Multiple sequence alignment - TraesCS7D01G229700

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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 TraesCS7D01G229700 chr7D 100.000 2348 0 0 1 2348 190128210 190130557 0.000000e+00 4337.0
1 TraesCS7D01G229700 chr7B 88.917 1570 98 37 584 2107 334797947 334799486 0.000000e+00 1866.0
2 TraesCS7D01G229700 chr7B 89.792 529 44 7 1 528 334797421 334797940 0.000000e+00 669.0
3 TraesCS7D01G229700 chr7B 87.791 172 18 3 2098 2268 450584066 450584235 5.120000e-47 198.0
4 TraesCS7D01G229700 chr7B 100.000 41 0 0 2283 2323 334801290 334801330 2.500000e-10 76.8
5 TraesCS7D01G229700 chr7A 86.614 1270 99 30 624 1846 199004239 199005484 0.000000e+00 1338.0
6 TraesCS7D01G229700 chr7A 87.591 274 19 8 232 496 199003927 199004194 1.050000e-78 303.0
7 TraesCS7D01G229700 chr7A 90.789 152 10 4 2094 2243 343843700 343843849 1.420000e-47 200.0
8 TraesCS7D01G229700 chr7A 86.792 159 12 2 99 248 199003752 199003910 4.010000e-38 169.0
9 TraesCS7D01G229700 chr7A 90.909 66 5 1 2253 2317 199005676 199005741 1.160000e-13 87.9
10 TraesCS7D01G229700 chr7A 86.154 65 4 1 522 581 7041086 7041150 5.420000e-07 65.8
11 TraesCS7D01G229700 chr1D 96.154 130 5 0 2103 2232 469558682 469558811 1.830000e-51 213.0
12 TraesCS7D01G229700 chr3D 94.815 135 7 0 2099 2233 283321118 283321252 6.570000e-51 211.0
13 TraesCS7D01G229700 chr3D 91.837 147 11 1 2086 2232 496172901 496172756 1.100000e-48 204.0
14 TraesCS7D01G229700 chr3A 93.571 140 7 2 2095 2233 348834583 348834445 8.500000e-50 207.0
15 TraesCS7D01G229700 chrUn 92.361 144 11 0 2097 2240 74542127 74542270 3.060000e-49 206.0
16 TraesCS7D01G229700 chr2B 92.361 144 10 1 2103 2246 548925139 548924997 1.100000e-48 204.0
17 TraesCS7D01G229700 chr3B 90.385 156 12 3 2079 2233 741865824 741865977 3.960000e-48 202.0
18 TraesCS7D01G229700 chr3B 90.741 54 3 2 541 594 697073792 697073741 1.160000e-08 71.3
19 TraesCS7D01G229700 chr1A 95.455 44 2 0 539 582 119144542 119144499 1.160000e-08 71.3
20 TraesCS7D01G229700 chr6A 95.349 43 2 0 539 581 375012052 375012094 4.190000e-08 69.4
21 TraesCS7D01G229700 chr6A 95.349 43 2 0 539 581 375063387 375063429 4.190000e-08 69.4
22 TraesCS7D01G229700 chr6B 90.385 52 4 1 541 591 162181222 162181273 1.510000e-07 67.6
23 TraesCS7D01G229700 chr2A 91.667 48 4 0 541 588 605114963 605114916 1.510000e-07 67.6
24 TraesCS7D01G229700 chr2A 90.196 51 4 1 541 591 694958676 694958627 5.420000e-07 65.8
25 TraesCS7D01G229700 chr6D 90.000 50 5 0 541 590 78275820 78275771 5.420000e-07 65.8


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 TraesCS7D01G229700 chr7D 190128210 190130557 2347 False 4337.000 4337 100.0000 1 2348 1 chr7D.!!$F1 2347
1 TraesCS7D01G229700 chr7B 334797421 334801330 3909 False 870.600 1866 92.9030 1 2323 3 chr7B.!!$F2 2322
2 TraesCS7D01G229700 chr7A 199003752 199005741 1989 False 474.475 1338 87.9765 99 2317 4 chr7A.!!$F3 2218

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
665 740 0.105039 CAGTAGGCGGGAACTCCATC 59.895 60.0 0.0 0.0 37.91 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2215 2446 0.337082 TGATACTCCCTCCGTCCCAA 59.663 55.0 0.0 0.0 0.0 4.12 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
22 23 2.161030 GCCGTAGTATCCTACTCCCTG 58.839 57.143 0.00 0.00 41.24 4.45
56 58 3.430042 AACAATCTGTGTGCTCAGGAT 57.570 42.857 0.00 0.00 40.60 3.24
72 74 5.359194 TCAGGATAAAGAACATCACCTCC 57.641 43.478 0.00 0.00 0.00 4.30
78 80 0.898789 AGAACATCACCTCCGACGGT 60.899 55.000 14.79 0.00 37.93 4.83
80 82 0.395312 AACATCACCTCCGACGGTTT 59.605 50.000 14.79 0.00 34.29 3.27
81 83 0.320421 ACATCACCTCCGACGGTTTG 60.320 55.000 14.79 9.56 34.29 2.93
83 85 0.395312 ATCACCTCCGACGGTTTGTT 59.605 50.000 14.79 2.22 34.29 2.83
91 93 1.877443 CCGACGGTTTGTTCTGGATTT 59.123 47.619 5.48 0.00 0.00 2.17
120 122 1.422269 GCCGCAATTTGCAATGCTG 59.578 52.632 20.56 15.37 45.36 4.41
153 155 0.657840 GCGCAATTTAGTCGGCTCAT 59.342 50.000 0.30 0.00 0.00 2.90
213 215 0.521735 GAAAGGGCACGCAGGTTTAG 59.478 55.000 0.00 0.00 0.00 1.85
216 218 0.179001 AGGGCACGCAGGTTTAGTTT 60.179 50.000 0.00 0.00 0.00 2.66
242 253 2.490902 GGGGTCAACCAGGAAGAAATGT 60.491 50.000 0.89 0.00 42.91 2.71
252 296 3.519510 CAGGAAGAAATGTGGGAGAGGTA 59.480 47.826 0.00 0.00 0.00 3.08
267 311 5.189145 GGGAGAGGTAATCTTGTGAGGTTAA 59.811 44.000 0.00 0.00 38.84 2.01
268 312 6.126739 GGGAGAGGTAATCTTGTGAGGTTAAT 60.127 42.308 0.00 0.00 38.84 1.40
340 385 1.079503 GCCGTAAACTGGAGCTCAAG 58.920 55.000 17.08 17.08 0.00 3.02
342 387 2.353406 GCCGTAAACTGGAGCTCAAGTA 60.353 50.000 24.24 6.92 0.00 2.24
432 479 2.126307 CACTGACGGACGAGCCAG 60.126 66.667 0.00 5.49 35.94 4.85
473 521 1.233019 CCGCCATCTTCATCACCATC 58.767 55.000 0.00 0.00 0.00 3.51
490 565 8.789762 CATCACCATCTTGCAGAAAATATATGA 58.210 33.333 0.00 0.00 0.00 2.15
553 628 9.931698 TTTATAGAGGGAGTAGTGATCTAAACA 57.068 33.333 0.00 0.00 0.00 2.83
554 629 7.826918 ATAGAGGGAGTAGTGATCTAAACAC 57.173 40.000 0.00 0.00 38.38 3.32
556 631 6.257586 AGAGGGAGTAGTGATCTAAACACTT 58.742 40.000 0.00 0.00 44.69 3.16
557 632 6.726764 AGAGGGAGTAGTGATCTAAACACTTT 59.273 38.462 0.00 0.00 44.69 2.66
558 633 7.235812 AGAGGGAGTAGTGATCTAAACACTTTT 59.764 37.037 0.00 0.00 44.69 2.27
559 634 8.431910 AGGGAGTAGTGATCTAAACACTTTTA 57.568 34.615 0.00 0.00 44.69 1.52
560 635 9.047947 AGGGAGTAGTGATCTAAACACTTTTAT 57.952 33.333 0.00 0.00 44.69 1.40
619 694 9.733556 AAATGTAGAATATTGCATCGGGTATAA 57.266 29.630 0.00 0.00 0.00 0.98
656 731 1.144057 GTGGATCACAGTAGGCGGG 59.856 63.158 0.00 0.00 34.08 6.13
665 740 0.105039 CAGTAGGCGGGAACTCCATC 59.895 60.000 0.00 0.00 37.91 3.51
667 742 2.131709 TAGGCGGGAACTCCATCGG 61.132 63.158 0.00 0.00 37.91 4.18
714 790 3.107402 TGGTAGTGAATCTGGAGCTCT 57.893 47.619 14.64 0.00 0.00 4.09
716 792 3.954904 TGGTAGTGAATCTGGAGCTCTAC 59.045 47.826 14.64 4.63 0.00 2.59
738 814 8.487028 TCTACCAGAAACTTTCTCTTTCTCTTT 58.513 33.333 0.67 0.00 38.11 2.52
796 877 2.669434 TCACGCCGATTAGTAGCAAAAC 59.331 45.455 0.00 0.00 0.00 2.43
847 928 0.730265 ACTTGTTTGACTTTCGCGCA 59.270 45.000 8.75 0.00 0.00 6.09
955 1036 0.386476 CTGCAGCACACACAAACCAT 59.614 50.000 0.00 0.00 0.00 3.55
962 1043 2.226437 GCACACACAAACCATAGACCAG 59.774 50.000 0.00 0.00 0.00 4.00
963 1044 2.813754 CACACACAAACCATAGACCAGG 59.186 50.000 0.00 0.00 0.00 4.45
966 1047 2.158534 ACACAAACCATAGACCAGGCAA 60.159 45.455 0.00 0.00 0.00 4.52
986 1067 1.004440 AAGCCAAGGAGCGTGAGAC 60.004 57.895 0.00 0.00 38.01 3.36
1477 1610 5.405571 GGCAGAGTATTCGTGTATATGTTGG 59.594 44.000 0.00 0.00 0.00 3.77
1489 1622 7.972277 TCGTGTATATGTTGGTTCTTCTTAGTC 59.028 37.037 0.00 0.00 0.00 2.59
1491 1624 7.494952 GTGTATATGTTGGTTCTTCTTAGTCCC 59.505 40.741 0.00 0.00 0.00 4.46
1498 1631 4.202430 TGGTTCTTCTTAGTCCCCTGTTTC 60.202 45.833 0.00 0.00 0.00 2.78
1579 1720 6.509997 GCAAAATTTGGTGTTGTCTAAGCAAG 60.510 38.462 7.89 0.00 35.42 4.01
1580 1721 3.708563 TTTGGTGTTGTCTAAGCAAGC 57.291 42.857 0.00 0.00 35.42 4.01
1592 1733 5.764686 TGTCTAAGCAAGCTTCTTTGATTGA 59.235 36.000 11.05 4.96 37.27 2.57
1614 1766 1.081892 CTGCTTGTGGGAGTTGATCG 58.918 55.000 0.00 0.00 0.00 3.69
1663 1852 2.802247 TCTTCATGATTTATGCGCTCGG 59.198 45.455 9.73 0.00 36.70 4.63
1734 1923 8.612619 AGCGTGAATGGTAAGACTAATATTTTG 58.387 33.333 0.00 0.00 0.00 2.44
1771 1962 0.674895 GCCAGGTCACATGAGTCCAC 60.675 60.000 0.00 0.00 0.00 4.02
1774 1965 1.070601 CAGGTCACATGAGTCCACACA 59.929 52.381 0.00 0.00 0.00 3.72
1807 1998 4.797868 TCAACGAACCGTACCGTAAATATG 59.202 41.667 0.00 0.00 39.99 1.78
1858 2049 3.969976 TCTGCCTGTTATATGCCTCTCTT 59.030 43.478 0.00 0.00 0.00 2.85
1862 2053 6.658849 TGCCTGTTATATGCCTCTCTTTTTA 58.341 36.000 0.00 0.00 0.00 1.52
1863 2054 6.542370 TGCCTGTTATATGCCTCTCTTTTTAC 59.458 38.462 0.00 0.00 0.00 2.01
1865 2056 6.202954 CCTGTTATATGCCTCTCTTTTTACGG 59.797 42.308 0.00 0.00 0.00 4.02
1970 2166 3.991367 ACGGTATGTAGCCATTAGAAGC 58.009 45.455 0.00 0.00 32.29 3.86
1990 2186 6.879458 AGAAGCGATTTTAAGAACCTGTGTAT 59.121 34.615 0.00 0.00 0.00 2.29
1995 2191 7.168637 GCGATTTTAAGAACCTGTGTATATCGA 59.831 37.037 0.00 0.00 0.00 3.59
2030 2226 8.637986 TCATAAAACTTAGCCAAAAAGACATGT 58.362 29.630 0.00 0.00 0.00 3.21
2060 2256 7.022979 TCTGCAAAATATGACAAAAGATCACG 58.977 34.615 0.00 0.00 0.00 4.35
2068 2264 1.333619 ACAAAAGATCACGCACACACC 59.666 47.619 0.00 0.00 0.00 4.16
2070 2266 0.889186 AAAGATCACGCACACACCCC 60.889 55.000 0.00 0.00 0.00 4.95
2112 2343 9.981460 AAATGAGAAAATTAAGATGTACTCCCT 57.019 29.630 0.00 0.00 0.00 4.20
2113 2344 9.620259 AATGAGAAAATTAAGATGTACTCCCTC 57.380 33.333 0.00 0.00 0.00 4.30
2114 2345 7.565680 TGAGAAAATTAAGATGTACTCCCTCC 58.434 38.462 0.00 0.00 0.00 4.30
2115 2346 6.583562 AGAAAATTAAGATGTACTCCCTCCG 58.416 40.000 0.00 0.00 0.00 4.63
2116 2347 5.952347 AAATTAAGATGTACTCCCTCCGT 57.048 39.130 0.00 0.00 0.00 4.69
2117 2348 5.952347 AATTAAGATGTACTCCCTCCGTT 57.048 39.130 0.00 0.00 0.00 4.44
2118 2349 5.952347 ATTAAGATGTACTCCCTCCGTTT 57.048 39.130 0.00 0.00 0.00 3.60
2119 2350 3.889520 AAGATGTACTCCCTCCGTTTC 57.110 47.619 0.00 0.00 0.00 2.78
2120 2351 2.816411 AGATGTACTCCCTCCGTTTCA 58.184 47.619 0.00 0.00 0.00 2.69
2121 2352 3.170717 AGATGTACTCCCTCCGTTTCAA 58.829 45.455 0.00 0.00 0.00 2.69
2122 2353 3.581332 AGATGTACTCCCTCCGTTTCAAA 59.419 43.478 0.00 0.00 0.00 2.69
2123 2354 3.842007 TGTACTCCCTCCGTTTCAAAA 57.158 42.857 0.00 0.00 0.00 2.44
2124 2355 4.360951 TGTACTCCCTCCGTTTCAAAAT 57.639 40.909 0.00 0.00 0.00 1.82
2125 2356 4.721132 TGTACTCCCTCCGTTTCAAAATT 58.279 39.130 0.00 0.00 0.00 1.82
2126 2357 4.758165 TGTACTCCCTCCGTTTCAAAATTC 59.242 41.667 0.00 0.00 0.00 2.17
2127 2358 3.154710 ACTCCCTCCGTTTCAAAATTCC 58.845 45.455 0.00 0.00 0.00 3.01
2128 2359 3.181433 ACTCCCTCCGTTTCAAAATTCCT 60.181 43.478 0.00 0.00 0.00 3.36
2129 2360 3.153919 TCCCTCCGTTTCAAAATTCCTG 58.846 45.455 0.00 0.00 0.00 3.86
2130 2361 2.890945 CCCTCCGTTTCAAAATTCCTGT 59.109 45.455 0.00 0.00 0.00 4.00
2131 2362 3.057526 CCCTCCGTTTCAAAATTCCTGTC 60.058 47.826 0.00 0.00 0.00 3.51
2132 2363 3.821033 CCTCCGTTTCAAAATTCCTGTCT 59.179 43.478 0.00 0.00 0.00 3.41
2133 2364 4.278419 CCTCCGTTTCAAAATTCCTGTCTT 59.722 41.667 0.00 0.00 0.00 3.01
2134 2365 5.472137 CCTCCGTTTCAAAATTCCTGTCTTA 59.528 40.000 0.00 0.00 0.00 2.10
2135 2366 6.016610 CCTCCGTTTCAAAATTCCTGTCTTAA 60.017 38.462 0.00 0.00 0.00 1.85
2136 2367 7.336161 TCCGTTTCAAAATTCCTGTCTTAAA 57.664 32.000 0.00 0.00 0.00 1.52
2137 2368 7.947282 TCCGTTTCAAAATTCCTGTCTTAAAT 58.053 30.769 0.00 0.00 0.00 1.40
2138 2369 8.417884 TCCGTTTCAAAATTCCTGTCTTAAATT 58.582 29.630 0.00 0.00 0.00 1.82
2139 2370 9.040939 CCGTTTCAAAATTCCTGTCTTAAATTT 57.959 29.630 0.00 0.00 34.86 1.82
2140 2371 9.848172 CGTTTCAAAATTCCTGTCTTAAATTTG 57.152 29.630 0.00 0.00 33.95 2.32
2151 2382 9.158233 TCCTGTCTTAAATTTGTCTAAATACGG 57.842 33.333 0.00 0.00 35.50 4.02
2152 2383 9.158233 CCTGTCTTAAATTTGTCTAAATACGGA 57.842 33.333 0.00 0.00 35.50 4.69
2153 2384 9.968743 CTGTCTTAAATTTGTCTAAATACGGAC 57.031 33.333 0.00 0.00 35.50 4.79
2154 2385 8.649841 TGTCTTAAATTTGTCTAAATACGGACG 58.350 33.333 0.00 0.00 35.50 4.79
2155 2386 8.650714 GTCTTAAATTTGTCTAAATACGGACGT 58.349 33.333 0.00 1.98 35.50 4.34
2156 2387 9.853555 TCTTAAATTTGTCTAAATACGGACGTA 57.146 29.630 7.05 7.05 35.50 3.57
2159 2390 8.706492 AAATTTGTCTAAATACGGACGTATCA 57.294 30.769 16.60 8.14 40.08 2.15
2160 2391 8.706492 AATTTGTCTAAATACGGACGTATCAA 57.294 30.769 16.60 12.90 40.08 2.57
2161 2392 7.745022 TTTGTCTAAATACGGACGTATCAAG 57.255 36.000 16.60 15.63 40.08 3.02
2162 2393 6.441093 TGTCTAAATACGGACGTATCAAGT 57.559 37.500 16.60 6.67 40.08 3.16
2163 2394 6.489675 TGTCTAAATACGGACGTATCAAGTC 58.510 40.000 16.60 13.94 40.08 3.01
2164 2395 6.093909 TGTCTAAATACGGACGTATCAAGTCA 59.906 38.462 16.60 15.77 40.08 3.41
2165 2396 6.413235 GTCTAAATACGGACGTATCAAGTCAC 59.587 42.308 16.60 9.09 40.08 3.67
2166 2397 2.811902 TACGGACGTATCAAGTCACG 57.188 50.000 0.00 0.00 43.63 4.35
2179 2410 9.494479 CGTATCAAGTCACGTTTTAGTATTAGA 57.506 33.333 0.00 0.00 33.56 2.10
2186 2417 9.962783 AGTCACGTTTTAGTATTAGATACATCC 57.037 33.333 0.00 0.00 38.21 3.51
2187 2418 8.899776 GTCACGTTTTAGTATTAGATACATCCG 58.100 37.037 0.00 0.00 38.21 4.18
2188 2419 8.623903 TCACGTTTTAGTATTAGATACATCCGT 58.376 33.333 0.00 0.00 38.21 4.69
2189 2420 9.882996 CACGTTTTAGTATTAGATACATCCGTA 57.117 33.333 0.00 0.00 38.21 4.02
2207 2438 9.530633 ACATCCGTATCTAGACAAATTTAAGAC 57.469 33.333 0.00 0.00 0.00 3.01
2208 2439 9.529325 CATCCGTATCTAGACAAATTTAAGACA 57.471 33.333 0.00 0.00 0.00 3.41
2210 2441 9.582431 TCCGTATCTAGACAAATTTAAGACAAG 57.418 33.333 0.00 0.00 0.00 3.16
2211 2442 9.582431 CCGTATCTAGACAAATTTAAGACAAGA 57.418 33.333 0.00 0.00 0.00 3.02
2219 2450 9.546428 AGACAAATTTAAGACAAGAATTTTGGG 57.454 29.630 0.00 0.00 33.39 4.12
2220 2451 9.541143 GACAAATTTAAGACAAGAATTTTGGGA 57.459 29.630 0.00 0.00 33.39 4.37
2221 2452 9.325198 ACAAATTTAAGACAAGAATTTTGGGAC 57.675 29.630 0.00 0.00 33.39 4.46
2222 2453 8.487176 CAAATTTAAGACAAGAATTTTGGGACG 58.513 33.333 0.00 0.00 32.35 4.79
2223 2454 5.699097 TTAAGACAAGAATTTTGGGACGG 57.301 39.130 0.00 0.00 0.00 4.79
2224 2455 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
2225 2456 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
2226 2457 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
2227 2458 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
2228 2459 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
2229 2460 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
2230 2461 1.004394 GAATTTTGGGACGGAGGGAGT 59.996 52.381 0.00 0.00 0.00 3.85
2231 2462 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
2323 4307 8.656849 GTTTCAACTCAATATGTAGACGAATGT 58.343 33.333 0.00 0.00 0.00 2.71
2324 4308 9.863845 TTTCAACTCAATATGTAGACGAATGTA 57.136 29.630 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 4.558226 ATCCTGAGCACACAGATTGTTA 57.442 40.909 7.06 0.00 39.94 2.41
42 44 4.318332 TGTTCTTTATCCTGAGCACACAG 58.682 43.478 0.00 0.00 37.61 3.66
45 47 4.937620 GTGATGTTCTTTATCCTGAGCACA 59.062 41.667 0.00 0.00 0.00 4.57
56 58 2.094390 CCGTCGGAGGTGATGTTCTTTA 60.094 50.000 4.91 0.00 0.00 1.85
72 74 3.619233 AAAATCCAGAACAAACCGTCG 57.381 42.857 0.00 0.00 0.00 5.12
129 131 2.094752 AGCCGACTAAATTGCGCAAATT 60.095 40.909 28.81 26.83 40.32 1.82
139 141 6.046593 TCGATTTTGTATGAGCCGACTAAAT 58.953 36.000 0.00 0.00 34.93 1.40
173 175 2.596904 AGTGCCATATCGCTAAACGT 57.403 45.000 0.00 0.00 44.19 3.99
205 207 4.581868 TGACCCCGAATAAACTAAACCTG 58.418 43.478 0.00 0.00 0.00 4.00
213 215 2.089201 CCTGGTTGACCCCGAATAAAC 58.911 52.381 0.00 0.00 34.29 2.01
216 218 1.557832 CTTCCTGGTTGACCCCGAATA 59.442 52.381 0.00 0.00 34.29 1.75
242 253 3.107601 CCTCACAAGATTACCTCTCCCA 58.892 50.000 0.00 0.00 31.03 4.37
252 296 4.275936 GCGGCATATTAACCTCACAAGATT 59.724 41.667 0.00 0.00 0.00 2.40
267 311 2.093816 AGATGATGATCACGCGGCATAT 60.094 45.455 12.47 0.00 0.00 1.78
268 312 1.273327 AGATGATGATCACGCGGCATA 59.727 47.619 12.47 0.00 0.00 3.14
397 443 2.716424 AGTGGATTTGGACAGGGAGAAA 59.284 45.455 0.00 0.00 0.00 2.52
432 479 2.171209 GACCTTTGGCATGGCAACCC 62.171 60.000 32.02 17.59 0.00 4.11
528 603 9.352191 GTGTTTAGATCACTACTCCCTCTATAA 57.648 37.037 0.00 0.00 33.59 0.98
529 604 8.725256 AGTGTTTAGATCACTACTCCCTCTATA 58.275 37.037 0.00 0.00 43.17 1.31
530 605 7.588169 AGTGTTTAGATCACTACTCCCTCTAT 58.412 38.462 0.00 0.00 43.17 1.98
531 606 6.971340 AGTGTTTAGATCACTACTCCCTCTA 58.029 40.000 0.00 0.00 43.17 2.43
532 607 5.833340 AGTGTTTAGATCACTACTCCCTCT 58.167 41.667 0.00 0.00 43.17 3.69
533 608 6.532988 AAGTGTTTAGATCACTACTCCCTC 57.467 41.667 0.00 0.00 44.03 4.30
534 609 6.936968 AAAGTGTTTAGATCACTACTCCCT 57.063 37.500 0.00 0.00 44.03 4.20
561 636 9.435570 ACTTACATACTCCCTATGTGAACTAAT 57.564 33.333 3.68 0.00 44.50 1.73
562 637 8.834004 ACTTACATACTCCCTATGTGAACTAA 57.166 34.615 3.68 0.00 44.50 2.24
564 639 9.435570 AATACTTACATACTCCCTATGTGAACT 57.564 33.333 3.68 0.00 44.50 3.01
565 640 9.477484 CAATACTTACATACTCCCTATGTGAAC 57.523 37.037 3.68 0.00 44.50 3.18
566 641 9.209048 ACAATACTTACATACTCCCTATGTGAA 57.791 33.333 3.68 0.00 44.50 3.18
567 642 8.777578 ACAATACTTACATACTCCCTATGTGA 57.222 34.615 3.68 0.00 44.50 3.58
588 663 8.514594 CCCGATGCAATATTCTACATTTACAAT 58.485 33.333 0.00 0.00 0.00 2.71
589 664 7.500892 ACCCGATGCAATATTCTACATTTACAA 59.499 33.333 0.00 0.00 0.00 2.41
590 665 6.995686 ACCCGATGCAATATTCTACATTTACA 59.004 34.615 0.00 0.00 0.00 2.41
591 666 7.435068 ACCCGATGCAATATTCTACATTTAC 57.565 36.000 0.00 0.00 0.00 2.01
593 668 9.733556 TTATACCCGATGCAATATTCTACATTT 57.266 29.630 0.00 0.00 0.00 2.32
594 669 9.733556 TTTATACCCGATGCAATATTCTACATT 57.266 29.630 0.00 0.00 0.00 2.71
595 670 9.733556 TTTTATACCCGATGCAATATTCTACAT 57.266 29.630 0.00 0.00 0.00 2.29
596 671 9.214957 CTTTTATACCCGATGCAATATTCTACA 57.785 33.333 0.00 0.00 0.00 2.74
652 727 2.107141 CTCCGATGGAGTTCCCGC 59.893 66.667 4.65 0.00 44.25 6.13
665 740 1.986378 GCGTCCGATTGATATTCTCCG 59.014 52.381 0.00 0.00 0.00 4.63
680 755 1.885163 CTACCATATCCCCGGCGTCC 61.885 65.000 6.01 0.00 0.00 4.79
714 790 8.893727 CAAAAGAGAAAGAGAAAGTTTCTGGTA 58.106 33.333 22.68 0.00 42.95 3.25
716 792 7.989826 TCAAAAGAGAAAGAGAAAGTTTCTGG 58.010 34.615 22.68 0.00 42.95 3.86
738 814 2.577563 TGGAATGCCATCTTCCTCTCAA 59.422 45.455 0.00 0.00 42.27 3.02
815 896 4.099419 GTCAAACAAGTGGGTTGGAAAGAT 59.901 41.667 0.00 0.00 40.90 2.40
938 1019 1.879380 TCTATGGTTTGTGTGTGCTGC 59.121 47.619 0.00 0.00 0.00 5.25
963 1044 1.968540 ACGCTCCTTGGCTTCTTGC 60.969 57.895 0.00 0.00 41.94 4.01
966 1047 1.188219 TCTCACGCTCCTTGGCTTCT 61.188 55.000 0.00 0.00 0.00 2.85
1116 1237 4.443266 GTCGGCAGCGAGAAGGCT 62.443 66.667 0.00 0.00 46.13 4.58
1217 1338 4.856607 CGGAGAACTCGAGCGGCC 62.857 72.222 13.61 8.19 0.00 6.13
1224 1345 1.038130 AGATGACCCCGGAGAACTCG 61.038 60.000 0.73 0.00 0.00 4.18
1368 1489 1.150536 CGAGGAGGAGGAGGAGGAG 59.849 68.421 0.00 0.00 0.00 3.69
1369 1490 1.619975 ACGAGGAGGAGGAGGAGGA 60.620 63.158 0.00 0.00 0.00 3.71
1370 1491 1.152839 GACGAGGAGGAGGAGGAGG 60.153 68.421 0.00 0.00 0.00 4.30
1477 1610 5.230323 AGAAACAGGGGACTAAGAAGAAC 57.770 43.478 0.00 0.00 40.21 3.01
1579 1720 3.930634 AGCAGGTTCAATCAAAGAAGC 57.069 42.857 0.00 0.00 42.23 3.86
1580 1721 4.980434 CACAAGCAGGTTCAATCAAAGAAG 59.020 41.667 0.00 0.00 0.00 2.85
1592 1733 0.550914 TCAACTCCCACAAGCAGGTT 59.449 50.000 0.00 0.00 0.00 3.50
1614 1766 7.783042 TCTAAAGGAGAATAACTTGCCTAGAC 58.217 38.462 0.00 0.00 0.00 2.59
1644 1833 2.560504 ACCGAGCGCATAAATCATGAA 58.439 42.857 11.47 0.00 36.69 2.57
1774 1965 2.224113 ACGGTTCGTTGAACACATAGGT 60.224 45.455 11.39 0.00 43.54 3.08
1807 1998 1.358759 CACACAAGGAAACGGTGCC 59.641 57.895 0.00 0.00 42.07 5.01
1882 2078 8.205131 GGTTGTAACCGTGATATTTGAGTAAT 57.795 34.615 0.00 0.00 39.66 1.89
1906 2102 1.047002 TGGGCAAGACACCAAAATGG 58.953 50.000 0.00 0.00 45.02 3.16
1970 2166 8.570096 TCGATATACACAGGTTCTTAAAATCG 57.430 34.615 0.00 0.00 0.00 3.34
1995 2191 8.700439 TTGGCTAAGTTTTATGAAGTAGGTTT 57.300 30.769 0.00 0.00 0.00 3.27
2046 2242 2.031560 GTGTGTGCGTGATCTTTTGTCA 59.968 45.455 0.00 0.00 0.00 3.58
2060 2256 0.538516 TATTGTGTGGGGGTGTGTGC 60.539 55.000 0.00 0.00 0.00 4.57
2096 2327 5.424252 TGAAACGGAGGGAGTACATCTTAAT 59.576 40.000 0.00 0.00 0.00 1.40
2107 2338 3.191371 CAGGAATTTTGAAACGGAGGGAG 59.809 47.826 0.00 0.00 0.00 4.30
2108 2339 3.153919 CAGGAATTTTGAAACGGAGGGA 58.846 45.455 0.00 0.00 0.00 4.20
2109 2340 2.890945 ACAGGAATTTTGAAACGGAGGG 59.109 45.455 0.00 0.00 0.00 4.30
2110 2341 3.821033 AGACAGGAATTTTGAAACGGAGG 59.179 43.478 0.00 0.00 0.00 4.30
2111 2342 5.438761 AAGACAGGAATTTTGAAACGGAG 57.561 39.130 0.00 0.00 0.00 4.63
2112 2343 6.945938 TTAAGACAGGAATTTTGAAACGGA 57.054 33.333 0.00 0.00 0.00 4.69
2113 2344 8.587952 AATTTAAGACAGGAATTTTGAAACGG 57.412 30.769 0.00 0.00 0.00 4.44
2114 2345 9.848172 CAAATTTAAGACAGGAATTTTGAAACG 57.152 29.630 0.00 0.00 32.35 3.60
2125 2356 9.158233 CCGTATTTAGACAAATTTAAGACAGGA 57.842 33.333 0.00 0.00 35.88 3.86
2126 2357 9.158233 TCCGTATTTAGACAAATTTAAGACAGG 57.842 33.333 0.00 0.00 35.88 4.00
2127 2358 9.968743 GTCCGTATTTAGACAAATTTAAGACAG 57.031 33.333 0.00 0.00 35.88 3.51
2128 2359 8.649841 CGTCCGTATTTAGACAAATTTAAGACA 58.350 33.333 0.00 0.00 35.88 3.41
2129 2360 8.650714 ACGTCCGTATTTAGACAAATTTAAGAC 58.349 33.333 0.00 0.00 35.88 3.01
2130 2361 8.761575 ACGTCCGTATTTAGACAAATTTAAGA 57.238 30.769 0.00 0.00 35.88 2.10
2133 2364 9.800433 TGATACGTCCGTATTTAGACAAATTTA 57.200 29.630 13.05 0.00 40.93 1.40
2134 2365 8.706492 TGATACGTCCGTATTTAGACAAATTT 57.294 30.769 13.05 0.00 40.93 1.82
2135 2366 8.706492 TTGATACGTCCGTATTTAGACAAATT 57.294 30.769 13.05 0.00 40.93 1.82
2136 2367 7.977853 ACTTGATACGTCCGTATTTAGACAAAT 59.022 33.333 19.75 7.37 40.93 2.32
2137 2368 7.315142 ACTTGATACGTCCGTATTTAGACAAA 58.685 34.615 19.75 6.90 40.93 2.83
2138 2369 6.855836 ACTTGATACGTCCGTATTTAGACAA 58.144 36.000 19.75 14.72 40.93 3.18
2139 2370 6.093909 TGACTTGATACGTCCGTATTTAGACA 59.906 38.462 19.75 17.59 40.93 3.41
2140 2371 6.413235 GTGACTTGATACGTCCGTATTTAGAC 59.587 42.308 19.75 16.10 40.93 2.59
2141 2372 6.489675 GTGACTTGATACGTCCGTATTTAGA 58.510 40.000 19.75 6.97 40.93 2.10
2142 2373 5.394613 CGTGACTTGATACGTCCGTATTTAG 59.605 44.000 13.05 14.18 40.93 1.85
2143 2374 5.265477 CGTGACTTGATACGTCCGTATTTA 58.735 41.667 13.05 4.22 40.93 1.40
2144 2375 4.100529 CGTGACTTGATACGTCCGTATTT 58.899 43.478 13.05 0.00 40.93 1.40
2145 2376 3.688272 CGTGACTTGATACGTCCGTATT 58.312 45.455 13.05 0.00 40.93 1.89
2146 2377 3.329743 CGTGACTTGATACGTCCGTAT 57.670 47.619 11.81 11.81 43.24 3.06
2147 2378 2.811902 CGTGACTTGATACGTCCGTA 57.188 50.000 1.60 1.60 35.70 4.02
2148 2379 3.689224 CGTGACTTGATACGTCCGT 57.311 52.632 0.00 0.00 35.70 4.69
2153 2384 9.494479 TCTAATACTAAAACGTGACTTGATACG 57.506 33.333 0.00 0.00 45.19 3.06
2160 2391 9.962783 GGATGTATCTAATACTAAAACGTGACT 57.037 33.333 0.00 0.00 36.70 3.41
2161 2392 8.899776 CGGATGTATCTAATACTAAAACGTGAC 58.100 37.037 0.00 0.00 36.70 3.67
2162 2393 8.623903 ACGGATGTATCTAATACTAAAACGTGA 58.376 33.333 0.00 0.00 36.70 4.35
2163 2394 8.792831 ACGGATGTATCTAATACTAAAACGTG 57.207 34.615 0.00 0.00 36.70 4.49
2181 2412 9.530633 GTCTTAAATTTGTCTAGATACGGATGT 57.469 33.333 0.00 0.00 0.00 3.06
2182 2413 9.529325 TGTCTTAAATTTGTCTAGATACGGATG 57.471 33.333 0.00 0.00 0.00 3.51
2184 2415 9.582431 CTTGTCTTAAATTTGTCTAGATACGGA 57.418 33.333 0.00 0.00 0.00 4.69
2185 2416 9.582431 TCTTGTCTTAAATTTGTCTAGATACGG 57.418 33.333 0.00 0.00 0.00 4.02
2193 2424 9.546428 CCCAAAATTCTTGTCTTAAATTTGTCT 57.454 29.630 0.00 0.00 33.95 3.41
2194 2425 9.541143 TCCCAAAATTCTTGTCTTAAATTTGTC 57.459 29.630 0.00 0.00 33.95 3.18
2195 2426 9.325198 GTCCCAAAATTCTTGTCTTAAATTTGT 57.675 29.630 0.00 0.00 33.95 2.83
2196 2427 8.487176 CGTCCCAAAATTCTTGTCTTAAATTTG 58.513 33.333 0.00 0.00 33.95 2.32
2197 2428 7.655732 CCGTCCCAAAATTCTTGTCTTAAATTT 59.344 33.333 0.00 0.00 34.86 1.82
2198 2429 7.014808 TCCGTCCCAAAATTCTTGTCTTAAATT 59.985 33.333 0.00 0.00 0.00 1.82
2199 2430 6.492087 TCCGTCCCAAAATTCTTGTCTTAAAT 59.508 34.615 0.00 0.00 0.00 1.40
2200 2431 5.828859 TCCGTCCCAAAATTCTTGTCTTAAA 59.171 36.000 0.00 0.00 0.00 1.52
2201 2432 5.378332 TCCGTCCCAAAATTCTTGTCTTAA 58.622 37.500 0.00 0.00 0.00 1.85
2202 2433 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
2203 2434 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
2204 2435 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
2205 2436 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
2206 2437 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
2207 2438 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
2208 2439 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
2209 2440 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
2210 2441 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
2211 2442 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
2212 2443 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
2213 2444 1.835531 GATACTCCCTCCGTCCCAAAA 59.164 52.381 0.00 0.00 0.00 2.44
2214 2445 1.273381 TGATACTCCCTCCGTCCCAAA 60.273 52.381 0.00 0.00 0.00 3.28
2215 2446 0.337082 TGATACTCCCTCCGTCCCAA 59.663 55.000 0.00 0.00 0.00 4.12
2216 2447 0.561184 ATGATACTCCCTCCGTCCCA 59.439 55.000 0.00 0.00 0.00 4.37
2217 2448 1.718280 AATGATACTCCCTCCGTCCC 58.282 55.000 0.00 0.00 0.00 4.46
2218 2449 3.134081 TGAAAATGATACTCCCTCCGTCC 59.866 47.826 0.00 0.00 0.00 4.79
2219 2450 4.402056 TGAAAATGATACTCCCTCCGTC 57.598 45.455 0.00 0.00 0.00 4.79
2220 2451 4.837093 TTGAAAATGATACTCCCTCCGT 57.163 40.909 0.00 0.00 0.00 4.69
2221 2452 6.374333 TCTTTTTGAAAATGATACTCCCTCCG 59.626 38.462 2.54 0.00 0.00 4.63
2222 2453 7.703058 TCTTTTTGAAAATGATACTCCCTCC 57.297 36.000 2.54 0.00 0.00 4.30
2223 2454 9.981114 TTTTCTTTTTGAAAATGATACTCCCTC 57.019 29.630 7.01 0.00 46.20 4.30
2267 2498 9.356433 CACATGCAATTTTTGAGTAATATGACA 57.644 29.630 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.