Multiple sequence alignment - TraesCS5A01G356100

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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 TraesCS5A01G356100 chr5A 100.000 7979 0 0 1 7979 558542460 558550438 0.000000e+00 14735
1 TraesCS5A01G356100 chr5A 80.821 1340 186 43 3650 4966 558545649 558546940 0.000000e+00 985
2 TraesCS5A01G356100 chr5A 80.821 1340 186 43 3190 4481 558546109 558547425 0.000000e+00 985
3 TraesCS5A01G356100 chr5A 82.260 823 111 20 4151 4966 558545673 558546467 0.000000e+00 678
4 TraesCS5A01G356100 chr5A 82.260 823 111 20 3214 4008 558546610 558547425 0.000000e+00 678
5 TraesCS5A01G356100 chr5A 83.518 631 86 13 2905 3520 558545028 558545655 2.500000e-159 573
6 TraesCS5A01G356100 chr5A 83.518 631 86 13 2569 3196 558545364 558545979 2.500000e-159 573
7 TraesCS5A01G356100 chr5A 83.662 355 47 8 4613 4966 558545654 558545998 2.780000e-84 324
8 TraesCS5A01G356100 chr5A 83.662 355 47 8 3195 3539 558547072 558547425 2.780000e-84 324
9 TraesCS5A01G356100 chr5A 81.416 339 57 5 3650 3986 558545318 558545652 1.020000e-68 272
10 TraesCS5A01G356100 chr5A 81.416 339 57 5 2859 3193 558546109 558546445 1.020000e-68 272
11 TraesCS5A01G356100 chr5A 82.034 295 47 6 4653 4942 558545026 558545319 6.180000e-61 246
12 TraesCS5A01G356100 chr5A 82.034 295 47 6 2567 2860 558547112 558547401 6.180000e-61 246
13 TraesCS5A01G356100 chr5A 81.169 308 53 4 4637 4942 558545346 558545650 8.000000e-60 243
14 TraesCS5A01G356100 chr5A 81.169 308 53 4 2887 3191 558547096 558547401 8.000000e-60 243
15 TraesCS5A01G356100 chr5A 79.743 311 48 11 3687 3986 558545015 558545321 2.260000e-50 211
16 TraesCS5A01G356100 chr5A 79.545 308 54 7 2556 2862 558546146 558546445 2.260000e-50 211
17 TraesCS5A01G356100 chr5D 92.148 2560 130 32 4976 7504 442336662 442339181 0.000000e+00 3548
18 TraesCS5A01G356100 chr5D 93.031 2052 69 39 1 2021 442330568 442332576 0.000000e+00 2929
19 TraesCS5A01G356100 chr5D 85.846 1413 145 30 2653 4030 442333657 442335049 0.000000e+00 1450
20 TraesCS5A01G356100 chr5D 86.851 867 86 19 3599 4447 442335268 442336124 0.000000e+00 944
21 TraesCS5A01G356100 chr5D 85.279 788 102 13 4151 4932 442335345 442336124 0.000000e+00 800
22 TraesCS5A01G356100 chr5D 81.304 813 117 21 3190 3973 442335317 442336123 1.890000e-175 627
23 TraesCS5A01G356100 chr5D 82.589 649 98 11 2556 3196 442333901 442334542 6.990000e-155 558
24 TraesCS5A01G356100 chr5D 78.767 876 138 32 3650 4503 442334200 442335049 1.960000e-150 544
25 TraesCS5A01G356100 chr5D 89.640 444 14 18 7537 7979 442339182 442339594 3.280000e-148 536
26 TraesCS5A01G356100 chr5D 83.986 562 73 13 2974 3520 442333647 442334206 2.550000e-144 523
27 TraesCS5A01G356100 chr5D 83.964 555 28 25 2056 2569 442332941 442333475 7.250000e-130 475
28 TraesCS5A01G356100 chr5D 86.429 420 45 10 4554 4970 442335268 442335678 4.390000e-122 449
29 TraesCS5A01G356100 chr5D 82.263 327 45 10 3191 3505 442335799 442336124 3.670000e-68 270
30 TraesCS5A01G356100 chr5D 80.870 345 53 9 2859 3196 442335317 442335655 7.940000e-65 259
31 TraesCS5A01G356100 chr5D 81.470 313 44 9 2556 2865 442335354 442335655 2.220000e-60 244
32 TraesCS5A01G356100 chr5D 78.834 326 63 4 2860 3180 442335799 442336123 1.740000e-51 215
33 TraesCS5A01G356100 chr5D 80.427 281 47 7 2572 2849 442335848 442336123 2.920000e-49 207
34 TraesCS5A01G356100 chr5B 89.424 2846 165 72 5190 7967 538546626 538549403 0.000000e+00 3463
35 TraesCS5A01G356100 chr5B 90.384 2631 87 65 1 2569 538541213 538543739 0.000000e+00 3304
36 TraesCS5A01G356100 chr5B 79.604 657 97 21 4304 4941 538544966 538545604 3.420000e-118 436
37 TraesCS5A01G356100 chr5B 76.583 679 116 25 3364 4012 538544968 538545633 4.610000e-87 333
38 TraesCS5A01G356100 chr5B 86.228 167 22 1 3029 3195 538544958 538545123 6.360000e-41 180
39 TraesCS5A01G356100 chr6A 92.214 411 27 3 1242 1648 471800550 471800959 1.930000e-160 577
40 TraesCS5A01G356100 chr6D 92.556 403 27 1 1242 1641 332499019 332499421 6.940000e-160 575
41 TraesCS5A01G356100 chr6B 91.587 416 32 1 1235 1647 487835482 487835067 8.980000e-159 571
42 TraesCS5A01G356100 chr2A 91.667 408 31 1 1243 1647 657813645 657813238 5.410000e-156 562
43 TraesCS5A01G356100 chr2A 92.208 77 6 0 5869 5945 657811017 657810941 8.470000e-20 110
44 TraesCS5A01G356100 chr2D 91.422 408 32 1 1243 1647 513765038 513764631 2.520000e-154 556
45 TraesCS5A01G356100 chr2D 92.208 77 6 0 5869 5945 513762406 513762330 8.470000e-20 110
46 TraesCS5A01G356100 chr2B 91.176 408 33 3 1243 1647 605381366 605380959 1.170000e-152 551
47 TraesCS5A01G356100 chr2B 92.208 77 6 0 5869 5945 605378723 605378647 8.470000e-20 110
48 TraesCS5A01G356100 chr3B 88.943 407 44 1 1240 1645 222318452 222318858 1.200000e-137 501
49 TraesCS5A01G356100 chr7D 90.000 90 3 6 2327 2416 44039822 44039739 2.350000e-20 111
50 TraesCS5A01G356100 chr4A 88.889 90 4 6 2327 2416 655243504 655243421 1.100000e-18 106
51 TraesCS5A01G356100 chr4A 96.774 62 2 0 5870 5931 34787351 34787290 3.940000e-18 104
52 TraesCS5A01G356100 chr4D 96.774 62 2 0 5870 5931 433393144 433393083 3.940000e-18 104
53 TraesCS5A01G356100 chr4B 96.774 62 2 0 5870 5931 531580472 531580411 3.940000e-18 104


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 TraesCS5A01G356100 chr5A 558542460 558550438 7978 False 14735.000000 14735 100.000000 1 7979 1 chr5A.!!$F1 7978
1 TraesCS5A01G356100 chr5A 558545015 558547425 2410 False 441.500000 985 81.815500 2556 4966 16 chr5A.!!$F2 2410
2 TraesCS5A01G356100 chr5D 442330568 442339594 9026 False 857.529412 3548 84.335176 1 7979 17 chr5D.!!$F1 7978
3 TraesCS5A01G356100 chr5B 538541213 538549403 8190 False 1543.200000 3463 84.444600 1 7967 5 chr5B.!!$F1 7966
4 TraesCS5A01G356100 chr2A 657810941 657813645 2704 True 336.000000 562 91.937500 1243 5945 2 chr2A.!!$R1 4702
5 TraesCS5A01G356100 chr2D 513762330 513765038 2708 True 333.000000 556 91.815000 1243 5945 2 chr2D.!!$R1 4702
6 TraesCS5A01G356100 chr2B 605378647 605381366 2719 True 330.500000 551 91.692000 1243 5945 2 chr2B.!!$R1 4702

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
545 555 0.320421 TTTCCTCCTTCCTTGCGTCG 60.320 55.000 0.00 0.00 0.00 5.12 F
1848 2032 0.035534 TTGACGGGTGGTGATGGATG 60.036 55.000 0.00 0.00 0.00 3.51 F
2277 2941 0.107017 CATGGATCCCCACCTGTGTC 60.107 60.000 9.90 0.00 46.98 3.67 F
2434 3134 0.807496 CTGGCCTGCTGTTAGCTTTC 59.193 55.000 3.32 0.00 42.97 2.62 F
2435 3135 0.955428 TGGCCTGCTGTTAGCTTTCG 60.955 55.000 3.32 0.00 42.97 3.46 F
2536 3412 1.006832 GTGTCATGTACATGCCGGTC 58.993 55.000 27.71 15.88 41.10 4.79 F
5453 7985 1.141665 GCCCGCATCCAAATCAACC 59.858 57.895 0.00 0.00 0.00 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2025 2214 0.104120 TCTCTCGCTCTCTCCTCTCG 59.896 60.000 0.00 0.00 0.00 4.04 R
5150 7617 8.516234 TCTGTGTATCTCTCTCTTTCTAAACAC 58.484 37.037 0.00 0.00 35.31 3.32 R
5415 7946 0.319469 GGCTATGGAAGAGCTCGCTC 60.319 60.000 8.37 10.83 43.03 5.03 R
5450 7982 1.555967 CAAATCCCCCAATCGTGGTT 58.444 50.000 0.00 0.00 44.30 3.67 R
5453 7985 1.815866 GCCAAATCCCCCAATCGTG 59.184 57.895 0.00 0.00 0.00 4.35 R
5644 8180 5.103687 TCAAACATGATACATGCATTGTGC 58.896 37.500 19.82 0.00 45.29 4.57 R
7513 10371 0.040336 CAGTCTGTGCTTGCTTGCTG 60.040 55.000 0.00 0.00 0.00 4.41 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
51 52 3.787001 CCCCCGCTCTCCTCCAAC 61.787 72.222 0.00 0.00 0.00 3.77
52 53 3.787001 CCCCGCTCTCCTCCAACC 61.787 72.222 0.00 0.00 0.00 3.77
53 54 3.787001 CCCGCTCTCCTCCAACCC 61.787 72.222 0.00 0.00 0.00 4.11
146 150 6.043590 AGAGAGAGAGAAGAGAGCAGATATCA 59.956 42.308 5.32 0.00 0.00 2.15
211 215 3.440415 GCAACAAGCGGGTAGGGC 61.440 66.667 0.00 0.00 0.00 5.19
269 274 5.062934 TCACGCACCGTTTTCTATATCTTTG 59.937 40.000 0.00 0.00 38.32 2.77
363 368 4.466827 GTTTGGTTCCTTTTCCTCCACTA 58.533 43.478 0.00 0.00 0.00 2.74
430 438 1.876799 CTCTCTCTCTCGTGTGTGTGT 59.123 52.381 0.00 0.00 0.00 3.72
436 444 0.459411 TCTCGTGTGTGTGTGTGTGG 60.459 55.000 0.00 0.00 0.00 4.17
544 554 2.010497 GATTTCCTCCTTCCTTGCGTC 58.990 52.381 0.00 0.00 0.00 5.19
545 555 0.320421 TTTCCTCCTTCCTTGCGTCG 60.320 55.000 0.00 0.00 0.00 5.12
546 556 2.781595 TTCCTCCTTCCTTGCGTCGC 62.782 60.000 11.10 11.10 0.00 5.19
573 583 1.528309 GAGGGTGTTGTGTGGGTGG 60.528 63.158 0.00 0.00 0.00 4.61
681 691 5.013704 TGGTTTGTCCTCTACATACATGGTT 59.986 40.000 0.00 0.00 40.60 3.67
879 892 0.898320 TTGTGCTCTCTAGACTGGGC 59.102 55.000 0.00 0.00 0.00 5.36
931 944 2.266055 CTCGGCTCACCTGAACCC 59.734 66.667 0.00 0.00 0.00 4.11
932 945 2.525629 TCGGCTCACCTGAACCCA 60.526 61.111 0.00 0.00 0.00 4.51
933 946 2.111999 CTCGGCTCACCTGAACCCAA 62.112 60.000 0.00 0.00 0.00 4.12
934 947 1.966451 CGGCTCACCTGAACCCAAC 60.966 63.158 0.00 0.00 0.00 3.77
935 948 1.456287 GGCTCACCTGAACCCAACT 59.544 57.895 0.00 0.00 0.00 3.16
972 985 3.084786 AGCAATTGGAGGAAGCTGTTAC 58.915 45.455 7.72 0.00 33.67 2.50
986 999 7.175119 AGGAAGCTGTTACCTAATCTTGTTTTC 59.825 37.037 0.00 0.00 31.78 2.29
994 1007 8.727910 GTTACCTAATCTTGTTTTCTTCCGATT 58.272 33.333 0.00 0.00 0.00 3.34
1156 1172 6.055588 CCAAGTGAGTAATTAATCCGTCCAT 58.944 40.000 10.23 0.00 0.00 3.41
1160 1176 7.659186 AGTGAGTAATTAATCCGTCCATCTAC 58.341 38.462 10.23 0.00 0.00 2.59
1162 1178 8.790718 GTGAGTAATTAATCCGTCCATCTACTA 58.209 37.037 10.23 0.00 0.00 1.82
1163 1179 9.529823 TGAGTAATTAATCCGTCCATCTACTAT 57.470 33.333 10.23 0.00 0.00 2.12
1169 1185 9.756571 ATTAATCCGTCCATCTACTATTCTACT 57.243 33.333 0.00 0.00 0.00 2.57
1170 1186 7.690952 AATCCGTCCATCTACTATTCTACTC 57.309 40.000 0.00 0.00 0.00 2.59
1171 1187 5.558818 TCCGTCCATCTACTATTCTACTCC 58.441 45.833 0.00 0.00 0.00 3.85
1172 1188 5.072736 TCCGTCCATCTACTATTCTACTCCA 59.927 44.000 0.00 0.00 0.00 3.86
1175 1191 7.610692 CCGTCCATCTACTATTCTACTCCATTA 59.389 40.741 0.00 0.00 0.00 1.90
1231 1256 8.515695 TTAATTGAGTATCGGTCTCTCTGTAA 57.484 34.615 3.18 0.00 38.61 2.41
1232 1257 7.589958 AATTGAGTATCGGTCTCTCTGTAAT 57.410 36.000 3.18 0.00 38.61 1.89
1650 1822 2.966516 CACCCTCTTCTCCAGGTATACC 59.033 54.545 14.54 14.54 0.00 2.73
1651 1823 2.590611 ACCCTCTTCTCCAGGTATACCA 59.409 50.000 23.87 2.37 38.89 3.25
1652 1824 3.210074 ACCCTCTTCTCCAGGTATACCAT 59.790 47.826 23.87 6.38 38.89 3.55
1653 1825 3.580458 CCCTCTTCTCCAGGTATACCATG 59.420 52.174 23.87 17.09 38.89 3.66
1656 1828 3.388024 TCTTCTCCAGGTATACCATGCAC 59.612 47.826 23.87 0.00 38.89 4.57
1673 1851 1.451927 ACGCACGCCATTGATCCAT 60.452 52.632 0.00 0.00 0.00 3.41
1674 1852 1.280746 CGCACGCCATTGATCCATC 59.719 57.895 0.00 0.00 0.00 3.51
1675 1853 1.656441 GCACGCCATTGATCCATCC 59.344 57.895 0.00 0.00 0.00 3.51
1676 1854 0.820891 GCACGCCATTGATCCATCCT 60.821 55.000 0.00 0.00 0.00 3.24
1709 1887 7.439157 AGATCGATGTTTCAGTTCATTTTCA 57.561 32.000 0.54 0.00 0.00 2.69
1717 1896 9.683069 ATGTTTCAGTTCATTTTCAGTTCATAC 57.317 29.630 0.00 0.00 0.00 2.39
1763 1945 4.609947 TGTTCGATTTTGGATATGCATGC 58.390 39.130 11.82 11.82 0.00 4.06
1799 1981 5.163581 GGTCATGATGAAACTTTGATGAGGG 60.164 44.000 0.00 0.00 0.00 4.30
1843 2027 0.611200 TCGATTTGACGGGTGGTGAT 59.389 50.000 0.00 0.00 0.00 3.06
1848 2032 0.035534 TTGACGGGTGGTGATGGATG 60.036 55.000 0.00 0.00 0.00 3.51
1849 2033 1.153168 GACGGGTGGTGATGGATGG 60.153 63.158 0.00 0.00 0.00 3.51
1850 2034 1.615124 ACGGGTGGTGATGGATGGA 60.615 57.895 0.00 0.00 0.00 3.41
1851 2035 0.988145 ACGGGTGGTGATGGATGGAT 60.988 55.000 0.00 0.00 0.00 3.41
1852 2036 0.535780 CGGGTGGTGATGGATGGATG 60.536 60.000 0.00 0.00 0.00 3.51
1853 2037 0.178981 GGGTGGTGATGGATGGATGG 60.179 60.000 0.00 0.00 0.00 3.51
1854 2038 0.846015 GGTGGTGATGGATGGATGGA 59.154 55.000 0.00 0.00 0.00 3.41
1855 2039 1.477558 GGTGGTGATGGATGGATGGAC 60.478 57.143 0.00 0.00 0.00 4.02
1868 2052 0.976641 GATGGACGGATGGGATGCTA 59.023 55.000 0.00 0.00 0.00 3.49
1872 2056 1.758440 GACGGATGGGATGCTAGCCA 61.758 60.000 13.29 2.69 0.00 4.75
1947 2131 0.563173 TAGGGACATGGGCTAGCTCT 59.437 55.000 17.26 0.00 0.00 4.09
1992 2181 2.658268 GCGCGCAACTTTTGGCTT 60.658 55.556 29.10 0.00 0.00 4.35
2025 2214 0.254178 TTGGATTCCCTGCAGAGAGC 59.746 55.000 17.39 3.32 45.96 4.09
2034 2224 4.234019 GCAGAGAGCGAGAGGAGA 57.766 61.111 0.00 0.00 0.00 3.71
2038 2228 0.179045 AGAGAGCGAGAGGAGAGAGC 60.179 60.000 0.00 0.00 0.00 4.09
2258 2922 3.589881 GCATCGACCTGGCATGGC 61.590 66.667 13.29 13.29 0.00 4.40
2259 2923 2.124612 CATCGACCTGGCATGGCA 60.125 61.111 21.97 21.97 0.00 4.92
2260 2924 1.527611 CATCGACCTGGCATGGCAT 60.528 57.895 23.59 9.00 0.00 4.40
2261 2925 1.527611 ATCGACCTGGCATGGCATG 60.528 57.895 23.59 22.99 0.00 4.06
2262 2926 2.971095 ATCGACCTGGCATGGCATGG 62.971 60.000 27.48 24.93 0.00 3.66
2271 2935 1.532316 CATGGCATGGATCCCCACC 60.532 63.158 19.80 8.19 46.98 4.61
2275 2939 1.454479 GCATGGATCCCCACCTGTG 60.454 63.158 9.90 0.00 46.98 3.66
2277 2941 0.107017 CATGGATCCCCACCTGTGTC 60.107 60.000 9.90 0.00 46.98 3.67
2303 2967 2.569059 GTGATGACATACATGCTGCCT 58.431 47.619 0.00 0.00 39.56 4.75
2319 2983 2.125753 CTGCAGCACTCCCGTCTC 60.126 66.667 0.00 0.00 0.00 3.36
2320 2984 2.917227 TGCAGCACTCCCGTCTCA 60.917 61.111 0.00 0.00 0.00 3.27
2321 2985 2.125753 GCAGCACTCCCGTCTCAG 60.126 66.667 0.00 0.00 0.00 3.35
2322 2986 2.125753 CAGCACTCCCGTCTCAGC 60.126 66.667 0.00 0.00 0.00 4.26
2325 2989 4.056125 CACTCCCGTCTCAGCGCA 62.056 66.667 11.47 0.00 0.00 6.09
2399 3091 2.247311 GCAAAGTCATGCCAAGTACG 57.753 50.000 0.00 0.00 40.49 3.67
2401 3093 2.739913 GCAAAGTCATGCCAAGTACGTA 59.260 45.455 0.00 0.00 40.49 3.57
2434 3134 0.807496 CTGGCCTGCTGTTAGCTTTC 59.193 55.000 3.32 0.00 42.97 2.62
2435 3135 0.955428 TGGCCTGCTGTTAGCTTTCG 60.955 55.000 3.32 0.00 42.97 3.46
2438 3138 2.007049 GCCTGCTGTTAGCTTTCGCTA 61.007 52.381 0.00 0.00 46.79 4.26
2505 3381 2.179267 GCTGCTGCGGCTTTTACC 59.821 61.111 25.48 0.00 39.59 2.85
2517 3393 2.223340 GGCTTTTACCTGATGCATGTCG 60.223 50.000 2.46 0.00 0.00 4.35
2536 3412 1.006832 GTGTCATGTACATGCCGGTC 58.993 55.000 27.71 15.88 41.10 4.79
2553 3429 4.562082 CCGGTCTTGTCTTACATGTAACA 58.438 43.478 14.35 10.03 0.00 2.41
4966 6690 8.592809 AGGGTAACTTCATCATTATTTGCAAAA 58.407 29.630 17.19 0.11 0.00 2.44
4967 6691 9.382275 GGGTAACTTCATCATTATTTGCAAAAT 57.618 29.630 17.19 2.96 0.00 1.82
5173 7690 9.646427 ATTGTGTTTAGAAAGAGAGAGATACAC 57.354 33.333 0.00 0.00 34.37 2.90
5174 7691 8.178313 TGTGTTTAGAAAGAGAGAGATACACA 57.822 34.615 0.00 0.00 39.58 3.72
5175 7692 8.300286 TGTGTTTAGAAAGAGAGAGATACACAG 58.700 37.037 0.00 0.00 37.72 3.66
5176 7693 8.516234 GTGTTTAGAAAGAGAGAGATACACAGA 58.484 37.037 0.00 0.00 34.06 3.41
5177 7694 8.735315 TGTTTAGAAAGAGAGAGATACACAGAG 58.265 37.037 0.00 0.00 0.00 3.35
5178 7695 8.952278 GTTTAGAAAGAGAGAGATACACAGAGA 58.048 37.037 0.00 0.00 0.00 3.10
5179 7696 8.731275 TTAGAAAGAGAGAGATACACAGAGAG 57.269 38.462 0.00 0.00 0.00 3.20
5180 7697 6.957631 AGAAAGAGAGAGATACACAGAGAGA 58.042 40.000 0.00 0.00 0.00 3.10
5181 7698 7.050377 AGAAAGAGAGAGATACACAGAGAGAG 58.950 42.308 0.00 0.00 0.00 3.20
5182 7699 5.296151 AGAGAGAGATACACAGAGAGAGG 57.704 47.826 0.00 0.00 0.00 3.69
5183 7700 4.103153 AGAGAGAGATACACAGAGAGAGGG 59.897 50.000 0.00 0.00 0.00 4.30
5184 7701 3.138283 AGAGAGATACACAGAGAGAGGGG 59.862 52.174 0.00 0.00 0.00 4.79
5215 7732 2.032894 CGGTGTGTTGCTACAAGACAAG 60.033 50.000 11.31 6.05 35.69 3.16
5415 7946 4.868067 AGTACCTAAATTATCAGCCGACG 58.132 43.478 0.00 0.00 0.00 5.12
5439 7970 2.029666 CTCTTCCATAGCCGCCCG 59.970 66.667 0.00 0.00 0.00 6.13
5440 7971 4.235762 TCTTCCATAGCCGCCCGC 62.236 66.667 0.00 0.00 37.98 6.13
5441 7972 4.545706 CTTCCATAGCCGCCCGCA 62.546 66.667 0.00 0.00 41.38 5.69
5450 7982 2.828095 CCGCCCGCATCCAAATCA 60.828 61.111 0.00 0.00 0.00 2.57
5453 7985 1.141665 GCCCGCATCCAAATCAACC 59.858 57.895 0.00 0.00 0.00 3.77
5483 8018 3.433740 GGGGATTTGGCGTTCTCTTAGAT 60.434 47.826 0.00 0.00 0.00 1.98
5488 8023 6.201234 GGATTTGGCGTTCTCTTAGATAAGAC 59.799 42.308 0.00 0.00 37.40 3.01
5519 8054 7.639113 TGTTTAAAAAGAAAGAGAGAAGGCA 57.361 32.000 0.00 0.00 0.00 4.75
5618 8154 4.095483 CAGTTCATCACCTGATTAGCCAAC 59.905 45.833 0.00 0.00 32.72 3.77
5641 8177 6.390504 ACTAATTCCATATACTCCCCTGTGA 58.609 40.000 0.00 0.00 0.00 3.58
5643 8179 6.786843 AATTCCATATACTCCCCTGTGATT 57.213 37.500 0.00 0.00 0.00 2.57
5644 8180 5.567037 TTCCATATACTCCCCTGTGATTG 57.433 43.478 0.00 0.00 0.00 2.67
5647 8183 2.717639 ATACTCCCCTGTGATTGCAC 57.282 50.000 0.00 0.00 45.35 4.57
5706 8257 7.441890 TGCTGAAATTTATTTGTAGGTCGAA 57.558 32.000 0.00 0.00 0.00 3.71
5707 8258 8.050778 TGCTGAAATTTATTTGTAGGTCGAAT 57.949 30.769 0.00 0.00 34.77 3.34
5716 8267 3.048337 TGTAGGTCGAATTTTCGCCTT 57.952 42.857 23.62 8.33 46.94 4.35
5855 8416 6.121590 AGGCATGGAAAGTTTTTGACATTTT 58.878 32.000 0.00 0.00 0.00 1.82
6090 8893 2.429930 CTCAACCTTGGTGGCGGA 59.570 61.111 0.00 0.00 40.22 5.54
6091 8894 1.228124 CTCAACCTTGGTGGCGGAA 60.228 57.895 0.00 0.00 40.22 4.30
6253 9056 2.050350 CATGGCAACCAGGGCTCTG 61.050 63.158 6.61 6.61 36.75 3.35
6475 9281 3.675348 ATGGAAATGGAGAGAATGGCA 57.325 42.857 0.00 0.00 0.00 4.92
6507 9313 2.760385 GGCAGCGTCCTAGGAGGT 60.760 66.667 27.70 17.31 36.53 3.85
6618 9424 4.498520 CAGATGGGCGCGACGACT 62.499 66.667 12.10 3.92 34.07 4.18
7145 9974 9.981460 ATTAGTTTCTTGGGTAATCTTTCATCT 57.019 29.630 0.00 0.00 0.00 2.90
7146 9975 7.693969 AGTTTCTTGGGTAATCTTTCATCTG 57.306 36.000 0.00 0.00 0.00 2.90
7147 9976 7.234355 AGTTTCTTGGGTAATCTTTCATCTGT 58.766 34.615 0.00 0.00 0.00 3.41
7149 9978 9.010029 GTTTCTTGGGTAATCTTTCATCTGTTA 57.990 33.333 0.00 0.00 0.00 2.41
7151 9980 9.753674 TTCTTGGGTAATCTTTCATCTGTTAAT 57.246 29.630 0.00 0.00 0.00 1.40
7283 10113 3.588842 TCTCCTTGGAACTTGGATGTGAT 59.411 43.478 0.00 0.00 31.31 3.06
7284 10114 3.944015 CTCCTTGGAACTTGGATGTGATC 59.056 47.826 0.00 0.00 31.31 2.92
7285 10115 2.679837 CCTTGGAACTTGGATGTGATCG 59.320 50.000 0.00 0.00 0.00 3.69
7286 10116 3.599343 CTTGGAACTTGGATGTGATCGA 58.401 45.455 0.00 0.00 0.00 3.59
7287 10117 3.251479 TGGAACTTGGATGTGATCGAG 57.749 47.619 0.00 0.00 0.00 4.04
7288 10118 2.831526 TGGAACTTGGATGTGATCGAGA 59.168 45.455 0.00 0.00 0.00 4.04
7289 10119 3.452264 TGGAACTTGGATGTGATCGAGAT 59.548 43.478 0.00 0.00 0.00 2.75
7290 10120 3.806521 GGAACTTGGATGTGATCGAGATG 59.193 47.826 0.00 0.00 0.00 2.90
7291 10121 4.437239 GAACTTGGATGTGATCGAGATGT 58.563 43.478 0.00 0.00 0.00 3.06
7292 10122 3.790091 ACTTGGATGTGATCGAGATGTG 58.210 45.455 0.00 0.00 0.00 3.21
7293 10123 3.448660 ACTTGGATGTGATCGAGATGTGA 59.551 43.478 0.00 0.00 0.00 3.58
7294 10124 4.081476 ACTTGGATGTGATCGAGATGTGAA 60.081 41.667 0.00 0.00 0.00 3.18
7295 10125 4.050852 TGGATGTGATCGAGATGTGAAG 57.949 45.455 0.00 0.00 0.00 3.02
7296 10126 3.701040 TGGATGTGATCGAGATGTGAAGA 59.299 43.478 0.00 0.00 0.00 2.87
7297 10127 4.047822 GGATGTGATCGAGATGTGAAGAC 58.952 47.826 0.00 0.00 0.00 3.01
7298 10128 3.510388 TGTGATCGAGATGTGAAGACC 57.490 47.619 0.00 0.00 0.00 3.85
7299 10129 2.159379 TGTGATCGAGATGTGAAGACCG 60.159 50.000 0.00 0.00 0.00 4.79
7373 10203 1.334689 CCTGCTTGATACATGCATGCG 60.335 52.381 26.53 4.36 42.13 4.73
7374 10204 1.332686 CTGCTTGATACATGCATGCGT 59.667 47.619 26.53 15.11 42.13 5.24
7375 10205 1.064357 TGCTTGATACATGCATGCGTG 59.936 47.619 33.18 33.18 39.10 5.34
7397 10231 2.182842 GCCTGCGCTAATGTCTGGG 61.183 63.158 9.73 0.00 0.00 4.45
7438 10272 9.788960 GTATACGATTCAATATCTATGTCAGCA 57.211 33.333 0.00 0.00 0.00 4.41
7440 10274 5.631096 ACGATTCAATATCTATGTCAGCACG 59.369 40.000 0.00 0.00 0.00 5.34
7443 10277 3.006859 TCAATATCTATGTCAGCACGGGG 59.993 47.826 0.00 0.00 0.00 5.73
7504 10362 5.674933 CTTTCAAAGCTTAAAGGACGACT 57.325 39.130 12.18 0.00 0.00 4.18
7506 10364 3.399330 TCAAAGCTTAAAGGACGACTGG 58.601 45.455 0.00 0.00 0.00 4.00
7508 10366 0.036294 AGCTTAAAGGACGACTGGGC 60.036 55.000 0.00 0.00 0.00 5.36
7509 10367 0.036294 GCTTAAAGGACGACTGGGCT 60.036 55.000 0.00 0.00 0.00 5.19
7510 10368 1.206371 GCTTAAAGGACGACTGGGCTA 59.794 52.381 0.00 0.00 0.00 3.93
7513 10371 2.693267 AAAGGACGACTGGGCTAATC 57.307 50.000 0.00 0.00 0.00 1.75
7514 10372 1.568504 AAGGACGACTGGGCTAATCA 58.431 50.000 0.00 0.00 0.00 2.57
7515 10373 1.115467 AGGACGACTGGGCTAATCAG 58.885 55.000 0.00 0.00 38.16 2.90
7528 10386 3.132629 CTAATCAGCAAGCAAGCACAG 57.867 47.619 3.19 0.00 36.85 3.66
7529 10387 1.612676 AATCAGCAAGCAAGCACAGA 58.387 45.000 3.19 0.00 36.85 3.41
7530 10388 0.879765 ATCAGCAAGCAAGCACAGAC 59.120 50.000 3.19 0.00 36.85 3.51
7531 10389 0.179037 TCAGCAAGCAAGCACAGACT 60.179 50.000 3.19 0.00 36.85 3.24
7532 10390 0.040336 CAGCAAGCAAGCACAGACTG 60.040 55.000 0.00 0.00 36.85 3.51
7540 10398 3.963222 GCACAGACTGCAGAGTGG 58.037 61.111 27.06 15.42 46.29 4.00
7541 10399 1.670406 GCACAGACTGCAGAGTGGG 60.670 63.158 27.06 21.98 46.29 4.61
7542 10400 1.670406 CACAGACTGCAGAGTGGGC 60.670 63.158 23.35 0.00 30.16 5.36
7543 10401 2.142761 ACAGACTGCAGAGTGGGCA 61.143 57.895 23.35 0.00 39.32 5.36
7544 10402 1.298993 CAGACTGCAGAGTGGGCAT 59.701 57.895 23.35 0.00 41.06 4.40
7545 10403 0.322277 CAGACTGCAGAGTGGGCATT 60.322 55.000 23.35 0.00 41.06 3.56
7546 10404 1.065926 CAGACTGCAGAGTGGGCATTA 60.066 52.381 23.35 0.00 41.06 1.90
7605 10463 1.524863 GGCTGGATGGATGCATCAGC 61.525 60.000 27.56 27.56 42.57 4.26
7608 10466 0.816421 TGGATGGATGCATCAGCGTG 60.816 55.000 27.25 0.00 46.23 5.34
7609 10467 0.816825 GGATGGATGCATCAGCGTGT 60.817 55.000 27.25 6.72 46.23 4.49
7610 10468 1.541015 GGATGGATGCATCAGCGTGTA 60.541 52.381 27.25 5.51 46.23 2.90
7645 10503 0.962855 TCTCAGGCGAGACCAGACAG 60.963 60.000 5.20 0.00 43.55 3.51
7688 10546 5.824624 GGAAGATACAAGCAGATGATCCAAA 59.175 40.000 0.00 0.00 0.00 3.28
7764 10622 3.403038 GCTATGGTTGTGACTTGTGAGT 58.597 45.455 0.00 0.00 39.32 3.41
7765 10623 3.187227 GCTATGGTTGTGACTTGTGAGTG 59.813 47.826 0.00 0.00 35.88 3.51
7771 10630 4.202182 GGTTGTGACTTGTGAGTGGTACTA 60.202 45.833 0.00 0.00 35.88 1.82
7772 10631 4.579454 TGTGACTTGTGAGTGGTACTAC 57.421 45.455 0.19 0.19 35.88 2.73
7777 10636 6.206243 GTGACTTGTGAGTGGTACTACTAGAA 59.794 42.308 12.36 4.71 35.88 2.10
7786 10645 4.159879 GTGGTACTACTAGAATGCACCACT 59.840 45.833 20.79 1.79 46.94 4.00
7787 10646 5.359009 GTGGTACTACTAGAATGCACCACTA 59.641 44.000 20.79 2.76 46.94 2.74
7788 10647 5.593095 TGGTACTACTAGAATGCACCACTAG 59.407 44.000 16.77 16.77 39.32 2.57
7789 10648 5.826737 GGTACTACTAGAATGCACCACTAGA 59.173 44.000 22.04 10.58 37.58 2.43
7790 10649 6.016943 GGTACTACTAGAATGCACCACTAGAG 60.017 46.154 22.04 17.53 37.58 2.43
7791 10650 5.511363 ACTACTAGAATGCACCACTAGAGT 58.489 41.667 22.04 17.94 37.58 3.24
7794 10662 5.511363 ACTAGAATGCACCACTAGAGTACT 58.489 41.667 22.04 0.00 37.58 2.73
7867 10736 1.971962 CGATCGTCTGCAAGCAAAAAC 59.028 47.619 7.03 0.00 0.00 2.43
7883 10752 1.389609 AAACTGCTTGCACTGCTGCT 61.390 50.000 16.48 3.58 44.57 4.24
7889 10758 0.603172 CTTGCACTGCTGCTCTCACT 60.603 55.000 1.98 0.00 44.57 3.41
7890 10759 0.883370 TTGCACTGCTGCTCTCACTG 60.883 55.000 1.98 0.00 44.57 3.66
7931 10800 2.338015 GGCTGAGGCACCACACATG 61.338 63.158 0.00 0.00 40.87 3.21
7932 10801 2.986306 GCTGAGGCACCACACATGC 61.986 63.158 0.00 0.00 42.62 4.06
7933 10802 1.601477 CTGAGGCACCACACATGCA 60.601 57.895 0.00 0.00 45.27 3.96
7934 10803 0.963856 CTGAGGCACCACACATGCAT 60.964 55.000 0.00 0.00 45.27 3.96
7939 10808 2.439135 AGGCACCACACATGCATATAGA 59.561 45.455 0.00 0.00 45.27 1.98
7941 10810 3.494924 GGCACCACACATGCATATAGAGA 60.495 47.826 0.00 0.00 45.27 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 3.787001 GGGGGTTGGAGGAGAGCG 61.787 72.222 0.00 0.00 0.00 5.03
223 227 1.490490 TCCGATGGAGAATTTGGGAGG 59.510 52.381 0.00 0.00 0.00 4.30
225 229 3.201930 TGATTCCGATGGAGAATTTGGGA 59.798 43.478 0.00 0.00 34.12 4.37
269 274 4.698056 GGGGACGACGACGATAAC 57.302 61.111 15.32 1.17 42.66 1.89
380 385 2.434774 GGTTGGGGAAAGGCGAGT 59.565 61.111 0.00 0.00 0.00 4.18
430 438 1.379176 CAACACACCCACCCACACA 60.379 57.895 0.00 0.00 0.00 3.72
436 444 1.136110 CTCAAAACCAACACACCCACC 59.864 52.381 0.00 0.00 0.00 4.61
546 556 2.587753 AACACCCTCGCACACACG 60.588 61.111 0.00 0.00 0.00 4.49
556 566 2.600731 CCACCCACACAACACCCT 59.399 61.111 0.00 0.00 0.00 4.34
558 568 0.466555 TAAGCCACCCACACAACACC 60.467 55.000 0.00 0.00 0.00 4.16
573 583 3.578716 TCCACAGGTATCTGCCTATAAGC 59.421 47.826 1.90 0.00 44.59 3.09
585 595 4.141390 GGGAGATGACAAATCCACAGGTAT 60.141 45.833 10.53 0.00 34.62 2.73
775 785 8.582437 TCTAAAAGACAAACGAAAGAGAGGATA 58.418 33.333 0.00 0.00 0.00 2.59
879 892 1.002868 CCAGTCCAAGCCTGTCCAG 60.003 63.158 0.00 0.00 0.00 3.86
931 944 1.193644 TGTTTGTCGTCGTCGAGTTG 58.806 50.000 4.68 0.00 46.96 3.16
932 945 1.850441 CTTGTTTGTCGTCGTCGAGTT 59.150 47.619 4.68 0.00 46.96 3.01
933 946 1.474017 CTTGTTTGTCGTCGTCGAGT 58.526 50.000 4.68 0.00 46.96 4.18
934 947 0.158928 GCTTGTTTGTCGTCGTCGAG 59.841 55.000 4.68 0.00 46.96 4.04
935 948 0.525882 TGCTTGTTTGTCGTCGTCGA 60.526 50.000 0.00 0.00 44.12 4.20
986 999 1.242076 GGCCATGGATGAATCGGAAG 58.758 55.000 18.40 0.00 0.00 3.46
1232 1257 5.548406 CATCAGGATCTGCATCAATACAGA 58.452 41.667 0.00 0.00 46.34 3.41
1563 1591 1.374758 CTTCCAGTCCGACTGCACC 60.375 63.158 21.26 0.00 44.63 5.01
1650 1822 2.601628 ATCAATGGCGTGCGTGCATG 62.602 55.000 9.66 9.66 36.28 4.06
1651 1823 2.327002 GATCAATGGCGTGCGTGCAT 62.327 55.000 0.00 0.00 36.28 3.96
1652 1824 3.037992 GATCAATGGCGTGCGTGCA 62.038 57.895 2.25 0.00 36.28 4.57
1653 1825 2.277501 GATCAATGGCGTGCGTGC 60.278 61.111 0.00 0.00 0.00 5.34
1656 1828 1.280746 GATGGATCAATGGCGTGCG 59.719 57.895 0.00 0.00 0.00 5.34
1673 1851 1.409064 CATCGATCTTGGACGGAAGGA 59.591 52.381 0.00 0.00 0.00 3.36
1674 1852 1.137086 ACATCGATCTTGGACGGAAGG 59.863 52.381 0.00 0.00 0.00 3.46
1675 1853 2.586258 ACATCGATCTTGGACGGAAG 57.414 50.000 0.00 0.00 0.00 3.46
1676 1854 3.259064 GAAACATCGATCTTGGACGGAA 58.741 45.455 0.00 0.00 0.00 4.30
1709 1887 0.321671 AGCACACGCCTGTATGAACT 59.678 50.000 0.00 0.00 39.83 3.01
1717 1896 2.010145 ACAGTATAAGCACACGCCTG 57.990 50.000 0.00 0.00 39.83 4.85
1763 1945 1.298602 TCATGACCCAATCATTCGCG 58.701 50.000 0.00 0.00 46.54 5.87
1843 2027 1.418097 CCCATCCGTCCATCCATCCA 61.418 60.000 0.00 0.00 0.00 3.41
1848 2032 1.302832 GCATCCCATCCGTCCATCC 60.303 63.158 0.00 0.00 0.00 3.51
1849 2033 0.976641 TAGCATCCCATCCGTCCATC 59.023 55.000 0.00 0.00 0.00 3.51
1850 2034 0.979665 CTAGCATCCCATCCGTCCAT 59.020 55.000 0.00 0.00 0.00 3.41
1851 2035 1.758440 GCTAGCATCCCATCCGTCCA 61.758 60.000 10.63 0.00 0.00 4.02
1852 2036 1.004440 GCTAGCATCCCATCCGTCC 60.004 63.158 10.63 0.00 0.00 4.79
1853 2037 1.004440 GGCTAGCATCCCATCCGTC 60.004 63.158 18.24 0.00 0.00 4.79
1854 2038 1.130054 ATGGCTAGCATCCCATCCGT 61.130 55.000 18.24 0.00 37.24 4.69
1855 2039 0.904649 TATGGCTAGCATCCCATCCG 59.095 55.000 18.24 0.00 40.84 4.18
1868 2052 4.737346 AGGCAGCTACCTATGGCT 57.263 55.556 2.71 0.00 44.90 4.75
1872 2056 2.797285 AACCCTAGGCAGCTACCTAT 57.203 50.000 13.33 0.00 41.49 2.57
1932 2116 0.249238 CACGAGAGCTAGCCCATGTC 60.249 60.000 12.13 1.43 0.00 3.06
1947 2131 0.736636 ACACACAGACTCGAACACGA 59.263 50.000 0.00 0.00 34.81 4.35
1964 2153 2.247437 TTGCGCGCACACACATACA 61.247 52.632 36.72 13.60 0.00 2.29
2025 2214 0.104120 TCTCTCGCTCTCTCCTCTCG 59.896 60.000 0.00 0.00 0.00 4.04
2034 2224 3.470709 CATTCTCTCTCTCTCTCGCTCT 58.529 50.000 0.00 0.00 0.00 4.09
2038 2228 3.565482 CCTTCCATTCTCTCTCTCTCTCG 59.435 52.174 0.00 0.00 0.00 4.04
2224 2759 0.822811 TGCAGATGAGAGAGAGTGGC 59.177 55.000 0.00 0.00 0.00 5.01
2258 2922 0.107017 GACACAGGTGGGGATCCATG 60.107 60.000 15.23 6.36 46.09 3.66
2259 2923 0.253347 AGACACAGGTGGGGATCCAT 60.253 55.000 15.23 0.00 46.09 3.41
2260 2924 0.475632 AAGACACAGGTGGGGATCCA 60.476 55.000 15.23 0.00 41.58 3.41
2261 2925 0.253327 GAAGACACAGGTGGGGATCC 59.747 60.000 1.92 1.92 34.19 3.36
2262 2926 0.984230 TGAAGACACAGGTGGGGATC 59.016 55.000 4.24 0.00 34.19 3.36
2271 2935 2.742774 TGTCATCACGTGAAGACACAG 58.257 47.619 38.53 17.73 44.62 3.66
2275 2939 4.259970 GCATGTATGTCATCACGTGAAGAC 60.260 45.833 35.13 35.13 41.58 3.01
2277 2941 3.867493 AGCATGTATGTCATCACGTGAAG 59.133 43.478 24.13 19.02 38.90 3.02
2315 2979 3.200593 CCATGGCTGCGCTGAGAC 61.201 66.667 19.32 5.98 0.00 3.36
2417 3117 1.796796 CGAAAGCTAACAGCAGGCC 59.203 57.895 0.00 0.00 45.56 5.19
2434 3134 4.240623 GCTGATTGCAAGCTAGCTAGCG 62.241 54.545 34.01 24.04 46.89 4.26
2435 3135 1.263752 GCTGATTGCAAGCTAGCTAGC 59.736 52.381 33.96 33.96 44.73 3.42
2505 3381 2.732001 CATGACACGACATGCATCAG 57.268 50.000 0.00 0.00 40.54 2.90
2553 3429 8.958506 CATCGCCCTAACTAACTATAGTAATCT 58.041 37.037 5.65 0.00 41.57 2.40
5150 7617 8.516234 TCTGTGTATCTCTCTCTTTCTAAACAC 58.484 37.037 0.00 0.00 35.31 3.32
5159 7626 5.397899 CCCTCTCTCTGTGTATCTCTCTCTT 60.398 48.000 0.00 0.00 0.00 2.85
5188 7705 1.376683 TAGCAACACACCGGATGGC 60.377 57.895 9.46 6.04 39.70 4.40
5199 7716 3.311322 CCGAAACTTGTCTTGTAGCAACA 59.689 43.478 0.00 0.00 0.00 3.33
5262 7780 2.036604 TCGCATCACAAACTACTGGACA 59.963 45.455 0.00 0.00 0.00 4.02
5415 7946 0.319469 GGCTATGGAAGAGCTCGCTC 60.319 60.000 8.37 10.83 43.03 5.03
5439 7970 3.181397 CAATCGTGGTTGATTTGGATGC 58.819 45.455 0.00 0.00 36.46 3.91
5440 7971 3.429272 CCCAATCGTGGTTGATTTGGATG 60.429 47.826 1.68 0.00 44.30 3.51
5441 7972 2.760092 CCCAATCGTGGTTGATTTGGAT 59.240 45.455 1.68 0.00 44.30 3.41
5450 7982 1.555967 CAAATCCCCCAATCGTGGTT 58.444 50.000 0.00 0.00 44.30 3.67
5453 7985 1.815866 GCCAAATCCCCCAATCGTG 59.184 57.895 0.00 0.00 0.00 4.35
5618 8154 6.935240 TCACAGGGGAGTATATGGAATTAG 57.065 41.667 0.00 0.00 0.00 1.73
5644 8180 5.103687 TCAAACATGATACATGCATTGTGC 58.896 37.500 19.82 0.00 45.29 4.57
5706 8257 9.573133 CTAGTCAAATTAAATCAAGGCGAAAAT 57.427 29.630 0.00 0.00 0.00 1.82
5707 8258 8.026607 CCTAGTCAAATTAAATCAAGGCGAAAA 58.973 33.333 0.00 0.00 0.00 2.29
5716 8267 8.523915 ACATGCATCCTAGTCAAATTAAATCA 57.476 30.769 0.00 0.00 0.00 2.57
5855 8416 1.295357 CCTGCATGCGTACGTGGAAA 61.295 55.000 17.90 0.00 32.20 3.13
5988 8791 2.249535 CGCCATGCCGGAGAGATTG 61.250 63.158 5.05 0.00 36.49 2.67
6016 8819 4.785453 GTCTGGGAAGCCGCTGGG 62.785 72.222 0.00 0.00 0.00 4.45
6019 8822 2.543067 GATTGGTCTGGGAAGCCGCT 62.543 60.000 0.00 0.00 0.00 5.52
6129 8932 2.136878 CATGGAGGACCCCGAGGAG 61.137 68.421 0.00 0.00 36.73 3.69
6198 9001 4.314440 TCGGCAAAGTCCTGCGCT 62.314 61.111 9.73 0.00 43.60 5.92
6201 9004 1.078143 ATCCTCGGCAAAGTCCTGC 60.078 57.895 0.00 0.00 41.85 4.85
6229 9032 1.228831 CCTGGTTGCCATGGGAACA 60.229 57.895 39.37 27.32 46.12 3.18
6291 9097 1.926511 GCTGGTCCGGAAGTTGCATG 61.927 60.000 5.23 0.00 0.00 4.06
6336 9142 4.218417 CCAAGGTTCAGGAGGTTGTTATTG 59.782 45.833 0.00 0.00 0.00 1.90
7167 9996 2.884639 GCTAGTTTGCCAAAGAGGACAA 59.115 45.455 0.00 0.00 41.22 3.18
7254 10083 3.702048 TTCCAAGGAGACCGGCGG 61.702 66.667 27.06 27.06 0.00 6.13
7255 10084 2.434359 GTTCCAAGGAGACCGGCG 60.434 66.667 0.00 0.00 0.00 6.46
7283 10113 0.809385 GTCCGGTCTTCACATCTCGA 59.191 55.000 0.00 0.00 0.00 4.04
7284 10114 0.179134 GGTCCGGTCTTCACATCTCG 60.179 60.000 0.00 0.00 0.00 4.04
7285 10115 0.179134 CGGTCCGGTCTTCACATCTC 60.179 60.000 2.34 0.00 0.00 2.75
7286 10116 1.605058 CCGGTCCGGTCTTCACATCT 61.605 60.000 23.02 0.00 42.73 2.90
7287 10117 1.153628 CCGGTCCGGTCTTCACATC 60.154 63.158 23.02 0.00 42.73 3.06
7288 10118 2.978824 CCGGTCCGGTCTTCACAT 59.021 61.111 23.02 0.00 42.73 3.21
7376 10206 0.306840 CAGACATTAGCGCAGGCATG 59.693 55.000 11.47 8.37 43.41 4.06
7381 10211 0.108186 TCACCCAGACATTAGCGCAG 60.108 55.000 11.47 0.00 0.00 5.18
7397 10231 8.239998 TGAATCGTATACTCTGATGATCATCAC 58.760 37.037 30.27 18.86 42.42 3.06
7418 10252 5.349817 CCCGTGCTGACATAGATATTGAATC 59.650 44.000 0.00 0.00 0.00 2.52
7422 10256 3.244215 ACCCCGTGCTGACATAGATATTG 60.244 47.826 0.00 0.00 0.00 1.90
7438 10272 5.265989 ACCAACATGAAATATAAACCCCGT 58.734 37.500 0.00 0.00 0.00 5.28
7440 10274 7.847096 AGAAACCAACATGAAATATAAACCCC 58.153 34.615 0.00 0.00 0.00 4.95
7493 10327 3.101437 TGATTAGCCCAGTCGTCCTTTA 58.899 45.455 0.00 0.00 0.00 1.85
7508 10366 2.745821 TCTGTGCTTGCTTGCTGATTAG 59.254 45.455 3.47 0.00 0.00 1.73
7509 10367 2.485426 GTCTGTGCTTGCTTGCTGATTA 59.515 45.455 3.47 0.00 0.00 1.75
7510 10368 1.268899 GTCTGTGCTTGCTTGCTGATT 59.731 47.619 3.47 0.00 0.00 2.57
7513 10371 0.040336 CAGTCTGTGCTTGCTTGCTG 60.040 55.000 0.00 0.00 0.00 4.41
7514 10372 2.328235 CAGTCTGTGCTTGCTTGCT 58.672 52.632 0.00 0.00 0.00 3.91
7515 10373 4.937781 CAGTCTGTGCTTGCTTGC 57.062 55.556 0.00 0.00 0.00 4.01
7524 10382 1.670406 GCCCACTCTGCAGTCTGTG 60.670 63.158 14.67 18.99 0.00 3.66
7525 10383 1.486997 ATGCCCACTCTGCAGTCTGT 61.487 55.000 14.67 8.66 42.92 3.41
7526 10384 0.322277 AATGCCCACTCTGCAGTCTG 60.322 55.000 14.67 9.81 42.92 3.51
7527 10385 1.279496 TAATGCCCACTCTGCAGTCT 58.721 50.000 14.67 0.00 42.92 3.24
7528 10386 2.113860 TTAATGCCCACTCTGCAGTC 57.886 50.000 14.67 0.00 42.92 3.51
7529 10387 2.584835 TTTAATGCCCACTCTGCAGT 57.415 45.000 14.67 0.00 42.92 4.40
7530 10388 4.498682 GCTAATTTAATGCCCACTCTGCAG 60.499 45.833 7.63 7.63 42.92 4.41
7531 10389 3.381272 GCTAATTTAATGCCCACTCTGCA 59.619 43.478 0.00 0.00 43.97 4.41
7532 10390 3.633986 AGCTAATTTAATGCCCACTCTGC 59.366 43.478 0.00 0.00 0.00 4.26
7533 10391 4.037208 CCAGCTAATTTAATGCCCACTCTG 59.963 45.833 0.00 0.00 0.00 3.35
7534 10392 4.210331 CCAGCTAATTTAATGCCCACTCT 58.790 43.478 0.00 0.00 0.00 3.24
7535 10393 3.954258 ACCAGCTAATTTAATGCCCACTC 59.046 43.478 0.00 0.00 0.00 3.51
7536 10394 3.981212 ACCAGCTAATTTAATGCCCACT 58.019 40.909 0.00 0.00 0.00 4.00
7537 10395 4.261031 CGTACCAGCTAATTTAATGCCCAC 60.261 45.833 0.00 0.00 0.00 4.61
7538 10396 3.880490 CGTACCAGCTAATTTAATGCCCA 59.120 43.478 0.00 0.00 0.00 5.36
7539 10397 3.881089 ACGTACCAGCTAATTTAATGCCC 59.119 43.478 0.00 0.00 0.00 5.36
7540 10398 4.024302 GGACGTACCAGCTAATTTAATGCC 60.024 45.833 0.00 0.00 38.79 4.40
7541 10399 4.814771 AGGACGTACCAGCTAATTTAATGC 59.185 41.667 0.00 0.00 42.04 3.56
7542 10400 6.046593 TGAGGACGTACCAGCTAATTTAATG 58.953 40.000 0.00 0.00 42.04 1.90
7543 10401 6.229936 TGAGGACGTACCAGCTAATTTAAT 57.770 37.500 0.00 0.00 42.04 1.40
7544 10402 5.657474 CTGAGGACGTACCAGCTAATTTAA 58.343 41.667 0.00 0.00 42.04 1.52
7545 10403 4.441079 GCTGAGGACGTACCAGCTAATTTA 60.441 45.833 25.27 0.00 46.96 1.40
7546 10404 3.679083 GCTGAGGACGTACCAGCTAATTT 60.679 47.826 25.27 0.00 46.96 1.82
7608 10466 5.236047 CCTGAGACCTACATACACGTACTAC 59.764 48.000 0.00 0.00 0.00 2.73
7609 10467 5.363101 CCTGAGACCTACATACACGTACTA 58.637 45.833 0.00 0.00 0.00 1.82
7610 10468 4.197750 CCTGAGACCTACATACACGTACT 58.802 47.826 0.00 0.00 0.00 2.73
7617 10475 2.573369 TCTCGCCTGAGACCTACATAC 58.427 52.381 0.00 0.00 46.25 2.39
7645 10503 2.358737 CCCCTGTCGTGTGCTTCC 60.359 66.667 0.00 0.00 0.00 3.46
7724 10582 3.847602 AGAGCTAGCAGCAGCGGG 61.848 66.667 18.83 0.00 45.56 6.13
7764 10622 4.350245 AGTGGTGCATTCTAGTAGTACCA 58.650 43.478 14.09 14.09 34.61 3.25
7765 10623 5.826737 TCTAGTGGTGCATTCTAGTAGTACC 59.173 44.000 16.52 10.41 34.55 3.34
7771 10630 5.511363 AGTACTCTAGTGGTGCATTCTAGT 58.489 41.667 16.52 8.49 34.55 2.57
7772 10631 6.768861 AGTAGTACTCTAGTGGTGCATTCTAG 59.231 42.308 0.00 13.13 34.32 2.43
7777 10636 7.899648 AATTAGTAGTACTCTAGTGGTGCAT 57.100 36.000 5.96 0.00 32.70 3.96
7786 10645 9.650539 ATCGAGCGAATAATTAGTAGTACTCTA 57.349 33.333 5.96 0.00 0.00 2.43
7787 10646 7.959689 TCGAGCGAATAATTAGTAGTACTCT 57.040 36.000 5.96 0.00 0.00 3.24
7788 10647 8.658609 AGATCGAGCGAATAATTAGTAGTACTC 58.341 37.037 5.96 0.00 0.00 2.59
7789 10648 8.550710 AGATCGAGCGAATAATTAGTAGTACT 57.449 34.615 8.14 8.14 0.00 2.73
7790 10649 9.053135 CAAGATCGAGCGAATAATTAGTAGTAC 57.947 37.037 0.00 0.00 0.00 2.73
7791 10650 8.235226 CCAAGATCGAGCGAATAATTAGTAGTA 58.765 37.037 0.00 0.00 0.00 1.82
7794 10662 6.978338 ACCAAGATCGAGCGAATAATTAGTA 58.022 36.000 0.00 0.00 0.00 1.82
7806 10674 1.078143 AGGCCAACCAAGATCGAGC 60.078 57.895 5.01 0.00 39.06 5.03
7889 10758 1.294857 CGGATCACAACACACACACA 58.705 50.000 0.00 0.00 0.00 3.72
7890 10759 0.586319 CCGGATCACAACACACACAC 59.414 55.000 0.00 0.00 0.00 3.82
7931 10800 8.406297 TGTATACGTCAATCCATCTCTATATGC 58.594 37.037 0.00 0.00 0.00 3.14
7939 10808 7.385205 GCTACATTTGTATACGTCAATCCATCT 59.615 37.037 0.00 0.00 0.00 2.90
7941 10810 6.426937 GGCTACATTTGTATACGTCAATCCAT 59.573 38.462 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.