Multiple sequence alignment - TraesCS7A01G170700

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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 TraesCS7A01G170700 chr7A 100.000 3128 0 0 705 3832 126592561 126595688 0.000000e+00 5777
1 TraesCS7A01G170700 chr7A 76.314 1427 283 45 1400 2798 126860787 126862186 0.000000e+00 712
2 TraesCS7A01G170700 chr7A 100.000 364 0 0 1 364 126591857 126592220 0.000000e+00 673
3 TraesCS7A01G170700 chr7D 90.081 2228 123 49 705 2858 123740113 123737910 0.000000e+00 2800
4 TraesCS7A01G170700 chr7D 76.045 1436 277 51 1400 2798 124293377 124294782 0.000000e+00 684
5 TraesCS7A01G170700 chr7D 90.526 190 5 5 164 353 123740286 123740110 4.950000e-59 239
6 TraesCS7A01G170700 chr7B 94.203 1656 56 13 1242 2858 85151017 85149363 0.000000e+00 2490
7 TraesCS7A01G170700 chr7B 94.659 880 41 5 2956 3832 698921176 698920300 0.000000e+00 1360
8 TraesCS7A01G170700 chr7B 94.558 882 40 5 2956 3832 693384795 693383917 0.000000e+00 1356
9 TraesCS7A01G170700 chr7B 77.176 1310 259 32 1400 2684 85940685 85941979 0.000000e+00 726
10 TraesCS7A01G170700 chr7B 85.689 559 32 20 711 1257 85151560 85151038 2.600000e-151 545
11 TraesCS7A01G170700 chr7B 85.538 325 30 7 32 353 85151873 85151563 1.330000e-84 324
12 TraesCS7A01G170700 chr6A 94.161 959 52 4 2876 3832 420585766 420584810 0.000000e+00 1458
13 TraesCS7A01G170700 chr1A 93.118 959 62 4 2876 3832 33754409 33755365 0.000000e+00 1402
14 TraesCS7A01G170700 chr6B 92.241 812 45 6 3023 3832 68409241 68408446 0.000000e+00 1134
15 TraesCS7A01G170700 chr6B 92.166 217 15 1 3599 3813 565388165 565388381 4.810000e-79 305
16 TraesCS7A01G170700 chr1D 92.093 215 17 0 3599 3813 65839959 65840173 1.730000e-78 303
17 TraesCS7A01G170700 chr2D 91.403 221 12 5 3599 3817 648360398 648360613 2.890000e-76 296
18 TraesCS7A01G170700 chr5D 90.045 221 19 2 3599 3817 547753044 547753263 2.250000e-72 283


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 TraesCS7A01G170700 chr7A 126591857 126595688 3831 False 3225.000000 5777 100.000000 1 3832 2 chr7A.!!$F2 3831
1 TraesCS7A01G170700 chr7A 126860787 126862186 1399 False 712.000000 712 76.314000 1400 2798 1 chr7A.!!$F1 1398
2 TraesCS7A01G170700 chr7D 123737910 123740286 2376 True 1519.500000 2800 90.303500 164 2858 2 chr7D.!!$R1 2694
3 TraesCS7A01G170700 chr7D 124293377 124294782 1405 False 684.000000 684 76.045000 1400 2798 1 chr7D.!!$F1 1398
4 TraesCS7A01G170700 chr7B 698920300 698921176 876 True 1360.000000 1360 94.659000 2956 3832 1 chr7B.!!$R2 876
5 TraesCS7A01G170700 chr7B 693383917 693384795 878 True 1356.000000 1356 94.558000 2956 3832 1 chr7B.!!$R1 876
6 TraesCS7A01G170700 chr7B 85149363 85151873 2510 True 1119.666667 2490 88.476667 32 2858 3 chr7B.!!$R3 2826
7 TraesCS7A01G170700 chr7B 85940685 85941979 1294 False 726.000000 726 77.176000 1400 2684 1 chr7B.!!$F1 1284
8 TraesCS7A01G170700 chr6A 420584810 420585766 956 True 1458.000000 1458 94.161000 2876 3832 1 chr6A.!!$R1 956
9 TraesCS7A01G170700 chr1A 33754409 33755365 956 False 1402.000000 1402 93.118000 2876 3832 1 chr1A.!!$F1 956
10 TraesCS7A01G170700 chr6B 68408446 68409241 795 True 1134.000000 1134 92.241000 3023 3832 1 chr6B.!!$R1 809

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
363 367 0.318275 GCAAACGATCACCCGCAAAA 60.318 50.0 0.0 0.00 0.00 2.44 F
1386 1482 0.463295 ATCCACCTGCAGCAGAATCG 60.463 55.0 24.9 9.42 32.44 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2159 2276 0.029167 GTAGGAGTCGTAGAAGCGCC 59.971 60.0 2.29 0.0 39.69 6.53 R
2917 3068 0.034616 CTGAGATGGGGGATCGAAGC 59.965 60.0 0.00 0.0 36.04 3.86 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
21 22 3.893720 GGCCTCAGAATTTATGCATTCG 58.106 45.455 3.54 0.00 38.10 3.34
22 23 3.316308 GGCCTCAGAATTTATGCATTCGT 59.684 43.478 3.54 0.00 38.10 3.85
23 24 4.202050 GGCCTCAGAATTTATGCATTCGTT 60.202 41.667 3.54 0.00 38.10 3.85
24 25 5.343249 GCCTCAGAATTTATGCATTCGTTT 58.657 37.500 3.54 0.00 38.10 3.60
25 26 5.807011 GCCTCAGAATTTATGCATTCGTTTT 59.193 36.000 3.54 0.00 38.10 2.43
26 27 6.020360 GCCTCAGAATTTATGCATTCGTTTTC 60.020 38.462 3.54 2.19 38.10 2.29
27 28 7.028962 CCTCAGAATTTATGCATTCGTTTTCA 58.971 34.615 3.54 0.00 38.10 2.69
28 29 7.008628 CCTCAGAATTTATGCATTCGTTTTCAC 59.991 37.037 3.54 0.00 38.10 3.18
29 30 7.366513 TCAGAATTTATGCATTCGTTTTCACA 58.633 30.769 3.54 0.00 38.10 3.58
30 31 7.864882 TCAGAATTTATGCATTCGTTTTCACAA 59.135 29.630 3.54 0.00 38.10 3.33
60 61 7.972623 ATAGAAAGAAATACGACAACTCTCG 57.027 36.000 0.00 0.00 39.68 4.04
76 77 4.184629 ACTCTCGATTTCTTTCATTCCCG 58.815 43.478 0.00 0.00 0.00 5.14
81 82 3.181500 CGATTTCTTTCATTCCCGTTCCC 60.181 47.826 0.00 0.00 0.00 3.97
88 89 3.162147 TCATTCCCGTTCCCATTTTCA 57.838 42.857 0.00 0.00 0.00 2.69
91 92 3.449746 TTCCCGTTCCCATTTTCATCT 57.550 42.857 0.00 0.00 0.00 2.90
92 93 3.449746 TCCCGTTCCCATTTTCATCTT 57.550 42.857 0.00 0.00 0.00 2.40
95 96 3.509575 CCCGTTCCCATTTTCATCTTTCA 59.490 43.478 0.00 0.00 0.00 2.69
96 97 4.160252 CCCGTTCCCATTTTCATCTTTCAT 59.840 41.667 0.00 0.00 0.00 2.57
99 100 6.318648 CCGTTCCCATTTTCATCTTTCATCTA 59.681 38.462 0.00 0.00 0.00 1.98
121 123 0.679640 TGGCTTATTTGGTCGCCCAG 60.680 55.000 0.00 0.00 43.15 4.45
136 138 1.536073 CCCAGTTGACCTCTCTCGCA 61.536 60.000 0.00 0.00 0.00 5.10
141 143 1.135517 GTTGACCTCTCTCGCAGTCTC 60.136 57.143 0.00 0.00 0.00 3.36
144 146 0.679640 ACCTCTCTCGCAGTCTCCAG 60.680 60.000 0.00 0.00 0.00 3.86
194 198 0.527565 ATGTGCTCAAATTCACCGGC 59.472 50.000 0.00 0.00 32.51 6.13
195 199 1.212751 GTGCTCAAATTCACCGGCC 59.787 57.895 0.00 0.00 0.00 6.13
196 200 2.331893 TGCTCAAATTCACCGGCCG 61.332 57.895 21.04 21.04 0.00 6.13
197 201 3.051392 GCTCAAATTCACCGGCCGG 62.051 63.158 42.17 42.17 42.03 6.13
251 255 5.537300 AGATTGCATCGAACTACCAGTAT 57.463 39.130 0.00 0.00 0.00 2.12
252 256 5.292765 AGATTGCATCGAACTACCAGTATG 58.707 41.667 0.00 0.00 0.00 2.39
253 257 4.465632 TTGCATCGAACTACCAGTATGT 57.534 40.909 0.00 0.00 0.00 2.29
254 258 5.585820 TTGCATCGAACTACCAGTATGTA 57.414 39.130 0.00 0.00 0.00 2.29
255 259 4.928601 TGCATCGAACTACCAGTATGTAC 58.071 43.478 0.00 0.00 0.00 2.90
256 260 4.643334 TGCATCGAACTACCAGTATGTACT 59.357 41.667 0.00 0.00 36.90 2.73
267 271 6.374565 ACCAGTATGTACTCTACATCGAAC 57.625 41.667 0.00 0.00 45.83 3.95
268 272 5.007430 ACCAGTATGTACTCTACATCGAACG 59.993 44.000 0.00 0.00 45.83 3.95
269 273 5.007430 CCAGTATGTACTCTACATCGAACGT 59.993 44.000 0.00 0.00 45.83 3.99
312 316 0.528466 GCGCTTCCATCGATCTGTCA 60.528 55.000 0.00 0.00 0.00 3.58
353 357 2.411547 CCAACGAAGTGAGCAAACGATC 60.412 50.000 0.00 0.00 45.00 3.69
354 358 2.148916 ACGAAGTGAGCAAACGATCA 57.851 45.000 0.00 0.00 42.51 2.92
358 362 1.787847 GTGAGCAAACGATCACCCG 59.212 57.895 0.00 0.00 42.66 5.28
359 363 2.032634 TGAGCAAACGATCACCCGC 61.033 57.895 0.00 0.00 0.00 6.13
360 364 2.031919 AGCAAACGATCACCCGCA 59.968 55.556 0.00 0.00 0.00 5.69
361 365 1.573829 GAGCAAACGATCACCCGCAA 61.574 55.000 0.00 0.00 0.00 4.85
362 366 1.169661 AGCAAACGATCACCCGCAAA 61.170 50.000 0.00 0.00 0.00 3.68
363 367 0.318275 GCAAACGATCACCCGCAAAA 60.318 50.000 0.00 0.00 0.00 2.44
742 749 0.876342 GGCCAGCTACACGCATCTAC 60.876 60.000 0.00 0.00 42.61 2.59
743 750 0.876342 GCCAGCTACACGCATCTACC 60.876 60.000 0.00 0.00 42.61 3.18
744 751 0.747255 CCAGCTACACGCATCTACCT 59.253 55.000 0.00 0.00 42.61 3.08
745 752 1.954382 CCAGCTACACGCATCTACCTA 59.046 52.381 0.00 0.00 42.61 3.08
746 753 2.287668 CCAGCTACACGCATCTACCTAC 60.288 54.545 0.00 0.00 42.61 3.18
780 797 1.271926 ACCAACTAGGCCAACATGGTC 60.272 52.381 15.23 0.00 44.07 4.02
847 864 5.936956 GGTCAACTCATCATCTTTCTCAAGT 59.063 40.000 0.00 0.00 0.00 3.16
848 865 7.099764 GGTCAACTCATCATCTTTCTCAAGTA 58.900 38.462 0.00 0.00 0.00 2.24
849 866 7.277539 GGTCAACTCATCATCTTTCTCAAGTAG 59.722 40.741 0.00 0.00 0.00 2.57
850 867 8.031864 GTCAACTCATCATCTTTCTCAAGTAGA 58.968 37.037 0.00 0.00 0.00 2.59
851 868 8.249638 TCAACTCATCATCTTTCTCAAGTAGAG 58.750 37.037 0.00 0.00 46.14 2.43
852 869 7.716799 ACTCATCATCTTTCTCAAGTAGAGT 57.283 36.000 0.00 0.00 44.98 3.24
866 883 8.201464 TCTCAAGTAGAGTAGTACAGATCTGAG 58.799 40.741 29.27 10.04 44.98 3.35
867 884 6.764085 TCAAGTAGAGTAGTACAGATCTGAGC 59.236 42.308 29.27 19.09 0.00 4.26
869 886 6.654959 AGTAGAGTAGTACAGATCTGAGCAA 58.345 40.000 29.27 8.90 0.00 3.91
876 893 6.543430 AGTACAGATCTGAGCAAGAAATCT 57.457 37.500 29.27 4.55 38.79 2.40
877 894 7.652524 AGTACAGATCTGAGCAAGAAATCTA 57.347 36.000 29.27 3.54 38.79 1.98
878 895 7.488322 AGTACAGATCTGAGCAAGAAATCTAC 58.512 38.462 29.27 15.00 38.79 2.59
879 896 5.347342 ACAGATCTGAGCAAGAAATCTACG 58.653 41.667 29.27 0.00 38.79 3.51
904 921 5.579718 ACACACGATCTACTGTAGTATTGC 58.420 41.667 14.11 1.23 0.00 3.56
908 925 7.913821 CACACGATCTACTGTAGTATTGCTTAA 59.086 37.037 14.11 0.00 0.00 1.85
909 926 8.630917 ACACGATCTACTGTAGTATTGCTTAAT 58.369 33.333 14.11 0.00 0.00 1.40
949 968 3.116079 TGTTAACCAAGAGACGGTTCC 57.884 47.619 2.48 0.00 43.36 3.62
981 1000 4.215349 GCTAGGAAGCCACTGCAG 57.785 61.111 13.48 13.48 43.40 4.41
993 1023 2.783135 CCACTGCAGGAGAAAGCTAAA 58.217 47.619 19.93 0.00 0.00 1.85
1018 1048 1.741706 AGATGGACAAGAAATGCAGCG 59.258 47.619 0.00 0.00 0.00 5.18
1031 1061 2.701780 GCAGCGGAGAGGAGTCGAA 61.702 63.158 0.00 0.00 0.00 3.71
1044 1074 1.079750 GTCGAACTGGCTGGAGGTC 60.080 63.158 0.00 0.00 0.00 3.85
1249 1288 2.284190 GAGGAGGTAATTGCAGTCTGC 58.716 52.381 18.32 18.32 45.29 4.26
1386 1482 0.463295 ATCCACCTGCAGCAGAATCG 60.463 55.000 24.90 9.42 32.44 3.34
1395 1491 1.806542 GCAGCAGAATCGTCCAAGAAA 59.193 47.619 0.00 0.00 0.00 2.52
1396 1492 2.421424 GCAGCAGAATCGTCCAAGAAAT 59.579 45.455 0.00 0.00 0.00 2.17
1397 1493 3.119708 GCAGCAGAATCGTCCAAGAAATT 60.120 43.478 0.00 0.00 0.00 1.82
1439 1535 1.739338 CTCCTCCCAGGATTCGACGG 61.739 65.000 0.00 0.00 44.81 4.79
1520 1616 1.099295 ACGCCGTATCTCATCGACCA 61.099 55.000 0.00 0.00 0.00 4.02
1617 1713 3.622060 ATCCGGGGTGAAAGGCGTG 62.622 63.158 0.00 0.00 0.00 5.34
1721 1832 2.586079 CTACGCCATGCTCACCGG 60.586 66.667 0.00 0.00 0.00 5.28
1829 1940 3.854669 CCCGCTCCAGGGCTACAG 61.855 72.222 0.00 0.00 45.72 2.74
2159 2276 2.124983 CGTCTGGGGCATGGTCAG 60.125 66.667 0.00 0.00 0.00 3.51
2244 2361 2.030562 AAGGACGACAAGCCGGTG 59.969 61.111 1.90 0.00 0.00 4.94
2770 2921 4.489771 GGTGCCTCATGTCCGGGG 62.490 72.222 0.00 0.00 0.00 5.73
2803 2954 1.280421 GTCTTGGGGTCTGAAGCTCAT 59.720 52.381 0.00 0.00 32.30 2.90
2840 2991 5.005779 CGAGAAGGATGTGTAGAATTTTCGG 59.994 44.000 0.00 0.00 0.00 4.30
2852 3003 5.338614 AGAATTTTCGGTCACAGTTTACG 57.661 39.130 0.00 0.00 0.00 3.18
2858 3009 1.733389 CGGTCACAGTTTACGCCGTAT 60.733 52.381 0.00 0.00 35.11 3.06
2859 3010 2.477694 CGGTCACAGTTTACGCCGTATA 60.478 50.000 0.00 0.00 35.11 1.47
2860 3011 3.709987 GGTCACAGTTTACGCCGTATAT 58.290 45.455 0.00 0.00 0.00 0.86
2861 3012 3.732721 GGTCACAGTTTACGCCGTATATC 59.267 47.826 0.00 0.00 0.00 1.63
2862 3013 4.498682 GGTCACAGTTTACGCCGTATATCT 60.499 45.833 0.00 0.00 0.00 1.98
2863 3014 4.674211 GTCACAGTTTACGCCGTATATCTC 59.326 45.833 0.00 0.00 0.00 2.75
2864 3015 4.577693 TCACAGTTTACGCCGTATATCTCT 59.422 41.667 0.00 0.00 0.00 3.10
2865 3016 5.759763 TCACAGTTTACGCCGTATATCTCTA 59.240 40.000 0.00 0.00 0.00 2.43
2866 3017 5.850128 CACAGTTTACGCCGTATATCTCTAC 59.150 44.000 0.00 0.00 0.00 2.59
2867 3018 5.762218 ACAGTTTACGCCGTATATCTCTACT 59.238 40.000 0.00 0.00 0.00 2.57
2868 3019 6.931281 ACAGTTTACGCCGTATATCTCTACTA 59.069 38.462 0.00 0.00 0.00 1.82
2869 3020 7.605691 ACAGTTTACGCCGTATATCTCTACTAT 59.394 37.037 0.00 0.00 0.00 2.12
2870 3021 8.449397 CAGTTTACGCCGTATATCTCTACTATT 58.551 37.037 0.00 0.00 0.00 1.73
2871 3022 9.658799 AGTTTACGCCGTATATCTCTACTATTA 57.341 33.333 0.00 0.00 0.00 0.98
2899 3050 9.268282 AGTCTACTATTAAAAGAGGATCCAACA 57.732 33.333 15.82 0.00 33.66 3.33
2908 3059 3.033909 AGAGGATCCAACATCGTGATGA 58.966 45.455 15.82 0.00 37.87 2.92
2917 3068 2.814269 ACATCGTGATGATTCGACCTG 58.186 47.619 16.33 0.00 41.20 4.00
2930 3081 2.285368 ACCTGCTTCGATCCCCCA 60.285 61.111 0.00 0.00 0.00 4.96
2931 3082 1.694169 ACCTGCTTCGATCCCCCAT 60.694 57.895 0.00 0.00 0.00 4.00
2932 3083 1.072159 CCTGCTTCGATCCCCCATC 59.928 63.158 0.00 0.00 0.00 3.51
2968 3119 1.737735 GCAGGCCAAAATCCAACGC 60.738 57.895 5.01 0.00 0.00 4.84
3009 3160 0.249120 CCAACTCAGCCCACATACGA 59.751 55.000 0.00 0.00 0.00 3.43
3091 3247 2.737376 GACAACCCACGACGAGGC 60.737 66.667 5.72 0.00 0.00 4.70
3106 3262 1.474330 GAGGCCCATCGACCAAAAAT 58.526 50.000 0.00 0.00 0.00 1.82
3131 3287 0.738975 CACCTACGAGCTCCATCGAA 59.261 55.000 8.47 0.00 45.56 3.71
3192 3348 2.110352 TCGCGTACGAGCTCCATCA 61.110 57.895 21.65 0.00 45.12 3.07
3207 3364 1.663388 ATCAACTCGCGAACGCACA 60.663 52.632 11.33 4.08 42.06 4.57
3208 3365 1.617755 ATCAACTCGCGAACGCACAG 61.618 55.000 11.33 14.87 42.06 3.66
3236 3393 2.965147 GATCAAACGCCAGCGCACA 61.965 57.895 11.47 0.00 44.19 4.57
3361 3518 2.342279 CCAGGAAGTCGCCGTTCA 59.658 61.111 0.00 0.00 0.00 3.18
3432 3589 3.145551 GCCGGGAAGTCGCCTCTA 61.146 66.667 2.18 0.00 0.00 2.43
3479 3636 5.145564 CCCTCATCATCCAAAATCCAAGAT 58.854 41.667 0.00 0.00 0.00 2.40
3482 3639 4.823442 TCATCATCCAAAATCCAAGATCCG 59.177 41.667 0.00 0.00 0.00 4.18
3483 3640 3.554934 TCATCCAAAATCCAAGATCCGG 58.445 45.455 0.00 0.00 0.00 5.14
3510 3667 0.470766 AAGGTAACCCAGTCGCACAA 59.529 50.000 0.00 0.00 37.17 3.33
3574 3731 1.897802 ACCGTACTTCTTCCCAATCGT 59.102 47.619 0.00 0.00 0.00 3.73
3586 3743 1.007271 CAATCGTAGCCGCCGATCT 60.007 57.895 5.20 0.00 43.75 2.75
3813 3970 9.872721 TCCTATAAATACAACAACGATGTACAA 57.127 29.630 0.00 0.00 39.40 2.41
3814 3971 9.910511 CCTATAAATACAACAACGATGTACAAC 57.089 33.333 0.00 0.00 39.40 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.316308 ACGAATGCATAAATTCTGAGGCC 59.684 43.478 0.00 0.00 34.90 5.19
1 2 4.558538 ACGAATGCATAAATTCTGAGGC 57.441 40.909 0.00 0.00 34.90 4.70
2 3 7.008628 GTGAAAACGAATGCATAAATTCTGAGG 59.991 37.037 0.00 0.00 34.90 3.86
3 4 7.538334 TGTGAAAACGAATGCATAAATTCTGAG 59.462 33.333 0.00 0.00 34.90 3.35
4 5 7.366513 TGTGAAAACGAATGCATAAATTCTGA 58.633 30.769 0.00 0.00 34.90 3.27
5 6 7.565450 TGTGAAAACGAATGCATAAATTCTG 57.435 32.000 0.00 0.00 34.90 3.02
6 7 8.761575 ATTGTGAAAACGAATGCATAAATTCT 57.238 26.923 0.00 0.00 34.90 2.40
7 8 9.810231 AAATTGTGAAAACGAATGCATAAATTC 57.190 25.926 0.00 1.87 33.92 2.17
14 15 9.684448 TCTATAAAAATTGTGAAAACGAATGCA 57.316 25.926 0.00 0.00 0.00 3.96
49 50 5.769967 ATGAAAGAAATCGAGAGTTGTCG 57.230 39.130 0.00 0.00 41.51 4.35
52 53 5.446473 CGGGAATGAAAGAAATCGAGAGTTG 60.446 44.000 0.00 0.00 0.00 3.16
54 55 4.184629 CGGGAATGAAAGAAATCGAGAGT 58.815 43.478 0.00 0.00 0.00 3.24
56 57 4.202245 ACGGGAATGAAAGAAATCGAGA 57.798 40.909 0.00 0.00 0.00 4.04
57 58 4.201822 GGAACGGGAATGAAAGAAATCGAG 60.202 45.833 0.00 0.00 0.00 4.04
60 61 3.761752 TGGGAACGGGAATGAAAGAAATC 59.238 43.478 0.00 0.00 0.00 2.17
76 77 8.286191 AGTAGATGAAAGATGAAAATGGGAAC 57.714 34.615 0.00 0.00 0.00 3.62
81 82 7.769220 AGCCAAGTAGATGAAAGATGAAAATG 58.231 34.615 0.00 0.00 0.00 2.32
88 89 7.836183 ACCAAATAAGCCAAGTAGATGAAAGAT 59.164 33.333 0.00 0.00 0.00 2.40
91 92 6.093495 CGACCAAATAAGCCAAGTAGATGAAA 59.907 38.462 0.00 0.00 0.00 2.69
92 93 5.584649 CGACCAAATAAGCCAAGTAGATGAA 59.415 40.000 0.00 0.00 0.00 2.57
95 96 3.877508 GCGACCAAATAAGCCAAGTAGAT 59.122 43.478 0.00 0.00 0.00 1.98
96 97 3.267483 GCGACCAAATAAGCCAAGTAGA 58.733 45.455 0.00 0.00 0.00 2.59
121 123 0.885196 AGACTGCGAGAGAGGTCAAC 59.115 55.000 0.00 0.00 36.87 3.18
136 138 0.694771 TGATGGCTTTGCTGGAGACT 59.305 50.000 0.00 0.00 0.00 3.24
141 143 1.213537 CCGTTGATGGCTTTGCTGG 59.786 57.895 0.00 0.00 0.00 4.85
144 146 3.334078 CATCCGTTGATGGCTTTGC 57.666 52.632 0.00 0.00 43.90 3.68
206 210 5.283060 ACGATTCATTAATTAGCGCATCC 57.717 39.130 11.47 0.00 0.00 3.51
251 255 2.995939 ACGACGTTCGATGTAGAGTACA 59.004 45.455 13.06 0.00 43.74 2.90
252 256 3.592309 GACGACGTTCGATGTAGAGTAC 58.408 50.000 0.13 0.00 43.74 2.73
253 257 2.279921 CGACGACGTTCGATGTAGAGTA 59.720 50.000 0.13 0.00 43.74 2.59
254 258 1.060266 CGACGACGTTCGATGTAGAGT 59.940 52.381 0.13 0.95 43.74 3.24
255 259 1.591632 CCGACGACGTTCGATGTAGAG 60.592 57.143 11.09 0.00 43.74 2.43
256 260 0.371301 CCGACGACGTTCGATGTAGA 59.629 55.000 11.09 0.00 43.74 2.59
269 273 4.063967 ATTGCGCTCCACCGACGA 62.064 61.111 9.73 0.00 0.00 4.20
312 316 7.444183 TCGTTGGAGAGAATCAGTTGTTAAATT 59.556 33.333 0.00 0.00 37.82 1.82
704 708 1.386525 CCATTGGGCTGGTTCCATCG 61.387 60.000 0.00 0.00 33.82 3.84
705 709 1.044790 CCCATTGGGCTGGTTCCATC 61.045 60.000 9.28 0.00 35.35 3.51
706 710 1.002017 CCCATTGGGCTGGTTCCAT 59.998 57.895 9.28 0.00 35.35 3.41
707 711 2.444696 CCCATTGGGCTGGTTCCA 59.555 61.111 9.28 0.00 35.35 3.53
742 749 1.435577 GTTAACGGTGCAGTGGTAGG 58.564 55.000 0.00 0.00 0.00 3.18
743 750 1.270412 TGGTTAACGGTGCAGTGGTAG 60.270 52.381 0.00 0.00 0.00 3.18
744 751 0.757512 TGGTTAACGGTGCAGTGGTA 59.242 50.000 0.00 0.00 0.00 3.25
745 752 0.107116 TTGGTTAACGGTGCAGTGGT 60.107 50.000 0.00 0.00 0.00 4.16
746 753 0.309612 GTTGGTTAACGGTGCAGTGG 59.690 55.000 0.00 0.00 0.00 4.00
780 797 0.459237 CTAGACTTGGCGCCAGAGTG 60.459 60.000 34.00 25.40 0.00 3.51
811 828 2.092861 TGAGTTGACCGTCCCAAAAAGA 60.093 45.455 0.00 0.00 0.00 2.52
812 829 2.294074 TGAGTTGACCGTCCCAAAAAG 58.706 47.619 0.00 0.00 0.00 2.27
813 830 2.421751 TGAGTTGACCGTCCCAAAAA 57.578 45.000 0.00 0.00 0.00 1.94
847 864 6.890293 TCTTGCTCAGATCTGTACTACTCTA 58.110 40.000 21.92 0.00 0.00 2.43
848 865 5.750524 TCTTGCTCAGATCTGTACTACTCT 58.249 41.667 21.92 0.00 0.00 3.24
849 866 6.443934 TTCTTGCTCAGATCTGTACTACTC 57.556 41.667 21.92 5.81 0.00 2.59
850 867 6.842437 TTTCTTGCTCAGATCTGTACTACT 57.158 37.500 21.92 0.00 0.00 2.57
851 868 7.488322 AGATTTCTTGCTCAGATCTGTACTAC 58.512 38.462 21.92 8.96 0.00 2.73
852 869 7.652524 AGATTTCTTGCTCAGATCTGTACTA 57.347 36.000 21.92 11.17 0.00 1.82
866 883 4.227177 CGTGTGTACGTAGATTTCTTGC 57.773 45.455 0.00 0.00 44.99 4.01
876 893 7.203218 ATACTACAGTAGATCGTGTGTACGTA 58.797 38.462 14.94 0.00 41.33 3.57
877 894 6.045318 ATACTACAGTAGATCGTGTGTACGT 58.955 40.000 14.94 0.00 41.33 3.57
878 895 6.522233 ATACTACAGTAGATCGTGTGTACG 57.478 41.667 14.94 0.00 41.64 3.67
879 896 6.632035 GCAATACTACAGTAGATCGTGTGTAC 59.368 42.308 14.94 0.00 33.52 2.90
900 917 8.296713 CCAGTGTTTGTACTGTAATTAAGCAAT 58.703 33.333 0.00 0.00 45.12 3.56
902 919 6.768861 ACCAGTGTTTGTACTGTAATTAAGCA 59.231 34.615 0.00 0.00 45.12 3.91
903 920 7.198306 ACCAGTGTTTGTACTGTAATTAAGC 57.802 36.000 0.00 0.00 45.12 3.09
945 964 4.489306 AGCTATGTGACCTTAAGGGAAC 57.511 45.455 25.31 20.97 40.27 3.62
949 968 5.740513 GCTTCCTAGCTATGTGACCTTAAGG 60.741 48.000 20.42 20.42 44.27 2.69
981 1000 3.696548 CCATCTTGGGTTTAGCTTTCTCC 59.303 47.826 0.00 0.00 32.67 3.71
993 1023 2.827921 GCATTTCTTGTCCATCTTGGGT 59.172 45.455 0.00 0.00 38.32 4.51
1018 1048 0.968393 AGCCAGTTCGACTCCTCTCC 60.968 60.000 0.00 0.00 0.00 3.71
1031 1061 2.681778 CCTCGACCTCCAGCCAGT 60.682 66.667 0.00 0.00 0.00 4.00
1058 1088 2.626780 GCCTTCTTCCCCGTGCAAC 61.627 63.158 0.00 0.00 0.00 4.17
1078 1117 2.272146 CCTGGGGTTGACGATGGG 59.728 66.667 0.00 0.00 0.00 4.00
1386 1482 4.691216 AGAAGCACGTCTAATTTCTTGGAC 59.309 41.667 0.00 0.00 38.95 4.02
1395 1491 0.541863 CCCCCAGAAGCACGTCTAAT 59.458 55.000 0.00 0.00 0.00 1.73
1396 1492 1.980052 CCCCCAGAAGCACGTCTAA 59.020 57.895 0.00 0.00 0.00 2.10
1397 1493 3.708210 CCCCCAGAAGCACGTCTA 58.292 61.111 0.00 0.00 0.00 2.59
1938 2055 3.723554 GAGCTTGTTCTCGACGGAT 57.276 52.632 0.00 0.00 0.00 4.18
2159 2276 0.029167 GTAGGAGTCGTAGAAGCGCC 59.971 60.000 2.29 0.00 39.69 6.53
2163 2280 4.515361 TCTTGAGGTAGGAGTCGTAGAAG 58.485 47.826 0.00 0.00 39.69 2.85
2244 2361 2.034104 TCTGATCCAAGATGTGCTGC 57.966 50.000 0.00 0.00 0.00 5.25
2770 2921 0.445436 CCAAGACATGTCTTCGCAGC 59.555 55.000 33.24 3.44 46.13 5.25
2803 2954 0.741326 CTTCTCGGAGATCGGCTCAA 59.259 55.000 8.81 0.00 45.81 3.02
2840 2991 4.604976 AGATATACGGCGTAAACTGTGAC 58.395 43.478 24.81 9.46 0.00 3.67
2873 3024 9.268282 TGTTGGATCCTCTTTTAATAGTAGACT 57.732 33.333 14.23 0.00 0.00 3.24
2887 3038 3.033909 TCATCACGATGTTGGATCCTCT 58.966 45.455 14.23 0.00 39.72 3.69
2889 3040 4.384056 GAATCATCACGATGTTGGATCCT 58.616 43.478 14.23 0.00 39.72 3.24
2895 3046 3.000623 CAGGTCGAATCATCACGATGTTG 59.999 47.826 6.91 0.00 40.50 3.33
2899 3050 1.410517 AGCAGGTCGAATCATCACGAT 59.589 47.619 0.00 0.00 40.50 3.73
2917 3068 0.034616 CTGAGATGGGGGATCGAAGC 59.965 60.000 0.00 0.00 36.04 3.86
2930 3081 1.336440 CTCGAGCGATGGTTCTGAGAT 59.664 52.381 0.00 0.00 31.20 2.75
2931 3082 0.735471 CTCGAGCGATGGTTCTGAGA 59.265 55.000 0.00 0.00 31.20 3.27
2932 3083 0.869454 GCTCGAGCGATGGTTCTGAG 60.869 60.000 23.61 8.24 32.03 3.35
2968 3119 1.812571 GTTGTACATGGGCTGAGTTGG 59.187 52.381 0.00 0.00 0.00 3.77
3039 3191 3.045142 GGTGACCTCGTTCGTGGA 58.955 61.111 17.95 0.00 0.00 4.02
3069 3225 1.299620 CGTCGTGGGTTGTCGAACT 60.300 57.895 0.00 0.00 37.81 3.01
3075 3231 4.309950 GGCCTCGTCGTGGGTTGT 62.310 66.667 14.77 0.00 0.00 3.32
3091 3247 3.006323 TGGTTTGATTTTTGGTCGATGGG 59.994 43.478 0.00 0.00 0.00 4.00
3106 3262 0.606604 GGAGCTCGTAGGTGGTTTGA 59.393 55.000 7.83 0.00 0.00 2.69
3148 3304 1.640917 ACTGGCGTTTCTCTCCCTAA 58.359 50.000 0.00 0.00 0.00 2.69
3149 3305 1.640917 AACTGGCGTTTCTCTCCCTA 58.359 50.000 0.00 0.00 0.00 3.53
3192 3348 3.702555 GCTGTGCGTTCGCGAGTT 61.703 61.111 9.59 0.00 44.71 3.01
3207 3364 1.153549 GTTTGATCTCCTCGGCGCT 60.154 57.895 7.64 0.00 0.00 5.92
3208 3365 2.517450 CGTTTGATCTCCTCGGCGC 61.517 63.158 0.00 0.00 0.00 6.53
3236 3393 2.485795 GCGAGTCGATGGAGCTCCT 61.486 63.158 32.28 18.41 36.82 3.69
3289 3446 1.592400 CTCCTTGGCGTCGTAGGACA 61.592 60.000 15.36 0.00 43.61 4.02
3312 3469 3.458163 GGGTCGATGGAGGTCGCA 61.458 66.667 0.00 0.00 41.22 5.10
3314 3471 4.570663 GCGGGTCGATGGAGGTCG 62.571 72.222 0.00 0.00 42.74 4.79
3336 3493 2.426023 GACTTCCTGGTGGCGTGT 59.574 61.111 0.00 0.00 0.00 4.49
3479 3636 4.700448 TACCTTGGGACGGCCGGA 62.700 66.667 31.76 7.27 33.83 5.14
3482 3639 2.045634 GGTTACCTTGGGACGGCC 60.046 66.667 0.00 0.00 0.00 6.13
3483 3640 2.045634 GGGTTACCTTGGGACGGC 60.046 66.667 0.00 0.00 0.00 5.68
3586 3743 2.884639 GTCAAGAAGCTTGGTTTGCCTA 59.115 45.455 2.10 0.00 35.27 3.93
3632 3789 2.422597 TCGTCCATGCAAGTAAACCAG 58.577 47.619 0.00 0.00 0.00 4.00
3658 3815 8.246430 TGAGTGAGTTAAGTAAAGAGAGGAAA 57.754 34.615 0.00 0.00 0.00 3.13


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

AutoCloner maintained by Alex Coulton.