Multiple sequence alignment - TraesCS2B01G183400

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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 TraesCS2B01G183400 chr2B 100.000 3686 0 0 1 3686 158622020 158618335 0.000000e+00 6807.0
1 TraesCS2B01G183400 chr2A 93.872 2611 135 8 989 3597 104872801 104870214 0.000000e+00 3912.0
2 TraesCS2B01G183400 chr2A 90.381 603 39 3 1 602 104873849 104873265 0.000000e+00 774.0
3 TraesCS2B01G183400 chr2D 94.518 1733 86 4 1053 2782 108924346 108922620 0.000000e+00 2665.0
4 TraesCS2B01G183400 chr2D 89.479 941 76 10 1 935 108925541 108924618 0.000000e+00 1168.0
5 TraesCS2B01G183400 chr2D 91.234 867 44 10 2824 3686 108922619 108921781 0.000000e+00 1151.0
6 TraesCS2B01G183400 chr5D 97.561 41 1 0 644 684 174829480 174829520 1.840000e-08 71.3
7 TraesCS2B01G183400 chr5B 100.000 38 0 0 647 684 173855736 173855699 1.840000e-08 71.3
8 TraesCS2B01G183400 chr5A 100.000 38 0 0 647 684 167115696 167115659 1.840000e-08 71.3


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 TraesCS2B01G183400 chr2B 158618335 158622020 3685 True 6807.000000 6807 100.000000 1 3686 1 chr2B.!!$R1 3685
1 TraesCS2B01G183400 chr2A 104870214 104873849 3635 True 2343.000000 3912 92.126500 1 3597 2 chr2A.!!$R1 3596
2 TraesCS2B01G183400 chr2D 108921781 108925541 3760 True 1661.333333 2665 91.743667 1 3686 3 chr2D.!!$R1 3685

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
680 686 0.238289 GAAGTTGACGTGCACCATGG 59.762 55.0 11.19 11.19 0.0 3.66 F
1951 2111 0.474184 CACAGGGACTCTTGTGGGTT 59.526 55.0 1.42 0.00 34.6 4.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2181 2341 0.392706 ACAAGGATATCGCGGCATCA 59.607 50.0 18.35 0.0 0.0 3.07 R
3218 3380 0.324285 CTGCAGCTCTTCCCAGAAGT 59.676 55.0 0.00 0.0 0.0 3.01 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
85 86 3.225940 CCTTGGCTTCTTGAAGGTCTTT 58.774 45.455 11.70 0.00 32.94 2.52
163 164 5.120053 TCAGATACAACACAAGCACATAACG 59.880 40.000 0.00 0.00 0.00 3.18
164 165 2.399396 ACAACACAAGCACATAACGC 57.601 45.000 0.00 0.00 0.00 4.84
168 169 2.761559 ACACAAGCACATAACGCAGTA 58.238 42.857 0.00 0.00 45.00 2.74
173 174 5.629020 CACAAGCACATAACGCAGTAAAATT 59.371 36.000 0.00 0.00 45.00 1.82
176 177 6.007936 AGCACATAACGCAGTAAAATTTCA 57.992 33.333 0.00 0.00 45.00 2.69
200 201 2.094286 TGGAAATGGCATGGCTTAAACG 60.094 45.455 21.08 0.00 0.00 3.60
206 207 1.530856 GCATGGCTTAAACGCGTAAC 58.469 50.000 14.46 0.00 0.00 2.50
221 222 2.737679 GCGTAACCGTTAAGCAGGAGAT 60.738 50.000 20.18 0.00 39.84 2.75
222 223 3.489738 GCGTAACCGTTAAGCAGGAGATA 60.490 47.826 20.18 0.00 39.84 1.98
232 233 6.978659 CGTTAAGCAGGAGATAAACACTATGA 59.021 38.462 0.00 0.00 0.00 2.15
235 236 9.547753 TTAAGCAGGAGATAAACACTATGAATC 57.452 33.333 0.00 0.00 0.00 2.52
237 238 7.215789 AGCAGGAGATAAACACTATGAATCAG 58.784 38.462 0.00 0.00 0.00 2.90
242 243 7.172361 GGAGATAAACACTATGAATCAGAAGCC 59.828 40.741 0.00 0.00 0.00 4.35
243 244 7.568349 AGATAAACACTATGAATCAGAAGCCA 58.432 34.615 0.00 0.00 0.00 4.75
244 245 7.714377 AGATAAACACTATGAATCAGAAGCCAG 59.286 37.037 0.00 0.00 0.00 4.85
402 406 9.151471 TCATAACCAAAATCTCTCGTTTTAGAG 57.849 33.333 0.00 0.00 43.72 2.43
449 453 4.021016 AGTCTACAAATCTTCTTCGCCACT 60.021 41.667 0.00 0.00 0.00 4.00
457 461 0.759959 TTCTTCGCCACTGGGTACAA 59.240 50.000 0.00 0.00 36.17 2.41
459 463 1.349688 TCTTCGCCACTGGGTACAAAT 59.650 47.619 0.00 0.00 36.17 2.32
462 466 1.800681 GCCACTGGGTACAAATCGC 59.199 57.895 0.00 0.00 36.17 4.58
512 516 2.289547 GGAACGAAACTAAGCTGTTGCA 59.710 45.455 0.00 0.00 42.74 4.08
555 559 1.550524 ACGCTGCCTCATGAAACTAGA 59.449 47.619 0.00 0.00 0.00 2.43
585 589 1.152652 GGATCGGCCCAGAGAGAGA 60.153 63.158 0.00 0.00 0.00 3.10
605 609 4.265630 CGCCGTTCAGCATACGCG 62.266 66.667 3.53 3.53 45.49 6.01
680 686 0.238289 GAAGTTGACGTGCACCATGG 59.762 55.000 11.19 11.19 0.00 3.66
713 719 4.609247 GATCGCTCGGGTCGTCGG 62.609 72.222 0.00 0.00 0.00 4.79
788 794 5.071370 AGGACGAGGCGATATTATATAGGG 58.929 45.833 0.00 0.00 0.00 3.53
803 809 2.789323 TAGGGGAGGGCTAAACCTAG 57.211 55.000 0.00 0.00 42.10 3.02
821 827 3.781307 TTCGGTCTGATGGGCCGG 61.781 66.667 8.77 0.00 44.97 6.13
830 836 4.759205 ATGGGCCGGGCTTTGGAC 62.759 66.667 28.80 10.51 0.00 4.02
834 840 2.650778 GCCGGGCTTTGGACTTTG 59.349 61.111 12.87 0.00 0.00 2.77
836 842 2.650778 CGGGCTTTGGACTTTGGC 59.349 61.111 0.00 0.00 0.00 4.52
837 843 2.931068 CGGGCTTTGGACTTTGGCC 61.931 63.158 0.00 0.00 41.80 5.36
839 845 1.533994 GGCTTTGGACTTTGGCCCT 60.534 57.895 0.00 0.00 37.12 5.19
840 846 1.536073 GGCTTTGGACTTTGGCCCTC 61.536 60.000 0.00 0.00 37.12 4.30
841 847 0.540597 GCTTTGGACTTTGGCCCTCT 60.541 55.000 0.00 0.00 0.00 3.69
842 848 2.001076 CTTTGGACTTTGGCCCTCTT 57.999 50.000 0.00 0.00 0.00 2.85
843 849 2.319844 CTTTGGACTTTGGCCCTCTTT 58.680 47.619 0.00 0.00 0.00 2.52
844 850 1.703411 TTGGACTTTGGCCCTCTTTG 58.297 50.000 0.00 0.00 0.00 2.77
845 851 0.827507 TGGACTTTGGCCCTCTTTGC 60.828 55.000 0.00 0.00 0.00 3.68
846 852 0.540597 GGACTTTGGCCCTCTTTGCT 60.541 55.000 0.00 0.00 0.00 3.91
847 853 1.332195 GACTTTGGCCCTCTTTGCTT 58.668 50.000 0.00 0.00 0.00 3.91
848 854 2.514803 GACTTTGGCCCTCTTTGCTTA 58.485 47.619 0.00 0.00 0.00 3.09
888 894 2.758770 TAACGGCGAGGCAGACACAC 62.759 60.000 16.62 0.00 0.00 3.82
922 928 1.850441 CGTAATAAGGCCGTGAACTCG 59.150 52.381 0.00 0.00 0.00 4.18
935 941 1.945776 GAACTCGAAGCAGCGAACGG 61.946 60.000 2.63 3.69 40.13 4.44
936 942 3.181967 CTCGAAGCAGCGAACGGG 61.182 66.667 2.63 2.54 40.13 5.28
937 943 4.735132 TCGAAGCAGCGAACGGGG 62.735 66.667 8.52 0.00 37.35 5.73
947 953 4.980805 GAACGGGGCGCACTCACA 62.981 66.667 10.74 0.00 0.00 3.58
948 954 4.988598 AACGGGGCGCACTCACAG 62.989 66.667 10.74 0.00 0.00 3.66
973 979 2.719354 AAAAACACCTCACCGCGC 59.281 55.556 0.00 0.00 0.00 6.86
974 980 3.175976 AAAAACACCTCACCGCGCG 62.176 57.895 25.67 25.67 0.00 6.86
975 981 4.903010 AAACACCTCACCGCGCGT 62.903 61.111 29.95 14.24 0.00 6.01
1188 1348 4.914420 CTGCCCTACGCGCTCTCG 62.914 72.222 5.73 0.00 42.08 4.04
1220 1380 2.833151 ATTCCGTGCCCCACCCTCTA 62.833 60.000 0.00 0.00 0.00 2.43
1383 1543 2.125106 GCCAAGAACTCCGGCGAT 60.125 61.111 9.30 0.00 35.79 4.58
1489 1649 1.374631 TGCCACTTCTACTGCTGCG 60.375 57.895 0.00 0.00 0.00 5.18
1491 1651 0.951040 GCCACTTCTACTGCTGCGTT 60.951 55.000 0.00 0.00 0.00 4.84
1530 1690 3.390135 GCGGAGGATGTTCGATGAAATA 58.610 45.455 0.00 0.00 0.00 1.40
1674 1834 2.485795 GGTTGTCGCCTTGGTTGCA 61.486 57.895 0.00 0.00 0.00 4.08
1696 1856 1.003233 GGGTGGCAAGGAGAGTCAC 60.003 63.158 0.00 0.00 0.00 3.67
1812 1972 3.748568 GTGCAAAGAAGGTCTTCGAAGAT 59.251 43.478 29.29 15.01 43.97 2.40
1833 1993 1.533469 CGACGAGGAGGGACTTGGTT 61.533 60.000 0.00 0.00 41.55 3.67
1836 1996 1.076677 ACGAGGAGGGACTTGGTTCTA 59.923 52.381 0.00 0.00 41.55 2.10
1893 2053 1.213678 CAGATTGAGGAGGCAATGGGA 59.786 52.381 0.00 0.00 38.53 4.37
1921 2081 3.245948 GGATAGGATGAGACAGGAGGGAT 60.246 52.174 0.00 0.00 0.00 3.85
1951 2111 0.474184 CACAGGGACTCTTGTGGGTT 59.526 55.000 1.42 0.00 34.60 4.11
1971 2131 2.505777 CTCTCTGCGTGTGGAGCG 60.506 66.667 0.00 0.00 37.44 5.03
2112 2272 3.507622 AGGAGGCAATTGCAGTCTTTTAC 59.492 43.478 30.32 10.73 44.36 2.01
2119 2279 3.980646 TTGCAGTCTTTTACGCAATGT 57.019 38.095 0.00 0.00 40.30 2.71
2175 2335 0.780494 TGGGGTTGGGGGTTAATGGA 60.780 55.000 0.00 0.00 0.00 3.41
2181 2341 2.041216 GTTGGGGGTTAATGGACAGTCT 59.959 50.000 0.00 0.00 0.00 3.24
2197 2357 0.244994 GTCTGATGCCGCGATATCCT 59.755 55.000 8.23 0.00 0.00 3.24
2202 2362 1.461127 GATGCCGCGATATCCTTGTTC 59.539 52.381 8.23 0.00 0.00 3.18
2204 2364 1.557443 GCCGCGATATCCTTGTTCCG 61.557 60.000 8.23 0.00 0.00 4.30
2214 2374 0.597568 CCTTGTTCCGCTCAATGCAA 59.402 50.000 0.00 0.00 43.06 4.08
2221 2381 0.592637 CCGCTCAATGCAACAAGACA 59.407 50.000 0.00 0.00 43.06 3.41
2244 2404 2.485426 TGTCACTCCTAACGAGGTTACG 59.515 50.000 0.00 0.00 44.19 3.18
2300 2460 4.072839 GGGTTAGTGTTTGAAGGGAAGAG 58.927 47.826 0.00 0.00 0.00 2.85
2331 2491 0.598065 GCATGGTCCGGAAATATGGC 59.402 55.000 5.23 1.49 0.00 4.40
2332 2492 1.247567 CATGGTCCGGAAATATGGCC 58.752 55.000 5.23 0.88 0.00 5.36
2334 2494 1.809133 TGGTCCGGAAATATGGCCTA 58.191 50.000 5.23 0.00 0.00 3.93
2443 2603 3.274586 CGTCCCATGGCGATGCTG 61.275 66.667 6.09 0.00 0.00 4.41
2448 2608 3.214123 CATGGCGATGCTGTGGGG 61.214 66.667 0.00 0.00 0.00 4.96
2523 2683 3.909662 GTGCAGGCACGATTGGAT 58.090 55.556 8.84 0.00 37.19 3.41
2544 2704 2.085118 CCATGGGCAATTACCATCCA 57.915 50.000 2.85 0.13 45.33 3.41
2559 2719 5.919348 ACCATCCATCAGATACCATTCTT 57.081 39.130 0.00 0.00 32.37 2.52
2578 2738 2.223537 TCTGTCGAACGCATATGCAT 57.776 45.000 26.52 15.05 42.21 3.96
2636 2796 2.673775 TCACAAGGGCAGAAAATGGA 57.326 45.000 0.00 0.00 0.00 3.41
2673 2833 1.679977 GGGCTGCAGCTCCATTGAA 60.680 57.895 35.82 0.00 41.70 2.69
2728 2890 0.790207 CAACGACCACCAACTGATCG 59.210 55.000 0.00 0.00 38.71 3.69
2755 2917 1.731709 TGGACTGTCGATGCGAAAATG 59.268 47.619 1.07 0.00 37.72 2.32
2761 2923 4.143115 ACTGTCGATGCGAAAATGTACTTG 60.143 41.667 0.00 0.00 37.72 3.16
2765 2927 2.697431 TGCGAAAATGTACTTGTGCC 57.303 45.000 0.00 0.00 0.00 5.01
2779 2941 0.396435 TGTGCCCAGGTGACTAACAG 59.604 55.000 0.00 0.00 40.21 3.16
2794 2956 7.255625 GGTGACTAACAGCAGTATCATCATCTA 60.256 40.741 0.00 0.00 45.12 1.98
2795 2957 8.303156 GTGACTAACAGCAGTATCATCATCTAT 58.697 37.037 0.00 0.00 0.00 1.98
2811 2973 9.269453 TCATCATCTATACTGATTTTTGCTGAG 57.731 33.333 0.00 0.00 31.00 3.35
2812 2974 9.269453 CATCATCTATACTGATTTTTGCTGAGA 57.731 33.333 0.00 0.00 31.00 3.27
2813 2975 8.883954 TCATCTATACTGATTTTTGCTGAGAG 57.116 34.615 0.00 0.00 0.00 3.20
2814 2976 7.440556 TCATCTATACTGATTTTTGCTGAGAGC 59.559 37.037 0.00 0.00 42.82 4.09
2860 3022 6.989169 GCAGTTATCAGATACAAGATTCAGGT 59.011 38.462 0.00 0.00 0.00 4.00
2869 3031 7.281774 CAGATACAAGATTCAGGTGTAAAGCAT 59.718 37.037 0.00 0.00 31.85 3.79
2936 3098 3.436704 ACAGATTGGAGTTTACATGCACG 59.563 43.478 0.00 0.00 0.00 5.34
3034 3196 6.593807 TGTGTTATGTACTTAAACCCTGTGT 58.406 36.000 2.99 0.00 0.00 3.72
3035 3197 6.483974 TGTGTTATGTACTTAAACCCTGTGTG 59.516 38.462 2.99 0.00 0.00 3.82
3036 3198 5.998981 TGTTATGTACTTAAACCCTGTGTGG 59.001 40.000 2.99 0.00 0.00 4.17
3106 3268 3.439857 CTTGGAAGGATTGGGAACTCA 57.560 47.619 0.00 0.00 0.00 3.41
3122 3284 2.540515 ACTCATTTACTGGCGACATCG 58.459 47.619 0.00 0.00 41.51 3.84
3174 3336 5.417580 GCCTTGTTACACTATTGGAAATCCA 59.582 40.000 0.00 0.00 45.94 3.41
3196 3358 1.684450 TGGTCTTGTGACAGTTCGCTA 59.316 47.619 0.00 0.00 44.61 4.26
3210 3372 3.449018 AGTTCGCTATCTTCAGTGGATGT 59.551 43.478 0.00 0.00 0.00 3.06
3213 3375 3.570125 TCGCTATCTTCAGTGGATGTAGG 59.430 47.826 0.00 0.00 0.00 3.18
3218 3380 5.762179 ATCTTCAGTGGATGTAGGTGAAA 57.238 39.130 0.00 0.00 0.00 2.69
3223 3385 4.593206 TCAGTGGATGTAGGTGAAACTTCT 59.407 41.667 0.00 0.00 36.74 2.85
3322 3484 2.553028 GGTGATGACTGGTGAATGTGGT 60.553 50.000 0.00 0.00 0.00 4.16
3555 3717 1.400846 GCATCAGTGATGAAGTGCTGG 59.599 52.381 32.61 7.08 42.09 4.85
3572 3734 3.136443 TGCTGGGGAAGTGTATTATCTGG 59.864 47.826 0.00 0.00 0.00 3.86
3597 3759 9.338622 GGGCAGTGATAATAGTGTAAATTACTT 57.661 33.333 4.67 0.00 0.00 2.24
3601 3763 9.899661 AGTGATAATAGTGTAAATTACTTGGCA 57.100 29.630 4.67 0.00 0.00 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 86 2.064434 TTTGTTGTGGTGCAGATGGA 57.936 45.000 0.00 0.00 0.00 3.41
123 124 4.778534 ATCTGATTGTTCTTGTTGGCTG 57.221 40.909 0.00 0.00 0.00 4.85
125 126 5.627499 TGTATCTGATTGTTCTTGTTGGC 57.373 39.130 0.00 0.00 0.00 4.52
173 174 1.275856 GCCATGCCATTTCCACTTGAA 59.724 47.619 0.00 0.00 0.00 2.69
176 177 1.648116 AAGCCATGCCATTTCCACTT 58.352 45.000 0.00 0.00 0.00 3.16
200 201 0.997196 CTCCTGCTTAACGGTTACGC 59.003 55.000 19.06 19.06 46.04 4.42
206 207 4.504858 AGTGTTTATCTCCTGCTTAACGG 58.495 43.478 0.00 0.00 0.00 4.44
221 222 5.586243 GCTGGCTTCTGATTCATAGTGTTTA 59.414 40.000 0.00 0.00 0.00 2.01
222 223 4.397417 GCTGGCTTCTGATTCATAGTGTTT 59.603 41.667 0.00 0.00 0.00 2.83
232 233 1.023513 GCACGAGCTGGCTTCTGATT 61.024 55.000 0.00 0.00 37.91 2.57
244 245 2.394708 TGCGAGATAATTAGCACGAGC 58.605 47.619 21.82 12.19 42.56 5.03
262 264 6.092259 AGGACGTGTAGTTTAGAATTTGATGC 59.908 38.462 0.00 0.00 0.00 3.91
402 406 0.392461 TGGTACGGAGCAGATTTGGC 60.392 55.000 0.00 0.00 0.00 4.52
414 418 2.048444 TGTAGACTAGCCTGGTACGG 57.952 55.000 0.00 0.00 0.00 4.02
449 453 2.568062 TGAACTAGGCGATTTGTACCCA 59.432 45.455 0.00 0.00 0.00 4.51
457 461 2.628178 TGATCGGATGAACTAGGCGATT 59.372 45.455 0.00 0.00 0.00 3.34
459 463 1.687563 TGATCGGATGAACTAGGCGA 58.312 50.000 0.00 0.00 0.00 5.54
462 466 4.513442 TGGTTTTGATCGGATGAACTAGG 58.487 43.478 0.00 0.00 0.00 3.02
506 510 4.941263 GGTGTCTGTTATAGGATTGCAACA 59.059 41.667 0.00 0.00 0.00 3.33
507 511 4.941263 TGGTGTCTGTTATAGGATTGCAAC 59.059 41.667 0.00 0.00 0.00 4.17
512 516 6.407202 GTCTGTTGGTGTCTGTTATAGGATT 58.593 40.000 0.00 0.00 0.00 3.01
555 559 2.615240 GGGCCGATCCAAATTTGCTTTT 60.615 45.455 12.92 0.00 36.21 2.27
585 589 1.516386 CGTATGCTGAACGGCGTCT 60.516 57.895 15.17 3.30 36.71 4.18
605 609 4.261495 GTCGTCGTAATGCGCGCC 62.261 66.667 30.77 12.28 41.07 6.53
610 614 0.650512 CACCCATGTCGTCGTAATGC 59.349 55.000 0.00 0.00 0.00 3.56
645 651 3.314541 ACTTCTACCGCAACTGTAAGG 57.685 47.619 0.00 0.00 39.30 2.69
788 794 1.138464 CCGAACTAGGTTTAGCCCTCC 59.862 57.143 0.00 0.00 38.26 4.30
821 827 1.533994 AGGGCCAAAGTCCAAAGCC 60.534 57.895 6.18 0.00 41.85 4.35
830 836 2.417787 GCATAAGCAAAGAGGGCCAAAG 60.418 50.000 6.18 0.00 41.58 2.77
831 837 1.550072 GCATAAGCAAAGAGGGCCAAA 59.450 47.619 6.18 0.00 41.58 3.28
845 851 2.216898 GCTCACTAGGGCTTGCATAAG 58.783 52.381 0.00 0.00 36.97 1.73
846 852 1.134098 GGCTCACTAGGGCTTGCATAA 60.134 52.381 0.00 0.00 0.00 1.90
847 853 0.469917 GGCTCACTAGGGCTTGCATA 59.530 55.000 0.00 0.00 0.00 3.14
848 854 1.225704 GGCTCACTAGGGCTTGCAT 59.774 57.895 0.00 0.00 0.00 3.96
899 905 0.806884 TTCACGGCCTTATTACGCGG 60.807 55.000 12.47 0.00 0.00 6.46
956 962 2.719354 GCGCGGTGAGGTGTTTTT 59.281 55.556 8.83 0.00 0.00 1.94
957 963 3.645975 CGCGCGGTGAGGTGTTTT 61.646 61.111 24.84 0.00 0.00 2.43
958 964 4.903010 ACGCGCGGTGAGGTGTTT 62.903 61.111 35.22 5.42 0.00 2.83
1255 1415 2.131067 CCGAGGAGAAGGAGGGAGC 61.131 68.421 0.00 0.00 0.00 4.70
1257 1417 2.042843 GCCGAGGAGAAGGAGGGA 60.043 66.667 0.00 0.00 0.00 4.20
1489 1649 1.677633 CGTCCCCCATGTTCCCAAC 60.678 63.158 0.00 0.00 0.00 3.77
1491 1651 4.041762 GCGTCCCCCATGTTCCCA 62.042 66.667 0.00 0.00 0.00 4.37
1530 1690 1.908793 CACGGTGTCCCTCTCAGGT 60.909 63.158 0.00 0.00 31.93 4.00
1596 1756 2.047274 AACATCTCCACCACCGCG 60.047 61.111 0.00 0.00 0.00 6.46
1601 1761 1.375908 GCGCTGAACATCTCCACCA 60.376 57.895 0.00 0.00 0.00 4.17
1659 1819 2.918345 GCATGCAACCAAGGCGACA 61.918 57.895 14.21 0.00 0.00 4.35
1689 1849 1.002888 CTGAACCCATGCAGTGACTCT 59.997 52.381 0.00 0.00 0.00 3.24
1696 1856 1.236616 TTGACGCTGAACCCATGCAG 61.237 55.000 0.00 0.00 35.28 4.41
1753 1913 4.569676 TCCTAGAATACATCCCCTCCAA 57.430 45.455 0.00 0.00 0.00 3.53
1812 1972 2.282958 AAGTCCCTCCTCGTCGCA 60.283 61.111 0.00 0.00 0.00 5.10
1833 1993 7.989170 CAGCTATCCACCATGCAATTATATAGA 59.011 37.037 0.00 0.00 0.00 1.98
1836 1996 5.359009 GCAGCTATCCACCATGCAATTATAT 59.641 40.000 0.00 0.00 36.88 0.86
1875 2035 2.626743 CAATCCCATTGCCTCCTCAATC 59.373 50.000 0.00 0.00 34.68 2.67
1893 2053 3.649981 CCTGTCTCATCCTATCCACCAAT 59.350 47.826 0.00 0.00 0.00 3.16
1921 2081 3.020984 GAGTCCCTGTGTTTGGTTTCAA 58.979 45.455 0.00 0.00 0.00 2.69
1951 2111 1.005748 CTCCACACGCAGAGAGCAA 60.006 57.895 0.00 0.00 46.13 3.91
1971 2131 2.202974 GGTACGATTGCCCCCGAC 60.203 66.667 0.00 0.00 0.00 4.79
2119 2279 1.221566 CCATCACATCCCTGTCGCA 59.778 57.895 0.00 0.00 31.62 5.10
2175 2335 0.676184 ATATCGCGGCATCAGACTGT 59.324 50.000 6.13 0.00 0.00 3.55
2181 2341 0.392706 ACAAGGATATCGCGGCATCA 59.607 50.000 18.35 0.00 0.00 3.07
2204 2364 2.033801 ACACTGTCTTGTTGCATTGAGC 59.966 45.455 0.00 0.00 45.96 4.26
2214 2374 3.243434 CGTTAGGAGTGACACTGTCTTGT 60.243 47.826 14.14 0.00 33.15 3.16
2244 2404 1.689959 CATTCAGCACCGCAAGAAAC 58.310 50.000 0.00 0.00 43.02 2.78
2305 2465 1.822114 TTCCGGACCATGCACTCGAA 61.822 55.000 1.83 0.00 0.00 3.71
2311 2471 1.979855 CCATATTTCCGGACCATGCA 58.020 50.000 1.83 0.00 0.00 3.96
2331 2491 2.100197 TGTTCGGTGTGAGGAGATAGG 58.900 52.381 0.00 0.00 0.00 2.57
2332 2492 2.755655 AGTGTTCGGTGTGAGGAGATAG 59.244 50.000 0.00 0.00 0.00 2.08
2334 2494 1.633774 AGTGTTCGGTGTGAGGAGAT 58.366 50.000 0.00 0.00 0.00 2.75
2443 2603 3.146847 CAAGTAAAGTTCTCCACCCCAC 58.853 50.000 0.00 0.00 0.00 4.61
2448 2608 2.226674 GGCTGCAAGTAAAGTTCTCCAC 59.773 50.000 0.50 0.00 35.30 4.02
2544 2704 6.276847 GTTCGACAGAAGAATGGTATCTGAT 58.723 40.000 8.84 0.00 42.48 2.90
2559 2719 2.223537 ATGCATATGCGTTCGACAGA 57.776 45.000 22.21 2.10 45.83 3.41
2578 2738 1.304052 CATCCCAACGGCCTTCCAA 60.304 57.895 0.00 0.00 0.00 3.53
2636 2796 1.611673 CCGCTTCTTTCCTGTCCATGT 60.612 52.381 0.00 0.00 0.00 3.21
2673 2833 7.345914 AGCAAGGTTAGATATTAGGAAGACACT 59.654 37.037 0.00 0.00 0.00 3.55
2728 2890 0.798776 CATCGACAGTCCAACCTTGC 59.201 55.000 0.00 0.00 0.00 4.01
2755 2917 0.396811 AGTCACCTGGGCACAAGTAC 59.603 55.000 0.00 0.00 0.00 2.73
2761 2923 0.955919 GCTGTTAGTCACCTGGGCAC 60.956 60.000 0.00 0.00 0.00 5.01
2765 2927 3.195610 TGATACTGCTGTTAGTCACCTGG 59.804 47.826 0.09 0.00 32.19 4.45
2811 2973 6.624423 GCACATGTATGGATAATGGATTGCTC 60.624 42.308 0.00 0.00 0.00 4.26
2812 2974 5.184479 GCACATGTATGGATAATGGATTGCT 59.816 40.000 0.00 0.00 0.00 3.91
2813 2975 5.047872 TGCACATGTATGGATAATGGATTGC 60.048 40.000 0.00 0.00 0.00 3.56
2814 2976 6.208007 ACTGCACATGTATGGATAATGGATTG 59.792 38.462 0.00 0.00 0.00 2.67
2815 2977 6.309357 ACTGCACATGTATGGATAATGGATT 58.691 36.000 0.00 0.00 0.00 3.01
2817 2979 5.308976 ACTGCACATGTATGGATAATGGA 57.691 39.130 0.00 0.00 0.00 3.41
2818 2980 7.391275 TGATAACTGCACATGTATGGATAATGG 59.609 37.037 0.00 0.00 0.00 3.16
2819 2981 8.326680 TGATAACTGCACATGTATGGATAATG 57.673 34.615 0.00 0.00 0.00 1.90
2820 2982 8.377799 TCTGATAACTGCACATGTATGGATAAT 58.622 33.333 0.00 0.00 0.00 1.28
2821 2983 7.734942 TCTGATAACTGCACATGTATGGATAA 58.265 34.615 0.00 0.00 0.00 1.75
2822 2984 7.301868 TCTGATAACTGCACATGTATGGATA 57.698 36.000 0.00 0.00 0.00 2.59
2893 3055 6.378564 TCTGTCTCCGAATCTTGATCTTAACT 59.621 38.462 0.00 0.00 0.00 2.24
3034 3196 1.075050 ACTAGTGAGGAAGACGGTCCA 59.925 52.381 4.14 0.00 40.48 4.02
3035 3197 1.473278 CACTAGTGAGGAAGACGGTCC 59.527 57.143 18.45 0.00 38.03 4.46
3036 3198 1.135344 GCACTAGTGAGGAAGACGGTC 60.135 57.143 27.08 0.00 0.00 4.79
3122 3284 3.053896 GTACCCAACACCAGCGGC 61.054 66.667 0.00 0.00 0.00 6.53
3174 3336 1.806623 GCGAACTGTCACAAGACCAGT 60.807 52.381 0.00 0.00 44.33 4.00
3196 3358 5.249393 AGTTTCACCTACATCCACTGAAGAT 59.751 40.000 0.00 0.00 0.00 2.40
3210 3372 3.008049 GCTCTTCCCAGAAGTTTCACCTA 59.992 47.826 4.38 0.00 0.00 3.08
3213 3375 2.810852 CAGCTCTTCCCAGAAGTTTCAC 59.189 50.000 4.38 0.00 0.00 3.18
3218 3380 0.324285 CTGCAGCTCTTCCCAGAAGT 59.676 55.000 0.00 0.00 0.00 3.01
3245 3407 0.754217 CAATGCTATGCTGCCCCACT 60.754 55.000 0.00 0.00 0.00 4.00
3322 3484 2.371841 AGTGTTCCCAGTACAGCATTCA 59.628 45.455 0.00 0.00 0.00 2.57
3446 3608 2.736081 GCATGCTTCGCAATGAAATCCA 60.736 45.455 11.37 0.00 43.62 3.41
3555 3717 3.136626 ACTGCCCAGATAATACACTTCCC 59.863 47.826 1.69 0.00 0.00 3.97


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

AutoCloner maintained by Alex Coulton.