Multiple sequence alignment - TraesCS4B01G305400

Loading Multiple Alignment...

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 TraesCS4B01G305400 chr4B 100.000 3007 0 0 1 3007 594149060 594152066 0.000000e+00 5553.0
1 TraesCS4B01G305400 chr4D 94.714 1154 40 9 882 2028 472158801 472159940 0.000000e+00 1773.0
2 TraesCS4B01G305400 chr4D 89.703 437 29 7 2121 2545 472159958 472160390 7.330000e-151 544.0
3 TraesCS4B01G305400 chr4D 83.565 432 27 11 2617 3007 472160506 472160934 6.130000e-97 364.0
4 TraesCS4B01G305400 chr4D 86.555 119 14 1 765 883 472158655 472158771 2.430000e-26 130.0
5 TraesCS4B01G305400 chr4A 88.656 1384 76 43 905 2246 679068318 679069662 0.000000e+00 1611.0
6 TraesCS4B01G305400 chr4A 88.030 802 54 13 2239 3007 679069739 679070531 0.000000e+00 911.0
7 TraesCS4B01G305400 chr4A 82.857 105 16 1 776 880 679068126 679068228 3.190000e-15 93.5
8 TraesCS4B01G305400 chr6D 92.363 694 50 3 1 693 413175334 413176025 0.000000e+00 985.0
9 TraesCS4B01G305400 chr3B 91.919 693 55 1 1 693 53816714 53817405 0.000000e+00 968.0
10 TraesCS4B01G305400 chrUn 91.582 689 54 3 1 687 212867265 212867951 0.000000e+00 948.0
11 TraesCS4B01G305400 chrUn 91.001 689 58 3 1 687 24838620 24839306 0.000000e+00 926.0
12 TraesCS4B01G305400 chr5A 90.607 692 62 3 3 693 662320770 662321459 0.000000e+00 915.0
13 TraesCS4B01G305400 chr7D 90.476 693 60 3 1 693 116836358 116835672 0.000000e+00 909.0
14 TraesCS4B01G305400 chr3D 89.899 693 69 1 1 693 515813761 515814452 0.000000e+00 891.0
15 TraesCS4B01G305400 chr7B 88.873 692 76 1 1 692 665381479 665380789 0.000000e+00 850.0
16 TraesCS4B01G305400 chr2B 88.023 693 82 1 1 693 569964728 569965419 0.000000e+00 819.0


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 TraesCS4B01G305400 chr4B 594149060 594152066 3006 False 5553.000000 5553 100.000000 1 3007 1 chr4B.!!$F1 3006
1 TraesCS4B01G305400 chr4D 472158655 472160934 2279 False 702.750000 1773 88.634250 765 3007 4 chr4D.!!$F1 2242
2 TraesCS4B01G305400 chr4A 679068126 679070531 2405 False 871.833333 1611 86.514333 776 3007 3 chr4A.!!$F1 2231
3 TraesCS4B01G305400 chr6D 413175334 413176025 691 False 985.000000 985 92.363000 1 693 1 chr6D.!!$F1 692
4 TraesCS4B01G305400 chr3B 53816714 53817405 691 False 968.000000 968 91.919000 1 693 1 chr3B.!!$F1 692
5 TraesCS4B01G305400 chrUn 212867265 212867951 686 False 948.000000 948 91.582000 1 687 1 chrUn.!!$F2 686
6 TraesCS4B01G305400 chrUn 24838620 24839306 686 False 926.000000 926 91.001000 1 687 1 chrUn.!!$F1 686
7 TraesCS4B01G305400 chr5A 662320770 662321459 689 False 915.000000 915 90.607000 3 693 1 chr5A.!!$F1 690
8 TraesCS4B01G305400 chr7D 116835672 116836358 686 True 909.000000 909 90.476000 1 693 1 chr7D.!!$R1 692
9 TraesCS4B01G305400 chr3D 515813761 515814452 691 False 891.000000 891 89.899000 1 693 1 chr3D.!!$F1 692
10 TraesCS4B01G305400 chr7B 665380789 665381479 690 True 850.000000 850 88.873000 1 692 1 chr7B.!!$R1 691
11 TraesCS4B01G305400 chr2B 569964728 569965419 691 False 819.000000 819 88.023000 1 693 1 chr2B.!!$F1 692

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
594 600 1.323271 TGCGGTGACTTGGGCAAAAA 61.323 50.0 0.0 0.0 31.5 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2248 2469 0.040425 GTGCGTTTGTGTGACCATCC 60.04 55.0 0.0 0.0 0.0 3.51 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
31 33 8.722480 TGGAAGAGATACTGTATTGTTTCATG 57.278 34.615 1.22 0.00 0.00 3.07
38 40 9.201127 AGATACTGTATTGTTTCATGATGATCG 57.799 33.333 0.00 0.00 0.00 3.69
102 104 9.753674 TTAACAAATTATCTTTGGTGAGGATCT 57.246 29.630 0.00 0.00 32.68 2.75
146 149 9.801873 CACATAAAGATTTTAATACACAAGGGG 57.198 33.333 0.00 0.00 0.00 4.79
240 243 4.320608 ACCGTAAACACTCCGTTTCTAA 57.679 40.909 0.00 0.00 44.78 2.10
245 248 5.332808 CGTAAACACTCCGTTTCTAACCAAG 60.333 44.000 0.00 0.00 44.78 3.61
325 328 2.042162 AGTGCATCCAGGAATTCCAACT 59.958 45.455 26.22 13.48 38.89 3.16
373 376 6.895782 ACTGAATATTCAAGGGAACCGATTA 58.104 36.000 18.47 0.00 43.34 1.75
398 403 8.671987 ATAATACTGTGCCTATGTAATCCTCT 57.328 34.615 0.00 0.00 0.00 3.69
422 427 9.710979 TCTTTACGTTGCACAATATTATAAAGC 57.289 29.630 0.00 0.00 30.66 3.51
445 450 5.945784 GCCTTGGATATTGTATGGCTAATGA 59.054 40.000 0.00 0.00 36.32 2.57
459 464 2.307768 CTAATGACGTCTCCCCTAGCA 58.692 52.381 17.92 0.00 0.00 3.49
592 598 1.733402 CTTGCGGTGACTTGGGCAAA 61.733 55.000 0.00 0.00 43.91 3.68
594 600 1.323271 TGCGGTGACTTGGGCAAAAA 61.323 50.000 0.00 0.00 31.50 1.94
632 638 9.394767 AGATATTTGTTGTGTAATATCTGTGCA 57.605 29.630 13.62 0.00 45.49 4.57
660 666 7.502895 ACATACCGTCATTCTCTACTGATAACT 59.497 37.037 0.00 0.00 0.00 2.24
693 699 8.359642 GCCATTTACTCATAAGGCATTTATTCA 58.640 33.333 0.00 0.00 41.63 2.57
694 700 9.903682 CCATTTACTCATAAGGCATTTATTCAG 57.096 33.333 0.00 0.00 29.37 3.02
723 729 8.779354 AAAGTATGAATATTAGATTCGGAGCC 57.221 34.615 0.00 0.00 0.00 4.70
724 730 6.565234 AGTATGAATATTAGATTCGGAGCCG 58.435 40.000 1.74 1.74 41.35 5.52
739 745 2.555123 GCCGAAGCTCAATGGTTGA 58.445 52.632 0.00 0.00 36.40 3.18
755 761 9.311916 TCAATGGTTGAGTAAAGAACAATTTTG 57.688 29.630 0.00 0.00 34.08 2.44
756 762 9.097257 CAATGGTTGAGTAAAGAACAATTTTGT 57.903 29.630 0.00 0.00 44.72 2.83
763 769 9.730420 TGAGTAAAGAACAATTTTGTAAAGAGC 57.270 29.630 0.00 0.00 41.31 4.09
768 774 4.766404 ACAATTTTGTAAAGAGCCGGAG 57.234 40.909 5.05 0.00 40.16 4.63
778 784 2.008242 AGAGCCGGAGAGAGCATTAT 57.992 50.000 5.05 0.00 0.00 1.28
782 788 3.209410 AGCCGGAGAGAGCATTATTTTG 58.791 45.455 5.05 0.00 0.00 2.44
787 793 5.413833 CCGGAGAGAGCATTATTTTGCATAT 59.586 40.000 0.00 0.00 45.23 1.78
788 794 6.402983 CCGGAGAGAGCATTATTTTGCATATC 60.403 42.308 0.00 0.00 45.23 1.63
792 798 7.827701 AGAGAGCATTATTTTGCATATCATGG 58.172 34.615 0.00 0.00 45.23 3.66
794 800 6.045072 AGCATTATTTTGCATATCATGGGG 57.955 37.500 0.00 0.00 45.23 4.96
797 803 2.475339 TTTTGCATATCATGGGGGCT 57.525 45.000 0.00 0.00 0.00 5.19
820 826 8.299570 GGCTAAATAACATGAATATGTCCTTGG 58.700 37.037 0.00 0.00 46.54 3.61
821 827 8.850156 GCTAAATAACATGAATATGTCCTTGGT 58.150 33.333 0.00 0.00 46.54 3.67
826 832 1.922447 TGAATATGTCCTTGGTGGCCT 59.078 47.619 3.32 0.00 35.26 5.19
827 833 2.311542 TGAATATGTCCTTGGTGGCCTT 59.688 45.455 3.32 0.00 35.26 4.35
919 992 2.299013 GTTCCAACACCAAAATCCCTCC 59.701 50.000 0.00 0.00 0.00 4.30
1016 1089 2.475519 CGCGCCAATAAAACAGTACCAG 60.476 50.000 0.00 0.00 0.00 4.00
1025 1098 2.434884 CAGTACCAGCTGGCACCG 60.435 66.667 33.06 19.00 39.32 4.94
1026 1099 2.923035 AGTACCAGCTGGCACCGT 60.923 61.111 33.06 15.48 39.32 4.83
1027 1100 2.742372 GTACCAGCTGGCACCGTG 60.742 66.667 33.06 7.55 39.32 4.94
1028 1101 4.697756 TACCAGCTGGCACCGTGC 62.698 66.667 33.06 15.50 44.08 5.34
1157 1233 1.145377 ACCGCCAAGAACACGAACT 59.855 52.632 0.00 0.00 0.00 3.01
1164 1240 2.680841 CCAAGAACACGAACTCCAACAA 59.319 45.455 0.00 0.00 0.00 2.83
1233 1311 3.250040 TCGAGCTGATTACGATCGATTCA 59.750 43.478 24.34 18.41 37.48 2.57
1239 1317 5.277058 GCTGATTACGATCGATTCAAGCTTT 60.277 40.000 24.34 0.00 34.91 3.51
1579 1657 1.539157 CAGAAGCCAAGGGAAAGGAC 58.461 55.000 0.00 0.00 0.00 3.85
1597 1678 2.161486 CGGCGAGGCGAAGAAGAAG 61.161 63.158 13.92 0.00 0.00 2.85
1598 1679 1.215647 GGCGAGGCGAAGAAGAAGA 59.784 57.895 0.00 0.00 0.00 2.87
1599 1680 0.389948 GGCGAGGCGAAGAAGAAGAA 60.390 55.000 0.00 0.00 0.00 2.52
1957 2051 7.180322 AGGAGAAGCATACATATATGGTGAG 57.820 40.000 16.96 5.25 46.47 3.51
2052 2152 8.754991 AGTTTCTCTAGCATAGTATGTACTGT 57.245 34.615 11.73 0.00 40.38 3.55
2053 2153 8.625651 AGTTTCTCTAGCATAGTATGTACTGTG 58.374 37.037 11.73 11.26 44.94 3.66
2054 2154 8.407064 GTTTCTCTAGCATAGTATGTACTGTGT 58.593 37.037 11.73 7.56 44.28 3.72
2055 2155 7.497925 TCTCTAGCATAGTATGTACTGTGTG 57.502 40.000 11.73 7.74 44.28 3.82
2056 2156 7.280356 TCTCTAGCATAGTATGTACTGTGTGA 58.720 38.462 11.73 11.24 44.28 3.58
2058 2158 8.465273 TCTAGCATAGTATGTACTGTGTGAAT 57.535 34.615 11.73 5.57 44.28 2.57
2060 2160 6.283694 AGCATAGTATGTACTGTGTGAATGG 58.716 40.000 11.73 0.00 44.28 3.16
2061 2161 5.050091 GCATAGTATGTACTGTGTGAATGGC 60.050 44.000 11.73 0.10 44.28 4.40
2062 2162 4.826274 AGTATGTACTGTGTGAATGGCT 57.174 40.909 0.00 0.00 34.72 4.75
2063 2163 5.165961 AGTATGTACTGTGTGAATGGCTT 57.834 39.130 0.00 0.00 34.72 4.35
2084 2189 5.107453 GCTTCTGGGATTCACGAATTATACG 60.107 44.000 0.00 0.00 0.00 3.06
2086 2191 5.526115 TCTGGGATTCACGAATTATACGAC 58.474 41.667 0.00 0.00 34.70 4.34
2089 2194 5.163488 TGGGATTCACGAATTATACGACAGT 60.163 40.000 0.00 0.00 34.70 3.55
2097 2202 7.328982 TCACGAATTATACGACAGTTTTGCTTA 59.671 33.333 0.00 0.00 34.70 3.09
2099 2204 8.662141 ACGAATTATACGACAGTTTTGCTTAAT 58.338 29.630 0.00 0.00 34.70 1.40
2105 2210 8.950403 ATACGACAGTTTTGCTTAATTTTCTC 57.050 30.769 0.00 0.00 0.00 2.87
2152 2282 6.913873 TTGGTACTTGTTACTTGTTCTGAC 57.086 37.500 0.00 0.00 0.00 3.51
2153 2283 5.045215 TGGTACTTGTTACTTGTTCTGACG 58.955 41.667 0.00 0.00 0.00 4.35
2154 2284 5.163530 TGGTACTTGTTACTTGTTCTGACGA 60.164 40.000 0.00 0.00 0.00 4.20
2155 2285 5.174579 GGTACTTGTTACTTGTTCTGACGAC 59.825 44.000 0.00 0.00 0.00 4.34
2156 2286 3.795101 ACTTGTTACTTGTTCTGACGACG 59.205 43.478 0.00 0.00 0.00 5.12
2157 2287 2.121786 TGTTACTTGTTCTGACGACGC 58.878 47.619 0.00 0.00 0.00 5.19
2167 2301 1.003866 TCTGACGACGCATATGAGACG 60.004 52.381 24.08 24.08 38.61 4.18
2174 2308 4.085195 CGACGCATATGAGACGAAGATAG 58.915 47.826 22.15 0.00 35.51 2.08
2183 2317 2.812591 GAGACGAAGATAGCATACGGGA 59.187 50.000 0.00 0.00 0.00 5.14
2198 2332 1.480954 ACGGGAGCGATTGAACATACT 59.519 47.619 0.00 0.00 0.00 2.12
2199 2333 2.691526 ACGGGAGCGATTGAACATACTA 59.308 45.455 0.00 0.00 0.00 1.82
2200 2334 3.321111 ACGGGAGCGATTGAACATACTAT 59.679 43.478 0.00 0.00 0.00 2.12
2202 2336 3.433615 GGGAGCGATTGAACATACTATGC 59.566 47.826 0.00 0.00 0.00 3.14
2218 2355 7.615365 ACATACTATGCAAAAATCAGGAGGAAA 59.385 33.333 0.00 0.00 0.00 3.13
2242 2463 6.515272 AGAAAGGAATGTTTGCATCGTATT 57.485 33.333 0.00 0.00 33.50 1.89
2246 2467 4.699735 AGGAATGTTTGCATCGTATTCACA 59.300 37.500 12.50 0.00 33.50 3.58
2248 2469 3.447752 TGTTTGCATCGTATTCACACG 57.552 42.857 0.00 0.00 43.28 4.49
2282 2504 5.634020 ACAAACGCACTGATAGAAGAGTTAC 59.366 40.000 0.00 0.00 0.00 2.50
2378 2603 3.552684 CCATTTTCTCGGCTGCTTTTCAA 60.553 43.478 0.00 0.00 0.00 2.69
2385 2610 4.024048 TCTCGGCTGCTTTTCAACTTTTAG 60.024 41.667 0.00 0.00 0.00 1.85
2386 2611 3.630312 TCGGCTGCTTTTCAACTTTTAGT 59.370 39.130 0.00 0.00 0.00 2.24
2387 2612 4.817464 TCGGCTGCTTTTCAACTTTTAGTA 59.183 37.500 0.00 0.00 0.00 1.82
2433 2658 0.965866 AGCTGGTTGTCTCGATCCGA 60.966 55.000 0.00 0.00 0.00 4.55
2522 2754 1.005294 GACACGTACGCCGACACAAT 61.005 55.000 16.72 0.00 40.70 2.71
2589 2870 0.237761 CACGTCGGTCGAACTCTCTT 59.762 55.000 0.00 0.00 42.86 2.85
2590 2871 0.516439 ACGTCGGTCGAACTCTCTTC 59.484 55.000 0.00 0.00 42.86 2.87
2591 2872 0.797542 CGTCGGTCGAACTCTCTTCT 59.202 55.000 0.00 0.00 42.86 2.85
2592 2873 1.464355 CGTCGGTCGAACTCTCTTCTG 60.464 57.143 0.00 0.00 42.86 3.02
2593 2874 1.536331 GTCGGTCGAACTCTCTTCTGT 59.464 52.381 0.00 0.00 0.00 3.41
2600 2881 6.202937 GGTCGAACTCTCTTCTGTACATATG 58.797 44.000 0.00 0.00 0.00 1.78
2615 2896 3.545703 ACATATGGACCAAAGTAGCTGC 58.454 45.455 7.80 0.00 0.00 5.25
2620 2901 0.670546 GACCAAAGTAGCTGCGCTCA 60.671 55.000 9.73 0.00 40.44 4.26
2622 2903 0.390340 CCAAAGTAGCTGCGCTCAGA 60.390 55.000 8.15 0.00 42.95 3.27
2626 2907 0.820226 AGTAGCTGCGCTCAGATGAA 59.180 50.000 8.15 0.00 42.95 2.57
2685 2980 2.556287 GGCGACAACGGAAGCAAG 59.444 61.111 0.00 0.00 40.15 4.01
2724 3019 0.389426 GTGTACGACCGGCACAGAAT 60.389 55.000 0.00 0.00 33.70 2.40
2725 3020 0.319083 TGTACGACCGGCACAGAATT 59.681 50.000 0.00 0.00 0.00 2.17
2791 3116 5.503662 TTACCGAATACGAACAGCTGATA 57.496 39.130 23.35 7.44 42.66 2.15
2792 3117 3.966154 ACCGAATACGAACAGCTGATAG 58.034 45.455 23.35 12.07 42.66 2.08
2793 3118 2.726760 CCGAATACGAACAGCTGATAGC 59.273 50.000 23.35 5.29 41.08 2.97
2860 3185 3.087781 TGAAATGGTTGCATCCGATTGA 58.912 40.909 9.25 0.00 0.00 2.57
2920 3259 8.090831 CCGAATCAAGATTAGAATATGTCTCCA 58.909 37.037 4.74 0.00 37.84 3.86
2980 3330 0.823356 AACCATGGTGACTGGTGCAC 60.823 55.000 20.60 8.80 46.29 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 8.948631 TCATGAAACAATACAGTATCTCTTCC 57.051 34.615 0.00 0.00 0.00 3.46
16 17 5.585844 TGCGATCATCATGAAACAATACAGT 59.414 36.000 0.00 0.00 0.00 3.55
17 18 6.051646 TGCGATCATCATGAAACAATACAG 57.948 37.500 0.00 0.00 0.00 2.74
31 33 4.029418 CACGATGTTGTTTTTGCGATCATC 59.971 41.667 0.00 0.00 0.00 2.92
38 40 3.301771 GCAGTTCACGATGTTGTTTTTGC 60.302 43.478 0.00 0.00 0.00 3.68
102 104 2.136298 TGGTTTGTCCACAAGCAAGA 57.864 45.000 8.34 0.00 41.93 3.02
139 142 1.709115 GGAAGGTTAAGGTCCCCTTGT 59.291 52.381 5.78 0.00 44.44 3.16
173 176 3.280938 TTCTGGCCCAATCCCGTGG 62.281 63.158 0.00 0.00 38.51 4.94
175 178 0.912487 TAGTTCTGGCCCAATCCCGT 60.912 55.000 0.00 0.00 0.00 5.28
240 243 4.102524 TGACTCATTACACTGGAACTTGGT 59.897 41.667 0.00 0.00 0.00 3.67
245 248 4.273148 ACCTGACTCATTACACTGGAAC 57.727 45.455 0.00 0.00 0.00 3.62
340 343 6.260050 TCCCTTGAATATTCAGTTTATGCGAC 59.740 38.462 17.28 0.00 38.61 5.19
373 376 8.671987 AGAGGATTACATAGGCACAGTATTAT 57.328 34.615 0.00 0.00 0.00 1.28
398 403 8.679100 AGGCTTTATAATATTGTGCAACGTAAA 58.321 29.630 0.00 0.00 42.39 2.01
422 427 6.092670 CGTCATTAGCCATACAATATCCAAGG 59.907 42.308 0.00 0.00 0.00 3.61
445 450 4.024670 GGATATATTGCTAGGGGAGACGT 58.975 47.826 0.00 0.00 0.00 4.34
575 581 1.323271 TTTTTGCCCAAGTCACCGCA 61.323 50.000 0.00 0.00 0.00 5.69
592 598 9.206870 ACAACAAATATCTGCAATCGAATTTTT 57.793 25.926 0.00 0.00 0.00 1.94
594 600 7.814107 ACACAACAAATATCTGCAATCGAATTT 59.186 29.630 0.00 0.00 0.00 1.82
595 601 7.315142 ACACAACAAATATCTGCAATCGAATT 58.685 30.769 0.00 0.00 0.00 2.17
596 602 6.855836 ACACAACAAATATCTGCAATCGAAT 58.144 32.000 0.00 0.00 0.00 3.34
632 638 4.948004 TCAGTAGAGAATGACGGTATGTGT 59.052 41.667 0.00 0.00 0.00 3.72
697 703 9.220767 GGCTCCGAATCTAATATTCATACTTTT 57.779 33.333 0.00 0.00 0.00 2.27
698 704 7.545965 CGGCTCCGAATCTAATATTCATACTTT 59.454 37.037 1.35 0.00 42.83 2.66
699 705 7.036220 CGGCTCCGAATCTAATATTCATACTT 58.964 38.462 1.35 0.00 42.83 2.24
700 706 6.377429 TCGGCTCCGAATCTAATATTCATACT 59.623 38.462 8.76 0.00 46.01 2.12
701 707 6.561614 TCGGCTCCGAATCTAATATTCATAC 58.438 40.000 8.76 0.00 46.01 2.39
702 708 6.769134 TCGGCTCCGAATCTAATATTCATA 57.231 37.500 8.76 0.00 46.01 2.15
703 709 5.661056 TCGGCTCCGAATCTAATATTCAT 57.339 39.130 8.76 0.00 46.01 2.57
721 727 2.555123 TCAACCATTGAGCTTCGGC 58.445 52.632 0.00 0.00 42.17 5.54
729 735 9.311916 CAAAATTGTTCTTTACTCAACCATTGA 57.688 29.630 0.00 0.00 38.17 2.57
730 736 9.097257 ACAAAATTGTTCTTTACTCAACCATTG 57.903 29.630 0.00 0.00 38.47 2.82
737 743 9.730420 GCTCTTTACAAAATTGTTCTTTACTCA 57.270 29.630 3.85 0.00 42.35 3.41
738 744 9.181805 GGCTCTTTACAAAATTGTTCTTTACTC 57.818 33.333 3.85 0.00 42.35 2.59
739 745 7.860872 CGGCTCTTTACAAAATTGTTCTTTACT 59.139 33.333 3.85 0.00 42.35 2.24
740 746 7.114388 CCGGCTCTTTACAAAATTGTTCTTTAC 59.886 37.037 3.85 0.00 42.35 2.01
741 747 7.013464 TCCGGCTCTTTACAAAATTGTTCTTTA 59.987 33.333 3.85 0.00 42.35 1.85
742 748 5.983118 CCGGCTCTTTACAAAATTGTTCTTT 59.017 36.000 3.85 0.00 42.35 2.52
743 749 5.300792 TCCGGCTCTTTACAAAATTGTTCTT 59.699 36.000 3.85 0.00 42.35 2.52
744 750 4.825085 TCCGGCTCTTTACAAAATTGTTCT 59.175 37.500 3.85 0.00 42.35 3.01
745 751 5.048991 TCTCCGGCTCTTTACAAAATTGTTC 60.049 40.000 3.85 0.00 42.35 3.18
746 752 4.825085 TCTCCGGCTCTTTACAAAATTGTT 59.175 37.500 3.85 0.00 42.35 2.83
747 753 4.394729 TCTCCGGCTCTTTACAAAATTGT 58.605 39.130 0.00 4.01 44.86 2.71
748 754 4.695455 TCTCTCCGGCTCTTTACAAAATTG 59.305 41.667 0.00 0.00 0.00 2.32
749 755 4.906618 TCTCTCCGGCTCTTTACAAAATT 58.093 39.130 0.00 0.00 0.00 1.82
750 756 4.508662 CTCTCTCCGGCTCTTTACAAAAT 58.491 43.478 0.00 0.00 0.00 1.82
751 757 3.864921 GCTCTCTCCGGCTCTTTACAAAA 60.865 47.826 0.00 0.00 0.00 2.44
752 758 2.353803 GCTCTCTCCGGCTCTTTACAAA 60.354 50.000 0.00 0.00 0.00 2.83
753 759 1.204941 GCTCTCTCCGGCTCTTTACAA 59.795 52.381 0.00 0.00 0.00 2.41
754 760 0.818296 GCTCTCTCCGGCTCTTTACA 59.182 55.000 0.00 0.00 0.00 2.41
755 761 0.818296 TGCTCTCTCCGGCTCTTTAC 59.182 55.000 0.00 0.00 0.00 2.01
756 762 1.781786 ATGCTCTCTCCGGCTCTTTA 58.218 50.000 0.00 0.00 0.00 1.85
757 763 0.908198 AATGCTCTCTCCGGCTCTTT 59.092 50.000 0.00 0.00 0.00 2.52
758 764 1.781786 TAATGCTCTCTCCGGCTCTT 58.218 50.000 0.00 0.00 0.00 2.85
759 765 2.008242 ATAATGCTCTCTCCGGCTCT 57.992 50.000 0.00 0.00 0.00 4.09
760 766 2.829741 AATAATGCTCTCTCCGGCTC 57.170 50.000 0.00 0.00 0.00 4.70
761 767 3.209410 CAAAATAATGCTCTCTCCGGCT 58.791 45.455 0.00 0.00 0.00 5.52
762 768 2.287248 GCAAAATAATGCTCTCTCCGGC 60.287 50.000 0.00 0.00 43.06 6.13
763 769 2.945008 TGCAAAATAATGCTCTCTCCGG 59.055 45.455 0.00 0.00 46.54 5.14
768 774 7.033791 CCCATGATATGCAAAATAATGCTCTC 58.966 38.462 0.00 0.00 46.54 3.20
778 784 2.475339 AGCCCCCATGATATGCAAAA 57.525 45.000 0.00 0.00 0.00 2.44
782 788 5.016173 TGTTATTTAGCCCCCATGATATGC 58.984 41.667 0.00 0.00 0.00 3.14
787 793 4.805140 TCATGTTATTTAGCCCCCATGA 57.195 40.909 0.00 0.00 37.08 3.07
788 794 7.178983 ACATATTCATGTTATTTAGCCCCCATG 59.821 37.037 0.00 0.00 42.98 3.66
792 798 6.948309 AGGACATATTCATGTTATTTAGCCCC 59.052 38.462 0.00 0.00 45.58 5.80
794 800 8.299570 CCAAGGACATATTCATGTTATTTAGCC 58.700 37.037 0.00 0.00 45.58 3.93
797 803 9.130661 CCACCAAGGACATATTCATGTTATTTA 57.869 33.333 0.00 0.00 45.58 1.40
919 992 0.991920 TCCTTTTCCTGCCTAGTGGG 59.008 55.000 0.00 0.00 38.36 4.61
990 1063 2.227865 ACTGTTTTATTGGCGCGTCAAT 59.772 40.909 37.33 37.33 40.15 2.57
1016 1089 4.030452 GAGTTGCACGGTGCCAGC 62.030 66.667 28.57 18.17 44.23 4.85
1025 1098 1.845809 CGCAAGAGGTGGAGTTGCAC 61.846 60.000 7.04 0.00 45.62 4.57
1026 1099 1.597854 CGCAAGAGGTGGAGTTGCA 60.598 57.895 7.04 0.00 45.62 4.08
1027 1100 1.301716 TCGCAAGAGGTGGAGTTGC 60.302 57.895 0.00 0.00 45.01 4.17
1157 1233 1.541379 TCGATCCTCGTCTTGTTGGA 58.459 50.000 0.00 0.00 41.35 3.53
1164 1240 0.938713 GTGTCGATCGATCCTCGTCT 59.061 55.000 22.50 0.00 41.35 4.18
1233 1311 2.283101 TCCGCATGGCCAAAGCTT 60.283 55.556 25.34 0.00 39.73 3.74
1579 1657 2.126071 TTCTTCTTCGCCTCGCCG 60.126 61.111 0.00 0.00 0.00 6.46
1597 1678 1.805869 TCTTGCTGCTGCTCTTCTTC 58.194 50.000 17.00 0.00 40.48 2.87
1598 1679 2.152830 CTTCTTGCTGCTGCTCTTCTT 58.847 47.619 17.00 0.00 40.48 2.52
1599 1680 1.347050 TCTTCTTGCTGCTGCTCTTCT 59.653 47.619 17.00 0.00 40.48 2.85
1768 1852 1.903860 TGGTTCGTATGGTTGGTAGCT 59.096 47.619 0.00 0.00 0.00 3.32
1771 1855 2.237643 AGCATGGTTCGTATGGTTGGTA 59.762 45.455 0.00 0.00 32.80 3.25
1855 1949 5.869753 TCAAGCTCAAGAAGAATACTTGC 57.130 39.130 0.00 0.00 42.76 4.01
1991 2091 7.970384 ACACGTTAATTTACATCCATACACTG 58.030 34.615 0.00 0.00 0.00 3.66
2028 2128 8.407064 ACACAGTACATACTATGCTAGAGAAAC 58.593 37.037 0.00 0.00 34.18 2.78
2030 2130 7.773690 TCACACAGTACATACTATGCTAGAGAA 59.226 37.037 0.00 0.00 34.18 2.87
2031 2131 7.280356 TCACACAGTACATACTATGCTAGAGA 58.720 38.462 0.00 0.00 34.18 3.10
2032 2132 7.497925 TCACACAGTACATACTATGCTAGAG 57.502 40.000 0.00 0.00 34.18 2.43
2033 2133 7.875327 TTCACACAGTACATACTATGCTAGA 57.125 36.000 0.00 0.00 34.18 2.43
2047 2147 2.290260 CCCAGAAGCCATTCACACAGTA 60.290 50.000 0.00 0.00 37.94 2.74
2051 2151 2.134789 ATCCCAGAAGCCATTCACAC 57.865 50.000 0.00 0.00 37.94 3.82
2052 2152 2.041485 TGAATCCCAGAAGCCATTCACA 59.959 45.455 0.00 0.00 37.94 3.58
2053 2153 2.424956 GTGAATCCCAGAAGCCATTCAC 59.575 50.000 7.64 7.64 44.66 3.18
2054 2154 2.726821 GTGAATCCCAGAAGCCATTCA 58.273 47.619 0.00 0.00 37.94 2.57
2055 2155 1.672881 CGTGAATCCCAGAAGCCATTC 59.327 52.381 0.00 0.00 35.52 2.67
2056 2156 1.281867 TCGTGAATCCCAGAAGCCATT 59.718 47.619 0.00 0.00 0.00 3.16
2058 2158 0.690192 TTCGTGAATCCCAGAAGCCA 59.310 50.000 0.00 0.00 0.00 4.75
2060 2160 5.107453 CGTATAATTCGTGAATCCCAGAAGC 60.107 44.000 0.00 0.00 0.00 3.86
2061 2161 6.144080 GTCGTATAATTCGTGAATCCCAGAAG 59.856 42.308 0.00 0.00 0.00 2.85
2062 2162 5.981315 GTCGTATAATTCGTGAATCCCAGAA 59.019 40.000 0.00 0.00 0.00 3.02
2063 2163 5.068067 TGTCGTATAATTCGTGAATCCCAGA 59.932 40.000 0.00 0.00 0.00 3.86
2084 2189 5.685511 TGCGAGAAAATTAAGCAAAACTGTC 59.314 36.000 0.00 0.00 34.66 3.51
2086 2191 6.695292 ATGCGAGAAAATTAAGCAAAACTG 57.305 33.333 0.00 0.00 41.37 3.16
2089 2194 6.919721 AGGTATGCGAGAAAATTAAGCAAAA 58.080 32.000 0.00 0.00 41.37 2.44
2097 2202 5.010282 AGACCAAAGGTATGCGAGAAAATT 58.990 37.500 0.00 0.00 35.25 1.82
2099 2204 4.015872 AGACCAAAGGTATGCGAGAAAA 57.984 40.909 0.00 0.00 35.25 2.29
2105 2210 4.000988 AGTAACAAGACCAAAGGTATGCG 58.999 43.478 0.00 0.00 35.25 4.73
2152 2282 2.384899 TCTTCGTCTCATATGCGTCG 57.615 50.000 6.07 6.07 0.00 5.12
2153 2283 3.849145 GCTATCTTCGTCTCATATGCGTC 59.151 47.826 0.00 0.00 0.00 5.19
2154 2284 3.253432 TGCTATCTTCGTCTCATATGCGT 59.747 43.478 0.00 0.00 0.00 5.24
2155 2285 3.826466 TGCTATCTTCGTCTCATATGCG 58.174 45.455 0.00 0.00 0.00 4.73
2156 2286 5.453909 CGTATGCTATCTTCGTCTCATATGC 59.546 44.000 0.00 0.00 0.00 3.14
2157 2287 5.968261 CCGTATGCTATCTTCGTCTCATATG 59.032 44.000 0.00 0.00 0.00 1.78
2167 2301 1.540267 TCGCTCCCGTATGCTATCTTC 59.460 52.381 0.00 0.00 35.54 2.87
2174 2308 0.582005 GTTCAATCGCTCCCGTATGC 59.418 55.000 0.00 0.00 35.54 3.14
2183 2317 6.435430 TTTTGCATAGTATGTTCAATCGCT 57.565 33.333 11.73 0.00 0.00 4.93
2198 2332 7.537596 TTCTTTTCCTCCTGATTTTTGCATA 57.462 32.000 0.00 0.00 0.00 3.14
2199 2333 6.423776 TTCTTTTCCTCCTGATTTTTGCAT 57.576 33.333 0.00 0.00 0.00 3.96
2200 2334 5.867903 TTCTTTTCCTCCTGATTTTTGCA 57.132 34.783 0.00 0.00 0.00 4.08
2202 2336 7.054491 TCCTTTCTTTTCCTCCTGATTTTTG 57.946 36.000 0.00 0.00 0.00 2.44
2218 2355 4.853924 ACGATGCAAACATTCCTTTCTT 57.146 36.364 0.00 0.00 36.35 2.52
2242 2463 0.466124 TTGTGTGACCATCCGTGTGA 59.534 50.000 0.00 0.00 0.00 3.58
2246 2467 1.503818 GCGTTTGTGTGACCATCCGT 61.504 55.000 0.00 0.00 0.00 4.69
2248 2469 0.040425 GTGCGTTTGTGTGACCATCC 60.040 55.000 0.00 0.00 0.00 3.51
2282 2504 5.236911 GCAGAGAAGCAATCATAGAAGGAAG 59.763 44.000 0.00 0.00 0.00 3.46
2378 2603 2.835764 TGGATCACCGGCTACTAAAAGT 59.164 45.455 0.00 0.00 39.42 2.66
2385 2610 0.104304 AACGATGGATCACCGGCTAC 59.896 55.000 0.00 0.00 39.42 3.58
2386 2611 0.828022 AAACGATGGATCACCGGCTA 59.172 50.000 0.00 0.00 39.42 3.93
2387 2612 0.462047 GAAACGATGGATCACCGGCT 60.462 55.000 0.00 0.00 39.42 5.52
2433 2658 1.029681 GGCCAAGACGGAAACAAGTT 58.970 50.000 0.00 0.00 36.56 2.66
2475 2707 0.179034 GAGCTGCCTTACCCATCCAG 60.179 60.000 0.00 0.00 0.00 3.86
2522 2754 3.256879 TGTTTTTCATGGCGGCTATTCAA 59.743 39.130 11.43 0.00 0.00 2.69
2589 2870 5.661312 AGCTACTTTGGTCCATATGTACAGA 59.339 40.000 0.33 0.00 0.00 3.41
2590 2871 5.755375 CAGCTACTTTGGTCCATATGTACAG 59.245 44.000 0.33 0.00 0.00 2.74
2591 2872 5.670485 CAGCTACTTTGGTCCATATGTACA 58.330 41.667 0.00 0.00 0.00 2.90
2592 2873 4.511826 GCAGCTACTTTGGTCCATATGTAC 59.488 45.833 1.24 0.00 0.00 2.90
2593 2874 4.703897 GCAGCTACTTTGGTCCATATGTA 58.296 43.478 1.24 0.00 0.00 2.29
2615 2896 1.413767 CGTTCCCGTTCATCTGAGCG 61.414 60.000 9.16 9.16 46.11 5.03
2620 2901 0.171903 CGTACCGTTCCCGTTCATCT 59.828 55.000 0.00 0.00 0.00 2.90
2622 2903 0.388907 CACGTACCGTTCCCGTTCAT 60.389 55.000 0.00 0.00 38.32 2.57
2626 2907 4.362476 GCCACGTACCGTTCCCGT 62.362 66.667 0.00 0.00 38.32 5.28
2674 2969 1.073923 ACATTCCTCCTTGCTTCCGTT 59.926 47.619 0.00 0.00 0.00 4.44
2685 2980 3.044059 GCTGCACGCACATTCCTCC 62.044 63.158 0.00 0.00 38.92 4.30
2718 3013 6.019748 TCCTCTGACCTTCTCTTAATTCTGT 58.980 40.000 0.00 0.00 0.00 3.41
2724 3019 4.489737 TGGTTCCTCTGACCTTCTCTTAA 58.510 43.478 0.00 0.00 38.04 1.85
2725 3020 4.127918 TGGTTCCTCTGACCTTCTCTTA 57.872 45.455 0.00 0.00 38.04 2.10
2840 3165 3.699067 CTCAATCGGATGCAACCATTTC 58.301 45.455 14.03 0.00 0.00 2.17
2954 3303 1.072505 GTCACCATGGTTCCACCGT 59.927 57.895 16.84 0.00 42.58 4.83


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

AutoCloner maintained by Alex Coulton.