Multiple sequence alignment - TraesCS1B01G137700

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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 TraesCS1B01G137700 chr1B 100.000 5472 0 0 1 5472 176782830 176788301 0.000000e+00 10105.0
1 TraesCS1B01G137700 chr1B 95.665 692 29 1 4782 5472 61990124 61989433 0.000000e+00 1110.0
2 TraesCS1B01G137700 chr1B 85.714 63 6 2 4681 4742 638978332 638978272 4.580000e-06 63.9
3 TraesCS1B01G137700 chr1D 94.262 1429 47 12 955 2373 115366404 115367807 0.000000e+00 2152.0
4 TraesCS1B01G137700 chr1D 94.057 875 33 9 3732 4602 115369352 115370211 0.000000e+00 1310.0
5 TraesCS1B01G137700 chr1D 92.385 499 12 11 2554 3040 115367984 115368468 0.000000e+00 688.0
6 TraesCS1B01G137700 chr1D 89.804 510 18 18 3230 3726 115368542 115369030 1.670000e-174 623.0
7 TraesCS1B01G137700 chr1D 96.875 96 3 0 2444 2539 115367903 115367998 1.580000e-35 161.0
8 TraesCS1B01G137700 chr1D 83.626 171 25 3 3047 3214 276793539 276793709 2.040000e-34 158.0
9 TraesCS1B01G137700 chr1D 84.118 170 17 5 4623 4783 115370199 115370367 7.340000e-34 156.0
10 TraesCS1B01G137700 chr1D 100.000 31 0 0 2369 2399 115367877 115367907 2.130000e-04 58.4
11 TraesCS1B01G137700 chr1A 92.221 1324 52 21 994 2298 126511770 126513061 0.000000e+00 1827.0
12 TraesCS1B01G137700 chr1A 91.429 1120 37 15 3534 4602 126514872 126515983 0.000000e+00 1482.0
13 TraesCS1B01G137700 chr1A 96.005 876 34 1 1 876 507909940 507910814 0.000000e+00 1423.0
14 TraesCS1B01G137700 chr1A 91.485 505 17 11 2553 3047 126513727 126514215 0.000000e+00 671.0
15 TraesCS1B01G137700 chr1A 88.158 228 7 8 3211 3418 126514262 126514489 2.530000e-63 254.0
16 TraesCS1B01G137700 chr1A 93.976 83 4 1 2294 2375 126513321 126513403 2.070000e-24 124.0
17 TraesCS1B01G137700 chr1A 98.182 55 1 0 2485 2539 126513688 126513742 4.510000e-16 97.1
18 TraesCS1B01G137700 chr1A 85.484 62 0 2 3433 3494 126514528 126514580 7.660000e-04 56.5
19 TraesCS1B01G137700 chr3A 96.804 876 27 1 1 876 746391403 746390529 0.000000e+00 1461.0
20 TraesCS1B01G137700 chr3A 93.488 691 44 1 4783 5472 721553474 721552784 0.000000e+00 1026.0
21 TraesCS1B01G137700 chr3A 84.356 326 44 5 1360 1683 100018817 100018497 4.120000e-81 313.0
22 TraesCS1B01G137700 chr3A 83.626 171 25 3 3047 3214 705790278 705790448 2.040000e-34 158.0
23 TraesCS1B01G137700 chr6D 96.481 881 29 2 1 880 436309647 436310526 0.000000e+00 1454.0
24 TraesCS1B01G137700 chr6D 83.626 171 23 5 3048 3214 91526341 91526172 7.340000e-34 156.0
25 TraesCS1B01G137700 chr7D 96.136 880 34 0 1 880 620136940 620137819 0.000000e+00 1437.0
26 TraesCS1B01G137700 chr7D 83.626 171 25 3 3047 3214 176959067 176959237 2.040000e-34 158.0
27 TraesCS1B01G137700 chr4A 96.119 876 28 2 1 876 37027926 37028795 0.000000e+00 1424.0
28 TraesCS1B01G137700 chr7A 95.886 875 35 1 1 875 681490812 681489939 0.000000e+00 1415.0
29 TraesCS1B01G137700 chr7A 95.776 876 37 0 1 876 560975630 560974755 0.000000e+00 1413.0
30 TraesCS1B01G137700 chr7A 93.632 691 43 1 4783 5472 704263869 704263179 0.000000e+00 1031.0
31 TraesCS1B01G137700 chr2A 95.886 875 34 2 3 876 670452806 670453679 0.000000e+00 1415.0
32 TraesCS1B01G137700 chr2A 93.957 695 41 1 4779 5472 721588050 721587356 0.000000e+00 1050.0
33 TraesCS1B01G137700 chr5D 96.793 842 25 2 1 841 98248958 98248118 0.000000e+00 1404.0
34 TraesCS1B01G137700 chr3B 96.961 691 20 1 4783 5472 11915158 11914468 0.000000e+00 1158.0
35 TraesCS1B01G137700 chr3B 82.209 326 48 7 1360 1683 131496137 131496454 6.980000e-69 272.0
36 TraesCS1B01G137700 chr4B 96.816 691 21 1 4783 5472 119326275 119325585 0.000000e+00 1153.0
37 TraesCS1B01G137700 chr4B 96.527 691 23 1 4783 5472 142928074 142927384 0.000000e+00 1142.0
38 TraesCS1B01G137700 chr6B 96.093 691 26 1 4783 5472 114073566 114072876 0.000000e+00 1125.0
39 TraesCS1B01G137700 chr6B 82.857 175 26 4 3043 3214 565365244 565365417 2.640000e-33 154.0
40 TraesCS1B01G137700 chr7B 95.389 694 31 1 4780 5472 746160530 746161223 0.000000e+00 1103.0
41 TraesCS1B01G137700 chr3D 83.742 326 43 7 1360 1683 83942900 83942583 3.200000e-77 300.0
42 TraesCS1B01G137700 chr3D 83.436 326 44 7 1360 1683 83923445 83923128 1.490000e-75 294.0
43 TraesCS1B01G137700 chr3D 83.721 172 23 5 3047 3214 601830767 601830937 2.040000e-34 158.0
44 TraesCS1B01G137700 chr2B 84.831 178 23 4 3041 3214 210653972 210654149 5.630000e-40 176.0
45 TraesCS1B01G137700 chrUn 83.529 170 25 3 3048 3214 36388037 36388206 7.340000e-34 156.0
46 TraesCS1B01G137700 chrUn 83.529 170 25 3 3048 3214 304606832 304607001 7.340000e-34 156.0


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 TraesCS1B01G137700 chr1B 176782830 176788301 5471 False 10105.000000 10105 100.000000 1 5472 1 chr1B.!!$F1 5471
1 TraesCS1B01G137700 chr1B 61989433 61990124 691 True 1110.000000 1110 95.665000 4782 5472 1 chr1B.!!$R1 690
2 TraesCS1B01G137700 chr1D 115366404 115370367 3963 False 735.485714 2152 93.071571 955 4783 7 chr1D.!!$F2 3828
3 TraesCS1B01G137700 chr1A 507909940 507910814 874 False 1423.000000 1423 96.005000 1 876 1 chr1A.!!$F1 875
4 TraesCS1B01G137700 chr1A 126511770 126515983 4213 False 644.514286 1827 91.562143 994 4602 7 chr1A.!!$F2 3608
5 TraesCS1B01G137700 chr3A 746390529 746391403 874 True 1461.000000 1461 96.804000 1 876 1 chr3A.!!$R3 875
6 TraesCS1B01G137700 chr3A 721552784 721553474 690 True 1026.000000 1026 93.488000 4783 5472 1 chr3A.!!$R2 689
7 TraesCS1B01G137700 chr6D 436309647 436310526 879 False 1454.000000 1454 96.481000 1 880 1 chr6D.!!$F1 879
8 TraesCS1B01G137700 chr7D 620136940 620137819 879 False 1437.000000 1437 96.136000 1 880 1 chr7D.!!$F2 879
9 TraesCS1B01G137700 chr4A 37027926 37028795 869 False 1424.000000 1424 96.119000 1 876 1 chr4A.!!$F1 875
10 TraesCS1B01G137700 chr7A 681489939 681490812 873 True 1415.000000 1415 95.886000 1 875 1 chr7A.!!$R2 874
11 TraesCS1B01G137700 chr7A 560974755 560975630 875 True 1413.000000 1413 95.776000 1 876 1 chr7A.!!$R1 875
12 TraesCS1B01G137700 chr7A 704263179 704263869 690 True 1031.000000 1031 93.632000 4783 5472 1 chr7A.!!$R3 689
13 TraesCS1B01G137700 chr2A 670452806 670453679 873 False 1415.000000 1415 95.886000 3 876 1 chr2A.!!$F1 873
14 TraesCS1B01G137700 chr2A 721587356 721588050 694 True 1050.000000 1050 93.957000 4779 5472 1 chr2A.!!$R1 693
15 TraesCS1B01G137700 chr5D 98248118 98248958 840 True 1404.000000 1404 96.793000 1 841 1 chr5D.!!$R1 840
16 TraesCS1B01G137700 chr3B 11914468 11915158 690 True 1158.000000 1158 96.961000 4783 5472 1 chr3B.!!$R1 689
17 TraesCS1B01G137700 chr4B 119325585 119326275 690 True 1153.000000 1153 96.816000 4783 5472 1 chr4B.!!$R1 689
18 TraesCS1B01G137700 chr4B 142927384 142928074 690 True 1142.000000 1142 96.527000 4783 5472 1 chr4B.!!$R2 689
19 TraesCS1B01G137700 chr6B 114072876 114073566 690 True 1125.000000 1125 96.093000 4783 5472 1 chr6B.!!$R1 689
20 TraesCS1B01G137700 chr7B 746160530 746161223 693 False 1103.000000 1103 95.389000 4780 5472 1 chr7B.!!$F1 692

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
942 947 0.034574 ACTCAGCCCACACACACAAA 60.035 50.0 0.00 0.00 0.00 2.83 F
2232 2268 0.235665 CACTACAACGTTGCTGCCAG 59.764 55.0 27.61 17.73 0.00 4.85 F
2631 3162 1.247567 CGGCCATTTGGTATCCATCC 58.752 55.0 2.24 0.00 37.57 3.51 F
3459 4048 0.037734 CCAACACCCTAGTTCCCCAC 59.962 60.0 0.00 0.00 0.00 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2245 2281 0.036306 AAAAATCGAGGGAGTGCGGT 59.964 50.0 0.00 0.0 0.00 5.68 R
3440 4029 0.037734 GTGGGGAACTAGGGTGTTGG 59.962 60.0 0.00 0.0 0.00 3.77 R
4169 5370 0.389426 CCAACGTCGACCCGAAAGAT 60.389 55.0 10.58 0.0 37.72 2.40 R
4894 6112 0.385473 CCGCGCGAAATCACTTGTTT 60.385 50.0 34.63 0.0 0.00 2.83 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
72 73 2.727123 TCAAAGACTGGGTTTGCTGA 57.273 45.000 0.00 0.00 35.29 4.26
166 167 4.158949 TGAAGCATCAGAAAATGTGGATGG 59.841 41.667 0.00 0.00 38.03 3.51
407 408 0.178992 TGCAAAGTTCAGGGGGAGTG 60.179 55.000 0.00 0.00 0.00 3.51
427 428 6.147437 AGTGAAATCCCAAGTTATAACCCA 57.853 37.500 12.05 0.00 0.00 4.51
483 484 7.951591 TCTTTTTCCCTTTATGAGTTTTCCAG 58.048 34.615 0.00 0.00 0.00 3.86
821 826 4.326255 GGGTCTCCCACATTGCAG 57.674 61.111 0.00 0.00 44.65 4.41
846 851 8.336801 GTGGAACTAGTGGATCATTTAAACTT 57.663 34.615 0.00 0.00 0.00 2.66
918 923 9.783081 AAAAATTGGCTGTTCATTAAGAAGAAT 57.217 25.926 0.00 0.00 36.78 2.40
919 924 9.783081 AAAATTGGCTGTTCATTAAGAAGAATT 57.217 25.926 0.00 0.00 36.78 2.17
923 928 8.862325 TGGCTGTTCATTAAGAAGAATTAAGA 57.138 30.769 0.00 0.00 36.78 2.10
924 929 8.730680 TGGCTGTTCATTAAGAAGAATTAAGAC 58.269 33.333 0.00 0.00 36.78 3.01
925 930 8.951243 GGCTGTTCATTAAGAAGAATTAAGACT 58.049 33.333 0.00 0.00 36.78 3.24
926 931 9.980780 GCTGTTCATTAAGAAGAATTAAGACTC 57.019 33.333 0.00 0.00 36.78 3.36
929 934 9.980780 GTTCATTAAGAAGAATTAAGACTCAGC 57.019 33.333 0.00 0.00 36.78 4.26
930 935 8.723942 TCATTAAGAAGAATTAAGACTCAGCC 57.276 34.615 0.00 0.00 0.00 4.85
931 936 7.770897 TCATTAAGAAGAATTAAGACTCAGCCC 59.229 37.037 0.00 0.00 0.00 5.19
932 937 5.505181 AAGAAGAATTAAGACTCAGCCCA 57.495 39.130 0.00 0.00 0.00 5.36
933 938 4.837972 AGAAGAATTAAGACTCAGCCCAC 58.162 43.478 0.00 0.00 0.00 4.61
934 939 4.287067 AGAAGAATTAAGACTCAGCCCACA 59.713 41.667 0.00 0.00 0.00 4.17
935 940 3.944087 AGAATTAAGACTCAGCCCACAC 58.056 45.455 0.00 0.00 0.00 3.82
936 941 3.327757 AGAATTAAGACTCAGCCCACACA 59.672 43.478 0.00 0.00 0.00 3.72
937 942 2.543777 TTAAGACTCAGCCCACACAC 57.456 50.000 0.00 0.00 0.00 3.82
938 943 1.419381 TAAGACTCAGCCCACACACA 58.581 50.000 0.00 0.00 0.00 3.72
939 944 0.179045 AAGACTCAGCCCACACACAC 60.179 55.000 0.00 0.00 0.00 3.82
940 945 1.146041 GACTCAGCCCACACACACA 59.854 57.895 0.00 0.00 0.00 3.72
941 946 0.463654 GACTCAGCCCACACACACAA 60.464 55.000 0.00 0.00 0.00 3.33
942 947 0.034574 ACTCAGCCCACACACACAAA 60.035 50.000 0.00 0.00 0.00 2.83
943 948 1.102154 CTCAGCCCACACACACAAAA 58.898 50.000 0.00 0.00 0.00 2.44
944 949 1.476085 CTCAGCCCACACACACAAAAA 59.524 47.619 0.00 0.00 0.00 1.94
980 985 0.318955 GTAGTACAACACCACCGCGT 60.319 55.000 4.92 0.00 0.00 6.01
981 986 0.318869 TAGTACAACACCACCGCGTG 60.319 55.000 4.92 3.32 39.75 5.34
992 997 1.080298 ACCGCGTGGCTACTACAAC 60.080 57.895 16.69 0.00 39.70 3.32
1022 1027 2.034879 CACACACATCTCACCGCCC 61.035 63.158 0.00 0.00 0.00 6.13
1040 1045 3.777925 CGCAGACCGCTTGTTCCG 61.778 66.667 0.00 0.00 39.08 4.30
1059 1064 2.618709 CCGAGTTCCAACAAAAGAGCTT 59.381 45.455 0.00 0.00 0.00 3.74
1208 1220 4.807039 GCGCTCCTTAACCGCCGA 62.807 66.667 0.00 0.00 41.72 5.54
1723 1750 2.574929 GCCACCACCATACGACGA 59.425 61.111 0.00 0.00 0.00 4.20
1730 1757 0.854853 CACCATACGACGACGACGAC 60.855 60.000 25.15 7.02 42.66 4.34
1773 1800 4.335647 CTGCTGGACGTGCCCCTT 62.336 66.667 4.04 0.00 34.97 3.95
2031 2058 5.915196 GTCTCTGCTTGGTTAAACATGTTTC 59.085 40.000 26.46 13.59 34.23 2.78
2035 2062 3.740832 GCTTGGTTAAACATGTTTCTGCC 59.259 43.478 26.46 23.62 34.23 4.85
2056 2083 4.927425 GCCGTGTCTTGTTAGTTAATCTCA 59.073 41.667 0.00 0.00 0.00 3.27
2081 2108 2.408271 ACATCGTCATGGCAGTGATT 57.592 45.000 5.99 0.00 33.82 2.57
2089 2116 4.392047 GTCATGGCAGTGATTCCATCATA 58.608 43.478 0.00 0.00 40.88 2.15
2091 2118 4.103627 TCATGGCAGTGATTCCATCATACT 59.896 41.667 0.00 0.00 40.88 2.12
2092 2119 4.077300 TGGCAGTGATTCCATCATACTC 57.923 45.455 0.00 0.00 42.04 2.59
2093 2120 3.181451 TGGCAGTGATTCCATCATACTCC 60.181 47.826 0.00 0.00 42.04 3.85
2094 2121 3.072184 GGCAGTGATTCCATCATACTCCT 59.928 47.826 0.00 0.00 42.04 3.69
2095 2122 4.284490 GGCAGTGATTCCATCATACTCCTA 59.716 45.833 0.00 0.00 42.04 2.94
2096 2123 5.233988 GCAGTGATTCCATCATACTCCTAC 58.766 45.833 0.00 0.00 42.04 3.18
2097 2124 5.465051 CAGTGATTCCATCATACTCCTACG 58.535 45.833 0.00 0.00 42.04 3.51
2109 2136 6.363065 TCATACTCCTACGTCCTGTTAGAAT 58.637 40.000 0.00 0.00 0.00 2.40
2198 2234 7.336679 AGAAATGGAATCATTGACGTGTTGATA 59.663 33.333 0.00 0.00 42.29 2.15
2232 2268 0.235665 CACTACAACGTTGCTGCCAG 59.764 55.000 27.61 17.73 0.00 4.85
2240 2276 4.158384 CAACGTTGCTGCCAGTTTAATAG 58.842 43.478 16.51 0.00 0.00 1.73
2241 2277 3.408634 ACGTTGCTGCCAGTTTAATAGT 58.591 40.909 0.00 0.00 0.00 2.12
2242 2278 4.571919 ACGTTGCTGCCAGTTTAATAGTA 58.428 39.130 0.00 0.00 0.00 1.82
2243 2279 4.630069 ACGTTGCTGCCAGTTTAATAGTAG 59.370 41.667 0.00 0.00 0.00 2.57
2244 2280 4.630069 CGTTGCTGCCAGTTTAATAGTAGT 59.370 41.667 0.00 0.00 0.00 2.73
2245 2281 5.808540 CGTTGCTGCCAGTTTAATAGTAGTA 59.191 40.000 0.00 0.00 0.00 1.82
2247 2283 5.667466 TGCTGCCAGTTTAATAGTAGTACC 58.333 41.667 0.00 0.00 0.00 3.34
2436 2819 9.672673 TCTCAATTAAACTAGTAGTAGTACGGT 57.327 33.333 10.68 3.37 38.66 4.83
2569 3096 3.106054 TGCGGGGTAGTAATACCAGAAA 58.894 45.455 20.30 1.32 41.83 2.52
2629 3160 3.073798 TGATACGGCCATTTGGTATCCAT 59.926 43.478 19.16 0.00 41.00 3.41
2630 3161 1.981256 ACGGCCATTTGGTATCCATC 58.019 50.000 2.24 0.00 37.57 3.51
2631 3162 1.247567 CGGCCATTTGGTATCCATCC 58.752 55.000 2.24 0.00 37.57 3.51
2632 3163 1.478471 CGGCCATTTGGTATCCATCCA 60.478 52.381 2.24 0.00 37.57 3.41
2633 3164 2.676748 GGCCATTTGGTATCCATCCAA 58.323 47.619 0.00 0.00 42.29 3.53
2634 3165 3.242011 GGCCATTTGGTATCCATCCAAT 58.758 45.455 0.00 0.00 43.25 3.16
2635 3166 4.415596 GGCCATTTGGTATCCATCCAATA 58.584 43.478 0.00 0.00 43.25 1.90
2636 3167 5.025453 GGCCATTTGGTATCCATCCAATAT 58.975 41.667 0.00 0.00 43.25 1.28
2637 3168 5.484998 GGCCATTTGGTATCCATCCAATATT 59.515 40.000 0.00 0.00 43.25 1.28
2683 3218 1.507141 AAGGCGCGAGGTCAAAACTG 61.507 55.000 12.10 0.00 0.00 3.16
2747 3290 1.672881 GGTGAGGCAAATCATTCGAGG 59.327 52.381 0.00 0.00 0.00 4.63
2761 3304 2.265904 CGAGGATGGCATGGCATGG 61.266 63.158 36.49 19.25 0.00 3.66
2964 3509 3.190535 TGCTCGAGGTAAAGGAAAAATGC 59.809 43.478 15.58 0.00 0.00 3.56
3004 3550 2.020720 TGTTTCTGTGCGTTTGACCAT 58.979 42.857 0.00 0.00 0.00 3.55
3048 3594 5.767816 TCATACGCACATGATACAGTAGT 57.232 39.130 0.00 0.00 29.93 2.73
3049 3595 6.870971 TCATACGCACATGATACAGTAGTA 57.129 37.500 0.00 0.00 29.93 1.82
3050 3596 7.448748 TCATACGCACATGATACAGTAGTAT 57.551 36.000 0.00 0.00 43.49 2.12
3051 3597 7.882179 TCATACGCACATGATACAGTAGTATT 58.118 34.615 0.00 0.00 40.95 1.89
3052 3598 9.005777 TCATACGCACATGATACAGTAGTATTA 57.994 33.333 0.00 0.00 40.95 0.98
3053 3599 9.062674 CATACGCACATGATACAGTAGTATTAC 57.937 37.037 0.00 0.00 40.95 1.89
3054 3600 6.444633 ACGCACATGATACAGTAGTATTACC 58.555 40.000 0.00 0.00 40.95 2.85
3056 3602 6.802348 CGCACATGATACAGTAGTATTACCTC 59.198 42.308 0.00 0.00 40.95 3.85
3057 3603 7.091443 GCACATGATACAGTAGTATTACCTCC 58.909 42.308 0.00 0.00 40.95 4.30
3058 3604 7.306213 CACATGATACAGTAGTATTACCTCCG 58.694 42.308 0.00 0.00 40.95 4.63
3060 3606 6.872628 TGATACAGTAGTATTACCTCCGTG 57.127 41.667 0.00 0.00 40.95 4.94
3063 3609 5.769484 ACAGTAGTATTACCTCCGTGATG 57.231 43.478 0.00 0.00 0.00 3.07
3064 3610 4.583489 ACAGTAGTATTACCTCCGTGATGG 59.417 45.833 0.00 0.00 40.09 3.51
3065 3611 4.583489 CAGTAGTATTACCTCCGTGATGGT 59.417 45.833 0.00 0.00 39.52 3.55
3066 3612 5.068723 CAGTAGTATTACCTCCGTGATGGTT 59.931 44.000 0.00 0.00 39.52 3.67
3067 3613 5.659971 AGTAGTATTACCTCCGTGATGGTTT 59.340 40.000 0.00 0.00 39.52 3.27
3070 3616 7.133133 AGTATTACCTCCGTGATGGTTTATT 57.867 36.000 0.00 0.00 39.52 1.40
3074 3620 5.431179 ACCTCCGTGATGGTTTATTAGTT 57.569 39.130 0.00 0.00 39.52 2.24
3075 3621 5.425630 ACCTCCGTGATGGTTTATTAGTTC 58.574 41.667 0.00 0.00 39.52 3.01
3076 3622 4.814771 CCTCCGTGATGGTTTATTAGTTCC 59.185 45.833 0.00 0.00 39.52 3.62
3077 3623 5.396436 CCTCCGTGATGGTTTATTAGTTCCT 60.396 44.000 0.00 0.00 39.52 3.36
3078 3624 6.057321 TCCGTGATGGTTTATTAGTTCCTT 57.943 37.500 0.00 0.00 39.52 3.36
3080 3626 6.373216 TCCGTGATGGTTTATTAGTTCCTTTG 59.627 38.462 0.00 0.00 39.52 2.77
3081 3627 6.150474 CCGTGATGGTTTATTAGTTCCTTTGT 59.850 38.462 0.00 0.00 0.00 2.83
3082 3628 7.334921 CCGTGATGGTTTATTAGTTCCTTTGTA 59.665 37.037 0.00 0.00 0.00 2.41
3179 3725 9.804758 AAATTAGTATTTGAACGTGGTTTTCAA 57.195 25.926 0.00 0.00 40.42 2.69
3211 3757 6.922247 TTTTTGTGACATGCATGAACATTT 57.078 29.167 32.75 9.47 31.64 2.32
3212 3758 6.922247 TTTTGTGACATGCATGAACATTTT 57.078 29.167 32.75 8.66 31.64 1.82
3213 3759 5.908916 TTGTGACATGCATGAACATTTTG 57.091 34.783 32.75 5.04 31.64 2.44
3397 3960 4.953940 TGCACCAAAATCCTTTAGCTTT 57.046 36.364 0.00 0.00 0.00 3.51
3430 4019 7.645058 AGGTGGGTTATATGTTTCATTTCTG 57.355 36.000 0.00 0.00 0.00 3.02
3456 4045 1.980036 TGTACCAACACCCTAGTTCCC 59.020 52.381 0.00 0.00 0.00 3.97
3457 4046 1.280133 GTACCAACACCCTAGTTCCCC 59.720 57.143 0.00 0.00 0.00 4.81
3458 4047 0.402272 ACCAACACCCTAGTTCCCCA 60.402 55.000 0.00 0.00 0.00 4.96
3459 4048 0.037734 CCAACACCCTAGTTCCCCAC 59.962 60.000 0.00 0.00 0.00 4.61
3460 4049 0.768622 CAACACCCTAGTTCCCCACA 59.231 55.000 0.00 0.00 0.00 4.17
3461 4050 0.769247 AACACCCTAGTTCCCCACAC 59.231 55.000 0.00 0.00 0.00 3.82
3462 4051 1.295423 CACCCTAGTTCCCCACACG 59.705 63.158 0.00 0.00 0.00 4.49
3463 4052 1.916777 ACCCTAGTTCCCCACACGG 60.917 63.158 0.00 0.00 0.00 4.94
3494 4083 1.827969 CTGTGGGATCCTTCTCTTCGT 59.172 52.381 12.58 0.00 0.00 3.85
3503 4092 3.728845 TCCTTCTCTTCGTTTGTCCTTG 58.271 45.455 0.00 0.00 0.00 3.61
3507 4096 1.946768 CTCTTCGTTTGTCCTTGGCAA 59.053 47.619 0.00 0.00 0.00 4.52
3521 4110 2.645838 TGGCAAGATGAGATTAGGGC 57.354 50.000 0.00 0.00 0.00 5.19
3525 4114 2.224967 GCAAGATGAGATTAGGGCCCAT 60.225 50.000 27.56 10.04 0.00 4.00
3530 4119 1.462238 AGATTAGGGCCCATCCGCT 60.462 57.895 27.56 11.60 34.94 5.52
3643 4484 1.739466 CGCAGTGGTACTTCGTAGGTA 59.261 52.381 0.00 0.00 30.48 3.08
3726 4598 5.023452 AGACCTGAGTATGTTGGTGATACA 58.977 41.667 0.00 0.00 32.30 2.29
3727 4599 5.086104 ACCTGAGTATGTTGGTGATACAC 57.914 43.478 0.00 0.00 0.00 2.90
3728 4600 4.112634 CCTGAGTATGTTGGTGATACACG 58.887 47.826 0.00 0.00 34.83 4.49
3729 4601 4.142249 CCTGAGTATGTTGGTGATACACGA 60.142 45.833 0.00 0.00 34.83 4.35
3730 4602 4.740268 TGAGTATGTTGGTGATACACGAC 58.260 43.478 0.00 0.00 34.83 4.34
3780 4968 0.659957 GCCGTTGATTCTGATGGCTC 59.340 55.000 13.35 0.00 43.17 4.70
4043 5235 0.553862 TCTCACCTCCTCCTCCTCCT 60.554 60.000 0.00 0.00 0.00 3.69
4168 5369 3.798380 CATCCGCATGCTTCGTCA 58.202 55.556 17.13 0.00 0.00 4.35
4169 5370 2.089017 CATCCGCATGCTTCGTCAA 58.911 52.632 17.13 0.00 0.00 3.18
4171 5372 0.940126 ATCCGCATGCTTCGTCAATC 59.060 50.000 17.13 0.00 0.00 2.67
4172 5373 0.108186 TCCGCATGCTTCGTCAATCT 60.108 50.000 17.13 0.00 0.00 2.40
4294 5501 2.283173 GGGCTGTTCAAGTGGGGG 60.283 66.667 0.00 0.00 0.00 5.40
4579 5787 5.591067 TGGTTTGGAATCTTAACGACACTTT 59.409 36.000 0.00 0.00 0.00 2.66
4598 5806 4.989168 ACTTTTGTCGTTTTAGCTCGATCT 59.011 37.500 0.00 0.00 38.32 2.75
4602 5810 5.306532 TGTCGTTTTAGCTCGATCTTAGT 57.693 39.130 0.00 0.00 38.32 2.24
4604 5812 6.154445 TGTCGTTTTAGCTCGATCTTAGTTT 58.846 36.000 0.00 0.00 38.32 2.66
4606 5814 7.170320 TGTCGTTTTAGCTCGATCTTAGTTTTT 59.830 33.333 0.00 0.00 38.32 1.94
4630 5838 8.782533 TTTTTCTTTTTAGAAACAGCTCGATC 57.217 30.769 0.11 0.00 37.50 3.69
4631 5839 6.481954 TTCTTTTTAGAAACAGCTCGATCC 57.518 37.500 0.00 0.00 0.00 3.36
4632 5840 5.794894 TCTTTTTAGAAACAGCTCGATCCT 58.205 37.500 0.00 0.00 0.00 3.24
4633 5841 6.231211 TCTTTTTAGAAACAGCTCGATCCTT 58.769 36.000 0.00 0.00 0.00 3.36
4634 5842 5.862924 TTTTAGAAACAGCTCGATCCTTG 57.137 39.130 0.00 0.00 0.00 3.61
4635 5843 1.731720 AGAAACAGCTCGATCCTTGC 58.268 50.000 0.00 0.00 0.00 4.01
4636 5844 1.277557 AGAAACAGCTCGATCCTTGCT 59.722 47.619 0.00 0.00 37.56 3.91
4638 5846 4.928398 CAGCTCGATCCTTGCTGT 57.072 55.556 13.78 0.00 46.23 4.40
4639 5847 2.381109 CAGCTCGATCCTTGCTGTG 58.619 57.895 13.78 0.00 46.23 3.66
4657 5865 0.941542 TGAAACTAACGCTGCGCTTT 59.058 45.000 23.51 12.54 0.00 3.51
4660 5868 0.602905 AACTAACGCTGCGCTTTCCT 60.603 50.000 23.51 0.00 0.00 3.36
4675 5883 2.314071 TTCCTTCAGAGGGGTCGTTA 57.686 50.000 0.00 0.00 43.72 3.18
4676 5884 2.544844 TCCTTCAGAGGGGTCGTTAT 57.455 50.000 0.00 0.00 43.72 1.89
4678 5886 3.985127 TCCTTCAGAGGGGTCGTTATAA 58.015 45.455 0.00 0.00 43.72 0.98
4696 5904 6.194876 CGTTATAACAGTCTTGCTAAGTCTCG 59.805 42.308 15.67 0.00 0.00 4.04
4697 5905 5.646577 ATAACAGTCTTGCTAAGTCTCGT 57.353 39.130 0.00 0.00 0.00 4.18
4698 5906 4.323553 AACAGTCTTGCTAAGTCTCGTT 57.676 40.909 0.00 0.00 0.00 3.85
4700 5908 5.646577 ACAGTCTTGCTAAGTCTCGTTAT 57.353 39.130 0.00 0.00 0.00 1.89
4701 5909 5.642686 ACAGTCTTGCTAAGTCTCGTTATC 58.357 41.667 0.00 0.00 0.00 1.75
4706 5923 4.371855 TGCTAAGTCTCGTTATCTGTGG 57.628 45.455 0.00 0.00 0.00 4.17
4710 5927 4.657436 AAGTCTCGTTATCTGTGGGATC 57.343 45.455 0.00 0.00 35.98 3.36
4713 5930 4.098654 AGTCTCGTTATCTGTGGGATCTTG 59.901 45.833 0.00 0.00 35.98 3.02
4714 5931 3.126831 CTCGTTATCTGTGGGATCTTGC 58.873 50.000 0.00 0.00 35.98 4.01
4723 5940 3.548770 TGTGGGATCTTGCATTGAGATC 58.451 45.455 15.65 15.65 45.61 2.75
4727 5944 3.874400 GATCTTGCATTGAGATCCGTG 57.126 47.619 13.71 0.00 42.28 4.94
4741 5958 9.626045 ATTGAGATCCGTGTAAAATTTTCTTTC 57.374 29.630 6.72 0.00 0.00 2.62
4744 5961 7.593825 AGATCCGTGTAAAATTTTCTTTCCAG 58.406 34.615 6.72 0.00 0.00 3.86
4799 6016 4.644234 TCAGTGGAGTGAATTGCAAGAAAA 59.356 37.500 4.94 0.00 0.00 2.29
4838 6056 4.799564 TCTTGCAGAAAACAACTTGGTT 57.200 36.364 0.00 0.00 0.00 3.67
4848 6066 6.925165 AGAAAACAACTTGGTTGCTAATCATG 59.075 34.615 0.00 0.00 46.20 3.07
4918 6136 1.205568 GTGATTTCGCGCGGTTGAA 59.794 52.632 31.69 19.17 0.00 2.69
4964 6182 3.031457 GCGTGACGTGGCGTAACA 61.031 61.111 6.91 0.00 40.91 2.41
5317 6535 1.779061 TTTTGCCTCCTCCTTCGGCT 61.779 55.000 0.00 0.00 44.09 5.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 73 9.495572 CTGAATACTTCCTTCAAAGTACTCTTT 57.504 33.333 0.00 0.00 42.78 2.52
107 108 6.154706 AGTGATAACTGGAAGGACTCGTTTAT 59.845 38.462 0.00 0.00 39.30 1.40
166 167 3.633525 TGTGGCCAATCATTCTATGAAGC 59.366 43.478 7.24 0.00 43.50 3.86
261 262 9.219603 CCTCTTACATTTCTGTAATTCACAAGA 57.780 33.333 0.00 0.00 44.65 3.02
407 408 6.816136 CCAATGGGTTATAACTTGGGATTTC 58.184 40.000 20.04 2.03 31.64 2.17
676 681 7.000472 TCTCAACACTCTCCTTTGATCAATTT 59.000 34.615 9.40 0.00 0.00 1.82
687 692 8.571336 CATGTTTTTATTTCTCAACACTCTCCT 58.429 33.333 0.00 0.00 32.10 3.69
690 695 8.902806 TCACATGTTTTTATTTCTCAACACTCT 58.097 29.630 0.00 0.00 32.10 3.24
821 826 7.923414 AGTTTAAATGATCCACTAGTTCCAC 57.077 36.000 0.00 0.00 0.00 4.02
846 851 8.506168 AGTGAAAGTAAAAGAGACACATGAAA 57.494 30.769 0.00 0.00 0.00 2.69
892 897 9.783081 ATTCTTCTTAATGAACAGCCAATTTTT 57.217 25.926 0.00 0.00 0.00 1.94
893 898 9.783081 AATTCTTCTTAATGAACAGCCAATTTT 57.217 25.926 0.00 0.00 0.00 1.82
897 902 9.295825 TCTTAATTCTTCTTAATGAACAGCCAA 57.704 29.630 0.00 0.00 0.00 4.52
898 903 8.730680 GTCTTAATTCTTCTTAATGAACAGCCA 58.269 33.333 0.00 0.00 0.00 4.75
899 904 8.951243 AGTCTTAATTCTTCTTAATGAACAGCC 58.049 33.333 0.00 0.00 0.00 4.85
900 905 9.980780 GAGTCTTAATTCTTCTTAATGAACAGC 57.019 33.333 0.00 0.00 0.00 4.40
903 908 9.980780 GCTGAGTCTTAATTCTTCTTAATGAAC 57.019 33.333 0.00 0.00 0.00 3.18
904 909 9.167311 GGCTGAGTCTTAATTCTTCTTAATGAA 57.833 33.333 0.00 0.00 0.00 2.57
905 910 7.770897 GGGCTGAGTCTTAATTCTTCTTAATGA 59.229 37.037 0.00 0.00 0.00 2.57
906 911 7.554118 TGGGCTGAGTCTTAATTCTTCTTAATG 59.446 37.037 0.00 0.00 0.00 1.90
907 912 7.554476 GTGGGCTGAGTCTTAATTCTTCTTAAT 59.446 37.037 0.00 0.00 0.00 1.40
908 913 6.879458 GTGGGCTGAGTCTTAATTCTTCTTAA 59.121 38.462 0.00 0.00 0.00 1.85
909 914 6.013725 TGTGGGCTGAGTCTTAATTCTTCTTA 60.014 38.462 0.00 0.00 0.00 2.10
910 915 5.221925 TGTGGGCTGAGTCTTAATTCTTCTT 60.222 40.000 0.00 0.00 0.00 2.52
911 916 4.287067 TGTGGGCTGAGTCTTAATTCTTCT 59.713 41.667 0.00 0.00 0.00 2.85
912 917 4.393371 GTGTGGGCTGAGTCTTAATTCTTC 59.607 45.833 0.00 0.00 0.00 2.87
913 918 4.202461 TGTGTGGGCTGAGTCTTAATTCTT 60.202 41.667 0.00 0.00 0.00 2.52
914 919 3.327757 TGTGTGGGCTGAGTCTTAATTCT 59.672 43.478 0.00 0.00 0.00 2.40
915 920 3.437049 GTGTGTGGGCTGAGTCTTAATTC 59.563 47.826 0.00 0.00 0.00 2.17
916 921 3.181445 TGTGTGTGGGCTGAGTCTTAATT 60.181 43.478 0.00 0.00 0.00 1.40
917 922 2.371841 TGTGTGTGGGCTGAGTCTTAAT 59.628 45.455 0.00 0.00 0.00 1.40
918 923 1.765904 TGTGTGTGGGCTGAGTCTTAA 59.234 47.619 0.00 0.00 0.00 1.85
919 924 1.070134 GTGTGTGTGGGCTGAGTCTTA 59.930 52.381 0.00 0.00 0.00 2.10
920 925 0.179045 GTGTGTGTGGGCTGAGTCTT 60.179 55.000 0.00 0.00 0.00 3.01
921 926 1.337384 TGTGTGTGTGGGCTGAGTCT 61.337 55.000 0.00 0.00 0.00 3.24
922 927 0.463654 TTGTGTGTGTGGGCTGAGTC 60.464 55.000 0.00 0.00 0.00 3.36
923 928 0.034574 TTTGTGTGTGTGGGCTGAGT 60.035 50.000 0.00 0.00 0.00 3.41
924 929 1.102154 TTTTGTGTGTGTGGGCTGAG 58.898 50.000 0.00 0.00 0.00 3.35
925 930 1.550327 TTTTTGTGTGTGTGGGCTGA 58.450 45.000 0.00 0.00 0.00 4.26
943 948 7.676947 TGTACTACATGGAGCTAGTTCTTTTT 58.323 34.615 4.32 0.00 0.00 1.94
944 949 7.241042 TGTACTACATGGAGCTAGTTCTTTT 57.759 36.000 4.32 0.00 0.00 2.27
945 950 6.852420 TGTACTACATGGAGCTAGTTCTTT 57.148 37.500 4.32 0.00 0.00 2.52
946 951 6.210784 TGTTGTACTACATGGAGCTAGTTCTT 59.789 38.462 4.32 0.00 0.00 2.52
947 952 5.715279 TGTTGTACTACATGGAGCTAGTTCT 59.285 40.000 4.32 0.00 0.00 3.01
948 953 5.805994 GTGTTGTACTACATGGAGCTAGTTC 59.194 44.000 13.21 0.00 0.00 3.01
949 954 5.337330 GGTGTTGTACTACATGGAGCTAGTT 60.337 44.000 13.21 0.00 0.00 2.24
950 955 4.159879 GGTGTTGTACTACATGGAGCTAGT 59.840 45.833 13.21 1.76 0.00 2.57
951 956 4.159693 TGGTGTTGTACTACATGGAGCTAG 59.840 45.833 13.21 0.00 0.00 3.42
952 957 4.081862 GTGGTGTTGTACTACATGGAGCTA 60.082 45.833 13.21 0.00 40.22 3.32
953 958 2.903784 TGGTGTTGTACTACATGGAGCT 59.096 45.455 13.21 0.00 0.00 4.09
964 969 2.932905 CACGCGGTGGTGTTGTAC 59.067 61.111 12.47 0.00 33.82 2.90
980 985 5.182380 GCCATAAAACTTGTTGTAGTAGCCA 59.818 40.000 0.00 0.00 0.00 4.75
981 986 5.182380 TGCCATAAAACTTGTTGTAGTAGCC 59.818 40.000 0.00 0.00 0.00 3.93
992 997 5.125100 AGATGTGTGTGCCATAAAACTTG 57.875 39.130 0.00 0.00 0.00 3.16
1040 1045 3.243535 CCCAAGCTCTTTTGTTGGAACTC 60.244 47.826 0.00 0.00 43.01 3.01
1101 1113 1.570857 ATTGGGTTGGCGATGGAGGA 61.571 55.000 0.00 0.00 0.00 3.71
1107 1119 1.754234 GGAGCATTGGGTTGGCGAT 60.754 57.895 0.00 0.00 0.00 4.58
1715 1742 1.341802 GTCGTCGTCGTCGTCGTAT 59.658 57.895 18.44 0.00 45.27 3.06
1773 1800 2.661537 CGCACCAGACGAAGCACA 60.662 61.111 0.00 0.00 0.00 4.57
2000 2027 2.816958 CAAGCAGAGACGCCGCAT 60.817 61.111 0.00 0.00 0.00 4.73
2016 2043 2.952978 ACGGCAGAAACATGTTTAACCA 59.047 40.909 23.33 0.00 32.11 3.67
2031 2058 4.929808 AGATTAACTAACAAGACACGGCAG 59.070 41.667 0.00 0.00 0.00 4.85
2035 2062 6.399669 CGGTTGAGATTAACTAACAAGACACG 60.400 42.308 0.00 0.00 0.00 4.49
2081 2108 3.117625 ACAGGACGTAGGAGTATGATGGA 60.118 47.826 0.00 0.00 0.00 3.41
2089 2116 6.404074 CGTTTATTCTAACAGGACGTAGGAGT 60.404 42.308 0.00 0.00 0.00 3.85
2091 2118 5.163622 CCGTTTATTCTAACAGGACGTAGGA 60.164 44.000 0.00 0.00 0.00 2.94
2092 2119 5.039333 CCGTTTATTCTAACAGGACGTAGG 58.961 45.833 0.00 0.00 0.00 3.18
2093 2120 5.644644 ACCGTTTATTCTAACAGGACGTAG 58.355 41.667 0.00 0.00 0.00 3.51
2094 2121 5.415701 AGACCGTTTATTCTAACAGGACGTA 59.584 40.000 0.00 0.00 0.00 3.57
2095 2122 4.219288 AGACCGTTTATTCTAACAGGACGT 59.781 41.667 0.00 0.00 0.00 4.34
2096 2123 4.741342 AGACCGTTTATTCTAACAGGACG 58.259 43.478 0.00 0.00 0.00 4.79
2097 2124 4.797349 CGAGACCGTTTATTCTAACAGGAC 59.203 45.833 0.00 0.00 0.00 3.85
2109 2136 1.807981 CATGGCGCGAGACCGTTTA 60.808 57.895 12.10 0.00 39.67 2.01
2232 2268 5.068329 AGGGAGTGCGGTACTACTATTAAAC 59.932 44.000 8.41 0.00 40.36 2.01
2240 2276 0.745845 TCGAGGGAGTGCGGTACTAC 60.746 60.000 0.00 0.00 40.53 2.73
2241 2277 0.182061 ATCGAGGGAGTGCGGTACTA 59.818 55.000 0.00 0.00 40.53 1.82
2242 2278 0.683504 AATCGAGGGAGTGCGGTACT 60.684 55.000 0.00 0.00 44.02 2.73
2243 2279 0.175073 AAATCGAGGGAGTGCGGTAC 59.825 55.000 0.00 0.00 0.00 3.34
2244 2280 0.899720 AAAATCGAGGGAGTGCGGTA 59.100 50.000 0.00 0.00 0.00 4.02
2245 2281 0.036306 AAAAATCGAGGGAGTGCGGT 59.964 50.000 0.00 0.00 0.00 5.68
2410 2793 9.672673 ACCGTACTACTACTAGTTTAATTGAGA 57.327 33.333 0.00 0.00 34.79 3.27
2413 2796 9.638300 CGTACCGTACTACTACTAGTTTAATTG 57.362 37.037 0.00 0.00 34.79 2.32
2414 2797 9.379791 ACGTACCGTACTACTACTAGTTTAATT 57.620 33.333 0.00 0.00 38.73 1.40
2415 2798 8.943909 ACGTACCGTACTACTACTAGTTTAAT 57.056 34.615 0.00 0.00 38.73 1.40
2416 2799 9.512435 CTACGTACCGTACTACTACTAGTTTAA 57.488 37.037 0.00 0.00 41.54 1.52
2417 2800 8.680903 ACTACGTACCGTACTACTACTAGTTTA 58.319 37.037 0.00 0.00 41.54 2.01
2418 2801 7.545489 ACTACGTACCGTACTACTACTAGTTT 58.455 38.462 0.00 0.00 41.54 2.66
2419 2802 7.098074 ACTACGTACCGTACTACTACTAGTT 57.902 40.000 0.00 0.00 41.54 2.24
2420 2803 6.696441 ACTACGTACCGTACTACTACTAGT 57.304 41.667 0.00 0.00 41.54 2.57
2421 2804 7.863666 ACTACTACGTACCGTACTACTACTAG 58.136 42.308 7.10 0.00 41.54 2.57
2422 2805 7.798596 ACTACTACGTACCGTACTACTACTA 57.201 40.000 7.10 0.00 41.54 1.82
2423 2806 6.696441 ACTACTACGTACCGTACTACTACT 57.304 41.667 7.10 0.00 41.54 2.57
2424 2807 8.505625 AGATACTACTACGTACCGTACTACTAC 58.494 40.741 7.10 0.00 41.54 2.73
2425 2808 8.618702 AGATACTACTACGTACCGTACTACTA 57.381 38.462 7.10 0.00 41.54 1.82
2426 2809 7.446013 AGAGATACTACTACGTACCGTACTACT 59.554 40.741 7.10 0.00 41.54 2.57
2427 2810 7.586747 AGAGATACTACTACGTACCGTACTAC 58.413 42.308 7.10 0.00 41.54 2.73
2428 2811 7.747155 AGAGATACTACTACGTACCGTACTA 57.253 40.000 7.10 0.00 41.54 1.82
2429 2812 6.642707 AGAGATACTACTACGTACCGTACT 57.357 41.667 7.10 0.00 41.54 2.73
2430 2813 6.363896 GGAAGAGATACTACTACGTACCGTAC 59.636 46.154 0.00 0.00 41.54 3.67
2431 2814 6.448006 GGAAGAGATACTACTACGTACCGTA 58.552 44.000 0.00 0.00 41.54 4.02
2432 2815 5.293560 GGAAGAGATACTACTACGTACCGT 58.706 45.833 0.00 0.00 44.35 4.83
2433 2816 4.688413 GGGAAGAGATACTACTACGTACCG 59.312 50.000 0.00 0.00 0.00 4.02
2434 2817 5.000591 GGGGAAGAGATACTACTACGTACC 58.999 50.000 0.00 0.00 0.00 3.34
2435 2818 5.468409 GTGGGGAAGAGATACTACTACGTAC 59.532 48.000 0.00 0.00 0.00 3.67
2436 2819 5.367937 AGTGGGGAAGAGATACTACTACGTA 59.632 44.000 0.00 0.00 0.00 3.57
2437 2820 4.165758 AGTGGGGAAGAGATACTACTACGT 59.834 45.833 0.00 0.00 0.00 3.57
2438 2821 4.716794 AGTGGGGAAGAGATACTACTACG 58.283 47.826 0.00 0.00 0.00 3.51
2439 2822 5.302313 CCAAGTGGGGAAGAGATACTACTAC 59.698 48.000 0.00 0.00 0.00 2.73
2440 2823 5.455872 CCAAGTGGGGAAGAGATACTACTA 58.544 45.833 0.00 0.00 0.00 1.82
2441 2824 4.290942 CCAAGTGGGGAAGAGATACTACT 58.709 47.826 0.00 0.00 0.00 2.57
2442 2825 4.674281 CCAAGTGGGGAAGAGATACTAC 57.326 50.000 0.00 0.00 0.00 2.73
2474 2857 5.065218 AGCCAATTTTTGATAGTAGCGACTG 59.935 40.000 10.02 0.00 36.28 3.51
2545 3072 3.518705 TCTGGTATTACTACCCCGCAAAA 59.481 43.478 6.81 0.00 46.01 2.44
2546 3073 3.106054 TCTGGTATTACTACCCCGCAAA 58.894 45.455 6.81 0.00 46.01 3.68
2547 3074 2.749600 TCTGGTATTACTACCCCGCAA 58.250 47.619 6.81 0.00 46.01 4.85
2549 3076 3.825143 TTTCTGGTATTACTACCCCGC 57.175 47.619 6.81 0.00 46.01 6.13
2550 3077 4.514066 GCAATTTCTGGTATTACTACCCCG 59.486 45.833 6.81 0.00 46.01 5.73
2551 3078 5.691896 AGCAATTTCTGGTATTACTACCCC 58.308 41.667 6.81 0.00 46.01 4.95
2612 3143 1.247567 GGATGGATACCAAATGGCCG 58.752 55.000 0.00 0.00 36.95 6.13
2683 3218 2.005451 CTGACTACAGTGCAATGCTCC 58.995 52.381 15.18 1.84 39.11 4.70
2747 3290 1.005037 CATGCCATGCCATGCCATC 60.005 57.895 3.39 0.00 36.52 3.51
2766 3309 6.441093 AACCACAGAACTTGCATACATATG 57.559 37.500 0.00 0.00 36.78 1.78
2767 3310 5.590259 GGAACCACAGAACTTGCATACATAT 59.410 40.000 0.00 0.00 0.00 1.78
2768 3311 4.941263 GGAACCACAGAACTTGCATACATA 59.059 41.667 0.00 0.00 0.00 2.29
2769 3312 3.758554 GGAACCACAGAACTTGCATACAT 59.241 43.478 0.00 0.00 0.00 2.29
2942 3487 3.190535 GCATTTTTCCTTTACCTCGAGCA 59.809 43.478 6.99 0.00 0.00 4.26
2964 3509 3.249687 GGGTGTACTTCCAGCCTTG 57.750 57.895 2.31 0.00 46.97 3.61
3004 3550 5.657745 TGATACGGTCCAACCTGAATTACTA 59.342 40.000 0.00 0.00 35.66 1.82
3047 3593 8.146412 ACTAATAAACCATCACGGAGGTAATAC 58.854 37.037 0.00 0.00 37.07 1.89
3048 3594 8.253867 ACTAATAAACCATCACGGAGGTAATA 57.746 34.615 0.00 0.00 37.07 0.98
3049 3595 7.133133 ACTAATAAACCATCACGGAGGTAAT 57.867 36.000 0.00 0.00 37.07 1.89
3050 3596 6.549433 ACTAATAAACCATCACGGAGGTAA 57.451 37.500 0.00 0.00 37.07 2.85
3051 3597 6.407299 GGAACTAATAAACCATCACGGAGGTA 60.407 42.308 0.00 0.00 37.07 3.08
3052 3598 5.425630 GAACTAATAAACCATCACGGAGGT 58.574 41.667 0.00 0.00 40.61 3.85
3053 3599 4.814771 GGAACTAATAAACCATCACGGAGG 59.185 45.833 0.00 0.00 38.63 4.30
3054 3600 5.671493 AGGAACTAATAAACCATCACGGAG 58.329 41.667 0.00 0.00 36.02 4.63
3056 3602 6.150474 ACAAAGGAACTAATAAACCATCACGG 59.850 38.462 0.00 0.00 38.49 4.94
3057 3603 7.141100 ACAAAGGAACTAATAAACCATCACG 57.859 36.000 0.00 0.00 38.49 4.35
3153 3699 9.804758 TTGAAAACCACGTTCAAATACTAATTT 57.195 25.926 0.00 0.00 40.96 1.82
3154 3700 9.804758 TTTGAAAACCACGTTCAAATACTAATT 57.195 25.926 7.99 0.00 45.44 1.40
3188 3734 6.922247 AAATGTTCATGCATGTCACAAAAA 57.078 29.167 27.12 12.63 0.00 1.94
3189 3735 6.238402 CCAAAATGTTCATGCATGTCACAAAA 60.238 34.615 27.12 12.93 0.00 2.44
3190 3736 5.236695 CCAAAATGTTCATGCATGTCACAAA 59.763 36.000 27.12 13.95 0.00 2.83
3191 3737 4.750598 CCAAAATGTTCATGCATGTCACAA 59.249 37.500 27.12 14.26 0.00 3.33
3192 3738 4.308265 CCAAAATGTTCATGCATGTCACA 58.692 39.130 26.19 26.19 0.00 3.58
3193 3739 3.123959 GCCAAAATGTTCATGCATGTCAC 59.876 43.478 25.43 21.75 0.00 3.67
3194 3740 3.007074 AGCCAAAATGTTCATGCATGTCA 59.993 39.130 25.43 23.31 0.00 3.58
3195 3741 3.592059 AGCCAAAATGTTCATGCATGTC 58.408 40.909 25.43 19.05 0.00 3.06
3196 3742 3.688694 AGCCAAAATGTTCATGCATGT 57.311 38.095 25.43 4.01 0.00 3.21
3197 3743 4.717991 CAAAGCCAAAATGTTCATGCATG 58.282 39.130 21.07 21.07 0.00 4.06
3198 3744 3.189702 GCAAAGCCAAAATGTTCATGCAT 59.810 39.130 0.00 0.00 0.00 3.96
3199 3745 2.548904 GCAAAGCCAAAATGTTCATGCA 59.451 40.909 0.00 0.00 0.00 3.96
3200 3746 2.411806 CGCAAAGCCAAAATGTTCATGC 60.412 45.455 0.00 0.00 0.00 4.06
3201 3747 2.411806 GCGCAAAGCCAAAATGTTCATG 60.412 45.455 0.30 0.00 40.81 3.07
3202 3748 1.799994 GCGCAAAGCCAAAATGTTCAT 59.200 42.857 0.30 0.00 40.81 2.57
3203 3749 1.216122 GCGCAAAGCCAAAATGTTCA 58.784 45.000 0.30 0.00 40.81 3.18
3368 3931 7.172361 GCTAAAGGATTTTGGTGCAAAACATAA 59.828 33.333 0.00 0.00 44.40 1.90
3418 3983 8.564574 GTTGGTACACTATTCAGAAATGAAACA 58.435 33.333 0.00 0.00 39.29 2.83
3419 3984 8.564574 TGTTGGTACACTATTCAGAAATGAAAC 58.435 33.333 0.00 0.00 39.29 2.78
3440 4029 0.037734 GTGGGGAACTAGGGTGTTGG 59.962 60.000 0.00 0.00 0.00 3.77
3494 4083 3.507162 TCTCATCTTGCCAAGGACAAA 57.493 42.857 4.30 0.00 0.00 2.83
3503 4092 1.546548 GGGCCCTAATCTCATCTTGCC 60.547 57.143 17.04 0.00 36.92 4.52
3507 4096 2.273619 GGATGGGCCCTAATCTCATCT 58.726 52.381 25.70 0.00 35.76 2.90
3521 4110 1.000283 GTGTAGATCTGAGCGGATGGG 60.000 57.143 5.18 0.00 0.00 4.00
3525 4114 2.573369 GTAGGTGTAGATCTGAGCGGA 58.427 52.381 5.18 0.00 0.00 5.54
3530 4119 3.377253 AACGGGTAGGTGTAGATCTGA 57.623 47.619 5.18 0.00 0.00 3.27
3643 4484 2.056906 AAACCCAGCTCTCGCCAAGT 62.057 55.000 0.00 0.00 36.60 3.16
3726 4598 1.728426 GCGCAACTCGTGTAGTCGT 60.728 57.895 0.30 0.00 37.50 4.34
3727 4599 1.396543 GAGCGCAACTCGTGTAGTCG 61.397 60.000 11.47 0.00 37.50 4.18
3728 4600 2.350833 GAGCGCAACTCGTGTAGTC 58.649 57.895 11.47 0.00 37.50 2.59
3729 4601 4.554163 GAGCGCAACTCGTGTAGT 57.446 55.556 11.47 0.00 41.49 2.73
3812 5004 4.087892 GCGCTCCTCCTTGCTGGA 62.088 66.667 0.00 0.00 43.86 3.86
4163 5364 0.883153 TCGACCCGAAAGATTGACGA 59.117 50.000 0.00 0.00 31.06 4.20
4164 5365 0.989890 GTCGACCCGAAAGATTGACG 59.010 55.000 3.51 0.00 37.72 4.35
4166 5367 0.599558 ACGTCGACCCGAAAGATTGA 59.400 50.000 10.58 0.00 37.72 2.57
4167 5368 1.126113 CAACGTCGACCCGAAAGATTG 59.874 52.381 10.58 0.00 37.72 2.67
4168 5369 1.425412 CAACGTCGACCCGAAAGATT 58.575 50.000 10.58 0.00 37.72 2.40
4169 5370 0.389426 CCAACGTCGACCCGAAAGAT 60.389 55.000 10.58 0.00 37.72 2.40
4171 5372 0.877213 AACCAACGTCGACCCGAAAG 60.877 55.000 10.58 0.00 37.72 2.62
4172 5373 1.143620 AACCAACGTCGACCCGAAA 59.856 52.632 10.58 0.00 37.72 3.46
4294 5501 3.047877 CCACCGAACAGGAACGCC 61.048 66.667 0.00 0.00 45.00 5.68
4331 5538 2.675772 GGAGTCGTCCACCCTCGT 60.676 66.667 0.00 0.00 43.31 4.18
4579 5787 5.706916 ACTAAGATCGAGCTAAAACGACAA 58.293 37.500 2.34 0.00 41.17 3.18
4606 5814 7.228706 AGGATCGAGCTGTTTCTAAAAAGAAAA 59.771 33.333 0.00 0.00 39.20 2.29
4607 5815 6.710744 AGGATCGAGCTGTTTCTAAAAAGAAA 59.289 34.615 0.00 0.00 35.67 2.52
4608 5816 6.231211 AGGATCGAGCTGTTTCTAAAAAGAA 58.769 36.000 0.00 0.00 0.00 2.52
4609 5817 5.794894 AGGATCGAGCTGTTTCTAAAAAGA 58.205 37.500 0.00 0.00 0.00 2.52
4610 5818 6.310197 CAAGGATCGAGCTGTTTCTAAAAAG 58.690 40.000 0.00 0.00 0.00 2.27
4611 5819 5.334879 GCAAGGATCGAGCTGTTTCTAAAAA 60.335 40.000 0.00 0.00 0.00 1.94
4612 5820 4.154195 GCAAGGATCGAGCTGTTTCTAAAA 59.846 41.667 0.00 0.00 0.00 1.52
4613 5821 3.684788 GCAAGGATCGAGCTGTTTCTAAA 59.315 43.478 0.00 0.00 0.00 1.85
4614 5822 3.055819 AGCAAGGATCGAGCTGTTTCTAA 60.056 43.478 0.00 0.00 37.20 2.10
4615 5823 2.497675 AGCAAGGATCGAGCTGTTTCTA 59.502 45.455 0.00 0.00 37.20 2.10
4616 5824 1.277557 AGCAAGGATCGAGCTGTTTCT 59.722 47.619 0.00 0.00 37.20 2.52
4617 5825 1.731720 AGCAAGGATCGAGCTGTTTC 58.268 50.000 0.00 0.00 37.20 2.78
4618 5826 3.944476 AGCAAGGATCGAGCTGTTT 57.056 47.368 0.00 0.00 37.20 2.83
4622 5830 0.610174 TTCACAGCAAGGATCGAGCT 59.390 50.000 0.00 0.00 39.63 4.09
4623 5831 1.129437 GTTTCACAGCAAGGATCGAGC 59.871 52.381 0.00 0.00 0.00 5.03
4624 5832 2.693069 AGTTTCACAGCAAGGATCGAG 58.307 47.619 0.00 0.00 0.00 4.04
4625 5833 2.839486 AGTTTCACAGCAAGGATCGA 57.161 45.000 0.00 0.00 0.00 3.59
4626 5834 3.181530 CGTTAGTTTCACAGCAAGGATCG 60.182 47.826 0.00 0.00 0.00 3.69
4627 5835 3.424962 GCGTTAGTTTCACAGCAAGGATC 60.425 47.826 0.00 0.00 0.00 3.36
4628 5836 2.484264 GCGTTAGTTTCACAGCAAGGAT 59.516 45.455 0.00 0.00 0.00 3.24
4629 5837 1.871039 GCGTTAGTTTCACAGCAAGGA 59.129 47.619 0.00 0.00 0.00 3.36
4630 5838 1.873591 AGCGTTAGTTTCACAGCAAGG 59.126 47.619 0.00 0.00 0.00 3.61
4631 5839 2.908634 CAGCGTTAGTTTCACAGCAAG 58.091 47.619 0.00 0.00 0.00 4.01
4632 5840 1.002900 GCAGCGTTAGTTTCACAGCAA 60.003 47.619 0.00 0.00 0.00 3.91
4633 5841 0.586319 GCAGCGTTAGTTTCACAGCA 59.414 50.000 0.00 0.00 0.00 4.41
4634 5842 0.451135 CGCAGCGTTAGTTTCACAGC 60.451 55.000 6.65 0.00 0.00 4.40
4635 5843 3.639222 CGCAGCGTTAGTTTCACAG 57.361 52.632 6.65 0.00 0.00 3.66
4657 5865 2.544844 ATAACGACCCCTCTGAAGGA 57.455 50.000 0.00 0.00 46.67 3.36
4660 5868 4.091549 ACTGTTATAACGACCCCTCTGAA 58.908 43.478 10.92 0.00 0.00 3.02
4675 5883 5.646577 ACGAGACTTAGCAAGACTGTTAT 57.353 39.130 0.00 0.00 33.75 1.89
4676 5884 5.449107 AACGAGACTTAGCAAGACTGTTA 57.551 39.130 0.00 0.00 33.75 2.41
4678 5886 5.416326 AGATAACGAGACTTAGCAAGACTGT 59.584 40.000 0.00 0.00 33.75 3.55
4696 5904 4.883585 TCAATGCAAGATCCCACAGATAAC 59.116 41.667 0.00 0.00 34.42 1.89
4697 5905 5.104402 TCTCAATGCAAGATCCCACAGATAA 60.104 40.000 0.00 0.00 34.42 1.75
4698 5906 4.409901 TCTCAATGCAAGATCCCACAGATA 59.590 41.667 0.00 0.00 34.42 1.98
4700 5908 2.573009 TCTCAATGCAAGATCCCACAGA 59.427 45.455 0.00 0.00 0.00 3.41
4701 5909 2.995283 TCTCAATGCAAGATCCCACAG 58.005 47.619 0.00 0.00 0.00 3.66
4710 5927 4.944962 TTTACACGGATCTCAATGCAAG 57.055 40.909 0.00 0.00 0.00 4.01
4713 5930 7.029563 AGAAAATTTTACACGGATCTCAATGC 58.970 34.615 2.75 0.00 0.00 3.56
4714 5931 8.970691 AAGAAAATTTTACACGGATCTCAATG 57.029 30.769 2.75 0.00 0.00 2.82
4723 5940 7.764695 AAACTGGAAAGAAAATTTTACACGG 57.235 32.000 2.75 1.37 28.28 4.94
4777 5994 4.572985 TTTCTTGCAATTCACTCCACTG 57.427 40.909 0.00 0.00 0.00 3.66
4838 6056 4.381825 GGTGGATTTTGCACATGATTAGCA 60.382 41.667 0.00 0.91 40.73 3.49
4848 6066 2.126502 CCGCGGTGGATTTTGCAC 60.127 61.111 19.50 0.00 42.00 4.57
4894 6112 0.385473 CCGCGCGAAATCACTTGTTT 60.385 50.000 34.63 0.00 0.00 2.83
5035 6253 0.616111 AGGACGGAGCAGATCTGGTT 60.616 55.000 27.10 12.85 41.93 3.67
5268 6486 1.079127 CGTCGGATTGGCCTTCACT 60.079 57.895 3.32 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.