Multiple sequence alignment - TraesCS3B01G590300

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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 TraesCS3B01G590300 chr3B 100.000 3887 0 0 1 3887 815356291 815360177 0.000000e+00 7179
1 TraesCS3B01G590300 chr3B 96.747 2121 57 7 1307 3425 815275278 815273168 0.000000e+00 3524
2 TraesCS3B01G590300 chr3B 91.408 710 36 2 1 709 815276823 815276138 0.000000e+00 950
3 TraesCS3B01G590300 chr3B 91.170 453 20 2 3453 3887 815273166 815272716 7.190000e-167 597
4 TraesCS3B01G590300 chr3B 87.973 291 29 3 1006 1293 815275621 815275334 4.810000e-89 339
5 TraesCS3B01G590300 chr3B 78.027 446 42 27 569 996 815276073 815275666 3.020000e-56 230
6 TraesCS3B01G590300 chr3A 94.028 2813 119 17 1115 3887 737479016 737476213 0.000000e+00 4218
7 TraesCS3B01G590300 chr3A 80.037 541 41 28 316 808 737479808 737479287 4.810000e-89 339
8 TraesCS3B01G590300 chr3A 97.126 174 5 0 146 319 737501299 737501126 1.060000e-75 294
9 TraesCS3B01G590300 chr3A 96.689 151 5 0 1 151 737505937 737505787 6.450000e-63 252
10 TraesCS3B01G590300 chr3D 89.924 3156 164 69 1 3094 606635175 606632112 0.000000e+00 3925
11 TraesCS3B01G590300 chr3D 94.634 820 22 4 3088 3887 606628285 606627468 0.000000e+00 1251
12 TraesCS3B01G590300 chr3D 87.000 500 61 3 1 500 606642498 606642993 9.430000e-156 560


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 TraesCS3B01G590300 chr3B 815356291 815360177 3886 False 7179.0 7179 100.0000 1 3887 1 chr3B.!!$F1 3886
1 TraesCS3B01G590300 chr3B 815272716 815276823 4107 True 1128.0 3524 89.0650 1 3887 5 chr3B.!!$R1 3886
2 TraesCS3B01G590300 chr3A 737476213 737479808 3595 True 2278.5 4218 87.0325 316 3887 2 chr3A.!!$R3 3571
3 TraesCS3B01G590300 chr3D 606627468 606635175 7707 True 2588.0 3925 92.2790 1 3887 2 chr3D.!!$R1 3886

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
888 1131 0.042731 TCCTCCTCCGTTTCCTCCAT 59.957 55.0 0.0 0.0 0.00 3.41 F
892 1135 0.179000 CCTCCGTTTCCTCCATCAGG 59.821 60.0 0.0 0.0 45.15 3.86 F
1264 1568 0.312416 GGACGACGGATCTGATGGAG 59.688 60.0 9.0 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1713 2060 3.386932 TCCAGATTGCTATTTTGGGCT 57.613 42.857 10.92 0.00 0.0 5.19 R
1854 2201 3.723235 CTCCTCACGGCCGGTCATG 62.723 68.421 31.76 18.91 0.0 3.07 R
3253 7447 2.334838 GTAGATGGTCAACGTGTGGTC 58.665 52.381 0.00 0.00 0.0 4.02 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
30 31 1.006086 TGCATCTTGTGGTTATCGCG 58.994 50.000 0.00 0.00 0.00 5.87
69 71 4.455366 GAGGGGTCCTCCGAGAAA 57.545 61.111 2.65 0.00 44.36 2.52
218 220 3.188786 GACGACATGAGTGCCGGC 61.189 66.667 22.73 22.73 35.37 6.13
221 223 2.046892 GACATGAGTGCCGGCTGT 60.047 61.111 29.70 23.03 0.00 4.40
270 272 3.406595 GACTAGCCGCTTGCCCCAT 62.407 63.158 0.00 0.00 42.71 4.00
344 346 3.041940 CGCCTTTCGGTCACGCTT 61.042 61.111 0.00 0.00 40.69 4.68
464 466 0.582482 CGGTCGTACGGAGATGAGAG 59.418 60.000 16.52 0.00 0.00 3.20
583 585 9.929180 TTTACTAAGAAGATCGGATATGGATTG 57.071 33.333 0.00 0.00 0.00 2.67
584 586 6.940739 ACTAAGAAGATCGGATATGGATTGG 58.059 40.000 0.00 0.00 0.00 3.16
585 587 4.213564 AGAAGATCGGATATGGATTGGC 57.786 45.455 0.00 0.00 0.00 4.52
586 588 3.584406 AGAAGATCGGATATGGATTGGCA 59.416 43.478 0.00 0.00 0.00 4.92
587 589 3.340814 AGATCGGATATGGATTGGCAC 57.659 47.619 0.00 0.00 0.00 5.01
588 590 2.002586 GATCGGATATGGATTGGCACG 58.997 52.381 0.00 0.00 0.00 5.34
589 591 1.044611 TCGGATATGGATTGGCACGA 58.955 50.000 0.00 0.00 0.00 4.35
590 592 1.623311 TCGGATATGGATTGGCACGAT 59.377 47.619 0.00 0.00 0.00 3.73
591 593 2.002586 CGGATATGGATTGGCACGATC 58.997 52.381 0.00 0.00 0.00 3.69
592 594 2.612721 CGGATATGGATTGGCACGATCA 60.613 50.000 1.90 0.00 0.00 2.92
593 595 3.411446 GGATATGGATTGGCACGATCAA 58.589 45.455 1.90 0.00 0.00 2.57
594 596 4.012374 GGATATGGATTGGCACGATCAAT 58.988 43.478 1.90 0.00 37.52 2.57
595 597 5.185454 GGATATGGATTGGCACGATCAATA 58.815 41.667 1.90 0.88 35.26 1.90
596 598 5.824624 GGATATGGATTGGCACGATCAATAT 59.175 40.000 8.25 8.25 34.37 1.28
597 599 6.017605 GGATATGGATTGGCACGATCAATATC 60.018 42.308 19.63 19.63 41.78 1.63
598 600 3.411446 TGGATTGGCACGATCAATATCC 58.589 45.455 4.06 4.06 35.26 2.59
599 601 3.181446 TGGATTGGCACGATCAATATCCA 60.181 43.478 8.75 8.75 35.26 3.41
600 602 4.012374 GGATTGGCACGATCAATATCCAT 58.988 43.478 5.85 0.00 35.26 3.41
601 603 4.095483 GGATTGGCACGATCAATATCCATC 59.905 45.833 5.85 0.00 35.26 3.51
602 604 2.687370 TGGCACGATCAATATCCATCG 58.313 47.619 12.49 12.49 46.03 3.84
603 605 2.002586 GGCACGATCAATATCCATCGG 58.997 52.381 16.53 9.30 45.08 4.18
604 606 2.353704 GGCACGATCAATATCCATCGGA 60.354 50.000 16.53 0.00 45.08 4.55
605 607 3.525537 GCACGATCAATATCCATCGGAT 58.474 45.455 16.53 0.43 45.08 4.18
606 608 3.935203 GCACGATCAATATCCATCGGATT 59.065 43.478 16.53 0.00 45.08 3.01
699 930 0.179181 CGTGCACGTACGTACCTCAT 60.179 55.000 30.50 0.57 39.13 2.90
700 931 1.062440 CGTGCACGTACGTACCTCATA 59.938 52.381 30.50 0.00 39.13 2.15
701 932 2.713011 GTGCACGTACGTACCTCATAG 58.287 52.381 22.34 7.18 0.00 2.23
702 933 2.096496 GTGCACGTACGTACCTCATAGT 59.904 50.000 22.34 7.90 0.00 2.12
703 934 2.749076 TGCACGTACGTACCTCATAGTT 59.251 45.455 22.34 0.00 0.00 2.24
704 935 3.191162 TGCACGTACGTACCTCATAGTTT 59.809 43.478 22.34 0.00 0.00 2.66
705 936 3.788163 GCACGTACGTACCTCATAGTTTC 59.212 47.826 22.34 2.23 0.00 2.78
706 937 4.024438 CACGTACGTACCTCATAGTTTCG 58.976 47.826 22.34 6.23 0.00 3.46
716 947 1.624813 TCATAGTTTCGGTTTCGGGGT 59.375 47.619 0.00 0.00 36.95 4.95
731 962 7.521261 CGGTTTCGGGGTTTAAACAAACTTATA 60.521 37.037 19.57 0.00 37.33 0.98
732 963 7.809331 GGTTTCGGGGTTTAAACAAACTTATAG 59.191 37.037 19.57 1.45 37.33 1.31
733 964 7.451501 TTCGGGGTTTAAACAAACTTATAGG 57.548 36.000 19.57 0.00 33.37 2.57
734 965 6.777782 TCGGGGTTTAAACAAACTTATAGGA 58.222 36.000 19.57 0.36 33.37 2.94
735 966 6.880529 TCGGGGTTTAAACAAACTTATAGGAG 59.119 38.462 19.57 0.00 33.37 3.69
736 967 6.656270 CGGGGTTTAAACAAACTTATAGGAGT 59.344 38.462 19.57 0.00 33.37 3.85
737 968 7.823799 CGGGGTTTAAACAAACTTATAGGAGTA 59.176 37.037 19.57 0.00 33.37 2.59
738 969 9.690913 GGGGTTTAAACAAACTTATAGGAGTAT 57.309 33.333 19.57 0.00 33.37 2.12
748 979 6.352016 ACTTATAGGAGTATCTCGTACGGA 57.648 41.667 16.52 11.97 38.38 4.69
805 1036 0.460109 GCCGGCAATTCCAATTCACC 60.460 55.000 24.80 0.00 34.01 4.02
808 1039 1.271934 CGGCAATTCCAATTCACCACA 59.728 47.619 0.00 0.00 34.01 4.17
826 1057 1.080025 AAGTAAGTCTGACGGCGGC 60.080 57.895 13.24 9.67 0.00 6.53
827 1058 2.502692 AAGTAAGTCTGACGGCGGCC 62.503 60.000 11.74 9.54 0.00 6.13
828 1059 2.992689 TAAGTCTGACGGCGGCCA 60.993 61.111 20.71 7.23 0.00 5.36
829 1060 3.291101 TAAGTCTGACGGCGGCCAC 62.291 63.158 20.71 7.13 0.00 5.01
885 1128 0.964358 TCGTCCTCCTCCGTTTCCTC 60.964 60.000 0.00 0.00 0.00 3.71
888 1131 0.042731 TCCTCCTCCGTTTCCTCCAT 59.957 55.000 0.00 0.00 0.00 3.41
889 1132 0.466124 CCTCCTCCGTTTCCTCCATC 59.534 60.000 0.00 0.00 0.00 3.51
890 1133 1.195115 CTCCTCCGTTTCCTCCATCA 58.805 55.000 0.00 0.00 0.00 3.07
891 1134 1.137872 CTCCTCCGTTTCCTCCATCAG 59.862 57.143 0.00 0.00 0.00 2.90
892 1135 0.179000 CCTCCGTTTCCTCCATCAGG 59.821 60.000 0.00 0.00 45.15 3.86
893 1136 0.905357 CTCCGTTTCCTCCATCAGGT 59.095 55.000 0.00 0.00 43.95 4.00
895 1138 2.101582 CTCCGTTTCCTCCATCAGGTAG 59.898 54.545 0.00 0.00 43.95 3.18
896 1139 1.139058 CCGTTTCCTCCATCAGGTAGG 59.861 57.143 0.00 0.00 43.95 3.18
897 1140 1.831736 CGTTTCCTCCATCAGGTAGGT 59.168 52.381 0.00 0.00 43.95 3.08
898 1141 3.028850 CGTTTCCTCCATCAGGTAGGTA 58.971 50.000 0.00 0.00 43.95 3.08
899 1142 3.181478 CGTTTCCTCCATCAGGTAGGTAC 60.181 52.174 0.00 0.00 43.95 3.34
900 1143 3.769189 TTCCTCCATCAGGTAGGTACA 57.231 47.619 0.00 0.00 43.95 2.90
901 1144 3.314307 TCCTCCATCAGGTAGGTACAG 57.686 52.381 0.00 0.00 43.95 2.74
908 1151 1.076513 TCAGGTAGGTACAGCTCACCA 59.923 52.381 14.93 0.80 38.62 4.17
912 1155 1.204941 GTAGGTACAGCTCACCACCTG 59.795 57.143 14.93 0.00 41.49 4.00
913 1156 1.376037 GGTACAGCTCACCACCTGC 60.376 63.158 8.84 0.00 36.01 4.85
914 1157 1.376037 GTACAGCTCACCACCTGCC 60.376 63.158 0.00 0.00 32.37 4.85
915 1158 2.942796 TACAGCTCACCACCTGCCG 61.943 63.158 0.00 0.00 32.37 5.69
928 1185 1.238439 CCTGCCGGCGATATTTTCAT 58.762 50.000 23.90 0.00 0.00 2.57
937 1194 5.334105 CCGGCGATATTTTCATTCTTCGATT 60.334 40.000 9.30 0.00 0.00 3.34
944 1201 9.522454 GATATTTTCATTCTTCGATTCGATGAC 57.478 33.333 20.36 5.50 39.17 3.06
945 1202 5.375544 TTTCATTCTTCGATTCGATGACG 57.624 39.130 20.36 15.43 39.17 4.35
947 1204 1.556564 TTCTTCGATTCGATGACGCC 58.443 50.000 20.36 0.00 39.17 5.68
957 1214 2.021457 TCGATGACGCCTCAATCTGTA 58.979 47.619 0.00 0.00 39.58 2.74
959 1216 2.728318 CGATGACGCCTCAATCTGTATG 59.272 50.000 0.00 0.00 0.00 2.39
996 1253 3.119849 GGATGTTGGTTTGATCTTGACCG 60.120 47.826 0.00 0.00 36.22 4.79
998 1255 0.871722 TTGGTTTGATCTTGACCGCG 59.128 50.000 0.00 0.00 36.22 6.46
1068 1369 2.360475 GAAGGCACCTGCAGGGAC 60.360 66.667 35.42 25.72 44.36 4.46
1073 1374 2.765969 CACCTGCAGGGACCCAAT 59.234 61.111 35.42 11.03 40.27 3.16
1134 1435 2.499685 GGCGCTACGTGGGAGAAT 59.500 61.111 7.64 0.00 0.00 2.40
1158 1462 1.441738 TGACGACGAGATTCGGTACA 58.558 50.000 0.00 0.00 45.59 2.90
1160 1464 1.662629 GACGACGAGATTCGGTACAGA 59.337 52.381 0.00 0.00 45.59 3.41
1203 1507 0.946221 CCGTAGCGCCATGGAGATTC 60.946 60.000 20.86 10.15 0.00 2.52
1264 1568 0.312416 GGACGACGGATCTGATGGAG 59.688 60.000 9.00 0.00 0.00 3.86
1295 1599 2.930950 TGGAACTTCCAAGTCAACCAG 58.069 47.619 8.15 0.00 45.00 4.00
1297 1601 2.879026 GGAACTTCCAAGTCAACCAGTC 59.121 50.000 2.62 0.00 38.57 3.51
1298 1602 3.433740 GGAACTTCCAAGTCAACCAGTCT 60.434 47.826 2.62 0.00 38.57 3.24
1305 1645 4.469945 TCCAAGTCAACCAGTCTTATAGGG 59.530 45.833 0.00 0.00 0.00 3.53
1330 1676 2.289694 GCTGCTTCTGTACCCAAGAAGA 60.290 50.000 20.15 8.54 40.89 2.87
1331 1677 3.330267 CTGCTTCTGTACCCAAGAAGAC 58.670 50.000 20.15 13.50 40.89 3.01
1332 1678 2.288825 TGCTTCTGTACCCAAGAAGACG 60.289 50.000 20.15 2.62 40.89 4.18
1344 1690 3.318017 CAAGAAGACGACGAAGGTTGAT 58.682 45.455 0.00 0.00 0.00 2.57
1379 1725 1.406898 TCGTGCAATGCCAAAGAACAA 59.593 42.857 1.53 0.00 0.00 2.83
1418 1764 1.512734 GCGTCATGGCTTCTTTGCG 60.513 57.895 0.00 0.00 0.00 4.85
1582 1928 2.224621 CCTGGAGTTCATGTTGGTGACT 60.225 50.000 0.00 0.00 0.00 3.41
1684 2031 1.626356 GGGCAGGACATGTCTAGCCA 61.626 60.000 38.28 0.00 44.91 4.75
1713 2060 2.012414 GTCGTACGCGCAACAGTCA 61.012 57.895 11.24 0.00 38.14 3.41
1724 2071 2.414559 CGCAACAGTCAGCCCAAAATAG 60.415 50.000 0.00 0.00 0.00 1.73
1752 2099 4.661222 TGGATTTCTTGCTACATGTTGGA 58.339 39.130 2.30 0.00 0.00 3.53
1854 2201 5.106869 TGTGCGTGTCATTTATAGGTTTGTC 60.107 40.000 0.00 0.00 0.00 3.18
2001 2348 2.855180 CAACCGAGCATCAACATTCAC 58.145 47.619 0.00 0.00 33.17 3.18
2951 3298 3.997762 TCGGCCGTGTTGCTTTATATAT 58.002 40.909 27.15 0.00 0.00 0.86
2952 3299 5.136816 TCGGCCGTGTTGCTTTATATATA 57.863 39.130 27.15 0.00 0.00 0.86
2953 3300 5.726397 TCGGCCGTGTTGCTTTATATATAT 58.274 37.500 27.15 0.00 0.00 0.86
2954 3301 6.865411 TCGGCCGTGTTGCTTTATATATATA 58.135 36.000 27.15 0.00 0.00 0.86
3001 3359 9.333724 TCTTTTTCGGTACTAGATTTTCTTGTT 57.666 29.630 0.00 0.00 34.49 2.83
3191 7384 6.869315 TTCTTAACGTGTGGATCAAAATCA 57.131 33.333 0.00 0.00 33.21 2.57
3193 7386 3.559238 AACGTGTGGATCAAAATCAGC 57.441 42.857 0.00 0.00 33.21 4.26
3253 7447 9.734620 TGTTTGATGACATTTCTTGTTTCTTAG 57.265 29.630 0.00 0.00 39.18 2.18
3273 7467 2.029290 AGACCACACGTTGACCATCTAC 60.029 50.000 0.00 0.00 0.00 2.59
3283 7477 5.421056 ACGTTGACCATCTACCATCTTTCTA 59.579 40.000 0.00 0.00 0.00 2.10
3405 7604 4.082949 CCTAGAAACCAACCGAAAATGTCC 60.083 45.833 0.00 0.00 0.00 4.02
3409 7608 0.243636 CCAACCGAAAATGTCCAGCC 59.756 55.000 0.00 0.00 0.00 4.85
3589 7788 3.441572 CAGATGTTACTTTTGGCTCCCAG 59.558 47.826 0.00 0.00 33.81 4.45
3690 7889 6.381133 TGAACACTAGCAGATTATTGAGAGGA 59.619 38.462 0.00 0.00 0.00 3.71
3706 7905 1.299089 GGAAAACACAGCCACGCAC 60.299 57.895 0.00 0.00 0.00 5.34
3766 7965 5.420725 ACTTGTATATTCACAGTCAGCCA 57.579 39.130 0.00 0.00 0.00 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 4.553547 GCGATAACCACAAGATGCAAGATC 60.554 45.833 0.00 0.00 0.00 2.75
69 71 8.632906 ATCTTGTCTCTGTTCAGAAAATCATT 57.367 30.769 4.09 0.00 0.00 2.57
84 86 3.439154 TCAGAGAGCCAATCTTGTCTCT 58.561 45.455 3.31 3.31 45.37 3.10
218 220 2.590007 GCTGGATAGCCGCCACAG 60.590 66.667 2.94 0.00 44.33 3.66
241 243 2.728817 GCTAGTCGGATCCCACGG 59.271 66.667 6.06 3.76 0.00 4.94
255 257 4.504596 CCATGGGGCAAGCGGCTA 62.505 66.667 1.35 0.00 44.01 3.93
444 446 0.176449 TCTCATCTCCGTACGACCGA 59.824 55.000 18.76 10.08 0.00 4.69
464 466 0.811616 CAAGATCTACCGTGGCTGCC 60.812 60.000 12.87 12.87 0.00 4.85
542 544 5.996513 TCTTAGTAAACGATCGAGGAGCTAT 59.003 40.000 24.34 2.29 0.00 2.97
583 585 2.002586 CCGATGGATATTGATCGTGCC 58.997 52.381 13.31 0.00 39.88 5.01
584 586 2.959516 TCCGATGGATATTGATCGTGC 58.040 47.619 13.31 0.00 39.88 5.34
585 587 6.036083 GGTAAATCCGATGGATATTGATCGTG 59.964 42.308 13.31 7.50 42.27 4.35
586 588 6.070767 AGGTAAATCCGATGGATATTGATCGT 60.071 38.462 13.31 2.03 42.27 3.73
587 589 6.341316 AGGTAAATCCGATGGATATTGATCG 58.659 40.000 0.00 9.32 42.27 3.69
588 590 8.567285 AAAGGTAAATCCGATGGATATTGATC 57.433 34.615 0.00 0.00 42.27 2.92
594 596 9.316594 TCTGTATAAAGGTAAATCCGATGGATA 57.683 33.333 0.00 0.00 42.27 2.59
595 597 8.202461 TCTGTATAAAGGTAAATCCGATGGAT 57.798 34.615 0.00 0.00 45.46 3.41
596 598 7.606135 TCTGTATAAAGGTAAATCCGATGGA 57.394 36.000 0.00 0.00 41.99 3.41
597 599 8.848474 ATTCTGTATAAAGGTAAATCCGATGG 57.152 34.615 0.00 0.00 41.99 3.51
682 913 2.358957 ACTATGAGGTACGTACGTGCA 58.641 47.619 32.30 22.73 32.33 4.57
699 930 2.636647 AAACCCCGAAACCGAAACTA 57.363 45.000 0.00 0.00 0.00 2.24
700 931 2.636647 TAAACCCCGAAACCGAAACT 57.363 45.000 0.00 0.00 0.00 2.66
701 932 3.181492 TGTTTAAACCCCGAAACCGAAAC 60.181 43.478 15.59 0.00 35.17 2.78
702 933 3.019564 TGTTTAAACCCCGAAACCGAAA 58.980 40.909 15.59 0.00 35.17 3.46
703 934 2.648059 TGTTTAAACCCCGAAACCGAA 58.352 42.857 15.59 0.00 35.17 4.30
704 935 2.338577 TGTTTAAACCCCGAAACCGA 57.661 45.000 15.59 0.00 35.17 4.69
705 936 3.114809 GTTTGTTTAAACCCCGAAACCG 58.885 45.455 15.59 0.00 40.19 4.44
706 937 4.389890 AGTTTGTTTAAACCCCGAAACC 57.610 40.909 20.07 9.20 45.77 3.27
731 962 1.417145 AGCTCCGTACGAGATACTCCT 59.583 52.381 18.76 1.33 41.63 3.69
732 963 1.532007 CAGCTCCGTACGAGATACTCC 59.468 57.143 18.76 0.00 41.63 3.85
733 964 1.069771 GCAGCTCCGTACGAGATACTC 60.070 57.143 18.76 0.00 41.63 2.59
734 965 0.945813 GCAGCTCCGTACGAGATACT 59.054 55.000 18.76 9.67 41.63 2.12
735 966 0.945813 AGCAGCTCCGTACGAGATAC 59.054 55.000 18.76 6.00 41.63 2.24
736 967 2.538512 TAGCAGCTCCGTACGAGATA 57.461 50.000 18.76 1.36 41.63 1.98
737 968 1.334243 GTTAGCAGCTCCGTACGAGAT 59.666 52.381 18.76 8.25 41.63 2.75
738 969 0.731417 GTTAGCAGCTCCGTACGAGA 59.269 55.000 18.76 11.38 41.63 4.04
748 979 2.290323 ACGGGAGATTTTGTTAGCAGCT 60.290 45.455 0.00 0.00 0.00 4.24
781 1012 0.899717 ATTGGAATTGCCGGCTGTGT 60.900 50.000 29.70 10.31 40.66 3.72
805 1036 1.060713 CGCCGTCAGACTTACTTGTG 58.939 55.000 0.00 0.00 0.00 3.33
808 1039 1.080025 GCCGCCGTCAGACTTACTT 60.080 57.895 0.00 0.00 0.00 2.24
828 1059 4.594854 TTGCCGGCATGGTGGTGT 62.595 61.111 33.25 0.00 41.21 4.16
829 1060 4.054825 GTTGCCGGCATGGTGGTG 62.055 66.667 33.25 0.00 41.21 4.17
863 1097 1.104630 GAAACGGAGGAGGACGAGAT 58.895 55.000 0.00 0.00 0.00 2.75
885 1128 2.101582 GTGAGCTGTACCTACCTGATGG 59.898 54.545 0.00 0.00 39.83 3.51
888 1131 1.076513 TGGTGAGCTGTACCTACCTGA 59.923 52.381 15.64 0.00 39.01 3.86
889 1132 1.204941 GTGGTGAGCTGTACCTACCTG 59.795 57.143 15.64 0.00 39.01 4.00
890 1133 1.558233 GTGGTGAGCTGTACCTACCT 58.442 55.000 15.64 0.00 39.01 3.08
891 1134 0.535797 GGTGGTGAGCTGTACCTACC 59.464 60.000 15.64 15.77 39.01 3.18
892 1135 1.204941 CAGGTGGTGAGCTGTACCTAC 59.795 57.143 15.64 12.00 41.42 3.18
893 1136 1.557099 CAGGTGGTGAGCTGTACCTA 58.443 55.000 15.64 2.70 41.42 3.08
908 1151 0.107410 TGAAAATATCGCCGGCAGGT 60.107 50.000 28.98 17.99 40.50 4.00
912 1155 3.555518 GAAGAATGAAAATATCGCCGGC 58.444 45.455 19.07 19.07 0.00 6.13
913 1156 3.493129 TCGAAGAATGAAAATATCGCCGG 59.507 43.478 0.00 0.00 0.00 6.13
914 1157 4.708868 TCGAAGAATGAAAATATCGCCG 57.291 40.909 0.00 0.00 0.00 6.46
915 1158 5.785599 CGAATCGAAGAATGAAAATATCGCC 59.214 40.000 0.00 0.00 43.58 5.54
916 1159 6.581370 TCGAATCGAAGAATGAAAATATCGC 58.419 36.000 1.57 0.00 43.58 4.58
918 1161 9.522454 GTCATCGAATCGAAGAATGAAAATATC 57.478 33.333 12.22 0.00 43.58 1.63
919 1162 8.217115 CGTCATCGAATCGAAGAATGAAAATAT 58.783 33.333 12.22 0.00 39.99 1.28
928 1185 1.134367 AGGCGTCATCGAATCGAAGAA 59.866 47.619 12.22 0.00 39.99 2.52
937 1194 0.817654 ACAGATTGAGGCGTCATCGA 59.182 50.000 10.35 0.00 39.71 3.59
944 1201 0.940126 GCACCATACAGATTGAGGCG 59.060 55.000 0.00 0.00 0.00 5.52
945 1202 1.945394 CTGCACCATACAGATTGAGGC 59.055 52.381 0.00 0.00 37.32 4.70
947 1204 3.118482 AGACCTGCACCATACAGATTGAG 60.118 47.826 0.00 0.00 37.32 3.02
957 1214 0.339859 TCCCTAGAGACCTGCACCAT 59.660 55.000 0.00 0.00 0.00 3.55
959 1216 0.755686 CATCCCTAGAGACCTGCACC 59.244 60.000 0.00 0.00 0.00 5.01
1052 1353 3.971702 GGTCCCTGCAGGTGCCTT 61.972 66.667 30.63 0.00 41.18 4.35
1060 1361 1.228831 CCACAATTGGGTCCCTGCA 60.229 57.895 10.00 0.00 39.57 4.41
1061 1362 0.541764 TTCCACAATTGGGTCCCTGC 60.542 55.000 10.00 0.00 44.11 4.85
1062 1363 1.549203 CTTCCACAATTGGGTCCCTG 58.451 55.000 10.00 1.30 44.11 4.45
1063 1364 0.251787 GCTTCCACAATTGGGTCCCT 60.252 55.000 10.00 0.00 44.11 4.20
1068 1369 1.270785 GGTTTGGCTTCCACAATTGGG 60.271 52.381 10.83 5.34 44.11 4.12
1073 1374 1.133637 TGCTAGGTTTGGCTTCCACAA 60.134 47.619 0.00 0.00 30.78 3.33
1079 1380 0.251341 CTGGGTGCTAGGTTTGGCTT 60.251 55.000 0.00 0.00 0.00 4.35
1080 1381 1.380302 CTGGGTGCTAGGTTTGGCT 59.620 57.895 0.00 0.00 0.00 4.75
1103 1404 3.782244 CGCCGTTGCACTGAGAGC 61.782 66.667 0.00 0.00 37.32 4.09
1134 1435 2.485426 ACCGAATCTCGTCGTCAAACTA 59.515 45.455 0.00 0.00 38.40 2.24
1158 1462 2.361610 CCCTTGCGGCAACCATCT 60.362 61.111 12.11 0.00 0.00 2.90
1203 1507 1.523758 GCCGCTTATACCCAATCTGG 58.476 55.000 0.00 0.00 37.25 3.86
1290 1594 1.490910 GCAGCCCCTATAAGACTGGTT 59.509 52.381 0.00 0.00 0.00 3.67
1293 1597 1.542108 GCAGCAGCCCCTATAAGACTG 60.542 57.143 0.00 0.00 33.58 3.51
1294 1598 0.761802 GCAGCAGCCCCTATAAGACT 59.238 55.000 0.00 0.00 33.58 3.24
1295 1599 0.761802 AGCAGCAGCCCCTATAAGAC 59.238 55.000 0.00 0.00 43.56 3.01
1297 1601 1.419387 AGAAGCAGCAGCCCCTATAAG 59.581 52.381 0.00 0.00 43.56 1.73
1298 1602 1.141657 CAGAAGCAGCAGCCCCTATAA 59.858 52.381 0.00 0.00 43.56 0.98
1305 1645 1.746991 GGGTACAGAAGCAGCAGCC 60.747 63.158 0.00 0.00 43.56 4.85
1330 1676 1.897802 ACCCTTATCAACCTTCGTCGT 59.102 47.619 0.00 0.00 0.00 4.34
1331 1677 2.094390 TCACCCTTATCAACCTTCGTCG 60.094 50.000 0.00 0.00 0.00 5.12
1332 1678 3.604875 TCACCCTTATCAACCTTCGTC 57.395 47.619 0.00 0.00 0.00 4.20
1344 1690 1.202371 GCACGATGACGATCACCCTTA 60.202 52.381 0.00 0.00 42.66 2.69
1379 1725 0.610174 TTCTCTGCTGATGGCGACTT 59.390 50.000 0.00 0.00 45.43 3.01
1418 1764 3.887110 CCTGTAAATTACCCGGAATTCCC 59.113 47.826 19.01 1.17 0.00 3.97
1453 1799 1.453155 TTGCATTTCGCCTTCTCCTC 58.547 50.000 0.00 0.00 41.33 3.71
1455 1801 4.105486 GTTTATTGCATTTCGCCTTCTCC 58.895 43.478 0.00 0.00 41.33 3.71
1464 1810 9.362539 AGATCATGTTCTTGTTTATTGCATTTC 57.637 29.630 0.16 0.00 0.00 2.17
1713 2060 3.386932 TCCAGATTGCTATTTTGGGCT 57.613 42.857 10.92 0.00 0.00 5.19
1724 2071 4.970662 TGTAGCAAGAAATCCAGATTGC 57.029 40.909 0.65 0.65 46.50 3.56
1854 2201 3.723235 CTCCTCACGGCCGGTCATG 62.723 68.421 31.76 18.91 0.00 3.07
2951 3298 7.069085 AGACTTTCGCCCCGCTTTATATATATA 59.931 37.037 0.00 0.00 0.00 0.86
2952 3299 5.985911 ACTTTCGCCCCGCTTTATATATAT 58.014 37.500 0.00 0.00 0.00 0.86
2953 3300 5.186409 AGACTTTCGCCCCGCTTTATATATA 59.814 40.000 0.00 0.00 0.00 0.86
2954 3301 4.020485 AGACTTTCGCCCCGCTTTATATAT 60.020 41.667 0.00 0.00 0.00 0.86
3158 7351 8.710835 ATCCACACGTTAAGAAACAAAATTTT 57.289 26.923 0.00 0.00 35.16 1.82
3161 7354 7.033530 TGATCCACACGTTAAGAAACAAAAT 57.966 32.000 0.00 0.00 35.16 1.82
3191 7384 4.759693 TGTATGTCACGGAATTTCAAAGCT 59.240 37.500 0.00 0.00 0.00 3.74
3193 7386 6.029607 CCATGTATGTCACGGAATTTCAAAG 58.970 40.000 0.00 0.00 29.90 2.77
3253 7447 2.334838 GTAGATGGTCAACGTGTGGTC 58.665 52.381 0.00 0.00 0.00 4.02
3273 7467 6.682423 TGTACACAATGCATAGAAAGATGG 57.318 37.500 0.00 0.00 0.00 3.51
3283 7477 4.582869 AGACACTCATGTACACAATGCAT 58.417 39.130 0.00 0.00 39.95 3.96
3362 7560 3.648545 AGGTATTCTGGGAGCCTGATAAC 59.351 47.826 0.00 0.00 31.78 1.89
3363 7561 3.941629 AGGTATTCTGGGAGCCTGATAA 58.058 45.455 0.00 0.00 31.78 1.75
3690 7889 2.407210 CGTGCGTGGCTGTGTTTT 59.593 55.556 0.00 0.00 0.00 2.43
3706 7905 4.618965 GGTTAGTCTTAAGTAGCATCCCG 58.381 47.826 1.63 0.00 0.00 5.14
3718 7917 5.818857 GGCATTATTTCCACGGTTAGTCTTA 59.181 40.000 0.00 0.00 0.00 2.10


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

AutoCloner maintained by Alex Coulton.