Multiple sequence alignment - TraesCS3D01G158900

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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 TraesCS3D01G158900 chr3D 100.000 2939 0 0 1 2939 127902987 127905925 0.000000e+00 5428.0
1 TraesCS3D01G158900 chr3D 84.795 1197 159 13 1091 2270 68037110 68035920 0.000000e+00 1181.0
2 TraesCS3D01G158900 chr3D 82.016 645 73 15 485 1094 68037695 68037059 2.610000e-140 508.0
3 TraesCS3D01G158900 chr3D 74.062 320 60 17 782 1082 71116345 71116030 3.100000e-20 110.0
4 TraesCS3D01G158900 chr3D 94.340 53 3 0 1090 1142 127904028 127904080 6.750000e-12 82.4
5 TraesCS3D01G158900 chr3A 88.773 2966 269 28 1 2939 138806245 138809173 0.000000e+00 3574.0
6 TraesCS3D01G158900 chr3A 84.010 1157 167 7 1092 2235 79875651 79874500 0.000000e+00 1096.0
7 TraesCS3D01G158900 chr3A 83.333 1194 176 13 1092 2270 79802403 79801218 0.000000e+00 1081.0
8 TraesCS3D01G158900 chr3A 83.027 1196 180 15 1092 2270 79905209 79904020 0.000000e+00 1062.0
9 TraesCS3D01G158900 chr3A 83.413 627 72 16 485 1094 79876212 79875601 1.190000e-153 553.0
10 TraesCS3D01G158900 chr3A 82.547 636 76 20 485 1094 79802979 79802353 7.210000e-146 527.0
11 TraesCS3D01G158900 chr3A 81.417 635 84 17 485 1094 79905784 79905159 3.400000e-134 488.0
12 TraesCS3D01G158900 chr3A 76.056 355 73 12 1696 2044 80103296 80103644 1.080000e-39 174.0
13 TraesCS3D01G158900 chr3A 98.113 53 1 0 1090 1142 138807297 138807349 3.120000e-15 93.5
14 TraesCS3D01G158900 chr3B 90.461 1866 147 18 1090 2938 182203490 182205341 0.000000e+00 2431.0
15 TraesCS3D01G158900 chr3B 90.947 950 75 6 148 1094 182202601 182203542 0.000000e+00 1267.0
16 TraesCS3D01G158900 chr3B 84.425 1130 161 7 1091 2210 113983680 113984804 0.000000e+00 1098.0
17 TraesCS3D01G158900 chr3B 81.596 614 76 18 504 1094 113983132 113983731 9.530000e-130 473.0
18 TraesCS3D01G158900 chr3B 88.462 104 12 0 12 115 182202499 182202602 3.070000e-25 126.0
19 TraesCS3D01G158900 chr3B 73.375 323 57 21 782 1082 116438027 116437712 3.120000e-15 93.5
20 TraesCS3D01G158900 chr7A 86.437 494 51 8 2346 2825 80836589 80837080 7.210000e-146 527.0
21 TraesCS3D01G158900 chr7A 85.542 498 55 8 2347 2830 470750959 470750465 3.380000e-139 505.0
22 TraesCS3D01G158900 chr5A 85.602 507 57 8 2335 2828 634103861 634104364 4.340000e-143 518.0
23 TraesCS3D01G158900 chr5A 85.513 497 55 8 2346 2828 389606992 389607485 1.220000e-138 503.0
24 TraesCS3D01G158900 chr5B 85.685 496 54 7 2346 2826 655376062 655375569 9.400000e-140 507.0
25 TraesCS3D01G158900 chr5B 85.336 491 57 8 2346 2823 341180599 341180111 7.320000e-136 494.0
26 TraesCS3D01G158900 chr4A 85.132 491 58 6 2351 2828 301969455 301968967 3.400000e-134 488.0
27 TraesCS3D01G158900 chr2A 75.561 847 172 24 1385 2207 545800750 545801585 4.590000e-103 385.0
28 TraesCS3D01G158900 chr7D 77.833 203 34 4 2636 2827 10118167 10117965 6.660000e-22 115.0


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 TraesCS3D01G158900 chr3D 127902987 127905925 2938 False 2755.200000 5428 97.170000 1 2939 2 chr3D.!!$F1 2938
1 TraesCS3D01G158900 chr3D 68035920 68037695 1775 True 844.500000 1181 83.405500 485 2270 2 chr3D.!!$R2 1785
2 TraesCS3D01G158900 chr3A 138806245 138809173 2928 False 1833.750000 3574 93.443000 1 2939 2 chr3A.!!$F2 2938
3 TraesCS3D01G158900 chr3A 79874500 79876212 1712 True 824.500000 1096 83.711500 485 2235 2 chr3A.!!$R2 1750
4 TraesCS3D01G158900 chr3A 79801218 79802979 1761 True 804.000000 1081 82.940000 485 2270 2 chr3A.!!$R1 1785
5 TraesCS3D01G158900 chr3A 79904020 79905784 1764 True 775.000000 1062 82.222000 485 2270 2 chr3A.!!$R3 1785
6 TraesCS3D01G158900 chr3B 182202499 182205341 2842 False 1274.666667 2431 89.956667 12 2938 3 chr3B.!!$F2 2926
7 TraesCS3D01G158900 chr3B 113983132 113984804 1672 False 785.500000 1098 83.010500 504 2210 2 chr3B.!!$F1 1706
8 TraesCS3D01G158900 chr5A 634103861 634104364 503 False 518.000000 518 85.602000 2335 2828 1 chr5A.!!$F2 493
9 TraesCS3D01G158900 chr2A 545800750 545801585 835 False 385.000000 385 75.561000 1385 2207 1 chr2A.!!$F1 822

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
76 77 0.037303 ACTTGGCATGCTACAGTGCT 59.963 50.0 18.92 0.0 41.04 4.40 F
1560 1667 0.250081 GAGAGCCGGATGATGGTTCC 60.250 60.0 5.05 0.0 37.43 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1730 1846 0.035630 AGGTGAGGACTGCATGCTTC 60.036 55.0 20.33 14.71 0.0 3.86 R
2830 2975 0.167908 TCAATTAGCCAAGCGTTGCG 59.832 50.0 0.00 0.00 0.0 4.85 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
21 22 2.094675 GCCTATGTGGTTCATTGTGCT 58.905 47.619 0.00 0.00 37.91 4.40
50 51 7.502120 AATGGATCACAATTATTTCTCCTCG 57.498 36.000 0.00 0.00 0.00 4.63
76 77 0.037303 ACTTGGCATGCTACAGTGCT 59.963 50.000 18.92 0.00 41.04 4.40
94 95 6.024049 CAGTGCTGCTACTAAAAGTTATTGC 58.976 40.000 0.00 0.00 0.00 3.56
95 96 5.705441 AGTGCTGCTACTAAAAGTTATTGCA 59.295 36.000 0.00 0.00 0.00 4.08
98 99 6.599244 TGCTGCTACTAAAAGTTATTGCAGAT 59.401 34.615 14.57 0.00 46.40 2.90
116 117 3.611549 CAGATGAGTGTCGTGTGATTCTG 59.388 47.826 0.00 0.00 29.02 3.02
184 185 9.524106 TTTCATATGATTGACATGCATTTTCTC 57.476 29.630 6.17 0.00 39.77 2.87
217 218 5.763204 AGGTGATTGTGATACGTGTTCTTTT 59.237 36.000 0.00 0.00 0.00 2.27
240 241 1.949799 ATGAAGCCTGGACTCACTCT 58.050 50.000 0.00 0.00 0.00 3.24
275 276 3.822167 CGACCTATCCTCCTCCTAGAAAC 59.178 52.174 0.00 0.00 0.00 2.78
328 329 7.225523 TGTCGTTCAAAGTACAAACTACTTC 57.774 36.000 0.00 0.00 36.82 3.01
329 330 7.037438 TGTCGTTCAAAGTACAAACTACTTCT 58.963 34.615 0.00 0.00 36.82 2.85
342 343 4.408182 ACTACTTCTGTGCTTGACTTGT 57.592 40.909 0.00 0.00 0.00 3.16
376 379 1.745653 TGACTCACTATGCAGTCTCGG 59.254 52.381 0.00 0.00 39.92 4.63
424 428 2.340210 TTGGTAGTCTGCAGCAAACA 57.660 45.000 9.47 2.36 30.91 2.83
433 437 2.502510 CAGCAAACATGCGCGGTC 60.503 61.111 8.83 0.00 40.27 4.79
472 476 2.362802 GCATGCCTTGCGCTAAAAC 58.637 52.632 9.73 0.00 42.54 2.43
478 482 1.134694 CTTGCGCTAAAACCTCGGC 59.865 57.895 9.73 0.00 0.00 5.54
481 485 3.192922 CGCTAAAACCTCGGCCCG 61.193 66.667 0.00 0.00 0.00 6.13
483 487 2.267961 CTAAAACCTCGGCCCGCT 59.732 61.111 0.00 0.00 0.00 5.52
526 534 5.875910 ACAATCTTTGCTCTCTTCATCTCTG 59.124 40.000 0.00 0.00 0.00 3.35
528 536 5.070770 TCTTTGCTCTCTTCATCTCTGTC 57.929 43.478 0.00 0.00 0.00 3.51
566 598 6.477053 TCTCTACCTCTCAAAGATCCATTG 57.523 41.667 3.08 3.08 0.00 2.82
567 599 5.028549 TCTACCTCTCAAAGATCCATTGC 57.971 43.478 4.38 0.00 0.00 3.56
583 615 5.765510 TCCATTGCCAATACTAGTTTGGAT 58.234 37.500 27.21 16.50 45.35 3.41
584 616 6.905736 TCCATTGCCAATACTAGTTTGGATA 58.094 36.000 27.21 18.60 45.35 2.59
975 1025 5.881923 TCACCTTATGTAATACCCTCCAC 57.118 43.478 0.00 0.00 0.00 4.02
988 1038 1.522668 CCTCCACAAGCATCAAACGA 58.477 50.000 0.00 0.00 0.00 3.85
1085 1143 7.073725 TCCTAATGGCTCCTATCCTAACATTTT 59.926 37.037 0.00 0.00 0.00 1.82
1086 1144 6.966534 AATGGCTCCTATCCTAACATTTTG 57.033 37.500 0.00 0.00 0.00 2.44
1087 1145 4.207165 TGGCTCCTATCCTAACATTTTGC 58.793 43.478 0.00 0.00 0.00 3.68
1088 1146 3.570125 GGCTCCTATCCTAACATTTTGCC 59.430 47.826 0.00 0.00 0.00 4.52
1089 1147 3.570125 GCTCCTATCCTAACATTTTGCCC 59.430 47.826 0.00 0.00 0.00 5.36
1090 1148 4.689983 GCTCCTATCCTAACATTTTGCCCT 60.690 45.833 0.00 0.00 0.00 5.19
1091 1149 5.449553 CTCCTATCCTAACATTTTGCCCTT 58.550 41.667 0.00 0.00 0.00 3.95
1092 1150 5.200483 TCCTATCCTAACATTTTGCCCTTG 58.800 41.667 0.00 0.00 0.00 3.61
1093 1151 3.893326 ATCCTAACATTTTGCCCTTGC 57.107 42.857 0.00 0.00 38.26 4.01
1094 1152 2.888212 TCCTAACATTTTGCCCTTGCT 58.112 42.857 0.00 0.00 38.71 3.91
1095 1153 4.040936 TCCTAACATTTTGCCCTTGCTA 57.959 40.909 0.00 0.00 38.71 3.49
1096 1154 4.016444 TCCTAACATTTTGCCCTTGCTAG 58.984 43.478 0.00 0.00 38.71 3.42
1097 1155 3.763897 CCTAACATTTTGCCCTTGCTAGT 59.236 43.478 0.00 0.00 38.71 2.57
1098 1156 4.947388 CCTAACATTTTGCCCTTGCTAGTA 59.053 41.667 0.00 0.00 38.71 1.82
1099 1157 5.066505 CCTAACATTTTGCCCTTGCTAGTAG 59.933 44.000 0.00 0.00 38.71 2.57
1100 1158 2.755103 ACATTTTGCCCTTGCTAGTAGC 59.245 45.455 15.56 15.56 42.82 3.58
1101 1159 2.879103 TTTTGCCCTTGCTAGTAGCT 57.121 45.000 22.34 0.00 42.97 3.32
1102 1160 3.992943 TTTTGCCCTTGCTAGTAGCTA 57.007 42.857 22.34 14.39 42.97 3.32
1103 1161 4.503714 TTTTGCCCTTGCTAGTAGCTAT 57.496 40.909 22.34 0.00 42.97 2.97
1104 1162 3.475566 TTGCCCTTGCTAGTAGCTATG 57.524 47.619 22.34 12.03 42.97 2.23
1105 1163 1.694150 TGCCCTTGCTAGTAGCTATGG 59.306 52.381 22.34 20.38 42.97 2.74
1106 1164 1.971357 GCCCTTGCTAGTAGCTATGGA 59.029 52.381 24.59 3.89 42.97 3.41
1107 1165 2.569404 GCCCTTGCTAGTAGCTATGGAT 59.431 50.000 24.59 0.00 42.97 3.41
1108 1166 3.368948 GCCCTTGCTAGTAGCTATGGATC 60.369 52.174 24.59 14.16 42.97 3.36
1109 1167 3.196685 CCCTTGCTAGTAGCTATGGATCC 59.803 52.174 22.34 4.20 42.97 3.36
1110 1168 4.093011 CCTTGCTAGTAGCTATGGATCCT 58.907 47.826 22.34 0.89 42.97 3.24
1111 1169 5.265191 CCTTGCTAGTAGCTATGGATCCTA 58.735 45.833 22.34 0.00 42.97 2.94
1112 1170 5.717178 CCTTGCTAGTAGCTATGGATCCTAA 59.283 44.000 22.34 4.17 42.97 2.69
1113 1171 6.382570 CCTTGCTAGTAGCTATGGATCCTAAT 59.617 42.308 22.34 1.09 42.97 1.73
1114 1172 6.782082 TGCTAGTAGCTATGGATCCTAATG 57.218 41.667 22.34 1.91 42.97 1.90
1115 1173 5.658634 TGCTAGTAGCTATGGATCCTAATGG 59.341 44.000 22.34 2.01 42.97 3.16
1116 1174 5.452636 GCTAGTAGCTATGGATCCTAATGGC 60.453 48.000 15.16 12.50 38.45 4.40
1117 1175 4.693420 AGTAGCTATGGATCCTAATGGCT 58.307 43.478 21.64 21.64 42.48 4.75
1118 1176 3.996921 AGCTATGGATCCTAATGGCTG 57.003 47.619 18.59 1.29 38.94 4.85
1119 1177 2.026449 AGCTATGGATCCTAATGGCTGC 60.026 50.000 18.59 9.52 38.94 5.25
1120 1178 2.026449 GCTATGGATCCTAATGGCTGCT 60.026 50.000 14.23 0.00 0.00 4.24
1121 1179 3.198635 GCTATGGATCCTAATGGCTGCTA 59.801 47.826 14.23 0.00 0.00 3.49
1122 1180 4.141528 GCTATGGATCCTAATGGCTGCTAT 60.142 45.833 14.23 0.00 0.00 2.97
1123 1181 3.988976 TGGATCCTAATGGCTGCTATC 57.011 47.619 14.23 0.00 0.00 2.08
1124 1182 2.573462 TGGATCCTAATGGCTGCTATCC 59.427 50.000 14.23 0.00 34.23 2.59
1125 1183 2.843113 GGATCCTAATGGCTGCTATCCT 59.157 50.000 3.84 0.00 32.17 3.24
1126 1184 4.033709 GGATCCTAATGGCTGCTATCCTA 58.966 47.826 3.84 0.00 32.17 2.94
1127 1185 4.471386 GGATCCTAATGGCTGCTATCCTAA 59.529 45.833 3.84 0.00 32.17 2.69
1128 1186 4.891992 TCCTAATGGCTGCTATCCTAAC 57.108 45.455 0.00 0.00 0.00 2.34
1129 1187 4.231273 TCCTAATGGCTGCTATCCTAACA 58.769 43.478 0.00 0.00 0.00 2.41
1130 1188 4.846367 TCCTAATGGCTGCTATCCTAACAT 59.154 41.667 0.00 0.00 0.00 2.71
1131 1189 5.310594 TCCTAATGGCTGCTATCCTAACATT 59.689 40.000 0.00 0.68 0.00 2.71
1132 1190 6.006449 CCTAATGGCTGCTATCCTAACATTT 58.994 40.000 0.00 0.00 0.00 2.32
1144 1250 2.695147 CCTAACATTTCCCCCTTGCATC 59.305 50.000 0.00 0.00 0.00 3.91
1191 1297 7.224557 GCCATGCCGATATTAAAAGATTTTGTT 59.775 33.333 0.82 0.00 0.00 2.83
1207 1313 0.541764 TGTTGCCCTTGAATCCCCAC 60.542 55.000 0.00 0.00 0.00 4.61
1318 1424 7.308770 CCATGATTCCATACCAATCACATACAC 60.309 40.741 0.00 0.00 41.86 2.90
1382 1488 7.068716 CCCTAATCCTTTATCCTTGGACAAAAG 59.931 40.741 14.55 14.55 32.16 2.27
1472 1579 2.566724 GGCAAAATTTGTCCATGGAGGA 59.433 45.455 16.81 3.42 46.75 3.71
1526 1633 9.410556 AGAACCAAAATTAATTGTTCATTCTCG 57.589 29.630 22.15 0.00 0.00 4.04
1560 1667 0.250081 GAGAGCCGGATGATGGTTCC 60.250 60.000 5.05 0.00 37.43 3.62
1614 1721 6.038997 GAGGTAAACTCACTACCACATCTT 57.961 41.667 2.10 0.00 45.85 2.40
1633 1740 8.960591 CACATCTTGGTTTCTTTATTATCCTGT 58.039 33.333 0.00 0.00 0.00 4.00
1668 1784 3.981071 AGTACTATGCAGCAGGAACAA 57.019 42.857 0.00 0.00 0.00 2.83
1671 1787 5.070001 AGTACTATGCAGCAGGAACAAAAA 58.930 37.500 0.00 0.00 0.00 1.94
1730 1846 1.109609 GTACCTACCCCTGGTTCTCG 58.890 60.000 0.00 0.00 38.88 4.04
1821 1937 5.663556 TGATAGTGGTATTACACATGGTCCA 59.336 40.000 0.00 0.00 43.72 4.02
1914 2030 2.099141 TGAGTTCGCATAGCAAAGCT 57.901 45.000 0.00 0.00 43.41 3.74
1949 2067 1.001378 ACAAAGTTGATCTTGCCACGC 60.001 47.619 0.00 0.00 36.40 5.34
2108 2231 4.307259 AGAAGCCCAAGGGTGAAGATATA 58.693 43.478 7.05 0.00 37.65 0.86
2175 2302 5.923733 TTGTGTTGTTGTTTCCCTATGTT 57.076 34.783 0.00 0.00 0.00 2.71
2186 2313 9.406828 GTTGTTTCCCTATGTTAACAAAAGATC 57.593 33.333 13.23 2.87 40.80 2.75
2213 2340 2.516906 TGATGGTCGTGTACTACACCA 58.483 47.619 12.79 11.33 45.93 4.17
2245 2375 8.043113 TCCATATAAGGTGCATCAGTATTCATC 58.957 37.037 0.00 0.00 0.00 2.92
2330 2462 6.316390 GTCATCCTACTTAACAATGGAACCTG 59.684 42.308 0.00 0.00 0.00 4.00
2349 2481 1.350684 TGCACATTCTTCTGGCCACTA 59.649 47.619 0.00 0.00 0.00 2.74
2364 2496 4.721776 TGGCCACTATTCAAGTATTCTCCT 59.278 41.667 0.00 0.00 35.76 3.69
2403 2535 4.502604 GGGCCAGTTAATCGCTACTCATAA 60.503 45.833 4.39 0.00 0.00 1.90
2411 2543 1.760029 TCGCTACTCATAACATGGCCA 59.240 47.619 8.56 8.56 0.00 5.36
2428 2560 2.548480 GGCCAAATCGAATAGCACCTAC 59.452 50.000 0.00 0.00 0.00 3.18
2500 2633 4.546829 TTAGTTGTCAGGCCGTTAATCT 57.453 40.909 0.00 0.00 0.00 2.40
2564 2697 1.677552 CACGTAACCCCTTCCAGCT 59.322 57.895 0.00 0.00 0.00 4.24
2624 2758 8.964476 TTTACCTCCTCTCTATGCTTTTAATG 57.036 34.615 0.00 0.00 0.00 1.90
2674 2810 1.118838 AGCTGGGAGCATGAGAGTAC 58.881 55.000 0.00 0.00 45.56 2.73
2684 2820 6.183360 GGGAGCATGAGAGTACGGTATAATAG 60.183 46.154 0.00 0.00 0.00 1.73
2686 2822 7.120873 GGAGCATGAGAGTACGGTATAATAGAA 59.879 40.741 0.00 0.00 0.00 2.10
2755 2900 8.496916 ACTAATGGTTTAATCCGGTTAATAGGT 58.503 33.333 0.00 0.00 32.56 3.08
2796 2941 0.175073 ATCCTAAACCGACCGAGCAC 59.825 55.000 0.00 0.00 0.00 4.40
2813 2958 4.439153 CGAGCACCTACCTGTTAACGATTA 60.439 45.833 0.26 0.00 0.00 1.75
2830 2975 6.170675 ACGATTACTTGAACATTGCTTCTC 57.829 37.500 0.00 0.00 0.00 2.87
2854 2999 4.236935 CAACGCTTGGCTAATTGACAAAT 58.763 39.130 0.00 0.00 44.14 2.32
2896 3041 3.243771 ACACTTAAACTCTCACTCCACCG 60.244 47.826 0.00 0.00 0.00 4.94
2899 3044 0.249911 AAACTCTCACTCCACCGCAC 60.250 55.000 0.00 0.00 0.00 5.34
2914 3060 1.178534 CGCACCCCACATTCTGGTTT 61.179 55.000 0.00 0.00 38.60 3.27
2925 3071 3.958147 ACATTCTGGTTTCTCGGGTTTTT 59.042 39.130 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 5.414454 TCCATTAGTAAGCACAATGAACCAC 59.586 40.000 0.00 0.00 32.54 4.16
13 14 6.682423 TGTGATCCATTAGTAAGCACAATG 57.318 37.500 0.00 0.00 32.54 2.82
14 15 7.886629 ATTGTGATCCATTAGTAAGCACAAT 57.113 32.000 11.20 11.20 45.05 2.71
50 51 4.396166 ACTGTAGCATGCCAAGTAATCAAC 59.604 41.667 15.66 0.00 0.00 3.18
76 77 7.824289 ACTCATCTGCAATAACTTTTAGTAGCA 59.176 33.333 0.00 0.00 0.00 3.49
94 95 3.611549 CAGAATCACACGACACTCATCTG 59.388 47.826 0.00 0.00 0.00 2.90
95 96 3.256879 ACAGAATCACACGACACTCATCT 59.743 43.478 0.00 0.00 0.00 2.90
98 99 2.360801 TCACAGAATCACACGACACTCA 59.639 45.455 0.00 0.00 0.00 3.41
116 117 3.309954 GCCGGTAGTCATTTTCATCTCAC 59.690 47.826 1.90 0.00 0.00 3.51
182 183 7.805542 CGTATCACAATCACCTTGACTATAGAG 59.194 40.741 6.78 0.00 38.29 2.43
184 185 7.379797 CACGTATCACAATCACCTTGACTATAG 59.620 40.741 0.00 0.00 38.29 1.31
217 218 3.445008 AGTGAGTCCAGGCTTCATTCTA 58.555 45.455 0.00 0.00 0.00 2.10
240 241 3.562973 GGATAGGTCGTGACACTCGATTA 59.437 47.826 3.68 0.00 39.45 1.75
328 329 2.292267 AGGTCAACAAGTCAAGCACAG 58.708 47.619 0.00 0.00 0.00 3.66
329 330 2.418368 AGGTCAACAAGTCAAGCACA 57.582 45.000 0.00 0.00 0.00 4.57
342 343 3.388024 AGTGAGTCAGCTTTGTAGGTCAA 59.612 43.478 0.00 0.00 0.00 3.18
424 428 2.953821 CAAAGTTGGACCGCGCAT 59.046 55.556 8.75 0.00 0.00 4.73
433 437 1.106944 ACCAAGCGGTCCAAAGTTGG 61.107 55.000 3.51 3.51 44.71 3.77
446 450 4.272100 CAAGGCATGCAACCAAGC 57.728 55.556 21.36 0.00 35.05 4.01
466 470 0.529992 CTAGCGGGCCGAGGTTTTAG 60.530 60.000 33.44 15.49 0.00 1.85
472 476 2.356818 CTTTCTCTAGCGGGCCGAGG 62.357 65.000 33.44 18.11 0.00 4.63
478 482 5.419155 TCCATATATGTCTTTCTCTAGCGGG 59.581 44.000 11.73 0.00 0.00 6.13
481 485 9.364989 GATTGTCCATATATGTCTTTCTCTAGC 57.635 37.037 11.73 0.00 0.00 3.42
526 534 8.596781 AGGTAGAGATAGAGATAGAGAGAGAC 57.403 42.308 0.00 0.00 0.00 3.36
528 536 8.830915 AGAGGTAGAGATAGAGATAGAGAGAG 57.169 42.308 0.00 0.00 0.00 3.20
566 598 9.626045 GCAAAATATATCCAAACTAGTATTGGC 57.374 33.333 22.13 10.05 45.63 4.52
674 721 7.225341 GCATGTTCTCTTTTGTTGGAAGAAAAT 59.775 33.333 0.00 0.00 31.86 1.82
975 1025 3.242543 GCTAGGATGTCGTTTGATGCTTG 60.243 47.826 0.00 0.00 0.00 4.01
988 1038 6.946583 AGAATGAAATGCATATGCTAGGATGT 59.053 34.615 27.13 8.60 42.66 3.06
1028 1086 6.656693 AGCTACTAGCAAGATCAACAATTTGT 59.343 34.615 10.73 0.00 45.56 2.83
1085 1143 1.694150 CCATAGCTACTAGCAAGGGCA 59.306 52.381 10.73 0.00 45.56 5.36
1086 1144 1.971357 TCCATAGCTACTAGCAAGGGC 59.029 52.381 10.73 0.00 45.56 5.19
1087 1145 3.196685 GGATCCATAGCTACTAGCAAGGG 59.803 52.174 6.95 7.94 45.56 3.95
1088 1146 4.093011 AGGATCCATAGCTACTAGCAAGG 58.907 47.826 15.82 8.58 45.56 3.61
1089 1147 6.842437 TTAGGATCCATAGCTACTAGCAAG 57.158 41.667 15.82 0.00 45.56 4.01
1090 1148 6.155221 CCATTAGGATCCATAGCTACTAGCAA 59.845 42.308 15.82 0.00 39.92 3.91
1091 1149 5.658634 CCATTAGGATCCATAGCTACTAGCA 59.341 44.000 15.82 0.00 39.92 3.49
1092 1150 5.452636 GCCATTAGGATCCATAGCTACTAGC 60.453 48.000 15.82 0.00 38.31 3.42
1093 1151 5.896678 AGCCATTAGGATCCATAGCTACTAG 59.103 44.000 15.82 0.00 36.89 2.57
1094 1152 5.658634 CAGCCATTAGGATCCATAGCTACTA 59.341 44.000 15.82 0.00 36.89 1.82
1095 1153 4.469227 CAGCCATTAGGATCCATAGCTACT 59.531 45.833 15.82 0.00 36.89 2.57
1096 1154 4.764172 CAGCCATTAGGATCCATAGCTAC 58.236 47.826 15.82 0.00 36.89 3.58
1097 1155 3.198635 GCAGCCATTAGGATCCATAGCTA 59.801 47.826 15.82 0.00 36.89 3.32
1098 1156 2.026449 GCAGCCATTAGGATCCATAGCT 60.026 50.000 15.82 11.43 36.89 3.32
1099 1157 2.026449 AGCAGCCATTAGGATCCATAGC 60.026 50.000 15.82 9.23 36.89 2.97
1100 1158 3.996921 AGCAGCCATTAGGATCCATAG 57.003 47.619 15.82 0.27 36.89 2.23
1101 1159 4.410228 GGATAGCAGCCATTAGGATCCATA 59.590 45.833 15.82 0.72 34.79 2.74
1102 1160 3.201708 GGATAGCAGCCATTAGGATCCAT 59.798 47.826 15.82 1.47 34.79 3.41
1103 1161 2.573462 GGATAGCAGCCATTAGGATCCA 59.427 50.000 15.82 0.00 34.79 3.41
1104 1162 2.843113 AGGATAGCAGCCATTAGGATCC 59.157 50.000 2.48 2.48 34.84 3.36
1105 1163 5.046304 TGTTAGGATAGCAGCCATTAGGATC 60.046 44.000 0.00 0.00 36.89 3.36
1106 1164 4.846367 TGTTAGGATAGCAGCCATTAGGAT 59.154 41.667 0.00 0.00 36.89 3.24
1107 1165 4.231273 TGTTAGGATAGCAGCCATTAGGA 58.769 43.478 0.00 0.00 36.89 2.94
1108 1166 4.623932 TGTTAGGATAGCAGCCATTAGG 57.376 45.455 0.00 0.00 38.23 2.69
1109 1167 6.150140 GGAAATGTTAGGATAGCAGCCATTAG 59.850 42.308 0.00 0.00 34.53 1.73
1110 1168 6.003950 GGAAATGTTAGGATAGCAGCCATTA 58.996 40.000 0.00 0.00 34.53 1.90
1111 1169 4.829492 GGAAATGTTAGGATAGCAGCCATT 59.171 41.667 0.00 0.00 34.53 3.16
1112 1170 4.401925 GGAAATGTTAGGATAGCAGCCAT 58.598 43.478 0.00 0.00 34.53 4.40
1113 1171 3.435026 GGGAAATGTTAGGATAGCAGCCA 60.435 47.826 0.00 0.00 34.53 4.75
1114 1172 3.149981 GGGAAATGTTAGGATAGCAGCC 58.850 50.000 0.00 0.00 34.53 4.85
1115 1173 3.149981 GGGGAAATGTTAGGATAGCAGC 58.850 50.000 0.00 0.00 34.53 5.25
1116 1174 3.395941 AGGGGGAAATGTTAGGATAGCAG 59.604 47.826 0.00 0.00 34.53 4.24
1117 1175 3.403322 AGGGGGAAATGTTAGGATAGCA 58.597 45.455 0.00 0.00 35.85 3.49
1118 1176 4.145052 CAAGGGGGAAATGTTAGGATAGC 58.855 47.826 0.00 0.00 0.00 2.97
1119 1177 4.145052 GCAAGGGGGAAATGTTAGGATAG 58.855 47.826 0.00 0.00 0.00 2.08
1120 1178 3.529734 TGCAAGGGGGAAATGTTAGGATA 59.470 43.478 0.00 0.00 0.00 2.59
1121 1179 2.314549 TGCAAGGGGGAAATGTTAGGAT 59.685 45.455 0.00 0.00 0.00 3.24
1122 1180 1.713647 TGCAAGGGGGAAATGTTAGGA 59.286 47.619 0.00 0.00 0.00 2.94
1123 1181 2.230130 TGCAAGGGGGAAATGTTAGG 57.770 50.000 0.00 0.00 0.00 2.69
1124 1182 3.364549 TGATGCAAGGGGGAAATGTTAG 58.635 45.455 0.00 0.00 0.00 2.34
1125 1183 3.464720 TGATGCAAGGGGGAAATGTTA 57.535 42.857 0.00 0.00 0.00 2.41
1126 1184 2.323999 TGATGCAAGGGGGAAATGTT 57.676 45.000 0.00 0.00 0.00 2.71
1127 1185 2.181975 CTTGATGCAAGGGGGAAATGT 58.818 47.619 0.00 0.00 37.77 2.71
1128 1186 1.134610 GCTTGATGCAAGGGGGAAATG 60.135 52.381 9.01 0.00 41.31 2.32
1129 1187 1.197812 GCTTGATGCAAGGGGGAAAT 58.802 50.000 9.01 0.00 41.31 2.17
1130 1188 2.669878 GCTTGATGCAAGGGGGAAA 58.330 52.632 9.01 0.00 41.31 3.13
1131 1189 4.440145 GCTTGATGCAAGGGGGAA 57.560 55.556 9.01 0.00 41.31 3.97
1144 1250 0.445436 GTCGTGCCTCTCAATGCTTG 59.555 55.000 0.00 0.00 0.00 4.01
1191 1297 1.517538 ATGGTGGGGATTCAAGGGCA 61.518 55.000 0.00 0.00 0.00 5.36
1207 1313 5.933617 TCCTATTGAAGGTGAATCTGATGG 58.066 41.667 0.00 0.00 46.62 3.51
1318 1424 2.264794 GGGTAGTGGTGCGAGGTG 59.735 66.667 0.00 0.00 0.00 4.00
1472 1579 6.406370 TGGAGTAACGATGTGAAGAATGAAT 58.594 36.000 0.00 0.00 0.00 2.57
1478 1585 4.951254 TGTTTGGAGTAACGATGTGAAGA 58.049 39.130 0.00 0.00 0.00 2.87
1524 1631 1.134007 TCTCCCATAGCGGTAAGTCGA 60.134 52.381 0.00 0.00 0.00 4.20
1526 1633 1.000052 GCTCTCCCATAGCGGTAAGTC 60.000 57.143 0.00 0.00 0.00 3.01
1560 1667 7.201794 ACATGCTTGATGTCCATCTTAAAGATG 60.202 37.037 6.60 0.00 41.91 2.90
1624 1731 7.669722 ACTTGGTGTGAATGTTTACAGGATAAT 59.330 33.333 0.00 0.00 0.00 1.28
1633 1740 6.937465 TGCATAGTACTTGGTGTGAATGTTTA 59.063 34.615 0.00 0.00 0.00 2.01
1730 1846 0.035630 AGGTGAGGACTGCATGCTTC 60.036 55.000 20.33 14.71 0.00 3.86
1821 1937 2.939756 TGTGTACTTGCGTGATGTTGTT 59.060 40.909 0.00 0.00 0.00 2.83
1914 2030 6.539173 TCAACTTTGTAGGCTTTTCATCCTA 58.461 36.000 0.00 0.00 34.02 2.94
2108 2231 7.446106 TCCTATAGTTTCACACCCACATAAT 57.554 36.000 0.00 0.00 0.00 1.28
2186 2313 3.861840 AGTACACGACCATCAAAGATGG 58.138 45.455 21.26 21.26 44.54 3.51
2302 2432 7.339466 GGTTCCATTGTTAAGTAGGATGACAAT 59.661 37.037 0.00 0.00 40.46 2.71
2325 2457 1.251251 GCCAGAAGAATGTGCAGGTT 58.749 50.000 0.00 0.00 0.00 3.50
2330 2462 2.113860 TAGTGGCCAGAAGAATGTGC 57.886 50.000 5.11 0.00 0.00 4.57
2364 2496 5.765510 ACTGGCCCATTAACTGATTAATCA 58.234 37.500 17.07 17.07 38.67 2.57
2403 2535 2.358898 GTGCTATTCGATTTGGCCATGT 59.641 45.455 6.09 0.00 0.00 3.21
2411 2543 3.071167 GGGGAGTAGGTGCTATTCGATTT 59.929 47.826 0.00 0.00 0.00 2.17
2428 2560 2.413837 CTGACAAGTTAACACGGGGAG 58.586 52.381 8.61 0.00 0.00 4.30
2500 2633 1.348064 CCCGATAATGGGCCAGTAGA 58.652 55.000 19.41 0.00 43.70 2.59
2547 2680 1.551019 GGAGCTGGAAGGGGTTACGT 61.551 60.000 0.00 0.00 0.00 3.57
2564 2697 2.609747 AGCTATTAAGGAGCGGATGGA 58.390 47.619 6.52 0.00 44.98 3.41
2624 2758 2.298729 ACCCAAACATGTTGCCATACAC 59.701 45.455 12.82 0.00 0.00 2.90
2693 2832 9.289782 GAATAGGAACTTGCCAACATATATCTT 57.710 33.333 0.00 0.00 41.75 2.40
2773 2918 2.100418 GCTCGGTCGGTTTAGGATTAGT 59.900 50.000 0.00 0.00 0.00 2.24
2777 2922 0.175073 GTGCTCGGTCGGTTTAGGAT 59.825 55.000 0.00 0.00 0.00 3.24
2796 2941 6.869913 TGTTCAAGTAATCGTTAACAGGTAGG 59.130 38.462 6.39 0.00 0.00 3.18
2830 2975 0.167908 TCAATTAGCCAAGCGTTGCG 59.832 50.000 0.00 0.00 0.00 4.85
2836 2981 5.573337 AGAGATTTGTCAATTAGCCAAGC 57.427 39.130 0.00 0.00 0.00 4.01
2854 2999 4.894114 GTGTGGGTAGGCTAAATCTAGAGA 59.106 45.833 0.00 0.00 0.00 3.10
2874 3019 3.243771 CGGTGGAGTGAGAGTTTAAGTGT 60.244 47.826 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.