Multiple sequence alignment - TraesCS5A01G351400

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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 TraesCS5A01G351400 chr5A 100.000 4503 0 0 1 4503 554086312 554081810 0.000000e+00 8316
1 TraesCS5A01G351400 chr5A 80.995 1468 243 27 3053 4503 554060534 554059086 0.000000e+00 1133
2 TraesCS5A01G351400 chr5A 80.814 1475 233 41 3064 4503 554201380 554199921 0.000000e+00 1110
3 TraesCS5A01G351400 chr5A 77.173 1967 391 39 725 2669 554063336 554061406 0.000000e+00 1092
4 TraesCS5A01G351400 chr5A 72.833 946 213 34 1052 1980 553487671 553486753 2.650000e-72 283
5 TraesCS5A01G351400 chr5D 92.746 1930 127 9 982 2908 438523718 438521799 0.000000e+00 2776
6 TraesCS5A01G351400 chr5D 85.992 2570 310 28 138 2669 438548256 438545699 0.000000e+00 2706
7 TraesCS5A01G351400 chr5D 92.884 1602 87 14 2911 4503 438521762 438520179 0.000000e+00 2302
8 TraesCS5A01G351400 chr5D 82.741 1547 235 27 2974 4503 438605351 438603820 0.000000e+00 1349
9 TraesCS5A01G351400 chr5D 82.879 1466 217 29 3053 4501 438545242 438543794 0.000000e+00 1286
10 TraesCS5A01G351400 chr5D 83.045 1445 210 26 3077 4503 438559120 438557693 0.000000e+00 1279
11 TraesCS5A01G351400 chr5D 82.240 1464 224 24 3053 4503 438455282 438453842 0.000000e+00 1230
12 TraesCS5A01G351400 chr5D 80.932 1395 230 30 3131 4503 438722367 438720987 0.000000e+00 1070
13 TraesCS5A01G351400 chr5D 77.263 1878 370 38 823 2668 438457478 438455626 0.000000e+00 1050
14 TraesCS5A01G351400 chr5B 89.913 1834 139 25 2701 4503 533390098 533388280 0.000000e+00 2320
15 TraesCS5A01G351400 chr5B 81.549 1962 326 32 725 2668 533392206 533390263 0.000000e+00 1585
16 TraesCS5A01G351400 chr5B 83.075 1548 209 30 2971 4503 533383964 533382455 0.000000e+00 1358
17 TraesCS5A01G351400 chr5B 82.288 1547 241 28 2974 4503 533509431 533507901 0.000000e+00 1308
18 TraesCS5A01G351400 chr5B 79.989 1779 311 26 923 2671 533386025 533384262 0.000000e+00 1271
19 TraesCS5A01G351400 chr5B 80.226 1593 260 38 2926 4503 533089349 533087797 0.000000e+00 1146
20 TraesCS5A01G351400 chr5B 80.369 1462 255 28 3064 4503 533494297 533492846 0.000000e+00 1081
21 TraesCS5A01G351400 chr5B 77.173 1967 365 49 725 2633 533511768 533509828 0.000000e+00 1068
22 TraesCS5A01G351400 chr5B 77.387 1592 327 25 835 2408 533093419 533091843 0.000000e+00 915
23 TraesCS5A01G351400 chrUn 79.712 1878 317 38 823 2665 63296508 63294660 0.000000e+00 1299
24 TraesCS5A01G351400 chrUn 81.730 1549 235 27 2971 4503 63292121 63290605 0.000000e+00 1249


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 TraesCS5A01G351400 chr5A 554081810 554086312 4502 True 8316.0 8316 100.0000 1 4503 1 chr5A.!!$R2 4502
1 TraesCS5A01G351400 chr5A 554059086 554063336 4250 True 1112.5 1133 79.0840 725 4503 2 chr5A.!!$R4 3778
2 TraesCS5A01G351400 chr5A 554199921 554201380 1459 True 1110.0 1110 80.8140 3064 4503 1 chr5A.!!$R3 1439
3 TraesCS5A01G351400 chr5A 553486753 553487671 918 True 283.0 283 72.8330 1052 1980 1 chr5A.!!$R1 928
4 TraesCS5A01G351400 chr5D 438520179 438523718 3539 True 2539.0 2776 92.8150 982 4503 2 chr5D.!!$R5 3521
5 TraesCS5A01G351400 chr5D 438543794 438548256 4462 True 1996.0 2706 84.4355 138 4501 2 chr5D.!!$R6 4363
6 TraesCS5A01G351400 chr5D 438603820 438605351 1531 True 1349.0 1349 82.7410 2974 4503 1 chr5D.!!$R2 1529
7 TraesCS5A01G351400 chr5D 438557693 438559120 1427 True 1279.0 1279 83.0450 3077 4503 1 chr5D.!!$R1 1426
8 TraesCS5A01G351400 chr5D 438453842 438457478 3636 True 1140.0 1230 79.7515 823 4503 2 chr5D.!!$R4 3680
9 TraesCS5A01G351400 chr5D 438720987 438722367 1380 True 1070.0 1070 80.9320 3131 4503 1 chr5D.!!$R3 1372
10 TraesCS5A01G351400 chr5B 533382455 533392206 9751 True 1633.5 2320 83.6315 725 4503 4 chr5B.!!$R3 3778
11 TraesCS5A01G351400 chr5B 533507901 533511768 3867 True 1188.0 1308 79.7305 725 4503 2 chr5B.!!$R4 3778
12 TraesCS5A01G351400 chr5B 533492846 533494297 1451 True 1081.0 1081 80.3690 3064 4503 1 chr5B.!!$R1 1439
13 TraesCS5A01G351400 chr5B 533087797 533093419 5622 True 1030.5 1146 78.8065 835 4503 2 chr5B.!!$R2 3668
14 TraesCS5A01G351400 chrUn 63290605 63296508 5903 True 1274.0 1299 80.7210 823 4503 2 chrUn.!!$R1 3680

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
424 427 0.321346 TGAAGACCGAAGAGCATGCA 59.679 50.0 21.98 0.0 0.00 3.96 F
1298 1361 0.617413 ATGCTCTCCCTCACCAACAG 59.383 55.0 0.00 0.0 0.00 3.16 F
1954 2030 0.312729 TTACTGCGACGAGACAGCAA 59.687 50.0 0.00 0.0 40.63 3.91 F
2215 2291 1.287425 GTACCGCAATGTGAGTAGCC 58.713 55.0 0.00 0.0 0.00 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1371 1437 0.178955 TTGGGGTAGACGAGTCCACA 60.179 55.000 4.4 0.0 32.39 4.17 R
2899 8061 0.027455 CGCATGTTTGACACACACGT 59.973 50.000 0.0 0.0 38.61 4.49 R
2900 8062 0.657077 CCGCATGTTTGACACACACG 60.657 55.000 0.0 0.0 38.61 4.49 R
3867 15115 1.483004 TCTCGCCATACCAAAATCCGA 59.517 47.619 0.0 0.0 0.00 4.55 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
103 104 8.901472 ATAATTACATCTAGATCTGTAGGCCA 57.099 34.615 5.01 0.00 0.00 5.36
104 105 7.805083 AATTACATCTAGATCTGTAGGCCAT 57.195 36.000 5.01 0.00 0.00 4.40
105 106 8.901472 AATTACATCTAGATCTGTAGGCCATA 57.099 34.615 5.01 0.00 0.00 2.74
106 107 9.499369 AATTACATCTAGATCTGTAGGCCATAT 57.501 33.333 5.01 0.00 0.00 1.78
108 109 9.990868 TTACATCTAGATCTGTAGGCCATATAA 57.009 33.333 5.01 0.00 0.00 0.98
113 114 9.990868 TCTAGATCTGTAGGCCATATAATAACA 57.009 33.333 5.01 0.00 0.00 2.41
116 117 9.105844 AGATCTGTAGGCCATATAATAACAACT 57.894 33.333 5.01 0.00 0.00 3.16
135 136 8.472007 AACAACTATAAACATTGGAACCAAGA 57.528 30.769 11.88 0.00 39.47 3.02
136 137 8.472007 ACAACTATAAACATTGGAACCAAGAA 57.528 30.769 11.88 0.00 39.47 2.52
137 138 9.088987 ACAACTATAAACATTGGAACCAAGAAT 57.911 29.630 11.88 4.09 39.47 2.40
138 139 9.927668 CAACTATAAACATTGGAACCAAGAATT 57.072 29.630 11.88 8.49 39.47 2.17
206 207 1.734465 GCATCGCAATATGTAGAGGCC 59.266 52.381 0.00 0.00 34.79 5.19
272 273 9.386010 CAAAACCATCATTACATTCCAATGAAT 57.614 29.630 6.29 0.08 43.58 2.57
310 311 5.241506 TCGCTCTCAGAATGGAAATTTTTGT 59.758 36.000 0.00 0.00 36.16 2.83
330 331 6.949578 TTGTTCACTTGAAGAAAAAGCTTG 57.050 33.333 0.00 0.00 34.88 4.01
354 357 5.059833 AGGACAGAATGAGTCAGACAAAAC 58.940 41.667 2.66 0.00 39.69 2.43
358 361 5.698545 ACAGAATGAGTCAGACAAAACTAGC 59.301 40.000 2.66 0.00 39.69 3.42
399 402 4.323417 TGAGTTTCCATAAGCACGTTGAT 58.677 39.130 0.00 0.00 0.00 2.57
424 427 0.321346 TGAAGACCGAAGAGCATGCA 59.679 50.000 21.98 0.00 0.00 3.96
449 452 1.672363 TCTGCAAGTTCACACAGCAAG 59.328 47.619 0.00 0.00 36.24 4.01
457 460 0.946528 TCACACAGCAAGCACATGTC 59.053 50.000 0.00 0.00 0.00 3.06
514 517 3.931578 ACTGTAGTTGTTGGCTGAGATC 58.068 45.455 0.00 0.00 0.00 2.75
548 554 9.060347 GCAGGTAAAATATAGGGTAGTAAAACC 57.940 37.037 0.00 0.00 38.94 3.27
625 631 2.033424 GCTTTCTGTGAAAGGAACGCTT 59.967 45.455 18.05 0.00 35.04 4.68
636 642 5.242838 TGAAAGGAACGCTTGGATAACAAAT 59.757 36.000 0.00 0.00 38.91 2.32
646 652 6.361481 CGCTTGGATAACAAATGATGCATAAG 59.639 38.462 0.00 0.00 38.91 1.73
650 656 6.832900 TGGATAACAAATGATGCATAAGTGGA 59.167 34.615 0.00 0.00 0.00 4.02
695 701 6.377080 TCACCCATGTCTCACTAATCTAGAT 58.623 40.000 0.00 0.00 0.00 1.98
792 802 3.300388 ACTCCAACTGACTCTTGACTCA 58.700 45.455 0.00 0.00 0.00 3.41
797 807 1.264557 ACTGACTCTTGACTCACGACG 59.735 52.381 0.00 0.00 0.00 5.12
941 968 3.181507 GCTTTCTCGCATTTGACAGCATA 60.182 43.478 0.00 0.00 36.40 3.14
977 1037 7.668886 CCTATAGCTAGTTAGGGCTTAGTAACA 59.331 40.741 11.30 0.00 39.65 2.41
1023 1083 2.421248 GGATTCAAAGGCTCTCCTCTGG 60.421 54.545 0.00 0.00 43.40 3.86
1025 1085 1.270907 TCAAAGGCTCTCCTCTGGTC 58.729 55.000 0.00 0.00 43.40 4.02
1068 1128 2.248280 TTCTGCCGTTTAGTGCTTCA 57.752 45.000 0.00 0.00 0.00 3.02
1071 1131 2.028112 TCTGCCGTTTAGTGCTTCAGAT 60.028 45.455 0.00 0.00 0.00 2.90
1178 1241 0.984230 TCCAACTCCACTCCATCCAC 59.016 55.000 0.00 0.00 0.00 4.02
1220 1283 2.303022 ACAACGACATCCCTGAGTTCAT 59.697 45.455 0.00 0.00 0.00 2.57
1256 1319 2.203422 CCGTGAAACCCCAGCCAA 60.203 61.111 0.00 0.00 0.00 4.52
1273 1336 2.033424 GCCAACAACAACACTTCCTCTC 59.967 50.000 0.00 0.00 0.00 3.20
1278 1341 1.507140 ACAACACTTCCTCTCCACCA 58.493 50.000 0.00 0.00 0.00 4.17
1298 1361 0.617413 ATGCTCTCCCTCACCAACAG 59.383 55.000 0.00 0.00 0.00 3.16
1371 1437 2.342910 CGCCTAACGTGACAACTACT 57.657 50.000 0.00 0.00 36.87 2.57
1376 1445 3.005050 CCTAACGTGACAACTACTGTGGA 59.995 47.826 0.00 0.00 38.84 4.02
1413 1482 1.966451 GGTGCTTCTGAACACCGGG 60.966 63.158 19.18 0.00 46.32 5.73
1526 1595 1.000731 CAAATCCAACACGCCCAACAT 59.999 47.619 0.00 0.00 0.00 2.71
1591 1660 1.527370 GGGCGCTTCTCCTATGGTT 59.473 57.895 7.64 0.00 0.00 3.67
1650 1723 0.966920 GAGAGAACTTGGTGTCCCGA 59.033 55.000 0.00 0.00 0.00 5.14
1668 1741 1.983119 GAAGCATCCCATGGACCGGA 61.983 60.000 15.22 1.34 32.98 5.14
1821 1897 2.281070 ACAAGGCTGGTGCTGACG 60.281 61.111 0.00 0.00 39.59 4.35
1954 2030 0.312729 TTACTGCGACGAGACAGCAA 59.687 50.000 0.00 0.00 40.63 3.91
2085 2161 3.195698 GGCGGTAGCTTCTTGGCG 61.196 66.667 0.00 0.00 44.37 5.69
2102 2178 1.674322 CGTTGCCGGGGATGAAGTT 60.674 57.895 2.18 0.00 0.00 2.66
2215 2291 1.287425 GTACCGCAATGTGAGTAGCC 58.713 55.000 0.00 0.00 0.00 3.93
2425 2544 7.331089 TCTAGTTCTATGAGTCATAGCCCTA 57.669 40.000 28.41 25.39 42.33 3.53
2505 2651 4.973168 AGATTGTGCTGTCAGTTTTAGGA 58.027 39.130 0.93 0.00 0.00 2.94
2510 2656 4.127171 GTGCTGTCAGTTTTAGGAAGTGA 58.873 43.478 0.93 0.00 0.00 3.41
2563 2709 4.464069 TGGTTAAAATGCCAAGGTATGC 57.536 40.909 0.00 0.00 0.00 3.14
2686 3807 3.416156 CCTCTAAGCCCCTTGAATATGC 58.584 50.000 0.00 0.00 0.00 3.14
2691 3812 4.476628 AAGCCCCTTGAATATGCAAAAG 57.523 40.909 0.00 0.00 0.00 2.27
2693 3814 4.095946 AGCCCCTTGAATATGCAAAAGAA 58.904 39.130 0.00 0.00 0.00 2.52
2694 3815 4.718276 AGCCCCTTGAATATGCAAAAGAAT 59.282 37.500 0.00 0.00 0.00 2.40
2712 3955 3.380004 AGAATTTCAGTTTTGTGTGCGGA 59.620 39.130 0.00 0.00 0.00 5.54
2845 8001 5.699001 GTCGGGTTTGGAAATAAAAAGCAAT 59.301 36.000 0.00 0.00 35.89 3.56
2883 8039 4.264253 CATGGACTCAAGGAAAGCATGTA 58.736 43.478 0.00 0.00 0.00 2.29
2936 8253 4.260139 TGCGGTCTGTGTTTTCTATGTA 57.740 40.909 0.00 0.00 0.00 2.29
2944 8261 8.443937 GGTCTGTGTTTTCTATGTAAACTGATC 58.556 37.037 0.00 0.00 36.64 2.92
2947 8264 8.771920 TGTGTTTTCTATGTAAACTGATCGAT 57.228 30.769 0.00 0.00 36.64 3.59
2948 8265 9.863845 TGTGTTTTCTATGTAAACTGATCGATA 57.136 29.630 0.00 0.00 36.64 2.92
3050 8401 3.463048 AGGAATGGAAATGAGCACCTT 57.537 42.857 0.00 0.00 0.00 3.50
3129 8493 1.400494 GGGAACATGACATTACCGTGC 59.600 52.381 0.00 0.00 0.00 5.34
3179 8543 8.515414 GGAGAAAGCACAAGATTATAAGTTTGT 58.485 33.333 10.13 10.13 34.31 2.83
3629 14865 6.821160 ACAAGAGCTTAGATTCTAGCCTTTTC 59.179 38.462 9.91 4.16 38.14 2.29
3764 15012 6.098266 GGTTTAATATCATCAAAGGGGTTGCT 59.902 38.462 0.00 0.00 37.13 3.91
3848 15096 7.161773 AGTTGGAAATATCTTGTTGGATGTG 57.838 36.000 0.00 0.00 0.00 3.21
3867 15115 7.177878 GGATGTGGATATGAAACCCAAGATAT 58.822 38.462 0.00 0.00 0.00 1.63
3890 15138 3.315191 CGGATTTTGGTATGGCGAGAATT 59.685 43.478 0.00 0.00 0.00 2.17
3927 15175 3.062763 CAAAATGCAAATACCCAACGCA 58.937 40.909 0.00 0.00 36.95 5.24
3956 15204 5.072193 TGGCACATAGTGAGTATCCATTGAT 59.928 40.000 0.58 0.00 35.23 2.57
4340 15615 1.557443 GACCAACGAACTGCCAGACG 61.557 60.000 0.00 6.62 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 78 9.326489 TGGCCTACAGATCTAGATGTAATTATT 57.674 33.333 10.74 0.00 31.81 1.40
78 79 8.901472 TGGCCTACAGATCTAGATGTAATTAT 57.099 34.615 10.74 0.00 31.81 1.28
79 80 8.901472 ATGGCCTACAGATCTAGATGTAATTA 57.099 34.615 10.74 0.00 31.81 1.40
80 81 7.805083 ATGGCCTACAGATCTAGATGTAATT 57.195 36.000 10.74 0.00 31.81 1.40
82 83 9.990868 TTATATGGCCTACAGATCTAGATGTAA 57.009 33.333 10.74 0.00 32.34 2.41
87 88 9.990868 TGTTATTATATGGCCTACAGATCTAGA 57.009 33.333 3.32 0.00 32.34 2.43
90 91 9.105844 AGTTGTTATTATATGGCCTACAGATCT 57.894 33.333 3.32 0.00 32.34 2.75
109 110 9.575868 TCTTGGTTCCAATGTTTATAGTTGTTA 57.424 29.630 4.67 0.00 0.00 2.41
110 111 8.472007 TCTTGGTTCCAATGTTTATAGTTGTT 57.528 30.769 4.67 0.00 0.00 2.83
111 112 8.472007 TTCTTGGTTCCAATGTTTATAGTTGT 57.528 30.769 4.67 0.00 0.00 3.32
112 113 9.927668 AATTCTTGGTTCCAATGTTTATAGTTG 57.072 29.630 4.67 0.00 0.00 3.16
117 118 9.625747 AACAAAATTCTTGGTTCCAATGTTTAT 57.374 25.926 4.67 0.00 0.00 1.40
119 120 7.936496 AACAAAATTCTTGGTTCCAATGTTT 57.064 28.000 4.67 4.50 0.00 2.83
120 121 8.264347 AGTAACAAAATTCTTGGTTCCAATGTT 58.736 29.630 17.23 17.23 31.28 2.71
121 122 7.791029 AGTAACAAAATTCTTGGTTCCAATGT 58.209 30.769 4.67 3.05 0.00 2.71
122 123 7.925483 TGAGTAACAAAATTCTTGGTTCCAATG 59.075 33.333 4.67 2.46 0.00 2.82
123 124 8.017418 TGAGTAACAAAATTCTTGGTTCCAAT 57.983 30.769 4.67 0.00 0.00 3.16
124 125 7.123547 ACTGAGTAACAAAATTCTTGGTTCCAA 59.876 33.333 4.17 4.17 0.00 3.53
125 126 6.605594 ACTGAGTAACAAAATTCTTGGTTCCA 59.394 34.615 0.00 0.00 0.00 3.53
126 127 6.918022 CACTGAGTAACAAAATTCTTGGTTCC 59.082 38.462 0.00 0.00 0.00 3.62
127 128 7.644157 GTCACTGAGTAACAAAATTCTTGGTTC 59.356 37.037 0.00 0.00 0.00 3.62
128 129 7.339466 AGTCACTGAGTAACAAAATTCTTGGTT 59.661 33.333 0.00 0.00 0.00 3.67
129 130 6.828785 AGTCACTGAGTAACAAAATTCTTGGT 59.171 34.615 0.00 2.19 0.00 3.67
130 131 7.264373 AGTCACTGAGTAACAAAATTCTTGG 57.736 36.000 0.00 0.00 0.00 3.61
131 132 9.013490 CAAAGTCACTGAGTAACAAAATTCTTG 57.987 33.333 0.00 0.61 0.00 3.02
132 133 8.956426 TCAAAGTCACTGAGTAACAAAATTCTT 58.044 29.630 0.00 0.00 0.00 2.52
133 134 8.398665 GTCAAAGTCACTGAGTAACAAAATTCT 58.601 33.333 0.00 0.00 0.00 2.40
134 135 8.398665 AGTCAAAGTCACTGAGTAACAAAATTC 58.601 33.333 0.00 0.00 0.00 2.17
135 136 8.281212 AGTCAAAGTCACTGAGTAACAAAATT 57.719 30.769 0.00 0.00 0.00 1.82
136 137 7.865706 AGTCAAAGTCACTGAGTAACAAAAT 57.134 32.000 0.00 0.00 0.00 1.82
137 138 7.681939 AAGTCAAAGTCACTGAGTAACAAAA 57.318 32.000 0.00 0.00 0.00 2.44
138 139 8.958119 ATAAGTCAAAGTCACTGAGTAACAAA 57.042 30.769 0.00 0.00 0.00 2.83
139 140 8.958119 AATAAGTCAAAGTCACTGAGTAACAA 57.042 30.769 0.00 0.00 0.00 2.83
272 273 5.077134 TGAGAGCGAGAATGAAGATTCAA 57.923 39.130 0.00 0.00 40.59 2.69
301 302 9.611284 GCTTTTTCTTCAAGTGAACAAAAATTT 57.389 25.926 15.65 0.00 39.42 1.82
310 311 5.652014 TCCTCAAGCTTTTTCTTCAAGTGAA 59.348 36.000 0.00 0.00 0.00 3.18
330 331 4.527509 TTGTCTGACTCATTCTGTCCTC 57.472 45.455 9.51 0.00 33.83 3.71
354 357 2.058798 ACGTTGAATGTCACACGCTAG 58.941 47.619 10.65 0.00 35.72 3.42
358 361 3.675481 TCAAAACGTTGAATGTCACACG 58.325 40.909 0.00 9.72 40.87 4.49
399 402 1.135373 GCTCTTCGGTCTTCACATCGA 60.135 52.381 0.00 0.00 0.00 3.59
424 427 3.144506 CTGTGTGAACTTGCAGAGGAAT 58.855 45.455 0.00 0.00 0.00 3.01
449 452 4.153986 CAATTTCTCGTTCAGACATGTGC 58.846 43.478 1.15 0.00 0.00 4.57
457 460 2.411547 GGCACGACAATTTCTCGTTCAG 60.412 50.000 5.38 0.00 42.42 3.02
548 554 7.550551 TGAGCTATTGAGTTTTGACCATTAGAG 59.449 37.037 0.00 0.00 0.00 2.43
625 631 6.832900 TCCACTTATGCATCATTTGTTATCCA 59.167 34.615 0.19 0.00 0.00 3.41
636 642 5.614308 AGATTTCGATCCACTTATGCATCA 58.386 37.500 0.19 0.00 0.00 3.07
646 652 5.277538 GCATCAAACCTAGATTTCGATCCAC 60.278 44.000 0.00 0.00 0.00 4.02
650 656 5.674525 TGAGCATCAAACCTAGATTTCGAT 58.325 37.500 0.00 0.00 45.97 3.59
792 802 0.956633 TCTAGAAGTGTTGGCGTCGT 59.043 50.000 0.00 0.00 0.00 4.34
797 807 8.593492 AATTTTGAAATTCTAGAAGTGTTGGC 57.407 30.769 11.53 0.00 33.54 4.52
966 994 6.366061 CAGGCAAAAATCTTTGTTACTAAGCC 59.634 38.462 1.83 0.00 43.34 4.35
977 1037 3.119849 CGATCGGTCAGGCAAAAATCTTT 60.120 43.478 7.38 0.00 0.00 2.52
1023 1083 1.746220 ACGATCAGAGCTACAGTGGAC 59.254 52.381 0.00 0.00 0.00 4.02
1025 1085 2.949451 AACGATCAGAGCTACAGTGG 57.051 50.000 0.00 0.00 0.00 4.00
1068 1128 1.613630 AGGGACAAGCCGGTCATCT 60.614 57.895 1.90 0.00 39.59 2.90
1071 1131 3.636231 CCAGGGACAAGCCGGTCA 61.636 66.667 1.90 0.00 39.59 4.02
1178 1241 2.650322 ACCATATGCCAAGGTAAACCG 58.350 47.619 0.00 0.00 42.08 4.44
1220 1283 2.853705 GGTTAGCAACCCACACAACTA 58.146 47.619 6.76 0.00 46.12 2.24
1256 1319 2.421529 GGTGGAGAGGAAGTGTTGTTGT 60.422 50.000 0.00 0.00 0.00 3.32
1273 1336 0.393537 GTGAGGGAGAGCATTGGTGG 60.394 60.000 0.00 0.00 0.00 4.61
1278 1341 1.004044 CTGTTGGTGAGGGAGAGCATT 59.996 52.381 0.00 0.00 0.00 3.56
1298 1361 6.991531 ACCTTCAGAGATGATAAGATTTGAGC 59.008 38.462 0.00 0.00 0.00 4.26
1371 1437 0.178955 TTGGGGTAGACGAGTCCACA 60.179 55.000 4.40 0.00 32.39 4.17
1376 1445 2.643232 GCCGTTGGGGTAGACGAGT 61.643 63.158 0.00 0.00 41.53 4.18
1413 1482 3.404899 TGACAACCGGATAACAAGGTTC 58.595 45.455 9.46 0.00 45.52 3.62
1526 1595 1.007734 GACACCAGACGCTCGACAA 60.008 57.895 0.00 0.00 0.00 3.18
1591 1660 1.407656 AAGGCTGTGTCTGGGTCGAA 61.408 55.000 0.00 0.00 0.00 3.71
1650 1723 1.355718 ATCCGGTCCATGGGATGCTT 61.356 55.000 13.02 0.00 41.43 3.91
1668 1741 6.620877 TGGTCTACACTCATTACTTGGAAT 57.379 37.500 0.00 0.00 0.00 3.01
1677 1750 3.815401 GCTGTTGTTGGTCTACACTCATT 59.185 43.478 0.00 0.00 0.00 2.57
1810 1886 1.148310 CCAAAGTACGTCAGCACCAG 58.852 55.000 0.00 0.00 0.00 4.00
1954 2030 2.203153 GCACGTTGGGACTGGTGT 60.203 61.111 0.00 0.00 33.09 4.16
2085 2161 1.092348 GTAACTTCATCCCCGGCAAC 58.908 55.000 0.00 0.00 0.00 4.17
2215 2291 0.534412 ATGTCTCCTCTGAACCTGCG 59.466 55.000 0.00 0.00 0.00 5.18
2505 2651 8.913487 TGCATATGAATATGAGAACATCACTT 57.087 30.769 6.97 0.00 41.91 3.16
2510 2656 9.961264 AAGAGATGCATATGAATATGAGAACAT 57.039 29.630 6.97 7.42 42.05 2.71
2589 2743 8.950210 ACATTCTCATAAGGTTGTCAAATACAG 58.050 33.333 0.00 0.00 39.87 2.74
2630 2784 5.964958 AGTACATGACCAATTCCAAGTTG 57.035 39.130 0.00 0.00 0.00 3.16
2686 3807 5.953205 CGCACACAAAACTGAAATTCTTTTG 59.047 36.000 14.78 14.78 39.66 2.44
2691 3812 3.701241 TCCGCACACAAAACTGAAATTC 58.299 40.909 0.00 0.00 0.00 2.17
2693 3814 4.320608 AATCCGCACACAAAACTGAAAT 57.679 36.364 0.00 0.00 0.00 2.17
2694 3815 3.791973 AATCCGCACACAAAACTGAAA 57.208 38.095 0.00 0.00 0.00 2.69
2899 8061 0.027455 CGCATGTTTGACACACACGT 59.973 50.000 0.00 0.00 38.61 4.49
2900 8062 0.657077 CCGCATGTTTGACACACACG 60.657 55.000 0.00 0.00 38.61 4.49
2905 8095 0.944386 ACAGACCGCATGTTTGACAC 59.056 50.000 0.00 0.00 33.42 3.67
2907 8097 0.944386 ACACAGACCGCATGTTTGAC 59.056 50.000 0.00 0.00 33.42 3.18
2950 8267 6.916360 AAATTCCCACACAAGACAATATGT 57.084 33.333 0.00 0.00 0.00 2.29
2961 8308 1.678627 CCACGTCAAAATTCCCACACA 59.321 47.619 0.00 0.00 0.00 3.72
3026 8376 4.952335 AGGTGCTCATTTCCATTCCTTTAG 59.048 41.667 0.00 0.00 0.00 1.85
3425 8806 3.412386 GACTTGCTGACCACCTAACAAT 58.588 45.455 0.00 0.00 0.00 2.71
3517 14753 4.690280 CCAAGTTTCTGTGTTGCAGTTTTT 59.310 37.500 0.00 0.00 45.23 1.94
3629 14865 9.811655 CATGCTTTATTATTAGAATGTGTACCG 57.188 33.333 0.00 0.00 0.00 4.02
3764 15012 4.087182 CGTGAAGATATAGAAGCCCCCTA 58.913 47.826 0.00 0.00 0.00 3.53
3794 15042 3.502211 CCCTATGAATTATGGTGAACCGC 59.498 47.826 0.00 0.00 39.43 5.68
3848 15096 6.049955 TCCGATATCTTGGGTTTCATATCC 57.950 41.667 0.34 0.00 0.00 2.59
3867 15115 1.483004 TCTCGCCATACCAAAATCCGA 59.517 47.619 0.00 0.00 0.00 4.55
3927 15175 5.602561 TGGATACTCACTATGTGCCAACTAT 59.397 40.000 0.00 0.00 32.98 2.12
4340 15615 7.547370 GTCTGGTGAAGTATCTATAATGGATGC 59.453 40.741 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.