Multiple sequence alignment - TraesCS1A01G193100

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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 TraesCS1A01G193100 chr1A 100.000 4497 0 0 1 4497 348847703 348852199 0.000000e+00 8305.0
1 TraesCS1A01G193100 chr1D 97.911 1484 27 3 790 2271 276749030 276750511 0.000000e+00 2566.0
2 TraesCS1A01G193100 chr1D 91.584 606 40 6 2378 2978 276750514 276751113 0.000000e+00 826.0
3 TraesCS1A01G193100 chr1D 88.889 486 54 0 1055 1540 276719347 276719832 2.320000e-167 599.0
4 TraesCS1A01G193100 chr1D 81.658 567 81 17 30 585 464251911 464251357 2.470000e-122 449.0
5 TraesCS1A01G193100 chr1D 89.305 374 16 8 4146 4497 276770767 276771138 8.870000e-122 448.0
6 TraesCS1A01G193100 chr1D 85.928 334 27 6 3018 3332 276751109 276751441 5.570000e-89 339.0
7 TraesCS1A01G193100 chr1D 79.294 425 50 26 3753 4161 276769669 276770071 3.450000e-66 263.0
8 TraesCS1A01G193100 chr1D 88.028 142 14 2 3620 3760 276753284 276753423 1.000000e-36 165.0
9 TraesCS1A01G193100 chr1D 88.550 131 11 4 631 759 276748817 276748945 6.020000e-34 156.0
10 TraesCS1A01G193100 chr1B 95.333 857 39 1 1416 2271 375859021 375859877 0.000000e+00 1360.0
11 TraesCS1A01G193100 chr1B 86.904 985 76 31 3538 4497 375861030 375861986 0.000000e+00 1055.0
12 TraesCS1A01G193100 chr1B 93.838 568 33 1 864 1429 375856719 375857286 0.000000e+00 854.0
13 TraesCS1A01G193100 chr1B 93.241 577 31 5 2407 2978 375859901 375860474 0.000000e+00 843.0
14 TraesCS1A01G193100 chr1B 83.396 530 60 18 3018 3532 375860470 375860986 2.450000e-127 466.0
15 TraesCS1A01G193100 chr1B 96.429 112 4 0 2263 2374 687253938 687254049 7.680000e-43 185.0
16 TraesCS1A01G193100 chr2B 80.623 578 81 24 28 587 438881767 438881203 6.960000e-113 418.0
17 TraesCS1A01G193100 chr2B 89.394 132 9 5 2246 2374 30654844 30654715 1.290000e-35 161.0
18 TraesCS1A01G193100 chr7D 80.438 593 73 29 22 586 609407741 609408318 3.240000e-111 412.0
19 TraesCS1A01G193100 chrUn 80.565 566 82 20 28 579 433904926 433904375 1.160000e-110 411.0
20 TraesCS1A01G193100 chr3A 80.526 570 82 21 25 579 227980271 227980826 1.160000e-110 411.0
21 TraesCS1A01G193100 chr3A 80.141 569 85 20 25 579 227981096 227981650 2.520000e-107 399.0
22 TraesCS1A01G193100 chr3A 93.548 124 6 2 2252 2374 581267906 581268028 2.760000e-42 183.0
23 TraesCS1A01G193100 chr3A 82.576 132 18 5 2245 2374 15608267 15608395 1.320000e-20 111.0
24 TraesCS1A01G193100 chr2D 81.518 514 69 22 4 506 568269772 568270270 2.520000e-107 399.0
25 TraesCS1A01G193100 chr2D 95.455 44 2 0 2976 3019 590238979 590238936 2.240000e-08 71.3
26 TraesCS1A01G193100 chr3D 82.195 483 67 14 31 505 475298737 475298266 9.060000e-107 398.0
27 TraesCS1A01G193100 chr3D 92.424 132 7 3 2258 2388 134497299 134497428 7.680000e-43 185.0
28 TraesCS1A01G193100 chr3D 92.913 127 7 2 2250 2376 433565979 433566103 2.760000e-42 183.0
29 TraesCS1A01G193100 chr4B 78.268 589 87 28 22 586 110289942 110289371 1.550000e-89 340.0
30 TraesCS1A01G193100 chr4B 80.303 132 24 2 1022 1152 110252294 110252424 1.030000e-16 99.0
31 TraesCS1A01G193100 chr4B 97.561 41 1 0 2976 3016 70256631 70256671 2.240000e-08 71.3
32 TraesCS1A01G193100 chr7B 76.291 426 68 27 342 751 107086075 107086483 3.550000e-46 196.0
33 TraesCS1A01G193100 chr7B 76.758 327 50 23 447 759 489413450 489413764 4.660000e-35 159.0
34 TraesCS1A01G193100 chr4A 95.833 120 3 2 2265 2383 281354302 281354420 4.590000e-45 193.0
35 TraesCS1A01G193100 chr4A 89.630 135 10 4 2246 2378 366478503 366478635 7.740000e-38 169.0
36 TraesCS1A01G193100 chr5D 98.131 107 2 0 2268 2374 29168310 29168204 2.140000e-43 187.0
37 TraesCS1A01G193100 chr5D 94.215 121 5 2 2257 2376 424123538 424123657 2.760000e-42 183.0
38 TraesCS1A01G193100 chr5D 97.500 40 1 0 2977 3016 381914488 381914449 8.070000e-08 69.4
39 TraesCS1A01G193100 chr5D 97.436 39 1 0 2978 3016 56125640 56125678 2.900000e-07 67.6
40 TraesCS1A01G193100 chr5D 95.122 41 2 0 2976 3016 69354264 69354224 1.040000e-06 65.8
41 TraesCS1A01G193100 chr2A 93.496 123 6 2 2259 2380 469455716 469455595 9.940000e-42 182.0
42 TraesCS1A01G193100 chr2A 87.879 132 10 6 2246 2374 728810362 728810234 2.800000e-32 150.0
43 TraesCS1A01G193100 chr2A 97.500 40 1 0 2977 3016 733925427 733925466 8.070000e-08 69.4
44 TraesCS1A01G193100 chr6A 94.783 115 6 0 2260 2374 20748515 20748401 3.570000e-41 180.0
45 TraesCS1A01G193100 chr3B 86.719 128 15 2 2249 2374 593563562 593563689 1.690000e-29 141.0
46 TraesCS1A01G193100 chr3B 73.475 377 82 16 2472 2842 20544909 20545273 4.720000e-25 126.0
47 TraesCS1A01G193100 chr7A 82.090 134 19 5 2247 2377 55874178 55874047 4.760000e-20 110.0
48 TraesCS1A01G193100 chr5B 82.677 127 19 3 2249 2374 11766897 11766773 4.760000e-20 110.0
49 TraesCS1A01G193100 chr5B 93.182 44 3 0 2973 3016 1739572 1739529 1.040000e-06 65.8
50 TraesCS1A01G193100 chr5A 93.182 44 3 0 2973 3016 10910 10867 1.040000e-06 65.8
51 TraesCS1A01G193100 chr6B 93.182 44 2 1 2972 3015 601132187 601132145 3.760000e-06 63.9


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 TraesCS1A01G193100 chr1A 348847703 348852199 4496 False 8305.0 8305 100.0000 1 4497 1 chr1A.!!$F1 4496
1 TraesCS1A01G193100 chr1D 276748817 276753423 4606 False 810.4 2566 90.4002 631 3760 5 chr1D.!!$F2 3129
2 TraesCS1A01G193100 chr1D 464251357 464251911 554 True 449.0 449 81.6580 30 585 1 chr1D.!!$R1 555
3 TraesCS1A01G193100 chr1D 276769669 276771138 1469 False 355.5 448 84.2995 3753 4497 2 chr1D.!!$F3 744
4 TraesCS1A01G193100 chr1B 375856719 375861986 5267 False 915.6 1360 90.5424 864 4497 5 chr1B.!!$F2 3633
5 TraesCS1A01G193100 chr2B 438881203 438881767 564 True 418.0 418 80.6230 28 587 1 chr2B.!!$R2 559
6 TraesCS1A01G193100 chr7D 609407741 609408318 577 False 412.0 412 80.4380 22 586 1 chr7D.!!$F1 564
7 TraesCS1A01G193100 chrUn 433904375 433904926 551 True 411.0 411 80.5650 28 579 1 chrUn.!!$R1 551
8 TraesCS1A01G193100 chr3A 227980271 227981650 1379 False 405.0 411 80.3335 25 579 2 chr3A.!!$F3 554
9 TraesCS1A01G193100 chr4B 110289371 110289942 571 True 340.0 340 78.2680 22 586 1 chr4B.!!$R1 564

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
700 1653 0.476611 AAGGAGGTTGGAGCTTCCCT 60.477 55.000 0.00 0.0 35.03 4.20 F
953 1962 0.788995 ATATCGCTCGTACCGTCTCG 59.211 55.000 0.00 0.0 0.00 4.04 F
2245 5006 1.067354 CAAATCTGAAACCCTGCTGGC 60.067 52.381 3.63 0.0 37.83 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2341 5102 1.274167 TCCGAATTACTTGTCGCAGGT 59.726 47.619 0.00 0.91 35.93 4.00 R
2342 5103 2.004583 TCCGAATTACTTGTCGCAGG 57.995 50.000 0.00 0.00 35.93 4.85 R
3654 7992 0.035152 TGCCATGGCCTTGTACTGAG 60.035 55.000 33.44 2.36 41.09 3.35 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
110 112 8.440059 GTGATCAACATTTTCTTGTATACACGA 58.560 33.333 4.68 6.51 0.00 4.35
115 117 9.605955 CAACATTTTCTTGTATACACGATCAAA 57.394 29.630 12.36 11.06 0.00 2.69
208 255 9.959775 TTTTTCAAAATACACGTTCAACATTTC 57.040 25.926 0.00 0.00 0.00 2.17
431 1127 9.311916 CTCAACATTTTCAAATACCTGTTCAAA 57.688 29.630 0.00 0.00 0.00 2.69
593 1546 9.950680 ACTTGTTCAACACATTTTTATAGAGTG 57.049 29.630 0.00 0.00 34.43 3.51
669 1622 9.631452 AAAAAGAAAACAGAGAACAGAAAGAAG 57.369 29.630 0.00 0.00 0.00 2.85
673 1626 9.014297 AGAAAACAGAGAACAGAAAGAAGAAAA 57.986 29.630 0.00 0.00 0.00 2.29
674 1627 9.283420 GAAAACAGAGAACAGAAAGAAGAAAAG 57.717 33.333 0.00 0.00 0.00 2.27
675 1628 6.370433 ACAGAGAACAGAAAGAAGAAAAGC 57.630 37.500 0.00 0.00 0.00 3.51
688 1641 5.204292 AGAAGAAAAGCAGAAAAAGGAGGT 58.796 37.500 0.00 0.00 0.00 3.85
700 1653 0.476611 AAGGAGGTTGGAGCTTCCCT 60.477 55.000 0.00 0.00 35.03 4.20
703 1656 1.536662 AGGTTGGAGCTTCCCTCGT 60.537 57.895 0.00 0.00 41.71 4.18
709 1662 3.672295 GAGCTTCCCTCGTGGCTGG 62.672 68.421 0.00 0.00 35.01 4.85
759 1713 2.183046 GAGGCTGCCGTCTGTCTC 59.817 66.667 13.96 0.00 36.10 3.36
911 1920 1.979155 CCGTCACTCTCAGCCTCCA 60.979 63.158 0.00 0.00 0.00 3.86
932 1941 3.402681 ACCCATCTCCGCCTGGTG 61.403 66.667 0.00 0.00 36.30 4.17
953 1962 0.788995 ATATCGCTCGTACCGTCTCG 59.211 55.000 0.00 0.00 0.00 4.04
982 1991 4.514577 CAAGCCGATCCGACGCCT 62.515 66.667 0.00 0.00 0.00 5.52
1016 2025 1.078848 GAATGCCTGAGAGCGTGGT 60.079 57.895 0.00 0.00 34.65 4.16
1228 2237 4.037446 TCTGGTTTGTTAATTCGCTGCTTT 59.963 37.500 0.00 0.00 0.00 3.51
1290 2301 1.453762 CCTACCTCGACGACCCATCC 61.454 65.000 0.00 0.00 0.00 3.51
1460 4220 4.438744 CGCTGGTATGAAATTTGAGGAACC 60.439 45.833 0.00 0.00 0.00 3.62
2002 4763 2.627863 TGTATGTTGCCAATTCGCAC 57.372 45.000 0.00 0.00 38.83 5.34
2021 4782 5.088739 CGCACTTGAACCATTATGTTTCTC 58.911 41.667 4.26 0.00 0.00 2.87
2245 5006 1.067354 CAAATCTGAAACCCTGCTGGC 60.067 52.381 3.63 0.00 37.83 4.85
2264 5025 3.054139 TGGCAGCTTCTATTCCATTCAGT 60.054 43.478 0.00 0.00 0.00 3.41
2265 5026 4.164030 TGGCAGCTTCTATTCCATTCAGTA 59.836 41.667 0.00 0.00 0.00 2.74
2271 5032 9.202273 CAGCTTCTATTCCATTCAGTATTACTC 57.798 37.037 0.00 0.00 0.00 2.59
2272 5033 8.371699 AGCTTCTATTCCATTCAGTATTACTCC 58.628 37.037 0.00 0.00 0.00 3.85
2273 5034 7.604545 GCTTCTATTCCATTCAGTATTACTCCC 59.395 40.741 0.00 0.00 0.00 4.30
2274 5035 8.798975 TTCTATTCCATTCAGTATTACTCCCT 57.201 34.615 0.00 0.00 0.00 4.20
2275 5036 8.423906 TCTATTCCATTCAGTATTACTCCCTC 57.576 38.462 0.00 0.00 0.00 4.30
2276 5037 5.888982 TTCCATTCAGTATTACTCCCTCC 57.111 43.478 0.00 0.00 0.00 4.30
2277 5038 3.895656 TCCATTCAGTATTACTCCCTCCG 59.104 47.826 0.00 0.00 0.00 4.63
2278 5039 3.641906 CCATTCAGTATTACTCCCTCCGT 59.358 47.826 0.00 0.00 0.00 4.69
2279 5040 4.101119 CCATTCAGTATTACTCCCTCCGTT 59.899 45.833 0.00 0.00 0.00 4.44
2280 5041 4.996788 TTCAGTATTACTCCCTCCGTTC 57.003 45.455 0.00 0.00 0.00 3.95
2281 5042 3.294214 TCAGTATTACTCCCTCCGTTCC 58.706 50.000 0.00 0.00 0.00 3.62
2282 5043 3.028850 CAGTATTACTCCCTCCGTTCCA 58.971 50.000 0.00 0.00 0.00 3.53
2283 5044 3.449737 CAGTATTACTCCCTCCGTTCCAA 59.550 47.826 0.00 0.00 0.00 3.53
2284 5045 4.081309 CAGTATTACTCCCTCCGTTCCAAA 60.081 45.833 0.00 0.00 0.00 3.28
2285 5046 4.720273 AGTATTACTCCCTCCGTTCCAAAT 59.280 41.667 0.00 0.00 0.00 2.32
2286 5047 4.586306 ATTACTCCCTCCGTTCCAAATT 57.414 40.909 0.00 0.00 0.00 1.82
2287 5048 5.703730 ATTACTCCCTCCGTTCCAAATTA 57.296 39.130 0.00 0.00 0.00 1.40
2288 5049 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
2289 5050 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
2290 5051 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
2291 5052 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
2292 5053 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
2293 5054 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
2294 5055 3.581755 CTCCGTTCCAAATTACTCGTCA 58.418 45.455 0.00 0.00 0.00 4.35
2295 5056 3.319755 TCCGTTCCAAATTACTCGTCAC 58.680 45.455 0.00 0.00 0.00 3.67
2296 5057 3.061322 CCGTTCCAAATTACTCGTCACA 58.939 45.455 0.00 0.00 0.00 3.58
2297 5058 3.122948 CCGTTCCAAATTACTCGTCACAG 59.877 47.826 0.00 0.00 0.00 3.66
2298 5059 3.985279 CGTTCCAAATTACTCGTCACAGA 59.015 43.478 0.00 0.00 0.00 3.41
2299 5060 4.446385 CGTTCCAAATTACTCGTCACAGAA 59.554 41.667 0.00 0.00 0.00 3.02
2300 5061 5.050634 CGTTCCAAATTACTCGTCACAGAAA 60.051 40.000 0.00 0.00 0.00 2.52
2301 5062 6.347402 CGTTCCAAATTACTCGTCACAGAAAT 60.347 38.462 0.00 0.00 0.00 2.17
2302 5063 7.148705 CGTTCCAAATTACTCGTCACAGAAATA 60.149 37.037 0.00 0.00 0.00 1.40
2303 5064 7.827819 TCCAAATTACTCGTCACAGAAATAG 57.172 36.000 0.00 0.00 0.00 1.73
2304 5065 7.608153 TCCAAATTACTCGTCACAGAAATAGA 58.392 34.615 0.00 0.00 0.00 1.98
2305 5066 8.258007 TCCAAATTACTCGTCACAGAAATAGAT 58.742 33.333 0.00 0.00 0.00 1.98
2306 5067 8.331022 CCAAATTACTCGTCACAGAAATAGATG 58.669 37.037 0.00 0.00 0.00 2.90
2307 5068 8.873830 CAAATTACTCGTCACAGAAATAGATGT 58.126 33.333 0.00 0.00 0.00 3.06
2310 5071 9.900710 ATTACTCGTCACAGAAATAGATGTATC 57.099 33.333 0.00 0.00 0.00 2.24
2311 5072 7.575414 ACTCGTCACAGAAATAGATGTATCT 57.425 36.000 0.00 0.00 40.86 1.98
2312 5073 8.678593 ACTCGTCACAGAAATAGATGTATCTA 57.321 34.615 4.22 4.22 43.00 1.98
2313 5074 8.779303 ACTCGTCACAGAAATAGATGTATCTAG 58.221 37.037 7.57 0.00 42.20 2.43
2314 5075 8.904099 TCGTCACAGAAATAGATGTATCTAGA 57.096 34.615 7.57 0.00 42.20 2.43
2315 5076 9.338622 TCGTCACAGAAATAGATGTATCTAGAA 57.661 33.333 0.00 0.00 42.20 2.10
2316 5077 9.388346 CGTCACAGAAATAGATGTATCTAGAAC 57.612 37.037 0.00 0.00 42.20 3.01
2346 5107 6.537453 ACATCTAGATACATCCATACCTGC 57.463 41.667 4.54 0.00 0.00 4.85
2347 5108 5.126222 ACATCTAGATACATCCATACCTGCG 59.874 44.000 4.54 0.00 0.00 5.18
2348 5109 4.918588 TCTAGATACATCCATACCTGCGA 58.081 43.478 0.00 0.00 0.00 5.10
2349 5110 3.944055 AGATACATCCATACCTGCGAC 57.056 47.619 0.00 0.00 0.00 5.19
2350 5111 3.230976 AGATACATCCATACCTGCGACA 58.769 45.455 0.00 0.00 0.00 4.35
2351 5112 3.641436 AGATACATCCATACCTGCGACAA 59.359 43.478 0.00 0.00 0.00 3.18
2352 5113 2.315925 ACATCCATACCTGCGACAAG 57.684 50.000 0.00 0.00 0.00 3.16
2353 5114 1.555075 ACATCCATACCTGCGACAAGT 59.445 47.619 0.00 0.00 0.00 3.16
2354 5115 2.764010 ACATCCATACCTGCGACAAGTA 59.236 45.455 0.00 0.00 0.00 2.24
2355 5116 3.196901 ACATCCATACCTGCGACAAGTAA 59.803 43.478 0.00 0.00 0.00 2.24
2356 5117 4.141711 ACATCCATACCTGCGACAAGTAAT 60.142 41.667 0.00 0.00 0.00 1.89
2357 5118 4.481368 TCCATACCTGCGACAAGTAATT 57.519 40.909 0.00 0.00 0.00 1.40
2358 5119 4.439057 TCCATACCTGCGACAAGTAATTC 58.561 43.478 0.00 0.00 0.00 2.17
2359 5120 3.245284 CCATACCTGCGACAAGTAATTCG 59.755 47.826 0.00 0.00 38.31 3.34
2360 5121 1.722011 ACCTGCGACAAGTAATTCGG 58.278 50.000 0.00 0.00 35.73 4.30
2361 5122 1.274167 ACCTGCGACAAGTAATTCGGA 59.726 47.619 0.00 0.00 35.73 4.55
2362 5123 2.289195 ACCTGCGACAAGTAATTCGGAA 60.289 45.455 0.00 0.00 35.02 4.30
2363 5124 2.936498 CCTGCGACAAGTAATTCGGAAT 59.064 45.455 0.00 0.00 35.02 3.01
2364 5125 3.242413 CCTGCGACAAGTAATTCGGAATG 60.242 47.826 3.59 0.00 35.02 2.67
2365 5126 2.675844 TGCGACAAGTAATTCGGAATGG 59.324 45.455 3.59 0.00 35.73 3.16
2366 5127 2.933906 GCGACAAGTAATTCGGAATGGA 59.066 45.455 3.59 0.00 35.73 3.41
2367 5128 3.001330 GCGACAAGTAATTCGGAATGGAG 59.999 47.826 3.59 0.00 35.73 3.86
2368 5129 3.555956 CGACAAGTAATTCGGAATGGAGG 59.444 47.826 3.59 0.00 0.00 4.30
2369 5130 3.877508 GACAAGTAATTCGGAATGGAGGG 59.122 47.826 3.59 0.00 0.00 4.30
2370 5131 3.521937 ACAAGTAATTCGGAATGGAGGGA 59.478 43.478 3.59 0.00 0.00 4.20
2371 5132 4.130118 CAAGTAATTCGGAATGGAGGGAG 58.870 47.826 3.59 0.00 0.00 4.30
2372 5133 3.385115 AGTAATTCGGAATGGAGGGAGT 58.615 45.455 3.59 0.00 0.00 3.85
2373 5134 4.553678 AGTAATTCGGAATGGAGGGAGTA 58.446 43.478 3.59 0.00 0.00 2.59
2374 5135 3.840124 AATTCGGAATGGAGGGAGTAC 57.160 47.619 3.59 0.00 0.00 2.73
2375 5136 2.544844 TTCGGAATGGAGGGAGTACT 57.455 50.000 0.00 0.00 0.00 2.73
2376 5137 2.544844 TCGGAATGGAGGGAGTACTT 57.455 50.000 0.00 0.00 0.00 2.24
2400 5161 9.268268 CTTATCAAGTACTTACAAAGTTGGACA 57.732 33.333 8.04 0.00 42.81 4.02
2402 5163 8.691661 ATCAAGTACTTACAAAGTTGGACATT 57.308 30.769 8.04 0.00 42.81 2.71
2403 5164 7.925993 TCAAGTACTTACAAAGTTGGACATTG 58.074 34.615 8.04 0.00 42.81 2.82
2405 5166 8.402472 CAAGTACTTACAAAGTTGGACATTGAA 58.598 33.333 8.04 0.00 42.81 2.69
2470 5231 5.128499 CAGGGATTTTAAATGGTGCCATACA 59.872 40.000 3.90 0.00 35.31 2.29
2520 5281 3.360340 GTGGTGTCTGGCTGCTGC 61.360 66.667 7.10 7.10 38.76 5.25
2591 5352 5.946377 AGGCTTACCCTTCAACTTAGATTTG 59.054 40.000 0.00 0.00 43.06 2.32
2592 5353 5.944007 GGCTTACCCTTCAACTTAGATTTGA 59.056 40.000 0.00 0.00 0.00 2.69
2655 5416 0.874390 GAAGTCGCCATTGCAGTTGA 59.126 50.000 0.59 0.00 37.32 3.18
2670 5431 7.509141 TTGCAGTTGATTGATTTCAGTTAGA 57.491 32.000 0.00 0.00 0.00 2.10
2730 5491 4.260170 AGATGAAAGCTACAAGCCAAGAG 58.740 43.478 0.00 0.00 43.77 2.85
2738 5499 4.829492 AGCTACAAGCCAAGAGAACAATTT 59.171 37.500 0.00 0.00 43.77 1.82
2747 5508 5.572896 GCCAAGAGAACAATTTTTGGTATCG 59.427 40.000 3.79 0.00 43.11 2.92
2779 5540 5.824243 AAAGTAGTCGAAATCAAGTGTCG 57.176 39.130 0.00 0.00 36.12 4.35
2865 5626 6.770303 TGATCTTATTGACAACCAACAGAACA 59.230 34.615 0.00 0.00 37.63 3.18
2866 5627 6.618287 TCTTATTGACAACCAACAGAACAG 57.382 37.500 0.00 0.00 37.63 3.16
2871 5632 1.472480 ACAACCAACAGAACAGTGTGC 59.528 47.619 0.00 0.00 0.00 4.57
2872 5633 1.472082 CAACCAACAGAACAGTGTGCA 59.528 47.619 3.49 0.00 0.00 4.57
2928 5692 8.041323 ACACTGATTATGTTTCTTCCTCGTAAT 58.959 33.333 0.00 0.00 0.00 1.89
2978 5742 9.850628 GTAAAATTTACCAATGGAAGAAGGTAC 57.149 33.333 6.16 0.00 36.42 3.34
2980 5744 7.939784 AATTTACCAATGGAAGAAGGTACTC 57.060 36.000 6.16 0.00 38.49 2.59
2981 5745 5.431179 TTACCAATGGAAGAAGGTACTCC 57.569 43.478 6.16 0.00 38.49 3.85
2997 5761 6.838382 AGGTACTCCTTCTGTAAACAAATGT 58.162 36.000 0.00 0.00 42.12 2.71
2998 5762 7.970102 AGGTACTCCTTCTGTAAACAAATGTA 58.030 34.615 0.00 0.00 42.12 2.29
2999 5763 8.434392 AGGTACTCCTTCTGTAAACAAATGTAA 58.566 33.333 0.00 0.00 42.12 2.41
3000 5764 8.718734 GGTACTCCTTCTGTAAACAAATGTAAG 58.281 37.037 0.00 0.00 0.00 2.34
3001 5765 9.485206 GTACTCCTTCTGTAAACAAATGTAAGA 57.515 33.333 0.00 0.00 0.00 2.10
3002 5766 8.379457 ACTCCTTCTGTAAACAAATGTAAGAC 57.621 34.615 0.00 0.00 0.00 3.01
3003 5767 7.170998 ACTCCTTCTGTAAACAAATGTAAGACG 59.829 37.037 0.00 0.00 0.00 4.18
3004 5768 6.987992 TCCTTCTGTAAACAAATGTAAGACGT 59.012 34.615 0.00 0.00 0.00 4.34
3005 5769 7.496591 TCCTTCTGTAAACAAATGTAAGACGTT 59.503 33.333 0.00 0.00 0.00 3.99
3006 5770 8.126700 CCTTCTGTAAACAAATGTAAGACGTTT 58.873 33.333 0.00 0.00 37.78 3.60
3007 5771 9.498307 CTTCTGTAAACAAATGTAAGACGTTTT 57.502 29.630 0.00 0.00 35.31 2.43
3010 5774 9.377383 CTGTAAACAAATGTAAGACGTTTTAGG 57.623 33.333 0.00 0.00 35.31 2.69
3011 5775 8.891720 TGTAAACAAATGTAAGACGTTTTAGGT 58.108 29.630 0.00 0.00 35.31 3.08
3012 5776 9.373750 GTAAACAAATGTAAGACGTTTTAGGTC 57.626 33.333 0.00 0.00 35.31 3.85
3013 5777 7.556733 AACAAATGTAAGACGTTTTAGGTCA 57.443 32.000 0.00 0.00 35.31 4.02
3014 5778 6.951643 ACAAATGTAAGACGTTTTAGGTCAC 58.048 36.000 0.00 0.00 35.31 3.67
3015 5779 6.764560 ACAAATGTAAGACGTTTTAGGTCACT 59.235 34.615 0.00 0.00 35.31 3.41
3016 5780 6.780706 AATGTAAGACGTTTTAGGTCACTG 57.219 37.500 0.00 0.00 35.60 3.66
3017 5781 5.518848 TGTAAGACGTTTTAGGTCACTGA 57.481 39.130 0.00 0.00 35.60 3.41
3018 5782 5.526115 TGTAAGACGTTTTAGGTCACTGAG 58.474 41.667 0.00 0.00 35.60 3.35
3019 5783 3.662247 AGACGTTTTAGGTCACTGAGG 57.338 47.619 0.00 0.00 35.60 3.86
3020 5784 3.228453 AGACGTTTTAGGTCACTGAGGA 58.772 45.455 0.00 0.00 35.60 3.71
3069 5833 8.757877 TGGATATTTTAAATTTGGAGAAGTGGG 58.242 33.333 0.00 0.00 0.00 4.61
3090 5854 4.502950 GGGCATTCCAACATTTTGTGAAGA 60.503 41.667 0.00 0.00 35.00 2.87
3193 5957 4.196626 CACCATTGTGCATCCTTTTGAT 57.803 40.909 0.00 0.00 35.31 2.57
3217 5981 3.506067 GCTAATGCCACCATACATTACCC 59.494 47.826 0.00 0.00 37.63 3.69
3222 5986 1.766496 CCACCATACATTACCCGGACT 59.234 52.381 0.73 0.00 0.00 3.85
3227 5991 3.492656 CCATACATTACCCGGACTCACAG 60.493 52.174 0.73 0.00 0.00 3.66
3228 5992 0.902531 ACATTACCCGGACTCACAGG 59.097 55.000 0.73 0.00 0.00 4.00
3238 6018 0.535335 GACTCACAGGGGCGAATGTA 59.465 55.000 0.00 0.00 0.00 2.29
3245 6025 2.508300 ACAGGGGCGAATGTAAATAGGT 59.492 45.455 0.00 0.00 0.00 3.08
3257 6037 7.064609 CGAATGTAAATAGGTCTGCAAAAGAGA 59.935 37.037 0.00 0.00 34.84 3.10
3258 6038 7.617041 ATGTAAATAGGTCTGCAAAAGAGAC 57.383 36.000 0.00 0.00 39.38 3.36
3264 6044 4.636249 AGGTCTGCAAAAGAGACAGTTAG 58.364 43.478 5.52 0.00 41.50 2.34
3281 6062 8.652290 AGACAGTTAGGACTTTTTATCAGTTCT 58.348 33.333 0.00 0.00 34.24 3.01
3303 6085 9.486857 GTTCTATTTTAACGAAGCATCCTTTAC 57.513 33.333 0.00 0.00 0.00 2.01
3360 7627 5.095145 TCAACCATCTCAGAGATTTCCTG 57.905 43.478 10.51 6.26 31.32 3.86
3369 7636 4.569943 TCAGAGATTTCCTGTACTGCAAC 58.430 43.478 0.00 0.00 33.57 4.17
3370 7637 4.284490 TCAGAGATTTCCTGTACTGCAACT 59.716 41.667 0.00 0.00 33.57 3.16
3430 7724 9.831737 ATCAATTGTATCTTCTCGTTTCTTTTG 57.168 29.630 5.13 0.00 0.00 2.44
3512 7806 3.198872 GAGTAGTTTCAGCTGGCATACC 58.801 50.000 15.13 0.00 0.00 2.73
3516 7810 1.130561 GTTTCAGCTGGCATACCGTTC 59.869 52.381 15.13 0.00 39.70 3.95
3517 7811 0.613260 TTCAGCTGGCATACCGTTCT 59.387 50.000 15.13 0.00 39.70 3.01
3519 7813 0.729116 CAGCTGGCATACCGTTCTTG 59.271 55.000 5.57 0.00 39.70 3.02
3532 7828 5.280654 ACCGTTCTTGGTTTACAGACTTA 57.719 39.130 0.00 0.00 39.99 2.24
3533 7829 5.861727 ACCGTTCTTGGTTTACAGACTTAT 58.138 37.500 0.00 0.00 39.99 1.73
3534 7830 5.930569 ACCGTTCTTGGTTTACAGACTTATC 59.069 40.000 0.00 0.00 39.99 1.75
3535 7831 5.350640 CCGTTCTTGGTTTACAGACTTATCC 59.649 44.000 0.00 0.00 0.00 2.59
3552 7886 2.665000 CCACCAGGATCGTGTGCT 59.335 61.111 13.98 0.00 36.89 4.40
3580 7914 5.190677 CCTACCCCGTTTGTATGAAAATCT 58.809 41.667 0.00 0.00 0.00 2.40
3615 7949 2.069273 CAGCTGGACTAGGTTTGAACG 58.931 52.381 5.57 0.00 34.17 3.95
3631 7969 0.537188 AACGCCATCCTAGTCTGGTG 59.463 55.000 16.03 16.03 46.27 4.17
3634 7972 1.626356 GCCATCCTAGTCTGGTGGCA 61.626 60.000 14.78 0.00 45.23 4.92
3636 7974 0.179000 CATCCTAGTCTGGTGGCACC 59.821 60.000 29.75 29.75 39.22 5.01
3641 7979 4.626081 GTCTGGTGGCACCGCTGT 62.626 66.667 30.14 0.00 42.58 4.40
3643 7981 3.663176 CTGGTGGCACCGCTGTTG 61.663 66.667 30.14 12.61 42.58 3.33
3645 7983 2.672996 GGTGGCACCGCTGTTGAT 60.673 61.111 22.83 0.00 0.00 2.57
3654 7992 1.880027 ACCGCTGTTGATTTCCTGAAC 59.120 47.619 0.00 0.00 0.00 3.18
3678 8017 2.158755 AGTACAAGGCCATGGCATCTAC 60.159 50.000 36.56 28.41 44.11 2.59
3679 8018 0.921896 ACAAGGCCATGGCATCTACT 59.078 50.000 36.56 21.67 44.11 2.57
3682 8021 3.909995 ACAAGGCCATGGCATCTACTATA 59.090 43.478 36.56 0.00 44.11 1.31
3689 8028 6.462207 GGCCATGGCATCTACTATATCACTAG 60.462 46.154 36.56 0.00 44.11 2.57
3690 8029 6.322456 GCCATGGCATCTACTATATCACTAGA 59.678 42.308 32.08 0.00 41.49 2.43
3697 8036 8.620416 GCATCTACTATATCACTAGATGACTGG 58.380 40.741 19.27 0.00 43.42 4.00
3751 8091 1.086634 CAGGTCGGCAGCTAGCTTTC 61.087 60.000 16.46 9.90 44.79 2.62
3768 8108 4.937620 AGCTTTCGATCTTCACTTTATGCA 59.062 37.500 0.00 0.00 0.00 3.96
3793 8133 0.319728 GCTCTTGCTCTCTGGTGTCA 59.680 55.000 0.00 0.00 36.03 3.58
3806 8146 0.312102 GGTGTCAAGCTCAACAAGGC 59.688 55.000 2.93 0.00 0.00 4.35
3809 8149 1.405105 TGTCAAGCTCAACAAGGCAAC 59.595 47.619 0.00 0.00 0.00 4.17
3819 8159 4.930963 TCAACAAGGCAACACATTAACTG 58.069 39.130 0.00 0.00 41.41 3.16
3822 8162 6.488344 TCAACAAGGCAACACATTAACTGATA 59.512 34.615 0.00 0.00 41.41 2.15
3873 8224 0.759346 GACTGTGGTAGGCCTATGGG 59.241 60.000 17.38 7.59 35.27 4.00
3898 8249 3.244457 ACCTTAACTGAACTTCTTCCGGG 60.244 47.826 0.00 0.00 0.00 5.73
3908 8259 2.832733 ACTTCTTCCGGGAACTTCCTAG 59.167 50.000 5.09 2.84 36.57 3.02
3998 8366 8.999431 ACATAAATGTTACTCTCGTGATGTTTT 58.001 29.630 0.00 0.00 37.90 2.43
3999 8367 9.825972 CATAAATGTTACTCTCGTGATGTTTTT 57.174 29.630 0.00 0.00 0.00 1.94
4018 8386 5.399604 TTTTTCTTTCGAAACGGACTCTC 57.600 39.130 6.47 0.00 38.77 3.20
4019 8387 2.327081 TCTTTCGAAACGGACTCTCG 57.673 50.000 6.47 0.00 0.00 4.04
4020 8388 1.605710 TCTTTCGAAACGGACTCTCGT 59.394 47.619 6.47 0.00 46.08 4.18
4021 8389 1.714460 CTTTCGAAACGGACTCTCGTG 59.286 52.381 6.47 0.00 43.07 4.35
4022 8390 0.946528 TTCGAAACGGACTCTCGTGA 59.053 50.000 0.00 0.00 43.07 4.35
4023 8391 1.162698 TCGAAACGGACTCTCGTGAT 58.837 50.000 0.00 0.00 43.07 3.06
4024 8392 1.135774 TCGAAACGGACTCTCGTGATG 60.136 52.381 0.00 0.00 43.07 3.07
4025 8393 1.401148 CGAAACGGACTCTCGTGATGT 60.401 52.381 0.00 0.00 43.07 3.06
4026 8394 2.673833 GAAACGGACTCTCGTGATGTT 58.326 47.619 0.00 0.00 43.07 2.71
4027 8395 2.814280 AACGGACTCTCGTGATGTTT 57.186 45.000 0.00 0.00 43.07 2.83
4088 8461 1.722464 CATGCATCGTTTTGGCTGTTG 59.278 47.619 0.00 0.00 0.00 3.33
4173 9257 4.874396 GTCCGTGTCTTATTAAGAAAGGGG 59.126 45.833 25.03 16.39 46.26 4.79
4193 9277 2.269172 GGAAGAACTAGGCGTACTTGC 58.731 52.381 0.00 0.00 0.00 4.01
4195 9279 3.323243 GAAGAACTAGGCGTACTTGCAA 58.677 45.455 0.00 0.00 36.28 4.08
4212 9296 1.727857 GCAATTTGTTACAGGACCGCG 60.728 52.381 0.00 0.00 0.00 6.46
4224 9308 0.450184 GGACCGCGTGCATTAACAAT 59.550 50.000 4.92 0.00 0.00 2.71
4277 9361 3.669023 GCGTTGCTTTCAGATTGAGAAGG 60.669 47.826 0.00 0.00 0.00 3.46
4294 9378 2.203266 GGATGCCTGGCTACCTGC 60.203 66.667 21.03 3.69 41.94 4.85
4423 9529 1.939974 CGATGGAATTTCGCTCCTGA 58.060 50.000 0.00 0.00 33.77 3.86
4473 9579 7.390718 GGCTTTTATTAGTGACTGAAAAGGAGA 59.609 37.037 20.69 0.00 37.51 3.71
4474 9580 8.447053 GCTTTTATTAGTGACTGAAAAGGAGAG 58.553 37.037 20.69 6.39 37.51 3.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
98 100 8.655970 TCAGACAATTTTGATCGTGTATACAAG 58.344 33.333 7.25 9.97 0.00 3.16
110 112 7.592938 TGAATAAGCGTTCAGACAATTTTGAT 58.407 30.769 0.00 0.00 33.41 2.57
115 117 6.312399 TGTTGAATAAGCGTTCAGACAATT 57.688 33.333 11.19 0.00 39.13 2.32
403 757 8.134895 TGAACAGGTATTTGAAAATGTTGAGTC 58.865 33.333 6.09 0.00 0.00 3.36
405 759 8.870160 TTGAACAGGTATTTGAAAATGTTGAG 57.130 30.769 6.09 0.00 0.00 3.02
646 1599 8.567285 TTCTTCTTTCTGTTCTCTGTTTTCTT 57.433 30.769 0.00 0.00 0.00 2.52
669 1622 4.099419 TCCAACCTCCTTTTTCTGCTTTTC 59.901 41.667 0.00 0.00 0.00 2.29
673 1626 2.868899 CTCCAACCTCCTTTTTCTGCT 58.131 47.619 0.00 0.00 0.00 4.24
674 1627 1.270826 GCTCCAACCTCCTTTTTCTGC 59.729 52.381 0.00 0.00 0.00 4.26
675 1628 2.868899 AGCTCCAACCTCCTTTTTCTG 58.131 47.619 0.00 0.00 0.00 3.02
688 1641 3.068881 CCACGAGGGAAGCTCCAA 58.931 61.111 0.00 0.00 38.64 3.53
712 1665 4.227134 AGCTCTACATGGGCCGCG 62.227 66.667 0.00 0.00 0.00 6.46
742 1695 2.183046 GAGACAGACGGCAGCCTC 59.817 66.667 10.54 6.33 0.00 4.70
743 1696 3.753434 CGAGACAGACGGCAGCCT 61.753 66.667 10.54 0.00 0.00 4.58
751 1705 1.068250 GCCCCTATGCGAGACAGAC 59.932 63.158 0.00 0.00 0.00 3.51
785 1751 4.114997 CGAAATGTGCGGTGGGCC 62.115 66.667 0.00 0.00 42.61 5.80
786 1752 4.114997 CCGAAATGTGCGGTGGGC 62.115 66.667 0.00 0.00 43.66 5.36
956 1965 1.001393 GATCGGCTTGGGGTTGGAA 60.001 57.895 0.00 0.00 0.00 3.53
1290 2301 2.280524 TCAACGTTGAGGGGTGCG 60.281 61.111 26.53 0.00 32.50 5.34
1460 4220 3.985925 GCAGCTTGAAAAATTCAGAGTGG 59.014 43.478 0.00 0.00 41.38 4.00
2002 4763 8.660373 GTCTACAGAGAAACATAATGGTTCAAG 58.340 37.037 0.00 0.00 46.12 3.02
2021 4782 7.113658 ACCAACTATTAGGTGATGTCTACAG 57.886 40.000 10.39 0.00 33.95 2.74
2245 5006 9.202273 GAGTAATACTGAATGGAATAGAAGCTG 57.798 37.037 0.00 0.00 0.00 4.24
2264 5025 5.703730 AATTTGGAACGGAGGGAGTAATA 57.296 39.130 0.00 0.00 0.00 0.98
2265 5026 4.586306 AATTTGGAACGGAGGGAGTAAT 57.414 40.909 0.00 0.00 0.00 1.89
2271 5032 2.277084 CGAGTAATTTGGAACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
2272 5033 2.928116 GACGAGTAATTTGGAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
2273 5034 3.367025 GTGACGAGTAATTTGGAACGGAG 59.633 47.826 0.00 0.00 0.00 4.63
2274 5035 3.243805 TGTGACGAGTAATTTGGAACGGA 60.244 43.478 0.00 0.00 0.00 4.69
2275 5036 3.061322 TGTGACGAGTAATTTGGAACGG 58.939 45.455 0.00 0.00 0.00 4.44
2276 5037 3.985279 TCTGTGACGAGTAATTTGGAACG 59.015 43.478 0.00 0.00 0.00 3.95
2277 5038 5.917541 TTCTGTGACGAGTAATTTGGAAC 57.082 39.130 0.00 0.00 0.00 3.62
2278 5039 8.092068 TCTATTTCTGTGACGAGTAATTTGGAA 58.908 33.333 0.00 0.00 0.00 3.53
2279 5040 7.608153 TCTATTTCTGTGACGAGTAATTTGGA 58.392 34.615 0.00 0.00 0.00 3.53
2280 5041 7.827819 TCTATTTCTGTGACGAGTAATTTGG 57.172 36.000 0.00 0.00 0.00 3.28
2281 5042 8.873830 ACATCTATTTCTGTGACGAGTAATTTG 58.126 33.333 0.00 0.00 0.00 2.32
2284 5045 9.900710 GATACATCTATTTCTGTGACGAGTAAT 57.099 33.333 0.00 0.00 0.00 1.89
2285 5046 9.121658 AGATACATCTATTTCTGTGACGAGTAA 57.878 33.333 0.00 0.00 34.85 2.24
2286 5047 8.678593 AGATACATCTATTTCTGTGACGAGTA 57.321 34.615 0.00 0.00 34.85 2.59
2287 5048 7.575414 AGATACATCTATTTCTGTGACGAGT 57.425 36.000 0.00 0.00 34.85 4.18
2288 5049 8.994170 TCTAGATACATCTATTTCTGTGACGAG 58.006 37.037 0.00 0.00 38.60 4.18
2289 5050 8.904099 TCTAGATACATCTATTTCTGTGACGA 57.096 34.615 0.00 0.00 38.60 4.20
2290 5051 9.388346 GTTCTAGATACATCTATTTCTGTGACG 57.612 37.037 0.00 0.00 38.60 4.35
2320 5081 8.700051 GCAGGTATGGATGTATCTAGATGTATT 58.300 37.037 15.79 0.00 0.00 1.89
2321 5082 7.013750 CGCAGGTATGGATGTATCTAGATGTAT 59.986 40.741 15.79 9.11 0.00 2.29
2322 5083 6.318900 CGCAGGTATGGATGTATCTAGATGTA 59.681 42.308 15.79 4.44 0.00 2.29
2323 5084 5.126222 CGCAGGTATGGATGTATCTAGATGT 59.874 44.000 15.79 1.25 0.00 3.06
2324 5085 5.358160 TCGCAGGTATGGATGTATCTAGATG 59.642 44.000 15.79 0.00 0.00 2.90
2325 5086 5.358442 GTCGCAGGTATGGATGTATCTAGAT 59.642 44.000 10.73 10.73 0.00 1.98
2326 5087 4.700692 GTCGCAGGTATGGATGTATCTAGA 59.299 45.833 0.00 0.00 0.00 2.43
2327 5088 4.459337 TGTCGCAGGTATGGATGTATCTAG 59.541 45.833 0.00 0.00 0.00 2.43
2328 5089 4.403734 TGTCGCAGGTATGGATGTATCTA 58.596 43.478 0.00 0.00 0.00 1.98
2329 5090 3.230976 TGTCGCAGGTATGGATGTATCT 58.769 45.455 0.00 0.00 0.00 1.98
2330 5091 3.660501 TGTCGCAGGTATGGATGTATC 57.339 47.619 0.00 0.00 0.00 2.24
2331 5092 3.388024 ACTTGTCGCAGGTATGGATGTAT 59.612 43.478 0.00 0.00 0.00 2.29
2332 5093 2.764010 ACTTGTCGCAGGTATGGATGTA 59.236 45.455 0.00 0.00 0.00 2.29
2333 5094 1.555075 ACTTGTCGCAGGTATGGATGT 59.445 47.619 0.00 0.00 0.00 3.06
2334 5095 2.315925 ACTTGTCGCAGGTATGGATG 57.684 50.000 0.00 0.00 0.00 3.51
2335 5096 4.689612 ATTACTTGTCGCAGGTATGGAT 57.310 40.909 3.46 0.00 0.00 3.41
2336 5097 4.439057 GAATTACTTGTCGCAGGTATGGA 58.561 43.478 3.46 0.00 0.00 3.41
2337 5098 3.245284 CGAATTACTTGTCGCAGGTATGG 59.755 47.826 3.46 0.00 0.00 2.74
2338 5099 3.245284 CCGAATTACTTGTCGCAGGTATG 59.755 47.826 3.46 0.00 35.93 2.39
2339 5100 3.131577 TCCGAATTACTTGTCGCAGGTAT 59.868 43.478 3.46 0.00 35.93 2.73
2340 5101 2.492881 TCCGAATTACTTGTCGCAGGTA 59.507 45.455 0.00 0.00 35.93 3.08
2341 5102 1.274167 TCCGAATTACTTGTCGCAGGT 59.726 47.619 0.00 0.91 35.93 4.00
2342 5103 2.004583 TCCGAATTACTTGTCGCAGG 57.995 50.000 0.00 0.00 35.93 4.85
2343 5104 3.242413 CCATTCCGAATTACTTGTCGCAG 60.242 47.826 0.00 0.00 35.93 5.18
2344 5105 2.675844 CCATTCCGAATTACTTGTCGCA 59.324 45.455 0.00 0.00 35.93 5.10
2345 5106 2.933906 TCCATTCCGAATTACTTGTCGC 59.066 45.455 0.00 0.00 35.93 5.19
2346 5107 3.555956 CCTCCATTCCGAATTACTTGTCG 59.444 47.826 0.00 0.00 37.01 4.35
2347 5108 3.877508 CCCTCCATTCCGAATTACTTGTC 59.122 47.826 0.00 0.00 0.00 3.18
2348 5109 3.521937 TCCCTCCATTCCGAATTACTTGT 59.478 43.478 0.00 0.00 0.00 3.16
2349 5110 4.130118 CTCCCTCCATTCCGAATTACTTG 58.870 47.826 0.00 0.00 0.00 3.16
2350 5111 3.780850 ACTCCCTCCATTCCGAATTACTT 59.219 43.478 0.00 0.00 0.00 2.24
2351 5112 3.385115 ACTCCCTCCATTCCGAATTACT 58.615 45.455 0.00 0.00 0.00 2.24
2352 5113 3.840124 ACTCCCTCCATTCCGAATTAC 57.160 47.619 0.00 0.00 0.00 1.89
2353 5114 4.553678 AGTACTCCCTCCATTCCGAATTA 58.446 43.478 0.00 0.00 0.00 1.40
2354 5115 3.385115 AGTACTCCCTCCATTCCGAATT 58.615 45.455 0.00 0.00 0.00 2.17
2355 5116 3.047695 AGTACTCCCTCCATTCCGAAT 57.952 47.619 0.00 0.00 0.00 3.34
2356 5117 2.544844 AGTACTCCCTCCATTCCGAA 57.455 50.000 0.00 0.00 0.00 4.30
2357 5118 2.544844 AAGTACTCCCTCCATTCCGA 57.455 50.000 0.00 0.00 0.00 4.55
2358 5119 3.895656 TGATAAGTACTCCCTCCATTCCG 59.104 47.826 0.00 0.00 0.00 4.30
2359 5120 5.367060 ACTTGATAAGTACTCCCTCCATTCC 59.633 44.000 0.00 0.00 40.69 3.01
2360 5121 6.487299 ACTTGATAAGTACTCCCTCCATTC 57.513 41.667 0.00 0.00 40.69 2.67
2373 5134 9.269453 GTCCAACTTTGTAAGTACTTGATAAGT 57.731 33.333 18.56 18.16 41.91 2.24
2374 5135 9.268268 TGTCCAACTTTGTAAGTACTTGATAAG 57.732 33.333 18.56 17.61 41.91 1.73
2375 5136 9.787435 ATGTCCAACTTTGTAAGTACTTGATAA 57.213 29.630 18.56 7.53 41.91 1.75
2376 5137 9.787435 AATGTCCAACTTTGTAAGTACTTGATA 57.213 29.630 18.56 2.41 41.91 2.15
2629 5390 2.360483 TGCAATGGCGACTTCAAAGAAA 59.640 40.909 0.00 0.00 45.35 2.52
2642 5403 4.247258 TGAAATCAATCAACTGCAATGGC 58.753 39.130 0.00 0.00 41.68 4.40
2730 5491 9.626045 AAGATTCTTCGATACCAAAAATTGTTC 57.374 29.630 0.00 0.00 0.00 3.18
2779 5540 4.142293 GGTGAATCCTTTCATCTTCCTTGC 60.142 45.833 0.00 0.00 43.49 4.01
2843 5604 6.038161 CACTGTTCTGTTGGTTGTCAATAAGA 59.962 38.462 0.00 0.00 37.73 2.10
2845 5606 5.650266 ACACTGTTCTGTTGGTTGTCAATAA 59.350 36.000 0.00 0.00 37.73 1.40
2865 5626 4.342862 ACTTACAATCAGACTGCACACT 57.657 40.909 0.00 0.00 0.00 3.55
2866 5627 5.696724 AGTTACTTACAATCAGACTGCACAC 59.303 40.000 0.00 0.00 0.00 3.82
2978 5742 7.170998 ACGTCTTACATTTGTTTACAGAAGGAG 59.829 37.037 0.00 0.00 0.00 3.69
2979 5743 6.987992 ACGTCTTACATTTGTTTACAGAAGGA 59.012 34.615 0.00 0.00 0.00 3.36
2980 5744 7.186021 ACGTCTTACATTTGTTTACAGAAGG 57.814 36.000 0.00 0.00 0.00 3.46
2981 5745 9.498307 AAAACGTCTTACATTTGTTTACAGAAG 57.502 29.630 0.00 0.00 32.84 2.85
2984 5748 9.377383 CCTAAAACGTCTTACATTTGTTTACAG 57.623 33.333 0.00 0.00 32.84 2.74
2985 5749 8.891720 ACCTAAAACGTCTTACATTTGTTTACA 58.108 29.630 0.00 0.00 32.84 2.41
2986 5750 9.373750 GACCTAAAACGTCTTACATTTGTTTAC 57.626 33.333 0.00 0.00 32.84 2.01
2987 5751 9.107177 TGACCTAAAACGTCTTACATTTGTTTA 57.893 29.630 0.00 0.00 32.84 2.01
2988 5752 7.911727 GTGACCTAAAACGTCTTACATTTGTTT 59.088 33.333 0.00 0.00 34.46 2.83
2989 5753 7.281549 AGTGACCTAAAACGTCTTACATTTGTT 59.718 33.333 0.00 0.00 0.00 2.83
2990 5754 6.764560 AGTGACCTAAAACGTCTTACATTTGT 59.235 34.615 0.00 0.00 0.00 2.83
2991 5755 7.042321 TCAGTGACCTAAAACGTCTTACATTTG 60.042 37.037 0.00 0.00 0.00 2.32
2992 5756 6.987992 TCAGTGACCTAAAACGTCTTACATTT 59.012 34.615 0.00 0.00 0.00 2.32
2993 5757 6.518493 TCAGTGACCTAAAACGTCTTACATT 58.482 36.000 0.00 0.00 0.00 2.71
2994 5758 6.092955 TCAGTGACCTAAAACGTCTTACAT 57.907 37.500 0.00 0.00 0.00 2.29
2995 5759 5.508489 CCTCAGTGACCTAAAACGTCTTACA 60.508 44.000 0.00 0.00 0.00 2.41
2996 5760 4.922103 CCTCAGTGACCTAAAACGTCTTAC 59.078 45.833 0.00 0.00 0.00 2.34
2997 5761 4.828939 TCCTCAGTGACCTAAAACGTCTTA 59.171 41.667 0.00 0.00 0.00 2.10
2998 5762 3.640029 TCCTCAGTGACCTAAAACGTCTT 59.360 43.478 0.00 0.00 0.00 3.01
2999 5763 3.228453 TCCTCAGTGACCTAAAACGTCT 58.772 45.455 0.00 0.00 0.00 4.18
3000 5764 3.655276 TCCTCAGTGACCTAAAACGTC 57.345 47.619 0.00 0.00 0.00 4.34
3001 5765 3.576982 TGATCCTCAGTGACCTAAAACGT 59.423 43.478 0.00 0.00 0.00 3.99
3002 5766 4.188247 TGATCCTCAGTGACCTAAAACG 57.812 45.455 0.00 0.00 0.00 3.60
3003 5767 7.824779 ACTAATTGATCCTCAGTGACCTAAAAC 59.175 37.037 0.00 0.00 0.00 2.43
3004 5768 7.918076 ACTAATTGATCCTCAGTGACCTAAAA 58.082 34.615 0.00 0.00 0.00 1.52
3005 5769 7.496346 ACTAATTGATCCTCAGTGACCTAAA 57.504 36.000 0.00 0.00 0.00 1.85
3006 5770 7.496346 AACTAATTGATCCTCAGTGACCTAA 57.504 36.000 0.00 0.00 0.00 2.69
3007 5771 7.496346 AAACTAATTGATCCTCAGTGACCTA 57.504 36.000 0.00 0.00 0.00 3.08
3008 5772 6.380079 AAACTAATTGATCCTCAGTGACCT 57.620 37.500 0.00 0.00 0.00 3.85
3009 5773 7.331791 ACTAAACTAATTGATCCTCAGTGACC 58.668 38.462 0.00 0.00 0.00 4.02
3010 5774 8.035394 TGACTAAACTAATTGATCCTCAGTGAC 58.965 37.037 0.00 0.00 0.00 3.67
3011 5775 8.134202 TGACTAAACTAATTGATCCTCAGTGA 57.866 34.615 0.00 0.00 0.00 3.41
3012 5776 8.777865 TTGACTAAACTAATTGATCCTCAGTG 57.222 34.615 0.00 0.00 0.00 3.66
3013 5777 9.442047 CTTTGACTAAACTAATTGATCCTCAGT 57.558 33.333 0.00 0.00 0.00 3.41
3014 5778 9.442047 ACTTTGACTAAACTAATTGATCCTCAG 57.558 33.333 0.00 0.00 0.00 3.35
3062 5826 3.683365 AAATGTTGGAATGCCCACTTC 57.317 42.857 0.00 0.00 46.62 3.01
3069 5833 6.035327 GCTATCTTCACAAAATGTTGGAATGC 59.965 38.462 0.00 1.38 39.22 3.56
3122 5886 6.480651 GCTTGGACCTAGCTTTAGATTCTTAC 59.519 42.308 19.25 0.00 35.74 2.34
3161 5925 3.482722 CACAATGGTGCAAGATGAGAC 57.517 47.619 0.00 0.00 38.37 3.36
3193 5957 4.582656 GGTAATGTATGGTGGCATTAGCAA 59.417 41.667 16.55 0.00 46.60 3.91
3217 5981 3.019003 ATTCGCCCCTGTGAGTCCG 62.019 63.158 0.00 0.00 31.46 4.79
3222 5986 2.799126 ATTTACATTCGCCCCTGTGA 57.201 45.000 0.00 0.00 0.00 3.58
3227 5991 3.139077 CAGACCTATTTACATTCGCCCC 58.861 50.000 0.00 0.00 0.00 5.80
3228 5992 2.548480 GCAGACCTATTTACATTCGCCC 59.452 50.000 0.00 0.00 0.00 6.13
3238 6018 5.625150 ACTGTCTCTTTTGCAGACCTATTT 58.375 37.500 1.06 0.00 39.78 1.40
3245 6025 4.345257 AGTCCTAACTGTCTCTTTTGCAGA 59.655 41.667 0.00 0.00 33.32 4.26
3281 6062 7.599630 ACGTAAAGGATGCTTCGTTAAAATA 57.400 32.000 7.72 0.00 30.10 1.40
3289 6070 3.185594 TGTTGAACGTAAAGGATGCTTCG 59.814 43.478 0.00 3.07 0.00 3.79
3303 6085 8.767085 TCAACTTAACCTAGTTATTGTTGAACG 58.233 33.333 21.10 0.00 41.96 3.95
3347 6130 4.284490 AGTTGCAGTACAGGAAATCTCTGA 59.716 41.667 0.00 0.00 36.22 3.27
3352 7619 4.154918 CCTTCAGTTGCAGTACAGGAAATC 59.845 45.833 0.00 0.00 0.00 2.17
3360 7627 4.327680 AGGAAATCCTTCAGTTGCAGTAC 58.672 43.478 0.00 0.00 46.09 2.73
3427 7721 1.304052 CATGGAAGGCCGGACCAAA 60.304 57.895 19.07 0.00 43.14 3.28
3512 7806 5.350640 GGGATAAGTCTGTAAACCAAGAACG 59.649 44.000 0.00 0.00 0.00 3.95
3516 7810 4.941873 GGTGGGATAAGTCTGTAAACCAAG 59.058 45.833 0.00 0.00 0.00 3.61
3517 7811 4.351407 TGGTGGGATAAGTCTGTAAACCAA 59.649 41.667 0.00 0.00 32.46 3.67
3519 7813 4.514401 CTGGTGGGATAAGTCTGTAAACC 58.486 47.826 0.00 0.00 0.00 3.27
3534 7830 2.436646 GCACACGATCCTGGTGGG 60.437 66.667 7.81 3.27 41.73 4.61
3535 7831 1.003355 AAGCACACGATCCTGGTGG 60.003 57.895 7.81 0.00 39.69 4.61
3552 7886 1.727062 TACAAACGGGGTAGGGACAA 58.273 50.000 0.00 0.00 0.00 3.18
3631 7969 1.212751 GGAAATCAACAGCGGTGCC 59.787 57.895 15.82 1.60 0.00 5.01
3634 7972 1.880027 GTTCAGGAAATCAACAGCGGT 59.120 47.619 0.00 0.00 0.00 5.68
3636 7974 2.807967 TGAGTTCAGGAAATCAACAGCG 59.192 45.455 9.46 0.00 41.62 5.18
3654 7992 0.035152 TGCCATGGCCTTGTACTGAG 60.035 55.000 33.44 2.36 41.09 3.35
3679 8018 9.588096 ACATAACACCAGTCATCTAGTGATATA 57.412 33.333 0.00 0.00 39.48 0.86
3682 8021 6.798427 ACATAACACCAGTCATCTAGTGAT 57.202 37.500 0.00 0.00 39.48 3.06
3689 8028 4.331968 TGGGAAACATAACACCAGTCATC 58.668 43.478 0.00 0.00 0.00 2.92
3690 8029 4.380843 TGGGAAACATAACACCAGTCAT 57.619 40.909 0.00 0.00 0.00 3.06
3697 8036 5.975693 TTCTTCCATGGGAAACATAACAC 57.024 39.130 13.02 0.00 41.54 3.32
3701 8041 7.093945 GCTTTACTTTCTTCCATGGGAAACATA 60.094 37.037 13.02 5.48 41.54 2.29
3768 8108 1.270732 CCAGAGAGCAAGAGCACACTT 60.271 52.381 0.00 0.00 45.49 3.16
3784 8124 2.564771 CTTGTTGAGCTTGACACCAGA 58.435 47.619 2.92 0.00 0.00 3.86
3785 8125 1.605710 CCTTGTTGAGCTTGACACCAG 59.394 52.381 2.92 0.35 0.00 4.00
3793 8133 1.473258 TGTGTTGCCTTGTTGAGCTT 58.527 45.000 0.00 0.00 0.00 3.74
3831 8171 0.622665 AGTTCCTTCCTCAGGCATGG 59.377 55.000 0.00 0.00 43.55 3.66
3833 8173 1.004044 CACAGTTCCTTCCTCAGGCAT 59.996 52.381 0.00 0.00 43.55 4.40
3835 8175 0.322008 CCACAGTTCCTTCCTCAGGC 60.322 60.000 0.00 0.00 43.55 4.85
3836 8176 1.002544 GTCCACAGTTCCTTCCTCAGG 59.997 57.143 0.00 0.00 45.64 3.86
3848 8199 1.481056 GGCCTACCACAGTCCACAGT 61.481 60.000 0.00 0.00 35.26 3.55
3849 8200 1.194781 AGGCCTACCACAGTCCACAG 61.195 60.000 1.29 0.00 39.06 3.66
3850 8201 0.115547 TAGGCCTACCACAGTCCACA 59.884 55.000 8.91 0.00 39.06 4.17
3851 8202 1.139058 CATAGGCCTACCACAGTCCAC 59.861 57.143 16.61 0.00 39.06 4.02
3852 8203 1.496060 CATAGGCCTACCACAGTCCA 58.504 55.000 16.61 0.00 39.06 4.02
3853 8204 0.759346 CCATAGGCCTACCACAGTCC 59.241 60.000 16.61 0.00 39.06 3.85
3854 8205 0.759346 CCCATAGGCCTACCACAGTC 59.241 60.000 16.61 0.00 39.06 3.51
3869 8220 1.628846 AGTTCAGTTAAGGTCGCCCAT 59.371 47.619 0.00 0.00 0.00 4.00
3873 8224 3.432592 GGAAGAAGTTCAGTTAAGGTCGC 59.567 47.826 5.50 0.00 33.93 5.19
3888 8239 2.832733 ACTAGGAAGTTCCCGGAAGAAG 59.167 50.000 18.65 7.32 37.19 2.85
3898 8249 6.035758 CAGCGGTTAATGTAACTAGGAAGTTC 59.964 42.308 0.00 0.00 42.42 3.01
3908 8259 3.434637 CAATGGCAGCGGTTAATGTAAC 58.565 45.455 0.00 0.00 37.94 2.50
3999 8367 2.033801 ACGAGAGTCCGTTTCGAAAGAA 59.966 45.455 11.66 0.00 46.53 2.52
4000 8368 1.605710 ACGAGAGTCCGTTTCGAAAGA 59.394 47.619 11.66 3.07 44.19 2.52
4001 8369 2.047679 ACGAGAGTCCGTTTCGAAAG 57.952 50.000 11.66 5.66 44.19 2.62
4012 8380 9.856939 ACATGGAGTGTAAACATCACGAGAGTC 62.857 44.444 0.00 0.00 40.71 3.36
4013 8381 8.190385 ACATGGAGTGTAAACATCACGAGAGT 62.190 42.308 0.00 0.00 42.80 3.24
4014 8382 4.174411 TGGAGTGTAAACATCACGAGAG 57.826 45.455 0.00 0.00 40.28 3.20
4015 8383 4.021456 ACATGGAGTGTAAACATCACGAGA 60.021 41.667 0.00 0.00 39.91 4.04
4016 8384 4.091945 CACATGGAGTGTAAACATCACGAG 59.908 45.833 0.00 0.00 43.40 4.18
4017 8385 3.993736 CACATGGAGTGTAAACATCACGA 59.006 43.478 0.00 0.00 43.40 4.35
4018 8386 4.326413 CACATGGAGTGTAAACATCACG 57.674 45.455 0.00 0.00 43.40 4.35
4088 8461 4.261909 CCAAATTTGAGCCTCTATGCATCC 60.262 45.833 19.86 0.00 0.00 3.51
4173 9257 2.269172 GCAAGTACGCCTAGTTCTTCC 58.731 52.381 0.00 0.00 38.21 3.46
4193 9277 1.533731 ACGCGGTCCTGTAACAAATTG 59.466 47.619 12.47 0.00 0.00 2.32
4195 9279 1.153353 CACGCGGTCCTGTAACAAAT 58.847 50.000 12.47 0.00 0.00 2.32
4212 9296 4.641989 AGGTCATCAGGATTGTTAATGCAC 59.358 41.667 0.00 0.00 0.00 4.57
4224 9308 4.406972 CCTCTTGTTATCAGGTCATCAGGA 59.593 45.833 0.00 0.00 0.00 3.86
4277 9361 2.203266 GCAGGTAGCCAGGCATCC 60.203 66.667 15.80 15.24 37.23 3.51
4294 9378 0.526524 GTCTACCGTAGCAGCAGCAG 60.527 60.000 3.17 0.00 45.49 4.24
4393 9499 2.706339 ATTCCATCGCTCTGCTTTCT 57.294 45.000 0.00 0.00 0.00 2.52
4423 9529 3.011949 CACGTTTTAAAGGTGCTGCAT 57.988 42.857 15.83 0.00 39.94 3.96
4473 9579 0.900647 CCTCTATCGATTCCCGGCCT 60.901 60.000 1.71 0.00 39.14 5.19
4474 9580 0.898789 TCCTCTATCGATTCCCGGCC 60.899 60.000 1.71 0.00 39.14 6.13


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

AutoCloner maintained by Alex Coulton.