Multiple sequence alignment - TraesCS1D01G087500

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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 TraesCS1D01G087500 chr1D 100.000 5544 0 0 1 5544 72899141 72904684 0.000000e+00 10238
1 TraesCS1D01G087500 chr1D 91.444 187 13 2 5278 5464 73051331 73051514 2.560000e-63 254
2 TraesCS1D01G087500 chr1B 93.562 4784 194 55 807 5544 115275355 115280070 0.000000e+00 7023
3 TraesCS1D01G087500 chr1B 79.368 601 57 33 56 627 115274614 115275176 1.470000e-95 361
4 TraesCS1D01G087500 chr1A 93.329 2773 111 30 2808 5544 72780885 72783619 0.000000e+00 4028
5 TraesCS1D01G087500 chr1A 87.532 2775 166 73 3 2675 72777948 72780644 0.000000e+00 3042


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 TraesCS1D01G087500 chr1D 72899141 72904684 5543 False 10238 10238 100.0000 1 5544 1 chr1D.!!$F1 5543
1 TraesCS1D01G087500 chr1B 115274614 115280070 5456 False 3692 7023 86.4650 56 5544 2 chr1B.!!$F1 5488
2 TraesCS1D01G087500 chr1A 72777948 72783619 5671 False 3535 4028 90.4305 3 5544 2 chr1A.!!$F1 5541

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
527 570 0.113776 ACGGTCCCCTCTTACACAGA 59.886 55.000 0.0 0.0 0.00 3.41 F
1122 1289 0.035439 CCAGGTACATCCCACACCAC 60.035 60.000 0.0 0.0 36.75 4.16 F
1123 1290 0.690192 CAGGTACATCCCACACCACA 59.310 55.000 0.0 0.0 36.75 4.17 F
1125 1292 0.690762 GGTACATCCCACACCACACT 59.309 55.000 0.0 0.0 32.32 3.55 F
1131 1298 0.988832 TCCCACACCACACTAATCCC 59.011 55.000 0.0 0.0 0.00 3.85 F
1132 1299 0.991920 CCCACACCACACTAATCCCT 59.008 55.000 0.0 0.0 0.00 4.20 F
2414 2630 1.288633 TCGAAGGGGATACAGGGTACA 59.711 52.381 0.0 0.0 39.74 2.90 F
4284 4703 1.037579 AGAGGCGATGATGGACGACA 61.038 55.000 0.0 0.0 40.24 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2199 2407 2.191641 GGCCAGGCTAAGCTCTGG 59.808 66.667 12.43 13.59 44.20 3.86 R
2771 2991 1.949547 GCAAGAGCTCACAGCCTCAAT 60.950 52.381 17.77 0.00 43.77 2.57 R
2806 3026 2.938451 TGCAAATCGAGCCTTGATAGTG 59.062 45.455 8.43 0.00 0.00 2.74 R
3083 3491 3.193267 ACGGCCAAACGTCTAAGTATGTA 59.807 43.478 2.24 0.00 45.08 2.29 R
3284 3694 1.531149 ACGACCATGTTTCGCAGAAAG 59.469 47.619 12.56 0.00 45.90 2.62 R
3329 3739 9.895138 TTAGTATATTTACCTCACCCTTTTCAC 57.105 33.333 0.00 0.00 0.00 3.18 R
4417 4836 0.604780 ACAACTTCGCATCAGCAGCT 60.605 50.000 0.00 0.00 42.27 4.24 R
5118 5555 0.389817 TACACTCCTGCATGCGACAC 60.390 55.000 14.09 0.00 0.00 3.67 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
41 42 3.414700 CAAGTGTGCTCCGTCGGC 61.415 66.667 6.34 0.00 0.00 5.54
54 55 1.514087 GTCGGCGGGACATAGTTGA 59.486 57.895 7.21 0.00 45.36 3.18
66 67 4.213482 GGACATAGTTGACAACGAGCTTTT 59.787 41.667 12.54 0.00 36.23 2.27
181 183 7.012704 GGACATGTGATACTTAGTACTCCGTTA 59.987 40.741 1.15 0.00 0.00 3.18
371 402 9.720769 ATTTTTCGAAAAACTATACTCTCTCCA 57.279 29.630 32.14 10.02 40.33 3.86
376 408 7.123697 TCGAAAAACTATACTCTCTCCATTCCA 59.876 37.037 0.00 0.00 0.00 3.53
382 414 8.783660 ACTATACTCTCTCCATTCCATTACAA 57.216 34.615 0.00 0.00 0.00 2.41
411 443 3.732048 ATAAATGGGTTGGTTCGACCT 57.268 42.857 4.52 0.00 39.58 3.85
412 444 4.847990 ATAAATGGGTTGGTTCGACCTA 57.152 40.909 4.52 0.00 39.58 3.08
438 480 1.383386 TTATAGGGGCCAGGCACGA 60.383 57.895 15.19 0.55 29.41 4.35
439 481 1.692173 TTATAGGGGCCAGGCACGAC 61.692 60.000 15.19 0.00 29.41 4.34
477 519 3.036084 CACAGGTCGTGCCGTGTC 61.036 66.667 11.78 0.00 43.70 3.67
527 570 0.113776 ACGGTCCCCTCTTACACAGA 59.886 55.000 0.00 0.00 0.00 3.41
603 646 4.207165 GGCTGCTTTGGACCTATATTCAA 58.793 43.478 0.00 0.00 0.00 2.69
665 714 2.179547 CGTGTTGTGCCTGCACTCA 61.180 57.895 21.62 17.03 46.30 3.41
823 948 3.322191 AAACCTGCCTAAAACCTTCCA 57.678 42.857 0.00 0.00 0.00 3.53
824 949 3.322191 AACCTGCCTAAAACCTTCCAA 57.678 42.857 0.00 0.00 0.00 3.53
917 1055 1.001378 CGAACACAGGCTTTTTCCCAG 60.001 52.381 0.00 0.00 0.00 4.45
1120 1287 1.077716 GCCAGGTACATCCCACACC 60.078 63.158 0.00 0.00 36.75 4.16
1122 1289 0.035439 CCAGGTACATCCCACACCAC 60.035 60.000 0.00 0.00 36.75 4.16
1123 1290 0.690192 CAGGTACATCCCACACCACA 59.310 55.000 0.00 0.00 36.75 4.17
1125 1292 0.690762 GGTACATCCCACACCACACT 59.309 55.000 0.00 0.00 32.32 3.55
1126 1293 1.903860 GGTACATCCCACACCACACTA 59.096 52.381 0.00 0.00 32.32 2.74
1127 1294 2.303600 GGTACATCCCACACCACACTAA 59.696 50.000 0.00 0.00 32.32 2.24
1128 1295 3.054655 GGTACATCCCACACCACACTAAT 60.055 47.826 0.00 0.00 32.32 1.73
1129 1296 3.350219 ACATCCCACACCACACTAATC 57.650 47.619 0.00 0.00 0.00 1.75
1130 1297 2.026262 ACATCCCACACCACACTAATCC 60.026 50.000 0.00 0.00 0.00 3.01
1131 1298 0.988832 TCCCACACCACACTAATCCC 59.011 55.000 0.00 0.00 0.00 3.85
1132 1299 0.991920 CCCACACCACACTAATCCCT 59.008 55.000 0.00 0.00 0.00 4.20
1133 1300 1.354368 CCCACACCACACTAATCCCTT 59.646 52.381 0.00 0.00 0.00 3.95
1138 1305 3.888930 ACACCACACTAATCCCTTTTGTG 59.111 43.478 0.00 0.00 43.81 3.33
1160 1339 4.227300 TGGGTAGCACATATCAAACTTCCT 59.773 41.667 0.00 0.00 0.00 3.36
1184 1373 2.729882 GCCACCTATGCGTTAGTAATCG 59.270 50.000 0.00 0.00 0.00 3.34
1187 1376 4.321750 CCACCTATGCGTTAGTAATCGGAT 60.322 45.833 13.26 13.26 40.69 4.18
1219 1408 3.772853 TTGCCGCTGCTGGTTCAGT 62.773 57.895 0.70 0.00 38.71 3.41
1269 1458 4.451241 CATACGCCATGCTCTGCT 57.549 55.556 0.00 0.00 0.00 4.24
1290 1482 2.025155 TCTGTGCAGTAGGCTAGTAGC 58.975 52.381 14.09 14.09 45.15 3.58
1304 1496 6.557568 AGGCTAGTAGCAGAGGTAAGATTAT 58.442 40.000 23.24 0.00 44.75 1.28
1318 1510 6.826741 AGGTAAGATTATACGGCAAACACATT 59.173 34.615 0.00 0.00 0.00 2.71
1319 1511 7.988599 AGGTAAGATTATACGGCAAACACATTA 59.011 33.333 0.00 0.00 0.00 1.90
1320 1512 8.066000 GGTAAGATTATACGGCAAACACATTAC 58.934 37.037 0.00 0.00 0.00 1.89
1321 1513 7.618502 AAGATTATACGGCAAACACATTACA 57.381 32.000 0.00 0.00 0.00 2.41
1322 1514 7.011828 AGATTATACGGCAAACACATTACAC 57.988 36.000 0.00 0.00 0.00 2.90
1323 1515 6.596106 AGATTATACGGCAAACACATTACACA 59.404 34.615 0.00 0.00 0.00 3.72
1324 1516 6.745159 TTATACGGCAAACACATTACACAT 57.255 33.333 0.00 0.00 0.00 3.21
1325 1517 3.281341 ACGGCAAACACATTACACATG 57.719 42.857 0.00 0.00 0.00 3.21
1326 1518 2.621055 ACGGCAAACACATTACACATGT 59.379 40.909 0.00 0.00 0.00 3.21
1382 1575 3.638160 TCAGAAAGCTTTTCTGGCATGTT 59.362 39.130 25.26 0.00 44.43 2.71
1384 1577 4.812626 CAGAAAGCTTTTCTGGCATGTTTT 59.187 37.500 14.05 0.00 41.54 2.43
1385 1578 5.295045 CAGAAAGCTTTTCTGGCATGTTTTT 59.705 36.000 14.05 0.00 41.54 1.94
1386 1579 5.525012 AGAAAGCTTTTCTGGCATGTTTTTC 59.475 36.000 14.05 0.00 0.00 2.29
1502 1700 3.272581 ACTAGCTCTCTAGAACACGGTC 58.727 50.000 6.36 0.00 43.95 4.79
1577 1777 4.201589 ACAAAGATACGAAAATGCGTCGAG 60.202 41.667 0.00 0.00 44.39 4.04
1578 1778 2.460918 AGATACGAAAATGCGTCGAGG 58.539 47.619 0.00 0.00 44.39 4.63
2045 2251 2.724977 TAGCTGAGGCGGAATTATCG 57.275 50.000 0.00 0.00 44.37 2.92
2158 2364 9.415544 TCTCAATAATCGAGTATTGACATGATG 57.584 33.333 32.99 24.66 42.72 3.07
2199 2407 1.727857 CGGTTTGTGCGCAGAATAACC 60.728 52.381 24.16 24.16 31.66 2.85
2414 2630 1.288633 TCGAAGGGGATACAGGGTACA 59.711 52.381 0.00 0.00 39.74 2.90
2499 2715 1.452651 CATTCAGGTCAGCGGGCAT 60.453 57.895 0.00 0.00 0.00 4.40
2510 2727 3.859386 GTCAGCGGGCATTTTTATTCTTG 59.141 43.478 0.00 0.00 0.00 3.02
2718 2938 6.462487 CCTTGCATTCTATTTTCTGCCATCAT 60.462 38.462 0.00 0.00 33.70 2.45
2723 2943 7.914346 GCATTCTATTTTCTGCCATCATATAGC 59.086 37.037 0.00 0.00 0.00 2.97
2734 2954 9.605275 TCTGCCATCATATAGCATTTTAGATAC 57.395 33.333 0.00 0.00 35.64 2.24
2806 3026 3.339141 CTCTTGCCCTTTGTAGAGAACC 58.661 50.000 0.00 0.00 37.00 3.62
3077 3485 4.680171 AGCGTATTTTTAACTGCCTGAC 57.320 40.909 0.00 0.00 0.00 3.51
3083 3491 7.625606 GCGTATTTTTAACTGCCTGACATAGTT 60.626 37.037 0.00 0.00 38.19 2.24
3284 3694 8.779354 AGTCTCTGTTCAAGTAAATGGTTATC 57.221 34.615 0.00 0.00 0.00 1.75
3329 3739 7.328493 GTCATAAAAATTTCTTGTCTTTCCCGG 59.672 37.037 0.00 0.00 0.00 5.73
3501 3911 7.687941 AGGAAAAGGAACACATGTAATACAG 57.312 36.000 0.00 0.00 0.00 2.74
3590 4000 8.034804 AGGCAAACATGGAAATGAATAACTTAC 58.965 33.333 0.00 0.00 0.00 2.34
3640 4050 7.346751 AGAAAGCAAGAATAAGGTTTGTTCA 57.653 32.000 0.00 0.00 35.79 3.18
3690 4100 9.575783 GGTTTCAGTACATTTCTGTTTGTAAAA 57.424 29.630 0.00 0.00 36.79 1.52
3868 4278 1.546923 CCACAGCTTTGGATGAATGCA 59.453 47.619 14.02 0.00 39.24 3.96
3995 4406 8.845227 AGAGAGACATAGTGTGAGTATTGTATG 58.155 37.037 0.00 0.00 0.00 2.39
4095 4514 6.879400 AGCACTACTCTAAGAACCTTATTGG 58.121 40.000 0.00 0.00 42.93 3.16
4097 4516 6.049790 CACTACTCTAAGAACCTTATTGGGC 58.950 44.000 0.00 0.00 41.11 5.36
4270 4689 6.807789 AGTACTTTGTATGCTACTTAGAGGC 58.192 40.000 0.00 0.00 0.00 4.70
4284 4703 1.037579 AGAGGCGATGATGGACGACA 61.038 55.000 0.00 0.00 40.24 4.35
4369 4788 2.339769 GGAGGTCCTGTGGCCTATATT 58.660 52.381 3.32 0.00 34.81 1.28
4462 4881 0.605050 TCAACATTACCAGCAGCGCA 60.605 50.000 11.47 0.00 0.00 6.09
4570 4989 0.669932 GTGAGTGCAGCTCCTGTCAG 60.670 60.000 11.99 0.00 43.48 3.51
4581 5000 2.545946 GCTCCTGTCAGTCTGTTTTGAC 59.454 50.000 0.00 0.00 43.07 3.18
4667 5086 5.632034 AGTCTGTCCTAAAGTGTTTCCTT 57.368 39.130 0.00 0.00 0.00 3.36
4668 5087 5.612351 AGTCTGTCCTAAAGTGTTTCCTTC 58.388 41.667 0.00 0.00 0.00 3.46
4691 5123 2.992543 TGTGTTCTTTTGTGCTTTGTGC 59.007 40.909 0.00 0.00 43.25 4.57
4692 5124 3.253230 GTGTTCTTTTGTGCTTTGTGCT 58.747 40.909 0.00 0.00 43.37 4.40
4693 5125 3.061161 GTGTTCTTTTGTGCTTTGTGCTG 59.939 43.478 0.00 0.00 43.37 4.41
4694 5126 2.582728 TCTTTTGTGCTTTGTGCTGG 57.417 45.000 0.00 0.00 43.37 4.85
4695 5127 1.824230 TCTTTTGTGCTTTGTGCTGGT 59.176 42.857 0.00 0.00 43.37 4.00
4696 5128 1.928503 CTTTTGTGCTTTGTGCTGGTG 59.071 47.619 0.00 0.00 43.37 4.17
4697 5129 0.459934 TTTGTGCTTTGTGCTGGTGC 60.460 50.000 0.00 0.00 43.37 5.01
4698 5130 1.321805 TTGTGCTTTGTGCTGGTGCT 61.322 50.000 0.00 0.00 43.37 4.40
4699 5131 1.008079 GTGCTTTGTGCTGGTGCTC 60.008 57.895 0.00 0.00 43.37 4.26
4700 5132 1.152902 TGCTTTGTGCTGGTGCTCT 60.153 52.632 0.00 0.00 43.37 4.09
4701 5133 1.285023 GCTTTGTGCTGGTGCTCTG 59.715 57.895 0.00 0.00 40.48 3.35
4702 5134 1.450531 GCTTTGTGCTGGTGCTCTGT 61.451 55.000 0.00 0.00 40.48 3.41
4703 5135 0.309922 CTTTGTGCTGGTGCTCTGTG 59.690 55.000 0.00 0.00 40.48 3.66
4843 5276 9.186323 CAGATTACTACTATTTGACTTCCATCG 57.814 37.037 0.00 0.00 0.00 3.84
4852 5289 2.571212 TGACTTCCATCGCTTTGTTGT 58.429 42.857 0.00 0.00 0.00 3.32
4860 5297 3.236816 CATCGCTTTGTTGTTAAGCCAG 58.763 45.455 0.00 0.00 43.93 4.85
5039 5476 3.822735 CTGGTCAACAAATCCATCACACT 59.177 43.478 0.00 0.00 0.00 3.55
5065 5502 7.576750 ACACTAGTTAATTATGTGTGTGACG 57.423 36.000 0.00 0.00 39.90 4.35
5118 5555 2.283298 ACATCTAAATGTCTGCTGGCG 58.717 47.619 0.00 0.00 42.59 5.69
5122 5559 1.394917 CTAAATGTCTGCTGGCGTGTC 59.605 52.381 0.00 0.00 0.00 3.67
5247 5692 0.387929 CTATTTGCATGCCAGCCAGG 59.612 55.000 16.68 0.00 41.84 4.45
5412 5857 3.989566 GACTACCGCGTCCGTGTCG 62.990 68.421 4.92 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 2.259618 CTCGTTGTCAACTATGTCCCG 58.740 52.381 13.67 0.00 0.00 5.14
54 55 2.033299 CACCATGTGAAAAGCTCGTTGT 59.967 45.455 0.00 0.00 35.23 3.32
351 382 7.265673 TGGAATGGAGAGAGTATAGTTTTTCG 58.734 38.462 0.00 0.00 0.00 3.46
361 392 7.687837 GCAGATTGTAATGGAATGGAGAGAGTA 60.688 40.741 0.00 0.00 0.00 2.59
362 393 6.590068 CAGATTGTAATGGAATGGAGAGAGT 58.410 40.000 0.00 0.00 0.00 3.24
363 394 5.469421 GCAGATTGTAATGGAATGGAGAGAG 59.531 44.000 0.00 0.00 0.00 3.20
364 395 5.104402 TGCAGATTGTAATGGAATGGAGAGA 60.104 40.000 0.00 0.00 0.00 3.10
365 396 5.128205 TGCAGATTGTAATGGAATGGAGAG 58.872 41.667 0.00 0.00 0.00 3.20
366 397 5.114764 TGCAGATTGTAATGGAATGGAGA 57.885 39.130 0.00 0.00 0.00 3.71
367 398 6.401047 AATGCAGATTGTAATGGAATGGAG 57.599 37.500 0.00 0.00 0.00 3.86
368 399 9.585369 TTATAATGCAGATTGTAATGGAATGGA 57.415 29.630 0.00 0.00 0.00 3.41
376 408 9.985730 CAACCCATTTATAATGCAGATTGTAAT 57.014 29.630 0.00 0.00 28.60 1.89
382 414 6.239008 CGAACCAACCCATTTATAATGCAGAT 60.239 38.462 0.00 0.00 0.00 2.90
411 443 0.475048 GGCCCCTATAACCCAGGCTA 60.475 60.000 0.00 0.00 43.36 3.93
412 444 1.774631 GGCCCCTATAACCCAGGCT 60.775 63.158 0.00 0.00 43.36 4.58
445 487 2.283298 CCTGTGTACTTAGCATGCCTG 58.717 52.381 15.66 7.37 0.00 4.85
446 488 1.909302 ACCTGTGTACTTAGCATGCCT 59.091 47.619 15.66 4.37 0.00 4.75
447 489 2.280628 GACCTGTGTACTTAGCATGCC 58.719 52.381 15.66 0.00 0.00 4.40
448 490 1.927174 CGACCTGTGTACTTAGCATGC 59.073 52.381 10.51 10.51 0.00 4.06
449 491 2.923655 CACGACCTGTGTACTTAGCATG 59.076 50.000 0.00 0.00 43.88 4.06
450 492 3.232213 CACGACCTGTGTACTTAGCAT 57.768 47.619 0.00 0.00 43.88 3.79
451 493 2.717580 CACGACCTGTGTACTTAGCA 57.282 50.000 0.00 0.00 43.88 3.49
538 581 3.315949 AGCGGGCTAAACGGGTCA 61.316 61.111 0.00 0.00 0.00 4.02
631 674 4.099824 CAACACGGCCGTTTAATTATTCC 58.900 43.478 32.11 0.00 0.00 3.01
632 675 4.555747 CACAACACGGCCGTTTAATTATTC 59.444 41.667 32.11 0.00 0.00 1.75
635 678 2.350580 GCACAACACGGCCGTTTAATTA 60.351 45.455 32.11 0.00 0.00 1.40
636 679 1.600912 GCACAACACGGCCGTTTAATT 60.601 47.619 32.11 17.77 0.00 1.40
637 680 0.039888 GCACAACACGGCCGTTTAAT 60.040 50.000 32.11 12.49 0.00 1.40
638 681 1.355916 GCACAACACGGCCGTTTAA 59.644 52.632 32.11 0.00 0.00 1.52
639 682 2.544698 GGCACAACACGGCCGTTTA 61.545 57.895 32.11 0.00 40.93 2.01
640 683 3.894947 GGCACAACACGGCCGTTT 61.895 61.111 32.11 22.15 40.93 3.60
702 751 0.941542 TTTATAATCAGGGCGTGCGC 59.058 50.000 8.17 8.17 41.06 6.09
703 752 2.032894 CACTTTATAATCAGGGCGTGCG 60.033 50.000 1.51 0.00 0.00 5.34
704 753 2.943033 ACACTTTATAATCAGGGCGTGC 59.057 45.455 1.51 0.00 0.00 5.34
709 758 3.139077 GCCCGACACTTTATAATCAGGG 58.861 50.000 8.29 8.29 39.29 4.45
832 957 6.808357 TCTAGGAAAGGTTTTAGGTAGGAGA 58.192 40.000 0.00 0.00 0.00 3.71
930 1068 2.359850 TGTGATGCAAGCGACCCC 60.360 61.111 0.00 0.00 0.00 4.95
933 1071 1.965930 TGGGTGTGATGCAAGCGAC 60.966 57.895 0.00 0.00 0.00 5.19
1040 1207 3.123620 GCTTGAGGTGGAGCAGCG 61.124 66.667 0.00 0.00 38.73 5.18
1138 1305 4.576463 CAGGAAGTTTGATATGTGCTACCC 59.424 45.833 0.00 0.00 0.00 3.69
1255 1444 1.744368 CAGAAGCAGAGCATGGCGT 60.744 57.895 0.00 0.00 34.54 5.68
1269 1458 2.427453 GCTACTAGCCTACTGCACAGAA 59.573 50.000 4.31 0.00 44.83 3.02
1282 1471 7.414319 CCGTATAATCTTACCTCTGCTACTAGC 60.414 44.444 0.61 0.61 42.82 3.42
1290 1482 6.018994 GTGTTTGCCGTATAATCTTACCTCTG 60.019 42.308 0.00 0.00 0.00 3.35
1304 1496 3.815962 ACATGTGTAATGTGTTTGCCGTA 59.184 39.130 0.00 0.00 0.00 4.02
1318 1510 4.130857 CAACCCACACTGTTACATGTGTA 58.869 43.478 9.11 0.00 44.43 2.90
1319 1511 2.948979 CAACCCACACTGTTACATGTGT 59.051 45.455 9.11 15.89 46.79 3.72
1320 1512 3.210227 TCAACCCACACTGTTACATGTG 58.790 45.455 9.11 15.72 44.79 3.21
1321 1513 3.569194 TCAACCCACACTGTTACATGT 57.431 42.857 2.69 2.69 0.00 3.21
1322 1514 3.366273 GCATCAACCCACACTGTTACATG 60.366 47.826 0.00 0.00 0.00 3.21
1323 1515 2.819608 GCATCAACCCACACTGTTACAT 59.180 45.455 0.00 0.00 0.00 2.29
1324 1516 2.158682 AGCATCAACCCACACTGTTACA 60.159 45.455 0.00 0.00 0.00 2.41
1325 1517 2.484264 GAGCATCAACCCACACTGTTAC 59.516 50.000 0.00 0.00 33.17 2.50
1326 1518 2.105649 TGAGCATCAACCCACACTGTTA 59.894 45.455 0.00 0.00 45.97 2.41
1449 1647 4.041938 AGAACCCCGAAACCATACAACTAA 59.958 41.667 0.00 0.00 0.00 2.24
1502 1700 8.660373 GGATATCCTTGTTAGCTATTTCAATCG 58.340 37.037 14.97 0.00 0.00 3.34
1799 2000 9.685828 GGTTATTTTAGTGCATAAGTTTTGTGA 57.314 29.630 0.00 0.00 0.00 3.58
2045 2251 8.659925 AGAGTTCATCAATCACAATATCTGAC 57.340 34.615 0.00 0.00 0.00 3.51
2158 2364 4.092968 CCGCAAAATGGACTACTTCAGTAC 59.907 45.833 0.00 0.00 37.72 2.73
2199 2407 2.191641 GGCCAGGCTAAGCTCTGG 59.808 66.667 12.43 13.59 44.20 3.86
2335 2551 6.750148 ACTTACTGGATTCGAGGATACATTC 58.250 40.000 0.60 0.00 41.41 2.67
2414 2630 9.193806 ACATGTATTTCAAGATTTAGAGCCATT 57.806 29.630 0.00 0.00 0.00 3.16
2493 2709 3.189285 CCTGCAAGAATAAAAATGCCCG 58.811 45.455 0.00 0.00 38.00 6.13
2499 2715 4.584325 AGACAGCACCTGCAAGAATAAAAA 59.416 37.500 0.00 0.00 45.16 1.94
2510 2727 2.647297 GCCAAAGACAGCACCTGC 59.353 61.111 0.00 0.00 42.49 4.85
2771 2991 1.949547 GCAAGAGCTCACAGCCTCAAT 60.950 52.381 17.77 0.00 43.77 2.57
2806 3026 2.938451 TGCAAATCGAGCCTTGATAGTG 59.062 45.455 8.43 0.00 0.00 2.74
3068 3476 6.546428 AAGTATGTAACTATGTCAGGCAGT 57.454 37.500 0.00 0.00 37.50 4.40
3077 3485 7.042925 GGCCAAACGTCTAAGTATGTAACTATG 60.043 40.741 0.00 0.00 37.50 2.23
3083 3491 3.193267 ACGGCCAAACGTCTAAGTATGTA 59.807 43.478 2.24 0.00 45.08 2.29
3284 3694 1.531149 ACGACCATGTTTCGCAGAAAG 59.469 47.619 12.56 0.00 45.90 2.62
3329 3739 9.895138 TTAGTATATTTACCTCACCCTTTTCAC 57.105 33.333 0.00 0.00 0.00 3.18
3501 3911 4.970662 ACCTGCATAATCACACACATTC 57.029 40.909 0.00 0.00 0.00 2.67
3712 4122 5.336451 CGCTATCTATATGCTACACCAACCA 60.336 44.000 0.00 0.00 0.00 3.67
3800 4210 2.851263 TAATGGTGCCACTCGTCTTT 57.149 45.000 0.00 0.00 0.00 2.52
3805 4215 0.880278 CGGGATAATGGTGCCACTCG 60.880 60.000 0.00 0.00 0.00 4.18
4039 4458 3.564053 TTAGTTTCAGGAACCAACGGT 57.436 42.857 0.00 0.00 39.13 4.83
4095 4514 3.493524 GGCTACTCATTCTCTAACAGGCC 60.494 52.174 0.00 0.00 0.00 5.19
4097 4516 5.830991 AGTAGGCTACTCATTCTCTAACAGG 59.169 44.000 21.30 0.00 32.47 4.00
4270 4689 3.000623 CACTTTCATGTCGTCCATCATCG 59.999 47.826 0.00 0.00 0.00 3.84
4284 4703 1.246649 TGCCGCATTGACACTTTCAT 58.753 45.000 0.00 0.00 32.84 2.57
4369 4788 1.024046 CATTCCGAATGACCGTGGCA 61.024 55.000 14.95 0.00 41.46 4.92
4378 4797 3.189080 TGAAAGTGTCTGCATTCCGAATG 59.811 43.478 15.63 15.63 41.85 2.67
4417 4836 0.604780 ACAACTTCGCATCAGCAGCT 60.605 50.000 0.00 0.00 42.27 4.24
4429 4848 6.183360 TGGTAATGTTGACAACAGACAACTTC 60.183 38.462 24.25 12.42 45.95 3.01
4462 4881 2.646798 AGGAAGAAAACTGGATGGAGCT 59.353 45.455 0.00 0.00 0.00 4.09
4466 4885 5.945784 TCATGTAAGGAAGAAAACTGGATGG 59.054 40.000 0.00 0.00 0.00 3.51
4468 4887 7.637511 AGATCATGTAAGGAAGAAAACTGGAT 58.362 34.615 0.00 0.00 0.00 3.41
4540 4959 1.802960 CTGCACTCACCAGCAACTTAG 59.197 52.381 0.00 0.00 40.73 2.18
4570 4989 4.531659 AAGTAGCAACGTCAAAACAGAC 57.468 40.909 0.00 0.00 35.19 3.51
4667 5086 3.509575 ACAAAGCACAAAAGAACACAGGA 59.490 39.130 0.00 0.00 0.00 3.86
4668 5087 3.613737 CACAAAGCACAAAAGAACACAGG 59.386 43.478 0.00 0.00 0.00 4.00
4691 5123 2.996249 ATATGGACACAGAGCACCAG 57.004 50.000 0.00 0.00 35.84 4.00
4692 5124 2.840038 AGAATATGGACACAGAGCACCA 59.160 45.455 0.00 0.00 36.83 4.17
4693 5125 3.462021 GAGAATATGGACACAGAGCACC 58.538 50.000 0.00 0.00 0.00 5.01
4694 5126 3.119291 CGAGAATATGGACACAGAGCAC 58.881 50.000 0.00 0.00 0.00 4.40
4695 5127 3.023832 TCGAGAATATGGACACAGAGCA 58.976 45.455 0.00 0.00 0.00 4.26
4696 5128 3.717400 TCGAGAATATGGACACAGAGC 57.283 47.619 0.00 0.00 0.00 4.09
4697 5129 8.459521 GATTTATCGAGAATATGGACACAGAG 57.540 38.462 0.00 0.00 0.00 3.35
4810 5243 9.201989 AGTCAAATAGTAGTAATCTGGATGTGA 57.798 33.333 0.00 0.00 0.00 3.58
4811 5244 9.823647 AAGTCAAATAGTAGTAATCTGGATGTG 57.176 33.333 0.00 0.00 0.00 3.21
4813 5246 9.482627 GGAAGTCAAATAGTAGTAATCTGGATG 57.517 37.037 0.00 0.00 0.00 3.51
4814 5247 9.213777 TGGAAGTCAAATAGTAGTAATCTGGAT 57.786 33.333 0.00 0.00 0.00 3.41
4815 5248 8.603898 TGGAAGTCAAATAGTAGTAATCTGGA 57.396 34.615 0.00 0.00 0.00 3.86
4816 5249 9.482627 GATGGAAGTCAAATAGTAGTAATCTGG 57.517 37.037 0.00 0.00 0.00 3.86
4817 5250 9.186323 CGATGGAAGTCAAATAGTAGTAATCTG 57.814 37.037 0.00 0.00 0.00 2.90
4819 5252 7.868415 AGCGATGGAAGTCAAATAGTAGTAATC 59.132 37.037 0.00 0.00 0.00 1.75
4820 5253 7.727181 AGCGATGGAAGTCAAATAGTAGTAAT 58.273 34.615 0.00 0.00 0.00 1.89
4821 5254 7.108841 AGCGATGGAAGTCAAATAGTAGTAA 57.891 36.000 0.00 0.00 0.00 2.24
4822 5255 6.710597 AGCGATGGAAGTCAAATAGTAGTA 57.289 37.500 0.00 0.00 0.00 1.82
4823 5256 5.599999 AGCGATGGAAGTCAAATAGTAGT 57.400 39.130 0.00 0.00 0.00 2.73
4824 5257 6.313905 ACAAAGCGATGGAAGTCAAATAGTAG 59.686 38.462 0.00 0.00 0.00 2.57
4843 5276 1.269051 ACGCTGGCTTAACAACAAAGC 60.269 47.619 0.00 0.00 46.90 3.51
4852 5289 0.878416 AAAATGCGACGCTGGCTTAA 59.122 45.000 22.08 0.00 0.00 1.85
4860 5297 0.729140 CCAGACCAAAAATGCGACGC 60.729 55.000 14.19 14.19 0.00 5.19
5039 5476 9.131416 CGTCACACACATAATTAACTAGTGTTA 57.869 33.333 0.00 0.00 41.08 2.41
5118 5555 0.389817 TACACTCCTGCATGCGACAC 60.390 55.000 14.09 0.00 0.00 3.67
5122 5559 1.863454 GAGATTACACTCCTGCATGCG 59.137 52.381 14.09 7.87 0.00 4.73
5210 5654 6.019801 GCAAATAGACTACATAACAGGACACG 60.020 42.308 0.00 0.00 0.00 4.49
5247 5692 7.450124 ACATCAATAGAATCATTGAGATGCC 57.550 36.000 11.55 0.00 45.51 4.40
5364 5809 1.067212 GCAACGAGATACTCCATCGGT 59.933 52.381 0.00 0.00 40.67 4.69
5412 5857 1.125847 CGTGTTTATTTCGCAGCGGC 61.126 55.000 16.42 0.00 0.00 6.53


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

AutoCloner maintained by Alex Coulton.