Multiple sequence alignment - TraesCS5B01G559300

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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 TraesCS5B01G559300 chr5B 100.000 7685 0 0 1 7685 706312144 706304460 0.000000e+00 14192.0
1 TraesCS5B01G559300 chr5B 86.364 484 37 10 1361 1840 516604646 516604188 1.150000e-137 501.0
2 TraesCS5B01G559300 chr5B 86.713 429 28 12 1416 1840 444453992 444453589 4.230000e-122 449.0
3 TraesCS5B01G559300 chr5B 88.655 238 16 4 1836 2065 444453499 444453265 5.870000e-71 279.0
4 TraesCS5B01G559300 chr5B 88.655 238 16 4 1836 2065 516604098 516603864 5.870000e-71 279.0
5 TraesCS5B01G559300 chr5B 90.260 154 12 1 5014 5164 706306879 706306726 1.690000e-46 198.0
6 TraesCS5B01G559300 chr5B 90.260 154 12 1 5266 5419 706307131 706306981 1.690000e-46 198.0
7 TraesCS5B01G559300 chr5B 97.674 86 2 0 5181 5266 706306879 706306964 1.730000e-31 148.0
8 TraesCS5B01G559300 chr5B 91.667 60 4 1 654 713 579367353 579367411 1.780000e-11 82.4
9 TraesCS5B01G559300 chr4A 93.188 2701 93 15 4598 7267 608607044 608609684 0.000000e+00 3884.0
10 TraesCS5B01G559300 chr4A 92.893 2012 68 28 2242 4196 608604015 608606008 0.000000e+00 2854.0
11 TraesCS5B01G559300 chr4A 93.168 483 23 8 1836 2317 608603558 608604031 0.000000e+00 701.0
12 TraesCS5B01G559300 chr4A 82.830 827 52 27 1039 1840 608602707 608603468 0.000000e+00 658.0
13 TraesCS5B01G559300 chr4A 96.429 364 13 0 4209 4572 608606691 608607054 1.100000e-167 601.0
14 TraesCS5B01G559300 chr4A 89.800 451 18 11 7249 7685 608609740 608610176 3.130000e-153 553.0
15 TraesCS5B01G559300 chr4A 93.056 144 10 0 5276 5419 608607456 608607599 2.170000e-50 211.0
16 TraesCS5B01G559300 chr4A 92.857 140 7 1 5028 5164 608607704 608607843 4.700000e-47 200.0
17 TraesCS5B01G559300 chr4A 86.528 193 8 4 1 175 608601717 608601909 6.080000e-46 196.0
18 TraesCS5B01G559300 chr4A 89.362 141 11 4 497 635 608601929 608602067 2.850000e-39 174.0
19 TraesCS5B01G559300 chr4A 80.672 238 21 9 7025 7238 608609080 608609316 2.220000e-35 161.0
20 TraesCS5B01G559300 chr5D 93.935 2572 79 18 4599 7146 563856096 563853578 0.000000e+00 3814.0
21 TraesCS5B01G559300 chr5D 93.848 2422 77 22 1836 4202 563859139 563856735 0.000000e+00 3581.0
22 TraesCS5B01G559300 chr5D 88.182 660 48 19 1 644 563861331 563860686 0.000000e+00 760.0
23 TraesCS5B01G559300 chr5D 83.924 790 62 24 752 1497 563860268 563859500 0.000000e+00 695.0
24 TraesCS5B01G559300 chr5D 96.154 364 14 0 4209 4572 563856450 563856087 5.130000e-166 595.0
25 TraesCS5B01G559300 chr5D 91.489 423 23 5 7263 7685 563853554 563853145 3.110000e-158 569.0
26 TraesCS5B01G559300 chr5D 90.260 154 12 1 5014 5164 563855454 563855301 1.690000e-46 198.0
27 TraesCS5B01G559300 chr5D 82.243 214 19 8 7043 7238 563854037 563853825 4.770000e-37 167.0
28 TraesCS5B01G559300 chr2B 92.283 635 34 3 6363 6986 248123239 248122609 0.000000e+00 887.0
29 TraesCS5B01G559300 chr2B 85.537 484 37 14 1361 1840 321107186 321107640 6.980000e-130 475.0
30 TraesCS5B01G559300 chr2B 89.520 229 13 4 1836 2056 321107730 321107955 5.870000e-71 279.0
31 TraesCS5B01G559300 chr2B 90.500 200 16 2 7270 7466 248107195 248106996 2.130000e-65 261.0
32 TraesCS5B01G559300 chr2B 83.871 155 11 4 6987 7129 248107468 248107316 1.350000e-27 135.0
33 TraesCS5B01G559300 chr4D 88.211 475 27 9 1370 1840 446552293 446551844 2.440000e-149 540.0
34 TraesCS5B01G559300 chr4D 87.104 473 32 10 1372 1840 99933444 99933891 6.880000e-140 508.0
35 TraesCS5B01G559300 chr4D 89.956 229 12 4 1836 2056 99933981 99934206 1.260000e-72 285.0
36 TraesCS5B01G559300 chr7B 86.570 484 35 13 1361 1840 656487796 656487339 2.470000e-139 507.0
37 TraesCS5B01G559300 chr7B 89.256 242 19 4 1601 1840 574901010 574900774 5.830000e-76 296.0
38 TraesCS5B01G559300 chr7B 89.496 238 14 4 1836 2065 656487249 656487015 2.710000e-74 291.0
39 TraesCS5B01G559300 chr7B 89.121 239 14 5 1836 2065 574900684 574900449 3.510000e-73 287.0
40 TraesCS5B01G559300 chr7B 91.667 96 8 0 5175 5270 208662025 208661930 4.840000e-27 134.0
41 TraesCS5B01G559300 chr3B 86.737 475 34 11 1370 1840 375546982 375547431 1.150000e-137 501.0
42 TraesCS5B01G559300 chr3B 97.778 45 1 0 665 709 679508907 679508863 2.300000e-10 78.7
43 TraesCS5B01G559300 chr7A 86.364 484 34 13 1361 1840 919351 918896 4.140000e-137 499.0
44 TraesCS5B01G559300 chr7A 89.956 229 11 5 1836 2056 662679531 662679755 1.260000e-72 285.0
45 TraesCS5B01G559300 chr7A 95.833 48 2 0 663 710 35450318 35450271 2.300000e-10 78.7
46 TraesCS5B01G559300 chr1B 86.157 484 37 11 1361 1840 606229134 606229591 5.360000e-136 496.0
47 TraesCS5B01G559300 chr1B 95.833 96 2 1 5173 5268 493871971 493871878 3.710000e-33 154.0
48 TraesCS5B01G559300 chr1B 97.674 86 2 0 5181 5266 493871880 493871965 1.730000e-31 148.0
49 TraesCS5B01G559300 chr1B 93.617 94 4 1 5173 5266 296488085 296487994 1.040000e-28 139.0
50 TraesCS5B01G559300 chr3A 93.427 213 14 0 1361 1573 373433234 373433446 4.480000e-82 316.0
51 TraesCS5B01G559300 chr3A 90.830 229 10 4 1836 2056 171149908 171150133 5.830000e-76 296.0
52 TraesCS5B01G559300 chr3A 89.496 238 14 4 1836 2065 545676644 545676410 2.710000e-74 291.0
53 TraesCS5B01G559300 chr3A 89.076 238 15 4 1836 2065 58078623 58078389 1.260000e-72 285.0
54 TraesCS5B01G559300 chr3A 89.394 66 7 0 656 721 28890882 28890947 4.940000e-12 84.2
55 TraesCS5B01G559300 chr3A 93.478 46 3 0 659 704 594867085 594867130 1.380000e-07 69.4
56 TraesCS5B01G559300 chr2A 93.427 213 14 0 1361 1573 59861697 59861909 4.480000e-82 316.0
57 TraesCS5B01G559300 chr1D 90.830 229 10 4 1836 2056 308935760 308935985 5.830000e-76 296.0
58 TraesCS5B01G559300 chr1A 89.496 238 14 4 1836 2065 181970942 181970708 2.710000e-74 291.0
59 TraesCS5B01G559300 chr1A 89.520 229 13 5 1836 2056 359190467 359190692 5.870000e-71 279.0
60 TraesCS5B01G559300 chr5A 91.080 213 19 0 1361 1573 506442617 506442829 9.760000e-74 289.0
61 TraesCS5B01G559300 chr5A 93.617 94 5 1 5175 5268 444560945 444560853 1.040000e-28 139.0
62 TraesCS5B01G559300 chr7D 93.000 100 7 0 5169 5268 570655789 570655888 6.210000e-31 147.0
63 TraesCS5B01G559300 chr7D 96.512 86 3 0 5181 5266 419793198 419793113 8.040000e-30 143.0
64 TraesCS5B01G559300 chr7D 90.323 62 5 1 651 711 550028200 550028261 6.390000e-11 80.5
65 TraesCS5B01G559300 chr7D 97.500 40 1 0 515 554 107663204 107663165 1.380000e-07 69.4
66 TraesCS5B01G559300 chr6D 94.231 52 3 0 659 710 427717398 427717449 6.390000e-11 80.5
67 TraesCS5B01G559300 chr3D 92.593 54 4 0 657 710 516183345 516183292 2.300000e-10 78.7
68 TraesCS5B01G559300 chr2D 87.097 62 7 1 650 710 119181115 119181054 1.380000e-07 69.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G559300 chr5B 706304460 706312144 7684 True 14192.000000 14192 100.000000 1 7685 1 chr5B.!!$R1 7684
1 TraesCS5B01G559300 chr5B 516603864 516604646 782 True 390.000000 501 87.509500 1361 2065 2 chr5B.!!$R3 704
2 TraesCS5B01G559300 chr5B 444453265 444453992 727 True 364.000000 449 87.684000 1416 2065 2 chr5B.!!$R2 649
3 TraesCS5B01G559300 chr4A 608601717 608610176 8459 False 926.636364 3884 90.071182 1 7685 11 chr4A.!!$F1 7684
4 TraesCS5B01G559300 chr5D 563853145 563861331 8186 True 1297.375000 3814 90.004375 1 7685 8 chr5D.!!$R1 7684
5 TraesCS5B01G559300 chr2B 248122609 248123239 630 True 887.000000 887 92.283000 6363 6986 1 chr2B.!!$R1 623
6 TraesCS5B01G559300 chr2B 321107186 321107955 769 False 377.000000 475 87.528500 1361 2056 2 chr2B.!!$F1 695
7 TraesCS5B01G559300 chr4D 99933444 99934206 762 False 396.500000 508 88.530000 1372 2056 2 chr4D.!!$F1 684
8 TraesCS5B01G559300 chr7B 656487015 656487796 781 True 399.000000 507 88.033000 1361 2065 2 chr7B.!!$R3 704
9 TraesCS5B01G559300 chr7B 574900449 574901010 561 True 291.500000 296 89.188500 1601 2065 2 chr7B.!!$R2 464

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
567 588 0.988832 TGGAAACAGGCTATCCCGTT 59.011 50.000 9.80 0.0 39.21 4.44 F
1355 1782 0.168788 CCGCAGGCTGTACATTGTTG 59.831 55.000 17.16 0.0 46.14 3.33 F
2014 2550 0.391661 TCTGGGACTCGCTTGCATTC 60.392 55.000 0.00 0.0 0.00 2.67 F
3243 3840 1.454847 TTGTGAACAGGTGTGGGCC 60.455 57.895 0.00 0.0 0.00 5.80 F
4029 4671 0.253327 CCCTTGCCTCCTTAGTGACC 59.747 60.000 0.00 0.0 0.00 4.02 F
4505 5825 1.673760 CGAATGTCGCTTTTGGTGTG 58.326 50.000 0.00 0.0 31.14 3.82 F
6248 7580 1.720533 ACAGGTAACCCTCACTCCCTA 59.279 52.381 0.00 0.0 39.89 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2286 2822 0.607620 TGTGACGTGCTGATCATGGA 59.392 50.0 0.00 0.00 36.01 3.41 R
2952 3547 0.673644 CCTGGACTACCTTTGCCACG 60.674 60.0 0.00 0.00 37.04 4.94 R
3447 4044 0.108585 TGAACTTCACAGCCTCCCAC 59.891 55.0 0.00 0.00 0.00 4.61 R
4493 5813 1.544686 GTGTCAACACACCAAAAGCG 58.455 50.0 8.37 0.00 46.49 4.68 R
5750 7080 1.068121 CCTTGGGGTTCTCCTTCAGT 58.932 55.0 0.00 0.00 35.33 3.41 R
6276 7608 0.250038 ATGCGGCTATGCTACACCTG 60.250 55.0 0.00 0.00 35.36 4.00 R
7532 8977 0.110056 TCTTAGAACGACGACGGCAC 60.110 55.0 12.58 2.66 44.46 5.01 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 44 2.957402 AAGGGAAAGTGCTCATGACA 57.043 45.000 0.00 0.00 0.00 3.58
159 179 6.572519 AGCGTATTTGCAAAATATGGTCATT 58.427 32.000 17.19 0.00 37.31 2.57
160 180 6.476380 AGCGTATTTGCAAAATATGGTCATTG 59.524 34.615 17.19 0.00 37.31 2.82
350 370 5.437289 TCATGTGTCTGAAAAATGTCCAC 57.563 39.130 0.00 0.00 0.00 4.02
385 405 5.353394 AATACTCGCCAGGTTTCAATAGA 57.647 39.130 0.00 0.00 0.00 1.98
470 491 8.931385 TCAAAATCAAAAGAAGAAAACCAGAG 57.069 30.769 0.00 0.00 0.00 3.35
523 544 5.457140 TCAAACATTTCATTAACGGCACTC 58.543 37.500 0.00 0.00 0.00 3.51
567 588 0.988832 TGGAAACAGGCTATCCCGTT 59.011 50.000 9.80 0.00 39.21 4.44
568 589 1.353022 TGGAAACAGGCTATCCCGTTT 59.647 47.619 9.80 0.00 40.48 3.60
579 600 4.399934 GGCTATCCCGTTTTGTATTTTCCA 59.600 41.667 0.00 0.00 0.00 3.53
582 603 6.039382 GCTATCCCGTTTTGTATTTTCCATCT 59.961 38.462 0.00 0.00 0.00 2.90
586 607 8.356000 TCCCGTTTTGTATTTTCCATCTTTAT 57.644 30.769 0.00 0.00 0.00 1.40
660 724 8.970691 AAAAACTGTTCCTATGAATTGAATCG 57.029 30.769 0.00 0.00 31.98 3.34
675 739 5.447624 TTGAATCGTAGACTTGACACTGA 57.552 39.130 0.00 0.00 42.51 3.41
731 1098 5.116180 TCTGTAAATGTTTAGATGCCCTCG 58.884 41.667 0.00 0.00 0.00 4.63
732 1099 4.196193 TGTAAATGTTTAGATGCCCTCGG 58.804 43.478 0.00 0.00 0.00 4.63
795 1162 6.121776 TGACCAGCCAGAGATAAACTTTTA 57.878 37.500 0.00 0.00 0.00 1.52
825 1193 4.215613 GGTTCACCAGACATAAACTTGGAC 59.784 45.833 0.00 0.00 35.64 4.02
828 1196 4.020573 TCACCAGACATAAACTTGGACGAT 60.021 41.667 0.00 0.00 0.00 3.73
836 1204 6.184789 ACATAAACTTGGACGATATTTGGGT 58.815 36.000 0.00 0.00 0.00 4.51
837 1205 7.340256 ACATAAACTTGGACGATATTTGGGTA 58.660 34.615 0.00 0.00 0.00 3.69
841 1209 7.712204 AACTTGGACGATATTTGGGTAAAAT 57.288 32.000 0.00 0.00 41.47 1.82
842 1210 8.810990 AACTTGGACGATATTTGGGTAAAATA 57.189 30.769 0.00 0.00 43.28 1.40
876 1244 3.725485 CGTATACGGCTGTTGGTGA 57.275 52.632 17.61 0.00 35.37 4.02
877 1245 1.999048 CGTATACGGCTGTTGGTGAA 58.001 50.000 17.61 0.00 35.37 3.18
878 1246 2.339418 CGTATACGGCTGTTGGTGAAA 58.661 47.619 17.61 0.00 35.37 2.69
879 1247 2.933906 CGTATACGGCTGTTGGTGAAAT 59.066 45.455 17.61 0.00 35.37 2.17
880 1248 4.114073 CGTATACGGCTGTTGGTGAAATA 58.886 43.478 17.61 0.00 35.37 1.40
881 1249 4.567558 CGTATACGGCTGTTGGTGAAATAA 59.432 41.667 17.61 0.00 35.37 1.40
890 1258 7.255242 CGGCTGTTGGTGAAATAATTGAGATAT 60.255 37.037 0.00 0.00 0.00 1.63
942 1317 3.539560 GAGAGCGATACGGGCCGAC 62.540 68.421 35.78 21.05 0.00 4.79
958 1345 1.607801 CGACCTCTCAGCCCATCACA 61.608 60.000 0.00 0.00 0.00 3.58
980 1367 2.278013 CCTAAGTCGCCGTCGCTC 60.278 66.667 0.00 0.00 35.26 5.03
988 1375 2.413765 GCCGTCGCTCCCTTCTAG 59.586 66.667 0.00 0.00 0.00 2.43
1030 1419 4.715523 CGCGCCCCCTTTCCAGAA 62.716 66.667 0.00 0.00 0.00 3.02
1121 1528 4.439472 GCGCAACAAGGTACGCCG 62.439 66.667 0.30 0.00 45.35 6.46
1143 1550 2.282958 TCCTCCGCGACTGGTCTT 60.283 61.111 8.23 0.00 0.00 3.01
1145 1552 2.125912 CTCCGCGACTGGTCTTGG 60.126 66.667 8.23 1.32 0.00 3.61
1146 1553 2.915659 TCCGCGACTGGTCTTGGT 60.916 61.111 8.23 0.00 0.00 3.67
1151 1558 1.202154 CGCGACTGGTCTTGGTAGTAG 60.202 57.143 0.00 0.00 0.00 2.57
1206 1613 4.814294 ACGCGGTCGCCTTGGATC 62.814 66.667 12.47 0.00 39.84 3.36
1256 1680 3.959991 GAAGGAGGAGGCACGTGGC 62.960 68.421 32.77 32.77 43.74 5.01
1355 1782 0.168788 CCGCAGGCTGTACATTGTTG 59.831 55.000 17.16 0.00 46.14 3.33
1395 1822 3.790256 GATTCGCCGATTGCCGTGC 62.790 63.158 0.00 0.00 36.24 5.34
1523 1950 5.293324 CACGATGTCTCCATCCGAAAATTTA 59.707 40.000 0.00 0.00 43.87 1.40
1569 1996 1.082117 AAGCGTCCGTAAATCTGCCG 61.082 55.000 0.00 0.00 0.00 5.69
1575 2002 1.373590 CCGTAAATCTGCCGTTGGGG 61.374 60.000 0.00 0.00 39.58 4.96
1584 2011 2.125106 CCGTTGGGGCTAGCTGAC 60.125 66.667 15.72 5.81 0.00 3.51
1585 2012 2.125106 CGTTGGGGCTAGCTGACC 60.125 66.667 15.72 14.79 45.48 4.02
1590 2017 3.787001 GGGCTAGCTGACCGCCTT 61.787 66.667 15.72 0.00 43.29 4.35
1710 2137 2.973224 CAGAACTTTGCGTGTACATTGC 59.027 45.455 14.20 14.20 0.00 3.56
1718 2145 1.201812 GCGTGTACATTGCGACTTCAG 60.202 52.381 8.39 0.00 0.00 3.02
1731 2158 2.128035 GACTTCAGATATTGCGGGTCG 58.872 52.381 0.00 0.00 0.00 4.79
1781 2210 6.262273 TCAGTTTTGCCCTGTTAACTAGAAAG 59.738 38.462 7.22 0.00 30.19 2.62
1805 2235 9.529325 AAGCCTTTTCTTGTTTTCTTGTTATAC 57.471 29.630 0.00 0.00 0.00 1.47
1853 2380 7.040132 TGCAATGGTGAACAAGTGTATTTATGA 60.040 33.333 0.00 0.00 0.00 2.15
1877 2404 8.423349 TGATTCAGAATGGAAAACAATCAAACT 58.577 29.630 0.00 0.00 31.58 2.66
1994 2530 5.009911 TCCTGAACAACATCCAAGAACATTG 59.990 40.000 0.00 0.00 0.00 2.82
2004 2540 3.077359 CCAAGAACATTGTCTGGGACTC 58.923 50.000 4.51 0.00 40.83 3.36
2014 2550 0.391661 TCTGGGACTCGCTTGCATTC 60.392 55.000 0.00 0.00 0.00 2.67
2169 2705 4.223320 TGACGAAGAAACAAAAGATGCC 57.777 40.909 0.00 0.00 0.00 4.40
2186 2722 5.831103 AGATGCCCTTGAAAATCTTCCTAA 58.169 37.500 0.00 0.00 0.00 2.69
2223 2759 7.939039 CCTGGTGACTGTATCCATAAATAACAT 59.061 37.037 4.34 0.00 0.00 2.71
2300 2891 3.242543 GCTTACTTTCCATGATCAGCACG 60.243 47.826 0.09 0.00 0.00 5.34
2567 3159 3.962063 GTTCCTCCCCCTTGTTTTTACAA 59.038 43.478 0.00 0.00 0.00 2.41
2605 3200 9.289303 CTTTTAGTTACCATATTGTTGATGTGC 57.711 33.333 0.00 0.00 0.00 4.57
2638 3233 8.908903 TGGCCTTGTTATTATATTTTCGTTGAT 58.091 29.630 3.32 0.00 0.00 2.57
2889 3484 3.368739 GCATTGTTTTCAGGGAATCTGGG 60.369 47.826 0.00 0.00 43.53 4.45
3173 3770 5.396362 CAGTTTGCAGTTTAGTTTGACATCG 59.604 40.000 0.00 0.00 0.00 3.84
3215 3812 3.263489 TGGTTGACAACGGTGTTTCTA 57.737 42.857 7.93 0.00 38.41 2.10
3243 3840 1.454847 TTGTGAACAGGTGTGGGCC 60.455 57.895 0.00 0.00 0.00 5.80
3264 3861 5.994668 GGCCTATAAGAAAACATCTGAGGAG 59.005 44.000 0.00 0.00 38.79 3.69
3414 4011 9.294614 GATCAAAGAATCAAGGGCTATCTTTAT 57.705 33.333 0.00 0.00 38.04 1.40
3447 4044 6.757237 AGTTGTTCCTATATCATCTGCTGAG 58.243 40.000 0.00 0.00 37.28 3.35
3626 4248 4.232188 TCGATACACCTAGTCCTTCAGT 57.768 45.455 0.00 0.00 0.00 3.41
3664 4286 7.523873 GCCAGTTAATAAGCTGAAACTTTTCCT 60.524 37.037 0.00 0.00 36.36 3.36
3669 4291 9.744468 TTAATAAGCTGAAACTTTTCCTTGTTC 57.256 29.630 0.00 0.00 36.36 3.18
3703 4325 5.745294 CCATCGTTTTGAGGCATAGAAATTG 59.255 40.000 0.00 0.00 0.00 2.32
3717 4339 6.593382 GCATAGAAATTGCAACCATTTTACCA 59.407 34.615 0.00 0.00 39.90 3.25
3723 4360 1.269309 GCAACCATTTTACCACGTGCA 60.269 47.619 10.91 0.00 0.00 4.57
3727 4364 2.625790 ACCATTTTACCACGTGCATTGT 59.374 40.909 10.91 5.14 0.00 2.71
3828 4465 9.520515 AGGATTATATTTGGTAAGCACTTATGG 57.479 33.333 0.00 0.00 0.00 2.74
3943 4580 4.382577 GGTTGGACAAACAAATGGTTGACT 60.383 41.667 17.52 0.00 45.19 3.41
3999 4641 4.528596 TGCTAGGAGCCTAGAAATACATCC 59.471 45.833 24.19 6.45 46.56 3.51
4001 4643 5.337169 GCTAGGAGCCTAGAAATACATCCTG 60.337 48.000 24.19 0.00 46.56 3.86
4029 4671 0.253327 CCCTTGCCTCCTTAGTGACC 59.747 60.000 0.00 0.00 0.00 4.02
4096 4745 5.567138 ATTAATTGGAGGAAACTTCTGCG 57.433 39.130 0.00 0.00 44.43 5.18
4167 4816 2.842208 TTGAAGACGTTGCAAACCAG 57.158 45.000 0.00 0.00 46.28 4.00
4207 4872 4.584638 ATTGTTGGGTAAGCATCTGGTA 57.415 40.909 0.00 0.00 0.00 3.25
4224 5544 4.825085 TCTGGTAAAATCCCAACTTGTGTC 59.175 41.667 0.00 0.00 0.00 3.67
4225 5545 3.892588 TGGTAAAATCCCAACTTGTGTCC 59.107 43.478 0.00 0.00 0.00 4.02
4275 5595 3.499537 TGAGCTGCACACTATCTTTGTTG 59.500 43.478 1.02 0.00 0.00 3.33
4441 5761 5.448360 CCTTAGCTAGAGCAATGCAAGAAAC 60.448 44.000 8.35 0.00 45.16 2.78
4493 5813 3.174375 GAGGCAAAATCAAGCGAATGTC 58.826 45.455 0.00 0.00 0.00 3.06
4505 5825 1.673760 CGAATGTCGCTTTTGGTGTG 58.326 50.000 0.00 0.00 31.14 3.82
4544 5864 5.803552 TCATCAGTGAACAATGTGGTATGA 58.196 37.500 0.00 2.23 0.00 2.15
4553 5873 7.867403 GTGAACAATGTGGTATGAACTTCATTT 59.133 33.333 9.57 0.00 38.26 2.32
4556 5876 8.402798 ACAATGTGGTATGAACTTCATTTGTA 57.597 30.769 9.57 0.00 38.26 2.41
4561 5881 7.095397 TGTGGTATGAACTTCATTTGTAACTCG 60.095 37.037 9.57 0.00 38.26 4.18
4562 5882 6.128391 TGGTATGAACTTCATTTGTAACTCGC 60.128 38.462 9.57 0.00 38.26 5.03
4563 5883 5.940192 ATGAACTTCATTTGTAACTCGCA 57.060 34.783 0.00 0.00 32.13 5.10
4564 5884 5.743026 TGAACTTCATTTGTAACTCGCAA 57.257 34.783 0.00 0.00 0.00 4.85
4565 5885 6.312399 TGAACTTCATTTGTAACTCGCAAT 57.688 33.333 0.00 0.00 0.00 3.56
4566 5886 6.734137 TGAACTTCATTTGTAACTCGCAATT 58.266 32.000 0.00 0.00 0.00 2.32
4567 5887 6.636447 TGAACTTCATTTGTAACTCGCAATTG 59.364 34.615 0.00 0.00 0.00 2.32
4568 5888 6.312399 ACTTCATTTGTAACTCGCAATTGA 57.688 33.333 10.34 0.00 35.66 2.57
4569 5889 6.913170 ACTTCATTTGTAACTCGCAATTGAT 58.087 32.000 10.34 0.00 36.64 2.57
4570 5890 6.803320 ACTTCATTTGTAACTCGCAATTGATG 59.197 34.615 10.34 0.17 36.64 3.07
4571 5891 5.639757 TCATTTGTAACTCGCAATTGATGG 58.360 37.500 10.34 0.00 33.83 3.51
4572 5892 5.414144 TCATTTGTAACTCGCAATTGATGGA 59.586 36.000 10.34 1.89 33.83 3.41
4573 5893 5.895636 TTTGTAACTCGCAATTGATGGAT 57.104 34.783 10.34 0.00 0.00 3.41
4574 5894 5.895636 TTGTAACTCGCAATTGATGGATT 57.104 34.783 10.34 0.00 0.00 3.01
4575 5895 5.895636 TGTAACTCGCAATTGATGGATTT 57.104 34.783 10.34 6.10 0.00 2.17
4576 5896 6.266168 TGTAACTCGCAATTGATGGATTTT 57.734 33.333 10.34 2.59 0.00 1.82
4577 5897 7.384439 TGTAACTCGCAATTGATGGATTTTA 57.616 32.000 10.34 1.75 0.00 1.52
4578 5898 7.995289 TGTAACTCGCAATTGATGGATTTTAT 58.005 30.769 10.34 0.00 0.00 1.40
4579 5899 7.914871 TGTAACTCGCAATTGATGGATTTTATG 59.085 33.333 10.34 0.00 0.00 1.90
4580 5900 5.835257 ACTCGCAATTGATGGATTTTATGG 58.165 37.500 10.34 0.00 0.00 2.74
4581 5901 5.199024 TCGCAATTGATGGATTTTATGGG 57.801 39.130 10.34 0.00 0.00 4.00
4582 5902 4.648762 TCGCAATTGATGGATTTTATGGGT 59.351 37.500 10.34 0.00 0.00 4.51
4583 5903 4.746115 CGCAATTGATGGATTTTATGGGTG 59.254 41.667 10.34 0.00 0.00 4.61
4584 5904 5.058490 GCAATTGATGGATTTTATGGGTGG 58.942 41.667 10.34 0.00 0.00 4.61
4585 5905 4.961438 ATTGATGGATTTTATGGGTGGC 57.039 40.909 0.00 0.00 0.00 5.01
4586 5906 3.686227 TGATGGATTTTATGGGTGGCT 57.314 42.857 0.00 0.00 0.00 4.75
4587 5907 4.805140 TGATGGATTTTATGGGTGGCTA 57.195 40.909 0.00 0.00 0.00 3.93
4588 5908 5.337956 TGATGGATTTTATGGGTGGCTAT 57.662 39.130 0.00 0.00 0.00 2.97
4589 5909 5.714863 TGATGGATTTTATGGGTGGCTATT 58.285 37.500 0.00 0.00 0.00 1.73
4590 5910 6.142498 TGATGGATTTTATGGGTGGCTATTT 58.858 36.000 0.00 0.00 0.00 1.40
4591 5911 6.614906 TGATGGATTTTATGGGTGGCTATTTT 59.385 34.615 0.00 0.00 0.00 1.82
4592 5912 6.882768 TGGATTTTATGGGTGGCTATTTTT 57.117 33.333 0.00 0.00 0.00 1.94
4641 5961 5.591099 ACCTGTTCAAGCAATTGTTTACTG 58.409 37.500 7.25 7.36 0.00 2.74
4644 5964 5.960113 TGTTCAAGCAATTGTTTACTGTGT 58.040 33.333 7.25 0.00 0.00 3.72
4708 6028 4.128925 TGAGGACATCAGAGATTTTCCG 57.871 45.455 0.00 0.00 32.77 4.30
4846 6166 2.564062 CAGGCCTGATTTCACACCAAAT 59.436 45.455 29.88 0.00 0.00 2.32
4849 6169 2.094026 GCCTGATTTCACACCAAATCCC 60.094 50.000 3.99 0.00 40.66 3.85
4861 6181 2.158173 ACCAAATCCCATGTTGGAGGTT 60.158 45.455 17.23 2.78 46.11 3.50
4877 6197 6.509418 TGGAGGTTGAATACTGCAATTTAC 57.491 37.500 0.00 0.00 31.93 2.01
4880 6200 7.885922 TGGAGGTTGAATACTGCAATTTACTAA 59.114 33.333 0.00 0.00 31.93 2.24
4881 6201 8.736244 GGAGGTTGAATACTGCAATTTACTAAA 58.264 33.333 0.00 0.00 0.00 1.85
4977 6297 6.854892 CACACTTGCTATTTTTCAGTTCTGAG 59.145 38.462 2.77 0.00 0.00 3.35
4980 6300 5.947228 TGCTATTTTTCAGTTCTGAGGTG 57.053 39.130 2.77 0.00 0.00 4.00
4987 6307 2.609747 TCAGTTCTGAGGTGGTAGCTT 58.390 47.619 0.00 0.00 0.00 3.74
5750 7080 7.437748 TCCAAAATTTAGGCAAATCTTTCGAA 58.562 30.769 0.00 0.00 33.09 3.71
5970 7300 3.149196 TGGTCAAGCTAAAAAGCCAGAG 58.851 45.455 0.00 0.00 34.90 3.35
6021 7351 3.467803 AGAGGTTCTGTTTCCTTCAACG 58.532 45.455 0.00 0.00 33.83 4.10
6047 7377 2.027385 GGTTGGGAAGATTGGAGATGC 58.973 52.381 0.00 0.00 0.00 3.91
6098 7428 2.692557 TGGCAGAGAGATCTAGCTCAAC 59.307 50.000 12.58 5.17 37.37 3.18
6240 7570 6.152932 TGTATAATCGAACAGGTAACCCTC 57.847 41.667 0.00 0.00 39.89 4.30
6241 7571 5.657745 TGTATAATCGAACAGGTAACCCTCA 59.342 40.000 0.00 0.00 39.89 3.86
6248 7580 1.720533 ACAGGTAACCCTCACTCCCTA 59.279 52.381 0.00 0.00 39.89 3.53
6269 7601 9.220906 TCCCTATGGTTATTTACTTCAGTGTAT 57.779 33.333 0.00 0.00 0.00 2.29
6280 7612 8.874744 TTTACTTCAGTGTATAGTAGTCAGGT 57.125 34.615 0.00 0.00 0.00 4.00
6281 7613 6.761099 ACTTCAGTGTATAGTAGTCAGGTG 57.239 41.667 0.00 0.00 0.00 4.00
6282 7614 6.246919 ACTTCAGTGTATAGTAGTCAGGTGT 58.753 40.000 0.00 0.00 0.00 4.16
6283 7615 7.400439 ACTTCAGTGTATAGTAGTCAGGTGTA 58.600 38.462 0.00 0.00 0.00 2.90
6284 7616 7.553402 ACTTCAGTGTATAGTAGTCAGGTGTAG 59.447 40.741 0.00 0.00 0.00 2.74
6285 7617 5.821470 TCAGTGTATAGTAGTCAGGTGTAGC 59.179 44.000 0.00 0.00 0.00 3.58
6286 7618 5.589050 CAGTGTATAGTAGTCAGGTGTAGCA 59.411 44.000 0.00 0.00 0.00 3.49
6287 7619 6.263392 CAGTGTATAGTAGTCAGGTGTAGCAT 59.737 42.308 0.00 0.00 0.00 3.79
6288 7620 7.444487 CAGTGTATAGTAGTCAGGTGTAGCATA 59.556 40.741 0.00 0.00 0.00 3.14
6289 7621 7.662258 AGTGTATAGTAGTCAGGTGTAGCATAG 59.338 40.741 0.00 0.00 0.00 2.23
6290 7622 5.968528 ATAGTAGTCAGGTGTAGCATAGC 57.031 43.478 0.00 0.00 0.00 2.97
6291 7623 2.959707 AGTAGTCAGGTGTAGCATAGCC 59.040 50.000 0.00 0.00 0.00 3.93
6346 7678 8.668510 AGAGCATGTGGACATAGTTAATTTAG 57.331 34.615 0.00 0.00 34.26 1.85
6361 7693 2.113860 TTTAGACATGCCTGGTCAGC 57.886 50.000 0.00 0.00 37.74 4.26
6365 7697 3.807538 CATGCCTGGTCAGCACGC 61.808 66.667 0.00 0.00 44.40 5.34
6418 7750 6.055588 CGGAGGAATATAACCAGTTTGTGAT 58.944 40.000 0.00 0.00 0.00 3.06
6447 7779 6.573289 GCTTTATGAGAGACTGAAGAAGGTGA 60.573 42.308 0.00 0.00 0.00 4.02
6608 7940 7.131227 TCCTATTCTTACCATTAATTTCCCCCA 59.869 37.037 0.00 0.00 0.00 4.96
6696 8028 1.198713 CTGAGTAGCATGGGTCTGGT 58.801 55.000 0.00 0.00 0.00 4.00
6796 8140 4.525996 TGGTATCTGATTTGATGGTGTGG 58.474 43.478 0.00 0.00 0.00 4.17
6889 8233 4.236935 CAACCGTCATGAAAGGGAAAATG 58.763 43.478 19.14 8.74 0.00 2.32
6892 8236 3.694072 CCGTCATGAAAGGGAAAATGCTA 59.306 43.478 9.93 0.00 0.00 3.49
6939 8283 2.558554 CTAGTCCCAGGTTGCGACGG 62.559 65.000 0.00 0.00 0.00 4.79
6996 8340 1.006281 TCTTTGGCTGCCAGGATCAAT 59.994 47.619 22.17 0.00 33.81 2.57
7036 8388 3.149196 CACTGAAACAGTAGCATGGGTT 58.851 45.455 4.08 0.00 43.43 4.11
7049 8401 0.473501 ATGGGTTTGGGTGGCATTGT 60.474 50.000 0.00 0.00 0.00 2.71
7084 8436 6.599356 TCTAACATCAGTTTAGCTGTACCA 57.401 37.500 0.00 0.00 45.23 3.25
7085 8437 6.395629 TCTAACATCAGTTTAGCTGTACCAC 58.604 40.000 0.00 0.00 45.23 4.16
7119 8475 5.587443 TGTTCTGAAGCTTGGTCATGATATG 59.413 40.000 2.10 0.00 0.00 1.78
7159 8515 1.273688 CGACGAACACGCCATTATCA 58.726 50.000 0.00 0.00 0.00 2.15
7167 8523 2.679837 ACACGCCATTATCAAAGCTCTG 59.320 45.455 0.00 0.00 0.00 3.35
7260 8692 4.139786 GGGCAATCTAATCTCAGCATTCA 58.860 43.478 0.00 0.00 0.00 2.57
7265 8697 7.169308 GGCAATCTAATCTCAGCATTCAATTTG 59.831 37.037 0.00 0.00 0.00 2.32
7296 8733 3.821033 GAGTAAACATCCCAGCAGTGTTT 59.179 43.478 7.69 7.69 45.15 2.83
7325 8762 6.889198 ACACCAATAGAGCACATATAACAGT 58.111 36.000 0.00 0.00 0.00 3.55
7410 8851 3.450578 ACACAAAAACAAGCTCTGCATG 58.549 40.909 0.00 0.00 33.24 4.06
7448 8890 5.235516 GCTAACTAGTTTCAGCCAGTACAA 58.764 41.667 14.49 0.00 0.00 2.41
7487 8929 7.875327 ATTTAGAGTACAACAACAACAAGGT 57.125 32.000 0.00 0.00 0.00 3.50
7516 8961 3.091545 CAAAAAGCTATTCAGGCAGGGA 58.908 45.455 0.00 0.00 0.00 4.20
7530 8975 2.143419 AGGGACATGGAGGCGGATC 61.143 63.158 0.00 0.00 0.00 3.36
7531 8976 2.427753 GGACATGGAGGCGGATCC 59.572 66.667 0.00 0.00 40.03 3.36
7532 8977 2.029666 GACATGGAGGCGGATCCG 59.970 66.667 30.03 30.03 42.77 4.18
7533 8978 2.764128 ACATGGAGGCGGATCCGT 60.764 61.111 33.33 16.73 42.77 4.69
7534 8979 2.280389 CATGGAGGCGGATCCGTG 60.280 66.667 33.33 19.53 46.97 4.94
7535 8980 4.241555 ATGGAGGCGGATCCGTGC 62.242 66.667 33.33 21.05 42.77 5.34
7657 9102 1.153005 GCTGAATGCCTCCTCCAGG 60.153 63.158 0.00 0.00 46.82 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 44 0.323087 GGGGCGTTAATGGTTGTCCT 60.323 55.000 0.00 0.00 34.23 3.85
127 146 9.877137 CATATTTTGCAAATACGCTATGAACTA 57.123 29.630 13.65 0.00 0.00 2.24
129 149 7.647715 ACCATATTTTGCAAATACGCTATGAAC 59.352 33.333 13.65 0.00 0.00 3.18
338 358 2.723124 ATGCACGGTGGACATTTTTC 57.277 45.000 10.60 0.00 0.00 2.29
508 529 0.320858 TGCCGAGTGCCGTTAATGAA 60.321 50.000 0.00 0.00 40.16 2.57
509 530 0.739462 CTGCCGAGTGCCGTTAATGA 60.739 55.000 0.00 0.00 40.16 2.57
523 544 1.066002 CACATAAATTCAGGCCTGCCG 59.934 52.381 28.91 12.28 41.95 5.69
640 661 7.923344 AGTCTACGATTCAATTCATAGGAACAG 59.077 37.037 0.00 0.00 35.46 3.16
642 663 8.543774 CAAGTCTACGATTCAATTCATAGGAAC 58.456 37.037 0.00 0.00 35.46 3.62
645 666 7.706607 TGTCAAGTCTACGATTCAATTCATAGG 59.293 37.037 0.00 0.00 0.00 2.57
646 667 8.535592 GTGTCAAGTCTACGATTCAATTCATAG 58.464 37.037 0.00 0.00 0.00 2.23
648 669 7.063898 CAGTGTCAAGTCTACGATTCAATTCAT 59.936 37.037 0.00 0.00 0.00 2.57
657 721 3.445450 AGCATCAGTGTCAAGTCTACGAT 59.555 43.478 0.00 0.00 0.00 3.73
660 724 3.175152 CGAGCATCAGTGTCAAGTCTAC 58.825 50.000 0.00 0.00 33.17 2.59
675 739 4.460948 AAATCCAGAAAAATGCGAGCAT 57.539 36.364 4.52 4.52 38.46 3.79
784 1151 9.974980 TGGTGAACCTCAAAATAAAAGTTTATC 57.025 29.630 0.37 0.00 33.00 1.75
795 1162 6.777580 AGTTTATGTCTGGTGAACCTCAAAAT 59.222 34.615 0.37 0.00 36.82 1.82
866 1234 9.241317 CAATATCTCAATTATTTCACCAACAGC 57.759 33.333 0.00 0.00 0.00 4.40
872 1240 9.899226 GCCTAACAATATCTCAATTATTTCACC 57.101 33.333 0.00 0.00 0.00 4.02
873 1241 9.899226 GGCCTAACAATATCTCAATTATTTCAC 57.101 33.333 0.00 0.00 0.00 3.18
874 1242 9.077885 GGGCCTAACAATATCTCAATTATTTCA 57.922 33.333 0.84 0.00 0.00 2.69
875 1243 9.301897 AGGGCCTAACAATATCTCAATTATTTC 57.698 33.333 2.82 0.00 0.00 2.17
877 1245 9.740710 GTAGGGCCTAACAATATCTCAATTATT 57.259 33.333 16.44 0.00 0.00 1.40
878 1246 8.041323 CGTAGGGCCTAACAATATCTCAATTAT 58.959 37.037 16.44 0.00 0.00 1.28
879 1247 7.233962 TCGTAGGGCCTAACAATATCTCAATTA 59.766 37.037 16.44 0.00 0.00 1.40
880 1248 6.042781 TCGTAGGGCCTAACAATATCTCAATT 59.957 38.462 16.44 0.00 0.00 2.32
881 1249 5.542635 TCGTAGGGCCTAACAATATCTCAAT 59.457 40.000 16.44 0.00 0.00 2.57
890 1258 1.902556 GCCTCGTAGGGCCTAACAA 59.097 57.895 16.44 2.66 45.92 2.83
910 1278 2.363795 TCTCCAGCCCGTACCAGG 60.364 66.667 0.00 0.00 0.00 4.45
913 1281 4.208686 CGCTCTCCAGCCCGTACC 62.209 72.222 0.00 0.00 43.56 3.34
914 1282 1.170919 TATCGCTCTCCAGCCCGTAC 61.171 60.000 0.00 0.00 43.56 3.67
926 1301 4.642542 GGTCGGCCCGTATCGCTC 62.643 72.222 1.63 0.00 0.00 5.03
942 1317 1.222936 GGTGTGATGGGCTGAGAGG 59.777 63.158 0.00 0.00 0.00 3.69
980 1367 3.293311 TCGACGTGTTTTCTAGAAGGG 57.707 47.619 5.12 0.00 0.00 3.95
988 1375 1.509162 GCGGCATCGACGTGTTTTC 60.509 57.895 0.00 0.00 35.91 2.29
1014 1403 3.062466 GTTCTGGAAAGGGGGCGC 61.062 66.667 0.00 0.00 0.00 6.53
1015 1404 1.971695 GTGTTCTGGAAAGGGGGCG 60.972 63.158 0.00 0.00 0.00 6.13
1016 1405 1.971695 CGTGTTCTGGAAAGGGGGC 60.972 63.158 0.00 0.00 0.00 5.80
1017 1406 1.303317 CCGTGTTCTGGAAAGGGGG 60.303 63.158 0.00 0.00 0.00 5.40
1020 1409 1.235724 GGTTCCGTGTTCTGGAAAGG 58.764 55.000 0.00 0.00 46.53 3.11
1022 1411 0.178533 ACGGTTCCGTGTTCTGGAAA 59.821 50.000 16.22 0.00 46.53 3.13
1129 1536 1.592400 CTACCAAGACCAGTCGCGGA 61.592 60.000 6.13 0.00 32.42 5.54
1132 1539 1.469423 GCTACTACCAAGACCAGTCGC 60.469 57.143 0.00 0.00 34.09 5.19
1135 1542 2.302157 GGTTGCTACTACCAAGACCAGT 59.698 50.000 0.00 0.00 35.67 4.00
1136 1543 2.301870 TGGTTGCTACTACCAAGACCAG 59.698 50.000 0.00 0.00 42.50 4.00
1137 1544 2.038033 GTGGTTGCTACTACCAAGACCA 59.962 50.000 3.46 0.00 46.62 4.02
1138 1545 2.696506 GTGGTTGCTACTACCAAGACC 58.303 52.381 3.46 0.00 46.62 3.85
1139 1546 2.334838 CGTGGTTGCTACTACCAAGAC 58.665 52.381 9.02 0.00 46.62 3.01
1143 1550 1.976898 CCCGTGGTTGCTACTACCA 59.023 57.895 9.02 3.23 43.20 3.25
1145 1552 1.449070 GGCCCGTGGTTGCTACTAC 60.449 63.158 4.75 4.75 32.84 2.73
1146 1553 1.268992 ATGGCCCGTGGTTGCTACTA 61.269 55.000 0.00 0.00 0.00 1.82
1151 1558 2.261361 GAAATGGCCCGTGGTTGC 59.739 61.111 0.00 0.00 0.00 4.17
1265 1689 2.339769 CCCCTCTATTCCCCTTGTAGG 58.660 57.143 0.00 0.00 34.30 3.18
1294 1718 3.558931 ACACATGAGCGATGGGAAATA 57.441 42.857 0.00 0.00 37.74 1.40
1295 1719 2.425143 ACACATGAGCGATGGGAAAT 57.575 45.000 0.00 0.00 37.74 2.17
1395 1822 2.673523 CAGAACCAGCCCCTCCTG 59.326 66.667 0.00 0.00 0.00 3.86
1507 1934 7.141363 GGTCAATCATAAATTTTCGGATGGAG 58.859 38.462 0.00 0.00 0.00 3.86
1523 1950 4.329638 TGTATTGGGTTGGGTCAATCAT 57.670 40.909 0.00 0.00 35.50 2.45
1569 1996 2.125106 CGGTCAGCTAGCCCCAAC 60.125 66.667 12.13 4.49 0.00 3.77
1710 2137 2.128035 GACCCGCAATATCTGAAGTCG 58.872 52.381 0.00 0.00 0.00 4.18
1718 2145 2.413112 CACATGATCGACCCGCAATATC 59.587 50.000 0.00 0.00 0.00 1.63
1731 2158 9.685828 GATAAGTAGGAAGTTAGTCACATGATC 57.314 37.037 0.00 0.00 0.00 2.92
1781 2210 9.181805 GAGTATAACAAGAAAACAAGAAAAGGC 57.818 33.333 0.00 0.00 0.00 4.35
1804 2234 8.210946 TGCATTAAAACCTATATGCTGTAGAGT 58.789 33.333 0.00 0.00 42.85 3.24
1805 2235 8.607441 TGCATTAAAACCTATATGCTGTAGAG 57.393 34.615 0.00 0.00 42.85 2.43
1853 2380 9.918630 CTAGTTTGATTGTTTTCCATTCTGAAT 57.081 29.630 0.00 0.00 0.00 2.57
1877 2404 7.067008 GCATGCTAAGGAGGAAAACAATAACTA 59.933 37.037 11.37 0.00 0.00 2.24
1994 2530 0.674895 AATGCAAGCGAGTCCCAGAC 60.675 55.000 0.00 0.00 0.00 3.51
2056 2592 8.611757 GTGTGTTTCTGCATACATACATCAATA 58.388 33.333 14.45 0.00 36.67 1.90
2058 2594 6.429385 TGTGTGTTTCTGCATACATACATCAA 59.571 34.615 16.69 1.94 40.11 2.57
2061 2597 6.816134 TTGTGTGTTTCTGCATACATACAT 57.184 33.333 19.42 0.00 43.00 2.29
2062 2598 6.429385 TCATTGTGTGTTTCTGCATACATACA 59.571 34.615 16.69 16.69 42.23 2.29
2063 2599 6.742718 GTCATTGTGTGTTTCTGCATACATAC 59.257 38.462 13.21 13.21 39.54 2.39
2064 2600 6.128035 GGTCATTGTGTGTTTCTGCATACATA 60.128 38.462 0.00 0.00 39.54 2.29
2133 2669 9.037417 GTTTCTTCGTCAACAACTTTAATATCG 57.963 33.333 0.00 0.00 0.00 2.92
2255 2791 6.261826 AGCAAATGTAATAACAGATGGCTCTC 59.738 38.462 0.00 0.00 39.49 3.20
2286 2822 0.607620 TGTGACGTGCTGATCATGGA 59.392 50.000 0.00 0.00 36.01 3.41
2290 2826 1.270252 ACATGTGTGACGTGCTGATCA 60.270 47.619 0.00 0.00 38.65 2.92
2300 2891 2.880890 AGGAGCTCAAAACATGTGTGAC 59.119 45.455 17.19 2.29 0.00 3.67
2367 2958 4.344102 TGGGGATATGAACTAGTAGCACAC 59.656 45.833 0.00 0.00 0.00 3.82
2605 3200 2.652941 AATAACAAGGCCACATTGCG 57.347 45.000 5.01 0.00 0.00 4.85
2648 3243 5.998363 AGTCAAGGAATTCCACTAACTGAAC 59.002 40.000 26.22 10.28 38.89 3.18
2865 3460 4.491676 CAGATTCCCTGAAAACAATGCAG 58.508 43.478 0.00 0.00 45.78 4.41
2889 3484 6.325919 TCCATTACAGAATTGTGTTGAACC 57.674 37.500 14.05 0.00 38.23 3.62
2937 3532 1.689273 GCCACGGACCTATCTCTGAAT 59.311 52.381 0.00 0.00 0.00 2.57
2952 3547 0.673644 CCTGGACTACCTTTGCCACG 60.674 60.000 0.00 0.00 37.04 4.94
3173 3770 5.525378 CCAACTGGAACACTAATGAGATAGC 59.475 44.000 0.00 0.00 37.39 2.97
3205 3802 2.699954 AGGCATCAAGTAGAAACACCG 58.300 47.619 0.00 0.00 0.00 4.94
3215 3812 2.233271 CCTGTTCACAAGGCATCAAGT 58.767 47.619 0.00 0.00 0.00 3.16
3264 3861 5.791336 ACTTCTTCAAAGTGGGGAATTTC 57.209 39.130 0.00 0.00 0.00 2.17
3414 4011 5.724370 TGATATAGGAACAACTTGAGGACCA 59.276 40.000 0.00 0.00 0.00 4.02
3447 4044 0.108585 TGAACTTCACAGCCTCCCAC 59.891 55.000 0.00 0.00 0.00 4.61
3605 4226 4.232188 ACTGAAGGACTAGGTGTATCGA 57.768 45.455 0.00 0.00 0.00 3.59
3606 4227 4.158025 ACAACTGAAGGACTAGGTGTATCG 59.842 45.833 0.00 0.00 42.68 2.92
3626 4248 9.238368 AGCTTATTAACTGGCAAAATAGTACAA 57.762 29.630 0.00 0.00 0.00 2.41
3664 4286 6.767524 AAACGATGGCATATAAAGGAACAA 57.232 33.333 0.00 0.00 0.00 2.83
3669 4291 5.762045 CCTCAAAACGATGGCATATAAAGG 58.238 41.667 0.00 0.00 0.00 3.11
3703 4325 1.269309 TGCACGTGGTAAAATGGTTGC 60.269 47.619 18.88 0.00 0.00 4.17
3717 4339 1.678635 CCCCCATCACAATGCACGT 60.679 57.895 0.00 0.00 0.00 4.49
3723 4360 6.325352 AGAATATTTATGCCCCCATCACAAT 58.675 36.000 0.00 0.00 32.85 2.71
3727 4364 6.718593 ACTAGAATATTTATGCCCCCATCA 57.281 37.500 0.00 0.00 32.85 3.07
3839 4476 7.344910 TGAAAACCGCATCAATTATGTTTTC 57.655 32.000 15.14 15.14 37.94 2.29
3884 4521 6.772605 TGATTCTTTTTCCTGACATCTCTGA 58.227 36.000 0.00 0.00 0.00 3.27
3999 4641 2.168728 GGAGGCAAGGGTAGTAAGACAG 59.831 54.545 0.00 0.00 0.00 3.51
4001 4643 2.468915 AGGAGGCAAGGGTAGTAAGAC 58.531 52.381 0.00 0.00 0.00 3.01
4054 4697 7.766219 TTAATTAGTTCTCACGATTGTAGCC 57.234 36.000 0.00 0.00 0.00 3.93
4090 4739 7.476667 TGAATAACAAAGAAAGAAACGCAGAA 58.523 30.769 0.00 0.00 0.00 3.02
4207 4872 4.482990 AGATGGACACAAGTTGGGATTTT 58.517 39.130 13.26 0.00 0.00 1.82
4224 5544 7.444629 TGAGTTGAGAATTTTTCTGAGATGG 57.555 36.000 0.00 0.00 40.87 3.51
4225 5545 8.727910 TGATGAGTTGAGAATTTTTCTGAGATG 58.272 33.333 0.00 0.00 40.87 2.90
4315 5635 3.527937 AGTAGAAAGGGGACTGCCTTAA 58.472 45.455 0.00 0.00 42.68 1.85
4493 5813 1.544686 GTGTCAACACACCAAAAGCG 58.455 50.000 8.37 0.00 46.49 4.68
4505 5825 5.349817 CACTGATGAGATGTTAGGTGTCAAC 59.650 44.000 0.00 0.00 0.00 3.18
4514 5834 6.372381 CCACATTGTTCACTGATGAGATGTTA 59.628 38.462 0.00 0.00 34.83 2.41
4544 5864 6.734137 TCAATTGCGAGTTACAAATGAAGTT 58.266 32.000 0.00 0.00 34.78 2.66
4553 5873 5.895636 AAATCCATCAATTGCGAGTTACA 57.104 34.783 0.00 0.00 0.00 2.41
4556 5876 6.275335 CCATAAAATCCATCAATTGCGAGTT 58.725 36.000 0.00 0.00 0.00 3.01
4561 5881 5.058490 CCACCCATAAAATCCATCAATTGC 58.942 41.667 0.00 0.00 0.00 3.56
4562 5882 5.058490 GCCACCCATAAAATCCATCAATTG 58.942 41.667 0.00 0.00 0.00 2.32
4563 5883 4.970640 AGCCACCCATAAAATCCATCAATT 59.029 37.500 0.00 0.00 0.00 2.32
4564 5884 4.559726 AGCCACCCATAAAATCCATCAAT 58.440 39.130 0.00 0.00 0.00 2.57
4565 5885 3.992999 AGCCACCCATAAAATCCATCAA 58.007 40.909 0.00 0.00 0.00 2.57
4566 5886 3.686227 AGCCACCCATAAAATCCATCA 57.314 42.857 0.00 0.00 0.00 3.07
4567 5887 6.670695 AAATAGCCACCCATAAAATCCATC 57.329 37.500 0.00 0.00 0.00 3.51
4568 5888 7.450323 AAAAATAGCCACCCATAAAATCCAT 57.550 32.000 0.00 0.00 0.00 3.41
4569 5889 6.882768 AAAAATAGCCACCCATAAAATCCA 57.117 33.333 0.00 0.00 0.00 3.41
4589 5909 6.825610 AGTTACCCATCAATTGCTTCAAAAA 58.174 32.000 0.00 0.00 0.00 1.94
4590 5910 6.418057 AGTTACCCATCAATTGCTTCAAAA 57.582 33.333 0.00 0.00 0.00 2.44
4591 5911 6.348950 CGTAGTTACCCATCAATTGCTTCAAA 60.349 38.462 0.00 0.00 0.00 2.69
4592 5912 5.123186 CGTAGTTACCCATCAATTGCTTCAA 59.877 40.000 0.00 0.00 0.00 2.69
4593 5913 4.634004 CGTAGTTACCCATCAATTGCTTCA 59.366 41.667 0.00 0.00 0.00 3.02
4594 5914 4.873827 TCGTAGTTACCCATCAATTGCTTC 59.126 41.667 0.00 0.00 0.00 3.86
4595 5915 4.839121 TCGTAGTTACCCATCAATTGCTT 58.161 39.130 0.00 0.00 0.00 3.91
4596 5916 4.481368 TCGTAGTTACCCATCAATTGCT 57.519 40.909 0.00 0.00 0.00 3.91
4610 5930 3.188159 TGCTTGAACAGGTTCGTAGTT 57.812 42.857 7.58 0.00 42.28 2.24
4644 5964 2.592102 AAAGGAATCTGGCTGCAAGA 57.408 45.000 9.58 9.58 34.07 3.02
4702 6022 1.871039 CTGAAGGAGCGAAACGGAAAA 59.129 47.619 0.00 0.00 0.00 2.29
4846 6166 3.591527 AGTATTCAACCTCCAACATGGGA 59.408 43.478 0.00 0.00 38.32 4.37
4849 6169 3.758023 TGCAGTATTCAACCTCCAACATG 59.242 43.478 0.00 0.00 0.00 3.21
4909 6229 7.826747 AGGGGAAAAGGCATATACTAAGAAAT 58.173 34.615 0.00 0.00 0.00 2.17
4917 6237 5.248380 AGATGAGGGGAAAAGGCATATAC 57.752 43.478 0.00 0.00 0.00 1.47
4925 6245 6.003950 TCACTAAACAAGATGAGGGGAAAAG 58.996 40.000 0.00 0.00 0.00 2.27
4926 6246 5.947663 TCACTAAACAAGATGAGGGGAAAA 58.052 37.500 0.00 0.00 0.00 2.29
4959 6279 4.762251 ACCACCTCAGAACTGAAAAATAGC 59.238 41.667 6.01 0.00 39.39 2.97
5750 7080 1.068121 CCTTGGGGTTCTCCTTCAGT 58.932 55.000 0.00 0.00 35.33 3.41
5970 7300 2.371510 AGCCTTCTCTGCATAAGGATCC 59.628 50.000 20.92 2.48 44.27 3.36
6021 7351 2.308866 TCCAATCTTCCCAACCTTCTCC 59.691 50.000 0.00 0.00 0.00 3.71
6047 7377 7.656948 TGGCTTCAAAATCTTTAACAGGATTTG 59.343 33.333 9.53 0.00 40.58 2.32
6098 7428 2.827322 TCAATTGCCTTCTGAACCCATG 59.173 45.455 0.00 0.00 0.00 3.66
6237 7567 6.749036 AGTAAATAACCATAGGGAGTGAGG 57.251 41.667 0.00 0.00 38.05 3.86
6240 7570 7.495934 CACTGAAGTAAATAACCATAGGGAGTG 59.504 40.741 0.00 0.00 38.05 3.51
6241 7571 7.182206 ACACTGAAGTAAATAACCATAGGGAGT 59.818 37.037 0.00 0.00 38.05 3.85
6269 7601 4.142790 GGCTATGCTACACCTGACTACTA 58.857 47.826 0.00 0.00 0.00 1.82
6270 7602 2.959707 GGCTATGCTACACCTGACTACT 59.040 50.000 0.00 0.00 0.00 2.57
6271 7603 2.287668 CGGCTATGCTACACCTGACTAC 60.288 54.545 0.00 0.00 0.00 2.73
6272 7604 1.954382 CGGCTATGCTACACCTGACTA 59.046 52.381 0.00 0.00 0.00 2.59
6273 7605 0.747255 CGGCTATGCTACACCTGACT 59.253 55.000 0.00 0.00 0.00 3.41
6274 7606 0.876342 GCGGCTATGCTACACCTGAC 60.876 60.000 0.00 0.00 0.00 3.51
6275 7607 1.326951 TGCGGCTATGCTACACCTGA 61.327 55.000 0.00 0.00 35.36 3.86
6276 7608 0.250038 ATGCGGCTATGCTACACCTG 60.250 55.000 0.00 0.00 35.36 4.00
6277 7609 1.273606 CTATGCGGCTATGCTACACCT 59.726 52.381 0.00 0.00 35.36 4.00
6278 7610 1.673033 CCTATGCGGCTATGCTACACC 60.673 57.143 0.00 0.00 35.36 4.16
6279 7611 1.000955 ACCTATGCGGCTATGCTACAC 59.999 52.381 0.00 0.00 35.61 2.90
6280 7612 1.272490 GACCTATGCGGCTATGCTACA 59.728 52.381 0.00 0.00 35.61 2.74
6281 7613 1.404315 GGACCTATGCGGCTATGCTAC 60.404 57.143 0.00 0.00 35.61 3.58
6282 7614 0.895530 GGACCTATGCGGCTATGCTA 59.104 55.000 0.00 0.00 35.61 3.49
6283 7615 0.833834 AGGACCTATGCGGCTATGCT 60.834 55.000 0.00 0.00 35.61 3.79
6284 7616 0.895530 TAGGACCTATGCGGCTATGC 59.104 55.000 0.00 0.00 35.61 3.14
6285 7617 2.497675 ACATAGGACCTATGCGGCTATG 59.502 50.000 32.79 16.04 45.33 2.23
6286 7618 2.821437 ACATAGGACCTATGCGGCTAT 58.179 47.619 32.79 15.59 45.33 2.97
6287 7619 2.304221 ACATAGGACCTATGCGGCTA 57.696 50.000 32.79 0.00 45.33 3.93
6288 7620 1.424638 AACATAGGACCTATGCGGCT 58.575 50.000 32.79 16.54 45.33 5.52
6289 7621 2.256117 AAACATAGGACCTATGCGGC 57.744 50.000 32.79 0.00 45.33 6.53
6290 7622 6.877611 AAATAAAACATAGGACCTATGCGG 57.122 37.500 32.79 16.23 45.33 5.69
6291 7623 9.268268 TCTTAAATAAAACATAGGACCTATGCG 57.732 33.333 32.79 16.86 45.33 4.73
6327 7659 7.282224 GGCATGTCTAAATTAACTATGTCCACA 59.718 37.037 0.00 0.00 0.00 4.17
6346 7678 2.393768 CGTGCTGACCAGGCATGTC 61.394 63.158 0.00 0.00 41.86 3.06
6361 7693 5.475273 ACAAATGACAGATTAGATGCGTG 57.525 39.130 0.00 0.00 0.00 5.34
6365 7697 9.605275 TCCTAAGAACAAATGACAGATTAGATG 57.395 33.333 0.00 0.00 0.00 2.90
6410 7742 8.940952 AGTCTCTCATAAAGCTTAATCACAAAC 58.059 33.333 0.00 0.00 0.00 2.93
6418 7750 8.037758 CCTTCTTCAGTCTCTCATAAAGCTTAA 58.962 37.037 0.00 0.00 0.00 1.85
6603 7935 0.751277 TGCGTGCAAATAGATGGGGG 60.751 55.000 0.00 0.00 0.00 5.40
6608 7940 1.262417 CATCGCTGCGTGCAAATAGAT 59.738 47.619 22.48 1.36 43.06 1.98
6796 8140 0.093705 GTTCATCGCAACTCGTCTGC 59.906 55.000 0.00 0.00 39.67 4.26
6889 8233 8.425703 AGAGGATTTCTAAATTCCACTAGTAGC 58.574 37.037 0.00 0.00 33.23 3.58
6892 8236 8.152023 ACAGAGGATTTCTAAATTCCACTAGT 57.848 34.615 0.00 0.00 33.83 2.57
7036 8388 1.702401 TCTACTGACAATGCCACCCAA 59.298 47.619 0.00 0.00 0.00 4.12
7084 8436 2.744202 GCTTCAGAACATGAACCATCGT 59.256 45.455 0.00 0.00 43.09 3.73
7085 8437 3.005554 AGCTTCAGAACATGAACCATCG 58.994 45.455 0.00 0.00 43.09 3.84
7140 8496 1.273688 TGATAATGGCGTGTTCGTCG 58.726 50.000 0.00 0.00 45.30 5.12
7155 8511 4.522789 GGGTTCCAAAACAGAGCTTTGATA 59.477 41.667 11.85 0.00 36.12 2.15
7159 8515 2.039418 GGGGTTCCAAAACAGAGCTTT 58.961 47.619 0.00 0.00 37.10 3.51
7167 8523 0.321346 CATGCTGGGGGTTCCAAAAC 59.679 55.000 0.00 0.00 46.51 2.43
7187 8544 4.932799 TCACGACGGTCATGAATTTACATT 59.067 37.500 4.17 0.00 0.00 2.71
7265 8697 7.272978 TGCTGGGATGTTTACTCTAAGATAAC 58.727 38.462 0.00 0.00 0.00 1.89
7285 8722 1.873591 GGTGTCACTAAACACTGCTGG 59.126 52.381 2.35 0.00 46.96 4.85
7296 8733 6.731292 ATATGTGCTCTATTGGTGTCACTA 57.269 37.500 2.35 0.00 0.00 2.74
7311 8748 7.056635 AGGCAAAGATTACTGTTATATGTGCT 58.943 34.615 14.07 1.39 0.00 4.40
7312 8749 7.012327 TGAGGCAAAGATTACTGTTATATGTGC 59.988 37.037 7.79 7.79 0.00 4.57
7325 8762 4.289672 ACTTCTTCCCTGAGGCAAAGATTA 59.710 41.667 13.23 2.21 0.00 1.75
7410 8851 1.065345 GTTAGCCAGGAAGAGGGTTCC 60.065 57.143 0.00 0.00 38.04 3.62
7487 8929 3.495331 TGAATAGCTTTTTGGGTGCTCA 58.505 40.909 0.00 0.00 38.15 4.26
7516 8961 2.764128 ACGGATCCGCCTCCATGT 60.764 61.111 33.62 9.08 44.19 3.21
7532 8977 0.110056 TCTTAGAACGACGACGGCAC 60.110 55.000 12.58 2.66 44.46 5.01
7533 8978 0.592637 TTCTTAGAACGACGACGGCA 59.407 50.000 12.58 0.00 44.46 5.69
7534 8979 1.844962 GATTCTTAGAACGACGACGGC 59.155 52.381 12.58 0.00 44.46 5.68
7535 8980 2.097142 AGGATTCTTAGAACGACGACGG 59.903 50.000 12.58 0.00 44.46 4.79
7536 8981 3.402058 AGGATTCTTAGAACGACGACG 57.598 47.619 5.58 5.58 45.75 5.12
7537 8982 4.483311 ACAAGGATTCTTAGAACGACGAC 58.517 43.478 0.00 0.00 0.00 4.34
7538 8983 4.458295 AGACAAGGATTCTTAGAACGACGA 59.542 41.667 0.00 0.00 0.00 4.20
7600 9045 2.818132 GCCCAGGAGATCAGGACG 59.182 66.667 0.00 0.00 0.00 4.79
7657 9102 0.179000 AGGTTGAGATCGTGATGGGC 59.821 55.000 0.00 0.00 0.00 5.36


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

AutoCloner maintained by Alex Coulton.