Multiple sequence alignment - TraesCS7A01G152400

Loading Multiple Alignment...

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 TraesCS7A01G152400 chr7A 100.000 3180 0 0 1 3180 105768416 105765237 0.000000e+00 5873
1 TraesCS7A01G152400 chr7A 95.197 2207 80 10 50 2254 105779203 105777021 0.000000e+00 3465
2 TraesCS7A01G152400 chr7A 90.641 780 59 3 1350 2128 105773887 105773121 0.000000e+00 1024
3 TraesCS7A01G152400 chr7A 98.158 380 7 0 2256 2635 105776965 105776586 0.000000e+00 664
4 TraesCS7A01G152400 chr7A 85.969 449 49 9 455 899 105779890 105780328 4.800000e-128 468
5 TraesCS7A01G152400 chr7A 93.506 154 8 1 3027 3180 105776152 105776001 8.870000e-56 228
6 TraesCS7A01G152400 chr7D 93.601 3141 143 25 50 3180 101799970 101796878 0.000000e+00 4634
7 TraesCS7A01G152400 chr7D 79.733 1347 232 30 589 1915 143976174 143974849 0.000000e+00 937
8 TraesCS7A01G152400 chr7D 77.778 1359 254 32 592 1926 152947181 152948515 0.000000e+00 793
9 TraesCS7A01G152400 chr7D 85.178 506 59 10 400 899 101800208 101800703 3.660000e-139 505
10 TraesCS7A01G152400 chr7D 83.284 341 43 9 2307 2637 143950214 143949878 5.160000e-78 302
11 TraesCS7A01G152400 chr7B 92.978 2478 143 14 50 2520 59181426 59178973 0.000000e+00 3583
12 TraesCS7A01G152400 chr7B 86.747 415 42 9 496 899 59304959 59305371 1.740000e-122 449
13 TraesCS7A01G152400 chr7B 76.316 646 97 32 2015 2612 107823012 107823649 8.630000e-76 294
14 TraesCS7A01G152400 chr3D 78.356 1922 307 59 522 2380 39121133 39119258 0.000000e+00 1144
15 TraesCS7A01G152400 chr3D 80.997 321 39 12 2330 2637 39031852 39031541 5.300000e-58 235
16 TraesCS7A01G152400 chr3B 79.070 1720 278 45 522 2205 61916753 61915080 0.000000e+00 1107
17 TraesCS7A01G152400 chr3B 79.191 692 109 23 989 1649 61896885 61896198 6.260000e-122 448
18 TraesCS7A01G152400 chrUn 77.531 1353 253 36 579 1907 29901335 29900010 0.000000e+00 767
19 TraesCS7A01G152400 chr5A 76.736 1354 259 38 579 1907 706406862 706405540 0.000000e+00 704
20 TraesCS7A01G152400 chr5A 77.343 1099 215 25 802 1881 459004098 459003015 1.250000e-173 619
21 TraesCS7A01G152400 chr5B 77.285 1127 229 20 788 1901 423366570 423365458 3.460000e-179 638
22 TraesCS7A01G152400 chr4B 74.954 1090 226 38 807 1867 667832451 667833522 1.040000e-124 457


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 TraesCS7A01G152400 chr7A 105765237 105768416 3179 True 5873.00 5873 100.0000 1 3180 1 chr7A.!!$R1 3179
1 TraesCS7A01G152400 chr7A 105773121 105779203 6082 True 1345.25 3465 94.3755 50 3180 4 chr7A.!!$R2 3130
2 TraesCS7A01G152400 chr7D 101796878 101799970 3092 True 4634.00 4634 93.6010 50 3180 1 chr7D.!!$R1 3130
3 TraesCS7A01G152400 chr7D 143974849 143976174 1325 True 937.00 937 79.7330 589 1915 1 chr7D.!!$R3 1326
4 TraesCS7A01G152400 chr7D 152947181 152948515 1334 False 793.00 793 77.7780 592 1926 1 chr7D.!!$F2 1334
5 TraesCS7A01G152400 chr7B 59178973 59181426 2453 True 3583.00 3583 92.9780 50 2520 1 chr7B.!!$R1 2470
6 TraesCS7A01G152400 chr7B 107823012 107823649 637 False 294.00 294 76.3160 2015 2612 1 chr7B.!!$F2 597
7 TraesCS7A01G152400 chr3D 39119258 39121133 1875 True 1144.00 1144 78.3560 522 2380 1 chr3D.!!$R2 1858
8 TraesCS7A01G152400 chr3B 61915080 61916753 1673 True 1107.00 1107 79.0700 522 2205 1 chr3B.!!$R2 1683
9 TraesCS7A01G152400 chr3B 61896198 61896885 687 True 448.00 448 79.1910 989 1649 1 chr3B.!!$R1 660
10 TraesCS7A01G152400 chrUn 29900010 29901335 1325 True 767.00 767 77.5310 579 1907 1 chrUn.!!$R1 1328
11 TraesCS7A01G152400 chr5A 706405540 706406862 1322 True 704.00 704 76.7360 579 1907 1 chr5A.!!$R2 1328
12 TraesCS7A01G152400 chr5A 459003015 459004098 1083 True 619.00 619 77.3430 802 1881 1 chr5A.!!$R1 1079
13 TraesCS7A01G152400 chr5B 423365458 423366570 1112 True 638.00 638 77.2850 788 1901 1 chr5B.!!$R1 1113
14 TraesCS7A01G152400 chr4B 667832451 667833522 1071 False 457.00 457 74.9540 807 1867 1 chr4B.!!$F1 1060

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
42 43 0.029567 CTCTAGGCGACATCCACGAC 59.970 60.0 0.0 0.0 39.24 4.34 F
530 534 0.322187 GTTCGCCCCTAAAGCCAAGA 60.322 55.0 0.0 0.0 0.00 3.02 F
1961 2025 0.035439 CTACCACCATGACCACCACC 60.035 60.0 0.0 0.0 0.00 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1377 1408 0.620700 TTGGTCTTCTCCCCCTAGGC 60.621 60.000 2.05 0.0 34.51 3.93 R
2089 2156 0.541863 ACCTGGCCAAAGTATCCTCG 59.458 55.000 7.01 0.0 0.00 4.63 R
2799 2987 1.473257 GGAGTTAGCATCATGTCGGCA 60.473 52.381 0.00 0.0 0.00 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
17 18 2.595655 AAGCGCCTATTCACCCCC 59.404 61.111 2.29 0.00 0.00 5.40
36 37 3.460995 CCCCCTCTAGGCGACATC 58.539 66.667 0.00 0.00 0.00 3.06
37 38 2.210711 CCCCCTCTAGGCGACATCC 61.211 68.421 0.00 0.00 0.00 3.51
38 39 1.457643 CCCCTCTAGGCGACATCCA 60.458 63.158 0.00 0.00 0.00 3.41
39 40 1.742768 CCCTCTAGGCGACATCCAC 59.257 63.158 0.00 0.00 0.00 4.02
40 41 1.360551 CCTCTAGGCGACATCCACG 59.639 63.158 0.00 0.00 0.00 4.94
41 42 1.101635 CCTCTAGGCGACATCCACGA 61.102 60.000 0.00 0.00 0.00 4.35
42 43 0.029567 CTCTAGGCGACATCCACGAC 59.970 60.000 0.00 0.00 39.24 4.34
43 44 1.065928 CTAGGCGACATCCACGACC 59.934 63.158 0.00 0.00 39.85 4.79
44 45 1.379443 TAGGCGACATCCACGACCT 60.379 57.895 0.00 0.00 39.85 3.85
45 46 0.968901 TAGGCGACATCCACGACCTT 60.969 55.000 0.00 0.00 39.85 3.50
46 47 1.375523 GGCGACATCCACGACCTTT 60.376 57.895 0.00 0.00 32.13 3.11
47 48 1.359459 GGCGACATCCACGACCTTTC 61.359 60.000 0.00 0.00 32.13 2.62
48 49 0.669318 GCGACATCCACGACCTTTCA 60.669 55.000 0.00 0.00 0.00 2.69
117 118 7.050377 TGATTCACTTCTAGTTGGATCATTCC 58.950 38.462 8.01 0.00 42.94 3.01
129 130 1.401905 GATCATTCCTGTCCGCAAACC 59.598 52.381 0.00 0.00 0.00 3.27
167 168 6.075280 CCATTGTCCGTTAAGTTTAACTTCG 58.925 40.000 14.03 12.05 39.51 3.79
252 253 8.293867 ACATAAATAACGTAACTTGTTGCACAT 58.706 29.630 0.00 0.00 0.00 3.21
253 254 6.984740 AAATAACGTAACTTGTTGCACATG 57.015 33.333 0.00 0.00 0.00 3.21
278 279 6.739550 GTGTGCTAATATAACAACCGACAAAC 59.260 38.462 0.00 0.00 0.00 2.93
285 286 8.851541 AATATAACAACCGACAAACTTTAGGA 57.148 30.769 0.00 0.00 0.00 2.94
324 325 4.644103 TCTTAGAAATACGAAGACCCCG 57.356 45.455 0.00 0.00 35.83 5.73
345 346 4.398044 CCGGATAATGTTGGCCCATTATAC 59.602 45.833 20.74 20.20 44.23 1.47
480 484 4.221924 TGGTATCCATCCGTATATGGTGTG 59.778 45.833 10.85 10.58 45.67 3.82
494 498 0.604243 GGTGTGTATGTGGGCAACGA 60.604 55.000 0.00 0.00 37.60 3.85
507 511 3.243367 TGGGCAACGAGTCATTTTTCTTG 60.243 43.478 0.00 0.00 37.60 3.02
509 513 4.023536 GGGCAACGAGTCATTTTTCTTGTA 60.024 41.667 0.00 0.00 37.60 2.41
530 534 0.322187 GTTCGCCCCTAAAGCCAAGA 60.322 55.000 0.00 0.00 0.00 3.02
722 734 5.393027 CCCATAGCAAGATAAACAACACACC 60.393 44.000 0.00 0.00 0.00 4.16
798 811 4.396357 AAACATCCACCCATCCACTTTA 57.604 40.909 0.00 0.00 0.00 1.85
815 831 9.990868 ATCCACTTTAAGTAGGGACAAATTAAT 57.009 29.630 6.36 0.00 0.00 1.40
968 986 2.120909 CCCCCAATACTTGCGCCAG 61.121 63.158 4.18 5.76 0.00 4.85
1198 1225 0.676782 CGAGAAGGCGAAAATGGGGT 60.677 55.000 0.00 0.00 0.00 4.95
1283 1310 4.849329 CACGACCGCCGGCTACTC 62.849 72.222 26.68 14.43 43.93 2.59
1376 1406 2.384375 TGGTCTTCTACAAGGGTAGGGA 59.616 50.000 2.37 0.00 45.76 4.20
1377 1408 3.032459 GGTCTTCTACAAGGGTAGGGAG 58.968 54.545 2.37 2.19 45.76 4.30
1498 1529 3.801293 GCCATTAATGCATCTTCCAAGGC 60.801 47.826 10.11 4.20 0.00 4.35
1645 1701 4.006319 GCAGGATATTCCATAAGAGCACC 58.994 47.826 0.00 0.00 39.61 5.01
1960 2024 0.981183 TCTACCACCATGACCACCAC 59.019 55.000 0.00 0.00 0.00 4.16
1961 2025 0.035439 CTACCACCATGACCACCACC 60.035 60.000 0.00 0.00 0.00 4.61
1962 2026 0.768609 TACCACCATGACCACCACCA 60.769 55.000 0.00 0.00 0.00 4.17
1963 2027 1.603455 CCACCATGACCACCACCAC 60.603 63.158 0.00 0.00 0.00 4.16
1964 2028 1.603455 CACCATGACCACCACCACC 60.603 63.158 0.00 0.00 0.00 4.61
1965 2029 2.081787 ACCATGACCACCACCACCA 61.082 57.895 0.00 0.00 0.00 4.17
1966 2030 1.303561 CCATGACCACCACCACCAG 60.304 63.158 0.00 0.00 0.00 4.00
1967 2031 1.973281 CATGACCACCACCACCAGC 60.973 63.158 0.00 0.00 0.00 4.85
1968 2032 2.459969 ATGACCACCACCACCAGCA 61.460 57.895 0.00 0.00 0.00 4.41
2006 2070 6.817641 ACAACAACAACACATGATTCAAATGT 59.182 30.769 0.00 0.00 38.81 2.71
2012 2076 5.239359 ACACATGATTCAAATGTCGATGG 57.761 39.130 0.00 0.00 36.10 3.51
2089 2156 1.200483 CGTCATCCATAGTGTCGCAC 58.800 55.000 2.28 2.28 34.10 5.34
2113 2180 2.369394 GATACTTTGGCCAGGTTGAGG 58.631 52.381 16.67 0.51 0.00 3.86
2179 2270 1.268283 TGGGTACGGATGGCATGTGA 61.268 55.000 3.81 0.00 0.00 3.58
2423 2601 4.386652 GCTACATTTGCATGTGTTCCAAAG 59.613 41.667 9.42 3.02 43.92 2.77
2670 2858 4.454161 ACACAATACTGACGCAAATGCTAA 59.546 37.500 3.63 0.00 39.32 3.09
2671 2859 4.788100 CACAATACTGACGCAAATGCTAAC 59.212 41.667 3.63 0.00 39.32 2.34
2672 2860 4.454161 ACAATACTGACGCAAATGCTAACA 59.546 37.500 3.63 0.71 39.32 2.41
2673 2861 2.969443 ACTGACGCAAATGCTAACAC 57.031 45.000 3.63 0.00 39.32 3.32
2674 2862 2.217750 ACTGACGCAAATGCTAACACA 58.782 42.857 3.63 0.00 39.32 3.72
2675 2863 2.032030 ACTGACGCAAATGCTAACACAC 60.032 45.455 3.63 0.00 39.32 3.82
2676 2864 1.070242 TGACGCAAATGCTAACACACG 60.070 47.619 3.63 0.00 39.32 4.49
2677 2865 0.385473 ACGCAAATGCTAACACACGC 60.385 50.000 3.63 0.00 39.32 5.34
2715 2903 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2717 2905 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2718 2906 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2722 2910 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2724 2912 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2726 2914 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2727 2915 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2729 2917 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2731 2919 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2732 2920 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2733 2921 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2734 2922 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2735 2923 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2736 2924 0.179227 CACACACACACACACACACG 60.179 55.000 0.00 0.00 0.00 4.49
2737 2925 1.225991 CACACACACACACACACGC 60.226 57.895 0.00 0.00 0.00 5.34
2738 2926 1.375396 ACACACACACACACACGCT 60.375 52.632 0.00 0.00 0.00 5.07
2739 2927 1.348250 CACACACACACACACGCTC 59.652 57.895 0.00 0.00 0.00 5.03
2740 2928 2.164663 ACACACACACACACGCTCG 61.165 57.895 0.00 0.00 0.00 5.03
2741 2929 3.261951 ACACACACACACGCTCGC 61.262 61.111 0.00 0.00 0.00 5.03
2742 2930 4.339809 CACACACACACGCTCGCG 62.340 66.667 10.06 10.06 46.03 5.87
2766 2954 1.748647 CGCCCTATAACACGTGCACG 61.749 60.000 35.99 35.99 46.33 5.34
2799 2987 4.008330 CCATGTGAGCTTGAAGAGATTGT 58.992 43.478 0.00 0.00 0.00 2.71
2801 2989 2.810274 TGTGAGCTTGAAGAGATTGTGC 59.190 45.455 0.00 0.00 0.00 4.57
2831 3019 4.244425 TGCTAACTCCTCGAATATGAGC 57.756 45.455 0.00 0.00 34.56 4.26
2835 3023 3.567576 ACTCCTCGAATATGAGCGATG 57.432 47.619 0.00 0.00 35.81 3.84
2925 3113 3.574284 TGCGTTGAAATGCTAATGCTT 57.426 38.095 8.59 0.00 41.45 3.91
3059 3290 9.862371 TCTATTCTAACATCTCACTTCTTTCAC 57.138 33.333 0.00 0.00 0.00 3.18
3101 3332 3.252701 GCAGAGCATCAAGGATAATGTGG 59.747 47.826 0.00 0.00 37.82 4.17
3103 3334 3.461085 AGAGCATCAAGGATAATGTGGGT 59.539 43.478 0.00 0.00 37.82 4.51
3106 3337 3.067180 GCATCAAGGATAATGTGGGTGTG 59.933 47.826 0.00 0.00 0.00 3.82
3107 3338 2.722094 TCAAGGATAATGTGGGTGTGC 58.278 47.619 0.00 0.00 0.00 4.57
3170 3403 9.423061 ACATGACTAGTTGAAAAATAATTTGCC 57.577 29.630 0.00 0.00 0.00 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.595655 GGGGGTGAATAGGCGCTT 59.404 61.111 7.64 0.52 0.00 4.68
19 20 2.210711 GGATGTCGCCTAGAGGGGG 61.211 68.421 12.32 0.23 46.90 5.40
21 22 1.742768 GTGGATGTCGCCTAGAGGG 59.257 63.158 0.00 0.00 35.18 4.30
22 23 1.101635 TCGTGGATGTCGCCTAGAGG 61.102 60.000 0.00 0.00 38.53 3.69
23 24 0.029567 GTCGTGGATGTCGCCTAGAG 59.970 60.000 0.00 0.00 0.00 2.43
24 25 1.381928 GGTCGTGGATGTCGCCTAGA 61.382 60.000 0.00 0.00 0.00 2.43
25 26 1.065928 GGTCGTGGATGTCGCCTAG 59.934 63.158 0.00 0.00 0.00 3.02
26 27 0.968901 AAGGTCGTGGATGTCGCCTA 60.969 55.000 0.00 0.00 35.25 3.93
27 28 1.827399 AAAGGTCGTGGATGTCGCCT 61.827 55.000 0.00 0.00 36.79 5.52
28 29 1.359459 GAAAGGTCGTGGATGTCGCC 61.359 60.000 0.00 0.00 0.00 5.54
29 30 0.669318 TGAAAGGTCGTGGATGTCGC 60.669 55.000 0.00 0.00 0.00 5.19
30 31 1.459592 GTTGAAAGGTCGTGGATGTCG 59.540 52.381 0.00 0.00 0.00 4.35
31 32 2.489971 TGTTGAAAGGTCGTGGATGTC 58.510 47.619 0.00 0.00 0.00 3.06
32 33 2.616842 GTTGTTGAAAGGTCGTGGATGT 59.383 45.455 0.00 0.00 0.00 3.06
33 34 2.878406 AGTTGTTGAAAGGTCGTGGATG 59.122 45.455 0.00 0.00 0.00 3.51
34 35 3.208747 AGTTGTTGAAAGGTCGTGGAT 57.791 42.857 0.00 0.00 0.00 3.41
35 36 2.702592 AGTTGTTGAAAGGTCGTGGA 57.297 45.000 0.00 0.00 0.00 4.02
36 37 4.124238 TCTTAGTTGTTGAAAGGTCGTGG 58.876 43.478 0.00 0.00 0.00 4.94
37 38 5.728351 TTCTTAGTTGTTGAAAGGTCGTG 57.272 39.130 0.00 0.00 0.00 4.35
38 39 5.644636 TGTTTCTTAGTTGTTGAAAGGTCGT 59.355 36.000 0.00 0.00 31.48 4.34
39 40 6.114221 TGTTTCTTAGTTGTTGAAAGGTCG 57.886 37.500 0.00 0.00 31.48 4.79
40 41 7.535997 ACTTGTTTCTTAGTTGTTGAAAGGTC 58.464 34.615 0.00 0.00 31.48 3.85
41 42 7.462571 ACTTGTTTCTTAGTTGTTGAAAGGT 57.537 32.000 0.00 0.00 31.48 3.50
42 43 8.173321 CAACTTGTTTCTTAGTTGTTGAAAGG 57.827 34.615 0.00 0.00 43.83 3.11
117 118 2.632377 ACTATCATGGTTTGCGGACAG 58.368 47.619 0.00 0.00 0.00 3.51
129 130 4.991056 CGGACAATGGGTCTTACTATCATG 59.009 45.833 0.00 0.00 46.16 3.07
252 253 5.480205 TGTCGGTTGTTATATTAGCACACA 58.520 37.500 0.00 0.00 0.00 3.72
253 254 6.411630 TTGTCGGTTGTTATATTAGCACAC 57.588 37.500 0.00 0.00 0.00 3.82
324 325 6.151144 GTCAGTATAATGGGCCAACATTATCC 59.849 42.308 22.96 15.72 45.95 2.59
345 346 7.578310 AGTTGATGGATTATCATTTGGTCAG 57.422 36.000 0.00 0.00 44.90 3.51
480 484 2.024176 ATGACTCGTTGCCCACATAC 57.976 50.000 0.00 0.00 0.00 2.39
494 498 4.215613 GGCGAACCTACAAGAAAAATGACT 59.784 41.667 0.00 0.00 0.00 3.41
507 511 0.463295 GGCTTTAGGGGCGAACCTAC 60.463 60.000 5.18 0.00 42.63 3.18
509 513 1.785353 TTGGCTTTAGGGGCGAACCT 61.785 55.000 3.74 3.74 44.75 3.50
530 534 3.255642 AGTGTGTGCTTCTGTTGTTGTTT 59.744 39.130 0.00 0.00 0.00 2.83
722 734 1.359459 GCTCCCTCGCCTTTACAACG 61.359 60.000 0.00 0.00 0.00 4.10
786 798 3.521937 TGTCCCTACTTAAAGTGGATGGG 59.478 47.826 0.00 0.00 31.70 4.00
798 811 7.232534 TGTGCTTTGATTAATTTGTCCCTACTT 59.767 33.333 0.00 0.00 0.00 2.24
815 831 4.791411 GCCTTGACGTTTTATGTGCTTTGA 60.791 41.667 0.00 0.00 0.00 2.69
968 986 4.086457 TCTTTGGGAAATTGGTTCTAGGC 58.914 43.478 0.00 0.00 36.40 3.93
1198 1225 5.262804 GGAGAAGAAGTACCACTCCTTCTA 58.737 45.833 7.67 0.00 45.01 2.10
1283 1310 0.955919 GTCCTTTCCAGTGGCCTTCG 60.956 60.000 3.51 0.00 0.00 3.79
1376 1406 1.315216 GGTCTTCTCCCCCTAGGCT 59.685 63.158 2.05 0.00 34.51 4.58
1377 1408 0.620700 TTGGTCTTCTCCCCCTAGGC 60.621 60.000 2.05 0.00 34.51 3.93
1498 1529 9.366216 TGAGTACTACTAGCATGTGTTTAAATG 57.634 33.333 0.00 0.00 0.00 2.32
1557 1613 9.534565 CAGTGCAAATCAACTATGTATAGTAGT 57.465 33.333 5.06 0.00 42.47 2.73
1645 1701 3.193691 ACATCACTACCTTCTTGAGTCCG 59.806 47.826 0.00 0.00 0.00 4.79
1961 2025 3.738246 CTGCTGCTGCTGCTGGTG 61.738 66.667 27.67 13.98 40.48 4.17
1967 2031 1.660575 GTTGTTGCTGCTGCTGCTG 60.661 57.895 27.67 16.73 40.48 4.41
1968 2032 1.669049 TTGTTGTTGCTGCTGCTGCT 61.669 50.000 27.67 0.00 40.48 4.24
2006 2070 2.560105 CACCTATCTGCATCTCCATCGA 59.440 50.000 0.00 0.00 0.00 3.59
2012 2076 3.006644 TCATCTGCACCTATCTGCATCTC 59.993 47.826 0.00 0.00 46.05 2.75
2089 2156 0.541863 ACCTGGCCAAAGTATCCTCG 59.458 55.000 7.01 0.00 0.00 4.63
2179 2270 9.775854 CTTGGATCATCTGATTATCAGTACTTT 57.224 33.333 20.09 4.98 44.58 2.66
2220 2335 8.959705 ATATACCGATCGATCTTGTGATAGTA 57.040 34.615 22.43 5.81 32.19 1.82
2221 2336 7.867305 ATATACCGATCGATCTTGTGATAGT 57.133 36.000 22.43 3.52 32.19 2.12
2423 2601 2.559668 TGGTGTACACACTGCTAGGTAC 59.440 50.000 26.51 5.99 45.73 3.34
2521 2709 9.509855 TCGTTTCCAAATAAAATACACATATGC 57.490 29.630 1.58 0.00 0.00 3.14
2640 2828 6.795098 TTGCGTCAGTATTGTGTTTCTATT 57.205 33.333 0.00 0.00 0.00 1.73
2659 2847 2.560706 GTGCGTGTGTTAGCATTTGCG 61.561 52.381 0.00 0.00 45.69 4.85
2670 2858 1.669437 TGTGTGTGTGTGCGTGTGT 60.669 52.632 0.00 0.00 0.00 3.72
2671 2859 1.225991 GTGTGTGTGTGTGCGTGTG 60.226 57.895 0.00 0.00 0.00 3.82
2672 2860 1.669437 TGTGTGTGTGTGTGCGTGT 60.669 52.632 0.00 0.00 0.00 4.49
2673 2861 1.225991 GTGTGTGTGTGTGTGCGTG 60.226 57.895 0.00 0.00 0.00 5.34
2674 2862 1.669437 TGTGTGTGTGTGTGTGCGT 60.669 52.632 0.00 0.00 0.00 5.24
2675 2863 1.225991 GTGTGTGTGTGTGTGTGCG 60.226 57.895 0.00 0.00 0.00 5.34
2676 2864 0.454285 GTGTGTGTGTGTGTGTGTGC 60.454 55.000 0.00 0.00 0.00 4.57
2677 2865 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2715 2903 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2717 2905 0.179227 CGTGTGTGTGTGTGTGTGTG 60.179 55.000 0.00 0.00 0.00 3.82
2718 2906 1.906994 GCGTGTGTGTGTGTGTGTGT 61.907 55.000 0.00 0.00 0.00 3.72
2722 2910 2.164663 CGAGCGTGTGTGTGTGTGT 61.165 57.895 0.00 0.00 0.00 3.72
2724 2912 3.261951 GCGAGCGTGTGTGTGTGT 61.262 61.111 0.00 0.00 0.00 3.72
2742 2930 3.996888 GTGTTATAGGGCGCGCGC 61.997 66.667 44.40 44.40 41.06 6.86
2743 2931 3.688330 CGTGTTATAGGGCGCGCG 61.688 66.667 28.44 28.44 0.00 6.86
2744 2932 2.584143 ACGTGTTATAGGGCGCGC 60.584 61.111 25.94 25.94 41.61 6.86
2745 2933 2.867091 GCACGTGTTATAGGGCGCG 61.867 63.158 18.38 0.00 43.25 6.86
2746 2934 1.812093 TGCACGTGTTATAGGGCGC 60.812 57.895 18.38 0.00 0.00 6.53
2788 2976 2.028203 TCATGTCGGCACAATCTCTTCA 60.028 45.455 0.00 0.00 35.64 3.02
2799 2987 1.473257 GGAGTTAGCATCATGTCGGCA 60.473 52.381 0.00 0.00 0.00 5.69
2801 2989 2.748605 GAGGAGTTAGCATCATGTCGG 58.251 52.381 0.00 0.00 0.00 4.79
2831 3019 4.512571 TGCAACATCAGTGATATTCCATCG 59.487 41.667 5.03 0.00 0.00 3.84
2835 3023 9.188588 CATATTTTGCAACATCAGTGATATTCC 57.811 33.333 5.03 0.00 0.00 3.01
2869 3057 5.633830 ATTCTCATCAATCAACGCAACTT 57.366 34.783 0.00 0.00 0.00 2.66
2875 3063 6.369005 GCCATCTTATTCTCATCAATCAACG 58.631 40.000 0.00 0.00 0.00 4.10
2925 3113 8.916062 TGTATACATCCGGATTTTGAACTAGTA 58.084 33.333 16.19 10.90 0.00 1.82


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

AutoCloner maintained by Alex Coulton.