Multiple sequence alignment - TraesCS4B01G206300

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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 TraesCS4B01G206300 chr4B 100.000 4855 0 0 1 4855 438383283 438378429 0.000000e+00 8966.0
1 TraesCS4B01G206300 chr4B 87.352 253 13 5 983 1218 438607113 438606863 6.190000e-69 272.0
2 TraesCS4B01G206300 chr4A 92.791 3482 115 55 1446 4855 109843550 109846967 0.000000e+00 4915.0
3 TraesCS4B01G206300 chr4A 91.923 520 13 7 895 1389 109843045 109843560 0.000000e+00 701.0
4 TraesCS4B01G206300 chr4A 86.561 253 15 5 983 1218 109787629 109787879 1.340000e-65 261.0
5 TraesCS4B01G206300 chr4D 93.768 2712 90 20 2024 4703 354889476 354886812 0.000000e+00 3999.0
6 TraesCS4B01G206300 chr4D 93.660 836 31 3 879 1699 354890815 354889987 0.000000e+00 1230.0
7 TraesCS4B01G206300 chr4D 97.619 168 4 0 4688 4855 354884067 354883900 6.150000e-74 289.0
8 TraesCS4B01G206300 chr4D 89.451 237 13 4 1710 1938 354889816 354889584 6.150000e-74 289.0
9 TraesCS4B01G206300 chr5B 94.118 816 29 6 1 800 656042156 656041344 0.000000e+00 1223.0
10 TraesCS4B01G206300 chr5B 96.795 156 4 1 674 828 532188567 532188412 4.820000e-65 259.0
11 TraesCS4B01G206300 chr2B 79.905 1468 270 19 2136 3584 731250947 731252408 0.000000e+00 1053.0
12 TraesCS4B01G206300 chr2B 85.429 501 49 13 358 835 143614618 143614119 2.610000e-137 499.0
13 TraesCS4B01G206300 chr2B 90.741 216 20 0 114 329 143636912 143636697 6.150000e-74 289.0
14 TraesCS4B01G206300 chr2B 82.773 238 32 4 590 825 104949943 104950173 2.290000e-48 204.0
15 TraesCS4B01G206300 chr2B 87.963 108 13 0 585 692 165096264 165096371 1.420000e-25 128.0
16 TraesCS4B01G206300 chr2D 79.700 1468 273 19 2136 3584 601109038 601110499 0.000000e+00 1037.0
17 TraesCS4B01G206300 chr2A 79.671 1461 259 23 2138 3584 734595309 734596745 0.000000e+00 1018.0
18 TraesCS4B01G206300 chr2A 79.144 1472 278 20 2138 3589 734586438 734587900 0.000000e+00 990.0
19 TraesCS4B01G206300 chr3A 89.708 719 65 5 114 825 569227699 569226983 0.000000e+00 909.0
20 TraesCS4B01G206300 chr6B 78.099 1452 284 16 2136 3579 647930968 647929543 0.000000e+00 889.0
21 TraesCS4B01G206300 chr6B 77.438 1046 209 15 2142 3163 647708788 647709830 2.500000e-167 599.0
22 TraesCS4B01G206300 chr6B 83.459 266 22 9 970 1214 647837380 647837116 1.360000e-55 228.0
23 TraesCS4B01G206300 chr6B 85.135 222 18 5 1011 1217 647588904 647589125 3.810000e-51 213.0
24 TraesCS4B01G206300 chr6B 83.004 253 25 6 984 1218 647691022 647691274 3.810000e-51 213.0
25 TraesCS4B01G206300 chr6B 82.819 227 17 13 970 1175 647952491 647952266 2.980000e-42 183.0
26 TraesCS4B01G206300 chr6B 78.909 275 39 8 968 1224 647932905 647932632 8.360000e-38 169.0
27 TraesCS4B01G206300 chr7A 88.904 730 47 10 114 825 79601032 79600319 0.000000e+00 869.0
28 TraesCS4B01G206300 chr3B 88.267 733 67 11 114 829 762826770 762827500 0.000000e+00 859.0
29 TraesCS4B01G206300 chr5A 88.251 732 53 11 111 825 42284212 42284927 0.000000e+00 845.0
30 TraesCS4B01G206300 chr3D 86.765 544 59 11 290 825 561470155 561469617 1.160000e-165 593.0
31 TraesCS4B01G206300 chr3D 90.659 182 17 0 114 295 561488838 561488657 4.850000e-60 243.0
32 TraesCS4B01G206300 chr6A 76.776 887 169 27 2142 2999 575464803 575465681 3.420000e-126 462.0
33 TraesCS4B01G206300 chr6A 85.833 240 32 2 593 830 7716025 7716264 2.240000e-63 254.0
34 TraesCS4B01G206300 chr6A 83.083 266 24 8 970 1215 575200279 575200015 6.320000e-54 222.0
35 TraesCS4B01G206300 chr6A 84.848 231 18 6 1004 1218 574911641 574911870 2.940000e-52 217.0
36 TraesCS4B01G206300 chr6A 82.819 227 17 14 970 1175 575143358 575143133 2.980000e-42 183.0
37 TraesCS4B01G206300 chr6D 88.066 243 26 3 585 825 463616104 463616345 7.950000e-73 285.0
38 TraesCS4B01G206300 chr6D 83.794 253 23 6 984 1218 429666501 429666753 1.760000e-54 224.0
39 TraesCS4B01G206300 chr6D 98.230 113 1 1 1 112 12747844 12747732 3.830000e-46 196.0
40 TraesCS4B01G206300 chr6D 85.492 193 20 7 637 824 447243700 447243511 1.380000e-45 195.0
41 TraesCS4B01G206300 chr6D 97.321 112 3 0 1 112 118581135 118581024 1.780000e-44 191.0
42 TraesCS4B01G206300 chr1D 98.214 112 2 0 1 112 58121760 58121649 3.830000e-46 196.0
43 TraesCS4B01G206300 chr1D 97.321 112 3 0 1 112 241265352 241265241 1.780000e-44 191.0
44 TraesCS4B01G206300 chr1D 97.321 112 2 1 1 112 418891668 418891558 6.410000e-44 189.0
45 TraesCS4B01G206300 chrUn 85.405 185 25 2 642 824 291742402 291742586 1.780000e-44 191.0
46 TraesCS4B01G206300 chrUn 94.828 116 2 4 1 116 462660137 462660248 1.390000e-40 178.0
47 TraesCS4B01G206300 chr1B 94.828 116 2 4 1 116 520347480 520347369 1.390000e-40 178.0
48 TraesCS4B01G206300 chr1B 94.828 116 2 4 1 116 547176526 547176415 1.390000e-40 178.0
49 TraesCS4B01G206300 chr1A 84.375 160 20 4 323 479 255847233 255847390 8.420000e-33 152.0
50 TraesCS4B01G206300 chr5D 89.474 76 7 1 4518 4592 443503672 443503597 1.440000e-15 95.3


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 TraesCS4B01G206300 chr4B 438378429 438383283 4854 True 8966.00 8966 100.0000 1 4855 1 chr4B.!!$R1 4854
1 TraesCS4B01G206300 chr4A 109843045 109846967 3922 False 2808.00 4915 92.3570 895 4855 2 chr4A.!!$F2 3960
2 TraesCS4B01G206300 chr4D 354883900 354890815 6915 True 1451.75 3999 93.6245 879 4855 4 chr4D.!!$R1 3976
3 TraesCS4B01G206300 chr5B 656041344 656042156 812 True 1223.00 1223 94.1180 1 800 1 chr5B.!!$R2 799
4 TraesCS4B01G206300 chr2B 731250947 731252408 1461 False 1053.00 1053 79.9050 2136 3584 1 chr2B.!!$F3 1448
5 TraesCS4B01G206300 chr2D 601109038 601110499 1461 False 1037.00 1037 79.7000 2136 3584 1 chr2D.!!$F1 1448
6 TraesCS4B01G206300 chr2A 734595309 734596745 1436 False 1018.00 1018 79.6710 2138 3584 1 chr2A.!!$F2 1446
7 TraesCS4B01G206300 chr2A 734586438 734587900 1462 False 990.00 990 79.1440 2138 3589 1 chr2A.!!$F1 1451
8 TraesCS4B01G206300 chr3A 569226983 569227699 716 True 909.00 909 89.7080 114 825 1 chr3A.!!$R1 711
9 TraesCS4B01G206300 chr6B 647708788 647709830 1042 False 599.00 599 77.4380 2142 3163 1 chr6B.!!$F3 1021
10 TraesCS4B01G206300 chr6B 647929543 647932905 3362 True 529.00 889 78.5040 968 3579 2 chr6B.!!$R3 2611
11 TraesCS4B01G206300 chr7A 79600319 79601032 713 True 869.00 869 88.9040 114 825 1 chr7A.!!$R1 711
12 TraesCS4B01G206300 chr3B 762826770 762827500 730 False 859.00 859 88.2670 114 829 1 chr3B.!!$F1 715
13 TraesCS4B01G206300 chr5A 42284212 42284927 715 False 845.00 845 88.2510 111 825 1 chr5A.!!$F1 714
14 TraesCS4B01G206300 chr3D 561469617 561470155 538 True 593.00 593 86.7650 290 825 1 chr3D.!!$R1 535
15 TraesCS4B01G206300 chr6A 575464803 575465681 878 False 462.00 462 76.7760 2142 2999 1 chr6A.!!$F3 857

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
400 406 0.392998 AGCGATGGCGAATGGAAAGT 60.393 50.0 0.0 0.0 46.35 2.66 F
1288 1339 0.528249 GGCCTTGTGTGCTTGTGTTG 60.528 55.0 0.0 0.0 0.00 3.33 F
1427 1488 0.890683 AGGCAAAACTATGTGCTGGC 59.109 50.0 0.0 0.0 40.70 4.85 F
2914 4323 0.109086 CACGTCGAGAAGTGCCTCAT 60.109 55.0 0.0 0.0 34.36 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1417 1478 0.181114 GATCAGGTGGCCAGCACATA 59.819 55.0 34.87 17.85 0.00 2.29 R
2914 4323 0.250234 CTTCTCCACCTTGGCATCGA 59.750 55.0 0.00 0.00 37.47 3.59 R
3101 4510 0.846693 AGTCCTGCACCTTCTGGTTT 59.153 50.0 0.00 0.00 46.05 3.27 R
3882 5309 0.034670 GGCAGCAAAGGGAGTGAGAT 60.035 55.0 0.00 0.00 0.00 2.75 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
51 52 1.060409 CTGTGTTTTTGTTGCAACCGC 59.940 47.619 26.14 16.55 39.24 5.68
164 167 4.179579 GGCGATGCGAAACAGGCC 62.180 66.667 0.00 0.00 42.51 5.19
210 213 1.217244 GGATGCTACAACCGGTCGT 59.783 57.895 8.04 5.05 0.00 4.34
231 234 1.511305 GAGATGCTGGAACCGACGA 59.489 57.895 0.00 0.00 0.00 4.20
251 254 4.127040 CGAGGAGCTGCGAGCAGT 62.127 66.667 23.79 12.28 45.56 4.40
400 406 0.392998 AGCGATGGCGAATGGAAAGT 60.393 50.000 0.00 0.00 46.35 2.66
757 788 3.396911 GATCTGACGGTCTCGCGCA 62.397 63.158 8.75 0.00 40.63 6.09
839 872 7.865706 CCAGTGCTGGTCTAAAATTAATACT 57.134 36.000 9.96 0.00 45.53 2.12
840 873 8.958119 CCAGTGCTGGTCTAAAATTAATACTA 57.042 34.615 9.96 0.00 45.53 1.82
841 874 9.561069 CCAGTGCTGGTCTAAAATTAATACTAT 57.439 33.333 9.96 0.00 45.53 2.12
863 896 9.668497 ACTATAAACTGGAGTCTATTTTGGAAC 57.332 33.333 2.60 0.00 0.00 3.62
864 897 7.939784 ATAAACTGGAGTCTATTTTGGAACC 57.060 36.000 2.60 0.00 0.00 3.62
865 898 3.939066 ACTGGAGTCTATTTTGGAACCG 58.061 45.455 0.00 0.00 0.00 4.44
866 899 3.581332 ACTGGAGTCTATTTTGGAACCGA 59.419 43.478 0.00 0.00 0.00 4.69
867 900 4.184629 CTGGAGTCTATTTTGGAACCGAG 58.815 47.826 0.00 0.00 0.00 4.63
868 901 3.055385 TGGAGTCTATTTTGGAACCGAGG 60.055 47.826 0.00 0.00 0.00 4.63
869 902 3.532542 GAGTCTATTTTGGAACCGAGGG 58.467 50.000 0.00 0.00 0.00 4.30
870 903 3.178865 AGTCTATTTTGGAACCGAGGGA 58.821 45.455 0.00 0.00 0.00 4.20
871 904 3.197983 AGTCTATTTTGGAACCGAGGGAG 59.802 47.826 0.00 0.00 0.00 4.30
872 905 3.055312 GTCTATTTTGGAACCGAGGGAGT 60.055 47.826 0.00 0.00 0.00 3.85
873 906 4.161001 GTCTATTTTGGAACCGAGGGAGTA 59.839 45.833 0.00 0.00 0.00 2.59
874 907 4.778958 TCTATTTTGGAACCGAGGGAGTAA 59.221 41.667 0.00 0.00 0.00 2.24
875 908 3.860968 TTTTGGAACCGAGGGAGTAAA 57.139 42.857 0.00 0.00 0.00 2.01
876 909 4.376225 TTTTGGAACCGAGGGAGTAAAT 57.624 40.909 0.00 0.00 0.00 1.40
877 910 3.343941 TTGGAACCGAGGGAGTAAATG 57.656 47.619 0.00 0.00 0.00 2.32
886 919 4.511826 CCGAGGGAGTAAATGTGAAATAGC 59.488 45.833 0.00 0.00 0.00 2.97
892 925 7.451566 AGGGAGTAAATGTGAAATAGCAAAACT 59.548 33.333 0.00 0.00 0.00 2.66
1005 1038 4.393155 TGTTGCGCGGAGATGGCT 62.393 61.111 8.83 0.00 0.00 4.75
1021 1057 4.421479 CTGGCGCGAAGGACGACT 62.421 66.667 12.10 0.00 45.77 4.18
1288 1339 0.528249 GGCCTTGTGTGCTTGTGTTG 60.528 55.000 0.00 0.00 0.00 3.33
1302 1363 6.092122 GTGCTTGTGTTGCATACATAGACTTA 59.908 38.462 5.29 0.00 42.69 2.24
1340 1401 1.335810 GGTCATATGTCTACACGCCGA 59.664 52.381 1.90 0.00 0.00 5.54
1391 1452 2.166459 TCTTCGTGCTAGCTAGTGCATT 59.834 45.455 21.62 0.00 41.45 3.56
1397 1458 4.208047 CGTGCTAGCTAGTGCATTCTAAAG 59.792 45.833 21.62 0.00 41.45 1.85
1404 1465 4.637977 GCTAGTGCATTCTAAAGGCTTCTT 59.362 41.667 0.00 0.00 39.41 2.52
1417 1478 5.614324 AAGGCTTCTTTAAAGGCAAAACT 57.386 34.783 15.13 4.25 44.29 2.66
1427 1488 0.890683 AGGCAAAACTATGTGCTGGC 59.109 50.000 0.00 0.00 40.70 4.85
1536 1597 1.573829 ATTGTGCCACGGCGTTACAG 61.574 55.000 11.19 0.00 45.51 2.74
1588 1655 1.883678 TGAGCTTGATCAGATCCCCA 58.116 50.000 8.00 0.00 37.08 4.96
1833 3102 2.851824 CAGGTTTTTGACGAGCAAACAC 59.148 45.455 12.82 12.82 45.64 3.32
1847 3116 4.813027 AGCAAACACTGAATGGCTTATTG 58.187 39.130 0.00 0.00 0.00 1.90
1910 3179 4.771590 TTGAAAGCTCGATGCAAATTCT 57.228 36.364 9.09 0.00 45.94 2.40
1967 3271 3.187227 CGCTTAGCCATCAACCATATCAC 59.813 47.826 0.00 0.00 0.00 3.06
1995 3299 6.925211 ACAACATCGAGTATGACATATAGGG 58.075 40.000 0.00 0.00 39.07 3.53
2305 3691 1.654317 GTTGCTGCAGAGATCTCCTG 58.346 55.000 20.43 16.35 34.88 3.86
2828 4237 2.086869 CTCCACGATGGCATTGACTTT 58.913 47.619 21.46 0.00 37.47 2.66
2914 4323 0.109086 CACGTCGAGAAGTGCCTCAT 60.109 55.000 0.00 0.00 34.36 2.90
3268 4683 5.114081 GCCTTACACAACCATATACGACTT 58.886 41.667 0.00 0.00 0.00 3.01
3467 4882 1.139058 ACGACTGGAAACAAGAGCAGT 59.861 47.619 0.00 0.00 42.06 4.40
3603 5024 3.730715 CGACAAGGACAAGAAACAAATGC 59.269 43.478 0.00 0.00 0.00 3.56
3617 5038 4.961438 ACAAATGCAGAAGGAAAATGGT 57.039 36.364 0.00 0.00 0.00 3.55
3672 5093 1.468520 TGGTAAAGAAGAAGCGCATGC 59.531 47.619 11.47 7.91 43.24 4.06
3729 5150 7.093945 ACAAGAAGCAAGTAAAGAAGGAAAACA 60.094 33.333 0.00 0.00 0.00 2.83
3758 5179 1.494721 TGGTTGAGCAAGGAGGAGTTT 59.505 47.619 0.00 0.00 0.00 2.66
3765 5186 0.603707 CAAGGAGGAGTTTGAGCGCA 60.604 55.000 11.47 0.00 0.00 6.09
3768 5189 0.674895 GGAGGAGTTTGAGCGCATGT 60.675 55.000 11.47 0.00 0.00 3.21
3870 5297 4.556699 GCTCGTAAGGTTTTCAATGCACTT 60.557 41.667 0.00 0.00 38.47 3.16
3871 5298 5.334569 GCTCGTAAGGTTTTCAATGCACTTA 60.335 40.000 0.00 0.00 38.47 2.24
3872 5299 6.621316 TCGTAAGGTTTTCAATGCACTTAA 57.379 33.333 0.00 0.00 38.47 1.85
3873 5300 6.664515 TCGTAAGGTTTTCAATGCACTTAAG 58.335 36.000 0.00 0.00 38.47 1.85
3874 5301 5.342259 CGTAAGGTTTTCAATGCACTTAAGC 59.658 40.000 1.29 0.00 0.00 3.09
3875 5302 9.068445 TCGTAAGGTTTTCAATGCACTTAAGCA 62.068 37.037 1.29 0.00 44.00 3.91
3882 5309 2.999356 TGCACTTAAGCAACGCTCA 58.001 47.368 1.29 0.00 42.46 4.26
3883 5310 1.522668 TGCACTTAAGCAACGCTCAT 58.477 45.000 1.29 0.00 42.46 2.90
3884 5311 1.464608 TGCACTTAAGCAACGCTCATC 59.535 47.619 1.29 0.00 42.46 2.92
3885 5312 1.734465 GCACTTAAGCAACGCTCATCT 59.266 47.619 1.29 0.00 38.25 2.90
3886 5313 2.222908 GCACTTAAGCAACGCTCATCTC 60.223 50.000 1.29 0.00 38.25 2.75
3887 5314 2.995939 CACTTAAGCAACGCTCATCTCA 59.004 45.455 1.29 0.00 38.25 3.27
3888 5315 2.996621 ACTTAAGCAACGCTCATCTCAC 59.003 45.455 1.29 0.00 38.25 3.51
3889 5316 3.257393 CTTAAGCAACGCTCATCTCACT 58.743 45.455 0.00 0.00 38.25 3.41
3899 5326 2.630158 CTCATCTCACTCCCTTTGCTG 58.370 52.381 0.00 0.00 0.00 4.41
3915 5342 1.064537 TGCTGCCATGGATGCTTAGAA 60.065 47.619 18.40 0.00 0.00 2.10
3924 5351 6.148480 GCCATGGATGCTTAGAATAGTTACTG 59.852 42.308 18.40 0.00 0.00 2.74
4184 5613 5.771666 ACAAGAAATCATACATATGGCCAGG 59.228 40.000 13.05 5.88 34.50 4.45
4200 5629 1.821136 CCAGGAAATTGGTGGAGCTTC 59.179 52.381 0.00 0.00 32.60 3.86
4208 5637 1.289380 GGTGGAGCTTCTTCGTCGT 59.711 57.895 0.00 0.00 0.00 4.34
4210 5639 0.784778 GTGGAGCTTCTTCGTCGTTG 59.215 55.000 0.00 0.00 0.00 4.10
4220 5649 3.049912 TCTTCGTCGTTGACATTCACAG 58.950 45.455 0.00 0.00 32.09 3.66
4243 5672 3.942748 TGAAGCGTGTAATCCCATTTACC 59.057 43.478 0.00 0.00 32.24 2.85
4257 5686 4.420168 CCATTTACCGCTGTACATTTTGG 58.580 43.478 0.00 0.00 0.00 3.28
4268 5697 4.318332 TGTACATTTTGGTGCAGAGAGAG 58.682 43.478 0.00 0.00 0.00 3.20
4279 5708 4.481463 GTGCAGAGAGAGTGAAGTAAGAC 58.519 47.826 0.00 0.00 0.00 3.01
4298 5727 1.625315 ACATCCAGCTGCTACACTTCA 59.375 47.619 8.66 0.00 0.00 3.02
4300 5729 1.342074 TCCAGCTGCTACACTTCAGT 58.658 50.000 8.66 0.00 33.09 3.41
4313 5742 7.880713 TGCTACACTTCAGTTTGGTTATATCAA 59.119 33.333 0.00 0.00 0.00 2.57
4363 5792 3.938963 ACGCCTTTACAGGTATGACATTG 59.061 43.478 0.00 0.00 43.18 2.82
4574 6004 5.426504 CTCTGAAGATGCTAGTTGATGGTT 58.573 41.667 0.00 0.00 0.00 3.67
4665 6108 1.635817 TTGCCTGGAGCTGATACCCC 61.636 60.000 0.00 0.00 44.23 4.95
4805 9008 7.119997 GTGTTATGCGTCATATTTTGAGACTC 58.880 38.462 0.00 0.00 34.17 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 4.843147 TGCAACAAAAACACAGAGATACG 58.157 39.130 0.00 0.00 0.00 3.06
51 52 4.574599 AGGTTGCAAGCTTTTTACTCTG 57.425 40.909 24.96 0.00 31.69 3.35
210 213 1.680989 TCGGTTCCAGCATCTCCGA 60.681 57.895 0.00 0.00 46.14 4.55
231 234 4.887987 GCTCGCAGCTCCTCGCAT 62.888 66.667 0.00 0.00 42.61 4.73
251 254 0.527600 CAGTTGTAGCATCGCCGCTA 60.528 55.000 1.93 1.93 43.56 4.26
295 298 0.664466 GCTTCCAGCAAAAGAACGCC 60.664 55.000 0.00 0.00 41.89 5.68
400 406 3.534554 CAAATCGACTCCATGGACATGA 58.465 45.455 11.44 8.92 41.20 3.07
535 544 2.280592 GTCGTCGTGCCCAAGGTT 60.281 61.111 0.00 0.00 0.00 3.50
734 764 1.657751 CGAGACCGTCAGATCCAGCA 61.658 60.000 0.40 0.00 0.00 4.41
757 788 2.729479 CCAGCTGTCCGATCTGGCT 61.729 63.158 13.81 0.00 40.63 4.75
789 821 4.337060 GCGCCGGCCGAAAGTTTT 62.337 61.111 30.73 0.00 40.02 2.43
837 870 9.668497 GTTCCAAAATAGACTCCAGTTTATAGT 57.332 33.333 0.00 0.00 0.00 2.12
838 871 9.110502 GGTTCCAAAATAGACTCCAGTTTATAG 57.889 37.037 0.00 0.00 0.00 1.31
839 872 7.767198 CGGTTCCAAAATAGACTCCAGTTTATA 59.233 37.037 0.00 0.00 0.00 0.98
840 873 6.598064 CGGTTCCAAAATAGACTCCAGTTTAT 59.402 38.462 0.00 0.00 0.00 1.40
841 874 5.935789 CGGTTCCAAAATAGACTCCAGTTTA 59.064 40.000 0.00 0.00 0.00 2.01
842 875 4.760204 CGGTTCCAAAATAGACTCCAGTTT 59.240 41.667 0.00 0.00 0.00 2.66
843 876 4.041198 TCGGTTCCAAAATAGACTCCAGTT 59.959 41.667 0.00 0.00 0.00 3.16
844 877 3.581332 TCGGTTCCAAAATAGACTCCAGT 59.419 43.478 0.00 0.00 0.00 4.00
845 878 4.184629 CTCGGTTCCAAAATAGACTCCAG 58.815 47.826 0.00 0.00 0.00 3.86
846 879 3.055385 CCTCGGTTCCAAAATAGACTCCA 60.055 47.826 0.00 0.00 0.00 3.86
847 880 3.532542 CCTCGGTTCCAAAATAGACTCC 58.467 50.000 0.00 0.00 0.00 3.85
848 881 3.197116 TCCCTCGGTTCCAAAATAGACTC 59.803 47.826 0.00 0.00 0.00 3.36
849 882 3.178865 TCCCTCGGTTCCAAAATAGACT 58.821 45.455 0.00 0.00 0.00 3.24
850 883 3.055312 ACTCCCTCGGTTCCAAAATAGAC 60.055 47.826 0.00 0.00 0.00 2.59
851 884 3.178865 ACTCCCTCGGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
852 885 3.629142 ACTCCCTCGGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
853 886 5.502089 TTTACTCCCTCGGTTCCAAAATA 57.498 39.130 0.00 0.00 0.00 1.40
854 887 4.376225 TTTACTCCCTCGGTTCCAAAAT 57.624 40.909 0.00 0.00 0.00 1.82
855 888 3.860968 TTTACTCCCTCGGTTCCAAAA 57.139 42.857 0.00 0.00 0.00 2.44
856 889 3.073356 ACATTTACTCCCTCGGTTCCAAA 59.927 43.478 0.00 0.00 0.00 3.28
857 890 2.640826 ACATTTACTCCCTCGGTTCCAA 59.359 45.455 0.00 0.00 0.00 3.53
858 891 2.027561 CACATTTACTCCCTCGGTTCCA 60.028 50.000 0.00 0.00 0.00 3.53
859 892 2.235402 TCACATTTACTCCCTCGGTTCC 59.765 50.000 0.00 0.00 0.00 3.62
860 893 3.604875 TCACATTTACTCCCTCGGTTC 57.395 47.619 0.00 0.00 0.00 3.62
861 894 4.360951 TTTCACATTTACTCCCTCGGTT 57.639 40.909 0.00 0.00 0.00 4.44
862 895 4.569719 ATTTCACATTTACTCCCTCGGT 57.430 40.909 0.00 0.00 0.00 4.69
863 896 4.511826 GCTATTTCACATTTACTCCCTCGG 59.488 45.833 0.00 0.00 0.00 4.63
864 897 5.116180 TGCTATTTCACATTTACTCCCTCG 58.884 41.667 0.00 0.00 0.00 4.63
865 898 7.391148 TTTGCTATTTCACATTTACTCCCTC 57.609 36.000 0.00 0.00 0.00 4.30
866 899 7.451566 AGTTTTGCTATTTCACATTTACTCCCT 59.548 33.333 0.00 0.00 0.00 4.20
867 900 7.542130 CAGTTTTGCTATTTCACATTTACTCCC 59.458 37.037 0.00 0.00 0.00 4.30
868 901 8.296713 TCAGTTTTGCTATTTCACATTTACTCC 58.703 33.333 0.00 0.00 0.00 3.85
869 902 9.677567 TTCAGTTTTGCTATTTCACATTTACTC 57.322 29.630 0.00 0.00 0.00 2.59
1005 1038 4.717629 CAGTCGTCCTTCGCGCCA 62.718 66.667 0.00 0.00 39.67 5.69
1288 1339 4.039245 TGAGGGCACTAAGTCTATGTATGC 59.961 45.833 0.00 0.00 0.00 3.14
1302 1363 1.599047 CGACCATCTTGAGGGCACT 59.401 57.895 0.00 0.00 31.91 4.40
1340 1401 1.597461 GTCCCTCAGCTTTAGCCGT 59.403 57.895 0.00 0.00 43.38 5.68
1351 1412 0.259065 ATAGCTCTGGACGTCCCTCA 59.741 55.000 31.19 12.59 35.38 3.86
1391 1452 6.969993 TTTGCCTTTAAAGAAGCCTTTAGA 57.030 33.333 16.98 0.00 43.43 2.10
1397 1458 6.366061 CACATAGTTTTGCCTTTAAAGAAGCC 59.634 38.462 16.98 3.00 0.00 4.35
1404 1465 4.560513 GCCAGCACATAGTTTTGCCTTTAA 60.561 41.667 0.00 0.00 39.75 1.52
1417 1478 0.181114 GATCAGGTGGCCAGCACATA 59.819 55.000 34.87 17.85 0.00 2.29
1536 1597 2.813172 GGACTCTACTGCGGTCTATACC 59.187 54.545 0.00 0.00 42.95 2.73
1588 1655 3.295973 GTCTAGGCTCAGAGAAGATGGT 58.704 50.000 0.00 0.00 0.00 3.55
1715 2415 9.781834 TTTGTTAGTTTTCAGTGACACTAAATG 57.218 29.630 19.19 0.00 34.34 2.32
1847 3116 2.849880 TCGAATGGCATAGCAAAAGC 57.150 45.000 0.00 0.00 0.00 3.51
1995 3299 4.525912 ATGCTTTTCCATGAAACAGGAC 57.474 40.909 0.00 0.00 32.62 3.85
2244 3630 1.099689 TACTGCACCACGATCATCGA 58.900 50.000 15.60 0.00 43.74 3.59
2305 3691 2.460918 GCATCTTCATCAGCAACATGC 58.539 47.619 0.00 0.00 45.46 4.06
2356 3742 0.669318 GATGACGGCGTTCTTCACCA 60.669 55.000 16.19 5.80 0.00 4.17
2828 4237 1.134521 GCACGAGTGATGGTCCCATAA 60.135 52.381 7.50 0.00 36.70 1.90
2914 4323 0.250234 CTTCTCCACCTTGGCATCGA 59.750 55.000 0.00 0.00 37.47 3.59
3101 4510 0.846693 AGTCCTGCACCTTCTGGTTT 59.153 50.000 0.00 0.00 46.05 3.27
3268 4683 1.816863 GAAGGTCACGCTGGTCTGGA 61.817 60.000 0.00 0.00 0.00 3.86
3467 4882 2.447630 ACCCTTGTCGATGGTGACA 58.552 52.632 0.00 0.00 46.63 3.58
3603 5024 3.160679 ACCCTCACCATTTTCCTTCTG 57.839 47.619 0.00 0.00 0.00 3.02
3617 5038 1.073722 CTTGCTCAGCCAACCCTCA 59.926 57.895 0.00 0.00 0.00 3.86
3679 5100 2.030185 TCGGACTTGTACTTCTCAGCAC 60.030 50.000 0.00 0.00 0.00 4.40
3729 5150 2.310538 CTTGCTCAACCAACCTTCCTT 58.689 47.619 0.00 0.00 0.00 3.36
3758 5179 2.168326 TCTTCTTCAACATGCGCTCA 57.832 45.000 9.73 0.00 0.00 4.26
3765 5186 3.569701 ACCATGCGTTTCTTCTTCAACAT 59.430 39.130 0.00 0.00 0.00 2.71
3768 5189 3.210227 TCACCATGCGTTTCTTCTTCAA 58.790 40.909 0.00 0.00 0.00 2.69
3870 5297 2.417379 GGAGTGAGATGAGCGTTGCTTA 60.417 50.000 0.00 0.00 39.88 3.09
3871 5298 1.674221 GGAGTGAGATGAGCGTTGCTT 60.674 52.381 0.00 0.00 39.88 3.91
3872 5299 0.108424 GGAGTGAGATGAGCGTTGCT 60.108 55.000 0.00 0.00 43.88 3.91
3873 5300 1.086634 GGGAGTGAGATGAGCGTTGC 61.087 60.000 0.00 0.00 0.00 4.17
3874 5301 0.534412 AGGGAGTGAGATGAGCGTTG 59.466 55.000 0.00 0.00 0.00 4.10
3875 5302 1.270907 AAGGGAGTGAGATGAGCGTT 58.729 50.000 0.00 0.00 0.00 4.84
3876 5303 1.066573 CAAAGGGAGTGAGATGAGCGT 60.067 52.381 0.00 0.00 0.00 5.07
3877 5304 1.649664 CAAAGGGAGTGAGATGAGCG 58.350 55.000 0.00 0.00 0.00 5.03
3878 5305 1.065564 AGCAAAGGGAGTGAGATGAGC 60.066 52.381 0.00 0.00 0.00 4.26
3879 5306 2.630158 CAGCAAAGGGAGTGAGATGAG 58.370 52.381 0.00 0.00 0.00 2.90
3880 5307 1.339438 GCAGCAAAGGGAGTGAGATGA 60.339 52.381 0.00 0.00 0.00 2.92
3881 5308 1.093159 GCAGCAAAGGGAGTGAGATG 58.907 55.000 0.00 0.00 0.00 2.90
3882 5309 0.034670 GGCAGCAAAGGGAGTGAGAT 60.035 55.000 0.00 0.00 0.00 2.75
3883 5310 1.376466 GGCAGCAAAGGGAGTGAGA 59.624 57.895 0.00 0.00 0.00 3.27
3884 5311 0.323178 ATGGCAGCAAAGGGAGTGAG 60.323 55.000 0.00 0.00 0.00 3.51
3885 5312 0.609957 CATGGCAGCAAAGGGAGTGA 60.610 55.000 0.00 0.00 0.00 3.41
3886 5313 1.601419 CCATGGCAGCAAAGGGAGTG 61.601 60.000 0.00 0.00 0.00 3.51
3887 5314 1.304713 CCATGGCAGCAAAGGGAGT 60.305 57.895 0.00 0.00 0.00 3.85
3888 5315 0.396695 ATCCATGGCAGCAAAGGGAG 60.397 55.000 6.96 0.00 0.00 4.30
3889 5316 0.685131 CATCCATGGCAGCAAAGGGA 60.685 55.000 6.96 3.43 0.00 4.20
3899 5326 6.148480 CAGTAACTATTCTAAGCATCCATGGC 59.852 42.308 6.96 0.00 0.00 4.40
3915 5342 7.667557 TGCAAAGAAGTACTGTCAGTAACTAT 58.332 34.615 14.33 1.57 31.62 2.12
3924 5351 5.277538 CCAGAAGTTGCAAAGAAGTACTGTC 60.278 44.000 0.00 0.00 0.00 3.51
3936 5363 0.968405 GCCCATTCCAGAAGTTGCAA 59.032 50.000 0.00 0.00 0.00 4.08
4035 5464 8.441608 TGCATTTTACAAAACATATACGTACGT 58.558 29.630 25.98 25.98 0.00 3.57
4036 5465 8.717920 GTGCATTTTACAAAACATATACGTACG 58.282 33.333 15.01 15.01 0.00 3.67
4037 5466 9.544314 TGTGCATTTTACAAAACATATACGTAC 57.456 29.630 0.00 0.00 0.00 3.67
4184 5613 2.814336 ACGAAGAAGCTCCACCAATTTC 59.186 45.455 0.00 0.00 0.00 2.17
4200 5629 2.794910 ACTGTGAATGTCAACGACGAAG 59.205 45.455 0.00 0.00 34.95 3.79
4208 5637 2.287644 CACGCTTCACTGTGAATGTCAA 59.712 45.455 22.28 0.64 35.59 3.18
4210 5639 1.867233 ACACGCTTCACTGTGAATGTC 59.133 47.619 22.28 13.60 35.59 3.06
4220 5649 4.201881 GGTAAATGGGATTACACGCTTCAC 60.202 45.833 0.00 0.00 37.48 3.18
4243 5672 1.535028 TCTGCACCAAAATGTACAGCG 59.465 47.619 0.33 0.00 31.04 5.18
4257 5686 4.022762 TGTCTTACTTCACTCTCTCTGCAC 60.023 45.833 0.00 0.00 0.00 4.57
4268 5697 2.675348 GCAGCTGGATGTCTTACTTCAC 59.325 50.000 17.12 0.00 0.00 3.18
4279 5708 2.277969 CTGAAGTGTAGCAGCTGGATG 58.722 52.381 17.12 0.00 0.00 3.51
4313 5742 6.238320 GCGCAACAGATATGATTTTCTTCTCT 60.238 38.462 0.30 0.00 0.00 3.10
4379 5808 7.556275 AGTTTACAGATGGTGAAGTTTGAAGAA 59.444 33.333 0.00 0.00 0.00 2.52
4380 5809 7.012327 CAGTTTACAGATGGTGAAGTTTGAAGA 59.988 37.037 0.00 0.00 0.00 2.87
4381 5810 7.134815 CAGTTTACAGATGGTGAAGTTTGAAG 58.865 38.462 0.00 0.00 0.00 3.02
4574 6004 0.319083 CAGCCAAGAATGCAGCCAAA 59.681 50.000 0.00 0.00 0.00 3.28
4665 6108 1.030488 TCTACGGCTTCACTCCTCGG 61.030 60.000 0.00 0.00 0.00 4.63
4805 9008 2.154462 CCTAGACCAGCAAACAACCAG 58.846 52.381 0.00 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.