Multiple sequence alignment - TraesCS1D01G274000

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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 TraesCS1D01G274000 chr1D 100.000 4048 0 0 1 4048 368323519 368319472 0.000000e+00 7476.0
1 TraesCS1D01G274000 chr1D 84.795 2361 173 96 412 2660 369904541 369902255 0.000000e+00 2200.0
2 TraesCS1D01G274000 chr1D 93.236 547 35 2 2658 3202 369899931 369899385 0.000000e+00 804.0
3 TraesCS1D01G274000 chr1D 92.537 268 13 4 108 373 369904806 369904544 1.060000e-100 377.0
4 TraesCS1D01G274000 chr1D 96.429 140 5 0 108 247 368332681 368332542 8.750000e-57 231.0
5 TraesCS1D01G274000 chr1D 92.593 108 8 0 1 108 383688338 383688231 5.420000e-34 156.0
6 TraesCS1D01G274000 chr1B 88.916 3239 202 70 108 3264 492358941 492355778 0.000000e+00 3847.0
7 TraesCS1D01G274000 chr1B 94.356 567 29 1 3485 4048 492335842 492335276 0.000000e+00 867.0
8 TraesCS1D01G274000 chr1B 92.254 142 7 1 3352 3489 492355699 492355558 8.870000e-47 198.0
9 TraesCS1D01G274000 chr1A 87.743 2366 162 59 108 2431 467260786 467258507 0.000000e+00 2645.0
10 TraesCS1D01G274000 chr1A 94.444 576 32 0 3473 4048 467257820 467257245 0.000000e+00 887.0
11 TraesCS1D01G274000 chr1A 90.816 392 19 3 2868 3259 467258216 467257842 3.610000e-140 508.0
12 TraesCS1D01G274000 chr1A 86.061 330 18 13 2467 2796 467258513 467258212 3.020000e-86 329.0
13 TraesCS1D01G274000 chr1A 92.821 195 12 1 109 303 468593539 468593347 8.570000e-72 281.0
14 TraesCS1D01G274000 chr1A 79.710 345 32 17 333 651 468593267 468592935 8.810000e-52 215.0
15 TraesCS1D01G274000 chr1A 94.286 105 6 0 4 108 366983611 366983507 1.160000e-35 161.0
16 TraesCS1D01G274000 chr1A 93.519 108 7 0 1 108 579580997 579581104 1.160000e-35 161.0
17 TraesCS1D01G274000 chr1A 92.593 108 8 0 1 108 288504489 288504596 5.420000e-34 156.0
18 TraesCS1D01G274000 chr3A 92.857 224 15 1 990 1213 627275625 627275847 1.400000e-84 324.0
19 TraesCS1D01G274000 chr3A 83.410 217 31 1 998 1214 107618001 107617790 3.190000e-46 196.0
20 TraesCS1D01G274000 chr3A 95.062 81 4 0 1304 1384 627275942 627276022 1.180000e-25 128.0
21 TraesCS1D01G274000 chr3A 88.571 70 8 0 1531 1600 627276288 627276357 7.210000e-13 86.1
22 TraesCS1D01G274000 chr3D 92.694 219 16 0 995 1213 484345581 484345799 2.350000e-82 316.0
23 TraesCS1D01G274000 chr3D 93.827 81 5 0 1304 1384 484345906 484345986 5.490000e-24 122.0
24 TraesCS1D01G274000 chr3D 86.667 75 10 0 1531 1605 484346249 484346323 2.590000e-12 84.2
25 TraesCS1D01G274000 chr3B 91.781 219 18 0 995 1213 647177884 647178102 5.080000e-79 305.0
26 TraesCS1D01G274000 chr3B 91.667 96 6 2 1304 1398 647178235 647178329 9.130000e-27 132.0
27 TraesCS1D01G274000 chr3B 90.000 70 7 0 1531 1600 647178615 647178684 1.550000e-14 91.6
28 TraesCS1D01G274000 chr5D 83.871 217 29 2 998 1214 10495641 10495431 6.860000e-48 202.0
29 TraesCS1D01G274000 chr5D 83.871 217 30 1 998 1214 511490990 511490779 6.860000e-48 202.0
30 TraesCS1D01G274000 chr5A 95.370 108 5 0 1 108 224443488 224443595 5.380000e-39 172.0
31 TraesCS1D01G274000 chr5A 100.000 28 0 0 3261 3288 422040380 422040353 7.000000e-03 52.8
32 TraesCS1D01G274000 chr2D 95.370 108 5 0 1 108 516931983 516931876 5.380000e-39 172.0
33 TraesCS1D01G274000 chr2D 94.444 108 5 1 1 108 66132231 66132337 9.000000e-37 165.0
34 TraesCS1D01G274000 chr2D 100.000 28 0 0 3230 3257 467965480 467965453 7.000000e-03 52.8
35 TraesCS1D01G274000 chr7A 94.444 108 6 0 1 108 186631422 186631529 2.500000e-37 167.0
36 TraesCS1D01G274000 chr4D 93.333 105 7 0 4 108 485018157 485018053 5.420000e-34 156.0
37 TraesCS1D01G274000 chr6D 82.143 140 20 1 1074 1213 443355408 443355542 9.190000e-22 115.0
38 TraesCS1D01G274000 chr6D 92.982 57 4 0 1541 1597 468860022 468859966 2.590000e-12 84.2
39 TraesCS1D01G274000 chr4B 100.000 29 0 0 3231 3259 664760580 664760552 2.000000e-03 54.7
40 TraesCS1D01G274000 chr4A 100.000 28 0 0 3261 3288 629483234 629483207 7.000000e-03 52.8
41 TraesCS1D01G274000 chr2B 100.000 28 0 0 3261 3288 790751474 790751447 7.000000e-03 52.8
42 TraesCS1D01G274000 chr2A 100.000 28 0 0 3237 3264 696242077 696242050 7.000000e-03 52.8


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 TraesCS1D01G274000 chr1D 368319472 368323519 4047 True 7476.00 7476 100.000000 1 4048 1 chr1D.!!$R1 4047
1 TraesCS1D01G274000 chr1D 369899385 369904806 5421 True 1127.00 2200 90.189333 108 3202 3 chr1D.!!$R4 3094
2 TraesCS1D01G274000 chr1B 492355558 492358941 3383 True 2022.50 3847 90.585000 108 3489 2 chr1B.!!$R2 3381
3 TraesCS1D01G274000 chr1B 492335276 492335842 566 True 867.00 867 94.356000 3485 4048 1 chr1B.!!$R1 563
4 TraesCS1D01G274000 chr1A 467257245 467260786 3541 True 1092.25 2645 89.766000 108 4048 4 chr1A.!!$R2 3940
5 TraesCS1D01G274000 chr1A 468592935 468593539 604 True 248.00 281 86.265500 109 651 2 chr1A.!!$R3 542

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
701 795 0.166814 GCACAAGCGCTTCCAGTAAG 59.833 55.0 22.21 9.9 38.32 2.34 F
1263 1420 0.382515 CGAGTCCCTTTCTCGCCTAG 59.617 60.0 2.59 0.0 45.77 3.02 F
1548 1732 0.663568 AGTACTGCGTGTGCTTCGAC 60.664 55.0 0.00 0.0 38.47 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1593 1777 0.384309 TAAGAGGAGCGCATACCGTG 59.616 55.0 11.47 0.0 39.71 4.94 R
2633 2894 0.395311 CCAGCCTCAGGAATGCACAT 60.395 55.0 0.00 0.0 0.00 3.21 R
3297 5931 0.105862 CCCCTCCCTGGTATGACGTA 60.106 60.0 0.00 0.0 0.00 3.57 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
18 19 2.968737 TCTTCTTCTCGCAGGAGCT 58.031 52.632 0.00 0.00 40.26 4.09
19 20 0.814457 TCTTCTTCTCGCAGGAGCTC 59.186 55.000 4.71 4.71 40.26 4.09
20 21 0.817013 CTTCTTCTCGCAGGAGCTCT 59.183 55.000 14.64 0.00 40.26 4.09
21 22 1.204467 CTTCTTCTCGCAGGAGCTCTT 59.796 52.381 14.64 2.08 40.26 2.85
22 23 1.261480 TCTTCTCGCAGGAGCTCTTT 58.739 50.000 14.64 0.00 40.26 2.52
23 24 1.620819 TCTTCTCGCAGGAGCTCTTTT 59.379 47.619 14.64 0.00 40.26 2.27
24 25 2.826128 TCTTCTCGCAGGAGCTCTTTTA 59.174 45.455 14.64 0.00 40.26 1.52
25 26 3.258372 TCTTCTCGCAGGAGCTCTTTTAA 59.742 43.478 14.64 0.00 40.26 1.52
26 27 3.895232 TCTCGCAGGAGCTCTTTTAAT 57.105 42.857 14.64 0.00 40.26 1.40
27 28 3.786635 TCTCGCAGGAGCTCTTTTAATC 58.213 45.455 14.64 0.00 40.26 1.75
28 29 2.537625 CTCGCAGGAGCTCTTTTAATCG 59.462 50.000 14.64 7.98 39.10 3.34
29 30 1.004504 CGCAGGAGCTCTTTTAATCGC 60.005 52.381 14.64 3.54 39.10 4.58
30 31 2.009774 GCAGGAGCTCTTTTAATCGCA 58.990 47.619 14.64 0.00 37.91 5.10
31 32 2.615912 GCAGGAGCTCTTTTAATCGCAT 59.384 45.455 14.64 0.00 37.91 4.73
32 33 3.303659 GCAGGAGCTCTTTTAATCGCATC 60.304 47.826 14.64 0.00 37.91 3.91
33 34 4.125703 CAGGAGCTCTTTTAATCGCATCT 58.874 43.478 14.64 0.00 0.00 2.90
34 35 4.210955 CAGGAGCTCTTTTAATCGCATCTC 59.789 45.833 14.64 0.00 0.00 2.75
35 36 3.496507 GGAGCTCTTTTAATCGCATCTCC 59.503 47.826 14.64 0.00 0.00 3.71
36 37 3.126831 AGCTCTTTTAATCGCATCTCCG 58.873 45.455 0.00 0.00 0.00 4.63
37 38 2.348966 GCTCTTTTAATCGCATCTCCGC 60.349 50.000 0.00 0.00 0.00 5.54
38 39 2.866156 CTCTTTTAATCGCATCTCCGCA 59.134 45.455 0.00 0.00 0.00 5.69
39 40 3.466836 TCTTTTAATCGCATCTCCGCAT 58.533 40.909 0.00 0.00 0.00 4.73
40 41 3.494626 TCTTTTAATCGCATCTCCGCATC 59.505 43.478 0.00 0.00 0.00 3.91
41 42 2.820059 TTAATCGCATCTCCGCATCT 57.180 45.000 0.00 0.00 0.00 2.90
42 43 3.934457 TTAATCGCATCTCCGCATCTA 57.066 42.857 0.00 0.00 0.00 1.98
43 44 2.820059 AATCGCATCTCCGCATCTAA 57.180 45.000 0.00 0.00 0.00 2.10
44 45 3.325293 AATCGCATCTCCGCATCTAAT 57.675 42.857 0.00 0.00 0.00 1.73
45 46 2.820059 TCGCATCTCCGCATCTAATT 57.180 45.000 0.00 0.00 0.00 1.40
46 47 3.111853 TCGCATCTCCGCATCTAATTT 57.888 42.857 0.00 0.00 0.00 1.82
47 48 4.251543 TCGCATCTCCGCATCTAATTTA 57.748 40.909 0.00 0.00 0.00 1.40
48 49 4.627058 TCGCATCTCCGCATCTAATTTAA 58.373 39.130 0.00 0.00 0.00 1.52
49 50 4.447724 TCGCATCTCCGCATCTAATTTAAC 59.552 41.667 0.00 0.00 0.00 2.01
50 51 4.211164 CGCATCTCCGCATCTAATTTAACA 59.789 41.667 0.00 0.00 0.00 2.41
51 52 5.106948 CGCATCTCCGCATCTAATTTAACAT 60.107 40.000 0.00 0.00 0.00 2.71
52 53 6.082338 GCATCTCCGCATCTAATTTAACATG 58.918 40.000 0.00 0.00 0.00 3.21
53 54 6.073058 GCATCTCCGCATCTAATTTAACATGA 60.073 38.462 0.00 0.00 0.00 3.07
54 55 7.520453 GCATCTCCGCATCTAATTTAACATGAA 60.520 37.037 0.00 0.00 0.00 2.57
55 56 7.482654 TCTCCGCATCTAATTTAACATGAAG 57.517 36.000 0.00 0.00 0.00 3.02
56 57 7.047891 TCTCCGCATCTAATTTAACATGAAGT 58.952 34.615 0.00 0.00 0.00 3.01
57 58 7.552687 TCTCCGCATCTAATTTAACATGAAGTT 59.447 33.333 0.00 0.00 44.27 2.66
58 59 7.693952 TCCGCATCTAATTTAACATGAAGTTC 58.306 34.615 0.00 0.00 41.64 3.01
59 60 6.912591 CCGCATCTAATTTAACATGAAGTTCC 59.087 38.462 0.00 0.00 41.64 3.62
60 61 6.628856 CGCATCTAATTTAACATGAAGTTCCG 59.371 38.462 0.00 0.00 41.64 4.30
61 62 7.472543 GCATCTAATTTAACATGAAGTTCCGT 58.527 34.615 0.00 0.00 41.64 4.69
62 63 7.968405 GCATCTAATTTAACATGAAGTTCCGTT 59.032 33.333 0.00 11.29 41.64 4.44
63 64 9.277565 CATCTAATTTAACATGAAGTTCCGTTG 57.722 33.333 14.78 6.93 41.64 4.10
64 65 8.610248 TCTAATTTAACATGAAGTTCCGTTGA 57.390 30.769 14.78 6.78 41.64 3.18
65 66 9.058174 TCTAATTTAACATGAAGTTCCGTTGAA 57.942 29.630 14.78 13.38 41.64 2.69
66 67 9.840427 CTAATTTAACATGAAGTTCCGTTGAAT 57.160 29.630 14.78 14.61 41.64 2.57
67 68 8.742554 AATTTAACATGAAGTTCCGTTGAATC 57.257 30.769 17.90 0.00 41.64 2.52
68 69 7.504924 TTTAACATGAAGTTCCGTTGAATCT 57.495 32.000 14.78 0.00 41.64 2.40
69 70 8.610248 TTTAACATGAAGTTCCGTTGAATCTA 57.390 30.769 14.78 0.00 41.64 1.98
70 71 6.727824 AACATGAAGTTCCGTTGAATCTAG 57.272 37.500 0.00 0.00 34.74 2.43
71 72 5.178797 ACATGAAGTTCCGTTGAATCTAGG 58.821 41.667 0.00 0.00 31.98 3.02
72 73 5.046591 ACATGAAGTTCCGTTGAATCTAGGA 60.047 40.000 0.00 0.00 31.98 2.94
73 74 5.677319 TGAAGTTCCGTTGAATCTAGGAT 57.323 39.130 0.00 0.00 31.98 3.24
74 75 5.661458 TGAAGTTCCGTTGAATCTAGGATC 58.339 41.667 0.00 0.00 31.98 3.36
75 76 5.186992 TGAAGTTCCGTTGAATCTAGGATCA 59.813 40.000 0.00 0.00 31.98 2.92
76 77 5.878406 AGTTCCGTTGAATCTAGGATCAT 57.122 39.130 0.00 0.00 31.98 2.45
77 78 5.605534 AGTTCCGTTGAATCTAGGATCATG 58.394 41.667 0.00 0.00 31.98 3.07
78 79 4.607293 TCCGTTGAATCTAGGATCATGG 57.393 45.455 0.00 0.00 0.00 3.66
79 80 4.223144 TCCGTTGAATCTAGGATCATGGA 58.777 43.478 0.00 0.00 31.73 3.41
80 81 4.039245 TCCGTTGAATCTAGGATCATGGAC 59.961 45.833 0.00 0.00 30.19 4.02
81 82 4.039730 CCGTTGAATCTAGGATCATGGACT 59.960 45.833 0.00 0.00 0.00 3.85
82 83 5.226396 CGTTGAATCTAGGATCATGGACTC 58.774 45.833 0.00 0.00 0.00 3.36
83 84 5.226396 GTTGAATCTAGGATCATGGACTCG 58.774 45.833 0.00 0.00 0.00 4.18
84 85 3.829026 TGAATCTAGGATCATGGACTCGG 59.171 47.826 0.00 0.00 0.00 4.63
85 86 1.621992 TCTAGGATCATGGACTCGGC 58.378 55.000 0.00 0.00 0.00 5.54
86 87 1.145945 TCTAGGATCATGGACTCGGCT 59.854 52.381 0.00 0.00 0.00 5.52
87 88 1.967066 CTAGGATCATGGACTCGGCTT 59.033 52.381 0.00 0.00 0.00 4.35
88 89 1.207791 AGGATCATGGACTCGGCTTT 58.792 50.000 0.00 0.00 0.00 3.51
89 90 1.561542 AGGATCATGGACTCGGCTTTT 59.438 47.619 0.00 0.00 0.00 2.27
90 91 2.771943 AGGATCATGGACTCGGCTTTTA 59.228 45.455 0.00 0.00 0.00 1.52
91 92 2.872858 GGATCATGGACTCGGCTTTTAC 59.127 50.000 0.00 0.00 0.00 2.01
92 93 3.531538 GATCATGGACTCGGCTTTTACA 58.468 45.455 0.00 0.00 0.00 2.41
93 94 3.627395 TCATGGACTCGGCTTTTACAT 57.373 42.857 0.00 0.00 0.00 2.29
94 95 3.531538 TCATGGACTCGGCTTTTACATC 58.468 45.455 0.00 0.00 0.00 3.06
95 96 2.396590 TGGACTCGGCTTTTACATCC 57.603 50.000 0.00 0.00 0.00 3.51
96 97 1.626321 TGGACTCGGCTTTTACATCCA 59.374 47.619 0.00 0.00 32.39 3.41
97 98 2.039216 TGGACTCGGCTTTTACATCCAA 59.961 45.455 0.00 0.00 31.90 3.53
98 99 2.678336 GGACTCGGCTTTTACATCCAAG 59.322 50.000 0.00 0.00 0.00 3.61
99 100 2.678336 GACTCGGCTTTTACATCCAAGG 59.322 50.000 0.00 0.00 0.00 3.61
100 101 1.401905 CTCGGCTTTTACATCCAAGGC 59.598 52.381 0.00 0.00 41.13 4.35
101 102 0.455815 CGGCTTTTACATCCAAGGCC 59.544 55.000 0.00 0.00 41.42 5.19
102 103 1.852633 GGCTTTTACATCCAAGGCCT 58.147 50.000 0.00 0.00 39.17 5.19
103 104 1.478105 GGCTTTTACATCCAAGGCCTG 59.522 52.381 5.69 0.00 39.17 4.85
104 105 2.446435 GCTTTTACATCCAAGGCCTGA 58.554 47.619 5.69 0.00 0.00 3.86
105 106 2.825532 GCTTTTACATCCAAGGCCTGAA 59.174 45.455 5.69 0.00 0.00 3.02
106 107 3.448660 GCTTTTACATCCAAGGCCTGAAT 59.551 43.478 5.69 0.00 0.00 2.57
136 137 0.817634 TCCAACAGTCGGCCAAACAG 60.818 55.000 2.24 0.00 0.00 3.16
316 351 1.694150 GATGGCCACTCCTACATAGCA 59.306 52.381 8.16 0.00 35.26 3.49
317 352 0.830648 TGGCCACTCCTACATAGCAC 59.169 55.000 0.00 0.00 35.26 4.40
318 353 0.249489 GGCCACTCCTACATAGCACG 60.249 60.000 0.00 0.00 0.00 5.34
319 354 0.876342 GCCACTCCTACATAGCACGC 60.876 60.000 0.00 0.00 0.00 5.34
512 579 3.124466 TCATTAGTCAACCGAATGCAACG 59.876 43.478 9.21 9.21 31.86 4.10
532 599 1.817099 GCTTGACAGGGATGCTCGG 60.817 63.158 0.00 0.00 0.00 4.63
560 644 9.890352 CCTTTTTCTTCTTCTTCTTTATCACTG 57.110 33.333 0.00 0.00 0.00 3.66
581 665 5.142061 TGTACGTGTAAACACATGAGGAT 57.858 39.130 13.30 0.00 46.75 3.24
701 795 0.166814 GCACAAGCGCTTCCAGTAAG 59.833 55.000 22.21 9.90 38.32 2.34
705 799 3.684788 CACAAGCGCTTCCAGTAAGTAAT 59.315 43.478 22.21 0.00 37.53 1.89
718 816 5.112686 CAGTAAGTAATCCAGTTGCTCCTC 58.887 45.833 0.00 0.00 30.83 3.71
722 820 0.551131 AATCCAGTTGCTCCTCCCCT 60.551 55.000 0.00 0.00 0.00 4.79
878 985 4.569180 CGGATGCCGCCTCCCATT 62.569 66.667 8.92 0.00 41.17 3.16
997 1154 3.080121 AGGCCAGGCGAGAAGAGG 61.080 66.667 5.01 0.00 0.00 3.69
1240 1397 2.355513 GCACACATGATCCAAGTCCTCT 60.356 50.000 0.00 0.00 0.00 3.69
1243 1400 3.133721 ACACATGATCCAAGTCCTCTAGC 59.866 47.826 0.00 0.00 0.00 3.42
1261 1418 3.289525 CGAGTCCCTTTCTCGCCT 58.710 61.111 2.59 0.00 45.77 5.52
1262 1419 2.490165 CGAGTCCCTTTCTCGCCTA 58.510 57.895 2.59 0.00 45.77 3.93
1263 1420 0.382515 CGAGTCCCTTTCTCGCCTAG 59.617 60.000 2.59 0.00 45.77 3.02
1404 1575 2.300956 TGCACTCTTCTCACTCTCCT 57.699 50.000 0.00 0.00 0.00 3.69
1405 1576 3.441500 TGCACTCTTCTCACTCTCCTA 57.558 47.619 0.00 0.00 0.00 2.94
1411 1588 4.704540 ACTCTTCTCACTCTCCTACACATG 59.295 45.833 0.00 0.00 0.00 3.21
1509 1693 2.892425 GAGGCGGCCATCTTCGTG 60.892 66.667 23.09 0.00 0.00 4.35
1548 1732 0.663568 AGTACTGCGTGTGCTTCGAC 60.664 55.000 0.00 0.00 38.47 4.20
1620 1805 1.025812 GCGCTCCTCTTACTCTGCTA 58.974 55.000 0.00 0.00 0.00 3.49
1656 1842 2.417719 CTACCTGTTGACTGGTTCAGC 58.582 52.381 16.33 0.00 44.38 4.26
1660 1846 2.224606 CTGTTGACTGGTTCAGCACAT 58.775 47.619 0.00 0.00 40.27 3.21
1690 1876 3.772060 AACGAAGGTACTATGTCGACC 57.228 47.619 14.12 0.00 38.49 4.79
1696 1882 3.209410 AGGTACTATGTCGACCGGTTAG 58.791 50.000 9.42 8.80 36.02 2.34
1728 1921 1.130373 TGATCGGCGTTTTCATTCTGC 59.870 47.619 6.85 0.00 0.00 4.26
1744 1937 5.423290 TCATTCTGCTCTGTAGATCTTTGGA 59.577 40.000 0.00 0.00 0.00 3.53
1865 2058 3.275143 TGCACGGTAATTATGTTCCCTG 58.725 45.455 0.00 0.00 0.00 4.45
1892 2088 8.506168 TGATGTATTTTCACTCCCATTACTTC 57.494 34.615 0.00 0.00 0.00 3.01
1921 2118 4.712337 ACCTCTTCATCCTAGATTCAACGT 59.288 41.667 0.00 0.00 0.00 3.99
1993 2190 3.871485 CTTCACTCTTGATCCTTCCCTG 58.129 50.000 0.00 0.00 0.00 4.45
1996 2193 1.081174 ACTCTTGATCCTTCCCTGGGA 59.919 52.381 12.53 12.53 37.26 4.37
2080 2288 9.994432 GTCCTTTCTACAATTTATTCACTGATG 57.006 33.333 0.00 0.00 0.00 3.07
2101 2309 4.783764 GTGCAACAAAAGGTTAGCCTAT 57.216 40.909 0.00 0.00 40.12 2.57
2408 2657 2.365293 GCAAACTGAAACCCTTCCACAT 59.635 45.455 0.00 0.00 0.00 3.21
2425 2674 7.012138 CCTTCCACATCTAATTCAGTCTGATTG 59.988 40.741 2.68 0.00 0.00 2.67
2428 2686 6.018098 CCACATCTAATTCAGTCTGATTGCTC 60.018 42.308 2.68 0.00 0.00 4.26
2429 2687 6.018098 CACATCTAATTCAGTCTGATTGCTCC 60.018 42.308 2.68 0.00 0.00 4.70
2431 2689 5.668471 TCTAATTCAGTCTGATTGCTCCTG 58.332 41.667 2.68 0.00 0.00 3.86
2443 2701 5.376625 TGATTGCTCCTGTTTTACTGAACT 58.623 37.500 0.00 0.00 0.00 3.01
2445 2703 5.499139 TTGCTCCTGTTTTACTGAACTTG 57.501 39.130 0.00 0.00 0.00 3.16
2448 2706 6.530120 TGCTCCTGTTTTACTGAACTTGATA 58.470 36.000 0.00 0.00 0.00 2.15
2449 2707 6.650807 TGCTCCTGTTTTACTGAACTTGATAG 59.349 38.462 0.00 0.00 0.00 2.08
2455 2713 8.850454 TGTTTTACTGAACTTGATAGTTTTGC 57.150 30.769 0.00 0.00 44.51 3.68
2456 2714 8.682710 TGTTTTACTGAACTTGATAGTTTTGCT 58.317 29.630 0.00 0.00 44.51 3.91
2462 2720 8.292448 ACTGAACTTGATAGTTTTGCTATGTTG 58.708 33.333 0.00 0.00 44.51 3.33
2633 2894 3.466836 CCAGCTGATTACGCTTATCCAA 58.533 45.455 17.39 0.00 35.07 3.53
2656 5243 0.322816 GCATTCCTGAGGCTGGTGAA 60.323 55.000 0.00 0.00 0.00 3.18
2744 5331 1.608590 CAGTCTTTCACCGGCAAACAT 59.391 47.619 0.00 0.00 0.00 2.71
2859 5446 9.982651 ATGTGCTATTTTACAGAATCGTAGTAT 57.017 29.630 0.00 0.00 0.00 2.12
2860 5447 9.459640 TGTGCTATTTTACAGAATCGTAGTATC 57.540 33.333 0.00 0.00 0.00 2.24
2876 5463 9.684448 ATCGTAGTATCATCTTAACTTCATGTG 57.316 33.333 0.00 0.00 0.00 3.21
3027 5614 5.352284 AGGAGATTAAATCACTGTACGCTG 58.648 41.667 0.00 0.00 0.00 5.18
3079 5667 4.393062 CCTGAAGACACATACACATGTTCC 59.607 45.833 0.00 0.00 42.98 3.62
3086 5674 3.314045 ACATACACATGTTCCGCATCGG 61.314 50.000 0.00 0.00 42.98 4.18
3102 5690 4.494199 CGCATCGGGTAGCTAAAAGAAAAG 60.494 45.833 0.00 0.00 0.00 2.27
3315 5949 1.038280 GTACGTCATACCAGGGAGGG 58.962 60.000 0.00 0.00 43.89 4.30
3316 5950 0.105862 TACGTCATACCAGGGAGGGG 60.106 60.000 0.00 0.00 43.89 4.79
3317 5951 1.382695 CGTCATACCAGGGAGGGGT 60.383 63.158 0.00 0.00 43.89 4.95
3318 5952 0.981277 CGTCATACCAGGGAGGGGTT 60.981 60.000 0.00 0.00 43.89 4.11
3319 5953 0.837940 GTCATACCAGGGAGGGGTTC 59.162 60.000 0.00 0.00 43.89 3.62
3320 5954 0.327191 TCATACCAGGGAGGGGTTCC 60.327 60.000 0.00 0.00 46.00 3.62
3339 5973 1.852633 CCCAAGGGAACAATCCTTCC 58.147 55.000 0.00 0.00 45.77 3.46
3347 5981 3.621558 GGAACAATCCTTCCCTTAGGTG 58.378 50.000 0.00 0.00 42.93 4.00
3348 5982 3.621558 GAACAATCCTTCCCTTAGGTGG 58.378 50.000 0.00 0.00 36.63 4.61
3349 5983 2.644151 ACAATCCTTCCCTTAGGTGGT 58.356 47.619 0.00 0.00 36.63 4.16
3350 5984 2.308866 ACAATCCTTCCCTTAGGTGGTG 59.691 50.000 0.00 0.00 36.63 4.17
3357 5991 2.173519 TCCCTTAGGTGGTGTCTAACG 58.826 52.381 0.00 0.00 0.00 3.18
3363 5997 2.313317 AGGTGGTGTCTAACGAGTGAA 58.687 47.619 0.00 0.00 0.00 3.18
3370 6004 3.979495 GTGTCTAACGAGTGAACGATTGT 59.021 43.478 0.00 0.00 37.03 2.71
3383 6017 5.346281 GTGAACGATTGTGTTTTGACCAAAA 59.654 36.000 4.00 4.00 37.90 2.44
3422 6056 1.461849 ACGGACCACACCCCCTTAA 60.462 57.895 0.00 0.00 0.00 1.85
3439 6073 4.952335 CCCTTAATTTTCTCTCATGGCTGT 59.048 41.667 0.00 0.00 0.00 4.40
3581 6219 2.163010 CCTCATGCATTCAGACACCAAC 59.837 50.000 0.00 0.00 0.00 3.77
3588 6226 4.515191 TGCATTCAGACACCAACTAAGTTC 59.485 41.667 0.00 0.00 0.00 3.01
3590 6228 2.750948 TCAGACACCAACTAAGTTCGC 58.249 47.619 0.00 0.00 0.00 4.70
3665 6303 8.364142 CCTGGTCATATTAAACAGAACCAAAAA 58.636 33.333 2.11 0.00 0.00 1.94
3694 6332 2.093973 ACCAGGACTTACTGATCAAGCG 60.094 50.000 0.00 0.00 40.97 4.68
3842 6480 2.849502 GCAAGACAACGAAACCTCAACG 60.850 50.000 0.00 0.00 0.00 4.10
3844 6482 3.107642 AGACAACGAAACCTCAACGAT 57.892 42.857 0.00 0.00 0.00 3.73
3855 6493 1.354040 CTCAACGATCTGGACACAGC 58.646 55.000 0.00 0.00 44.54 4.40
3884 6525 8.985315 TGGTCTGCATAAATCTGAAATTCTAT 57.015 30.769 0.00 0.00 0.00 1.98
3940 6581 0.762418 TGTCCATCTCCACCACGTTT 59.238 50.000 0.00 0.00 0.00 3.60
3982 6623 1.983907 CTTCGTCACAGACATCGCG 59.016 57.895 0.00 0.00 32.09 5.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.814457 GAGCTCCTGCGAGAAGAAGA 59.186 55.000 0.87 0.00 45.42 2.87
1 2 0.817013 AGAGCTCCTGCGAGAAGAAG 59.183 55.000 10.93 0.00 45.42 2.85
2 3 1.261480 AAGAGCTCCTGCGAGAAGAA 58.739 50.000 10.93 0.00 45.42 2.52
3 4 1.261480 AAAGAGCTCCTGCGAGAAGA 58.739 50.000 10.93 0.00 45.42 2.87
4 5 2.091852 AAAAGAGCTCCTGCGAGAAG 57.908 50.000 10.93 0.00 45.42 2.85
5 6 3.678056 TTAAAAGAGCTCCTGCGAGAA 57.322 42.857 10.93 0.00 45.42 2.87
6 7 3.735208 CGATTAAAAGAGCTCCTGCGAGA 60.735 47.826 10.93 0.00 45.42 4.04
7 8 2.537625 CGATTAAAAGAGCTCCTGCGAG 59.462 50.000 10.93 0.00 45.42 5.03
8 9 2.540515 CGATTAAAAGAGCTCCTGCGA 58.459 47.619 10.93 0.00 45.42 5.10
9 10 1.004504 GCGATTAAAAGAGCTCCTGCG 60.005 52.381 10.93 6.25 45.42 5.18
10 11 2.009774 TGCGATTAAAAGAGCTCCTGC 58.990 47.619 10.93 3.79 40.05 4.85
11 12 4.125703 AGATGCGATTAAAAGAGCTCCTG 58.874 43.478 10.93 0.00 0.00 3.86
12 13 4.376146 GAGATGCGATTAAAAGAGCTCCT 58.624 43.478 10.93 0.00 0.00 3.69
13 14 3.496507 GGAGATGCGATTAAAAGAGCTCC 59.503 47.826 10.93 0.00 33.45 4.70
14 15 3.183373 CGGAGATGCGATTAAAAGAGCTC 59.817 47.826 5.27 5.27 0.00 4.09
15 16 3.126831 CGGAGATGCGATTAAAAGAGCT 58.873 45.455 0.00 0.00 0.00 4.09
16 17 2.348966 GCGGAGATGCGATTAAAAGAGC 60.349 50.000 0.00 0.00 0.00 4.09
17 18 2.866156 TGCGGAGATGCGATTAAAAGAG 59.134 45.455 0.00 0.00 37.81 2.85
18 19 2.899976 TGCGGAGATGCGATTAAAAGA 58.100 42.857 0.00 0.00 37.81 2.52
19 20 3.496130 AGATGCGGAGATGCGATTAAAAG 59.504 43.478 0.00 0.00 37.81 2.27
20 21 3.466836 AGATGCGGAGATGCGATTAAAA 58.533 40.909 0.00 0.00 37.81 1.52
21 22 3.111853 AGATGCGGAGATGCGATTAAA 57.888 42.857 0.00 0.00 37.81 1.52
22 23 2.820059 AGATGCGGAGATGCGATTAA 57.180 45.000 0.00 0.00 37.81 1.40
23 24 3.934457 TTAGATGCGGAGATGCGATTA 57.066 42.857 0.00 0.00 37.81 1.75
24 25 2.820059 TTAGATGCGGAGATGCGATT 57.180 45.000 0.00 0.00 37.81 3.34
25 26 3.325293 AATTAGATGCGGAGATGCGAT 57.675 42.857 0.00 0.00 37.81 4.58
26 27 2.820059 AATTAGATGCGGAGATGCGA 57.180 45.000 0.00 0.00 37.81 5.10
27 28 4.211164 TGTTAAATTAGATGCGGAGATGCG 59.789 41.667 0.00 0.00 37.81 4.73
28 29 5.673337 TGTTAAATTAGATGCGGAGATGC 57.327 39.130 0.00 0.00 0.00 3.91
29 30 7.425577 TCATGTTAAATTAGATGCGGAGATG 57.574 36.000 0.00 0.00 0.00 2.90
30 31 7.716998 ACTTCATGTTAAATTAGATGCGGAGAT 59.283 33.333 0.00 0.00 0.00 2.75
31 32 7.047891 ACTTCATGTTAAATTAGATGCGGAGA 58.952 34.615 0.00 0.00 0.00 3.71
32 33 7.251704 ACTTCATGTTAAATTAGATGCGGAG 57.748 36.000 0.00 0.00 0.00 4.63
33 34 7.201696 GGAACTTCATGTTAAATTAGATGCGGA 60.202 37.037 0.00 0.00 39.30 5.54
34 35 6.912591 GGAACTTCATGTTAAATTAGATGCGG 59.087 38.462 0.00 0.00 39.30 5.69
35 36 6.628856 CGGAACTTCATGTTAAATTAGATGCG 59.371 38.462 0.00 0.00 39.30 4.73
36 37 7.472543 ACGGAACTTCATGTTAAATTAGATGC 58.527 34.615 0.00 0.00 39.30 3.91
37 38 9.277565 CAACGGAACTTCATGTTAAATTAGATG 57.722 33.333 0.00 0.00 39.30 2.90
38 39 9.226606 TCAACGGAACTTCATGTTAAATTAGAT 57.773 29.630 0.00 0.00 39.30 1.98
39 40 8.610248 TCAACGGAACTTCATGTTAAATTAGA 57.390 30.769 0.00 0.00 39.30 2.10
40 41 9.840427 ATTCAACGGAACTTCATGTTAAATTAG 57.160 29.630 0.00 0.00 39.30 1.73
41 42 9.834628 GATTCAACGGAACTTCATGTTAAATTA 57.165 29.630 0.00 0.00 39.30 1.40
42 43 8.576442 AGATTCAACGGAACTTCATGTTAAATT 58.424 29.630 0.00 0.00 39.30 1.82
43 44 8.110860 AGATTCAACGGAACTTCATGTTAAAT 57.889 30.769 0.00 0.00 39.30 1.40
44 45 7.504924 AGATTCAACGGAACTTCATGTTAAA 57.495 32.000 0.00 0.00 39.30 1.52
45 46 7.333423 CCTAGATTCAACGGAACTTCATGTTAA 59.667 37.037 0.00 0.00 39.30 2.01
46 47 6.816640 CCTAGATTCAACGGAACTTCATGTTA 59.183 38.462 0.00 0.00 39.30 2.41
47 48 5.643777 CCTAGATTCAACGGAACTTCATGTT 59.356 40.000 0.00 0.00 42.38 2.71
48 49 5.046591 TCCTAGATTCAACGGAACTTCATGT 60.047 40.000 0.00 0.00 35.46 3.21
49 50 5.419542 TCCTAGATTCAACGGAACTTCATG 58.580 41.667 0.00 0.00 35.46 3.07
50 51 5.677319 TCCTAGATTCAACGGAACTTCAT 57.323 39.130 0.00 0.00 35.46 2.57
51 52 5.186992 TGATCCTAGATTCAACGGAACTTCA 59.813 40.000 0.00 0.00 35.46 3.02
52 53 5.661458 TGATCCTAGATTCAACGGAACTTC 58.339 41.667 0.00 0.00 35.46 3.01
53 54 5.677319 TGATCCTAGATTCAACGGAACTT 57.323 39.130 0.00 0.00 35.46 2.66
54 55 5.453903 CCATGATCCTAGATTCAACGGAACT 60.454 44.000 0.00 0.00 35.46 3.01
55 56 4.752101 CCATGATCCTAGATTCAACGGAAC 59.248 45.833 0.00 0.00 35.46 3.62
56 57 4.653801 TCCATGATCCTAGATTCAACGGAA 59.346 41.667 0.00 0.00 37.45 4.30
57 58 4.039245 GTCCATGATCCTAGATTCAACGGA 59.961 45.833 0.00 2.33 0.00 4.69
58 59 4.039730 AGTCCATGATCCTAGATTCAACGG 59.960 45.833 0.00 0.00 0.00 4.44
59 60 5.207110 AGTCCATGATCCTAGATTCAACG 57.793 43.478 0.00 0.00 0.00 4.10
60 61 5.226396 CGAGTCCATGATCCTAGATTCAAC 58.774 45.833 0.00 0.00 0.00 3.18
61 62 4.281941 CCGAGTCCATGATCCTAGATTCAA 59.718 45.833 0.00 0.00 0.00 2.69
62 63 3.829026 CCGAGTCCATGATCCTAGATTCA 59.171 47.826 0.00 0.00 0.00 2.57
63 64 3.367910 GCCGAGTCCATGATCCTAGATTC 60.368 52.174 0.00 0.00 0.00 2.52
64 65 2.564947 GCCGAGTCCATGATCCTAGATT 59.435 50.000 0.00 0.00 0.00 2.40
65 66 2.175202 GCCGAGTCCATGATCCTAGAT 58.825 52.381 0.00 0.00 0.00 1.98
66 67 1.145945 AGCCGAGTCCATGATCCTAGA 59.854 52.381 0.00 0.00 0.00 2.43
67 68 1.626686 AGCCGAGTCCATGATCCTAG 58.373 55.000 0.00 0.00 0.00 3.02
68 69 2.088104 AAGCCGAGTCCATGATCCTA 57.912 50.000 0.00 0.00 0.00 2.94
69 70 1.207791 AAAGCCGAGTCCATGATCCT 58.792 50.000 0.00 0.00 0.00 3.24
70 71 2.044123 AAAAGCCGAGTCCATGATCC 57.956 50.000 0.00 0.00 0.00 3.36
71 72 3.531538 TGTAAAAGCCGAGTCCATGATC 58.468 45.455 0.00 0.00 0.00 2.92
72 73 3.627395 TGTAAAAGCCGAGTCCATGAT 57.373 42.857 0.00 0.00 0.00 2.45
73 74 3.531538 GATGTAAAAGCCGAGTCCATGA 58.468 45.455 0.00 0.00 0.00 3.07
74 75 2.614057 GGATGTAAAAGCCGAGTCCATG 59.386 50.000 0.00 0.00 0.00 3.66
75 76 2.238646 TGGATGTAAAAGCCGAGTCCAT 59.761 45.455 0.00 0.00 37.03 3.41
76 77 1.626321 TGGATGTAAAAGCCGAGTCCA 59.374 47.619 0.00 0.00 37.03 4.02
77 78 2.396590 TGGATGTAAAAGCCGAGTCC 57.603 50.000 0.00 0.00 37.03 3.85
78 79 2.678336 CCTTGGATGTAAAAGCCGAGTC 59.322 50.000 0.00 0.00 43.53 3.36
79 80 2.711542 CCTTGGATGTAAAAGCCGAGT 58.288 47.619 0.00 0.00 43.53 4.18
80 81 1.401905 GCCTTGGATGTAAAAGCCGAG 59.598 52.381 0.00 0.00 44.51 4.63
81 82 1.459450 GCCTTGGATGTAAAAGCCGA 58.541 50.000 0.00 0.00 37.03 5.54
82 83 0.455815 GGCCTTGGATGTAAAAGCCG 59.544 55.000 0.00 0.00 37.03 5.52
83 84 1.478105 CAGGCCTTGGATGTAAAAGCC 59.522 52.381 0.00 0.00 33.66 4.35
84 85 2.446435 TCAGGCCTTGGATGTAAAAGC 58.554 47.619 0.00 0.00 0.00 3.51
85 86 5.221126 GCTATTCAGGCCTTGGATGTAAAAG 60.221 44.000 0.00 0.00 0.00 2.27
86 87 4.644685 GCTATTCAGGCCTTGGATGTAAAA 59.355 41.667 0.00 0.00 0.00 1.52
87 88 4.207165 GCTATTCAGGCCTTGGATGTAAA 58.793 43.478 0.00 0.00 0.00 2.01
88 89 3.201930 TGCTATTCAGGCCTTGGATGTAA 59.798 43.478 0.00 0.00 0.00 2.41
89 90 2.777114 TGCTATTCAGGCCTTGGATGTA 59.223 45.455 0.00 0.00 0.00 2.29
90 91 1.565759 TGCTATTCAGGCCTTGGATGT 59.434 47.619 0.00 0.00 0.00 3.06
91 92 2.353357 TGCTATTCAGGCCTTGGATG 57.647 50.000 0.00 0.00 0.00 3.51
92 93 2.941480 CTTGCTATTCAGGCCTTGGAT 58.059 47.619 0.00 1.32 0.00 3.41
93 94 1.683011 GCTTGCTATTCAGGCCTTGGA 60.683 52.381 0.00 0.00 41.43 3.53
94 95 0.743097 GCTTGCTATTCAGGCCTTGG 59.257 55.000 0.00 0.00 41.43 3.61
95 96 1.466856 TGCTTGCTATTCAGGCCTTG 58.533 50.000 0.00 0.00 46.08 3.61
96 97 2.220653 TTGCTTGCTATTCAGGCCTT 57.779 45.000 0.00 0.00 46.08 4.35
97 98 2.449137 ATTGCTTGCTATTCAGGCCT 57.551 45.000 0.00 0.00 46.08 5.19
98 99 2.223900 GGAATTGCTTGCTATTCAGGCC 60.224 50.000 23.22 0.00 46.08 5.19
99 100 2.428171 TGGAATTGCTTGCTATTCAGGC 59.572 45.455 23.22 12.02 46.73 4.85
100 101 4.082081 TGTTGGAATTGCTTGCTATTCAGG 60.082 41.667 23.22 0.00 33.43 3.86
101 102 5.063180 TGTTGGAATTGCTTGCTATTCAG 57.937 39.130 23.22 0.00 33.43 3.02
102 103 4.523943 ACTGTTGGAATTGCTTGCTATTCA 59.476 37.500 23.22 12.02 33.43 2.57
103 104 5.064441 ACTGTTGGAATTGCTTGCTATTC 57.936 39.130 17.09 17.09 0.00 1.75
104 105 4.379813 CGACTGTTGGAATTGCTTGCTATT 60.380 41.667 0.00 2.27 0.00 1.73
105 106 3.127548 CGACTGTTGGAATTGCTTGCTAT 59.872 43.478 0.00 0.00 0.00 2.97
106 107 2.483877 CGACTGTTGGAATTGCTTGCTA 59.516 45.455 0.00 0.00 0.00 3.49
136 137 1.372872 GCCACGGTTCCAATGTTGC 60.373 57.895 0.00 0.00 0.00 4.17
316 351 3.895025 CAACAGCTGCTATGGCGT 58.105 55.556 15.27 0.00 42.25 5.68
437 500 3.919223 ACGAACGGATAGATAGGCTTC 57.081 47.619 0.00 0.00 0.00 3.86
441 504 4.832590 AGACAACGAACGGATAGATAGG 57.167 45.455 0.00 0.00 0.00 2.57
451 514 4.150980 TGGCATTAAAGTAGACAACGAACG 59.849 41.667 0.00 0.00 0.00 3.95
452 515 5.178809 AGTGGCATTAAAGTAGACAACGAAC 59.821 40.000 0.00 0.00 0.00 3.95
453 516 5.302360 AGTGGCATTAAAGTAGACAACGAA 58.698 37.500 0.00 0.00 0.00 3.85
454 517 4.890088 AGTGGCATTAAAGTAGACAACGA 58.110 39.130 0.00 0.00 0.00 3.85
512 579 1.364626 CGAGCATCCCTGTCAAGCAC 61.365 60.000 0.00 0.00 0.00 4.40
532 599 7.810282 GTGATAAAGAAGAAGAAGAAAAAGGCC 59.190 37.037 0.00 0.00 0.00 5.19
581 665 1.464734 GACTCGACCTGATCCTGTGA 58.535 55.000 0.00 0.00 0.00 3.58
701 795 1.134068 GGGGAGGAGCAACTGGATTAC 60.134 57.143 0.00 0.00 0.00 1.89
705 799 1.151810 AAGGGGAGGAGCAACTGGA 60.152 57.895 0.00 0.00 0.00 3.86
718 816 1.002502 GTGTCCGGGAAAGAAGGGG 60.003 63.158 0.00 0.00 0.00 4.79
722 820 0.032952 CAGACGTGTCCGGGAAAGAA 59.967 55.000 0.00 0.00 38.78 2.52
753 851 2.598632 GCGTGGATATGCTCGGCAC 61.599 63.158 18.27 0.83 43.04 5.01
754 852 1.460273 TAGCGTGGATATGCTCGGCA 61.460 55.000 18.27 1.01 45.95 5.69
755 853 1.009389 GTAGCGTGGATATGCTCGGC 61.009 60.000 18.27 11.41 45.95 5.54
833 940 1.134371 GCCCGGAGATTGATATAGGCC 60.134 57.143 0.73 0.00 32.93 5.19
840 947 4.609018 CGCGGCCCGGAGATTGAT 62.609 66.667 4.77 0.00 0.00 2.57
878 985 1.368203 TGTTAGAGATGGGAGGGGGAA 59.632 52.381 0.00 0.00 0.00 3.97
883 990 3.181450 GGATGGTTGTTAGAGATGGGAGG 60.181 52.174 0.00 0.00 0.00 4.30
982 1118 1.398958 ATCTCCTCTTCTCGCCTGGC 61.399 60.000 9.11 9.11 0.00 4.85
1260 1417 5.904080 GCGCAGACATTAATAAACAAGCTAG 59.096 40.000 0.30 0.00 0.00 3.42
1261 1418 5.501736 CGCGCAGACATTAATAAACAAGCTA 60.502 40.000 8.75 0.00 0.00 3.32
1262 1419 4.662145 GCGCAGACATTAATAAACAAGCT 58.338 39.130 0.30 0.00 0.00 3.74
1263 1420 3.478516 CGCGCAGACATTAATAAACAAGC 59.521 43.478 8.75 0.00 0.00 4.01
1404 1575 5.622180 TGTAGTTTACTTTGCCCATGTGTA 58.378 37.500 0.00 0.00 0.00 2.90
1405 1576 4.465886 TGTAGTTTACTTTGCCCATGTGT 58.534 39.130 0.00 0.00 0.00 3.72
1411 1588 5.007682 TCAGGATTGTAGTTTACTTTGCCC 58.992 41.667 0.00 0.00 0.00 5.36
1473 1657 1.069159 TCGTTCTCTTCAGACACGAGC 60.069 52.381 0.00 0.00 37.31 5.03
1593 1777 0.384309 TAAGAGGAGCGCATACCGTG 59.616 55.000 11.47 0.00 39.71 4.94
1671 1857 1.667724 CGGTCGACATAGTACCTTCGT 59.332 52.381 18.91 0.00 33.20 3.85
1672 1858 1.003116 CCGGTCGACATAGTACCTTCG 60.003 57.143 18.91 7.20 0.00 3.79
1673 1859 2.019984 ACCGGTCGACATAGTACCTTC 58.980 52.381 18.91 0.00 0.00 3.46
1690 1876 5.913514 CCGATCAGATAACAGTAACTAACCG 59.086 44.000 0.00 0.00 0.00 4.44
1696 1882 3.703420 ACGCCGATCAGATAACAGTAAC 58.297 45.455 0.00 0.00 0.00 2.50
1744 1937 7.397221 TGTCCTTGTCTTTGATCATGTAGATT 58.603 34.615 0.00 0.00 37.00 2.40
1805 1998 3.945434 GCCAGCGGCGATCATGTG 61.945 66.667 12.98 0.00 39.62 3.21
1865 2058 8.682936 AGTAATGGGAGTGAAAATACATCATC 57.317 34.615 0.00 0.00 0.00 2.92
1892 2088 1.765314 CTAGGATGAAGAGGTGGGGTG 59.235 57.143 0.00 0.00 0.00 4.61
1921 2118 0.948678 GCTGCGGTAAACCAGAACAA 59.051 50.000 0.00 0.00 35.14 2.83
1993 2190 4.040584 GGATGGGTAAGTATGAACTCTCCC 59.959 50.000 9.59 9.59 43.32 4.30
1996 2193 4.631234 TGGGATGGGTAAGTATGAACTCT 58.369 43.478 0.00 0.00 33.75 3.24
2123 2338 2.884012 TGTTTGGTATCTGCACAACCAG 59.116 45.455 9.37 0.00 43.82 4.00
2203 2418 5.805486 TGAAATGAGATGTACTGCGTACTTC 59.195 40.000 18.28 18.28 40.87 3.01
2399 2648 5.982356 TCAGACTGAATTAGATGTGGAAGG 58.018 41.667 1.64 0.00 0.00 3.46
2408 2657 5.188555 ACAGGAGCAATCAGACTGAATTAGA 59.811 40.000 9.70 0.00 33.57 2.10
2425 2674 5.948992 ATCAAGTTCAGTAAAACAGGAGC 57.051 39.130 0.00 0.00 0.00 4.70
2428 2686 9.450807 CAAAACTATCAAGTTCAGTAAAACAGG 57.549 33.333 0.00 0.00 45.37 4.00
2429 2687 8.958043 GCAAAACTATCAAGTTCAGTAAAACAG 58.042 33.333 0.00 0.00 45.37 3.16
2443 2701 7.040478 AGCAGAACAACATAGCAAAACTATCAA 60.040 33.333 0.00 0.00 39.71 2.57
2445 2703 6.846350 AGCAGAACAACATAGCAAAACTATC 58.154 36.000 0.00 0.00 39.71 2.08
2448 2706 4.022849 GGAGCAGAACAACATAGCAAAACT 60.023 41.667 0.00 0.00 0.00 2.66
2449 2707 4.022849 AGGAGCAGAACAACATAGCAAAAC 60.023 41.667 0.00 0.00 0.00 2.43
2455 2713 4.825422 TCAGAAGGAGCAGAACAACATAG 58.175 43.478 0.00 0.00 0.00 2.23
2456 2714 4.890158 TCAGAAGGAGCAGAACAACATA 57.110 40.909 0.00 0.00 0.00 2.29
2462 2720 6.809630 ACTAAAATTCAGAAGGAGCAGAAC 57.190 37.500 0.00 0.00 0.00 3.01
2633 2894 0.395311 CCAGCCTCAGGAATGCACAT 60.395 55.000 0.00 0.00 0.00 3.21
2656 5243 6.861065 ACAGAACACTGAAAATACGACATT 57.139 33.333 0.00 0.00 35.80 2.71
2744 5331 0.988832 AATTCAGTGGCCTTACCCGA 59.011 50.000 3.32 0.00 37.83 5.14
2781 5368 2.758736 AGTAGAAAGTGCTGCTCTGG 57.241 50.000 4.83 0.00 0.00 3.86
2852 5439 9.684448 ATCACATGAAGTTAAGATGATACTACG 57.316 33.333 0.00 0.00 0.00 3.51
2859 5446 6.880529 TCAGCAATCACATGAAGTTAAGATGA 59.119 34.615 0.00 0.00 0.00 2.92
2860 5447 7.080353 TCAGCAATCACATGAAGTTAAGATG 57.920 36.000 0.00 0.00 0.00 2.90
2876 5463 1.796617 GCACGCCAAAGATCAGCAATC 60.797 52.381 0.00 0.00 34.30 2.67
3079 5667 2.218953 TCTTTTAGCTACCCGATGCG 57.781 50.000 0.00 0.00 0.00 4.73
3086 5674 8.242053 GGAACATAACCTTTTCTTTTAGCTACC 58.758 37.037 0.00 0.00 0.00 3.18
3089 5677 6.569801 GCGGAACATAACCTTTTCTTTTAGCT 60.570 38.462 0.00 0.00 0.00 3.32
3102 5690 1.136169 GTCACAACGCGGAACATAACC 60.136 52.381 12.47 0.00 0.00 2.85
3264 5898 5.997384 GGAGTACTCCCTCTGTAAAGAAA 57.003 43.478 28.87 0.00 43.94 2.52
3278 5912 1.465794 ACCGCTCTCTTGGAGTACTC 58.534 55.000 14.87 14.87 43.62 2.59
3297 5931 0.105862 CCCCTCCCTGGTATGACGTA 60.106 60.000 0.00 0.00 0.00 3.57
3300 5934 0.837940 GAACCCCTCCCTGGTATGAC 59.162 60.000 0.00 0.00 34.15 3.06
3301 5935 0.327191 GGAACCCCTCCCTGGTATGA 60.327 60.000 0.00 0.00 38.44 2.15
3302 5936 2.231642 GGAACCCCTCCCTGGTATG 58.768 63.158 0.00 0.00 38.44 2.39
3303 5937 4.854042 GGAACCCCTCCCTGGTAT 57.146 61.111 0.00 0.00 38.44 2.73
3319 5953 1.619704 GGAAGGATTGTTCCCTTGGGG 60.620 57.143 5.78 0.00 43.59 4.96
3320 5954 1.852633 GGAAGGATTGTTCCCTTGGG 58.147 55.000 0.00 0.00 43.59 4.12
3326 5960 3.621558 CACCTAAGGGAAGGATTGTTCC 58.378 50.000 0.00 0.00 44.81 3.62
3327 5961 3.010250 ACCACCTAAGGGAAGGATTGTTC 59.990 47.826 0.00 0.00 39.15 3.18
3328 5962 2.993863 ACCACCTAAGGGAAGGATTGTT 59.006 45.455 0.00 0.00 39.15 2.83
3329 5963 2.308866 CACCACCTAAGGGAAGGATTGT 59.691 50.000 0.00 0.00 39.15 2.71
3330 5964 2.308866 ACACCACCTAAGGGAAGGATTG 59.691 50.000 0.00 0.00 39.15 2.67
3331 5965 2.576648 GACACCACCTAAGGGAAGGATT 59.423 50.000 0.00 0.00 39.15 3.01
3332 5966 2.197465 GACACCACCTAAGGGAAGGAT 58.803 52.381 0.00 0.00 39.15 3.24
3333 5967 1.151413 AGACACCACCTAAGGGAAGGA 59.849 52.381 0.00 0.00 39.15 3.36
3334 5968 1.657804 AGACACCACCTAAGGGAAGG 58.342 55.000 0.00 0.00 42.82 3.46
3335 5969 3.368116 CGTTAGACACCACCTAAGGGAAG 60.368 52.174 0.00 0.00 36.25 3.46
3336 5970 2.564062 CGTTAGACACCACCTAAGGGAA 59.436 50.000 0.00 0.00 36.25 3.97
3337 5971 2.173519 CGTTAGACACCACCTAAGGGA 58.826 52.381 0.00 0.00 36.25 4.20
3338 5972 2.165845 CTCGTTAGACACCACCTAAGGG 59.834 54.545 0.00 0.00 34.54 3.95
3339 5973 2.824341 ACTCGTTAGACACCACCTAAGG 59.176 50.000 0.00 0.00 34.87 2.69
3340 5974 3.504906 TCACTCGTTAGACACCACCTAAG 59.495 47.826 0.00 0.00 0.00 2.18
3341 5975 3.489355 TCACTCGTTAGACACCACCTAA 58.511 45.455 0.00 0.00 0.00 2.69
3342 5976 3.144657 TCACTCGTTAGACACCACCTA 57.855 47.619 0.00 0.00 0.00 3.08
3343 5977 1.991121 TCACTCGTTAGACACCACCT 58.009 50.000 0.00 0.00 0.00 4.00
3344 5978 2.401351 GTTCACTCGTTAGACACCACC 58.599 52.381 0.00 0.00 0.00 4.61
3345 5979 2.049228 CGTTCACTCGTTAGACACCAC 58.951 52.381 0.00 0.00 0.00 4.16
3346 5980 1.948834 TCGTTCACTCGTTAGACACCA 59.051 47.619 0.00 0.00 0.00 4.17
3347 5981 2.693797 TCGTTCACTCGTTAGACACC 57.306 50.000 0.00 0.00 0.00 4.16
3348 5982 3.979495 ACAATCGTTCACTCGTTAGACAC 59.021 43.478 0.00 0.00 0.00 3.67
3349 5983 3.978855 CACAATCGTTCACTCGTTAGACA 59.021 43.478 0.00 0.00 0.00 3.41
3350 5984 3.979495 ACACAATCGTTCACTCGTTAGAC 59.021 43.478 0.00 0.00 0.00 2.59
3357 5991 4.201871 TGGTCAAAACACAATCGTTCACTC 60.202 41.667 0.00 0.00 0.00 3.51
3363 5997 6.370166 ACAAATTTTGGTCAAAACACAATCGT 59.630 30.769 13.42 1.02 42.32 3.73
3383 6017 4.298332 GTGATCGGAAGTGCAAAACAAAT 58.702 39.130 0.00 0.00 0.00 2.32
3422 6056 3.015327 GCTGACAGCCATGAGAGAAAAT 58.985 45.455 17.01 0.00 34.48 1.82
3439 6073 3.765381 TGTTGGAATTGATCTTGGCTGA 58.235 40.909 0.00 0.00 0.00 4.26
3581 6219 1.676014 CCAGTCCCCTTGCGAACTTAG 60.676 57.143 0.00 0.00 0.00 2.18
3588 6226 0.821711 TTTTGTCCAGTCCCCTTGCG 60.822 55.000 0.00 0.00 0.00 4.85
3590 6228 0.951558 CGTTTTGTCCAGTCCCCTTG 59.048 55.000 0.00 0.00 0.00 3.61
3665 6303 4.228824 TCAGTAAGTCCTGGTGGTAGTTT 58.771 43.478 0.00 0.00 33.14 2.66
3694 6332 0.745845 ATGAGCCTGGTCGTGCATTC 60.746 55.000 0.00 0.00 0.00 2.67
3842 6480 1.271054 ACCAGTTGCTGTGTCCAGATC 60.271 52.381 0.00 0.00 41.50 2.75
3844 6482 0.106708 GACCAGTTGCTGTGTCCAGA 59.893 55.000 0.00 0.00 41.50 3.86
3855 6493 5.885230 TTCAGATTTATGCAGACCAGTTG 57.115 39.130 0.00 0.00 0.00 3.16
3884 6525 7.944729 AACAAGAGGTACGTAATAAGGTAGA 57.055 36.000 0.00 0.00 0.00 2.59
3940 6581 2.031012 CGTGGCAGAGACAAGGCA 59.969 61.111 0.00 0.00 38.03 4.75
3982 6623 2.586792 CTAGTGCACCAGGCCTCC 59.413 66.667 14.63 0.00 43.89 4.30


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

AutoCloner maintained by Alex Coulton.