Multiple sequence alignment - TraesCS3B01G238900

Loading Multiple Alignment...

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 TraesCS3B01G238900 chr3B 100.000 2899 0 0 1 2899 376501876 376504774 0.000000e+00 5354
1 TraesCS3B01G238900 chr3B 90.591 1371 123 6 149 1514 40495001 40496370 0.000000e+00 1812
2 TraesCS3B01G238900 chr3B 90.057 1408 127 11 149 1547 115675888 115674485 0.000000e+00 1812
3 TraesCS3B01G238900 chr3B 86.961 951 86 26 1954 2899 453570074 453569157 0.000000e+00 1035
4 TraesCS3B01G238900 chr4B 92.725 1402 86 5 149 1547 155757504 155758892 0.000000e+00 2010
5 TraesCS3B01G238900 chr4B 89.668 1297 99 17 1606 2899 155758895 155760159 0.000000e+00 1620
6 TraesCS3B01G238900 chr4B 88.812 1305 117 18 1606 2899 595412282 595413568 0.000000e+00 1574
7 TraesCS3B01G238900 chr4B 85.953 1196 130 28 1722 2899 451474946 451476121 0.000000e+00 1243
8 TraesCS3B01G238900 chr4B 87.020 1094 115 19 1812 2899 503289835 503288763 0.000000e+00 1208
9 TraesCS3B01G238900 chrUn 91.026 1404 119 7 149 1547 79020275 79018874 0.000000e+00 1888
10 TraesCS3B01G238900 chrUn 89.530 1404 141 6 149 1547 41660889 41662291 0.000000e+00 1773
11 TraesCS3B01G238900 chrUn 98.333 60 1 0 1546 1605 246699231 246699172 3.950000e-19 106
12 TraesCS3B01G238900 chr1B 90.754 1406 123 7 146 1547 149476467 149475065 0.000000e+00 1869
13 TraesCS3B01G238900 chr1B 90.979 1308 92 16 1606 2899 566776560 566775265 0.000000e+00 1738
14 TraesCS3B01G238900 chr1B 86.055 1298 130 34 1610 2899 346596052 346597306 0.000000e+00 1347
15 TraesCS3B01G238900 chr1B 98.333 60 1 0 1546 1605 49787160 49787101 3.950000e-19 106
16 TraesCS3B01G238900 chr1B 98.333 60 1 0 1546 1605 49815595 49815654 3.950000e-19 106
17 TraesCS3B01G238900 chr6B 91.088 1369 113 8 149 1514 105723281 105724643 0.000000e+00 1844
18 TraesCS3B01G238900 chr6B 88.276 1305 127 19 1610 2899 440009122 440010415 0.000000e+00 1539
19 TraesCS3B01G238900 chr6B 89.016 1220 117 10 1687 2899 272297144 272295935 0.000000e+00 1495
20 TraesCS3B01G238900 chr2B 89.372 1402 139 7 149 1547 298275750 298277144 0.000000e+00 1755
21 TraesCS3B01G238900 chr7B 88.730 1402 151 5 149 1547 476088097 476086700 0.000000e+00 1707
22 TraesCS3B01G238900 chr7D 88.659 1305 111 24 1609 2899 281329506 281328225 0.000000e+00 1555
23 TraesCS3B01G238900 chr7D 96.000 150 5 1 1 150 592113251 592113103 2.890000e-60 243
24 TraesCS3B01G238900 chr7D 95.395 152 6 1 1 152 428043839 428043689 1.040000e-59 241
25 TraesCS3B01G238900 chr4D 90.008 1181 77 23 1606 2776 358036848 358035699 0.000000e+00 1489
26 TraesCS3B01G238900 chr4D 96.053 152 4 2 1 151 95809708 95809858 2.230000e-61 246
27 TraesCS3B01G238900 chr4D 98.333 60 1 0 1546 1605 241247367 241247426 3.950000e-19 106
28 TraesCS3B01G238900 chr2D 87.203 1305 113 28 1606 2898 181665687 181664425 0.000000e+00 1435
29 TraesCS3B01G238900 chr2D 86.687 1307 112 36 1606 2899 209708144 209706887 0.000000e+00 1393
30 TraesCS3B01G238900 chr5B 90.995 955 65 16 1954 2899 586882725 586883667 0.000000e+00 1267
31 TraesCS3B01G238900 chr5B 98.333 60 1 0 1546 1605 695875928 695875869 3.950000e-19 106
32 TraesCS3B01G238900 chr6A 84.158 1193 139 34 1722 2899 509870083 509871240 0.000000e+00 1110
33 TraesCS3B01G238900 chr6A 97.241 145 4 0 1 145 473643007 473642863 2.230000e-61 246
34 TraesCS3B01G238900 chr4A 83.863 1196 159 25 1721 2899 113199403 113200581 0.000000e+00 1109
35 TraesCS3B01G238900 chr1D 83.183 1219 152 34 1712 2899 288163524 288164720 0.000000e+00 1066
36 TraesCS3B01G238900 chr1D 95.513 156 5 1 1 154 350277711 350277556 6.200000e-62 248
37 TraesCS3B01G238900 chr7A 80.171 1286 181 44 1650 2898 404878703 404877455 0.000000e+00 894
38 TraesCS3B01G238900 chr7A 93.373 166 7 4 1 164 78315945 78316108 2.890000e-60 243
39 TraesCS3B01G238900 chr3D 97.241 145 4 0 1 145 431705657 431705801 2.230000e-61 246
40 TraesCS3B01G238900 chr3D 95.425 153 7 0 1 153 576231508 576231356 8.020000e-61 244
41 TraesCS3B01G238900 chr3D 98.333 60 1 0 1546 1605 202626457 202626398 3.950000e-19 106
42 TraesCS3B01G238900 chr3D 98.333 60 1 0 1546 1605 498442838 498442897 3.950000e-19 106
43 TraesCS3B01G238900 chr5D 96.026 151 5 1 1 150 492714694 492714844 8.020000e-61 244
44 TraesCS3B01G238900 chr6D 98.333 60 1 0 1546 1605 370008462 370008403 3.950000e-19 106
45 TraesCS3B01G238900 chr6D 98.333 60 1 0 1546 1605 430467750 430467691 3.950000e-19 106


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 TraesCS3B01G238900 chr3B 376501876 376504774 2898 False 5354 5354 100.0000 1 2899 1 chr3B.!!$F2 2898
1 TraesCS3B01G238900 chr3B 40495001 40496370 1369 False 1812 1812 90.5910 149 1514 1 chr3B.!!$F1 1365
2 TraesCS3B01G238900 chr3B 115674485 115675888 1403 True 1812 1812 90.0570 149 1547 1 chr3B.!!$R1 1398
3 TraesCS3B01G238900 chr3B 453569157 453570074 917 True 1035 1035 86.9610 1954 2899 1 chr3B.!!$R2 945
4 TraesCS3B01G238900 chr4B 155757504 155760159 2655 False 1815 2010 91.1965 149 2899 2 chr4B.!!$F3 2750
5 TraesCS3B01G238900 chr4B 595412282 595413568 1286 False 1574 1574 88.8120 1606 2899 1 chr4B.!!$F2 1293
6 TraesCS3B01G238900 chr4B 451474946 451476121 1175 False 1243 1243 85.9530 1722 2899 1 chr4B.!!$F1 1177
7 TraesCS3B01G238900 chr4B 503288763 503289835 1072 True 1208 1208 87.0200 1812 2899 1 chr4B.!!$R1 1087
8 TraesCS3B01G238900 chrUn 79018874 79020275 1401 True 1888 1888 91.0260 149 1547 1 chrUn.!!$R1 1398
9 TraesCS3B01G238900 chrUn 41660889 41662291 1402 False 1773 1773 89.5300 149 1547 1 chrUn.!!$F1 1398
10 TraesCS3B01G238900 chr1B 149475065 149476467 1402 True 1869 1869 90.7540 146 1547 1 chr1B.!!$R2 1401
11 TraesCS3B01G238900 chr1B 566775265 566776560 1295 True 1738 1738 90.9790 1606 2899 1 chr1B.!!$R3 1293
12 TraesCS3B01G238900 chr1B 346596052 346597306 1254 False 1347 1347 86.0550 1610 2899 1 chr1B.!!$F2 1289
13 TraesCS3B01G238900 chr6B 105723281 105724643 1362 False 1844 1844 91.0880 149 1514 1 chr6B.!!$F1 1365
14 TraesCS3B01G238900 chr6B 440009122 440010415 1293 False 1539 1539 88.2760 1610 2899 1 chr6B.!!$F2 1289
15 TraesCS3B01G238900 chr6B 272295935 272297144 1209 True 1495 1495 89.0160 1687 2899 1 chr6B.!!$R1 1212
16 TraesCS3B01G238900 chr2B 298275750 298277144 1394 False 1755 1755 89.3720 149 1547 1 chr2B.!!$F1 1398
17 TraesCS3B01G238900 chr7B 476086700 476088097 1397 True 1707 1707 88.7300 149 1547 1 chr7B.!!$R1 1398
18 TraesCS3B01G238900 chr7D 281328225 281329506 1281 True 1555 1555 88.6590 1609 2899 1 chr7D.!!$R1 1290
19 TraesCS3B01G238900 chr4D 358035699 358036848 1149 True 1489 1489 90.0080 1606 2776 1 chr4D.!!$R1 1170
20 TraesCS3B01G238900 chr2D 181664425 181665687 1262 True 1435 1435 87.2030 1606 2898 1 chr2D.!!$R1 1292
21 TraesCS3B01G238900 chr2D 209706887 209708144 1257 True 1393 1393 86.6870 1606 2899 1 chr2D.!!$R2 1293
22 TraesCS3B01G238900 chr5B 586882725 586883667 942 False 1267 1267 90.9950 1954 2899 1 chr5B.!!$F1 945
23 TraesCS3B01G238900 chr6A 509870083 509871240 1157 False 1110 1110 84.1580 1722 2899 1 chr6A.!!$F1 1177
24 TraesCS3B01G238900 chr4A 113199403 113200581 1178 False 1109 1109 83.8630 1721 2899 1 chr4A.!!$F1 1178
25 TraesCS3B01G238900 chr1D 288163524 288164720 1196 False 1066 1066 83.1830 1712 2899 1 chr1D.!!$F1 1187
26 TraesCS3B01G238900 chr7A 404877455 404878703 1248 True 894 894 80.1710 1650 2898 1 chr7A.!!$R1 1248

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
40 41 0.179222 GTGCTAACGCTTCCGCTTTC 60.179 55.0 0.00 0.0 38.22 2.62 F
73 74 0.404812 ACGTAGACACACTCTCCCCT 59.595 55.0 0.00 0.0 0.00 4.79 F
109 110 0.736636 ACCATGATCTTGCATGTGCG 59.263 50.0 3.07 0.0 43.16 5.34 F
545 553 0.753111 GGATTCCAAGGCCATTCGCT 60.753 55.0 5.01 0.0 37.74 4.93 F
898 906 0.885879 ATGTCATGTGCAAGTGCCTG 59.114 50.0 0.00 0.0 41.18 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1489 1498 0.609131 ATGCCACTAACAGGGTGTGC 60.609 55.000 0.0 0.0 34.18 4.57 R
1583 1592 0.620556 AGCCATTCTCACAACGGGAT 59.379 50.000 0.0 0.0 0.00 3.85 R
1584 1593 1.207089 CTAGCCATTCTCACAACGGGA 59.793 52.381 0.0 0.0 0.00 5.14 R
1586 1595 2.093973 ACTCTAGCCATTCTCACAACGG 60.094 50.000 0.0 0.0 0.00 4.44 R
2516 2589 2.487934 CGATCCAGGGAACATGACATC 58.512 52.381 0.0 0.0 0.00 3.06 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 2.273370 ACGACTACATCAATCGCGTT 57.727 45.000 5.77 0.00 39.47 4.84
21 22 1.917955 ACGACTACATCAATCGCGTTG 59.082 47.619 5.77 10.48 39.47 4.10
22 23 1.917955 CGACTACATCAATCGCGTTGT 59.082 47.619 5.77 6.34 38.95 3.32
23 24 2.284457 CGACTACATCAATCGCGTTGTG 60.284 50.000 5.77 12.50 38.95 3.33
24 25 1.393539 ACTACATCAATCGCGTTGTGC 59.606 47.619 5.77 0.00 38.95 4.57
25 26 1.660607 CTACATCAATCGCGTTGTGCT 59.339 47.619 5.77 0.00 43.27 4.40
26 27 1.720805 ACATCAATCGCGTTGTGCTA 58.279 45.000 5.77 0.00 43.27 3.49
27 28 2.073056 ACATCAATCGCGTTGTGCTAA 58.927 42.857 5.77 0.00 43.27 3.09
28 29 2.159707 ACATCAATCGCGTTGTGCTAAC 60.160 45.455 5.77 0.00 43.27 2.34
29 30 0.436913 TCAATCGCGTTGTGCTAACG 59.563 50.000 18.25 18.25 45.56 3.18
35 36 1.129809 CGTTGTGCTAACGCTTCCG 59.870 57.895 12.46 0.00 36.82 4.30
36 37 1.154469 GTTGTGCTAACGCTTCCGC 60.154 57.895 0.00 0.00 38.22 5.54
37 38 1.301401 TTGTGCTAACGCTTCCGCT 60.301 52.632 0.00 0.00 38.22 5.52
38 39 0.882927 TTGTGCTAACGCTTCCGCTT 60.883 50.000 0.00 0.00 38.22 4.68
39 40 0.882927 TGTGCTAACGCTTCCGCTTT 60.883 50.000 0.00 0.00 38.22 3.51
40 41 0.179222 GTGCTAACGCTTCCGCTTTC 60.179 55.000 0.00 0.00 38.22 2.62
41 42 1.058903 GCTAACGCTTCCGCTTTCG 59.941 57.895 0.00 0.00 38.22 3.46
64 65 2.760634 TACGAGGGTACGTAGACACA 57.239 50.000 0.00 0.00 44.72 3.72
65 66 1.160137 ACGAGGGTACGTAGACACAC 58.840 55.000 0.00 0.00 44.72 3.82
66 67 1.271054 ACGAGGGTACGTAGACACACT 60.271 52.381 0.00 0.00 44.72 3.55
67 68 1.396301 CGAGGGTACGTAGACACACTC 59.604 57.143 8.17 8.17 40.93 3.51
68 69 2.709213 GAGGGTACGTAGACACACTCT 58.291 52.381 10.55 0.00 41.06 3.24
69 70 2.677337 GAGGGTACGTAGACACACTCTC 59.323 54.545 10.55 4.79 41.06 3.20
70 71 1.742268 GGGTACGTAGACACACTCTCC 59.258 57.143 0.00 0.00 0.00 3.71
71 72 1.742268 GGTACGTAGACACACTCTCCC 59.258 57.143 0.00 0.00 0.00 4.30
72 73 1.742268 GTACGTAGACACACTCTCCCC 59.258 57.143 0.00 0.00 0.00 4.81
73 74 0.404812 ACGTAGACACACTCTCCCCT 59.595 55.000 0.00 0.00 0.00 4.79
74 75 1.096416 CGTAGACACACTCTCCCCTC 58.904 60.000 0.00 0.00 0.00 4.30
75 76 1.340211 CGTAGACACACTCTCCCCTCT 60.340 57.143 0.00 0.00 0.00 3.69
76 77 2.371306 GTAGACACACTCTCCCCTCTC 58.629 57.143 0.00 0.00 0.00 3.20
77 78 0.780637 AGACACACTCTCCCCTCTCA 59.219 55.000 0.00 0.00 0.00 3.27
78 79 1.360852 AGACACACTCTCCCCTCTCAT 59.639 52.381 0.00 0.00 0.00 2.90
79 80 2.183679 GACACACTCTCCCCTCTCATT 58.816 52.381 0.00 0.00 0.00 2.57
80 81 1.905215 ACACACTCTCCCCTCTCATTG 59.095 52.381 0.00 0.00 0.00 2.82
81 82 0.908198 ACACTCTCCCCTCTCATTGC 59.092 55.000 0.00 0.00 0.00 3.56
82 83 1.202330 CACTCTCCCCTCTCATTGCT 58.798 55.000 0.00 0.00 0.00 3.91
83 84 2.292521 ACACTCTCCCCTCTCATTGCTA 60.293 50.000 0.00 0.00 0.00 3.49
84 85 2.971330 CACTCTCCCCTCTCATTGCTAT 59.029 50.000 0.00 0.00 0.00 2.97
85 86 2.971330 ACTCTCCCCTCTCATTGCTATG 59.029 50.000 1.30 1.30 0.00 2.23
86 87 1.696336 TCTCCCCTCTCATTGCTATGC 59.304 52.381 3.00 0.00 0.00 3.14
87 88 1.419012 CTCCCCTCTCATTGCTATGCA 59.581 52.381 3.00 0.00 36.47 3.96
88 89 2.040012 CTCCCCTCTCATTGCTATGCAT 59.960 50.000 3.79 3.79 38.76 3.96
89 90 2.039480 TCCCCTCTCATTGCTATGCATC 59.961 50.000 0.19 0.00 38.76 3.91
90 91 2.224695 CCCCTCTCATTGCTATGCATCA 60.225 50.000 0.19 0.00 38.76 3.07
91 92 2.812591 CCCTCTCATTGCTATGCATCAC 59.187 50.000 0.19 0.00 38.76 3.06
92 93 2.812591 CCTCTCATTGCTATGCATCACC 59.187 50.000 0.19 0.00 38.76 4.02
93 94 3.473625 CTCTCATTGCTATGCATCACCA 58.526 45.455 0.19 0.00 38.76 4.17
94 95 4.072839 CTCTCATTGCTATGCATCACCAT 58.927 43.478 0.19 0.00 38.76 3.55
95 96 3.818773 TCTCATTGCTATGCATCACCATG 59.181 43.478 0.19 4.57 38.76 3.66
96 97 3.818773 CTCATTGCTATGCATCACCATGA 59.181 43.478 0.19 8.77 38.76 3.07
97 98 4.403734 TCATTGCTATGCATCACCATGAT 58.596 39.130 0.19 0.00 38.76 2.45
98 99 4.457949 TCATTGCTATGCATCACCATGATC 59.542 41.667 0.19 0.00 38.76 2.92
99 100 3.782656 TGCTATGCATCACCATGATCT 57.217 42.857 0.19 0.00 34.28 2.75
100 101 4.094830 TGCTATGCATCACCATGATCTT 57.905 40.909 0.19 0.00 34.28 2.40
101 102 3.818773 TGCTATGCATCACCATGATCTTG 59.181 43.478 0.19 1.60 34.28 3.02
102 103 3.366070 GCTATGCATCACCATGATCTTGC 60.366 47.826 0.19 0.00 34.28 4.01
103 104 2.131776 TGCATCACCATGATCTTGCA 57.868 45.000 3.07 8.61 37.51 4.08
104 105 2.661718 TGCATCACCATGATCTTGCAT 58.338 42.857 3.07 0.00 35.67 3.96
105 106 2.360801 TGCATCACCATGATCTTGCATG 59.639 45.455 3.07 0.00 44.05 4.06
106 107 2.361119 GCATCACCATGATCTTGCATGT 59.639 45.455 3.07 0.00 43.16 3.21
107 108 3.795488 GCATCACCATGATCTTGCATGTG 60.795 47.826 3.07 6.61 43.16 3.21
108 109 1.746787 TCACCATGATCTTGCATGTGC 59.253 47.619 3.07 0.00 43.16 4.57
109 110 0.736636 ACCATGATCTTGCATGTGCG 59.263 50.000 3.07 0.00 43.16 5.34
110 111 0.736636 CCATGATCTTGCATGTGCGT 59.263 50.000 3.07 0.00 43.16 5.24
111 112 1.941975 CCATGATCTTGCATGTGCGTA 59.058 47.619 3.07 0.00 43.16 4.42
112 113 2.032290 CCATGATCTTGCATGTGCGTAG 60.032 50.000 3.07 1.03 43.16 3.51
113 114 1.655484 TGATCTTGCATGTGCGTAGG 58.345 50.000 0.01 0.00 45.83 3.18
114 115 1.206849 TGATCTTGCATGTGCGTAGGA 59.793 47.619 0.01 0.00 45.83 2.94
115 116 2.158914 TGATCTTGCATGTGCGTAGGAT 60.159 45.455 0.01 1.84 45.83 3.24
116 117 2.401583 TCTTGCATGTGCGTAGGATT 57.598 45.000 0.01 0.00 45.83 3.01
117 118 2.710377 TCTTGCATGTGCGTAGGATTT 58.290 42.857 0.01 0.00 45.83 2.17
118 119 3.081061 TCTTGCATGTGCGTAGGATTTT 58.919 40.909 0.01 0.00 45.83 1.82
119 120 3.505680 TCTTGCATGTGCGTAGGATTTTT 59.494 39.130 0.01 0.00 45.83 1.94
140 141 4.769859 TTTTGCAATTACTACGTTCCCC 57.230 40.909 0.00 0.00 0.00 4.81
141 142 3.420300 TTGCAATTACTACGTTCCCCA 57.580 42.857 0.00 0.00 0.00 4.96
142 143 3.420300 TGCAATTACTACGTTCCCCAA 57.580 42.857 0.00 0.00 0.00 4.12
143 144 3.075884 TGCAATTACTACGTTCCCCAAC 58.924 45.455 0.00 0.00 0.00 3.77
144 145 3.075884 GCAATTACTACGTTCCCCAACA 58.924 45.455 0.00 0.00 32.14 3.33
145 146 3.120095 GCAATTACTACGTTCCCCAACAC 60.120 47.826 0.00 0.00 32.14 3.32
146 147 4.066490 CAATTACTACGTTCCCCAACACA 58.934 43.478 0.00 0.00 32.14 3.72
147 148 4.563140 ATTACTACGTTCCCCAACACAT 57.437 40.909 0.00 0.00 32.14 3.21
198 200 3.654414 AGCGATTGTGTTAGGCTATAGC 58.346 45.455 16.78 16.78 41.14 2.97
224 228 8.611757 CCTAGGTTTTTCTTGTTTTCATTTTGG 58.388 33.333 0.00 0.00 0.00 3.28
233 237 7.327214 TCTTGTTTTCATTTTGGGCCATATAC 58.673 34.615 7.26 0.17 0.00 1.47
266 270 3.850173 TCTCTAGCCATTAACCCCTGTTT 59.150 43.478 0.00 0.00 35.87 2.83
322 330 2.158813 GCGGGTTGGATTATCCTCTCAA 60.159 50.000 12.91 0.00 37.46 3.02
531 539 5.827797 TCCTACTTGCCATATTTGTGGATTC 59.172 40.000 0.00 0.00 42.02 2.52
545 553 0.753111 GGATTCCAAGGCCATTCGCT 60.753 55.000 5.01 0.00 37.74 4.93
546 554 1.106285 GATTCCAAGGCCATTCGCTT 58.894 50.000 5.01 0.00 37.74 4.68
706 714 3.244215 TGAGATCTCACCGTTTGCTTCTT 60.244 43.478 21.67 0.00 34.14 2.52
779 787 7.928167 TGCACCACAACAATTTTATTCACATTA 59.072 29.630 0.00 0.00 0.00 1.90
827 835 6.248433 AGATGTGTCCAATGGAGTTAAATGT 58.752 36.000 0.27 0.00 29.39 2.71
881 889 4.880120 ACCTGATGAGTCATTAGTGCAATG 59.120 41.667 20.14 8.89 44.69 2.82
897 905 1.271379 CAATGTCATGTGCAAGTGCCT 59.729 47.619 0.00 0.00 41.18 4.75
898 906 0.885879 ATGTCATGTGCAAGTGCCTG 59.114 50.000 0.00 0.00 41.18 4.85
909 917 2.223433 GCAAGTGCCTGCATAAGATGAC 60.223 50.000 0.00 0.00 42.17 3.06
1089 1097 5.877012 CACTGGTAGCACTATTTCTTCACAT 59.123 40.000 0.00 0.00 0.00 3.21
1191 1199 2.698855 GCCTTGAGCAAGAGATACCA 57.301 50.000 11.61 0.00 42.97 3.25
1194 1202 3.683847 GCCTTGAGCAAGAGATACCACAT 60.684 47.826 11.61 0.00 42.97 3.21
1236 1244 6.171921 AGAAGACAAGGAACAAGATGATCAG 58.828 40.000 0.09 0.00 0.00 2.90
1246 1254 2.328819 AGATGATCAGGAGCTGCAAC 57.671 50.000 8.35 0.00 0.00 4.17
1267 1275 4.792068 ACTCCCAAGTGATCAAGTTGAAA 58.208 39.130 10.14 0.00 41.10 2.69
1372 1380 5.469084 GTCATACATGAGCATGATGTGTCAT 59.531 40.000 16.70 6.60 44.51 3.06
1462 1471 5.192927 TGCCATCACTTAAGGTAGATTTGG 58.807 41.667 7.53 8.34 0.00 3.28
1489 1498 6.387041 ACTATTTGCTTGGACATGATCATG 57.613 37.500 29.95 29.95 44.15 3.07
1547 1556 4.038763 TGATCACAGTTACTTTCCTCGTGT 59.961 41.667 0.00 0.00 0.00 4.49
1549 1558 4.116961 TCACAGTTACTTTCCTCGTGTTG 58.883 43.478 0.00 0.00 0.00 3.33
1550 1559 3.869246 CACAGTTACTTTCCTCGTGTTGT 59.131 43.478 0.00 0.00 0.00 3.32
1551 1560 5.045215 CACAGTTACTTTCCTCGTGTTGTA 58.955 41.667 0.00 0.00 0.00 2.41
1552 1561 5.521010 CACAGTTACTTTCCTCGTGTTGTAA 59.479 40.000 0.00 0.00 0.00 2.41
1553 1562 6.202188 CACAGTTACTTTCCTCGTGTTGTAAT 59.798 38.462 0.00 0.00 0.00 1.89
1554 1563 6.423001 ACAGTTACTTTCCTCGTGTTGTAATC 59.577 38.462 0.00 0.00 0.00 1.75
1555 1564 6.645415 CAGTTACTTTCCTCGTGTTGTAATCT 59.355 38.462 0.00 0.00 0.00 2.40
1556 1565 6.867293 AGTTACTTTCCTCGTGTTGTAATCTC 59.133 38.462 0.00 0.00 0.00 2.75
1557 1566 5.470047 ACTTTCCTCGTGTTGTAATCTCT 57.530 39.130 0.00 0.00 0.00 3.10
1558 1567 5.855045 ACTTTCCTCGTGTTGTAATCTCTT 58.145 37.500 0.00 0.00 0.00 2.85
1559 1568 5.927115 ACTTTCCTCGTGTTGTAATCTCTTC 59.073 40.000 0.00 0.00 0.00 2.87
1560 1569 5.723672 TTCCTCGTGTTGTAATCTCTTCT 57.276 39.130 0.00 0.00 0.00 2.85
1561 1570 5.312120 TCCTCGTGTTGTAATCTCTTCTC 57.688 43.478 0.00 0.00 0.00 2.87
1562 1571 4.765339 TCCTCGTGTTGTAATCTCTTCTCA 59.235 41.667 0.00 0.00 0.00 3.27
1563 1572 5.419155 TCCTCGTGTTGTAATCTCTTCTCAT 59.581 40.000 0.00 0.00 0.00 2.90
1564 1573 6.071334 TCCTCGTGTTGTAATCTCTTCTCATT 60.071 38.462 0.00 0.00 0.00 2.57
1565 1574 6.035435 CCTCGTGTTGTAATCTCTTCTCATTG 59.965 42.308 0.00 0.00 0.00 2.82
1566 1575 6.455647 TCGTGTTGTAATCTCTTCTCATTGT 58.544 36.000 0.00 0.00 0.00 2.71
1567 1576 6.586463 TCGTGTTGTAATCTCTTCTCATTGTC 59.414 38.462 0.00 0.00 0.00 3.18
1568 1577 6.587990 CGTGTTGTAATCTCTTCTCATTGTCT 59.412 38.462 0.00 0.00 0.00 3.41
1569 1578 7.116948 CGTGTTGTAATCTCTTCTCATTGTCTT 59.883 37.037 0.00 0.00 0.00 3.01
1570 1579 8.778358 GTGTTGTAATCTCTTCTCATTGTCTTT 58.222 33.333 0.00 0.00 0.00 2.52
1571 1580 8.777413 TGTTGTAATCTCTTCTCATTGTCTTTG 58.223 33.333 0.00 0.00 0.00 2.77
1572 1581 8.778358 GTTGTAATCTCTTCTCATTGTCTTTGT 58.222 33.333 0.00 0.00 0.00 2.83
1573 1582 8.908786 TGTAATCTCTTCTCATTGTCTTTGTT 57.091 30.769 0.00 0.00 0.00 2.83
1574 1583 8.993121 TGTAATCTCTTCTCATTGTCTTTGTTC 58.007 33.333 0.00 0.00 0.00 3.18
1575 1584 6.718454 ATCTCTTCTCATTGTCTTTGTTCG 57.282 37.500 0.00 0.00 0.00 3.95
1576 1585 4.449068 TCTCTTCTCATTGTCTTTGTTCGC 59.551 41.667 0.00 0.00 0.00 4.70
1577 1586 4.380531 TCTTCTCATTGTCTTTGTTCGCT 58.619 39.130 0.00 0.00 0.00 4.93
1578 1587 4.816385 TCTTCTCATTGTCTTTGTTCGCTT 59.184 37.500 0.00 0.00 0.00 4.68
1579 1588 5.296780 TCTTCTCATTGTCTTTGTTCGCTTT 59.703 36.000 0.00 0.00 0.00 3.51
1580 1589 6.481976 TCTTCTCATTGTCTTTGTTCGCTTTA 59.518 34.615 0.00 0.00 0.00 1.85
1581 1590 6.801539 TCTCATTGTCTTTGTTCGCTTTAT 57.198 33.333 0.00 0.00 0.00 1.40
1582 1591 7.202016 TCTCATTGTCTTTGTTCGCTTTATT 57.798 32.000 0.00 0.00 0.00 1.40
1583 1592 8.317891 TCTCATTGTCTTTGTTCGCTTTATTA 57.682 30.769 0.00 0.00 0.00 0.98
1584 1593 8.946085 TCTCATTGTCTTTGTTCGCTTTATTAT 58.054 29.630 0.00 0.00 0.00 1.28
1585 1594 9.214953 CTCATTGTCTTTGTTCGCTTTATTATC 57.785 33.333 0.00 0.00 0.00 1.75
1586 1595 8.181573 TCATTGTCTTTGTTCGCTTTATTATCC 58.818 33.333 0.00 0.00 0.00 2.59
1587 1596 6.431198 TGTCTTTGTTCGCTTTATTATCCC 57.569 37.500 0.00 0.00 0.00 3.85
1588 1597 5.064198 TGTCTTTGTTCGCTTTATTATCCCG 59.936 40.000 0.00 0.00 0.00 5.14
1589 1598 5.064325 GTCTTTGTTCGCTTTATTATCCCGT 59.936 40.000 0.00 0.00 0.00 5.28
1590 1599 5.644636 TCTTTGTTCGCTTTATTATCCCGTT 59.355 36.000 0.00 0.00 0.00 4.44
1591 1600 4.868450 TGTTCGCTTTATTATCCCGTTG 57.132 40.909 0.00 0.00 0.00 4.10
1592 1601 4.255301 TGTTCGCTTTATTATCCCGTTGT 58.745 39.130 0.00 0.00 0.00 3.32
1593 1602 4.093703 TGTTCGCTTTATTATCCCGTTGTG 59.906 41.667 0.00 0.00 0.00 3.33
1594 1603 4.126208 TCGCTTTATTATCCCGTTGTGA 57.874 40.909 0.00 0.00 0.00 3.58
1595 1604 4.116961 TCGCTTTATTATCCCGTTGTGAG 58.883 43.478 0.00 0.00 0.00 3.51
1596 1605 4.116961 CGCTTTATTATCCCGTTGTGAGA 58.883 43.478 0.00 0.00 0.00 3.27
1597 1606 4.569162 CGCTTTATTATCCCGTTGTGAGAA 59.431 41.667 0.00 0.00 0.00 2.87
1598 1607 5.236478 CGCTTTATTATCCCGTTGTGAGAAT 59.764 40.000 0.00 0.00 0.00 2.40
1599 1608 6.430451 GCTTTATTATCCCGTTGTGAGAATG 58.570 40.000 0.00 0.00 0.00 2.67
1600 1609 6.513393 GCTTTATTATCCCGTTGTGAGAATGG 60.513 42.308 0.00 0.00 0.00 3.16
1601 1610 2.325583 TATCCCGTTGTGAGAATGGC 57.674 50.000 0.00 0.00 0.00 4.40
1602 1611 0.620556 ATCCCGTTGTGAGAATGGCT 59.379 50.000 0.00 0.00 0.00 4.75
1603 1612 1.271856 TCCCGTTGTGAGAATGGCTA 58.728 50.000 0.00 0.00 0.00 3.93
1604 1613 1.207089 TCCCGTTGTGAGAATGGCTAG 59.793 52.381 0.00 0.00 0.00 3.42
1692 1701 5.222079 TCATGTTAGTGTTCACCTTGCTA 57.778 39.130 0.00 0.00 0.00 3.49
1709 1718 7.227512 CACCTTGCTAATTTCTACCATCCTAAG 59.772 40.741 0.00 0.00 0.00 2.18
1928 1943 1.619654 CAAGGGGCACACATGAAGAA 58.380 50.000 0.00 0.00 0.00 2.52
1929 1944 1.542915 CAAGGGGCACACATGAAGAAG 59.457 52.381 0.00 0.00 0.00 2.85
1930 1945 1.067295 AGGGGCACACATGAAGAAGA 58.933 50.000 0.00 0.00 0.00 2.87
1952 1967 5.046014 AGAGTGAAGATGGAGTATGCTTGTT 60.046 40.000 0.00 0.00 0.00 2.83
2041 2089 2.170166 GCTGTTTCATGACCCATTCCA 58.830 47.619 0.00 0.00 0.00 3.53
2126 2184 4.436113 AAATGTTGCCCCACTGATTTTT 57.564 36.364 0.00 0.00 0.00 1.94
2210 2272 5.528690 GTGATCTACATATTGCTTGCTTGGA 59.471 40.000 0.00 0.00 0.00 3.53
2233 2296 9.905713 TGGATGAAATTAGTGAAAGCTATTAGT 57.094 29.630 0.00 0.00 0.00 2.24
2303 2368 7.915293 TCATTTTCTGCTTTTACCTCGATAA 57.085 32.000 0.00 0.00 0.00 1.75
2336 2401 8.621532 TCATTAAGTGTTAGATGCTGAGTTTT 57.378 30.769 0.00 0.00 0.00 2.43
2399 2465 7.177568 CACTATGGACTAGTATGCTATGTTCCT 59.822 40.741 0.00 1.02 38.68 3.36
2867 2975 1.621992 TAGGAACCATTTGGCGCAAA 58.378 45.000 10.83 0.00 39.32 3.68
2868 2976 0.975887 AGGAACCATTTGGCGCAAAT 59.024 45.000 10.83 10.73 43.71 2.32
2870 2978 2.564947 AGGAACCATTTGGCGCAAATAA 59.435 40.909 10.83 0.00 41.40 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.103007 CAACGCGATTGATGTAGTCGTA 58.897 45.455 15.93 0.00 41.23 3.43
2 3 1.917955 ACAACGCGATTGATGTAGTCG 59.082 47.619 15.93 0.00 41.23 4.18
3 4 2.534939 GCACAACGCGATTGATGTAGTC 60.535 50.000 15.93 0.00 41.23 2.59
4 5 1.393539 GCACAACGCGATTGATGTAGT 59.606 47.619 15.93 0.00 41.23 2.73
5 6 2.077155 GCACAACGCGATTGATGTAG 57.923 50.000 15.93 6.09 41.23 2.74
34 35 1.226603 CCCTCGTAGACCGAAAGCG 60.227 63.158 0.00 0.00 46.75 4.68
35 36 1.098050 TACCCTCGTAGACCGAAAGC 58.902 55.000 0.00 0.00 46.75 3.51
36 37 1.063174 CGTACCCTCGTAGACCGAAAG 59.937 57.143 0.00 0.00 46.75 2.62
37 38 1.086696 CGTACCCTCGTAGACCGAAA 58.913 55.000 0.00 0.00 46.75 3.46
38 39 0.036388 ACGTACCCTCGTAGACCGAA 60.036 55.000 0.00 0.00 46.75 4.30
39 40 0.821517 TACGTACCCTCGTAGACCGA 59.178 55.000 0.00 0.00 45.00 4.69
40 41 3.362581 TACGTACCCTCGTAGACCG 57.637 57.895 0.00 0.00 43.80 4.79
45 46 2.028112 AGTGTGTCTACGTACCCTCGTA 60.028 50.000 0.00 0.00 43.80 3.43
46 47 1.160137 GTGTGTCTACGTACCCTCGT 58.840 55.000 0.00 0.00 45.97 4.18
47 48 1.396301 GAGTGTGTCTACGTACCCTCG 59.604 57.143 0.00 0.00 0.00 4.63
48 49 2.677337 GAGAGTGTGTCTACGTACCCTC 59.323 54.545 0.00 0.00 34.71 4.30
49 50 2.617532 GGAGAGTGTGTCTACGTACCCT 60.618 54.545 0.00 0.00 34.71 4.34
50 51 1.742268 GGAGAGTGTGTCTACGTACCC 59.258 57.143 0.00 0.00 34.71 3.69
51 52 1.742268 GGGAGAGTGTGTCTACGTACC 59.258 57.143 0.00 0.00 36.91 3.34
52 53 1.742268 GGGGAGAGTGTGTCTACGTAC 59.258 57.143 0.00 0.00 36.91 3.67
53 54 1.632409 AGGGGAGAGTGTGTCTACGTA 59.368 52.381 0.00 0.00 36.91 3.57
54 55 0.404812 AGGGGAGAGTGTGTCTACGT 59.595 55.000 0.00 0.00 36.91 3.57
55 56 1.096416 GAGGGGAGAGTGTGTCTACG 58.904 60.000 0.00 0.00 36.91 3.51
56 57 2.291024 TGAGAGGGGAGAGTGTGTCTAC 60.291 54.545 0.00 0.00 34.71 2.59
57 58 1.993301 TGAGAGGGGAGAGTGTGTCTA 59.007 52.381 0.00 0.00 34.71 2.59
58 59 0.780637 TGAGAGGGGAGAGTGTGTCT 59.219 55.000 0.00 0.00 38.71 3.41
59 60 1.859302 ATGAGAGGGGAGAGTGTGTC 58.141 55.000 0.00 0.00 0.00 3.67
60 61 1.905215 CAATGAGAGGGGAGAGTGTGT 59.095 52.381 0.00 0.00 0.00 3.72
61 62 1.406614 GCAATGAGAGGGGAGAGTGTG 60.407 57.143 0.00 0.00 0.00 3.82
62 63 0.908198 GCAATGAGAGGGGAGAGTGT 59.092 55.000 0.00 0.00 0.00 3.55
63 64 1.202330 AGCAATGAGAGGGGAGAGTG 58.798 55.000 0.00 0.00 0.00 3.51
64 65 2.856760 TAGCAATGAGAGGGGAGAGT 57.143 50.000 0.00 0.00 0.00 3.24
65 66 2.289569 GCATAGCAATGAGAGGGGAGAG 60.290 54.545 0.00 0.00 34.84 3.20
66 67 1.696336 GCATAGCAATGAGAGGGGAGA 59.304 52.381 0.00 0.00 34.84 3.71
67 68 1.419012 TGCATAGCAATGAGAGGGGAG 59.581 52.381 0.00 0.00 34.76 4.30
68 69 1.510492 TGCATAGCAATGAGAGGGGA 58.490 50.000 0.00 0.00 34.76 4.81
69 70 2.224695 TGATGCATAGCAATGAGAGGGG 60.225 50.000 0.00 0.00 43.62 4.79
70 71 2.812591 GTGATGCATAGCAATGAGAGGG 59.187 50.000 0.00 0.00 43.62 4.30
71 72 2.812591 GGTGATGCATAGCAATGAGAGG 59.187 50.000 0.00 0.00 43.62 3.69
72 73 3.473625 TGGTGATGCATAGCAATGAGAG 58.526 45.455 0.00 0.00 43.62 3.20
73 74 3.564053 TGGTGATGCATAGCAATGAGA 57.436 42.857 0.00 0.00 43.62 3.27
74 75 3.818773 TCATGGTGATGCATAGCAATGAG 59.181 43.478 13.21 5.62 43.62 2.90
75 76 3.822940 TCATGGTGATGCATAGCAATGA 58.177 40.909 13.21 13.21 43.62 2.57
76 77 4.459337 AGATCATGGTGATGCATAGCAATG 59.541 41.667 0.00 5.10 43.62 2.82
77 78 4.663334 AGATCATGGTGATGCATAGCAAT 58.337 39.130 0.00 0.00 43.62 3.56
78 79 4.094830 AGATCATGGTGATGCATAGCAA 57.905 40.909 0.00 0.00 43.62 3.91
79 80 3.782656 AGATCATGGTGATGCATAGCA 57.217 42.857 0.00 4.86 44.86 3.49
80 81 3.366070 GCAAGATCATGGTGATGCATAGC 60.366 47.826 0.00 0.00 37.20 2.97
81 82 3.818773 TGCAAGATCATGGTGATGCATAG 59.181 43.478 10.42 0.00 35.67 2.23
82 83 3.822940 TGCAAGATCATGGTGATGCATA 58.177 40.909 10.42 0.00 35.67 3.14
83 84 2.661718 TGCAAGATCATGGTGATGCAT 58.338 42.857 10.42 0.00 35.67 3.96
84 85 2.131776 TGCAAGATCATGGTGATGCA 57.868 45.000 10.42 10.42 37.51 3.96
85 86 2.361119 ACATGCAAGATCATGGTGATGC 59.639 45.455 5.77 5.77 46.02 3.91
86 87 3.795488 GCACATGCAAGATCATGGTGATG 60.795 47.826 9.18 0.66 46.02 3.07
87 88 2.361119 GCACATGCAAGATCATGGTGAT 59.639 45.455 9.18 0.00 46.02 3.06
88 89 1.746787 GCACATGCAAGATCATGGTGA 59.253 47.619 9.18 0.00 46.02 4.02
89 90 1.533129 CGCACATGCAAGATCATGGTG 60.533 52.381 4.49 1.26 46.02 4.17
90 91 0.736636 CGCACATGCAAGATCATGGT 59.263 50.000 4.49 0.00 46.02 3.55
91 92 0.736636 ACGCACATGCAAGATCATGG 59.263 50.000 4.49 0.00 46.02 3.66
92 93 2.032290 CCTACGCACATGCAAGATCATG 60.032 50.000 4.49 0.00 46.86 3.07
93 94 2.158914 TCCTACGCACATGCAAGATCAT 60.159 45.455 4.49 0.00 42.21 2.45
94 95 1.206849 TCCTACGCACATGCAAGATCA 59.793 47.619 4.49 0.00 42.21 2.92
95 96 1.939974 TCCTACGCACATGCAAGATC 58.060 50.000 4.49 0.00 42.21 2.75
96 97 2.627515 ATCCTACGCACATGCAAGAT 57.372 45.000 4.49 0.00 42.21 2.40
97 98 2.401583 AATCCTACGCACATGCAAGA 57.598 45.000 4.49 0.00 42.21 3.02
98 99 3.492421 AAAATCCTACGCACATGCAAG 57.508 42.857 4.49 0.69 42.21 4.01
99 100 3.932545 AAAAATCCTACGCACATGCAA 57.067 38.095 4.49 0.00 42.21 4.08
118 119 4.583489 TGGGGAACGTAGTAATTGCAAAAA 59.417 37.500 1.71 0.00 45.00 1.94
119 120 4.142790 TGGGGAACGTAGTAATTGCAAAA 58.857 39.130 1.71 0.00 45.00 2.44
120 121 3.752665 TGGGGAACGTAGTAATTGCAAA 58.247 40.909 1.71 0.00 45.00 3.68
121 122 3.420300 TGGGGAACGTAGTAATTGCAA 57.580 42.857 0.00 0.00 45.00 4.08
122 123 3.075884 GTTGGGGAACGTAGTAATTGCA 58.924 45.455 0.00 0.00 45.00 4.08
123 124 3.075884 TGTTGGGGAACGTAGTAATTGC 58.924 45.455 0.00 0.00 45.00 3.56
124 125 4.066490 TGTGTTGGGGAACGTAGTAATTG 58.934 43.478 0.00 0.00 45.00 2.32
125 126 4.354893 TGTGTTGGGGAACGTAGTAATT 57.645 40.909 0.00 0.00 45.00 1.40
126 127 4.563140 ATGTGTTGGGGAACGTAGTAAT 57.437 40.909 0.00 0.00 45.00 1.89
127 128 4.354893 AATGTGTTGGGGAACGTAGTAA 57.645 40.909 0.00 0.00 45.00 2.24
128 129 4.354893 AAATGTGTTGGGGAACGTAGTA 57.645 40.909 0.00 0.00 45.00 1.82
129 130 7.180165 CCAAAAATGTGTTGGGGAACGTAGT 62.180 44.000 0.00 0.00 42.34 2.73
130 131 4.295051 CAAAAATGTGTTGGGGAACGTAG 58.705 43.478 0.00 0.00 0.00 3.51
131 132 3.068307 CCAAAAATGTGTTGGGGAACGTA 59.932 43.478 0.00 0.00 41.64 3.57
132 133 2.159028 CCAAAAATGTGTTGGGGAACGT 60.159 45.455 0.00 0.00 41.64 3.99
133 134 2.478831 CCAAAAATGTGTTGGGGAACG 58.521 47.619 0.00 0.00 41.64 3.95
134 135 2.217750 GCCAAAAATGTGTTGGGGAAC 58.782 47.619 5.41 0.00 44.87 3.62
135 136 2.629336 GCCAAAAATGTGTTGGGGAA 57.371 45.000 5.41 0.00 44.87 3.97
138 139 1.227342 GGCGCCAAAAATGTGTTGGG 61.227 55.000 24.80 0.00 44.87 4.12
140 141 0.873743 ACGGCGCCAAAAATGTGTTG 60.874 50.000 28.98 7.69 0.00 3.33
141 142 0.179097 AACGGCGCCAAAAATGTGTT 60.179 45.000 28.98 16.52 0.00 3.32
142 143 0.873743 CAACGGCGCCAAAAATGTGT 60.874 50.000 28.98 10.68 0.00 3.72
143 144 1.851978 CAACGGCGCCAAAAATGTG 59.148 52.632 28.98 9.93 0.00 3.21
144 145 1.953642 GCAACGGCGCCAAAAATGT 60.954 52.632 28.98 12.36 0.00 2.71
145 146 2.852507 GCAACGGCGCCAAAAATG 59.147 55.556 28.98 17.36 0.00 2.32
198 200 8.611757 CCAAAATGAAAACAAGAAAAACCTAGG 58.388 33.333 7.41 7.41 0.00 3.02
233 237 9.593134 GGTTAATGGCTAGAGATATATCACAAG 57.407 37.037 15.08 9.12 0.00 3.16
296 303 3.436243 AGGATAATCCAACCCGCAAAAA 58.564 40.909 0.00 0.00 39.61 1.94
303 310 6.183360 CCATTTTTGAGAGGATAATCCAACCC 60.183 42.308 0.00 0.00 39.61 4.11
412 420 5.578727 GCCGAGCTAAATCATCTAATCGATT 59.421 40.000 16.15 16.15 33.27 3.34
531 539 2.182537 GCAAGCGAATGGCCTTGG 59.817 61.111 3.32 0.00 45.17 3.61
619 627 7.035004 CACCCATATGAGTAATTGTTTTGGTG 58.965 38.462 3.65 4.55 0.00 4.17
706 714 7.090319 ACCTAAATCCCTGCATATGATTACA 57.910 36.000 6.97 0.00 0.00 2.41
779 787 4.162320 CCTGGTGTTGAGGTACATGAGTAT 59.838 45.833 0.00 0.00 31.84 2.12
827 835 1.422024 TCGGTTGACCAAATGGAGGAA 59.578 47.619 6.42 0.00 38.94 3.36
881 889 1.080974 GCAGGCACTTGCACATGAC 60.081 57.895 0.00 0.00 44.36 3.06
897 905 3.133691 GCCATCGAAGTCATCTTATGCA 58.866 45.455 0.00 0.00 33.64 3.96
898 906 3.133691 TGCCATCGAAGTCATCTTATGC 58.866 45.455 0.00 0.00 33.64 3.14
901 909 5.301805 TGTCTATGCCATCGAAGTCATCTTA 59.698 40.000 0.00 0.00 33.64 2.10
909 917 2.799412 GAGCTTGTCTATGCCATCGAAG 59.201 50.000 0.00 0.00 0.00 3.79
1089 1097 3.520721 TCCCAGAATTGCTCATCTCAAGA 59.479 43.478 0.00 0.00 0.00 3.02
1207 1215 7.509546 TCATCTTGTTCCTTGTCTTCTAGTTT 58.490 34.615 0.00 0.00 0.00 2.66
1246 1254 5.300286 AGTTTTCAACTTGATCACTTGGGAG 59.700 40.000 10.92 1.26 39.04 4.30
1267 1275 7.350382 TCTTCAGGAGTAGTAGATGATGAGTT 58.650 38.462 0.00 0.00 0.00 3.01
1372 1380 5.222027 TGTCATCAAGAGGATTGGGTAAACA 60.222 40.000 0.00 0.00 32.57 2.83
1462 1471 7.315142 TGATCATGTCCAAGCAAATAGTTTTC 58.685 34.615 0.00 0.00 0.00 2.29
1489 1498 0.609131 ATGCCACTAACAGGGTGTGC 60.609 55.000 0.00 0.00 34.18 4.57
1547 1556 8.908786 ACAAAGACAATGAGAAGAGATTACAA 57.091 30.769 0.00 0.00 0.00 2.41
1549 1558 8.165428 CGAACAAAGACAATGAGAAGAGATTAC 58.835 37.037 0.00 0.00 0.00 1.89
1550 1559 7.148573 GCGAACAAAGACAATGAGAAGAGATTA 60.149 37.037 0.00 0.00 0.00 1.75
1551 1560 6.348050 GCGAACAAAGACAATGAGAAGAGATT 60.348 38.462 0.00 0.00 0.00 2.40
1552 1561 5.121454 GCGAACAAAGACAATGAGAAGAGAT 59.879 40.000 0.00 0.00 0.00 2.75
1553 1562 4.449068 GCGAACAAAGACAATGAGAAGAGA 59.551 41.667 0.00 0.00 0.00 3.10
1554 1563 4.450419 AGCGAACAAAGACAATGAGAAGAG 59.550 41.667 0.00 0.00 0.00 2.85
1555 1564 4.380531 AGCGAACAAAGACAATGAGAAGA 58.619 39.130 0.00 0.00 0.00 2.87
1556 1565 4.739046 AGCGAACAAAGACAATGAGAAG 57.261 40.909 0.00 0.00 0.00 2.85
1557 1566 5.499139 AAAGCGAACAAAGACAATGAGAA 57.501 34.783 0.00 0.00 0.00 2.87
1558 1567 6.801539 ATAAAGCGAACAAAGACAATGAGA 57.198 33.333 0.00 0.00 0.00 3.27
1559 1568 9.214953 GATAATAAAGCGAACAAAGACAATGAG 57.785 33.333 0.00 0.00 0.00 2.90
1560 1569 8.181573 GGATAATAAAGCGAACAAAGACAATGA 58.818 33.333 0.00 0.00 0.00 2.57
1561 1570 7.432252 GGGATAATAAAGCGAACAAAGACAATG 59.568 37.037 0.00 0.00 0.00 2.82
1562 1571 7.480810 GGGATAATAAAGCGAACAAAGACAAT 58.519 34.615 0.00 0.00 0.00 2.71
1563 1572 6.402766 CGGGATAATAAAGCGAACAAAGACAA 60.403 38.462 0.00 0.00 0.00 3.18
1564 1573 5.064198 CGGGATAATAAAGCGAACAAAGACA 59.936 40.000 0.00 0.00 0.00 3.41
1565 1574 5.064325 ACGGGATAATAAAGCGAACAAAGAC 59.936 40.000 0.00 0.00 0.00 3.01
1566 1575 5.180271 ACGGGATAATAAAGCGAACAAAGA 58.820 37.500 0.00 0.00 0.00 2.52
1567 1576 5.479716 ACGGGATAATAAAGCGAACAAAG 57.520 39.130 0.00 0.00 0.00 2.77
1568 1577 5.181622 ACAACGGGATAATAAAGCGAACAAA 59.818 36.000 0.00 0.00 0.00 2.83
1569 1578 4.696402 ACAACGGGATAATAAAGCGAACAA 59.304 37.500 0.00 0.00 0.00 2.83
1570 1579 4.093703 CACAACGGGATAATAAAGCGAACA 59.906 41.667 0.00 0.00 0.00 3.18
1571 1580 4.330620 TCACAACGGGATAATAAAGCGAAC 59.669 41.667 0.00 0.00 0.00 3.95
1572 1581 4.505808 TCACAACGGGATAATAAAGCGAA 58.494 39.130 0.00 0.00 0.00 4.70
1573 1582 4.116961 CTCACAACGGGATAATAAAGCGA 58.883 43.478 0.00 0.00 0.00 4.93
1574 1583 4.116961 TCTCACAACGGGATAATAAAGCG 58.883 43.478 0.00 0.00 0.00 4.68
1575 1584 6.430451 CATTCTCACAACGGGATAATAAAGC 58.570 40.000 0.00 0.00 0.00 3.51
1576 1585 6.513393 GCCATTCTCACAACGGGATAATAAAG 60.513 42.308 0.00 0.00 0.00 1.85
1577 1586 5.298276 GCCATTCTCACAACGGGATAATAAA 59.702 40.000 0.00 0.00 0.00 1.40
1578 1587 4.819630 GCCATTCTCACAACGGGATAATAA 59.180 41.667 0.00 0.00 0.00 1.40
1579 1588 4.102524 AGCCATTCTCACAACGGGATAATA 59.897 41.667 0.00 0.00 0.00 0.98
1580 1589 3.117888 AGCCATTCTCACAACGGGATAAT 60.118 43.478 0.00 0.00 0.00 1.28
1581 1590 2.238646 AGCCATTCTCACAACGGGATAA 59.761 45.455 0.00 0.00 0.00 1.75
1582 1591 1.837439 AGCCATTCTCACAACGGGATA 59.163 47.619 0.00 0.00 0.00 2.59
1583 1592 0.620556 AGCCATTCTCACAACGGGAT 59.379 50.000 0.00 0.00 0.00 3.85
1584 1593 1.207089 CTAGCCATTCTCACAACGGGA 59.793 52.381 0.00 0.00 0.00 5.14
1585 1594 1.207089 TCTAGCCATTCTCACAACGGG 59.793 52.381 0.00 0.00 0.00 5.28
1586 1595 2.093973 ACTCTAGCCATTCTCACAACGG 60.094 50.000 0.00 0.00 0.00 4.44
1587 1596 3.238108 ACTCTAGCCATTCTCACAACG 57.762 47.619 0.00 0.00 0.00 4.10
1588 1597 4.826556 AGAACTCTAGCCATTCTCACAAC 58.173 43.478 0.00 0.00 0.00 3.32
1589 1598 6.577103 CATAGAACTCTAGCCATTCTCACAA 58.423 40.000 6.32 0.00 34.55 3.33
1590 1599 5.452496 GCATAGAACTCTAGCCATTCTCACA 60.452 44.000 6.32 0.00 34.55 3.58
1591 1600 4.987912 GCATAGAACTCTAGCCATTCTCAC 59.012 45.833 6.32 0.00 34.55 3.51
1592 1601 4.898265 AGCATAGAACTCTAGCCATTCTCA 59.102 41.667 6.32 0.00 34.55 3.27
1593 1602 5.467035 AGCATAGAACTCTAGCCATTCTC 57.533 43.478 6.32 0.00 34.55 2.87
1594 1603 5.885449 AAGCATAGAACTCTAGCCATTCT 57.115 39.130 7.74 7.74 36.64 2.40
1595 1604 7.875041 TCATTAAGCATAGAACTCTAGCCATTC 59.125 37.037 0.00 0.00 0.00 2.67
1596 1605 7.739825 TCATTAAGCATAGAACTCTAGCCATT 58.260 34.615 0.00 0.00 0.00 3.16
1597 1606 7.308450 TCATTAAGCATAGAACTCTAGCCAT 57.692 36.000 0.00 0.00 0.00 4.40
1598 1607 6.731292 TCATTAAGCATAGAACTCTAGCCA 57.269 37.500 0.00 0.00 0.00 4.75
1599 1608 7.495934 TGTTTCATTAAGCATAGAACTCTAGCC 59.504 37.037 0.00 0.00 0.00 3.93
1600 1609 8.425577 TGTTTCATTAAGCATAGAACTCTAGC 57.574 34.615 0.00 0.00 0.00 3.42
1683 1692 5.440610 AGGATGGTAGAAATTAGCAAGGTG 58.559 41.667 0.00 0.00 0.00 4.00
1692 1701 5.300286 GCACATGCTTAGGATGGTAGAAATT 59.700 40.000 17.56 0.00 38.21 1.82
1928 1943 4.469227 ACAAGCATACTCCATCTTCACTCT 59.531 41.667 0.00 0.00 0.00 3.24
1929 1944 4.764172 ACAAGCATACTCCATCTTCACTC 58.236 43.478 0.00 0.00 0.00 3.51
1930 1945 4.833478 ACAAGCATACTCCATCTTCACT 57.167 40.909 0.00 0.00 0.00 3.41
1952 1967 2.549754 CGGCTCTTCTTCTTTTGCTTCA 59.450 45.455 0.00 0.00 0.00 3.02
2126 2184 5.945191 TCTCATCAAGCACCATATGTCAAAA 59.055 36.000 1.24 0.00 0.00 2.44
2303 2368 8.709308 AGCATCTAACACTTAATGATCTAGGTT 58.291 33.333 0.00 0.00 0.00 3.50
2399 2465 2.627945 GTTCACATGCTACCGATCCAA 58.372 47.619 0.00 0.00 0.00 3.53
2496 2564 4.500499 TCCTACTGTAGGTAGTCAGACC 57.500 50.000 28.21 0.00 46.32 3.85
2516 2589 2.487934 CGATCCAGGGAACATGACATC 58.512 52.381 0.00 0.00 0.00 3.06
2678 2778 3.132289 CGAGAACATGGTATACACCTGGT 59.868 47.826 5.01 0.00 45.98 4.00


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

AutoCloner maintained by Alex Coulton.