Multiple sequence alignment - TraesCS7B01G319500

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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 TraesCS7B01G319500 chr7B 100.000 2712 0 0 1 2712 569440936 569438225 0.000000e+00 5009.0
1 TraesCS7B01G319500 chr7B 94.851 1340 30 15 988 2309 569481808 569480490 0.000000e+00 2056.0
2 TraesCS7B01G319500 chr7B 84.870 1150 93 41 1106 2216 591684290 591685397 0.000000e+00 1085.0
3 TraesCS7B01G319500 chr7B 83.425 1267 108 50 1106 2309 591057006 591055779 0.000000e+00 1083.0
4 TraesCS7B01G319500 chr7B 85.222 1015 89 37 1156 2127 633001104 633002100 0.000000e+00 987.0
5 TraesCS7B01G319500 chr7B 89.825 629 25 14 161 780 569482537 569481939 0.000000e+00 771.0
6 TraesCS7B01G319500 chr7B 100.000 136 0 0 2972 3107 569437965 569437830 5.140000e-63 252.0
7 TraesCS7B01G319500 chr7B 99.265 136 1 0 2972 3107 395639667 395639802 2.390000e-61 246.0
8 TraesCS7B01G319500 chr7B 93.902 164 8 1 2550 2711 530005565 530005728 2.390000e-61 246.0
9 TraesCS7B01G319500 chr7B 92.500 160 11 1 2550 2709 395639146 395639304 8.670000e-56 228.0
10 TraesCS7B01G319500 chr7B 96.269 134 5 0 2972 3105 530006021 530006154 1.450000e-53 220.0
11 TraesCS7B01G319500 chr7B 90.643 171 7 5 2550 2712 568483930 568483761 5.220000e-53 219.0
12 TraesCS7B01G319500 chr7B 95.946 74 3 0 66 139 569482607 569482534 1.510000e-23 121.0
13 TraesCS7B01G319500 chr7B 87.692 65 8 0 988 1052 587464440 587464504 3.320000e-10 76.8
14 TraesCS7B01G319500 chr7B 87.692 65 8 0 988 1052 587479550 587479614 3.320000e-10 76.8
15 TraesCS7B01G319500 chr7B 87.692 65 8 0 988 1052 587503719 587503783 3.320000e-10 76.8
16 TraesCS7B01G319500 chr7B 95.455 44 1 1 2398 2441 591055736 591055694 5.560000e-08 69.4
17 TraesCS7B01G319500 chr7B 93.333 45 2 1 2397 2441 569480448 569480405 7.190000e-07 65.8
18 TraesCS7B01G319500 chr7D 91.819 1589 79 23 988 2554 530430909 530429350 0.000000e+00 2167.0
19 TraesCS7B01G319500 chr7D 84.899 1490 113 53 1116 2545 530361678 530360241 0.000000e+00 1402.0
20 TraesCS7B01G319500 chr7D 82.798 1401 102 69 1124 2423 548324917 548326279 0.000000e+00 1123.0
21 TraesCS7B01G319500 chr7D 85.119 1176 82 48 1009 2109 548560595 548561752 0.000000e+00 1116.0
22 TraesCS7B01G319500 chr7D 85.546 1017 82 32 1155 2127 573969167 573970162 0.000000e+00 1003.0
23 TraesCS7B01G319500 chr7D 90.385 780 28 12 194 973 530431627 530430895 0.000000e+00 981.0
24 TraesCS7B01G319500 chr7D 86.490 792 88 11 184 973 543730788 543731562 0.000000e+00 852.0
25 TraesCS7B01G319500 chr7D 86.172 781 86 10 194 973 548550336 548551095 0.000000e+00 824.0
26 TraesCS7B01G319500 chr7D 95.238 84 4 0 66 149 548351145 548351228 1.940000e-27 134.0
27 TraesCS7B01G319500 chr7D 92.647 68 5 0 988 1055 548324823 548324890 7.090000e-17 99.0
28 TraesCS7B01G319500 chr7D 93.333 60 4 0 1097 1156 573969078 573969137 4.270000e-14 89.8
29 TraesCS7B01G319500 chr7D 96.154 52 2 0 66 117 530433821 530433770 5.520000e-13 86.1
30 TraesCS7B01G319500 chr7D 97.500 40 1 0 66 105 548068666 548068627 5.560000e-08 69.4
31 TraesCS7B01G319500 chr7D 97.222 36 1 0 114 149 548323911 548323946 9.300000e-06 62.1
32 TraesCS7B01G319500 chr7A 80.698 2378 191 130 194 2441 630670765 630673004 0.000000e+00 1602.0
33 TraesCS7B01G319500 chr7A 82.171 1621 168 70 988 2524 632265626 632267209 0.000000e+00 1280.0
34 TraesCS7B01G319500 chr7A 83.866 1221 95 51 988 2125 632187871 632189072 0.000000e+00 1070.0
35 TraesCS7B01G319500 chr7A 86.940 781 79 10 194 973 625641565 625642323 0.000000e+00 856.0
36 TraesCS7B01G319500 chr7A 87.206 766 78 10 212 973 625674356 625675105 0.000000e+00 854.0
37 TraesCS7B01G319500 chr7A 86.996 769 59 11 206 973 631653316 631652588 0.000000e+00 828.0
38 TraesCS7B01G319500 chr7A 90.328 610 43 10 1158 1762 631872502 631871904 0.000000e+00 785.0
39 TraesCS7B01G319500 chr7A 83.409 657 48 23 202 845 632187167 632187775 1.260000e-153 553.0
40 TraesCS7B01G319500 chr7A 81.438 598 46 32 1897 2441 631849533 631848948 2.210000e-116 429.0
41 TraesCS7B01G319500 chr7A 87.778 180 12 4 988 1157 631878003 631877824 5.250000e-48 202.0
42 TraesCS7B01G319500 chr7A 82.174 230 17 11 2235 2441 632190131 632190359 3.180000e-40 176.0
43 TraesCS7B01G319500 chr7A 94.048 84 5 0 66 149 630669089 630669172 9.040000e-26 128.0
44 TraesCS7B01G319500 chr7A 89.888 89 4 2 66 149 631878411 631878323 3.280000e-20 110.0
45 TraesCS7B01G319500 chr7A 88.889 90 4 2 66 149 632265194 632265283 4.240000e-19 106.0
46 TraesCS7B01G319500 chr7A 96.364 55 2 0 95 149 617552440 617552386 1.190000e-14 91.6
47 TraesCS7B01G319500 chrUn 83.568 1491 129 64 1106 2524 337590886 337589440 0.000000e+00 1290.0
48 TraesCS7B01G319500 chrUn 84.223 1274 100 50 988 2216 355335464 355334247 0.000000e+00 1146.0
49 TraesCS7B01G319500 chr1D 87.176 772 79 11 206 973 110904567 110905322 0.000000e+00 859.0
50 TraesCS7B01G319500 chr1D 92.754 69 3 2 988 1055 110905308 110905375 7.090000e-17 99.0
51 TraesCS7B01G319500 chr6B 86.369 785 82 13 191 973 694680357 694681118 0.000000e+00 833.0
52 TraesCS7B01G319500 chr6B 86.154 65 9 0 988 1052 694681104 694681168 1.550000e-08 71.3
53 TraesCS7B01G319500 chr1B 86.528 772 84 11 206 973 169024351 169025106 0.000000e+00 832.0
54 TraesCS7B01G319500 chr1B 97.778 135 3 0 2972 3106 442181977 442182111 1.860000e-57 233.0
55 TraesCS7B01G319500 chr1B 97.059 136 4 0 2972 3107 161379855 161379990 2.410000e-56 230.0
56 TraesCS7B01G319500 chr1B 90.173 173 6 6 2550 2712 161379593 161379764 6.750000e-52 215.0
57 TraesCS7B01G319500 chr1B 90.533 169 7 5 2551 2711 562470538 562470705 6.750000e-52 215.0
58 TraesCS7B01G319500 chr2B 93.413 167 7 1 2550 2712 442534026 442533860 8.610000e-61 244.0
59 TraesCS7B01G319500 chr4B 99.254 134 1 0 2972 3105 185875143 185875276 3.100000e-60 243.0
60 TraesCS7B01G319500 chr5B 99.242 132 1 0 2976 3107 344238421 344238290 4.000000e-59 239.0
61 TraesCS7B01G319500 chr5B 97.794 136 3 0 2972 3107 106355071 106355206 5.180000e-58 235.0
62 TraesCS7B01G319500 chr5B 90.805 174 12 3 2538 2709 106354487 106354658 2.410000e-56 230.0
63 TraesCS7B01G319500 chr5B 92.405 158 11 1 2555 2712 344238937 344238781 1.120000e-54 224.0
64 TraesCS7B01G319500 chr4A 96.324 136 5 0 2972 3107 656817784 656817649 1.120000e-54 224.0
65 TraesCS7B01G319500 chr4A 95.588 136 6 0 2972 3107 436436909 436436774 5.220000e-53 219.0
66 TraesCS7B01G319500 chr3B 90.058 171 8 5 2550 2712 550976637 550976806 2.430000e-51 213.0


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 TraesCS7B01G319500 chr7B 569437830 569440936 3106 True 2630.500000 5009 100.000000 1 3107 2 chr7B.!!$R2 3106
1 TraesCS7B01G319500 chr7B 591684290 591685397 1107 False 1085.000000 1085 84.870000 1106 2216 1 chr7B.!!$F4 1110
2 TraesCS7B01G319500 chr7B 633001104 633002100 996 False 987.000000 987 85.222000 1156 2127 1 chr7B.!!$F5 971
3 TraesCS7B01G319500 chr7B 569480405 569482607 2202 True 753.450000 2056 93.488750 66 2441 4 chr7B.!!$R3 2375
4 TraesCS7B01G319500 chr7B 591055694 591057006 1312 True 576.200000 1083 89.440000 1106 2441 2 chr7B.!!$R4 1335
5 TraesCS7B01G319500 chr7B 395639146 395639802 656 False 237.000000 246 95.882500 2550 3107 2 chr7B.!!$F6 557
6 TraesCS7B01G319500 chr7B 530005565 530006154 589 False 233.000000 246 95.085500 2550 3105 2 chr7B.!!$F7 555
7 TraesCS7B01G319500 chr7D 530360241 530361678 1437 True 1402.000000 1402 84.899000 1116 2545 1 chr7D.!!$R1 1429
8 TraesCS7B01G319500 chr7D 548560595 548561752 1157 False 1116.000000 1116 85.119000 1009 2109 1 chr7D.!!$F4 1100
9 TraesCS7B01G319500 chr7D 530429350 530433821 4471 True 1078.033333 2167 92.786000 66 2554 3 chr7D.!!$R3 2488
10 TraesCS7B01G319500 chr7D 543730788 543731562 774 False 852.000000 852 86.490000 184 973 1 chr7D.!!$F1 789
11 TraesCS7B01G319500 chr7D 548550336 548551095 759 False 824.000000 824 86.172000 194 973 1 chr7D.!!$F3 779
12 TraesCS7B01G319500 chr7D 573969078 573970162 1084 False 546.400000 1003 89.439500 1097 2127 2 chr7D.!!$F6 1030
13 TraesCS7B01G319500 chr7D 548323911 548326279 2368 False 428.033333 1123 90.889000 114 2423 3 chr7D.!!$F5 2309
14 TraesCS7B01G319500 chr7A 630669089 630673004 3915 False 865.000000 1602 87.373000 66 2441 2 chr7A.!!$F3 2375
15 TraesCS7B01G319500 chr7A 625641565 625642323 758 False 856.000000 856 86.940000 194 973 1 chr7A.!!$F1 779
16 TraesCS7B01G319500 chr7A 625674356 625675105 749 False 854.000000 854 87.206000 212 973 1 chr7A.!!$F2 761
17 TraesCS7B01G319500 chr7A 631652588 631653316 728 True 828.000000 828 86.996000 206 973 1 chr7A.!!$R2 767
18 TraesCS7B01G319500 chr7A 631871904 631872502 598 True 785.000000 785 90.328000 1158 1762 1 chr7A.!!$R4 604
19 TraesCS7B01G319500 chr7A 632265194 632267209 2015 False 693.000000 1280 85.530000 66 2524 2 chr7A.!!$F5 2458
20 TraesCS7B01G319500 chr7A 632187167 632190359 3192 False 599.666667 1070 83.149667 202 2441 3 chr7A.!!$F4 2239
21 TraesCS7B01G319500 chr7A 631848948 631849533 585 True 429.000000 429 81.438000 1897 2441 1 chr7A.!!$R3 544
22 TraesCS7B01G319500 chrUn 337589440 337590886 1446 True 1290.000000 1290 83.568000 1106 2524 1 chrUn.!!$R1 1418
23 TraesCS7B01G319500 chrUn 355334247 355335464 1217 True 1146.000000 1146 84.223000 988 2216 1 chrUn.!!$R2 1228
24 TraesCS7B01G319500 chr1D 110904567 110905375 808 False 479.000000 859 89.965000 206 1055 2 chr1D.!!$F1 849
25 TraesCS7B01G319500 chr6B 694680357 694681168 811 False 452.150000 833 86.261500 191 1052 2 chr6B.!!$F1 861
26 TraesCS7B01G319500 chr1B 169024351 169025106 755 False 832.000000 832 86.528000 206 973 1 chr1B.!!$F1 767
27 TraesCS7B01G319500 chr5B 106354487 106355206 719 False 232.500000 235 94.299500 2538 3107 2 chr5B.!!$F1 569
28 TraesCS7B01G319500 chr5B 344238290 344238937 647 True 231.500000 239 95.823500 2555 3107 2 chr5B.!!$R1 552

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
495 4076 0.251916 TTCCCAGGCTTGATGTACCG 59.748 55.0 0.0 0.0 0.0 4.02 F
1100 4790 0.469917 CGAGGGGAGTACATGGCAAT 59.530 55.0 0.0 0.0 0.0 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1908 5746 1.153667 CTCCGAGCAGAACTCAGCC 60.154 63.158 0.0 0.0 46.63 4.85 R
2593 7547 0.482446 TCTGGATTGTTGGCTTGGGT 59.518 50.000 0.0 0.0 0.00 4.51 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
19 20 2.973419 GACGCTATTACGCTAGCTCT 57.027 50.000 13.93 0.00 41.61 4.09
21 22 4.603231 GACGCTATTACGCTAGCTCTAT 57.397 45.455 13.93 5.44 41.61 1.98
22 23 4.972201 GACGCTATTACGCTAGCTCTATT 58.028 43.478 13.93 1.64 41.61 1.73
23 24 4.724303 ACGCTATTACGCTAGCTCTATTG 58.276 43.478 13.93 5.23 41.61 1.90
24 25 3.544285 CGCTATTACGCTAGCTCTATTGC 59.456 47.826 13.93 13.07 41.61 3.56
25 26 4.486090 GCTATTACGCTAGCTCTATTGCA 58.514 43.478 13.93 0.00 40.79 4.08
26 27 4.560819 GCTATTACGCTAGCTCTATTGCAG 59.439 45.833 13.93 1.09 40.79 4.41
27 28 4.855715 ATTACGCTAGCTCTATTGCAGA 57.144 40.909 13.93 0.00 34.99 4.26
28 29 2.500509 ACGCTAGCTCTATTGCAGAC 57.499 50.000 13.93 0.00 34.99 3.51
29 30 1.268794 ACGCTAGCTCTATTGCAGACG 60.269 52.381 13.93 0.00 34.99 4.18
30 31 1.135867 GCTAGCTCTATTGCAGACGC 58.864 55.000 7.70 0.00 39.24 5.19
52 53 4.663444 GCGGATGCTATCTTCGCT 57.337 55.556 0.00 0.00 42.62 4.93
53 54 3.794690 GCGGATGCTATCTTCGCTA 57.205 52.632 0.00 0.00 42.62 4.26
54 55 2.285827 GCGGATGCTATCTTCGCTAT 57.714 50.000 0.00 0.00 42.62 2.97
55 56 2.611518 GCGGATGCTATCTTCGCTATT 58.388 47.619 0.00 0.00 42.62 1.73
56 57 2.600867 GCGGATGCTATCTTCGCTATTC 59.399 50.000 0.00 0.00 42.62 1.75
57 58 2.848887 CGGATGCTATCTTCGCTATTCG 59.151 50.000 0.00 0.00 40.15 3.34
58 59 3.426292 CGGATGCTATCTTCGCTATTCGA 60.426 47.826 0.00 0.00 46.88 3.71
69 70 3.986277 TCGCTATTCGAAACTATTCCCC 58.014 45.455 0.00 0.00 45.36 4.81
140 147 2.027385 GGAGGAATGGAAATGCACTCC 58.973 52.381 9.35 9.35 36.60 3.85
141 148 2.027385 GAGGAATGGAAATGCACTCCC 58.973 52.381 12.96 3.99 31.32 4.30
142 149 1.358787 AGGAATGGAAATGCACTCCCA 59.641 47.619 12.96 9.28 31.32 4.37
143 150 2.178580 GGAATGGAAATGCACTCCCAA 58.821 47.619 12.96 0.00 31.77 4.12
144 151 2.167075 GGAATGGAAATGCACTCCCAAG 59.833 50.000 12.96 0.00 31.77 3.61
145 152 2.610438 ATGGAAATGCACTCCCAAGT 57.390 45.000 12.96 0.00 35.60 3.16
188 195 4.323792 CCAAGTGATGAGGTAGAATGTGGT 60.324 45.833 0.00 0.00 0.00 4.16
189 196 4.744795 AGTGATGAGGTAGAATGTGGTC 57.255 45.455 0.00 0.00 0.00 4.02
192 3753 3.130516 TGATGAGGTAGAATGTGGTCGTC 59.869 47.826 0.00 0.00 0.00 4.20
250 3811 1.536073 TTCTCAGGAGCTGGTCGGTG 61.536 60.000 0.00 1.46 31.51 4.94
384 3954 2.167219 CCATGTACCAGAGCGTGCG 61.167 63.158 0.00 0.00 0.00 5.34
481 4062 3.014085 GCCGACGAGGATGTTCCCA 62.014 63.158 0.00 0.00 45.00 4.37
494 4075 1.004277 TGTTCCCAGGCTTGATGTACC 59.996 52.381 0.00 0.00 0.00 3.34
495 4076 0.251916 TTCCCAGGCTTGATGTACCG 59.748 55.000 0.00 0.00 0.00 4.02
496 4077 0.907704 TCCCAGGCTTGATGTACCGT 60.908 55.000 0.00 0.00 0.00 4.83
497 4078 0.828022 CCCAGGCTTGATGTACCGTA 59.172 55.000 0.00 0.00 0.00 4.02
498 4079 1.472728 CCCAGGCTTGATGTACCGTAC 60.473 57.143 0.00 1.40 0.00 3.67
644 4232 4.717629 CGACGTGCTCCAAGCCGA 62.718 66.667 13.94 0.00 41.51 5.54
645 4233 2.811317 GACGTGCTCCAAGCCGAG 60.811 66.667 13.94 1.70 41.51 4.63
646 4234 3.575351 GACGTGCTCCAAGCCGAGT 62.575 63.158 13.94 4.41 41.51 4.18
972 4645 2.104331 GGCGTGGTCGTCGATCAT 59.896 61.111 12.08 0.00 39.49 2.45
973 4646 1.518572 GGCGTGGTCGTCGATCATT 60.519 57.895 12.08 0.00 39.49 2.57
974 4647 1.082117 GGCGTGGTCGTCGATCATTT 61.082 55.000 12.08 0.00 39.49 2.32
975 4648 0.719465 GCGTGGTCGTCGATCATTTT 59.281 50.000 12.08 0.00 39.49 1.82
976 4649 1.127951 GCGTGGTCGTCGATCATTTTT 59.872 47.619 12.08 0.00 39.49 1.94
1055 4728 3.404438 GACGGTGGCCATGGGGTA 61.404 66.667 9.72 0.00 36.17 3.69
1100 4790 0.469917 CGAGGGGAGTACATGGCAAT 59.530 55.000 0.00 0.00 0.00 3.56
2257 7170 3.711086 AGCTCGTATGCATGTTCTGTAG 58.289 45.455 10.16 0.00 34.99 2.74
2296 7211 6.474819 TGACGAATTGAAAGCGAGATTTAA 57.525 33.333 0.00 0.00 0.00 1.52
2347 7284 0.890683 CCTGTTGGGAAAGATGTGGC 59.109 55.000 0.00 0.00 37.23 5.01
2385 7324 1.060937 GCACGCACCTAAGCAATCG 59.939 57.895 0.00 0.00 0.00 3.34
2402 7348 4.148871 GCAATCGACAAAGCTTTCCTTTTC 59.851 41.667 9.23 0.40 41.75 2.29
2446 7394 2.997980 TGTTCAGACTTGCAGTCCAAA 58.002 42.857 11.24 5.31 46.18 3.28
2452 7400 0.381801 ACTTGCAGTCCAAAGTTGCG 59.618 50.000 0.00 0.00 40.62 4.85
2496 7446 6.441274 TGACAAATTCTCATCTTGCTGTTTC 58.559 36.000 0.00 0.00 0.00 2.78
2498 7450 7.047460 ACAAATTCTCATCTTGCTGTTTCTT 57.953 32.000 0.00 0.00 0.00 2.52
2502 7454 5.874895 TCTCATCTTGCTGTTTCTTGATG 57.125 39.130 0.00 0.00 34.40 3.07
2547 7501 7.392766 ACCATGATATAGATCCACAAAAGGA 57.607 36.000 0.00 0.00 43.01 3.36
2611 7565 2.214376 TACCCAAGCCAACAATCCAG 57.786 50.000 0.00 0.00 0.00 3.86
2664 7621 4.193090 AGTACACACACACGATCCAAAAA 58.807 39.130 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 5.797934 GTCTGCAATAGAGCTAGCGTAATAG 59.202 44.000 9.55 0.95 35.70 1.73
5 6 5.617087 CGTCTGCAATAGAGCTAGCGTAATA 60.617 44.000 9.55 1.44 35.70 0.98
6 7 4.551388 GTCTGCAATAGAGCTAGCGTAAT 58.449 43.478 9.55 0.81 35.70 1.89
7 8 3.548214 CGTCTGCAATAGAGCTAGCGTAA 60.548 47.826 9.55 0.00 35.70 3.18
8 9 2.031944 CGTCTGCAATAGAGCTAGCGTA 60.032 50.000 9.55 5.67 35.70 4.42
9 10 1.268794 CGTCTGCAATAGAGCTAGCGT 60.269 52.381 9.55 3.25 35.70 5.07
10 11 1.403493 CGTCTGCAATAGAGCTAGCG 58.597 55.000 9.55 0.00 35.70 4.26
11 12 1.135867 GCGTCTGCAATAGAGCTAGC 58.864 55.000 6.62 6.62 42.15 3.42
35 36 2.285827 ATAGCGAAGATAGCATCCGC 57.714 50.000 0.00 0.00 45.39 5.54
36 37 2.848887 CGAATAGCGAAGATAGCATCCG 59.151 50.000 0.00 0.00 44.57 4.18
49 50 2.729882 CGGGGAATAGTTTCGAATAGCG 59.270 50.000 0.00 0.00 42.69 4.26
50 51 3.064931 CCGGGGAATAGTTTCGAATAGC 58.935 50.000 0.00 0.00 32.28 2.97
51 52 3.064931 GCCGGGGAATAGTTTCGAATAG 58.935 50.000 2.18 0.00 32.28 1.73
52 53 2.435069 TGCCGGGGAATAGTTTCGAATA 59.565 45.455 2.18 0.00 32.28 1.75
53 54 1.210967 TGCCGGGGAATAGTTTCGAAT 59.789 47.619 2.18 0.00 32.28 3.34
54 55 0.614294 TGCCGGGGAATAGTTTCGAA 59.386 50.000 2.18 0.00 32.28 3.71
55 56 0.177141 CTGCCGGGGAATAGTTTCGA 59.823 55.000 2.18 0.00 32.28 3.71
56 57 0.107848 ACTGCCGGGGAATAGTTTCG 60.108 55.000 2.18 0.00 32.28 3.46
57 58 2.994186 TACTGCCGGGGAATAGTTTC 57.006 50.000 2.18 0.00 0.00 2.78
58 59 3.724732 TTTACTGCCGGGGAATAGTTT 57.275 42.857 2.18 0.00 0.00 2.66
59 60 3.945640 ATTTACTGCCGGGGAATAGTT 57.054 42.857 2.18 0.00 0.00 2.24
60 61 3.743269 CGAATTTACTGCCGGGGAATAGT 60.743 47.826 2.18 0.00 0.00 2.12
61 62 2.806244 CGAATTTACTGCCGGGGAATAG 59.194 50.000 2.18 0.00 0.00 1.73
62 63 2.171027 ACGAATTTACTGCCGGGGAATA 59.829 45.455 2.18 0.00 0.00 1.75
63 64 1.064979 ACGAATTTACTGCCGGGGAAT 60.065 47.619 2.18 0.00 0.00 3.01
64 65 0.325602 ACGAATTTACTGCCGGGGAA 59.674 50.000 2.18 0.00 0.00 3.97
69 70 6.519353 TGTATATTGACGAATTTACTGCCG 57.481 37.500 0.00 0.00 31.05 5.69
161 168 3.474798 TCTACCTCATCACTTGGGAGT 57.525 47.619 0.00 0.00 36.25 3.85
162 169 4.163078 ACATTCTACCTCATCACTTGGGAG 59.837 45.833 0.00 0.00 0.00 4.30
163 170 4.080919 CACATTCTACCTCATCACTTGGGA 60.081 45.833 0.00 0.00 0.00 4.37
164 171 4.194640 CACATTCTACCTCATCACTTGGG 58.805 47.826 0.00 0.00 0.00 4.12
188 195 1.324005 TGTATGGCATCCACGGACGA 61.324 55.000 1.65 0.00 35.80 4.20
189 196 1.142965 TGTATGGCATCCACGGACG 59.857 57.895 1.65 0.00 35.80 4.79
192 3753 3.717899 CGTGTATGGCATCCACGG 58.282 61.111 30.52 16.22 45.97 4.94
263 3824 2.745884 CGGCGAGCCATTGTTCCA 60.746 61.111 15.03 0.00 35.37 3.53
495 4076 2.202837 GGCATCGTCCACCGGTAC 60.203 66.667 6.87 0.93 37.11 3.34
496 4077 2.680707 TGGCATCGTCCACCGGTA 60.681 61.111 6.87 0.00 37.11 4.02
641 4229 2.433838 CAGTGCAGCCTCACTCGG 60.434 66.667 5.57 0.00 44.81 4.63
643 4231 1.741032 GAGCAGTGCAGCCTCACTC 60.741 63.158 19.20 0.00 44.81 3.51
645 4233 3.117171 CGAGCAGTGCAGCCTCAC 61.117 66.667 19.20 0.00 37.24 3.51
646 4234 4.383861 CCGAGCAGTGCAGCCTCA 62.384 66.667 19.20 0.00 34.23 3.86
854 4502 3.712881 GTCGTCAAGGTGCGCCAC 61.713 66.667 20.59 7.16 37.19 5.01
857 4505 3.764049 GTCGTCGTCAAGGTGCGC 61.764 66.667 0.00 0.00 0.00 6.09
858 4506 3.458579 CGTCGTCGTCAAGGTGCG 61.459 66.667 0.00 0.00 0.00 5.34
859 4507 3.764049 GCGTCGTCGTCAAGGTGC 61.764 66.667 3.66 0.00 39.49 5.01
860 4508 3.103911 GGCGTCGTCGTCAAGGTG 61.104 66.667 0.88 0.00 41.67 4.00
861 4509 4.695231 CGGCGTCGTCGTCAAGGT 62.695 66.667 11.83 0.00 42.21 3.50
973 4646 5.238868 TCGACGACCACCATTTTATCAAAAA 59.761 36.000 0.00 0.00 38.87 1.94
974 4647 4.755629 TCGACGACCACCATTTTATCAAAA 59.244 37.500 0.00 0.00 34.41 2.44
975 4648 4.316645 TCGACGACCACCATTTTATCAAA 58.683 39.130 0.00 0.00 0.00 2.69
976 4649 3.927854 TCGACGACCACCATTTTATCAA 58.072 40.909 0.00 0.00 0.00 2.57
977 4650 3.596310 TCGACGACCACCATTTTATCA 57.404 42.857 0.00 0.00 0.00 2.15
978 4651 4.116961 TGATCGACGACCACCATTTTATC 58.883 43.478 0.00 0.00 0.00 1.75
979 4652 4.131649 TGATCGACGACCACCATTTTAT 57.868 40.909 0.00 0.00 0.00 1.40
980 4653 3.596310 TGATCGACGACCACCATTTTA 57.404 42.857 0.00 0.00 0.00 1.52
981 4654 2.465860 TGATCGACGACCACCATTTT 57.534 45.000 0.00 0.00 0.00 1.82
982 4655 2.279741 CATGATCGACGACCACCATTT 58.720 47.619 0.00 0.00 0.00 2.32
983 4656 1.473257 CCATGATCGACGACCACCATT 60.473 52.381 0.00 0.00 0.00 3.16
984 4657 0.104855 CCATGATCGACGACCACCAT 59.895 55.000 0.00 0.00 0.00 3.55
985 4658 1.515487 CCATGATCGACGACCACCA 59.485 57.895 0.00 0.00 0.00 4.17
986 4659 1.883084 GCCATGATCGACGACCACC 60.883 63.158 0.00 0.00 0.00 4.61
1258 4991 2.925966 AATTGGGAAGGAAGATGGCA 57.074 45.000 0.00 0.00 0.00 4.92
1908 5746 1.153667 CTCCGAGCAGAACTCAGCC 60.154 63.158 0.00 0.00 46.63 4.85
2231 7131 3.865745 AGAACATGCATACGAGCTACAAC 59.134 43.478 0.00 0.00 34.99 3.32
2232 7132 3.865164 CAGAACATGCATACGAGCTACAA 59.135 43.478 0.00 0.00 34.99 2.41
2257 7170 4.966850 TCGTCAACTTCTTTCGATCAAC 57.033 40.909 0.00 0.00 0.00 3.18
2296 7211 8.611654 AATTTTTCTTTGCAGATTTGTAGCAT 57.388 26.923 0.00 0.00 38.19 3.79
2385 7324 6.908870 AATTGTGAAAAGGAAAGCTTTGTC 57.091 33.333 18.30 8.69 0.00 3.18
2394 7333 7.835822 TGAGAACTCAAAATTGTGAAAAGGAA 58.164 30.769 0.00 0.00 36.53 3.36
2402 7348 6.075762 TGGACATGAGAACTCAAAATTGTG 57.924 37.500 8.59 4.33 43.58 3.33
2446 7394 6.925165 ACTTTGATTGAATTCAAATCGCAACT 59.075 30.769 23.91 5.69 42.87 3.16
2470 7419 5.766222 ACAGCAAGATGAGAATTTGTCAAC 58.234 37.500 0.00 0.00 0.00 3.18
2479 7428 5.766670 ACATCAAGAAACAGCAAGATGAGAA 59.233 36.000 0.00 0.00 37.05 2.87
2496 7446 4.625311 TCGCACACATGTAGTTACATCAAG 59.375 41.667 0.00 0.00 44.57 3.02
2498 7450 3.924073 GTCGCACACATGTAGTTACATCA 59.076 43.478 0.00 0.00 44.57 3.07
2502 7454 4.451557 GTTTGTCGCACACATGTAGTTAC 58.548 43.478 0.00 0.00 33.90 2.50
2590 7544 2.428171 CTGGATTGTTGGCTTGGGTATG 59.572 50.000 0.00 0.00 0.00 2.39
2593 7547 0.482446 TCTGGATTGTTGGCTTGGGT 59.518 50.000 0.00 0.00 0.00 4.51
2611 7565 1.368850 GCGTGCGTGTGAACCTTTC 60.369 57.895 0.00 0.00 0.00 2.62


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

AutoCloner maintained by Alex Coulton.