Multiple sequence alignment - TraesCS5D01G411800

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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 TraesCS5D01G411800 chr5D 100.000 3675 0 0 1 3675 475208615 475212289 0.000000e+00 6787.0
1 TraesCS5D01G411800 chr5D 91.304 46 3 1 3001 3046 486618929 486618885 1.100000e-05 62.1
2 TraesCS5D01G411800 chr5A 89.994 3198 168 70 532 3675 594350241 594353340 0.000000e+00 3993.0
3 TraesCS5D01G411800 chr5A 81.299 385 39 20 65 420 594349765 594350145 7.770000e-72 281.0
4 TraesCS5D01G411800 chr5B 89.838 2834 132 75 532 3293 582425095 582427844 0.000000e+00 3494.0
5 TraesCS5D01G411800 chr5B 90.830 458 28 5 16 464 582424481 582424933 5.250000e-168 601.0
6 TraesCS5D01G411800 chr5B 94.215 363 16 3 3318 3675 582427842 582428204 1.930000e-152 549.0
7 TraesCS5D01G411800 chr6A 100.000 28 0 0 3104 3131 52808529 52808556 7.000000e-03 52.8


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 TraesCS5D01G411800 chr5D 475208615 475212289 3674 False 6787 6787 100.000000 1 3675 1 chr5D.!!$F1 3674
1 TraesCS5D01G411800 chr5A 594349765 594353340 3575 False 2137 3993 85.646500 65 3675 2 chr5A.!!$F1 3610
2 TraesCS5D01G411800 chr5B 582424481 582428204 3723 False 1548 3494 91.627667 16 3675 3 chr5B.!!$F1 3659

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
897 1083 0.250513 GCATCACGGTTCCTTCCTCT 59.749 55.0 0.00 0.00 0.0 3.69 F
1451 1687 0.315544 TTCGGATTTTATTCGCGCGC 60.316 50.0 27.95 23.91 0.0 6.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2646 2896 0.244178 GCTATAGCCTACCGACCTGC 59.756 60.0 14.13 0.0 34.31 4.85 R
3062 3319 0.106015 AAAAGGGCAGTTCAGCAGGT 60.106 50.0 0.00 0.0 35.83 4.00 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
28 29 3.349488 TTATCTGCACGGATGTCTACG 57.651 47.619 2.12 0.00 0.00 3.51
31 32 2.294979 TCTGCACGGATGTCTACGTAT 58.705 47.619 0.00 0.00 42.04 3.06
35 36 3.816523 TGCACGGATGTCTACGTATGATA 59.183 43.478 0.00 0.00 42.04 2.15
40 41 4.844522 CGGATGTCTACGTATGATAACACG 59.155 45.833 0.00 0.00 43.63 4.49
94 95 6.858993 GTCTAAGTCGATCGAGATTTAGCAAT 59.141 38.462 20.09 1.06 39.08 3.56
96 97 4.302455 AGTCGATCGAGATTTAGCAATGG 58.698 43.478 20.09 0.00 0.00 3.16
128 137 2.941891 TTCTGCTTTTTCACGTAGCG 57.058 45.000 3.03 0.00 37.73 4.26
139 148 5.712217 TTTCACGTAGCGAGATTAAATGG 57.288 39.130 0.00 0.00 0.00 3.16
165 184 2.838736 ACAGACAAAGTAGTGCCACTG 58.161 47.619 7.83 0.00 0.00 3.66
282 302 4.814900 ATCGACAGTGCCGATGTC 57.185 55.556 13.85 3.61 44.06 3.06
322 343 0.861837 AACTCTCTCTTTTGCGTGCG 59.138 50.000 0.00 0.00 0.00 5.34
354 390 3.215244 CGTGACATAAACTCGTGTTTGC 58.785 45.455 22.25 11.24 45.01 3.68
392 428 2.774439 ACAAAGCGTGTAAGCAAAGG 57.226 45.000 0.00 0.00 39.29 3.11
408 445 0.896226 AAGGCACCTCGGTTCTAGAC 59.104 55.000 0.00 0.00 0.00 2.59
434 471 0.603569 TCCACGGAAGAGAAGAGCAC 59.396 55.000 0.00 0.00 0.00 4.40
438 475 0.605589 CGGAAGAGAAGAGCACCACT 59.394 55.000 0.00 0.00 0.00 4.00
439 476 1.671261 CGGAAGAGAAGAGCACCACTG 60.671 57.143 0.00 0.00 0.00 3.66
440 477 1.437625 GAAGAGAAGAGCACCACTGC 58.562 55.000 0.00 0.00 44.63 4.40
441 478 0.761187 AAGAGAAGAGCACCACTGCA 59.239 50.000 0.00 0.00 46.97 4.41
478 515 3.855689 GGCAACAAGTGTATGCATTCT 57.144 42.857 3.54 0.00 41.80 2.40
479 516 4.178545 GGCAACAAGTGTATGCATTCTT 57.821 40.909 3.54 5.11 41.80 2.52
480 517 4.168760 GGCAACAAGTGTATGCATTCTTC 58.831 43.478 3.54 0.00 41.80 2.87
481 518 4.082571 GGCAACAAGTGTATGCATTCTTCT 60.083 41.667 3.54 0.08 41.80 2.85
482 519 4.855388 GCAACAAGTGTATGCATTCTTCTG 59.145 41.667 3.54 8.37 39.81 3.02
483 520 5.563475 GCAACAAGTGTATGCATTCTTCTGT 60.563 40.000 3.54 0.84 39.81 3.41
484 521 6.441274 CAACAAGTGTATGCATTCTTCTGTT 58.559 36.000 3.54 7.38 0.00 3.16
485 522 6.005583 ACAAGTGTATGCATTCTTCTGTTG 57.994 37.500 3.54 3.12 0.00 3.33
487 524 6.262944 ACAAGTGTATGCATTCTTCTGTTGAA 59.737 34.615 3.54 0.00 0.00 2.69
490 527 7.715657 AGTGTATGCATTCTTCTGTTGAAAAA 58.284 30.769 3.54 0.00 0.00 1.94
491 528 7.649306 AGTGTATGCATTCTTCTGTTGAAAAAC 59.351 33.333 3.54 0.00 0.00 2.43
512 602 5.819825 ACAACAACAAGAAAGAAGAGGAC 57.180 39.130 0.00 0.00 0.00 3.85
526 616 3.586100 AGAGGACGAAGAAGAAGAAGC 57.414 47.619 0.00 0.00 0.00 3.86
527 617 2.894126 AGAGGACGAAGAAGAAGAAGCA 59.106 45.455 0.00 0.00 0.00 3.91
528 618 3.056891 AGAGGACGAAGAAGAAGAAGCAG 60.057 47.826 0.00 0.00 0.00 4.24
529 619 2.630580 AGGACGAAGAAGAAGAAGCAGT 59.369 45.455 0.00 0.00 0.00 4.40
530 620 2.734079 GGACGAAGAAGAAGAAGCAGTG 59.266 50.000 0.00 0.00 0.00 3.66
538 669 0.944386 GAAGAAGCAGTGCGAAACCA 59.056 50.000 10.00 0.00 0.00 3.67
545 676 2.261361 GTGCGAAACCAATGGGCC 59.739 61.111 3.55 0.00 37.90 5.80
546 677 3.369400 TGCGAAACCAATGGGCCG 61.369 61.111 3.55 5.05 37.90 6.13
547 678 4.128388 GCGAAACCAATGGGCCGG 62.128 66.667 3.55 0.00 37.90 6.13
894 1080 3.486263 CGCATCACGGTTCCTTCC 58.514 61.111 0.00 0.00 38.44 3.46
895 1081 1.079127 CGCATCACGGTTCCTTCCT 60.079 57.895 0.00 0.00 38.44 3.36
896 1082 1.084370 CGCATCACGGTTCCTTCCTC 61.084 60.000 0.00 0.00 38.44 3.71
897 1083 0.250513 GCATCACGGTTCCTTCCTCT 59.749 55.000 0.00 0.00 0.00 3.69
898 1084 1.740718 GCATCACGGTTCCTTCCTCTC 60.741 57.143 0.00 0.00 0.00 3.20
899 1085 1.827969 CATCACGGTTCCTTCCTCTCT 59.172 52.381 0.00 0.00 0.00 3.10
900 1086 1.546961 TCACGGTTCCTTCCTCTCTC 58.453 55.000 0.00 0.00 0.00 3.20
901 1087 1.075698 TCACGGTTCCTTCCTCTCTCT 59.924 52.381 0.00 0.00 0.00 3.10
902 1088 1.474879 CACGGTTCCTTCCTCTCTCTC 59.525 57.143 0.00 0.00 0.00 3.20
903 1089 1.356398 ACGGTTCCTTCCTCTCTCTCT 59.644 52.381 0.00 0.00 0.00 3.10
904 1090 2.021457 CGGTTCCTTCCTCTCTCTCTC 58.979 57.143 0.00 0.00 0.00 3.20
928 1114 4.892345 TCTCTCTCTCTCTCTCTCTCTCAG 59.108 50.000 0.00 0.00 0.00 3.35
929 1115 3.963374 TCTCTCTCTCTCTCTCTCTCAGG 59.037 52.174 0.00 0.00 0.00 3.86
987 1173 3.854669 AGCTCGCAGATTCCCCCG 61.855 66.667 0.00 0.00 33.89 5.73
1051 1237 3.439260 CCACATTCCTATCCTCCTCCTCT 60.439 52.174 0.00 0.00 0.00 3.69
1052 1238 3.831911 CACATTCCTATCCTCCTCCTCTC 59.168 52.174 0.00 0.00 0.00 3.20
1069 1273 1.618837 TCTCCAACCAGACTTTCTCCG 59.381 52.381 0.00 0.00 0.00 4.63
1090 1294 1.596934 CGCTACCAGCTTCCTTCCA 59.403 57.895 0.00 0.00 39.60 3.53
1095 1300 0.915364 ACCAGCTTCCTTCCATCCTC 59.085 55.000 0.00 0.00 0.00 3.71
1097 1302 1.211456 CAGCTTCCTTCCATCCTCCT 58.789 55.000 0.00 0.00 0.00 3.69
1099 1304 1.843206 AGCTTCCTTCCATCCTCCTTC 59.157 52.381 0.00 0.00 0.00 3.46
1101 1306 2.486716 CTTCCTTCCATCCTCCTTCCT 58.513 52.381 0.00 0.00 0.00 3.36
1151 1365 1.071814 GTGGCGTGTTCCCTGGTTA 59.928 57.895 0.00 0.00 0.00 2.85
1157 1383 1.734163 GTGTTCCCTGGTTATCCGTG 58.266 55.000 0.00 0.00 36.30 4.94
1163 1389 0.725117 CCTGGTTATCCGTGCGTTTC 59.275 55.000 0.00 0.00 36.30 2.78
1386 1612 3.770040 CTCGCCGATGGTGGGTGA 61.770 66.667 0.00 0.00 41.55 4.02
1403 1629 2.280628 GTGACCAATCCGTTCATCCTC 58.719 52.381 0.00 0.00 0.00 3.71
1447 1683 8.609478 TTAATTTCTGTTCGGATTTTATTCGC 57.391 30.769 0.00 0.00 0.00 4.70
1448 1684 3.918258 TCTGTTCGGATTTTATTCGCG 57.082 42.857 0.00 0.00 0.00 5.87
1449 1685 2.029970 TCTGTTCGGATTTTATTCGCGC 59.970 45.455 0.00 0.00 0.00 6.86
1450 1686 1.267136 TGTTCGGATTTTATTCGCGCG 60.267 47.619 26.76 26.76 0.00 6.86
1451 1687 0.315544 TTCGGATTTTATTCGCGCGC 60.316 50.000 27.95 23.91 0.00 6.86
1452 1688 1.721133 CGGATTTTATTCGCGCGCC 60.721 57.895 27.95 16.89 0.00 6.53
1453 1689 1.721133 GGATTTTATTCGCGCGCCG 60.721 57.895 27.95 20.60 38.61 6.46
1454 1690 1.721133 GATTTTATTCGCGCGCCGG 60.721 57.895 27.95 13.23 37.59 6.13
1455 1691 3.800323 ATTTTATTCGCGCGCCGGC 62.800 57.895 27.95 19.07 37.59 6.13
1637 1873 3.829044 CGCCGATCCCGTGGTACA 61.829 66.667 0.00 0.00 0.00 2.90
1697 1937 7.653713 TCGCTCTGGTTTGATCTTTATTATCTC 59.346 37.037 0.00 0.00 0.00 2.75
1699 1939 7.716998 GCTCTGGTTTGATCTTTATTATCTCCA 59.283 37.037 0.00 0.00 0.00 3.86
1700 1940 9.790344 CTCTGGTTTGATCTTTATTATCTCCAT 57.210 33.333 0.00 0.00 0.00 3.41
1728 1968 4.708868 TGTTGCTATGCGATACGATTTC 57.291 40.909 0.00 0.00 0.00 2.17
1731 1971 5.293324 TGTTGCTATGCGATACGATTTCTTT 59.707 36.000 0.00 0.00 0.00 2.52
1732 1972 5.328886 TGCTATGCGATACGATTTCTTTG 57.671 39.130 0.00 0.00 0.00 2.77
1733 1973 4.808895 TGCTATGCGATACGATTTCTTTGT 59.191 37.500 0.00 0.00 0.00 2.83
1734 1974 5.980715 TGCTATGCGATACGATTTCTTTGTA 59.019 36.000 0.00 0.00 0.00 2.41
1735 1975 6.477360 TGCTATGCGATACGATTTCTTTGTAA 59.523 34.615 0.00 0.00 0.00 2.41
1767 2007 0.970640 TCCTGACCGAAACGAATCCA 59.029 50.000 0.00 0.00 0.00 3.41
1768 2008 1.553248 TCCTGACCGAAACGAATCCAT 59.447 47.619 0.00 0.00 0.00 3.41
1769 2009 2.027561 TCCTGACCGAAACGAATCCATT 60.028 45.455 0.00 0.00 0.00 3.16
1770 2010 2.351726 CCTGACCGAAACGAATCCATTC 59.648 50.000 0.00 0.00 0.00 2.67
1797 2037 1.273606 TCGGTTTCAGAAGGAGCAGAG 59.726 52.381 0.00 0.00 0.00 3.35
1992 2232 1.068352 AGGCAGTTTTCTCCCCCTGT 61.068 55.000 0.00 0.00 0.00 4.00
2187 2427 6.818142 ACTTGAGCCATAATTTAACCAAATGC 59.182 34.615 0.00 0.00 34.53 3.56
2199 2439 4.970662 AACCAAATGCTAGCTGTATGTG 57.029 40.909 17.23 6.50 0.00 3.21
2200 2440 2.684881 ACCAAATGCTAGCTGTATGTGC 59.315 45.455 17.23 0.00 0.00 4.57
2201 2441 2.947652 CCAAATGCTAGCTGTATGTGCT 59.052 45.455 17.23 0.00 43.79 4.40
2202 2442 4.129380 CCAAATGCTAGCTGTATGTGCTA 58.871 43.478 17.23 0.00 41.46 3.49
2203 2443 4.024556 CCAAATGCTAGCTGTATGTGCTAC 60.025 45.833 17.23 0.00 41.46 3.58
2291 2537 2.376518 ACTCCAAAGCAAATCAGGGAGA 59.623 45.455 12.09 0.00 43.58 3.71
2361 2607 7.208064 TCCAGGTTAGCAATAGTTTTATCCT 57.792 36.000 0.00 0.00 0.00 3.24
2644 2894 0.733223 GCGACAGTTCCGAGGAAGAC 60.733 60.000 4.57 0.00 34.49 3.01
2818 3075 1.156736 GGATATTGGGCGTTGATCCG 58.843 55.000 0.00 0.00 0.00 4.18
2886 3143 3.159460 GCTTTGTTTCGCGAGCGC 61.159 61.111 9.59 0.00 39.59 5.92
2987 3244 4.077300 TGCTGTGTTGAGAACTTGAGAT 57.923 40.909 0.00 0.00 0.00 2.75
2988 3245 3.811497 TGCTGTGTTGAGAACTTGAGATG 59.189 43.478 0.00 0.00 0.00 2.90
2989 3246 4.060900 GCTGTGTTGAGAACTTGAGATGA 58.939 43.478 0.00 0.00 0.00 2.92
3061 3318 2.159014 TGTTCAGCGTCAACCTTGTACT 60.159 45.455 0.00 0.00 0.00 2.73
3062 3319 3.068448 TGTTCAGCGTCAACCTTGTACTA 59.932 43.478 0.00 0.00 0.00 1.82
3063 3320 3.293311 TCAGCGTCAACCTTGTACTAC 57.707 47.619 0.00 0.00 0.00 2.73
3131 3399 4.926832 TGAAATTTCATCAGCAACAGCATG 59.073 37.500 16.91 0.00 35.23 4.06
3132 3400 5.510009 TGAAATTTCATCAGCAACAGCATGT 60.510 36.000 16.91 0.00 41.83 3.21
3133 3401 7.281658 TGAAATTTCATCAGCAACAGCATGTC 61.282 38.462 16.91 0.00 39.85 3.06
3134 3402 9.554162 TGAAATTTCATCAGCAACAGCATGTCA 62.554 37.037 16.91 0.00 39.85 3.58
3156 3424 1.298859 ATCGCAGCAAAACCGAGGTC 61.299 55.000 0.00 0.00 34.21 3.85
3176 3444 3.045634 TCCTCTGAACCAAAGGAACTCA 58.954 45.455 0.00 0.00 38.49 3.41
3296 3568 4.174305 CCTTTCGGGGCTGTTTGT 57.826 55.556 0.00 0.00 0.00 2.83
3297 3569 1.659794 CCTTTCGGGGCTGTTTGTG 59.340 57.895 0.00 0.00 0.00 3.33
3298 3570 0.821711 CCTTTCGGGGCTGTTTGTGA 60.822 55.000 0.00 0.00 0.00 3.58
3299 3571 1.028905 CTTTCGGGGCTGTTTGTGAA 58.971 50.000 0.00 0.00 0.00 3.18
3300 3572 1.001378 CTTTCGGGGCTGTTTGTGAAG 60.001 52.381 0.00 0.00 0.00 3.02
3301 3573 1.452145 TTCGGGGCTGTTTGTGAAGC 61.452 55.000 0.00 0.00 38.76 3.86
3302 3574 2.644992 GGGGCTGTTTGTGAAGCG 59.355 61.111 0.00 0.00 40.46 4.68
3303 3575 1.896660 GGGGCTGTTTGTGAAGCGA 60.897 57.895 0.00 0.00 40.46 4.93
3304 3576 1.576421 GGGCTGTTTGTGAAGCGAG 59.424 57.895 0.00 0.00 40.46 5.03
3305 3577 1.166531 GGGCTGTTTGTGAAGCGAGT 61.167 55.000 0.00 0.00 40.46 4.18
3306 3578 1.508632 GGCTGTTTGTGAAGCGAGTA 58.491 50.000 0.00 0.00 40.46 2.59
3307 3579 1.871039 GGCTGTTTGTGAAGCGAGTAA 59.129 47.619 0.00 0.00 40.46 2.24
3308 3580 2.289547 GGCTGTTTGTGAAGCGAGTAAA 59.710 45.455 0.00 0.00 40.46 2.01
3309 3581 3.058224 GGCTGTTTGTGAAGCGAGTAAAT 60.058 43.478 0.00 0.00 40.46 1.40
3310 3582 4.153475 GGCTGTTTGTGAAGCGAGTAAATA 59.847 41.667 0.00 0.00 40.46 1.40
3311 3583 5.163754 GGCTGTTTGTGAAGCGAGTAAATAT 60.164 40.000 0.00 0.00 40.46 1.28
3312 3584 6.314784 GCTGTTTGTGAAGCGAGTAAATATT 58.685 36.000 0.00 0.00 0.00 1.28
3313 3585 6.801862 GCTGTTTGTGAAGCGAGTAAATATTT 59.198 34.615 5.89 5.89 0.00 1.40
3314 3586 7.007456 GCTGTTTGTGAAGCGAGTAAATATTTC 59.993 37.037 3.39 0.00 0.00 2.17
3315 3587 7.866729 TGTTTGTGAAGCGAGTAAATATTTCA 58.133 30.769 3.39 0.00 0.00 2.69
3316 3588 8.015087 TGTTTGTGAAGCGAGTAAATATTTCAG 58.985 33.333 3.39 0.00 0.00 3.02
3567 3874 1.002366 GCTGTCTGTGCTTATCCACG 58.998 55.000 0.00 0.00 38.55 4.94
3573 3880 0.464036 TGTGCTTATCCACGGCCTAG 59.536 55.000 0.00 0.00 38.55 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.225603 AGACATCCGTGCAGATAAATTATTTT 57.774 30.769 0.00 0.00 0.00 1.82
1 2 7.807977 AGACATCCGTGCAGATAAATTATTT 57.192 32.000 0.00 0.00 0.00 1.40
2 3 7.116376 CGTAGACATCCGTGCAGATAAATTATT 59.884 37.037 0.00 0.00 0.00 1.40
3 4 6.586463 CGTAGACATCCGTGCAGATAAATTAT 59.414 38.462 0.00 0.00 0.00 1.28
4 5 5.918576 CGTAGACATCCGTGCAGATAAATTA 59.081 40.000 0.00 0.00 0.00 1.40
5 6 4.745125 CGTAGACATCCGTGCAGATAAATT 59.255 41.667 0.00 0.00 0.00 1.82
6 7 4.202121 ACGTAGACATCCGTGCAGATAAAT 60.202 41.667 0.00 0.00 35.69 1.40
7 8 3.129813 ACGTAGACATCCGTGCAGATAAA 59.870 43.478 0.00 0.00 35.69 1.40
8 9 2.686405 ACGTAGACATCCGTGCAGATAA 59.314 45.455 0.00 0.00 35.69 1.75
9 10 2.294979 ACGTAGACATCCGTGCAGATA 58.705 47.619 0.00 0.00 35.69 1.98
10 11 1.103803 ACGTAGACATCCGTGCAGAT 58.896 50.000 0.00 0.00 35.69 2.90
11 12 1.741528 TACGTAGACATCCGTGCAGA 58.258 50.000 0.00 0.00 37.91 4.26
12 13 2.032924 TCATACGTAGACATCCGTGCAG 59.967 50.000 0.08 0.00 37.91 4.41
13 14 2.018515 TCATACGTAGACATCCGTGCA 58.981 47.619 0.08 0.00 37.91 4.57
14 15 2.768833 TCATACGTAGACATCCGTGC 57.231 50.000 0.08 0.00 37.91 5.34
19 20 9.770503 ATATTCGTGTTATCATACGTAGACATC 57.229 33.333 0.08 0.00 40.87 3.06
35 36 9.745880 AGTCTTAATCGATGTTATATTCGTGTT 57.254 29.630 0.00 0.00 36.74 3.32
80 81 3.924114 TTCCCCATTGCTAAATCTCGA 57.076 42.857 0.00 0.00 0.00 4.04
128 137 5.745227 TGTCTGTTCTCCCCATTTAATCTC 58.255 41.667 0.00 0.00 0.00 2.75
139 148 3.067833 GCACTACTTTGTCTGTTCTCCC 58.932 50.000 0.00 0.00 0.00 4.30
165 184 0.788391 CCTCAGCAAAACGTACGACC 59.212 55.000 24.41 4.87 0.00 4.79
282 302 0.722848 GTAATTACGTGCACCACCCG 59.277 55.000 12.15 0.95 0.00 5.28
322 343 0.601576 TATGTCACGTGGTGGTGCAC 60.602 55.000 17.00 8.80 37.83 4.57
354 390 7.044966 CGCTTTGTTTTGTTTCTTACTGTACAG 60.045 37.037 21.44 21.44 0.00 2.74
451 488 1.440938 TACACTTGTTGCCACGGTGC 61.441 55.000 1.68 0.00 34.49 5.01
483 520 8.879342 TCTTCTTTCTTGTTGTTGTTTTTCAA 57.121 26.923 0.00 0.00 0.00 2.69
484 521 7.598493 CCTCTTCTTTCTTGTTGTTGTTTTTCA 59.402 33.333 0.00 0.00 0.00 2.69
485 522 7.812669 TCCTCTTCTTTCTTGTTGTTGTTTTTC 59.187 33.333 0.00 0.00 0.00 2.29
487 524 7.090808 GTCCTCTTCTTTCTTGTTGTTGTTTT 58.909 34.615 0.00 0.00 0.00 2.43
490 527 4.332819 CGTCCTCTTCTTTCTTGTTGTTGT 59.667 41.667 0.00 0.00 0.00 3.32
491 528 4.570772 TCGTCCTCTTCTTTCTTGTTGTTG 59.429 41.667 0.00 0.00 0.00 3.33
500 590 5.774630 TCTTCTTCTTCGTCCTCTTCTTTC 58.225 41.667 0.00 0.00 0.00 2.62
512 602 1.125748 CGCACTGCTTCTTCTTCTTCG 59.874 52.381 0.00 0.00 0.00 3.79
526 616 1.080569 GCCCATTGGTTTCGCACTG 60.081 57.895 1.20 0.00 0.00 3.66
527 617 2.275380 GGCCCATTGGTTTCGCACT 61.275 57.895 1.20 0.00 0.00 4.40
528 618 2.261361 GGCCCATTGGTTTCGCAC 59.739 61.111 1.20 0.00 0.00 5.34
529 619 3.369400 CGGCCCATTGGTTTCGCA 61.369 61.111 0.00 0.00 0.00 5.10
530 620 4.128388 CCGGCCCATTGGTTTCGC 62.128 66.667 0.00 0.00 0.00 4.70
555 686 2.697431 GGATCTTCTCCGATCGTCAG 57.303 55.000 15.09 9.58 40.52 3.51
608 739 1.857318 CGTGCATGGCGGTTTAACCA 61.857 55.000 14.97 0.00 38.47 3.67
666 809 5.181245 CCAAGTATAGCCAACGGAATTATGG 59.819 44.000 0.00 0.00 37.29 2.74
744 910 5.697473 TTCTCACGCACCATTTCATTTTA 57.303 34.783 0.00 0.00 0.00 1.52
749 915 0.874390 GCTTCTCACGCACCATTTCA 59.126 50.000 0.00 0.00 0.00 2.69
855 1024 3.335729 GTGGGGTGGTGGGTAGGG 61.336 72.222 0.00 0.00 0.00 3.53
856 1025 3.712907 CGTGGGGTGGTGGGTAGG 61.713 72.222 0.00 0.00 0.00 3.18
857 1026 4.404098 GCGTGGGGTGGTGGGTAG 62.404 72.222 0.00 0.00 0.00 3.18
894 1080 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
895 1081 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
896 1082 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
897 1083 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
898 1084 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
899 1085 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
900 1086 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
901 1087 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
902 1088 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
903 1089 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
904 1090 4.892345 TGAGAGAGAGAGAGAGAGAGAGAG 59.108 50.000 0.00 0.00 0.00 3.20
1051 1237 1.618837 CTCGGAGAAAGTCTGGTTGGA 59.381 52.381 0.00 0.00 34.09 3.53
1052 1238 1.941668 GCTCGGAGAAAGTCTGGTTGG 60.942 57.143 9.69 0.00 34.09 3.77
1090 1294 3.095347 GCGGCGAAGGAAGGAGGAT 62.095 63.158 12.98 0.00 0.00 3.24
1163 1389 3.762247 CCAGCCCCATGCAAACGG 61.762 66.667 0.00 0.00 44.83 4.44
1381 1607 1.379527 GATGAACGGATTGGTCACCC 58.620 55.000 0.00 0.00 0.00 4.61
1382 1608 1.065418 AGGATGAACGGATTGGTCACC 60.065 52.381 0.00 0.00 0.00 4.02
1385 1611 2.691409 TGAGGATGAACGGATTGGTC 57.309 50.000 0.00 0.00 0.00 4.02
1386 1612 2.421952 CCATGAGGATGAACGGATTGGT 60.422 50.000 0.00 0.00 36.89 3.67
1414 1640 9.541143 AAATCCGAACAGAAATTAAACAAACAT 57.459 25.926 0.00 0.00 0.00 2.71
1415 1641 8.934507 AAATCCGAACAGAAATTAAACAAACA 57.065 26.923 0.00 0.00 0.00 2.83
1421 1647 9.068008 GCGAATAAAATCCGAACAGAAATTAAA 57.932 29.630 0.00 0.00 0.00 1.52
1424 1650 5.737290 CGCGAATAAAATCCGAACAGAAATT 59.263 36.000 0.00 0.00 0.00 1.82
1425 1651 5.263185 CGCGAATAAAATCCGAACAGAAAT 58.737 37.500 0.00 0.00 0.00 2.17
1429 1655 2.363220 GCGCGAATAAAATCCGAACAG 58.637 47.619 12.10 0.00 0.00 3.16
1434 1670 1.721133 GGCGCGCGAATAAAATCCG 60.721 57.895 37.18 0.41 0.00 4.18
1452 1688 4.692475 AGGGAAACGAACCGGCCG 62.692 66.667 21.04 21.04 0.00 6.13
1453 1689 3.053896 CAGGGAAACGAACCGGCC 61.054 66.667 0.00 0.00 0.00 6.13
1454 1690 2.031465 TCAGGGAAACGAACCGGC 59.969 61.111 0.00 0.00 0.00 6.13
1455 1691 2.025418 CGTCAGGGAAACGAACCGG 61.025 63.158 0.00 0.00 42.62 5.28
1456 1692 2.664436 GCGTCAGGGAAACGAACCG 61.664 63.158 0.00 0.00 42.62 4.44
1457 1693 2.322830 GGCGTCAGGGAAACGAACC 61.323 63.158 0.00 0.00 42.62 3.62
1458 1694 0.883370 AAGGCGTCAGGGAAACGAAC 60.883 55.000 0.00 0.00 42.62 3.95
1459 1695 0.882927 CAAGGCGTCAGGGAAACGAA 60.883 55.000 0.00 0.00 42.62 3.85
1460 1696 1.301401 CAAGGCGTCAGGGAAACGA 60.301 57.895 0.00 0.00 42.62 3.85
1461 1697 1.597027 ACAAGGCGTCAGGGAAACG 60.597 57.895 0.00 0.00 42.87 3.60
1462 1698 1.949257 CACAAGGCGTCAGGGAAAC 59.051 57.895 0.00 0.00 0.00 2.78
1463 1699 1.896660 GCACAAGGCGTCAGGGAAA 60.897 57.895 0.00 0.00 0.00 3.13
1464 1700 2.281484 GCACAAGGCGTCAGGGAA 60.281 61.111 0.00 0.00 0.00 3.97
1632 1868 3.056035 ACGGAAAGGAGTGAAGATGTACC 60.056 47.826 0.00 0.00 0.00 3.34
1637 1873 4.625607 AGAAACGGAAAGGAGTGAAGAT 57.374 40.909 0.00 0.00 0.00 2.40
1697 1937 5.922739 TCGCATAGCAACAACTTATATGG 57.077 39.130 0.00 0.00 0.00 2.74
1699 1939 7.088272 TCGTATCGCATAGCAACAACTTATAT 58.912 34.615 0.00 0.00 0.00 0.86
1700 1940 6.440436 TCGTATCGCATAGCAACAACTTATA 58.560 36.000 0.00 0.00 0.00 0.98
1744 1984 2.823924 TTCGTTTCGGTCAGGATTGA 57.176 45.000 0.00 0.00 0.00 2.57
1746 1986 2.027561 TGGATTCGTTTCGGTCAGGATT 60.028 45.455 0.00 0.00 0.00 3.01
1767 2007 6.003950 TCCTTCTGAAACCGAAGAAATGAAT 58.996 36.000 0.00 0.00 40.15 2.57
1768 2008 5.373222 TCCTTCTGAAACCGAAGAAATGAA 58.627 37.500 0.00 0.00 40.15 2.57
1769 2009 4.968259 TCCTTCTGAAACCGAAGAAATGA 58.032 39.130 0.00 0.00 40.15 2.57
1770 2010 4.378874 GCTCCTTCTGAAACCGAAGAAATG 60.379 45.833 0.00 0.00 40.15 2.32
1797 2037 3.378399 GACAGGGCGCTCTCCTTCC 62.378 68.421 6.94 0.00 31.06 3.46
1860 2100 4.789075 GCATTGCACGGCAGCTGG 62.789 66.667 17.12 1.57 40.61 4.85
1894 2134 1.448013 GTCCCTGCCGAAGTACTGC 60.448 63.158 0.00 0.00 0.00 4.40
1900 2140 1.738099 CTTGTCGTCCCTGCCGAAG 60.738 63.158 0.00 0.00 35.89 3.79
1992 2232 3.822192 CCTGATGGCGGTCGTCGA 61.822 66.667 0.00 0.00 42.43 4.20
2180 2420 2.947652 AGCACATACAGCTAGCATTTGG 59.052 45.455 18.83 5.84 41.32 3.28
2187 2427 6.434596 CAACTAGAGTAGCACATACAGCTAG 58.565 44.000 0.00 0.00 44.54 3.42
2199 2439 4.995124 TCGAATGTTCCAACTAGAGTAGC 58.005 43.478 0.00 0.00 0.00 3.58
2200 2440 7.884816 TTTTCGAATGTTCCAACTAGAGTAG 57.115 36.000 0.00 0.00 0.00 2.57
2201 2441 8.842358 ATTTTTCGAATGTTCCAACTAGAGTA 57.158 30.769 0.00 0.00 0.00 2.59
2202 2442 7.745620 ATTTTTCGAATGTTCCAACTAGAGT 57.254 32.000 0.00 0.00 0.00 3.24
2291 2537 3.698040 GTGAGGCCATCAACTTTCATCAT 59.302 43.478 5.01 0.00 40.43 2.45
2365 2611 7.317842 TGATTGTTCACAAAAATTTGCACAT 57.682 28.000 5.82 0.00 41.79 3.21
2644 2894 0.892358 TATAGCCTACCGACCTGCCG 60.892 60.000 0.00 0.00 0.00 5.69
2646 2896 0.244178 GCTATAGCCTACCGACCTGC 59.756 60.000 14.13 0.00 34.31 4.85
2886 3143 0.609131 AATTGGTGGTCTGCCCGAAG 60.609 55.000 0.00 0.00 35.15 3.79
2987 3244 7.759489 AAAACTGTAGCACCTTTATTCATCA 57.241 32.000 0.00 0.00 0.00 3.07
2988 3245 7.062255 GCAAAAACTGTAGCACCTTTATTCATC 59.938 37.037 0.00 0.00 0.00 2.92
2989 3246 6.868339 GCAAAAACTGTAGCACCTTTATTCAT 59.132 34.615 0.00 0.00 0.00 2.57
3061 3318 0.771127 AAAGGGCAGTTCAGCAGGTA 59.229 50.000 0.00 0.00 35.83 3.08
3062 3319 0.106015 AAAAGGGCAGTTCAGCAGGT 60.106 50.000 0.00 0.00 35.83 4.00
3063 3320 0.600057 GAAAAGGGCAGTTCAGCAGG 59.400 55.000 0.00 0.00 35.83 4.85
3131 3399 0.730494 GGTTTTGCTGCGATGCTGAC 60.730 55.000 0.00 0.00 0.00 3.51
3132 3400 1.580942 GGTTTTGCTGCGATGCTGA 59.419 52.632 0.00 0.00 0.00 4.26
3133 3401 1.798725 CGGTTTTGCTGCGATGCTG 60.799 57.895 0.00 0.00 0.00 4.41
3134 3402 1.915614 CTCGGTTTTGCTGCGATGCT 61.916 55.000 0.00 0.00 0.00 3.79
3135 3403 1.512734 CTCGGTTTTGCTGCGATGC 60.513 57.895 0.00 0.00 0.00 3.91
3136 3404 1.135315 CCTCGGTTTTGCTGCGATG 59.865 57.895 0.00 0.00 0.00 3.84
3137 3405 1.298859 GACCTCGGTTTTGCTGCGAT 61.299 55.000 0.00 0.00 0.00 4.58
3138 3406 1.959226 GACCTCGGTTTTGCTGCGA 60.959 57.895 0.00 0.00 0.00 5.10
3156 3424 3.492102 TGAGTTCCTTTGGTTCAGAGG 57.508 47.619 0.00 0.00 37.12 3.69
3176 3444 1.377725 CCATGGCGCTCTTGTCCTT 60.378 57.895 7.64 0.00 0.00 3.36
3199 3467 1.351153 CGAAGGAGAAAACGGAGAGC 58.649 55.000 0.00 0.00 0.00 4.09
3290 3562 7.866729 TGAAATATTTACTCGCTTCACAAACA 58.133 30.769 0.00 0.00 0.00 2.83
3291 3563 8.015658 ACTGAAATATTTACTCGCTTCACAAAC 58.984 33.333 0.00 0.00 0.00 2.93
3292 3564 8.015087 CACTGAAATATTTACTCGCTTCACAAA 58.985 33.333 0.00 0.00 0.00 2.83
3293 3565 7.172532 ACACTGAAATATTTACTCGCTTCACAA 59.827 33.333 0.00 0.00 0.00 3.33
3294 3566 6.649141 ACACTGAAATATTTACTCGCTTCACA 59.351 34.615 0.00 0.00 0.00 3.58
3295 3567 7.061752 ACACTGAAATATTTACTCGCTTCAC 57.938 36.000 0.00 0.00 0.00 3.18
3296 3568 6.312918 GGACACTGAAATATTTACTCGCTTCA 59.687 38.462 0.00 0.00 0.00 3.02
3297 3569 6.312918 TGGACACTGAAATATTTACTCGCTTC 59.687 38.462 0.00 0.00 0.00 3.86
3298 3570 6.170506 TGGACACTGAAATATTTACTCGCTT 58.829 36.000 0.00 0.00 0.00 4.68
3299 3571 5.730550 TGGACACTGAAATATTTACTCGCT 58.269 37.500 0.00 0.00 0.00 4.93
3300 3572 5.006746 CCTGGACACTGAAATATTTACTCGC 59.993 44.000 0.00 0.00 0.00 5.03
3301 3573 5.006746 GCCTGGACACTGAAATATTTACTCG 59.993 44.000 0.00 0.00 0.00 4.18
3302 3574 5.006746 CGCCTGGACACTGAAATATTTACTC 59.993 44.000 0.00 0.00 0.00 2.59
3303 3575 4.876107 CGCCTGGACACTGAAATATTTACT 59.124 41.667 0.00 0.00 0.00 2.24
3304 3576 4.873827 TCGCCTGGACACTGAAATATTTAC 59.126 41.667 0.00 0.00 0.00 2.01
3305 3577 4.873827 GTCGCCTGGACACTGAAATATTTA 59.126 41.667 0.00 0.00 45.36 1.40
3306 3578 3.689649 GTCGCCTGGACACTGAAATATTT 59.310 43.478 0.00 0.00 45.36 1.40
3307 3579 3.270877 GTCGCCTGGACACTGAAATATT 58.729 45.455 0.00 0.00 45.36 1.28
3308 3580 2.906354 GTCGCCTGGACACTGAAATAT 58.094 47.619 0.00 0.00 45.36 1.28
3309 3581 2.380084 GTCGCCTGGACACTGAAATA 57.620 50.000 0.00 0.00 45.36 1.40
3310 3582 3.233355 GTCGCCTGGACACTGAAAT 57.767 52.632 0.00 0.00 45.36 2.17
3311 3583 4.771127 GTCGCCTGGACACTGAAA 57.229 55.556 0.00 0.00 45.36 2.69
3567 3874 7.010552 CGAATCAATACTGCATTATACTAGGCC 59.989 40.741 0.00 0.00 0.00 5.19
3573 3880 6.009474 CGTGCGAATCAATACTGCATTATAC 58.991 40.000 0.00 0.00 37.93 1.47


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

AutoCloner maintained by Alex Coulton.