Multiple sequence alignment - TraesCS7D01G013200

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 TraesCS7D01G013200 chr7D 100.000 4699 0 0 1 4699 5519574 5514876 0.000000e+00 8678.0
1 TraesCS7D01G013200 chr7D 100.000 3156 0 0 5131 8286 5514444 5511289 0.000000e+00 5829.0
2 TraesCS7D01G013200 chr7D 80.220 1456 231 33 1264 2691 1705556 1706982 0.000000e+00 1040.0
3 TraesCS7D01G013200 chr7D 81.863 204 33 4 2490 2691 1062703 1062904 1.430000e-37 169.0
4 TraesCS7D01G013200 chr4A 95.612 3168 94 15 5131 8285 736520412 736523547 0.000000e+00 5038.0
5 TraesCS7D01G013200 chr4A 95.883 1943 61 9 891 2816 734625400 734627340 0.000000e+00 3127.0
6 TraesCS7D01G013200 chr4A 95.780 1943 63 9 891 2816 736515874 736517814 0.000000e+00 3116.0
7 TraesCS7D01G013200 chr4A 98.512 1478 22 0 5164 6641 734651863 734653340 0.000000e+00 2608.0
8 TraesCS7D01G013200 chr4A 93.608 1627 67 16 3102 4699 736518398 736520016 0.000000e+00 2394.0
9 TraesCS7D01G013200 chr4A 95.127 1498 63 5 3202 4699 734650029 734651516 0.000000e+00 2353.0
10 TraesCS7D01G013200 chr4A 83.709 2173 286 40 5263 7376 744470457 744468294 0.000000e+00 1989.0
11 TraesCS7D01G013200 chr4A 97.519 1048 26 0 6637 7684 734676451 734677498 0.000000e+00 1792.0
12 TraesCS7D01G013200 chr4A 80.164 1956 300 50 5260 7179 743562571 743564474 0.000000e+00 1382.0
13 TraesCS7D01G013200 chr4A 91.601 762 34 14 1 746 736514860 736515607 0.000000e+00 1026.0
14 TraesCS7D01G013200 chr4A 91.350 763 35 14 1 746 734624144 734624892 0.000000e+00 1014.0
15 TraesCS7D01G013200 chr4A 77.830 1493 201 72 1267 2691 744473888 744472458 0.000000e+00 804.0
16 TraesCS7D01G013200 chr4A 89.655 609 44 8 7678 8285 734679328 734679918 0.000000e+00 758.0
17 TraesCS7D01G013200 chr4A 73.848 738 145 29 3935 4657 743557887 743558591 4.970000e-62 250.0
18 TraesCS7D01G013200 chr4A 94.340 159 5 3 239 397 736512980 736513134 2.990000e-59 241.0
19 TraesCS7D01G013200 chr4A 96.350 137 4 1 751 886 736515667 736515803 3.010000e-54 224.0
20 TraesCS7D01G013200 chr4A 93.571 140 4 5 751 886 734624952 734625090 3.920000e-48 204.0
21 TraesCS7D01G013200 chr4A 76.963 382 43 19 812 1152 744474446 744474069 8.550000e-40 176.0
22 TraesCS7D01G013200 chr4A 97.000 100 3 0 2815 2914 736518186 736518285 1.430000e-37 169.0
23 TraesCS7D01G013200 chr4A 89.147 129 14 0 5131 5259 744470642 744470514 2.390000e-35 161.0
24 TraesCS7D01G013200 chr4A 92.727 110 6 2 2949 3058 734627800 734627907 3.100000e-34 158.0
25 TraesCS7D01G013200 chr4A 95.000 100 4 1 3102 3200 734627911 734628010 1.110000e-33 156.0
26 TraesCS7D01G013200 chr4A 91.818 110 7 2 2949 3058 736518287 736518394 1.440000e-32 152.0
27 TraesCS7D01G013200 chr4A 97.647 85 2 0 2830 2914 734627714 734627798 6.700000e-31 147.0
28 TraesCS7D01G013200 chr4A 96.250 80 2 1 667 746 736513154 736513232 6.750000e-26 130.0
29 TraesCS7D01G013200 chr7B 85.150 1899 254 19 5303 7184 645250372 645248485 0.000000e+00 1919.0
30 TraesCS7D01G013200 chr7B 74.960 1258 243 42 999 2199 611613087 611614329 5.740000e-141 512.0
31 TraesCS7D01G013200 chr7B 75.531 1083 202 38 1264 2306 645252810 645251751 2.710000e-129 473.0
32 TraesCS7D01G013200 chr7B 85.305 279 35 5 2418 2691 1038489 1038212 4.900000e-72 283.0
33 TraesCS7D01G013200 chr1B 80.558 1898 307 39 5312 7171 903781 905654 0.000000e+00 1404.0
34 TraesCS7D01G013200 chr1B 81.854 1532 206 39 1191 2690 898768 900259 0.000000e+00 1223.0
35 TraesCS7D01G013200 chr1B 84.615 130 17 2 5133 5259 902843 902972 8.730000e-25 126.0
36 TraesCS7D01G013200 chr2B 76.658 1945 374 48 5269 7184 59630499 59628606 0.000000e+00 1003.0
37 TraesCS7D01G013200 chr2B 77.140 1168 211 30 3246 4388 755985907 755987043 1.960000e-175 627.0
38 TraesCS7D01G013200 chr2B 75.842 1010 183 35 1657 2627 755972013 755973000 2.730000e-124 457.0
39 TraesCS7D01G013200 chr2B 77.740 292 50 11 1297 1577 59647254 59646967 1.850000e-36 165.0
40 TraesCS7D01G013200 chr2B 97.436 39 0 1 8 46 391159062 391159025 1.930000e-06 65.8
41 TraesCS7D01G013200 chr2B 100.000 29 0 0 5220 5248 59635669 59635641 4.000000e-03 54.7
42 TraesCS7D01G013200 chr2A 83.909 926 125 14 5405 6320 2411592 2410681 0.000000e+00 863.0
43 TraesCS7D01G013200 chr2A 97.727 44 1 0 2926 2969 602449762 602449805 8.920000e-10 76.8
44 TraesCS7D01G013200 chr2D 82.679 993 146 14 5340 6320 2506362 2507340 0.000000e+00 857.0
45 TraesCS7D01G013200 chr6A 80.684 1082 174 22 1244 2307 1882097 1881033 0.000000e+00 808.0
46 TraesCS7D01G013200 chr6A 78.914 313 62 2 1244 1555 3336247 3335938 8.430000e-50 209.0
47 TraesCS7D01G013200 chr6A 86.466 133 16 2 3074 3204 1880645 1880513 2.410000e-30 145.0
48 TraesCS7D01G013200 chr6B 77.041 1176 221 28 3246 4397 5875280 5874130 1.520000e-176 630.0
49 TraesCS7D01G013200 chr6B 77.747 1092 184 36 1258 2306 731593 730518 4.250000e-172 616.0
50 TraesCS7D01G013200 chr6B 75.421 1009 186 36 1657 2627 5887952 5886968 4.590000e-117 433.0
51 TraesCS7D01G013200 chr6B 85.560 277 32 7 2418 2688 29939928 29939654 4.900000e-72 283.0
52 TraesCS7D01G013200 chr6B 73.874 777 141 44 3903 4657 8431333 8430597 3.840000e-63 254.0
53 TraesCS7D01G013200 chr6B 83.957 187 30 0 991 1177 29941390 29941204 6.610000e-41 180.0
54 TraesCS7D01G013200 chr6B 76.972 317 66 6 1261 1575 3179933 3180244 3.070000e-39 174.0
55 TraesCS7D01G013200 chr6B 73.926 349 74 14 6645 6986 3198135 3198473 3.140000e-24 124.0
56 TraesCS7D01G013200 chr6B 87.342 79 10 0 4514 4592 10730208 10730130 3.180000e-14 91.6
57 TraesCS7D01G013200 chr7A 78.662 867 119 32 1446 2273 656880 656041 4.430000e-142 516.0
58 TraesCS7D01G013200 chrUn 85.556 270 32 6 1649 1912 265070813 265071081 8.190000e-70 276.0
59 TraesCS7D01G013200 chrUn 85.556 270 32 6 1649 1912 276378568 276378300 8.190000e-70 276.0
60 TraesCS7D01G013200 chrUn 85.556 270 32 6 1649 1912 309411218 309411486 8.190000e-70 276.0
61 TraesCS7D01G013200 chrUn 85.556 270 32 6 1649 1912 309427952 309427684 8.190000e-70 276.0
62 TraesCS7D01G013200 chrUn 85.556 270 32 6 1649 1912 322037018 322037286 8.190000e-70 276.0
63 TraesCS7D01G013200 chrUn 97.561 41 0 1 8 48 45106350 45106311 1.490000e-07 69.4
64 TraesCS7D01G013200 chr6D 82.707 133 21 2 5259 5390 20587744 20587875 5.250000e-22 117.0
65 TraesCS7D01G013200 chr6D 86.420 81 11 0 4512 4592 5728876 5728796 1.150000e-13 89.8
66 TraesCS7D01G013200 chr5A 81.457 151 9 10 2831 2967 92201079 92201224 1.140000e-18 106.0
67 TraesCS7D01G013200 chr5A 88.462 78 3 6 2895 2971 143577045 143577117 1.150000e-13 89.8
68 TraesCS7D01G013200 chr5B 90.476 63 5 1 2814 2875 103333233 103333295 1.920000e-11 82.4
69 TraesCS7D01G013200 chr4B 97.561 41 0 1 8 48 598464881 598464842 1.490000e-07 69.4


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 TraesCS7D01G013200 chr7D 5511289 5519574 8285 True 7253.500000 8678 100.000000 1 8286 2 chr7D.!!$R1 8285
1 TraesCS7D01G013200 chr7D 1705556 1706982 1426 False 1040.000000 1040 80.220000 1264 2691 1 chr7D.!!$F2 1427
2 TraesCS7D01G013200 chr4A 734650029 734653340 3311 False 2480.500000 2608 96.819500 3202 6641 2 chr4A.!!$F2 3439
3 TraesCS7D01G013200 chr4A 736512980 736523547 10567 False 1387.777778 5038 94.706556 1 8285 9 chr4A.!!$F4 8284
4 TraesCS7D01G013200 chr4A 734676451 734679918 3467 False 1275.000000 1792 93.587000 6637 8285 2 chr4A.!!$F3 1648
5 TraesCS7D01G013200 chr4A 743557887 743564474 6587 False 816.000000 1382 77.006000 3935 7179 2 chr4A.!!$F5 3244
6 TraesCS7D01G013200 chr4A 734624144 734628010 3866 False 801.000000 3127 94.363000 1 3200 6 chr4A.!!$F1 3199
7 TraesCS7D01G013200 chr4A 744468294 744474446 6152 True 782.500000 1989 81.912250 812 7376 4 chr4A.!!$R1 6564
8 TraesCS7D01G013200 chr7B 645248485 645252810 4325 True 1196.000000 1919 80.340500 1264 7184 2 chr7B.!!$R2 5920
9 TraesCS7D01G013200 chr7B 611613087 611614329 1242 False 512.000000 512 74.960000 999 2199 1 chr7B.!!$F1 1200
10 TraesCS7D01G013200 chr1B 898768 905654 6886 False 917.666667 1404 82.342333 1191 7171 3 chr1B.!!$F1 5980
11 TraesCS7D01G013200 chr2B 59628606 59630499 1893 True 1003.000000 1003 76.658000 5269 7184 1 chr2B.!!$R1 1915
12 TraesCS7D01G013200 chr2B 755985907 755987043 1136 False 627.000000 627 77.140000 3246 4388 1 chr2B.!!$F2 1142
13 TraesCS7D01G013200 chr2B 755972013 755973000 987 False 457.000000 457 75.842000 1657 2627 1 chr2B.!!$F1 970
14 TraesCS7D01G013200 chr2A 2410681 2411592 911 True 863.000000 863 83.909000 5405 6320 1 chr2A.!!$R1 915
15 TraesCS7D01G013200 chr2D 2506362 2507340 978 False 857.000000 857 82.679000 5340 6320 1 chr2D.!!$F1 980
16 TraesCS7D01G013200 chr6A 1880513 1882097 1584 True 476.500000 808 83.575000 1244 3204 2 chr6A.!!$R2 1960
17 TraesCS7D01G013200 chr6B 5874130 5875280 1150 True 630.000000 630 77.041000 3246 4397 1 chr6B.!!$R2 1151
18 TraesCS7D01G013200 chr6B 730518 731593 1075 True 616.000000 616 77.747000 1258 2306 1 chr6B.!!$R1 1048
19 TraesCS7D01G013200 chr6B 5886968 5887952 984 True 433.000000 433 75.421000 1657 2627 1 chr6B.!!$R3 970
20 TraesCS7D01G013200 chr6B 8430597 8431333 736 True 254.000000 254 73.874000 3903 4657 1 chr6B.!!$R4 754
21 TraesCS7D01G013200 chr6B 29939654 29941390 1736 True 231.500000 283 84.758500 991 2688 2 chr6B.!!$R6 1697
22 TraesCS7D01G013200 chr7A 656041 656880 839 True 516.000000 516 78.662000 1446 2273 1 chr7A.!!$R1 827

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
886 2841 0.313672 GTGCCGAAATTGCTTGGTGA 59.686 50.000 0.00 0.00 0.00 4.02 F
887 2842 1.067635 GTGCCGAAATTGCTTGGTGAT 60.068 47.619 0.00 0.00 0.00 3.06 F
1009 3290 1.480954 TCTAGTTCTGAATGCGGGACC 59.519 52.381 0.00 0.00 28.14 4.46 F
1200 3481 1.583495 GAGCCCACTAAAACACCGCC 61.583 60.000 0.00 0.00 0.00 6.13 F
2828 5855 2.032528 ATGTGGTCCTGCGTGGTG 59.967 61.111 0.00 0.00 37.07 4.17 F
3844 7885 1.210155 GGCGTGCAAGGACAATGTC 59.790 57.895 4.51 4.51 0.00 3.06 F
4404 8457 1.470979 GCCAAAGCTGCCATTGATGAG 60.471 52.381 15.02 2.62 35.50 2.90 F
5653 13482 1.611673 GCAAGCCTTCTAGCTGGTGAA 60.612 52.381 0.00 0.00 44.11 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2503 5056 2.598589 GTATTGTAGCAACGTCGGTGA 58.401 47.619 16.01 0.00 0.00 4.02 R
2840 5867 5.705441 AGTTTACATTCTCGCCTGAAAATCA 59.295 36.000 0.00 0.00 0.00 2.57 R
2941 5968 0.171231 TCGAACACGCAGGAGATCTG 59.829 55.000 0.00 0.00 46.03 2.90 R
2943 5970 0.452184 TCTCGAACACGCAGGAGATC 59.548 55.000 0.00 0.00 31.00 2.75 R
3859 7900 0.252197 GGTAGGTGGAAATCACGGCT 59.748 55.000 0.00 0.00 46.96 5.52 R
5890 13720 0.592637 TTTCTGCAACATCCACTGCG 59.407 50.000 0.00 0.00 41.63 5.18 R
6508 14367 1.523758 CTTGTAGGGTGCACAAGGAC 58.476 55.000 20.43 10.97 45.92 3.85 R
7656 15576 0.181114 ATGGTGGCATACTCGCACAT 59.819 50.000 0.00 0.00 0.00 3.21 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
40 1921 2.499693 TGCCGAGTTGGATTAGACATCA 59.500 45.455 0.00 0.00 42.00 3.07
48 1929 6.306987 AGTTGGATTAGACATCACAGGTTTT 58.693 36.000 0.00 0.00 0.00 2.43
123 2009 3.030652 CGTTCTTGGTGTGGTGCC 58.969 61.111 0.00 0.00 0.00 5.01
159 2045 2.634940 CAGAAGAGAAGGACCAGGTTGA 59.365 50.000 0.00 0.00 0.00 3.18
162 2048 4.352298 AGAAGAGAAGGACCAGGTTGAAAT 59.648 41.667 0.00 0.00 0.00 2.17
165 2051 5.073428 AGAGAAGGACCAGGTTGAAATTTC 58.927 41.667 11.41 11.41 0.00 2.17
245 2131 7.605691 AGTCCAGTCTTTGTTAATGAGAAGATG 59.394 37.037 0.00 0.00 31.52 2.90
361 2247 1.007600 TGATCTTGAGAGGAGGGCTCA 59.992 52.381 0.00 0.00 40.41 4.26
466 2352 1.305930 ATCTTGGCCGGTCGAAAAGC 61.306 55.000 0.00 0.00 0.00 3.51
468 2354 0.672401 CTTGGCCGGTCGAAAAGCTA 60.672 55.000 0.00 0.00 0.00 3.32
474 2360 1.269621 CCGGTCGAAAAGCTATCCGAT 60.270 52.381 8.25 0.00 40.29 4.18
475 2361 2.470821 CGGTCGAAAAGCTATCCGATT 58.529 47.619 0.91 0.00 40.29 3.34
476 2362 2.471743 CGGTCGAAAAGCTATCCGATTC 59.528 50.000 0.91 3.81 40.29 2.52
481 2367 4.338400 TCGAAAAGCTATCCGATTCTCTCA 59.662 41.667 0.00 0.00 0.00 3.27
483 2369 5.596845 GAAAAGCTATCCGATTCTCTCACT 58.403 41.667 0.00 0.00 0.00 3.41
484 2370 5.606348 AAAGCTATCCGATTCTCTCACTT 57.394 39.130 0.00 0.00 0.00 3.16
497 2383 2.373502 CTCTCACTTTTTCCCCACTCCT 59.626 50.000 0.00 0.00 0.00 3.69
565 2451 2.663196 AGGTTGCGGCTACCTGTC 59.337 61.111 30.54 7.74 44.25 3.51
567 2453 1.003718 GGTTGCGGCTACCTGTCTT 60.004 57.895 23.46 0.00 32.75 3.01
574 2460 1.725164 CGGCTACCTGTCTTTCGTTTC 59.275 52.381 0.00 0.00 0.00 2.78
599 2485 4.047059 TGCCGACGTCGTCCCTTC 62.047 66.667 33.49 16.34 37.74 3.46
600 2486 4.790861 GCCGACGTCGTCCCTTCC 62.791 72.222 33.49 10.94 37.74 3.46
607 2493 1.898885 GTCGTCCCTTCCTCTTCCC 59.101 63.158 0.00 0.00 0.00 3.97
630 2520 1.134753 CTTTGCTTGCCACTCAACACA 59.865 47.619 0.00 0.00 0.00 3.72
738 2634 2.711009 CCTATGCAAAGGTATCCCCTCA 59.289 50.000 0.00 0.00 45.47 3.86
746 2642 3.252554 AGGTATCCCCTCATCTCTGAC 57.747 52.381 0.00 0.00 40.71 3.51
747 2643 2.520120 AGGTATCCCCTCATCTCTGACA 59.480 50.000 0.00 0.00 40.71 3.58
748 2644 3.051803 AGGTATCCCCTCATCTCTGACAA 60.052 47.826 0.00 0.00 40.71 3.18
749 2645 3.070302 GGTATCCCCTCATCTCTGACAAC 59.930 52.174 0.00 0.00 0.00 3.32
763 2714 6.971602 TCTCTGACAACAGTAACAGTAAGAG 58.028 40.000 0.00 0.00 43.81 2.85
851 2806 8.839310 AGATTATATTTCCGAAGAACCATCTG 57.161 34.615 0.00 0.00 35.59 2.90
886 2841 0.313672 GTGCCGAAATTGCTTGGTGA 59.686 50.000 0.00 0.00 0.00 4.02
887 2842 1.067635 GTGCCGAAATTGCTTGGTGAT 60.068 47.619 0.00 0.00 0.00 3.06
888 2843 2.163412 GTGCCGAAATTGCTTGGTGATA 59.837 45.455 0.00 0.00 0.00 2.15
988 3251 9.344772 TCTCAAGCAAACTTACTTTTACCATTA 57.655 29.630 0.00 0.00 33.74 1.90
1009 3290 1.480954 TCTAGTTCTGAATGCGGGACC 59.519 52.381 0.00 0.00 28.14 4.46
1097 3378 4.703575 ACAGGACATCACCAATGATTTCTG 59.296 41.667 4.05 6.58 43.40 3.02
1101 3382 5.163683 GGACATCACCAATGATTTCTGTGAG 60.164 44.000 7.65 4.09 43.40 3.51
1180 3461 7.819415 CCATTCACAAACTACTTACAGATCTCA 59.181 37.037 0.00 0.00 0.00 3.27
1184 3465 6.529829 CACAAACTACTTACAGATCTCAGAGC 59.470 42.308 0.00 0.00 0.00 4.09
1200 3481 1.583495 GAGCCCACTAAAACACCGCC 61.583 60.000 0.00 0.00 0.00 6.13
1462 3885 2.143419 GGAGGCTGGGTCCGATGAT 61.143 63.158 0.00 0.00 0.00 2.45
1480 3903 6.250527 CCGATGATTTTAAATTGGTCAACGTC 59.749 38.462 15.09 0.00 34.60 4.34
1678 4143 8.237811 TGTTCTATCATTGCTCAGTATGTAGA 57.762 34.615 0.00 0.00 37.40 2.59
1684 4149 7.930513 TCATTGCTCAGTATGTAGATTAACG 57.069 36.000 0.00 0.00 37.40 3.18
1699 4169 5.480205 AGATTAACGAAACTCCTCACCTTC 58.520 41.667 0.00 0.00 0.00 3.46
2419 4971 7.067372 ACACCATGACATGAACATATAGTTTGG 59.933 37.037 17.24 4.93 41.51 3.28
2503 5056 2.249139 GGAGACACAGGTGGAGTAAGT 58.751 52.381 4.24 0.00 34.19 2.24
2701 5345 6.245115 TGTAATCAAACTGCAGTTGAGATG 57.755 37.500 31.91 26.08 38.44 2.90
2744 5398 5.337578 AACAGCCAACTAACATTGTGTTT 57.662 34.783 0.20 0.00 41.45 2.83
2790 5444 8.823220 ACATTGGTTAGCTAATCATAAACCTT 57.177 30.769 19.87 2.05 40.22 3.50
2828 5855 2.032528 ATGTGGTCCTGCGTGGTG 59.967 61.111 0.00 0.00 37.07 4.17
2876 5903 8.167345 GCGAGAATGTAAACTAAGAACTTTACC 58.833 37.037 0.00 0.00 33.60 2.85
2923 5950 7.433708 GGGTTCTTGTCCCATTTAAAATTTG 57.566 36.000 0.00 0.00 44.05 2.32
2924 5951 6.072728 GGGTTCTTGTCCCATTTAAAATTTGC 60.073 38.462 0.00 0.00 44.05 3.68
2925 5952 6.072728 GGTTCTTGTCCCATTTAAAATTTGCC 60.073 38.462 0.00 0.00 0.00 4.52
2926 5953 6.432403 TCTTGTCCCATTTAAAATTTGCCT 57.568 33.333 0.00 0.00 0.00 4.75
2927 5954 6.836242 TCTTGTCCCATTTAAAATTTGCCTT 58.164 32.000 0.00 0.00 0.00 4.35
2928 5955 7.967908 TCTTGTCCCATTTAAAATTTGCCTTA 58.032 30.769 0.00 0.00 0.00 2.69
2929 5956 8.432805 TCTTGTCCCATTTAAAATTTGCCTTAA 58.567 29.630 0.00 0.00 0.00 1.85
2930 5957 8.980481 TTGTCCCATTTAAAATTTGCCTTAAA 57.020 26.923 0.00 0.00 32.96 1.52
2931 5958 9.579932 TTGTCCCATTTAAAATTTGCCTTAAAT 57.420 25.926 0.00 0.00 40.67 1.40
2942 5969 9.593134 AAAATTTGCCTTAAATAATGATACGCA 57.407 25.926 0.00 0.00 38.01 5.24
2943 5970 8.801715 AATTTGCCTTAAATAATGATACGCAG 57.198 30.769 0.00 0.00 38.01 5.18
2944 5971 7.561021 TTTGCCTTAAATAATGATACGCAGA 57.439 32.000 0.00 0.00 0.00 4.26
2945 5972 7.744087 TTGCCTTAAATAATGATACGCAGAT 57.256 32.000 0.00 0.00 0.00 2.90
2946 5973 7.364522 TGCCTTAAATAATGATACGCAGATC 57.635 36.000 0.00 0.00 0.00 2.75
2947 5974 7.161404 TGCCTTAAATAATGATACGCAGATCT 58.839 34.615 0.00 0.00 0.00 2.75
2959 5986 2.658538 CAGATCTCCTGCGTGTTCG 58.341 57.895 0.00 0.00 35.89 3.95
3058 6085 9.429359 GTTTCATTAAGAAGTTGAGATCAGAGA 57.571 33.333 0.00 0.00 37.57 3.10
3066 6093 8.359875 AGAAGTTGAGATCAGAGAACTAATGA 57.640 34.615 0.00 0.00 0.00 2.57
3067 6094 8.811017 AGAAGTTGAGATCAGAGAACTAATGAA 58.189 33.333 0.00 0.00 0.00 2.57
3068 6095 9.598517 GAAGTTGAGATCAGAGAACTAATGAAT 57.401 33.333 0.00 0.00 0.00 2.57
3069 6096 9.956640 AAGTTGAGATCAGAGAACTAATGAATT 57.043 29.630 0.00 0.00 0.00 2.17
3073 6100 9.948964 TGAGATCAGAGAACTAATGAATTTTGA 57.051 29.630 0.00 0.00 0.00 2.69
3078 6105 9.212641 TCAGAGAACTAATGAATTTTGAGTCAG 57.787 33.333 0.00 0.00 0.00 3.51
3100 6127 8.837389 GTCAGTTATTCAACTCTAAGGTTTTGT 58.163 33.333 0.00 0.00 43.30 2.83
3331 7144 5.502544 GCTCGAGCTACATTTTACATTGGAC 60.503 44.000 29.88 0.00 38.21 4.02
3361 7177 5.627182 AGGAGATGTCATGCTCAGTTAAT 57.373 39.130 11.81 0.00 32.83 1.40
3467 7286 2.401766 CCACCAGGATGCAACGAGC 61.402 63.158 0.00 0.00 40.02 5.03
3487 7306 5.220359 CGAGCATCTTGTTCAGATAACAGTG 60.220 44.000 0.00 0.00 40.67 3.66
3488 7307 4.394300 AGCATCTTGTTCAGATAACAGTGC 59.606 41.667 12.80 12.80 40.67 4.40
3489 7308 4.154737 GCATCTTGTTCAGATAACAGTGCA 59.845 41.667 14.49 0.00 40.67 4.57
3490 7309 5.673068 GCATCTTGTTCAGATAACAGTGCAG 60.673 44.000 14.49 2.35 40.67 4.41
3491 7310 4.318332 TCTTGTTCAGATAACAGTGCAGG 58.682 43.478 0.00 0.00 0.00 4.85
3492 7311 2.426522 TGTTCAGATAACAGTGCAGGC 58.573 47.619 0.00 0.00 0.00 4.85
3646 7471 5.393461 GGTTGATGAGGTGAATTTGATGGTC 60.393 44.000 0.00 0.00 0.00 4.02
3647 7472 4.920999 TGATGAGGTGAATTTGATGGTCA 58.079 39.130 0.00 0.00 0.00 4.02
3665 7511 5.993106 GGTCAAATATGAGCCTGTTAGTC 57.007 43.478 0.00 0.00 46.07 2.59
3702 7548 4.390556 AGCCGAGGCAGTCTCCCT 62.391 66.667 17.18 0.00 44.88 4.20
3796 7837 4.752661 TTACTTCGTTGTTTATGGTGCC 57.247 40.909 0.00 0.00 0.00 5.01
3825 7866 8.388484 ACATCAATTCCAGCATCTATAAAGAC 57.612 34.615 0.00 0.00 33.57 3.01
3844 7885 1.210155 GGCGTGCAAGGACAATGTC 59.790 57.895 4.51 4.51 0.00 3.06
3850 7891 3.374745 GTGCAAGGACAATGTCACAAAG 58.625 45.455 15.86 1.42 33.68 2.77
3859 7900 7.907389 AGGACAATGTCACAAAGAACTAGATA 58.093 34.615 15.86 0.00 33.68 1.98
3865 7906 4.563184 GTCACAAAGAACTAGATAGCCGTG 59.437 45.833 0.00 0.00 0.00 4.94
3875 7916 2.119495 AGATAGCCGTGATTTCCACCT 58.881 47.619 0.00 0.00 42.76 4.00
4106 8147 2.721971 AAGGTGTCAGAGGTGCAGCG 62.722 60.000 10.78 0.00 35.02 5.18
4287 8331 1.656587 AGGGCAAGAGTCACCATACA 58.343 50.000 0.00 0.00 0.00 2.29
4323 8370 6.531240 TGATCAAAGACAAAAGCAAACAAGTC 59.469 34.615 0.00 0.00 0.00 3.01
4404 8457 1.470979 GCCAAAGCTGCCATTGATGAG 60.471 52.381 15.02 2.62 35.50 2.90
4603 8656 2.277084 ACGAGCTTAAAGCCCAATACG 58.723 47.619 0.00 0.00 43.77 3.06
5653 13482 1.611673 GCAAGCCTTCTAGCTGGTGAA 60.612 52.381 0.00 0.00 44.11 3.18
5890 13720 4.691216 GTGAGTACAAATGGTCTTCTGGAC 59.309 45.833 0.00 0.00 43.79 4.02
6075 13910 6.825721 GTGATTGATGGTTCTAAGGTTGAGAT 59.174 38.462 0.00 0.00 0.00 2.75
6280 14121 2.097110 ACAACTACCTGGACCTCACA 57.903 50.000 0.00 0.00 0.00 3.58
6508 14367 0.246635 ACGGGATCGACAGGTTGAAG 59.753 55.000 0.00 0.00 40.11 3.02
7380 15300 4.530553 TCATGCCACCTCTAACTTACTTGA 59.469 41.667 0.00 0.00 0.00 3.02
7442 15362 4.215908 TGCTCAAGTCGTCCCTATTATCT 58.784 43.478 0.00 0.00 0.00 1.98
7488 15408 4.286297 AGCTTAATGGTGCAGACTACAA 57.714 40.909 0.00 0.00 0.00 2.41
7518 15438 8.512138 GCTTAATTGATGTGGTTGTTACTTAGT 58.488 33.333 0.00 0.00 0.00 2.24
7524 15444 8.911918 TGATGTGGTTGTTACTTAGTGTATTT 57.088 30.769 0.00 0.00 0.00 1.40
7525 15445 8.995220 TGATGTGGTTGTTACTTAGTGTATTTC 58.005 33.333 0.00 0.00 0.00 2.17
7592 15512 6.656270 GTGGATGAAATATATGATGTCCTGCA 59.344 38.462 8.21 0.00 0.00 4.41
7633 15553 2.734175 CGAGTGGCGAGCTACAACAATA 60.734 50.000 13.77 0.00 44.57 1.90
7637 15557 4.099573 AGTGGCGAGCTACAACAATACTAT 59.900 41.667 13.77 0.00 0.00 2.12
7651 15571 9.019656 ACAACAATACTATTAGAACAAATGCCA 57.980 29.630 0.00 0.00 0.00 4.92
7664 15584 3.004002 ACAAATGCCATGATATGTGCGAG 59.996 43.478 0.00 0.00 31.73 5.03
7684 17440 3.164268 AGTATGCCACCATGAAGCAAAA 58.836 40.909 8.09 0.00 40.46 2.44
7685 17441 3.577848 AGTATGCCACCATGAAGCAAAAA 59.422 39.130 8.09 0.00 40.46 1.94
7705 17461 3.758755 AGTGAGTGTCATCAAGCAGAA 57.241 42.857 0.00 0.00 0.00 3.02
7811 17568 1.002033 CTGTGGAAGCAGAAGCACAAC 60.002 52.381 0.00 0.00 45.49 3.32
7818 17575 0.955428 GCAGAAGCACAACGGGATCA 60.955 55.000 0.00 0.00 41.58 2.92
7822 17579 1.062587 GAAGCACAACGGGATCAATCG 59.937 52.381 0.00 0.00 0.00 3.34
7823 17580 0.249120 AGCACAACGGGATCAATCGA 59.751 50.000 8.87 0.00 0.00 3.59
7824 17581 1.083489 GCACAACGGGATCAATCGAA 58.917 50.000 8.87 0.00 0.00 3.71
7825 17582 1.670811 GCACAACGGGATCAATCGAAT 59.329 47.619 8.87 0.00 0.00 3.34
7826 17583 2.286418 GCACAACGGGATCAATCGAATC 60.286 50.000 8.87 0.00 0.00 2.52
7827 17584 2.935849 CACAACGGGATCAATCGAATCA 59.064 45.455 8.87 0.00 0.00 2.57
7828 17585 3.373748 CACAACGGGATCAATCGAATCAA 59.626 43.478 8.87 0.00 0.00 2.57
7829 17586 4.035558 CACAACGGGATCAATCGAATCAAT 59.964 41.667 8.87 0.00 0.00 2.57
7830 17587 4.273480 ACAACGGGATCAATCGAATCAATC 59.727 41.667 8.87 0.00 0.00 2.67
7831 17588 3.403038 ACGGGATCAATCGAATCAATCC 58.597 45.455 8.87 9.71 36.06 3.01
7832 17589 3.181455 ACGGGATCAATCGAATCAATCCA 60.181 43.478 16.53 0.00 38.10 3.41
7833 17590 4.005650 CGGGATCAATCGAATCAATCCAT 58.994 43.478 16.53 0.00 38.10 3.41
7834 17591 4.093998 CGGGATCAATCGAATCAATCCATC 59.906 45.833 16.53 4.71 38.10 3.51
7835 17592 5.251764 GGGATCAATCGAATCAATCCATCT 58.748 41.667 16.53 0.00 38.10 2.90
7836 17593 5.709164 GGGATCAATCGAATCAATCCATCTT 59.291 40.000 16.53 0.00 38.10 2.40
7837 17594 6.128063 GGGATCAATCGAATCAATCCATCTTC 60.128 42.308 16.53 1.67 38.10 2.87
7838 17595 6.654161 GGATCAATCGAATCAATCCATCTTCT 59.346 38.462 12.16 0.00 36.67 2.85
7839 17596 7.148440 GGATCAATCGAATCAATCCATCTTCTC 60.148 40.741 12.16 0.00 36.67 2.87
7840 17597 5.994054 TCAATCGAATCAATCCATCTTCTCC 59.006 40.000 0.00 0.00 0.00 3.71
7843 17600 4.410228 TCGAATCAATCCATCTTCTCCCTT 59.590 41.667 0.00 0.00 0.00 3.95
7863 17620 2.701551 TCCTTCCTTCCTTCCAGTGAA 58.298 47.619 0.00 0.00 0.00 3.18
7893 17650 9.370126 GACGAGAATTACAATACAATGCAATAC 57.630 33.333 0.00 0.00 0.00 1.89
7895 17652 9.158364 CGAGAATTACAATACAATGCAATACAC 57.842 33.333 0.00 0.00 0.00 2.90
7901 17658 4.801147 ATACAATGCAATACACAGAGCG 57.199 40.909 0.00 0.00 0.00 5.03
7919 17676 1.398071 GCGTTAAGCTTTCCGTGTCAC 60.398 52.381 3.20 0.00 44.04 3.67
7930 17687 1.003355 CGTGTCACCCTGATTGCCT 60.003 57.895 0.00 0.00 0.00 4.75
7935 17692 1.963515 GTCACCCTGATTGCCTGTTTT 59.036 47.619 0.00 0.00 0.00 2.43
7937 17694 1.068333 CACCCTGATTGCCTGTTTTCG 60.068 52.381 0.00 0.00 0.00 3.46
7940 17697 0.454957 CTGATTGCCTGTTTTCGCCG 60.455 55.000 0.00 0.00 0.00 6.46
8035 17800 2.017668 AACCCTGTGTTGGCATCCCA 62.018 55.000 0.00 0.00 40.06 4.37
8061 17826 2.802787 AGCCAGTTAATCCTCGATCG 57.197 50.000 9.36 9.36 0.00 3.69
8079 17844 0.870393 CGCTGTCTTGCATGTGAACT 59.130 50.000 0.00 0.00 0.00 3.01
8104 17869 2.123428 GGCAGCAATACCCAGCAGG 61.123 63.158 0.00 0.00 43.78 4.85
8171 17936 4.450419 CCACTCTCTCTTTTGCTAGTGTTG 59.550 45.833 0.00 0.00 34.02 3.33
8175 17940 5.050490 TCTCTCTTTTGCTAGTGTTGTCAC 58.950 41.667 0.00 0.00 44.15 3.67
8190 17955 7.189693 GTGTTGTCACTGAAATGTCTATGAA 57.810 36.000 0.00 0.00 40.98 2.57
8201 17966 7.289310 TGAAATGTCTATGAATAATCTGGGCA 58.711 34.615 0.00 0.00 0.00 5.36
8213 17978 2.283101 TGGGCATGGTGGCTTGTC 60.283 61.111 3.50 0.00 43.20 3.18
8245 18010 3.581024 TGTTCATGCAAAATCTGGCTC 57.419 42.857 0.00 0.00 0.00 4.70
8281 18046 5.972973 CGAGGCACGTGTTGTTAATACTATA 59.027 40.000 18.38 0.00 37.22 1.31
8285 18050 9.001542 AGGCACGTGTTGTTAATACTATAAAAA 57.998 29.630 18.38 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 1888 1.296715 CTCGGCACCTAAACCAGCT 59.703 57.895 0.00 0.00 0.00 4.24
40 1921 6.319658 CCATCTTCTATGCATGTAAAACCTGT 59.680 38.462 10.16 0.00 0.00 4.00
48 1929 3.136260 TGCCACCATCTTCTATGCATGTA 59.864 43.478 10.16 0.00 0.00 2.29
150 2036 6.560003 AAGAAAAGGAAATTTCAACCTGGT 57.440 33.333 19.49 0.00 40.89 4.00
159 2045 7.904558 AGGACTCTGAAAGAAAAGGAAATTT 57.095 32.000 0.00 0.00 46.34 1.82
162 2048 7.718334 AAAAGGACTCTGAAAGAAAAGGAAA 57.282 32.000 0.00 0.00 46.34 3.13
165 2051 5.750547 GCAAAAAGGACTCTGAAAGAAAAGG 59.249 40.000 0.00 0.00 46.34 3.11
276 2162 7.431249 CATGGGATCTTTTGTCCTCATTATTG 58.569 38.462 0.00 0.00 36.00 1.90
293 2179 2.520260 GGGGCTGTGCATGGGATC 60.520 66.667 0.00 0.00 0.00 3.36
297 2183 2.757099 GAAGGGGGCTGTGCATGG 60.757 66.667 0.00 0.00 0.00 3.66
361 2247 6.183360 GCTGTAGCAGAATTATTGTGATTGGT 60.183 38.462 6.26 0.00 41.59 3.67
466 2352 5.755861 GGGAAAAAGTGAGAGAATCGGATAG 59.244 44.000 0.00 0.00 42.67 2.08
468 2354 4.518249 GGGAAAAAGTGAGAGAATCGGAT 58.482 43.478 0.00 0.00 42.67 4.18
474 2360 3.181443 GGAGTGGGGAAAAAGTGAGAGAA 60.181 47.826 0.00 0.00 0.00 2.87
475 2361 2.372172 GGAGTGGGGAAAAAGTGAGAGA 59.628 50.000 0.00 0.00 0.00 3.10
476 2362 2.373502 AGGAGTGGGGAAAAAGTGAGAG 59.626 50.000 0.00 0.00 0.00 3.20
481 2367 3.197983 CGAGATAGGAGTGGGGAAAAAGT 59.802 47.826 0.00 0.00 0.00 2.66
483 2369 2.093128 GCGAGATAGGAGTGGGGAAAAA 60.093 50.000 0.00 0.00 0.00 1.94
484 2370 1.485066 GCGAGATAGGAGTGGGGAAAA 59.515 52.381 0.00 0.00 0.00 2.29
554 2440 1.725164 GAAACGAAAGACAGGTAGCCG 59.275 52.381 0.00 0.00 0.00 5.52
562 2448 1.342174 ACCTAGGCGAAACGAAAGACA 59.658 47.619 9.30 0.00 0.00 3.41
563 2449 1.725164 CACCTAGGCGAAACGAAAGAC 59.275 52.381 9.30 0.00 0.00 3.01
565 2451 0.442699 GCACCTAGGCGAAACGAAAG 59.557 55.000 9.30 0.00 0.00 2.62
567 2453 1.375013 GGCACCTAGGCGAAACGAA 60.375 57.895 9.30 0.00 33.57 3.85
607 2493 1.114722 TTGAGTGGCAAGCAAAGGGG 61.115 55.000 0.00 0.00 31.55 4.79
621 2507 1.069765 CGAGGTGGCTGTGTTGAGT 59.930 57.895 0.00 0.00 0.00 3.41
630 2520 4.694233 CACTGCTGCGAGGTGGCT 62.694 66.667 10.78 0.00 0.00 4.75
650 2540 1.072965 AGAAGGCTTGGTTGACTCCAG 59.927 52.381 3.46 0.00 38.80 3.86
685 2575 1.217057 ACCAGAGCACCATCCCCATT 61.217 55.000 0.00 0.00 0.00 3.16
738 2634 7.448777 TCTCTTACTGTTACTGTTGTCAGAGAT 59.551 37.037 13.68 0.00 43.76 2.75
746 2642 7.095607 GGAACACATCTCTTACTGTTACTGTTG 60.096 40.741 0.00 0.00 0.00 3.33
747 2643 6.929606 GGAACACATCTCTTACTGTTACTGTT 59.070 38.462 0.00 0.00 0.00 3.16
748 2644 6.267928 AGGAACACATCTCTTACTGTTACTGT 59.732 38.462 0.00 0.00 36.60 3.55
749 2645 6.587990 CAGGAACACATCTCTTACTGTTACTG 59.412 42.308 7.11 7.11 44.92 2.74
763 2714 0.801251 GCACAGAGCAGGAACACATC 59.199 55.000 0.00 0.00 44.79 3.06
792 2743 1.339535 GGGAGCAGAGAGGAAACCAAG 60.340 57.143 0.00 0.00 0.00 3.61
838 2793 2.625737 AGATGCACAGATGGTTCTTCG 58.374 47.619 0.00 0.00 0.00 3.79
851 2806 3.126858 TCGGCACATTAAAGAAGATGCAC 59.873 43.478 0.00 0.00 33.14 4.57
886 2841 7.321717 AGATTTAGCCCTGTATGTGTGATAT 57.678 36.000 0.00 0.00 0.00 1.63
887 2842 6.239600 GGAGATTTAGCCCTGTATGTGTGATA 60.240 42.308 0.00 0.00 0.00 2.15
888 2843 5.455326 GGAGATTTAGCCCTGTATGTGTGAT 60.455 44.000 0.00 0.00 0.00 3.06
988 3251 2.103263 GGTCCCGCATTCAGAACTAGAT 59.897 50.000 0.00 0.00 0.00 1.98
1009 3290 1.442769 ATACGCTCCAGCACACTTTG 58.557 50.000 0.00 0.00 42.21 2.77
1097 3378 1.468914 GGCCGATTTTGTTCTCCTCAC 59.531 52.381 0.00 0.00 0.00 3.51
1101 3382 0.811281 CCTGGCCGATTTTGTTCTCC 59.189 55.000 0.00 0.00 0.00 3.71
1180 3461 0.605589 GCGGTGTTTTAGTGGGCTCT 60.606 55.000 0.00 0.00 0.00 4.09
1184 3465 2.329614 CCGGCGGTGTTTTAGTGGG 61.330 63.158 19.97 0.00 0.00 4.61
1462 3885 6.928979 TCTCTGACGTTGACCAATTTAAAA 57.071 33.333 0.00 0.00 0.00 1.52
1678 4143 5.485209 AGAAGGTGAGGAGTTTCGTTAAT 57.515 39.130 0.00 0.00 0.00 1.40
1739 4213 4.433186 TGTCATAGCGTTTTTCCCATTG 57.567 40.909 0.00 0.00 0.00 2.82
2503 5056 2.598589 GTATTGTAGCAACGTCGGTGA 58.401 47.619 16.01 0.00 0.00 4.02
2701 5345 8.384365 GCTGTTTTACACTTAATTAGCTCTCTC 58.616 37.037 0.00 0.00 0.00 3.20
2790 5444 6.014242 CACATCCTGGATTATGCTAACCTAGA 60.014 42.308 6.42 0.00 0.00 2.43
2840 5867 5.705441 AGTTTACATTCTCGCCTGAAAATCA 59.295 36.000 0.00 0.00 0.00 2.57
2916 5943 9.593134 TGCGTATCATTATTTAAGGCAAATTTT 57.407 25.926 0.00 0.00 37.93 1.82
2917 5944 9.248291 CTGCGTATCATTATTTAAGGCAAATTT 57.752 29.630 0.00 0.00 37.93 1.82
2918 5945 8.629158 TCTGCGTATCATTATTTAAGGCAAATT 58.371 29.630 0.00 0.00 37.93 1.82
2919 5946 8.165239 TCTGCGTATCATTATTTAAGGCAAAT 57.835 30.769 0.00 0.00 40.10 2.32
2920 5947 7.561021 TCTGCGTATCATTATTTAAGGCAAA 57.439 32.000 0.00 0.00 0.00 3.68
2921 5948 7.661437 AGATCTGCGTATCATTATTTAAGGCAA 59.339 33.333 0.00 0.00 0.00 4.52
2922 5949 7.161404 AGATCTGCGTATCATTATTTAAGGCA 58.839 34.615 0.00 0.00 0.00 4.75
2923 5950 7.201565 GGAGATCTGCGTATCATTATTTAAGGC 60.202 40.741 0.00 0.00 0.00 4.35
2924 5951 8.037758 AGGAGATCTGCGTATCATTATTTAAGG 58.962 37.037 8.74 0.00 0.00 2.69
2925 5952 8.867935 CAGGAGATCTGCGTATCATTATTTAAG 58.132 37.037 8.74 0.00 36.60 1.85
2926 5953 8.763049 CAGGAGATCTGCGTATCATTATTTAA 57.237 34.615 8.74 0.00 36.60 1.52
2941 5968 0.171231 TCGAACACGCAGGAGATCTG 59.829 55.000 0.00 0.00 46.03 2.90
2942 5969 0.453793 CTCGAACACGCAGGAGATCT 59.546 55.000 0.00 0.00 0.00 2.75
2943 5970 0.452184 TCTCGAACACGCAGGAGATC 59.548 55.000 0.00 0.00 31.00 2.75
2944 5971 0.888619 TTCTCGAACACGCAGGAGAT 59.111 50.000 0.00 0.00 35.63 2.75
2945 5972 0.671796 TTTCTCGAACACGCAGGAGA 59.328 50.000 0.00 0.00 33.96 3.71
2946 5973 1.497991 TTTTCTCGAACACGCAGGAG 58.502 50.000 0.00 0.00 0.00 3.69
2947 5974 1.942677 TTTTTCTCGAACACGCAGGA 58.057 45.000 0.00 0.00 0.00 3.86
3068 6095 9.273016 CCTTAGAGTTGAATAACTGACTCAAAA 57.727 33.333 5.31 0.00 46.79 2.44
3069 6096 8.429641 ACCTTAGAGTTGAATAACTGACTCAAA 58.570 33.333 5.31 0.00 46.79 2.69
3073 6100 9.057089 CAAAACCTTAGAGTTGAATAACTGACT 57.943 33.333 0.00 0.00 46.79 3.41
3074 6101 8.837389 ACAAAACCTTAGAGTTGAATAACTGAC 58.163 33.333 0.00 0.00 46.79 3.51
3087 6114 8.221965 AGAACCAAAGTAACAAAACCTTAGAG 57.778 34.615 0.00 0.00 0.00 2.43
3124 6151 5.638234 GCGGGTTAAGATTAGCTAACCTATG 59.362 44.000 8.70 3.15 41.14 2.23
3129 6156 5.228665 CCTAGCGGGTTAAGATTAGCTAAC 58.771 45.833 8.70 3.23 36.86 2.34
3207 6236 5.419788 TGCACTATTTTCAGAAAGGATGCAT 59.580 36.000 16.33 0.00 34.62 3.96
3209 6238 5.098211 GTGCACTATTTTCAGAAAGGATGC 58.902 41.667 10.32 12.94 0.00 3.91
3331 7144 4.375272 AGCATGACATCTCCTTGTTATCG 58.625 43.478 0.00 0.00 0.00 2.92
3361 7177 2.488347 GGCCTTTGTCCTGTTGGTTAGA 60.488 50.000 0.00 0.00 34.23 2.10
3446 7265 2.048023 CGTTGCATCCTGGTGGCAT 61.048 57.895 13.95 0.00 37.39 4.40
3467 7286 5.163784 CCTGCACTGTTATCTGAACAAGATG 60.164 44.000 0.00 0.00 45.64 2.90
3488 7307 3.430565 TATCCTGTCGCTGCGCCTG 62.431 63.158 18.65 10.33 0.00 4.85
3489 7308 3.144120 CTATCCTGTCGCTGCGCCT 62.144 63.158 18.65 0.00 0.00 5.52
3490 7309 2.659897 CTATCCTGTCGCTGCGCC 60.660 66.667 18.65 6.66 0.00 6.53
3491 7310 2.659897 CCTATCCTGTCGCTGCGC 60.660 66.667 18.65 13.09 0.00 6.09
3492 7311 2.028190 CCCTATCCTGTCGCTGCG 59.972 66.667 17.25 17.25 0.00 5.18
3646 7471 5.109210 TGTCGACTAACAGGCTCATATTTG 58.891 41.667 17.92 0.00 0.00 2.32
3647 7472 5.339008 TGTCGACTAACAGGCTCATATTT 57.661 39.130 17.92 0.00 0.00 1.40
3665 7511 1.515521 GGCAAACTGGGGTCTTGTCG 61.516 60.000 0.00 0.00 0.00 4.35
3702 7548 7.058525 AGATTATTTGATGAAGCTCACCATGA 58.941 34.615 0.00 0.00 0.00 3.07
3767 7754 9.834628 ACCATAAACAACGAAGTAATAACATTG 57.165 29.630 0.00 0.00 45.00 2.82
3771 7758 6.744082 GGCACCATAAACAACGAAGTAATAAC 59.256 38.462 0.00 0.00 45.00 1.89
3775 7762 4.135306 TGGCACCATAAACAACGAAGTAA 58.865 39.130 0.00 0.00 45.00 2.24
3791 7778 1.106285 GGAATTGATGTCCTGGCACC 58.894 55.000 0.00 0.00 31.94 5.01
3796 7837 3.552875 AGATGCTGGAATTGATGTCCTG 58.447 45.455 0.00 0.00 36.03 3.86
3825 7866 2.176546 CATTGTCCTTGCACGCCG 59.823 61.111 0.00 0.00 0.00 6.46
3844 7885 4.744570 TCACGGCTATCTAGTTCTTTGTG 58.255 43.478 0.00 0.00 0.00 3.33
3850 7891 4.745620 GTGGAAATCACGGCTATCTAGTTC 59.254 45.833 0.00 0.00 36.56 3.01
3859 7900 0.252197 GGTAGGTGGAAATCACGGCT 59.748 55.000 0.00 0.00 46.96 5.52
3865 7906 7.176690 TGAAAATTCTTCTGGTAGGTGGAAATC 59.823 37.037 0.00 0.00 0.00 2.17
3875 7916 6.826668 TGACTCTGTGAAAATTCTTCTGGTA 58.173 36.000 0.00 0.00 0.00 3.25
4106 8147 2.124695 GGTCATCGAGGTTGCCCC 60.125 66.667 0.00 0.00 0.00 5.80
4287 8331 6.899393 TTGTCTTTGATCAAGTTGCCTATT 57.101 33.333 8.41 0.00 33.66 1.73
4323 8370 0.318120 ACTTTTTGGCCGCATCTTGG 59.682 50.000 0.00 0.00 0.00 3.61
4404 8457 4.515191 TCATACATAGCCAAAATCCGAAGC 59.485 41.667 0.00 0.00 0.00 3.86
4547 8600 1.688197 CAAGTGTGGTCTTGCCCAATT 59.312 47.619 0.00 0.00 38.35 2.32
4585 8638 4.381411 AGATCGTATTGGGCTTTAAGCTC 58.619 43.478 16.89 13.80 43.59 4.09
4603 8656 8.941977 ACCAACCAAAACAAAAGTTTTAAGATC 58.058 29.630 0.00 0.00 35.09 2.75
5890 13720 0.592637 TTTCTGCAACATCCACTGCG 59.407 50.000 0.00 0.00 41.63 5.18
6508 14367 1.523758 CTTGTAGGGTGCACAAGGAC 58.476 55.000 20.43 10.97 45.92 3.85
7150 15036 0.671251 TTTGTTTAAGGGTGCCAGCG 59.329 50.000 0.00 0.00 0.00 5.18
7418 15338 3.914426 AATAGGGACGACTTGAGCAAT 57.086 42.857 0.00 0.00 0.00 3.56
7419 15339 4.649674 AGATAATAGGGACGACTTGAGCAA 59.350 41.667 0.00 0.00 0.00 3.91
7468 15388 5.371115 TTTTGTAGTCTGCACCATTAAGC 57.629 39.130 0.00 0.00 0.00 3.09
7488 15408 5.806654 ACAACCACATCAATTAAGCCTTT 57.193 34.783 0.00 0.00 0.00 3.11
7524 15444 6.018262 GCCGTGTTTGCTTGTATCAATATAGA 60.018 38.462 0.00 0.00 0.00 1.98
7525 15445 6.136071 GCCGTGTTTGCTTGTATCAATATAG 58.864 40.000 0.00 0.00 0.00 1.31
7592 15512 2.157738 GAGCCAGAAGAGCATTTGTGT 58.842 47.619 0.00 0.00 0.00 3.72
7633 15553 9.578576 ACATATCATGGCATTTGTTCTAATAGT 57.421 29.630 0.00 0.00 33.60 2.12
7637 15557 6.506147 GCACATATCATGGCATTTGTTCTAA 58.494 36.000 0.00 0.00 33.60 2.10
7651 15571 3.329386 GTGGCATACTCGCACATATCAT 58.671 45.455 0.00 0.00 0.00 2.45
7656 15576 0.181114 ATGGTGGCATACTCGCACAT 59.819 50.000 0.00 0.00 0.00 3.21
7664 15584 3.591196 TTTTGCTTCATGGTGGCATAC 57.409 42.857 8.46 0.00 35.84 2.39
7684 17440 3.758755 TCTGCTTGATGACACTCACTT 57.241 42.857 0.00 0.00 0.00 3.16
7685 17441 3.758755 TTCTGCTTGATGACACTCACT 57.241 42.857 0.00 0.00 0.00 3.41
7811 17568 3.402110 TGGATTGATTCGATTGATCCCG 58.598 45.455 12.34 0.00 36.32 5.14
7818 17575 5.072872 AGGGAGAAGATGGATTGATTCGATT 59.927 40.000 0.00 0.00 0.00 3.34
7822 17579 5.069318 GGAAGGGAGAAGATGGATTGATTC 58.931 45.833 0.00 0.00 0.00 2.52
7823 17580 4.730904 AGGAAGGGAGAAGATGGATTGATT 59.269 41.667 0.00 0.00 0.00 2.57
7824 17581 4.314238 AGGAAGGGAGAAGATGGATTGAT 58.686 43.478 0.00 0.00 0.00 2.57
7825 17582 3.740780 AGGAAGGGAGAAGATGGATTGA 58.259 45.455 0.00 0.00 0.00 2.57
7826 17583 4.459330 GAAGGAAGGGAGAAGATGGATTG 58.541 47.826 0.00 0.00 0.00 2.67
7827 17584 3.461458 GGAAGGAAGGGAGAAGATGGATT 59.539 47.826 0.00 0.00 0.00 3.01
7828 17585 3.052329 GGAAGGAAGGGAGAAGATGGAT 58.948 50.000 0.00 0.00 0.00 3.41
7829 17586 2.046447 AGGAAGGAAGGGAGAAGATGGA 59.954 50.000 0.00 0.00 0.00 3.41
7830 17587 2.486716 AGGAAGGAAGGGAGAAGATGG 58.513 52.381 0.00 0.00 0.00 3.51
7831 17588 3.118075 GGAAGGAAGGAAGGGAGAAGATG 60.118 52.174 0.00 0.00 0.00 2.90
7832 17589 3.119319 GGAAGGAAGGAAGGGAGAAGAT 58.881 50.000 0.00 0.00 0.00 2.40
7833 17590 2.114506 AGGAAGGAAGGAAGGGAGAAGA 59.885 50.000 0.00 0.00 0.00 2.87
7834 17591 2.556766 AGGAAGGAAGGAAGGGAGAAG 58.443 52.381 0.00 0.00 0.00 2.85
7835 17592 2.743131 AGGAAGGAAGGAAGGGAGAA 57.257 50.000 0.00 0.00 0.00 2.87
7836 17593 2.552367 GAAGGAAGGAAGGAAGGGAGA 58.448 52.381 0.00 0.00 0.00 3.71
7837 17594 1.562008 GGAAGGAAGGAAGGAAGGGAG 59.438 57.143 0.00 0.00 0.00 4.30
7838 17595 1.132201 TGGAAGGAAGGAAGGAAGGGA 60.132 52.381 0.00 0.00 0.00 4.20
7839 17596 1.283321 CTGGAAGGAAGGAAGGAAGGG 59.717 57.143 0.00 0.00 0.00 3.95
7840 17597 1.988846 ACTGGAAGGAAGGAAGGAAGG 59.011 52.381 0.00 0.00 39.30 3.46
7843 17600 2.415983 TCACTGGAAGGAAGGAAGGA 57.584 50.000 0.00 0.00 39.30 3.36
7863 17620 7.549134 TGCATTGTATTGTAATTCTCGTCTTCT 59.451 33.333 0.00 0.00 0.00 2.85
7869 17626 9.158364 GTGTATTGCATTGTATTGTAATTCTCG 57.842 33.333 0.00 0.00 34.40 4.04
7901 17658 1.534163 GGGTGACACGGAAAGCTTAAC 59.466 52.381 0.00 0.00 0.00 2.01
7919 17676 0.109132 GCGAAAACAGGCAATCAGGG 60.109 55.000 0.00 0.00 0.00 4.45
7930 17687 3.597728 GGGTTGCCGGCGAAAACA 61.598 61.111 24.47 4.13 0.00 2.83
7940 17697 2.360475 GAGGCTGACTGGGTTGCC 60.360 66.667 0.00 0.00 45.21 4.52
8035 17800 7.545965 CGATCGAGGATTAACTGGCTAAAATAT 59.454 37.037 10.26 0.00 0.00 1.28
8061 17826 2.095869 CAGAGTTCACATGCAAGACAGC 60.096 50.000 0.00 0.00 0.00 4.40
8150 17915 5.163405 TGACAACACTAGCAAAAGAGAGAGT 60.163 40.000 0.00 0.00 0.00 3.24
8151 17916 5.176590 GTGACAACACTAGCAAAAGAGAGAG 59.823 44.000 0.00 0.00 42.99 3.20
8175 17940 7.446319 TGCCCAGATTATTCATAGACATTTCAG 59.554 37.037 0.00 0.00 0.00 3.02
8190 17955 0.855598 AGCCACCATGCCCAGATTAT 59.144 50.000 0.00 0.00 0.00 1.28
8201 17966 4.047125 CCCCGGACAAGCCACCAT 62.047 66.667 0.73 0.00 35.94 3.55
8237 18002 2.748132 CGAGTGAGTCCTAGAGCCAGAT 60.748 54.545 0.00 0.00 0.00 2.90
8245 18010 0.736053 GTGCCTCGAGTGAGTCCTAG 59.264 60.000 12.31 0.00 40.85 3.02


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

AutoCloner maintained by Alex Coulton.