Multiple sequence alignment - TraesCS5A01G409300

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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 TraesCS5A01G409300 chr5A 100.000 9174 0 0 1 9174 598890958 598900131 0.000000e+00 16942.0
1 TraesCS5A01G409300 chr5A 85.275 3151 367 59 2812 5912 42108661 42105558 0.000000e+00 3158.0
2 TraesCS5A01G409300 chr5A 87.337 1303 141 22 7224 8516 42104284 42102996 0.000000e+00 1471.0
3 TraesCS5A01G409300 chr5A 85.915 1207 150 13 6008 7209 42105540 42104349 0.000000e+00 1269.0
4 TraesCS5A01G409300 chr5A 88.660 97 5 4 833 923 599395492 599395396 7.530000e-21 113.0
5 TraesCS5A01G409300 chr5A 76.812 207 30 10 160 349 675961029 675961234 5.860000e-17 100.0
6 TraesCS5A01G409300 chr5D 96.446 7709 191 34 821 8518 480422531 480430167 0.000000e+00 12641.0
7 TraesCS5A01G409300 chr5D 85.188 2363 265 49 3605 5912 53929167 53926835 0.000000e+00 2346.0
8 TraesCS5A01G409300 chr5D 87.653 1304 136 23 7224 8516 53925560 53924271 0.000000e+00 1493.0
9 TraesCS5A01G409300 chr5D 86.010 1208 149 13 6008 7210 53926817 53925625 0.000000e+00 1277.0
10 TraesCS5A01G409300 chr5D 85.242 847 99 22 2812 3648 53932414 53931584 0.000000e+00 848.0
11 TraesCS5A01G409300 chr5D 92.754 483 13 13 196 661 480421803 480422280 0.000000e+00 678.0
12 TraesCS5A01G409300 chr5D 93.396 106 3 4 68 173 521497433 521497534 4.440000e-33 154.0
13 TraesCS5A01G409300 chr5D 77.295 207 29 8 160 349 302853301 302853506 1.260000e-18 106.0
14 TraesCS5A01G409300 chr5D 89.873 79 3 3 833 906 480496374 480496296 7.580000e-16 97.1
15 TraesCS5A01G409300 chr5D 86.154 65 6 3 1 65 380174030 380174091 5.940000e-07 67.6
16 TraesCS5A01G409300 chr2D 83.883 4517 509 118 2812 7211 13764207 13759793 0.000000e+00 4106.0
17 TraesCS5A01G409300 chr2D 90.192 1091 99 8 7422 8508 13759711 13758625 0.000000e+00 1415.0
18 TraesCS5A01G409300 chr2A 83.650 4520 511 128 2812 7210 15955236 15950824 0.000000e+00 4043.0
19 TraesCS5A01G409300 chr2A 89.121 1103 99 16 7422 8518 15950740 15949653 0.000000e+00 1352.0
20 TraesCS5A01G409300 chr2A 89.908 109 9 2 48 156 768095534 768095428 1.240000e-28 139.0
21 TraesCS5A01G409300 chr2B 84.509 3189 357 74 2812 5922 25025577 25022448 0.000000e+00 3025.0
22 TraesCS5A01G409300 chr2B 89.655 1131 106 11 7392 8518 25020557 25019434 0.000000e+00 1430.0
23 TraesCS5A01G409300 chr2B 98.892 632 6 1 8515 9145 458074038 458073407 0.000000e+00 1127.0
24 TraesCS5A01G409300 chr2B 85.662 1088 129 23 6137 7211 25021941 25020868 0.000000e+00 1120.0
25 TraesCS5A01G409300 chr2B 83.120 468 38 7 821 1279 753883794 753884229 1.120000e-103 388.0
26 TraesCS5A01G409300 chr2B 82.692 468 39 14 821 1279 773634422 773634856 2.420000e-100 377.0
27 TraesCS5A01G409300 chr2B 77.778 216 29 11 151 349 790027045 790026832 2.090000e-21 115.0
28 TraesCS5A01G409300 chr2B 75.714 210 33 8 160 352 495815073 495814865 1.270000e-13 89.8
29 TraesCS5A01G409300 chr2B 81.081 111 19 2 6008 6118 25022033 25021925 4.560000e-13 87.9
30 TraesCS5A01G409300 chr2B 90.909 66 5 1 1 65 791473740 791473675 4.560000e-13 87.9
31 TraesCS5A01G409300 chr2B 95.918 49 1 1 18 65 31818373 31818421 2.750000e-10 78.7
32 TraesCS5A01G409300 chr5B 85.618 2086 247 41 2812 4865 56571076 56569012 0.000000e+00 2141.0
33 TraesCS5A01G409300 chr5B 87.956 1262 134 17 7262 8516 56565883 56564633 0.000000e+00 1472.0
34 TraesCS5A01G409300 chr5B 85.797 1211 143 20 6008 7210 56567156 56565967 0.000000e+00 1256.0
35 TraesCS5A01G409300 chr5B 84.165 922 113 25 5028 5930 56568062 56567155 0.000000e+00 863.0
36 TraesCS5A01G409300 chr5B 83.974 468 34 7 821 1279 502517075 502517510 2.380000e-110 411.0
37 TraesCS5A01G409300 chr5B 91.720 157 13 0 4860 5016 56568360 56568204 1.550000e-52 219.0
38 TraesCS5A01G409300 chr5B 92.233 103 4 3 58 160 389177503 389177601 9.600000e-30 143.0
39 TraesCS5A01G409300 chr5B 84.375 96 8 5 5928 6017 686200357 686200451 4.560000e-13 87.9
40 TraesCS5A01G409300 chr4A 99.842 631 1 0 8515 9145 154511004 154510374 0.000000e+00 1160.0
41 TraesCS5A01G409300 chr4A 99.528 635 3 0 8515 9149 352498543 352497909 0.000000e+00 1157.0
42 TraesCS5A01G409300 chr4A 82.766 470 36 12 821 1279 702447253 702446818 2.420000e-100 377.0
43 TraesCS5A01G409300 chr4A 77.619 210 29 9 160 352 560904120 560903912 2.710000e-20 111.0
44 TraesCS5A01G409300 chr1A 99.683 631 2 0 8515 9145 53879483 53880113 0.000000e+00 1155.0
45 TraesCS5A01G409300 chr1A 86.154 65 6 3 1 65 53667409 53667470 5.940000e-07 67.6
46 TraesCS5A01G409300 chr7B 99.525 631 3 0 8515 9145 108532520 108531890 0.000000e+00 1149.0
47 TraesCS5A01G409300 chr7B 85.600 375 33 10 915 1279 26099558 26099195 3.130000e-99 374.0
48 TraesCS5A01G409300 chr7B 85.503 338 30 6 951 1279 681707935 681707608 1.480000e-87 335.0
49 TraesCS5A01G409300 chr7B 91.429 105 7 2 68 171 292378851 292378748 9.600000e-30 143.0
50 TraesCS5A01G409300 chr7B 95.161 62 3 0 1207 1268 681707634 681707573 2.110000e-16 99.0
51 TraesCS5A01G409300 chr7B 84.091 88 8 6 5928 6009 709586931 709587018 7.640000e-11 80.5
52 TraesCS5A01G409300 chr7B 91.071 56 3 1 13 66 606834697 606834642 3.550000e-09 75.0
53 TraesCS5A01G409300 chr3A 99.367 632 4 0 8515 9146 453669774 453670405 0.000000e+00 1146.0
54 TraesCS5A01G409300 chr7A 99.205 629 4 1 8518 9145 608719249 608718621 0.000000e+00 1133.0
55 TraesCS5A01G409300 chr7A 96.197 631 24 0 8515 9145 120973395 120972765 0.000000e+00 1033.0
56 TraesCS5A01G409300 chr7A 89.076 119 6 6 63 180 695622857 695622745 3.450000e-29 141.0
57 TraesCS5A01G409300 chr7A 86.316 95 13 0 161 255 206757205 206757299 4.530000e-18 104.0
58 TraesCS5A01G409300 chr7A 92.424 66 3 2 2 65 4554284 4554349 9.810000e-15 93.5
59 TraesCS5A01G409300 chr6B 98.574 631 9 0 8515 9145 77786576 77787206 0.000000e+00 1116.0
60 TraesCS5A01G409300 chr6B 82.906 468 39 11 821 1279 125470577 125470142 5.200000e-102 383.0
61 TraesCS5A01G409300 chr6B 82.301 113 15 5 152 263 479295786 479295894 9.810000e-15 93.5
62 TraesCS5A01G409300 chr6B 79.612 103 19 2 248 349 41569240 41569341 1.280000e-08 73.1
63 TraesCS5A01G409300 chr1B 85.753 372 34 8 917 1279 556490242 556490603 8.700000e-100 375.0
64 TraesCS5A01G409300 chr1B 83.696 92 8 6 5926 6010 429910734 429910825 7.640000e-11 80.5
65 TraesCS5A01G409300 chr4B 85.302 381 35 9 910 1279 196361567 196361937 3.130000e-99 374.0
66 TraesCS5A01G409300 chr4B 86.170 94 6 6 5930 6017 551262868 551262960 2.730000e-15 95.3
67 TraesCS5A01G409300 chr3B 97.753 89 2 0 68 156 18672948 18673036 4.440000e-33 154.0
68 TraesCS5A01G409300 chr3B 77.512 209 30 7 160 352 642461747 642461540 9.740000e-20 110.0
69 TraesCS5A01G409300 chr3B 76.744 215 31 8 152 349 571760204 571760416 1.630000e-17 102.0
70 TraesCS5A01G409300 chr6D 93.269 104 5 2 53 156 248003988 248004089 1.600000e-32 152.0
71 TraesCS5A01G409300 chr6D 86.364 88 6 3 5928 6009 456406460 456406373 3.530000e-14 91.6
72 TraesCS5A01G409300 chr3D 97.727 88 2 0 65 152 37369008 37369095 1.600000e-32 152.0
73 TraesCS5A01G409300 chr3D 95.789 95 3 1 58 152 505561847 505561940 1.600000e-32 152.0
74 TraesCS5A01G409300 chr3D 85.577 104 14 1 160 263 465841580 465841478 3.500000e-19 108.0
75 TraesCS5A01G409300 chr4D 77.295 207 29 8 160 349 252186816 252187021 1.260000e-18 106.0
76 TraesCS5A01G409300 chr4D 84.706 85 7 6 5931 6009 218516199 218516283 7.640000e-11 80.5
77 TraesCS5A01G409300 chrUn 93.651 63 3 1 4 65 29463856 29463794 9.810000e-15 93.5
78 TraesCS5A01G409300 chrUn 92.424 66 4 1 1 65 60528931 60528996 9.810000e-15 93.5
79 TraesCS5A01G409300 chr6A 84.848 99 7 6 833 923 80804929 80805027 9.810000e-15 93.5
80 TraesCS5A01G409300 chr6A 81.818 88 10 6 5928 6009 555519676 555519589 1.650000e-07 69.4
81 TraesCS5A01G409300 chr6A 86.154 65 6 3 1 65 24776545 24776606 5.940000e-07 67.6
82 TraesCS5A01G409300 chr7D 83.158 95 14 2 248 341 29555956 29556049 1.640000e-12 86.1
83 TraesCS5A01G409300 chr1D 85.526 76 5 6 5945 6014 408769339 408769264 3.550000e-09 75.0


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 TraesCS5A01G409300 chr5A 598890958 598900131 9173 False 16942.000 16942 100.000000 1 9174 1 chr5A.!!$F1 9173
1 TraesCS5A01G409300 chr5A 42102996 42108661 5665 True 1966.000 3158 86.175667 2812 8516 3 chr5A.!!$R2 5704
2 TraesCS5A01G409300 chr5D 480421803 480430167 8364 False 6659.500 12641 94.600000 196 8518 2 chr5D.!!$F4 8322
3 TraesCS5A01G409300 chr5D 53924271 53932414 8143 True 1491.000 2346 86.023250 2812 8516 4 chr5D.!!$R2 5704
4 TraesCS5A01G409300 chr2D 13758625 13764207 5582 True 2760.500 4106 87.037500 2812 8508 2 chr2D.!!$R1 5696
5 TraesCS5A01G409300 chr2A 15949653 15955236 5583 True 2697.500 4043 86.385500 2812 8518 2 chr2A.!!$R2 5706
6 TraesCS5A01G409300 chr2B 25019434 25025577 6143 True 1415.725 3025 85.226750 2812 8518 4 chr2B.!!$R5 5706
7 TraesCS5A01G409300 chr2B 458073407 458074038 631 True 1127.000 1127 98.892000 8515 9145 1 chr2B.!!$R1 630
8 TraesCS5A01G409300 chr5B 56564633 56571076 6443 True 1190.200 2141 87.051200 2812 8516 5 chr5B.!!$R1 5704
9 TraesCS5A01G409300 chr4A 154510374 154511004 630 True 1160.000 1160 99.842000 8515 9145 1 chr4A.!!$R1 630
10 TraesCS5A01G409300 chr4A 352497909 352498543 634 True 1157.000 1157 99.528000 8515 9149 1 chr4A.!!$R2 634
11 TraesCS5A01G409300 chr1A 53879483 53880113 630 False 1155.000 1155 99.683000 8515 9145 1 chr1A.!!$F2 630
12 TraesCS5A01G409300 chr7B 108531890 108532520 630 True 1149.000 1149 99.525000 8515 9145 1 chr7B.!!$R2 630
13 TraesCS5A01G409300 chr3A 453669774 453670405 631 False 1146.000 1146 99.367000 8515 9146 1 chr3A.!!$F1 631
14 TraesCS5A01G409300 chr7A 608718621 608719249 628 True 1133.000 1133 99.205000 8518 9145 1 chr7A.!!$R2 627
15 TraesCS5A01G409300 chr7A 120972765 120973395 630 True 1033.000 1033 96.197000 8515 9145 1 chr7A.!!$R1 630
16 TraesCS5A01G409300 chr6B 77786576 77787206 630 False 1116.000 1116 98.574000 8515 9145 1 chr6B.!!$F2 630

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
652 669 0.767375 CCATGGATCCTCCCGAATGT 59.233 55.000 14.23 0.00 35.03 2.71 F
1481 1623 1.712977 CCCTTCTGCATGCTTCGCTC 61.713 60.000 20.33 0.00 0.00 5.03 F
1994 2137 1.217882 GTAAGACTGCGCTGTGTGTT 58.782 50.000 25.37 18.05 0.00 3.32 F
2624 2767 1.119684 TACATCCGGTCCACATCCTG 58.880 55.000 0.00 0.00 0.00 3.86 F
2793 2939 1.548357 CCTGCAGGACTGTAGTGCCT 61.548 60.000 29.88 0.00 40.94 4.75 F
4538 7217 3.070018 AGAAGCAGTACACAATGCAGTC 58.930 45.455 7.48 4.57 45.01 3.51 F
5199 8677 0.232303 CACTCGCGACAGTTTTGGTC 59.768 55.000 3.71 0.00 0.00 4.02 F
6150 10005 0.245539 ATTGCATGCCTGTTCACTGC 59.754 50.000 16.68 0.00 0.00 4.40 F
6439 10319 0.539438 CCCTTAGGCAGGCAACAACA 60.539 55.000 0.00 0.00 42.29 3.33 F
6488 10368 0.977108 TGGGGATCAAATTGGCCTGC 60.977 55.000 3.32 0.00 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1680 1823 0.168788 CCACGAATGTCTTGCGCATT 59.831 50.000 12.75 0.49 39.04 3.56 R
2327 2470 0.758734 TATGCTCAACCCCATCGGAG 59.241 55.000 0.00 0.00 34.64 4.63 R
3494 3685 1.456296 GTCCAAACCGGTATCCAACC 58.544 55.000 8.00 0.00 45.77 3.77 R
4262 6932 2.027100 CCTCTCTTTCCCTAAAGCGGTT 60.027 50.000 0.00 0.00 41.64 4.44 R
4677 7365 1.002366 GACAATACAGGCTCAGTGCG 58.998 55.000 0.00 0.00 44.05 5.34 R
5881 9394 0.956410 TTACACCAATGAACCCGCCG 60.956 55.000 0.00 0.00 0.00 6.46 R
6948 10837 1.152756 AAGGCCACCCAACTGTGAC 60.153 57.895 5.01 0.00 38.55 3.67 R
7598 11654 2.805099 GCTGCAGATTTTATCTCCTCCG 59.195 50.000 20.43 0.00 37.58 4.63 R
8168 12227 0.181587 TCTTTCCAGGCCGTTCAACA 59.818 50.000 0.00 0.00 0.00 3.33 R
8433 12497 2.299297 AGTCTGGTCGTACAAAAGAGGG 59.701 50.000 0.00 0.00 0.00 4.30 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
21 22 4.085357 CCAGATTTTCGATGTATCCCCA 57.915 45.455 0.00 0.00 0.00 4.96
22 23 4.655963 CCAGATTTTCGATGTATCCCCAT 58.344 43.478 0.00 0.00 0.00 4.00
23 24 4.456911 CCAGATTTTCGATGTATCCCCATG 59.543 45.833 0.00 0.00 0.00 3.66
24 25 5.308014 CAGATTTTCGATGTATCCCCATGA 58.692 41.667 0.00 0.00 0.00 3.07
25 26 5.764686 CAGATTTTCGATGTATCCCCATGAA 59.235 40.000 0.00 0.00 0.00 2.57
26 27 5.765182 AGATTTTCGATGTATCCCCATGAAC 59.235 40.000 0.00 0.00 0.00 3.18
27 28 4.495690 TTTCGATGTATCCCCATGAACA 57.504 40.909 0.00 0.00 0.00 3.18
28 29 4.705110 TTCGATGTATCCCCATGAACAT 57.295 40.909 0.00 0.00 35.34 2.71
29 30 4.705110 TCGATGTATCCCCATGAACATT 57.295 40.909 0.00 0.00 32.87 2.71
30 31 5.816955 TCGATGTATCCCCATGAACATTA 57.183 39.130 0.00 0.00 32.87 1.90
31 32 6.373005 TCGATGTATCCCCATGAACATTAT 57.627 37.500 0.00 0.00 32.87 1.28
32 33 6.778821 TCGATGTATCCCCATGAACATTATT 58.221 36.000 0.00 0.00 32.87 1.40
33 34 6.654582 TCGATGTATCCCCATGAACATTATTG 59.345 38.462 0.00 0.00 32.87 1.90
34 35 6.654582 CGATGTATCCCCATGAACATTATTGA 59.345 38.462 0.00 0.00 32.87 2.57
35 36 7.148356 CGATGTATCCCCATGAACATTATTGAG 60.148 40.741 0.00 0.00 32.87 3.02
36 37 6.910191 TGTATCCCCATGAACATTATTGAGT 58.090 36.000 0.00 0.00 0.00 3.41
37 38 8.040002 TGTATCCCCATGAACATTATTGAGTA 57.960 34.615 0.00 0.00 0.00 2.59
38 39 8.498575 TGTATCCCCATGAACATTATTGAGTAA 58.501 33.333 0.00 0.00 0.00 2.24
39 40 9.520515 GTATCCCCATGAACATTATTGAGTAAT 57.479 33.333 0.00 0.00 33.23 1.89
94 95 8.817876 ACTCCCTCCATAAACTAATATAAGAGC 58.182 37.037 0.00 0.00 0.00 4.09
95 96 7.837863 TCCCTCCATAAACTAATATAAGAGCG 58.162 38.462 0.00 0.00 0.00 5.03
96 97 7.453752 TCCCTCCATAAACTAATATAAGAGCGT 59.546 37.037 0.00 0.00 0.00 5.07
97 98 8.095169 CCCTCCATAAACTAATATAAGAGCGTT 58.905 37.037 0.00 0.00 0.00 4.84
98 99 9.490379 CCTCCATAAACTAATATAAGAGCGTTT 57.510 33.333 0.00 0.00 0.00 3.60
190 191 9.827198 ATCAATATAATAAGATTCAAAGGGGCA 57.173 29.630 0.00 0.00 0.00 5.36
191 192 9.300681 TCAATATAATAAGATTCAAAGGGGCAG 57.699 33.333 0.00 0.00 0.00 4.85
192 193 9.300681 CAATATAATAAGATTCAAAGGGGCAGA 57.699 33.333 0.00 0.00 0.00 4.26
194 195 9.692325 ATATAATAAGATTCAAAGGGGCAGATC 57.308 33.333 0.00 0.00 0.00 2.75
246 247 2.888513 CAACGATTTGGACTGCTCTG 57.111 50.000 0.00 0.00 0.00 3.35
250 251 1.938577 CGATTTGGACTGCTCTGATGG 59.061 52.381 0.00 0.00 0.00 3.51
271 287 5.439721 TGGTGAGTGCTGCAATTAATATCT 58.560 37.500 2.77 0.00 0.00 1.98
442 458 2.860735 ACGACTAGCGATCAATTCAAGC 59.139 45.455 12.46 0.00 44.57 4.01
444 460 3.462021 GACTAGCGATCAATTCAAGCCT 58.538 45.455 0.00 0.00 0.00 4.58
445 461 3.462021 ACTAGCGATCAATTCAAGCCTC 58.538 45.455 0.00 0.00 0.00 4.70
448 464 1.748591 GCGATCAATTCAAGCCTCCCT 60.749 52.381 0.00 0.00 0.00 4.20
449 465 2.485479 GCGATCAATTCAAGCCTCCCTA 60.485 50.000 0.00 0.00 0.00 3.53
450 466 3.808618 GCGATCAATTCAAGCCTCCCTAT 60.809 47.826 0.00 0.00 0.00 2.57
451 467 3.999663 CGATCAATTCAAGCCTCCCTATC 59.000 47.826 0.00 0.00 0.00 2.08
453 469 3.122480 TCAATTCAAGCCTCCCTATCCA 58.878 45.455 0.00 0.00 0.00 3.41
454 470 3.137176 TCAATTCAAGCCTCCCTATCCAG 59.863 47.826 0.00 0.00 0.00 3.86
493 509 1.340088 TGCCTTACAGTGTCCCGTTA 58.660 50.000 0.00 0.00 0.00 3.18
547 564 2.187163 GGCCTGAGGAACCGCTAC 59.813 66.667 0.65 0.00 0.00 3.58
602 619 1.662876 CGCCGTGGTGAGATGTTTTTG 60.663 52.381 0.00 0.00 0.00 2.44
651 668 1.059098 TCCATGGATCCTCCCGAATG 58.941 55.000 11.44 6.90 35.03 2.67
652 669 0.767375 CCATGGATCCTCCCGAATGT 59.233 55.000 14.23 0.00 35.03 2.71
655 672 3.181445 CCATGGATCCTCCCGAATGTAAA 60.181 47.826 14.23 0.00 35.03 2.01
656 673 4.460263 CATGGATCCTCCCGAATGTAAAA 58.540 43.478 14.23 0.00 35.03 1.52
657 674 4.577988 TGGATCCTCCCGAATGTAAAAA 57.422 40.909 14.23 0.00 35.03 1.94
750 768 2.851045 GAGCAAACCCCTTCCCCA 59.149 61.111 0.00 0.00 0.00 4.96
781 799 2.606519 CCTCCCGACCCTTCCACA 60.607 66.667 0.00 0.00 0.00 4.17
782 800 2.663196 CTCCCGACCCTTCCACAC 59.337 66.667 0.00 0.00 0.00 3.82
789 807 2.125766 GACCCTTCCACACCCACTCC 62.126 65.000 0.00 0.00 0.00 3.85
911 1053 4.574271 CCCCGGCCCCGTTATTCC 62.574 72.222 5.93 0.00 37.81 3.01
912 1054 4.922026 CCCGGCCCCGTTATTCCG 62.922 72.222 5.93 0.00 41.41 4.30
1183 1325 4.877378 ATGCATTGTCTGATTGTTGGTT 57.123 36.364 0.00 0.00 0.00 3.67
1247 1389 9.005777 GTCTGATTGTTGGTAGTTTGGTATTAA 57.994 33.333 0.00 0.00 0.00 1.40
1269 1411 3.822594 TGAATTGGTGTACGCATTGTC 57.177 42.857 8.97 1.02 0.00 3.18
1279 1421 3.812609 TGTACGCATTGTCTGATTGTTGT 59.187 39.130 0.00 0.00 0.00 3.32
1335 1477 9.877178 ACATCTGTAATTTCTTGTTCCTACTAG 57.123 33.333 0.00 0.00 0.00 2.57
1338 1480 9.085645 TCTGTAATTTCTTGTTCCTACTAGACA 57.914 33.333 0.00 0.00 36.17 3.41
1339 1481 9.877178 CTGTAATTTCTTGTTCCTACTAGACAT 57.123 33.333 0.00 0.00 36.17 3.06
1354 1496 7.602644 CCTACTAGACATATCTGAGACAGAGAC 59.397 44.444 0.00 0.00 44.08 3.36
1481 1623 1.712977 CCCTTCTGCATGCTTCGCTC 61.713 60.000 20.33 0.00 0.00 5.03
1501 1643 5.353938 GCTCGTGTGTAAGGATTGGTATAA 58.646 41.667 0.00 0.00 0.00 0.98
1503 1645 6.314400 GCTCGTGTGTAAGGATTGGTATAAAA 59.686 38.462 0.00 0.00 0.00 1.52
1504 1646 7.012044 GCTCGTGTGTAAGGATTGGTATAAAAT 59.988 37.037 0.00 0.00 0.00 1.82
1505 1647 8.428186 TCGTGTGTAAGGATTGGTATAAAATC 57.572 34.615 2.18 2.18 34.00 2.17
1506 1648 8.041919 TCGTGTGTAAGGATTGGTATAAAATCA 58.958 33.333 10.18 0.00 36.03 2.57
1507 1649 8.836413 CGTGTGTAAGGATTGGTATAAAATCAT 58.164 33.333 10.18 2.53 36.03 2.45
1527 1669 3.190383 TCTCAGATCCTGGTTTCCTCA 57.810 47.619 0.00 0.00 31.51 3.86
1601 1744 6.332635 AGTTTGATGGTGGGGATGATATAGAA 59.667 38.462 0.00 0.00 0.00 2.10
1661 1804 4.901197 TGGCAAGTACCTATTGACTTCA 57.099 40.909 1.37 0.00 36.59 3.02
1680 1823 4.627284 TCATTTTCGGGTGGTCTTAGAA 57.373 40.909 0.00 0.00 0.00 2.10
1751 1894 2.734755 TCGCCATCTCCAATCCATTT 57.265 45.000 0.00 0.00 0.00 2.32
1764 1907 7.557719 TCTCCAATCCATTTATGAAGAGTTTCC 59.442 37.037 0.00 0.00 32.09 3.13
1775 1918 2.270352 AGAGTTTCCGCACATTTCCA 57.730 45.000 0.00 0.00 0.00 3.53
1793 1936 2.298661 ACTAGCCCCACCTTTCCGG 61.299 63.158 0.00 0.00 39.35 5.14
1833 1976 6.775142 TCATTGTGGTGATTTTTACCTCTTCA 59.225 34.615 0.00 0.00 39.01 3.02
1865 2008 2.797087 CGTAGTCCGCGTGGTTATCATT 60.797 50.000 16.01 0.00 36.30 2.57
1904 2047 7.776933 TCTGCATATTCAGTTATGTGTTCTC 57.223 36.000 2.21 0.00 35.63 2.87
1911 2054 6.812879 TTCAGTTATGTGTTCTCGAGTCTA 57.187 37.500 13.13 0.00 0.00 2.59
1939 2082 6.606395 ACTTGGATAGAGTATAGAAACACCGT 59.394 38.462 0.00 0.00 0.00 4.83
1994 2137 1.217882 GTAAGACTGCGCTGTGTGTT 58.782 50.000 25.37 18.05 0.00 3.32
2044 2187 7.912056 TTGATGGATTCTTAGTGAAAGTCAG 57.088 36.000 0.00 0.00 38.29 3.51
2078 2221 2.475155 TCTGCATCTGTCATCCCTCTT 58.525 47.619 0.00 0.00 0.00 2.85
2170 2313 3.804518 TGTTGATGGTTTCGACATTCG 57.195 42.857 0.00 0.00 42.69 3.34
2300 2443 1.669115 CACGTCAAGGAGTGGCTGG 60.669 63.158 0.00 0.00 34.93 4.85
2327 2470 5.164606 AGTTTTTGACAATGTACGGTGTC 57.835 39.130 17.55 17.55 43.66 3.67
2371 2514 4.599720 TCATGGGGATTAATGGTGTTGA 57.400 40.909 0.00 0.00 0.00 3.18
2426 2569 4.454504 ACAGTGACGTTAATTGGATCCAAC 59.545 41.667 29.32 16.27 38.88 3.77
2433 2576 5.646360 ACGTTAATTGGATCCAACGAAGAAT 59.354 36.000 32.76 14.67 44.85 2.40
2479 2622 3.854994 ACCTCTTGGATCCCTTCATTTCT 59.145 43.478 9.90 0.00 37.04 2.52
2480 2623 4.205587 CCTCTTGGATCCCTTCATTTCTG 58.794 47.826 9.90 0.00 34.57 3.02
2482 2625 4.848357 TCTTGGATCCCTTCATTTCTGAC 58.152 43.478 9.90 0.00 0.00 3.51
2499 2642 7.486802 TTTCTGACTTTAAAGGTTAGTTCCG 57.513 36.000 19.14 3.75 0.00 4.30
2515 2658 8.358895 GGTTAGTTCCGCTACTATTCTTTCTAT 58.641 37.037 0.00 0.00 31.09 1.98
2579 2722 3.007940 TGCATGCCAAGTACTTCAGTAGT 59.992 43.478 16.68 0.00 41.04 2.73
2585 2728 7.182817 TGCCAAGTACTTCAGTAGTATCAAT 57.817 36.000 4.77 0.00 41.26 2.57
2591 2734 9.862371 AAGTACTTCAGTAGTATCAATGAGTTG 57.138 33.333 1.12 0.00 41.26 3.16
2592 2735 9.244292 AGTACTTCAGTAGTATCAATGAGTTGA 57.756 33.333 0.00 0.00 41.26 3.18
2594 2737 8.994429 ACTTCAGTAGTATCAATGAGTTGAAG 57.006 34.615 13.99 13.99 46.67 3.02
2595 2738 7.547370 ACTTCAGTAGTATCAATGAGTTGAAGC 59.453 37.037 14.81 0.00 46.67 3.86
2597 2740 8.293699 TCAGTAGTATCAATGAGTTGAAGCTA 57.706 34.615 0.00 0.00 46.67 3.32
2599 2742 9.539825 CAGTAGTATCAATGAGTTGAAGCTATT 57.460 33.333 0.00 0.00 46.67 1.73
2600 2743 9.757227 AGTAGTATCAATGAGTTGAAGCTATTC 57.243 33.333 0.00 0.00 46.67 1.75
2601 2744 9.757227 GTAGTATCAATGAGTTGAAGCTATTCT 57.243 33.333 0.00 0.00 46.67 2.40
2611 2754 9.547753 TGAGTTGAAGCTATTCTAATTACATCC 57.452 33.333 0.00 0.00 36.33 3.51
2624 2767 1.119684 TACATCCGGTCCACATCCTG 58.880 55.000 0.00 0.00 0.00 3.86
2665 2811 7.762382 AGCTCCAGTAAAAATGTAAATAGTGC 58.238 34.615 0.00 0.00 0.00 4.40
2675 2821 8.986477 AAAATGTAAATAGTGCTTTCATGGTC 57.014 30.769 0.00 0.00 0.00 4.02
2731 2877 8.475639 TGTATGTTATCTCTTAACTGGAACCTC 58.524 37.037 0.00 0.00 40.77 3.85
2736 2882 3.006967 TCTCTTAACTGGAACCTCTGCAC 59.993 47.826 0.00 0.00 0.00 4.57
2793 2939 1.548357 CCTGCAGGACTGTAGTGCCT 61.548 60.000 29.88 0.00 40.94 4.75
2835 2982 9.730705 TGATTGTCTTGATACATTTCTTCTTCT 57.269 29.630 0.00 0.00 0.00 2.85
3351 3519 7.609760 TCAAACAGCGATAAAACATCTGTAT 57.390 32.000 0.00 0.00 37.04 2.29
3353 3522 8.817100 TCAAACAGCGATAAAACATCTGTATAG 58.183 33.333 0.00 0.00 37.04 1.31
3494 3685 5.725110 ATTATTTGACTTACAGCTGCTCG 57.275 39.130 15.27 4.29 0.00 5.03
3530 3721 3.365265 CCACACCTTGCCGAAGCC 61.365 66.667 0.00 0.00 38.69 4.35
3670 6323 5.560724 TGCTTCTCTGTGGCTTTAAGTTAT 58.439 37.500 0.00 0.00 0.00 1.89
3776 6430 7.496529 TGCTTTGGAATATGTAAGCTATGAC 57.503 36.000 0.00 0.00 42.56 3.06
4100 6757 7.435192 GCTTACTGCACTTTAACAATCTTGTTT 59.565 33.333 13.06 0.00 44.15 2.83
4250 6920 4.642437 TGTTTGATTGTTCACAGGCTTGTA 59.358 37.500 0.00 0.00 35.25 2.41
4262 6932 4.688879 CACAGGCTTGTACGAAGTTAATCA 59.311 41.667 0.00 0.00 45.11 2.57
4480 7150 9.819267 GTCTAGGTAAGCAAAATATCTGTTACT 57.181 33.333 0.00 0.00 0.00 2.24
4538 7217 3.070018 AGAAGCAGTACACAATGCAGTC 58.930 45.455 7.48 4.57 45.01 3.51
4601 7280 3.285745 GTTAAAACTTGGCACGACTTCG 58.714 45.455 0.00 0.00 46.33 3.79
4657 7345 4.225267 ACTTGTTATGGTTAGAGGGAGGTG 59.775 45.833 0.00 0.00 0.00 4.00
5046 8522 6.236017 TCTGTTTTAACTTGCCGTCTATTG 57.764 37.500 0.00 0.00 0.00 1.90
5117 8593 5.416013 GCATTTACTAGGATTCTTATGGCCC 59.584 44.000 0.00 0.00 0.00 5.80
5186 8664 7.171678 AGCTATTATCTTTGATAAACCACTCGC 59.828 37.037 4.43 0.00 0.00 5.03
5191 8669 1.990799 TGATAAACCACTCGCGACAG 58.009 50.000 3.71 0.00 0.00 3.51
5197 8675 1.157870 ACCACTCGCGACAGTTTTGG 61.158 55.000 3.71 7.60 0.00 3.28
5199 8677 0.232303 CACTCGCGACAGTTTTGGTC 59.768 55.000 3.71 0.00 0.00 4.02
5513 8997 2.425143 TGGCCAATCAAGATCAGGTC 57.575 50.000 0.61 0.68 0.00 3.85
5542 9026 1.146566 CCCTCCCCTACGTACATACCT 59.853 57.143 0.00 0.00 0.00 3.08
5686 9180 5.294552 GTCATGCCTATCCTTACTTGTTGAC 59.705 44.000 0.00 0.00 0.00 3.18
5693 9187 5.762179 ATCCTTACTTGTTGACAGGATGA 57.238 39.130 0.00 0.00 39.69 2.92
5719 9213 6.035650 GCTATGAAATAACACGACTTACAGCA 59.964 38.462 0.00 0.00 0.00 4.41
5856 9352 1.746470 TGATCAGTGCATCTTGCTGG 58.254 50.000 0.00 0.00 45.31 4.85
5881 9394 2.620585 GCTGGGATAGAGATGGTTTTGC 59.379 50.000 0.00 0.00 0.00 3.68
6150 10005 0.245539 ATTGCATGCCTGTTCACTGC 59.754 50.000 16.68 0.00 0.00 4.40
6439 10319 0.539438 CCCTTAGGCAGGCAACAACA 60.539 55.000 0.00 0.00 42.29 3.33
6449 10329 1.073923 AGGCAACAACAGGAACCCTAG 59.926 52.381 0.00 0.00 41.41 3.02
6488 10368 0.977108 TGGGGATCAAATTGGCCTGC 60.977 55.000 3.32 0.00 0.00 4.85
6571 10453 4.133078 AGCTTTCTTCAACAACTCTCCAG 58.867 43.478 0.00 0.00 0.00 3.86
6762 10646 6.899393 ATTTTGATCAGGAGTGCTTTGTTA 57.101 33.333 0.00 0.00 0.00 2.41
6835 10724 9.050154 ACTTGATTTCTTTATTCCCCAATTGAT 57.950 29.630 7.12 0.00 0.00 2.57
6923 10812 4.574892 ACAACCTTTGAAACTTTGTTGGG 58.425 39.130 0.00 0.00 37.87 4.12
6960 10849 1.762708 CCAAACAGTCACAGTTGGGT 58.237 50.000 0.00 0.00 35.69 4.51
7079 10968 4.274459 GCTCGAAGGCATTCTAAATGATGT 59.726 41.667 9.71 0.00 32.93 3.06
7119 11010 2.811410 AGGCTTTTCCTGATCATGCAA 58.189 42.857 0.00 0.00 45.54 4.08
7241 11204 5.252547 TGCTGTCTATTTGTTTCCTATGCA 58.747 37.500 0.00 0.00 0.00 3.96
7259 11222 5.869753 ATGCATTCCGCTGTTCTTATATC 57.130 39.130 0.00 0.00 43.06 1.63
7374 11339 4.270008 GTTAGTGCTTGGTTATGATGGGT 58.730 43.478 0.00 0.00 0.00 4.51
7401 11451 7.594015 GTCTGCAGATCTTTATTATTTGCCATG 59.406 37.037 21.47 0.00 0.00 3.66
7598 11654 6.521151 AATTGAATCATTCCAGTCACCTTC 57.479 37.500 0.00 0.00 0.00 3.46
7599 11655 3.599343 TGAATCATTCCAGTCACCTTCG 58.401 45.455 0.00 0.00 0.00 3.79
8080 12139 7.492077 ACTCCATGATATGAGATCTAATGCA 57.508 36.000 2.42 1.73 0.00 3.96
8088 12147 5.608676 ATGAGATCTAATGCAGCATTTCG 57.391 39.130 25.54 16.49 35.54 3.46
8433 12497 2.147150 GGTCTTGTTCCTGAACTGCTC 58.853 52.381 11.03 1.00 41.67 4.26
9161 13227 4.701956 AAAAAGTTATGATCTGGCGGTG 57.298 40.909 0.00 0.00 0.00 4.94
9162 13228 1.668419 AAGTTATGATCTGGCGGTGC 58.332 50.000 0.00 0.00 0.00 5.01
9163 13229 0.833287 AGTTATGATCTGGCGGTGCT 59.167 50.000 0.00 0.00 0.00 4.40
9164 13230 2.039418 AGTTATGATCTGGCGGTGCTA 58.961 47.619 0.00 0.00 0.00 3.49
9165 13231 2.135933 GTTATGATCTGGCGGTGCTAC 58.864 52.381 0.00 0.00 0.00 3.58
9166 13232 1.408969 TATGATCTGGCGGTGCTACA 58.591 50.000 0.00 0.00 0.00 2.74
9167 13233 0.761187 ATGATCTGGCGGTGCTACAT 59.239 50.000 0.00 0.00 0.00 2.29
9168 13234 0.179076 TGATCTGGCGGTGCTACATG 60.179 55.000 0.00 0.00 0.00 3.21
9169 13235 1.502163 GATCTGGCGGTGCTACATGC 61.502 60.000 0.00 0.00 43.25 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.085357 TGGGGATACATCGAAAATCTGG 57.915 45.455 0.00 0.00 39.74 3.86
1 2 5.308014 TCATGGGGATACATCGAAAATCTG 58.692 41.667 0.00 0.00 39.74 2.90
2 3 5.567037 TCATGGGGATACATCGAAAATCT 57.433 39.130 0.00 0.00 39.74 2.40
3 4 5.530915 TGTTCATGGGGATACATCGAAAATC 59.469 40.000 0.00 0.00 39.74 2.17
4 5 5.445069 TGTTCATGGGGATACATCGAAAAT 58.555 37.500 0.00 0.00 39.74 1.82
5 6 4.849518 TGTTCATGGGGATACATCGAAAA 58.150 39.130 0.00 0.00 39.74 2.29
6 7 4.495690 TGTTCATGGGGATACATCGAAA 57.504 40.909 0.00 0.00 39.74 3.46
7 8 4.705110 ATGTTCATGGGGATACATCGAA 57.295 40.909 0.00 0.00 39.74 3.71
8 9 4.705110 AATGTTCATGGGGATACATCGA 57.295 40.909 0.00 0.00 39.74 3.59
9 10 6.654582 TCAATAATGTTCATGGGGATACATCG 59.345 38.462 0.00 0.00 39.74 3.84
10 11 7.667219 ACTCAATAATGTTCATGGGGATACATC 59.333 37.037 0.00 0.00 39.74 3.06
11 12 7.529555 ACTCAATAATGTTCATGGGGATACAT 58.470 34.615 0.00 0.00 39.74 2.29
12 13 6.910191 ACTCAATAATGTTCATGGGGATACA 58.090 36.000 0.00 0.00 39.74 2.29
13 14 8.918202 TTACTCAATAATGTTCATGGGGATAC 57.082 34.615 0.00 0.00 0.00 2.24
68 69 8.817876 GCTCTTATATTAGTTTATGGAGGGAGT 58.182 37.037 0.00 0.00 0.00 3.85
69 70 7.976734 CGCTCTTATATTAGTTTATGGAGGGAG 59.023 40.741 0.00 0.00 33.23 4.30
70 71 7.453752 ACGCTCTTATATTAGTTTATGGAGGGA 59.546 37.037 0.00 0.00 34.22 4.20
71 72 7.612677 ACGCTCTTATATTAGTTTATGGAGGG 58.387 38.462 0.00 0.00 35.06 4.30
72 73 9.490379 AAACGCTCTTATATTAGTTTATGGAGG 57.510 33.333 0.00 0.00 31.14 4.30
164 165 9.827198 TGCCCCTTTGAATCTTATTATATTGAT 57.173 29.630 0.00 0.00 0.00 2.57
165 166 9.300681 CTGCCCCTTTGAATCTTATTATATTGA 57.699 33.333 0.00 0.00 0.00 2.57
166 167 9.300681 TCTGCCCCTTTGAATCTTATTATATTG 57.699 33.333 0.00 0.00 0.00 1.90
168 169 9.692325 GATCTGCCCCTTTGAATCTTATTATAT 57.308 33.333 0.00 0.00 0.00 0.86
169 170 8.668653 TGATCTGCCCCTTTGAATCTTATTATA 58.331 33.333 0.00 0.00 0.00 0.98
170 171 7.529555 TGATCTGCCCCTTTGAATCTTATTAT 58.470 34.615 0.00 0.00 0.00 1.28
171 172 6.910191 TGATCTGCCCCTTTGAATCTTATTA 58.090 36.000 0.00 0.00 0.00 0.98
172 173 5.769835 TGATCTGCCCCTTTGAATCTTATT 58.230 37.500 0.00 0.00 0.00 1.40
173 174 5.393068 TGATCTGCCCCTTTGAATCTTAT 57.607 39.130 0.00 0.00 0.00 1.73
174 175 4.860802 TGATCTGCCCCTTTGAATCTTA 57.139 40.909 0.00 0.00 0.00 2.10
175 176 3.744940 TGATCTGCCCCTTTGAATCTT 57.255 42.857 0.00 0.00 0.00 2.40
176 177 3.744940 TTGATCTGCCCCTTTGAATCT 57.255 42.857 0.00 0.00 0.00 2.40
177 178 4.806640 TTTTGATCTGCCCCTTTGAATC 57.193 40.909 0.00 0.00 0.00 2.52
178 179 6.872585 TTATTTTGATCTGCCCCTTTGAAT 57.127 33.333 0.00 0.00 0.00 2.57
179 180 6.669154 AGATTATTTTGATCTGCCCCTTTGAA 59.331 34.615 0.00 0.00 32.79 2.69
180 181 6.197168 AGATTATTTTGATCTGCCCCTTTGA 58.803 36.000 0.00 0.00 32.79 2.69
181 182 6.475596 AGATTATTTTGATCTGCCCCTTTG 57.524 37.500 0.00 0.00 32.79 2.77
182 183 5.300286 CGAGATTATTTTGATCTGCCCCTTT 59.700 40.000 0.00 0.00 34.13 3.11
183 184 4.823989 CGAGATTATTTTGATCTGCCCCTT 59.176 41.667 0.00 0.00 34.13 3.95
184 185 4.103153 TCGAGATTATTTTGATCTGCCCCT 59.897 41.667 0.00 0.00 34.13 4.79
185 186 4.214332 GTCGAGATTATTTTGATCTGCCCC 59.786 45.833 0.00 0.00 34.13 5.80
186 187 4.214332 GGTCGAGATTATTTTGATCTGCCC 59.786 45.833 0.00 0.00 34.13 5.36
187 188 4.816385 TGGTCGAGATTATTTTGATCTGCC 59.184 41.667 0.00 0.00 34.13 4.85
188 189 5.991328 TGGTCGAGATTATTTTGATCTGC 57.009 39.130 0.00 0.00 34.13 4.26
189 190 7.719778 TGATGGTCGAGATTATTTTGATCTG 57.280 36.000 0.00 0.00 34.13 2.90
190 191 8.737168 TTTGATGGTCGAGATTATTTTGATCT 57.263 30.769 0.00 0.00 36.60 2.75
191 192 9.604626 GATTTGATGGTCGAGATTATTTTGATC 57.395 33.333 0.00 0.00 0.00 2.92
192 193 9.123902 TGATTTGATGGTCGAGATTATTTTGAT 57.876 29.630 0.00 0.00 0.00 2.57
193 194 8.504812 TGATTTGATGGTCGAGATTATTTTGA 57.495 30.769 0.00 0.00 0.00 2.69
194 195 7.859377 CCTGATTTGATGGTCGAGATTATTTTG 59.141 37.037 0.00 0.00 0.00 2.44
245 246 1.913778 AATTGCAGCACTCACCATCA 58.086 45.000 0.00 0.00 0.00 3.07
246 247 4.644103 ATTAATTGCAGCACTCACCATC 57.356 40.909 0.00 0.00 0.00 3.51
250 251 7.482654 TGTAGATATTAATTGCAGCACTCAC 57.517 36.000 0.00 0.00 0.00 3.51
271 287 4.630505 TGGCGCTAACGTTCATATTTTGTA 59.369 37.500 2.82 0.00 42.83 2.41
281 297 0.793861 TGTGATTGGCGCTAACGTTC 59.206 50.000 8.88 3.21 42.83 3.95
285 301 2.919666 ATTGTGTGATTGGCGCTAAC 57.080 45.000 8.88 3.70 0.00 2.34
375 391 6.600822 TCAGGACACTAGTAACCTGTATGTAC 59.399 42.308 29.88 11.26 46.68 2.90
376 392 6.724351 TCAGGACACTAGTAACCTGTATGTA 58.276 40.000 29.88 17.56 46.68 2.29
377 393 5.577100 TCAGGACACTAGTAACCTGTATGT 58.423 41.667 29.88 10.72 46.68 2.29
378 394 6.525578 TTCAGGACACTAGTAACCTGTATG 57.474 41.667 29.88 16.57 46.68 2.39
379 395 7.549147 TTTTCAGGACACTAGTAACCTGTAT 57.451 36.000 29.88 8.46 46.68 2.29
422 438 2.219674 GGCTTGAATTGATCGCTAGTCG 59.780 50.000 0.00 0.00 40.15 4.18
426 442 2.485479 GGGAGGCTTGAATTGATCGCTA 60.485 50.000 0.00 0.00 0.00 4.26
444 460 2.446848 GCTGCTGCCTGGATAGGGA 61.447 63.158 3.85 0.00 44.75 4.20
445 461 2.112718 GCTGCTGCCTGGATAGGG 59.887 66.667 3.85 0.00 44.75 3.53
448 464 4.897357 CGCGCTGCTGCCTGGATA 62.897 66.667 5.56 0.00 35.36 2.59
477 493 4.451629 AGATGTAACGGGACACTGTAAG 57.548 45.455 0.00 0.00 42.29 2.34
493 509 1.376649 AAGAAGAGGGCCCAAGATGT 58.623 50.000 27.56 0.00 0.00 3.06
547 564 2.289694 CCTGGCCCAGATAGTATTTCCG 60.290 54.545 13.74 0.00 32.44 4.30
602 619 6.690194 ATATCATCTCACCAGCTCAAAAAC 57.310 37.500 0.00 0.00 0.00 2.43
676 693 8.989653 TTCGACCAGTTTTTCTTTACATTTTT 57.010 26.923 0.00 0.00 0.00 1.94
677 694 8.989653 TTTCGACCAGTTTTTCTTTACATTTT 57.010 26.923 0.00 0.00 0.00 1.82
678 695 9.594478 AATTTCGACCAGTTTTTCTTTACATTT 57.406 25.926 0.00 0.00 0.00 2.32
680 697 9.893305 CTAATTTCGACCAGTTTTTCTTTACAT 57.107 29.630 0.00 0.00 0.00 2.29
681 698 7.858879 GCTAATTTCGACCAGTTTTTCTTTACA 59.141 33.333 0.00 0.00 0.00 2.41
682 699 7.858879 TGCTAATTTCGACCAGTTTTTCTTTAC 59.141 33.333 0.00 0.00 0.00 2.01
683 700 7.932335 TGCTAATTTCGACCAGTTTTTCTTTA 58.068 30.769 0.00 0.00 0.00 1.85
684 701 6.801575 TGCTAATTTCGACCAGTTTTTCTTT 58.198 32.000 0.00 0.00 0.00 2.52
685 702 6.385649 TGCTAATTTCGACCAGTTTTTCTT 57.614 33.333 0.00 0.00 0.00 2.52
686 703 6.385649 TTGCTAATTTCGACCAGTTTTTCT 57.614 33.333 0.00 0.00 0.00 2.52
687 704 5.117135 GCTTGCTAATTTCGACCAGTTTTTC 59.883 40.000 0.00 0.00 0.00 2.29
688 705 4.982295 GCTTGCTAATTTCGACCAGTTTTT 59.018 37.500 0.00 0.00 0.00 1.94
750 768 1.192803 GGGAGGTTTCTGGAGACGGT 61.193 60.000 0.00 0.00 38.16 4.83
781 799 3.542602 AGGTGAGGGGGAGTGGGT 61.543 66.667 0.00 0.00 0.00 4.51
782 800 2.689034 GAGGTGAGGGGGAGTGGG 60.689 72.222 0.00 0.00 0.00 4.61
789 807 1.386485 ATGATGGGGAGGTGAGGGG 60.386 63.158 0.00 0.00 0.00 4.79
916 1058 4.574271 GGAATAACGGGGCCGGGG 62.574 72.222 16.11 0.92 44.69 5.73
917 1059 4.922026 CGGAATAACGGGGCCGGG 62.922 72.222 16.11 3.70 44.69 5.73
968 1110 4.367023 CGGAGGCGGAAACACGGA 62.367 66.667 0.00 0.00 0.00 4.69
1110 1252 2.083167 AATTGCAAATGCCACTTCCG 57.917 45.000 1.71 0.00 41.18 4.30
1219 1361 5.197451 ACCAAACTACCAACAATCAGACAA 58.803 37.500 0.00 0.00 0.00 3.18
1247 1389 4.458989 AGACAATGCGTACACCAATTCAAT 59.541 37.500 0.00 0.00 0.00 2.57
1252 1394 3.052455 TCAGACAATGCGTACACCAAT 57.948 42.857 0.00 0.00 0.00 3.16
1269 1411 6.458751 GGTTATCACAGCCATACAACAATCAG 60.459 42.308 0.00 0.00 0.00 2.90
1300 1442 9.003658 ACAAGAAATTACAGATGTTACTTCCAG 57.996 33.333 0.00 0.00 0.00 3.86
1320 1462 9.126151 CTCAGATATGTCTAGTAGGAACAAGAA 57.874 37.037 0.00 0.00 32.09 2.52
1332 1474 5.989168 ACGTCTCTGTCTCAGATATGTCTAG 59.011 44.000 0.00 0.00 39.92 2.43
1333 1475 5.919755 ACGTCTCTGTCTCAGATATGTCTA 58.080 41.667 0.00 0.00 39.92 2.59
1334 1476 4.776349 ACGTCTCTGTCTCAGATATGTCT 58.224 43.478 0.00 0.00 39.92 3.41
1335 1477 4.572795 TGACGTCTCTGTCTCAGATATGTC 59.427 45.833 17.92 20.46 45.50 3.06
1336 1478 4.334203 GTGACGTCTCTGTCTCAGATATGT 59.666 45.833 17.92 8.87 39.92 2.29
1337 1479 4.260990 GGTGACGTCTCTGTCTCAGATATG 60.261 50.000 17.92 2.16 39.92 1.78
1338 1480 3.880490 GGTGACGTCTCTGTCTCAGATAT 59.120 47.826 17.92 0.00 39.92 1.63
1339 1481 3.271729 GGTGACGTCTCTGTCTCAGATA 58.728 50.000 17.92 0.00 39.92 1.98
1340 1482 2.088423 GGTGACGTCTCTGTCTCAGAT 58.912 52.381 17.92 0.00 39.92 2.90
1341 1483 1.202770 TGGTGACGTCTCTGTCTCAGA 60.203 52.381 17.92 0.00 39.64 3.27
1354 1496 2.051345 GCAGCCGTTTTGGTGACG 60.051 61.111 0.00 0.00 41.21 4.35
1481 1623 8.203937 TGATTTTATACCAATCCTTACACACG 57.796 34.615 2.66 0.00 30.64 4.49
1501 1643 5.193325 AGGAAACCAGGATCTGAGATGATTT 59.807 40.000 0.00 0.00 32.44 2.17
1503 1645 4.305524 AGGAAACCAGGATCTGAGATGAT 58.694 43.478 0.00 0.00 32.44 2.45
1504 1646 3.708631 GAGGAAACCAGGATCTGAGATGA 59.291 47.826 0.00 0.00 32.44 2.92
1505 1647 3.453717 TGAGGAAACCAGGATCTGAGATG 59.546 47.826 0.00 0.00 32.44 2.90
1506 1648 3.729108 TGAGGAAACCAGGATCTGAGAT 58.271 45.455 0.00 0.00 32.44 2.75
1507 1649 3.190383 TGAGGAAACCAGGATCTGAGA 57.810 47.619 0.00 0.00 32.44 3.27
1573 1716 2.094675 CATCCCCACCATCAAACTCAC 58.905 52.381 0.00 0.00 0.00 3.51
1601 1744 1.097547 GCAGTGGCAGCGGTATGAAT 61.098 55.000 0.00 0.00 40.72 2.57
1646 1789 5.878669 ACCCGAAAATGAAGTCAATAGGTAC 59.121 40.000 0.00 0.00 0.00 3.34
1648 1791 4.700213 CACCCGAAAATGAAGTCAATAGGT 59.300 41.667 0.00 0.00 0.00 3.08
1661 1804 4.157840 GCATTTCTAAGACCACCCGAAAAT 59.842 41.667 0.00 0.00 0.00 1.82
1680 1823 0.168788 CCACGAATGTCTTGCGCATT 59.831 50.000 12.75 0.49 39.04 3.56
1751 1894 4.394920 GGAAATGTGCGGAAACTCTTCATA 59.605 41.667 0.00 0.00 32.75 2.15
1764 1907 1.376609 GGGGCTAGTGGAAATGTGCG 61.377 60.000 0.00 0.00 0.00 5.34
1775 1918 2.298661 CCGGAAAGGTGGGGCTAGT 61.299 63.158 0.00 0.00 34.51 2.57
1793 1936 5.011329 ACCACAATGATGGCCATGAATATTC 59.989 40.000 26.56 8.33 44.33 1.75
1833 1976 2.795175 CGGACTACGCTATCACCATT 57.205 50.000 0.00 0.00 34.82 3.16
1860 2003 4.523173 CAGAAGATTAGCCATGGCAATGAT 59.477 41.667 37.18 23.50 44.88 2.45
1865 2008 1.064537 TGCAGAAGATTAGCCATGGCA 60.065 47.619 37.18 19.62 44.88 4.92
1904 2047 9.577110 CTATACTCTATCCAAGTACTAGACTCG 57.423 40.741 0.00 0.00 37.44 4.18
1911 2054 9.134055 GGTGTTTCTATACTCTATCCAAGTACT 57.866 37.037 0.00 0.00 32.30 2.73
1939 2082 5.016173 CCCCAAGAGAAATACCAACATCAA 58.984 41.667 0.00 0.00 0.00 2.57
2044 2187 4.036498 CAGATGCAGAACAATCCTCCATTC 59.964 45.833 0.00 0.00 0.00 2.67
2078 2221 3.896888 GCCATTCATATGACCCATTTGGA 59.103 43.478 4.48 0.00 38.00 3.53
2170 2313 8.088981 AGGTATCTGACAAATACGACCATATTC 58.911 37.037 0.00 0.00 31.62 1.75
2300 2443 3.057806 CGTACATTGTCAAAAACTCCCCC 60.058 47.826 0.00 0.00 0.00 5.40
2327 2470 0.758734 TATGCTCAACCCCATCGGAG 59.241 55.000 0.00 0.00 34.64 4.63
2332 2475 5.266788 CCATGATAATATGCTCAACCCCAT 58.733 41.667 0.00 0.00 0.00 4.00
2338 2481 9.192642 CATTAATCCCCATGATAATATGCTCAA 57.807 33.333 0.00 0.00 31.83 3.02
2426 2569 9.846248 AAAGGTGAAATCTCAATTAATTCTTCG 57.154 29.630 0.00 0.00 31.88 3.79
2433 2576 8.141268 GGTGACAAAAGGTGAAATCTCAATTAA 58.859 33.333 0.00 0.00 31.88 1.40
2479 2622 4.964593 AGCGGAACTAACCTTTAAAGTCA 58.035 39.130 14.03 0.00 0.00 3.41
2480 2623 6.162079 AGTAGCGGAACTAACCTTTAAAGTC 58.838 40.000 14.03 3.90 30.90 3.01
2482 2625 8.713737 AATAGTAGCGGAACTAACCTTTAAAG 57.286 34.615 8.32 8.32 35.65 1.85
2497 2640 5.635700 GCTGGAATAGAAAGAATAGTAGCGG 59.364 44.000 0.00 0.00 0.00 5.52
2499 2642 8.614469 AATGCTGGAATAGAAAGAATAGTAGC 57.386 34.615 0.00 0.00 0.00 3.58
2550 2693 2.554032 AGTACTTGGCATGCAAGTCAAC 59.446 45.455 27.49 22.56 41.43 3.18
2585 2728 9.547753 GGATGTAATTAGAATAGCTTCAACTCA 57.452 33.333 0.00 0.00 33.56 3.41
2591 2734 6.590677 GGACCGGATGTAATTAGAATAGCTTC 59.409 42.308 9.46 0.00 0.00 3.86
2592 2735 6.042781 TGGACCGGATGTAATTAGAATAGCTT 59.957 38.462 9.46 0.00 0.00 3.74
2594 2737 5.638234 GTGGACCGGATGTAATTAGAATAGC 59.362 44.000 9.46 0.00 0.00 2.97
2595 2738 6.755206 TGTGGACCGGATGTAATTAGAATAG 58.245 40.000 9.46 0.00 0.00 1.73
2597 2740 5.623956 TGTGGACCGGATGTAATTAGAAT 57.376 39.130 9.46 0.00 0.00 2.40
2599 2742 4.039973 GGATGTGGACCGGATGTAATTAGA 59.960 45.833 9.46 0.00 0.00 2.10
2600 2743 4.040461 AGGATGTGGACCGGATGTAATTAG 59.960 45.833 9.46 0.00 0.00 1.73
2601 2744 3.971305 AGGATGTGGACCGGATGTAATTA 59.029 43.478 9.46 0.00 0.00 1.40
2602 2745 2.777692 AGGATGTGGACCGGATGTAATT 59.222 45.455 9.46 0.00 0.00 1.40
2603 2746 2.104792 CAGGATGTGGACCGGATGTAAT 59.895 50.000 9.46 0.00 0.00 1.89
2604 2747 1.484653 CAGGATGTGGACCGGATGTAA 59.515 52.381 9.46 0.00 0.00 2.41
2605 2748 1.119684 CAGGATGTGGACCGGATGTA 58.880 55.000 9.46 0.00 0.00 2.29
2606 2749 1.907739 CAGGATGTGGACCGGATGT 59.092 57.895 9.46 0.00 0.00 3.06
2607 2750 4.863707 CAGGATGTGGACCGGATG 57.136 61.111 9.46 0.00 0.00 3.51
2624 2767 9.956720 TTACTGGAGCTTCGTACTAATAATAAC 57.043 33.333 0.00 0.00 0.00 1.89
2665 2811 4.576053 TCAAGTGACAACAGACCATGAAAG 59.424 41.667 0.00 0.00 0.00 2.62
2675 2821 9.376075 AGTTAATAGATCATCAAGTGACAACAG 57.624 33.333 0.00 0.00 40.28 3.16
2793 2939 3.261580 CAATCATAAGTCGTGCCAGTGA 58.738 45.455 0.00 0.00 0.00 3.41
2834 2981 5.039333 CAGCACTCTTTTCCTGTCAAAAAG 58.961 41.667 4.10 4.10 42.46 2.27
2835 2982 4.704540 TCAGCACTCTTTTCCTGTCAAAAA 59.295 37.500 0.00 0.00 0.00 1.94
2836 2983 4.269183 TCAGCACTCTTTTCCTGTCAAAA 58.731 39.130 0.00 0.00 0.00 2.44
2896 3045 4.200838 TCACGTTGCCAGATCTATCAAA 57.799 40.909 9.56 0.00 0.00 2.69
2995 3144 2.487762 CCATACCAATGCACGAAACAGT 59.512 45.455 0.00 0.00 0.00 3.55
3276 3428 6.770785 TCAGTACAAGCTGTTATGAACCTTTT 59.229 34.615 0.00 0.00 37.70 2.27
3277 3429 6.296026 TCAGTACAAGCTGTTATGAACCTTT 58.704 36.000 0.00 0.00 37.70 3.11
3353 3522 9.178758 GGGTATATTATCCAACCAGATTCATTC 57.821 37.037 0.00 0.00 33.46 2.67
3494 3685 1.456296 GTCCAAACCGGTATCCAACC 58.544 55.000 8.00 0.00 45.77 3.77
3670 6323 2.378886 TCGAGGGCCTATAAGATGGAGA 59.621 50.000 5.73 0.00 0.00 3.71
3776 6430 5.598416 TCATGCTATCGGTGATATTAGGG 57.402 43.478 0.00 0.00 0.00 3.53
4006 6663 5.745312 ACAACATCTGAGGACAAGATACA 57.255 39.130 0.00 0.00 0.00 2.29
4122 6779 6.899393 AACATCAATAACAATATGGCCGAT 57.101 33.333 0.00 0.00 0.00 4.18
4250 6920 4.390909 CCTAAAGCGGTTGATTAACTTCGT 59.609 41.667 0.00 0.00 36.99 3.85
4262 6932 2.027100 CCTCTCTTTCCCTAAAGCGGTT 60.027 50.000 0.00 0.00 41.64 4.44
4538 7217 5.063564 GGCTATTAGTCCAAACAGAGAAACG 59.936 44.000 0.00 0.00 0.00 3.60
4601 7280 9.188588 CAGATAATGATTTTTGCATCCATGTAC 57.811 33.333 0.00 0.00 0.00 2.90
4604 7283 6.929049 AGCAGATAATGATTTTTGCATCCATG 59.071 34.615 9.69 0.00 34.17 3.66
4677 7365 1.002366 GACAATACAGGCTCAGTGCG 58.998 55.000 0.00 0.00 44.05 5.34
5117 8593 0.606401 AACACAGAGGGCGAATGTGG 60.606 55.000 15.83 2.64 46.74 4.17
5186 8664 8.676928 ACTAATGAGTAACGACCAAAACTGTCG 61.677 40.741 10.87 10.87 46.52 4.35
5191 8669 6.774354 TGACTAATGAGTAACGACCAAAAC 57.226 37.500 0.00 0.00 35.45 2.43
5197 8675 8.796278 GTTCAGTAATGACTAATGAGTAACGAC 58.204 37.037 0.00 0.00 36.07 4.34
5199 8677 7.513196 GCGTTCAGTAATGACTAATGAGTAACG 60.513 40.741 6.35 6.35 38.46 3.18
5200 8678 7.274904 TGCGTTCAGTAATGACTAATGAGTAAC 59.725 37.037 0.00 0.00 36.07 2.50
5201 8679 7.317390 TGCGTTCAGTAATGACTAATGAGTAA 58.683 34.615 0.00 0.00 36.07 2.24
5202 8680 6.859017 TGCGTTCAGTAATGACTAATGAGTA 58.141 36.000 0.00 0.00 36.07 2.59
5203 8681 5.720202 TGCGTTCAGTAATGACTAATGAGT 58.280 37.500 0.00 0.00 36.07 3.41
5204 8682 6.647212 TTGCGTTCAGTAATGACTAATGAG 57.353 37.500 0.00 0.00 36.07 2.90
5207 8685 5.703592 TGGTTTGCGTTCAGTAATGACTAAT 59.296 36.000 0.00 0.00 33.32 1.73
5513 8997 1.790818 GTAGGGGAGGGAGTGGTTAG 58.209 60.000 0.00 0.00 0.00 2.34
5557 9051 3.853355 AACAGAATAGCATGAGAGGGG 57.147 47.619 0.00 0.00 0.00 4.79
5559 9053 4.201990 GGCAAAACAGAATAGCATGAGAGG 60.202 45.833 0.00 0.00 0.00 3.69
5686 9180 5.985530 TCGTGTTATTTCATAGCTCATCCTG 59.014 40.000 0.00 0.00 0.00 3.86
5693 9187 6.255887 GCTGTAAGTCGTGTTATTTCATAGCT 59.744 38.462 0.00 0.00 35.30 3.32
5719 9213 3.503748 GCAGTTGATTGCTTACCTTGACT 59.496 43.478 0.00 0.00 40.89 3.41
5856 9352 1.771255 ACCATCTCTATCCCAGCAACC 59.229 52.381 0.00 0.00 0.00 3.77
5881 9394 0.956410 TTACACCAATGAACCCGCCG 60.956 55.000 0.00 0.00 0.00 6.46
5939 9452 8.394877 CCAAAAACGCTCTTATATTATGACACA 58.605 33.333 0.00 0.00 0.00 3.72
5942 9455 7.376072 GTGCCAAAAACGCTCTTATATTATGAC 59.624 37.037 0.00 0.00 0.00 3.06
5943 9456 7.066404 TGTGCCAAAAACGCTCTTATATTATGA 59.934 33.333 0.00 0.00 0.00 2.15
6000 9848 7.060421 CCACACAAATATATTGGTACTCCCTT 58.940 38.462 5.13 0.00 0.00 3.95
6082 9937 2.478894 ACATAACAGTCTGAAAACGCCG 59.521 45.455 6.91 0.00 0.00 6.46
6118 9973 3.535561 GCATGCAATCACCTAGTACAGT 58.464 45.455 14.21 0.00 0.00 3.55
6449 10329 5.765182 CCCCATATGTAACAACCAGAGAATC 59.235 44.000 1.24 0.00 0.00 2.52
6488 10368 8.815565 TCAGCTATTATAGTCTCATAAGAGGG 57.184 38.462 0.94 0.00 42.34 4.30
6571 10453 3.624861 CAGTCATCATGGTAGGCAGAAAC 59.375 47.826 0.00 0.00 0.00 2.78
6762 10646 1.178276 CCTCTAGTGCTCGTCCTTGT 58.822 55.000 0.00 0.00 0.00 3.16
6807 10694 9.586435 CAATTGGGGAATAAAGAAATCAAGTAC 57.414 33.333 0.00 0.00 0.00 2.73
6835 10724 5.042463 TGTAACAGAAACAATGTCCTCCA 57.958 39.130 0.00 0.00 0.00 3.86
6923 10812 1.340991 TGGCAGTGGAAATAAGGGAGC 60.341 52.381 0.00 0.00 0.00 4.70
6948 10837 1.152756 AAGGCCACCCAACTGTGAC 60.153 57.895 5.01 0.00 38.55 3.67
7119 11010 4.402155 TGCAAATCTGGTGAACAAAAGACT 59.598 37.500 0.00 0.00 0.00 3.24
7172 11063 3.156293 AGCAAGGCATGTTATGTCAACA 58.844 40.909 0.00 0.00 37.34 3.33
7241 11204 8.939929 CACATAATGATATAAGAACAGCGGAAT 58.060 33.333 0.00 0.00 0.00 3.01
7259 11222 4.577693 ACCAATAGCAGCAGACACATAATG 59.422 41.667 0.00 0.00 0.00 1.90
7374 11339 6.602803 TGGCAAATAATAAAGATCTGCAGACA 59.397 34.615 20.97 3.34 0.00 3.41
7401 11451 5.883673 TCAAACATAGGTATGCAGTTAACCC 59.116 40.000 0.88 0.00 37.19 4.11
7598 11654 2.805099 GCTGCAGATTTTATCTCCTCCG 59.195 50.000 20.43 0.00 37.58 4.63
7599 11655 3.813443 TGCTGCAGATTTTATCTCCTCC 58.187 45.455 20.43 0.00 37.58 4.30
8080 12139 9.950680 CATTCCTACAAAATTATACGAAATGCT 57.049 29.630 0.00 0.00 0.00 3.79
8168 12227 0.181587 TCTTTCCAGGCCGTTCAACA 59.818 50.000 0.00 0.00 0.00 3.33
8273 12333 6.890293 AGGAAGATTGGTTAGTAAGGATGTC 58.110 40.000 0.00 0.00 0.00 3.06
8433 12497 2.299297 AGTCTGGTCGTACAAAAGAGGG 59.701 50.000 0.00 0.00 0.00 4.30
9149 13215 0.179076 CATGTAGCACCGCCAGATCA 60.179 55.000 0.00 0.00 0.00 2.92
9150 13216 1.502163 GCATGTAGCACCGCCAGATC 61.502 60.000 0.00 0.00 44.79 2.75
9151 13217 1.524621 GCATGTAGCACCGCCAGAT 60.525 57.895 0.00 0.00 44.79 2.90
9152 13218 2.125147 GCATGTAGCACCGCCAGA 60.125 61.111 0.00 0.00 44.79 3.86


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

AutoCloner maintained by Alex Coulton.