Multiple sequence alignment - TraesCS6B01G020200

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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 TraesCS6B01G020200 chr6B 100.000 2561 0 0 1 2561 12592606 12590046 0.000000e+00 4730
1 TraesCS6B01G020200 chr6B 83.846 130 15 5 104 228 14252430 14252558 4.480000e-23 119
2 TraesCS6B01G020200 chr3D 88.758 2126 218 13 104 2217 121209333 121211449 0.000000e+00 2582
3 TraesCS6B01G020200 chr3D 87.172 2136 231 25 104 2217 562217395 562219509 0.000000e+00 2386
4 TraesCS6B01G020200 chr3D 86.544 2118 248 24 104 2206 586295524 586293429 0.000000e+00 2298
5 TraesCS6B01G020200 chr1D 87.816 2134 229 24 104 2217 415632886 415630764 0.000000e+00 2471
6 TraesCS6B01G020200 chr7B 89.591 1931 186 10 296 2217 544722121 544724045 0.000000e+00 2438
7 TraesCS6B01G020200 chr7B 89.441 1790 180 8 433 2217 593631558 593629773 0.000000e+00 2250
8 TraesCS6B01G020200 chr7B 80.478 251 32 10 104 345 593632113 593631871 2.620000e-40 176
9 TraesCS6B01G020200 chr6D 87.512 2130 231 25 104 2217 146941220 146943330 0.000000e+00 2427
10 TraesCS6B01G020200 chr1A 87.166 2096 235 18 134 2217 105913253 105915326 0.000000e+00 2350
11 TraesCS6B01G020200 chr1A 99.133 346 3 0 2216 2561 337013482 337013827 7.780000e-175 623
12 TraesCS6B01G020200 chr1A 82.726 521 58 13 104 616 287538651 287538155 3.910000e-118 435
13 TraesCS6B01G020200 chr3B 89.686 1784 174 8 440 2217 566826265 566828044 0.000000e+00 2266
14 TraesCS6B01G020200 chr3B 84.102 1692 199 46 104 1775 527650525 527648884 0.000000e+00 1570
15 TraesCS6B01G020200 chr3B 99.709 344 1 0 2218 2561 244740742 244741085 4.650000e-177 630
16 TraesCS6B01G020200 chr3B 98.867 353 2 1 2211 2561 571879067 571879419 1.670000e-176 628
17 TraesCS6B01G020200 chr2A 79.921 1763 252 47 113 1825 613268971 613267261 0.000000e+00 1201
18 TraesCS6B01G020200 chr7A 99.712 347 1 0 2215 2561 231557537 231557191 9.990000e-179 636
19 TraesCS6B01G020200 chr7A 99.709 344 1 0 2218 2561 200612412 200612069 4.650000e-177 630
20 TraesCS6B01G020200 chr7A 99.709 344 1 0 2218 2561 200615105 200614762 4.650000e-177 630
21 TraesCS6B01G020200 chr7A 99.419 344 2 0 2218 2561 231554868 231554525 2.160000e-175 625
22 TraesCS6B01G020200 chr5A 99.709 344 1 0 2218 2561 509048558 509048901 4.650000e-177 630
23 TraesCS6B01G020200 chr5A 99.709 344 1 0 2218 2561 509051067 509051410 4.650000e-177 630
24 TraesCS6B01G020200 chr5A 99.709 344 1 0 2218 2561 586156785 586157128 4.650000e-177 630
25 TraesCS6B01G020200 chr4A 99.424 347 2 0 2215 2561 729270133 729270479 4.650000e-177 630
26 TraesCS6B01G020200 chr4A 99.709 344 1 0 2218 2561 729272667 729273010 4.650000e-177 630
27 TraesCS6B01G020200 chr1B 95.349 344 16 0 2218 2561 643389916 643389573 4.820000e-152 547
28 TraesCS6B01G020200 chr1B 92.174 345 25 2 2216 2560 643387250 643386908 1.070000e-133 486
29 TraesCS6B01G020200 chr1B 82.734 139 16 4 104 236 662204710 662204574 1.610000e-22 117
30 TraesCS6B01G020200 chr7D 84.672 137 15 4 104 236 572265528 572265394 5.750000e-27 132
31 TraesCS6B01G020200 chr5B 81.633 147 21 5 104 245 281063380 281063235 1.610000e-22 117


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 TraesCS6B01G020200 chr6B 12590046 12592606 2560 True 4730.0 4730 100.0000 1 2561 1 chr6B.!!$R1 2560
1 TraesCS6B01G020200 chr3D 121209333 121211449 2116 False 2582.0 2582 88.7580 104 2217 1 chr3D.!!$F1 2113
2 TraesCS6B01G020200 chr3D 562217395 562219509 2114 False 2386.0 2386 87.1720 104 2217 1 chr3D.!!$F2 2113
3 TraesCS6B01G020200 chr3D 586293429 586295524 2095 True 2298.0 2298 86.5440 104 2206 1 chr3D.!!$R1 2102
4 TraesCS6B01G020200 chr1D 415630764 415632886 2122 True 2471.0 2471 87.8160 104 2217 1 chr1D.!!$R1 2113
5 TraesCS6B01G020200 chr7B 544722121 544724045 1924 False 2438.0 2438 89.5910 296 2217 1 chr7B.!!$F1 1921
6 TraesCS6B01G020200 chr7B 593629773 593632113 2340 True 1213.0 2250 84.9595 104 2217 2 chr7B.!!$R1 2113
7 TraesCS6B01G020200 chr6D 146941220 146943330 2110 False 2427.0 2427 87.5120 104 2217 1 chr6D.!!$F1 2113
8 TraesCS6B01G020200 chr1A 105913253 105915326 2073 False 2350.0 2350 87.1660 134 2217 1 chr1A.!!$F1 2083
9 TraesCS6B01G020200 chr3B 566826265 566828044 1779 False 2266.0 2266 89.6860 440 2217 1 chr3B.!!$F2 1777
10 TraesCS6B01G020200 chr3B 527648884 527650525 1641 True 1570.0 1570 84.1020 104 1775 1 chr3B.!!$R1 1671
11 TraesCS6B01G020200 chr2A 613267261 613268971 1710 True 1201.0 1201 79.9210 113 1825 1 chr2A.!!$R1 1712
12 TraesCS6B01G020200 chr7A 231554525 231557537 3012 True 630.5 636 99.5655 2215 2561 2 chr7A.!!$R2 346
13 TraesCS6B01G020200 chr7A 200612069 200615105 3036 True 630.0 630 99.7090 2218 2561 2 chr7A.!!$R1 343
14 TraesCS6B01G020200 chr5A 509048558 509051410 2852 False 630.0 630 99.7090 2218 2561 2 chr5A.!!$F2 343
15 TraesCS6B01G020200 chr4A 729270133 729273010 2877 False 630.0 630 99.5665 2215 2561 2 chr4A.!!$F1 346
16 TraesCS6B01G020200 chr1B 643386908 643389916 3008 True 516.5 547 93.7615 2216 2561 2 chr1B.!!$R2 345

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
391 434 0.035739 TCCGGTAAAGACAAGCCACC 59.964 55.0 0.0 0.0 0.0 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1948 2260 0.319083 TCTTCTTTCTAACGCCGGCA 59.681 50.0 28.98 5.9 0.0 5.69 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 4.882671 ATCGTTCAACATTGGTATGCTC 57.117 40.909 0.00 0.00 35.03 4.26
22 23 3.669536 TCGTTCAACATTGGTATGCTCA 58.330 40.909 0.00 0.00 35.03 4.26
23 24 3.435327 TCGTTCAACATTGGTATGCTCAC 59.565 43.478 0.00 0.00 35.03 3.51
24 25 3.426159 CGTTCAACATTGGTATGCTCACC 60.426 47.826 0.74 0.74 39.20 4.02
25 26 2.722094 TCAACATTGGTATGCTCACCC 58.278 47.619 5.04 0.00 37.84 4.61
26 27 2.040947 TCAACATTGGTATGCTCACCCA 59.959 45.455 5.04 0.00 37.84 4.51
27 28 2.128771 ACATTGGTATGCTCACCCAC 57.871 50.000 5.04 0.00 37.84 4.61
28 29 1.354031 ACATTGGTATGCTCACCCACA 59.646 47.619 5.04 0.00 37.84 4.17
29 30 2.019249 CATTGGTATGCTCACCCACAG 58.981 52.381 5.04 0.00 37.84 3.66
30 31 0.327924 TTGGTATGCTCACCCACAGG 59.672 55.000 5.04 0.00 37.84 4.00
31 32 1.452108 GGTATGCTCACCCACAGGC 60.452 63.158 0.00 0.00 36.11 4.85
32 33 1.299648 GTATGCTCACCCACAGGCA 59.700 57.895 0.00 0.00 39.06 4.75
33 34 0.107017 GTATGCTCACCCACAGGCAT 60.107 55.000 0.00 0.00 45.57 4.40
34 35 0.107066 TATGCTCACCCACAGGCATG 60.107 55.000 0.00 0.00 43.84 4.06
35 36 2.753043 GCTCACCCACAGGCATGG 60.753 66.667 2.31 0.00 39.71 3.66
36 37 2.753043 CTCACCCACAGGCATGGC 60.753 66.667 12.14 12.14 38.55 4.40
46 47 2.041612 GGCATGGCCCATTCCCTT 60.042 61.111 8.35 0.00 44.06 3.95
47 48 2.437396 GGCATGGCCCATTCCCTTG 61.437 63.158 8.35 0.00 44.06 3.61
48 49 3.097921 GCATGGCCCATTCCCTTGC 62.098 63.158 0.00 0.00 43.38 4.01
49 50 1.686455 CATGGCCCATTCCCTTGCA 60.686 57.895 0.00 0.00 0.00 4.08
50 51 1.080722 ATGGCCCATTCCCTTGCAA 59.919 52.632 0.00 0.00 0.00 4.08
51 52 1.266867 ATGGCCCATTCCCTTGCAAC 61.267 55.000 0.00 0.00 0.00 4.17
52 53 2.573340 GCCCATTCCCTTGCAACG 59.427 61.111 0.00 0.00 0.00 4.10
53 54 1.976474 GCCCATTCCCTTGCAACGA 60.976 57.895 0.00 0.00 0.00 3.85
54 55 1.322538 GCCCATTCCCTTGCAACGAT 61.323 55.000 0.00 0.00 0.00 3.73
55 56 1.185315 CCCATTCCCTTGCAACGATT 58.815 50.000 0.00 0.00 0.00 3.34
56 57 1.550072 CCCATTCCCTTGCAACGATTT 59.450 47.619 0.00 0.00 0.00 2.17
57 58 2.417243 CCCATTCCCTTGCAACGATTTC 60.417 50.000 0.00 0.00 0.00 2.17
58 59 2.493278 CCATTCCCTTGCAACGATTTCT 59.507 45.455 0.00 0.00 0.00 2.52
59 60 3.694072 CCATTCCCTTGCAACGATTTCTA 59.306 43.478 0.00 0.00 0.00 2.10
60 61 4.157656 CCATTCCCTTGCAACGATTTCTAA 59.842 41.667 0.00 0.00 0.00 2.10
61 62 5.335127 CATTCCCTTGCAACGATTTCTAAG 58.665 41.667 0.00 0.00 0.00 2.18
62 63 4.280436 TCCCTTGCAACGATTTCTAAGA 57.720 40.909 0.00 0.00 0.00 2.10
63 64 4.253685 TCCCTTGCAACGATTTCTAAGAG 58.746 43.478 0.00 0.00 0.00 2.85
64 65 3.181506 CCCTTGCAACGATTTCTAAGAGC 60.182 47.826 0.00 0.00 0.00 4.09
65 66 3.436704 CCTTGCAACGATTTCTAAGAGCA 59.563 43.478 0.00 0.00 0.00 4.26
66 67 4.083324 CCTTGCAACGATTTCTAAGAGCAA 60.083 41.667 0.00 0.00 38.28 3.91
67 68 4.404507 TGCAACGATTTCTAAGAGCAAC 57.595 40.909 0.00 0.00 0.00 4.17
68 69 4.065088 TGCAACGATTTCTAAGAGCAACT 58.935 39.130 0.00 0.00 0.00 3.16
69 70 4.152402 TGCAACGATTTCTAAGAGCAACTC 59.848 41.667 0.00 0.00 0.00 3.01
70 71 4.436183 GCAACGATTTCTAAGAGCAACTCC 60.436 45.833 0.00 0.00 0.00 3.85
71 72 3.512680 ACGATTTCTAAGAGCAACTCCG 58.487 45.455 0.00 0.00 0.00 4.63
72 73 3.192844 ACGATTTCTAAGAGCAACTCCGA 59.807 43.478 0.00 0.00 0.00 4.55
73 74 3.548268 CGATTTCTAAGAGCAACTCCGAC 59.452 47.826 0.00 0.00 0.00 4.79
74 75 2.631418 TTCTAAGAGCAACTCCGACG 57.369 50.000 0.00 0.00 0.00 5.12
75 76 0.809385 TCTAAGAGCAACTCCGACGG 59.191 55.000 7.84 7.84 0.00 4.79
76 77 0.179134 CTAAGAGCAACTCCGACGGG 60.179 60.000 15.25 7.45 0.00 5.28
77 78 1.601419 TAAGAGCAACTCCGACGGGG 61.601 60.000 13.59 13.59 37.02 5.73
95 96 3.484547 CGGTCCAACGCGCTAACC 61.485 66.667 5.73 8.32 0.00 2.85
96 97 3.122971 GGTCCAACGCGCTAACCC 61.123 66.667 5.73 0.00 0.00 4.11
97 98 2.357760 GTCCAACGCGCTAACCCA 60.358 61.111 5.73 0.00 0.00 4.51
98 99 1.962306 GTCCAACGCGCTAACCCAA 60.962 57.895 5.73 0.00 0.00 4.12
99 100 1.227883 TCCAACGCGCTAACCCAAA 60.228 52.632 5.73 0.00 0.00 3.28
100 101 1.081708 CCAACGCGCTAACCCAAAC 60.082 57.895 5.73 0.00 0.00 2.93
101 102 1.439693 CAACGCGCTAACCCAAACG 60.440 57.895 5.73 0.00 0.00 3.60
102 103 2.609759 AACGCGCTAACCCAAACGG 61.610 57.895 5.73 0.00 37.81 4.44
184 193 0.949105 GATTTGTGTCGGTGCGGACT 60.949 55.000 7.11 0.00 37.81 3.85
191 200 3.432588 CGGTGCGGACTCGAGACT 61.433 66.667 21.68 0.00 39.00 3.24
199 214 0.110147 GGACTCGAGACTGACACACG 60.110 60.000 21.68 0.00 0.00 4.49
203 218 2.354656 GAGACTGACACACGCGCA 60.355 61.111 5.73 0.00 0.00 6.09
215 231 3.854669 CGCGCATTCTCCTCCCCT 61.855 66.667 8.75 0.00 0.00 4.79
382 425 2.884179 ATCGCCCCCTCCGGTAAAGA 62.884 60.000 0.00 0.00 0.00 2.52
389 432 0.323629 CCTCCGGTAAAGACAAGCCA 59.676 55.000 0.00 0.00 0.00 4.75
391 434 0.035739 TCCGGTAAAGACAAGCCACC 59.964 55.000 0.00 0.00 0.00 4.61
393 436 0.958876 CGGTAAAGACAAGCCACCCC 60.959 60.000 0.00 0.00 0.00 4.95
394 437 0.611062 GGTAAAGACAAGCCACCCCC 60.611 60.000 0.00 0.00 0.00 5.40
395 438 0.404426 GTAAAGACAAGCCACCCCCT 59.596 55.000 0.00 0.00 0.00 4.79
396 439 0.696501 TAAAGACAAGCCACCCCCTC 59.303 55.000 0.00 0.00 0.00 4.30
514 783 1.384989 GCGGACGAGAGGGATGAAGA 61.385 60.000 0.00 0.00 0.00 2.87
515 784 1.323412 CGGACGAGAGGGATGAAGAT 58.677 55.000 0.00 0.00 0.00 2.40
527 796 2.355837 GAAGATATCGCGGCGGCA 60.356 61.111 23.46 10.92 39.92 5.69
560 832 3.595691 CTCGCAACAAGAGGTCACT 57.404 52.632 0.00 0.00 32.38 3.41
691 963 2.398554 CGTTCCCTTGGATGGTGCG 61.399 63.158 0.00 0.00 0.00 5.34
835 1107 3.197790 CGCGCCCATTGACCTCAG 61.198 66.667 0.00 0.00 0.00 3.35
865 1138 2.581354 GCTGGTGGCTCGTCATCT 59.419 61.111 0.00 0.00 38.06 2.90
962 1235 4.194720 GCCTCCAGCGACGACGAT 62.195 66.667 12.29 0.40 42.66 3.73
964 1241 1.874019 CCTCCAGCGACGACGATTG 60.874 63.158 12.29 8.25 42.66 2.67
1194 1475 1.178276 GCAAGAGGAAGAGGACGAGA 58.822 55.000 0.00 0.00 0.00 4.04
1197 1478 0.623723 AGAGGAAGAGGACGAGAGCT 59.376 55.000 0.00 0.00 0.00 4.09
1217 1498 0.698818 ACATCGAAGGGGAGCCTTTT 59.301 50.000 0.00 0.00 0.00 2.27
1219 1500 1.745653 CATCGAAGGGGAGCCTTTTTC 59.254 52.381 0.00 0.00 0.00 2.29
1226 1507 1.286257 GGGGAGCCTTTTTCTGAGGAT 59.714 52.381 0.00 0.00 36.33 3.24
1337 1618 2.079925 GAGTGTTGGAGAGACATTGGC 58.920 52.381 0.00 0.00 0.00 4.52
1420 1701 2.028112 AGTTCCATGAGCGCAAGAAGTA 60.028 45.455 11.47 0.00 43.02 2.24
1440 1721 0.101040 TCCGCCGTACCAAATCGTAG 59.899 55.000 0.00 0.00 0.00 3.51
1475 1756 3.074412 GGTGTCCATTTCGAAGTGATGT 58.926 45.455 20.95 0.00 0.00 3.06
1485 1766 3.632333 TCGAAGTGATGTAGGGTGATCT 58.368 45.455 0.00 0.00 0.00 2.75
1524 1805 0.469494 TTGTGCCACTCTTGAGAGCA 59.531 50.000 7.91 13.12 45.79 4.26
1624 1912 6.000542 CGTTTATGCTTGCGTGTTTATTTTG 58.999 36.000 0.00 0.00 0.00 2.44
1625 1913 5.508124 TTATGCTTGCGTGTTTATTTTGC 57.492 34.783 0.00 0.00 0.00 3.68
1661 1953 7.570507 GCCAATATGCTTGCATGAAATACATTG 60.571 37.037 17.26 15.09 37.07 2.82
1689 1998 4.320870 CATTTCAAGCTTTGGAGGCATTT 58.679 39.130 0.00 0.00 0.00 2.32
1707 2016 4.262420 GCATTTAAGGTCCAACACAATGGT 60.262 41.667 0.00 0.00 41.46 3.55
1734 2043 2.496899 TCAACCTCTCCCATTGCTTC 57.503 50.000 0.00 0.00 0.00 3.86
1743 2052 2.173356 CTCCCATTGCTTCAGGGTCATA 59.827 50.000 0.00 0.00 43.31 2.15
1747 2056 4.222588 CCCATTGCTTCAGGGTCATAAAAA 59.777 41.667 0.00 0.00 37.81 1.94
1792 2101 4.124351 CCGCCCTCAAGTCGCGTA 62.124 66.667 5.77 0.00 44.29 4.42
1900 2212 2.481212 GCGTGGAATGCCTTGATCA 58.519 52.632 0.00 0.00 45.05 2.92
1948 2260 0.041982 GGACTCAAGGGAGGAGGAGT 59.958 60.000 0.00 0.00 45.81 3.85
1959 2271 2.202756 GAGGAGTGCCGGCGTTAG 60.203 66.667 23.90 0.00 39.96 2.34
2004 2316 1.207791 TGGAGATCCAAAGGAGGAGC 58.792 55.000 0.00 0.00 44.35 4.70
2082 2394 3.164268 AGCCAAGATGCTAGAGATCGAT 58.836 45.455 0.00 0.00 40.56 3.59
2092 2404 1.521457 GAGATCGATGCCGCCAACA 60.521 57.895 0.54 0.00 35.37 3.33
2118 2430 1.581447 CAAGGCGAAAGAAGTGGCC 59.419 57.895 0.00 0.00 45.91 5.36
2149 2461 2.088674 GATGACCGGGGTGGAGATCG 62.089 65.000 6.32 0.00 42.00 3.69
2175 2487 1.044611 TGGATCTCAACACCGTGTCA 58.955 50.000 4.23 0.00 0.00 3.58
2190 2502 1.059584 TGTCACCAAGGAAGAGGCCA 61.060 55.000 5.01 0.00 0.00 5.36
2208 2520 4.016444 GGCCATGGTTCAAGAAGATGTAA 58.984 43.478 14.67 0.00 0.00 2.41
2368 5378 0.036010 GGAGCAAGCTTCAGGTAGCA 60.036 55.000 0.00 0.00 43.68 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.094887 GTGAGCATACCAATGTTGAACGAT 59.905 41.667 0.00 0.00 35.38 3.73
1 2 3.435327 GTGAGCATACCAATGTTGAACGA 59.565 43.478 0.00 0.00 35.38 3.85
3 4 3.119495 GGGTGAGCATACCAATGTTGAAC 60.119 47.826 10.99 0.00 42.69 3.18
4 5 3.088532 GGGTGAGCATACCAATGTTGAA 58.911 45.455 10.99 0.00 42.69 2.69
5 6 2.040947 TGGGTGAGCATACCAATGTTGA 59.959 45.455 10.99 0.00 42.69 3.18
6 7 2.164219 GTGGGTGAGCATACCAATGTTG 59.836 50.000 10.99 0.00 42.69 3.33
7 8 2.224992 TGTGGGTGAGCATACCAATGTT 60.225 45.455 10.99 0.00 42.69 2.71
8 9 1.354031 TGTGGGTGAGCATACCAATGT 59.646 47.619 10.99 0.00 42.69 2.71
9 10 2.019249 CTGTGGGTGAGCATACCAATG 58.981 52.381 10.99 0.00 42.69 2.82
10 11 1.064463 CCTGTGGGTGAGCATACCAAT 60.064 52.381 10.99 0.00 42.69 3.16
11 12 0.327924 CCTGTGGGTGAGCATACCAA 59.672 55.000 10.99 0.00 42.69 3.67
12 13 1.990424 CCTGTGGGTGAGCATACCA 59.010 57.895 10.99 0.00 42.69 3.25
13 14 1.452108 GCCTGTGGGTGAGCATACC 60.452 63.158 1.01 1.01 40.10 2.73
14 15 0.107017 ATGCCTGTGGGTGAGCATAC 60.107 55.000 0.00 0.00 43.85 2.39
15 16 0.107066 CATGCCTGTGGGTGAGCATA 60.107 55.000 0.00 0.00 43.85 3.14
16 17 1.379443 CATGCCTGTGGGTGAGCAT 60.379 57.895 0.00 0.00 46.50 3.79
17 18 2.034532 CATGCCTGTGGGTGAGCA 59.965 61.111 0.00 0.00 40.00 4.26
18 19 2.753043 CCATGCCTGTGGGTGAGC 60.753 66.667 0.00 0.00 35.55 4.26
19 20 2.753043 GCCATGCCTGTGGGTGAG 60.753 66.667 2.57 0.00 39.73 3.51
20 21 4.365111 GGCCATGCCTGTGGGTGA 62.365 66.667 0.00 0.00 46.69 4.02
30 31 3.097921 GCAAGGGAATGGGCCATGC 62.098 63.158 22.01 19.37 35.90 4.06
31 32 1.266160 TTGCAAGGGAATGGGCCATG 61.266 55.000 22.01 9.19 0.00 3.66
32 33 1.080722 TTGCAAGGGAATGGGCCAT 59.919 52.632 14.78 14.78 0.00 4.40
33 34 1.912763 GTTGCAAGGGAATGGGCCA 60.913 57.895 9.61 9.61 0.00 5.36
34 35 2.981302 GTTGCAAGGGAATGGGCC 59.019 61.111 0.00 0.00 0.00 5.80
35 36 1.322538 ATCGTTGCAAGGGAATGGGC 61.323 55.000 18.38 0.00 0.00 5.36
36 37 1.185315 AATCGTTGCAAGGGAATGGG 58.815 50.000 18.38 0.00 0.00 4.00
37 38 2.493278 AGAAATCGTTGCAAGGGAATGG 59.507 45.455 18.38 0.00 0.00 3.16
38 39 3.855689 AGAAATCGTTGCAAGGGAATG 57.144 42.857 18.38 0.00 0.00 2.67
39 40 5.253330 TCTTAGAAATCGTTGCAAGGGAAT 58.747 37.500 18.38 3.58 0.00 3.01
40 41 4.647611 TCTTAGAAATCGTTGCAAGGGAA 58.352 39.130 18.38 1.15 0.00 3.97
41 42 4.253685 CTCTTAGAAATCGTTGCAAGGGA 58.746 43.478 18.38 10.64 0.00 4.20
42 43 3.181506 GCTCTTAGAAATCGTTGCAAGGG 60.182 47.826 18.38 5.23 0.00 3.95
43 44 3.436704 TGCTCTTAGAAATCGTTGCAAGG 59.563 43.478 12.91 12.91 0.00 3.61
44 45 4.668576 TGCTCTTAGAAATCGTTGCAAG 57.331 40.909 0.00 0.00 0.00 4.01
45 46 4.515191 AGTTGCTCTTAGAAATCGTTGCAA 59.485 37.500 0.00 0.00 36.93 4.08
46 47 4.065088 AGTTGCTCTTAGAAATCGTTGCA 58.935 39.130 0.00 0.00 0.00 4.08
47 48 4.436183 GGAGTTGCTCTTAGAAATCGTTGC 60.436 45.833 0.00 0.00 0.00 4.17
48 49 4.201628 CGGAGTTGCTCTTAGAAATCGTTG 60.202 45.833 0.00 0.00 0.00 4.10
49 50 3.927142 CGGAGTTGCTCTTAGAAATCGTT 59.073 43.478 0.00 0.00 0.00 3.85
50 51 3.192844 TCGGAGTTGCTCTTAGAAATCGT 59.807 43.478 0.00 0.00 0.00 3.73
51 52 3.548268 GTCGGAGTTGCTCTTAGAAATCG 59.452 47.826 0.00 0.00 0.00 3.34
52 53 3.548268 CGTCGGAGTTGCTCTTAGAAATC 59.452 47.826 0.00 0.00 0.00 2.17
53 54 3.512680 CGTCGGAGTTGCTCTTAGAAAT 58.487 45.455 0.00 0.00 0.00 2.17
54 55 2.352421 CCGTCGGAGTTGCTCTTAGAAA 60.352 50.000 4.91 0.00 0.00 2.52
55 56 1.201647 CCGTCGGAGTTGCTCTTAGAA 59.798 52.381 4.91 0.00 0.00 2.10
56 57 0.809385 CCGTCGGAGTTGCTCTTAGA 59.191 55.000 4.91 0.00 0.00 2.10
57 58 0.179134 CCCGTCGGAGTTGCTCTTAG 60.179 60.000 14.39 0.00 0.00 2.18
58 59 1.601419 CCCCGTCGGAGTTGCTCTTA 61.601 60.000 14.39 0.00 0.00 2.10
59 60 2.657237 CCCGTCGGAGTTGCTCTT 59.343 61.111 14.39 0.00 0.00 2.85
60 61 3.382832 CCCCGTCGGAGTTGCTCT 61.383 66.667 14.39 0.00 0.00 4.09
78 79 3.484547 GGTTAGCGCGTTGGACCG 61.485 66.667 8.43 0.00 0.00 4.79
79 80 3.122971 GGGTTAGCGCGTTGGACC 61.123 66.667 17.79 17.79 0.00 4.46
80 81 1.508808 TTTGGGTTAGCGCGTTGGAC 61.509 55.000 8.43 5.32 0.00 4.02
81 82 1.227883 TTTGGGTTAGCGCGTTGGA 60.228 52.632 8.43 0.00 0.00 3.53
82 83 1.081708 GTTTGGGTTAGCGCGTTGG 60.082 57.895 8.43 0.00 0.00 3.77
83 84 1.439693 CGTTTGGGTTAGCGCGTTG 60.440 57.895 8.43 0.00 0.00 4.10
84 85 2.609759 CCGTTTGGGTTAGCGCGTT 61.610 57.895 8.43 3.54 0.00 4.84
85 86 2.992607 TTCCGTTTGGGTTAGCGCGT 62.993 55.000 8.43 0.00 37.00 6.01
86 87 1.843734 TTTCCGTTTGGGTTAGCGCG 61.844 55.000 0.00 0.00 37.00 6.86
87 88 0.386352 GTTTCCGTTTGGGTTAGCGC 60.386 55.000 0.00 0.00 37.00 5.92
88 89 0.110554 CGTTTCCGTTTGGGTTAGCG 60.111 55.000 0.00 0.00 37.00 4.26
89 90 0.239082 CCGTTTCCGTTTGGGTTAGC 59.761 55.000 0.00 0.00 37.00 3.09
90 91 1.532437 GTCCGTTTCCGTTTGGGTTAG 59.468 52.381 0.00 0.00 37.00 2.34
91 92 1.592064 GTCCGTTTCCGTTTGGGTTA 58.408 50.000 0.00 0.00 37.00 2.85
92 93 1.438562 CGTCCGTTTCCGTTTGGGTT 61.439 55.000 0.00 0.00 37.00 4.11
93 94 1.888638 CGTCCGTTTCCGTTTGGGT 60.889 57.895 0.00 0.00 37.00 4.51
94 95 2.940561 CGTCCGTTTCCGTTTGGG 59.059 61.111 0.00 0.00 35.24 4.12
95 96 2.250190 GCGTCCGTTTCCGTTTGG 59.750 61.111 0.00 0.00 0.00 3.28
96 97 2.127906 CGCGTCCGTTTCCGTTTG 60.128 61.111 0.00 0.00 0.00 2.93
97 98 4.004241 GCGCGTCCGTTTCCGTTT 62.004 61.111 8.43 0.00 36.67 3.60
184 193 2.251371 CGCGTGTGTCAGTCTCGA 59.749 61.111 0.00 0.00 0.00 4.04
191 200 2.027073 GGAGAATGCGCGTGTGTCA 61.027 57.895 8.43 0.00 0.00 3.58
199 214 2.203126 CAGGGGAGGAGAATGCGC 60.203 66.667 0.00 0.00 0.00 6.09
203 218 2.368878 GGCCCAGGGGAGGAGAAT 60.369 66.667 7.91 0.00 37.50 2.40
349 392 2.104132 CGATCGTCATGCCGGACA 59.896 61.111 5.05 2.56 37.66 4.02
377 420 0.696501 GAGGGGGTGGCTTGTCTTTA 59.303 55.000 0.00 0.00 0.00 1.85
419 462 1.080705 CGTCTTCTTCGGCTTCGGT 60.081 57.895 0.00 0.00 34.13 4.69
422 465 0.388649 TCAGCGTCTTCTTCGGCTTC 60.389 55.000 0.00 0.00 0.00 3.86
493 762 3.147595 CATCCCTCTCGTCCGCCA 61.148 66.667 0.00 0.00 0.00 5.69
543 815 2.750948 GTTAGTGACCTCTTGTTGCGA 58.249 47.619 0.00 0.00 0.00 5.10
548 820 0.320697 GGGCGTTAGTGACCTCTTGT 59.679 55.000 0.00 0.00 0.00 3.16
703 975 4.228567 TGCAAGCCGACACGTGGA 62.229 61.111 21.57 0.00 0.00 4.02
827 1099 2.421314 CGTGTGGCACTGAGGTCA 59.579 61.111 19.83 0.00 31.34 4.02
850 1123 1.607801 CTCCAGATGACGAGCCACCA 61.608 60.000 0.00 0.00 0.00 4.17
865 1138 2.342279 CGTTTCCTCGTGCCTCCA 59.658 61.111 0.00 0.00 0.00 3.86
1194 1475 1.403687 GGCTCCCCTTCGATGTAGCT 61.404 60.000 13.52 0.00 0.00 3.32
1217 1498 1.942776 TGGTGAGCTCATCCTCAGAA 58.057 50.000 24.06 1.03 42.14 3.02
1219 1500 1.406614 GGTTGGTGAGCTCATCCTCAG 60.407 57.143 24.06 0.00 42.14 3.35
1226 1507 1.228245 GGCTTGGTTGGTGAGCTCA 60.228 57.895 13.74 13.74 36.66 4.26
1304 1585 5.470098 TCTCCAACACTCACAAATAAGCTTC 59.530 40.000 0.00 0.00 0.00 3.86
1368 1649 4.616953 ACGCGAATCCAAAAAGTTGAATT 58.383 34.783 15.93 0.00 36.83 2.17
1420 1701 0.746063 TACGATTTGGTACGGCGGAT 59.254 50.000 13.24 0.00 0.00 4.18
1475 1756 4.093743 TGCACTCTTGTTAGATCACCCTA 58.906 43.478 0.00 0.00 0.00 3.53
1485 1766 5.861251 CACAAAACTTGTTGCACTCTTGTTA 59.139 36.000 0.00 0.00 43.23 2.41
1574 1856 1.321474 CACAAAAGAGGGCAGCTTGA 58.679 50.000 0.00 0.00 0.00 3.02
1624 1912 4.261578 AGCATATTGGCAAATGGTATGC 57.738 40.909 25.31 25.31 43.08 3.14
1625 1913 4.449743 GCAAGCATATTGGCAAATGGTATG 59.550 41.667 19.68 16.23 33.66 2.39
1661 1953 2.825532 TCCAAAGCTTGAAATGCCTACC 59.174 45.455 0.00 0.00 37.80 3.18
1689 1998 5.067273 CACTTACCATTGTGTTGGACCTTA 58.933 41.667 0.00 0.00 39.25 2.69
1707 2016 2.334977 TGGGAGAGGTTGAAGCACTTA 58.665 47.619 0.00 0.00 0.00 2.24
1747 2056 1.605712 CGCCTTGAACTTCTCCTCGTT 60.606 52.381 0.00 0.00 0.00 3.85
1792 2101 4.351054 CACGGCTTGCTTCCCCCT 62.351 66.667 0.00 0.00 0.00 4.79
1847 2156 1.338200 CCTCCTTGGAGTTGGTCTTCG 60.338 57.143 14.77 0.00 38.35 3.79
1900 2212 2.202236 ATCATGCCCTCCACGCTTGT 62.202 55.000 0.00 0.00 34.11 3.16
1948 2260 0.319083 TCTTCTTTCTAACGCCGGCA 59.681 50.000 28.98 5.90 0.00 5.69
1959 2271 3.057946 AGGCGTTCATTTGCTCTTCTTTC 60.058 43.478 0.00 0.00 0.00 2.62
2004 2316 1.227089 CTCCGCGTCCATCTCAAGG 60.227 63.158 4.92 0.00 0.00 3.61
2082 2394 2.904866 GTCTTGGTGTTGGCGGCA 60.905 61.111 7.97 7.97 0.00 5.69
2092 2404 0.472471 TCTTTCGCCTTGGTCTTGGT 59.528 50.000 0.00 0.00 0.00 3.67
2118 2430 1.953138 GGTCATCATGCTCGCGAGG 60.953 63.158 35.10 20.11 0.00 4.63
2149 2461 2.427506 GGTGTTGAGATCCACCTTCAC 58.572 52.381 10.62 3.98 46.17 3.18
2175 2487 1.693640 CCATGGCCTCTTCCTTGGT 59.306 57.895 3.32 0.00 43.03 3.67
2190 2502 3.941483 CGGCTTACATCTTCTTGAACCAT 59.059 43.478 0.00 0.00 0.00 3.55
2208 2520 1.750399 GGCCACATCAATGTCGGCT 60.750 57.895 23.49 0.00 45.64 5.52
2368 5378 4.262894 CCCTATTCGTAACATATGCCCTGT 60.263 45.833 1.58 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.