Multiple sequence alignment - TraesCS2A01G344100

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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 TraesCS2A01G344100 chr2A 100.000 3101 0 0 1 3101 580853008 580849908 0.000000e+00 5727.0
1 TraesCS2A01G344100 chr2D 91.884 2797 119 34 1 2750 413778236 413775501 0.000000e+00 3808.0
2 TraesCS2A01G344100 chr2D 84.451 328 19 7 2783 3099 413775515 413775209 8.410000e-76 294.0
3 TraesCS2A01G344100 chr2B 92.747 1627 61 16 1 1602 486986393 486984799 0.000000e+00 2298.0
4 TraesCS2A01G344100 chr2B 90.025 1193 86 20 1600 2772 486984584 486983405 0.000000e+00 1513.0
5 TraesCS2A01G344100 chr2B 86.190 210 10 5 2824 3023 486983174 486982974 3.130000e-50 209.0
6 TraesCS2A01G344100 chr2B 97.500 80 2 0 3019 3098 486977635 486977556 1.500000e-28 137.0
7 TraesCS2A01G344100 chr5A 89.157 83 9 0 19 101 433312029 433312111 1.520000e-18 104.0
8 TraesCS2A01G344100 chr3D 84.270 89 12 2 12 99 517891907 517891994 5.510000e-13 86.1
9 TraesCS2A01G344100 chr3A 84.091 88 14 0 12 99 653521808 653521895 5.510000e-13 86.1


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 TraesCS2A01G344100 chr2A 580849908 580853008 3100 True 5727 5727 100.0000 1 3101 1 chr2A.!!$R1 3100
1 TraesCS2A01G344100 chr2D 413775209 413778236 3027 True 2051 3808 88.1675 1 3099 2 chr2D.!!$R1 3098
2 TraesCS2A01G344100 chr2B 486982974 486986393 3419 True 1340 2298 89.6540 1 3023 3 chr2B.!!$R2 3022

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
617 636 0.316204 GACCGACCGAACCTCTCAAA 59.684 55.0 0.0 0.0 0.0 2.69 F
618 637 0.754472 ACCGACCGAACCTCTCAAAA 59.246 50.0 0.0 0.0 0.0 2.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1997 2267 0.247736 CTTGTCCTCCTTCTCCGGTG 59.752 60.0 0.00 0.0 0.00 4.94 R
2104 2374 0.462581 GTCCGGATTGCTCATGCTCA 60.463 55.0 7.81 0.0 40.48 4.26 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
227 228 1.904771 CATGCCCAACTACCTCGGA 59.095 57.895 0.00 0.00 0.00 4.55
252 253 0.934496 GGTCTAAACGCGCATGCATA 59.066 50.000 19.57 1.51 42.97 3.14
253 254 1.531149 GGTCTAAACGCGCATGCATAT 59.469 47.619 19.57 0.00 42.97 1.78
254 255 2.563976 GTCTAAACGCGCATGCATATG 58.436 47.619 19.57 6.21 42.97 1.78
406 422 5.377478 TCTTTTCTGGAGTTCTCTTTTCCC 58.623 41.667 0.00 0.00 0.00 3.97
432 448 9.773328 CTGGTAAATGATTAAGTGTATGTTGTG 57.227 33.333 0.00 0.00 0.00 3.33
433 449 9.508642 TGGTAAATGATTAAGTGTATGTTGTGA 57.491 29.630 0.00 0.00 0.00 3.58
434 450 9.988350 GGTAAATGATTAAGTGTATGTTGTGAG 57.012 33.333 0.00 0.00 0.00 3.51
437 453 9.897744 AAATGATTAAGTGTATGTTGTGAGTTG 57.102 29.630 0.00 0.00 0.00 3.16
438 454 8.621532 ATGATTAAGTGTATGTTGTGAGTTGT 57.378 30.769 0.00 0.00 0.00 3.32
452 468 7.066887 TGTTGTGAGTTGTGACATTGATTAACT 59.933 33.333 0.00 0.00 0.00 2.24
504 520 1.202110 GCGTCTGCGTTGCTACTACTA 60.202 52.381 0.00 0.00 40.81 1.82
505 521 2.438583 CGTCTGCGTTGCTACTACTAC 58.561 52.381 0.00 0.00 0.00 2.73
506 522 2.095532 CGTCTGCGTTGCTACTACTACT 59.904 50.000 0.00 0.00 0.00 2.57
510 526 3.021695 TGCGTTGCTACTACTACTCCAT 58.978 45.455 0.00 0.00 0.00 3.41
615 634 1.975407 GGACCGACCGAACCTCTCA 60.975 63.158 0.00 0.00 0.00 3.27
616 635 1.530013 GGACCGACCGAACCTCTCAA 61.530 60.000 0.00 0.00 0.00 3.02
617 636 0.316204 GACCGACCGAACCTCTCAAA 59.684 55.000 0.00 0.00 0.00 2.69
618 637 0.754472 ACCGACCGAACCTCTCAAAA 59.246 50.000 0.00 0.00 0.00 2.44
650 669 2.803956 ACGTACGCATTAGCTTGTGTTT 59.196 40.909 16.72 0.00 40.60 2.83
651 670 3.989167 ACGTACGCATTAGCTTGTGTTTA 59.011 39.130 16.72 0.00 40.60 2.01
652 671 4.448395 ACGTACGCATTAGCTTGTGTTTAA 59.552 37.500 16.72 0.00 40.60 1.52
653 672 5.013236 CGTACGCATTAGCTTGTGTTTAAG 58.987 41.667 9.73 0.00 40.60 1.85
654 673 5.389098 CGTACGCATTAGCTTGTGTTTAAGT 60.389 40.000 9.73 1.89 40.60 2.24
655 674 5.432885 ACGCATTAGCTTGTGTTTAAGTT 57.567 34.783 0.00 0.00 37.01 2.66
810 829 5.051816 ACAAACTGCAATGAACTGGAATTG 58.948 37.500 1.23 0.00 36.95 2.32
819 838 6.017275 GCAATGAACTGGAATTGATAGAGGAG 60.017 42.308 0.00 0.00 36.13 3.69
825 844 3.900601 TGGAATTGATAGAGGAGAGAGCC 59.099 47.826 0.00 0.00 0.00 4.70
935 954 2.774351 CCCATCCTCCCCACCCTC 60.774 72.222 0.00 0.00 0.00 4.30
1013 1043 1.047002 AAGAGGATGGGCTCGATCAG 58.953 55.000 0.00 0.00 0.00 2.90
1027 1057 1.797211 GATCAGGAGGCGGGAGTACG 61.797 65.000 0.00 0.00 0.00 3.67
1035 1065 4.678396 CGGGAGTACGCTTACGAC 57.322 61.111 0.00 0.00 43.93 4.34
1036 1066 1.297158 CGGGAGTACGCTTACGACG 60.297 63.158 0.00 0.00 43.93 5.12
1037 1067 1.584742 GGGAGTACGCTTACGACGC 60.585 63.158 0.00 0.00 43.93 5.19
1164 1200 5.001232 TGCTCAATTTCAGTACCCACTTAC 58.999 41.667 0.00 0.00 30.46 2.34
1183 1219 6.037062 CACTTACATATGGTTCTTGAATCGCA 59.963 38.462 7.80 0.00 0.00 5.10
1284 1320 8.397575 TGCATTTTTGTGTTAGGATTGTAGTA 57.602 30.769 0.00 0.00 0.00 1.82
1328 1364 5.769662 GCCATAGGAAATCATGATGGTTACA 59.230 40.000 9.46 0.00 39.45 2.41
1367 1414 4.853924 ACAGTTGGTTTCATGGATTCAC 57.146 40.909 0.00 0.00 0.00 3.18
1391 1438 5.070981 CACTTGGATCCCTTGCTAGATCTTA 59.929 44.000 9.90 0.00 39.12 2.10
1456 1504 8.850007 TCCAGTCTAGCACTAATACATAGTAG 57.150 38.462 0.00 0.00 43.12 2.57
1461 1509 5.730296 AGCACTAATACATAGTAGGCCTG 57.270 43.478 17.99 0.25 43.12 4.85
1523 1571 9.535878 GTAAGATCTTGAGAAATTTAGATCCGT 57.464 33.333 18.47 12.71 42.44 4.69
1527 1575 8.600449 ATCTTGAGAAATTTAGATCCGTGATC 57.400 34.615 5.94 5.94 39.17 2.92
1638 1903 4.755411 AGATGCAAAAGCCAGATGATTTG 58.245 39.130 0.00 0.00 36.19 2.32
1670 1937 7.285401 CACATATTTGGGGAGCAACTTACTTAT 59.715 37.037 0.00 0.00 0.00 1.73
1737 2004 1.087501 GCGGTCTCAATTTCCTGGTC 58.912 55.000 0.00 0.00 0.00 4.02
1853 2123 2.945456 TCACCGAGGTAGTAGCATCAT 58.055 47.619 1.58 0.00 0.00 2.45
1899 2169 9.699410 TTGATTCCTCTCATGTTATTTTACCAT 57.301 29.630 0.00 0.00 0.00 3.55
1909 2179 9.778741 TCATGTTATTTTACCATCACTCTATCC 57.221 33.333 0.00 0.00 0.00 2.59
1920 2190 3.338249 TCACTCTATCCAAAGTGCAAGC 58.662 45.455 0.00 0.00 42.10 4.01
2008 2278 2.046892 CACTGGCACCGGAGAAGG 60.047 66.667 9.46 0.00 37.30 3.46
2017 2287 0.905337 ACCGGAGAAGGAGGACAAGG 60.905 60.000 9.46 0.00 34.73 3.61
2028 2298 4.717313 GACAAGGCCCCGACCACC 62.717 72.222 0.00 0.00 0.00 4.61
2047 2317 2.594303 CAACGCCTCCAACAGCCA 60.594 61.111 0.00 0.00 0.00 4.75
2055 2325 2.990967 CCAACAGCCACCGCCAAT 60.991 61.111 0.00 0.00 34.57 3.16
2104 2374 0.674895 GCCATCAGGAAAGTGAGCGT 60.675 55.000 0.00 0.00 36.89 5.07
2122 2392 0.462581 GTGAGCATGAGCAATCCGGA 60.463 55.000 6.61 6.61 45.49 5.14
2125 2395 2.537560 GCATGAGCAATCCGGACGG 61.538 63.158 6.12 3.96 41.58 4.79
2179 2449 4.101448 GCGTCCTGCCCATCTGGT 62.101 66.667 0.00 0.00 37.76 4.00
2216 2486 5.912396 TGAATAATCGTGTGTTTGTTTGCTC 59.088 36.000 0.00 0.00 0.00 4.26
2232 2510 3.520290 TGCTCGTATGTGAACCTAAGG 57.480 47.619 0.00 0.00 0.00 2.69
2234 2512 2.429610 GCTCGTATGTGAACCTAAGGGA 59.570 50.000 0.00 0.00 36.25 4.20
2259 2538 2.695666 CTGTATTCCTCCTCCGTGATGT 59.304 50.000 0.00 0.00 0.00 3.06
2263 2542 1.141881 CCTCCTCCGTGATGTTCCG 59.858 63.158 0.00 0.00 0.00 4.30
2294 2573 6.375736 TGAACCATCCATTTCGTTTAATGCTA 59.624 34.615 0.00 0.00 34.81 3.49
2304 2583 5.146482 TCGTTTAATGCTATGGCGTTTAC 57.854 39.130 14.14 11.31 44.28 2.01
2327 2606 0.450482 GTTCGTTCCAATGCGTGTCG 60.450 55.000 0.00 0.00 0.00 4.35
2358 2638 2.299993 TGCATCTCTCATGTTCCGAC 57.700 50.000 0.00 0.00 0.00 4.79
2388 2669 3.552890 CGGTCTATTCATCGAATGCCTGA 60.553 47.826 0.00 0.00 33.95 3.86
2405 2686 6.757897 TGCCTGAATATTTCACGAGAAAAT 57.242 33.333 12.02 5.99 46.06 1.82
2409 2690 7.857885 GCCTGAATATTTCACGAGAAAATTAGG 59.142 37.037 12.02 15.32 46.06 2.69
2504 2790 7.394872 CAAAGAACTAGAAATCACGATAGCAC 58.605 38.462 0.00 0.00 42.67 4.40
2531 2817 4.457810 CTCACGTTGCACATAACTGAAAG 58.542 43.478 0.00 0.00 42.29 2.62
2554 2840 2.493675 GCAGCACCATCTCCGATATCTA 59.506 50.000 0.34 0.00 0.00 1.98
2555 2841 3.674682 GCAGCACCATCTCCGATATCTAC 60.675 52.174 0.34 0.00 0.00 2.59
2556 2842 3.761218 CAGCACCATCTCCGATATCTACT 59.239 47.826 0.34 0.00 0.00 2.57
2557 2843 4.944317 CAGCACCATCTCCGATATCTACTA 59.056 45.833 0.34 0.00 0.00 1.82
2558 2844 4.944930 AGCACCATCTCCGATATCTACTAC 59.055 45.833 0.34 0.00 0.00 2.73
2559 2845 4.944930 GCACCATCTCCGATATCTACTACT 59.055 45.833 0.34 0.00 0.00 2.57
2605 2895 0.514691 CCTCTTGCGTGTTCTTGCTC 59.485 55.000 0.00 0.00 0.00 4.26
2607 2897 1.194098 CTCTTGCGTGTTCTTGCTCAG 59.806 52.381 0.00 0.00 0.00 3.35
2649 2939 3.679980 CACTGGTGACCGAGATTAACAAG 59.320 47.826 7.84 0.00 0.00 3.16
2660 2950 8.438676 ACCGAGATTAACAAGAAATCCATAAG 57.561 34.615 0.00 0.00 34.50 1.73
2671 2961 8.637986 ACAAGAAATCCATAAGTTGTTAAAGCA 58.362 29.630 0.00 0.00 0.00 3.91
2688 2978 2.268298 AGCAATCGACGTTATGTCCAC 58.732 47.619 0.00 0.00 45.23 4.02
2754 3044 1.127951 CAACCGATGTTGTAGCCGTTC 59.872 52.381 0.00 0.00 45.51 3.95
2762 3052 4.545823 TGTTGTAGCCGTTCTCAAAAAG 57.454 40.909 0.00 0.00 0.00 2.27
2794 3084 6.885735 AAGAAAAGAAAAACCGATGTTGTG 57.114 33.333 0.00 0.00 34.13 3.33
2795 3085 5.348164 AGAAAAGAAAAACCGATGTTGTGG 58.652 37.500 0.00 0.00 34.13 4.17
2796 3086 2.793278 AGAAAAACCGATGTTGTGGC 57.207 45.000 0.00 0.00 34.13 5.01
2829 3119 0.170339 GCCATGCGTGTTAGGGTTTC 59.830 55.000 4.96 0.00 0.00 2.78
2958 3449 2.561373 CGCTTTCGGTTCTTGGCC 59.439 61.111 0.00 0.00 0.00 5.36
3005 3496 2.289195 CCAAACTTGTGATGGCAATGCT 60.289 45.455 4.82 0.00 0.00 3.79
3016 3507 2.476051 CAATGCTGGTCGTCGCAC 59.524 61.111 0.00 0.00 39.21 5.34
3063 3554 2.004808 TAGCGTGGCGTGATCCTCAG 62.005 60.000 0.00 0.00 0.00 3.35
3080 3571 5.680619 TCCTCAGAGTCAACTTTTTGCTTA 58.319 37.500 0.00 0.00 32.17 3.09
3081 3572 5.527582 TCCTCAGAGTCAACTTTTTGCTTAC 59.472 40.000 0.00 0.00 32.17 2.34
3093 3584 1.036707 TTGCTTACACAAGTTGGGCC 58.963 50.000 4.63 0.00 34.00 5.80
3099 3590 2.124693 CACAAGTTGGGCCCGTTGT 61.125 57.895 24.46 24.46 33.37 3.32
3100 3591 1.380650 ACAAGTTGGGCCCGTTGTT 60.381 52.632 24.46 11.07 28.62 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 1.592590 CGTAGTAGAGCGTCTTGAGCG 60.593 57.143 0.00 0.00 40.04 5.03
227 228 1.803334 TGCGCGTTTAGACCTTGAAT 58.197 45.000 8.43 0.00 0.00 2.57
406 422 9.773328 CACAACATACACTTAATCATTTACCAG 57.227 33.333 0.00 0.00 0.00 4.00
432 448 6.801539 TCCAGTTAATCAATGTCACAACTC 57.198 37.500 0.00 0.00 0.00 3.01
433 449 7.581213 TTTCCAGTTAATCAATGTCACAACT 57.419 32.000 0.00 0.00 0.00 3.16
434 450 8.702438 CATTTTCCAGTTAATCAATGTCACAAC 58.298 33.333 0.00 0.00 0.00 3.32
435 451 8.420222 ACATTTTCCAGTTAATCAATGTCACAA 58.580 29.630 0.00 0.00 30.75 3.33
436 452 7.950512 ACATTTTCCAGTTAATCAATGTCACA 58.049 30.769 0.00 0.00 30.75 3.58
452 468 5.302568 GGGCATCTGAATGATACATTTTCCA 59.697 40.000 0.00 0.00 34.61 3.53
504 520 9.918630 GCAAATATGAGCATAAAATAATGGAGT 57.081 29.630 0.00 0.00 0.00 3.85
506 522 9.917129 CAGCAAATATGAGCATAAAATAATGGA 57.083 29.630 2.90 0.00 0.00 3.41
510 526 8.196103 TGTGCAGCAAATATGAGCATAAAATAA 58.804 29.630 0.00 0.00 39.94 1.40
525 541 3.825014 AGAAGTTGAGATGTGCAGCAAAT 59.175 39.130 0.00 0.00 0.00 2.32
584 600 2.579738 GGTCCCTTCTGTCTCGGC 59.420 66.667 0.00 0.00 0.00 5.54
616 635 6.431198 AATGCGTACGTGGAGATTATTTTT 57.569 33.333 17.90 0.00 0.00 1.94
617 636 6.292703 GCTAATGCGTACGTGGAGATTATTTT 60.293 38.462 17.90 0.00 0.00 1.82
618 637 5.176958 GCTAATGCGTACGTGGAGATTATTT 59.823 40.000 17.90 0.00 0.00 1.40
650 669 4.530875 TGTTTTGACCCGGGTTAAACTTA 58.469 39.130 37.89 26.81 34.19 2.24
651 670 3.363627 TGTTTTGACCCGGGTTAAACTT 58.636 40.909 37.89 18.60 34.19 2.66
652 671 3.015675 TGTTTTGACCCGGGTTAAACT 57.984 42.857 37.89 19.22 34.19 2.66
653 672 3.797451 TTGTTTTGACCCGGGTTAAAC 57.203 42.857 35.37 35.37 34.19 2.01
654 673 3.768215 AGTTTGTTTTGACCCGGGTTAAA 59.232 39.130 33.26 33.26 32.92 1.52
655 674 3.363627 AGTTTGTTTTGACCCGGGTTAA 58.636 40.909 30.89 28.20 0.00 2.01
810 829 1.582610 CGGCGGCTCTCTCCTCTATC 61.583 65.000 7.61 0.00 0.00 2.08
843 862 3.653344 GTGCATAGTGAGAAGTGACACA 58.347 45.455 8.59 0.00 39.18 3.72
1019 1049 1.584742 GCGTCGTAAGCGTACTCCC 60.585 63.158 8.19 0.00 38.71 4.30
1027 1057 3.236137 GTCGTCGGCGTCGTAAGC 61.236 66.667 24.03 10.81 39.49 3.09
1029 1059 3.353114 CTCGTCGTCGGCGTCGTAA 62.353 63.158 26.20 9.40 46.29 3.18
1033 1063 4.808238 GTCCTCGTCGTCGGCGTC 62.808 72.222 19.81 1.92 39.49 5.19
1036 1066 2.862347 AAATCGTCCTCGTCGTCGGC 62.862 60.000 1.55 0.00 38.33 5.54
1037 1067 0.860618 GAAATCGTCCTCGTCGTCGG 60.861 60.000 1.55 0.00 38.33 4.79
1164 1200 4.705492 CGATGCGATTCAAGAACCATATG 58.295 43.478 0.00 0.00 0.00 1.78
1256 1292 6.815089 ACAATCCTAACACAAAAATGCAGAA 58.185 32.000 0.00 0.00 0.00 3.02
1367 1414 3.390639 AGATCTAGCAAGGGATCCAAGTG 59.609 47.826 15.23 9.06 39.12 3.16
1391 1438 7.154656 TCTATGAGCATACGAGCAAAATACAT 58.845 34.615 0.00 0.00 36.85 2.29
1456 1504 1.484038 TTTTGCCCATACATCAGGCC 58.516 50.000 0.00 0.00 46.55 5.19
1461 1509 5.700832 TGTCGATCTATTTTGCCCATACATC 59.299 40.000 0.00 0.00 0.00 3.06
1523 1571 9.803507 ATATATTCAGATTGAAGCTTTGGATCA 57.196 29.630 0.00 0.00 40.05 2.92
1638 1903 3.142174 GCTCCCCAAATATGTGAGTAGC 58.858 50.000 0.00 0.00 0.00 3.58
1640 1905 4.227300 AGTTGCTCCCCAAATATGTGAGTA 59.773 41.667 0.00 0.00 34.68 2.59
1853 2123 9.541143 GAATCAAAGGTAAAACAATCAAAGGAA 57.459 29.630 0.00 0.00 0.00 3.36
1899 2169 3.244526 TGCTTGCACTTTGGATAGAGTGA 60.245 43.478 7.61 0.00 44.65 3.41
1909 2179 4.032672 TGAACGATTTTTGCTTGCACTTTG 59.967 37.500 0.00 0.00 0.00 2.77
1911 2181 3.551485 GTGAACGATTTTTGCTTGCACTT 59.449 39.130 0.00 0.00 0.00 3.16
1920 2190 7.995998 CCGAACTTAATTTGTGAACGATTTTTG 59.004 33.333 0.00 0.00 0.00 2.44
1993 2263 2.581354 CTCCTTCTCCGGTGCCAG 59.419 66.667 0.00 0.00 0.00 4.85
1997 2267 0.247736 CTTGTCCTCCTTCTCCGGTG 59.752 60.000 0.00 0.00 0.00 4.94
2008 2278 4.097361 GGTCGGGGCCTTGTCCTC 62.097 72.222 0.84 0.00 0.00 3.71
2028 2298 4.389576 GCTGTTGGAGGCGTTGCG 62.390 66.667 0.00 0.00 0.00 4.85
2041 2311 2.974692 TTCACATTGGCGGTGGCTGT 62.975 55.000 4.32 0.00 39.81 4.40
2047 2317 1.675641 GCTCCTTCACATTGGCGGT 60.676 57.895 0.00 0.00 0.00 5.68
2055 2325 2.853542 TGGGGCTGCTCCTTCACA 60.854 61.111 21.13 0.00 34.39 3.58
2094 2364 1.436600 CTCATGCTCACGCTCACTTT 58.563 50.000 0.00 0.00 36.97 2.66
2104 2374 0.462581 GTCCGGATTGCTCATGCTCA 60.463 55.000 7.81 0.00 40.48 4.26
2122 2392 5.751990 CAGTTACTACAACTTCTTGAACCGT 59.248 40.000 0.00 0.00 0.00 4.83
2125 2395 5.049612 GGGCAGTTACTACAACTTCTTGAAC 60.050 44.000 0.00 0.00 0.00 3.18
2155 2425 0.686441 ATGGGCAGGACGCTACTACA 60.686 55.000 0.00 0.00 41.91 2.74
2202 2472 3.623510 TCACATACGAGCAAACAAACACA 59.376 39.130 0.00 0.00 0.00 3.72
2216 2486 3.181478 GGTCTCCCTTAGGTTCACATACG 60.181 52.174 0.00 0.00 0.00 3.06
2232 2510 2.321719 GGAGGAGGAATACAGGTCTCC 58.678 57.143 0.00 0.00 44.46 3.71
2234 2512 1.288335 ACGGAGGAGGAATACAGGTCT 59.712 52.381 0.00 0.00 0.00 3.85
2259 2538 0.746563 GGATGGTTCATTCGGCGGAA 60.747 55.000 7.21 9.32 36.41 4.30
2263 2542 2.541588 CGAAATGGATGGTTCATTCGGC 60.542 50.000 0.00 0.00 34.15 5.54
2294 2573 3.304190 GGAACGAACAAAGTAAACGCCAT 60.304 43.478 0.00 0.00 0.00 4.40
2304 2583 2.043411 CACGCATTGGAACGAACAAAG 58.957 47.619 0.00 0.00 0.00 2.77
2358 2638 1.151777 ATGAATAGACCGCGCCAACG 61.152 55.000 0.00 0.00 44.07 4.10
2405 2686 7.495901 TGTGAAATCTTCAACAAATTGCCTAA 58.504 30.769 0.00 0.00 42.15 2.69
2409 2690 7.588488 CCAAATGTGAAATCTTCAACAAATTGC 59.412 33.333 0.00 0.00 42.15 3.56
2504 2790 1.067693 TATGTGCAACGTGAGCGAAG 58.932 50.000 8.48 0.00 42.39 3.79
2557 2843 9.008965 TGTGTGTGTTTTGCATTAAGATATAGT 57.991 29.630 0.00 0.00 0.00 2.12
2558 2844 9.838975 TTGTGTGTGTTTTGCATTAAGATATAG 57.161 29.630 0.00 0.00 0.00 1.31
2559 2845 9.619316 GTTGTGTGTGTTTTGCATTAAGATATA 57.381 29.630 0.00 0.00 0.00 0.86
2576 2866 1.095228 ACGCAAGAGGGTTGTGTGTG 61.095 55.000 3.26 0.00 41.07 3.82
2605 2895 1.806542 ACGTTGCTAAGCATGAACCTG 59.193 47.619 0.00 0.00 38.76 4.00
2607 2897 1.729149 GCACGTTGCTAAGCATGAACC 60.729 52.381 0.00 0.00 40.96 3.62
2649 2939 8.798153 CGATTGCTTTAACAACTTATGGATTTC 58.202 33.333 0.00 0.00 31.03 2.17
2660 2950 6.075280 ACATAACGTCGATTGCTTTAACAAC 58.925 36.000 0.00 0.00 31.03 3.32
2671 2961 5.597806 ACATATGTGGACATAACGTCGATT 58.402 37.500 7.78 0.00 46.42 3.34
2722 3012 1.444119 ATCGGTTGCGTGCACTGTTT 61.444 50.000 16.19 0.00 0.00 2.83
2724 3014 2.280797 ATCGGTTGCGTGCACTGT 60.281 55.556 16.19 0.00 0.00 3.55
2771 3061 5.810074 CCACAACATCGGTTTTTCTTTTCTT 59.190 36.000 0.00 0.00 34.21 2.52
2772 3062 5.348164 CCACAACATCGGTTTTTCTTTTCT 58.652 37.500 0.00 0.00 34.21 2.52
2773 3063 4.026062 GCCACAACATCGGTTTTTCTTTTC 60.026 41.667 0.00 0.00 34.21 2.29
2774 3064 3.868661 GCCACAACATCGGTTTTTCTTTT 59.131 39.130 0.00 0.00 34.21 2.27
2775 3065 3.453424 GCCACAACATCGGTTTTTCTTT 58.547 40.909 0.00 0.00 34.21 2.52
2776 3066 2.223947 GGCCACAACATCGGTTTTTCTT 60.224 45.455 0.00 0.00 34.21 2.52
2777 3067 1.339929 GGCCACAACATCGGTTTTTCT 59.660 47.619 0.00 0.00 34.21 2.52
2778 3068 1.067821 TGGCCACAACATCGGTTTTTC 59.932 47.619 0.00 0.00 34.21 2.29
2779 3069 1.115467 TGGCCACAACATCGGTTTTT 58.885 45.000 0.00 0.00 34.21 1.94
2780 3070 1.000731 CATGGCCACAACATCGGTTTT 59.999 47.619 8.16 0.00 34.21 2.43
2781 3071 0.602562 CATGGCCACAACATCGGTTT 59.397 50.000 8.16 0.00 34.21 3.27
2782 3072 1.250154 CCATGGCCACAACATCGGTT 61.250 55.000 8.16 0.00 37.87 4.44
2783 3073 1.678635 CCATGGCCACAACATCGGT 60.679 57.895 8.16 0.00 0.00 4.69
2811 3101 0.446222 CGAAACCCTAACACGCATGG 59.554 55.000 0.00 0.00 0.00 3.66
2822 3112 2.197324 TGGCAAAGGCGAAACCCT 59.803 55.556 0.00 0.00 42.47 4.34
2829 3119 3.365265 GGTCAGGTGGCAAAGGCG 61.365 66.667 0.00 0.00 42.47 5.52
2928 3418 0.457337 GAAAGCGCAAGGAAGCCATG 60.457 55.000 11.47 0.00 38.28 3.66
2930 3420 2.616330 CGAAAGCGCAAGGAAGCCA 61.616 57.895 11.47 0.00 38.28 4.75
3005 3496 4.337060 CACCGAGTGCGACGACCA 62.337 66.667 0.00 0.00 40.82 4.02
3050 3541 0.532573 TTGACTCTGAGGATCACGCC 59.467 55.000 9.85 0.00 42.56 5.68
3063 3554 6.322491 ACTTGTGTAAGCAAAAAGTTGACTC 58.678 36.000 0.00 0.00 37.43 3.36
3080 3571 2.124693 CAACGGGCCCAACTTGTGT 61.125 57.895 24.92 6.48 0.00 3.72
3081 3572 1.671901 AACAACGGGCCCAACTTGTG 61.672 55.000 24.92 11.92 0.00 3.33


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

AutoCloner maintained by Alex Coulton.