Multiple sequence alignment - TraesCS5D01G203800

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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 TraesCS5D01G203800 chr5D 100.000 4359 0 0 1 4359 309007529 309003171 0.000000e+00 8050.0
1 TraesCS5D01G203800 chr5D 100.000 34 0 0 3122 3155 3040005 3040038 3.640000e-06 63.9
2 TraesCS5D01G203800 chr5A 90.697 2010 99 31 1471 3438 389071140 389073103 0.000000e+00 2595.0
3 TraesCS5D01G203800 chr5A 90.576 1475 73 29 1 1433 389069687 389071137 0.000000e+00 1893.0
4 TraesCS5D01G203800 chr5A 91.270 126 10 1 3996 4121 389073677 389073801 2.080000e-38 171.0
5 TraesCS5D01G203800 chr5A 94.382 89 5 0 3912 4000 48918164 48918076 2.110000e-28 137.0
6 TraesCS5D01G203800 chr5B 93.183 1599 70 11 1863 3426 354240637 354239043 0.000000e+00 2313.0
7 TraesCS5D01G203800 chr5B 89.460 1518 79 36 379 1869 354242157 354240694 0.000000e+00 1842.0
8 TraesCS5D01G203800 chr5B 92.784 388 15 4 1 375 354242583 354242196 2.290000e-152 549.0
9 TraesCS5D01G203800 chr5B 84.282 439 65 4 3478 3913 354239045 354238608 4.030000e-115 425.0
10 TraesCS5D01G203800 chr5B 81.739 115 16 5 4181 4295 629893470 629893579 1.670000e-14 91.6
11 TraesCS5D01G203800 chr6B 92.683 246 11 3 1188 1433 255097119 255096881 8.970000e-92 348.0
12 TraesCS5D01G203800 chr6B 93.450 229 13 2 4130 4358 446411726 446411952 5.400000e-89 339.0
13 TraesCS5D01G203800 chr6B 88.372 215 12 7 1471 1685 87322033 87321832 3.370000e-61 246.0
14 TraesCS5D01G203800 chr6B 87.907 215 13 7 1471 1685 255096878 255096677 1.570000e-59 241.0
15 TraesCS5D01G203800 chr6B 87.402 127 9 3 1056 1180 255097282 255097161 5.880000e-29 139.0
16 TraesCS5D01G203800 chr6B 96.386 83 3 0 3912 3994 1952051 1952133 2.110000e-28 137.0
17 TraesCS5D01G203800 chr6B 91.549 71 4 1 1112 1180 87322385 87322315 3.590000e-16 97.1
18 TraesCS5D01G203800 chr6B 88.000 75 5 4 2540 2612 460209798 460209870 7.770000e-13 86.1
19 TraesCS5D01G203800 chr4A 92.683 246 11 3 1188 1433 198002173 198001935 8.970000e-92 348.0
20 TraesCS5D01G203800 chr4A 87.907 215 13 7 1471 1685 198001932 198001731 1.570000e-59 241.0
21 TraesCS5D01G203800 chr4A 93.617 94 6 0 3906 3999 737382244 737382337 1.630000e-29 141.0
22 TraesCS5D01G203800 chr4A 91.549 71 4 1 1112 1180 198002284 198002214 3.590000e-16 97.1
23 TraesCS5D01G203800 chr2D 92.683 246 11 3 1188 1433 118801130 118800892 8.970000e-92 348.0
24 TraesCS5D01G203800 chr2D 87.925 265 17 11 1471 1735 118800889 118800640 9.160000e-77 298.0
25 TraesCS5D01G203800 chr2D 85.938 128 11 3 1055 1180 118801295 118801173 3.540000e-26 130.0
26 TraesCS5D01G203800 chr3B 92.946 241 9 4 1188 1427 169825955 169826188 1.160000e-90 344.0
27 TraesCS5D01G203800 chr3B 84.932 146 11 5 1471 1616 169826197 169826331 2.110000e-28 137.0
28 TraesCS5D01G203800 chr3B 95.349 86 4 0 3909 3994 652291748 652291833 2.110000e-28 137.0
29 TraesCS5D01G203800 chr3B 94.203 69 3 1 4219 4287 787345846 787345913 2.140000e-18 104.0
30 TraesCS5D01G203800 chr7B 92.917 240 10 3 1188 1427 374717242 374717474 4.170000e-90 342.0
31 TraesCS5D01G203800 chr7B 91.870 246 13 3 1188 1433 705711814 705711576 1.940000e-88 337.0
32 TraesCS5D01G203800 chr7B 87.907 215 13 7 1471 1685 374717483 374717684 1.570000e-59 241.0
33 TraesCS5D01G203800 chr7B 87.442 215 14 7 1471 1685 705711573 705711372 7.290000e-58 235.0
34 TraesCS5D01G203800 chr7B 87.500 128 9 3 1055 1180 705711977 705711855 1.630000e-29 141.0
35 TraesCS5D01G203800 chr7B 91.549 71 4 1 1112 1180 374717131 374717201 3.590000e-16 97.1
36 TraesCS5D01G203800 chr7A 92.500 240 11 3 1188 1427 133317083 133317315 1.940000e-88 337.0
37 TraesCS5D01G203800 chr7A 87.442 215 14 9 1471 1685 133317324 133317525 7.290000e-58 235.0
38 TraesCS5D01G203800 chr7A 91.549 71 4 1 1112 1180 133316972 133317042 3.590000e-16 97.1
39 TraesCS5D01G203800 chr6D 93.392 227 13 1 4135 4359 472641095 472641321 6.990000e-88 335.0
40 TraesCS5D01G203800 chr6D 87.075 147 12 5 4132 4276 470143842 470143701 4.510000e-35 159.0
41 TraesCS5D01G203800 chr6D 88.000 75 5 4 2540 2612 296824533 296824461 7.770000e-13 86.1
42 TraesCS5D01G203800 chr7D 88.584 219 25 0 4136 4354 597223350 597223568 2.580000e-67 267.0
43 TraesCS5D01G203800 chr7D 91.667 96 7 1 3904 3998 405186285 405186380 9.840000e-27 132.0
44 TraesCS5D01G203800 chr7D 89.831 59 5 1 3105 3162 130138175 130138233 1.680000e-09 75.0
45 TraesCS5D01G203800 chr1D 86.607 224 22 7 4132 4352 115572832 115572614 1.570000e-59 241.0
46 TraesCS5D01G203800 chr1D 92.473 93 7 0 3905 3997 464771381 464771289 2.730000e-27 134.0
47 TraesCS5D01G203800 chr1A 96.429 84 3 0 3911 3994 344497663 344497746 5.880000e-29 139.0
48 TraesCS5D01G203800 chr2B 94.382 89 5 0 3910 3998 648033141 648033053 2.110000e-28 137.0
49 TraesCS5D01G203800 chr1B 96.386 83 3 0 3912 3994 214173684 214173766 2.110000e-28 137.0
50 TraesCS5D01G203800 chr2A 93.151 73 3 2 4216 4287 759793215 759793144 5.960000e-19 106.0
51 TraesCS5D01G203800 chr4B 78.882 161 21 9 4130 4287 561592836 561592986 3.590000e-16 97.1
52 TraesCS5D01G203800 chr6A 88.000 75 5 4 2540 2612 423533558 423533486 7.770000e-13 86.1


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 TraesCS5D01G203800 chr5D 309003171 309007529 4358 True 8050.000000 8050 100.000000 1 4359 1 chr5D.!!$R1 4358
1 TraesCS5D01G203800 chr5A 389069687 389073801 4114 False 1553.000000 2595 90.847667 1 4121 3 chr5A.!!$F1 4120
2 TraesCS5D01G203800 chr5B 354238608 354242583 3975 True 1282.250000 2313 89.927250 1 3913 4 chr5B.!!$R1 3912
3 TraesCS5D01G203800 chr6B 255096677 255097282 605 True 242.666667 348 89.330667 1056 1685 3 chr6B.!!$R2 629
4 TraesCS5D01G203800 chr4A 198001731 198002284 553 True 228.700000 348 90.713000 1112 1685 3 chr4A.!!$R1 573
5 TraesCS5D01G203800 chr2D 118800640 118801295 655 True 258.666667 348 88.848667 1055 1735 3 chr2D.!!$R1 680
6 TraesCS5D01G203800 chr7B 705711372 705711977 605 True 237.666667 337 88.937333 1055 1685 3 chr7B.!!$R1 630
7 TraesCS5D01G203800 chr7B 374717131 374717684 553 False 226.700000 342 90.791000 1112 1685 3 chr7B.!!$F1 573
8 TraesCS5D01G203800 chr7A 133316972 133317525 553 False 223.033333 337 90.497000 1112 1685 3 chr7A.!!$F1 573

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
552 610 0.035056 CCCAAGAGATCAGCCCGTTT 60.035 55.0 0.0 0.0 0.00 3.60 F
607 670 0.599991 TGTACTGCACGCACTCCTTG 60.600 55.0 0.0 0.0 0.00 3.61 F
1762 1909 0.104120 TGATAATCACGTCCGGCAGG 59.896 55.0 0.0 0.0 39.46 4.85 F
2749 3004 1.403814 CTGACCCTCGGCTGATTCTA 58.596 55.0 0.0 0.0 0.00 2.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1762 1909 0.035630 ACCACTCTGATCTTGGCTGC 60.036 55.000 0.0 0.0 33.25 5.25 R
1804 1951 1.269448 GGCCGATGCTTTTCTTGACAA 59.731 47.619 0.0 0.0 37.74 3.18 R
3171 3435 1.270839 CCACCATCCACAAGAACGTCT 60.271 52.381 0.0 0.0 0.00 4.18 R
3983 4351 0.249363 GGCGTCTATTCCCTCCGTTC 60.249 60.000 0.0 0.0 0.00 3.95 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
38 39 9.731819 ATAAGGTCACGCTGAATATTATATACG 57.268 33.333 0.00 0.00 0.00 3.06
46 47 6.453791 CGCTGAATATTATATACGCACACACC 60.454 42.308 0.00 0.00 0.00 4.16
173 186 1.198759 CCTCCGTTTCTTCCTCCCCA 61.199 60.000 0.00 0.00 0.00 4.96
250 264 5.728471 CAATGCACCAACCATTAACCAATA 58.272 37.500 0.00 0.00 32.03 1.90
360 378 2.537625 GCAATCTCACACTACTGATCGC 59.462 50.000 0.00 0.00 0.00 4.58
446 499 0.666274 TCCACACGCTTTGCTACTCG 60.666 55.000 0.00 0.00 0.00 4.18
495 548 1.066430 TCTTTGCCAACGCTAGTAGGG 60.066 52.381 12.42 12.42 35.36 3.53
523 576 3.597728 GGCGCGTCTCCTCCTAGG 61.598 72.222 8.43 0.82 36.46 3.02
549 602 1.445095 CTCCCAAGAGATCAGCCCG 59.555 63.158 0.00 0.00 43.39 6.13
552 610 0.035056 CCCAAGAGATCAGCCCGTTT 60.035 55.000 0.00 0.00 0.00 3.60
607 670 0.599991 TGTACTGCACGCACTCCTTG 60.600 55.000 0.00 0.00 0.00 3.61
622 685 1.515020 CTTGCTCCTGTCCTCTCCG 59.485 63.158 0.00 0.00 0.00 4.63
633 712 0.677098 TCCTCTCCGTCTCTTCCGTG 60.677 60.000 0.00 0.00 0.00 4.94
672 759 3.499737 CGCCGTGCATTCAGGTCC 61.500 66.667 0.00 0.00 0.00 4.46
688 775 2.511600 CCCACGATCGGTTCAGGC 60.512 66.667 20.98 0.00 0.00 4.85
768 856 2.086869 CGCTGGGATTGATTTGTCTGT 58.913 47.619 0.00 0.00 0.00 3.41
770 858 3.350833 GCTGGGATTGATTTGTCTGTCT 58.649 45.455 0.00 0.00 0.00 3.41
771 859 3.376546 GCTGGGATTGATTTGTCTGTCTC 59.623 47.826 0.00 0.00 0.00 3.36
892 981 7.495901 TGACTAGAGCAAGGAATATCTTTGAG 58.504 38.462 6.42 0.00 35.74 3.02
893 982 7.124901 TGACTAGAGCAAGGAATATCTTTGAGT 59.875 37.037 6.42 1.34 35.74 3.41
895 984 5.679601 AGAGCAAGGAATATCTTTGAGTCC 58.320 41.667 6.42 0.00 35.74 3.85
896 985 5.190528 AGAGCAAGGAATATCTTTGAGTCCA 59.809 40.000 6.42 0.00 35.74 4.02
989 1078 2.740055 CGCAGACCGCAGAAAGCT 60.740 61.111 0.00 0.00 42.60 3.74
1005 1094 1.195115 AGCTTCGGGCAGTAATCTCA 58.805 50.000 4.35 0.00 44.79 3.27
1006 1095 1.555075 AGCTTCGGGCAGTAATCTCAA 59.445 47.619 4.35 0.00 44.79 3.02
1007 1096 1.666189 GCTTCGGGCAGTAATCTCAAC 59.334 52.381 0.00 0.00 41.35 3.18
1008 1097 2.935238 GCTTCGGGCAGTAATCTCAACA 60.935 50.000 0.00 0.00 41.35 3.33
1009 1098 2.672961 TCGGGCAGTAATCTCAACAG 57.327 50.000 0.00 0.00 0.00 3.16
1010 1099 1.207089 TCGGGCAGTAATCTCAACAGG 59.793 52.381 0.00 0.00 0.00 4.00
1011 1100 1.383523 GGGCAGTAATCTCAACAGGC 58.616 55.000 0.00 0.00 0.00 4.85
1012 1101 1.340017 GGGCAGTAATCTCAACAGGCA 60.340 52.381 0.00 0.00 31.63 4.75
1013 1102 2.436417 GGCAGTAATCTCAACAGGCAA 58.564 47.619 0.00 0.00 0.00 4.52
1014 1103 2.819608 GGCAGTAATCTCAACAGGCAAA 59.180 45.455 0.00 0.00 0.00 3.68
1015 1104 3.119708 GGCAGTAATCTCAACAGGCAAAG 60.120 47.826 0.00 0.00 0.00 2.77
1091 1180 4.072131 GCTTGACCAGTTGAATCCTTGTA 58.928 43.478 0.00 0.00 0.00 2.41
1098 1187 4.460382 CCAGTTGAATCCTTGTAAGTGCAT 59.540 41.667 0.00 0.00 0.00 3.96
1102 1191 2.736670 ATCCTTGTAAGTGCATCCCC 57.263 50.000 0.00 0.00 0.00 4.81
1103 1192 1.668826 TCCTTGTAAGTGCATCCCCT 58.331 50.000 0.00 0.00 0.00 4.79
1104 1193 1.992557 TCCTTGTAAGTGCATCCCCTT 59.007 47.619 0.00 0.00 0.00 3.95
1105 1194 2.094675 CCTTGTAAGTGCATCCCCTTG 58.905 52.381 0.00 0.00 0.00 3.61
1106 1195 2.555227 CCTTGTAAGTGCATCCCCTTGT 60.555 50.000 0.00 0.00 0.00 3.16
1107 1196 2.969821 TGTAAGTGCATCCCCTTGTT 57.030 45.000 0.00 0.00 0.00 2.83
1108 1197 3.237268 TGTAAGTGCATCCCCTTGTTT 57.763 42.857 0.00 0.00 0.00 2.83
1428 1574 1.439679 CTCAAAGACGGGCAGGTAAC 58.560 55.000 0.00 0.00 0.00 2.50
1465 1611 4.435877 CGAAATACGTACGGCTCTTACTTC 59.564 45.833 21.06 7.05 37.22 3.01
1497 1643 5.418840 AGAAGATGGTGTTGTTTTTGTCACT 59.581 36.000 0.00 0.00 0.00 3.41
1614 1760 8.487176 GTGGTGTTTTTGTCATTTAGCTTTATG 58.513 33.333 0.00 0.00 0.00 1.90
1762 1909 0.104120 TGATAATCACGTCCGGCAGG 59.896 55.000 0.00 0.00 39.46 4.85
1821 1968 4.409570 CATCCTTGTCAAGAAAAGCATCG 58.590 43.478 14.42 0.00 0.00 3.84
1856 2003 7.083858 CAGTCAAATACGATCAAACACCAATT 58.916 34.615 0.00 0.00 0.00 2.32
1954 2179 6.231211 CACCTACTTTCAGTCCAACTAATGT 58.769 40.000 0.00 0.00 0.00 2.71
1973 2198 4.291540 TGTGTTCTTGTTGCTGTGAATC 57.708 40.909 0.00 0.00 0.00 2.52
2274 2499 4.320456 CTGCACTCCACCACCGCT 62.320 66.667 0.00 0.00 0.00 5.52
2464 2689 2.125310 CGCTGGTAATGGCCACGA 60.125 61.111 8.16 0.00 36.14 4.35
2662 2892 1.912043 CCTCAGGACCAGAACCTCATT 59.088 52.381 0.00 0.00 35.35 2.57
2683 2937 2.225142 TGTCAAGGTACTCTCTCTGCCT 60.225 50.000 0.00 0.00 38.49 4.75
2690 2944 2.605601 TCTCTCTGCCTGCTGCCA 60.606 61.111 0.00 0.00 40.16 4.92
2692 2946 4.383861 TCTCTGCCTGCTGCCACG 62.384 66.667 0.00 0.00 40.16 4.94
2749 3004 1.403814 CTGACCCTCGGCTGATTCTA 58.596 55.000 0.00 0.00 0.00 2.10
2871 3126 2.047655 TCGGTGTCCATGTTCGCC 60.048 61.111 6.83 6.83 0.00 5.54
3023 3278 1.691196 TTGCTTGGTTCAGTCTTGGG 58.309 50.000 0.00 0.00 0.00 4.12
3061 3325 3.900601 AGAGGAAGAAGATGGCGATACAT 59.099 43.478 0.00 0.00 0.00 2.29
3083 3347 7.120716 ACATAATTTTAGTACCCCGTTCCATT 58.879 34.615 0.00 0.00 0.00 3.16
3171 3435 1.262151 GAGTAACTTTTCGTTGCGCCA 59.738 47.619 4.18 0.00 42.25 5.69
3233 3497 3.758554 TGAAATGAGAGGGCTTAGTTTGC 59.241 43.478 0.00 0.00 0.00 3.68
3309 3576 1.613925 GGAGGGAGCAAGTGGTTTTTC 59.386 52.381 0.00 0.00 0.00 2.29
3337 3604 8.698973 TCTTTTGGATTTGTACAGATGGTTAA 57.301 30.769 3.18 0.00 0.00 2.01
3363 3630 8.650143 AATCCCTGACTTTTGTATTATTGTGT 57.350 30.769 0.00 0.00 0.00 3.72
3423 3690 9.912634 AATATAAAATAAAGTCAATCATGGCGG 57.087 29.630 0.00 0.00 35.88 6.13
3507 3873 8.358148 ACACTTTCAAGAAGAGATAAACGTCTA 58.642 33.333 0.00 0.00 0.00 2.59
3516 3882 6.798315 AGAGATAAACGTCTAAGCGCTATA 57.202 37.500 12.05 4.66 34.88 1.31
3522 3888 3.692576 ACGTCTAAGCGCTATAGTTGTG 58.307 45.455 12.05 8.82 34.88 3.33
3543 3909 5.652014 TGTGACAGTCTGGACAAAGATTTTT 59.348 36.000 4.53 0.00 0.00 1.94
3575 3941 4.334481 TGTCGAGACTAGCAACGAATATCA 59.666 41.667 4.78 0.65 36.57 2.15
3582 3948 6.090898 AGACTAGCAACGAATATCAACACAAC 59.909 38.462 0.00 0.00 0.00 3.32
3585 3951 4.515191 AGCAACGAATATCAACACAACAGT 59.485 37.500 0.00 0.00 0.00 3.55
3595 3961 9.772973 AATATCAACACAACAGTAAGTAGACAA 57.227 29.630 0.00 0.00 0.00 3.18
3608 3974 7.169308 CAGTAAGTAGACAACGTCTTCAACAAT 59.831 37.037 1.36 0.00 40.28 2.71
3616 3982 6.791303 ACAACGTCTTCAACAATGTAACAAT 58.209 32.000 0.00 0.00 0.00 2.71
3621 3987 6.363088 CGTCTTCAACAATGTAACAATGCAAT 59.637 34.615 0.00 0.00 0.00 3.56
3625 3991 8.429493 TTCAACAATGTAACAATGCAATTTCA 57.571 26.923 0.00 0.00 31.22 2.69
3650 4016 1.680338 GCTGAGCCCGACCAATAAAT 58.320 50.000 0.00 0.00 0.00 1.40
3653 4019 3.016736 CTGAGCCCGACCAATAAATGTT 58.983 45.455 0.00 0.00 0.00 2.71
3655 4021 4.196193 TGAGCCCGACCAATAAATGTTAG 58.804 43.478 0.00 0.00 0.00 2.34
3658 4024 3.314357 GCCCGACCAATAAATGTTAGGAC 59.686 47.826 0.00 0.00 0.00 3.85
3660 4026 4.574828 CCCGACCAATAAATGTTAGGACAG 59.425 45.833 0.00 0.00 39.58 3.51
3661 4027 5.183228 CCGACCAATAAATGTTAGGACAGT 58.817 41.667 0.00 0.00 39.58 3.55
3668 4034 9.226606 CCAATAAATGTTAGGACAGTAGTTTCA 57.773 33.333 0.00 0.00 39.58 2.69
3672 4038 5.117355 TGTTAGGACAGTAGTTTCACTCG 57.883 43.478 0.00 0.00 0.00 4.18
3673 4039 2.726832 AGGACAGTAGTTTCACTCGC 57.273 50.000 0.00 0.00 0.00 5.03
3675 4041 2.563179 AGGACAGTAGTTTCACTCGCAT 59.437 45.455 0.00 0.00 0.00 4.73
3701 4068 7.609760 TGAAGCGTGTTCTAATCAACATATT 57.390 32.000 2.04 0.00 38.53 1.28
3740 4107 2.121538 TCGCATCCGCTAGCACTCT 61.122 57.895 16.45 0.00 35.30 3.24
3760 4127 6.828785 CACTCTATGCCAAAACTAAAGGGTAT 59.171 38.462 0.00 0.00 0.00 2.73
3761 4128 6.828785 ACTCTATGCCAAAACTAAAGGGTATG 59.171 38.462 0.00 0.00 0.00 2.39
3763 4130 7.054124 TCTATGCCAAAACTAAAGGGTATGAG 58.946 38.462 0.00 0.00 0.00 2.90
3783 4151 4.043310 TGAGAGATTGGTGGGACATCTTTT 59.957 41.667 0.00 0.00 42.15 2.27
3805 4173 1.098050 CCTTAGACCATTGCCACTGC 58.902 55.000 0.00 0.00 38.26 4.40
3809 4177 0.610232 AGACCATTGCCACTGCCTTC 60.610 55.000 0.00 0.00 36.33 3.46
3831 4199 1.153549 GGTCTGTCCATGTCTCGGC 60.154 63.158 0.00 0.00 35.97 5.54
3837 4205 2.058001 TCCATGTCTCGGCGTGGAT 61.058 57.895 11.61 0.99 46.33 3.41
3860 4228 1.228521 CCACTGCCATTCCACACCA 60.229 57.895 0.00 0.00 0.00 4.17
3863 4231 2.672651 TGCCATTCCACACCAGCG 60.673 61.111 0.00 0.00 0.00 5.18
3871 4239 3.406361 CACACCAGCGCGAGTCAC 61.406 66.667 12.10 0.00 0.00 3.67
3876 4244 2.029288 CCAGCGCGAGTCACATTGT 61.029 57.895 12.10 0.00 0.00 2.71
3878 4246 0.642291 CAGCGCGAGTCACATTGTAG 59.358 55.000 12.10 0.00 0.00 2.74
3890 4258 5.819379 AGTCACATTGTAGCATTCACCATAG 59.181 40.000 0.00 0.00 0.00 2.23
3905 4273 2.563179 ACCATAGTATTGGAGCCGCTAG 59.437 50.000 0.00 0.00 39.25 3.42
3913 4281 1.360911 GGAGCCGCTAGAGTGCTAC 59.639 63.158 8.89 6.46 34.99 3.58
3914 4282 1.104577 GGAGCCGCTAGAGTGCTACT 61.105 60.000 10.52 0.00 34.99 2.57
3915 4283 0.309612 GAGCCGCTAGAGTGCTACTC 59.690 60.000 8.89 7.88 45.38 2.59
3916 4284 1.104577 AGCCGCTAGAGTGCTACTCC 61.105 60.000 11.24 0.00 46.18 3.85
3917 4285 2.034607 CCGCTAGAGTGCTACTCCC 58.965 63.158 11.24 2.59 46.18 4.30
3918 4286 0.466555 CCGCTAGAGTGCTACTCCCT 60.467 60.000 11.24 0.01 46.18 4.20
3919 4287 0.948678 CGCTAGAGTGCTACTCCCTC 59.051 60.000 11.24 0.00 46.18 4.30
3920 4288 1.324383 GCTAGAGTGCTACTCCCTCC 58.676 60.000 11.24 0.00 46.18 4.30
3921 4289 1.600023 CTAGAGTGCTACTCCCTCCG 58.400 60.000 11.24 0.00 46.18 4.63
3922 4290 0.917533 TAGAGTGCTACTCCCTCCGT 59.082 55.000 11.24 0.00 46.18 4.69
3923 4291 0.394625 AGAGTGCTACTCCCTCCGTC 60.395 60.000 11.24 0.00 46.18 4.79
3924 4292 1.380112 AGTGCTACTCCCTCCGTCC 60.380 63.158 0.00 0.00 0.00 4.79
3925 4293 2.043248 TGCTACTCCCTCCGTCCC 60.043 66.667 0.00 0.00 0.00 4.46
3926 4294 2.043248 GCTACTCCCTCCGTCCCA 60.043 66.667 0.00 0.00 0.00 4.37
3927 4295 1.684734 GCTACTCCCTCCGTCCCAA 60.685 63.158 0.00 0.00 0.00 4.12
3928 4296 1.262640 GCTACTCCCTCCGTCCCAAA 61.263 60.000 0.00 0.00 0.00 3.28
3929 4297 1.272807 CTACTCCCTCCGTCCCAAAA 58.727 55.000 0.00 0.00 0.00 2.44
3930 4298 1.838077 CTACTCCCTCCGTCCCAAAAT 59.162 52.381 0.00 0.00 0.00 1.82
3931 4299 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
3932 4300 1.838077 ACTCCCTCCGTCCCAAAATAG 59.162 52.381 0.00 0.00 0.00 1.73
3933 4301 2.116238 CTCCCTCCGTCCCAAAATAGA 58.884 52.381 0.00 0.00 0.00 1.98
3934 4302 2.706190 CTCCCTCCGTCCCAAAATAGAT 59.294 50.000 0.00 0.00 0.00 1.98
3935 4303 3.901844 CTCCCTCCGTCCCAAAATAGATA 59.098 47.826 0.00 0.00 0.00 1.98
3936 4304 4.300345 TCCCTCCGTCCCAAAATAGATAA 58.700 43.478 0.00 0.00 0.00 1.75
3937 4305 4.102054 TCCCTCCGTCCCAAAATAGATAAC 59.898 45.833 0.00 0.00 0.00 1.89
3938 4306 4.102681 CCCTCCGTCCCAAAATAGATAACT 59.897 45.833 0.00 0.00 0.00 2.24
3939 4307 5.298347 CCTCCGTCCCAAAATAGATAACTC 58.702 45.833 0.00 0.00 0.00 3.01
3940 4308 5.163343 CCTCCGTCCCAAAATAGATAACTCA 60.163 44.000 0.00 0.00 0.00 3.41
3941 4309 6.302535 TCCGTCCCAAAATAGATAACTCAA 57.697 37.500 0.00 0.00 0.00 3.02
3942 4310 6.110707 TCCGTCCCAAAATAGATAACTCAAC 58.889 40.000 0.00 0.00 0.00 3.18
3943 4311 6.070424 TCCGTCCCAAAATAGATAACTCAACT 60.070 38.462 0.00 0.00 0.00 3.16
3944 4312 6.598064 CCGTCCCAAAATAGATAACTCAACTT 59.402 38.462 0.00 0.00 0.00 2.66
3945 4313 7.120726 CCGTCCCAAAATAGATAACTCAACTTT 59.879 37.037 0.00 0.00 0.00 2.66
3946 4314 7.962918 CGTCCCAAAATAGATAACTCAACTTTG 59.037 37.037 0.00 0.00 0.00 2.77
3947 4315 8.793592 GTCCCAAAATAGATAACTCAACTTTGT 58.206 33.333 0.00 0.00 0.00 2.83
3988 4356 8.943909 AAGTTAGGTCATCTATTTTAGAACGG 57.056 34.615 0.00 0.00 38.50 4.44
3989 4357 8.302515 AGTTAGGTCATCTATTTTAGAACGGA 57.697 34.615 0.00 0.00 38.50 4.69
3990 4358 8.414778 AGTTAGGTCATCTATTTTAGAACGGAG 58.585 37.037 0.00 0.00 38.50 4.63
3991 4359 6.163135 AGGTCATCTATTTTAGAACGGAGG 57.837 41.667 0.00 0.00 38.50 4.30
3992 4360 5.070580 AGGTCATCTATTTTAGAACGGAGGG 59.929 44.000 0.00 0.00 38.50 4.30
3993 4361 5.070047 GGTCATCTATTTTAGAACGGAGGGA 59.930 44.000 0.00 0.00 38.50 4.20
3994 4362 6.407752 GGTCATCTATTTTAGAACGGAGGGAA 60.408 42.308 0.00 0.00 38.50 3.97
3999 4367 7.949434 TCTATTTTAGAACGGAGGGAATAGAC 58.051 38.462 0.00 0.00 32.64 2.59
4007 4375 2.280186 GGGAATAGACGCCAGCGG 60.280 66.667 17.33 0.00 44.69 5.52
4008 4376 2.280186 GGAATAGACGCCAGCGGG 60.280 66.667 17.33 0.00 44.69 6.13
4026 4394 4.265056 GAACCACCGGTGCACCCT 62.265 66.667 29.75 12.73 35.34 4.34
4040 4408 2.754552 TGCACCCTTTACTCATCAATGC 59.245 45.455 0.00 0.00 0.00 3.56
4047 4415 4.816385 CCTTTACTCATCAATGCCATACGT 59.184 41.667 0.00 0.00 0.00 3.57
4093 4461 2.421739 CTATGGCCGTTCCCCTCG 59.578 66.667 0.77 0.00 0.00 4.63
4106 4474 3.924114 TCCCCTCGCAATAGATGAAAA 57.076 42.857 0.00 0.00 0.00 2.29
4107 4475 4.437682 TCCCCTCGCAATAGATGAAAAT 57.562 40.909 0.00 0.00 0.00 1.82
4124 4492 8.255905 AGATGAAAATTCCATTTGAGTTGATCC 58.744 33.333 0.00 0.00 31.77 3.36
4125 4493 7.300556 TGAAAATTCCATTTGAGTTGATCCA 57.699 32.000 0.00 0.00 31.77 3.41
4126 4494 7.380536 TGAAAATTCCATTTGAGTTGATCCAG 58.619 34.615 0.00 0.00 31.77 3.86
4127 4495 6.923199 AAATTCCATTTGAGTTGATCCAGT 57.077 33.333 0.00 0.00 0.00 4.00
4128 4496 6.923199 AATTCCATTTGAGTTGATCCAGTT 57.077 33.333 0.00 0.00 0.00 3.16
4129 4497 5.710513 TTCCATTTGAGTTGATCCAGTTG 57.289 39.130 0.00 0.00 0.00 3.16
4130 4498 4.984295 TCCATTTGAGTTGATCCAGTTGA 58.016 39.130 0.00 0.00 0.00 3.18
4131 4499 5.384336 TCCATTTGAGTTGATCCAGTTGAA 58.616 37.500 0.00 0.00 0.00 2.69
4132 4500 5.832595 TCCATTTGAGTTGATCCAGTTGAAA 59.167 36.000 0.00 0.00 0.00 2.69
4133 4501 6.016024 TCCATTTGAGTTGATCCAGTTGAAAG 60.016 38.462 0.00 0.00 0.00 2.62
4134 4502 6.016024 CCATTTGAGTTGATCCAGTTGAAAGA 60.016 38.462 0.00 0.00 0.00 2.52
4135 4503 6.624352 TTTGAGTTGATCCAGTTGAAAGAG 57.376 37.500 0.00 0.00 0.00 2.85
4136 4504 4.645535 TGAGTTGATCCAGTTGAAAGAGG 58.354 43.478 0.00 0.00 0.00 3.69
4137 4505 3.416156 AGTTGATCCAGTTGAAAGAGGC 58.584 45.455 0.00 0.00 0.00 4.70
4138 4506 2.489722 GTTGATCCAGTTGAAAGAGGCC 59.510 50.000 0.00 0.00 0.00 5.19
4139 4507 1.004745 TGATCCAGTTGAAAGAGGCCC 59.995 52.381 0.00 0.00 0.00 5.80
4140 4508 0.332972 ATCCAGTTGAAAGAGGCCCC 59.667 55.000 0.00 0.00 0.00 5.80
4141 4509 1.675641 CCAGTTGAAAGAGGCCCCG 60.676 63.158 0.00 0.00 0.00 5.73
4142 4510 2.034221 AGTTGAAAGAGGCCCCGC 59.966 61.111 0.00 0.00 0.00 6.13
4143 4511 3.431725 GTTGAAAGAGGCCCCGCG 61.432 66.667 0.00 0.00 0.00 6.46
4185 4553 3.179265 CGCACGTCGTTGCCCTAG 61.179 66.667 12.18 0.00 39.53 3.02
4186 4554 3.488090 GCACGTCGTTGCCCTAGC 61.488 66.667 0.00 0.00 36.42 3.42
4187 4555 3.179265 CACGTCGTTGCCCTAGCG 61.179 66.667 0.00 0.00 44.31 4.26
4199 4567 4.778143 CTAGCGCCGCCACCCTTT 62.778 66.667 4.98 0.00 0.00 3.11
4200 4568 4.770874 TAGCGCCGCCACCCTTTC 62.771 66.667 4.98 0.00 0.00 2.62
4202 4570 4.770874 GCGCCGCCACCCTTTCTA 62.771 66.667 0.00 0.00 0.00 2.10
4203 4571 2.818274 CGCCGCCACCCTTTCTAC 60.818 66.667 0.00 0.00 0.00 2.59
4204 4572 2.669240 GCCGCCACCCTTTCTACT 59.331 61.111 0.00 0.00 0.00 2.57
4205 4573 1.002502 GCCGCCACCCTTTCTACTT 60.003 57.895 0.00 0.00 0.00 2.24
4206 4574 1.025113 GCCGCCACCCTTTCTACTTC 61.025 60.000 0.00 0.00 0.00 3.01
4207 4575 0.392595 CCGCCACCCTTTCTACTTCC 60.393 60.000 0.00 0.00 0.00 3.46
4208 4576 0.613777 CGCCACCCTTTCTACTTCCT 59.386 55.000 0.00 0.00 0.00 3.36
4209 4577 1.405661 CGCCACCCTTTCTACTTCCTC 60.406 57.143 0.00 0.00 0.00 3.71
4210 4578 1.065345 GCCACCCTTTCTACTTCCTCC 60.065 57.143 0.00 0.00 0.00 4.30
4211 4579 2.552367 CCACCCTTTCTACTTCCTCCT 58.448 52.381 0.00 0.00 0.00 3.69
4212 4580 2.502130 CCACCCTTTCTACTTCCTCCTC 59.498 54.545 0.00 0.00 0.00 3.71
4213 4581 2.502130 CACCCTTTCTACTTCCTCCTCC 59.498 54.545 0.00 0.00 0.00 4.30
4214 4582 2.387510 ACCCTTTCTACTTCCTCCTCCT 59.612 50.000 0.00 0.00 0.00 3.69
4215 4583 2.769095 CCCTTTCTACTTCCTCCTCCTG 59.231 54.545 0.00 0.00 0.00 3.86
4216 4584 2.169561 CCTTTCTACTTCCTCCTCCTGC 59.830 54.545 0.00 0.00 0.00 4.85
4217 4585 1.867363 TTCTACTTCCTCCTCCTGCC 58.133 55.000 0.00 0.00 0.00 4.85
4218 4586 0.395862 TCTACTTCCTCCTCCTGCCG 60.396 60.000 0.00 0.00 0.00 5.69
4219 4587 2.022240 CTACTTCCTCCTCCTGCCGC 62.022 65.000 0.00 0.00 0.00 6.53
4220 4588 4.521062 CTTCCTCCTCCTGCCGCG 62.521 72.222 0.00 0.00 0.00 6.46
4288 4656 4.475135 GGCGGGGCTTCTCCTCAC 62.475 72.222 0.00 0.00 33.78 3.51
4289 4657 4.821589 GCGGGGCTTCTCCTCACG 62.822 72.222 0.00 0.00 33.78 4.35
4290 4658 3.068691 CGGGGCTTCTCCTCACGA 61.069 66.667 0.00 0.00 33.78 4.35
4291 4659 2.579738 GGGGCTTCTCCTCACGAC 59.420 66.667 0.00 0.00 34.56 4.34
4292 4660 2.182030 GGGCTTCTCCTCACGACG 59.818 66.667 0.00 0.00 34.39 5.12
4293 4661 2.182030 GGCTTCTCCTCACGACGG 59.818 66.667 0.00 0.00 0.00 4.79
4294 4662 2.507324 GCTTCTCCTCACGACGGC 60.507 66.667 0.00 0.00 0.00 5.68
4295 4663 2.995872 GCTTCTCCTCACGACGGCT 61.996 63.158 0.00 0.00 0.00 5.52
4296 4664 1.137825 CTTCTCCTCACGACGGCTC 59.862 63.158 0.00 0.00 0.00 4.70
4297 4665 2.272918 CTTCTCCTCACGACGGCTCC 62.273 65.000 0.00 0.00 0.00 4.70
4298 4666 3.827898 CTCCTCACGACGGCTCCC 61.828 72.222 0.00 0.00 0.00 4.30
4320 4688 2.358615 TGCAGGGCAGCAGTTACG 60.359 61.111 0.00 0.00 40.11 3.18
4321 4689 2.358737 GCAGGGCAGCAGTTACGT 60.359 61.111 0.00 0.00 0.00 3.57
4322 4690 2.680913 GCAGGGCAGCAGTTACGTG 61.681 63.158 0.00 0.00 0.00 4.49
4323 4691 2.034879 CAGGGCAGCAGTTACGTGG 61.035 63.158 0.00 0.00 0.00 4.94
4324 4692 2.214216 AGGGCAGCAGTTACGTGGA 61.214 57.895 0.00 0.00 0.00 4.02
4325 4693 1.741770 GGGCAGCAGTTACGTGGAG 60.742 63.158 0.00 0.00 0.00 3.86
4326 4694 1.004918 GGCAGCAGTTACGTGGAGT 60.005 57.895 0.00 0.00 0.00 3.85
4327 4695 0.602905 GGCAGCAGTTACGTGGAGTT 60.603 55.000 0.00 0.00 0.00 3.01
4328 4696 0.512952 GCAGCAGTTACGTGGAGTTG 59.487 55.000 0.00 0.00 0.00 3.16
4329 4697 0.512952 CAGCAGTTACGTGGAGTTGC 59.487 55.000 0.00 1.10 35.06 4.17
4330 4698 0.944311 AGCAGTTACGTGGAGTTGCG 60.944 55.000 0.00 0.00 38.69 4.85
4331 4699 1.219522 GCAGTTACGTGGAGTTGCGT 61.220 55.000 0.00 0.00 44.02 5.24
4332 4700 1.214367 CAGTTACGTGGAGTTGCGTT 58.786 50.000 0.00 0.00 41.77 4.84
4333 4701 1.070843 CAGTTACGTGGAGTTGCGTTG 60.071 52.381 0.00 0.00 41.77 4.10
4334 4702 1.202440 AGTTACGTGGAGTTGCGTTGA 60.202 47.619 0.00 0.00 41.77 3.18
4335 4703 1.071041 GTTACGTGGAGTTGCGTTGAC 60.071 52.381 0.00 0.00 41.77 3.18
4336 4704 0.935831 TACGTGGAGTTGCGTTGACG 60.936 55.000 0.00 0.00 41.77 4.35
4352 4720 4.160635 CGCGACCCGTCAATTGGC 62.161 66.667 0.00 1.91 0.00 4.52
4353 4721 4.160635 GCGACCCGTCAATTGGCG 62.161 66.667 25.04 25.04 43.72 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 6.530534 GCGTATATAATATTCAGCGTGACCTT 59.469 38.462 0.00 0.00 0.00 3.50
17 18 6.307077 TGTGCGTATATAATATTCAGCGTGAC 59.693 38.462 0.00 0.00 0.00 3.67
21 22 6.453791 GGTGTGTGCGTATATAATATTCAGCG 60.454 42.308 0.00 0.00 0.00 5.18
35 36 2.760634 ATCTTCATGGTGTGTGCGTA 57.239 45.000 0.00 0.00 0.00 4.42
38 39 4.436050 CGTAGAAATCTTCATGGTGTGTGC 60.436 45.833 0.00 0.00 0.00 4.57
46 47 7.757173 TCTTCTGAACTCGTAGAAATCTTCATG 59.243 37.037 0.00 0.00 34.09 3.07
173 186 3.624777 GATGGTGAGTGATTGGGACATT 58.375 45.455 0.00 0.00 39.30 2.71
250 264 1.077169 GGTGGATTGGAAGGAGGGTTT 59.923 52.381 0.00 0.00 0.00 3.27
523 576 2.950309 TGATCTCTTGGGAGCTACGTAC 59.050 50.000 0.00 0.00 39.31 3.67
549 602 7.929245 GGATTCAGAGATAAGAACCTAGGAAAC 59.071 40.741 17.98 6.15 0.00 2.78
552 610 6.928202 AGGATTCAGAGATAAGAACCTAGGA 58.072 40.000 17.98 0.00 0.00 2.94
607 670 1.379309 AGACGGAGAGGACAGGAGC 60.379 63.158 0.00 0.00 0.00 4.70
608 671 0.254747 AGAGACGGAGAGGACAGGAG 59.745 60.000 0.00 0.00 0.00 3.69
611 674 1.099689 GGAAGAGACGGAGAGGACAG 58.900 60.000 0.00 0.00 0.00 3.51
672 759 2.885644 CGCCTGAACCGATCGTGG 60.886 66.667 15.09 8.87 0.00 4.94
688 775 2.031516 CACTGGAGACAAGGCTGCG 61.032 63.158 0.00 0.00 42.06 5.18
768 856 6.311445 GCAAGTATCAGAAATTCAGAACGAGA 59.689 38.462 0.00 0.00 0.00 4.04
770 858 5.931724 TGCAAGTATCAGAAATTCAGAACGA 59.068 36.000 0.00 0.00 0.00 3.85
771 859 6.169419 TGCAAGTATCAGAAATTCAGAACG 57.831 37.500 0.00 0.00 0.00 3.95
872 961 5.190528 TGGACTCAAAGATATTCCTTGCTCT 59.809 40.000 0.00 0.00 0.00 4.09
892 981 8.571336 CAATATACCTTTCCTTGATCAATGGAC 58.429 37.037 19.90 0.00 0.00 4.02
893 982 7.725397 CCAATATACCTTTCCTTGATCAATGGA 59.275 37.037 17.56 17.56 0.00 3.41
895 984 8.696043 TCCAATATACCTTTCCTTGATCAATG 57.304 34.615 8.96 6.49 0.00 2.82
896 985 9.887862 ATTCCAATATACCTTTCCTTGATCAAT 57.112 29.630 8.96 0.00 0.00 2.57
956 1045 3.467119 CGCCTTCGTCGTTGTCGG 61.467 66.667 0.00 0.00 37.69 4.79
989 1078 2.354704 CCTGTTGAGATTACTGCCCGAA 60.355 50.000 0.00 0.00 0.00 4.30
994 1083 3.753272 TCTTTGCCTGTTGAGATTACTGC 59.247 43.478 0.00 0.00 0.00 4.40
1005 1094 4.402155 TGTTGAACATCTTCTTTGCCTGTT 59.598 37.500 0.00 0.00 33.02 3.16
1006 1095 3.953612 TGTTGAACATCTTCTTTGCCTGT 59.046 39.130 0.00 0.00 0.00 4.00
1007 1096 4.572985 TGTTGAACATCTTCTTTGCCTG 57.427 40.909 0.00 0.00 0.00 4.85
1008 1097 4.402155 TGTTGTTGAACATCTTCTTTGCCT 59.598 37.500 0.00 0.00 37.15 4.75
1009 1098 4.681744 TGTTGTTGAACATCTTCTTTGCC 58.318 39.130 0.00 0.00 37.15 4.52
1091 1180 2.397597 ACAAAACAAGGGGATGCACTT 58.602 42.857 0.00 0.00 0.00 3.16
1098 1187 3.035363 GGAAGGAAACAAAACAAGGGGA 58.965 45.455 0.00 0.00 0.00 4.81
1102 1191 4.736126 AGTGGGAAGGAAACAAAACAAG 57.264 40.909 0.00 0.00 0.00 3.16
1103 1192 5.221742 ACAAAGTGGGAAGGAAACAAAACAA 60.222 36.000 0.00 0.00 0.00 2.83
1104 1193 4.284746 ACAAAGTGGGAAGGAAACAAAACA 59.715 37.500 0.00 0.00 0.00 2.83
1105 1194 4.827692 ACAAAGTGGGAAGGAAACAAAAC 58.172 39.130 0.00 0.00 0.00 2.43
1106 1195 5.221742 ACAACAAAGTGGGAAGGAAACAAAA 60.222 36.000 0.00 0.00 0.00 2.44
1107 1196 4.284746 ACAACAAAGTGGGAAGGAAACAAA 59.715 37.500 0.00 0.00 0.00 2.83
1108 1197 3.835395 ACAACAAAGTGGGAAGGAAACAA 59.165 39.130 0.00 0.00 0.00 2.83
1351 1497 2.839486 TGAGGTTCTTGTCGCTGAAT 57.161 45.000 0.00 0.00 0.00 2.57
1428 1574 4.698276 CGTATTTCGTGTGGAAACTGAAG 58.302 43.478 0.00 0.00 46.81 3.02
1465 1611 4.330250 ACAACACCATCTTCTGAATCTGG 58.670 43.478 13.76 13.76 0.00 3.86
1497 1643 5.642063 CCTGAATTCCGAAAACTGTAGCTAA 59.358 40.000 2.27 0.00 0.00 3.09
1762 1909 0.035630 ACCACTCTGATCTTGGCTGC 60.036 55.000 0.00 0.00 33.25 5.25
1804 1951 1.269448 GGCCGATGCTTTTCTTGACAA 59.731 47.619 0.00 0.00 37.74 3.18
1821 1968 1.544246 GTATTTGACTGGTGGTTGGCC 59.456 52.381 0.00 0.00 0.00 5.36
1954 2179 3.202097 TCGATTCACAGCAACAAGAACA 58.798 40.909 0.00 0.00 0.00 3.18
2251 2476 1.835267 TGGTGGAGTGCAGGTACGT 60.835 57.895 0.00 0.00 0.00 3.57
2464 2689 2.525784 TGCAAAAATGGTGCAGGGT 58.474 47.368 0.00 0.00 46.76 4.34
2498 2724 3.329889 TGCAGCCAGGAACCCGAT 61.330 61.111 0.00 0.00 0.00 4.18
2662 2892 2.171840 GGCAGAGAGAGTACCTTGACA 58.828 52.381 0.00 0.00 0.00 3.58
2749 3004 3.069980 GAGCACGAGCCGGACAGAT 62.070 63.158 5.05 0.00 43.56 2.90
2790 3045 2.815647 CGCAGCTTCTTCCGGTCC 60.816 66.667 0.00 0.00 0.00 4.46
3000 3255 3.243201 CCAAGACTGAACCAAGCAAAGAC 60.243 47.826 0.00 0.00 0.00 3.01
3023 3278 6.631962 TCTTCCTCTTCCTCGAGTAAAAATC 58.368 40.000 12.31 0.00 0.00 2.17
3061 3325 6.719301 TGAATGGAACGGGGTACTAAAATTA 58.281 36.000 0.00 0.00 0.00 1.40
3083 3347 9.929180 GTACTAGATCAGCCACAATTAATATGA 57.071 33.333 0.00 0.00 0.00 2.15
3127 3391 5.243730 CCCTTCAATCCATATTAATTGCCGT 59.756 40.000 0.00 0.00 33.76 5.68
3130 3394 7.530426 ACTCCCTTCAATCCATATTAATTGC 57.470 36.000 0.00 0.00 33.76 3.56
3171 3435 1.270839 CCACCATCCACAAGAACGTCT 60.271 52.381 0.00 0.00 0.00 4.18
3256 3522 2.275318 CGACAGGGCAGATTTCTTCTC 58.725 52.381 0.00 0.00 29.93 2.87
3309 3576 7.661040 ACCATCTGTACAAATCCAAAAGAAAG 58.339 34.615 0.00 0.00 0.00 2.62
3337 3604 9.088987 ACACAATAATACAAAAGTCAGGGATTT 57.911 29.630 0.00 0.00 0.00 2.17
3458 3823 7.593644 GTGTTGTTGCGGAAGAAGTAAATTTAT 59.406 33.333 0.00 0.00 0.00 1.40
3464 3829 3.537580 AGTGTTGTTGCGGAAGAAGTAA 58.462 40.909 0.00 0.00 0.00 2.24
3507 3873 3.193691 AGACTGTCACAACTATAGCGCTT 59.806 43.478 18.68 6.25 0.00 4.68
3516 3882 3.197766 TCTTTGTCCAGACTGTCACAACT 59.802 43.478 10.88 0.00 0.00 3.16
3522 3888 7.530863 GGATAAAAATCTTTGTCCAGACTGTC 58.469 38.462 2.61 0.00 46.74 3.51
3543 3909 5.032327 TGCTAGTCTCGACAACTAGGATA 57.968 43.478 22.55 0.00 44.17 2.59
3575 3941 5.413499 ACGTTGTCTACTTACTGTTGTGTT 58.587 37.500 0.00 0.00 0.00 3.32
3582 3948 5.975344 TGTTGAAGACGTTGTCTACTTACTG 59.025 40.000 12.58 0.00 42.59 2.74
3585 3951 6.982141 ACATTGTTGAAGACGTTGTCTACTTA 59.018 34.615 12.58 4.73 42.59 2.24
3595 3961 5.212194 GCATTGTTACATTGTTGAAGACGT 58.788 37.500 8.69 0.00 0.00 4.34
3608 3974 5.159925 CCGTGATGAAATTGCATTGTTACA 58.840 37.500 0.00 0.00 0.00 2.41
3616 3982 1.469703 CTCAGCCGTGATGAAATTGCA 59.530 47.619 0.00 0.00 30.18 4.08
3621 3987 4.301505 GGCTCAGCCGTGATGAAA 57.698 55.556 0.00 0.00 39.62 2.69
3672 4038 4.722194 TGATTAGAACACGCTTCAAATGC 58.278 39.130 0.00 0.00 0.00 3.56
3673 4039 6.142139 TGTTGATTAGAACACGCTTCAAATG 58.858 36.000 0.00 0.00 30.75 2.32
3675 4041 5.743026 TGTTGATTAGAACACGCTTCAAA 57.257 34.783 0.00 0.00 30.75 2.69
3701 4068 5.693814 CGACTATCGAATGATCTGTCATCA 58.306 41.667 0.00 0.00 44.20 3.07
3740 4107 6.964464 TCTCATACCCTTTAGTTTTGGCATA 58.036 36.000 0.00 0.00 0.00 3.14
3751 4118 4.412199 CCCACCAATCTCTCATACCCTTTA 59.588 45.833 0.00 0.00 0.00 1.85
3760 4127 2.837947 AGATGTCCCACCAATCTCTCA 58.162 47.619 0.00 0.00 0.00 3.27
3761 4128 3.922171 AAGATGTCCCACCAATCTCTC 57.078 47.619 0.00 0.00 0.00 3.20
3763 4130 4.156739 GTGAAAAGATGTCCCACCAATCTC 59.843 45.833 0.00 0.00 0.00 2.75
3783 4151 1.985159 AGTGGCAATGGTCTAAGGTGA 59.015 47.619 0.00 0.00 0.00 4.02
3805 4173 0.254178 CATGGACAGACCCCTGAAGG 59.746 60.000 0.00 0.00 43.02 3.46
3809 4177 0.539051 GAGACATGGACAGACCCCTG 59.461 60.000 0.00 0.00 45.76 4.45
3837 4205 2.220586 TGGAATGGCAGTGGTCGGA 61.221 57.895 0.00 0.00 0.00 4.55
3860 4228 1.078759 GCTACAATGTGACTCGCGCT 61.079 55.000 5.56 0.00 0.00 5.92
3863 4231 2.672874 TGAATGCTACAATGTGACTCGC 59.327 45.455 0.00 0.00 0.00 5.03
3871 4239 7.445096 TCCAATACTATGGTGAATGCTACAATG 59.555 37.037 0.00 0.00 41.46 2.82
3876 4244 5.513094 GGCTCCAATACTATGGTGAATGCTA 60.513 44.000 0.00 0.00 41.46 3.49
3878 4246 3.503748 GGCTCCAATACTATGGTGAATGC 59.496 47.826 0.00 0.00 41.46 3.56
3890 4258 1.870167 GCACTCTAGCGGCTCCAATAC 60.870 57.143 5.39 0.00 0.00 1.89
3905 4273 1.385756 GGACGGAGGGAGTAGCACTC 61.386 65.000 7.52 7.52 46.76 3.51
3913 4281 2.116238 TCTATTTTGGGACGGAGGGAG 58.884 52.381 0.00 0.00 0.00 4.30
3914 4282 2.257391 TCTATTTTGGGACGGAGGGA 57.743 50.000 0.00 0.00 0.00 4.20
3915 4283 4.102681 AGTTATCTATTTTGGGACGGAGGG 59.897 45.833 0.00 0.00 0.00 4.30
3916 4284 5.163343 TGAGTTATCTATTTTGGGACGGAGG 60.163 44.000 0.00 0.00 0.00 4.30
3917 4285 5.914033 TGAGTTATCTATTTTGGGACGGAG 58.086 41.667 0.00 0.00 0.00 4.63
3918 4286 5.943349 TGAGTTATCTATTTTGGGACGGA 57.057 39.130 0.00 0.00 0.00 4.69
3919 4287 6.113411 AGTTGAGTTATCTATTTTGGGACGG 58.887 40.000 0.00 0.00 0.00 4.79
3920 4288 7.611213 AAGTTGAGTTATCTATTTTGGGACG 57.389 36.000 0.00 0.00 0.00 4.79
3921 4289 8.793592 ACAAAGTTGAGTTATCTATTTTGGGAC 58.206 33.333 10.53 0.00 40.00 4.46
3922 4290 8.934023 ACAAAGTTGAGTTATCTATTTTGGGA 57.066 30.769 10.53 0.00 40.00 4.37
3962 4330 9.379791 CCGTTCTAAAATAGATGACCTAACTTT 57.620 33.333 0.00 0.00 34.22 2.66
3963 4331 8.755977 TCCGTTCTAAAATAGATGACCTAACTT 58.244 33.333 0.00 0.00 34.22 2.66
3964 4332 8.302515 TCCGTTCTAAAATAGATGACCTAACT 57.697 34.615 0.00 0.00 34.22 2.24
3965 4333 7.652507 CCTCCGTTCTAAAATAGATGACCTAAC 59.347 40.741 0.00 0.00 34.22 2.34
3966 4334 7.201974 CCCTCCGTTCTAAAATAGATGACCTAA 60.202 40.741 0.00 0.00 34.22 2.69
3967 4335 6.267014 CCCTCCGTTCTAAAATAGATGACCTA 59.733 42.308 0.00 0.00 34.22 3.08
3968 4336 5.070580 CCCTCCGTTCTAAAATAGATGACCT 59.929 44.000 0.00 0.00 34.22 3.85
3969 4337 5.070047 TCCCTCCGTTCTAAAATAGATGACC 59.930 44.000 0.00 0.00 34.22 4.02
3970 4338 6.158023 TCCCTCCGTTCTAAAATAGATGAC 57.842 41.667 0.00 0.00 34.22 3.06
3971 4339 6.801718 TTCCCTCCGTTCTAAAATAGATGA 57.198 37.500 0.00 0.00 34.22 2.92
3972 4340 8.585881 TCTATTCCCTCCGTTCTAAAATAGATG 58.414 37.037 0.00 0.00 32.29 2.90
3973 4341 8.586744 GTCTATTCCCTCCGTTCTAAAATAGAT 58.413 37.037 0.00 0.00 36.90 1.98
3974 4342 7.255381 CGTCTATTCCCTCCGTTCTAAAATAGA 60.255 40.741 0.00 0.00 33.90 1.98
3975 4343 6.862090 CGTCTATTCCCTCCGTTCTAAAATAG 59.138 42.308 0.00 0.00 0.00 1.73
3976 4344 6.736794 GCGTCTATTCCCTCCGTTCTAAAATA 60.737 42.308 0.00 0.00 0.00 1.40
3977 4345 5.598769 CGTCTATTCCCTCCGTTCTAAAAT 58.401 41.667 0.00 0.00 0.00 1.82
3978 4346 4.678840 GCGTCTATTCCCTCCGTTCTAAAA 60.679 45.833 0.00 0.00 0.00 1.52
3979 4347 3.181483 GCGTCTATTCCCTCCGTTCTAAA 60.181 47.826 0.00 0.00 0.00 1.85
3980 4348 2.360165 GCGTCTATTCCCTCCGTTCTAA 59.640 50.000 0.00 0.00 0.00 2.10
3981 4349 1.952296 GCGTCTATTCCCTCCGTTCTA 59.048 52.381 0.00 0.00 0.00 2.10
3982 4350 0.745468 GCGTCTATTCCCTCCGTTCT 59.255 55.000 0.00 0.00 0.00 3.01
3983 4351 0.249363 GGCGTCTATTCCCTCCGTTC 60.249 60.000 0.00 0.00 0.00 3.95
3984 4352 0.974010 TGGCGTCTATTCCCTCCGTT 60.974 55.000 0.00 0.00 0.00 4.44
3985 4353 1.380785 TGGCGTCTATTCCCTCCGT 60.381 57.895 0.00 0.00 0.00 4.69
3986 4354 1.364171 CTGGCGTCTATTCCCTCCG 59.636 63.158 0.00 0.00 0.00 4.63
3987 4355 1.069935 GCTGGCGTCTATTCCCTCC 59.930 63.158 0.00 0.00 0.00 4.30
3988 4356 1.300233 CGCTGGCGTCTATTCCCTC 60.300 63.158 6.83 0.00 34.35 4.30
3989 4357 2.797278 CCGCTGGCGTCTATTCCCT 61.797 63.158 13.84 0.00 37.81 4.20
3990 4358 2.280186 CCGCTGGCGTCTATTCCC 60.280 66.667 13.84 0.00 37.81 3.97
3991 4359 2.280186 CCCGCTGGCGTCTATTCC 60.280 66.667 13.84 0.00 37.81 3.01
3992 4360 2.280186 CCCCGCTGGCGTCTATTC 60.280 66.667 13.84 0.00 37.81 1.75
3993 4361 2.363975 TTCCCCGCTGGCGTCTATT 61.364 57.895 13.84 0.00 37.81 1.73
3994 4362 2.762459 TTCCCCGCTGGCGTCTAT 60.762 61.111 13.84 0.00 37.81 1.98
4016 4384 1.338674 TGATGAGTAAAGGGTGCACCG 60.339 52.381 29.08 0.00 46.96 4.94
4021 4389 3.355378 TGGCATTGATGAGTAAAGGGTG 58.645 45.455 0.00 0.00 0.00 4.61
4026 4394 5.448496 GCAACGTATGGCATTGATGAGTAAA 60.448 40.000 4.78 0.00 0.00 2.01
4093 4461 8.937634 ACTCAAATGGAATTTTCATCTATTGC 57.062 30.769 0.00 0.00 46.10 3.56
4106 4474 6.012113 TCAACTGGATCAACTCAAATGGAAT 58.988 36.000 0.00 0.00 0.00 3.01
4107 4475 5.384336 TCAACTGGATCAACTCAAATGGAA 58.616 37.500 0.00 0.00 0.00 3.53
4121 4489 0.332972 GGGGCCTCTTTCAACTGGAT 59.667 55.000 0.84 0.00 0.00 3.41
4122 4490 1.767692 GGGGCCTCTTTCAACTGGA 59.232 57.895 0.84 0.00 0.00 3.86
4123 4491 1.675641 CGGGGCCTCTTTCAACTGG 60.676 63.158 0.00 0.00 0.00 4.00
4124 4492 2.335712 GCGGGGCCTCTTTCAACTG 61.336 63.158 0.00 0.00 0.00 3.16
4125 4493 2.034221 GCGGGGCCTCTTTCAACT 59.966 61.111 0.00 0.00 0.00 3.16
4126 4494 3.431725 CGCGGGGCCTCTTTCAAC 61.432 66.667 0.00 0.00 0.00 3.18
4168 4536 3.179265 CTAGGGCAACGACGTGCG 61.179 66.667 0.00 0.00 45.91 5.34
4169 4537 3.488090 GCTAGGGCAACGACGTGC 61.488 66.667 0.00 7.57 44.14 5.34
4170 4538 3.179265 CGCTAGGGCAACGACGTG 61.179 66.667 0.00 0.00 38.60 4.49
4182 4550 4.778143 AAAGGGTGGCGGCGCTAG 62.778 66.667 32.30 2.71 0.00 3.42
4183 4551 4.770874 GAAAGGGTGGCGGCGCTA 62.771 66.667 32.30 24.91 0.00 4.26
4185 4553 4.770874 TAGAAAGGGTGGCGGCGC 62.771 66.667 26.17 26.17 0.00 6.53
4186 4554 2.798148 AAGTAGAAAGGGTGGCGGCG 62.798 60.000 0.51 0.51 0.00 6.46
4187 4555 1.002502 AAGTAGAAAGGGTGGCGGC 60.003 57.895 0.00 0.00 0.00 6.53
4188 4556 0.392595 GGAAGTAGAAAGGGTGGCGG 60.393 60.000 0.00 0.00 0.00 6.13
4189 4557 0.613777 AGGAAGTAGAAAGGGTGGCG 59.386 55.000 0.00 0.00 0.00 5.69
4190 4558 1.065345 GGAGGAAGTAGAAAGGGTGGC 60.065 57.143 0.00 0.00 0.00 5.01
4191 4559 2.502130 GAGGAGGAAGTAGAAAGGGTGG 59.498 54.545 0.00 0.00 0.00 4.61
4192 4560 2.502130 GGAGGAGGAAGTAGAAAGGGTG 59.498 54.545 0.00 0.00 0.00 4.61
4193 4561 2.387510 AGGAGGAGGAAGTAGAAAGGGT 59.612 50.000 0.00 0.00 0.00 4.34
4194 4562 2.769095 CAGGAGGAGGAAGTAGAAAGGG 59.231 54.545 0.00 0.00 0.00 3.95
4195 4563 2.169561 GCAGGAGGAGGAAGTAGAAAGG 59.830 54.545 0.00 0.00 0.00 3.11
4196 4564 2.169561 GGCAGGAGGAGGAAGTAGAAAG 59.830 54.545 0.00 0.00 0.00 2.62
4197 4565 2.188817 GGCAGGAGGAGGAAGTAGAAA 58.811 52.381 0.00 0.00 0.00 2.52
4198 4566 1.867363 GGCAGGAGGAGGAAGTAGAA 58.133 55.000 0.00 0.00 0.00 2.10
4199 4567 0.395862 CGGCAGGAGGAGGAAGTAGA 60.396 60.000 0.00 0.00 0.00 2.59
4200 4568 2.022240 GCGGCAGGAGGAGGAAGTAG 62.022 65.000 0.00 0.00 0.00 2.57
4201 4569 2.058595 GCGGCAGGAGGAGGAAGTA 61.059 63.158 0.00 0.00 0.00 2.24
4202 4570 3.394836 GCGGCAGGAGGAGGAAGT 61.395 66.667 0.00 0.00 0.00 3.01
4203 4571 4.521062 CGCGGCAGGAGGAGGAAG 62.521 72.222 0.00 0.00 0.00 3.46
4271 4639 4.475135 GTGAGGAGAAGCCCCGCC 62.475 72.222 0.00 0.00 37.37 6.13
4272 4640 4.821589 CGTGAGGAGAAGCCCCGC 62.822 72.222 0.00 0.00 37.37 6.13
4273 4641 3.068691 TCGTGAGGAGAAGCCCCG 61.069 66.667 0.00 0.00 37.37 5.73
4274 4642 2.579738 GTCGTGAGGAGAAGCCCC 59.420 66.667 0.00 0.00 37.37 5.80
4275 4643 2.182030 CGTCGTGAGGAGAAGCCC 59.818 66.667 0.00 0.00 37.37 5.19
4276 4644 2.182030 CCGTCGTGAGGAGAAGCC 59.818 66.667 0.00 0.00 0.00 4.35
4277 4645 2.507324 GCCGTCGTGAGGAGAAGC 60.507 66.667 0.00 0.00 0.00 3.86
4278 4646 1.137825 GAGCCGTCGTGAGGAGAAG 59.862 63.158 0.00 0.00 0.00 2.85
4279 4647 2.341101 GGAGCCGTCGTGAGGAGAA 61.341 63.158 0.00 0.00 0.00 2.87
4280 4648 2.750637 GGAGCCGTCGTGAGGAGA 60.751 66.667 0.00 0.00 0.00 3.71
4281 4649 3.827898 GGGAGCCGTCGTGAGGAG 61.828 72.222 0.00 0.00 0.00 3.69
4303 4671 2.358615 CGTAACTGCTGCCCTGCA 60.359 61.111 0.00 0.03 41.05 4.41
4304 4672 2.358737 ACGTAACTGCTGCCCTGC 60.359 61.111 0.00 0.00 0.00 4.85
4305 4673 2.034879 CCACGTAACTGCTGCCCTG 61.035 63.158 0.00 0.00 0.00 4.45
4306 4674 2.172483 CTCCACGTAACTGCTGCCCT 62.172 60.000 0.00 0.00 0.00 5.19
4307 4675 1.741770 CTCCACGTAACTGCTGCCC 60.742 63.158 0.00 0.00 0.00 5.36
4308 4676 0.602905 AACTCCACGTAACTGCTGCC 60.603 55.000 0.00 0.00 0.00 4.85
4309 4677 0.512952 CAACTCCACGTAACTGCTGC 59.487 55.000 0.00 0.00 0.00 5.25
4310 4678 0.512952 GCAACTCCACGTAACTGCTG 59.487 55.000 0.00 0.00 0.00 4.41
4311 4679 0.944311 CGCAACTCCACGTAACTGCT 60.944 55.000 0.00 0.00 0.00 4.24
4312 4680 1.219522 ACGCAACTCCACGTAACTGC 61.220 55.000 0.00 0.00 41.48 4.40
4313 4681 1.070843 CAACGCAACTCCACGTAACTG 60.071 52.381 0.00 0.00 42.68 3.16
4314 4682 1.202440 TCAACGCAACTCCACGTAACT 60.202 47.619 0.00 0.00 42.68 2.24
4315 4683 1.071041 GTCAACGCAACTCCACGTAAC 60.071 52.381 0.00 0.00 42.68 2.50
4316 4684 1.210870 GTCAACGCAACTCCACGTAA 58.789 50.000 0.00 0.00 42.68 3.18
4317 4685 0.935831 CGTCAACGCAACTCCACGTA 60.936 55.000 0.00 0.00 42.68 3.57
4318 4686 2.235016 CGTCAACGCAACTCCACGT 61.235 57.895 0.00 0.00 46.07 4.49
4319 4687 2.544359 CGTCAACGCAACTCCACG 59.456 61.111 0.00 0.00 0.00 4.94
4329 4697 4.986587 TGACGGGTCGCGTCAACG 62.987 66.667 34.46 11.93 42.41 4.10
4330 4698 2.659244 TTGACGGGTCGCGTCAAC 60.659 61.111 38.49 19.49 46.91 3.18
4332 4700 2.024868 CAATTGACGGGTCGCGTCA 61.025 57.895 33.39 33.39 43.45 4.35
4333 4701 2.736682 CCAATTGACGGGTCGCGTC 61.737 63.158 29.48 29.48 36.95 5.19
4334 4702 2.740826 CCAATTGACGGGTCGCGT 60.741 61.111 15.47 15.47 0.00 6.01
4335 4703 4.160635 GCCAATTGACGGGTCGCG 62.161 66.667 7.12 7.88 0.00 5.87
4336 4704 4.160635 CGCCAATTGACGGGTCGC 62.161 66.667 7.12 0.00 0.00 5.19
4337 4705 1.813753 ATCGCCAATTGACGGGTCG 60.814 57.895 14.32 2.78 0.00 4.79
4338 4706 1.714899 CCATCGCCAATTGACGGGTC 61.715 60.000 14.32 0.00 0.00 4.46
4339 4707 1.748879 CCATCGCCAATTGACGGGT 60.749 57.895 14.32 0.92 0.00 5.28
4340 4708 2.480610 CCCATCGCCAATTGACGGG 61.481 63.158 14.32 8.24 0.00 5.28
4341 4709 3.110139 CCCATCGCCAATTGACGG 58.890 61.111 14.32 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.