Multiple sequence alignment - TraesCS1A01G330000

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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 TraesCS1A01G330000 chr1A 100.000 2351 0 0 1 2351 518863059 518860709 0.000000e+00 4342.0
1 TraesCS1A01G330000 chr1A 94.726 929 48 1 1 929 569487760 569488687 0.000000e+00 1443.0
2 TraesCS1A01G330000 chr1A 94.295 929 52 1 1 929 569523052 569523979 0.000000e+00 1421.0
3 TraesCS1A01G330000 chr1A 88.889 126 10 3 1467 1588 518668068 518667943 4.050000e-33 152.0
4 TraesCS1A01G330000 chr1A 83.439 157 15 10 1433 1585 544125186 544125335 4.080000e-28 135.0
5 TraesCS1A01G330000 chr1A 93.421 76 3 2 1584 1657 518950329 518950254 6.870000e-21 111.0
6 TraesCS1A01G330000 chr1A 93.421 76 3 2 1584 1657 518950549 518950474 6.870000e-21 111.0
7 TraesCS1A01G330000 chr5A 95.910 929 38 0 1 929 100648770 100647842 0.000000e+00 1506.0
8 TraesCS1A01G330000 chr5A 94.941 929 47 0 1 929 6919977 6920905 0.000000e+00 1456.0
9 TraesCS1A01G330000 chr5A 94.086 930 55 0 1 930 14988867 14989796 0.000000e+00 1413.0
10 TraesCS1A01G330000 chr5A 84.459 148 17 4 1439 1585 59616842 59616984 8.760000e-30 141.0
11 TraesCS1A01G330000 chr7A 95.479 929 42 0 1 929 180346432 180345504 0.000000e+00 1483.0
12 TraesCS1A01G330000 chr2A 94.635 932 50 0 1 932 52224775 52225706 0.000000e+00 1445.0
13 TraesCS1A01G330000 chr2A 94.403 929 49 2 1 929 52200685 52201610 0.000000e+00 1424.0
14 TraesCS1A01G330000 chr4A 94.612 928 49 1 2 929 624595310 624594384 0.000000e+00 1435.0
15 TraesCS1A01G330000 chr1D 90.999 711 41 8 1617 2319 422932551 422931856 0.000000e+00 937.0
16 TraesCS1A01G330000 chr1D 88.300 453 29 9 1584 2028 422932979 422932543 2.680000e-144 521.0
17 TraesCS1A01G330000 chr1D 90.793 391 25 4 998 1378 422933777 422933388 1.610000e-141 512.0
18 TraesCS1A01G330000 chr1D 84.164 341 35 10 989 1314 422992318 422992654 1.750000e-81 313.0
19 TraesCS1A01G330000 chr1D 86.224 196 24 2 990 1185 422994654 422994462 2.370000e-50 209.0
20 TraesCS1A01G330000 chr1D 88.189 127 12 3 1465 1588 422837418 422837292 5.230000e-32 148.0
21 TraesCS1A01G330000 chr1D 86.555 119 12 2 1394 1512 421864706 421864820 6.820000e-26 128.0
22 TraesCS1A01G330000 chr1D 93.671 79 2 3 1584 1659 423030814 423030736 5.310000e-22 115.0
23 TraesCS1A01G330000 chr1D 97.059 34 1 0 1408 1441 422992983 422993016 9.080000e-05 58.4
24 TraesCS1A01G330000 chr1B 91.680 625 43 6 1584 2203 571757250 571756630 0.000000e+00 857.0
25 TraesCS1A01G330000 chr1B 90.172 407 23 7 986 1376 571758049 571757644 4.480000e-142 514.0
26 TraesCS1A01G330000 chr1B 94.954 218 11 0 2134 2351 571756631 571756414 2.240000e-90 342.0
27 TraesCS1A01G330000 chr1B 86.528 193 22 2 1394 1585 570723952 570724141 2.370000e-50 209.0
28 TraesCS1A01G330000 chr1B 85.567 194 16 8 1394 1585 570836212 570836395 2.380000e-45 193.0
29 TraesCS1A01G330000 chr1B 88.112 143 12 4 985 1125 572110760 572110621 5.200000e-37 165.0
30 TraesCS1A01G330000 chr1B 88.983 118 11 2 1467 1582 567120086 567120203 6.770000e-31 145.0
31 TraesCS1A01G330000 chr1B 87.200 125 15 1 1465 1588 572141279 572141155 8.760000e-30 141.0
32 TraesCS1A01G330000 chr1B 94.595 74 3 1 1584 1656 570836452 570836525 1.910000e-21 113.0
33 TraesCS1A01G330000 chr1B 92.958 71 3 2 1584 1654 571444296 571444228 4.130000e-18 102.0
34 TraesCS1A01G330000 chr1B 96.721 61 2 0 1584 1644 571497096 571497036 4.130000e-18 102.0
35 TraesCS1A01G330000 chr1B 93.939 66 4 0 1584 1649 572145000 572144935 1.490000e-17 100.0
36 TraesCS1A01G330000 chr1B 95.161 62 3 0 1584 1645 570724198 570724259 5.350000e-17 99.0
37 TraesCS1A01G330000 chr5B 84.459 148 18 4 1439 1585 74659020 74659163 8.760000e-30 141.0


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 TraesCS1A01G330000 chr1A 518860709 518863059 2350 True 4342.000000 4342 100.000000 1 2351 1 chr1A.!!$R2 2350
1 TraesCS1A01G330000 chr1A 569487760 569488687 927 False 1443.000000 1443 94.726000 1 929 1 chr1A.!!$F2 928
2 TraesCS1A01G330000 chr1A 569523052 569523979 927 False 1421.000000 1421 94.295000 1 929 1 chr1A.!!$F3 928
3 TraesCS1A01G330000 chr5A 100647842 100648770 928 True 1506.000000 1506 95.910000 1 929 1 chr5A.!!$R1 928
4 TraesCS1A01G330000 chr5A 6919977 6920905 928 False 1456.000000 1456 94.941000 1 929 1 chr5A.!!$F1 928
5 TraesCS1A01G330000 chr5A 14988867 14989796 929 False 1413.000000 1413 94.086000 1 930 1 chr5A.!!$F2 929
6 TraesCS1A01G330000 chr7A 180345504 180346432 928 True 1483.000000 1483 95.479000 1 929 1 chr7A.!!$R1 928
7 TraesCS1A01G330000 chr2A 52224775 52225706 931 False 1445.000000 1445 94.635000 1 932 1 chr2A.!!$F2 931
8 TraesCS1A01G330000 chr2A 52200685 52201610 925 False 1424.000000 1424 94.403000 1 929 1 chr2A.!!$F1 928
9 TraesCS1A01G330000 chr4A 624594384 624595310 926 True 1435.000000 1435 94.612000 2 929 1 chr4A.!!$R1 927
10 TraesCS1A01G330000 chr1D 422931856 422933777 1921 True 656.666667 937 90.030667 998 2319 3 chr1D.!!$R4 1321
11 TraesCS1A01G330000 chr1B 571756414 571758049 1635 True 571.000000 857 92.268667 986 2351 3 chr1B.!!$R4 1365

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
943 944 0.178873 TAACAGGCACCTCTTCCCCT 60.179 55.0 0.0 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2237 2989 0.323629 GATCCTTTGTGGTCGGTGGA 59.676 55.0 0.0 0.0 37.07 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
37 38 2.432300 GCCCTCCAAGTAGCGGCTA 61.432 63.158 5.42 5.42 36.65 3.93
90 91 2.431260 GTAGTTGTCCGGCGCGAA 60.431 61.111 12.10 0.00 0.00 4.70
625 626 1.742768 GATTGGAGCGTCCGGAGAT 59.257 57.895 3.06 0.00 40.17 2.75
650 651 2.687566 CCTACGGGGAAGTGGGCT 60.688 66.667 0.00 0.00 35.99 5.19
789 790 1.134818 TGCAGCGGAAGACATCGTAAT 60.135 47.619 0.00 0.00 0.00 1.89
801 802 9.915629 GGAAGACATCGTAATCTAAACTGATAT 57.084 33.333 0.00 0.00 0.00 1.63
932 933 6.994496 ACTACGTATATACAGTCTAACAGGCA 59.006 38.462 13.22 0.00 0.00 4.75
933 934 6.069684 ACGTATATACAGTCTAACAGGCAC 57.930 41.667 13.22 0.00 0.00 5.01
934 935 5.009410 ACGTATATACAGTCTAACAGGCACC 59.991 44.000 13.22 0.00 0.00 5.01
935 936 5.241064 CGTATATACAGTCTAACAGGCACCT 59.759 44.000 13.22 0.00 0.00 4.00
936 937 5.793030 ATATACAGTCTAACAGGCACCTC 57.207 43.478 0.00 0.00 0.00 3.85
937 938 2.016905 ACAGTCTAACAGGCACCTCT 57.983 50.000 0.00 0.00 0.00 3.69
938 939 2.330216 ACAGTCTAACAGGCACCTCTT 58.670 47.619 0.00 0.00 0.00 2.85
939 940 2.300437 ACAGTCTAACAGGCACCTCTTC 59.700 50.000 0.00 0.00 0.00 2.87
940 941 1.903183 AGTCTAACAGGCACCTCTTCC 59.097 52.381 0.00 0.00 0.00 3.46
941 942 1.066071 GTCTAACAGGCACCTCTTCCC 60.066 57.143 0.00 0.00 0.00 3.97
942 943 0.253327 CTAACAGGCACCTCTTCCCC 59.747 60.000 0.00 0.00 0.00 4.81
943 944 0.178873 TAACAGGCACCTCTTCCCCT 60.179 55.000 0.00 0.00 0.00 4.79
944 945 1.492993 AACAGGCACCTCTTCCCCTC 61.493 60.000 0.00 0.00 0.00 4.30
945 946 1.920325 CAGGCACCTCTTCCCCTCA 60.920 63.158 0.00 0.00 0.00 3.86
946 947 1.083706 AGGCACCTCTTCCCCTCAT 59.916 57.895 0.00 0.00 0.00 2.90
947 948 1.225704 GGCACCTCTTCCCCTCATG 59.774 63.158 0.00 0.00 0.00 3.07
948 949 1.566298 GGCACCTCTTCCCCTCATGT 61.566 60.000 0.00 0.00 0.00 3.21
949 950 1.204146 GCACCTCTTCCCCTCATGTA 58.796 55.000 0.00 0.00 0.00 2.29
950 951 1.559682 GCACCTCTTCCCCTCATGTAA 59.440 52.381 0.00 0.00 0.00 2.41
951 952 2.173569 GCACCTCTTCCCCTCATGTAAT 59.826 50.000 0.00 0.00 0.00 1.89
952 953 3.372025 GCACCTCTTCCCCTCATGTAATT 60.372 47.826 0.00 0.00 0.00 1.40
953 954 4.202441 CACCTCTTCCCCTCATGTAATTG 58.798 47.826 0.00 0.00 0.00 2.32
954 955 3.217626 CCTCTTCCCCTCATGTAATTGC 58.782 50.000 0.00 0.00 0.00 3.56
955 956 3.217626 CTCTTCCCCTCATGTAATTGCC 58.782 50.000 0.00 0.00 0.00 4.52
956 957 1.949525 CTTCCCCTCATGTAATTGCCG 59.050 52.381 0.00 0.00 0.00 5.69
957 958 0.465460 TCCCCTCATGTAATTGCCGC 60.465 55.000 0.00 0.00 0.00 6.53
958 959 0.466189 CCCCTCATGTAATTGCCGCT 60.466 55.000 0.00 0.00 0.00 5.52
959 960 0.947244 CCCTCATGTAATTGCCGCTC 59.053 55.000 0.00 0.00 0.00 5.03
960 961 0.947244 CCTCATGTAATTGCCGCTCC 59.053 55.000 0.00 0.00 0.00 4.70
961 962 1.475751 CCTCATGTAATTGCCGCTCCT 60.476 52.381 0.00 0.00 0.00 3.69
962 963 2.224281 CCTCATGTAATTGCCGCTCCTA 60.224 50.000 0.00 0.00 0.00 2.94
963 964 3.557898 CCTCATGTAATTGCCGCTCCTAT 60.558 47.826 0.00 0.00 0.00 2.57
964 965 3.664107 TCATGTAATTGCCGCTCCTATC 58.336 45.455 0.00 0.00 0.00 2.08
965 966 3.070878 TCATGTAATTGCCGCTCCTATCA 59.929 43.478 0.00 0.00 0.00 2.15
966 967 3.552132 TGTAATTGCCGCTCCTATCAA 57.448 42.857 0.00 0.00 0.00 2.57
967 968 3.466836 TGTAATTGCCGCTCCTATCAAG 58.533 45.455 0.00 0.00 0.00 3.02
968 969 3.133901 TGTAATTGCCGCTCCTATCAAGA 59.866 43.478 0.00 0.00 0.00 3.02
969 970 2.540265 ATTGCCGCTCCTATCAAGAG 57.460 50.000 0.00 0.00 0.00 2.85
970 971 1.485124 TTGCCGCTCCTATCAAGAGA 58.515 50.000 0.00 0.00 32.86 3.10
971 972 1.485124 TGCCGCTCCTATCAAGAGAA 58.515 50.000 0.00 0.00 32.86 2.87
972 973 1.410517 TGCCGCTCCTATCAAGAGAAG 59.589 52.381 0.00 0.00 32.86 2.85
973 974 1.270041 GCCGCTCCTATCAAGAGAAGG 60.270 57.143 0.00 0.00 35.24 3.46
974 975 1.270041 CCGCTCCTATCAAGAGAAGGC 60.270 57.143 0.00 0.00 32.86 4.35
975 976 1.410517 CGCTCCTATCAAGAGAAGGCA 59.589 52.381 0.00 0.00 32.86 4.75
976 977 2.801342 CGCTCCTATCAAGAGAAGGCAC 60.801 54.545 0.00 0.00 32.86 5.01
977 978 2.169352 GCTCCTATCAAGAGAAGGCACA 59.831 50.000 0.00 0.00 32.86 4.57
978 979 3.791245 CTCCTATCAAGAGAAGGCACAC 58.209 50.000 0.00 0.00 32.86 3.82
979 980 3.173151 TCCTATCAAGAGAAGGCACACA 58.827 45.455 0.00 0.00 0.00 3.72
980 981 3.776969 TCCTATCAAGAGAAGGCACACAT 59.223 43.478 0.00 0.00 0.00 3.21
981 982 4.962362 TCCTATCAAGAGAAGGCACACATA 59.038 41.667 0.00 0.00 0.00 2.29
982 983 5.604231 TCCTATCAAGAGAAGGCACACATAT 59.396 40.000 0.00 0.00 0.00 1.78
983 984 6.100279 TCCTATCAAGAGAAGGCACACATATT 59.900 38.462 0.00 0.00 0.00 1.28
984 985 7.290014 TCCTATCAAGAGAAGGCACACATATTA 59.710 37.037 0.00 0.00 0.00 0.98
988 989 7.791029 TCAAGAGAAGGCACACATATTACATA 58.209 34.615 0.00 0.00 0.00 2.29
1007 1008 4.770531 ACATATATCAGCAGCAATGGCAAT 59.229 37.500 0.00 0.00 44.61 3.56
1015 1016 0.384309 AGCAATGGCAATGATCAGCG 59.616 50.000 6.76 0.00 44.61 5.18
1126 1127 1.271597 CCTCCAAGGACCACAAGAAGG 60.272 57.143 0.00 0.00 37.67 3.46
1127 1128 0.110486 TCCAAGGACCACAAGAAGGC 59.890 55.000 0.00 0.00 0.00 4.35
1308 1315 0.173708 CCTTCCACAGCGTCTACTCC 59.826 60.000 0.00 0.00 0.00 3.85
1373 1392 2.304180 CACCACCACCATCTTCTTCTCT 59.696 50.000 0.00 0.00 0.00 3.10
1382 1603 5.702670 CACCATCTTCTTCTCTGCTGTTTAA 59.297 40.000 0.00 0.00 0.00 1.52
1388 1609 3.580458 TCTTCTCTGCTGTTTAAGGAGCT 59.420 43.478 8.71 0.00 43.79 4.09
1391 1612 5.483685 TCTCTGCTGTTTAAGGAGCTTAA 57.516 39.130 8.71 0.00 43.79 1.85
1412 1633 1.200020 CTGAACGGGAATTGGCAAGAC 59.800 52.381 5.96 1.90 0.00 3.01
1435 1656 9.178758 AGACATAAACATCCCTTGAATTTACTC 57.821 33.333 0.00 0.00 0.00 2.59
1460 1681 0.598158 TTTGTACGGTGCTGTCGTCC 60.598 55.000 0.00 0.00 41.38 4.79
1470 1691 4.288234 TGTCGTCCCTGACAAGGT 57.712 55.556 0.00 0.00 45.40 3.50
1484 1705 1.741145 ACAAGGTCGTTTGTTTCGCTT 59.259 42.857 0.00 0.00 38.05 4.68
1485 1706 2.223180 ACAAGGTCGTTTGTTTCGCTTC 60.223 45.455 0.00 0.00 38.05 3.86
1486 1707 0.942252 AGGTCGTTTGTTTCGCTTCC 59.058 50.000 0.00 0.00 0.00 3.46
1488 1709 0.383860 GTCGTTTGTTTCGCTTCCGG 60.384 55.000 0.00 0.00 34.56 5.14
1489 1710 0.530211 TCGTTTGTTTCGCTTCCGGA 60.530 50.000 0.00 0.00 34.56 5.14
1490 1711 0.305313 CGTTTGTTTCGCTTCCGGAA 59.695 50.000 17.73 17.73 34.56 4.30
1496 1717 0.941542 TTTCGCTTCCGGAACAACAG 59.058 50.000 14.35 3.92 34.56 3.16
1545 1769 3.552294 GCGTAGGTCTCATAGCTGAAAAC 59.448 47.826 0.00 0.00 37.13 2.43
1547 1771 3.963428 AGGTCTCATAGCTGAAAACGT 57.037 42.857 0.00 0.00 33.68 3.99
1566 1790 0.402887 TGAGTGGTCCTGAGGTCGTA 59.597 55.000 0.00 0.00 0.00 3.43
1582 1806 2.935201 GTCGTAAGTTCGAGCCTCTCTA 59.065 50.000 0.00 0.00 40.52 2.43
1583 1807 2.935201 TCGTAAGTTCGAGCCTCTCTAC 59.065 50.000 0.00 0.00 34.85 2.59
1585 1809 2.217510 AAGTTCGAGCCTCTCTACCA 57.782 50.000 0.00 0.00 0.00 3.25
1587 1811 1.174783 GTTCGAGCCTCTCTACCACA 58.825 55.000 0.00 0.00 0.00 4.17
1589 1813 1.464734 TCGAGCCTCTCTACCACAAG 58.535 55.000 0.00 0.00 0.00 3.16
1632 2309 0.687354 ACCGAGCATGTCTGAACCTT 59.313 50.000 0.00 0.00 0.00 3.50
1729 2412 3.041211 AGCATGCCATCCTCTGTAACTA 58.959 45.455 15.66 0.00 0.00 2.24
1793 2477 7.088905 TGACCTCTACTTCTTTAAACACGATC 58.911 38.462 0.00 0.00 0.00 3.69
1834 2518 7.817962 TCTTCAGTTGCCTAAGTAACTATGTTC 59.182 37.037 0.00 0.00 45.85 3.18
1887 2571 4.824289 TGTAGTCCTTTCGGTGGATAAAC 58.176 43.478 0.00 0.00 35.87 2.01
1889 2573 2.910977 AGTCCTTTCGGTGGATAAACCT 59.089 45.455 0.00 0.00 38.14 3.50
1890 2574 3.007635 GTCCTTTCGGTGGATAAACCTG 58.992 50.000 0.00 0.00 38.14 4.00
1891 2575 2.640826 TCCTTTCGGTGGATAAACCTGT 59.359 45.455 0.00 0.00 38.14 4.00
1960 2644 1.971167 GTGCGTGAATCAAGGGCCA 60.971 57.895 6.18 0.00 0.00 5.36
1976 2660 2.102252 GGGCCATGTTCAGTTTGAAACA 59.898 45.455 11.02 0.00 38.22 2.83
1977 2661 3.431486 GGGCCATGTTCAGTTTGAAACAA 60.431 43.478 11.02 0.00 38.22 2.83
1980 2664 5.988561 GGCCATGTTCAGTTTGAAACAATTA 59.011 36.000 11.02 0.00 38.22 1.40
1988 2672 8.974408 GTTCAGTTTGAAACAATTAATACCACC 58.026 33.333 11.02 0.00 38.22 4.61
2015 2699 7.717436 TGTCAGTCATGAGTAATGTTTGGTTTA 59.283 33.333 1.86 0.00 35.66 2.01
2024 2708 8.417106 TGAGTAATGTTTGGTTTATTTGAGCAA 58.583 29.630 0.00 0.00 33.16 3.91
2045 2729 7.727181 AGCAACTCCTATTATTCGTAGACAAT 58.273 34.615 0.00 0.00 34.32 2.71
2087 2771 7.614192 CCCTACTAGAAACCATACAAAACCATT 59.386 37.037 0.00 0.00 0.00 3.16
2098 2782 8.415553 ACCATACAAAACCATTGATGATATGTG 58.584 33.333 0.00 0.00 0.00 3.21
2139 2891 3.694535 ATAGCTGTTTCGAGGACTACG 57.305 47.619 0.00 0.00 0.00 3.51
2173 2925 7.502120 AATGTCTCAGAAATGCATATGTACC 57.498 36.000 0.00 0.00 0.00 3.34
2237 2989 2.823959 TGGTAAGGAGGGTGTTCGTAT 58.176 47.619 0.00 0.00 0.00 3.06
2240 2992 1.946984 AAGGAGGGTGTTCGTATCCA 58.053 50.000 0.00 0.00 32.21 3.41
2288 3040 2.690778 GGCACCACGCTTGTCCATC 61.691 63.158 0.00 0.00 41.91 3.51
2338 3090 3.727079 CGTCTGCGTCTTTACATACGAGT 60.727 47.826 0.00 0.00 41.55 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 0.039911 AGGTCTTGCCTCTACTCCGT 59.960 55.000 0.00 0.00 46.96 4.69
90 91 4.210158 ACCTGCTACCGGTGAAGT 57.790 55.556 19.93 4.45 32.41 3.01
100 101 3.369756 CGTTTTATTTCTCGCACCTGCTA 59.630 43.478 0.00 0.00 39.32 3.49
399 400 2.362120 ACTACTACCAGGCGCCGT 60.362 61.111 23.20 16.87 0.00 5.68
444 445 4.728102 CGCCGCAACCCTACACGA 62.728 66.667 0.00 0.00 0.00 4.35
667 668 3.580193 CCCCTCGCGACGACGTAT 61.580 66.667 3.71 0.00 41.98 3.06
801 802 7.841282 TTTCCAAACCCTATGTTTTACATGA 57.159 32.000 0.00 0.00 44.80 3.07
823 824 1.053424 TAGGGTGTCGAGCCAGTTTT 58.947 50.000 8.07 0.00 42.81 2.43
932 933 3.372025 GCAATTACATGAGGGGAAGAGGT 60.372 47.826 0.00 0.00 0.00 3.85
933 934 3.217626 GCAATTACATGAGGGGAAGAGG 58.782 50.000 0.00 0.00 0.00 3.69
934 935 3.217626 GGCAATTACATGAGGGGAAGAG 58.782 50.000 0.00 0.00 0.00 2.85
935 936 2.421388 CGGCAATTACATGAGGGGAAGA 60.421 50.000 0.00 0.00 0.00 2.87
936 937 1.949525 CGGCAATTACATGAGGGGAAG 59.050 52.381 0.00 0.00 0.00 3.46
937 938 2.021723 GCGGCAATTACATGAGGGGAA 61.022 52.381 0.00 0.00 0.00 3.97
938 939 0.465460 GCGGCAATTACATGAGGGGA 60.465 55.000 0.00 0.00 0.00 4.81
939 940 0.466189 AGCGGCAATTACATGAGGGG 60.466 55.000 0.00 0.00 0.00 4.79
940 941 0.947244 GAGCGGCAATTACATGAGGG 59.053 55.000 0.00 0.00 0.00 4.30
941 942 0.947244 GGAGCGGCAATTACATGAGG 59.053 55.000 0.00 0.00 0.00 3.86
942 943 1.959042 AGGAGCGGCAATTACATGAG 58.041 50.000 0.00 0.00 0.00 2.90
943 944 3.070878 TGATAGGAGCGGCAATTACATGA 59.929 43.478 0.00 0.00 0.00 3.07
944 945 3.402110 TGATAGGAGCGGCAATTACATG 58.598 45.455 1.45 0.00 0.00 3.21
945 946 3.769739 TGATAGGAGCGGCAATTACAT 57.230 42.857 1.45 0.00 0.00 2.29
946 947 3.133901 TCTTGATAGGAGCGGCAATTACA 59.866 43.478 1.45 0.00 0.00 2.41
947 948 3.728845 TCTTGATAGGAGCGGCAATTAC 58.271 45.455 1.45 0.00 0.00 1.89
948 949 3.641436 TCTCTTGATAGGAGCGGCAATTA 59.359 43.478 1.45 0.00 0.00 1.40
949 950 2.435805 TCTCTTGATAGGAGCGGCAATT 59.564 45.455 1.45 0.00 0.00 2.32
950 951 2.042464 TCTCTTGATAGGAGCGGCAAT 58.958 47.619 1.45 0.00 0.00 3.56
951 952 1.485124 TCTCTTGATAGGAGCGGCAA 58.515 50.000 1.45 0.00 0.00 4.52
952 953 1.410517 CTTCTCTTGATAGGAGCGGCA 59.589 52.381 1.45 0.00 0.00 5.69
953 954 1.270041 CCTTCTCTTGATAGGAGCGGC 60.270 57.143 0.00 0.00 0.00 6.53
954 955 1.270041 GCCTTCTCTTGATAGGAGCGG 60.270 57.143 0.00 0.00 0.00 5.52
955 956 1.410517 TGCCTTCTCTTGATAGGAGCG 59.589 52.381 0.00 0.00 0.00 5.03
956 957 2.169352 TGTGCCTTCTCTTGATAGGAGC 59.831 50.000 0.00 0.00 0.00 4.70
957 958 3.196469 TGTGTGCCTTCTCTTGATAGGAG 59.804 47.826 0.00 0.00 0.00 3.69
958 959 3.173151 TGTGTGCCTTCTCTTGATAGGA 58.827 45.455 0.00 0.00 0.00 2.94
959 960 3.616956 TGTGTGCCTTCTCTTGATAGG 57.383 47.619 0.00 0.00 0.00 2.57
960 961 7.928167 TGTAATATGTGTGCCTTCTCTTGATAG 59.072 37.037 0.00 0.00 0.00 2.08
961 962 7.791029 TGTAATATGTGTGCCTTCTCTTGATA 58.209 34.615 0.00 0.00 0.00 2.15
962 963 6.653020 TGTAATATGTGTGCCTTCTCTTGAT 58.347 36.000 0.00 0.00 0.00 2.57
963 964 6.048732 TGTAATATGTGTGCCTTCTCTTGA 57.951 37.500 0.00 0.00 0.00 3.02
964 965 6.932356 ATGTAATATGTGTGCCTTCTCTTG 57.068 37.500 0.00 0.00 0.00 3.02
967 968 9.875691 TGATATATGTAATATGTGTGCCTTCTC 57.124 33.333 0.00 0.00 40.40 2.87
968 969 9.881649 CTGATATATGTAATATGTGTGCCTTCT 57.118 33.333 0.00 0.00 40.40 2.85
969 970 8.607459 GCTGATATATGTAATATGTGTGCCTTC 58.393 37.037 0.00 0.00 40.40 3.46
970 971 8.102676 TGCTGATATATGTAATATGTGTGCCTT 58.897 33.333 0.00 0.00 40.40 4.35
971 972 7.623630 TGCTGATATATGTAATATGTGTGCCT 58.376 34.615 0.00 0.00 40.40 4.75
972 973 7.466455 GCTGCTGATATATGTAATATGTGTGCC 60.466 40.741 0.00 0.00 40.40 5.01
973 974 7.064966 TGCTGCTGATATATGTAATATGTGTGC 59.935 37.037 0.00 0.00 40.40 4.57
974 975 8.483307 TGCTGCTGATATATGTAATATGTGTG 57.517 34.615 0.00 0.00 40.40 3.82
975 976 9.676861 ATTGCTGCTGATATATGTAATATGTGT 57.323 29.630 0.00 0.00 40.40 3.72
976 977 9.931210 CATTGCTGCTGATATATGTAATATGTG 57.069 33.333 0.00 0.00 40.40 3.21
977 978 9.117183 CCATTGCTGCTGATATATGTAATATGT 57.883 33.333 0.00 0.00 40.40 2.29
978 979 8.074370 GCCATTGCTGCTGATATATGTAATATG 58.926 37.037 0.00 0.00 35.73 1.78
979 980 7.776500 TGCCATTGCTGCTGATATATGTAATAT 59.224 33.333 0.00 0.00 39.83 1.28
980 981 7.111466 TGCCATTGCTGCTGATATATGTAATA 58.889 34.615 0.00 0.00 38.71 0.98
981 982 5.947566 TGCCATTGCTGCTGATATATGTAAT 59.052 36.000 0.00 0.00 38.71 1.89
982 983 5.315348 TGCCATTGCTGCTGATATATGTAA 58.685 37.500 0.00 0.00 38.71 2.41
983 984 4.909001 TGCCATTGCTGCTGATATATGTA 58.091 39.130 0.00 0.00 38.71 2.29
984 985 3.758425 TGCCATTGCTGCTGATATATGT 58.242 40.909 0.00 0.00 38.71 2.29
988 989 3.227614 TCATTGCCATTGCTGCTGATAT 58.772 40.909 0.00 0.00 38.71 1.63
1007 1008 4.758251 CGGTGGTGGCGCTGATCA 62.758 66.667 7.64 0.00 0.00 2.92
1244 1251 4.512914 GGATCCACCCCAGCAGGC 62.513 72.222 6.95 0.00 0.00 4.85
1308 1315 1.009900 GCCGTCGTCGAGGATGTAG 60.010 63.158 22.07 11.51 39.71 2.74
1339 1346 1.595382 GTGGTGTTCAGAGCGTGCT 60.595 57.895 0.00 0.00 0.00 4.40
1340 1347 2.607892 GGTGGTGTTCAGAGCGTGC 61.608 63.158 0.00 0.00 0.00 5.34
1373 1392 4.968259 TCAGTTAAGCTCCTTAAACAGCA 58.032 39.130 7.80 0.00 37.62 4.41
1382 1603 1.640917 TCCCGTTCAGTTAAGCTCCT 58.359 50.000 0.00 0.00 0.00 3.69
1388 1609 2.865079 TGCCAATTCCCGTTCAGTTAA 58.135 42.857 0.00 0.00 0.00 2.01
1391 1612 1.202879 TCTTGCCAATTCCCGTTCAGT 60.203 47.619 0.00 0.00 0.00 3.41
1412 1633 8.292444 TGGAGTAAATTCAAGGGATGTTTATG 57.708 34.615 0.00 0.00 0.00 1.90
1435 1656 2.083774 ACAGCACCGTACAAATCATGG 58.916 47.619 0.00 0.00 0.00 3.66
1469 1690 0.383860 CCGGAAGCGAAACAAACGAC 60.384 55.000 0.00 0.00 0.00 4.34
1470 1691 0.530211 TCCGGAAGCGAAACAAACGA 60.530 50.000 0.00 0.00 0.00 3.85
1484 1705 2.824880 CCCCACCTGTTGTTCCGGA 61.825 63.158 0.00 0.00 0.00 5.14
1485 1706 2.282180 CCCCACCTGTTGTTCCGG 60.282 66.667 0.00 0.00 0.00 5.14
1486 1707 1.896660 CACCCCACCTGTTGTTCCG 60.897 63.158 0.00 0.00 0.00 4.30
1488 1709 1.106944 CACCACCCCACCTGTTGTTC 61.107 60.000 0.00 0.00 0.00 3.18
1489 1710 1.076339 CACCACCCCACCTGTTGTT 60.076 57.895 0.00 0.00 0.00 2.83
1490 1711 2.600731 CACCACCCCACCTGTTGT 59.399 61.111 0.00 0.00 0.00 3.32
1545 1769 1.587054 GACCTCAGGACCACTCACG 59.413 63.158 0.00 0.00 0.00 4.35
1547 1771 0.402887 TACGACCTCAGGACCACTCA 59.597 55.000 0.00 0.00 0.00 3.41
1553 1777 1.808945 TCGAACTTACGACCTCAGGAC 59.191 52.381 0.00 0.00 37.37 3.85
1566 1790 1.819903 GTGGTAGAGAGGCTCGAACTT 59.180 52.381 9.22 0.00 35.36 2.66
1583 1807 3.861840 ACGAATCAGATGTACCTTGTGG 58.138 45.455 0.00 0.00 39.83 4.17
1585 1809 4.801330 TGACGAATCAGATGTACCTTGT 57.199 40.909 0.00 0.00 0.00 3.16
1603 1884 0.798776 CATGCTCGGTTTCACCTGAC 59.201 55.000 0.00 0.00 35.66 3.51
1615 1896 1.081892 CCAAGGTTCAGACATGCTCG 58.918 55.000 0.00 0.00 0.00 5.03
1621 1902 4.503714 AAAGAAGACCAAGGTTCAGACA 57.496 40.909 0.00 0.00 0.00 3.41
1661 2344 1.729267 AACACCAGGGCATGAAGGGT 61.729 55.000 0.00 0.00 0.00 4.34
1729 2412 2.575279 AGAAGCAGTCATGGGATTCTGT 59.425 45.455 11.00 0.00 0.00 3.41
1771 2454 6.395629 TGGATCGTGTTTAAAGAAGTAGAGG 58.604 40.000 0.00 0.00 0.00 3.69
1793 2477 6.204359 CAACTGAAGATTCAAGACACTTTGG 58.796 40.000 0.00 0.00 36.64 3.28
1834 2518 5.924825 TGAGATAGCATCATGATTGAAGACG 59.075 40.000 5.16 0.00 34.96 4.18
1889 2573 8.856247 CGCGCTATAATACAACATATTCTTACA 58.144 33.333 5.56 0.00 0.00 2.41
1890 2574 8.318876 CCGCGCTATAATACAACATATTCTTAC 58.681 37.037 5.56 0.00 0.00 2.34
1891 2575 8.245491 TCCGCGCTATAATACAACATATTCTTA 58.755 33.333 5.56 0.00 0.00 2.10
1976 2660 6.957631 TCATGACTGACAGGTGGTATTAATT 58.042 36.000 7.51 0.00 0.00 1.40
1977 2661 6.156949 ACTCATGACTGACAGGTGGTATTAAT 59.843 38.462 7.51 0.00 0.00 1.40
1980 2664 3.840666 ACTCATGACTGACAGGTGGTATT 59.159 43.478 7.51 0.00 0.00 1.89
1988 2672 5.702670 ACCAAACATTACTCATGACTGACAG 59.297 40.000 0.00 0.00 36.24 3.51
2015 2699 8.421784 TCTACGAATAATAGGAGTTGCTCAAAT 58.578 33.333 0.00 0.00 31.08 2.32
2087 2771 8.482128 TGTATAACTGGACAACACATATCATCA 58.518 33.333 0.00 0.00 0.00 3.07
2123 2807 1.811359 AGGTCGTAGTCCTCGAAACAG 59.189 52.381 0.96 0.00 44.07 3.16
2139 2891 7.280876 TGCATTTCTGAGACATTTATACAGGTC 59.719 37.037 0.00 0.00 0.00 3.85
2173 2925 3.618351 AGCTCATCTGTTTGGAATGAGG 58.382 45.455 12.14 0.00 39.16 3.86
2221 2973 1.553704 GTGGATACGAACACCCTCCTT 59.446 52.381 0.00 0.00 42.51 3.36
2237 2989 0.323629 GATCCTTTGTGGTCGGTGGA 59.676 55.000 0.00 0.00 37.07 4.02
2240 2992 0.768622 TTGGATCCTTTGTGGTCGGT 59.231 50.000 14.23 0.00 37.07 4.69
2242 2994 1.165270 GGTTGGATCCTTTGTGGTCG 58.835 55.000 14.23 0.00 37.07 4.79
2288 3040 3.063997 ACTGAAAGACGCAGACACTTTTG 59.936 43.478 0.00 0.00 37.43 2.44


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

AutoCloner maintained by Alex Coulton.