Multiple sequence alignment - TraesCS7A01G448500

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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 TraesCS7A01G448500 chr7A 100.000 3455 0 0 1 3455 642898185 642901639 0.000000e+00 6381.0
1 TraesCS7A01G448500 chr7A 94.167 960 38 13 1 953 26777763 26776815 0.000000e+00 1447.0
2 TraesCS7A01G448500 chr7A 91.507 942 54 9 1 922 247107926 247108861 0.000000e+00 1273.0
3 TraesCS7A01G448500 chr7A 87.699 943 105 9 951 1887 642938841 642939778 0.000000e+00 1088.0
4 TraesCS7A01G448500 chr7A 86.567 603 74 3 2567 3168 642940524 642941120 0.000000e+00 658.0
5 TraesCS7A01G448500 chr7A 82.875 654 86 14 2533 3173 642941611 642942251 6.470000e-157 564.0
6 TraesCS7A01G448500 chr7A 90.251 359 24 6 1891 2238 642939811 642940169 3.140000e-125 459.0
7 TraesCS7A01G448500 chr7A 90.123 81 6 1 2536 2616 642941652 642941730 1.700000e-18 104.0
8 TraesCS7A01G448500 chrUn 92.063 2104 106 17 991 3051 86730134 86732219 0.000000e+00 2904.0
9 TraesCS7A01G448500 chrUn 82.883 111 18 1 2495 2604 86731722 86731832 7.890000e-17 99.0
10 TraesCS7A01G448500 chr7D 90.812 1970 96 25 1253 3173 557344839 557346772 0.000000e+00 2556.0
11 TraesCS7A01G448500 chr7D 88.213 1298 112 15 958 2240 557783433 557782162 0.000000e+00 1511.0
12 TraesCS7A01G448500 chr7D 87.487 943 101 11 951 1887 557397400 557398331 0.000000e+00 1072.0
13 TraesCS7A01G448500 chr7D 86.544 654 65 15 2527 3173 557781866 557781229 0.000000e+00 699.0
14 TraesCS7A01G448500 chr7D 81.054 892 110 30 2331 3173 557400812 557401693 0.000000e+00 656.0
15 TraesCS7A01G448500 chr7D 84.466 618 74 9 2567 3168 557399067 557399678 1.070000e-164 590.0
16 TraesCS7A01G448500 chr7D 89.694 359 26 6 1891 2238 557398364 557398722 6.800000e-122 448.0
17 TraesCS7A01G448500 chr7D 82.888 374 44 7 2320 2677 557782115 557781746 5.560000e-83 318.0
18 TraesCS7A01G448500 chr7D 93.048 187 13 0 2537 2723 557781826 557781640 1.220000e-69 274.0
19 TraesCS7A01G448500 chr7D 83.395 271 34 3 2320 2589 557398769 557399029 1.240000e-59 241.0
20 TraesCS7A01G448500 chr7D 82.061 262 37 9 1984 2240 557400502 557400758 7.510000e-52 215.0
21 TraesCS7A01G448500 chr7D 88.462 104 6 1 951 1054 557380778 557380875 1.680000e-23 121.0
22 TraesCS7A01G448500 chr7D 81.081 111 20 1 2495 2604 557346159 557346269 1.710000e-13 87.9
23 TraesCS7A01G448500 chr7D 100.000 29 0 0 1026 1054 557380882 557380910 2.000000e-03 54.7
24 TraesCS7A01G448500 chr7B 90.573 1676 94 21 1560 3192 605101705 605103359 0.000000e+00 2161.0
25 TraesCS7A01G448500 chr7B 86.811 925 109 9 951 1867 605420212 605421131 0.000000e+00 1020.0
26 TraesCS7A01G448500 chr7B 93.878 539 33 0 1026 1564 605098431 605098969 0.000000e+00 813.0
27 TraesCS7A01G448500 chr7B 85.572 603 80 3 2567 3168 605421898 605422494 2.930000e-175 625.0
28 TraesCS7A01G448500 chr7B 90.251 359 24 6 1891 2238 605421185 605421543 3.140000e-125 459.0
29 TraesCS7A01G448500 chr7B 90.977 266 18 4 967 1227 605089336 605089600 1.530000e-93 353.0
30 TraesCS7A01G448500 chr7B 82.721 272 44 3 2320 2589 605421590 605421860 4.460000e-59 239.0
31 TraesCS7A01G448500 chr7B 81.992 261 37 9 1981 2236 605424374 605424629 2.700000e-51 213.0
32 TraesCS7A01G448500 chr7B 87.952 166 14 2 3008 3173 605425369 605425528 1.270000e-44 191.0
33 TraesCS7A01G448500 chr7B 93.827 81 5 0 951 1031 605089989 605090069 4.680000e-24 122.0
34 TraesCS7A01G448500 chr7B 88.462 78 4 1 3383 3455 605108507 605108584 4.750000e-14 89.8
35 TraesCS7A01G448500 chr3A 95.299 936 24 3 1 920 460150841 460149910 0.000000e+00 1467.0
36 TraesCS7A01G448500 chr3A 93.416 972 34 13 1 953 533975145 533976105 0.000000e+00 1413.0
37 TraesCS7A01G448500 chr3A 96.639 119 4 0 3191 3309 638983644 638983762 7.560000e-47 198.0
38 TraesCS7A01G448500 chr2A 92.570 996 35 7 1 957 607478578 607479573 0.000000e+00 1393.0
39 TraesCS7A01G448500 chr2A 92.476 957 36 4 2 922 261186346 261185390 0.000000e+00 1336.0
40 TraesCS7A01G448500 chr2A 91.684 938 28 11 1 923 42148194 42147292 0.000000e+00 1254.0
41 TraesCS7A01G448500 chr2A 96.639 119 4 0 3191 3309 606523804 606523686 7.560000e-47 198.0
42 TraesCS7A01G448500 chr5A 92.999 957 31 5 2 922 524220050 524221006 0.000000e+00 1363.0
43 TraesCS7A01G448500 chr5A 92.812 946 39 9 1 922 688857863 688858803 0.000000e+00 1343.0
44 TraesCS7A01G448500 chr5A 93.795 838 42 8 1 836 495325839 495325010 0.000000e+00 1251.0
45 TraesCS7A01G448500 chr5A 75.146 342 72 10 1906 2238 442277586 442277923 7.730000e-32 148.0
46 TraesCS7A01G448500 chr5A 100.000 37 0 0 917 953 524221030 524221066 6.190000e-08 69.4
47 TraesCS7A01G448500 chr4A 92.765 926 49 17 1 921 558484367 558485279 0.000000e+00 1323.0
48 TraesCS7A01G448500 chr6A 92.222 900 46 12 1 899 594743376 594744252 0.000000e+00 1253.0
49 TraesCS7A01G448500 chr6A 94.010 818 30 3 44 845 40529487 40530301 0.000000e+00 1221.0
50 TraesCS7A01G448500 chr6A 95.161 124 6 0 3188 3311 581974192 581974315 2.720000e-46 196.0
51 TraesCS7A01G448500 chr2B 89.020 929 66 28 18 922 517693871 517692955 0.000000e+00 1118.0
52 TraesCS7A01G448500 chr2B 95.868 121 5 0 3189 3309 518048444 518048324 2.720000e-46 196.0
53 TraesCS7A01G448500 chr2B 97.619 42 1 0 912 953 416833408 416833449 4.780000e-09 73.1
54 TraesCS7A01G448500 chr2B 100.000 37 0 0 915 951 517692933 517692897 6.190000e-08 69.4
55 TraesCS7A01G448500 chr5B 88.519 932 69 28 18 922 660198284 660197364 0.000000e+00 1094.0
56 TraesCS7A01G448500 chr1B 88.292 931 73 28 18 922 665814916 665813996 0.000000e+00 1083.0
57 TraesCS7A01G448500 chr2D 97.479 119 3 0 3190 3308 12692358 12692240 1.630000e-48 204.0
58 TraesCS7A01G448500 chr2D 95.868 121 4 1 3191 3310 437904054 437903934 9.780000e-46 195.0
59 TraesCS7A01G448500 chr3D 94.488 127 7 0 3187 3313 445035129 445035255 2.720000e-46 196.0
60 TraesCS7A01G448500 chr3D 95.122 123 6 0 3191 3313 14846671 14846793 9.780000e-46 195.0
61 TraesCS7A01G448500 chr1D 95.122 123 6 0 3188 3310 329739812 329739690 9.780000e-46 195.0
62 TraesCS7A01G448500 chr5D 75.166 302 66 7 1942 2238 341031947 341032244 2.160000e-27 134.0
63 TraesCS7A01G448500 chr6B 100.000 39 0 0 915 953 275922734 275922696 4.780000e-09 73.1
64 TraesCS7A01G448500 chr1A 91.667 48 2 2 908 955 64850102 64850057 8.000000e-07 65.8


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 TraesCS7A01G448500 chr7A 642898185 642901639 3454 False 6381.000000 6381 100.000000 1 3455 1 chr7A.!!$F2 3454
1 TraesCS7A01G448500 chr7A 26776815 26777763 948 True 1447.000000 1447 94.167000 1 953 1 chr7A.!!$R1 952
2 TraesCS7A01G448500 chr7A 247107926 247108861 935 False 1273.000000 1273 91.507000 1 922 1 chr7A.!!$F1 921
3 TraesCS7A01G448500 chr7A 642938841 642942251 3410 False 574.600000 1088 87.503000 951 3173 5 chr7A.!!$F3 2222
4 TraesCS7A01G448500 chrUn 86730134 86732219 2085 False 1501.500000 2904 87.473000 991 3051 2 chrUn.!!$F1 2060
5 TraesCS7A01G448500 chr7D 557344839 557346772 1933 False 1321.950000 2556 85.946500 1253 3173 2 chr7D.!!$F1 1920
6 TraesCS7A01G448500 chr7D 557781229 557783433 2204 True 700.500000 1511 87.673250 958 3173 4 chr7D.!!$R1 2215
7 TraesCS7A01G448500 chr7D 557397400 557401693 4293 False 537.000000 1072 84.692833 951 3173 6 chr7D.!!$F3 2222
8 TraesCS7A01G448500 chr7B 605098431 605103359 4928 False 1487.000000 2161 92.225500 1026 3192 2 chr7B.!!$F3 2166
9 TraesCS7A01G448500 chr7B 605420212 605425528 5316 False 457.833333 1020 85.883167 951 3173 6 chr7B.!!$F4 2222
10 TraesCS7A01G448500 chr7B 605089336 605090069 733 False 237.500000 353 92.402000 951 1227 2 chr7B.!!$F2 276
11 TraesCS7A01G448500 chr3A 460149910 460150841 931 True 1467.000000 1467 95.299000 1 920 1 chr3A.!!$R1 919
12 TraesCS7A01G448500 chr3A 533975145 533976105 960 False 1413.000000 1413 93.416000 1 953 1 chr3A.!!$F1 952
13 TraesCS7A01G448500 chr2A 607478578 607479573 995 False 1393.000000 1393 92.570000 1 957 1 chr2A.!!$F1 956
14 TraesCS7A01G448500 chr2A 261185390 261186346 956 True 1336.000000 1336 92.476000 2 922 1 chr2A.!!$R2 920
15 TraesCS7A01G448500 chr2A 42147292 42148194 902 True 1254.000000 1254 91.684000 1 923 1 chr2A.!!$R1 922
16 TraesCS7A01G448500 chr5A 688857863 688858803 940 False 1343.000000 1343 92.812000 1 922 1 chr5A.!!$F2 921
17 TraesCS7A01G448500 chr5A 495325010 495325839 829 True 1251.000000 1251 93.795000 1 836 1 chr5A.!!$R1 835
18 TraesCS7A01G448500 chr5A 524220050 524221066 1016 False 716.200000 1363 96.499500 2 953 2 chr5A.!!$F3 951
19 TraesCS7A01G448500 chr4A 558484367 558485279 912 False 1323.000000 1323 92.765000 1 921 1 chr4A.!!$F1 920
20 TraesCS7A01G448500 chr6A 594743376 594744252 876 False 1253.000000 1253 92.222000 1 899 1 chr6A.!!$F3 898
21 TraesCS7A01G448500 chr6A 40529487 40530301 814 False 1221.000000 1221 94.010000 44 845 1 chr6A.!!$F1 801
22 TraesCS7A01G448500 chr2B 517692897 517693871 974 True 593.700000 1118 94.510000 18 951 2 chr2B.!!$R2 933
23 TraesCS7A01G448500 chr5B 660197364 660198284 920 True 1094.000000 1094 88.519000 18 922 1 chr5B.!!$R1 904
24 TraesCS7A01G448500 chr1B 665813996 665814916 920 True 1083.000000 1083 88.292000 18 922 1 chr1B.!!$R1 904

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
214 236 0.548031 ATGTCCAGCCACCGATCATT 59.452 50.0 0.0 0.0 0.00 2.57 F
1678 4624 0.748367 CCTCCTCTCCGTCATCGTCA 60.748 60.0 0.0 0.0 35.01 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1696 4642 0.328258 GCAAGGGTTAGGCTCCTCAA 59.672 55.0 0.00 0.0 32.02 3.02 R
3289 6451 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.0 5.23 0.0 44.66 3.13 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
79 81 6.354130 AGGTATTTTACATCGGTGCAACTAT 58.646 36.000 0.00 0.00 36.74 2.12
214 236 0.548031 ATGTCCAGCCACCGATCATT 59.452 50.000 0.00 0.00 0.00 2.57
521 543 3.966215 GCTTGCTGGAGCGTGTAA 58.034 55.556 0.00 0.00 45.83 2.41
536 558 6.131544 AGCGTGTAAACATCTTGAAAGTTT 57.868 33.333 0.00 0.00 38.79 2.66
620 642 2.693762 CGTCCCTTACGTGCCGAGA 61.694 63.158 0.00 0.00 46.72 4.04
625 647 1.210931 CTTACGTGCCGAGACCGAA 59.789 57.895 0.00 0.00 38.22 4.30
845 994 4.101790 CGGCGCGCCAAATCTTGT 62.102 61.111 45.26 0.00 35.37 3.16
937 1131 3.411351 CGTCGTTTGGGGCGTCTG 61.411 66.667 0.00 0.00 0.00 3.51
938 1132 2.280592 GTCGTTTGGGGCGTCTGT 60.281 61.111 0.00 0.00 0.00 3.41
939 1133 1.890510 GTCGTTTGGGGCGTCTGTT 60.891 57.895 0.00 0.00 0.00 3.16
940 1134 1.890041 TCGTTTGGGGCGTCTGTTG 60.890 57.895 0.00 0.00 0.00 3.33
941 1135 2.903547 CGTTTGGGGCGTCTGTTGG 61.904 63.158 0.00 0.00 0.00 3.77
942 1136 1.527380 GTTTGGGGCGTCTGTTGGA 60.527 57.895 0.00 0.00 0.00 3.53
943 1137 1.228124 TTTGGGGCGTCTGTTGGAG 60.228 57.895 0.00 0.00 0.00 3.86
944 1138 1.701031 TTTGGGGCGTCTGTTGGAGA 61.701 55.000 0.00 0.00 0.00 3.71
945 1139 1.488705 TTGGGGCGTCTGTTGGAGAT 61.489 55.000 0.00 0.00 31.63 2.75
946 1140 1.450312 GGGGCGTCTGTTGGAGATG 60.450 63.158 0.00 0.00 40.33 2.90
1170 1376 2.828549 AAATCCGCCATCCGCACC 60.829 61.111 0.00 0.00 37.30 5.01
1417 1623 2.524394 ACCTGCACGTCCACCTCT 60.524 61.111 0.00 0.00 0.00 3.69
1678 4624 0.748367 CCTCCTCTCCGTCATCGTCA 60.748 60.000 0.00 0.00 35.01 4.35
1707 4653 1.553690 GGGCACACTTGAGGAGCCTA 61.554 60.000 0.00 0.00 44.60 3.93
1722 4672 0.036875 GCCTAACCCTTGCAGAGTGT 59.963 55.000 0.00 0.00 0.00 3.55
1800 4750 4.891727 AGCGGCGCCTACATTCCG 62.892 66.667 30.40 9.64 44.29 4.30
1805 4755 2.588877 CGCCTACATTCCGGCCTG 60.589 66.667 0.00 0.00 43.38 4.85
1935 4918 5.507985 GCTTCAACTGCTAACCAATTTGTCT 60.508 40.000 0.00 0.00 0.00 3.41
2059 5062 7.393216 ACTGATAAACTTCTTCTTGCAGAGAT 58.607 34.615 0.00 0.00 33.49 2.75
2163 5166 2.602257 TGTTCGCAATGGAGATCGAT 57.398 45.000 0.00 0.00 0.00 3.59
2309 5330 2.977405 ATTTGTGCAGCTTCGACTTC 57.023 45.000 0.00 0.00 0.00 3.01
2329 5351 5.864474 ACTTCGTATACAAGCTGTCAAAGAG 59.136 40.000 3.32 0.00 0.00 2.85
2341 5363 4.201990 GCTGTCAAAGAGATTGCCTTATGG 60.202 45.833 0.00 0.00 38.98 2.74
2539 5606 1.532868 CAGAGCAAGAAACAACGGAGG 59.467 52.381 0.00 0.00 0.00 4.30
2546 5613 4.065088 CAAGAAACAACGGAGGAAGATGA 58.935 43.478 0.00 0.00 0.00 2.92
2607 5734 3.295973 AGAGCTGTTAGAGGGAGATGAC 58.704 50.000 0.00 0.00 0.00 3.06
2618 5745 1.967779 GGGAGATGACCTAGAGGAAGC 59.032 57.143 1.60 0.00 38.94 3.86
2639 5766 2.783135 GCTGTCAGAGGGAATTGAACA 58.217 47.619 3.32 0.00 0.00 3.18
2665 5792 2.990740 AGAGTTGTCAGAGGGAGAGT 57.009 50.000 0.00 0.00 0.00 3.24
2740 5882 1.140652 GAGGGCAATCAGAGGAAGAGG 59.859 57.143 0.00 0.00 0.00 3.69
2754 5896 2.708325 GGAAGAGGCAATAGAGGATGGT 59.292 50.000 0.00 0.00 0.00 3.55
2843 5985 6.993786 GCTAGTAAGCCTTTTCTTGAAGAT 57.006 37.500 0.00 0.00 43.40 2.40
2885 6027 6.038997 ACTGATACTGTTTACTCCCAAGAC 57.961 41.667 0.00 0.00 0.00 3.01
2924 6066 7.748677 TGGCTTCAGAAGGATCATATGAATAA 58.251 34.615 9.99 0.00 30.13 1.40
2958 6100 6.931838 TCTTGAAAGAAAACTATCGCCTCTA 58.068 36.000 0.00 0.00 30.73 2.43
2997 6139 7.251281 CGAATGTTCAGATAGTACTCAGTGAA 58.749 38.462 0.00 4.14 0.00 3.18
3107 6250 7.039270 TGCGAAATATCAGAAACTAGCAACTA 58.961 34.615 0.00 0.00 0.00 2.24
3108 6251 7.010183 TGCGAAATATCAGAAACTAGCAACTAC 59.990 37.037 0.00 0.00 0.00 2.73
3109 6252 7.222999 GCGAAATATCAGAAACTAGCAACTACT 59.777 37.037 0.00 0.00 0.00 2.57
3110 6253 9.731819 CGAAATATCAGAAACTAGCAACTACTA 57.268 33.333 0.00 0.00 0.00 1.82
3138 6281 3.817647 AGGCAAGACAAAGAACAAGCTAG 59.182 43.478 0.00 0.00 0.00 3.42
3192 6354 0.743097 ACGTCGTCTGGGCCTTATAC 59.257 55.000 4.53 0.00 0.00 1.47
3194 6356 1.001597 CGTCGTCTGGGCCTTATACTC 60.002 57.143 4.53 0.00 0.00 2.59
3195 6357 1.340568 GTCGTCTGGGCCTTATACTCC 59.659 57.143 4.53 0.00 0.00 3.85
3196 6358 0.680061 CGTCTGGGCCTTATACTCCC 59.320 60.000 4.53 0.00 40.47 4.30
3197 6359 1.758123 CGTCTGGGCCTTATACTCCCT 60.758 57.143 4.53 0.00 40.69 4.20
3198 6360 1.972075 GTCTGGGCCTTATACTCCCTC 59.028 57.143 4.53 0.00 40.69 4.30
3199 6361 1.132817 TCTGGGCCTTATACTCCCTCC 60.133 57.143 4.53 0.00 40.69 4.30
3200 6362 0.471211 TGGGCCTTATACTCCCTCCG 60.471 60.000 4.53 0.00 40.69 4.63
3201 6363 0.471401 GGGCCTTATACTCCCTCCGT 60.471 60.000 0.84 0.00 37.08 4.69
3202 6364 0.967662 GGCCTTATACTCCCTCCGTC 59.032 60.000 0.00 0.00 0.00 4.79
3203 6365 0.967662 GCCTTATACTCCCTCCGTCC 59.032 60.000 0.00 0.00 0.00 4.79
3204 6366 1.245732 CCTTATACTCCCTCCGTCCG 58.754 60.000 0.00 0.00 0.00 4.79
3205 6367 1.245732 CTTATACTCCCTCCGTCCGG 58.754 60.000 0.00 0.00 0.00 5.14
3206 6368 0.846015 TTATACTCCCTCCGTCCGGA 59.154 55.000 0.00 0.00 42.90 5.14
3207 6369 0.846015 TATACTCCCTCCGTCCGGAA 59.154 55.000 5.23 0.00 44.66 4.30
3208 6370 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
3209 6371 0.251742 TACTCCCTCCGTCCGGAAAA 60.252 55.000 5.23 0.00 44.66 2.29
3210 6372 1.218316 CTCCCTCCGTCCGGAAAAG 59.782 63.158 5.23 3.59 44.66 2.27
3211 6373 2.436115 CCCTCCGTCCGGAAAAGC 60.436 66.667 5.23 0.00 44.66 3.51
3212 6374 2.663196 CCTCCGTCCGGAAAAGCT 59.337 61.111 5.23 0.00 44.66 3.74
3213 6375 1.003718 CCTCCGTCCGGAAAAGCTT 60.004 57.895 5.23 0.00 44.66 3.74
3214 6376 1.298859 CCTCCGTCCGGAAAAGCTTG 61.299 60.000 5.23 0.00 44.66 4.01
3215 6377 0.602905 CTCCGTCCGGAAAAGCTTGT 60.603 55.000 5.23 0.00 44.66 3.16
3216 6378 0.601841 TCCGTCCGGAAAAGCTTGTC 60.602 55.000 5.23 8.23 42.05 3.18
3217 6379 1.574702 CCGTCCGGAAAAGCTTGTCC 61.575 60.000 24.00 24.00 37.50 4.02
3218 6380 1.574702 CGTCCGGAAAAGCTTGTCCC 61.575 60.000 26.94 13.97 0.00 4.46
3219 6381 0.250770 GTCCGGAAAAGCTTGTCCCT 60.251 55.000 26.94 0.00 0.00 4.20
3220 6382 0.036306 TCCGGAAAAGCTTGTCCCTC 59.964 55.000 26.94 5.77 0.00 4.30
3221 6383 0.250727 CCGGAAAAGCTTGTCCCTCA 60.251 55.000 26.94 0.00 0.00 3.86
3222 6384 1.604604 CGGAAAAGCTTGTCCCTCAA 58.395 50.000 26.94 0.00 34.61 3.02
3223 6385 1.953686 CGGAAAAGCTTGTCCCTCAAA 59.046 47.619 26.94 0.00 35.48 2.69
3224 6386 2.558359 CGGAAAAGCTTGTCCCTCAAAT 59.442 45.455 26.94 0.00 35.48 2.32
3225 6387 3.612479 CGGAAAAGCTTGTCCCTCAAATG 60.612 47.826 26.94 9.69 35.48 2.32
3226 6388 3.306294 GGAAAAGCTTGTCCCTCAAATGG 60.306 47.826 23.49 0.00 35.48 3.16
3227 6389 2.978156 AAGCTTGTCCCTCAAATGGA 57.022 45.000 0.00 0.00 35.48 3.41
3228 6390 3.463048 AAGCTTGTCCCTCAAATGGAT 57.537 42.857 0.00 0.00 35.48 3.41
3229 6391 2.731572 AGCTTGTCCCTCAAATGGATG 58.268 47.619 0.00 0.00 35.48 3.51
3230 6392 2.042162 AGCTTGTCCCTCAAATGGATGT 59.958 45.455 0.00 0.00 35.48 3.06
3231 6393 3.266772 AGCTTGTCCCTCAAATGGATGTA 59.733 43.478 0.00 0.00 35.48 2.29
3232 6394 4.079558 AGCTTGTCCCTCAAATGGATGTAT 60.080 41.667 0.00 0.00 35.48 2.29
3233 6395 4.276926 GCTTGTCCCTCAAATGGATGTATC 59.723 45.833 0.00 0.00 35.48 2.24
3234 6396 5.688807 CTTGTCCCTCAAATGGATGTATCT 58.311 41.667 0.00 0.00 35.48 1.98
3235 6397 6.688922 GCTTGTCCCTCAAATGGATGTATCTA 60.689 42.308 0.00 0.00 35.48 1.98
3236 6398 6.823286 TGTCCCTCAAATGGATGTATCTAA 57.177 37.500 0.00 0.00 33.65 2.10
3237 6399 6.591935 TGTCCCTCAAATGGATGTATCTAAC 58.408 40.000 0.00 0.00 33.65 2.34
3238 6400 6.157820 TGTCCCTCAAATGGATGTATCTAACA 59.842 38.462 0.00 0.00 43.86 2.41
3239 6401 6.483640 GTCCCTCAAATGGATGTATCTAACAC 59.516 42.308 0.00 0.00 42.09 3.32
3240 6402 5.765182 CCCTCAAATGGATGTATCTAACACC 59.235 44.000 0.00 0.00 42.09 4.16
3241 6403 6.356556 CCTCAAATGGATGTATCTAACACCA 58.643 40.000 0.00 0.00 42.09 4.17
3242 6404 6.828273 CCTCAAATGGATGTATCTAACACCAA 59.172 38.462 0.00 0.00 42.09 3.67
3243 6405 7.012704 CCTCAAATGGATGTATCTAACACCAAG 59.987 40.741 0.00 0.00 42.09 3.61
3244 6406 7.402054 TCAAATGGATGTATCTAACACCAAGT 58.598 34.615 0.00 0.00 42.09 3.16
3245 6407 7.888021 TCAAATGGATGTATCTAACACCAAGTT 59.112 33.333 0.00 0.00 42.09 2.66
3246 6408 9.173021 CAAATGGATGTATCTAACACCAAGTTA 57.827 33.333 0.00 0.00 42.09 2.24
3258 6420 5.995565 ACACCAAGTTAGTGCTAGATACA 57.004 39.130 0.99 0.00 38.87 2.29
3259 6421 6.546428 ACACCAAGTTAGTGCTAGATACAT 57.454 37.500 0.99 0.00 38.87 2.29
3260 6422 6.574350 ACACCAAGTTAGTGCTAGATACATC 58.426 40.000 0.99 0.00 38.87 3.06
3261 6423 5.986135 CACCAAGTTAGTGCTAGATACATCC 59.014 44.000 0.00 0.00 0.00 3.51
3262 6424 5.661312 ACCAAGTTAGTGCTAGATACATCCA 59.339 40.000 0.00 0.00 0.00 3.41
3263 6425 6.327626 ACCAAGTTAGTGCTAGATACATCCAT 59.672 38.462 0.00 0.00 0.00 3.41
3264 6426 7.147479 ACCAAGTTAGTGCTAGATACATCCATT 60.147 37.037 0.00 0.00 0.00 3.16
3265 6427 7.716998 CCAAGTTAGTGCTAGATACATCCATTT 59.283 37.037 0.00 0.00 0.00 2.32
3266 6428 8.554528 CAAGTTAGTGCTAGATACATCCATTTG 58.445 37.037 0.00 0.00 0.00 2.32
3267 6429 8.023021 AGTTAGTGCTAGATACATCCATTTGA 57.977 34.615 0.00 0.00 0.00 2.69
3268 6430 8.147058 AGTTAGTGCTAGATACATCCATTTGAG 58.853 37.037 0.00 0.00 0.00 3.02
3269 6431 5.862845 AGTGCTAGATACATCCATTTGAGG 58.137 41.667 0.00 0.00 0.00 3.86
3270 6432 4.999950 GTGCTAGATACATCCATTTGAGGG 59.000 45.833 0.00 0.00 0.00 4.30
3271 6433 4.907269 TGCTAGATACATCCATTTGAGGGA 59.093 41.667 0.00 0.00 39.14 4.20
3272 6434 5.221722 TGCTAGATACATCCATTTGAGGGAC 60.222 44.000 0.00 0.00 37.23 4.46
3273 6435 5.221722 GCTAGATACATCCATTTGAGGGACA 60.222 44.000 0.00 0.00 37.23 4.02
3274 6436 5.715439 AGATACATCCATTTGAGGGACAA 57.285 39.130 0.00 0.00 37.23 3.18
3275 6437 5.688807 AGATACATCCATTTGAGGGACAAG 58.311 41.667 0.00 0.00 39.77 3.16
3276 6438 3.814504 ACATCCATTTGAGGGACAAGT 57.185 42.857 0.00 0.00 39.77 3.16
3277 6439 4.118168 ACATCCATTTGAGGGACAAGTT 57.882 40.909 0.00 0.00 39.77 2.66
3278 6440 4.482990 ACATCCATTTGAGGGACAAGTTT 58.517 39.130 0.00 0.00 39.77 2.66
3279 6441 4.281688 ACATCCATTTGAGGGACAAGTTTG 59.718 41.667 0.00 0.00 39.77 2.93
3280 6442 3.230134 TCCATTTGAGGGACAAGTTTGG 58.770 45.455 0.00 0.00 39.77 3.28
3281 6443 2.299867 CCATTTGAGGGACAAGTTTGGG 59.700 50.000 0.00 0.00 39.77 4.12
3282 6444 3.230134 CATTTGAGGGACAAGTTTGGGA 58.770 45.455 0.00 0.00 39.77 4.37
3283 6445 2.358322 TTGAGGGACAAGTTTGGGAC 57.642 50.000 0.00 0.00 34.20 4.46
3284 6446 1.217916 TGAGGGACAAGTTTGGGACA 58.782 50.000 0.00 0.00 0.00 4.02
3285 6447 2.024846 TTGAGGGACAAGTTTGGGACAA 60.025 45.455 0.00 0.00 37.48 3.18
3286 6448 3.939454 TTGAGGGACAAGTTTGGGACAAG 60.939 47.826 0.00 0.00 37.48 3.16
3287 6449 6.408971 TTGAGGGACAAGTTTGGGACAAGT 62.409 45.833 0.00 0.00 37.48 3.16
3288 6450 7.809906 TTGAGGGACAAGTTTGGGACAAGTT 62.810 44.000 0.00 0.00 37.48 2.66
3297 6459 1.682740 TGGGACAAGTTTTTCCGGAC 58.317 50.000 1.83 0.00 31.92 4.79
3298 6460 0.589708 GGGACAAGTTTTTCCGGACG 59.410 55.000 1.83 0.00 32.00 4.79
3299 6461 0.589708 GGACAAGTTTTTCCGGACGG 59.410 55.000 1.83 3.96 0.00 4.79
3300 6462 1.585297 GACAAGTTTTTCCGGACGGA 58.415 50.000 1.83 9.76 43.52 4.69
3301 6463 1.529865 GACAAGTTTTTCCGGACGGAG 59.470 52.381 13.64 3.15 46.06 4.63
3302 6464 0.872388 CAAGTTTTTCCGGACGGAGG 59.128 55.000 13.64 0.00 46.06 4.30
3303 6465 0.250597 AAGTTTTTCCGGACGGAGGG 60.251 55.000 13.64 0.00 46.06 4.30
3304 6466 1.123246 AGTTTTTCCGGACGGAGGGA 61.123 55.000 13.64 1.83 46.06 4.20
3305 6467 0.672711 GTTTTTCCGGACGGAGGGAG 60.673 60.000 13.64 0.00 46.06 4.30
3306 6468 1.123246 TTTTTCCGGACGGAGGGAGT 61.123 55.000 13.64 0.00 46.06 3.85
3307 6469 0.251742 TTTTCCGGACGGAGGGAGTA 60.252 55.000 13.64 0.00 46.06 2.59
3308 6470 0.032813 TTTCCGGACGGAGGGAGTAT 60.033 55.000 13.64 0.00 46.06 2.12
3309 6471 0.032813 TTCCGGACGGAGGGAGTATT 60.033 55.000 13.64 0.00 46.06 1.89
3310 6472 0.032813 TCCGGACGGAGGGAGTATTT 60.033 55.000 9.76 0.00 39.76 1.40
3311 6473 0.828677 CCGGACGGAGGGAGTATTTT 59.171 55.000 4.40 0.00 37.50 1.82
3312 6474 1.472728 CCGGACGGAGGGAGTATTTTG 60.473 57.143 4.40 0.00 37.50 2.44
3313 6475 1.664873 GGACGGAGGGAGTATTTTGC 58.335 55.000 0.00 0.00 0.00 3.68
3314 6476 1.065709 GGACGGAGGGAGTATTTTGCA 60.066 52.381 0.00 0.00 0.00 4.08
3315 6477 2.280628 GACGGAGGGAGTATTTTGCAG 58.719 52.381 0.00 0.00 0.00 4.41
3320 6482 4.270008 GGAGGGAGTATTTTGCAGCTTAA 58.730 43.478 0.00 0.00 0.00 1.85
3321 6483 4.096532 GGAGGGAGTATTTTGCAGCTTAAC 59.903 45.833 0.00 0.00 0.00 2.01
3333 6495 4.822026 TGCAGCTTAACTCCTTAAGACTC 58.178 43.478 3.36 0.00 41.01 3.36
3335 6497 5.012148 TGCAGCTTAACTCCTTAAGACTCTT 59.988 40.000 3.36 0.00 41.01 2.85
3337 6499 7.093289 TGCAGCTTAACTCCTTAAGACTCTTAT 60.093 37.037 3.36 0.00 41.01 1.73
3339 6501 9.959749 CAGCTTAACTCCTTAAGACTCTTATAG 57.040 37.037 3.36 1.78 41.01 1.31
3368 6598 2.489938 TGACTGGGACTTGTTATGCC 57.510 50.000 0.00 0.00 0.00 4.40
3372 6615 2.505819 ACTGGGACTTGTTATGCCCTAG 59.494 50.000 0.00 0.00 41.28 3.02
3378 6621 4.261801 GACTTGTTATGCCCTAGCTTTGA 58.738 43.478 0.00 0.00 40.80 2.69
3379 6622 4.010349 ACTTGTTATGCCCTAGCTTTGAC 58.990 43.478 0.00 0.00 40.80 3.18
3385 6652 3.053831 TGCCCTAGCTTTGACTTGTAC 57.946 47.619 0.00 0.00 40.80 2.90
3386 6653 2.290071 TGCCCTAGCTTTGACTTGTACC 60.290 50.000 0.00 0.00 40.80 3.34
3402 6669 6.173339 ACTTGTACCTCAATCAGTTGGTATG 58.827 40.000 0.00 0.00 37.39 2.39
3431 6698 7.840489 ACGAGTGTTGCAATTTTATTTTTCAG 58.160 30.769 0.59 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
109 111 3.887621 AGTTTCTATCTAGTTGCGCCA 57.112 42.857 4.18 0.00 0.00 5.69
214 236 3.620286 CGTTCTTCACGCCGAACA 58.380 55.556 0.00 0.00 43.37 3.18
312 334 4.373116 GGAGGACACGCGAAGGCA 62.373 66.667 15.93 0.00 39.92 4.75
521 543 5.106157 CGGCCAGATAAACTTTCAAGATGTT 60.106 40.000 2.24 0.00 0.00 2.71
625 647 4.070552 GCTCTGGCGAACTCCGGT 62.071 66.667 0.00 0.00 39.04 5.28
923 1117 2.637025 CAACAGACGCCCCAAACG 59.363 61.111 0.00 0.00 0.00 3.60
924 1118 1.515521 CTCCAACAGACGCCCCAAAC 61.516 60.000 0.00 0.00 0.00 2.93
925 1119 1.228124 CTCCAACAGACGCCCCAAA 60.228 57.895 0.00 0.00 0.00 3.28
926 1120 1.488705 ATCTCCAACAGACGCCCCAA 61.489 55.000 0.00 0.00 32.26 4.12
927 1121 1.918293 ATCTCCAACAGACGCCCCA 60.918 57.895 0.00 0.00 32.26 4.96
929 1123 2.109126 GCATCTCCAACAGACGCCC 61.109 63.158 0.00 0.00 33.99 6.13
930 1124 1.078848 AGCATCTCCAACAGACGCC 60.079 57.895 0.00 0.00 41.57 5.68
940 1134 3.540974 ACCTCCGGTTAAGAGCATCTCC 61.541 54.545 0.00 0.00 37.15 3.71
941 1135 1.757699 ACCTCCGGTTAAGAGCATCTC 59.242 52.381 0.00 0.00 37.15 2.75
942 1136 1.757699 GACCTCCGGTTAAGAGCATCT 59.242 52.381 0.00 0.00 42.56 2.90
943 1137 1.202545 GGACCTCCGGTTAAGAGCATC 60.203 57.143 0.00 0.00 35.25 3.91
944 1138 0.831307 GGACCTCCGGTTAAGAGCAT 59.169 55.000 0.00 0.00 35.25 3.79
945 1139 2.283824 GGACCTCCGGTTAAGAGCA 58.716 57.895 0.00 0.00 35.25 4.26
1270 1476 1.677552 GCTCCAGGGTTTCGAGGAA 59.322 57.895 0.00 0.00 0.00 3.36
1417 1623 1.529438 GATGTTGAAGACGCGGTTTGA 59.471 47.619 12.47 0.00 0.00 2.69
1517 1723 2.203788 AGTGGGCGGAGAAGGACA 60.204 61.111 0.00 0.00 0.00 4.02
1663 4609 4.672550 CGTGACGATGACGGAGAG 57.327 61.111 0.00 0.00 44.46 3.20
1696 4642 0.328258 GCAAGGGTTAGGCTCCTCAA 59.672 55.000 0.00 0.00 32.02 3.02
1935 4918 0.609662 GGGTAAGCACGGTGAGGTTA 59.390 55.000 13.29 3.31 0.00 2.85
2042 5034 4.996122 CAGACAATCTCTGCAAGAAGAAGT 59.004 41.667 3.27 3.24 46.34 3.01
2059 5062 1.785041 GCACGAGCTTTGGCAGACAA 61.785 55.000 0.00 0.00 41.70 3.18
2112 5115 4.214971 TGAAGCTCTCTCAAATTCAGCAAC 59.785 41.667 0.00 0.00 32.17 4.17
2163 5166 9.275398 AGGAAAGTGTAAATGTCGTTTATGTTA 57.725 29.630 0.65 0.00 34.93 2.41
2309 5330 6.700020 CAATCTCTTTGACAGCTTGTATACG 58.300 40.000 0.00 0.00 37.53 3.06
2341 5363 3.308438 ACTGAATGCATTTGTCAAGGC 57.692 42.857 14.33 0.00 40.26 4.35
2452 5474 4.140782 TGGTTCATCCTCTGGCCTATACTA 60.141 45.833 3.32 0.00 37.07 1.82
2454 5476 2.972713 TGGTTCATCCTCTGGCCTATAC 59.027 50.000 3.32 0.00 37.07 1.47
2529 5551 1.625818 AGCTCATCTTCCTCCGTTGTT 59.374 47.619 0.00 0.00 0.00 2.83
2530 5552 1.270907 AGCTCATCTTCCTCCGTTGT 58.729 50.000 0.00 0.00 0.00 3.32
2539 5606 3.891366 AGCTCTTCCTCTAGCTCATCTTC 59.109 47.826 0.00 0.00 45.92 2.87
2579 5706 2.430332 CCCTCTAACAGCTCTTCCTCTG 59.570 54.545 0.00 0.00 36.45 3.35
2607 5734 0.102120 CTGACAGCGCTTCCTCTAGG 59.898 60.000 7.50 0.00 0.00 3.02
2618 5745 1.734465 GTTCAATTCCCTCTGACAGCG 59.266 52.381 0.00 0.00 0.00 5.18
2639 5766 1.889829 CCTCTGACAACTCTTCCTCGT 59.110 52.381 0.00 0.00 0.00 4.18
2665 5792 6.298361 TCTGTGATTGATTTTCTTCAGGTGA 58.702 36.000 0.00 0.00 0.00 4.02
2740 5882 2.157738 GCCATCACCATCCTCTATTGC 58.842 52.381 0.00 0.00 0.00 3.56
2754 5896 3.181440 ACAGAAGGTTCTCAAAGCCATCA 60.181 43.478 0.00 0.00 34.74 3.07
2843 5985 5.382616 TCAGTTGGTTGAGACTAGTAGACA 58.617 41.667 3.59 0.00 0.00 3.41
2958 6100 1.073923 ACATTCGGTGAGGCCTTTCTT 59.926 47.619 6.77 0.00 34.25 2.52
2997 6139 3.746751 GCTGGATTGCACTATCATCAGGT 60.747 47.826 1.02 0.00 0.00 4.00
3107 6250 7.676947 TGTTCTTTGTCTTGCCTAATACTAGT 58.323 34.615 0.00 0.00 0.00 2.57
3108 6251 8.547967 TTGTTCTTTGTCTTGCCTAATACTAG 57.452 34.615 0.00 0.00 0.00 2.57
3109 6252 7.119262 GCTTGTTCTTTGTCTTGCCTAATACTA 59.881 37.037 0.00 0.00 0.00 1.82
3110 6253 6.072452 GCTTGTTCTTTGTCTTGCCTAATACT 60.072 38.462 0.00 0.00 0.00 2.12
3111 6254 6.072452 AGCTTGTTCTTTGTCTTGCCTAATAC 60.072 38.462 0.00 0.00 0.00 1.89
3112 6255 6.003950 AGCTTGTTCTTTGTCTTGCCTAATA 58.996 36.000 0.00 0.00 0.00 0.98
3192 6354 1.218316 CTTTTCCGGACGGAGGGAG 59.782 63.158 13.64 9.15 46.06 4.30
3194 6356 2.436115 GCTTTTCCGGACGGAGGG 60.436 66.667 13.64 8.97 46.06 4.30
3195 6357 1.003718 AAGCTTTTCCGGACGGAGG 60.004 57.895 13.64 9.30 46.06 4.30
3196 6358 0.602905 ACAAGCTTTTCCGGACGGAG 60.603 55.000 13.64 3.27 46.06 4.63
3197 6359 0.601841 GACAAGCTTTTCCGGACGGA 60.602 55.000 1.83 9.76 43.52 4.69
3198 6360 1.574702 GGACAAGCTTTTCCGGACGG 61.575 60.000 15.65 3.96 0.00 4.79
3199 6361 1.574702 GGGACAAGCTTTTCCGGACG 61.575 60.000 22.30 0.00 32.00 4.79
3200 6362 0.250770 AGGGACAAGCTTTTCCGGAC 60.251 55.000 22.30 11.02 32.00 4.79
3201 6363 0.036306 GAGGGACAAGCTTTTCCGGA 59.964 55.000 22.30 0.00 32.00 5.14
3202 6364 0.250727 TGAGGGACAAGCTTTTCCGG 60.251 55.000 22.30 0.00 32.00 5.14
3203 6365 1.604604 TTGAGGGACAAGCTTTTCCG 58.395 50.000 22.30 2.85 34.20 4.30
3204 6366 3.306294 CCATTTGAGGGACAAGCTTTTCC 60.306 47.826 21.34 21.34 39.77 3.13
3205 6367 3.573967 TCCATTTGAGGGACAAGCTTTTC 59.426 43.478 3.91 3.91 39.77 2.29
3206 6368 3.575805 TCCATTTGAGGGACAAGCTTTT 58.424 40.909 0.00 0.00 39.77 2.27
3207 6369 3.243359 TCCATTTGAGGGACAAGCTTT 57.757 42.857 0.00 0.00 39.77 3.51
3208 6370 2.978156 TCCATTTGAGGGACAAGCTT 57.022 45.000 0.00 0.00 39.77 3.74
3209 6371 2.042162 ACATCCATTTGAGGGACAAGCT 59.958 45.455 0.00 0.00 39.77 3.74
3210 6372 2.450476 ACATCCATTTGAGGGACAAGC 58.550 47.619 0.00 0.00 39.77 4.01
3211 6373 5.688807 AGATACATCCATTTGAGGGACAAG 58.311 41.667 0.00 0.00 39.77 3.16
3212 6374 5.715439 AGATACATCCATTTGAGGGACAA 57.285 39.130 0.00 0.00 37.23 3.18
3213 6375 6.157820 TGTTAGATACATCCATTTGAGGGACA 59.842 38.462 0.00 0.00 37.23 4.02
3214 6376 6.483640 GTGTTAGATACATCCATTTGAGGGAC 59.516 42.308 0.00 0.00 39.39 4.46
3215 6377 6.409234 GGTGTTAGATACATCCATTTGAGGGA 60.409 42.308 0.00 0.00 39.39 4.20
3216 6378 5.765182 GGTGTTAGATACATCCATTTGAGGG 59.235 44.000 0.00 0.00 39.39 4.30
3217 6379 6.356556 TGGTGTTAGATACATCCATTTGAGG 58.643 40.000 0.00 0.00 37.04 3.86
3218 6380 7.554118 ACTTGGTGTTAGATACATCCATTTGAG 59.446 37.037 0.00 0.00 37.04 3.02
3219 6381 7.402054 ACTTGGTGTTAGATACATCCATTTGA 58.598 34.615 0.00 0.00 37.04 2.69
3220 6382 7.630242 ACTTGGTGTTAGATACATCCATTTG 57.370 36.000 0.00 0.00 37.04 2.32
3234 6396 7.470935 TGTATCTAGCACTAACTTGGTGTTA 57.529 36.000 7.08 4.74 39.89 2.41
3235 6397 6.354794 TGTATCTAGCACTAACTTGGTGTT 57.645 37.500 7.08 3.82 42.31 3.32
3236 6398 5.995565 TGTATCTAGCACTAACTTGGTGT 57.004 39.130 7.08 0.00 37.07 4.16
3237 6399 5.986135 GGATGTATCTAGCACTAACTTGGTG 59.014 44.000 0.97 0.97 37.70 4.17
3238 6400 5.661312 TGGATGTATCTAGCACTAACTTGGT 59.339 40.000 0.00 0.00 0.00 3.67
3239 6401 6.161855 TGGATGTATCTAGCACTAACTTGG 57.838 41.667 0.00 0.00 0.00 3.61
3240 6402 8.554528 CAAATGGATGTATCTAGCACTAACTTG 58.445 37.037 0.00 0.00 0.00 3.16
3241 6403 8.486210 TCAAATGGATGTATCTAGCACTAACTT 58.514 33.333 0.00 0.00 0.00 2.66
3242 6404 8.023021 TCAAATGGATGTATCTAGCACTAACT 57.977 34.615 0.00 0.00 0.00 2.24
3243 6405 7.386299 CCTCAAATGGATGTATCTAGCACTAAC 59.614 40.741 0.00 0.00 0.00 2.34
3244 6406 7.445121 CCTCAAATGGATGTATCTAGCACTAA 58.555 38.462 0.00 0.00 0.00 2.24
3245 6407 6.014242 CCCTCAAATGGATGTATCTAGCACTA 60.014 42.308 0.00 0.00 0.00 2.74
3246 6408 5.221803 CCCTCAAATGGATGTATCTAGCACT 60.222 44.000 0.00 0.00 0.00 4.40
3247 6409 4.999950 CCCTCAAATGGATGTATCTAGCAC 59.000 45.833 0.00 0.00 0.00 4.40
3248 6410 4.907269 TCCCTCAAATGGATGTATCTAGCA 59.093 41.667 0.00 0.00 0.00 3.49
3249 6411 5.221722 TGTCCCTCAAATGGATGTATCTAGC 60.222 44.000 0.00 0.00 33.65 3.42
3250 6412 6.425210 TGTCCCTCAAATGGATGTATCTAG 57.575 41.667 0.00 0.00 33.65 2.43
3251 6413 6.386927 ACTTGTCCCTCAAATGGATGTATCTA 59.613 38.462 0.00 0.00 35.48 1.98
3252 6414 5.192522 ACTTGTCCCTCAAATGGATGTATCT 59.807 40.000 0.00 0.00 35.48 1.98
3253 6415 5.440610 ACTTGTCCCTCAAATGGATGTATC 58.559 41.667 0.00 0.00 35.48 2.24
3254 6416 5.456921 ACTTGTCCCTCAAATGGATGTAT 57.543 39.130 0.00 0.00 35.48 2.29
3255 6417 4.927267 ACTTGTCCCTCAAATGGATGTA 57.073 40.909 0.00 0.00 35.48 2.29
3256 6418 3.814504 ACTTGTCCCTCAAATGGATGT 57.185 42.857 0.00 0.00 35.48 3.06
3257 6419 4.322198 CCAAACTTGTCCCTCAAATGGATG 60.322 45.833 0.00 0.00 36.92 3.51
3258 6420 3.834231 CCAAACTTGTCCCTCAAATGGAT 59.166 43.478 0.00 0.00 36.92 3.41
3259 6421 3.230134 CCAAACTTGTCCCTCAAATGGA 58.770 45.455 0.00 0.00 36.92 3.41
3260 6422 2.299867 CCCAAACTTGTCCCTCAAATGG 59.700 50.000 0.00 0.00 35.48 3.16
3261 6423 3.005791 GTCCCAAACTTGTCCCTCAAATG 59.994 47.826 0.00 0.00 35.48 2.32
3262 6424 3.230976 GTCCCAAACTTGTCCCTCAAAT 58.769 45.455 0.00 0.00 35.48 2.32
3263 6425 2.024846 TGTCCCAAACTTGTCCCTCAAA 60.025 45.455 0.00 0.00 35.48 2.69
3264 6426 1.566703 TGTCCCAAACTTGTCCCTCAA 59.433 47.619 0.00 0.00 34.61 3.02
3265 6427 1.217916 TGTCCCAAACTTGTCCCTCA 58.782 50.000 0.00 0.00 0.00 3.86
3266 6428 2.230660 CTTGTCCCAAACTTGTCCCTC 58.769 52.381 0.00 0.00 0.00 4.30
3267 6429 1.569072 ACTTGTCCCAAACTTGTCCCT 59.431 47.619 0.00 0.00 0.00 4.20
3268 6430 2.067365 ACTTGTCCCAAACTTGTCCC 57.933 50.000 0.00 0.00 0.00 4.46
3269 6431 4.465632 AAAACTTGTCCCAAACTTGTCC 57.534 40.909 0.00 0.00 0.00 4.02
3270 6432 4.868171 GGAAAAACTTGTCCCAAACTTGTC 59.132 41.667 0.00 0.00 0.00 3.18
3271 6433 4.619628 CGGAAAAACTTGTCCCAAACTTGT 60.620 41.667 0.00 0.00 0.00 3.16
3272 6434 3.862845 CGGAAAAACTTGTCCCAAACTTG 59.137 43.478 0.00 0.00 0.00 3.16
3273 6435 3.118920 CCGGAAAAACTTGTCCCAAACTT 60.119 43.478 0.00 0.00 0.00 2.66
3274 6436 2.429250 CCGGAAAAACTTGTCCCAAACT 59.571 45.455 0.00 0.00 0.00 2.66
3275 6437 2.427812 TCCGGAAAAACTTGTCCCAAAC 59.572 45.455 0.00 0.00 0.00 2.93
3276 6438 2.427812 GTCCGGAAAAACTTGTCCCAAA 59.572 45.455 5.23 0.00 0.00 3.28
3277 6439 2.025898 GTCCGGAAAAACTTGTCCCAA 58.974 47.619 5.23 0.00 0.00 4.12
3278 6440 1.682740 GTCCGGAAAAACTTGTCCCA 58.317 50.000 5.23 0.00 0.00 4.37
3279 6441 0.589708 CGTCCGGAAAAACTTGTCCC 59.410 55.000 5.23 0.00 0.00 4.46
3280 6442 0.589708 CCGTCCGGAAAAACTTGTCC 59.410 55.000 5.23 0.00 37.50 4.02
3281 6443 1.529865 CTCCGTCCGGAAAAACTTGTC 59.470 52.381 5.23 0.00 44.66 3.18
3282 6444 1.589803 CTCCGTCCGGAAAAACTTGT 58.410 50.000 5.23 0.00 44.66 3.16
3283 6445 0.872388 CCTCCGTCCGGAAAAACTTG 59.128 55.000 5.23 0.00 44.66 3.16
3284 6446 0.250597 CCCTCCGTCCGGAAAAACTT 60.251 55.000 5.23 0.00 44.66 2.66
3285 6447 1.123246 TCCCTCCGTCCGGAAAAACT 61.123 55.000 5.23 0.00 44.66 2.66
3286 6448 0.672711 CTCCCTCCGTCCGGAAAAAC 60.673 60.000 5.23 0.00 44.66 2.43
3287 6449 1.123246 ACTCCCTCCGTCCGGAAAAA 61.123 55.000 5.23 0.00 44.66 1.94
3288 6450 0.251742 TACTCCCTCCGTCCGGAAAA 60.252 55.000 5.23 0.00 44.66 2.29
3289 6451 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
3290 6452 0.032813 AATACTCCCTCCGTCCGGAA 60.033 55.000 5.23 0.00 44.66 4.30
3291 6453 0.032813 AAATACTCCCTCCGTCCGGA 60.033 55.000 0.00 0.00 42.90 5.14
3292 6454 0.828677 AAAATACTCCCTCCGTCCGG 59.171 55.000 0.00 0.00 0.00 5.14
3293 6455 1.935933 CAAAATACTCCCTCCGTCCG 58.064 55.000 0.00 0.00 0.00 4.79
3294 6456 1.065709 TGCAAAATACTCCCTCCGTCC 60.066 52.381 0.00 0.00 0.00 4.79
3295 6457 2.280628 CTGCAAAATACTCCCTCCGTC 58.719 52.381 0.00 0.00 0.00 4.79
3296 6458 1.679032 GCTGCAAAATACTCCCTCCGT 60.679 52.381 0.00 0.00 0.00 4.69
3297 6459 1.017387 GCTGCAAAATACTCCCTCCG 58.983 55.000 0.00 0.00 0.00 4.63
3298 6460 2.426842 AGCTGCAAAATACTCCCTCC 57.573 50.000 1.02 0.00 0.00 4.30
3299 6461 4.944317 AGTTAAGCTGCAAAATACTCCCTC 59.056 41.667 1.02 0.00 0.00 4.30
3300 6462 4.923415 AGTTAAGCTGCAAAATACTCCCT 58.077 39.130 1.02 0.00 0.00 4.20
3301 6463 4.096532 GGAGTTAAGCTGCAAAATACTCCC 59.903 45.833 19.64 9.02 42.65 4.30
3302 6464 4.944317 AGGAGTTAAGCTGCAAAATACTCC 59.056 41.667 21.35 21.35 46.63 3.85
3303 6465 6.502136 AAGGAGTTAAGCTGCAAAATACTC 57.498 37.500 1.02 7.08 38.09 2.59
3304 6466 7.883311 TCTTAAGGAGTTAAGCTGCAAAATACT 59.117 33.333 1.02 0.00 43.43 2.12
3305 6467 7.963465 GTCTTAAGGAGTTAAGCTGCAAAATAC 59.037 37.037 1.02 0.00 43.43 1.89
3306 6468 7.883311 AGTCTTAAGGAGTTAAGCTGCAAAATA 59.117 33.333 1.02 0.00 43.43 1.40
3307 6469 6.717084 AGTCTTAAGGAGTTAAGCTGCAAAAT 59.283 34.615 1.02 0.00 43.43 1.82
3308 6470 6.062095 AGTCTTAAGGAGTTAAGCTGCAAAA 58.938 36.000 1.02 0.00 43.43 2.44
3309 6471 5.621193 AGTCTTAAGGAGTTAAGCTGCAAA 58.379 37.500 1.02 0.00 43.43 3.68
3310 6472 5.012148 AGAGTCTTAAGGAGTTAAGCTGCAA 59.988 40.000 1.02 0.00 43.43 4.08
3311 6473 4.528596 AGAGTCTTAAGGAGTTAAGCTGCA 59.471 41.667 1.02 0.00 43.43 4.41
3312 6474 5.079689 AGAGTCTTAAGGAGTTAAGCTGC 57.920 43.478 1.85 0.00 43.43 5.25
3313 6475 9.959749 CTATAAGAGTCTTAAGGAGTTAAGCTG 57.040 37.037 16.37 0.00 43.43 4.24
3314 6476 9.924010 TCTATAAGAGTCTTAAGGAGTTAAGCT 57.076 33.333 16.37 0.00 43.43 3.74
3337 6499 7.861629 ACAAGTCCCAGTCATGATATTTTCTA 58.138 34.615 0.00 0.00 0.00 2.10
3339 6501 7.396540 AACAAGTCCCAGTCATGATATTTTC 57.603 36.000 0.00 0.00 0.00 2.29
3341 6503 7.013655 GCATAACAAGTCCCAGTCATGATATTT 59.986 37.037 0.00 0.00 0.00 1.40
3343 6505 6.000219 GCATAACAAGTCCCAGTCATGATAT 59.000 40.000 0.00 0.00 0.00 1.63
3344 6506 5.368145 GCATAACAAGTCCCAGTCATGATA 58.632 41.667 0.00 0.00 0.00 2.15
3347 6509 2.684881 GGCATAACAAGTCCCAGTCATG 59.315 50.000 0.00 0.00 0.00 3.07
3350 6512 1.282157 AGGGCATAACAAGTCCCAGTC 59.718 52.381 0.00 0.00 41.22 3.51
3355 6585 3.283259 AAGCTAGGGCATAACAAGTCC 57.717 47.619 0.00 0.00 41.70 3.85
3368 6598 4.537135 TGAGGTACAAGTCAAAGCTAGG 57.463 45.455 0.00 0.00 0.00 3.02
3372 6615 4.757149 ACTGATTGAGGTACAAGTCAAAGC 59.243 41.667 8.18 5.43 42.02 3.51
3378 6621 4.706842 ACCAACTGATTGAGGTACAAGT 57.293 40.909 0.00 0.00 42.02 3.16
3379 6622 5.586243 CCATACCAACTGATTGAGGTACAAG 59.414 44.000 0.00 0.00 42.02 3.16
3385 6652 3.003394 TGCCATACCAACTGATTGAGG 57.997 47.619 0.00 0.00 38.15 3.86
3386 6653 3.181507 CGTTGCCATACCAACTGATTGAG 60.182 47.826 3.89 0.00 42.17 3.02


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

AutoCloner maintained by Alex Coulton.