Multiple sequence alignment - TraesCS5D01G233200

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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 TraesCS5D01G233200 chr5D 100.000 1991 0 0 850 2840 340760261 340758271 0.000000e+00 3677.0
1 TraesCS5D01G233200 chr5D 100.000 512 0 0 1 512 340761110 340760599 0.000000e+00 946.0
2 TraesCS5D01G233200 chr5B 96.986 1526 38 5 850 2372 399812942 399811422 0.000000e+00 2556.0
3 TraesCS5D01G233200 chr5B 96.561 378 4 3 2464 2840 399811422 399811053 4.020000e-173 617.0
4 TraesCS5D01G233200 chr5B 91.146 384 19 9 136 512 399813376 399813001 9.080000e-140 507.0
5 TraesCS5D01G233200 chr5B 94.118 102 6 0 2367 2468 194782576 194782475 3.790000e-34 156.0
6 TraesCS5D01G233200 chr5B 91.304 115 7 3 2357 2468 33626350 33626236 1.360000e-33 154.0
7 TraesCS5D01G233200 chr5B 87.671 73 8 1 2689 2761 118961371 118961300 1.810000e-12 84.2
8 TraesCS5D01G233200 chr5A 93.721 1529 71 13 850 2370 441704938 441703427 0.000000e+00 2268.0
9 TraesCS5D01G233200 chr5A 89.374 527 30 15 1 512 441705507 441704992 8.580000e-180 640.0
10 TraesCS5D01G233200 chr5A 90.517 116 9 1 2578 2693 441703347 441703234 4.900000e-33 152.0
11 TraesCS5D01G233200 chr4A 93.519 108 6 1 2362 2469 584930955 584931061 2.930000e-35 159.0
12 TraesCS5D01G233200 chr4A 93.396 106 7 0 2368 2473 650040979 650040874 1.050000e-34 158.0
13 TraesCS5D01G233200 chr4A 93.396 106 5 2 2361 2465 650040874 650040978 3.790000e-34 156.0
14 TraesCS5D01G233200 chr7B 93.458 107 6 1 2367 2472 190338586 190338692 1.050000e-34 158.0
15 TraesCS5D01G233200 chr2D 93.333 105 6 1 2366 2470 107204179 107204076 1.360000e-33 154.0
16 TraesCS5D01G233200 chr2D 92.593 108 7 1 2364 2470 166808335 166808228 1.360000e-33 154.0
17 TraesCS5D01G233200 chr2D 100.000 47 0 0 2689 2735 529010332 529010286 1.400000e-13 87.9
18 TraesCS5D01G233200 chr6A 94.845 97 5 0 2369 2465 600701848 600701752 4.900000e-33 152.0
19 TraesCS5D01G233200 chr6A 96.226 53 2 0 2683 2735 51882721 51882669 1.400000e-13 87.9
20 TraesCS5D01G233200 chr7A 91.111 90 8 0 2153 2242 14840656 14840567 3.840000e-24 122.0
21 TraesCS5D01G233200 chr6B 91.111 90 8 0 2153 2242 697663100 697663011 3.840000e-24 122.0
22 TraesCS5D01G233200 chr6B 93.103 58 3 1 2680 2737 524465520 524465576 1.810000e-12 84.2
23 TraesCS5D01G233200 chr4D 91.111 90 8 0 2151 2240 320593822 320593733 3.840000e-24 122.0
24 TraesCS5D01G233200 chr3B 91.111 90 8 0 2150 2239 112281273 112281184 3.840000e-24 122.0
25 TraesCS5D01G233200 chr3B 91.111 90 8 0 2153 2242 403459254 403459343 3.840000e-24 122.0
26 TraesCS5D01G233200 chrUn 88.889 99 10 1 2140 2238 101630787 101630884 1.380000e-23 121.0
27 TraesCS5D01G233200 chrUn 89.706 68 2 4 2673 2735 37403218 37403285 6.520000e-12 82.4
28 TraesCS5D01G233200 chr3A 91.011 89 8 0 2150 2238 78732143 78732055 1.380000e-23 121.0
29 TraesCS5D01G233200 chr3A 95.000 60 1 2 2676 2735 231001822 231001879 3.010000e-15 93.5
30 TraesCS5D01G233200 chr1B 90.110 91 9 0 2151 2241 181305374 181305284 4.970000e-23 119.0
31 TraesCS5D01G233200 chr7D 98.246 57 1 0 2409 2465 634069486 634069542 1.800000e-17 100.0
32 TraesCS5D01G233200 chr2B 90.667 75 6 1 2409 2482 589794250 589794324 6.480000e-17 99.0
33 TraesCS5D01G233200 chr2B 98.077 52 1 0 2684 2735 166044576 166044525 1.080000e-14 91.6
34 TraesCS5D01G233200 chr6D 96.226 53 2 0 2683 2735 41237300 41237248 1.400000e-13 87.9


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 TraesCS5D01G233200 chr5D 340758271 340761110 2839 True 2311.500000 3677 100.000000 1 2840 2 chr5D.!!$R1 2839
1 TraesCS5D01G233200 chr5B 399811053 399813376 2323 True 1226.666667 2556 94.897667 136 2840 3 chr5B.!!$R4 2704
2 TraesCS5D01G233200 chr5A 441703234 441705507 2273 True 1020.000000 2268 91.204000 1 2693 3 chr5A.!!$R1 2692

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
24 25 0.106149 AAGAGTCGGGTTTCGTTGCT 59.894 50.0 0.0 0.0 40.32 3.91 F
120 122 0.309612 ATTCGTTGCAAACCACGGAC 59.690 50.0 0.0 0.0 46.28 4.79 F
1716 1737 1.340399 ATCAGGCAGGCTCCGATTCA 61.340 55.0 0.0 0.0 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1083 1104 1.283181 GTCGACGATCTCCCGGATG 59.717 63.158 0.73 0.00 34.33 3.51 R
1722 1743 2.095252 GTTGAAGGAGAGCGCGGTC 61.095 63.158 29.78 29.78 0.00 4.79 R
2723 2747 6.989169 CCTTGCTAAATGCTAAGTAGTGATCT 59.011 38.462 0.00 0.00 43.37 2.75 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 1.860676 TTCACAAGAGTCGGGTTTCG 58.139 50.000 0.00 0.00 40.90 3.46
22 23 1.260561 CACAAGAGTCGGGTTTCGTTG 59.739 52.381 0.00 0.00 40.32 4.10
24 25 0.106149 AAGAGTCGGGTTTCGTTGCT 59.894 50.000 0.00 0.00 40.32 3.91
25 26 0.963962 AGAGTCGGGTTTCGTTGCTA 59.036 50.000 0.00 0.00 40.32 3.49
50 51 1.060698 GTATCTTTTCACCGCGACAGC 59.939 52.381 8.23 0.00 40.74 4.40
54 55 0.947180 TTTTCACCGCGACAGCCTAC 60.947 55.000 8.23 0.00 41.18 3.18
60 61 0.997196 CCGCGACAGCCTACTTTTAC 59.003 55.000 8.23 0.00 41.18 2.01
61 62 0.997196 CGCGACAGCCTACTTTTACC 59.003 55.000 0.00 0.00 41.18 2.85
67 68 4.517832 CGACAGCCTACTTTTACCCTTTTT 59.482 41.667 0.00 0.00 0.00 1.94
120 122 0.309612 ATTCGTTGCAAACCACGGAC 59.690 50.000 0.00 0.00 46.28 4.79
138 140 5.626543 CACGGACATTTTTCATGTGAAGAAG 59.373 40.000 5.21 1.49 32.72 2.85
148 150 6.551385 TTCATGTGAAGAAGAAGAAGAAGC 57.449 37.500 0.00 0.00 0.00 3.86
219 221 6.211515 CAAGTCAAAGAAAACCCTCTTCATG 58.788 40.000 0.00 0.00 34.49 3.07
376 394 4.722535 AGAAGGCGCCCCTCCTCA 62.723 66.667 26.15 0.00 41.90 3.86
377 395 3.717294 GAAGGCGCCCCTCCTCAA 61.717 66.667 26.15 0.00 41.90 3.02
378 396 3.689002 GAAGGCGCCCCTCCTCAAG 62.689 68.421 26.15 0.00 41.90 3.02
421 439 3.068064 GACCCACCATTTGCGGGG 61.068 66.667 0.00 0.00 44.96 5.73
1593 1614 4.111577 ACCTCATCAGGATTTACTTCCCA 58.888 43.478 0.00 0.00 43.65 4.37
1611 1632 3.381590 TCCCAGTGATCTACGACATCAAG 59.618 47.826 0.00 0.00 31.98 3.02
1716 1737 1.340399 ATCAGGCAGGCTCCGATTCA 61.340 55.000 0.00 0.00 0.00 2.57
1722 1743 1.088340 CAGGCTCCGATTCACTGCTG 61.088 60.000 0.00 0.00 0.00 4.41
1785 1806 4.083271 GGCGGATTAACTGAGAAATATGCC 60.083 45.833 9.57 9.57 31.98 4.40
1905 1926 2.157738 AGAAACCTGTCTGCTGAATGC 58.842 47.619 0.00 0.00 43.25 3.56
1968 1990 6.656693 AGGTATCACTTTTCTCTCAATTGTGG 59.343 38.462 5.13 0.25 0.00 4.17
2004 2026 7.732025 TGAGTTTGTTTAGGTTAGATGACTGA 58.268 34.615 0.00 0.00 0.00 3.41
2026 2048 7.041508 ACTGAGTTTTTGTTGTTTGATTTTGCA 60.042 29.630 0.00 0.00 0.00 4.08
2053 2075 5.941733 TGAAGTTGATGGAATGATGAAACG 58.058 37.500 0.00 0.00 0.00 3.60
2054 2076 5.473162 TGAAGTTGATGGAATGATGAAACGT 59.527 36.000 0.00 0.00 0.00 3.99
2055 2077 5.300969 AGTTGATGGAATGATGAAACGTG 57.699 39.130 0.00 0.00 0.00 4.49
2074 2096 6.466885 ACGTGCTCTAGATACTGGTTAAAT 57.533 37.500 0.00 0.00 0.00 1.40
2075 2097 6.505272 ACGTGCTCTAGATACTGGTTAAATC 58.495 40.000 0.00 0.00 0.00 2.17
2076 2098 6.321690 ACGTGCTCTAGATACTGGTTAAATCT 59.678 38.462 0.00 0.00 34.44 2.40
2097 2120 6.737720 TCTACCTATGCTGATTCTTCACAT 57.262 37.500 0.00 0.00 32.27 3.21
2099 2122 5.363562 ACCTATGCTGATTCTTCACATGA 57.636 39.130 0.00 0.00 30.98 3.07
2111 2134 5.808366 TCTTCACATGACCTGTAGAGTTT 57.192 39.130 0.00 0.00 35.91 2.66
2119 2142 6.706270 ACATGACCTGTAGAGTTTAACACTTG 59.294 38.462 0.00 0.00 35.91 3.16
2120 2143 6.474140 TGACCTGTAGAGTTTAACACTTGA 57.526 37.500 0.00 0.00 35.01 3.02
2121 2144 7.062749 TGACCTGTAGAGTTTAACACTTGAT 57.937 36.000 0.00 0.00 35.01 2.57
2122 2145 8.185506 TGACCTGTAGAGTTTAACACTTGATA 57.814 34.615 0.00 0.00 35.01 2.15
2162 2185 4.188247 TCTTTTGTCATGTACTCCCTCG 57.812 45.455 0.00 0.00 0.00 4.63
2181 2204 6.325545 TCCCTCGGTAAAGAAATATAAGAGCA 59.674 38.462 0.00 0.00 0.00 4.26
2197 2220 4.070630 AGAGCATTTGGATCACTAGAGC 57.929 45.455 0.00 0.00 33.23 4.09
2371 2394 7.835181 ACTAGTTGGTTCAAGCTATCTAGTACT 59.165 37.037 0.00 0.00 36.27 2.73
2372 2395 7.102847 AGTTGGTTCAAGCTATCTAGTACTC 57.897 40.000 0.00 0.00 0.00 2.59
2373 2396 6.097129 AGTTGGTTCAAGCTATCTAGTACTCC 59.903 42.308 0.00 0.00 0.00 3.85
2374 2397 4.894114 TGGTTCAAGCTATCTAGTACTCCC 59.106 45.833 0.00 0.00 0.00 4.30
2375 2398 5.141910 GGTTCAAGCTATCTAGTACTCCCT 58.858 45.833 0.00 0.00 0.00 4.20
2376 2399 5.242171 GGTTCAAGCTATCTAGTACTCCCTC 59.758 48.000 0.00 0.00 0.00 4.30
2377 2400 4.988029 TCAAGCTATCTAGTACTCCCTCC 58.012 47.826 0.00 0.00 0.00 4.30
2378 2401 3.706600 AGCTATCTAGTACTCCCTCCG 57.293 52.381 0.00 0.00 0.00 4.63
2379 2402 2.981081 AGCTATCTAGTACTCCCTCCGT 59.019 50.000 0.00 0.00 0.00 4.69
2380 2403 3.395273 AGCTATCTAGTACTCCCTCCGTT 59.605 47.826 0.00 0.00 0.00 4.44
2381 2404 3.752747 GCTATCTAGTACTCCCTCCGTTC 59.247 52.174 0.00 0.00 0.00 3.95
2382 2405 2.725221 TCTAGTACTCCCTCCGTTCC 57.275 55.000 0.00 0.00 0.00 3.62
2383 2406 1.918262 TCTAGTACTCCCTCCGTTCCA 59.082 52.381 0.00 0.00 0.00 3.53
2384 2407 2.309755 TCTAGTACTCCCTCCGTTCCAA 59.690 50.000 0.00 0.00 0.00 3.53
2385 2408 2.019807 AGTACTCCCTCCGTTCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
2386 2409 1.900486 AGTACTCCCTCCGTTCCAAAG 59.100 52.381 0.00 0.00 0.00 2.77
2387 2410 1.622312 GTACTCCCTCCGTTCCAAAGT 59.378 52.381 0.00 0.00 0.00 2.66
2388 2411 2.019807 ACTCCCTCCGTTCCAAAGTA 57.980 50.000 0.00 0.00 0.00 2.24
2389 2412 1.900486 ACTCCCTCCGTTCCAAAGTAG 59.100 52.381 0.00 0.00 0.00 2.57
2390 2413 2.176889 CTCCCTCCGTTCCAAAGTAGA 58.823 52.381 0.00 0.00 0.00 2.59
2391 2414 2.766828 CTCCCTCCGTTCCAAAGTAGAT 59.233 50.000 0.00 0.00 0.00 1.98
2392 2415 2.500098 TCCCTCCGTTCCAAAGTAGATG 59.500 50.000 0.00 0.00 0.00 2.90
2393 2416 2.500098 CCCTCCGTTCCAAAGTAGATGA 59.500 50.000 0.00 0.00 0.00 2.92
2394 2417 3.134804 CCCTCCGTTCCAAAGTAGATGAT 59.865 47.826 0.00 0.00 0.00 2.45
2395 2418 4.384208 CCCTCCGTTCCAAAGTAGATGATT 60.384 45.833 0.00 0.00 0.00 2.57
2396 2419 4.811557 CCTCCGTTCCAAAGTAGATGATTC 59.188 45.833 0.00 0.00 0.00 2.52
2397 2420 5.414789 TCCGTTCCAAAGTAGATGATTCA 57.585 39.130 0.00 0.00 0.00 2.57
2398 2421 5.800296 TCCGTTCCAAAGTAGATGATTCAA 58.200 37.500 0.00 0.00 0.00 2.69
2399 2422 5.642063 TCCGTTCCAAAGTAGATGATTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
2400 2423 5.643777 CCGTTCCAAAGTAGATGATTCAACT 59.356 40.000 1.83 1.83 0.00 3.16
2401 2424 6.149474 CCGTTCCAAAGTAGATGATTCAACTT 59.851 38.462 1.47 0.00 33.72 2.66
2402 2425 7.308589 CCGTTCCAAAGTAGATGATTCAACTTT 60.309 37.037 8.49 8.49 41.56 2.66
2406 2429 7.558435 CAAAGTAGATGATTCAACTTTGTGC 57.442 36.000 22.77 0.18 46.99 4.57
2407 2430 7.365741 CAAAGTAGATGATTCAACTTTGTGCT 58.634 34.615 22.77 2.09 46.99 4.40
2408 2431 8.506437 CAAAGTAGATGATTCAACTTTGTGCTA 58.494 33.333 22.77 0.00 46.99 3.49
2409 2432 8.621532 AAGTAGATGATTCAACTTTGTGCTAA 57.378 30.769 1.47 0.00 0.00 3.09
2410 2433 8.034058 AGTAGATGATTCAACTTTGTGCTAAC 57.966 34.615 1.47 0.00 0.00 2.34
2411 2434 7.880195 AGTAGATGATTCAACTTTGTGCTAACT 59.120 33.333 1.47 0.00 0.00 2.24
2412 2435 7.516198 AGATGATTCAACTTTGTGCTAACTT 57.484 32.000 0.00 0.00 0.00 2.66
2413 2436 7.945134 AGATGATTCAACTTTGTGCTAACTTT 58.055 30.769 0.00 0.00 0.00 2.66
2414 2437 9.066892 AGATGATTCAACTTTGTGCTAACTTTA 57.933 29.630 0.00 0.00 0.00 1.85
2415 2438 9.846248 GATGATTCAACTTTGTGCTAACTTTAT 57.154 29.630 0.00 0.00 0.00 1.40
2451 2474 9.003658 AGTACAAAGTTGAGTCATCTATTTTGG 57.996 33.333 14.35 0.00 40.00 3.28
2452 2475 8.999431 GTACAAAGTTGAGTCATCTATTTTGGA 58.001 33.333 14.35 6.88 40.00 3.53
2453 2476 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53
2454 2477 9.082313 ACAAAGTTGAGTCATCTATTTTGGAAT 57.918 29.630 14.35 0.00 40.00 3.01
2455 2478 9.350357 CAAAGTTGAGTCATCTATTTTGGAATG 57.650 33.333 4.14 0.00 35.65 2.67
2456 2479 7.636150 AGTTGAGTCATCTATTTTGGAATGG 57.364 36.000 1.70 0.00 0.00 3.16
2457 2480 7.405292 AGTTGAGTCATCTATTTTGGAATGGA 58.595 34.615 1.70 0.00 37.20 3.41
2458 2481 7.555554 AGTTGAGTCATCTATTTTGGAATGGAG 59.444 37.037 1.70 0.00 36.39 3.86
2459 2482 6.359804 TGAGTCATCTATTTTGGAATGGAGG 58.640 40.000 0.00 0.00 36.39 4.30
2460 2483 5.699143 AGTCATCTATTTTGGAATGGAGGG 58.301 41.667 0.00 0.00 36.39 4.30
2587 2610 3.401182 GAGATTAAGCAGAGATGGCCAG 58.599 50.000 13.05 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 6.509677 GCGGTGAAAAGATACACTATAGCAAC 60.510 42.308 0.00 0.00 37.22 4.17
22 23 4.148348 CGCGGTGAAAAGATACACTATAGC 59.852 45.833 0.00 0.00 37.22 2.97
24 25 5.163632 TGTCGCGGTGAAAAGATACACTATA 60.164 40.000 6.13 0.00 37.22 1.31
25 26 4.110482 GTCGCGGTGAAAAGATACACTAT 58.890 43.478 6.13 0.00 37.22 2.12
89 91 8.678199 TGGTTTGCAACGAATATATTAACATCA 58.322 29.630 0.00 0.00 0.00 3.07
90 92 8.953990 GTGGTTTGCAACGAATATATTAACATC 58.046 33.333 0.00 0.00 0.00 3.06
95 97 5.816258 TCCGTGGTTTGCAACGAATATATTA 59.184 36.000 10.13 0.00 44.42 0.98
101 103 0.309612 GTCCGTGGTTTGCAACGAAT 59.690 50.000 10.13 0.00 44.42 3.34
120 122 9.740239 TTCTTCTTCTTCTTCACATGAAAAATG 57.260 29.630 0.00 0.00 33.07 2.32
138 140 5.855925 GCTTTTCTTTAGCTGCTTCTTCTTC 59.144 40.000 7.79 0.00 35.74 2.87
148 150 6.467723 TTTCTCTACGCTTTTCTTTAGCTG 57.532 37.500 0.00 0.00 36.49 4.24
219 221 3.867857 TGGTTTTGTTTTGCTTCTTCCC 58.132 40.909 0.00 0.00 0.00 3.97
251 261 2.031870 AGGAAAACAAGGGAAGTGTGC 58.968 47.619 0.00 0.00 0.00 4.57
361 376 3.721706 CTTGAGGAGGGGCGCCTT 61.722 66.667 28.56 15.62 32.83 4.35
376 394 4.722700 ATTGCCGGCCGACAGCTT 62.723 61.111 30.73 10.75 43.05 3.74
491 509 1.396594 GGGGAAGAAGAGGGGAGGA 59.603 63.158 0.00 0.00 0.00 3.71
933 954 4.847444 GAAGCCTCGGAGCTGGGC 62.847 72.222 0.00 0.00 44.11 5.36
1083 1104 1.283181 GTCGACGATCTCCCGGATG 59.717 63.158 0.73 0.00 34.33 3.51
1563 1584 4.399004 AATCCTGATGAGGTCGAAGAAG 57.601 45.455 0.00 0.00 39.69 2.85
1593 1614 3.445450 AGTGCTTGATGTCGTAGATCACT 59.555 43.478 0.00 0.00 40.67 3.41
1611 1632 4.634184 ATTGCAGAATCTCATCAAGTGC 57.366 40.909 0.00 0.00 0.00 4.40
1722 1743 2.095252 GTTGAAGGAGAGCGCGGTC 61.095 63.158 29.78 29.78 0.00 4.79
1785 1806 2.888594 CCTAGACCATACAACACACCG 58.111 52.381 0.00 0.00 0.00 4.94
1898 1919 5.919272 ATAATCAGACATCACGCATTCAG 57.081 39.130 0.00 0.00 0.00 3.02
1905 1926 6.309980 GCAAGAGGATATAATCAGACATCACG 59.690 42.308 0.00 0.00 0.00 4.35
1948 1970 6.591935 AGTACCACAATTGAGAGAAAAGTGA 58.408 36.000 13.59 0.00 0.00 3.41
2004 2026 6.527372 GCATGCAAAATCAAACAACAAAAACT 59.473 30.769 14.21 0.00 0.00 2.66
2026 2048 5.198207 TCATCATTCCATCAACTTCAGCAT 58.802 37.500 0.00 0.00 0.00 3.79
2053 2075 8.083462 GGTAGATTTAACCAGTATCTAGAGCAC 58.917 40.741 0.00 0.00 36.96 4.40
2054 2076 8.005388 AGGTAGATTTAACCAGTATCTAGAGCA 58.995 37.037 0.00 0.00 39.64 4.26
2055 2077 8.411991 AGGTAGATTTAACCAGTATCTAGAGC 57.588 38.462 0.00 0.00 39.64 4.09
2074 2096 6.324770 TCATGTGAAGAATCAGCATAGGTAGA 59.675 38.462 0.00 0.00 35.88 2.59
2075 2097 6.423302 GTCATGTGAAGAATCAGCATAGGTAG 59.577 42.308 0.00 0.00 35.88 3.18
2076 2098 6.283694 GTCATGTGAAGAATCAGCATAGGTA 58.716 40.000 0.00 0.00 35.88 3.08
2097 2120 6.474140 TCAAGTGTTAAACTCTACAGGTCA 57.526 37.500 0.00 0.00 38.56 4.02
2099 2122 8.418597 TCTATCAAGTGTTAAACTCTACAGGT 57.581 34.615 0.00 0.00 38.56 4.00
2181 2204 6.479884 AGAAAACTGCTCTAGTGATCCAAAT 58.520 36.000 0.00 0.00 40.26 2.32
2371 2394 2.314071 TCTACTTTGGAACGGAGGGA 57.686 50.000 0.00 0.00 0.00 4.20
2372 2395 2.500098 TCATCTACTTTGGAACGGAGGG 59.500 50.000 0.00 0.00 0.00 4.30
2373 2396 3.887621 TCATCTACTTTGGAACGGAGG 57.112 47.619 0.00 0.00 0.00 4.30
2374 2397 5.419542 TGAATCATCTACTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
2375 2398 5.414789 TGAATCATCTACTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
2376 2399 5.643777 AGTTGAATCATCTACTTTGGAACGG 59.356 40.000 0.00 0.00 38.27 4.44
2377 2400 6.727824 AGTTGAATCATCTACTTTGGAACG 57.272 37.500 0.00 0.00 38.27 3.95
2385 2408 7.880195 AGTTAGCACAAAGTTGAATCATCTACT 59.120 33.333 0.00 0.00 42.33 2.57
2386 2409 8.034058 AGTTAGCACAAAGTTGAATCATCTAC 57.966 34.615 0.00 0.00 0.00 2.59
2387 2410 8.621532 AAGTTAGCACAAAGTTGAATCATCTA 57.378 30.769 0.00 0.00 0.00 1.98
2388 2411 7.516198 AAGTTAGCACAAAGTTGAATCATCT 57.484 32.000 0.00 0.00 0.00 2.90
2389 2412 9.846248 ATAAAGTTAGCACAAAGTTGAATCATC 57.154 29.630 0.00 0.00 0.00 2.92
2425 2448 9.003658 CCAAAATAGATGACTCAACTTTGTACT 57.996 33.333 0.00 0.00 0.00 2.73
2426 2449 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
2427 2450 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
2428 2451 8.463930 TTCCAAAATAGATGACTCAACTTTGT 57.536 30.769 0.00 0.00 0.00 2.83
2429 2452 9.350357 CATTCCAAAATAGATGACTCAACTTTG 57.650 33.333 0.00 0.00 0.00 2.77
2430 2453 8.526147 CCATTCCAAAATAGATGACTCAACTTT 58.474 33.333 0.00 0.00 0.00 2.66
2431 2454 7.890127 TCCATTCCAAAATAGATGACTCAACTT 59.110 33.333 0.00 0.00 0.00 2.66
2432 2455 7.405292 TCCATTCCAAAATAGATGACTCAACT 58.595 34.615 0.00 0.00 0.00 3.16
2433 2456 7.201767 CCTCCATTCCAAAATAGATGACTCAAC 60.202 40.741 0.00 0.00 0.00 3.18
2434 2457 6.830324 CCTCCATTCCAAAATAGATGACTCAA 59.170 38.462 0.00 0.00 0.00 3.02
2435 2458 6.359804 CCTCCATTCCAAAATAGATGACTCA 58.640 40.000 0.00 0.00 0.00 3.41
2436 2459 5.767168 CCCTCCATTCCAAAATAGATGACTC 59.233 44.000 0.00 0.00 0.00 3.36
2437 2460 5.433051 TCCCTCCATTCCAAAATAGATGACT 59.567 40.000 0.00 0.00 0.00 3.41
2438 2461 5.694995 TCCCTCCATTCCAAAATAGATGAC 58.305 41.667 0.00 0.00 0.00 3.06
2439 2462 5.433051 ACTCCCTCCATTCCAAAATAGATGA 59.567 40.000 0.00 0.00 0.00 2.92
2440 2463 5.699143 ACTCCCTCCATTCCAAAATAGATG 58.301 41.667 0.00 0.00 0.00 2.90
2441 2464 7.654287 ATACTCCCTCCATTCCAAAATAGAT 57.346 36.000 0.00 0.00 0.00 1.98
2442 2465 7.465900 AATACTCCCTCCATTCCAAAATAGA 57.534 36.000 0.00 0.00 0.00 1.98
2447 2470 9.057911 CCTATATAATACTCCCTCCATTCCAAA 57.942 37.037 0.00 0.00 0.00 3.28
2448 2471 8.191110 ACCTATATAATACTCCCTCCATTCCAA 58.809 37.037 0.00 0.00 0.00 3.53
2449 2472 7.729350 ACCTATATAATACTCCCTCCATTCCA 58.271 38.462 0.00 0.00 0.00 3.53
2450 2473 7.290481 GGACCTATATAATACTCCCTCCATTCC 59.710 44.444 0.00 0.00 0.00 3.01
2451 2474 7.844779 TGGACCTATATAATACTCCCTCCATTC 59.155 40.741 0.00 0.00 0.00 2.67
2452 2475 7.729350 TGGACCTATATAATACTCCCTCCATT 58.271 38.462 0.00 0.00 0.00 3.16
2453 2476 7.312162 TGGACCTATATAATACTCCCTCCAT 57.688 40.000 0.00 0.00 0.00 3.41
2454 2477 6.746456 TGGACCTATATAATACTCCCTCCA 57.254 41.667 0.00 0.00 0.00 3.86
2455 2478 6.042208 GCATGGACCTATATAATACTCCCTCC 59.958 46.154 0.00 0.00 0.00 4.30
2456 2479 6.841755 AGCATGGACCTATATAATACTCCCTC 59.158 42.308 0.00 0.00 0.00 4.30
2457 2480 6.757317 AGCATGGACCTATATAATACTCCCT 58.243 40.000 0.00 0.00 0.00 4.20
2458 2481 7.419172 GGAAGCATGGACCTATATAATACTCCC 60.419 44.444 0.00 0.00 0.00 4.30
2459 2482 7.125811 TGGAAGCATGGACCTATATAATACTCC 59.874 40.741 0.00 0.00 0.00 3.85
2460 2483 8.079211 TGGAAGCATGGACCTATATAATACTC 57.921 38.462 0.00 0.00 0.00 2.59
2723 2747 6.989169 CCTTGCTAAATGCTAAGTAGTGATCT 59.011 38.462 0.00 0.00 43.37 2.75
2750 2774 9.173939 GTTTCTTGACTTATTGACATTTGACAG 57.826 33.333 0.00 0.00 0.00 3.51
2751 2775 8.902806 AGTTTCTTGACTTATTGACATTTGACA 58.097 29.630 0.00 0.00 0.00 3.58
2752 2776 9.736023 AAGTTTCTTGACTTATTGACATTTGAC 57.264 29.630 0.00 0.00 38.06 3.18
2755 2779 9.750125 GGAAAGTTTCTTGACTTATTGACATTT 57.250 29.630 15.05 0.00 38.86 2.32
2756 2780 8.360390 GGGAAAGTTTCTTGACTTATTGACATT 58.640 33.333 15.05 0.00 38.86 2.71


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

AutoCloner maintained by Alex Coulton.