Multiple sequence alignment - TraesCS2A01G017400

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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 TraesCS2A01G017400 chr2A 100.000 4876 0 0 1 4876 8146731 8151606 0.000000e+00 9005.0
1 TraesCS2A01G017400 chr2A 91.861 1155 66 9 927 2065 30552987 30551845 0.000000e+00 1587.0
2 TraesCS2A01G017400 chr2A 94.635 727 38 1 3148 3874 30550652 30549927 0.000000e+00 1125.0
3 TraesCS2A01G017400 chr2A 82.428 626 74 23 4262 4876 7788060 7788660 9.360000e-142 514.0
4 TraesCS2A01G017400 chr2A 84.519 478 37 12 2683 3153 30551130 30550683 5.790000e-119 438.0
5 TraesCS2A01G017400 chr2A 88.728 346 33 3 4338 4680 7743592 7743934 7.550000e-113 418.0
6 TraesCS2A01G017400 chr2A 91.429 280 17 2 2059 2335 30551702 30551427 1.280000e-100 377.0
7 TraesCS2A01G017400 chr2A 91.038 212 19 0 2370 2581 30551338 30551127 2.220000e-73 287.0
8 TraesCS2A01G017400 chr2A 78.652 267 39 10 3878 4131 9066098 9065837 1.400000e-35 161.0
9 TraesCS2A01G017400 chr2A 78.378 259 38 11 3878 4121 8628656 8628911 8.450000e-33 152.0
10 TraesCS2A01G017400 chr2A 85.333 150 15 4 1181 1330 753250412 753250270 1.090000e-31 148.0
11 TraesCS2A01G017400 chr2A 81.461 178 28 4 3898 4074 8632203 8632376 1.830000e-29 141.0
12 TraesCS2A01G017400 chr2A 95.122 41 1 1 2878 2918 8149572 8149611 4.070000e-06 63.9
13 TraesCS2A01G017400 chr2A 95.122 41 1 1 2842 2881 8149608 8149648 4.070000e-06 63.9
14 TraesCS2A01G017400 chr2B 92.630 1574 81 16 3337 4876 11992888 11994460 0.000000e+00 2231.0
15 TraesCS2A01G017400 chr2B 91.090 1156 73 15 927 2065 46091836 46090694 0.000000e+00 1537.0
16 TraesCS2A01G017400 chr2B 97.069 887 8 2 627 1510 11991094 11991965 0.000000e+00 1478.0
17 TraesCS2A01G017400 chr2B 97.396 845 16 2 1493 2335 11991980 11992820 0.000000e+00 1434.0
18 TraesCS2A01G017400 chr2B 95.736 727 30 1 3148 3874 46089501 46088776 0.000000e+00 1170.0
19 TraesCS2A01G017400 chr2B 98.392 622 9 1 1 621 11990358 11990979 0.000000e+00 1092.0
20 TraesCS2A01G017400 chr2B 85.215 629 70 15 4262 4876 11402200 11402819 4.140000e-175 625.0
21 TraesCS2A01G017400 chr2B 84.728 478 36 16 2683 3153 46089979 46089532 1.250000e-120 444.0
22 TraesCS2A01G017400 chr2B 90.000 280 21 2 2059 2335 46090551 46090276 6.000000e-94 355.0
23 TraesCS2A01G017400 chr2B 78.481 474 78 12 4262 4728 212577512 212577968 6.180000e-74 289.0
24 TraesCS2A01G017400 chr2B 90.566 212 20 0 2370 2581 46090187 46089976 1.030000e-71 281.0
25 TraesCS2A01G017400 chr2B 81.395 344 50 10 3878 4213 11401862 11402199 8.040000e-68 268.0
26 TraesCS2A01G017400 chr2B 82.456 285 38 10 4416 4698 11397473 11397747 6.310000e-59 239.0
27 TraesCS2A01G017400 chr2B 98.148 108 2 0 2578 2685 514395766 514395873 6.440000e-44 189.0
28 TraesCS2A01G017400 chr2B 78.808 302 46 12 3899 4185 138997098 138996800 2.320000e-43 187.0
29 TraesCS2A01G017400 chr2B 81.818 187 21 3 4541 4727 138995106 138995279 1.410000e-30 145.0
30 TraesCS2A01G017400 chr2B 75.817 306 47 13 1193 1497 762500750 762500471 3.960000e-26 130.0
31 TraesCS2A01G017400 chr2B 88.732 71 7 1 4660 4729 11995424 11995494 8.700000e-13 86.1
32 TraesCS2A01G017400 chr2D 89.189 1443 88 35 627 2020 8974067 8972644 0.000000e+00 1738.0
33 TraesCS2A01G017400 chr2D 92.121 1155 63 10 927 2065 28733240 28732098 0.000000e+00 1604.0
34 TraesCS2A01G017400 chr2D 93.750 880 38 6 3440 4307 8960225 8959351 0.000000e+00 1304.0
35 TraesCS2A01G017400 chr2D 95.323 727 33 1 3148 3874 28730905 28730180 0.000000e+00 1153.0
36 TraesCS2A01G017400 chr2D 94.676 601 27 5 4277 4875 8839057 8838460 0.000000e+00 928.0
37 TraesCS2A01G017400 chr2D 90.545 624 36 8 3474 4081 8839849 8839233 0.000000e+00 804.0
38 TraesCS2A01G017400 chr2D 90.485 536 41 4 4341 4876 8959045 8958520 0.000000e+00 699.0
39 TraesCS2A01G017400 chr2D 85.056 629 63 20 4262 4876 8684932 8685543 3.230000e-171 612.0
40 TraesCS2A01G017400 chr2D 91.951 410 26 5 2683 3086 8848914 8848506 7.080000e-158 568.0
41 TraesCS2A01G017400 chr2D 95.364 302 12 2 3148 3448 8970468 8970168 3.410000e-131 479.0
42 TraesCS2A01G017400 chr2D 91.786 280 16 2 2059 2335 28731955 28731680 2.750000e-102 383.0
43 TraesCS2A01G017400 chr2D 91.007 278 20 4 2878 3153 28731210 28730936 2.140000e-98 370.0
44 TraesCS2A01G017400 chr2D 91.038 212 19 0 2370 2581 28731591 28731380 2.220000e-73 287.0
45 TraesCS2A01G017400 chr2D 92.708 192 14 0 1874 2065 8849653 8849462 1.340000e-70 278.0
46 TraesCS2A01G017400 chr2D 95.376 173 8 0 2059 2231 8849319 8849147 4.810000e-70 276.0
47 TraesCS2A01G017400 chr2D 93.583 187 8 1 2146 2332 8971170 8970988 4.810000e-70 276.0
48 TraesCS2A01G017400 chr2D 92.737 179 10 3 2370 2546 8970896 8970719 6.260000e-64 255.0
49 TraesCS2A01G017400 chr2D 87.678 211 12 4 2683 2879 28731383 28731173 2.930000e-57 233.0
50 TraesCS2A01G017400 chr2D 84.711 242 11 5 2910 3150 8970721 8970505 8.220000e-53 219.0
51 TraesCS2A01G017400 chr2D 80.524 267 34 11 3878 4131 9751968 9751707 6.440000e-44 189.0
52 TraesCS2A01G017400 chr2D 89.796 147 14 1 481 627 8974284 8974139 2.320000e-43 187.0
53 TraesCS2A01G017400 chr2D 95.745 94 4 0 3385 3478 8848509 8848416 8.450000e-33 152.0
54 TraesCS2A01G017400 chr2D 90.698 86 6 2 33 118 8974463 8974380 3.990000e-21 113.0
55 TraesCS2A01G017400 chr3D 88.889 1080 65 18 954 2020 564002933 564001896 0.000000e+00 1279.0
56 TraesCS2A01G017400 chr3D 95.159 785 35 3 4095 4876 564001655 564000871 0.000000e+00 1236.0
57 TraesCS2A01G017400 chr3D 90.640 203 13 5 433 632 564003447 564003248 1.040000e-66 265.0
58 TraesCS2A01G017400 chr3D 81.781 247 15 13 627 844 564003181 564002936 3.880000e-41 180.0
59 TraesCS2A01G017400 chr3D 87.234 141 15 1 4733 4873 563994955 563994818 1.820000e-34 158.0
60 TraesCS2A01G017400 chr5B 79.263 434 75 12 1082 1512 429902587 429903008 6.180000e-74 289.0
61 TraesCS2A01G017400 chr5B 97.273 110 3 0 2576 2685 245831285 245831394 2.320000e-43 187.0
62 TraesCS2A01G017400 chr5B 95.495 111 5 0 2576 2686 338943131 338943241 1.390000e-40 178.0
63 TraesCS2A01G017400 chrUn 97.222 108 3 0 2578 2685 51452239 51452132 3.000000e-42 183.0
64 TraesCS2A01G017400 chr4B 97.196 107 3 0 2576 2682 583994599 583994493 1.080000e-41 182.0
65 TraesCS2A01G017400 chr1B 96.330 109 4 0 2578 2686 589055517 589055409 3.880000e-41 180.0
66 TraesCS2A01G017400 chr1B 94.393 107 6 0 2579 2685 99134451 99134557 1.090000e-36 165.0
67 TraesCS2A01G017400 chr7D 96.296 108 4 0 2579 2686 267124058 267124165 1.390000e-40 178.0
68 TraesCS2A01G017400 chr4A 94.545 110 6 0 2576 2685 657141711 657141820 2.330000e-38 171.0


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 TraesCS2A01G017400 chr2A 8146731 8151606 4875 False 3044.266667 9005 96.748000 1 4876 3 chr2A.!!$F3 4875
1 TraesCS2A01G017400 chr2A 30549927 30552987 3060 True 762.800000 1587 90.696400 927 3874 5 chr2A.!!$R3 2947
2 TraesCS2A01G017400 chr2A 7788060 7788660 600 False 514.000000 514 82.428000 4262 4876 1 chr2A.!!$F2 614
3 TraesCS2A01G017400 chr2B 11990358 11995494 5136 False 1264.220000 2231 94.843800 1 4876 5 chr2B.!!$F6 4875
4 TraesCS2A01G017400 chr2B 46088776 46091836 3060 True 757.400000 1537 90.424000 927 3874 5 chr2B.!!$R3 2947
5 TraesCS2A01G017400 chr2B 11401862 11402819 957 False 446.500000 625 83.305000 3878 4876 2 chr2B.!!$F5 998
6 TraesCS2A01G017400 chr2D 8958520 8960225 1705 True 1001.500000 1304 92.117500 3440 4876 2 chr2D.!!$R4 1436
7 TraesCS2A01G017400 chr2D 8838460 8839849 1389 True 866.000000 928 92.610500 3474 4875 2 chr2D.!!$R2 1401
8 TraesCS2A01G017400 chr2D 28730180 28733240 3060 True 671.666667 1604 91.492167 927 3874 6 chr2D.!!$R6 2947
9 TraesCS2A01G017400 chr2D 8684932 8685543 611 False 612.000000 612 85.056000 4262 4876 1 chr2D.!!$F1 614
10 TraesCS2A01G017400 chr2D 8970168 8974463 4295 True 466.714286 1738 90.868286 33 3448 7 chr2D.!!$R5 3415
11 TraesCS2A01G017400 chr2D 8848416 8849653 1237 True 318.500000 568 93.945000 1874 3478 4 chr2D.!!$R3 1604
12 TraesCS2A01G017400 chr3D 564000871 564003447 2576 True 740.000000 1279 89.117250 433 4876 4 chr3D.!!$R2 4443

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
171 172 0.313672 TCGTGTGATTTTGCCCTTGC 59.686 50.000 0.00 0.00 38.26 4.01 F
311 312 1.480545 ACCTTGAATTATTTGCCGCCC 59.519 47.619 0.00 0.00 0.00 6.13 F
1475 1660 1.615392 ACATTGCAAAAGAGGCACCTC 59.385 47.619 1.71 8.74 41.75 3.85 F
2306 3918 0.323087 TCGATCAGACAACCCGGAGA 60.323 55.000 0.73 0.00 0.00 3.71 F
2879 4562 0.386838 AAACTCCAGCAAGCAAGCAC 59.613 50.000 3.19 0.00 36.85 4.40 F
3603 5365 0.174845 TGACGCGATAAAGGAGTGGG 59.825 55.000 15.93 0.00 0.00 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1942 2170 1.063567 CCTACTCTCTGCTGGGGTAGT 60.064 57.143 13.92 4.81 0.00 2.73 R
2255 3867 0.543749 GATGGTAGTGCTTCCAGGCT 59.456 55.000 4.03 0.00 37.14 4.58 R
2548 4216 0.253044 AATGCGGATAGTGCAGGTGT 59.747 50.000 0.00 0.00 46.98 4.16 R
3573 5335 0.033504 ATCGCGTCAAGTGAGGTTGT 59.966 50.000 5.77 0.00 43.34 3.32 R
3771 5558 1.900545 GCAGAAGGCTCGTACCCCTT 61.901 60.000 6.78 6.78 43.87 3.95 R
4508 6621 3.004734 CGATGCTTTTCTCCTGTTTTGGT 59.995 43.478 0.00 0.00 0.00 3.67 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
76 77 8.305046 TCTATTTTTCCCATCCCTTTGTATTG 57.695 34.615 0.00 0.00 0.00 1.90
139 140 3.126514 CACTGATGGACACTTCTGAATGC 59.873 47.826 0.00 0.00 0.00 3.56
171 172 0.313672 TCGTGTGATTTTGCCCTTGC 59.686 50.000 0.00 0.00 38.26 4.01
182 183 2.520260 CCCTTGCATGCTAGCCCC 60.520 66.667 21.80 0.57 0.00 5.80
311 312 1.480545 ACCTTGAATTATTTGCCGCCC 59.519 47.619 0.00 0.00 0.00 6.13
621 634 5.993748 TTCTTTTTCCTCTCTCTCTCTCC 57.006 43.478 0.00 0.00 0.00 3.71
622 635 5.004361 TCTTTTTCCTCTCTCTCTCTCCA 57.996 43.478 0.00 0.00 0.00 3.86
623 636 4.770010 TCTTTTTCCTCTCTCTCTCTCCAC 59.230 45.833 0.00 0.00 0.00 4.02
624 637 3.816398 TTTCCTCTCTCTCTCTCCACA 57.184 47.619 0.00 0.00 0.00 4.17
625 638 3.816398 TTCCTCTCTCTCTCTCCACAA 57.184 47.619 0.00 0.00 0.00 3.33
754 915 2.658802 CTGTGTCTTGTCATCGAGAACG 59.341 50.000 0.00 0.00 36.04 3.95
962 1128 4.033990 TCAGACGATTGCACTAGCTAAG 57.966 45.455 0.00 0.00 42.74 2.18
1209 1394 2.624838 CACAGCTCTGGATGTTTGGTTT 59.375 45.455 1.66 0.00 40.34 3.27
1475 1660 1.615392 ACATTGCAAAAGAGGCACCTC 59.385 47.619 1.71 8.74 41.75 3.85
1515 1736 4.666512 ACATGGGCAGAAAAGTTATCTGT 58.333 39.130 0.00 0.00 44.88 3.41
1606 1830 8.298854 CCACAAAGATCATATGTGTGAAAAAGA 58.701 33.333 19.58 0.00 42.17 2.52
2255 3867 3.869065 CGGGCTTAGGTTGAGTCAAATA 58.131 45.455 7.25 1.01 0.00 1.40
2277 3889 1.492176 CCTGGAAGCACTACCATCCAT 59.508 52.381 0.00 0.00 40.94 3.41
2305 3917 0.530744 TTCGATCAGACAACCCGGAG 59.469 55.000 0.73 0.00 0.00 4.63
2306 3918 0.323087 TCGATCAGACAACCCGGAGA 60.323 55.000 0.73 0.00 0.00 3.71
2307 3919 0.747255 CGATCAGACAACCCGGAGAT 59.253 55.000 0.73 0.00 0.00 2.75
2308 3920 1.536922 CGATCAGACAACCCGGAGATG 60.537 57.143 0.73 0.45 0.00 2.90
2395 4061 4.256920 TCTAGGTCTTCAAATGAGCTTGC 58.743 43.478 0.00 0.00 41.66 4.01
2420 4086 7.253983 GCTGCATAAAAGAATGTGAATGATGTG 60.254 37.037 0.00 0.00 0.00 3.21
2423 4089 4.460948 AAAGAATGTGAATGATGTGCCC 57.539 40.909 0.00 0.00 0.00 5.36
2447 4114 4.703645 TTCGAGAGAGTTGGTGATACAG 57.296 45.455 0.00 0.00 43.69 2.74
2496 4163 6.043127 TCTCTTACCTATTTATGGCAGCATGA 59.957 38.462 0.00 0.00 39.69 3.07
2531 4199 6.869695 TGTTTCTACTGTTAAGAGTGTGACA 58.130 36.000 15.18 10.98 0.00 3.58
2538 4206 3.118408 TGTTAAGAGTGTGACAAGCCACT 60.118 43.478 0.00 0.00 44.31 4.00
2542 4210 0.687354 AGTGTGACAAGCCACTAGGG 59.313 55.000 0.00 0.00 40.03 3.53
2570 4238 1.745087 ACCTGCACTATCCGCATTTTG 59.255 47.619 0.00 0.00 39.02 2.44
2577 4245 5.804473 TGCACTATCCGCATTTTGTTTAATG 59.196 36.000 0.00 0.00 38.31 1.90
2578 4246 5.804979 GCACTATCCGCATTTTGTTTAATGT 59.195 36.000 0.00 0.00 37.72 2.71
2579 4247 6.970043 GCACTATCCGCATTTTGTTTAATGTA 59.030 34.615 0.00 0.00 37.72 2.29
2580 4248 7.044314 GCACTATCCGCATTTTGTTTAATGTAC 60.044 37.037 0.00 0.00 37.72 2.90
2581 4249 8.181573 CACTATCCGCATTTTGTTTAATGTACT 58.818 33.333 0.00 0.00 37.72 2.73
2582 4250 8.395633 ACTATCCGCATTTTGTTTAATGTACTC 58.604 33.333 0.00 0.00 37.72 2.59
2583 4251 5.945155 TCCGCATTTTGTTTAATGTACTCC 58.055 37.500 0.00 0.00 37.72 3.85
2584 4252 5.099575 CCGCATTTTGTTTAATGTACTCCC 58.900 41.667 0.00 0.00 37.72 4.30
2585 4253 5.105917 CCGCATTTTGTTTAATGTACTCCCT 60.106 40.000 0.00 0.00 37.72 4.20
2586 4254 6.027749 CGCATTTTGTTTAATGTACTCCCTC 58.972 40.000 0.00 0.00 37.72 4.30
2587 4255 6.330278 GCATTTTGTTTAATGTACTCCCTCC 58.670 40.000 0.00 0.00 37.72 4.30
2588 4256 6.551736 CATTTTGTTTAATGTACTCCCTCCG 58.448 40.000 0.00 0.00 32.17 4.63
2589 4257 4.895668 TTGTTTAATGTACTCCCTCCGT 57.104 40.909 0.00 0.00 0.00 4.69
2590 4258 4.895668 TGTTTAATGTACTCCCTCCGTT 57.104 40.909 0.00 0.00 0.00 4.44
2591 4259 4.824289 TGTTTAATGTACTCCCTCCGTTC 58.176 43.478 0.00 0.00 0.00 3.95
2592 4260 4.529377 TGTTTAATGTACTCCCTCCGTTCT 59.471 41.667 0.00 0.00 0.00 3.01
2593 4261 4.730949 TTAATGTACTCCCTCCGTTCTG 57.269 45.455 0.00 0.00 0.00 3.02
2594 4262 2.526888 ATGTACTCCCTCCGTTCTGA 57.473 50.000 0.00 0.00 0.00 3.27
2595 4263 2.297698 TGTACTCCCTCCGTTCTGAA 57.702 50.000 0.00 0.00 0.00 3.02
2596 4264 2.816411 TGTACTCCCTCCGTTCTGAAT 58.184 47.619 0.00 0.00 0.00 2.57
2597 4265 3.170717 TGTACTCCCTCCGTTCTGAATT 58.829 45.455 0.00 0.00 0.00 2.17
2598 4266 4.346730 TGTACTCCCTCCGTTCTGAATTA 58.653 43.478 0.00 0.00 0.00 1.40
2599 4267 3.889520 ACTCCCTCCGTTCTGAATTAC 57.110 47.619 0.00 0.00 0.00 1.89
2600 4268 3.442076 ACTCCCTCCGTTCTGAATTACT 58.558 45.455 0.00 0.00 0.00 2.24
2601 4269 3.838903 ACTCCCTCCGTTCTGAATTACTT 59.161 43.478 0.00 0.00 0.00 2.24
2602 4270 4.184629 CTCCCTCCGTTCTGAATTACTTG 58.815 47.826 0.00 0.00 0.00 3.16
2603 4271 3.581332 TCCCTCCGTTCTGAATTACTTGT 59.419 43.478 0.00 0.00 0.00 3.16
2604 4272 3.933332 CCCTCCGTTCTGAATTACTTGTC 59.067 47.826 0.00 0.00 0.00 3.18
2605 4273 3.612860 CCTCCGTTCTGAATTACTTGTCG 59.387 47.826 0.00 0.00 0.00 4.35
2606 4274 2.991190 TCCGTTCTGAATTACTTGTCGC 59.009 45.455 0.00 0.00 0.00 5.19
2607 4275 2.993899 CCGTTCTGAATTACTTGTCGCT 59.006 45.455 0.00 0.00 0.00 4.93
2608 4276 3.060895 CCGTTCTGAATTACTTGTCGCTC 59.939 47.826 0.00 0.00 0.00 5.03
2609 4277 3.673338 CGTTCTGAATTACTTGTCGCTCA 59.327 43.478 0.00 0.00 0.00 4.26
2610 4278 4.149922 CGTTCTGAATTACTTGTCGCTCAA 59.850 41.667 0.00 0.00 34.61 3.02
2618 4286 1.800805 CTTGTCGCTCAAGTGGATGT 58.199 50.000 10.54 0.00 45.89 3.06
2619 4287 2.959516 CTTGTCGCTCAAGTGGATGTA 58.040 47.619 10.54 0.00 45.89 2.29
2620 4288 3.525537 CTTGTCGCTCAAGTGGATGTAT 58.474 45.455 10.54 0.00 45.89 2.29
2621 4289 3.165058 TGTCGCTCAAGTGGATGTATC 57.835 47.619 0.00 0.00 0.00 2.24
2622 4290 2.760650 TGTCGCTCAAGTGGATGTATCT 59.239 45.455 0.00 0.00 0.00 1.98
2623 4291 3.951680 TGTCGCTCAAGTGGATGTATCTA 59.048 43.478 0.00 0.00 0.00 1.98
2624 4292 4.401202 TGTCGCTCAAGTGGATGTATCTAA 59.599 41.667 0.00 0.00 0.00 2.10
2625 4293 4.740695 GTCGCTCAAGTGGATGTATCTAAC 59.259 45.833 0.00 0.00 0.00 2.34
2626 4294 4.401202 TCGCTCAAGTGGATGTATCTAACA 59.599 41.667 0.00 0.00 43.86 2.41
2627 4295 4.504461 CGCTCAAGTGGATGTATCTAACAC 59.496 45.833 0.00 0.00 42.09 3.32
2628 4296 5.665459 GCTCAAGTGGATGTATCTAACACT 58.335 41.667 0.00 0.00 42.09 3.55
2629 4297 6.459710 CGCTCAAGTGGATGTATCTAACACTA 60.460 42.308 0.00 0.00 42.09 2.74
2630 4298 7.437748 GCTCAAGTGGATGTATCTAACACTAT 58.562 38.462 0.00 0.00 42.09 2.12
2631 4299 7.928706 GCTCAAGTGGATGTATCTAACACTATT 59.071 37.037 0.00 0.00 42.09 1.73
2632 4300 9.823647 CTCAAGTGGATGTATCTAACACTATTT 57.176 33.333 0.00 0.00 42.09 1.40
2638 4306 9.056005 TGGATGTATCTAACACTATTTTGATGC 57.944 33.333 0.00 0.00 42.09 3.91
2639 4307 9.277783 GGATGTATCTAACACTATTTTGATGCT 57.722 33.333 0.00 0.00 42.09 3.79
2649 4317 8.839310 ACACTATTTTGATGCTAGATACATCC 57.161 34.615 0.00 0.00 42.68 3.51
2650 4318 8.432013 ACACTATTTTGATGCTAGATACATCCA 58.568 33.333 0.00 0.00 42.68 3.41
2651 4319 9.445878 CACTATTTTGATGCTAGATACATCCAT 57.554 33.333 0.00 0.00 42.68 3.41
2655 4323 8.750515 TTTTGATGCTAGATACATCCATTTGA 57.249 30.769 0.00 0.00 42.68 2.69
2656 4324 7.974482 TTGATGCTAGATACATCCATTTGAG 57.026 36.000 0.00 0.00 42.68 3.02
2657 4325 5.936372 TGATGCTAGATACATCCATTTGAGC 59.064 40.000 0.00 0.00 42.68 4.26
2658 4326 4.309933 TGCTAGATACATCCATTTGAGCG 58.690 43.478 0.00 0.00 0.00 5.03
2659 4327 4.039124 TGCTAGATACATCCATTTGAGCGA 59.961 41.667 0.00 0.00 0.00 4.93
2660 4328 4.387256 GCTAGATACATCCATTTGAGCGAC 59.613 45.833 0.00 0.00 0.00 5.19
2661 4329 4.406648 AGATACATCCATTTGAGCGACA 57.593 40.909 0.00 0.00 0.00 4.35
2662 4330 4.769688 AGATACATCCATTTGAGCGACAA 58.230 39.130 0.00 0.00 36.65 3.18
2663 4331 4.813161 AGATACATCCATTTGAGCGACAAG 59.187 41.667 0.00 0.00 39.77 3.16
2664 4332 2.783135 ACATCCATTTGAGCGACAAGT 58.217 42.857 0.00 0.00 39.77 3.16
2665 4333 3.937814 ACATCCATTTGAGCGACAAGTA 58.062 40.909 0.00 0.00 39.77 2.24
2666 4334 4.323417 ACATCCATTTGAGCGACAAGTAA 58.677 39.130 0.00 0.00 39.77 2.24
2667 4335 4.943705 ACATCCATTTGAGCGACAAGTAAT 59.056 37.500 0.00 0.00 39.77 1.89
2668 4336 5.415701 ACATCCATTTGAGCGACAAGTAATT 59.584 36.000 0.00 0.00 39.77 1.40
2669 4337 5.545658 TCCATTTGAGCGACAAGTAATTC 57.454 39.130 0.00 0.00 39.77 2.17
2670 4338 4.092821 TCCATTTGAGCGACAAGTAATTCG 59.907 41.667 0.00 0.00 39.77 3.34
2671 4339 4.334443 CATTTGAGCGACAAGTAATTCGG 58.666 43.478 0.00 0.00 39.77 4.30
2672 4340 3.306917 TTGAGCGACAAGTAATTCGGA 57.693 42.857 0.00 0.00 35.73 4.55
2673 4341 3.306917 TGAGCGACAAGTAATTCGGAA 57.693 42.857 0.00 0.00 35.73 4.30
2674 4342 2.991190 TGAGCGACAAGTAATTCGGAAC 59.009 45.455 0.00 0.00 35.73 3.62
2675 4343 5.891084 TTGAGCGACAAGTAATTCGGAACG 61.891 45.833 0.00 0.00 43.18 3.95
2707 4376 2.167693 CTGGCATGCCATTCTCAAATGT 59.832 45.455 38.47 0.00 46.15 2.71
2708 4377 2.568062 TGGCATGCCATTCTCAAATGTT 59.432 40.909 35.59 0.00 41.89 2.71
2709 4378 3.008157 TGGCATGCCATTCTCAAATGTTT 59.992 39.130 35.59 0.00 41.89 2.83
2710 4379 3.372822 GGCATGCCATTCTCAAATGTTTG 59.627 43.478 32.08 0.00 40.63 2.93
2712 4381 4.092383 GCATGCCATTCTCAAATGTTTGAC 59.908 41.667 6.36 0.00 41.88 3.18
2830 4504 1.090728 GCAAGTAGCTTCAAGGGAGC 58.909 55.000 0.00 0.00 41.15 4.70
2876 4559 2.985406 GAGAAACTCCAGCAAGCAAG 57.015 50.000 0.00 0.00 0.00 4.01
2877 4560 0.957362 AGAAACTCCAGCAAGCAAGC 59.043 50.000 0.00 0.00 0.00 4.01
2878 4561 0.670162 GAAACTCCAGCAAGCAAGCA 59.330 50.000 3.19 0.00 36.85 3.91
2879 4562 0.386838 AAACTCCAGCAAGCAAGCAC 59.613 50.000 3.19 0.00 36.85 4.40
2880 4563 1.458639 AACTCCAGCAAGCAAGCACC 61.459 55.000 3.19 0.00 36.85 5.01
2881 4564 2.598394 TCCAGCAAGCAAGCACCC 60.598 61.111 3.19 0.00 36.85 4.61
2882 4565 2.599578 CCAGCAAGCAAGCACCCT 60.600 61.111 3.19 0.00 36.85 4.34
2883 4566 2.205152 CCAGCAAGCAAGCACCCTT 61.205 57.895 3.19 0.00 36.85 3.95
2893 4576 2.154462 CAAGCACCCTTGTTACTCAGG 58.846 52.381 0.00 0.00 42.76 3.86
2894 4577 1.729586 AGCACCCTTGTTACTCAGGA 58.270 50.000 3.22 0.00 0.00 3.86
2895 4578 1.625818 AGCACCCTTGTTACTCAGGAG 59.374 52.381 3.22 0.00 0.00 3.69
2896 4579 1.623811 GCACCCTTGTTACTCAGGAGA 59.376 52.381 2.79 0.00 0.00 3.71
2897 4580 2.038557 GCACCCTTGTTACTCAGGAGAA 59.961 50.000 2.79 0.00 0.00 2.87
2898 4581 3.496160 GCACCCTTGTTACTCAGGAGAAA 60.496 47.826 2.79 0.00 0.00 2.52
2899 4582 4.065789 CACCCTTGTTACTCAGGAGAAAC 58.934 47.826 2.79 0.00 0.00 2.78
2900 4583 3.974642 ACCCTTGTTACTCAGGAGAAACT 59.025 43.478 2.79 0.00 0.00 2.66
2901 4584 4.040584 ACCCTTGTTACTCAGGAGAAACTC 59.959 45.833 2.79 0.00 0.00 3.01
2999 4719 3.993736 GAGAAAGCTGACAGGAACTCTTC 59.006 47.826 4.26 1.42 34.60 2.87
3083 4803 9.031537 TCATGTACGGGAATATAGAACATATGT 57.968 33.333 1.41 1.41 0.00 2.29
3123 4843 7.635971 GCAGAGAAAGAAATGATTACCCTCCTA 60.636 40.741 0.00 0.00 0.00 2.94
3127 4847 9.225682 AGAAAGAAATGATTACCCTCCTACATA 57.774 33.333 0.00 0.00 0.00 2.29
3228 4988 3.803231 CCTGATGAGATTGAAGAAGAGCG 59.197 47.826 0.00 0.00 0.00 5.03
3533 5293 3.000041 TGACATGGCTATCGTGTTCAAC 59.000 45.455 0.00 0.00 44.95 3.18
3573 5335 1.735973 CGCATCGACTCCATCCAGA 59.264 57.895 0.00 0.00 0.00 3.86
3603 5365 0.174845 TGACGCGATAAAGGAGTGGG 59.825 55.000 15.93 0.00 0.00 4.61
3771 5558 5.627735 GCAGAGGAAACATAGGAATCAGACA 60.628 44.000 0.00 0.00 0.00 3.41
3933 5729 4.078537 TCAATCAAGAAGGAATCGCCAAA 58.921 39.130 0.00 0.00 40.02 3.28
4137 5945 3.056749 AGAACTCGTGTAATGTGACCCTC 60.057 47.826 0.00 0.00 0.00 4.30
4187 5995 0.827089 TGTGTTCAAGTGGCCATGGG 60.827 55.000 9.72 0.56 0.00 4.00
4213 6021 8.340443 GGAAACCATTTTACGGAGTGATTATAC 58.660 37.037 0.00 0.00 45.73 1.47
4243 6051 5.231702 TCCGATCAAAAATAAGTGTCGTGA 58.768 37.500 0.00 0.00 0.00 4.35
4508 6621 7.701924 CAGAACACACTTTAAATTTGAAGCTGA 59.298 33.333 19.50 0.00 0.00 4.26
4577 6700 2.432628 CCGACGGTTCAGGAGTGC 60.433 66.667 5.48 0.00 0.00 4.40
4845 6973 7.868922 TCGTAAATTTTAGACTGTCTTGTGCTA 59.131 33.333 16.53 0.00 0.00 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
139 140 3.058160 CACGAGCAAAGCTGGGGG 61.058 66.667 6.01 0.00 39.88 5.40
182 183 0.107654 GTTGGATCGACCTCAAGGGG 60.108 60.000 0.29 0.00 40.27 4.79
285 286 3.694566 GGCAAATAATTCAAGGTCGGTCT 59.305 43.478 0.00 0.00 0.00 3.85
386 388 7.358765 CGTCTTTGCTTAGCAGATGATACATAC 60.359 40.741 7.08 0.00 40.61 2.39
621 634 3.825308 CAATCGAGGTGACCATTTTGTG 58.175 45.455 3.63 0.00 0.00 3.33
622 635 2.228822 GCAATCGAGGTGACCATTTTGT 59.771 45.455 3.63 0.00 0.00 2.83
623 636 2.228582 TGCAATCGAGGTGACCATTTTG 59.771 45.455 3.63 3.41 0.00 2.44
624 637 2.513753 TGCAATCGAGGTGACCATTTT 58.486 42.857 3.63 0.00 0.00 1.82
625 638 2.198827 TGCAATCGAGGTGACCATTT 57.801 45.000 3.63 0.00 0.00 2.32
793 955 6.583562 GTGGTCTAGAGCCTTATACAAATGT 58.416 40.000 18.90 0.00 0.00 2.71
962 1128 6.038356 CCAACTGCAGGAAAATTGATGATAC 58.962 40.000 19.93 0.00 0.00 2.24
1209 1394 8.906867 GTTTCTGGAAATTCATCATATCCAAGA 58.093 33.333 0.00 0.00 39.54 3.02
1475 1660 3.140325 TGTTTCAAGGAGCTTACCCTG 57.860 47.619 0.00 0.00 33.55 4.45
1515 1736 3.814625 TGCAAGTTGTACACAGATCCAA 58.185 40.909 4.48 0.00 0.00 3.53
1606 1830 3.262915 AGAGATGAAGTTAGGCAAGCAGT 59.737 43.478 0.00 0.00 0.00 4.40
1942 2170 1.063567 CCTACTCTCTGCTGGGGTAGT 60.064 57.143 13.92 4.81 0.00 2.73
1996 2229 4.009675 CCTGGTTTACATGCTGCTAAAGA 58.990 43.478 0.00 0.00 0.00 2.52
2255 3867 0.543749 GATGGTAGTGCTTCCAGGCT 59.456 55.000 4.03 0.00 37.14 4.58
2281 3893 2.338500 GGGTTGTCTGATCGAAGTGTC 58.662 52.381 0.00 0.00 0.00 3.67
2290 3902 0.833287 CCATCTCCGGGTTGTCTGAT 59.167 55.000 0.00 0.00 0.00 2.90
2305 3917 2.172293 AGCTCTTCCTTGGACATCCATC 59.828 50.000 0.34 0.00 46.97 3.51
2306 3918 2.172293 GAGCTCTTCCTTGGACATCCAT 59.828 50.000 6.43 0.00 46.97 3.41
2307 3919 1.556911 GAGCTCTTCCTTGGACATCCA 59.443 52.381 6.43 0.00 45.94 3.41
2308 3920 1.134250 GGAGCTCTTCCTTGGACATCC 60.134 57.143 14.64 0.00 43.16 3.51
2336 3988 1.274416 ACCCCCATCAAGCCTTCTAGA 60.274 52.381 0.00 0.00 0.00 2.43
2349 4001 0.776080 AGAACCAGAACCACCCCCAT 60.776 55.000 0.00 0.00 0.00 4.00
2395 4061 7.253983 GCACATCATTCACATTCTTTTATGCAG 60.254 37.037 0.00 0.00 0.00 4.41
2420 4086 1.757699 ACCAACTCTCTCGAATAGGGC 59.242 52.381 0.00 0.00 0.00 5.19
2423 4089 6.378710 TGTATCACCAACTCTCTCGAATAG 57.621 41.667 0.00 0.00 0.00 1.73
2447 4114 2.507471 ACCTTCATTCCTCTGATCCACC 59.493 50.000 0.00 0.00 0.00 4.61
2496 4163 5.520748 ACAGTAGAAACATGGAAAGGGAT 57.479 39.130 0.00 0.00 0.00 3.85
2538 4206 2.434331 GCAGGTGTGGTTGCCCTA 59.566 61.111 0.00 0.00 34.28 3.53
2542 4210 0.804989 GATAGTGCAGGTGTGGTTGC 59.195 55.000 0.00 0.00 40.67 4.17
2548 4216 0.253044 AATGCGGATAGTGCAGGTGT 59.747 50.000 0.00 0.00 46.98 4.16
2570 4238 4.868734 CAGAACGGAGGGAGTACATTAAAC 59.131 45.833 0.00 0.00 0.00 2.01
2577 4245 3.889520 AATTCAGAACGGAGGGAGTAC 57.110 47.619 0.00 0.00 0.00 2.73
2578 4246 4.607239 AGTAATTCAGAACGGAGGGAGTA 58.393 43.478 0.00 0.00 0.00 2.59
2579 4247 3.442076 AGTAATTCAGAACGGAGGGAGT 58.558 45.455 0.00 0.00 0.00 3.85
2580 4248 4.184629 CAAGTAATTCAGAACGGAGGGAG 58.815 47.826 0.00 0.00 0.00 4.30
2581 4249 3.581332 ACAAGTAATTCAGAACGGAGGGA 59.419 43.478 0.00 0.00 0.00 4.20
2582 4250 3.933332 GACAAGTAATTCAGAACGGAGGG 59.067 47.826 0.00 0.00 0.00 4.30
2583 4251 3.612860 CGACAAGTAATTCAGAACGGAGG 59.387 47.826 0.00 0.00 0.00 4.30
2584 4252 3.060895 GCGACAAGTAATTCAGAACGGAG 59.939 47.826 0.00 0.00 0.00 4.63
2585 4253 2.991190 GCGACAAGTAATTCAGAACGGA 59.009 45.455 0.00 0.00 0.00 4.69
2586 4254 2.993899 AGCGACAAGTAATTCAGAACGG 59.006 45.455 0.00 0.00 0.00 4.44
2587 4255 3.673338 TGAGCGACAAGTAATTCAGAACG 59.327 43.478 0.00 0.00 0.00 3.95
2588 4256 5.591643 TTGAGCGACAAGTAATTCAGAAC 57.408 39.130 0.00 0.00 34.20 3.01
2600 4268 3.195610 AGATACATCCACTTGAGCGACAA 59.804 43.478 0.00 0.00 36.97 3.18
2601 4269 2.760650 AGATACATCCACTTGAGCGACA 59.239 45.455 0.00 0.00 0.00 4.35
2602 4270 3.444703 AGATACATCCACTTGAGCGAC 57.555 47.619 0.00 0.00 0.00 5.19
2603 4271 4.401202 TGTTAGATACATCCACTTGAGCGA 59.599 41.667 0.00 0.00 0.00 4.93
2604 4272 4.504461 GTGTTAGATACATCCACTTGAGCG 59.496 45.833 0.00 0.00 39.39 5.03
2605 4273 5.665459 AGTGTTAGATACATCCACTTGAGC 58.335 41.667 0.00 0.00 39.39 4.26
2606 4274 9.823647 AAATAGTGTTAGATACATCCACTTGAG 57.176 33.333 0.00 0.00 39.39 3.02
2612 4280 9.056005 GCATCAAAATAGTGTTAGATACATCCA 57.944 33.333 0.00 0.00 39.39 3.41
2613 4281 9.277783 AGCATCAAAATAGTGTTAGATACATCC 57.722 33.333 0.00 0.00 39.39 3.51
2623 4291 9.277783 GGATGTATCTAGCATCAAAATAGTGTT 57.722 33.333 9.99 0.00 43.17 3.32
2624 4292 8.432013 TGGATGTATCTAGCATCAAAATAGTGT 58.568 33.333 9.99 0.00 43.17 3.55
2625 4293 8.837788 TGGATGTATCTAGCATCAAAATAGTG 57.162 34.615 9.99 0.00 43.17 2.74
2629 4297 9.358406 TCAAATGGATGTATCTAGCATCAAAAT 57.642 29.630 9.99 0.61 43.17 1.82
2630 4298 8.750515 TCAAATGGATGTATCTAGCATCAAAA 57.249 30.769 9.99 0.00 43.17 2.44
2631 4299 7.040892 GCTCAAATGGATGTATCTAGCATCAAA 60.041 37.037 9.99 0.63 43.17 2.69
2632 4300 6.429078 GCTCAAATGGATGTATCTAGCATCAA 59.571 38.462 9.99 0.98 43.17 2.57
2633 4301 5.936372 GCTCAAATGGATGTATCTAGCATCA 59.064 40.000 9.99 0.00 43.17 3.07
2634 4302 5.063186 CGCTCAAATGGATGTATCTAGCATC 59.937 44.000 0.00 1.37 41.30 3.91
2635 4303 4.934001 CGCTCAAATGGATGTATCTAGCAT 59.066 41.667 0.00 0.00 0.00 3.79
2636 4304 4.039124 TCGCTCAAATGGATGTATCTAGCA 59.961 41.667 0.00 0.00 0.00 3.49
2637 4305 4.387256 GTCGCTCAAATGGATGTATCTAGC 59.613 45.833 0.00 0.00 0.00 3.42
2638 4306 5.532557 TGTCGCTCAAATGGATGTATCTAG 58.467 41.667 0.00 0.00 0.00 2.43
2639 4307 5.529581 TGTCGCTCAAATGGATGTATCTA 57.470 39.130 0.00 0.00 0.00 1.98
2640 4308 4.406648 TGTCGCTCAAATGGATGTATCT 57.593 40.909 0.00 0.00 0.00 1.98
2641 4309 4.572389 ACTTGTCGCTCAAATGGATGTATC 59.428 41.667 0.00 0.00 35.48 2.24
2642 4310 4.517285 ACTTGTCGCTCAAATGGATGTAT 58.483 39.130 0.00 0.00 35.48 2.29
2643 4311 3.937814 ACTTGTCGCTCAAATGGATGTA 58.062 40.909 0.00 0.00 35.48 2.29
2644 4312 2.783135 ACTTGTCGCTCAAATGGATGT 58.217 42.857 0.00 0.00 35.48 3.06
2645 4313 4.944962 TTACTTGTCGCTCAAATGGATG 57.055 40.909 0.00 0.00 35.48 3.51
2646 4314 5.220662 CGAATTACTTGTCGCTCAAATGGAT 60.221 40.000 0.00 0.00 35.48 3.41
2647 4315 4.092821 CGAATTACTTGTCGCTCAAATGGA 59.907 41.667 0.00 0.00 35.48 3.41
2648 4316 4.334443 CGAATTACTTGTCGCTCAAATGG 58.666 43.478 0.00 0.00 35.48 3.16
2649 4317 4.092821 TCCGAATTACTTGTCGCTCAAATG 59.907 41.667 0.00 0.00 35.93 2.32
2650 4318 4.250464 TCCGAATTACTTGTCGCTCAAAT 58.750 39.130 0.00 0.00 35.93 2.32
2651 4319 3.655486 TCCGAATTACTTGTCGCTCAAA 58.345 40.909 0.00 0.00 35.93 2.69
2652 4320 3.306917 TCCGAATTACTTGTCGCTCAA 57.693 42.857 0.00 0.00 35.93 3.02
2653 4321 2.991190 GTTCCGAATTACTTGTCGCTCA 59.009 45.455 0.00 0.00 35.93 4.26
2654 4322 2.027688 CGTTCCGAATTACTTGTCGCTC 59.972 50.000 0.00 0.00 35.93 5.03
2655 4323 1.990563 CGTTCCGAATTACTTGTCGCT 59.009 47.619 0.00 0.00 35.93 4.93
2656 4324 1.060122 CCGTTCCGAATTACTTGTCGC 59.940 52.381 0.00 0.00 35.93 5.19
2657 4325 2.597305 CTCCGTTCCGAATTACTTGTCG 59.403 50.000 0.00 0.00 37.01 4.35
2658 4326 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
2659 4327 2.354403 CCCTCCGTTCCGAATTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
2660 4328 2.093869 TCCCTCCGTTCCGAATTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
2661 4329 2.167900 CTCCCTCCGTTCCGAATTACTT 59.832 50.000 0.00 0.00 0.00 2.24
2662 4330 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
2663 4331 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
2664 4332 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
2665 4333 1.479730 GTACTCCCTCCGTTCCGAATT 59.520 52.381 0.00 0.00 0.00 2.17
2666 4334 1.109609 GTACTCCCTCCGTTCCGAAT 58.890 55.000 0.00 0.00 0.00 3.34
2667 4335 0.967380 GGTACTCCCTCCGTTCCGAA 60.967 60.000 0.00 0.00 0.00 4.30
2668 4336 1.379044 GGTACTCCCTCCGTTCCGA 60.379 63.158 0.00 0.00 0.00 4.55
2669 4337 1.379576 AGGTACTCCCTCCGTTCCG 60.380 63.158 0.00 0.00 40.71 4.30
2670 4338 1.328430 CCAGGTACTCCCTCCGTTCC 61.328 65.000 0.00 0.00 43.86 3.62
2671 4339 1.957765 GCCAGGTACTCCCTCCGTTC 61.958 65.000 0.00 0.00 43.86 3.95
2672 4340 1.988406 GCCAGGTACTCCCTCCGTT 60.988 63.158 0.00 0.00 43.86 4.44
2673 4341 2.363925 GCCAGGTACTCCCTCCGT 60.364 66.667 0.00 0.00 43.86 4.69
2674 4342 1.762460 ATGCCAGGTACTCCCTCCG 60.762 63.158 0.00 0.00 43.86 4.63
2675 4343 1.832912 CATGCCAGGTACTCCCTCC 59.167 63.158 0.00 0.00 43.86 4.30
2676 4344 1.147153 GCATGCCAGGTACTCCCTC 59.853 63.158 6.36 0.00 43.86 4.30
2678 4346 2.193248 GGCATGCCAGGTACTCCC 59.807 66.667 32.08 0.00 34.60 4.30
2679 4347 2.998097 TGGCATGCCAGGTACTCC 59.002 61.111 35.59 6.59 41.89 3.85
2740 4414 6.428159 GGATCCTTTGAGCGTAATGTAATCAT 59.572 38.462 3.84 0.00 35.59 2.45
2741 4415 5.758296 GGATCCTTTGAGCGTAATGTAATCA 59.242 40.000 3.84 0.00 0.00 2.57
2751 4425 1.079127 CCGTGGATCCTTTGAGCGT 60.079 57.895 14.23 0.00 0.00 5.07
2871 4554 1.142870 TGAGTAACAAGGGTGCTTGCT 59.857 47.619 0.00 0.00 37.83 3.91
2875 4558 1.625818 CTCCTGAGTAACAAGGGTGCT 59.374 52.381 0.00 0.00 0.00 4.40
2876 4559 1.623811 TCTCCTGAGTAACAAGGGTGC 59.376 52.381 0.00 0.00 0.00 5.01
2877 4560 4.065789 GTTTCTCCTGAGTAACAAGGGTG 58.934 47.826 10.61 0.00 38.22 4.61
2878 4561 3.974642 AGTTTCTCCTGAGTAACAAGGGT 59.025 43.478 15.92 0.00 39.99 4.34
2879 4562 4.563786 GGAGTTTCTCCTGAGTAACAAGGG 60.564 50.000 15.92 0.00 46.41 3.95
2880 4563 4.570930 GGAGTTTCTCCTGAGTAACAAGG 58.429 47.826 15.92 0.00 46.41 3.61
2893 4576 3.254166 TGCTTTGATTGCTGGAGTTTCTC 59.746 43.478 0.00 0.00 0.00 2.87
2894 4577 3.005155 GTGCTTTGATTGCTGGAGTTTCT 59.995 43.478 0.00 0.00 0.00 2.52
2895 4578 3.311966 GTGCTTTGATTGCTGGAGTTTC 58.688 45.455 0.00 0.00 0.00 2.78
2896 4579 2.036346 GGTGCTTTGATTGCTGGAGTTT 59.964 45.455 0.00 0.00 0.00 2.66
2897 4580 1.615392 GGTGCTTTGATTGCTGGAGTT 59.385 47.619 0.00 0.00 0.00 3.01
2898 4581 1.251251 GGTGCTTTGATTGCTGGAGT 58.749 50.000 0.00 0.00 0.00 3.85
2899 4582 1.250328 TGGTGCTTTGATTGCTGGAG 58.750 50.000 0.00 0.00 0.00 3.86
2900 4583 1.702182 TTGGTGCTTTGATTGCTGGA 58.298 45.000 0.00 0.00 0.00 3.86
2901 4584 2.529780 TTTGGTGCTTTGATTGCTGG 57.470 45.000 0.00 0.00 0.00 4.85
2902 4585 3.196463 TGTTTTGGTGCTTTGATTGCTG 58.804 40.909 0.00 0.00 0.00 4.41
2903 4586 3.540314 TGTTTTGGTGCTTTGATTGCT 57.460 38.095 0.00 0.00 0.00 3.91
2904 4587 4.590226 CTTTGTTTTGGTGCTTTGATTGC 58.410 39.130 0.00 0.00 0.00 3.56
2905 4588 4.094590 TGCTTTGTTTTGGTGCTTTGATTG 59.905 37.500 0.00 0.00 0.00 2.67
2906 4589 4.260170 TGCTTTGTTTTGGTGCTTTGATT 58.740 34.783 0.00 0.00 0.00 2.57
2907 4590 3.871485 TGCTTTGTTTTGGTGCTTTGAT 58.129 36.364 0.00 0.00 0.00 2.57
2908 4591 3.325293 TGCTTTGTTTTGGTGCTTTGA 57.675 38.095 0.00 0.00 0.00 2.69
3024 4744 4.187694 CTCATCAGCCCTTGAAGTAGAAC 58.812 47.826 0.00 0.00 39.77 3.01
3096 4816 5.196695 AGGGTAATCATTTCTTTCTCTGCC 58.803 41.667 0.00 0.00 0.00 4.85
3123 4843 8.466798 CATGATATGATTGTGCAATGGATATGT 58.533 33.333 1.77 0.00 0.00 2.29
3127 4847 6.911250 ACATGATATGATTGTGCAATGGAT 57.089 33.333 0.00 0.00 0.00 3.41
3509 5269 4.260985 TGAACACGATAGCCATGTCAAAT 58.739 39.130 0.00 0.00 42.67 2.32
3533 5293 3.929610 GGAGAACATCCTTCTTGAAGTCG 59.070 47.826 9.21 0.90 45.64 4.18
3573 5335 0.033504 ATCGCGTCAAGTGAGGTTGT 59.966 50.000 5.77 0.00 43.34 3.32
3603 5365 2.069273 CTTGAGATCGGTGGTGTCAAC 58.931 52.381 0.00 0.00 0.00 3.18
3614 5376 5.334802 CCTGCTCTCATAGTACTTGAGATCG 60.335 48.000 25.03 19.16 46.26 3.69
3771 5558 1.900545 GCAGAAGGCTCGTACCCCTT 61.901 60.000 6.78 6.78 43.87 3.95
3933 5729 4.666512 AGCAATTACCCAGATGTTTCACT 58.333 39.130 0.00 0.00 0.00 3.41
4099 5906 9.268268 ACACGAGTTCTGAACAAAATTAGATTA 57.732 29.630 21.50 0.00 0.00 1.75
4159 5967 4.380867 GGCCACTTGAACACATCTATTTGG 60.381 45.833 0.00 0.00 0.00 3.28
4164 5972 3.346315 CATGGCCACTTGAACACATCTA 58.654 45.455 8.16 0.00 0.00 1.98
4187 5995 5.638596 AATCACTCCGTAAAATGGTTTCC 57.361 39.130 0.00 0.00 0.00 3.13
4213 6021 5.065218 CACTTATTTTTGATCGGAGGGAGTG 59.935 44.000 0.00 0.00 0.00 3.51
4243 6051 2.438392 GGTACTCCCTCCGATCCAAAAT 59.562 50.000 0.00 0.00 0.00 1.82
4437 6550 9.520515 AATCCATAAACTAGACAACACTTGAAT 57.479 29.630 0.00 0.00 0.00 2.57
4458 6571 4.705110 TGTTCAGAAGTTCCAGAATCCA 57.295 40.909 10.48 4.16 0.00 3.41
4508 6621 3.004734 CGATGCTTTTCTCCTGTTTTGGT 59.995 43.478 0.00 0.00 0.00 3.67
4839 6967 4.562757 GGTCAGAACAGTTACCATAGCACA 60.563 45.833 0.00 0.00 32.04 4.57


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

AutoCloner maintained by Alex Coulton.