Multiple sequence alignment - TraesCS7A01G511500

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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 TraesCS7A01G511500 chr7A 100.000 3107 0 0 1 3107 699125965 699129071 0 5738
1 TraesCS7A01G511500 chr7A 92.129 902 62 5 2206 3107 538762099 538762991 0 1264
2 TraesCS7A01G511500 chr7A 91.444 900 71 5 2208 3107 183473547 183472654 0 1230
3 TraesCS7A01G511500 chr7B 93.226 1240 84 0 969 2208 691966003 691967242 0 1825
4 TraesCS7A01G511500 chr7B 92.581 1240 92 0 969 2208 691999535 692000774 0 1781
5 TraesCS7A01G511500 chr7B 91.935 1240 100 0 969 2208 691927865 691929104 0 1736
6 TraesCS7A01G511500 chr3A 97.211 968 24 3 1 968 653571572 653572536 0 1635
7 TraesCS7A01G511500 chr3A 97.107 968 28 0 1 968 519040651 519039684 0 1633
8 TraesCS7A01G511500 chr3A 96.904 969 29 1 1 968 600163199 600164167 0 1622
9 TraesCS7A01G511500 chr3A 96.619 976 29 1 1 972 198900631 198899656 0 1616
10 TraesCS7A01G511500 chr3A 96.798 968 31 0 1 968 739481070 739480103 0 1616
11 TraesCS7A01G511500 chr6A 97.004 968 29 0 1 968 548555139 548554172 0 1628
12 TraesCS7A01G511500 chr2A 97.004 968 28 1 1 968 676692746 676691780 0 1626
13 TraesCS7A01G511500 chr2A 96.901 968 29 1 1 968 732702174 732703140 0 1620
14 TraesCS7A01G511500 chr2A 96.804 970 29 1 1 968 495989286 495988317 0 1618
15 TraesCS7A01G511500 chr2A 94.333 900 40 3 2208 3107 714970498 714971386 0 1369
16 TraesCS7A01G511500 chr1A 92.707 905 59 3 2208 3107 51002047 51001145 0 1299
17 TraesCS7A01G511500 chr1A 92.240 915 55 6 2208 3107 51057575 51056662 0 1282
18 TraesCS7A01G511500 chr1A 92.000 900 67 2 2208 3107 553504480 553505374 0 1258
19 TraesCS7A01G511500 chr1A 91.232 901 72 3 2208 3107 51051943 51051049 0 1219
20 TraesCS7A01G511500 chr3D 92.350 902 60 4 2208 3107 17716705 17715811 0 1275
21 TraesCS7A01G511500 chr4D 91.769 899 71 3 2208 3103 56727163 56728061 0 1247


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 TraesCS7A01G511500 chr7A 699125965 699129071 3106 False 5738 5738 100.000 1 3107 1 chr7A.!!$F2 3106
1 TraesCS7A01G511500 chr7A 538762099 538762991 892 False 1264 1264 92.129 2206 3107 1 chr7A.!!$F1 901
2 TraesCS7A01G511500 chr7A 183472654 183473547 893 True 1230 1230 91.444 2208 3107 1 chr7A.!!$R1 899
3 TraesCS7A01G511500 chr7B 691966003 691967242 1239 False 1825 1825 93.226 969 2208 1 chr7B.!!$F2 1239
4 TraesCS7A01G511500 chr7B 691999535 692000774 1239 False 1781 1781 92.581 969 2208 1 chr7B.!!$F3 1239
5 TraesCS7A01G511500 chr7B 691927865 691929104 1239 False 1736 1736 91.935 969 2208 1 chr7B.!!$F1 1239
6 TraesCS7A01G511500 chr3A 653571572 653572536 964 False 1635 1635 97.211 1 968 1 chr3A.!!$F2 967
7 TraesCS7A01G511500 chr3A 519039684 519040651 967 True 1633 1633 97.107 1 968 1 chr3A.!!$R2 967
8 TraesCS7A01G511500 chr3A 600163199 600164167 968 False 1622 1622 96.904 1 968 1 chr3A.!!$F1 967
9 TraesCS7A01G511500 chr3A 198899656 198900631 975 True 1616 1616 96.619 1 972 1 chr3A.!!$R1 971
10 TraesCS7A01G511500 chr3A 739480103 739481070 967 True 1616 1616 96.798 1 968 1 chr3A.!!$R3 967
11 TraesCS7A01G511500 chr6A 548554172 548555139 967 True 1628 1628 97.004 1 968 1 chr6A.!!$R1 967
12 TraesCS7A01G511500 chr2A 676691780 676692746 966 True 1626 1626 97.004 1 968 1 chr2A.!!$R2 967
13 TraesCS7A01G511500 chr2A 732702174 732703140 966 False 1620 1620 96.901 1 968 1 chr2A.!!$F2 967
14 TraesCS7A01G511500 chr2A 495988317 495989286 969 True 1618 1618 96.804 1 968 1 chr2A.!!$R1 967
15 TraesCS7A01G511500 chr2A 714970498 714971386 888 False 1369 1369 94.333 2208 3107 1 chr2A.!!$F1 899
16 TraesCS7A01G511500 chr1A 51001145 51002047 902 True 1299 1299 92.707 2208 3107 1 chr1A.!!$R1 899
17 TraesCS7A01G511500 chr1A 51056662 51057575 913 True 1282 1282 92.240 2208 3107 1 chr1A.!!$R3 899
18 TraesCS7A01G511500 chr1A 553504480 553505374 894 False 1258 1258 92.000 2208 3107 1 chr1A.!!$F1 899
19 TraesCS7A01G511500 chr1A 51051049 51051943 894 True 1219 1219 91.232 2208 3107 1 chr1A.!!$R2 899
20 TraesCS7A01G511500 chr3D 17715811 17716705 894 True 1275 1275 92.350 2208 3107 1 chr3D.!!$R1 899
21 TraesCS7A01G511500 chr4D 56727163 56728061 898 False 1247 1247 91.769 2208 3103 1 chr4D.!!$F1 895

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
371 372 1.012486 GGTTAGGTGTCGCGTTCTGG 61.012 60.0 5.77 0.0 0.0 3.86 F
1024 1034 0.250467 CACTCCCCAGAACACACAGG 60.250 60.0 0.00 0.0 0.0 4.00 F
1699 1709 0.379669 GCCGATGAGGTTCAAGCATG 59.620 55.0 0.00 0.0 43.7 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1338 1348 0.465460 TGTTGAACACCACAGGAGGC 60.465 55.0 0.0 0.0 0.00 4.70 R
2081 2091 0.753479 TTTTCGAGCCTTGGTTGCCA 60.753 50.0 0.0 0.0 0.00 4.92 R
3056 3095 0.588252 CAAAGAACTGTGGCAGGACG 59.412 55.0 0.0 0.0 35.51 4.79 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
371 372 1.012486 GGTTAGGTGTCGCGTTCTGG 61.012 60.000 5.77 0.00 0.00 3.86
597 598 6.032956 TCTAACCAGACGTACAATTGTCAT 57.967 37.500 15.85 1.22 37.58 3.06
625 626 3.923017 GGAACTGGTCCAACAAATCAG 57.077 47.619 6.92 0.00 46.97 2.90
662 663 2.989571 ACTGGTTTCATCCTTCCCTTCT 59.010 45.455 0.00 0.00 0.00 2.85
794 795 6.759272 TCCTTACTACATTGCTGCTATTAGG 58.241 40.000 0.00 0.00 0.00 2.69
853 854 5.409211 GTTTGCCTAGTGTAGTCTACCTTC 58.591 45.833 7.56 0.00 0.00 3.46
930 932 8.968242 GTTTTGAAGACTTTCATAAAAATCGCT 58.032 29.630 0.00 0.00 42.60 4.93
992 1002 2.601266 CCGGTTAGTTTTTGCACTCACG 60.601 50.000 0.00 0.00 0.00 4.35
1008 1018 0.677731 CACGAACCATCATGGCCACT 60.678 55.000 8.16 0.00 42.67 4.00
1022 1032 1.836391 CCACTCCCCAGAACACACA 59.164 57.895 0.00 0.00 0.00 3.72
1024 1034 0.250467 CACTCCCCAGAACACACAGG 60.250 60.000 0.00 0.00 0.00 4.00
1088 1098 3.619483 ACACACTCGTTCAAAATCGACAA 59.381 39.130 0.00 0.00 32.65 3.18
1092 1102 5.694910 ACACTCGTTCAAAATCGACAAGTAT 59.305 36.000 0.00 0.00 32.65 2.12
1094 1104 5.120208 ACTCGTTCAAAATCGACAAGTATGG 59.880 40.000 0.00 0.00 32.65 2.74
1099 1109 4.764823 TCAAAATCGACAAGTATGGCCTTT 59.235 37.500 3.32 0.00 0.00 3.11
1110 1120 3.841870 GGCCTTTATCGGGGCTTG 58.158 61.111 0.00 0.00 46.80 4.01
1113 1123 1.828224 CCTTTATCGGGGCTTGGGC 60.828 63.158 0.00 0.00 37.82 5.36
1116 1126 2.487274 TTTATCGGGGCTTGGGCGTT 62.487 55.000 0.00 0.00 39.81 4.84
1146 1156 0.606604 TCCAGTCCGCTAACTTCACC 59.393 55.000 0.00 0.00 0.00 4.02
1181 1191 1.264749 TGGTGCATCCGCTTCTACCT 61.265 55.000 0.00 0.00 39.64 3.08
1199 1209 2.879462 CGACGGCTACAACGAGGC 60.879 66.667 0.00 0.00 38.61 4.70
1205 1215 1.470979 CGGCTACAACGAGGCTAACAT 60.471 52.381 0.00 0.00 39.80 2.71
1212 1222 6.294065 GCTACAACGAGGCTAACATAGACTAT 60.294 42.308 0.00 0.00 46.40 2.12
1218 1228 5.563085 CGAGGCTAACATAGACTATGTGTCC 60.563 48.000 25.24 23.11 46.40 4.02
1228 1238 4.235360 AGACTATGTGTCCGTTTTTCTCG 58.765 43.478 0.00 0.00 46.46 4.04
1255 1265 3.146104 AGACCAAGAACATTGAGGTGG 57.854 47.619 0.00 0.00 31.57 4.61
1263 1273 1.825191 CATTGAGGTGGGGGCGATG 60.825 63.158 0.00 0.00 0.00 3.84
1290 1300 1.404391 CTGATGCTGGTCAATCAAGCC 59.596 52.381 0.00 0.00 0.00 4.35
1294 1304 2.646930 TGCTGGTCAATCAAGCCATAG 58.353 47.619 0.00 0.00 0.00 2.23
1354 1364 1.770110 AGGCCTCCTGTGGTGTTCA 60.770 57.895 0.00 0.00 29.57 3.18
1376 1386 1.136252 CACTCGCAATGACAAACTCGG 60.136 52.381 0.00 0.00 0.00 4.63
1441 1451 3.879295 AGGCTCATCATACATTTTGGACG 59.121 43.478 0.00 0.00 0.00 4.79
1451 1461 4.749245 ACATTTTGGACGACTCAATCAC 57.251 40.909 0.00 0.00 0.00 3.06
1461 1471 1.349627 CTCAATCACCGTCGCATGC 59.650 57.895 7.91 7.91 0.00 4.06
1503 1513 0.625683 AGGATGCCAAGGAGGTGGAT 60.626 55.000 0.00 0.00 41.65 3.41
1513 1523 1.685224 GAGGTGGATGCTGGGTTGA 59.315 57.895 0.00 0.00 0.00 3.18
1523 1533 0.605319 GCTGGGTTGATCGGTGACAA 60.605 55.000 0.00 0.00 0.00 3.18
1533 1543 4.251246 GGTGACAACCAAGTGCCA 57.749 55.556 0.00 0.00 46.75 4.92
1572 1582 6.308566 TGCTAACCTTAGTAAATTGTTGGGT 58.691 36.000 0.00 0.00 33.32 4.51
1574 1584 7.088272 GCTAACCTTAGTAAATTGTTGGGTTG 58.912 38.462 9.56 0.00 37.12 3.77
1612 1622 4.641094 ACGTGTGTTTCAAGGTCCAAAATA 59.359 37.500 0.00 0.00 0.00 1.40
1635 1645 3.389329 AGGTATTCCATGCTCACGAGATT 59.611 43.478 0.00 0.00 35.89 2.40
1641 1651 3.006217 TCCATGCTCACGAGATTATCCTG 59.994 47.826 0.00 0.00 0.00 3.86
1685 1695 2.487532 CGGAGTTCTACGGGCCGAT 61.488 63.158 35.78 19.33 44.43 4.18
1690 1700 1.380785 TTCTACGGGCCGATGAGGT 60.381 57.895 35.78 11.90 43.70 3.85
1693 1703 1.672854 CTACGGGCCGATGAGGTTCA 61.673 60.000 35.78 4.49 43.70 3.18
1699 1709 0.379669 GCCGATGAGGTTCAAGCATG 59.620 55.000 0.00 0.00 43.70 4.06
1702 1712 1.407299 CGATGAGGTTCAAGCATGGGA 60.407 52.381 0.00 0.00 0.00 4.37
1705 1715 1.144708 TGAGGTTCAAGCATGGGAACA 59.855 47.619 6.82 0.00 43.96 3.18
1728 1738 9.491675 AACATCAAAAACATTGAAGATATGCAA 57.508 25.926 0.00 0.00 31.55 4.08
1767 1777 2.899900 ACTGCTCCACTTCATCTACACA 59.100 45.455 0.00 0.00 0.00 3.72
1774 1784 3.175152 CACTTCATCTACACAGACTCGC 58.825 50.000 0.00 0.00 32.25 5.03
1821 1831 2.224670 TGGTGGGTACGAAGAAATGCTT 60.225 45.455 0.00 0.00 40.25 3.91
1822 1832 3.008157 TGGTGGGTACGAAGAAATGCTTA 59.992 43.478 0.00 0.00 36.83 3.09
1848 1858 2.871182 TACTCGTGGCTGCAGATAAG 57.129 50.000 20.43 7.57 0.00 1.73
1853 1863 1.528586 CGTGGCTGCAGATAAGTATGC 59.471 52.381 20.43 0.00 42.78 3.14
1854 1864 2.804572 CGTGGCTGCAGATAAGTATGCT 60.805 50.000 20.43 0.00 42.90 3.79
1875 1885 8.985315 ATGCTATGAAAAGGATGAAGTCAATA 57.015 30.769 0.00 0.00 0.00 1.90
1879 1889 7.649533 ATGAAAAGGATGAAGTCAATATGCA 57.350 32.000 0.00 0.00 0.00 3.96
1882 1892 6.461110 AAAGGATGAAGTCAATATGCAAGG 57.539 37.500 0.00 0.00 0.00 3.61
1931 1941 1.128692 GACTGTGGCGACAACATTAGC 59.871 52.381 2.34 0.00 46.06 3.09
1990 2000 9.656040 AAGATGCTTGCATTAAATTTATCAACA 57.344 25.926 9.59 6.13 0.00 3.33
2019 2029 1.243342 ATGTGGATGGTGTGGTTGCG 61.243 55.000 0.00 0.00 0.00 4.85
2037 2047 3.592059 TGCGAGTAAAGGGTATCAACAC 58.408 45.455 0.00 0.00 0.00 3.32
2040 2050 4.181578 CGAGTAAAGGGTATCAACACCTG 58.818 47.826 0.00 0.00 38.73 4.00
2048 2058 3.440522 GGGTATCAACACCTGAAAAGAGC 59.559 47.826 0.00 0.00 37.67 4.09
2061 2071 5.221722 CCTGAAAAGAGCATGCCCTACTATA 60.222 44.000 15.66 0.00 0.00 1.31
2066 2076 5.832539 AGAGCATGCCCTACTATATTTGT 57.167 39.130 15.66 0.00 0.00 2.83
2081 2091 8.367660 ACTATATTTGTCGATATGTGGGAGAT 57.632 34.615 0.00 0.00 0.00 2.75
2101 2111 0.039165 GGCAACCAAGGCTCGAAAAG 60.039 55.000 0.00 0.00 0.00 2.27
2228 2238 8.951243 AGTTCTGCTGGAATTTAGTCTATTTTC 58.049 33.333 0.00 0.00 36.24 2.29
2314 2328 4.226394 TGCAAGGCAAGGGATACTACTAAA 59.774 41.667 0.00 0.00 34.76 1.85
2626 2665 2.559840 CTGCTGGCTGTTCGCTTG 59.440 61.111 0.00 0.00 39.13 4.01
2757 2796 3.131478 CGCCACCGGTTCCATTCC 61.131 66.667 2.97 0.00 0.00 3.01
2881 2920 3.096852 GGTGATAAGGTTTTTGGGGAGG 58.903 50.000 0.00 0.00 0.00 4.30
2885 2924 0.267658 AAGGTTTTTGGGGAGGGCTT 59.732 50.000 0.00 0.00 0.00 4.35
3056 3095 8.408743 ACGTATTTATGCTCTTTCTGTTAGAC 57.591 34.615 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
346 347 1.670083 GCGACACCTAACCGGCTTT 60.670 57.895 0.00 0.00 35.61 3.51
347 348 2.047560 GCGACACCTAACCGGCTT 60.048 61.111 0.00 0.00 35.61 4.35
359 360 2.434185 GATGCCCAGAACGCGACA 60.434 61.111 15.93 0.00 0.00 4.35
371 372 1.747355 CCACAATGTCTCTTGGATGCC 59.253 52.381 0.00 0.00 0.00 4.40
574 575 5.456548 TGACAATTGTACGTCTGGTTAGA 57.543 39.130 11.95 0.00 33.18 2.10
625 626 2.128035 CCAGTGACTCGTTGAAGACAC 58.872 52.381 0.00 0.00 40.66 3.67
662 663 6.053005 CACAAGGACCAACAGTAAGTAAAGA 58.947 40.000 0.00 0.00 0.00 2.52
853 854 1.967319 AACCTATTACCATGCAGCGG 58.033 50.000 3.41 3.41 0.00 5.52
890 892 3.936902 TCAAAACGTGGAAGTTTCGAG 57.063 42.857 0.00 0.00 42.81 4.04
992 1002 0.753111 GGGAGTGGCCATGATGGTTC 60.753 60.000 9.72 6.67 40.46 3.62
1008 1018 1.836391 CACCTGTGTGTTCTGGGGA 59.164 57.895 0.00 0.00 37.72 4.81
1032 1042 0.103208 CTGGGACGTAGACTGATGCC 59.897 60.000 0.00 0.00 0.00 4.40
1074 1084 4.156008 AGGCCATACTTGTCGATTTTGAAC 59.844 41.667 5.01 0.00 0.00 3.18
1088 1098 0.400594 GCCCCGATAAAGGCCATACT 59.599 55.000 5.01 0.00 43.76 2.12
1099 1109 3.404438 AACGCCCAAGCCCCGATA 61.404 61.111 0.00 0.00 34.57 2.92
1107 1117 2.336088 CAGTTGCCAACGCCCAAG 59.664 61.111 1.20 0.00 36.23 3.61
1110 1120 3.631487 GATGCAGTTGCCAACGCCC 62.631 63.158 17.34 8.92 41.18 6.13
1113 1123 1.210931 CTGGATGCAGTTGCCAACG 59.789 57.895 5.98 0.00 41.18 4.10
1116 1126 1.303561 GGACTGGATGCAGTTGCCA 60.304 57.895 21.67 0.00 41.18 4.92
1146 1156 2.102749 CATTCATGGCCGCCAACG 59.897 61.111 18.00 11.08 36.95 4.10
1181 1191 2.872557 CCTCGTTGTAGCCGTCGA 59.127 61.111 0.00 0.00 0.00 4.20
1199 1209 8.475331 AAAAACGGACACATAGTCTATGTTAG 57.525 34.615 20.72 13.92 46.69 2.34
1205 1215 5.181811 TCGAGAAAAACGGACACATAGTCTA 59.818 40.000 0.00 0.00 46.72 2.59
1212 1222 1.202486 AGCTCGAGAAAAACGGACACA 60.202 47.619 18.75 0.00 0.00 3.72
1218 1228 2.155924 GGTCTTGAGCTCGAGAAAAACG 59.844 50.000 31.15 6.52 38.07 3.60
1228 1238 4.067896 TCAATGTTCTTGGTCTTGAGCTC 58.932 43.478 6.82 6.82 0.00 4.09
1255 1265 2.146342 CATCAGATTGTACATCGCCCC 58.854 52.381 0.00 0.00 0.00 5.80
1263 1273 4.877823 TGATTGACCAGCATCAGATTGTAC 59.122 41.667 0.00 0.00 0.00 2.90
1290 1300 2.173669 CAACACCGGCGGCTCTATG 61.174 63.158 28.71 19.05 0.00 2.23
1336 1346 1.352622 TTGAACACCACAGGAGGCCT 61.353 55.000 3.86 3.86 0.00 5.19
1338 1348 0.465460 TGTTGAACACCACAGGAGGC 60.465 55.000 0.00 0.00 0.00 4.70
1354 1364 2.032894 CGAGTTTGTCATTGCGAGTGTT 60.033 45.455 0.00 0.00 0.00 3.32
1376 1386 1.302431 GCAACAAAACCCCATGCCC 60.302 57.895 0.00 0.00 0.00 5.36
1441 1451 0.647410 CATGCGACGGTGATTGAGTC 59.353 55.000 0.00 0.00 0.00 3.36
1451 1461 1.019278 AGTAAGGTTGCATGCGACGG 61.019 55.000 27.71 0.00 0.00 4.79
1503 1513 1.003839 GTCACCGATCAACCCAGCA 60.004 57.895 0.00 0.00 0.00 4.41
1523 1533 2.034066 CGGATGGTGGCACTTGGT 59.966 61.111 18.45 0.86 0.00 3.67
1572 1582 1.414919 ACGTCAGCTCCCTTTGTACAA 59.585 47.619 3.59 3.59 0.00 2.41
1574 1584 1.270147 ACACGTCAGCTCCCTTTGTAC 60.270 52.381 0.00 0.00 0.00 2.90
1612 1622 2.766263 TCTCGTGAGCATGGAATACCTT 59.234 45.455 0.00 0.00 37.04 3.50
1635 1645 2.734591 GACCGCATCGCCAGGATA 59.265 61.111 0.00 0.00 32.85 2.59
1655 1665 1.827399 GAACTCCGCCCAGAAGACCA 61.827 60.000 0.00 0.00 0.00 4.02
1685 1695 1.144708 TGTTCCCATGCTTGAACCTCA 59.855 47.619 14.53 0.00 40.06 3.86
1690 1700 4.952071 TTTTGATGTTCCCATGCTTGAA 57.048 36.364 0.22 0.00 0.00 2.69
1693 1703 4.686191 TGTTTTTGATGTTCCCATGCTT 57.314 36.364 0.00 0.00 0.00 3.91
1699 1709 9.090692 CATATCTTCAATGTTTTTGATGTTCCC 57.909 33.333 0.00 0.00 0.00 3.97
1702 1712 9.491675 TTGCATATCTTCAATGTTTTTGATGTT 57.508 25.926 0.00 0.00 0.00 2.71
1705 1715 7.550196 GGGTTGCATATCTTCAATGTTTTTGAT 59.450 33.333 0.00 0.00 0.00 2.57
1728 1738 1.203149 AGTCCTCTAAAGACACCGGGT 60.203 52.381 6.32 0.00 36.68 5.28
1767 1777 2.441164 ATCGGAGGCAGCGAGTCT 60.441 61.111 0.00 0.00 32.36 3.24
1774 1784 1.144936 GGTCCTTCATCGGAGGCAG 59.855 63.158 0.00 0.00 32.70 4.85
1821 1831 1.742411 GCAGCCACGAGTAAATGCCTA 60.742 52.381 0.00 0.00 0.00 3.93
1822 1832 1.026718 GCAGCCACGAGTAAATGCCT 61.027 55.000 0.00 0.00 0.00 4.75
1833 1843 1.528586 GCATACTTATCTGCAGCCACG 59.471 52.381 9.47 0.00 38.28 4.94
1848 1858 7.792374 TGACTTCATCCTTTTCATAGCATAC 57.208 36.000 0.00 0.00 0.00 2.39
1853 1863 8.843262 TGCATATTGACTTCATCCTTTTCATAG 58.157 33.333 0.00 0.00 0.00 2.23
1854 1864 8.750515 TGCATATTGACTTCATCCTTTTCATA 57.249 30.769 0.00 0.00 0.00 2.15
1875 1885 1.767681 TGGCAAAGTTTTCCCTTGCAT 59.232 42.857 1.61 0.00 0.00 3.96
1879 1889 2.319844 CCTCTGGCAAAGTTTTCCCTT 58.680 47.619 1.61 0.00 0.00 3.95
1882 1892 3.132111 TCAAACCTCTGGCAAAGTTTTCC 59.868 43.478 0.00 0.00 30.27 3.13
1990 2000 3.330701 ACACCATCCACATTACTCAAGGT 59.669 43.478 0.00 0.00 0.00 3.50
2000 2010 1.243342 CGCAACCACACCATCCACAT 61.243 55.000 0.00 0.00 0.00 3.21
2019 2029 5.416271 TCAGGTGTTGATACCCTTTACTC 57.584 43.478 0.00 0.00 41.83 2.59
2037 2047 2.019984 GTAGGGCATGCTCTTTTCAGG 58.980 52.381 28.24 0.00 0.00 3.86
2040 2050 7.229506 ACAAATATAGTAGGGCATGCTCTTTTC 59.770 37.037 28.24 16.35 0.00 2.29
2048 2058 7.981789 ACATATCGACAAATATAGTAGGGCATG 59.018 37.037 0.00 0.00 0.00 4.06
2061 2071 4.645535 CCATCTCCCACATATCGACAAAT 58.354 43.478 0.00 0.00 0.00 2.32
2066 2076 1.715785 TGCCATCTCCCACATATCGA 58.284 50.000 0.00 0.00 0.00 3.59
2081 2091 0.753479 TTTTCGAGCCTTGGTTGCCA 60.753 50.000 0.00 0.00 0.00 4.92
2129 2139 5.932303 GGCATCAAGTGAAGTAACTACTCAA 59.068 40.000 0.00 0.00 34.99 3.02
2130 2140 5.011635 TGGCATCAAGTGAAGTAACTACTCA 59.988 40.000 0.00 0.00 34.99 3.41
2200 2210 8.499403 AATAGACTAAATTCCAGCAGAACTTC 57.501 34.615 0.00 0.00 37.29 3.01
2228 2238 2.948979 TGAAATAGTTATTGGGCTGCCG 59.051 45.455 13.40 0.00 0.00 5.69
2314 2328 4.910458 ACTAGCAATGTGGGACTAAACT 57.090 40.909 0.00 0.00 0.00 2.66
2480 2519 2.044946 GGCTCATTCCCGCAACCT 60.045 61.111 0.00 0.00 0.00 3.50
2626 2665 1.657822 GAAACGAAGAGATGGAGGCC 58.342 55.000 0.00 0.00 0.00 5.19
2670 2709 2.240493 TTATAGGCGCAAGAGAAGGC 57.760 50.000 10.83 0.00 43.02 4.35
2885 2924 1.134075 GAAGTCAGTAGTCGCGCGA 59.866 57.895 31.40 31.40 0.00 5.87
3056 3095 0.588252 CAAAGAACTGTGGCAGGACG 59.412 55.000 0.00 0.00 35.51 4.79


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

AutoCloner maintained by Alex Coulton.