Multiple sequence alignment - TraesCS6B01G346900

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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 TraesCS6B01G346900 chr6B 100.000 3454 0 0 1 3454 610815015 610818468 0.000000e+00 6379.0
1 TraesCS6B01G346900 chr6B 97.771 942 18 2 2513 3454 500321361 500320423 0.000000e+00 1620.0
2 TraesCS6B01G346900 chr6B 97.569 946 19 2 2512 3453 610825789 610826734 0.000000e+00 1616.0
3 TraesCS6B01G346900 chr6B 93.617 235 14 1 2178 2412 611331208 611331441 1.970000e-92 350.0
4 TraesCS6B01G346900 chr6B 93.651 63 4 0 2120 2182 611321656 611321718 1.020000e-15 95.3
5 TraesCS6B01G346900 chr5D 88.942 1664 135 19 412 2050 435613353 435611714 0.000000e+00 2008.0
6 TraesCS6B01G346900 chr5D 83.243 185 30 1 2256 2440 31271204 31271021 5.930000e-38 169.0
7 TraesCS6B01G346900 chr1D 88.582 1664 141 19 412 2050 249580462 249578823 0.000000e+00 1975.0
8 TraesCS6B01G346900 chr7B 97.782 947 18 3 2510 3454 629909704 629908759 0.000000e+00 1629.0
9 TraesCS6B01G346900 chr7B 97.773 943 19 2 2512 3454 629901438 629900498 0.000000e+00 1624.0
10 TraesCS6B01G346900 chr7B 97.354 945 23 1 2512 3454 174519401 174518457 0.000000e+00 1605.0
11 TraesCS6B01G346900 chr4A 97.775 944 20 1 2512 3454 664868054 664867111 0.000000e+00 1626.0
12 TraesCS6B01G346900 chr4A 100.000 30 0 0 2087 2116 559062505 559062534 4.820000e-04 56.5
13 TraesCS6B01G346900 chr6D 89.587 1306 86 20 1 1281 406339896 406341176 0.000000e+00 1613.0
14 TraesCS6B01G346900 chr6D 92.978 826 50 2 1265 2087 406341273 406342093 0.000000e+00 1197.0
15 TraesCS6B01G346900 chr6D 93.048 374 24 2 2124 2497 407201959 407202330 2.340000e-151 545.0
16 TraesCS6B01G346900 chr6D 86.842 380 25 14 2120 2493 406342095 406342455 5.370000e-108 401.0
17 TraesCS6B01G346900 chr4B 97.452 942 23 1 2513 3454 523958018 523958958 0.000000e+00 1605.0
18 TraesCS6B01G346900 chr2B 97.257 948 24 2 2509 3454 426951523 426950576 0.000000e+00 1605.0
19 TraesCS6B01G346900 chr2B 97.452 942 23 1 2513 3454 481361725 481360785 0.000000e+00 1605.0
20 TraesCS6B01G346900 chr6A 87.906 1108 94 19 1014 2087 552763873 552764974 0.000000e+00 1267.0
21 TraesCS6B01G346900 chr6A 93.800 629 35 3 3 628 552762965 552763592 0.000000e+00 942.0
22 TraesCS6B01G346900 chr6A 93.651 252 16 0 673 924 552763590 552763841 9.050000e-101 377.0
23 TraesCS6B01G346900 chr6A 87.550 249 28 3 2251 2497 552772395 552772642 5.640000e-73 285.0
24 TraesCS6B01G346900 chr2D 100.000 33 0 0 2087 2119 607510122 607510090 1.040000e-05 62.1
25 TraesCS6B01G346900 chr2A 96.970 33 1 0 2087 2119 568400729 568400697 4.820000e-04 56.5
26 TraesCS6B01G346900 chr1B 100.000 29 0 0 2092 2120 539455103 539455075 2.000000e-03 54.7


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 TraesCS6B01G346900 chr6B 610815015 610818468 3453 False 6379.000000 6379 100.000000 1 3454 1 chr6B.!!$F1 3453
1 TraesCS6B01G346900 chr6B 500320423 500321361 938 True 1620.000000 1620 97.771000 2513 3454 1 chr6B.!!$R1 941
2 TraesCS6B01G346900 chr6B 610825789 610826734 945 False 1616.000000 1616 97.569000 2512 3453 1 chr6B.!!$F2 941
3 TraesCS6B01G346900 chr5D 435611714 435613353 1639 True 2008.000000 2008 88.942000 412 2050 1 chr5D.!!$R2 1638
4 TraesCS6B01G346900 chr1D 249578823 249580462 1639 True 1975.000000 1975 88.582000 412 2050 1 chr1D.!!$R1 1638
5 TraesCS6B01G346900 chr7B 629908759 629909704 945 True 1629.000000 1629 97.782000 2510 3454 1 chr7B.!!$R3 944
6 TraesCS6B01G346900 chr7B 629900498 629901438 940 True 1624.000000 1624 97.773000 2512 3454 1 chr7B.!!$R2 942
7 TraesCS6B01G346900 chr7B 174518457 174519401 944 True 1605.000000 1605 97.354000 2512 3454 1 chr7B.!!$R1 942
8 TraesCS6B01G346900 chr4A 664867111 664868054 943 True 1626.000000 1626 97.775000 2512 3454 1 chr4A.!!$R1 942
9 TraesCS6B01G346900 chr6D 406339896 406342455 2559 False 1070.333333 1613 89.802333 1 2493 3 chr6D.!!$F2 2492
10 TraesCS6B01G346900 chr4B 523958018 523958958 940 False 1605.000000 1605 97.452000 2513 3454 1 chr4B.!!$F1 941
11 TraesCS6B01G346900 chr2B 426950576 426951523 947 True 1605.000000 1605 97.257000 2509 3454 1 chr2B.!!$R1 945
12 TraesCS6B01G346900 chr2B 481360785 481361725 940 True 1605.000000 1605 97.452000 2513 3454 1 chr2B.!!$R2 941
13 TraesCS6B01G346900 chr6A 552762965 552764974 2009 False 862.000000 1267 91.785667 3 2087 3 chr6A.!!$F2 2084

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
813 818 0.035317 TCTGCATCTGACGGCAACTT 59.965 50.0 0.0 0.0 39.93 2.66 F
2138 2306 0.521291 TACGTACGTACAGCCCACAC 59.479 55.0 23.6 0.0 0.00 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2267 2439 0.178992 CAACCCTCCACAGGCTTCAA 60.179 55.000 0.0 0.0 38.72 2.69 R
3104 3282 3.261897 AGTTGAGTGTTGGGGAGACTATG 59.738 47.826 0.0 0.0 30.90 2.23 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
35 36 6.016777 AGCTTTTCATTCAGACATCGAGTTTT 60.017 34.615 0.00 0.00 0.00 2.43
120 121 3.248024 ACAGGTATCACCAAAGAGGACA 58.752 45.455 0.00 0.00 41.95 4.02
257 258 2.468831 GCTTTTGCAAAACGTGGATGA 58.531 42.857 20.46 0.00 46.58 2.92
290 291 4.036352 CGTCCGTTCTAACAGCTATCTTC 58.964 47.826 0.00 0.00 0.00 2.87
292 293 5.652518 GTCCGTTCTAACAGCTATCTTCTT 58.347 41.667 0.00 0.00 0.00 2.52
293 294 5.517054 GTCCGTTCTAACAGCTATCTTCTTG 59.483 44.000 0.00 0.00 0.00 3.02
357 358 0.389426 CACGCTACAGGCCGTACTTT 60.389 55.000 0.00 0.00 37.74 2.66
392 393 3.508762 CTTCCATGAAGCTCAATGCAAC 58.491 45.455 0.00 0.00 45.94 4.17
407 408 1.436983 GCAACGCCAGTAGCCATACC 61.437 60.000 0.00 0.00 38.78 2.73
409 410 1.324740 AACGCCAGTAGCCATACCGA 61.325 55.000 0.00 0.00 38.78 4.69
410 411 1.324740 ACGCCAGTAGCCATACCGAA 61.325 55.000 0.00 0.00 38.78 4.30
474 475 3.304525 GGTAGACATAATCTGACGACGGG 60.305 52.174 0.00 0.00 38.49 5.28
494 495 0.600255 CGAATGCCCCTATCGTGTCC 60.600 60.000 0.00 0.00 0.00 4.02
530 532 0.322816 ACTGTGGGCTTGCAGTATGG 60.323 55.000 7.20 0.00 43.30 2.74
549 551 5.635278 ATGGATTCAGTCATGTGGTGATA 57.365 39.130 0.00 0.00 39.48 2.15
599 604 3.938963 CTGACGTGGTTATTATGTTGGCT 59.061 43.478 0.00 0.00 0.00 4.75
612 617 4.946784 ATGTTGGCTCGAATGAAGTTAC 57.053 40.909 0.00 0.00 0.00 2.50
687 692 0.107654 GCGATGAGCCTGTAACCCTT 60.108 55.000 0.00 0.00 40.81 3.95
803 808 1.671328 CAGCTGTTGGATCTGCATCTG 59.329 52.381 5.25 0.00 35.31 2.90
804 809 1.558294 AGCTGTTGGATCTGCATCTGA 59.442 47.619 0.00 0.00 35.31 3.27
805 810 1.669779 GCTGTTGGATCTGCATCTGAC 59.330 52.381 0.00 0.00 33.55 3.51
806 811 1.931841 CTGTTGGATCTGCATCTGACG 59.068 52.381 0.00 0.00 0.00 4.35
807 812 1.293924 GTTGGATCTGCATCTGACGG 58.706 55.000 0.00 0.00 0.00 4.79
808 813 0.462581 TTGGATCTGCATCTGACGGC 60.463 55.000 0.00 0.00 0.00 5.68
809 814 1.144716 GGATCTGCATCTGACGGCA 59.855 57.895 0.00 0.00 38.52 5.69
810 815 0.462581 GGATCTGCATCTGACGGCAA 60.463 55.000 0.00 0.00 39.93 4.52
811 816 0.654683 GATCTGCATCTGACGGCAAC 59.345 55.000 0.00 0.00 39.93 4.17
812 817 0.251354 ATCTGCATCTGACGGCAACT 59.749 50.000 0.00 0.00 39.93 3.16
813 818 0.035317 TCTGCATCTGACGGCAACTT 59.965 50.000 0.00 0.00 39.93 2.66
816 821 1.001974 TGCATCTGACGGCAACTTACT 59.998 47.619 0.00 0.00 37.03 2.24
881 896 3.557054 GCTGATGTTGGTCTTCCTGTGTA 60.557 47.826 0.00 0.00 34.23 2.90
884 899 2.778299 TGTTGGTCTTCCTGTGTATGC 58.222 47.619 0.00 0.00 34.23 3.14
1028 1045 2.090887 ACCGAGTATAAACCCTAGCCCT 60.091 50.000 0.00 0.00 0.00 5.19
1029 1046 3.140895 ACCGAGTATAAACCCTAGCCCTA 59.859 47.826 0.00 0.00 0.00 3.53
1039 1056 1.202818 CCCTAGCCCTAATGTTCTGGC 60.203 57.143 0.00 0.00 44.35 4.85
1108 1126 3.466836 CCACAAAGTGTGCTACTCTGAA 58.533 45.455 2.77 0.00 46.51 3.02
1116 1134 8.506437 CAAAGTGTGCTACTCTGAATGATTTTA 58.494 33.333 0.00 0.00 39.18 1.52
1153 1171 5.046231 CCCTCTTTAGTTCTTCAGGCTAGTT 60.046 44.000 0.00 0.00 0.00 2.24
1215 1253 3.623060 AGCAATTCGTCATGTGTGATACC 59.377 43.478 0.00 0.00 36.60 2.73
1316 1462 4.630111 AGTACGCTATAGCTAGTCGAGTT 58.370 43.478 21.98 0.00 39.32 3.01
1386 1532 2.033675 CGTACGTATCACCATGTGGCTA 59.966 50.000 7.22 0.00 39.32 3.93
1389 1535 2.159099 ACGTATCACCATGTGGCTACTG 60.159 50.000 0.64 0.00 39.32 2.74
1646 1798 4.704833 GCCGCTCCAGCAGACCAA 62.705 66.667 0.00 0.00 42.21 3.67
1721 1873 4.961511 GGTGACGGACGTGCAGCA 62.962 66.667 8.11 0.81 0.00 4.41
1759 1917 2.582498 GCTACAGCTACGGCGTGG 60.582 66.667 24.86 22.17 44.37 4.94
1813 1971 4.689549 TCCGCCGGGACCTCTCAA 62.690 66.667 1.90 0.00 37.43 3.02
1816 1974 3.394836 GCCGGGACCTCTCAAGCT 61.395 66.667 2.18 0.00 0.00 3.74
1934 2102 3.148279 GGTCGTGGCCTCGGAGAT 61.148 66.667 25.62 0.00 33.89 2.75
2047 2215 3.054361 AGACTGCGTTGGGGATAAAATCT 60.054 43.478 0.00 0.00 0.00 2.40
2087 2255 2.187163 GCTCGCCAAGGAGGTACC 59.813 66.667 2.73 2.73 40.61 3.34
2106 2274 9.822185 GAGGTACCTCCGTTTTAAAATAGATAA 57.178 33.333 28.87 0.00 41.99 1.75
2107 2275 9.605275 AGGTACCTCCGTTTTAAAATAGATAAC 57.395 33.333 9.21 0.00 41.99 1.89
2108 2276 8.830580 GGTACCTCCGTTTTAAAATAGATAACC 58.169 37.037 4.06 7.94 0.00 2.85
2109 2277 7.870509 ACCTCCGTTTTAAAATAGATAACCC 57.129 36.000 3.52 0.00 0.00 4.11
2110 2278 7.404481 ACCTCCGTTTTAAAATAGATAACCCA 58.596 34.615 3.52 0.00 0.00 4.51
2111 2279 7.889600 ACCTCCGTTTTAAAATAGATAACCCAA 59.110 33.333 3.52 0.00 0.00 4.12
2112 2280 8.186163 CCTCCGTTTTAAAATAGATAACCCAAC 58.814 37.037 3.52 0.00 0.00 3.77
2113 2281 8.866970 TCCGTTTTAAAATAGATAACCCAACT 57.133 30.769 3.52 0.00 0.00 3.16
2114 2282 9.299465 TCCGTTTTAAAATAGATAACCCAACTT 57.701 29.630 3.52 0.00 0.00 2.66
2115 2283 9.917129 CCGTTTTAAAATAGATAACCCAACTTT 57.083 29.630 3.52 0.00 0.00 2.66
2137 2305 1.462616 ATACGTACGTACAGCCCACA 58.537 50.000 28.99 7.24 33.01 4.17
2138 2306 0.521291 TACGTACGTACAGCCCACAC 59.479 55.000 23.60 0.00 0.00 3.82
2139 2307 1.798725 CGTACGTACAGCCCACACG 60.799 63.158 24.50 6.92 41.32 4.49
2188 2356 7.727331 CAAAATTGCAAATCCTTCCTTTACA 57.273 32.000 1.71 0.00 0.00 2.41
2189 2357 7.799784 CAAAATTGCAAATCCTTCCTTTACAG 58.200 34.615 1.71 0.00 0.00 2.74
2190 2358 6.916360 AATTGCAAATCCTTCCTTTACAGA 57.084 33.333 1.71 0.00 0.00 3.41
2192 2360 4.985538 TGCAAATCCTTCCTTTACAGAGT 58.014 39.130 0.00 0.00 0.00 3.24
2194 2362 5.473504 TGCAAATCCTTCCTTTACAGAGTTC 59.526 40.000 0.00 0.00 0.00 3.01
2195 2363 5.106118 GCAAATCCTTCCTTTACAGAGTTCC 60.106 44.000 0.00 0.00 0.00 3.62
2196 2364 6.241645 CAAATCCTTCCTTTACAGAGTTCCT 58.758 40.000 0.00 0.00 0.00 3.36
2197 2365 6.455690 AATCCTTCCTTTACAGAGTTCCTT 57.544 37.500 0.00 0.00 0.00 3.36
2198 2366 5.906772 TCCTTCCTTTACAGAGTTCCTTT 57.093 39.130 0.00 0.00 0.00 3.11
2199 2367 6.262056 TCCTTCCTTTACAGAGTTCCTTTT 57.738 37.500 0.00 0.00 0.00 2.27
2200 2368 6.296803 TCCTTCCTTTACAGAGTTCCTTTTC 58.703 40.000 0.00 0.00 0.00 2.29
2201 2369 6.101296 TCCTTCCTTTACAGAGTTCCTTTTCT 59.899 38.462 0.00 0.00 0.00 2.52
2202 2370 6.773200 CCTTCCTTTACAGAGTTCCTTTTCTT 59.227 38.462 0.00 0.00 0.00 2.52
2203 2371 7.285629 CCTTCCTTTACAGAGTTCCTTTTCTTT 59.714 37.037 0.00 0.00 0.00 2.52
2204 2372 8.589701 TTCCTTTACAGAGTTCCTTTTCTTTT 57.410 30.769 0.00 0.00 0.00 2.27
2205 2373 9.689501 TTCCTTTACAGAGTTCCTTTTCTTTTA 57.310 29.630 0.00 0.00 0.00 1.52
2206 2374 9.117183 TCCTTTACAGAGTTCCTTTTCTTTTAC 57.883 33.333 0.00 0.00 0.00 2.01
2207 2375 8.350722 CCTTTACAGAGTTCCTTTTCTTTTACC 58.649 37.037 0.00 0.00 0.00 2.85
2208 2376 9.121658 CTTTACAGAGTTCCTTTTCTTTTACCT 57.878 33.333 0.00 0.00 0.00 3.08
2210 2378 9.774413 TTACAGAGTTCCTTTTCTTTTACCTAG 57.226 33.333 0.00 0.00 0.00 3.02
2211 2379 8.030913 ACAGAGTTCCTTTTCTTTTACCTAGA 57.969 34.615 0.00 0.00 0.00 2.43
2212 2380 8.661345 ACAGAGTTCCTTTTCTTTTACCTAGAT 58.339 33.333 0.00 0.00 0.00 1.98
2235 2403 1.527034 TGAACCTGCTGCATGAACTC 58.473 50.000 11.93 5.88 0.00 3.01
2238 2406 0.607489 ACCTGCTGCATGAACTCACC 60.607 55.000 11.93 0.00 0.00 4.02
2248 2416 3.181486 GCATGAACTCACCTGATCGAGTA 60.181 47.826 0.00 0.00 41.60 2.59
2249 2417 4.500545 GCATGAACTCACCTGATCGAGTAT 60.501 45.833 0.00 0.00 41.60 2.12
2250 2418 5.595885 CATGAACTCACCTGATCGAGTATT 58.404 41.667 1.98 0.00 41.60 1.89
2283 2455 1.303643 GGTTGAAGCCTGTGGAGGG 60.304 63.158 0.00 0.00 40.19 4.30
2309 2481 3.411446 CACTGGCACTAAGGATGTTTGA 58.589 45.455 0.00 0.00 0.00 2.69
2329 2501 2.526304 TTGCCCGATGTCTGCTATAC 57.474 50.000 0.00 0.00 0.00 1.47
2332 2504 2.224042 TGCCCGATGTCTGCTATACAAG 60.224 50.000 0.00 0.00 0.00 3.16
2372 2544 9.535878 GAGGTATATGCATAAGTATCTTAAGGC 57.464 37.037 11.13 0.00 0.00 4.35
2391 2564 0.680921 CCCGGCTTCCATTGTCACAT 60.681 55.000 0.00 0.00 0.00 3.21
2397 2570 3.005684 GGCTTCCATTGTCACATGAACAA 59.994 43.478 16.74 16.74 0.00 2.83
2429 2602 7.604164 AGATTTGTTAGATAATATCGGGCACTG 59.396 37.037 0.00 0.00 0.00 3.66
2433 2606 6.268158 TGTTAGATAATATCGGGCACTGGTAA 59.732 38.462 0.00 0.00 32.07 2.85
2461 2635 7.166473 GTGTTTCAGCTGCAATAATAATGCTAC 59.834 37.037 9.47 0.00 44.14 3.58
2469 2643 8.348507 GCTGCAATAATAATGCTACTTTCTTCT 58.651 33.333 1.79 0.00 44.14 2.85
2493 2667 5.036117 TGAGCTTGTAAGTTTTCTCCACT 57.964 39.130 0.00 0.00 0.00 4.00
2494 2668 5.437060 TGAGCTTGTAAGTTTTCTCCACTT 58.563 37.500 0.00 0.00 38.13 3.16
2495 2669 5.527582 TGAGCTTGTAAGTTTTCTCCACTTC 59.472 40.000 0.00 0.00 35.95 3.01
2496 2670 5.437060 AGCTTGTAAGTTTTCTCCACTTCA 58.563 37.500 0.00 0.00 35.95 3.02
2497 2671 5.529060 AGCTTGTAAGTTTTCTCCACTTCAG 59.471 40.000 0.00 0.00 35.95 3.02
2498 2672 5.278022 GCTTGTAAGTTTTCTCCACTTCAGG 60.278 44.000 0.00 0.00 35.95 3.86
2499 2673 4.134563 TGTAAGTTTTCTCCACTTCAGGC 58.865 43.478 0.00 0.00 35.95 4.85
2500 2674 3.584733 AAGTTTTCTCCACTTCAGGCT 57.415 42.857 0.00 0.00 27.49 4.58
2501 2675 3.133141 AGTTTTCTCCACTTCAGGCTC 57.867 47.619 0.00 0.00 0.00 4.70
2502 2676 2.155279 GTTTTCTCCACTTCAGGCTCC 58.845 52.381 0.00 0.00 0.00 4.70
2503 2677 0.321671 TTTCTCCACTTCAGGCTCCG 59.678 55.000 0.00 0.00 0.00 4.63
2504 2678 0.832135 TTCTCCACTTCAGGCTCCGT 60.832 55.000 0.00 0.00 0.00 4.69
2505 2679 0.832135 TCTCCACTTCAGGCTCCGTT 60.832 55.000 0.00 0.00 0.00 4.44
2506 2680 0.035458 CTCCACTTCAGGCTCCGTTT 59.965 55.000 0.00 0.00 0.00 3.60
2507 2681 0.250295 TCCACTTCAGGCTCCGTTTG 60.250 55.000 0.00 0.00 0.00 2.93
2727 2904 3.332968 AGTAAAGGGAAGGGTTTGGAGA 58.667 45.455 0.00 0.00 0.00 3.71
2796 2973 2.037251 GGTGGTGCTATCGTACATCCAT 59.963 50.000 0.00 0.00 0.00 3.41
3104 3282 3.254166 TCCTTGCTCTTGTGCTTCAAATC 59.746 43.478 0.00 0.00 35.48 2.17
3150 3328 7.729431 ACTCTCTCTCATATGATTTGGATCTGA 59.271 37.037 5.72 0.00 33.28 3.27
3405 3584 1.201647 GGACCGATTCAACAGACTCGA 59.798 52.381 6.78 0.00 36.81 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
105 106 3.139077 GACGTTTGTCCTCTTTGGTGAT 58.861 45.455 0.00 0.00 39.30 3.06
120 121 0.322546 GCTTCATCCCAGGGACGTTT 60.323 55.000 11.70 0.00 32.98 3.60
257 258 6.334989 TGTTAGAACGGACGATACAATTGAT 58.665 36.000 13.59 1.08 0.00 2.57
272 273 6.326375 AGACAAGAAGATAGCTGTTAGAACG 58.674 40.000 0.00 0.00 0.00 3.95
290 291 6.205464 TCTCCTGAAAATAGCACAAAGACAAG 59.795 38.462 0.00 0.00 0.00 3.16
292 293 5.620206 TCTCCTGAAAATAGCACAAAGACA 58.380 37.500 0.00 0.00 0.00 3.41
293 294 5.703130 ACTCTCCTGAAAATAGCACAAAGAC 59.297 40.000 0.00 0.00 0.00 3.01
357 358 0.541998 TGGAAGCCTCGTCCTCTCAA 60.542 55.000 0.94 0.00 36.03 3.02
387 388 0.742990 GTATGGCTACTGGCGTTGCA 60.743 55.000 14.62 0.00 42.50 4.08
392 393 0.597637 CTTCGGTATGGCTACTGGCG 60.598 60.000 4.01 0.00 42.94 5.69
407 408 2.410053 GCGGCAGCTAGATTATTCTTCG 59.590 50.000 0.00 0.00 41.01 3.79
435 436 5.761234 TGTCTACCAGTCAAACAATGTAACC 59.239 40.000 0.00 0.00 0.00 2.85
474 475 3.642755 CACGATAGGGGCATTCGC 58.357 61.111 0.00 0.00 43.77 4.70
494 495 4.926238 CCACAGTACAACAGAGCTTAAGAG 59.074 45.833 6.67 0.00 0.00 2.85
530 532 5.824624 ACCAATATCACCACATGACTGAATC 59.175 40.000 0.00 0.00 41.24 2.52
549 551 3.832527 ACTACCAAGTCAGCAAACCAAT 58.167 40.909 0.00 0.00 0.00 3.16
599 604 3.239587 TGGCATCGTAACTTCATTCGA 57.760 42.857 0.00 0.00 36.77 3.71
612 617 2.282407 TGACATCAGAACATGGCATCG 58.718 47.619 0.00 0.00 36.83 3.84
687 692 9.702494 CTGACATATGCTATACTTCAGATTCAA 57.298 33.333 10.28 0.00 32.42 2.69
803 808 0.438830 CGAAGCAGTAAGTTGCCGTC 59.561 55.000 0.00 0.00 45.18 4.79
804 809 0.249741 ACGAAGCAGTAAGTTGCCGT 60.250 50.000 0.00 0.00 45.18 5.68
805 810 0.865769 AACGAAGCAGTAAGTTGCCG 59.134 50.000 0.00 0.00 45.18 5.69
806 811 1.871039 TCAACGAAGCAGTAAGTTGCC 59.129 47.619 0.00 0.00 45.18 4.52
807 812 2.663063 GCTCAACGAAGCAGTAAGTTGC 60.663 50.000 0.00 0.00 42.42 4.17
808 813 2.802816 AGCTCAACGAAGCAGTAAGTTG 59.197 45.455 10.78 1.22 45.00 3.16
809 814 2.802816 CAGCTCAACGAAGCAGTAAGTT 59.197 45.455 10.78 0.00 45.00 2.66
810 815 2.408050 CAGCTCAACGAAGCAGTAAGT 58.592 47.619 10.78 0.00 45.00 2.24
811 816 1.127582 GCAGCTCAACGAAGCAGTAAG 59.872 52.381 10.78 0.00 45.00 2.34
812 817 1.148310 GCAGCTCAACGAAGCAGTAA 58.852 50.000 10.78 0.00 45.00 2.24
813 818 0.670546 GGCAGCTCAACGAAGCAGTA 60.671 55.000 10.78 0.00 45.00 2.74
816 821 1.669115 GAGGCAGCTCAACGAAGCA 60.669 57.895 10.78 0.00 45.00 3.91
862 877 3.375299 GCATACACAGGAAGACCAACATC 59.625 47.826 0.00 0.00 38.94 3.06
881 896 2.481952 GCTCTTCTCGTGTTTCAAGCAT 59.518 45.455 0.00 0.00 0.00 3.79
884 899 3.060003 CAGTGCTCTTCTCGTGTTTCAAG 60.060 47.826 0.00 0.00 0.00 3.02
968 984 0.680061 CCCTCGGTATACTGGGCTTC 59.320 60.000 11.82 0.00 32.49 3.86
1028 1045 2.576191 ACTTAGGCCAGCCAGAACATTA 59.424 45.455 12.03 0.00 38.92 1.90
1029 1046 1.355720 ACTTAGGCCAGCCAGAACATT 59.644 47.619 12.03 0.00 38.92 2.71
1039 1056 0.753262 AGGATACGCACTTAGGCCAG 59.247 55.000 5.01 0.00 46.39 4.85
1108 1126 8.118600 AGAGGGGAGAAATTCAGTTAAAATCAT 58.881 33.333 0.00 0.00 0.00 2.45
1116 1134 6.455690 ACTAAAGAGGGGAGAAATTCAGTT 57.544 37.500 0.00 0.00 0.00 3.16
1215 1253 3.304928 GGACATGGCTTCAACTTCAACTG 60.305 47.826 0.00 0.00 0.00 3.16
1316 1462 2.202610 CTCACGCCGCGAGAATCA 60.203 61.111 21.79 0.00 31.84 2.57
1353 1499 2.100216 CGTACGTACGGGGTTCGG 59.900 66.667 34.54 9.16 45.30 4.30
1386 1532 3.520721 TGTGGTGGATGATCTTGATCAGT 59.479 43.478 16.86 7.18 33.59 3.41
1389 1535 4.711399 TCATGTGGTGGATGATCTTGATC 58.289 43.478 3.82 3.82 0.00 2.92
1780 1938 3.797353 GATGAGGCGGGCCAGGAA 61.797 66.667 12.97 0.00 38.92 3.36
2047 2215 2.741878 GCCGAATCCGAGAATCTTGGAA 60.742 50.000 22.14 7.16 45.99 3.53
2087 2255 8.953313 AGTTGGGTTATCTATTTTAAAACGGAG 58.047 33.333 1.97 1.74 0.00 4.63
2088 2256 8.866970 AGTTGGGTTATCTATTTTAAAACGGA 57.133 30.769 1.97 5.09 0.00 4.69
2089 2257 9.917129 AAAGTTGGGTTATCTATTTTAAAACGG 57.083 29.630 1.97 0.00 0.00 4.44
2097 2265 9.895138 ACGTATACAAAGTTGGGTTATCTATTT 57.105 29.630 3.32 0.00 0.00 1.40
2099 2267 9.971922 GTACGTATACAAAGTTGGGTTATCTAT 57.028 33.333 0.00 0.00 0.00 1.98
2100 2268 8.128582 CGTACGTATACAAAGTTGGGTTATCTA 58.871 37.037 7.22 0.00 0.00 1.98
2101 2269 6.974622 CGTACGTATACAAAGTTGGGTTATCT 59.025 38.462 7.22 0.00 0.00 1.98
2102 2270 6.751888 ACGTACGTATACAAAGTTGGGTTATC 59.248 38.462 21.41 0.00 0.00 1.75
2103 2271 6.630071 ACGTACGTATACAAAGTTGGGTTAT 58.370 36.000 21.41 0.00 0.00 1.89
2104 2272 6.019779 ACGTACGTATACAAAGTTGGGTTA 57.980 37.500 21.41 0.00 0.00 2.85
2105 2273 4.881920 ACGTACGTATACAAAGTTGGGTT 58.118 39.130 21.41 0.00 0.00 4.11
2106 2274 4.519540 ACGTACGTATACAAAGTTGGGT 57.480 40.909 21.41 0.00 0.00 4.51
2107 2275 5.398169 TGTACGTACGTATACAAAGTTGGG 58.602 41.667 29.05 0.00 32.82 4.12
2108 2276 5.003778 GCTGTACGTACGTATACAAAGTTGG 59.996 44.000 29.05 14.45 31.09 3.77
2109 2277 5.003778 GGCTGTACGTACGTATACAAAGTTG 59.996 44.000 29.05 15.07 31.09 3.16
2110 2278 5.095490 GGCTGTACGTACGTATACAAAGTT 58.905 41.667 29.05 2.13 31.09 2.66
2111 2279 4.438744 GGGCTGTACGTACGTATACAAAGT 60.439 45.833 29.05 2.89 31.09 2.66
2112 2280 4.037690 GGGCTGTACGTACGTATACAAAG 58.962 47.826 29.05 20.60 31.09 2.77
2113 2281 3.441922 TGGGCTGTACGTACGTATACAAA 59.558 43.478 29.05 12.32 31.09 2.83
2114 2282 3.013219 TGGGCTGTACGTACGTATACAA 58.987 45.455 29.05 15.02 31.09 2.41
2115 2283 2.354510 GTGGGCTGTACGTACGTATACA 59.645 50.000 29.05 24.01 32.82 2.29
2116 2284 2.354510 TGTGGGCTGTACGTACGTATAC 59.645 50.000 29.05 20.87 32.82 1.47
2117 2285 2.354510 GTGTGGGCTGTACGTACGTATA 59.645 50.000 29.05 25.01 32.82 1.47
2118 2286 1.133025 GTGTGGGCTGTACGTACGTAT 59.867 52.381 29.05 7.54 32.82 3.06
2139 2307 2.205074 CATGCACGGTGATTCTACTCC 58.795 52.381 13.29 0.00 0.00 3.85
2168 2336 6.012745 ACTCTGTAAAGGAAGGATTTGCAAT 58.987 36.000 0.00 0.00 32.92 3.56
2169 2337 5.385198 ACTCTGTAAAGGAAGGATTTGCAA 58.615 37.500 0.00 0.00 32.92 4.08
2170 2338 4.985538 ACTCTGTAAAGGAAGGATTTGCA 58.014 39.130 0.00 0.00 32.45 4.08
2171 2339 5.106118 GGAACTCTGTAAAGGAAGGATTTGC 60.106 44.000 0.00 0.00 0.00 3.68
2172 2340 6.241645 AGGAACTCTGTAAAGGAAGGATTTG 58.758 40.000 0.00 0.00 0.00 2.32
2173 2341 6.455690 AGGAACTCTGTAAAGGAAGGATTT 57.544 37.500 0.00 0.00 0.00 2.17
2174 2342 6.455690 AAGGAACTCTGTAAAGGAAGGATT 57.544 37.500 0.00 0.00 38.49 3.01
2175 2343 6.455690 AAAGGAACTCTGTAAAGGAAGGAT 57.544 37.500 0.00 0.00 38.49 3.24
2176 2344 5.906772 AAAGGAACTCTGTAAAGGAAGGA 57.093 39.130 0.00 0.00 38.49 3.36
2178 2346 7.809546 AAGAAAAGGAACTCTGTAAAGGAAG 57.190 36.000 0.00 0.00 38.49 3.46
2181 2349 8.350722 GGTAAAAGAAAAGGAACTCTGTAAAGG 58.649 37.037 0.00 0.00 38.49 3.11
2182 2350 9.121658 AGGTAAAAGAAAAGGAACTCTGTAAAG 57.878 33.333 0.00 0.00 38.49 1.85
2186 2354 8.030913 TCTAGGTAAAAGAAAAGGAACTCTGT 57.969 34.615 0.00 0.00 38.49 3.41
2198 2366 9.174166 GCAGGTTCAAATATCTAGGTAAAAGAA 57.826 33.333 0.00 0.00 0.00 2.52
2199 2367 8.548877 AGCAGGTTCAAATATCTAGGTAAAAGA 58.451 33.333 0.00 0.00 0.00 2.52
2200 2368 8.616076 CAGCAGGTTCAAATATCTAGGTAAAAG 58.384 37.037 0.00 0.00 0.00 2.27
2201 2369 7.067008 GCAGCAGGTTCAAATATCTAGGTAAAA 59.933 37.037 0.00 0.00 0.00 1.52
2202 2370 6.542370 GCAGCAGGTTCAAATATCTAGGTAAA 59.458 38.462 0.00 0.00 0.00 2.01
2203 2371 6.055588 GCAGCAGGTTCAAATATCTAGGTAA 58.944 40.000 0.00 0.00 0.00 2.85
2204 2372 5.130311 TGCAGCAGGTTCAAATATCTAGGTA 59.870 40.000 0.00 0.00 0.00 3.08
2205 2373 4.080356 TGCAGCAGGTTCAAATATCTAGGT 60.080 41.667 0.00 0.00 0.00 3.08
2206 2374 4.454678 TGCAGCAGGTTCAAATATCTAGG 58.545 43.478 0.00 0.00 0.00 3.02
2207 2375 5.761726 TCATGCAGCAGGTTCAAATATCTAG 59.238 40.000 6.99 0.00 0.00 2.43
2208 2376 5.683681 TCATGCAGCAGGTTCAAATATCTA 58.316 37.500 6.99 0.00 0.00 1.98
2209 2377 4.529897 TCATGCAGCAGGTTCAAATATCT 58.470 39.130 6.99 0.00 0.00 1.98
2210 2378 4.906065 TCATGCAGCAGGTTCAAATATC 57.094 40.909 6.99 0.00 0.00 1.63
2211 2379 4.708421 AGTTCATGCAGCAGGTTCAAATAT 59.292 37.500 6.99 0.00 0.00 1.28
2212 2380 4.081406 AGTTCATGCAGCAGGTTCAAATA 58.919 39.130 6.99 0.00 0.00 1.40
2235 2403 4.092529 GCATGCATAATACTCGATCAGGTG 59.907 45.833 14.21 0.00 0.00 4.00
2238 2406 3.241900 GCGCATGCATAATACTCGATCAG 60.242 47.826 19.57 0.00 42.15 2.90
2267 2439 0.178992 CAACCCTCCACAGGCTTCAA 60.179 55.000 0.00 0.00 38.72 2.69
2309 2481 2.368548 TGTATAGCAGACATCGGGCAAT 59.631 45.455 0.00 0.00 0.00 3.56
2329 2501 3.552875 ACCTCCATTCATCTGCATCTTG 58.447 45.455 0.00 0.00 0.00 3.02
2332 2504 5.296283 GCATATACCTCCATTCATCTGCATC 59.704 44.000 0.00 0.00 0.00 3.91
2370 2542 3.140814 GACAATGGAAGCCGGGCC 61.141 66.667 17.02 0.15 0.00 5.80
2372 2544 0.680921 ATGTGACAATGGAAGCCGGG 60.681 55.000 2.18 0.00 0.00 5.73
2414 2587 3.908103 ACCTTACCAGTGCCCGATATTAT 59.092 43.478 0.00 0.00 0.00 1.28
2415 2588 3.070446 CACCTTACCAGTGCCCGATATTA 59.930 47.826 0.00 0.00 0.00 0.98
2416 2589 2.124411 ACCTTACCAGTGCCCGATATT 58.876 47.619 0.00 0.00 0.00 1.28
2422 2595 1.244816 GAAACACCTTACCAGTGCCC 58.755 55.000 0.00 0.00 38.87 5.36
2429 2602 1.604604 TGCAGCTGAAACACCTTACC 58.395 50.000 20.43 0.00 0.00 2.85
2433 2606 6.567050 CATTATTATTGCAGCTGAAACACCT 58.433 36.000 20.43 0.00 0.00 4.00
2461 2635 8.917415 AAAACTTACAAGCTCAAAGAAGAAAG 57.083 30.769 9.04 0.00 0.00 2.62
2469 2643 5.885912 AGTGGAGAAAACTTACAAGCTCAAA 59.114 36.000 0.00 0.00 0.00 2.69
2493 2667 2.224670 ACAATACCAAACGGAGCCTGAA 60.225 45.455 0.00 0.00 0.00 3.02
2494 2668 1.349688 ACAATACCAAACGGAGCCTGA 59.650 47.619 0.00 0.00 0.00 3.86
2495 2669 1.821216 ACAATACCAAACGGAGCCTG 58.179 50.000 0.00 0.00 0.00 4.85
2496 2670 2.093128 CCTACAATACCAAACGGAGCCT 60.093 50.000 0.00 0.00 0.00 4.58
2497 2671 2.093341 TCCTACAATACCAAACGGAGCC 60.093 50.000 0.00 0.00 0.00 4.70
2498 2672 2.934553 GTCCTACAATACCAAACGGAGC 59.065 50.000 0.00 0.00 0.00 4.70
2499 2673 3.197116 AGGTCCTACAATACCAAACGGAG 59.803 47.826 0.00 0.00 38.30 4.63
2500 2674 3.175594 AGGTCCTACAATACCAAACGGA 58.824 45.455 0.00 0.00 38.30 4.69
2501 2675 3.622166 AGGTCCTACAATACCAAACGG 57.378 47.619 0.00 0.00 38.30 4.44
2502 2676 4.571919 TCAAGGTCCTACAATACCAAACG 58.428 43.478 0.00 0.00 38.30 3.60
2503 2677 6.002082 ACTTCAAGGTCCTACAATACCAAAC 58.998 40.000 0.00 0.00 38.30 2.93
2504 2678 6.195600 ACTTCAAGGTCCTACAATACCAAA 57.804 37.500 0.00 0.00 38.30 3.28
2505 2679 5.836024 ACTTCAAGGTCCTACAATACCAA 57.164 39.130 0.00 0.00 38.30 3.67
2506 2680 6.499350 ACTTACTTCAAGGTCCTACAATACCA 59.501 38.462 0.00 0.00 38.70 3.25
2507 2681 6.944096 ACTTACTTCAAGGTCCTACAATACC 58.056 40.000 0.00 0.00 38.70 2.73
2673 2850 4.524316 TGCATGCTTTAATTTCTGCTGT 57.476 36.364 20.33 0.00 0.00 4.40
2727 2904 4.298332 GTGTCTCCAATTGCGTTTGAATT 58.702 39.130 0.00 0.00 0.00 2.17
3013 3191 4.314740 CTAGATTGGCTAGGTGTCACTC 57.685 50.000 2.35 0.00 42.41 3.51
3104 3282 3.261897 AGTTGAGTGTTGGGGAGACTATG 59.738 47.826 0.00 0.00 30.90 2.23
3150 3328 4.934797 TCCACTCAAATCCTCTTTCCAT 57.065 40.909 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.