Multiple sequence alignment - TraesCS5A01G211900

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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 TraesCS5A01G211900 chr5A 100.000 2696 0 0 1 2696 427088759 427086064 0.000000e+00 4979.0
1 TraesCS5A01G211900 chr5D 91.776 1836 95 19 833 2652 329509439 329511234 0.000000e+00 2503.0
2 TraesCS5A01G211900 chr5D 87.590 556 37 11 46 578 329508327 329508873 1.370000e-172 616.0
3 TraesCS5A01G211900 chr5B 93.112 1147 56 11 833 1971 382700511 382701642 0.000000e+00 1659.0
4 TraesCS5A01G211900 chr5B 90.173 346 24 4 288 632 382699926 382700262 2.460000e-120 442.0
5 TraesCS5A01G211900 chr5B 90.625 64 5 1 1648 1711 382730110 382730172 1.720000e-12 84.2


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 TraesCS5A01G211900 chr5A 427086064 427088759 2695 True 4979.0 4979 100.0000 1 2696 1 chr5A.!!$R1 2695
1 TraesCS5A01G211900 chr5D 329508327 329511234 2907 False 1559.5 2503 89.6830 46 2652 2 chr5D.!!$F1 2606
2 TraesCS5A01G211900 chr5B 382699926 382701642 1716 False 1050.5 1659 91.6425 288 1971 2 chr5B.!!$F2 1683

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
755 829 0.036164 TTGTGTTCCGCCTAGCACAT 59.964 50.0 3.92 0.0 40.82 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2648 3014 0.45541 GTGCAATTGATAAGCCGGCA 59.545 50.0 31.54 9.64 0.0 5.69 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
26 27 2.753055 TCAAACCGTGATCGATTGGA 57.247 45.000 16.36 0.00 39.71 3.53
27 28 3.260475 TCAAACCGTGATCGATTGGAT 57.740 42.857 16.36 4.68 39.71 3.41
28 29 4.394439 TCAAACCGTGATCGATTGGATA 57.606 40.909 16.36 0.28 39.71 2.59
29 30 4.368315 TCAAACCGTGATCGATTGGATAG 58.632 43.478 16.36 7.41 39.71 2.08
30 31 4.098807 TCAAACCGTGATCGATTGGATAGA 59.901 41.667 16.36 9.06 39.71 1.98
31 32 4.665833 AACCGTGATCGATTGGATAGAA 57.334 40.909 16.36 0.00 39.71 2.10
32 33 3.978687 ACCGTGATCGATTGGATAGAAC 58.021 45.455 16.36 0.00 39.71 3.01
33 34 2.980476 CCGTGATCGATTGGATAGAACG 59.020 50.000 0.00 0.77 39.71 3.95
34 35 3.550233 CCGTGATCGATTGGATAGAACGT 60.550 47.826 0.00 0.00 36.00 3.99
35 36 4.042398 CGTGATCGATTGGATAGAACGTT 58.958 43.478 0.00 0.00 39.71 3.99
36 37 4.146616 CGTGATCGATTGGATAGAACGTTC 59.853 45.833 20.71 20.71 39.71 3.95
37 38 5.041287 GTGATCGATTGGATAGAACGTTCA 58.959 41.667 28.78 15.65 34.82 3.18
38 39 5.174035 GTGATCGATTGGATAGAACGTTCAG 59.826 44.000 28.78 9.11 34.82 3.02
39 40 4.976224 TCGATTGGATAGAACGTTCAGA 57.024 40.909 28.78 17.08 0.00 3.27
40 41 4.669318 TCGATTGGATAGAACGTTCAGAC 58.331 43.478 28.78 17.87 0.00 3.51
41 42 6.012492 ATCGATTGGATAGAACGTTCAGACG 61.012 44.000 28.78 19.63 43.68 4.18
86 87 0.523072 ATGCTCGTGTCATGCCAAAC 59.477 50.000 0.00 0.00 0.00 2.93
87 88 1.210155 GCTCGTGTCATGCCAAACC 59.790 57.895 0.00 0.00 0.00 3.27
88 89 1.497278 CTCGTGTCATGCCAAACCG 59.503 57.895 0.00 0.00 0.00 4.44
89 90 0.948623 CTCGTGTCATGCCAAACCGA 60.949 55.000 0.00 0.00 0.00 4.69
90 91 0.321210 TCGTGTCATGCCAAACCGAT 60.321 50.000 0.00 0.00 0.00 4.18
91 92 1.066787 TCGTGTCATGCCAAACCGATA 60.067 47.619 0.00 0.00 0.00 2.92
92 93 1.939934 CGTGTCATGCCAAACCGATAT 59.060 47.619 0.00 0.00 0.00 1.63
93 94 3.127589 CGTGTCATGCCAAACCGATATA 58.872 45.455 0.00 0.00 0.00 0.86
94 95 3.059868 CGTGTCATGCCAAACCGATATAC 60.060 47.826 0.00 0.00 0.00 1.47
95 96 4.127171 GTGTCATGCCAAACCGATATACT 58.873 43.478 0.00 0.00 0.00 2.12
96 97 4.211374 GTGTCATGCCAAACCGATATACTC 59.789 45.833 0.00 0.00 0.00 2.59
97 98 3.746492 GTCATGCCAAACCGATATACTCC 59.254 47.826 0.00 0.00 0.00 3.85
98 99 2.519377 TGCCAAACCGATATACTCCG 57.481 50.000 0.00 0.00 0.00 4.63
115 116 2.761208 CTCCGTATCTCTGGTGGTTTCT 59.239 50.000 0.00 0.00 0.00 2.52
135 136 7.856556 GTTTCTTTTCTCAAACCAAACACAAA 58.143 30.769 0.00 0.00 0.00 2.83
136 137 7.414814 TTCTTTTCTCAAACCAAACACAAAC 57.585 32.000 0.00 0.00 0.00 2.93
137 138 6.516718 TCTTTTCTCAAACCAAACACAAACA 58.483 32.000 0.00 0.00 0.00 2.83
171 172 1.458445 GTACGCCGAAGTTGGAAGAAC 59.542 52.381 0.00 0.00 0.00 3.01
214 215 1.477295 AGCGAAACGGTTTCCCAAAAA 59.523 42.857 23.75 0.00 36.30 1.94
217 218 3.302805 GCGAAACGGTTTCCCAAAAATTG 60.303 43.478 23.75 10.42 36.30 2.32
238 239 2.636462 CACAAACGCGGCACATCA 59.364 55.556 12.47 0.00 0.00 3.07
250 251 3.574614 CGGCACATCACATATCACGATA 58.425 45.455 0.00 0.00 0.00 2.92
252 253 3.364920 GGCACATCACATATCACGATACG 59.635 47.826 0.00 0.00 0.00 3.06
279 300 7.005062 ACAAGAAAATAATTCTCGACCGATG 57.995 36.000 0.00 0.00 0.00 3.84
281 302 7.762615 ACAAGAAAATAATTCTCGACCGATGTA 59.237 33.333 0.00 0.00 0.00 2.29
316 337 1.134560 GGAGCCACGAAGTAGTACCAG 59.865 57.143 0.00 0.00 41.61 4.00
357 378 2.030562 CAGCCGGTTCCGTCAACT 59.969 61.111 1.90 0.00 35.06 3.16
358 379 1.597027 CAGCCGGTTCCGTCAACTT 60.597 57.895 1.90 0.00 35.06 2.66
373 394 2.892425 CTTGCCATCTCGACCGCC 60.892 66.667 0.00 0.00 0.00 6.13
411 432 2.435410 CATGCTGACGCTGGCTCA 60.435 61.111 0.00 0.00 36.97 4.26
469 490 0.468214 TCGATTCCGAGCATCTCCCT 60.468 55.000 0.00 0.00 40.30 4.20
470 491 0.038709 CGATTCCGAGCATCTCCCTC 60.039 60.000 0.00 0.00 38.22 4.30
481 502 3.610669 CTCCCTCGCAGATCCCCG 61.611 72.222 0.00 0.00 33.89 5.73
548 570 4.946157 ACAGCTCCCATTAACTGAAGATTG 59.054 41.667 0.00 0.00 34.25 2.67
549 571 3.950395 AGCTCCCATTAACTGAAGATTGC 59.050 43.478 0.00 0.00 0.00 3.56
560 582 3.005155 ACTGAAGATTGCCTCTTTTGCAC 59.995 43.478 0.00 0.00 44.42 4.57
578 600 2.594962 CGCACGCACCTCGACTTTT 61.595 57.895 0.00 0.00 41.67 2.27
581 603 2.251642 ACGCACCTCGACTTTTGCC 61.252 57.895 0.00 0.00 41.67 4.52
623 670 7.323420 GTCCAAGGATTTCTTTATTTTGGGAG 58.677 38.462 0.00 0.00 35.48 4.30
626 673 7.039082 CCAAGGATTTCTTTATTTTGGGAGACA 60.039 37.037 0.00 0.00 32.41 3.41
630 677 9.803315 GGATTTCTTTATTTTGGGAGACAATAC 57.197 33.333 0.00 0.00 39.21 1.89
652 717 4.877323 ACTTTTCAAGAAAGTGGACGAC 57.123 40.909 3.57 0.00 38.88 4.34
662 727 0.670546 AGTGGACGACAAATGCCTCG 60.671 55.000 0.00 0.00 35.96 4.63
663 728 1.375396 TGGACGACAAATGCCTCGG 60.375 57.895 0.00 0.00 34.07 4.63
678 743 3.325870 GCCTCGGCAGCTTTAAAATTTT 58.674 40.909 8.75 8.75 41.49 1.82
683 748 4.926832 TCGGCAGCTTTAAAATTTTAAGCC 59.073 37.500 26.61 26.61 37.11 4.35
744 818 3.412386 AGTAGCAACTGGATTGTGTTCC 58.588 45.455 0.00 0.00 40.77 3.62
755 829 0.036164 TTGTGTTCCGCCTAGCACAT 59.964 50.000 3.92 0.00 40.82 3.21
757 831 0.727398 GTGTTCCGCCTAGCACATTC 59.273 55.000 0.00 0.00 32.62 2.67
759 833 1.009829 GTTCCGCCTAGCACATTCTG 58.990 55.000 0.00 0.00 0.00 3.02
769 843 1.840181 GCACATTCTGCATGCATCAG 58.160 50.000 22.97 10.20 46.29 2.90
824 909 6.134535 TGTTTACCTAATCCAACATCCACT 57.865 37.500 0.00 0.00 0.00 4.00
857 1201 6.449698 ACTAAACTGCAAACTCCATCATTTG 58.550 36.000 0.00 0.00 38.57 2.32
885 1229 4.142004 CCGCCACCTATATATACACTTCCC 60.142 50.000 0.00 0.00 0.00 3.97
930 1274 7.120285 CACTATCCTCATCATTCACAACAAACT 59.880 37.037 0.00 0.00 0.00 2.66
933 1277 5.239306 TCCTCATCATTCACAACAAACTCAC 59.761 40.000 0.00 0.00 0.00 3.51
935 1279 6.063640 TCATCATTCACAACAAACTCACAG 57.936 37.500 0.00 0.00 0.00 3.66
941 1285 3.689161 TCACAACAAACTCACAGACCAAG 59.311 43.478 0.00 0.00 0.00 3.61
1169 1520 1.346722 CTCCTCCAACAAACTACCCGT 59.653 52.381 0.00 0.00 0.00 5.28
1419 1770 2.876219 GACAGGGACGAGGACGAC 59.124 66.667 0.00 0.00 42.66 4.34
1420 1771 1.970114 GACAGGGACGAGGACGACA 60.970 63.158 0.00 0.00 42.66 4.35
1733 2084 8.675705 TGATGTGTATAATGTGGTTAGGATTG 57.324 34.615 0.00 0.00 0.00 2.67
1793 2144 6.040729 CCTTCAATTTGGGCATGTCATATGTA 59.959 38.462 0.00 0.00 0.00 2.29
1794 2145 7.256048 CCTTCAATTTGGGCATGTCATATGTAT 60.256 37.037 0.00 0.00 0.00 2.29
1795 2146 6.983984 TCAATTTGGGCATGTCATATGTATG 58.016 36.000 0.00 14.37 35.04 2.39
1796 2147 6.550481 TCAATTTGGGCATGTCATATGTATGT 59.450 34.615 17.68 2.21 35.26 2.29
1797 2148 5.771153 TTTGGGCATGTCATATGTATGTG 57.229 39.130 17.68 9.00 35.26 3.21
1809 2160 9.426837 TGTCATATGTATGTGATGTGTATCATG 57.573 33.333 1.90 0.00 44.62 3.07
1941 2293 1.246056 TTCCATGGCTTGCACTGCTC 61.246 55.000 6.96 2.66 0.00 4.26
1986 2339 8.182227 CCCTTTTGTTCTCTCGGTTTATTTATC 58.818 37.037 0.00 0.00 0.00 1.75
1988 2341 9.760660 CTTTTGTTCTCTCGGTTTATTTATCTG 57.239 33.333 0.00 0.00 0.00 2.90
1989 2342 9.496873 TTTTGTTCTCTCGGTTTATTTATCTGA 57.503 29.630 0.00 0.00 0.00 3.27
1990 2343 8.475331 TTGTTCTCTCGGTTTATTTATCTGAC 57.525 34.615 0.00 0.00 0.00 3.51
1991 2344 6.750501 TGTTCTCTCGGTTTATTTATCTGACG 59.249 38.462 0.00 0.00 0.00 4.35
1992 2345 6.688637 TCTCTCGGTTTATTTATCTGACGA 57.311 37.500 0.00 0.00 0.00 4.20
1993 2346 7.092137 TCTCTCGGTTTATTTATCTGACGAA 57.908 36.000 0.00 0.00 0.00 3.85
1994 2347 6.971184 TCTCTCGGTTTATTTATCTGACGAAC 59.029 38.462 0.00 0.00 0.00 3.95
1997 2350 5.577945 TCGGTTTATTTATCTGACGAACACC 59.422 40.000 0.00 0.00 0.00 4.16
1998 2351 5.499652 CGGTTTATTTATCTGACGAACACCG 60.500 44.000 0.00 0.00 45.44 4.94
2014 2368 6.143278 ACGAACACCGCTTTCAAAATAAATTC 59.857 34.615 0.00 0.00 43.32 2.17
2017 2371 7.350110 ACACCGCTTTCAAAATAAATTCATG 57.650 32.000 0.00 0.00 0.00 3.07
2056 2416 5.188163 TCCGGTGGATGAGTTATCTTTGTAA 59.812 40.000 0.00 0.00 36.03 2.41
2057 2417 6.055588 CCGGTGGATGAGTTATCTTTGTAAT 58.944 40.000 0.00 0.00 36.03 1.89
2058 2418 7.070198 TCCGGTGGATGAGTTATCTTTGTAATA 59.930 37.037 0.00 0.00 36.03 0.98
2152 2514 7.265673 TCTCTTGTATACTTTATCTGGTGCAC 58.734 38.462 8.80 8.80 0.00 4.57
2209 2571 4.828939 GTCATTCCCAGCATCCATGATTTA 59.171 41.667 0.00 0.00 0.00 1.40
2210 2572 5.048224 GTCATTCCCAGCATCCATGATTTAG 60.048 44.000 0.00 0.00 0.00 1.85
2268 2630 4.426736 TCAATATGAGATGCAGGCTCAA 57.573 40.909 21.44 13.31 44.71 3.02
2270 2632 2.627515 TATGAGATGCAGGCTCAACC 57.372 50.000 21.44 0.00 44.71 3.77
2278 2640 1.798735 CAGGCTCAACCGAATGCAG 59.201 57.895 0.00 0.00 46.52 4.41
2289 2651 2.687935 ACCGAATGCAGAAAACTTGTGT 59.312 40.909 0.00 0.00 0.00 3.72
2331 2693 2.777459 TGGGCTCCTGGGTTTTAAAA 57.223 45.000 0.00 0.00 0.00 1.52
2342 2704 7.475299 TCCTGGGTTTTAAAAGAGTTCCATAT 58.525 34.615 0.00 0.00 0.00 1.78
2379 2741 8.397575 GATTTGGATCCTTAGGAATTTAGGAC 57.602 38.462 14.23 0.00 40.68 3.85
2398 2760 4.037923 AGGACCACTTTGCACACTATTTTG 59.962 41.667 0.00 0.00 0.00 2.44
2413 2775 8.526147 CACACTATTTTGGAGGAGAATTTTCAT 58.474 33.333 0.00 0.00 0.00 2.57
2483 2847 8.755018 CATTAAACGCTATTTGATCCAAATTCC 58.245 33.333 9.78 2.41 40.60 3.01
2652 3018 2.287103 CAGTGATGTGAAGATGATGCCG 59.713 50.000 0.00 0.00 0.00 5.69
2653 3019 1.600957 GTGATGTGAAGATGATGCCGG 59.399 52.381 0.00 0.00 0.00 6.13
2654 3020 0.590195 GATGTGAAGATGATGCCGGC 59.410 55.000 22.73 22.73 0.00 6.13
2655 3021 0.182061 ATGTGAAGATGATGCCGGCT 59.818 50.000 29.70 13.55 0.00 5.52
2656 3022 0.035152 TGTGAAGATGATGCCGGCTT 60.035 50.000 29.70 22.95 0.00 4.35
2657 3023 1.209261 TGTGAAGATGATGCCGGCTTA 59.791 47.619 29.70 14.27 0.00 3.09
2658 3024 2.158769 TGTGAAGATGATGCCGGCTTAT 60.159 45.455 29.70 18.59 0.00 1.73
2659 3025 2.481952 GTGAAGATGATGCCGGCTTATC 59.518 50.000 29.70 25.12 0.00 1.75
2660 3026 2.104622 TGAAGATGATGCCGGCTTATCA 59.895 45.455 26.31 26.31 37.68 2.15
2661 3027 2.936919 AGATGATGCCGGCTTATCAA 57.063 45.000 27.42 14.68 36.93 2.57
2662 3028 3.430042 AGATGATGCCGGCTTATCAAT 57.570 42.857 27.42 18.45 36.93 2.57
2663 3029 3.759581 AGATGATGCCGGCTTATCAATT 58.240 40.909 27.42 17.80 36.93 2.32
2664 3030 3.504906 AGATGATGCCGGCTTATCAATTG 59.495 43.478 27.42 0.00 36.93 2.32
2665 3031 1.337703 TGATGCCGGCTTATCAATTGC 59.662 47.619 29.70 7.21 30.84 3.56
2666 3032 1.337703 GATGCCGGCTTATCAATTGCA 59.662 47.619 29.70 1.81 0.00 4.08
2667 3033 0.455410 TGCCGGCTTATCAATTGCAC 59.545 50.000 29.70 0.00 0.00 4.57
2668 3034 0.455410 GCCGGCTTATCAATTGCACA 59.545 50.000 22.15 0.00 0.00 4.57
2669 3035 1.067516 GCCGGCTTATCAATTGCACAT 59.932 47.619 22.15 0.00 0.00 3.21
2670 3036 2.481795 GCCGGCTTATCAATTGCACATT 60.482 45.455 22.15 0.00 0.00 2.71
2671 3037 3.784338 CCGGCTTATCAATTGCACATTT 58.216 40.909 0.00 0.00 0.00 2.32
2672 3038 4.736168 GCCGGCTTATCAATTGCACATTTA 60.736 41.667 22.15 0.00 0.00 1.40
2673 3039 5.531634 CCGGCTTATCAATTGCACATTTAT 58.468 37.500 0.00 0.00 0.00 1.40
2674 3040 5.984926 CCGGCTTATCAATTGCACATTTATT 59.015 36.000 0.00 0.00 0.00 1.40
2675 3041 6.479660 CCGGCTTATCAATTGCACATTTATTT 59.520 34.615 0.00 0.00 0.00 1.40
2676 3042 7.651304 CCGGCTTATCAATTGCACATTTATTTA 59.349 33.333 0.00 0.00 0.00 1.40
2677 3043 9.029243 CGGCTTATCAATTGCACATTTATTTAA 57.971 29.630 0.00 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.753055 TCCAATCGATCACGGTTTGA 57.247 45.000 0.00 0.00 41.08 2.69
8 9 4.368315 TCTATCCAATCGATCACGGTTTG 58.632 43.478 0.00 0.00 41.08 2.93
9 10 4.665833 TCTATCCAATCGATCACGGTTT 57.334 40.909 0.00 0.00 41.08 3.27
10 11 4.369182 GTTCTATCCAATCGATCACGGTT 58.631 43.478 0.00 0.00 43.97 4.44
11 12 3.550233 CGTTCTATCCAATCGATCACGGT 60.550 47.826 0.00 0.00 40.21 4.83
12 13 2.980476 CGTTCTATCCAATCGATCACGG 59.020 50.000 0.00 0.00 40.21 4.94
13 14 3.629058 ACGTTCTATCCAATCGATCACG 58.371 45.455 0.00 0.62 36.12 4.35
14 15 5.041287 TGAACGTTCTATCCAATCGATCAC 58.959 41.667 27.32 0.00 30.98 3.06
15 16 5.067283 TCTGAACGTTCTATCCAATCGATCA 59.933 40.000 27.32 3.36 33.77 2.92
16 17 5.399892 GTCTGAACGTTCTATCCAATCGATC 59.600 44.000 27.32 0.00 31.92 3.69
17 18 5.282510 GTCTGAACGTTCTATCCAATCGAT 58.717 41.667 27.32 0.00 34.73 3.59
18 19 4.669318 GTCTGAACGTTCTATCCAATCGA 58.331 43.478 27.32 3.82 0.00 3.59
19 20 3.482472 CGTCTGAACGTTCTATCCAATCG 59.518 47.826 27.32 15.87 43.94 3.34
33 34 3.050275 GCTGCCCCACGTCTGAAC 61.050 66.667 0.00 0.00 0.00 3.18
34 35 3.555324 TGCTGCCCCACGTCTGAA 61.555 61.111 0.00 0.00 0.00 3.02
35 36 4.314440 GTGCTGCCCCACGTCTGA 62.314 66.667 0.00 0.00 0.00 3.27
41 42 2.672996 ATCAACGTGCTGCCCCAC 60.673 61.111 0.00 0.00 0.00 4.61
42 43 2.359850 GATCAACGTGCTGCCCCA 60.360 61.111 0.00 0.00 0.00 4.96
43 44 2.359850 TGATCAACGTGCTGCCCC 60.360 61.111 0.00 0.00 0.00 5.80
44 45 1.965930 TGTGATCAACGTGCTGCCC 60.966 57.895 0.00 0.00 0.00 5.36
45 46 1.207593 GTGTGATCAACGTGCTGCC 59.792 57.895 0.00 0.00 0.00 4.85
46 47 1.154599 CGTGTGATCAACGTGCTGC 60.155 57.895 17.02 0.00 0.00 5.25
47 48 0.436150 CTCGTGTGATCAACGTGCTG 59.564 55.000 21.46 11.88 0.00 4.41
48 49 0.313987 TCTCGTGTGATCAACGTGCT 59.686 50.000 21.46 0.00 0.00 4.40
94 95 2.761208 AGAAACCACCAGAGATACGGAG 59.239 50.000 0.00 0.00 0.00 4.63
95 96 2.816411 AGAAACCACCAGAGATACGGA 58.184 47.619 0.00 0.00 0.00 4.69
96 97 3.611766 AAGAAACCACCAGAGATACGG 57.388 47.619 0.00 0.00 0.00 4.02
97 98 5.238583 AGAAAAGAAACCACCAGAGATACG 58.761 41.667 0.00 0.00 0.00 3.06
98 99 6.231211 TGAGAAAAGAAACCACCAGAGATAC 58.769 40.000 0.00 0.00 0.00 2.24
115 116 6.049149 TGTGTTTGTGTTTGGTTTGAGAAAA 58.951 32.000 0.00 0.00 0.00 2.29
163 164 2.435069 TCCGTAACCACAAGTTCTTCCA 59.565 45.455 0.00 0.00 40.05 3.53
192 193 4.373771 GGGAAACCGTTTCGCTCT 57.626 55.556 25.85 0.00 45.79 4.09
214 215 2.953821 CCGCGTTTGTGCTCCAAT 59.046 55.556 4.92 0.00 31.81 3.16
217 218 4.683334 GTGCCGCGTTTGTGCTCC 62.683 66.667 4.92 0.00 0.00 4.70
224 225 1.330521 GATATGTGATGTGCCGCGTTT 59.669 47.619 4.92 0.00 0.00 3.60
238 239 8.692110 TTTTCTTGTTACGTATCGTGATATGT 57.308 30.769 16.54 16.54 43.65 2.29
250 251 7.411157 CGGTCGAGAATTATTTTCTTGTTACGT 60.411 37.037 0.00 0.00 32.91 3.57
252 253 7.956558 TCGGTCGAGAATTATTTTCTTGTTAC 58.043 34.615 0.00 0.00 32.91 2.50
279 300 2.156098 CTCCTGTAGGCCGAGAGATAC 58.844 57.143 11.86 0.96 34.44 2.24
281 302 0.825840 GCTCCTGTAGGCCGAGAGAT 60.826 60.000 11.86 0.00 34.44 2.75
316 337 1.303155 GGGCCTGCCTGAGATATGC 60.303 63.158 8.29 0.00 36.10 3.14
357 378 4.812476 CGGCGGTCGAGATGGCAA 62.812 66.667 0.00 0.00 42.43 4.52
411 432 0.773644 ATATCCCATTTCCGCAGCCT 59.226 50.000 0.00 0.00 0.00 4.58
481 502 3.595758 CCCGGAATTGGCATCGGC 61.596 66.667 0.73 0.00 41.02 5.54
548 570 2.427410 CGTGCGTGCAAAAGAGGC 60.427 61.111 0.00 0.00 0.00 4.70
549 571 2.427410 GCGTGCGTGCAAAAGAGG 60.427 61.111 0.00 0.00 34.15 3.69
560 582 2.594962 AAAAGTCGAGGTGCGTGCG 61.595 57.895 0.00 0.00 41.80 5.34
578 600 1.950909 CCTGTAAACAGAAAACCGGCA 59.049 47.619 11.69 0.00 46.59 5.69
581 603 3.207778 TGGACCTGTAAACAGAAAACCG 58.792 45.455 11.69 0.00 46.59 4.44
662 727 4.926832 TCGGCTTAAAATTTTAAAGCTGCC 59.073 37.500 26.61 26.61 37.11 4.85
663 728 6.460664 TTCGGCTTAAAATTTTAAAGCTGC 57.539 33.333 27.63 23.32 35.51 5.25
729 795 0.110486 AGGCGGAACACAATCCAGTT 59.890 50.000 0.00 0.00 39.61 3.16
731 797 1.656652 CTAGGCGGAACACAATCCAG 58.343 55.000 0.00 0.00 39.61 3.86
755 829 2.679450 GCAAAACTGATGCATGCAGAA 58.321 42.857 26.69 15.20 43.29 3.02
782 856 3.808728 ACAAGTGCACTGATACACAACT 58.191 40.909 22.49 0.00 39.30 3.16
783 857 4.552166 AACAAGTGCACTGATACACAAC 57.448 40.909 22.49 0.00 39.30 3.32
785 859 4.513692 GGTAAACAAGTGCACTGATACACA 59.486 41.667 22.49 0.00 39.30 3.72
857 1201 4.809426 GTGTATATATAGGTGGCGGAATGC 59.191 45.833 0.00 0.00 45.38 3.56
885 1229 4.366684 GGAGGGTGGGCTTGGGTG 62.367 72.222 0.00 0.00 0.00 4.61
930 1274 1.194781 GGAGGAGGCTTGGTCTGTGA 61.195 60.000 0.00 0.00 0.00 3.58
933 1277 0.251634 GAAGGAGGAGGCTTGGTCTG 59.748 60.000 0.00 0.00 0.00 3.51
935 1279 0.912006 AGGAAGGAGGAGGCTTGGTC 60.912 60.000 0.00 0.00 0.00 4.02
941 1285 2.683768 TCAAGATAGGAAGGAGGAGGC 58.316 52.381 0.00 0.00 0.00 4.70
1030 1381 1.908637 TAGAGGGGGAAGGCCATGGA 61.909 60.000 18.40 0.00 35.15 3.41
1366 1717 0.179205 CCGTCAACTACTCCGTCGTC 60.179 60.000 0.00 0.00 0.00 4.20
1371 1722 1.513586 GACGCCGTCAACTACTCCG 60.514 63.158 13.23 0.00 32.09 4.63
1380 1731 2.032634 GCATTTCCTGACGCCGTCA 61.033 57.895 20.04 20.04 40.50 4.35
1401 1752 2.745100 TCGTCCTCGTCCCTGTCG 60.745 66.667 0.00 0.00 38.33 4.35
1551 1902 2.822399 CGGTACCAGCCCAGATCC 59.178 66.667 13.54 0.00 0.00 3.36
1733 2084 2.039879 ACCCACCTAATCACAGTCCAAC 59.960 50.000 0.00 0.00 0.00 3.77
1793 2144 5.455755 CCCTCTTCCATGATACACATCACAT 60.456 44.000 0.00 0.00 43.89 3.21
1794 2145 4.141642 CCCTCTTCCATGATACACATCACA 60.142 45.833 0.00 0.00 43.89 3.58
1795 2146 4.384056 CCCTCTTCCATGATACACATCAC 58.616 47.826 0.00 0.00 43.89 3.06
1796 2147 3.181451 GCCCTCTTCCATGATACACATCA 60.181 47.826 0.00 0.00 45.15 3.07
1797 2148 3.406764 GCCCTCTTCCATGATACACATC 58.593 50.000 0.00 0.00 37.07 3.06
1809 2160 4.168291 CAGCCTCGGCCCTCTTCC 62.168 72.222 3.92 0.00 43.17 3.46
1930 2282 2.703416 TGTAATGGAGAGCAGTGCAAG 58.297 47.619 19.20 0.00 0.00 4.01
1941 2293 3.713764 AGGGTCAGAAGGATGTAATGGAG 59.286 47.826 0.00 0.00 0.00 3.86
1986 2339 0.934496 TTGAAAGCGGTGTTCGTCAG 59.066 50.000 0.00 0.00 41.72 3.51
1988 2341 2.461897 TTTTGAAAGCGGTGTTCGTC 57.538 45.000 0.00 0.00 41.72 4.20
1989 2342 4.555348 TTATTTTGAAAGCGGTGTTCGT 57.445 36.364 0.00 0.00 41.72 3.85
1990 2343 6.143118 TGAATTTATTTTGAAAGCGGTGTTCG 59.857 34.615 0.00 0.00 42.76 3.95
1991 2344 7.401484 TGAATTTATTTTGAAAGCGGTGTTC 57.599 32.000 0.00 0.00 0.00 3.18
1992 2345 7.571059 GCATGAATTTATTTTGAAAGCGGTGTT 60.571 33.333 0.00 0.00 0.00 3.32
1993 2346 6.128580 GCATGAATTTATTTTGAAAGCGGTGT 60.129 34.615 0.00 0.00 0.00 4.16
1994 2347 6.091169 AGCATGAATTTATTTTGAAAGCGGTG 59.909 34.615 0.00 0.00 0.00 4.94
1997 2350 7.842721 GCTAAGCATGAATTTATTTTGAAAGCG 59.157 33.333 0.00 0.00 0.00 4.68
1998 2351 8.876790 AGCTAAGCATGAATTTATTTTGAAAGC 58.123 29.630 0.00 0.00 0.00 3.51
2014 2368 2.606725 CGGAGAACTGAAGCTAAGCATG 59.393 50.000 0.00 0.00 0.00 4.06
2017 2371 1.066787 ACCGGAGAACTGAAGCTAAGC 60.067 52.381 9.46 0.00 0.00 3.09
2167 2529 7.147915 GGAATGACCTGCAAAACTCCATAAATA 60.148 37.037 0.00 0.00 35.41 1.40
2209 2571 9.061435 TGAATTTTTCCAAGTTTGTGAAAAACT 57.939 25.926 21.98 16.94 42.67 2.66
2210 2572 9.838975 ATGAATTTTTCCAAGTTTGTGAAAAAC 57.161 25.926 21.98 16.05 42.67 2.43
2268 2630 2.687935 ACACAAGTTTTCTGCATTCGGT 59.312 40.909 0.00 0.00 0.00 4.69
2270 2632 4.601019 AGAACACAAGTTTTCTGCATTCG 58.399 39.130 1.13 0.00 38.30 3.34
2278 2640 6.128282 TGTGAGAACTGAGAACACAAGTTTTC 60.128 38.462 0.00 0.00 38.30 2.29
2289 2651 6.016860 CCATTGTGATTTGTGAGAACTGAGAA 60.017 38.462 0.00 0.00 0.00 2.87
2331 2693 7.921041 TCCTCTACAAATCATATGGAACTCT 57.079 36.000 2.13 0.00 0.00 3.24
2368 2730 3.572255 TGTGCAAAGTGGTCCTAAATTCC 59.428 43.478 0.00 0.00 0.00 3.01
2379 2741 4.549458 CTCCAAAATAGTGTGCAAAGTGG 58.451 43.478 0.00 0.00 0.00 4.00
2398 2760 4.848357 TGAGTGGATGAAAATTCTCCTCC 58.152 43.478 0.00 0.00 0.00 4.30
2451 2814 8.773645 TGGATCAAATAGCGTTTAATGTCATAG 58.226 33.333 0.00 0.00 0.00 2.23
2452 2815 8.669946 TGGATCAAATAGCGTTTAATGTCATA 57.330 30.769 0.00 0.00 0.00 2.15
2453 2816 7.566760 TGGATCAAATAGCGTTTAATGTCAT 57.433 32.000 0.00 0.00 0.00 3.06
2483 2847 8.567285 AGAAACATAGGATTAGAAAACCACAG 57.433 34.615 0.00 0.00 0.00 3.66
2549 2915 8.677148 AGGCATTGGTTATATACTTGTAGTTG 57.323 34.615 0.00 0.00 0.00 3.16
2631 2997 2.287103 CGGCATCATCTTCACATCACTG 59.713 50.000 0.00 0.00 0.00 3.66
2645 3011 1.337703 GCAATTGATAAGCCGGCATCA 59.662 47.619 31.54 26.05 0.00 3.07
2648 3014 0.455410 GTGCAATTGATAAGCCGGCA 59.545 50.000 31.54 9.64 0.00 5.69


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

AutoCloner maintained by Alex Coulton.