Multiple sequence alignment - TraesCS5B01G528200

Loading Multiple Alignment...

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 TraesCS5B01G528200 chr5B 100.000 5509 0 0 1 5509 687164280 687158772 0.000000e+00 10174.0
1 TraesCS5B01G528200 chr5B 86.337 505 60 7 5012 5509 107368786 107368284 4.850000e-150 542.0
2 TraesCS5B01G528200 chr5B 85.499 531 62 10 4985 5509 469978482 469977961 1.750000e-149 540.0
3 TraesCS5B01G528200 chr5D 94.052 2757 93 23 2164 4904 544700490 544703191 0.000000e+00 4117.0
4 TraesCS5B01G528200 chr5D 95.533 2194 59 9 6 2166 544698200 544700387 0.000000e+00 3472.0
5 TraesCS5B01G528200 chr4A 93.753 2273 93 17 2732 4982 624631806 624634051 0.000000e+00 3365.0
6 TraesCS5B01G528200 chr4A 84.668 437 47 12 2213 2635 577046090 577045660 8.540000e-113 418.0
7 TraesCS5B01G528200 chr4A 90.909 308 24 3 2786 3092 577045603 577045299 1.430000e-110 411.0
8 TraesCS5B01G528200 chr1A 90.419 1002 49 16 4002 4982 569447374 569446399 0.000000e+00 1275.0
9 TraesCS5B01G528200 chr1A 83.505 1067 176 0 2971 4037 9362640 9363706 0.000000e+00 996.0
10 TraesCS5B01G528200 chr1A 86.541 899 64 26 404 1272 569448766 569447895 0.000000e+00 937.0
11 TraesCS5B01G528200 chr1A 87.218 399 25 17 11 386 569450252 569449857 1.100000e-116 431.0
12 TraesCS5B01G528200 chr1A 86.306 314 38 3 373 685 569449808 569449499 2.460000e-88 337.0
13 TraesCS5B01G528200 chr1A 92.537 201 12 1 404 604 569449488 569449291 9.030000e-73 285.0
14 TraesCS5B01G528200 chr1A 79.630 378 63 8 307 683 569447857 569447493 5.470000e-65 259.0
15 TraesCS5B01G528200 chrUn 83.244 1116 176 9 2971 4082 238779951 238778843 0.000000e+00 1014.0
16 TraesCS5B01G528200 chrUn 83.244 1116 176 9 2971 4082 240356323 240357431 0.000000e+00 1014.0
17 TraesCS5B01G528200 chr3D 83.199 1113 180 6 2967 4077 27878186 27877079 0.000000e+00 1013.0
18 TraesCS5B01G528200 chr3D 84.499 529 75 5 4987 5509 130515623 130515096 2.940000e-142 516.0
19 TraesCS5B01G528200 chr4D 87.279 904 71 14 1136 2021 26253078 26253955 0.000000e+00 992.0
20 TraesCS5B01G528200 chr4D 82.975 605 61 14 2036 2635 26254067 26254634 4.920000e-140 508.0
21 TraesCS5B01G528200 chr4D 89.286 308 23 3 2786 3092 26254691 26254989 1.450000e-100 377.0
22 TraesCS5B01G528200 chr4D 87.363 182 19 2 877 1057 26252778 26252956 7.230000e-49 206.0
23 TraesCS5B01G528200 chr4D 98.333 60 0 1 2695 2753 26254633 26254692 2.710000e-18 104.0
24 TraesCS5B01G528200 chr1D 83.118 1084 179 3 2972 4053 7879249 7880330 0.000000e+00 985.0
25 TraesCS5B01G528200 chr1D 82.841 1084 184 2 2971 4053 7348536 7347454 0.000000e+00 970.0
26 TraesCS5B01G528200 chr1D 87.238 478 52 6 5037 5509 192916796 192916323 2.260000e-148 536.0
27 TraesCS5B01G528200 chr1D 91.304 46 4 0 1671 1716 7350366 7350321 4.610000e-06 63.9
28 TraesCS5B01G528200 chr1B 83.118 1084 179 3 2972 4053 10074728 10075809 0.000000e+00 985.0
29 TraesCS5B01G528200 chr4B 85.015 1001 95 16 1153 2133 38792631 38793596 0.000000e+00 966.0
30 TraesCS5B01G528200 chr4B 85.880 432 45 8 2213 2632 38793627 38794054 3.920000e-121 446.0
31 TraesCS5B01G528200 chr4B 89.644 309 22 6 2786 3092 38794114 38794414 8.660000e-103 385.0
32 TraesCS5B01G528200 chr4B 86.559 186 20 3 877 1060 38792313 38792495 3.370000e-47 200.0
33 TraesCS5B01G528200 chr4B 94.118 68 1 2 2689 2753 38794048 38794115 3.510000e-17 100.0
34 TraesCS5B01G528200 chr2B 86.142 534 66 6 4983 5509 767023237 767023769 2.230000e-158 569.0
35 TraesCS5B01G528200 chr2B 89.474 57 6 0 4988 5044 233255225 233255281 7.650000e-09 73.1
36 TraesCS5B01G528200 chr6D 85.851 523 60 8 4990 5506 425910603 425911117 1.350000e-150 544.0
37 TraesCS5B01G528200 chr6D 86.820 478 58 3 5037 5509 396015922 396015445 3.780000e-146 529.0
38 TraesCS5B01G528200 chr2D 85.393 534 60 7 4988 5506 139483758 139484288 6.280000e-149 538.0
39 TraesCS5B01G528200 chr7D 86.820 478 58 3 5037 5509 638409564 638409087 3.780000e-146 529.0


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 TraesCS5B01G528200 chr5B 687158772 687164280 5508 True 10174.000000 10174 100.0000 1 5509 1 chr5B.!!$R3 5508
1 TraesCS5B01G528200 chr5B 107368284 107368786 502 True 542.000000 542 86.3370 5012 5509 1 chr5B.!!$R1 497
2 TraesCS5B01G528200 chr5B 469977961 469978482 521 True 540.000000 540 85.4990 4985 5509 1 chr5B.!!$R2 524
3 TraesCS5B01G528200 chr5D 544698200 544703191 4991 False 3794.500000 4117 94.7925 6 4904 2 chr5D.!!$F1 4898
4 TraesCS5B01G528200 chr4A 624631806 624634051 2245 False 3365.000000 3365 93.7530 2732 4982 1 chr4A.!!$F1 2250
5 TraesCS5B01G528200 chr4A 577045299 577046090 791 True 414.500000 418 87.7885 2213 3092 2 chr4A.!!$R1 879
6 TraesCS5B01G528200 chr1A 9362640 9363706 1066 False 996.000000 996 83.5050 2971 4037 1 chr1A.!!$F1 1066
7 TraesCS5B01G528200 chr1A 569446399 569450252 3853 True 587.333333 1275 87.1085 11 4982 6 chr1A.!!$R1 4971
8 TraesCS5B01G528200 chrUn 238778843 238779951 1108 True 1014.000000 1014 83.2440 2971 4082 1 chrUn.!!$R1 1111
9 TraesCS5B01G528200 chrUn 240356323 240357431 1108 False 1014.000000 1014 83.2440 2971 4082 1 chrUn.!!$F1 1111
10 TraesCS5B01G528200 chr3D 27877079 27878186 1107 True 1013.000000 1013 83.1990 2967 4077 1 chr3D.!!$R1 1110
11 TraesCS5B01G528200 chr3D 130515096 130515623 527 True 516.000000 516 84.4990 4987 5509 1 chr3D.!!$R2 522
12 TraesCS5B01G528200 chr4D 26252778 26254989 2211 False 437.400000 992 89.0472 877 3092 5 chr4D.!!$F1 2215
13 TraesCS5B01G528200 chr1D 7879249 7880330 1081 False 985.000000 985 83.1180 2972 4053 1 chr1D.!!$F1 1081
14 TraesCS5B01G528200 chr1D 7347454 7350366 2912 True 516.950000 970 87.0725 1671 4053 2 chr1D.!!$R2 2382
15 TraesCS5B01G528200 chr1B 10074728 10075809 1081 False 985.000000 985 83.1180 2972 4053 1 chr1B.!!$F1 1081
16 TraesCS5B01G528200 chr4B 38792313 38794414 2101 False 419.400000 966 88.2432 877 3092 5 chr4B.!!$F1 2215
17 TraesCS5B01G528200 chr2B 767023237 767023769 532 False 569.000000 569 86.1420 4983 5509 1 chr2B.!!$F2 526
18 TraesCS5B01G528200 chr6D 425910603 425911117 514 False 544.000000 544 85.8510 4990 5506 1 chr6D.!!$F1 516
19 TraesCS5B01G528200 chr2D 139483758 139484288 530 False 538.000000 538 85.3930 4988 5506 1 chr2D.!!$F1 518

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
874 1981 0.107703 CATACCCAGCGTGTGACCAT 60.108 55.000 0.00 0.00 35.70 3.55 F
1069 2178 0.764890 AAGGCTACCAGCTCAACACA 59.235 50.000 0.00 0.00 41.99 3.72 F
1299 2461 1.102809 TGGCCACAGCTTCAACAGTG 61.103 55.000 0.00 0.00 39.73 3.66 F
1356 2518 1.374505 CCGGTGCAGCAAAAATGGG 60.375 57.895 17.33 2.89 0.00 4.00 F
2205 3978 2.969821 TGTTTCCCCTAGCAACATGT 57.030 45.000 0.00 0.00 0.00 3.21 F
3224 5401 0.393808 GGGCGAGCTACCAAATGGAA 60.394 55.000 6.42 0.00 38.94 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2341 4124 4.153117 GCCCGCATCATCTGATAAAACTAG 59.847 45.833 0.00 0.0 32.63 2.57 R
2753 4718 4.576873 TGTGAACCTGCAAATACGAAAGAA 59.423 37.500 0.00 0.0 0.00 2.52 R
3205 5382 0.393808 TTCCATTTGGTAGCTCGCCC 60.394 55.000 0.00 0.0 36.34 6.13 R
3224 5401 3.199508 AGCATCTTGACAGCTACAGGAAT 59.800 43.478 8.47 0.0 36.73 3.01 R
3831 6009 0.666913 GTCCTGGCGAGCGATAACTA 59.333 55.000 0.00 0.0 0.00 2.24 R
4905 7112 0.108138 AGTAGTGGAGGCGCATTCAC 60.108 55.000 25.50 25.5 0.00 3.18 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
138 139 4.637483 TGTTCTGCCTTCTTTTCAAGTG 57.363 40.909 0.00 0.00 0.00 3.16
162 163 5.276584 GCACTCTTGTAATGCTACGATTCTG 60.277 44.000 0.00 0.00 36.40 3.02
302 335 2.953648 AGTTTCCGTAACACCCCAAAAG 59.046 45.455 1.24 0.00 39.30 2.27
381 415 6.233434 TGACAATCTTTACAGAAGATGCACT 58.767 36.000 2.34 0.00 37.11 4.40
432 528 7.504924 TCAAGGAAATACACGACAAATTCTT 57.495 32.000 0.00 0.00 0.00 2.52
443 539 6.202954 ACACGACAAATTCTTCTTCGAAGAAT 59.797 34.615 34.19 21.10 45.87 2.40
451 547 5.097742 TCTTCTTCGAAGAATGGCCAATA 57.902 39.130 34.19 14.26 45.90 1.90
462 558 4.223477 AGAATGGCCAATACAAATTGTGCT 59.777 37.500 10.96 0.00 40.84 4.40
482 1586 5.049167 TGCTGAACATGGATTTGTGTTTTC 58.951 37.500 0.00 0.00 38.57 2.29
586 1690 6.544928 TTCTCACATAGCAACTATTCCTCA 57.455 37.500 0.00 0.00 0.00 3.86
619 1723 4.513406 ATTTATTTCCGCAACCCCTCTA 57.487 40.909 0.00 0.00 0.00 2.43
678 1782 2.763933 ACAATCACACTCAGACAGCTG 58.236 47.619 13.48 13.48 43.67 4.24
770 1874 2.619931 TCACCTTCATGTCCTTCTCCA 58.380 47.619 0.00 0.00 0.00 3.86
814 1921 9.827411 GAGTAAGTCCAAGTTGTATTCAATTTC 57.173 33.333 1.45 0.00 35.92 2.17
847 1954 0.870393 GGTGCCACGATAGATGCATG 59.130 55.000 2.46 0.00 44.75 4.06
864 1971 2.292267 CATGTTCTGTCCATACCCAGC 58.708 52.381 0.00 0.00 0.00 4.85
874 1981 0.107703 CATACCCAGCGTGTGACCAT 60.108 55.000 0.00 0.00 35.70 3.55
985 2092 1.001293 TGGACTGCAGCAAGTCTACAG 59.999 52.381 15.27 0.00 44.98 2.74
1012 2119 2.427453 CTCAGACCACTATAACACGGCT 59.573 50.000 0.00 0.00 0.00 5.52
1056 2165 2.284331 TCCTCGGGCACAAGGCTA 60.284 61.111 0.00 0.00 44.01 3.93
1069 2178 0.764890 AAGGCTACCAGCTCAACACA 59.235 50.000 0.00 0.00 41.99 3.72
1096 2205 9.193806 AGTGGCTCTGTTAATTTCATCAATAAT 57.806 29.630 0.00 0.00 0.00 1.28
1110 2220 9.681692 TTTCATCAATAATCGCCAATCATTTAG 57.318 29.630 0.00 0.00 0.00 1.85
1211 2370 1.702957 ACCTTTCCATCTCCGGTTCAA 59.297 47.619 0.00 0.00 0.00 2.69
1212 2371 2.084546 CCTTTCCATCTCCGGTTCAAC 58.915 52.381 0.00 0.00 0.00 3.18
1213 2372 2.552155 CCTTTCCATCTCCGGTTCAACA 60.552 50.000 0.00 0.00 0.00 3.33
1246 2408 7.285401 TGACTAAATTTCTTTCCATAGCCATCC 59.715 37.037 0.00 0.00 0.00 3.51
1299 2461 1.102809 TGGCCACAGCTTCAACAGTG 61.103 55.000 0.00 0.00 39.73 3.66
1356 2518 1.374505 CCGGTGCAGCAAAAATGGG 60.375 57.895 17.33 2.89 0.00 4.00
1502 2664 4.592778 TGTCACTGCCATAGATTATAGCCA 59.407 41.667 0.00 0.00 0.00 4.75
2205 3978 2.969821 TGTTTCCCCTAGCAACATGT 57.030 45.000 0.00 0.00 0.00 3.21
2211 3984 5.765576 TTCCCCTAGCAACATGTAGTTAA 57.234 39.130 0.00 0.00 38.74 2.01
2333 4116 8.658609 AGCAATGTAAAATTATGCATGTTCAAC 58.341 29.630 10.16 6.86 39.42 3.18
2951 5127 6.132056 GCTTTCTATCATAAGACAATGTGCG 58.868 40.000 0.00 0.00 0.00 5.34
3054 5231 5.797934 CACTCTATCTTTCACTGAAGACGAC 59.202 44.000 0.00 0.00 38.39 4.34
3152 5329 8.207545 ACACTTTCTCTGAAGTTAAGAAGATGT 58.792 33.333 0.00 1.15 37.76 3.06
3205 5382 6.706270 GTGGTGGATATGGAAGTGTATACAAG 59.294 42.308 7.25 0.00 0.00 3.16
3224 5401 0.393808 GGGCGAGCTACCAAATGGAA 60.394 55.000 6.42 0.00 38.94 3.53
3305 5482 4.009675 TGAAGTTGCAACTATTGGGCTAG 58.990 43.478 31.31 0.00 38.57 3.42
3392 5569 5.673337 TTATGAATTCATGCCTAACGAGC 57.327 39.130 27.59 0.00 37.15 5.03
3394 5571 1.261619 GAATTCATGCCTAACGAGCCG 59.738 52.381 0.00 0.00 0.00 5.52
3697 5875 3.614390 CGGAGCTATATTCCCGGAACTTC 60.614 52.174 0.73 0.00 38.42 3.01
3771 5949 1.757699 GATGGTGAGTGGTAGGAGGAC 59.242 57.143 0.00 0.00 0.00 3.85
3830 6008 2.301296 CTCCCGGAATGCATCTATGAGT 59.699 50.000 0.73 0.00 0.00 3.41
3831 6009 2.705658 TCCCGGAATGCATCTATGAGTT 59.294 45.455 0.73 0.00 0.00 3.01
3842 6020 6.382608 TGCATCTATGAGTTAGTTATCGCTC 58.617 40.000 0.00 0.00 0.00 5.03
3940 6118 1.678970 GTGCATCCAGTGGAACCCC 60.679 63.158 17.71 5.42 37.80 4.95
3944 6122 0.323725 CATCCAGTGGAACCCCAAGG 60.324 60.000 17.71 0.00 45.59 3.61
4096 6275 6.968904 CACCATGATTTTAGTCTACATGTTGC 59.031 38.462 2.30 0.00 37.29 4.17
4117 6296 3.056607 GCTTGGTATTGGACAGCACAAAT 60.057 43.478 0.00 0.00 0.00 2.32
4240 6420 4.820897 TCAGTAGTATGGTTGCTTGTCAG 58.179 43.478 0.00 0.00 0.00 3.51
4286 6466 5.426689 TCCTGACAGCTGAGATACAAAAT 57.573 39.130 23.35 0.00 0.00 1.82
4292 6475 6.481313 TGACAGCTGAGATACAAAATATCTGC 59.519 38.462 23.35 4.06 34.68 4.26
4390 6573 4.827835 CCATGAAGAAGATGAAGGCATGAT 59.172 41.667 0.00 0.00 35.02 2.45
4447 6630 9.436957 TTCTCCCGATATAAGAAAATGATTAGC 57.563 33.333 0.00 0.00 0.00 3.09
4472 6655 0.529378 CATGCTTTGCCTCCCAGAAC 59.471 55.000 0.00 0.00 0.00 3.01
4483 6666 1.417890 CTCCCAGAACACACACCTTCT 59.582 52.381 0.00 0.00 0.00 2.85
4539 6728 3.369147 CACTGCAGTTTTCTAGATCCGTG 59.631 47.826 18.94 0.00 0.00 4.94
4545 6734 4.003648 AGTTTTCTAGATCCGTGCCAAAG 58.996 43.478 0.00 0.00 0.00 2.77
4546 6735 3.973206 TTTCTAGATCCGTGCCAAAGA 57.027 42.857 0.00 0.00 0.00 2.52
4666 6856 2.480555 GAACACATGAAGGGCGCG 59.519 61.111 0.00 0.00 0.00 6.86
4743 6950 3.470888 CAGGAGGCCTACACCGGG 61.471 72.222 19.90 3.52 29.64 5.73
4802 7009 1.065491 AGATCATGCCGGCAACAACTA 60.065 47.619 36.33 15.40 0.00 2.24
4803 7010 1.331756 GATCATGCCGGCAACAACTAG 59.668 52.381 36.33 16.66 0.00 2.57
4804 7011 0.036164 TCATGCCGGCAACAACTAGT 59.964 50.000 36.33 11.92 0.00 2.57
4905 7112 3.231222 CGGAGTTAGGCGTACTTCG 57.769 57.895 8.05 8.05 38.18 3.79
4906 7113 0.449388 CGGAGTTAGGCGTACTTCGT 59.551 55.000 12.67 0.00 39.28 3.85
4934 7141 2.364647 GCCTCCACTACTATAAGGCGTT 59.635 50.000 0.00 0.00 42.74 4.84
4950 7157 1.503542 GTTGTCTCCCGCTGCAATG 59.496 57.895 0.00 0.00 0.00 2.82
4957 7164 2.672651 CCGCTGCAATGGGTGTGA 60.673 61.111 0.00 0.00 0.00 3.58
4958 7165 2.048023 CCGCTGCAATGGGTGTGAT 61.048 57.895 0.00 0.00 0.00 3.06
4978 7188 6.776116 TGTGATATACGTTACCCTTGAGATCT 59.224 38.462 0.00 0.00 0.00 2.75
4982 7192 4.246712 ACGTTACCCTTGAGATCTAGGA 57.753 45.455 12.47 0.00 40.59 2.94
4983 7193 4.805744 ACGTTACCCTTGAGATCTAGGAT 58.194 43.478 12.47 0.00 40.59 3.24
4984 7194 5.950023 ACGTTACCCTTGAGATCTAGGATA 58.050 41.667 12.47 0.00 40.59 2.59
4985 7195 5.769162 ACGTTACCCTTGAGATCTAGGATAC 59.231 44.000 12.47 6.79 40.59 2.24
5023 7233 1.534729 GGACTTTGCAAATCCGACCT 58.465 50.000 13.23 0.00 0.00 3.85
5059 7279 2.764314 GCGTCTGCGGGCATTGATT 61.764 57.895 0.00 0.00 38.78 2.57
5092 7315 2.803670 CGCGTCGTCATCCGTGTT 60.804 61.111 0.00 0.00 37.94 3.32
5096 7319 1.415374 CGTCGTCATCCGTGTTTCTT 58.585 50.000 0.00 0.00 37.94 2.52
5103 7326 6.474427 GTCGTCATCCGTGTTTCTTATATTCA 59.526 38.462 0.00 0.00 37.94 2.57
5107 7330 8.665685 GTCATCCGTGTTTCTTATATTCAAACT 58.334 33.333 0.00 0.00 32.28 2.66
5112 7335 8.601476 CCGTGTTTCTTATATTCAAACTCCTAC 58.399 37.037 0.00 0.00 32.28 3.18
5136 7360 4.556233 TCATACTATAGCATGCAACGTCC 58.444 43.478 21.98 0.00 0.00 4.79
5158 7382 5.127194 TCCATCAAACTACGTAGATCAGCTT 59.873 40.000 28.74 8.74 0.00 3.74
5218 7443 2.814919 ACCAAAGTTCACACAAACGACA 59.185 40.909 0.00 0.00 34.27 4.35
5344 7570 1.218316 GTGGAGGAGCGTCCGATTT 59.782 57.895 4.92 0.00 42.75 2.17
5348 7574 1.134907 GGAGGAGCGTCCGATTTGTTA 60.135 52.381 0.00 0.00 42.75 2.41
5358 7584 3.700038 GTCCGATTTGTTAGAGGAGGAGA 59.300 47.826 0.00 0.00 0.00 3.71
5359 7585 4.342665 GTCCGATTTGTTAGAGGAGGAGAT 59.657 45.833 0.00 0.00 0.00 2.75
5387 7616 1.595993 CGAAAGAGGAGGAGCCGACA 61.596 60.000 0.00 0.00 43.43 4.35
5396 7625 0.965866 AGGAGCCGACAATGACGAGA 60.966 55.000 6.69 0.00 0.00 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.609061 CCAGGGGCGTCATCATCATAC 60.609 57.143 0.00 0.00 0.00 2.39
4 5 0.976641 TATCCAGGGGCGTCATCATC 59.023 55.000 0.00 0.00 0.00 2.92
9 10 1.758440 GCTGATATCCAGGGGCGTCA 61.758 60.000 0.00 0.00 43.13 4.35
138 139 4.806247 AGAATCGTAGCATTACAAGAGTGC 59.194 41.667 0.00 0.00 39.10 4.40
162 163 8.932791 TGTTTCTTTTTCTATCATAAGGACGAC 58.067 33.333 0.00 0.00 0.00 4.34
191 192 3.173965 AGTGACTGCCACCTGTTATACT 58.826 45.455 0.00 0.00 46.87 2.12
302 335 6.971184 CCTTATGAGATGACAGCACAAATTTC 59.029 38.462 0.00 0.00 0.00 2.17
371 405 3.691118 TGTGGCAGAATAAGTGCATCTTC 59.309 43.478 5.04 0.00 43.12 2.87
432 528 4.214986 TGTATTGGCCATTCTTCGAAGA 57.785 40.909 23.74 23.74 0.00 2.87
443 539 2.896044 TCAGCACAATTTGTATTGGCCA 59.104 40.909 0.00 0.00 44.42 5.36
451 547 4.877378 ATCCATGTTCAGCACAATTTGT 57.123 36.364 0.00 0.00 39.50 2.83
462 558 6.047870 CCAAGAAAACACAAATCCATGTTCA 58.952 36.000 0.00 0.00 38.08 3.18
482 1586 9.578576 TCAAAAGATAAATCTATCATCCCCAAG 57.421 33.333 0.00 0.00 37.05 3.61
586 1690 5.654650 TGCGGAAATAAATAACTGATTGGGT 59.345 36.000 0.00 0.00 0.00 4.51
619 1723 1.051812 CCCGTCCCATCTTATCTGCT 58.948 55.000 0.00 0.00 0.00 4.24
678 1782 1.741770 CAGCCTCCTGCCGTGTTAC 60.742 63.158 0.00 0.00 42.71 2.50
770 1874 6.942576 ACTTACTCATCTTGGTTTGCTGTAAT 59.057 34.615 0.00 0.00 0.00 1.89
814 1921 3.059051 CGTGGCACCAAAATTCCAAATTG 60.059 43.478 12.86 0.00 0.00 2.32
824 1931 1.742831 GCATCTATCGTGGCACCAAAA 59.257 47.619 12.86 0.00 0.00 2.44
847 1954 0.249398 ACGCTGGGTATGGACAGAAC 59.751 55.000 0.00 0.00 36.86 3.01
864 1971 3.003171 TGTCATGTTCAAATGGTCACACG 59.997 43.478 0.00 0.00 0.00 4.49
985 2092 5.162075 GTGTTATAGTGGTCTGAGTGTGAC 58.838 45.833 0.00 0.00 0.00 3.67
1012 2119 0.895100 GGTTGTGAATGCAGCCTCCA 60.895 55.000 0.00 0.00 36.89 3.86
1022 2129 4.256920 CGAGGAGAATTCTGGTTGTGAAT 58.743 43.478 14.00 0.00 35.88 2.57
1056 2165 1.103398 GCCACTTGTGTTGAGCTGGT 61.103 55.000 0.00 0.00 0.00 4.00
1069 2178 6.899393 TTGATGAAATTAACAGAGCCACTT 57.101 33.333 0.00 0.00 0.00 3.16
1096 2205 8.408043 AAATGGAATATCTAAATGATTGGCGA 57.592 30.769 0.00 0.00 36.65 5.54
1211 2370 8.378565 TGGAAAGAAATTTAGTCATCTCTCTGT 58.621 33.333 0.00 0.00 0.00 3.41
1212 2371 8.783833 TGGAAAGAAATTTAGTCATCTCTCTG 57.216 34.615 0.00 0.00 0.00 3.35
1246 2408 4.511527 TGGCTGAGAAGAAAAGCTATGAG 58.488 43.478 0.00 0.00 37.12 2.90
1299 2461 2.586648 AGAAATCTTGGTCACCCCAC 57.413 50.000 0.00 0.00 45.19 4.61
1356 2518 1.521681 CGGAAACCGGATCTCAGGC 60.522 63.158 9.46 0.00 44.15 4.85
1536 2698 6.888632 AGATGAACTTCTGAACTTTATGGCAT 59.111 34.615 4.88 4.88 0.00 4.40
2211 3984 7.043458 CGCACAATTCTGAAACTTGTAAACATT 60.043 33.333 8.57 0.00 32.14 2.71
2333 4116 9.205719 CATCATCTGATAAAACTAGAGGACATG 57.794 37.037 0.00 0.00 34.58 3.21
2341 4124 4.153117 GCCCGCATCATCTGATAAAACTAG 59.847 45.833 0.00 0.00 32.63 2.57
2422 4216 7.125792 AGATTGATTAGGGTAAGGTAGTGTG 57.874 40.000 0.00 0.00 0.00 3.82
2750 4715 5.529430 TGAACCTGCAAATACGAAAGAAGAA 59.471 36.000 0.00 0.00 0.00 2.52
2753 4718 4.576873 TGTGAACCTGCAAATACGAAAGAA 59.423 37.500 0.00 0.00 0.00 2.52
2951 5127 7.713507 TGCATAAATACAGTGTACAGGTAATCC 59.286 37.037 4.80 0.00 0.00 3.01
3152 5329 2.624838 AGTTAACCTTGAACCGTCTCGA 59.375 45.455 0.88 0.00 0.00 4.04
3205 5382 0.393808 TTCCATTTGGTAGCTCGCCC 60.394 55.000 0.00 0.00 36.34 6.13
3224 5401 3.199508 AGCATCTTGACAGCTACAGGAAT 59.800 43.478 8.47 0.00 36.73 3.01
3305 5482 4.261031 GCGGACAATATTTGTATGGTGGAC 60.261 45.833 0.00 0.00 45.52 4.02
3392 5569 5.788450 AGAGAATATGTATTTCTCCAGCGG 58.212 41.667 9.23 0.00 0.00 5.52
3394 5571 5.347364 GCGAGAGAATATGTATTTCTCCAGC 59.653 44.000 9.23 10.75 32.48 4.85
3771 5949 3.073228 TCAGTCCTTGGGTCTGAGG 57.927 57.895 8.88 0.00 41.42 3.86
3830 6008 1.066605 GTCCTGGCGAGCGATAACTAA 59.933 52.381 0.00 0.00 0.00 2.24
3831 6009 0.666913 GTCCTGGCGAGCGATAACTA 59.333 55.000 0.00 0.00 0.00 2.24
3964 6142 3.137544 TCCCTGTCAACATGTTTACCACT 59.862 43.478 17.93 0.00 0.00 4.00
4096 6275 4.789012 ATTTGTGCTGTCCAATACCAAG 57.211 40.909 0.00 0.00 0.00 3.61
4286 6466 8.362464 ACAGAATATAAGGTAATCGGCAGATA 57.638 34.615 0.00 0.00 35.74 1.98
4292 6475 9.976511 TGAAACTACAGAATATAAGGTAATCGG 57.023 33.333 0.00 0.00 0.00 4.18
4390 6573 2.286872 GTAGATTCCGGAGTGACGAGA 58.713 52.381 3.25 0.00 35.47 4.04
4472 6655 1.691976 TGTAGGGACAGAAGGTGTGTG 59.308 52.381 0.00 0.00 40.56 3.82
4483 6666 5.640147 ACAGATCCAAAAATTGTAGGGACA 58.360 37.500 0.00 0.00 0.00 4.02
4539 6728 3.251972 CCAAGAGAGTGTCTTTCTTTGGC 59.748 47.826 0.00 0.00 43.54 4.52
4545 6734 4.329462 ACAGACCAAGAGAGTGTCTTTC 57.671 45.455 0.00 0.00 43.54 2.62
4546 6735 5.871396 TTACAGACCAAGAGAGTGTCTTT 57.129 39.130 0.00 0.00 43.54 2.52
4672 6862 2.500646 GCTCTGCTCCTCTGCCTC 59.499 66.667 0.00 0.00 0.00 4.70
4675 6865 4.527583 CCGGCTCTGCTCCTCTGC 62.528 72.222 0.00 0.00 0.00 4.26
4676 6866 2.757508 TCCGGCTCTGCTCCTCTG 60.758 66.667 0.00 0.00 0.00 3.35
4677 6867 2.757917 GTCCGGCTCTGCTCCTCT 60.758 66.667 0.00 0.00 0.00 3.69
4678 6868 4.200283 CGTCCGGCTCTGCTCCTC 62.200 72.222 0.00 0.00 0.00 3.71
4679 6869 4.742649 TCGTCCGGCTCTGCTCCT 62.743 66.667 0.00 0.00 0.00 3.69
4680 6870 2.962697 GAATCGTCCGGCTCTGCTCC 62.963 65.000 0.00 0.00 0.00 4.70
4681 6871 1.590259 GAATCGTCCGGCTCTGCTC 60.590 63.158 0.00 0.00 0.00 4.26
4682 6872 2.496817 GAATCGTCCGGCTCTGCT 59.503 61.111 0.00 0.00 0.00 4.24
4727 6925 4.798682 CCCCGGTGTAGGCCTCCT 62.799 72.222 9.68 0.00 37.71 3.69
4802 7009 1.213013 CGCTGCCGTCTCAAGTACT 59.787 57.895 0.00 0.00 0.00 2.73
4803 7010 0.388134 TTCGCTGCCGTCTCAAGTAC 60.388 55.000 0.00 0.00 35.54 2.73
4804 7011 0.388134 GTTCGCTGCCGTCTCAAGTA 60.388 55.000 0.00 0.00 35.54 2.24
4905 7112 0.108138 AGTAGTGGAGGCGCATTCAC 60.108 55.000 25.50 25.50 0.00 3.18
4906 7113 1.480789 TAGTAGTGGAGGCGCATTCA 58.519 50.000 10.83 3.35 0.00 2.57
4934 7141 2.046023 CCATTGCAGCGGGAGACA 60.046 61.111 0.00 0.00 0.00 3.41
4950 7157 4.099881 TCAAGGGTAACGTATATCACACCC 59.900 45.833 0.00 0.00 45.00 4.61
4957 7164 7.696981 TCCTAGATCTCAAGGGTAACGTATAT 58.303 38.462 11.01 0.00 33.40 0.86
4958 7165 7.083062 TCCTAGATCTCAAGGGTAACGTATA 57.917 40.000 11.01 0.00 33.40 1.47
4978 7188 5.279206 GCTGCAGATGCTCTTAAGTATCCTA 60.279 44.000 20.43 0.00 43.47 2.94
4982 7192 3.737850 GGCTGCAGATGCTCTTAAGTAT 58.262 45.455 20.43 0.00 42.66 2.12
4983 7193 2.481969 CGGCTGCAGATGCTCTTAAGTA 60.482 50.000 20.43 0.00 42.66 2.24
4984 7194 1.741732 CGGCTGCAGATGCTCTTAAGT 60.742 52.381 20.43 0.00 42.66 2.24
4985 7195 0.935898 CGGCTGCAGATGCTCTTAAG 59.064 55.000 20.43 0.00 42.66 1.85
4998 7208 0.733909 GATTTGCAAAGTCCGGCTGC 60.734 55.000 18.19 3.43 36.60 5.25
5020 7230 1.451387 CCGCGGGCATTTAAGAGGT 60.451 57.895 20.10 0.00 0.00 3.85
5023 7233 1.812093 CGTCCGCGGGCATTTAAGA 60.812 57.895 31.65 0.93 0.00 2.10
5046 7266 3.459965 GCCCAATCAATGCCCGCA 61.460 61.111 0.00 0.00 0.00 5.69
5054 7274 1.522668 CTTGAGACGTGCCCAATCAA 58.477 50.000 0.00 0.00 0.00 2.57
5059 7279 4.680237 CGGCTTGAGACGTGCCCA 62.680 66.667 8.15 0.00 42.66 5.36
5081 7304 8.665685 AGTTTGAATATAAGAAACACGGATGAC 58.334 33.333 0.00 0.00 32.96 3.06
5082 7305 8.786826 AGTTTGAATATAAGAAACACGGATGA 57.213 30.769 0.00 0.00 32.96 2.92
5103 7326 8.037758 GCATGCTATAGTATGATGTAGGAGTTT 58.962 37.037 28.64 0.00 39.98 2.66
5107 7330 7.323420 GTTGCATGCTATAGTATGATGTAGGA 58.677 38.462 28.64 4.66 39.98 2.94
5112 7335 5.062683 GGACGTTGCATGCTATAGTATGATG 59.937 44.000 28.64 18.14 39.98 3.07
5136 7360 5.172232 CGAAGCTGATCTACGTAGTTTGATG 59.828 44.000 21.53 9.77 37.78 3.07
5158 7382 6.112734 ACTATTGTGCAATTTCTATGTCCGA 58.887 36.000 2.56 0.00 32.50 4.55
5250 7475 4.290155 CGGAAGTGGTGAAGTTGATTTTG 58.710 43.478 0.00 0.00 0.00 2.44
5344 7570 3.280295 GACGACATCTCCTCCTCTAACA 58.720 50.000 0.00 0.00 0.00 2.41
5348 7574 0.253610 ACGACGACATCTCCTCCTCT 59.746 55.000 0.00 0.00 0.00 3.69
5372 7601 0.324738 TCATTGTCGGCTCCTCCTCT 60.325 55.000 0.00 0.00 0.00 3.69
5373 7602 0.179097 GTCATTGTCGGCTCCTCCTC 60.179 60.000 0.00 0.00 0.00 3.71
5374 7603 1.901085 GTCATTGTCGGCTCCTCCT 59.099 57.895 0.00 0.00 0.00 3.69
5382 7611 0.246635 AAGGGTCTCGTCATTGTCGG 59.753 55.000 3.59 0.00 0.00 4.79
5387 7616 0.250513 GCCTCAAGGGTCTCGTCATT 59.749 55.000 0.00 0.00 37.43 2.57
5396 7625 4.021925 GTCCAGCGCCTCAAGGGT 62.022 66.667 2.29 0.00 37.43 4.34


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

AutoCloner maintained by Alex Coulton.