Multiple sequence alignment - TraesCS2A01G167800

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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 TraesCS2A01G167800 chr2A 100.000 2552 0 0 1 2552 120777434 120774883 0.000000e+00 4713.0
1 TraesCS2A01G167800 chr2A 92.408 461 32 3 1 459 736477390 736476931 0.000000e+00 654.0
2 TraesCS2A01G167800 chr2A 85.714 70 5 4 397 463 737730632 737730699 4.560000e-08 69.4
3 TraesCS2A01G167800 chr2D 89.432 1514 63 33 602 2052 118895625 118894146 0.000000e+00 1820.0
4 TraesCS2A01G167800 chr2D 89.775 489 29 12 2074 2552 118894173 118893696 7.810000e-170 606.0
5 TraesCS2A01G167800 chr2D 83.402 241 19 12 2132 2363 118876813 118876585 1.200000e-48 204.0
6 TraesCS2A01G167800 chr2D 87.129 101 5 2 492 584 118895708 118895608 9.650000e-20 108.0
7 TraesCS2A01G167800 chr2D 95.833 48 2 0 461 508 118895769 118895722 7.570000e-11 78.7
8 TraesCS2A01G167800 chr2B 92.408 922 50 12 658 1566 170972148 170971234 0.000000e+00 1297.0
9 TraesCS2A01G167800 chr2B 89.355 310 21 9 2136 2437 170956103 170955798 1.850000e-101 379.0
10 TraesCS2A01G167800 chr2B 93.478 46 2 1 2496 2540 170954562 170954517 1.640000e-07 67.6
11 TraesCS2A01G167800 chr4A 89.263 475 38 9 1 463 629945376 629945849 1.320000e-162 582.0
12 TraesCS2A01G167800 chr6A 86.383 470 36 9 1 463 58006603 58007051 2.950000e-134 488.0
13 TraesCS2A01G167800 chr4D 90.323 217 16 4 249 463 433348986 433348773 1.930000e-71 279.0
14 TraesCS2A01G167800 chr4D 95.146 103 4 1 1 103 433349381 433349280 7.310000e-36 161.0
15 TraesCS2A01G167800 chr4D 89.474 57 6 0 399 455 504084300 504084356 3.520000e-09 73.1
16 TraesCS2A01G167800 chr3B 93.976 166 8 2 1 166 20723313 20723150 1.520000e-62 250.0
17 TraesCS2A01G167800 chr3B 89.071 183 19 1 281 462 20722755 20722573 2.550000e-55 226.0
18 TraesCS2A01G167800 chr4B 94.194 155 6 3 1 155 352170884 352170733 1.530000e-57 233.0
19 TraesCS2A01G167800 chr4B 87.435 191 22 2 273 461 352170478 352170288 4.270000e-53 219.0
20 TraesCS2A01G167800 chr3D 89.714 175 13 4 1 173 596722636 596722465 4.270000e-53 219.0
21 TraesCS2A01G167800 chr1A 84.286 210 17 5 217 421 9303472 9303670 9.320000e-45 191.0
22 TraesCS2A01G167800 chr1A 91.339 127 10 1 1 126 9303022 9303148 3.380000e-39 172.0
23 TraesCS2A01G167800 chr6B 94.231 52 3 0 413 464 211217670 211217619 2.100000e-11 80.5
24 TraesCS2A01G167800 chr5B 85.075 67 6 3 399 463 648740180 648740244 5.890000e-07 65.8


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 TraesCS2A01G167800 chr2A 120774883 120777434 2551 True 4713.000 4713 100.00000 1 2552 1 chr2A.!!$R1 2551
1 TraesCS2A01G167800 chr2D 118893696 118895769 2073 True 653.175 1820 90.54225 461 2552 4 chr2D.!!$R2 2091
2 TraesCS2A01G167800 chr2B 170971234 170972148 914 True 1297.000 1297 92.40800 658 1566 1 chr2B.!!$R1 908
3 TraesCS2A01G167800 chr2B 170954517 170956103 1586 True 223.300 379 91.41650 2136 2540 2 chr2B.!!$R2 404
4 TraesCS2A01G167800 chr4D 433348773 433349381 608 True 220.000 279 92.73450 1 463 2 chr4D.!!$R1 462
5 TraesCS2A01G167800 chr3B 20722573 20723313 740 True 238.000 250 91.52350 1 462 2 chr3B.!!$R1 461
6 TraesCS2A01G167800 chr4B 352170288 352170884 596 True 226.000 233 90.81450 1 461 2 chr4B.!!$R1 460

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
933 1279 0.108804 ACCGTACATCTCAACGCAGG 60.109 55.0 0.0 0.0 37.78 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2070 2461 0.107897 GCACCATACGGATGTGACCA 60.108 55.0 6.92 0.0 35.59 4.02 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
124 125 1.142870 CATGCGAAGGATTAGGGGGAA 59.857 52.381 0.00 0.00 35.32 3.97
156 157 1.683365 GGTTGCTGGGCATGGACAT 60.683 57.895 0.00 0.00 38.76 3.06
166 167 1.146930 CATGGACATGGGGGAGACG 59.853 63.158 4.39 0.00 35.24 4.18
167 168 1.002921 ATGGACATGGGGGAGACGA 59.997 57.895 0.00 0.00 0.00 4.20
168 169 1.050988 ATGGACATGGGGGAGACGAG 61.051 60.000 0.00 0.00 0.00 4.18
169 170 2.435693 GGACATGGGGGAGACGAGG 61.436 68.421 0.00 0.00 0.00 4.63
170 171 2.365635 ACATGGGGGAGACGAGGG 60.366 66.667 0.00 0.00 0.00 4.30
171 172 3.164269 CATGGGGGAGACGAGGGG 61.164 72.222 0.00 0.00 0.00 4.79
172 173 4.499116 ATGGGGGAGACGAGGGGG 62.499 72.222 0.00 0.00 0.00 5.40
194 195 3.103911 GTGGAGACGCGACAACGG 61.104 66.667 15.93 0.00 40.15 4.44
199 200 4.405173 GACGCGACAACGGCGAAC 62.405 66.667 15.93 0.30 40.20 3.95
200 201 4.936823 ACGCGACAACGGCGAACT 62.937 61.111 15.93 0.00 40.20 3.01
201 202 4.117372 CGCGACAACGGCGAACTC 62.117 66.667 16.62 2.95 39.71 3.01
202 203 3.774702 GCGACAACGGCGAACTCC 61.775 66.667 16.62 0.00 40.15 3.85
211 212 4.047059 GCGAACTCCGACCCACGA 62.047 66.667 0.00 0.00 45.77 4.35
212 213 2.882876 CGAACTCCGACCCACGAT 59.117 61.111 0.00 0.00 45.77 3.73
213 214 1.516386 CGAACTCCGACCCACGATG 60.516 63.158 0.00 0.00 45.77 3.84
214 215 1.153628 GAACTCCGACCCACGATGG 60.154 63.158 0.00 0.00 45.77 3.51
235 236 4.415332 GGCGACGGCGAACTCTGA 62.415 66.667 18.90 0.00 41.24 3.27
236 237 3.173240 GCGACGGCGAACTCTGAC 61.173 66.667 18.90 0.00 40.82 3.51
237 238 2.870161 CGACGGCGAACTCTGACG 60.870 66.667 16.62 2.21 40.82 4.35
238 239 2.559840 GACGGCGAACTCTGACGA 59.440 61.111 16.62 0.00 0.00 4.20
239 240 1.796749 GACGGCGAACTCTGACGAC 60.797 63.158 16.62 0.00 0.00 4.34
241 242 2.504244 GGCGAACTCTGACGACGG 60.504 66.667 0.00 0.00 0.00 4.79
242 243 2.504244 GCGAACTCTGACGACGGG 60.504 66.667 0.00 0.00 0.00 5.28
243 244 2.178521 CGAACTCTGACGACGGGG 59.821 66.667 0.00 0.00 0.00 5.73
244 245 2.572284 GAACTCTGACGACGGGGG 59.428 66.667 0.00 0.00 0.00 5.40
245 246 3.644399 GAACTCTGACGACGGGGGC 62.644 68.421 0.00 0.00 0.00 5.80
297 578 3.884774 GGTGGGCGGGGCATGATA 61.885 66.667 0.00 0.00 0.00 2.15
322 604 0.334676 ATTTGATGGGGCGAGGGAAA 59.665 50.000 0.00 0.00 0.00 3.13
359 641 1.847328 GGAACGATGGGTGGGAAAAT 58.153 50.000 0.00 0.00 0.00 1.82
365 647 1.134946 GATGGGTGGGAAAATGAAGCG 59.865 52.381 0.00 0.00 0.00 4.68
367 649 0.610785 GGGTGGGAAAATGAAGCGGA 60.611 55.000 0.00 0.00 0.00 5.54
383 665 1.819229 GGAGAAGCTGATCTGGCGA 59.181 57.895 1.46 0.00 34.52 5.54
470 752 0.839946 ATCAGCGCCCTTCCTGTAAT 59.160 50.000 2.29 0.00 0.00 1.89
479 761 1.393539 CCTTCCTGTAATGTCGTTGCG 59.606 52.381 0.00 0.00 0.00 4.85
519 831 2.453521 AGTTCCTACACGGCTACATGA 58.546 47.619 0.00 0.00 0.00 3.07
532 846 2.428890 GCTACATGACCTAGCAGTCTGT 59.571 50.000 0.00 7.22 37.22 3.41
540 854 2.114616 CCTAGCAGTCTGTTCCCATCT 58.885 52.381 0.93 0.00 0.00 2.90
541 855 2.503356 CCTAGCAGTCTGTTCCCATCTT 59.497 50.000 0.93 0.00 0.00 2.40
554 868 1.482182 CCCATCTTGAGTCGGTGATCA 59.518 52.381 0.00 0.00 0.00 2.92
564 884 2.439156 GGTGATCAGGCAGCCACC 60.439 66.667 15.80 8.31 41.72 4.61
581 901 1.608590 CACCAGCAAAAGTCACCGATT 59.391 47.619 0.00 0.00 0.00 3.34
582 902 1.880027 ACCAGCAAAAGTCACCGATTC 59.120 47.619 0.00 0.00 0.00 2.52
583 903 2.154462 CCAGCAAAAGTCACCGATTCT 58.846 47.619 0.00 0.00 0.00 2.40
584 904 2.554032 CCAGCAAAAGTCACCGATTCTT 59.446 45.455 0.00 0.00 0.00 2.52
585 905 3.004734 CCAGCAAAAGTCACCGATTCTTT 59.995 43.478 0.00 0.00 33.61 2.52
586 906 4.499696 CCAGCAAAAGTCACCGATTCTTTT 60.500 41.667 0.00 0.00 40.50 2.27
587 907 5.043248 CAGCAAAAGTCACCGATTCTTTTT 58.957 37.500 0.00 0.00 38.70 1.94
588 908 5.173854 CAGCAAAAGTCACCGATTCTTTTTC 59.826 40.000 0.00 0.00 38.70 2.29
589 909 5.067805 AGCAAAAGTCACCGATTCTTTTTCT 59.932 36.000 0.00 0.00 38.70 2.52
590 910 5.748630 GCAAAAGTCACCGATTCTTTTTCTT 59.251 36.000 0.00 0.00 38.70 2.52
591 911 6.255670 GCAAAAGTCACCGATTCTTTTTCTTT 59.744 34.615 0.00 0.00 38.70 2.52
592 912 7.201522 GCAAAAGTCACCGATTCTTTTTCTTTT 60.202 33.333 0.00 0.00 38.70 2.27
593 913 8.655970 CAAAAGTCACCGATTCTTTTTCTTTTT 58.344 29.630 0.00 0.00 38.70 1.94
613 933 2.810439 TTGAAGGGCAAAATTCACCG 57.190 45.000 0.00 0.00 35.25 4.94
614 934 1.988293 TGAAGGGCAAAATTCACCGA 58.012 45.000 0.00 0.00 30.67 4.69
625 945 4.471904 AAATTCACCGATCTGTGCTCTA 57.528 40.909 12.05 0.00 36.17 2.43
667 997 0.818296 TAGCTTCGTGCCCTCTTCTC 59.182 55.000 0.00 0.00 44.23 2.87
682 1012 1.945354 TTCTCGGAGATGGGACGCAC 61.945 60.000 8.81 0.00 33.89 5.34
685 1015 4.530857 GGAGATGGGACGCACGGG 62.531 72.222 0.00 0.00 0.00 5.28
686 1016 3.458163 GAGATGGGACGCACGGGA 61.458 66.667 0.00 0.00 0.00 5.14
829 1168 4.789075 GCGCGGCCACTCTAACGA 62.789 66.667 8.83 0.00 0.00 3.85
830 1169 2.126228 CGCGGCCACTCTAACGAA 60.126 61.111 2.24 0.00 0.00 3.85
879 1224 1.742761 ATATTTGCTCTGTGTGCGCT 58.257 45.000 9.73 0.00 0.00 5.92
904 1250 1.064906 CATCCTGCACCCATCTCAACT 60.065 52.381 0.00 0.00 0.00 3.16
905 1251 0.615331 TCCTGCACCCATCTCAACTC 59.385 55.000 0.00 0.00 0.00 3.01
906 1252 0.617413 CCTGCACCCATCTCAACTCT 59.383 55.000 0.00 0.00 0.00 3.24
907 1253 1.833630 CCTGCACCCATCTCAACTCTA 59.166 52.381 0.00 0.00 0.00 2.43
908 1254 2.158986 CCTGCACCCATCTCAACTCTAG 60.159 54.545 0.00 0.00 0.00 2.43
930 1276 2.353889 TCTCTACCGTACATCTCAACGC 59.646 50.000 0.00 0.00 37.78 4.84
933 1279 0.108804 ACCGTACATCTCAACGCAGG 60.109 55.000 0.00 0.00 37.78 4.85
939 1285 3.989698 ATCTCAACGCAGGCGACGG 62.990 63.158 21.62 8.95 42.83 4.79
969 1325 2.105930 CTCTCCAGCCGCTACAGC 59.894 66.667 0.00 0.00 37.78 4.40
1330 1695 3.458579 CCGTCACGCTCGTGTTCG 61.459 66.667 19.95 21.80 45.55 3.95
1473 1838 0.243907 ACTCCGTCATGAAGGTCGTG 59.756 55.000 24.48 15.90 34.78 4.35
1571 1938 9.176181 CTTCTAGCAAAAGTACTCGATATTCTC 57.824 37.037 0.00 0.00 0.00 2.87
1572 1939 8.221965 TCTAGCAAAAGTACTCGATATTCTCA 57.778 34.615 0.00 0.00 0.00 3.27
1573 1940 8.683615 TCTAGCAAAAGTACTCGATATTCTCAA 58.316 33.333 0.00 0.00 0.00 3.02
1577 1944 9.267096 GCAAAAGTACTCGATATTCTCAAAAAG 57.733 33.333 0.00 0.00 0.00 2.27
1735 2102 9.585099 TGGTAATAAGATTGATTGACAAATTGC 57.415 29.630 0.00 0.00 42.03 3.56
1786 2153 1.808945 CTGCAATTCCAGTGACCTGAC 59.191 52.381 0.00 0.00 41.50 3.51
1787 2154 0.798776 GCAATTCCAGTGACCTGACG 59.201 55.000 0.00 0.00 41.50 4.35
1797 2164 2.806244 AGTGACCTGACGTAAATGTTGC 59.194 45.455 0.00 0.00 0.00 4.17
1827 2194 3.215151 TCCCACACGCTAATGAACAAAA 58.785 40.909 0.00 0.00 0.00 2.44
1875 2244 3.402628 ACAAATCCAGTCGTTGCTAGT 57.597 42.857 0.00 0.00 0.00 2.57
1930 2299 5.797934 CGTAAGTTGTTCTGCTTTGAAAACA 59.202 36.000 0.00 0.00 0.00 2.83
1931 2300 6.472163 CGTAAGTTGTTCTGCTTTGAAAACAT 59.528 34.615 0.00 0.00 32.16 2.71
1940 2331 5.527951 TCTGCTTTGAAAACATTACGTGGTA 59.472 36.000 0.00 0.00 0.00 3.25
1946 2337 4.214545 TGAAAACATTACGTGGTAGCCAAG 59.785 41.667 0.00 0.00 38.88 3.61
1947 2338 2.396590 ACATTACGTGGTAGCCAAGG 57.603 50.000 0.00 0.00 37.32 3.61
2020 2411 4.260375 CGGCTTTGATAACCTTCGATTCAG 60.260 45.833 0.00 0.00 0.00 3.02
2041 2432 3.264193 AGCACTCACAATCCATGGTTCTA 59.736 43.478 12.58 0.00 0.00 2.10
2052 2443 4.093743 TCCATGGTTCTACTAGAAGTGCA 58.906 43.478 12.58 0.00 34.42 4.57
2053 2444 4.160439 TCCATGGTTCTACTAGAAGTGCAG 59.840 45.833 12.58 0.00 34.42 4.41
2055 2446 3.774734 TGGTTCTACTAGAAGTGCAGGA 58.225 45.455 0.00 0.00 34.42 3.86
2056 2447 4.157246 TGGTTCTACTAGAAGTGCAGGAA 58.843 43.478 0.00 0.00 34.42 3.36
2057 2448 4.220821 TGGTTCTACTAGAAGTGCAGGAAG 59.779 45.833 0.00 0.00 34.42 3.46
2058 2449 4.177783 GTTCTACTAGAAGTGCAGGAAGC 58.822 47.826 0.00 0.00 38.21 3.86
2059 2450 3.832490 TTCTACTAGAAGTGCAGGAAGCA 59.168 43.478 0.00 0.00 45.48 3.91
2079 2470 3.118454 CGGGTGCGTGGTCACATC 61.118 66.667 1.90 0.00 38.66 3.06
2080 2471 2.746277 GGGTGCGTGGTCACATCC 60.746 66.667 1.90 0.86 38.66 3.51
2081 2472 3.118454 GGTGCGTGGTCACATCCG 61.118 66.667 1.90 0.00 38.66 4.18
2082 2473 2.357034 GTGCGTGGTCACATCCGT 60.357 61.111 1.90 0.00 36.97 4.69
2083 2474 1.080366 GTGCGTGGTCACATCCGTA 60.080 57.895 1.90 0.00 36.97 4.02
2084 2475 0.459585 GTGCGTGGTCACATCCGTAT 60.460 55.000 1.90 0.00 36.97 3.06
2085 2476 0.459411 TGCGTGGTCACATCCGTATG 60.459 55.000 1.90 0.00 39.17 2.39
2086 2477 1.151777 GCGTGGTCACATCCGTATGG 61.152 60.000 0.00 0.00 37.43 2.74
2087 2478 0.174845 CGTGGTCACATCCGTATGGT 59.825 55.000 0.00 0.00 37.43 3.55
2088 2479 1.651987 GTGGTCACATCCGTATGGTG 58.348 55.000 0.00 1.66 37.43 4.17
2089 2480 0.107897 TGGTCACATCCGTATGGTGC 60.108 55.000 0.00 0.00 37.43 5.01
2090 2481 0.178068 GGTCACATCCGTATGGTGCT 59.822 55.000 0.00 0.00 37.43 4.40
2091 2482 1.411246 GGTCACATCCGTATGGTGCTA 59.589 52.381 0.00 0.00 37.43 3.49
2092 2483 2.470821 GTCACATCCGTATGGTGCTAC 58.529 52.381 0.00 0.00 37.43 3.58
2093 2484 2.100916 GTCACATCCGTATGGTGCTACT 59.899 50.000 0.00 0.00 37.43 2.57
2094 2485 3.317149 GTCACATCCGTATGGTGCTACTA 59.683 47.826 0.00 0.00 37.43 1.82
2095 2486 3.317149 TCACATCCGTATGGTGCTACTAC 59.683 47.826 0.00 0.00 37.43 2.73
2096 2487 3.067601 CACATCCGTATGGTGCTACTACA 59.932 47.826 0.00 0.00 37.43 2.74
2097 2488 3.702548 ACATCCGTATGGTGCTACTACAA 59.297 43.478 0.00 0.00 37.43 2.41
2098 2489 4.202121 ACATCCGTATGGTGCTACTACAAG 60.202 45.833 0.00 0.00 37.43 3.16
2099 2490 3.359033 TCCGTATGGTGCTACTACAAGT 58.641 45.455 0.00 0.00 36.30 3.16
2100 2491 3.765511 TCCGTATGGTGCTACTACAAGTT 59.234 43.478 0.00 0.00 36.30 2.66
2101 2492 4.949238 TCCGTATGGTGCTACTACAAGTTA 59.051 41.667 0.00 0.00 36.30 2.24
2102 2493 5.039333 CCGTATGGTGCTACTACAAGTTAC 58.961 45.833 0.00 0.00 0.00 2.50
2103 2494 5.163581 CCGTATGGTGCTACTACAAGTTACT 60.164 44.000 0.00 0.00 0.00 2.24
2104 2495 5.970023 CGTATGGTGCTACTACAAGTTACTC 59.030 44.000 0.00 0.00 0.00 2.59
2105 2496 4.430137 TGGTGCTACTACAAGTTACTCG 57.570 45.455 0.00 0.00 0.00 4.18
2106 2497 3.822735 TGGTGCTACTACAAGTTACTCGT 59.177 43.478 0.00 0.00 0.00 4.18
2181 2572 0.390472 TGTGTCGCTTGTGTGTGTCA 60.390 50.000 0.00 0.00 0.00 3.58
2294 2696 2.650778 CCGCTGTTTCCTTTGCCC 59.349 61.111 0.00 0.00 0.00 5.36
2358 2762 1.882912 TACATATCGTACGTCCGGCT 58.117 50.000 16.05 0.00 0.00 5.52
2463 2872 4.233635 GCTCGCATCGCCAAGCTG 62.234 66.667 0.00 0.00 0.00 4.24
2464 2873 4.233635 CTCGCATCGCCAAGCTGC 62.234 66.667 0.00 0.00 0.00 5.25
2496 2905 1.689582 CGCCTCCCCTTTCCCTACT 60.690 63.158 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 1.202639 TCGCAACTCTGAATGTGGTGT 60.203 47.619 4.48 0.00 0.00 4.16
91 92 2.028420 TCGCATGCTTCTACTGCAAT 57.972 45.000 17.13 0.00 44.01 3.56
92 93 1.733912 CTTCGCATGCTTCTACTGCAA 59.266 47.619 17.13 0.00 44.01 4.08
124 125 1.687612 CAACCATGCACCTCCTCCT 59.312 57.895 0.00 0.00 0.00 3.69
144 145 3.753319 CCCCCATGTCCATGCCCA 61.753 66.667 1.64 0.00 37.49 5.36
174 175 2.081212 GTTGTCGCGTCTCCACTCG 61.081 63.158 5.77 0.00 31.73 4.18
175 176 2.081212 CGTTGTCGCGTCTCCACTC 61.081 63.158 5.77 0.00 0.00 3.51
176 177 2.050351 CGTTGTCGCGTCTCCACT 60.050 61.111 5.77 0.00 0.00 4.00
177 178 3.103911 CCGTTGTCGCGTCTCCAC 61.104 66.667 5.77 0.00 35.54 4.02
181 182 4.634133 TTCGCCGTTGTCGCGTCT 62.634 61.111 5.77 0.00 37.64 4.18
182 183 4.405173 GTTCGCCGTTGTCGCGTC 62.405 66.667 5.77 0.00 37.64 5.19
183 184 4.936823 AGTTCGCCGTTGTCGCGT 62.937 61.111 5.77 0.00 37.64 6.01
184 185 4.117372 GAGTTCGCCGTTGTCGCG 62.117 66.667 0.00 0.00 37.70 5.87
185 186 3.774702 GGAGTTCGCCGTTGTCGC 61.775 66.667 0.00 0.00 35.54 5.19
186 187 3.467119 CGGAGTTCGCCGTTGTCG 61.467 66.667 6.81 0.00 46.07 4.35
194 195 3.352338 ATCGTGGGTCGGAGTTCGC 62.352 63.158 0.00 0.00 40.32 4.70
195 196 1.516386 CATCGTGGGTCGGAGTTCG 60.516 63.158 0.00 0.00 40.32 3.95
196 197 1.153628 CCATCGTGGGTCGGAGTTC 60.154 63.158 0.00 0.00 40.32 3.01
197 198 2.978824 CCATCGTGGGTCGGAGTT 59.021 61.111 0.00 0.00 40.32 3.01
218 219 4.415332 TCAGAGTTCGCCGTCGCC 62.415 66.667 0.00 0.00 35.26 5.54
219 220 3.173240 GTCAGAGTTCGCCGTCGC 61.173 66.667 0.00 0.00 35.26 5.19
220 221 2.870161 CGTCAGAGTTCGCCGTCG 60.870 66.667 0.00 0.00 0.00 5.12
221 222 1.796749 GTCGTCAGAGTTCGCCGTC 60.797 63.158 0.00 0.00 0.00 4.79
222 223 2.254651 GTCGTCAGAGTTCGCCGT 59.745 61.111 0.00 0.00 0.00 5.68
223 224 2.870161 CGTCGTCAGAGTTCGCCG 60.870 66.667 0.00 0.00 0.00 6.46
224 225 2.504244 CCGTCGTCAGAGTTCGCC 60.504 66.667 0.00 0.00 0.00 5.54
225 226 2.504244 CCCGTCGTCAGAGTTCGC 60.504 66.667 0.00 0.00 0.00 4.70
226 227 2.178521 CCCCGTCGTCAGAGTTCG 59.821 66.667 0.00 0.00 0.00 3.95
227 228 2.572284 CCCCCGTCGTCAGAGTTC 59.428 66.667 0.00 0.00 0.00 3.01
228 229 3.692406 GCCCCCGTCGTCAGAGTT 61.692 66.667 0.00 0.00 0.00 3.01
286 567 0.321671 AATCGACCTATCATGCCCCG 59.678 55.000 0.00 0.00 0.00 5.73
295 576 1.270839 CGCCCCATCAAATCGACCTAT 60.271 52.381 0.00 0.00 0.00 2.57
296 577 0.105964 CGCCCCATCAAATCGACCTA 59.894 55.000 0.00 0.00 0.00 3.08
297 578 1.153168 CGCCCCATCAAATCGACCT 60.153 57.895 0.00 0.00 0.00 3.85
322 604 2.376109 TCCGAGCGAGTAGGAGAAAAT 58.624 47.619 0.00 0.00 0.00 1.82
355 637 2.783135 TCAGCTTCTCCGCTTCATTTT 58.217 42.857 0.00 0.00 38.41 1.82
356 638 2.479566 TCAGCTTCTCCGCTTCATTT 57.520 45.000 0.00 0.00 38.41 2.32
359 641 1.134877 CAGATCAGCTTCTCCGCTTCA 60.135 52.381 0.00 0.00 38.41 3.02
365 647 0.176680 TTCGCCAGATCAGCTTCTCC 59.823 55.000 6.24 0.00 0.00 3.71
367 649 0.459237 CGTTCGCCAGATCAGCTTCT 60.459 55.000 6.24 0.00 0.00 2.85
470 752 1.670730 ATGCATGTCCGCAACGACA 60.671 52.632 0.00 1.21 46.87 4.35
479 761 1.456296 TCTGAACTGCATGCATGTCC 58.544 50.000 26.79 10.09 0.00 4.02
519 831 3.475932 TGGGAACAGACTGCTAGGT 57.524 52.632 1.25 0.00 35.01 3.08
532 846 1.639722 TCACCGACTCAAGATGGGAA 58.360 50.000 0.00 0.00 0.00 3.97
540 854 0.247460 CTGCCTGATCACCGACTCAA 59.753 55.000 0.00 0.00 0.00 3.02
541 855 1.893062 CTGCCTGATCACCGACTCA 59.107 57.895 0.00 0.00 0.00 3.41
554 868 2.123338 TTTTGCTGGTGGCTGCCT 60.123 55.556 21.03 0.00 42.39 4.75
564 884 3.904136 AAGAATCGGTGACTTTTGCTG 57.096 42.857 0.00 0.00 0.00 4.41
593 913 2.695666 TCGGTGAATTTTGCCCTTCAAA 59.304 40.909 0.00 0.00 42.50 2.69
594 914 2.311463 TCGGTGAATTTTGCCCTTCAA 58.689 42.857 0.00 0.00 33.45 2.69
595 915 1.988293 TCGGTGAATTTTGCCCTTCA 58.012 45.000 0.00 0.00 0.00 3.02
596 916 2.755103 AGATCGGTGAATTTTGCCCTTC 59.245 45.455 0.00 0.00 0.00 3.46
597 917 2.493278 CAGATCGGTGAATTTTGCCCTT 59.507 45.455 0.00 0.00 0.00 3.95
598 918 2.094675 CAGATCGGTGAATTTTGCCCT 58.905 47.619 0.00 0.00 0.00 5.19
599 919 1.818674 ACAGATCGGTGAATTTTGCCC 59.181 47.619 0.00 0.00 0.00 5.36
600 920 2.867429 CACAGATCGGTGAATTTTGCC 58.133 47.619 19.83 0.00 41.32 4.52
601 921 2.095059 AGCACAGATCGGTGAATTTTGC 60.095 45.455 27.24 11.52 41.32 3.68
602 922 3.438087 AGAGCACAGATCGGTGAATTTTG 59.562 43.478 27.24 1.84 41.32 2.44
603 923 3.679389 AGAGCACAGATCGGTGAATTTT 58.321 40.909 27.24 8.29 41.32 1.82
604 924 3.340814 AGAGCACAGATCGGTGAATTT 57.659 42.857 27.24 10.53 41.32 1.82
605 925 3.701542 TCTAGAGCACAGATCGGTGAATT 59.298 43.478 27.24 12.82 41.32 2.17
606 926 3.067461 GTCTAGAGCACAGATCGGTGAAT 59.933 47.826 27.24 15.53 41.32 2.57
607 927 2.423892 GTCTAGAGCACAGATCGGTGAA 59.576 50.000 27.24 9.66 41.32 3.18
608 928 2.017782 GTCTAGAGCACAGATCGGTGA 58.982 52.381 27.24 7.46 41.32 4.02
609 929 2.020720 AGTCTAGAGCACAGATCGGTG 58.979 52.381 20.14 20.14 41.72 4.94
610 930 2.294074 GAGTCTAGAGCACAGATCGGT 58.706 52.381 0.00 0.00 0.00 4.69
611 931 1.262950 CGAGTCTAGAGCACAGATCGG 59.737 57.143 0.00 0.00 0.00 4.18
612 932 2.033236 GTCGAGTCTAGAGCACAGATCG 60.033 54.545 0.00 0.00 0.00 3.69
613 933 2.289547 GGTCGAGTCTAGAGCACAGATC 59.710 54.545 7.22 0.00 36.27 2.75
614 934 2.294074 GGTCGAGTCTAGAGCACAGAT 58.706 52.381 7.22 0.00 36.27 2.90
667 997 4.873129 CCGTGCGTCCCATCTCCG 62.873 72.222 0.00 0.00 0.00 4.63
682 1012 3.922640 GCCTGCTAGCTCCTCCCG 61.923 72.222 17.23 0.00 0.00 5.14
685 1015 2.108771 GCAGCCTGCTAGCTCCTC 59.891 66.667 17.23 2.62 42.61 3.71
686 1016 2.686470 TGCAGCCTGCTAGCTCCT 60.686 61.111 18.96 6.41 45.31 3.69
788 1127 3.065233 GGGACATATGTCACGTACGTACA 59.935 47.826 31.51 22.95 46.47 2.90
824 1163 0.111617 CGTTGCGCTCGTTTTCGTTA 60.112 50.000 9.73 0.00 44.46 3.18
825 1164 1.367195 CGTTGCGCTCGTTTTCGTT 60.367 52.632 9.73 0.00 44.46 3.85
826 1165 2.244382 CGTTGCGCTCGTTTTCGT 59.756 55.556 9.73 0.00 44.46 3.85
886 1232 0.615331 GAGTTGAGATGGGTGCAGGA 59.385 55.000 0.00 0.00 0.00 3.86
904 1250 5.866159 TGAGATGTACGGTAGAGACTAGA 57.134 43.478 0.00 0.00 0.00 2.43
905 1251 5.050904 CGTTGAGATGTACGGTAGAGACTAG 60.051 48.000 0.00 0.00 34.30 2.57
906 1252 4.807834 CGTTGAGATGTACGGTAGAGACTA 59.192 45.833 0.00 0.00 34.30 2.59
907 1253 3.622163 CGTTGAGATGTACGGTAGAGACT 59.378 47.826 0.00 0.00 34.30 3.24
908 1254 3.788135 GCGTTGAGATGTACGGTAGAGAC 60.788 52.174 0.00 0.00 38.17 3.36
969 1325 2.386661 ACAAGAACGTGGAGCTATGG 57.613 50.000 0.00 0.00 0.00 2.74
981 1337 2.427410 CCGCTGCGCAACAAGAAC 60.427 61.111 18.00 0.00 0.00 3.01
983 1339 3.899981 ATCCCGCTGCGCAACAAGA 62.900 57.895 18.00 6.90 0.00 3.02
998 1358 1.153349 GACGGTGAGAAGGCCATCC 60.153 63.158 5.01 0.00 0.00 3.51
1489 1854 0.243907 ATCCTGAACACGACCGTCTG 59.756 55.000 0.00 0.00 0.00 3.51
1579 1946 8.961634 ACTACTTTTGCTTCTTCTTCTCTTTTT 58.038 29.630 0.00 0.00 0.00 1.94
1580 1947 8.512966 ACTACTTTTGCTTCTTCTTCTCTTTT 57.487 30.769 0.00 0.00 0.00 2.27
1581 1948 7.042389 CGACTACTTTTGCTTCTTCTTCTCTTT 60.042 37.037 0.00 0.00 0.00 2.52
1582 1949 6.422400 CGACTACTTTTGCTTCTTCTTCTCTT 59.578 38.462 0.00 0.00 0.00 2.85
1583 1950 5.923684 CGACTACTTTTGCTTCTTCTTCTCT 59.076 40.000 0.00 0.00 0.00 3.10
1584 1951 5.921408 TCGACTACTTTTGCTTCTTCTTCTC 59.079 40.000 0.00 0.00 0.00 2.87
1585 1952 5.844004 TCGACTACTTTTGCTTCTTCTTCT 58.156 37.500 0.00 0.00 0.00 2.85
1586 1953 6.183360 GGATCGACTACTTTTGCTTCTTCTTC 60.183 42.308 0.00 0.00 0.00 2.87
1587 1954 5.639931 GGATCGACTACTTTTGCTTCTTCTT 59.360 40.000 0.00 0.00 0.00 2.52
1588 1955 5.172205 GGATCGACTACTTTTGCTTCTTCT 58.828 41.667 0.00 0.00 0.00 2.85
1589 1956 4.031878 CGGATCGACTACTTTTGCTTCTTC 59.968 45.833 0.00 0.00 0.00 2.87
1590 1957 3.927142 CGGATCGACTACTTTTGCTTCTT 59.073 43.478 0.00 0.00 0.00 2.52
1591 1958 3.192844 TCGGATCGACTACTTTTGCTTCT 59.807 43.478 0.00 0.00 0.00 2.85
1592 1959 3.508762 TCGGATCGACTACTTTTGCTTC 58.491 45.455 0.00 0.00 0.00 3.86
1593 1960 3.587797 TCGGATCGACTACTTTTGCTT 57.412 42.857 0.00 0.00 0.00 3.91
1594 1961 3.707793 GATCGGATCGACTACTTTTGCT 58.292 45.455 1.62 0.00 39.18 3.91
1621 1988 4.220382 AGAAGATCGGATAGATGGAGCAAG 59.780 45.833 0.00 0.00 40.26 4.01
1673 2040 5.175859 CACACAACGACACTAGGGATAAAT 58.824 41.667 0.00 0.00 0.00 1.40
1679 2046 1.497991 CACACACAACGACACTAGGG 58.502 55.000 0.00 0.00 0.00 3.53
1734 2101 6.073440 TCCGTACAAAATCTCAAAGTTACAGC 60.073 38.462 0.00 0.00 0.00 4.40
1735 2102 7.360101 CCTCCGTACAAAATCTCAAAGTTACAG 60.360 40.741 0.00 0.00 0.00 2.74
1786 2153 3.428534 GGAAAAGGCAAGCAACATTTACG 59.571 43.478 0.00 0.00 0.00 3.18
1787 2154 3.745975 GGGAAAAGGCAAGCAACATTTAC 59.254 43.478 0.00 0.00 0.00 2.01
1797 2164 1.007387 GCGTGTGGGAAAAGGCAAG 60.007 57.895 0.00 0.00 0.00 4.01
1866 2235 5.794687 TCATTTATGTCCAACTAGCAACG 57.205 39.130 0.00 0.00 0.00 4.10
1875 2244 4.457257 TGAACACGCATCATTTATGTCCAA 59.543 37.500 0.00 0.00 37.93 3.53
1919 2288 4.615541 GCTACCACGTAATGTTTTCAAAGC 59.384 41.667 0.00 0.00 0.00 3.51
1922 2291 4.135306 TGGCTACCACGTAATGTTTTCAA 58.865 39.130 0.00 0.00 0.00 2.69
1923 2292 3.741249 TGGCTACCACGTAATGTTTTCA 58.259 40.909 0.00 0.00 0.00 2.69
1924 2293 4.379082 CCTTGGCTACCACGTAATGTTTTC 60.379 45.833 0.00 0.00 30.78 2.29
1926 2295 3.078837 CCTTGGCTACCACGTAATGTTT 58.921 45.455 0.00 0.00 30.78 2.83
1928 2297 1.626825 ACCTTGGCTACCACGTAATGT 59.373 47.619 0.00 0.00 30.78 2.71
1930 2299 1.065709 CCACCTTGGCTACCACGTAAT 60.066 52.381 0.00 0.00 30.78 1.89
1931 2300 0.322322 CCACCTTGGCTACCACGTAA 59.678 55.000 0.00 0.00 30.78 3.18
1940 2331 1.995376 ATCGTTTTTCCACCTTGGCT 58.005 45.000 0.00 0.00 37.47 4.75
1946 2337 3.719173 TTGTCCAATCGTTTTTCCACC 57.281 42.857 0.00 0.00 0.00 4.61
1994 2385 0.377203 GAAGGTTATCAAAGCCGGCG 59.623 55.000 23.20 7.22 33.43 6.46
2020 2411 2.440409 AGAACCATGGATTGTGAGTGC 58.560 47.619 21.47 0.00 0.00 4.40
2062 2453 3.118454 GATGTGACCACGCACCCG 61.118 66.667 0.00 0.00 39.38 5.28
2063 2454 2.746277 GGATGTGACCACGCACCC 60.746 66.667 0.00 0.00 39.38 4.61
2064 2455 2.495366 TACGGATGTGACCACGCACC 62.495 60.000 0.00 0.00 39.38 5.01
2065 2456 0.459585 ATACGGATGTGACCACGCAC 60.460 55.000 0.00 0.00 39.38 5.34
2066 2457 0.459411 CATACGGATGTGACCACGCA 60.459 55.000 0.00 0.00 40.86 5.24
2067 2458 1.151777 CCATACGGATGTGACCACGC 61.152 60.000 6.92 0.00 0.00 5.34
2068 2459 0.174845 ACCATACGGATGTGACCACG 59.825 55.000 6.92 0.00 35.59 4.94
2069 2460 1.651987 CACCATACGGATGTGACCAC 58.348 55.000 6.92 0.00 35.59 4.16
2070 2461 0.107897 GCACCATACGGATGTGACCA 60.108 55.000 6.92 0.00 35.59 4.02
2071 2462 0.178068 AGCACCATACGGATGTGACC 59.822 55.000 6.92 0.00 35.59 4.02
2072 2463 2.100916 AGTAGCACCATACGGATGTGAC 59.899 50.000 6.92 1.25 35.59 3.67
2073 2464 2.384828 AGTAGCACCATACGGATGTGA 58.615 47.619 6.92 0.00 35.59 3.58
2074 2465 2.890808 AGTAGCACCATACGGATGTG 57.109 50.000 6.92 6.37 35.59 3.21
2075 2466 3.293337 TGTAGTAGCACCATACGGATGT 58.707 45.455 6.92 0.00 35.59 3.06
2076 2467 4.202121 ACTTGTAGTAGCACCATACGGATG 60.202 45.833 0.00 0.00 35.59 3.51
2077 2468 3.958798 ACTTGTAGTAGCACCATACGGAT 59.041 43.478 0.00 0.00 35.59 4.18
2078 2469 3.359033 ACTTGTAGTAGCACCATACGGA 58.641 45.455 0.00 0.00 35.59 4.69
2079 2470 3.795623 ACTTGTAGTAGCACCATACGG 57.204 47.619 0.00 0.00 38.77 4.02
2080 2471 5.888105 AGTAACTTGTAGTAGCACCATACG 58.112 41.667 0.00 0.00 0.00 3.06
2081 2472 5.970023 CGAGTAACTTGTAGTAGCACCATAC 59.030 44.000 0.00 0.00 0.00 2.39
2082 2473 5.649395 ACGAGTAACTTGTAGTAGCACCATA 59.351 40.000 0.00 0.00 0.00 2.74
2083 2474 4.461781 ACGAGTAACTTGTAGTAGCACCAT 59.538 41.667 0.00 0.00 0.00 3.55
2084 2475 3.822735 ACGAGTAACTTGTAGTAGCACCA 59.177 43.478 0.00 0.00 0.00 4.17
2085 2476 4.431661 ACGAGTAACTTGTAGTAGCACC 57.568 45.455 0.00 0.00 0.00 5.01
2086 2477 5.931532 TGTACGAGTAACTTGTAGTAGCAC 58.068 41.667 0.00 0.00 31.77 4.40
2087 2478 6.372381 TGATGTACGAGTAACTTGTAGTAGCA 59.628 38.462 0.00 0.00 31.77 3.49
2088 2479 6.779117 TGATGTACGAGTAACTTGTAGTAGC 58.221 40.000 0.00 0.00 31.77 3.58
2089 2480 7.972527 ACTGATGTACGAGTAACTTGTAGTAG 58.027 38.462 0.00 0.00 31.77 2.57
2090 2481 7.912056 ACTGATGTACGAGTAACTTGTAGTA 57.088 36.000 0.00 0.00 31.77 1.82
2091 2482 6.814506 ACTGATGTACGAGTAACTTGTAGT 57.185 37.500 0.00 0.00 31.77 2.73
2092 2483 7.082602 ACAACTGATGTACGAGTAACTTGTAG 58.917 38.462 0.00 0.00 41.63 2.74
2093 2484 6.973843 ACAACTGATGTACGAGTAACTTGTA 58.026 36.000 0.00 0.00 41.63 2.41
2094 2485 5.839621 ACAACTGATGTACGAGTAACTTGT 58.160 37.500 0.00 0.00 41.63 3.16
2095 2486 7.862741 TTACAACTGATGTACGAGTAACTTG 57.137 36.000 0.00 0.00 44.11 3.16
2096 2487 9.485206 AATTTACAACTGATGTACGAGTAACTT 57.515 29.630 0.00 0.00 44.11 2.66
2099 2490 9.064804 CGTAATTTACAACTGATGTACGAGTAA 57.935 33.333 7.31 0.00 44.11 2.24
2100 2491 7.218773 GCGTAATTTACAACTGATGTACGAGTA 59.781 37.037 12.48 1.01 44.11 2.59
2101 2492 6.034256 GCGTAATTTACAACTGATGTACGAGT 59.966 38.462 12.48 1.77 44.11 4.18
2102 2493 6.034150 TGCGTAATTTACAACTGATGTACGAG 59.966 38.462 12.48 0.00 44.11 4.18
2103 2494 5.862860 TGCGTAATTTACAACTGATGTACGA 59.137 36.000 12.48 0.28 44.11 3.43
2104 2495 6.085121 TGCGTAATTTACAACTGATGTACG 57.915 37.500 7.31 6.10 44.11 3.67
2105 2496 7.057149 ACTGCGTAATTTACAACTGATGTAC 57.943 36.000 7.31 0.00 44.11 2.90
2106 2497 6.311935 GGACTGCGTAATTTACAACTGATGTA 59.688 38.462 7.31 0.00 43.63 2.29
2181 2572 1.140312 TGGGTGAAGTGAAGAAGCCT 58.860 50.000 0.00 0.00 0.00 4.58
2279 2680 1.005748 GCAGGGCAAAGGAAACAGC 60.006 57.895 0.00 0.00 0.00 4.40
2280 2681 1.667722 GGCAGGGCAAAGGAAACAG 59.332 57.895 0.00 0.00 0.00 3.16
2294 2696 1.817099 GTTCTCGGCTCATGGGCAG 60.817 63.158 21.47 16.72 40.90 4.85
2358 2762 1.829849 CCACAGAGGATTCTCAGCTGA 59.170 52.381 17.19 17.19 42.34 4.26
2492 2901 6.431234 AGGTGGAGATTGTGCTTTTTAAGTAG 59.569 38.462 0.00 0.00 0.00 2.57
2496 2905 4.522789 GGAGGTGGAGATTGTGCTTTTTAA 59.477 41.667 0.00 0.00 0.00 1.52


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

AutoCloner maintained by Alex Coulton.