Multiple sequence alignment - TraesCS4D01G208300

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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 TraesCS4D01G208300 chr4D 100.000 4609 0 0 1 4609 358714178 358718786 0.000000e+00 8512
1 TraesCS4D01G208300 chr4A 92.126 3480 134 52 1218 4604 106583151 106579719 0.000000e+00 4780
2 TraesCS4D01G208300 chr4A 95.285 509 12 5 691 1188 106583658 106583151 0.000000e+00 797
3 TraesCS4D01G208300 chr4B 93.031 3286 109 44 1218 4438 442586327 442589557 0.000000e+00 4689
4 TraesCS4D01G208300 chr4B 92.950 539 22 6 655 1188 442585800 442586327 0.000000e+00 771
5 TraesCS4D01G208300 chr4B 82.799 593 92 6 3 591 88158941 88159527 5.280000e-144 521
6 TraesCS4D01G208300 chr4B 96.450 169 6 0 4434 4602 442590581 442590749 3.510000e-71 279
7 TraesCS4D01G208300 chr2D 86.655 592 69 8 3 591 302781970 302782554 0.000000e+00 647
8 TraesCS4D01G208300 chr2D 81.218 591 104 5 3 591 262148392 262148977 1.940000e-128 470
9 TraesCS4D01G208300 chr2D 78.229 542 111 6 51 589 468847533 468848070 1.590000e-89 340
10 TraesCS4D01G208300 chr1A 79.865 591 117 2 2 591 478344304 478344893 9.160000e-117 431
11 TraesCS4D01G208300 chr2B 78.078 593 123 6 3 591 466009526 466008937 7.290000e-98 368
12 TraesCS4D01G208300 chr6D 77.654 537 108 11 58 589 289036438 289036967 2.680000e-82 316
13 TraesCS4D01G208300 chr5B 76.241 564 124 8 3 562 336323227 336322670 1.620000e-74 291
14 TraesCS4D01G208300 chr5D 80.495 323 60 3 271 591 70642806 70643127 1.280000e-60 244


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 TraesCS4D01G208300 chr4D 358714178 358718786 4608 False 8512.0 8512 100.000000 1 4609 1 chr4D.!!$F1 4608
1 TraesCS4D01G208300 chr4A 106579719 106583658 3939 True 2788.5 4780 93.705500 691 4604 2 chr4A.!!$R1 3913
2 TraesCS4D01G208300 chr4B 442585800 442590749 4949 False 1913.0 4689 94.143667 655 4602 3 chr4B.!!$F2 3947
3 TraesCS4D01G208300 chr4B 88158941 88159527 586 False 521.0 521 82.799000 3 591 1 chr4B.!!$F1 588
4 TraesCS4D01G208300 chr2D 302781970 302782554 584 False 647.0 647 86.655000 3 591 1 chr2D.!!$F2 588
5 TraesCS4D01G208300 chr2D 262148392 262148977 585 False 470.0 470 81.218000 3 591 1 chr2D.!!$F1 588
6 TraesCS4D01G208300 chr2D 468847533 468848070 537 False 340.0 340 78.229000 51 589 1 chr2D.!!$F3 538
7 TraesCS4D01G208300 chr1A 478344304 478344893 589 False 431.0 431 79.865000 2 591 1 chr1A.!!$F1 589
8 TraesCS4D01G208300 chr2B 466008937 466009526 589 True 368.0 368 78.078000 3 591 1 chr2B.!!$R1 588
9 TraesCS4D01G208300 chr6D 289036438 289036967 529 False 316.0 316 77.654000 58 589 1 chr6D.!!$F1 531
10 TraesCS4D01G208300 chr5B 336322670 336323227 557 True 291.0 291 76.241000 3 562 1 chr5B.!!$R1 559

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
594 600 0.171903 CAGCGCCTTCCCAAGAAATG 59.828 55.0 2.29 0.0 0.0 2.32 F
1190 1210 0.035739 GGCCACCTCCAAGTACGAAA 59.964 55.0 0.00 0.0 0.0 3.46 F
1290 1311 0.179100 ATCTCCGGTGTGCTGATTCG 60.179 55.0 0.00 0.0 0.0 3.34 F
1292 1313 1.078759 CTCCGGTGTGCTGATTCGTC 61.079 60.0 0.00 0.0 0.0 4.20 F
3140 3227 1.313772 CATCGACATCTCCCTCGTCT 58.686 55.0 0.00 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2267 2297 1.066908 ACGAACCAACACAATGGCTTG 59.933 47.619 0.0 0.0 44.75 4.01 R
3140 3227 0.669318 GAACAAGATCCGCACCGTCA 60.669 55.000 0.0 0.0 0.00 4.35 R
3399 3493 1.088340 TCCTCGTCCTCGTCATCGTC 61.088 60.000 0.0 0.0 38.33 4.20 R
3400 3494 1.078637 TCCTCGTCCTCGTCATCGT 60.079 57.895 0.0 0.0 38.33 3.73 R
4035 4147 0.039618 AGCACAATCGGACCCCAAAT 59.960 50.000 0.0 0.0 0.00 2.32 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
56 57 2.415010 CGCAGAGCATCCGTAGCT 59.585 61.111 0.00 0.00 46.82 3.32
107 108 1.906333 GGCAAAGAAGGCCGGGAAA 60.906 57.895 2.18 0.00 42.39 3.13
326 329 3.225235 GGCTTCTCGATGCCTCCT 58.775 61.111 14.53 0.00 45.21 3.69
327 330 1.227497 GGCTTCTCGATGCCTCCTG 60.227 63.158 14.53 0.00 45.21 3.86
332 335 1.175347 TCTCGATGCCTCCTGATCCG 61.175 60.000 0.00 0.00 0.00 4.18
382 386 4.400961 GCAGCTCCGCCACCTTCT 62.401 66.667 0.00 0.00 0.00 2.85
390 394 1.032114 CCGCCACCTTCTCCCAAATC 61.032 60.000 0.00 0.00 0.00 2.17
393 397 1.272704 GCCACCTTCTCCCAAATCCTT 60.273 52.381 0.00 0.00 0.00 3.36
394 398 2.728007 CCACCTTCTCCCAAATCCTTC 58.272 52.381 0.00 0.00 0.00 3.46
428 434 1.135915 GCCTTCATCTCTCTCTGCGAA 59.864 52.381 0.00 0.00 0.00 4.70
592 598 2.268076 GCAGCGCCTTCCCAAGAAA 61.268 57.895 2.29 0.00 0.00 2.52
593 599 1.598701 GCAGCGCCTTCCCAAGAAAT 61.599 55.000 2.29 0.00 0.00 2.17
594 600 0.171903 CAGCGCCTTCCCAAGAAATG 59.828 55.000 2.29 0.00 0.00 2.32
606 612 4.456280 CCAAGAAATGGTTTAGGCCTTC 57.544 45.455 12.58 0.00 44.85 3.46
607 613 4.089361 CCAAGAAATGGTTTAGGCCTTCT 58.911 43.478 12.58 0.97 44.85 2.85
608 614 5.261216 CCAAGAAATGGTTTAGGCCTTCTA 58.739 41.667 12.58 0.00 44.85 2.10
609 615 5.893824 CCAAGAAATGGTTTAGGCCTTCTAT 59.106 40.000 12.58 2.73 44.85 1.98
610 616 7.060421 CCAAGAAATGGTTTAGGCCTTCTATA 58.940 38.462 12.58 0.00 44.85 1.31
611 617 7.559897 CCAAGAAATGGTTTAGGCCTTCTATAA 59.440 37.037 12.58 0.00 44.85 0.98
612 618 8.624776 CAAGAAATGGTTTAGGCCTTCTATAAG 58.375 37.037 12.58 0.00 0.00 1.73
613 619 8.102484 AGAAATGGTTTAGGCCTTCTATAAGA 57.898 34.615 12.58 0.00 34.37 2.10
614 620 8.557450 AGAAATGGTTTAGGCCTTCTATAAGAA 58.443 33.333 12.58 0.00 34.37 2.52
615 621 9.185680 GAAATGGTTTAGGCCTTCTATAAGAAA 57.814 33.333 12.58 0.00 33.19 2.52
616 622 9.715119 AAATGGTTTAGGCCTTCTATAAGAAAT 57.285 29.630 12.58 0.00 33.19 2.17
625 631 9.920946 AGGCCTTCTATAAGAAATAAAATGACA 57.079 29.630 0.00 0.00 33.19 3.58
646 652 9.833917 ATGACATGCATATCAAATCCTATAGAG 57.166 33.333 12.45 0.00 34.82 2.43
647 653 9.039165 TGACATGCATATCAAATCCTATAGAGA 57.961 33.333 4.88 0.00 0.00 3.10
648 654 9.881649 GACATGCATATCAAATCCTATAGAGAA 57.118 33.333 0.00 0.00 0.00 2.87
653 659 9.598517 GCATATCAAATCCTATAGAGAAAGAGG 57.401 37.037 0.00 0.00 0.00 3.69
728 738 9.793259 CCTATAAATCAAACAAGGCCTTATCTA 57.207 33.333 20.00 0.00 0.00 1.98
1188 1208 2.642254 CGGCCACCTCCAAGTACGA 61.642 63.158 2.24 0.00 0.00 3.43
1189 1209 1.675219 GGCCACCTCCAAGTACGAA 59.325 57.895 0.00 0.00 0.00 3.85
1190 1210 0.035739 GGCCACCTCCAAGTACGAAA 59.964 55.000 0.00 0.00 0.00 3.46
1191 1211 1.439679 GCCACCTCCAAGTACGAAAG 58.560 55.000 0.00 0.00 0.00 2.62
1192 1212 1.439679 CCACCTCCAAGTACGAAAGC 58.560 55.000 0.00 0.00 0.00 3.51
1193 1213 1.270625 CCACCTCCAAGTACGAAAGCA 60.271 52.381 0.00 0.00 0.00 3.91
1194 1214 2.069273 CACCTCCAAGTACGAAAGCAG 58.931 52.381 0.00 0.00 0.00 4.24
1195 1215 1.968493 ACCTCCAAGTACGAAAGCAGA 59.032 47.619 0.00 0.00 0.00 4.26
1196 1216 2.367567 ACCTCCAAGTACGAAAGCAGAA 59.632 45.455 0.00 0.00 0.00 3.02
1197 1217 3.181458 ACCTCCAAGTACGAAAGCAGAAA 60.181 43.478 0.00 0.00 0.00 2.52
1198 1218 3.186613 CCTCCAAGTACGAAAGCAGAAAC 59.813 47.826 0.00 0.00 0.00 2.78
1199 1219 3.135994 TCCAAGTACGAAAGCAGAAACC 58.864 45.455 0.00 0.00 0.00 3.27
1200 1220 2.875933 CCAAGTACGAAAGCAGAAACCA 59.124 45.455 0.00 0.00 0.00 3.67
1201 1221 3.314080 CCAAGTACGAAAGCAGAAACCAA 59.686 43.478 0.00 0.00 0.00 3.67
1202 1222 4.023193 CCAAGTACGAAAGCAGAAACCAAT 60.023 41.667 0.00 0.00 0.00 3.16
1203 1223 5.147162 CAAGTACGAAAGCAGAAACCAATC 58.853 41.667 0.00 0.00 0.00 2.67
1204 1224 4.642429 AGTACGAAAGCAGAAACCAATCT 58.358 39.130 0.00 0.00 0.00 2.40
1206 1226 2.554032 ACGAAAGCAGAAACCAATCTGG 59.446 45.455 6.46 0.00 45.60 3.86
1207 1227 2.669391 CGAAAGCAGAAACCAATCTGGC 60.669 50.000 6.46 0.00 45.60 4.85
1208 1228 1.999648 AAGCAGAAACCAATCTGGCA 58.000 45.000 6.46 0.00 45.60 4.92
1209 1229 1.251251 AGCAGAAACCAATCTGGCAC 58.749 50.000 6.46 0.00 45.60 5.01
1210 1230 0.244721 GCAGAAACCAATCTGGCACC 59.755 55.000 6.46 0.00 45.60 5.01
1211 1231 1.915141 CAGAAACCAATCTGGCACCT 58.085 50.000 0.00 0.00 42.67 4.00
1212 1232 2.242043 CAGAAACCAATCTGGCACCTT 58.758 47.619 0.00 0.00 42.67 3.50
1213 1233 2.029649 CAGAAACCAATCTGGCACCTTG 60.030 50.000 0.00 0.00 42.67 3.61
1214 1234 0.681175 AAACCAATCTGGCACCTTGC 59.319 50.000 0.00 0.00 42.67 4.01
1215 1235 1.526575 AACCAATCTGGCACCTTGCG 61.527 55.000 0.00 0.00 46.21 4.85
1216 1236 1.973281 CCAATCTGGCACCTTGCGT 60.973 57.895 0.00 0.00 46.21 5.24
1217 1237 1.210931 CAATCTGGCACCTTGCGTG 59.789 57.895 0.00 0.00 46.21 5.34
1252 1272 3.319198 GTGCTCCTCCCCGTCCAA 61.319 66.667 0.00 0.00 0.00 3.53
1258 1278 1.192146 TCCTCCCCGTCCAACTTCTG 61.192 60.000 0.00 0.00 0.00 3.02
1266 1286 1.774217 TCCAACTTCTGGCCACCCT 60.774 57.895 0.00 0.00 45.98 4.34
1267 1287 0.474854 TCCAACTTCTGGCCACCCTA 60.475 55.000 0.00 0.00 45.98 3.53
1290 1311 0.179100 ATCTCCGGTGTGCTGATTCG 60.179 55.000 0.00 0.00 0.00 3.34
1292 1313 1.078759 CTCCGGTGTGCTGATTCGTC 61.079 60.000 0.00 0.00 0.00 4.20
1309 1330 1.531149 CGTCTGTTTGCTTAGGTGGTG 59.469 52.381 0.00 0.00 0.00 4.17
1367 1388 2.123897 ACCGCCACAAGCAGGTTT 60.124 55.556 0.00 0.00 43.05 3.27
1382 1403 2.597217 TTTGCCACGCTTCCCCTG 60.597 61.111 0.00 0.00 0.00 4.45
1592 1616 1.396996 CCTAATGGCGTTTTCCGTCTG 59.603 52.381 0.00 0.00 43.10 3.51
1593 1617 2.073816 CTAATGGCGTTTTCCGTCTGT 58.926 47.619 0.00 0.00 43.10 3.41
2019 2044 1.746220 CCCTTCTCACTCTCAGTACCG 59.254 57.143 0.00 0.00 0.00 4.02
2029 2054 2.599082 CTCTCAGTACCGAAAATCGCAC 59.401 50.000 0.00 0.00 38.82 5.34
2035 2060 2.415697 ACCGAAAATCGCACCTTTTG 57.584 45.000 0.00 0.00 38.82 2.44
2061 2086 1.986698 GCAAAAGCTGCGACATTGAT 58.013 45.000 11.81 0.00 42.37 2.57
2200 2225 3.041940 CTCCGTTGGGTGCGTCAC 61.042 66.667 1.92 1.92 33.83 3.67
2201 2226 3.800685 CTCCGTTGGGTGCGTCACA 62.801 63.158 11.20 0.00 35.86 3.58
2243 2268 3.490761 CCACTGAATTCCAACACCACAAC 60.491 47.826 2.27 0.00 0.00 3.32
2267 2297 6.034591 CACCAATTCTTCAGCAAATGATCTC 58.965 40.000 0.00 0.00 37.89 2.75
2279 2309 4.619863 GCAAATGATCTCAAGCCATTGTGT 60.620 41.667 0.00 0.00 37.68 3.72
2285 2315 2.622942 TCTCAAGCCATTGTGTTGGTTC 59.377 45.455 0.00 0.00 39.11 3.62
2309 2343 6.761242 TCGTCTAATCTATGTGGATTGGTTTG 59.239 38.462 2.31 0.00 36.69 2.93
2384 2418 1.493950 CGCTGCTGAATCCGTCATCC 61.494 60.000 0.00 0.00 35.07 3.51
2603 2650 3.420893 TGCCTTGCAAATTACTGCTACT 58.579 40.909 0.00 0.00 43.07 2.57
2604 2651 4.584874 TGCCTTGCAAATTACTGCTACTA 58.415 39.130 0.00 0.00 43.07 1.82
2605 2652 4.635765 TGCCTTGCAAATTACTGCTACTAG 59.364 41.667 0.00 0.00 43.07 2.57
2610 2661 9.542462 CCTTGCAAATTACTGCTACTAGTATTA 57.458 33.333 2.33 0.00 43.07 0.98
2778 2838 6.015180 TCTCAATCAAGATTGGTTTTCAAGGG 60.015 38.462 19.46 0.00 46.08 3.95
2959 3025 5.733109 GCGTACGTACCAGTACTAGTTTAAC 59.267 44.000 19.67 0.00 43.42 2.01
3140 3227 1.313772 CATCGACATCTCCCTCGTCT 58.686 55.000 0.00 0.00 0.00 4.18
3410 3504 2.648102 GGCGACGACGATGACGAG 60.648 66.667 12.29 0.00 42.66 4.18
3443 3540 2.125350 GAAGGCAGGCTGGAGTCG 60.125 66.667 17.64 0.00 0.00 4.18
3533 3630 3.646976 CTCATGGGCAGCATCGCG 61.647 66.667 0.00 0.00 0.00 5.87
3638 3735 4.828925 GGCCGAGCCTCTCAGCAC 62.829 72.222 7.58 0.00 46.69 4.40
3663 3760 5.937540 TCATTCATTCACTCACCGTGTTATT 59.062 36.000 0.00 0.00 44.16 1.40
3936 4047 3.871594 GAGAACCCAGTACAAATCCATCG 59.128 47.826 0.00 0.00 0.00 3.84
3958 4069 2.265367 TGTGCTCTCCCTCCATGTAAA 58.735 47.619 0.00 0.00 0.00 2.01
4002 4114 1.884067 GCTCAGGTGTTCCCTTCCTTG 60.884 57.143 0.00 0.00 42.73 3.61
4004 4116 2.106511 CTCAGGTGTTCCCTTCCTTGAA 59.893 50.000 0.00 0.00 42.73 2.69
4022 4134 3.892284 TGAAGGTTGGTTTCTGCAAGTA 58.108 40.909 0.00 0.00 33.76 2.24
4041 4153 6.948353 CAAGTATTGTCGAGTGATATTTGGG 58.052 40.000 0.00 0.00 42.34 4.12
4042 4154 5.611374 AGTATTGTCGAGTGATATTTGGGG 58.389 41.667 0.00 0.00 0.00 4.96
4043 4155 3.992943 TTGTCGAGTGATATTTGGGGT 57.007 42.857 0.00 0.00 0.00 4.95
4186 4303 1.181098 AAGCACCACACCTTCATGGC 61.181 55.000 0.00 0.00 39.84 4.40
4298 4417 5.498069 CGAAAATGAAATGAGCAGCGAAATG 60.498 40.000 0.00 0.00 0.00 2.32
4324 4451 1.284982 GCAGCAGGAGTGTGTGTACG 61.285 60.000 0.00 0.00 0.00 3.67
4359 4490 2.124507 TTGGCAGGAGCTAAACCGCT 62.125 55.000 0.00 0.00 44.33 5.52
4361 4492 2.109126 GCAGGAGCTAAACCGCTGG 61.109 63.158 0.00 0.00 41.08 4.85
4566 5735 2.203437 AGGGGTGCCAAAACGTCC 60.203 61.111 0.00 0.00 0.00 4.79
4583 5752 0.677731 TCCTCTTGCCAGAAATGCGG 60.678 55.000 0.00 0.00 0.00 5.69
4595 5764 2.439507 AGAAATGCGGGGATGTATGTCT 59.560 45.455 0.00 0.00 0.00 3.41
4604 5773 2.438021 GGGATGTATGTCTTGGCAGGTA 59.562 50.000 0.00 0.00 0.00 3.08
4605 5774 3.118038 GGGATGTATGTCTTGGCAGGTAA 60.118 47.826 0.00 0.00 0.00 2.85
4606 5775 4.523083 GGATGTATGTCTTGGCAGGTAAA 58.477 43.478 0.00 0.00 0.00 2.01
4607 5776 4.335594 GGATGTATGTCTTGGCAGGTAAAC 59.664 45.833 0.00 0.00 0.00 2.01
4608 5777 4.359434 TGTATGTCTTGGCAGGTAAACA 57.641 40.909 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 1.405526 GCTGTGGAGTCTTTCGCCATA 60.406 52.381 0.00 0.00 46.81 2.74
107 108 2.762043 GAGCCCGAGGAGGAAGCT 60.762 66.667 0.00 0.00 45.00 3.74
144 145 1.400530 GGGATCCAATCTCCCGACGT 61.401 60.000 15.23 0.00 42.94 4.34
152 153 3.142393 CGCGAGGGGATCCAATCT 58.858 61.111 15.23 7.66 34.83 2.40
178 179 2.899339 GATCCTCCAGCCGCTTGC 60.899 66.667 0.00 0.00 41.71 4.01
326 329 0.911769 ATGCCTGGAAGAACGGATCA 59.088 50.000 0.00 0.00 34.07 2.92
327 330 1.943340 GAATGCCTGGAAGAACGGATC 59.057 52.381 0.00 0.00 34.07 3.36
373 377 0.332972 AGGATTTGGGAGAAGGTGGC 59.667 55.000 0.00 0.00 0.00 5.01
382 386 3.716872 GAGGTAGATGGAAGGATTTGGGA 59.283 47.826 0.00 0.00 0.00 4.37
428 434 1.172812 GGCGGCAACTCAGGAAGTTT 61.173 55.000 3.07 0.00 46.26 2.66
556 562 3.536917 CGCCCCGTAGCTGGATGA 61.537 66.667 0.00 0.00 0.00 2.92
599 605 9.920946 TGTCATTTTATTTCTTATAGAAGGCCT 57.079 29.630 0.00 0.00 35.37 5.19
620 626 9.833917 CTCTATAGGATTTGATATGCATGTCAT 57.166 33.333 24.49 12.51 39.17 3.06
621 627 9.039165 TCTCTATAGGATTTGATATGCATGTCA 57.961 33.333 20.85 20.85 0.00 3.58
622 628 9.881649 TTCTCTATAGGATTTGATATGCATGTC 57.118 33.333 15.93 15.93 0.00 3.06
627 633 9.598517 CCTCTTTCTCTATAGGATTTGATATGC 57.401 37.037 0.00 0.00 0.00 3.14
643 649 9.599056 TGAATCAGATGATATACCTCTTTCTCT 57.401 33.333 0.00 0.00 33.73 3.10
649 655 9.781425 ACCTTATGAATCAGATGATATACCTCT 57.219 33.333 0.00 0.00 33.73 3.69
699 709 5.837829 AGGCCTTGTTTGATTTATAGGGAA 58.162 37.500 0.00 0.00 0.00 3.97
728 738 1.327690 ACACACTGTCACCGTCACCT 61.328 55.000 0.00 0.00 0.00 4.00
763 773 5.106791 CCTTTCGCATGCTAGGATATTTCAG 60.107 44.000 19.85 0.10 0.00 3.02
1188 1208 2.036346 GTGCCAGATTGGTTTCTGCTTT 59.964 45.455 0.00 0.00 41.50 3.51
1189 1209 1.615392 GTGCCAGATTGGTTTCTGCTT 59.385 47.619 0.00 0.00 41.50 3.91
1190 1210 1.251251 GTGCCAGATTGGTTTCTGCT 58.749 50.000 0.00 0.00 41.50 4.24
1191 1211 0.244721 GGTGCCAGATTGGTTTCTGC 59.755 55.000 0.00 0.00 41.50 4.26
1192 1212 1.915141 AGGTGCCAGATTGGTTTCTG 58.085 50.000 0.00 0.00 40.46 3.02
1193 1213 2.242043 CAAGGTGCCAGATTGGTTTCT 58.758 47.619 0.00 0.00 40.46 2.52
1194 1214 1.337167 GCAAGGTGCCAGATTGGTTTC 60.337 52.381 0.00 0.00 40.46 2.78
1195 1215 0.681175 GCAAGGTGCCAGATTGGTTT 59.319 50.000 0.00 0.00 40.46 3.27
1196 1216 1.526575 CGCAAGGTGCCAGATTGGTT 61.527 55.000 0.00 0.00 41.12 3.67
1197 1217 1.973281 CGCAAGGTGCCAGATTGGT 60.973 57.895 0.00 0.00 41.12 3.67
1198 1218 1.973281 ACGCAAGGTGCCAGATTGG 60.973 57.895 0.00 0.00 41.12 3.16
1199 1219 1.210931 CACGCAAGGTGCCAGATTG 59.789 57.895 0.00 0.00 41.12 2.67
1200 1220 1.973281 CCACGCAAGGTGCCAGATT 60.973 57.895 0.00 0.00 45.62 2.40
1201 1221 2.360350 CCACGCAAGGTGCCAGAT 60.360 61.111 0.00 0.00 45.62 2.90
1202 1222 3.414136 AACCACGCAAGGTGCCAGA 62.414 57.895 0.00 0.00 45.62 3.86
1203 1223 2.906897 AACCACGCAAGGTGCCAG 60.907 61.111 0.00 0.00 45.62 4.85
1204 1224 2.904866 GAACCACGCAAGGTGCCA 60.905 61.111 0.00 0.00 45.62 4.92
1252 1272 2.263895 TACATAGGGTGGCCAGAAGT 57.736 50.000 5.11 1.68 0.00 3.01
1258 1278 0.608640 CGGAGATACATAGGGTGGCC 59.391 60.000 0.00 0.00 0.00 5.36
1266 1286 2.661718 TCAGCACACCGGAGATACATA 58.338 47.619 9.46 0.00 0.00 2.29
1267 1287 1.485124 TCAGCACACCGGAGATACAT 58.515 50.000 9.46 0.00 0.00 2.29
1290 1311 2.548480 GACACCACCTAAGCAAACAGAC 59.452 50.000 0.00 0.00 0.00 3.51
1292 1313 1.880027 GGACACCACCTAAGCAAACAG 59.120 52.381 0.00 0.00 0.00 3.16
1367 1388 3.842925 GAACAGGGGAAGCGTGGCA 62.843 63.158 0.00 0.00 0.00 4.92
1369 1390 1.376037 GAGAACAGGGGAAGCGTGG 60.376 63.158 0.00 0.00 0.00 4.94
1382 1403 1.079057 GGGCGACAGGGAAGAGAAC 60.079 63.158 0.00 0.00 0.00 3.01
1507 1529 2.045926 AGTCTCACATTGGCGCCC 60.046 61.111 26.77 6.44 0.00 6.13
1592 1616 2.501723 ACATCAGGATCTGTACACCCAC 59.498 50.000 0.00 0.00 32.61 4.61
1593 1617 2.832838 ACATCAGGATCTGTACACCCA 58.167 47.619 0.00 0.00 32.61 4.51
2019 2044 3.915437 TCCTCAAAAGGTGCGATTTTC 57.085 42.857 0.00 0.00 43.82 2.29
2200 2225 4.094590 TGGTGTTTTTGCAAGAAAATGCTG 59.905 37.500 3.66 0.00 46.54 4.41
2201 2226 4.094739 GTGGTGTTTTTGCAAGAAAATGCT 59.905 37.500 3.66 0.00 46.54 3.79
2243 2268 5.962433 AGATCATTTGCTGAAGAATTGGTG 58.038 37.500 0.00 0.00 37.44 4.17
2267 2297 1.066908 ACGAACCAACACAATGGCTTG 59.933 47.619 0.00 0.00 44.75 4.01
2279 2309 5.925506 TCCACATAGATTAGACGAACCAA 57.074 39.130 0.00 0.00 0.00 3.67
2285 2315 6.538742 ACAAACCAATCCACATAGATTAGACG 59.461 38.462 0.00 0.00 34.69 4.18
2309 2343 6.226787 CACCTCATATGGAATTCTCCTGTAC 58.773 44.000 5.23 0.00 42.94 2.90
2375 2409 3.838271 GGCTCTGCGGATGACGGA 61.838 66.667 0.00 0.00 44.51 4.69
2384 2418 1.668294 CCATACTAGGGGCTCTGCG 59.332 63.158 0.00 0.00 0.00 5.18
2598 2645 6.750148 AGGTCAGCAATGTAATACTAGTAGC 58.250 40.000 8.85 4.48 0.00 3.58
2601 2648 6.154534 TGTGAGGTCAGCAATGTAATACTAGT 59.845 38.462 0.00 0.00 0.00 2.57
2603 2650 6.338146 GTGTGAGGTCAGCAATGTAATACTA 58.662 40.000 0.00 0.00 0.00 1.82
2604 2651 5.178797 GTGTGAGGTCAGCAATGTAATACT 58.821 41.667 0.00 0.00 0.00 2.12
2605 2652 4.032900 CGTGTGAGGTCAGCAATGTAATAC 59.967 45.833 0.00 0.00 0.00 1.89
2610 2661 1.230635 GCGTGTGAGGTCAGCAATGT 61.231 55.000 0.00 0.00 0.00 2.71
2778 2838 4.020751 TGATGAGCTCTGGGATAATGCTAC 60.021 45.833 16.19 0.00 33.83 3.58
3096 3168 2.173669 CGGGATCGTGCATGTGGAC 61.174 63.158 5.68 0.00 0.00 4.02
3140 3227 0.669318 GAACAAGATCCGCACCGTCA 60.669 55.000 0.00 0.00 0.00 4.35
3399 3493 1.088340 TCCTCGTCCTCGTCATCGTC 61.088 60.000 0.00 0.00 38.33 4.20
3400 3494 1.078637 TCCTCGTCCTCGTCATCGT 60.079 57.895 0.00 0.00 38.33 3.73
3401 3495 1.644372 CTCCTCGTCCTCGTCATCG 59.356 63.158 0.00 0.00 38.33 3.84
3402 3496 0.464013 TCCTCCTCGTCCTCGTCATC 60.464 60.000 0.00 0.00 38.33 2.92
3403 3497 0.034380 TTCCTCCTCGTCCTCGTCAT 60.034 55.000 0.00 0.00 38.33 3.06
3404 3498 0.677098 CTTCCTCCTCGTCCTCGTCA 60.677 60.000 0.00 0.00 38.33 4.35
3410 3504 1.107945 CTTCTCCTTCCTCCTCGTCC 58.892 60.000 0.00 0.00 0.00 4.79
3533 3630 2.301505 CATCTTGCCGATGGACGAC 58.698 57.895 5.44 0.00 44.69 4.34
3663 3760 2.598205 CGACGTATCATGACGCTTCGTA 60.598 50.000 14.77 0.00 46.87 3.43
3845 3946 2.969300 TTCAACAACTCCACGGGGGC 62.969 60.000 2.42 0.00 36.21 5.80
3936 4047 0.835941 ACATGGAGGGAGAGCACATC 59.164 55.000 0.00 0.00 0.00 3.06
4002 4114 5.221244 ACAATACTTGCAGAAACCAACCTTC 60.221 40.000 0.00 0.00 0.00 3.46
4004 4116 4.215109 ACAATACTTGCAGAAACCAACCT 58.785 39.130 0.00 0.00 0.00 3.50
4009 4121 3.746492 ACTCGACAATACTTGCAGAAACC 59.254 43.478 0.00 0.00 0.00 3.27
4022 4134 4.451900 GACCCCAAATATCACTCGACAAT 58.548 43.478 0.00 0.00 0.00 2.71
4025 4137 2.802057 CGGACCCCAAATATCACTCGAC 60.802 54.545 0.00 0.00 0.00 4.20
4027 4139 1.411246 TCGGACCCCAAATATCACTCG 59.589 52.381 0.00 0.00 0.00 4.18
4028 4140 3.771577 ATCGGACCCCAAATATCACTC 57.228 47.619 0.00 0.00 0.00 3.51
4029 4141 3.202151 ACAATCGGACCCCAAATATCACT 59.798 43.478 0.00 0.00 0.00 3.41
4031 4143 3.550820 CACAATCGGACCCCAAATATCA 58.449 45.455 0.00 0.00 0.00 2.15
4033 4145 2.091885 AGCACAATCGGACCCCAAATAT 60.092 45.455 0.00 0.00 0.00 1.28
4035 4147 0.039618 AGCACAATCGGACCCCAAAT 59.960 50.000 0.00 0.00 0.00 2.32
4036 4148 0.178975 AAGCACAATCGGACCCCAAA 60.179 50.000 0.00 0.00 0.00 3.28
4037 4149 0.178975 AAAGCACAATCGGACCCCAA 60.179 50.000 0.00 0.00 0.00 4.12
4038 4150 0.608035 GAAAGCACAATCGGACCCCA 60.608 55.000 0.00 0.00 0.00 4.96
4039 4151 0.322546 AGAAAGCACAATCGGACCCC 60.323 55.000 0.00 0.00 0.00 4.95
4040 4152 0.804989 CAGAAAGCACAATCGGACCC 59.195 55.000 0.00 0.00 0.00 4.46
4041 4153 1.808411 TCAGAAAGCACAATCGGACC 58.192 50.000 0.00 0.00 0.00 4.46
4042 4154 3.686726 AGATTCAGAAAGCACAATCGGAC 59.313 43.478 0.00 0.00 31.64 4.79
4043 4155 3.686241 CAGATTCAGAAAGCACAATCGGA 59.314 43.478 0.00 0.00 31.64 4.55
4186 4303 0.322975 CTGACTGGGGACAAGACAGG 59.677 60.000 0.00 0.00 42.06 4.00
4234 4351 1.520666 GTACACTCCACCCATCCCG 59.479 63.158 0.00 0.00 0.00 5.14
4298 4417 1.079266 CACTCCTGCTGCTCAGTCC 60.079 63.158 0.00 0.00 41.25 3.85
4315 4434 0.175989 TTGTGCCTGTCGTACACACA 59.824 50.000 0.00 0.00 43.57 3.72
4324 4451 1.285023 CAAGCTGCTTGTGCCTGTC 59.715 57.895 29.38 0.00 36.79 3.51
4359 4490 1.893137 CTGCACTCTACACTACACCCA 59.107 52.381 0.00 0.00 0.00 4.51
4361 4492 3.367498 CCTTCTGCACTCTACACTACACC 60.367 52.174 0.00 0.00 0.00 4.16
4508 5677 4.623167 CGTGATGTCAAGTCGATTCTCTTT 59.377 41.667 0.00 0.00 0.00 2.52
4566 5735 1.660560 CCCCGCATTTCTGGCAAGAG 61.661 60.000 0.00 0.00 32.79 2.85
4583 5752 1.212935 ACCTGCCAAGACATACATCCC 59.787 52.381 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.