Multiple sequence alignment - TraesCS2D01G165600

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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 TraesCS2D01G165600 chr2D 100.000 2207 0 0 1 2207 109792442 109794648 0.000000e+00 4076.0
1 TraesCS2D01G165600 chr2D 84.038 852 135 1 1357 2207 353585708 353584857 0.000000e+00 819.0
2 TraesCS2D01G165600 chr2D 85.229 677 44 22 156 779 109901083 109901756 0.000000e+00 645.0
3 TraesCS2D01G165600 chr2D 90.238 420 33 7 933 1347 109902020 109902436 1.930000e-150 542.0
4 TraesCS2D01G165600 chr2D 88.542 384 33 9 932 1307 109737599 109737979 2.580000e-124 455.0
5 TraesCS2D01G165600 chr2B 88.173 854 97 4 1356 2207 441922723 441923574 0.000000e+00 1014.0
6 TraesCS2D01G165600 chr2B 86.754 687 85 6 1356 2039 258696013 258696696 0.000000e+00 760.0
7 TraesCS2D01G165600 chr2B 79.813 857 160 9 1358 2205 329010517 329009665 1.450000e-171 612.0
8 TraesCS2D01G165600 chr2B 89.320 412 38 5 940 1347 159319083 159319492 1.510000e-141 512.0
9 TraesCS2D01G165600 chr2B 81.669 671 51 37 177 779 159318061 159318727 1.970000e-135 492.0
10 TraesCS2D01G165600 chr2B 76.841 842 173 21 1356 2187 88189420 88188591 2.580000e-124 455.0
11 TraesCS2D01G165600 chr2B 87.435 382 42 4 932 1308 159300169 159300549 3.370000e-118 435.0
12 TraesCS2D01G165600 chr2B 95.000 100 5 0 1 100 730032162 730032261 8.160000e-35 158.0
13 TraesCS2D01G165600 chr2B 86.207 58 6 2 66 122 634958902 634958958 6.580000e-06 62.1
14 TraesCS2D01G165600 chr7B 88.989 554 58 3 1355 1906 74388683 74388131 0.000000e+00 682.0
15 TraesCS2D01G165600 chr3B 85.645 620 86 3 1365 1982 591363005 591363623 0.000000e+00 649.0
16 TraesCS2D01G165600 chr3B 72.150 614 144 25 1356 1954 549388001 549388602 6.310000e-36 161.0
17 TraesCS2D01G165600 chr3B 89.286 56 5 1 58 113 632432118 632432172 3.930000e-08 69.4
18 TraesCS2D01G165600 chr3B 87.719 57 6 1 58 114 216208671 216208616 5.090000e-07 65.8
19 TraesCS2D01G165600 chr6B 80.234 855 148 13 1356 2207 207810553 207809717 6.690000e-175 623.0
20 TraesCS2D01G165600 chr6B 95.000 40 2 0 58 97 480262411 480262450 1.830000e-06 63.9
21 TraesCS2D01G165600 chr2A 82.632 737 60 26 171 842 105540359 105541092 6.790000e-165 590.0
22 TraesCS2D01G165600 chr2A 88.498 426 37 6 932 1347 105541258 105541681 2.530000e-139 505.0
23 TraesCS2D01G165600 chr2A 88.158 380 32 8 932 1306 105531792 105532163 7.230000e-120 440.0
24 TraesCS2D01G165600 chr2A 85.042 361 50 4 932 1291 105522786 105523143 4.480000e-97 364.0
25 TraesCS2D01G165600 chr2A 85.223 291 29 8 377 653 105531049 105531339 9.970000e-74 287.0
26 TraesCS2D01G165600 chr2A 86.339 183 18 7 470 648 105522175 105522354 2.240000e-45 193.0
27 TraesCS2D01G165600 chr3D 78.416 644 130 7 1357 1998 540906720 540907356 5.670000e-111 411.0
28 TraesCS2D01G165600 chr6D 78.864 440 90 3 1357 1796 254206923 254207359 5.960000e-76 294.0
29 TraesCS2D01G165600 chr5A 97.500 40 1 0 61 100 495141458 495141419 3.930000e-08 69.4
30 TraesCS2D01G165600 chr7A 97.222 36 1 0 65 100 700113240 700113205 6.580000e-06 62.1
31 TraesCS2D01G165600 chr4B 89.583 48 3 2 67 114 85607924 85607879 2.370000e-05 60.2
32 TraesCS2D01G165600 chr3A 89.583 48 4 1 67 114 519256166 519256120 2.370000e-05 60.2


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 TraesCS2D01G165600 chr2D 109792442 109794648 2206 False 4076.0 4076 100.0000 1 2207 1 chr2D.!!$F2 2206
1 TraesCS2D01G165600 chr2D 353584857 353585708 851 True 819.0 819 84.0380 1357 2207 1 chr2D.!!$R1 850
2 TraesCS2D01G165600 chr2D 109901083 109902436 1353 False 593.5 645 87.7335 156 1347 2 chr2D.!!$F3 1191
3 TraesCS2D01G165600 chr2B 441922723 441923574 851 False 1014.0 1014 88.1730 1356 2207 1 chr2B.!!$F3 851
4 TraesCS2D01G165600 chr2B 258696013 258696696 683 False 760.0 760 86.7540 1356 2039 1 chr2B.!!$F2 683
5 TraesCS2D01G165600 chr2B 329009665 329010517 852 True 612.0 612 79.8130 1358 2205 1 chr2B.!!$R2 847
6 TraesCS2D01G165600 chr2B 159318061 159319492 1431 False 502.0 512 85.4945 177 1347 2 chr2B.!!$F6 1170
7 TraesCS2D01G165600 chr2B 88188591 88189420 829 True 455.0 455 76.8410 1356 2187 1 chr2B.!!$R1 831
8 TraesCS2D01G165600 chr7B 74388131 74388683 552 True 682.0 682 88.9890 1355 1906 1 chr7B.!!$R1 551
9 TraesCS2D01G165600 chr3B 591363005 591363623 618 False 649.0 649 85.6450 1365 1982 1 chr3B.!!$F2 617
10 TraesCS2D01G165600 chr6B 207809717 207810553 836 True 623.0 623 80.2340 1356 2207 1 chr6B.!!$R1 851
11 TraesCS2D01G165600 chr2A 105540359 105541681 1322 False 547.5 590 85.5650 171 1347 2 chr2A.!!$F3 1176
12 TraesCS2D01G165600 chr2A 105531049 105532163 1114 False 363.5 440 86.6905 377 1306 2 chr2A.!!$F2 929
13 TraesCS2D01G165600 chr2A 105522175 105523143 968 False 278.5 364 85.6905 470 1291 2 chr2A.!!$F1 821
14 TraesCS2D01G165600 chr3D 540906720 540907356 636 False 411.0 411 78.4160 1357 1998 1 chr3D.!!$F1 641

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
119 120 0.178947 AGAGATAGGAGGGGGAAGCG 60.179 60.0 0.0 0.0 0.0 4.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1978 2353 0.107214 CCCTTTTGGCGCCTCATCTA 60.107 55.0 29.7 1.94 38.58 1.98 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
64 65 4.554036 GCGGACTGCCCCAGGATC 62.554 72.222 0.00 0.00 37.76 3.36
65 66 2.765807 CGGACTGCCCCAGGATCT 60.766 66.667 0.00 0.00 35.51 2.75
66 67 2.914289 GGACTGCCCCAGGATCTG 59.086 66.667 0.00 0.00 35.51 2.90
74 75 4.864334 CCAGGATCTGGTGGCCGC 62.864 72.222 8.12 8.12 45.82 6.53
75 76 4.864334 CAGGATCTGGTGGCCGCC 62.864 72.222 29.34 29.34 0.00 6.13
112 113 2.346597 GGCACGAGAGATAGGAGGG 58.653 63.158 0.00 0.00 0.00 4.30
113 114 1.182385 GGCACGAGAGATAGGAGGGG 61.182 65.000 0.00 0.00 0.00 4.79
114 115 1.182385 GCACGAGAGATAGGAGGGGG 61.182 65.000 0.00 0.00 0.00 5.40
115 116 0.478942 CACGAGAGATAGGAGGGGGA 59.521 60.000 0.00 0.00 0.00 4.81
116 117 1.133450 CACGAGAGATAGGAGGGGGAA 60.133 57.143 0.00 0.00 0.00 3.97
117 118 1.146152 ACGAGAGATAGGAGGGGGAAG 59.854 57.143 0.00 0.00 0.00 3.46
118 119 1.639722 GAGAGATAGGAGGGGGAAGC 58.360 60.000 0.00 0.00 0.00 3.86
119 120 0.178947 AGAGATAGGAGGGGGAAGCG 60.179 60.000 0.00 0.00 0.00 4.68
120 121 0.178958 GAGATAGGAGGGGGAAGCGA 60.179 60.000 0.00 0.00 0.00 4.93
121 122 0.178947 AGATAGGAGGGGGAAGCGAG 60.179 60.000 0.00 0.00 0.00 5.03
122 123 1.822114 GATAGGAGGGGGAAGCGAGC 61.822 65.000 0.00 0.00 0.00 5.03
123 124 2.605535 ATAGGAGGGGGAAGCGAGCA 62.606 60.000 0.00 0.00 0.00 4.26
124 125 2.605535 TAGGAGGGGGAAGCGAGCAT 62.606 60.000 0.00 0.00 0.00 3.79
125 126 2.110006 GAGGGGGAAGCGAGCATC 59.890 66.667 0.00 0.00 0.00 3.91
126 127 2.366167 AGGGGGAAGCGAGCATCT 60.366 61.111 0.00 0.00 0.00 2.90
127 128 2.203126 GGGGGAAGCGAGCATCTG 60.203 66.667 0.00 0.00 0.00 2.90
128 129 2.586792 GGGGAAGCGAGCATCTGT 59.413 61.111 0.00 0.00 0.00 3.41
129 130 1.817099 GGGGAAGCGAGCATCTGTG 60.817 63.158 0.00 0.00 0.00 3.66
138 139 2.180017 GCATCTGTGCCGGCTTTG 59.820 61.111 29.70 17.61 45.76 2.77
139 140 2.334946 GCATCTGTGCCGGCTTTGA 61.335 57.895 29.70 21.50 45.76 2.69
140 141 1.798735 CATCTGTGCCGGCTTTGAG 59.201 57.895 29.70 17.11 0.00 3.02
141 142 0.674581 CATCTGTGCCGGCTTTGAGA 60.675 55.000 29.70 21.62 0.00 3.27
142 143 0.392193 ATCTGTGCCGGCTTTGAGAG 60.392 55.000 29.70 15.27 0.00 3.20
143 144 1.302033 CTGTGCCGGCTTTGAGAGT 60.302 57.895 29.70 0.00 0.00 3.24
144 145 0.886490 CTGTGCCGGCTTTGAGAGTT 60.886 55.000 29.70 0.00 0.00 3.01
145 146 0.465460 TGTGCCGGCTTTGAGAGTTT 60.465 50.000 29.70 0.00 0.00 2.66
146 147 0.238553 GTGCCGGCTTTGAGAGTTTC 59.761 55.000 29.70 0.00 0.00 2.78
147 148 1.227999 TGCCGGCTTTGAGAGTTTCG 61.228 55.000 29.70 0.00 0.00 3.46
148 149 1.228657 GCCGGCTTTGAGAGTTTCGT 61.229 55.000 22.15 0.00 0.00 3.85
149 150 1.226746 CCGGCTTTGAGAGTTTCGTT 58.773 50.000 0.00 0.00 0.00 3.85
150 151 1.069906 CCGGCTTTGAGAGTTTCGTTG 60.070 52.381 0.00 0.00 0.00 4.10
151 152 1.597663 CGGCTTTGAGAGTTTCGTTGT 59.402 47.619 0.00 0.00 0.00 3.32
152 153 2.599848 CGGCTTTGAGAGTTTCGTTGTG 60.600 50.000 0.00 0.00 0.00 3.33
153 154 2.376032 GCTTTGAGAGTTTCGTTGTGC 58.624 47.619 0.00 0.00 0.00 4.57
154 155 2.854805 GCTTTGAGAGTTTCGTTGTGCC 60.855 50.000 0.00 0.00 0.00 5.01
260 261 4.508124 CCATCACGATCTAAACCAACTAGC 59.492 45.833 0.00 0.00 0.00 3.42
265 266 6.147164 TCACGATCTAAACCAACTAGCTTTTG 59.853 38.462 0.00 0.00 0.00 2.44
277 278 6.262273 CCAACTAGCTTTTGAACTCCTAAACA 59.738 38.462 8.89 0.00 0.00 2.83
284 285 7.502561 AGCTTTTGAACTCCTAAACATAACAGT 59.497 33.333 0.00 0.00 0.00 3.55
287 288 7.962964 TTGAACTCCTAAACATAACAGTCAG 57.037 36.000 0.00 0.00 0.00 3.51
396 423 6.654161 AGACATGTTCTCTTTTTCTCCTCATG 59.346 38.462 0.00 0.00 36.99 3.07
549 584 1.341209 GGGGCCTGAAAAGTTGACAAG 59.659 52.381 0.84 0.00 0.00 3.16
559 594 4.574599 AAAGTTGACAAGAGCAACATCC 57.425 40.909 0.00 0.00 46.05 3.51
591 628 1.285641 GAATGTGTGGTTGCCGTGG 59.714 57.895 0.00 0.00 0.00 4.94
604 641 3.659092 CGTGGGAAGCTTGCGCAA 61.659 61.111 23.48 23.48 39.10 4.85
615 652 1.145162 CTTGCGCAAACACGGCTTTT 61.145 50.000 25.01 0.00 0.00 2.27
621 658 2.599082 CGCAAACACGGCTTTTAAACAA 59.401 40.909 0.00 0.00 0.00 2.83
622 659 3.244111 CGCAAACACGGCTTTTAAACAAT 59.756 39.130 0.00 0.00 0.00 2.71
624 661 5.564768 GCAAACACGGCTTTTAAACAATTT 58.435 33.333 0.00 0.00 0.00 1.82
625 662 6.508088 CGCAAACACGGCTTTTAAACAATTTA 60.508 34.615 0.00 0.00 0.00 1.40
655 726 8.492673 TGTTTAGCATTGCCTATATATACTGC 57.507 34.615 4.70 3.54 0.00 4.40
656 727 8.100164 TGTTTAGCATTGCCTATATATACTGCA 58.900 33.333 4.70 7.72 0.00 4.41
657 728 8.946085 GTTTAGCATTGCCTATATATACTGCAA 58.054 33.333 19.60 19.60 44.96 4.08
662 733 9.330063 GCATTGCCTATATATACTGCAAAGATA 57.670 33.333 20.53 6.31 44.17 1.98
679 773 2.945668 AGATATTCGGAAAGCAAGCCAC 59.054 45.455 0.00 0.00 0.00 5.01
680 774 1.459450 TATTCGGAAAGCAAGCCACC 58.541 50.000 0.00 0.00 0.00 4.61
762 867 8.597167 TCTTTCTTGAGAAGATCCTTGTCATTA 58.403 33.333 7.26 0.00 37.38 1.90
830 983 1.478510 CTGTACTCACGGGCATCTCTT 59.521 52.381 0.00 0.00 0.00 2.85
847 1000 7.428562 CATCTCTTGCAAAATGATCGTAAAC 57.571 36.000 0.00 0.00 0.00 2.01
848 1001 5.938322 TCTCTTGCAAAATGATCGTAAACC 58.062 37.500 0.00 0.00 0.00 3.27
849 1002 5.471797 TCTCTTGCAAAATGATCGTAAACCA 59.528 36.000 0.00 0.00 0.00 3.67
923 1258 5.298989 TGTTCCAAAAGTTGAGCCTAGTA 57.701 39.130 0.00 0.00 0.00 1.82
928 1263 7.448748 TCCAAAAGTTGAGCCTAGTAAATTC 57.551 36.000 0.00 0.00 0.00 2.17
929 1264 7.001674 TCCAAAAGTTGAGCCTAGTAAATTCA 58.998 34.615 0.00 0.00 0.00 2.57
930 1265 7.040686 TCCAAAAGTTGAGCCTAGTAAATTCAC 60.041 37.037 0.00 0.00 0.00 3.18
956 1305 0.895100 TTTGGCTGATGCTGACCACC 60.895 55.000 0.00 0.00 39.59 4.61
967 1318 1.470098 GCTGACCACCAAGCACTATTG 59.530 52.381 0.00 0.00 0.00 1.90
1109 1466 1.376037 GGCCGGACCTCAAAGTCAG 60.376 63.158 5.05 0.00 38.59 3.51
1110 1467 1.671742 GCCGGACCTCAAAGTCAGA 59.328 57.895 5.05 0.00 38.59 3.27
1140 1497 3.924686 CGGTAGGAAGTATTGTGACACAC 59.075 47.826 8.05 0.00 34.56 3.82
1145 1502 3.302555 GAAGTATTGTGACACACGACGA 58.697 45.455 8.05 0.00 37.14 4.20
1146 1503 3.358707 AGTATTGTGACACACGACGAA 57.641 42.857 8.05 0.00 37.14 3.85
1164 1521 0.601841 AAGATTTGAACCGCGTCCGT 60.602 50.000 4.92 0.00 0.00 4.69
1178 1535 1.605451 TCCGTGTCTGGGTCGACAT 60.605 57.895 18.91 0.00 44.84 3.06
1275 1635 0.828022 ATCGTCCAGTTAATCGGCCA 59.172 50.000 2.24 0.00 0.00 5.36
1280 1640 3.813166 CGTCCAGTTAATCGGCCAAATAT 59.187 43.478 2.24 0.00 0.00 1.28
1333 1695 1.030488 TGTGGGTGTTTCGCGGAAAA 61.030 50.000 0.00 0.00 33.14 2.29
1334 1696 0.312729 GTGGGTGTTTCGCGGAAAAT 59.687 50.000 0.00 0.00 33.14 1.82
1335 1697 0.312416 TGGGTGTTTCGCGGAAAATG 59.688 50.000 0.00 0.00 33.14 2.32
1336 1698 0.312729 GGGTGTTTCGCGGAAAATGT 59.687 50.000 0.00 0.00 33.14 2.71
1337 1699 1.536331 GGGTGTTTCGCGGAAAATGTA 59.464 47.619 0.00 0.00 33.14 2.29
1338 1700 2.162809 GGGTGTTTCGCGGAAAATGTAT 59.837 45.455 0.00 0.00 33.14 2.29
1339 1701 3.168193 GGTGTTTCGCGGAAAATGTATG 58.832 45.455 0.00 0.00 33.14 2.39
1340 1702 3.168193 GTGTTTCGCGGAAAATGTATGG 58.832 45.455 0.00 0.00 33.14 2.74
1341 1703 3.075148 TGTTTCGCGGAAAATGTATGGA 58.925 40.909 0.00 0.00 33.14 3.41
1342 1704 3.692101 TGTTTCGCGGAAAATGTATGGAT 59.308 39.130 0.00 0.00 33.14 3.41
1343 1705 3.961477 TTCGCGGAAAATGTATGGATG 57.039 42.857 6.13 0.00 0.00 3.51
1344 1706 2.912771 TCGCGGAAAATGTATGGATGT 58.087 42.857 6.13 0.00 0.00 3.06
1345 1707 2.611751 TCGCGGAAAATGTATGGATGTG 59.388 45.455 6.13 0.00 0.00 3.21
1346 1708 2.354510 CGCGGAAAATGTATGGATGTGT 59.645 45.455 0.00 0.00 0.00 3.72
1347 1709 3.181501 CGCGGAAAATGTATGGATGTGTT 60.182 43.478 0.00 0.00 0.00 3.32
1348 1710 4.034626 CGCGGAAAATGTATGGATGTGTTA 59.965 41.667 0.00 0.00 0.00 2.41
1349 1711 5.277779 CGCGGAAAATGTATGGATGTGTTAT 60.278 40.000 0.00 0.00 0.00 1.89
1350 1712 5.914635 GCGGAAAATGTATGGATGTGTTATG 59.085 40.000 0.00 0.00 0.00 1.90
1351 1713 6.459573 GCGGAAAATGTATGGATGTGTTATGT 60.460 38.462 0.00 0.00 0.00 2.29
1352 1714 7.254966 GCGGAAAATGTATGGATGTGTTATGTA 60.255 37.037 0.00 0.00 0.00 2.29
1353 1715 8.616942 CGGAAAATGTATGGATGTGTTATGTAA 58.383 33.333 0.00 0.00 0.00 2.41
1397 1759 6.188400 TGTTGCGTATCTTTGCATTGATAA 57.812 33.333 9.74 0.00 41.42 1.75
1480 1850 1.028868 GCAAGTGAGCATGGGAGGAC 61.029 60.000 0.00 0.00 0.00 3.85
1543 1913 8.833717 GGATAACTAGTCCTAAGCCTTTGGCTA 61.834 44.444 11.80 4.89 44.52 3.93
1617 1987 2.625737 CTCGATGGCTGAATGTTGTCT 58.374 47.619 0.00 0.00 0.00 3.41
1658 2029 0.181587 TTCCACAAAGACCAGGCGAA 59.818 50.000 0.00 0.00 0.00 4.70
1744 2115 0.741221 CCAGGCGTAGAAGCTTGTCC 60.741 60.000 2.10 0.00 41.83 4.02
1934 2309 4.101448 GCAGCGGTCCATGGAGGT 62.101 66.667 16.81 7.35 39.02 3.85
1954 2329 1.902938 AAGCCAGAGGAAGAACTTGC 58.097 50.000 0.00 0.00 0.00 4.01
2018 2393 2.343163 GACCCTGTCGATCTGGCGAG 62.343 65.000 0.00 0.00 41.49 5.03
2061 2437 3.826236 GCAGTATAGATGCCATTGCTG 57.174 47.619 0.00 0.00 37.73 4.41
2082 2458 5.570844 GCTGGTCCACTTCCAAGTTATCTTA 60.571 44.000 0.00 0.00 37.08 2.10
2094 2470 3.303049 AGTTATCTTATCGGGGTCGGTT 58.697 45.455 0.00 0.00 36.95 4.44
2109 2485 3.640000 GTTGTCAGCTGCACGCGT 61.640 61.111 5.58 5.58 45.59 6.01
2140 2517 3.181524 CGCCAAAGTTCGACGTATTCAAT 60.182 43.478 0.00 0.00 0.00 2.57
2150 2528 1.134640 ACGTATTCAATAGTGGCGGCA 60.135 47.619 7.97 7.97 0.00 5.69
2153 2531 0.546122 ATTCAATAGTGGCGGCAGGA 59.454 50.000 13.91 2.93 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 4.554036 GATCCTGGGGCAGTCCGC 62.554 72.222 0.00 0.00 44.87 5.54
48 49 2.765807 AGATCCTGGGGCAGTCCG 60.766 66.667 0.00 0.00 36.01 4.79
49 50 2.914289 CAGATCCTGGGGCAGTCC 59.086 66.667 0.00 0.00 0.00 3.85
58 59 4.864334 GGCGGCCACCAGATCCTG 62.864 72.222 15.62 0.00 0.00 3.86
89 90 1.007964 CTATCTCTCGTGCCGCTGG 60.008 63.158 0.00 0.00 0.00 4.85
90 91 1.007964 CCTATCTCTCGTGCCGCTG 60.008 63.158 0.00 0.00 0.00 5.18
91 92 1.152943 TCCTATCTCTCGTGCCGCT 60.153 57.895 0.00 0.00 0.00 5.52
92 93 1.284408 CTCCTATCTCTCGTGCCGC 59.716 63.158 0.00 0.00 0.00 6.53
93 94 1.519751 CCCTCCTATCTCTCGTGCCG 61.520 65.000 0.00 0.00 0.00 5.69
94 95 1.182385 CCCCTCCTATCTCTCGTGCC 61.182 65.000 0.00 0.00 0.00 5.01
95 96 1.182385 CCCCCTCCTATCTCTCGTGC 61.182 65.000 0.00 0.00 0.00 5.34
96 97 0.478942 TCCCCCTCCTATCTCTCGTG 59.521 60.000 0.00 0.00 0.00 4.35
97 98 1.146152 CTTCCCCCTCCTATCTCTCGT 59.854 57.143 0.00 0.00 0.00 4.18
98 99 1.917872 CTTCCCCCTCCTATCTCTCG 58.082 60.000 0.00 0.00 0.00 4.04
99 100 1.639722 GCTTCCCCCTCCTATCTCTC 58.360 60.000 0.00 0.00 0.00 3.20
100 101 0.178947 CGCTTCCCCCTCCTATCTCT 60.179 60.000 0.00 0.00 0.00 3.10
101 102 0.178958 TCGCTTCCCCCTCCTATCTC 60.179 60.000 0.00 0.00 0.00 2.75
102 103 0.178947 CTCGCTTCCCCCTCCTATCT 60.179 60.000 0.00 0.00 0.00 1.98
103 104 1.822114 GCTCGCTTCCCCCTCCTATC 61.822 65.000 0.00 0.00 0.00 2.08
104 105 1.839296 GCTCGCTTCCCCCTCCTAT 60.839 63.158 0.00 0.00 0.00 2.57
105 106 2.444140 GCTCGCTTCCCCCTCCTA 60.444 66.667 0.00 0.00 0.00 2.94
106 107 4.722535 TGCTCGCTTCCCCCTCCT 62.723 66.667 0.00 0.00 0.00 3.69
107 108 3.468326 GATGCTCGCTTCCCCCTCC 62.468 68.421 0.00 0.00 0.00 4.30
108 109 2.110006 GATGCTCGCTTCCCCCTC 59.890 66.667 0.00 0.00 0.00 4.30
109 110 2.366167 AGATGCTCGCTTCCCCCT 60.366 61.111 1.68 0.00 0.00 4.79
110 111 2.203126 CAGATGCTCGCTTCCCCC 60.203 66.667 1.68 0.00 0.00 5.40
111 112 1.817099 CACAGATGCTCGCTTCCCC 60.817 63.158 1.68 0.00 0.00 4.81
112 113 3.805267 CACAGATGCTCGCTTCCC 58.195 61.111 1.68 0.00 0.00 3.97
122 123 0.674581 TCTCAAAGCCGGCACAGATG 60.675 55.000 31.54 18.75 0.00 2.90
123 124 0.392193 CTCTCAAAGCCGGCACAGAT 60.392 55.000 31.54 3.61 0.00 2.90
124 125 1.004560 CTCTCAAAGCCGGCACAGA 60.005 57.895 31.54 20.97 0.00 3.41
125 126 0.886490 AACTCTCAAAGCCGGCACAG 60.886 55.000 31.54 17.80 0.00 3.66
126 127 0.465460 AAACTCTCAAAGCCGGCACA 60.465 50.000 31.54 7.91 0.00 4.57
127 128 0.238553 GAAACTCTCAAAGCCGGCAC 59.761 55.000 31.54 0.00 0.00 5.01
128 129 1.227999 CGAAACTCTCAAAGCCGGCA 61.228 55.000 31.54 6.61 0.00 5.69
129 130 1.228657 ACGAAACTCTCAAAGCCGGC 61.229 55.000 21.89 21.89 0.00 6.13
130 131 1.069906 CAACGAAACTCTCAAAGCCGG 60.070 52.381 0.00 0.00 0.00 6.13
131 132 1.597663 ACAACGAAACTCTCAAAGCCG 59.402 47.619 0.00 0.00 0.00 5.52
132 133 2.854805 GCACAACGAAACTCTCAAAGCC 60.855 50.000 0.00 0.00 0.00 4.35
133 134 2.376032 GCACAACGAAACTCTCAAAGC 58.624 47.619 0.00 0.00 0.00 3.51
134 135 2.599848 CGGCACAACGAAACTCTCAAAG 60.600 50.000 0.00 0.00 35.47 2.77
135 136 1.329292 CGGCACAACGAAACTCTCAAA 59.671 47.619 0.00 0.00 35.47 2.69
136 137 0.934496 CGGCACAACGAAACTCTCAA 59.066 50.000 0.00 0.00 35.47 3.02
137 138 0.878523 CCGGCACAACGAAACTCTCA 60.879 55.000 0.00 0.00 35.47 3.27
138 139 1.860078 CCGGCACAACGAAACTCTC 59.140 57.895 0.00 0.00 35.47 3.20
139 140 2.251642 GCCGGCACAACGAAACTCT 61.252 57.895 24.80 0.00 35.47 3.24
140 141 2.251371 GCCGGCACAACGAAACTC 59.749 61.111 24.80 0.00 35.47 3.01
141 142 2.203153 AGCCGGCACAACGAAACT 60.203 55.556 31.54 0.00 35.47 2.66
142 143 2.051345 CAGCCGGCACAACGAAAC 60.051 61.111 31.54 0.00 35.47 2.78
143 144 3.283684 CCAGCCGGCACAACGAAA 61.284 61.111 31.54 0.00 35.47 3.46
144 145 4.555709 ACCAGCCGGCACAACGAA 62.556 61.111 31.54 0.00 34.57 3.85
153 154 2.809861 ATCACTTCTGCACCAGCCGG 62.810 60.000 0.00 0.00 41.13 6.13
154 155 1.376424 ATCACTTCTGCACCAGCCG 60.376 57.895 0.00 0.00 41.13 5.52
260 261 8.836413 TGACTGTTATGTTTAGGAGTTCAAAAG 58.164 33.333 0.00 0.00 0.00 2.27
265 266 6.698380 TCCTGACTGTTATGTTTAGGAGTTC 58.302 40.000 0.00 0.00 33.12 3.01
318 319 3.186909 CGTGAATTATCGAGGAGTGCAA 58.813 45.455 0.00 0.00 0.00 4.08
372 395 6.622462 GCATGAGGAGAAAAAGAGAACATGTC 60.622 42.308 0.00 0.00 36.19 3.06
396 423 2.368439 TGCAATGACTAAGTGATGGGC 58.632 47.619 0.00 0.00 0.00 5.36
528 563 0.260230 TGTCAACTTTTCAGGCCCCA 59.740 50.000 0.00 0.00 0.00 4.96
549 584 0.099436 GCATGTTCGGGATGTTGCTC 59.901 55.000 0.00 0.00 0.00 4.26
559 594 0.516877 ACATTCACGTGCATGTTCGG 59.483 50.000 25.11 4.62 27.64 4.30
631 668 8.492673 TGCAGTATATATAGGCAATGCTAAAC 57.507 34.615 13.82 0.00 33.68 2.01
648 719 6.989759 TGCTTTCCGAATATCTTTGCAGTATA 59.010 34.615 0.00 0.00 0.00 1.47
653 724 4.675146 GCTTGCTTTCCGAATATCTTTGCA 60.675 41.667 0.00 0.00 0.00 4.08
655 726 4.142403 TGGCTTGCTTTCCGAATATCTTTG 60.142 41.667 0.00 0.00 0.00 2.77
656 727 4.016444 TGGCTTGCTTTCCGAATATCTTT 58.984 39.130 0.00 0.00 0.00 2.52
657 728 3.378427 GTGGCTTGCTTTCCGAATATCTT 59.622 43.478 0.00 0.00 0.00 2.40
662 733 1.586154 CGGTGGCTTGCTTTCCGAAT 61.586 55.000 14.13 0.00 43.22 3.34
663 734 2.258013 CGGTGGCTTGCTTTCCGAA 61.258 57.895 14.13 0.00 43.22 4.30
664 735 2.668212 CGGTGGCTTGCTTTCCGA 60.668 61.111 14.13 0.00 43.22 4.55
665 736 4.404654 GCGGTGGCTTGCTTTCCG 62.405 66.667 14.66 14.66 43.37 4.30
679 773 3.616821 TGTGATTTGATCGTTTCTAGCGG 59.383 43.478 0.00 0.00 0.00 5.52
680 774 4.840401 TGTGATTTGATCGTTTCTAGCG 57.160 40.909 0.00 0.00 0.00 4.26
787 893 9.295825 ACAGGTGACAAATTTCATAGACAAATA 57.704 29.630 0.00 0.00 0.00 1.40
808 961 0.614979 AGATGCCCGTGAGTACAGGT 60.615 55.000 0.00 0.00 0.00 4.00
811 964 1.204704 CAAGAGATGCCCGTGAGTACA 59.795 52.381 0.00 0.00 0.00 2.90
830 983 7.151999 ACTATTGGTTTACGATCATTTTGCA 57.848 32.000 0.00 0.00 0.00 4.08
890 1136 9.702726 CTCAACTTTTGGAACATGTAATATACG 57.297 33.333 0.00 0.00 39.30 3.06
893 1139 7.397192 AGGCTCAACTTTTGGAACATGTAATAT 59.603 33.333 0.00 0.00 39.30 1.28
895 1141 5.539955 AGGCTCAACTTTTGGAACATGTAAT 59.460 36.000 0.00 0.00 39.30 1.89
903 1149 7.504238 TGAATTTACTAGGCTCAACTTTTGGAA 59.496 33.333 0.00 0.00 0.00 3.53
923 1258 6.128117 GCATCAGCCAAATGAATTGTGAATTT 60.128 34.615 0.00 0.00 37.32 1.82
928 1263 3.616821 CAGCATCAGCCAAATGAATTGTG 59.383 43.478 0.00 0.00 43.56 3.33
929 1264 3.512329 TCAGCATCAGCCAAATGAATTGT 59.488 39.130 0.00 0.00 43.56 2.71
930 1265 3.863424 GTCAGCATCAGCCAAATGAATTG 59.137 43.478 0.00 0.00 43.56 2.32
1109 1466 4.684484 ATACTTCCTACCGGGACAATTC 57.316 45.455 6.32 0.00 45.03 2.17
1110 1467 4.226620 ACAATACTTCCTACCGGGACAATT 59.773 41.667 6.32 0.00 45.03 2.32
1140 1497 0.246757 CGCGGTTCAAATCTTCGTCG 60.247 55.000 0.00 0.00 0.00 5.12
1145 1502 0.601841 ACGGACGCGGTTCAAATCTT 60.602 50.000 12.47 0.00 0.00 2.40
1146 1503 1.005394 ACGGACGCGGTTCAAATCT 60.005 52.632 12.47 0.00 0.00 2.40
1214 1571 7.078228 GCTTTTATTCCAGTCGGCTAATTATG 58.922 38.462 0.00 0.00 0.00 1.90
1215 1572 6.206829 GGCTTTTATTCCAGTCGGCTAATTAT 59.793 38.462 0.00 0.00 0.00 1.28
1225 1582 2.760092 TGCATGGGCTTTTATTCCAGTC 59.240 45.455 0.00 0.00 41.91 3.51
1280 1640 9.679661 TTTTCTTCAGAATGTACCATGCTTATA 57.320 29.630 0.00 0.00 37.40 0.98
1312 1674 1.716826 TTCCGCGAAACACCCACAAC 61.717 55.000 8.23 0.00 0.00 3.32
1317 1679 0.312729 ACATTTTCCGCGAAACACCC 59.687 50.000 8.23 0.00 30.83 4.61
1397 1759 4.887655 CCCACTGTAACTCCTTTTTCAACT 59.112 41.667 0.00 0.00 0.00 3.16
1452 1819 1.004918 GCTCACTTGCACCCTACGT 60.005 57.895 0.00 0.00 0.00 3.57
1480 1850 1.805945 GTACCGAGGCTGAGCAACG 60.806 63.158 6.82 11.06 0.00 4.10
1658 2029 1.005215 CAAACTCCCTCATTGCCCTCT 59.995 52.381 0.00 0.00 0.00 3.69
1744 2115 2.594303 TTCACAGCCAACCGCCTG 60.594 61.111 0.00 0.00 38.78 4.85
1756 2127 1.598962 GCAGACTGCCAGCTTCACA 60.599 57.895 17.01 0.00 37.42 3.58
1775 2146 3.359033 TGGCATGAAATTCTCTCTTGGG 58.641 45.455 0.00 0.00 0.00 4.12
1934 2309 2.639839 AGCAAGTTCTTCCTCTGGCTTA 59.360 45.455 0.00 0.00 37.66 3.09
1954 2329 3.058160 CTGGGCTCCCGCAAACAG 61.058 66.667 0.00 0.00 39.42 3.16
1978 2353 0.107214 CCCTTTTGGCGCCTCATCTA 60.107 55.000 29.70 1.94 38.58 1.98
2001 2376 2.415010 CTCGCCAGATCGACAGGG 59.585 66.667 0.00 0.00 34.46 4.45
2061 2437 5.753921 CGATAAGATAACTTGGAAGTGGACC 59.246 44.000 0.00 0.00 39.66 4.46
2082 2458 2.978824 CTGACAACCGACCCCGAT 59.021 61.111 0.00 0.00 38.22 4.18
2094 2470 3.639008 CAACGCGTGCAGCTGACA 61.639 61.111 20.43 12.49 45.59 3.58
2109 2485 2.065906 GAACTTTGGCGGCGAACCAA 62.066 55.000 12.98 13.52 45.37 3.67
2150 2528 2.592993 CCACGACACCATGGGTCCT 61.593 63.158 18.09 7.74 31.02 3.85
2153 2531 1.416401 GATATCCACGACACCATGGGT 59.584 52.381 18.09 11.25 36.56 4.51


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

AutoCloner maintained by Alex Coulton.