Multiple sequence alignment - TraesCS5A01G403400

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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 TraesCS5A01G403400 chr5A 100.000 4457 0 0 1 4457 595893274 595897730 0.000000e+00 8231
1 TraesCS5A01G403400 chr5D 92.258 4495 187 70 47 4457 476459664 476464081 0.000000e+00 6224
2 TraesCS5A01G403400 chr5D 84.659 176 25 2 2908 3082 458632622 458632796 1.650000e-39 174
3 TraesCS5A01G403400 chr5B 91.964 4542 201 69 16 4457 583910429 583914906 0.000000e+00 6215
4 TraesCS5A01G403400 chr5B 85.227 176 24 2 2908 3082 562048319 562048493 3.540000e-41 180
5 TraesCS5A01G403400 chr1B 81.071 280 51 2 3787 4065 678259509 678259787 5.800000e-54 222
6 TraesCS5A01G403400 chr1B 81.818 176 30 2 2908 3082 520245315 520245489 3.590000e-31 147
7 TraesCS5A01G403400 chr1D 80.714 280 52 2 3787 4065 487168521 487168799 2.700000e-52 217
8 TraesCS5A01G403400 chr1A 80.714 280 52 2 3787 4065 584676043 584676321 2.700000e-52 217
9 TraesCS5A01G403400 chr1A 81.818 176 30 2 2908 3082 64844670 64844844 3.590000e-31 147
10 TraesCS5A01G403400 chr4A 84.091 176 26 2 2908 3082 532161998 532162172 7.670000e-38 169
11 TraesCS5A01G403400 chr7D 83.523 176 27 2 2908 3082 332692750 332692924 3.570000e-36 163
12 TraesCS5A01G403400 chr2D 83.815 173 26 2 2911 3082 601056257 601056086 3.570000e-36 163


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 TraesCS5A01G403400 chr5A 595893274 595897730 4456 False 8231 8231 100.000 1 4457 1 chr5A.!!$F1 4456
1 TraesCS5A01G403400 chr5D 476459664 476464081 4417 False 6224 6224 92.258 47 4457 1 chr5D.!!$F2 4410
2 TraesCS5A01G403400 chr5B 583910429 583914906 4477 False 6215 6215 91.964 16 4457 1 chr5B.!!$F2 4441

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
565 591 0.106708 TGAGCTTCACTCTTTGCCGT 59.893 50.000 0.00 0.0 46.41 5.68 F
982 1068 0.179000 AATGCCTTAGCGGAGAGTGG 59.821 55.000 0.00 0.0 44.31 4.00 F
1510 1616 0.392461 TGCAGTTCCCGCTAATGTCC 60.392 55.000 0.00 0.0 0.00 4.02 F
2867 2973 1.070108 CCATCTTGATCGATGCTTGCG 60.070 52.381 0.54 0.0 39.51 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2044 2150 0.039617 CGCCGGCATTTTTCTTGTGA 60.040 50.000 28.98 0.00 0.00 3.58 R
2870 2976 0.674581 CTTCTGAGCACCGGCATTGA 60.675 55.000 0.00 0.00 44.61 2.57 R
3048 3154 0.671781 GCTGGAGCTGCTCGAAGAAA 60.672 55.000 26.04 8.65 38.21 2.52 R
4400 4536 1.067142 ACCTGCTCGACGAAATGCTTA 60.067 47.619 8.74 0.00 0.00 3.09 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
29 30 2.614057 CCAGTCAGGCCGTTCAAATATC 59.386 50.000 0.00 0.00 0.00 1.63
31 32 3.557595 CAGTCAGGCCGTTCAAATATCTC 59.442 47.826 0.00 0.00 0.00 2.75
32 33 3.452627 AGTCAGGCCGTTCAAATATCTCT 59.547 43.478 0.00 0.00 0.00 3.10
35 36 3.041946 AGGCCGTTCAAATATCTCTCCT 58.958 45.455 0.00 0.00 0.00 3.69
37 38 4.282195 AGGCCGTTCAAATATCTCTCCTAG 59.718 45.833 0.00 0.00 0.00 3.02
83 84 4.421058 GCGAGTTCAAAGTTCAAAAACCT 58.579 39.130 0.00 0.00 35.92 3.50
84 85 4.265320 GCGAGTTCAAAGTTCAAAAACCTG 59.735 41.667 0.00 0.00 35.92 4.00
85 86 4.265320 CGAGTTCAAAGTTCAAAAACCTGC 59.735 41.667 0.00 0.00 35.92 4.85
86 87 5.146010 AGTTCAAAGTTCAAAAACCTGCA 57.854 34.783 0.00 0.00 35.92 4.41
87 88 5.170748 AGTTCAAAGTTCAAAAACCTGCAG 58.829 37.500 6.78 6.78 35.92 4.41
110 111 1.771255 AGGCTTCACTGTTCTTGGTCT 59.229 47.619 0.00 0.00 0.00 3.85
140 141 2.027745 TGTCTGACAGAGAAAGATGGCC 60.028 50.000 5.10 0.00 30.26 5.36
151 152 2.795231 AAGATGGCCGGATCATATGG 57.205 50.000 5.05 0.00 0.00 2.74
152 153 1.661463 AGATGGCCGGATCATATGGT 58.339 50.000 5.05 0.00 0.00 3.55
153 154 2.832838 AGATGGCCGGATCATATGGTA 58.167 47.619 5.05 0.00 0.00 3.25
235 236 2.808567 GCGAGATTCCCTTCATTCCTCC 60.809 54.545 0.00 0.00 0.00 4.30
323 345 1.517832 CGTGATCCAGACAGTCCCC 59.482 63.158 0.00 0.00 0.00 4.81
364 386 6.303839 AGAGCTGGTTTACAAATGGAGTAAA 58.696 36.000 0.00 0.00 38.66 2.01
371 393 6.804783 GGTTTACAAATGGAGTAAATTGTCGG 59.195 38.462 0.00 0.00 41.74 4.79
381 403 6.070995 TGGAGTAAATTGTCGGTGAGTTATCT 60.071 38.462 0.00 0.00 0.00 1.98
383 405 7.434602 GGAGTAAATTGTCGGTGAGTTATCTAC 59.565 40.741 0.00 0.00 0.00 2.59
385 407 8.529476 AGTAAATTGTCGGTGAGTTATCTACTT 58.471 33.333 0.00 0.00 37.17 2.24
386 408 7.596749 AAATTGTCGGTGAGTTATCTACTTG 57.403 36.000 0.00 0.00 37.17 3.16
398 420 9.074576 TGAGTTATCTACTTGTCTTGTTGAGTA 57.925 33.333 0.00 0.00 37.17 2.59
400 422 8.305317 AGTTATCTACTTGTCTTGTTGAGTACC 58.695 37.037 0.00 0.00 31.29 3.34
425 448 4.679654 CACTGTAAAAATCTTGGCGTTTCC 59.320 41.667 0.00 0.00 0.00 3.13
453 479 1.669760 CCGGGAAACTGCTGCGTTA 60.670 57.895 9.54 0.00 34.42 3.18
484 510 1.531058 CCGGCGCTACAAGTTTTATGC 60.531 52.381 7.64 0.00 0.00 3.14
507 533 4.366684 GGTTGGGAGGGCCAGGTG 62.367 72.222 6.18 0.00 35.15 4.00
533 559 4.054455 CCGAACACGTGAACGGCG 62.054 66.667 30.98 21.43 44.95 6.46
560 586 3.570550 ACTCTACGTGAGCTTCACTCTTT 59.429 43.478 12.90 0.88 44.85 2.52
561 587 3.902150 TCTACGTGAGCTTCACTCTTTG 58.098 45.455 0.00 2.36 44.85 2.77
563 589 0.514691 CGTGAGCTTCACTCTTTGCC 59.485 55.000 12.45 0.00 44.85 4.52
564 590 0.514691 GTGAGCTTCACTCTTTGCCG 59.485 55.000 8.50 0.00 46.41 5.69
565 591 0.106708 TGAGCTTCACTCTTTGCCGT 59.893 50.000 0.00 0.00 46.41 5.68
566 592 0.514691 GAGCTTCACTCTTTGCCGTG 59.485 55.000 0.00 0.00 42.62 4.94
567 593 0.886490 AGCTTCACTCTTTGCCGTGG 60.886 55.000 0.00 0.00 0.00 4.94
568 594 1.166531 GCTTCACTCTTTGCCGTGGT 61.167 55.000 0.00 0.00 0.00 4.16
678 704 4.152580 GCTGCTCAAACTGTAGTTTAGGAC 59.847 45.833 9.47 2.06 45.54 3.85
689 715 5.464168 TGTAGTTTAGGACAAAGCGAGTAC 58.536 41.667 0.00 0.00 0.00 2.73
690 716 4.868314 AGTTTAGGACAAAGCGAGTACT 57.132 40.909 0.00 0.00 33.87 2.73
691 717 4.807443 AGTTTAGGACAAAGCGAGTACTC 58.193 43.478 13.18 13.18 31.28 2.59
692 718 3.863142 TTAGGACAAAGCGAGTACTCC 57.137 47.619 17.23 9.91 31.28 3.85
693 719 1.926108 AGGACAAAGCGAGTACTCCT 58.074 50.000 17.23 11.98 0.00 3.69
694 720 1.819903 AGGACAAAGCGAGTACTCCTC 59.180 52.381 17.23 9.24 36.80 3.71
695 721 1.135053 GGACAAAGCGAGTACTCCTCC 60.135 57.143 17.23 8.86 36.82 4.30
696 722 1.819903 GACAAAGCGAGTACTCCTCCT 59.180 52.381 17.23 8.23 36.82 3.69
697 723 1.819903 ACAAAGCGAGTACTCCTCCTC 59.180 52.381 17.23 2.04 36.82 3.71
698 724 1.135333 CAAAGCGAGTACTCCTCCTCC 59.865 57.143 17.23 0.00 36.82 4.30
699 725 0.626916 AAGCGAGTACTCCTCCTCCT 59.373 55.000 17.23 1.82 36.82 3.69
700 726 0.181824 AGCGAGTACTCCTCCTCCTC 59.818 60.000 17.23 0.00 36.82 3.71
729 760 5.357878 TCCTGCTGCTGGTTGAATAATAAAG 59.642 40.000 22.62 0.00 0.00 1.85
731 762 6.441093 TGCTGCTGGTTGAATAATAAAGAG 57.559 37.500 0.00 0.00 0.00 2.85
785 820 2.159517 GGATACGTGCTTTTGAGGCAAG 60.160 50.000 0.00 0.00 41.54 4.01
786 821 0.591170 TACGTGCTTTTGAGGCAAGC 59.409 50.000 0.00 0.67 45.92 4.01
789 824 3.354678 GCTTTTGAGGCAAGCGGA 58.645 55.556 0.00 0.00 37.51 5.54
850 894 1.075600 GTCTCCCTCCTCCCTCCTG 60.076 68.421 0.00 0.00 0.00 3.86
860 904 1.413077 CCTCCCTCCTGTAATCGGAAC 59.587 57.143 0.00 0.00 0.00 3.62
897 941 2.256117 AATACAGGCGCCAGAATACC 57.744 50.000 31.54 0.00 0.00 2.73
950 1006 2.726351 CCGTCCTCCTGCTCCTTCC 61.726 68.421 0.00 0.00 0.00 3.46
951 1007 1.984570 CGTCCTCCTGCTCCTTCCA 60.985 63.158 0.00 0.00 0.00 3.53
952 1008 1.599576 GTCCTCCTGCTCCTTCCAC 59.400 63.158 0.00 0.00 0.00 4.02
953 1009 1.984570 TCCTCCTGCTCCTTCCACG 60.985 63.158 0.00 0.00 0.00 4.94
955 1011 3.997064 CTCCTGCTCCTTCCACGCG 62.997 68.421 3.53 3.53 0.00 6.01
956 1012 4.069232 CCTGCTCCTTCCACGCGA 62.069 66.667 15.93 0.00 0.00 5.87
957 1013 2.811317 CTGCTCCTTCCACGCGAC 60.811 66.667 15.93 0.00 0.00 5.19
974 1054 2.591715 CCCCCGAATGCCTTAGCG 60.592 66.667 0.00 0.00 44.31 4.26
982 1068 0.179000 AATGCCTTAGCGGAGAGTGG 59.821 55.000 0.00 0.00 44.31 4.00
986 1072 1.608717 CCTTAGCGGAGAGTGGCTGT 61.609 60.000 0.00 0.00 40.32 4.40
988 1074 0.898326 TTAGCGGAGAGTGGCTGTGA 60.898 55.000 0.00 0.00 40.32 3.58
1039 1131 3.826282 CCAAGGGCAAGAGGGAGA 58.174 61.111 0.00 0.00 0.00 3.71
1157 1252 2.980568 TGGCGTTCCGTGATCTTTAAT 58.019 42.857 0.00 0.00 34.14 1.40
1161 1256 4.557301 GGCGTTCCGTGATCTTTAATTTTG 59.443 41.667 0.00 0.00 0.00 2.44
1165 1261 7.490055 CGTTCCGTGATCTTTAATTTTGTTTG 58.510 34.615 0.00 0.00 0.00 2.93
1166 1262 7.166804 CGTTCCGTGATCTTTAATTTTGTTTGT 59.833 33.333 0.00 0.00 0.00 2.83
1167 1263 7.922505 TCCGTGATCTTTAATTTTGTTTGTG 57.077 32.000 0.00 0.00 0.00 3.33
1168 1264 6.419413 TCCGTGATCTTTAATTTTGTTTGTGC 59.581 34.615 0.00 0.00 0.00 4.57
1171 1267 7.788846 CGTGATCTTTAATTTTGTTTGTGCTTG 59.211 33.333 0.00 0.00 0.00 4.01
1172 1268 8.603181 GTGATCTTTAATTTTGTTTGTGCTTGT 58.397 29.630 0.00 0.00 0.00 3.16
1173 1269 8.602328 TGATCTTTAATTTTGTTTGTGCTTGTG 58.398 29.630 0.00 0.00 0.00 3.33
1174 1270 6.770076 TCTTTAATTTTGTTTGTGCTTGTGC 58.230 32.000 0.00 0.00 40.20 4.57
1175 1271 6.593382 TCTTTAATTTTGTTTGTGCTTGTGCT 59.407 30.769 0.00 0.00 40.48 4.40
1261 1357 2.749621 CCATCTCCACAAGGTTAGTTGC 59.250 50.000 0.00 0.00 35.89 4.17
1364 1470 4.791974 CATTCTTGTTTGTCTTGCTCTCC 58.208 43.478 0.00 0.00 0.00 3.71
1365 1471 2.483876 TCTTGTTTGTCTTGCTCTCCG 58.516 47.619 0.00 0.00 0.00 4.63
1366 1472 2.158957 TCTTGTTTGTCTTGCTCTCCGT 60.159 45.455 0.00 0.00 0.00 4.69
1396 1502 1.413382 CAATCTCGCTCGTATCTGCC 58.587 55.000 0.00 0.00 0.00 4.85
1444 1550 3.438087 CACTGCGGTTCTTGATCTTGAAT 59.562 43.478 0.00 0.00 0.00 2.57
1445 1551 4.074970 ACTGCGGTTCTTGATCTTGAATT 58.925 39.130 0.00 0.00 0.00 2.17
1446 1552 4.083110 ACTGCGGTTCTTGATCTTGAATTG 60.083 41.667 0.00 0.00 0.00 2.32
1447 1553 4.071423 TGCGGTTCTTGATCTTGAATTGA 58.929 39.130 0.00 0.00 0.00 2.57
1448 1554 4.518590 TGCGGTTCTTGATCTTGAATTGAA 59.481 37.500 0.00 0.00 0.00 2.69
1510 1616 0.392461 TGCAGTTCCCGCTAATGTCC 60.392 55.000 0.00 0.00 0.00 4.02
1590 1696 2.040359 GGGAGGGGAGGAGGAAGG 60.040 72.222 0.00 0.00 0.00 3.46
1648 1754 4.373116 GTGCTGGAGGCGGACGAA 62.373 66.667 0.00 0.00 45.43 3.85
1837 1943 4.612412 AACCTCGTTTCCCGCGCA 62.612 61.111 8.75 0.00 36.19 6.09
2017 2123 1.454479 CTTCGGCTGGCCCATCAAT 60.454 57.895 0.00 0.00 0.00 2.57
2134 2240 1.502990 CGTTCACCCGTGTCATTGCA 61.503 55.000 0.00 0.00 0.00 4.08
2173 2279 2.683933 GGCCCTGAGGTCCTCGAA 60.684 66.667 14.34 0.00 32.35 3.71
2209 2315 2.512896 GCCAAGCGATCCATCCCT 59.487 61.111 0.00 0.00 0.00 4.20
2452 2558 1.220749 GGCTTCCCGTGACATGCTA 59.779 57.895 0.00 0.00 0.00 3.49
2867 2973 1.070108 CCATCTTGATCGATGCTTGCG 60.070 52.381 0.54 0.00 39.51 4.85
2870 2976 1.434622 CTTGATCGATGCTTGCGGCT 61.435 55.000 0.54 0.00 42.39 5.52
2886 2992 2.758089 GCTCAATGCCGGTGCTCAG 61.758 63.158 1.90 0.00 38.71 3.35
3048 3154 4.189580 ACGGTGGTGCAGGTGCTT 62.190 61.111 3.18 0.00 42.66 3.91
3135 3241 0.987294 CAGGCCAAGGAGAGGAAGAA 59.013 55.000 5.01 0.00 0.00 2.52
3141 3247 1.134848 CAAGGAGAGGAAGAAGGCGAG 60.135 57.143 0.00 0.00 0.00 5.03
3310 3419 1.814772 CGCTGCTGGGGATAGAGGAG 61.815 65.000 0.00 0.00 0.00 3.69
3311 3420 2.056985 CTGCTGGGGATAGAGGAGC 58.943 63.158 0.00 0.00 0.00 4.70
3312 3421 1.814772 CTGCTGGGGATAGAGGAGCG 61.815 65.000 0.00 0.00 32.05 5.03
3613 3722 3.990092 TCAGATTTCGTTGTAGCAGTGT 58.010 40.909 0.00 0.00 0.00 3.55
3614 3723 3.987868 TCAGATTTCGTTGTAGCAGTGTC 59.012 43.478 0.00 0.00 0.00 3.67
3615 3724 2.987149 AGATTTCGTTGTAGCAGTGTCG 59.013 45.455 0.00 0.00 0.00 4.35
3688 3816 4.336889 TGTTCTCTCCACTTACACAAGG 57.663 45.455 0.00 0.00 35.97 3.61
3695 3823 2.955660 TCCACTTACACAAGGCCAAAAG 59.044 45.455 5.01 1.30 35.97 2.27
3720 3850 4.529109 GCCAAAATTTACAGGCTTGGTA 57.471 40.909 17.34 0.00 43.70 3.25
3732 3862 3.055530 CAGGCTTGGTAGAGACACTGAAT 60.056 47.826 0.00 0.00 0.00 2.57
3735 3866 4.870991 GGCTTGGTAGAGACACTGAATTAC 59.129 45.833 0.00 0.00 0.00 1.89
3736 3867 4.870991 GCTTGGTAGAGACACTGAATTACC 59.129 45.833 0.00 0.00 0.00 2.85
3738 3869 4.422057 TGGTAGAGACACTGAATTACCCA 58.578 43.478 0.00 0.00 31.68 4.51
3739 3870 4.466370 TGGTAGAGACACTGAATTACCCAG 59.534 45.833 0.00 0.00 37.64 4.45
3740 3871 4.466726 GGTAGAGACACTGAATTACCCAGT 59.533 45.833 0.00 0.00 44.92 4.00
3741 3872 5.655532 GGTAGAGACACTGAATTACCCAGTA 59.344 44.000 0.00 0.00 42.44 2.74
3742 3873 6.154021 GGTAGAGACACTGAATTACCCAGTAA 59.846 42.308 0.00 0.00 42.44 2.24
3743 3874 6.875972 AGAGACACTGAATTACCCAGTAAT 57.124 37.500 0.00 0.00 42.44 1.89
3744 3875 6.879400 AGAGACACTGAATTACCCAGTAATC 58.121 40.000 0.72 0.00 42.44 1.75
3745 3876 6.440647 AGAGACACTGAATTACCCAGTAATCA 59.559 38.462 0.72 1.57 42.44 2.57
3746 3877 6.644347 AGACACTGAATTACCCAGTAATCAG 58.356 40.000 16.63 16.63 42.44 2.90
3755 3886 8.840200 AATTACCCAGTAATCAGTAAGAGAGA 57.160 34.615 0.72 0.00 37.69 3.10
3764 3895 8.986991 AGTAATCAGTAAGAGAGAAATGGATGT 58.013 33.333 0.00 0.00 0.00 3.06
3771 3902 5.447778 AGAGAGAAATGGATGTCAATGGT 57.552 39.130 0.00 0.00 0.00 3.55
3772 3903 5.191426 AGAGAGAAATGGATGTCAATGGTG 58.809 41.667 0.00 0.00 0.00 4.17
3773 3904 3.698040 AGAGAAATGGATGTCAATGGTGC 59.302 43.478 0.00 0.00 0.00 5.01
3895 4031 3.257561 CGATGAGCTTGACGGCGG 61.258 66.667 13.24 0.00 37.29 6.13
4005 4141 0.807667 GCTCGCTGTGGTACATGAGG 60.808 60.000 0.00 0.00 44.52 3.86
4014 4150 3.147595 TACATGAGGGCGCGCTCT 61.148 61.111 41.95 37.66 0.00 4.09
4246 4382 2.874648 GATCCTGTGCACGATGGGCA 62.875 60.000 13.13 0.00 39.32 5.36
4286 4422 2.664851 CGTGGACTTGGCGAGCAA 60.665 61.111 0.37 0.00 0.00 3.91
4293 4429 4.617520 TTGGCGAGCAAGCGGTGA 62.618 61.111 0.00 0.00 38.18 4.02
4422 4558 1.067142 AGCATTTCGTCGAGCAGGTTA 60.067 47.619 7.58 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.101448 GCCTGACTGGGCGGTGAT 62.101 66.667 0.01 0.00 42.82 3.06
8 9 2.107950 TATTTGAACGGCCTGACTGG 57.892 50.000 0.00 0.00 39.35 4.00
9 10 3.535561 AGATATTTGAACGGCCTGACTG 58.464 45.455 0.00 0.00 0.00 3.51
10 11 3.452627 AGAGATATTTGAACGGCCTGACT 59.547 43.478 0.00 0.00 0.00 3.41
11 12 3.798202 AGAGATATTTGAACGGCCTGAC 58.202 45.455 0.00 0.00 0.00 3.51
12 13 3.181465 GGAGAGATATTTGAACGGCCTGA 60.181 47.826 0.00 0.00 0.00 3.86
13 14 3.134458 GGAGAGATATTTGAACGGCCTG 58.866 50.000 0.00 0.00 0.00 4.85
14 15 3.041946 AGGAGAGATATTTGAACGGCCT 58.958 45.455 0.00 0.00 0.00 5.19
18 19 4.985409 GTGCCTAGGAGAGATATTTGAACG 59.015 45.833 14.75 0.00 0.00 3.95
29 30 2.105930 GCTGCGTGCCTAGGAGAG 59.894 66.667 14.75 2.98 35.15 3.20
31 32 2.510238 GTGCTGCGTGCCTAGGAG 60.510 66.667 14.75 0.77 42.00 3.69
32 33 4.435436 CGTGCTGCGTGCCTAGGA 62.435 66.667 14.75 0.00 42.00 2.94
51 52 4.144681 GAACTCGCGCTGCTGCTG 62.145 66.667 14.03 8.34 36.97 4.41
52 53 4.669842 TGAACTCGCGCTGCTGCT 62.670 61.111 14.03 0.00 36.97 4.24
58 59 1.295792 TTGAACTTTGAACTCGCGCT 58.704 45.000 5.56 0.00 0.00 5.92
61 62 4.265320 CAGGTTTTTGAACTTTGAACTCGC 59.735 41.667 0.00 0.00 0.00 5.03
83 84 2.281970 CAGTGAAGCCTGCCTGCA 60.282 61.111 0.00 0.00 0.00 4.41
84 85 1.860484 GAACAGTGAAGCCTGCCTGC 61.860 60.000 0.00 0.00 35.83 4.85
85 86 0.250640 AGAACAGTGAAGCCTGCCTG 60.251 55.000 0.00 0.00 35.83 4.85
86 87 0.475906 AAGAACAGTGAAGCCTGCCT 59.524 50.000 0.00 0.00 35.83 4.75
87 88 0.595095 CAAGAACAGTGAAGCCTGCC 59.405 55.000 0.00 0.00 35.83 4.85
95 96 4.442706 GTCAAGAAGACCAAGAACAGTGA 58.557 43.478 0.00 0.00 41.56 3.41
110 111 3.566351 TCTCTGTCAGACAGGTCAAGAA 58.434 45.455 27.15 8.02 45.94 2.52
140 141 5.419542 CCACCATTACTACCATATGATCCG 58.580 45.833 3.65 0.00 0.00 4.18
151 152 2.210116 CGTCCATGCCACCATTACTAC 58.790 52.381 0.00 0.00 0.00 2.73
152 153 1.834896 ACGTCCATGCCACCATTACTA 59.165 47.619 0.00 0.00 0.00 1.82
153 154 0.618458 ACGTCCATGCCACCATTACT 59.382 50.000 0.00 0.00 0.00 2.24
235 236 2.536928 GCTGATTAAGCGCTAACAACGG 60.537 50.000 12.05 8.12 43.45 4.44
323 345 2.490115 GCTCTAGGATGGTAGTGATCCG 59.510 54.545 0.00 0.00 43.78 4.18
364 386 6.153000 AGACAAGTAGATAACTCACCGACAAT 59.847 38.462 0.00 0.00 37.50 2.71
371 393 7.868415 ACTCAACAAGACAAGTAGATAACTCAC 59.132 37.037 0.00 0.00 37.50 3.51
381 403 5.128171 AGTGTGGTACTCAACAAGACAAGTA 59.872 40.000 0.00 0.00 33.17 2.24
383 405 4.271049 CAGTGTGGTACTCAACAAGACAAG 59.729 45.833 0.00 0.00 37.60 3.16
385 407 3.196901 ACAGTGTGGTACTCAACAAGACA 59.803 43.478 0.00 0.00 37.60 3.41
386 408 3.793559 ACAGTGTGGTACTCAACAAGAC 58.206 45.455 0.00 0.00 37.60 3.01
398 420 3.004315 CGCCAAGATTTTTACAGTGTGGT 59.996 43.478 5.88 0.00 0.00 4.16
400 422 4.223320 ACGCCAAGATTTTTACAGTGTG 57.777 40.909 5.88 0.00 0.00 3.82
484 510 4.410400 GCCCTCCCAACCACCTCG 62.410 72.222 0.00 0.00 0.00 4.63
507 533 1.082117 CACGTGTTCGGTATGCCTCC 61.082 60.000 7.58 0.00 41.85 4.30
533 559 0.389166 AAGCTCACGTAGAGTGCTGC 60.389 55.000 13.91 0.00 46.06 5.25
560 586 2.058001 ATCAGGATCGACCACGGCA 61.058 57.895 6.78 0.00 42.04 5.69
561 587 1.592669 CATCAGGATCGACCACGGC 60.593 63.158 6.78 0.00 42.04 5.68
563 589 1.592669 GCCATCAGGATCGACCACG 60.593 63.158 6.78 0.00 42.04 4.94
564 590 1.592669 CGCCATCAGGATCGACCAC 60.593 63.158 6.78 0.00 42.04 4.16
565 591 1.115326 ATCGCCATCAGGATCGACCA 61.115 55.000 6.78 0.00 42.04 4.02
566 592 0.888619 TATCGCCATCAGGATCGACC 59.111 55.000 0.00 0.00 33.26 4.79
567 593 1.269723 TGTATCGCCATCAGGATCGAC 59.730 52.381 0.00 0.00 33.26 4.20
568 594 1.269723 GTGTATCGCCATCAGGATCGA 59.730 52.381 0.00 0.00 36.89 3.59
689 715 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
690 716 1.087725 AGGAGGAGGAGGAGGAGGA 59.912 63.158 0.00 0.00 0.00 3.71
691 717 1.232792 CAGGAGGAGGAGGAGGAGG 59.767 68.421 0.00 0.00 0.00 4.30
692 718 1.457455 GCAGGAGGAGGAGGAGGAG 60.457 68.421 0.00 0.00 0.00 3.69
693 719 1.938596 AGCAGGAGGAGGAGGAGGA 60.939 63.158 0.00 0.00 0.00 3.71
694 720 1.761667 CAGCAGGAGGAGGAGGAGG 60.762 68.421 0.00 0.00 0.00 4.30
695 721 2.433994 GCAGCAGGAGGAGGAGGAG 61.434 68.421 0.00 0.00 0.00 3.69
696 722 2.364842 GCAGCAGGAGGAGGAGGA 60.365 66.667 0.00 0.00 0.00 3.71
697 723 2.365370 AGCAGCAGGAGGAGGAGG 60.365 66.667 0.00 0.00 0.00 4.30
698 724 2.733669 CCAGCAGCAGGAGGAGGAG 61.734 68.421 0.00 0.00 0.00 3.69
699 725 2.686470 CCAGCAGCAGGAGGAGGA 60.686 66.667 0.00 0.00 0.00 3.71
700 726 2.600729 AACCAGCAGCAGGAGGAGG 61.601 63.158 11.55 0.00 0.00 4.30
789 824 0.250467 TTTCTTTGAGCTCTGCCGCT 60.250 50.000 16.19 0.00 44.33 5.52
791 826 1.068954 GGTTTTCTTTGAGCTCTGCCG 60.069 52.381 16.19 1.00 0.00 5.69
792 827 1.956477 TGGTTTTCTTTGAGCTCTGCC 59.044 47.619 16.19 5.99 0.00 4.85
797 832 3.616821 GCGTTTTTGGTTTTCTTTGAGCT 59.383 39.130 0.00 0.00 0.00 4.09
799 834 3.929610 TGGCGTTTTTGGTTTTCTTTGAG 59.070 39.130 0.00 0.00 0.00 3.02
800 835 3.926616 TGGCGTTTTTGGTTTTCTTTGA 58.073 36.364 0.00 0.00 0.00 2.69
860 904 5.120399 TGTATTAGGTGCGGAGTTAAATGG 58.880 41.667 0.00 0.00 0.00 3.16
890 934 2.590092 GCGTGCCCCTGGTATTCT 59.410 61.111 0.00 0.00 0.00 2.40
897 941 1.735360 CAATAATGGCGTGCCCCTG 59.265 57.895 8.69 0.00 34.56 4.45
936 992 2.581354 CGTGGAAGGAGCAGGAGG 59.419 66.667 0.00 0.00 0.00 4.30
953 1009 3.394635 TAAGGCATTCGGGGGTCGC 62.395 63.158 0.00 0.00 39.05 5.19
955 1011 1.526225 GCTAAGGCATTCGGGGGTC 60.526 63.158 0.00 0.00 38.54 4.46
956 1012 2.595655 GCTAAGGCATTCGGGGGT 59.404 61.111 0.00 0.00 38.54 4.95
957 1013 2.591715 CGCTAAGGCATTCGGGGG 60.592 66.667 0.00 0.00 38.60 5.40
974 1054 0.463620 GATCCTCACAGCCACTCTCC 59.536 60.000 0.00 0.00 0.00 3.71
982 1068 2.669808 ATCGCGACGATCCTCACAGC 62.670 60.000 12.93 0.00 43.45 4.40
986 1072 0.040067 CATCATCGCGACGATCCTCA 60.040 55.000 15.72 0.00 45.19 3.86
988 1074 1.372251 GCATCATCGCGACGATCCT 60.372 57.895 15.72 0.00 45.19 3.24
1157 1252 2.665537 CGAAGCACAAGCACAAACAAAA 59.334 40.909 0.00 0.00 45.49 2.44
1161 1256 1.208642 GCCGAAGCACAAGCACAAAC 61.209 55.000 0.00 0.00 45.49 2.93
1165 1261 2.253452 CTGCCGAAGCACAAGCAC 59.747 61.111 0.00 0.00 46.52 4.40
1166 1262 2.979676 CCTGCCGAAGCACAAGCA 60.980 61.111 0.00 0.00 46.52 3.91
1167 1263 2.463675 GAACCTGCCGAAGCACAAGC 62.464 60.000 0.00 0.00 46.52 4.01
1168 1264 0.886490 AGAACCTGCCGAAGCACAAG 60.886 55.000 0.00 0.00 46.52 3.16
1171 1267 3.257933 CAGAACCTGCCGAAGCAC 58.742 61.111 0.00 0.00 46.52 4.40
1261 1357 5.342433 CAGAGTAGAGACAAGATTCAGCAG 58.658 45.833 0.00 0.00 0.00 4.24
1365 1471 2.125512 AGATTGGCAGCGGACGAC 60.126 61.111 0.00 0.00 0.00 4.34
1366 1472 2.184322 GAGATTGGCAGCGGACGA 59.816 61.111 0.00 0.00 0.00 4.20
1422 1528 2.416747 TCAAGATCAAGAACCGCAGTG 58.583 47.619 0.00 0.00 0.00 3.66
1444 1550 1.068194 CGCCGGCCACTTTAATTTCAA 60.068 47.619 23.46 0.00 0.00 2.69
1445 1551 0.523966 CGCCGGCCACTTTAATTTCA 59.476 50.000 23.46 0.00 0.00 2.69
1446 1552 0.179148 CCGCCGGCCACTTTAATTTC 60.179 55.000 23.46 0.00 0.00 2.17
1447 1553 1.887301 CCGCCGGCCACTTTAATTT 59.113 52.632 23.46 0.00 0.00 1.82
1448 1554 2.706834 GCCGCCGGCCACTTTAATT 61.707 57.895 23.46 0.00 44.06 1.40
1510 1616 2.670414 GTCGTGGATCTTCTTGCTCTTG 59.330 50.000 0.00 0.00 0.00 3.02
1590 1696 3.174265 CTGCCCCCTCATCCTCCC 61.174 72.222 0.00 0.00 0.00 4.30
1837 1943 1.738099 GTGCGACATGAAGCGGTCT 60.738 57.895 0.00 0.00 35.87 3.85
2044 2150 0.039617 CGCCGGCATTTTTCTTGTGA 60.040 50.000 28.98 0.00 0.00 3.58
2200 2306 1.308128 TGACAGCCCAGGGATGGAT 60.308 57.895 27.93 7.73 44.23 3.41
2870 2976 0.674581 CTTCTGAGCACCGGCATTGA 60.675 55.000 0.00 0.00 44.61 2.57
3048 3154 0.671781 GCTGGAGCTGCTCGAAGAAA 60.672 55.000 26.04 8.65 38.21 2.52
3084 3190 3.768185 ATTCGCCACGATCGTCCGG 62.768 63.158 27.29 23.11 35.23 5.14
3294 3400 1.834378 CGCTCCTCTATCCCCAGCA 60.834 63.158 0.00 0.00 0.00 4.41
3297 3403 2.524394 GCCGCTCCTCTATCCCCA 60.524 66.667 0.00 0.00 0.00 4.96
3502 3611 6.976925 AGCAAAGAATCAAGAGAACAAAACAG 59.023 34.615 0.00 0.00 0.00 3.16
3613 3722 0.323302 TGCATTACCCAGCAAGACGA 59.677 50.000 0.00 0.00 37.90 4.20
3614 3723 1.331756 GATGCATTACCCAGCAAGACG 59.668 52.381 0.00 0.00 44.88 4.18
3615 3724 2.368439 TGATGCATTACCCAGCAAGAC 58.632 47.619 0.00 0.00 44.88 3.01
3688 3816 1.608055 AATTTTGGCAGGCTTTTGGC 58.392 45.000 0.00 3.68 46.43 4.52
3715 3845 4.841813 TGGGTAATTCAGTGTCTCTACCAA 59.158 41.667 12.35 2.79 0.00 3.67
3720 3850 6.440647 TGATTACTGGGTAATTCAGTGTCTCT 59.559 38.462 8.20 0.00 44.24 3.10
3732 3862 8.660295 TTTCTCTCTTACTGATTACTGGGTAA 57.340 34.615 0.00 0.00 32.36 2.85
3735 3866 6.989169 CCATTTCTCTCTTACTGATTACTGGG 59.011 42.308 0.00 0.00 0.00 4.45
3736 3867 7.786030 TCCATTTCTCTCTTACTGATTACTGG 58.214 38.462 0.00 0.00 0.00 4.00
3738 3869 8.986991 ACATCCATTTCTCTCTTACTGATTACT 58.013 33.333 0.00 0.00 0.00 2.24
3739 3870 9.255304 GACATCCATTTCTCTCTTACTGATTAC 57.745 37.037 0.00 0.00 0.00 1.89
3740 3871 8.981659 TGACATCCATTTCTCTCTTACTGATTA 58.018 33.333 0.00 0.00 0.00 1.75
3741 3872 7.855375 TGACATCCATTTCTCTCTTACTGATT 58.145 34.615 0.00 0.00 0.00 2.57
3742 3873 7.429374 TGACATCCATTTCTCTCTTACTGAT 57.571 36.000 0.00 0.00 0.00 2.90
3743 3874 6.857437 TGACATCCATTTCTCTCTTACTGA 57.143 37.500 0.00 0.00 0.00 3.41
3744 3875 7.012138 CCATTGACATCCATTTCTCTCTTACTG 59.988 40.741 0.00 0.00 0.00 2.74
3745 3876 7.052873 CCATTGACATCCATTTCTCTCTTACT 58.947 38.462 0.00 0.00 0.00 2.24
3746 3877 6.825721 ACCATTGACATCCATTTCTCTCTTAC 59.174 38.462 0.00 0.00 0.00 2.34
3755 3886 1.477700 CCGCACCATTGACATCCATTT 59.522 47.619 0.00 0.00 0.00 2.32
3764 3895 2.350895 CCTCCACCGCACCATTGA 59.649 61.111 0.00 0.00 0.00 2.57
3773 3904 4.436998 GGTGAGACGCCTCCACCG 62.437 72.222 0.00 0.00 38.66 4.94
3957 4093 4.681978 GCGTTCGGGCTGGTGAGT 62.682 66.667 0.00 0.00 0.00 3.41
4014 4150 4.077184 ATCGACGAGGCCGCCAAA 62.077 61.111 13.15 0.00 39.95 3.28
4246 4382 2.207924 GGTACTCCGGGATCGCCAT 61.208 63.158 0.00 0.00 35.15 4.40
4286 4422 2.282251 TCAGACGAGGTCACCGCT 60.282 61.111 0.00 0.00 34.60 5.52
4326 4462 1.874345 CGGTCCTCCAGTGCTACGTT 61.874 60.000 0.00 0.00 0.00 3.99
4399 4535 1.324736 CCTGCTCGACGAAATGCTTAC 59.675 52.381 8.74 0.00 0.00 2.34
4400 4536 1.067142 ACCTGCTCGACGAAATGCTTA 60.067 47.619 8.74 0.00 0.00 3.09
4422 4558 2.344203 CGACCTCGAGGGAGCAGTT 61.344 63.158 34.04 12.49 43.02 3.16


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

AutoCloner maintained by Alex Coulton.