Multiple sequence alignment - TraesCS4B01G310000

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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 TraesCS4B01G310000 chr4B 100.000 2372 0 0 1 2372 600522017 600519646 0.000000e+00 4381
1 TraesCS4B01G310000 chr4B 82.270 846 120 15 545 1365 483944612 483943772 0.000000e+00 704
2 TraesCS4B01G310000 chr4B 83.046 637 69 21 1365 2000 377155525 377154927 2.070000e-150 542
3 TraesCS4B01G310000 chr4A 89.643 1400 108 8 1 1368 574833796 574832402 0.000000e+00 1748
4 TraesCS4B01G310000 chr4A 83.077 325 37 11 155 463 661048403 661048081 1.800000e-71 279
5 TraesCS4B01G310000 chr7A 89.500 1400 109 17 1 1368 120481063 120479670 0.000000e+00 1736
6 TraesCS4B01G310000 chr7D 90.376 665 62 2 1369 2033 553059258 553059920 0.000000e+00 872
7 TraesCS4B01G310000 chr7D 90.566 212 19 1 2142 2353 553060129 553060339 1.800000e-71 279
8 TraesCS4B01G310000 chr4D 82.423 842 119 11 545 1363 394356031 394355196 0.000000e+00 708
9 TraesCS4B01G310000 chr4D 86.567 201 23 2 2157 2353 278162398 278162198 3.970000e-53 219
10 TraesCS4B01G310000 chr2D 86.635 636 82 3 1365 2000 485098607 485097975 0.000000e+00 701
11 TraesCS4B01G310000 chr2D 87.685 203 25 0 2170 2372 485097984 485097782 1.100000e-58 237
12 TraesCS4B01G310000 chr2D 86.364 198 26 1 2156 2353 598019136 598019332 5.130000e-52 215
13 TraesCS4B01G310000 chr2D 86.364 198 26 1 2156 2353 598047327 598047523 5.130000e-52 215
14 TraesCS4B01G310000 chr3D 85.063 636 69 12 1365 2000 443313879 443314488 2.000000e-175 625
15 TraesCS4B01G310000 chr3D 88.177 203 24 0 2170 2372 443314479 443314681 2.360000e-60 243
16 TraesCS4B01G310000 chr1D 83.962 636 76 12 1365 2000 126865088 126864479 9.450000e-164 586
17 TraesCS4B01G310000 chr1D 88.670 203 23 0 2170 2372 126864488 126864286 5.060000e-62 248
18 TraesCS4B01G310000 chr3A 84.009 469 69 6 900 1366 11121219 11120755 1.670000e-121 446
19 TraesCS4B01G310000 chr1B 84.342 281 44 0 1749 2029 571158923 571159203 2.320000e-70 276
20 TraesCS4B01G310000 chr2B 93.889 180 11 0 2190 2369 649205801 649205980 3.000000e-69 272
21 TraesCS4B01G310000 chr6B 81.786 280 43 1 1750 2029 440761013 440760742 6.600000e-56 228
22 TraesCS4B01G310000 chr3B 84.906 212 31 1 2142 2353 9163199 9163409 1.850000e-51 213


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 TraesCS4B01G310000 chr4B 600519646 600522017 2371 True 4381.0 4381 100.000 1 2372 1 chr4B.!!$R3 2371
1 TraesCS4B01G310000 chr4B 483943772 483944612 840 True 704.0 704 82.270 545 1365 1 chr4B.!!$R2 820
2 TraesCS4B01G310000 chr4B 377154927 377155525 598 True 542.0 542 83.046 1365 2000 1 chr4B.!!$R1 635
3 TraesCS4B01G310000 chr4A 574832402 574833796 1394 True 1748.0 1748 89.643 1 1368 1 chr4A.!!$R1 1367
4 TraesCS4B01G310000 chr7A 120479670 120481063 1393 True 1736.0 1736 89.500 1 1368 1 chr7A.!!$R1 1367
5 TraesCS4B01G310000 chr7D 553059258 553060339 1081 False 575.5 872 90.471 1369 2353 2 chr7D.!!$F1 984
6 TraesCS4B01G310000 chr4D 394355196 394356031 835 True 708.0 708 82.423 545 1363 1 chr4D.!!$R2 818
7 TraesCS4B01G310000 chr2D 485097782 485098607 825 True 469.0 701 87.160 1365 2372 2 chr2D.!!$R1 1007
8 TraesCS4B01G310000 chr3D 443313879 443314681 802 False 434.0 625 86.620 1365 2372 2 chr3D.!!$F1 1007
9 TraesCS4B01G310000 chr1D 126864286 126865088 802 True 417.0 586 86.316 1365 2372 2 chr1D.!!$R1 1007

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
141 142 0.310854 CCGTTCTTTGCCCAGTTGAC 59.689 55.0 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2070 2157 0.251916 TCGGGCAGGACATAAGTTGG 59.748 55.0 0.0 0.0 0.0 3.77 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 4.184629 GCTTGTCGTCTCTTGGTTGATAT 58.815 43.478 0.00 0.00 0.00 1.63
45 46 2.877097 TGGTTGATATGTGTGTGCCT 57.123 45.000 0.00 0.00 0.00 4.75
57 58 0.322975 GTGTGCCTGTCCTCTGATGT 59.677 55.000 0.00 0.00 0.00 3.06
60 61 0.837691 TGCCTGTCCTCTGATGTGGT 60.838 55.000 0.00 0.00 0.00 4.16
66 67 1.899814 GTCCTCTGATGTGGTGGTGTA 59.100 52.381 0.00 0.00 0.00 2.90
71 72 3.997021 CTCTGATGTGGTGGTGTAGTTTC 59.003 47.826 0.00 0.00 0.00 2.78
75 76 4.020573 TGATGTGGTGGTGTAGTTTCTAGG 60.021 45.833 0.00 0.00 0.00 3.02
82 83 4.022503 GTGGTGTAGTTTCTAGGTTCGACT 60.023 45.833 0.00 0.00 0.00 4.18
94 95 1.303888 TTCGACTGACGGCTAGGGT 60.304 57.895 0.00 0.00 42.82 4.34
102 103 1.353022 TGACGGCTAGGGTTGGATTTT 59.647 47.619 0.00 0.00 0.00 1.82
105 106 2.167662 CGGCTAGGGTTGGATTTTTGT 58.832 47.619 0.00 0.00 0.00 2.83
123 124 1.065199 TGTTGTGGATGATGCCTCTCC 60.065 52.381 0.00 0.00 0.00 3.71
135 136 1.374947 CCTCTCCGTTCTTTGCCCA 59.625 57.895 0.00 0.00 0.00 5.36
141 142 0.310854 CCGTTCTTTGCCCAGTTGAC 59.689 55.000 0.00 0.00 0.00 3.18
195 196 5.461737 GGCTCTGATCTACTCTCGATTTTTG 59.538 44.000 0.00 0.00 0.00 2.44
197 198 7.197017 GCTCTGATCTACTCTCGATTTTTGTA 58.803 38.462 0.00 0.00 0.00 2.41
205 206 9.404848 TCTACTCTCGATTTTTGTAATCTCCTA 57.595 33.333 0.00 0.00 0.00 2.94
216 217 9.859427 TTTTTGTAATCTCCTATTGATTGCTTG 57.141 29.630 0.00 0.00 37.40 4.01
225 226 7.178983 TCTCCTATTGATTGCTTGGATTTGTTT 59.821 33.333 0.00 0.00 0.00 2.83
231 232 1.611491 TGCTTGGATTTGTTTCCGTCC 59.389 47.619 0.00 0.00 38.74 4.79
253 254 1.223487 GCGCAGGATTGGGGTTAGA 59.777 57.895 0.30 0.00 37.70 2.10
281 282 1.376812 GATTTGGCCCTCGGTCGTT 60.377 57.895 0.00 0.00 0.00 3.85
286 287 4.353437 GCCCTCGGTCGTTGTCGT 62.353 66.667 0.00 0.00 38.33 4.34
302 303 0.820482 TCGTGTCGTCCTGGTCTTCA 60.820 55.000 0.00 0.00 0.00 3.02
332 333 1.077501 ATTGGATCTGGTGCGGGTG 60.078 57.895 0.00 0.00 0.00 4.61
347 348 1.463553 GGGTGTTTCTTGCTGGGGTG 61.464 60.000 0.00 0.00 0.00 4.61
366 367 0.391597 GTCTGTTGACGGTCCTTGGA 59.608 55.000 5.55 0.00 33.15 3.53
370 371 0.391597 GTTGACGGTCCTTGGACAGA 59.608 55.000 22.87 2.67 0.00 3.41
377 378 3.262420 CGGTCCTTGGACAGATACTTTG 58.738 50.000 19.90 0.00 0.00 2.77
380 381 3.686726 GTCCTTGGACAGATACTTTGCTG 59.313 47.826 14.34 0.00 38.10 4.41
422 425 1.186200 TGCCTCTATGCTCGTCTTGT 58.814 50.000 0.00 0.00 0.00 3.16
424 427 1.929836 GCCTCTATGCTCGTCTTGTTG 59.070 52.381 0.00 0.00 0.00 3.33
427 430 3.589988 CTCTATGCTCGTCTTGTTGGTT 58.410 45.455 0.00 0.00 0.00 3.67
428 431 3.325870 TCTATGCTCGTCTTGTTGGTTG 58.674 45.455 0.00 0.00 0.00 3.77
430 433 2.605837 TGCTCGTCTTGTTGGTTGTA 57.394 45.000 0.00 0.00 0.00 2.41
431 434 2.907634 TGCTCGTCTTGTTGGTTGTAA 58.092 42.857 0.00 0.00 0.00 2.41
433 436 3.880490 TGCTCGTCTTGTTGGTTGTAATT 59.120 39.130 0.00 0.00 0.00 1.40
435 438 4.783242 CTCGTCTTGTTGGTTGTAATTGG 58.217 43.478 0.00 0.00 0.00 3.16
438 441 4.737765 CGTCTTGTTGGTTGTAATTGGTTG 59.262 41.667 0.00 0.00 0.00 3.77
439 442 5.656480 GTCTTGTTGGTTGTAATTGGTTGT 58.344 37.500 0.00 0.00 0.00 3.32
440 443 6.458478 CGTCTTGTTGGTTGTAATTGGTTGTA 60.458 38.462 0.00 0.00 0.00 2.41
441 444 7.259161 GTCTTGTTGGTTGTAATTGGTTGTAA 58.741 34.615 0.00 0.00 0.00 2.41
459 462 4.917385 TGTAATGGTTGTTGCATAGGAGT 58.083 39.130 0.00 0.00 0.00 3.85
460 463 4.699735 TGTAATGGTTGTTGCATAGGAGTG 59.300 41.667 0.00 0.00 0.00 3.51
465 470 4.759693 TGGTTGTTGCATAGGAGTGTTTAG 59.240 41.667 0.00 0.00 0.00 1.85
468 473 6.128363 GGTTGTTGCATAGGAGTGTTTAGTAC 60.128 42.308 0.00 0.00 0.00 2.73
605 637 7.117236 TGTTTAGATAAAGTGGTTCGTGCTTAG 59.883 37.037 0.00 0.00 0.00 2.18
630 662 1.147817 AGGGGTTTGCTTTGACTGGAT 59.852 47.619 0.00 0.00 0.00 3.41
641 673 6.620678 TGCTTTGACTGGATGCTATTTTTAC 58.379 36.000 0.00 0.00 0.00 2.01
650 682 8.107095 ACTGGATGCTATTTTTACTTTGTAGGA 58.893 33.333 0.00 0.00 0.00 2.94
692 724 4.901250 TCCTGGATATATGTCTCAGCAACA 59.099 41.667 10.48 0.00 0.00 3.33
732 764 2.663852 GTCGTGTTCCGGGGTGTG 60.664 66.667 0.00 0.00 37.11 3.82
832 887 4.875536 GGTGAATTATGCATTTTGGTTCCC 59.124 41.667 3.54 3.52 0.00 3.97
875 930 2.903784 GGGGCTTTTAGTTTGGGTGATT 59.096 45.455 0.00 0.00 0.00 2.57
884 939 2.554032 AGTTTGGGTGATTTGCTTCTCG 59.446 45.455 0.00 0.00 0.00 4.04
892 947 4.752101 GGTGATTTGCTTCTCGTATATGCT 59.248 41.667 0.00 0.00 0.00 3.79
897 952 8.888716 TGATTTGCTTCTCGTATATGCTTTTTA 58.111 29.630 0.00 0.00 0.00 1.52
923 978 6.299805 TCCTATCTAGATGCTTTGTGTTGT 57.700 37.500 15.79 0.00 0.00 3.32
928 983 6.942532 TCTAGATGCTTTGTGTTGTTCTTT 57.057 33.333 0.00 0.00 0.00 2.52
959 1014 3.071479 TGATCTAACGTTTGTTCCTGGC 58.929 45.455 5.91 0.00 39.54 4.85
993 1049 4.781775 TTCTTGTGAGGAGTGGGTTTAA 57.218 40.909 0.00 0.00 0.00 1.52
1006 1062 6.109156 AGTGGGTTTAATTTTTGATGGGTC 57.891 37.500 0.00 0.00 0.00 4.46
1011 1067 8.885346 TGGGTTTAATTTTTGATGGGTCTTATT 58.115 29.630 0.00 0.00 0.00 1.40
1018 1074 7.732222 TTTTTGATGGGTCTTATTTATGGCT 57.268 32.000 0.00 0.00 0.00 4.75
1034 1090 0.961019 GGCTGGATGTTTGCTGTGAA 59.039 50.000 0.00 0.00 0.00 3.18
1067 1123 1.996292 CATCTGTTGGATGTCGTCGT 58.004 50.000 0.00 0.00 44.88 4.34
1160 1216 4.221703 AGTCGAGATTGAGGTTGATGTTCT 59.778 41.667 0.00 0.00 0.00 3.01
1282 1338 2.560981 CAAGGGGTGTATGGGTTTGTTC 59.439 50.000 0.00 0.00 0.00 3.18
1380 1436 6.038825 CGTTGGTCAGGGCATAATTACAATAA 59.961 38.462 0.00 0.00 0.00 1.40
1382 1438 8.421002 GTTGGTCAGGGCATAATTACAATAAAT 58.579 33.333 0.00 0.00 0.00 1.40
1415 1471 2.154462 ACGAACCTCAAGAAATGCCAG 58.846 47.619 0.00 0.00 0.00 4.85
1426 1482 2.168936 AGAAATGCCAGAGAGAGCTCAG 59.831 50.000 17.77 0.00 43.81 3.35
1482 1538 3.119708 GCGTGCAGAATCCTTTCAGAAAT 60.120 43.478 0.00 0.00 34.08 2.17
1496 1552 3.786635 TCAGAAATAGCTCGCCTCTTTC 58.213 45.455 0.00 5.98 37.08 2.62
1512 1568 2.678836 TCTTTCACCGCGACAAAGAAAA 59.321 40.909 18.73 5.89 34.04 2.29
1553 1609 1.415659 GATGATAGCACTCCAGCACCT 59.584 52.381 0.00 0.00 36.85 4.00
1554 1610 0.538584 TGATAGCACTCCAGCACCTG 59.461 55.000 0.00 0.00 36.85 4.00
1585 1641 5.812642 GTCAACGAATCAGAGGTAATCATGT 59.187 40.000 0.00 0.00 0.00 3.21
1606 1662 4.619336 TGTTGTTGTTCTGCTTTTCGTTTC 59.381 37.500 0.00 0.00 0.00 2.78
1614 1670 1.268352 TGCTTTTCGTTTCCATTCCGG 59.732 47.619 0.00 0.00 0.00 5.14
1633 1700 3.056891 CCGGCAATACCAAATGTTGTCTT 60.057 43.478 0.00 0.00 39.03 3.01
1634 1701 4.156922 CCGGCAATACCAAATGTTGTCTTA 59.843 41.667 0.00 0.00 39.03 2.10
1635 1702 5.092781 CGGCAATACCAAATGTTGTCTTAC 58.907 41.667 0.00 0.00 39.03 2.34
1636 1703 5.335269 CGGCAATACCAAATGTTGTCTTACA 60.335 40.000 0.00 0.00 39.03 2.41
1637 1704 6.624861 CGGCAATACCAAATGTTGTCTTACAT 60.625 38.462 0.00 0.00 38.21 2.29
1638 1705 7.414651 CGGCAATACCAAATGTTGTCTTACATA 60.415 37.037 0.00 0.00 36.55 2.29
1639 1706 7.700656 GGCAATACCAAATGTTGTCTTACATAC 59.299 37.037 0.00 0.00 36.68 2.39
1640 1707 8.240682 GCAATACCAAATGTTGTCTTACATACA 58.759 33.333 0.00 0.00 37.76 2.29
1657 1724 9.161629 CTTACATACAACTGACCATTTACATCA 57.838 33.333 0.00 0.00 0.00 3.07
1671 1738 4.524802 TTACATCAAGGATGGCCTCAAT 57.475 40.909 3.32 0.00 46.28 2.57
1697 1764 3.536917 CGGCTCGCTCCCACCATA 61.537 66.667 0.00 0.00 0.00 2.74
1734 1801 1.501582 AGTAACATGCCCTCCCTCTC 58.498 55.000 0.00 0.00 0.00 3.20
1747 1814 1.560146 TCCCTCTCGCTCTTCAGACTA 59.440 52.381 0.00 0.00 0.00 2.59
1793 1860 3.495670 TTGTTGTTTTCCCAGTGAACG 57.504 42.857 0.00 0.00 31.05 3.95
1928 1995 9.298250 TCATATGTAGTACCCTTAGATTCACTC 57.702 37.037 1.90 0.00 0.00 3.51
1944 2011 2.282958 TCCTCGGACCTTGCTCGT 60.283 61.111 0.00 0.00 0.00 4.18
2003 2070 3.181462 TGGTCCTTATAGCATGCTGAGTG 60.181 47.826 30.42 16.39 0.00 3.51
2007 2074 6.049149 GTCCTTATAGCATGCTGAGTGTAAA 58.951 40.000 30.42 7.81 0.00 2.01
2016 2083 2.371841 TGCTGAGTGTAAATCCCTGTGT 59.628 45.455 0.00 0.00 0.00 3.72
2025 2092 1.398692 AATCCCTGTGTTGCGTTGTT 58.601 45.000 0.00 0.00 0.00 2.83
2029 2096 1.600164 CCCTGTGTTGCGTTGTTGATG 60.600 52.381 0.00 0.00 0.00 3.07
2040 2127 3.312421 GCGTTGTTGATGTATACATGCCT 59.688 43.478 22.93 0.00 36.57 4.75
2044 2131 6.258160 GTTGTTGATGTATACATGCCTTGTC 58.742 40.000 22.93 8.14 39.87 3.18
2047 2134 5.357742 TGATGTATACATGCCTTGTCTGT 57.642 39.130 22.93 0.00 39.87 3.41
2065 2152 1.133513 TGTCATTGCCACCCTCTTTGT 60.134 47.619 0.00 0.00 0.00 2.83
2068 2155 2.173519 CATTGCCACCCTCTTTGTGAT 58.826 47.619 0.00 0.00 35.74 3.06
2069 2156 1.619654 TTGCCACCCTCTTTGTGATG 58.380 50.000 0.00 0.00 35.74 3.07
2070 2157 0.895100 TGCCACCCTCTTTGTGATGC 60.895 55.000 0.00 0.00 35.74 3.91
2072 2159 0.251297 CCACCCTCTTTGTGATGCCA 60.251 55.000 0.00 0.00 35.74 4.92
2086 2192 1.678101 GATGCCAACTTATGTCCTGCC 59.322 52.381 0.00 0.00 0.00 4.85
2088 2194 1.376609 GCCAACTTATGTCCTGCCCG 61.377 60.000 0.00 0.00 0.00 6.13
2090 2196 1.656652 CAACTTATGTCCTGCCCGAG 58.343 55.000 0.00 0.00 0.00 4.63
2102 2208 1.938577 CTGCCCGAGACTTGAATGATG 59.061 52.381 0.00 0.00 0.00 3.07
2106 2212 4.343814 TGCCCGAGACTTGAATGATGTATA 59.656 41.667 0.00 0.00 0.00 1.47
2115 2221 8.093307 AGACTTGAATGATGTATATGCTCGATT 58.907 33.333 0.00 0.00 0.00 3.34
2116 2222 8.613060 ACTTGAATGATGTATATGCTCGATTT 57.387 30.769 0.00 0.00 0.00 2.17
2117 2223 8.715998 ACTTGAATGATGTATATGCTCGATTTC 58.284 33.333 0.00 0.00 0.00 2.17
2123 2229 8.837788 TGATGTATATGCTCGATTTCTTCAAT 57.162 30.769 0.00 0.00 0.00 2.57
2124 2230 9.927668 TGATGTATATGCTCGATTTCTTCAATA 57.072 29.630 0.00 0.00 0.00 1.90
2132 2238 7.445121 TGCTCGATTTCTTCAATACATCCTAT 58.555 34.615 0.00 0.00 0.00 2.57
2190 2360 6.410942 TGTATCATGCTAGCTCAGTGTTAT 57.589 37.500 17.23 0.00 0.00 1.89
2197 2367 6.486253 TGCTAGCTCAGTGTTATTTTCTTG 57.514 37.500 17.23 0.00 0.00 3.02
2207 2377 9.944663 TCAGTGTTATTTTCTTGTGTATTGTTC 57.055 29.630 0.00 0.00 0.00 3.18
2208 2378 9.729023 CAGTGTTATTTTCTTGTGTATTGTTCA 57.271 29.630 0.00 0.00 0.00 3.18
2261 2431 2.917701 TTTATCTGGTGTTGCATGCG 57.082 45.000 14.09 0.00 0.00 4.73
2264 2434 0.606130 ATCTGGTGTTGCATGCGTCA 60.606 50.000 14.09 11.72 0.00 4.35
2269 2439 2.491298 TGGTGTTGCATGCGTCAATATT 59.509 40.909 14.09 0.00 0.00 1.28
2273 2443 0.385029 TGCATGCGTCAATATTGCCC 59.615 50.000 14.09 3.05 32.39 5.36
2286 2456 1.064003 ATTGCCCGTGGATATGCCTA 58.936 50.000 0.00 0.00 37.63 3.93
2294 2464 4.323792 CCCGTGGATATGCCTATGAATCTT 60.324 45.833 0.00 0.00 37.63 2.40
2295 2465 4.633126 CCGTGGATATGCCTATGAATCTTG 59.367 45.833 0.00 0.00 37.63 3.02
2355 2525 1.153628 GACGGGGATGACGTTGGAG 60.154 63.158 0.00 0.00 45.68 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 4.657824 ACGACAAGCGGGGACACG 62.658 66.667 0.00 0.00 46.49 4.49
10 11 1.738099 CCAAGAGACGACAAGCGGG 60.738 63.158 0.00 0.00 46.49 6.13
35 36 1.048160 TCAGAGGACAGGCACACACA 61.048 55.000 0.00 0.00 0.00 3.72
45 46 0.686789 CACCACCACATCAGAGGACA 59.313 55.000 0.00 0.00 0.00 4.02
57 58 3.006110 CGAACCTAGAAACTACACCACCA 59.994 47.826 0.00 0.00 0.00 4.17
60 61 4.022589 CAGTCGAACCTAGAAACTACACCA 60.023 45.833 0.00 0.00 0.00 4.17
66 67 2.228343 CCGTCAGTCGAACCTAGAAACT 59.772 50.000 0.00 0.00 42.86 2.66
71 72 1.331138 CTAGCCGTCAGTCGAACCTAG 59.669 57.143 0.00 0.00 42.86 3.02
75 76 1.139095 CCCTAGCCGTCAGTCGAAC 59.861 63.158 0.00 0.00 42.86 3.95
82 83 0.988832 AAATCCAACCCTAGCCGTCA 59.011 50.000 0.00 0.00 0.00 4.35
94 95 4.996122 GCATCATCCACAACAAAAATCCAA 59.004 37.500 0.00 0.00 0.00 3.53
102 103 2.618816 GGAGAGGCATCATCCACAACAA 60.619 50.000 0.00 0.00 33.08 2.83
105 106 0.178767 CGGAGAGGCATCATCCACAA 59.821 55.000 14.38 0.00 32.31 3.33
123 124 1.002468 CAGTCAACTGGGCAAAGAACG 60.002 52.381 2.08 0.00 40.20 3.95
135 136 1.134580 CCTCATCCATCGCAGTCAACT 60.135 52.381 0.00 0.00 0.00 3.16
141 142 2.251409 AATCACCTCATCCATCGCAG 57.749 50.000 0.00 0.00 0.00 5.18
195 196 7.992754 ATCCAAGCAATCAATAGGAGATTAC 57.007 36.000 0.00 0.00 34.14 1.89
197 198 7.343833 ACAAATCCAAGCAATCAATAGGAGATT 59.656 33.333 0.00 0.00 36.19 2.40
205 206 4.931002 CGGAAACAAATCCAAGCAATCAAT 59.069 37.500 0.00 0.00 39.61 2.57
216 217 1.664874 GCAACGGACGGAAACAAATCC 60.665 52.381 0.00 0.00 36.05 3.01
231 232 3.814268 CCCCAATCCTGCGCAACG 61.814 66.667 13.05 4.39 0.00 4.10
253 254 1.203100 AGGGCCAAATCTCAGCAAACT 60.203 47.619 6.18 0.00 0.00 2.66
281 282 1.105167 AAGACCAGGACGACACGACA 61.105 55.000 0.00 0.00 0.00 4.35
286 287 0.827925 AGCTGAAGACCAGGACGACA 60.828 55.000 0.00 0.00 43.13 4.35
332 333 0.954452 CAGACACCCCAGCAAGAAAC 59.046 55.000 0.00 0.00 0.00 2.78
347 348 0.391597 TCCAAGGACCGTCAACAGAC 59.608 55.000 0.00 0.00 0.00 3.51
366 367 7.530426 AAAAAGAATCCAGCAAAGTATCTGT 57.470 32.000 0.00 0.00 0.00 3.41
396 399 4.039730 AGACGAGCATAGAGGCAAACATAT 59.960 41.667 0.00 0.00 35.83 1.78
398 401 2.169352 AGACGAGCATAGAGGCAAACAT 59.831 45.455 0.00 0.00 35.83 2.71
402 405 1.550524 ACAAGACGAGCATAGAGGCAA 59.449 47.619 0.00 0.00 35.83 4.52
422 425 6.732896 ACCATTACAACCAATTACAACCAA 57.267 33.333 0.00 0.00 0.00 3.67
424 427 6.517605 ACAACCATTACAACCAATTACAACC 58.482 36.000 0.00 0.00 0.00 3.77
427 430 5.986135 GCAACAACCATTACAACCAATTACA 59.014 36.000 0.00 0.00 0.00 2.41
428 431 5.986135 TGCAACAACCATTACAACCAATTAC 59.014 36.000 0.00 0.00 0.00 1.89
430 433 5.028549 TGCAACAACCATTACAACCAATT 57.971 34.783 0.00 0.00 0.00 2.32
431 434 4.679373 TGCAACAACCATTACAACCAAT 57.321 36.364 0.00 0.00 0.00 3.16
433 436 4.219507 CCTATGCAACAACCATTACAACCA 59.780 41.667 0.00 0.00 0.00 3.67
435 438 5.183140 ACTCCTATGCAACAACCATTACAAC 59.817 40.000 0.00 0.00 0.00 3.32
438 441 4.700213 ACACTCCTATGCAACAACCATTAC 59.300 41.667 0.00 0.00 0.00 1.89
439 442 4.917385 ACACTCCTATGCAACAACCATTA 58.083 39.130 0.00 0.00 0.00 1.90
440 443 3.766545 ACACTCCTATGCAACAACCATT 58.233 40.909 0.00 0.00 0.00 3.16
441 444 3.439857 ACACTCCTATGCAACAACCAT 57.560 42.857 0.00 0.00 0.00 3.55
459 462 1.965643 ACAGGACTGCCGTACTAAACA 59.034 47.619 0.00 0.00 39.96 2.83
460 463 2.735134 CAACAGGACTGCCGTACTAAAC 59.265 50.000 0.00 0.00 39.96 2.01
465 470 1.263217 CAAACAACAGGACTGCCGTAC 59.737 52.381 0.00 0.00 39.96 3.67
468 473 1.069022 CATCAAACAACAGGACTGCCG 60.069 52.381 0.00 0.00 39.96 5.69
605 637 1.611977 GTCAAAGCAAACCCCTACACC 59.388 52.381 0.00 0.00 0.00 4.16
630 662 7.829211 AGCAGATCCTACAAAGTAAAAATAGCA 59.171 33.333 0.00 0.00 0.00 3.49
641 673 4.874966 CCTCAAGAAGCAGATCCTACAAAG 59.125 45.833 0.00 0.00 0.00 2.77
650 682 3.416156 GGACAAACCTCAAGAAGCAGAT 58.584 45.455 0.00 0.00 35.41 2.90
692 724 5.072329 ACACATAAGCTAGAATACCAGCCAT 59.928 40.000 0.00 0.00 38.61 4.40
732 764 2.845752 TATCAACCGGCGTGCTCACC 62.846 60.000 6.01 0.00 0.00 4.02
742 774 9.825972 GTATACATGAATTCAAATATCAACCGG 57.174 33.333 13.09 0.00 0.00 5.28
827 882 1.816074 TAAATCAGCACACCGGGAAC 58.184 50.000 6.32 0.00 0.00 3.62
832 887 1.670811 GGACCATAAATCAGCACACCG 59.329 52.381 0.00 0.00 0.00 4.94
875 930 9.716507 GAAATAAAAAGCATATACGAGAAGCAA 57.283 29.630 0.00 0.00 0.00 3.91
897 952 7.831193 ACAACACAAAGCATCTAGATAGGAAAT 59.169 33.333 4.54 0.00 0.00 2.17
904 959 7.516198 AAAGAACAACACAAAGCATCTAGAT 57.484 32.000 0.00 0.00 0.00 1.98
908 963 5.964758 TCAAAAGAACAACACAAAGCATCT 58.035 33.333 0.00 0.00 0.00 2.90
910 965 6.091169 CAGTTCAAAAGAACAACACAAAGCAT 59.909 34.615 10.56 0.00 37.52 3.79
923 978 8.378172 ACGTTAGATCATTCAGTTCAAAAGAA 57.622 30.769 0.00 0.00 0.00 2.52
928 983 7.490962 ACAAACGTTAGATCATTCAGTTCAA 57.509 32.000 0.00 0.00 0.00 2.69
980 1036 5.248248 CCCATCAAAAATTAAACCCACTCCT 59.752 40.000 0.00 0.00 0.00 3.69
993 1049 8.206189 CAGCCATAAATAAGACCCATCAAAAAT 58.794 33.333 0.00 0.00 0.00 1.82
1006 1062 5.981315 CAGCAAACATCCAGCCATAAATAAG 59.019 40.000 0.00 0.00 0.00 1.73
1011 1067 2.492881 CACAGCAAACATCCAGCCATAA 59.507 45.455 0.00 0.00 0.00 1.90
1018 1074 4.619973 GAACAATTCACAGCAAACATCCA 58.380 39.130 0.00 0.00 0.00 3.41
1034 1090 4.142622 CCAACAGATGCACATACGAACAAT 60.143 41.667 0.00 0.00 0.00 2.71
1160 1216 2.224843 ACTGTCAATGCATCACTCCCAA 60.225 45.455 0.00 0.00 0.00 4.12
1380 1436 3.000727 GGTTCGTCGAGTTGGAATCATT 58.999 45.455 0.00 0.00 0.00 2.57
1382 1438 1.616865 AGGTTCGTCGAGTTGGAATCA 59.383 47.619 0.00 0.00 0.00 2.57
1426 1482 2.751166 TGACCAGAACTGCTTAGCTC 57.249 50.000 5.60 0.00 0.00 4.09
1431 1487 2.775890 CACTGATGACCAGAACTGCTT 58.224 47.619 0.00 0.00 45.78 3.91
1482 1538 1.511305 CGGTGAAAGAGGCGAGCTA 59.489 57.895 0.00 0.00 0.00 3.32
1496 1552 0.660300 GCCTTTTCTTTGTCGCGGTG 60.660 55.000 6.13 0.00 0.00 4.94
1512 1568 1.830477 GTCACTCTCTGAATGAGGCCT 59.170 52.381 3.86 3.86 42.86 5.19
1553 1609 4.452114 CCTCTGATTCGTTGACACATTTCA 59.548 41.667 0.00 0.00 0.00 2.69
1554 1610 4.452455 ACCTCTGATTCGTTGACACATTTC 59.548 41.667 0.00 0.00 0.00 2.17
1585 1641 4.170256 GGAAACGAAAAGCAGAACAACAA 58.830 39.130 0.00 0.00 0.00 2.83
1606 1662 2.430332 ACATTTGGTATTGCCGGAATGG 59.570 45.455 5.05 6.31 42.65 3.16
1614 1670 8.240682 TGTATGTAAGACAACATTTGGTATTGC 58.759 33.333 0.00 0.00 40.52 3.56
1633 1700 9.161629 CTTGATGTAAATGGTCAGTTGTATGTA 57.838 33.333 0.00 0.00 0.00 2.29
1634 1701 7.121168 CCTTGATGTAAATGGTCAGTTGTATGT 59.879 37.037 0.00 0.00 0.00 2.29
1635 1702 7.336679 TCCTTGATGTAAATGGTCAGTTGTATG 59.663 37.037 0.00 0.00 0.00 2.39
1636 1703 7.402054 TCCTTGATGTAAATGGTCAGTTGTAT 58.598 34.615 0.00 0.00 0.00 2.29
1637 1704 6.774673 TCCTTGATGTAAATGGTCAGTTGTA 58.225 36.000 0.00 0.00 0.00 2.41
1638 1705 5.630121 TCCTTGATGTAAATGGTCAGTTGT 58.370 37.500 0.00 0.00 0.00 3.32
1639 1706 6.405065 CCATCCTTGATGTAAATGGTCAGTTG 60.405 42.308 3.62 0.00 38.28 3.16
1640 1707 5.653769 CCATCCTTGATGTAAATGGTCAGTT 59.346 40.000 3.62 0.00 38.28 3.16
1641 1708 5.195940 CCATCCTTGATGTAAATGGTCAGT 58.804 41.667 3.62 0.00 38.28 3.41
1642 1709 4.037208 GCCATCCTTGATGTAAATGGTCAG 59.963 45.833 3.62 0.00 38.28 3.51
1643 1710 3.953612 GCCATCCTTGATGTAAATGGTCA 59.046 43.478 3.62 0.00 38.28 4.02
1644 1711 3.319122 GGCCATCCTTGATGTAAATGGTC 59.681 47.826 0.00 0.00 38.28 4.02
1645 1712 3.052642 AGGCCATCCTTGATGTAAATGGT 60.053 43.478 5.01 0.00 40.66 3.55
1649 1716 4.314522 TTGAGGCCATCCTTGATGTAAA 57.685 40.909 5.01 0.00 44.46 2.01
1651 1718 3.459227 TCATTGAGGCCATCCTTGATGTA 59.541 43.478 5.01 0.00 44.46 2.29
1657 1724 1.341383 GGTGTCATTGAGGCCATCCTT 60.341 52.381 5.01 0.00 44.46 3.36
1696 1763 4.521130 ACTTGTCTGATGCTTCTTCGTA 57.479 40.909 0.88 0.00 0.00 3.43
1697 1764 3.393089 ACTTGTCTGATGCTTCTTCGT 57.607 42.857 0.88 0.00 0.00 3.85
1734 1801 1.906757 CTGCACTAGTCTGAAGAGCG 58.093 55.000 0.00 0.00 33.82 5.03
1747 1814 3.068165 TGAGTAACGCATATAGCTGCACT 59.932 43.478 1.02 0.00 42.40 4.40
1928 1995 1.878656 AAGACGAGCAAGGTCCGAGG 61.879 60.000 0.00 0.00 34.97 4.63
1944 2011 3.937814 AGGACGACAATTGTATGCAAGA 58.062 40.909 11.95 0.00 38.10 3.02
1982 2049 3.181461 ACACTCAGCATGCTATAAGGACC 60.181 47.826 22.19 0.00 34.76 4.46
2003 2070 2.292292 ACAACGCAACACAGGGATTTAC 59.708 45.455 0.00 0.00 0.00 2.01
2007 2074 0.667993 CAACAACGCAACACAGGGAT 59.332 50.000 0.00 0.00 0.00 3.85
2016 2083 4.438065 GGCATGTATACATCAACAACGCAA 60.438 41.667 15.60 0.00 33.61 4.85
2025 2092 5.104982 TGACAGACAAGGCATGTATACATCA 60.105 40.000 15.60 4.51 44.12 3.07
2029 2096 5.504665 GCAATGACAGACAAGGCATGTATAC 60.505 44.000 0.00 0.00 44.12 1.47
2040 2127 0.478072 AGGGTGGCAATGACAGACAA 59.522 50.000 0.00 0.00 0.00 3.18
2044 2131 1.542915 CAAAGAGGGTGGCAATGACAG 59.457 52.381 0.00 0.00 0.00 3.51
2047 2134 1.144708 TCACAAAGAGGGTGGCAATGA 59.855 47.619 0.00 0.00 36.90 2.57
2065 2152 2.368439 GCAGGACATAAGTTGGCATCA 58.632 47.619 0.00 0.00 33.62 3.07
2068 2155 0.323360 GGGCAGGACATAAGTTGGCA 60.323 55.000 0.00 0.00 33.62 4.92
2069 2156 1.376609 CGGGCAGGACATAAGTTGGC 61.377 60.000 0.00 0.00 32.10 4.52
2070 2157 0.251916 TCGGGCAGGACATAAGTTGG 59.748 55.000 0.00 0.00 0.00 3.77
2072 2159 1.207329 GTCTCGGGCAGGACATAAGTT 59.793 52.381 0.00 0.00 33.19 2.66
2086 2192 6.162079 AGCATATACATCATTCAAGTCTCGG 58.838 40.000 0.00 0.00 0.00 4.63
2088 2194 7.087007 TCGAGCATATACATCATTCAAGTCTC 58.913 38.462 0.00 0.00 0.00 3.36
2090 2196 7.824704 ATCGAGCATATACATCATTCAAGTC 57.175 36.000 0.00 0.00 0.00 3.01
2106 2212 6.294473 AGGATGTATTGAAGAAATCGAGCAT 58.706 36.000 0.00 0.00 0.00 3.79
2175 2345 6.073003 ACACAAGAAAATAACACTGAGCTAGC 60.073 38.462 6.62 6.62 0.00 3.42
2259 2429 1.092921 TCCACGGGCAATATTGACGC 61.093 55.000 23.96 18.60 36.95 5.19
2261 2431 3.119849 GCATATCCACGGGCAATATTGAC 60.120 47.826 19.73 16.63 34.70 3.18
2264 2434 2.041620 AGGCATATCCACGGGCAATATT 59.958 45.455 0.00 0.00 37.29 1.28
2269 2439 0.324614 CATAGGCATATCCACGGGCA 59.675 55.000 0.00 0.00 37.29 5.36
2273 2443 5.349817 GTCAAGATTCATAGGCATATCCACG 59.650 44.000 0.00 0.00 37.29 4.94
2286 2456 7.934855 AAAGCAGTTAGATGTCAAGATTCAT 57.065 32.000 0.00 0.00 0.00 2.57
2294 2464 6.291377 GGGATGATAAAGCAGTTAGATGTCA 58.709 40.000 0.00 0.00 0.00 3.58
2295 2465 5.703130 GGGGATGATAAAGCAGTTAGATGTC 59.297 44.000 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.