Multiple sequence alignment - TraesCS6D01G338800

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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 TraesCS6D01G338800 chr6D 100.000 3560 0 0 1 3560 438828905 438832464 0.000000e+00 6575.0
1 TraesCS6D01G338800 chr6D 80.870 115 20 2 342 455 417890214 417890101 4.900000e-14 89.8
2 TraesCS6D01G338800 chr6B 91.288 1894 130 17 913 2782 663985175 663987057 0.000000e+00 2551.0
3 TraesCS6D01G338800 chr6B 84.954 864 69 33 94 905 663984272 663985126 0.000000e+00 819.0
4 TraesCS6D01G338800 chr6B 89.568 278 24 2 2787 3062 663987096 663987370 7.310000e-92 348.0
5 TraesCS6D01G338800 chr6B 77.720 193 24 12 3046 3226 575318132 575317947 2.260000e-17 100.0
6 TraesCS6D01G338800 chr6A 90.986 1886 126 13 911 2778 587684986 587686845 0.000000e+00 2501.0
7 TraesCS6D01G338800 chr6A 94.730 778 30 7 2787 3560 587686892 587687662 0.000000e+00 1199.0
8 TraesCS6D01G338800 chr6A 92.000 50 4 0 651 700 587645283 587645332 1.770000e-08 71.3
9 TraesCS6D01G338800 chr7A 79.167 1416 197 56 1057 2417 103051824 103053196 0.000000e+00 891.0
10 TraesCS6D01G338800 chr7D 79.405 1345 187 49 1122 2417 100884992 100886295 0.000000e+00 867.0
11 TraesCS6D01G338800 chr7D 83.077 130 17 5 353 480 129804616 129804490 2.900000e-21 113.0
12 TraesCS6D01G338800 chr7B 78.329 1412 213 52 1057 2417 56497751 56496382 0.000000e+00 826.0
13 TraesCS6D01G338800 chr2D 91.463 82 5 2 3396 3476 13182518 13182438 1.040000e-20 111.0
14 TraesCS6D01G338800 chr2D 78.125 128 26 2 494 620 468867830 468867704 2.950000e-11 80.5
15 TraesCS6D01G338800 chr5B 100.000 34 0 0 3414 3447 270681891 270681924 2.970000e-06 63.9
16 TraesCS6D01G338800 chr2B 96.875 32 0 1 520 550 617928726 617928695 6.000000e-03 52.8


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 TraesCS6D01G338800 chr6D 438828905 438832464 3559 False 6575.000000 6575 100.000000 1 3560 1 chr6D.!!$F1 3559
1 TraesCS6D01G338800 chr6B 663984272 663987370 3098 False 1239.333333 2551 88.603333 94 3062 3 chr6B.!!$F1 2968
2 TraesCS6D01G338800 chr6A 587684986 587687662 2676 False 1850.000000 2501 92.858000 911 3560 2 chr6A.!!$F2 2649
3 TraesCS6D01G338800 chr7A 103051824 103053196 1372 False 891.000000 891 79.167000 1057 2417 1 chr7A.!!$F1 1360
4 TraesCS6D01G338800 chr7D 100884992 100886295 1303 False 867.000000 867 79.405000 1122 2417 1 chr7D.!!$F1 1295
5 TraesCS6D01G338800 chr7B 56496382 56497751 1369 True 826.000000 826 78.329000 1057 2417 1 chr7B.!!$R1 1360

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
572 580 0.104672 TGGTGGGAGGAGGTTCAAGA 60.105 55.0 0.00 0.0 0.00 3.02 F
1390 1505 0.108615 CTGTCGGAGGCGATGACTTT 60.109 55.0 7.38 0.0 33.81 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2491 2646 0.731855 GGTCTACCGTTGCACTCGAC 60.732 60.0 11.33 2.72 0.00 4.20 R
2968 3181 0.947180 TGAAGTGCCGCGGACTTAAC 60.947 55.0 33.48 21.59 33.71 2.01 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
28 29 7.780008 ATGGTCATAATTTCGAACAATACGA 57.220 32.000 0.00 0.00 31.39 3.43
29 30 7.598189 TGGTCATAATTTCGAACAATACGAA 57.402 32.000 0.00 0.00 45.65 3.85
40 41 7.774224 TCGAACAATACGAAAATCAATGTTG 57.226 32.000 0.00 0.00 36.84 3.33
41 42 7.577107 TCGAACAATACGAAAATCAATGTTGA 58.423 30.769 0.00 0.00 37.95 3.18
42 43 7.744276 TCGAACAATACGAAAATCAATGTTGAG 59.256 33.333 1.65 0.00 37.44 3.02
43 44 7.460120 CGAACAATACGAAAATCAATGTTGAGC 60.460 37.037 1.65 0.00 41.08 4.26
44 45 6.092748 ACAATACGAAAATCAATGTTGAGCC 58.907 36.000 1.65 0.00 41.08 4.70
45 46 5.895636 ATACGAAAATCAATGTTGAGCCA 57.104 34.783 1.65 0.00 41.08 4.75
46 47 3.900941 ACGAAAATCAATGTTGAGCCAC 58.099 40.909 1.65 0.00 41.08 5.01
47 48 3.569701 ACGAAAATCAATGTTGAGCCACT 59.430 39.130 1.65 0.00 41.08 4.00
48 49 4.037923 ACGAAAATCAATGTTGAGCCACTT 59.962 37.500 1.65 0.00 41.08 3.16
49 50 4.383649 CGAAAATCAATGTTGAGCCACTTG 59.616 41.667 1.65 0.00 41.08 3.16
50 51 4.942761 AAATCAATGTTGAGCCACTTGT 57.057 36.364 1.65 0.00 41.08 3.16
51 52 4.942761 AATCAATGTTGAGCCACTTGTT 57.057 36.364 1.65 0.00 41.08 2.83
52 53 4.942761 ATCAATGTTGAGCCACTTGTTT 57.057 36.364 1.65 0.00 41.08 2.83
53 54 6.403866 AATCAATGTTGAGCCACTTGTTTA 57.596 33.333 1.65 0.00 41.08 2.01
54 55 5.181690 TCAATGTTGAGCCACTTGTTTAC 57.818 39.130 0.00 0.00 32.50 2.01
55 56 4.642437 TCAATGTTGAGCCACTTGTTTACA 59.358 37.500 0.00 0.00 32.50 2.41
56 57 5.301551 TCAATGTTGAGCCACTTGTTTACAT 59.698 36.000 0.00 0.00 32.50 2.29
57 58 6.488344 TCAATGTTGAGCCACTTGTTTACATA 59.512 34.615 0.00 0.00 32.50 2.29
58 59 6.892658 ATGTTGAGCCACTTGTTTACATAA 57.107 33.333 0.00 0.00 0.00 1.90
59 60 6.701145 TGTTGAGCCACTTGTTTACATAAA 57.299 33.333 0.00 0.00 0.00 1.40
60 61 6.734137 TGTTGAGCCACTTGTTTACATAAAG 58.266 36.000 0.00 0.00 0.00 1.85
61 62 5.371115 TGAGCCACTTGTTTACATAAAGC 57.629 39.130 0.00 0.00 0.00 3.51
62 63 5.070001 TGAGCCACTTGTTTACATAAAGCT 58.930 37.500 0.00 0.00 0.00 3.74
63 64 5.534654 TGAGCCACTTGTTTACATAAAGCTT 59.465 36.000 0.00 0.00 0.00 3.74
64 65 6.040391 TGAGCCACTTGTTTACATAAAGCTTT 59.960 34.615 17.30 17.30 0.00 3.51
65 66 6.816136 AGCCACTTGTTTACATAAAGCTTTT 58.184 32.000 18.47 1.60 0.00 2.27
66 67 7.947282 AGCCACTTGTTTACATAAAGCTTTTA 58.053 30.769 18.47 0.49 0.00 1.52
67 68 8.585018 AGCCACTTGTTTACATAAAGCTTTTAT 58.415 29.630 18.47 6.20 0.00 1.40
68 69 8.860128 GCCACTTGTTTACATAAAGCTTTTATC 58.140 33.333 18.47 2.68 0.00 1.75
69 70 9.906660 CCACTTGTTTACATAAAGCTTTTATCA 57.093 29.630 18.47 0.00 0.00 2.15
84 85 9.502091 AAGCTTTTATCATCAGTTTAGTGTACA 57.498 29.630 0.00 0.00 0.00 2.90
85 86 9.672673 AGCTTTTATCATCAGTTTAGTGTACAT 57.327 29.630 0.00 0.00 0.00 2.29
86 87 9.922305 GCTTTTATCATCAGTTTAGTGTACATC 57.078 33.333 0.00 0.00 0.00 3.06
118 119 2.161609 GGTAGGTTATTGTGCACAGTGC 59.838 50.000 23.66 19.37 45.29 4.40
142 143 7.436376 TGCGAAATAGAGAGTATGATTGTTCAG 59.564 37.037 0.00 0.00 34.73 3.02
153 154 3.084039 TGATTGTTCAGAGTGAATGCCC 58.916 45.455 0.00 0.00 38.79 5.36
154 155 1.522668 TTGTTCAGAGTGAATGCCCG 58.477 50.000 0.00 0.00 38.79 6.13
176 177 4.396790 CGTCAGCTAAGAGGGTCCTATATC 59.603 50.000 0.00 0.00 0.00 1.63
177 178 4.396790 GTCAGCTAAGAGGGTCCTATATCG 59.603 50.000 0.00 0.00 0.00 2.92
249 257 7.759489 TCAAAAATATGTAGACAAGGTTGCT 57.241 32.000 0.00 0.00 0.00 3.91
250 258 7.592938 TCAAAAATATGTAGACAAGGTTGCTG 58.407 34.615 0.00 0.00 0.00 4.41
280 288 3.064207 ACTTCATGCGTCGTGTTTGTAT 58.936 40.909 0.00 0.00 0.00 2.29
281 289 3.122948 ACTTCATGCGTCGTGTTTGTATC 59.877 43.478 0.00 0.00 0.00 2.24
287 295 3.437741 TGCGTCGTGTTTGTATCTCTCTA 59.562 43.478 0.00 0.00 0.00 2.43
296 304 8.587950 CGTGTTTGTATCTCTCTACATTTTCTC 58.412 37.037 0.00 0.00 31.94 2.87
322 330 6.918892 AAATATGTACGCTATCTTTGTGCA 57.081 33.333 0.00 0.00 32.88 4.57
323 331 7.496529 AAATATGTACGCTATCTTTGTGCAT 57.503 32.000 0.00 1.17 41.00 3.96
324 332 7.496529 AATATGTACGCTATCTTTGTGCATT 57.503 32.000 0.00 0.00 39.24 3.56
326 334 3.305897 TGTACGCTATCTTTGTGCATTCG 59.694 43.478 0.00 0.00 0.00 3.34
327 335 1.062587 ACGCTATCTTTGTGCATTCGC 59.937 47.619 0.00 0.00 39.24 4.70
363 371 1.059264 GTCGCCTGACTTTCGAATTCG 59.941 52.381 21.78 21.78 42.08 3.34
369 377 3.064207 CTGACTTTCGAATTCGGGTCAA 58.936 45.455 30.72 18.58 40.15 3.18
386 394 5.971202 CGGGTCAATCGAATTTAATTGAAGG 59.029 40.000 14.47 6.71 41.99 3.46
391 399 8.458843 GTCAATCGAATTTAATTGAAGGGAGAA 58.541 33.333 14.47 0.00 41.99 2.87
393 401 9.076596 CAATCGAATTTAATTGAAGGGAGAAAC 57.923 33.333 0.00 0.00 35.35 2.78
398 406 7.610580 ATTTAATTGAAGGGAGAAACAACCA 57.389 32.000 0.00 0.00 0.00 3.67
399 407 6.648879 TTAATTGAAGGGAGAAACAACCAG 57.351 37.500 0.00 0.00 0.00 4.00
426 434 4.774503 AGAAGCTCGCTGGCAGGC 62.775 66.667 17.64 11.40 34.17 4.85
429 437 2.657102 GAAGCTCGCTGGCAGGCTAT 62.657 60.000 17.64 7.48 34.40 2.97
435 443 2.109799 CTGGCAGGCTATCCCACG 59.890 66.667 6.61 0.00 35.39 4.94
448 456 5.194432 GCTATCCCACGATCTATCTTAGGA 58.806 45.833 0.00 0.00 0.00 2.94
455 463 4.528596 CACGATCTATCTTAGGATTGGGGT 59.471 45.833 0.00 0.00 33.71 4.95
457 465 5.012148 ACGATCTATCTTAGGATTGGGGTTG 59.988 44.000 0.00 0.00 33.71 3.77
470 478 2.445155 GGTTGGGGGAGGCAACAT 59.555 61.111 0.00 0.00 41.41 2.71
472 480 1.984026 GTTGGGGGAGGCAACATGG 60.984 63.158 0.00 0.00 41.41 3.66
487 495 3.358932 ATGGCGGTGGTGGGGATTC 62.359 63.158 0.00 0.00 0.00 2.52
492 500 4.090588 GTGGTGGGGATTCGCCGA 62.091 66.667 14.39 2.14 39.47 5.54
495 503 2.582436 GTGGGGATTCGCCGAAGA 59.418 61.111 14.39 0.00 39.47 2.87
496 504 1.078708 GTGGGGATTCGCCGAAGAA 60.079 57.895 14.39 0.00 39.47 2.52
533 541 1.152139 AGGAGCTAGAGGGATGGCC 60.152 63.158 0.00 0.00 0.00 5.36
553 561 4.796231 GGGCGACGACAGCACGAT 62.796 66.667 1.63 0.00 37.03 3.73
556 564 2.126463 CGACGACAGCACGATGGT 60.126 61.111 5.12 0.00 37.03 3.55
572 580 0.104672 TGGTGGGAGGAGGTTCAAGA 60.105 55.000 0.00 0.00 0.00 3.02
575 583 2.041755 GGTGGGAGGAGGTTCAAGAAAT 59.958 50.000 0.00 0.00 0.00 2.17
585 593 3.825611 CAAGAAATGGCGGGGCGG 61.826 66.667 0.00 0.00 0.00 6.13
684 714 2.033299 AGTTGTGCACGTTGAATCAAGG 59.967 45.455 13.13 13.38 35.67 3.61
691 721 3.423123 GCACGTTGAATCAAGGTCTAACG 60.423 47.826 17.14 8.83 39.86 3.18
750 799 5.708230 TGTTTTATAGCCATTCCTTCGTGTT 59.292 36.000 0.00 0.00 0.00 3.32
763 812 3.614616 CCTTCGTGTTTGTATCTCTCTGC 59.385 47.826 0.00 0.00 0.00 4.26
815 867 1.140852 AGGTGCACTTTGTCTACTGCA 59.859 47.619 17.98 0.00 37.30 4.41
842 894 2.753043 CCAGGAGCTTGCCGCATT 60.753 61.111 0.00 0.00 42.61 3.56
843 895 2.488355 CAGGAGCTTGCCGCATTG 59.512 61.111 0.00 0.00 42.61 2.82
853 905 4.330620 AGCTTGCCGCATTGAAAATTAATG 59.669 37.500 0.00 0.00 42.61 1.90
860 912 5.809562 CCGCATTGAAAATTAATGGCAGTAA 59.190 36.000 10.06 10.06 36.33 2.24
889 941 0.179097 GGTGGCGCCAAGAAAACAAA 60.179 50.000 34.66 0.00 37.17 2.83
905 957 8.045750 AGAAAACAAACATAACGTCAATTTCG 57.954 30.769 0.00 0.00 0.00 3.46
908 960 7.825627 AACAAACATAACGTCAATTTCGTAC 57.174 32.000 5.98 0.00 40.69 3.67
909 961 6.946165 ACAAACATAACGTCAATTTCGTACA 58.054 32.000 5.98 0.00 40.69 2.90
910 962 7.067116 ACAAACATAACGTCAATTTCGTACAG 58.933 34.615 5.98 2.84 40.69 2.74
911 963 6.774354 AACATAACGTCAATTTCGTACAGT 57.226 33.333 5.98 3.32 40.69 3.55
915 1008 2.729882 ACGTCAATTTCGTACAGTCTGC 59.270 45.455 0.00 0.00 39.78 4.26
965 1058 2.737376 GTGAACCTCGTGTCCCGC 60.737 66.667 0.00 0.00 36.19 6.13
988 1081 3.130160 GCTGCAGCACTAGCCACC 61.130 66.667 33.36 0.00 43.56 4.61
992 1085 2.270205 CAGCACTAGCCACCCCAG 59.730 66.667 0.00 0.00 43.56 4.45
993 1086 2.203998 AGCACTAGCCACCCCAGT 60.204 61.111 0.00 0.00 43.56 4.00
994 1087 1.080354 AGCACTAGCCACCCCAGTA 59.920 57.895 0.00 0.00 43.56 2.74
1372 1487 2.338984 GTTCGTCTCACGGTGGCT 59.661 61.111 8.50 0.00 42.81 4.75
1378 1493 3.680786 CTCACGGTGGCTGTCGGA 61.681 66.667 8.50 0.00 0.00 4.55
1390 1505 0.108615 CTGTCGGAGGCGATGACTTT 60.109 55.000 7.38 0.00 33.81 2.66
1393 1508 1.218047 CGGAGGCGATGACTTTGGA 59.782 57.895 0.00 0.00 0.00 3.53
1396 1511 1.139853 GGAGGCGATGACTTTGGAGAT 59.860 52.381 0.00 0.00 0.00 2.75
1580 1716 1.009829 CTCCAGCTACGTGCATTTCC 58.990 55.000 0.00 0.00 45.94 3.13
1632 1768 2.172483 ATCGGCGCTGACAAGAAGGT 62.172 55.000 23.67 0.00 0.00 3.50
1642 1781 0.544697 ACAAGAAGGTGGTGGACGTT 59.455 50.000 0.00 0.00 35.34 3.99
1645 1784 0.544697 AGAAGGTGGTGGACGTTGTT 59.455 50.000 0.00 0.00 32.75 2.83
1823 1971 4.787280 AGGAGCTGCTAGGCCGGT 62.787 66.667 5.69 0.00 0.00 5.28
1912 2060 3.475494 TGGGCCGGTATCGTGCAT 61.475 61.111 1.90 0.00 35.37 3.96
2036 2185 1.845205 AACTGCCTGGGTCTCTGCT 60.845 57.895 0.00 0.00 0.00 4.24
2058 2207 3.237741 GGAGGAGGCGGAGGATGG 61.238 72.222 0.00 0.00 0.00 3.51
2059 2208 2.444895 GAGGAGGCGGAGGATGGT 60.445 66.667 0.00 0.00 0.00 3.55
2060 2209 2.444895 AGGAGGCGGAGGATGGTC 60.445 66.667 0.00 0.00 0.00 4.02
2067 2219 3.771160 GGAGGATGGTCACGGCGT 61.771 66.667 6.77 6.77 0.00 5.68
2118 2270 4.193334 CTGGCACGCGATCGAGGA 62.193 66.667 21.57 0.57 39.41 3.71
2386 2541 2.444706 CGAGGGGAGATGGAGGCA 60.445 66.667 0.00 0.00 0.00 4.75
2572 2727 1.194781 ACGAGTTGGAGCAGGTGGAT 61.195 55.000 0.00 0.00 0.00 3.41
2576 2731 0.678048 GTTGGAGCAGGTGGATGGAC 60.678 60.000 0.00 0.00 0.00 4.02
2673 2829 4.507710 ACTGCTGTGTCGATTGTGAATAT 58.492 39.130 0.00 0.00 0.00 1.28
2710 2877 5.924254 GCCATAGCACTTATCGTACACAATA 59.076 40.000 0.00 0.00 39.53 1.90
2713 2880 7.063426 CCATAGCACTTATCGTACACAATATGG 59.937 40.741 0.00 0.00 31.66 2.74
2784 2963 1.024046 TTCATGAATGCACGACCGGG 61.024 55.000 6.32 0.00 0.00 5.73
2837 3050 7.040478 TCCAAGATTACTGTCAAATGGTTCAAG 60.040 37.037 0.00 0.00 0.00 3.02
2864 3077 7.171630 TCTAAGTCTAAGTCCATCTTCAACC 57.828 40.000 0.00 0.00 37.56 3.77
2890 3103 2.776312 TCGAATCGGACTCACTATGC 57.224 50.000 1.76 0.00 0.00 3.14
2925 3138 4.974275 CGAATACGAAAGTCGGACATGTAT 59.026 41.667 11.27 9.26 45.59 2.29
3123 3339 9.003658 ACTTGAATCCAACTTATGTTCTAGTTG 57.996 33.333 7.76 7.76 46.77 3.16
3125 3341 8.547967 TGAATCCAACTTATGTTCTAGTTGTC 57.452 34.615 12.38 5.93 46.13 3.18
3136 3352 5.484715 TGTTCTAGTTGTCCCCTTTAATCG 58.515 41.667 0.00 0.00 0.00 3.34
3143 3359 2.372504 TGTCCCCTTTAATCGTCCACAA 59.627 45.455 0.00 0.00 0.00 3.33
3150 3366 4.155826 CCTTTAATCGTCCACAAATGCTCA 59.844 41.667 0.00 0.00 0.00 4.26
3155 3371 4.406648 TCGTCCACAAATGCTCATCTAT 57.593 40.909 0.00 0.00 0.00 1.98
3159 3375 5.237996 CGTCCACAAATGCTCATCTATTCAT 59.762 40.000 0.00 0.00 0.00 2.57
3189 3405 0.734253 GCTCATGAGTTGCTCGACGT 60.734 55.000 23.38 0.00 32.35 4.34
3247 3463 6.089920 ACGTTAACTGCAAAAAGAAAAAGC 57.910 33.333 3.71 0.00 0.00 3.51
3290 3506 6.625740 CGGACTTTGAATTGCAAGTTGGATAT 60.626 38.462 4.94 0.00 37.87 1.63
3306 3522 5.188327 TGGATATGATCACTCGTGTTCTC 57.812 43.478 0.00 0.62 32.17 2.87
3321 3537 4.137543 GTGTTCTCAAATTCCAGACCAGT 58.862 43.478 0.00 0.00 0.00 4.00
3512 3728 5.344743 TCTAACCAACTGGCTTAGAGATG 57.655 43.478 12.77 0.00 39.32 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 7.780008 TCGTATTGTTCGAAATTATGACCAT 57.220 32.000 0.00 0.00 34.36 3.55
5 6 7.598189 TTCGTATTGTTCGAAATTATGACCA 57.402 32.000 0.00 0.00 42.83 4.02
15 16 8.070769 TCAACATTGATTTTCGTATTGTTCGAA 58.929 29.630 0.00 0.00 37.60 3.71
16 17 7.577107 TCAACATTGATTTTCGTATTGTTCGA 58.423 30.769 0.00 0.00 32.05 3.71
17 18 7.460120 GCTCAACATTGATTTTCGTATTGTTCG 60.460 37.037 0.00 0.00 36.46 3.95
18 19 7.201350 GGCTCAACATTGATTTTCGTATTGTTC 60.201 37.037 0.00 0.00 36.46 3.18
19 20 6.586082 GGCTCAACATTGATTTTCGTATTGTT 59.414 34.615 0.00 0.00 36.46 2.83
20 21 6.092748 GGCTCAACATTGATTTTCGTATTGT 58.907 36.000 0.00 0.00 36.46 2.71
21 22 6.033831 GTGGCTCAACATTGATTTTCGTATTG 59.966 38.462 0.00 0.00 36.46 1.90
22 23 6.071952 AGTGGCTCAACATTGATTTTCGTATT 60.072 34.615 0.00 0.00 36.46 1.89
23 24 5.415701 AGTGGCTCAACATTGATTTTCGTAT 59.584 36.000 0.00 0.00 36.46 3.06
24 25 4.759693 AGTGGCTCAACATTGATTTTCGTA 59.240 37.500 0.00 0.00 36.46 3.43
25 26 3.569701 AGTGGCTCAACATTGATTTTCGT 59.430 39.130 0.00 0.00 36.46 3.85
26 27 4.164822 AGTGGCTCAACATTGATTTTCG 57.835 40.909 0.00 0.00 36.46 3.46
27 28 5.291971 ACAAGTGGCTCAACATTGATTTTC 58.708 37.500 0.00 0.00 36.46 2.29
28 29 5.280654 ACAAGTGGCTCAACATTGATTTT 57.719 34.783 0.00 0.00 36.46 1.82
29 30 4.942761 ACAAGTGGCTCAACATTGATTT 57.057 36.364 0.00 0.00 36.46 2.17
30 31 4.942761 AACAAGTGGCTCAACATTGATT 57.057 36.364 0.00 0.00 36.46 2.57
31 32 4.942761 AAACAAGTGGCTCAACATTGAT 57.057 36.364 0.00 0.00 36.46 2.57
32 33 4.642437 TGTAAACAAGTGGCTCAACATTGA 59.358 37.500 0.00 0.00 35.57 2.57
33 34 4.930963 TGTAAACAAGTGGCTCAACATTG 58.069 39.130 0.00 0.00 0.00 2.82
34 35 5.789643 ATGTAAACAAGTGGCTCAACATT 57.210 34.783 0.00 0.00 0.00 2.71
35 36 6.892658 TTATGTAAACAAGTGGCTCAACAT 57.107 33.333 0.00 0.00 0.00 2.71
36 37 6.701145 TTTATGTAAACAAGTGGCTCAACA 57.299 33.333 0.00 0.00 0.00 3.33
37 38 5.629435 GCTTTATGTAAACAAGTGGCTCAAC 59.371 40.000 0.00 0.00 0.00 3.18
38 39 5.534654 AGCTTTATGTAAACAAGTGGCTCAA 59.465 36.000 0.00 0.00 0.00 3.02
39 40 5.070001 AGCTTTATGTAAACAAGTGGCTCA 58.930 37.500 0.00 0.00 0.00 4.26
40 41 5.629079 AGCTTTATGTAAACAAGTGGCTC 57.371 39.130 0.00 0.00 0.00 4.70
41 42 6.405278 AAAGCTTTATGTAAACAAGTGGCT 57.595 33.333 10.72 0.00 0.00 4.75
42 43 8.757164 ATAAAAGCTTTATGTAAACAAGTGGC 57.243 30.769 13.10 0.00 0.00 5.01
43 44 9.906660 TGATAAAAGCTTTATGTAAACAAGTGG 57.093 29.630 13.10 0.00 0.00 4.00
58 59 9.502091 TGTACACTAAACTGATGATAAAAGCTT 57.498 29.630 0.00 0.00 0.00 3.74
59 60 9.672673 ATGTACACTAAACTGATGATAAAAGCT 57.327 29.630 0.00 0.00 0.00 3.74
60 61 9.922305 GATGTACACTAAACTGATGATAAAAGC 57.078 33.333 0.00 0.00 0.00 3.51
77 78 9.824216 ACCTACCTATATACAATGATGTACACT 57.176 33.333 0.00 0.00 44.47 3.55
85 86 9.938280 GCACAATAACCTACCTATATACAATGA 57.062 33.333 0.00 0.00 0.00 2.57
86 87 9.719355 TGCACAATAACCTACCTATATACAATG 57.281 33.333 0.00 0.00 0.00 2.82
87 88 9.720769 GTGCACAATAACCTACCTATATACAAT 57.279 33.333 13.17 0.00 0.00 2.71
88 89 8.706521 TGTGCACAATAACCTACCTATATACAA 58.293 33.333 19.28 0.00 0.00 2.41
89 90 8.252624 TGTGCACAATAACCTACCTATATACA 57.747 34.615 19.28 0.00 0.00 2.29
90 91 8.365647 ACTGTGCACAATAACCTACCTATATAC 58.634 37.037 21.98 0.00 0.00 1.47
91 92 8.364894 CACTGTGCACAATAACCTACCTATATA 58.635 37.037 21.98 0.00 0.00 0.86
92 93 7.217200 CACTGTGCACAATAACCTACCTATAT 58.783 38.462 21.98 0.00 0.00 0.86
93 94 6.578944 CACTGTGCACAATAACCTACCTATA 58.421 40.000 21.98 0.00 0.00 1.31
94 95 5.428253 CACTGTGCACAATAACCTACCTAT 58.572 41.667 21.98 0.00 0.00 2.57
95 96 4.827692 CACTGTGCACAATAACCTACCTA 58.172 43.478 21.98 0.00 0.00 3.08
96 97 3.674997 CACTGTGCACAATAACCTACCT 58.325 45.455 21.98 0.00 0.00 3.08
118 119 9.179552 CTCTGAACAATCATACTCTCTATTTCG 57.820 37.037 0.00 0.00 34.37 3.46
142 143 0.175760 TAGCTGACGGGCATTCACTC 59.824 55.000 0.00 0.00 34.17 3.51
153 154 2.054232 TAGGACCCTCTTAGCTGACG 57.946 55.000 0.00 0.00 0.00 4.35
154 155 4.396790 CGATATAGGACCCTCTTAGCTGAC 59.603 50.000 0.00 0.00 0.00 3.51
176 177 1.378514 CTTTGGATGGGTCCCACCG 60.379 63.158 14.57 1.02 44.41 4.94
177 178 1.682344 GCTTTGGATGGGTCCCACC 60.682 63.158 14.57 16.82 44.41 4.61
223 224 8.637986 AGCAACCTTGTCTACATATTTTTGAAA 58.362 29.630 0.00 0.00 0.00 2.69
228 229 5.476599 TGCAGCAACCTTGTCTACATATTTT 59.523 36.000 0.00 0.00 0.00 1.82
259 267 1.295792 ACAAACACGACGCATGAAGT 58.704 45.000 0.00 0.00 0.00 3.01
264 272 3.119459 AGAGAGATACAAACACGACGCAT 60.119 43.478 0.00 0.00 0.00 4.73
296 304 7.696035 TGCACAAAGATAGCGTACATATTTTTG 59.304 33.333 19.32 19.32 39.13 2.44
327 335 1.328680 GCGACTGACCTGCATGTATTG 59.671 52.381 0.00 0.00 0.00 1.90
329 337 0.179073 GGCGACTGACCTGCATGTAT 60.179 55.000 0.00 0.00 0.00 2.29
330 338 1.218047 GGCGACTGACCTGCATGTA 59.782 57.895 0.00 0.00 0.00 2.29
331 339 2.046892 GGCGACTGACCTGCATGT 60.047 61.111 0.00 0.00 0.00 3.21
363 371 6.096282 TCCCTTCAATTAAATTCGATTGACCC 59.904 38.462 13.14 0.00 40.78 4.46
369 377 8.348285 TGTTTCTCCCTTCAATTAAATTCGAT 57.652 30.769 0.00 0.00 0.00 3.59
378 386 4.803452 TCTGGTTGTTTCTCCCTTCAATT 58.197 39.130 0.00 0.00 0.00 2.32
386 394 1.003696 CTCCCCTCTGGTTGTTTCTCC 59.996 57.143 0.00 0.00 34.77 3.71
391 399 1.068121 CTTCCTCCCCTCTGGTTGTT 58.932 55.000 0.00 0.00 34.77 2.83
393 401 1.280421 CTTCTTCCTCCCCTCTGGTTG 59.720 57.143 0.00 0.00 34.77 3.77
398 406 0.686112 CGAGCTTCTTCCTCCCCTCT 60.686 60.000 0.00 0.00 0.00 3.69
399 407 1.819905 CGAGCTTCTTCCTCCCCTC 59.180 63.158 0.00 0.00 0.00 4.30
429 437 4.772624 CCAATCCTAAGATAGATCGTGGGA 59.227 45.833 11.77 11.77 46.19 4.37
435 443 5.280727 CCCAACCCCAATCCTAAGATAGATC 60.281 48.000 0.00 0.00 30.42 2.75
448 456 3.683518 GCCTCCCCCAACCCCAAT 61.684 66.667 0.00 0.00 0.00 3.16
455 463 2.444696 CCATGTTGCCTCCCCCAA 59.555 61.111 0.00 0.00 0.00 4.12
470 478 4.041762 GAATCCCCACCACCGCCA 62.042 66.667 0.00 0.00 0.00 5.69
515 523 1.152139 GGCCATCCCTCTAGCTCCT 60.152 63.158 0.00 0.00 0.00 3.69
547 555 2.187946 CTCCTCCCACCATCGTGC 59.812 66.667 0.00 0.00 38.79 5.34
551 559 0.991920 TTGAACCTCCTCCCACCATC 59.008 55.000 0.00 0.00 0.00 3.51
553 561 0.104672 TCTTGAACCTCCTCCCACCA 60.105 55.000 0.00 0.00 0.00 4.17
556 564 2.041620 CCATTTCTTGAACCTCCTCCCA 59.958 50.000 0.00 0.00 0.00 4.37
559 567 1.740025 CGCCATTTCTTGAACCTCCTC 59.260 52.381 0.00 0.00 0.00 3.71
630 660 1.817209 GATCTATCCCCGATCCGCC 59.183 63.158 0.00 0.00 32.94 6.13
637 667 1.617322 TCAACCTCGATCTATCCCCG 58.383 55.000 0.00 0.00 0.00 5.73
691 721 4.965119 ATTTAAGCGGTCAATCTCAACC 57.035 40.909 0.00 0.00 0.00 3.77
722 770 5.007724 CGAAGGAATGGCTATAAAACAGTCC 59.992 44.000 0.00 0.00 46.52 3.85
728 776 6.207810 ACAAACACGAAGGAATGGCTATAAAA 59.792 34.615 0.00 0.00 0.00 1.52
730 778 5.250200 ACAAACACGAAGGAATGGCTATAA 58.750 37.500 0.00 0.00 0.00 0.98
778 827 1.547372 ACCTTGTCGGTAGCGTACATT 59.453 47.619 14.79 3.13 46.73 2.71
789 841 0.307760 GACAAAGTGCACCTTGTCGG 59.692 55.000 33.86 12.34 39.35 4.79
808 860 1.026182 TGGCGCTTTGGATGCAGTAG 61.026 55.000 7.64 0.00 0.00 2.57
815 867 2.439156 GCTCCTGGCGCTTTGGAT 60.439 61.111 7.64 0.00 0.00 3.41
833 885 3.373439 GCCATTAATTTTCAATGCGGCAA 59.627 39.130 6.82 0.00 33.00 4.52
853 905 4.682787 GCCACCTCAATAATTTTACTGCC 58.317 43.478 0.00 0.00 0.00 4.85
860 912 1.846007 TGGCGCCACCTCAATAATTT 58.154 45.000 29.03 0.00 40.22 1.82
870 922 0.179097 TTTGTTTTCTTGGCGCCACC 60.179 50.000 32.95 13.26 39.84 4.61
889 941 6.089016 CAGACTGTACGAAATTGACGTTATGT 59.911 38.462 14.29 10.84 43.62 2.29
905 957 2.087009 GTGGACGCGCAGACTGTAC 61.087 63.158 5.73 0.00 0.00 2.90
974 1067 3.984193 CTGGGGTGGCTAGTGCTGC 62.984 68.421 0.00 0.00 39.59 5.25
988 1081 1.001597 GCTACCTCGAATCGTACTGGG 60.002 57.143 1.52 1.70 0.00 4.45
992 1085 2.286891 GGTCTGCTACCTCGAATCGTAC 60.287 54.545 1.52 0.00 45.75 3.67
993 1086 1.945394 GGTCTGCTACCTCGAATCGTA 59.055 52.381 1.52 0.00 45.75 3.43
994 1087 0.739561 GGTCTGCTACCTCGAATCGT 59.260 55.000 1.52 0.00 45.75 3.73
1342 1457 2.870161 CGAACAGAGTCGCCGTCG 60.870 66.667 0.00 0.00 33.66 5.12
1378 1493 2.102252 GAGATCTCCAAAGTCATCGCCT 59.898 50.000 12.00 0.00 0.00 5.52
1466 1581 3.717294 CACTCCCCAAGACCCCCG 61.717 72.222 0.00 0.00 0.00 5.73
1475 1590 2.203280 CACGGCAAACACTCCCCA 60.203 61.111 0.00 0.00 0.00 4.96
1632 1768 2.589442 GCGGAACAACGTCCACCA 60.589 61.111 0.00 0.00 37.56 4.17
1642 1781 4.287781 TCGAACAGCGGCGGAACA 62.288 61.111 9.78 0.00 41.33 3.18
1808 1956 2.512515 CAACCGGCCTAGCAGCTC 60.513 66.667 0.00 0.00 0.00 4.09
1823 1971 4.735132 CTCGACGCGCTTCCCCAA 62.735 66.667 5.73 0.00 0.00 4.12
1945 2093 1.234615 CGAACCCAAACTGATGCCGT 61.235 55.000 0.00 0.00 0.00 5.68
1957 2105 3.931247 CACCCGGTCACGAACCCA 61.931 66.667 0.00 0.00 46.27 4.51
2029 2178 2.283173 TCCTCCACGCAGCAGAGA 60.283 61.111 5.80 0.00 0.00 3.10
2049 2198 4.873129 CGCCGTGACCATCCTCCG 62.873 72.222 0.00 0.00 0.00 4.63
2371 2526 1.064824 GGAATGCCTCCATCTCCCCT 61.065 60.000 0.00 0.00 44.67 4.79
2491 2646 0.731855 GGTCTACCGTTGCACTCGAC 60.732 60.000 11.33 2.72 0.00 4.20
2492 2647 1.582968 GGTCTACCGTTGCACTCGA 59.417 57.895 11.33 0.00 0.00 4.04
2673 2829 4.420522 TGCTATGGCAGTACATGATTGA 57.579 40.909 0.00 0.00 44.28 2.57
2710 2877 3.287482 CAAAACGCCTTGCAACCAT 57.713 47.368 0.00 0.00 0.00 3.55
2731 2899 4.217983 ACGAAAGGAGAAACGATCTACACT 59.782 41.667 7.73 0.27 42.03 3.55
2733 2901 4.458295 AGACGAAAGGAGAAACGATCTACA 59.542 41.667 7.73 0.00 42.03 2.74
2736 2908 3.759618 AGAGACGAAAGGAGAAACGATCT 59.240 43.478 0.00 0.00 42.61 2.75
2837 3050 6.810911 TGAAGATGGACTTAGACTTAGATGC 58.189 40.000 0.00 0.00 39.13 3.91
2864 3077 2.585247 GTCCGATTCGAAGGCGGG 60.585 66.667 30.07 17.31 44.87 6.13
2925 3138 3.541632 GGCGAAAGTTTGATGGATAGGA 58.458 45.455 0.00 0.00 0.00 2.94
2968 3181 0.947180 TGAAGTGCCGCGGACTTAAC 60.947 55.000 33.48 21.59 33.71 2.01
3109 3325 9.110502 GATTAAAGGGGACAACTAGAACATAAG 57.889 37.037 0.00 0.00 0.00 1.73
3123 3339 2.773993 TGTGGACGATTAAAGGGGAC 57.226 50.000 0.00 0.00 0.00 4.46
3125 3341 3.428862 GCATTTGTGGACGATTAAAGGGG 60.429 47.826 0.00 0.00 0.00 4.79
3136 3352 6.630444 ATGAATAGATGAGCATTTGTGGAC 57.370 37.500 0.00 0.00 0.00 4.02
3155 3371 7.750229 ACTCATGAGCAGTTTAAGAAATGAA 57.250 32.000 22.83 0.00 32.82 2.57
3159 3375 5.532406 AGCAACTCATGAGCAGTTTAAGAAA 59.468 36.000 22.83 0.00 31.40 2.52
3189 3405 8.634335 TTGTCCAGATAAATCAACAGATTTGA 57.366 30.769 12.35 0.35 40.97 2.69
3247 3463 1.068333 CCGGCAATGTTTGAGGAGTTG 60.068 52.381 0.00 0.00 33.60 3.16
3290 3506 4.690748 GGAATTTGAGAACACGAGTGATCA 59.309 41.667 10.50 8.07 35.20 2.92
3306 3522 4.582869 TGAGATCACTGGTCTGGAATTTG 58.417 43.478 0.00 0.00 0.00 2.32
3321 3537 5.768980 AGGAGGTCTGAAATTTGAGATCA 57.231 39.130 18.46 0.00 0.00 2.92
3443 3659 5.303589 AGAAATGATGTGGATAGGCATTTGG 59.696 40.000 0.00 0.00 38.75 3.28
3512 3728 0.651031 GCGCGACCTTTATCAAGACC 59.349 55.000 12.10 0.00 30.57 3.85


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

AutoCloner maintained by Alex Coulton.