Multiple sequence alignment - TraesCS2A01G309700

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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 TraesCS2A01G309700 chr2A 100.000 3957 0 0 1 3957 532868753 532864797 0.000000e+00 7308
1 TraesCS2A01G309700 chr2D 90.428 4064 165 86 1 3957 394801510 394797564 0.000000e+00 5144
2 TraesCS2A01G309700 chr2B 89.448 3753 167 96 317 3957 467873630 467869995 0.000000e+00 4525
3 TraesCS2A01G309700 chr2B 85.758 330 16 12 1 326 467873965 467873663 1.770000e-83 320


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 TraesCS2A01G309700 chr2A 532864797 532868753 3956 True 7308.0 7308 100.000 1 3957 1 chr2A.!!$R1 3956
1 TraesCS2A01G309700 chr2D 394797564 394801510 3946 True 5144.0 5144 90.428 1 3957 1 chr2D.!!$R1 3956
2 TraesCS2A01G309700 chr2B 467869995 467873965 3970 True 2422.5 4525 87.603 1 3957 2 chr2B.!!$R1 3956

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
847 945 0.252012 CCTCTGACCTCACCTCACCT 60.252 60.0 0.0 0.0 0.00 4.00 F
1447 1589 0.035739 TCAAGGACGGCAAGGTAACC 59.964 55.0 0.0 0.0 37.17 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2154 2343 0.036858 GCTCGAGTGAAGGAAAGGCT 60.037 55.0 15.13 0.0 0.00 4.58 R
3137 3346 0.246910 GGGGTTCTTCCTCGACTCAC 59.753 60.0 0.00 0.0 36.25 3.51 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
43 44 7.544804 AGATGCAGTGTCATATCTGGTTATA 57.455 36.000 0.00 0.00 32.94 0.98
44 45 8.143673 AGATGCAGTGTCATATCTGGTTATAT 57.856 34.615 0.00 0.00 32.94 0.86
60 61 9.487442 TCTGGTTATATGCATATATCACCACTA 57.513 33.333 30.06 22.67 43.57 2.74
69 70 3.843893 ATATCACCACTAGCATGTGCA 57.156 42.857 7.83 0.00 45.16 4.57
77 78 2.352651 CACTAGCATGTGCACACCATAC 59.647 50.000 24.37 9.89 45.16 2.39
81 82 1.066002 GCATGTGCACACCATACCATC 59.934 52.381 24.37 0.00 41.59 3.51
82 83 2.367486 CATGTGCACACCATACCATCA 58.633 47.619 24.37 0.00 0.00 3.07
83 84 2.804986 TGTGCACACCATACCATCAT 57.195 45.000 17.42 0.00 0.00 2.45
124 125 7.094890 GCACTGAAGCAGCAGAAACATATATAT 60.095 37.037 12.11 0.00 39.20 0.86
125 126 9.428097 CACTGAAGCAGCAGAAACATATATATA 57.572 33.333 12.11 0.00 39.20 0.86
207 208 3.769369 ATCTCCAGCCAGCGCCATG 62.769 63.158 2.29 0.00 34.57 3.66
208 209 4.478371 CTCCAGCCAGCGCCATGA 62.478 66.667 2.29 0.00 34.57 3.07
209 210 3.769369 CTCCAGCCAGCGCCATGAT 62.769 63.158 2.29 0.00 34.57 2.45
210 211 2.111669 CCAGCCAGCGCCATGATA 59.888 61.111 2.29 0.00 34.57 2.15
211 212 1.526686 CCAGCCAGCGCCATGATAA 60.527 57.895 2.29 0.00 34.57 1.75
212 213 0.892358 CCAGCCAGCGCCATGATAAT 60.892 55.000 2.29 0.00 34.57 1.28
213 214 1.611410 CCAGCCAGCGCCATGATAATA 60.611 52.381 2.29 0.00 34.57 0.98
214 215 2.153645 CAGCCAGCGCCATGATAATAA 58.846 47.619 2.29 0.00 34.57 1.40
215 216 2.161012 CAGCCAGCGCCATGATAATAAG 59.839 50.000 2.29 0.00 34.57 1.73
216 217 2.038952 AGCCAGCGCCATGATAATAAGA 59.961 45.455 2.29 0.00 34.57 2.10
217 218 2.813754 GCCAGCGCCATGATAATAAGAA 59.186 45.455 2.29 0.00 0.00 2.52
218 219 3.253188 GCCAGCGCCATGATAATAAGAAA 59.747 43.478 2.29 0.00 0.00 2.52
219 220 4.261572 GCCAGCGCCATGATAATAAGAAAA 60.262 41.667 2.29 0.00 0.00 2.29
220 221 5.735922 GCCAGCGCCATGATAATAAGAAAAA 60.736 40.000 2.29 0.00 0.00 1.94
221 222 5.916883 CCAGCGCCATGATAATAAGAAAAAG 59.083 40.000 2.29 0.00 0.00 2.27
222 223 5.400485 CAGCGCCATGATAATAAGAAAAAGC 59.600 40.000 2.29 0.00 0.00 3.51
223 224 5.067674 AGCGCCATGATAATAAGAAAAAGCA 59.932 36.000 2.29 0.00 0.00 3.91
224 225 5.748152 GCGCCATGATAATAAGAAAAAGCAA 59.252 36.000 0.00 0.00 0.00 3.91
248 249 1.530655 AAGGCAGGAAACGGTTGGG 60.531 57.895 0.00 0.00 0.00 4.12
282 283 1.136252 CGAATCCACGTGCTGACTTTG 60.136 52.381 10.91 0.00 0.00 2.77
294 295 2.076863 CTGACTTTGTTTAGCCCCTCG 58.923 52.381 0.00 0.00 0.00 4.63
295 296 1.271163 TGACTTTGTTTAGCCCCTCGG 60.271 52.381 0.00 0.00 0.00 4.63
359 405 7.308951 CGGGTCAAATGGTTTTCAATTAGTACT 60.309 37.037 0.00 0.00 0.00 2.73
360 406 9.016438 GGGTCAAATGGTTTTCAATTAGTACTA 57.984 33.333 0.00 0.00 0.00 1.82
361 407 9.836076 GGTCAAATGGTTTTCAATTAGTACTAC 57.164 33.333 0.91 0.00 0.00 2.73
364 410 9.755064 CAAATGGTTTTCAATTAGTACTACGAG 57.245 33.333 0.91 0.00 0.00 4.18
401 447 4.031426 CACCAACGCTAAGATAACGAGAAC 59.969 45.833 0.00 0.00 0.00 3.01
402 448 3.239941 CCAACGCTAAGATAACGAGAACG 59.760 47.826 0.00 0.00 45.75 3.95
408 454 5.548250 GCTAAGATAACGAGAACGGTTTTG 58.452 41.667 0.00 0.00 44.46 2.44
419 465 2.573340 GGTTTTGCTGGCCGATGG 59.427 61.111 0.00 0.00 0.00 3.51
427 477 1.908619 TGCTGGCCGATGGTATGATAT 59.091 47.619 0.00 0.00 0.00 1.63
428 478 2.283298 GCTGGCCGATGGTATGATATG 58.717 52.381 0.00 0.00 0.00 1.78
429 479 2.093500 GCTGGCCGATGGTATGATATGA 60.093 50.000 0.00 0.00 0.00 2.15
430 480 3.432749 GCTGGCCGATGGTATGATATGAT 60.433 47.826 0.00 0.00 0.00 2.45
431 481 4.124970 CTGGCCGATGGTATGATATGATG 58.875 47.826 0.00 0.00 0.00 3.07
508 560 2.357034 CTGGTGGTGTCGAACGGG 60.357 66.667 0.00 0.00 0.00 5.28
590 665 2.191846 AGGAGGGGGAGGGGAAAGA 61.192 63.158 0.00 0.00 0.00 2.52
591 666 1.230182 GGAGGGGGAGGGGAAAGAA 60.230 63.158 0.00 0.00 0.00 2.52
592 667 0.849540 GGAGGGGGAGGGGAAAGAAA 60.850 60.000 0.00 0.00 0.00 2.52
593 668 0.626382 GAGGGGGAGGGGAAAGAAAG 59.374 60.000 0.00 0.00 0.00 2.62
667 742 2.040606 TGGGCCCACTACTCCTCC 59.959 66.667 24.45 0.00 0.00 4.30
676 751 2.158667 CCACTACTCCTCCTCTCTCTCC 60.159 59.091 0.00 0.00 0.00 3.71
728 826 4.179599 GGAGGGGAGGGGAGGAGG 62.180 77.778 0.00 0.00 0.00 4.30
774 872 2.428171 CCGGGTCATCAAATCAAATGCT 59.572 45.455 0.00 0.00 0.00 3.79
782 880 5.294306 TCATCAAATCAAATGCTCGTACTCC 59.706 40.000 0.00 0.00 0.00 3.85
841 939 4.459089 GCCGCCTCTGACCTCACC 62.459 72.222 0.00 0.00 0.00 4.02
842 940 2.681778 CCGCCTCTGACCTCACCT 60.682 66.667 0.00 0.00 0.00 4.00
843 941 2.716017 CCGCCTCTGACCTCACCTC 61.716 68.421 0.00 0.00 0.00 3.85
844 942 1.979155 CGCCTCTGACCTCACCTCA 60.979 63.158 0.00 0.00 0.00 3.86
845 943 1.594310 GCCTCTGACCTCACCTCAC 59.406 63.158 0.00 0.00 0.00 3.51
846 944 1.893919 GCCTCTGACCTCACCTCACC 61.894 65.000 0.00 0.00 0.00 4.02
847 945 0.252012 CCTCTGACCTCACCTCACCT 60.252 60.000 0.00 0.00 0.00 4.00
848 946 1.181786 CTCTGACCTCACCTCACCTC 58.818 60.000 0.00 0.00 0.00 3.85
849 947 0.482887 TCTGACCTCACCTCACCTCA 59.517 55.000 0.00 0.00 0.00 3.86
850 948 0.605589 CTGACCTCACCTCACCTCAC 59.394 60.000 0.00 0.00 0.00 3.51
851 949 0.832135 TGACCTCACCTCACCTCACC 60.832 60.000 0.00 0.00 0.00 4.02
852 950 0.543174 GACCTCACCTCACCTCACCT 60.543 60.000 0.00 0.00 0.00 4.00
853 951 0.543174 ACCTCACCTCACCTCACCTC 60.543 60.000 0.00 0.00 0.00 3.85
854 952 0.542938 CCTCACCTCACCTCACCTCA 60.543 60.000 0.00 0.00 0.00 3.86
855 953 1.566211 CTCACCTCACCTCACCTCAT 58.434 55.000 0.00 0.00 0.00 2.90
897 995 2.279741 GCACTCGCAGTCATAATTCCA 58.720 47.619 0.00 0.00 38.36 3.53
902 1000 5.403766 CACTCGCAGTCATAATTCCATCTAC 59.596 44.000 0.00 0.00 0.00 2.59
947 1053 4.079850 CGAGGACCTGCTGCTGCT 62.080 66.667 17.00 0.00 40.48 4.24
949 1055 4.719106 AGGACCTGCTGCTGCTGC 62.719 66.667 22.51 22.51 40.48 5.25
950 1056 4.719106 GGACCTGCTGCTGCTGCT 62.719 66.667 27.67 11.62 40.48 4.24
953 1059 4.717313 CCTGCTGCTGCTGCTGGA 62.717 66.667 36.74 17.94 45.18 3.86
971 1077 3.165875 TGGAGTTTGTCTGGTAGAGAGG 58.834 50.000 0.00 0.00 0.00 3.69
972 1078 3.181422 TGGAGTTTGTCTGGTAGAGAGGA 60.181 47.826 0.00 0.00 0.00 3.71
973 1079 3.445805 GGAGTTTGTCTGGTAGAGAGGAG 59.554 52.174 0.00 0.00 0.00 3.69
974 1080 4.337145 GAGTTTGTCTGGTAGAGAGGAGA 58.663 47.826 0.00 0.00 0.00 3.71
975 1081 4.340617 AGTTTGTCTGGTAGAGAGGAGAG 58.659 47.826 0.00 0.00 0.00 3.20
976 1082 3.374042 TTGTCTGGTAGAGAGGAGAGG 57.626 52.381 0.00 0.00 0.00 3.69
977 1083 2.563406 TGTCTGGTAGAGAGGAGAGGA 58.437 52.381 0.00 0.00 0.00 3.71
978 1084 2.507886 TGTCTGGTAGAGAGGAGAGGAG 59.492 54.545 0.00 0.00 0.00 3.69
979 1085 2.775384 GTCTGGTAGAGAGGAGAGGAGA 59.225 54.545 0.00 0.00 0.00 3.71
980 1086 3.045634 TCTGGTAGAGAGGAGAGGAGAG 58.954 54.545 0.00 0.00 0.00 3.20
1144 1256 0.396278 CCCTTCCTTCCCTTCCATGC 60.396 60.000 0.00 0.00 0.00 4.06
1147 1259 1.006400 CTTCCTTCCCTTCCATGCCTT 59.994 52.381 0.00 0.00 0.00 4.35
1148 1260 1.084018 TCCTTCCCTTCCATGCCTTT 58.916 50.000 0.00 0.00 0.00 3.11
1149 1261 1.005924 TCCTTCCCTTCCATGCCTTTC 59.994 52.381 0.00 0.00 0.00 2.62
1150 1262 1.006400 CCTTCCCTTCCATGCCTTTCT 59.994 52.381 0.00 0.00 0.00 2.52
1151 1263 2.558350 CCTTCCCTTCCATGCCTTTCTT 60.558 50.000 0.00 0.00 0.00 2.52
1152 1264 2.999185 TCCCTTCCATGCCTTTCTTT 57.001 45.000 0.00 0.00 0.00 2.52
1153 1265 4.344104 CTTCCCTTCCATGCCTTTCTTTA 58.656 43.478 0.00 0.00 0.00 1.85
1154 1266 3.968265 TCCCTTCCATGCCTTTCTTTAG 58.032 45.455 0.00 0.00 0.00 1.85
1155 1267 3.591527 TCCCTTCCATGCCTTTCTTTAGA 59.408 43.478 0.00 0.00 0.00 2.10
1156 1268 4.230502 TCCCTTCCATGCCTTTCTTTAGAT 59.769 41.667 0.00 0.00 0.00 1.98
1167 1279 8.641498 TGCCTTTCTTTAGATTGAATTCTCTT 57.359 30.769 7.05 0.00 0.00 2.85
1168 1280 8.734386 TGCCTTTCTTTAGATTGAATTCTCTTC 58.266 33.333 7.05 1.28 0.00 2.87
1181 1293 1.521457 CTCTTCAATGGCGCGGCTA 60.521 57.895 33.23 19.80 0.00 3.93
1229 1341 3.829886 TTGCTCTGTTAATTTGCTCGG 57.170 42.857 0.00 0.00 0.00 4.63
1312 1424 1.584495 CGATCGTCATCGCCCCATA 59.416 57.895 7.03 0.00 45.28 2.74
1313 1425 0.038618 CGATCGTCATCGCCCCATAA 60.039 55.000 7.03 0.00 45.28 1.90
1320 1434 4.020573 TCGTCATCGCCCCATAATTAATCT 60.021 41.667 0.00 0.00 36.96 2.40
1347 1487 4.738998 TCCCCATTGCTGCCACGG 62.739 66.667 0.00 0.00 0.00 4.94
1374 1516 8.014322 TGCTCTGTACTAAAATCTTAACAACG 57.986 34.615 0.00 0.00 0.00 4.10
1379 1521 9.741168 CTGTACTAAAATCTTAACAACGTCATG 57.259 33.333 0.00 0.00 0.00 3.07
1447 1589 0.035739 TCAAGGACGGCAAGGTAACC 59.964 55.000 0.00 0.00 37.17 2.85
1501 1654 1.661112 GCCTCGCATTCAGTACTTCAC 59.339 52.381 0.00 0.00 0.00 3.18
1504 1657 2.926200 CTCGCATTCAGTACTTCACCAG 59.074 50.000 0.00 0.00 0.00 4.00
1566 1719 2.101783 CACTTTGGCTATCCATTGGCA 58.898 47.619 0.00 0.00 43.05 4.92
1570 1723 0.557238 TGGCTATCCATTGGCACCAT 59.443 50.000 0.00 0.00 37.47 3.55
1700 1864 2.028925 AAAGGCCGCCGCTTTTTG 59.971 55.556 3.05 0.00 41.11 2.44
1846 2010 9.372369 GCAGGGTAAATAATAATCTGCTAGTAG 57.628 37.037 0.63 0.63 41.75 2.57
1927 2091 0.250234 TCACTGACTACTGCATGCCC 59.750 55.000 16.68 0.00 0.00 5.36
2040 2228 2.133520 AGATGTCCAATGCTCCCAGAT 58.866 47.619 0.00 0.00 0.00 2.90
2055 2244 8.593945 TGCTCCCAGATTTCATTACTAATTTT 57.406 30.769 0.00 0.00 0.00 1.82
2101 2290 1.048724 TCTCAAGCCTATCCCGGTGG 61.049 60.000 0.00 0.00 0.00 4.61
2151 2340 2.210424 GATCAGCAGGTGAGCCTCT 58.790 57.895 6.60 0.00 44.97 3.69
2152 2341 0.104671 GATCAGCAGGTGAGCCTCTC 59.895 60.000 6.60 0.00 44.97 3.20
2153 2342 0.616964 ATCAGCAGGTGAGCCTCTCA 60.617 55.000 8.56 0.00 44.97 3.27
2154 2343 0.833409 TCAGCAGGTGAGCCTCTCAA 60.833 55.000 0.00 0.00 44.97 3.02
2155 2344 0.391395 CAGCAGGTGAGCCTCTCAAG 60.391 60.000 0.00 0.00 44.97 3.02
2161 2357 1.447945 GTGAGCCTCTCAAGCCTTTC 58.552 55.000 0.00 0.00 42.46 2.62
2202 2398 4.891627 TTTGTTCAAAGTCGATGAAGCA 57.108 36.364 0.23 0.76 37.46 3.91
2284 2481 7.769044 TCATGGGTCTAAAGCTCAGTTAATAAC 59.231 37.037 0.00 0.00 0.00 1.89
2325 2522 3.125146 TGCTTGCTGCTTCAGTAAATACG 59.875 43.478 0.00 0.00 43.37 3.06
2361 2558 2.749441 GCTGCCTGTCCTTGCTCC 60.749 66.667 0.00 0.00 0.00 4.70
2377 2574 5.456619 CCTTGCTCCTCCCATTATGTATCAA 60.457 44.000 0.00 0.00 0.00 2.57
2447 2644 6.142798 CAGTGCATTCATTGTGTCTTTGTAAC 59.857 38.462 0.00 0.00 0.00 2.50
2498 2700 3.256136 AGCTGATACCTGATAGTAACCGC 59.744 47.826 0.00 0.00 0.00 5.68
2673 2875 0.531532 ATAGCTGCTGTCGATGGCAC 60.532 55.000 13.43 8.38 34.57 5.01
2759 2965 0.379669 ATTACCGCACCGTCGTCTAG 59.620 55.000 0.00 0.00 0.00 2.43
2809 3018 2.111756 CTTCGCTTGCTGTTGTGTTTC 58.888 47.619 0.00 0.00 0.00 2.78
2818 3027 3.128589 TGCTGTTGTGTTTCTTTCAGGTC 59.871 43.478 0.00 0.00 0.00 3.85
3143 3352 0.890996 CCTTGTTGGGCTGGTGAGTC 60.891 60.000 0.00 0.00 0.00 3.36
3344 3553 3.698029 TGAGAAAAGAACAGCACAAGC 57.302 42.857 0.00 0.00 42.56 4.01
3454 3663 3.057736 CCGTCTATGTATTGTACTCCCGG 60.058 52.174 0.00 0.00 0.00 5.73
3457 3666 5.048224 CGTCTATGTATTGTACTCCCGGATT 60.048 44.000 0.73 0.00 0.00 3.01
3608 3820 0.698238 CAAAGGTGGGTGAGGATCCA 59.302 55.000 15.82 0.00 0.00 3.41
3621 3833 4.889409 GTGAGGATCCAAGCCATTGAAATA 59.111 41.667 15.82 0.00 38.83 1.40
3669 3882 1.765230 CCCGTCTTCCTACTGCTACT 58.235 55.000 0.00 0.00 0.00 2.57
3670 3883 1.405821 CCCGTCTTCCTACTGCTACTG 59.594 57.143 0.00 0.00 0.00 2.74
3671 3884 2.093106 CCGTCTTCCTACTGCTACTGT 58.907 52.381 0.00 0.00 0.00 3.55
3675 3888 4.155462 CGTCTTCCTACTGCTACTGTTGTA 59.845 45.833 0.00 0.00 0.00 2.41
3676 3889 5.163642 CGTCTTCCTACTGCTACTGTTGTAT 60.164 44.000 0.00 0.00 0.00 2.29
3682 3897 8.942338 TCCTACTGCTACTGTTGTATTTTATG 57.058 34.615 0.00 0.00 0.00 1.90
3696 3911 9.677567 GTTGTATTTTATGGTTGTATGCATAGG 57.322 33.333 6.67 0.00 0.00 2.57
3713 3928 0.538287 AGGTGCAAGTTCCTTCTGCC 60.538 55.000 0.00 0.00 0.00 4.85
3714 3929 0.823356 GGTGCAAGTTCCTTCTGCCA 60.823 55.000 0.00 0.00 0.00 4.92
3729 3944 4.299586 TCTGCCATTCTACATTTCACCA 57.700 40.909 0.00 0.00 0.00 4.17
3857 4072 5.301551 ACATTAGTTGGAATTGTCAGCAACA 59.698 36.000 0.00 0.00 37.44 3.33
3862 4077 3.146066 TGGAATTGTCAGCAACAGTACC 58.854 45.455 0.00 0.00 39.58 3.34
3865 4080 3.769739 ATTGTCAGCAACAGTACCTGA 57.230 42.857 0.00 0.12 39.58 3.86
3926 4141 9.895138 AATAAAATGAAGGAGCAGCATAAAAAT 57.105 25.926 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 5.878669 CACATGCTAGTGGTGATATATGCAT 59.121 40.000 3.79 3.79 39.99 3.96
44 45 5.240121 CACATGCTAGTGGTGATATATGCA 58.760 41.667 0.00 0.00 35.88 3.96
53 54 0.518636 GTGTGCACATGCTAGTGGTG 59.481 55.000 24.69 6.30 42.66 4.17
60 61 0.038021 TGGTATGGTGTGCACATGCT 59.962 50.000 24.69 12.60 42.66 3.79
69 70 4.623886 GCGGATATGATGATGGTATGGTGT 60.624 45.833 0.00 0.00 0.00 4.16
77 78 1.091771 GGCCGCGGATATGATGATGG 61.092 60.000 33.48 0.00 0.00 3.51
81 82 2.393768 GCTGGCCGCGGATATGATG 61.394 63.158 33.48 11.67 0.00 3.07
82 83 2.046892 GCTGGCCGCGGATATGAT 60.047 61.111 33.48 0.00 0.00 2.45
83 84 3.545574 TGCTGGCCGCGGATATGA 61.546 61.111 33.48 5.81 43.27 2.15
124 125 2.559231 TGCGTATCCTGCGGATTATGTA 59.441 45.455 13.95 3.76 39.79 2.29
125 126 1.343142 TGCGTATCCTGCGGATTATGT 59.657 47.619 13.95 0.00 39.79 2.29
224 225 1.828595 ACCGTTTCCTGCCTTGTTTTT 59.171 42.857 0.00 0.00 0.00 1.94
233 234 2.613506 CGTCCCAACCGTTTCCTGC 61.614 63.158 0.00 0.00 0.00 4.85
248 249 3.836176 ATTCGGCGCGGGATACGTC 62.836 63.158 15.48 0.00 46.52 4.34
305 310 2.356313 GATCGCGGGCATGATCGT 60.356 61.111 6.13 0.00 32.46 3.73
359 405 5.834169 TGGTGATTATTATGTTCGCTCGTA 58.166 37.500 0.00 0.00 0.00 3.43
360 406 4.689071 TGGTGATTATTATGTTCGCTCGT 58.311 39.130 0.00 0.00 0.00 4.18
361 407 5.432157 GTTGGTGATTATTATGTTCGCTCG 58.568 41.667 0.00 0.00 0.00 5.03
364 410 3.966218 GCGTTGGTGATTATTATGTTCGC 59.034 43.478 0.00 0.00 0.00 4.70
395 441 1.082104 GCCAGCAAAACCGTTCTCG 60.082 57.895 0.00 0.00 0.00 4.04
402 448 0.963355 TACCATCGGCCAGCAAAACC 60.963 55.000 2.24 0.00 0.00 3.27
408 454 2.093500 TCATATCATACCATCGGCCAGC 60.093 50.000 2.24 0.00 0.00 4.85
419 465 5.319139 GCGTTGCATCACATCATATCATAC 58.681 41.667 0.00 0.00 0.00 2.39
427 477 1.496835 CACGCGTTGCATCACATCA 59.503 52.632 10.22 0.00 0.00 3.07
428 478 1.226101 CCACGCGTTGCATCACATC 60.226 57.895 10.22 0.00 0.00 3.06
429 479 2.869646 CCACGCGTTGCATCACAT 59.130 55.556 10.22 0.00 0.00 3.21
430 480 4.024143 GCCACGCGTTGCATCACA 62.024 61.111 28.17 0.00 0.00 3.58
476 526 2.892425 CAGAGAATCGCCACCGGC 60.892 66.667 0.00 0.00 46.75 6.13
508 560 0.541063 TTTTCTCCCTTTTCCCCGGC 60.541 55.000 0.00 0.00 0.00 6.13
590 665 2.282783 GGGGCACGGGAAATGCTTT 61.283 57.895 0.00 0.00 42.93 3.51
591 666 2.679996 GGGGCACGGGAAATGCTT 60.680 61.111 0.00 0.00 42.93 3.91
592 667 3.978193 TGGGGCACGGGAAATGCT 61.978 61.111 0.00 0.00 42.93 3.79
593 668 3.758931 GTGGGGCACGGGAAATGC 61.759 66.667 0.00 0.00 42.62 3.56
649 724 2.066999 GGAGGAGTAGTGGGCCCAG 61.067 68.421 29.55 0.00 0.00 4.45
650 725 2.040606 GGAGGAGTAGTGGGCCCA 59.959 66.667 24.45 24.45 0.00 5.36
662 737 1.010793 AGAGAGGGAGAGAGAGGAGGA 59.989 57.143 0.00 0.00 0.00 3.71
667 742 1.133792 GTGGGAGAGAGGGAGAGAGAG 60.134 61.905 0.00 0.00 0.00 3.20
676 751 4.200283 GCGAGCGTGGGAGAGAGG 62.200 72.222 0.00 0.00 0.00 3.69
728 826 1.654954 CTGCAGGCCAGTGATGAAGC 61.655 60.000 5.01 0.00 36.79 3.86
774 872 1.305623 GAGGTGGGAGGGAGTACGA 59.694 63.158 0.00 0.00 0.00 3.43
841 939 2.426738 GAGTGAGATGAGGTGAGGTGAG 59.573 54.545 0.00 0.00 0.00 3.51
842 940 2.451490 GAGTGAGATGAGGTGAGGTGA 58.549 52.381 0.00 0.00 0.00 4.02
843 941 1.480137 GGAGTGAGATGAGGTGAGGTG 59.520 57.143 0.00 0.00 0.00 4.00
844 942 1.859302 GGAGTGAGATGAGGTGAGGT 58.141 55.000 0.00 0.00 0.00 3.85
845 943 0.743688 CGGAGTGAGATGAGGTGAGG 59.256 60.000 0.00 0.00 0.00 3.86
846 944 0.743688 CCGGAGTGAGATGAGGTGAG 59.256 60.000 0.00 0.00 0.00 3.51
847 945 0.039764 ACCGGAGTGAGATGAGGTGA 59.960 55.000 9.46 0.00 0.00 4.02
848 946 2.584673 ACCGGAGTGAGATGAGGTG 58.415 57.895 9.46 0.00 0.00 4.00
902 1000 7.449086 CCCTCCTACTAGTGGTAAGAAAGATAG 59.551 44.444 5.39 0.00 0.00 2.08
946 1052 2.300152 TCTACCAGACAAACTCCAGCAG 59.700 50.000 0.00 0.00 0.00 4.24
947 1053 2.300152 CTCTACCAGACAAACTCCAGCA 59.700 50.000 0.00 0.00 0.00 4.41
949 1055 3.194542 CCTCTCTACCAGACAAACTCCAG 59.805 52.174 0.00 0.00 0.00 3.86
950 1056 3.165875 CCTCTCTACCAGACAAACTCCA 58.834 50.000 0.00 0.00 0.00 3.86
952 1058 4.337145 TCTCCTCTCTACCAGACAAACTC 58.663 47.826 0.00 0.00 0.00 3.01
953 1059 4.340617 CTCTCCTCTCTACCAGACAAACT 58.659 47.826 0.00 0.00 0.00 2.66
971 1077 1.421646 CCTCTCCTCTCCTCTCCTCTC 59.578 61.905 0.00 0.00 0.00 3.20
972 1078 1.010793 TCCTCTCCTCTCCTCTCCTCT 59.989 57.143 0.00 0.00 0.00 3.69
973 1079 1.421646 CTCCTCTCCTCTCCTCTCCTC 59.578 61.905 0.00 0.00 0.00 3.71
974 1080 1.010793 TCTCCTCTCCTCTCCTCTCCT 59.989 57.143 0.00 0.00 0.00 3.69
975 1081 1.421646 CTCTCCTCTCCTCTCCTCTCC 59.578 61.905 0.00 0.00 0.00 3.71
976 1082 1.421646 CCTCTCCTCTCCTCTCCTCTC 59.578 61.905 0.00 0.00 0.00 3.20
977 1083 1.522900 CCTCTCCTCTCCTCTCCTCT 58.477 60.000 0.00 0.00 0.00 3.69
978 1084 0.478507 CCCTCTCCTCTCCTCTCCTC 59.521 65.000 0.00 0.00 0.00 3.71
979 1085 0.047176 TCCCTCTCCTCTCCTCTCCT 59.953 60.000 0.00 0.00 0.00 3.69
980 1086 0.478507 CTCCCTCTCCTCTCCTCTCC 59.521 65.000 0.00 0.00 0.00 3.71
1148 1260 8.680903 GCCATTGAAGAGAATTCAATCTAAAGA 58.319 33.333 8.44 0.00 44.60 2.52
1149 1261 7.642978 CGCCATTGAAGAGAATTCAATCTAAAG 59.357 37.037 8.44 2.88 44.60 1.85
1150 1262 7.475015 CGCCATTGAAGAGAATTCAATCTAAA 58.525 34.615 8.44 2.43 44.60 1.85
1151 1263 6.458751 GCGCCATTGAAGAGAATTCAATCTAA 60.459 38.462 8.44 0.00 44.60 2.10
1152 1264 5.008019 GCGCCATTGAAGAGAATTCAATCTA 59.992 40.000 8.44 0.49 44.60 1.98
1153 1265 4.201990 GCGCCATTGAAGAGAATTCAATCT 60.202 41.667 8.44 0.00 44.60 2.40
1154 1266 4.040376 GCGCCATTGAAGAGAATTCAATC 58.960 43.478 8.44 3.41 44.60 2.67
1155 1267 3.488047 CGCGCCATTGAAGAGAATTCAAT 60.488 43.478 8.44 9.45 46.59 2.57
1156 1268 2.159531 CGCGCCATTGAAGAGAATTCAA 60.160 45.455 8.44 5.58 41.91 2.69
1167 1279 0.746204 TTGAATAGCCGCGCCATTGA 60.746 50.000 0.00 0.00 0.00 2.57
1168 1280 0.311790 ATTGAATAGCCGCGCCATTG 59.688 50.000 0.00 0.00 0.00 2.82
1181 1293 1.478105 GGCGGCAGAGGAAAATTGAAT 59.522 47.619 3.07 0.00 0.00 2.57
1242 1354 3.058432 CACACATGCTGTTCAAGAGAAGG 60.058 47.826 0.00 0.00 33.63 3.46
1269 1381 2.625737 TGCTCTCTATCTGCAGTTTGC 58.374 47.619 14.67 10.02 45.29 3.68
1270 1382 6.128876 CGATTATGCTCTCTATCTGCAGTTTG 60.129 42.308 14.67 6.75 40.18 2.93
1271 1383 5.925397 CGATTATGCTCTCTATCTGCAGTTT 59.075 40.000 14.67 5.37 40.18 2.66
1306 1418 7.233553 GGAAGGAAAGGAAGATTAATTATGGGG 59.766 40.741 0.00 0.00 0.00 4.96
1312 1424 6.165742 TGGGGAAGGAAAGGAAGATTAATT 57.834 37.500 0.00 0.00 0.00 1.40
1313 1425 5.813965 TGGGGAAGGAAAGGAAGATTAAT 57.186 39.130 0.00 0.00 0.00 1.40
1320 1434 1.432807 AGCAATGGGGAAGGAAAGGAA 59.567 47.619 0.00 0.00 0.00 3.36
1347 1487 9.595357 GTTGTTAAGATTTTAGTACAGAGCAAC 57.405 33.333 0.00 0.00 0.00 4.17
1374 1516 1.811266 ACGGCGATGACTGCATGAC 60.811 57.895 16.62 0.00 34.11 3.06
1379 1521 3.188786 GTCCACGGCGATGACTGC 61.189 66.667 16.62 0.00 0.00 4.40
1447 1589 1.135024 CAGGGCGGATGGAATTTGTTG 60.135 52.381 0.00 0.00 0.00 3.33
1527 1680 9.785982 CCAAAGTGGGGAAAATAAAAGAAAATA 57.214 29.630 0.00 0.00 32.67 1.40
1537 1690 4.017037 TGGATAGCCAAAGTGGGGAAAATA 60.017 41.667 0.00 0.00 42.49 1.40
1635 1796 3.267597 AAAACCCTCACGCGCATGC 62.268 57.895 5.73 7.91 37.91 4.06
1636 1797 1.442520 CAAAACCCTCACGCGCATG 60.443 57.895 5.73 0.97 0.00 4.06
1637 1798 1.896660 ACAAAACCCTCACGCGCAT 60.897 52.632 5.73 0.00 0.00 4.73
1638 1799 2.515057 ACAAAACCCTCACGCGCA 60.515 55.556 5.73 0.00 0.00 6.09
1688 1852 2.181525 CCCATCAAAAAGCGGCGG 59.818 61.111 9.78 0.00 0.00 6.13
1712 1876 1.636988 AGACGGCGAGTTTTTATCCG 58.363 50.000 16.62 0.00 45.04 4.18
1845 2009 6.828785 ACAGGTGAAAGAAAACAATCAGTACT 59.171 34.615 0.00 0.00 0.00 2.73
1846 2010 6.912591 CACAGGTGAAAGAAAACAATCAGTAC 59.087 38.462 0.00 0.00 0.00 2.73
1847 2011 6.039270 CCACAGGTGAAAGAAAACAATCAGTA 59.961 38.462 0.00 0.00 0.00 2.74
1927 2091 1.009900 GTCGTAGCCGGTCATCTCG 60.010 63.158 1.90 0.22 33.95 4.04
2012 2181 4.643784 GGAGCATTGGACATCTTCTTTCAT 59.356 41.667 0.00 0.00 0.00 2.57
2055 2244 0.109532 TGGCCTGAAAACGTCCATGA 59.890 50.000 3.32 0.00 0.00 3.07
2091 2280 0.685131 ACATGACGACCACCGGGATA 60.685 55.000 6.32 0.00 43.93 2.59
2101 2290 0.167470 TTCTCCGACGACATGACGAC 59.833 55.000 23.72 16.33 37.99 4.34
2151 2340 1.691976 TCGAGTGAAGGAAAGGCTTGA 59.308 47.619 0.00 0.00 0.00 3.02
2152 2341 2.072298 CTCGAGTGAAGGAAAGGCTTG 58.928 52.381 3.62 0.00 0.00 4.01
2153 2342 1.609320 GCTCGAGTGAAGGAAAGGCTT 60.609 52.381 15.13 0.00 0.00 4.35
2154 2343 0.036858 GCTCGAGTGAAGGAAAGGCT 60.037 55.000 15.13 0.00 0.00 4.58
2155 2344 0.320771 TGCTCGAGTGAAGGAAAGGC 60.321 55.000 15.13 0.00 0.00 4.35
2161 2357 2.322355 AATGGATGCTCGAGTGAAGG 57.678 50.000 15.13 0.00 0.00 3.46
2202 2398 2.644628 TTTTTGCCCCCACCCCCATT 62.645 55.000 0.00 0.00 0.00 3.16
2284 2481 1.935873 CACTGTGGCTACGAATCCATG 59.064 52.381 0.00 0.00 34.47 3.66
2325 2522 2.681848 AGCATAATGAACTGACTGCAGC 59.318 45.455 15.27 7.45 46.26 5.25
2361 2558 8.588472 TCACTGATACTTGATACATAATGGGAG 58.412 37.037 0.00 0.00 0.00 4.30
2377 2574 6.947733 TGGGATGTTCAAAATTCACTGATACT 59.052 34.615 0.00 0.00 0.00 2.12
2447 2644 8.424918 AGGATTCTGTATAGTACAATCAACAGG 58.575 37.037 0.00 0.00 38.38 4.00
2498 2700 2.962421 TGTCCCCAGCAAAAAGTTAAGG 59.038 45.455 0.00 0.00 0.00 2.69
2728 2934 3.391049 GTGCGGTAATAAGATGGAGGTC 58.609 50.000 0.00 0.00 0.00 3.85
2759 2965 0.741221 GTCCTGGAACATCAGACGGC 60.741 60.000 0.00 0.00 38.20 5.68
2809 3018 0.969894 ACGAGTGGAGGACCTGAAAG 59.030 55.000 0.00 0.00 37.04 2.62
2994 3203 1.133407 CGACACAAGAGCTACTCCTCC 59.867 57.143 0.00 0.00 32.17 4.30
3137 3346 0.246910 GGGGTTCTTCCTCGACTCAC 59.753 60.000 0.00 0.00 36.25 3.51
3143 3352 2.158943 GGATACAAGGGGTTCTTCCTCG 60.159 54.545 0.00 0.00 42.70 4.63
3344 3553 6.402222 AGATCTGGTGCTACTTTTAAGTCAG 58.598 40.000 0.00 0.89 40.37 3.51
3437 3646 5.364446 ACACAATCCGGGAGTACAATACATA 59.636 40.000 0.00 0.00 0.00 2.29
3476 3685 3.424962 GCAATTTCGCTGTCTGAACTACC 60.425 47.826 0.00 0.00 0.00 3.18
3608 3820 7.567458 AGGCAATATTGTTATTTCAATGGCTT 58.433 30.769 16.61 0.00 37.40 4.35
3670 3883 9.677567 CCTATGCATACAACCATAAAATACAAC 57.322 33.333 1.16 0.00 0.00 3.32
3671 3884 9.415008 ACCTATGCATACAACCATAAAATACAA 57.585 29.630 1.16 0.00 0.00 2.41
3710 3925 4.641541 CAGATGGTGAAATGTAGAATGGCA 59.358 41.667 0.00 0.00 0.00 4.92
3729 3944 3.771216 AGAATTTGCACCTCAACCAGAT 58.229 40.909 0.00 0.00 33.73 2.90
3857 4072 3.658725 AGGTGCTTATCCATCAGGTACT 58.341 45.455 0.00 0.00 43.88 2.73
3862 4077 5.233083 TCCAATAGGTGCTTATCCATCAG 57.767 43.478 0.00 0.00 35.89 2.90
3865 4080 8.448008 TCTATTTTCCAATAGGTGCTTATCCAT 58.552 33.333 2.84 0.00 41.66 3.41
3926 4141 8.204836 GGGACAAATAGTAATAGAGAAAGCTGA 58.795 37.037 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.