Multiple sequence alignment - TraesCS7D01G246800

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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 TraesCS7D01G246800 chr7D 100.000 2800 0 0 1491 4290 216081840 216079041 0.000000e+00 5171
1 TraesCS7D01G246800 chr7D 100.000 1221 0 0 1 1221 216083330 216082110 0.000000e+00 2255
2 TraesCS7D01G246800 chr7D 91.954 87 4 2 2519 2602 234073673 234073759 7.540000e-23 119
3 TraesCS7D01G246800 chr7B 93.982 1695 62 12 2593 4273 184300726 184302394 0.000000e+00 2529
4 TraesCS7D01G246800 chr7B 96.405 1224 33 5 1 1221 184298367 184299582 0.000000e+00 2006
5 TraesCS7D01G246800 chr7B 97.108 657 12 5 1870 2521 184300074 184300728 0.000000e+00 1101
6 TraesCS7D01G246800 chr7B 93.789 483 24 4 1491 1969 184299594 184300074 0.000000e+00 721
7 TraesCS7D01G246800 chr7A 97.061 1225 25 5 1 1221 229144256 229143039 0.000000e+00 2052
8 TraesCS7D01G246800 chr7A 94.605 1316 38 13 2593 3901 229141685 229140396 0.000000e+00 2006
9 TraesCS7D01G246800 chr7A 95.344 902 34 5 1491 2386 229143028 229142129 0.000000e+00 1426
10 TraesCS7D01G246800 chr7A 94.408 304 15 2 3898 4201 229138995 229138694 2.340000e-127 466
11 TraesCS7D01G246800 chr7A 92.361 144 7 1 2382 2521 229141826 229141683 7.270000e-48 202
12 TraesCS7D01G246800 chr7A 96.104 77 2 1 4198 4274 229138534 229138459 1.620000e-24 124
13 TraesCS7D01G246800 chr5B 92.347 196 15 0 988 1183 450842129 450841934 3.270000e-71 279
14 TraesCS7D01G246800 chr5D 93.122 189 13 0 995 1183 377534597 377534409 1.170000e-70 278
15 TraesCS7D01G246800 chr5A 93.122 189 13 0 995 1183 478322171 478321983 1.170000e-70 278
16 TraesCS7D01G246800 chr3D 96.296 81 2 1 2520 2600 169888215 169888136 9.680000e-27 132
17 TraesCS7D01G246800 chr4D 93.750 80 3 1 2521 2598 478990757 478990678 7.540000e-23 119
18 TraesCS7D01G246800 chr4D 93.671 79 3 2 2518 2594 478990679 478990757 2.710000e-22 117
19 TraesCS7D01G246800 chr6B 93.506 77 5 0 2519 2595 149447177 149447253 9.750000e-22 115
20 TraesCS7D01G246800 chr6B 93.506 77 5 0 2520 2596 693939386 693939310 9.750000e-22 115
21 TraesCS7D01G246800 chr6B 86.139 101 8 3 2515 2610 135505593 135505692 2.110000e-18 104
22 TraesCS7D01G246800 chr6D 93.590 78 2 1 2519 2596 469492338 469492412 3.510000e-21 113
23 TraesCS7D01G246800 chr6D 93.590 78 2 1 2519 2596 469511146 469511220 3.510000e-21 113


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 TraesCS7D01G246800 chr7D 216079041 216083330 4289 True 3713.00 5171 100.0000 1 4290 2 chr7D.!!$R1 4289
1 TraesCS7D01G246800 chr7B 184298367 184302394 4027 False 1589.25 2529 95.3210 1 4273 4 chr7B.!!$F1 4272
2 TraesCS7D01G246800 chr7A 229138459 229144256 5797 True 1046.00 2052 94.9805 1 4274 6 chr7A.!!$R1 4273

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
838 846 0.749091 CATCCGCCTCATCCAAGCAA 60.749 55.000 0.00 0.0 0.0 3.91 F
899 907 0.810426 GAATTCCGGCGTCCTCTTCC 60.810 60.000 6.01 0.0 0.0 3.46 F
1044 1052 1.124780 TGGACAGGTTCGTGAAGGAA 58.875 50.000 0.00 0.0 0.0 3.36 F
2796 3223 1.338105 CGCACCAGAAGATTGTCTCCA 60.338 52.381 0.00 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1757 1769 0.034477 CCCCTGACGCCCTTGTAAAT 60.034 55.000 0.0 0.0 0.0 1.40 R
2242 2355 0.544357 TCCCACTCCCAGTACACAGG 60.544 60.000 0.0 0.0 0.0 4.00 R
2843 3270 3.607741 TCACCACCACGTTTCAACTTTA 58.392 40.909 0.0 0.0 0.0 1.85 R
3901 4357 2.114411 GGCGGTCACTGGGGAAAA 59.886 61.111 0.0 0.0 0.0 2.29 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
216 217 3.194968 GGAACTGAACCGACTAATCAGGA 59.805 47.826 6.92 0.00 43.79 3.86
317 318 6.414408 CTGAAATATCACAGCGAGAAACTT 57.586 37.500 0.00 0.00 0.00 2.66
455 456 4.508047 GGCAAGGTGATCATAATCAGGGAT 60.508 45.833 0.00 0.00 42.53 3.85
518 519 3.130693 GTGGCGACTATTGGTAGAGAAGT 59.869 47.826 0.00 0.00 0.00 3.01
521 522 5.419788 TGGCGACTATTGGTAGAGAAGTTAA 59.580 40.000 0.00 0.00 0.00 2.01
522 523 5.747675 GGCGACTATTGGTAGAGAAGTTAAC 59.252 44.000 0.00 0.00 0.00 2.01
523 524 6.327934 GCGACTATTGGTAGAGAAGTTAACA 58.672 40.000 8.61 0.00 0.00 2.41
524 525 6.253083 GCGACTATTGGTAGAGAAGTTAACAC 59.747 42.308 8.61 1.57 0.00 3.32
525 526 7.536855 CGACTATTGGTAGAGAAGTTAACACT 58.463 38.462 8.61 6.70 33.11 3.55
526 527 7.485277 CGACTATTGGTAGAGAAGTTAACACTG 59.515 40.741 8.61 0.00 31.60 3.66
606 607 3.648339 TTTCTTTGCAACTCAGATGCC 57.352 42.857 4.19 0.00 43.16 4.40
721 723 8.840321 CAGTCAAAAGAACAAAGATAAAGGAGA 58.160 33.333 0.00 0.00 0.00 3.71
795 801 1.109323 GCGGCCATAAAGAAGCCCAT 61.109 55.000 2.24 0.00 44.13 4.00
838 846 0.749091 CATCCGCCTCATCCAAGCAA 60.749 55.000 0.00 0.00 0.00 3.91
858 866 1.748493 AGCAAAGCCGAAACAGAACAA 59.252 42.857 0.00 0.00 0.00 2.83
876 884 1.792118 AAGGAAAGAAACGCGCCCAC 61.792 55.000 5.73 0.00 0.00 4.61
899 907 0.810426 GAATTCCGGCGTCCTCTTCC 60.810 60.000 6.01 0.00 0.00 3.46
1044 1052 1.124780 TGGACAGGTTCGTGAAGGAA 58.875 50.000 0.00 0.00 0.00 3.36
1170 1178 2.038007 TGGAAGGCCGAGCTCTCT 59.962 61.111 12.85 3.75 36.79 3.10
1519 1528 2.741985 CGCCACCGTGATCAGCAA 60.742 61.111 0.00 0.00 0.00 3.91
1521 1530 1.647545 CGCCACCGTGATCAGCAATT 61.648 55.000 0.00 0.00 0.00 2.32
1558 1567 2.146342 CGATCGAGAATGGGGGAAATG 58.854 52.381 10.26 0.00 0.00 2.32
1703 1715 5.173774 TGTCTTTCAGTTTCTTGTGATGC 57.826 39.130 0.00 0.00 0.00 3.91
1718 1730 3.499537 TGTGATGCTAAACTGCAGAAGTG 59.500 43.478 23.35 8.84 46.71 3.16
1749 1761 4.878397 AGAGATTATTGCTTGCTTTACGCT 59.122 37.500 0.00 0.00 40.11 5.07
1757 1769 5.001237 TGCTTGCTTTACGCTGTAGTATA 57.999 39.130 0.00 0.00 40.11 1.47
1758 1770 5.597806 TGCTTGCTTTACGCTGTAGTATAT 58.402 37.500 0.00 0.00 40.11 0.86
1759 1771 6.046593 TGCTTGCTTTACGCTGTAGTATATT 58.953 36.000 0.00 0.00 40.11 1.28
1760 1772 6.537301 TGCTTGCTTTACGCTGTAGTATATTT 59.463 34.615 0.00 0.00 40.11 1.40
1816 1828 8.976471 TCTTCAGTTACGTAGAGAATATAGTCG 58.024 37.037 0.00 0.00 0.00 4.18
2055 2167 9.236691 GATTGTGCATGTAAATATGGTTACTTG 57.763 33.333 0.00 8.05 39.95 3.16
2242 2355 1.369625 CAACGTATGAAGCACCTCCC 58.630 55.000 0.00 0.00 0.00 4.30
2315 2430 2.046285 GGTGACAAAGCGGGGATGG 61.046 63.158 0.00 0.00 0.00 3.51
2521 2948 8.254508 TGTTTTGGCTATTATTTTCCATGGTAC 58.745 33.333 12.58 0.00 0.00 3.34
2522 2949 8.474831 GTTTTGGCTATTATTTTCCATGGTACT 58.525 33.333 12.58 0.00 0.00 2.73
2523 2950 7.817418 TTGGCTATTATTTTCCATGGTACTC 57.183 36.000 12.58 0.00 0.00 2.59
2524 2951 6.303839 TGGCTATTATTTTCCATGGTACTCC 58.696 40.000 12.58 1.75 0.00 3.85
2525 2952 5.710567 GGCTATTATTTTCCATGGTACTCCC 59.289 44.000 12.58 0.00 0.00 4.30
2526 2953 6.467339 GGCTATTATTTTCCATGGTACTCCCT 60.467 42.308 12.58 0.00 0.00 4.20
2527 2954 6.655425 GCTATTATTTTCCATGGTACTCCCTC 59.345 42.308 12.58 0.00 0.00 4.30
2528 2955 6.848562 ATTATTTTCCATGGTACTCCCTCT 57.151 37.500 12.58 0.00 0.00 3.69
2529 2956 4.510167 ATTTTCCATGGTACTCCCTCTG 57.490 45.455 12.58 0.00 0.00 3.35
2530 2957 2.642171 TTCCATGGTACTCCCTCTGT 57.358 50.000 12.58 0.00 0.00 3.41
2531 2958 3.769189 TTCCATGGTACTCCCTCTGTA 57.231 47.619 12.58 0.00 0.00 2.74
2532 2959 3.769189 TCCATGGTACTCCCTCTGTAA 57.231 47.619 12.58 0.00 0.00 2.41
2533 2960 4.069312 TCCATGGTACTCCCTCTGTAAA 57.931 45.455 12.58 0.00 0.00 2.01
2534 2961 4.030913 TCCATGGTACTCCCTCTGTAAAG 58.969 47.826 12.58 0.00 0.00 1.85
2535 2962 4.030913 CCATGGTACTCCCTCTGTAAAGA 58.969 47.826 2.57 0.00 0.00 2.52
2536 2963 4.469945 CCATGGTACTCCCTCTGTAAAGAA 59.530 45.833 2.57 0.00 0.00 2.52
2537 2964 5.045869 CCATGGTACTCCCTCTGTAAAGAAA 60.046 44.000 2.57 0.00 0.00 2.52
2538 2965 6.353082 CCATGGTACTCCCTCTGTAAAGAAAT 60.353 42.308 2.57 0.00 0.00 2.17
2539 2966 7.147549 CCATGGTACTCCCTCTGTAAAGAAATA 60.148 40.741 2.57 0.00 0.00 1.40
2540 2967 7.989947 TGGTACTCCCTCTGTAAAGAAATAT 57.010 36.000 0.00 0.00 0.00 1.28
2541 2968 9.670442 ATGGTACTCCCTCTGTAAAGAAATATA 57.330 33.333 0.00 0.00 0.00 0.86
2542 2969 9.496710 TGGTACTCCCTCTGTAAAGAAATATAA 57.503 33.333 0.00 0.00 0.00 0.98
2543 2970 9.761504 GGTACTCCCTCTGTAAAGAAATATAAC 57.238 37.037 0.00 0.00 0.00 1.89
2546 2973 9.047947 ACTCCCTCTGTAAAGAAATATAACAGT 57.952 33.333 0.00 0.00 38.88 3.55
2547 2974 9.319143 CTCCCTCTGTAAAGAAATATAACAGTG 57.681 37.037 0.00 0.00 38.88 3.66
2548 2975 8.822805 TCCCTCTGTAAAGAAATATAACAGTGT 58.177 33.333 0.00 0.00 38.88 3.55
2549 2976 9.449719 CCCTCTGTAAAGAAATATAACAGTGTT 57.550 33.333 14.05 14.05 38.88 3.32
2589 3016 8.649973 AACGCTCTTATATTTCTTTACAGAGG 57.350 34.615 0.00 0.00 0.00 3.69
2590 3017 7.210873 ACGCTCTTATATTTCTTTACAGAGGG 58.789 38.462 8.36 8.36 42.53 4.30
2591 3018 7.069578 ACGCTCTTATATTTCTTTACAGAGGGA 59.930 37.037 14.96 0.00 40.49 4.20
2592 3019 7.596995 CGCTCTTATATTTCTTTACAGAGGGAG 59.403 40.741 4.76 0.00 40.49 4.30
2593 3020 8.425703 GCTCTTATATTTCTTTACAGAGGGAGT 58.574 37.037 0.00 0.00 0.00 3.85
2648 3075 2.668457 CCTAAGTTGCTTGCTGACTACG 59.332 50.000 0.00 0.00 0.00 3.51
2746 3173 5.178061 TGAGCACATATTCACAGGTTGTAG 58.822 41.667 0.00 0.00 0.00 2.74
2765 3192 7.803189 GGTTGTAGTCATAATGAACAAACAGTG 59.197 37.037 0.00 0.00 35.79 3.66
2796 3223 1.338105 CGCACCAGAAGATTGTCTCCA 60.338 52.381 0.00 0.00 0.00 3.86
2811 3238 6.968263 TTGTCTCCAGAGATCATAACCTAG 57.032 41.667 0.00 0.00 39.97 3.02
2823 3250 6.615726 AGATCATAACCTAGGAGCCAAAACTA 59.384 38.462 17.98 0.00 0.00 2.24
2843 3270 8.814038 AAACTAAATCATAACCTGAGCTCATT 57.186 30.769 18.63 12.38 37.28 2.57
2879 3306 4.104102 TGGTGGTGAGGTCTTCAAACTAAT 59.896 41.667 0.00 0.00 37.61 1.73
2883 3310 7.393515 GGTGGTGAGGTCTTCAAACTAATAAAT 59.606 37.037 0.00 0.00 37.61 1.40
2886 3313 9.010029 GGTGAGGTCTTCAAACTAATAAATCAA 57.990 33.333 0.00 0.00 37.61 2.57
2989 3428 3.067833 GCCAACAGACTAACTCAAGGAC 58.932 50.000 0.00 0.00 0.00 3.85
2994 3433 3.974642 ACAGACTAACTCAAGGACCCTTT 59.025 43.478 0.00 0.00 33.42 3.11
2995 3434 4.202367 ACAGACTAACTCAAGGACCCTTTG 60.202 45.833 0.00 0.00 33.42 2.77
3058 3509 7.833682 TCTTTAGGGAATGTCATTATTGCTTCA 59.166 33.333 0.00 0.00 0.00 3.02
3064 3515 7.864379 GGGAATGTCATTATTGCTTCATAGTTG 59.136 37.037 0.00 0.00 0.00 3.16
3092 3543 3.513515 GCTTTGGGGACATTTAACATGGA 59.486 43.478 0.00 0.00 42.32 3.41
3319 3770 0.908180 AGGGTGGCACCAGTAGTACC 60.908 60.000 35.69 17.08 41.02 3.34
3346 3797 6.398095 GTTATTTTAAGCCTTGCACCTGATT 58.602 36.000 0.00 0.00 0.00 2.57
3541 3996 6.604171 TGGCTTCCAATTATCATCACAGTAT 58.396 36.000 0.00 0.00 0.00 2.12
3720 4175 4.825422 TCAAGATTCAGTTGTGCTCCTAG 58.175 43.478 0.00 0.00 0.00 3.02
3919 5779 3.835790 TTTTCCCCAGTGACCGCCG 62.836 63.158 0.00 0.00 0.00 6.46
3979 5840 3.692576 CTCCTGATAACGACTGTTACCG 58.307 50.000 0.00 0.00 43.03 4.02
4147 6010 6.509656 TCCGGTGTGCAGTAGTAATAAATAG 58.490 40.000 0.00 0.00 0.00 1.73
4148 6011 6.321945 TCCGGTGTGCAGTAGTAATAAATAGA 59.678 38.462 0.00 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 7.409661 GCATATGTATTTGACAACAATATGCGC 60.410 37.037 18.30 0.00 42.78 6.09
404 405 0.039437 TGGAGACGAGCTTCACGAAC 60.039 55.000 0.00 0.00 34.70 3.95
518 519 2.285083 GCCAGTGTGTGTCAGTGTTAA 58.715 47.619 0.00 0.00 43.72 2.01
521 522 0.035534 TTGCCAGTGTGTGTCAGTGT 60.036 50.000 0.00 0.00 43.72 3.55
522 523 0.659427 CTTGCCAGTGTGTGTCAGTG 59.341 55.000 0.00 0.00 44.54 3.66
523 524 0.464373 CCTTGCCAGTGTGTGTCAGT 60.464 55.000 0.00 0.00 0.00 3.41
524 525 1.789078 GCCTTGCCAGTGTGTGTCAG 61.789 60.000 0.00 0.00 0.00 3.51
525 526 1.823470 GCCTTGCCAGTGTGTGTCA 60.823 57.895 0.00 0.00 0.00 3.58
526 527 1.510480 GAGCCTTGCCAGTGTGTGTC 61.510 60.000 0.00 0.00 0.00 3.67
795 801 0.544697 GGGAAAGAGATACGGCCCAA 59.455 55.000 0.00 0.00 35.63 4.12
838 846 1.388547 TGTTCTGTTTCGGCTTTGCT 58.611 45.000 0.00 0.00 0.00 3.91
858 866 2.112297 TGGGCGCGTTTCTTTCCT 59.888 55.556 8.43 0.00 0.00 3.36
876 884 2.585247 GGACGCCGGAATTCCTCG 60.585 66.667 25.00 25.00 36.31 4.63
899 907 2.514824 GGCTTCTAGGGCTTGCGG 60.515 66.667 8.14 0.00 0.00 5.69
973 981 2.551912 GCCTCAACAACCACCACCG 61.552 63.158 0.00 0.00 0.00 4.94
1044 1052 2.604686 TCCAGCGCCTCCTTGAGT 60.605 61.111 2.29 0.00 0.00 3.41
1170 1178 4.170062 CTCGTTACCTCGCGGCGA 62.170 66.667 24.84 24.84 0.00 5.54
1501 1509 2.520465 ATTGCTGATCACGGTGGCGA 62.520 55.000 8.50 3.97 0.00 5.54
1502 1510 1.647545 AATTGCTGATCACGGTGGCG 61.648 55.000 8.50 0.00 0.00 5.69
1509 1518 4.933330 AGATGATGCAAATTGCTGATCAC 58.067 39.130 18.93 13.93 45.31 3.06
1558 1567 3.126879 TGCCGCTGCAGCATACAC 61.127 61.111 36.03 20.38 44.23 2.90
1578 1587 6.861065 ATAGTACACTGAAACACAAACCAG 57.139 37.500 0.00 0.00 0.00 4.00
1741 1753 8.975439 CCCTTGTAAATATACTACAGCGTAAAG 58.025 37.037 0.00 0.00 31.17 1.85
1746 1758 4.384846 CGCCCTTGTAAATATACTACAGCG 59.615 45.833 11.91 11.91 35.06 5.18
1749 1761 6.461927 CCTGACGCCCTTGTAAATATACTACA 60.462 42.308 0.00 0.00 32.98 2.74
1757 1769 0.034477 CCCCTGACGCCCTTGTAAAT 60.034 55.000 0.00 0.00 0.00 1.40
1758 1770 1.128809 TCCCCTGACGCCCTTGTAAA 61.129 55.000 0.00 0.00 0.00 2.01
1759 1771 1.128809 TTCCCCTGACGCCCTTGTAA 61.129 55.000 0.00 0.00 0.00 2.41
1760 1772 0.912487 ATTCCCCTGACGCCCTTGTA 60.912 55.000 0.00 0.00 0.00 2.41
1816 1828 5.105837 ACCTGTAAGTCACCTTTCTACGATC 60.106 44.000 0.00 0.00 31.89 3.69
1861 1873 1.980765 AGGACCAATGCTTCTCAGACA 59.019 47.619 0.00 0.00 0.00 3.41
2087 2199 2.035449 TCACCAAGACTCAACTACCACG 59.965 50.000 0.00 0.00 0.00 4.94
2203 2316 4.291540 TGCAGTGTCATTTTCTTGTGTC 57.708 40.909 0.00 0.00 0.00 3.67
2242 2355 0.544357 TCCCACTCCCAGTACACAGG 60.544 60.000 0.00 0.00 0.00 4.00
2446 2873 5.804979 GCACAATTATGTAATGTGGTTGTCC 59.195 40.000 7.19 0.00 37.82 4.02
2521 2948 9.319143 CACTGTTATATTTCTTTACAGAGGGAG 57.681 37.037 0.00 0.00 38.74 4.30
2522 2949 8.822805 ACACTGTTATATTTCTTTACAGAGGGA 58.177 33.333 0.00 0.00 38.74 4.20
2523 2950 9.449719 AACACTGTTATATTTCTTTACAGAGGG 57.550 33.333 0.00 0.00 38.74 4.30
2563 2990 9.099454 CCTCTGTAAAGAAATATAAGAGCGTTT 57.901 33.333 0.00 0.00 0.00 3.60
2564 2991 7.711339 CCCTCTGTAAAGAAATATAAGAGCGTT 59.289 37.037 0.00 0.00 0.00 4.84
2565 2992 7.069578 TCCCTCTGTAAAGAAATATAAGAGCGT 59.930 37.037 0.00 0.00 0.00 5.07
2566 2993 7.434492 TCCCTCTGTAAAGAAATATAAGAGCG 58.566 38.462 0.00 0.00 0.00 5.03
2567 2994 8.425703 ACTCCCTCTGTAAAGAAATATAAGAGC 58.574 37.037 0.00 0.00 0.00 4.09
2574 3001 9.765295 ACTAGTTACTCCCTCTGTAAAGAAATA 57.235 33.333 0.00 0.00 32.58 1.40
2575 3002 8.667592 ACTAGTTACTCCCTCTGTAAAGAAAT 57.332 34.615 0.00 0.00 32.58 2.17
2576 3003 9.592196 TTACTAGTTACTCCCTCTGTAAAGAAA 57.408 33.333 0.00 0.00 32.58 2.52
2577 3004 9.240734 CTTACTAGTTACTCCCTCTGTAAAGAA 57.759 37.037 0.00 0.00 32.58 2.52
2578 3005 8.389366 ACTTACTAGTTACTCCCTCTGTAAAGA 58.611 37.037 0.00 0.00 32.58 2.52
2579 3006 8.460428 CACTTACTAGTTACTCCCTCTGTAAAG 58.540 40.741 0.00 0.00 32.58 1.85
2580 3007 7.094032 GCACTTACTAGTTACTCCCTCTGTAAA 60.094 40.741 0.00 0.00 32.58 2.01
2581 3008 6.376581 GCACTTACTAGTTACTCCCTCTGTAA 59.623 42.308 0.00 0.00 30.26 2.41
2582 3009 5.884792 GCACTTACTAGTTACTCCCTCTGTA 59.115 44.000 0.00 0.00 30.26 2.74
2583 3010 4.705991 GCACTTACTAGTTACTCCCTCTGT 59.294 45.833 0.00 0.00 30.26 3.41
2584 3011 4.098196 GGCACTTACTAGTTACTCCCTCTG 59.902 50.000 0.00 0.00 30.26 3.35
2585 3012 4.264262 TGGCACTTACTAGTTACTCCCTCT 60.264 45.833 0.00 0.00 30.26 3.69
2586 3013 4.021916 TGGCACTTACTAGTTACTCCCTC 58.978 47.826 0.00 0.00 30.26 4.30
2587 3014 4.057063 TGGCACTTACTAGTTACTCCCT 57.943 45.455 0.00 0.00 30.26 4.20
2588 3015 4.020839 TGTTGGCACTTACTAGTTACTCCC 60.021 45.833 0.00 0.00 30.26 4.30
2589 3016 5.143376 TGTTGGCACTTACTAGTTACTCC 57.857 43.478 0.00 0.00 30.26 3.85
2590 3017 8.248945 TCTTATGTTGGCACTTACTAGTTACTC 58.751 37.037 0.00 0.00 30.26 2.59
2591 3018 8.130671 TCTTATGTTGGCACTTACTAGTTACT 57.869 34.615 0.00 0.00 30.26 2.24
2592 3019 8.818057 CATCTTATGTTGGCACTTACTAGTTAC 58.182 37.037 0.00 0.00 30.26 2.50
2593 3020 7.494625 GCATCTTATGTTGGCACTTACTAGTTA 59.505 37.037 0.00 0.00 30.26 2.24
2746 3173 5.376854 AGCCACTGTTTGTTCATTATGAC 57.623 39.130 0.00 0.00 0.00 3.06
2796 3223 4.477536 TGGCTCCTAGGTTATGATCTCT 57.522 45.455 9.08 0.00 0.00 3.10
2811 3238 6.377146 TCAGGTTATGATTTAGTTTTGGCTCC 59.623 38.462 0.00 0.00 31.12 4.70
2823 3250 8.814038 ACTTTAATGAGCTCAGGTTATGATTT 57.186 30.769 22.96 10.34 37.28 2.17
2843 3270 3.607741 TCACCACCACGTTTCAACTTTA 58.392 40.909 0.00 0.00 0.00 1.85
2887 3314 8.200792 GCTCTAATTGGAGATTACCATATCGAT 58.799 37.037 21.83 2.16 39.82 3.59
2888 3315 7.178451 TGCTCTAATTGGAGATTACCATATCGA 59.822 37.037 21.83 0.00 39.82 3.59
2889 3316 7.323420 TGCTCTAATTGGAGATTACCATATCG 58.677 38.462 21.83 0.00 39.82 2.92
2890 3317 9.507329 TTTGCTCTAATTGGAGATTACCATATC 57.493 33.333 21.83 1.52 39.82 1.63
2891 3318 9.289782 GTTTGCTCTAATTGGAGATTACCATAT 57.710 33.333 21.83 0.00 39.82 1.78
2892 3319 7.719633 GGTTTGCTCTAATTGGAGATTACCATA 59.280 37.037 21.83 3.29 39.82 2.74
2893 3320 6.547510 GGTTTGCTCTAATTGGAGATTACCAT 59.452 38.462 21.83 0.00 39.82 3.55
2894 3321 5.885912 GGTTTGCTCTAATTGGAGATTACCA 59.114 40.000 21.83 7.40 38.24 3.25
2895 3322 5.885912 TGGTTTGCTCTAATTGGAGATTACC 59.114 40.000 21.83 20.80 35.52 2.85
2896 3323 7.573968 ATGGTTTGCTCTAATTGGAGATTAC 57.426 36.000 21.83 13.91 35.52 1.89
2897 3324 8.494433 ACTATGGTTTGCTCTAATTGGAGATTA 58.506 33.333 21.83 5.07 35.52 1.75
2994 3433 6.739331 AACATAGGAAATGTTTGAAACCCA 57.261 33.333 5.50 0.00 38.97 4.51
2995 3434 8.527810 TGATAACATAGGAAATGTTTGAAACCC 58.472 33.333 5.50 0.00 41.81 4.11
3058 3509 4.210331 GTCCCCAAAGCATGATCAACTAT 58.790 43.478 0.00 0.00 0.00 2.12
3064 3515 5.105392 TGTTAAATGTCCCCAAAGCATGATC 60.105 40.000 0.00 0.00 0.00 2.92
3142 3593 5.713861 CAGATTCTCCCTTTCCATTTTCAGT 59.286 40.000 0.00 0.00 0.00 3.41
3145 3596 5.264395 TCCAGATTCTCCCTTTCCATTTTC 58.736 41.667 0.00 0.00 0.00 2.29
3319 3770 3.507786 GTGCAAGGCTTAAAATAACGGG 58.492 45.455 0.00 0.00 0.00 5.28
3346 3797 2.585330 TCTTGTGCTGCTCCAATTTGA 58.415 42.857 0.00 0.00 0.00 2.69
3541 3996 2.398588 CTGGACCTAACATGGCTCCTA 58.601 52.381 0.00 0.00 32.35 2.94
3737 4192 3.519107 TCCAGATGCTAATCAAGGTCACA 59.481 43.478 0.00 0.00 35.03 3.58
3744 4199 4.824479 TGAGTGTCCAGATGCTAATCAA 57.176 40.909 0.00 0.00 35.03 2.57
3901 4357 2.114411 GGCGGTCACTGGGGAAAA 59.886 61.111 0.00 0.00 0.00 2.29
3919 5779 2.303311 CCTAGCTAACCCTAATGCCTCC 59.697 54.545 0.00 0.00 0.00 4.30
3922 5782 4.158015 TCTACCTAGCTAACCCTAATGCC 58.842 47.826 0.00 0.00 0.00 4.40
3929 5789 4.715792 ACCTTCTTTCTACCTAGCTAACCC 59.284 45.833 0.00 0.00 0.00 4.11
3930 5790 5.936187 ACCTTCTTTCTACCTAGCTAACC 57.064 43.478 0.00 0.00 0.00 2.85
3932 5792 6.321690 CAGCTACCTTCTTTCTACCTAGCTAA 59.678 42.308 0.00 0.00 34.96 3.09
4147 6010 5.159209 CAAAATTGCATTCTCAGGACTGTC 58.841 41.667 0.00 0.00 0.00 3.51
4148 6011 4.021719 CCAAAATTGCATTCTCAGGACTGT 60.022 41.667 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.