Multiple sequence alignment - TraesCS1A01G127500

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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 TraesCS1A01G127500 chr1A 100.000 4176 0 0 1 4176 154698585 154702760 0.000000e+00 7712.0
1 TraesCS1A01G127500 chr1A 72.930 809 198 21 2067 2866 578356382 578355586 1.150000e-65 261.0
2 TraesCS1A01G127500 chr1D 95.969 2208 57 13 1100 3297 137969251 137967066 0.000000e+00 3555.0
3 TraesCS1A01G127500 chr1D 91.033 736 55 8 3449 4176 137961279 137960547 0.000000e+00 983.0
4 TraesCS1A01G127500 chr1D 88.469 529 33 12 558 1075 137969841 137969330 7.670000e-172 614.0
5 TraesCS1A01G127500 chr1D 90.786 369 18 4 19 377 137970208 137969846 2.920000e-131 479.0
6 TraesCS1A01G127500 chr1D 96.855 159 5 0 3295 3453 137966829 137966671 2.480000e-67 267.0
7 TraesCS1A01G127500 chr1B 91.625 2209 82 31 1978 4176 212410429 212408314 0.000000e+00 2959.0
8 TraesCS1A01G127500 chr1B 96.082 638 16 2 1291 1924 212411092 212410460 0.000000e+00 1031.0
9 TraesCS1A01G127500 chr1B 89.323 384 21 12 558 932 212415074 212414702 8.180000e-127 464.0
10 TraesCS1A01G127500 chr1B 87.903 372 11 18 27 377 212415437 212415079 1.400000e-109 407.0
11 TraesCS1A01G127500 chr1B 96.020 201 8 0 1100 1300 212414212 212414012 1.120000e-85 327.0
12 TraesCS1A01G127500 chr1B 90.714 140 12 1 936 1075 212414429 212414291 7.130000e-43 185.0
13 TraesCS1A01G127500 chr3D 81.410 780 135 10 2028 2802 129025158 129025932 2.740000e-176 628.0
14 TraesCS1A01G127500 chr3D 78.508 791 147 18 2022 2802 310683026 310683803 8.060000e-137 497.0
15 TraesCS1A01G127500 chr3B 81.258 779 138 8 2028 2802 183083329 183084103 1.270000e-174 623.0
16 TraesCS1A01G127500 chr3B 78.543 755 139 18 2058 2802 410774942 410774201 3.780000e-130 475.0
17 TraesCS1A01G127500 chr3B 96.407 167 5 1 377 542 252667055 252666889 1.480000e-69 274.0
18 TraesCS1A01G127500 chr3B 98.026 152 3 0 377 528 4767806 4767957 8.900000e-67 265.0
19 TraesCS1A01G127500 chr3A 80.922 781 137 12 2028 2802 140806702 140805928 1.280000e-169 606.0
20 TraesCS1A01G127500 chr3A 78.046 788 150 19 2025 2802 421720853 421720079 3.780000e-130 475.0
21 TraesCS1A01G127500 chr2B 98.193 166 3 0 377 542 73314186 73314021 1.470000e-74 291.0
22 TraesCS1A01G127500 chr2B 98.182 165 3 0 378 542 73316189 73316025 5.280000e-74 289.0
23 TraesCS1A01G127500 chr2B 94.737 171 6 2 377 547 541895855 541896022 3.200000e-66 263.0
24 TraesCS1A01G127500 chr2B 77.405 447 82 18 2250 2685 594846327 594845889 8.970000e-62 248.0
25 TraesCS1A01G127500 chr5B 94.578 166 9 0 377 542 625131369 625131204 1.490000e-64 257.0
26 TraesCS1A01G127500 chr5B 97.059 34 1 0 3987 4020 531355274 531355307 1.620000e-04 58.4
27 TraesCS1A01G127500 chr2A 77.528 445 85 15 2250 2685 651609361 651608923 1.930000e-63 254.0
28 TraesCS1A01G127500 chr6B 93.064 173 11 1 377 549 233686981 233686810 6.930000e-63 252.0
29 TraesCS1A01G127500 chr6B 92.857 168 11 1 377 543 696238999 696238832 4.170000e-60 243.0
30 TraesCS1A01G127500 chr7D 94.937 158 7 1 377 533 36446635 36446792 3.220000e-61 246.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G127500 chr1A 154698585 154702760 4175 False 7712.00 7712 100.00000 1 4176 1 chr1A.!!$F1 4175
1 TraesCS1A01G127500 chr1A 578355586 578356382 796 True 261.00 261 72.93000 2067 2866 1 chr1A.!!$R1 799
2 TraesCS1A01G127500 chr1D 137966671 137970208 3537 True 1228.75 3555 93.01975 19 3453 4 chr1D.!!$R2 3434
3 TraesCS1A01G127500 chr1D 137960547 137961279 732 True 983.00 983 91.03300 3449 4176 1 chr1D.!!$R1 727
4 TraesCS1A01G127500 chr1B 212408314 212415437 7123 True 895.50 2959 91.94450 27 4176 6 chr1B.!!$R1 4149
5 TraesCS1A01G127500 chr3D 129025158 129025932 774 False 628.00 628 81.41000 2028 2802 1 chr3D.!!$F1 774
6 TraesCS1A01G127500 chr3D 310683026 310683803 777 False 497.00 497 78.50800 2022 2802 1 chr3D.!!$F2 780
7 TraesCS1A01G127500 chr3B 183083329 183084103 774 False 623.00 623 81.25800 2028 2802 1 chr3B.!!$F2 774
8 TraesCS1A01G127500 chr3B 410774201 410774942 741 True 475.00 475 78.54300 2058 2802 1 chr3B.!!$R2 744
9 TraesCS1A01G127500 chr3A 140805928 140806702 774 True 606.00 606 80.92200 2028 2802 1 chr3A.!!$R1 774
10 TraesCS1A01G127500 chr3A 421720079 421720853 774 True 475.00 475 78.04600 2025 2802 1 chr3A.!!$R2 777
11 TraesCS1A01G127500 chr2B 73314021 73316189 2168 True 290.00 291 98.18750 377 542 2 chr2B.!!$R2 165

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
341 363 0.108186 CAGCCAGAAGGACGCATACA 60.108 55.000 0.00 0.0 36.89 2.29 F
810 832 0.173029 CTGACGCTGATGCTCTGAGT 59.827 55.000 6.53 0.0 36.97 3.41 F
830 852 0.249398 ACGTACTTCCATGCCTGTCC 59.751 55.000 0.00 0.0 0.00 4.02 F
831 853 0.806102 CGTACTTCCATGCCTGTCCG 60.806 60.000 0.00 0.0 0.00 4.79 F
1307 1663 1.079750 GGGTGAGTCAGTCTTCCGC 60.080 63.158 0.00 0.0 0.00 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2017 5306 0.456142 CCGACGACTGAAGCAATCGA 60.456 55.000 5.26 0.0 39.16 3.59 R
2018 5307 0.456142 TCCGACGACTGAAGCAATCG 60.456 55.000 0.00 0.0 41.60 3.34 R
2341 5875 0.962356 CCATGGCCAGGAACAGACAC 60.962 60.000 21.32 0.0 0.00 3.67 R
2518 6377 2.983592 CCCACGAAGTTGCCCACC 60.984 66.667 0.00 0.0 41.61 4.61 R
3269 7472 3.488384 CGCAAGCAAACTTTTGTACTCCA 60.488 43.478 3.74 0.0 40.24 3.86 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
57 58 1.384222 CCTTGAATTAGGCCGCCACC 61.384 60.000 13.15 0.00 0.00 4.61
160 161 1.164041 ACTTTGGGTGCCTCGTTTCG 61.164 55.000 0.00 0.00 0.00 3.46
226 242 0.858135 GAAGCTCTCGTGTAGCGTCG 60.858 60.000 0.00 0.00 44.87 5.12
332 354 1.078143 GTAGTGCCCAGCCAGAAGG 60.078 63.158 0.00 0.00 38.23 3.46
341 363 0.108186 CAGCCAGAAGGACGCATACA 60.108 55.000 0.00 0.00 36.89 2.29
342 364 0.833287 AGCCAGAAGGACGCATACAT 59.167 50.000 0.00 0.00 36.89 2.29
344 366 1.871080 CCAGAAGGACGCATACATCC 58.129 55.000 0.00 0.00 36.89 3.51
345 367 1.138859 CCAGAAGGACGCATACATCCA 59.861 52.381 0.00 0.00 37.47 3.41
346 368 2.477825 CAGAAGGACGCATACATCCAG 58.522 52.381 0.00 0.00 37.47 3.86
347 369 1.202580 AGAAGGACGCATACATCCAGC 60.203 52.381 0.00 0.00 37.47 4.85
348 370 0.833287 AAGGACGCATACATCCAGCT 59.167 50.000 0.00 0.00 37.47 4.24
349 371 0.390860 AGGACGCATACATCCAGCTC 59.609 55.000 0.00 0.00 37.47 4.09
350 372 0.601311 GGACGCATACATCCAGCTCC 60.601 60.000 0.00 0.00 34.87 4.70
351 373 0.390860 GACGCATACATCCAGCTCCT 59.609 55.000 0.00 0.00 0.00 3.69
352 374 0.390860 ACGCATACATCCAGCTCCTC 59.609 55.000 0.00 0.00 0.00 3.71
379 401 4.753516 TTTCCGAGGATGACACATATGT 57.246 40.909 1.41 1.41 43.71 2.29
380 402 4.753516 TTCCGAGGATGACACATATGTT 57.246 40.909 5.37 0.00 39.95 2.71
381 403 5.862678 TTCCGAGGATGACACATATGTTA 57.137 39.130 5.37 0.00 39.95 2.41
542 564 5.744171 TCAGCCATCTCATAGCTTTTACAA 58.256 37.500 0.00 0.00 33.70 2.41
543 565 5.586243 TCAGCCATCTCATAGCTTTTACAAC 59.414 40.000 0.00 0.00 33.70 3.32
544 566 5.355071 CAGCCATCTCATAGCTTTTACAACA 59.645 40.000 0.00 0.00 33.70 3.33
547 569 7.227512 AGCCATCTCATAGCTTTTACAACATAC 59.772 37.037 0.00 0.00 31.27 2.39
548 570 7.012327 GCCATCTCATAGCTTTTACAACATACA 59.988 37.037 0.00 0.00 0.00 2.29
549 571 8.554528 CCATCTCATAGCTTTTACAACATACAG 58.445 37.037 0.00 0.00 0.00 2.74
550 572 7.539712 TCTCATAGCTTTTACAACATACAGC 57.460 36.000 0.00 0.00 0.00 4.40
551 573 7.331026 TCTCATAGCTTTTACAACATACAGCT 58.669 34.615 0.00 0.00 40.65 4.24
552 574 7.492669 TCTCATAGCTTTTACAACATACAGCTC 59.507 37.037 0.00 0.00 38.54 4.09
554 576 4.911390 AGCTTTTACAACATACAGCTCCT 58.089 39.130 0.00 0.00 31.93 3.69
555 577 6.049955 AGCTTTTACAACATACAGCTCCTA 57.950 37.500 0.00 0.00 31.93 2.94
556 578 6.109359 AGCTTTTACAACATACAGCTCCTAG 58.891 40.000 0.00 0.00 31.93 3.02
638 660 1.476891 GAACCAGCCAGTCATCGACTA 59.523 52.381 0.00 0.00 41.37 2.59
662 684 0.713883 CCATATACGAACGGCGCATC 59.286 55.000 10.83 4.80 46.04 3.91
691 713 5.396750 TTTAAAAGCCAAACACAAATCGC 57.603 34.783 0.00 0.00 0.00 4.58
724 746 0.185901 ACATGCTTTGTCCACCACCT 59.814 50.000 0.00 0.00 30.89 4.00
725 747 1.331214 CATGCTTTGTCCACCACCTT 58.669 50.000 0.00 0.00 0.00 3.50
726 748 1.000060 CATGCTTTGTCCACCACCTTG 60.000 52.381 0.00 0.00 0.00 3.61
727 749 1.363807 GCTTTGTCCACCACCTTGC 59.636 57.895 0.00 0.00 0.00 4.01
728 750 1.391157 GCTTTGTCCACCACCTTGCA 61.391 55.000 0.00 0.00 0.00 4.08
795 817 3.801114 AAAGGGTTTTGTGCTTCTGAC 57.199 42.857 0.00 0.00 0.00 3.51
809 831 0.455005 TCTGACGCTGATGCTCTGAG 59.545 55.000 0.00 0.00 36.97 3.35
810 832 0.173029 CTGACGCTGATGCTCTGAGT 59.827 55.000 6.53 0.00 36.97 3.41
811 833 1.403323 CTGACGCTGATGCTCTGAGTA 59.597 52.381 6.53 1.58 36.97 2.59
812 834 1.133216 TGACGCTGATGCTCTGAGTAC 59.867 52.381 6.53 0.00 36.97 2.73
829 851 2.165845 AGTACGTACTTCCATGCCTGTC 59.834 50.000 22.45 0.00 31.13 3.51
830 852 0.249398 ACGTACTTCCATGCCTGTCC 59.751 55.000 0.00 0.00 0.00 4.02
831 853 0.806102 CGTACTTCCATGCCTGTCCG 60.806 60.000 0.00 0.00 0.00 4.79
832 854 1.090052 GTACTTCCATGCCTGTCCGC 61.090 60.000 0.00 0.00 0.00 5.54
909 942 2.178580 TGGGATTTTTAGGCAAGGCAG 58.821 47.619 0.00 0.00 0.00 4.85
933 966 4.806247 AGAAGCTCTACCGATTTCATTTCG 59.194 41.667 0.00 0.00 36.38 3.46
1024 1326 1.681264 ACAGTTTGGCTTTGGCACTAC 59.319 47.619 0.00 0.00 37.98 2.73
1039 1341 4.515191 TGGCACTACTAAGTTTGCAGAAAG 59.485 41.667 4.85 0.00 31.97 2.62
1044 1346 7.513968 CACTACTAAGTTTGCAGAAAGACATC 58.486 38.462 0.00 0.00 31.97 3.06
1052 1354 2.813172 TGCAGAAAGACATCGATTTGCA 59.187 40.909 0.00 0.00 37.91 4.08
1063 1365 6.204688 AGACATCGATTTGCACTTGAAAGTTA 59.795 34.615 0.00 0.00 37.08 2.24
1075 1377 5.765182 CACTTGAAAGTTAGGATGGTGACTT 59.235 40.000 0.00 0.00 37.08 3.01
1076 1378 5.765182 ACTTGAAAGTTAGGATGGTGACTTG 59.235 40.000 0.00 0.00 35.21 3.16
1077 1379 4.651778 TGAAAGTTAGGATGGTGACTTGG 58.348 43.478 0.00 0.00 33.02 3.61
1079 1381 5.014123 TGAAAGTTAGGATGGTGACTTGGAT 59.986 40.000 0.00 0.00 33.02 3.41
1080 1382 4.494091 AGTTAGGATGGTGACTTGGATG 57.506 45.455 0.00 0.00 0.00 3.51
1081 1383 4.104086 AGTTAGGATGGTGACTTGGATGA 58.896 43.478 0.00 0.00 0.00 2.92
1085 1387 4.040047 AGGATGGTGACTTGGATGATGTA 58.960 43.478 0.00 0.00 0.00 2.29
1087 1389 5.846164 AGGATGGTGACTTGGATGATGTATA 59.154 40.000 0.00 0.00 0.00 1.47
1088 1390 6.013898 AGGATGGTGACTTGGATGATGTATAG 60.014 42.308 0.00 0.00 0.00 1.31
1089 1391 6.239714 GGATGGTGACTTGGATGATGTATAGT 60.240 42.308 0.00 0.00 0.00 2.12
1091 1393 6.348498 TGGTGACTTGGATGATGTATAGTTG 58.652 40.000 0.00 0.00 0.00 3.16
1093 1395 7.125053 TGGTGACTTGGATGATGTATAGTTGTA 59.875 37.037 0.00 0.00 0.00 2.41
1095 1397 8.198109 GTGACTTGGATGATGTATAGTTGTACT 58.802 37.037 0.00 0.00 0.00 2.73
1096 1398 8.414003 TGACTTGGATGATGTATAGTTGTACTC 58.586 37.037 0.00 0.00 0.00 2.59
1102 1458 8.857098 GGATGATGTATAGTTGTACTCCACTTA 58.143 37.037 0.00 0.00 0.00 2.24
1128 1484 2.025969 CACTCGCTCTGTGCAGGTG 61.026 63.158 2.42 6.18 43.06 4.00
1129 1485 3.117171 CTCGCTCTGTGCAGGTGC 61.117 66.667 2.42 0.00 43.06 5.01
1200 1556 3.379445 TCCCTCCTCGCCAACGTC 61.379 66.667 0.00 0.00 41.18 4.34
1253 1609 4.559063 CCCGATGCAGAGCCCCAG 62.559 72.222 0.00 0.00 0.00 4.45
1301 1657 4.436998 CGCCCGGGTGAGTCAGTC 62.437 72.222 30.98 3.10 0.00 3.51
1305 1661 1.592223 CCGGGTGAGTCAGTCTTCC 59.408 63.158 0.00 0.00 0.00 3.46
1306 1662 1.213013 CGGGTGAGTCAGTCTTCCG 59.787 63.158 0.00 0.00 0.00 4.30
1307 1663 1.079750 GGGTGAGTCAGTCTTCCGC 60.080 63.158 0.00 0.00 0.00 5.54
1583 4872 2.825836 CGGAAGCAGGCCATGTCC 60.826 66.667 5.01 5.01 0.00 4.02
1820 5109 3.708544 CCGGTTAGCACCCCCGAA 61.709 66.667 0.00 0.00 44.41 4.30
1949 5238 7.364200 CACTACTTCTTCTTCTTCTTCTTCGA 58.636 38.462 0.00 0.00 0.00 3.71
1998 5287 1.137872 CCCTCCCATTCGAGTCTCAAG 59.862 57.143 0.00 0.00 0.00 3.02
2014 5303 5.238214 AGTCTCAAGATTCTGAAACTTGTGC 59.762 40.000 28.28 22.47 40.89 4.57
2015 5304 4.212004 TCTCAAGATTCTGAAACTTGTGCG 59.788 41.667 28.28 20.74 40.89 5.34
2016 5305 4.126437 TCAAGATTCTGAAACTTGTGCGA 58.874 39.130 28.28 14.42 40.89 5.10
2017 5306 4.756642 TCAAGATTCTGAAACTTGTGCGAT 59.243 37.500 28.28 1.31 40.89 4.58
2018 5307 4.935885 AGATTCTGAAACTTGTGCGATC 57.064 40.909 0.00 0.00 0.00 3.69
2098 5387 3.781307 CGGTTCCCCATCTCGGCA 61.781 66.667 0.00 0.00 0.00 5.69
2518 6377 1.597027 GTCCAACCACCTGTCCGTG 60.597 63.158 0.00 0.00 0.00 4.94
2854 6907 3.515316 CTCGTTGTCGTGGTGGGCT 62.515 63.158 0.00 0.00 38.33 5.19
3136 7334 2.667536 AGCAGCAGCAAGGACGTG 60.668 61.111 3.17 0.00 45.49 4.49
3186 7384 2.093288 CAGAAGCTTGATGGAGTGGCTA 60.093 50.000 2.10 0.00 32.64 3.93
3259 7462 4.770531 CACTTGGTGGGATAGGATACGATA 59.229 45.833 0.00 0.00 46.39 2.92
3260 7463 4.771054 ACTTGGTGGGATAGGATACGATAC 59.229 45.833 0.00 0.00 46.39 2.24
3261 7464 3.349927 TGGTGGGATAGGATACGATACG 58.650 50.000 0.00 0.00 46.39 3.06
3263 7466 4.205587 GGTGGGATAGGATACGATACGAT 58.794 47.826 0.00 0.00 46.39 3.73
3264 7467 4.275443 GGTGGGATAGGATACGATACGATC 59.725 50.000 0.00 0.00 46.39 3.69
3356 7882 6.017523 GGCATAGAATAAGCAAAGAAGGTCTC 60.018 42.308 0.00 0.00 36.93 3.36
3372 7898 3.575687 AGGTCTCTTTGGAATTTGCAAGG 59.424 43.478 6.44 6.44 0.00 3.61
3498 8029 5.874895 TCTACCTCGGACGATATACAATG 57.125 43.478 0.00 0.00 0.00 2.82
3510 8041 6.682746 ACGATATACAATGTGTTTTGGCAAA 58.317 32.000 8.93 8.93 0.00 3.68
3599 8130 3.977427 GACCCAACAAAATTGGTCTGAC 58.023 45.455 0.00 0.00 43.16 3.51
3624 8156 2.222398 CGCAAAAAGCAACGAAAACGTT 60.222 40.909 0.00 0.00 46.13 3.99
3625 8157 3.719474 CGCAAAAAGCAACGAAAACGTTT 60.719 39.130 7.96 7.96 46.13 3.60
3839 8378 6.642683 ACACGACGATACCTAAAGAAAATG 57.357 37.500 0.00 0.00 0.00 2.32
3844 8383 7.042925 ACGACGATACCTAAAGAAAATGCATAC 60.043 37.037 0.00 0.00 0.00 2.39
3920 8479 4.859798 AGCGAACGAAAACACAATGAAAAA 59.140 33.333 0.00 0.00 0.00 1.94
3986 8546 8.905702 GCAATGAAATGTTACTCTAAAACACAG 58.094 33.333 0.00 0.00 39.51 3.66
4027 8587 4.268405 GGTTGAAGCACATTGAAACACAAG 59.732 41.667 0.00 0.00 42.02 3.16
4037 8597 5.816777 ACATTGAAACACAAGGAAACATTGG 59.183 36.000 0.00 0.00 41.97 3.16
4122 8682 3.255642 CGGTCATGGTTCCAATGAAGTTT 59.744 43.478 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 9.996554 CCTAATTCAAGGAAGTTGGTTATTTTT 57.003 29.630 0.00 0.00 39.15 1.94
24 25 8.094548 GCCTAATTCAAGGAAGTTGGTTATTTT 58.905 33.333 8.25 0.00 39.15 1.82
57 58 0.601841 AGAGTAACGTGCGTTTGGGG 60.602 55.000 15.16 0.00 39.31 4.96
98 99 4.460263 TGCACATTTACAGGAGTTTCAGT 58.540 39.130 0.00 0.00 0.00 3.41
149 150 2.261671 GCTCTCCGAAACGAGGCA 59.738 61.111 0.00 0.00 0.00 4.75
160 161 0.540923 ACAGATCTTGGCAGCTCTCC 59.459 55.000 0.00 0.00 0.00 3.71
226 242 5.838531 ACTAGCAGTGAATACTACTCCAC 57.161 43.478 0.00 0.00 34.74 4.02
332 354 0.390860 AGGAGCTGGATGTATGCGTC 59.609 55.000 0.00 0.00 0.00 5.19
444 466 3.309265 GGAGGGAGAGAGACTTGGAGTAA 60.309 52.174 0.00 0.00 0.00 2.24
542 564 3.139397 AGCTAGGACTAGGAGCTGTATGT 59.861 47.826 8.33 0.00 44.77 2.29
543 565 3.761897 AGCTAGGACTAGGAGCTGTATG 58.238 50.000 8.33 0.00 44.77 2.39
544 566 5.174037 CTAGCTAGGACTAGGAGCTGTAT 57.826 47.826 13.32 0.00 45.94 2.29
638 660 2.400399 CGCCGTTCGTATATGGTGATT 58.600 47.619 0.00 0.00 36.94 2.57
662 684 5.537188 TGTGTTTGGCTTTTAAATAGGCAG 58.463 37.500 18.65 3.93 46.93 4.85
710 732 1.331214 ATGCAAGGTGGTGGACAAAG 58.669 50.000 0.00 0.00 0.00 2.77
712 734 1.039068 CAATGCAAGGTGGTGGACAA 58.961 50.000 0.00 0.00 0.00 3.18
724 746 0.469705 AGGCAGGGAACACAATGCAA 60.470 50.000 0.00 0.00 40.46 4.08
725 747 1.153524 AGGCAGGGAACACAATGCA 59.846 52.632 0.00 0.00 40.46 3.96
726 748 1.588082 CAGGCAGGGAACACAATGC 59.412 57.895 0.00 0.00 37.95 3.56
727 749 1.588082 GCAGGCAGGGAACACAATG 59.412 57.895 0.00 0.00 0.00 2.82
728 750 1.607467 GGCAGGCAGGGAACACAAT 60.607 57.895 0.00 0.00 0.00 2.71
795 817 6.491005 AAGTACGTACTCAGAGCATCAGCG 62.491 50.000 27.51 0.00 40.00 5.18
809 831 2.537401 GACAGGCATGGAAGTACGTAC 58.463 52.381 18.10 18.10 0.00 3.67
810 832 1.479323 GGACAGGCATGGAAGTACGTA 59.521 52.381 2.31 0.00 0.00 3.57
811 833 0.249398 GGACAGGCATGGAAGTACGT 59.751 55.000 2.31 0.00 0.00 3.57
812 834 0.806102 CGGACAGGCATGGAAGTACG 60.806 60.000 2.31 0.00 31.42 3.67
829 851 4.603946 GTTAGGCTAGGCGGGCGG 62.604 72.222 11.10 0.00 36.85 6.13
830 852 3.379865 TTGTTAGGCTAGGCGGGCG 62.380 63.158 11.10 0.00 36.85 6.13
831 853 1.818363 GTTGTTAGGCTAGGCGGGC 60.818 63.158 11.10 5.45 0.00 6.13
832 854 1.520787 CGTTGTTAGGCTAGGCGGG 60.521 63.158 11.10 0.00 0.00 6.13
909 942 5.051374 CGAAATGAAATCGGTAGAGCTTCTC 60.051 44.000 0.00 0.00 36.68 2.87
947 1249 9.090692 CAGATTTGGCTTTATATTTCACCTTTG 57.909 33.333 0.00 0.00 0.00 2.77
954 1256 7.536622 CGATCAGCAGATTTGGCTTTATATTTC 59.463 37.037 0.00 0.00 40.23 2.17
995 1297 1.210155 GCCAAACTGTCCATGTCGC 59.790 57.895 0.00 0.00 0.00 5.19
1024 1326 5.845985 TCGATGTCTTTCTGCAAACTTAG 57.154 39.130 0.00 0.00 0.00 2.18
1039 1341 4.787598 ACTTTCAAGTGCAAATCGATGTC 58.212 39.130 0.00 0.00 37.98 3.06
1044 1346 5.356882 TCCTAACTTTCAAGTGCAAATCG 57.643 39.130 0.00 0.00 39.66 3.34
1052 1354 5.568620 AGTCACCATCCTAACTTTCAAGT 57.431 39.130 0.00 0.00 42.04 3.16
1063 1365 2.848694 ACATCATCCAAGTCACCATCCT 59.151 45.455 0.00 0.00 0.00 3.24
1075 1377 6.839134 AGTGGAGTACAACTATACATCATCCA 59.161 38.462 0.00 0.00 0.00 3.41
1076 1378 7.291411 AGTGGAGTACAACTATACATCATCC 57.709 40.000 0.00 0.00 0.00 3.51
1077 1379 9.900710 CTAAGTGGAGTACAACTATACATCATC 57.099 37.037 0.00 0.00 0.00 2.92
1079 1381 8.818622 ACTAAGTGGAGTACAACTATACATCA 57.181 34.615 0.00 0.00 0.00 3.07
1080 1382 9.733219 GAACTAAGTGGAGTACAACTATACATC 57.267 37.037 0.00 0.00 0.00 3.06
1081 1383 9.476928 AGAACTAAGTGGAGTACAACTATACAT 57.523 33.333 0.00 0.00 0.00 2.29
1085 1387 7.450634 TGTGAGAACTAAGTGGAGTACAACTAT 59.549 37.037 0.00 0.00 0.00 2.12
1087 1389 5.597182 TGTGAGAACTAAGTGGAGTACAACT 59.403 40.000 0.00 0.00 0.00 3.16
1088 1390 5.690857 GTGTGAGAACTAAGTGGAGTACAAC 59.309 44.000 0.00 0.00 0.00 3.32
1089 1391 5.597182 AGTGTGAGAACTAAGTGGAGTACAA 59.403 40.000 0.00 0.00 0.00 2.41
1091 1393 5.617308 CGAGTGTGAGAACTAAGTGGAGTAC 60.617 48.000 0.00 0.00 0.00 2.73
1093 1395 3.253677 CGAGTGTGAGAACTAAGTGGAGT 59.746 47.826 0.00 0.00 0.00 3.85
1095 1397 2.030185 GCGAGTGTGAGAACTAAGTGGA 60.030 50.000 0.00 0.00 0.00 4.02
1096 1398 2.029828 AGCGAGTGTGAGAACTAAGTGG 60.030 50.000 0.00 0.00 0.00 4.00
1102 1458 1.000827 CACAGAGCGAGTGTGAGAACT 60.001 52.381 9.73 0.00 46.99 3.01
1128 1484 4.521062 ATGGCTCGCTCAGACGGC 62.521 66.667 0.00 0.00 28.76 5.68
1129 1485 2.584418 CATGGCTCGCTCAGACGG 60.584 66.667 0.00 0.00 28.76 4.79
1227 1583 4.343323 TGCATCGGGGTGGTGGTG 62.343 66.667 0.00 0.00 0.00 4.17
1230 1586 2.124983 CTCTGCATCGGGGTGGTG 60.125 66.667 0.00 0.00 0.00 4.17
1307 1663 3.584052 CCGTACGAGGGAGCGGAG 61.584 72.222 18.76 0.00 46.33 4.63
1336 4621 3.015327 CCAAGCTCCATTTCTTCTCAGG 58.985 50.000 0.00 0.00 0.00 3.86
1341 4626 4.012374 TCATGTCCAAGCTCCATTTCTTC 58.988 43.478 0.00 0.00 0.00 2.87
1489 4778 2.181777 GCAGGCTGATCGACACGA 59.818 61.111 20.86 0.00 41.13 4.35
1496 4785 1.953138 CGACGATGGCAGGCTGATC 60.953 63.158 20.86 12.28 0.00 2.92
1608 4897 3.036084 CTGCGCGAACCTCACGTT 61.036 61.111 12.10 0.00 37.41 3.99
1681 4970 1.065928 CTACCCATCCGTCTCACGC 59.934 63.158 0.00 0.00 40.91 5.34
1820 5109 1.684049 CTGGGCGAACTCCTCCTCT 60.684 63.158 0.00 0.00 0.00 3.69
1949 5238 3.928992 GCATGATAATGTGATCGACCGAT 59.071 43.478 4.42 4.42 37.59 4.18
1998 5287 3.367932 TCGATCGCACAAGTTTCAGAATC 59.632 43.478 11.09 0.00 0.00 2.52
2014 5303 1.514811 GACGACTGAAGCAATCGATCG 59.485 52.381 9.36 9.36 39.16 3.69
2015 5304 1.514811 CGACGACTGAAGCAATCGATC 59.485 52.381 5.26 0.00 39.16 3.69
2016 5305 1.550065 CGACGACTGAAGCAATCGAT 58.450 50.000 5.26 0.00 39.16 3.59
2017 5306 0.456142 CCGACGACTGAAGCAATCGA 60.456 55.000 5.26 0.00 39.16 3.59
2018 5307 0.456142 TCCGACGACTGAAGCAATCG 60.456 55.000 0.00 0.00 41.60 3.34
2098 5387 1.445942 CCCGAGGCACATACCGAAT 59.554 57.895 0.00 0.00 33.69 3.34
2161 5450 2.599281 TGCAGGAACTCGGTCGGA 60.599 61.111 0.00 0.00 34.60 4.55
2203 5492 1.003118 CCCACGGAGATGAACCAAAGA 59.997 52.381 0.00 0.00 0.00 2.52
2341 5875 0.962356 CCATGGCCAGGAACAGACAC 60.962 60.000 21.32 0.00 0.00 3.67
2393 5977 3.760035 CGCGTACCAGAGCCAGGT 61.760 66.667 0.00 0.00 43.14 4.00
2518 6377 2.983592 CCCACGAAGTTGCCCACC 60.984 66.667 0.00 0.00 41.61 4.61
3263 7466 7.127175 AAGCAAACTTTTGTACTCCAGTACGA 61.127 38.462 11.41 7.44 42.60 3.43
3264 7467 5.007332 AAGCAAACTTTTGTACTCCAGTACG 59.993 40.000 11.41 1.35 42.60 3.67
3265 7468 6.199393 CAAGCAAACTTTTGTACTCCAGTAC 58.801 40.000 9.58 9.58 41.69 2.73
3266 7469 5.220970 GCAAGCAAACTTTTGTACTCCAGTA 60.221 40.000 3.74 0.00 40.24 2.74
3267 7470 4.440112 GCAAGCAAACTTTTGTACTCCAGT 60.440 41.667 3.74 0.00 40.24 4.00
3269 7472 3.488384 CGCAAGCAAACTTTTGTACTCCA 60.488 43.478 3.74 0.00 40.24 3.86
3356 7882 5.047519 AGTGAGATCCTTGCAAATTCCAAAG 60.048 40.000 0.00 0.00 0.00 2.77
3372 7898 1.550976 ACGGAGGTTTCCAGTGAGATC 59.449 52.381 0.00 0.00 44.26 2.75
3498 8029 8.631676 ATCAAAATTCAAATTTGCCAAAACAC 57.368 26.923 13.54 0.00 38.53 3.32
3543 8074 4.511454 TGGAGCGCATATTTCATACAAGTC 59.489 41.667 11.47 0.00 0.00 3.01
3599 8130 3.394062 CGTTGCTTTTTGCGGGCG 61.394 61.111 0.00 0.00 46.63 6.13
3624 8156 2.171237 CCTATCCTGATGTGCACCTCAA 59.829 50.000 22.65 11.69 0.00 3.02
3625 8157 1.764723 CCTATCCTGATGTGCACCTCA 59.235 52.381 21.43 21.43 0.00 3.86
3701 8233 7.470289 CAACGAATTTTGTTGGGTTTTATCA 57.530 32.000 18.18 0.00 42.27 2.15
3722 8260 6.910433 CACCATAACGTTTATAGCATTCCAAC 59.090 38.462 5.91 0.00 0.00 3.77
3779 8317 8.270080 TGTAAATGTTTCACTTTGTGTCACTA 57.730 30.769 4.27 0.00 34.79 2.74
3781 8319 7.097047 CGATGTAAATGTTTCACTTTGTGTCAC 60.097 37.037 0.00 0.00 34.79 3.67
3866 8425 9.632638 ACATGTATTAGGCATAGTTGATTTTCT 57.367 29.630 0.00 0.00 0.00 2.52
3870 8429 9.407380 TCAAACATGTATTAGGCATAGTTGATT 57.593 29.630 0.00 0.00 30.31 2.57
3871 8430 8.978874 TCAAACATGTATTAGGCATAGTTGAT 57.021 30.769 0.00 0.00 30.31 2.57
3872 8431 8.800370 TTCAAACATGTATTAGGCATAGTTGA 57.200 30.769 0.00 0.00 31.89 3.18
3873 8432 7.645340 GCTTCAAACATGTATTAGGCATAGTTG 59.355 37.037 0.00 0.00 0.00 3.16
3874 8433 7.467267 CGCTTCAAACATGTATTAGGCATAGTT 60.467 37.037 0.00 0.00 0.00 2.24
3875 8434 6.017934 CGCTTCAAACATGTATTAGGCATAGT 60.018 38.462 0.00 0.00 0.00 2.12
3876 8435 6.202762 TCGCTTCAAACATGTATTAGGCATAG 59.797 38.462 0.00 0.00 0.00 2.23
3877 8436 6.052360 TCGCTTCAAACATGTATTAGGCATA 58.948 36.000 0.00 0.00 0.00 3.14
3878 8437 4.881273 TCGCTTCAAACATGTATTAGGCAT 59.119 37.500 0.00 0.00 0.00 4.40
3879 8438 4.257731 TCGCTTCAAACATGTATTAGGCA 58.742 39.130 0.00 0.00 0.00 4.75
3880 8439 4.875544 TCGCTTCAAACATGTATTAGGC 57.124 40.909 0.00 0.81 0.00 3.93
3881 8440 5.062934 TCGTTCGCTTCAAACATGTATTAGG 59.937 40.000 0.00 0.00 0.00 2.69
3882 8441 6.089920 TCGTTCGCTTCAAACATGTATTAG 57.910 37.500 0.00 0.00 0.00 1.73
3883 8442 6.469139 TTCGTTCGCTTCAAACATGTATTA 57.531 33.333 0.00 0.00 0.00 0.98
3884 8443 5.351233 TTCGTTCGCTTCAAACATGTATT 57.649 34.783 0.00 0.00 0.00 1.89
3885 8444 5.351233 TTTCGTTCGCTTCAAACATGTAT 57.649 34.783 0.00 0.00 0.00 2.29
3986 8546 4.938226 TCAACCAATTTTGTTGGGTTTCAC 59.062 37.500 14.50 0.00 41.49 3.18
4027 8587 2.888834 AAGTGCACACCAATGTTTCC 57.111 45.000 21.04 0.00 36.72 3.13
4096 8656 2.009774 CATTGGAACCATGACCGAGAC 58.990 52.381 0.00 0.00 0.00 3.36
4106 8666 5.659079 ACCAAAGTAAACTTCATTGGAACCA 59.341 36.000 15.64 0.00 35.79 3.67


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

AutoCloner maintained by Alex Coulton.