Multiple sequence alignment - TraesCS4B01G085700

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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 TraesCS4B01G085700 chr4B 100.000 3836 0 0 1 3836 86060699 86064534 0.000000e+00 7084
1 TraesCS4B01G085700 chr4D 92.151 2255 104 24 1 2225 57474156 57476367 0.000000e+00 3116
2 TraesCS4B01G085700 chr4D 87.265 1649 116 47 2219 3836 57476884 57478469 0.000000e+00 1796
3 TraesCS4B01G085700 chr4A 91.607 2228 141 25 18 2225 539300515 539298314 0.000000e+00 3037
4 TraesCS4B01G085700 chr4A 91.085 673 44 12 2219 2887 539297797 539297137 0.000000e+00 896
5 TraesCS4B01G085700 chr4A 83.103 580 39 35 2961 3524 539297136 539296600 1.250000e-129 473
6 TraesCS4B01G085700 chr4A 88.889 324 26 4 3515 3836 539296214 539295899 1.290000e-104 390
7 TraesCS4B01G085700 chr6B 91.820 1247 70 15 2373 3604 551794517 551795746 0.000000e+00 1709
8 TraesCS4B01G085700 chr6B 94.902 1020 51 1 1207 2225 551792826 551793845 0.000000e+00 1594
9 TraesCS4B01G085700 chr6B 91.164 928 47 17 1 903 551791520 551792437 0.000000e+00 1227
10 TraesCS4B01G085700 chr6B 89.520 229 16 4 3611 3836 551795881 551796104 2.260000e-72 283
11 TraesCS4B01G085700 chr6B 95.376 173 4 3 2219 2389 551794332 551794502 4.880000e-69 272
12 TraesCS4B01G085700 chr6B 88.789 223 11 3 919 1132 551792612 551792829 1.060000e-65 261


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 TraesCS4B01G085700 chr4B 86060699 86064534 3835 False 7084 7084 100.0000 1 3836 1 chr4B.!!$F1 3835
1 TraesCS4B01G085700 chr4D 57474156 57478469 4313 False 2456 3116 89.7080 1 3836 2 chr4D.!!$F1 3835
2 TraesCS4B01G085700 chr4A 539295899 539300515 4616 True 1199 3037 88.6710 18 3836 4 chr4A.!!$R1 3818
3 TraesCS4B01G085700 chr6B 551791520 551796104 4584 False 891 1709 91.9285 1 3836 6 chr6B.!!$F1 3835

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
975 1200 0.868406 GAAACCCAACTCAGTCAGCG 59.132 55.0 0.0 0.0 0.0 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2915 3727 0.326238 TAGAGGATGGTGGGTGGGAC 60.326 60.0 0.0 0.0 0.0 4.46 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
22 23 5.893897 CAGCTAGAGGAAAAGAAAGCATT 57.106 39.130 0.00 0.00 32.42 3.56
38 39 2.306512 AGCATTTAACAGGGGAACGGTA 59.693 45.455 0.00 0.00 0.00 4.02
72 73 7.218228 TCACAAACAACTGAGCATGATAAAT 57.782 32.000 0.00 0.00 0.00 1.40
176 177 6.116711 TCTACACTTTGCAGGGTTACATAA 57.883 37.500 0.00 0.00 37.94 1.90
258 261 4.437239 AGATAACAGGCAGCATATATCGC 58.563 43.478 0.00 0.48 0.00 4.58
262 265 2.093216 GGCAGCATATATCGCCAGC 58.907 57.895 10.98 10.85 44.25 4.85
263 266 1.699656 GGCAGCATATATCGCCAGCG 61.700 60.000 5.50 5.50 44.25 5.18
264 267 1.712081 CAGCATATATCGCCAGCGC 59.288 57.895 7.27 0.00 39.59 5.92
265 268 1.015607 CAGCATATATCGCCAGCGCA 61.016 55.000 11.47 0.00 39.59 6.09
276 279 1.321148 CGCCAGCGCAAAATTATTGTG 59.679 47.619 11.47 0.00 34.03 3.33
303 306 1.865865 CACCCTGGTGCGTATGTATC 58.134 55.000 2.89 0.00 39.39 2.24
307 310 3.154710 CCCTGGTGCGTATGTATCTCTA 58.845 50.000 0.00 0.00 0.00 2.43
309 312 4.547532 CCTGGTGCGTATGTATCTCTAAC 58.452 47.826 0.00 0.00 0.00 2.34
310 313 4.547532 CTGGTGCGTATGTATCTCTAACC 58.452 47.826 0.00 0.00 0.00 2.85
311 314 4.212716 TGGTGCGTATGTATCTCTAACCT 58.787 43.478 0.00 0.00 0.00 3.50
312 315 4.037565 TGGTGCGTATGTATCTCTAACCTG 59.962 45.833 0.00 0.00 0.00 4.00
313 316 4.277672 GGTGCGTATGTATCTCTAACCTGA 59.722 45.833 0.00 0.00 0.00 3.86
314 317 5.453648 GTGCGTATGTATCTCTAACCTGAG 58.546 45.833 0.00 0.00 35.52 3.35
315 318 5.238868 GTGCGTATGTATCTCTAACCTGAGA 59.761 44.000 0.00 0.00 45.71 3.27
330 333 8.055790 TCTAACCTGAGAGAGATGTATTCTTCA 58.944 37.037 0.00 0.00 33.74 3.02
521 524 7.016153 AGTCCACCATTAACATGAAGTAGAA 57.984 36.000 0.00 0.00 31.07 2.10
545 548 7.277174 AGAATCGGAAACTTTCAAATTGTCT 57.723 32.000 3.93 0.00 0.00 3.41
553 556 4.461198 ACTTTCAAATTGTCTCCCGACTT 58.539 39.130 0.00 0.00 40.86 3.01
565 568 2.035632 TCCCGACTTGTTTTTGCCATT 58.964 42.857 0.00 0.00 0.00 3.16
580 583 5.818136 TTGCCATTGTTAGCTGAATCTAC 57.182 39.130 0.00 0.00 0.00 2.59
616 619 4.143030 GCAACACTAGTGTAACATGAGCAG 60.143 45.833 28.13 9.46 44.13 4.24
668 700 5.627499 TTTTTGCTGAGAGATTAATGCGT 57.373 34.783 0.00 0.00 0.00 5.24
669 701 4.864916 TTTGCTGAGAGATTAATGCGTC 57.135 40.909 0.00 0.00 0.00 5.19
670 702 3.808466 TGCTGAGAGATTAATGCGTCT 57.192 42.857 0.00 0.00 0.00 4.18
671 703 3.451526 TGCTGAGAGATTAATGCGTCTG 58.548 45.455 0.00 0.00 0.00 3.51
672 704 3.131046 TGCTGAGAGATTAATGCGTCTGA 59.869 43.478 0.00 0.00 0.00 3.27
673 705 4.115516 GCTGAGAGATTAATGCGTCTGAA 58.884 43.478 0.00 0.00 0.00 3.02
674 706 4.749099 GCTGAGAGATTAATGCGTCTGAAT 59.251 41.667 0.00 0.00 0.00 2.57
675 707 5.333187 GCTGAGAGATTAATGCGTCTGAATG 60.333 44.000 0.00 0.00 0.00 2.67
676 708 5.052481 TGAGAGATTAATGCGTCTGAATGG 58.948 41.667 0.00 0.00 0.00 3.16
677 709 3.812053 AGAGATTAATGCGTCTGAATGGC 59.188 43.478 0.00 0.00 0.00 4.40
803 837 3.278574 GCAATGTAGCCATGTAGGTGAA 58.721 45.455 0.00 0.00 40.61 3.18
887 953 6.419980 TCAAATGTTTCAAGCAAACCAAAG 57.580 33.333 0.00 0.00 43.52 2.77
903 969 7.566868 GCAAACCAAAGAAATTTCGACATGTAC 60.567 37.037 12.42 0.00 0.00 2.90
904 970 5.685841 ACCAAAGAAATTTCGACATGTACG 58.314 37.500 12.42 4.78 0.00 3.67
906 972 6.424509 ACCAAAGAAATTTCGACATGTACGTA 59.575 34.615 12.42 0.00 0.00 3.57
907 973 7.041916 ACCAAAGAAATTTCGACATGTACGTAA 60.042 33.333 12.42 5.35 0.00 3.18
908 974 7.799447 CCAAAGAAATTTCGACATGTACGTAAA 59.201 33.333 12.42 7.75 0.00 2.01
909 975 8.615585 CAAAGAAATTTCGACATGTACGTAAAC 58.384 33.333 12.42 0.00 0.00 2.01
910 976 7.647907 AGAAATTTCGACATGTACGTAAACT 57.352 32.000 12.42 4.35 0.00 2.66
912 978 8.553696 AGAAATTTCGACATGTACGTAAACTTT 58.446 29.630 12.42 3.92 0.00 2.66
913 979 9.161684 GAAATTTCGACATGTACGTAAACTTTT 57.838 29.630 0.00 3.31 0.00 2.27
914 980 8.483743 AATTTCGACATGTACGTAAACTTTTG 57.516 30.769 0.00 0.00 0.00 2.44
915 981 6.586868 TTCGACATGTACGTAAACTTTTGT 57.413 33.333 0.00 0.00 0.00 2.83
916 982 7.691430 TTCGACATGTACGTAAACTTTTGTA 57.309 32.000 0.00 0.00 0.00 2.41
975 1200 0.868406 GAAACCCAACTCAGTCAGCG 59.132 55.000 0.00 0.00 0.00 5.18
980 1216 3.616721 AACTCAGTCAGCGGCGGT 61.617 61.111 5.44 5.44 0.00 5.68
982 1218 3.753434 CTCAGTCAGCGGCGGTCT 61.753 66.667 9.40 0.46 0.00 3.85
983 1219 3.978723 CTCAGTCAGCGGCGGTCTG 62.979 68.421 18.30 18.30 0.00 3.51
984 1220 4.056125 CAGTCAGCGGCGGTCTGA 62.056 66.667 19.28 15.86 38.16 3.27
985 1221 3.753434 AGTCAGCGGCGGTCTGAG 61.753 66.667 15.89 2.77 40.82 3.35
986 1222 4.803426 GTCAGCGGCGGTCTGAGG 62.803 72.222 15.89 2.40 40.82 3.86
1631 1880 3.423154 CTTGTTCGGTCAGGCGGC 61.423 66.667 0.00 0.00 0.00 6.53
1632 1881 3.883744 CTTGTTCGGTCAGGCGGCT 62.884 63.158 5.25 5.25 0.00 5.52
1655 1904 0.669318 GTGTTCGGCTCGATGGTTGA 60.669 55.000 0.00 0.00 35.23 3.18
1704 1953 0.396435 TGATCAGTTTCCTGCCGTGT 59.604 50.000 0.00 0.00 38.66 4.49
1756 2005 1.628340 AGATGGTTCATGGGTTCGTGA 59.372 47.619 0.00 0.00 37.15 4.35
1869 2118 2.896854 GATGGAATGGCTGCGCGA 60.897 61.111 12.10 0.00 0.00 5.87
2076 2325 0.958091 CTAGGAGTCATGGGCTCGAG 59.042 60.000 8.45 8.45 34.00 4.04
2135 2384 2.352503 GCAAAATGTGGCGAGATTGT 57.647 45.000 0.00 0.00 0.00 2.71
2228 2999 3.040965 CCAACCATGGTGAGCAAGT 57.959 52.632 20.60 0.00 42.18 3.16
2349 3122 3.006430 TCACAGGCTCGTGATAAACTGAA 59.994 43.478 13.41 0.00 40.94 3.02
2423 3227 2.093181 GGAAGGCCGCCCAATTAAAATT 60.093 45.455 5.55 0.00 0.00 1.82
2448 3252 4.855715 TGAACCGTTGCATTATTGGAAA 57.144 36.364 0.00 0.00 34.74 3.13
2571 3379 2.159448 GCCAAACAAAAACCAAAGTGGC 60.159 45.455 0.00 0.00 42.67 5.01
2602 3410 0.962356 ACGGGTACTGGACGACGATT 60.962 55.000 11.83 0.00 40.47 3.34
2731 3540 3.412386 AGTCACAGTGCTATTTTCCACC 58.588 45.455 0.00 0.00 32.48 4.61
2746 3555 1.064134 CACCGAGATGCATCGACGA 59.936 57.895 33.41 0.00 45.56 4.20
2748 3557 0.385751 ACCGAGATGCATCGACGATT 59.614 50.000 33.41 23.16 45.56 3.34
2749 3558 0.780596 CCGAGATGCATCGACGATTG 59.219 55.000 33.41 21.16 45.56 2.67
2802 3611 3.496130 CCGATGGCAGATGACTGATTAAC 59.504 47.826 0.00 0.00 46.03 2.01
2840 3649 2.626683 TCATGCTAGTGGGATGAGTCCA 60.627 50.000 6.59 0.00 45.56 4.02
2841 3650 4.510219 TCATGCTAGTGGGATGAGTCCAG 61.510 52.174 6.59 0.00 45.56 3.86
2842 3651 6.720549 TCATGCTAGTGGGATGAGTCCAGA 62.721 50.000 6.59 0.00 45.56 3.86
2853 3662 0.106217 GAGTCCAGAGGAGAGGAGGG 60.106 65.000 0.00 0.00 33.85 4.30
2858 3667 0.859760 CAGAGGAGAGGAGGGAGGAT 59.140 60.000 0.00 0.00 0.00 3.24
2942 3754 2.900546 CCCACCATCCTCTATACTGGAC 59.099 54.545 0.00 0.00 34.90 4.02
2954 3766 6.349445 CCTCTATACTGGACGCGAAAGAATAT 60.349 42.308 15.93 5.97 0.00 1.28
3048 3873 7.508687 TCTAGCATATTTTGTATTGCTCTCCA 58.491 34.615 0.00 0.00 43.94 3.86
3049 3874 6.382869 AGCATATTTTGTATTGCTCTCCAC 57.617 37.500 0.00 0.00 41.38 4.02
3056 3881 2.301870 TGTATTGCTCTCCACGGAAGTT 59.698 45.455 0.00 0.00 46.40 2.66
3124 3956 2.027192 GCTCCCAGGATAGTGTTTGTGA 60.027 50.000 0.00 0.00 0.00 3.58
3178 4014 7.920682 AGTGTGCATTCGTTTTTCTCTAAAAAT 59.079 29.630 0.00 0.00 44.22 1.82
3448 4303 2.288030 ACGTGTTGGCACTAGTGAGTAC 60.288 50.000 27.08 18.25 43.16 2.73
3449 4304 2.030185 CGTGTTGGCACTAGTGAGTACT 60.030 50.000 27.08 0.00 43.16 2.73
3450 4305 3.552273 CGTGTTGGCACTAGTGAGTACTT 60.552 47.826 27.08 0.00 43.16 2.24
3451 4306 4.320714 CGTGTTGGCACTAGTGAGTACTTA 60.321 45.833 27.08 3.06 43.16 2.24
3529 4779 1.546099 CCATGCTATGCCATGCCACTA 60.546 52.381 0.00 0.00 40.92 2.74
3545 4795 6.747414 TGCCACTACATTATCATTAGGTCT 57.253 37.500 0.00 0.00 0.00 3.85
3568 4818 4.171005 TGTCATCGTGGTCGTCTAAATTC 58.829 43.478 0.00 0.00 38.33 2.17
3588 4838 0.247185 ATGCCGCATTTGGACCTTTG 59.753 50.000 0.00 0.00 0.00 2.77
3650 5028 7.582319 GTGAATTTAAATTTGGCAGTTTGAACG 59.418 33.333 14.45 0.00 0.00 3.95
3692 5072 8.983307 ATGAAAACACAAACAAATGCAAAAAT 57.017 23.077 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 7.176690 CCCTGTTAAATGCTTTCTTTTCCTCTA 59.823 37.037 0.00 0.00 0.00 2.43
22 23 2.607499 TGACTACCGTTCCCCTGTTAA 58.393 47.619 0.00 0.00 0.00 2.01
38 39 7.141363 GCTCAGTTGTTTGTGAATAAATGACT 58.859 34.615 0.00 0.00 36.50 3.41
207 208 7.546358 TGCTGGTTTATTCAGGTAAATCATTG 58.454 34.615 0.00 0.00 34.98 2.82
258 261 3.573598 TGACACAATAATTTTGCGCTGG 58.426 40.909 9.73 0.00 0.00 4.85
260 263 6.865726 TGTAAATGACACAATAATTTTGCGCT 59.134 30.769 9.73 0.00 31.20 5.92
261 264 7.043454 TGTAAATGACACAATAATTTTGCGC 57.957 32.000 0.00 0.00 31.20 6.09
276 279 0.802494 CGCACCAGGGTGTAAATGAC 59.198 55.000 18.99 0.69 46.90 3.06
303 306 8.463930 AAGAATACATCTCTCTCAGGTTAGAG 57.536 38.462 0.00 0.00 43.72 2.43
307 310 7.673641 ATGAAGAATACATCTCTCTCAGGTT 57.326 36.000 0.00 0.00 37.42 3.50
309 312 7.499292 ACAATGAAGAATACATCTCTCTCAGG 58.501 38.462 0.00 0.00 37.42 3.86
310 313 8.945481 AACAATGAAGAATACATCTCTCTCAG 57.055 34.615 0.00 0.00 37.42 3.35
311 314 7.984050 GGAACAATGAAGAATACATCTCTCTCA 59.016 37.037 0.00 0.00 37.42 3.27
312 315 7.984050 TGGAACAATGAAGAATACATCTCTCTC 59.016 37.037 0.00 0.00 33.04 3.20
313 316 7.855375 TGGAACAATGAAGAATACATCTCTCT 58.145 34.615 0.00 0.00 33.04 3.10
314 317 7.226325 CCTGGAACAATGAAGAATACATCTCTC 59.774 40.741 0.00 0.00 38.70 3.20
315 318 7.052873 CCTGGAACAATGAAGAATACATCTCT 58.947 38.462 0.00 0.00 38.70 3.10
330 333 4.218417 CGATTCAACCTTTCCTGGAACAAT 59.782 41.667 9.04 1.25 38.70 2.71
521 524 7.277174 AGACAATTTGAAAGTTTCCGATTCT 57.723 32.000 13.01 4.82 0.00 2.40
545 548 1.698506 ATGGCAAAAACAAGTCGGGA 58.301 45.000 0.00 0.00 0.00 5.14
553 556 4.662468 TCAGCTAACAATGGCAAAAACA 57.338 36.364 0.00 0.00 35.08 2.83
565 568 4.353777 ACTCTGGGTAGATTCAGCTAACA 58.646 43.478 0.00 0.00 29.50 2.41
580 583 2.175202 AGTGTTGCTAGAGACTCTGGG 58.825 52.381 15.55 8.79 0.00 4.45
672 704 4.444838 TAGTGTCGCGGCGCCATT 62.445 61.111 28.98 17.98 0.00 3.16
675 707 3.688475 TTAGTAGTGTCGCGGCGCC 62.688 63.158 27.87 19.07 0.00 6.53
676 708 1.143969 ATTTAGTAGTGTCGCGGCGC 61.144 55.000 24.21 24.21 0.00 6.53
677 709 0.570734 CATTTAGTAGTGTCGCGGCG 59.429 55.000 17.70 17.70 0.00 6.46
678 710 1.636988 ACATTTAGTAGTGTCGCGGC 58.363 50.000 2.29 2.29 0.00 6.53
679 711 2.222729 GCAACATTTAGTAGTGTCGCGG 60.223 50.000 6.13 0.00 0.00 6.46
680 712 2.410392 TGCAACATTTAGTAGTGTCGCG 59.590 45.455 0.00 0.00 0.00 5.87
681 713 4.398549 TTGCAACATTTAGTAGTGTCGC 57.601 40.909 0.00 0.00 0.00 5.19
682 714 4.838642 CGTTTGCAACATTTAGTAGTGTCG 59.161 41.667 0.00 0.00 0.00 4.35
683 715 5.744490 ACGTTTGCAACATTTAGTAGTGTC 58.256 37.500 0.00 0.00 0.00 3.67
684 716 5.744666 ACGTTTGCAACATTTAGTAGTGT 57.255 34.783 0.00 0.00 0.00 3.55
685 717 6.419090 CAACGTTTGCAACATTTAGTAGTG 57.581 37.500 0.00 0.00 0.00 2.74
803 837 5.617528 TTTGATGCCATTATGAAATGCCT 57.382 34.783 0.00 0.00 41.06 4.75
872 938 6.035542 GTCGAAATTTCTTTGGTTTGCTTGAA 59.964 34.615 15.92 0.00 0.00 2.69
887 953 8.703823 AAAGTTTACGTACATGTCGAAATTTC 57.296 30.769 19.74 8.20 0.00 2.17
903 969 4.901881 CGGCTTCTTGTACAAAAGTTTACG 59.098 41.667 21.20 17.81 0.00 3.18
904 970 5.813717 ACGGCTTCTTGTACAAAAGTTTAC 58.186 37.500 21.20 13.43 0.00 2.01
906 972 4.976224 ACGGCTTCTTGTACAAAAGTTT 57.024 36.364 21.20 10.59 0.00 2.66
907 973 4.024302 GCTACGGCTTCTTGTACAAAAGTT 60.024 41.667 21.20 13.62 35.22 2.66
908 974 3.497262 GCTACGGCTTCTTGTACAAAAGT 59.503 43.478 21.20 13.25 35.22 2.66
909 975 3.496884 TGCTACGGCTTCTTGTACAAAAG 59.503 43.478 10.03 15.42 39.59 2.27
910 976 3.468770 TGCTACGGCTTCTTGTACAAAA 58.531 40.909 10.03 6.43 39.59 2.44
912 978 2.823924 TGCTACGGCTTCTTGTACAA 57.176 45.000 8.28 8.28 39.59 2.41
913 979 4.368315 CATATGCTACGGCTTCTTGTACA 58.632 43.478 0.00 0.00 39.59 2.90
914 980 3.184581 GCATATGCTACGGCTTCTTGTAC 59.815 47.826 20.64 0.00 39.59 2.90
915 981 3.390135 GCATATGCTACGGCTTCTTGTA 58.610 45.455 20.64 0.00 39.59 2.41
916 982 2.213499 GCATATGCTACGGCTTCTTGT 58.787 47.619 20.64 0.00 39.59 3.16
975 1200 2.997897 ACCTCACCTCAGACCGCC 60.998 66.667 0.00 0.00 0.00 6.13
980 1216 1.133167 TCTGTTGGACCTCACCTCAGA 60.133 52.381 0.00 0.00 38.28 3.27
982 1218 1.625315 CATCTGTTGGACCTCACCTCA 59.375 52.381 0.00 0.00 0.00 3.86
983 1219 1.677217 GCATCTGTTGGACCTCACCTC 60.677 57.143 0.00 0.00 0.00 3.85
984 1220 0.326264 GCATCTGTTGGACCTCACCT 59.674 55.000 0.00 0.00 0.00 4.00
985 1221 0.678048 GGCATCTGTTGGACCTCACC 60.678 60.000 0.00 0.00 0.00 4.02
986 1222 0.678048 GGGCATCTGTTGGACCTCAC 60.678 60.000 0.00 0.00 0.00 3.51
1099 1344 1.233369 CGTGGATAGGGAGGAGGGT 59.767 63.158 0.00 0.00 0.00 4.34
1359 1608 0.822164 GGTATGTGTAGCAGTCCGGT 59.178 55.000 0.00 0.00 0.00 5.28
1438 1687 3.692406 GAACCTCACCGCGTCCCT 61.692 66.667 4.92 0.00 0.00 4.20
1631 1880 3.989698 ATCGAGCCGAACACCGCAG 62.990 63.158 1.44 0.00 39.99 5.18
1632 1881 4.063967 ATCGAGCCGAACACCGCA 62.064 61.111 1.44 0.00 39.99 5.69
1645 1894 2.668632 GCCCTGGTCAACCATCGA 59.331 61.111 1.58 0.00 46.46 3.59
1704 1953 0.615331 GACATTCCTGTCCCTGCAGA 59.385 55.000 17.39 0.00 45.06 4.26
1713 1962 1.078848 GGCAGCGAGACATTCCTGT 60.079 57.895 0.00 0.00 38.67 4.00
1756 2005 0.749454 GCATCGAACCCCAGCTTGAT 60.749 55.000 0.00 0.00 0.00 2.57
1806 2055 0.747644 TCCCGCACTTGCCATACATG 60.748 55.000 0.00 0.00 37.91 3.21
1869 2118 1.147600 GTTCCAGGACACCACGGTT 59.852 57.895 0.00 0.00 0.00 4.44
1917 2166 4.235762 ATCGCCCGAACCCCATCG 62.236 66.667 0.00 0.00 42.37 3.84
2076 2325 1.663074 GCCGATCCTCGCATCAGTC 60.663 63.158 0.00 0.00 38.82 3.51
2135 2384 2.946329 TCAAAAGCCTGTCTTGCGTAAA 59.054 40.909 0.00 0.00 34.67 2.01
2145 2394 1.202405 CGCAAACCTTCAAAAGCCTGT 60.202 47.619 0.00 0.00 0.00 4.00
2228 2999 8.154856 ACAGTCTAACCTAAAACTTGCATCTAA 58.845 33.333 0.00 0.00 0.00 2.10
2383 3156 5.536916 CCTTCCCCATTGTACAGTTAACAAA 59.463 40.000 8.61 0.00 40.05 2.83
2423 3227 4.460731 TCCAATAATGCAACGGTTCATCAA 59.539 37.500 0.00 0.00 0.00 2.57
2448 3252 6.409704 TCTGCAGCTCTAATGTAAAATCACT 58.590 36.000 9.47 0.00 0.00 3.41
2602 3410 3.181455 CCATTATTCCTCACCGATCACCA 60.181 47.826 0.00 0.00 0.00 4.17
2655 3463 8.899427 TGAAACAAATTTCTATGCCAATCAAA 57.101 26.923 1.82 0.00 44.02 2.69
2731 3540 1.758783 TCAATCGTCGATGCATCTCG 58.241 50.000 23.73 24.34 39.99 4.04
2765 3574 2.069273 CATCGGCGTTCTTGTTTCTCT 58.931 47.619 6.85 0.00 0.00 3.10
2802 3611 9.606631 ACTAGCATGAGAAAGGAAAAAGTATAG 57.393 33.333 0.00 0.00 0.00 1.31
2818 3627 2.036992 GGACTCATCCCACTAGCATGAG 59.963 54.545 15.20 15.20 46.16 2.90
2838 3647 1.232792 CCTCCCTCCTCTCCTCTGG 59.767 68.421 0.00 0.00 0.00 3.86
2840 3649 2.542257 TATCCTCCCTCCTCTCCTCT 57.458 55.000 0.00 0.00 0.00 3.69
2841 3650 3.141272 TCTTTATCCTCCCTCCTCTCCTC 59.859 52.174 0.00 0.00 0.00 3.71
2842 3651 3.143406 TCTTTATCCTCCCTCCTCTCCT 58.857 50.000 0.00 0.00 0.00 3.69
2843 3652 3.621682 TCTTTATCCTCCCTCCTCTCC 57.378 52.381 0.00 0.00 0.00 3.71
2844 3653 4.552674 ACTTCTTTATCCTCCCTCCTCTC 58.447 47.826 0.00 0.00 0.00 3.20
2848 3657 3.054361 TGCAACTTCTTTATCCTCCCTCC 60.054 47.826 0.00 0.00 0.00 4.30
2853 3662 5.473504 TCCAGTTTGCAACTTCTTTATCCTC 59.526 40.000 0.00 0.00 40.46 3.71
2858 3667 7.106439 TCATTTCCAGTTTGCAACTTCTTTA 57.894 32.000 0.00 0.00 40.46 1.85
2915 3727 0.326238 TAGAGGATGGTGGGTGGGAC 60.326 60.000 0.00 0.00 0.00 4.46
2917 3729 1.978580 GTATAGAGGATGGTGGGTGGG 59.021 57.143 0.00 0.00 0.00 4.61
2942 3754 4.499399 TCTCGTTCTTCATATTCTTTCGCG 59.501 41.667 0.00 0.00 0.00 5.87
2954 3766 6.418956 CGATTTGAAACTTTCTCGTTCTTCA 58.581 36.000 3.22 0.00 0.00 3.02
3031 3856 3.950397 TCCGTGGAGAGCAATACAAAAT 58.050 40.909 0.00 0.00 0.00 1.82
3032 3857 3.410631 TCCGTGGAGAGCAATACAAAA 57.589 42.857 0.00 0.00 0.00 2.44
3048 3873 4.853924 AATTCAGAATGCAAACTTCCGT 57.146 36.364 0.00 0.00 34.76 4.69
3049 3874 6.529463 AAAAATTCAGAATGCAAACTTCCG 57.471 33.333 0.00 0.00 34.76 4.30
3074 3899 8.835439 TGCAAAATGCTAGATTATGAATCGTTA 58.165 29.630 3.78 0.00 45.31 3.18
3124 3956 6.036083 CGAACTTTATATACTGTGCTGTTGCT 59.964 38.462 0.00 0.00 40.48 3.91
3178 4014 5.355910 GCACTGAGTTCCCGGAATTTATTTA 59.644 40.000 0.73 0.00 0.00 1.40
3189 4027 1.961277 GGTGTGCACTGAGTTCCCG 60.961 63.158 19.41 0.00 0.00 5.14
3191 4029 2.543777 TAAGGTGTGCACTGAGTTCC 57.456 50.000 19.41 10.36 0.00 3.62
3251 4091 6.514048 GCAATGAATAGAGATACTTTGGGTGC 60.514 42.308 0.00 0.00 0.00 5.01
3263 4103 6.753913 ACCCTGATTAGCAATGAATAGAGA 57.246 37.500 0.00 0.00 0.00 3.10
3310 4152 1.326055 ACCCTCCCCTCCATGTACTA 58.674 55.000 0.00 0.00 0.00 1.82
3344 4197 1.846007 TATGCTGAACCGGGCATTTT 58.154 45.000 19.05 0.00 45.41 1.82
3448 4303 9.979270 GATATCGACCTTGCATTCAATATTAAG 57.021 33.333 0.00 0.00 0.00 1.85
3449 4304 9.725019 AGATATCGACCTTGCATTCAATATTAA 57.275 29.630 0.00 0.00 0.00 1.40
3450 4305 9.725019 AAGATATCGACCTTGCATTCAATATTA 57.275 29.630 0.00 0.00 0.00 0.98
3451 4306 8.627208 AAGATATCGACCTTGCATTCAATATT 57.373 30.769 0.00 0.00 0.00 1.28
3529 4779 7.439356 CACGATGACAAGACCTAATGATAATGT 59.561 37.037 0.00 0.00 0.00 2.71
3545 4795 3.646611 TTTAGACGACCACGATGACAA 57.353 42.857 0.00 0.00 42.66 3.18
3568 4818 0.247185 AAAGGTCCAAATGCGGCATG 59.753 50.000 17.43 6.41 0.00 4.06
3588 4838 4.593157 TCAAGTTCAACATAAACACGTGC 58.407 39.130 17.22 0.00 0.00 5.34
3665 5043 8.807667 TTTTGCATTTGTTTGTGTTTTCATTT 57.192 23.077 0.00 0.00 0.00 2.32
3667 5045 8.983307 ATTTTTGCATTTGTTTGTGTTTTCAT 57.017 23.077 0.00 0.00 0.00 2.57
3668 5046 9.897744 TTATTTTTGCATTTGTTTGTGTTTTCA 57.102 22.222 0.00 0.00 0.00 2.69
3692 5072 6.036191 GGCACGTGGTTTTCTTTTTCAAATTA 59.964 34.615 18.88 0.00 0.00 1.40
3773 5153 4.314740 TGGAAGCAAGCGTAATTGTTTT 57.685 36.364 0.00 0.00 34.29 2.43
3774 5154 4.022416 TGATGGAAGCAAGCGTAATTGTTT 60.022 37.500 0.00 0.46 36.47 2.83
3775 5155 3.505680 TGATGGAAGCAAGCGTAATTGTT 59.494 39.130 0.00 0.00 32.56 2.83


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

AutoCloner maintained by Alex Coulton.