Multiple sequence alignment - TraesCS5D01G137000

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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 TraesCS5D01G137000 chr5D 100.000 3527 0 0 1 3527 217754035 217757561 0.000000e+00 6514.0
1 TraesCS5D01G137000 chr5D 95.082 183 7 1 2859 3041 47952387 47952207 1.600000e-73 287.0
2 TraesCS5D01G137000 chr5D 94.175 103 6 0 3425 3527 2231663 2231765 1.310000e-34 158.0
3 TraesCS5D01G137000 chr5D 93.220 59 3 1 249 306 51179473 51179531 6.270000e-13 86.1
4 TraesCS5D01G137000 chr5D 90.000 60 5 1 247 305 517972692 517972751 3.780000e-10 76.8
5 TraesCS5D01G137000 chr5A 94.091 2826 110 26 64 2856 290547062 290549863 0.000000e+00 4241.0
6 TraesCS5D01G137000 chr5A 92.000 225 11 4 3064 3284 290549901 290550122 3.420000e-80 309.0
7 TraesCS5D01G137000 chr5A 93.684 190 9 3 2859 3046 649783051 649783239 7.450000e-72 281.0
8 TraesCS5D01G137000 chr5A 95.652 69 3 0 1 69 481684037 481683969 1.030000e-20 111.0
9 TraesCS5D01G137000 chr5B 95.149 2680 93 22 184 2841 233921458 233924122 0.000000e+00 4194.0
10 TraesCS5D01G137000 chr5B 90.331 362 28 5 3064 3423 233924251 233924607 5.330000e-128 468.0
11 TraesCS5D01G137000 chr5B 95.652 69 3 0 1 69 252298937 252298869 1.030000e-20 111.0
12 TraesCS5D01G137000 chr5B 95.652 69 3 0 1 69 676179132 676179200 1.030000e-20 111.0
13 TraesCS5D01G137000 chr5B 95.652 69 2 1 1 69 252299223 252299156 3.720000e-20 110.0
14 TraesCS5D01G137000 chr5B 91.379 58 2 3 255 310 369889677 369889733 3.780000e-10 76.8
15 TraesCS5D01G137000 chr2A 90.233 1505 130 6 995 2492 749448079 749446585 0.000000e+00 1949.0
16 TraesCS5D01G137000 chr2A 89.940 1511 136 5 1000 2504 749523741 749525241 0.000000e+00 1934.0
17 TraesCS5D01G137000 chr2A 94.366 71 4 0 1 71 28828206 28828136 3.720000e-20 110.0
18 TraesCS5D01G137000 chr2D 89.761 1504 138 7 1000 2497 618532333 618530840 0.000000e+00 1910.0
19 TraesCS5D01G137000 chr2D 91.364 1320 105 5 1188 2507 618645451 618646761 0.000000e+00 1797.0
20 TraesCS5D01G137000 chr2D 90.000 60 5 1 248 306 24344403 24344462 3.780000e-10 76.8
21 TraesCS5D01G137000 chr2B 89.660 1499 139 5 1000 2492 755038359 755036871 0.000000e+00 1895.0
22 TraesCS5D01G137000 chr2B 90.373 966 75 7 1000 1958 755054585 755055539 0.000000e+00 1253.0
23 TraesCS5D01G137000 chr2B 90.074 544 54 0 1949 2492 755056005 755056548 0.000000e+00 706.0
24 TraesCS5D01G137000 chr2B 92.523 107 7 1 3421 3527 161669153 161669048 6.100000e-33 152.0
25 TraesCS5D01G137000 chr2B 91.139 79 5 2 1 77 64703996 64703918 4.820000e-19 106.0
26 TraesCS5D01G137000 chr4D 83.256 1511 214 22 1012 2498 115543837 115542342 0.000000e+00 1352.0
27 TraesCS5D01G137000 chr4D 94.149 188 8 3 2857 3042 449889199 449889385 2.070000e-72 283.0
28 TraesCS5D01G137000 chr4A 82.548 1507 232 17 1012 2498 461353990 461355485 0.000000e+00 1297.0
29 TraesCS5D01G137000 chr4A 95.082 183 7 2 2859 3041 91002274 91002454 1.600000e-73 287.0
30 TraesCS5D01G137000 chr6D 95.676 185 6 2 2859 3042 219091356 219091539 2.660000e-76 296.0
31 TraesCS5D01G137000 chr7D 94.709 189 8 2 2858 3045 31996925 31996738 3.440000e-75 292.0
32 TraesCS5D01G137000 chr7D 92.746 193 12 2 2853 3043 629623521 629623713 9.640000e-71 278.0
33 TraesCS5D01G137000 chr1A 95.109 184 7 2 2859 3041 589956815 589956633 4.450000e-74 289.0
34 TraesCS5D01G137000 chr1A 96.970 66 2 0 1 66 497923582 497923517 1.030000e-20 111.0
35 TraesCS5D01G137000 chr1D 95.082 183 7 1 2859 3041 445668760 445668580 1.600000e-73 287.0
36 TraesCS5D01G137000 chr1D 94.444 54 3 0 255 308 451033039 451032986 2.260000e-12 84.2
37 TraesCS5D01G137000 chr3D 98.058 103 2 0 3425 3527 393107646 393107748 2.800000e-41 180.0
38 TraesCS5D01G137000 chr3D 98.438 64 1 0 3 66 496683770 496683707 2.880000e-21 113.0
39 TraesCS5D01G137000 chr3D 100.000 33 0 0 170 202 391575787 391575819 1.060000e-05 62.1
40 TraesCS5D01G137000 chr1B 95.050 101 5 0 3425 3525 116117158 116117258 3.640000e-35 159.0
41 TraesCS5D01G137000 chr1B 94.231 104 6 0 3424 3527 574738776 574738673 3.640000e-35 159.0
42 TraesCS5D01G137000 chr1B 91.228 57 3 2 255 309 574353828 574353772 3.780000e-10 76.8
43 TraesCS5D01G137000 chr7A 94.175 103 6 0 3425 3527 5475199 5475097 1.310000e-34 158.0
44 TraesCS5D01G137000 chr3B 92.523 107 7 1 3421 3527 326582096 326581991 6.100000e-33 152.0
45 TraesCS5D01G137000 chr3B 92.233 103 7 1 3421 3523 316562084 316561983 1.020000e-30 145.0
46 TraesCS5D01G137000 chr3B 95.652 69 3 0 1 69 417053562 417053630 1.030000e-20 111.0
47 TraesCS5D01G137000 chr3B 91.228 57 3 2 255 309 144944030 144944086 3.780000e-10 76.8
48 TraesCS5D01G137000 chr3B 91.228 57 3 2 255 309 275995420 275995364 3.780000e-10 76.8
49 TraesCS5D01G137000 chr7B 90.291 103 10 0 3425 3527 179887735 179887633 6.140000e-28 135.0


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 TraesCS5D01G137000 chr5D 217754035 217757561 3526 False 6514.0 6514 100.0000 1 3527 1 chr5D.!!$F3 3526
1 TraesCS5D01G137000 chr5A 290547062 290550122 3060 False 2275.0 4241 93.0455 64 3284 2 chr5A.!!$F2 3220
2 TraesCS5D01G137000 chr5B 233921458 233924607 3149 False 2331.0 4194 92.7400 184 3423 2 chr5B.!!$F3 3239
3 TraesCS5D01G137000 chr2A 749446585 749448079 1494 True 1949.0 1949 90.2330 995 2492 1 chr2A.!!$R2 1497
4 TraesCS5D01G137000 chr2A 749523741 749525241 1500 False 1934.0 1934 89.9400 1000 2504 1 chr2A.!!$F1 1504
5 TraesCS5D01G137000 chr2D 618530840 618532333 1493 True 1910.0 1910 89.7610 1000 2497 1 chr2D.!!$R1 1497
6 TraesCS5D01G137000 chr2D 618645451 618646761 1310 False 1797.0 1797 91.3640 1188 2507 1 chr2D.!!$F2 1319
7 TraesCS5D01G137000 chr2B 755036871 755038359 1488 True 1895.0 1895 89.6600 1000 2492 1 chr2B.!!$R3 1492
8 TraesCS5D01G137000 chr2B 755054585 755056548 1963 False 979.5 1253 90.2235 1000 2492 2 chr2B.!!$F1 1492
9 TraesCS5D01G137000 chr4D 115542342 115543837 1495 True 1352.0 1352 83.2560 1012 2498 1 chr4D.!!$R1 1486
10 TraesCS5D01G137000 chr4A 461353990 461355485 1495 False 1297.0 1297 82.5480 1012 2498 1 chr4A.!!$F2 1486

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
963 1000 0.967380 ATCTGCTTTCCCCTTTGCCG 60.967 55.0 0.0 0.0 0.00 5.69 F
1470 1518 0.467474 AGATCGTCGCCCATGAGGTA 60.467 55.0 0.0 0.0 38.26 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2029 2570 0.392595 TGCAGGCTCTTGAGATGCTG 60.393 55.000 20.68 0.0 37.76 4.41 R
3418 4001 1.068895 TGGACGGAGCGAGTAACAAAA 59.931 47.619 0.00 0.0 0.00 2.44 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
25 26 7.809665 ACATAAGCAAAAATTTCTTGGAATGC 58.190 30.769 12.13 0.00 0.00 3.56
26 27 4.996062 AGCAAAAATTTCTTGGAATGCG 57.004 36.364 12.13 0.00 37.61 4.73
27 28 3.187022 AGCAAAAATTTCTTGGAATGCGC 59.813 39.130 0.00 0.00 37.61 6.09
28 29 3.187022 GCAAAAATTTCTTGGAATGCGCT 59.813 39.130 9.73 0.00 0.00 5.92
29 30 4.388469 GCAAAAATTTCTTGGAATGCGCTA 59.612 37.500 9.73 0.00 0.00 4.26
30 31 5.063817 GCAAAAATTTCTTGGAATGCGCTAT 59.936 36.000 9.73 0.00 0.00 2.97
31 32 6.471839 CAAAAATTTCTTGGAATGCGCTATG 58.528 36.000 9.73 0.00 0.00 2.23
32 33 4.989279 AATTTCTTGGAATGCGCTATGT 57.011 36.364 9.73 0.00 0.00 2.29
33 34 4.989279 ATTTCTTGGAATGCGCTATGTT 57.011 36.364 9.73 0.00 0.00 2.71
34 35 6.449635 AATTTCTTGGAATGCGCTATGTTA 57.550 33.333 9.73 0.00 0.00 2.41
35 36 4.875544 TTCTTGGAATGCGCTATGTTAC 57.124 40.909 9.73 0.00 0.00 2.50
36 37 4.137116 TCTTGGAATGCGCTATGTTACT 57.863 40.909 9.73 0.00 0.00 2.24
37 38 3.871006 TCTTGGAATGCGCTATGTTACTG 59.129 43.478 9.73 0.00 0.00 2.74
38 39 3.260475 TGGAATGCGCTATGTTACTGT 57.740 42.857 9.73 0.00 0.00 3.55
39 40 3.194861 TGGAATGCGCTATGTTACTGTC 58.805 45.455 9.73 0.00 0.00 3.51
40 41 3.118775 TGGAATGCGCTATGTTACTGTCT 60.119 43.478 9.73 0.00 0.00 3.41
41 42 4.098807 TGGAATGCGCTATGTTACTGTCTA 59.901 41.667 9.73 0.00 0.00 2.59
42 43 5.047847 GGAATGCGCTATGTTACTGTCTAA 58.952 41.667 9.73 0.00 0.00 2.10
43 44 5.175856 GGAATGCGCTATGTTACTGTCTAAG 59.824 44.000 9.73 0.00 0.00 2.18
44 45 4.713824 TGCGCTATGTTACTGTCTAAGT 57.286 40.909 9.73 0.00 43.40 2.24
45 46 5.068234 TGCGCTATGTTACTGTCTAAGTT 57.932 39.130 9.73 0.00 40.56 2.66
46 47 6.198650 TGCGCTATGTTACTGTCTAAGTTA 57.801 37.500 9.73 0.00 40.56 2.24
47 48 6.032094 TGCGCTATGTTACTGTCTAAGTTAC 58.968 40.000 9.73 0.00 40.56 2.50
48 49 6.127814 TGCGCTATGTTACTGTCTAAGTTACT 60.128 38.462 9.73 0.00 38.87 2.24
49 50 6.414402 GCGCTATGTTACTGTCTAAGTTACTC 59.586 42.308 0.00 0.00 38.87 2.59
50 51 6.911511 CGCTATGTTACTGTCTAAGTTACTCC 59.088 42.308 0.00 0.00 38.87 3.85
51 52 7.201835 GCTATGTTACTGTCTAAGTTACTCCC 58.798 42.308 0.00 0.00 38.87 4.30
52 53 7.147949 GCTATGTTACTGTCTAAGTTACTCCCA 60.148 40.741 0.00 0.00 38.87 4.37
53 54 6.336842 TGTTACTGTCTAAGTTACTCCCAC 57.663 41.667 0.00 0.00 38.87 4.61
54 55 6.073314 TGTTACTGTCTAAGTTACTCCCACT 58.927 40.000 0.00 0.00 38.87 4.00
55 56 7.233632 TGTTACTGTCTAAGTTACTCCCACTA 58.766 38.462 0.00 0.00 38.87 2.74
56 57 7.892241 TGTTACTGTCTAAGTTACTCCCACTAT 59.108 37.037 0.00 0.00 38.87 2.12
57 58 6.777213 ACTGTCTAAGTTACTCCCACTATG 57.223 41.667 0.00 0.00 34.57 2.23
58 59 6.491383 ACTGTCTAAGTTACTCCCACTATGA 58.509 40.000 0.00 0.00 34.57 2.15
59 60 6.377712 ACTGTCTAAGTTACTCCCACTATGAC 59.622 42.308 0.00 0.00 34.57 3.06
60 61 6.491383 TGTCTAAGTTACTCCCACTATGACT 58.509 40.000 0.00 0.00 32.36 3.41
61 62 7.636579 TGTCTAAGTTACTCCCACTATGACTA 58.363 38.462 0.00 0.00 32.36 2.59
62 63 7.774157 TGTCTAAGTTACTCCCACTATGACTAG 59.226 40.741 0.00 0.00 32.36 2.57
70 71 5.724854 ACTCCCACTATGACTAGCCTAAAAA 59.275 40.000 0.00 0.00 0.00 1.94
73 74 4.809426 CCACTATGACTAGCCTAAAAACCG 59.191 45.833 0.00 0.00 0.00 4.44
75 76 2.103537 TGACTAGCCTAAAAACCGGC 57.896 50.000 0.00 0.00 0.00 6.13
97 99 5.523916 GGCTCAACGATAACTGTCACATATT 59.476 40.000 0.00 0.00 0.00 1.28
169 180 6.309357 ACCAGATATGTACCATTGATTGCAT 58.691 36.000 0.00 0.00 0.00 3.96
174 185 9.754382 AGATATGTACCATTGATTGCATTTTTC 57.246 29.630 0.00 0.00 0.00 2.29
175 186 9.531942 GATATGTACCATTGATTGCATTTTTCA 57.468 29.630 0.00 0.00 0.00 2.69
244 255 6.212235 CAATAGCCATTACACAACACACAAA 58.788 36.000 0.00 0.00 0.00 2.83
245 256 4.040445 AGCCATTACACAACACACAAAC 57.960 40.909 0.00 0.00 0.00 2.93
247 258 4.081972 AGCCATTACACAACACACAAACAA 60.082 37.500 0.00 0.00 0.00 2.83
249 260 5.293079 GCCATTACACAACACACAAACAATT 59.707 36.000 0.00 0.00 0.00 2.32
250 261 6.477033 GCCATTACACAACACACAAACAATTA 59.523 34.615 0.00 0.00 0.00 1.40
251 262 7.515998 GCCATTACACAACACACAAACAATTAC 60.516 37.037 0.00 0.00 0.00 1.89
253 264 5.652994 ACACAACACACAAACAATTACCT 57.347 34.783 0.00 0.00 0.00 3.08
256 267 4.953579 ACAACACACAAACAATTACCTCCT 59.046 37.500 0.00 0.00 0.00 3.69
401 435 5.833131 ACAACACTACATGAGAAATTGGGTT 59.167 36.000 0.00 0.00 0.00 4.11
462 496 9.778993 CAATTTCTACAAAGATATTGGACACAG 57.221 33.333 9.41 0.00 42.66 3.66
567 602 5.757099 TCTAAAATCCGAAAAGAGGGAGT 57.243 39.130 0.00 0.00 35.40 3.85
570 605 5.500546 AAAATCCGAAAAGAGGGAGTAGT 57.499 39.130 0.00 0.00 35.40 2.73
612 647 1.070843 CGAGCACGATCAAAACGTTGT 60.071 47.619 0.00 0.00 42.07 3.32
657 692 1.669604 GGGAGGAGCGGAAAAAGATC 58.330 55.000 0.00 0.00 0.00 2.75
658 693 1.065418 GGGAGGAGCGGAAAAAGATCA 60.065 52.381 0.00 0.00 0.00 2.92
674 710 9.448294 GAAAAAGATCATCTTAATCATGTGCTC 57.552 33.333 0.00 0.00 35.27 4.26
704 740 2.350738 TGTCATGCAGAGTCCGTCA 58.649 52.632 0.00 0.00 0.00 4.35
820 857 2.465855 GTTGGGTTGTTTAAAGCACCG 58.534 47.619 8.87 0.00 0.00 4.94
946 983 1.080705 CCGGAACCCGCTCGATATC 60.081 63.158 0.00 0.00 46.86 1.63
963 1000 0.967380 ATCTGCTTTCCCCTTTGCCG 60.967 55.000 0.00 0.00 0.00 5.69
992 1029 1.890894 TCGTGAGAGCAGCTAACCC 59.109 57.895 0.00 0.00 34.84 4.11
1470 1518 0.467474 AGATCGTCGCCCATGAGGTA 60.467 55.000 0.00 0.00 38.26 3.08
2029 2570 1.079336 GACAAGCCCTCCACGTACC 60.079 63.158 0.00 0.00 0.00 3.34
2537 3078 9.890629 TGCAGACTTCAAATAATTACTAGTGAT 57.109 29.630 5.39 0.00 0.00 3.06
2663 3218 9.977762 GTGATTTCCAAAATTTCATGCTTAATC 57.022 29.630 0.00 0.00 0.00 1.75
2671 3226 8.474577 CAAAATTTCATGCTTAATCGTGCTATC 58.525 33.333 0.00 0.00 0.00 2.08
2675 3230 7.961325 TTCATGCTTAATCGTGCTATCATTA 57.039 32.000 0.00 0.00 0.00 1.90
2681 3236 7.169813 TGCTTAATCGTGCTATCATTACAGAAG 59.830 37.037 0.00 0.00 0.00 2.85
2810 3368 5.957771 TTTCTATGGCTGATACTCCACTT 57.042 39.130 0.00 0.00 34.81 3.16
2824 3382 5.913137 ACTCCACTTTCTGACTGAGATAG 57.087 43.478 0.00 0.00 36.20 2.08
2845 3403 9.927081 AGATAGGTTTCATCATCCAAGTATTTT 57.073 29.630 0.00 0.00 0.00 1.82
2869 3427 9.856162 TTTAGTAATAAAACAAAGGGTCTGTCT 57.144 29.630 0.00 0.00 0.00 3.41
2872 3430 8.101419 AGTAATAAAACAAAGGGTCTGTCTAGG 58.899 37.037 0.00 0.00 0.00 3.02
2873 3431 6.697641 ATAAAACAAAGGGTCTGTCTAGGA 57.302 37.500 0.00 0.00 0.00 2.94
2874 3432 4.353383 AAACAAAGGGTCTGTCTAGGAC 57.647 45.455 0.00 0.00 0.00 3.85
2876 3434 2.633481 ACAAAGGGTCTGTCTAGGACAC 59.367 50.000 0.00 0.00 37.67 3.67
2877 3435 2.632996 CAAAGGGTCTGTCTAGGACACA 59.367 50.000 3.18 0.00 39.36 3.72
2880 3438 2.313342 AGGGTCTGTCTAGGACACATCT 59.687 50.000 3.18 0.00 39.36 2.90
2882 3440 3.886505 GGGTCTGTCTAGGACACATCTAG 59.113 52.174 0.00 0.00 37.67 2.43
2883 3441 4.385421 GGGTCTGTCTAGGACACATCTAGA 60.385 50.000 0.00 0.00 37.67 2.43
2885 3443 6.466038 GGGTCTGTCTAGGACACATCTAGATA 60.466 46.154 4.54 1.80 43.25 1.98
2886 3444 7.172342 GGTCTGTCTAGGACACATCTAGATAT 58.828 42.308 4.54 0.00 43.25 1.63
2887 3445 7.120579 GGTCTGTCTAGGACACATCTAGATATG 59.879 44.444 9.51 9.51 43.25 1.78
2888 3446 7.880713 GTCTGTCTAGGACACATCTAGATATGA 59.119 40.741 17.82 0.00 43.25 2.15
2889 3447 7.880713 TCTGTCTAGGACACATCTAGATATGAC 59.119 40.741 17.82 11.19 43.25 3.06
2891 3449 8.166726 TGTCTAGGACACATCTAGATATGACAT 58.833 37.037 17.82 11.49 43.25 3.06
2893 3451 9.898152 TCTAGGACACATCTAGATATGACATAG 57.102 37.037 21.26 21.26 38.50 2.23
2894 3452 9.679661 CTAGGACACATCTAGATATGACATAGT 57.320 37.037 19.89 5.05 37.08 2.12
2895 3453 8.948401 AGGACACATCTAGATATGACATAGTT 57.052 34.615 17.82 0.00 0.00 2.24
2913 3471 8.011844 ACATAGTTATGTCACATCTAAGCTGA 57.988 34.615 0.00 0.00 42.96 4.26
2914 3472 8.646004 ACATAGTTATGTCACATCTAAGCTGAT 58.354 33.333 0.00 0.00 42.96 2.90
2915 3473 8.923683 CATAGTTATGTCACATCTAAGCTGATG 58.076 37.037 11.48 11.48 46.61 3.07
2924 3482 5.481200 CATCTAAGCTGATGTCCACTTTG 57.519 43.478 5.99 0.00 39.05 2.77
2925 3483 4.623932 TCTAAGCTGATGTCCACTTTGT 57.376 40.909 0.00 0.00 0.00 2.83
2926 3484 4.973168 TCTAAGCTGATGTCCACTTTGTT 58.027 39.130 0.00 0.00 0.00 2.83
2927 3485 5.376625 TCTAAGCTGATGTCCACTTTGTTT 58.623 37.500 0.00 0.00 0.00 2.83
2928 3486 3.996150 AGCTGATGTCCACTTTGTTTG 57.004 42.857 0.00 0.00 0.00 2.93
2929 3487 3.290710 AGCTGATGTCCACTTTGTTTGT 58.709 40.909 0.00 0.00 0.00 2.83
2930 3488 3.067180 AGCTGATGTCCACTTTGTTTGTG 59.933 43.478 0.00 0.00 35.39 3.33
2991 3549 9.575783 GTTGCTAGATTATATACTTGTAGGAGC 57.424 37.037 0.00 0.00 0.00 4.70
2992 3550 9.535170 TTGCTAGATTATATACTTGTAGGAGCT 57.465 33.333 0.00 0.00 0.00 4.09
2993 3551 9.535170 TGCTAGATTATATACTTGTAGGAGCTT 57.465 33.333 0.00 0.00 0.00 3.74
3001 3559 8.941995 ATATACTTGTAGGAGCTTAGATGTGA 57.058 34.615 0.00 0.00 0.00 3.58
3002 3560 5.331876 ACTTGTAGGAGCTTAGATGTGAC 57.668 43.478 0.00 0.00 0.00 3.67
3003 3561 4.772624 ACTTGTAGGAGCTTAGATGTGACA 59.227 41.667 0.00 0.00 0.00 3.58
3004 3562 5.423610 ACTTGTAGGAGCTTAGATGTGACAT 59.576 40.000 0.00 0.00 0.00 3.06
3005 3563 5.521906 TGTAGGAGCTTAGATGTGACATC 57.478 43.478 17.46 17.46 0.00 3.06
3006 3564 4.342378 TGTAGGAGCTTAGATGTGACATCC 59.658 45.833 21.05 6.49 0.00 3.51
3007 3565 3.652055 AGGAGCTTAGATGTGACATCCT 58.348 45.455 21.05 11.37 0.00 3.24
3008 3566 4.036518 AGGAGCTTAGATGTGACATCCTT 58.963 43.478 21.05 7.22 31.97 3.36
3009 3567 5.211973 AGGAGCTTAGATGTGACATCCTTA 58.788 41.667 21.05 6.22 31.97 2.69
3010 3568 5.663106 AGGAGCTTAGATGTGACATCCTTAA 59.337 40.000 21.05 13.11 31.97 1.85
3011 3569 6.156949 AGGAGCTTAGATGTGACATCCTTAAA 59.843 38.462 21.05 10.18 31.97 1.52
3012 3570 6.823689 GGAGCTTAGATGTGACATCCTTAAAA 59.176 38.462 21.05 8.00 0.00 1.52
3013 3571 7.336931 GGAGCTTAGATGTGACATCCTTAAAAA 59.663 37.037 21.05 6.46 0.00 1.94
3075 3654 5.722021 TTGCCTTGGGAAAATAACTTCTC 57.278 39.130 0.00 0.00 0.00 2.87
3088 3667 7.721286 AAATAACTTCTCCTCGAGCATTATG 57.279 36.000 6.99 0.00 0.00 1.90
3089 3668 3.104843 ACTTCTCCTCGAGCATTATGC 57.895 47.619 9.46 9.46 45.46 3.14
3116 3695 9.991906 AATCATTTACCTTATAGCGCTAGTAAA 57.008 29.630 27.71 27.71 35.04 2.01
3146 3729 5.018695 AGCATTTTTCTCTTACGTTCACG 57.981 39.130 0.00 0.00 46.33 4.35
3198 3781 5.290885 CGAACCGATGAATACAACTGATTGA 59.709 40.000 0.00 0.00 39.30 2.57
3202 3785 8.055279 ACCGATGAATACAACTGATTGATTTT 57.945 30.769 0.00 0.00 39.30 1.82
3296 3879 9.026121 TCTAATATCTTAAGAATCCTTCCTCGG 57.974 37.037 9.71 0.00 33.94 4.63
3300 3883 6.651975 TCTTAAGAATCCTTCCTCGGTATC 57.348 41.667 1.68 0.00 33.94 2.24
3302 3885 4.946478 AAGAATCCTTCCTCGGTATCAG 57.054 45.455 0.00 0.00 0.00 2.90
3309 3892 4.888239 TCCTTCCTCGGTATCAGAAGTAAG 59.112 45.833 0.00 0.00 35.10 2.34
3333 3916 8.874744 AGATATCAAATCCATGGAGTTATTGG 57.125 34.615 25.91 14.37 30.91 3.16
3363 3946 1.550524 TGATTAGCTCCGCACTCAACT 59.449 47.619 0.00 0.00 0.00 3.16
3370 3953 2.661979 GCTCCGCACTCAACTAAAAACG 60.662 50.000 0.00 0.00 0.00 3.60
3373 3956 3.374678 TCCGCACTCAACTAAAAACGTTT 59.625 39.130 7.96 7.96 0.00 3.60
3374 3957 4.099824 CCGCACTCAACTAAAAACGTTTT 58.900 39.130 20.26 20.26 0.00 2.43
3376 3959 5.275556 CCGCACTCAACTAAAAACGTTTTTC 60.276 40.000 35.13 19.70 40.53 2.29
3377 3960 5.510323 CGCACTCAACTAAAAACGTTTTTCT 59.490 36.000 35.13 21.84 40.53 2.52
3378 3961 6.033091 CGCACTCAACTAAAAACGTTTTTCTT 59.967 34.615 35.13 25.32 40.53 2.52
3385 3968 4.811969 AAAAACGTTTTTCTTGTCCCCT 57.188 36.364 28.62 7.24 35.61 4.79
3418 4001 4.040952 AGTGAAGTTGCCAATCTCACTAGT 59.959 41.667 17.76 0.00 35.53 2.57
3423 4006 5.133221 AGTTGCCAATCTCACTAGTTTTGT 58.867 37.500 0.00 0.00 0.00 2.83
3424 4007 5.594317 AGTTGCCAATCTCACTAGTTTTGTT 59.406 36.000 0.00 0.00 0.00 2.83
3425 4008 6.770785 AGTTGCCAATCTCACTAGTTTTGTTA 59.229 34.615 0.00 0.00 0.00 2.41
3426 4009 6.554334 TGCCAATCTCACTAGTTTTGTTAC 57.446 37.500 0.00 0.00 0.00 2.50
3427 4010 6.296026 TGCCAATCTCACTAGTTTTGTTACT 58.704 36.000 0.00 0.00 0.00 2.24
3428 4011 6.426937 TGCCAATCTCACTAGTTTTGTTACTC 59.573 38.462 0.00 0.00 0.00 2.59
3429 4012 6.401153 GCCAATCTCACTAGTTTTGTTACTCG 60.401 42.308 0.00 0.00 0.00 4.18
3430 4013 6.401153 CCAATCTCACTAGTTTTGTTACTCGC 60.401 42.308 0.00 0.00 0.00 5.03
3431 4014 5.449107 TCTCACTAGTTTTGTTACTCGCT 57.551 39.130 0.00 0.00 0.00 4.93
3432 4015 5.458891 TCTCACTAGTTTTGTTACTCGCTC 58.541 41.667 0.00 0.00 0.00 5.03
3433 4016 4.553323 TCACTAGTTTTGTTACTCGCTCC 58.447 43.478 0.00 0.00 0.00 4.70
3434 4017 3.364023 CACTAGTTTTGTTACTCGCTCCG 59.636 47.826 0.00 0.00 0.00 4.63
3435 4018 2.521105 AGTTTTGTTACTCGCTCCGT 57.479 45.000 0.00 0.00 0.00 4.69
3436 4019 2.401351 AGTTTTGTTACTCGCTCCGTC 58.599 47.619 0.00 0.00 0.00 4.79
3437 4020 1.458445 GTTTTGTTACTCGCTCCGTCC 59.542 52.381 0.00 0.00 0.00 4.79
3438 4021 0.675083 TTTGTTACTCGCTCCGTCCA 59.325 50.000 0.00 0.00 0.00 4.02
3439 4022 0.242825 TTGTTACTCGCTCCGTCCAG 59.757 55.000 0.00 0.00 0.00 3.86
3440 4023 1.139095 GTTACTCGCTCCGTCCAGG 59.861 63.158 0.00 0.00 42.97 4.45
3441 4024 1.303888 TTACTCGCTCCGTCCAGGT 60.304 57.895 0.00 0.00 41.99 4.00
3442 4025 1.592400 TTACTCGCTCCGTCCAGGTG 61.592 60.000 0.00 0.00 41.99 4.00
3448 4031 1.443407 CTCCGTCCAGGTGCATAGG 59.557 63.158 0.00 0.00 41.99 2.57
3449 4032 2.032860 CTCCGTCCAGGTGCATAGGG 62.033 65.000 0.00 0.00 41.99 3.53
3450 4033 2.203070 CGTCCAGGTGCATAGGGC 60.203 66.667 0.00 0.00 45.13 5.19
3465 4048 5.555017 GCATAGGGCATCTTAGAGAATTCA 58.445 41.667 8.44 0.00 43.97 2.57
3466 4049 5.642919 GCATAGGGCATCTTAGAGAATTCAG 59.357 44.000 8.44 0.00 43.97 3.02
3467 4050 4.703379 AGGGCATCTTAGAGAATTCAGG 57.297 45.455 8.44 0.00 0.00 3.86
3468 4051 4.302067 AGGGCATCTTAGAGAATTCAGGA 58.698 43.478 8.44 0.00 0.00 3.86
3469 4052 4.912744 AGGGCATCTTAGAGAATTCAGGAT 59.087 41.667 8.44 0.00 0.00 3.24
3470 4053 5.372066 AGGGCATCTTAGAGAATTCAGGATT 59.628 40.000 8.44 0.00 0.00 3.01
3471 4054 6.067350 GGGCATCTTAGAGAATTCAGGATTT 58.933 40.000 8.44 0.00 0.00 2.17
3472 4055 6.206438 GGGCATCTTAGAGAATTCAGGATTTC 59.794 42.308 8.44 0.00 0.00 2.17
3473 4056 6.997476 GGCATCTTAGAGAATTCAGGATTTCT 59.003 38.462 8.44 6.23 34.74 2.52
3474 4057 8.153550 GGCATCTTAGAGAATTCAGGATTTCTA 58.846 37.037 8.44 2.17 32.91 2.10
3475 4058 9.553064 GCATCTTAGAGAATTCAGGATTTCTAA 57.447 33.333 8.44 9.72 32.91 2.10
3488 4071 7.649973 TCAGGATTTCTAAGAGTATAAGTCGC 58.350 38.462 0.00 0.00 0.00 5.19
3489 4072 7.502895 TCAGGATTTCTAAGAGTATAAGTCGCT 59.497 37.037 0.00 0.00 0.00 4.93
3490 4073 8.784994 CAGGATTTCTAAGAGTATAAGTCGCTA 58.215 37.037 0.00 0.00 0.00 4.26
3491 4074 9.523168 AGGATTTCTAAGAGTATAAGTCGCTAT 57.477 33.333 0.00 0.00 0.00 2.97
3495 4078 9.947669 TTTCTAAGAGTATAAGTCGCTATTGTC 57.052 33.333 0.00 0.00 0.00 3.18
3496 4079 8.672823 TCTAAGAGTATAAGTCGCTATTGTCA 57.327 34.615 0.00 0.00 0.00 3.58
3497 4080 9.117183 TCTAAGAGTATAAGTCGCTATTGTCAA 57.883 33.333 0.00 0.00 0.00 3.18
3498 4081 9.900710 CTAAGAGTATAAGTCGCTATTGTCAAT 57.099 33.333 3.06 3.06 0.00 2.57
3500 4083 8.804688 AGAGTATAAGTCGCTATTGTCAATTC 57.195 34.615 2.79 0.00 0.00 2.17
3501 4084 7.591795 AGAGTATAAGTCGCTATTGTCAATTCG 59.408 37.037 2.79 8.24 0.00 3.34
3502 4085 3.658351 AAGTCGCTATTGTCAATTCGC 57.342 42.857 2.79 6.44 0.00 4.70
3503 4086 2.616960 AGTCGCTATTGTCAATTCGCA 58.383 42.857 2.79 0.00 0.00 5.10
3504 4087 3.000041 AGTCGCTATTGTCAATTCGCAA 59.000 40.909 2.79 0.00 0.00 4.85
3505 4088 3.062639 AGTCGCTATTGTCAATTCGCAAG 59.937 43.478 2.79 0.00 0.00 4.01
3521 4104 5.092554 TCGCAAGAGGTGGTAATTAATCA 57.907 39.130 0.00 0.00 45.01 2.57
3522 4105 4.873827 TCGCAAGAGGTGGTAATTAATCAC 59.126 41.667 10.21 10.21 45.01 3.06
3523 4106 4.260212 CGCAAGAGGTGGTAATTAATCACG 60.260 45.833 11.64 0.00 43.02 4.35
3524 4107 4.634443 GCAAGAGGTGGTAATTAATCACGT 59.366 41.667 12.34 12.34 32.65 4.49
3525 4108 5.447279 GCAAGAGGTGGTAATTAATCACGTG 60.447 44.000 9.94 9.94 32.65 4.49
3526 4109 5.670792 AGAGGTGGTAATTAATCACGTGA 57.329 39.130 22.48 22.48 32.65 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 6.957077 CGCATTCCAAGAAATTTTTGCTTATG 59.043 34.615 0.00 4.79 0.00 1.90
3 4 5.107143 GCGCATTCCAAGAAATTTTTGCTTA 60.107 36.000 0.30 0.00 0.00 3.09
4 5 4.319694 GCGCATTCCAAGAAATTTTTGCTT 60.320 37.500 0.30 0.00 0.00 3.91
6 7 3.187022 AGCGCATTCCAAGAAATTTTTGC 59.813 39.130 11.47 0.00 0.00 3.68
7 8 4.996062 AGCGCATTCCAAGAAATTTTTG 57.004 36.364 11.47 0.00 0.00 2.44
8 9 6.165577 ACATAGCGCATTCCAAGAAATTTTT 58.834 32.000 11.47 0.00 0.00 1.94
9 10 5.723295 ACATAGCGCATTCCAAGAAATTTT 58.277 33.333 11.47 0.00 0.00 1.82
11 12 4.989279 ACATAGCGCATTCCAAGAAATT 57.011 36.364 11.47 0.00 0.00 1.82
12 13 4.989279 AACATAGCGCATTCCAAGAAAT 57.011 36.364 11.47 0.00 0.00 2.17
13 14 4.941263 AGTAACATAGCGCATTCCAAGAAA 59.059 37.500 11.47 0.00 0.00 2.52
14 15 4.332543 CAGTAACATAGCGCATTCCAAGAA 59.667 41.667 11.47 0.00 0.00 2.52
15 16 3.871006 CAGTAACATAGCGCATTCCAAGA 59.129 43.478 11.47 0.00 0.00 3.02
16 17 3.623060 ACAGTAACATAGCGCATTCCAAG 59.377 43.478 11.47 0.00 0.00 3.61
17 18 3.605634 ACAGTAACATAGCGCATTCCAA 58.394 40.909 11.47 0.00 0.00 3.53
18 19 3.118775 AGACAGTAACATAGCGCATTCCA 60.119 43.478 11.47 0.00 0.00 3.53
19 20 3.458189 AGACAGTAACATAGCGCATTCC 58.542 45.455 11.47 0.00 0.00 3.01
20 21 5.749109 ACTTAGACAGTAACATAGCGCATTC 59.251 40.000 11.47 0.00 31.97 2.67
21 22 5.661458 ACTTAGACAGTAACATAGCGCATT 58.339 37.500 11.47 0.20 31.97 3.56
22 23 5.263968 ACTTAGACAGTAACATAGCGCAT 57.736 39.130 11.47 0.00 31.97 4.73
23 24 4.713824 ACTTAGACAGTAACATAGCGCA 57.286 40.909 11.47 0.00 31.97 6.09
24 25 6.264088 AGTAACTTAGACAGTAACATAGCGC 58.736 40.000 0.00 0.00 32.94 5.92
25 26 6.911511 GGAGTAACTTAGACAGTAACATAGCG 59.088 42.308 0.00 0.00 32.94 4.26
26 27 7.147949 TGGGAGTAACTTAGACAGTAACATAGC 60.148 40.741 0.00 0.00 32.94 2.97
27 28 8.189460 GTGGGAGTAACTTAGACAGTAACATAG 58.811 40.741 0.00 0.00 32.94 2.23
28 29 7.892241 AGTGGGAGTAACTTAGACAGTAACATA 59.108 37.037 0.00 0.00 32.94 2.29
29 30 6.724905 AGTGGGAGTAACTTAGACAGTAACAT 59.275 38.462 0.00 0.00 32.94 2.71
30 31 6.073314 AGTGGGAGTAACTTAGACAGTAACA 58.927 40.000 0.00 0.00 32.94 2.41
31 32 6.587206 AGTGGGAGTAACTTAGACAGTAAC 57.413 41.667 0.00 0.00 32.94 2.50
32 33 8.111545 TCATAGTGGGAGTAACTTAGACAGTAA 58.888 37.037 0.00 0.00 32.94 2.24
33 34 7.555554 GTCATAGTGGGAGTAACTTAGACAGTA 59.444 40.741 0.00 0.00 32.94 2.74
34 35 6.377712 GTCATAGTGGGAGTAACTTAGACAGT 59.622 42.308 0.00 0.00 37.30 3.55
35 36 6.603997 AGTCATAGTGGGAGTAACTTAGACAG 59.396 42.308 0.00 0.00 34.91 3.51
36 37 6.491383 AGTCATAGTGGGAGTAACTTAGACA 58.509 40.000 0.00 0.00 34.91 3.41
37 38 7.255208 GCTAGTCATAGTGGGAGTAACTTAGAC 60.255 44.444 0.00 0.00 33.72 2.59
38 39 6.771749 GCTAGTCATAGTGGGAGTAACTTAGA 59.228 42.308 0.00 0.00 0.00 2.10
39 40 6.016108 GGCTAGTCATAGTGGGAGTAACTTAG 60.016 46.154 0.00 0.00 0.00 2.18
40 41 5.832060 GGCTAGTCATAGTGGGAGTAACTTA 59.168 44.000 0.00 0.00 0.00 2.24
41 42 4.650131 GGCTAGTCATAGTGGGAGTAACTT 59.350 45.833 0.00 0.00 0.00 2.66
42 43 4.079096 AGGCTAGTCATAGTGGGAGTAACT 60.079 45.833 0.00 0.00 0.00 2.24
43 44 4.216708 AGGCTAGTCATAGTGGGAGTAAC 58.783 47.826 0.00 0.00 0.00 2.50
44 45 4.537945 AGGCTAGTCATAGTGGGAGTAA 57.462 45.455 0.00 0.00 0.00 2.24
45 46 5.658198 TTAGGCTAGTCATAGTGGGAGTA 57.342 43.478 0.00 0.00 0.00 2.59
46 47 4.537945 TTAGGCTAGTCATAGTGGGAGT 57.462 45.455 0.00 0.00 0.00 3.85
47 48 5.871396 TTTTAGGCTAGTCATAGTGGGAG 57.129 43.478 0.00 0.00 0.00 4.30
48 49 5.104652 GGTTTTTAGGCTAGTCATAGTGGGA 60.105 44.000 0.00 0.00 0.00 4.37
49 50 5.123936 GGTTTTTAGGCTAGTCATAGTGGG 58.876 45.833 0.00 0.00 0.00 4.61
50 51 4.809426 CGGTTTTTAGGCTAGTCATAGTGG 59.191 45.833 0.00 0.00 0.00 4.00
51 52 4.809426 CCGGTTTTTAGGCTAGTCATAGTG 59.191 45.833 0.00 0.00 0.00 2.74
52 53 5.019785 CCGGTTTTTAGGCTAGTCATAGT 57.980 43.478 0.00 0.00 0.00 2.12
70 71 0.606604 ACAGTTATCGTTGAGCCGGT 59.393 50.000 1.90 0.00 0.00 5.28
73 74 2.683968 TGTGACAGTTATCGTTGAGCC 58.316 47.619 0.00 0.00 0.00 4.70
133 138 9.283768 TGGTACATATCTGGTAAGCATTTATTG 57.716 33.333 0.00 0.00 0.00 1.90
154 165 8.254178 TCAATGAAAAATGCAATCAATGGTAC 57.746 30.769 0.00 0.00 0.00 3.34
230 241 6.183360 GGAGGTAATTGTTTGTGTGTTGTGTA 60.183 38.462 0.00 0.00 0.00 2.90
231 242 5.393678 GGAGGTAATTGTTTGTGTGTTGTGT 60.394 40.000 0.00 0.00 0.00 3.72
244 255 5.750352 TTTAGGAACGAGGAGGTAATTGT 57.250 39.130 0.00 0.00 0.00 2.71
245 256 9.991906 TTATATTTAGGAACGAGGAGGTAATTG 57.008 33.333 0.00 0.00 0.00 2.32
247 258 9.377238 ACTTATATTTAGGAACGAGGAGGTAAT 57.623 33.333 0.00 0.00 0.00 1.89
249 260 8.223330 AGACTTATATTTAGGAACGAGGAGGTA 58.777 37.037 0.00 0.00 0.00 3.08
250 261 7.068061 AGACTTATATTTAGGAACGAGGAGGT 58.932 38.462 0.00 0.00 0.00 3.85
251 262 7.527568 AGACTTATATTTAGGAACGAGGAGG 57.472 40.000 0.00 0.00 0.00 4.30
350 383 9.986833 TTCGTGTTATGTGATTATTTCATTCTG 57.013 29.630 0.00 0.00 36.54 3.02
355 388 9.388346 GTTGTTTCGTGTTATGTGATTATTTCA 57.612 29.630 0.00 0.00 0.00 2.69
356 389 9.388346 TGTTGTTTCGTGTTATGTGATTATTTC 57.612 29.630 0.00 0.00 0.00 2.17
357 390 9.176181 GTGTTGTTTCGTGTTATGTGATTATTT 57.824 29.630 0.00 0.00 0.00 1.40
360 393 7.485418 AGTGTTGTTTCGTGTTATGTGATTA 57.515 32.000 0.00 0.00 0.00 1.75
365 398 6.480651 TCATGTAGTGTTGTTTCGTGTTATGT 59.519 34.615 0.00 0.00 0.00 2.29
413 447 2.936498 CTCCGGCTTCATTTTCATACGT 59.064 45.455 0.00 0.00 0.00 3.57
462 496 6.887626 TGTGGGTATTAAAACTTCCTGAAC 57.112 37.500 0.00 0.00 0.00 3.18
567 602 7.256286 GTTCGCTACTAAATCAGAAAGGACTA 58.744 38.462 0.00 0.00 0.00 2.59
570 605 5.100259 CGTTCGCTACTAAATCAGAAAGGA 58.900 41.667 0.00 0.00 0.00 3.36
612 647 6.456315 CGTGTTCATATCATTTTTCGGCTACA 60.456 38.462 0.00 0.00 0.00 2.74
657 692 4.514441 GTCCCTGAGCACATGATTAAGATG 59.486 45.833 0.00 0.00 0.00 2.90
658 693 4.445448 GGTCCCTGAGCACATGATTAAGAT 60.445 45.833 0.00 0.00 0.00 2.40
674 710 0.962356 GCATGACAGTTGGGTCCCTG 60.962 60.000 10.00 1.30 36.97 4.45
704 740 0.915872 TGGATGACAGCTGGGTCCAT 60.916 55.000 24.46 18.14 36.97 3.41
841 878 4.585216 TGGGTGGACGGGGGAAGT 62.585 66.667 0.00 0.00 0.00 3.01
943 980 1.681780 CGGCAAAGGGGAAAGCAGATA 60.682 52.381 0.00 0.00 0.00 1.98
946 983 1.463553 AACGGCAAAGGGGAAAGCAG 61.464 55.000 0.00 0.00 0.00 4.24
963 1000 1.060726 CTCTCACGAGTCGCACGAAC 61.061 60.000 13.59 0.00 32.47 3.95
1436 1484 1.948145 CGATCTTGTAGGCGTAGGAGT 59.052 52.381 0.00 0.00 0.00 3.85
1812 1860 2.301583 GGAGAGGAGGTCATGGCTATTC 59.698 54.545 0.00 0.00 0.00 1.75
2019 2560 0.817654 TGAGATGCTGGTACGTGGAG 59.182 55.000 0.00 0.00 0.00 3.86
2029 2570 0.392595 TGCAGGCTCTTGAGATGCTG 60.393 55.000 20.68 0.00 37.76 4.41
2283 2824 4.101856 ACACTGGGTACTTATACAGGCTT 58.898 43.478 0.00 0.00 35.34 4.35
2292 2833 1.626825 GCCTGGAACACTGGGTACTTA 59.373 52.381 0.00 0.00 38.54 2.24
2537 3078 4.400884 ACATTGTTAGCGCATCCCAATTTA 59.599 37.500 11.47 0.00 0.00 1.40
2614 3169 6.359617 CACGGTGAACATTAACTGATGAAAAC 59.640 38.462 0.74 0.00 0.00 2.43
2663 3218 6.074088 GGTTGATCTTCTGTAATGATAGCACG 60.074 42.308 0.00 0.00 0.00 5.34
2671 3226 6.403636 CCCTTTTCGGTTGATCTTCTGTAATG 60.404 42.308 0.00 0.00 0.00 1.90
2675 3230 3.072476 TCCCTTTTCGGTTGATCTTCTGT 59.928 43.478 0.00 0.00 0.00 3.41
2681 3236 2.791655 ACCTTCCCTTTTCGGTTGATC 58.208 47.619 0.00 0.00 0.00 2.92
2758 3313 7.661847 GGAGGATTTCGGTCTATGAATTTATGT 59.338 37.037 0.00 0.00 0.00 2.29
2810 3368 6.857437 TGATGAAACCTATCTCAGTCAGAA 57.143 37.500 0.00 0.00 33.62 3.02
2846 3404 8.101419 CCTAGACAGACCCTTTGTTTTATTACT 58.899 37.037 0.00 0.00 0.00 2.24
2847 3405 8.098912 TCCTAGACAGACCCTTTGTTTTATTAC 58.901 37.037 0.00 0.00 0.00 1.89
2848 3406 8.098912 GTCCTAGACAGACCCTTTGTTTTATTA 58.901 37.037 0.00 0.00 32.09 0.98
2850 3408 6.043938 TGTCCTAGACAGACCCTTTGTTTTAT 59.956 38.462 0.00 0.00 37.67 1.40
2852 3410 4.165372 TGTCCTAGACAGACCCTTTGTTTT 59.835 41.667 0.00 0.00 37.67 2.43
2853 3411 3.714798 TGTCCTAGACAGACCCTTTGTTT 59.285 43.478 0.00 0.00 37.67 2.83
2854 3412 3.071167 GTGTCCTAGACAGACCCTTTGTT 59.929 47.826 0.00 0.00 43.57 2.83
2855 3413 2.633481 GTGTCCTAGACAGACCCTTTGT 59.367 50.000 0.00 0.00 43.57 2.83
2856 3414 2.632996 TGTGTCCTAGACAGACCCTTTG 59.367 50.000 0.00 0.00 43.57 2.77
2859 3417 2.313342 AGATGTGTCCTAGACAGACCCT 59.687 50.000 0.00 0.00 43.57 4.34
2860 3418 2.741145 AGATGTGTCCTAGACAGACCC 58.259 52.381 0.00 0.00 43.57 4.46
2861 3419 4.783055 TCTAGATGTGTCCTAGACAGACC 58.217 47.826 0.00 0.00 43.57 3.85
2862 3420 7.880713 TCATATCTAGATGTGTCCTAGACAGAC 59.119 40.741 23.88 0.00 43.57 3.51
2863 3421 7.880713 GTCATATCTAGATGTGTCCTAGACAGA 59.119 40.741 23.88 0.00 43.57 3.41
2864 3422 7.663493 TGTCATATCTAGATGTGTCCTAGACAG 59.337 40.741 23.88 0.73 43.57 3.51
2866 3424 7.987750 TGTCATATCTAGATGTGTCCTAGAC 57.012 40.000 23.88 15.91 43.57 2.59
2867 3425 9.898152 CTATGTCATATCTAGATGTGTCCTAGA 57.102 37.037 23.88 8.33 44.50 2.43
2868 3426 9.679661 ACTATGTCATATCTAGATGTGTCCTAG 57.320 37.037 23.88 23.41 35.97 3.02
2870 3428 8.948401 AACTATGTCATATCTAGATGTGTCCT 57.052 34.615 23.88 15.89 32.61 3.85
2889 3447 8.923683 CATCAGCTTAGATGTGACATAACTATG 58.076 37.037 0.00 0.92 40.35 2.23
2903 3461 5.171339 ACAAAGTGGACATCAGCTTAGAT 57.829 39.130 0.00 0.00 0.00 1.98
2904 3462 4.623932 ACAAAGTGGACATCAGCTTAGA 57.376 40.909 0.00 0.00 0.00 2.10
2905 3463 5.009010 ACAAACAAAGTGGACATCAGCTTAG 59.991 40.000 0.00 0.00 0.00 2.18
2906 3464 4.887071 ACAAACAAAGTGGACATCAGCTTA 59.113 37.500 0.00 0.00 0.00 3.09
2908 3466 3.067180 CACAAACAAAGTGGACATCAGCT 59.933 43.478 0.00 0.00 33.43 4.24
2965 3523 9.575783 GCTCCTACAAGTATATAATCTAGCAAC 57.424 37.037 0.00 0.00 0.00 4.17
2966 3524 9.535170 AGCTCCTACAAGTATATAATCTAGCAA 57.465 33.333 0.00 0.00 0.00 3.91
2967 3525 9.535170 AAGCTCCTACAAGTATATAATCTAGCA 57.465 33.333 0.00 0.00 0.00 3.49
2976 3534 8.798402 GTCACATCTAAGCTCCTACAAGTATAT 58.202 37.037 0.00 0.00 0.00 0.86
2977 3535 7.778382 TGTCACATCTAAGCTCCTACAAGTATA 59.222 37.037 0.00 0.00 0.00 1.47
2978 3536 6.607600 TGTCACATCTAAGCTCCTACAAGTAT 59.392 38.462 0.00 0.00 0.00 2.12
2979 3537 5.949952 TGTCACATCTAAGCTCCTACAAGTA 59.050 40.000 0.00 0.00 0.00 2.24
2980 3538 4.772624 TGTCACATCTAAGCTCCTACAAGT 59.227 41.667 0.00 0.00 0.00 3.16
2981 3539 5.330455 TGTCACATCTAAGCTCCTACAAG 57.670 43.478 0.00 0.00 0.00 3.16
2982 3540 5.163405 GGATGTCACATCTAAGCTCCTACAA 60.163 44.000 17.46 0.00 0.00 2.41
2983 3541 4.342378 GGATGTCACATCTAAGCTCCTACA 59.658 45.833 17.46 0.00 0.00 2.74
2984 3542 4.586841 AGGATGTCACATCTAAGCTCCTAC 59.413 45.833 17.46 0.00 30.26 3.18
2985 3543 4.809193 AGGATGTCACATCTAAGCTCCTA 58.191 43.478 17.46 0.00 30.26 2.94
2986 3544 3.652055 AGGATGTCACATCTAAGCTCCT 58.348 45.455 17.46 2.78 0.00 3.69
2987 3545 4.414337 AAGGATGTCACATCTAAGCTCC 57.586 45.455 17.46 0.18 0.00 4.70
2988 3546 7.849804 TTTTAAGGATGTCACATCTAAGCTC 57.150 36.000 17.46 0.00 0.00 4.09
3015 3573 9.376075 ACAGTTTGTCTAATTCACATCTAGATG 57.624 33.333 27.63 27.63 44.15 2.90
3021 3579 9.944663 TGTTTTACAGTTTGTCTAATTCACATC 57.055 29.630 0.00 0.00 0.00 3.06
3031 3589 9.040939 GGCAATATTTTGTTTTACAGTTTGTCT 57.959 29.630 0.00 0.00 35.17 3.41
3032 3590 9.040939 AGGCAATATTTTGTTTTACAGTTTGTC 57.959 29.630 0.00 0.00 35.17 3.18
3033 3591 8.956533 AGGCAATATTTTGTTTTACAGTTTGT 57.043 26.923 0.00 0.00 35.17 2.83
3034 3592 9.649024 CAAGGCAATATTTTGTTTTACAGTTTG 57.351 29.630 0.00 0.00 35.17 2.93
3035 3593 8.835439 CCAAGGCAATATTTTGTTTTACAGTTT 58.165 29.630 0.00 0.00 35.17 2.66
3036 3594 7.443879 CCCAAGGCAATATTTTGTTTTACAGTT 59.556 33.333 0.00 0.00 35.17 3.16
3037 3595 6.934083 CCCAAGGCAATATTTTGTTTTACAGT 59.066 34.615 0.00 0.00 35.17 3.55
3038 3596 7.158021 TCCCAAGGCAATATTTTGTTTTACAG 58.842 34.615 0.00 0.00 35.17 2.74
3039 3597 7.067496 TCCCAAGGCAATATTTTGTTTTACA 57.933 32.000 0.00 0.00 35.17 2.41
3075 3654 4.761235 AATGATTGCATAATGCTCGAGG 57.239 40.909 15.58 0.00 45.31 4.63
3088 3667 5.613358 AGCGCTATAAGGTAAATGATTGC 57.387 39.130 8.99 0.00 0.00 3.56
3089 3668 7.891183 ACTAGCGCTATAAGGTAAATGATTG 57.109 36.000 19.19 2.56 0.00 2.67
3116 3695 9.744468 AACGTAAGAGAAAAATGCTTGTATTTT 57.256 25.926 4.09 4.09 40.25 1.82
3198 3781 7.724061 ACGTTATTAGCCAGGGATATCAAAAAT 59.276 33.333 4.83 0.00 0.00 1.82
3202 3785 5.818678 ACGTTATTAGCCAGGGATATCAA 57.181 39.130 4.83 0.00 0.00 2.57
3300 3883 9.217278 CTCCATGGATTTGATATCTTACTTCTG 57.783 37.037 16.63 0.00 0.00 3.02
3302 3885 9.566432 AACTCCATGGATTTGATATCTTACTTC 57.434 33.333 16.63 0.00 0.00 3.01
3309 3892 8.734386 GTCCAATAACTCCATGGATTTGATATC 58.266 37.037 23.75 8.95 44.55 1.63
3321 3904 1.837439 TGGCTCGTCCAATAACTCCAT 59.163 47.619 0.00 0.00 43.21 3.41
3331 3914 1.486310 AGCTAATCATTGGCTCGTCCA 59.514 47.619 1.62 0.00 44.83 4.02
3332 3915 2.246719 AGCTAATCATTGGCTCGTCC 57.753 50.000 1.62 0.00 44.83 4.79
3349 3932 7.918254 AAACGTTTTTAGTTGAGTGCGGAGC 62.918 44.000 7.96 0.00 42.94 4.70
3353 3936 5.510323 AGAAAAACGTTTTTAGTTGAGTGCG 59.490 36.000 32.57 0.00 40.21 5.34
3354 3937 6.864560 AGAAAAACGTTTTTAGTTGAGTGC 57.135 33.333 32.57 19.30 40.21 4.40
3363 3946 5.918426 AGGGGACAAGAAAAACGTTTTTA 57.082 34.783 32.57 0.00 40.21 1.52
3370 3953 6.531923 AGACTAAGTAGGGGACAAGAAAAAC 58.468 40.000 0.00 0.00 0.00 2.43
3373 3956 6.436532 CACTAGACTAAGTAGGGGACAAGAAA 59.563 42.308 0.00 0.00 0.00 2.52
3374 3957 5.950549 CACTAGACTAAGTAGGGGACAAGAA 59.049 44.000 0.00 0.00 0.00 2.52
3376 3959 5.507637 TCACTAGACTAAGTAGGGGACAAG 58.492 45.833 0.00 0.00 0.00 3.16
3377 3960 5.525454 TCACTAGACTAAGTAGGGGACAA 57.475 43.478 0.00 0.00 0.00 3.18
3378 3961 5.014966 ACTTCACTAGACTAAGTAGGGGACA 59.985 44.000 0.00 0.00 31.84 4.02
3385 3968 6.659745 TTGGCAACTTCACTAGACTAAGTA 57.340 37.500 0.00 0.00 33.24 2.24
3418 4001 1.068895 TGGACGGAGCGAGTAACAAAA 59.931 47.619 0.00 0.00 0.00 2.44
3423 4006 1.303888 ACCTGGACGGAGCGAGTAA 60.304 57.895 0.00 0.00 36.31 2.24
3424 4007 2.044555 CACCTGGACGGAGCGAGTA 61.045 63.158 0.00 0.00 36.31 2.59
3425 4008 3.374402 CACCTGGACGGAGCGAGT 61.374 66.667 0.00 0.00 36.31 4.18
3426 4009 4.803426 GCACCTGGACGGAGCGAG 62.803 72.222 0.00 0.00 39.59 5.03
3430 4013 1.443407 CCTATGCACCTGGACGGAG 59.557 63.158 0.00 0.00 36.31 4.63
3431 4014 2.063979 CCCTATGCACCTGGACGGA 61.064 63.158 0.00 0.00 36.31 4.69
3432 4015 2.505982 CCCTATGCACCTGGACGG 59.494 66.667 0.00 0.00 39.35 4.79
3433 4016 2.203070 GCCCTATGCACCTGGACG 60.203 66.667 0.00 0.00 40.77 4.79
3442 4025 5.555017 TGAATTCTCTAAGATGCCCTATGC 58.445 41.667 7.05 0.00 41.77 3.14
3443 4026 6.013898 TCCTGAATTCTCTAAGATGCCCTATG 60.014 42.308 7.05 0.00 0.00 2.23
3444 4027 6.087456 TCCTGAATTCTCTAAGATGCCCTAT 58.913 40.000 7.05 0.00 0.00 2.57
3445 4028 5.467738 TCCTGAATTCTCTAAGATGCCCTA 58.532 41.667 7.05 0.00 0.00 3.53
3446 4029 4.302067 TCCTGAATTCTCTAAGATGCCCT 58.698 43.478 7.05 0.00 0.00 5.19
3447 4030 4.696479 TCCTGAATTCTCTAAGATGCCC 57.304 45.455 7.05 0.00 0.00 5.36
3448 4031 6.997476 AGAAATCCTGAATTCTCTAAGATGCC 59.003 38.462 7.05 0.00 30.16 4.40
3449 4032 9.553064 TTAGAAATCCTGAATTCTCTAAGATGC 57.447 33.333 7.05 0.00 37.16 3.91
3462 4045 8.136165 GCGACTTATACTCTTAGAAATCCTGAA 58.864 37.037 0.00 0.00 0.00 3.02
3463 4046 7.502895 AGCGACTTATACTCTTAGAAATCCTGA 59.497 37.037 0.00 0.00 0.00 3.86
3464 4047 7.653647 AGCGACTTATACTCTTAGAAATCCTG 58.346 38.462 0.00 0.00 0.00 3.86
3465 4048 7.826918 AGCGACTTATACTCTTAGAAATCCT 57.173 36.000 0.00 0.00 0.00 3.24
3469 4052 9.947669 GACAATAGCGACTTATACTCTTAGAAA 57.052 33.333 0.00 0.00 0.00 2.52
3470 4053 9.117183 TGACAATAGCGACTTATACTCTTAGAA 57.883 33.333 0.00 0.00 0.00 2.10
3471 4054 8.672823 TGACAATAGCGACTTATACTCTTAGA 57.327 34.615 0.00 0.00 0.00 2.10
3472 4055 9.900710 ATTGACAATAGCGACTTATACTCTTAG 57.099 33.333 0.00 0.00 0.00 2.18
3474 4057 9.250624 GAATTGACAATAGCGACTTATACTCTT 57.749 33.333 0.00 0.00 0.00 2.85
3475 4058 7.591795 CGAATTGACAATAGCGACTTATACTCT 59.408 37.037 14.68 0.00 0.00 3.24
3476 4059 7.617528 GCGAATTGACAATAGCGACTTATACTC 60.618 40.741 20.85 3.51 0.00 2.59
3477 4060 6.144080 GCGAATTGACAATAGCGACTTATACT 59.856 38.462 20.85 0.00 0.00 2.12
3478 4061 6.074516 TGCGAATTGACAATAGCGACTTATAC 60.075 38.462 20.85 7.36 0.00 1.47
3479 4062 5.980715 TGCGAATTGACAATAGCGACTTATA 59.019 36.000 20.85 4.00 0.00 0.98
3480 4063 4.808895 TGCGAATTGACAATAGCGACTTAT 59.191 37.500 20.85 0.00 0.00 1.73
3481 4064 4.177783 TGCGAATTGACAATAGCGACTTA 58.822 39.130 20.85 5.08 0.00 2.24
3482 4065 3.000041 TGCGAATTGACAATAGCGACTT 59.000 40.909 20.85 0.00 0.00 3.01
3483 4066 2.616960 TGCGAATTGACAATAGCGACT 58.383 42.857 20.85 0.00 0.00 4.18
3484 4067 3.062099 TCTTGCGAATTGACAATAGCGAC 59.938 43.478 20.85 14.41 0.00 5.19
3485 4068 3.258228 TCTTGCGAATTGACAATAGCGA 58.742 40.909 20.85 17.48 0.00 4.93
3486 4069 3.544834 CCTCTTGCGAATTGACAATAGCG 60.545 47.826 17.97 16.64 0.00 4.26
3487 4070 3.375299 ACCTCTTGCGAATTGACAATAGC 59.625 43.478 16.96 16.96 0.00 2.97
3488 4071 4.201851 CCACCTCTTGCGAATTGACAATAG 60.202 45.833 0.00 0.36 0.00 1.73
3489 4072 3.689161 CCACCTCTTGCGAATTGACAATA 59.311 43.478 0.00 0.00 0.00 1.90
3490 4073 2.489329 CCACCTCTTGCGAATTGACAAT 59.511 45.455 0.00 0.00 0.00 2.71
3491 4074 1.879380 CCACCTCTTGCGAATTGACAA 59.121 47.619 0.00 0.00 0.00 3.18
3492 4075 1.202758 ACCACCTCTTGCGAATTGACA 60.203 47.619 0.00 0.00 0.00 3.58
3493 4076 1.523758 ACCACCTCTTGCGAATTGAC 58.476 50.000 0.00 0.00 0.00 3.18
3494 4077 3.410631 TTACCACCTCTTGCGAATTGA 57.589 42.857 0.00 0.00 0.00 2.57
3495 4078 4.701956 AATTACCACCTCTTGCGAATTG 57.298 40.909 0.00 0.00 0.00 2.32
3496 4079 6.601613 TGATTAATTACCACCTCTTGCGAATT 59.398 34.615 0.00 0.00 0.00 2.17
3497 4080 6.038271 GTGATTAATTACCACCTCTTGCGAAT 59.962 38.462 0.00 0.00 0.00 3.34
3498 4081 5.353123 GTGATTAATTACCACCTCTTGCGAA 59.647 40.000 0.00 0.00 0.00 4.70
3499 4082 4.873827 GTGATTAATTACCACCTCTTGCGA 59.126 41.667 0.00 0.00 0.00 5.10
3500 4083 4.260212 CGTGATTAATTACCACCTCTTGCG 60.260 45.833 4.90 0.00 0.00 4.85
3501 4084 4.634443 ACGTGATTAATTACCACCTCTTGC 59.366 41.667 4.90 0.00 0.00 4.01
3502 4085 5.872617 TCACGTGATTAATTACCACCTCTTG 59.127 40.000 15.76 4.98 0.00 3.02
3503 4086 6.045072 TCACGTGATTAATTACCACCTCTT 57.955 37.500 15.76 0.00 0.00 2.85
3504 4087 5.670792 TCACGTGATTAATTACCACCTCT 57.329 39.130 15.76 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.