Multiple sequence alignment - TraesCS1B01G223200

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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 TraesCS1B01G223200 chr1B 100.000 4639 0 0 1 4639 400665120 400669758 0 8567
1 TraesCS1B01G223200 chr1D 93.180 4619 246 31 49 4639 298010528 298015105 0 6721
2 TraesCS1B01G223200 chr1A 94.687 3162 144 9 49 3204 371083848 371086991 0 4887
3 TraesCS1B01G223200 chr1A 95.218 1443 53 9 3206 4639 371087480 371088915 0 2268


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 TraesCS1B01G223200 chr1B 400665120 400669758 4638 False 8567.0 8567 100.0000 1 4639 1 chr1B.!!$F1 4638
1 TraesCS1B01G223200 chr1D 298010528 298015105 4577 False 6721.0 6721 93.1800 49 4639 1 chr1D.!!$F1 4590
2 TraesCS1B01G223200 chr1A 371083848 371088915 5067 False 3577.5 4887 94.9525 49 4639 2 chr1A.!!$F1 4590

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
581 597 0.321653 AAGAAGTGCGGCTCGGATTT 60.322 50.000 0.00 0.0 29.54 2.17 F
582 598 1.021390 AGAAGTGCGGCTCGGATTTG 61.021 55.000 0.00 0.0 26.94 2.32 F
659 675 1.111277 TTCGATTCCCATCTGCGAGA 58.889 50.000 0.00 0.0 32.22 4.04 F
1197 1230 1.374252 TCTTCCTTCAAGACGCCGC 60.374 57.895 0.00 0.0 36.08 6.53 F
2694 2727 0.909623 ACGGGTTACCAAGGGATGAG 59.090 55.000 2.98 0.0 36.13 2.90 F
3317 3841 0.823356 TCCAACTGTTGAAGCAGGGC 60.823 55.000 21.49 0.0 40.59 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1674 1707 0.682209 CAGGATGAAGGCCAACAGGG 60.682 60.000 5.01 0.0 39.69 4.45 R
2034 2067 1.918609 GTCGGCGATGAAGTAACTGTC 59.081 52.381 14.79 0.0 0.00 3.51 R
2626 2659 1.486310 TGTACCAGGTGATGATCCAGC 59.514 52.381 0.76 0.0 34.97 4.85 R
2907 2940 0.451383 TGTGATAAATGCACGCAGGC 59.549 50.000 0.00 0.0 39.07 4.85 R
3584 4108 0.179012 TGACCACCGGAGTTTTTCCC 60.179 55.000 9.46 0.0 43.63 3.97 R
4335 4865 0.695462 TGCATGACCCTAGGATGGCT 60.695 55.000 11.48 0.0 0.00 4.75 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
84 86 0.400213 TTTACAGCCACAGACCCCTG 59.600 55.000 0.00 0.00 45.76 4.45
85 87 0.472925 TTACAGCCACAGACCCCTGA 60.473 55.000 0.00 0.00 43.02 3.86
93 95 2.608988 AGACCCCTGAGGCTGGTG 60.609 66.667 4.03 0.00 40.58 4.17
94 96 4.416738 GACCCCTGAGGCTGGTGC 62.417 72.222 4.03 0.00 40.58 5.01
100 102 4.662961 TGAGGCTGGTGCGACACG 62.663 66.667 0.00 0.00 40.82 4.49
108 110 4.367023 GTGCGACACGGGCCTACA 62.367 66.667 0.84 0.00 0.00 2.74
116 118 1.073284 ACACGGGCCTACAAAGATGTT 59.927 47.619 0.84 0.00 41.05 2.71
149 151 4.404654 GGAGCAGCCCAAAACGCG 62.405 66.667 3.53 3.53 0.00 6.01
185 188 4.553156 CGGATCGCTCTTTACAGTCTAGTC 60.553 50.000 0.00 0.00 0.00 2.59
186 189 4.261280 GGATCGCTCTTTACAGTCTAGTCC 60.261 50.000 0.00 0.00 0.00 3.85
210 213 3.906846 CCCCTGCCTCTATCTATTTCACT 59.093 47.826 0.00 0.00 0.00 3.41
211 214 4.020662 CCCCTGCCTCTATCTATTTCACTC 60.021 50.000 0.00 0.00 0.00 3.51
223 226 0.809385 TTTCACTCTCGTCCCTAGCG 59.191 55.000 0.00 0.00 0.00 4.26
224 227 1.030488 TTCACTCTCGTCCCTAGCGG 61.030 60.000 0.00 0.00 0.00 5.52
225 228 2.829458 ACTCTCGTCCCTAGCGGC 60.829 66.667 0.00 0.00 0.00 6.53
226 229 3.955101 CTCTCGTCCCTAGCGGCG 61.955 72.222 0.51 0.51 33.90 6.46
227 230 4.478371 TCTCGTCCCTAGCGGCGA 62.478 66.667 12.98 3.78 37.68 5.54
274 277 5.125417 TGGGAATCTCCATTTCATTTTCGTC 59.875 40.000 0.00 0.00 38.64 4.20
536 539 5.887754 ACTTTTTAGGAGGAACTAATGGCA 58.112 37.500 0.00 0.00 41.55 4.92
574 590 1.604278 GTTTCTTCAAGAAGTGCGGCT 59.396 47.619 9.44 0.00 35.37 5.52
575 591 1.512926 TTCTTCAAGAAGTGCGGCTC 58.487 50.000 9.44 0.00 39.38 4.70
576 592 0.667487 TCTTCAAGAAGTGCGGCTCG 60.667 55.000 9.44 0.00 39.38 5.03
577 593 1.630244 CTTCAAGAAGTGCGGCTCGG 61.630 60.000 0.00 0.00 33.87 4.63
578 594 2.048222 CAAGAAGTGCGGCTCGGA 60.048 61.111 0.00 0.00 0.00 4.55
579 595 1.448540 CAAGAAGTGCGGCTCGGAT 60.449 57.895 0.00 0.00 0.00 4.18
580 596 1.021390 CAAGAAGTGCGGCTCGGATT 61.021 55.000 0.00 0.00 0.00 3.01
581 597 0.321653 AAGAAGTGCGGCTCGGATTT 60.322 50.000 0.00 0.00 29.54 2.17
582 598 1.021390 AGAAGTGCGGCTCGGATTTG 61.021 55.000 0.00 0.00 26.94 2.32
583 599 1.982073 GAAGTGCGGCTCGGATTTGG 61.982 60.000 0.00 0.00 26.94 3.28
584 600 2.746277 GTGCGGCTCGGATTTGGT 60.746 61.111 0.00 0.00 0.00 3.67
585 601 2.745884 TGCGGCTCGGATTTGGTG 60.746 61.111 0.00 0.00 0.00 4.17
586 602 4.179579 GCGGCTCGGATTTGGTGC 62.180 66.667 0.00 0.00 0.00 5.01
587 603 2.745884 CGGCTCGGATTTGGTGCA 60.746 61.111 0.00 0.00 0.00 4.57
588 604 2.753966 CGGCTCGGATTTGGTGCAG 61.754 63.158 0.00 0.00 0.00 4.41
589 605 1.377202 GGCTCGGATTTGGTGCAGA 60.377 57.895 0.00 0.00 0.00 4.26
590 606 1.372087 GGCTCGGATTTGGTGCAGAG 61.372 60.000 0.00 0.00 0.00 3.35
591 607 1.986575 GCTCGGATTTGGTGCAGAGC 61.987 60.000 4.79 4.79 43.11 4.09
592 608 1.372087 CTCGGATTTGGTGCAGAGCC 61.372 60.000 0.00 0.00 0.00 4.70
593 609 2.753966 CGGATTTGGTGCAGAGCCG 61.754 63.158 0.00 0.00 40.71 5.52
594 610 2.486966 GATTTGGTGCAGAGCCGC 59.513 61.111 0.00 0.00 0.00 6.53
605 621 4.247380 GAGCCGCAGATGGGAGGG 62.247 72.222 0.00 0.00 0.00 4.30
630 646 2.587522 GGTTCCTTTTCTGCTGACCTT 58.412 47.619 0.00 0.00 0.00 3.50
659 675 1.111277 TTCGATTCCCATCTGCGAGA 58.889 50.000 0.00 0.00 32.22 4.04
687 703 2.683362 CCTTTCCTCGAATGGTTTAGCC 59.317 50.000 0.00 0.00 33.78 3.93
734 750 9.350951 TGTGATCCGAGAGTAGATTTAGATTTA 57.649 33.333 0.00 0.00 0.00 1.40
852 874 7.775561 GTGGATATGACCTATTTTTCTTGGACT 59.224 37.037 0.00 0.00 0.00 3.85
874 896 4.806892 TGATTTGATGCATAGGATGGGTT 58.193 39.130 0.00 0.00 0.00 4.11
899 921 7.708998 TGAGTTTTAAGCTCGTAAAATGGTTT 58.291 30.769 6.61 0.00 35.86 3.27
928 950 4.094294 TGCCGAACTTGATACAAACTATGC 59.906 41.667 0.00 0.00 0.00 3.14
933 955 8.612619 CCGAACTTGATACAAACTATGCTTATT 58.387 33.333 0.00 0.00 0.00 1.40
987 1020 7.002250 TGTCATCTTTTCTCTCTTCTGATGT 57.998 36.000 0.00 0.00 33.67 3.06
1016 1049 7.307337 GCAATGTATTATGGTTTTAATGCAGGC 60.307 37.037 0.00 0.00 37.51 4.85
1031 1064 2.123982 GGCTTCCTGCATGGGGAG 60.124 66.667 0.00 0.00 45.15 4.30
1137 1170 2.987125 CCGGATGGAAACTCGGGT 59.013 61.111 0.00 0.00 38.93 5.28
1156 1189 2.033448 AAATGCGCCTCAACCGGA 59.967 55.556 9.46 0.00 0.00 5.14
1182 1215 5.993441 CCCAAATTTTCATTGCAAGAGTCTT 59.007 36.000 4.94 0.00 0.00 3.01
1197 1230 1.374252 TCTTCCTTCAAGACGCCGC 60.374 57.895 0.00 0.00 36.08 6.53
1266 1299 1.549620 CAGAGCTCCAGTGATGTCAGT 59.450 52.381 10.93 0.00 0.00 3.41
1304 1337 3.067645 AGAGGGGAGGAGGAAATTAGG 57.932 52.381 0.00 0.00 0.00 2.69
1390 1423 3.904136 CAAGTGGAGCTTACTTGGTTG 57.096 47.619 25.48 10.33 46.97 3.77
1654 1687 2.049433 GCAGCAGCAGCAAAGGTG 60.049 61.111 4.63 1.03 45.49 4.00
1674 1707 1.805943 GCAATGTCAAATTGCCAACCC 59.194 47.619 0.32 0.00 46.21 4.11
1992 2025 6.092807 GTGGTATCTCAAGATCTGAACAAACC 59.907 42.308 0.00 1.82 36.05 3.27
1999 2032 2.379907 AGATCTGAACAAACCCCCACAT 59.620 45.455 0.00 0.00 0.00 3.21
2012 2045 2.301346 CCCCACATCTAAATGCCAGAC 58.699 52.381 0.00 0.00 36.26 3.51
2013 2046 2.357050 CCCCACATCTAAATGCCAGACA 60.357 50.000 0.00 0.00 36.26 3.41
2026 2059 1.763770 CAGACAAGTGGGGAAGCCT 59.236 57.895 0.00 0.00 0.00 4.58
2034 2067 2.386100 TGGGGAAGCCTGGCCTATG 61.386 63.158 16.57 0.00 0.00 2.23
2058 2091 1.918609 GTTACTTCATCGCCGACTCAC 59.081 52.381 0.00 0.00 0.00 3.51
2103 2136 1.606224 CCTGACAATGGTGCTTTTGGC 60.606 52.381 0.00 0.00 42.22 4.52
2295 2328 5.876651 TGCATGTGTCTTCCTATCTGTAT 57.123 39.130 0.00 0.00 0.00 2.29
2337 2370 8.588290 ATGGTATTTTAAATAACTCAGCCACA 57.412 30.769 13.09 0.00 0.00 4.17
2406 2439 4.865365 GCTGTTGATAGAGTTCAGTGTACC 59.135 45.833 0.00 0.00 0.00 3.34
2466 2499 6.550854 AGAATTCAATCTCTAGGGAGTCTCTG 59.449 42.308 8.44 0.00 40.29 3.35
2595 2628 1.813862 GCTGTTGTAGTCCAAGTGCCA 60.814 52.381 0.00 0.00 32.51 4.92
2694 2727 0.909623 ACGGGTTACCAAGGGATGAG 59.090 55.000 2.98 0.00 36.13 2.90
2730 2763 5.837437 TCACCGTTACTTAACCGTCTAAAA 58.163 37.500 0.00 0.00 32.69 1.52
2778 2811 1.203162 TGGGACATGTCTTGCCCAATT 60.203 47.619 24.50 0.00 44.00 2.32
2796 2829 4.213906 CCAATTGTTGTCCTTGAAAATGCC 59.786 41.667 4.43 0.00 0.00 4.40
2807 2840 7.283127 TGTCCTTGAAAATGCCTATGATAGTTC 59.717 37.037 0.00 0.00 0.00 3.01
2866 2899 5.531287 CCCATGGAGCTATTTGTTAAGGTAC 59.469 44.000 15.22 0.00 0.00 3.34
2907 2940 5.957220 CACATCACGTGTTTGATTATTACCG 59.043 40.000 22.06 0.81 39.62 4.02
2912 2945 3.691498 GTGTTTGATTATTACCGCCTGC 58.309 45.455 0.00 0.00 0.00 4.85
2931 2965 2.159430 TGCGTGCATTTATCACAGTGAC 59.841 45.455 5.05 0.00 34.27 3.67
2934 2968 4.271049 GCGTGCATTTATCACAGTGACTAT 59.729 41.667 5.05 0.00 34.27 2.12
2982 3016 1.818674 CCCCCAACTTCATTAGCACAC 59.181 52.381 0.00 0.00 0.00 3.82
2983 3017 1.468520 CCCCAACTTCATTAGCACACG 59.531 52.381 0.00 0.00 0.00 4.49
2984 3018 1.468520 CCCAACTTCATTAGCACACGG 59.531 52.381 0.00 0.00 0.00 4.94
3072 3106 6.040209 TCCCTGTTTTAGTTATACTTGCGA 57.960 37.500 0.00 0.00 0.00 5.10
3118 3155 3.589988 ACTTCTTGACGAATGCACTAGG 58.410 45.455 0.00 0.00 0.00 3.02
3235 3759 8.868916 CAACAACAATGCACTAGTTAAAACTTT 58.131 29.630 0.00 0.00 40.37 2.66
3236 3760 8.996024 ACAACAATGCACTAGTTAAAACTTTT 57.004 26.923 0.00 0.00 40.37 2.27
3317 3841 0.823356 TCCAACTGTTGAAGCAGGGC 60.823 55.000 21.49 0.00 40.59 5.19
3354 3878 2.517959 CTGCCCTTTCCATGAAAGTCA 58.482 47.619 13.75 10.48 45.12 3.41
3563 4087 5.548056 AGGATCAGTAACAGGGAAAGAGAAA 59.452 40.000 0.00 0.00 0.00 2.52
3584 4108 6.770303 AGAAAAAGAAAGTGAAGAGGAGGAAG 59.230 38.462 0.00 0.00 0.00 3.46
3629 4153 2.276309 CTCCCTTCTCACCCATGGGC 62.276 65.000 31.73 0.00 39.32 5.36
3973 4501 4.039852 TGACCACTGCTCTTGTATACAACA 59.960 41.667 14.35 10.17 35.88 3.33
4162 4692 0.027979 CATGACCAAACCGCGCATAG 59.972 55.000 8.75 0.00 0.00 2.23
4331 4861 2.507484 TCAGTCAATTCTTGGGTGCTG 58.493 47.619 0.00 0.00 0.00 4.41
4335 4865 1.155859 AATTCTTGGGTGCTGGCCA 59.844 52.632 4.71 4.71 0.00 5.36
4381 4914 3.467483 ACCTGGACCCTGAGTAGATATGA 59.533 47.826 0.00 0.00 0.00 2.15
4390 4923 8.095452 ACCCTGAGTAGATATGATCAAAGTTT 57.905 34.615 0.00 0.00 0.00 2.66
4452 4986 3.315191 GCCTGACTTTTCTTGTAAGCACA 59.685 43.478 0.00 0.00 0.00 4.57
4529 5063 0.616891 TGTCATCTGCTCACCTGCAT 59.383 50.000 0.00 0.00 42.48 3.96
4564 5098 3.282021 GCAAAGATGGGTTATCAGCTGA 58.718 45.455 20.79 20.79 38.31 4.26
4615 5149 4.458989 GGCCATTTTCTGTGTGTATTCTGA 59.541 41.667 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 8.220559 GGCCCATGTACCATCTATATTATCAAT 58.779 37.037 0.00 0.00 0.00 2.57
38 39 7.405858 AGGCCCATGTACCATCTATATTATCAA 59.594 37.037 0.00 0.00 0.00 2.57
39 40 6.908593 AGGCCCATGTACCATCTATATTATCA 59.091 38.462 0.00 0.00 0.00 2.15
40 41 7.380423 AGGCCCATGTACCATCTATATTATC 57.620 40.000 0.00 0.00 0.00 1.75
41 42 7.771506 AAGGCCCATGTACCATCTATATTAT 57.228 36.000 0.00 0.00 0.00 1.28
42 43 7.582909 AAAGGCCCATGTACCATCTATATTA 57.417 36.000 0.00 0.00 0.00 0.98
43 44 6.468972 AAAGGCCCATGTACCATCTATATT 57.531 37.500 0.00 0.00 0.00 1.28
44 45 6.468972 AAAAGGCCCATGTACCATCTATAT 57.531 37.500 0.00 0.00 0.00 0.86
45 46 5.922960 AAAAGGCCCATGTACCATCTATA 57.077 39.130 0.00 0.00 0.00 1.31
46 47 4.814224 AAAAGGCCCATGTACCATCTAT 57.186 40.909 0.00 0.00 0.00 1.98
47 48 4.475381 TGTAAAAGGCCCATGTACCATCTA 59.525 41.667 0.00 0.00 0.00 1.98
68 69 2.122413 TCAGGGGTCTGTGGCTGT 60.122 61.111 0.00 0.00 41.59 4.40
70 71 2.608988 CCTCAGGGGTCTGTGGCT 60.609 66.667 2.20 0.00 44.49 4.75
93 95 2.357760 TTTGTAGGCCCGTGTCGC 60.358 61.111 0.00 0.00 0.00 5.19
94 96 0.108329 ATCTTTGTAGGCCCGTGTCG 60.108 55.000 0.00 0.00 0.00 4.35
100 102 1.204704 GGCAAACATCTTTGTAGGCCC 59.795 52.381 0.00 0.00 43.89 5.80
193 196 5.699097 ACGAGAGTGAAATAGATAGAGGC 57.301 43.478 0.00 0.00 46.97 4.70
210 213 4.478371 TCGCCGCTAGGGACGAGA 62.478 66.667 14.02 0.02 38.71 4.04
274 277 1.338020 GGGAAATATTCTTGGCGGCTG 59.662 52.381 11.43 3.13 0.00 4.85
329 332 1.072331 AGGCAGTGGACTTTACTGGTG 59.928 52.381 7.19 0.00 44.36 4.17
574 590 1.377202 GGCTCTGCACCAAATCCGA 60.377 57.895 0.00 0.00 0.00 4.55
575 591 2.753966 CGGCTCTGCACCAAATCCG 61.754 63.158 0.00 0.00 0.00 4.18
576 592 3.056313 GCGGCTCTGCACCAAATCC 62.056 63.158 0.00 0.00 34.15 3.01
577 593 2.262471 CTGCGGCTCTGCACCAAATC 62.262 60.000 0.00 0.00 40.62 2.17
578 594 2.282391 TGCGGCTCTGCACCAAAT 60.282 55.556 0.00 0.00 40.62 2.32
579 595 2.753009 ATCTGCGGCTCTGCACCAAA 62.753 55.000 0.00 0.00 40.62 3.28
580 596 3.258228 ATCTGCGGCTCTGCACCAA 62.258 57.895 0.00 0.00 40.62 3.67
581 597 3.709633 ATCTGCGGCTCTGCACCA 61.710 61.111 0.00 0.00 40.62 4.17
582 598 3.200593 CATCTGCGGCTCTGCACC 61.201 66.667 0.00 0.00 40.62 5.01
583 599 3.200593 CCATCTGCGGCTCTGCAC 61.201 66.667 0.00 0.00 40.62 4.57
584 600 4.478371 CCCATCTGCGGCTCTGCA 62.478 66.667 0.00 3.13 43.95 4.41
585 601 4.166888 TCCCATCTGCGGCTCTGC 62.167 66.667 0.00 0.00 0.00 4.26
586 602 2.108566 CTCCCATCTGCGGCTCTG 59.891 66.667 0.00 0.00 0.00 3.35
587 603 3.160047 CCTCCCATCTGCGGCTCT 61.160 66.667 0.00 0.00 0.00 4.09
588 604 4.247380 CCCTCCCATCTGCGGCTC 62.247 72.222 0.00 0.00 0.00 4.70
591 607 3.554342 CTCCCCTCCCATCTGCGG 61.554 72.222 0.00 0.00 0.00 5.69
592 608 3.554342 CCTCCCCTCCCATCTGCG 61.554 72.222 0.00 0.00 0.00 5.18
593 609 3.174265 CCCTCCCCTCCCATCTGC 61.174 72.222 0.00 0.00 0.00 4.26
594 610 2.449322 CCCCTCCCCTCCCATCTG 60.449 72.222 0.00 0.00 0.00 2.90
605 621 0.405973 AGCAGAAAAGGAACCCCTCC 59.594 55.000 0.00 0.00 43.48 4.30
659 675 3.264450 ACCATTCGAGGAAAGGATGAACT 59.736 43.478 6.63 0.00 34.49 3.01
687 703 4.330894 ACACAGCACATTATCACTGAATCG 59.669 41.667 0.00 0.00 34.25 3.34
756 772 3.433615 CCTAAGTTTCAAGAGGAACAGCG 59.566 47.826 0.00 0.00 34.56 5.18
852 874 4.458256 ACCCATCCTATGCATCAAATCA 57.542 40.909 0.19 0.00 0.00 2.57
874 896 6.870971 ACCATTTTACGAGCTTAAAACTCA 57.129 33.333 5.65 0.00 34.53 3.41
899 921 2.037902 TGTATCAAGTTCGGCAGTGGAA 59.962 45.455 0.00 0.00 0.00 3.53
903 925 3.740115 AGTTTGTATCAAGTTCGGCAGT 58.260 40.909 0.00 0.00 0.00 4.40
933 955 8.394121 GCATCAGTTTTTATCCAACAACAAAAA 58.606 29.630 0.00 0.00 0.00 1.94
938 960 7.538678 CAGTAGCATCAGTTTTTATCCAACAAC 59.461 37.037 0.00 0.00 0.00 3.32
941 963 7.094805 TGACAGTAGCATCAGTTTTTATCCAAC 60.095 37.037 0.00 0.00 0.00 3.77
952 985 6.047511 AGAAAAGATGACAGTAGCATCAGT 57.952 37.500 0.00 0.00 43.50 3.41
987 1020 8.473219 TGCATTAAAACCATAATACATTGCTCA 58.527 29.630 0.00 0.00 0.00 4.26
1016 1049 2.123982 GGCTCCCCATGCAGGAAG 60.124 66.667 0.00 0.00 41.22 3.46
1022 1055 2.514824 GAGAACGGCTCCCCATGC 60.515 66.667 0.00 0.00 37.69 4.06
1137 1170 2.331893 CCGGTTGAGGCGCATTTCA 61.332 57.895 10.83 7.10 0.00 2.69
1156 1189 6.013984 AGACTCTTGCAATGAAAATTTGGGAT 60.014 34.615 0.00 0.00 0.00 3.85
1182 1215 3.626680 CTCGCGGCGTCTTGAAGGA 62.627 63.158 22.90 0.00 0.00 3.36
1197 1230 3.198872 GCTATCTTCTGGGTTTTCCTCG 58.801 50.000 0.00 0.00 40.46 4.63
1266 1299 5.024118 CCCTCTTGGAGTTTCCTTAGTCTA 58.976 45.833 0.00 0.00 37.46 2.59
1304 1337 8.472683 AAACGCATCTCTTTCATATATAGAGC 57.527 34.615 6.23 1.99 36.27 4.09
1390 1423 2.680913 ATGAACTGCTCCGTTGCGC 61.681 57.895 0.00 0.00 35.36 6.09
1402 1435 1.620819 AGACCTCGACTTGCATGAACT 59.379 47.619 6.60 0.00 0.00 3.01
1674 1707 0.682209 CAGGATGAAGGCCAACAGGG 60.682 60.000 5.01 0.00 39.69 4.45
1825 1858 9.657419 ATCCAAAATTTTCTTAAATGCACTAGG 57.343 29.630 0.00 0.00 34.27 3.02
1992 2025 2.301346 GTCTGGCATTTAGATGTGGGG 58.699 52.381 0.00 0.00 35.63 4.96
1999 2032 2.290896 CCCCACTTGTCTGGCATTTAGA 60.291 50.000 0.00 0.00 0.00 2.10
2012 2045 2.677875 GCCAGGCTTCCCCACTTG 60.678 66.667 3.29 0.00 35.39 3.16
2013 2046 3.984732 GGCCAGGCTTCCCCACTT 61.985 66.667 12.43 0.00 35.39 3.16
2026 2059 4.441495 CGATGAAGTAACTGTCATAGGCCA 60.441 45.833 5.01 0.00 34.61 5.36
2034 2067 1.918609 GTCGGCGATGAAGTAACTGTC 59.081 52.381 14.79 0.00 0.00 3.51
2058 2091 4.022935 TCCAGTTTAAGAACAGCATGCAAG 60.023 41.667 21.98 14.52 42.53 4.01
2103 2136 4.065789 GACCCTTGGTACAGAACTCAAAG 58.934 47.826 0.00 0.00 42.39 2.77
2295 2328 8.924511 AAATACCATCTTCTTCAACTTCAGAA 57.075 30.769 0.00 0.00 0.00 3.02
2337 2370 5.493133 TGTCATACAAAACAAACTCGCTT 57.507 34.783 0.00 0.00 0.00 4.68
2406 2439 2.113860 ATGGTGGTTGAGTGGAATCG 57.886 50.000 0.00 0.00 0.00 3.34
2466 2499 4.928615 CGCTCCATCTGATTATTTCTCTCC 59.071 45.833 0.00 0.00 0.00 3.71
2595 2628 3.459710 TGGGACCGGGTTTTATGAAAT 57.540 42.857 6.32 0.00 0.00 2.17
2626 2659 1.486310 TGTACCAGGTGATGATCCAGC 59.514 52.381 0.76 0.00 34.97 4.85
2694 2727 1.258445 ACGGTGATGGACTGGTCTCC 61.258 60.000 0.67 0.00 34.90 3.71
2730 2763 2.852075 TCACACCTTCCCCCGCTT 60.852 61.111 0.00 0.00 0.00 4.68
2778 2811 5.076182 TCATAGGCATTTTCAAGGACAACA 58.924 37.500 0.00 0.00 0.00 3.33
2796 2829 6.865726 CAGAATCGACCCAAGAACTATCATAG 59.134 42.308 0.00 0.00 0.00 2.23
2807 2840 3.251479 TCATCACAGAATCGACCCAAG 57.749 47.619 0.00 0.00 0.00 3.61
2889 2922 3.372822 CAGGCGGTAATAATCAAACACGT 59.627 43.478 0.00 0.00 0.00 4.49
2907 2940 0.451383 TGTGATAAATGCACGCAGGC 59.549 50.000 0.00 0.00 39.07 4.85
2912 2945 5.973651 ATAGTCACTGTGATAAATGCACG 57.026 39.130 14.37 0.00 39.07 5.34
3147 3184 6.734137 TCAACAGTTGGATTACACAAATGAC 58.266 36.000 13.52 0.00 44.10 3.06
3317 3841 1.882623 GCAGGGAGAACTTCTTGGTTG 59.117 52.381 0.00 0.00 0.00 3.77
3354 3878 5.259632 CACTGAGAAATCTCCTTTCCCATT 58.740 41.667 7.91 0.00 43.66 3.16
3563 4087 4.202514 CCCTTCCTCCTCTTCACTTTCTTT 60.203 45.833 0.00 0.00 0.00 2.52
3584 4108 0.179012 TGACCACCGGAGTTTTTCCC 60.179 55.000 9.46 0.00 43.63 3.97
3629 4153 6.925610 TGGCAAAAATACTGCTATACTCTG 57.074 37.500 0.00 0.00 39.82 3.35
3753 4277 4.640771 TCCTTATGGACAAGACAGCTTT 57.359 40.909 0.00 0.00 37.46 3.51
3973 4501 1.677217 GCAGTCCAAAAGGAGAGCGAT 60.677 52.381 0.00 0.00 0.00 4.58
4162 4692 5.585047 ACAGAAACTGAACACTGAAACTACC 59.415 40.000 5.76 0.00 35.18 3.18
4219 4749 2.287608 GCAAGCACCTACAACTTGAACC 60.288 50.000 6.18 0.00 42.71 3.62
4319 4849 2.115910 CTGGCCAGCACCCAAGAA 59.884 61.111 22.33 0.00 30.66 2.52
4331 4861 2.774351 ACCCTAGGATGGCTGGCC 60.774 66.667 11.48 4.43 0.00 5.36
4335 4865 0.695462 TGCATGACCCTAGGATGGCT 60.695 55.000 11.48 0.00 0.00 4.75
4360 4893 4.119556 TCATATCTACTCAGGGTCCAGG 57.880 50.000 0.00 0.00 0.00 4.45
4381 4914 8.871686 ACGCTAAAAATCTTGAAAACTTTGAT 57.128 26.923 0.00 0.00 0.00 2.57
4390 4923 7.667043 ACATGTCTACGCTAAAAATCTTGAA 57.333 32.000 0.00 0.00 0.00 2.69
4401 4935 7.549134 AGATCAAAATTCAACATGTCTACGCTA 59.451 33.333 0.00 0.00 0.00 4.26
4564 5098 1.456287 GTCCAAACCCTGCTCCTGT 59.544 57.895 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.