Multiple sequence alignment - TraesCS1B01G275400

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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 TraesCS1B01G275400 chr1B 100.000 4423 0 0 1 4423 482716670 482712248 0.000000e+00 8168.0
1 TraesCS1B01G275400 chr1D 93.369 2428 86 25 1 2391 360481323 360478934 0.000000e+00 3522.0
2 TraesCS1B01G275400 chr1D 88.989 1553 78 33 2386 3884 360478840 360477327 0.000000e+00 1834.0
3 TraesCS1B01G275400 chr1D 86.421 1031 58 35 3424 4423 360477774 360476795 0.000000e+00 1053.0
4 TraesCS1B01G275400 chr1A 90.720 1444 72 22 2363 3766 460331895 460330474 0.000000e+00 1868.0
5 TraesCS1B01G275400 chr1A 94.532 823 21 9 1539 2349 460332815 460332005 0.000000e+00 1249.0
6 TraesCS1B01G275400 chr1A 94.190 809 31 4 704 1497 460333631 460332824 0.000000e+00 1219.0
7 TraesCS1B01G275400 chr1A 89.474 665 42 14 1 656 460334256 460333611 0.000000e+00 815.0
8 TraesCS1B01G275400 chr1A 85.625 480 32 15 3972 4423 460330178 460329708 1.860000e-128 470.0
9 TraesCS1B01G275400 chr1A 91.071 56 5 0 3831 3886 460330317 460330262 4.740000e-10 76.8
10 TraesCS1B01G275400 chr3D 83.544 79 13 0 27 105 490834436 490834514 1.710000e-09 75.0
11 TraesCS1B01G275400 chr3B 83.544 79 13 0 27 105 652734768 652734846 1.710000e-09 75.0
12 TraesCS1B01G275400 chr3A 83.544 79 13 0 27 105 633052905 633052983 1.710000e-09 75.0


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 TraesCS1B01G275400 chr1B 482712248 482716670 4422 True 8168.000000 8168 100.000000 1 4423 1 chr1B.!!$R1 4422
1 TraesCS1B01G275400 chr1D 360476795 360481323 4528 True 2136.333333 3522 89.593000 1 4423 3 chr1D.!!$R1 4422
2 TraesCS1B01G275400 chr1A 460329708 460334256 4548 True 949.633333 1868 90.935333 1 4423 6 chr1A.!!$R1 4422

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
375 396 0.615850 AGGTAGGACTTTGGAGCAGC 59.384 55.000 0.0 0.0 0.0 5.25 F
1047 1086 0.462789 AGACGTTTGGTTCCGACAGT 59.537 50.000 0.0 0.0 0.0 3.55 F
1049 1088 0.462789 ACGTTTGGTTCCGACAGTCT 59.537 50.000 0.0 0.0 0.0 3.24 F
1050 1089 1.134610 ACGTTTGGTTCCGACAGTCTT 60.135 47.619 0.0 0.0 0.0 3.01 F
2768 3092 1.269621 GCAATGCTCATGGAATCCTGC 60.270 52.381 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1274 1330 3.318275 AGAACAGCACTGTAAGAGAACGA 59.682 43.478 3.26 0.0 44.13 3.85 R
2495 2799 0.550914 ACCAAAACCTGAGTGGCTGA 59.449 50.000 0.00 0.0 40.22 4.26 R
2752 3076 0.627451 AAGGCAGGATTCCATGAGCA 59.373 50.000 5.29 0.0 0.00 4.26 R
3033 3357 0.941542 AACCACACATTTCCGTGACG 59.058 50.000 0.00 0.0 39.34 4.35 R
4254 4762 0.320421 TGGAAGCTCCGTGTTACTGC 60.320 55.000 0.00 0.0 40.17 4.40 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
141 155 2.033602 TGCGTCTCGTCTCTCCCA 59.966 61.111 0.00 0.00 0.00 4.37
142 156 2.333417 TGCGTCTCGTCTCTCCCAC 61.333 63.158 0.00 0.00 0.00 4.61
143 157 3.053849 GCGTCTCGTCTCTCCCACC 62.054 68.421 0.00 0.00 0.00 4.61
144 158 2.408241 CGTCTCGTCTCTCCCACCC 61.408 68.421 0.00 0.00 0.00 4.61
145 159 2.053277 GTCTCGTCTCTCCCACCCC 61.053 68.421 0.00 0.00 0.00 4.95
146 160 2.037367 CTCGTCTCTCCCACCCCA 59.963 66.667 0.00 0.00 0.00 4.96
147 161 2.283676 TCGTCTCTCCCACCCCAC 60.284 66.667 0.00 0.00 0.00 4.61
148 162 3.391382 CGTCTCTCCCACCCCACC 61.391 72.222 0.00 0.00 0.00 4.61
149 163 3.009714 GTCTCTCCCACCCCACCC 61.010 72.222 0.00 0.00 0.00 4.61
150 164 4.348495 TCTCTCCCACCCCACCCC 62.348 72.222 0.00 0.00 0.00 4.95
151 165 4.675303 CTCTCCCACCCCACCCCA 62.675 72.222 0.00 0.00 0.00 4.96
152 166 4.995058 TCTCCCACCCCACCCCAC 62.995 72.222 0.00 0.00 0.00 4.61
163 177 4.217266 ACCCCACCCCACCTCCTT 62.217 66.667 0.00 0.00 0.00 3.36
164 178 3.661648 CCCCACCCCACCTCCTTG 61.662 72.222 0.00 0.00 0.00 3.61
165 179 2.858974 CCCACCCCACCTCCTTGT 60.859 66.667 0.00 0.00 0.00 3.16
166 180 2.757077 CCACCCCACCTCCTTGTC 59.243 66.667 0.00 0.00 0.00 3.18
167 181 2.757077 CACCCCACCTCCTTGTCC 59.243 66.667 0.00 0.00 0.00 4.02
168 182 2.531942 ACCCCACCTCCTTGTCCC 60.532 66.667 0.00 0.00 0.00 4.46
375 396 0.615850 AGGTAGGACTTTGGAGCAGC 59.384 55.000 0.00 0.00 0.00 5.25
393 414 3.654020 GAGCGCATTGGGGATCGC 61.654 66.667 11.47 0.06 46.95 4.58
531 555 1.549203 TGCATTTCTTCCTTGCTCCC 58.451 50.000 0.00 0.00 37.28 4.30
557 581 5.803461 CACCTTTAATGTCACATTCAGCATG 59.197 40.000 6.21 2.73 39.07 4.06
572 596 2.289820 CAGCATGGATGTCTCGGAAATG 59.710 50.000 0.00 0.00 0.00 2.32
640 664 3.132289 TGTTATTTGTTGCACCGGGAAAA 59.868 39.130 6.32 0.00 0.00 2.29
647 671 2.208132 TGCACCGGGAAAATGTATGT 57.792 45.000 6.32 0.00 0.00 2.29
656 680 8.145767 CACCGGGAAAATGTATGTAATAGACTA 58.854 37.037 6.32 0.00 0.00 2.59
671 698 8.582437 TGTAATAGACTACTGTTAGCTTGTTGT 58.418 33.333 0.00 0.00 32.10 3.32
681 708 6.602009 ACTGTTAGCTTGTTGTCCTTTAAACT 59.398 34.615 0.00 0.00 0.00 2.66
683 710 7.254852 TGTTAGCTTGTTGTCCTTTAAACTTG 58.745 34.615 0.00 0.00 0.00 3.16
711 738 6.035975 GCATATTTGTTACACCAGGAAAATGC 59.964 38.462 0.00 0.00 0.00 3.56
740 767 2.569404 AGACTCCCTTCTGTTAGCTTGG 59.431 50.000 0.00 0.00 0.00 3.61
741 768 2.303311 GACTCCCTTCTGTTAGCTTGGT 59.697 50.000 0.00 0.00 0.00 3.67
757 784 4.341235 AGCTTGGTTCCCTTAAACTTTCAC 59.659 41.667 0.00 0.00 0.00 3.18
765 792 9.895138 GGTTCCCTTAAACTTTCACTGTATATA 57.105 33.333 0.00 0.00 0.00 0.86
893 932 3.213206 TGTTGCTTCTGTCATTCCAGT 57.787 42.857 0.00 0.00 34.02 4.00
1044 1083 2.265683 GGATAGACGTTTGGTTCCGAC 58.734 52.381 0.00 0.00 0.00 4.79
1045 1084 2.353011 GGATAGACGTTTGGTTCCGACA 60.353 50.000 0.00 0.00 0.00 4.35
1046 1085 2.427232 TAGACGTTTGGTTCCGACAG 57.573 50.000 0.00 0.00 0.00 3.51
1047 1086 0.462789 AGACGTTTGGTTCCGACAGT 59.537 50.000 0.00 0.00 0.00 3.55
1048 1087 0.857287 GACGTTTGGTTCCGACAGTC 59.143 55.000 0.00 0.00 0.00 3.51
1049 1088 0.462789 ACGTTTGGTTCCGACAGTCT 59.537 50.000 0.00 0.00 0.00 3.24
1050 1089 1.134610 ACGTTTGGTTCCGACAGTCTT 60.135 47.619 0.00 0.00 0.00 3.01
1051 1090 1.937899 CGTTTGGTTCCGACAGTCTTT 59.062 47.619 0.00 0.00 0.00 2.52
1052 1091 2.353579 CGTTTGGTTCCGACAGTCTTTT 59.646 45.455 0.00 0.00 0.00 2.27
1053 1092 3.545426 CGTTTGGTTCCGACAGTCTTTTC 60.545 47.826 0.00 0.00 0.00 2.29
1054 1093 2.249844 TGGTTCCGACAGTCTTTTCC 57.750 50.000 0.00 0.00 0.00 3.13
1055 1094 1.766496 TGGTTCCGACAGTCTTTTCCT 59.234 47.619 0.00 0.00 0.00 3.36
1056 1095 2.171870 TGGTTCCGACAGTCTTTTCCTT 59.828 45.455 0.00 0.00 0.00 3.36
1057 1096 2.806818 GGTTCCGACAGTCTTTTCCTTC 59.193 50.000 0.00 0.00 0.00 3.46
1083 1138 2.290071 ACTGTATGTGGTGGCACTAACC 60.290 50.000 18.45 0.54 38.26 2.85
1130 1185 2.095263 GGAAATCGCTAACTTTGCTGCA 60.095 45.455 0.00 0.00 0.00 4.41
1490 1546 5.006153 ACGCTTGCATAGTACTGTGAATA 57.994 39.130 22.39 5.79 0.00 1.75
1967 2038 8.478066 TGCATAGTAACACAGATGAACTATCTT 58.522 33.333 0.00 0.00 43.68 2.40
2000 2071 5.172205 TGATCGATGTTTATGTTCGTTGGA 58.828 37.500 0.54 0.00 34.60 3.53
2057 2128 9.871238 ATACGTAACATAGACTGAAGAACATTT 57.129 29.630 0.00 0.00 0.00 2.32
2239 2318 2.817844 GTTCAAGGTAACGGCTTTGGAT 59.182 45.455 0.00 0.00 46.39 3.41
2299 2380 4.512571 TGCTTTACTTTCCGTCTTACAACC 59.487 41.667 0.00 0.00 0.00 3.77
2302 2383 6.548441 TTTACTTTCCGTCTTACAACCATG 57.452 37.500 0.00 0.00 0.00 3.66
2355 2436 5.540337 TGGTTATTTTGGGAATGTGCAGTAA 59.460 36.000 0.00 0.00 0.00 2.24
2357 2438 7.102993 GGTTATTTTGGGAATGTGCAGTAAAT 58.897 34.615 0.00 0.00 0.00 1.40
2358 2439 8.254508 GGTTATTTTGGGAATGTGCAGTAAATA 58.745 33.333 0.00 0.00 0.00 1.40
2492 2796 6.072112 TGCAATCTTTGTGTTTCCTAGAAC 57.928 37.500 0.00 0.00 0.00 3.01
2493 2797 5.592282 TGCAATCTTTGTGTTTCCTAGAACA 59.408 36.000 0.00 0.00 37.20 3.18
2541 2845 2.297033 CACAGTAAACCTTGCAGCCATT 59.703 45.455 0.00 0.00 0.00 3.16
2569 2873 6.119536 ACAACAATCACTCAAGTTTACCTGA 58.880 36.000 0.00 0.00 0.00 3.86
2615 2919 1.829533 CTGTGGTGTTGCCTGGCTT 60.830 57.895 21.03 0.00 38.35 4.35
2682 2987 4.885907 CACTCATAGTAAGGGTTAGACGGA 59.114 45.833 0.00 0.00 0.00 4.69
2696 3001 6.478016 GGGTTAGACGGACTATTATTGTGTTC 59.522 42.308 0.00 0.00 0.00 3.18
2750 3074 2.752030 AGAGCCAGGACTATAGTTGCA 58.248 47.619 6.88 0.00 0.00 4.08
2751 3075 3.107601 AGAGCCAGGACTATAGTTGCAA 58.892 45.455 6.88 0.00 0.00 4.08
2752 3076 3.713764 AGAGCCAGGACTATAGTTGCAAT 59.286 43.478 6.88 0.00 0.00 3.56
2753 3077 3.812053 GAGCCAGGACTATAGTTGCAATG 59.188 47.826 6.88 2.39 0.00 2.82
2754 3078 2.291741 GCCAGGACTATAGTTGCAATGC 59.708 50.000 6.88 0.00 0.00 3.56
2755 3079 3.813443 CCAGGACTATAGTTGCAATGCT 58.187 45.455 6.88 0.00 0.00 3.79
2756 3080 3.812053 CCAGGACTATAGTTGCAATGCTC 59.188 47.826 6.88 0.00 0.00 4.26
2757 3081 4.445453 CAGGACTATAGTTGCAATGCTCA 58.555 43.478 6.88 0.00 0.00 4.26
2758 3082 5.061853 CAGGACTATAGTTGCAATGCTCAT 58.938 41.667 6.88 0.00 0.00 2.90
2759 3083 5.049612 CAGGACTATAGTTGCAATGCTCATG 60.050 44.000 6.88 0.00 0.00 3.07
2760 3084 4.214971 GGACTATAGTTGCAATGCTCATGG 59.785 45.833 6.88 0.00 0.00 3.66
2761 3085 5.039920 ACTATAGTTGCAATGCTCATGGA 57.960 39.130 6.82 0.00 0.00 3.41
2762 3086 5.439721 ACTATAGTTGCAATGCTCATGGAA 58.560 37.500 6.82 0.00 0.00 3.53
2763 3087 6.066690 ACTATAGTTGCAATGCTCATGGAAT 58.933 36.000 6.82 0.00 30.70 3.01
2764 3088 3.795623 AGTTGCAATGCTCATGGAATC 57.204 42.857 6.82 0.00 30.70 2.52
2765 3089 2.429610 AGTTGCAATGCTCATGGAATCC 59.570 45.455 6.82 0.00 30.70 3.01
2766 3090 2.429610 GTTGCAATGCTCATGGAATCCT 59.570 45.455 6.82 0.00 30.70 3.24
2767 3091 2.028876 TGCAATGCTCATGGAATCCTG 58.971 47.619 6.82 0.00 0.00 3.86
2768 3092 1.269621 GCAATGCTCATGGAATCCTGC 60.270 52.381 0.00 0.00 0.00 4.85
2776 3100 4.722220 CTCATGGAATCCTGCCTTCATTA 58.278 43.478 0.00 0.00 0.00 1.90
2926 3250 2.995939 CGCTAAGCTGATTGTCAAGTGA 59.004 45.455 0.00 0.00 0.00 3.41
2953 3277 5.678132 TCAGTCGATCCATTATTGCATTG 57.322 39.130 0.00 0.00 0.00 2.82
2957 3281 3.004629 TCGATCCATTATTGCATTGCACC 59.995 43.478 11.66 0.00 38.71 5.01
3033 3357 4.921470 TCGTCAAAATCCGACTCAAATC 57.079 40.909 0.00 0.00 0.00 2.17
3054 3378 2.601266 CGTCACGGAAATGTGTGGTTTC 60.601 50.000 0.00 0.00 40.74 2.78
3063 3387 6.310956 CGGAAATGTGTGGTTTCGTTACTATA 59.689 38.462 0.00 0.00 36.64 1.31
3115 3439 3.582998 AAGACATGGTGGATGGTATGG 57.417 47.619 0.00 0.00 36.23 2.74
3132 3456 0.323725 TGGCTGCATTTCCTCCCTTC 60.324 55.000 0.50 0.00 0.00 3.46
3151 3475 5.775195 CCCTTCCTGACCTTTTTAAACATCT 59.225 40.000 0.00 0.00 0.00 2.90
3266 3590 2.202919 CACGCGGATGAGGATGCA 60.203 61.111 12.47 0.00 0.00 3.96
3308 3632 2.113433 CAGGTCTGCTGCTGATGGC 61.113 63.158 12.42 0.22 42.22 4.40
3445 3798 1.221466 TGAGACGCTTGAAGGCAACG 61.221 55.000 0.00 0.00 46.39 4.10
3472 3825 1.855295 AATCATGGTGCCTCAATGCA 58.145 45.000 0.00 0.00 39.37 3.96
3590 3948 5.222631 CCTTGTAATTGTTGAGACTTTGGC 58.777 41.667 0.00 0.00 0.00 4.52
3679 4041 4.370917 CAAGGACCCAAGTTTTGAACATG 58.629 43.478 0.00 0.00 0.00 3.21
3792 4154 6.379386 TCACATACAGTAGTTCGTTCAGAAG 58.621 40.000 0.00 0.00 39.95 2.85
3829 4283 6.183360 GCAAGAGCAAAATATGTCTAGCAAGA 60.183 38.462 0.00 0.00 41.58 3.02
3840 4294 7.448420 ATATGTCTAGCAAGAAGCACATATGT 58.552 34.615 1.41 1.41 43.26 2.29
3841 4295 7.387122 ATATGTCTAGCAAGAAGCACATATGTG 59.613 37.037 28.07 28.07 43.26 3.21
3970 4447 1.105457 ATGGGCACATGTTCGGATTG 58.895 50.000 0.00 0.00 35.57 2.67
3978 4455 3.186409 CACATGTTCGGATTGTCGTTCTT 59.814 43.478 0.00 0.00 0.00 2.52
4043 4520 9.872757 TTTGACGTTAAACAATTGATTACTCTC 57.127 29.630 13.59 5.67 0.00 3.20
4100 4585 3.818210 TCAGTCAACTCTCACTCTCAGTC 59.182 47.826 0.00 0.00 0.00 3.51
4137 4622 3.392616 ACAATGTCCATGGTCTATCCTCC 59.607 47.826 12.58 0.00 37.07 4.30
4236 4737 3.774702 GCGAAGGCGACGTTGACC 61.775 66.667 4.56 6.59 40.82 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
146 160 4.217266 AAGGAGGTGGGGTGGGGT 62.217 66.667 0.00 0.00 0.00 4.95
147 161 3.661648 CAAGGAGGTGGGGTGGGG 61.662 72.222 0.00 0.00 0.00 4.96
148 162 2.858974 ACAAGGAGGTGGGGTGGG 60.859 66.667 0.00 0.00 0.00 4.61
149 163 2.757077 GACAAGGAGGTGGGGTGG 59.243 66.667 0.00 0.00 0.00 4.61
150 164 2.757077 GGACAAGGAGGTGGGGTG 59.243 66.667 0.00 0.00 0.00 4.61
151 165 2.531942 GGGACAAGGAGGTGGGGT 60.532 66.667 0.00 0.00 0.00 4.95
152 166 3.339093 GGGGACAAGGAGGTGGGG 61.339 72.222 0.00 0.00 0.00 4.96
153 167 3.339093 GGGGGACAAGGAGGTGGG 61.339 72.222 0.00 0.00 0.00 4.61
167 181 2.445654 GGGCAGAGAGAGAGGGGG 60.446 72.222 0.00 0.00 0.00 5.40
168 182 2.445654 GGGGCAGAGAGAGAGGGG 60.446 72.222 0.00 0.00 0.00 4.79
375 396 3.341043 CGATCCCCAATGCGCTCG 61.341 66.667 9.73 2.46 0.00 5.03
393 414 2.671177 CGGAGCTCAACAACCAGCG 61.671 63.158 17.19 2.24 40.84 5.18
531 555 4.406069 CTGAATGTGACATTAAAGGTGCG 58.594 43.478 11.28 0.00 0.00 5.34
557 581 2.972625 TGTCACATTTCCGAGACATCC 58.027 47.619 0.00 0.00 36.20 3.51
572 596 5.106555 CCCTTGTACAGTCAATGATTGTCAC 60.107 44.000 14.63 11.55 34.49 3.67
647 671 8.248945 GGACAACAAGCTAACAGTAGTCTATTA 58.751 37.037 0.00 0.00 0.00 0.98
656 680 6.602009 AGTTTAAAGGACAACAAGCTAACAGT 59.398 34.615 0.00 0.00 0.00 3.55
681 708 6.007076 TCCTGGTGTAACAAATATGCTTCAA 58.993 36.000 0.00 0.00 39.98 2.69
683 710 6.509418 TTCCTGGTGTAACAAATATGCTTC 57.491 37.500 0.00 0.00 39.98 3.86
697 724 1.340088 TGCATGCATTTTCCTGGTGT 58.660 45.000 18.46 0.00 0.00 4.16
711 738 4.148128 ACAGAAGGGAGTCTATTGCATG 57.852 45.455 0.00 0.00 0.00 4.06
893 932 6.783708 ACACTGGAAAAGGTTGAAATGTAA 57.216 33.333 0.00 0.00 0.00 2.41
1044 1083 7.607991 ACATACAGTAATGGAAGGAAAAGACTG 59.392 37.037 0.00 0.00 39.14 3.51
1045 1084 7.607991 CACATACAGTAATGGAAGGAAAAGACT 59.392 37.037 0.00 0.00 0.00 3.24
1046 1085 7.148239 CCACATACAGTAATGGAAGGAAAAGAC 60.148 40.741 8.09 0.00 33.80 3.01
1047 1086 6.884295 CCACATACAGTAATGGAAGGAAAAGA 59.116 38.462 8.09 0.00 33.80 2.52
1048 1087 6.659242 ACCACATACAGTAATGGAAGGAAAAG 59.341 38.462 17.47 0.00 36.04 2.27
1049 1088 6.432783 CACCACATACAGTAATGGAAGGAAAA 59.567 38.462 17.47 0.00 36.04 2.29
1050 1089 5.943416 CACCACATACAGTAATGGAAGGAAA 59.057 40.000 17.47 0.00 36.04 3.13
1051 1090 5.496556 CACCACATACAGTAATGGAAGGAA 58.503 41.667 17.47 0.00 36.04 3.36
1052 1091 4.080582 CCACCACATACAGTAATGGAAGGA 60.081 45.833 17.47 0.00 36.83 3.36
1053 1092 4.199310 CCACCACATACAGTAATGGAAGG 58.801 47.826 17.47 14.46 36.83 3.46
1054 1093 3.627577 GCCACCACATACAGTAATGGAAG 59.372 47.826 17.47 10.61 36.83 3.46
1055 1094 3.009584 TGCCACCACATACAGTAATGGAA 59.990 43.478 17.47 0.00 36.83 3.53
1056 1095 2.573915 TGCCACCACATACAGTAATGGA 59.426 45.455 17.47 0.00 36.83 3.41
1057 1096 2.682856 GTGCCACCACATACAGTAATGG 59.317 50.000 11.24 11.24 41.67 3.16
1083 1138 5.452078 ACAACCACTGGAAATTGTACATG 57.548 39.130 0.71 0.00 33.59 3.21
1130 1185 0.254747 TAGCAGGGGCAAAAGCGTAT 59.745 50.000 0.00 0.00 44.61 3.06
1274 1330 3.318275 AGAACAGCACTGTAAGAGAACGA 59.682 43.478 3.26 0.00 44.13 3.85
1583 1652 4.553547 GCTGCATAAAGTAGAAATCCTGCG 60.554 45.833 0.00 0.00 32.34 5.18
1967 2038 9.607988 AACATAAACATCGATCATACCTTGTTA 57.392 29.630 0.00 0.00 0.00 2.41
2038 2109 7.516198 AGCAAAAATGTTCTTCAGTCTATGT 57.484 32.000 0.00 0.00 0.00 2.29
2102 2181 7.752239 CAGAAGTAAACAATACCAAGCTGAATG 59.248 37.037 0.00 0.00 0.00 2.67
2103 2182 7.575720 GCAGAAGTAAACAATACCAAGCTGAAT 60.576 37.037 0.00 0.00 0.00 2.57
2299 2380 7.910162 CCTGGATCGTTTTATTTAGTCAACATG 59.090 37.037 0.00 0.00 0.00 3.21
2302 2383 6.596497 TCCCTGGATCGTTTTATTTAGTCAAC 59.404 38.462 0.00 0.00 0.00 3.18
2358 2439 8.700051 ACTAAAGTACAGATTGACATCTAGCAT 58.300 33.333 0.00 0.00 37.71 3.79
2466 2741 6.061441 TCTAGGAAACACAAAGATTGCAAGA 58.939 36.000 4.94 0.00 0.00 3.02
2492 2796 1.605710 CAAAACCTGAGTGGCTGAGTG 59.394 52.381 0.00 0.00 40.22 3.51
2493 2797 1.477558 CCAAAACCTGAGTGGCTGAGT 60.478 52.381 0.00 0.00 40.22 3.41
2494 2798 1.242076 CCAAAACCTGAGTGGCTGAG 58.758 55.000 0.00 0.00 40.22 3.35
2495 2799 0.550914 ACCAAAACCTGAGTGGCTGA 59.449 50.000 0.00 0.00 40.22 4.26
2496 2800 0.954452 GACCAAAACCTGAGTGGCTG 59.046 55.000 0.00 0.00 40.22 4.85
2497 2801 0.846693 AGACCAAAACCTGAGTGGCT 59.153 50.000 0.00 0.00 40.22 4.75
2498 2802 1.338020 CAAGACCAAAACCTGAGTGGC 59.662 52.381 0.00 0.00 40.22 5.01
2499 2803 1.338020 GCAAGACCAAAACCTGAGTGG 59.662 52.381 0.00 0.00 42.93 4.00
2541 2845 9.787435 AGGTAAACTTGAGTGATTGTTGTAATA 57.213 29.630 0.00 0.00 0.00 0.98
2750 3074 1.217183 AGGCAGGATTCCATGAGCATT 59.783 47.619 5.29 0.00 0.00 3.56
2751 3075 0.851469 AGGCAGGATTCCATGAGCAT 59.149 50.000 5.29 0.00 0.00 3.79
2752 3076 0.627451 AAGGCAGGATTCCATGAGCA 59.373 50.000 5.29 0.00 0.00 4.26
2753 3077 1.316651 GAAGGCAGGATTCCATGAGC 58.683 55.000 5.29 3.40 0.00 4.26
2754 3078 2.723322 TGAAGGCAGGATTCCATGAG 57.277 50.000 5.29 0.00 0.00 2.90
2755 3079 3.675348 AATGAAGGCAGGATTCCATGA 57.325 42.857 5.29 0.00 0.00 3.07
2756 3080 5.074804 TCATAATGAAGGCAGGATTCCATG 58.925 41.667 5.29 1.90 0.00 3.66
2757 3081 5.322754 CTCATAATGAAGGCAGGATTCCAT 58.677 41.667 5.29 0.00 0.00 3.41
2758 3082 4.446745 CCTCATAATGAAGGCAGGATTCCA 60.447 45.833 5.29 0.00 0.00 3.53
2759 3083 4.077822 CCTCATAATGAAGGCAGGATTCC 58.922 47.826 0.00 0.00 0.00 3.01
2760 3084 4.978099 TCCTCATAATGAAGGCAGGATTC 58.022 43.478 0.00 0.00 0.00 2.52
2761 3085 5.074102 TCATCCTCATAATGAAGGCAGGATT 59.926 40.000 0.00 0.00 33.17 3.01
2762 3086 4.600547 TCATCCTCATAATGAAGGCAGGAT 59.399 41.667 0.00 0.00 35.54 3.24
2763 3087 3.975982 TCATCCTCATAATGAAGGCAGGA 59.024 43.478 0.00 0.00 30.37 3.86
2764 3088 4.325119 CTCATCCTCATAATGAAGGCAGG 58.675 47.826 0.00 0.00 32.96 4.85
2765 3089 4.202440 ACCTCATCCTCATAATGAAGGCAG 60.202 45.833 0.00 0.00 32.96 4.85
2766 3090 3.718434 ACCTCATCCTCATAATGAAGGCA 59.282 43.478 0.00 0.00 32.96 4.75
2767 3091 4.070716 CACCTCATCCTCATAATGAAGGC 58.929 47.826 0.00 0.00 32.96 4.35
2768 3092 4.103785 ACCACCTCATCCTCATAATGAAGG 59.896 45.833 0.00 0.00 32.96 3.46
2776 3100 4.040047 TGACATAACCACCTCATCCTCAT 58.960 43.478 0.00 0.00 0.00 2.90
2819 3143 7.433708 AAATCGTGTTGTCAGACATTCATAA 57.566 32.000 3.45 1.10 0.00 1.90
2890 3214 4.342378 AGCTTAGCGGATAGAAGATGTGAA 59.658 41.667 0.00 0.00 0.00 3.18
2957 3281 2.480224 AATGATCCGCAGCATTTTCG 57.520 45.000 0.00 0.00 0.00 3.46
3033 3357 0.941542 AACCACACATTTCCGTGACG 59.058 50.000 0.00 0.00 39.34 4.35
3054 3378 5.240713 ACGTCCCAGAAAGTATAGTAACG 57.759 43.478 0.00 0.00 0.00 3.18
3063 3387 1.141053 AGCAGAAACGTCCCAGAAAGT 59.859 47.619 0.00 0.00 0.00 2.66
3115 3439 0.033699 AGGAAGGGAGGAAATGCAGC 60.034 55.000 0.00 0.00 0.00 5.25
3132 3456 8.171164 AGAAGAAGATGTTTAAAAAGGTCAGG 57.829 34.615 0.00 0.00 0.00 3.86
3151 3475 8.519799 AGGTGTCATTTCAAGTAAAAGAAGAA 57.480 30.769 0.00 0.00 0.00 2.52
3223 3547 3.815401 AGGAATTCGGATAGGCAAATTCG 59.185 43.478 0.00 0.00 38.44 3.34
3230 3554 3.493503 CGTGTTTAGGAATTCGGATAGGC 59.506 47.826 0.00 0.00 0.00 3.93
3338 3662 1.134250 GCAGACCTGAGAGGAATTCCC 60.134 57.143 21.22 12.37 37.67 3.97
3374 3698 1.407936 CCCTCGATGATGACCTGAGT 58.592 55.000 0.00 0.00 0.00 3.41
3445 3798 1.895131 AGGCACCATGATTTGACCAAC 59.105 47.619 0.00 0.00 0.00 3.77
3472 3825 6.161167 AGATTCTTCCCTTCCCAGGTATAAT 58.839 40.000 0.00 0.00 38.79 1.28
3507 3865 2.960163 ACCTAAGGAGTTCTATCCGGG 58.040 52.381 0.00 0.00 44.65 5.73
3508 3866 5.105064 TCAAAACCTAAGGAGTTCTATCCGG 60.105 44.000 0.00 0.00 44.65 5.14
3590 3948 2.582052 TGTAAGCCCCAAACTTCTGTG 58.418 47.619 0.00 0.00 0.00 3.66
3721 4083 3.046087 CTGTGGCTCACTGCGGTG 61.046 66.667 20.12 20.12 44.05 4.94
3723 4085 2.433838 CTCTGTGGCTCACTGCGG 60.434 66.667 6.83 0.00 44.05 5.69
3724 4086 2.433838 CCTCTGTGGCTCACTGCG 60.434 66.667 6.83 2.26 44.05 5.18
3817 4179 5.526479 CACATATGTGCTTCTTGCTAGACAT 59.474 40.000 22.27 1.67 43.37 3.06
3841 4295 2.168521 TGATGCAGCTGTAGGGTTCTAC 59.831 50.000 16.64 0.00 44.57 2.59
3897 4351 5.278758 CGGGAAGGTTTAGCAATCTCAAAAA 60.279 40.000 0.00 0.00 0.00 1.94
3898 4352 4.217550 CGGGAAGGTTTAGCAATCTCAAAA 59.782 41.667 0.00 0.00 0.00 2.44
3899 4353 3.756434 CGGGAAGGTTTAGCAATCTCAAA 59.244 43.478 0.00 0.00 0.00 2.69
3900 4354 3.343617 CGGGAAGGTTTAGCAATCTCAA 58.656 45.455 0.00 0.00 0.00 3.02
3901 4355 2.355716 CCGGGAAGGTTTAGCAATCTCA 60.356 50.000 0.00 0.00 34.51 3.27
3902 4356 2.093128 TCCGGGAAGGTTTAGCAATCTC 60.093 50.000 0.00 0.00 41.99 2.75
3903 4357 1.913419 TCCGGGAAGGTTTAGCAATCT 59.087 47.619 0.00 0.00 41.99 2.40
3904 4358 2.413310 TCCGGGAAGGTTTAGCAATC 57.587 50.000 0.00 0.00 41.99 2.67
3905 4359 2.443416 GTTCCGGGAAGGTTTAGCAAT 58.557 47.619 10.35 0.00 41.99 3.56
3906 4360 1.878948 CGTTCCGGGAAGGTTTAGCAA 60.879 52.381 18.87 0.00 41.99 3.91
3907 4361 0.320946 CGTTCCGGGAAGGTTTAGCA 60.321 55.000 18.87 0.00 41.99 3.49
3908 4362 1.642037 GCGTTCCGGGAAGGTTTAGC 61.642 60.000 25.38 13.82 41.99 3.09
3909 4363 0.320946 TGCGTTCCGGGAAGGTTTAG 60.321 55.000 25.38 8.91 41.99 1.85
3910 4364 0.325602 ATGCGTTCCGGGAAGGTTTA 59.674 50.000 25.38 15.24 41.99 2.01
3933 4387 4.712476 CCCATGAGAACTCCTAAGGAATG 58.288 47.826 0.00 0.00 0.00 2.67
3939 4393 2.265367 TGTGCCCATGAGAACTCCTAA 58.735 47.619 0.00 0.00 0.00 2.69
3978 4455 1.402968 GATAGGCCGACTACGTTGACA 59.597 52.381 3.44 0.00 37.88 3.58
4065 4542 6.862209 AGAGTTGACTGACATCTAGTGATTC 58.138 40.000 0.00 0.00 0.00 2.52
4068 4545 5.182190 GTGAGAGTTGACTGACATCTAGTGA 59.818 44.000 0.00 0.00 0.00 3.41
4100 4585 0.744414 ATTGTCGCCATTCGGAGGTG 60.744 55.000 0.00 0.00 39.05 4.00
4137 4622 0.667487 TCTTTTGGAGCTCTCGCACG 60.667 55.000 14.64 0.00 39.10 5.34
4254 4762 0.320421 TGGAAGCTCCGTGTTACTGC 60.320 55.000 0.00 0.00 40.17 4.40
4257 4765 2.067013 GTTCTGGAAGCTCCGTGTTAC 58.933 52.381 0.00 0.00 40.17 2.50
4264 4772 2.342179 CTTTCGAGTTCTGGAAGCTCC 58.658 52.381 0.00 0.00 36.96 4.70
4265 4773 2.342179 CCTTTCGAGTTCTGGAAGCTC 58.658 52.381 0.00 0.00 0.00 4.09


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

AutoCloner maintained by Alex Coulton.