Multiple sequence alignment - TraesCS1A01G383100

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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 TraesCS1A01G383100 chr1A 100.000 9872 0 0 1 9872 553972579 553962708 0.000000e+00 18231.0
1 TraesCS1A01G383100 chr1A 83.370 920 106 21 607 1491 553958520 553957613 0.000000e+00 808.0
2 TraesCS1A01G383100 chr1A 87.482 687 67 8 8254 8940 553957317 553956650 0.000000e+00 774.0
3 TraesCS1A01G383100 chr1A 85.227 440 53 9 1788 2219 27004531 27004966 9.100000e-120 442.0
4 TraesCS1A01G383100 chr1A 89.170 277 28 1 1790 2064 26975425 26975701 2.640000e-90 344.0
5 TraesCS1A01G383100 chr1A 86.164 159 13 6 1501 1650 27002829 27002987 7.930000e-36 163.0
6 TraesCS1A01G383100 chr1A 93.220 59 4 0 1734 1792 541449211 541449153 4.910000e-13 87.9
7 TraesCS1A01G383100 chr4B 99.552 5579 22 2 2520 8098 522305090 522299515 0.000000e+00 10161.0
8 TraesCS1A01G383100 chr4B 100.000 158 0 0 7921 8078 83028772 83028615 9.700000e-75 292.0
9 TraesCS1A01G383100 chr1B 99.408 5577 33 0 2521 8097 577191690 577197266 0.000000e+00 10117.0
10 TraesCS1A01G383100 chr1B 86.901 1565 112 40 14 1504 636740180 636738635 0.000000e+00 1668.0
11 TraesCS1A01G383100 chr1B 93.862 782 45 3 8210 8991 636738642 636737864 0.000000e+00 1175.0
12 TraesCS1A01G383100 chr1B 76.951 1935 426 17 4825 6750 28053247 28055170 0.000000e+00 1085.0
13 TraesCS1A01G383100 chr1B 82.073 926 118 32 601 1491 636727450 636726538 0.000000e+00 747.0
14 TraesCS1A01G383100 chr1B 86.402 478 41 7 1788 2244 658321811 658321337 1.480000e-137 501.0
15 TraesCS1A01G383100 chr1B 86.842 152 16 3 1507 1656 610900916 610901065 6.130000e-37 167.0
16 TraesCS1A01G383100 chr1B 91.489 47 3 1 9197 9243 636751166 636751121 8.280000e-06 63.9
17 TraesCS1A01G383100 chr5B 99.372 5577 35 0 2521 8097 703533750 703539326 0.000000e+00 10105.0
18 TraesCS1A01G383100 chr5B 83.459 133 15 4 1 132 382734468 382734594 6.260000e-22 117.0
19 TraesCS1A01G383100 chrUn 99.071 4413 26 2 3684 8096 42485227 42480830 0.000000e+00 7908.0
20 TraesCS1A01G383100 chrUn 99.473 1707 9 0 2521 4227 377611496 377609790 0.000000e+00 3103.0
21 TraesCS1A01G383100 chrUn 99.520 1457 7 0 5529 6985 398153955 398152499 0.000000e+00 2652.0
22 TraesCS1A01G383100 chrUn 90.373 1018 61 9 1505 2489 284349693 284348680 0.000000e+00 1303.0
23 TraesCS1A01G383100 chrUn 90.373 1018 61 9 1505 2489 311024094 311023081 0.000000e+00 1303.0
24 TraesCS1A01G383100 chrUn 92.982 114 8 0 8097 8210 284348695 284348582 6.130000e-37 167.0
25 TraesCS1A01G383100 chrUn 92.982 114 8 0 8097 8210 311023096 311022983 6.130000e-37 167.0
26 TraesCS1A01G383100 chr7B 99.674 3984 12 1 4013 7996 342421758 342417776 0.000000e+00 7284.0
27 TraesCS1A01G383100 chr7B 99.536 1078 5 0 2519 3596 342422846 342421769 0.000000e+00 1964.0
28 TraesCS1A01G383100 chr7B 73.584 3725 914 65 3755 7443 610827988 610824298 0.000000e+00 1363.0
29 TraesCS1A01G383100 chr7B 86.008 486 39 10 1788 2244 583374546 583374061 2.480000e-135 494.0
30 TraesCS1A01G383100 chr7B 87.719 57 7 0 4890 4946 440230581 440230637 6.400000e-07 67.6
31 TraesCS1A01G383100 chr1D 92.303 1689 70 23 8210 9872 462114611 462112957 0.000000e+00 2344.0
32 TraesCS1A01G383100 chr1D 74.391 3241 783 45 4210 7427 203362688 203365904 0.000000e+00 1343.0
33 TraesCS1A01G383100 chr1D 87.954 1046 79 18 472 1481 462116039 462115005 0.000000e+00 1190.0
34 TraesCS1A01G383100 chr1D 82.728 909 111 30 607 1480 462108326 462107429 0.000000e+00 767.0
35 TraesCS1A01G383100 chr1D 86.541 691 74 4 8254 8940 462106819 462106144 0.000000e+00 743.0
36 TraesCS1A01G383100 chr1D 85.587 562 45 13 1788 2319 439089205 439089760 3.110000e-154 556.0
37 TraesCS1A01G383100 chr1D 81.364 660 85 14 849 1480 462093304 462092655 4.120000e-138 503.0
38 TraesCS1A01G383100 chr1D 85.143 350 34 5 8447 8795 462092192 462091860 9.490000e-90 342.0
39 TraesCS1A01G383100 chr1D 88.235 153 14 4 1505 1656 445362833 445362684 7.880000e-41 180.0
40 TraesCS1A01G383100 chr1D 91.111 90 8 0 8447 8536 462081288 462081377 1.350000e-23 122.0
41 TraesCS1A01G383100 chr1D 90.000 90 9 0 8447 8536 462081931 462081842 6.260000e-22 117.0
42 TraesCS1A01G383100 chr3B 93.679 1408 85 4 5478 6884 72197745 72199149 0.000000e+00 2104.0
43 TraesCS1A01G383100 chr3B 92.273 440 31 3 6929 7366 72221311 72221749 1.090000e-173 621.0
44 TraesCS1A01G383100 chr3B 84.711 242 16 5 2029 2253 284568055 284567818 1.290000e-53 222.0
45 TraesCS1A01G383100 chr3B 88.608 79 6 2 2413 2489 284567106 284567029 1.060000e-14 93.5
46 TraesCS1A01G383100 chr3A 73.980 3724 886 74 3748 7431 626678402 626674722 0.000000e+00 1432.0
47 TraesCS1A01G383100 chr2A 90.564 1028 61 11 1495 2489 47922608 47921584 0.000000e+00 1328.0
48 TraesCS1A01G383100 chr2A 96.296 297 11 0 7799 8095 78462775 78462479 1.150000e-133 488.0
49 TraesCS1A01G383100 chr2A 83.333 270 36 6 1001 1267 24397403 24397140 3.560000e-59 241.0
50 TraesCS1A01G383100 chr2A 90.598 117 8 2 8097 8213 47921599 47921486 1.720000e-32 152.0
51 TraesCS1A01G383100 chr2A 80.233 172 33 1 54 225 36803954 36804124 2.890000e-25 128.0
52 TraesCS1A01G383100 chr6B 95.031 805 40 0 6486 7290 683819809 683820613 0.000000e+00 1266.0
53 TraesCS1A01G383100 chr6B 95.245 736 31 3 7361 8094 683823354 683824087 0.000000e+00 1162.0
54 TraesCS1A01G383100 chr2D 90.244 861 57 11 1505 2341 433685562 433684705 0.000000e+00 1099.0
55 TraesCS1A01G383100 chr2D 77.799 527 99 12 8270 8793 22789843 22789332 9.630000e-80 309.0
56 TraesCS1A01G383100 chr2D 89.686 223 20 1 3473 3692 343533420 343533198 2.100000e-71 281.0
57 TraesCS1A01G383100 chr2D 94.631 149 5 1 2330 2475 433683301 433683153 2.770000e-55 228.0
58 TraesCS1A01G383100 chr2D 79.853 273 47 5 999 1267 22790457 22790189 1.010000e-44 193.0
59 TraesCS1A01G383100 chr2D 98.000 50 1 0 2426 2475 433683094 433683045 4.910000e-13 87.9
60 TraesCS1A01G383100 chr3D 95.238 525 10 3 6921 7443 566941634 566942145 0.000000e+00 817.0
61 TraesCS1A01G383100 chr3D 96.755 493 10 2 7488 7976 566942145 566942635 0.000000e+00 817.0
62 TraesCS1A01G383100 chr3D 79.824 1021 186 13 2524 3531 603625557 603624544 0.000000e+00 726.0
63 TraesCS1A01G383100 chr3D 78.524 908 174 15 3746 4646 603624224 603623331 2.390000e-160 577.0
64 TraesCS1A01G383100 chr3D 97.674 43 1 0 1733 1775 56280069 56280027 3.820000e-09 75.0
65 TraesCS1A01G383100 chr3D 97.674 43 1 0 1733 1775 56289696 56289654 3.820000e-09 75.0
66 TraesCS1A01G383100 chr3D 97.674 43 1 0 1733 1775 56291334 56291292 3.820000e-09 75.0
67 TraesCS1A01G383100 chr5A 80.343 992 182 9 2537 3522 599395863 599396847 0.000000e+00 739.0
68 TraesCS1A01G383100 chr5A 79.134 1016 194 13 2524 3531 291744447 291743442 0.000000e+00 686.0
69 TraesCS1A01G383100 chr5A 80.147 816 151 10 3748 4559 599397178 599397986 5.100000e-167 599.0
70 TraesCS1A01G383100 chr5A 83.616 177 27 2 7675 7850 539955412 539955587 2.210000e-36 165.0
71 TraesCS1A01G383100 chr5A 80.930 215 29 11 1 210 621020139 621020346 1.030000e-34 159.0
72 TraesCS1A01G383100 chr5D 79.980 1009 185 13 2524 3522 513363190 513364191 0.000000e+00 728.0
73 TraesCS1A01G383100 chr5D 84.568 486 40 9 1788 2245 394086695 394086217 5.440000e-122 449.0
74 TraesCS1A01G383100 chr5D 77.512 209 33 13 1 206 329608610 329608807 8.100000e-21 113.0
75 TraesCS1A01G383100 chr2B 85.504 476 45 7 1788 2243 138024031 138023560 8.970000e-130 475.0
76 TraesCS1A01G383100 chr2B 84.697 379 22 9 1959 2321 750109806 750110164 7.340000e-91 346.0
77 TraesCS1A01G383100 chr2B 77.288 590 128 6 8267 8853 39156845 39157431 9.490000e-90 342.0
78 TraesCS1A01G383100 chr2B 80.370 270 44 7 1001 1267 39156256 39156519 7.820000e-46 196.0
79 TraesCS1A01G383100 chr2B 96.552 58 2 0 1730 1787 750108893 750108950 8.160000e-16 97.1
80 TraesCS1A01G383100 chr7A 96.441 281 9 1 7817 8096 721702905 721702625 6.990000e-126 462.0
81 TraesCS1A01G383100 chr7A 80.899 178 26 8 4 178 132286493 132286321 6.220000e-27 134.0
82 TraesCS1A01G383100 chr7A 81.560 141 21 5 3 140 335188285 335188423 2.910000e-20 111.0
83 TraesCS1A01G383100 chr4A 92.105 152 12 0 1505 1656 579061907 579061756 2.160000e-51 215.0
84 TraesCS1A01G383100 chr4D 80.214 187 23 11 1 178 12693911 12694092 2.890000e-25 128.0
85 TraesCS1A01G383100 chr6A 81.410 156 21 7 1 153 85539758 85539908 4.840000e-23 121.0
86 TraesCS1A01G383100 chr6D 77.533 227 31 16 1 218 67958450 67958665 1.740000e-22 119.0


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 TraesCS1A01G383100 chr1A 553962708 553972579 9871 True 18231.000000 18231 100.000000 1 9872 1 chr1A.!!$R2 9871
1 TraesCS1A01G383100 chr1A 553956650 553958520 1870 True 791.000000 808 85.426000 607 8940 2 chr1A.!!$R3 8333
2 TraesCS1A01G383100 chr1A 27002829 27004966 2137 False 302.500000 442 85.695500 1501 2219 2 chr1A.!!$F2 718
3 TraesCS1A01G383100 chr4B 522299515 522305090 5575 True 10161.000000 10161 99.552000 2520 8098 1 chr4B.!!$R2 5578
4 TraesCS1A01G383100 chr1B 577191690 577197266 5576 False 10117.000000 10117 99.408000 2521 8097 1 chr1B.!!$F2 5576
5 TraesCS1A01G383100 chr1B 636737864 636740180 2316 True 1421.500000 1668 90.381500 14 8991 2 chr1B.!!$R4 8977
6 TraesCS1A01G383100 chr1B 28053247 28055170 1923 False 1085.000000 1085 76.951000 4825 6750 1 chr1B.!!$F1 1925
7 TraesCS1A01G383100 chr1B 636726538 636727450 912 True 747.000000 747 82.073000 601 1491 1 chr1B.!!$R1 890
8 TraesCS1A01G383100 chr5B 703533750 703539326 5576 False 10105.000000 10105 99.372000 2521 8097 1 chr5B.!!$F2 5576
9 TraesCS1A01G383100 chrUn 42480830 42485227 4397 True 7908.000000 7908 99.071000 3684 8096 1 chrUn.!!$R1 4412
10 TraesCS1A01G383100 chrUn 377609790 377611496 1706 True 3103.000000 3103 99.473000 2521 4227 1 chrUn.!!$R2 1706
11 TraesCS1A01G383100 chrUn 398152499 398153955 1456 True 2652.000000 2652 99.520000 5529 6985 1 chrUn.!!$R3 1456
12 TraesCS1A01G383100 chrUn 284348582 284349693 1111 True 735.000000 1303 91.677500 1505 8210 2 chrUn.!!$R4 6705
13 TraesCS1A01G383100 chrUn 311022983 311024094 1111 True 735.000000 1303 91.677500 1505 8210 2 chrUn.!!$R5 6705
14 TraesCS1A01G383100 chr7B 342417776 342422846 5070 True 4624.000000 7284 99.605000 2519 7996 2 chr7B.!!$R3 5477
15 TraesCS1A01G383100 chr7B 610824298 610827988 3690 True 1363.000000 1363 73.584000 3755 7443 1 chr7B.!!$R2 3688
16 TraesCS1A01G383100 chr1D 462112957 462116039 3082 True 1767.000000 2344 90.128500 472 9872 2 chr1D.!!$R5 9400
17 TraesCS1A01G383100 chr1D 203362688 203365904 3216 False 1343.000000 1343 74.391000 4210 7427 1 chr1D.!!$F1 3217
18 TraesCS1A01G383100 chr1D 462106144 462108326 2182 True 755.000000 767 84.634500 607 8940 2 chr1D.!!$R4 8333
19 TraesCS1A01G383100 chr1D 439089205 439089760 555 False 556.000000 556 85.587000 1788 2319 1 chr1D.!!$F2 531
20 TraesCS1A01G383100 chr1D 462091860 462093304 1444 True 422.500000 503 83.253500 849 8795 2 chr1D.!!$R3 7946
21 TraesCS1A01G383100 chr3B 72197745 72199149 1404 False 2104.000000 2104 93.679000 5478 6884 1 chr3B.!!$F1 1406
22 TraesCS1A01G383100 chr3A 626674722 626678402 3680 True 1432.000000 1432 73.980000 3748 7431 1 chr3A.!!$R1 3683
23 TraesCS1A01G383100 chr2A 47921486 47922608 1122 True 740.000000 1328 90.581000 1495 8213 2 chr2A.!!$R3 6718
24 TraesCS1A01G383100 chr6B 683819809 683824087 4278 False 1214.000000 1266 95.138000 6486 8094 2 chr6B.!!$F1 1608
25 TraesCS1A01G383100 chr2D 433683045 433685562 2517 True 471.633333 1099 94.291667 1505 2475 3 chr2D.!!$R3 970
26 TraesCS1A01G383100 chr2D 22789332 22790457 1125 True 251.000000 309 78.826000 999 8793 2 chr2D.!!$R2 7794
27 TraesCS1A01G383100 chr3D 566941634 566942635 1001 False 817.000000 817 95.996500 6921 7976 2 chr3D.!!$F1 1055
28 TraesCS1A01G383100 chr3D 603623331 603625557 2226 True 651.500000 726 79.174000 2524 4646 2 chr3D.!!$R3 2122
29 TraesCS1A01G383100 chr5A 291743442 291744447 1005 True 686.000000 686 79.134000 2524 3531 1 chr5A.!!$R1 1007
30 TraesCS1A01G383100 chr5A 599395863 599397986 2123 False 669.000000 739 80.245000 2537 4559 2 chr5A.!!$F3 2022
31 TraesCS1A01G383100 chr5D 513363190 513364191 1001 False 728.000000 728 79.980000 2524 3522 1 chr5D.!!$F2 998
32 TraesCS1A01G383100 chr2B 39156256 39157431 1175 False 269.000000 342 78.829000 1001 8853 2 chr2B.!!$F1 7852
33 TraesCS1A01G383100 chr2B 750108893 750110164 1271 False 221.550000 346 90.624500 1730 2321 2 chr2B.!!$F2 591

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
402 440 0.035056 CTGGAGGTGGGTCATGTTCC 60.035 60.000 0.00 0.0 0.00 3.62 F
1182 1247 1.078143 GGAGAGGGTGCATCGCTTT 60.078 57.895 0.00 0.0 39.46 3.51 F
2440 6356 0.108207 ATGCTATGGGCTGAGACTGC 59.892 55.000 0.00 0.0 42.39 4.40 F
2504 6420 0.403271 AGGCAGAGCTCCAAACACAT 59.597 50.000 10.93 0.0 0.00 3.21 F
2505 6421 0.807496 GGCAGAGCTCCAAACACATC 59.193 55.000 10.93 0.0 0.00 3.06 F
2876 6802 0.942410 GGTAAGCTGAACACGACGCA 60.942 55.000 0.00 0.0 0.00 5.24 F
5468 9508 4.085357 TGCATCGAAGGTATTGGCTAAT 57.915 40.909 0.00 0.0 0.00 1.73 F
6167 10210 1.378250 CTTGGGCCTGCCTTCTGAG 60.378 63.158 4.53 0.0 36.10 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1715 2204 0.250727 GCACTTCACCCTTGCCTACA 60.251 55.000 0.00 0.0 0.00 2.74 R
2516 6432 0.106116 AAGCGAGAGGGTAGGTAGGG 60.106 60.000 0.00 0.0 0.00 3.53 R
4752 8790 1.142688 ACTGATCCAAAGGTGGCCCT 61.143 55.000 0.00 0.0 45.54 5.19 R
4968 9007 2.668185 TTTCGGGCACTCGCTTTCCA 62.668 55.000 0.00 0.0 38.60 3.53 R
5468 9508 1.066143 GGGAGAATGAGTTTGAGCCGA 60.066 52.381 0.00 0.0 0.00 5.54 R
6167 10210 1.376037 CTCCTTCGTTCTGCCCACC 60.376 63.158 0.00 0.0 0.00 4.61 R
8105 14829 0.328258 GCTCTTGACCCCAGCCTAAA 59.672 55.000 0.00 0.0 0.00 1.85 R
9251 16002 0.179100 AGTGATGTGATCGGCGAAGG 60.179 55.000 15.93 0.0 0.00 3.46 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
76 83 6.356417 CACGAAAAATGTACAACGTGTATGA 58.644 36.000 22.07 0.00 43.47 2.15
79 86 8.710551 ACGAAAAATGTACAACGTGTATGAATA 58.289 29.630 0.00 0.00 35.05 1.75
182 190 8.708742 GTTCCTAATGTGTAAGAAAAATTTGCC 58.291 33.333 0.00 0.00 0.00 4.52
186 194 5.921004 TGTGTAAGAAAAATTTGCCATGC 57.079 34.783 0.00 0.00 0.00 4.06
187 195 4.754114 TGTGTAAGAAAAATTTGCCATGCC 59.246 37.500 0.00 0.00 0.00 4.40
211 219 7.698130 GCCTATGAAAAATGTAGACATGTGTTC 59.302 37.037 1.15 0.00 36.56 3.18
216 224 9.645059 TGAAAAATGTAGACATGTGTTCAAAAA 57.355 25.926 1.15 0.00 36.56 1.94
218 226 9.868277 AAAAATGTAGACATGTGTTCAAAAAGA 57.132 25.926 1.15 0.00 36.56 2.52
219 227 9.520204 AAAATGTAGACATGTGTTCAAAAAGAG 57.480 29.630 1.15 0.00 36.56 2.85
220 228 8.450578 AATGTAGACATGTGTTCAAAAAGAGA 57.549 30.769 1.15 0.00 36.56 3.10
225 233 8.466086 AGACATGTGTTCAAAAAGAGAAAAAC 57.534 30.769 1.15 0.00 0.00 2.43
227 235 9.567848 GACATGTGTTCAAAAAGAGAAAAACTA 57.432 29.630 1.15 0.00 0.00 2.24
266 295 7.590279 ACGAGAAAGAAACAAAGAAAACAAGA 58.410 30.769 0.00 0.00 0.00 3.02
267 296 8.244113 ACGAGAAAGAAACAAAGAAAACAAGAT 58.756 29.630 0.00 0.00 0.00 2.40
269 298 9.573133 GAGAAAGAAACAAAGAAAACAAGATGA 57.427 29.630 0.00 0.00 0.00 2.92
270 299 9.927668 AGAAAGAAACAAAGAAAACAAGATGAA 57.072 25.926 0.00 0.00 0.00 2.57
277 306 8.917415 ACAAAGAAAACAAGATGAAAGAGAAC 57.083 30.769 0.00 0.00 0.00 3.01
284 317 7.761651 AACAAGATGAAAGAGAACAAAAAGC 57.238 32.000 0.00 0.00 0.00 3.51
288 321 7.105241 AGATGAAAGAGAACAAAAAGCAACT 57.895 32.000 0.00 0.00 0.00 3.16
319 352 5.870706 ACAAAGAAAAACCAAAGGAAACCA 58.129 33.333 0.00 0.00 0.00 3.67
343 376 4.453819 TGCAAAACAGTGGAAACCAAAAAG 59.546 37.500 0.00 0.00 34.18 2.27
346 384 5.738619 AAACAGTGGAAACCAAAAAGACT 57.261 34.783 0.00 0.00 34.18 3.24
351 389 2.955660 TGGAAACCAAAAAGACTGCGAT 59.044 40.909 0.00 0.00 0.00 4.58
353 391 4.580995 TGGAAACCAAAAAGACTGCGATAA 59.419 37.500 0.00 0.00 0.00 1.75
357 395 7.810759 GGAAACCAAAAAGACTGCGATAAATAA 59.189 33.333 0.00 0.00 0.00 1.40
362 400 7.905493 CCAAAAAGACTGCGATAAATAACTCTC 59.095 37.037 0.00 0.00 0.00 3.20
370 408 4.692135 CGATAAATAACTCTCGCATGCAC 58.308 43.478 19.57 0.00 0.00 4.57
372 410 5.611197 CGATAAATAACTCTCGCATGCACAG 60.611 44.000 19.57 12.80 0.00 3.66
378 416 4.377708 TCGCATGCACAGGACGCT 62.378 61.111 19.57 0.00 0.00 5.07
379 417 4.156622 CGCATGCACAGGACGCTG 62.157 66.667 19.57 0.00 0.00 5.18
380 418 3.807538 GCATGCACAGGACGCTGG 61.808 66.667 14.21 0.00 0.00 4.85
381 419 2.046988 CATGCACAGGACGCTGGA 60.047 61.111 0.00 0.00 0.00 3.86
382 420 1.672030 CATGCACAGGACGCTGGAA 60.672 57.895 0.00 0.00 0.00 3.53
383 421 1.672356 ATGCACAGGACGCTGGAAC 60.672 57.895 0.00 0.00 0.00 3.62
384 422 2.031163 GCACAGGACGCTGGAACT 59.969 61.111 0.00 0.00 0.00 3.01
385 423 2.320587 GCACAGGACGCTGGAACTG 61.321 63.158 0.00 0.00 37.01 3.16
386 424 1.669115 CACAGGACGCTGGAACTGG 60.669 63.158 0.00 0.00 35.34 4.00
387 425 1.837051 ACAGGACGCTGGAACTGGA 60.837 57.895 0.00 0.00 35.34 3.86
388 426 1.079543 CAGGACGCTGGAACTGGAG 60.080 63.158 0.00 0.00 0.00 3.86
389 427 2.266055 GGACGCTGGAACTGGAGG 59.734 66.667 0.00 0.00 0.00 4.30
402 440 0.035056 CTGGAGGTGGGTCATGTTCC 60.035 60.000 0.00 0.00 0.00 3.62
435 474 8.661352 AAAAGTGACTGGTCCAAATAAAAATG 57.339 30.769 0.00 0.00 0.00 2.32
439 478 6.863126 GTGACTGGTCCAAATAAAAATGTCAG 59.137 38.462 5.34 0.00 32.51 3.51
448 487 2.399396 AAAAATGTCAGGCAACGACG 57.601 45.000 0.00 0.00 41.13 5.12
455 494 2.030096 TGTCAGGCAACGACGTACATTA 60.030 45.455 0.00 0.00 41.13 1.90
459 498 3.000078 CAGGCAACGACGTACATTATGTC 60.000 47.826 0.00 0.00 46.39 3.06
468 507 5.445407 CGACGTACATTATGTCCCAACAAAG 60.445 44.000 0.00 0.00 40.72 2.77
522 561 6.150318 CAGTAACGCGTAGGAAATCATCTAT 58.850 40.000 14.46 0.00 0.00 1.98
524 563 7.169308 CAGTAACGCGTAGGAAATCATCTATTT 59.831 37.037 14.46 0.00 40.59 1.40
594 634 5.551233 AGAGAAAATCGAGTCAATGAACCA 58.449 37.500 0.00 0.00 0.00 3.67
652 710 3.491598 AAGGCGACAAGGTGGTGGG 62.492 63.158 0.00 0.00 0.00 4.61
841 901 3.620428 CTACGTGCATCGCCAGCG 61.620 66.667 5.50 5.50 44.19 5.18
921 983 1.895020 AAAGACATGTCCCCGCGCTA 61.895 55.000 22.21 0.00 0.00 4.26
924 986 2.108976 CATGTCCCCGCGCTACAT 59.891 61.111 5.56 7.00 34.22 2.29
943 1005 4.300803 ACATCGGCGAACGCTATATAAAA 58.699 39.130 15.93 0.00 43.86 1.52
961 1023 4.829064 AAAAACGTCTACACATGCATGT 57.171 36.364 26.61 26.61 42.84 3.21
996 1058 2.608752 GGTGTGTGTAGATCGTTCGGTT 60.609 50.000 0.00 0.00 0.00 4.44
997 1059 2.660236 GTGTGTGTAGATCGTTCGGTTC 59.340 50.000 0.00 0.00 0.00 3.62
1133 1198 2.665185 GTTCCGCGAGTGGCAAGT 60.665 61.111 8.23 0.00 43.84 3.16
1171 1236 2.363018 TGAGCACGGAGGAGAGGG 60.363 66.667 0.00 0.00 0.00 4.30
1175 1240 2.997315 CACGGAGGAGAGGGTGCA 60.997 66.667 0.00 0.00 0.00 4.57
1182 1247 1.078143 GGAGAGGGTGCATCGCTTT 60.078 57.895 0.00 0.00 39.46 3.51
1215 1280 2.477357 CGACAACGTGGAGTACATCGAT 60.477 50.000 0.00 0.00 35.12 3.59
1302 1400 1.811679 GTCCTACGAAGCTGCCAGC 60.812 63.158 9.13 9.13 42.84 4.85
1320 1418 1.618837 AGCGATGATACGGGCATTACT 59.381 47.619 0.00 0.00 0.00 2.24
1356 1454 4.357947 GACGCCGAGCTGTGGTCA 62.358 66.667 0.00 0.00 0.00 4.02
1364 1462 4.760047 GCTGTGGTCATCCGGCGT 62.760 66.667 6.01 0.00 36.30 5.68
1366 1464 3.295304 CTGTGGTCATCCGGCGTCA 62.295 63.158 6.01 0.00 36.30 4.35
1549 2035 1.228831 CTGGGGTCAACCAATGCCA 60.229 57.895 0.89 0.00 40.68 4.92
1621 2107 3.712016 AAACCCAAAAATATGCCCACC 57.288 42.857 0.00 0.00 0.00 4.61
1628 2114 5.163216 CCCAAAAATATGCCCACCATAACAT 60.163 40.000 0.00 0.00 39.71 2.71
1639 2127 8.862325 TGCCCACCATAACATAATAGAAATAG 57.138 34.615 0.00 0.00 0.00 1.73
1715 2204 2.205152 ACGGTGTTACAGTCCGCCT 61.205 57.895 13.20 0.00 46.92 5.52
1732 2221 0.693049 CCTGTAGGCAAGGGTGAAGT 59.307 55.000 0.00 0.00 0.00 3.01
1825 3848 5.733620 ATTTGATGTGTGATCTTGCCTTT 57.266 34.783 0.00 0.00 0.00 3.11
1829 3852 2.229792 TGTGTGATCTTGCCTTTGTCC 58.770 47.619 0.00 0.00 0.00 4.02
1837 3860 0.396974 TTGCCTTTGTCCAACTGGCT 60.397 50.000 18.14 0.00 39.44 4.75
1994 4446 0.393132 TGTTGGTGCGTGAGACCAAA 60.393 50.000 7.13 0.00 45.73 3.28
2004 4456 3.064820 GCGTGAGACCAAAAGAAACTGAA 59.935 43.478 0.00 0.00 0.00 3.02
2012 4464 9.452065 GAGACCAAAAGAAACTGAAAAAGATAC 57.548 33.333 0.00 0.00 0.00 2.24
2143 4634 0.953960 GGGATCGCCTTGTTTGTCGT 60.954 55.000 0.00 0.00 0.00 4.34
2197 4688 1.688311 GGGTGGGGAAAAGAATAGGCC 60.688 57.143 0.00 0.00 0.00 5.19
2382 6295 1.003355 GCCTTGTGTGCTGGAGCTA 60.003 57.895 0.00 0.00 42.66 3.32
2440 6356 0.108207 ATGCTATGGGCTGAGACTGC 59.892 55.000 0.00 0.00 42.39 4.40
2501 6417 2.949177 TTTAGGCAGAGCTCCAAACA 57.051 45.000 10.93 0.00 0.00 2.83
2502 6418 2.185004 TTAGGCAGAGCTCCAAACAC 57.815 50.000 10.93 0.00 0.00 3.32
2503 6419 1.055849 TAGGCAGAGCTCCAAACACA 58.944 50.000 10.93 0.00 0.00 3.72
2504 6420 0.403271 AGGCAGAGCTCCAAACACAT 59.597 50.000 10.93 0.00 0.00 3.21
2505 6421 0.807496 GGCAGAGCTCCAAACACATC 59.193 55.000 10.93 0.00 0.00 3.06
2506 6422 1.612726 GGCAGAGCTCCAAACACATCT 60.613 52.381 10.93 0.00 0.00 2.90
2507 6423 1.467734 GCAGAGCTCCAAACACATCTG 59.532 52.381 10.93 0.00 37.74 2.90
2508 6424 2.082231 CAGAGCTCCAAACACATCTGG 58.918 52.381 10.93 0.00 32.44 3.86
2509 6425 1.980765 AGAGCTCCAAACACATCTGGA 59.019 47.619 10.93 0.00 39.47 3.86
2510 6426 2.373169 AGAGCTCCAAACACATCTGGAA 59.627 45.455 10.93 0.00 41.20 3.53
2511 6427 3.009916 AGAGCTCCAAACACATCTGGAAT 59.990 43.478 10.93 0.00 41.20 3.01
2512 6428 3.350833 AGCTCCAAACACATCTGGAATC 58.649 45.455 0.00 0.00 41.20 2.52
2513 6429 3.009916 AGCTCCAAACACATCTGGAATCT 59.990 43.478 0.00 0.00 41.20 2.40
2514 6430 4.225942 AGCTCCAAACACATCTGGAATCTA 59.774 41.667 0.00 0.00 41.20 1.98
2515 6431 5.104193 AGCTCCAAACACATCTGGAATCTAT 60.104 40.000 0.00 0.00 41.20 1.98
2516 6432 5.238214 GCTCCAAACACATCTGGAATCTATC 59.762 44.000 0.00 0.00 41.20 2.08
2657 6576 2.821366 GCTGTGATCGGGTGGCTG 60.821 66.667 0.00 0.00 0.00 4.85
2876 6802 0.942410 GGTAAGCTGAACACGACGCA 60.942 55.000 0.00 0.00 0.00 5.24
3900 7934 9.533253 CAATGAAAATCTTAAGTTGGAACTGTT 57.467 29.630 1.63 0.00 39.66 3.16
4752 8790 4.349503 ACTTGCAGCGATGGGGCA 62.350 61.111 1.46 0.00 35.41 5.36
5468 9508 4.085357 TGCATCGAAGGTATTGGCTAAT 57.915 40.909 0.00 0.00 0.00 1.73
6167 10210 1.378250 CTTGGGCCTGCCTTCTGAG 60.378 63.158 4.53 0.00 36.10 3.35
7588 14304 1.923395 CAGTTCCCACAGGCCCCTA 60.923 63.158 0.00 0.00 0.00 3.53
8136 14860 2.229784 GGTCAAGAGCAACTTTGATGGG 59.770 50.000 0.00 0.00 36.61 4.00
8204 14928 4.017808 AGTGTCCATACTAGAGCTTCGTT 58.982 43.478 0.00 0.00 0.00 3.85
8210 14934 4.498345 CCATACTAGAGCTTCGTTCCTGAC 60.498 50.000 0.00 0.00 0.00 3.51
8212 14936 3.158676 ACTAGAGCTTCGTTCCTGACTT 58.841 45.455 0.00 0.00 0.00 3.01
8213 14937 3.574826 ACTAGAGCTTCGTTCCTGACTTT 59.425 43.478 0.00 0.00 0.00 2.66
8214 14938 4.765856 ACTAGAGCTTCGTTCCTGACTTTA 59.234 41.667 0.00 0.00 0.00 1.85
8215 14939 3.915536 AGAGCTTCGTTCCTGACTTTAC 58.084 45.455 0.00 0.00 0.00 2.01
8216 14940 2.994578 GAGCTTCGTTCCTGACTTTACC 59.005 50.000 0.00 0.00 0.00 2.85
8217 14941 2.633481 AGCTTCGTTCCTGACTTTACCT 59.367 45.455 0.00 0.00 0.00 3.08
8218 14942 3.071167 AGCTTCGTTCCTGACTTTACCTT 59.929 43.478 0.00 0.00 0.00 3.50
8219 14943 3.186613 GCTTCGTTCCTGACTTTACCTTG 59.813 47.826 0.00 0.00 0.00 3.61
8220 14944 4.377897 CTTCGTTCCTGACTTTACCTTGT 58.622 43.478 0.00 0.00 0.00 3.16
8221 14945 4.411256 TCGTTCCTGACTTTACCTTGTT 57.589 40.909 0.00 0.00 0.00 2.83
8222 14946 5.534207 TCGTTCCTGACTTTACCTTGTTA 57.466 39.130 0.00 0.00 0.00 2.41
8223 14947 6.105397 TCGTTCCTGACTTTACCTTGTTAT 57.895 37.500 0.00 0.00 0.00 1.89
8226 14950 7.599998 TCGTTCCTGACTTTACCTTGTTATAAC 59.400 37.037 8.75 8.75 0.00 1.89
8235 14959 8.036575 ACTTTACCTTGTTATAACTATGCACGA 58.963 33.333 16.33 0.00 0.00 4.35
8347 15071 1.306141 ATCAGGACGGGGAAGCTGA 60.306 57.895 0.00 0.00 0.00 4.26
8352 15076 3.011517 ACGGGGAAGCTGATGCCT 61.012 61.111 0.00 0.00 40.80 4.75
8647 15371 0.729116 CGGCATGCAGTTCTACAAGG 59.271 55.000 21.36 0.00 0.00 3.61
8706 15430 4.430765 GCCGTCACCATCGTCGGT 62.431 66.667 0.00 0.00 44.07 4.69
8799 15529 2.588877 GGCTACATCCGCATGCGT 60.589 61.111 35.55 21.36 37.81 5.24
8943 15677 1.889573 GCTCGCCTACTGGGATTGC 60.890 63.158 0.00 0.00 37.23 3.56
8954 15688 0.038166 TGGGATTGCTTCAGGACCAC 59.962 55.000 0.00 0.00 0.00 4.16
9025 15760 9.494271 GCAATAACACTATCCATCTAATGAAGA 57.506 33.333 0.00 0.00 39.02 2.87
9104 15855 4.748600 GGGACTACATACGGAGCAAAATAC 59.251 45.833 0.00 0.00 0.00 1.89
9107 15858 6.135290 ACTACATACGGAGCAAAATACGTA 57.865 37.500 0.00 0.00 44.51 3.57
9118 15869 7.201496 CGGAGCAAAATACGTAAATCTACACTT 60.201 37.037 0.00 0.00 0.00 3.16
9243 15994 8.562892 CAACTTTGATGGTTATAGCCTTAGATG 58.437 37.037 7.19 0.00 0.00 2.90
9244 15995 7.227156 ACTTTGATGGTTATAGCCTTAGATGG 58.773 38.462 7.19 0.00 0.00 3.51
9247 15998 7.865530 TGATGGTTATAGCCTTAGATGGTTA 57.134 36.000 7.19 0.00 0.00 2.85
9249 16000 9.555411 TGATGGTTATAGCCTTAGATGGTTATA 57.445 33.333 7.19 0.00 35.57 0.98
9252 16003 8.989131 TGGTTATAGCCTTAGATGGTTATATCC 58.011 37.037 7.19 13.14 41.24 2.59
9253 16004 9.214962 GGTTATAGCCTTAGATGGTTATATCCT 57.785 37.037 12.92 0.00 39.68 3.24
9256 16007 6.287589 AGCCTTAGATGGTTATATCCTTCG 57.712 41.667 9.10 0.00 36.94 3.79
9259 16010 3.594603 AGATGGTTATATCCTTCGCCG 57.405 47.619 9.10 0.00 36.94 6.46
9260 16011 3.162666 AGATGGTTATATCCTTCGCCGA 58.837 45.455 9.10 0.00 36.94 5.54
9262 16013 3.587797 TGGTTATATCCTTCGCCGATC 57.412 47.619 1.59 0.00 0.00 3.69
9263 16014 2.894765 TGGTTATATCCTTCGCCGATCA 59.105 45.455 1.59 0.00 0.00 2.92
9264 16015 3.251571 GGTTATATCCTTCGCCGATCAC 58.748 50.000 0.00 0.00 0.00 3.06
9265 16016 3.305813 GGTTATATCCTTCGCCGATCACA 60.306 47.826 0.00 0.00 0.00 3.58
9266 16017 4.495422 GTTATATCCTTCGCCGATCACAT 58.505 43.478 0.00 0.00 0.00 3.21
9267 16018 2.724977 TATCCTTCGCCGATCACATC 57.275 50.000 0.00 0.00 0.00 3.06
9268 16019 0.752658 ATCCTTCGCCGATCACATCA 59.247 50.000 0.00 0.00 0.00 3.07
9269 16020 0.179111 TCCTTCGCCGATCACATCAC 60.179 55.000 0.00 0.00 0.00 3.06
9270 16021 0.179100 CCTTCGCCGATCACATCACT 60.179 55.000 0.00 0.00 0.00 3.41
9271 16022 1.203928 CTTCGCCGATCACATCACTC 58.796 55.000 0.00 0.00 0.00 3.51
9272 16023 0.179111 TTCGCCGATCACATCACTCC 60.179 55.000 0.00 0.00 0.00 3.85
9273 16024 1.141665 CGCCGATCACATCACTCCA 59.858 57.895 0.00 0.00 0.00 3.86
9274 16025 0.249615 CGCCGATCACATCACTCCAT 60.250 55.000 0.00 0.00 0.00 3.41
9275 16026 1.224075 GCCGATCACATCACTCCATG 58.776 55.000 0.00 0.00 0.00 3.66
9276 16027 1.224075 CCGATCACATCACTCCATGC 58.776 55.000 0.00 0.00 0.00 4.06
9277 16028 1.473788 CCGATCACATCACTCCATGCA 60.474 52.381 0.00 0.00 0.00 3.96
9278 16029 2.282407 CGATCACATCACTCCATGCAA 58.718 47.619 0.00 0.00 0.00 4.08
9279 16030 2.679336 CGATCACATCACTCCATGCAAA 59.321 45.455 0.00 0.00 0.00 3.68
9280 16031 3.127376 CGATCACATCACTCCATGCAAAA 59.873 43.478 0.00 0.00 0.00 2.44
9281 16032 4.379708 CGATCACATCACTCCATGCAAAAA 60.380 41.667 0.00 0.00 0.00 1.94
9306 16057 2.612212 ACACGTGTAAGAGGCAAACAAG 59.388 45.455 21.98 0.00 0.00 3.16
9316 16067 1.299089 GCAAACAAGCCACCACGTC 60.299 57.895 0.00 0.00 0.00 4.34
9322 16073 2.439960 AAGCCACCACGTCACTCCA 61.440 57.895 0.00 0.00 0.00 3.86
9333 16084 2.832129 ACGTCACTCCACCTTCACATAT 59.168 45.455 0.00 0.00 0.00 1.78
9334 16085 3.190079 CGTCACTCCACCTTCACATATG 58.810 50.000 0.00 0.00 0.00 1.78
9378 16136 8.725148 GCCGATCTTGTTGATAATAATTGAGAT 58.275 33.333 0.00 0.00 35.14 2.75
9447 16205 4.570369 TCCACTAATGACACGTGCAATATG 59.430 41.667 17.22 11.31 0.00 1.78
9486 16244 7.806960 ACACTCATCTAAAACTAGACAACGTAC 59.193 37.037 0.00 0.00 0.00 3.67
9511 16269 7.873505 ACACACTAGAAAGAGAAAAGACATACC 59.126 37.037 0.00 0.00 0.00 2.73
9546 16305 1.259609 TTTTTGAGATGGGCAGCCAG 58.740 50.000 15.19 0.00 0.00 4.85
9606 16365 7.290110 TGGACACATATCGAAAGTAGATCAT 57.710 36.000 0.00 0.00 0.00 2.45
9615 16374 9.847706 ATATCGAAAGTAGATCATGTACACATC 57.152 33.333 0.00 2.94 33.61 3.06
9650 16410 8.627208 AAGAAAACTTATGAGCAGATCTTTCA 57.373 30.769 8.68 8.68 0.00 2.69
9695 16455 4.807834 GGCGAACCTACAAGGAAATACTAC 59.192 45.833 0.00 0.00 37.67 2.73
9697 16457 5.870978 GCGAACCTACAAGGAAATACTACAA 59.129 40.000 0.00 0.00 37.67 2.41
9720 16480 4.965200 AGAAAGTGTAGCCTCAGTTCTT 57.035 40.909 0.38 0.00 31.58 2.52
9724 16484 2.829120 AGTGTAGCCTCAGTTCTTCCTC 59.171 50.000 0.00 0.00 0.00 3.71
9774 16534 0.392706 ATTATGCCGCCGAGACATGA 59.607 50.000 0.00 0.00 0.00 3.07
9816 16576 0.036732 ACGCTTCAAGGATGGCTTGA 59.963 50.000 0.00 0.00 38.83 3.02
9852 16613 1.265236 TGGATGGGTACGTTTACGGT 58.735 50.000 7.24 0.00 44.95 4.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 9.549509 GTACATTTTTCGTGCATATCTAAAACA 57.450 29.630 0.00 0.00 0.00 2.83
40 41 9.549509 TGTACATTTTTCGTGCATATCTAAAAC 57.450 29.630 0.00 0.00 0.00 2.43
43 44 7.900864 CGTTGTACATTTTTCGTGCATATCTAA 59.099 33.333 0.00 0.00 0.00 2.10
45 46 6.128391 ACGTTGTACATTTTTCGTGCATATCT 60.128 34.615 0.00 0.00 0.00 1.98
46 47 6.019152 ACGTTGTACATTTTTCGTGCATATC 58.981 36.000 0.00 0.00 0.00 1.63
48 49 5.140872 CACGTTGTACATTTTTCGTGCATA 58.859 37.500 17.58 0.00 41.04 3.14
49 50 3.971871 CACGTTGTACATTTTTCGTGCAT 59.028 39.130 17.58 0.00 41.04 3.96
50 51 3.355270 CACGTTGTACATTTTTCGTGCA 58.645 40.909 17.58 0.00 41.04 4.57
51 52 3.990978 CACGTTGTACATTTTTCGTGC 57.009 42.857 17.58 0.00 41.04 5.34
156 164 8.708742 GGCAAATTTTTCTTACACATTAGGAAC 58.291 33.333 0.00 0.00 0.00 3.62
180 188 5.067674 TGTCTACATTTTTCATAGGCATGGC 59.932 40.000 12.14 12.14 32.61 4.40
186 194 8.729756 TGAACACATGTCTACATTTTTCATAGG 58.270 33.333 0.00 0.00 33.61 2.57
266 295 6.866480 TCAGTTGCTTTTTGTTCTCTTTCAT 58.134 32.000 0.00 0.00 0.00 2.57
267 296 6.266168 TCAGTTGCTTTTTGTTCTCTTTCA 57.734 33.333 0.00 0.00 0.00 2.69
269 298 9.651913 TTTATTCAGTTGCTTTTTGTTCTCTTT 57.348 25.926 0.00 0.00 0.00 2.52
270 299 9.651913 TTTTATTCAGTTGCTTTTTGTTCTCTT 57.348 25.926 0.00 0.00 0.00 2.85
271 300 9.087424 GTTTTATTCAGTTGCTTTTTGTTCTCT 57.913 29.630 0.00 0.00 0.00 3.10
288 321 9.726438 TCCTTTGGTTTTTCTTTGTTTTATTCA 57.274 25.926 0.00 0.00 0.00 2.57
307 340 3.539604 TGTTTTGCATGGTTTCCTTTGG 58.460 40.909 0.00 0.00 0.00 3.28
319 352 3.902881 TTGGTTTCCACTGTTTTGCAT 57.097 38.095 0.00 0.00 30.78 3.96
351 389 3.871006 CCTGTGCATGCGAGAGTTATTTA 59.129 43.478 14.09 0.00 0.00 1.40
353 391 2.093500 TCCTGTGCATGCGAGAGTTATT 60.093 45.455 14.09 0.00 0.00 1.40
357 395 1.079543 GTCCTGTGCATGCGAGAGT 60.080 57.895 14.09 0.00 0.00 3.24
362 400 4.156622 CAGCGTCCTGTGCATGCG 62.157 66.667 14.09 0.00 34.31 4.73
370 408 1.079543 CTCCAGTTCCAGCGTCCTG 60.080 63.158 0.00 0.00 38.85 3.86
372 410 2.266055 CCTCCAGTTCCAGCGTCC 59.734 66.667 0.00 0.00 0.00 4.79
378 416 0.475632 ATGACCCACCTCCAGTTCCA 60.476 55.000 0.00 0.00 0.00 3.53
379 417 0.035056 CATGACCCACCTCCAGTTCC 60.035 60.000 0.00 0.00 0.00 3.62
380 418 0.693049 ACATGACCCACCTCCAGTTC 59.307 55.000 0.00 0.00 0.00 3.01
381 419 1.073923 GAACATGACCCACCTCCAGTT 59.926 52.381 0.00 0.00 0.00 3.16
382 420 0.693049 GAACATGACCCACCTCCAGT 59.307 55.000 0.00 0.00 0.00 4.00
383 421 0.035056 GGAACATGACCCACCTCCAG 60.035 60.000 0.00 0.00 0.00 3.86
384 422 0.770166 TGGAACATGACCCACCTCCA 60.770 55.000 0.00 0.00 0.00 3.86
385 423 0.035056 CTGGAACATGACCCACCTCC 60.035 60.000 0.00 0.00 38.20 4.30
386 424 0.678048 GCTGGAACATGACCCACCTC 60.678 60.000 0.00 0.00 38.20 3.85
387 425 1.136329 AGCTGGAACATGACCCACCT 61.136 55.000 0.00 0.00 38.20 4.00
388 426 0.618458 TAGCTGGAACATGACCCACC 59.382 55.000 0.00 0.00 38.20 4.61
389 427 2.489938 TTAGCTGGAACATGACCCAC 57.510 50.000 0.00 1.83 38.20 4.61
422 461 5.010112 TCGTTGCCTGACATTTTTATTTGGA 59.990 36.000 0.00 0.00 0.00 3.53
424 463 5.164196 CGTCGTTGCCTGACATTTTTATTTG 60.164 40.000 1.76 0.00 36.11 2.32
435 474 1.425412 AATGTACGTCGTTGCCTGAC 58.575 50.000 1.78 0.00 0.00 3.51
439 478 2.283351 GGACATAATGTACGTCGTTGCC 59.717 50.000 1.78 0.00 0.00 4.52
448 487 7.653647 TGAAACTTTGTTGGGACATAATGTAC 58.346 34.615 0.00 0.00 39.30 2.90
455 494 5.079643 AGCTATGAAACTTTGTTGGGACAT 58.920 37.500 0.00 0.00 39.30 3.06
459 498 5.957842 TGTAGCTATGAAACTTTGTTGGG 57.042 39.130 0.00 0.00 0.00 4.12
468 507 4.259970 CGCAGTGACATGTAGCTATGAAAC 60.260 45.833 0.00 1.85 0.00 2.78
522 561 8.398743 AGATGATTTCTCCTTTTTAGGGGTAAA 58.601 33.333 0.00 0.00 0.00 2.01
524 563 7.525158 AGATGATTTCTCCTTTTTAGGGGTA 57.475 36.000 0.00 0.00 0.00 3.69
574 614 5.179368 TGTCTGGTTCATTGACTCGATTTTC 59.821 40.000 0.00 0.00 0.00 2.29
575 615 5.063204 TGTCTGGTTCATTGACTCGATTTT 58.937 37.500 0.00 0.00 0.00 1.82
594 634 0.879765 CGTCCTCAACCGTACTGTCT 59.120 55.000 0.00 0.00 0.00 3.41
652 710 0.596082 ACTGCAATGTACCGGTTTGC 59.404 50.000 27.88 27.88 44.59 3.68
688 746 2.348666 GCCGTGCACACTAACATAGAAG 59.651 50.000 18.64 0.00 0.00 2.85
690 748 1.273886 TGCCGTGCACACTAACATAGA 59.726 47.619 18.64 0.00 31.71 1.98
771 829 0.390866 CTTGGTCTCGTCATGCAGCT 60.391 55.000 0.00 0.00 0.00 4.24
892 954 0.534203 ACATGTCTTTCGCCGGTGTT 60.534 50.000 16.01 0.00 0.00 3.32
921 983 3.564235 TTATATAGCGTTCGCCGATGT 57.436 42.857 13.54 8.47 39.56 3.06
924 986 3.180189 CGTTTTTATATAGCGTTCGCCGA 59.820 43.478 13.54 2.83 39.56 5.54
931 993 7.306399 GCATGTGTAGACGTTTTTATATAGCGT 60.306 37.037 0.00 0.00 38.55 5.07
943 1005 3.812609 TCAAACATGCATGTGTAGACGTT 59.187 39.130 31.98 17.73 41.61 3.99
961 1023 1.013596 CACACCGACTTGTGCTCAAA 58.986 50.000 2.44 0.00 40.51 2.69
996 1058 0.182537 CGGGGGACAAAGCCATATGA 59.817 55.000 3.65 0.00 0.00 2.15
997 1059 0.823356 CCGGGGGACAAAGCCATATG 60.823 60.000 0.00 0.00 0.00 1.78
1123 1188 1.436195 TTGTGCGTGACTTGCCACTC 61.436 55.000 0.00 0.00 35.02 3.51
1133 1198 2.843352 TACGTCCGGTTGTGCGTGA 61.843 57.895 0.00 0.00 38.10 4.35
1171 1236 1.128692 GTACACCTGAAAGCGATGCAC 59.871 52.381 0.00 0.00 0.00 4.57
1175 1240 0.739813 GCGGTACACCTGAAAGCGAT 60.740 55.000 0.00 0.00 36.28 4.58
1182 1247 1.007038 GTTGTCGCGGTACACCTGA 60.007 57.895 6.13 0.00 0.00 3.86
1293 1382 1.300465 CGTATCATCGCTGGCAGCT 60.300 57.895 34.17 19.44 39.60 4.24
1302 1400 3.363970 GCAAAGTAATGCCCGTATCATCG 60.364 47.826 0.00 0.00 40.49 3.84
1356 1454 1.669049 TACCATCGTTGACGCCGGAT 61.669 55.000 5.05 0.00 39.60 4.18
1364 1462 1.207089 CCAAGGAGCTACCATCGTTGA 59.793 52.381 9.29 0.00 42.36 3.18
1366 1464 1.482593 CTCCAAGGAGCTACCATCGTT 59.517 52.381 2.68 0.00 42.04 3.85
1527 2006 1.892329 GCATTGGTTGACCCCAGTGAT 60.892 52.381 6.87 0.00 43.00 3.06
1628 2114 8.719596 TGTTACCCTTGGATGCTATTTCTATTA 58.280 33.333 0.00 0.00 0.00 0.98
1693 2182 1.135315 GCGGACTGTAACACCGTGATA 60.135 52.381 5.28 0.00 46.95 2.15
1715 2204 0.250727 GCACTTCACCCTTGCCTACA 60.251 55.000 0.00 0.00 0.00 2.74
1732 2221 7.600960 TGCATATTTTCACTCTTTATGTTGCA 58.399 30.769 0.00 0.00 0.00 4.08
1825 3848 2.297701 GACTTCAAAGCCAGTTGGACA 58.702 47.619 1.45 0.00 37.39 4.02
1829 3852 1.610522 CAGGGACTTCAAAGCCAGTTG 59.389 52.381 5.85 0.00 34.60 3.16
1837 3860 1.704628 TGATCTGGCAGGGACTTCAAA 59.295 47.619 15.73 0.00 34.60 2.69
1994 4446 5.531287 ACGCCAGTATCTTTTTCAGTTTCTT 59.469 36.000 0.00 0.00 0.00 2.52
2004 4456 2.629051 GCAGGTACGCCAGTATCTTTT 58.371 47.619 0.00 0.00 41.26 2.27
2143 4634 3.626222 CCCTAATCCCCAATTTCCAACGA 60.626 47.826 0.00 0.00 0.00 3.85
2197 4688 3.257561 CGCCGTCTCATCGCCTTG 61.258 66.667 0.00 0.00 0.00 3.61
2424 6340 0.538584 TGTGCAGTCTCAGCCCATAG 59.461 55.000 0.00 0.00 0.00 2.23
2440 6356 4.487948 CACCAGCTAATTGTCCAATTGTG 58.512 43.478 14.02 9.60 40.83 3.33
2485 6401 0.403271 ATGTGTTTGGAGCTCTGCCT 59.597 50.000 14.64 0.00 0.00 4.75
2486 6402 0.807496 GATGTGTTTGGAGCTCTGCC 59.193 55.000 14.64 0.00 0.00 4.85
2487 6403 1.467734 CAGATGTGTTTGGAGCTCTGC 59.532 52.381 14.64 0.00 0.00 4.26
2488 6404 2.082231 CCAGATGTGTTTGGAGCTCTG 58.918 52.381 14.64 0.00 36.55 3.35
2489 6405 1.980765 TCCAGATGTGTTTGGAGCTCT 59.019 47.619 14.64 0.00 38.53 4.09
2490 6406 2.479566 TCCAGATGTGTTTGGAGCTC 57.520 50.000 4.71 4.71 38.53 4.09
2491 6407 2.957402 TTCCAGATGTGTTTGGAGCT 57.043 45.000 0.00 0.00 43.89 4.09
2492 6408 3.350833 AGATTCCAGATGTGTTTGGAGC 58.649 45.455 0.00 0.00 43.89 4.70
2493 6409 5.762218 GGATAGATTCCAGATGTGTTTGGAG 59.238 44.000 0.00 0.00 43.89 3.86
2494 6410 5.684704 GGATAGATTCCAGATGTGTTTGGA 58.315 41.667 0.00 0.00 44.74 3.53
2507 6423 4.295506 AGAGGGTAGGTAGGGATAGATTCC 59.704 50.000 0.00 0.00 44.62 3.01
2508 6424 5.512298 GAGAGGGTAGGTAGGGATAGATTC 58.488 50.000 0.00 0.00 0.00 2.52
2509 6425 4.018233 CGAGAGGGTAGGTAGGGATAGATT 60.018 50.000 0.00 0.00 0.00 2.40
2510 6426 3.524380 CGAGAGGGTAGGTAGGGATAGAT 59.476 52.174 0.00 0.00 0.00 1.98
2511 6427 2.911636 CGAGAGGGTAGGTAGGGATAGA 59.088 54.545 0.00 0.00 0.00 1.98
2512 6428 2.618559 GCGAGAGGGTAGGTAGGGATAG 60.619 59.091 0.00 0.00 0.00 2.08
2513 6429 1.353694 GCGAGAGGGTAGGTAGGGATA 59.646 57.143 0.00 0.00 0.00 2.59
2514 6430 0.112801 GCGAGAGGGTAGGTAGGGAT 59.887 60.000 0.00 0.00 0.00 3.85
2515 6431 0.992431 AGCGAGAGGGTAGGTAGGGA 60.992 60.000 0.00 0.00 0.00 4.20
2516 6432 0.106116 AAGCGAGAGGGTAGGTAGGG 60.106 60.000 0.00 0.00 0.00 3.53
2517 6433 2.506444 CTAAGCGAGAGGGTAGGTAGG 58.494 57.143 0.00 0.00 0.00 3.18
2657 6576 0.168568 GAACGTCGAGTGGAGAGGAC 59.831 60.000 0.00 0.00 0.00 3.85
2876 6802 1.749334 CGCCGAGGAGCTAAAGGGAT 61.749 60.000 0.00 0.00 0.00 3.85
4752 8790 1.142688 ACTGATCCAAAGGTGGCCCT 61.143 55.000 0.00 0.00 45.54 5.19
4968 9007 2.668185 TTTCGGGCACTCGCTTTCCA 62.668 55.000 0.00 0.00 38.60 3.53
5468 9508 1.066143 GGGAGAATGAGTTTGAGCCGA 60.066 52.381 0.00 0.00 0.00 5.54
6167 10210 1.376037 CTCCTTCGTTCTGCCCACC 60.376 63.158 0.00 0.00 0.00 4.61
7588 14304 1.975407 GCATCAGGTTGCAGCCAGT 60.975 57.895 22.64 3.93 42.31 4.00
8103 14827 2.817839 GCTCTTGACCCCAGCCTAAAAA 60.818 50.000 0.00 0.00 0.00 1.94
8104 14828 1.271926 GCTCTTGACCCCAGCCTAAAA 60.272 52.381 0.00 0.00 0.00 1.52
8105 14829 0.328258 GCTCTTGACCCCAGCCTAAA 59.672 55.000 0.00 0.00 0.00 1.85
8106 14830 0.840288 TGCTCTTGACCCCAGCCTAA 60.840 55.000 0.00 0.00 31.68 2.69
8107 14831 0.840288 TTGCTCTTGACCCCAGCCTA 60.840 55.000 0.00 0.00 31.68 3.93
8108 14832 2.156098 TTGCTCTTGACCCCAGCCT 61.156 57.895 0.00 0.00 31.68 4.58
8121 14845 1.130561 GTACGCCCATCAAAGTTGCTC 59.869 52.381 0.00 0.00 0.00 4.26
8122 14846 1.165270 GTACGCCCATCAAAGTTGCT 58.835 50.000 0.00 0.00 0.00 3.91
8136 14860 4.679662 TCCAGTATTTGAAGCTAGTACGC 58.320 43.478 0.00 0.00 0.00 4.42
8210 14934 8.415192 TCGTGCATAGTTATAACAAGGTAAAG 57.585 34.615 17.65 3.39 0.00 1.85
8212 14936 7.439955 CCATCGTGCATAGTTATAACAAGGTAA 59.560 37.037 17.65 0.00 0.00 2.85
8213 14937 6.926826 CCATCGTGCATAGTTATAACAAGGTA 59.073 38.462 17.65 1.89 0.00 3.08
8214 14938 5.758296 CCATCGTGCATAGTTATAACAAGGT 59.242 40.000 17.65 0.00 0.00 3.50
8215 14939 5.758296 ACCATCGTGCATAGTTATAACAAGG 59.242 40.000 17.65 7.13 0.00 3.61
8216 14940 6.844696 ACCATCGTGCATAGTTATAACAAG 57.155 37.500 17.65 7.79 0.00 3.16
8217 14941 8.719560 TTAACCATCGTGCATAGTTATAACAA 57.280 30.769 17.65 0.00 0.00 2.83
8218 14942 7.042321 GCTTAACCATCGTGCATAGTTATAACA 60.042 37.037 17.65 4.52 0.00 2.41
8219 14943 7.042321 TGCTTAACCATCGTGCATAGTTATAAC 60.042 37.037 7.57 7.57 0.00 1.89
8220 14944 6.987404 TGCTTAACCATCGTGCATAGTTATAA 59.013 34.615 0.00 0.00 0.00 0.98
8221 14945 6.517605 TGCTTAACCATCGTGCATAGTTATA 58.482 36.000 0.00 0.00 0.00 0.98
8222 14946 5.364778 TGCTTAACCATCGTGCATAGTTAT 58.635 37.500 0.00 0.00 0.00 1.89
8223 14947 4.760878 TGCTTAACCATCGTGCATAGTTA 58.239 39.130 0.00 0.00 0.00 2.24
8226 14950 4.273235 TCAATGCTTAACCATCGTGCATAG 59.727 41.667 0.00 0.00 42.57 2.23
8235 14959 7.363793 GGGACAAAATAGTCAATGCTTAACCAT 60.364 37.037 0.00 0.00 40.29 3.55
8307 15031 2.937149 CCAGTTCAGAGTCTCGATCGTA 59.063 50.000 15.94 1.59 0.00 3.43
8347 15071 2.795110 GCTGCTCCGAGAGAGGCAT 61.795 63.158 0.00 0.00 43.46 4.40
8559 15283 0.461339 GCATTTCGGGCTCGTTCCTA 60.461 55.000 5.57 0.00 37.69 2.94
8908 15642 4.189231 GCGAGCTTACTTAATTGGGAAGA 58.811 43.478 8.74 0.00 0.00 2.87
8943 15677 2.290071 ACAATAACGGGTGGTCCTGAAG 60.290 50.000 0.00 0.00 42.46 3.02
8954 15688 3.915437 AGTTCAGCAAACAATAACGGG 57.085 42.857 5.00 0.00 40.56 5.28
9025 15760 7.716998 ACTGAAGAGTAATGAATGTCAAAGTGT 59.283 33.333 0.00 0.00 0.00 3.55
9180 15931 6.408206 CCTCAAATTACTCCCTCCGTTTCTAT 60.408 42.308 0.00 0.00 0.00 1.98
9243 15994 3.251571 GTGATCGGCGAAGGATATAACC 58.748 50.000 15.93 0.00 0.00 2.85
9244 15995 3.909430 TGTGATCGGCGAAGGATATAAC 58.091 45.455 15.93 0.00 0.00 1.89
9247 15998 2.562738 TGATGTGATCGGCGAAGGATAT 59.437 45.455 15.93 4.33 0.00 1.63
9249 16000 0.752658 TGATGTGATCGGCGAAGGAT 59.247 50.000 15.93 3.52 0.00 3.24
9251 16002 0.179100 AGTGATGTGATCGGCGAAGG 60.179 55.000 15.93 0.00 0.00 3.46
9252 16003 1.203928 GAGTGATGTGATCGGCGAAG 58.796 55.000 15.93 0.00 0.00 3.79
9253 16004 0.179111 GGAGTGATGTGATCGGCGAA 60.179 55.000 15.93 0.00 0.00 4.70
9254 16005 1.319614 TGGAGTGATGTGATCGGCGA 61.320 55.000 13.87 13.87 0.00 5.54
9255 16006 0.249615 ATGGAGTGATGTGATCGGCG 60.250 55.000 0.00 0.00 0.00 6.46
9256 16007 1.224075 CATGGAGTGATGTGATCGGC 58.776 55.000 0.00 0.00 0.00 5.54
9259 16010 4.707030 TTTTGCATGGAGTGATGTGATC 57.293 40.909 0.00 0.00 0.00 2.92
9281 16032 4.082679 TGTTTGCCTCTTACACGTGTTTTT 60.083 37.500 28.55 3.69 0.00 1.94
9282 16033 3.440872 TGTTTGCCTCTTACACGTGTTTT 59.559 39.130 28.55 4.12 0.00 2.43
9283 16034 3.011119 TGTTTGCCTCTTACACGTGTTT 58.989 40.909 28.55 4.99 0.00 2.83
9284 16035 2.634600 TGTTTGCCTCTTACACGTGTT 58.365 42.857 28.55 11.17 0.00 3.32
9285 16036 2.319136 TGTTTGCCTCTTACACGTGT 57.681 45.000 26.52 26.52 0.00 4.49
9286 16037 2.602217 GCTTGTTTGCCTCTTACACGTG 60.602 50.000 15.48 15.48 0.00 4.49
9287 16038 1.602377 GCTTGTTTGCCTCTTACACGT 59.398 47.619 0.00 0.00 0.00 4.49
9288 16039 2.316119 GCTTGTTTGCCTCTTACACG 57.684 50.000 0.00 0.00 0.00 4.49
9306 16057 2.665185 GTGGAGTGACGTGGTGGC 60.665 66.667 0.00 0.00 0.00 5.01
9316 16067 3.272574 AGCATATGTGAAGGTGGAGTG 57.727 47.619 4.29 0.00 0.00 3.51
9333 16084 5.543714 TCGGCGAAGGATATATTTTTAGCA 58.456 37.500 7.35 0.00 0.00 3.49
9334 16085 6.535508 AGATCGGCGAAGGATATATTTTTAGC 59.464 38.462 15.93 6.67 0.00 3.09
9410 16168 2.614829 AGTGGACTTGTTTGTACGCT 57.385 45.000 0.00 0.00 36.85 5.07
9464 16222 7.592533 GTGTGTACGTTGTCTAGTTTTAGATGA 59.407 37.037 0.00 0.00 38.17 2.92
9486 16244 8.091449 AGGTATGTCTTTTCTCTTTCTAGTGTG 58.909 37.037 0.00 0.00 0.00 3.82
9529 16288 1.000521 CCTGGCTGCCCATCTCAAA 60.001 57.895 17.53 0.00 41.21 2.69
9543 16302 3.623060 CACGTATCATTGGAAAGACCTGG 59.377 47.826 0.00 0.00 39.86 4.45
9546 16305 3.006940 TGCACGTATCATTGGAAAGACC 58.993 45.455 0.00 0.00 39.54 3.85
9606 16365 8.612619 GTTTTCTTTCTTCTTCTGATGTGTACA 58.387 33.333 0.00 0.00 0.00 2.90
9615 16374 8.562892 TGCTCATAAGTTTTCTTTCTTCTTCTG 58.437 33.333 0.00 0.00 40.91 3.02
9659 16419 0.785979 GTTCGCCGATTTACACGTGT 59.214 50.000 26.52 26.52 0.00 4.49
9674 16434 7.894376 TTTGTAGTATTTCCTTGTAGGTTCG 57.106 36.000 0.00 0.00 36.53 3.95
9695 16455 5.529060 AGAACTGAGGCTACACTTTCTTTTG 59.471 40.000 0.00 0.00 0.00 2.44
9697 16457 5.297569 AGAACTGAGGCTACACTTTCTTT 57.702 39.130 0.00 0.00 0.00 2.52
9705 16465 2.889512 TGAGGAAGAACTGAGGCTACA 58.110 47.619 0.00 0.00 0.00 2.74
9732 16492 8.723942 AATATGCTCATCGTTAGAGTTTCTTT 57.276 30.769 0.00 0.00 35.55 2.52
9733 16493 9.988815 ATAATATGCTCATCGTTAGAGTTTCTT 57.011 29.630 0.00 0.00 35.55 2.52
9774 16534 3.281359 GAAGCATGGCGGCCGTTTT 62.281 57.895 28.70 9.19 0.00 2.43
9816 16576 1.358787 TCCAACTCCATTTCAGGCCAT 59.641 47.619 5.01 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.