Multiple sequence alignment - TraesCS6B01G183500

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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 TraesCS6B01G183500 chr6B 100.000 4571 0 0 1 4571 205233255 205237825 0.000000e+00 8442.0
1 TraesCS6B01G183500 chr6B 96.774 31 1 0 2972 3002 512874263 512874293 8.000000e-03 52.8
2 TraesCS6B01G183500 chr6A 96.235 2975 90 15 1147 4111 144247196 144250158 0.000000e+00 4854.0
3 TraesCS6B01G183500 chr6A 92.952 227 11 3 800 1023 144246758 144246982 4.410000e-85 326.0
4 TraesCS6B01G183500 chr6A 95.413 109 3 2 4112 4220 144250268 144250374 6.080000e-39 172.0
5 TraesCS6B01G183500 chr6A 94.444 108 5 1 4387 4494 144251809 144251915 1.020000e-36 165.0
6 TraesCS6B01G183500 chr6A 100.000 30 0 0 2973 3002 450464545 450464516 6.390000e-04 56.5
7 TraesCS6B01G183500 chr6D 96.699 2757 61 21 839 3579 115771486 115774228 0.000000e+00 4560.0
8 TraesCS6B01G183500 chr6D 88.226 654 75 2 150 802 41162295 41161643 0.000000e+00 780.0
9 TraesCS6B01G183500 chr6D 88.136 649 69 7 158 802 41156922 41156278 0.000000e+00 765.0
10 TraesCS6B01G183500 chr6D 90.980 510 37 4 3603 4111 115777696 115778197 0.000000e+00 678.0
11 TraesCS6B01G183500 chr6D 91.667 156 10 2 4367 4519 115778453 115778608 3.580000e-51 213.0
12 TraesCS6B01G183500 chr6D 96.970 99 3 0 4112 4210 115778309 115778407 2.830000e-37 167.0
13 TraesCS6B01G183500 chr6D 100.000 32 0 0 4540 4571 58745175 58745206 4.940000e-05 60.2
14 TraesCS6B01G183500 chr6D 100.000 28 0 0 2975 3002 313281233 313281206 8.000000e-03 52.8
15 TraesCS6B01G183500 chr4D 92.824 655 46 1 150 803 336509189 336509843 0.000000e+00 948.0
16 TraesCS6B01G183500 chr4D 89.755 654 60 5 157 803 55295912 55296565 0.000000e+00 830.0
17 TraesCS6B01G183500 chr7D 89.771 655 65 2 150 803 556613289 556613942 0.000000e+00 837.0
18 TraesCS6B01G183500 chr7D 87.253 659 81 3 146 803 549094027 549094683 0.000000e+00 749.0
19 TraesCS6B01G183500 chr7D 78.472 288 46 13 1479 1756 583066179 583065898 1.690000e-39 174.0
20 TraesCS6B01G183500 chr7D 86.458 96 13 0 2609 2704 583064643 583064548 6.250000e-19 106.0
21 TraesCS6B01G183500 chr5B 89.506 648 61 5 157 803 615008519 615009160 0.000000e+00 813.0
22 TraesCS6B01G183500 chr5B 93.893 131 7 1 4219 4348 2581647 2581777 3.610000e-46 196.0
23 TraesCS6B01G183500 chr5B 93.893 131 7 1 4215 4344 262477193 262477323 3.610000e-46 196.0
24 TraesCS6B01G183500 chr5B 88.119 101 12 0 1488 1588 322200171 322200271 2.230000e-23 121.0
25 TraesCS6B01G183500 chr1A 88.598 649 72 2 156 803 560337282 560337929 0.000000e+00 787.0
26 TraesCS6B01G183500 chr1A 100.000 32 0 0 4540 4571 26058855 26058886 4.940000e-05 60.2
27 TraesCS6B01G183500 chr1A 100.000 32 0 0 4540 4571 150009816 150009785 4.940000e-05 60.2
28 TraesCS6B01G183500 chr1A 100.000 32 0 0 4540 4571 394306034 394306003 4.940000e-05 60.2
29 TraesCS6B01G183500 chr1D 87.386 658 77 4 150 803 439753530 439754185 0.000000e+00 750.0
30 TraesCS6B01G183500 chr1D 100.000 32 0 0 4540 4571 308698725 308698756 4.940000e-05 60.2
31 TraesCS6B01G183500 chr1D 100.000 32 0 0 4540 4571 463782318 463782349 4.940000e-05 60.2
32 TraesCS6B01G183500 chr4B 94.656 131 6 1 4218 4347 237908075 237908205 7.750000e-48 202.0
33 TraesCS6B01G183500 chr4B 93.750 128 7 1 4219 4345 63765696 63765823 1.680000e-44 191.0
34 TraesCS6B01G183500 chr4B 100.000 32 0 0 4540 4571 22638931 22638900 4.940000e-05 60.2
35 TraesCS6B01G183500 chr2B 91.724 145 9 3 4218 4359 353470441 353470297 1.000000e-46 198.0
36 TraesCS6B01G183500 chr1B 94.531 128 6 1 4218 4344 203424184 203424311 3.610000e-46 196.0
37 TraesCS6B01G183500 chr1B 93.233 133 7 2 4217 4348 62060254 62060385 1.300000e-45 195.0
38 TraesCS6B01G183500 chr5D 93.233 133 8 1 4219 4350 542695707 542695575 1.300000e-45 195.0
39 TraesCS6B01G183500 chr5D 88.119 101 12 0 1488 1588 284893667 284893767 2.230000e-23 121.0
40 TraesCS6B01G183500 chr5D 100.000 32 0 0 4540 4571 15481131 15481162 4.940000e-05 60.2
41 TraesCS6B01G183500 chr7B 93.130 131 8 1 4219 4349 720120589 720120718 1.680000e-44 191.0
42 TraesCS6B01G183500 chr7B 77.778 288 48 12 1479 1756 650613795 650613514 3.660000e-36 163.0
43 TraesCS6B01G183500 chr7A 90.000 110 11 0 1479 1588 674816467 674816358 4.770000e-30 143.0
44 TraesCS6B01G183500 chr7A 86.458 96 13 0 2609 2704 674814958 674814863 6.250000e-19 106.0
45 TraesCS6B01G183500 chr5A 87.129 101 13 0 1488 1588 376464418 376464518 1.040000e-21 115.0
46 TraesCS6B01G183500 chr3D 100.000 32 0 0 4540 4571 21374059 21374028 4.940000e-05 60.2


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 TraesCS6B01G183500 chr6B 205233255 205237825 4570 False 8442.00 8442 100.000 1 4571 1 chr6B.!!$F1 4570
1 TraesCS6B01G183500 chr6A 144246758 144251915 5157 False 1379.25 4854 94.761 800 4494 4 chr6A.!!$F1 3694
2 TraesCS6B01G183500 chr6D 115771486 115778608 7122 False 1404.50 4560 94.079 839 4519 4 chr6D.!!$F2 3680
3 TraesCS6B01G183500 chr6D 41161643 41162295 652 True 780.00 780 88.226 150 802 1 chr6D.!!$R2 652
4 TraesCS6B01G183500 chr6D 41156278 41156922 644 True 765.00 765 88.136 158 802 1 chr6D.!!$R1 644
5 TraesCS6B01G183500 chr4D 336509189 336509843 654 False 948.00 948 92.824 150 803 1 chr4D.!!$F2 653
6 TraesCS6B01G183500 chr4D 55295912 55296565 653 False 830.00 830 89.755 157 803 1 chr4D.!!$F1 646
7 TraesCS6B01G183500 chr7D 556613289 556613942 653 False 837.00 837 89.771 150 803 1 chr7D.!!$F2 653
8 TraesCS6B01G183500 chr7D 549094027 549094683 656 False 749.00 749 87.253 146 803 1 chr7D.!!$F1 657
9 TraesCS6B01G183500 chr5B 615008519 615009160 641 False 813.00 813 89.506 157 803 1 chr5B.!!$F4 646
10 TraesCS6B01G183500 chr1A 560337282 560337929 647 False 787.00 787 88.598 156 803 1 chr1A.!!$F2 647
11 TraesCS6B01G183500 chr1D 439753530 439754185 655 False 750.00 750 87.386 150 803 1 chr1D.!!$F2 653

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
22 23 0.324943 CCTCGGGGACAGTGATTTGT 59.675 55.000 0.00 0.0 33.58 2.83 F
180 181 1.148498 GAGGTTATTCCCCGGCCTG 59.852 63.158 0.00 0.0 36.75 4.85 F
440 449 1.964552 CTCTCTGGCATCCATTGGAC 58.035 55.000 7.76 0.0 32.98 4.02 F
1203 1308 0.178767 CTATAGCCAGCCACACAGCA 59.821 55.000 0.00 0.0 34.23 4.41 F
2791 2907 0.324552 CCATCAAGGACATTGGCCCA 60.325 55.000 4.44 0.0 41.22 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1184 1288 0.178767 TGCTGTGTGGCTGGCTATAG 59.821 55.000 2.00 0.00 0.00 1.31 R
1185 1289 0.178767 CTGCTGTGTGGCTGGCTATA 59.821 55.000 2.00 0.00 0.00 1.31 R
1663 1774 0.947180 GGCGTCGCCTCTACAACAAA 60.947 55.000 28.98 0.00 46.69 2.83 R
3183 3302 1.379443 TAGATCACCGACGGGCTGT 60.379 57.895 20.00 0.00 36.48 4.40 R
4523 9597 0.108992 ACATGCATGCTTTTGCCGAG 60.109 50.000 26.53 1.32 46.87 4.63 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
17 18 2.997315 CTGCCTCGGGGACAGTGA 60.997 66.667 4.80 0.00 34.42 3.41
18 19 2.284625 TGCCTCGGGGACAGTGAT 60.285 61.111 4.80 0.00 33.58 3.06
19 20 1.903877 CTGCCTCGGGGACAGTGATT 61.904 60.000 4.80 0.00 34.42 2.57
20 21 1.299976 GCCTCGGGGACAGTGATTT 59.700 57.895 4.80 0.00 33.58 2.17
21 22 1.026718 GCCTCGGGGACAGTGATTTG 61.027 60.000 4.80 0.00 33.58 2.32
22 23 0.324943 CCTCGGGGACAGTGATTTGT 59.675 55.000 0.00 0.00 33.58 2.83
23 24 1.271379 CCTCGGGGACAGTGATTTGTT 60.271 52.381 0.00 0.00 33.58 2.83
24 25 1.806542 CTCGGGGACAGTGATTTGTTG 59.193 52.381 0.00 0.00 0.00 3.33
25 26 1.418264 TCGGGGACAGTGATTTGTTGA 59.582 47.619 0.00 0.00 0.00 3.18
26 27 2.158740 TCGGGGACAGTGATTTGTTGAA 60.159 45.455 0.00 0.00 0.00 2.69
27 28 2.621055 CGGGGACAGTGATTTGTTGAAA 59.379 45.455 0.00 0.00 0.00 2.69
28 29 3.067461 CGGGGACAGTGATTTGTTGAAAA 59.933 43.478 0.00 0.00 0.00 2.29
29 30 4.440802 CGGGGACAGTGATTTGTTGAAAAA 60.441 41.667 0.00 0.00 0.00 1.94
30 31 5.049828 GGGGACAGTGATTTGTTGAAAAAG 58.950 41.667 0.00 0.00 0.00 2.27
31 32 5.163457 GGGGACAGTGATTTGTTGAAAAAGA 60.163 40.000 0.00 0.00 0.00 2.52
32 33 6.337356 GGGACAGTGATTTGTTGAAAAAGAA 58.663 36.000 0.00 0.00 0.00 2.52
33 34 6.816140 GGGACAGTGATTTGTTGAAAAAGAAA 59.184 34.615 0.00 0.00 0.00 2.52
34 35 7.333174 GGGACAGTGATTTGTTGAAAAAGAAAA 59.667 33.333 0.00 0.00 0.00 2.29
35 36 8.882736 GGACAGTGATTTGTTGAAAAAGAAAAT 58.117 29.630 0.00 0.00 0.00 1.82
36 37 9.906111 GACAGTGATTTGTTGAAAAAGAAAATC 57.094 29.630 0.00 0.00 35.05 2.17
37 38 9.434420 ACAGTGATTTGTTGAAAAAGAAAATCA 57.566 25.926 0.00 5.30 38.74 2.57
44 45 9.890352 TTTGTTGAAAAAGAAAATCAAAACCAG 57.110 25.926 0.00 0.00 35.07 4.00
45 46 7.525759 TGTTGAAAAAGAAAATCAAAACCAGC 58.474 30.769 0.00 0.00 35.07 4.85
46 47 6.343226 TGAAAAAGAAAATCAAAACCAGCG 57.657 33.333 0.00 0.00 0.00 5.18
47 48 5.293079 TGAAAAAGAAAATCAAAACCAGCGG 59.707 36.000 0.00 0.00 0.00 5.52
48 49 4.400529 AAAGAAAATCAAAACCAGCGGT 57.599 36.364 0.00 0.00 37.65 5.68
65 66 9.850198 AACCAGCGGTTTTATAAATACCTATAA 57.150 29.630 18.89 0.00 44.33 0.98
66 67 9.276590 ACCAGCGGTTTTATAAATACCTATAAC 57.723 33.333 18.89 6.13 27.29 1.89
67 68 9.275398 CCAGCGGTTTTATAAATACCTATAACA 57.725 33.333 18.89 0.00 0.00 2.41
78 79 7.748691 AAATACCTATAACAAACGTGGTGTT 57.251 32.000 18.60 18.60 44.59 3.32
89 90 4.769859 AACGTGGTGTTTTTGTGTAACT 57.230 36.364 0.00 0.00 37.59 2.24
90 91 4.769859 ACGTGGTGTTTTTGTGTAACTT 57.230 36.364 0.00 0.00 38.04 2.66
91 92 5.876612 ACGTGGTGTTTTTGTGTAACTTA 57.123 34.783 0.00 0.00 38.04 2.24
92 93 5.630061 ACGTGGTGTTTTTGTGTAACTTAC 58.370 37.500 0.00 0.00 38.04 2.34
93 94 5.412286 ACGTGGTGTTTTTGTGTAACTTACT 59.588 36.000 0.00 0.00 38.04 2.24
94 95 5.961263 CGTGGTGTTTTTGTGTAACTTACTC 59.039 40.000 0.71 0.00 38.04 2.59
95 96 6.183360 CGTGGTGTTTTTGTGTAACTTACTCT 60.183 38.462 0.71 0.00 38.04 3.24
96 97 6.964934 GTGGTGTTTTTGTGTAACTTACTCTG 59.035 38.462 0.71 0.00 38.04 3.35
97 98 6.655848 TGGTGTTTTTGTGTAACTTACTCTGT 59.344 34.615 0.71 0.00 38.04 3.41
98 99 7.175293 TGGTGTTTTTGTGTAACTTACTCTGTT 59.825 33.333 0.71 0.00 38.04 3.16
99 100 8.024865 GGTGTTTTTGTGTAACTTACTCTGTTT 58.975 33.333 0.71 0.00 38.04 2.83
129 130 7.897864 AGTCCAGTTAATCCTACTACATATGC 58.102 38.462 1.58 0.00 0.00 3.14
130 131 7.509318 AGTCCAGTTAATCCTACTACATATGCA 59.491 37.037 1.58 0.00 0.00 3.96
131 132 8.314751 GTCCAGTTAATCCTACTACATATGCAT 58.685 37.037 3.79 3.79 0.00 3.96
132 133 8.314021 TCCAGTTAATCCTACTACATATGCATG 58.686 37.037 10.16 0.00 38.21 4.06
133 134 8.314021 CCAGTTAATCCTACTACATATGCATGA 58.686 37.037 10.16 0.00 35.96 3.07
134 135 9.710900 CAGTTAATCCTACTACATATGCATGAA 57.289 33.333 10.16 0.00 35.96 2.57
135 136 9.712305 AGTTAATCCTACTACATATGCATGAAC 57.288 33.333 10.16 0.00 35.96 3.18
136 137 9.489084 GTTAATCCTACTACATATGCATGAACA 57.511 33.333 10.16 0.00 35.96 3.18
138 139 8.783833 AATCCTACTACATATGCATGAACATC 57.216 34.615 10.16 0.00 35.96 3.06
139 140 7.544804 TCCTACTACATATGCATGAACATCT 57.455 36.000 10.16 0.00 35.96 2.90
140 141 8.650143 TCCTACTACATATGCATGAACATCTA 57.350 34.615 10.16 0.00 35.96 1.98
141 142 9.259832 TCCTACTACATATGCATGAACATCTAT 57.740 33.333 10.16 0.00 35.96 1.98
142 143 9.310716 CCTACTACATATGCATGAACATCTATG 57.689 37.037 10.16 4.85 35.96 2.23
145 146 9.955102 ACTACATATGCATGAACATCTATGAAT 57.045 29.630 10.16 0.00 35.96 2.57
180 181 1.148498 GAGGTTATTCCCCGGCCTG 59.852 63.158 0.00 0.00 36.75 4.85
218 220 6.462500 TGCATGCGGCCATTTTATTAATAAT 58.538 32.000 14.09 0.00 43.89 1.28
319 325 4.992319 CCACAACCGGCGATATAAAGATAA 59.008 41.667 9.30 0.00 0.00 1.75
352 361 9.959721 AACTAAACACCTGTCTTATTACATGAT 57.040 29.630 0.00 0.00 0.00 2.45
424 433 3.658725 AGACCCAGTAACCATATGCTCT 58.341 45.455 0.00 0.00 0.00 4.09
440 449 1.964552 CTCTCTGGCATCCATTGGAC 58.035 55.000 7.76 0.00 32.98 4.02
498 507 5.758784 CCCGGAAGATAACCTACAAGAAATC 59.241 44.000 0.73 0.00 0.00 2.17
618 629 3.074412 CTCAACTCCATTTAGCCACGTT 58.926 45.455 0.00 0.00 0.00 3.99
622 633 2.009774 CTCCATTTAGCCACGTTCCAG 58.990 52.381 0.00 0.00 0.00 3.86
677 688 5.128171 TGTTAAACGCTATATGGACAGACCT 59.872 40.000 0.00 0.00 39.86 3.85
724 735 8.303876 GGCAATCAAGAAAGAGGTGTTTAATAA 58.696 33.333 0.00 0.00 0.00 1.40
763 774 4.518970 AGAAGCTACATCTTCGAGATCCTC 59.481 45.833 0.00 0.00 45.28 3.71
788 799 5.067413 TCCAGTTACGTTTTGCCAAATTGTA 59.933 36.000 0.00 0.00 0.00 2.41
860 871 3.750652 GCTTTTCTTCTGTCTTCCTCTGG 59.249 47.826 0.00 0.00 0.00 3.86
914 925 3.670627 CGATGATGCTCGATCGTATTGGA 60.671 47.826 15.94 5.98 41.12 3.53
1077 1091 3.591023 GCTTTGTAGGTGAAGACTCCTC 58.409 50.000 0.00 0.00 40.07 3.71
1153 1257 4.083590 GCAAGCGAGAAAGAAAGAAGACAT 60.084 41.667 0.00 0.00 0.00 3.06
1183 1287 2.680841 CGCAGACCTAGCTAGCTATAGG 59.319 54.545 25.84 25.84 43.61 2.57
1184 1288 2.425668 GCAGACCTAGCTAGCTATAGGC 59.574 54.545 26.93 21.76 42.04 3.93
1201 1306 2.997899 GCTATAGCCAGCCACACAG 58.002 57.895 14.13 0.00 35.40 3.66
1202 1307 1.162800 GCTATAGCCAGCCACACAGC 61.163 60.000 14.13 0.00 35.40 4.40
1203 1308 0.178767 CTATAGCCAGCCACACAGCA 59.821 55.000 0.00 0.00 34.23 4.41
1204 1309 0.178767 TATAGCCAGCCACACAGCAG 59.821 55.000 0.00 0.00 34.23 4.24
1205 1310 3.783020 TATAGCCAGCCACACAGCAGC 62.783 57.143 0.00 0.00 35.27 5.25
1207 1312 3.362797 CCAGCCACACAGCAGCAG 61.363 66.667 0.00 0.00 34.23 4.24
1212 1317 3.284449 CACACAGCAGCAGCAGCA 61.284 61.111 12.92 0.00 45.49 4.41
1213 1318 2.978565 ACACAGCAGCAGCAGCAG 60.979 61.111 12.92 6.60 45.49 4.24
1250 1355 1.349357 GCAACAAGAAGGGGTCTCTCT 59.651 52.381 0.00 0.00 34.56 3.10
1610 1719 2.802719 GGCTCCAAAACCCTTCATGTA 58.197 47.619 0.00 0.00 0.00 2.29
1613 1722 3.440522 GCTCCAAAACCCTTCATGTACTC 59.559 47.826 0.00 0.00 0.00 2.59
1616 1725 3.408634 CAAAACCCTTCATGTACTCCGT 58.591 45.455 0.00 0.00 0.00 4.69
1628 1737 1.732259 GTACTCCGTGCTGGTCATTTG 59.268 52.381 0.00 0.00 39.52 2.32
1663 1774 3.411446 TCCATCGCTGAGAATTTTGTGT 58.589 40.909 0.00 0.00 0.00 3.72
1851 1962 3.143728 CACATGCATGCTGGCTAATCTA 58.856 45.455 26.53 0.00 34.04 1.98
2101 2212 2.852449 TCAGGCATAATGGGGAGAAACT 59.148 45.455 0.00 0.00 0.00 2.66
2440 2555 1.347707 CTGAGCACCTTACCACCTTCA 59.652 52.381 0.00 0.00 0.00 3.02
2472 2587 6.540189 GCTCATGCTCCTCAACTTTTAGATAA 59.460 38.462 0.00 0.00 36.03 1.75
2791 2907 0.324552 CCATCAAGGACATTGGCCCA 60.325 55.000 4.44 0.00 41.22 5.36
2836 2952 2.184579 GACCTGCACCTCTACGGC 59.815 66.667 0.00 0.00 35.61 5.68
3296 3415 4.333913 AGTATAGCTTGAGTGCATGGAG 57.666 45.455 0.00 0.00 34.99 3.86
3399 3521 7.187824 TGATGCTCAAGGTCTAACTAAGATT 57.812 36.000 0.00 0.00 36.36 2.40
3489 3611 1.746470 TGGTGATCTTGCATGCTGAG 58.254 50.000 20.33 16.30 0.00 3.35
3581 3703 0.850100 TGGTTGGGTCTGGAACATGT 59.150 50.000 0.00 0.00 38.20 3.21
3587 3709 2.040947 TGGGTCTGGAACATGTGCATAA 59.959 45.455 6.08 0.00 38.20 1.90
3651 7217 5.049954 GTGCAAATGTAACTTCGGACACTTA 60.050 40.000 0.00 0.00 0.00 2.24
3670 7236 7.088905 ACACTTACCTTCGTATCAACTAACAG 58.911 38.462 0.00 0.00 0.00 3.16
3784 7351 4.756135 CACAGCCAAATTATTGCAAAACCT 59.244 37.500 1.71 0.00 35.10 3.50
3813 7380 8.696043 AACACTGGCACAACATATATGATATT 57.304 30.769 19.63 0.49 38.70 1.28
3818 7385 7.819644 TGGCACAACATATATGATATTTGCTC 58.180 34.615 19.63 12.26 31.92 4.26
3845 7412 9.079833 GCATGCATAATAAGGCTATAAAATGTG 57.920 33.333 14.21 0.00 32.35 3.21
3953 7520 5.924475 ATGTTCCAAAGTTCGTAACTCTG 57.076 39.130 1.58 0.00 41.91 3.35
3984 7551 9.833182 GTTAGTGTAGTAACTTAGTACCTTCAC 57.167 37.037 10.18 10.65 34.43 3.18
4069 7636 3.078837 GCATGGGTTTTTAGGTCTTCGA 58.921 45.455 0.00 0.00 0.00 3.71
4081 7648 4.516365 AGGTCTTCGATTTGACTAACGT 57.484 40.909 11.61 0.00 34.01 3.99
4089 7656 6.268797 TCGATTTGACTAACGTAATCATGC 57.731 37.500 7.14 0.00 0.00 4.06
4108 7675 5.767665 TCATGCGGTATATGCCACTAAAAAT 59.232 36.000 10.70 0.00 0.00 1.82
4109 7676 6.937465 TCATGCGGTATATGCCACTAAAAATA 59.063 34.615 10.70 0.00 0.00 1.40
4110 7677 7.609918 TCATGCGGTATATGCCACTAAAAATAT 59.390 33.333 10.70 0.00 0.00 1.28
4210 7889 3.502595 CGCCTTACAGATTCGGATAGAGA 59.497 47.826 0.00 0.00 0.00 3.10
4211 7890 4.378978 CGCCTTACAGATTCGGATAGAGAG 60.379 50.000 0.00 0.00 0.00 3.20
4212 7891 4.082463 GCCTTACAGATTCGGATAGAGAGG 60.082 50.000 0.00 0.00 0.00 3.69
4213 7892 4.461081 CCTTACAGATTCGGATAGAGAGGG 59.539 50.000 0.00 0.00 0.00 4.30
4214 7893 2.883026 ACAGATTCGGATAGAGAGGGG 58.117 52.381 0.00 0.00 0.00 4.79
4215 7894 2.178106 ACAGATTCGGATAGAGAGGGGT 59.822 50.000 0.00 0.00 0.00 4.95
4216 7895 3.398292 ACAGATTCGGATAGAGAGGGGTA 59.602 47.826 0.00 0.00 0.00 3.69
4217 7896 4.013728 CAGATTCGGATAGAGAGGGGTAG 58.986 52.174 0.00 0.00 0.00 3.18
4218 7897 3.658705 AGATTCGGATAGAGAGGGGTAGT 59.341 47.826 0.00 0.00 0.00 2.73
4219 7898 4.850963 AGATTCGGATAGAGAGGGGTAGTA 59.149 45.833 0.00 0.00 0.00 1.82
4220 7899 4.363991 TTCGGATAGAGAGGGGTAGTAC 57.636 50.000 0.00 0.00 0.00 2.73
4221 7900 3.596101 TCGGATAGAGAGGGGTAGTACT 58.404 50.000 0.00 0.00 0.00 2.73
4222 7901 3.582208 TCGGATAGAGAGGGGTAGTACTC 59.418 52.174 0.00 0.00 0.00 2.59
4223 7902 3.307621 CGGATAGAGAGGGGTAGTACTCC 60.308 56.522 11.67 11.67 39.74 3.85
4224 7903 3.010472 GGATAGAGAGGGGTAGTACTCCC 59.990 56.522 16.07 15.75 40.56 4.30
4230 7909 2.070305 GGGGTAGTACTCCCTCTGTC 57.930 60.000 22.23 8.32 44.07 3.51
4231 7910 1.411359 GGGGTAGTACTCCCTCTGTCC 60.411 61.905 22.23 5.85 44.07 4.02
4232 7911 1.677942 GGTAGTACTCCCTCTGTCCG 58.322 60.000 0.00 0.00 0.00 4.79
4233 7912 1.211457 GGTAGTACTCCCTCTGTCCGA 59.789 57.143 0.00 0.00 0.00 4.55
4234 7913 2.356535 GGTAGTACTCCCTCTGTCCGAA 60.357 54.545 0.00 0.00 0.00 4.30
4235 7914 2.599408 AGTACTCCCTCTGTCCGAAA 57.401 50.000 0.00 0.00 0.00 3.46
4236 7915 2.885616 AGTACTCCCTCTGTCCGAAAA 58.114 47.619 0.00 0.00 0.00 2.29
4237 7916 3.442076 AGTACTCCCTCTGTCCGAAAAT 58.558 45.455 0.00 0.00 0.00 1.82
4238 7917 4.607239 AGTACTCCCTCTGTCCGAAAATA 58.393 43.478 0.00 0.00 0.00 1.40
4239 7918 3.889520 ACTCCCTCTGTCCGAAAATAC 57.110 47.619 0.00 0.00 0.00 1.89
4240 7919 3.442076 ACTCCCTCTGTCCGAAAATACT 58.558 45.455 0.00 0.00 0.00 2.12
4241 7920 3.838903 ACTCCCTCTGTCCGAAAATACTT 59.161 43.478 0.00 0.00 0.00 2.24
4242 7921 5.021458 ACTCCCTCTGTCCGAAAATACTTA 58.979 41.667 0.00 0.00 0.00 2.24
4243 7922 5.661759 ACTCCCTCTGTCCGAAAATACTTAT 59.338 40.000 0.00 0.00 0.00 1.73
4244 7923 6.158023 TCCCTCTGTCCGAAAATACTTATC 57.842 41.667 0.00 0.00 0.00 1.75
4245 7924 5.659525 TCCCTCTGTCCGAAAATACTTATCA 59.340 40.000 0.00 0.00 0.00 2.15
4246 7925 6.326583 TCCCTCTGTCCGAAAATACTTATCAT 59.673 38.462 0.00 0.00 0.00 2.45
4247 7926 6.647067 CCCTCTGTCCGAAAATACTTATCATC 59.353 42.308 0.00 0.00 0.00 2.92
4248 7927 7.210174 CCTCTGTCCGAAAATACTTATCATCA 58.790 38.462 0.00 0.00 0.00 3.07
4249 7928 7.710907 CCTCTGTCCGAAAATACTTATCATCAA 59.289 37.037 0.00 0.00 0.00 2.57
4250 7929 9.098355 CTCTGTCCGAAAATACTTATCATCAAA 57.902 33.333 0.00 0.00 0.00 2.69
4251 7930 9.443323 TCTGTCCGAAAATACTTATCATCAAAA 57.557 29.630 0.00 0.00 0.00 2.44
4254 7933 9.450807 GTCCGAAAATACTTATCATCAAAATGG 57.549 33.333 0.00 0.00 33.42 3.16
4255 7934 9.402320 TCCGAAAATACTTATCATCAAAATGGA 57.598 29.630 0.00 0.00 33.42 3.41
4296 7975 9.900710 CTAGAACTAAAATGCATCTAGATACGT 57.099 33.333 18.14 0.00 41.22 3.57
4297 7976 8.804688 AGAACTAAAATGCATCTAGATACGTC 57.195 34.615 18.14 9.53 0.00 4.34
4298 7977 8.634444 AGAACTAAAATGCATCTAGATACGTCT 58.366 33.333 18.14 10.94 38.52 4.18
4299 7978 8.804688 AACTAAAATGCATCTAGATACGTCTC 57.195 34.615 18.14 0.00 35.87 3.36
4300 7979 7.371936 ACTAAAATGCATCTAGATACGTCTCC 58.628 38.462 18.14 0.00 35.87 3.71
4301 7980 6.412362 AAAATGCATCTAGATACGTCTCCT 57.588 37.500 4.54 0.00 35.87 3.69
4302 7981 6.412362 AAATGCATCTAGATACGTCTCCTT 57.588 37.500 4.54 0.00 35.87 3.36
4303 7982 5.637006 ATGCATCTAGATACGTCTCCTTC 57.363 43.478 4.54 0.00 35.87 3.46
4304 7983 4.720046 TGCATCTAGATACGTCTCCTTCT 58.280 43.478 4.54 0.00 35.87 2.85
4305 7984 5.866207 TGCATCTAGATACGTCTCCTTCTA 58.134 41.667 4.54 0.00 35.87 2.10
4306 7985 6.477253 TGCATCTAGATACGTCTCCTTCTAT 58.523 40.000 4.54 0.00 35.87 1.98
4307 7986 6.596106 TGCATCTAGATACGTCTCCTTCTATC 59.404 42.308 4.54 0.00 35.87 2.08
4308 7987 6.037830 GCATCTAGATACGTCTCCTTCTATCC 59.962 46.154 4.54 0.00 35.87 2.59
4309 7988 6.683312 TCTAGATACGTCTCCTTCTATCCA 57.317 41.667 0.00 0.00 35.87 3.41
4310 7989 7.260387 TCTAGATACGTCTCCTTCTATCCAT 57.740 40.000 0.00 0.00 35.87 3.41
4311 7990 7.691213 TCTAGATACGTCTCCTTCTATCCATT 58.309 38.462 0.00 0.00 35.87 3.16
4312 7991 8.164733 TCTAGATACGTCTCCTTCTATCCATTT 58.835 37.037 0.00 0.00 35.87 2.32
4313 7992 7.604657 AGATACGTCTCCTTCTATCCATTTT 57.395 36.000 0.00 0.00 0.00 1.82
4314 7993 7.437748 AGATACGTCTCCTTCTATCCATTTTG 58.562 38.462 0.00 0.00 0.00 2.44
4315 7994 5.677319 ACGTCTCCTTCTATCCATTTTGA 57.323 39.130 0.00 0.00 0.00 2.69
4316 7995 6.240549 ACGTCTCCTTCTATCCATTTTGAT 57.759 37.500 0.00 0.00 0.00 2.57
4317 7996 6.051717 ACGTCTCCTTCTATCCATTTTGATG 58.948 40.000 0.00 0.00 0.00 3.07
4318 7997 6.127054 ACGTCTCCTTCTATCCATTTTGATGA 60.127 38.462 0.00 0.00 0.00 2.92
4319 7998 6.201806 CGTCTCCTTCTATCCATTTTGATGAC 59.798 42.308 0.00 0.00 0.00 3.06
4320 7999 7.050377 GTCTCCTTCTATCCATTTTGATGACA 58.950 38.462 0.00 0.00 0.00 3.58
4321 8000 7.554118 GTCTCCTTCTATCCATTTTGATGACAA 59.446 37.037 0.00 0.00 0.00 3.18
4322 8001 7.772292 TCTCCTTCTATCCATTTTGATGACAAG 59.228 37.037 0.00 0.00 37.32 3.16
4323 8002 7.405292 TCCTTCTATCCATTTTGATGACAAGT 58.595 34.615 0.00 0.00 37.32 3.16
4324 8003 8.548025 TCCTTCTATCCATTTTGATGACAAGTA 58.452 33.333 0.00 0.00 37.32 2.24
4325 8004 9.347240 CCTTCTATCCATTTTGATGACAAGTAT 57.653 33.333 0.00 0.00 37.32 2.12
4331 8010 7.829725 TCCATTTTGATGACAAGTATTTCTGG 58.170 34.615 0.00 0.00 37.32 3.86
4332 8011 7.669304 TCCATTTTGATGACAAGTATTTCTGGA 59.331 33.333 0.00 0.00 37.32 3.86
4333 8012 7.756722 CCATTTTGATGACAAGTATTTCTGGAC 59.243 37.037 0.00 0.00 37.32 4.02
4334 8013 6.480524 TTTGATGACAAGTATTTCTGGACG 57.519 37.500 0.00 0.00 37.32 4.79
4335 8014 4.503910 TGATGACAAGTATTTCTGGACGG 58.496 43.478 0.00 0.00 0.00 4.79
4336 8015 4.221924 TGATGACAAGTATTTCTGGACGGA 59.778 41.667 0.00 0.00 0.00 4.69
4339 8018 2.236395 ACAAGTATTTCTGGACGGAGGG 59.764 50.000 0.00 0.00 0.00 4.30
4459 9530 1.138036 CAACATGCATGCTCACGGG 59.862 57.895 26.53 0.29 0.00 5.28
4460 9531 2.048023 AACATGCATGCTCACGGGG 61.048 57.895 26.53 0.00 0.00 5.73
4466 9537 0.388520 GCATGCTCACGGGGAAAAAC 60.389 55.000 11.37 0.00 0.00 2.43
4467 9541 0.109781 CATGCTCACGGGGAAAAACG 60.110 55.000 0.00 0.00 0.00 3.60
4508 9582 6.461110 AATTAGTGATCATGAAAAGCCAGG 57.539 37.500 0.00 0.00 0.00 4.45
4522 9596 2.765969 CAGGGCAACTGGGACCAT 59.234 61.111 0.00 0.00 43.70 3.55
4523 9597 1.379044 CAGGGCAACTGGGACCATC 60.379 63.158 0.00 0.00 43.70 3.51
4524 9598 1.542375 AGGGCAACTGGGACCATCT 60.542 57.895 0.00 0.00 0.00 2.90
4525 9599 1.077429 GGGCAACTGGGACCATCTC 60.077 63.158 0.00 0.00 0.00 2.75
4526 9600 1.450312 GGCAACTGGGACCATCTCG 60.450 63.158 0.00 0.00 0.00 4.04
4527 9601 1.450312 GCAACTGGGACCATCTCGG 60.450 63.158 0.00 0.00 42.50 4.63
4528 9602 1.450312 CAACTGGGACCATCTCGGC 60.450 63.158 0.00 0.00 39.03 5.54
4529 9603 1.918293 AACTGGGACCATCTCGGCA 60.918 57.895 0.00 0.00 39.03 5.69
4530 9604 1.488705 AACTGGGACCATCTCGGCAA 61.489 55.000 0.00 0.00 39.03 4.52
4531 9605 1.299648 CTGGGACCATCTCGGCAAA 59.700 57.895 0.00 0.00 39.03 3.68
4532 9606 0.322456 CTGGGACCATCTCGGCAAAA 60.322 55.000 0.00 0.00 39.03 2.44
4533 9607 0.322456 TGGGACCATCTCGGCAAAAG 60.322 55.000 0.00 0.00 39.03 2.27
4534 9608 1.657751 GGGACCATCTCGGCAAAAGC 61.658 60.000 0.00 0.00 39.03 3.51
4535 9609 0.960364 GGACCATCTCGGCAAAAGCA 60.960 55.000 0.00 0.00 39.03 3.91
4536 9610 1.098050 GACCATCTCGGCAAAAGCAT 58.902 50.000 0.00 0.00 39.03 3.79
4537 9611 0.813184 ACCATCTCGGCAAAAGCATG 59.187 50.000 0.00 0.00 39.03 4.06
4538 9612 0.526954 CCATCTCGGCAAAAGCATGC 60.527 55.000 10.51 10.51 45.67 4.06
4547 9621 3.449322 GCAAAAGCATGCATGTTTGAG 57.551 42.857 31.49 24.96 45.70 3.02
4548 9622 3.061322 GCAAAAGCATGCATGTTTGAGA 58.939 40.909 31.49 0.00 45.70 3.27
4549 9623 3.682858 GCAAAAGCATGCATGTTTGAGAT 59.317 39.130 31.49 16.30 45.70 2.75
4550 9624 4.865925 GCAAAAGCATGCATGTTTGAGATA 59.134 37.500 31.49 0.00 45.70 1.98
4551 9625 5.005394 GCAAAAGCATGCATGTTTGAGATAG 59.995 40.000 31.49 18.86 45.70 2.08
4552 9626 5.909621 AAAGCATGCATGTTTGAGATAGT 57.090 34.783 26.65 8.80 31.44 2.12
4553 9627 5.496133 AAGCATGCATGTTTGAGATAGTC 57.504 39.130 25.59 6.24 29.82 2.59
4554 9628 4.778579 AGCATGCATGTTTGAGATAGTCT 58.221 39.130 26.79 8.68 0.00 3.24
4555 9629 5.191426 AGCATGCATGTTTGAGATAGTCTT 58.809 37.500 26.79 0.00 0.00 3.01
4556 9630 5.296283 AGCATGCATGTTTGAGATAGTCTTC 59.704 40.000 26.79 5.24 0.00 2.87
4557 9631 5.065602 GCATGCATGTTTGAGATAGTCTTCA 59.934 40.000 26.79 0.00 0.00 3.02
4558 9632 6.484540 CATGCATGTTTGAGATAGTCTTCAC 58.515 40.000 18.91 0.00 0.00 3.18
4559 9633 5.550290 TGCATGTTTGAGATAGTCTTCACA 58.450 37.500 0.00 0.00 0.00 3.58
4560 9634 5.997129 TGCATGTTTGAGATAGTCTTCACAA 59.003 36.000 0.00 0.00 0.00 3.33
4561 9635 6.486320 TGCATGTTTGAGATAGTCTTCACAAA 59.514 34.615 0.00 0.00 34.99 2.83
4562 9636 7.175467 TGCATGTTTGAGATAGTCTTCACAAAT 59.825 33.333 0.00 0.00 38.09 2.32
4563 9637 7.484007 GCATGTTTGAGATAGTCTTCACAAATG 59.516 37.037 0.00 0.00 38.09 2.32
4564 9638 8.509690 CATGTTTGAGATAGTCTTCACAAATGT 58.490 33.333 0.00 0.00 38.09 2.71
4565 9639 9.725019 ATGTTTGAGATAGTCTTCACAAATGTA 57.275 29.630 0.00 0.00 38.09 2.29
4566 9640 9.208022 TGTTTGAGATAGTCTTCACAAATGTAG 57.792 33.333 0.00 0.00 38.09 2.74
4567 9641 9.424319 GTTTGAGATAGTCTTCACAAATGTAGA 57.576 33.333 0.00 0.00 38.09 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.903877 AATCACTGTCCCCGAGGCAG 61.904 60.000 5.59 5.59 40.84 4.85
1 2 1.488705 AAATCACTGTCCCCGAGGCA 61.489 55.000 0.00 0.00 0.00 4.75
2 3 1.026718 CAAATCACTGTCCCCGAGGC 61.027 60.000 0.00 0.00 0.00 4.70
3 4 0.324943 ACAAATCACTGTCCCCGAGG 59.675 55.000 0.00 0.00 0.00 4.63
4 5 1.806542 CAACAAATCACTGTCCCCGAG 59.193 52.381 0.00 0.00 0.00 4.63
5 6 1.418264 TCAACAAATCACTGTCCCCGA 59.582 47.619 0.00 0.00 0.00 5.14
6 7 1.890876 TCAACAAATCACTGTCCCCG 58.109 50.000 0.00 0.00 0.00 5.73
7 8 4.664150 TTTTCAACAAATCACTGTCCCC 57.336 40.909 0.00 0.00 0.00 4.81
8 9 5.901552 TCTTTTTCAACAAATCACTGTCCC 58.098 37.500 0.00 0.00 0.00 4.46
9 10 7.826260 TTTCTTTTTCAACAAATCACTGTCC 57.174 32.000 0.00 0.00 0.00 4.02
10 11 9.906111 GATTTTCTTTTTCAACAAATCACTGTC 57.094 29.630 0.00 0.00 35.04 3.51
11 12 9.434420 TGATTTTCTTTTTCAACAAATCACTGT 57.566 25.926 0.00 0.00 38.39 3.55
18 19 9.890352 CTGGTTTTGATTTTCTTTTTCAACAAA 57.110 25.926 0.00 0.00 0.00 2.83
19 20 8.020244 GCTGGTTTTGATTTTCTTTTTCAACAA 58.980 29.630 0.00 0.00 0.00 2.83
20 21 7.525759 GCTGGTTTTGATTTTCTTTTTCAACA 58.474 30.769 0.00 0.00 0.00 3.33
21 22 6.682441 CGCTGGTTTTGATTTTCTTTTTCAAC 59.318 34.615 0.00 0.00 0.00 3.18
22 23 6.183360 CCGCTGGTTTTGATTTTCTTTTTCAA 60.183 34.615 0.00 0.00 0.00 2.69
23 24 5.293079 CCGCTGGTTTTGATTTTCTTTTTCA 59.707 36.000 0.00 0.00 0.00 2.69
24 25 5.293324 ACCGCTGGTTTTGATTTTCTTTTTC 59.707 36.000 0.00 0.00 27.29 2.29
25 26 5.182487 ACCGCTGGTTTTGATTTTCTTTTT 58.818 33.333 0.00 0.00 27.29 1.94
26 27 4.765273 ACCGCTGGTTTTGATTTTCTTTT 58.235 34.783 0.00 0.00 27.29 2.27
27 28 4.400529 ACCGCTGGTTTTGATTTTCTTT 57.599 36.364 0.00 0.00 27.29 2.52
28 29 4.400529 AACCGCTGGTTTTGATTTTCTT 57.599 36.364 7.08 0.00 44.33 2.52
40 41 9.276590 GTTATAGGTATTTATAAAACCGCTGGT 57.723 33.333 16.88 0.00 38.37 4.00
41 42 9.275398 TGTTATAGGTATTTATAAAACCGCTGG 57.725 33.333 16.88 0.00 38.37 4.85
52 53 9.452287 AACACCACGTTTGTTATAGGTATTTAT 57.548 29.630 10.00 0.00 35.38 1.40
53 54 8.845413 AACACCACGTTTGTTATAGGTATTTA 57.155 30.769 10.00 0.00 35.38 1.40
54 55 7.748691 AACACCACGTTTGTTATAGGTATTT 57.251 32.000 10.00 0.00 35.38 1.40
55 56 7.748691 AAACACCACGTTTGTTATAGGTATT 57.251 32.000 11.72 0.00 46.22 1.89
68 69 4.769859 AGTTACACAAAAACACCACGTT 57.230 36.364 0.00 0.00 40.50 3.99
69 70 4.769859 AAGTTACACAAAAACACCACGT 57.230 36.364 0.00 0.00 0.00 4.49
70 71 5.871539 AGTAAGTTACACAAAAACACCACG 58.128 37.500 15.28 0.00 0.00 4.94
71 72 6.964934 CAGAGTAAGTTACACAAAAACACCAC 59.035 38.462 15.28 0.00 0.00 4.16
72 73 6.655848 ACAGAGTAAGTTACACAAAAACACCA 59.344 34.615 15.28 0.00 0.00 4.17
73 74 7.080353 ACAGAGTAAGTTACACAAAAACACC 57.920 36.000 15.28 0.00 0.00 4.16
74 75 8.959734 AAACAGAGTAAGTTACACAAAAACAC 57.040 30.769 15.28 0.00 0.00 3.32
103 104 9.021807 GCATATGTAGTAGGATTAACTGGACTA 57.978 37.037 4.29 0.00 0.00 2.59
104 105 7.509318 TGCATATGTAGTAGGATTAACTGGACT 59.491 37.037 4.29 0.00 0.00 3.85
105 106 7.667557 TGCATATGTAGTAGGATTAACTGGAC 58.332 38.462 4.29 0.00 0.00 4.02
106 107 7.849322 TGCATATGTAGTAGGATTAACTGGA 57.151 36.000 4.29 0.00 0.00 3.86
107 108 8.314021 TCATGCATATGTAGTAGGATTAACTGG 58.686 37.037 0.00 0.00 35.73 4.00
108 109 9.710900 TTCATGCATATGTAGTAGGATTAACTG 57.289 33.333 0.00 0.00 35.73 3.16
109 110 9.712305 GTTCATGCATATGTAGTAGGATTAACT 57.288 33.333 0.00 0.00 35.73 2.24
110 111 9.489084 TGTTCATGCATATGTAGTAGGATTAAC 57.511 33.333 0.00 0.00 35.73 2.01
112 113 9.875691 GATGTTCATGCATATGTAGTAGGATTA 57.124 33.333 0.00 0.00 35.73 1.75
113 114 8.600668 AGATGTTCATGCATATGTAGTAGGATT 58.399 33.333 0.00 0.00 35.73 3.01
114 115 8.143673 AGATGTTCATGCATATGTAGTAGGAT 57.856 34.615 0.00 0.00 35.73 3.24
115 116 7.544804 AGATGTTCATGCATATGTAGTAGGA 57.455 36.000 0.00 0.00 35.73 2.94
116 117 9.310716 CATAGATGTTCATGCATATGTAGTAGG 57.689 37.037 0.00 0.00 35.73 3.18
119 120 9.955102 ATTCATAGATGTTCATGCATATGTAGT 57.045 29.630 0.00 0.00 35.73 2.73
148 149 8.822805 GGGGAATAACCTCCTTTTCTTAAAAAT 58.177 33.333 0.00 0.00 38.98 1.82
154 155 3.308904 CCGGGGAATAACCTCCTTTTCTT 60.309 47.826 0.00 0.00 35.24 2.52
218 220 7.505585 ACTTGGAGACTTTGGTGAATTATTTGA 59.494 33.333 0.00 0.00 0.00 2.69
284 290 0.535553 GGTTGTGGCTGTCCCGTTTA 60.536 55.000 0.00 0.00 35.87 2.01
341 347 5.240623 GGTTTGGATGGCGATCATGTAATAA 59.759 40.000 11.07 0.00 35.97 1.40
352 361 1.969064 CAACCGGTTTGGATGGCGA 60.969 57.895 19.55 0.00 42.00 5.54
424 433 1.211212 CTCAGTCCAATGGATGCCAGA 59.789 52.381 4.81 0.00 36.75 3.86
436 445 1.419381 TGTGGTTGCTACTCAGTCCA 58.581 50.000 0.00 0.00 0.00 4.02
440 449 2.165641 TCCGTATGTGGTTGCTACTCAG 59.834 50.000 0.00 0.00 0.00 3.35
532 542 6.891306 ATTAGGGCTATATGGAACTGCATA 57.109 37.500 0.00 0.00 0.00 3.14
618 629 1.831106 AGCATCCACACGTTATCTGGA 59.169 47.619 4.04 4.04 38.47 3.86
622 633 4.277672 TCCTACTAGCATCCACACGTTATC 59.722 45.833 0.00 0.00 0.00 1.75
724 735 7.052248 TGTAGCTTCTGTGATCATGATGAATT 58.948 34.615 14.30 4.79 0.00 2.17
763 774 3.701532 TTTGGCAAAACGTAACTGGAG 57.298 42.857 10.83 0.00 0.00 3.86
824 835 9.860898 ACAGAAGAAAAGCCAATATATTGTTTC 57.139 29.630 21.20 21.27 36.06 2.78
827 838 8.814038 AGACAGAAGAAAAGCCAATATATTGT 57.186 30.769 21.20 5.15 36.06 2.71
834 845 4.734266 AGGAAGACAGAAGAAAAGCCAAT 58.266 39.130 0.00 0.00 0.00 3.16
835 846 4.137543 GAGGAAGACAGAAGAAAAGCCAA 58.862 43.478 0.00 0.00 0.00 4.52
836 847 3.392616 AGAGGAAGACAGAAGAAAAGCCA 59.607 43.478 0.00 0.00 0.00 4.75
837 848 3.750652 CAGAGGAAGACAGAAGAAAAGCC 59.249 47.826 0.00 0.00 0.00 4.35
882 893 1.585668 GAGCATCATCGACACTGTTCG 59.414 52.381 0.00 6.19 36.10 3.95
995 1009 3.684628 TCGAAGGCTCCCCCTCCT 61.685 66.667 0.00 0.00 45.62 3.69
1077 1091 0.737715 CCGTCCCTCTCTTTCTTGCG 60.738 60.000 0.00 0.00 0.00 4.85
1093 1107 3.194861 GGCTTTTGCTTTCTTTTTCCGT 58.805 40.909 0.00 0.00 46.54 4.69
1094 1108 3.001228 GTGGCTTTTGCTTTCTTTTTCCG 59.999 43.478 0.00 0.00 46.54 4.30
1153 1257 1.534476 TAGGTCTGCGTTGGGGTGA 60.534 57.895 0.00 0.00 0.00 4.02
1183 1287 1.162800 GCTGTGTGGCTGGCTATAGC 61.163 60.000 16.78 16.78 42.94 2.97
1184 1288 0.178767 TGCTGTGTGGCTGGCTATAG 59.821 55.000 2.00 0.00 0.00 1.31
1185 1289 0.178767 CTGCTGTGTGGCTGGCTATA 59.821 55.000 2.00 0.00 0.00 1.31
1186 1290 1.077930 CTGCTGTGTGGCTGGCTAT 60.078 57.895 2.00 0.00 0.00 2.97
1187 1291 2.348620 CTGCTGTGTGGCTGGCTA 59.651 61.111 2.00 0.00 0.00 3.93
1205 1310 4.086178 GTCGTGCTGCTGCTGCTG 62.086 66.667 27.67 20.72 40.48 4.41
1212 1317 4.363990 CCTCGTGGTCGTGCTGCT 62.364 66.667 0.00 0.00 38.33 4.24
1216 1321 4.980805 TTGCCCTCGTGGTCGTGC 62.981 66.667 2.33 0.00 38.33 5.34
1613 1722 2.507339 AAAACAAATGACCAGCACGG 57.493 45.000 0.00 0.00 42.50 4.94
1645 1756 5.186996 ACAAACACAAAATTCTCAGCGAT 57.813 34.783 0.00 0.00 0.00 4.58
1663 1774 0.947180 GGCGTCGCCTCTACAACAAA 60.947 55.000 28.98 0.00 46.69 2.83
1851 1962 5.534207 TTCTGCACATGAAAAGACCAAAT 57.466 34.783 0.00 0.00 0.00 2.32
2101 2212 7.889469 ACTAACTGATTAACCTACTCGTTCAA 58.111 34.615 0.00 0.00 0.00 2.69
2187 2298 3.888583 ACGGTAAAGGAAAAGTGGTGAA 58.111 40.909 0.00 0.00 0.00 3.18
2384 2496 9.827411 GTTGAGTAAACTTCCTAATGCTTTTAG 57.173 33.333 0.00 0.00 35.75 1.85
2728 2844 3.684413 CGTGGTTGCCTAGGGATTTGTAT 60.684 47.826 11.72 0.00 0.00 2.29
2791 2907 2.685999 GGGAAGCCCATGGAAGCT 59.314 61.111 15.22 11.92 44.65 3.74
3183 3302 1.379443 TAGATCACCGACGGGCTGT 60.379 57.895 20.00 0.00 36.48 4.40
3399 3521 7.868922 AGAACACGTACAATTACACAACAGATA 59.131 33.333 0.00 0.00 0.00 1.98
3489 3611 1.610554 ATGCATGGAAGCTTGCCACC 61.611 55.000 15.98 5.19 38.44 4.61
3557 3679 4.186077 TGTTCCAGACCCAACCAATAAA 57.814 40.909 0.00 0.00 0.00 1.40
3581 3703 6.596106 AGCAATGCAAGAATCAAAATTATGCA 59.404 30.769 8.35 11.24 44.86 3.96
3587 3709 5.178623 CACACAGCAATGCAAGAATCAAAAT 59.821 36.000 8.35 0.00 0.00 1.82
3651 7217 6.342338 AGTTCTGTTAGTTGATACGAAGGT 57.658 37.500 0.00 0.00 0.00 3.50
3703 7270 9.922477 TTTCTCTCGGTGTATATATATCCTGAT 57.078 33.333 0.00 0.00 0.00 2.90
3784 7351 2.949177 ATGTTGTGCCAGTGTTCCTA 57.051 45.000 0.00 0.00 0.00 2.94
3818 7385 7.970061 ACATTTTATAGCCTTATTATGCATGCG 59.030 33.333 14.09 0.00 0.00 4.73
3845 7412 1.726791 ACGAGATTGCACGTCATCAAC 59.273 47.619 0.00 0.00 36.63 3.18
3846 7413 2.078849 ACGAGATTGCACGTCATCAA 57.921 45.000 0.00 0.00 36.63 2.57
3916 7483 9.528489 ACTTTGGAACATAACATAAACATAGGT 57.472 29.630 0.00 0.00 39.30 3.08
3923 7490 9.881529 GTTACGAACTTTGGAACATAACATAAA 57.118 29.630 0.00 0.00 39.30 1.40
3924 7491 9.275398 AGTTACGAACTTTGGAACATAACATAA 57.725 29.630 6.85 0.00 39.04 1.90
3925 7492 8.836268 AGTTACGAACTTTGGAACATAACATA 57.164 30.769 6.85 0.00 39.04 2.29
3926 7493 7.660208 AGAGTTACGAACTTTGGAACATAACAT 59.340 33.333 6.85 0.00 43.03 2.71
3927 7494 6.987992 AGAGTTACGAACTTTGGAACATAACA 59.012 34.615 6.85 0.00 43.03 2.41
3928 7495 7.288672 CAGAGTTACGAACTTTGGAACATAAC 58.711 38.462 6.85 0.00 43.03 1.89
4023 7590 4.016444 GCCTTACAAACTCAATGGATGGA 58.984 43.478 0.00 0.00 29.42 3.41
4069 7636 4.873827 ACCGCATGATTACGTTAGTCAAAT 59.126 37.500 0.00 0.00 0.00 2.32
4081 7648 4.551702 AGTGGCATATACCGCATGATTA 57.448 40.909 8.26 0.00 42.97 1.75
4110 7677 9.660180 TCACTAACAAAACATGTGCTATATACA 57.340 29.630 0.00 0.00 42.99 2.29
4118 7797 6.033341 TCAACTTCACTAACAAAACATGTGC 58.967 36.000 0.00 0.00 42.99 4.57
4213 7892 1.211457 TCGGACAGAGGGAGTACTACC 59.789 57.143 17.30 17.30 0.00 3.18
4214 7893 2.706339 TCGGACAGAGGGAGTACTAC 57.294 55.000 0.00 0.00 0.00 2.73
4215 7894 3.726557 TTTCGGACAGAGGGAGTACTA 57.273 47.619 0.00 0.00 0.00 1.82
4216 7895 2.599408 TTTCGGACAGAGGGAGTACT 57.401 50.000 0.00 0.00 0.00 2.73
4217 7896 3.889520 ATTTTCGGACAGAGGGAGTAC 57.110 47.619 0.00 0.00 0.00 2.73
4218 7897 4.607239 AGTATTTTCGGACAGAGGGAGTA 58.393 43.478 0.00 0.00 0.00 2.59
4219 7898 3.442076 AGTATTTTCGGACAGAGGGAGT 58.558 45.455 0.00 0.00 0.00 3.85
4220 7899 4.473477 AAGTATTTTCGGACAGAGGGAG 57.527 45.455 0.00 0.00 0.00 4.30
4221 7900 5.659525 TGATAAGTATTTTCGGACAGAGGGA 59.340 40.000 0.00 0.00 0.00 4.20
4222 7901 5.914033 TGATAAGTATTTTCGGACAGAGGG 58.086 41.667 0.00 0.00 0.00 4.30
4223 7902 7.210174 TGATGATAAGTATTTTCGGACAGAGG 58.790 38.462 0.00 0.00 0.00 3.69
4224 7903 8.648557 TTGATGATAAGTATTTTCGGACAGAG 57.351 34.615 0.00 0.00 0.00 3.35
4225 7904 9.443323 TTTTGATGATAAGTATTTTCGGACAGA 57.557 29.630 0.00 0.00 0.00 3.41
4228 7907 9.450807 CCATTTTGATGATAAGTATTTTCGGAC 57.549 33.333 0.00 0.00 0.00 4.79
4229 7908 9.402320 TCCATTTTGATGATAAGTATTTTCGGA 57.598 29.630 0.00 0.00 0.00 4.55
4270 7949 9.900710 ACGTATCTAGATGCATTTTAGTTCTAG 57.099 33.333 19.22 6.29 38.03 2.43
4271 7950 9.894783 GACGTATCTAGATGCATTTTAGTTCTA 57.105 33.333 19.22 0.00 0.00 2.10
4272 7951 8.634444 AGACGTATCTAGATGCATTTTAGTTCT 58.366 33.333 19.22 0.00 31.46 3.01
4273 7952 8.804688 AGACGTATCTAGATGCATTTTAGTTC 57.195 34.615 19.22 3.99 31.46 3.01
4274 7953 7.868415 GGAGACGTATCTAGATGCATTTTAGTT 59.132 37.037 19.22 4.58 34.34 2.24
4275 7954 7.231722 AGGAGACGTATCTAGATGCATTTTAGT 59.768 37.037 19.22 8.66 34.34 2.24
4276 7955 7.598278 AGGAGACGTATCTAGATGCATTTTAG 58.402 38.462 19.22 6.74 34.34 1.85
4277 7956 7.526142 AGGAGACGTATCTAGATGCATTTTA 57.474 36.000 19.22 0.00 34.34 1.52
4278 7957 6.412362 AGGAGACGTATCTAGATGCATTTT 57.588 37.500 19.22 2.52 34.34 1.82
4279 7958 6.266558 AGAAGGAGACGTATCTAGATGCATTT 59.733 38.462 19.22 0.00 34.34 2.32
4280 7959 5.772672 AGAAGGAGACGTATCTAGATGCATT 59.227 40.000 19.22 6.63 34.34 3.56
4281 7960 5.321102 AGAAGGAGACGTATCTAGATGCAT 58.679 41.667 19.22 0.00 34.34 3.96
4282 7961 4.720046 AGAAGGAGACGTATCTAGATGCA 58.280 43.478 19.22 0.00 34.34 3.96
4283 7962 6.037830 GGATAGAAGGAGACGTATCTAGATGC 59.962 46.154 15.79 13.06 34.34 3.91
4284 7963 7.106890 TGGATAGAAGGAGACGTATCTAGATG 58.893 42.308 15.79 1.92 34.34 2.90
4285 7964 7.260387 TGGATAGAAGGAGACGTATCTAGAT 57.740 40.000 10.44 10.73 34.34 1.98
4286 7965 6.683312 TGGATAGAAGGAGACGTATCTAGA 57.317 41.667 10.44 0.00 34.34 2.43
4287 7966 7.931578 AATGGATAGAAGGAGACGTATCTAG 57.068 40.000 10.44 0.00 34.34 2.43
4288 7967 8.577296 CAAAATGGATAGAAGGAGACGTATCTA 58.423 37.037 10.44 3.89 34.34 1.98
4289 7968 7.287927 TCAAAATGGATAGAAGGAGACGTATCT 59.712 37.037 10.44 0.00 38.15 1.98
4290 7969 7.434492 TCAAAATGGATAGAAGGAGACGTATC 58.566 38.462 0.37 0.37 0.00 2.24
4291 7970 7.361457 TCAAAATGGATAGAAGGAGACGTAT 57.639 36.000 0.00 0.00 0.00 3.06
4292 7971 6.785337 TCAAAATGGATAGAAGGAGACGTA 57.215 37.500 0.00 0.00 0.00 3.57
4293 7972 5.677319 TCAAAATGGATAGAAGGAGACGT 57.323 39.130 0.00 0.00 0.00 4.34
4294 7973 6.201806 GTCATCAAAATGGATAGAAGGAGACG 59.798 42.308 0.00 0.00 33.42 4.18
4295 7974 7.050377 TGTCATCAAAATGGATAGAAGGAGAC 58.950 38.462 0.00 0.00 33.42 3.36
4296 7975 7.199167 TGTCATCAAAATGGATAGAAGGAGA 57.801 36.000 0.00 0.00 33.42 3.71
4297 7976 7.555554 ACTTGTCATCAAAATGGATAGAAGGAG 59.444 37.037 0.00 0.00 33.42 3.69
4298 7977 7.405292 ACTTGTCATCAAAATGGATAGAAGGA 58.595 34.615 0.00 0.00 33.42 3.36
4299 7978 7.636150 ACTTGTCATCAAAATGGATAGAAGG 57.364 36.000 0.00 0.00 33.42 3.46
4305 7984 8.472413 CCAGAAATACTTGTCATCAAAATGGAT 58.528 33.333 0.00 0.00 33.42 3.41
4306 7985 7.669304 TCCAGAAATACTTGTCATCAAAATGGA 59.331 33.333 0.00 0.00 33.42 3.41
4307 7986 7.756722 GTCCAGAAATACTTGTCATCAAAATGG 59.243 37.037 0.00 0.00 33.42 3.16
4308 7987 7.482743 CGTCCAGAAATACTTGTCATCAAAATG 59.517 37.037 0.00 0.00 32.87 2.32
4309 7988 7.362056 CCGTCCAGAAATACTTGTCATCAAAAT 60.362 37.037 0.00 0.00 32.87 1.82
4310 7989 6.072728 CCGTCCAGAAATACTTGTCATCAAAA 60.073 38.462 0.00 0.00 32.87 2.44
4311 7990 5.411361 CCGTCCAGAAATACTTGTCATCAAA 59.589 40.000 0.00 0.00 32.87 2.69
4312 7991 4.935205 CCGTCCAGAAATACTTGTCATCAA 59.065 41.667 0.00 0.00 0.00 2.57
4313 7992 4.221924 TCCGTCCAGAAATACTTGTCATCA 59.778 41.667 0.00 0.00 0.00 3.07
4314 7993 4.755411 TCCGTCCAGAAATACTTGTCATC 58.245 43.478 0.00 0.00 0.00 2.92
4315 7994 4.383118 CCTCCGTCCAGAAATACTTGTCAT 60.383 45.833 0.00 0.00 0.00 3.06
4316 7995 3.056107 CCTCCGTCCAGAAATACTTGTCA 60.056 47.826 0.00 0.00 0.00 3.58
4317 7996 3.522553 CCTCCGTCCAGAAATACTTGTC 58.477 50.000 0.00 0.00 0.00 3.18
4318 7997 2.236395 CCCTCCGTCCAGAAATACTTGT 59.764 50.000 0.00 0.00 0.00 3.16
4319 7998 2.500098 TCCCTCCGTCCAGAAATACTTG 59.500 50.000 0.00 0.00 0.00 3.16
4320 7999 2.766828 CTCCCTCCGTCCAGAAATACTT 59.233 50.000 0.00 0.00 0.00 2.24
4321 8000 2.292323 ACTCCCTCCGTCCAGAAATACT 60.292 50.000 0.00 0.00 0.00 2.12
4322 8001 2.108970 ACTCCCTCCGTCCAGAAATAC 58.891 52.381 0.00 0.00 0.00 1.89
4323 8002 2.544844 ACTCCCTCCGTCCAGAAATA 57.455 50.000 0.00 0.00 0.00 1.40
4324 8003 2.544844 TACTCCCTCCGTCCAGAAAT 57.455 50.000 0.00 0.00 0.00 2.17
4325 8004 2.108168 CATACTCCCTCCGTCCAGAAA 58.892 52.381 0.00 0.00 0.00 2.52
4326 8005 1.006758 ACATACTCCCTCCGTCCAGAA 59.993 52.381 0.00 0.00 0.00 3.02
4327 8006 0.629596 ACATACTCCCTCCGTCCAGA 59.370 55.000 0.00 0.00 0.00 3.86
4328 8007 2.359981 TACATACTCCCTCCGTCCAG 57.640 55.000 0.00 0.00 0.00 3.86
4329 8008 3.323774 AATACATACTCCCTCCGTCCA 57.676 47.619 0.00 0.00 0.00 4.02
4330 8009 5.245526 ACATTAATACATACTCCCTCCGTCC 59.754 44.000 0.00 0.00 0.00 4.79
4331 8010 6.342338 ACATTAATACATACTCCCTCCGTC 57.658 41.667 0.00 0.00 0.00 4.79
4332 8011 5.245526 GGACATTAATACATACTCCCTCCGT 59.754 44.000 0.00 0.00 0.00 4.69
4333 8012 5.480772 AGGACATTAATACATACTCCCTCCG 59.519 44.000 0.00 0.00 0.00 4.63
4334 8013 6.936968 AGGACATTAATACATACTCCCTCC 57.063 41.667 0.00 0.00 0.00 4.30
4335 8014 7.736893 ACAAGGACATTAATACATACTCCCTC 58.263 38.462 0.00 0.00 0.00 4.30
4336 8015 7.569111 AGACAAGGACATTAATACATACTCCCT 59.431 37.037 0.00 0.00 0.00 4.20
4369 8052 6.430925 TCATTTGTTGTCGAAGATGGAGATTT 59.569 34.615 0.00 0.00 40.67 2.17
4370 8053 5.939883 TCATTTGTTGTCGAAGATGGAGATT 59.060 36.000 0.00 0.00 40.67 2.40
4372 8055 4.893608 TCATTTGTTGTCGAAGATGGAGA 58.106 39.130 0.00 0.00 40.67 3.71
4373 8056 5.180117 AGTTCATTTGTTGTCGAAGATGGAG 59.820 40.000 0.00 0.00 40.67 3.86
4374 8057 5.049474 CAGTTCATTTGTTGTCGAAGATGGA 60.049 40.000 0.00 0.00 40.67 3.41
4383 8082 8.801715 AATACATGTTCAGTTCATTTGTTGTC 57.198 30.769 2.30 0.00 0.00 3.18
4459 9530 2.285544 GCACACATTTGCACGTTTTTCC 60.286 45.455 0.00 0.00 42.49 3.13
4460 9531 2.602660 AGCACACATTTGCACGTTTTTC 59.397 40.909 0.00 0.00 45.62 2.29
4466 9537 0.238025 TAGCAGCACACATTTGCACG 59.762 50.000 0.00 0.00 45.62 5.34
4467 9541 2.420628 TTAGCAGCACACATTTGCAC 57.579 45.000 0.00 0.00 45.62 4.57
4508 9582 1.450312 CGAGATGGTCCCAGTTGCC 60.450 63.158 0.00 0.00 0.00 4.52
4519 9593 0.526954 GCATGCTTTTGCCGAGATGG 60.527 55.000 11.37 0.00 46.87 3.51
4520 9594 0.171679 TGCATGCTTTTGCCGAGATG 59.828 50.000 20.33 0.00 46.87 2.90
4521 9595 1.108776 ATGCATGCTTTTGCCGAGAT 58.891 45.000 20.33 0.00 46.87 2.75
4522 9596 0.171679 CATGCATGCTTTTGCCGAGA 59.828 50.000 20.33 0.00 46.87 4.04
4523 9597 0.108992 ACATGCATGCTTTTGCCGAG 60.109 50.000 26.53 1.32 46.87 4.63
4524 9598 0.317799 AACATGCATGCTTTTGCCGA 59.682 45.000 26.53 0.00 46.87 5.54
4525 9599 1.136197 CAAACATGCATGCTTTTGCCG 60.136 47.619 26.53 4.74 46.87 5.69
4526 9600 2.144730 TCAAACATGCATGCTTTTGCC 58.855 42.857 26.36 0.00 46.87 4.52
4528 9602 6.097356 ACTATCTCAAACATGCATGCTTTTG 58.903 36.000 26.53 26.02 0.00 2.44
4529 9603 6.152323 AGACTATCTCAAACATGCATGCTTTT 59.848 34.615 26.53 16.91 0.00 2.27
4530 9604 5.651139 AGACTATCTCAAACATGCATGCTTT 59.349 36.000 26.53 20.56 0.00 3.51
4531 9605 5.191426 AGACTATCTCAAACATGCATGCTT 58.809 37.500 26.53 18.08 0.00 3.91
4532 9606 4.778579 AGACTATCTCAAACATGCATGCT 58.221 39.130 26.53 12.25 0.00 3.79
4533 9607 5.065602 TGAAGACTATCTCAAACATGCATGC 59.934 40.000 26.53 11.82 0.00 4.06
4534 9608 6.093082 TGTGAAGACTATCTCAAACATGCATG 59.907 38.462 25.09 25.09 0.00 4.06
4535 9609 6.175471 TGTGAAGACTATCTCAAACATGCAT 58.825 36.000 0.00 0.00 0.00 3.96
4536 9610 5.550290 TGTGAAGACTATCTCAAACATGCA 58.450 37.500 0.00 0.00 0.00 3.96
4537 9611 6.486253 TTGTGAAGACTATCTCAAACATGC 57.514 37.500 0.00 0.00 31.85 4.06
4538 9612 8.509690 ACATTTGTGAAGACTATCTCAAACATG 58.490 33.333 12.69 0.00 42.28 3.21
4539 9613 8.627208 ACATTTGTGAAGACTATCTCAAACAT 57.373 30.769 12.69 6.05 42.28 2.71
4540 9614 9.208022 CTACATTTGTGAAGACTATCTCAAACA 57.792 33.333 12.69 0.00 42.28 2.83
4541 9615 9.424319 TCTACATTTGTGAAGACTATCTCAAAC 57.576 33.333 12.69 0.00 42.28 2.93
4542 9616 9.424319 GTCTACATTTGTGAAGACTATCTCAAA 57.576 33.333 12.75 12.75 43.09 2.69
4543 9617 8.035394 GGTCTACATTTGTGAAGACTATCTCAA 58.965 37.037 11.46 0.00 38.69 3.02
4544 9618 7.178451 TGGTCTACATTTGTGAAGACTATCTCA 59.822 37.037 11.46 1.69 38.69 3.27
4545 9619 7.548097 TGGTCTACATTTGTGAAGACTATCTC 58.452 38.462 11.46 0.00 38.69 2.75
4546 9620 7.482169 TGGTCTACATTTGTGAAGACTATCT 57.518 36.000 11.46 0.00 38.69 1.98


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

AutoCloner maintained by Alex Coulton.