Multiple sequence alignment - TraesCS3D01G210900

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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 TraesCS3D01G210900 chr3D 100.000 4060 0 0 2154 6213 281002891 281006950 0.000000e+00 7498.0
1 TraesCS3D01G210900 chr3D 100.000 1997 0 0 1 1997 281000738 281002734 0.000000e+00 3688.0
2 TraesCS3D01G210900 chr3D 90.783 575 51 1 5641 6213 480355919 480356493 0.000000e+00 767.0
3 TraesCS3D01G210900 chr3D 94.737 114 2 2 4148 4257 138182971 138182858 2.300000e-39 174.0
4 TraesCS3D01G210900 chr3D 94.690 113 4 1 4147 4257 394956403 394956515 2.300000e-39 174.0
5 TraesCS3D01G210900 chr3D 77.705 305 50 13 4 297 523939955 523940252 2.980000e-38 171.0
6 TraesCS3D01G210900 chr3D 75.896 307 46 15 4 294 348153962 348153668 1.410000e-26 132.0
7 TraesCS3D01G210900 chr3D 91.111 90 4 3 4184 4271 142073060 142072973 1.090000e-22 119.0
8 TraesCS3D01G210900 chr3D 74.866 187 41 5 554 737 115629553 115629736 5.160000e-11 80.5
9 TraesCS3D01G210900 chr3A 94.513 1859 37 18 2154 4003 366881754 366883556 0.000000e+00 2808.0
10 TraesCS3D01G210900 chr3A 95.530 1141 27 2 4255 5372 366885361 366886500 0.000000e+00 1803.0
11 TraesCS3D01G210900 chr3A 97.921 962 15 3 1037 1997 366880805 366881762 0.000000e+00 1661.0
12 TraesCS3D01G210900 chr3A 91.389 929 58 14 2 919 366871206 366872123 0.000000e+00 1253.0
13 TraesCS3D01G210900 chr3A 97.091 275 6 1 5368 5642 366886985 366887257 4.390000e-126 462.0
14 TraesCS3D01G210900 chr3A 93.413 167 8 2 3989 4152 366885201 366885367 1.730000e-60 244.0
15 TraesCS3D01G210900 chr3A 94.690 113 4 1 4147 4257 117944654 117944542 2.300000e-39 174.0
16 TraesCS3D01G210900 chr3A 91.736 121 7 2 4139 4257 373020641 373020522 1.390000e-36 165.0
17 TraesCS3D01G210900 chr3A 95.122 82 2 1 4192 4271 154188091 154188010 1.820000e-25 128.0
18 TraesCS3D01G210900 chr3A 87.912 91 7 2 4190 4278 520438060 520437972 3.060000e-18 104.0
19 TraesCS3D01G210900 chr3B 95.608 1366 34 11 4268 5609 369105939 369107302 0.000000e+00 2167.0
20 TraesCS3D01G210900 chr3B 96.348 1150 30 2 2154 3300 369104022 369105162 0.000000e+00 1881.0
21 TraesCS3D01G210900 chr3B 90.520 1097 37 18 749 1799 369102388 369103463 0.000000e+00 1387.0
22 TraesCS3D01G210900 chr3B 89.895 574 55 3 5639 6211 313808934 313809505 0.000000e+00 736.0
23 TraesCS3D01G210900 chr3B 94.272 419 19 3 3739 4152 369105508 369105926 2.440000e-178 636.0
24 TraesCS3D01G210900 chr3B 91.530 366 7 7 3331 3693 369105162 369105506 3.370000e-132 483.0
25 TraesCS3D01G210900 chr3B 94.211 190 4 1 1808 1997 369103848 369104030 3.670000e-72 283.0
26 TraesCS3D01G210900 chr3B 88.421 95 8 2 4184 4276 114721581 114721674 1.830000e-20 111.0
27 TraesCS3D01G210900 chr5D 90.609 575 53 1 5639 6213 400366374 400366947 0.000000e+00 761.0
28 TraesCS3D01G210900 chr5D 91.358 162 12 1 3904 4063 279302713 279302874 2.920000e-53 220.0
29 TraesCS3D01G210900 chr5D 80.405 296 42 15 4 291 67871646 67871359 1.750000e-50 211.0
30 TraesCS3D01G210900 chr5D 90.244 164 13 2 3903 4063 319325106 319324943 1.750000e-50 211.0
31 TraesCS3D01G210900 chr5D 80.135 297 39 11 2 291 327479871 327480154 2.940000e-48 204.0
32 TraesCS3D01G210900 chr2D 90.796 565 48 3 5641 6202 186954401 186954964 0.000000e+00 752.0
33 TraesCS3D01G210900 chr2D 90.295 577 49 4 5641 6213 353544574 353544001 0.000000e+00 749.0
34 TraesCS3D01G210900 chr2D 90.087 575 54 3 5641 6213 387480937 387480364 0.000000e+00 743.0
35 TraesCS3D01G210900 chr2D 84.896 192 23 4 3904 4092 63736937 63737125 8.220000e-44 189.0
36 TraesCS3D01G210900 chr2D 79.195 298 39 15 17 295 512920862 512920569 1.060000e-42 185.0
37 TraesCS3D01G210900 chr2D 89.130 92 8 1 4190 4279 566134746 566134655 5.090000e-21 113.0
38 TraesCS3D01G210900 chr2D 100.000 28 0 0 3784 3811 73099244 73099217 1.100000e-02 52.8
39 TraesCS3D01G210900 chr6D 90.214 562 49 4 5641 6200 372780550 372779993 0.000000e+00 728.0
40 TraesCS3D01G210900 chr4D 88.927 578 60 4 5638 6213 115402212 115401637 0.000000e+00 710.0
41 TraesCS3D01G210900 chr5B 87.024 578 69 6 5636 6211 22029980 22030553 0.000000e+00 647.0
42 TraesCS3D01G210900 chr5B 81.145 297 40 15 4 291 228279482 228279193 2.250000e-54 224.0
43 TraesCS3D01G210900 chr5B 91.250 80 5 1 4184 4261 678507303 678507382 2.370000e-19 108.0
44 TraesCS3D01G210900 chr7D 90.741 162 13 1 3904 4063 397555077 397554916 1.360000e-51 215.0
45 TraesCS3D01G210900 chr7D 80.524 267 39 13 30 290 18763443 18763702 6.360000e-45 193.0
46 TraesCS3D01G210900 chr7D 97.345 113 0 2 4147 4257 335401380 335401491 8.220000e-44 189.0
47 TraesCS3D01G210900 chr7D 95.726 117 1 3 4144 4257 55399014 55399129 1.060000e-42 185.0
48 TraesCS3D01G210900 chr2A 90.741 162 13 2 3904 4063 342647560 342647399 1.360000e-51 215.0
49 TraesCS3D01G210900 chr2A 90.741 162 13 1 3904 4063 758586738 758586577 1.360000e-51 215.0
50 TraesCS3D01G210900 chr6A 90.303 165 12 2 3904 4064 64321677 64321513 4.880000e-51 213.0
51 TraesCS3D01G210900 chr6A 79.468 263 43 11 33 290 64174809 64174553 6.400000e-40 176.0
52 TraesCS3D01G210900 chr6A 81.757 148 20 7 147 291 613579163 613579306 3.940000e-22 117.0
53 TraesCS3D01G210900 chr4B 90.184 163 14 1 3903 4063 586319224 586319062 1.750000e-50 211.0
54 TraesCS3D01G210900 chr4B 80.405 296 42 15 4 290 615835922 615836210 1.750000e-50 211.0
55 TraesCS3D01G210900 chr4B 94.690 113 4 1 4148 4258 424274397 424274509 2.300000e-39 174.0
56 TraesCS3D01G210900 chr4B 83.761 117 12 7 177 291 617881109 617881220 3.060000e-18 104.0
57 TraesCS3D01G210900 chr7B 79.801 302 38 19 4 291 363289280 363289572 1.370000e-46 198.0
58 TraesCS3D01G210900 chr1B 79.110 292 49 11 4 290 658523895 658524179 2.290000e-44 191.0
59 TraesCS3D01G210900 chr2B 78.689 305 40 18 4 294 51674976 51674683 4.950000e-41 180.0
60 TraesCS3D01G210900 chr2B 95.536 112 3 1 4148 4257 42279755 42279866 1.780000e-40 178.0
61 TraesCS3D01G210900 chr2B 90.698 86 4 4 4187 4271 82190843 82190761 1.830000e-20 111.0
62 TraesCS3D01G210900 chr4A 79.401 267 42 13 30 290 512181352 512181611 6.400000e-40 176.0
63 TraesCS3D01G210900 chr7A 93.750 112 5 1 4148 4257 501658162 501658273 3.850000e-37 167.0
64 TraesCS3D01G210900 chr5A 89.062 128 10 3 4146 4270 215146887 215147013 8.340000e-34 156.0
65 TraesCS3D01G210900 chr1A 77.211 294 42 19 3 282 556141173 556140891 1.400000e-31 148.0
66 TraesCS3D01G210900 chrUn 84.848 132 16 1 160 291 42625187 42625314 5.050000e-26 130.0
67 TraesCS3D01G210900 chrUn 84.848 132 16 1 160 291 42903056 42902929 5.050000e-26 130.0
68 TraesCS3D01G210900 chr6B 88.889 90 6 3 4184 4271 26619093 26619180 2.370000e-19 108.0


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 TraesCS3D01G210900 chr3D 281000738 281006950 6212 False 5593.0 7498 100.000000 1 6213 2 chr3D.!!$F5 6212
1 TraesCS3D01G210900 chr3D 480355919 480356493 574 False 767.0 767 90.783000 5641 6213 1 chr3D.!!$F3 572
2 TraesCS3D01G210900 chr3A 366880805 366887257 6452 False 1395.6 2808 95.693600 1037 5642 5 chr3A.!!$F2 4605
3 TraesCS3D01G210900 chr3A 366871206 366872123 917 False 1253.0 1253 91.389000 2 919 1 chr3A.!!$F1 917
4 TraesCS3D01G210900 chr3B 369102388 369107302 4914 False 1139.5 2167 93.748167 749 5609 6 chr3B.!!$F3 4860
5 TraesCS3D01G210900 chr3B 313808934 313809505 571 False 736.0 736 89.895000 5639 6211 1 chr3B.!!$F2 572
6 TraesCS3D01G210900 chr5D 400366374 400366947 573 False 761.0 761 90.609000 5639 6213 1 chr5D.!!$F3 574
7 TraesCS3D01G210900 chr2D 186954401 186954964 563 False 752.0 752 90.796000 5641 6202 1 chr2D.!!$F2 561
8 TraesCS3D01G210900 chr2D 353544001 353544574 573 True 749.0 749 90.295000 5641 6213 1 chr2D.!!$R2 572
9 TraesCS3D01G210900 chr2D 387480364 387480937 573 True 743.0 743 90.087000 5641 6213 1 chr2D.!!$R3 572
10 TraesCS3D01G210900 chr6D 372779993 372780550 557 True 728.0 728 90.214000 5641 6200 1 chr6D.!!$R1 559
11 TraesCS3D01G210900 chr4D 115401637 115402212 575 True 710.0 710 88.927000 5638 6213 1 chr4D.!!$R1 575
12 TraesCS3D01G210900 chr5B 22029980 22030553 573 False 647.0 647 87.024000 5636 6211 1 chr5B.!!$F1 575

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
100 103 0.747255 ACCACTGTAGCCTATCAGCG 59.253 55.000 0.00 0.0 38.01 5.18 F
785 797 0.989602 TCTCCACGGACTGGACTAGA 59.010 55.000 0.00 0.0 44.99 2.43 F
1731 1795 2.432146 TGACGCTTCTTGGCTGATATCT 59.568 45.455 3.98 0.0 0.00 1.98 F
3454 3900 0.531974 GCTGGCATGCATCATTTGGG 60.532 55.000 21.36 0.0 0.00 4.12 F
4760 6883 0.251832 TCTTCTCGACCCTCAAGGCT 60.252 55.000 0.00 0.0 40.58 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1016 1055 0.985490 CCCTCCCTCCCTCTTCTTGG 60.985 65.0 0.00 0.00 0.00 3.61 R
2155 2595 0.603707 TTGAAGCTCAAGTCCAGCCG 60.604 55.0 0.00 0.00 37.63 5.52 R
3565 4011 0.098376 GTGACTACCGGAGTGTAGCG 59.902 60.0 9.46 0.00 41.57 4.26 R
4832 6955 2.279935 ACACAATTACCCCGAAAGCA 57.720 45.0 0.00 0.00 0.00 3.91 R
5938 8581 1.947597 TAATAACGAGTGCCGGCCGT 61.948 55.0 26.77 23.63 43.93 5.68 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
98 101 7.865706 AAAAATTACCACTGTAGCCTATCAG 57.134 36.000 0.00 0.00 37.65 2.90
100 103 0.747255 ACCACTGTAGCCTATCAGCG 59.253 55.000 0.00 0.00 38.01 5.18
105 108 1.101635 TGTAGCCTATCAGCGAGCGT 61.102 55.000 0.00 0.00 38.01 5.07
116 119 1.062440 CAGCGAGCGTCATTTTGCATA 59.938 47.619 0.00 0.00 0.00 3.14
120 123 2.440501 GAGCGTCATTTTGCATAACCG 58.559 47.619 0.00 0.00 0.00 4.44
123 126 1.797348 CGTCATTTTGCATAACCGCCC 60.797 52.381 0.00 0.00 0.00 6.13
124 127 1.203523 GTCATTTTGCATAACCGCCCA 59.796 47.619 0.00 0.00 0.00 5.36
126 129 2.499289 TCATTTTGCATAACCGCCCATT 59.501 40.909 0.00 0.00 0.00 3.16
127 130 3.701542 TCATTTTGCATAACCGCCCATTA 59.298 39.130 0.00 0.00 0.00 1.90
205 208 9.347240 CATCACCTCCATCTAAAAGACATATTT 57.653 33.333 0.00 0.00 0.00 1.40
222 225 8.076178 AGACATATTTCAAAAGTTTTCTCACCG 58.924 33.333 0.00 0.00 0.00 4.94
230 233 2.548295 TTTTCTCACCGCGCCCAAC 61.548 57.895 0.00 0.00 0.00 3.77
243 246 4.389576 CCAACCAGCTTGCGCGAC 62.390 66.667 12.10 0.88 42.32 5.19
341 344 5.053811 TCATGCGACTGTCTTGTTAGAAAA 58.946 37.500 6.21 0.00 30.65 2.29
351 354 9.628500 ACTGTCTTGTTAGAAAATTTAGGACTT 57.372 29.630 0.00 0.00 30.65 3.01
389 394 8.702438 GTGTATCCAAACACTTGATTTGATTTG 58.298 33.333 0.01 0.00 45.12 2.32
401 406 8.025445 ACTTGATTTGATTTGCAGATTAGACAC 58.975 33.333 0.00 0.00 0.00 3.67
406 411 8.846943 TTTGATTTGCAGATTAGACACTTAGA 57.153 30.769 0.00 0.00 0.00 2.10
435 440 6.650390 AGTTTGCCAGGCTTTACAAATTATTG 59.350 34.615 14.15 0.00 42.46 1.90
438 443 5.178061 GCCAGGCTTTACAAATTATTGCTT 58.822 37.500 3.29 0.00 40.34 3.91
500 505 1.595466 AGTATGACGAGGCTACTCCG 58.405 55.000 0.00 0.00 40.77 4.63
503 508 1.437772 ATGACGAGGCTACTCCGACG 61.438 60.000 0.00 0.00 40.77 5.12
531 536 3.509967 TCCCGTATATCATGCTCGACAAT 59.490 43.478 0.00 0.00 0.00 2.71
544 549 1.134936 TCGACAATGGTGATACACGGG 60.135 52.381 0.00 0.00 34.83 5.28
604 610 3.023832 AGGGTGCTTGGGAAATAAATCG 58.976 45.455 0.00 0.00 0.00 3.34
728 739 8.776680 TTTTTCTAAACAACTTCGTAAGCATC 57.223 30.769 0.00 0.00 37.18 3.91
747 758 2.923121 TCTAGCATTGCAGGTGGATTC 58.077 47.619 11.91 0.00 0.00 2.52
754 765 1.619654 TGCAGGTGGATTCCAAACAG 58.380 50.000 7.05 2.02 34.18 3.16
785 797 0.989602 TCTCCACGGACTGGACTAGA 59.010 55.000 0.00 0.00 44.99 2.43
1122 1161 4.724602 TCGTGTGCCGCTCTCTGC 62.725 66.667 0.00 0.00 36.19 4.26
1606 1650 3.136123 CTCTGCCATTGCCACGGG 61.136 66.667 0.00 0.00 36.33 5.28
1703 1767 4.575885 TGATCCTAAAACGAGTTCTTGGG 58.424 43.478 0.00 0.00 0.00 4.12
1731 1795 2.432146 TGACGCTTCTTGGCTGATATCT 59.568 45.455 3.98 0.00 0.00 1.98
1732 1796 3.636764 TGACGCTTCTTGGCTGATATCTA 59.363 43.478 3.98 0.00 0.00 1.98
1733 1797 4.233789 GACGCTTCTTGGCTGATATCTAG 58.766 47.826 3.98 1.40 0.00 2.43
1830 2270 4.216257 ACTGCTGTTAATGTTGATGTGTCC 59.784 41.667 0.00 0.00 0.00 4.02
1835 2275 6.478344 GCTGTTAATGTTGATGTGTCCAAAAA 59.522 34.615 0.00 0.00 0.00 1.94
2746 3190 1.002087 AGGCGAACAAGGAATCGTTCT 59.998 47.619 0.00 0.00 39.49 3.01
2909 3353 1.202245 GCAGTACTTCTCGGAGCTGAG 60.202 57.143 12.05 0.00 37.33 3.35
2928 3372 5.320277 CTGAGTCTCCTGGGAAAGAAAAAT 58.680 41.667 0.00 0.00 0.00 1.82
3111 3555 1.296392 CAACATCGTGGGGCTGAGA 59.704 57.895 0.00 0.00 0.00 3.27
3300 3744 2.362077 GGGCATTGCTAAAGGTATGGTG 59.638 50.000 8.82 0.00 0.00 4.17
3301 3745 2.362077 GGCATTGCTAAAGGTATGGTGG 59.638 50.000 8.82 0.00 0.00 4.61
3303 3747 3.290710 CATTGCTAAAGGTATGGTGGCT 58.709 45.455 0.00 0.00 0.00 4.75
3304 3748 4.460263 CATTGCTAAAGGTATGGTGGCTA 58.540 43.478 0.00 0.00 0.00 3.93
3305 3749 3.838244 TGCTAAAGGTATGGTGGCTAG 57.162 47.619 0.00 0.00 0.00 3.42
3307 3751 3.118408 TGCTAAAGGTATGGTGGCTAGTG 60.118 47.826 0.00 0.00 0.00 2.74
3411 3855 4.816392 TGCATTCGTACTGTACTGTCAAT 58.184 39.130 15.35 4.17 0.00 2.57
3454 3900 0.531974 GCTGGCATGCATCATTTGGG 60.532 55.000 21.36 0.00 0.00 4.12
3455 3901 0.531974 CTGGCATGCATCATTTGGGC 60.532 55.000 21.36 0.00 0.00 5.36
3456 3902 0.978667 TGGCATGCATCATTTGGGCT 60.979 50.000 21.36 0.00 0.00 5.19
3457 3903 1.042229 GGCATGCATCATTTGGGCTA 58.958 50.000 21.36 0.00 0.00 3.93
3458 3904 1.621814 GGCATGCATCATTTGGGCTAT 59.378 47.619 21.36 0.00 0.00 2.97
3459 3905 2.827322 GGCATGCATCATTTGGGCTATA 59.173 45.455 21.36 0.00 0.00 1.31
3460 3906 3.258872 GGCATGCATCATTTGGGCTATAA 59.741 43.478 21.36 0.00 0.00 0.98
3461 3907 4.491676 GCATGCATCATTTGGGCTATAAG 58.508 43.478 14.21 0.00 0.00 1.73
3462 3908 4.491676 CATGCATCATTTGGGCTATAAGC 58.508 43.478 0.00 0.00 41.46 3.09
3463 3909 3.836146 TGCATCATTTGGGCTATAAGCT 58.164 40.909 0.00 0.00 41.99 3.74
3464 3910 4.217510 TGCATCATTTGGGCTATAAGCTT 58.782 39.130 3.48 3.48 41.99 3.74
3465 3911 4.038282 TGCATCATTTGGGCTATAAGCTTG 59.962 41.667 9.86 0.00 41.99 4.01
3466 3912 4.560108 GCATCATTTGGGCTATAAGCTTGG 60.560 45.833 9.86 0.22 41.99 3.61
3505 3951 4.931601 TCCAATCAGTTTCTCAGTTCATCG 59.068 41.667 0.00 0.00 0.00 3.84
3511 3957 7.625828 TCAGTTTCTCAGTTCATCGATACTA 57.374 36.000 0.00 0.00 0.00 1.82
3512 3958 7.473366 TCAGTTTCTCAGTTCATCGATACTAC 58.527 38.462 0.00 0.00 0.00 2.73
3513 3959 7.337184 TCAGTTTCTCAGTTCATCGATACTACT 59.663 37.037 0.00 0.00 0.00 2.57
3514 3960 8.613482 CAGTTTCTCAGTTCATCGATACTACTA 58.387 37.037 0.00 0.00 0.00 1.82
3515 3961 8.614346 AGTTTCTCAGTTCATCGATACTACTAC 58.386 37.037 0.00 0.00 0.00 2.73
3516 3962 8.614346 GTTTCTCAGTTCATCGATACTACTACT 58.386 37.037 0.00 0.00 0.00 2.57
3517 3963 7.716768 TCTCAGTTCATCGATACTACTACTG 57.283 40.000 0.00 6.07 34.55 2.74
3565 4011 2.325583 TCGGGAAACATGTGATAGGC 57.674 50.000 0.00 0.00 0.00 3.93
3639 4085 3.505293 AGCTCTGCTTGCTTTTCTTTAGG 59.495 43.478 0.00 0.00 37.52 2.69
3705 4155 7.492669 CACATAGCCATATTTATTACTCCCTCG 59.507 40.741 0.00 0.00 0.00 4.63
3706 4156 7.180408 ACATAGCCATATTTATTACTCCCTCGT 59.820 37.037 0.00 0.00 0.00 4.18
3707 4157 6.038997 AGCCATATTTATTACTCCCTCGTC 57.961 41.667 0.00 0.00 0.00 4.20
3710 4160 5.408356 CATATTTATTACTCCCTCGTCCCG 58.592 45.833 0.00 0.00 0.00 5.14
3711 4161 2.442236 TTATTACTCCCTCGTCCCGT 57.558 50.000 0.00 0.00 0.00 5.28
3712 4162 3.576078 TTATTACTCCCTCGTCCCGTA 57.424 47.619 0.00 0.00 0.00 4.02
3714 4164 2.442236 TTACTCCCTCGTCCCGTAAT 57.558 50.000 0.00 0.00 0.00 1.89
3767 4220 6.998074 AGAACACAAGTAATCATCCAGAACAA 59.002 34.615 0.00 0.00 0.00 2.83
3803 4257 7.982354 CCTAAGTACTCCCTCTGTAAAGAAATG 59.018 40.741 0.00 0.00 0.00 2.32
3846 4300 5.574970 AAAGAAATATGAGGCCTCCTAGG 57.425 43.478 29.95 0.82 38.80 3.02
3924 4378 4.261952 GCTACTCCCTCCGTTCCTAAATAC 60.262 50.000 0.00 0.00 0.00 1.89
4137 6252 4.370917 GTGAAGTAAGGACCACGTACAAA 58.629 43.478 0.00 0.00 36.63 2.83
4146 6261 6.677781 AGGACCACGTACAAATTTATCATG 57.322 37.500 0.00 0.00 0.00 3.07
4147 6262 6.177610 AGGACCACGTACAAATTTATCATGT 58.822 36.000 0.00 0.00 0.00 3.21
4148 6263 7.332557 AGGACCACGTACAAATTTATCATGTA 58.667 34.615 0.00 0.00 0.00 2.29
4149 6264 7.279313 AGGACCACGTACAAATTTATCATGTAC 59.721 37.037 7.14 7.14 43.66 2.90
4150 6265 7.279313 GGACCACGTACAAATTTATCATGTACT 59.721 37.037 12.99 0.00 44.47 2.73
4151 6266 8.193250 ACCACGTACAAATTTATCATGTACTC 57.807 34.615 12.99 0.00 44.47 2.59
4152 6267 7.279313 ACCACGTACAAATTTATCATGTACTCC 59.721 37.037 12.99 0.00 44.47 3.85
4153 6268 7.254658 CCACGTACAAATTTATCATGTACTCCC 60.255 40.741 12.99 0.00 44.47 4.30
4154 6269 7.494625 CACGTACAAATTTATCATGTACTCCCT 59.505 37.037 12.99 0.00 44.47 4.20
4155 6270 7.709613 ACGTACAAATTTATCATGTACTCCCTC 59.290 37.037 12.99 0.00 44.47 4.30
4156 6271 7.170998 CGTACAAATTTATCATGTACTCCCTCC 59.829 40.741 12.99 0.00 44.47 4.30
4157 6272 6.055588 ACAAATTTATCATGTACTCCCTCCG 58.944 40.000 0.00 0.00 0.00 4.63
4158 6273 5.888982 AATTTATCATGTACTCCCTCCGT 57.111 39.130 0.00 0.00 0.00 4.69
4159 6274 5.888982 ATTTATCATGTACTCCCTCCGTT 57.111 39.130 0.00 0.00 0.00 4.44
4160 6275 4.931661 TTATCATGTACTCCCTCCGTTC 57.068 45.455 0.00 0.00 0.00 3.95
4161 6276 1.481871 TCATGTACTCCCTCCGTTCC 58.518 55.000 0.00 0.00 0.00 3.62
4162 6277 1.191535 CATGTACTCCCTCCGTTCCA 58.808 55.000 0.00 0.00 0.00 3.53
4163 6278 1.553248 CATGTACTCCCTCCGTTCCAA 59.447 52.381 0.00 0.00 0.00 3.53
4164 6279 1.719529 TGTACTCCCTCCGTTCCAAA 58.280 50.000 0.00 0.00 0.00 3.28
4165 6280 2.262637 TGTACTCCCTCCGTTCCAAAT 58.737 47.619 0.00 0.00 0.00 2.32
4166 6281 2.640826 TGTACTCCCTCCGTTCCAAATT 59.359 45.455 0.00 0.00 0.00 1.82
4167 6282 3.839490 TGTACTCCCTCCGTTCCAAATTA 59.161 43.478 0.00 0.00 0.00 1.40
4168 6283 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
4169 6284 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
4170 6285 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
4171 6286 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
4172 6287 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
4173 6288 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
4174 6289 2.597305 CTCCGTTCCAAATTACTCGTCG 59.403 50.000 0.00 0.00 0.00 5.12
4175 6290 2.030007 TCCGTTCCAAATTACTCGTCGT 60.030 45.455 0.00 0.00 0.00 4.34
4176 6291 2.091588 CCGTTCCAAATTACTCGTCGTG 59.908 50.000 0.00 0.00 0.00 4.35
4177 6292 2.091588 CGTTCCAAATTACTCGTCGTGG 59.908 50.000 0.00 0.00 0.00 4.94
4178 6293 3.062042 GTTCCAAATTACTCGTCGTGGT 58.938 45.455 0.00 0.00 0.00 4.16
4179 6294 3.389925 TCCAAATTACTCGTCGTGGTT 57.610 42.857 0.00 0.00 0.00 3.67
4180 6295 3.731089 TCCAAATTACTCGTCGTGGTTT 58.269 40.909 0.00 0.00 0.00 3.27
4181 6296 4.128643 TCCAAATTACTCGTCGTGGTTTT 58.871 39.130 0.00 0.00 0.00 2.43
4182 6297 5.295950 TCCAAATTACTCGTCGTGGTTTTA 58.704 37.500 0.00 0.00 0.00 1.52
4183 6298 5.406175 TCCAAATTACTCGTCGTGGTTTTAG 59.594 40.000 0.00 0.00 0.00 1.85
4184 6299 5.178067 CCAAATTACTCGTCGTGGTTTTAGT 59.822 40.000 0.00 0.00 0.00 2.24
4185 6300 6.293027 CCAAATTACTCGTCGTGGTTTTAGTT 60.293 38.462 0.00 0.00 0.00 2.24
4186 6301 6.457851 AATTACTCGTCGTGGTTTTAGTTC 57.542 37.500 0.00 0.00 0.00 3.01
4187 6302 3.441496 ACTCGTCGTGGTTTTAGTTCA 57.559 42.857 0.00 0.00 0.00 3.18
4188 6303 3.784338 ACTCGTCGTGGTTTTAGTTCAA 58.216 40.909 0.00 0.00 0.00 2.69
4189 6304 4.183101 ACTCGTCGTGGTTTTAGTTCAAA 58.817 39.130 0.00 0.00 0.00 2.69
4190 6305 4.812626 ACTCGTCGTGGTTTTAGTTCAAAT 59.187 37.500 0.00 0.00 0.00 2.32
4191 6306 5.295045 ACTCGTCGTGGTTTTAGTTCAAATT 59.705 36.000 0.00 0.00 0.00 1.82
4192 6307 6.121613 TCGTCGTGGTTTTAGTTCAAATTT 57.878 33.333 0.00 0.00 0.00 1.82
4193 6308 7.011295 ACTCGTCGTGGTTTTAGTTCAAATTTA 59.989 33.333 0.00 0.00 0.00 1.40
4194 6309 7.125113 TCGTCGTGGTTTTAGTTCAAATTTAC 58.875 34.615 0.00 0.00 0.00 2.01
4195 6310 7.011295 TCGTCGTGGTTTTAGTTCAAATTTACT 59.989 33.333 0.00 0.00 0.00 2.24
4196 6311 7.319615 CGTCGTGGTTTTAGTTCAAATTTACTC 59.680 37.037 0.00 0.00 0.00 2.59
4197 6312 7.319615 GTCGTGGTTTTAGTTCAAATTTACTCG 59.680 37.037 0.00 0.00 0.00 4.18
4198 6313 7.011295 TCGTGGTTTTAGTTCAAATTTACTCGT 59.989 33.333 0.00 0.00 0.00 4.18
4199 6314 7.319615 CGTGGTTTTAGTTCAAATTTACTCGTC 59.680 37.037 0.00 0.00 0.00 4.20
4200 6315 7.319615 GTGGTTTTAGTTCAAATTTACTCGTCG 59.680 37.037 0.00 0.00 0.00 5.12
4201 6316 7.011295 TGGTTTTAGTTCAAATTTACTCGTCGT 59.989 33.333 0.00 0.00 0.00 4.34
4202 6317 7.319615 GGTTTTAGTTCAAATTTACTCGTCGTG 59.680 37.037 0.00 0.00 0.00 4.35
4203 6318 4.985044 AGTTCAAATTTACTCGTCGTGG 57.015 40.909 0.00 0.00 0.00 4.94
4204 6319 4.374399 AGTTCAAATTTACTCGTCGTGGT 58.626 39.130 0.00 0.00 0.00 4.16
4205 6320 4.812626 AGTTCAAATTTACTCGTCGTGGTT 59.187 37.500 0.00 0.00 0.00 3.67
4206 6321 5.295045 AGTTCAAATTTACTCGTCGTGGTTT 59.705 36.000 0.00 0.00 0.00 3.27
4207 6322 5.738118 TCAAATTTACTCGTCGTGGTTTT 57.262 34.783 0.00 0.00 0.00 2.43
4208 6323 6.841443 TCAAATTTACTCGTCGTGGTTTTA 57.159 33.333 0.00 0.00 0.00 1.52
4209 6324 6.879962 TCAAATTTACTCGTCGTGGTTTTAG 58.120 36.000 0.00 0.00 0.00 1.85
4210 6325 6.479660 TCAAATTTACTCGTCGTGGTTTTAGT 59.520 34.615 0.00 0.00 0.00 2.24
4211 6326 6.849588 AATTTACTCGTCGTGGTTTTAGTT 57.150 33.333 0.00 0.00 0.00 2.24
4212 6327 5.888412 TTTACTCGTCGTGGTTTTAGTTC 57.112 39.130 0.00 0.00 0.00 3.01
4213 6328 3.441496 ACTCGTCGTGGTTTTAGTTCA 57.559 42.857 0.00 0.00 0.00 3.18
4214 6329 3.784338 ACTCGTCGTGGTTTTAGTTCAA 58.216 40.909 0.00 0.00 0.00 2.69
4215 6330 4.183101 ACTCGTCGTGGTTTTAGTTCAAA 58.817 39.130 0.00 0.00 0.00 2.69
4216 6331 4.812626 ACTCGTCGTGGTTTTAGTTCAAAT 59.187 37.500 0.00 0.00 0.00 2.32
4217 6332 5.295045 ACTCGTCGTGGTTTTAGTTCAAATT 59.705 36.000 0.00 0.00 0.00 1.82
4218 6333 6.479660 ACTCGTCGTGGTTTTAGTTCAAATTA 59.520 34.615 0.00 0.00 0.00 1.40
4219 6334 7.011295 ACTCGTCGTGGTTTTAGTTCAAATTAA 59.989 33.333 0.00 0.00 0.00 1.40
4220 6335 7.125113 TCGTCGTGGTTTTAGTTCAAATTAAC 58.875 34.615 0.00 0.00 0.00 2.01
4221 6336 7.011295 TCGTCGTGGTTTTAGTTCAAATTAACT 59.989 33.333 0.00 0.00 42.31 2.24
4222 6337 8.274939 CGTCGTGGTTTTAGTTCAAATTAACTA 58.725 33.333 0.00 0.00 40.20 2.24
4223 6338 9.934190 GTCGTGGTTTTAGTTCAAATTAACTAA 57.066 29.630 8.77 8.77 45.59 2.24
4232 6347 9.934190 TTAGTTCAAATTAACTAAAACCACGAC 57.066 29.630 9.98 0.00 44.77 4.34
4233 6348 7.127686 AGTTCAAATTAACTAAAACCACGACG 58.872 34.615 0.00 0.00 37.93 5.12
4234 6349 6.841443 TCAAATTAACTAAAACCACGACGA 57.159 33.333 0.00 0.00 0.00 4.20
4235 6350 6.879962 TCAAATTAACTAAAACCACGACGAG 58.120 36.000 0.00 0.00 0.00 4.18
4236 6351 6.479660 TCAAATTAACTAAAACCACGACGAGT 59.520 34.615 0.00 0.00 0.00 4.18
4237 6352 7.651304 TCAAATTAACTAAAACCACGACGAGTA 59.349 33.333 0.00 0.00 0.00 2.59
4238 6353 7.945033 AATTAACTAAAACCACGACGAGTAA 57.055 32.000 0.00 0.00 0.00 2.24
4239 6354 8.538409 AATTAACTAAAACCACGACGAGTAAT 57.462 30.769 0.00 0.00 0.00 1.89
4240 6355 7.945033 TTAACTAAAACCACGACGAGTAATT 57.055 32.000 0.00 1.08 0.00 1.40
4241 6356 6.849588 AACTAAAACCACGACGAGTAATTT 57.150 33.333 0.00 0.34 0.00 1.82
4242 6357 6.219302 ACTAAAACCACGACGAGTAATTTG 57.781 37.500 0.00 2.39 0.00 2.32
4243 6358 4.477302 AAAACCACGACGAGTAATTTGG 57.523 40.909 0.00 0.00 0.00 3.28
4244 6359 3.389925 AACCACGACGAGTAATTTGGA 57.610 42.857 0.00 0.00 0.00 3.53
4245 6360 3.389925 ACCACGACGAGTAATTTGGAA 57.610 42.857 0.00 0.00 0.00 3.53
4246 6361 3.062042 ACCACGACGAGTAATTTGGAAC 58.938 45.455 0.00 0.00 0.00 3.62
4247 6362 2.091588 CCACGACGAGTAATTTGGAACG 59.908 50.000 0.00 0.00 0.00 3.95
4248 6363 2.091588 CACGACGAGTAATTTGGAACGG 59.908 50.000 0.00 0.00 0.00 4.44
4249 6364 2.030007 ACGACGAGTAATTTGGAACGGA 60.030 45.455 0.00 0.00 0.00 4.69
4250 6365 2.597305 CGACGAGTAATTTGGAACGGAG 59.403 50.000 0.00 0.00 0.00 4.63
4251 6366 2.928116 GACGAGTAATTTGGAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
4252 6367 2.277084 CGAGTAATTTGGAACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
4253 6368 2.093869 CGAGTAATTTGGAACGGAGGGA 60.094 50.000 0.00 0.00 0.00 4.20
4356 6478 9.113876 CTTAAAACACACTCATTACGGAAATTC 57.886 33.333 0.00 0.00 0.00 2.17
4592 6715 7.607005 CAAGGTTACGTATCGATGTTTACTTC 58.393 38.462 8.54 0.00 0.00 3.01
4760 6883 0.251832 TCTTCTCGACCCTCAAGGCT 60.252 55.000 0.00 0.00 40.58 4.58
4832 6955 3.632604 TCTCGGAGAAGAGCGATGTTTAT 59.367 43.478 4.96 0.00 38.12 1.40
4863 6986 5.357032 GGGGTAATTGTGTTTCAGATACTGG 59.643 44.000 0.00 0.00 31.51 4.00
5401 8036 5.013079 TGACTCCCAAGTGTACAATCAATCT 59.987 40.000 0.00 0.00 35.28 2.40
5497 8132 2.167281 GTCCTTGAGAGCATGTGAGCTA 59.833 50.000 0.00 0.00 46.75 3.32
5828 8465 0.462225 TGTCGTCGCCTTGGTTTTGA 60.462 50.000 0.00 0.00 0.00 2.69
5836 8473 1.754226 GCCTTGGTTTTGACACTCCAA 59.246 47.619 0.00 0.00 38.13 3.53
5938 8581 3.910490 GCTGGTTTTGGCACGCCA 61.910 61.111 6.67 6.67 45.63 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.759436 TAGATGAAGGCGAGGACCCC 60.759 60.000 0.00 0.00 0.00 4.95
74 77 6.318900 GCTGATAGGCTACAGTGGTAATTTTT 59.681 38.462 18.72 0.00 36.62 1.94
75 78 5.823045 GCTGATAGGCTACAGTGGTAATTTT 59.177 40.000 18.72 0.00 36.62 1.82
76 79 5.368989 GCTGATAGGCTACAGTGGTAATTT 58.631 41.667 18.72 0.00 36.62 1.82
77 80 4.501571 CGCTGATAGGCTACAGTGGTAATT 60.502 45.833 20.45 0.00 39.84 1.40
78 81 3.005897 CGCTGATAGGCTACAGTGGTAAT 59.994 47.826 20.45 0.00 39.84 1.89
95 98 1.227342 TGCAAAATGACGCTCGCTGA 61.227 50.000 0.00 0.00 0.00 4.26
98 101 1.840141 GTTATGCAAAATGACGCTCGC 59.160 47.619 0.00 0.00 0.00 5.03
100 103 2.440501 CGGTTATGCAAAATGACGCTC 58.559 47.619 0.00 0.00 0.00 5.03
105 108 1.550327 TGGGCGGTTATGCAAAATGA 58.450 45.000 0.00 0.00 36.28 2.57
137 140 2.192263 AGAAGAAGGTGAGGATCCCAC 58.808 52.381 19.58 19.58 0.00 4.61
197 200 7.148967 GCGGTGAGAAAACTTTTGAAATATGTC 60.149 37.037 0.00 0.00 0.00 3.06
205 208 1.268335 GCGCGGTGAGAAAACTTTTGA 60.268 47.619 8.83 0.00 0.00 2.69
238 241 2.601398 CCAGCTATGCCATGTCGCG 61.601 63.158 0.00 0.00 0.00 5.87
241 244 1.027357 CCAACCAGCTATGCCATGTC 58.973 55.000 0.00 0.00 0.00 3.06
243 246 1.737816 GCCAACCAGCTATGCCATG 59.262 57.895 0.00 0.00 0.00 3.66
401 406 3.350833 AGCCTGGCAAACTTGATCTAAG 58.649 45.455 22.65 0.00 42.30 2.18
406 411 3.230134 TGTAAAGCCTGGCAAACTTGAT 58.770 40.909 22.65 0.00 0.00 2.57
435 440 6.304356 TGAACACATAATAGCATAGCAAGC 57.696 37.500 0.00 0.00 0.00 4.01
438 443 7.140705 GCAAATGAACACATAATAGCATAGCA 58.859 34.615 0.00 0.00 0.00 3.49
500 505 3.909776 TGATATACGGGACACATCGTC 57.090 47.619 0.00 0.00 44.57 4.20
503 508 4.177026 GAGCATGATATACGGGACACATC 58.823 47.826 0.00 0.00 0.00 3.06
531 536 4.460683 GCCGCCCGTGTATCACCA 62.461 66.667 0.00 0.00 0.00 4.17
659 665 8.893219 TCATTGCCTATGTATACAAAGAAGAG 57.107 34.615 10.14 1.22 35.64 2.85
717 728 3.530535 TGCAATGCTAGATGCTTACGAA 58.469 40.909 6.82 0.00 42.97 3.85
728 739 1.952296 GGAATCCACCTGCAATGCTAG 59.048 52.381 6.82 2.23 0.00 3.42
754 765 4.074526 TGGAGAGCAGTCGCAGGC 62.075 66.667 0.00 0.00 42.27 4.85
785 797 3.609175 CGAACTGAACATTTTGCGTCCAT 60.609 43.478 0.00 0.00 0.00 3.41
1011 1050 1.078848 CTCCCTCTTCTTGGTGCGG 60.079 63.158 0.00 0.00 0.00 5.69
1016 1055 0.985490 CCCTCCCTCCCTCTTCTTGG 60.985 65.000 0.00 0.00 0.00 3.61
1606 1650 4.644103 ATCAATCCAAGCAATGCTGTAC 57.356 40.909 9.14 0.00 39.62 2.90
1703 1767 2.030805 AGCCAAGAAGCGTCAATCAAAC 60.031 45.455 1.61 0.00 38.01 2.93
2153 2593 3.909086 AAGCTCAAGTCCAGCCGCC 62.909 63.158 0.00 0.00 37.63 6.13
2154 2594 2.359230 AAGCTCAAGTCCAGCCGC 60.359 61.111 0.00 0.00 37.63 6.53
2155 2595 0.603707 TTGAAGCTCAAGTCCAGCCG 60.604 55.000 0.00 0.00 37.63 5.52
2595 3039 2.586792 GCCAGAAGGATCACCGCT 59.413 61.111 0.00 0.00 41.83 5.52
2746 3190 4.639171 TGACGACGCGCTCTTGCA 62.639 61.111 5.73 0.00 39.64 4.08
2838 3282 4.316823 AGGCTCGGGGACACCTCA 62.317 66.667 0.00 0.00 36.97 3.86
2909 3353 4.832823 TGGAATTTTTCTTTCCCAGGAGAC 59.167 41.667 0.00 0.00 41.68 3.36
3111 3555 2.600729 CCTGGAGCAGCAGAACCCT 61.601 63.158 0.00 0.00 0.00 4.34
3183 3627 1.299541 CTGCAACGTCCAAGAAGTGT 58.700 50.000 0.00 0.00 0.00 3.55
3252 3696 2.291043 GGACACCCTCGTGGACCAT 61.291 63.158 4.76 0.00 44.86 3.55
3300 3744 1.107945 GACAGAGAGGGACACTAGCC 58.892 60.000 0.00 0.00 0.00 3.93
3301 3745 1.474879 GTGACAGAGAGGGACACTAGC 59.525 57.143 0.00 0.00 0.00 3.42
3303 3747 2.108425 ACAGTGACAGAGAGGGACACTA 59.892 50.000 0.00 0.00 39.33 2.74
3304 3748 1.133325 ACAGTGACAGAGAGGGACACT 60.133 52.381 0.00 0.00 41.52 3.55
3305 3749 1.271102 GACAGTGACAGAGAGGGACAC 59.729 57.143 0.00 0.00 0.00 3.67
3307 3751 1.917872 AGACAGTGACAGAGAGGGAC 58.082 55.000 0.00 0.00 0.00 4.46
3411 3855 1.064003 TGCTTCTCAGGCAGGGTTTA 58.936 50.000 0.00 0.00 34.56 2.01
3454 3900 2.620115 TGCATTCTGCCAAGCTTATAGC 59.380 45.455 0.00 3.27 44.23 2.97
3455 3901 3.628942 TGTGCATTCTGCCAAGCTTATAG 59.371 43.478 0.00 0.00 44.23 1.31
3456 3902 3.378112 GTGTGCATTCTGCCAAGCTTATA 59.622 43.478 0.00 0.00 44.23 0.98
3457 3903 2.165030 GTGTGCATTCTGCCAAGCTTAT 59.835 45.455 0.00 0.00 44.23 1.73
3458 3904 1.541147 GTGTGCATTCTGCCAAGCTTA 59.459 47.619 0.00 0.00 44.23 3.09
3459 3905 0.316204 GTGTGCATTCTGCCAAGCTT 59.684 50.000 0.00 0.00 44.23 3.74
3460 3906 0.824595 TGTGTGCATTCTGCCAAGCT 60.825 50.000 0.00 0.00 44.23 3.74
3461 3907 0.245539 ATGTGTGCATTCTGCCAAGC 59.754 50.000 0.00 0.00 44.23 4.01
3462 3908 1.271379 ACATGTGTGCATTCTGCCAAG 59.729 47.619 0.00 0.00 44.23 3.61
3463 3909 1.270274 GACATGTGTGCATTCTGCCAA 59.730 47.619 1.15 0.00 44.23 4.52
3464 3910 0.883153 GACATGTGTGCATTCTGCCA 59.117 50.000 1.15 0.00 44.23 4.92
3465 3911 0.171903 GGACATGTGTGCATTCTGCC 59.828 55.000 1.15 0.00 44.23 4.85
3466 3912 0.883153 TGGACATGTGTGCATTCTGC 59.117 50.000 1.15 0.00 41.48 4.26
3476 3922 4.758674 ACTGAGAAACTGATTGGACATGTG 59.241 41.667 1.15 0.00 0.00 3.21
3565 4011 0.098376 GTGACTACCGGAGTGTAGCG 59.902 60.000 9.46 0.00 41.57 4.26
3639 4085 0.612174 GGCAGGGGTTTTCCTCCTTC 60.612 60.000 0.00 0.00 42.67 3.46
3705 4155 5.596268 AAAAACGTCTTACATTACGGGAC 57.404 39.130 0.00 0.00 43.25 4.46
3767 4220 7.016072 CAGAGGGAGTACTTAGGATGATTTGAT 59.984 40.741 0.00 0.00 0.00 2.57
3834 4288 2.687003 ATAGTGACCTAGGAGGCCTC 57.313 55.000 25.59 25.59 39.63 4.70
3837 4291 7.778185 TCTAATTTATAGTGACCTAGGAGGC 57.222 40.000 17.98 4.90 39.63 4.70
4052 6167 2.589720 TGAAAGACGGTACTCACTCCA 58.410 47.619 0.00 0.00 0.00 3.86
4137 6252 5.221661 GGAACGGAGGGAGTACATGATAAAT 60.222 44.000 0.00 0.00 0.00 1.40
4146 6261 3.345508 AATTTGGAACGGAGGGAGTAC 57.654 47.619 0.00 0.00 0.00 2.73
4147 6262 4.098894 AGTAATTTGGAACGGAGGGAGTA 58.901 43.478 0.00 0.00 0.00 2.59
4148 6263 2.910977 AGTAATTTGGAACGGAGGGAGT 59.089 45.455 0.00 0.00 0.00 3.85
4149 6264 3.532542 GAGTAATTTGGAACGGAGGGAG 58.467 50.000 0.00 0.00 0.00 4.30
4150 6265 2.093869 CGAGTAATTTGGAACGGAGGGA 60.094 50.000 0.00 0.00 0.00 4.20
4151 6266 2.277084 CGAGTAATTTGGAACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
4152 6267 2.928116 GACGAGTAATTTGGAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
4153 6268 2.597305 CGACGAGTAATTTGGAACGGAG 59.403 50.000 0.00 0.00 0.00 4.63
4154 6269 2.030007 ACGACGAGTAATTTGGAACGGA 60.030 45.455 0.00 0.00 0.00 4.69
4155 6270 2.091588 CACGACGAGTAATTTGGAACGG 59.908 50.000 0.00 0.00 0.00 4.44
4156 6271 2.091588 CCACGACGAGTAATTTGGAACG 59.908 50.000 0.00 0.00 0.00 3.95
4157 6272 3.062042 ACCACGACGAGTAATTTGGAAC 58.938 45.455 0.00 0.00 0.00 3.62
4158 6273 3.389925 ACCACGACGAGTAATTTGGAA 57.610 42.857 0.00 0.00 0.00 3.53
4159 6274 3.389925 AACCACGACGAGTAATTTGGA 57.610 42.857 0.00 0.00 0.00 3.53
4160 6275 4.477302 AAAACCACGACGAGTAATTTGG 57.523 40.909 0.00 0.00 0.00 3.28
4161 6276 6.219302 ACTAAAACCACGACGAGTAATTTG 57.781 37.500 0.00 2.39 0.00 2.32
4162 6277 6.479660 TGAACTAAAACCACGACGAGTAATTT 59.520 34.615 0.00 0.34 0.00 1.82
4163 6278 5.984926 TGAACTAAAACCACGACGAGTAATT 59.015 36.000 0.00 1.08 0.00 1.40
4164 6279 5.531634 TGAACTAAAACCACGACGAGTAAT 58.468 37.500 0.00 0.00 0.00 1.89
4165 6280 4.930963 TGAACTAAAACCACGACGAGTAA 58.069 39.130 0.00 0.00 0.00 2.24
4166 6281 4.566545 TGAACTAAAACCACGACGAGTA 57.433 40.909 0.00 0.00 0.00 2.59
4167 6282 3.441496 TGAACTAAAACCACGACGAGT 57.559 42.857 0.00 0.00 0.00 4.18
4168 6283 4.782252 TTTGAACTAAAACCACGACGAG 57.218 40.909 0.00 0.00 0.00 4.18
4169 6284 5.738118 AATTTGAACTAAAACCACGACGA 57.262 34.783 0.00 0.00 0.00 4.20
4170 6285 7.127686 AGTAAATTTGAACTAAAACCACGACG 58.872 34.615 0.00 0.00 0.00 5.12
4171 6286 7.319615 CGAGTAAATTTGAACTAAAACCACGAC 59.680 37.037 0.00 0.00 0.00 4.34
4172 6287 7.011295 ACGAGTAAATTTGAACTAAAACCACGA 59.989 33.333 0.00 0.00 0.00 4.35
4173 6288 7.127686 ACGAGTAAATTTGAACTAAAACCACG 58.872 34.615 0.00 0.00 0.00 4.94
4174 6289 7.319615 CGACGAGTAAATTTGAACTAAAACCAC 59.680 37.037 0.00 0.00 0.00 4.16
4175 6290 7.011295 ACGACGAGTAAATTTGAACTAAAACCA 59.989 33.333 0.00 0.00 0.00 3.67
4176 6291 7.319615 CACGACGAGTAAATTTGAACTAAAACC 59.680 37.037 0.00 0.00 0.00 3.27
4177 6292 7.319615 CCACGACGAGTAAATTTGAACTAAAAC 59.680 37.037 0.00 0.00 0.00 2.43
4178 6293 7.011295 ACCACGACGAGTAAATTTGAACTAAAA 59.989 33.333 0.00 0.00 0.00 1.52
4179 6294 6.479660 ACCACGACGAGTAAATTTGAACTAAA 59.520 34.615 0.00 0.00 0.00 1.85
4180 6295 5.984926 ACCACGACGAGTAAATTTGAACTAA 59.015 36.000 0.00 0.00 0.00 2.24
4181 6296 5.531634 ACCACGACGAGTAAATTTGAACTA 58.468 37.500 0.00 0.00 0.00 2.24
4182 6297 4.374399 ACCACGACGAGTAAATTTGAACT 58.626 39.130 0.00 0.00 0.00 3.01
4183 6298 4.720530 ACCACGACGAGTAAATTTGAAC 57.279 40.909 0.00 0.00 0.00 3.18
4184 6299 5.738118 AAACCACGACGAGTAAATTTGAA 57.262 34.783 0.00 0.00 0.00 2.69
4185 6300 5.738118 AAAACCACGACGAGTAAATTTGA 57.262 34.783 0.00 0.00 0.00 2.69
4186 6301 6.652245 ACTAAAACCACGACGAGTAAATTTG 58.348 36.000 0.00 0.24 0.00 2.32
4187 6302 6.849588 ACTAAAACCACGACGAGTAAATTT 57.150 33.333 0.00 0.00 0.00 1.82
4188 6303 6.479660 TGAACTAAAACCACGACGAGTAAATT 59.520 34.615 0.00 0.00 0.00 1.82
4189 6304 5.984926 TGAACTAAAACCACGACGAGTAAAT 59.015 36.000 0.00 0.00 0.00 1.40
4190 6305 5.347342 TGAACTAAAACCACGACGAGTAAA 58.653 37.500 0.00 0.00 0.00 2.01
4191 6306 4.930963 TGAACTAAAACCACGACGAGTAA 58.069 39.130 0.00 0.00 0.00 2.24
4192 6307 4.566545 TGAACTAAAACCACGACGAGTA 57.433 40.909 0.00 0.00 0.00 2.59
4193 6308 3.441496 TGAACTAAAACCACGACGAGT 57.559 42.857 0.00 0.00 0.00 4.18
4194 6309 4.782252 TTTGAACTAAAACCACGACGAG 57.218 40.909 0.00 0.00 0.00 4.18
4195 6310 5.738118 AATTTGAACTAAAACCACGACGA 57.262 34.783 0.00 0.00 0.00 4.20
4196 6311 7.127686 AGTTAATTTGAACTAAAACCACGACG 58.872 34.615 0.00 0.00 37.90 5.12
4197 6312 9.934190 TTAGTTAATTTGAACTAAAACCACGAC 57.066 29.630 9.98 0.00 44.84 4.34
4206 6321 9.934190 GTCGTGGTTTTAGTTAATTTGAACTAA 57.066 29.630 8.77 8.77 45.67 2.24
4207 6322 8.274939 CGTCGTGGTTTTAGTTAATTTGAACTA 58.725 33.333 0.00 0.00 40.22 2.24
4208 6323 7.011295 TCGTCGTGGTTTTAGTTAATTTGAACT 59.989 33.333 0.00 0.00 42.35 3.01
4209 6324 7.125113 TCGTCGTGGTTTTAGTTAATTTGAAC 58.875 34.615 0.00 0.00 0.00 3.18
4210 6325 7.011295 ACTCGTCGTGGTTTTAGTTAATTTGAA 59.989 33.333 0.00 0.00 0.00 2.69
4211 6326 6.479660 ACTCGTCGTGGTTTTAGTTAATTTGA 59.520 34.615 0.00 0.00 0.00 2.69
4212 6327 6.652245 ACTCGTCGTGGTTTTAGTTAATTTG 58.348 36.000 0.00 0.00 0.00 2.32
4213 6328 6.849588 ACTCGTCGTGGTTTTAGTTAATTT 57.150 33.333 0.00 0.00 0.00 1.82
4214 6329 7.945033 TTACTCGTCGTGGTTTTAGTTAATT 57.055 32.000 0.00 0.00 0.00 1.40
4215 6330 8.538409 AATTACTCGTCGTGGTTTTAGTTAAT 57.462 30.769 0.00 0.00 0.00 1.40
4216 6331 7.945033 AATTACTCGTCGTGGTTTTAGTTAA 57.055 32.000 0.00 0.00 0.00 2.01
4217 6332 7.095691 CCAAATTACTCGTCGTGGTTTTAGTTA 60.096 37.037 0.00 0.00 0.00 2.24
4218 6333 6.293027 CCAAATTACTCGTCGTGGTTTTAGTT 60.293 38.462 0.00 0.00 0.00 2.24
4219 6334 5.178067 CCAAATTACTCGTCGTGGTTTTAGT 59.822 40.000 0.00 0.00 0.00 2.24
4220 6335 5.406175 TCCAAATTACTCGTCGTGGTTTTAG 59.594 40.000 0.00 0.00 0.00 1.85
4221 6336 5.295950 TCCAAATTACTCGTCGTGGTTTTA 58.704 37.500 0.00 0.00 0.00 1.52
4222 6337 4.128643 TCCAAATTACTCGTCGTGGTTTT 58.871 39.130 0.00 0.00 0.00 2.43
4223 6338 3.731089 TCCAAATTACTCGTCGTGGTTT 58.269 40.909 0.00 0.00 0.00 3.27
4224 6339 3.389925 TCCAAATTACTCGTCGTGGTT 57.610 42.857 0.00 0.00 0.00 3.67
4225 6340 3.062042 GTTCCAAATTACTCGTCGTGGT 58.938 45.455 0.00 0.00 0.00 4.16
4226 6341 2.091588 CGTTCCAAATTACTCGTCGTGG 59.908 50.000 0.00 0.00 0.00 4.94
4227 6342 2.091588 CCGTTCCAAATTACTCGTCGTG 59.908 50.000 0.00 0.00 0.00 4.35
4228 6343 2.030007 TCCGTTCCAAATTACTCGTCGT 60.030 45.455 0.00 0.00 0.00 4.34
4229 6344 2.597305 CTCCGTTCCAAATTACTCGTCG 59.403 50.000 0.00 0.00 0.00 5.12
4230 6345 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
4231 6346 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
4232 6347 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
4233 6348 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
4234 6349 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
4235 6350 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
4236 6351 3.118519 GCTACTCCCTCCGTTCCAAATTA 60.119 47.826 0.00 0.00 0.00 1.40
4237 6352 2.355818 GCTACTCCCTCCGTTCCAAATT 60.356 50.000 0.00 0.00 0.00 1.82
4238 6353 1.209747 GCTACTCCCTCCGTTCCAAAT 59.790 52.381 0.00 0.00 0.00 2.32
4239 6354 0.611714 GCTACTCCCTCCGTTCCAAA 59.388 55.000 0.00 0.00 0.00 3.28
4240 6355 0.252103 AGCTACTCCCTCCGTTCCAA 60.252 55.000 0.00 0.00 0.00 3.53
4241 6356 0.683504 GAGCTACTCCCTCCGTTCCA 60.684 60.000 0.00 0.00 0.00 3.53
4242 6357 0.396001 AGAGCTACTCCCTCCGTTCC 60.396 60.000 0.00 0.00 0.00 3.62
4243 6358 0.741915 CAGAGCTACTCCCTCCGTTC 59.258 60.000 0.00 0.00 0.00 3.95
4244 6359 0.331954 TCAGAGCTACTCCCTCCGTT 59.668 55.000 0.00 0.00 0.00 4.44
4245 6360 0.331954 TTCAGAGCTACTCCCTCCGT 59.668 55.000 0.00 0.00 0.00 4.69
4246 6361 1.407258 CTTTCAGAGCTACTCCCTCCG 59.593 57.143 0.00 0.00 0.00 4.63
4247 6362 2.462723 ACTTTCAGAGCTACTCCCTCC 58.537 52.381 0.00 0.00 0.00 4.30
4248 6363 4.545208 AAACTTTCAGAGCTACTCCCTC 57.455 45.455 0.00 0.00 0.00 4.30
4249 6364 4.595350 AGAAAACTTTCAGAGCTACTCCCT 59.405 41.667 5.07 0.00 39.61 4.20
4250 6365 4.900684 AGAAAACTTTCAGAGCTACTCCC 58.099 43.478 5.07 0.00 39.61 4.30
4251 6366 6.869315 AAAGAAAACTTTCAGAGCTACTCC 57.131 37.500 5.07 0.00 39.61 3.85
4356 6478 3.494251 GTGCTTTACTTTGGGCATTGTTG 59.506 43.478 0.00 0.00 37.05 3.33
4563 6686 4.110482 ACATCGATACGTAACCTTGCTTC 58.890 43.478 0.00 0.00 0.00 3.86
4576 6699 7.772332 ATTCCTGTGAAGTAAACATCGATAC 57.228 36.000 0.00 0.00 33.05 2.24
4592 6715 4.201657 TGTGCAGATATCCAATTCCTGTG 58.798 43.478 0.00 0.00 0.00 3.66
4832 6955 2.279935 ACACAATTACCCCGAAAGCA 57.720 45.000 0.00 0.00 0.00 3.91
4863 6986 3.165890 GCATCGTTTTACTTTTACCCGC 58.834 45.455 0.00 0.00 0.00 6.13
5104 7250 7.463054 AGTGACCCTAGATAAGTACTCCTAA 57.537 40.000 0.00 0.00 0.00 2.69
5401 8036 2.676632 ACTGGTACACGTGAACACAA 57.323 45.000 25.01 9.41 0.00 3.33
5496 8131 6.653020 ACAAGACAAGACAGCAATCCATATA 58.347 36.000 0.00 0.00 0.00 0.86
5497 8132 5.503927 ACAAGACAAGACAGCAATCCATAT 58.496 37.500 0.00 0.00 0.00 1.78
5727 8362 6.690530 CACTGCCAATCCAAATCTAAAAGAA 58.309 36.000 0.00 0.00 0.00 2.52
5756 8391 2.152297 TAAAGTGGGTCGGCGCGTTA 62.152 55.000 8.43 0.00 0.00 3.18
5836 8473 3.656045 CAAACCTTTCCCGCGCGT 61.656 61.111 29.95 4.74 0.00 6.01
5938 8581 1.947597 TAATAACGAGTGCCGGCCGT 61.948 55.000 26.77 23.63 43.93 5.68
5947 8590 3.445857 GAGCGCCTTCTTAATAACGAGT 58.554 45.455 2.29 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.