Multiple sequence alignment - TraesCS3B01G404000

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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 TraesCS3B01G404000 chr3B 100.000 4211 0 0 1 4211 638359864 638355654 0.000000e+00 7777.0
1 TraesCS3B01G404000 chr3A 90.506 4171 197 72 168 4210 621895909 621891810 0.000000e+00 5325.0
2 TraesCS3B01G404000 chr3A 85.965 114 5 2 58 171 621896267 621896165 1.240000e-20 111.0
3 TraesCS3B01G404000 chr3A 95.652 46 2 0 1 46 560432336 560432291 1.620000e-09 75.0
4 TraesCS3B01G404000 chr3A 92.157 51 3 1 1 50 716809875 716809925 2.100000e-08 71.3
5 TraesCS3B01G404000 chr3D 88.616 4278 263 90 38 4210 478655918 478651760 0.000000e+00 4996.0
6 TraesCS3B01G404000 chr1D 88.551 428 27 5 2613 3019 372360598 372361024 2.260000e-137 499.0
7 TraesCS3B01G404000 chr1D 95.652 46 2 0 1 46 222282756 222282711 1.620000e-09 75.0
8 TraesCS3B01G404000 chr1B 89.673 397 20 4 2613 2988 497274561 497274957 1.760000e-133 486.0
9 TraesCS3B01G404000 chr1A 88.780 410 25 4 2610 2998 471730046 471730455 2.280000e-132 483.0
10 TraesCS3B01G404000 chr1A 95.652 46 2 0 1 46 425901231 425901186 1.620000e-09 75.0
11 TraesCS3B01G404000 chr1A 93.617 47 3 0 1 47 266349285 266349239 2.100000e-08 71.3
12 TraesCS3B01G404000 chr5B 88.579 359 37 4 2610 2966 446996501 446996857 2.330000e-117 433.0
13 TraesCS3B01G404000 chr5D 87.879 363 39 5 2606 2966 374391709 374392068 5.030000e-114 422.0
14 TraesCS3B01G404000 chr5A 87.989 358 41 2 2610 2966 476225331 476225687 5.030000e-114 422.0
15 TraesCS3B01G404000 chr5A 97.727 44 1 0 1 44 616368596 616368553 4.510000e-10 76.8
16 TraesCS3B01G404000 chr5A 93.750 48 2 1 1 47 535243547 535243500 2.100000e-08 71.3
17 TraesCS3B01G404000 chr7B 85.974 385 50 4 2614 2996 544481052 544480670 3.920000e-110 409.0
18 TraesCS3B01G404000 chr7A 95.556 45 2 0 1 45 39576554 39576510 5.840000e-09 73.1
19 TraesCS3B01G404000 chr6B 93.750 48 2 1 1 47 465696027 465695980 2.100000e-08 71.3


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 TraesCS3B01G404000 chr3B 638355654 638359864 4210 True 7777 7777 100.0000 1 4211 1 chr3B.!!$R1 4210
1 TraesCS3B01G404000 chr3A 621891810 621896267 4457 True 2718 5325 88.2355 58 4210 2 chr3A.!!$R2 4152
2 TraesCS3B01G404000 chr3D 478651760 478655918 4158 True 4996 4996 88.6160 38 4210 1 chr3D.!!$R1 4172

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
880 1191 0.027979 CGCGCACATTGACATTAGGG 59.972 55.0 8.75 0.00 0.0 3.53 F
909 1223 0.035343 CCGTTCCTCTTTCCCCTTCC 60.035 60.0 0.00 0.00 0.0 3.46 F
1061 1392 0.179936 CTCCATGGAAGGTGAGCTCC 59.820 60.0 17.00 2.19 0.0 4.70 F
1287 1621 0.750546 CATGATCACCCTGCACCTGG 60.751 60.0 0.00 0.00 0.0 4.45 F
3172 3571 0.468226 TGCAAGAGGAACAACGAGGT 59.532 50.0 0.00 0.00 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2357 2719 0.177373 GGAAAGGTGGCTACTACCGG 59.823 60.000 0.00 0.0 43.06 5.28 R
2510 2872 2.900122 AGGCGTTTTCATGATCGTTG 57.100 45.000 0.00 0.0 0.00 4.10 R
3078 3460 7.517575 CGAGCGTGGATATGATCTATGTAGTAG 60.518 44.444 0.00 0.0 0.00 2.57 R
3176 3575 4.503296 CCCCTTATTGCGCTATCACTTACT 60.503 45.833 9.73 0.0 0.00 2.24 R
4092 4523 1.293924 CAGATAAAGCTGCCACCTCG 58.706 55.000 0.00 0.0 0.00 4.63 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 6.312399 CATCTAGATGTGTCCTAGACAGAC 57.688 45.833 22.42 0.00 43.57 3.51
36 37 4.783055 TCTAGATGTGTCCTAGACAGACC 58.217 47.826 0.00 0.00 43.57 3.85
37 38 2.741145 AGATGTGTCCTAGACAGACCC 58.259 52.381 0.00 0.00 43.57 4.46
38 39 2.043115 AGATGTGTCCTAGACAGACCCA 59.957 50.000 0.00 0.00 43.57 4.51
39 40 2.391926 TGTGTCCTAGACAGACCCAA 57.608 50.000 0.00 0.00 43.57 4.12
40 41 2.684943 TGTGTCCTAGACAGACCCAAA 58.315 47.619 0.00 0.00 43.57 3.28
41 42 3.042682 TGTGTCCTAGACAGACCCAAAA 58.957 45.455 0.00 0.00 43.57 2.44
98 106 0.108585 AGTTGGACCGCAATGTGACT 59.891 50.000 0.00 0.00 0.00 3.41
133 142 2.626840 TGCCTTTTTGGTTTCTTGTGC 58.373 42.857 0.00 0.00 38.35 4.57
165 174 5.824904 AATCTGGATTTGAGATTTCACCG 57.175 39.130 0.00 0.00 36.91 4.94
220 490 5.518487 CAGTTTTTCTTTTACACCGCAACAT 59.482 36.000 0.00 0.00 0.00 2.71
326 604 5.163513 GCATGTGTATGAAAAAGTCCCAAG 58.836 41.667 0.00 0.00 36.36 3.61
367 650 3.409856 GGCTGTCGCGCACATAAT 58.590 55.556 8.75 0.00 36.88 1.28
368 651 2.600388 GGCTGTCGCGCACATAATA 58.400 52.632 8.75 0.00 36.88 0.98
445 739 1.475280 GCTTGACCCCCGAATTAAACC 59.525 52.381 0.00 0.00 0.00 3.27
466 760 2.029288 CACAGACCGCGCACATTCT 61.029 57.895 8.75 0.00 0.00 2.40
592 899 4.143333 CCGCACCTCCCCTGTACG 62.143 72.222 0.00 0.00 0.00 3.67
850 1161 1.663161 GCCGCTTCGTTTTCTTCAAGG 60.663 52.381 0.00 0.00 0.00 3.61
851 1162 1.602377 CCGCTTCGTTTTCTTCAAGGT 59.398 47.619 0.00 0.00 0.00 3.50
860 1171 4.446385 CGTTTTCTTCAAGGTCGTGACATA 59.554 41.667 2.00 0.00 0.00 2.29
861 1172 5.611844 CGTTTTCTTCAAGGTCGTGACATAC 60.612 44.000 2.00 0.00 0.00 2.39
880 1191 0.027979 CGCGCACATTGACATTAGGG 59.972 55.000 8.75 0.00 0.00 3.53
883 1194 1.942657 CGCACATTGACATTAGGGAGG 59.057 52.381 0.00 0.00 0.00 4.30
884 1195 1.678101 GCACATTGACATTAGGGAGGC 59.322 52.381 0.00 0.00 0.00 4.70
885 1196 2.684927 GCACATTGACATTAGGGAGGCT 60.685 50.000 0.00 0.00 0.00 4.58
886 1197 2.947652 CACATTGACATTAGGGAGGCTG 59.052 50.000 0.00 0.00 0.00 4.85
887 1198 1.952296 CATTGACATTAGGGAGGCTGC 59.048 52.381 0.00 0.00 0.00 5.25
888 1199 1.289160 TTGACATTAGGGAGGCTGCT 58.711 50.000 5.84 0.00 0.00 4.24
889 1200 0.543277 TGACATTAGGGAGGCTGCTG 59.457 55.000 5.84 0.00 0.00 4.41
907 1221 1.379146 GCCGTTCCTCTTTCCCCTT 59.621 57.895 0.00 0.00 0.00 3.95
909 1223 0.035343 CCGTTCCTCTTTCCCCTTCC 60.035 60.000 0.00 0.00 0.00 3.46
952 1266 4.733542 CGCCACCAAACCCCCGAT 62.734 66.667 0.00 0.00 0.00 4.18
957 1271 1.064314 CCACCAAACCCCCGATATCAA 60.064 52.381 3.12 0.00 0.00 2.57
960 1274 1.133792 CCAAACCCCCGATATCAAGCT 60.134 52.381 3.12 0.00 0.00 3.74
987 1301 9.653516 AGCTATATATACTGCATATTCTCCAGT 57.346 33.333 10.28 0.00 42.10 4.00
1002 1316 1.004560 CAGTCCCTGCAAAGCGAGA 60.005 57.895 0.00 0.00 0.00 4.04
1006 1320 2.037136 CCCTGCAAAGCGAGACCTG 61.037 63.158 0.00 0.00 0.00 4.00
1011 1325 2.346803 TGCAAAGCGAGACCTGTATTC 58.653 47.619 0.00 0.00 0.00 1.75
1012 1326 2.028112 TGCAAAGCGAGACCTGTATTCT 60.028 45.455 0.00 0.00 0.00 2.40
1013 1327 3.194755 TGCAAAGCGAGACCTGTATTCTA 59.805 43.478 0.00 0.00 0.00 2.10
1014 1328 4.181578 GCAAAGCGAGACCTGTATTCTAA 58.818 43.478 0.00 0.00 0.00 2.10
1015 1329 4.268884 GCAAAGCGAGACCTGTATTCTAAG 59.731 45.833 0.00 0.00 0.00 2.18
1033 1364 2.517875 ATCAAGATGGGGCTGCGC 60.518 61.111 8.35 8.35 0.00 6.09
1059 1390 0.252881 TCCTCCATGGAAGGTGAGCT 60.253 55.000 17.00 0.00 42.94 4.09
1061 1392 0.179936 CTCCATGGAAGGTGAGCTCC 59.820 60.000 17.00 2.19 0.00 4.70
1088 1419 1.355066 CTCGCCTTTCTTCGAGTGGC 61.355 60.000 3.76 0.00 44.95 5.01
1090 1421 1.355066 CGCCTTTCTTCGAGTGGCTC 61.355 60.000 12.06 0.00 41.25 4.70
1144 1478 1.166129 CGTCGACTTTCTCCTCCTCA 58.834 55.000 14.70 0.00 0.00 3.86
1147 1481 2.755655 GTCGACTTTCTCCTCCTCATCA 59.244 50.000 8.70 0.00 0.00 3.07
1153 1487 1.988293 TCTCCTCCTCATCATCGTCC 58.012 55.000 0.00 0.00 0.00 4.79
1165 1499 2.058001 ATCGTCCATGGCGTCTGGA 61.058 57.895 22.22 4.37 40.49 3.86
1168 1502 2.606213 TCCATGGCGTCTGGACCA 60.606 61.111 6.96 0.00 37.87 4.02
1171 1505 1.078214 CATGGCGTCTGGACCACAT 60.078 57.895 0.00 0.00 39.19 3.21
1173 1507 3.127533 GGCGTCTGGACCACATGC 61.128 66.667 5.42 5.42 0.00 4.06
1177 1511 1.448540 GTCTGGACCACATGCGGAG 60.449 63.158 6.80 0.00 34.14 4.63
1178 1512 2.124983 CTGGACCACATGCGGAGG 60.125 66.667 6.80 0.00 0.00 4.30
1179 1513 2.606213 TGGACCACATGCGGAGGA 60.606 61.111 6.80 0.00 0.00 3.71
1180 1514 2.125106 GGACCACATGCGGAGGAC 60.125 66.667 6.80 0.00 0.00 3.85
1182 1516 4.082523 ACCACATGCGGAGGACGG 62.083 66.667 6.80 0.00 44.51 4.79
1198 1532 3.075005 GGAGGTGCCGCTCAGGTA 61.075 66.667 0.00 0.00 43.70 3.08
1199 1533 2.496817 GAGGTGCCGCTCAGGTAG 59.503 66.667 0.00 0.00 43.70 3.18
1200 1534 2.037367 AGGTGCCGCTCAGGTAGA 59.963 61.111 0.00 0.00 43.70 2.59
1201 1535 1.381872 AGGTGCCGCTCAGGTAGAT 60.382 57.895 0.00 0.00 43.70 1.98
1202 1536 1.227380 GGTGCCGCTCAGGTAGATG 60.227 63.158 0.00 0.00 43.70 2.90
1213 1547 1.884926 GGTAGATGGCAGCAGCGTC 60.885 63.158 5.19 0.00 43.41 5.19
1225 1559 4.088762 AGCGTCGCATGTTTGCCG 62.089 61.111 21.09 0.00 46.57 5.69
1287 1621 0.750546 CATGATCACCCTGCACCTGG 60.751 60.000 0.00 0.00 0.00 4.45
1450 1787 1.099689 GTGACGAAGAGGAGGAGGAG 58.900 60.000 0.00 0.00 0.00 3.69
1456 1793 2.373836 CGAAGAGGAGGAGGAGGAGATA 59.626 54.545 0.00 0.00 0.00 1.98
1466 1803 4.418526 AGGAGGAGGAGATAGATGAGTTGA 59.581 45.833 0.00 0.00 0.00 3.18
1472 1809 6.232581 AGGAGATAGATGAGTTGAAACCTG 57.767 41.667 0.00 0.00 0.00 4.00
1474 1811 6.098124 AGGAGATAGATGAGTTGAAACCTGAG 59.902 42.308 0.00 0.00 0.00 3.35
1510 1847 1.066502 GTGGAGGCAGAGGAGAAAGAC 60.067 57.143 0.00 0.00 0.00 3.01
1536 1873 2.892425 CGAGCCAATGGTCTCGGC 60.892 66.667 26.77 3.91 46.62 5.54
1539 1876 2.825836 GCCAATGGTCTCGGCAGG 60.826 66.667 0.00 0.00 45.52 4.85
1541 1878 1.299648 CCAATGGTCTCGGCAGGAA 59.700 57.895 0.00 0.00 0.00 3.36
1615 1952 4.828409 CCCATGGGCTGCGAATAT 57.172 55.556 20.41 0.00 0.00 1.28
1696 2033 7.547370 GTCTGTAACAAGAGCTTCAACAGATAT 59.453 37.037 15.83 0.00 42.51 1.63
1747 2084 8.926710 ACGTCTATTTTGCATGCTCTTATATAC 58.073 33.333 20.33 11.91 0.00 1.47
1752 2089 3.942829 TGCATGCTCTTATATACTGCCC 58.057 45.455 20.33 0.00 0.00 5.36
1769 2108 1.404035 GCCCCGCCTTAGTTATTGTTG 59.596 52.381 0.00 0.00 0.00 3.33
1782 2121 9.965824 CTTAGTTATTGTTGGTTCTGTTTTCAT 57.034 29.630 0.00 0.00 0.00 2.57
1783 2122 9.959749 TTAGTTATTGTTGGTTCTGTTTTCATC 57.040 29.630 0.00 0.00 0.00 2.92
1791 2130 4.518970 TGGTTCTGTTTTCATCTAAGCCAC 59.481 41.667 0.00 0.00 0.00 5.01
1805 2144 3.951979 AAGCCACGATTCGATTGATTC 57.048 42.857 13.95 0.00 0.00 2.52
1821 2160 9.428097 TCGATTGATTCTGTGATAATATTGGAG 57.572 33.333 0.00 0.00 0.00 3.86
1903 2256 5.507149 CGAATGAGAGAACCGAGATCATCTT 60.507 44.000 0.00 0.00 30.51 2.40
1923 2276 6.068473 TCTTAGCTCGCTAACATAATTCGA 57.932 37.500 7.25 0.00 35.06 3.71
1964 2317 4.024048 CCATATCATAGTGTTTTGGTCGCC 60.024 45.833 0.00 0.00 0.00 5.54
1965 2318 2.851263 TCATAGTGTTTTGGTCGCCT 57.149 45.000 0.00 0.00 0.00 5.52
1966 2319 2.422597 TCATAGTGTTTTGGTCGCCTG 58.577 47.619 0.00 0.00 0.00 4.85
1967 2320 1.135689 CATAGTGTTTTGGTCGCCTGC 60.136 52.381 0.00 0.00 0.00 4.85
1968 2321 0.887387 TAGTGTTTTGGTCGCCTGCC 60.887 55.000 0.00 0.00 0.00 4.85
1969 2322 2.909965 TGTTTTGGTCGCCTGCCC 60.910 61.111 0.00 0.00 0.00 5.36
1970 2323 4.038080 GTTTTGGTCGCCTGCCCG 62.038 66.667 0.00 0.00 0.00 6.13
1999 2352 4.702131 CCCAAATCTTAACCAACTCTCCAG 59.298 45.833 0.00 0.00 0.00 3.86
2000 2353 5.316987 CCAAATCTTAACCAACTCTCCAGT 58.683 41.667 0.00 0.00 0.00 4.00
2002 2355 6.234177 CAAATCTTAACCAACTCTCCAGTCT 58.766 40.000 0.00 0.00 29.93 3.24
2003 2356 5.669164 ATCTTAACCAACTCTCCAGTCTC 57.331 43.478 0.00 0.00 29.93 3.36
2004 2357 3.833070 TCTTAACCAACTCTCCAGTCTCC 59.167 47.826 0.00 0.00 29.93 3.71
2005 2358 2.103153 AACCAACTCTCCAGTCTCCA 57.897 50.000 0.00 0.00 29.93 3.86
2006 2359 1.343069 ACCAACTCTCCAGTCTCCAC 58.657 55.000 0.00 0.00 29.93 4.02
2007 2360 1.342074 CCAACTCTCCAGTCTCCACA 58.658 55.000 0.00 0.00 29.93 4.17
2008 2361 1.905215 CCAACTCTCCAGTCTCCACAT 59.095 52.381 0.00 0.00 29.93 3.21
2086 2441 2.146342 CACACACCATCAAGGACACTC 58.854 52.381 0.00 0.00 41.22 3.51
2087 2442 2.050144 ACACACCATCAAGGACACTCT 58.950 47.619 0.00 0.00 41.22 3.24
2095 2450 4.508662 CATCAAGGACACTCTAGGTTTCC 58.491 47.826 7.93 7.93 43.23 3.13
2107 2462 5.134725 TCTAGGTTTCCCGGATAACTAGT 57.865 43.478 22.38 0.00 35.12 2.57
2108 2463 5.136105 TCTAGGTTTCCCGGATAACTAGTC 58.864 45.833 22.38 4.91 35.12 2.59
2132 2487 4.511246 ACCCGGCCGGTAGATCGA 62.511 66.667 40.52 0.00 45.97 3.59
2263 2625 1.817740 CGGGTGTTTGGTGTCTGGATT 60.818 52.381 0.00 0.00 0.00 3.01
2357 2719 1.226888 GATCACCAGTACGCCGTCC 60.227 63.158 0.00 0.00 0.00 4.79
2378 2740 0.900421 GGTAGTAGCCACCTTTCCGT 59.100 55.000 0.00 0.00 32.98 4.69
2422 2784 9.938280 CCCAAACATGTATATATATATACCCGG 57.062 37.037 28.33 21.89 42.70 5.73
2510 2872 3.687200 ACGAACAACGAAAATTCACACC 58.313 40.909 0.00 0.00 45.77 4.16
3078 3460 2.737830 GGGCCGTCTAGCTGATCC 59.262 66.667 0.00 0.00 0.00 3.36
3096 3484 9.573166 AGCTGATCCTACTACATAGATCATATC 57.427 37.037 2.30 0.00 32.10 1.63
3146 3545 6.150396 TGATTTCATCATACATGCAATGCA 57.850 33.333 11.44 11.44 40.63 3.96
3171 3570 1.813513 ATGCAAGAGGAACAACGAGG 58.186 50.000 0.00 0.00 0.00 4.63
3172 3571 0.468226 TGCAAGAGGAACAACGAGGT 59.532 50.000 0.00 0.00 0.00 3.85
3173 3572 1.689813 TGCAAGAGGAACAACGAGGTA 59.310 47.619 0.00 0.00 0.00 3.08
3174 3573 2.067013 GCAAGAGGAACAACGAGGTAC 58.933 52.381 0.00 0.00 0.00 3.34
3176 3575 3.057033 GCAAGAGGAACAACGAGGTACTA 60.057 47.826 0.00 0.00 41.55 1.82
3346 3746 5.790593 CTTCACAGGCTAACTAAACTGGTA 58.209 41.667 0.00 0.00 35.34 3.25
3390 3790 3.829886 TCGCATTTTGAACATGAGACC 57.170 42.857 0.00 0.00 0.00 3.85
3549 3953 9.703892 AACATTTGTGCAAGCAATAACTATAAA 57.296 25.926 0.00 0.00 0.00 1.40
3719 4123 9.109393 CTTCTCATTTAATTGATTCCGGAGTTA 57.891 33.333 3.34 0.00 0.00 2.24
3734 4138 4.151867 CCGGAGTTAAAGCTTTGTCAGTAC 59.848 45.833 22.02 8.16 0.00 2.73
3853 4259 8.579850 AGCAATTAATAGAACAAAGATGGTCA 57.420 30.769 0.00 0.00 46.21 4.02
3961 4368 9.988815 AAACATTGTTTATAATTGTAAGTGGCA 57.011 25.926 12.98 0.00 0.00 4.92
3996 4427 6.491745 TGCCACCACAAGTTTTATCTATTTCA 59.508 34.615 0.00 0.00 0.00 2.69
4124 4555 2.148916 TTATCTGGCGCATTCTACGG 57.851 50.000 10.83 0.00 0.00 4.02
4134 4565 4.909880 GGCGCATTCTACGGAAATAAAATC 59.090 41.667 10.83 0.00 34.90 2.17
4135 4566 4.909880 GCGCATTCTACGGAAATAAAATCC 59.090 41.667 0.30 0.00 34.90 3.01
4148 4579 9.012448 CGGAAATAAAATCCCAATTTTACGTAC 57.988 33.333 0.00 0.00 45.44 3.67
4172 4608 8.773404 ACACAATAGGTTATGTCTTAGTGTTC 57.227 34.615 0.00 0.00 33.19 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 5.240623 GGTCTGTCTAGGACACATCTAGATG 59.759 48.000 27.63 27.63 43.25 2.90
13 14 5.381757 GGTCTGTCTAGGACACATCTAGAT 58.618 45.833 0.00 0.00 43.25 1.98
14 15 4.385421 GGGTCTGTCTAGGACACATCTAGA 60.385 50.000 0.00 0.00 37.67 2.43
15 16 3.886505 GGGTCTGTCTAGGACACATCTAG 59.113 52.174 0.00 0.00 37.67 2.43
16 17 3.268595 TGGGTCTGTCTAGGACACATCTA 59.731 47.826 0.00 0.00 41.46 1.98
17 18 2.043115 TGGGTCTGTCTAGGACACATCT 59.957 50.000 0.00 0.00 41.46 2.90
18 19 2.457598 TGGGTCTGTCTAGGACACATC 58.542 52.381 0.00 0.00 41.46 3.06
19 20 2.623418 TGGGTCTGTCTAGGACACAT 57.377 50.000 0.00 0.00 41.46 3.21
20 21 2.391926 TTGGGTCTGTCTAGGACACA 57.608 50.000 0.00 0.00 44.14 3.72
21 22 3.764237 TTTTGGGTCTGTCTAGGACAC 57.236 47.619 0.00 0.00 37.67 3.67
98 106 2.969821 AGGCAAACCCAGTGTTGATA 57.030 45.000 0.00 0.00 37.23 2.15
165 174 5.126067 AGAAACATGTGCCCATCATACTAC 58.874 41.667 0.00 0.00 0.00 2.73
220 490 3.470709 CTCACTCACTCTGGCTGAAAAA 58.529 45.455 0.00 0.00 0.00 1.94
326 604 6.313658 CCCTAGCCTATGTTTTTGATTTTTGC 59.686 38.462 0.00 0.00 0.00 3.68
366 649 2.165845 GTGCCGTGTTCTCACCTAGTAT 59.834 50.000 0.00 0.00 41.09 2.12
367 650 1.542915 GTGCCGTGTTCTCACCTAGTA 59.457 52.381 0.00 0.00 41.09 1.82
368 651 0.317479 GTGCCGTGTTCTCACCTAGT 59.683 55.000 0.00 0.00 41.09 2.57
592 899 2.920869 CCATACGATCGTGTGCGC 59.079 61.111 32.13 0.00 36.18 6.09
860 1171 0.726827 CCTAATGTCAATGTGCGCGT 59.273 50.000 8.43 0.00 0.00 6.01
861 1172 0.027979 CCCTAATGTCAATGTGCGCG 59.972 55.000 0.00 0.00 0.00 6.86
883 1194 1.916697 GAAAGAGGAACGGCAGCAGC 61.917 60.000 0.00 0.00 41.10 5.25
884 1195 1.301677 GGAAAGAGGAACGGCAGCAG 61.302 60.000 0.00 0.00 0.00 4.24
885 1196 1.302511 GGAAAGAGGAACGGCAGCA 60.303 57.895 0.00 0.00 0.00 4.41
886 1197 2.041115 GGGAAAGAGGAACGGCAGC 61.041 63.158 0.00 0.00 0.00 5.25
887 1198 1.377333 GGGGAAAGAGGAACGGCAG 60.377 63.158 0.00 0.00 0.00 4.85
888 1199 1.423794 AAGGGGAAAGAGGAACGGCA 61.424 55.000 0.00 0.00 0.00 5.69
889 1200 0.677098 GAAGGGGAAAGAGGAACGGC 60.677 60.000 0.00 0.00 0.00 5.68
891 1202 0.984995 AGGAAGGGGAAAGAGGAACG 59.015 55.000 0.00 0.00 0.00 3.95
892 1203 1.282447 GGAGGAAGGGGAAAGAGGAAC 59.718 57.143 0.00 0.00 0.00 3.62
907 1221 1.079490 AGAAGACTGGGATGTGGAGGA 59.921 52.381 0.00 0.00 0.00 3.71
909 1223 1.484240 GGAGAAGACTGGGATGTGGAG 59.516 57.143 0.00 0.00 0.00 3.86
985 1299 1.004440 GTCTCGCTTTGCAGGGACT 60.004 57.895 0.00 0.00 37.07 3.85
987 1301 2.217038 AGGTCTCGCTTTGCAGGGA 61.217 57.895 0.00 0.00 39.61 4.20
1002 1316 6.043706 CCCCATCTTGATCTTAGAATACAGGT 59.956 42.308 0.00 0.00 0.00 4.00
1006 1320 5.936956 CAGCCCCATCTTGATCTTAGAATAC 59.063 44.000 0.00 0.00 0.00 1.89
1011 1325 2.502295 GCAGCCCCATCTTGATCTTAG 58.498 52.381 0.00 0.00 0.00 2.18
1012 1326 1.202687 CGCAGCCCCATCTTGATCTTA 60.203 52.381 0.00 0.00 0.00 2.10
1013 1327 0.465097 CGCAGCCCCATCTTGATCTT 60.465 55.000 0.00 0.00 0.00 2.40
1014 1328 1.147824 CGCAGCCCCATCTTGATCT 59.852 57.895 0.00 0.00 0.00 2.75
1015 1329 3.741860 CGCAGCCCCATCTTGATC 58.258 61.111 0.00 0.00 0.00 2.92
1033 1364 3.731547 TCCATGGAGGAGCAGGTG 58.268 61.111 11.44 0.00 43.07 4.00
1041 1372 0.179936 GAGCTCACCTTCCATGGAGG 59.820 60.000 21.90 21.90 39.47 4.30
1043 1374 0.252881 AGGAGCTCACCTTCCATGGA 60.253 55.000 17.19 11.44 36.86 3.41
1059 1390 2.781595 GAAAGGCGAGGCGACAAGGA 62.782 60.000 0.00 0.00 37.34 3.36
1061 1392 0.951040 AAGAAAGGCGAGGCGACAAG 60.951 55.000 0.00 0.00 37.34 3.16
1100 1431 4.493747 CGAGGAGGACGGCGAACC 62.494 72.222 16.62 16.74 0.00 3.62
1101 1432 3.398353 CTCGAGGAGGACGGCGAAC 62.398 68.421 16.62 5.56 32.16 3.95
1102 1433 2.888464 ATCTCGAGGAGGACGGCGAA 62.888 60.000 16.62 0.00 32.16 4.70
1138 1472 1.607509 GCCATGGACGATGATGAGGAG 60.608 57.143 18.40 0.00 33.31 3.69
1144 1478 0.249615 CAGACGCCATGGACGATGAT 60.250 55.000 27.68 11.09 33.31 2.45
1147 1481 2.058001 TCCAGACGCCATGGACGAT 61.058 57.895 27.68 16.27 41.96 3.73
1153 1487 1.078214 ATGTGGTCCAGACGCCATG 60.078 57.895 0.00 0.00 37.09 3.66
1165 1499 4.082523 CCGTCCTCCGCATGTGGT 62.083 66.667 24.28 0.00 34.38 4.16
1167 1501 2.202797 CTCCGTCCTCCGCATGTG 60.203 66.667 0.00 0.00 34.38 3.21
1168 1502 3.461773 CCTCCGTCCTCCGCATGT 61.462 66.667 0.00 0.00 34.38 3.21
1181 1515 3.075005 TACCTGAGCGGCACCTCC 61.075 66.667 1.45 0.00 35.61 4.30
1182 1516 1.395826 ATCTACCTGAGCGGCACCTC 61.396 60.000 1.45 0.00 35.61 3.85
1183 1517 1.381872 ATCTACCTGAGCGGCACCT 60.382 57.895 1.45 0.00 35.61 4.00
1184 1518 1.227380 CATCTACCTGAGCGGCACC 60.227 63.158 1.45 0.00 35.61 5.01
1185 1519 1.227380 CCATCTACCTGAGCGGCAC 60.227 63.158 1.45 0.00 35.61 5.01
1186 1520 3.094062 GCCATCTACCTGAGCGGCA 62.094 63.158 1.45 0.00 43.11 5.69
1187 1521 2.280457 GCCATCTACCTGAGCGGC 60.280 66.667 0.00 0.00 39.16 6.53
1188 1522 1.068753 CTGCCATCTACCTGAGCGG 59.931 63.158 0.00 0.00 39.35 5.52
1189 1523 1.593750 GCTGCCATCTACCTGAGCG 60.594 63.158 0.00 0.00 0.00 5.03
1190 1524 0.532417 CTGCTGCCATCTACCTGAGC 60.532 60.000 0.00 0.00 0.00 4.26
1191 1525 0.532417 GCTGCTGCCATCTACCTGAG 60.532 60.000 3.85 0.00 0.00 3.35
1192 1526 1.524002 GCTGCTGCCATCTACCTGA 59.476 57.895 3.85 0.00 0.00 3.86
1193 1527 1.886313 CGCTGCTGCCATCTACCTG 60.886 63.158 10.24 0.00 35.36 4.00
1194 1528 2.303549 GACGCTGCTGCCATCTACCT 62.304 60.000 10.24 0.00 35.36 3.08
1195 1529 1.884926 GACGCTGCTGCCATCTACC 60.885 63.158 10.24 0.00 35.36 3.18
1196 1530 2.233654 CGACGCTGCTGCCATCTAC 61.234 63.158 10.24 0.00 35.36 2.59
1197 1531 2.104928 CGACGCTGCTGCCATCTA 59.895 61.111 10.24 0.00 35.36 1.98
1213 1547 4.409218 AGCAGCGGCAAACATGCG 62.409 61.111 12.44 0.00 43.41 4.73
1287 1621 3.743899 GCCCATGATCTCTTCCTTGACTC 60.744 52.174 0.00 0.00 0.00 3.36
1396 1730 2.543978 CTTCCTCCTGGCCCTCCTCT 62.544 65.000 0.00 0.00 0.00 3.69
1450 1787 6.227298 TCAGGTTTCAACTCATCTATCTCC 57.773 41.667 0.00 0.00 0.00 3.71
1456 1793 3.777106 TGCTCAGGTTTCAACTCATCT 57.223 42.857 0.00 0.00 0.00 2.90
1472 1809 0.610232 ACCTTGCAACCTCCATGCTC 60.610 55.000 0.00 0.00 44.14 4.26
1474 1811 1.588082 CACCTTGCAACCTCCATGC 59.412 57.895 0.00 0.00 44.08 4.06
1525 1862 1.139853 GATCTTCCTGCCGAGACCATT 59.860 52.381 0.00 0.00 0.00 3.16
1526 1863 0.755686 GATCTTCCTGCCGAGACCAT 59.244 55.000 0.00 0.00 0.00 3.55
1536 1873 2.414481 CTGACGCTGTTTGATCTTCCTG 59.586 50.000 0.00 0.00 0.00 3.86
1537 1874 2.693069 CTGACGCTGTTTGATCTTCCT 58.307 47.619 0.00 0.00 0.00 3.36
1539 1876 1.800586 TGCTGACGCTGTTTGATCTTC 59.199 47.619 0.00 0.00 36.97 2.87
1541 1878 1.736126 CATGCTGACGCTGTTTGATCT 59.264 47.619 0.00 0.00 36.97 2.75
1574 1911 3.474570 GCCCTCTGCTCCGACCAT 61.475 66.667 0.00 0.00 36.87 3.55
1612 1949 1.292223 CGGCGTCGGGATCCAATAT 59.708 57.895 15.23 0.00 0.00 1.28
1669 2006 3.802139 TGTTGAAGCTCTTGTTACAGACG 59.198 43.478 0.00 0.00 0.00 4.18
1722 2059 9.144747 AGTATATAAGAGCATGCAAAATAGACG 57.855 33.333 21.98 0.00 0.00 4.18
1747 2084 1.308998 CAATAACTAAGGCGGGGCAG 58.691 55.000 0.00 0.00 0.00 4.85
1749 2086 1.404035 CAACAATAACTAAGGCGGGGC 59.596 52.381 0.00 0.00 0.00 5.80
1752 2089 4.007659 AGAACCAACAATAACTAAGGCGG 58.992 43.478 0.00 0.00 0.00 6.13
1769 2108 4.378459 CGTGGCTTAGATGAAAACAGAACC 60.378 45.833 0.00 0.00 0.00 3.62
1782 2121 3.793797 TCAATCGAATCGTGGCTTAGA 57.206 42.857 1.52 0.00 0.00 2.10
1783 2122 4.747108 AGAATCAATCGAATCGTGGCTTAG 59.253 41.667 1.52 0.00 0.00 2.18
1805 2144 6.603237 TTTGCGTCTCCAATATTATCACAG 57.397 37.500 0.00 0.00 0.00 3.66
1821 2160 5.826586 TCTAGATCATCTCTCTTTTGCGTC 58.173 41.667 0.00 0.00 35.28 5.19
1861 2208 6.837992 TCATTCGCTGGACTTAATTTTGTAC 58.162 36.000 0.00 0.00 0.00 2.90
1862 2209 6.876789 TCTCATTCGCTGGACTTAATTTTGTA 59.123 34.615 0.00 0.00 0.00 2.41
1863 2210 5.705441 TCTCATTCGCTGGACTTAATTTTGT 59.295 36.000 0.00 0.00 0.00 2.83
1864 2211 6.092670 TCTCTCATTCGCTGGACTTAATTTTG 59.907 38.462 0.00 0.00 0.00 2.44
1903 2256 5.177725 TGTCGAATTATGTTAGCGAGCTA 57.822 39.130 0.00 0.00 0.00 3.32
1946 2299 2.422597 CAGGCGACCAAAACACTATGA 58.577 47.619 0.00 0.00 0.00 2.15
1967 2320 2.566111 TAAGATTTGGGGCAGCCGGG 62.566 60.000 5.00 0.00 0.00 5.73
1968 2321 0.682855 TTAAGATTTGGGGCAGCCGG 60.683 55.000 5.00 0.00 0.00 6.13
1969 2322 0.455815 GTTAAGATTTGGGGCAGCCG 59.544 55.000 5.00 0.00 0.00 5.52
1970 2323 0.824109 GGTTAAGATTTGGGGCAGCC 59.176 55.000 1.26 1.26 0.00 4.85
1971 2324 1.555967 TGGTTAAGATTTGGGGCAGC 58.444 50.000 0.00 0.00 0.00 5.25
1999 2352 5.107220 CGTTTGTAACCAAGTATGTGGAGAC 60.107 44.000 0.00 0.00 41.65 3.36
2000 2353 4.992319 CGTTTGTAACCAAGTATGTGGAGA 59.008 41.667 0.00 0.00 41.65 3.71
2002 2355 4.958509 TCGTTTGTAACCAAGTATGTGGA 58.041 39.130 0.00 0.00 41.65 4.02
2003 2356 4.153475 CCTCGTTTGTAACCAAGTATGTGG 59.847 45.833 0.00 0.00 44.92 4.17
2004 2357 4.992319 TCCTCGTTTGTAACCAAGTATGTG 59.008 41.667 0.00 0.00 0.00 3.21
2005 2358 5.217978 TCCTCGTTTGTAACCAAGTATGT 57.782 39.130 0.00 0.00 0.00 2.29
2006 2359 4.092968 GCTCCTCGTTTGTAACCAAGTATG 59.907 45.833 0.00 0.00 0.00 2.39
2007 2360 4.251268 GCTCCTCGTTTGTAACCAAGTAT 58.749 43.478 0.00 0.00 0.00 2.12
2008 2361 3.069872 TGCTCCTCGTTTGTAACCAAGTA 59.930 43.478 0.00 0.00 0.00 2.24
2131 2486 1.270274 TGCATGCAAGGTGTTCACATC 59.730 47.619 20.30 0.00 0.00 3.06
2132 2487 1.271379 CTGCATGCAAGGTGTTCACAT 59.729 47.619 22.88 0.00 0.00 3.21
2156 2513 3.555956 CGGTGTTGGGAGATAGATTTTCG 59.444 47.826 0.00 0.00 0.00 3.46
2160 2517 2.100916 CGACGGTGTTGGGAGATAGATT 59.899 50.000 0.00 0.00 0.00 2.40
2263 2625 4.316823 AGACGAGCCCTGGGTCCA 62.317 66.667 15.56 0.00 39.23 4.02
2357 2719 0.177373 GGAAAGGTGGCTACTACCGG 59.823 60.000 0.00 0.00 43.06 5.28
2378 2740 6.434652 TGTTTGGGTTTCAGAGTTGTTCTTTA 59.565 34.615 0.00 0.00 32.41 1.85
2510 2872 2.900122 AGGCGTTTTCATGATCGTTG 57.100 45.000 0.00 0.00 0.00 4.10
3078 3460 7.517575 CGAGCGTGGATATGATCTATGTAGTAG 60.518 44.444 0.00 0.00 0.00 2.57
3163 3562 6.038050 GCTATCACTTACTAGTACCTCGTTGT 59.962 42.308 0.91 0.00 31.96 3.32
3171 3570 7.537991 CCTTATTGCGCTATCACTTACTAGTAC 59.462 40.741 9.73 0.00 31.96 2.73
3172 3571 7.309012 CCCTTATTGCGCTATCACTTACTAGTA 60.309 40.741 9.73 0.00 31.96 1.82
3173 3572 6.448006 CCTTATTGCGCTATCACTTACTAGT 58.552 40.000 9.73 0.00 34.00 2.57
3174 3573 5.864474 CCCTTATTGCGCTATCACTTACTAG 59.136 44.000 9.73 0.00 0.00 2.57
3175 3574 5.279306 CCCCTTATTGCGCTATCACTTACTA 60.279 44.000 9.73 0.00 0.00 1.82
3176 3575 4.503296 CCCCTTATTGCGCTATCACTTACT 60.503 45.833 9.73 0.00 0.00 2.24
3346 3746 8.358148 CGATGTATACAGTACTAGGTCCAAATT 58.642 37.037 11.91 0.00 0.00 1.82
3371 3771 3.837213 AGGTCTCATGTTCAAAATGCG 57.163 42.857 0.00 0.00 0.00 4.73
3698 4102 8.190784 AGCTTTAACTCCGGAATCAATTAAATG 58.809 33.333 5.23 7.34 0.00 2.32
3719 4123 4.947388 TGAACCAAGTACTGACAAAGCTTT 59.053 37.500 5.69 5.69 0.00 3.51
3734 4138 9.180678 GTTGTCATTTTGTTACTATGAACCAAG 57.819 33.333 0.00 0.00 30.72 3.61
3790 4194 8.952278 GGGTTGTGTGACATAAAAATGATACTA 58.048 33.333 0.00 0.00 0.00 1.82
3811 4215 4.566545 TTGCTTGATAATATGCGGGTTG 57.433 40.909 0.00 0.00 0.00 3.77
3961 4368 3.134442 ACTTGTGGTGGCATGTTTCAAAT 59.866 39.130 0.00 0.00 0.00 2.32
4045 4476 7.765307 ACGATTAAGCAAATTGAGATGACAAT 58.235 30.769 0.00 0.00 41.43 2.71
4092 4523 1.293924 CAGATAAAGCTGCCACCTCG 58.706 55.000 0.00 0.00 0.00 4.63
4134 4565 6.746745 ACCTATTGTGTACGTAAAATTGGG 57.253 37.500 20.72 16.30 31.67 4.12
4135 4566 9.710979 CATAACCTATTGTGTACGTAAAATTGG 57.289 33.333 17.74 17.74 33.06 3.16
4148 4579 9.088512 GAGAACACTAAGACATAACCTATTGTG 57.911 37.037 0.00 0.00 33.37 3.33


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

AutoCloner maintained by Alex Coulton.