Multiple sequence alignment - TraesCS2D01G398700

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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 TraesCS2D01G398700 chr2D 100.000 5742 0 0 1 5742 511915295 511921036 0.000000e+00 10604.0
1 TraesCS2D01G398700 chr2D 84.404 327 49 2 3493 3818 431928504 431928829 2.580000e-83 320.0
2 TraesCS2D01G398700 chr2D 95.122 41 2 0 694 734 553897259 553897219 1.340000e-06 65.8
3 TraesCS2D01G398700 chr2D 97.297 37 1 0 694 730 326212680 326212644 4.800000e-06 63.9
4 TraesCS2D01G398700 chr2D 92.500 40 3 0 694 733 255682502 255682463 2.230000e-04 58.4
5 TraesCS2D01G398700 chr2A 92.322 3295 147 41 1 3238 655029362 655032607 0.000000e+00 4586.0
6 TraesCS2D01G398700 chr2A 93.818 1100 40 13 4481 5564 655032883 655033970 0.000000e+00 1629.0
7 TraesCS2D01G398700 chr2A 92.262 168 10 3 3317 3481 218122415 218122248 9.620000e-58 235.0
8 TraesCS2D01G398700 chr2A 87.940 199 18 2 4284 4476 655032613 655032811 4.480000e-56 230.0
9 TraesCS2D01G398700 chr2A 81.513 119 19 2 4172 4287 57141817 57141935 1.700000e-15 95.3
10 TraesCS2D01G398700 chr2B 92.836 1661 89 15 3519 5156 601177844 601179497 0.000000e+00 2381.0
11 TraesCS2D01G398700 chr2B 94.098 1169 52 6 2081 3241 601176229 601177388 0.000000e+00 1760.0
12 TraesCS2D01G398700 chr2B 94.166 977 33 11 739 1706 601175224 601176185 0.000000e+00 1467.0
13 TraesCS2D01G398700 chr2B 92.414 290 17 5 3235 3520 601177451 601177739 5.360000e-110 409.0
14 TraesCS2D01G398700 chr2B 78.698 169 30 6 5570 5736 698971526 698971362 2.190000e-19 108.0
15 TraesCS2D01G398700 chr2B 95.082 61 3 0 1728 1788 601176175 601176235 4.740000e-16 97.1
16 TraesCS2D01G398700 chr2B 85.714 84 9 2 4204 4284 68825163 68825080 1.030000e-12 86.1
17 TraesCS2D01G398700 chr2B 97.297 37 1 0 694 730 58979343 58979307 4.800000e-06 63.9
18 TraesCS2D01G398700 chr2B 97.297 37 1 0 694 730 280475873 280475909 4.800000e-06 63.9
19 TraesCS2D01G398700 chr7A 86.310 336 46 0 3485 3820 201534740 201535075 3.270000e-97 366.0
20 TraesCS2D01G398700 chr7A 85.806 310 43 1 3511 3820 124366839 124367147 1.540000e-85 327.0
21 TraesCS2D01G398700 chr7A 92.814 167 9 3 3317 3480 115736425 115736259 7.440000e-59 239.0
22 TraesCS2D01G398700 chr4A 86.984 315 40 1 3504 3817 685343431 685343745 2.550000e-93 353.0
23 TraesCS2D01G398700 chr4A 96.970 33 1 0 698 730 149042799 149042767 8.040000e-04 56.5
24 TraesCS2D01G398700 chr4D 89.455 275 28 1 3487 3760 352290370 352290096 4.260000e-91 346.0
25 TraesCS2D01G398700 chr3B 88.014 292 31 4 3483 3772 492571762 492572051 5.510000e-90 342.0
26 TraesCS2D01G398700 chr7B 85.670 321 46 0 3496 3816 337574720 337575040 7.130000e-89 339.0
27 TraesCS2D01G398700 chr7B 97.297 37 1 0 694 730 500726001 500726037 4.800000e-06 63.9
28 TraesCS2D01G398700 chr7B 97.297 37 1 0 694 730 594954654 594954690 4.800000e-06 63.9
29 TraesCS2D01G398700 chr4B 86.349 315 38 2 3504 3818 605519776 605520085 7.130000e-89 339.0
30 TraesCS2D01G398700 chr4B 97.297 37 1 0 694 730 54741054 54741090 4.800000e-06 63.9
31 TraesCS2D01G398700 chr6A 92.169 166 11 2 3317 3480 85268227 85268062 3.460000e-57 233.0
32 TraesCS2D01G398700 chr6A 86.528 193 25 1 4553 4744 473743313 473743121 1.620000e-50 211.0
33 TraesCS2D01G398700 chr6A 86.932 176 21 2 2829 3003 473744906 473744732 4.540000e-46 196.0
34 TraesCS2D01G398700 chr6A 81.250 112 17 2 4171 4278 501798136 501798247 2.850000e-13 87.9
35 TraesCS2D01G398700 chr6A 100.000 30 0 0 5687 5716 422269203 422269232 8.040000e-04 56.5
36 TraesCS2D01G398700 chr7D 91.667 168 11 2 3317 3481 194481929 194482096 4.480000e-56 230.0
37 TraesCS2D01G398700 chr7D 82.022 178 27 5 5565 5740 178011352 178011178 4.640000e-31 147.0
38 TraesCS2D01G398700 chr5B 90.395 177 12 5 3317 3490 275235285 275235459 1.610000e-55 228.0
39 TraesCS2D01G398700 chr5B 76.596 141 29 4 5567 5706 458896410 458896547 2.220000e-09 75.0
40 TraesCS2D01G398700 chr5B 97.143 35 1 0 696 730 596081672 596081706 6.210000e-05 60.2
41 TraesCS2D01G398700 chr5B 97.143 35 1 0 696 730 596670798 596670764 6.210000e-05 60.2
42 TraesCS2D01G398700 chr3D 91.124 169 12 3 3317 3483 92209323 92209490 5.790000e-55 226.0
43 TraesCS2D01G398700 chr3A 87.940 199 13 9 3317 3510 593351776 593351584 2.080000e-54 224.0
44 TraesCS2D01G398700 chr3A 87.374 198 18 5 3300 3491 581251498 581251694 2.690000e-53 220.0
45 TraesCS2D01G398700 chr6D 88.068 176 19 2 2829 3003 334344627 334344453 2.100000e-49 207.0
46 TraesCS2D01G398700 chr6D 84.974 193 28 1 4553 4744 334342988 334342796 1.630000e-45 195.0
47 TraesCS2D01G398700 chr6B 86.010 193 26 1 4553 4744 485873584 485873776 7.540000e-49 206.0
48 TraesCS2D01G398700 chr6B 87.500 176 18 3 2829 3002 485871978 485872151 3.510000e-47 200.0
49 TraesCS2D01G398700 chr6B 84.762 105 13 3 4173 4274 651392998 651393102 1.020000e-17 102.0
50 TraesCS2D01G398700 chr1A 82.857 140 21 3 5567 5705 37613655 37613792 7.810000e-24 122.0
51 TraesCS2D01G398700 chr1A 88.235 51 6 0 5689 5739 66331221 66331171 1.730000e-05 62.1
52 TraesCS2D01G398700 chr1A 100.000 28 0 0 703 730 60352529 60352502 1.000000e-02 52.8
53 TraesCS2D01G398700 chr5D 84.553 123 14 4 4166 4284 119662619 119662740 3.640000e-22 117.0
54 TraesCS2D01G398700 chr5D 83.721 86 11 3 4204 4286 409290434 409290349 1.720000e-10 78.7
55 TraesCS2D01G398700 chr5D 97.297 37 1 0 694 730 543767847 543767883 4.800000e-06 63.9
56 TraesCS2D01G398700 chrUn 81.513 119 16 6 4172 4286 30134380 30134264 6.130000e-15 93.5
57 TraesCS2D01G398700 chr5A 85.057 87 8 5 4204 4286 702685159 702685074 3.690000e-12 84.2
58 TraesCS2D01G398700 chr5A 97.297 37 1 0 694 730 360086301 360086337 4.800000e-06 63.9
59 TraesCS2D01G398700 chr1D 97.500 40 1 0 694 733 230670288 230670327 1.030000e-07 69.4
60 TraesCS2D01G398700 chr1D 78.723 94 18 2 5583 5676 459047724 459047633 1.730000e-05 62.1
61 TraesCS2D01G398700 chr1B 100.000 32 0 0 703 734 642494852 642494883 6.210000e-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 TraesCS2D01G398700 chr2D 511915295 511921036 5741 False 10604.000000 10604 100.0000 1 5742 1 chr2D.!!$F2 5741
1 TraesCS2D01G398700 chr2A 655029362 655033970 4608 False 2148.333333 4586 91.3600 1 5564 3 chr2A.!!$F2 5563
2 TraesCS2D01G398700 chr2B 601175224 601179497 4273 False 1222.820000 2381 93.7192 739 5156 5 chr2B.!!$F2 4417
3 TraesCS2D01G398700 chr6A 473743121 473744906 1785 True 203.500000 211 86.7300 2829 4744 2 chr6A.!!$R2 1915
4 TraesCS2D01G398700 chr6D 334342796 334344627 1831 True 201.000000 207 86.5210 2829 4744 2 chr6D.!!$R1 1915
5 TraesCS2D01G398700 chr6B 485871978 485873776 1798 False 203.000000 206 86.7550 2829 4744 2 chr6B.!!$F2 1915

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
44 45 0.317160 CACTAGCTGGAACGACCACA 59.683 55.000 3.17 0.0 44.64 4.17 F
345 346 1.003718 GCCACCTCCACGCTAAAGT 60.004 57.895 0.00 0.0 0.00 2.66 F
1908 1956 0.250295 CGGTGAAGCAAGGAAGGTGA 60.250 55.000 0.00 0.0 0.00 4.02 F
3819 5177 0.035725 TCATGCTCTGGCTCAACAGG 60.036 55.000 0.00 0.0 38.98 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1879 1910 0.250252 TGCTTCACCGCTGAACATCA 60.250 50.0 0.0 0.0 32.68 3.07 R
2308 2363 0.038892 AGATGCTTTGCCAAACTGCG 60.039 50.0 0.0 0.0 0.00 5.18 R
3862 5227 0.248336 CAACGCCACGTCTATCGCTA 60.248 55.0 0.0 0.0 39.99 4.26 R
5582 7048 0.102120 GGCTCAGTCTCTCGATGGTG 59.898 60.0 0.0 0.0 0.00 4.17 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
44 45 0.317160 CACTAGCTGGAACGACCACA 59.683 55.000 3.17 0.00 44.64 4.17
64 65 2.004120 TCACACCACCACCACCCTT 61.004 57.895 0.00 0.00 0.00 3.95
67 68 1.528309 CACCACCACCACCCTTGTC 60.528 63.158 0.00 0.00 0.00 3.18
90 91 3.771160 GAGACCCGCACGACCCAT 61.771 66.667 0.00 0.00 0.00 4.00
97 98 1.441729 CGCACGACCCATATCTGGT 59.558 57.895 0.00 0.00 41.37 4.00
105 106 1.128200 CCCATATCTGGTCACCCGAA 58.872 55.000 0.00 0.00 41.37 4.30
156 157 3.719121 CCACCTGGTGAGAGGGAG 58.281 66.667 27.94 5.51 37.45 4.30
161 162 2.680352 TGGTGAGAGGGAGGCGAC 60.680 66.667 0.00 0.00 0.00 5.19
163 164 4.500116 GTGAGAGGGAGGCGACGC 62.500 72.222 12.43 12.43 0.00 5.19
167 168 4.430765 GAGGGAGGCGACGCGAAA 62.431 66.667 15.93 0.00 0.00 3.46
168 169 4.436998 AGGGAGGCGACGCGAAAG 62.437 66.667 15.93 4.23 0.00 2.62
190 191 3.777925 CGGAAAGTGTCGCGCCTG 61.778 66.667 0.00 0.00 0.00 4.85
219 220 1.797713 CGTCGGCAAAGAATCGAGCTA 60.798 52.381 0.00 0.00 33.41 3.32
234 235 3.144285 CTACCACCCCACACGTGT 58.856 61.111 17.22 17.22 0.00 4.49
273 274 2.438434 CCATCGCCACCCAACCTC 60.438 66.667 0.00 0.00 0.00 3.85
345 346 1.003718 GCCACCTCCACGCTAAAGT 60.004 57.895 0.00 0.00 0.00 2.66
388 392 1.827969 CTCCGAGTTTCCAGATCCAGT 59.172 52.381 0.00 0.00 0.00 4.00
409 413 2.280552 AACGCGTTGCCCTCCTCTA 61.281 57.895 26.00 0.00 0.00 2.43
414 418 1.142097 GTTGCCCTCCTCTAGCGAC 59.858 63.158 0.00 0.00 33.98 5.19
431 435 1.480205 GACGAAACGAACACGAGGAA 58.520 50.000 0.00 0.00 0.00 3.36
567 571 4.851179 GGATTCCGGCGTGTCCCC 62.851 72.222 6.01 0.00 0.00 4.81
569 573 3.400599 GATTCCGGCGTGTCCCCAT 62.401 63.158 6.01 0.00 0.00 4.00
642 646 9.144298 TGTGTACTCCCTCTATAAAGAAATAGG 57.856 37.037 0.00 0.00 31.50 2.57
645 649 9.377238 GTACTCCCTCTATAAAGAAATAGGGAA 57.623 37.037 9.11 0.00 40.32 3.97
646 650 8.871570 ACTCCCTCTATAAAGAAATAGGGAAA 57.128 34.615 9.11 0.00 40.32 3.13
660 664 8.298140 AGAAATAGGGAAATAACGATCTCTACG 58.702 37.037 0.00 0.00 31.69 3.51
672 676 9.991388 ATAACGATCTCTACGCTCTTATATTTC 57.009 33.333 0.00 0.00 0.00 2.17
725 729 4.214332 GCTCTTATATTTCTTTGCGGAGGG 59.786 45.833 0.00 0.00 0.00 4.30
875 892 2.124320 AACCCGCATTCCCCATCG 60.124 61.111 0.00 0.00 0.00 3.84
881 898 1.502231 CGCATTCCCCATCGTAGAAG 58.498 55.000 0.00 0.00 43.58 2.85
1097 1118 3.188786 GCAGCGTAGAGGCAACGG 61.189 66.667 8.71 0.00 46.39 4.44
1555 1576 3.877508 CGTCAGGTAATTGGAGGGATTTC 59.122 47.826 0.00 0.00 0.00 2.17
1560 1581 5.016831 AGGTAATTGGAGGGATTTCACAAC 58.983 41.667 0.00 0.00 0.00 3.32
1564 1585 3.350219 TGGAGGGATTTCACAACTAGC 57.650 47.619 0.00 0.00 0.00 3.42
1675 1704 8.842358 TCCTAATTGATTTTTCGTCAAGTAGT 57.158 30.769 16.91 0.00 45.54 2.73
1678 1707 5.934935 TTGATTTTTCGTCAAGTAGTCCC 57.065 39.130 0.00 0.00 32.23 4.46
1708 1737 7.539712 ACGGTAGTGATAACTTTGATTGATG 57.460 36.000 0.00 0.00 0.00 3.07
1823 1854 5.853572 ATACAGTTCTCTACCCCCAAAAA 57.146 39.130 0.00 0.00 0.00 1.94
1828 1859 7.935405 ACAGTTCTCTACCCCCAAAAATTATA 58.065 34.615 0.00 0.00 0.00 0.98
1829 1860 7.832685 ACAGTTCTCTACCCCCAAAAATTATAC 59.167 37.037 0.00 0.00 0.00 1.47
1880 1911 6.140303 CCATGGATGGTTTCTTAATCTGTG 57.860 41.667 5.56 0.00 43.05 3.66
1889 1920 6.072508 TGGTTTCTTAATCTGTGATGTTCAGC 60.073 38.462 0.00 0.00 33.48 4.26
1891 1922 4.183865 TCTTAATCTGTGATGTTCAGCGG 58.816 43.478 0.00 0.00 33.48 5.52
1908 1956 0.250295 CGGTGAAGCAAGGAAGGTGA 60.250 55.000 0.00 0.00 0.00 4.02
1913 1961 2.172505 TGAAGCAAGGAAGGTGAAGTGA 59.827 45.455 0.00 0.00 0.00 3.41
1915 1963 3.515602 AGCAAGGAAGGTGAAGTGAAT 57.484 42.857 0.00 0.00 0.00 2.57
1916 1964 3.837355 AGCAAGGAAGGTGAAGTGAATT 58.163 40.909 0.00 0.00 0.00 2.17
1926 1974 6.824305 AGGTGAAGTGAATTTTCATGGTAG 57.176 37.500 0.00 0.00 39.73 3.18
1929 1977 6.431234 GGTGAAGTGAATTTTCATGGTAGAGT 59.569 38.462 0.00 0.00 39.73 3.24
1970 2018 7.012894 TGTGAAGTTTAGTTTGGTCTGTTATGG 59.987 37.037 0.00 0.00 0.00 2.74
1973 2021 4.650972 TTAGTTTGGTCTGTTATGGCCT 57.349 40.909 3.32 0.00 0.00 5.19
2104 2152 6.863645 GGCATAAGTTTCTCTTCCTTGTTTTC 59.136 38.462 0.00 0.00 37.56 2.29
2153 2201 5.801350 TTCTTCTGCTCGATAAAACATGG 57.199 39.130 0.00 0.00 0.00 3.66
2164 2212 9.419297 GCTCGATAAAACATGGTAGTGATTATA 57.581 33.333 0.00 0.00 0.00 0.98
2181 2229 6.312918 GTGATTATAAGTGTCACATCGGTTGT 59.687 38.462 5.62 0.00 41.35 3.32
2276 2326 9.241317 CAATATTTCCATTATGTCTTGTTCAGC 57.759 33.333 0.00 0.00 0.00 4.26
2337 2392 1.817357 CAAAGCATCTGGAGTCTGCA 58.183 50.000 5.05 0.00 38.37 4.41
2490 2545 7.279615 TCAACTGTCCTTATTTCTTCTGTTCA 58.720 34.615 0.00 0.00 0.00 3.18
2678 2734 6.291377 TGATCAGGTATGGCTTTCAAGTATC 58.709 40.000 0.00 0.00 0.00 2.24
2686 2742 9.289782 GGTATGGCTTTCAAGTATCTGAAATAT 57.710 33.333 0.00 0.00 42.78 1.28
2690 2746 6.039717 GGCTTTCAAGTATCTGAAATATGGCA 59.960 38.462 0.00 0.00 42.78 4.92
2871 2947 7.447374 TGATATTCGCCAAATTCCGAAATAT 57.553 32.000 11.01 9.59 45.17 1.28
3131 3999 6.784176 TGTTGGTTCATCATTTATCATGACG 58.216 36.000 0.00 0.00 0.00 4.35
3154 4166 4.461781 GGAATCATGCCCAATCAATAGGAG 59.538 45.833 0.00 0.00 0.00 3.69
3217 4397 2.236489 AATACCTGGCTTTGGTGCAT 57.764 45.000 0.00 0.00 38.42 3.96
3252 4502 3.686016 TGGGAAAGTACATTTGCTCCTC 58.314 45.455 0.00 0.00 39.09 3.71
3290 4540 8.358895 CGTTTTTAACCAATCCCCTAAACTTAA 58.641 33.333 0.00 0.00 0.00 1.85
3305 4555 8.019094 CCCTAAACTTAACGGAGTACATTTTTG 58.981 37.037 0.00 0.00 45.00 2.44
3309 4559 8.623310 AACTTAACGGAGTACATTTTTGTTTG 57.377 30.769 0.00 0.00 45.00 2.93
3317 4567 6.144078 AGTACATTTTTGTTTGGGTCTGTC 57.856 37.500 0.00 0.00 0.00 3.51
3370 4620 8.600449 AAGTGACTCAATCAAACTAGAAAGAG 57.400 34.615 0.00 0.00 39.72 2.85
3394 4645 9.122613 GAGAAAGAAAAAGACAACAGAATATGC 57.877 33.333 0.00 0.00 0.00 3.14
3407 4658 5.359756 ACAGAATATGCTTGCACGAATCTA 58.640 37.500 0.00 0.00 0.00 1.98
3409 4660 6.132056 CAGAATATGCTTGCACGAATCTAAC 58.868 40.000 0.00 0.00 0.00 2.34
3410 4661 5.817296 AGAATATGCTTGCACGAATCTAACA 59.183 36.000 0.00 0.00 0.00 2.41
3506 4758 8.586879 TTTTGTTTTTCCCAAATCTTTCCAAT 57.413 26.923 0.00 0.00 32.28 3.16
3508 4760 8.586879 TTGTTTTTCCCAAATCTTTCCAATTT 57.413 26.923 0.00 0.00 0.00 1.82
3554 4912 9.106286 CAACTACATATTTGCACGCATATTAAG 57.894 33.333 0.29 0.00 0.00 1.85
3559 4917 5.772825 ATTTGCACGCATATTAAGTCCAT 57.227 34.783 0.00 0.00 0.00 3.41
3560 4918 4.811555 TTGCACGCATATTAAGTCCATC 57.188 40.909 0.00 0.00 0.00 3.51
3564 4922 4.378770 GCACGCATATTAAGTCCATCCATG 60.379 45.833 0.00 0.00 0.00 3.66
3744 5102 3.135348 TCATCTTGGAGCTGGGTATGAAG 59.865 47.826 0.00 0.00 0.00 3.02
3772 5130 2.736721 GTTCTCTATTCTGTGTTGCGCA 59.263 45.455 5.66 5.66 0.00 6.09
3799 5157 5.308825 AGGAATCCTTGTATCCTATTTGCG 58.691 41.667 0.00 0.00 41.74 4.85
3809 5167 2.554142 TCCTATTTGCGTCATGCTCTG 58.446 47.619 0.00 0.00 46.63 3.35
3818 5176 1.085091 GTCATGCTCTGGCTCAACAG 58.915 55.000 0.00 0.00 39.59 3.16
3819 5177 0.035725 TCATGCTCTGGCTCAACAGG 60.036 55.000 0.00 0.00 38.98 4.00
3820 5178 0.322277 CATGCTCTGGCTCAACAGGT 60.322 55.000 0.00 0.00 38.98 4.00
3862 5227 0.249489 GGCGATGTTGAGCCGATACT 60.249 55.000 0.00 0.00 44.22 2.12
3869 5234 3.143728 TGTTGAGCCGATACTAGCGATA 58.856 45.455 0.00 0.00 0.00 2.92
3872 5237 3.001414 TGAGCCGATACTAGCGATAGAC 58.999 50.000 15.85 4.65 39.76 2.59
3888 5253 2.740714 GACGTGGCGTTGAGATGGC 61.741 63.158 0.00 0.00 41.37 4.40
3910 5275 1.738099 CAGTGCACGGTGAGGCTAC 60.738 63.158 13.29 2.44 0.00 3.58
3941 5306 2.357517 CGAGCCGCTTTCCAGTGT 60.358 61.111 0.00 0.00 0.00 3.55
3948 5313 1.272781 CGCTTTCCAGTGTCGAGATC 58.727 55.000 0.00 0.00 0.00 2.75
3974 5339 2.616330 CGGCGGCTTTTGAGCTTGA 61.616 57.895 7.61 0.00 34.73 3.02
3981 5346 2.603953 GCTTTTGAGCTTGATTCCAGC 58.396 47.619 1.55 1.55 0.00 4.85
4021 5386 3.465403 CTCGGACTGGGGCAGGAG 61.465 72.222 0.00 0.00 35.51 3.69
4056 5421 3.311110 GAGGCAGTGGGGTGTCGA 61.311 66.667 0.00 0.00 0.00 4.20
4085 5450 2.033194 GGGTAGTCGCCACAGCAAC 61.033 63.158 0.00 0.00 39.83 4.17
4147 5512 1.971695 GTGAGGGGGCCGAAACTTG 60.972 63.158 0.00 0.00 0.00 3.16
4160 5525 0.605589 AAACTTGTACTCAGCCGGGC 60.606 55.000 12.11 12.11 0.00 6.13
4199 5564 8.745590 GGATAAATTTTCCTGCACTAAAGGTTA 58.254 33.333 0.00 0.00 36.14 2.85
4208 5573 5.531287 CCTGCACTAAAGGTTATATGGGTTC 59.469 44.000 0.00 0.00 0.00 3.62
4235 5600 0.611714 TGCCGGTTAGAGGAGGAAAC 59.388 55.000 1.90 0.00 0.00 2.78
4313 5686 4.164294 GCATGACTTCAGTTTTCATCAGC 58.836 43.478 0.00 0.00 0.00 4.26
4429 5802 3.120338 ACAACATCATTTTCCGCACTACG 60.120 43.478 0.00 0.00 43.15 3.51
4447 5820 5.050363 CACTACGTTTCTGTTGTTGTGCTAT 60.050 40.000 0.00 0.00 33.88 2.97
4460 5834 6.463995 TGTTGTGCTATCTGGTTTTTCTTT 57.536 33.333 0.00 0.00 0.00 2.52
4486 5927 6.235231 ACTTTCGACAGGATATAACCATGT 57.765 37.500 3.23 3.27 0.00 3.21
4507 5948 6.735678 TGTTGTATCGTTTGCATAAGTGAT 57.264 33.333 0.00 0.00 0.00 3.06
4540 5981 9.778741 TGATATTAGTACAAGAATTCCATCCAC 57.221 33.333 0.65 0.00 0.00 4.02
4840 6282 4.400251 CCCAAATGTGCTGATAGTGTCAAT 59.600 41.667 0.00 0.00 36.14 2.57
5162 6613 9.916360 TCTTGACTGGTACTCTTATATCTTACA 57.084 33.333 0.00 0.00 0.00 2.41
5211 6662 1.139498 TGGTTGCCATGGAAGGGAGA 61.139 55.000 18.40 0.00 43.46 3.71
5227 6678 5.171339 AGGGAGAACTGTTCGTAGTACTA 57.829 43.478 14.35 0.00 34.02 1.82
5292 6751 6.128007 ACAGTGGTTTGAGTGTTCAGTAAAAG 60.128 38.462 0.00 0.00 34.15 2.27
5294 6753 5.124936 GTGGTTTGAGTGTTCAGTAAAAGGT 59.875 40.000 0.00 0.00 34.15 3.50
5301 6761 8.740123 TGAGTGTTCAGTAAAAGGTGAAATAA 57.260 30.769 0.00 0.00 34.52 1.40
5325 6785 4.116961 CGAAATGTAGCCGTTCTGGAATA 58.883 43.478 0.00 0.00 42.00 1.75
5335 6795 5.702670 AGCCGTTCTGGAATATCACATAATG 59.297 40.000 0.00 0.00 42.00 1.90
5336 6796 5.106555 GCCGTTCTGGAATATCACATAATGG 60.107 44.000 9.69 9.69 42.00 3.16
5337 6797 6.230472 CCGTTCTGGAATATCACATAATGGA 58.770 40.000 8.90 0.00 42.00 3.41
5338 6798 6.369890 CCGTTCTGGAATATCACATAATGGAG 59.630 42.308 8.90 0.00 42.00 3.86
5339 6799 6.369890 CGTTCTGGAATATCACATAATGGAGG 59.630 42.308 0.00 0.00 0.00 4.30
5340 6800 7.453393 GTTCTGGAATATCACATAATGGAGGA 58.547 38.462 0.00 0.00 0.00 3.71
5375 6835 0.610174 GTCTGCTGGTCTGTGATCCA 59.390 55.000 0.00 0.00 0.00 3.41
5380 6840 0.743701 CTGGTCTGTGATCCAGCAGC 60.744 60.000 6.38 0.00 43.45 5.25
5389 6849 3.628942 TGTGATCCAGCAGCATTGAATAC 59.371 43.478 0.00 0.00 0.00 1.89
5391 6851 3.628942 TGATCCAGCAGCATTGAATACAC 59.371 43.478 0.00 0.00 0.00 2.90
5394 6854 1.406539 CAGCAGCATTGAATACACCCC 59.593 52.381 0.00 0.00 0.00 4.95
5395 6855 1.005805 AGCAGCATTGAATACACCCCA 59.994 47.619 0.00 0.00 0.00 4.96
5396 6856 1.406539 GCAGCATTGAATACACCCCAG 59.593 52.381 0.00 0.00 0.00 4.45
5397 6857 2.945440 GCAGCATTGAATACACCCCAGA 60.945 50.000 0.00 0.00 0.00 3.86
5438 6901 0.331278 TCAAATCACCTCCCCGCAAT 59.669 50.000 0.00 0.00 0.00 3.56
5440 6903 1.134946 CAAATCACCTCCCCGCAATTC 59.865 52.381 0.00 0.00 0.00 2.17
5459 6922 6.794636 GCAATTCTCTCTTCTTTTCGAGAAAC 59.205 38.462 4.88 0.00 43.56 2.78
5480 6943 1.140852 CACCTCCTTTGTGGACAGACA 59.859 52.381 0.00 0.00 40.56 3.41
5481 6944 1.141053 ACCTCCTTTGTGGACAGACAC 59.859 52.381 0.00 0.00 40.56 3.67
5483 6946 0.472471 TCCTTTGTGGACAGACACCC 59.528 55.000 0.00 0.00 40.56 4.61
5536 7002 1.193323 CACCAGATGAGCAGGAGACT 58.807 55.000 0.00 0.00 46.44 3.24
5559 7025 9.121658 GACTTACCATCGATGACCAGATATATA 57.878 37.037 26.86 0.93 0.00 0.86
5586 7052 9.678981 AATTATACCCTACCTCTATAAACACCA 57.321 33.333 0.00 0.00 0.00 4.17
5587 7053 9.854303 ATTATACCCTACCTCTATAAACACCAT 57.146 33.333 0.00 0.00 0.00 3.55
5588 7054 7.793948 ATACCCTACCTCTATAAACACCATC 57.206 40.000 0.00 0.00 0.00 3.51
5589 7055 4.587684 ACCCTACCTCTATAAACACCATCG 59.412 45.833 0.00 0.00 0.00 3.84
5590 7056 4.831155 CCCTACCTCTATAAACACCATCGA 59.169 45.833 0.00 0.00 0.00 3.59
5591 7057 5.047943 CCCTACCTCTATAAACACCATCGAG 60.048 48.000 0.00 0.00 0.00 4.04
5592 7058 5.768662 CCTACCTCTATAAACACCATCGAGA 59.231 44.000 0.00 0.00 0.00 4.04
5593 7059 5.776173 ACCTCTATAAACACCATCGAGAG 57.224 43.478 0.00 0.00 0.00 3.20
5595 7061 5.299782 ACCTCTATAAACACCATCGAGAGAC 59.700 44.000 0.00 0.00 46.97 3.36
5596 7062 5.533154 CCTCTATAAACACCATCGAGAGACT 59.467 44.000 0.00 0.00 46.97 3.24
5597 7063 6.378710 TCTATAAACACCATCGAGAGACTG 57.621 41.667 0.00 0.00 46.97 3.51
5598 7064 6.120220 TCTATAAACACCATCGAGAGACTGA 58.880 40.000 0.00 0.00 46.97 3.41
5599 7065 3.584406 AAACACCATCGAGAGACTGAG 57.416 47.619 0.00 0.00 46.97 3.35
5600 7066 0.814457 ACACCATCGAGAGACTGAGC 59.186 55.000 0.00 0.00 46.97 4.26
5601 7067 0.102120 CACCATCGAGAGACTGAGCC 59.898 60.000 0.00 0.00 46.97 4.70
5602 7068 0.323816 ACCATCGAGAGACTGAGCCA 60.324 55.000 0.00 0.00 46.97 4.75
5603 7069 0.385029 CCATCGAGAGACTGAGCCAG 59.615 60.000 0.00 1.16 46.97 4.85
5604 7070 0.248990 CATCGAGAGACTGAGCCAGC 60.249 60.000 0.00 0.00 46.97 4.85
5605 7071 0.682532 ATCGAGAGACTGAGCCAGCA 60.683 55.000 0.00 0.00 46.97 4.41
5606 7072 0.682532 TCGAGAGACTGAGCCAGCAT 60.683 55.000 2.50 0.00 34.37 3.79
5607 7073 1.028130 CGAGAGACTGAGCCAGCATA 58.972 55.000 2.50 0.00 34.37 3.14
5608 7074 1.612950 CGAGAGACTGAGCCAGCATAT 59.387 52.381 2.50 0.00 34.37 1.78
5609 7075 2.351641 CGAGAGACTGAGCCAGCATATC 60.352 54.545 2.50 0.00 34.37 1.63
5610 7076 2.627221 GAGAGACTGAGCCAGCATATCA 59.373 50.000 2.50 0.00 34.37 2.15
5611 7077 3.241156 AGAGACTGAGCCAGCATATCAT 58.759 45.455 2.50 0.00 34.37 2.45
5612 7078 3.647113 AGAGACTGAGCCAGCATATCATT 59.353 43.478 2.50 0.00 34.37 2.57
5613 7079 4.102838 AGAGACTGAGCCAGCATATCATTT 59.897 41.667 2.50 0.00 34.37 2.32
5614 7080 4.789807 AGACTGAGCCAGCATATCATTTT 58.210 39.130 2.50 0.00 34.37 1.82
5615 7081 5.933617 AGACTGAGCCAGCATATCATTTTA 58.066 37.500 2.50 0.00 34.37 1.52
5616 7082 6.359804 AGACTGAGCCAGCATATCATTTTAA 58.640 36.000 2.50 0.00 34.37 1.52
5617 7083 6.830324 AGACTGAGCCAGCATATCATTTTAAA 59.170 34.615 2.50 0.00 34.37 1.52
5618 7084 7.340232 AGACTGAGCCAGCATATCATTTTAAAA 59.660 33.333 2.51 2.51 34.37 1.52
5619 7085 7.839907 ACTGAGCCAGCATATCATTTTAAAAA 58.160 30.769 4.44 0.00 34.37 1.94
5620 7086 8.480501 ACTGAGCCAGCATATCATTTTAAAAAT 58.519 29.630 4.44 0.00 34.37 1.82
5621 7087 9.321562 CTGAGCCAGCATATCATTTTAAAAATT 57.678 29.630 4.44 0.00 0.00 1.82
5622 7088 9.669887 TGAGCCAGCATATCATTTTAAAAATTT 57.330 25.926 4.44 0.00 0.00 1.82
5641 7107 7.500807 AAATTTATGAAATCACCGTAAACGC 57.499 32.000 0.00 0.00 38.18 4.84
5642 7108 4.603231 TTATGAAATCACCGTAAACGCC 57.397 40.909 0.00 0.00 38.18 5.68
5643 7109 2.172851 TGAAATCACCGTAAACGCCT 57.827 45.000 0.00 0.00 38.18 5.52
5644 7110 2.496111 TGAAATCACCGTAAACGCCTT 58.504 42.857 0.00 0.00 38.18 4.35
5645 7111 2.481185 TGAAATCACCGTAAACGCCTTC 59.519 45.455 0.00 0.00 38.18 3.46
5646 7112 1.073177 AATCACCGTAAACGCCTTCG 58.927 50.000 0.00 0.00 42.43 3.79
5672 7138 3.971620 CGTGAACGTTTCGTCTCAC 57.028 52.632 0.46 17.97 39.99 3.51
5673 7139 1.474017 CGTGAACGTTTCGTCTCACT 58.526 50.000 21.55 1.51 41.14 3.41
5674 7140 1.187271 CGTGAACGTTTCGTCTCACTG 59.813 52.381 21.55 15.95 41.14 3.66
5675 7141 2.456989 GTGAACGTTTCGTCTCACTGA 58.543 47.619 0.46 0.00 39.99 3.41
5676 7142 2.215812 GTGAACGTTTCGTCTCACTGAC 59.784 50.000 0.46 0.00 39.99 3.51
5677 7143 2.159352 TGAACGTTTCGTCTCACTGACA 60.159 45.455 0.46 0.00 45.60 3.58
5678 7144 1.836383 ACGTTTCGTCTCACTGACAC 58.164 50.000 0.00 0.00 45.60 3.67
5679 7145 1.133598 ACGTTTCGTCTCACTGACACA 59.866 47.619 0.00 0.00 45.60 3.72
5680 7146 1.517276 CGTTTCGTCTCACTGACACAC 59.483 52.381 0.00 0.00 45.60 3.82
5681 7147 2.536365 GTTTCGTCTCACTGACACACA 58.464 47.619 0.00 0.00 45.60 3.72
5682 7148 2.927477 GTTTCGTCTCACTGACACACAA 59.073 45.455 0.00 0.00 45.60 3.33
5683 7149 2.203800 TCGTCTCACTGACACACAAC 57.796 50.000 0.00 0.00 45.60 3.32
5684 7150 1.474879 TCGTCTCACTGACACACAACA 59.525 47.619 0.00 0.00 45.60 3.33
5685 7151 1.588404 CGTCTCACTGACACACAACAC 59.412 52.381 0.00 0.00 45.60 3.32
5686 7152 1.933853 GTCTCACTGACACACAACACC 59.066 52.381 0.00 0.00 44.73 4.16
5687 7153 0.930310 CTCACTGACACACAACACCG 59.070 55.000 0.00 0.00 0.00 4.94
5688 7154 0.533032 TCACTGACACACAACACCGA 59.467 50.000 0.00 0.00 0.00 4.69
5689 7155 1.066787 TCACTGACACACAACACCGAA 60.067 47.619 0.00 0.00 0.00 4.30
5690 7156 1.735018 CACTGACACACAACACCGAAA 59.265 47.619 0.00 0.00 0.00 3.46
5691 7157 2.160615 CACTGACACACAACACCGAAAA 59.839 45.455 0.00 0.00 0.00 2.29
5692 7158 3.013921 ACTGACACACAACACCGAAAAT 58.986 40.909 0.00 0.00 0.00 1.82
5693 7159 3.064820 ACTGACACACAACACCGAAAATC 59.935 43.478 0.00 0.00 0.00 2.17
5694 7160 2.356382 TGACACACAACACCGAAAATCC 59.644 45.455 0.00 0.00 0.00 3.01
5695 7161 2.616842 GACACACAACACCGAAAATCCT 59.383 45.455 0.00 0.00 0.00 3.24
5696 7162 3.810941 GACACACAACACCGAAAATCCTA 59.189 43.478 0.00 0.00 0.00 2.94
5697 7163 4.200874 ACACACAACACCGAAAATCCTAA 58.799 39.130 0.00 0.00 0.00 2.69
5698 7164 4.641094 ACACACAACACCGAAAATCCTAAA 59.359 37.500 0.00 0.00 0.00 1.85
5699 7165 5.125739 ACACACAACACCGAAAATCCTAAAA 59.874 36.000 0.00 0.00 0.00 1.52
5700 7166 6.183360 ACACACAACACCGAAAATCCTAAAAT 60.183 34.615 0.00 0.00 0.00 1.82
5701 7167 7.013464 ACACACAACACCGAAAATCCTAAAATA 59.987 33.333 0.00 0.00 0.00 1.40
5702 7168 7.863375 CACACAACACCGAAAATCCTAAAATAA 59.137 33.333 0.00 0.00 0.00 1.40
5703 7169 8.414778 ACACAACACCGAAAATCCTAAAATAAA 58.585 29.630 0.00 0.00 0.00 1.40
5704 7170 9.418045 CACAACACCGAAAATCCTAAAATAAAT 57.582 29.630 0.00 0.00 0.00 1.40
5705 7171 9.990360 ACAACACCGAAAATCCTAAAATAAATT 57.010 25.926 0.00 0.00 0.00 1.82
5737 7203 8.803397 AAATATGACCACTAGAACTTAAACCC 57.197 34.615 0.00 0.00 0.00 4.11
5738 7204 7.750947 ATATGACCACTAGAACTTAAACCCT 57.249 36.000 0.00 0.00 0.00 4.34
5739 7205 5.223449 TGACCACTAGAACTTAAACCCTG 57.777 43.478 0.00 0.00 0.00 4.45
5740 7206 4.903049 TGACCACTAGAACTTAAACCCTGA 59.097 41.667 0.00 0.00 0.00 3.86
5741 7207 5.546499 TGACCACTAGAACTTAAACCCTGAT 59.454 40.000 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.000270 TGGCAGTGGTGTGGTGTTT 60.000 52.632 0.00 0.00 0.00 2.83
44 45 2.752807 GGGTGGTGGTGGTGTGACT 61.753 63.158 0.00 0.00 0.00 3.41
97 98 0.748729 GTTGGTGGTTGTTCGGGTGA 60.749 55.000 0.00 0.00 0.00 4.02
102 103 1.259507 CACTACGTTGGTGGTTGTTCG 59.740 52.381 11.82 0.00 35.45 3.95
105 106 0.107606 TGCACTACGTTGGTGGTTGT 60.108 50.000 18.39 0.00 35.45 3.32
145 146 3.827898 CGTCGCCTCCCTCTCACC 61.828 72.222 0.00 0.00 0.00 4.02
151 152 4.436998 CTTTCGCGTCGCCTCCCT 62.437 66.667 12.44 0.00 0.00 4.20
156 157 4.736631 GGTTGCTTTCGCGTCGCC 62.737 66.667 12.44 0.00 39.65 5.54
161 162 1.440353 CTTTCCGGTTGCTTTCGCG 60.440 57.895 0.00 0.00 39.65 5.87
163 164 0.661020 ACACTTTCCGGTTGCTTTCG 59.339 50.000 0.00 0.00 0.00 3.46
164 165 1.333791 CGACACTTTCCGGTTGCTTTC 60.334 52.381 0.00 0.00 0.00 2.62
166 167 1.782028 GCGACACTTTCCGGTTGCTT 61.782 55.000 0.00 0.00 40.50 3.91
167 168 2.251642 GCGACACTTTCCGGTTGCT 61.252 57.895 0.00 0.00 40.50 3.91
168 169 2.251371 GCGACACTTTCCGGTTGC 59.749 61.111 0.00 0.00 37.26 4.17
169 170 2.549282 CGCGACACTTTCCGGTTG 59.451 61.111 0.00 0.00 0.00 3.77
170 171 3.343421 GCGCGACACTTTCCGGTT 61.343 61.111 12.10 0.00 0.00 4.44
173 174 3.777925 CAGGCGCGACACTTTCCG 61.778 66.667 17.71 0.00 0.00 4.30
174 175 3.423154 CCAGGCGCGACACTTTCC 61.423 66.667 17.71 0.47 0.00 3.13
175 176 3.423154 CCCAGGCGCGACACTTTC 61.423 66.667 17.71 0.00 0.00 2.62
201 202 1.470979 GGTAGCTCGATTCTTTGCCGA 60.471 52.381 0.00 0.00 0.00 5.54
204 205 1.666189 GGTGGTAGCTCGATTCTTTGC 59.334 52.381 0.00 0.00 0.00 3.68
219 220 2.124487 CAACACGTGTGGGGTGGT 60.124 61.111 24.16 0.52 39.69 4.16
254 255 3.061848 GGTTGGGTGGCGATGGTG 61.062 66.667 0.00 0.00 0.00 4.17
256 257 2.438434 GAGGTTGGGTGGCGATGG 60.438 66.667 0.00 0.00 0.00 3.51
258 259 2.671070 CTGAGGTTGGGTGGCGAT 59.329 61.111 0.00 0.00 0.00 4.58
269 270 1.827399 CTACGTGGTTGGCCTGAGGT 61.827 60.000 3.32 0.00 35.27 3.85
273 274 2.746277 GGCTACGTGGTTGGCCTG 60.746 66.667 3.32 0.00 41.20 4.85
388 392 2.357760 GGAGGGCAACGCGTTGTA 60.358 61.111 41.95 0.00 42.31 2.41
409 413 1.266786 CTCGTGTTCGTTTCGTCGCT 61.267 55.000 0.00 0.00 38.33 4.93
414 418 0.505655 GGTTCCTCGTGTTCGTTTCG 59.494 55.000 0.00 0.00 38.33 3.46
511 515 1.774631 CCCCCATCCTACCTTCCCC 60.775 68.421 0.00 0.00 0.00 4.81
567 571 1.347050 CCCTGCATCACCTCTCCTATG 59.653 57.143 0.00 0.00 0.00 2.23
569 573 0.399091 CCCCTGCATCACCTCTCCTA 60.399 60.000 0.00 0.00 0.00 2.94
580 584 0.033796 CACATTGACTCCCCCTGCAT 60.034 55.000 0.00 0.00 0.00 3.96
581 585 1.133181 TCACATTGACTCCCCCTGCA 61.133 55.000 0.00 0.00 0.00 4.41
641 645 4.023021 AGAGCGTAGAGATCGTTATTTCCC 60.023 45.833 0.00 0.00 40.85 3.97
642 646 5.110940 AGAGCGTAGAGATCGTTATTTCC 57.889 43.478 0.00 0.00 40.85 3.13
646 650 9.991388 GAAATATAAGAGCGTAGAGATCGTTAT 57.009 33.333 0.00 0.00 40.85 1.89
649 653 7.675962 AGAAATATAAGAGCGTAGAGATCGT 57.324 36.000 0.00 0.00 40.85 3.73
650 654 8.958175 AAAGAAATATAAGAGCGTAGAGATCG 57.042 34.615 0.00 0.00 40.85 3.69
660 664 9.651913 CTCCTCTCCATAAAGAAATATAAGAGC 57.348 37.037 0.00 0.00 30.43 4.09
672 676 2.540265 ATGCGCTCCTCTCCATAAAG 57.460 50.000 9.73 0.00 0.00 1.85
715 719 2.572556 TGGTTATTACTCCCTCCGCAAA 59.427 45.455 0.00 0.00 0.00 3.68
718 722 1.070289 CCTGGTTATTACTCCCTCCGC 59.930 57.143 0.00 0.00 0.00 5.54
753 757 6.981762 TTGCAATTTCACAACAATCAACTT 57.018 29.167 0.00 0.00 0.00 2.66
754 758 7.927629 AGTATTGCAATTTCACAACAATCAACT 59.072 29.630 18.75 6.58 33.31 3.16
755 759 8.005466 CAGTATTGCAATTTCACAACAATCAAC 58.995 33.333 18.75 4.21 33.31 3.18
756 760 7.171167 CCAGTATTGCAATTTCACAACAATCAA 59.829 33.333 18.75 0.00 33.31 2.57
757 761 6.645827 CCAGTATTGCAATTTCACAACAATCA 59.354 34.615 18.75 0.00 33.31 2.57
758 762 6.867816 TCCAGTATTGCAATTTCACAACAATC 59.132 34.615 18.75 0.00 33.31 2.67
759 763 6.646240 GTCCAGTATTGCAATTTCACAACAAT 59.354 34.615 18.75 0.00 35.31 2.71
760 764 5.982516 GTCCAGTATTGCAATTTCACAACAA 59.017 36.000 18.75 0.00 0.00 2.83
761 765 5.527951 GTCCAGTATTGCAATTTCACAACA 58.472 37.500 18.75 0.00 0.00 3.33
762 766 4.616802 CGTCCAGTATTGCAATTTCACAAC 59.383 41.667 18.75 8.46 0.00 3.32
763 767 4.517075 TCGTCCAGTATTGCAATTTCACAA 59.483 37.500 18.75 0.00 0.00 3.33
764 768 4.068599 TCGTCCAGTATTGCAATTTCACA 58.931 39.130 18.75 0.00 0.00 3.58
765 769 4.154195 ACTCGTCCAGTATTGCAATTTCAC 59.846 41.667 18.75 10.01 31.37 3.18
766 770 4.323417 ACTCGTCCAGTATTGCAATTTCA 58.677 39.130 18.75 0.00 31.37 2.69
767 771 4.946784 ACTCGTCCAGTATTGCAATTTC 57.053 40.909 18.75 11.32 31.37 2.17
875 892 0.616891 TTTTCCTCCCCCGCTTCTAC 59.383 55.000 0.00 0.00 0.00 2.59
881 898 4.442454 CCCCTTTTCCTCCCCCGC 62.442 72.222 0.00 0.00 0.00 6.13
1080 1101 3.188786 CCGTTGCCTCTACGCTGC 61.189 66.667 0.00 0.00 37.67 5.25
1555 1576 4.201724 GCTTAGAAATGTCCGCTAGTTGTG 60.202 45.833 0.00 0.00 0.00 3.33
1560 1581 3.786635 ACAGCTTAGAAATGTCCGCTAG 58.213 45.455 0.00 0.00 0.00 3.42
1564 1585 4.201822 GCCTAAACAGCTTAGAAATGTCCG 60.202 45.833 0.00 0.00 39.66 4.79
1656 1683 5.617252 AGGGACTACTTGACGAAAAATCAA 58.383 37.500 0.00 0.00 36.02 2.57
1675 1704 0.260816 ATCACTACCGTGGCTAGGGA 59.739 55.000 16.40 0.00 41.53 4.20
1678 1707 4.650754 AAGTTATCACTACCGTGGCTAG 57.349 45.455 0.00 0.00 41.53 3.42
1823 1854 6.889198 ACATACTGTTGCAGGACTGTATAAT 58.111 36.000 16.23 8.63 40.47 1.28
1828 1859 3.492102 AACATACTGTTGCAGGACTGT 57.508 42.857 6.35 6.35 39.45 3.55
1879 1910 0.250252 TGCTTCACCGCTGAACATCA 60.250 50.000 0.00 0.00 32.68 3.07
1880 1911 0.874390 TTGCTTCACCGCTGAACATC 59.126 50.000 0.00 0.00 32.68 3.06
1889 1920 0.250295 TCACCTTCCTTGCTTCACCG 60.250 55.000 0.00 0.00 0.00 4.94
1891 1922 2.291741 CACTTCACCTTCCTTGCTTCAC 59.708 50.000 0.00 0.00 0.00 3.18
1908 1956 7.721399 AGAACACTCTACCATGAAAATTCACTT 59.279 33.333 0.00 0.00 40.49 3.16
1916 1964 9.653287 CTGTATTTAGAACACTCTACCATGAAA 57.347 33.333 0.00 0.00 33.73 2.69
1926 1974 8.366671 ACTTCACAACTGTATTTAGAACACTC 57.633 34.615 0.00 0.00 0.00 3.51
1970 2018 3.821033 ACACCTAAACAAGATGAACAGGC 59.179 43.478 0.00 0.00 0.00 4.85
1973 2021 7.441157 CAGAAGTACACCTAAACAAGATGAACA 59.559 37.037 0.00 0.00 0.00 3.18
2065 2113 0.393820 TATGCCAGCATGATCGCAGA 59.606 50.000 15.29 0.88 39.69 4.26
2066 2114 1.197036 CTTATGCCAGCATGATCGCAG 59.803 52.381 15.29 0.00 39.69 5.18
2067 2115 1.232119 CTTATGCCAGCATGATCGCA 58.768 50.000 15.29 5.54 39.69 5.10
2153 2201 7.201145 ACCGATGTGACACTTATAATCACTAC 58.799 38.462 15.32 9.94 42.65 2.73
2164 2212 2.639065 ACAACAACCGATGTGACACTT 58.361 42.857 7.20 0.00 42.99 3.16
2276 2326 8.908786 AACCACAATGATATAATCAGGTACAG 57.091 34.615 0.00 0.00 43.53 2.74
2308 2363 0.038892 AGATGCTTTGCCAAACTGCG 60.039 50.000 0.00 0.00 0.00 5.18
2337 2392 8.906867 CACCATATGAAGGAGAACATTGTATTT 58.093 33.333 3.65 0.00 0.00 1.40
2686 2742 6.149973 GCAAGCATCTATAGATTGTATTGCCA 59.850 38.462 24.23 0.00 31.21 4.92
2690 2746 9.040259 TCCTAGCAAGCATCTATAGATTGTATT 57.960 33.333 12.75 3.12 31.21 1.89
2698 2754 5.421693 ACTGGATCCTAGCAAGCATCTATAG 59.578 44.000 14.23 0.00 0.00 1.31
2773 2849 7.683578 ACTAATAGCAAGATTGGCATATGAGA 58.316 34.615 6.97 0.00 0.00 3.27
2871 2947 5.368523 AGGTTCATCCATCCTACGGAATTTA 59.631 40.000 0.00 0.00 39.02 1.40
3131 3999 4.410099 TCCTATTGATTGGGCATGATTCC 58.590 43.478 0.00 0.00 0.00 3.01
3154 4166 7.610865 TGAAACAGAATCATGGTTTTATTCCC 58.389 34.615 0.00 0.00 35.08 3.97
3269 4519 5.945191 CCGTTAAGTTTAGGGGATTGGTTAA 59.055 40.000 0.00 0.00 0.00 2.01
3278 4528 4.806640 TGTACTCCGTTAAGTTTAGGGG 57.193 45.455 1.11 0.00 0.00 4.79
3290 4540 3.955551 ACCCAAACAAAAATGTACTCCGT 59.044 39.130 0.00 0.00 0.00 4.69
3305 4555 3.003480 GCACATCTAGACAGACCCAAAC 58.997 50.000 0.00 0.00 32.25 2.93
3308 4558 1.195115 GGCACATCTAGACAGACCCA 58.805 55.000 0.00 0.00 32.25 4.51
3309 4559 0.466124 GGGCACATCTAGACAGACCC 59.534 60.000 0.00 0.30 32.25 4.46
3317 4567 4.960938 TGCAATAACTAGGGCACATCTAG 58.039 43.478 0.00 0.00 39.88 2.43
3343 4593 9.698309 TCTTTCTAGTTTGATTGAGTCACTTAG 57.302 33.333 0.00 0.00 36.32 2.18
3370 4620 9.468532 AAGCATATTCTGTTGTCTTTTTCTTTC 57.531 29.630 0.00 0.00 0.00 2.62
3385 4636 4.808077 AGATTCGTGCAAGCATATTCTG 57.192 40.909 0.00 0.00 0.00 3.02
3392 4643 5.871465 TTTATGTTAGATTCGTGCAAGCA 57.129 34.783 0.00 0.00 0.00 3.91
3394 4645 8.894409 TTGATTTTATGTTAGATTCGTGCAAG 57.106 30.769 0.00 0.00 0.00 4.01
3491 4743 9.771534 TGTAAACTAAAATTGGAAAGATTTGGG 57.228 29.630 0.00 0.00 0.00 4.12
3544 4902 7.848223 TTATCATGGATGGACTTAATATGCG 57.152 36.000 0.00 0.00 0.00 4.73
3554 4912 7.502226 TGTGAACCTTAATTATCATGGATGGAC 59.498 37.037 0.00 0.00 0.00 4.02
3559 4917 8.821686 ATTGTGTGAACCTTAATTATCATGGA 57.178 30.769 0.00 0.00 0.00 3.41
3560 4918 9.520204 GAATTGTGTGAACCTTAATTATCATGG 57.480 33.333 0.00 0.00 0.00 3.66
3564 4922 8.447833 TCGTGAATTGTGTGAACCTTAATTATC 58.552 33.333 0.00 0.00 0.00 1.75
3626 4984 5.838531 ACCCTTTCGTGTGTTTGAATTTA 57.161 34.783 0.00 0.00 0.00 1.40
3642 5000 5.243954 GCTCTTTACTTCATTGGAACCCTTT 59.756 40.000 0.00 0.00 0.00 3.11
3651 5009 9.017669 GCTTTTATCATGCTCTTTACTTCATTG 57.982 33.333 0.00 0.00 0.00 2.82
3744 5102 5.061920 ACACAGAATAGAGAACCGAGAAC 57.938 43.478 0.00 0.00 0.00 3.01
3772 5130 2.683768 AGGATACAAGGATTCCTCGCT 58.316 47.619 5.48 0.00 34.80 4.93
3775 5133 5.409826 CGCAAATAGGATACAAGGATTCCTC 59.590 44.000 5.48 0.00 40.37 3.71
3799 5157 1.085091 CTGTTGAGCCAGAGCATGAC 58.915 55.000 0.00 0.00 43.56 3.06
3809 5167 4.329545 TCCGCCACCTGTTGAGCC 62.330 66.667 0.00 0.00 0.00 4.70
3862 5227 0.248336 CAACGCCACGTCTATCGCTA 60.248 55.000 0.00 0.00 39.99 4.26
3869 5234 1.079819 CCATCTCAACGCCACGTCT 60.080 57.895 0.00 0.00 39.99 4.18
3872 5237 3.499737 GGCCATCTCAACGCCACG 61.500 66.667 0.00 0.00 42.52 4.94
3910 5275 0.031449 GGCTCGGATCTTCTTCCTCG 59.969 60.000 0.00 0.00 33.30 4.63
4020 5385 3.382832 CTTCGTCCTCGCCACCCT 61.383 66.667 0.00 0.00 36.96 4.34
4021 5386 4.452733 CCTTCGTCCTCGCCACCC 62.453 72.222 0.00 0.00 36.96 4.61
4032 5397 3.322466 CCCACTGCCTCCCTTCGT 61.322 66.667 0.00 0.00 0.00 3.85
4056 5421 4.691359 ACTACCCACCGCCTCCGT 62.691 66.667 0.00 0.00 0.00 4.69
4068 5433 3.562635 GTTGCTGTGGCGACTACC 58.437 61.111 0.00 0.00 46.41 3.18
4128 5493 3.546714 AAGTTTCGGCCCCCTCACG 62.547 63.158 0.00 0.00 0.00 4.35
4147 5512 4.208686 CTCCGCCCGGCTGAGTAC 62.209 72.222 19.87 0.00 35.66 2.73
4199 5564 0.396811 GCACCTAGCCGAACCCATAT 59.603 55.000 0.00 0.00 37.23 1.78
4222 5587 4.921644 AAATTCCGGTTTCCTCCTCTAA 57.078 40.909 0.00 0.00 0.00 2.10
4313 5686 3.745975 TGGTTTGATGCTCGTAGTTCTTG 59.254 43.478 0.00 0.00 0.00 3.02
4429 5802 4.275936 ACCAGATAGCACAACAACAGAAAC 59.724 41.667 0.00 0.00 0.00 2.78
4447 5820 6.072397 TGTCGAAAGTTGAAAGAAAAACCAGA 60.072 34.615 0.00 0.00 0.00 3.86
4460 5834 6.288941 TGGTTATATCCTGTCGAAAGTTGA 57.711 37.500 1.04 0.00 0.00 3.18
4522 5963 6.375455 ACAATGAGTGGATGGAATTCTTGTAC 59.625 38.462 5.23 0.00 0.00 2.90
4533 5974 0.734889 GGCGAACAATGAGTGGATGG 59.265 55.000 0.00 0.00 0.00 3.51
4540 5981 3.495193 CATTGACAAGGCGAACAATGAG 58.505 45.455 17.57 0.97 46.81 2.90
4840 6282 6.114187 AGTCACCTTTAAGACATGACATGA 57.886 37.500 22.19 0.00 41.72 3.07
5036 6478 3.392616 ACTATATCCCTGGCCTGTTTCAG 59.607 47.826 3.32 0.00 0.00 3.02
5042 6484 1.276421 CGGAACTATATCCCTGGCCTG 59.724 57.143 3.32 2.54 36.00 4.85
5211 6662 5.443185 TTGCACTAGTACTACGAACAGTT 57.557 39.130 0.00 0.00 0.00 3.16
5227 6678 4.537015 GTTTACTGAAGCGAAATTGCACT 58.463 39.130 0.00 0.00 37.31 4.40
5267 6718 3.350219 ACTGAACACTCAAACCACTGT 57.650 42.857 0.00 0.00 0.00 3.55
5274 6725 7.455641 TTTCACCTTTTACTGAACACTCAAA 57.544 32.000 0.00 0.00 0.00 2.69
5276 6727 8.740123 TTATTTCACCTTTTACTGAACACTCA 57.260 30.769 0.00 0.00 0.00 3.41
5292 6751 5.007332 ACGGCTACATTTCGATTATTTCACC 59.993 40.000 0.00 0.00 0.00 4.02
5294 6753 6.537301 AGAACGGCTACATTTCGATTATTTCA 59.463 34.615 0.00 0.00 0.00 2.69
5301 6761 2.167693 TCCAGAACGGCTACATTTCGAT 59.832 45.455 0.00 0.00 33.14 3.59
5325 6785 3.906846 GTCCTCCTCCTCCATTATGTGAT 59.093 47.826 0.00 0.00 0.00 3.06
5335 6795 2.760385 CGTGGGTCCTCCTCCTCC 60.760 72.222 0.00 0.00 36.20 4.30
5336 6796 2.760385 CCGTGGGTCCTCCTCCTC 60.760 72.222 0.00 0.00 36.20 3.71
5337 6797 3.175714 AACCGTGGGTCCTCCTCCT 62.176 63.158 0.00 0.00 33.12 3.69
5338 6798 2.606826 AACCGTGGGTCCTCCTCC 60.607 66.667 0.00 0.00 33.12 4.30
5339 6799 2.168666 GACAACCGTGGGTCCTCCTC 62.169 65.000 0.00 0.00 33.12 3.71
5340 6800 2.122547 ACAACCGTGGGTCCTCCT 60.123 61.111 0.00 0.00 33.12 3.69
5375 6835 1.005805 TGGGGTGTATTCAATGCTGCT 59.994 47.619 0.00 0.00 0.00 4.24
5380 6840 2.288666 CGGTCTGGGGTGTATTCAATG 58.711 52.381 0.00 0.00 0.00 2.82
5389 6849 3.402681 ATCTGGCGGTCTGGGGTG 61.403 66.667 0.00 0.00 0.00 4.61
5391 6851 1.987807 AATCATCTGGCGGTCTGGGG 61.988 60.000 0.00 0.00 0.00 4.96
5394 6854 1.579698 CTGAATCATCTGGCGGTCTG 58.420 55.000 0.00 0.00 0.00 3.51
5395 6855 0.467384 CCTGAATCATCTGGCGGTCT 59.533 55.000 0.00 0.00 37.78 3.85
5396 6856 0.465705 TCCTGAATCATCTGGCGGTC 59.534 55.000 0.00 0.00 42.71 4.79
5397 6857 0.911769 TTCCTGAATCATCTGGCGGT 59.088 50.000 0.00 0.00 42.71 5.68
5438 6901 5.753921 GTGGTTTCTCGAAAAGAAGAGAGAA 59.246 40.000 3.01 3.01 44.69 2.87
5440 6903 4.449405 GGTGGTTTCTCGAAAAGAAGAGAG 59.551 45.833 0.00 0.00 44.69 3.20
5564 7030 6.436532 CGATGGTGTTTATAGAGGTAGGGTAT 59.563 42.308 0.00 0.00 0.00 2.73
5565 7031 5.771666 CGATGGTGTTTATAGAGGTAGGGTA 59.228 44.000 0.00 0.00 0.00 3.69
5566 7032 4.587684 CGATGGTGTTTATAGAGGTAGGGT 59.412 45.833 0.00 0.00 0.00 4.34
5567 7033 4.831155 TCGATGGTGTTTATAGAGGTAGGG 59.169 45.833 0.00 0.00 0.00 3.53
5568 7034 5.768662 TCTCGATGGTGTTTATAGAGGTAGG 59.231 44.000 0.00 0.00 30.97 3.18
5569 7035 6.711194 TCTCTCGATGGTGTTTATAGAGGTAG 59.289 42.308 0.00 0.00 30.97 3.18
5570 7036 6.485984 GTCTCTCGATGGTGTTTATAGAGGTA 59.514 42.308 0.00 0.00 30.97 3.08
5571 7037 5.299782 GTCTCTCGATGGTGTTTATAGAGGT 59.700 44.000 0.00 0.00 30.97 3.85
5572 7038 5.533154 AGTCTCTCGATGGTGTTTATAGAGG 59.467 44.000 0.00 0.00 30.97 3.69
5573 7039 6.261158 TCAGTCTCTCGATGGTGTTTATAGAG 59.739 42.308 0.00 0.00 0.00 2.43
5574 7040 6.120220 TCAGTCTCTCGATGGTGTTTATAGA 58.880 40.000 0.00 0.00 0.00 1.98
5575 7041 6.378710 TCAGTCTCTCGATGGTGTTTATAG 57.621 41.667 0.00 0.00 0.00 1.31
5576 7042 5.221067 GCTCAGTCTCTCGATGGTGTTTATA 60.221 44.000 0.00 0.00 0.00 0.98
5577 7043 4.440802 GCTCAGTCTCTCGATGGTGTTTAT 60.441 45.833 0.00 0.00 0.00 1.40
5578 7044 3.119459 GCTCAGTCTCTCGATGGTGTTTA 60.119 47.826 0.00 0.00 0.00 2.01
5579 7045 2.353208 GCTCAGTCTCTCGATGGTGTTT 60.353 50.000 0.00 0.00 0.00 2.83
5580 7046 1.203523 GCTCAGTCTCTCGATGGTGTT 59.796 52.381 0.00 0.00 0.00 3.32
5581 7047 0.814457 GCTCAGTCTCTCGATGGTGT 59.186 55.000 0.00 0.00 0.00 4.16
5582 7048 0.102120 GGCTCAGTCTCTCGATGGTG 59.898 60.000 0.00 0.00 0.00 4.17
5583 7049 0.323816 TGGCTCAGTCTCTCGATGGT 60.324 55.000 0.00 0.00 0.00 3.55
5584 7050 0.385029 CTGGCTCAGTCTCTCGATGG 59.615 60.000 0.00 0.00 0.00 3.51
5585 7051 0.248990 GCTGGCTCAGTCTCTCGATG 60.249 60.000 4.45 0.00 33.43 3.84
5586 7052 0.682532 TGCTGGCTCAGTCTCTCGAT 60.683 55.000 4.45 0.00 33.43 3.59
5587 7053 0.682532 ATGCTGGCTCAGTCTCTCGA 60.683 55.000 4.45 0.00 33.43 4.04
5588 7054 1.028130 TATGCTGGCTCAGTCTCTCG 58.972 55.000 4.45 0.00 33.43 4.04
5589 7055 2.627221 TGATATGCTGGCTCAGTCTCTC 59.373 50.000 4.45 0.00 33.43 3.20
5590 7056 2.675583 TGATATGCTGGCTCAGTCTCT 58.324 47.619 4.45 0.00 33.43 3.10
5591 7057 3.681593 ATGATATGCTGGCTCAGTCTC 57.318 47.619 4.45 0.00 33.43 3.36
5592 7058 4.434545 AAATGATATGCTGGCTCAGTCT 57.565 40.909 4.45 0.00 33.43 3.24
5593 7059 6.624352 TTAAAATGATATGCTGGCTCAGTC 57.376 37.500 4.45 0.00 33.43 3.51
5594 7060 7.408756 TTTTAAAATGATATGCTGGCTCAGT 57.591 32.000 0.00 0.00 33.43 3.41
5595 7061 8.882415 ATTTTTAAAATGATATGCTGGCTCAG 57.118 30.769 1.76 0.00 34.12 3.35
5596 7062 9.669887 AAATTTTTAAAATGATATGCTGGCTCA 57.330 25.926 3.51 0.00 0.00 4.26
5615 7081 8.429299 GCGTTTACGGTGATTTCATAAATTTTT 58.571 29.630 4.29 0.00 40.23 1.94
5616 7082 7.062488 GGCGTTTACGGTGATTTCATAAATTTT 59.938 33.333 4.29 0.00 40.23 1.82
5617 7083 6.528774 GGCGTTTACGGTGATTTCATAAATTT 59.471 34.615 4.29 0.00 40.23 1.82
5618 7084 6.031471 GGCGTTTACGGTGATTTCATAAATT 58.969 36.000 4.29 0.00 40.23 1.82
5619 7085 5.355910 AGGCGTTTACGGTGATTTCATAAAT 59.644 36.000 4.29 0.00 40.23 1.40
5620 7086 4.696402 AGGCGTTTACGGTGATTTCATAAA 59.304 37.500 4.29 0.00 40.23 1.40
5621 7087 4.255301 AGGCGTTTACGGTGATTTCATAA 58.745 39.130 4.29 0.00 40.23 1.90
5622 7088 3.864243 AGGCGTTTACGGTGATTTCATA 58.136 40.909 4.29 0.00 40.23 2.15
5623 7089 2.706890 AGGCGTTTACGGTGATTTCAT 58.293 42.857 4.29 0.00 40.23 2.57
5624 7090 2.172851 AGGCGTTTACGGTGATTTCA 57.827 45.000 4.29 0.00 40.23 2.69
5625 7091 2.473376 CGAAGGCGTTTACGGTGATTTC 60.473 50.000 4.29 0.00 40.23 2.17
5626 7092 1.461897 CGAAGGCGTTTACGGTGATTT 59.538 47.619 4.29 0.00 40.23 2.17
5627 7093 1.073177 CGAAGGCGTTTACGGTGATT 58.927 50.000 4.29 0.00 40.23 2.57
5628 7094 2.745728 CGAAGGCGTTTACGGTGAT 58.254 52.632 4.29 0.00 40.23 3.06
5629 7095 4.248402 CGAAGGCGTTTACGGTGA 57.752 55.556 4.29 0.00 40.23 4.02
5654 7120 1.187271 CAGTGAGACGAAACGTTCACG 59.813 52.381 20.50 20.50 44.20 4.35
5655 7121 2.215812 GTCAGTGAGACGAAACGTTCAC 59.784 50.000 20.16 20.16 41.37 3.18
5656 7122 2.456989 GTCAGTGAGACGAAACGTTCA 58.543 47.619 0.00 0.00 41.37 3.18
5667 7133 1.470805 CGGTGTTGTGTGTCAGTGAGA 60.471 52.381 0.00 0.00 0.00 3.27
5668 7134 0.930310 CGGTGTTGTGTGTCAGTGAG 59.070 55.000 0.00 0.00 0.00 3.51
5669 7135 0.533032 TCGGTGTTGTGTGTCAGTGA 59.467 50.000 0.00 0.00 0.00 3.41
5670 7136 1.364721 TTCGGTGTTGTGTGTCAGTG 58.635 50.000 0.00 0.00 0.00 3.66
5671 7137 2.102070 TTTCGGTGTTGTGTGTCAGT 57.898 45.000 0.00 0.00 0.00 3.41
5672 7138 3.548014 GGATTTTCGGTGTTGTGTGTCAG 60.548 47.826 0.00 0.00 0.00 3.51
5673 7139 2.356382 GGATTTTCGGTGTTGTGTGTCA 59.644 45.455 0.00 0.00 0.00 3.58
5674 7140 2.616842 AGGATTTTCGGTGTTGTGTGTC 59.383 45.455 0.00 0.00 0.00 3.67
5675 7141 2.650322 AGGATTTTCGGTGTTGTGTGT 58.350 42.857 0.00 0.00 0.00 3.72
5676 7142 4.822036 TTAGGATTTTCGGTGTTGTGTG 57.178 40.909 0.00 0.00 0.00 3.82
5677 7143 5.838531 TTTTAGGATTTTCGGTGTTGTGT 57.161 34.783 0.00 0.00 0.00 3.72
5678 7144 8.804688 TTTATTTTAGGATTTTCGGTGTTGTG 57.195 30.769 0.00 0.00 0.00 3.33
5679 7145 9.990360 AATTTATTTTAGGATTTTCGGTGTTGT 57.010 25.926 0.00 0.00 0.00 3.32
5711 7177 9.895138 GGGTTTAAGTTCTAGTGGTCATATTTA 57.105 33.333 0.00 0.00 0.00 1.40
5712 7178 8.612145 AGGGTTTAAGTTCTAGTGGTCATATTT 58.388 33.333 0.00 0.00 0.00 1.40
5713 7179 8.047310 CAGGGTTTAAGTTCTAGTGGTCATATT 58.953 37.037 0.00 0.00 0.00 1.28
5714 7180 7.402071 TCAGGGTTTAAGTTCTAGTGGTCATAT 59.598 37.037 0.00 0.00 0.00 1.78
5715 7181 6.727231 TCAGGGTTTAAGTTCTAGTGGTCATA 59.273 38.462 0.00 0.00 0.00 2.15
5716 7182 5.546499 TCAGGGTTTAAGTTCTAGTGGTCAT 59.454 40.000 0.00 0.00 0.00 3.06
5717 7183 4.903049 TCAGGGTTTAAGTTCTAGTGGTCA 59.097 41.667 0.00 0.00 0.00 4.02
5718 7184 5.479124 TCAGGGTTTAAGTTCTAGTGGTC 57.521 43.478 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.