Multiple sequence alignment - TraesCS2D01G187400

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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 TraesCS2D01G187400 chr2D 100.000 4958 0 0 1 4958 131275956 131280913 0.000000e+00 9156.0
1 TraesCS2D01G187400 chr2D 96.190 210 8 0 1 210 35257423 35257632 1.320000e-90 344.0
2 TraesCS2D01G187400 chr2D 96.154 208 8 0 1 208 573910179 573910386 1.710000e-89 340.0
3 TraesCS2D01G187400 chr2B 90.767 1603 84 35 953 2524 184772582 184774151 0.000000e+00 2082.0
4 TraesCS2D01G187400 chr2B 93.493 1337 61 10 2618 3933 184774163 184775494 0.000000e+00 1964.0
5 TraesCS2D01G187400 chr2B 89.926 814 51 19 3937 4731 197591405 197592206 0.000000e+00 1020.0
6 TraesCS2D01G187400 chr2B 88.107 824 74 13 3938 4742 712500096 712499278 0.000000e+00 957.0
7 TraesCS2D01G187400 chr2B 92.308 169 10 2 4741 4908 184775490 184775656 2.310000e-58 237.0
8 TraesCS2D01G187400 chr2A 89.814 1345 84 24 969 2290 137931544 137932858 0.000000e+00 1676.0
9 TraesCS2D01G187400 chr2A 88.520 1054 90 15 2291 3330 137932895 137933931 0.000000e+00 1247.0
10 TraesCS2D01G187400 chr2A 84.694 490 54 10 3333 3810 137933978 137934458 2.090000e-128 470.0
11 TraesCS2D01G187400 chr2A 89.109 303 27 4 1928 2225 4005370 4005069 6.060000e-99 372.0
12 TraesCS2D01G187400 chr6A 84.893 1218 131 37 1234 2427 5321615 5320427 0.000000e+00 1181.0
13 TraesCS2D01G187400 chr6A 89.269 848 54 19 3938 4770 27092079 27091254 0.000000e+00 1027.0
14 TraesCS2D01G187400 chr6A 89.701 301 25 3 1927 2222 370232962 370233261 3.620000e-101 379.0
15 TraesCS2D01G187400 chr6A 94.313 211 10 2 2306 2516 247559572 247559780 6.190000e-84 322.0
16 TraesCS2D01G187400 chr6A 81.818 385 51 11 3387 3762 5319431 5319057 6.240000e-79 305.0
17 TraesCS2D01G187400 chr6A 94.231 104 3 2 1318 1421 247559278 247559378 6.650000e-34 156.0
18 TraesCS2D01G187400 chr6A 95.455 88 3 1 1318 1405 247615594 247615680 6.690000e-29 139.0
19 TraesCS2D01G187400 chr6D 86.704 1083 94 32 1234 2293 5978570 5977515 0.000000e+00 1157.0
20 TraesCS2D01G187400 chr6D 95.238 210 10 0 1 210 107936730 107936521 2.860000e-87 333.0
21 TraesCS2D01G187400 chr6D 80.535 411 57 13 3395 3794 5976653 5976255 1.350000e-75 294.0
22 TraesCS2D01G187400 chr6D 83.688 282 29 7 1066 1333 471075106 471075384 2.960000e-62 250.0
23 TraesCS2D01G187400 chr4B 89.333 825 62 14 3938 4742 374732101 374731283 0.000000e+00 1013.0
24 TraesCS2D01G187400 chr4B 89.701 301 25 4 1927 2222 626991693 626991992 3.620000e-101 379.0
25 TraesCS2D01G187400 chr3B 88.672 821 73 11 3946 4746 431151287 431152107 0.000000e+00 983.0
26 TraesCS2D01G187400 chr3B 88.527 828 60 22 3949 4742 698605507 698606333 0.000000e+00 970.0
27 TraesCS2D01G187400 chr6B 89.407 793 63 14 3970 4742 18271202 18271993 0.000000e+00 979.0
28 TraesCS2D01G187400 chr6B 88.527 828 65 19 3938 4742 626806915 626807735 0.000000e+00 976.0
29 TraesCS2D01G187400 chr6B 82.985 1099 117 44 1233 2293 11288850 11287784 0.000000e+00 929.0
30 TraesCS2D01G187400 chr6B 87.302 819 82 12 2523 3330 125020469 125021276 0.000000e+00 917.0
31 TraesCS2D01G187400 chr6B 80.000 420 50 18 3387 3793 11286589 11286191 3.780000e-71 279.0
32 TraesCS2D01G187400 chr6B 91.358 162 13 1 1927 2088 546202239 546202079 2.320000e-53 220.0
33 TraesCS2D01G187400 chr6B 87.898 157 18 1 1177 1333 719480436 719480281 3.050000e-42 183.0
34 TraesCS2D01G187400 chr6B 85.000 80 6 3 1433 1512 70047798 70047725 5.320000e-10 76.8
35 TraesCS2D01G187400 chr1B 88.739 817 65 17 3949 4742 26702334 26701522 0.000000e+00 974.0
36 TraesCS2D01G187400 chr1B 86.043 738 91 11 210 939 477496287 477497020 0.000000e+00 782.0
37 TraesCS2D01G187400 chr1D 87.790 819 78 12 2523 3330 360102498 360103305 0.000000e+00 939.0
38 TraesCS2D01G187400 chr1D 95.714 210 9 0 1 210 352189147 352188938 6.150000e-89 339.0
39 TraesCS2D01G187400 chr5B 87.348 822 82 12 2523 3333 206760374 206759564 0.000000e+00 922.0
40 TraesCS2D01G187400 chr5B 86.285 751 87 12 210 948 682192130 682191384 0.000000e+00 802.0
41 TraesCS2D01G187400 chr7D 87.226 822 83 12 2523 3333 636195912 636195102 0.000000e+00 917.0
42 TraesCS2D01G187400 chr7D 86.877 823 84 14 2523 3333 64418799 64417989 0.000000e+00 900.0
43 TraesCS2D01G187400 chr7D 86.861 822 86 13 2523 3333 636113640 636112830 0.000000e+00 900.0
44 TraesCS2D01G187400 chr7D 86.804 826 83 13 2523 3333 636156800 636155986 0.000000e+00 898.0
45 TraesCS2D01G187400 chr7D 89.366 536 50 3 1761 2290 329811554 329812088 0.000000e+00 667.0
46 TraesCS2D01G187400 chr7D 86.280 379 38 10 1288 1665 329811193 329811558 2.780000e-107 399.0
47 TraesCS2D01G187400 chr7D 94.444 36 1 1 929 964 629617948 629617982 2.000000e-03 54.7
48 TraesCS2D01G187400 chr5D 87.728 766 77 14 209 967 484815039 484814284 0.000000e+00 878.0
49 TraesCS2D01G187400 chr5D 88.563 682 71 5 210 885 545912364 545911684 0.000000e+00 821.0
50 TraesCS2D01G187400 chr5D 88.513 679 72 5 213 885 253549868 253550546 0.000000e+00 817.0
51 TraesCS2D01G187400 chr3D 89.337 694 60 13 208 892 137020006 137020694 0.000000e+00 859.0
52 TraesCS2D01G187400 chr3D 94.444 216 11 1 3 218 551073687 551073473 1.030000e-86 331.0
53 TraesCS2D01G187400 chr3D 95.152 165 7 1 2352 2516 519930490 519930653 4.920000e-65 259.0
54 TraesCS2D01G187400 chr5A 86.345 747 85 15 210 945 489841906 489841166 0.000000e+00 798.0
55 TraesCS2D01G187400 chr5A 94.787 211 10 1 2306 2516 161403997 161403788 1.330000e-85 327.0
56 TraesCS2D01G187400 chr5A 95.192 104 4 1 1318 1421 179212536 179212434 3.970000e-36 163.0
57 TraesCS2D01G187400 chr7B 85.600 750 89 15 197 939 116481372 116482109 0.000000e+00 769.0
58 TraesCS2D01G187400 chr7B 90.333 300 23 4 1927 2221 701399776 701400074 6.020000e-104 388.0
59 TraesCS2D01G187400 chr7B 89.474 304 26 4 1927 2225 645437115 645436813 3.620000e-101 379.0
60 TraesCS2D01G187400 chr7B 96.154 208 8 0 1 208 446648500 446648293 1.710000e-89 340.0
61 TraesCS2D01G187400 chr4D 85.317 756 96 13 208 955 324234281 324233533 0.000000e+00 767.0
62 TraesCS2D01G187400 chr4D 95.673 208 8 1 1 208 426602345 426602551 2.860000e-87 333.0
63 TraesCS2D01G187400 chr4D 94.787 211 11 0 1 211 508493468 508493258 3.700000e-86 329.0
64 TraesCS2D01G187400 chr1A 88.158 304 30 4 1927 2225 502074931 502074629 1.700000e-94 357.0
65 TraesCS2D01G187400 chr7A 94.811 212 10 1 1 212 149422175 149421965 3.700000e-86 329.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G187400 chr2D 131275956 131280913 4957 False 9156.000000 9156 100.000000 1 4958 1 chr2D.!!$F2 4957
1 TraesCS2D01G187400 chr2B 184772582 184775656 3074 False 1427.666667 2082 92.189333 953 4908 3 chr2B.!!$F2 3955
2 TraesCS2D01G187400 chr2B 197591405 197592206 801 False 1020.000000 1020 89.926000 3937 4731 1 chr2B.!!$F1 794
3 TraesCS2D01G187400 chr2B 712499278 712500096 818 True 957.000000 957 88.107000 3938 4742 1 chr2B.!!$R1 804
4 TraesCS2D01G187400 chr2A 137931544 137934458 2914 False 1131.000000 1676 87.676000 969 3810 3 chr2A.!!$F1 2841
5 TraesCS2D01G187400 chr6A 27091254 27092079 825 True 1027.000000 1027 89.269000 3938 4770 1 chr6A.!!$R1 832
6 TraesCS2D01G187400 chr6A 5319057 5321615 2558 True 743.000000 1181 83.355500 1234 3762 2 chr6A.!!$R2 2528
7 TraesCS2D01G187400 chr6A 247559278 247559780 502 False 239.000000 322 94.272000 1318 2516 2 chr6A.!!$F3 1198
8 TraesCS2D01G187400 chr6D 5976255 5978570 2315 True 725.500000 1157 83.619500 1234 3794 2 chr6D.!!$R2 2560
9 TraesCS2D01G187400 chr4B 374731283 374732101 818 True 1013.000000 1013 89.333000 3938 4742 1 chr4B.!!$R1 804
10 TraesCS2D01G187400 chr3B 431151287 431152107 820 False 983.000000 983 88.672000 3946 4746 1 chr3B.!!$F1 800
11 TraesCS2D01G187400 chr3B 698605507 698606333 826 False 970.000000 970 88.527000 3949 4742 1 chr3B.!!$F2 793
12 TraesCS2D01G187400 chr6B 18271202 18271993 791 False 979.000000 979 89.407000 3970 4742 1 chr6B.!!$F1 772
13 TraesCS2D01G187400 chr6B 626806915 626807735 820 False 976.000000 976 88.527000 3938 4742 1 chr6B.!!$F3 804
14 TraesCS2D01G187400 chr6B 125020469 125021276 807 False 917.000000 917 87.302000 2523 3330 1 chr6B.!!$F2 807
15 TraesCS2D01G187400 chr6B 11286191 11288850 2659 True 604.000000 929 81.492500 1233 3793 2 chr6B.!!$R4 2560
16 TraesCS2D01G187400 chr1B 26701522 26702334 812 True 974.000000 974 88.739000 3949 4742 1 chr1B.!!$R1 793
17 TraesCS2D01G187400 chr1B 477496287 477497020 733 False 782.000000 782 86.043000 210 939 1 chr1B.!!$F1 729
18 TraesCS2D01G187400 chr1D 360102498 360103305 807 False 939.000000 939 87.790000 2523 3330 1 chr1D.!!$F1 807
19 TraesCS2D01G187400 chr5B 206759564 206760374 810 True 922.000000 922 87.348000 2523 3333 1 chr5B.!!$R1 810
20 TraesCS2D01G187400 chr5B 682191384 682192130 746 True 802.000000 802 86.285000 210 948 1 chr5B.!!$R2 738
21 TraesCS2D01G187400 chr7D 636195102 636195912 810 True 917.000000 917 87.226000 2523 3333 1 chr7D.!!$R4 810
22 TraesCS2D01G187400 chr7D 64417989 64418799 810 True 900.000000 900 86.877000 2523 3333 1 chr7D.!!$R1 810
23 TraesCS2D01G187400 chr7D 636112830 636113640 810 True 900.000000 900 86.861000 2523 3333 1 chr7D.!!$R2 810
24 TraesCS2D01G187400 chr7D 636155986 636156800 814 True 898.000000 898 86.804000 2523 3333 1 chr7D.!!$R3 810
25 TraesCS2D01G187400 chr7D 329811193 329812088 895 False 533.000000 667 87.823000 1288 2290 2 chr7D.!!$F2 1002
26 TraesCS2D01G187400 chr5D 484814284 484815039 755 True 878.000000 878 87.728000 209 967 1 chr5D.!!$R1 758
27 TraesCS2D01G187400 chr5D 545911684 545912364 680 True 821.000000 821 88.563000 210 885 1 chr5D.!!$R2 675
28 TraesCS2D01G187400 chr5D 253549868 253550546 678 False 817.000000 817 88.513000 213 885 1 chr5D.!!$F1 672
29 TraesCS2D01G187400 chr3D 137020006 137020694 688 False 859.000000 859 89.337000 208 892 1 chr3D.!!$F1 684
30 TraesCS2D01G187400 chr5A 489841166 489841906 740 True 798.000000 798 86.345000 210 945 1 chr5A.!!$R3 735
31 TraesCS2D01G187400 chr7B 116481372 116482109 737 False 769.000000 769 85.600000 197 939 1 chr7B.!!$F1 742
32 TraesCS2D01G187400 chr4D 324233533 324234281 748 True 767.000000 767 85.317000 208 955 1 chr4D.!!$R1 747

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
893 915 1.061131 CGATGACGTGGCAATCTGTTC 59.939 52.381 0.00 0.00 34.56 3.18 F
1068 1094 0.030092 CCCTCTGTTCCCCATCCCTA 60.030 60.000 0.00 0.00 0.00 3.53 F
1433 1491 0.306228 TGACGCCGTGTTGTGAATTG 59.694 50.000 0.00 0.00 0.00 2.32 F
1436 1494 0.306228 CGCCGTGTTGTGAATTGTGA 59.694 50.000 0.00 0.00 0.00 3.58 F
2239 2333 0.617820 ACCCTCCGAACAGGCTACAT 60.618 55.000 0.00 0.00 40.77 2.29 F
2991 3243 0.893447 AAAGAATCAAGGCTGCTGGC 59.107 50.000 9.27 9.27 40.90 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2269 2363 0.388134 GCTGTGCAATGCAGTGGAAG 60.388 55.000 16.93 13.57 40.08 3.46 R
2614 2823 2.158827 TGTAGAAGAGTTGCTGCAACCA 60.159 45.455 34.59 23.00 44.49 3.67 R
3141 3399 0.248012 CAAATGCATGCCTTCTGCCA 59.752 50.000 16.68 0.00 38.89 4.92 R
3309 3587 3.825014 AGAACAATTGAAGCACAGCTCAT 59.175 39.130 13.59 0.00 38.25 2.90 R
3587 3951 1.689243 CCGCCATCTCATCCTCACCA 61.689 60.000 0.00 0.00 0.00 4.17 R
4911 5367 0.103208 CCTCTACGCCACTGCTAAGG 59.897 60.000 0.00 0.00 34.43 2.69 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
18 19 2.043248 GGGGACAGGAGTAGGCGA 60.043 66.667 0.00 0.00 0.00 5.54
19 20 2.424733 GGGGACAGGAGTAGGCGAC 61.425 68.421 0.00 0.00 0.00 5.19
20 21 2.424733 GGGACAGGAGTAGGCGACC 61.425 68.421 0.00 0.00 0.00 4.79
21 22 2.772691 GGACAGGAGTAGGCGACCG 61.773 68.421 0.00 0.00 0.00 4.79
22 23 3.412879 GACAGGAGTAGGCGACCGC 62.413 68.421 5.75 5.75 41.06 5.68
23 24 4.554363 CAGGAGTAGGCGACCGCG 62.554 72.222 8.36 0.00 43.06 6.46
62 63 4.520846 CGCCGACGCAAATCAGGC 62.521 66.667 0.00 0.00 44.00 4.85
63 64 3.127533 GCCGACGCAAATCAGGCT 61.128 61.111 0.00 0.00 44.06 4.58
64 65 1.813753 GCCGACGCAAATCAGGCTA 60.814 57.895 0.00 0.00 44.06 3.93
65 66 1.366111 GCCGACGCAAATCAGGCTAA 61.366 55.000 0.00 0.00 44.06 3.09
66 67 1.083489 CCGACGCAAATCAGGCTAAA 58.917 50.000 0.00 0.00 0.00 1.85
67 68 1.466950 CCGACGCAAATCAGGCTAAAA 59.533 47.619 0.00 0.00 0.00 1.52
68 69 2.095466 CCGACGCAAATCAGGCTAAAAA 60.095 45.455 0.00 0.00 0.00 1.94
83 84 2.295904 AAAAATGGGCCGGGAATGG 58.704 52.632 2.18 0.00 0.00 3.16
84 85 1.271127 AAAAATGGGCCGGGAATGGG 61.271 55.000 2.18 0.00 0.00 4.00
85 86 2.469563 AAAATGGGCCGGGAATGGGT 62.470 55.000 2.18 0.00 0.00 4.51
86 87 2.871795 AAATGGGCCGGGAATGGGTC 62.872 60.000 2.18 0.00 0.00 4.46
102 103 4.965348 TCGCCCGCGGACGAAAAA 62.965 61.111 34.30 11.97 43.93 1.94
103 104 4.729798 CGCCCGCGGACGAAAAAC 62.730 66.667 30.91 4.71 43.93 2.43
106 107 3.037249 CCGCGGACGAAAAACGGA 61.037 61.111 24.07 0.00 46.71 4.69
107 108 3.285776 CCGCGGACGAAAAACGGAC 62.286 63.158 24.07 0.00 46.71 4.79
113 114 4.344109 CGAAAAACGGACGCGCGT 62.344 61.111 38.52 38.52 38.46 6.01
114 115 2.496171 GAAAAACGGACGCGCGTC 60.496 61.111 45.60 45.60 43.87 5.19
133 134 4.676586 GTTTGGGTCGGCGCGTTG 62.677 66.667 8.43 0.00 0.00 4.10
146 147 2.983592 CGTTGGGCCGCCTTTTCT 60.984 61.111 9.86 0.00 0.00 2.52
147 148 2.650778 GTTGGGCCGCCTTTTCTG 59.349 61.111 9.86 0.00 0.00 3.02
148 149 2.197324 TTGGGCCGCCTTTTCTGT 59.803 55.556 9.86 0.00 0.00 3.41
149 150 1.901464 TTGGGCCGCCTTTTCTGTC 60.901 57.895 9.86 0.00 0.00 3.51
150 151 3.062466 GGGCCGCCTTTTCTGTCC 61.062 66.667 9.86 0.00 0.00 4.02
151 152 3.431725 GGCCGCCTTTTCTGTCCG 61.432 66.667 0.71 0.00 0.00 4.79
152 153 4.103103 GCCGCCTTTTCTGTCCGC 62.103 66.667 0.00 0.00 0.00 5.54
153 154 3.788766 CCGCCTTTTCTGTCCGCG 61.789 66.667 0.00 0.00 42.37 6.46
154 155 4.445545 CGCCTTTTCTGTCCGCGC 62.446 66.667 0.00 0.00 36.02 6.86
155 156 4.103103 GCCTTTTCTGTCCGCGCC 62.103 66.667 0.00 0.00 0.00 6.53
156 157 3.788766 CCTTTTCTGTCCGCGCCG 61.789 66.667 0.00 0.00 0.00 6.46
157 158 2.736995 CTTTTCTGTCCGCGCCGA 60.737 61.111 0.00 0.00 0.00 5.54
158 159 3.011760 CTTTTCTGTCCGCGCCGAC 62.012 63.158 20.04 20.04 0.00 4.79
182 183 2.125832 GGACGACCGCGGATGAAA 60.126 61.111 35.90 0.00 43.17 2.69
183 184 1.520787 GGACGACCGCGGATGAAAT 60.521 57.895 35.90 8.10 43.17 2.17
184 185 1.636340 GACGACCGCGGATGAAATG 59.364 57.895 35.90 14.66 43.17 2.32
185 186 1.762222 GACGACCGCGGATGAAATGG 61.762 60.000 35.90 12.30 43.17 3.16
186 187 2.534019 CGACCGCGGATGAAATGGG 61.534 63.158 35.90 0.02 0.00 4.00
187 188 1.451387 GACCGCGGATGAAATGGGT 60.451 57.895 35.90 4.22 0.00 4.51
188 189 1.436983 GACCGCGGATGAAATGGGTC 61.437 60.000 35.90 11.13 37.40 4.46
189 190 2.534019 CCGCGGATGAAATGGGTCG 61.534 63.158 24.07 0.00 0.00 4.79
190 191 2.715624 GCGGATGAAATGGGTCGC 59.284 61.111 0.00 0.00 36.51 5.19
191 192 2.834618 GCGGATGAAATGGGTCGCC 61.835 63.158 0.00 0.00 37.62 5.54
192 193 2.186826 CGGATGAAATGGGTCGCCC 61.187 63.158 7.87 7.87 45.71 6.13
238 239 3.791973 TTTGCCACGTCAAAACAGATT 57.208 38.095 0.29 0.00 33.47 2.40
332 337 5.004922 TCCATTTTCACCATTAAATCCGC 57.995 39.130 0.00 0.00 0.00 5.54
359 364 6.316640 TCGACGAGATCTTCAAAACTAGATCT 59.683 38.462 12.93 12.93 46.88 2.75
425 435 2.783828 TGTTTACATTGTGGTTGCCG 57.216 45.000 0.00 0.00 0.00 5.69
435 446 3.128852 TGTGGTTGCCGTAGTGTTTAT 57.871 42.857 0.00 0.00 0.00 1.40
437 448 4.834534 TGTGGTTGCCGTAGTGTTTATAT 58.165 39.130 0.00 0.00 0.00 0.86
714 730 6.523201 GCAATAGACATGACAACTTTTAACCG 59.477 38.462 0.00 0.00 0.00 4.44
715 731 7.581476 CAATAGACATGACAACTTTTAACCGT 58.419 34.615 0.00 0.00 0.00 4.83
893 915 1.061131 CGATGACGTGGCAATCTGTTC 59.939 52.381 0.00 0.00 34.56 3.18
906 929 4.166523 CAATCTGTTCGCTTTAGAGACGA 58.833 43.478 0.00 0.00 32.40 4.20
939 962 1.275291 CCTTCCTATCACACGTGTGGT 59.725 52.381 39.88 37.34 45.65 4.16
956 979 3.119743 TGTGGTAGTTATCGACGTCCTTG 60.120 47.826 10.58 0.00 0.00 3.61
958 981 3.507233 TGGTAGTTATCGACGTCCTTGTT 59.493 43.478 10.58 0.00 0.00 2.83
995 1018 2.133359 AACATCAGCTCTGCCCAGCA 62.133 55.000 6.75 0.00 42.40 4.41
1004 1027 3.016971 TGCCCAGCAGCCCATAGT 61.017 61.111 0.00 0.00 33.32 2.12
1005 1028 2.203266 GCCCAGCAGCCCATAGTC 60.203 66.667 0.00 0.00 0.00 2.59
1006 1029 2.750657 GCCCAGCAGCCCATAGTCT 61.751 63.158 0.00 0.00 0.00 3.24
1038 1061 0.404040 CCCAGCCCACCAGAGTAAAA 59.596 55.000 0.00 0.00 0.00 1.52
1039 1062 1.534729 CCAGCCCACCAGAGTAAAAC 58.465 55.000 0.00 0.00 0.00 2.43
1040 1063 1.202879 CCAGCCCACCAGAGTAAAACA 60.203 52.381 0.00 0.00 0.00 2.83
1053 1079 2.643304 AGTAAAACACTCCCTTCCCCTC 59.357 50.000 0.00 0.00 28.33 4.30
1055 1081 1.068121 AAACACTCCCTTCCCCTCTG 58.932 55.000 0.00 0.00 0.00 3.35
1057 1083 0.104409 ACACTCCCTTCCCCTCTGTT 60.104 55.000 0.00 0.00 0.00 3.16
1061 1087 2.309504 CCCTTCCCCTCTGTTCCCC 61.310 68.421 0.00 0.00 0.00 4.81
1068 1094 0.030092 CCCTCTGTTCCCCATCCCTA 60.030 60.000 0.00 0.00 0.00 3.53
1071 1097 0.689745 TCTGTTCCCCATCCCTACGG 60.690 60.000 0.00 0.00 0.00 4.02
1179 1213 4.400961 AGAGCAAGCGCCCTCCAC 62.401 66.667 2.29 0.00 39.83 4.02
1183 1217 3.710722 CAAGCGCCCTCCACCTCT 61.711 66.667 2.29 0.00 0.00 3.69
1184 1218 3.710722 AAGCGCCCTCCACCTCTG 61.711 66.667 2.29 0.00 0.00 3.35
1189 1223 2.612115 CCCTCCACCTCTGCCCTT 60.612 66.667 0.00 0.00 0.00 3.95
1190 1224 2.234296 CCCTCCACCTCTGCCCTTT 61.234 63.158 0.00 0.00 0.00 3.11
1198 1244 2.032528 TCTGCCCTTTCACGCCAG 59.967 61.111 0.00 0.00 0.00 4.85
1210 1256 2.348998 CGCCAGAGCCAGGTTTCT 59.651 61.111 0.00 0.00 34.57 2.52
1220 1266 2.306219 AGCCAGGTTTCTTCTAGAACCC 59.694 50.000 0.00 0.00 37.08 4.11
1361 1419 1.613255 GCTCCCCTTCGAACCAAATCA 60.613 52.381 0.00 0.00 0.00 2.57
1367 1425 2.029380 CCTTCGAACCAAATCAAACCCC 60.029 50.000 0.00 0.00 0.00 4.95
1369 1427 2.667470 TCGAACCAAATCAAACCCCAA 58.333 42.857 0.00 0.00 0.00 4.12
1370 1428 2.362717 TCGAACCAAATCAAACCCCAAC 59.637 45.455 0.00 0.00 0.00 3.77
1371 1429 2.101582 CGAACCAAATCAAACCCCAACA 59.898 45.455 0.00 0.00 0.00 3.33
1372 1430 3.727726 GAACCAAATCAAACCCCAACAG 58.272 45.455 0.00 0.00 0.00 3.16
1430 1488 1.885388 CCTGACGCCGTGTTGTGAA 60.885 57.895 0.00 0.00 0.00 3.18
1431 1489 1.227999 CCTGACGCCGTGTTGTGAAT 61.228 55.000 0.00 0.00 0.00 2.57
1432 1490 0.586319 CTGACGCCGTGTTGTGAATT 59.414 50.000 0.00 0.00 0.00 2.17
1433 1491 0.306228 TGACGCCGTGTTGTGAATTG 59.694 50.000 0.00 0.00 0.00 2.32
1436 1494 0.306228 CGCCGTGTTGTGAATTGTGA 59.694 50.000 0.00 0.00 0.00 3.58
1482 1540 1.745264 CAGAGGATCCGGGAGAAGC 59.255 63.158 5.98 0.00 33.66 3.86
1589 1660 1.402968 CTGTCTCTCTCAGCAGAGCTC 59.597 57.143 5.27 5.27 45.46 4.09
1652 1735 5.874261 CAGTCTTTGTTGGTTTGGTTGATTT 59.126 36.000 0.00 0.00 0.00 2.17
1749 1832 4.159857 GCGTTACGAGGTATCTGATGATC 58.840 47.826 9.62 0.00 34.32 2.92
1797 1883 2.622942 ACTTGCTGTTTGGTGGTATGTG 59.377 45.455 0.00 0.00 0.00 3.21
1824 1910 4.019174 CAGGAAAGTCCAAGCATTATGGT 58.981 43.478 0.00 0.00 39.61 3.55
1904 1990 2.393764 GGCACACTGTATGTTTGTTGC 58.606 47.619 0.00 0.00 40.64 4.17
1914 2000 3.648339 ATGTTTGTTGCCTGCTTACAG 57.352 42.857 0.00 0.00 44.05 2.74
2049 2135 5.245751 AGTTCATGCCAAATTGTAATCACCA 59.754 36.000 0.00 0.00 0.00 4.17
2135 2222 9.871238 TCTTCTGTTTAGGAGTACACATTAATC 57.129 33.333 0.00 0.00 30.96 1.75
2212 2306 6.640518 TCTCTGTCATGGAATACTGTTTACC 58.359 40.000 0.00 0.00 0.00 2.85
2227 2321 1.105457 TTACCGTGACATACCCTCCG 58.895 55.000 0.00 0.00 0.00 4.63
2239 2333 0.617820 ACCCTCCGAACAGGCTACAT 60.618 55.000 0.00 0.00 40.77 2.29
2250 2344 6.238103 CCGAACAGGCTACATACATTTACTTG 60.238 42.308 0.00 0.00 0.00 3.16
2319 2455 2.102578 GCAAGCTCATTGGGGTAACAT 58.897 47.619 0.00 0.00 39.47 2.71
2590 2787 8.859090 TGCCTGTATTTATTATTGAATCCTTGG 58.141 33.333 0.00 0.00 0.00 3.61
2614 2823 7.498570 TGGTTCTTTTTGTGTACTTAATACGGT 59.501 33.333 0.00 0.00 36.47 4.83
2641 2850 2.992543 CAGCAACTCTTCTACAGCACTC 59.007 50.000 0.00 0.00 0.00 3.51
2664 2874 5.295045 TCGAGTTTTGTTTCCCTGTACTTTC 59.705 40.000 0.00 0.00 0.00 2.62
2688 2898 9.673454 TTCGTAACATATAGCTGTACATAGTTG 57.327 33.333 0.00 0.00 0.00 3.16
2712 2922 6.311445 TGCTGTTTCTTGCGTTTTGATTAAAA 59.689 30.769 0.00 0.00 33.57 1.52
2822 3067 2.014128 CGGGTAGCAATTGAACGGAAT 58.986 47.619 10.34 0.00 0.00 3.01
2847 3096 7.535489 AAGCTTAGTAAGGTAATTGCTAACG 57.465 36.000 14.72 0.00 40.04 3.18
2865 3114 1.063469 ACGACAACTGGAACGCAAAAG 59.937 47.619 0.00 0.00 0.00 2.27
2869 3118 4.664188 GACAACTGGAACGCAAAAGTTTA 58.336 39.130 0.00 0.00 34.00 2.01
2991 3243 0.893447 AAAGAATCAAGGCTGCTGGC 59.107 50.000 9.27 9.27 40.90 4.85
3010 3262 2.802816 GGCATCGATTATGAGTGTCCAC 59.197 50.000 0.00 0.00 37.86 4.02
3089 3345 6.482641 TCAGATCTGAAATAGCTCAGCAATTC 59.517 38.462 23.17 0.42 42.25 2.17
3172 3430 5.945784 AGGCATGCATTTGTAGTTTTCTAGA 59.054 36.000 21.36 0.00 32.55 2.43
3216 3477 9.530633 GTTACTGTGTAGGTCCTTGATAATTAG 57.469 37.037 0.00 0.00 0.00 1.73
3309 3587 7.441157 CGTCCCAGACTTTGCTTAATCATATTA 59.559 37.037 0.00 0.00 0.00 0.98
3330 3608 3.631145 TGAGCTGTGCTTCAATTGTTC 57.369 42.857 5.13 0.00 39.88 3.18
3438 3794 7.978975 TGAGGTAATAACAAAATATTTGCCTGC 59.021 33.333 0.39 0.00 33.47 4.85
3523 3880 9.499479 CAAGTTTGATGAGGATTAGCTATACAT 57.501 33.333 0.00 0.00 0.00 2.29
3587 3951 7.232534 TGAGTTAAACATGGCTGGTCTATTTTT 59.767 33.333 0.00 0.00 0.00 1.94
3658 4022 8.258007 TCTTCAGTGGATGTTGTATTAGGTAAG 58.742 37.037 0.00 0.00 0.00 2.34
3718 4093 6.642540 GTGGTGGAAAATGAATGACTTTCTTC 59.357 38.462 3.08 0.00 35.23 2.87
3814 4189 0.541392 TGCCATCGCTGTTACCTCAT 59.459 50.000 0.00 0.00 35.36 2.90
3815 4190 1.760029 TGCCATCGCTGTTACCTCATA 59.240 47.619 0.00 0.00 35.36 2.15
3816 4191 2.224042 TGCCATCGCTGTTACCTCATAG 60.224 50.000 0.00 0.00 35.36 2.23
3934 4309 7.867305 TGGATATCGGTAGTTCTATCATCTC 57.133 40.000 0.00 0.00 0.00 2.75
3935 4310 7.634718 TGGATATCGGTAGTTCTATCATCTCT 58.365 38.462 0.00 0.00 0.00 3.10
3984 4366 2.356673 GTTCGTCCGTCGCCCTTT 60.357 61.111 0.00 0.00 39.67 3.11
4038 4429 3.310774 CCGCAGTCCATCTTTAAGTCATG 59.689 47.826 0.00 0.00 0.00 3.07
4041 4432 4.521146 CAGTCCATCTTTAAGTCATGCCT 58.479 43.478 0.00 0.00 0.00 4.75
4047 4438 5.829924 CCATCTTTAAGTCATGCCTAACCAT 59.170 40.000 0.00 0.00 0.00 3.55
4051 4443 8.871629 TCTTTAAGTCATGCCTAACCATTTTA 57.128 30.769 0.00 0.00 0.00 1.52
4052 4444 9.303116 TCTTTAAGTCATGCCTAACCATTTTAA 57.697 29.630 0.00 0.00 0.00 1.52
4175 4572 3.127895 CCTTTCGGTTAATCAATCCGCAA 59.872 43.478 0.00 0.00 43.35 4.85
4225 4622 6.890558 TCTTTTAAACCGTAACTCCGATTTG 58.109 36.000 0.00 0.00 0.00 2.32
4334 4731 9.313118 CTATTAATTTGGGTGCAAACTTAATCC 57.687 33.333 7.73 0.00 30.36 3.01
4459 4865 2.023673 TGCACAACTCTGGAAAACCTG 58.976 47.619 0.00 0.00 0.00 4.00
4516 4922 1.751536 CGATTATGTGCGTGCGAGCA 61.752 55.000 1.54 1.54 45.96 4.26
4595 5043 4.437239 TGACCACATTCAAATGCGTTTTT 58.563 34.783 0.00 0.00 40.04 1.94
4693 5142 1.135199 TCTCGAGTCGTGGTTATTGGC 60.135 52.381 13.13 0.00 0.00 4.52
4742 5197 1.502190 GCACGGGCTCTTTTGCTAC 59.498 57.895 0.00 0.00 36.96 3.58
4753 5208 7.323420 GGGCTCTTTTGCTACTCATTAAAAAT 58.677 34.615 0.00 0.00 0.00 1.82
4754 5209 7.276438 GGGCTCTTTTGCTACTCATTAAAAATG 59.724 37.037 0.00 0.00 0.00 2.32
4755 5210 7.201470 GGCTCTTTTGCTACTCATTAAAAATGC 60.201 37.037 0.00 0.00 0.00 3.56
4853 5309 8.622157 TCGATAGTCAAAGTTAGAGAAGTATGG 58.378 37.037 0.00 0.00 37.40 2.74
4857 5313 6.651225 AGTCAAAGTTAGAGAAGTATGGTTGC 59.349 38.462 0.00 0.00 0.00 4.17
4860 5316 5.483685 AGTTAGAGAAGTATGGTTGCACA 57.516 39.130 0.00 0.00 0.00 4.57
4912 5368 9.005777 TGTAAAATTTACCACATGTCTTACTCC 57.994 33.333 12.72 0.00 0.00 3.85
4913 5369 9.227777 GTAAAATTTACCACATGTCTTACTCCT 57.772 33.333 4.61 0.00 0.00 3.69
4914 5370 8.706322 AAAATTTACCACATGTCTTACTCCTT 57.294 30.769 0.00 0.00 0.00 3.36
4915 5371 9.802039 AAAATTTACCACATGTCTTACTCCTTA 57.198 29.630 0.00 0.00 0.00 2.69
4916 5372 9.449719 AAATTTACCACATGTCTTACTCCTTAG 57.550 33.333 0.00 0.00 0.00 2.18
4917 5373 4.473477 ACCACATGTCTTACTCCTTAGC 57.527 45.455 0.00 0.00 0.00 3.09
4918 5374 3.838317 ACCACATGTCTTACTCCTTAGCA 59.162 43.478 0.00 0.00 0.00 3.49
4919 5375 4.081420 ACCACATGTCTTACTCCTTAGCAG 60.081 45.833 0.00 0.00 0.00 4.24
4920 5376 4.081420 CCACATGTCTTACTCCTTAGCAGT 60.081 45.833 0.00 0.00 0.00 4.40
4921 5377 4.867047 CACATGTCTTACTCCTTAGCAGTG 59.133 45.833 0.00 0.00 0.00 3.66
4922 5378 4.081420 ACATGTCTTACTCCTTAGCAGTGG 60.081 45.833 0.00 0.00 0.00 4.00
4923 5379 2.233922 TGTCTTACTCCTTAGCAGTGGC 59.766 50.000 0.00 0.00 41.61 5.01
4934 5390 3.226884 GCAGTGGCGTAGAGGAAAA 57.773 52.632 0.00 0.00 0.00 2.29
4935 5391 1.079503 GCAGTGGCGTAGAGGAAAAG 58.920 55.000 0.00 0.00 0.00 2.27
4936 5392 1.608283 GCAGTGGCGTAGAGGAAAAGT 60.608 52.381 0.00 0.00 0.00 2.66
4937 5393 2.353406 GCAGTGGCGTAGAGGAAAAGTA 60.353 50.000 0.00 0.00 0.00 2.24
4938 5394 3.863400 GCAGTGGCGTAGAGGAAAAGTAA 60.863 47.826 0.00 0.00 0.00 2.24
4939 5395 4.312443 CAGTGGCGTAGAGGAAAAGTAAA 58.688 43.478 0.00 0.00 0.00 2.01
4940 5396 4.935808 CAGTGGCGTAGAGGAAAAGTAAAT 59.064 41.667 0.00 0.00 0.00 1.40
4941 5397 5.063564 CAGTGGCGTAGAGGAAAAGTAAATC 59.936 44.000 0.00 0.00 0.00 2.17
4942 5398 4.933400 GTGGCGTAGAGGAAAAGTAAATCA 59.067 41.667 0.00 0.00 0.00 2.57
4943 5399 4.933400 TGGCGTAGAGGAAAAGTAAATCAC 59.067 41.667 0.00 0.00 0.00 3.06
4944 5400 4.933400 GGCGTAGAGGAAAAGTAAATCACA 59.067 41.667 0.00 0.00 0.00 3.58
4945 5401 5.585047 GGCGTAGAGGAAAAGTAAATCACAT 59.415 40.000 0.00 0.00 0.00 3.21
4946 5402 6.759827 GGCGTAGAGGAAAAGTAAATCACATA 59.240 38.462 0.00 0.00 0.00 2.29
4947 5403 7.254353 GGCGTAGAGGAAAAGTAAATCACATAC 60.254 40.741 0.00 0.00 0.00 2.39
4948 5404 7.514747 GCGTAGAGGAAAAGTAAATCACATACG 60.515 40.741 0.00 0.00 34.51 3.06
4949 5405 6.663944 AGAGGAAAAGTAAATCACATACGC 57.336 37.500 0.00 0.00 0.00 4.42
4950 5406 6.170506 AGAGGAAAAGTAAATCACATACGCA 58.829 36.000 0.00 0.00 0.00 5.24
4951 5407 6.823689 AGAGGAAAAGTAAATCACATACGCAT 59.176 34.615 0.00 0.00 0.00 4.73
4952 5408 7.985184 AGAGGAAAAGTAAATCACATACGCATA 59.015 33.333 0.00 0.00 0.00 3.14
4953 5409 8.142994 AGGAAAAGTAAATCACATACGCATAG 57.857 34.615 0.00 0.00 0.00 2.23
4954 5410 7.985184 AGGAAAAGTAAATCACATACGCATAGA 59.015 33.333 0.00 0.00 0.00 1.98
4955 5411 8.609176 GGAAAAGTAAATCACATACGCATAGAA 58.391 33.333 0.00 0.00 0.00 2.10
4956 5412 9.982291 GAAAAGTAAATCACATACGCATAGAAA 57.018 29.630 0.00 0.00 0.00 2.52
4957 5413 9.988350 AAAAGTAAATCACATACGCATAGAAAG 57.012 29.630 0.00 0.00 0.00 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.772691 CGGTCGCCTACTCCTGTCC 61.773 68.421 0.00 0.00 0.00 4.02
4 5 2.799371 CGGTCGCCTACTCCTGTC 59.201 66.667 0.00 0.00 0.00 3.51
5 6 3.450115 GCGGTCGCCTACTCCTGT 61.450 66.667 3.73 0.00 34.56 4.00
6 7 4.554363 CGCGGTCGCCTACTCCTG 62.554 72.222 9.85 0.00 37.98 3.86
45 46 4.520846 GCCTGATTTGCGTCGGCG 62.521 66.667 4.29 4.29 44.10 6.46
46 47 1.366111 TTAGCCTGATTTGCGTCGGC 61.366 55.000 0.00 0.00 37.76 5.54
47 48 1.083489 TTTAGCCTGATTTGCGTCGG 58.917 50.000 0.00 0.00 0.00 4.79
48 49 2.892373 TTTTAGCCTGATTTGCGTCG 57.108 45.000 0.00 0.00 0.00 5.12
65 66 1.271127 CCCATTCCCGGCCCATTTTT 61.271 55.000 0.00 0.00 0.00 1.94
66 67 1.688884 CCCATTCCCGGCCCATTTT 60.689 57.895 0.00 0.00 0.00 1.82
67 68 2.042025 CCCATTCCCGGCCCATTT 60.042 61.111 0.00 0.00 0.00 2.32
68 69 3.355344 ACCCATTCCCGGCCCATT 61.355 61.111 0.00 0.00 0.00 3.16
69 70 3.820843 GACCCATTCCCGGCCCAT 61.821 66.667 0.00 0.00 0.00 4.00
86 87 4.729798 GTTTTTCGTCCGCGGGCG 62.730 66.667 44.15 44.15 38.89 6.13
87 88 4.729798 CGTTTTTCGTCCGCGGGC 62.730 66.667 27.83 25.32 38.89 6.13
88 89 4.079748 CCGTTTTTCGTCCGCGGG 62.080 66.667 27.83 10.69 38.86 6.13
89 90 3.037249 TCCGTTTTTCGTCCGCGG 61.037 61.111 22.12 22.12 43.32 6.46
90 91 2.169327 GTCCGTTTTTCGTCCGCG 59.831 61.111 0.00 0.00 37.94 6.46
91 92 2.169327 CGTCCGTTTTTCGTCCGC 59.831 61.111 0.00 0.00 37.94 5.54
92 93 2.169327 GCGTCCGTTTTTCGTCCG 59.831 61.111 0.00 0.00 37.94 4.79
93 94 2.169327 CGCGTCCGTTTTTCGTCC 59.831 61.111 0.00 0.00 37.94 4.79
94 95 2.496171 GCGCGTCCGTTTTTCGTC 60.496 61.111 8.43 0.00 37.94 4.20
95 96 4.344109 CGCGCGTCCGTTTTTCGT 62.344 61.111 24.19 0.00 37.94 3.85
96 97 4.344109 ACGCGCGTCCGTTTTTCG 62.344 61.111 32.73 0.00 38.47 3.46
97 98 2.496171 GACGCGCGTCCGTTTTTC 60.496 61.111 44.30 23.38 42.24 2.29
116 117 4.676586 CAACGCGCCGACCCAAAC 62.677 66.667 5.73 0.00 0.00 2.93
129 130 2.983592 AGAAAAGGCGGCCCAACG 60.984 61.111 17.02 0.00 0.00 4.10
130 131 2.142357 GACAGAAAAGGCGGCCCAAC 62.142 60.000 17.02 5.20 0.00 3.77
131 132 1.901464 GACAGAAAAGGCGGCCCAA 60.901 57.895 17.02 0.00 0.00 4.12
132 133 2.282180 GACAGAAAAGGCGGCCCA 60.282 61.111 17.02 0.00 0.00 5.36
133 134 3.062466 GGACAGAAAAGGCGGCCC 61.062 66.667 17.02 0.00 0.00 5.80
134 135 3.431725 CGGACAGAAAAGGCGGCC 61.432 66.667 12.11 12.11 0.00 6.13
135 136 4.103103 GCGGACAGAAAAGGCGGC 62.103 66.667 0.00 0.00 0.00 6.53
136 137 3.788766 CGCGGACAGAAAAGGCGG 61.789 66.667 0.00 0.00 42.86 6.13
138 139 4.103103 GGCGCGGACAGAAAAGGC 62.103 66.667 8.83 0.00 0.00 4.35
139 140 3.788766 CGGCGCGGACAGAAAAGG 61.789 66.667 9.72 0.00 0.00 3.11
140 141 2.736995 TCGGCGCGGACAGAAAAG 60.737 61.111 14.27 0.00 0.00 2.27
141 142 3.039588 GTCGGCGCGGACAGAAAA 61.040 61.111 34.74 4.76 36.91 2.29
153 154 4.668118 TCGTCCGTTTGGGTCGGC 62.668 66.667 0.00 0.00 45.67 5.54
154 155 2.735857 GTCGTCCGTTTGGGTCGG 60.736 66.667 0.00 0.00 45.67 4.79
155 156 2.735857 GGTCGTCCGTTTGGGTCG 60.736 66.667 0.00 0.00 46.78 4.79
165 166 1.520787 ATTTCATCCGCGGTCGTCC 60.521 57.895 27.15 0.00 0.00 4.79
166 167 1.636340 CATTTCATCCGCGGTCGTC 59.364 57.895 27.15 0.00 0.00 4.20
167 168 1.813753 CCATTTCATCCGCGGTCGT 60.814 57.895 27.15 9.98 0.00 4.34
168 169 2.534019 CCCATTTCATCCGCGGTCG 61.534 63.158 27.15 17.54 0.00 4.79
169 170 1.436983 GACCCATTTCATCCGCGGTC 61.437 60.000 27.15 7.22 33.57 4.79
170 171 1.451387 GACCCATTTCATCCGCGGT 60.451 57.895 27.15 10.00 0.00 5.68
171 172 2.534019 CGACCCATTTCATCCGCGG 61.534 63.158 22.12 22.12 0.00 6.46
172 173 3.014036 CGACCCATTTCATCCGCG 58.986 61.111 0.00 0.00 0.00 6.46
173 174 2.715624 GCGACCCATTTCATCCGC 59.284 61.111 0.00 0.00 35.91 5.54
174 175 3.420943 GGCGACCCATTTCATCCG 58.579 61.111 0.00 0.00 0.00 4.18
186 187 1.212751 GCAACTTCAATGGGGCGAC 59.787 57.895 0.00 0.00 0.00 5.19
187 188 0.960364 GAGCAACTTCAATGGGGCGA 60.960 55.000 0.00 0.00 0.00 5.54
188 189 0.962356 AGAGCAACTTCAATGGGGCG 60.962 55.000 0.00 0.00 0.00 6.13
189 190 1.260544 AAGAGCAACTTCAATGGGGC 58.739 50.000 0.00 0.00 32.91 5.80
190 191 2.755103 GGTAAGAGCAACTTCAATGGGG 59.245 50.000 0.00 0.00 39.72 4.96
191 192 3.420893 TGGTAAGAGCAACTTCAATGGG 58.579 45.455 0.00 0.00 39.72 4.00
192 193 5.183713 TGAATGGTAAGAGCAACTTCAATGG 59.816 40.000 0.00 0.00 39.72 3.16
193 194 6.258230 TGAATGGTAAGAGCAACTTCAATG 57.742 37.500 0.00 0.00 39.72 2.82
194 195 7.472334 AATGAATGGTAAGAGCAACTTCAAT 57.528 32.000 0.00 0.00 39.72 2.57
195 196 6.899393 AATGAATGGTAAGAGCAACTTCAA 57.101 33.333 0.00 0.00 39.72 2.69
196 197 6.899393 AAATGAATGGTAAGAGCAACTTCA 57.101 33.333 0.00 0.00 39.72 3.02
197 198 6.089954 GCAAAATGAATGGTAAGAGCAACTTC 59.910 38.462 0.00 0.00 39.72 3.01
198 199 5.928264 GCAAAATGAATGGTAAGAGCAACTT 59.072 36.000 2.10 2.10 42.04 2.66
201 202 4.282957 TGGCAAAATGAATGGTAAGAGCAA 59.717 37.500 0.00 0.00 0.00 3.91
238 239 3.694072 CCAAAAAGATTCCCGCTGATGTA 59.306 43.478 0.00 0.00 0.00 2.29
332 337 3.839293 AGTTTTGAAGATCTCGTCGAGG 58.161 45.455 21.63 0.00 0.00 4.63
359 364 6.902224 ATTCGTCGAAACATATCAACATGA 57.098 33.333 12.40 0.00 0.00 3.07
389 395 6.757237 TGTAAACATCATGGCAACTTTTGAT 58.243 32.000 0.00 0.00 33.59 2.57
515 527 2.872842 GCACTTCAAATTGCCATGGCTT 60.873 45.455 35.53 21.06 42.51 4.35
530 542 4.579454 ATTGCCATGATACATGCACTTC 57.421 40.909 0.00 0.00 32.63 3.01
645 660 3.379372 ACACTGAAGTTGCCATGATATGC 59.621 43.478 0.00 0.00 0.00 3.14
840 862 9.414295 TGCATGTGAGAATCTTTTTAGATTTTG 57.586 29.630 2.26 0.00 38.50 2.44
868 890 0.744057 ATTGCCACGTCATCGCATGA 60.744 50.000 0.00 0.00 41.18 3.07
893 915 1.618861 CACCACTCGTCTCTAAAGCG 58.381 55.000 0.00 0.00 0.00 4.68
906 929 2.584391 GGAAGGGAGACGCACCACT 61.584 63.158 0.00 0.00 0.00 4.00
995 1018 4.388577 AAAACCAAAGAGACTATGGGCT 57.611 40.909 0.00 0.00 38.58 5.19
998 1021 4.640647 GGGCTAAAACCAAAGAGACTATGG 59.359 45.833 0.00 0.00 40.16 2.74
999 1022 5.253330 TGGGCTAAAACCAAAGAGACTATG 58.747 41.667 0.00 0.00 34.44 2.23
1000 1023 5.501156 CTGGGCTAAAACCAAAGAGACTAT 58.499 41.667 0.00 0.00 37.59 2.12
1002 1025 3.756117 CTGGGCTAAAACCAAAGAGACT 58.244 45.455 0.00 0.00 37.59 3.24
1003 1026 2.229062 GCTGGGCTAAAACCAAAGAGAC 59.771 50.000 0.00 0.00 37.59 3.36
1004 1027 2.514803 GCTGGGCTAAAACCAAAGAGA 58.485 47.619 0.00 0.00 37.59 3.10
1005 1028 1.546029 GGCTGGGCTAAAACCAAAGAG 59.454 52.381 0.00 0.00 37.59 2.85
1006 1029 1.627864 GGCTGGGCTAAAACCAAAGA 58.372 50.000 0.00 0.00 37.59 2.52
1038 1061 0.104409 AACAGAGGGGAAGGGAGTGT 60.104 55.000 0.00 0.00 0.00 3.55
1039 1062 0.615850 GAACAGAGGGGAAGGGAGTG 59.384 60.000 0.00 0.00 0.00 3.51
1040 1063 0.547954 GGAACAGAGGGGAAGGGAGT 60.548 60.000 0.00 0.00 0.00 3.85
1071 1097 2.068277 CTGGCGGCTAGGGTACGTAC 62.068 65.000 17.56 17.56 0.00 3.67
1172 1206 2.203549 GAAAGGGCAGAGGTGGAGGG 62.204 65.000 0.00 0.00 0.00 4.30
1176 1210 1.672356 CGTGAAAGGGCAGAGGTGG 60.672 63.158 0.00 0.00 0.00 4.61
1177 1211 2.328099 GCGTGAAAGGGCAGAGGTG 61.328 63.158 0.00 0.00 0.00 4.00
1188 1222 2.032528 CCTGGCTCTGGCGTGAAA 59.967 61.111 0.00 0.00 39.81 2.69
1189 1223 2.337879 AAACCTGGCTCTGGCGTGAA 62.338 55.000 0.00 0.00 39.81 3.18
1190 1224 2.731691 GAAACCTGGCTCTGGCGTGA 62.732 60.000 0.00 0.00 39.81 4.35
1198 1244 3.601435 GGTTCTAGAAGAAACCTGGCTC 58.399 50.000 5.12 0.00 35.94 4.70
1210 1256 1.171308 CCTCGACGTGGGTTCTAGAA 58.829 55.000 8.09 0.00 0.00 2.10
1220 1266 2.870161 CGCTCGAACCTCGACGTG 60.870 66.667 0.00 0.00 44.82 4.49
1361 1419 3.699538 GTGTTTTCTCTCTGTTGGGGTTT 59.300 43.478 0.00 0.00 0.00 3.27
1367 1425 3.785505 GCGTGTGTGTTTTCTCTCTGTTG 60.786 47.826 0.00 0.00 0.00 3.33
1369 1427 1.933853 GCGTGTGTGTTTTCTCTCTGT 59.066 47.619 0.00 0.00 0.00 3.41
1370 1428 1.933181 TGCGTGTGTGTTTTCTCTCTG 59.067 47.619 0.00 0.00 0.00 3.35
1371 1429 1.933853 GTGCGTGTGTGTTTTCTCTCT 59.066 47.619 0.00 0.00 0.00 3.10
1372 1430 1.332028 CGTGCGTGTGTGTTTTCTCTC 60.332 52.381 0.00 0.00 0.00 3.20
1589 1660 3.710722 ACCCCCTGCGCTTCTCTG 61.711 66.667 9.73 0.00 0.00 3.35
1611 1683 2.832129 GACTGTATCAGAACCAGACCCA 59.168 50.000 3.70 0.00 35.18 4.51
1652 1735 2.760092 ACTGCTGAAAGAAACCTGCAAA 59.240 40.909 0.00 0.00 36.93 3.68
1749 1832 0.657312 TCGCAGAAAACAGCACACAG 59.343 50.000 0.00 0.00 0.00 3.66
1797 1883 3.402628 TGCTTGGACTTTCCTGTCTAC 57.597 47.619 0.00 0.00 37.46 2.59
1824 1910 5.445069 TCAGGGTTCTCAAACTCAATGAAA 58.555 37.500 0.00 0.00 38.42 2.69
1904 1990 1.065199 TGCCAGGAATCTGTAAGCAGG 60.065 52.381 0.00 0.00 42.78 4.85
1914 2000 2.450476 ACCAAGAACATGCCAGGAATC 58.550 47.619 0.00 0.00 0.00 2.52
2049 2135 4.330250 ACAGAATTAAGCAGCACAGTCAT 58.670 39.130 0.00 0.00 0.00 3.06
2135 2222 9.784531 AGAATATATTGACCTCATTTAGTGGTG 57.215 33.333 1.78 0.00 43.87 4.17
2212 2306 0.528924 TGTTCGGAGGGTATGTCACG 59.471 55.000 0.00 0.00 0.00 4.35
2227 2321 7.843490 TCAAGTAAATGTATGTAGCCTGTTC 57.157 36.000 0.00 0.00 0.00 3.18
2250 2344 8.817876 AGTGGAAGAAATAGCCTAGGTAATATC 58.182 37.037 11.31 4.39 0.00 1.63
2259 2353 4.778213 ATGCAGTGGAAGAAATAGCCTA 57.222 40.909 0.00 0.00 0.00 3.93
2269 2363 0.388134 GCTGTGCAATGCAGTGGAAG 60.388 55.000 16.93 13.57 40.08 3.46
2319 2455 9.166173 CAATCAGAAAGTATCAACACCAATCTA 57.834 33.333 0.00 0.00 0.00 1.98
2385 2525 9.144747 CATTCACATATCACTTACTATGCCTAC 57.855 37.037 0.00 0.00 0.00 3.18
2489 2686 4.951715 AGATTGCCATCAATGCTTCAGTTA 59.048 37.500 0.01 0.00 42.60 2.24
2531 2728 2.939756 TCTAACACAAGACGCTTGCAAA 59.060 40.909 16.24 3.30 0.00 3.68
2540 2737 7.096477 GCACACAAATGAAATCTAACACAAGAC 60.096 37.037 0.00 0.00 0.00 3.01
2590 2787 7.799914 CCACCGTATTAAGTACACAAAAAGAAC 59.200 37.037 0.00 0.00 32.61 3.01
2614 2823 2.158827 TGTAGAAGAGTTGCTGCAACCA 60.159 45.455 34.59 23.00 44.49 3.67
2641 2850 5.494632 AAAGTACAGGGAAACAAAACTCG 57.505 39.130 0.00 0.00 0.00 4.18
2664 2874 7.808381 AGCAACTATGTACAGCTATATGTTACG 59.192 37.037 4.85 0.00 34.56 3.18
2688 2898 5.881637 TTAATCAAAACGCAAGAAACAGC 57.118 34.783 0.00 0.00 43.62 4.40
2740 2950 5.791336 AGAAGCGATACAAGATATGGACA 57.209 39.130 0.00 0.00 0.00 4.02
2822 3067 8.469200 TCGTTAGCAATTACCTTACTAAGCTTA 58.531 33.333 5.94 5.94 32.70 3.09
2847 3096 2.844122 ACTTTTGCGTTCCAGTTGTC 57.156 45.000 0.00 0.00 0.00 3.18
2869 3118 8.765219 CAACAGCTAATATTAATCTACAGCGTT 58.235 33.333 0.00 4.16 32.88 4.84
2991 3243 3.393800 GGGTGGACACTCATAATCGATG 58.606 50.000 0.00 0.00 36.82 3.84
3010 3262 5.335661 GCATCAAAGTGTTACTTACAAGGGG 60.336 44.000 0.00 0.00 37.47 4.79
3089 3345 4.637483 ATACCATTTCAATTCTGTGGCG 57.363 40.909 0.00 0.00 33.24 5.69
3132 3388 2.596346 TGCCTTCTGCCAAAGATGAAA 58.404 42.857 0.00 0.00 40.16 2.69
3135 3393 1.470979 GCATGCCTTCTGCCAAAGATG 60.471 52.381 6.36 0.00 40.16 2.90
3137 3395 0.540133 TGCATGCCTTCTGCCAAAGA 60.540 50.000 16.68 0.00 38.89 2.52
3140 3398 0.978151 AAATGCATGCCTTCTGCCAA 59.022 45.000 16.68 0.00 38.89 4.52
3141 3399 0.248012 CAAATGCATGCCTTCTGCCA 59.752 50.000 16.68 0.00 38.89 4.92
3146 3404 5.473039 AGAAAACTACAAATGCATGCCTTC 58.527 37.500 16.68 0.00 0.00 3.46
3309 3587 3.825014 AGAACAATTGAAGCACAGCTCAT 59.175 39.130 13.59 0.00 38.25 2.90
3399 3753 8.771920 TGTTATTACCTCACACACAATAGAAG 57.228 34.615 0.00 0.00 0.00 2.85
3438 3794 3.863142 AGCCAAGAAAGCATTAGCAAG 57.137 42.857 0.00 0.00 45.49 4.01
3523 3880 4.019051 CCCACTGGATATCCATCTGCATTA 60.019 45.833 24.73 0.00 46.46 1.90
3526 3883 1.701292 CCCACTGGATATCCATCTGCA 59.299 52.381 24.73 0.74 46.46 4.41
3587 3951 1.689243 CCGCCATCTCATCCTCACCA 61.689 60.000 0.00 0.00 0.00 4.17
3658 4022 5.237815 TCTTCACCAACATACATCAGTCAC 58.762 41.667 0.00 0.00 0.00 3.67
3718 4093 7.726033 AATATCTATAGTGAGGCAGGTAAGG 57.274 40.000 0.00 0.00 0.00 2.69
3850 4225 7.007723 TCCCCATTCCAAATTATATGGTGTAC 58.992 38.462 0.00 0.00 39.09 2.90
4015 4405 2.565391 TGACTTAAAGATGGACTGCGGA 59.435 45.455 0.00 0.00 0.00 5.54
4334 4731 1.153353 AAAACGGACCGTGCACTATG 58.847 50.000 22.53 5.81 39.99 2.23
4423 4829 3.274288 TGTGCATGCGTGGTTATCAATA 58.726 40.909 14.09 0.00 0.00 1.90
4524 4942 1.583451 CACACACACACGCAAGCAC 60.583 57.895 0.00 0.00 45.62 4.40
4525 4943 2.037702 ACACACACACACGCAAGCA 61.038 52.632 0.00 0.00 45.62 3.91
4526 4944 1.583451 CACACACACACACGCAAGC 60.583 57.895 0.00 0.00 45.62 4.01
4528 4946 0.951040 TCACACACACACACACGCAA 60.951 50.000 0.00 0.00 0.00 4.85
4529 4947 1.357991 CTCACACACACACACACGCA 61.358 55.000 0.00 0.00 0.00 5.24
4595 5043 2.221169 GGTCTCAATGCTCACACAACA 58.779 47.619 0.00 0.00 0.00 3.33
4812 5268 7.967890 TGACTATCGACATATAAACCGACTA 57.032 36.000 0.00 0.00 33.69 2.59
4908 5364 0.818296 CTACGCCACTGCTAAGGAGT 59.182 55.000 0.00 0.00 41.01 3.85
4909 5365 1.066303 CTCTACGCCACTGCTAAGGAG 59.934 57.143 0.00 0.00 34.43 3.69
4910 5366 1.103803 CTCTACGCCACTGCTAAGGA 58.896 55.000 0.00 0.00 34.43 3.36
4911 5367 0.103208 CCTCTACGCCACTGCTAAGG 59.897 60.000 0.00 0.00 34.43 2.69
4912 5368 1.103803 TCCTCTACGCCACTGCTAAG 58.896 55.000 0.00 0.00 34.43 2.18
4913 5369 1.552578 TTCCTCTACGCCACTGCTAA 58.447 50.000 0.00 0.00 34.43 3.09
4914 5370 1.552578 TTTCCTCTACGCCACTGCTA 58.447 50.000 0.00 0.00 34.43 3.49
4915 5371 0.685097 TTTTCCTCTACGCCACTGCT 59.315 50.000 0.00 0.00 34.43 4.24
4916 5372 1.079503 CTTTTCCTCTACGCCACTGC 58.920 55.000 0.00 0.00 0.00 4.40
4917 5373 2.457366 ACTTTTCCTCTACGCCACTG 57.543 50.000 0.00 0.00 0.00 3.66
4918 5374 4.612264 TTTACTTTTCCTCTACGCCACT 57.388 40.909 0.00 0.00 0.00 4.00
4919 5375 4.933400 TGATTTACTTTTCCTCTACGCCAC 59.067 41.667 0.00 0.00 0.00 5.01
4920 5376 4.933400 GTGATTTACTTTTCCTCTACGCCA 59.067 41.667 0.00 0.00 0.00 5.69
4921 5377 4.933400 TGTGATTTACTTTTCCTCTACGCC 59.067 41.667 0.00 0.00 0.00 5.68
4922 5378 6.663944 ATGTGATTTACTTTTCCTCTACGC 57.336 37.500 0.00 0.00 0.00 4.42
4923 5379 7.514747 GCGTATGTGATTTACTTTTCCTCTACG 60.515 40.741 0.00 0.00 0.00 3.51
4924 5380 7.277098 TGCGTATGTGATTTACTTTTCCTCTAC 59.723 37.037 0.00 0.00 0.00 2.59
4925 5381 7.324935 TGCGTATGTGATTTACTTTTCCTCTA 58.675 34.615 0.00 0.00 0.00 2.43
4926 5382 6.170506 TGCGTATGTGATTTACTTTTCCTCT 58.829 36.000 0.00 0.00 0.00 3.69
4927 5383 6.417191 TGCGTATGTGATTTACTTTTCCTC 57.583 37.500 0.00 0.00 0.00 3.71
4928 5384 7.985184 TCTATGCGTATGTGATTTACTTTTCCT 59.015 33.333 0.00 0.00 0.00 3.36
4929 5385 8.138365 TCTATGCGTATGTGATTTACTTTTCC 57.862 34.615 0.00 0.00 0.00 3.13
4930 5386 9.982291 TTTCTATGCGTATGTGATTTACTTTTC 57.018 29.630 0.00 0.00 0.00 2.29
4931 5387 9.988350 CTTTCTATGCGTATGTGATTTACTTTT 57.012 29.630 0.00 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.