Multiple sequence alignment - TraesCS5A01G466900

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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 TraesCS5A01G466900 chr5A 100.000 2942 0 0 1 2942 645128978 645126037 0.000000e+00 5433.0
1 TraesCS5A01G466900 chr5A 88.761 347 25 13 2581 2923 540263054 540262718 2.110000e-111 412.0
2 TraesCS5A01G466900 chr5A 84.028 432 46 16 2495 2923 641117499 641117088 7.640000e-106 394.0
3 TraesCS5A01G466900 chr5A 89.836 305 26 5 2640 2941 641056766 641056464 1.280000e-103 387.0
4 TraesCS5A01G466900 chr5D 90.403 1761 83 44 517 2207 517754587 517752843 0.000000e+00 2237.0
5 TraesCS5A01G466900 chr5D 92.188 512 23 9 29 527 517755312 517754805 0.000000e+00 708.0
6 TraesCS5A01G466900 chr5D 93.593 437 19 5 2485 2920 517672406 517671978 0.000000e+00 643.0
7 TraesCS5A01G466900 chr5D 84.222 450 48 16 2496 2941 513466455 513466025 1.630000e-112 416.0
8 TraesCS5A01G466900 chr5D 91.582 297 21 4 2626 2920 512894507 512894213 9.820000e-110 407.0
9 TraesCS5A01G466900 chr5D 88.438 320 29 8 2607 2923 425984802 425984488 2.140000e-101 379.0
10 TraesCS5A01G466900 chr5B 91.213 1673 91 38 573 2207 650339828 650338174 0.000000e+00 2224.0
11 TraesCS5A01G466900 chr5B 88.794 705 65 8 2240 2936 650166068 650165370 0.000000e+00 852.0
12 TraesCS5A01G466900 chr5B 87.699 439 33 8 42 467 650340464 650340034 2.630000e-135 492.0
13 TraesCS5A01G466900 chr5B 91.579 285 21 3 2638 2920 643976823 643976540 9.890000e-105 390.0
14 TraesCS5A01G466900 chr5B 88.060 67 4 3 2176 2242 661299404 661299466 3.140000e-10 76.8
15 TraesCS5A01G466900 chr5B 86.364 66 4 4 2178 2241 622738106 622738168 1.890000e-07 67.6
16 TraesCS5A01G466900 chr3A 73.582 723 146 35 1172 1882 579135112 579135801 4.900000e-58 235.0
17 TraesCS5A01G466900 chr3A 88.333 60 5 1 2178 2237 401026737 401026680 1.460000e-08 71.3
18 TraesCS5A01G466900 chr3D 73.481 724 143 37 1173 1882 439632841 439633529 8.200000e-56 228.0
19 TraesCS5A01G466900 chr3D 86.111 72 5 4 2173 2241 322435285 322435354 4.070000e-09 73.1
20 TraesCS5A01G466900 chr3D 100.000 33 0 0 2178 2210 389633246 389633214 8.800000e-06 62.1
21 TraesCS5A01G466900 chr3B 73.481 724 143 38 1173 1882 576303798 576304486 8.200000e-56 228.0
22 TraesCS5A01G466900 chr3B 87.692 65 5 2 2178 2241 396271879 396271941 4.070000e-09 73.1
23 TraesCS5A01G466900 chr3B 100.000 33 0 0 2178 2210 507132427 507132395 8.800000e-06 62.1
24 TraesCS5A01G466900 chr7D 97.059 34 1 0 1532 1565 191796260 191796227 1.140000e-04 58.4
25 TraesCS5A01G466900 chr7D 100.000 30 0 0 2178 2207 507424704 507424675 4.100000e-04 56.5
26 TraesCS5A01G466900 chr7B 97.059 34 1 0 1532 1565 337024094 337024061 1.140000e-04 58.4
27 TraesCS5A01G466900 chr7A 97.059 34 1 0 1532 1565 200509855 200509822 1.140000e-04 58.4
28 TraesCS5A01G466900 chr1A 96.875 32 0 1 1873 1904 537977645 537977675 5.000000e-03 52.8


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 TraesCS5A01G466900 chr5A 645126037 645128978 2941 True 5433.0 5433 100.0000 1 2942 1 chr5A.!!$R4 2941
1 TraesCS5A01G466900 chr5D 517752843 517755312 2469 True 1472.5 2237 91.2955 29 2207 2 chr5D.!!$R5 2178
2 TraesCS5A01G466900 chr5B 650338174 650340464 2290 True 1358.0 2224 89.4560 42 2207 2 chr5B.!!$R3 2165
3 TraesCS5A01G466900 chr5B 650165370 650166068 698 True 852.0 852 88.7940 2240 2936 1 chr5B.!!$R2 696
4 TraesCS5A01G466900 chr3A 579135112 579135801 689 False 235.0 235 73.5820 1172 1882 1 chr3A.!!$F1 710
5 TraesCS5A01G466900 chr3D 439632841 439633529 688 False 228.0 228 73.4810 1173 1882 1 chr3D.!!$F2 709
6 TraesCS5A01G466900 chr3B 576303798 576304486 688 False 228.0 228 73.4810 1173 1882 1 chr3B.!!$F2 709

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
147 148 0.03601 AGCTTGCCTGCGTGATAAGT 60.036 50.0 0.0 0.0 38.13 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2066 2490 0.584396 GATTGTTCGCGGTCACACAA 59.416 50.0 6.13 8.61 33.78 3.33 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
20 21 1.890552 ATCCTCTGCCTTCTGATGGT 58.109 50.000 10.85 0.00 0.00 3.55
21 22 2.550277 TCCTCTGCCTTCTGATGGTA 57.450 50.000 10.85 5.91 0.00 3.25
22 23 2.392662 TCCTCTGCCTTCTGATGGTAG 58.607 52.381 17.83 17.83 38.42 3.18
23 24 2.114616 CCTCTGCCTTCTGATGGTAGT 58.885 52.381 21.33 0.00 38.26 2.73
24 25 3.052869 TCCTCTGCCTTCTGATGGTAGTA 60.053 47.826 21.33 11.28 38.26 1.82
25 26 3.706594 CCTCTGCCTTCTGATGGTAGTAA 59.293 47.826 21.33 7.81 38.26 2.24
26 27 4.442192 CCTCTGCCTTCTGATGGTAGTAAC 60.442 50.000 21.33 2.71 38.26 2.50
27 28 4.353777 TCTGCCTTCTGATGGTAGTAACT 58.646 43.478 21.33 0.00 38.26 2.24
31 32 5.105064 TGCCTTCTGATGGTAGTAACTAACC 60.105 44.000 10.85 0.00 0.00 2.85
102 103 1.656095 CTGCGGAAGATTGAGAACGTC 59.344 52.381 0.00 0.00 0.00 4.34
105 106 1.732732 CGGAAGATTGAGAACGTCGCT 60.733 52.381 0.00 0.00 0.00 4.93
147 148 0.036010 AGCTTGCCTGCGTGATAAGT 60.036 50.000 0.00 0.00 38.13 2.24
153 154 1.002366 CCTGCGTGATAAGTGAGTGC 58.998 55.000 0.00 0.00 0.00 4.40
156 157 0.736325 GCGTGATAAGTGAGTGCGGT 60.736 55.000 0.00 0.00 0.00 5.68
175 177 3.189287 CGGTGAGATGTAGCTTGCTTTTT 59.811 43.478 0.00 0.00 0.00 1.94
186 188 2.126346 GCTTTTTGAGCGCGGCAT 60.126 55.556 8.83 0.00 42.46 4.40
187 189 2.438954 GCTTTTTGAGCGCGGCATG 61.439 57.895 8.83 0.00 42.46 4.06
208 211 1.434622 CCTAGCGCTGCCTTGACATG 61.435 60.000 22.90 0.00 0.00 3.21
404 419 3.149196 TCAAAGCAGGAGATGTGGTTTC 58.851 45.455 0.00 0.00 42.26 2.78
559 870 6.202954 CGGGGTATAACAGAATGAAGATGTTC 59.797 42.308 0.00 0.00 39.69 3.18
562 873 9.178758 GGGTATAACAGAATGAAGATGTTCTTT 57.821 33.333 4.03 3.85 39.69 2.52
621 964 6.234177 CAGGAACAAAGTCCAGTAGAGAAAT 58.766 40.000 0.00 0.00 40.48 2.17
622 965 7.386851 CAGGAACAAAGTCCAGTAGAGAAATA 58.613 38.462 0.00 0.00 40.48 1.40
623 966 8.043710 CAGGAACAAAGTCCAGTAGAGAAATAT 58.956 37.037 0.00 0.00 40.48 1.28
624 967 8.606830 AGGAACAAAGTCCAGTAGAGAAATATT 58.393 33.333 0.00 0.00 40.48 1.28
646 989 7.709149 ATTATATCCATCGAGTCATCTGTCA 57.291 36.000 0.00 0.00 0.00 3.58
647 990 7.524717 TTATATCCATCGAGTCATCTGTCAA 57.475 36.000 0.00 0.00 0.00 3.18
648 991 4.952071 ATCCATCGAGTCATCTGTCAAT 57.048 40.909 0.00 0.00 0.00 2.57
649 992 7.709149 ATATCCATCGAGTCATCTGTCAATA 57.291 36.000 0.00 0.00 0.00 1.90
650 993 6.602410 ATCCATCGAGTCATCTGTCAATAT 57.398 37.500 0.00 0.00 0.00 1.28
651 994 5.776744 TCCATCGAGTCATCTGTCAATATG 58.223 41.667 0.00 0.00 0.00 1.78
697 1041 3.223157 CTGCCACGAACAAACGAAATAC 58.777 45.455 0.00 0.00 37.03 1.89
698 1042 2.873472 TGCCACGAACAAACGAAATACT 59.127 40.909 0.00 0.00 37.03 2.12
699 1043 4.056740 TGCCACGAACAAACGAAATACTA 58.943 39.130 0.00 0.00 37.03 1.82
787 1131 1.667212 TGCAGCATGAACTAATCAGCG 59.333 47.619 0.00 0.00 42.53 5.18
798 1142 3.356290 ACTAATCAGCGCCAAAATCCTT 58.644 40.909 2.29 0.00 0.00 3.36
799 1143 2.947448 AATCAGCGCCAAAATCCTTC 57.053 45.000 2.29 0.00 0.00 3.46
800 1144 1.106285 ATCAGCGCCAAAATCCTTCC 58.894 50.000 2.29 0.00 0.00 3.46
802 1146 0.967380 CAGCGCCAAAATCCTTCCCT 60.967 55.000 2.29 0.00 0.00 4.20
803 1147 0.967380 AGCGCCAAAATCCTTCCCTG 60.967 55.000 2.29 0.00 0.00 4.45
804 1148 1.512694 CGCCAAAATCCTTCCCTGC 59.487 57.895 0.00 0.00 0.00 4.85
805 1149 0.967380 CGCCAAAATCCTTCCCTGCT 60.967 55.000 0.00 0.00 0.00 4.24
806 1150 0.820226 GCCAAAATCCTTCCCTGCTC 59.180 55.000 0.00 0.00 0.00 4.26
807 1151 1.478631 CCAAAATCCTTCCCTGCTCC 58.521 55.000 0.00 0.00 0.00 4.70
808 1152 1.006400 CCAAAATCCTTCCCTGCTCCT 59.994 52.381 0.00 0.00 0.00 3.69
810 1154 0.627986 AAATCCTTCCCTGCTCCTGG 59.372 55.000 0.00 0.00 0.00 4.45
811 1155 1.931007 AATCCTTCCCTGCTCCTGGC 61.931 60.000 0.00 0.00 42.22 4.85
812 1156 2.854420 ATCCTTCCCTGCTCCTGGCT 62.854 60.000 0.00 0.00 42.39 4.75
813 1157 2.271497 CTTCCCTGCTCCTGGCTG 59.729 66.667 0.00 0.00 42.39 4.85
957 1321 1.542547 GCTCCTAGGGTCTCTCTCTCG 60.543 61.905 9.46 0.00 0.00 4.04
961 1329 1.279749 TAGGGTCTCTCTCTCGGCCA 61.280 60.000 2.24 0.00 0.00 5.36
964 1332 1.379309 GTCTCTCTCTCGGCCACCT 60.379 63.158 2.24 0.00 0.00 4.00
969 1337 3.151022 CTCTCGGCCACCTCCTCC 61.151 72.222 2.24 0.00 0.00 4.30
974 1342 3.732849 GGCCACCTCCTCCTTGGG 61.733 72.222 0.00 0.00 36.20 4.12
976 1344 2.539081 GCCACCTCCTCCTTGGGTT 61.539 63.158 0.00 0.00 36.20 4.11
980 1348 2.670148 CCTCCTCCTTGGGTTCCCG 61.670 68.421 3.27 0.00 36.20 5.14
981 1349 3.327404 TCCTCCTTGGGTTCCCGC 61.327 66.667 3.27 0.00 36.20 6.13
982 1350 4.778143 CCTCCTTGGGTTCCCGCG 62.778 72.222 0.00 0.00 0.00 6.46
2005 2428 6.019762 AGTCGTCGTTGTTTCTTTTCTTTTC 58.980 36.000 0.00 0.00 0.00 2.29
2008 2431 4.027945 GTCGTTGTTTCTTTTCTTTTCGGC 60.028 41.667 0.00 0.00 0.00 5.54
2048 2472 0.726827 AACAAGTGTGTGACGCTGTG 59.273 50.000 0.00 0.00 38.11 3.66
2063 2487 1.471327 GCTGTGTTTGTGTTGGTGCAT 60.471 47.619 0.00 0.00 0.00 3.96
2065 2489 3.736433 GCTGTGTTTGTGTTGGTGCATTA 60.736 43.478 0.00 0.00 0.00 1.90
2066 2490 4.619973 CTGTGTTTGTGTTGGTGCATTAT 58.380 39.130 0.00 0.00 0.00 1.28
2090 2519 2.063266 GTGACCGCGAACAATCTTGTA 58.937 47.619 8.23 0.00 41.31 2.41
2096 2525 4.506654 ACCGCGAACAATCTTGTATGTATC 59.493 41.667 8.23 0.00 41.31 2.24
2100 2529 5.459107 GCGAACAATCTTGTATGTATCGACT 59.541 40.000 14.77 0.00 41.31 4.18
2132 2563 9.482627 AAACGGAATCTATACAGAGAAATCATC 57.517 33.333 0.00 0.00 33.22 2.92
2136 2567 9.598517 GGAATCTATACAGAGAAATCATCATCC 57.401 37.037 0.00 0.00 33.22 3.51
2147 2578 8.277197 AGAGAAATCATCATCCTACAAATTCCA 58.723 33.333 0.00 0.00 0.00 3.53
2155 2586 4.837093 TCCTACAAATTCCACCGAAGAT 57.163 40.909 0.00 0.00 0.00 2.40
2161 2592 4.700213 ACAAATTCCACCGAAGATAACTGG 59.300 41.667 0.00 0.00 0.00 4.00
2169 2600 4.030913 ACCGAAGATAACTGGATTCTCCA 58.969 43.478 0.00 0.00 45.98 3.86
2189 2620 3.370527 CCATGAACAATACTCCCTCCGTT 60.371 47.826 0.00 0.00 0.00 4.44
2190 2621 3.604875 TGAACAATACTCCCTCCGTTC 57.395 47.619 0.00 0.00 34.69 3.95
2191 2622 2.901192 TGAACAATACTCCCTCCGTTCA 59.099 45.455 0.00 0.00 40.12 3.18
2192 2623 3.259902 GAACAATACTCCCTCCGTTCAC 58.740 50.000 0.00 0.00 34.35 3.18
2207 2638 6.236017 TCCGTTCACAAATGTAAGATGTTC 57.764 37.500 0.00 0.00 0.00 3.18
2208 2639 5.995282 TCCGTTCACAAATGTAAGATGTTCT 59.005 36.000 0.00 0.00 0.00 3.01
2209 2640 7.156000 TCCGTTCACAAATGTAAGATGTTCTA 58.844 34.615 0.00 0.00 0.00 2.10
2210 2641 7.330946 TCCGTTCACAAATGTAAGATGTTCTAG 59.669 37.037 0.00 0.00 0.00 2.43
2211 2642 7.117812 CCGTTCACAAATGTAAGATGTTCTAGT 59.882 37.037 0.00 0.00 0.00 2.57
2212 2643 9.135843 CGTTCACAAATGTAAGATGTTCTAGTA 57.864 33.333 0.00 0.00 0.00 1.82
2226 2657 9.699703 AGATGTTCTAGTAACTTTTTCTGAGTC 57.300 33.333 0.00 0.00 0.00 3.36
2227 2658 9.477484 GATGTTCTAGTAACTTTTTCTGAGTCA 57.523 33.333 0.00 0.00 0.00 3.41
2228 2659 8.873215 TGTTCTAGTAACTTTTTCTGAGTCAG 57.127 34.615 14.36 14.36 0.00 3.51
2229 2660 8.692710 TGTTCTAGTAACTTTTTCTGAGTCAGA 58.307 33.333 19.10 19.10 38.87 3.27
2230 2661 9.699703 GTTCTAGTAACTTTTTCTGAGTCAGAT 57.300 33.333 23.23 10.03 40.39 2.90
2231 2662 9.698309 TTCTAGTAACTTTTTCTGAGTCAGATG 57.302 33.333 23.23 15.22 40.39 2.90
2232 2663 8.861086 TCTAGTAACTTTTTCTGAGTCAGATGT 58.139 33.333 23.23 15.79 40.39 3.06
2242 2673 9.817809 TTTTCTGAGTCAGATGTATATAACACC 57.182 33.333 23.23 0.00 42.09 4.16
2243 2674 7.526142 TCTGAGTCAGATGTATATAACACCC 57.474 40.000 19.10 0.00 42.09 4.61
2244 2675 7.066781 TCTGAGTCAGATGTATATAACACCCA 58.933 38.462 19.10 0.00 42.09 4.51
2245 2676 7.231519 TCTGAGTCAGATGTATATAACACCCAG 59.768 40.741 19.10 0.00 42.09 4.45
2284 2715 0.177836 AACTTTTGGGTGCAACAGGC 59.822 50.000 3.06 0.00 39.98 4.85
2286 2717 2.697992 CTTTTGGGTGCAACAGGCCG 62.698 60.000 3.06 0.00 43.89 6.13
2289 2721 2.909965 GGGTGCAACAGGCCGAAA 60.910 61.111 3.06 0.00 43.89 3.46
2315 2747 1.007387 CCAAAGGTGCAGCGGTTTC 60.007 57.895 10.78 0.00 0.00 2.78
2319 2751 2.200373 AAGGTGCAGCGGTTTCTTAT 57.800 45.000 10.78 0.00 0.00 1.73
2321 2753 0.179163 GGTGCAGCGGTTTCTTATGC 60.179 55.000 0.00 0.00 37.40 3.14
2349 2781 6.529125 CCATGCACATTAAGAGCAAAAGTAAG 59.471 38.462 0.00 0.00 46.76 2.34
2353 2785 7.138736 GCACATTAAGAGCAAAAGTAAGTGAA 58.861 34.615 0.00 0.00 33.66 3.18
2354 2786 7.113544 GCACATTAAGAGCAAAAGTAAGTGAAC 59.886 37.037 0.00 0.00 33.66 3.18
2357 2789 9.515020 CATTAAGAGCAAAAGTAAGTGAACAAA 57.485 29.630 0.00 0.00 0.00 2.83
2375 2807 5.876612 ACAAAATACGAGTACGAGAGACT 57.123 39.130 0.00 0.00 42.66 3.24
2379 2811 6.601741 AAATACGAGTACGAGAGACTTAGG 57.398 41.667 0.00 0.00 42.66 2.69
2414 2846 7.807977 TTTTTAGAATCAAGAGCAACAGTCT 57.192 32.000 0.00 0.00 0.00 3.24
2419 2851 6.501781 AGAATCAAGAGCAACAGTCTTTTTG 58.498 36.000 0.00 0.00 31.64 2.44
2448 2880 5.243426 CTCAAGAGCAGTAGTAAGAGACC 57.757 47.826 0.00 0.00 0.00 3.85
2449 2881 4.663334 TCAAGAGCAGTAGTAAGAGACCA 58.337 43.478 0.00 0.00 0.00 4.02
2450 2882 4.702612 TCAAGAGCAGTAGTAAGAGACCAG 59.297 45.833 0.00 0.00 0.00 4.00
2451 2883 4.577988 AGAGCAGTAGTAAGAGACCAGA 57.422 45.455 0.00 0.00 0.00 3.86
2452 2884 4.924625 AGAGCAGTAGTAAGAGACCAGAA 58.075 43.478 0.00 0.00 0.00 3.02
2453 2885 4.703093 AGAGCAGTAGTAAGAGACCAGAAC 59.297 45.833 0.00 0.00 0.00 3.01
2454 2886 4.408276 AGCAGTAGTAAGAGACCAGAACA 58.592 43.478 0.00 0.00 0.00 3.18
2455 2887 4.218852 AGCAGTAGTAAGAGACCAGAACAC 59.781 45.833 0.00 0.00 0.00 3.32
2456 2888 4.218852 GCAGTAGTAAGAGACCAGAACACT 59.781 45.833 0.00 0.00 0.00 3.55
2457 2889 5.704888 CAGTAGTAAGAGACCAGAACACTG 58.295 45.833 0.00 0.00 0.00 3.66
2502 2954 1.756538 ACAACACTGGGAAAAAGCTGG 59.243 47.619 0.00 0.00 0.00 4.85
2533 2985 2.109181 GCCCACACGCCTATCTCC 59.891 66.667 0.00 0.00 0.00 3.71
2549 3001 0.816825 CTCCCGTCATTCAGCCCATG 60.817 60.000 0.00 0.00 0.00 3.66
2659 3115 1.461897 GCTGCGCTTCGGTTTTTAGTA 59.538 47.619 9.73 0.00 0.00 1.82
2708 3165 1.353091 GGGGAGCCACTATAAGAGGG 58.647 60.000 0.00 0.00 0.00 4.30
2911 3368 7.066163 CCCCTGCCAATTCTTTGAAATTAAATC 59.934 37.037 0.00 0.00 34.60 2.17
2921 3378 8.940397 TCTTTGAAATTAAATCTTGGTCCTCT 57.060 30.769 0.00 0.00 0.00 3.69
2924 3381 8.477419 TTGAAATTAAATCTTGGTCCTCTGTT 57.523 30.769 0.00 0.00 0.00 3.16
2929 3386 1.140312 TCTTGGTCCTCTGTTTGGCT 58.860 50.000 0.00 0.00 0.00 4.75
2930 3387 1.072331 TCTTGGTCCTCTGTTTGGCTC 59.928 52.381 0.00 0.00 0.00 4.70
2936 3393 1.079503 CCTCTGTTTGGCTCGCTTAC 58.920 55.000 0.00 0.00 0.00 2.34
2937 3394 0.716108 CTCTGTTTGGCTCGCTTACG 59.284 55.000 0.00 0.00 42.01 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.051940 ACCATCAGAAGGCAGAGGATA 57.948 47.619 0.00 0.00 0.00 2.59
2 3 2.292521 ACTACCATCAGAAGGCAGAGGA 60.293 50.000 0.00 0.00 0.00 3.71
5 6 4.353777 AGTTACTACCATCAGAAGGCAGA 58.646 43.478 0.00 0.00 0.00 4.26
6 7 4.744795 AGTTACTACCATCAGAAGGCAG 57.255 45.455 0.00 0.00 0.00 4.85
7 8 5.105064 GGTTAGTTACTACCATCAGAAGGCA 60.105 44.000 0.00 0.00 0.00 4.75
8 9 5.105064 TGGTTAGTTACTACCATCAGAAGGC 60.105 44.000 8.79 0.00 0.00 4.35
9 10 6.540438 TGGTTAGTTACTACCATCAGAAGG 57.460 41.667 8.79 0.00 0.00 3.46
10 11 6.530534 CGTTGGTTAGTTACTACCATCAGAAG 59.469 42.308 12.15 1.00 31.71 2.85
11 12 6.392354 CGTTGGTTAGTTACTACCATCAGAA 58.608 40.000 12.15 0.00 31.71 3.02
12 13 5.622914 GCGTTGGTTAGTTACTACCATCAGA 60.623 44.000 12.15 0.00 31.71 3.27
13 14 4.565564 GCGTTGGTTAGTTACTACCATCAG 59.434 45.833 12.15 8.99 31.71 2.90
14 15 4.497300 GCGTTGGTTAGTTACTACCATCA 58.503 43.478 12.15 0.00 31.71 3.07
15 16 3.867493 GGCGTTGGTTAGTTACTACCATC 59.133 47.826 12.15 10.86 31.71 3.51
16 17 3.516700 AGGCGTTGGTTAGTTACTACCAT 59.483 43.478 12.15 0.00 31.71 3.55
17 18 2.899256 AGGCGTTGGTTAGTTACTACCA 59.101 45.455 8.79 8.79 0.00 3.25
18 19 3.599730 AGGCGTTGGTTAGTTACTACC 57.400 47.619 0.00 0.00 0.00 3.18
19 20 4.309933 ACAAGGCGTTGGTTAGTTACTAC 58.690 43.478 22.07 0.00 38.07 2.73
20 21 4.605640 ACAAGGCGTTGGTTAGTTACTA 57.394 40.909 22.07 0.00 38.07 1.82
21 22 3.480505 ACAAGGCGTTGGTTAGTTACT 57.519 42.857 22.07 0.00 38.07 2.24
22 23 5.624292 CATAACAAGGCGTTGGTTAGTTAC 58.376 41.667 22.07 0.00 38.63 2.50
23 24 4.154556 GCATAACAAGGCGTTGGTTAGTTA 59.845 41.667 22.07 11.71 38.63 2.24
24 25 3.057806 GCATAACAAGGCGTTGGTTAGTT 60.058 43.478 22.07 10.01 38.63 2.24
25 26 2.486592 GCATAACAAGGCGTTGGTTAGT 59.513 45.455 22.07 4.14 38.63 2.24
26 27 2.747446 AGCATAACAAGGCGTTGGTTAG 59.253 45.455 22.07 12.86 38.63 2.34
27 28 2.785562 AGCATAACAAGGCGTTGGTTA 58.214 42.857 22.07 16.75 38.63 2.85
31 32 4.980590 TGAAATAGCATAACAAGGCGTTG 58.019 39.130 17.21 17.21 38.63 4.10
102 103 0.872388 GGTTGTTTGGTCCAGTAGCG 59.128 55.000 0.00 0.00 0.00 4.26
105 106 0.535553 GCCGGTTGTTTGGTCCAGTA 60.536 55.000 1.90 0.00 0.00 2.74
147 148 0.173481 GCTACATCTCACCGCACTCA 59.827 55.000 0.00 0.00 0.00 3.41
153 154 2.015736 AAGCAAGCTACATCTCACCG 57.984 50.000 0.00 0.00 0.00 4.94
156 157 5.618056 CTCAAAAAGCAAGCTACATCTCA 57.382 39.130 0.00 0.00 0.00 3.27
175 177 3.430565 CTAGGACATGCCGCGCTCA 62.431 63.158 5.56 3.36 43.43 4.26
186 188 2.265739 CAAGGCAGCGCTAGGACA 59.734 61.111 10.99 0.00 0.00 4.02
187 189 1.811679 GTCAAGGCAGCGCTAGGAC 60.812 63.158 10.99 9.89 0.00 3.85
208 211 5.734720 TCCAGTGATTCAGTACTTTCATCC 58.265 41.667 0.00 0.00 0.00 3.51
361 366 9.995957 TTTGAATATTATTCAACACCATACACG 57.004 29.630 24.64 0.00 38.05 4.49
404 419 1.725641 TTAGCGGCAGTGAAGTCATG 58.274 50.000 1.45 0.00 0.00 3.07
506 588 3.334583 TGAAACATAGTGACAGGGCTC 57.665 47.619 0.00 0.00 0.00 4.70
510 592 5.049405 GGAACAGTTGAAACATAGTGACAGG 60.049 44.000 0.00 0.00 0.00 4.00
546 857 8.517878 TCCATCAGAAAAAGAACATCTTCATTC 58.482 33.333 9.07 9.07 35.27 2.67
559 870 8.876275 TCTTCATTTTGTTCCATCAGAAAAAG 57.124 30.769 0.00 0.00 33.14 2.27
562 873 7.954835 ACATCTTCATTTTGTTCCATCAGAAA 58.045 30.769 0.00 0.00 35.85 2.52
567 878 6.400303 CGCAAACATCTTCATTTTGTTCCATC 60.400 38.462 0.00 0.00 32.66 3.51
621 964 8.807948 TGACAGATGACTCGATGGATATAATA 57.192 34.615 0.00 0.00 0.00 0.98
622 965 7.709149 TGACAGATGACTCGATGGATATAAT 57.291 36.000 0.00 0.00 0.00 1.28
623 966 7.524717 TTGACAGATGACTCGATGGATATAA 57.475 36.000 0.00 0.00 0.00 0.98
624 967 7.709149 ATTGACAGATGACTCGATGGATATA 57.291 36.000 0.00 0.00 0.00 0.86
641 984 7.740519 TTGCGTCGATATATCATATTGACAG 57.259 36.000 19.47 14.77 37.92 3.51
642 985 7.254084 GCATTGCGTCGATATATCATATTGACA 60.254 37.037 19.47 7.16 37.92 3.58
643 986 7.059817 GCATTGCGTCGATATATCATATTGAC 58.940 38.462 13.11 13.31 35.82 3.18
644 987 6.756074 TGCATTGCGTCGATATATCATATTGA 59.244 34.615 13.11 0.00 0.00 2.57
645 988 6.936374 TGCATTGCGTCGATATATCATATTG 58.064 36.000 13.11 2.54 0.00 1.90
646 989 7.278646 ACTTGCATTGCGTCGATATATCATATT 59.721 33.333 13.11 0.00 0.00 1.28
647 990 6.758416 ACTTGCATTGCGTCGATATATCATAT 59.242 34.615 13.11 0.00 0.00 1.78
648 991 6.034898 CACTTGCATTGCGTCGATATATCATA 59.965 38.462 13.11 0.00 0.00 2.15
649 992 4.931601 ACTTGCATTGCGTCGATATATCAT 59.068 37.500 13.11 0.00 0.00 2.45
650 993 4.150451 CACTTGCATTGCGTCGATATATCA 59.850 41.667 13.11 0.00 0.00 2.15
651 994 4.434725 CCACTTGCATTGCGTCGATATATC 60.435 45.833 3.84 2.34 0.00 1.63
657 1000 2.324330 CCCACTTGCATTGCGTCGA 61.324 57.895 3.84 0.00 0.00 4.20
787 1131 0.820226 GAGCAGGGAAGGATTTTGGC 59.180 55.000 0.00 0.00 0.00 4.52
803 1147 1.069358 GTACTCATACCAGCCAGGAGC 59.931 57.143 0.00 0.00 41.22 4.70
804 1148 1.338337 CGTACTCATACCAGCCAGGAG 59.662 57.143 0.00 0.00 41.22 3.69
805 1149 1.341679 ACGTACTCATACCAGCCAGGA 60.342 52.381 0.00 0.00 41.22 3.86
806 1150 1.112113 ACGTACTCATACCAGCCAGG 58.888 55.000 0.00 0.00 45.67 4.45
807 1151 1.476891 ACACGTACTCATACCAGCCAG 59.523 52.381 0.00 0.00 0.00 4.85
808 1152 1.475280 GACACGTACTCATACCAGCCA 59.525 52.381 0.00 0.00 0.00 4.75
810 1154 2.539142 CGAGACACGTACTCATACCAGC 60.539 54.545 17.73 0.00 37.22 4.85
811 1155 2.031807 CCGAGACACGTACTCATACCAG 59.968 54.545 17.73 4.80 40.78 4.00
812 1156 2.011947 CCGAGACACGTACTCATACCA 58.988 52.381 17.73 0.00 40.78 3.25
813 1157 2.012673 ACCGAGACACGTACTCATACC 58.987 52.381 17.73 0.00 40.78 2.73
814 1158 2.417933 ACACCGAGACACGTACTCATAC 59.582 50.000 17.73 0.78 40.78 2.39
815 1159 2.703416 ACACCGAGACACGTACTCATA 58.297 47.619 17.73 0.00 40.78 2.15
859 1210 4.424566 GGCATGCACGCTGGTTGG 62.425 66.667 21.36 0.00 0.00 3.77
898 1258 4.446234 CTCGAAGTGTTTTAAGCTGAACG 58.554 43.478 0.00 0.00 0.00 3.95
902 1262 4.058817 AGTCCTCGAAGTGTTTTAAGCTG 58.941 43.478 0.00 0.00 0.00 4.24
957 1321 3.732849 CCCAAGGAGGAGGTGGCC 61.733 72.222 0.00 0.00 41.22 5.36
961 1329 4.252493 GGAACCCAAGGAGGAGGT 57.748 61.111 0.00 0.00 41.22 3.85
1191 1563 1.285578 GCTCTTTGAGCGTGATCTCC 58.714 55.000 3.73 0.00 45.85 3.71
1296 1690 1.146041 CGCGATGATGGGGAAGGAA 59.854 57.895 0.00 0.00 0.00 3.36
1971 2384 2.360165 ACAACGACGACTAACAACTCCT 59.640 45.455 0.00 0.00 0.00 3.69
1972 2385 2.735823 ACAACGACGACTAACAACTCC 58.264 47.619 0.00 0.00 0.00 3.85
2005 2428 3.296709 AAGGTAGCCACGTCTGCCG 62.297 63.158 5.87 0.00 42.68 5.69
2008 2431 0.732880 CACGAAGGTAGCCACGTCTG 60.733 60.000 10.23 0.00 36.91 3.51
2048 2472 4.808364 ACACAATAATGCACCAACACAAAC 59.192 37.500 0.00 0.00 0.00 2.93
2063 2487 1.867166 TGTTCGCGGTCACACAATAA 58.133 45.000 6.13 0.00 0.00 1.40
2065 2489 1.196808 GATTGTTCGCGGTCACACAAT 59.803 47.619 6.13 12.96 41.51 2.71
2066 2490 0.584396 GATTGTTCGCGGTCACACAA 59.416 50.000 6.13 8.61 33.78 3.33
2090 2519 5.063180 TCCGTTTACACAAGTCGATACAT 57.937 39.130 0.00 0.00 0.00 2.29
2096 2525 6.748658 TGTATAGATTCCGTTTACACAAGTCG 59.251 38.462 0.00 0.00 0.00 4.18
2100 2529 8.058667 TCTCTGTATAGATTCCGTTTACACAA 57.941 34.615 0.00 0.00 31.21 3.33
2132 2563 4.513442 TCTTCGGTGGAATTTGTAGGATG 58.487 43.478 0.00 0.00 0.00 3.51
2136 2567 6.037172 CCAGTTATCTTCGGTGGAATTTGTAG 59.963 42.308 0.00 0.00 0.00 2.74
2139 2570 4.941263 TCCAGTTATCTTCGGTGGAATTTG 59.059 41.667 0.00 0.00 34.30 2.32
2161 2592 5.934781 AGGGAGTATTGTTCATGGAGAATC 58.065 41.667 0.00 0.00 38.76 2.52
2169 2600 3.517901 TGAACGGAGGGAGTATTGTTCAT 59.482 43.478 1.80 0.00 40.31 2.57
2216 2647 9.817809 GGTGTTATATACATCTGACTCAGAAAA 57.182 33.333 12.83 2.33 44.04 2.29
2217 2648 8.421784 GGGTGTTATATACATCTGACTCAGAAA 58.578 37.037 12.83 2.67 44.04 2.52
2218 2649 7.563556 TGGGTGTTATATACATCTGACTCAGAA 59.436 37.037 12.83 0.00 44.04 3.02
2219 2650 7.066781 TGGGTGTTATATACATCTGACTCAGA 58.933 38.462 11.24 11.24 44.99 3.27
2220 2651 7.290110 TGGGTGTTATATACATCTGACTCAG 57.710 40.000 0.00 0.00 38.01 3.35
2221 2652 6.267699 CCTGGGTGTTATATACATCTGACTCA 59.732 42.308 0.00 0.00 38.01 3.41
2222 2653 6.267928 ACCTGGGTGTTATATACATCTGACTC 59.732 42.308 0.00 0.00 38.01 3.36
2223 2654 6.143915 ACCTGGGTGTTATATACATCTGACT 58.856 40.000 0.00 0.00 38.01 3.41
2224 2655 6.420913 ACCTGGGTGTTATATACATCTGAC 57.579 41.667 0.00 0.00 38.01 3.51
2225 2656 7.953493 TGATACCTGGGTGTTATATACATCTGA 59.047 37.037 2.07 0.00 38.01 3.27
2226 2657 8.134202 TGATACCTGGGTGTTATATACATCTG 57.866 38.462 2.07 0.00 38.01 2.90
2227 2658 7.093289 GCTGATACCTGGGTGTTATATACATCT 60.093 40.741 2.07 0.00 38.01 2.90
2228 2659 7.042335 GCTGATACCTGGGTGTTATATACATC 58.958 42.308 2.07 0.00 39.39 3.06
2229 2660 6.070194 GGCTGATACCTGGGTGTTATATACAT 60.070 42.308 2.07 0.00 39.39 2.29
2230 2661 5.247564 GGCTGATACCTGGGTGTTATATACA 59.752 44.000 2.07 0.00 0.00 2.29
2231 2662 5.623824 CGGCTGATACCTGGGTGTTATATAC 60.624 48.000 2.07 0.00 0.00 1.47
2232 2663 4.464951 CGGCTGATACCTGGGTGTTATATA 59.535 45.833 2.07 0.00 0.00 0.86
2233 2664 3.260884 CGGCTGATACCTGGGTGTTATAT 59.739 47.826 2.07 0.00 0.00 0.86
2234 2665 2.631062 CGGCTGATACCTGGGTGTTATA 59.369 50.000 2.07 0.00 0.00 0.98
2235 2666 1.416401 CGGCTGATACCTGGGTGTTAT 59.584 52.381 2.07 0.00 0.00 1.89
2236 2667 0.828022 CGGCTGATACCTGGGTGTTA 59.172 55.000 2.07 0.00 0.00 2.41
2237 2668 1.602237 CGGCTGATACCTGGGTGTT 59.398 57.895 2.07 0.00 0.00 3.32
2238 2669 2.367202 CCGGCTGATACCTGGGTGT 61.367 63.158 2.07 0.00 0.00 4.16
2239 2670 1.910580 AACCGGCTGATACCTGGGTG 61.911 60.000 0.00 0.00 0.00 4.61
2240 2671 1.205460 AAACCGGCTGATACCTGGGT 61.205 55.000 0.00 0.00 0.00 4.51
2241 2672 0.748005 CAAACCGGCTGATACCTGGG 60.748 60.000 0.00 0.00 0.00 4.45
2242 2673 0.035439 ACAAACCGGCTGATACCTGG 60.035 55.000 10.96 0.00 0.00 4.45
2243 2674 1.086696 CACAAACCGGCTGATACCTG 58.913 55.000 10.96 0.00 0.00 4.00
2244 2675 0.676782 GCACAAACCGGCTGATACCT 60.677 55.000 10.96 0.00 0.00 3.08
2245 2676 0.958382 TGCACAAACCGGCTGATACC 60.958 55.000 10.96 0.00 0.00 2.73
2267 2698 1.069596 GGCCTGTTGCACCCAAAAG 59.930 57.895 0.00 0.00 43.89 2.27
2284 2715 0.598065 CCTTTGGTGCCTCTTTTCGG 59.402 55.000 0.00 0.00 0.00 4.30
2297 2729 1.007387 GAAACCGCTGCACCTTTGG 60.007 57.895 0.00 0.00 0.00 3.28
2308 2740 1.724582 ATGGCCGCATAAGAAACCGC 61.725 55.000 0.00 0.00 0.00 5.68
2311 2743 0.455410 TGCATGGCCGCATAAGAAAC 59.545 50.000 0.59 0.00 36.86 2.78
2315 2747 0.386476 AATGTGCATGGCCGCATAAG 59.614 50.000 8.65 0.00 45.26 1.73
2319 2751 0.679321 TCTTAATGTGCATGGCCGCA 60.679 50.000 0.59 0.59 40.32 5.69
2321 2753 0.029834 GCTCTTAATGTGCATGGCCG 59.970 55.000 0.00 0.00 35.45 6.13
2349 2781 6.032251 GTCTCTCGTACTCGTATTTTGTTCAC 59.968 42.308 0.00 0.00 38.33 3.18
2353 2785 5.876612 AGTCTCTCGTACTCGTATTTTGT 57.123 39.130 0.00 0.00 38.33 2.83
2354 2786 6.906143 CCTAAGTCTCTCGTACTCGTATTTTG 59.094 42.308 0.00 0.00 38.33 2.44
2357 2789 5.055812 CCCTAAGTCTCTCGTACTCGTATT 58.944 45.833 0.00 0.00 38.33 1.89
2367 2799 4.657436 AACTATTGCCCTAAGTCTCTCG 57.343 45.455 0.00 0.00 0.00 4.04
2408 2840 3.808728 TGAGCTGCTACAAAAAGACTGT 58.191 40.909 0.15 0.00 0.00 3.55
2409 2841 4.512944 TCTTGAGCTGCTACAAAAAGACTG 59.487 41.667 0.15 0.00 0.00 3.51
2414 2846 3.213506 TGCTCTTGAGCTGCTACAAAAA 58.786 40.909 21.17 0.35 35.49 1.94
2419 2851 2.165437 ACTACTGCTCTTGAGCTGCTAC 59.835 50.000 23.12 0.00 37.27 3.58
2474 2906 6.592220 GCTTTTTCCCAGTGTTGTCTTAAAAA 59.408 34.615 0.00 0.00 0.00 1.94
2481 2933 2.223805 CCAGCTTTTTCCCAGTGTTGTC 60.224 50.000 0.00 0.00 0.00 3.18
2483 2935 1.756538 ACCAGCTTTTTCCCAGTGTTG 59.243 47.619 0.00 0.00 0.00 3.33
2486 2938 1.535462 CGTACCAGCTTTTTCCCAGTG 59.465 52.381 0.00 0.00 0.00 3.66
2490 2942 0.608308 AGCCGTACCAGCTTTTTCCC 60.608 55.000 0.00 0.00 37.24 3.97
2533 2985 1.586422 CTACATGGGCTGAATGACGG 58.414 55.000 0.00 0.00 0.00 4.79
2549 3001 1.271379 TGGGCTTGACTTTGCTCCTAC 60.271 52.381 0.00 0.00 0.00 3.18
2605 3061 3.249189 AAGCCGTGAAGGGAGCCA 61.249 61.111 0.00 0.00 41.48 4.75
2606 3062 2.436824 GAAGCCGTGAAGGGAGCC 60.437 66.667 0.00 0.00 41.48 4.70
2607 3063 2.035442 GTGAAGCCGTGAAGGGAGC 61.035 63.158 0.00 0.00 41.48 4.70
2608 3064 1.738099 CGTGAAGCCGTGAAGGGAG 60.738 63.158 0.00 0.00 41.48 4.30
2640 3096 2.159747 GGTACTAAAAACCGAAGCGCAG 60.160 50.000 11.47 0.00 0.00 5.18
2785 3242 1.546589 CCAAGTGCAATGTGGGCCAT 61.547 55.000 10.70 0.00 34.36 4.40
2899 3356 8.477419 AACAGAGGACCAAGATTTAATTTCAA 57.523 30.769 0.00 0.00 0.00 2.69
2901 3358 7.814587 CCAAACAGAGGACCAAGATTTAATTTC 59.185 37.037 0.00 0.00 0.00 2.17
2911 3368 1.528129 GAGCCAAACAGAGGACCAAG 58.472 55.000 0.00 0.00 0.00 3.61
2920 3377 2.822306 TCGTAAGCGAGCCAAACAG 58.178 52.632 0.00 0.00 42.81 3.16


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

AutoCloner maintained by Alex Coulton.