Multiple sequence alignment - TraesCS5D01G513400

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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 TraesCS5D01G513400 chr5D 100.000 3465 0 0 1 3465 537655444 537658908 0.000000e+00 6399.0
1 TraesCS5D01G513400 chr5D 95.643 482 20 1 2984 3465 97579217 97578737 0.000000e+00 773.0
2 TraesCS5D01G513400 chr5D 88.462 130 8 3 2669 2793 97579500 97579373 2.150000e-32 150.0
3 TraesCS5D01G513400 chr5D 83.974 156 7 8 2474 2614 97579921 97579769 2.170000e-27 134.0
4 TraesCS5D01G513400 chr5D 96.226 53 2 0 2936 2988 97579299 97579247 1.710000e-13 87.9
5 TraesCS5D01G513400 chr5D 97.368 38 0 1 1797 1833 45378160 45378123 2.890000e-06 63.9
6 TraesCS5D01G513400 chr4A 90.290 3553 180 54 1 3463 631899083 631902560 0.000000e+00 4497.0
7 TraesCS5D01G513400 chr5B 90.090 2664 123 63 1 2608 678312435 678315013 0.000000e+00 3326.0
8 TraesCS5D01G513400 chr5B 93.554 543 21 6 2936 3465 106953647 106953106 0.000000e+00 797.0
9 TraesCS5D01G513400 chr5B 93.902 492 19 3 2984 3465 105537702 105538192 0.000000e+00 732.0
10 TraesCS5D01G513400 chr5B 93.361 482 20 3 2984 3465 678315513 678315982 0.000000e+00 702.0
11 TraesCS5D01G513400 chr5B 89.785 186 6 6 2805 2979 678315291 678315474 3.480000e-55 226.0
12 TraesCS5D01G513400 chr5B 83.173 208 15 5 325 532 678205762 678205949 4.600000e-39 172.0
13 TraesCS5D01G513400 chr5B 79.508 244 33 9 2560 2793 105537326 105537562 1.290000e-34 158.0
14 TraesCS5D01G513400 chr5B 81.410 156 10 9 2474 2614 105537127 105537278 3.660000e-20 110.0
15 TraesCS5D01G513400 chr5B 97.872 47 1 0 2942 2988 105537626 105537672 7.970000e-12 82.4
16 TraesCS5D01G513400 chr5A 93.971 481 28 1 2985 3465 106164286 106164765 0.000000e+00 726.0
17 TraesCS5D01G513400 chr5A 96.226 53 2 0 2936 2988 106164201 106164253 1.710000e-13 87.9
18 TraesCS5D01G513400 chr5A 93.617 47 1 2 1789 1833 36331754 36331800 6.210000e-08 69.4


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 TraesCS5D01G513400 chr5D 537655444 537658908 3464 False 6399.000 6399 100.000000 1 3465 1 chr5D.!!$F1 3464
1 TraesCS5D01G513400 chr5D 97578737 97579921 1184 True 286.225 773 91.076250 2474 3465 4 chr5D.!!$R2 991
2 TraesCS5D01G513400 chr4A 631899083 631902560 3477 False 4497.000 4497 90.290000 1 3463 1 chr4A.!!$F1 3462
3 TraesCS5D01G513400 chr5B 678312435 678315982 3547 False 1418.000 3326 91.078667 1 3465 3 chr5B.!!$F3 3464
4 TraesCS5D01G513400 chr5B 106953106 106953647 541 True 797.000 797 93.554000 2936 3465 1 chr5B.!!$R1 529
5 TraesCS5D01G513400 chr5B 105537127 105538192 1065 False 270.600 732 88.173000 2474 3465 4 chr5B.!!$F2 991
6 TraesCS5D01G513400 chr5A 106164201 106164765 564 False 406.950 726 95.098500 2936 3465 2 chr5A.!!$F2 529

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
889 920 1.058748 CCGCTTTGTATCACGCACG 59.941 57.895 0.0 0.0 0.0 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2724 3135 0.179097 TCGCGCATGCCATTGTACTA 60.179 50.0 13.15 0.0 38.08 1.82 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
121 122 1.339824 CCATCTGCTATGCCCCATCTC 60.340 57.143 0.00 0.00 0.00 2.75
207 218 4.284178 ACTTGGATTGGATTGGATTGAGG 58.716 43.478 0.00 0.00 0.00 3.86
212 223 4.522022 GGATTGGATTGGATTGAGGATGAC 59.478 45.833 0.00 0.00 0.00 3.06
259 270 3.957497 AGTGCAAGACTACTAGATCAGGG 59.043 47.826 0.00 0.00 30.86 4.45
289 300 1.409064 TGTGTGAGAGACAGTCACCAC 59.591 52.381 2.66 8.00 43.19 4.16
291 302 1.409064 TGTGAGAGACAGTCACCACAC 59.591 52.381 14.76 14.59 43.19 3.82
334 345 3.756117 GATTGGACCTGAAAACCTCTGT 58.244 45.455 0.00 0.00 0.00 3.41
335 346 2.638480 TGGACCTGAAAACCTCTGTG 57.362 50.000 0.00 0.00 0.00 3.66
450 461 4.219944 TCACACTATCACCACCTTCTACAC 59.780 45.833 0.00 0.00 0.00 2.90
474 485 6.024049 CGTATGCTTTTCTCCTGATGAAAAC 58.976 40.000 0.00 0.00 38.15 2.43
476 487 5.850557 TGCTTTTCTCCTGATGAAAACAA 57.149 34.783 0.00 0.00 38.15 2.83
477 488 6.219417 TGCTTTTCTCCTGATGAAAACAAA 57.781 33.333 0.00 0.00 38.15 2.83
478 489 6.042143 TGCTTTTCTCCTGATGAAAACAAAC 58.958 36.000 0.00 0.00 38.15 2.93
479 490 5.463392 GCTTTTCTCCTGATGAAAACAAACC 59.537 40.000 0.00 0.00 38.15 3.27
480 491 6.537453 TTTTCTCCTGATGAAAACAAACCA 57.463 33.333 0.00 0.00 38.15 3.67
481 492 6.537453 TTTCTCCTGATGAAAACAAACCAA 57.463 33.333 0.00 0.00 31.45 3.67
482 493 6.729690 TTCTCCTGATGAAAACAAACCAAT 57.270 33.333 0.00 0.00 0.00 3.16
483 494 6.331369 TCTCCTGATGAAAACAAACCAATC 57.669 37.500 0.00 0.00 0.00 2.67
484 495 5.832595 TCTCCTGATGAAAACAAACCAATCA 59.167 36.000 0.00 0.00 0.00 2.57
485 496 6.016024 TCTCCTGATGAAAACAAACCAATCAG 60.016 38.462 0.00 0.00 35.39 2.90
486 497 5.232463 CCTGATGAAAACAAACCAATCAGG 58.768 41.667 13.46 13.46 45.09 3.86
487 498 5.212532 TGATGAAAACAAACCAATCAGGG 57.787 39.130 0.00 0.00 43.89 4.45
488 499 4.898265 TGATGAAAACAAACCAATCAGGGA 59.102 37.500 0.00 0.00 43.89 4.20
489 500 5.543405 TGATGAAAACAAACCAATCAGGGAT 59.457 36.000 0.00 0.00 43.89 3.85
490 501 5.212532 TGAAAACAAACCAATCAGGGATG 57.787 39.130 0.00 0.00 43.89 3.51
491 502 3.683365 AAACAAACCAATCAGGGATGC 57.317 42.857 0.00 0.00 43.89 3.91
492 503 1.560505 ACAAACCAATCAGGGATGCC 58.439 50.000 0.00 0.00 43.89 4.40
493 504 1.203162 ACAAACCAATCAGGGATGCCA 60.203 47.619 5.86 0.00 43.89 4.92
494 505 2.112998 CAAACCAATCAGGGATGCCAT 58.887 47.619 5.86 0.00 43.89 4.40
495 506 3.298619 CAAACCAATCAGGGATGCCATA 58.701 45.455 5.86 0.00 43.89 2.74
496 507 3.899360 CAAACCAATCAGGGATGCCATAT 59.101 43.478 5.86 0.00 43.89 1.78
534 545 4.903054 TGTCTGAATCAGCATTCTCAAGT 58.097 39.130 5.18 0.00 39.49 3.16
536 547 4.694509 GTCTGAATCAGCATTCTCAAGTGT 59.305 41.667 5.18 0.00 39.49 3.55
539 550 5.250982 TGAATCAGCATTCTCAAGTGTCAT 58.749 37.500 0.00 0.00 39.49 3.06
540 551 5.123344 TGAATCAGCATTCTCAAGTGTCATG 59.877 40.000 0.00 0.00 39.49 3.07
541 552 4.276058 TCAGCATTCTCAAGTGTCATGA 57.724 40.909 0.00 0.00 0.00 3.07
542 553 4.840271 TCAGCATTCTCAAGTGTCATGAT 58.160 39.130 0.00 0.00 0.00 2.45
543 554 4.634443 TCAGCATTCTCAAGTGTCATGATG 59.366 41.667 0.00 0.00 33.49 3.07
546 557 4.380128 GCATTCTCAAGTGTCATGATGCAA 60.380 41.667 0.00 0.00 32.98 4.08
547 558 5.678871 GCATTCTCAAGTGTCATGATGCAAT 60.679 40.000 0.00 0.00 32.98 3.56
548 559 6.459161 GCATTCTCAAGTGTCATGATGCAATA 60.459 38.462 0.00 0.00 32.98 1.90
549 560 7.649057 CATTCTCAAGTGTCATGATGCAATAT 58.351 34.615 0.00 0.00 0.00 1.28
550 561 8.780249 CATTCTCAAGTGTCATGATGCAATATA 58.220 33.333 0.00 0.00 0.00 0.86
551 562 7.719778 TCTCAAGTGTCATGATGCAATATAC 57.280 36.000 0.00 0.00 0.00 1.47
552 563 7.274447 TCTCAAGTGTCATGATGCAATATACA 58.726 34.615 0.00 0.00 0.00 2.29
553 564 7.935210 TCTCAAGTGTCATGATGCAATATACAT 59.065 33.333 0.00 0.00 0.00 2.29
554 565 9.211485 CTCAAGTGTCATGATGCAATATACATA 57.789 33.333 0.00 0.00 0.00 2.29
555 566 9.558396 TCAAGTGTCATGATGCAATATACATAA 57.442 29.630 0.00 0.00 0.00 1.90
628 642 4.257267 TCTTCTGCGACTGAAATGAGAA 57.743 40.909 0.00 0.00 0.00 2.87
695 725 5.241728 GCACCAGGTACATCTTTCTTCTTTT 59.758 40.000 0.00 0.00 0.00 2.27
870 901 1.818674 CCCCTATTGCTCGTGCTTTTT 59.181 47.619 11.19 0.00 40.48 1.94
889 920 1.058748 CCGCTTTGTATCACGCACG 59.941 57.895 0.00 0.00 0.00 5.34
1131 1172 3.706373 TCGTTGGGCAGGGAGAGC 61.706 66.667 0.00 0.00 0.00 4.09
1135 1176 1.847506 TTGGGCAGGGAGAGCTTCA 60.848 57.895 0.00 0.00 0.00 3.02
1141 1182 0.179936 CAGGGAGAGCTTCATGGGTC 59.820 60.000 0.00 0.00 0.00 4.46
1149 1190 0.517316 GCTTCATGGGTCGTGTTGTC 59.483 55.000 0.00 0.00 0.00 3.18
1158 1199 1.083209 TCGTGTTGTCGACGTCTCG 60.083 57.895 14.70 20.07 41.65 4.04
1159 1200 1.083209 CGTGTTGTCGACGTCTCGA 60.083 57.895 20.92 4.40 46.85 4.04
1210 1254 3.827898 GAGCCAGGGAGACGACGG 61.828 72.222 0.00 0.00 0.00 4.79
1215 1259 4.405671 AGGGAGACGACGGCTCGA 62.406 66.667 23.86 0.00 43.06 4.04
1518 1562 2.840753 AATCACCAACCCGGCCACT 61.841 57.895 2.24 0.00 39.03 4.00
1520 1564 1.279025 ATCACCAACCCGGCCACTAT 61.279 55.000 2.24 0.00 39.03 2.12
1715 1759 4.021925 GCAGGACGGGCTGGACTT 62.022 66.667 0.00 0.00 0.00 3.01
1969 2013 3.056107 ACTGTTAGCAACGCCTTCTGATA 60.056 43.478 0.00 0.00 0.00 2.15
2016 2060 2.624838 CAGGTTCAGGAACTTGCATGTT 59.375 45.455 17.08 17.08 40.60 2.71
2026 2070 2.079158 ACTTGCATGTTCCAGACATCG 58.921 47.619 0.00 0.00 45.88 3.84
2052 2096 5.048713 CAGGTTCAGGGTAAGAATGAACAAC 60.049 44.000 16.45 3.45 0.00 3.32
2092 2136 7.093354 GTCTCTAGAACACATGATCTTGTCAA 58.907 38.462 11.10 0.00 40.97 3.18
2113 2157 7.431960 TGTCAAGAATTTCAAATCAAACAGTCG 59.568 33.333 0.00 0.00 0.00 4.18
2127 2171 7.173863 TCAAACAGTCGAATTCTTACACTTC 57.826 36.000 3.52 0.00 0.00 3.01
2128 2172 6.984474 TCAAACAGTCGAATTCTTACACTTCT 59.016 34.615 3.52 0.00 0.00 2.85
2129 2173 7.494625 TCAAACAGTCGAATTCTTACACTTCTT 59.505 33.333 3.52 0.00 0.00 2.52
2130 2174 8.761497 CAAACAGTCGAATTCTTACACTTCTTA 58.239 33.333 3.52 0.00 0.00 2.10
2131 2175 8.882415 AACAGTCGAATTCTTACACTTCTTAA 57.118 30.769 3.52 0.00 0.00 1.85
2132 2176 8.522178 ACAGTCGAATTCTTACACTTCTTAAG 57.478 34.615 3.52 0.00 0.00 1.85
2133 2177 8.142551 ACAGTCGAATTCTTACACTTCTTAAGT 58.857 33.333 3.52 0.00 44.06 2.24
2134 2178 8.979574 CAGTCGAATTCTTACACTTCTTAAGTT 58.020 33.333 3.52 0.00 40.46 2.66
2158 2202 6.002082 TCTTATGCTAAGCTGATCATGCAAT 58.998 36.000 16.20 9.14 34.07 3.56
2161 2205 3.050619 GCTAAGCTGATCATGCAATTGC 58.949 45.455 23.69 23.69 42.50 3.56
2163 2207 0.384309 AGCTGATCATGCAATTGCGG 59.616 50.000 24.58 18.92 45.83 5.69
2199 2243 4.388499 CGGCTACAACCCGGCAGT 62.388 66.667 0.00 0.00 41.99 4.40
2203 2247 1.375523 CTACAACCCGGCAGTGACC 60.376 63.158 0.00 0.00 0.00 4.02
2414 2467 1.071987 CTGAACTGCAGCTGGGTCA 59.928 57.895 17.12 12.97 37.90 4.02
2482 2552 3.938653 GCATCCATGTGCTGATGTG 57.061 52.632 10.24 0.00 41.82 3.21
2485 2555 1.333931 CATCCATGTGCTGATGTGCTC 59.666 52.381 0.00 0.00 34.90 4.26
2520 2590 7.044181 ACATGATATTCACTTGTGTACAGAGG 58.956 38.462 0.00 0.00 0.00 3.69
2572 2656 2.103263 TGCCTGTGTGTGTGTGTGTATA 59.897 45.455 0.00 0.00 0.00 1.47
2573 2657 3.135225 GCCTGTGTGTGTGTGTGTATAA 58.865 45.455 0.00 0.00 0.00 0.98
2614 2803 9.608617 CAGAATGTTGCTTATAGCTATGAAATG 57.391 33.333 16.77 0.40 42.97 2.32
2709 3115 7.377766 TCATCTTCTTTTCCATTACCTTTCG 57.622 36.000 0.00 0.00 0.00 3.46
2724 3135 2.949644 CCTTTCGGACCTTTTGACACTT 59.050 45.455 0.00 0.00 0.00 3.16
2729 3140 4.874970 TCGGACCTTTTGACACTTAGTAC 58.125 43.478 0.00 0.00 0.00 2.73
2800 3212 8.585436 GCTAGTAAGAAGTAAGAAGTAAAAGCG 58.415 37.037 0.00 0.00 0.00 4.68
2900 3314 4.450419 CAGGAAACAGAAGTAGTTGCTCTG 59.550 45.833 0.00 0.00 34.85 3.35
2980 3403 8.584600 CAACTAGCTTACATCAAAACTACTACG 58.415 37.037 0.00 0.00 0.00 3.51
3042 3502 5.247792 TCCATCCTAGATGAGGTTCATGATG 59.752 44.000 6.15 3.85 46.76 3.07
3083 3543 2.093764 CCGAGCAAGATTCTTCACTCCT 60.094 50.000 15.47 1.94 0.00 3.69
3182 3642 7.278646 TCCTTGATGTTTCGAAGTGATTCTATG 59.721 37.037 0.00 0.00 0.00 2.23
3266 3726 0.538057 TGAACAGAAGGCCCTGCAAG 60.538 55.000 8.77 0.00 37.68 4.01
3357 3830 1.578206 GAAGGAAAGGCAGACACGGC 61.578 60.000 0.00 0.00 0.00 5.68
3409 3882 2.038557 GGACTAGGTTGGCAGAAGAACA 59.961 50.000 0.00 0.00 0.00 3.18
3432 3905 9.926158 AACATGCATAAAACAATCATTCTAACA 57.074 25.926 0.00 0.00 0.00 2.41
3447 3920 5.939764 TTCTAACAGACTACATCCATGCT 57.060 39.130 0.00 0.00 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
121 122 5.821204 AGAAGAAATTTCAGTGTTTGGACG 58.179 37.500 19.99 0.00 0.00 4.79
207 218 2.998670 CTGTGTGTCCATGTCAGTCATC 59.001 50.000 0.00 0.00 34.09 2.92
212 223 2.531522 TCACTGTGTGTCCATGTCAG 57.468 50.000 7.79 0.00 34.79 3.51
259 270 3.066621 TGTCTCTCACACACAAAAATGGC 59.933 43.478 0.00 0.00 0.00 4.40
289 300 2.032549 CGACAAAGGTGCTTTCTCTGTG 60.033 50.000 0.00 0.00 30.60 3.66
291 302 2.213499 ACGACAAAGGTGCTTTCTCTG 58.787 47.619 0.00 0.00 30.60 3.35
334 345 2.299867 GGGAAAAATGCTTTGCTCTCCA 59.700 45.455 0.00 0.00 0.00 3.86
335 346 2.564504 AGGGAAAAATGCTTTGCTCTCC 59.435 45.455 0.00 0.00 20.81 3.71
434 445 3.430374 GCATACGTGTAGAAGGTGGTGAT 60.430 47.826 0.00 0.00 0.00 3.06
450 461 5.801350 TTTCATCAGGAGAAAAGCATACG 57.199 39.130 0.00 0.00 32.47 3.06
474 485 1.559368 TGGCATCCCTGATTGGTTTG 58.441 50.000 0.00 0.00 0.00 2.93
476 487 3.899360 CAATATGGCATCCCTGATTGGTT 59.101 43.478 1.65 0.00 33.68 3.67
477 488 3.503365 CAATATGGCATCCCTGATTGGT 58.497 45.455 1.65 0.00 33.68 3.67
478 489 2.232941 GCAATATGGCATCCCTGATTGG 59.767 50.000 17.23 4.49 35.84 3.16
479 490 2.232941 GGCAATATGGCATCCCTGATTG 59.767 50.000 1.65 9.36 43.14 2.67
480 491 2.532843 GGCAATATGGCATCCCTGATT 58.467 47.619 1.65 0.00 43.14 2.57
481 492 2.226962 GGCAATATGGCATCCCTGAT 57.773 50.000 1.65 0.00 43.14 2.90
482 493 3.751767 GGCAATATGGCATCCCTGA 57.248 52.632 1.65 0.00 43.14 3.86
490 501 0.249996 GGTGGCAATGGCAATATGGC 60.250 55.000 12.09 14.96 43.71 4.40
491 502 0.393820 GGGTGGCAATGGCAATATGG 59.606 55.000 12.09 0.00 43.71 2.74
492 503 0.393820 GGGGTGGCAATGGCAATATG 59.606 55.000 12.09 0.00 43.71 1.78
493 504 0.265553 AGGGGTGGCAATGGCAATAT 59.734 50.000 12.09 0.00 43.71 1.28
494 505 0.687098 CAGGGGTGGCAATGGCAATA 60.687 55.000 12.09 0.00 43.71 1.90
495 506 1.991167 CAGGGGTGGCAATGGCAAT 60.991 57.895 12.09 0.00 43.71 3.56
496 507 2.604079 CAGGGGTGGCAATGGCAA 60.604 61.111 12.09 0.00 43.71 4.52
541 552 9.410556 GCGAAAAGGAATTTATGTATATTGCAT 57.589 29.630 0.00 0.00 0.00 3.96
542 553 7.865385 GGCGAAAAGGAATTTATGTATATTGCA 59.135 33.333 0.00 0.00 0.00 4.08
543 554 7.060633 CGGCGAAAAGGAATTTATGTATATTGC 59.939 37.037 0.00 0.00 0.00 3.56
546 557 7.739498 ACGGCGAAAAGGAATTTATGTATAT 57.261 32.000 16.62 0.00 0.00 0.86
547 558 8.836268 ATACGGCGAAAAGGAATTTATGTATA 57.164 30.769 16.62 0.00 0.00 1.47
548 559 7.739498 ATACGGCGAAAAGGAATTTATGTAT 57.261 32.000 16.62 0.00 0.00 2.29
549 560 7.556733 AATACGGCGAAAAGGAATTTATGTA 57.443 32.000 16.62 0.00 0.00 2.29
550 561 6.445357 AATACGGCGAAAAGGAATTTATGT 57.555 33.333 16.62 0.00 0.00 2.29
551 562 6.140108 CGAAATACGGCGAAAAGGAATTTATG 59.860 38.462 16.62 1.30 38.46 1.90
552 563 6.196571 CGAAATACGGCGAAAAGGAATTTAT 58.803 36.000 16.62 0.00 38.46 1.40
553 564 5.561993 CGAAATACGGCGAAAAGGAATTTA 58.438 37.500 16.62 0.00 38.46 1.40
554 565 4.408694 CGAAATACGGCGAAAAGGAATTT 58.591 39.130 16.62 7.36 38.46 1.82
555 566 4.011058 CGAAATACGGCGAAAAGGAATT 57.989 40.909 16.62 0.00 38.46 2.17
556 567 3.668596 CGAAATACGGCGAAAAGGAAT 57.331 42.857 16.62 0.00 38.46 3.01
623 637 8.939929 GTTATCTTGTCACTTTGATCATTCTCA 58.060 33.333 0.00 0.00 0.00 3.27
628 642 9.234827 TCAATGTTATCTTGTCACTTTGATCAT 57.765 29.630 0.00 0.00 32.55 2.45
695 725 1.203287 CACATCCTCTGCTGTCGAGAA 59.797 52.381 0.00 0.00 0.00 2.87
870 901 1.348538 CGTGCGTGATACAAAGCGGA 61.349 55.000 0.00 0.00 0.00 5.54
889 920 2.492088 AGGCGAAATTTAAAGGCTGGAC 59.508 45.455 13.49 0.00 38.11 4.02
920 951 1.781786 ATGCGAGGAGAAAGGAGCTA 58.218 50.000 0.00 0.00 0.00 3.32
1004 1045 4.775977 AGCTGAGAGCCGGAGCCT 62.776 66.667 5.05 0.00 43.77 4.58
1104 1145 4.430765 CCCAACGACCCGTCCTCG 62.431 72.222 0.00 0.00 39.99 4.63
1105 1146 4.754667 GCCCAACGACCCGTCCTC 62.755 72.222 0.00 0.00 39.99 3.71
1113 1154 2.266055 CTCTCCCTGCCCAACGAC 59.734 66.667 0.00 0.00 0.00 4.34
1114 1155 3.706373 GCTCTCCCTGCCCAACGA 61.706 66.667 0.00 0.00 0.00 3.85
1118 1159 1.617536 ATGAAGCTCTCCCTGCCCA 60.618 57.895 0.00 0.00 0.00 5.36
1131 1172 0.790207 CGACAACACGACCCATGAAG 59.210 55.000 0.00 0.00 35.09 3.02
1158 1199 3.984765 CGGCGCCGCGAATTACTC 61.985 66.667 38.48 0.00 0.00 2.59
1190 1234 4.779733 TCGTCTCCCTGGCTCCCC 62.780 72.222 0.00 0.00 0.00 4.81
1197 1241 4.180946 CGAGCCGTCGTCTCCCTG 62.181 72.222 0.00 0.00 41.57 4.45
1198 1242 4.405671 TCGAGCCGTCGTCTCCCT 62.406 66.667 0.00 0.00 46.85 4.20
1202 1246 3.488978 CGTCTCGAGCCGTCGTCT 61.489 66.667 7.87 0.00 46.85 4.18
1210 1254 3.524759 CGCGAACACGTCTCGAGC 61.525 66.667 18.22 1.89 38.61 5.03
1969 2013 0.605083 TCAGCAGCTCGTCAGTGATT 59.395 50.000 0.00 0.00 0.00 2.57
2026 2070 4.553330 TCATTCTTACCCTGAACCTGAC 57.447 45.455 0.00 0.00 0.00 3.51
2052 2096 7.953158 TTCTAGAGACATGTCTTGAACAAAG 57.047 36.000 28.46 16.00 42.37 2.77
2092 2136 9.185192 GAATTCGACTGTTTGATTTGAAATTCT 57.815 29.630 0.00 0.00 0.00 2.40
2127 2171 8.654230 TGATCAGCTTAGCATAAGAACTTAAG 57.346 34.615 7.07 0.00 0.00 1.85
2128 2172 9.049523 CATGATCAGCTTAGCATAAGAACTTAA 57.950 33.333 7.07 0.00 0.00 1.85
2129 2173 7.172190 GCATGATCAGCTTAGCATAAGAACTTA 59.828 37.037 7.07 0.00 0.00 2.24
2130 2174 6.017275 GCATGATCAGCTTAGCATAAGAACTT 60.017 38.462 7.07 0.00 0.00 2.66
2131 2175 5.469421 GCATGATCAGCTTAGCATAAGAACT 59.531 40.000 7.07 0.00 0.00 3.01
2132 2176 5.237996 TGCATGATCAGCTTAGCATAAGAAC 59.762 40.000 7.07 0.00 0.00 3.01
2133 2177 5.370679 TGCATGATCAGCTTAGCATAAGAA 58.629 37.500 7.07 0.00 0.00 2.52
2134 2178 4.964593 TGCATGATCAGCTTAGCATAAGA 58.035 39.130 7.07 0.00 0.00 2.10
2138 2182 4.796290 GCAATTGCATGATCAGCTTAGCAT 60.796 41.667 25.36 0.00 41.59 3.79
2158 2202 1.898094 AGAACTGCACATGCCGCAA 60.898 52.632 11.18 0.00 39.30 4.85
2197 2241 3.941188 CCTGTGGTGCCGGTCACT 61.941 66.667 22.54 0.00 44.98 3.41
2414 2467 4.141756 GGTGAACATCCAGATCAGAGACAT 60.142 45.833 0.00 0.00 28.79 3.06
2478 2531 2.936919 TGTCAACAAGAGGAGCACAT 57.063 45.000 0.00 0.00 0.00 3.21
2482 2552 5.819379 TGAATATCATGTCAACAAGAGGAGC 59.181 40.000 0.00 0.00 0.00 4.70
2485 2555 7.120285 ACAAGTGAATATCATGTCAACAAGAGG 59.880 37.037 0.00 0.00 0.00 3.69
2520 2590 8.924511 TTATCCCTCTGAATTCATTTATCCAC 57.075 34.615 8.96 0.00 0.00 4.02
2572 2656 1.273759 TCTGCTCAGCTCAGTCCATT 58.726 50.000 0.00 0.00 33.48 3.16
2573 2657 1.273759 TTCTGCTCAGCTCAGTCCAT 58.726 50.000 0.00 0.00 33.48 3.41
2614 2803 4.803098 ACTCCATACTCACCTAACACAC 57.197 45.455 0.00 0.00 0.00 3.82
2709 3115 6.072673 CCATTGTACTAAGTGTCAAAAGGTCC 60.073 42.308 0.00 0.00 0.00 4.46
2724 3135 0.179097 TCGCGCATGCCATTGTACTA 60.179 50.000 13.15 0.00 38.08 1.82
2729 3140 0.802994 ACAAATCGCGCATGCCATTG 60.803 50.000 13.15 12.18 31.96 2.82
2900 3314 9.790389 CCCTCAATTGTATATCGTAGATCTAAC 57.210 37.037 3.40 0.00 45.12 2.34
2980 3403 1.087501 GCAACACGAGAATCTTCCCC 58.912 55.000 0.00 0.00 0.00 4.81
3042 3502 6.675728 GCTCGGAAGATTTCATAAACAGAACC 60.676 42.308 0.00 0.00 40.84 3.62
3083 3543 4.036262 GTCACTCTAAAATGTGTTGGTGCA 59.964 41.667 0.00 0.00 35.82 4.57
3266 3726 8.128582 TCACATGATGTTTCTCTTGTAAACAAC 58.871 33.333 0.00 4.20 46.59 3.32
3357 3830 2.704464 TGGCAAGATGATGTCTGAGG 57.296 50.000 0.00 0.00 37.23 3.86
3409 3882 9.793252 GTCTGTTAGAATGATTGTTTTATGCAT 57.207 29.630 3.79 3.79 0.00 3.96
3432 3905 6.985653 ACATAGTAAGCATGGATGTAGTCT 57.014 37.500 0.00 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.