Multiple sequence alignment - TraesCS1B01G348200

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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 TraesCS1B01G348200 chr1B 100.000 3487 0 0 1 3487 577798577 577795091 0.000000e+00 6440.0
1 TraesCS1B01G348200 chr1D 90.860 1674 118 17 1842 3485 427235624 427233956 0.000000e+00 2211.0
2 TraesCS1B01G348200 chr1D 89.631 1408 94 15 475 1843 427238756 427237362 0.000000e+00 1744.0
3 TraesCS1B01G348200 chr1D 88.174 482 43 6 2 470 427239210 427238730 2.350000e-156 562.0
4 TraesCS1B01G348200 chr1A 89.604 1616 136 16 1895 3484 522501106 522499497 0.000000e+00 2025.0
5 TraesCS1B01G348200 chr1A 94.439 1079 54 4 802 1875 522502294 522501217 0.000000e+00 1655.0
6 TraesCS1B01G348200 chr1A 84.615 169 23 2 523 691 522502914 522502749 7.740000e-37 165.0
7 TraesCS1B01G348200 chr1A 89.381 113 8 4 1409 1519 95861379 95861489 4.690000e-29 139.0
8 TraesCS1B01G348200 chr5B 85.526 228 29 3 1074 1298 603873283 603873057 5.820000e-58 235.0
9 TraesCS1B01G348200 chr2B 82.759 174 24 4 1165 1335 51201764 51201594 2.170000e-32 150.0
10 TraesCS1B01G348200 chr2B 97.727 44 1 0 1083 1126 51201801 51201758 3.730000e-10 76.8
11 TraesCS1B01G348200 chr5A 90.566 106 8 2 1414 1519 545599858 545599755 4.690000e-29 139.0


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 TraesCS1B01G348200 chr1B 577795091 577798577 3486 True 6440.000000 6440 100.000000 1 3487 1 chr1B.!!$R1 3486
1 TraesCS1B01G348200 chr1D 427233956 427239210 5254 True 1505.666667 2211 89.555000 2 3485 3 chr1D.!!$R1 3483
2 TraesCS1B01G348200 chr1A 522499497 522502914 3417 True 1281.666667 2025 89.552667 523 3484 3 chr1A.!!$R1 2961


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
418 432 0.035317 TGCAATTCACTCGTGGAGCT 59.965 50.0 0.0 0.0 32.04 4.09 F
989 1375 0.036388 ATCAACCACCCTGCACGTAG 60.036 55.0 0.0 0.0 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2189 4414 0.172578 ATTCGTCGTCTCGCCAATCA 59.827 50.0 0.0 0.0 0.0 2.57 R
2594 4819 0.321298 TTGAAGGACAAGTAGGGCGC 60.321 55.0 0.0 0.0 34.2 6.53 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
24 25 5.828328 AGGAGGTCTTTCAAAACTTACAAGG 59.172 40.000 0.00 0.00 0.00 3.61
25 26 5.507482 GGAGGTCTTTCAAAACTTACAAGGC 60.507 44.000 0.00 0.00 0.00 4.35
26 27 4.341235 AGGTCTTTCAAAACTTACAAGGCC 59.659 41.667 0.00 0.00 39.19 5.19
58 61 6.839124 TTGTGCAAATCTGGTCTTTCATAT 57.161 33.333 0.00 0.00 0.00 1.78
99 102 5.034152 TGAACAAAAGTCGAGATGCAAAAC 58.966 37.500 0.00 0.00 0.00 2.43
112 115 7.064609 TCGAGATGCAAAACATAAAACTAGAGG 59.935 37.037 0.00 0.00 39.84 3.69
114 117 5.041951 TGCAAAACATAAAACTAGAGGCG 57.958 39.130 0.00 0.00 0.00 5.52
126 132 3.887352 ACTAGAGGCGATGACTTGACTA 58.113 45.455 0.00 0.00 0.00 2.59
134 140 5.053145 GGCGATGACTTGACTAGATTGAAT 58.947 41.667 0.00 0.00 0.00 2.57
155 161 6.985645 TGAATTGGAGATTTTTGTTGTCCTTG 59.014 34.615 0.00 0.00 0.00 3.61
168 174 3.936372 TGTCCTTGTGTGCTCTAGTAC 57.064 47.619 0.00 0.00 0.00 2.73
231 237 7.920151 AGTTAGATCTTGATTGACGAATGAGAG 59.080 37.037 0.00 0.00 0.00 3.20
232 238 6.219417 AGATCTTGATTGACGAATGAGAGT 57.781 37.500 0.00 0.00 0.00 3.24
256 262 7.381678 AGTTTGACTCGAAGAATGTAGTAACAC 59.618 37.037 0.00 0.00 38.78 3.32
294 300 9.599866 AAAATTAATGATAAGTAAAGCCAAGCC 57.400 29.630 0.00 0.00 0.00 4.35
344 358 3.713826 AGAAAAACCCGAAGCCATCTA 57.286 42.857 0.00 0.00 0.00 1.98
352 366 2.224606 CCGAAGCCATCTACATTGCAT 58.775 47.619 0.00 0.00 0.00 3.96
360 374 7.822161 AGCCATCTACATTGCATATGTTTTA 57.178 32.000 16.19 6.51 33.76 1.52
368 382 9.797473 CTACATTGCATATGTTTTACGATAGTG 57.203 33.333 16.19 0.00 40.81 2.74
382 396 4.649088 CGATAGTGTCACCACAATCCTA 57.351 45.455 0.00 0.00 44.39 2.94
384 398 2.743636 AGTGTCACCACAATCCTACG 57.256 50.000 0.00 0.00 44.39 3.51
394 408 3.564511 CACAATCCTACGGCAAACTTTG 58.435 45.455 0.00 0.00 0.00 2.77
398 412 2.215196 TCCTACGGCAAACTTTGTGAC 58.785 47.619 3.48 0.00 0.00 3.67
399 413 2.158871 TCCTACGGCAAACTTTGTGACT 60.159 45.455 3.48 0.00 0.00 3.41
400 414 2.032030 CCTACGGCAAACTTTGTGACTG 60.032 50.000 3.48 0.00 0.00 3.51
401 415 0.100503 ACGGCAAACTTTGTGACTGC 59.899 50.000 3.48 0.00 0.00 4.40
409 423 4.989279 AACTTTGTGACTGCAATTCACT 57.011 36.364 22.38 5.94 43.30 3.41
411 425 3.002656 ACTTTGTGACTGCAATTCACTCG 59.997 43.478 22.38 15.03 43.30 4.18
414 428 1.195448 GTGACTGCAATTCACTCGTGG 59.805 52.381 17.21 0.00 40.30 4.94
418 432 0.035317 TGCAATTCACTCGTGGAGCT 59.965 50.000 0.00 0.00 32.04 4.09
425 439 1.472878 TCACTCGTGGAGCTACATGTC 59.527 52.381 17.86 0.00 32.04 3.06
429 443 0.246360 CGTGGAGCTACATGTCACCA 59.754 55.000 10.27 5.38 0.00 4.17
437 451 4.460263 AGCTACATGTCACCAAACAAAGA 58.540 39.130 0.00 0.00 31.81 2.52
443 457 2.229062 TGTCACCAAACAAAGAACGCAA 59.771 40.909 0.00 0.00 0.00 4.85
444 458 4.969121 ATGTCACCAAACAAAGAACGCAAG 60.969 41.667 0.00 0.00 36.48 4.01
445 459 2.750166 TCACCAAACAAAGAACGCAAGA 59.250 40.909 0.00 0.00 43.62 3.02
446 460 2.851824 CACCAAACAAAGAACGCAAGAC 59.148 45.455 0.00 0.00 43.62 3.01
447 461 2.752903 ACCAAACAAAGAACGCAAGACT 59.247 40.909 0.00 0.00 43.62 3.24
448 462 3.942748 ACCAAACAAAGAACGCAAGACTA 59.057 39.130 0.00 0.00 43.62 2.59
449 463 4.201881 ACCAAACAAAGAACGCAAGACTAC 60.202 41.667 0.00 0.00 43.62 2.73
450 464 4.201871 CCAAACAAAGAACGCAAGACTACA 60.202 41.667 0.00 0.00 43.62 2.74
451 465 5.328691 CAAACAAAGAACGCAAGACTACAA 58.671 37.500 0.00 0.00 43.62 2.41
452 466 4.795970 ACAAAGAACGCAAGACTACAAG 57.204 40.909 0.00 0.00 43.62 3.16
453 467 4.439057 ACAAAGAACGCAAGACTACAAGA 58.561 39.130 0.00 0.00 43.62 3.02
454 468 4.270325 ACAAAGAACGCAAGACTACAAGAC 59.730 41.667 0.00 0.00 43.62 3.01
455 469 3.728076 AGAACGCAAGACTACAAGACA 57.272 42.857 0.00 0.00 43.62 3.41
456 470 3.643763 AGAACGCAAGACTACAAGACAG 58.356 45.455 0.00 0.00 43.62 3.51
457 471 1.784525 ACGCAAGACTACAAGACAGC 58.215 50.000 0.00 0.00 43.62 4.40
458 472 1.068588 ACGCAAGACTACAAGACAGCA 59.931 47.619 0.00 0.00 43.62 4.41
459 473 2.289072 ACGCAAGACTACAAGACAGCAT 60.289 45.455 0.00 0.00 43.62 3.79
460 474 2.346847 CGCAAGACTACAAGACAGCATC 59.653 50.000 0.00 0.00 43.02 3.91
461 475 3.594134 GCAAGACTACAAGACAGCATCT 58.406 45.455 0.00 0.00 40.46 2.90
462 476 5.383757 CGCAAGACTACAAGACAGCATCTT 61.384 45.833 0.00 0.00 45.47 2.40
463 477 4.092675 GCAAGACTACAAGACAGCATCTTC 59.907 45.833 0.47 0.00 44.99 2.87
464 478 5.233225 CAAGACTACAAGACAGCATCTTCA 58.767 41.667 0.47 0.00 44.99 3.02
465 479 5.474578 AGACTACAAGACAGCATCTTCAA 57.525 39.130 0.47 0.00 44.99 2.69
466 480 5.477510 AGACTACAAGACAGCATCTTCAAG 58.522 41.667 0.47 4.45 44.99 3.02
467 481 4.573900 ACTACAAGACAGCATCTTCAAGG 58.426 43.478 0.47 0.00 44.99 3.61
468 482 3.777106 ACAAGACAGCATCTTCAAGGA 57.223 42.857 0.47 0.00 44.99 3.36
469 483 3.672808 ACAAGACAGCATCTTCAAGGAG 58.327 45.455 0.47 0.00 44.99 3.69
470 484 3.072184 ACAAGACAGCATCTTCAAGGAGT 59.928 43.478 0.47 0.00 44.99 3.85
471 485 3.608316 AGACAGCATCTTCAAGGAGTC 57.392 47.619 0.00 0.00 31.62 3.36
472 486 2.094286 AGACAGCATCTTCAAGGAGTCG 60.094 50.000 0.00 0.00 31.62 4.18
473 487 1.620819 ACAGCATCTTCAAGGAGTCGT 59.379 47.619 0.00 0.00 0.00 4.34
495 509 4.963318 AGACTCCAAGACAACATCTTCA 57.037 40.909 0.00 0.00 44.99 3.02
498 512 4.392940 ACTCCAAGACAACATCTTCAAGG 58.607 43.478 0.00 0.00 44.99 3.61
501 515 4.103153 TCCAAGACAACATCTTCAAGGAGT 59.897 41.667 0.00 0.00 44.99 3.85
502 516 4.453819 CCAAGACAACATCTTCAAGGAGTC 59.546 45.833 0.00 0.00 44.99 3.36
509 524 2.011122 TCTTCAAGGAGTCGTCCCTT 57.989 50.000 0.00 0.00 45.26 3.95
516 531 0.179081 GGAGTCGTCCCTTGTATGCC 60.179 60.000 0.00 0.00 36.76 4.40
531 546 5.784578 TGTATGCCGATGTTGACTAGTAT 57.215 39.130 0.00 0.00 0.00 2.12
559 574 5.654650 CACAAAGTTAAACATGGGGGCTATA 59.345 40.000 0.00 0.00 0.00 1.31
575 590 3.697542 GGCTATAACCCACAAAACCGAAT 59.302 43.478 0.00 0.00 0.00 3.34
576 591 4.201980 GGCTATAACCCACAAAACCGAATC 60.202 45.833 0.00 0.00 0.00 2.52
614 634 1.135228 GGGAAAACAACGTGCACAGTT 60.135 47.619 18.64 17.92 0.00 3.16
626 646 2.813754 GTGCACAGTTTGATCTAGCCAA 59.186 45.455 13.17 0.00 0.00 4.52
677 711 3.926616 AGAATGTAACCTCGGTGTCAAG 58.073 45.455 0.00 0.00 0.00 3.02
737 790 2.159382 TGGCCAAACGAGAATTCTTCC 58.841 47.619 9.87 0.00 0.00 3.46
739 792 2.820197 GGCCAAACGAGAATTCTTCCTT 59.180 45.455 9.87 0.47 0.00 3.36
740 793 3.366374 GGCCAAACGAGAATTCTTCCTTG 60.366 47.826 9.87 12.17 0.00 3.61
781 1096 1.523938 GCTTCCGGTCCACCTATGC 60.524 63.158 0.00 0.00 0.00 3.14
905 1283 1.436600 GCATGAGTGGTGAGTGACTG 58.563 55.000 0.00 0.00 0.00 3.51
921 1299 4.160626 AGTGACTGGACAGACTATTTAGCC 59.839 45.833 6.29 0.00 0.00 3.93
971 1349 6.456501 ACAAGTACGAAGAACAAGCTAAGAT 58.543 36.000 0.00 0.00 0.00 2.40
988 1374 0.036765 GATCAACCACCCTGCACGTA 60.037 55.000 0.00 0.00 0.00 3.57
989 1375 0.036388 ATCAACCACCCTGCACGTAG 60.036 55.000 0.00 0.00 0.00 3.51
991 1377 0.319083 CAACCACCCTGCACGTAGTA 59.681 55.000 0.00 0.00 41.61 1.82
1005 1391 3.129813 CACGTAGTAAGTACTCCATGGCA 59.870 47.826 6.96 0.00 41.61 4.92
1199 1585 0.104934 ACCATTATCGCCCTCCCTCT 60.105 55.000 0.00 0.00 0.00 3.69
1203 1589 0.854218 TTATCGCCCTCCCTCTCTCT 59.146 55.000 0.00 0.00 0.00 3.10
1245 1631 4.429212 ATGCGCGTGCTCACCGTA 62.429 61.111 23.16 0.00 43.34 4.02
1264 1650 4.831307 CGGGCGTCTTCTCCGTCG 62.831 72.222 0.00 0.00 39.04 5.12
1266 1652 2.100603 GGCGTCTTCTCCGTCGAG 59.899 66.667 0.00 0.00 37.48 4.04
1323 1709 2.799371 GTCTACGGGCTCACCTCG 59.201 66.667 0.00 0.00 36.97 4.63
1372 1758 1.592400 GACATCGTCGGGACTGTCCA 61.592 60.000 26.94 7.70 38.64 4.02
1410 1796 3.998672 GACCCGAACCTCACCGCA 61.999 66.667 0.00 0.00 0.00 5.69
1497 1883 2.125106 GGCGAGGACATGTGGGAC 60.125 66.667 1.15 0.00 0.00 4.46
1536 1922 1.686355 CTCTGAGCAGGACGATAGGT 58.314 55.000 0.00 0.00 43.77 3.08
1576 1962 2.649034 GCTTCGTCGTGGAGGTGA 59.351 61.111 0.00 0.00 0.00 4.02
1776 2162 0.249699 TCGCCGGCGATATGTTTGAT 60.250 50.000 45.37 0.00 44.01 2.57
1834 2220 8.325787 AGGTAATTTCACATGTGTTCCATACTA 58.674 33.333 24.63 0.00 30.71 1.82
1861 3985 4.415881 TTAGTCGCCATGTGTTCCATAT 57.584 40.909 0.00 0.00 30.71 1.78
1864 3988 3.627577 AGTCGCCATGTGTTCCATATTTC 59.372 43.478 0.00 0.00 30.71 2.17
1875 3999 5.295787 GTGTTCCATATTTCCATTGCGAGTA 59.704 40.000 0.00 0.00 0.00 2.59
1876 4000 5.295787 TGTTCCATATTTCCATTGCGAGTAC 59.704 40.000 0.00 0.00 0.00 2.73
1877 4001 4.385825 TCCATATTTCCATTGCGAGTACC 58.614 43.478 0.00 0.00 0.00 3.34
1882 4060 3.520290 TTCCATTGCGAGTACCTACTG 57.480 47.619 0.00 0.00 36.50 2.74
2022 4242 4.762289 AAACCATAGAGCTTAGACCTGG 57.238 45.455 0.00 0.00 0.00 4.45
2039 4259 2.658285 CTGGCCTTTGCATATCAGGAA 58.342 47.619 3.32 0.00 40.13 3.36
2042 4262 3.117398 TGGCCTTTGCATATCAGGAAGAT 60.117 43.478 3.32 0.00 40.13 2.40
2076 4296 2.303600 ACTTTATTACCGAGGGCACACA 59.696 45.455 0.00 0.00 0.00 3.72
2102 4323 6.563381 CGACACTTACGTGCTTGATTAAGTTT 60.563 38.462 0.00 0.00 45.10 2.66
2103 4324 7.358600 CGACACTTACGTGCTTGATTAAGTTTA 60.359 37.037 0.00 0.00 45.10 2.01
2104 4325 8.319143 ACACTTACGTGCTTGATTAAGTTTAT 57.681 30.769 0.00 0.00 45.10 1.40
2207 4432 0.172578 ATGATTGGCGAGACGACGAA 59.827 50.000 0.00 0.00 37.93 3.85
2247 4472 1.340991 GGTGCAAAGAGGCAATCCCTA 60.341 52.381 0.00 0.00 46.60 3.53
2291 4516 6.547141 AGGTGATAATCATAAACATGGTGGTG 59.453 38.462 0.00 0.00 0.00 4.17
2306 4531 2.422945 GGTGGTGGGTTCTGAAAAGTCT 60.423 50.000 0.00 0.00 0.00 3.24
2365 4590 2.362397 TGTACGATCTCTTCCTCATGGC 59.638 50.000 0.00 0.00 0.00 4.40
2447 4672 5.483685 TCAGTGGCTACAATATCATACCC 57.516 43.478 2.02 0.00 0.00 3.69
2449 4674 3.000727 GTGGCTACAATATCATACCCGC 58.999 50.000 0.00 0.00 0.00 6.13
2590 4815 9.764363 ATGGTTTATATATATATGTGCACCTCG 57.236 33.333 15.69 0.00 0.00 4.63
2658 4884 5.465935 TCAAATTAGCCGGTTTCATGTTTC 58.534 37.500 1.90 0.00 0.00 2.78
2673 4899 6.220726 TCATGTTTCGGTCAGAGATGAATA 57.779 37.500 0.00 0.00 0.00 1.75
2718 4944 7.088589 AGTGTATGCATGTTACTCCAAATTC 57.911 36.000 10.16 0.00 0.00 2.17
2823 5058 6.160684 CCATGAATTGACACACATGACAAAT 58.839 36.000 0.00 0.00 42.41 2.32
2946 5182 4.336889 TCGTTGAATTCTCTGTGGTCTT 57.663 40.909 7.05 0.00 0.00 3.01
2968 5204 2.427453 GCCTTCATCGACCTCTGAAGTA 59.573 50.000 19.79 0.00 44.40 2.24
2981 5217 1.760613 CTGAAGTAACCGGGATGCCTA 59.239 52.381 6.32 0.00 0.00 3.93
3001 5237 5.418209 GCCTAGACTAGTGGACAAGAAACTA 59.582 44.000 0.00 0.00 0.00 2.24
3014 5250 7.990886 TGGACAAGAAACTACTAAGACACAAAT 59.009 33.333 0.00 0.00 0.00 2.32
3028 5264 3.067106 ACACAAATAGGCACACGAGAAG 58.933 45.455 0.00 0.00 0.00 2.85
3033 5269 5.147162 CAAATAGGCACACGAGAAGAAAAC 58.853 41.667 0.00 0.00 0.00 2.43
3052 5291 3.712091 ACGTCCGAATAAAGAGCTAGG 57.288 47.619 0.00 0.00 0.00 3.02
3099 5338 2.223144 TGGTCGTTTCAATTGCTTCTCG 59.777 45.455 0.00 1.78 0.00 4.04
3103 5342 3.428870 TCGTTTCAATTGCTTCTCGAGAC 59.571 43.478 16.36 5.25 0.00 3.36
3127 5366 8.927675 ACGAGTTAGATAGATCTCTTGGTAAT 57.072 34.615 0.00 0.00 38.32 1.89
3140 5379 8.812513 ATCTCTTGGTAATTTCAATGATCACA 57.187 30.769 0.00 0.00 0.00 3.58
3150 5389 6.897706 TTTCAATGATCACAGTGGATGAAA 57.102 33.333 0.00 8.03 41.57 2.69
3155 5394 4.582869 TGATCACAGTGGATGAAAGGAAG 58.417 43.478 0.00 0.00 0.00 3.46
3167 5406 2.987046 GAAAGGAAGCACACTTTCGTG 58.013 47.619 10.04 0.00 41.94 4.35
3343 5584 7.342769 TGGTCATGACTATGTAATAACGACT 57.657 36.000 24.50 0.00 35.73 4.18
3361 5602 4.863131 ACGACTTATTCCGACAGAATGAAC 59.137 41.667 0.00 0.00 45.11 3.18
3430 5671 4.192429 TCTCGTTGAGATGCATGAAAGA 57.808 40.909 2.46 1.17 33.35 2.52
3436 5677 5.570344 GTTGAGATGCATGAAAGAGACATG 58.430 41.667 2.46 0.00 45.19 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.828328 CCTTGTAAGTTTTGAAAGACCTCCT 59.172 40.000 0.00 0.00 0.00 3.69
45 48 8.103948 ACAGTGAAGAAAATATGAAAGACCAG 57.896 34.615 0.00 0.00 0.00 4.00
46 49 9.567776 TTACAGTGAAGAAAATATGAAAGACCA 57.432 29.630 0.00 0.00 0.00 4.02
58 61 6.751514 TGTTCAAGCTTACAGTGAAGAAAA 57.248 33.333 0.00 0.00 32.15 2.29
67 70 5.234329 TCTCGACTTTTGTTCAAGCTTACAG 59.766 40.000 0.00 0.00 0.00 2.74
99 102 6.019479 GTCAAGTCATCGCCTCTAGTTTTATG 60.019 42.308 0.00 0.00 0.00 1.90
112 115 6.417327 CAATTCAATCTAGTCAAGTCATCGC 58.583 40.000 0.00 0.00 0.00 4.58
114 117 7.984050 TCTCCAATTCAATCTAGTCAAGTCATC 59.016 37.037 0.00 0.00 0.00 2.92
126 132 7.874528 GGACAACAAAAATCTCCAATTCAATCT 59.125 33.333 0.00 0.00 0.00 2.40
134 140 5.186797 ACACAAGGACAACAAAAATCTCCAA 59.813 36.000 0.00 0.00 0.00 3.53
199 205 9.869757 TTCGTCAATCAAGATCTAACTTCATTA 57.130 29.630 0.00 0.00 0.00 1.90
221 227 3.917329 TCGAGTCAAACTCTCATTCGT 57.083 42.857 5.63 0.00 42.92 3.85
231 237 7.359014 GGTGTTACTACATTCTTCGAGTCAAAC 60.359 40.741 0.00 0.00 36.50 2.93
232 238 6.643770 GGTGTTACTACATTCTTCGAGTCAAA 59.356 38.462 0.00 0.00 36.50 2.69
333 347 4.453478 ACATATGCAATGTAGATGGCTTCG 59.547 41.667 10.43 0.00 28.60 3.79
336 350 6.720112 AAAACATATGCAATGTAGATGGCT 57.280 33.333 10.43 0.00 28.60 4.75
344 358 8.208718 ACACTATCGTAAAACATATGCAATGT 57.791 30.769 1.58 8.21 0.00 2.71
382 396 0.100503 GCAGTCACAAAGTTTGCCGT 59.899 50.000 15.59 0.00 0.00 5.68
384 398 2.292103 TTGCAGTCACAAAGTTTGCC 57.708 45.000 15.59 4.17 33.98 4.52
394 408 1.195448 CCACGAGTGAATTGCAGTCAC 59.805 52.381 19.71 19.71 45.44 3.67
398 412 0.445436 GCTCCACGAGTGAATTGCAG 59.555 55.000 4.59 0.00 31.39 4.41
399 413 0.035317 AGCTCCACGAGTGAATTGCA 59.965 50.000 4.59 0.00 31.39 4.08
400 414 1.661112 GTAGCTCCACGAGTGAATTGC 59.339 52.381 4.59 3.71 31.39 3.56
401 415 2.959516 TGTAGCTCCACGAGTGAATTG 58.040 47.619 4.59 0.00 31.39 2.32
409 423 0.530744 GGTGACATGTAGCTCCACGA 59.469 55.000 0.00 0.00 0.00 4.35
411 425 2.472695 TTGGTGACATGTAGCTCCAC 57.527 50.000 0.00 1.78 42.32 4.02
414 428 4.515191 TCTTTGTTTGGTGACATGTAGCTC 59.485 41.667 0.00 0.00 42.32 4.09
418 432 4.496673 GCGTTCTTTGTTTGGTGACATGTA 60.497 41.667 0.00 0.00 42.32 2.29
425 439 2.851824 GTCTTGCGTTCTTTGTTTGGTG 59.148 45.455 0.00 0.00 0.00 4.17
429 443 5.353123 TCTTGTAGTCTTGCGTTCTTTGTTT 59.647 36.000 0.00 0.00 0.00 2.83
437 451 2.135933 GCTGTCTTGTAGTCTTGCGTT 58.864 47.619 0.00 0.00 0.00 4.84
451 465 2.094286 CGACTCCTTGAAGATGCTGTCT 60.094 50.000 0.00 0.00 39.43 3.41
452 466 2.266554 CGACTCCTTGAAGATGCTGTC 58.733 52.381 0.00 0.00 0.00 3.51
453 467 1.620819 ACGACTCCTTGAAGATGCTGT 59.379 47.619 0.00 0.00 0.00 4.40
454 468 2.376808 ACGACTCCTTGAAGATGCTG 57.623 50.000 0.00 0.00 0.00 4.41
455 469 3.129638 GTCTACGACTCCTTGAAGATGCT 59.870 47.826 0.00 0.00 0.00 3.79
456 470 3.129638 AGTCTACGACTCCTTGAAGATGC 59.870 47.826 0.00 0.00 38.71 3.91
457 471 4.974368 AGTCTACGACTCCTTGAAGATG 57.026 45.455 0.00 0.00 38.71 2.90
467 481 8.007572 AGATGTTGTCTTGGAGTCTACGACTC 62.008 46.154 14.06 14.06 45.15 3.36
468 482 3.220110 TGTTGTCTTGGAGTCTACGACT 58.780 45.455 13.17 0.00 46.42 4.18
469 483 3.637998 TGTTGTCTTGGAGTCTACGAC 57.362 47.619 6.22 6.22 0.00 4.34
470 484 4.079970 AGATGTTGTCTTGGAGTCTACGA 58.920 43.478 0.00 0.00 31.47 3.43
471 485 4.442375 AGATGTTGTCTTGGAGTCTACG 57.558 45.455 0.00 0.00 31.47 3.51
485 499 2.996621 GGACGACTCCTTGAAGATGTTG 59.003 50.000 0.00 0.00 33.07 3.33
495 509 1.207329 GCATACAAGGGACGACTCCTT 59.793 52.381 0.00 0.00 44.76 3.36
498 512 0.527817 CGGCATACAAGGGACGACTC 60.528 60.000 0.00 0.00 0.00 3.36
501 515 0.104120 CATCGGCATACAAGGGACGA 59.896 55.000 0.00 0.00 34.70 4.20
502 516 0.179084 ACATCGGCATACAAGGGACG 60.179 55.000 0.00 0.00 0.00 4.79
509 524 5.784578 ATACTAGTCAACATCGGCATACA 57.215 39.130 0.00 0.00 0.00 2.29
516 531 9.302345 ACTTTGTGAATATACTAGTCAACATCG 57.698 33.333 0.00 0.00 34.28 3.84
531 546 5.046950 GCCCCCATGTTTAACTTTGTGAATA 60.047 40.000 0.00 0.00 0.00 1.75
543 558 3.132056 TGGGTTATAGCCCCCATGTTTA 58.868 45.455 21.00 0.00 46.06 2.01
559 574 1.960689 CCAGATTCGGTTTTGTGGGTT 59.039 47.619 0.00 0.00 0.00 4.11
569 584 0.620556 ATGTTGGCTCCAGATTCGGT 59.379 50.000 0.00 0.00 0.00 4.69
575 590 0.247460 CGTCAGATGTTGGCTCCAGA 59.753 55.000 0.00 0.00 0.00 3.86
576 591 0.742281 CCGTCAGATGTTGGCTCCAG 60.742 60.000 0.00 0.00 0.00 3.86
614 634 9.970395 CATAATTTAGCATTTTGGCTAGATCAA 57.030 29.630 0.00 0.00 46.25 2.57
626 646 7.710475 CGGGTGAAAATCCATAATTTAGCATTT 59.290 33.333 0.00 0.00 36.54 2.32
848 1226 7.116376 TCTCCGATTTTAATATTCATCACGAGC 59.884 37.037 0.00 0.00 0.00 5.03
885 1263 0.037882 AGTCACTCACCACTCATGCG 60.038 55.000 0.00 0.00 0.00 4.73
905 1283 3.118592 ACTGCTGGCTAAATAGTCTGTCC 60.119 47.826 0.00 0.00 30.69 4.02
921 1299 3.085533 AGCTATATCTCCGGTACTGCTG 58.914 50.000 0.00 0.00 0.00 4.41
971 1349 1.369692 CTACGTGCAGGGTGGTTGA 59.630 57.895 11.67 0.00 0.00 3.18
988 1374 3.195825 GTGAGTGCCATGGAGTACTTACT 59.804 47.826 18.40 6.99 39.71 2.24
989 1375 3.522553 GTGAGTGCCATGGAGTACTTAC 58.477 50.000 18.40 17.61 0.00 2.34
990 1376 2.500098 GGTGAGTGCCATGGAGTACTTA 59.500 50.000 18.40 10.06 0.00 2.24
991 1377 1.279271 GGTGAGTGCCATGGAGTACTT 59.721 52.381 18.40 1.37 0.00 2.24
1005 1391 1.585006 CTTGTAGTCGCCGGTGAGT 59.415 57.895 27.45 27.45 0.00 3.41
1245 1631 2.754658 ACGGAGAAGACGCCCGAT 60.755 61.111 7.06 0.00 45.58 4.18
1354 1740 1.595993 CTGGACAGTCCCGACGATGT 61.596 60.000 17.59 0.00 35.03 3.06
1372 1758 2.362369 CCATGAGGGACACGAGGCT 61.362 63.158 0.00 0.00 40.01 4.58
1461 1847 1.428448 CGTGGTGCATCTCGAAGAAA 58.572 50.000 16.07 0.00 34.09 2.52
1551 1937 3.973516 ACGACGAAGCGGCTGTCA 61.974 61.111 17.38 0.00 35.12 3.58
1596 1982 4.099170 CCGGAGAAGACGTCGCGT 62.099 66.667 10.46 4.60 45.10 6.01
1761 2147 4.457810 GAATGTGATCAAACATATCGCCG 58.542 43.478 0.00 0.00 39.89 6.46
1773 2159 2.595095 GCCGGGGGAATGTGATCA 59.405 61.111 2.18 0.00 0.00 2.92
1861 3985 3.857052 CAGTAGGTACTCGCAATGGAAA 58.143 45.455 0.00 0.00 41.75 3.13
1864 3988 1.137086 AGCAGTAGGTACTCGCAATGG 59.863 52.381 11.58 0.00 41.75 3.16
1875 3999 7.857404 AATGATACTAATACCAGCAGTAGGT 57.143 36.000 0.00 0.00 43.14 3.08
1876 4000 8.993121 CAAAATGATACTAATACCAGCAGTAGG 58.007 37.037 0.00 0.00 33.42 3.18
1877 4001 9.547753 ACAAAATGATACTAATACCAGCAGTAG 57.452 33.333 0.00 0.00 33.42 2.57
1882 4060 9.542462 TCTACACAAAATGATACTAATACCAGC 57.458 33.333 0.00 0.00 0.00 4.85
1946 4162 9.973450 CTATAAAGCTTCTATTAGTGCTTCAGA 57.027 33.333 19.02 12.21 43.80 3.27
1947 4163 9.973450 TCTATAAAGCTTCTATTAGTGCTTCAG 57.027 33.333 19.02 16.57 43.80 3.02
1951 4167 9.137459 TGAGTCTATAAAGCTTCTATTAGTGCT 57.863 33.333 0.00 7.70 37.37 4.40
1971 4187 8.827177 TGACTATATTTGACGTTTTTGAGTCT 57.173 30.769 12.20 0.00 38.16 3.24
1992 4208 7.982354 GTCTAAGCTCTATGGTTTTGTATGACT 59.018 37.037 0.00 0.00 37.56 3.41
2003 4219 2.043227 GCCAGGTCTAAGCTCTATGGT 58.957 52.381 0.00 0.00 0.00 3.55
2102 4323 9.348476 TGTAGGCTTGTGCATTCAATATTTATA 57.652 29.630 0.00 0.00 41.91 0.98
2103 4324 8.236585 TGTAGGCTTGTGCATTCAATATTTAT 57.763 30.769 0.00 0.00 41.91 1.40
2104 4325 7.637631 TGTAGGCTTGTGCATTCAATATTTA 57.362 32.000 0.00 0.00 41.91 1.40
2189 4414 0.172578 ATTCGTCGTCTCGCCAATCA 59.827 50.000 0.00 0.00 0.00 2.57
2207 4432 2.196749 CTTCGCAGTATCTTGACGCAT 58.803 47.619 0.00 0.00 0.00 4.73
2291 4516 3.082548 GCCCTTAGACTTTTCAGAACCC 58.917 50.000 0.00 0.00 0.00 4.11
2306 4531 7.403813 TCCTCCTTTTTAGTACTATTGCCCTTA 59.596 37.037 2.79 0.00 0.00 2.69
2365 4590 0.601558 TCGTTCACCTCCCTCGAAAG 59.398 55.000 0.00 0.00 0.00 2.62
2447 4672 0.387929 TGGACCTAATTCCTAGCGCG 59.612 55.000 0.00 0.00 36.51 6.86
2449 4674 4.499183 GATGATGGACCTAATTCCTAGCG 58.501 47.826 0.00 0.00 36.51 4.26
2588 4813 2.048597 CAAGTAGGGCGCACACGA 60.049 61.111 14.57 0.00 43.93 4.35
2590 4815 2.033194 GGACAAGTAGGGCGCACAC 61.033 63.158 14.57 8.43 0.00 3.82
2594 4819 0.321298 TTGAAGGACAAGTAGGGCGC 60.321 55.000 0.00 0.00 34.20 6.53
2924 5160 4.543590 AGACCACAGAGAATTCAACGAT 57.456 40.909 8.44 0.00 0.00 3.73
2946 5182 1.205655 CTTCAGAGGTCGATGAAGGCA 59.794 52.381 15.63 0.00 45.61 4.75
2968 5204 1.063114 ACTAGTCTAGGCATCCCGGTT 60.063 52.381 11.61 0.00 35.76 4.44
2981 5217 7.943447 TCTTAGTAGTTTCTTGTCCACTAGTCT 59.057 37.037 0.00 0.00 30.77 3.24
3001 5237 3.994392 CGTGTGCCTATTTGTGTCTTAGT 59.006 43.478 0.00 0.00 0.00 2.24
3014 5250 2.223876 ACGTTTTCTTCTCGTGTGCCTA 60.224 45.455 0.00 0.00 36.46 3.93
3028 5264 4.923264 AGCTCTTTATTCGGACGTTTTC 57.077 40.909 0.00 0.00 0.00 2.29
3033 5269 3.712091 ACCTAGCTCTTTATTCGGACG 57.288 47.619 0.00 0.00 0.00 4.79
3052 5291 5.596845 TCAAATTGGGTACAAGCTTGAAAC 58.403 37.500 32.50 25.75 40.49 2.78
3099 5338 6.708949 ACCAAGAGATCTATCTAACTCGTCTC 59.291 42.308 0.00 0.00 37.25 3.36
3127 5366 6.071784 CCTTTCATCCACTGTGATCATTGAAA 60.072 38.462 9.86 13.81 0.00 2.69
3137 5376 2.227388 GTGCTTCCTTTCATCCACTGTG 59.773 50.000 0.00 0.00 0.00 3.66
3138 5377 2.158623 TGTGCTTCCTTTCATCCACTGT 60.159 45.455 0.00 0.00 0.00 3.55
3140 5379 2.107204 AGTGTGCTTCCTTTCATCCACT 59.893 45.455 0.00 0.00 0.00 4.00
3189 5428 7.233348 AGTGACCATGTACAAAGGAAATCAATT 59.767 33.333 20.82 6.87 0.00 2.32
3192 5431 5.630121 AGTGACCATGTACAAAGGAAATCA 58.370 37.500 20.82 12.79 0.00 2.57
3343 5584 4.258543 GTGGGTTCATTCTGTCGGAATAA 58.741 43.478 6.58 0.00 42.20 1.40
3403 5644 2.677199 TGCATCTCAACGAGAAGACAC 58.323 47.619 0.00 0.00 42.27 3.67
3412 5653 3.681417 TGTCTCTTTCATGCATCTCAACG 59.319 43.478 0.00 0.00 0.00 4.10
3430 5671 6.175471 TGAGCATCTTGAATGTTACATGTCT 58.825 36.000 0.00 0.00 34.92 3.41



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

AutoCloner maintained by Alex Coulton.