Multiple sequence alignment - TraesCS3B01G360200

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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 TraesCS3B01G360200 chr3B 100.000 3019 0 0 1 3019 572243653 572246671 0.000000e+00 5576.0
1 TraesCS3B01G360200 chr3D 95.248 1410 53 8 1177 2577 436644700 436646104 0.000000e+00 2220.0
2 TraesCS3B01G360200 chr3D 95.301 1128 45 4 1 1128 436643580 436644699 0.000000e+00 1783.0
3 TraesCS3B01G360200 chr3D 90.026 391 27 9 2582 2968 436646633 436647015 2.090000e-136 496.0
4 TraesCS3B01G360200 chr3D 91.667 72 4 1 1126 1197 590371183 590371114 6.890000e-17 99.0
5 TraesCS3B01G360200 chr3A 93.738 1086 52 9 1935 3019 574980651 574981721 0.000000e+00 1615.0
6 TraesCS3B01G360200 chr3A 96.825 63 2 0 1121 1183 52198850 52198912 4.120000e-19 106.0
7 TraesCS3B01G360200 chr2B 95.385 65 3 0 1127 1191 731935949 731936013 1.480000e-18 104.0
8 TraesCS3B01G360200 chr6A 92.857 70 3 2 1114 1183 135929152 135929085 1.920000e-17 100.0
9 TraesCS3B01G360200 chr1A 92.857 70 3 2 1114 1183 407648560 407648627 1.920000e-17 100.0
10 TraesCS3B01G360200 chr7A 90.789 76 3 3 1109 1183 695093585 695093657 6.890000e-17 99.0
11 TraesCS3B01G360200 chr5B 91.667 72 4 2 1114 1183 262477338 262477267 6.890000e-17 99.0
12 TraesCS3B01G360200 chr1B 91.667 72 4 2 1117 1188 15235411 15235342 6.890000e-17 99.0
13 TraesCS3B01G360200 chr7B 88.750 80 5 3 1120 1197 517092893 517092970 8.910000e-16 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 TraesCS3B01G360200 chr3B 572243653 572246671 3018 False 5576.000000 5576 100.000 1 3019 1 chr3B.!!$F1 3018
1 TraesCS3B01G360200 chr3D 436643580 436647015 3435 False 1499.666667 2220 93.525 1 2968 3 chr3D.!!$F1 2967
2 TraesCS3B01G360200 chr3A 574980651 574981721 1070 False 1615.000000 1615 93.738 1935 3019 1 chr3A.!!$F2 1084

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
410 411 0.178953 AACAAGGCTTGGAGCACCAT 60.179 50.0 29.26 4.56 46.34 3.55 F
1145 1146 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.0 5.23 0.00 44.66 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1901 1906 0.179108 GGCTACACCAGACGACCATC 60.179 60.0 0.0 0.0 38.86 3.51 R
2062 2067 0.784495 TCAGTGGGAGTAGGTGTCCT 59.216 55.0 0.0 0.0 37.71 3.85 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
76 77 4.772886 ATCAAATTAGAGCGTAACCCCT 57.227 40.909 0.00 0.00 0.00 4.79
79 80 6.052405 TCAAATTAGAGCGTAACCCCTAAA 57.948 37.500 0.00 0.00 0.00 1.85
80 81 6.655930 TCAAATTAGAGCGTAACCCCTAAAT 58.344 36.000 0.00 0.00 0.00 1.40
115 116 9.612620 AATTAGATCGTCAAAACTGAAATTCAC 57.387 29.630 0.00 0.00 0.00 3.18
116 117 6.867662 AGATCGTCAAAACTGAAATTCACT 57.132 33.333 0.00 0.00 0.00 3.41
117 118 6.662616 AGATCGTCAAAACTGAAATTCACTG 58.337 36.000 0.00 0.00 0.00 3.66
249 250 1.009389 AAGACGTCGTAAGCTGCAGC 61.009 55.000 31.53 31.53 42.49 5.25
251 252 2.125912 CGTCGTAAGCTGCAGCCT 60.126 61.111 34.39 25.20 43.38 4.58
287 288 4.660938 GCACCTCCCCGGTTTGCT 62.661 66.667 0.00 0.00 46.37 3.91
310 311 3.071023 TCCTATTATTTCCCTGAGCGTGG 59.929 47.826 0.00 0.00 0.00 4.94
350 351 4.374702 CGTGCAGCACAAGGACGC 62.375 66.667 25.19 0.00 43.40 5.19
361 362 3.871248 AAGGACGCCGACGGGTTTC 62.871 63.158 17.22 8.45 46.04 2.78
365 366 4.675029 CGCCGACGGGTTTCAGGT 62.675 66.667 17.22 0.00 34.97 4.00
369 370 1.666872 CGACGGGTTTCAGGTGGTC 60.667 63.158 0.00 0.00 0.00 4.02
371 372 0.320508 GACGGGTTTCAGGTGGTCTC 60.321 60.000 0.00 0.00 0.00 3.36
377 378 0.596577 TTTCAGGTGGTCTCGTCGAG 59.403 55.000 16.33 16.33 0.00 4.04
410 411 0.178953 AACAAGGCTTGGAGCACCAT 60.179 50.000 29.26 4.56 46.34 3.55
448 449 3.207669 GGAGCATCTTGGCAGGCG 61.208 66.667 0.00 0.00 35.83 5.52
452 453 2.178890 GCATCTTGGCAGGCGAGAG 61.179 63.158 18.49 11.75 0.00 3.20
507 508 2.383855 CTGACCTTCTACCTGAGGGAG 58.616 57.143 3.67 3.67 43.90 4.30
528 529 0.746923 AGTCCATCGACATCGTCCGA 60.747 55.000 0.54 0.00 41.87 4.55
621 622 1.015109 TCGACTACATGAGCGAGGTC 58.985 55.000 0.00 0.00 32.40 3.85
745 746 3.231736 AGCCCGACGTGTCCAACT 61.232 61.111 0.00 0.00 0.00 3.16
777 778 1.072173 TGCAAGAAGCTGAAGCACCTA 59.928 47.619 4.90 0.00 45.94 3.08
780 781 2.941720 CAAGAAGCTGAAGCACCTATCC 59.058 50.000 4.90 0.00 45.16 2.59
793 794 1.840635 ACCTATCCCTGCAGAACCTTC 59.159 52.381 17.39 0.00 0.00 3.46
867 868 0.879765 AGCTTGTCATGTGCTTCTGC 59.120 50.000 0.00 0.00 40.20 4.26
891 892 4.681421 TTCGAGCTGAAGTGGCTG 57.319 55.556 0.00 0.00 40.40 4.85
934 935 2.757077 CCACCTGGTGTCCTTCCC 59.243 66.667 24.32 0.00 0.00 3.97
982 983 3.361977 GCTCCGCGGCTTTCCAAA 61.362 61.111 23.51 0.00 0.00 3.28
1120 1121 4.281947 GGGGCGCCGCTAGTAGAC 62.282 72.222 34.09 10.68 0.00 2.59
1132 1133 4.057432 CGCTAGTAGACTAGTGTACTCCC 58.943 52.174 30.01 21.47 46.53 4.30
1133 1134 4.202243 CGCTAGTAGACTAGTGTACTCCCT 60.202 50.000 30.01 13.71 46.53 4.20
1134 1135 5.299949 GCTAGTAGACTAGTGTACTCCCTC 58.700 50.000 30.01 16.45 45.85 4.30
1135 1136 4.776435 AGTAGACTAGTGTACTCCCTCC 57.224 50.000 23.34 0.85 35.06 4.30
1136 1137 2.713863 AGACTAGTGTACTCCCTCCG 57.286 55.000 0.00 0.00 0.00 4.63
1137 1138 1.914798 AGACTAGTGTACTCCCTCCGT 59.085 52.381 0.00 0.00 0.00 4.69
1138 1139 2.093021 AGACTAGTGTACTCCCTCCGTC 60.093 54.545 0.00 0.00 0.00 4.79
1139 1140 1.064832 ACTAGTGTACTCCCTCCGTCC 60.065 57.143 0.00 0.00 0.00 4.79
1140 1141 0.107508 TAGTGTACTCCCTCCGTCCG 60.108 60.000 0.00 0.00 0.00 4.79
1141 1142 2.044650 TGTACTCCCTCCGTCCGG 60.045 66.667 0.00 0.00 0.00 5.14
1142 1143 2.273449 GTACTCCCTCCGTCCGGA 59.727 66.667 0.00 0.00 42.90 5.14
1143 1144 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
1144 1145 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
1145 1146 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
1146 1147 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
1147 1148 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
1148 1149 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
1149 1150 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
1150 1151 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
1151 1152 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
1152 1153 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
1153 1154 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
1154 1155 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
1155 1156 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
1156 1157 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
1157 1158 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
1158 1159 4.390603 CGTCCGGAAATACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
1159 1160 5.106869 CGTCCGGAAATACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
1160 1161 6.403200 CGTCCGGAAATACTTGTCATCAAAAT 60.403 38.462 5.23 0.00 32.87 1.82
1161 1162 6.747280 GTCCGGAAATACTTGTCATCAAAATG 59.253 38.462 5.23 0.00 32.87 2.32
1162 1163 6.035843 CCGGAAATACTTGTCATCAAAATGG 58.964 40.000 0.00 0.00 33.42 3.16
1163 1164 6.127758 CCGGAAATACTTGTCATCAAAATGGA 60.128 38.462 0.00 0.00 33.42 3.41
1164 1165 7.416664 CCGGAAATACTTGTCATCAAAATGGAT 60.417 37.037 0.00 0.00 33.42 3.41
1165 1166 8.620416 CGGAAATACTTGTCATCAAAATGGATA 58.380 33.333 0.00 0.00 33.42 2.59
1171 1172 8.421249 ACTTGTCATCAAAATGGATAAAAGGA 57.579 30.769 0.00 0.00 33.42 3.36
1172 1173 8.526147 ACTTGTCATCAAAATGGATAAAAGGAG 58.474 33.333 0.00 0.00 33.42 3.69
1173 1174 8.648698 TTGTCATCAAAATGGATAAAAGGAGA 57.351 30.769 0.00 0.00 33.42 3.71
1174 1175 8.827832 TGTCATCAAAATGGATAAAAGGAGAT 57.172 30.769 0.00 0.00 33.42 2.75
1175 1176 8.689061 TGTCATCAAAATGGATAAAAGGAGATG 58.311 33.333 0.00 0.00 33.42 2.90
1292 1296 2.177594 AACTGGCTCCTCGGCTGAAG 62.178 60.000 0.00 0.00 39.86 3.02
1335 1339 3.782369 CGACAACATCAATGAAGAATGCG 59.218 43.478 0.00 0.00 0.00 4.73
1420 1425 5.493809 GGTAGTATAACCTGTTTTGCTGGA 58.506 41.667 2.37 0.00 39.25 3.86
1428 1433 2.232208 CCTGTTTTGCTGGAATTCCTCC 59.768 50.000 24.73 15.46 45.64 4.30
1802 1807 1.764854 GGAGGCCGTCCCCTATGAA 60.765 63.158 9.46 0.00 39.88 2.57
1829 1834 8.281212 ACCATCCAAGTTTTATTCAGTGATAC 57.719 34.615 0.00 0.00 0.00 2.24
1848 1853 6.862090 GTGATACCAAGTATAGAACCGATGAC 59.138 42.308 0.00 0.00 0.00 3.06
1884 1889 1.450848 CACTGCGACCCTGCATGAT 60.451 57.895 0.00 0.00 45.26 2.45
1890 1895 1.468054 GCGACCCTGCATGATTTGTTC 60.468 52.381 0.00 0.00 34.15 3.18
1901 1906 5.183713 TGCATGATTTGTTCCAACTTCCTAG 59.816 40.000 0.00 0.00 0.00 3.02
1904 1909 7.478322 CATGATTTGTTCCAACTTCCTAGATG 58.522 38.462 0.00 0.00 0.00 2.90
1925 1930 1.798813 GTCGTCTGGTGTAGCCTTTTG 59.201 52.381 0.00 0.00 38.35 2.44
1926 1931 0.517316 CGTCTGGTGTAGCCTTTTGC 59.483 55.000 0.00 0.00 41.71 3.68
1944 1949 7.318141 CCTTTTGCATATTGATTGACTGAACT 58.682 34.615 0.00 0.00 0.00 3.01
1976 1981 5.934043 TGTTCTTGGTACAGATCAACTCATG 59.066 40.000 0.00 0.00 42.39 3.07
2062 2067 1.443702 CGCGTCTTCATGGTCGACA 60.444 57.895 18.91 3.91 0.00 4.35
2155 2160 8.135529 GTGACAAGTCTAAGGCTTAAACAATTT 58.864 33.333 12.91 0.00 0.00 1.82
2196 2203 6.800890 AGGCTAAAAGATTTAAAGAGGGGAA 58.199 36.000 0.00 0.00 0.00 3.97
2206 2213 8.588472 AGATTTAAAGAGGGGAAAAACATGAAG 58.412 33.333 0.00 0.00 0.00 3.02
2316 2323 7.241376 CGGATCCAACTAAAAATGTCAACTAC 58.759 38.462 13.41 0.00 0.00 2.73
2371 2378 9.959721 AGAGTGTGGTGTGTATAAAAGATAATT 57.040 29.630 0.00 0.00 0.00 1.40
2411 2418 7.696992 ATTGGAAAAGGTGTAATAATGTCGT 57.303 32.000 0.00 0.00 0.00 4.34
2525 2537 4.612939 GCAGAACGAATACCAAAACTCACC 60.613 45.833 0.00 0.00 0.00 4.02
2694 3227 2.936202 AGCTCTCATCACTCCTCTCTC 58.064 52.381 0.00 0.00 0.00 3.20
2710 3243 2.946329 TCTCTCCTTCGCACAGATAGTC 59.054 50.000 0.00 0.00 0.00 2.59
2801 3334 4.707105 TCATATGGACGAGATTGCACAAT 58.293 39.130 2.13 0.00 0.00 2.71
2813 3346 3.485947 TTGCACAATTCACGCTAATCC 57.514 42.857 0.00 0.00 0.00 3.01
2874 3407 4.527564 GTCTTTGTGACACGATGGAAAAG 58.472 43.478 8.46 7.83 44.73 2.27
2934 3467 6.864165 GTGTAAGTTTTCTCACCAAACAAACA 59.136 34.615 0.00 0.00 36.71 2.83
2945 3478 4.097741 CACCAAACAAACACTCCTTCATCA 59.902 41.667 0.00 0.00 0.00 3.07
2979 3512 5.826643 ACCAATGTATTTTTGCCCTCTCTA 58.173 37.500 0.00 0.00 0.00 2.43
2998 3531 1.850755 TCCAGGTTGGAGGTTCCCC 60.851 63.158 0.00 0.00 42.67 4.81
3003 3536 1.759236 GTTGGAGGTTCCCCGTTCT 59.241 57.895 0.00 0.00 35.03 3.01
3004 3537 0.605589 GTTGGAGGTTCCCCGTTCTG 60.606 60.000 0.00 0.00 35.03 3.02
3010 3543 2.301009 GAGGTTCCCCGTTCTGAAAGTA 59.699 50.000 2.80 0.00 35.12 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
113 114 9.956720 AAATTGAGATTCAGTTTTCTTACAGTG 57.043 29.630 0.00 0.00 33.37 3.66
114 115 9.956720 CAAATTGAGATTCAGTTTTCTTACAGT 57.043 29.630 0.00 0.00 34.68 3.55
115 116 8.909671 GCAAATTGAGATTCAGTTTTCTTACAG 58.090 33.333 0.00 0.00 34.68 2.74
116 117 8.632679 AGCAAATTGAGATTCAGTTTTCTTACA 58.367 29.630 0.00 0.00 34.68 2.41
249 250 2.357517 AACCGTCTGCTTGCGAGG 60.358 61.111 2.37 0.00 0.00 4.63
251 252 1.664649 CTCAACCGTCTGCTTGCGA 60.665 57.895 0.00 0.00 0.00 5.10
287 288 4.444306 CCACGCTCAGGGAAATAATAGGAA 60.444 45.833 0.00 0.00 0.00 3.36
310 311 1.521681 GGCCGTGCATGTAGTCCTC 60.522 63.158 4.96 0.00 0.00 3.71
350 351 2.358247 CCACCTGAAACCCGTCGG 60.358 66.667 3.60 3.60 0.00 4.79
361 362 0.596577 TTTCTCGACGAGACCACCTG 59.403 55.000 26.54 0.00 38.51 4.00
365 366 0.039437 GCACTTTCTCGACGAGACCA 60.039 55.000 26.54 15.23 38.51 4.02
369 370 0.241213 TCCTGCACTTTCTCGACGAG 59.759 55.000 18.91 18.91 0.00 4.18
371 372 0.784778 GTTCCTGCACTTTCTCGACG 59.215 55.000 0.00 0.00 0.00 5.12
377 378 2.799562 GCCTTGTTGTTCCTGCACTTTC 60.800 50.000 0.00 0.00 0.00 2.62
410 411 2.755064 CGGATTGCACCATGGCCA 60.755 61.111 13.04 8.56 0.00 5.36
466 467 2.811514 GGAGCTGATGGATGGCGGA 61.812 63.158 0.00 0.00 0.00 5.54
507 508 0.030908 GGACGATGTCGATGGACTCC 59.969 60.000 9.67 3.99 43.79 3.85
584 585 0.392336 GATCTTCTCGCCCAGCATCT 59.608 55.000 0.00 0.00 0.00 2.90
604 605 1.532090 CGTGACCTCGCTCATGTAGTC 60.532 57.143 0.00 0.00 0.00 2.59
605 606 0.452184 CGTGACCTCGCTCATGTAGT 59.548 55.000 0.00 0.00 0.00 2.73
649 650 1.453379 CGCCGAGGTAGGAGAGGAA 60.453 63.158 0.00 0.00 32.51 3.36
696 697 2.740055 CTCTCCACGTGCAGGTGC 60.740 66.667 29.48 0.00 42.50 5.01
745 746 2.987282 TTCTTGCAGCGGTCGAGCAA 62.987 55.000 15.89 11.80 45.07 3.91
777 778 2.042162 ACAATGAAGGTTCTGCAGGGAT 59.958 45.455 15.13 0.00 0.00 3.85
780 781 1.542915 CCACAATGAAGGTTCTGCAGG 59.457 52.381 15.13 0.00 0.00 4.85
793 794 1.888512 CACCACCTCTTTCCCACAATG 59.111 52.381 0.00 0.00 0.00 2.82
902 903 2.125552 TGGCAATGACGAGCTCCG 60.126 61.111 8.47 6.07 45.44 4.63
910 911 1.244019 GGACACCAGGTGGCAATGAC 61.244 60.000 27.71 5.23 44.59 3.06
911 912 1.074775 GGACACCAGGTGGCAATGA 59.925 57.895 27.71 0.00 44.59 2.57
917 918 2.153401 TGGGAAGGACACCAGGTGG 61.153 63.158 24.13 1.68 37.94 4.61
941 942 2.432628 GAACAGCACCGGGTCTCG 60.433 66.667 6.32 0.18 38.88 4.04
1120 1121 1.677942 GGACGGAGGGAGTACACTAG 58.322 60.000 0.00 0.00 0.00 2.57
1128 1129 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
1129 1130 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
1130 1131 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
1131 1132 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
1132 1133 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
1133 1134 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
1134 1135 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
1135 1136 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
1136 1137 5.873179 TTTGATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
1137 1138 6.127758 CCATTTTGATGACAAGTATTTCCGGA 60.128 38.462 0.00 0.00 37.32 5.14
1138 1139 6.035843 CCATTTTGATGACAAGTATTTCCGG 58.964 40.000 0.00 0.00 37.32 5.14
1139 1140 6.851609 TCCATTTTGATGACAAGTATTTCCG 58.148 36.000 0.00 0.00 37.32 4.30
1145 1146 9.527157 TCCTTTTATCCATTTTGATGACAAGTA 57.473 29.630 0.00 0.00 37.32 2.24
1146 1147 8.421249 TCCTTTTATCCATTTTGATGACAAGT 57.579 30.769 0.00 0.00 37.32 3.16
1147 1148 8.742777 TCTCCTTTTATCCATTTTGATGACAAG 58.257 33.333 0.00 0.00 37.32 3.16
1148 1149 8.648698 TCTCCTTTTATCCATTTTGATGACAA 57.351 30.769 0.00 0.00 0.00 3.18
1149 1150 8.689061 CATCTCCTTTTATCCATTTTGATGACA 58.311 33.333 0.00 0.00 32.05 3.58
1150 1151 8.689972 ACATCTCCTTTTATCCATTTTGATGAC 58.310 33.333 0.00 0.00 33.85 3.06
1151 1152 8.827832 ACATCTCCTTTTATCCATTTTGATGA 57.172 30.769 0.00 0.00 33.85 2.92
1158 1159 9.823647 CGCTATATACATCTCCTTTTATCCATT 57.176 33.333 0.00 0.00 0.00 3.16
1159 1160 9.201989 TCGCTATATACATCTCCTTTTATCCAT 57.798 33.333 0.00 0.00 0.00 3.41
1160 1161 8.467598 GTCGCTATATACATCTCCTTTTATCCA 58.532 37.037 0.00 0.00 0.00 3.41
1161 1162 8.467598 TGTCGCTATATACATCTCCTTTTATCC 58.532 37.037 0.00 0.00 0.00 2.59
1162 1163 9.291664 GTGTCGCTATATACATCTCCTTTTATC 57.708 37.037 0.00 0.00 0.00 1.75
1163 1164 8.803235 TGTGTCGCTATATACATCTCCTTTTAT 58.197 33.333 0.00 0.00 0.00 1.40
1164 1165 8.173542 TGTGTCGCTATATACATCTCCTTTTA 57.826 34.615 0.00 0.00 0.00 1.52
1165 1166 7.050970 TGTGTCGCTATATACATCTCCTTTT 57.949 36.000 0.00 0.00 0.00 2.27
1166 1167 6.650427 TGTGTCGCTATATACATCTCCTTT 57.350 37.500 0.00 0.00 0.00 3.11
1167 1168 6.842437 ATGTGTCGCTATATACATCTCCTT 57.158 37.500 0.00 0.00 0.00 3.36
1168 1169 6.661377 AGAATGTGTCGCTATATACATCTCCT 59.339 38.462 0.00 0.00 32.97 3.69
1169 1170 6.857956 AGAATGTGTCGCTATATACATCTCC 58.142 40.000 0.00 0.00 32.97 3.71
1170 1171 7.810282 ACAAGAATGTGTCGCTATATACATCTC 59.190 37.037 0.00 0.00 38.69 2.75
1171 1172 7.661968 ACAAGAATGTGTCGCTATATACATCT 58.338 34.615 0.00 0.00 38.69 2.90
1172 1173 7.875316 ACAAGAATGTGTCGCTATATACATC 57.125 36.000 0.00 0.00 38.69 3.06
1173 1174 9.411801 CTTACAAGAATGTGTCGCTATATACAT 57.588 33.333 0.00 0.00 40.84 2.29
1174 1175 7.865889 CCTTACAAGAATGTGTCGCTATATACA 59.134 37.037 0.00 0.00 40.84 2.29
1175 1176 7.866393 ACCTTACAAGAATGTGTCGCTATATAC 59.134 37.037 0.00 0.00 40.84 1.47
1292 1296 3.530535 GAGCTTCAGAATCCTCAGGTTC 58.469 50.000 0.00 0.00 0.00 3.62
1420 1425 0.346932 TAGGCCAGGGAGGAGGAATT 59.653 55.000 5.01 0.00 41.22 2.17
1428 1433 1.524482 GTTCAGCTAGGCCAGGGAG 59.476 63.158 5.01 0.00 0.00 4.30
1503 1508 1.342074 TCCTTAGCATCCCATCCTCG 58.658 55.000 0.00 0.00 0.00 4.63
1511 1516 3.942115 GACCAGAAGTTTCCTTAGCATCC 59.058 47.826 0.00 0.00 0.00 3.51
1618 1623 6.633856 TCATATACTGCATGAACATATCGCT 58.366 36.000 0.00 0.00 29.55 4.93
1802 1807 6.542821 TCACTGAATAAAACTTGGATGGTCT 58.457 36.000 0.00 0.00 0.00 3.85
1829 1834 5.282510 GTCAGTCATCGGTTCTATACTTGG 58.717 45.833 0.00 0.00 0.00 3.61
1884 1889 5.313712 GACCATCTAGGAAGTTGGAACAAA 58.686 41.667 9.01 0.00 42.91 2.83
1890 1895 2.761208 AGACGACCATCTAGGAAGTTGG 59.239 50.000 0.00 1.76 44.90 3.77
1901 1906 0.179108 GGCTACACCAGACGACCATC 60.179 60.000 0.00 0.00 38.86 3.51
1904 1909 0.320697 AAAGGCTACACCAGACGACC 59.679 55.000 0.00 0.00 43.14 4.79
1925 1930 7.086376 ACACAAAGTTCAGTCAATCAATATGC 58.914 34.615 0.00 0.00 0.00 3.14
1926 1931 9.467258 AAACACAAAGTTCAGTCAATCAATATG 57.533 29.630 0.00 0.00 40.26 1.78
1944 1949 6.375736 TGATCTGTACCAAGAACAAACACAAA 59.624 34.615 0.00 0.00 0.00 2.83
2044 2049 1.406219 CTGTCGACCATGAAGACGCG 61.406 60.000 14.12 3.53 37.69 6.01
2062 2067 0.784495 TCAGTGGGAGTAGGTGTCCT 59.216 55.000 0.00 0.00 37.71 3.85
2155 2160 9.109393 CTTTTAGCCTAATAGCAAACTGTGATA 57.891 33.333 0.00 0.00 34.23 2.15
2196 2203 8.547967 ACTATGACACGATAACTTCATGTTTT 57.452 30.769 0.00 0.00 39.89 2.43
2266 2273 3.297134 ACCTGGCCATGTTCGAATATT 57.703 42.857 5.51 0.00 0.00 1.28
2316 2323 9.512435 CTAAGGCATAAAAGAAACATCTTGATG 57.488 33.333 8.87 8.87 31.93 3.07
2388 2395 7.513371 AACGACATTATTACACCTTTTCCAA 57.487 32.000 0.00 0.00 0.00 3.53
2433 2440 2.655090 TGTCCCAACAAGCATTCTCA 57.345 45.000 0.00 0.00 30.70 3.27
2485 2497 7.381323 TCGTTCTGCATGATTATGATAGATGT 58.619 34.615 0.85 0.00 36.36 3.06
2525 2537 7.883217 AGTAGATATGTGTATTCGGGTTGTAG 58.117 38.462 0.00 0.00 0.00 2.74
2694 3227 2.546795 GGATGGACTATCTGTGCGAAGG 60.547 54.545 0.00 0.00 40.08 3.46
2762 3295 3.957591 ATGATGATGCGACTGAGCTAT 57.042 42.857 0.00 0.00 38.13 2.97
2765 3298 2.671888 CCATATGATGATGCGACTGAGC 59.328 50.000 3.65 0.00 37.71 4.26
2801 3334 1.550524 AGAGCACTGGATTAGCGTGAA 59.449 47.619 0.00 0.00 0.00 3.18
2813 3346 3.875727 CCCAGATTACATTCAGAGCACTG 59.124 47.826 4.57 4.57 44.66 3.66
2899 3432 2.685804 AAACTTACACCCCGCCGCTT 62.686 55.000 0.00 0.00 0.00 4.68
2934 3467 7.405292 TGGTTAAATCTCAATGATGAAGGAGT 58.595 34.615 0.00 0.00 34.49 3.85


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

AutoCloner maintained by Alex Coulton.