Multiple sequence alignment - TraesCS7A01G249700

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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 TraesCS7A01G249700 chr7A 100.000 2969 0 0 1 2969 232387781 232390749 0.000000e+00 5483.0
1 TraesCS7A01G249700 chr7D 92.528 1499 84 12 804 2286 219847423 219848909 0.000000e+00 2122.0
2 TraesCS7A01G249700 chr7D 91.063 414 26 6 59 465 219843674 219844083 1.560000e-152 549.0
3 TraesCS7A01G249700 chr7D 76.538 780 171 11 1186 1962 572018288 572019058 1.650000e-112 416.0
4 TraesCS7A01G249700 chr7D 85.156 256 10 6 450 678 219844527 219844781 1.380000e-58 237.0
5 TraesCS7A01G249700 chr7D 94.286 140 7 1 682 821 219846108 219846246 2.320000e-51 213.0
6 TraesCS7A01G249700 chr7D 100.000 51 0 0 759 809 219846250 219846300 8.760000e-16 95.3
7 TraesCS7A01G249700 chr7B 87.944 1352 81 40 561 1904 179902671 179901394 0.000000e+00 1519.0
8 TraesCS7A01G249700 chr7B 90.051 392 21 8 1897 2288 179900054 179899681 2.660000e-135 492.0
9 TraesCS7A01G249700 chr7B 76.142 876 191 14 1092 1961 629019441 629020304 7.550000e-121 444.0
10 TraesCS7A01G249700 chr7B 83.544 395 54 4 44 436 179910817 179910432 2.810000e-95 359.0
11 TraesCS7A01G249700 chr7B 89.109 101 9 2 2460 2559 504815554 504815653 1.120000e-24 124.0
12 TraesCS7A01G249700 chr5A 95.603 614 26 1 2356 2969 482718638 482718026 0.000000e+00 983.0
13 TraesCS7A01G249700 chr3D 94.413 358 16 3 2616 2969 565800800 565800443 5.600000e-152 547.0
14 TraesCS7A01G249700 chr3D 93.785 354 20 2 2616 2969 369804120 369804471 5.630000e-147 531.0
15 TraesCS7A01G249700 chr3D 90.698 258 21 3 2356 2611 566967267 566967011 1.020000e-89 340.0
16 TraesCS7A01G249700 chr4A 94.398 357 16 4 2616 2969 717952854 717953209 2.010000e-151 545.0
17 TraesCS7A01G249700 chr6B 94.134 358 17 4 2616 2969 492220704 492220347 2.600000e-150 542.0
18 TraesCS7A01G249700 chr6B 93.575 358 19 4 2616 2969 392484221 392484578 5.630000e-147 531.0
19 TraesCS7A01G249700 chr6B 93.258 356 22 2 2616 2969 37233296 37232941 9.430000e-145 523.0
20 TraesCS7A01G249700 chr6B 93.220 354 24 0 2616 2969 6885669 6885316 3.390000e-144 521.0
21 TraesCS7A01G249700 chr2D 94.101 356 18 3 2616 2969 104151568 104151214 3.370000e-149 538.0
22 TraesCS7A01G249700 chr2D 77.132 516 96 18 1160 1662 18269632 18269126 2.250000e-71 279.0
23 TraesCS7A01G249700 chr1D 91.085 258 20 3 2356 2611 33992241 33991985 2.190000e-91 346.0
24 TraesCS7A01G249700 chr2B 77.692 520 87 24 1159 1662 30313388 30312882 1.040000e-74 291.0
25 TraesCS7A01G249700 chr2B 75.530 519 107 17 1157 1662 30418080 30417569 1.380000e-58 237.0
26 TraesCS7A01G249700 chr4B 88.372 215 21 4 2347 2559 634416412 634416200 3.800000e-64 255.0
27 TraesCS7A01G249700 chr4B 85.938 64 8 1 2460 2522 627529395 627529332 1.910000e-07 67.6
28 TraesCS7A01G249700 chr2A 74.143 642 135 24 1157 1781 19436304 19435677 1.380000e-58 237.0
29 TraesCS7A01G249700 chr3B 88.119 101 10 2 2460 2559 716242292 716242391 5.200000e-23 119.0
30 TraesCS7A01G249700 chr1A 79.518 166 27 7 1175 1336 540413928 540414090 8.700000e-21 111.0


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 TraesCS7A01G249700 chr7A 232387781 232390749 2968 False 5483.00 5483 100.0000 1 2969 1 chr7A.!!$F1 2968
1 TraesCS7A01G249700 chr7D 219843674 219848909 5235 False 643.26 2122 92.6066 59 2286 5 chr7D.!!$F2 2227
2 TraesCS7A01G249700 chr7D 572018288 572019058 770 False 416.00 416 76.5380 1186 1962 1 chr7D.!!$F1 776
3 TraesCS7A01G249700 chr7B 179899681 179902671 2990 True 1005.50 1519 88.9975 561 2288 2 chr7B.!!$R2 1727
4 TraesCS7A01G249700 chr7B 629019441 629020304 863 False 444.00 444 76.1420 1092 1961 1 chr7B.!!$F2 869
5 TraesCS7A01G249700 chr5A 482718026 482718638 612 True 983.00 983 95.6030 2356 2969 1 chr5A.!!$R1 613
6 TraesCS7A01G249700 chr2D 18269126 18269632 506 True 279.00 279 77.1320 1160 1662 1 chr2D.!!$R1 502
7 TraesCS7A01G249700 chr2B 30312882 30313388 506 True 291.00 291 77.6920 1159 1662 1 chr2B.!!$R1 503
8 TraesCS7A01G249700 chr2B 30417569 30418080 511 True 237.00 237 75.5300 1157 1662 1 chr2B.!!$R2 505
9 TraesCS7A01G249700 chr2A 19435677 19436304 627 True 237.00 237 74.1430 1157 1781 1 chr2A.!!$R1 624


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
971 3986 0.328592 ACCTGCTCGACCACTCTAGA 59.671 55.0 0.0 0.0 0.0 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2617 7008 0.676782 AGGGTAGATGTTGTTGCCGC 60.677 55.0 0.0 0.0 0.0 6.53 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
21 22 3.957468 GTGTTGCTTCCTCTGTTCTTTG 58.043 45.455 0.00 0.00 0.00 2.77
22 23 3.378427 GTGTTGCTTCCTCTGTTCTTTGT 59.622 43.478 0.00 0.00 0.00 2.83
23 24 3.378112 TGTTGCTTCCTCTGTTCTTTGTG 59.622 43.478 0.00 0.00 0.00 3.33
24 25 3.558931 TGCTTCCTCTGTTCTTTGTGA 57.441 42.857 0.00 0.00 0.00 3.58
25 26 4.090761 TGCTTCCTCTGTTCTTTGTGAT 57.909 40.909 0.00 0.00 0.00 3.06
26 27 5.227569 TGCTTCCTCTGTTCTTTGTGATA 57.772 39.130 0.00 0.00 0.00 2.15
27 28 4.997395 TGCTTCCTCTGTTCTTTGTGATAC 59.003 41.667 0.00 0.00 0.00 2.24
28 29 4.393371 GCTTCCTCTGTTCTTTGTGATACC 59.607 45.833 0.00 0.00 0.00 2.73
29 30 5.799213 CTTCCTCTGTTCTTTGTGATACCT 58.201 41.667 0.00 0.00 0.00 3.08
30 31 5.825593 TCCTCTGTTCTTTGTGATACCTT 57.174 39.130 0.00 0.00 0.00 3.50
31 32 6.187727 TCCTCTGTTCTTTGTGATACCTTT 57.812 37.500 0.00 0.00 0.00 3.11
32 33 6.601332 TCCTCTGTTCTTTGTGATACCTTTT 58.399 36.000 0.00 0.00 0.00 2.27
33 34 7.060421 TCCTCTGTTCTTTGTGATACCTTTTT 58.940 34.615 0.00 0.00 0.00 1.94
64 65 6.803154 AACCTTGTGATGCTTTCTAGTAAC 57.197 37.500 0.00 0.00 0.00 2.50
71 72 9.515226 TTGTGATGCTTTCTAGTAACCTTATTT 57.485 29.630 0.00 0.00 0.00 1.40
89 90 9.432982 ACCTTATTTCTTGGCCATTAATCAATA 57.567 29.630 6.09 1.34 0.00 1.90
95 96 9.956640 TTTCTTGGCCATTAATCAATATTGTTT 57.043 25.926 6.09 14.72 0.00 2.83
116 117 1.747355 GGCCTGACTTGATGTTGATGG 59.253 52.381 0.00 0.00 0.00 3.51
120 121 4.074259 CCTGACTTGATGTTGATGGTGAA 58.926 43.478 0.00 0.00 0.00 3.18
126 127 4.371624 TGATGTTGATGGTGAAGAAGGT 57.628 40.909 0.00 0.00 0.00 3.50
134 135 5.634118 TGATGGTGAAGAAGGTGAAGAAAT 58.366 37.500 0.00 0.00 0.00 2.17
137 138 5.065914 TGGTGAAGAAGGTGAAGAAATCTG 58.934 41.667 0.00 0.00 0.00 2.90
146 147 2.746362 GTGAAGAAATCTGTGCTGGAGG 59.254 50.000 0.00 0.00 0.00 4.30
152 153 1.351080 ATCTGTGCTGGAGGGGATGG 61.351 60.000 0.00 0.00 0.00 3.51
170 171 3.315140 TGGATCCGCAACCACCGA 61.315 61.111 7.39 0.00 0.00 4.69
186 193 1.966354 ACCGAGGAAGGTCGTTTAACT 59.034 47.619 0.00 0.00 41.46 2.24
265 273 2.189499 GCCCCGGCAGATGATTGAC 61.189 63.158 0.00 0.00 41.49 3.18
281 289 7.677745 AGATGATTGACCTATGGAGCTTATAGT 59.322 37.037 14.30 6.19 0.00 2.12
286 294 2.563179 CCTATGGAGCTTATAGTGCCGT 59.437 50.000 14.30 2.70 0.00 5.68
287 295 3.006967 CCTATGGAGCTTATAGTGCCGTT 59.993 47.826 14.30 0.00 0.00 4.44
289 297 2.627945 TGGAGCTTATAGTGCCGTTTG 58.372 47.619 0.00 0.00 0.00 2.93
290 298 1.940613 GGAGCTTATAGTGCCGTTTGG 59.059 52.381 0.00 0.00 38.77 3.28
291 299 2.629051 GAGCTTATAGTGCCGTTTGGT 58.371 47.619 0.00 0.00 37.67 3.67
292 300 2.608090 GAGCTTATAGTGCCGTTTGGTC 59.392 50.000 0.00 0.00 37.67 4.02
293 301 2.236395 AGCTTATAGTGCCGTTTGGTCT 59.764 45.455 0.00 0.00 37.67 3.85
307 315 1.946984 TGGTCTATTGGAAGTCCGGT 58.053 50.000 0.00 0.00 39.43 5.28
356 364 3.701205 TCTGTATTTCTGAGCTTGCCA 57.299 42.857 0.00 0.00 0.00 4.92
367 375 2.223782 TGAGCTTGCCATTGTGTGTTTC 60.224 45.455 0.00 0.00 0.00 2.78
422 430 3.764466 CAGCTCCGGCGAGAACCT 61.764 66.667 9.30 0.63 44.37 3.50
522 987 2.093973 CGATGTAGGTTTCTGCTGGTCT 60.094 50.000 0.00 0.00 0.00 3.85
529 994 2.157738 GTTTCTGCTGGTCTCATGCTT 58.842 47.619 0.00 0.00 0.00 3.91
545 1010 4.158394 TCATGCTTGAGTTCCATAAAAGCC 59.842 41.667 0.00 0.00 41.99 4.35
603 1094 3.881688 CTGCAAGGATTAATGACTCAGGG 59.118 47.826 0.00 0.00 0.00 4.45
698 2514 9.698309 ATAATTCAGAACGTGATATTGGTAGAG 57.302 33.333 0.00 0.00 34.17 2.43
755 2571 6.115446 TCATCAGCTGGAGTTACCTTATTTG 58.885 40.000 15.13 0.00 39.86 2.32
854 3864 1.470890 ACCGGACATGCAAATTAACGG 59.529 47.619 9.46 13.81 45.06 4.44
856 3866 2.477189 CCGGACATGCAAATTAACGGAC 60.477 50.000 0.00 0.00 42.42 4.79
857 3867 2.477189 CGGACATGCAAATTAACGGACC 60.477 50.000 0.00 0.00 0.00 4.46
907 3921 1.688735 TGCATCATTACTCTCCCTCCG 59.311 52.381 0.00 0.00 0.00 4.63
922 3936 1.800586 CCTCCGCACATACATGCATAC 59.199 52.381 0.00 0.00 46.47 2.39
962 3977 1.598130 AAAGTGGCACCTGCTCGAC 60.598 57.895 15.27 0.00 41.70 4.20
971 3986 0.328592 ACCTGCTCGACCACTCTAGA 59.671 55.000 0.00 0.00 0.00 2.43
985 4000 1.005630 CTAGATAGCTGCGTGCCCC 60.006 63.158 0.00 0.00 44.23 5.80
986 4001 1.748329 CTAGATAGCTGCGTGCCCCA 61.748 60.000 0.00 0.00 44.23 4.96
987 4002 1.121407 TAGATAGCTGCGTGCCCCAT 61.121 55.000 0.00 0.00 44.23 4.00
988 4003 1.963338 GATAGCTGCGTGCCCCATC 60.963 63.158 0.00 0.00 44.23 3.51
989 4004 3.482232 ATAGCTGCGTGCCCCATCC 62.482 63.158 0.00 0.00 44.23 3.51
1015 4030 1.451927 GCCATGGCCGAGATCAACA 60.452 57.895 27.24 0.00 34.56 3.33
1505 4532 1.736126 CAGCTGGCACTACATGAACAG 59.264 52.381 5.57 0.00 37.69 3.16
1526 4568 4.516195 GAGCGCCGACTTCTCCCC 62.516 72.222 2.29 0.00 0.00 4.81
1677 4719 3.785859 ATGATGGCCGACGCAGGT 61.786 61.111 0.00 0.00 36.38 4.00
1684 4726 2.813908 CCGACGCAGGTAAGCACC 60.814 66.667 0.00 0.00 46.19 5.01
1914 6303 3.181440 ACTTGACTGAGGAGATGGCAAAA 60.181 43.478 0.00 0.00 0.00 2.44
1980 6369 0.439985 CCTTCTGACGTGTGATTGCG 59.560 55.000 0.00 0.00 0.00 4.85
1999 6390 3.128589 TGCGTCTCTTTAATTTGATGGCC 59.871 43.478 0.00 0.00 0.00 5.36
2017 6408 1.404851 GCCACAGAGGTCTTCTACTGC 60.405 57.143 0.00 0.00 40.61 4.40
2111 6502 6.735678 TGTTAATGAATGATACGCACACTT 57.264 33.333 0.00 0.00 0.00 3.16
2113 6504 3.680642 ATGAATGATACGCACACTTGC 57.319 42.857 0.00 0.00 46.21 4.01
2158 6549 3.611530 GCATAAATCAGTTGTTGCCGTGT 60.612 43.478 0.00 0.00 0.00 4.49
2159 6550 2.490328 AAATCAGTTGTTGCCGTGTG 57.510 45.000 0.00 0.00 0.00 3.82
2211 6602 5.830912 TGGAAGTGAAAAATGTCATGTGTC 58.169 37.500 0.00 0.00 0.00 3.67
2229 6620 4.935205 TGTGTCTTCCTTATGAAATGGACG 59.065 41.667 0.00 0.00 31.58 4.79
2288 6679 3.945981 TTACCACGTCAAGAGCACATA 57.054 42.857 0.00 0.00 0.00 2.29
2289 6680 2.831685 ACCACGTCAAGAGCACATAA 57.168 45.000 0.00 0.00 0.00 1.90
2290 6681 2.688507 ACCACGTCAAGAGCACATAAG 58.311 47.619 0.00 0.00 0.00 1.73
2291 6682 2.002586 CCACGTCAAGAGCACATAAGG 58.997 52.381 0.00 0.00 0.00 2.69
2292 6683 1.394917 CACGTCAAGAGCACATAAGGC 59.605 52.381 0.00 0.00 0.00 4.35
2293 6684 1.009829 CGTCAAGAGCACATAAGGCC 58.990 55.000 0.00 0.00 0.00 5.19
2294 6685 1.406069 CGTCAAGAGCACATAAGGCCT 60.406 52.381 0.00 0.00 0.00 5.19
2295 6686 2.716217 GTCAAGAGCACATAAGGCCTT 58.284 47.619 24.18 24.18 0.00 4.35
2296 6687 2.680339 GTCAAGAGCACATAAGGCCTTC 59.320 50.000 24.49 7.21 0.00 3.46
2297 6688 2.573462 TCAAGAGCACATAAGGCCTTCT 59.427 45.455 24.49 12.84 0.00 2.85
2298 6689 3.009473 TCAAGAGCACATAAGGCCTTCTT 59.991 43.478 24.49 14.67 39.40 2.52
2299 6690 3.728385 AGAGCACATAAGGCCTTCTTT 57.272 42.857 24.49 1.61 36.93 2.52
2300 6691 3.350833 AGAGCACATAAGGCCTTCTTTG 58.649 45.455 24.49 19.86 36.93 2.77
2301 6692 3.009473 AGAGCACATAAGGCCTTCTTTGA 59.991 43.478 24.49 3.81 36.93 2.69
2302 6693 3.950395 GAGCACATAAGGCCTTCTTTGAT 59.050 43.478 24.49 14.82 36.93 2.57
2303 6694 4.347607 AGCACATAAGGCCTTCTTTGATT 58.652 39.130 24.49 5.05 36.93 2.57
2304 6695 4.400567 AGCACATAAGGCCTTCTTTGATTC 59.599 41.667 24.49 11.95 36.93 2.52
2305 6696 4.158394 GCACATAAGGCCTTCTTTGATTCA 59.842 41.667 24.49 0.18 36.93 2.57
2306 6697 5.163478 GCACATAAGGCCTTCTTTGATTCAT 60.163 40.000 24.49 3.14 36.93 2.57
2307 6698 6.039717 GCACATAAGGCCTTCTTTGATTCATA 59.960 38.462 24.49 0.00 36.93 2.15
2308 6699 7.416664 GCACATAAGGCCTTCTTTGATTCATAA 60.417 37.037 24.49 0.00 36.93 1.90
2309 6700 8.133627 CACATAAGGCCTTCTTTGATTCATAAG 58.866 37.037 24.49 0.00 36.93 1.73
2310 6701 8.055181 ACATAAGGCCTTCTTTGATTCATAAGA 58.945 33.333 24.49 0.00 36.93 2.10
2311 6702 9.075678 CATAAGGCCTTCTTTGATTCATAAGAT 57.924 33.333 24.49 0.19 36.93 2.40
2313 6704 8.688747 AAGGCCTTCTTTGATTCATAAGATAG 57.311 34.615 13.78 10.08 31.00 2.08
2314 6705 7.230027 AGGCCTTCTTTGATTCATAAGATAGG 58.770 38.462 0.00 19.06 34.88 2.57
2315 6706 7.072961 AGGCCTTCTTTGATTCATAAGATAGGA 59.927 37.037 22.52 9.50 34.33 2.94
2316 6707 7.721399 GGCCTTCTTTGATTCATAAGATAGGAA 59.279 37.037 22.52 9.16 34.33 3.36
2317 6708 9.125026 GCCTTCTTTGATTCATAAGATAGGAAA 57.875 33.333 22.52 8.91 34.33 3.13
2349 6740 1.034356 AAAAAGGGGAACGTTTCGGG 58.966 50.000 0.46 0.00 46.89 5.14
2350 6741 0.824595 AAAAGGGGAACGTTTCGGGG 60.825 55.000 0.46 0.00 46.89 5.73
2351 6742 3.855503 AAGGGGAACGTTTCGGGGC 62.856 63.158 0.46 0.00 34.05 5.80
2354 6745 4.994471 GGAACGTTTCGGGGCGGT 62.994 66.667 0.46 0.00 0.00 5.68
2375 6766 4.744316 GAACGATTCGGCCGGTAT 57.256 55.556 27.83 19.22 0.00 2.73
2464 6855 1.705186 CCCACTTTCTTCTTCCTCCCA 59.295 52.381 0.00 0.00 0.00 4.37
2467 6858 4.411013 CCACTTTCTTCTTCCTCCCAATT 58.589 43.478 0.00 0.00 0.00 2.32
2488 6879 0.263172 CCTCCTTCCCTCTCAGCCTA 59.737 60.000 0.00 0.00 0.00 3.93
2515 6906 1.144936 CTGGCCCTCGTCTTCATCC 59.855 63.158 0.00 0.00 0.00 3.51
2617 7008 3.227276 CCCACCCTCCCTCGATCG 61.227 72.222 9.36 9.36 0.00 3.69
2626 7017 2.813474 CCTCGATCGCGGCAACAA 60.813 61.111 11.81 0.00 38.28 2.83
2629 7020 1.695893 CTCGATCGCGGCAACAACAT 61.696 55.000 11.09 0.00 38.28 2.71
2630 7021 1.296867 CGATCGCGGCAACAACATC 60.297 57.895 6.13 0.00 0.00 3.06
2655 7046 3.449918 CCTTCTTCCTTCTCCCTCTCTT 58.550 50.000 0.00 0.00 0.00 2.85
2694 7085 0.753479 TCCCTTTTTGCTGCAACCGA 60.753 50.000 15.72 0.00 0.00 4.69
2700 7091 1.369839 TTTGCTGCAACCGACGACAA 61.370 50.000 15.72 0.00 0.00 3.18
2742 7133 1.153529 CGCCCGTGCTACAACCATA 60.154 57.895 0.00 0.00 34.43 2.74
2758 7149 1.053264 CATAGCCACAGGGAGGAGCT 61.053 60.000 0.00 0.00 35.59 4.09
2765 7156 1.073722 CAGGGAGGAGCTGCAACAA 59.926 57.895 8.35 0.00 0.00 2.83
2773 7164 1.226746 GAGCTGCAACAACGGTACTT 58.773 50.000 1.02 0.00 0.00 2.24
2917 7308 2.288152 GCTTCAACCCGCAGATGAAAAA 60.288 45.455 0.00 0.00 33.08 1.94
2928 7319 4.147653 CGCAGATGAAAAAGCTTCAAACAG 59.852 41.667 0.00 0.00 31.55 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.378427 ACAAAGAACAGAGGAAGCAACAC 59.622 43.478 0.00 0.00 0.00 3.32
1 2 3.378112 CACAAAGAACAGAGGAAGCAACA 59.622 43.478 0.00 0.00 0.00 3.33
2 3 3.627577 TCACAAAGAACAGAGGAAGCAAC 59.372 43.478 0.00 0.00 0.00 4.17
3 4 3.884895 TCACAAAGAACAGAGGAAGCAA 58.115 40.909 0.00 0.00 0.00 3.91
4 5 3.558931 TCACAAAGAACAGAGGAAGCA 57.441 42.857 0.00 0.00 0.00 3.91
5 6 4.393371 GGTATCACAAAGAACAGAGGAAGC 59.607 45.833 0.00 0.00 0.00 3.86
6 7 5.799213 AGGTATCACAAAGAACAGAGGAAG 58.201 41.667 0.00 0.00 0.00 3.46
7 8 5.825593 AGGTATCACAAAGAACAGAGGAA 57.174 39.130 0.00 0.00 0.00 3.36
8 9 5.825593 AAGGTATCACAAAGAACAGAGGA 57.174 39.130 0.00 0.00 0.00 3.71
9 10 6.884280 AAAAGGTATCACAAAGAACAGAGG 57.116 37.500 0.00 0.00 0.00 3.69
32 33 9.515226 AGAAAGCATCACAAGGTTAGTATAAAA 57.485 29.630 0.00 0.00 0.00 1.52
34 35 9.817809 CTAGAAAGCATCACAAGGTTAGTATAA 57.182 33.333 0.00 0.00 0.00 0.98
35 36 8.978472 ACTAGAAAGCATCACAAGGTTAGTATA 58.022 33.333 0.00 0.00 0.00 1.47
36 37 7.852263 ACTAGAAAGCATCACAAGGTTAGTAT 58.148 34.615 0.00 0.00 0.00 2.12
37 38 7.241042 ACTAGAAAGCATCACAAGGTTAGTA 57.759 36.000 0.00 0.00 0.00 1.82
38 39 6.115448 ACTAGAAAGCATCACAAGGTTAGT 57.885 37.500 0.00 0.00 0.00 2.24
39 40 7.064728 GGTTACTAGAAAGCATCACAAGGTTAG 59.935 40.741 0.00 0.00 0.00 2.34
40 41 6.877322 GGTTACTAGAAAGCATCACAAGGTTA 59.123 38.462 0.00 0.00 0.00 2.85
41 42 5.705905 GGTTACTAGAAAGCATCACAAGGTT 59.294 40.000 0.00 0.00 0.00 3.50
42 43 5.013183 AGGTTACTAGAAAGCATCACAAGGT 59.987 40.000 0.00 0.00 0.00 3.50
43 44 5.491982 AGGTTACTAGAAAGCATCACAAGG 58.508 41.667 0.00 0.00 0.00 3.61
44 45 8.723942 ATAAGGTTACTAGAAAGCATCACAAG 57.276 34.615 0.00 0.00 0.00 3.16
45 46 9.515226 AAATAAGGTTACTAGAAAGCATCACAA 57.485 29.630 0.00 0.00 0.00 3.33
46 47 9.162764 GAAATAAGGTTACTAGAAAGCATCACA 57.837 33.333 0.00 0.00 0.00 3.58
47 48 9.384764 AGAAATAAGGTTACTAGAAAGCATCAC 57.615 33.333 0.00 0.00 0.00 3.06
48 49 9.959721 AAGAAATAAGGTTACTAGAAAGCATCA 57.040 29.630 0.00 0.00 0.00 3.07
50 51 9.178758 CCAAGAAATAAGGTTACTAGAAAGCAT 57.821 33.333 0.00 0.00 0.00 3.79
51 52 7.120726 GCCAAGAAATAAGGTTACTAGAAAGCA 59.879 37.037 0.00 0.00 0.00 3.91
52 53 7.415318 GGCCAAGAAATAAGGTTACTAGAAAGC 60.415 40.741 0.00 0.00 0.00 3.51
53 54 7.610305 TGGCCAAGAAATAAGGTTACTAGAAAG 59.390 37.037 0.61 0.00 0.00 2.62
54 55 7.463431 TGGCCAAGAAATAAGGTTACTAGAAA 58.537 34.615 0.61 0.00 0.00 2.52
55 56 7.023171 TGGCCAAGAAATAAGGTTACTAGAA 57.977 36.000 0.61 0.00 0.00 2.10
56 57 6.630203 TGGCCAAGAAATAAGGTTACTAGA 57.370 37.500 0.61 0.00 0.00 2.43
57 58 7.881775 AATGGCCAAGAAATAAGGTTACTAG 57.118 36.000 10.96 0.00 0.00 2.57
71 72 7.986320 CCAAACAATATTGATTAATGGCCAAGA 59.014 33.333 22.16 0.00 31.84 3.02
89 90 3.233507 ACATCAAGTCAGGCCAAACAAT 58.766 40.909 5.01 0.00 0.00 2.71
95 96 2.439409 CATCAACATCAAGTCAGGCCA 58.561 47.619 5.01 0.00 0.00 5.36
116 117 5.561725 GCACAGATTTCTTCACCTTCTTCAC 60.562 44.000 0.00 0.00 0.00 3.18
120 121 4.070716 CAGCACAGATTTCTTCACCTTCT 58.929 43.478 0.00 0.00 0.00 2.85
126 127 2.290514 CCCTCCAGCACAGATTTCTTCA 60.291 50.000 0.00 0.00 0.00 3.02
134 135 1.997311 CCATCCCCTCCAGCACAGA 60.997 63.158 0.00 0.00 0.00 3.41
137 138 2.273449 CACCATCCCCTCCAGCAC 59.727 66.667 0.00 0.00 0.00 4.40
159 160 2.742372 CCTTCCTCGGTGGTTGCG 60.742 66.667 0.00 0.00 37.07 4.85
161 162 1.374252 CGACCTTCCTCGGTGGTTG 60.374 63.158 0.00 4.92 37.42 3.77
169 170 2.737252 CTGCAGTTAAACGACCTTCCTC 59.263 50.000 5.25 0.00 0.00 3.71
170 171 2.367567 TCTGCAGTTAAACGACCTTCCT 59.632 45.455 14.67 0.00 0.00 3.36
186 193 2.562738 TCTGGAAGATCGAACTTCTGCA 59.437 45.455 27.87 19.50 43.76 4.41
250 258 2.420642 CATAGGTCAATCATCTGCCGG 58.579 52.381 0.00 0.00 0.00 6.13
258 266 6.519043 GCACTATAAGCTCCATAGGTCAATCA 60.519 42.308 15.92 0.00 31.44 2.57
265 273 2.563179 ACGGCACTATAAGCTCCATAGG 59.437 50.000 15.92 8.69 31.44 2.57
281 289 2.224670 ACTTCCAATAGACCAAACGGCA 60.225 45.455 0.00 0.00 0.00 5.69
286 294 2.640826 ACCGGACTTCCAATAGACCAAA 59.359 45.455 9.46 0.00 35.14 3.28
287 295 2.027561 CACCGGACTTCCAATAGACCAA 60.028 50.000 9.46 0.00 35.14 3.67
289 297 1.134491 CCACCGGACTTCCAATAGACC 60.134 57.143 9.46 0.00 35.14 3.85
290 298 1.553704 ACCACCGGACTTCCAATAGAC 59.446 52.381 9.46 0.00 35.14 2.59
291 299 1.946984 ACCACCGGACTTCCAATAGA 58.053 50.000 9.46 0.00 35.14 1.98
292 300 2.764572 AGTACCACCGGACTTCCAATAG 59.235 50.000 9.46 0.00 35.14 1.73
293 301 2.498481 CAGTACCACCGGACTTCCAATA 59.502 50.000 9.46 0.00 35.14 1.90
307 315 7.120716 GGGAAATATAAAGGAAACCAGTACCA 58.879 38.462 0.00 0.00 0.00 3.25
343 351 1.610038 CACACAATGGCAAGCTCAGAA 59.390 47.619 0.00 0.00 0.00 3.02
356 364 4.338964 TCACATTCAGCAGAAACACACAAT 59.661 37.500 0.00 0.00 37.29 2.71
367 375 1.888215 ACACCACTCACATTCAGCAG 58.112 50.000 0.00 0.00 0.00 4.24
422 430 1.133199 ACCCAGCAAAAGAACCCATCA 60.133 47.619 0.00 0.00 0.00 3.07
522 987 4.158394 GGCTTTTATGGAACTCAAGCATGA 59.842 41.667 0.00 0.00 41.42 3.07
529 994 3.846588 AGGAGAGGCTTTTATGGAACTCA 59.153 43.478 0.00 0.00 0.00 3.41
585 1076 3.525199 ACAGCCCTGAGTCATTAATCCTT 59.475 43.478 1.69 0.00 0.00 3.36
586 1077 3.118531 ACAGCCCTGAGTCATTAATCCT 58.881 45.455 1.69 0.00 0.00 3.24
755 2571 0.529378 TAGCCGAAGTCGAAGGGAAC 59.471 55.000 1.43 0.00 43.02 3.62
884 3896 3.006752 GGAGGGAGAGTAATGATGCAGAG 59.993 52.174 0.00 0.00 0.00 3.35
922 3936 3.005554 GCTGGTATATATGGCACTGCAG 58.994 50.000 13.48 13.48 0.00 4.41
927 3941 4.216257 CCACTTTGCTGGTATATATGGCAC 59.784 45.833 0.00 0.00 32.47 5.01
962 3977 1.601663 GCACGCAGCTATCTAGAGTGG 60.602 57.143 0.00 0.00 41.15 4.00
985 4000 3.359523 CATGGCGGATGGCGGATG 61.360 66.667 0.00 0.00 44.92 3.51
986 4001 4.648626 CCATGGCGGATGGCGGAT 62.649 66.667 0.00 0.00 45.58 4.18
1015 4030 1.448540 CTTCCTCTGCGGCGTCATT 60.449 57.895 9.37 0.00 0.00 2.57
1505 4532 3.991536 GAGAAGTCGGCGCTCACCC 62.992 68.421 7.64 0.00 0.00 4.61
1526 4568 3.605749 AAGGTGGCGTCCATGTCGG 62.606 63.158 9.04 0.00 35.28 4.79
1590 4632 3.740397 CAGTACCCGCGGACGTGA 61.740 66.667 30.73 3.14 37.70 4.35
1684 4726 0.459237 AACTCGGCGAGCATCTTGAG 60.459 55.000 34.76 11.09 32.04 3.02
1755 4797 2.126071 CTACACAGGGCCACGACG 60.126 66.667 6.18 0.00 0.00 5.12
1827 4869 4.738998 TCCATGGGCAAGCCACCG 62.739 66.667 13.02 0.00 37.98 4.94
1833 4875 1.672881 GACGAATTCTCCATGGGCAAG 59.327 52.381 13.02 1.69 0.00 4.01
1878 4920 3.034635 AGTCAAGTGTGTCTTCCAGTCT 58.965 45.455 0.00 0.00 33.63 3.24
1914 6303 0.877071 CAACGATGCAGTCCAGCTTT 59.123 50.000 0.00 0.00 34.99 3.51
1980 6369 5.415701 TCTGTGGCCATCAAATTAAAGAGAC 59.584 40.000 9.72 0.00 0.00 3.36
1999 6390 2.822561 TCTGCAGTAGAAGACCTCTGTG 59.177 50.000 14.67 0.00 35.41 3.66
2017 6408 4.363138 TGCGAGTATGTAATTCAGCTCTG 58.637 43.478 0.00 0.00 33.20 3.35
2131 6522 5.804473 CGGCAACAACTGATTTATGCATTTA 59.196 36.000 3.54 0.00 33.04 1.40
2134 6525 3.193267 ACGGCAACAACTGATTTATGCAT 59.807 39.130 3.79 3.79 33.04 3.96
2135 6526 2.556189 ACGGCAACAACTGATTTATGCA 59.444 40.909 0.00 0.00 33.04 3.96
2158 6549 7.715249 ACTCTTCTCAAGTAGCATAAACAAACA 59.285 33.333 0.00 0.00 0.00 2.83
2159 6550 8.089115 ACTCTTCTCAAGTAGCATAAACAAAC 57.911 34.615 0.00 0.00 0.00 2.93
2211 6602 6.867662 AATAGCGTCCATTTCATAAGGAAG 57.132 37.500 0.00 0.00 36.72 3.46
2229 6620 7.482654 TGCATTATCTTCACACAGTAATAGC 57.517 36.000 0.00 0.00 0.00 2.97
2288 6679 7.723172 CCTATCTTATGAATCAAAGAAGGCCTT 59.277 37.037 20.65 20.65 35.47 4.35
2289 6680 7.072961 TCCTATCTTATGAATCAAAGAAGGCCT 59.927 37.037 0.00 0.00 35.47 5.19
2290 6681 7.227156 TCCTATCTTATGAATCAAAGAAGGCC 58.773 38.462 17.90 0.00 35.47 5.19
2291 6682 8.682936 TTCCTATCTTATGAATCAAAGAAGGC 57.317 34.615 17.90 0.00 35.47 4.35
2330 6721 1.034356 CCCGAAACGTTCCCCTTTTT 58.966 50.000 0.00 0.00 0.00 1.94
2331 6722 0.824595 CCCCGAAACGTTCCCCTTTT 60.825 55.000 0.00 0.00 0.00 2.27
2332 6723 1.228337 CCCCGAAACGTTCCCCTTT 60.228 57.895 0.00 0.00 0.00 3.11
2333 6724 2.433004 CCCCGAAACGTTCCCCTT 59.567 61.111 0.00 0.00 0.00 3.95
2334 6725 4.340246 GCCCCGAAACGTTCCCCT 62.340 66.667 0.00 0.00 0.00 4.79
2337 6728 4.994471 ACCGCCCCGAAACGTTCC 62.994 66.667 0.00 0.00 0.00 3.62
2338 6729 3.719144 CACCGCCCCGAAACGTTC 61.719 66.667 0.00 0.00 0.00 3.95
2349 6740 3.861263 GAATCGTTCGGCACCGCC 61.861 66.667 3.66 0.00 46.75 6.13
2428 6819 2.197465 GTGGGAGAAGATAAGGTGGGT 58.803 52.381 0.00 0.00 0.00 4.51
2464 6855 2.486716 CTGAGAGGGAAGGAGGGAATT 58.513 52.381 0.00 0.00 0.00 2.17
2467 6858 1.002274 GCTGAGAGGGAAGGAGGGA 59.998 63.158 0.00 0.00 0.00 4.20
2563 6954 1.151450 CAAGGGCACTGAGGTTGGT 59.849 57.895 0.00 0.00 0.00 3.67
2568 6959 3.970410 TGGGCAAGGGCACTGAGG 61.970 66.667 0.00 0.00 46.28 3.86
2617 7008 0.676782 AGGGTAGATGTTGTTGCCGC 60.677 55.000 0.00 0.00 0.00 6.53
2626 7017 4.034410 GGAGAAGGAAGAAGGGTAGATGT 58.966 47.826 0.00 0.00 0.00 3.06
2629 7020 2.660556 AGGGAGAAGGAAGAAGGGTAGA 59.339 50.000 0.00 0.00 0.00 2.59
2630 7021 3.035363 GAGGGAGAAGGAAGAAGGGTAG 58.965 54.545 0.00 0.00 0.00 3.18
2655 7046 1.398799 AGAGAGGAGGAGGAAAGGGA 58.601 55.000 0.00 0.00 0.00 4.20
2694 7085 3.645975 CCGCGTTTGGCTTGTCGT 61.646 61.111 4.92 0.00 40.44 4.34
2742 7133 3.007920 CAGCTCCTCCCTGTGGCT 61.008 66.667 0.00 0.00 0.00 4.75
2758 7149 1.139256 TCTCCAAGTACCGTTGTTGCA 59.861 47.619 0.00 0.00 0.00 4.08
2765 7156 1.045407 TGCAACTCTCCAAGTACCGT 58.955 50.000 0.00 0.00 37.17 4.83
2773 7164 2.250939 CGCCGTTTGCAACTCTCCA 61.251 57.895 0.00 0.00 41.33 3.86
2797 7188 1.806542 GTGTCCATGGTTGTAGCACAG 59.193 52.381 12.58 0.00 0.00 3.66
2798 7189 1.141858 TGTGTCCATGGTTGTAGCACA 59.858 47.619 12.58 14.34 33.71 4.57
2842 7233 2.639065 TCGTTGTCTGGTTGAAGCTTT 58.361 42.857 0.00 0.00 0.00 3.51
2860 7251 6.075280 CGGTTGTAACTTTTCCTGTATTTCG 58.925 40.000 0.00 0.00 0.00 3.46
2917 7308 6.150809 GGATTTCTCAATCTCTGTTTGAAGCT 59.849 38.462 0.00 0.00 39.17 3.74
2928 7319 4.616953 GTCGAGGAGGATTTCTCAATCTC 58.383 47.826 0.00 0.00 44.19 2.75



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

AutoCloner maintained by Alex Coulton.