Multiple sequence alignment - TraesCS2D01G123600

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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 TraesCS2D01G123600 chr2D 100.000 4957 0 0 1 4957 72443404 72438448 0.000000e+00 9154.0
1 TraesCS2D01G123600 chr2D 95.374 3956 98 32 442 4347 72702833 72698913 0.000000e+00 6213.0
2 TraesCS2D01G123600 chr2D 85.372 1251 123 31 3102 4333 72660204 72658995 0.000000e+00 1242.0
3 TraesCS2D01G123600 chr2D 98.632 585 8 0 4373 4957 72698916 72698332 0.000000e+00 1037.0
4 TraesCS2D01G123600 chr2D 84.066 728 71 25 3614 4337 72379042 72378356 0.000000e+00 660.0
5 TraesCS2D01G123600 chr2D 81.062 565 89 14 3109 3660 72373899 72373340 7.620000e-118 435.0
6 TraesCS2D01G123600 chr2D 80.354 565 93 14 3109 3660 72654380 72653821 3.570000e-111 412.0
7 TraesCS2D01G123600 chr2D 84.375 192 19 8 457 640 72609751 72609939 1.420000e-40 178.0
8 TraesCS2D01G123600 chr2D 90.323 124 12 0 183 306 72704585 72704462 3.970000e-36 163.0
9 TraesCS2D01G123600 chr2A 91.004 4313 263 56 432 4638 71351044 71346751 0.000000e+00 5699.0
10 TraesCS2D01G123600 chr2A 84.575 1342 120 40 3014 4334 71165588 71164313 0.000000e+00 1251.0
11 TraesCS2D01G123600 chr2A 82.506 846 133 12 1090 1923 71261771 71260929 0.000000e+00 728.0
12 TraesCS2D01G123600 chr2A 82.270 846 135 12 1090 1923 71209141 71208299 0.000000e+00 717.0
13 TraesCS2D01G123600 chr2A 86.392 485 45 8 1988 2455 71124383 71123903 1.230000e-140 510.0
14 TraesCS2D01G123600 chr2A 86.307 482 50 5 1988 2455 71166318 71165839 1.230000e-140 510.0
15 TraesCS2D01G123600 chr2A 82.378 471 64 11 905 1372 71269779 71269325 4.650000e-105 392.0
16 TraesCS2D01G123600 chr2A 81.953 471 66 11 905 1372 71220106 71219652 1.010000e-101 381.0
17 TraesCS2D01G123600 chr2A 89.338 272 27 2 4392 4662 71312344 71312074 1.710000e-89 340.0
18 TraesCS2D01G123600 chr2A 86.000 200 19 4 4724 4918 71157304 71157109 6.500000e-49 206.0
19 TraesCS2D01G123600 chr2A 81.026 195 21 8 4724 4918 71210062 71209884 1.860000e-29 141.0
20 TraesCS2D01G123600 chr2A 81.026 195 21 8 4724 4918 71262692 71262514 1.860000e-29 141.0
21 TraesCS2D01G123600 chr2A 87.736 106 12 1 2544 2649 71165813 71165709 6.740000e-24 122.0
22 TraesCS2D01G123600 chr2A 87.736 106 12 1 2544 2649 71218596 71218492 6.740000e-24 122.0
23 TraesCS2D01G123600 chr2B 95.041 2299 93 7 757 3052 109936797 109934517 0.000000e+00 3594.0
24 TraesCS2D01G123600 chr2B 92.186 2393 137 21 666 3052 109983496 109981148 0.000000e+00 3338.0
25 TraesCS2D01G123600 chr2B 92.881 1826 86 19 3006 4814 109934531 109932733 0.000000e+00 2612.0
26 TraesCS2D01G123600 chr2B 93.132 1427 73 10 3069 4494 109976428 109975026 0.000000e+00 2069.0
27 TraesCS2D01G123600 chr2B 83.841 1906 176 65 3014 4853 109875975 109874136 0.000000e+00 1692.0
28 TraesCS2D01G123600 chr2B 82.368 1985 181 80 3014 4918 109096551 109094656 0.000000e+00 1570.0
29 TraesCS2D01G123600 chr2B 85.237 1348 118 41 3014 4337 109760088 109758798 0.000000e+00 1312.0
30 TraesCS2D01G123600 chr2B 83.416 1206 146 35 645 1833 110067295 110068463 0.000000e+00 1070.0
31 TraesCS2D01G123600 chr2B 82.875 981 144 22 957 1923 109931487 109930517 0.000000e+00 859.0
32 TraesCS2D01G123600 chr2B 88.136 531 37 12 223 746 109937359 109936848 4.240000e-170 608.0
33 TraesCS2D01G123600 chr2B 86.228 501 46 9 1978 2455 109876724 109876224 5.690000e-144 521.0
34 TraesCS2D01G123600 chr2B 88.161 397 42 4 4353 4747 109193709 109193316 7.510000e-128 468.0
35 TraesCS2D01G123600 chr2B 94.526 274 8 4 406 672 109994733 109994460 2.760000e-112 416.0
36 TraesCS2D01G123600 chr2B 83.193 357 38 6 834 1189 109204464 109204129 1.730000e-79 307.0
37 TraesCS2D01G123600 chr2B 84.127 189 21 9 2544 2725 109195275 109195089 1.830000e-39 174.0
38 TraesCS2D01G123600 chr2B 91.000 100 8 1 1 99 109994854 109994755 3.110000e-27 134.0
39 TraesCS2D01G123600 chr2B 95.946 74 2 1 3006 3079 109981162 109981090 8.720000e-23 119.0
40 TraesCS2D01G123600 chrUn 93.378 1646 80 12 1237 2878 289939069 289940689 0.000000e+00 2409.0
41 TraesCS2D01G123600 chrUn 93.631 1570 80 6 3006 4560 289940899 289942463 0.000000e+00 2327.0
42 TraesCS2D01G123600 chrUn 84.241 1872 171 63 3014 4826 235538438 235540244 0.000000e+00 1709.0
43 TraesCS2D01G123600 chrUn 100.000 384 0 0 3353 3736 480865901 480866284 0.000000e+00 710.0
44 TraesCS2D01G123600 chrUn 86.427 501 45 9 1978 2455 235537689 235538189 1.220000e-145 527.0
45 TraesCS2D01G123600 chrUn 85.749 414 42 7 4546 4953 261752386 261752788 5.930000e-114 422.0
46 TraesCS2D01G123600 chrUn 80.531 565 92 14 3109 3660 289660414 289659855 7.670000e-113 418.0
47 TraesCS2D01G123600 chrUn 97.768 224 4 1 2830 3052 289940690 289940913 7.780000e-103 385.0
48 TraesCS2D01G123600 chrUn 80.952 294 14 21 252 543 352890091 352890344 1.410000e-45 195.0
49 TraesCS2D01G123600 chrUn 89.623 106 10 1 2544 2649 235538215 235538319 3.110000e-27 134.0
50 TraesCS2D01G123600 chr4B 86.194 268 34 3 2739 3005 464159012 464159277 2.260000e-73 287.0
51 TraesCS2D01G123600 chr3A 85.145 276 32 6 2739 3007 523754956 523754683 1.760000e-69 274.0
52 TraesCS2D01G123600 chr3B 84.116 277 35 6 2739 3007 528639797 528639522 4.920000e-65 259.0
53 TraesCS2D01G123600 chr5D 96.000 50 1 1 310 358 345940469 345940518 4.110000e-11 80.5
54 TraesCS2D01G123600 chr7A 94.872 39 2 0 310 348 49992463 49992501 1.490000e-05 62.1
55 TraesCS2D01G123600 chr4A 96.774 31 1 0 311 341 662230881 662230911 9.000000e-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 TraesCS2D01G123600 chr2D 72438448 72443404 4956 True 9154.000000 9154 100.000000 1 4957 1 chr2D.!!$R3 4956
1 TraesCS2D01G123600 chr2D 72698332 72704585 6253 True 2471.000000 6213 94.776333 183 4957 3 chr2D.!!$R6 4774
2 TraesCS2D01G123600 chr2D 72658995 72660204 1209 True 1242.000000 1242 85.372000 3102 4333 1 chr2D.!!$R5 1231
3 TraesCS2D01G123600 chr2D 72378356 72379042 686 True 660.000000 660 84.066000 3614 4337 1 chr2D.!!$R2 723
4 TraesCS2D01G123600 chr2D 72373340 72373899 559 True 435.000000 435 81.062000 3109 3660 1 chr2D.!!$R1 551
5 TraesCS2D01G123600 chr2D 72653821 72654380 559 True 412.000000 412 80.354000 3109 3660 1 chr2D.!!$R4 551
6 TraesCS2D01G123600 chr2A 71346751 71351044 4293 True 5699.000000 5699 91.004000 432 4638 1 chr2A.!!$R5 4206
7 TraesCS2D01G123600 chr2A 71164313 71166318 2005 True 627.666667 1251 86.206000 1988 4334 3 chr2A.!!$R6 2346
8 TraesCS2D01G123600 chr2A 71260929 71262692 1763 True 434.500000 728 81.766000 1090 4918 2 chr2A.!!$R9 3828
9 TraesCS2D01G123600 chr2A 71208299 71210062 1763 True 429.000000 717 81.648000 1090 4918 2 chr2A.!!$R7 3828
10 TraesCS2D01G123600 chr2A 71218492 71220106 1614 True 251.500000 381 84.844500 905 2649 2 chr2A.!!$R8 1744
11 TraesCS2D01G123600 chr2B 109975026 109976428 1402 True 2069.000000 2069 93.132000 3069 4494 1 chr2B.!!$R4 1425
12 TraesCS2D01G123600 chr2B 109930517 109937359 6842 True 1918.250000 3594 89.733250 223 4814 4 chr2B.!!$R7 4591
13 TraesCS2D01G123600 chr2B 109981090 109983496 2406 True 1728.500000 3338 94.066000 666 3079 2 chr2B.!!$R8 2413
14 TraesCS2D01G123600 chr2B 109094656 109096551 1895 True 1570.000000 1570 82.368000 3014 4918 1 chr2B.!!$R1 1904
15 TraesCS2D01G123600 chr2B 109758798 109760088 1290 True 1312.000000 1312 85.237000 3014 4337 1 chr2B.!!$R3 1323
16 TraesCS2D01G123600 chr2B 109874136 109876724 2588 True 1106.500000 1692 85.034500 1978 4853 2 chr2B.!!$R6 2875
17 TraesCS2D01G123600 chr2B 110067295 110068463 1168 False 1070.000000 1070 83.416000 645 1833 1 chr2B.!!$F1 1188
18 TraesCS2D01G123600 chr2B 109193316 109195275 1959 True 321.000000 468 86.144000 2544 4747 2 chr2B.!!$R5 2203
19 TraesCS2D01G123600 chrUn 289939069 289942463 3394 False 1707.000000 2409 94.925667 1237 4560 3 chrUn.!!$F5 3323
20 TraesCS2D01G123600 chrUn 235537689 235540244 2555 False 790.000000 1709 86.763667 1978 4826 3 chrUn.!!$F4 2848
21 TraesCS2D01G123600 chrUn 289659855 289660414 559 True 418.000000 418 80.531000 3109 3660 1 chrUn.!!$R1 551

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
136 137 0.109532 TCAAACAGGAACCCGATGCA 59.890 50.000 0.00 0.00 0.00 3.96 F
181 182 0.245539 CGACGGCTAGGGTTGAGAAA 59.754 55.000 0.00 0.00 0.00 2.52 F
183 184 0.613777 ACGGCTAGGGTTGAGAAAGG 59.386 55.000 0.00 0.00 0.00 3.11 F
192 193 0.884704 GTTGAGAAAGGCCACGCTCA 60.885 55.000 14.97 14.97 35.74 4.26 F
571 2088 1.200839 CAAACCGTGTCGTCGCTTC 59.799 57.895 0.00 0.00 0.00 3.86 F
1361 2970 1.409064 GTCCAGCGATGACTATGTGGA 59.591 52.381 0.06 0.00 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1383 2992 0.970427 TAGCAGTCCTGATCCACGCA 60.970 55.000 0.00 0.0 0.00 5.24 R
1851 3484 4.926244 TCTCTCTCTTATCATCGTTGTGC 58.074 43.478 0.00 0.0 0.00 4.57 R
1945 3596 9.888878 GTATCCAAAATTATCATCACTGATGTG 57.111 33.333 16.96 7.5 42.19 3.21 R
2828 4516 5.520748 AATGTGAAGGATAGGAACAGGTT 57.479 39.130 0.00 0.0 0.00 3.50 R
3736 5552 4.095782 TGCCACCTAAAACATATTTCGCTC 59.904 41.667 0.00 0.0 0.00 5.03 R
4018 5886 4.444449 GGTCCTTGCTAACTACATAAGGGG 60.444 50.000 0.00 0.0 38.69 4.79 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
22 23 4.685924 CCTTATTCCAACACATCATTGCC 58.314 43.478 0.00 0.00 0.00 4.52
23 24 2.945447 ATTCCAACACATCATTGCCG 57.055 45.000 0.00 0.00 0.00 5.69
24 25 0.243365 TTCCAACACATCATTGCCGC 59.757 50.000 0.00 0.00 0.00 6.53
25 26 1.153784 CCAACACATCATTGCCGCC 60.154 57.895 0.00 0.00 0.00 6.13
26 27 1.585517 CAACACATCATTGCCGCCA 59.414 52.632 0.00 0.00 0.00 5.69
27 28 0.733566 CAACACATCATTGCCGCCAC 60.734 55.000 0.00 0.00 0.00 5.01
28 29 1.876497 AACACATCATTGCCGCCACC 61.876 55.000 0.00 0.00 0.00 4.61
29 30 2.048023 CACATCATTGCCGCCACCT 61.048 57.895 0.00 0.00 0.00 4.00
30 31 1.750399 ACATCATTGCCGCCACCTC 60.750 57.895 0.00 0.00 0.00 3.85
32 33 1.105167 CATCATTGCCGCCACCTCAT 61.105 55.000 0.00 0.00 0.00 2.90
34 35 2.514592 ATTGCCGCCACCTCATCG 60.515 61.111 0.00 0.00 0.00 3.84
35 36 3.030168 ATTGCCGCCACCTCATCGA 62.030 57.895 0.00 0.00 0.00 3.59
36 37 2.329539 ATTGCCGCCACCTCATCGAT 62.330 55.000 0.00 0.00 0.00 3.59
37 38 2.969238 GCCGCCACCTCATCGATG 60.969 66.667 19.61 19.61 0.00 3.84
38 39 2.501128 CCGCCACCTCATCGATGT 59.499 61.111 24.09 3.08 0.00 3.06
39 40 1.153369 CCGCCACCTCATCGATGTT 60.153 57.895 24.09 8.06 0.00 2.71
42 43 1.807755 CGCCACCTCATCGATGTTGAT 60.808 52.381 24.09 3.84 0.00 2.57
43 44 1.600957 GCCACCTCATCGATGTTGATG 59.399 52.381 24.09 15.11 45.70 3.07
44 45 2.216046 CCACCTCATCGATGTTGATGG 58.784 52.381 24.09 19.55 44.68 3.51
45 46 2.216046 CACCTCATCGATGTTGATGGG 58.784 52.381 24.09 17.76 44.80 4.00
51 52 4.331108 TCATCGATGTTGATGGGAAAACA 58.669 39.130 24.09 0.00 44.68 2.83
52 53 4.764308 TCATCGATGTTGATGGGAAAACAA 59.236 37.500 24.09 0.00 44.68 2.83
54 55 5.521906 TCGATGTTGATGGGAAAACAAAA 57.478 34.783 0.00 0.00 39.57 2.44
57 58 5.610398 GATGTTGATGGGAAAACAAAACCT 58.390 37.500 0.00 0.00 39.57 3.50
58 59 6.515862 CGATGTTGATGGGAAAACAAAACCTA 60.516 38.462 0.00 0.00 39.57 3.08
59 60 6.546428 TGTTGATGGGAAAACAAAACCTAA 57.454 33.333 0.00 0.00 33.50 2.69
60 61 6.578023 TGTTGATGGGAAAACAAAACCTAAG 58.422 36.000 0.00 0.00 33.50 2.18
61 62 5.799827 TGATGGGAAAACAAAACCTAAGG 57.200 39.130 0.00 0.00 0.00 2.69
63 64 5.303333 TGATGGGAAAACAAAACCTAAGGAC 59.697 40.000 0.00 0.00 0.00 3.85
64 65 4.611367 TGGGAAAACAAAACCTAAGGACA 58.389 39.130 0.00 0.00 0.00 4.02
65 66 5.212745 TGGGAAAACAAAACCTAAGGACAT 58.787 37.500 0.00 0.00 0.00 3.06
66 67 6.374588 TGGGAAAACAAAACCTAAGGACATA 58.625 36.000 0.00 0.00 0.00 2.29
68 69 7.344871 TGGGAAAACAAAACCTAAGGACATAAA 59.655 33.333 0.00 0.00 0.00 1.40
69 70 8.205512 GGGAAAACAAAACCTAAGGACATAAAA 58.794 33.333 0.00 0.00 0.00 1.52
70 71 9.037737 GGAAAACAAAACCTAAGGACATAAAAC 57.962 33.333 0.00 0.00 0.00 2.43
71 72 8.637281 AAAACAAAACCTAAGGACATAAAACG 57.363 30.769 0.00 0.00 0.00 3.60
72 73 6.321848 ACAAAACCTAAGGACATAAAACGG 57.678 37.500 0.00 0.00 0.00 4.44
73 74 6.063404 ACAAAACCTAAGGACATAAAACGGA 58.937 36.000 0.00 0.00 0.00 4.69
74 75 6.546772 ACAAAACCTAAGGACATAAAACGGAA 59.453 34.615 0.00 0.00 0.00 4.30
75 76 7.231925 ACAAAACCTAAGGACATAAAACGGAAT 59.768 33.333 0.00 0.00 0.00 3.01
76 77 6.753107 AACCTAAGGACATAAAACGGAATG 57.247 37.500 0.00 0.00 0.00 2.67
77 78 5.190677 ACCTAAGGACATAAAACGGAATGG 58.809 41.667 0.00 0.00 0.00 3.16
78 79 4.578928 CCTAAGGACATAAAACGGAATGGG 59.421 45.833 0.00 0.00 0.00 4.00
79 80 2.375146 AGGACATAAAACGGAATGGGC 58.625 47.619 0.00 0.00 0.00 5.36
80 81 1.064952 GGACATAAAACGGAATGGGCG 59.935 52.381 0.00 0.00 0.00 6.13
81 82 1.064952 GACATAAAACGGAATGGGCGG 59.935 52.381 0.00 0.00 0.00 6.13
82 83 1.340211 ACATAAAACGGAATGGGCGGA 60.340 47.619 0.00 0.00 0.00 5.54
83 84 1.064952 CATAAAACGGAATGGGCGGAC 59.935 52.381 0.00 0.00 0.00 4.79
85 86 2.734948 AAAACGGAATGGGCGGACGA 62.735 55.000 0.00 0.00 0.00 4.20
86 87 3.659089 AACGGAATGGGCGGACGAG 62.659 63.158 0.00 0.00 0.00 4.18
87 88 4.143333 CGGAATGGGCGGACGAGT 62.143 66.667 0.00 0.00 0.00 4.18
88 89 2.202892 GGAATGGGCGGACGAGTC 60.203 66.667 0.00 0.00 0.00 3.36
89 90 2.202892 GAATGGGCGGACGAGTCC 60.203 66.667 12.07 12.07 46.18 3.85
90 91 3.735037 GAATGGGCGGACGAGTCCC 62.735 68.421 15.88 8.99 46.96 4.46
95 96 4.131088 GCGGACGAGTCCCCACTC 62.131 72.222 15.88 0.00 46.96 3.51
96 97 3.450115 CGGACGAGTCCCCACTCC 61.450 72.222 15.88 0.00 45.81 3.85
97 98 2.037527 GGACGAGTCCCCACTCCT 59.962 66.667 11.07 0.00 45.81 3.69
98 99 2.053277 GGACGAGTCCCCACTCCTC 61.053 68.421 11.07 0.00 45.81 3.71
99 100 1.000646 GACGAGTCCCCACTCCTCT 60.001 63.158 0.00 0.00 45.81 3.69
100 101 0.612453 GACGAGTCCCCACTCCTCTT 60.612 60.000 0.00 0.00 45.81 2.85
101 102 0.900647 ACGAGTCCCCACTCCTCTTG 60.901 60.000 0.00 0.00 45.81 3.02
102 103 1.599576 GAGTCCCCACTCCTCTTGC 59.400 63.158 0.00 0.00 43.14 4.01
103 104 0.907230 GAGTCCCCACTCCTCTTGCT 60.907 60.000 0.00 0.00 43.14 3.91
104 105 1.197430 AGTCCCCACTCCTCTTGCTG 61.197 60.000 0.00 0.00 0.00 4.41
105 106 2.045536 CCCCACTCCTCTTGCTGC 60.046 66.667 0.00 0.00 0.00 5.25
106 107 2.045536 CCCACTCCTCTTGCTGCC 60.046 66.667 0.00 0.00 0.00 4.85
107 108 2.435586 CCACTCCTCTTGCTGCCG 60.436 66.667 0.00 0.00 0.00 5.69
108 109 2.659016 CACTCCTCTTGCTGCCGA 59.341 61.111 0.00 0.00 0.00 5.54
109 110 1.220206 CACTCCTCTTGCTGCCGAT 59.780 57.895 0.00 0.00 0.00 4.18
110 111 1.088340 CACTCCTCTTGCTGCCGATG 61.088 60.000 0.00 0.00 0.00 3.84
111 112 1.260538 ACTCCTCTTGCTGCCGATGA 61.261 55.000 0.00 0.00 0.00 2.92
113 114 1.523258 CCTCTTGCTGCCGATGAGG 60.523 63.158 11.03 11.03 44.97 3.86
126 127 2.425143 GATGAGGCCATCAAACAGGA 57.575 50.000 5.01 0.00 46.48 3.86
127 128 2.726821 GATGAGGCCATCAAACAGGAA 58.273 47.619 5.01 0.00 46.48 3.36
128 129 1.909700 TGAGGCCATCAAACAGGAAC 58.090 50.000 5.01 0.00 34.02 3.62
130 131 0.251787 AGGCCATCAAACAGGAACCC 60.252 55.000 5.01 0.00 0.00 4.11
131 132 1.595093 GGCCATCAAACAGGAACCCG 61.595 60.000 0.00 0.00 0.00 5.28
132 133 0.608035 GCCATCAAACAGGAACCCGA 60.608 55.000 0.00 0.00 0.00 5.14
134 135 1.745087 CCATCAAACAGGAACCCGATG 59.255 52.381 0.00 0.00 0.00 3.84
135 136 1.133025 CATCAAACAGGAACCCGATGC 59.867 52.381 0.00 0.00 0.00 3.91
136 137 0.109532 TCAAACAGGAACCCGATGCA 59.890 50.000 0.00 0.00 0.00 3.96
137 138 0.958091 CAAACAGGAACCCGATGCAA 59.042 50.000 0.00 0.00 0.00 4.08
139 140 1.234615 AACAGGAACCCGATGCAACG 61.235 55.000 9.71 9.71 0.00 4.10
152 153 4.323477 CAACGGCGTGGGGGAGAA 62.323 66.667 15.70 0.00 0.00 2.87
153 154 3.562232 AACGGCGTGGGGGAGAAA 61.562 61.111 15.70 0.00 0.00 2.52
154 155 3.837570 AACGGCGTGGGGGAGAAAC 62.838 63.158 15.70 0.00 0.00 2.78
155 156 4.016706 CGGCGTGGGGGAGAAACT 62.017 66.667 0.00 0.00 0.00 2.66
156 157 2.434774 GGCGTGGGGGAGAAACTT 59.565 61.111 0.00 0.00 0.00 2.66
157 158 1.971695 GGCGTGGGGGAGAAACTTG 60.972 63.158 0.00 0.00 0.00 3.16
158 159 1.971695 GCGTGGGGGAGAAACTTGG 60.972 63.158 0.00 0.00 0.00 3.61
159 160 1.454539 CGTGGGGGAGAAACTTGGT 59.545 57.895 0.00 0.00 0.00 3.67
160 161 0.889186 CGTGGGGGAGAAACTTGGTG 60.889 60.000 0.00 0.00 0.00 4.17
162 163 1.606601 GGGGGAGAAACTTGGTGGC 60.607 63.158 0.00 0.00 0.00 5.01
164 165 1.072505 GGGAGAAACTTGGTGGCGA 59.927 57.895 0.00 0.00 0.00 5.54
165 166 1.235281 GGGAGAAACTTGGTGGCGAC 61.235 60.000 0.00 0.00 0.00 5.19
166 167 1.566018 GGAGAAACTTGGTGGCGACG 61.566 60.000 0.00 0.00 0.00 5.12
167 168 1.566018 GAGAAACTTGGTGGCGACGG 61.566 60.000 0.00 0.00 0.00 4.79
168 169 3.249973 GAAACTTGGTGGCGACGGC 62.250 63.158 15.43 15.43 38.90 5.68
169 170 3.767630 AAACTTGGTGGCGACGGCT 62.768 57.895 22.70 0.00 39.81 5.52
170 171 2.386064 AAACTTGGTGGCGACGGCTA 62.386 55.000 22.70 6.21 39.81 3.93
171 172 2.509336 CTTGGTGGCGACGGCTAG 60.509 66.667 22.70 10.37 39.81 3.42
172 173 4.077184 TTGGTGGCGACGGCTAGG 62.077 66.667 22.70 0.00 39.81 3.02
175 176 4.078516 GTGGCGACGGCTAGGGTT 62.079 66.667 22.70 0.00 39.81 4.11
176 177 4.077184 TGGCGACGGCTAGGGTTG 62.077 66.667 22.70 0.00 39.81 3.77
177 178 3.766691 GGCGACGGCTAGGGTTGA 61.767 66.667 15.00 0.00 39.81 3.18
178 179 2.202756 GCGACGGCTAGGGTTGAG 60.203 66.667 0.00 0.00 35.83 3.02
181 182 0.245539 CGACGGCTAGGGTTGAGAAA 59.754 55.000 0.00 0.00 0.00 2.52
182 183 1.736032 CGACGGCTAGGGTTGAGAAAG 60.736 57.143 0.00 0.00 0.00 2.62
183 184 0.613777 ACGGCTAGGGTTGAGAAAGG 59.386 55.000 0.00 0.00 0.00 3.11
191 192 1.578206 GGTTGAGAAAGGCCACGCTC 61.578 60.000 5.01 8.72 0.00 5.03
192 193 0.884704 GTTGAGAAAGGCCACGCTCA 60.885 55.000 14.97 14.97 35.74 4.26
206 207 2.845967 CACGCTCACTTTGACAACAAAC 59.154 45.455 0.00 0.00 40.47 2.93
210 211 4.485163 GCTCACTTTGACAACAAACTTGT 58.515 39.130 0.00 0.00 44.72 3.16
217 218 8.707839 CACTTTGACAACAAACTTGTGTTAATT 58.292 29.630 0.00 0.00 41.31 1.40
225 226 9.086336 CAACAAACTTGTGTTAATTCATGAAGT 57.914 29.630 14.54 14.05 41.31 3.01
254 255 9.787435 TTAATAGACAACATAGTGGTCAAGTTT 57.213 29.630 7.37 0.00 38.83 2.66
283 284 3.323403 CCCCCTGCACAAAAATTAAGTCA 59.677 43.478 0.00 0.00 0.00 3.41
408 1910 7.693952 TCACCAATTTAATGATCTAAACGCTC 58.306 34.615 0.00 0.00 0.00 5.03
473 1975 2.093152 GCCTTCTGATGCGCAATTTTTG 59.907 45.455 17.11 3.84 0.00 2.44
542 2059 6.012858 AGTGGGACATTTTACTCCAGATGTTA 60.013 38.462 0.00 0.00 44.52 2.41
571 2088 1.200839 CAAACCGTGTCGTCGCTTC 59.799 57.895 0.00 0.00 0.00 3.86
742 2281 1.825341 GGAATGCCCAAAGCCCATC 59.175 57.895 0.00 0.00 42.71 3.51
755 2294 3.455737 CCCATCGGCCCCATTTTAT 57.544 52.632 0.00 0.00 0.00 1.40
756 2295 1.715785 CCCATCGGCCCCATTTTATT 58.284 50.000 0.00 0.00 0.00 1.40
757 2296 2.046292 CCCATCGGCCCCATTTTATTT 58.954 47.619 0.00 0.00 0.00 1.40
758 2297 2.224257 CCCATCGGCCCCATTTTATTTG 60.224 50.000 0.00 0.00 0.00 2.32
760 2299 1.859302 TCGGCCCCATTTTATTTGCT 58.141 45.000 0.00 0.00 0.00 3.91
761 2300 1.480137 TCGGCCCCATTTTATTTGCTG 59.520 47.619 0.00 0.00 0.00 4.41
830 2424 6.418141 CCAAAATTTCGAATTTCAAAAGCGT 58.582 32.000 0.00 0.00 0.00 5.07
831 2425 7.306866 CCCAAAATTTCGAATTTCAAAAGCGTA 60.307 33.333 0.00 0.00 0.00 4.42
852 2446 1.534729 AAGAACTCCACGCCATTTCC 58.465 50.000 0.00 0.00 0.00 3.13
1361 2970 1.409064 GTCCAGCGATGACTATGTGGA 59.591 52.381 0.06 0.00 0.00 4.02
1378 2987 2.030981 GTGGACTTCGACGAGAAAGACT 60.031 50.000 0.00 0.00 38.57 3.24
1383 2992 3.256136 ACTTCGACGAGAAAGACTCCAAT 59.744 43.478 0.00 0.00 42.18 3.16
2472 4147 7.737869 TCTAGTGTCAATACCTGGTTACAAAA 58.262 34.615 3.84 0.00 0.00 2.44
2701 4388 7.014711 CAGTCATTATAAGAGAGTCTAAGGCCA 59.985 40.741 5.01 0.00 0.00 5.36
3351 5142 8.221100 GTGATTACATATTTGGTGTATGCTACG 58.779 37.037 0.00 0.00 33.79 3.51
3736 5552 2.559668 ACACATTGGCATGTTCCTGAAG 59.440 45.455 0.00 0.00 41.16 3.02
4018 5886 2.480555 CTGCCGCGATCAAACCAC 59.519 61.111 8.23 0.00 0.00 4.16
4237 6111 3.526931 TGCTTTCTTACCGGATCAGAG 57.473 47.619 9.46 0.00 0.00 3.35
4342 6291 7.418337 AGGGTTCATTTGTCAGTTTAAGTTT 57.582 32.000 0.00 0.00 0.00 2.66
4343 6292 8.528044 AGGGTTCATTTGTCAGTTTAAGTTTA 57.472 30.769 0.00 0.00 0.00 2.01
4344 6293 8.630037 AGGGTTCATTTGTCAGTTTAAGTTTAG 58.370 33.333 0.00 0.00 0.00 1.85
4345 6294 8.410912 GGGTTCATTTGTCAGTTTAAGTTTAGT 58.589 33.333 0.00 0.00 0.00 2.24
4385 6334 9.821662 ACGTTTTATATGCAGTAGAAAGAAAAC 57.178 29.630 0.00 0.00 33.20 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.685924 GGCAATGATGTGTTGGAATAAGG 58.314 43.478 0.00 0.00 0.00 2.69
1 2 4.353737 CGGCAATGATGTGTTGGAATAAG 58.646 43.478 0.00 0.00 0.00 1.73
4 5 1.135024 GCGGCAATGATGTGTTGGAAT 60.135 47.619 0.00 0.00 0.00 3.01
5 6 0.243365 GCGGCAATGATGTGTTGGAA 59.757 50.000 0.00 0.00 0.00 3.53
8 9 0.733566 GTGGCGGCAATGATGTGTTG 60.734 55.000 15.50 0.00 0.00 3.33
9 10 1.586028 GTGGCGGCAATGATGTGTT 59.414 52.632 15.50 0.00 0.00 3.32
10 11 2.342650 GGTGGCGGCAATGATGTGT 61.343 57.895 15.50 0.00 0.00 3.72
11 12 1.996786 GAGGTGGCGGCAATGATGTG 61.997 60.000 15.50 0.00 0.00 3.21
12 13 1.750399 GAGGTGGCGGCAATGATGT 60.750 57.895 15.50 0.00 0.00 3.06
13 14 1.105167 ATGAGGTGGCGGCAATGATG 61.105 55.000 15.50 0.00 0.00 3.07
14 15 0.820891 GATGAGGTGGCGGCAATGAT 60.821 55.000 15.50 4.99 0.00 2.45
15 16 1.451927 GATGAGGTGGCGGCAATGA 60.452 57.895 15.50 0.00 0.00 2.57
16 17 2.827051 CGATGAGGTGGCGGCAATG 61.827 63.158 15.50 0.00 0.00 2.82
18 19 3.030168 ATCGATGAGGTGGCGGCAA 62.030 57.895 15.50 0.00 0.00 4.52
20 21 2.969238 CATCGATGAGGTGGCGGC 60.969 66.667 21.02 0.00 0.00 6.53
21 22 1.153369 AACATCGATGAGGTGGCGG 60.153 57.895 31.33 2.03 34.56 6.13
22 23 0.460109 TCAACATCGATGAGGTGGCG 60.460 55.000 31.33 10.85 34.56 5.69
23 24 1.600957 CATCAACATCGATGAGGTGGC 59.399 52.381 31.33 0.00 44.67 5.01
24 25 2.216046 CCATCAACATCGATGAGGTGG 58.784 52.381 31.33 29.12 44.67 4.61
25 26 2.158914 TCCCATCAACATCGATGAGGTG 60.159 50.000 31.33 25.21 44.67 4.00
26 27 2.118679 TCCCATCAACATCGATGAGGT 58.881 47.619 31.33 16.40 44.67 3.85
27 28 2.916702 TCCCATCAACATCGATGAGG 57.083 50.000 31.33 20.88 44.67 3.86
28 29 4.395854 TGTTTTCCCATCAACATCGATGAG 59.604 41.667 31.33 21.49 44.67 2.90
29 30 4.331108 TGTTTTCCCATCAACATCGATGA 58.669 39.130 31.33 11.26 44.67 2.92
30 31 4.700268 TGTTTTCCCATCAACATCGATG 57.300 40.909 23.68 23.68 42.09 3.84
32 33 5.285651 GTTTTGTTTTCCCATCAACATCGA 58.714 37.500 0.00 0.00 32.96 3.59
34 35 5.610398 AGGTTTTGTTTTCCCATCAACATC 58.390 37.500 0.00 0.00 32.96 3.06
35 36 5.628797 AGGTTTTGTTTTCCCATCAACAT 57.371 34.783 0.00 0.00 32.96 2.71
36 37 6.407525 CCTTAGGTTTTGTTTTCCCATCAACA 60.408 38.462 0.00 0.00 0.00 3.33
37 38 5.989168 CCTTAGGTTTTGTTTTCCCATCAAC 59.011 40.000 0.00 0.00 0.00 3.18
38 39 5.900123 TCCTTAGGTTTTGTTTTCCCATCAA 59.100 36.000 0.00 0.00 0.00 2.57
39 40 5.303333 GTCCTTAGGTTTTGTTTTCCCATCA 59.697 40.000 0.00 0.00 0.00 3.07
42 43 4.611367 TGTCCTTAGGTTTTGTTTTCCCA 58.389 39.130 0.00 0.00 0.00 4.37
43 44 5.801531 ATGTCCTTAGGTTTTGTTTTCCC 57.198 39.130 0.00 0.00 0.00 3.97
44 45 9.037737 GTTTTATGTCCTTAGGTTTTGTTTTCC 57.962 33.333 0.00 0.00 0.00 3.13
45 46 8.748582 CGTTTTATGTCCTTAGGTTTTGTTTTC 58.251 33.333 0.00 0.00 0.00 2.29
46 47 7.707464 CCGTTTTATGTCCTTAGGTTTTGTTTT 59.293 33.333 0.00 0.00 0.00 2.43
47 48 7.068470 TCCGTTTTATGTCCTTAGGTTTTGTTT 59.932 33.333 0.00 0.00 0.00 2.83
48 49 6.546772 TCCGTTTTATGTCCTTAGGTTTTGTT 59.453 34.615 0.00 0.00 0.00 2.83
49 50 6.063404 TCCGTTTTATGTCCTTAGGTTTTGT 58.937 36.000 0.00 0.00 0.00 2.83
51 52 7.309560 CCATTCCGTTTTATGTCCTTAGGTTTT 60.310 37.037 0.00 0.00 0.00 2.43
52 53 6.152154 CCATTCCGTTTTATGTCCTTAGGTTT 59.848 38.462 0.00 0.00 0.00 3.27
54 55 5.190677 CCATTCCGTTTTATGTCCTTAGGT 58.809 41.667 0.00 0.00 0.00 3.08
57 58 3.949113 GCCCATTCCGTTTTATGTCCTTA 59.051 43.478 0.00 0.00 0.00 2.69
58 59 2.758423 GCCCATTCCGTTTTATGTCCTT 59.242 45.455 0.00 0.00 0.00 3.36
59 60 2.375146 GCCCATTCCGTTTTATGTCCT 58.625 47.619 0.00 0.00 0.00 3.85
60 61 1.064952 CGCCCATTCCGTTTTATGTCC 59.935 52.381 0.00 0.00 0.00 4.02
61 62 1.064952 CCGCCCATTCCGTTTTATGTC 59.935 52.381 0.00 0.00 0.00 3.06
63 64 1.064952 GTCCGCCCATTCCGTTTTATG 59.935 52.381 0.00 0.00 0.00 1.90
64 65 1.385528 GTCCGCCCATTCCGTTTTAT 58.614 50.000 0.00 0.00 0.00 1.40
65 66 1.020333 CGTCCGCCCATTCCGTTTTA 61.020 55.000 0.00 0.00 0.00 1.52
66 67 2.329614 CGTCCGCCCATTCCGTTTT 61.330 57.895 0.00 0.00 0.00 2.43
68 69 3.659089 CTCGTCCGCCCATTCCGTT 62.659 63.158 0.00 0.00 0.00 4.44
69 70 4.143333 CTCGTCCGCCCATTCCGT 62.143 66.667 0.00 0.00 0.00 4.69
70 71 4.143333 ACTCGTCCGCCCATTCCG 62.143 66.667 0.00 0.00 0.00 4.30
71 72 2.202892 GACTCGTCCGCCCATTCC 60.203 66.667 0.00 0.00 0.00 3.01
72 73 2.202892 GGACTCGTCCGCCCATTC 60.203 66.667 0.00 0.00 40.36 2.67
80 81 2.502329 AGAGGAGTGGGGACTCGTCC 62.502 65.000 17.11 7.57 46.75 4.79
81 82 0.612453 AAGAGGAGTGGGGACTCGTC 60.612 60.000 14.24 14.24 46.24 4.20
82 83 0.900647 CAAGAGGAGTGGGGACTCGT 60.901 60.000 0.00 0.00 37.61 4.18
83 84 1.893786 CAAGAGGAGTGGGGACTCG 59.106 63.158 0.00 0.00 37.61 4.18
85 86 1.159664 AGCAAGAGGAGTGGGGACT 59.840 57.895 0.00 0.00 0.00 3.85
86 87 1.298014 CAGCAAGAGGAGTGGGGAC 59.702 63.158 0.00 0.00 0.00 4.46
87 88 2.596851 GCAGCAAGAGGAGTGGGGA 61.597 63.158 0.00 0.00 0.00 4.81
88 89 2.045536 GCAGCAAGAGGAGTGGGG 60.046 66.667 0.00 0.00 0.00 4.96
89 90 2.045536 GGCAGCAAGAGGAGTGGG 60.046 66.667 0.00 0.00 0.00 4.61
90 91 2.249413 ATCGGCAGCAAGAGGAGTGG 62.249 60.000 0.00 0.00 0.00 4.00
91 92 1.088340 CATCGGCAGCAAGAGGAGTG 61.088 60.000 0.00 0.00 0.00 3.51
92 93 1.220206 CATCGGCAGCAAGAGGAGT 59.780 57.895 0.00 0.00 0.00 3.85
93 94 0.530211 CTCATCGGCAGCAAGAGGAG 60.530 60.000 14.55 14.55 38.62 3.69
94 95 1.519246 CTCATCGGCAGCAAGAGGA 59.481 57.895 0.00 0.00 0.00 3.71
95 96 1.523258 CCTCATCGGCAGCAAGAGG 60.523 63.158 7.13 7.13 39.83 3.69
96 97 4.121691 CCTCATCGGCAGCAAGAG 57.878 61.111 0.00 0.00 0.00 2.85
108 109 2.450476 GTTCCTGTTTGATGGCCTCAT 58.550 47.619 3.32 0.00 32.72 2.90
109 110 1.547675 GGTTCCTGTTTGATGGCCTCA 60.548 52.381 3.32 2.06 0.00 3.86
110 111 1.177401 GGTTCCTGTTTGATGGCCTC 58.823 55.000 3.32 0.00 0.00 4.70
111 112 0.251787 GGGTTCCTGTTTGATGGCCT 60.252 55.000 3.32 0.00 0.00 5.19
113 114 0.608035 TCGGGTTCCTGTTTGATGGC 60.608 55.000 0.00 0.00 0.00 4.40
114 115 1.745087 CATCGGGTTCCTGTTTGATGG 59.255 52.381 0.00 0.00 31.82 3.51
115 116 1.133025 GCATCGGGTTCCTGTTTGATG 59.867 52.381 0.00 0.00 37.01 3.07
116 117 1.271871 TGCATCGGGTTCCTGTTTGAT 60.272 47.619 0.00 0.00 0.00 2.57
117 118 0.109532 TGCATCGGGTTCCTGTTTGA 59.890 50.000 0.00 0.00 0.00 2.69
119 120 0.958822 GTTGCATCGGGTTCCTGTTT 59.041 50.000 0.00 0.00 0.00 2.83
120 121 1.234615 CGTTGCATCGGGTTCCTGTT 61.235 55.000 9.33 0.00 0.00 3.16
121 122 1.671054 CGTTGCATCGGGTTCCTGT 60.671 57.895 9.33 0.00 0.00 4.00
123 124 2.046314 CCGTTGCATCGGGTTCCT 60.046 61.111 25.40 0.00 45.88 3.36
135 136 3.835790 TTTCTCCCCCACGCCGTTG 62.836 63.158 0.00 0.00 0.00 4.10
136 137 3.562232 TTTCTCCCCCACGCCGTT 61.562 61.111 0.00 0.00 0.00 4.44
137 138 4.324991 GTTTCTCCCCCACGCCGT 62.325 66.667 0.00 0.00 0.00 5.68
139 140 1.971695 CAAGTTTCTCCCCCACGCC 60.972 63.158 0.00 0.00 0.00 5.68
140 141 1.971695 CCAAGTTTCTCCCCCACGC 60.972 63.158 0.00 0.00 0.00 5.34
141 142 0.889186 CACCAAGTTTCTCCCCCACG 60.889 60.000 0.00 0.00 0.00 4.94
142 143 0.539669 CCACCAAGTTTCTCCCCCAC 60.540 60.000 0.00 0.00 0.00 4.61
143 144 1.850549 CCACCAAGTTTCTCCCCCA 59.149 57.895 0.00 0.00 0.00 4.96
145 146 1.971695 CGCCACCAAGTTTCTCCCC 60.972 63.158 0.00 0.00 0.00 4.81
146 147 1.072505 TCGCCACCAAGTTTCTCCC 59.927 57.895 0.00 0.00 0.00 4.30
147 148 1.566018 CGTCGCCACCAAGTTTCTCC 61.566 60.000 0.00 0.00 0.00 3.71
149 150 1.597027 CCGTCGCCACCAAGTTTCT 60.597 57.895 0.00 0.00 0.00 2.52
151 152 2.386064 TAGCCGTCGCCACCAAGTTT 62.386 55.000 0.00 0.00 34.57 2.66
152 153 2.781595 CTAGCCGTCGCCACCAAGTT 62.782 60.000 0.00 0.00 34.57 2.66
153 154 3.296709 CTAGCCGTCGCCACCAAGT 62.297 63.158 0.00 0.00 34.57 3.16
154 155 2.509336 CTAGCCGTCGCCACCAAG 60.509 66.667 0.00 0.00 34.57 3.61
155 156 4.077184 CCTAGCCGTCGCCACCAA 62.077 66.667 0.00 0.00 34.57 3.67
158 159 4.078516 AACCCTAGCCGTCGCCAC 62.079 66.667 0.00 0.00 34.57 5.01
159 160 4.077184 CAACCCTAGCCGTCGCCA 62.077 66.667 0.00 0.00 34.57 5.69
160 161 3.718210 CTCAACCCTAGCCGTCGCC 62.718 68.421 0.00 0.00 34.57 5.54
162 163 0.245539 TTTCTCAACCCTAGCCGTCG 59.754 55.000 0.00 0.00 0.00 5.12
164 165 0.613777 CCTTTCTCAACCCTAGCCGT 59.386 55.000 0.00 0.00 0.00 5.68
165 166 0.744771 GCCTTTCTCAACCCTAGCCG 60.745 60.000 0.00 0.00 0.00 5.52
166 167 0.394488 GGCCTTTCTCAACCCTAGCC 60.394 60.000 0.00 0.00 0.00 3.93
167 168 0.328258 TGGCCTTTCTCAACCCTAGC 59.672 55.000 3.32 0.00 0.00 3.42
168 169 1.676014 CGTGGCCTTTCTCAACCCTAG 60.676 57.143 3.32 0.00 0.00 3.02
169 170 0.323629 CGTGGCCTTTCTCAACCCTA 59.676 55.000 3.32 0.00 0.00 3.53
170 171 1.073199 CGTGGCCTTTCTCAACCCT 59.927 57.895 3.32 0.00 0.00 4.34
171 172 2.626780 GCGTGGCCTTTCTCAACCC 61.627 63.158 3.32 0.00 0.00 4.11
172 173 1.578206 GAGCGTGGCCTTTCTCAACC 61.578 60.000 3.32 0.00 0.00 3.77
173 174 0.884704 TGAGCGTGGCCTTTCTCAAC 60.885 55.000 15.62 0.00 33.17 3.18
174 175 0.884704 GTGAGCGTGGCCTTTCTCAA 60.885 55.000 18.34 5.39 37.33 3.02
175 176 1.301716 GTGAGCGTGGCCTTTCTCA 60.302 57.895 14.49 14.49 33.64 3.27
176 177 0.603975 AAGTGAGCGTGGCCTTTCTC 60.604 55.000 3.32 8.01 0.00 2.87
177 178 0.179018 AAAGTGAGCGTGGCCTTTCT 60.179 50.000 3.32 0.00 0.00 2.52
178 179 0.040067 CAAAGTGAGCGTGGCCTTTC 60.040 55.000 3.32 0.00 0.00 2.62
181 182 1.598130 GTCAAAGTGAGCGTGGCCT 60.598 57.895 3.32 0.00 0.00 5.19
182 183 1.444119 TTGTCAAAGTGAGCGTGGCC 61.444 55.000 0.00 0.00 0.00 5.36
183 184 0.317020 GTTGTCAAAGTGAGCGTGGC 60.317 55.000 0.00 0.00 0.00 5.01
191 192 7.630470 TTAACACAAGTTTGTTGTCAAAGTG 57.370 32.000 11.37 6.10 43.69 3.16
192 193 8.825667 AATTAACACAAGTTTGTTGTCAAAGT 57.174 26.923 11.37 0.00 45.59 2.66
244 245 2.374170 GGGGGTCTAGAAAACTTGACCA 59.626 50.000 23.56 0.00 46.23 4.02
245 246 2.643304 AGGGGGTCTAGAAAACTTGACC 59.357 50.000 17.60 17.60 44.59 4.02
254 255 1.440618 TTTGTGCAGGGGGTCTAGAA 58.559 50.000 0.00 0.00 0.00 2.10
313 785 6.377996 TGGCTTATGTTCTTCATGTAGCATTT 59.622 34.615 13.97 0.00 42.20 2.32
367 839 8.575649 AAATTGGTGATCTAAACGGTCTTATT 57.424 30.769 0.00 0.00 0.00 1.40
425 1927 6.449830 AACCAGTTTAAGTGATACTCCCTT 57.550 37.500 0.72 0.00 0.00 3.95
440 1942 4.082026 GCATCAGAAGGCATAAACCAGTTT 60.082 41.667 0.86 0.86 32.82 2.66
473 1975 5.627499 TGCACACTTCTGTCCATTAATTC 57.373 39.130 0.00 0.00 0.00 2.17
542 2059 1.960689 ACACGGTTTGCTTTTGCCTAT 59.039 42.857 0.00 0.00 46.87 2.57
571 2088 3.806521 AGCTAATGCATTCTACTGCTTCG 59.193 43.478 16.86 0.00 42.75 3.79
632 2164 6.552008 ACTACAAAAATTCCCCATTCTCTCA 58.448 36.000 0.00 0.00 0.00 3.27
637 2169 8.570068 TGTACTACTACAAAAATTCCCCATTC 57.430 34.615 0.00 0.00 29.36 2.67
742 2281 1.938625 CAGCAAATAAAATGGGGCCG 58.061 50.000 0.00 0.00 0.00 6.13
830 2424 3.504520 GGAAATGGCGTGGAGTTCTTTTA 59.495 43.478 0.00 0.00 0.00 1.52
831 2425 2.296190 GGAAATGGCGTGGAGTTCTTTT 59.704 45.455 0.00 0.00 0.00 2.27
852 2446 2.268298 CAACTTACGGAGGGATTCGTG 58.732 52.381 0.00 0.00 40.05 4.35
1333 2942 4.479993 ATCGCTGGACTGCAGGCC 62.480 66.667 33.16 33.16 0.00 5.19
1361 2970 2.228059 TGGAGTCTTTCTCGTCGAAGT 58.772 47.619 0.00 0.00 43.60 3.01
1383 2992 0.970427 TAGCAGTCCTGATCCACGCA 60.970 55.000 0.00 0.00 0.00 5.24
1851 3484 4.926244 TCTCTCTCTTATCATCGTTGTGC 58.074 43.478 0.00 0.00 0.00 4.57
1945 3596 9.888878 GTATCCAAAATTATCATCACTGATGTG 57.111 33.333 16.96 7.50 42.19 3.21
2828 4516 5.520748 AATGTGAAGGATAGGAACAGGTT 57.479 39.130 0.00 0.00 0.00 3.50
3736 5552 4.095782 TGCCACCTAAAACATATTTCGCTC 59.904 41.667 0.00 0.00 0.00 5.03
4018 5886 4.444449 GGTCCTTGCTAACTACATAAGGGG 60.444 50.000 0.00 0.00 38.69 4.79
4278 6153 7.335491 GGAGTAAAATAACAAAGCGTATCTCG 58.665 38.462 0.00 0.00 43.12 4.04
4359 6308 9.821662 GTTTTCTTTCTACTGCATATAAAACGT 57.178 29.630 0.00 0.00 0.00 3.99
4360 6309 9.820229 TGTTTTCTTTCTACTGCATATAAAACG 57.180 29.630 0.00 0.00 37.20 3.60
4364 6313 9.502091 AGTGTGTTTTCTTTCTACTGCATATAA 57.498 29.630 0.00 0.00 0.00 0.98
4365 6314 9.502091 AAGTGTGTTTTCTTTCTACTGCATATA 57.498 29.630 0.00 0.00 0.00 0.86
4366 6315 7.986085 AGTGTGTTTTCTTTCTACTGCATAT 57.014 32.000 0.00 0.00 0.00 1.78
4367 6316 7.497579 TGAAGTGTGTTTTCTTTCTACTGCATA 59.502 33.333 0.00 0.00 0.00 3.14
4368 6317 6.318648 TGAAGTGTGTTTTCTTTCTACTGCAT 59.681 34.615 0.00 0.00 0.00 3.96
4369 6318 5.645929 TGAAGTGTGTTTTCTTTCTACTGCA 59.354 36.000 0.00 0.00 0.00 4.41
4370 6319 6.119144 TGAAGTGTGTTTTCTTTCTACTGC 57.881 37.500 0.00 0.00 0.00 4.40
4376 6325 9.944663 TGTTGTATATGAAGTGTGTTTTCTTTC 57.055 29.630 0.00 0.00 0.00 2.62
4385 6334 8.948631 ATTCTACCTGTTGTATATGAAGTGTG 57.051 34.615 0.00 0.00 0.00 3.82
4662 6620 5.815233 TCAGGGCAAATTGTTAAATTGGA 57.185 34.783 0.00 0.00 36.11 3.53


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

AutoCloner maintained by Alex Coulton.