Multiple sequence alignment - TraesCS1B01G415900

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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 TraesCS1B01G415900 chr1B 100.000 4979 0 0 1 4979 640869300 640864322 0.000000e+00 9195
1 TraesCS1B01G415900 chr1B 88.636 220 15 3 96 315 658466421 658466212 4.940000e-65 259
2 TraesCS1B01G415900 chr1B 93.789 161 10 0 841 1001 623387385 623387545 4.980000e-60 243
3 TraesCS1B01G415900 chr1B 93.443 122 5 2 262 383 640869104 640868986 1.420000e-40 178
4 TraesCS1B01G415900 chr1A 92.589 2186 89 21 1193 3337 556963028 556960875 0.000000e+00 3072
5 TraesCS1B01G415900 chr1A 95.976 1665 48 10 3330 4979 556958432 556956772 0.000000e+00 2686
6 TraesCS1B01G415900 chr1D 95.699 1581 57 6 3408 4979 464628014 464626436 0.000000e+00 2532
7 TraesCS1B01G415900 chr1D 94.570 884 30 6 2521 3399 464629233 464628363 0.000000e+00 1351
8 TraesCS1B01G415900 chr1D 89.356 1071 56 22 1193 2231 464630443 464629399 0.000000e+00 1293
9 TraesCS1B01G415900 chr1D 88.034 117 10 2 1035 1150 464630566 464630453 8.690000e-28 135
10 TraesCS1B01G415900 chr7D 89.315 496 34 13 257 747 460644004 460643523 5.510000e-169 604
11 TraesCS1B01G415900 chr7D 89.713 418 30 10 334 747 587872916 587873324 5.710000e-144 521
12 TraesCS1B01G415900 chr3D 88.889 504 32 13 257 747 135539605 135539113 2.570000e-167 599
13 TraesCS1B01G415900 chr3D 92.342 222 14 2 96 315 135539701 135539481 3.740000e-81 313
14 TraesCS1B01G415900 chr3D 89.091 220 12 4 96 315 54326445 54326238 3.820000e-66 263
15 TraesCS1B01G415900 chr3D 83.803 284 27 11 735 1000 586563595 586563313 8.270000e-63 252
16 TraesCS1B01G415900 chr6B 87.897 504 30 13 262 749 697136666 697137154 9.360000e-157 564
17 TraesCS1B01G415900 chr6B 88.300 453 25 11 313 749 697044786 697045226 7.390000e-143 518
18 TraesCS1B01G415900 chr6B 85.603 514 34 19 262 749 697275782 697276281 2.070000e-138 503
19 TraesCS1B01G415900 chr6B 93.607 219 12 2 97 315 697136568 697136784 4.810000e-85 326
20 TraesCS1B01G415900 chr6B 92.727 220 12 2 96 315 697275685 697275900 1.040000e-81 315
21 TraesCS1B01G415900 chr6B 93.789 161 8 2 841 999 451934583 451934423 1.790000e-59 241
22 TraesCS1B01G415900 chr3B 86.590 522 43 12 251 752 72474397 72473883 7.280000e-153 551
23 TraesCS1B01G415900 chr3B 89.286 224 18 4 96 315 72474484 72474263 4.910000e-70 276
24 TraesCS1B01G415900 chr3B 93.750 160 9 1 841 1000 72473831 72473673 6.440000e-59 239
25 TraesCS1B01G415900 chr4B 89.183 453 22 8 321 746 180991260 180990808 1.580000e-149 540
26 TraesCS1B01G415900 chr4B 87.940 199 17 4 96 291 180990973 180991167 1.390000e-55 228
27 TraesCS1B01G415900 chr2B 85.662 544 39 15 303 839 18162079 18161568 2.040000e-148 536
28 TraesCS1B01G415900 chr2B 90.110 182 16 1 96 277 18162226 18162047 8.330000e-58 235
29 TraesCS1B01G415900 chrUn 87.742 465 26 16 292 752 473649569 473649132 9.560000e-142 514
30 TraesCS1B01G415900 chr3A 88.736 435 27 5 313 747 717907712 717907300 3.440000e-141 512
31 TraesCS1B01G415900 chr3A 92.857 168 11 1 841 1008 717908086 717908252 4.980000e-60 243
32 TraesCS1B01G415900 chr3A 84.324 185 11 7 4348 4514 1309996 1309812 1.110000e-36 165
33 TraesCS1B01G415900 chr4A 81.713 689 52 37 354 1001 695109246 695109901 1.600000e-139 507
34 TraesCS1B01G415900 chr6A 92.236 322 17 6 429 749 510971624 510971938 2.730000e-122 449
35 TraesCS1B01G415900 chr7B 92.273 220 11 5 96 315 323844981 323845194 1.740000e-79 307
36 TraesCS1B01G415900 chr7B 89.683 126 7 4 262 387 323845079 323845198 6.670000e-34 156
37 TraesCS1B01G415900 chr2D 85.069 288 22 13 735 1002 604062233 604061947 1.770000e-69 274
38 TraesCS1B01G415900 chr5B 95.062 162 6 2 841 1000 116672490 116672651 2.300000e-63 254
39 TraesCS1B01G415900 chr5B 95.000 160 7 1 841 999 116671404 116671245 2.980000e-62 250
40 TraesCS1B01G415900 chr5D 93.125 160 10 1 841 999 458911964 458911805 3.000000e-57 233


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 TraesCS1B01G415900 chr1B 640864322 640869300 4978 True 4686.500000 9195 96.721500 1 4979 2 chr1B.!!$R2 4978
1 TraesCS1B01G415900 chr1A 556956772 556963028 6256 True 2879.000000 3072 94.282500 1193 4979 2 chr1A.!!$R1 3786
2 TraesCS1B01G415900 chr1D 464626436 464630566 4130 True 1327.750000 2532 91.914750 1035 4979 4 chr1D.!!$R1 3944
3 TraesCS1B01G415900 chr3D 135539113 135539701 588 True 456.000000 599 90.615500 96 747 2 chr3D.!!$R3 651
4 TraesCS1B01G415900 chr6B 697136568 697137154 586 False 445.000000 564 90.752000 97 749 2 chr6B.!!$F2 652
5 TraesCS1B01G415900 chr6B 697275685 697276281 596 False 409.000000 503 89.165000 96 749 2 chr6B.!!$F3 653
6 TraesCS1B01G415900 chr3B 72473673 72474484 811 True 355.333333 551 89.875333 96 1000 3 chr3B.!!$R1 904
7 TraesCS1B01G415900 chr2B 18161568 18162226 658 True 385.500000 536 87.886000 96 839 2 chr2B.!!$R1 743
8 TraesCS1B01G415900 chr4A 695109246 695109901 655 False 507.000000 507 81.713000 354 1001 1 chr4A.!!$F1 647

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
60 61 0.101759 TACCGCTGTTACGCCATCTC 59.898 55.0 0.0 0.0 0.00 2.75 F
70 71 0.107945 ACGCCATCTCTTCTTCAGCC 60.108 55.0 0.0 0.0 0.00 4.85 F
1022 1125 0.034767 TCCTCGCCGACTCTCCTTTA 60.035 55.0 0.0 0.0 0.00 1.85 F
1260 1364 0.179111 CGCCTCTGGATTACGCAGAA 60.179 55.0 0.0 0.0 0.00 3.02 F
1919 2048 0.392998 GCGTGGATCTGGTTGGTGAT 60.393 55.0 0.0 0.0 0.00 3.06 F
2571 2738 0.036952 ATGAGCACAACTCCTCACCG 60.037 55.0 0.0 0.0 45.61 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1003 1106 0.034767 TAAAGGAGAGTCGGCGAGGA 60.035 55.000 11.2 0.0 0.0 3.71 R
1237 1341 0.102481 GCGTAATCCAGAGGCGAAGA 59.898 55.000 0.0 0.0 0.0 2.87 R
1900 2016 0.392998 ATCACCAACCAGATCCACGC 60.393 55.000 0.0 0.0 0.0 5.34 R
2102 2248 1.202498 GCGGCTACCCTATTCGTCTTT 60.202 52.381 0.0 0.0 0.0 2.52 R
3464 6430 1.152735 TAGCAGAGGTAGGAGGGCG 60.153 63.158 0.0 0.0 0.0 6.13 R
4548 7521 0.461339 TGGATAACTCGCCCGCTTTC 60.461 55.000 0.0 0.0 0.0 2.62 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
26 27 9.871238 GACATAACTTGACTACCTTCTCAATAA 57.129 33.333 0.00 0.00 0.00 1.40
31 32 8.954950 ACTTGACTACCTTCTCAATAATGATG 57.045 34.615 0.00 0.00 34.37 3.07
32 33 7.497249 ACTTGACTACCTTCTCAATAATGATGC 59.503 37.037 0.00 0.00 34.37 3.91
33 34 7.129457 TGACTACCTTCTCAATAATGATGCT 57.871 36.000 0.00 0.00 34.37 3.79
34 35 7.212976 TGACTACCTTCTCAATAATGATGCTC 58.787 38.462 0.00 0.00 34.37 4.26
35 36 7.070447 TGACTACCTTCTCAATAATGATGCTCT 59.930 37.037 0.00 0.00 34.37 4.09
36 37 7.800092 ACTACCTTCTCAATAATGATGCTCTT 58.200 34.615 0.00 0.00 34.37 2.85
37 38 8.270744 ACTACCTTCTCAATAATGATGCTCTTT 58.729 33.333 0.00 0.00 34.37 2.52
38 39 7.565323 ACCTTCTCAATAATGATGCTCTTTC 57.435 36.000 0.00 0.00 34.37 2.62
39 40 7.344913 ACCTTCTCAATAATGATGCTCTTTCT 58.655 34.615 0.00 0.00 34.37 2.52
40 41 7.833183 ACCTTCTCAATAATGATGCTCTTTCTT 59.167 33.333 0.00 0.00 34.37 2.52
41 42 8.684520 CCTTCTCAATAATGATGCTCTTTCTTT 58.315 33.333 0.00 0.00 34.37 2.52
44 45 9.113838 TCTCAATAATGATGCTCTTTCTTTACC 57.886 33.333 0.00 0.00 34.37 2.85
45 46 7.919690 TCAATAATGATGCTCTTTCTTTACCG 58.080 34.615 0.00 0.00 0.00 4.02
46 47 4.622701 AATGATGCTCTTTCTTTACCGC 57.377 40.909 0.00 0.00 0.00 5.68
47 48 3.334583 TGATGCTCTTTCTTTACCGCT 57.665 42.857 0.00 0.00 0.00 5.52
48 49 3.002791 TGATGCTCTTTCTTTACCGCTG 58.997 45.455 0.00 0.00 0.00 5.18
49 50 2.543777 TGCTCTTTCTTTACCGCTGT 57.456 45.000 0.00 0.00 0.00 4.40
50 51 2.846193 TGCTCTTTCTTTACCGCTGTT 58.154 42.857 0.00 0.00 0.00 3.16
51 52 3.997762 TGCTCTTTCTTTACCGCTGTTA 58.002 40.909 0.00 0.00 0.00 2.41
52 53 3.744426 TGCTCTTTCTTTACCGCTGTTAC 59.256 43.478 0.00 0.00 0.00 2.50
53 54 3.181533 GCTCTTTCTTTACCGCTGTTACG 60.182 47.826 0.00 0.00 0.00 3.18
54 55 2.733026 TCTTTCTTTACCGCTGTTACGC 59.267 45.455 0.00 0.00 0.00 4.42
55 56 1.431496 TTCTTTACCGCTGTTACGCC 58.569 50.000 0.00 0.00 0.00 5.68
56 57 0.317799 TCTTTACCGCTGTTACGCCA 59.682 50.000 0.00 0.00 0.00 5.69
57 58 1.066716 TCTTTACCGCTGTTACGCCAT 60.067 47.619 0.00 0.00 0.00 4.40
58 59 1.326548 CTTTACCGCTGTTACGCCATC 59.673 52.381 0.00 0.00 0.00 3.51
59 60 0.533491 TTACCGCTGTTACGCCATCT 59.467 50.000 0.00 0.00 0.00 2.90
60 61 0.101759 TACCGCTGTTACGCCATCTC 59.898 55.000 0.00 0.00 0.00 2.75
61 62 1.141881 CCGCTGTTACGCCATCTCT 59.858 57.895 0.00 0.00 0.00 3.10
62 63 0.460284 CCGCTGTTACGCCATCTCTT 60.460 55.000 0.00 0.00 0.00 2.85
63 64 0.924090 CGCTGTTACGCCATCTCTTC 59.076 55.000 0.00 0.00 0.00 2.87
64 65 1.469940 CGCTGTTACGCCATCTCTTCT 60.470 52.381 0.00 0.00 0.00 2.85
65 66 2.622436 GCTGTTACGCCATCTCTTCTT 58.378 47.619 0.00 0.00 0.00 2.52
66 67 2.605366 GCTGTTACGCCATCTCTTCTTC 59.395 50.000 0.00 0.00 0.00 2.87
67 68 3.849911 CTGTTACGCCATCTCTTCTTCA 58.150 45.455 0.00 0.00 0.00 3.02
68 69 3.849911 TGTTACGCCATCTCTTCTTCAG 58.150 45.455 0.00 0.00 0.00 3.02
69 70 2.586258 TACGCCATCTCTTCTTCAGC 57.414 50.000 0.00 0.00 0.00 4.26
70 71 0.107945 ACGCCATCTCTTCTTCAGCC 60.108 55.000 0.00 0.00 0.00 4.85
71 72 1.150567 CGCCATCTCTTCTTCAGCCG 61.151 60.000 0.00 0.00 0.00 5.52
72 73 1.435408 GCCATCTCTTCTTCAGCCGC 61.435 60.000 0.00 0.00 0.00 6.53
73 74 1.150567 CCATCTCTTCTTCAGCCGCG 61.151 60.000 0.00 0.00 0.00 6.46
74 75 0.459237 CATCTCTTCTTCAGCCGCGT 60.459 55.000 4.92 0.00 0.00 6.01
75 76 0.459237 ATCTCTTCTTCAGCCGCGTG 60.459 55.000 4.92 0.00 0.00 5.34
76 77 2.048222 TCTTCTTCAGCCGCGTGG 60.048 61.111 11.67 11.67 38.77 4.94
86 87 3.777925 CCGCGTGGCAAACTCTCG 61.778 66.667 0.00 0.00 0.00 4.04
87 88 3.036084 CGCGTGGCAAACTCTCGT 61.036 61.111 0.00 0.00 0.00 4.18
88 89 2.853914 GCGTGGCAAACTCTCGTC 59.146 61.111 0.00 0.00 0.00 4.20
89 90 1.954146 GCGTGGCAAACTCTCGTCA 60.954 57.895 0.00 0.00 0.00 4.35
90 91 1.495584 GCGTGGCAAACTCTCGTCAA 61.496 55.000 0.00 0.00 0.00 3.18
91 92 0.934496 CGTGGCAAACTCTCGTCAAA 59.066 50.000 0.00 0.00 0.00 2.69
92 93 1.329292 CGTGGCAAACTCTCGTCAAAA 59.671 47.619 0.00 0.00 0.00 2.44
93 94 2.716398 GTGGCAAACTCTCGTCAAAAC 58.284 47.619 0.00 0.00 0.00 2.43
94 95 2.096819 GTGGCAAACTCTCGTCAAAACA 59.903 45.455 0.00 0.00 0.00 2.83
763 813 9.719355 AACAGAAAAGAACAACTAAAACCAAAT 57.281 25.926 0.00 0.00 0.00 2.32
795 851 2.163810 AAATGGCCACATGCACCTAT 57.836 45.000 8.16 0.00 43.89 2.57
807 863 1.301623 CACCTATTCGGCCCACCAA 59.698 57.895 0.00 0.00 35.61 3.67
816 872 3.140814 GCCCACCAAAGGCCGATC 61.141 66.667 0.00 0.00 45.16 3.69
1009 1112 1.763968 AAAATTAGCCCCTTCCTCGC 58.236 50.000 0.00 0.00 0.00 5.03
1010 1113 0.106669 AAATTAGCCCCTTCCTCGCC 60.107 55.000 0.00 0.00 0.00 5.54
1011 1114 2.325393 AATTAGCCCCTTCCTCGCCG 62.325 60.000 0.00 0.00 0.00 6.46
1012 1115 3.968837 TTAGCCCCTTCCTCGCCGA 62.969 63.158 0.00 0.00 0.00 5.54
1015 1118 3.839432 CCCCTTCCTCGCCGACTC 61.839 72.222 0.00 0.00 0.00 3.36
1016 1119 2.756283 CCCTTCCTCGCCGACTCT 60.756 66.667 0.00 0.00 0.00 3.24
1017 1120 2.776913 CCCTTCCTCGCCGACTCTC 61.777 68.421 0.00 0.00 0.00 3.20
1018 1121 2.776913 CCTTCCTCGCCGACTCTCC 61.777 68.421 0.00 0.00 0.00 3.71
1019 1122 1.751162 CTTCCTCGCCGACTCTCCT 60.751 63.158 0.00 0.00 0.00 3.69
1020 1123 1.304217 TTCCTCGCCGACTCTCCTT 60.304 57.895 0.00 0.00 0.00 3.36
1021 1124 0.898789 TTCCTCGCCGACTCTCCTTT 60.899 55.000 0.00 0.00 0.00 3.11
1022 1125 0.034767 TCCTCGCCGACTCTCCTTTA 60.035 55.000 0.00 0.00 0.00 1.85
1023 1126 0.382515 CCTCGCCGACTCTCCTTTAG 59.617 60.000 0.00 0.00 0.00 1.85
1024 1127 0.248702 CTCGCCGACTCTCCTTTAGC 60.249 60.000 0.00 0.00 0.00 3.09
1025 1128 1.227002 CGCCGACTCTCCTTTAGCC 60.227 63.158 0.00 0.00 0.00 3.93
1026 1129 1.227002 GCCGACTCTCCTTTAGCCG 60.227 63.158 0.00 0.00 0.00 5.52
1027 1130 1.664321 GCCGACTCTCCTTTAGCCGA 61.664 60.000 0.00 0.00 0.00 5.54
1028 1131 0.382515 CCGACTCTCCTTTAGCCGAG 59.617 60.000 0.00 0.00 0.00 4.63
1029 1132 1.380524 CGACTCTCCTTTAGCCGAGA 58.619 55.000 0.00 0.00 34.07 4.04
1098 1201 4.202223 TGTTCCGGGCTACATATTTCTCTC 60.202 45.833 0.00 0.00 0.00 3.20
1099 1202 2.897969 TCCGGGCTACATATTTCTCTCC 59.102 50.000 0.00 0.00 0.00 3.71
1104 1207 5.765182 CGGGCTACATATTTCTCTCCATTTT 59.235 40.000 0.00 0.00 0.00 1.82
1122 1225 6.213195 TCCATTTTCAACTTATGCCAGGAATT 59.787 34.615 0.00 0.00 0.00 2.17
1124 1227 7.064966 CCATTTTCAACTTATGCCAGGAATTTC 59.935 37.037 0.00 0.00 0.00 2.17
1125 1228 6.662865 TTTCAACTTATGCCAGGAATTTCA 57.337 33.333 0.00 0.00 0.00 2.69
1126 1229 6.662865 TTCAACTTATGCCAGGAATTTCAA 57.337 33.333 0.00 0.00 0.00 2.69
1127 1230 6.855763 TCAACTTATGCCAGGAATTTCAAT 57.144 33.333 0.00 0.00 0.00 2.57
1129 1232 7.322664 TCAACTTATGCCAGGAATTTCAATTC 58.677 34.615 3.97 3.97 43.12 2.17
1130 1233 6.855763 ACTTATGCCAGGAATTTCAATTCA 57.144 33.333 13.10 0.00 45.10 2.57
1139 1242 6.073819 CCAGGAATTTCAATTCAAAACCGAAC 60.074 38.462 13.10 0.00 45.10 3.95
1159 1262 1.270094 CGACAAATCGGCCCTATAGCA 60.270 52.381 0.00 0.00 44.99 3.49
1160 1263 2.805295 CGACAAATCGGCCCTATAGCAA 60.805 50.000 0.00 0.00 44.99 3.91
1161 1264 3.211045 GACAAATCGGCCCTATAGCAAA 58.789 45.455 0.00 0.00 0.00 3.68
1162 1265 3.626930 ACAAATCGGCCCTATAGCAAAA 58.373 40.909 0.00 0.00 0.00 2.44
1163 1266 4.215109 ACAAATCGGCCCTATAGCAAAAT 58.785 39.130 0.00 0.00 0.00 1.82
1164 1267 4.278419 ACAAATCGGCCCTATAGCAAAATC 59.722 41.667 0.00 0.00 0.00 2.17
1165 1268 2.163818 TCGGCCCTATAGCAAAATCG 57.836 50.000 0.00 0.00 0.00 3.34
1166 1269 1.414919 TCGGCCCTATAGCAAAATCGT 59.585 47.619 0.00 0.00 0.00 3.73
1167 1270 2.158871 TCGGCCCTATAGCAAAATCGTT 60.159 45.455 0.00 0.00 0.00 3.85
1168 1271 2.223377 CGGCCCTATAGCAAAATCGTTC 59.777 50.000 0.00 0.00 0.00 3.95
1169 1272 2.223377 GGCCCTATAGCAAAATCGTTCG 59.777 50.000 0.00 0.00 0.00 3.95
1170 1273 2.870411 GCCCTATAGCAAAATCGTTCGT 59.130 45.455 0.00 0.00 0.00 3.85
1171 1274 3.311596 GCCCTATAGCAAAATCGTTCGTT 59.688 43.478 0.00 0.00 0.00 3.85
1172 1275 4.201881 GCCCTATAGCAAAATCGTTCGTTT 60.202 41.667 0.00 0.00 0.00 3.60
1173 1276 5.675323 GCCCTATAGCAAAATCGTTCGTTTT 60.675 40.000 0.00 0.00 0.00 2.43
1174 1277 6.319399 CCCTATAGCAAAATCGTTCGTTTTT 58.681 36.000 7.78 7.78 0.00 1.94
1203 1306 2.225727 GAGGGAAGCAAAATCGTTCGTT 59.774 45.455 0.00 0.00 0.00 3.85
1204 1307 2.031157 AGGGAAGCAAAATCGTTCGTTG 60.031 45.455 0.00 0.00 0.00 4.10
1222 1325 3.467803 GTTGCAAAGCGTATCCCTATCT 58.532 45.455 0.00 0.00 0.00 1.98
1225 1329 2.613223 GCAAAGCGTATCCCTATCTCCC 60.613 54.545 0.00 0.00 0.00 4.30
1237 1341 2.385803 CTATCTCCCCCAACAGTACGT 58.614 52.381 0.00 0.00 0.00 3.57
1252 1356 1.134560 GTACGTCTTCGCCTCTGGATT 59.865 52.381 0.00 0.00 41.18 3.01
1260 1364 0.179111 CGCCTCTGGATTACGCAGAA 60.179 55.000 0.00 0.00 0.00 3.02
1267 1371 2.868583 CTGGATTACGCAGAACCTCATG 59.131 50.000 0.00 0.00 0.00 3.07
1780 1896 1.553704 GAGATCGGGTACAAGGTGGTT 59.446 52.381 0.00 0.00 0.00 3.67
1783 1899 1.302993 CGGGTACAAGGTGGTTGGG 60.303 63.158 0.00 0.00 40.90 4.12
1826 1942 1.899437 CTTCAAGCCCTACGAGCCCA 61.899 60.000 0.00 0.00 0.00 5.36
1848 1964 4.778415 CGCCGTCGTCCAGGTCTG 62.778 72.222 0.00 0.00 0.00 3.51
1850 1966 4.436998 CCGTCGTCCAGGTCTGCC 62.437 72.222 0.00 0.00 0.00 4.85
1851 1967 4.436998 CGTCGTCCAGGTCTGCCC 62.437 72.222 0.00 0.00 34.57 5.36
1852 1968 4.083862 GTCGTCCAGGTCTGCCCC 62.084 72.222 0.00 0.00 34.57 5.80
1900 2016 2.125512 CTTCGGTTCGGCTCTGGG 60.126 66.667 0.00 0.00 0.00 4.45
1919 2048 0.392998 GCGTGGATCTGGTTGGTGAT 60.393 55.000 0.00 0.00 0.00 3.06
1941 2070 2.024022 GTGCGCGTTGCTTGTTCA 59.976 55.556 8.43 0.00 46.63 3.18
1958 2087 1.753930 TCATGCAGATTGGTTCGCAT 58.246 45.000 0.00 0.00 41.79 4.73
2036 2165 5.351189 CGATGTGAATGACAAGGTAATGTGA 59.649 40.000 0.00 0.00 38.36 3.58
2102 2248 2.857186 TCAAGCTGCAACCTATGACA 57.143 45.000 1.02 0.00 0.00 3.58
2108 2254 2.159653 GCTGCAACCTATGACAAAGACG 60.160 50.000 0.00 0.00 0.00 4.18
2124 2270 1.202855 AGACGAATAGGGTAGCCGCTA 60.203 52.381 5.06 0.00 40.04 4.26
2127 2273 1.544691 CGAATAGGGTAGCCGCTATGT 59.455 52.381 5.06 0.00 43.75 2.29
2158 2304 3.515502 TCTCAAGTTGTAGTATGCAGGCT 59.484 43.478 2.11 0.00 27.68 4.58
2183 2329 3.760151 TCTTCTGTTCATTTGCTGATGGG 59.240 43.478 1.03 0.00 32.72 4.00
2293 2455 1.234615 TAGCACTTTGGTCCGCTTGC 61.235 55.000 0.00 0.00 35.93 4.01
2294 2456 2.555547 GCACTTTGGTCCGCTTGCT 61.556 57.895 0.00 0.00 0.00 3.91
2305 2467 2.083774 TCCGCTTGCTTTTGACCTATG 58.916 47.619 0.00 0.00 0.00 2.23
2357 2519 9.274065 GTATTGGTTCAAATTAGTCGTTCAATC 57.726 33.333 0.00 0.00 0.00 2.67
2405 2570 2.621338 TCGTCATGGAAGCTGCTTAAG 58.379 47.619 15.95 5.76 0.00 1.85
2406 2571 1.667724 CGTCATGGAAGCTGCTTAAGG 59.332 52.381 15.95 8.75 0.00 2.69
2428 2593 4.337274 GGGGTTGCTGTATAATGTACCAAC 59.663 45.833 0.00 0.00 0.00 3.77
2447 2612 6.958255 ACCAACAATTGAATTTTAAGCTTGC 58.042 32.000 13.59 0.00 0.00 4.01
2474 2640 5.734720 AGTGTATGGAGTATGGACTTGTTG 58.265 41.667 0.00 0.00 35.45 3.33
2500 2666 4.935702 ACATGAATTGTTGTGGTTGACAG 58.064 39.130 0.00 0.00 33.74 3.51
2510 2676 2.104111 TGTGGTTGACAGGTTGAGTAGG 59.896 50.000 0.00 0.00 0.00 3.18
2519 2685 5.360999 TGACAGGTTGAGTAGGACTATCATG 59.639 44.000 0.00 0.00 0.00 3.07
2571 2738 0.036952 ATGAGCACAACTCCTCACCG 60.037 55.000 0.00 0.00 45.61 4.94
2575 2742 1.145803 GCACAACTCCTCACCGTTAC 58.854 55.000 0.00 0.00 0.00 2.50
2585 2752 4.571919 TCCTCACCGTTACCATACTTTTG 58.428 43.478 0.00 0.00 0.00 2.44
2651 2818 5.864474 CAGTGAACCAGTGACTAGTTGATAC 59.136 44.000 0.14 0.00 36.99 2.24
2684 2851 8.046708 TGTAATGATTCCAGTAGCAAACATAGT 58.953 33.333 0.00 0.00 0.00 2.12
2714 2889 3.954200 TGCTTGTGCTTCTCATTCCATA 58.046 40.909 0.00 0.00 40.48 2.74
2718 2893 5.674525 CTTGTGCTTCTCATTCCATAGGTA 58.325 41.667 0.00 0.00 0.00 3.08
2719 2894 5.692115 TGTGCTTCTCATTCCATAGGTAA 57.308 39.130 0.00 0.00 0.00 2.85
2720 2895 6.252599 TGTGCTTCTCATTCCATAGGTAAT 57.747 37.500 0.00 0.00 0.00 1.89
2721 2896 6.662755 TGTGCTTCTCATTCCATAGGTAATT 58.337 36.000 0.00 0.00 0.00 1.40
2722 2897 7.118723 TGTGCTTCTCATTCCATAGGTAATTT 58.881 34.615 0.00 0.00 0.00 1.82
2723 2898 7.615365 TGTGCTTCTCATTCCATAGGTAATTTT 59.385 33.333 0.00 0.00 0.00 1.82
2724 2899 8.470002 GTGCTTCTCATTCCATAGGTAATTTTT 58.530 33.333 0.00 0.00 0.00 1.94
2725 2900 8.469200 TGCTTCTCATTCCATAGGTAATTTTTG 58.531 33.333 0.00 0.00 0.00 2.44
2746 2921 7.846644 TTTGAATTTTTCTGATGCTGTTGTT 57.153 28.000 0.00 0.00 0.00 2.83
2787 2962 8.068380 GTGCAGTTAGTTTTAAATCGAGTTCTT 58.932 33.333 0.00 0.00 0.00 2.52
2828 3003 4.020662 TCAAACAATAATTGGGAGGCCAAC 60.021 41.667 5.01 0.00 32.21 3.77
2924 3099 8.634335 TTTTCTGTCATGTTCATTAGAATGGA 57.366 30.769 2.52 0.00 37.03 3.41
3000 3175 7.956420 AAGTGTGTCTGATTAAATGTTACGA 57.044 32.000 0.00 0.00 0.00 3.43
3018 3193 6.584942 TGTTACGACTGCATTCTACAAACTAG 59.415 38.462 2.32 0.00 0.00 2.57
3084 3259 6.698008 TCCTTGTCTTAACATATTGCATGG 57.302 37.500 0.00 0.00 34.73 3.66
3088 3263 4.949238 TGTCTTAACATATTGCATGGCAGT 59.051 37.500 0.00 0.00 40.61 4.40
3107 3282 5.852827 GCAGTCTTCTTATTCTCTGCCTAT 58.147 41.667 0.00 0.00 41.26 2.57
3146 3321 5.939883 ACTGCATTTGAAAGCTGATGTACTA 59.060 36.000 11.05 0.00 34.35 1.82
3154 3329 9.587772 TTTGAAAGCTGATGTACTAGTCTATTC 57.412 33.333 0.00 0.00 0.00 1.75
3161 3336 7.041030 GCTGATGTACTAGTCTATTCTGCTACA 60.041 40.741 0.00 0.00 0.00 2.74
3806 6772 3.536956 ACCGTTTCAGTTCTCAGTCAA 57.463 42.857 0.00 0.00 0.00 3.18
3981 6947 5.153513 CGCTGTTGCTGCTTAAATTAAGAA 58.846 37.500 16.22 5.10 36.03 2.52
4098 7065 3.181510 ACGTGTCTGTTGCTTTTGTTCTC 60.182 43.478 0.00 0.00 0.00 2.87
4099 7066 3.181511 CGTGTCTGTTGCTTTTGTTCTCA 60.182 43.478 0.00 0.00 0.00 3.27
4154 7121 2.287909 GCCCTGTCTCTGTATCGTCATC 60.288 54.545 0.00 0.00 0.00 2.92
4280 7251 9.162764 GTTTATAGAGCTACACTGATTTTCCAA 57.837 33.333 0.00 0.00 0.00 3.53
4281 7252 9.905713 TTTATAGAGCTACACTGATTTTCCAAT 57.094 29.630 0.00 0.00 0.00 3.16
4282 7253 9.905713 TTATAGAGCTACACTGATTTTCCAATT 57.094 29.630 0.00 0.00 0.00 2.32
4352 7323 0.675837 CCTGCCATGTCCACTGTCTG 60.676 60.000 0.00 0.00 0.00 3.51
4420 7392 3.943034 CGAGATCTCGCGCCGTCT 61.943 66.667 30.41 3.67 46.50 4.18
4469 7441 5.241285 TGTTGTGTTTGTAGTCATGCATCAT 59.759 36.000 0.00 0.00 0.00 2.45
4539 7512 6.372381 TCCTTATACTTACCAAAGGCGTTTTC 59.628 38.462 0.70 0.00 38.70 2.29
4540 7513 6.373495 CCTTATACTTACCAAAGGCGTTTTCT 59.627 38.462 0.70 0.00 37.01 2.52
4542 7515 6.980051 ATACTTACCAAAGGCGTTTTCTAG 57.020 37.500 0.70 0.88 37.01 2.43
4544 7517 5.857268 ACTTACCAAAGGCGTTTTCTAGTA 58.143 37.500 0.70 0.01 37.01 1.82
4545 7518 6.290605 ACTTACCAAAGGCGTTTTCTAGTAA 58.709 36.000 0.70 7.32 37.01 2.24
4546 7519 6.203530 ACTTACCAAAGGCGTTTTCTAGTAAC 59.796 38.462 0.70 0.00 37.01 2.50
4547 7520 3.817084 ACCAAAGGCGTTTTCTAGTAACC 59.183 43.478 0.70 0.00 0.00 2.85
4548 7521 3.120442 CCAAAGGCGTTTTCTAGTAACCG 60.120 47.826 0.70 0.00 0.00 4.44
4663 7643 6.703607 CAGTAATCTGATCATGGTTACTCCAC 59.296 42.308 19.49 4.82 45.43 4.02
4833 7817 5.573219 CATGGGGAATAATCATTAGCCTCA 58.427 41.667 4.55 4.55 31.25 3.86
4859 7843 9.965902 ATCTCACTTTCCATGGATAATTATACC 57.034 33.333 17.06 6.19 0.00 2.73
4879 7863 4.297768 ACCCCCATTTCCTTTTGATATGG 58.702 43.478 5.09 5.09 46.48 2.74
4890 7874 4.020839 CCTTTTGATATGGCCATCAATCCC 60.021 45.833 24.80 6.74 42.83 3.85
4964 7948 3.802948 ATATGTCCTCTCACGTTCACC 57.197 47.619 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 9.388506 CATCATTATTGAGAAGGTAGTCAAGTT 57.611 33.333 0.00 0.00 36.16 2.66
6 7 7.497249 GCATCATTATTGAGAAGGTAGTCAAGT 59.503 37.037 0.00 0.00 36.16 3.16
7 8 7.714377 AGCATCATTATTGAGAAGGTAGTCAAG 59.286 37.037 0.00 0.00 36.16 3.02
8 9 7.568349 AGCATCATTATTGAGAAGGTAGTCAA 58.432 34.615 0.00 0.00 37.10 3.18
9 10 7.070447 AGAGCATCATTATTGAGAAGGTAGTCA 59.930 37.037 0.00 0.00 37.82 3.41
10 11 7.441017 AGAGCATCATTATTGAGAAGGTAGTC 58.559 38.462 0.00 0.00 37.82 2.59
11 12 7.372260 AGAGCATCATTATTGAGAAGGTAGT 57.628 36.000 0.00 0.00 37.82 2.73
12 13 8.674263 AAAGAGCATCATTATTGAGAAGGTAG 57.326 34.615 0.00 0.00 37.82 3.18
13 14 8.489489 AGAAAGAGCATCATTATTGAGAAGGTA 58.511 33.333 0.00 0.00 37.82 3.08
14 15 7.344913 AGAAAGAGCATCATTATTGAGAAGGT 58.655 34.615 0.00 0.00 37.82 3.50
15 16 7.804843 AGAAAGAGCATCATTATTGAGAAGG 57.195 36.000 0.00 0.00 37.82 3.46
18 19 9.113838 GGTAAAGAAAGAGCATCATTATTGAGA 57.886 33.333 0.00 0.00 37.82 3.27
19 20 8.066595 CGGTAAAGAAAGAGCATCATTATTGAG 58.933 37.037 0.00 0.00 37.82 3.02
20 21 7.467267 GCGGTAAAGAAAGAGCATCATTATTGA 60.467 37.037 0.00 0.00 37.82 2.57
21 22 6.634436 GCGGTAAAGAAAGAGCATCATTATTG 59.366 38.462 0.00 0.00 37.82 1.90
22 23 6.543831 AGCGGTAAAGAAAGAGCATCATTATT 59.456 34.615 0.00 0.00 37.82 1.40
23 24 6.017605 CAGCGGTAAAGAAAGAGCATCATTAT 60.018 38.462 0.00 0.00 37.82 1.28
24 25 5.294306 CAGCGGTAAAGAAAGAGCATCATTA 59.706 40.000 0.00 0.00 37.82 1.90
25 26 4.095483 CAGCGGTAAAGAAAGAGCATCATT 59.905 41.667 0.00 0.00 37.82 2.57
26 27 3.624861 CAGCGGTAAAGAAAGAGCATCAT 59.375 43.478 0.00 0.00 37.82 2.45
27 28 3.002791 CAGCGGTAAAGAAAGAGCATCA 58.997 45.455 0.00 0.00 37.82 3.07
28 29 3.003480 ACAGCGGTAAAGAAAGAGCATC 58.997 45.455 0.00 0.00 0.00 3.91
29 30 3.059352 ACAGCGGTAAAGAAAGAGCAT 57.941 42.857 0.00 0.00 0.00 3.79
30 31 2.543777 ACAGCGGTAAAGAAAGAGCA 57.456 45.000 0.00 0.00 0.00 4.26
31 32 3.181533 CGTAACAGCGGTAAAGAAAGAGC 60.182 47.826 0.00 0.00 0.00 4.09
32 33 3.181533 GCGTAACAGCGGTAAAGAAAGAG 60.182 47.826 0.00 0.00 0.00 2.85
33 34 2.733026 GCGTAACAGCGGTAAAGAAAGA 59.267 45.455 0.00 0.00 0.00 2.52
34 35 2.159747 GGCGTAACAGCGGTAAAGAAAG 60.160 50.000 0.00 0.00 38.18 2.62
35 36 1.799994 GGCGTAACAGCGGTAAAGAAA 59.200 47.619 0.00 0.00 38.18 2.52
36 37 1.270199 TGGCGTAACAGCGGTAAAGAA 60.270 47.619 0.00 0.00 38.18 2.52
37 38 0.317799 TGGCGTAACAGCGGTAAAGA 59.682 50.000 0.00 0.00 38.18 2.52
38 39 1.326548 GATGGCGTAACAGCGGTAAAG 59.673 52.381 0.00 0.00 38.18 1.85
39 40 1.066716 AGATGGCGTAACAGCGGTAAA 60.067 47.619 0.00 0.00 38.18 2.01
40 41 0.533491 AGATGGCGTAACAGCGGTAA 59.467 50.000 0.00 0.00 38.18 2.85
41 42 0.101759 GAGATGGCGTAACAGCGGTA 59.898 55.000 0.00 0.00 38.18 4.02
42 43 1.153628 GAGATGGCGTAACAGCGGT 60.154 57.895 0.00 0.00 38.18 5.68
43 44 0.460284 AAGAGATGGCGTAACAGCGG 60.460 55.000 0.00 0.00 38.18 5.52
44 45 0.924090 GAAGAGATGGCGTAACAGCG 59.076 55.000 0.00 0.00 38.18 5.18
45 46 2.301577 AGAAGAGATGGCGTAACAGC 57.698 50.000 0.00 0.00 0.00 4.40
46 47 3.849911 TGAAGAAGAGATGGCGTAACAG 58.150 45.455 0.00 0.00 0.00 3.16
47 48 3.849911 CTGAAGAAGAGATGGCGTAACA 58.150 45.455 0.00 0.00 0.00 2.41
48 49 2.605366 GCTGAAGAAGAGATGGCGTAAC 59.395 50.000 0.00 0.00 0.00 2.50
49 50 2.418746 GGCTGAAGAAGAGATGGCGTAA 60.419 50.000 0.00 0.00 0.00 3.18
50 51 1.137086 GGCTGAAGAAGAGATGGCGTA 59.863 52.381 0.00 0.00 0.00 4.42
51 52 0.107945 GGCTGAAGAAGAGATGGCGT 60.108 55.000 0.00 0.00 0.00 5.68
52 53 1.150567 CGGCTGAAGAAGAGATGGCG 61.151 60.000 0.00 0.00 37.17 5.69
53 54 1.435408 GCGGCTGAAGAAGAGATGGC 61.435 60.000 0.00 0.00 0.00 4.40
54 55 1.150567 CGCGGCTGAAGAAGAGATGG 61.151 60.000 0.00 0.00 0.00 3.51
55 56 0.459237 ACGCGGCTGAAGAAGAGATG 60.459 55.000 12.47 0.00 0.00 2.90
56 57 0.459237 CACGCGGCTGAAGAAGAGAT 60.459 55.000 12.47 0.00 0.00 2.75
57 58 1.080501 CACGCGGCTGAAGAAGAGA 60.081 57.895 12.47 0.00 0.00 3.10
58 59 2.097038 CCACGCGGCTGAAGAAGAG 61.097 63.158 12.47 0.00 0.00 2.85
59 60 2.048222 CCACGCGGCTGAAGAAGA 60.048 61.111 12.47 0.00 0.00 2.87
69 70 3.777925 CGAGAGTTTGCCACGCGG 61.778 66.667 12.47 0.00 0.00 6.46
70 71 3.036084 ACGAGAGTTTGCCACGCG 61.036 61.111 3.53 3.53 46.40 6.01
81 82 4.328440 CAGGAGCTATTGTTTTGACGAGAG 59.672 45.833 0.00 0.00 0.00 3.20
82 83 4.245660 CAGGAGCTATTGTTTTGACGAGA 58.754 43.478 0.00 0.00 0.00 4.04
83 84 3.372206 CCAGGAGCTATTGTTTTGACGAG 59.628 47.826 0.00 0.00 0.00 4.18
84 85 3.244422 ACCAGGAGCTATTGTTTTGACGA 60.244 43.478 0.00 0.00 0.00 4.20
85 86 3.074412 ACCAGGAGCTATTGTTTTGACG 58.926 45.455 0.00 0.00 0.00 4.35
86 87 4.072131 TCACCAGGAGCTATTGTTTTGAC 58.928 43.478 0.00 0.00 0.00 3.18
87 88 4.365514 TCACCAGGAGCTATTGTTTTGA 57.634 40.909 0.00 0.00 0.00 2.69
88 89 5.649782 ATTCACCAGGAGCTATTGTTTTG 57.350 39.130 0.00 0.00 0.00 2.44
89 90 8.494433 TCTATATTCACCAGGAGCTATTGTTTT 58.506 33.333 0.00 0.00 0.00 2.43
90 91 8.034313 TCTATATTCACCAGGAGCTATTGTTT 57.966 34.615 0.00 0.00 0.00 2.83
91 92 7.618019 TCTATATTCACCAGGAGCTATTGTT 57.382 36.000 0.00 0.00 0.00 2.83
92 93 7.805083 ATCTATATTCACCAGGAGCTATTGT 57.195 36.000 0.00 0.00 0.00 2.71
93 94 8.420222 CCTATCTATATTCACCAGGAGCTATTG 58.580 40.741 0.00 0.00 0.00 1.90
94 95 7.566879 CCCTATCTATATTCACCAGGAGCTATT 59.433 40.741 0.00 0.00 0.00 1.73
265 284 9.912634 AAGAATTTTCGTCATATTGTTTCACAT 57.087 25.926 0.00 0.00 0.00 3.21
266 285 9.743057 AAAGAATTTTCGTCATATTGTTTCACA 57.257 25.926 0.00 0.00 31.62 3.58
291 310 9.780413 GTTTCAAATTGTTTCATAAGCCAAAAA 57.220 25.926 0.00 0.00 0.00 1.94
292 311 8.950210 TGTTTCAAATTGTTTCATAAGCCAAAA 58.050 25.926 0.00 0.00 0.00 2.44
293 312 8.498054 TGTTTCAAATTGTTTCATAAGCCAAA 57.502 26.923 0.00 0.00 0.00 3.28
294 313 8.498054 TTGTTTCAAATTGTTTCATAAGCCAA 57.502 26.923 0.00 0.00 0.00 4.52
295 314 8.674263 ATTGTTTCAAATTGTTTCATAAGCCA 57.326 26.923 0.00 0.00 0.00 4.75
737 787 9.719355 ATTTGGTTTTAGTTGTTCTTTTCTGTT 57.281 25.926 0.00 0.00 0.00 3.16
763 813 6.227298 TGTGGCCATTTTTCTTTTTCTGTA 57.773 33.333 9.72 0.00 0.00 2.74
909 1011 9.660180 TTTTTAAAAATAATACACCATCAGCCC 57.340 29.630 9.31 0.00 0.00 5.19
1001 1104 1.316706 AAGGAGAGTCGGCGAGGAAG 61.317 60.000 11.20 0.00 0.00 3.46
1002 1105 0.898789 AAAGGAGAGTCGGCGAGGAA 60.899 55.000 11.20 0.00 0.00 3.36
1003 1106 0.034767 TAAAGGAGAGTCGGCGAGGA 60.035 55.000 11.20 0.00 0.00 3.71
1004 1107 0.382515 CTAAAGGAGAGTCGGCGAGG 59.617 60.000 11.20 0.00 0.00 4.63
1005 1108 0.248702 GCTAAAGGAGAGTCGGCGAG 60.249 60.000 11.20 0.00 0.00 5.03
1006 1109 1.664321 GGCTAAAGGAGAGTCGGCGA 61.664 60.000 4.99 4.99 0.00 5.54
1007 1110 1.227002 GGCTAAAGGAGAGTCGGCG 60.227 63.158 0.00 0.00 0.00 6.46
1008 1111 1.227002 CGGCTAAAGGAGAGTCGGC 60.227 63.158 0.00 0.00 38.37 5.54
1009 1112 0.382515 CTCGGCTAAAGGAGAGTCGG 59.617 60.000 0.00 0.00 42.26 4.79
1010 1113 1.380524 TCTCGGCTAAAGGAGAGTCG 58.619 55.000 0.00 0.00 43.34 4.18
1014 1117 2.933573 CTACCTCTCGGCTAAAGGAGA 58.066 52.381 3.33 0.00 37.69 3.71
1015 1118 1.338655 GCTACCTCTCGGCTAAAGGAG 59.661 57.143 3.33 0.00 34.16 3.69
1016 1119 1.400737 GCTACCTCTCGGCTAAAGGA 58.599 55.000 3.33 0.00 34.16 3.36
1017 1120 0.389757 GGCTACCTCTCGGCTAAAGG 59.610 60.000 0.00 0.00 36.21 3.11
1018 1121 1.112113 TGGCTACCTCTCGGCTAAAG 58.888 55.000 0.00 0.00 0.00 1.85
1019 1122 0.822164 GTGGCTACCTCTCGGCTAAA 59.178 55.000 0.00 0.00 0.00 1.85
1020 1123 0.323999 TGTGGCTACCTCTCGGCTAA 60.324 55.000 0.00 0.00 0.00 3.09
1021 1124 0.752009 CTGTGGCTACCTCTCGGCTA 60.752 60.000 0.00 0.00 0.00 3.93
1022 1125 2.037367 TGTGGCTACCTCTCGGCT 59.963 61.111 0.00 0.00 0.00 5.52
1023 1126 2.010582 CTCTGTGGCTACCTCTCGGC 62.011 65.000 0.00 0.00 0.00 5.54
1024 1127 0.394488 TCTCTGTGGCTACCTCTCGG 60.394 60.000 0.00 0.00 0.00 4.63
1025 1128 1.133407 GTTCTCTGTGGCTACCTCTCG 59.867 57.143 0.00 0.00 0.00 4.04
1026 1129 2.165437 CAGTTCTCTGTGGCTACCTCTC 59.835 54.545 0.00 0.00 36.97 3.20
1027 1130 2.175202 CAGTTCTCTGTGGCTACCTCT 58.825 52.381 0.00 0.00 36.97 3.69
1028 1131 2.165437 CTCAGTTCTCTGTGGCTACCTC 59.835 54.545 0.00 0.00 41.91 3.85
1029 1132 2.175202 CTCAGTTCTCTGTGGCTACCT 58.825 52.381 0.00 0.00 41.91 3.08
1030 1133 2.171840 TCTCAGTTCTCTGTGGCTACC 58.828 52.381 0.00 0.00 41.91 3.18
1031 1134 3.944055 TTCTCAGTTCTCTGTGGCTAC 57.056 47.619 0.00 0.00 41.91 3.58
1032 1135 5.016831 TGTATTCTCAGTTCTCTGTGGCTA 58.983 41.667 0.00 0.00 41.91 3.93
1033 1136 3.834813 TGTATTCTCAGTTCTCTGTGGCT 59.165 43.478 0.00 0.00 41.91 4.75
1034 1137 3.929610 GTGTATTCTCAGTTCTCTGTGGC 59.070 47.826 0.00 0.00 41.91 5.01
1035 1138 4.926238 GTGTGTATTCTCAGTTCTCTGTGG 59.074 45.833 0.00 0.00 41.91 4.17
1036 1139 5.532557 TGTGTGTATTCTCAGTTCTCTGTG 58.467 41.667 0.00 0.00 41.91 3.66
1037 1140 5.791336 TGTGTGTATTCTCAGTTCTCTGT 57.209 39.130 0.00 0.00 41.91 3.41
1038 1141 7.814587 TGTTATGTGTGTATTCTCAGTTCTCTG 59.185 37.037 0.00 0.00 42.54 3.35
1039 1142 7.896811 TGTTATGTGTGTATTCTCAGTTCTCT 58.103 34.615 0.00 0.00 0.00 3.10
1073 1176 4.850680 AGAAATATGTAGCCCGGAACAAA 58.149 39.130 0.73 0.00 0.00 2.83
1080 1183 4.543590 ATGGAGAGAAATATGTAGCCCG 57.456 45.455 0.00 0.00 0.00 6.13
1098 1201 5.404466 TTCCTGGCATAAGTTGAAAATGG 57.596 39.130 0.00 0.00 0.00 3.16
1099 1202 7.603404 TGAAATTCCTGGCATAAGTTGAAAATG 59.397 33.333 0.93 0.00 0.00 2.32
1104 1207 6.855763 ATTGAAATTCCTGGCATAAGTTGA 57.144 33.333 0.93 0.00 0.00 3.18
1112 1215 5.062528 GGTTTTGAATTGAAATTCCTGGCA 58.937 37.500 12.11 0.00 43.19 4.92
1114 1217 5.537188 TCGGTTTTGAATTGAAATTCCTGG 58.463 37.500 12.11 0.00 43.19 4.45
1122 1225 4.617808 TGTCGTTCGGTTTTGAATTGAA 57.382 36.364 0.00 0.00 0.00 2.69
1124 1227 5.385918 CGATTTGTCGTTCGGTTTTGAATTG 60.386 40.000 0.00 0.00 0.00 2.32
1125 1228 4.673311 CGATTTGTCGTTCGGTTTTGAATT 59.327 37.500 0.00 0.00 0.00 2.17
1126 1229 4.215965 CGATTTGTCGTTCGGTTTTGAAT 58.784 39.130 0.00 0.00 0.00 2.57
1127 1230 3.609475 CGATTTGTCGTTCGGTTTTGAA 58.391 40.909 0.00 0.00 0.00 2.69
1139 1242 1.270094 TGCTATAGGGCCGATTTGTCG 60.270 52.381 3.92 0.00 0.00 4.35
1150 1253 5.479716 AAACGAACGATTTTGCTATAGGG 57.520 39.130 1.04 0.00 0.00 3.53
1177 1280 4.664150 ACGATTTTGCTTCCCTCAAAAA 57.336 36.364 5.21 0.00 43.77 1.94
1178 1281 4.616953 GAACGATTTTGCTTCCCTCAAAA 58.383 39.130 3.79 3.79 44.40 2.44
1179 1282 3.304391 CGAACGATTTTGCTTCCCTCAAA 60.304 43.478 0.00 0.00 0.00 2.69
1180 1283 2.225491 CGAACGATTTTGCTTCCCTCAA 59.775 45.455 0.00 0.00 0.00 3.02
1181 1284 1.804151 CGAACGATTTTGCTTCCCTCA 59.196 47.619 0.00 0.00 0.00 3.86
1182 1285 1.804748 ACGAACGATTTTGCTTCCCTC 59.195 47.619 0.14 0.00 0.00 4.30
1183 1286 1.892209 ACGAACGATTTTGCTTCCCT 58.108 45.000 0.14 0.00 0.00 4.20
1184 1287 2.315901 CAACGAACGATTTTGCTTCCC 58.684 47.619 0.14 0.00 0.00 3.97
1185 1288 1.713932 GCAACGAACGATTTTGCTTCC 59.286 47.619 11.66 0.00 41.98 3.46
1186 1289 2.380660 TGCAACGAACGATTTTGCTTC 58.619 42.857 17.01 0.00 44.87 3.86
1187 1290 2.483583 TGCAACGAACGATTTTGCTT 57.516 40.000 17.01 0.00 44.87 3.91
1188 1291 2.483583 TTGCAACGAACGATTTTGCT 57.516 40.000 17.01 0.00 44.87 3.91
1189 1292 2.656368 GCTTTGCAACGAACGATTTTGC 60.656 45.455 7.19 11.91 44.84 3.68
1190 1293 2.407111 CGCTTTGCAACGAACGATTTTG 60.407 45.455 7.19 0.00 0.00 2.44
1191 1294 1.778591 CGCTTTGCAACGAACGATTTT 59.221 42.857 7.19 0.00 0.00 1.82
1203 1306 2.037251 GGAGATAGGGATACGCTTTGCA 59.963 50.000 0.00 0.00 37.60 4.08
1204 1307 2.613223 GGGAGATAGGGATACGCTTTGC 60.613 54.545 0.00 0.00 37.60 3.68
1222 1325 0.971386 GAAGACGTACTGTTGGGGGA 59.029 55.000 0.00 0.00 0.00 4.81
1225 1329 1.012486 GGCGAAGACGTACTGTTGGG 61.012 60.000 0.00 0.00 41.98 4.12
1237 1341 0.102481 GCGTAATCCAGAGGCGAAGA 59.898 55.000 0.00 0.00 0.00 2.87
1252 1356 2.416296 CGGTTACATGAGGTTCTGCGTA 60.416 50.000 0.00 0.00 0.00 4.42
1260 1364 2.553685 GGGGAAAACGGTTACATGAGGT 60.554 50.000 0.00 0.00 0.00 3.85
1267 1371 2.679934 CCGCGGGGAAAACGGTTAC 61.680 63.158 20.10 0.00 42.01 2.50
1316 1420 1.000496 AGGGTTTAAGGGAAGGGAGC 59.000 55.000 0.00 0.00 0.00 4.70
1826 1942 2.490217 CTGGACGACGGCGAAGAT 59.510 61.111 22.49 0.00 41.64 2.40
1854 1970 0.530870 GAAGAAGATTCGGGCCGGAG 60.531 60.000 27.98 0.00 0.00 4.63
1855 1971 1.520666 GAAGAAGATTCGGGCCGGA 59.479 57.895 27.98 20.48 0.00 5.14
1856 1972 1.523938 GGAAGAAGATTCGGGCCGG 60.524 63.158 27.98 7.65 0.00 6.13
1857 1973 1.883084 CGGAAGAAGATTCGGGCCG 60.883 63.158 22.51 22.51 35.20 6.13
1897 2013 2.350895 CAACCAGATCCACGCCCA 59.649 61.111 0.00 0.00 0.00 5.36
1900 2016 0.392998 ATCACCAACCAGATCCACGC 60.393 55.000 0.00 0.00 0.00 5.34
1919 2048 4.927782 AAGCAACGCGCACCCAGA 62.928 61.111 5.73 0.00 46.13 3.86
1941 2070 1.674441 CTGATGCGAACCAATCTGCAT 59.326 47.619 0.00 0.00 44.86 3.96
1958 2087 1.581934 CGTTGCTCACCTTGAACTGA 58.418 50.000 0.00 0.00 0.00 3.41
2036 2165 2.047274 CTCGTTCCGCCCATGTGT 60.047 61.111 0.00 0.00 0.00 3.72
2051 2180 7.218963 GGAAACAACATTCAATCGAAATAGCTC 59.781 37.037 0.00 0.00 34.01 4.09
2052 2181 7.029563 GGAAACAACATTCAATCGAAATAGCT 58.970 34.615 0.00 0.00 34.01 3.32
2053 2182 7.029563 AGGAAACAACATTCAATCGAAATAGC 58.970 34.615 0.00 0.00 34.01 2.97
2054 2183 8.236586 TGAGGAAACAACATTCAATCGAAATAG 58.763 33.333 0.00 0.00 34.01 1.73
2102 2248 1.202498 GCGGCTACCCTATTCGTCTTT 60.202 52.381 0.00 0.00 0.00 2.52
2108 2254 3.679824 AACATAGCGGCTACCCTATTC 57.320 47.619 12.67 0.00 0.00 1.75
2124 2270 6.992715 ACTACAACTTGAGAGCTTGTAAACAT 59.007 34.615 0.00 0.00 33.32 2.71
2127 2273 7.117812 GCATACTACAACTTGAGAGCTTGTAAA 59.882 37.037 0.00 0.00 33.32 2.01
2158 2304 6.095860 CCCATCAGCAAATGAACAGAAGATAA 59.904 38.462 0.25 0.00 42.53 1.75
2183 2329 8.958119 TTGAGGTTTGACCATAGTGATATAAC 57.042 34.615 0.00 0.00 41.95 1.89
2293 2455 6.659242 AGTTCCCAACATACATAGGTCAAAAG 59.341 38.462 0.00 0.00 0.00 2.27
2294 2456 6.432783 CAGTTCCCAACATACATAGGTCAAAA 59.567 38.462 0.00 0.00 0.00 2.44
2305 2467 6.713450 TCTTAAGTTTCCAGTTCCCAACATAC 59.287 38.462 1.63 0.00 0.00 2.39
2385 2550 2.621338 CTTAAGCAGCTTCCATGACGA 58.379 47.619 12.07 0.00 0.00 4.20
2387 2552 2.019984 CCCTTAAGCAGCTTCCATGAC 58.980 52.381 12.07 0.00 0.00 3.06
2405 2570 4.159244 TGGTACATTATACAGCAACCCC 57.841 45.455 0.00 0.00 0.00 4.95
2406 2571 4.944930 TGTTGGTACATTATACAGCAACCC 59.055 41.667 11.86 0.00 45.46 4.11
2428 2593 8.007716 CACTTCAGCAAGCTTAAAATTCAATTG 58.992 33.333 0.00 0.00 32.09 2.32
2441 2606 2.304180 ACTCCATACACTTCAGCAAGCT 59.696 45.455 0.00 0.00 32.09 3.74
2447 2612 5.860941 AGTCCATACTCCATACACTTCAG 57.139 43.478 0.00 0.00 0.00 3.02
2484 2650 3.360867 TCAACCTGTCAACCACAACAAT 58.639 40.909 0.00 0.00 33.31 2.71
2490 2656 2.367567 TCCTACTCAACCTGTCAACCAC 59.632 50.000 0.00 0.00 0.00 4.16
2493 2659 5.185249 TGATAGTCCTACTCAACCTGTCAAC 59.815 44.000 0.00 0.00 0.00 3.18
2500 2666 4.282195 CCCTCATGATAGTCCTACTCAACC 59.718 50.000 0.00 0.00 0.00 3.77
2510 2676 2.334023 AGAAGGCCCCTCATGATAGTC 58.666 52.381 0.00 0.00 0.00 2.59
2519 2685 4.098044 GCAACTAAAATAAGAAGGCCCCTC 59.902 45.833 0.00 0.00 0.00 4.30
2571 2738 7.147312 GGTGGGTTTAACAAAAGTATGGTAAC 58.853 38.462 0.00 0.00 32.41 2.50
2575 2742 5.793030 TGGTGGGTTTAACAAAAGTATGG 57.207 39.130 0.00 0.00 0.00 2.74
2585 2752 5.880887 TGGTTTGAAAAATGGTGGGTTTAAC 59.119 36.000 0.00 0.00 0.00 2.01
2684 2851 1.605710 GAAGCACAAGCAAGCAGAGAA 59.394 47.619 0.00 0.00 45.49 2.87
2714 2889 9.783081 AGCATCAGAAAAATTCAAAAATTACCT 57.217 25.926 0.00 0.00 33.93 3.08
2718 2893 9.724839 CAACAGCATCAGAAAAATTCAAAAATT 57.275 25.926 0.00 0.00 36.64 1.82
2719 2894 8.895737 ACAACAGCATCAGAAAAATTCAAAAAT 58.104 25.926 0.00 0.00 0.00 1.82
2720 2895 8.266392 ACAACAGCATCAGAAAAATTCAAAAA 57.734 26.923 0.00 0.00 0.00 1.94
2721 2896 7.846644 ACAACAGCATCAGAAAAATTCAAAA 57.153 28.000 0.00 0.00 0.00 2.44
2722 2897 7.846644 AACAACAGCATCAGAAAAATTCAAA 57.153 28.000 0.00 0.00 0.00 2.69
2723 2898 9.545105 AATAACAACAGCATCAGAAAAATTCAA 57.455 25.926 0.00 0.00 0.00 2.69
2724 2899 9.545105 AAATAACAACAGCATCAGAAAAATTCA 57.455 25.926 0.00 0.00 0.00 2.57
2725 2900 9.801714 CAAATAACAACAGCATCAGAAAAATTC 57.198 29.630 0.00 0.00 0.00 2.17
2746 2921 6.714810 ACTAACTGCACCAAGTGATTCAAATA 59.285 34.615 0.00 0.00 35.23 1.40
2828 3003 5.233902 GCATGAACAGTAGCATCAGTAAGAG 59.766 44.000 0.00 0.00 0.00 2.85
3000 3175 4.003648 GTGCCTAGTTTGTAGAATGCAGT 58.996 43.478 0.00 0.00 27.68 4.40
3018 3193 3.804036 TGTGTACATATTGCCTAGTGCC 58.196 45.455 0.00 0.00 40.16 5.01
3084 3259 4.135747 AGGCAGAGAATAAGAAGACTGC 57.864 45.455 0.00 0.00 46.31 4.40
3088 3263 9.201989 TCAGTAAATAGGCAGAGAATAAGAAGA 57.798 33.333 0.00 0.00 0.00 2.87
3107 3282 6.880529 TCAAATGCAGTGATCAGATCAGTAAA 59.119 34.615 18.75 11.30 40.85 2.01
3146 3321 9.757227 GTCTTAATGATTGTAGCAGAATAGACT 57.243 33.333 0.00 0.00 0.00 3.24
3154 3329 4.877823 TGCCAGTCTTAATGATTGTAGCAG 59.122 41.667 0.00 0.00 30.64 4.24
3161 3336 5.002464 GCACATTGCCAGTCTTAATGATT 57.998 39.130 0.00 0.00 37.42 2.57
3464 6430 1.152735 TAGCAGAGGTAGGAGGGCG 60.153 63.158 0.00 0.00 0.00 6.13
3922 6888 7.025963 GCTTATCTGTTCCTTCTTGTTGAATG 58.974 38.462 0.00 0.00 33.71 2.67
3981 6947 4.015084 CAGCAACCTTCCTTGATTCATCT 58.985 43.478 0.00 0.00 0.00 2.90
4154 7121 0.716108 CGAGAGGCTTGTGCGTTAAG 59.284 55.000 0.00 0.00 40.82 1.85
4305 7276 5.062528 TGTATCAGAACACATTCAACAGCA 58.937 37.500 0.00 0.00 37.29 4.41
4352 7323 9.525409 AGTTTCATTATTTATGCATTGAAGAGC 57.475 29.630 3.54 2.75 34.06 4.09
4420 7392 1.630369 AGTTACATCTGCAGAAGCCCA 59.370 47.619 22.50 2.30 41.13 5.36
4469 7441 6.522625 TTGTGAAAGACCAGATTGTCAAAA 57.477 33.333 0.00 0.00 37.73 2.44
4547 7520 1.488261 GGATAACTCGCCCGCTTTCG 61.488 60.000 0.00 0.00 0.00 3.46
4548 7521 0.461339 TGGATAACTCGCCCGCTTTC 60.461 55.000 0.00 0.00 0.00 2.62
4663 7643 4.760530 TGAGTGAATGGATAACTCCTGG 57.239 45.455 0.00 0.00 42.59 4.45
4833 7817 9.965902 GGTATAATTATCCATGGAAAGTGAGAT 57.034 33.333 20.67 9.05 0.00 2.75
4859 7843 3.071457 GGCCATATCAAAAGGAAATGGGG 59.929 47.826 0.00 0.00 0.00 4.96
4879 7863 0.815615 GTCTCCGTGGGATTGATGGC 60.816 60.000 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.