Multiple sequence alignment - TraesCS3D01G085300

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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 TraesCS3D01G085300 chr3D 100.000 2436 0 0 1 2436 42991465 42989030 0.000000e+00 4499.0
1 TraesCS3D01G085300 chr3D 97.373 609 16 0 1794 2402 2358209 2357601 0.000000e+00 1037.0
2 TraesCS3D01G085300 chr3D 92.776 263 19 0 1794 2056 315478391 315478653 4.920000e-102 381.0
3 TraesCS3D01G085300 chr2D 97.812 960 17 2 1464 2423 601606358 601605403 0.000000e+00 1653.0
4 TraesCS3D01G085300 chr2D 95.172 290 10 1 1797 2082 632564134 632563845 2.860000e-124 455.0
5 TraesCS3D01G085300 chr7D 97.704 958 18 3 1466 2423 49951248 49950295 0.000000e+00 1644.0
6 TraesCS3D01G085300 chr7D 91.228 57 3 2 479 534 510609194 510609249 2.600000e-10 76.8
7 TraesCS3D01G085300 chr3B 89.906 1169 42 22 1 1124 66864504 66863367 0.000000e+00 1435.0
8 TraesCS3D01G085300 chr3B 89.716 282 18 5 1188 1464 66863219 66862944 1.390000e-92 350.0
9 TraesCS3D01G085300 chr3B 95.588 68 3 0 1053 1120 66822126 66822059 2.560000e-20 110.0
10 TraesCS3D01G085300 chr1B 95.880 631 26 0 1794 2424 423108576 423107946 0.000000e+00 1022.0
11 TraesCS3D01G085300 chr1B 91.615 644 44 5 1794 2436 486551754 486552388 0.000000e+00 881.0
12 TraesCS3D01G085300 chr1B 95.796 333 12 2 1465 1796 423111039 423110708 9.910000e-149 536.0
13 TraesCS3D01G085300 chr3A 94.679 639 33 1 1794 2432 588510047 588510684 0.000000e+00 990.0
14 TraesCS3D01G085300 chr3A 94.595 333 15 2 1464 1796 588507588 588507917 1.670000e-141 512.0
15 TraesCS3D01G085300 chr4A 93.978 631 36 1 1794 2424 201549717 201549089 0.000000e+00 953.0
16 TraesCS3D01G085300 chr4A 91.566 332 23 3 1465 1796 201552174 201551848 1.030000e-123 453.0
17 TraesCS3D01G085300 chr4A 91.071 56 3 2 487 540 606747705 606747760 9.340000e-10 75.0
18 TraesCS3D01G085300 chr5A 96.059 406 15 1 2019 2424 606473995 606473591 0.000000e+00 660.0
19 TraesCS3D01G085300 chr5A 93.808 323 18 2 1474 1796 606479880 606479560 3.640000e-133 484.0
20 TraesCS3D01G085300 chr1D 90.497 463 30 9 1965 2424 276774003 276774454 1.250000e-167 599.0
21 TraesCS3D01G085300 chrUn 89.329 328 33 2 1465 1790 326827977 326828304 6.270000e-111 411.0
22 TraesCS3D01G085300 chrUn 88.922 334 35 2 1465 1796 329537189 329536856 6.270000e-111 411.0
23 TraesCS3D01G085300 chr7B 89.329 328 33 2 1465 1790 566745292 566745619 6.270000e-111 411.0
24 TraesCS3D01G085300 chr6D 95.833 48 2 0 487 534 460808330 460808283 7.220000e-11 78.7
25 TraesCS3D01G085300 chr6D 92.453 53 2 2 487 538 30395090 30395039 9.340000e-10 75.0
26 TraesCS3D01G085300 chr6D 92.453 53 3 1 487 538 54706631 54706683 9.340000e-10 75.0
27 TraesCS3D01G085300 chr6B 95.833 48 2 0 487 534 42749495 42749448 7.220000e-11 78.7
28 TraesCS3D01G085300 chr7A 91.071 56 3 2 487 540 672778889 672778944 9.340000e-10 75.0
29 TraesCS3D01G085300 chr1A 91.071 56 3 2 487 540 28831927 28831872 9.340000e-10 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 TraesCS3D01G085300 chr3D 42989030 42991465 2435 True 4499.0 4499 100.000 1 2436 1 chr3D.!!$R2 2435
1 TraesCS3D01G085300 chr3D 2357601 2358209 608 True 1037.0 1037 97.373 1794 2402 1 chr3D.!!$R1 608
2 TraesCS3D01G085300 chr2D 601605403 601606358 955 True 1653.0 1653 97.812 1464 2423 1 chr2D.!!$R1 959
3 TraesCS3D01G085300 chr7D 49950295 49951248 953 True 1644.0 1644 97.704 1466 2423 1 chr7D.!!$R1 957
4 TraesCS3D01G085300 chr3B 66862944 66864504 1560 True 892.5 1435 89.811 1 1464 2 chr3B.!!$R2 1463
5 TraesCS3D01G085300 chr1B 486551754 486552388 634 False 881.0 881 91.615 1794 2436 1 chr1B.!!$F1 642
6 TraesCS3D01G085300 chr1B 423107946 423111039 3093 True 779.0 1022 95.838 1465 2424 2 chr1B.!!$R1 959
7 TraesCS3D01G085300 chr3A 588507588 588510684 3096 False 751.0 990 94.637 1464 2432 2 chr3A.!!$F1 968
8 TraesCS3D01G085300 chr4A 201549089 201552174 3085 True 703.0 953 92.772 1465 2424 2 chr4A.!!$R1 959

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
214 225 0.036388 TTTGGATCTCGGCCACTCAC 60.036 55.0 2.24 0.0 34.56 3.51 F
1098 1144 0.321653 CCAAGAGAACCAACCCTCCG 60.322 60.0 0.00 0.0 0.00 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1318 1487 0.179059 TGGCGCAGTTGAAGAACAGA 60.179 50.000 10.83 0.00 34.17 3.41 R
1944 4253 4.282195 AGCTTACTCGGGATCCATCTAAAG 59.718 45.833 15.23 11.84 0.00 1.85 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
23 24 3.369157 GGTACAGGAATACGGATATGCCC 60.369 52.174 0.00 0.00 37.20 5.36
51 52 0.839946 ACACAAGCACTCCAGGTCTT 59.160 50.000 0.00 0.00 0.00 3.01
54 55 2.689983 CACAAGCACTCCAGGTCTTTTT 59.310 45.455 0.00 0.00 0.00 1.94
66 67 2.963101 AGGTCTTTTTGGGCCTTTGTAC 59.037 45.455 4.53 0.00 0.00 2.90
81 82 2.394930 TGTACATGCGGTGCTTATGT 57.605 45.000 0.00 0.00 38.48 2.29
108 109 9.154847 TGTTGAAGTGTTGATACTCATAGAATG 57.845 33.333 0.00 0.00 0.00 2.67
162 173 1.392589 AGGGTTTCTGTGCAGTGTTG 58.607 50.000 0.00 0.00 0.00 3.33
214 225 0.036388 TTTGGATCTCGGCCACTCAC 60.036 55.000 2.24 0.00 34.56 3.51
239 250 6.244654 TGTGATGTTGGGAGTATGATTTTCA 58.755 36.000 0.00 0.00 0.00 2.69
242 253 4.991776 TGTTGGGAGTATGATTTTCACCA 58.008 39.130 0.00 0.00 0.00 4.17
244 255 6.726379 TGTTGGGAGTATGATTTTCACCATA 58.274 36.000 0.00 0.00 0.00 2.74
290 301 6.723977 TGCATTTTAATCCCCTGTATATTCCC 59.276 38.462 0.00 0.00 0.00 3.97
326 337 1.694696 GGGAGCTGGACTTAGGGTATG 59.305 57.143 0.00 0.00 0.00 2.39
329 340 3.181464 GGAGCTGGACTTAGGGTATGTTC 60.181 52.174 0.00 0.00 0.00 3.18
396 407 4.436113 AAGGTTTTGTTTGCCAATGGAT 57.564 36.364 2.05 0.00 31.81 3.41
454 467 8.874744 AAACTACTCTGTATTGTAGTGTAGGA 57.125 34.615 14.77 0.00 45.74 2.94
455 468 8.508883 AACTACTCTGTATTGTAGTGTAGGAG 57.491 38.462 14.77 0.00 45.74 3.69
456 469 7.631933 ACTACTCTGTATTGTAGTGTAGGAGT 58.368 38.462 14.77 0.00 45.05 3.85
457 470 8.766476 ACTACTCTGTATTGTAGTGTAGGAGTA 58.234 37.037 14.77 0.00 45.05 2.59
462 475 9.470399 TCTGTATTGTAGTGTAGGAGTATTTGA 57.530 33.333 0.00 0.00 0.00 2.69
478 491 8.940952 GGAGTATTTGATATGGCAAGATTAGAC 58.059 37.037 0.00 0.00 0.00 2.59
485 498 9.944376 TTGATATGGCAAGATTAGACTAATACC 57.056 33.333 7.71 8.03 0.00 2.73
490 503 9.700831 ATGGCAAGATTAGACTAATACCTTTTT 57.299 29.630 7.71 0.00 0.00 1.94
491 504 9.174166 TGGCAAGATTAGACTAATACCTTTTTC 57.826 33.333 7.71 0.00 0.00 2.29
527 541 1.507562 TGCTTACCACATGTGTCACG 58.492 50.000 23.79 11.29 0.00 4.35
531 550 2.945984 CCACATGTGTCACGTGGC 59.054 61.111 25.31 14.58 43.43 5.01
561 580 8.627208 TTAGACTAATACCTAACATACCCTCG 57.373 38.462 0.00 0.00 0.00 4.63
641 664 7.791029 ACCTTCTGTTGTTCATAACCAAAAAT 58.209 30.769 0.00 0.00 0.00 1.82
669 692 7.848223 GGTACGGTACACTTTGGTTTATAAT 57.152 36.000 19.14 0.00 0.00 1.28
670 693 7.909267 GGTACGGTACACTTTGGTTTATAATC 58.091 38.462 19.14 0.00 0.00 1.75
671 694 6.990341 ACGGTACACTTTGGTTTATAATCC 57.010 37.500 5.72 5.72 0.00 3.01
672 695 6.474630 ACGGTACACTTTGGTTTATAATCCA 58.525 36.000 10.65 10.65 0.00 3.41
673 696 6.941436 ACGGTACACTTTGGTTTATAATCCAA 59.059 34.615 19.69 19.69 41.22 3.53
674 697 7.447853 ACGGTACACTTTGGTTTATAATCCAAA 59.552 33.333 27.49 27.49 46.93 3.28
675 698 7.751793 CGGTACACTTTGGTTTATAATCCAAAC 59.248 37.037 26.42 19.87 45.13 2.93
676 699 8.578151 GGTACACTTTGGTTTATAATCCAAACA 58.422 33.333 26.42 14.48 45.13 2.83
677 700 9.401873 GTACACTTTGGTTTATAATCCAAACAC 57.598 33.333 26.42 19.54 45.13 3.32
678 701 8.012957 ACACTTTGGTTTATAATCCAAACACA 57.987 30.769 26.42 13.68 45.13 3.72
679 702 8.478877 ACACTTTGGTTTATAATCCAAACACAA 58.521 29.630 26.42 13.40 45.13 3.33
680 703 8.760569 CACTTTGGTTTATAATCCAAACACAAC 58.239 33.333 26.42 3.14 45.13 3.32
681 704 7.929245 ACTTTGGTTTATAATCCAAACACAACC 59.071 33.333 26.42 11.17 45.13 3.77
702 725 1.464734 TAACCGCTCAGAGTCTCAGG 58.535 55.000 1.94 0.00 0.00 3.86
742 765 1.134220 TCTTCCGGTGAAGTGCTTGTT 60.134 47.619 0.00 0.00 46.66 2.83
761 784 3.182772 TGTTTGCTTGATGTGTACGTACG 59.817 43.478 20.18 15.01 0.00 3.67
896 924 2.516906 TCGTTTGTAATTCCCAACCCC 58.483 47.619 0.00 0.00 0.00 4.95
901 929 4.412060 TTGTAATTCCCAACCCCTGATT 57.588 40.909 0.00 0.00 0.00 2.57
987 1018 2.203714 CGATCCTCCCTCCCTCCC 60.204 72.222 0.00 0.00 0.00 4.30
988 1019 2.784654 CGATCCTCCCTCCCTCCCT 61.785 68.421 0.00 0.00 0.00 4.20
989 1020 1.157513 GATCCTCCCTCCCTCCCTC 59.842 68.421 0.00 0.00 0.00 4.30
990 1021 2.395180 GATCCTCCCTCCCTCCCTCC 62.395 70.000 0.00 0.00 0.00 4.30
991 1022 4.179599 CCTCCCTCCCTCCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
1085 1131 0.593128 CTCGTGCCAAAACCCAAGAG 59.407 55.000 0.00 0.00 32.81 2.85
1098 1144 0.321653 CCAAGAGAACCAACCCTCCG 60.322 60.000 0.00 0.00 0.00 4.63
1120 1166 1.227556 GTCCGCGCAATCAGGGTAT 60.228 57.895 8.75 0.00 0.00 2.73
1124 1170 1.356624 GCGCAATCAGGGTATGTGC 59.643 57.895 0.30 0.00 42.48 4.57
1125 1171 1.643292 CGCAATCAGGGTATGTGCG 59.357 57.895 1.69 1.69 37.93 5.34
1126 1172 1.089481 CGCAATCAGGGTATGTGCGT 61.089 55.000 8.10 0.00 39.12 5.24
1127 1173 0.378257 GCAATCAGGGTATGTGCGTG 59.622 55.000 0.00 0.00 0.00 5.34
1128 1174 1.737838 CAATCAGGGTATGTGCGTGT 58.262 50.000 0.00 0.00 0.00 4.49
1129 1175 2.899976 CAATCAGGGTATGTGCGTGTA 58.100 47.619 0.00 0.00 0.00 2.90
1130 1176 3.266636 CAATCAGGGTATGTGCGTGTAA 58.733 45.455 0.00 0.00 0.00 2.41
1131 1177 2.665649 TCAGGGTATGTGCGTGTAAG 57.334 50.000 0.00 0.00 0.00 2.34
1132 1178 1.006832 CAGGGTATGTGCGTGTAAGC 58.993 55.000 0.00 0.00 37.71 3.09
1133 1179 0.902531 AGGGTATGTGCGTGTAAGCT 59.097 50.000 0.00 0.00 38.13 3.74
1134 1180 2.104967 AGGGTATGTGCGTGTAAGCTA 58.895 47.619 0.00 0.00 38.13 3.32
1135 1181 2.698797 AGGGTATGTGCGTGTAAGCTAT 59.301 45.455 0.00 0.00 38.13 2.97
1136 1182 3.893200 AGGGTATGTGCGTGTAAGCTATA 59.107 43.478 0.00 0.00 38.13 1.31
1137 1183 4.342951 AGGGTATGTGCGTGTAAGCTATAA 59.657 41.667 0.00 0.00 38.13 0.98
1138 1184 5.051816 GGGTATGTGCGTGTAAGCTATAAA 58.948 41.667 0.00 0.00 38.13 1.40
1139 1185 5.699458 GGGTATGTGCGTGTAAGCTATAAAT 59.301 40.000 0.00 0.00 38.13 1.40
1140 1186 6.869913 GGGTATGTGCGTGTAAGCTATAAATA 59.130 38.462 0.00 0.00 38.13 1.40
1141 1187 7.385752 GGGTATGTGCGTGTAAGCTATAAATAA 59.614 37.037 0.00 0.00 38.13 1.40
1142 1188 8.932791 GGTATGTGCGTGTAAGCTATAAATAAT 58.067 33.333 0.00 0.00 38.13 1.28
1143 1189 9.953825 GTATGTGCGTGTAAGCTATAAATAATC 57.046 33.333 0.00 0.00 38.13 1.75
1144 1190 8.601845 ATGTGCGTGTAAGCTATAAATAATCA 57.398 30.769 0.00 0.00 38.13 2.57
1145 1191 8.426881 TGTGCGTGTAAGCTATAAATAATCAA 57.573 30.769 0.00 0.00 38.13 2.57
1146 1192 8.547894 TGTGCGTGTAAGCTATAAATAATCAAG 58.452 33.333 0.00 0.00 38.13 3.02
1147 1193 8.009974 GTGCGTGTAAGCTATAAATAATCAAGG 58.990 37.037 0.00 0.00 38.13 3.61
1148 1194 7.172532 TGCGTGTAAGCTATAAATAATCAAGGG 59.827 37.037 0.00 0.00 38.13 3.95
1149 1195 7.172703 GCGTGTAAGCTATAAATAATCAAGGGT 59.827 37.037 0.00 0.00 0.00 4.34
1150 1196 9.701098 CGTGTAAGCTATAAATAATCAAGGGTA 57.299 33.333 0.00 0.00 0.00 3.69
1155 1201 8.567285 AGCTATAAATAATCAAGGGTATGTGC 57.433 34.615 0.00 0.00 0.00 4.57
1156 1202 7.334421 AGCTATAAATAATCAAGGGTATGTGCG 59.666 37.037 0.00 0.00 0.00 5.34
1157 1203 7.119262 GCTATAAATAATCAAGGGTATGTGCGT 59.881 37.037 0.00 0.00 0.00 5.24
1158 1204 5.499139 AAATAATCAAGGGTATGTGCGTG 57.501 39.130 0.00 0.00 0.00 5.34
1164 1210 0.902531 AGGGTATGTGCGTGTAAGCT 59.097 50.000 0.00 0.00 38.13 3.74
1170 1216 6.380274 AGGGTATGTGCGTGTAAGCTATATAT 59.620 38.462 0.00 0.00 38.13 0.86
1171 1217 7.558807 AGGGTATGTGCGTGTAAGCTATATATA 59.441 37.037 0.00 0.00 38.13 0.86
1172 1218 8.358148 GGGTATGTGCGTGTAAGCTATATATAT 58.642 37.037 0.00 0.00 38.13 0.86
1218 1383 3.004839 GGAGCCTCACAAGTTCCTTTTTC 59.995 47.826 0.00 0.00 0.00 2.29
1219 1384 2.959030 AGCCTCACAAGTTCCTTTTTCC 59.041 45.455 0.00 0.00 0.00 3.13
1220 1385 2.959030 GCCTCACAAGTTCCTTTTTCCT 59.041 45.455 0.00 0.00 0.00 3.36
1223 1388 4.464947 CTCACAAGTTCCTTTTTCCTCCT 58.535 43.478 0.00 0.00 0.00 3.69
1224 1389 4.461198 TCACAAGTTCCTTTTTCCTCCTC 58.539 43.478 0.00 0.00 0.00 3.71
1278 1447 9.109393 TGTACTATTTATTGTCTTCATCTTGGC 57.891 33.333 0.00 0.00 0.00 4.52
1286 1455 2.096496 GTCTTCATCTTGGCGTTCATGG 59.904 50.000 0.00 0.00 0.00 3.66
1318 1487 1.752833 GGACAAGAACCACCTCCGT 59.247 57.895 0.00 0.00 0.00 4.69
1325 1494 0.680061 GAACCACCTCCGTCTGTTCT 59.320 55.000 0.00 0.00 32.07 3.01
1360 1529 2.659610 GTGCTCCTCTCGCTTGGT 59.340 61.111 0.00 0.00 0.00 3.67
1363 1532 0.108585 TGCTCCTCTCGCTTGGTTTT 59.891 50.000 0.00 0.00 0.00 2.43
1375 1544 0.958091 TTGGTTTTCCTGTCATGGCG 59.042 50.000 0.00 0.00 41.38 5.69
1387 1556 2.030274 TGTCATGGCGTATATCCTCACG 60.030 50.000 0.00 0.00 41.04 4.35
1459 1628 3.255725 CGTGGCTTACTTGTATTCCGAA 58.744 45.455 0.00 0.00 0.00 4.30
1496 1665 2.038033 CCAGGACGAAAAACTAGTGGGA 59.962 50.000 0.00 0.00 0.00 4.37
1611 1780 9.374960 GTGTCGAAGAAGCAAAATCATATAATC 57.625 33.333 0.00 0.00 39.69 1.75
1879 4188 1.005450 GGACAAGGTTGATAAGCCCCA 59.995 52.381 0.00 0.00 0.00 4.96
1915 4224 3.921104 TCTCCTAATCTCCTCATGCTGT 58.079 45.455 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 0.178961 GGCCCAAAAAGACCTGGAGT 60.179 55.000 0.00 0.00 34.35 3.85
51 52 1.000283 CGCATGTACAAAGGCCCAAAA 60.000 47.619 0.00 0.00 0.00 2.44
54 55 1.677300 CCGCATGTACAAAGGCCCA 60.677 57.895 0.00 0.00 0.00 5.36
66 67 2.095314 TCAACAACATAAGCACCGCATG 60.095 45.455 0.00 0.00 0.00 4.06
162 173 1.576356 GACCTCTCATCACGCATTCC 58.424 55.000 0.00 0.00 0.00 3.01
214 225 6.375174 TGAAAATCATACTCCCAACATCACAG 59.625 38.462 0.00 0.00 0.00 3.66
239 250 4.021544 ACCAATTTCACGCAACATTATGGT 60.022 37.500 0.00 0.00 32.86 3.55
242 253 6.565623 GCAAAACCAATTTCACGCAACATTAT 60.566 34.615 0.00 0.00 0.00 1.28
244 255 4.495514 GCAAAACCAATTTCACGCAACATT 60.496 37.500 0.00 0.00 0.00 2.71
290 301 3.698040 AGCTCCCAACAATATGAAAGCAG 59.302 43.478 0.00 0.00 33.05 4.24
428 441 9.964354 TCCTACACTACAATACAGAGTAGTTTA 57.036 33.333 2.74 1.50 46.36 2.01
452 465 8.940952 GTCTAATCTTGCCATATCAAATACTCC 58.059 37.037 0.00 0.00 0.00 3.85
453 466 9.717942 AGTCTAATCTTGCCATATCAAATACTC 57.282 33.333 0.00 0.00 0.00 2.59
485 498 9.264719 AGCAATCCAAACTATTCAAAGAAAAAG 57.735 29.630 0.00 0.00 0.00 2.27
490 503 7.450014 TGGTAAGCAATCCAAACTATTCAAAGA 59.550 33.333 0.00 0.00 0.00 2.52
491 504 7.542130 GTGGTAAGCAATCCAAACTATTCAAAG 59.458 37.037 0.00 0.00 35.38 2.77
527 541 9.169592 TGTTAGGTATTAGTCTAATTTTGCCAC 57.830 33.333 10.36 2.04 0.00 5.01
561 580 7.340999 TGGCCTTTGTTATTAGGAATAAAGACC 59.659 37.037 3.32 5.67 39.17 3.85
605 624 2.211279 AGAAGGTTGGCCCTCCCT 59.789 61.111 0.00 0.00 45.47 4.20
617 636 8.661352 AATTTTTGGTTATGAACAACAGAAGG 57.339 30.769 0.00 0.00 30.09 3.46
641 664 2.102252 ACCAAAGTGTACCGTACCGAAA 59.898 45.455 6.23 0.00 0.00 3.46
664 687 6.183360 GCGGTTATGGTTGTGTTTGGATTATA 60.183 38.462 0.00 0.00 0.00 0.98
665 688 5.393678 GCGGTTATGGTTGTGTTTGGATTAT 60.394 40.000 0.00 0.00 0.00 1.28
666 689 4.082679 GCGGTTATGGTTGTGTTTGGATTA 60.083 41.667 0.00 0.00 0.00 1.75
667 690 3.305744 GCGGTTATGGTTGTGTTTGGATT 60.306 43.478 0.00 0.00 0.00 3.01
668 691 2.230266 GCGGTTATGGTTGTGTTTGGAT 59.770 45.455 0.00 0.00 0.00 3.41
669 692 1.609555 GCGGTTATGGTTGTGTTTGGA 59.390 47.619 0.00 0.00 0.00 3.53
670 693 1.611491 AGCGGTTATGGTTGTGTTTGG 59.389 47.619 0.00 0.00 0.00 3.28
671 694 2.292016 TGAGCGGTTATGGTTGTGTTTG 59.708 45.455 0.00 0.00 0.00 2.93
672 695 2.552315 CTGAGCGGTTATGGTTGTGTTT 59.448 45.455 0.00 0.00 0.00 2.83
673 696 2.151202 CTGAGCGGTTATGGTTGTGTT 58.849 47.619 0.00 0.00 0.00 3.32
674 697 1.346395 TCTGAGCGGTTATGGTTGTGT 59.654 47.619 0.00 0.00 0.00 3.72
675 698 2.002586 CTCTGAGCGGTTATGGTTGTG 58.997 52.381 0.00 0.00 0.00 3.33
676 699 1.623811 ACTCTGAGCGGTTATGGTTGT 59.376 47.619 4.19 0.00 0.00 3.32
677 700 2.093973 AGACTCTGAGCGGTTATGGTTG 60.094 50.000 4.19 0.00 0.00 3.77
678 701 2.166664 GAGACTCTGAGCGGTTATGGTT 59.833 50.000 4.19 0.00 0.00 3.67
679 702 1.751924 GAGACTCTGAGCGGTTATGGT 59.248 52.381 4.19 0.00 0.00 3.55
680 703 1.751351 TGAGACTCTGAGCGGTTATGG 59.249 52.381 4.19 0.00 0.00 2.74
681 704 2.223688 CCTGAGACTCTGAGCGGTTATG 60.224 54.545 10.70 0.00 0.00 1.90
702 725 1.449778 GGCTAGTTGACGGGAAGGC 60.450 63.158 0.00 0.00 0.00 4.35
742 765 3.015934 ACGTACGTACACATCAAGCAA 57.984 42.857 21.41 0.00 0.00 3.91
761 784 7.798052 GCAGCGTTCTATTCTTAGTAGTAGTAC 59.202 40.741 0.00 0.00 0.00 2.73
772 795 3.003480 GTTCCTGCAGCGTTCTATTCTT 58.997 45.455 8.66 0.00 0.00 2.52
868 896 9.328845 GGTTGGGAATTACAAACGAATATAGTA 57.671 33.333 1.67 0.00 0.00 1.82
879 907 3.905493 TCAGGGGTTGGGAATTACAAA 57.095 42.857 0.00 0.00 0.00 2.83
880 908 4.412060 AATCAGGGGTTGGGAATTACAA 57.588 40.909 0.00 0.00 0.00 2.41
896 924 9.319143 AGGAGATTAACTTGAACGAATAATCAG 57.681 33.333 0.00 0.00 36.10 2.90
901 929 6.270815 CCGAGGAGATTAACTTGAACGAATA 58.729 40.000 0.00 0.00 0.00 1.75
934 965 7.111179 CGTCGAAAAACTTTATATCTCGATCGA 59.889 37.037 18.32 18.32 36.38 3.59
987 1018 4.201122 GGCATGGGCAGGAGGGAG 62.201 72.222 0.00 0.00 43.71 4.30
1064 1110 2.420466 CTTGGGTTTTGGCACGAGGC 62.420 60.000 0.00 0.00 43.74 4.70
1065 1111 0.821711 TCTTGGGTTTTGGCACGAGG 60.822 55.000 0.00 0.00 0.00 4.63
1077 1123 0.771755 GAGGGTTGGTTCTCTTGGGT 59.228 55.000 0.00 0.00 0.00 4.51
1098 1144 3.499737 CTGATTGCGCGGACCCAC 61.500 66.667 8.83 0.00 0.00 4.61
1120 1166 8.426881 TTGATTATTTATAGCTTACACGCACA 57.573 30.769 0.00 0.00 0.00 4.57
1124 1170 8.603242 ACCCTTGATTATTTATAGCTTACACG 57.397 34.615 0.00 0.00 0.00 4.49
1129 1175 9.014297 GCACATACCCTTGATTATTTATAGCTT 57.986 33.333 0.00 0.00 0.00 3.74
1130 1176 7.334421 CGCACATACCCTTGATTATTTATAGCT 59.666 37.037 0.00 0.00 0.00 3.32
1131 1177 7.119262 ACGCACATACCCTTGATTATTTATAGC 59.881 37.037 0.00 0.00 0.00 2.97
1132 1178 8.443160 CACGCACATACCCTTGATTATTTATAG 58.557 37.037 0.00 0.00 0.00 1.31
1133 1179 7.934665 ACACGCACATACCCTTGATTATTTATA 59.065 33.333 0.00 0.00 0.00 0.98
1134 1180 6.770785 ACACGCACATACCCTTGATTATTTAT 59.229 34.615 0.00 0.00 0.00 1.40
1135 1181 6.116806 ACACGCACATACCCTTGATTATTTA 58.883 36.000 0.00 0.00 0.00 1.40
1136 1182 4.947388 ACACGCACATACCCTTGATTATTT 59.053 37.500 0.00 0.00 0.00 1.40
1137 1183 4.523083 ACACGCACATACCCTTGATTATT 58.477 39.130 0.00 0.00 0.00 1.40
1138 1184 4.150897 ACACGCACATACCCTTGATTAT 57.849 40.909 0.00 0.00 0.00 1.28
1139 1185 3.620427 ACACGCACATACCCTTGATTA 57.380 42.857 0.00 0.00 0.00 1.75
1140 1186 2.489938 ACACGCACATACCCTTGATT 57.510 45.000 0.00 0.00 0.00 2.57
1141 1187 3.531538 CTTACACGCACATACCCTTGAT 58.468 45.455 0.00 0.00 0.00 2.57
1142 1188 2.933492 GCTTACACGCACATACCCTTGA 60.933 50.000 0.00 0.00 0.00 3.02
1143 1189 1.396996 GCTTACACGCACATACCCTTG 59.603 52.381 0.00 0.00 0.00 3.61
1144 1190 1.278127 AGCTTACACGCACATACCCTT 59.722 47.619 0.00 0.00 0.00 3.95
1145 1191 0.902531 AGCTTACACGCACATACCCT 59.097 50.000 0.00 0.00 0.00 4.34
1146 1192 2.589798 TAGCTTACACGCACATACCC 57.410 50.000 0.00 0.00 0.00 3.69
1208 1373 2.554462 GCACAGAGGAGGAAAAAGGAAC 59.446 50.000 0.00 0.00 0.00 3.62
1219 1384 1.739562 GAACGCCTGCACAGAGGAG 60.740 63.158 0.00 0.00 38.78 3.69
1220 1385 2.343758 GAACGCCTGCACAGAGGA 59.656 61.111 0.00 0.00 34.69 3.71
1264 1433 2.542020 TGAACGCCAAGATGAAGACA 57.458 45.000 0.00 0.00 0.00 3.41
1278 1447 1.635663 GCTCCGTGGAACCATGAACG 61.636 60.000 13.85 4.86 35.09 3.95
1286 1455 2.047179 GTCCCTGCTCCGTGGAAC 60.047 66.667 0.00 0.00 0.00 3.62
1318 1487 0.179059 TGGCGCAGTTGAAGAACAGA 60.179 50.000 10.83 0.00 34.17 3.41
1325 1494 2.361104 GGGGATGGCGCAGTTGAA 60.361 61.111 10.83 0.00 0.00 2.69
1360 1529 4.102524 AGGATATACGCCATGACAGGAAAA 59.897 41.667 0.00 0.00 0.00 2.29
1363 1532 2.826128 GAGGATATACGCCATGACAGGA 59.174 50.000 0.00 0.00 0.00 3.86
1404 1573 2.750350 CGCCCTGAGGTTGAGGTT 59.250 61.111 0.00 0.00 34.57 3.50
1405 1574 4.021925 GCGCCCTGAGGTTGAGGT 62.022 66.667 0.00 0.00 34.57 3.85
1406 1575 3.335356 ATGCGCCCTGAGGTTGAGG 62.335 63.158 4.18 0.00 34.57 3.86
1407 1576 2.110967 CATGCGCCCTGAGGTTGAG 61.111 63.158 4.18 0.00 34.57 3.02
1408 1577 2.046023 CATGCGCCCTGAGGTTGA 60.046 61.111 4.18 0.00 34.57 3.18
1409 1578 3.818787 GCATGCGCCCTGAGGTTG 61.819 66.667 4.18 0.00 34.57 3.77
1439 1608 3.373130 GGTTCGGAATACAAGTAAGCCAC 59.627 47.826 0.00 0.00 0.00 5.01
1442 1611 4.933400 TGAAGGTTCGGAATACAAGTAAGC 59.067 41.667 0.00 0.00 0.00 3.09
1879 4188 6.670027 AGATTAGGAGAAAGTACCTGACATGT 59.330 38.462 0.00 0.00 37.68 3.21
1944 4253 4.282195 AGCTTACTCGGGATCCATCTAAAG 59.718 45.833 15.23 11.84 0.00 1.85
2109 4422 6.963322 AGTTCTGCTGGGAGTAGAATAAAAT 58.037 36.000 7.29 0.00 45.99 1.82
2110 4423 6.013725 TGAGTTCTGCTGGGAGTAGAATAAAA 60.014 38.462 7.29 0.00 45.99 1.52


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

AutoCloner maintained by Alex Coulton.