Multiple sequence alignment - TraesCS6B01G023400

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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 TraesCS6B01G023400 chr6B 100.000 3155 0 0 1 3155 14339460 14342614 0.000000e+00 5827.0
1 TraesCS6B01G023400 chr6B 82.804 1227 182 23 959 2163 13818962 13817743 0.000000e+00 1070.0
2 TraesCS6B01G023400 chr6B 77.021 1336 236 45 969 2281 40658517 40657230 0.000000e+00 701.0
3 TraesCS6B01G023400 chr6B 76.929 1335 242 46 963 2266 14399903 14398604 0.000000e+00 699.0
4 TraesCS6B01G023400 chr6B 75.417 1200 252 30 987 2175 15264292 15263125 2.770000e-150 542.0
5 TraesCS6B01G023400 chr6B 79.223 746 127 21 987 1716 52997725 52996992 7.860000e-136 494.0
6 TraesCS6B01G023400 chr6B 75.102 735 159 24 1556 2281 41228581 41227862 3.930000e-84 322.0
7 TraesCS6B01G023400 chr6B 94.382 178 9 1 184 360 14354899 14355076 4.010000e-69 272.0
8 TraesCS6B01G023400 chr6B 82.533 229 37 2 2038 2266 40791277 40791052 6.900000e-47 198.0
9 TraesCS6B01G023400 chr6B 88.344 163 19 0 639 801 21353763 21353925 2.480000e-46 196.0
10 TraesCS6B01G023400 chr6B 82.096 229 38 2 2038 2266 40715840 40715615 3.210000e-45 193.0
11 TraesCS6B01G023400 chr6D 91.029 1672 89 16 1523 3155 7729142 7730791 0.000000e+00 2200.0
12 TraesCS6B01G023400 chr6D 82.866 1319 194 24 962 2266 7901239 7902539 0.000000e+00 1155.0
13 TraesCS6B01G023400 chr6D 90.577 849 52 11 849 1696 7728329 7729150 0.000000e+00 1099.0
14 TraesCS6B01G023400 chr6D 81.964 1059 142 19 1112 2159 7404835 7403815 0.000000e+00 852.0
15 TraesCS6B01G023400 chr6D 77.119 1333 268 31 953 2266 8894006 8895320 0.000000e+00 737.0
16 TraesCS6B01G023400 chr6D 77.553 1283 243 33 899 2159 7484885 7483626 0.000000e+00 732.0
17 TraesCS6B01G023400 chr6D 77.619 1260 208 49 969 2189 25018787 25017563 0.000000e+00 697.0
18 TraesCS6B01G023400 chr6D 76.942 1249 251 27 954 2180 7477212 7475979 0.000000e+00 676.0
19 TraesCS6B01G023400 chr6D 76.270 1319 267 31 973 2266 14689278 14687981 0.000000e+00 660.0
20 TraesCS6B01G023400 chr6D 89.021 419 37 3 122 538 7724715 7725126 7.810000e-141 510.0
21 TraesCS6B01G023400 chr6D 73.625 1164 275 21 1113 2266 14437809 14438950 1.350000e-113 420.0
22 TraesCS6B01G023400 chr6D 75.771 875 186 20 1404 2266 14518053 14518913 4.870000e-113 418.0
23 TraesCS6B01G023400 chr6D 75.529 850 193 14 1423 2266 8402232 8401392 1.360000e-108 403.0
24 TraesCS6B01G023400 chr6D 97.403 154 4 0 488 641 7725127 7725280 2.410000e-66 263.0
25 TraesCS6B01G023400 chr6A 80.349 1318 211 28 962 2266 8174948 8176230 0.000000e+00 955.0
26 TraesCS6B01G023400 chr6A 80.690 1072 160 24 957 2008 7224763 7223719 0.000000e+00 789.0
27 TraesCS6B01G023400 chr6A 77.030 1219 227 34 988 2180 8712241 8713432 0.000000e+00 651.0
28 TraesCS6B01G023400 chr6A 75.622 1206 255 29 987 2173 9461444 9462629 2.120000e-156 562.0
29 TraesCS6B01G023400 chr1B 93.232 591 35 4 2565 3153 27364066 27363479 0.000000e+00 865.0
30 TraesCS6B01G023400 chr1B 77.162 1318 249 37 975 2266 630644723 630646014 0.000000e+00 719.0
31 TraesCS6B01G023400 chr1B 75.524 1193 256 32 987 2159 662153019 662154195 1.280000e-153 553.0
32 TraesCS6B01G023400 chr7B 80.169 1180 205 19 982 2149 623951353 623950191 0.000000e+00 856.0
33 TraesCS6B01G023400 chr7B 89.157 166 16 2 636 801 377009959 377010122 4.120000e-49 206.0
34 TraesCS6B01G023400 chr7B 87.719 57 4 3 1 54 245854405 245854349 2.630000e-06 63.9
35 TraesCS6B01G023400 chr7A 79.453 1207 217 24 957 2150 657024860 657023672 0.000000e+00 826.0
36 TraesCS6B01G023400 chr7A 77.677 1102 215 22 1070 2157 162577916 162579000 0.000000e+00 643.0
37 TraesCS6B01G023400 chr7A 87.719 57 4 3 1 54 83936120 83936176 2.630000e-06 63.9
38 TraesCS6B01G023400 chr7D 79.544 1183 211 23 982 2150 568371562 568370397 0.000000e+00 815.0
39 TraesCS6B01G023400 chr1D 77.947 1179 228 26 991 2159 477165689 477166845 0.000000e+00 708.0
40 TraesCS6B01G023400 chr1D 91.275 149 13 0 658 806 481697981 481697833 1.480000e-48 204.0
41 TraesCS6B01G023400 chr3B 76.334 1331 255 36 960 2266 761047773 761046479 0.000000e+00 658.0
42 TraesCS6B01G023400 chr3B 86.982 169 22 0 638 806 43319259 43319091 1.160000e-44 191.0
43 TraesCS6B01G023400 chr3B 86.131 137 18 1 670 806 30937337 30937202 2.540000e-31 147.0
44 TraesCS6B01G023400 chr4D 90.419 167 15 1 639 804 490257548 490257714 5.300000e-53 219.0
45 TraesCS6B01G023400 chr4D 87.719 57 4 3 1 54 28237823 28237879 2.630000e-06 63.9
46 TraesCS6B01G023400 chr3D 89.759 166 17 0 641 806 459959591 459959426 2.470000e-51 213.0
47 TraesCS6B01G023400 chr3D 97.959 49 1 0 1 49 122572220 122572172 5.610000e-13 86.1
48 TraesCS6B01G023400 chr3D 96.154 52 1 1 1 52 422648353 422648403 2.020000e-12 84.2
49 TraesCS6B01G023400 chr1A 89.024 164 18 0 641 804 360460146 360459983 1.480000e-48 204.0
50 TraesCS6B01G023400 chr1A 90.741 54 2 2 1 51 58274636 58274583 5.650000e-08 69.4
51 TraesCS6B01G023400 chr3A 88.344 163 19 0 639 801 549614454 549614616 2.480000e-46 196.0
52 TraesCS6B01G023400 chr3A 93.478 46 3 0 1 46 638911028 638911073 5.650000e-08 69.4
53 TraesCS6B01G023400 chr4B 88.024 167 17 1 638 804 660100141 660099978 8.930000e-46 195.0
54 TraesCS6B01G023400 chr4A 97.826 46 1 0 1 46 632915955 632915910 2.610000e-11 80.5
55 TraesCS6B01G023400 chr4A 78.899 109 20 3 2489 2595 615609013 615608906 1.570000e-08 71.3
56 TraesCS6B01G023400 chr4A 87.719 57 4 3 1 54 585398072 585398128 2.630000e-06 63.9
57 TraesCS6B01G023400 chr2B 78.571 112 21 3 2486 2595 315682386 315682496 1.570000e-08 71.3


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 TraesCS6B01G023400 chr6B 14339460 14342614 3154 False 5827 5827 100.0000 1 3155 1 chr6B.!!$F1 3154
1 TraesCS6B01G023400 chr6B 13817743 13818962 1219 True 1070 1070 82.8040 959 2163 1 chr6B.!!$R1 1204
2 TraesCS6B01G023400 chr6B 40657230 40658517 1287 True 701 701 77.0210 969 2281 1 chr6B.!!$R4 1312
3 TraesCS6B01G023400 chr6B 14398604 14399903 1299 True 699 699 76.9290 963 2266 1 chr6B.!!$R2 1303
4 TraesCS6B01G023400 chr6B 15263125 15264292 1167 True 542 542 75.4170 987 2175 1 chr6B.!!$R3 1188
5 TraesCS6B01G023400 chr6B 52996992 52997725 733 True 494 494 79.2230 987 1716 1 chr6B.!!$R8 729
6 TraesCS6B01G023400 chr6B 41227862 41228581 719 True 322 322 75.1020 1556 2281 1 chr6B.!!$R7 725
7 TraesCS6B01G023400 chr6D 7901239 7902539 1300 False 1155 1155 82.8660 962 2266 1 chr6D.!!$F1 1304
8 TraesCS6B01G023400 chr6D 7724715 7730791 6076 False 1018 2200 92.0075 122 3155 4 chr6D.!!$F5 3033
9 TraesCS6B01G023400 chr6D 7403815 7404835 1020 True 852 852 81.9640 1112 2159 1 chr6D.!!$R1 1047
10 TraesCS6B01G023400 chr6D 8894006 8895320 1314 False 737 737 77.1190 953 2266 1 chr6D.!!$F2 1313
11 TraesCS6B01G023400 chr6D 7483626 7484885 1259 True 732 732 77.5530 899 2159 1 chr6D.!!$R3 1260
12 TraesCS6B01G023400 chr6D 25017563 25018787 1224 True 697 697 77.6190 969 2189 1 chr6D.!!$R6 1220
13 TraesCS6B01G023400 chr6D 7475979 7477212 1233 True 676 676 76.9420 954 2180 1 chr6D.!!$R2 1226
14 TraesCS6B01G023400 chr6D 14687981 14689278 1297 True 660 660 76.2700 973 2266 1 chr6D.!!$R5 1293
15 TraesCS6B01G023400 chr6D 14437809 14438950 1141 False 420 420 73.6250 1113 2266 1 chr6D.!!$F3 1153
16 TraesCS6B01G023400 chr6D 14518053 14518913 860 False 418 418 75.7710 1404 2266 1 chr6D.!!$F4 862
17 TraesCS6B01G023400 chr6D 8401392 8402232 840 True 403 403 75.5290 1423 2266 1 chr6D.!!$R4 843
18 TraesCS6B01G023400 chr6A 8174948 8176230 1282 False 955 955 80.3490 962 2266 1 chr6A.!!$F1 1304
19 TraesCS6B01G023400 chr6A 7223719 7224763 1044 True 789 789 80.6900 957 2008 1 chr6A.!!$R1 1051
20 TraesCS6B01G023400 chr6A 8712241 8713432 1191 False 651 651 77.0300 988 2180 1 chr6A.!!$F2 1192
21 TraesCS6B01G023400 chr6A 9461444 9462629 1185 False 562 562 75.6220 987 2173 1 chr6A.!!$F3 1186
22 TraesCS6B01G023400 chr1B 27363479 27364066 587 True 865 865 93.2320 2565 3153 1 chr1B.!!$R1 588
23 TraesCS6B01G023400 chr1B 630644723 630646014 1291 False 719 719 77.1620 975 2266 1 chr1B.!!$F1 1291
24 TraesCS6B01G023400 chr1B 662153019 662154195 1176 False 553 553 75.5240 987 2159 1 chr1B.!!$F2 1172
25 TraesCS6B01G023400 chr7B 623950191 623951353 1162 True 856 856 80.1690 982 2149 1 chr7B.!!$R2 1167
26 TraesCS6B01G023400 chr7A 657023672 657024860 1188 True 826 826 79.4530 957 2150 1 chr7A.!!$R1 1193
27 TraesCS6B01G023400 chr7A 162577916 162579000 1084 False 643 643 77.6770 1070 2157 1 chr7A.!!$F2 1087
28 TraesCS6B01G023400 chr7D 568370397 568371562 1165 True 815 815 79.5440 982 2150 1 chr7D.!!$R1 1168
29 TraesCS6B01G023400 chr1D 477165689 477166845 1156 False 708 708 77.9470 991 2159 1 chr1D.!!$F1 1168
30 TraesCS6B01G023400 chr3B 761046479 761047773 1294 True 658 658 76.3340 960 2266 1 chr3B.!!$R3 1306

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
944 3964 0.254178 GCAAATCTGGAGGAGGCTCA 59.746 55.0 17.69 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2180 5471 0.602638 TGAGCGCCCTACACAGTTTG 60.603 55.0 2.29 0.0 0.0 2.93 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
28 29 8.535690 AATAAGTGACTCAACTTTGTACTAGC 57.464 34.615 0.00 0.00 40.77 3.42
29 30 5.793030 AGTGACTCAACTTTGTACTAGCT 57.207 39.130 0.00 0.00 0.00 3.32
30 31 6.163135 AGTGACTCAACTTTGTACTAGCTT 57.837 37.500 0.00 0.00 0.00 3.74
31 32 6.583562 AGTGACTCAACTTTGTACTAGCTTT 58.416 36.000 0.00 0.00 0.00 3.51
32 33 7.723324 AGTGACTCAACTTTGTACTAGCTTTA 58.277 34.615 0.00 0.00 0.00 1.85
33 34 7.868415 AGTGACTCAACTTTGTACTAGCTTTAG 59.132 37.037 0.00 0.00 0.00 1.85
34 35 7.866393 GTGACTCAACTTTGTACTAGCTTTAGA 59.134 37.037 0.00 0.00 0.00 2.10
35 36 7.866393 TGACTCAACTTTGTACTAGCTTTAGAC 59.134 37.037 0.00 0.00 0.00 2.59
36 37 6.862090 ACTCAACTTTGTACTAGCTTTAGACG 59.138 38.462 0.00 0.00 0.00 4.18
37 38 6.154445 TCAACTTTGTACTAGCTTTAGACGG 58.846 40.000 0.00 0.00 0.00 4.79
38 39 5.972107 ACTTTGTACTAGCTTTAGACGGA 57.028 39.130 0.00 0.00 0.00 4.69
39 40 5.952033 ACTTTGTACTAGCTTTAGACGGAG 58.048 41.667 0.00 0.00 0.00 4.63
40 41 4.978083 TTGTACTAGCTTTAGACGGAGG 57.022 45.455 0.00 0.00 0.00 4.30
41 42 3.285484 TGTACTAGCTTTAGACGGAGGG 58.715 50.000 0.00 0.00 0.00 4.30
42 43 2.822707 ACTAGCTTTAGACGGAGGGA 57.177 50.000 0.00 0.00 0.00 4.20
43 44 2.657143 ACTAGCTTTAGACGGAGGGAG 58.343 52.381 0.00 0.00 0.00 4.30
44 45 2.025131 ACTAGCTTTAGACGGAGGGAGT 60.025 50.000 0.00 0.00 0.00 3.85
45 46 2.822707 AGCTTTAGACGGAGGGAGTA 57.177 50.000 0.00 0.00 0.00 2.59
46 47 2.377073 AGCTTTAGACGGAGGGAGTAC 58.623 52.381 0.00 0.00 0.00 2.73
47 48 2.025131 AGCTTTAGACGGAGGGAGTACT 60.025 50.000 0.00 0.00 0.00 2.73
48 49 2.759535 GCTTTAGACGGAGGGAGTACTT 59.240 50.000 0.00 0.00 0.00 2.24
49 50 3.195182 GCTTTAGACGGAGGGAGTACTTT 59.805 47.826 0.00 0.00 0.00 2.66
50 51 4.322574 GCTTTAGACGGAGGGAGTACTTTT 60.323 45.833 0.00 0.00 0.00 2.27
51 52 5.791666 CTTTAGACGGAGGGAGTACTTTTT 58.208 41.667 0.00 0.00 0.00 1.94
71 72 3.868619 TTTTGTGGGGTAACTAGTGCT 57.131 42.857 0.00 0.00 0.00 4.40
72 73 3.868619 TTTGTGGGGTAACTAGTGCTT 57.131 42.857 0.00 0.00 0.00 3.91
73 74 3.868619 TTGTGGGGTAACTAGTGCTTT 57.131 42.857 0.00 0.00 0.00 3.51
74 75 4.978438 TTGTGGGGTAACTAGTGCTTTA 57.022 40.909 0.00 0.00 0.00 1.85
75 76 5.508280 TTGTGGGGTAACTAGTGCTTTAT 57.492 39.130 0.00 0.00 0.00 1.40
76 77 5.508280 TGTGGGGTAACTAGTGCTTTATT 57.492 39.130 0.00 0.00 0.00 1.40
77 78 5.493809 TGTGGGGTAACTAGTGCTTTATTC 58.506 41.667 0.00 0.00 0.00 1.75
78 79 5.013287 TGTGGGGTAACTAGTGCTTTATTCA 59.987 40.000 0.00 0.00 0.00 2.57
79 80 5.941647 GTGGGGTAACTAGTGCTTTATTCAA 59.058 40.000 0.00 0.00 0.00 2.69
80 81 6.431852 GTGGGGTAACTAGTGCTTTATTCAAA 59.568 38.462 0.00 0.00 0.00 2.69
81 82 7.005296 TGGGGTAACTAGTGCTTTATTCAAAA 58.995 34.615 0.00 0.00 0.00 2.44
82 83 7.672239 TGGGGTAACTAGTGCTTTATTCAAAAT 59.328 33.333 0.00 0.00 0.00 1.82
83 84 8.528643 GGGGTAACTAGTGCTTTATTCAAAATT 58.471 33.333 0.00 0.00 0.00 1.82
84 85 9.569167 GGGTAACTAGTGCTTTATTCAAAATTC 57.431 33.333 0.00 0.00 0.00 2.17
111 112 8.538409 AAATTCAAAACATCAAGGATACAAGC 57.462 30.769 0.00 0.00 41.41 4.01
112 113 6.647334 TTCAAAACATCAAGGATACAAGCA 57.353 33.333 0.00 0.00 41.41 3.91
113 114 6.647334 TCAAAACATCAAGGATACAAGCAA 57.353 33.333 0.00 0.00 41.41 3.91
114 115 7.230849 TCAAAACATCAAGGATACAAGCAAT 57.769 32.000 0.00 0.00 41.41 3.56
115 116 7.092079 TCAAAACATCAAGGATACAAGCAATG 58.908 34.615 0.00 0.00 41.41 2.82
116 117 6.594788 AAACATCAAGGATACAAGCAATGT 57.405 33.333 0.67 0.67 46.36 2.71
117 118 5.824904 ACATCAAGGATACAAGCAATGTC 57.175 39.130 0.00 0.00 42.70 3.06
118 119 5.503927 ACATCAAGGATACAAGCAATGTCT 58.496 37.500 0.00 0.00 42.70 3.41
119 120 5.356190 ACATCAAGGATACAAGCAATGTCTG 59.644 40.000 0.00 0.00 42.70 3.51
120 121 4.264253 TCAAGGATACAAGCAATGTCTGG 58.736 43.478 0.00 0.00 42.70 3.86
123 124 3.521126 AGGATACAAGCAATGTCTGGACT 59.479 43.478 0.00 0.00 42.70 3.85
126 127 5.294552 GGATACAAGCAATGTCTGGACTAAC 59.705 44.000 0.00 0.00 42.70 2.34
138 139 4.489737 TCTGGACTAACAGAAAGGGAAGA 58.510 43.478 0.00 0.00 44.03 2.87
170 171 4.771590 AGCAATTGAATGAGCTTCGAAA 57.228 36.364 10.34 0.00 36.60 3.46
185 186 4.025313 GCTTCGAAATTGGACTCTCTATGC 60.025 45.833 0.00 0.00 0.00 3.14
191 192 5.344743 AATTGGACTCTCTATGCTCGAAA 57.655 39.130 0.00 0.00 0.00 3.46
204 205 4.273005 TGCTCGAAACAGAAAGAAACAC 57.727 40.909 0.00 0.00 0.00 3.32
205 206 3.938963 TGCTCGAAACAGAAAGAAACACT 59.061 39.130 0.00 0.00 0.00 3.55
257 258 2.833943 TGGCGAGATCATAGCATATGGT 59.166 45.455 12.78 12.78 0.00 3.55
264 265 6.424812 CGAGATCATAGCATATGGTGAAACAA 59.575 38.462 17.58 0.00 39.98 2.83
283 284 2.206576 ACTCCCTTCTTGATGTTGCC 57.793 50.000 0.00 0.00 0.00 4.52
286 287 1.089920 CCCTTCTTGATGTTGCCGAG 58.910 55.000 0.00 0.00 0.00 4.63
300 301 0.875059 GCCGAGGACTTTCCAAACAG 59.125 55.000 0.00 0.00 39.61 3.16
304 305 3.467803 CGAGGACTTTCCAAACAGTCTT 58.532 45.455 0.00 0.00 39.61 3.01
310 311 3.181458 ACTTTCCAAACAGTCTTAGGCGA 60.181 43.478 0.00 0.00 0.00 5.54
320 321 6.161855 ACAGTCTTAGGCGATGATCATTTA 57.838 37.500 10.14 0.00 0.00 1.40
348 349 2.102109 TAAGGTCGTGCGCAAGGGAA 62.102 55.000 23.00 0.86 38.28 3.97
350 351 2.332654 GGTCGTGCGCAAGGGAAAT 61.333 57.895 23.00 0.00 38.28 2.17
353 354 2.125952 GTGCGCAAGGGAAATGCC 60.126 61.111 14.00 0.00 40.72 4.40
354 355 2.283101 TGCGCAAGGGAAATGCCT 60.283 55.556 8.16 0.00 40.72 4.75
355 356 2.342650 TGCGCAAGGGAAATGCCTC 61.343 57.895 8.16 0.00 40.72 4.70
356 357 2.048603 GCGCAAGGGAAATGCCTCT 61.049 57.895 0.30 0.00 40.72 3.69
357 358 1.598701 GCGCAAGGGAAATGCCTCTT 61.599 55.000 0.30 0.00 40.72 2.85
358 359 0.890683 CGCAAGGGAAATGCCTCTTT 59.109 50.000 0.00 0.00 40.72 2.52
376 377 0.391528 TTCTTCGCTGCATGCTAGCA 60.392 50.000 29.02 21.85 41.18 3.49
388 389 3.715495 CATGCTAGCACTTCCAGAGTAG 58.285 50.000 22.07 0.00 36.65 2.57
391 392 2.167487 GCTAGCACTTCCAGAGTAGCTT 59.833 50.000 10.63 0.00 40.63 3.74
407 408 1.280421 AGCTTGATCAACCAGACCCTC 59.720 52.381 3.38 0.00 0.00 4.30
408 409 2.009042 GCTTGATCAACCAGACCCTCG 61.009 57.143 3.38 0.00 0.00 4.63
422 423 1.562575 CCCTCGAAAACAACCGTCGG 61.563 60.000 10.48 10.48 35.51 4.79
423 424 1.562575 CCTCGAAAACAACCGTCGGG 61.563 60.000 17.28 0.47 35.51 5.14
426 427 1.895231 GAAAACAACCGTCGGGGCT 60.895 57.895 17.28 0.00 40.62 5.19
434 435 2.737881 CCGTCGGGGCTCCCAAATA 61.738 63.158 2.34 0.00 45.83 1.40
440 441 0.927029 GGGGCTCCCAAATAGTTCCT 59.073 55.000 7.34 0.00 44.65 3.36
458 459 1.085091 CTTGCACCATCTCTGCAGAC 58.915 55.000 13.74 1.34 45.21 3.51
462 463 2.202987 CCATCTCTGCAGACCGCC 60.203 66.667 13.74 0.00 41.33 6.13
494 497 0.771755 ACCCCTTTGTCTCCCAGAAC 59.228 55.000 0.00 0.00 0.00 3.01
522 576 7.512992 AGATACCTCCTTCCACATTAATCTTG 58.487 38.462 0.00 0.00 0.00 3.02
555 609 1.214589 CGGAGGAATCCAACGTCGT 59.785 57.895 0.61 0.00 0.00 4.34
558 612 1.359459 GAGGAATCCAACGTCGTGGC 61.359 60.000 0.61 0.00 38.68 5.01
641 695 3.838903 AGGTCCTCCAAGTACCTGTTAAG 59.161 47.826 0.00 0.00 42.08 1.85
642 696 5.307003 AGGTCCTCCAAGTACCTGTTAAGG 61.307 50.000 0.00 0.00 42.08 2.69
654 708 4.701956 CCTGTTAAGGCCTTGTACAATG 57.298 45.455 28.77 18.73 36.56 2.82
655 709 3.119495 CCTGTTAAGGCCTTGTACAATGC 60.119 47.826 28.77 23.06 36.56 3.56
656 710 3.491342 TGTTAAGGCCTTGTACAATGCA 58.509 40.909 29.20 12.62 34.30 3.96
657 711 3.891977 TGTTAAGGCCTTGTACAATGCAA 59.108 39.130 29.20 16.86 34.30 4.08
664 718 3.648339 CTTGTACAATGCAAGGTGCTT 57.352 42.857 9.13 0.00 45.31 3.91
666 720 2.580962 TGTACAATGCAAGGTGCTTGA 58.419 42.857 14.87 0.00 45.31 3.02
667 721 2.954989 TGTACAATGCAAGGTGCTTGAA 59.045 40.909 14.87 0.00 45.31 2.69
668 722 2.806608 ACAATGCAAGGTGCTTGAAG 57.193 45.000 14.87 0.00 45.31 3.02
669 723 2.309613 ACAATGCAAGGTGCTTGAAGA 58.690 42.857 14.87 0.00 45.31 2.87
672 726 4.202284 ACAATGCAAGGTGCTTGAAGAAAT 60.202 37.500 14.87 0.00 45.31 2.17
673 727 5.010922 ACAATGCAAGGTGCTTGAAGAAATA 59.989 36.000 14.87 0.00 45.31 1.40
674 728 5.726980 ATGCAAGGTGCTTGAAGAAATAA 57.273 34.783 0.00 0.00 45.31 1.40
675 729 5.528043 TGCAAGGTGCTTGAAGAAATAAA 57.472 34.783 0.00 0.00 45.31 1.40
676 730 5.288804 TGCAAGGTGCTTGAAGAAATAAAC 58.711 37.500 0.00 0.00 45.31 2.01
677 731 4.686091 GCAAGGTGCTTGAAGAAATAAACC 59.314 41.667 0.00 0.00 43.42 3.27
678 732 5.738783 GCAAGGTGCTTGAAGAAATAAACCA 60.739 40.000 0.00 0.00 43.42 3.67
679 733 6.279882 CAAGGTGCTTGAAGAAATAAACCAA 58.720 36.000 0.00 0.00 43.42 3.67
680 734 6.089249 AGGTGCTTGAAGAAATAAACCAAG 57.911 37.500 0.00 0.00 37.76 3.61
681 735 5.598417 AGGTGCTTGAAGAAATAAACCAAGT 59.402 36.000 0.00 0.00 37.23 3.16
682 736 6.098266 AGGTGCTTGAAGAAATAAACCAAGTT 59.902 34.615 0.00 0.00 37.23 2.66
683 737 6.761242 GGTGCTTGAAGAAATAAACCAAGTTT 59.239 34.615 0.00 0.00 39.24 2.66
684 738 7.279981 GGTGCTTGAAGAAATAAACCAAGTTTT 59.720 33.333 0.00 0.00 37.01 2.43
685 739 8.664798 GTGCTTGAAGAAATAAACCAAGTTTTT 58.335 29.630 0.00 0.00 37.01 1.94
686 740 8.878769 TGCTTGAAGAAATAAACCAAGTTTTTC 58.121 29.630 0.00 0.00 37.01 2.29
687 741 9.098355 GCTTGAAGAAATAAACCAAGTTTTTCT 57.902 29.630 0.00 0.45 35.46 2.52
695 749 8.657074 AATAAACCAAGTTTTTCTTAAGCACC 57.343 30.769 0.00 0.00 37.01 5.01
696 750 4.301637 ACCAAGTTTTTCTTAAGCACCG 57.698 40.909 0.00 0.00 34.66 4.94
697 751 3.067601 ACCAAGTTTTTCTTAAGCACCGG 59.932 43.478 0.00 0.00 34.66 5.28
698 752 3.067601 CCAAGTTTTTCTTAAGCACCGGT 59.932 43.478 0.00 0.00 34.66 5.28
699 753 3.982576 AGTTTTTCTTAAGCACCGGTG 57.017 42.857 30.66 30.66 0.00 4.94
700 754 3.490249 AAGTTTTTCTTAAGCACCGGTGC 60.490 43.478 45.27 45.27 44.63 5.01
714 768 3.813166 CACCGGTGCTTATTTGTATAGGG 59.187 47.826 24.02 0.00 0.00 3.53
715 769 2.812011 CCGGTGCTTATTTGTATAGGGC 59.188 50.000 0.00 0.00 0.00 5.19
716 770 3.472652 CGGTGCTTATTTGTATAGGGCA 58.527 45.455 0.00 0.00 0.00 5.36
717 771 3.498397 CGGTGCTTATTTGTATAGGGCAG 59.502 47.826 0.00 0.00 31.94 4.85
718 772 4.714632 GGTGCTTATTTGTATAGGGCAGA 58.285 43.478 0.00 0.00 31.94 4.26
719 773 4.515567 GGTGCTTATTTGTATAGGGCAGAC 59.484 45.833 0.00 0.00 31.94 3.51
720 774 4.211374 GTGCTTATTTGTATAGGGCAGACG 59.789 45.833 0.00 0.00 31.94 4.18
721 775 3.186613 GCTTATTTGTATAGGGCAGACGC 59.813 47.826 0.00 0.00 37.44 5.19
722 776 4.632153 CTTATTTGTATAGGGCAGACGCT 58.368 43.478 0.00 0.00 42.59 5.07
723 777 3.560636 ATTTGTATAGGGCAGACGCTT 57.439 42.857 0.00 0.00 40.12 4.68
724 778 4.682778 ATTTGTATAGGGCAGACGCTTA 57.317 40.909 0.00 0.00 40.12 3.09
725 779 4.475051 TTTGTATAGGGCAGACGCTTAA 57.525 40.909 0.00 0.00 40.12 1.85
726 780 4.682778 TTGTATAGGGCAGACGCTTAAT 57.317 40.909 0.00 0.00 40.12 1.40
727 781 4.682778 TGTATAGGGCAGACGCTTAATT 57.317 40.909 0.00 0.00 40.12 1.40
728 782 5.794726 TGTATAGGGCAGACGCTTAATTA 57.205 39.130 0.00 0.00 40.12 1.40
729 783 5.779922 TGTATAGGGCAGACGCTTAATTAG 58.220 41.667 0.00 0.00 40.12 1.73
730 784 2.622064 AGGGCAGACGCTTAATTAGG 57.378 50.000 0.00 0.00 35.04 2.69
731 785 0.945099 GGGCAGACGCTTAATTAGGC 59.055 55.000 9.43 9.43 38.60 3.93
772 826 3.084070 CACTGGTGCTTCAGAAAAACC 57.916 47.619 12.54 6.89 38.11 3.27
773 827 2.031870 ACTGGTGCTTCAGAAAAACCC 58.968 47.619 12.54 0.00 38.11 4.11
774 828 2.031120 CTGGTGCTTCAGAAAAACCCA 58.969 47.619 10.23 2.22 36.93 4.51
775 829 2.430332 CTGGTGCTTCAGAAAAACCCAA 59.570 45.455 10.23 0.00 36.93 4.12
776 830 3.037549 TGGTGCTTCAGAAAAACCCAAT 58.962 40.909 10.23 0.00 0.00 3.16
777 831 3.454082 TGGTGCTTCAGAAAAACCCAATT 59.546 39.130 10.23 0.00 0.00 2.32
778 832 4.080638 TGGTGCTTCAGAAAAACCCAATTT 60.081 37.500 10.23 0.00 0.00 1.82
779 833 5.129485 TGGTGCTTCAGAAAAACCCAATTTA 59.871 36.000 10.23 0.00 0.00 1.40
780 834 6.183361 TGGTGCTTCAGAAAAACCCAATTTAT 60.183 34.615 10.23 0.00 0.00 1.40
781 835 6.710295 GGTGCTTCAGAAAAACCCAATTTATT 59.290 34.615 3.37 0.00 0.00 1.40
782 836 7.228507 GGTGCTTCAGAAAAACCCAATTTATTT 59.771 33.333 3.37 0.00 0.00 1.40
783 837 8.620416 GTGCTTCAGAAAAACCCAATTTATTTT 58.380 29.630 0.00 0.00 0.00 1.82
784 838 9.183368 TGCTTCAGAAAAACCCAATTTATTTTT 57.817 25.926 4.32 4.32 38.03 1.94
785 839 9.663904 GCTTCAGAAAAACCCAATTTATTTTTC 57.336 29.630 16.48 16.48 45.95 2.29
793 847 8.615878 AAACCCAATTTATTTTTCTAAGCACC 57.384 30.769 0.00 0.00 0.00 5.01
794 848 7.553504 ACCCAATTTATTTTTCTAAGCACCT 57.446 32.000 0.00 0.00 0.00 4.00
795 849 7.611770 ACCCAATTTATTTTTCTAAGCACCTC 58.388 34.615 0.00 0.00 0.00 3.85
796 850 7.041721 CCCAATTTATTTTTCTAAGCACCTCC 58.958 38.462 0.00 0.00 0.00 4.30
797 851 7.041721 CCAATTTATTTTTCTAAGCACCTCCC 58.958 38.462 0.00 0.00 0.00 4.30
798 852 7.093333 CCAATTTATTTTTCTAAGCACCTCCCT 60.093 37.037 0.00 0.00 0.00 4.20
799 853 8.966868 CAATTTATTTTTCTAAGCACCTCCCTA 58.033 33.333 0.00 0.00 0.00 3.53
800 854 9.541884 AATTTATTTTTCTAAGCACCTCCCTAA 57.458 29.630 0.00 0.00 0.00 2.69
801 855 8.943594 TTTATTTTTCTAAGCACCTCCCTAAA 57.056 30.769 0.00 0.00 0.00 1.85
810 864 2.936202 CACCTCCCTAAACATCATGGG 58.064 52.381 0.00 0.00 40.95 4.00
819 873 2.645838 AACATCATGGGCTATTCGCT 57.354 45.000 0.00 0.00 39.13 4.93
844 898 3.903282 CCGCCAAATCGCCCCATG 61.903 66.667 0.00 0.00 0.00 3.66
846 900 2.759560 GCCAAATCGCCCCATGGT 60.760 61.111 11.73 0.00 35.34 3.55
847 901 1.454847 GCCAAATCGCCCCATGGTA 60.455 57.895 11.73 0.00 35.34 3.25
944 3964 0.254178 GCAAATCTGGAGGAGGCTCA 59.746 55.000 17.69 0.00 0.00 4.26
1412 4531 1.358759 CCGCCAACAACAACCACTC 59.641 57.895 0.00 0.00 0.00 3.51
1762 5051 0.453793 CGCCGCCAAAATGGAATACA 59.546 50.000 0.00 0.00 40.96 2.29
1897 5187 0.602905 CGAGGTTGGACTGGAACCAC 60.603 60.000 0.00 0.00 44.71 4.16
2180 5471 4.405116 TCAATGGGCTATGAAAATTGGC 57.595 40.909 0.00 0.00 0.00 4.52
2268 5559 7.685481 TGTGTTCTTTTCCTAACTGGATGATA 58.315 34.615 0.00 0.00 45.68 2.15
2296 5587 8.948853 TTTTATCTGCTATTGACTTTTGAACG 57.051 30.769 0.00 0.00 0.00 3.95
2302 5593 4.556699 GCTATTGACTTTTGAACGCCAACT 60.557 41.667 0.00 0.00 33.85 3.16
2360 5651 5.560375 CGCCTGCAATCTCTGAAAATGATAG 60.560 44.000 0.00 0.00 0.00 2.08
2402 5693 6.202188 GTGTTTCTGACTTCCGTTTAAGATCA 59.798 38.462 0.00 0.00 0.00 2.92
2449 5740 6.729690 TCAATTTTCTGTTGAAACCAGGAT 57.270 33.333 0.00 0.00 41.34 3.24
2472 5763 3.430651 CCAGCAAACCAGAAAGCAAAAGA 60.431 43.478 0.00 0.00 0.00 2.52
2477 5768 5.118286 CAAACCAGAAAGCAAAAGAACCAT 58.882 37.500 0.00 0.00 0.00 3.55
2478 5769 5.357742 AACCAGAAAGCAAAAGAACCATT 57.642 34.783 0.00 0.00 0.00 3.16
2546 5837 4.711399 CTGAATTCTATCAGCATGTCCCA 58.289 43.478 7.05 0.00 40.31 4.37
2612 5903 6.398918 AGTACTAGCAGTTCAATGTTCGATT 58.601 36.000 0.00 0.00 0.00 3.34
2617 5908 8.730680 ACTAGCAGTTCAATGTTCGATTTTTAT 58.269 29.630 0.00 0.00 0.00 1.40
2656 5947 5.124645 TGTATTTCTGTTGGGTGTACGTTT 58.875 37.500 0.00 0.00 0.00 3.60
2694 5985 9.618890 CTTCCCTGTATTCTTCAAAGATTGATA 57.381 33.333 0.00 0.00 39.84 2.15
2783 6074 1.524355 CGAGGCTAAAGCATGATCGTG 59.476 52.381 10.76 10.76 44.36 4.35
2885 6214 2.497273 CACCCAATCCATTCAAGGAACC 59.503 50.000 0.00 0.00 41.92 3.62
2915 6244 3.309138 CAGAACATGCAGTGAGCTGATAC 59.691 47.826 0.00 0.00 45.28 2.24
2936 6265 9.225436 TGATACACAATTATGTTTGTTCAGCTA 57.775 29.630 0.00 0.00 37.73 3.32
3075 6406 5.970592 TCAAGTATCAACACTGATCCTGAG 58.029 41.667 0.00 0.00 41.57 3.35
3088 6419 5.129980 ACTGATCCTGAGACTTGCATGATAA 59.870 40.000 6.60 0.00 0.00 1.75
3090 6421 5.819379 TGATCCTGAGACTTGCATGATAAAC 59.181 40.000 6.60 0.00 0.00 2.01
3091 6422 5.426689 TCCTGAGACTTGCATGATAAACT 57.573 39.130 6.60 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 8.989980 GCTAGTACAAAGTTGAGTCACTTATTT 58.010 33.333 0.00 0.00 35.87 1.40
4 5 7.897864 AGCTAGTACAAAGTTGAGTCACTTAT 58.102 34.615 0.00 0.00 35.87 1.73
5 6 7.286215 AGCTAGTACAAAGTTGAGTCACTTA 57.714 36.000 0.00 0.00 35.87 2.24
6 7 6.163135 AGCTAGTACAAAGTTGAGTCACTT 57.837 37.500 0.00 0.00 38.74 3.16
7 8 5.793030 AGCTAGTACAAAGTTGAGTCACT 57.207 39.130 0.00 0.00 0.00 3.41
8 9 6.846325 AAAGCTAGTACAAAGTTGAGTCAC 57.154 37.500 0.00 0.00 0.00 3.67
9 10 7.866393 GTCTAAAGCTAGTACAAAGTTGAGTCA 59.134 37.037 0.00 0.00 0.00 3.41
10 11 7.060864 CGTCTAAAGCTAGTACAAAGTTGAGTC 59.939 40.741 0.00 0.00 0.00 3.36
11 12 6.862090 CGTCTAAAGCTAGTACAAAGTTGAGT 59.138 38.462 0.00 0.00 0.00 3.41
12 13 6.308282 CCGTCTAAAGCTAGTACAAAGTTGAG 59.692 42.308 0.00 0.00 0.00 3.02
13 14 6.016024 TCCGTCTAAAGCTAGTACAAAGTTGA 60.016 38.462 0.00 0.00 0.00 3.18
14 15 6.154445 TCCGTCTAAAGCTAGTACAAAGTTG 58.846 40.000 0.00 0.00 0.00 3.16
15 16 6.336842 TCCGTCTAAAGCTAGTACAAAGTT 57.663 37.500 0.00 0.00 0.00 2.66
16 17 5.105837 CCTCCGTCTAAAGCTAGTACAAAGT 60.106 44.000 0.00 0.00 0.00 2.66
17 18 5.341617 CCTCCGTCTAAAGCTAGTACAAAG 58.658 45.833 0.00 0.00 0.00 2.77
18 19 4.159135 CCCTCCGTCTAAAGCTAGTACAAA 59.841 45.833 0.00 0.00 0.00 2.83
19 20 3.698040 CCCTCCGTCTAAAGCTAGTACAA 59.302 47.826 0.00 0.00 0.00 2.41
20 21 3.054139 TCCCTCCGTCTAAAGCTAGTACA 60.054 47.826 0.00 0.00 0.00 2.90
21 22 3.549794 TCCCTCCGTCTAAAGCTAGTAC 58.450 50.000 0.00 0.00 0.00 2.73
22 23 3.201708 ACTCCCTCCGTCTAAAGCTAGTA 59.798 47.826 0.00 0.00 0.00 1.82
23 24 2.025131 ACTCCCTCCGTCTAAAGCTAGT 60.025 50.000 0.00 0.00 0.00 2.57
24 25 2.657143 ACTCCCTCCGTCTAAAGCTAG 58.343 52.381 0.00 0.00 0.00 3.42
25 26 2.822707 ACTCCCTCCGTCTAAAGCTA 57.177 50.000 0.00 0.00 0.00 3.32
26 27 2.025131 AGTACTCCCTCCGTCTAAAGCT 60.025 50.000 0.00 0.00 0.00 3.74
27 28 2.377073 AGTACTCCCTCCGTCTAAAGC 58.623 52.381 0.00 0.00 0.00 3.51
28 29 5.402997 AAAAGTACTCCCTCCGTCTAAAG 57.597 43.478 0.00 0.00 0.00 1.85
29 30 5.813513 AAAAAGTACTCCCTCCGTCTAAA 57.186 39.130 0.00 0.00 0.00 1.85
50 51 4.173290 AGCACTAGTTACCCCACAAAAA 57.827 40.909 0.00 0.00 0.00 1.94
51 52 3.868619 AGCACTAGTTACCCCACAAAA 57.131 42.857 0.00 0.00 0.00 2.44
52 53 3.868619 AAGCACTAGTTACCCCACAAA 57.131 42.857 0.00 0.00 0.00 2.83
53 54 3.868619 AAAGCACTAGTTACCCCACAA 57.131 42.857 0.00 0.00 0.00 3.33
54 55 5.013287 TGAATAAAGCACTAGTTACCCCACA 59.987 40.000 0.00 0.00 0.00 4.17
55 56 5.493809 TGAATAAAGCACTAGTTACCCCAC 58.506 41.667 0.00 0.00 0.00 4.61
56 57 5.765576 TGAATAAAGCACTAGTTACCCCA 57.234 39.130 0.00 0.00 0.00 4.96
57 58 7.457024 TTTTGAATAAAGCACTAGTTACCCC 57.543 36.000 0.00 0.00 0.00 4.95
58 59 9.569167 GAATTTTGAATAAAGCACTAGTTACCC 57.431 33.333 0.00 0.00 0.00 3.69
85 86 8.992073 GCTTGTATCCTTGATGTTTTGAATTTT 58.008 29.630 0.00 0.00 0.00 1.82
86 87 8.149647 TGCTTGTATCCTTGATGTTTTGAATTT 58.850 29.630 0.00 0.00 0.00 1.82
87 88 7.669427 TGCTTGTATCCTTGATGTTTTGAATT 58.331 30.769 0.00 0.00 0.00 2.17
88 89 7.230849 TGCTTGTATCCTTGATGTTTTGAAT 57.769 32.000 0.00 0.00 0.00 2.57
89 90 6.647334 TGCTTGTATCCTTGATGTTTTGAA 57.353 33.333 0.00 0.00 0.00 2.69
90 91 6.647334 TTGCTTGTATCCTTGATGTTTTGA 57.353 33.333 0.00 0.00 0.00 2.69
91 92 6.869913 ACATTGCTTGTATCCTTGATGTTTTG 59.130 34.615 0.00 0.00 36.57 2.44
92 93 6.996509 ACATTGCTTGTATCCTTGATGTTTT 58.003 32.000 0.00 0.00 36.57 2.43
93 94 6.435277 AGACATTGCTTGTATCCTTGATGTTT 59.565 34.615 0.00 0.00 39.18 2.83
94 95 5.948162 AGACATTGCTTGTATCCTTGATGTT 59.052 36.000 0.00 0.00 39.18 2.71
95 96 5.356190 CAGACATTGCTTGTATCCTTGATGT 59.644 40.000 0.00 0.00 39.18 3.06
96 97 5.220989 CCAGACATTGCTTGTATCCTTGATG 60.221 44.000 0.00 0.00 39.18 3.07
97 98 4.885907 CCAGACATTGCTTGTATCCTTGAT 59.114 41.667 0.00 0.00 39.18 2.57
98 99 4.019411 TCCAGACATTGCTTGTATCCTTGA 60.019 41.667 0.00 0.00 39.18 3.02
99 100 4.095483 GTCCAGACATTGCTTGTATCCTTG 59.905 45.833 0.00 0.00 39.18 3.61
100 101 4.018960 AGTCCAGACATTGCTTGTATCCTT 60.019 41.667 0.00 0.00 39.18 3.36
101 102 3.521126 AGTCCAGACATTGCTTGTATCCT 59.479 43.478 0.00 0.00 39.18 3.24
102 103 3.878778 AGTCCAGACATTGCTTGTATCC 58.121 45.455 0.00 0.00 39.18 2.59
103 104 5.874810 TGTTAGTCCAGACATTGCTTGTATC 59.125 40.000 0.00 0.00 39.18 2.24
104 105 5.804639 TGTTAGTCCAGACATTGCTTGTAT 58.195 37.500 0.00 0.00 39.18 2.29
105 106 5.011635 TCTGTTAGTCCAGACATTGCTTGTA 59.988 40.000 0.00 0.00 39.18 2.41
106 107 4.067896 CTGTTAGTCCAGACATTGCTTGT 58.932 43.478 0.00 0.00 42.79 3.16
107 108 4.318332 TCTGTTAGTCCAGACATTGCTTG 58.682 43.478 0.00 0.00 36.57 4.01
108 109 4.623932 TCTGTTAGTCCAGACATTGCTT 57.376 40.909 0.00 0.00 36.57 3.91
109 110 4.623932 TTCTGTTAGTCCAGACATTGCT 57.376 40.909 0.00 0.00 41.05 3.91
110 111 4.154918 CCTTTCTGTTAGTCCAGACATTGC 59.845 45.833 0.00 0.00 41.05 3.56
111 112 4.697352 CCCTTTCTGTTAGTCCAGACATTG 59.303 45.833 0.00 0.00 41.05 2.82
112 113 4.597507 TCCCTTTCTGTTAGTCCAGACATT 59.402 41.667 0.00 0.00 41.05 2.71
113 114 4.168101 TCCCTTTCTGTTAGTCCAGACAT 58.832 43.478 0.00 0.00 41.05 3.06
114 115 3.583228 TCCCTTTCTGTTAGTCCAGACA 58.417 45.455 0.00 0.00 41.05 3.41
115 116 4.283722 TCTTCCCTTTCTGTTAGTCCAGAC 59.716 45.833 0.00 0.00 41.05 3.51
116 117 4.489737 TCTTCCCTTTCTGTTAGTCCAGA 58.510 43.478 0.00 0.00 39.65 3.86
117 118 4.891992 TCTTCCCTTTCTGTTAGTCCAG 57.108 45.455 0.00 0.00 0.00 3.86
118 119 5.621193 CTTTCTTCCCTTTCTGTTAGTCCA 58.379 41.667 0.00 0.00 0.00 4.02
119 120 4.456222 GCTTTCTTCCCTTTCTGTTAGTCC 59.544 45.833 0.00 0.00 0.00 3.85
120 121 5.309638 AGCTTTCTTCCCTTTCTGTTAGTC 58.690 41.667 0.00 0.00 0.00 2.59
123 124 4.506802 GGGAGCTTTCTTCCCTTTCTGTTA 60.507 45.833 3.06 0.00 40.46 2.41
126 127 2.441410 GGGAGCTTTCTTCCCTTTCTG 58.559 52.381 3.06 0.00 40.46 3.02
170 171 4.160439 TGTTTCGAGCATAGAGAGTCCAAT 59.840 41.667 0.00 0.00 0.00 3.16
185 186 7.408132 TGATAGTGTTTCTTTCTGTTTCGAG 57.592 36.000 0.00 0.00 0.00 4.04
191 192 9.566432 AGATCTTTTGATAGTGTTTCTTTCTGT 57.434 29.630 0.00 0.00 39.67 3.41
219 220 6.736123 TCTCGCCAGATATTCAGTTTAGTAC 58.264 40.000 0.00 0.00 0.00 2.73
229 230 5.003692 TGCTATGATCTCGCCAGATATTC 57.996 43.478 0.00 0.00 39.71 1.75
233 234 4.202233 CCATATGCTATGATCTCGCCAGAT 60.202 45.833 0.00 0.00 42.59 2.90
237 238 3.118992 TCACCATATGCTATGATCTCGCC 60.119 47.826 0.00 0.00 0.00 5.54
257 258 4.792068 ACATCAAGAAGGGAGTTGTTTCA 58.208 39.130 0.00 0.00 0.00 2.69
264 265 1.611673 CGGCAACATCAAGAAGGGAGT 60.612 52.381 0.00 0.00 0.00 3.85
283 284 3.113260 AGACTGTTTGGAAAGTCCTCG 57.887 47.619 0.00 0.00 43.18 4.63
286 287 3.502595 GCCTAAGACTGTTTGGAAAGTCC 59.497 47.826 0.00 0.00 43.18 3.85
300 301 7.426929 ACATTAAATGATCATCGCCTAAGAC 57.573 36.000 9.06 0.00 0.00 3.01
320 321 2.864343 GCGCACGACCTTAATCTACATT 59.136 45.455 0.30 0.00 0.00 2.71
330 331 2.951475 TTTCCCTTGCGCACGACCTT 62.951 55.000 16.43 0.00 0.00 3.50
348 349 0.807496 GCAGCGAAGAAAGAGGCATT 59.193 50.000 0.00 0.00 0.00 3.56
350 351 0.321919 ATGCAGCGAAGAAAGAGGCA 60.322 50.000 0.00 0.00 0.00 4.75
353 354 3.600493 GCATGCAGCGAAGAAAGAG 57.400 52.632 14.21 0.00 0.00 2.85
376 377 4.323104 GGTTGATCAAGCTACTCTGGAAGT 60.323 45.833 26.44 0.00 42.33 3.01
388 389 1.743996 GAGGGTCTGGTTGATCAAGC 58.256 55.000 26.86 26.86 39.12 4.01
391 392 1.639722 TTCGAGGGTCTGGTTGATCA 58.360 50.000 0.00 0.00 0.00 2.92
407 408 2.940561 CCCCGACGGTTGTTTTCG 59.059 61.111 13.94 0.00 0.00 3.46
408 409 1.848932 GAGCCCCGACGGTTGTTTTC 61.849 60.000 13.94 0.00 0.00 2.29
422 423 2.379005 CAAGGAACTATTTGGGAGCCC 58.621 52.381 0.00 0.00 38.49 5.19
423 424 1.751351 GCAAGGAACTATTTGGGAGCC 59.249 52.381 0.00 0.00 38.49 4.70
426 427 2.109128 TGGTGCAAGGAACTATTTGGGA 59.891 45.455 0.00 0.00 38.49 4.37
469 470 4.660938 AGACAAAGGGGTGGCGGC 62.661 66.667 0.00 0.00 0.00 6.53
471 472 2.359975 GGAGACAAAGGGGTGGCG 60.360 66.667 0.00 0.00 0.00 5.69
472 473 2.035783 GGGAGACAAAGGGGTGGC 59.964 66.667 0.00 0.00 0.00 5.01
474 475 0.771127 TTCTGGGAGACAAAGGGGTG 59.229 55.000 0.00 0.00 0.00 4.61
494 497 6.485830 TTAATGTGGAAGGAGGTATCTCAG 57.514 41.667 5.14 0.00 41.69 3.35
522 576 1.226686 CTCCGCCTAGTGATGCATGC 61.227 60.000 11.82 11.82 0.00 4.06
555 609 3.317711 CACAAGTTAACATCACAAGGCCA 59.682 43.478 5.01 0.00 0.00 5.36
558 612 5.280945 CAACCACAAGTTAACATCACAAGG 58.719 41.667 8.61 3.01 36.18 3.61
654 708 4.686091 GGTTTATTTCTTCAAGCACCTTGC 59.314 41.667 0.22 0.00 45.46 4.01
655 709 5.841810 TGGTTTATTTCTTCAAGCACCTTG 58.158 37.500 0.00 0.00 42.25 3.61
656 710 6.098266 ACTTGGTTTATTTCTTCAAGCACCTT 59.902 34.615 0.00 0.00 38.56 3.50
657 711 5.598417 ACTTGGTTTATTTCTTCAAGCACCT 59.402 36.000 0.00 0.00 38.56 4.00
659 713 7.770801 AAACTTGGTTTATTTCTTCAAGCAC 57.229 32.000 0.00 0.00 38.56 4.40
660 714 8.785329 AAAAACTTGGTTTATTTCTTCAAGCA 57.215 26.923 0.00 0.00 38.56 3.91
661 715 9.098355 AGAAAAACTTGGTTTATTTCTTCAAGC 57.902 29.630 0.00 0.00 38.56 4.01
669 723 9.104965 GGTGCTTAAGAAAAACTTGGTTTATTT 57.895 29.630 6.67 0.00 39.38 1.40
672 726 6.267070 CGGTGCTTAAGAAAAACTTGGTTTA 58.733 36.000 6.67 0.00 39.38 2.01
673 727 5.106442 CGGTGCTTAAGAAAAACTTGGTTT 58.894 37.500 6.67 0.00 39.38 3.27
674 728 4.440940 CCGGTGCTTAAGAAAAACTTGGTT 60.441 41.667 6.67 0.00 39.38 3.67
675 729 3.067601 CCGGTGCTTAAGAAAAACTTGGT 59.932 43.478 6.67 0.00 39.38 3.67
676 730 3.067601 ACCGGTGCTTAAGAAAAACTTGG 59.932 43.478 6.12 7.29 39.38 3.61
677 731 4.041723 CACCGGTGCTTAAGAAAAACTTG 58.958 43.478 24.02 0.00 39.38 3.16
678 732 4.301637 CACCGGTGCTTAAGAAAAACTT 57.698 40.909 24.02 0.00 42.04 2.66
679 733 3.982576 CACCGGTGCTTAAGAAAAACT 57.017 42.857 24.02 0.00 0.00 2.66
692 746 3.813166 CCCTATACAAATAAGCACCGGTG 59.187 47.826 30.66 30.66 0.00 4.94
693 747 3.746432 GCCCTATACAAATAAGCACCGGT 60.746 47.826 0.00 0.00 0.00 5.28
694 748 2.812011 GCCCTATACAAATAAGCACCGG 59.188 50.000 0.00 0.00 0.00 5.28
695 749 3.472652 TGCCCTATACAAATAAGCACCG 58.527 45.455 0.00 0.00 0.00 4.94
696 750 4.515567 GTCTGCCCTATACAAATAAGCACC 59.484 45.833 0.00 0.00 0.00 5.01
697 751 4.211374 CGTCTGCCCTATACAAATAAGCAC 59.789 45.833 0.00 0.00 0.00 4.40
698 752 4.377021 CGTCTGCCCTATACAAATAAGCA 58.623 43.478 0.00 0.00 0.00 3.91
699 753 3.186613 GCGTCTGCCCTATACAAATAAGC 59.813 47.826 0.00 0.00 33.98 3.09
700 754 4.632153 AGCGTCTGCCCTATACAAATAAG 58.368 43.478 0.00 0.00 44.31 1.73
701 755 4.682778 AGCGTCTGCCCTATACAAATAA 57.317 40.909 0.00 0.00 44.31 1.40
702 756 4.682778 AAGCGTCTGCCCTATACAAATA 57.317 40.909 0.00 0.00 44.31 1.40
703 757 3.560636 AAGCGTCTGCCCTATACAAAT 57.439 42.857 0.00 0.00 44.31 2.32
704 758 4.475051 TTAAGCGTCTGCCCTATACAAA 57.525 40.909 0.00 0.00 44.31 2.83
705 759 4.682778 ATTAAGCGTCTGCCCTATACAA 57.317 40.909 0.00 0.00 44.31 2.41
706 760 4.682778 AATTAAGCGTCTGCCCTATACA 57.317 40.909 0.00 0.00 44.31 2.29
707 761 5.169295 CCTAATTAAGCGTCTGCCCTATAC 58.831 45.833 0.00 0.00 44.31 1.47
708 762 4.322499 GCCTAATTAAGCGTCTGCCCTATA 60.322 45.833 0.00 0.00 44.31 1.31
709 763 3.557264 GCCTAATTAAGCGTCTGCCCTAT 60.557 47.826 0.00 0.00 44.31 2.57
710 764 2.224209 GCCTAATTAAGCGTCTGCCCTA 60.224 50.000 0.00 0.00 44.31 3.53
711 765 1.475213 GCCTAATTAAGCGTCTGCCCT 60.475 52.381 0.00 0.00 44.31 5.19
712 766 0.945099 GCCTAATTAAGCGTCTGCCC 59.055 55.000 0.00 0.00 44.31 5.36
752 806 2.223805 GGGTTTTTCTGAAGCACCAGTG 60.224 50.000 17.20 0.00 35.71 3.66
753 807 2.031870 GGGTTTTTCTGAAGCACCAGT 58.968 47.619 17.20 0.00 35.71 4.00
754 808 2.031120 TGGGTTTTTCTGAAGCACCAG 58.969 47.619 17.20 0.00 35.55 4.00
755 809 2.151502 TGGGTTTTTCTGAAGCACCA 57.848 45.000 17.20 10.26 0.00 4.17
756 810 3.751479 ATTGGGTTTTTCTGAAGCACC 57.249 42.857 10.25 10.25 0.00 5.01
757 811 7.728847 AATAAATTGGGTTTTTCTGAAGCAC 57.271 32.000 0.00 0.00 0.00 4.40
758 812 8.744568 AAAATAAATTGGGTTTTTCTGAAGCA 57.255 26.923 0.00 0.00 0.00 3.91
759 813 9.663904 GAAAAATAAATTGGGTTTTTCTGAAGC 57.336 29.630 18.82 0.00 43.37 3.86
767 821 9.062524 GGTGCTTAGAAAAATAAATTGGGTTTT 57.937 29.630 0.00 0.00 0.00 2.43
768 822 8.436778 AGGTGCTTAGAAAAATAAATTGGGTTT 58.563 29.630 0.00 0.00 0.00 3.27
769 823 7.973402 AGGTGCTTAGAAAAATAAATTGGGTT 58.027 30.769 0.00 0.00 0.00 4.11
770 824 7.310423 GGAGGTGCTTAGAAAAATAAATTGGGT 60.310 37.037 0.00 0.00 0.00 4.51
771 825 7.041721 GGAGGTGCTTAGAAAAATAAATTGGG 58.958 38.462 0.00 0.00 0.00 4.12
772 826 7.041721 GGGAGGTGCTTAGAAAAATAAATTGG 58.958 38.462 0.00 0.00 0.00 3.16
773 827 7.840931 AGGGAGGTGCTTAGAAAAATAAATTG 58.159 34.615 0.00 0.00 0.00 2.32
774 828 9.541884 TTAGGGAGGTGCTTAGAAAAATAAATT 57.458 29.630 0.00 0.00 0.00 1.82
775 829 9.541884 TTTAGGGAGGTGCTTAGAAAAATAAAT 57.458 29.630 0.00 0.00 0.00 1.40
776 830 8.799367 GTTTAGGGAGGTGCTTAGAAAAATAAA 58.201 33.333 0.00 0.00 0.00 1.40
777 831 7.945664 TGTTTAGGGAGGTGCTTAGAAAAATAA 59.054 33.333 0.00 0.00 0.00 1.40
778 832 7.463431 TGTTTAGGGAGGTGCTTAGAAAAATA 58.537 34.615 0.00 0.00 0.00 1.40
779 833 6.311735 TGTTTAGGGAGGTGCTTAGAAAAAT 58.688 36.000 0.00 0.00 0.00 1.82
780 834 5.697067 TGTTTAGGGAGGTGCTTAGAAAAA 58.303 37.500 0.00 0.00 0.00 1.94
781 835 5.313280 TGTTTAGGGAGGTGCTTAGAAAA 57.687 39.130 0.00 0.00 0.00 2.29
782 836 4.986054 TGTTTAGGGAGGTGCTTAGAAA 57.014 40.909 0.00 0.00 0.00 2.52
783 837 4.534500 TGATGTTTAGGGAGGTGCTTAGAA 59.466 41.667 0.00 0.00 0.00 2.10
784 838 4.101114 TGATGTTTAGGGAGGTGCTTAGA 58.899 43.478 0.00 0.00 0.00 2.10
785 839 4.487714 TGATGTTTAGGGAGGTGCTTAG 57.512 45.455 0.00 0.00 0.00 2.18
786 840 4.385199 CCATGATGTTTAGGGAGGTGCTTA 60.385 45.833 0.00 0.00 0.00 3.09
787 841 3.624777 CATGATGTTTAGGGAGGTGCTT 58.375 45.455 0.00 0.00 0.00 3.91
788 842 2.092212 CCATGATGTTTAGGGAGGTGCT 60.092 50.000 0.00 0.00 0.00 4.40
789 843 2.301346 CCATGATGTTTAGGGAGGTGC 58.699 52.381 0.00 0.00 0.00 5.01
790 844 2.936202 CCCATGATGTTTAGGGAGGTG 58.064 52.381 0.00 0.00 44.30 4.00
791 845 1.215423 GCCCATGATGTTTAGGGAGGT 59.785 52.381 0.00 0.00 44.30 3.85
792 846 1.496429 AGCCCATGATGTTTAGGGAGG 59.504 52.381 0.00 0.00 44.30 4.30
793 847 4.647564 ATAGCCCATGATGTTTAGGGAG 57.352 45.455 0.00 0.00 44.30 4.30
794 848 4.504864 CGAATAGCCCATGATGTTTAGGGA 60.505 45.833 0.00 0.00 44.30 4.20
795 849 3.753272 CGAATAGCCCATGATGTTTAGGG 59.247 47.826 0.00 0.00 44.37 3.53
796 850 3.189287 GCGAATAGCCCATGATGTTTAGG 59.811 47.826 0.00 0.00 40.81 2.69
797 851 4.410492 GCGAATAGCCCATGATGTTTAG 57.590 45.455 0.00 0.00 40.81 1.85
819 873 2.331893 CGATTTGGCGGGCAAGACA 61.332 57.895 16.76 3.33 0.00 3.41
841 895 3.059188 GTGACTCGTTTGTGGTTACCATG 60.059 47.826 7.58 0.00 35.28 3.66
842 896 3.135994 GTGACTCGTTTGTGGTTACCAT 58.864 45.455 7.58 0.00 35.28 3.55
843 897 2.168936 AGTGACTCGTTTGTGGTTACCA 59.831 45.455 0.00 0.00 0.00 3.25
844 898 2.798847 GAGTGACTCGTTTGTGGTTACC 59.201 50.000 0.00 0.00 0.00 2.85
846 900 5.518848 TTAGAGTGACTCGTTTGTGGTTA 57.481 39.130 6.99 0.00 35.36 2.85
847 901 2.981859 AGAGTGACTCGTTTGTGGTT 57.018 45.000 6.99 0.00 35.36 3.67
936 3956 2.026879 GCGAGACGATGAGCCTCC 59.973 66.667 0.00 0.00 0.00 4.30
944 3964 1.065928 GGAACGATGGCGAGACGAT 59.934 57.895 5.29 0.00 41.64 3.73
1059 4116 3.151022 CGGTGGAGAGAGGGGAGC 61.151 72.222 0.00 0.00 0.00 4.70
1412 4531 2.235536 GACGACGGATTTGTTGCGGG 62.236 60.000 0.00 0.00 44.44 6.13
1762 5051 2.904434 ACCACCTAAACGTCTCCTTCAT 59.096 45.455 0.00 0.00 0.00 2.57
2180 5471 0.602638 TGAGCGCCCTACACAGTTTG 60.603 55.000 2.29 0.00 0.00 2.93
2289 5580 3.907927 CGACAAGTTGGCGTTCAAA 57.092 47.368 23.17 0.00 45.41 2.69
2296 5587 6.037172 ACTGAATAATACATCGACAAGTTGGC 59.963 38.462 7.96 2.47 0.00 4.52
2302 5593 9.952188 CTTCTCTACTGAATAATACATCGACAA 57.048 33.333 0.00 0.00 0.00 3.18
2360 5651 7.556275 TCAGAAACACAAATATATTCCAGGACC 59.444 37.037 0.00 0.00 0.00 4.46
2402 5693 1.365731 ACCCCCACATCCAATTTCCAT 59.634 47.619 0.00 0.00 0.00 3.41
2449 5740 1.774110 TTGCTTTCTGGTTTGCTGGA 58.226 45.000 0.00 0.00 0.00 3.86
2477 5768 6.381420 TGTTTTTAATGGAAACCAGGACAGAA 59.619 34.615 0.00 0.00 36.75 3.02
2478 5769 5.894393 TGTTTTTAATGGAAACCAGGACAGA 59.106 36.000 0.00 0.00 36.75 3.41
2546 5837 8.702163 AACAAAGAAGACGATGAAACAAAAAT 57.298 26.923 0.00 0.00 0.00 1.82
2629 5920 6.072893 ACGTACACCCAACAGAAATACATTTC 60.073 38.462 6.58 6.58 44.91 2.17
2634 5925 5.445845 CAAACGTACACCCAACAGAAATAC 58.554 41.667 0.00 0.00 0.00 1.89
2656 5947 3.312736 ACAGGGAAGAAGAAAAAGGCA 57.687 42.857 0.00 0.00 0.00 4.75
2694 5985 7.961326 ACCATAGAATTTAGGAACAAAGCAT 57.039 32.000 0.00 0.00 0.00 3.79
2767 6058 5.160699 TCATTTCACGATCATGCTTTAGC 57.839 39.130 0.00 0.00 42.50 3.09
2863 6192 1.851304 TCCTTGAATGGATTGGGTGC 58.149 50.000 0.00 0.00 0.00 5.01
2885 6214 1.200716 ACTGCATGTTCTGGATTTGCG 59.799 47.619 0.00 0.00 36.11 4.85
2915 6244 9.282247 GATCTTAGCTGAACAAACATAATTGTG 57.718 33.333 0.00 0.00 42.49 3.33
2970 6300 7.282224 TCTGTATTTAACTTGATATGGTGGCAC 59.718 37.037 9.70 9.70 0.00 5.01
3069 6400 5.426689 AGTTTATCATGCAAGTCTCAGGA 57.573 39.130 0.00 0.00 0.00 3.86
3075 6406 7.746475 GTGTGAAAGTAGTTTATCATGCAAGTC 59.254 37.037 0.00 0.00 0.00 3.01
3088 6419 7.328737 ACAAGTGTTCTAGTGTGAAAGTAGTT 58.671 34.615 0.00 0.00 33.97 2.24
3090 6421 7.772332 AACAAGTGTTCTAGTGTGAAAGTAG 57.228 36.000 0.00 0.00 31.64 2.57
3091 6422 8.447833 CAAAACAAGTGTTCTAGTGTGAAAGTA 58.552 33.333 0.00 0.00 37.25 2.24


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

AutoCloner maintained by Alex Coulton.