Multiple sequence alignment - TraesCS1D01G389700

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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 TraesCS1D01G389700 chr1D 100.000 4014 0 0 1 4014 461399542 461395529 0.000000e+00 7413.0
1 TraesCS1D01G389700 chr1D 76.635 933 184 24 1282 2194 459521540 459522458 6.030000e-133 484.0
2 TraesCS1D01G389700 chr1D 76.599 735 158 12 1294 2025 459626529 459625806 3.760000e-105 392.0
3 TraesCS1D01G389700 chr1D 78.458 506 90 14 1281 1776 460196484 460195988 3.010000e-81 313.0
4 TraesCS1D01G389700 chr1D 80.357 280 21 16 290 537 461342603 461342326 8.860000e-42 182.0
5 TraesCS1D01G389700 chr1D 81.301 246 20 10 1 220 461898762 461899007 4.120000e-40 176.0
6 TraesCS1D01G389700 chr1D 88.000 125 13 2 420 544 461899642 461899764 3.230000e-31 147.0
7 TraesCS1D01G389700 chr1A 94.754 3584 109 30 485 4014 552892874 552889316 0.000000e+00 5504.0
8 TraesCS1D01G389700 chr1A 77.643 908 163 31 1287 2167 552387484 552386590 2.140000e-142 516.0
9 TraesCS1D01G389700 chr1A 78.533 750 145 15 1282 2025 551531762 551532501 2.810000e-131 479.0
10 TraesCS1D01G389700 chr1A 76.518 741 154 18 1292 2025 551788034 551787307 1.750000e-103 387.0
11 TraesCS1D01G389700 chr1A 77.522 565 120 6 2435 2996 552964462 552963902 2.310000e-87 333.0
12 TraesCS1D01G389700 chr1A 93.363 226 8 2 1 220 552893914 552893690 1.080000e-85 327.0
13 TraesCS1D01G389700 chr1A 74.576 413 97 5 2589 2993 553567633 553568045 1.480000e-39 174.0
14 TraesCS1D01G389700 chr1A 78.652 267 22 23 251 499 552893502 552893253 1.160000e-30 145.0
15 TraesCS1D01G389700 chr1A 94.318 88 4 1 457 544 552966525 552966439 2.520000e-27 134.0
16 TraesCS1D01G389700 chr1A 82.979 141 10 7 3 129 553482269 553482409 9.120000e-22 115.0
17 TraesCS1D01G389700 chr1B 96.922 1267 39 0 1282 2548 634241758 634240492 0.000000e+00 2124.0
18 TraesCS1D01G389700 chr1B 94.035 855 35 5 3173 4014 634238791 634237940 0.000000e+00 1282.0
19 TraesCS1D01G389700 chr1B 96.926 618 17 1 2546 3163 634240438 634239823 0.000000e+00 1035.0
20 TraesCS1D01G389700 chr1B 78.965 908 157 23 1289 2168 634146372 634145471 4.470000e-164 588.0
21 TraesCS1D01G389700 chr1B 86.929 482 37 13 586 1041 634242745 634242264 5.950000e-143 518.0
22 TraesCS1D01G389700 chr1B 79.228 751 138 14 1282 2025 631716575 631717314 1.290000e-139 507.0
23 TraesCS1D01G389700 chr1B 92.920 226 10 4 1 220 634243316 634243091 1.390000e-84 324.0
24 TraesCS1D01G389700 chr1B 92.248 129 8 1 418 544 634243002 634242874 8.860000e-42 182.0
25 TraesCS1D01G389700 chr1B 74.693 407 100 2 2590 2993 636065072 636065478 1.150000e-40 178.0
26 TraesCS1D01G389700 chr1B 82.895 152 16 8 402 544 635383068 635383218 1.170000e-25 128.0
27 TraesCS1D01G389700 chr1B 87.179 117 9 5 434 544 635917064 635917180 1.170000e-25 128.0
28 TraesCS1D01G389700 chr1B 86.667 120 9 6 426 544 636127809 636127922 4.210000e-25 126.0
29 TraesCS1D01G389700 chr1B 100.000 29 0 0 1054 1082 542433083 542433111 2.000000e-03 54.7
30 TraesCS1D01G389700 chr4A 94.382 89 4 1 457 545 117091700 117091787 7.000000e-28 135.0
31 TraesCS1D01G389700 chr7D 94.118 85 5 0 460 544 47113862 47113778 3.260000e-26 130.0
32 TraesCS1D01G389700 chr7D 100.000 29 0 0 1054 1082 596074623 596074651 2.000000e-03 54.7
33 TraesCS1D01G389700 chr2D 91.045 67 5 1 2440 2506 632692929 632692994 5.530000e-14 89.8
34 TraesCS1D01G389700 chr2D 100.000 31 0 0 1054 1084 109030030 109030000 1.560000e-04 58.4
35 TraesCS1D01G389700 chr2B 95.000 40 2 0 1053 1092 142931584 142931545 3.350000e-06 63.9
36 TraesCS1D01G389700 chr3B 90.476 42 2 2 1054 1093 526693557 526693516 2.000000e-03 54.7


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 TraesCS1D01G389700 chr1D 461395529 461399542 4013 True 7413.000000 7413 100.000 1 4014 1 chr1D.!!$R4 4013
1 TraesCS1D01G389700 chr1D 459521540 459522458 918 False 484.000000 484 76.635 1282 2194 1 chr1D.!!$F1 912
2 TraesCS1D01G389700 chr1D 459625806 459626529 723 True 392.000000 392 76.599 1294 2025 1 chr1D.!!$R1 731
3 TraesCS1D01G389700 chr1A 552889316 552893914 4598 True 1992.000000 5504 88.923 1 4014 3 chr1A.!!$R3 4013
4 TraesCS1D01G389700 chr1A 552386590 552387484 894 True 516.000000 516 77.643 1287 2167 1 chr1A.!!$R2 880
5 TraesCS1D01G389700 chr1A 551531762 551532501 739 False 479.000000 479 78.533 1282 2025 1 chr1A.!!$F1 743
6 TraesCS1D01G389700 chr1A 551787307 551788034 727 True 387.000000 387 76.518 1292 2025 1 chr1A.!!$R1 733
7 TraesCS1D01G389700 chr1A 552963902 552966525 2623 True 233.500000 333 85.920 457 2996 2 chr1A.!!$R4 2539
8 TraesCS1D01G389700 chr1B 634237940 634243316 5376 True 910.833333 2124 93.330 1 4014 6 chr1B.!!$R2 4013
9 TraesCS1D01G389700 chr1B 634145471 634146372 901 True 588.000000 588 78.965 1289 2168 1 chr1B.!!$R1 879
10 TraesCS1D01G389700 chr1B 631716575 631717314 739 False 507.000000 507 79.228 1282 2025 1 chr1B.!!$F2 743

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
661 1330 0.464916 ACGGCCGAAACCTTCAAAGT 60.465 50.0 35.9 0.0 0.0 2.66 F
664 1333 0.668535 GCCGAAACCTTCAAAGTGCT 59.331 50.0 0.0 0.0 0.0 4.40 F
933 1727 0.671251 GAGATAGTGGACCAGAGGCG 59.329 60.0 0.0 0.0 0.0 5.52 F
934 1728 0.757188 AGATAGTGGACCAGAGGCGG 60.757 60.0 0.0 0.0 0.0 6.13 F
2893 4285 0.613572 TGTGCAGGACGTATCTCCCA 60.614 55.0 0.0 0.0 0.0 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1723 2872 0.519999 GAATCGAACTTGCAGCTGCG 60.520 55.000 32.11 21.70 45.83 5.18 R
2132 3462 1.402613 GCTCTCGACAGTTCCTAGGAC 59.597 57.143 12.22 7.12 0.00 3.85 R
2872 4264 1.139058 GGGAGATACGTCCTGCACATT 59.861 52.381 10.58 0.00 36.75 2.71 R
2920 4312 1.966901 TTCCGGCGATGCACCTACAT 61.967 55.000 9.30 0.00 0.00 2.29 R
3848 6271 1.686587 ACAGATGAACCGTGTCTCACA 59.313 47.619 1.00 0.00 33.40 3.58 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
105 106 5.735892 CAGAAAGCACAAATGATACATGTCG 59.264 40.000 0.00 0.00 0.00 4.35
124 125 5.049828 TGTCGTAACTGAATAGCATGATGG 58.950 41.667 0.00 0.00 0.00 3.51
129 130 8.581578 TCGTAACTGAATAGCATGATGGTTATA 58.418 33.333 1.20 0.00 0.00 0.98
156 163 5.691754 GGGAACATGAGTGTGAACAAAATTC 59.308 40.000 0.00 0.00 38.92 2.17
220 227 6.308015 TGTAAGTGCCAGTACCTAAATGAT 57.692 37.500 0.00 0.00 0.00 2.45
221 228 6.112734 TGTAAGTGCCAGTACCTAAATGATG 58.887 40.000 0.00 0.00 0.00 3.07
222 229 4.156455 AGTGCCAGTACCTAAATGATGG 57.844 45.455 0.00 0.00 0.00 3.51
223 230 3.780294 AGTGCCAGTACCTAAATGATGGA 59.220 43.478 0.00 0.00 0.00 3.41
224 231 4.227300 AGTGCCAGTACCTAAATGATGGAA 59.773 41.667 0.00 0.00 0.00 3.53
225 232 5.103940 AGTGCCAGTACCTAAATGATGGAAT 60.104 40.000 0.00 0.00 0.00 3.01
226 233 6.101150 AGTGCCAGTACCTAAATGATGGAATA 59.899 38.462 0.00 0.00 0.00 1.75
229 236 6.942576 GCCAGTACCTAAATGATGGAATATGT 59.057 38.462 0.00 0.00 0.00 2.29
230 237 7.094634 GCCAGTACCTAAATGATGGAATATGTG 60.095 40.741 0.00 0.00 0.00 3.21
232 239 8.777413 CAGTACCTAAATGATGGAATATGTGTG 58.223 37.037 0.00 0.00 0.00 3.82
236 243 9.425248 ACCTAAATGATGGAATATGTGTGAATT 57.575 29.630 0.00 0.00 0.00 2.17
237 244 9.903682 CCTAAATGATGGAATATGTGTGAATTC 57.096 33.333 0.00 0.00 0.00 2.17
242 249 9.811995 ATGATGGAATATGTGTGAATTCTTTTG 57.188 29.630 7.05 0.00 33.50 2.44
243 250 8.805175 TGATGGAATATGTGTGAATTCTTTTGT 58.195 29.630 7.05 0.00 33.50 2.83
244 251 9.294030 GATGGAATATGTGTGAATTCTTTTGTC 57.706 33.333 7.05 0.00 33.50 3.18
245 252 8.175925 TGGAATATGTGTGAATTCTTTTGTCA 57.824 30.769 7.05 0.00 33.50 3.58
246 253 8.298854 TGGAATATGTGTGAATTCTTTTGTCAG 58.701 33.333 7.05 0.00 33.50 3.51
267 434 1.182667 TACATCGACCAGGTGAGTGG 58.817 55.000 0.00 0.00 44.01 4.00
268 435 1.448540 CATCGACCAGGTGAGTGGC 60.449 63.158 0.00 0.00 41.90 5.01
315 482 2.281761 AGCCAAACTGTGCCTCGG 60.282 61.111 0.00 0.00 0.00 4.63
317 484 1.302192 GCCAAACTGTGCCTCGGTA 60.302 57.895 0.00 0.00 34.87 4.02
320 487 1.468520 CCAAACTGTGCCTCGGTATTG 59.531 52.381 0.00 0.00 34.87 1.90
341 509 7.571071 ATTGATTCTATCATCCACCTCTGAT 57.429 36.000 0.00 0.00 39.39 2.90
342 510 7.384524 TTGATTCTATCATCCACCTCTGATT 57.615 36.000 0.00 0.00 39.39 2.57
343 511 7.002250 TGATTCTATCATCCACCTCTGATTC 57.998 40.000 0.00 0.00 34.14 2.52
344 512 6.556116 TGATTCTATCATCCACCTCTGATTCA 59.444 38.462 0.00 0.00 34.14 2.57
345 513 7.237055 TGATTCTATCATCCACCTCTGATTCAT 59.763 37.037 0.00 0.00 34.14 2.57
346 514 6.602410 TCTATCATCCACCTCTGATTCATC 57.398 41.667 0.00 0.00 34.14 2.92
347 515 6.080009 TCTATCATCCACCTCTGATTCATCA 58.920 40.000 0.00 0.00 34.14 3.07
348 516 5.844773 ATCATCCACCTCTGATTCATCAT 57.155 39.130 0.00 0.00 36.02 2.45
349 517 5.224821 TCATCCACCTCTGATTCATCATC 57.775 43.478 0.00 0.00 36.02 2.92
350 518 4.041321 TCATCCACCTCTGATTCATCATCC 59.959 45.833 0.00 0.00 36.02 3.51
351 519 2.707791 TCCACCTCTGATTCATCATCCC 59.292 50.000 0.00 0.00 36.02 3.85
352 520 2.440627 CCACCTCTGATTCATCATCCCA 59.559 50.000 0.00 0.00 36.02 4.37
353 521 3.074094 CCACCTCTGATTCATCATCCCAT 59.926 47.826 0.00 0.00 36.02 4.00
354 522 4.325119 CACCTCTGATTCATCATCCCATC 58.675 47.826 0.00 0.00 36.02 3.51
355 523 4.041815 CACCTCTGATTCATCATCCCATCT 59.958 45.833 0.00 0.00 36.02 2.90
356 524 4.286549 ACCTCTGATTCATCATCCCATCTC 59.713 45.833 0.00 0.00 36.02 2.75
357 525 4.532916 CCTCTGATTCATCATCCCATCTCT 59.467 45.833 0.00 0.00 36.02 3.10
358 526 5.483811 CTCTGATTCATCATCCCATCTCTG 58.516 45.833 0.00 0.00 36.02 3.35
359 527 5.152934 TCTGATTCATCATCCCATCTCTGA 58.847 41.667 0.00 0.00 36.02 3.27
362 530 4.684484 TTCATCATCCCATCTCTGACAG 57.316 45.455 0.00 0.00 0.00 3.51
379 547 4.799678 TGACAGAGAGTTTCTTTCTAGCG 58.200 43.478 0.00 0.00 34.39 4.26
387 555 3.451178 AGTTTCTTTCTAGCGGCCATCTA 59.549 43.478 2.24 2.21 0.00 1.98
388 556 4.101741 AGTTTCTTTCTAGCGGCCATCTAT 59.898 41.667 2.24 0.00 0.00 1.98
389 557 3.667497 TCTTTCTAGCGGCCATCTATG 57.333 47.619 2.24 0.00 0.00 2.23
391 559 3.005897 TCTTTCTAGCGGCCATCTATGAC 59.994 47.826 2.24 0.00 0.00 3.06
392 560 0.881796 TCTAGCGGCCATCTATGACG 59.118 55.000 2.24 0.00 0.00 4.35
394 562 0.538746 TAGCGGCCATCTATGACGGA 60.539 55.000 2.24 0.00 0.00 4.69
395 563 1.373497 GCGGCCATCTATGACGGAG 60.373 63.158 2.24 0.00 0.00 4.63
415 601 5.932883 CGGAGTATAGAGTATAGACACAGCA 59.067 44.000 0.00 0.00 0.00 4.41
537 1119 7.574592 GCGGGAATACTTACCACTATACTACAG 60.575 44.444 0.00 0.00 0.00 2.74
538 1120 7.446625 CGGGAATACTTACCACTATACTACAGT 59.553 40.741 0.00 0.00 0.00 3.55
661 1330 0.464916 ACGGCCGAAACCTTCAAAGT 60.465 50.000 35.90 0.00 0.00 2.66
664 1333 0.668535 GCCGAAACCTTCAAAGTGCT 59.331 50.000 0.00 0.00 0.00 4.40
666 1335 2.481276 GCCGAAACCTTCAAAGTGCTTT 60.481 45.455 0.00 0.00 0.00 3.51
785 1472 6.037940 GCAGCATCATGTATGTATATCCCAAG 59.962 42.308 0.00 0.00 37.93 3.61
791 1478 6.492087 TCATGTATGTATATCCCAAGACGTCA 59.508 38.462 19.50 0.00 0.00 4.35
794 1481 2.359848 TGTATATCCCAAGACGTCACGG 59.640 50.000 19.50 16.71 0.00 4.94
800 1487 1.002250 CCAAGACGTCACGGTTCTCG 61.002 60.000 19.50 0.00 45.88 4.04
896 1685 4.809691 GCAAAGGTGGGACAATACTTACCT 60.810 45.833 0.00 0.00 44.16 3.08
933 1727 0.671251 GAGATAGTGGACCAGAGGCG 59.329 60.000 0.00 0.00 0.00 5.52
934 1728 0.757188 AGATAGTGGACCAGAGGCGG 60.757 60.000 0.00 0.00 0.00 6.13
935 1729 2.370647 GATAGTGGACCAGAGGCGGC 62.371 65.000 0.00 0.00 0.00 6.53
950 1744 4.235762 GGCTTCATCGGCCGGCTA 62.236 66.667 28.56 15.89 40.19 3.93
1053 1849 5.878116 CCCACAGGTATAATCTTGTTTTCGA 59.122 40.000 0.00 0.00 0.00 3.71
1099 1895 6.049790 GGGAGTAGAAAATAAGTAGTGCCTG 58.950 44.000 0.00 0.00 0.00 4.85
1100 1896 5.524281 GGAGTAGAAAATAAGTAGTGCCTGC 59.476 44.000 0.00 0.00 0.00 4.85
1102 1898 6.109359 AGTAGAAAATAAGTAGTGCCTGCTG 58.891 40.000 0.00 0.00 0.00 4.41
1121 2024 6.192234 TGCTGTTTTGTAACTTTACCGAAA 57.808 33.333 0.00 0.00 35.24 3.46
1184 2177 8.514330 AACCGCTATGTTTCCATAAGAAATTA 57.486 30.769 0.00 0.00 45.99 1.40
1323 2458 8.519526 ACAATCTAACTGTTGAAACTTGTCAAA 58.480 29.630 2.69 0.00 39.18 2.69
1723 2872 1.928503 TGTTCCGTTTTGTCTGACGAC 59.071 47.619 2.98 1.49 41.53 4.34
1856 3150 2.082140 TAGCGAGGAAGGATTAGGCA 57.918 50.000 0.00 0.00 0.00 4.75
2132 3462 3.272334 GCGCCAAGCTACCATCCG 61.272 66.667 0.00 0.00 44.04 4.18
2516 3846 3.928005 AGTCACTATCCACGTCTCCTA 57.072 47.619 0.00 0.00 0.00 2.94
2524 3854 4.912317 ATCCACGTCTCCTAGAGCTATA 57.088 45.455 0.00 0.00 0.00 1.31
2767 4159 5.304101 CCTAATCTACATCCTTGAGAGTGCT 59.696 44.000 0.00 0.00 0.00 4.40
2893 4285 0.613572 TGTGCAGGACGTATCTCCCA 60.614 55.000 0.00 0.00 0.00 4.37
2920 4312 2.282783 TAGAGCCGTGGAAGCTGCA 61.283 57.895 1.02 0.00 41.75 4.41
2944 4336 2.125552 TGCATCGCCGGAAGAGTG 60.126 61.111 5.05 5.64 0.00 3.51
3082 4474 7.315890 AGTAAAGCTTTGAACTAATTGCCATC 58.684 34.615 22.02 0.00 0.00 3.51
3149 4541 9.108284 GTGGGAAATCTTTCTTGATTTGAAAAA 57.892 29.630 7.13 0.00 43.97 1.94
3293 5708 9.840427 ATACTATATTTCCAAAATTACGCATGC 57.160 29.630 7.91 7.91 0.00 4.06
3407 5823 6.800408 GCATGCATGTGTGATATTCTGATTAC 59.200 38.462 26.79 0.79 0.00 1.89
3549 5967 4.081862 TCGAATCCGTAGACCATCAAGTTT 60.082 41.667 0.00 0.00 37.05 2.66
3582 6000 9.542462 TGCGCTACAATATCTTTAGTTCTTTAT 57.458 29.630 9.73 0.00 0.00 1.40
3723 6145 9.577110 TGTTTTTGAAGATGAATCTAATGATGC 57.423 29.630 0.00 0.00 35.76 3.91
3848 6271 6.069963 ACCTTTTAGATAGAAGATGTGTGCCT 60.070 38.462 0.00 0.00 0.00 4.75
3867 6290 2.332104 CTGTGAGACACGGTTCATCTG 58.668 52.381 0.00 0.00 37.14 2.90
3895 6318 3.885297 CCACCTATTGCATACCCTTCTTG 59.115 47.826 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
105 106 9.489084 TGTATAACCATCATGCTATTCAGTTAC 57.511 33.333 0.00 0.00 0.00 2.50
124 125 5.730550 TCACACTCATGTTCCCTGTATAAC 58.269 41.667 0.00 0.00 36.72 1.89
129 130 2.172505 TGTTCACACTCATGTTCCCTGT 59.827 45.455 0.00 0.00 36.72 4.00
220 227 8.175925 TGACAAAAGAATTCACACATATTCCA 57.824 30.769 8.44 0.00 32.43 3.53
221 228 8.514594 TCTGACAAAAGAATTCACACATATTCC 58.485 33.333 8.44 0.00 32.43 3.01
225 232 9.500785 TGTATCTGACAAAAGAATTCACACATA 57.499 29.630 8.44 0.00 34.15 2.29
226 233 8.394971 TGTATCTGACAAAAGAATTCACACAT 57.605 30.769 8.44 0.00 34.15 3.21
229 236 7.602265 TCGATGTATCTGACAAAAGAATTCACA 59.398 33.333 8.44 0.00 42.78 3.58
230 237 7.900352 GTCGATGTATCTGACAAAAGAATTCAC 59.100 37.037 8.44 0.00 42.78 3.18
232 239 7.064609 TGGTCGATGTATCTGACAAAAGAATTC 59.935 37.037 0.00 0.00 42.78 2.17
235 242 5.789521 TGGTCGATGTATCTGACAAAAGAA 58.210 37.500 14.20 0.00 42.78 2.52
236 243 5.400066 TGGTCGATGTATCTGACAAAAGA 57.600 39.130 14.20 0.00 42.78 2.52
237 244 4.568359 CCTGGTCGATGTATCTGACAAAAG 59.432 45.833 14.20 10.04 42.78 2.27
241 248 2.427095 CACCTGGTCGATGTATCTGACA 59.573 50.000 0.00 0.00 43.97 3.58
242 249 2.688446 TCACCTGGTCGATGTATCTGAC 59.312 50.000 0.00 7.73 33.07 3.51
243 250 2.952310 CTCACCTGGTCGATGTATCTGA 59.048 50.000 0.00 0.00 0.00 3.27
244 251 2.690497 ACTCACCTGGTCGATGTATCTG 59.310 50.000 0.00 0.00 0.00 2.90
245 252 2.690497 CACTCACCTGGTCGATGTATCT 59.310 50.000 0.00 0.00 0.00 1.98
246 253 2.223829 CCACTCACCTGGTCGATGTATC 60.224 54.545 0.00 0.00 0.00 2.24
267 434 2.205911 GATTAGGGAGCTCGTTCTTGC 58.794 52.381 7.83 0.00 0.00 4.01
268 435 2.432510 AGGATTAGGGAGCTCGTTCTTG 59.567 50.000 7.83 0.00 0.00 3.02
315 482 7.901029 TCAGAGGTGGATGATAGAATCAATAC 58.099 38.462 0.00 0.00 43.50 1.89
317 484 7.571071 ATCAGAGGTGGATGATAGAATCAAT 57.429 36.000 0.00 0.00 43.50 2.57
320 487 7.002250 TGAATCAGAGGTGGATGATAGAATC 57.998 40.000 0.00 0.00 35.11 2.52
341 509 4.292643 TCTGTCAGAGATGGGATGATGAA 58.707 43.478 0.00 0.00 0.00 2.57
342 510 3.896272 CTCTGTCAGAGATGGGATGATGA 59.104 47.826 23.29 0.00 45.07 2.92
343 511 3.896272 TCTCTGTCAGAGATGGGATGATG 59.104 47.826 25.68 0.15 45.77 3.07
344 512 4.196118 TCTCTGTCAGAGATGGGATGAT 57.804 45.455 25.68 0.00 45.77 2.45
345 513 3.677156 TCTCTGTCAGAGATGGGATGA 57.323 47.619 25.68 4.44 45.77 2.92
355 523 5.335269 CGCTAGAAAGAAACTCTCTGTCAGA 60.335 44.000 1.78 1.78 40.54 3.27
356 524 4.856487 CGCTAGAAAGAAACTCTCTGTCAG 59.144 45.833 0.00 0.00 40.54 3.51
357 525 4.321304 CCGCTAGAAAGAAACTCTCTGTCA 60.321 45.833 0.00 0.00 40.54 3.58
358 526 4.170256 CCGCTAGAAAGAAACTCTCTGTC 58.830 47.826 0.00 0.00 38.57 3.51
359 527 3.615351 GCCGCTAGAAAGAAACTCTCTGT 60.615 47.826 0.00 0.00 33.37 3.41
362 530 2.272678 GGCCGCTAGAAAGAAACTCTC 58.727 52.381 0.00 0.00 0.00 3.20
367 535 4.100963 TCATAGATGGCCGCTAGAAAGAAA 59.899 41.667 10.47 0.00 0.00 2.52
374 542 0.109086 CCGTCATAGATGGCCGCTAG 60.109 60.000 10.47 4.26 31.58 3.42
379 547 4.270834 TCTATACTCCGTCATAGATGGCC 58.729 47.826 0.00 0.00 38.52 5.36
387 555 7.677892 TGTGTCTATACTCTATACTCCGTCAT 58.322 38.462 0.00 0.00 0.00 3.06
388 556 7.059202 TGTGTCTATACTCTATACTCCGTCA 57.941 40.000 0.00 0.00 0.00 4.35
389 557 6.091169 GCTGTGTCTATACTCTATACTCCGTC 59.909 46.154 0.00 0.00 0.00 4.79
391 559 5.932883 TGCTGTGTCTATACTCTATACTCCG 59.067 44.000 0.00 0.00 0.00 4.63
392 560 7.162761 TCTGCTGTGTCTATACTCTATACTCC 58.837 42.308 0.00 0.00 0.00 3.85
394 562 9.581289 AATTCTGCTGTGTCTATACTCTATACT 57.419 33.333 0.00 0.00 0.00 2.12
409 595 9.897744 TTTTTCTCTGTATAAAATTCTGCTGTG 57.102 29.630 0.00 0.00 0.00 3.66
537 1119 2.201732 TCACGCTTTCTGTGAAGTCAC 58.798 47.619 4.43 4.43 42.99 3.67
538 1120 2.595124 TCACGCTTTCTGTGAAGTCA 57.405 45.000 0.00 0.00 42.99 3.41
547 1129 3.695830 TCCCTGTTTATCACGCTTTCT 57.304 42.857 0.00 0.00 0.00 2.52
549 1131 3.694566 GGAATCCCTGTTTATCACGCTTT 59.305 43.478 0.00 0.00 0.00 3.51
661 1330 2.048222 CCGTCGCCTGAGAAAGCA 60.048 61.111 0.00 0.00 0.00 3.91
664 1333 1.003839 ATTGCCGTCGCCTGAGAAA 60.004 52.632 0.00 0.00 0.00 2.52
666 1335 2.184322 GATTGCCGTCGCCTGAGA 59.816 61.111 0.00 0.00 0.00 3.27
791 1478 5.523809 TTTCTCCTAGAACACGAGAACCGT 61.524 45.833 7.61 0.00 41.19 4.83
794 1481 5.577554 GGATTTTCTCCTAGAACACGAGAAC 59.422 44.000 7.61 0.00 41.19 3.01
830 1616 1.740025 GAAAGGGAGCCGTGAATTCTG 59.260 52.381 7.05 0.00 0.00 3.02
896 1685 4.350368 TCTCCAATAATGCAGCGGATAA 57.650 40.909 0.00 0.00 0.00 1.75
934 1728 2.203015 TTAGCCGGCCGATGAAGC 60.203 61.111 30.73 21.56 0.00 3.86
935 1729 1.595382 CCTTAGCCGGCCGATGAAG 60.595 63.158 30.73 23.78 0.00 3.02
1053 1849 8.871570 TCCCTCCCTTTCTAAATATAAGTCTT 57.128 34.615 0.00 0.00 0.00 3.01
1099 1895 7.509050 TTTTTCGGTAAAGTTACAAAACAGC 57.491 32.000 3.75 0.00 38.12 4.40
1100 1896 9.894439 CAATTTTTCGGTAAAGTTACAAAACAG 57.106 29.630 3.75 0.00 38.12 3.16
1121 2024 5.682990 GCTGGATGGCATTCATGTACAATTT 60.683 40.000 9.34 0.00 35.97 1.82
1184 2177 1.660607 CGCGTGATACATGAAGCACTT 59.339 47.619 0.00 0.00 0.00 3.16
1723 2872 0.519999 GAATCGAACTTGCAGCTGCG 60.520 55.000 32.11 21.70 45.83 5.18
1856 3150 7.352738 AGGGAAGAAGATTTTGAGAGCAATAT 58.647 34.615 0.00 0.00 33.25 1.28
2132 3462 1.402613 GCTCTCGACAGTTCCTAGGAC 59.597 57.143 12.22 7.12 0.00 3.85
2298 3628 5.332743 TGGAACTTTGGCATTCTAAGGAAT 58.667 37.500 2.08 0.00 42.29 3.01
2516 3846 7.911651 ACATAGTAATTGGCACATATAGCTCT 58.088 34.615 0.00 0.00 39.30 4.09
2524 3854 8.802267 ACAAGTTTAACATAGTAATTGGCACAT 58.198 29.630 0.00 0.00 39.30 3.21
2579 3965 7.962441 ACCTGCATATACATTACACATGTAGA 58.038 34.615 0.00 0.00 37.84 2.59
2872 4264 1.139058 GGGAGATACGTCCTGCACATT 59.861 52.381 10.58 0.00 36.75 2.71
2920 4312 1.966901 TTCCGGCGATGCACCTACAT 61.967 55.000 9.30 0.00 0.00 2.29
2944 4336 3.337358 CTCAAATTCAACATTTGGGGGC 58.663 45.455 7.31 0.00 38.97 5.80
3028 4420 9.450807 GTAACCAATACTATGAATGAACATTGC 57.549 33.333 4.72 0.00 0.00 3.56
3082 4474 2.171448 CACCACTCTCCTCCCCTTTATG 59.829 54.545 0.00 0.00 0.00 1.90
3150 4542 4.686191 TTCCATGGCATGTTCAGTTTTT 57.314 36.364 24.80 0.00 0.00 1.94
3151 4543 4.686191 TTTCCATGGCATGTTCAGTTTT 57.314 36.364 24.80 0.00 0.00 2.43
3497 5915 3.884350 CCGATCTCGCCCGTTCGA 61.884 66.667 10.26 0.00 38.18 3.71
3582 6000 8.371699 CCTTGTAATTTTGAATGGGGAAAGTAA 58.628 33.333 0.00 0.00 0.00 2.24
3604 6026 5.607119 ACAAGTAGTCAAATTACGCCTTG 57.393 39.130 9.59 9.59 37.67 3.61
3848 6271 1.686587 ACAGATGAACCGTGTCTCACA 59.313 47.619 1.00 0.00 33.40 3.58
3867 6290 5.631119 AGGGTATGCAATAGGTGGAAATAC 58.369 41.667 0.00 0.00 0.00 1.89


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

AutoCloner maintained by Alex Coulton.