Multiple sequence alignment - TraesCS1B01G102300

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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 TraesCS1B01G102300 chr1B 100.000 5582 0 0 1 5582 112361587 112356006 0.000000e+00 10309
1 TraesCS1B01G102300 chr1B 98.144 2209 35 5 3240 5447 588507111 588509314 0.000000e+00 3847
2 TraesCS1B01G102300 chr1B 94.698 1886 79 12 2189 4071 16563984 16565851 0.000000e+00 2909
3 TraesCS1B01G102300 chr1B 92.706 1892 90 25 2189 4071 222201608 222199756 0.000000e+00 2686
4 TraesCS1B01G102300 chr1B 97.419 1201 30 1 308 1508 588505890 588507089 0.000000e+00 2045
5 TraesCS1B01G102300 chr1B 93.034 646 22 5 4799 5421 24024257 24024902 0.000000e+00 922
6 TraesCS1B01G102300 chr1B 98.706 309 3 1 1 308 569426201 569426509 1.060000e-151 547
7 TraesCS1B01G102300 chr1B 94.904 314 16 0 5108 5421 328503686 328503999 5.020000e-135 492
8 TraesCS1B01G102300 chr5A 98.272 5093 77 7 344 5429 504758547 504763635 0.000000e+00 8907
9 TraesCS1B01G102300 chr5A 98.086 2194 39 2 3240 5433 452277424 452275234 0.000000e+00 3816
10 TraesCS1B01G102300 chr5A 97.245 1198 32 1 311 1508 452278642 452277446 0.000000e+00 2028
11 TraesCS1B01G102300 chr5A 90.610 607 49 4 4109 4711 600887663 600888265 0.000000e+00 798
12 TraesCS1B01G102300 chr5A 94.048 84 5 0 5499 5582 74556964 74557047 1.630000e-25 128
13 TraesCS1B01G102300 chr4B 98.029 5124 92 5 311 5428 553360509 553355389 0.000000e+00 8894
14 TraesCS1B01G102300 chr4B 93.899 754 36 6 3324 4071 82169140 82169889 0.000000e+00 1129
15 TraesCS1B01G102300 chr3A 98.079 2186 38 3 3240 5425 743445640 743447821 0.000000e+00 3801
16 TraesCS1B01G102300 chr3A 97.007 1203 33 2 308 1508 743444417 743445618 0.000000e+00 2019
17 TraesCS1B01G102300 chr3A 89.249 1265 95 16 4083 5314 719529826 719531082 0.000000e+00 1544
18 TraesCS1B01G102300 chr3A 90.293 752 56 4 4468 5203 291177765 291178515 0.000000e+00 968
19 TraesCS1B01G102300 chr3A 98.382 309 3 2 1 308 704397778 704397471 4.920000e-150 542
20 TraesCS1B01G102300 chr3A 96.341 82 3 0 5501 5582 495025309 495025390 9.750000e-28 135
21 TraesCS1B01G102300 chr2B 97.325 2243 41 17 3240 5472 604468997 604466764 0.000000e+00 3792
22 TraesCS1B01G102300 chr2B 97.329 1198 31 1 311 1508 604470215 604469019 0.000000e+00 2034
23 TraesCS1B01G102300 chr2B 87.024 1156 97 12 4109 5245 568667422 568668543 0.000000e+00 1254
24 TraesCS1B01G102300 chr2B 97.799 318 5 2 1 316 57811 58128 1.060000e-151 547
25 TraesCS1B01G102300 chr2B 97.799 318 5 2 1 316 171910 172227 1.060000e-151 547
26 TraesCS1B01G102300 chr3B 93.016 1890 95 21 2189 4071 641067478 641069337 0.000000e+00 2724
27 TraesCS1B01G102300 chr3B 92.974 1893 89 20 2189 4071 457030929 457029071 0.000000e+00 2719
28 TraesCS1B01G102300 chr3B 93.914 1068 61 3 1141 2207 641066401 641067465 0.000000e+00 1609
29 TraesCS1B01G102300 chr3B 93.721 1067 62 4 1141 2206 457032007 457030945 0.000000e+00 1594
30 TraesCS1B01G102300 chr3B 98.089 314 4 2 1 312 71891712 71892025 3.800000e-151 545
31 TraesCS1B01G102300 chr4D 94.316 1777 86 12 1139 2908 115203890 115202122 0.000000e+00 2708
32 TraesCS1B01G102300 chr4D 93.055 1771 91 8 1142 2908 81177201 81175459 0.000000e+00 2560
33 TraesCS1B01G102300 chr4D 91.765 510 30 4 4109 4614 58913781 58914282 0.000000e+00 699
34 TraesCS1B01G102300 chr6A 92.812 1892 92 20 2189 4071 60386965 60385109 0.000000e+00 2700
35 TraesCS1B01G102300 chr6A 94.068 1770 94 7 1142 2908 617537419 617535658 0.000000e+00 2676
36 TraesCS1B01G102300 chr6A 93.721 1067 62 4 1141 2206 194805761 194806823 0.000000e+00 1594
37 TraesCS1B01G102300 chr6A 89.036 830 75 11 308 1134 194804199 194805015 0.000000e+00 1014
38 TraesCS1B01G102300 chr6A 86.842 152 10 10 5438 5582 155805999 155806147 1.610000e-35 161
39 TraesCS1B01G102300 chr6B 87.630 2304 196 44 1826 4071 655234254 655236526 0.000000e+00 2593
40 TraesCS1B01G102300 chr6B 95.141 638 16 3 4799 5421 187092828 187093465 0.000000e+00 992
41 TraesCS1B01G102300 chr7A 92.243 1779 100 7 1142 2908 608953993 608952241 0.000000e+00 2486
42 TraesCS1B01G102300 chr7A 93.908 1067 60 4 1141 2206 710684889 710683827 0.000000e+00 1605
43 TraesCS1B01G102300 chr7A 89.117 827 75 11 311 1134 710685771 710684957 0.000000e+00 1014
44 TraesCS1B01G102300 chr7A 98.433 319 3 2 1 317 30236522 30236204 1.360000e-155 560
45 TraesCS1B01G102300 chr7A 94.382 89 4 1 5495 5582 401611342 401611254 9.750000e-28 135
46 TraesCS1B01G102300 chr4A 86.532 2272 204 30 1826 4066 310427189 310424989 0.000000e+00 2407
47 TraesCS1B01G102300 chr4A 90.282 638 24 12 4799 5421 711819929 711819315 0.000000e+00 800
48 TraesCS1B01G102300 chr7B 87.288 944 88 7 2469 3392 740575632 740576563 0.000000e+00 1050
49 TraesCS1B01G102300 chr7B 88.686 875 75 8 2469 3323 740562091 740562961 0.000000e+00 1046
50 TraesCS1B01G102300 chr7B 88.571 875 76 8 2469 3323 740655353 740656223 0.000000e+00 1040
51 TraesCS1B01G102300 chr7B 97.742 310 5 2 1 309 32558854 32558546 2.960000e-147 532
52 TraesCS1B01G102300 chr5B 88.875 827 76 11 311 1134 471923304 471922491 0.000000e+00 1003
53 TraesCS1B01G102300 chr1A 98.113 318 3 3 1 315 474158244 474158561 8.170000e-153 551
54 TraesCS1B01G102300 chr2A 98.361 305 3 2 1 304 719353502 719353199 8.230000e-148 534


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 TraesCS1B01G102300 chr1B 112356006 112361587 5581 True 10309.0 10309 100.0000 1 5582 1 chr1B.!!$R1 5581
1 TraesCS1B01G102300 chr1B 588505890 588509314 3424 False 2946.0 3847 97.7815 308 5447 2 chr1B.!!$F5 5139
2 TraesCS1B01G102300 chr1B 16563984 16565851 1867 False 2909.0 2909 94.6980 2189 4071 1 chr1B.!!$F1 1882
3 TraesCS1B01G102300 chr1B 222199756 222201608 1852 True 2686.0 2686 92.7060 2189 4071 1 chr1B.!!$R2 1882
4 TraesCS1B01G102300 chr1B 24024257 24024902 645 False 922.0 922 93.0340 4799 5421 1 chr1B.!!$F2 622
5 TraesCS1B01G102300 chr5A 504758547 504763635 5088 False 8907.0 8907 98.2720 344 5429 1 chr5A.!!$F2 5085
6 TraesCS1B01G102300 chr5A 452275234 452278642 3408 True 2922.0 3816 97.6655 311 5433 2 chr5A.!!$R1 5122
7 TraesCS1B01G102300 chr5A 600887663 600888265 602 False 798.0 798 90.6100 4109 4711 1 chr5A.!!$F3 602
8 TraesCS1B01G102300 chr4B 553355389 553360509 5120 True 8894.0 8894 98.0290 311 5428 1 chr4B.!!$R1 5117
9 TraesCS1B01G102300 chr4B 82169140 82169889 749 False 1129.0 1129 93.8990 3324 4071 1 chr4B.!!$F1 747
10 TraesCS1B01G102300 chr3A 743444417 743447821 3404 False 2910.0 3801 97.5430 308 5425 2 chr3A.!!$F4 5117
11 TraesCS1B01G102300 chr3A 719529826 719531082 1256 False 1544.0 1544 89.2490 4083 5314 1 chr3A.!!$F3 1231
12 TraesCS1B01G102300 chr3A 291177765 291178515 750 False 968.0 968 90.2930 4468 5203 1 chr3A.!!$F1 735
13 TraesCS1B01G102300 chr2B 604466764 604470215 3451 True 2913.0 3792 97.3270 311 5472 2 chr2B.!!$R1 5161
14 TraesCS1B01G102300 chr2B 568667422 568668543 1121 False 1254.0 1254 87.0240 4109 5245 1 chr2B.!!$F3 1136
15 TraesCS1B01G102300 chr3B 641066401 641069337 2936 False 2166.5 2724 93.4650 1141 4071 2 chr3B.!!$F2 2930
16 TraesCS1B01G102300 chr3B 457029071 457032007 2936 True 2156.5 2719 93.3475 1141 4071 2 chr3B.!!$R1 2930
17 TraesCS1B01G102300 chr4D 115202122 115203890 1768 True 2708.0 2708 94.3160 1139 2908 1 chr4D.!!$R2 1769
18 TraesCS1B01G102300 chr4D 81175459 81177201 1742 True 2560.0 2560 93.0550 1142 2908 1 chr4D.!!$R1 1766
19 TraesCS1B01G102300 chr4D 58913781 58914282 501 False 699.0 699 91.7650 4109 4614 1 chr4D.!!$F1 505
20 TraesCS1B01G102300 chr6A 60385109 60386965 1856 True 2700.0 2700 92.8120 2189 4071 1 chr6A.!!$R1 1882
21 TraesCS1B01G102300 chr6A 617535658 617537419 1761 True 2676.0 2676 94.0680 1142 2908 1 chr6A.!!$R2 1766
22 TraesCS1B01G102300 chr6A 194804199 194806823 2624 False 1304.0 1594 91.3785 308 2206 2 chr6A.!!$F2 1898
23 TraesCS1B01G102300 chr6B 655234254 655236526 2272 False 2593.0 2593 87.6300 1826 4071 1 chr6B.!!$F2 2245
24 TraesCS1B01G102300 chr6B 187092828 187093465 637 False 992.0 992 95.1410 4799 5421 1 chr6B.!!$F1 622
25 TraesCS1B01G102300 chr7A 608952241 608953993 1752 True 2486.0 2486 92.2430 1142 2908 1 chr7A.!!$R3 1766
26 TraesCS1B01G102300 chr7A 710683827 710685771 1944 True 1309.5 1605 91.5125 311 2206 2 chr7A.!!$R4 1895
27 TraesCS1B01G102300 chr4A 310424989 310427189 2200 True 2407.0 2407 86.5320 1826 4066 1 chr4A.!!$R1 2240
28 TraesCS1B01G102300 chr4A 711819315 711819929 614 True 800.0 800 90.2820 4799 5421 1 chr4A.!!$R2 622
29 TraesCS1B01G102300 chr7B 740575632 740576563 931 False 1050.0 1050 87.2880 2469 3392 1 chr7B.!!$F2 923
30 TraesCS1B01G102300 chr7B 740562091 740562961 870 False 1046.0 1046 88.6860 2469 3323 1 chr7B.!!$F1 854
31 TraesCS1B01G102300 chr7B 740655353 740656223 870 False 1040.0 1040 88.5710 2469 3323 1 chr7B.!!$F3 854
32 TraesCS1B01G102300 chr5B 471922491 471923304 813 True 1003.0 1003 88.8750 311 1134 1 chr5B.!!$R1 823

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
95 96 0.035439 CCGGCTGGAGGTAAACACAT 60.035 55.000 5.28 0.00 37.49 3.21 F
268 269 0.657312 CTTCTGTTGCAACGCAGTCA 59.343 50.000 23.79 5.08 45.00 3.41 F
272 273 0.737804 TGTTGCAACGCAGTCAATGT 59.262 45.000 23.79 0.00 45.00 2.71 F
305 306 0.821711 AACGCACAGGCCTTTTGCTA 60.822 50.000 26.48 0.00 40.92 3.49 F
1336 1409 1.135915 CACTGAGGACCTTCTCATCCG 59.864 57.143 0.00 0.00 42.19 4.18 F
2978 3817 1.064017 ACTTTGGGTTCTTGGCACTCA 60.064 47.619 0.00 0.00 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1121 1132 2.042831 GGTGCATGGAGGTGCTGTC 61.043 63.158 0.0 0.0 45.27 3.51 R
1336 1409 2.159028 GGGTTACCTCTGATCTCTGTGC 60.159 54.545 0.0 0.0 0.00 4.57 R
1552 2303 6.010294 ACAGAGAACATGATGAGCAAAAAG 57.990 37.500 0.0 0.0 0.00 2.27 R
2978 3817 1.563924 TAGTCATAACCTGCACGGGT 58.436 50.000 0.0 0.0 42.05 5.28 R
3860 4723 6.722590 TCGAGCCAAGGGAATATTGTACTATA 59.277 38.462 0.0 0.0 0.00 1.31 R
5513 6439 0.753867 TGACGTACCACCAGAAGCAA 59.246 50.000 0.0 0.0 0.00 3.91 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
20 21 3.306917 TCGAGCACGATCCACTAAAAA 57.693 42.857 0.88 0.00 43.81 1.94
21 22 3.857052 TCGAGCACGATCCACTAAAAAT 58.143 40.909 0.88 0.00 43.81 1.82
22 23 5.001237 TCGAGCACGATCCACTAAAAATA 57.999 39.130 0.88 0.00 43.81 1.40
23 24 5.412640 TCGAGCACGATCCACTAAAAATAA 58.587 37.500 0.88 0.00 43.81 1.40
24 25 5.518847 TCGAGCACGATCCACTAAAAATAAG 59.481 40.000 0.88 0.00 43.81 1.73
25 26 5.291128 CGAGCACGATCCACTAAAAATAAGT 59.709 40.000 0.00 0.00 42.66 2.24
26 27 6.183360 CGAGCACGATCCACTAAAAATAAGTT 60.183 38.462 0.00 0.00 42.66 2.66
27 28 7.009815 CGAGCACGATCCACTAAAAATAAGTTA 59.990 37.037 0.00 0.00 42.66 2.24
28 29 8.556213 AGCACGATCCACTAAAAATAAGTTAA 57.444 30.769 0.00 0.00 0.00 2.01
29 30 9.174166 AGCACGATCCACTAAAAATAAGTTAAT 57.826 29.630 0.00 0.00 0.00 1.40
30 31 9.434559 GCACGATCCACTAAAAATAAGTTAATC 57.565 33.333 0.00 0.00 0.00 1.75
31 32 9.632969 CACGATCCACTAAAAATAAGTTAATCG 57.367 33.333 12.09 12.09 40.81 3.34
32 33 9.590451 ACGATCCACTAAAAATAAGTTAATCGA 57.410 29.630 17.18 0.00 39.17 3.59
34 35 9.865484 GATCCACTAAAAATAAGTTAATCGAGC 57.135 33.333 0.00 0.00 0.00 5.03
35 36 8.780846 TCCACTAAAAATAAGTTAATCGAGCA 57.219 30.769 0.00 0.00 0.00 4.26
36 37 9.391006 TCCACTAAAAATAAGTTAATCGAGCAT 57.609 29.630 0.00 0.00 0.00 3.79
37 38 9.438291 CCACTAAAAATAAGTTAATCGAGCATG 57.562 33.333 0.00 0.00 0.00 4.06
42 43 9.906660 AAAAATAAGTTAATCGAGCATGAAACA 57.093 25.926 0.00 0.00 0.00 2.83
43 44 9.559958 AAAATAAGTTAATCGAGCATGAAACAG 57.440 29.630 0.00 0.00 0.00 3.16
44 45 7.849804 ATAAGTTAATCGAGCATGAAACAGT 57.150 32.000 0.00 0.00 0.00 3.55
45 46 8.942338 ATAAGTTAATCGAGCATGAAACAGTA 57.058 30.769 0.00 0.00 0.00 2.74
46 47 6.648725 AGTTAATCGAGCATGAAACAGTAC 57.351 37.500 0.00 0.00 0.00 2.73
47 48 6.163476 AGTTAATCGAGCATGAAACAGTACA 58.837 36.000 0.00 0.00 0.00 2.90
48 49 6.818644 AGTTAATCGAGCATGAAACAGTACAT 59.181 34.615 0.00 0.00 0.00 2.29
49 50 7.334421 AGTTAATCGAGCATGAAACAGTACATT 59.666 33.333 0.00 0.00 0.00 2.71
50 51 4.926860 TCGAGCATGAAACAGTACATTG 57.073 40.909 0.00 0.00 0.00 2.82
51 52 4.565022 TCGAGCATGAAACAGTACATTGA 58.435 39.130 0.00 0.00 0.00 2.57
52 53 4.627035 TCGAGCATGAAACAGTACATTGAG 59.373 41.667 0.00 0.00 0.00 3.02
53 54 4.389992 CGAGCATGAAACAGTACATTGAGT 59.610 41.667 0.00 0.00 0.00 3.41
54 55 5.445142 CGAGCATGAAACAGTACATTGAGTC 60.445 44.000 0.00 0.00 0.00 3.36
55 56 4.697352 AGCATGAAACAGTACATTGAGTCC 59.303 41.667 0.00 0.00 0.00 3.85
56 57 4.436050 GCATGAAACAGTACATTGAGTCCG 60.436 45.833 0.00 0.00 0.00 4.79
57 58 4.594123 TGAAACAGTACATTGAGTCCGA 57.406 40.909 0.00 0.00 0.00 4.55
58 59 4.556233 TGAAACAGTACATTGAGTCCGAG 58.444 43.478 0.00 0.00 0.00 4.63
59 60 2.656560 ACAGTACATTGAGTCCGAGC 57.343 50.000 0.00 0.00 0.00 5.03
60 61 2.171840 ACAGTACATTGAGTCCGAGCT 58.828 47.619 0.00 0.00 0.00 4.09
61 62 2.563179 ACAGTACATTGAGTCCGAGCTT 59.437 45.455 0.00 0.00 0.00 3.74
62 63 3.006967 ACAGTACATTGAGTCCGAGCTTT 59.993 43.478 0.00 0.00 0.00 3.51
63 64 3.369147 CAGTACATTGAGTCCGAGCTTTG 59.631 47.826 0.00 0.00 0.00 2.77
64 65 2.550830 ACATTGAGTCCGAGCTTTGT 57.449 45.000 0.00 0.00 0.00 2.83
65 66 2.851195 ACATTGAGTCCGAGCTTTGTT 58.149 42.857 0.00 0.00 0.00 2.83
66 67 2.549754 ACATTGAGTCCGAGCTTTGTTG 59.450 45.455 0.00 0.00 0.00 3.33
67 68 2.613026 TTGAGTCCGAGCTTTGTTGA 57.387 45.000 0.00 0.00 0.00 3.18
68 69 1.865865 TGAGTCCGAGCTTTGTTGAC 58.134 50.000 0.00 0.00 0.00 3.18
69 70 1.138069 TGAGTCCGAGCTTTGTTGACA 59.862 47.619 0.00 0.00 0.00 3.58
70 71 1.795286 GAGTCCGAGCTTTGTTGACAG 59.205 52.381 0.00 0.00 0.00 3.51
71 72 0.235926 GTCCGAGCTTTGTTGACAGC 59.764 55.000 0.00 0.00 36.16 4.40
72 73 0.884704 TCCGAGCTTTGTTGACAGCC 60.885 55.000 0.00 0.00 36.62 4.85
73 74 1.576421 CGAGCTTTGTTGACAGCCC 59.424 57.895 0.00 0.00 36.62 5.19
74 75 0.886490 CGAGCTTTGTTGACAGCCCT 60.886 55.000 0.00 0.00 36.62 5.19
75 76 1.608025 CGAGCTTTGTTGACAGCCCTA 60.608 52.381 0.00 0.00 36.62 3.53
76 77 1.807142 GAGCTTTGTTGACAGCCCTAC 59.193 52.381 0.00 0.00 36.62 3.18
77 78 0.881796 GCTTTGTTGACAGCCCTACC 59.118 55.000 0.00 0.00 0.00 3.18
78 79 1.156736 CTTTGTTGACAGCCCTACCG 58.843 55.000 0.00 0.00 0.00 4.02
79 80 0.250553 TTTGTTGACAGCCCTACCGG 60.251 55.000 0.00 0.00 0.00 5.28
88 89 2.281091 CCCTACCGGCTGGAGGTA 59.719 66.667 21.41 9.48 42.81 3.08
89 90 1.382146 CCCTACCGGCTGGAGGTAA 60.382 63.158 21.41 0.00 42.97 2.85
90 91 0.979187 CCCTACCGGCTGGAGGTAAA 60.979 60.000 21.41 0.00 42.97 2.01
91 92 0.177373 CCTACCGGCTGGAGGTAAAC 59.823 60.000 21.41 0.00 42.97 2.01
92 93 0.899720 CTACCGGCTGGAGGTAAACA 59.100 55.000 21.41 0.00 42.97 2.83
93 94 0.609662 TACCGGCTGGAGGTAAACAC 59.390 55.000 21.41 0.00 40.91 3.32
94 95 1.373435 CCGGCTGGAGGTAAACACA 59.627 57.895 5.28 0.00 37.49 3.72
95 96 0.035439 CCGGCTGGAGGTAAACACAT 60.035 55.000 5.28 0.00 37.49 3.21
96 97 1.208535 CCGGCTGGAGGTAAACACATA 59.791 52.381 5.28 0.00 37.49 2.29
97 98 2.277084 CGGCTGGAGGTAAACACATAC 58.723 52.381 0.00 0.00 0.00 2.39
98 99 2.093658 CGGCTGGAGGTAAACACATACT 60.094 50.000 0.00 0.00 0.00 2.12
99 100 3.618997 CGGCTGGAGGTAAACACATACTT 60.619 47.826 0.00 0.00 0.00 2.24
100 101 4.332828 GGCTGGAGGTAAACACATACTTT 58.667 43.478 0.00 0.00 0.00 2.66
101 102 4.765339 GGCTGGAGGTAAACACATACTTTT 59.235 41.667 0.00 0.00 0.00 2.27
102 103 5.243060 GGCTGGAGGTAAACACATACTTTTT 59.757 40.000 0.00 0.00 0.00 1.94
103 104 6.379386 GCTGGAGGTAAACACATACTTTTTC 58.621 40.000 0.00 0.00 0.00 2.29
104 105 6.569801 GCTGGAGGTAAACACATACTTTTTCC 60.570 42.308 0.00 0.00 0.00 3.13
105 106 6.607019 TGGAGGTAAACACATACTTTTTCCT 58.393 36.000 0.00 0.00 35.76 3.36
106 107 7.064229 TGGAGGTAAACACATACTTTTTCCTT 58.936 34.615 0.00 0.00 33.87 3.36
107 108 7.562088 TGGAGGTAAACACATACTTTTTCCTTT 59.438 33.333 0.00 0.00 33.87 3.11
108 109 8.418662 GGAGGTAAACACATACTTTTTCCTTTT 58.581 33.333 0.00 0.00 33.87 2.27
109 110 9.811995 GAGGTAAACACATACTTTTTCCTTTTT 57.188 29.630 0.00 0.00 33.87 1.94
150 151 7.068692 ACTTGTACTAACGTTTATTCCATGC 57.931 36.000 5.91 0.00 0.00 4.06
151 152 6.651643 ACTTGTACTAACGTTTATTCCATGCA 59.348 34.615 5.91 0.00 0.00 3.96
152 153 7.335924 ACTTGTACTAACGTTTATTCCATGCAT 59.664 33.333 5.91 0.00 0.00 3.96
153 154 7.618502 TGTACTAACGTTTATTCCATGCATT 57.381 32.000 5.91 0.00 0.00 3.56
154 155 8.046294 TGTACTAACGTTTATTCCATGCATTT 57.954 30.769 5.91 0.00 0.00 2.32
155 156 8.516234 TGTACTAACGTTTATTCCATGCATTTT 58.484 29.630 5.91 0.00 0.00 1.82
156 157 9.006215 GTACTAACGTTTATTCCATGCATTTTC 57.994 33.333 5.91 0.00 0.00 2.29
157 158 7.598278 ACTAACGTTTATTCCATGCATTTTCA 58.402 30.769 5.91 0.00 0.00 2.69
158 159 8.250332 ACTAACGTTTATTCCATGCATTTTCAT 58.750 29.630 5.91 0.00 0.00 2.57
159 160 9.729023 CTAACGTTTATTCCATGCATTTTCATA 57.271 29.630 5.91 0.00 0.00 2.15
160 161 7.985634 ACGTTTATTCCATGCATTTTCATAC 57.014 32.000 0.00 0.00 0.00 2.39
161 162 7.542890 ACGTTTATTCCATGCATTTTCATACA 58.457 30.769 0.00 0.00 0.00 2.29
162 163 8.196771 ACGTTTATTCCATGCATTTTCATACAT 58.803 29.630 0.00 0.00 0.00 2.29
163 164 9.033481 CGTTTATTCCATGCATTTTCATACATT 57.967 29.630 0.00 0.00 0.00 2.71
262 263 5.701029 ATTTGTTTTCTTCTGTTGCAACG 57.299 34.783 23.79 17.92 0.00 4.10
263 264 2.525055 TGTTTTCTTCTGTTGCAACGC 58.475 42.857 23.79 2.38 0.00 4.84
264 265 2.095008 TGTTTTCTTCTGTTGCAACGCA 60.095 40.909 23.79 10.48 36.47 5.24
265 266 2.473530 TTTCTTCTGTTGCAACGCAG 57.526 45.000 23.79 16.65 40.61 5.18
267 268 0.937304 TCTTCTGTTGCAACGCAGTC 59.063 50.000 23.79 0.02 45.00 3.51
268 269 0.657312 CTTCTGTTGCAACGCAGTCA 59.343 50.000 23.79 5.08 45.00 3.41
269 270 1.063912 CTTCTGTTGCAACGCAGTCAA 59.936 47.619 23.79 7.80 45.00 3.18
270 271 1.308047 TCTGTTGCAACGCAGTCAAT 58.692 45.000 23.79 0.00 45.00 2.57
271 272 1.002576 TCTGTTGCAACGCAGTCAATG 60.003 47.619 23.79 6.16 45.00 2.82
272 273 0.737804 TGTTGCAACGCAGTCAATGT 59.262 45.000 23.79 0.00 45.00 2.71
273 274 1.133982 TGTTGCAACGCAGTCAATGTT 59.866 42.857 23.79 0.00 45.00 2.71
274 275 2.192624 GTTGCAACGCAGTCAATGTTT 58.807 42.857 14.90 0.00 45.00 2.83
275 276 2.575694 TGCAACGCAGTCAATGTTTT 57.424 40.000 0.00 0.00 45.00 2.43
276 277 2.458951 TGCAACGCAGTCAATGTTTTC 58.541 42.857 0.00 0.00 45.00 2.29
277 278 2.098934 TGCAACGCAGTCAATGTTTTCT 59.901 40.909 0.00 0.00 45.00 2.52
278 279 2.721090 GCAACGCAGTCAATGTTTTCTC 59.279 45.455 0.00 0.00 45.00 2.87
279 280 3.300009 CAACGCAGTCAATGTTTTCTCC 58.700 45.455 0.00 0.00 45.00 3.71
280 281 1.880027 ACGCAGTCAATGTTTTCTCCC 59.120 47.619 0.00 0.00 29.74 4.30
281 282 1.135972 CGCAGTCAATGTTTTCTCCCG 60.136 52.381 0.00 0.00 0.00 5.14
282 283 1.880027 GCAGTCAATGTTTTCTCCCGT 59.120 47.619 0.00 0.00 0.00 5.28
283 284 2.293399 GCAGTCAATGTTTTCTCCCGTT 59.707 45.455 0.00 0.00 0.00 4.44
284 285 3.853307 GCAGTCAATGTTTTCTCCCGTTG 60.853 47.826 0.00 0.00 0.00 4.10
285 286 2.293399 AGTCAATGTTTTCTCCCGTTGC 59.707 45.455 0.00 0.00 0.00 4.17
286 287 2.034053 GTCAATGTTTTCTCCCGTTGCA 59.966 45.455 0.00 0.00 0.00 4.08
287 288 2.690497 TCAATGTTTTCTCCCGTTGCAA 59.310 40.909 0.00 0.00 0.00 4.08
288 289 2.793278 ATGTTTTCTCCCGTTGCAAC 57.207 45.000 19.89 19.89 0.00 4.17
297 298 4.980903 CGTTGCAACGCACAGGCC 62.981 66.667 35.89 3.35 46.06 5.19
298 299 3.595758 GTTGCAACGCACAGGCCT 61.596 61.111 14.90 0.00 38.71 5.19
299 300 2.832661 TTGCAACGCACAGGCCTT 60.833 55.556 0.00 0.00 38.71 4.35
300 301 2.422231 TTGCAACGCACAGGCCTTT 61.422 52.632 0.00 0.00 38.71 3.11
301 302 1.954362 TTGCAACGCACAGGCCTTTT 61.954 50.000 0.00 0.00 38.71 2.27
302 303 1.950630 GCAACGCACAGGCCTTTTG 60.951 57.895 0.00 4.26 36.38 2.44
303 304 1.950630 CAACGCACAGGCCTTTTGC 60.951 57.895 21.81 21.81 36.38 3.68
304 305 2.127232 AACGCACAGGCCTTTTGCT 61.127 52.632 26.48 14.97 40.92 3.91
305 306 0.821711 AACGCACAGGCCTTTTGCTA 60.822 50.000 26.48 0.00 40.92 3.49
306 307 1.237285 ACGCACAGGCCTTTTGCTAG 61.237 55.000 26.48 17.55 40.92 3.42
309 310 2.159382 GCACAGGCCTTTTGCTAGTAA 58.841 47.619 23.66 0.00 40.92 2.24
342 343 2.631418 ACTGATTCTGGTCGTACGTG 57.369 50.000 16.05 4.73 0.00 4.49
384 385 7.694093 AGTCCCTCTGTTTCTAAGAAATCAAT 58.306 34.615 0.00 0.00 0.00 2.57
581 586 2.272146 CCGGTAATGGCAGCACCT 59.728 61.111 15.83 0.00 40.22 4.00
743 749 3.947841 GCGTCGTTGCACTTGCCA 61.948 61.111 0.00 0.00 41.18 4.92
787 793 2.719705 ACCACCCTCCACCTCAAATTTA 59.280 45.455 0.00 0.00 0.00 1.40
875 881 2.369860 AGCCAGTTTCAGTCACAGATCA 59.630 45.455 0.00 0.00 0.00 2.92
1060 1066 9.060347 CCTATTGCTTGACAAATGTATATCTGT 57.940 33.333 0.00 0.00 42.86 3.41
1100 1106 6.872020 TGTATGAAGAAGTTACAGTTAGGTGC 59.128 38.462 0.00 0.00 0.00 5.01
1258 1331 5.278169 GCAAACATGCTCTGTATTCTATGGG 60.278 44.000 0.00 0.00 36.98 4.00
1336 1409 1.135915 CACTGAGGACCTTCTCATCCG 59.864 57.143 0.00 0.00 42.19 4.18
1552 2303 8.871686 ATTTGGTTCTGTTCAACTTGAATTAC 57.128 30.769 7.47 4.30 38.79 1.89
1790 2544 9.271828 GATTTTTCTTGACAAACATATTGGGTT 57.728 29.630 0.00 0.00 0.00 4.11
2045 2826 3.884895 TCAGAAACCTGATGTGTGTGTT 58.115 40.909 0.00 0.00 35.88 3.32
2978 3817 1.064017 ACTTTGGGTTCTTGGCACTCA 60.064 47.619 0.00 0.00 0.00 3.41
3494 4346 7.067494 GCTTGAAATCTACATCTGGGTTACAAT 59.933 37.037 0.00 0.00 0.00 2.71
3860 4723 5.087323 TGGAGTGTTAATCTTCTCCTCTGT 58.913 41.667 10.66 0.00 44.57 3.41
4040 4919 3.152261 AGATTAGTCGAGGTTTGCGAG 57.848 47.619 0.00 0.00 38.59 5.03
4230 5109 7.669427 TCTTGACAACCAATTGATTTGCTAAT 58.331 30.769 7.12 0.00 39.30 1.73
4448 5331 4.046462 CGTTTCGGAGAACTTCTTGTACA 58.954 43.478 0.00 0.00 45.90 2.90
4531 5420 0.806102 TTTGCATAGAGCTCGGACGC 60.806 55.000 8.37 10.51 45.94 5.19
4732 5621 1.494721 TCCTTGCCAGGACAGTTCTTT 59.505 47.619 1.49 0.00 45.20 2.52
4868 5757 4.037208 CAGAAACTATAGCCCAAATGCAGG 59.963 45.833 0.00 0.00 0.00 4.85
5356 6274 9.173939 CAAGTCATGTTGTCAAAATTACTTCTC 57.826 33.333 11.01 0.00 0.00 2.87
5398 6324 2.113986 AGAATAGGCATGCCCCGC 59.886 61.111 33.14 19.35 36.58 6.13
5529 6455 1.933853 GCTATTGCTTCTGGTGGTACG 59.066 52.381 0.00 0.00 36.03 3.67
5530 6456 2.677037 GCTATTGCTTCTGGTGGTACGT 60.677 50.000 0.00 0.00 36.03 3.57
5531 6457 2.094762 ATTGCTTCTGGTGGTACGTC 57.905 50.000 0.00 0.00 0.00 4.34
5532 6458 0.753867 TTGCTTCTGGTGGTACGTCA 59.246 50.000 0.00 0.00 0.00 4.35
5533 6459 0.973632 TGCTTCTGGTGGTACGTCAT 59.026 50.000 0.00 0.00 0.00 3.06
5534 6460 2.172679 TGCTTCTGGTGGTACGTCATA 58.827 47.619 0.00 0.00 0.00 2.15
5535 6461 2.764010 TGCTTCTGGTGGTACGTCATAT 59.236 45.455 0.00 0.00 0.00 1.78
5536 6462 3.955551 TGCTTCTGGTGGTACGTCATATA 59.044 43.478 0.00 0.00 0.00 0.86
5537 6463 4.403113 TGCTTCTGGTGGTACGTCATATAA 59.597 41.667 0.00 0.00 0.00 0.98
5538 6464 5.069914 TGCTTCTGGTGGTACGTCATATAAT 59.930 40.000 0.00 0.00 0.00 1.28
5539 6465 5.989777 GCTTCTGGTGGTACGTCATATAATT 59.010 40.000 0.00 0.00 0.00 1.40
5540 6466 6.482308 GCTTCTGGTGGTACGTCATATAATTT 59.518 38.462 0.00 0.00 0.00 1.82
5541 6467 7.518370 GCTTCTGGTGGTACGTCATATAATTTG 60.518 40.741 0.00 0.00 0.00 2.32
5542 6468 5.756347 TCTGGTGGTACGTCATATAATTTGC 59.244 40.000 0.00 0.00 0.00 3.68
5543 6469 4.817464 TGGTGGTACGTCATATAATTTGCC 59.183 41.667 0.00 0.00 0.00 4.52
5544 6470 4.214758 GGTGGTACGTCATATAATTTGCCC 59.785 45.833 0.00 0.00 0.00 5.36
5545 6471 4.214758 GTGGTACGTCATATAATTTGCCCC 59.785 45.833 0.00 0.00 0.00 5.80
5546 6472 4.103469 TGGTACGTCATATAATTTGCCCCT 59.897 41.667 0.00 0.00 0.00 4.79
5547 6473 5.307456 TGGTACGTCATATAATTTGCCCCTA 59.693 40.000 0.00 0.00 0.00 3.53
5548 6474 6.183361 TGGTACGTCATATAATTTGCCCCTAA 60.183 38.462 0.00 0.00 0.00 2.69
5549 6475 6.711645 GGTACGTCATATAATTTGCCCCTAAA 59.288 38.462 0.00 0.00 0.00 1.85
5550 6476 6.628919 ACGTCATATAATTTGCCCCTAAAC 57.371 37.500 0.00 0.00 0.00 2.01
5551 6477 6.362248 ACGTCATATAATTTGCCCCTAAACT 58.638 36.000 0.00 0.00 0.00 2.66
5552 6478 6.831868 ACGTCATATAATTTGCCCCTAAACTT 59.168 34.615 0.00 0.00 0.00 2.66
5553 6479 7.138736 CGTCATATAATTTGCCCCTAAACTTG 58.861 38.462 0.00 0.00 0.00 3.16
5554 6480 6.923508 GTCATATAATTTGCCCCTAAACTTGC 59.076 38.462 0.00 0.00 0.00 4.01
5555 6481 6.838612 TCATATAATTTGCCCCTAAACTTGCT 59.161 34.615 0.00 0.00 0.00 3.91
5556 6482 8.001875 TCATATAATTTGCCCCTAAACTTGCTA 58.998 33.333 0.00 0.00 0.00 3.49
5557 6483 8.637986 CATATAATTTGCCCCTAAACTTGCTAA 58.362 33.333 0.00 0.00 0.00 3.09
5558 6484 5.816955 AATTTGCCCCTAAACTTGCTAAA 57.183 34.783 0.00 0.00 0.00 1.85
5559 6485 6.373005 AATTTGCCCCTAAACTTGCTAAAT 57.627 33.333 0.00 0.00 0.00 1.40
5560 6486 7.489239 AATTTGCCCCTAAACTTGCTAAATA 57.511 32.000 0.00 0.00 0.00 1.40
5561 6487 7.675161 ATTTGCCCCTAAACTTGCTAAATAT 57.325 32.000 0.00 0.00 0.00 1.28
5562 6488 7.489239 TTTGCCCCTAAACTTGCTAAATATT 57.511 32.000 0.00 0.00 0.00 1.28
5563 6489 8.596781 TTTGCCCCTAAACTTGCTAAATATTA 57.403 30.769 0.00 0.00 0.00 0.98
5564 6490 7.576861 TGCCCCTAAACTTGCTAAATATTAC 57.423 36.000 0.00 0.00 0.00 1.89
5565 6491 6.548251 TGCCCCTAAACTTGCTAAATATTACC 59.452 38.462 0.00 0.00 0.00 2.85
5566 6492 6.015688 GCCCCTAAACTTGCTAAATATTACCC 60.016 42.308 0.00 0.00 0.00 3.69
5567 6493 7.064229 CCCCTAAACTTGCTAAATATTACCCA 58.936 38.462 0.00 0.00 0.00 4.51
5568 6494 7.013942 CCCCTAAACTTGCTAAATATTACCCAC 59.986 40.741 0.00 0.00 0.00 4.61
5569 6495 7.013942 CCCTAAACTTGCTAAATATTACCCACC 59.986 40.741 0.00 0.00 0.00 4.61
5570 6496 7.558444 CCTAAACTTGCTAAATATTACCCACCA 59.442 37.037 0.00 0.00 0.00 4.17
5571 6497 7.784470 AAACTTGCTAAATATTACCCACCAA 57.216 32.000 0.00 0.00 0.00 3.67
5572 6498 7.971368 AACTTGCTAAATATTACCCACCAAT 57.029 32.000 0.00 0.00 0.00 3.16
5573 6499 7.346751 ACTTGCTAAATATTACCCACCAATG 57.653 36.000 0.00 0.00 0.00 2.82
5574 6500 5.782893 TGCTAAATATTACCCACCAATGC 57.217 39.130 0.00 0.00 0.00 3.56
5575 6501 4.586841 TGCTAAATATTACCCACCAATGCC 59.413 41.667 0.00 0.00 0.00 4.40
5576 6502 4.586841 GCTAAATATTACCCACCAATGCCA 59.413 41.667 0.00 0.00 0.00 4.92
5577 6503 5.245977 GCTAAATATTACCCACCAATGCCAT 59.754 40.000 0.00 0.00 0.00 4.40
5578 6504 5.806654 AAATATTACCCACCAATGCCATC 57.193 39.130 0.00 0.00 0.00 3.51
5579 6505 4.747265 ATATTACCCACCAATGCCATCT 57.253 40.909 0.00 0.00 0.00 2.90
5580 6506 5.858876 ATATTACCCACCAATGCCATCTA 57.141 39.130 0.00 0.00 0.00 1.98
5581 6507 4.747265 ATTACCCACCAATGCCATCTAT 57.253 40.909 0.00 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 6.663944 ACTTATTTTTAGTGGATCGTGCTC 57.336 37.500 0.00 0.00 0.00 4.26
3 4 8.556213 TTAACTTATTTTTAGTGGATCGTGCT 57.444 30.769 0.00 0.00 0.00 4.40
5 6 9.632969 CGATTAACTTATTTTTAGTGGATCGTG 57.367 33.333 0.00 0.00 36.96 4.35
6 7 9.590451 TCGATTAACTTATTTTTAGTGGATCGT 57.410 29.630 14.89 0.00 39.56 3.73
8 9 9.865484 GCTCGATTAACTTATTTTTAGTGGATC 57.135 33.333 0.00 0.00 0.00 3.36
9 10 9.391006 TGCTCGATTAACTTATTTTTAGTGGAT 57.609 29.630 0.00 0.00 0.00 3.41
10 11 8.780846 TGCTCGATTAACTTATTTTTAGTGGA 57.219 30.769 0.00 0.00 0.00 4.02
11 12 9.438291 CATGCTCGATTAACTTATTTTTAGTGG 57.562 33.333 0.00 0.00 0.00 4.00
16 17 9.906660 TGTTTCATGCTCGATTAACTTATTTTT 57.093 25.926 0.00 0.00 0.00 1.94
17 18 9.559958 CTGTTTCATGCTCGATTAACTTATTTT 57.440 29.630 0.00 0.00 0.00 1.82
18 19 8.730680 ACTGTTTCATGCTCGATTAACTTATTT 58.269 29.630 0.00 0.00 0.00 1.40
19 20 8.268850 ACTGTTTCATGCTCGATTAACTTATT 57.731 30.769 0.00 0.00 0.00 1.40
20 21 7.849804 ACTGTTTCATGCTCGATTAACTTAT 57.150 32.000 0.00 0.00 0.00 1.73
21 22 7.815549 TGTACTGTTTCATGCTCGATTAACTTA 59.184 33.333 0.00 0.00 0.00 2.24
22 23 6.649141 TGTACTGTTTCATGCTCGATTAACTT 59.351 34.615 0.00 0.00 0.00 2.66
23 24 6.163476 TGTACTGTTTCATGCTCGATTAACT 58.837 36.000 0.00 0.00 0.00 2.24
24 25 6.403333 TGTACTGTTTCATGCTCGATTAAC 57.597 37.500 0.00 0.00 0.00 2.01
25 26 7.333174 TCAATGTACTGTTTCATGCTCGATTAA 59.667 33.333 0.00 0.00 0.00 1.40
26 27 6.816140 TCAATGTACTGTTTCATGCTCGATTA 59.184 34.615 0.00 0.00 0.00 1.75
27 28 5.643348 TCAATGTACTGTTTCATGCTCGATT 59.357 36.000 0.00 0.00 0.00 3.34
28 29 5.178061 TCAATGTACTGTTTCATGCTCGAT 58.822 37.500 0.00 0.00 0.00 3.59
29 30 4.565022 TCAATGTACTGTTTCATGCTCGA 58.435 39.130 0.00 0.00 0.00 4.04
30 31 4.389992 ACTCAATGTACTGTTTCATGCTCG 59.610 41.667 0.00 0.00 0.00 5.03
31 32 5.163814 GGACTCAATGTACTGTTTCATGCTC 60.164 44.000 0.00 0.00 0.00 4.26
32 33 4.697352 GGACTCAATGTACTGTTTCATGCT 59.303 41.667 0.00 0.00 0.00 3.79
33 34 4.436050 CGGACTCAATGTACTGTTTCATGC 60.436 45.833 0.00 0.00 0.00 4.06
34 35 4.929211 TCGGACTCAATGTACTGTTTCATG 59.071 41.667 0.00 0.00 0.00 3.07
35 36 5.147330 TCGGACTCAATGTACTGTTTCAT 57.853 39.130 0.00 0.00 0.00 2.57
36 37 4.556233 CTCGGACTCAATGTACTGTTTCA 58.444 43.478 0.00 0.00 0.00 2.69
37 38 3.368236 GCTCGGACTCAATGTACTGTTTC 59.632 47.826 0.00 0.00 0.00 2.78
38 39 3.006967 AGCTCGGACTCAATGTACTGTTT 59.993 43.478 0.00 0.00 0.00 2.83
39 40 2.563179 AGCTCGGACTCAATGTACTGTT 59.437 45.455 0.00 0.00 0.00 3.16
40 41 2.171840 AGCTCGGACTCAATGTACTGT 58.828 47.619 0.00 0.00 0.00 3.55
41 42 2.949451 AGCTCGGACTCAATGTACTG 57.051 50.000 0.00 0.00 0.00 2.74
42 43 3.006967 ACAAAGCTCGGACTCAATGTACT 59.993 43.478 0.00 0.00 0.00 2.73
43 44 3.326747 ACAAAGCTCGGACTCAATGTAC 58.673 45.455 0.00 0.00 0.00 2.90
44 45 3.678056 ACAAAGCTCGGACTCAATGTA 57.322 42.857 0.00 0.00 0.00 2.29
45 46 2.549754 CAACAAAGCTCGGACTCAATGT 59.450 45.455 0.00 0.00 0.00 2.71
46 47 2.807967 TCAACAAAGCTCGGACTCAATG 59.192 45.455 0.00 0.00 0.00 2.82
47 48 2.808543 GTCAACAAAGCTCGGACTCAAT 59.191 45.455 0.00 0.00 0.00 2.57
48 49 2.210116 GTCAACAAAGCTCGGACTCAA 58.790 47.619 0.00 0.00 0.00 3.02
49 50 1.138069 TGTCAACAAAGCTCGGACTCA 59.862 47.619 0.00 0.00 0.00 3.41
50 51 1.795286 CTGTCAACAAAGCTCGGACTC 59.205 52.381 0.00 0.00 0.00 3.36
51 52 1.871080 CTGTCAACAAAGCTCGGACT 58.129 50.000 0.00 0.00 0.00 3.85
52 53 0.235926 GCTGTCAACAAAGCTCGGAC 59.764 55.000 0.00 0.00 36.47 4.79
53 54 0.884704 GGCTGTCAACAAAGCTCGGA 60.885 55.000 0.00 0.00 39.46 4.55
54 55 1.576421 GGCTGTCAACAAAGCTCGG 59.424 57.895 0.00 0.00 39.46 4.63
55 56 0.886490 AGGGCTGTCAACAAAGCTCG 60.886 55.000 0.00 0.00 44.98 5.03
56 57 1.807142 GTAGGGCTGTCAACAAAGCTC 59.193 52.381 0.00 0.00 40.40 4.09
57 58 1.545651 GGTAGGGCTGTCAACAAAGCT 60.546 52.381 0.00 0.00 39.46 3.74
58 59 0.881796 GGTAGGGCTGTCAACAAAGC 59.118 55.000 0.00 0.00 38.76 3.51
59 60 1.156736 CGGTAGGGCTGTCAACAAAG 58.843 55.000 0.00 0.00 0.00 2.77
60 61 0.250553 CCGGTAGGGCTGTCAACAAA 60.251 55.000 0.00 0.00 0.00 2.83
61 62 1.373435 CCGGTAGGGCTGTCAACAA 59.627 57.895 0.00 0.00 0.00 2.83
62 63 3.065306 CCGGTAGGGCTGTCAACA 58.935 61.111 0.00 0.00 0.00 3.33
71 72 0.979187 TTTACCTCCAGCCGGTAGGG 60.979 60.000 13.37 7.99 38.20 3.53
72 73 0.177373 GTTTACCTCCAGCCGGTAGG 59.823 60.000 1.90 5.52 38.20 3.18
73 74 0.899720 TGTTTACCTCCAGCCGGTAG 59.100 55.000 1.90 0.00 38.20 3.18
74 75 0.609662 GTGTTTACCTCCAGCCGGTA 59.390 55.000 1.90 0.00 35.98 4.02
75 76 1.373812 GTGTTTACCTCCAGCCGGT 59.626 57.895 1.90 0.00 38.55 5.28
76 77 0.035439 ATGTGTTTACCTCCAGCCGG 60.035 55.000 0.00 0.00 0.00 6.13
77 78 2.093658 AGTATGTGTTTACCTCCAGCCG 60.094 50.000 0.00 0.00 0.00 5.52
78 79 3.629142 AGTATGTGTTTACCTCCAGCC 57.371 47.619 0.00 0.00 0.00 4.85
79 80 5.959618 AAAAGTATGTGTTTACCTCCAGC 57.040 39.130 0.00 0.00 0.00 4.85
80 81 6.715264 AGGAAAAAGTATGTGTTTACCTCCAG 59.285 38.462 0.00 0.00 0.00 3.86
81 82 6.607019 AGGAAAAAGTATGTGTTTACCTCCA 58.393 36.000 0.00 0.00 0.00 3.86
82 83 7.520451 AAGGAAAAAGTATGTGTTTACCTCC 57.480 36.000 0.00 0.00 0.00 4.30
83 84 9.811995 AAAAAGGAAAAAGTATGTGTTTACCTC 57.188 29.630 0.00 0.00 0.00 3.85
124 125 8.823818 GCATGGAATAAACGTTAGTACAAGTAT 58.176 33.333 0.00 0.00 0.00 2.12
125 126 7.818446 TGCATGGAATAAACGTTAGTACAAGTA 59.182 33.333 0.00 0.00 0.00 2.24
126 127 6.651643 TGCATGGAATAAACGTTAGTACAAGT 59.348 34.615 0.00 0.00 0.00 3.16
127 128 7.067532 TGCATGGAATAAACGTTAGTACAAG 57.932 36.000 0.00 0.00 0.00 3.16
128 129 7.618502 ATGCATGGAATAAACGTTAGTACAA 57.381 32.000 0.00 0.00 0.00 2.41
129 130 7.618502 AATGCATGGAATAAACGTTAGTACA 57.381 32.000 0.00 0.00 0.00 2.90
130 131 8.905103 AAAATGCATGGAATAAACGTTAGTAC 57.095 30.769 0.00 0.00 0.00 2.73
131 132 8.731605 TGAAAATGCATGGAATAAACGTTAGTA 58.268 29.630 0.00 0.00 0.00 1.82
132 133 7.598278 TGAAAATGCATGGAATAAACGTTAGT 58.402 30.769 0.00 0.00 0.00 2.24
133 134 8.633075 ATGAAAATGCATGGAATAAACGTTAG 57.367 30.769 0.00 0.00 0.00 2.34
134 135 9.509855 GTATGAAAATGCATGGAATAAACGTTA 57.490 29.630 0.00 0.00 0.00 3.18
135 136 8.031864 TGTATGAAAATGCATGGAATAAACGTT 58.968 29.630 0.00 0.00 0.00 3.99
136 137 7.542890 TGTATGAAAATGCATGGAATAAACGT 58.457 30.769 0.00 0.00 0.00 3.99
137 138 7.984002 TGTATGAAAATGCATGGAATAAACG 57.016 32.000 0.00 0.00 0.00 3.60
236 237 8.327429 CGTTGCAACAGAAGAAAACAAATAATT 58.673 29.630 28.01 0.00 0.00 1.40
237 238 7.516627 GCGTTGCAACAGAAGAAAACAAATAAT 60.517 33.333 28.01 0.00 0.00 1.28
238 239 6.237701 GCGTTGCAACAGAAGAAAACAAATAA 60.238 34.615 28.01 0.00 0.00 1.40
239 240 5.231147 GCGTTGCAACAGAAGAAAACAAATA 59.769 36.000 28.01 0.00 0.00 1.40
240 241 4.032786 GCGTTGCAACAGAAGAAAACAAAT 59.967 37.500 28.01 0.00 0.00 2.32
241 242 3.366422 GCGTTGCAACAGAAGAAAACAAA 59.634 39.130 28.01 0.00 0.00 2.83
242 243 2.920490 GCGTTGCAACAGAAGAAAACAA 59.080 40.909 28.01 0.00 0.00 2.83
243 244 2.095008 TGCGTTGCAACAGAAGAAAACA 60.095 40.909 28.01 9.20 34.76 2.83
244 245 2.525055 TGCGTTGCAACAGAAGAAAAC 58.475 42.857 28.01 6.93 34.76 2.43
245 246 2.163412 ACTGCGTTGCAACAGAAGAAAA 59.837 40.909 28.01 4.24 38.41 2.29
246 247 1.742831 ACTGCGTTGCAACAGAAGAAA 59.257 42.857 28.01 5.22 38.41 2.52
247 248 1.330521 GACTGCGTTGCAACAGAAGAA 59.669 47.619 28.01 6.55 38.41 2.52
248 249 0.937304 GACTGCGTTGCAACAGAAGA 59.063 50.000 28.01 6.61 38.41 2.87
249 250 0.657312 TGACTGCGTTGCAACAGAAG 59.343 50.000 28.01 23.88 38.41 2.85
250 251 1.090728 TTGACTGCGTTGCAACAGAA 58.909 45.000 28.01 14.80 38.41 3.02
251 252 1.002576 CATTGACTGCGTTGCAACAGA 60.003 47.619 28.01 13.18 38.41 3.41
252 253 1.268692 ACATTGACTGCGTTGCAACAG 60.269 47.619 28.01 20.58 38.41 3.16
253 254 0.737804 ACATTGACTGCGTTGCAACA 59.262 45.000 28.01 9.88 38.41 3.33
254 255 1.838913 AACATTGACTGCGTTGCAAC 58.161 45.000 19.89 19.89 38.41 4.17
255 256 2.575694 AAACATTGACTGCGTTGCAA 57.424 40.000 0.00 0.00 38.41 4.08
256 257 2.098934 AGAAAACATTGACTGCGTTGCA 59.901 40.909 0.00 0.00 36.92 4.08
257 258 2.721090 GAGAAAACATTGACTGCGTTGC 59.279 45.455 0.00 0.00 0.00 4.17
258 259 3.300009 GGAGAAAACATTGACTGCGTTG 58.700 45.455 0.00 0.00 0.00 4.10
259 260 2.293399 GGGAGAAAACATTGACTGCGTT 59.707 45.455 0.00 0.00 0.00 4.84
260 261 1.880027 GGGAGAAAACATTGACTGCGT 59.120 47.619 0.00 0.00 0.00 5.24
261 262 1.135972 CGGGAGAAAACATTGACTGCG 60.136 52.381 0.00 0.00 0.00 5.18
262 263 1.880027 ACGGGAGAAAACATTGACTGC 59.120 47.619 0.00 0.00 0.00 4.40
263 264 3.853307 GCAACGGGAGAAAACATTGACTG 60.853 47.826 0.00 0.00 0.00 3.51
264 265 2.293399 GCAACGGGAGAAAACATTGACT 59.707 45.455 0.00 0.00 0.00 3.41
265 266 2.034053 TGCAACGGGAGAAAACATTGAC 59.966 45.455 0.00 0.00 0.00 3.18
266 267 2.302260 TGCAACGGGAGAAAACATTGA 58.698 42.857 0.00 0.00 0.00 2.57
267 268 2.791383 TGCAACGGGAGAAAACATTG 57.209 45.000 0.00 0.00 0.00 2.82
268 269 3.092334 GTTGCAACGGGAGAAAACATT 57.908 42.857 14.90 0.00 0.00 2.71
269 270 2.793278 GTTGCAACGGGAGAAAACAT 57.207 45.000 14.90 0.00 0.00 2.71
281 282 2.627510 AAAGGCCTGTGCGTTGCAAC 62.628 55.000 19.89 19.89 44.30 4.17
282 283 1.954362 AAAAGGCCTGTGCGTTGCAA 61.954 50.000 5.69 0.00 44.30 4.08
283 284 2.422231 AAAAGGCCTGTGCGTTGCA 61.422 52.632 5.69 0.00 44.30 4.08
284 285 1.950630 CAAAAGGCCTGTGCGTTGC 60.951 57.895 5.69 0.00 44.30 4.17
285 286 1.950630 GCAAAAGGCCTGTGCGTTG 60.951 57.895 22.20 14.85 44.30 4.10
286 287 0.821711 TAGCAAAAGGCCTGTGCGTT 60.822 50.000 27.44 17.90 46.85 4.84
287 288 1.228124 TAGCAAAAGGCCTGTGCGT 60.228 52.632 27.44 20.25 46.50 5.24
288 289 1.237285 ACTAGCAAAAGGCCTGTGCG 61.237 55.000 27.44 19.74 46.50 5.34
289 290 1.821216 TACTAGCAAAAGGCCTGTGC 58.179 50.000 26.97 26.97 46.50 4.57
290 291 6.699575 ATTATTACTAGCAAAAGGCCTGTG 57.300 37.500 5.69 9.50 46.50 3.66
291 292 8.817092 TTTATTATTACTAGCAAAAGGCCTGT 57.183 30.769 5.69 0.00 46.50 4.00
292 293 7.862873 GCTTTATTATTACTAGCAAAAGGCCTG 59.137 37.037 5.69 0.00 46.50 4.85
293 294 7.559897 TGCTTTATTATTACTAGCAAAAGGCCT 59.440 33.333 0.00 0.00 46.50 5.19
294 295 7.712797 TGCTTTATTATTACTAGCAAAAGGCC 58.287 34.615 0.00 0.00 46.50 5.19
295 296 8.621286 TCTGCTTTATTATTACTAGCAAAAGGC 58.379 33.333 0.00 0.00 40.90 4.35
309 310 9.717942 GACCAGAATCAGTATCTGCTTTATTAT 57.282 33.333 0.00 0.00 42.36 1.28
327 328 4.978083 ATTACTCACGTACGACCAGAAT 57.022 40.909 24.41 12.21 0.00 2.40
342 343 5.189180 AGGGACTCTGATGCAAAATTACTC 58.811 41.667 0.00 0.00 0.00 2.59
384 385 5.502079 TCACTTTAAAATAGGGATTGCGGA 58.498 37.500 0.00 0.00 0.00 5.54
581 586 2.517402 GGTGGAACGGTGGTGCAA 60.517 61.111 0.00 0.00 38.12 4.08
787 793 1.953559 ACACAAACACATGCTCGTCT 58.046 45.000 0.00 0.00 0.00 4.18
833 839 2.031068 TCGGACAAACACACAAACATCG 59.969 45.455 0.00 0.00 0.00 3.84
835 841 2.223479 GCTCGGACAAACACACAAACAT 60.223 45.455 0.00 0.00 0.00 2.71
875 881 8.321353 TGTATTCATGTGAGAGTTTACCTCAAT 58.679 33.333 0.00 0.00 43.12 2.57
911 917 8.419442 GCTTTGAATCATATGGAAGGAGATTTT 58.581 33.333 2.13 0.00 0.00 1.82
1121 1132 2.042831 GGTGCATGGAGGTGCTGTC 61.043 63.158 0.00 0.00 45.27 3.51
1336 1409 2.159028 GGGTTACCTCTGATCTCTGTGC 60.159 54.545 0.00 0.00 0.00 4.57
1552 2303 6.010294 ACAGAGAACATGATGAGCAAAAAG 57.990 37.500 0.00 0.00 0.00 2.27
2978 3817 1.563924 TAGTCATAACCTGCACGGGT 58.436 50.000 0.00 0.00 42.05 5.28
3494 4346 7.573096 GCGATGTTCTTAAATTCTGGACAAAGA 60.573 37.037 0.00 0.00 0.00 2.52
3860 4723 6.722590 TCGAGCCAAGGGAATATTGTACTATA 59.277 38.462 0.00 0.00 0.00 1.31
4448 5331 2.571653 ACCTATGCATACACACACACCT 59.428 45.455 1.16 0.00 0.00 4.00
4502 5391 2.162408 GCTCTATGCAAACTTGTGGGAC 59.838 50.000 0.00 0.00 42.31 4.46
4732 5621 2.036731 AGACCCGTCGTCCATGGA 59.963 61.111 11.44 11.44 43.08 3.41
5325 6243 6.949352 ATTTTGACAACATGACTTGTCTCT 57.051 33.333 22.53 8.27 46.97 3.10
5356 6274 4.718858 CAACACCAATCAGTTGCAAATG 57.281 40.909 20.41 20.41 38.69 2.32
5398 6324 1.134487 CAATACCCGTGCGTTGCAG 59.866 57.895 0.00 0.00 40.08 4.41
5509 6435 1.933853 CGTACCACCAGAAGCAATAGC 59.066 52.381 0.00 0.00 42.56 2.97
5510 6436 3.187700 GACGTACCACCAGAAGCAATAG 58.812 50.000 0.00 0.00 0.00 1.73
5511 6437 2.563620 TGACGTACCACCAGAAGCAATA 59.436 45.455 0.00 0.00 0.00 1.90
5512 6438 1.346395 TGACGTACCACCAGAAGCAAT 59.654 47.619 0.00 0.00 0.00 3.56
5513 6439 0.753867 TGACGTACCACCAGAAGCAA 59.246 50.000 0.00 0.00 0.00 3.91
5514 6440 0.973632 ATGACGTACCACCAGAAGCA 59.026 50.000 0.00 0.00 0.00 3.91
5515 6441 2.953466 TATGACGTACCACCAGAAGC 57.047 50.000 0.00 0.00 0.00 3.86
5516 6442 7.518370 GCAAATTATATGACGTACCACCAGAAG 60.518 40.741 0.00 0.00 0.00 2.85
5517 6443 6.259167 GCAAATTATATGACGTACCACCAGAA 59.741 38.462 0.00 0.00 0.00 3.02
5518 6444 5.756347 GCAAATTATATGACGTACCACCAGA 59.244 40.000 0.00 0.00 0.00 3.86
5519 6445 5.049680 GGCAAATTATATGACGTACCACCAG 60.050 44.000 0.00 0.00 0.00 4.00
5520 6446 4.817464 GGCAAATTATATGACGTACCACCA 59.183 41.667 0.00 0.00 0.00 4.17
5521 6447 4.214758 GGGCAAATTATATGACGTACCACC 59.785 45.833 0.00 0.00 0.00 4.61
5522 6448 4.214758 GGGGCAAATTATATGACGTACCAC 59.785 45.833 0.00 0.00 0.00 4.16
5523 6449 4.103469 AGGGGCAAATTATATGACGTACCA 59.897 41.667 0.00 0.00 0.00 3.25
5524 6450 4.648651 AGGGGCAAATTATATGACGTACC 58.351 43.478 0.00 0.00 0.00 3.34
5525 6451 7.443272 AGTTTAGGGGCAAATTATATGACGTAC 59.557 37.037 0.00 0.00 0.00 3.67
5526 6452 7.511268 AGTTTAGGGGCAAATTATATGACGTA 58.489 34.615 0.00 0.00 0.00 3.57
5527 6453 6.362248 AGTTTAGGGGCAAATTATATGACGT 58.638 36.000 0.00 0.00 0.00 4.34
5528 6454 6.877611 AGTTTAGGGGCAAATTATATGACG 57.122 37.500 0.00 0.00 0.00 4.35
5529 6455 6.923508 GCAAGTTTAGGGGCAAATTATATGAC 59.076 38.462 0.00 0.00 0.00 3.06
5530 6456 6.838612 AGCAAGTTTAGGGGCAAATTATATGA 59.161 34.615 0.00 0.00 0.00 2.15
5531 6457 7.054491 AGCAAGTTTAGGGGCAAATTATATG 57.946 36.000 0.00 0.00 0.00 1.78
5532 6458 8.776061 TTAGCAAGTTTAGGGGCAAATTATAT 57.224 30.769 0.00 0.00 0.00 0.86
5533 6459 8.596781 TTTAGCAAGTTTAGGGGCAAATTATA 57.403 30.769 0.00 0.00 0.00 0.98
5534 6460 7.489239 TTTAGCAAGTTTAGGGGCAAATTAT 57.511 32.000 0.00 0.00 0.00 1.28
5535 6461 6.919775 TTTAGCAAGTTTAGGGGCAAATTA 57.080 33.333 0.00 0.00 0.00 1.40
5536 6462 5.816955 TTTAGCAAGTTTAGGGGCAAATT 57.183 34.783 0.00 0.00 0.00 1.82
5537 6463 7.675161 ATATTTAGCAAGTTTAGGGGCAAAT 57.325 32.000 0.00 0.00 0.00 2.32
5538 6464 7.489239 AATATTTAGCAAGTTTAGGGGCAAA 57.511 32.000 0.00 0.00 0.00 3.68
5539 6465 7.068962 GGTAATATTTAGCAAGTTTAGGGGCAA 59.931 37.037 0.00 0.00 0.00 4.52
5540 6466 6.548251 GGTAATATTTAGCAAGTTTAGGGGCA 59.452 38.462 0.00 0.00 0.00 5.36
5541 6467 6.015688 GGGTAATATTTAGCAAGTTTAGGGGC 60.016 42.308 0.00 0.00 0.00 5.80
5542 6468 7.013942 GTGGGTAATATTTAGCAAGTTTAGGGG 59.986 40.741 0.00 0.00 0.00 4.79
5543 6469 7.013942 GGTGGGTAATATTTAGCAAGTTTAGGG 59.986 40.741 0.00 0.00 0.00 3.53
5544 6470 7.558444 TGGTGGGTAATATTTAGCAAGTTTAGG 59.442 37.037 0.00 0.00 0.00 2.69
5545 6471 8.514330 TGGTGGGTAATATTTAGCAAGTTTAG 57.486 34.615 0.00 0.00 0.00 1.85
5546 6472 8.880991 TTGGTGGGTAATATTTAGCAAGTTTA 57.119 30.769 0.00 0.00 0.00 2.01
5547 6473 7.784470 TTGGTGGGTAATATTTAGCAAGTTT 57.216 32.000 0.00 0.00 0.00 2.66
5548 6474 7.632680 GCATTGGTGGGTAATATTTAGCAAGTT 60.633 37.037 0.00 0.00 33.08 2.66
5549 6475 6.183360 GCATTGGTGGGTAATATTTAGCAAGT 60.183 38.462 0.00 0.00 33.08 3.16
5550 6476 6.215845 GCATTGGTGGGTAATATTTAGCAAG 58.784 40.000 0.00 0.00 33.08 4.01
5551 6477 5.069781 GGCATTGGTGGGTAATATTTAGCAA 59.930 40.000 0.00 1.60 33.93 3.91
5552 6478 4.586841 GGCATTGGTGGGTAATATTTAGCA 59.413 41.667 0.00 0.00 0.00 3.49
5553 6479 4.586841 TGGCATTGGTGGGTAATATTTAGC 59.413 41.667 0.00 0.00 0.00 3.09
5554 6480 6.721208 AGATGGCATTGGTGGGTAATATTTAG 59.279 38.462 0.00 0.00 0.00 1.85
5555 6481 6.619464 AGATGGCATTGGTGGGTAATATTTA 58.381 36.000 0.00 0.00 0.00 1.40
5556 6482 5.466819 AGATGGCATTGGTGGGTAATATTT 58.533 37.500 0.00 0.00 0.00 1.40
5557 6483 5.078683 AGATGGCATTGGTGGGTAATATT 57.921 39.130 0.00 0.00 0.00 1.28
5558 6484 4.747265 AGATGGCATTGGTGGGTAATAT 57.253 40.909 0.00 0.00 0.00 1.28
5559 6485 5.858876 ATAGATGGCATTGGTGGGTAATA 57.141 39.130 0.00 0.00 0.00 0.98
5560 6486 4.747265 ATAGATGGCATTGGTGGGTAAT 57.253 40.909 0.00 0.00 0.00 1.89


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

AutoCloner maintained by Alex Coulton.