Multiple sequence alignment - TraesCS7A01G095400

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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 TraesCS7A01G095400 chr7A 100.000 4104 0 0 855 4958 58232995 58237098 0.000000e+00 7579.0
1 TraesCS7A01G095400 chr7A 100.000 618 0 0 1 618 58232141 58232758 0.000000e+00 1142.0
2 TraesCS7A01G095400 chr7A 80.171 585 83 25 3359 3928 83292208 83291642 1.660000e-109 407.0
3 TraesCS7A01G095400 chr7A 85.677 384 52 1 1696 2079 83298825 83298445 7.730000e-108 401.0
4 TraesCS7A01G095400 chr7A 82.057 457 61 8 2222 2678 83298280 83297845 2.180000e-98 370.0
5 TraesCS7A01G095400 chr7A 87.043 301 39 0 1215 1515 83299210 83298910 1.710000e-89 340.0
6 TraesCS7A01G095400 chr7D 92.000 2750 154 23 1566 4307 54760605 54757914 0.000000e+00 3799.0
7 TraesCS7A01G095400 chr7D 92.522 789 47 7 859 1636 54761280 54760493 0.000000e+00 1120.0
8 TraesCS7A01G095400 chr7D 87.264 636 31 14 1 615 54762074 54761468 0.000000e+00 680.0
9 TraesCS7A01G095400 chr7D 79.198 1048 163 38 2801 3820 80714238 80713218 0.000000e+00 676.0
10 TraesCS7A01G095400 chr7D 86.473 621 45 17 4300 4891 54757674 54757064 0.000000e+00 645.0
11 TraesCS7A01G095400 chr7D 86.645 307 41 0 1215 1521 80715769 80715463 1.710000e-89 340.0
12 TraesCS7A01G095400 chr7D 92.647 68 5 0 4891 4958 54757034 54756967 1.140000e-16 99.0
13 TraesCS7A01G095400 chr4A 91.751 2376 157 19 1608 3976 670886798 670889141 0.000000e+00 3265.0
14 TraesCS7A01G095400 chr4A 92.510 761 41 12 856 1611 670886139 670886888 0.000000e+00 1075.0
15 TraesCS7A01G095400 chr4A 84.330 485 68 7 1015 1498 670942177 670942654 7.520000e-128 468.0
16 TraesCS7A01G095400 chr4A 85.854 410 58 0 2211 2620 670943329 670943738 2.120000e-118 436.0
17 TraesCS7A01G095400 chr4A 85.854 410 51 6 1689 2096 670942701 670943105 3.550000e-116 429.0
18 TraesCS7A01G095400 chr4A 86.103 331 24 12 4009 4339 670925054 670925362 2.210000e-88 337.0
19 TraesCS7A01G095400 chr4A 82.927 123 7 4 506 615 670885828 670885949 1.140000e-16 99.0
20 TraesCS7A01G095400 chr4A 100.000 34 0 0 273 306 606584322 606584289 4.140000e-06 63.9
21 TraesCS7A01G095400 chr6A 87.949 390 44 3 1696 2085 585971745 585972131 1.630000e-124 457.0
22 TraesCS7A01G095400 chr6A 85.556 450 48 5 1083 1516 585971120 585971568 5.850000e-124 455.0
23 TraesCS7A01G095400 chr6A 94.737 95 5 0 3355 3449 585973437 585973531 1.110000e-31 148.0
24 TraesCS7A01G095400 chrUn 82.752 516 71 7 3355 3870 108752198 108751701 1.270000e-120 444.0
25 TraesCS7A01G095400 chrUn 88.764 356 35 3 1697 2051 108746461 108746812 9.860000e-117 431.0
26 TraesCS7A01G095400 chrUn 83.971 418 59 3 2800 3209 108795245 108794828 1.290000e-105 394.0
27 TraesCS7A01G095400 chrUn 82.243 428 68 7 2252 2678 108747117 108747537 3.650000e-96 363.0
28 TraesCS7A01G095400 chrUn 85.065 308 43 3 1206 1513 108618599 108618903 1.340000e-80 311.0
29 TraesCS7A01G095400 chrUn 97.059 34 1 0 273 306 332851764 332851731 1.930000e-04 58.4
30 TraesCS7A01G095400 chr4B 86.616 396 49 2 1689 2084 665302209 665301818 7.620000e-118 435.0
31 TraesCS7A01G095400 chr4B 79.769 173 34 1 3656 3828 665300752 665300581 1.870000e-24 124.0
32 TraesCS7A01G095400 chr5A 85.930 398 52 2 1689 2086 704975083 704974690 5.930000e-114 422.0
33 TraesCS7A01G095400 chr5A 81.589 516 77 10 3355 3870 704950506 704951003 1.280000e-110 411.0
34 TraesCS7A01G095400 chr5A 83.447 441 63 3 2243 2682 705144081 705144512 7.730000e-108 401.0
35 TraesCS7A01G095400 chr5A 79.899 592 75 25 3348 3917 705146561 705147130 1.290000e-105 394.0
36 TraesCS7A01G095400 chr5A 81.647 425 70 8 2255 2678 704974426 704974009 3.670000e-91 346.0
37 TraesCS7A01G095400 chr5A 79.060 468 67 6 3355 3822 680216871 680216435 4.850000e-75 292.0
38 TraesCS7A01G095400 chr2D 84.527 433 56 5 2251 2682 584759225 584759647 7.680000e-113 418.0
39 TraesCS7A01G095400 chr7B 85.938 384 51 2 1696 2079 28062205 28061825 1.660000e-109 407.0
40 TraesCS7A01G095400 chr7B 79.167 600 94 25 3359 3944 28060144 28059562 2.160000e-103 387.0
41 TraesCS7A01G095400 chr7B 87.055 309 38 2 1215 1522 28062590 28062283 1.020000e-91 348.0
42 TraesCS7A01G095400 chr7B 84.641 306 38 6 2373 2678 28061157 28060861 3.750000e-76 296.0
43 TraesCS7A01G095400 chr7B 97.059 34 1 0 273 306 613240173 613240140 1.930000e-04 58.4
44 TraesCS7A01G095400 chr4D 82.051 468 66 7 3355 3822 499457956 499457507 2.800000e-102 383.0
45 TraesCS7A01G095400 chr4D 82.100 419 66 5 2810 3228 499458510 499458101 2.840000e-92 350.0
46 TraesCS7A01G095400 chr4D 81.542 428 67 2 2251 2678 499459039 499458624 4.750000e-90 342.0
47 TraesCS7A01G095400 chr3B 84.295 312 45 2 1204 1513 818314503 818314812 8.070000e-78 302.0
48 TraesCS7A01G095400 chr6D 100.000 34 0 0 273 306 355436620 355436653 4.140000e-06 63.9
49 TraesCS7A01G095400 chr1B 100.000 34 0 0 273 306 423640269 423640236 4.140000e-06 63.9
50 TraesCS7A01G095400 chr1B 97.059 34 1 0 273 306 29975403 29975370 1.930000e-04 58.4
51 TraesCS7A01G095400 chr1B 97.059 34 1 0 273 306 614972548 614972581 1.930000e-04 58.4
52 TraesCS7A01G095400 chr5D 97.059 34 1 0 273 306 134782126 134782159 1.930000e-04 58.4


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 TraesCS7A01G095400 chr7A 58232141 58237098 4957 False 4360.500000 7579 100.000000 1 4958 2 chr7A.!!$F1 4957
1 TraesCS7A01G095400 chr7A 83291642 83292208 566 True 407.000000 407 80.171000 3359 3928 1 chr7A.!!$R1 569
2 TraesCS7A01G095400 chr7A 83297845 83299210 1365 True 370.333333 401 84.925667 1215 2678 3 chr7A.!!$R2 1463
3 TraesCS7A01G095400 chr7D 54756967 54762074 5107 True 1268.600000 3799 90.181200 1 4958 5 chr7D.!!$R1 4957
4 TraesCS7A01G095400 chr7D 80713218 80715769 2551 True 508.000000 676 82.921500 1215 3820 2 chr7D.!!$R2 2605
5 TraesCS7A01G095400 chr4A 670885828 670889141 3313 False 1479.666667 3265 89.062667 506 3976 3 chr4A.!!$F2 3470
6 TraesCS7A01G095400 chr4A 670942177 670943738 1561 False 444.333333 468 85.346000 1015 2620 3 chr4A.!!$F3 1605
7 TraesCS7A01G095400 chr6A 585971120 585973531 2411 False 353.333333 457 89.414000 1083 3449 3 chr6A.!!$F1 2366
8 TraesCS7A01G095400 chrUn 108746461 108747537 1076 False 397.000000 431 85.503500 1697 2678 2 chrUn.!!$F2 981
9 TraesCS7A01G095400 chr4B 665300581 665302209 1628 True 279.500000 435 83.192500 1689 3828 2 chr4B.!!$R1 2139
10 TraesCS7A01G095400 chr5A 705144081 705147130 3049 False 397.500000 401 81.673000 2243 3917 2 chr5A.!!$F2 1674
11 TraesCS7A01G095400 chr5A 704974009 704975083 1074 True 384.000000 422 83.788500 1689 2678 2 chr5A.!!$R2 989
12 TraesCS7A01G095400 chr7B 28059562 28062590 3028 True 359.500000 407 84.200250 1215 3944 4 chr7B.!!$R2 2729
13 TraesCS7A01G095400 chr4D 499457507 499459039 1532 True 358.333333 383 81.897667 2251 3822 3 chr4D.!!$R1 1571

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
592 621 0.036010 AGCCATTCCGTCCTCTGTTG 60.036 55.000 0.00 0.00 0.00 3.33 F
1119 1166 0.036164 TGTGGAAGTGGCGCAAGTAT 59.964 50.000 10.83 0.00 41.68 2.12 F
1664 1813 0.034089 ATGGAGAAAGCCGGGGAAAG 60.034 55.000 2.18 0.00 0.00 2.62 F
2069 2254 1.376942 CTGGCTTGGTGCTCCTCAG 60.377 63.158 6.34 3.51 42.39 3.35 F
2756 3594 0.820226 AAGCTGCTGCGTCTATCTGA 59.180 50.000 1.35 0.00 45.42 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1645 1707 0.034089 CTTTCCCCGGCTTTCTCCAT 60.034 55.0 0.00 0.0 0.00 3.41 R
2069 2254 0.097674 CTTCGCCTGTAGCACAATGC 59.902 55.0 0.00 0.0 45.46 3.56 R
2737 3575 0.820226 TCAGATAGACGCAGCAGCTT 59.180 50.0 0.00 0.0 39.10 3.74 R
3282 5533 0.831307 ATCCTAGGGGCTCGAACAAC 59.169 55.0 9.46 0.0 0.00 3.32 R
4392 6992 0.033208 TCATCACCCCCTTGCATTCC 60.033 55.0 0.00 0.0 0.00 3.01 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
39 40 4.319477 CGTGAGTACATGGTCCTTGTTTTG 60.319 45.833 15.10 0.00 0.00 2.44
43 44 6.153680 TGAGTACATGGTCCTTGTTTTGTTTT 59.846 34.615 15.10 0.00 0.00 2.43
44 45 6.337356 AGTACATGGTCCTTGTTTTGTTTTG 58.663 36.000 15.10 0.00 0.00 2.44
45 46 5.159273 ACATGGTCCTTGTTTTGTTTTGT 57.841 34.783 4.56 0.00 0.00 2.83
46 47 4.934602 ACATGGTCCTTGTTTTGTTTTGTG 59.065 37.500 4.56 0.00 0.00 3.33
66 67 8.770438 TTTGTGTCTTGCTTTATTTTTCTGTT 57.230 26.923 0.00 0.00 0.00 3.16
77 78 9.237846 GCTTTATTTTTCTGTTGGCATAGATAC 57.762 33.333 3.25 0.00 0.00 2.24
136 137 9.877178 TCTTTTTAGAAATATCTGTCTGTCTCC 57.123 33.333 0.00 0.00 37.10 3.71
137 138 9.658799 CTTTTTAGAAATATCTGTCTGTCTCCA 57.341 33.333 0.00 0.00 37.10 3.86
139 140 9.658799 TTTTAGAAATATCTGTCTGTCTCCAAG 57.341 33.333 0.00 0.00 37.10 3.61
140 141 6.232581 AGAAATATCTGTCTGTCTCCAAGG 57.767 41.667 0.00 0.00 33.59 3.61
141 142 5.130145 AGAAATATCTGTCTGTCTCCAAGGG 59.870 44.000 0.00 0.00 33.59 3.95
142 143 1.577736 ATCTGTCTGTCTCCAAGGGG 58.422 55.000 0.00 0.00 0.00 4.79
143 144 0.191064 TCTGTCTGTCTCCAAGGGGT 59.809 55.000 0.00 0.00 34.93 4.95
144 145 0.610687 CTGTCTGTCTCCAAGGGGTC 59.389 60.000 0.00 0.00 34.93 4.46
145 146 0.191064 TGTCTGTCTCCAAGGGGTCT 59.809 55.000 0.00 0.00 34.93 3.85
146 147 0.610687 GTCTGTCTCCAAGGGGTCTG 59.389 60.000 0.00 0.00 34.93 3.51
147 148 0.191064 TCTGTCTCCAAGGGGTCTGT 59.809 55.000 0.00 0.00 34.93 3.41
148 149 0.610687 CTGTCTCCAAGGGGTCTGTC 59.389 60.000 0.00 0.00 34.93 3.51
149 150 0.191064 TGTCTCCAAGGGGTCTGTCT 59.809 55.000 0.00 0.00 34.93 3.41
150 151 0.899019 GTCTCCAAGGGGTCTGTCTC 59.101 60.000 0.00 0.00 34.93 3.36
151 152 0.252284 TCTCCAAGGGGTCTGTCTCC 60.252 60.000 0.00 0.00 36.82 3.71
152 153 0.545309 CTCCAAGGGGTCTGTCTCCA 60.545 60.000 0.00 0.00 39.70 3.86
173 174 4.142182 CCAAGGGGCACTACATGTAATTTG 60.142 45.833 7.06 5.82 0.00 2.32
220 221 1.412079 TTGCACTGGCCAAACAGATT 58.588 45.000 7.01 0.00 40.97 2.40
237 238 7.992754 AACAGATTGTCTAAAGCAAGATTCT 57.007 32.000 0.00 0.00 0.00 2.40
295 311 9.444600 TCCAAATAAGTGTCTCAACCTTAATAC 57.555 33.333 0.00 0.00 0.00 1.89
296 312 9.226606 CCAAATAAGTGTCTCAACCTTAATACA 57.773 33.333 0.00 0.00 0.00 2.29
316 332 5.945144 ACAACTTTATACCGGGTGTAGAT 57.055 39.130 10.66 0.00 31.61 1.98
348 364 3.327757 GTCCATGCCATCCTCCAACTATA 59.672 47.826 0.00 0.00 0.00 1.31
349 365 4.018960 GTCCATGCCATCCTCCAACTATAT 60.019 45.833 0.00 0.00 0.00 0.86
356 372 8.213489 TGCCATCCTCCAACTATATAATAACA 57.787 34.615 0.00 0.00 0.00 2.41
357 373 8.664992 TGCCATCCTCCAACTATATAATAACAA 58.335 33.333 0.00 0.00 0.00 2.83
390 406 6.954616 ATGTTACAATGCAATGATGTGTTG 57.045 33.333 9.20 0.00 32.71 3.33
453 469 5.284582 ACCAGAGTTATCTCCCAATCTTCT 58.715 41.667 0.00 0.00 41.26 2.85
469 485 7.063780 CCCAATCTTCTATGTGCATTTTGTTTC 59.936 37.037 0.00 0.00 0.00 2.78
476 492 7.243487 TCTATGTGCATTTTGTTTCGATCTTC 58.757 34.615 0.00 0.00 0.00 2.87
481 497 5.914635 TGCATTTTGTTTCGATCTTCTTCAC 59.085 36.000 0.00 0.00 0.00 3.18
489 505 4.084889 TCGATCTTCTTCACGACTTCTG 57.915 45.455 0.00 0.00 0.00 3.02
504 520 1.869767 CTTCTGTCCTATGGATTGCGC 59.130 52.381 0.00 0.00 32.73 6.09
584 613 4.868195 GCACAAAGCCATTCCGTC 57.132 55.556 0.00 0.00 37.23 4.79
589 618 1.089920 CAAAGCCATTCCGTCCTCTG 58.910 55.000 0.00 0.00 0.00 3.35
592 621 0.036010 AGCCATTCCGTCCTCTGTTG 60.036 55.000 0.00 0.00 0.00 3.33
610 639 1.550327 TGTCCTTGCACTCTCGAGAT 58.450 50.000 17.03 3.50 0.00 2.75
612 641 0.820226 TCCTTGCACTCTCGAGATGG 59.180 55.000 17.03 12.11 0.00 3.51
613 642 0.534412 CCTTGCACTCTCGAGATGGT 59.466 55.000 17.03 8.66 0.00 3.55
614 643 1.470632 CCTTGCACTCTCGAGATGGTC 60.471 57.143 17.03 6.39 0.00 4.02
615 644 1.476085 CTTGCACTCTCGAGATGGTCT 59.524 52.381 17.03 0.00 0.00 3.85
875 912 3.833729 TGAGCATCAATGGGGATGG 57.166 52.632 5.43 0.00 45.97 3.51
879 916 0.479815 GCATCAATGGGGATGGAGGA 59.520 55.000 5.43 0.00 43.85 3.71
880 917 1.820877 GCATCAATGGGGATGGAGGAC 60.821 57.143 5.43 0.00 43.85 3.85
881 918 1.779092 CATCAATGGGGATGGAGGACT 59.221 52.381 0.00 0.00 40.75 3.85
882 919 1.216064 TCAATGGGGATGGAGGACTG 58.784 55.000 0.00 0.00 0.00 3.51
886 923 0.621571 TGGGGATGGAGGACTGAAGG 60.622 60.000 0.00 0.00 0.00 3.46
891 928 0.539051 ATGGAGGACTGAAGGAAGCG 59.461 55.000 0.00 0.00 0.00 4.68
894 931 0.892063 GAGGACTGAAGGAAGCGTCT 59.108 55.000 0.00 0.00 0.00 4.18
960 1007 1.300465 CAGTCGCCATCATCCTCGG 60.300 63.158 0.00 0.00 0.00 4.63
961 1008 2.029666 GTCGCCATCATCCTCGGG 59.970 66.667 0.00 0.00 0.00 5.14
962 1009 3.928779 TCGCCATCATCCTCGGGC 61.929 66.667 0.00 0.00 42.98 6.13
1008 1055 9.866798 AGCATATAATATCACTGTATGTCACTG 57.133 33.333 0.00 0.00 0.00 3.66
1039 1086 1.202348 CGCCGATCATGGATACTGCTA 59.798 52.381 0.00 0.00 37.61 3.49
1042 1089 3.444034 GCCGATCATGGATACTGCTACTA 59.556 47.826 0.00 0.00 37.61 1.82
1069 1116 2.112815 GGAAAGGGAATCACGGCGG 61.113 63.158 13.24 0.00 0.00 6.13
1092 1139 1.063183 AGCAGCAGAAAGAGGACCTT 58.937 50.000 0.00 0.00 36.47 3.50
1119 1166 0.036164 TGTGGAAGTGGCGCAAGTAT 59.964 50.000 10.83 0.00 41.68 2.12
1131 1178 1.093159 GCAAGTATCTGCTGCTGCTT 58.907 50.000 17.00 4.53 39.34 3.91
1431 1493 2.270205 CTCATGGCCGCCTTCACT 59.730 61.111 11.61 0.00 0.00 3.41
1503 1565 2.430921 CTCGTCTTCGCCTGCGTT 60.431 61.111 11.68 0.00 40.74 4.84
1572 1634 2.660064 ATCCCTCGCGGACAAAGCT 61.660 57.895 6.13 0.00 46.09 3.74
1657 1719 2.124151 CCCCCATGGAGAAAGCCG 60.124 66.667 15.22 0.00 35.39 5.52
1659 1721 2.124151 CCCATGGAGAAAGCCGGG 60.124 66.667 15.22 0.00 0.00 5.73
1660 1722 2.124151 CCATGGAGAAAGCCGGGG 60.124 66.667 5.56 0.00 0.00 5.73
1662 1811 1.302949 CATGGAGAAAGCCGGGGAA 59.697 57.895 2.18 0.00 0.00 3.97
1664 1813 0.034089 ATGGAGAAAGCCGGGGAAAG 60.034 55.000 2.18 0.00 0.00 2.62
2069 2254 1.376942 CTGGCTTGGTGCTCCTCAG 60.377 63.158 6.34 3.51 42.39 3.35
2111 2314 2.029244 CCATGTACACGTTCGAGCAATC 59.971 50.000 0.00 0.00 0.00 2.67
2280 2719 2.434428 GAGGAGTCACGGTCACTTCTA 58.566 52.381 0.00 0.00 28.94 2.10
2283 2722 2.162008 GGAGTCACGGTCACTTCTACTC 59.838 54.545 0.00 0.00 32.92 2.59
2551 3383 2.758089 GCGCTCAAGACAGCCATGG 61.758 63.158 7.63 7.63 35.84 3.66
2663 3495 3.430929 GCCGTCTTTGTCTACTCCATCAT 60.431 47.826 0.00 0.00 0.00 2.45
2670 3502 4.743057 TGTCTACTCCATCATCAAGGTG 57.257 45.455 0.00 0.00 0.00 4.00
2688 3526 2.666207 GTGGCGTACACCCATGGA 59.334 61.111 15.22 0.00 44.49 3.41
2736 3574 4.498520 ATGTCGGACAGGCTCGCG 62.499 66.667 16.84 0.00 0.00 5.87
2756 3594 0.820226 AAGCTGCTGCGTCTATCTGA 59.180 50.000 1.35 0.00 45.42 3.27
3253 5504 4.978580 GGAGAGTCAATTGTTCAAAGTTGC 59.021 41.667 5.13 0.00 0.00 4.17
3254 5505 4.936891 AGAGTCAATTGTTCAAAGTTGCC 58.063 39.130 5.13 0.00 0.00 4.52
3255 5506 3.705604 AGTCAATTGTTCAAAGTTGCCG 58.294 40.909 5.13 0.00 0.00 5.69
3278 5529 2.125269 GCTTCCCGAGCGGCTAAA 60.125 61.111 0.60 0.00 42.46 1.85
3279 5530 2.174319 GCTTCCCGAGCGGCTAAAG 61.174 63.158 0.60 6.04 42.46 1.85
3280 5531 2.125269 TTCCCGAGCGGCTAAAGC 60.125 61.111 0.60 0.00 41.14 3.51
3281 5532 4.508128 TCCCGAGCGGCTAAAGCG 62.508 66.667 0.60 1.58 43.26 4.68
3342 5614 3.154827 ACCCGAAACAAAGGTGATGAT 57.845 42.857 0.00 0.00 30.97 2.45
3602 5946 0.032678 GCCTCCATCGTCGTCATCAT 59.967 55.000 0.00 0.00 0.00 2.45
3603 5947 1.775869 CCTCCATCGTCGTCATCATG 58.224 55.000 0.00 0.00 0.00 3.07
3604 5948 1.135046 CTCCATCGTCGTCATCATGC 58.865 55.000 0.00 0.00 0.00 4.06
3640 5984 2.066262 ACACCGTGAAGAAGCAATACG 58.934 47.619 5.28 0.00 34.78 3.06
3822 6175 3.832171 GCGCTGCTGTCGTTCGAG 61.832 66.667 0.00 0.00 0.00 4.04
3840 6193 3.766691 GCCGTGCGAGGGAAGGTA 61.767 66.667 0.00 0.00 0.00 3.08
3850 6203 1.487142 GAGGGAAGGTAAAGGAGCTCC 59.513 57.143 26.22 26.22 33.71 4.70
3860 6213 4.767255 GGAGCTCCCGGTGTGCAG 62.767 72.222 23.19 0.00 35.92 4.41
3882 6235 6.037610 GCAGGTACTTTTCTAACATGATGGAG 59.962 42.308 0.00 0.00 34.60 3.86
3921 6274 2.489938 TGGGAGTTAGCAATGGTGAC 57.510 50.000 0.00 0.00 0.00 3.67
3933 6286 2.498807 ATGGTGACGATGATCAGTCG 57.501 50.000 19.36 19.36 44.26 4.18
3976 6329 7.538678 GCGTGTAATCAATTGATTCTTCTTGTT 59.461 33.333 31.70 12.57 43.17 2.83
3977 6330 9.398170 CGTGTAATCAATTGATTCTTCTTGTTT 57.602 29.630 31.70 11.91 43.17 2.83
4079 6432 8.533569 TCATGTTACATCTAATGTAGTCCTGA 57.466 34.615 0.00 4.89 45.58 3.86
4105 6458 6.655078 AATAGACAAACCAAAACAGAGCAT 57.345 33.333 0.00 0.00 0.00 3.79
4109 6462 5.536161 AGACAAACCAAAACAGAGCATGTAT 59.464 36.000 0.00 0.00 43.00 2.29
4111 6464 6.581712 ACAAACCAAAACAGAGCATGTATTT 58.418 32.000 0.00 0.00 43.00 1.40
4113 6466 7.552330 ACAAACCAAAACAGAGCATGTATTTTT 59.448 29.630 0.00 0.00 43.00 1.94
4114 6467 7.481275 AACCAAAACAGAGCATGTATTTTTG 57.519 32.000 0.00 9.22 43.00 2.44
4116 6469 5.106987 CCAAAACAGAGCATGTATTTTTGCC 60.107 40.000 10.13 0.00 43.00 4.52
4119 6472 5.212532 ACAGAGCATGTATTTTTGCCAAA 57.787 34.783 0.00 0.00 41.60 3.28
4120 6473 5.797051 ACAGAGCATGTATTTTTGCCAAAT 58.203 33.333 0.00 0.00 41.60 2.32
4121 6474 5.640357 ACAGAGCATGTATTTTTGCCAAATG 59.360 36.000 0.00 0.00 41.60 2.32
4123 6476 6.369340 CAGAGCATGTATTTTTGCCAAATGAA 59.631 34.615 0.00 0.00 39.72 2.57
4124 6477 6.369615 AGAGCATGTATTTTTGCCAAATGAAC 59.630 34.615 0.00 0.00 39.72 3.18
4153 6506 4.040339 TCACAGGAAACTATGTGCTGAGAA 59.960 41.667 0.00 0.00 45.12 2.87
4154 6507 4.940046 CACAGGAAACTATGTGCTGAGAAT 59.060 41.667 0.00 0.00 40.27 2.40
4155 6508 5.413833 CACAGGAAACTATGTGCTGAGAATT 59.586 40.000 0.00 0.00 40.27 2.17
4156 6509 6.006449 ACAGGAAACTATGTGCTGAGAATTT 58.994 36.000 0.00 0.00 40.21 1.82
4157 6510 6.491403 ACAGGAAACTATGTGCTGAGAATTTT 59.509 34.615 0.00 0.00 40.21 1.82
4159 6512 8.514594 CAGGAAACTATGTGCTGAGAATTTTTA 58.485 33.333 0.00 0.00 40.21 1.52
4160 6513 8.734386 AGGAAACTATGTGCTGAGAATTTTTAG 58.266 33.333 0.00 0.00 40.61 1.85
4161 6514 7.486232 GGAAACTATGTGCTGAGAATTTTTAGC 59.514 37.037 5.86 5.86 36.72 3.09
4162 6515 7.693969 AACTATGTGCTGAGAATTTTTAGCT 57.306 32.000 12.98 0.00 37.10 3.32
4163 6516 7.313951 ACTATGTGCTGAGAATTTTTAGCTC 57.686 36.000 12.98 10.19 37.10 4.09
4164 6517 5.573337 ATGTGCTGAGAATTTTTAGCTCC 57.427 39.130 12.98 5.51 37.10 4.70
4165 6518 4.397420 TGTGCTGAGAATTTTTAGCTCCA 58.603 39.130 12.98 7.63 37.10 3.86
4166 6519 4.216257 TGTGCTGAGAATTTTTAGCTCCAC 59.784 41.667 12.98 4.96 37.10 4.02
4167 6520 4.216257 GTGCTGAGAATTTTTAGCTCCACA 59.784 41.667 12.98 0.00 37.10 4.17
4168 6521 5.012239 TGCTGAGAATTTTTAGCTCCACAT 58.988 37.500 12.98 0.00 37.10 3.21
4169 6522 5.106038 TGCTGAGAATTTTTAGCTCCACATG 60.106 40.000 12.98 0.00 37.10 3.21
4170 6523 5.678107 GCTGAGAATTTTTAGCTCCACATGG 60.678 44.000 5.59 0.00 33.53 3.66
4171 6524 5.569355 TGAGAATTTTTAGCTCCACATGGA 58.431 37.500 0.00 0.00 43.08 3.41
4172 6525 6.009589 TGAGAATTTTTAGCTCCACATGGAA 58.990 36.000 1.50 0.00 44.91 3.53
4173 6526 6.151648 TGAGAATTTTTAGCTCCACATGGAAG 59.848 38.462 1.50 0.00 44.91 3.46
4174 6527 4.725790 ATTTTTAGCTCCACATGGAAGC 57.274 40.909 1.50 7.95 44.91 3.86
4175 6528 3.439857 TTTTAGCTCCACATGGAAGCT 57.560 42.857 21.05 21.05 44.91 3.74
4176 6529 2.698855 TTAGCTCCACATGGAAGCTC 57.301 50.000 20.95 5.11 44.91 4.09
4177 6530 0.461548 TAGCTCCACATGGAAGCTCG 59.538 55.000 20.95 4.46 44.91 5.03
4178 6531 2.467826 GCTCCACATGGAAGCTCGC 61.468 63.158 1.50 0.00 44.91 5.03
4179 6532 1.078918 CTCCACATGGAAGCTCGCA 60.079 57.895 1.50 0.00 44.91 5.10
4180 6533 0.463295 CTCCACATGGAAGCTCGCAT 60.463 55.000 1.50 0.00 44.91 4.73
4181 6534 0.829990 TCCACATGGAAGCTCGCATA 59.170 50.000 0.00 0.00 42.18 3.14
4182 6535 1.202568 TCCACATGGAAGCTCGCATAG 60.203 52.381 0.00 0.00 42.18 2.23
4183 6536 1.224075 CACATGGAAGCTCGCATAGG 58.776 55.000 0.00 0.00 0.00 2.57
4184 6537 0.833287 ACATGGAAGCTCGCATAGGT 59.167 50.000 0.00 0.00 37.60 3.08
4186 6539 2.434336 ACATGGAAGCTCGCATAGGTTA 59.566 45.455 0.00 0.00 45.83 2.85
4187 6540 3.071602 ACATGGAAGCTCGCATAGGTTAT 59.928 43.478 0.00 0.00 45.83 1.89
4258 6611 1.224315 TCCATGCTGGATGAACCCG 59.776 57.895 10.99 0.00 42.67 5.28
4274 6627 0.950836 CCCGATTGAACAACTGCACA 59.049 50.000 0.00 0.00 0.00 4.57
4283 6636 3.181497 TGAACAACTGCACAGCTCTTTTC 60.181 43.478 0.00 0.00 0.00 2.29
4291 6644 0.886490 ACAGCTCTTTTCACCCTGCG 60.886 55.000 0.00 0.00 0.00 5.18
4325 6925 0.548031 TGGAAGGCCATCCATCTCAC 59.452 55.000 25.76 0.00 44.52 3.51
4326 6926 0.842635 GGAAGGCCATCCATCTCACT 59.157 55.000 22.26 0.00 39.42 3.41
4327 6927 2.050144 GGAAGGCCATCCATCTCACTA 58.950 52.381 22.26 0.00 39.42 2.74
4350 6950 9.165035 ACTACTCACTAGTCAGTAGAACAATAC 57.835 37.037 32.95 0.00 43.36 1.89
4358 6958 9.856488 CTAGTCAGTAGAACAATACTTAAGCAA 57.144 33.333 1.29 0.00 33.68 3.91
4376 6976 4.703899 GCAAAAACATGCAGAAGTTCAG 57.296 40.909 5.50 0.00 45.70 3.02
4381 6981 7.623925 GCAAAAACATGCAGAAGTTCAGAAAAA 60.624 33.333 5.50 0.00 45.70 1.94
4385 6985 5.357878 ACATGCAGAAGTTCAGAAAAACTCA 59.642 36.000 5.50 0.00 38.52 3.41
4389 6989 6.092748 GCAGAAGTTCAGAAAAACTCAAACA 58.907 36.000 5.50 0.00 38.52 2.83
4391 6991 7.308435 CAGAAGTTCAGAAAAACTCAAACACT 58.692 34.615 5.50 0.00 38.52 3.55
4392 6992 7.272084 CAGAAGTTCAGAAAAACTCAAACACTG 59.728 37.037 5.50 0.00 38.52 3.66
4403 7003 1.962807 TCAAACACTGGAATGCAAGGG 59.037 47.619 0.00 0.00 0.00 3.95
4407 7007 1.077265 ACTGGAATGCAAGGGGGTG 59.923 57.895 0.00 0.00 0.00 4.61
4416 7016 0.183492 GCAAGGGGGTGATGATGCTA 59.817 55.000 0.00 0.00 0.00 3.49
4421 7021 2.114323 AGGGGGTGATGATGCTAGGATA 59.886 50.000 0.00 0.00 0.00 2.59
4432 7032 8.874156 TGATGATGCTAGGATAGAAGTAATTGT 58.126 33.333 0.00 0.00 42.77 2.71
4446 7046 5.529581 AGTAATTGTCAAACCAAACAGGG 57.470 39.130 0.00 0.00 43.89 4.45
4451 7051 0.758685 TCAAACCAAACAGGGCCCAG 60.759 55.000 27.56 20.62 43.89 4.45
4475 7075 1.380785 TCCCTCCTAATGCGACGGT 60.381 57.895 0.00 0.00 0.00 4.83
4498 7098 3.516615 GCAGTCTGGCAGAACTAACTAG 58.483 50.000 20.62 8.24 0.00 2.57
4499 7099 3.056465 GCAGTCTGGCAGAACTAACTAGT 60.056 47.826 20.62 0.00 38.39 2.57
4500 7100 4.739195 CAGTCTGGCAGAACTAACTAGTC 58.261 47.826 20.62 2.35 34.99 2.59
4501 7101 3.764972 AGTCTGGCAGAACTAACTAGTCC 59.235 47.826 20.62 1.79 34.99 3.85
4502 7102 3.510360 GTCTGGCAGAACTAACTAGTCCA 59.490 47.826 20.62 0.00 34.99 4.02
4503 7103 4.021368 GTCTGGCAGAACTAACTAGTCCAA 60.021 45.833 20.62 0.00 34.99 3.53
4504 7104 4.220821 TCTGGCAGAACTAACTAGTCCAAG 59.779 45.833 16.28 0.00 34.99 3.61
4505 7105 3.901844 TGGCAGAACTAACTAGTCCAAGT 59.098 43.478 0.00 0.00 34.99 3.16
4506 7106 4.246458 GGCAGAACTAACTAGTCCAAGTG 58.754 47.826 0.00 0.00 34.99 3.16
4554 7154 7.789202 ATGCATAACAGGAGATAGATAGTGT 57.211 36.000 0.00 0.00 0.00 3.55
4555 7155 6.986250 TGCATAACAGGAGATAGATAGTGTG 58.014 40.000 0.00 0.00 0.00 3.82
4595 7195 4.458295 CAGCCTGGAGATTATTTATGCCAG 59.542 45.833 0.00 0.00 41.88 4.85
4604 7206 7.360438 GGAGATTATTTATGCCAGATGTTCGAC 60.360 40.741 0.00 0.00 0.00 4.20
4718 7320 6.272698 ACATTTTTAAAGCTGAAAGTTGCG 57.727 33.333 0.00 0.00 35.30 4.85
4724 7326 6.494893 TTAAAGCTGAAAGTTGCGACATAT 57.505 33.333 6.90 0.00 35.30 1.78
4730 7332 5.960105 GCTGAAAGTTGCGACATATTTCTAC 59.040 40.000 6.90 1.62 35.30 2.59
4733 7335 7.463544 TGAAAGTTGCGACATATTTCTACATG 58.536 34.615 6.90 0.00 32.42 3.21
4743 7349 7.598118 CGACATATTTCTACATGAGAATGCTCT 59.402 37.037 1.43 0.00 43.84 4.09
4747 7353 4.933505 TCTACATGAGAATGCTCTCCTG 57.066 45.455 1.43 6.68 46.67 3.86
4758 7364 3.189618 TGCTCTCCTGAATATGCACAG 57.810 47.619 0.00 0.00 0.00 3.66
4773 7400 1.614051 GCACAGGGTGATTGTCCATGA 60.614 52.381 0.00 0.00 38.79 3.07
4833 7462 5.065218 CAGTTGTCAGTGACCCAATATTAGC 59.935 44.000 20.43 1.55 0.00 3.09
4834 7463 4.835284 TGTCAGTGACCCAATATTAGCA 57.165 40.909 20.43 0.00 0.00 3.49
4919 7578 7.041167 TGTCAGACGAATCAACAGAAATTCATT 60.041 33.333 0.00 0.00 32.55 2.57
4930 7589 8.685427 TCAACAGAAATTCATTGACTCTTCAAA 58.315 29.630 8.14 0.00 45.01 2.69
4933 7592 8.302438 ACAGAAATTCATTGACTCTTCAAATCC 58.698 33.333 0.00 0.00 45.01 3.01
4953 7612 7.440523 AATCCATAACTCACAAGTCAAGAAC 57.559 36.000 0.00 0.00 33.48 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 8.655970 ACAGAAAAATAAAGCAAGACACAAAAC 58.344 29.630 0.00 0.00 0.00 2.43
43 44 6.756074 CCAACAGAAAAATAAAGCAAGACACA 59.244 34.615 0.00 0.00 0.00 3.72
44 45 6.292328 GCCAACAGAAAAATAAAGCAAGACAC 60.292 38.462 0.00 0.00 0.00 3.67
45 46 5.752955 GCCAACAGAAAAATAAAGCAAGACA 59.247 36.000 0.00 0.00 0.00 3.41
46 47 5.752955 TGCCAACAGAAAAATAAAGCAAGAC 59.247 36.000 0.00 0.00 0.00 3.01
66 67 9.710900 CTAGAAAACATGTATGTATCTATGCCA 57.289 33.333 15.17 2.74 40.80 4.92
131 132 0.899019 GAGACAGACCCCTTGGAGAC 59.101 60.000 0.00 0.00 34.81 3.36
133 134 0.545309 TGGAGACAGACCCCTTGGAG 60.545 60.000 0.00 0.00 35.01 3.86
134 135 0.104672 TTGGAGACAGACCCCTTGGA 60.105 55.000 0.00 0.00 44.54 3.53
135 136 0.326264 CTTGGAGACAGACCCCTTGG 59.674 60.000 0.00 0.00 44.54 3.61
136 137 0.326264 CCTTGGAGACAGACCCCTTG 59.674 60.000 0.00 0.00 44.54 3.61
137 138 0.842467 CCCTTGGAGACAGACCCCTT 60.842 60.000 0.00 0.00 44.54 3.95
138 139 1.229658 CCCTTGGAGACAGACCCCT 60.230 63.158 0.00 0.00 44.54 4.79
139 140 2.301738 CCCCTTGGAGACAGACCCC 61.302 68.421 0.00 0.00 44.54 4.95
140 141 2.972819 GCCCCTTGGAGACAGACCC 61.973 68.421 0.00 0.00 44.54 4.46
141 142 2.224159 TGCCCCTTGGAGACAGACC 61.224 63.158 0.00 0.00 44.54 3.85
142 143 1.003233 GTGCCCCTTGGAGACAGAC 60.003 63.158 0.00 0.00 44.54 3.51
143 144 0.116342 TAGTGCCCCTTGGAGACAGA 59.884 55.000 0.00 0.00 44.54 3.41
144 145 0.250513 GTAGTGCCCCTTGGAGACAG 59.749 60.000 0.00 0.00 44.54 3.51
145 146 0.472925 TGTAGTGCCCCTTGGAGACA 60.473 55.000 0.00 0.00 39.83 3.41
146 147 0.912486 ATGTAGTGCCCCTTGGAGAC 59.088 55.000 0.00 0.00 0.00 3.36
147 148 0.911769 CATGTAGTGCCCCTTGGAGA 59.088 55.000 0.00 0.00 0.00 3.71
148 149 0.620556 ACATGTAGTGCCCCTTGGAG 59.379 55.000 0.00 0.00 0.00 3.86
149 150 1.959710 TACATGTAGTGCCCCTTGGA 58.040 50.000 0.08 0.00 0.00 3.53
150 151 2.799126 TTACATGTAGTGCCCCTTGG 57.201 50.000 5.56 0.00 0.00 3.61
151 152 4.677779 GCAAATTACATGTAGTGCCCCTTG 60.678 45.833 19.76 13.09 0.00 3.61
152 153 3.447229 GCAAATTACATGTAGTGCCCCTT 59.553 43.478 19.76 2.81 0.00 3.95
237 238 7.178983 ACATCTCATTTCCTTCTTTATGGCAAA 59.821 33.333 0.00 0.00 0.00 3.68
270 271 9.226606 TGTATTAAGGTTGAGACACTTATTTGG 57.773 33.333 0.00 0.00 0.00 3.28
288 304 9.252962 CTACACCCGGTATAAAGTTGTATTAAG 57.747 37.037 0.00 0.00 0.00 1.85
291 307 7.422465 TCTACACCCGGTATAAAGTTGTATT 57.578 36.000 0.00 0.00 0.00 1.89
293 309 6.606796 TCATCTACACCCGGTATAAAGTTGTA 59.393 38.462 0.00 0.00 0.00 2.41
294 310 5.422970 TCATCTACACCCGGTATAAAGTTGT 59.577 40.000 0.00 0.00 0.00 3.32
295 311 5.909477 TCATCTACACCCGGTATAAAGTTG 58.091 41.667 0.00 0.00 0.00 3.16
296 312 6.742559 ATCATCTACACCCGGTATAAAGTT 57.257 37.500 0.00 0.00 0.00 2.66
298 314 6.812160 GCTAATCATCTACACCCGGTATAAAG 59.188 42.308 0.00 0.00 0.00 1.85
299 315 6.495872 AGCTAATCATCTACACCCGGTATAAA 59.504 38.462 0.00 0.00 0.00 1.40
316 332 2.804986 TGGCATGGACAAGCTAATCA 57.195 45.000 0.00 0.00 0.00 2.57
360 376 9.656040 ACATCATTGCATTGTAACATTTGTAAT 57.344 25.926 8.36 0.00 0.00 1.89
367 383 6.689554 TCAACACATCATTGCATTGTAACAT 58.310 32.000 8.36 0.00 0.00 2.71
368 384 6.081872 TCAACACATCATTGCATTGTAACA 57.918 33.333 8.36 0.00 0.00 2.41
377 393 8.114905 CGATCATCTATATCAACACATCATTGC 58.885 37.037 0.00 0.00 0.00 3.56
436 452 6.291377 TGCACATAGAAGATTGGGAGATAAC 58.709 40.000 0.00 0.00 0.00 1.89
453 469 7.144722 AGAAGATCGAAACAAAATGCACATA 57.855 32.000 0.00 0.00 0.00 2.29
469 485 3.827625 ACAGAAGTCGTGAAGAAGATCG 58.172 45.455 0.00 0.00 0.00 3.69
476 492 3.444034 TCCATAGGACAGAAGTCGTGAAG 59.556 47.826 0.00 0.00 45.92 3.02
481 497 3.126831 GCAATCCATAGGACAGAAGTCG 58.873 50.000 0.00 0.00 45.92 4.18
489 505 2.408050 CACTAGCGCAATCCATAGGAC 58.592 52.381 11.47 0.00 32.98 3.85
504 520 5.163814 GGCAAAGTATTCTTCAGTGCACTAG 60.164 44.000 21.20 14.85 36.94 2.57
584 613 1.071385 AGAGTGCAAGGACAACAGAGG 59.929 52.381 0.00 0.00 0.00 3.69
589 618 1.000163 TCTCGAGAGTGCAAGGACAAC 60.000 52.381 12.08 0.00 0.00 3.32
592 621 1.470632 CCATCTCGAGAGTGCAAGGAC 60.471 57.143 21.52 0.00 0.00 3.85
854 883 2.423803 CCATCCCCATTGATGCTCAGAA 60.424 50.000 0.00 0.00 40.66 3.02
873 910 0.832135 ACGCTTCCTTCAGTCCTCCA 60.832 55.000 0.00 0.00 0.00 3.86
875 912 0.892063 AGACGCTTCCTTCAGTCCTC 59.108 55.000 0.00 0.00 34.41 3.71
879 916 1.373497 CGCAGACGCTTCCTTCAGT 60.373 57.895 0.00 0.00 35.30 3.41
880 917 1.373497 ACGCAGACGCTTCCTTCAG 60.373 57.895 0.00 0.00 45.53 3.02
881 918 1.664649 CACGCAGACGCTTCCTTCA 60.665 57.895 0.00 0.00 45.53 3.02
882 919 3.016474 GCACGCAGACGCTTCCTTC 62.016 63.158 0.00 0.00 45.53 3.46
886 923 2.607892 AAAGGCACGCAGACGCTTC 61.608 57.895 0.00 0.00 45.53 3.86
891 928 1.089920 ATCATCAAAGGCACGCAGAC 58.910 50.000 0.00 0.00 0.00 3.51
894 931 0.810648 GGAATCATCAAAGGCACGCA 59.189 50.000 0.00 0.00 0.00 5.24
978 1025 8.713737 ACATACAGTGATATTATATGCTGCTG 57.286 34.615 0.00 10.97 0.00 4.41
1008 1055 4.807039 ATCGGCGCGGTGTGGTAC 62.807 66.667 15.06 0.00 0.00 3.34
1039 1086 4.446413 CTTTCCGGCCGGCGTAGT 62.446 66.667 39.89 0.00 34.68 2.73
1069 1116 0.671781 TCCTCTTTCTGCTGCTTCGC 60.672 55.000 0.00 0.00 0.00 4.70
1072 1119 1.063183 AGGTCCTCTTTCTGCTGCTT 58.937 50.000 0.00 0.00 0.00 3.91
1092 1139 0.108585 GCCACTTCCACAGGAACTCA 59.891 55.000 0.00 0.00 36.71 3.41
1272 1334 2.735762 GCAGTAGAAGAAGGCGGTGTAG 60.736 54.545 0.00 0.00 0.00 2.74
1559 1621 4.735132 CCCGAGCTTTGTCCGCGA 62.735 66.667 8.23 0.00 0.00 5.87
1590 1652 4.731853 TCCGAGGGGGATGTGGCA 62.732 66.667 0.00 0.00 40.94 4.92
1631 1693 4.900704 CCATGGGGGATGTGGCGG 62.901 72.222 2.85 0.00 40.01 6.13
1639 1701 2.679342 CGGCTTTCTCCATGGGGGA 61.679 63.158 12.98 0.00 45.89 4.81
1640 1702 2.124151 CGGCTTTCTCCATGGGGG 60.124 66.667 12.98 5.50 38.37 5.40
1641 1703 2.124151 CCGGCTTTCTCCATGGGG 60.124 66.667 13.02 9.18 0.00 4.96
1642 1704 2.124151 CCCGGCTTTCTCCATGGG 60.124 66.667 13.02 2.57 0.00 4.00
1643 1705 2.124151 CCCCGGCTTTCTCCATGG 60.124 66.667 4.97 4.97 0.00 3.66
1645 1707 0.034089 CTTTCCCCGGCTTTCTCCAT 60.034 55.000 0.00 0.00 0.00 3.41
2069 2254 0.097674 CTTCGCCTGTAGCACAATGC 59.902 55.000 0.00 0.00 45.46 3.56
2156 2359 0.242825 CGTGTCCGGCTCTTGTTCTA 59.757 55.000 0.00 0.00 0.00 2.10
2280 2719 4.990910 AGGGTGGCCAGCAGGAGT 62.991 66.667 34.28 11.75 36.89 3.85
2367 2806 1.302832 GATGTGATCCGGATGCCCC 60.303 63.158 24.82 7.91 0.00 5.80
2551 3383 2.429610 TGAGGCCGAATAGGTTCAGTAC 59.570 50.000 0.00 0.00 43.70 2.73
2663 3495 1.070105 GTGTACGCCACCACCTTGA 59.930 57.895 0.00 0.00 38.18 3.02
2699 3537 1.524621 CGGTGCATCCACTCCATCC 60.525 63.158 0.00 0.00 41.75 3.51
2736 3574 1.202348 TCAGATAGACGCAGCAGCTTC 60.202 52.381 0.00 0.00 39.16 3.86
2737 3575 0.820226 TCAGATAGACGCAGCAGCTT 59.180 50.000 0.00 0.00 39.10 3.74
2751 3589 4.096003 CCGGGTTGGCCGTCAGAT 62.096 66.667 0.00 0.00 34.97 2.90
3275 5526 0.952010 GGGCTCGAACAACCGCTTTA 60.952 55.000 0.00 0.00 0.00 1.85
3276 5527 2.258726 GGGCTCGAACAACCGCTTT 61.259 57.895 0.00 0.00 0.00 3.51
3277 5528 2.668550 GGGCTCGAACAACCGCTT 60.669 61.111 0.00 0.00 0.00 4.68
3278 5529 4.699522 GGGGCTCGAACAACCGCT 62.700 66.667 0.00 0.00 33.83 5.52
3279 5530 3.305177 TAGGGGCTCGAACAACCGC 62.305 63.158 0.00 0.00 36.70 5.68
3280 5531 1.153628 CTAGGGGCTCGAACAACCG 60.154 63.158 0.00 0.00 0.00 4.44
3281 5532 1.221021 CCTAGGGGCTCGAACAACC 59.779 63.158 0.00 0.00 0.00 3.77
3282 5533 0.831307 ATCCTAGGGGCTCGAACAAC 59.169 55.000 9.46 0.00 0.00 3.32
3323 5595 3.081061 TCATCATCACCTTTGTTTCGGG 58.919 45.455 0.00 0.00 0.00 5.14
3342 5614 1.847975 GCGTTTCGCGTACTGTTCA 59.152 52.632 5.77 0.00 44.55 3.18
3435 5758 2.726274 GTATCGTCGTCGCCCCAT 59.274 61.111 0.00 0.00 36.96 4.00
3478 5801 4.064768 TGGGCTTGCTGATGGGGG 62.065 66.667 0.00 0.00 0.00 5.40
3640 5984 3.491652 GGCGCTCTTCTTCACGGC 61.492 66.667 7.64 0.00 43.82 5.68
3804 6157 4.639171 TCGAACGACAGCAGCGCA 62.639 61.111 11.47 0.00 0.00 6.09
3840 6193 2.750350 CACACCGGGAGCTCCTTT 59.250 61.111 31.36 13.65 35.95 3.11
3850 6203 0.872388 GAAAAGTACCTGCACACCGG 59.128 55.000 0.00 0.00 0.00 5.28
3860 6213 8.451748 GTTTCTCCATCATGTTAGAAAAGTACC 58.548 37.037 11.95 0.34 39.08 3.34
3882 6235 2.265904 GGGCTTCCACACCCGTTTC 61.266 63.158 0.00 0.00 36.07 2.78
3921 6274 3.032609 GCGGCCGACTGATCATCG 61.033 66.667 33.48 16.02 39.33 3.84
4079 6432 8.177119 TGCTCTGTTTTGGTTTGTCTATTTAT 57.823 30.769 0.00 0.00 0.00 1.40
4105 6458 9.255304 GAAACTAGTTCATTTGGCAAAAATACA 57.745 29.630 17.70 0.00 36.15 2.29
4134 6487 7.530426 AAAAATTCTCAGCACATAGTTTCCT 57.470 32.000 0.00 0.00 0.00 3.36
4141 6494 6.094048 GTGGAGCTAAAAATTCTCAGCACATA 59.906 38.462 7.59 0.00 36.47 2.29
4144 6497 4.216257 TGTGGAGCTAAAAATTCTCAGCAC 59.784 41.667 7.59 0.00 36.47 4.40
4153 6506 4.347607 AGCTTCCATGTGGAGCTAAAAAT 58.652 39.130 18.25 1.69 46.36 1.82
4154 6507 3.758554 GAGCTTCCATGTGGAGCTAAAAA 59.241 43.478 19.15 0.00 46.36 1.94
4155 6508 3.347216 GAGCTTCCATGTGGAGCTAAAA 58.653 45.455 19.15 0.00 46.36 1.52
4156 6509 2.677902 CGAGCTTCCATGTGGAGCTAAA 60.678 50.000 19.15 0.00 46.36 1.85
4157 6510 1.134699 CGAGCTTCCATGTGGAGCTAA 60.135 52.381 19.15 0.00 46.36 3.09
4159 6512 1.220206 CGAGCTTCCATGTGGAGCT 59.780 57.895 19.18 19.18 46.36 4.09
4160 6513 2.467826 GCGAGCTTCCATGTGGAGC 61.468 63.158 12.59 12.59 46.36 4.70
4161 6514 0.463295 ATGCGAGCTTCCATGTGGAG 60.463 55.000 1.49 0.00 46.36 3.86
4162 6515 0.829990 TATGCGAGCTTCCATGTGGA 59.170 50.000 9.54 0.00 43.73 4.02
4163 6516 1.224075 CTATGCGAGCTTCCATGTGG 58.776 55.000 9.54 0.00 0.00 4.17
4164 6517 1.224075 CCTATGCGAGCTTCCATGTG 58.776 55.000 9.54 3.95 0.00 3.21
4165 6518 0.833287 ACCTATGCGAGCTTCCATGT 59.167 50.000 9.54 0.00 0.00 3.21
4166 6519 1.959042 AACCTATGCGAGCTTCCATG 58.041 50.000 9.54 0.00 0.00 3.66
4167 6520 3.324846 TCATAACCTATGCGAGCTTCCAT 59.675 43.478 5.53 5.53 36.14 3.41
4168 6521 2.698274 TCATAACCTATGCGAGCTTCCA 59.302 45.455 0.00 0.00 36.14 3.53
4169 6522 3.386768 TCATAACCTATGCGAGCTTCC 57.613 47.619 0.00 0.00 36.14 3.46
4170 6523 6.333416 TCATATCATAACCTATGCGAGCTTC 58.667 40.000 0.00 0.00 36.14 3.86
4171 6524 6.286240 TCATATCATAACCTATGCGAGCTT 57.714 37.500 0.00 0.00 36.14 3.74
4172 6525 5.921962 TCATATCATAACCTATGCGAGCT 57.078 39.130 0.00 0.00 36.14 4.09
4173 6526 6.758416 TCATTCATATCATAACCTATGCGAGC 59.242 38.462 0.00 0.00 36.14 5.03
4174 6527 8.707938 TTCATTCATATCATAACCTATGCGAG 57.292 34.615 0.00 0.00 36.14 5.03
4175 6528 9.671279 ATTTCATTCATATCATAACCTATGCGA 57.329 29.630 0.00 0.00 36.14 5.10
4181 6534 9.797642 TGTGCTATTTCATTCATATCATAACCT 57.202 29.630 0.00 0.00 0.00 3.50
4187 6540 9.440773 GTATCCTGTGCTATTTCATTCATATCA 57.559 33.333 0.00 0.00 0.00 2.15
4246 6599 2.710377 TGTTCAATCGGGTTCATCCAG 58.290 47.619 0.00 0.00 38.11 3.86
4258 6611 2.551459 AGAGCTGTGCAGTTGTTCAATC 59.449 45.455 0.00 0.00 0.00 2.67
4274 6627 4.386413 CGCAGGGTGAAAAGAGCT 57.614 55.556 0.00 0.00 0.00 4.09
4307 6660 0.842635 AGTGAGATGGATGGCCTTCC 59.157 55.000 27.15 27.15 38.73 3.46
4325 6925 9.386010 AGTATTGTTCTACTGACTAGTGAGTAG 57.614 37.037 32.09 32.09 44.99 2.57
4326 6926 9.736414 AAGTATTGTTCTACTGACTAGTGAGTA 57.264 33.333 19.35 19.35 37.78 2.59
4327 6927 8.638629 AAGTATTGTTCTACTGACTAGTGAGT 57.361 34.615 19.17 19.17 37.78 3.41
4350 6950 6.476380 TGAACTTCTGCATGTTTTTGCTTAAG 59.524 34.615 0.00 0.00 43.18 1.85
4355 6955 4.362279 TCTGAACTTCTGCATGTTTTTGC 58.638 39.130 0.00 0.00 43.07 3.68
4358 6958 7.099120 AGTTTTTCTGAACTTCTGCATGTTTT 58.901 30.769 0.00 0.00 36.49 2.43
4368 6968 6.528072 CCAGTGTTTGAGTTTTTCTGAACTTC 59.472 38.462 0.00 0.00 39.84 3.01
4374 6974 5.232838 GCATTCCAGTGTTTGAGTTTTTCTG 59.767 40.000 0.00 0.00 0.00 3.02
4376 6976 5.108517 TGCATTCCAGTGTTTGAGTTTTTC 58.891 37.500 0.00 0.00 0.00 2.29
4381 6981 2.624838 CCTTGCATTCCAGTGTTTGAGT 59.375 45.455 0.00 0.00 0.00 3.41
4385 6985 1.341080 CCCCTTGCATTCCAGTGTTT 58.659 50.000 0.00 0.00 0.00 2.83
4389 6989 1.077265 CACCCCCTTGCATTCCAGT 59.923 57.895 0.00 0.00 0.00 4.00
4391 6991 0.324552 CATCACCCCCTTGCATTCCA 60.325 55.000 0.00 0.00 0.00 3.53
4392 6992 0.033208 TCATCACCCCCTTGCATTCC 60.033 55.000 0.00 0.00 0.00 3.01
4403 7003 4.530161 ACTTCTATCCTAGCATCATCACCC 59.470 45.833 0.00 0.00 0.00 4.61
4407 7007 9.364989 GACAATTACTTCTATCCTAGCATCATC 57.635 37.037 0.00 0.00 0.00 2.92
4416 7016 8.793592 GTTTGGTTTGACAATTACTTCTATCCT 58.206 33.333 0.00 0.00 0.00 3.24
4421 7021 6.183360 CCCTGTTTGGTTTGACAATTACTTCT 60.183 38.462 0.00 0.00 0.00 2.85
4432 7032 0.758685 CTGGGCCCTGTTTGGTTTGA 60.759 55.000 25.70 0.00 0.00 2.69
4446 7046 2.400467 TAGGAGGGAGATTACTGGGC 57.600 55.000 0.00 0.00 0.00 5.36
4451 7051 3.612004 CGTCGCATTAGGAGGGAGATTAC 60.612 52.174 0.00 0.00 0.00 1.89
4475 7075 1.055849 TTAGTTCTGCCAGACTGCCA 58.944 50.000 0.00 0.00 0.00 4.92
4498 7098 5.643379 TTCATATTTCTTGCCACTTGGAC 57.357 39.130 0.00 0.00 37.39 4.02
4499 7099 4.158394 GCTTCATATTTCTTGCCACTTGGA 59.842 41.667 0.00 0.00 37.39 3.53
4500 7100 4.082081 TGCTTCATATTTCTTGCCACTTGG 60.082 41.667 0.00 0.00 38.53 3.61
4501 7101 4.860907 GTGCTTCATATTTCTTGCCACTTG 59.139 41.667 0.00 0.00 0.00 3.16
4502 7102 4.768968 AGTGCTTCATATTTCTTGCCACTT 59.231 37.500 0.00 0.00 0.00 3.16
4503 7103 4.338879 AGTGCTTCATATTTCTTGCCACT 58.661 39.130 0.00 0.00 0.00 4.00
4504 7104 4.708726 AGTGCTTCATATTTCTTGCCAC 57.291 40.909 0.00 0.00 0.00 5.01
4505 7105 8.518430 TTATTAGTGCTTCATATTTCTTGCCA 57.482 30.769 0.00 0.00 0.00 4.92
4506 7106 9.403110 CATTATTAGTGCTTCATATTTCTTGCC 57.597 33.333 0.00 0.00 0.00 4.52
4553 7153 1.772063 GCGTGTGTGAAGGGTGACAC 61.772 60.000 0.00 0.00 42.40 3.67
4554 7154 1.522806 GCGTGTGTGAAGGGTGACA 60.523 57.895 0.00 0.00 0.00 3.58
4555 7155 1.498865 CTGCGTGTGTGAAGGGTGAC 61.499 60.000 0.00 0.00 0.00 3.67
4595 7195 2.618053 AGAAATGTCGGGTCGAACATC 58.382 47.619 1.31 0.00 37.72 3.06
4604 7206 5.009210 TCCACAAAACTAAAGAAATGTCGGG 59.991 40.000 0.00 0.00 0.00 5.14
4669 7271 7.924358 AACATACTCATATAGGTGGGTGTTA 57.076 36.000 8.79 0.00 34.02 2.41
4702 7304 6.494893 AATATGTCGCAACTTTCAGCTTTA 57.505 33.333 0.00 0.00 0.00 1.85
4705 7307 4.697352 AGAAATATGTCGCAACTTTCAGCT 59.303 37.500 14.01 0.00 0.00 4.24
4710 7312 7.549134 TCTCATGTAGAAATATGTCGCAACTTT 59.451 33.333 0.00 0.00 0.00 2.66
4747 7353 3.316308 GGACAATCACCCTGTGCATATTC 59.684 47.826 0.00 0.00 35.41 1.75
4793 7420 9.772973 ACTGACAACTGTTACTGACATTAAATA 57.227 29.630 0.00 0.00 37.69 1.40
4810 7437 5.186198 GCTAATATTGGGTCACTGACAACT 58.814 41.667 11.34 0.00 33.68 3.16
4919 7578 6.768483 TGTGAGTTATGGATTTGAAGAGTCA 58.232 36.000 0.00 0.00 0.00 3.41
4930 7589 5.940470 GGTTCTTGACTTGTGAGTTATGGAT 59.060 40.000 0.00 0.00 35.88 3.41
4933 7592 5.527214 TGTGGTTCTTGACTTGTGAGTTATG 59.473 40.000 0.00 0.00 35.88 1.90
4937 7596 3.627395 TGTGGTTCTTGACTTGTGAGT 57.373 42.857 0.00 0.00 39.32 3.41


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

AutoCloner maintained by Alex Coulton.