Multiple sequence alignment - TraesCS5D01G379800

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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 TraesCS5D01G379800 chr5D 100.000 5637 0 0 1 5637 450631674 450637310 0.000000e+00 10410.0
1 TraesCS5D01G379800 chr5A 91.531 2279 127 31 2086 4314 569803290 569805552 0.000000e+00 3079.0
2 TraesCS5D01G379800 chr5A 82.013 1212 93 64 277 1446 569801325 569802453 0.000000e+00 915.0
3 TraesCS5D01G379800 chr5A 91.515 660 28 7 4330 4968 569805533 569806185 0.000000e+00 883.0
4 TraesCS5D01G379800 chr5A 84.318 491 44 15 1467 1942 569802542 569803014 3.100000e-122 449.0
5 TraesCS5D01G379800 chr5A 92.903 310 18 2 5330 5637 569806586 569806893 1.110000e-121 448.0
6 TraesCS5D01G379800 chr5A 86.154 260 21 11 4965 5217 569806209 569806460 3.350000e-67 267.0
7 TraesCS5D01G379800 chr5A 90.244 123 12 0 1922 2044 569803024 569803146 1.630000e-35 161.0
8 TraesCS5D01G379800 chr5B 89.297 2504 182 47 1460 3922 550558763 550561221 0.000000e+00 3061.0
9 TraesCS5D01G379800 chr5B 86.791 1128 73 37 152 1233 550557142 550558239 0.000000e+00 1188.0
10 TraesCS5D01G379800 chr5B 90.476 651 43 7 4330 4968 550561496 550562139 0.000000e+00 841.0
11 TraesCS5D01G379800 chr5B 88.329 377 24 10 4965 5321 550562163 550562539 8.670000e-118 435.0
12 TraesCS5D01G379800 chr5B 93.704 270 13 3 4048 4314 550561247 550561515 8.800000e-108 401.0
13 TraesCS5D01G379800 chr5B 92.509 267 20 0 5371 5637 550562555 550562821 3.190000e-102 383.0
14 TraesCS5D01G379800 chr2A 84.298 484 48 10 1465 1938 424923844 424923379 1.110000e-121 448.0
15 TraesCS5D01G379800 chr2A 88.095 126 13 2 1922 2047 424923366 424923243 1.270000e-31 148.0
16 TraesCS5D01G379800 chr6D 89.583 48 5 0 5245 5292 97863811 97863858 1.700000e-05 62.1


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 TraesCS5D01G379800 chr5D 450631674 450637310 5636 False 10410.0 10410 100.000000 1 5637 1 chr5D.!!$F1 5636
1 TraesCS5D01G379800 chr5A 569801325 569806893 5568 False 886.0 3079 88.382571 277 5637 7 chr5A.!!$F1 5360
2 TraesCS5D01G379800 chr5B 550557142 550562821 5679 False 1051.5 3061 90.184333 152 5637 6 chr5B.!!$F1 5485
3 TraesCS5D01G379800 chr2A 424923243 424923844 601 True 298.0 448 86.196500 1465 2047 2 chr2A.!!$R1 582

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
466 487 0.034477 AAAAACTCGGGCGGATCCAT 60.034 50.0 13.41 0.0 36.21 3.41 F
472 511 0.463654 TCGGGCGGATCCATGAAAAG 60.464 55.0 13.41 0.0 36.21 2.27 F
1447 1755 0.175302 AACCGTGTACGTGTGTTCCA 59.825 50.0 0.00 0.0 37.74 3.53 F
2985 3546 0.034767 TACTCCTCGTCGGTGATGGT 60.035 55.0 0.00 0.0 0.00 3.55 F
3129 3690 0.963962 CACATTTGCCCTTCAGTGCT 59.036 50.0 0.00 0.0 0.00 4.40 F
3198 3759 1.059098 TCTGGACAGTTGCCATCAGT 58.941 50.0 0.00 0.0 34.33 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1438 1743 0.751643 AGCACCCAGTTGGAACACAC 60.752 55.0 0.00 0.00 39.29 3.82 R
1485 1868 1.014352 CAACCATCCGGATTCGTTCC 58.986 55.0 16.19 0.00 41.59 3.62 R
3036 3597 0.840617 TGGCCCAACAACTGTACAGA 59.159 50.0 29.30 0.00 0.00 3.41 R
4001 4572 0.034059 GTGCAGACAGTGTGGTAGCT 59.966 55.0 0.00 0.00 0.00 3.32 R
4003 4574 0.392706 TGGTGCAGACAGTGTGGTAG 59.607 55.0 0.00 0.00 0.00 3.18 R
5050 5679 0.394080 AGGCATCCTCTTTGAGCTGC 60.394 55.0 0.00 10.06 36.65 5.25 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
107 108 9.448438 ACATATATTTGAAAACAGACTAGCACA 57.552 29.630 0.00 0.00 0.00 4.57
108 109 9.708222 CATATATTTGAAAACAGACTAGCACAC 57.292 33.333 0.00 0.00 0.00 3.82
109 110 7.744087 ATATTTGAAAACAGACTAGCACACA 57.256 32.000 0.00 0.00 0.00 3.72
110 111 6.639632 ATTTGAAAACAGACTAGCACACAT 57.360 33.333 0.00 0.00 0.00 3.21
111 112 6.449635 TTTGAAAACAGACTAGCACACATT 57.550 33.333 0.00 0.00 0.00 2.71
112 113 7.561021 TTTGAAAACAGACTAGCACACATTA 57.439 32.000 0.00 0.00 0.00 1.90
113 114 7.561021 TTGAAAACAGACTAGCACACATTAA 57.439 32.000 0.00 0.00 0.00 1.40
114 115 7.561021 TGAAAACAGACTAGCACACATTAAA 57.439 32.000 0.00 0.00 0.00 1.52
115 116 7.990917 TGAAAACAGACTAGCACACATTAAAA 58.009 30.769 0.00 0.00 0.00 1.52
116 117 8.462811 TGAAAACAGACTAGCACACATTAAAAA 58.537 29.630 0.00 0.00 0.00 1.94
368 372 4.464947 AGAAGTGAAGAACCCCAAAGAAG 58.535 43.478 0.00 0.00 0.00 2.85
462 483 1.003233 AGAAGAAAAACTCGGGCGGAT 59.997 47.619 0.00 0.00 0.00 4.18
463 484 1.397343 GAAGAAAAACTCGGGCGGATC 59.603 52.381 0.00 0.00 0.00 3.36
466 487 0.034477 AAAAACTCGGGCGGATCCAT 60.034 50.000 13.41 0.00 36.21 3.41
467 488 0.748005 AAAACTCGGGCGGATCCATG 60.748 55.000 13.41 0.00 36.21 3.66
472 511 0.463654 TCGGGCGGATCCATGAAAAG 60.464 55.000 13.41 0.00 36.21 2.27
478 517 3.945285 GGCGGATCCATGAAAAGAAACTA 59.055 43.478 13.41 0.00 34.01 2.24
538 578 1.127951 GTTAAGTCACACGAATGGCGG 59.872 52.381 0.00 0.00 46.49 6.13
558 598 2.627515 GAGATAGCTCCCATGCAACA 57.372 50.000 0.00 0.00 35.01 3.33
559 599 2.923121 GAGATAGCTCCCATGCAACAA 58.077 47.619 0.00 0.00 35.01 2.83
604 658 4.697756 ACCCGACGACGACCCGTA 62.698 66.667 9.28 0.00 43.49 4.02
605 659 3.204827 CCCGACGACGACCCGTAT 61.205 66.667 9.28 0.00 43.49 3.06
611 665 2.550101 CGACGACCCGTATCCCTCC 61.550 68.421 0.00 0.00 41.37 4.30
767 835 4.825679 CCTCCCTCCCTCCCCCAC 62.826 77.778 0.00 0.00 0.00 4.61
768 836 3.700350 CTCCCTCCCTCCCCCACT 61.700 72.222 0.00 0.00 0.00 4.00
770 838 3.700350 CCCTCCCTCCCCCACTCT 61.700 72.222 0.00 0.00 0.00 3.24
776 844 0.842467 CCCTCCCCCACTCTCAAAGT 60.842 60.000 0.00 0.00 39.44 2.66
935 1006 2.317609 CGGACCAAAGCCACTCACG 61.318 63.158 0.00 0.00 0.00 4.35
936 1007 1.966451 GGACCAAAGCCACTCACGG 60.966 63.158 0.00 0.00 0.00 4.94
1117 1195 1.151899 AGCCCTTACCAGGTGACCA 60.152 57.895 3.63 0.00 38.79 4.02
1149 1227 0.548989 TCCCTCTCCTCTCTCTTCCG 59.451 60.000 0.00 0.00 0.00 4.30
1203 1281 3.423154 CTGCCTTTGACCGCGACC 61.423 66.667 8.23 0.00 0.00 4.79
1234 1313 2.567049 CTGCTGCTCTTGCTTGCC 59.433 61.111 0.00 0.00 40.48 4.52
1235 1314 1.972223 CTGCTGCTCTTGCTTGCCT 60.972 57.895 0.00 0.00 40.48 4.75
1240 1319 2.759114 CTCTTGCTTGCCTGGGGA 59.241 61.111 0.00 0.00 0.00 4.81
1242 1321 1.228552 TCTTGCTTGCCTGGGGAAC 60.229 57.895 0.00 0.00 0.00 3.62
1321 1400 1.610673 GTGCCACAGAGGGAGAGGA 60.611 63.158 0.00 0.00 39.03 3.71
1329 1408 1.305718 GAGGGAGAGGAGTGCTGGT 60.306 63.158 0.00 0.00 0.00 4.00
1446 1754 0.854705 GAACCGTGTACGTGTGTTCC 59.145 55.000 0.00 0.00 34.38 3.62
1447 1755 0.175302 AACCGTGTACGTGTGTTCCA 59.825 50.000 0.00 0.00 37.74 3.53
1449 1757 0.578211 CCGTGTACGTGTGTTCCAAC 59.422 55.000 0.00 0.00 37.74 3.77
1451 1759 1.256895 CGTGTACGTGTGTTCCAACTG 59.743 52.381 0.00 0.00 34.11 3.16
1453 1761 1.223187 GTACGTGTGTTCCAACTGGG 58.777 55.000 0.00 0.00 35.41 4.45
1455 1763 0.746563 ACGTGTGTTCCAACTGGGTG 60.747 55.000 0.00 0.00 38.11 4.61
1456 1764 1.733526 GTGTGTTCCAACTGGGTGC 59.266 57.895 0.00 0.00 38.11 5.01
1457 1765 0.751643 GTGTGTTCCAACTGGGTGCT 60.752 55.000 0.00 0.00 38.11 4.40
1458 1766 0.751277 TGTGTTCCAACTGGGTGCTG 60.751 55.000 0.00 0.00 38.11 4.41
1473 1853 2.328289 CTGCGATGCTGCTCATGC 59.672 61.111 0.00 0.45 35.05 4.06
1485 1868 2.009051 TGCTCATGCGTAGAATTGGTG 58.991 47.619 0.00 0.00 43.34 4.17
1509 1898 1.379527 GAATCCGGATGGTTGTGGAC 58.620 55.000 19.95 0.00 36.30 4.02
1523 1912 2.853430 TGTGGACTGGGGTTGGTATAT 58.147 47.619 0.00 0.00 0.00 0.86
1524 1913 4.010253 TGTGGACTGGGGTTGGTATATA 57.990 45.455 0.00 0.00 0.00 0.86
1527 1916 4.657039 GTGGACTGGGGTTGGTATATAAGA 59.343 45.833 0.00 0.00 0.00 2.10
1528 1917 4.657039 TGGACTGGGGTTGGTATATAAGAC 59.343 45.833 0.00 0.00 0.00 3.01
1529 1918 4.906060 GGACTGGGGTTGGTATATAAGACT 59.094 45.833 0.00 0.00 0.00 3.24
1530 1919 5.221661 GGACTGGGGTTGGTATATAAGACTG 60.222 48.000 0.00 0.00 0.00 3.51
1531 1920 4.102681 ACTGGGGTTGGTATATAAGACTGC 59.897 45.833 0.00 0.00 0.00 4.40
1532 1921 4.041464 TGGGGTTGGTATATAAGACTGCA 58.959 43.478 0.00 0.00 0.00 4.41
1533 1922 4.141574 TGGGGTTGGTATATAAGACTGCAC 60.142 45.833 0.00 0.00 0.00 4.57
1534 1923 4.386711 GGGTTGGTATATAAGACTGCACC 58.613 47.826 0.00 0.00 0.00 5.01
1536 1925 5.306160 GGGTTGGTATATAAGACTGCACCTA 59.694 44.000 0.00 0.00 0.00 3.08
1537 1926 6.013639 GGGTTGGTATATAAGACTGCACCTAT 60.014 42.308 0.00 0.00 0.00 2.57
1538 1927 7.450903 GGTTGGTATATAAGACTGCACCTATT 58.549 38.462 0.00 0.00 0.00 1.73
1539 1928 7.387948 GGTTGGTATATAAGACTGCACCTATTG 59.612 40.741 0.00 0.00 0.00 1.90
1560 1949 3.070734 TGCCAGGTGTTTTAAATGTGCAT 59.929 39.130 0.00 0.00 0.00 3.96
1576 1965 0.308993 GCATACCGAAATGAGGCAGC 59.691 55.000 1.62 0.00 0.00 5.25
1598 1987 2.203480 TGCTCAAGTGGTTGGGGC 60.203 61.111 0.00 0.00 34.32 5.80
1619 2008 2.656069 GGCGGCCTACTTGAGTGGA 61.656 63.158 12.87 0.00 0.00 4.02
1637 2026 1.335872 GGAACCATGACTTTGTTGGCG 60.336 52.381 0.00 0.00 33.66 5.69
1654 2043 0.997196 GCGTTAGTTTGCCCGTAGAG 59.003 55.000 0.00 0.00 0.00 2.43
1724 2113 5.164233 TGACATTCTCAATTCTCTGACGAC 58.836 41.667 0.00 0.00 0.00 4.34
1870 2267 9.386010 TGGTACAGTTATTGTGATTACCAATAC 57.614 33.333 0.00 0.00 40.20 1.89
1916 2314 9.690434 GAATGAGATATCTGAAAAACAACGTAC 57.310 33.333 10.74 0.00 0.00 3.67
1920 2318 8.699283 AGATATCTGAAAAACAACGTACTACC 57.301 34.615 3.89 0.00 0.00 3.18
1998 2426 4.620567 GCAGCTTAATGTTGGGGTAAAAGG 60.621 45.833 0.00 0.00 0.00 3.11
1999 2427 4.081697 CAGCTTAATGTTGGGGTAAAAGGG 60.082 45.833 0.00 0.00 0.00 3.95
2015 2445 5.722021 AAAAGGGAAATAACTCGTTGCAT 57.278 34.783 0.00 0.00 0.00 3.96
2029 2459 5.406780 ACTCGTTGCATGTTTCTAAGAGAAG 59.593 40.000 2.86 0.00 35.37 2.85
2034 2464 8.113062 CGTTGCATGTTTCTAAGAGAAGATTAG 58.887 37.037 0.00 0.00 35.37 1.73
2044 2474 7.556844 TCTAAGAGAAGATTAGCACCGAAATT 58.443 34.615 0.00 0.00 31.57 1.82
2049 2479 5.888161 AGAAGATTAGCACCGAAATTCCAAT 59.112 36.000 0.00 0.00 0.00 3.16
2069 2503 5.395103 CCAATAGCCGATTTCATTTTGGGAA 60.395 40.000 0.00 0.00 31.00 3.97
2129 2661 0.109723 TTCACAAACTCCCCCTTCCG 59.890 55.000 0.00 0.00 0.00 4.30
2131 2663 0.179001 CACAAACTCCCCCTTCCGTT 60.179 55.000 0.00 0.00 0.00 4.44
2148 2680 4.693283 TCCGTTTGGCTTATAGACTGATG 58.307 43.478 0.00 0.00 34.14 3.07
2201 2733 8.446273 AGATCACAATCTTACGACATTTTTCTG 58.554 33.333 0.00 0.00 39.27 3.02
2222 2754 8.654230 TTCTGTTCTAGCATCATAAGTGAATC 57.346 34.615 0.00 0.00 38.01 2.52
2257 2789 4.205587 ACAAGATGGCAAGATCAATCCTC 58.794 43.478 0.00 0.00 0.00 3.71
2263 2795 2.641305 GCAAGATCAATCCTCACTGCT 58.359 47.619 0.00 0.00 0.00 4.24
2281 2813 2.012673 GCTGACTTGCATTAGTCCCTG 58.987 52.381 14.49 7.28 43.11 4.45
2282 2814 2.012673 CTGACTTGCATTAGTCCCTGC 58.987 52.381 14.49 0.00 43.11 4.85
2305 2839 7.868775 TGCATTTGCTTTAAGCTAGATATGAG 58.131 34.615 18.20 0.45 42.97 2.90
2365 2905 7.345653 ACATCTGTTAGAGATATGGGTTTCTGA 59.654 37.037 0.00 0.00 39.64 3.27
2454 3008 7.063308 CACCATGTTTGCTCCAACATAATTAAC 59.937 37.037 8.56 0.00 0.00 2.01
2463 3017 9.337396 TGCTCCAACATAATTAACTACTAATGG 57.663 33.333 0.00 0.00 30.24 3.16
2536 3090 1.112459 GCGACAGCTTTGAACAAACG 58.888 50.000 0.00 0.00 41.01 3.60
2555 3116 6.071616 ACAAACGCATACAAAATCCCATTACT 60.072 34.615 0.00 0.00 0.00 2.24
2566 3127 1.009829 CCCATTACTGACTTCGCTGC 58.990 55.000 0.00 0.00 0.00 5.25
2570 3131 3.189287 CCATTACTGACTTCGCTGCTTTT 59.811 43.478 0.00 0.00 0.00 2.27
2600 3161 5.178797 AGATTCCACTTCACTAATGTTCCG 58.821 41.667 0.00 0.00 0.00 4.30
2602 3163 4.819105 TCCACTTCACTAATGTTCCGAT 57.181 40.909 0.00 0.00 0.00 4.18
2735 3296 7.377928 CAGTTTCACAAAGATTCTGTTCATCAC 59.622 37.037 0.00 0.00 0.00 3.06
2778 3339 4.401925 CCCTCACAATCTTTCTTGGAGTT 58.598 43.478 0.00 0.00 0.00 3.01
2814 3375 1.269621 CCGAATCCTACCTACAAGCCG 60.270 57.143 0.00 0.00 0.00 5.52
2973 3534 3.610585 GCTGCGATGTAGTCATACTCCTC 60.611 52.174 0.00 0.00 34.06 3.71
2985 3546 0.034767 TACTCCTCGTCGGTGATGGT 60.035 55.000 0.00 0.00 0.00 3.55
3129 3690 0.963962 CACATTTGCCCTTCAGTGCT 59.036 50.000 0.00 0.00 0.00 4.40
3198 3759 1.059098 TCTGGACAGTTGCCATCAGT 58.941 50.000 0.00 0.00 34.33 3.41
3687 4248 3.072184 AGCTTGTTGATTCAGACCTCACT 59.928 43.478 0.00 0.00 0.00 3.41
3756 4317 1.607467 GGTTGCTGGTTCATGGGCT 60.607 57.895 0.00 0.00 0.00 5.19
3864 4425 1.354101 TCCCTCTCCGGCTGTTTTTA 58.646 50.000 0.00 0.00 0.00 1.52
3873 4434 6.005198 TCTCCGGCTGTTTTTATTTTTCCTA 58.995 36.000 0.00 0.00 0.00 2.94
3936 4507 2.490328 TGCTAGCAAACAGCAACAAC 57.510 45.000 16.84 0.00 45.71 3.32
3945 4516 4.672283 GCAAACAGCAACAACAAAAAGCAT 60.672 37.500 0.00 0.00 44.79 3.79
3948 4519 4.119136 ACAGCAACAACAAAAAGCATACC 58.881 39.130 0.00 0.00 0.00 2.73
3956 4527 7.675962 ACAACAAAAAGCATACCGTCTATTA 57.324 32.000 0.00 0.00 0.00 0.98
3964 4535 4.038883 AGCATACCGTCTATTAGTGAACCC 59.961 45.833 0.00 0.00 0.00 4.11
3975 4546 7.550196 GTCTATTAGTGAACCCGGTTGAATTTA 59.450 37.037 7.78 0.00 0.00 1.40
3978 4549 7.527568 TTAGTGAACCCGGTTGAATTTATTT 57.472 32.000 7.78 0.00 0.00 1.40
3989 4560 8.807581 CCGGTTGAATTTATTTTAATCTTCTGC 58.192 33.333 0.00 0.00 0.00 4.26
4006 4577 3.919216 TCTGCTGACAAGAAGAAGCTAC 58.081 45.455 0.00 0.00 34.90 3.58
4021 4592 0.951040 GCTACCACACTGTCTGCACC 60.951 60.000 0.00 0.00 0.00 5.01
4083 4656 8.549338 AAGAAGTAGCATAAACCTGTTTAGTC 57.451 34.615 8.32 3.29 38.30 2.59
4099 4672 6.146216 TGTTTAGTCCAACATTTTGCATACG 58.854 36.000 0.00 0.00 31.48 3.06
4102 4675 7.618502 TTAGTCCAACATTTTGCATACGTAT 57.381 32.000 1.14 1.14 0.00 3.06
4103 4676 5.879237 AGTCCAACATTTTGCATACGTATG 58.121 37.500 27.59 27.59 36.78 2.39
4125 4704 4.039004 TGCCACTACGTTTTAGGTAGTTGA 59.961 41.667 12.24 0.00 44.52 3.18
4136 4715 3.802948 AGGTAGTTGAGTCCATAAGCG 57.197 47.619 0.00 0.00 0.00 4.68
4204 4783 8.032451 GCCTTTACATTGCCTTTAGTGAAATTA 58.968 33.333 0.00 0.00 0.00 1.40
4205 4784 9.353999 CCTTTACATTGCCTTTAGTGAAATTAC 57.646 33.333 0.00 0.00 0.00 1.89
4311 4890 9.987726 ATTATCCAAAAGAAGAGAGATCCTTTT 57.012 29.630 0.00 0.00 38.81 2.27
4312 4891 7.936496 ATCCAAAAGAAGAGAGATCCTTTTC 57.064 36.000 0.00 4.88 36.90 2.29
4313 4892 6.241645 TCCAAAAGAAGAGAGATCCTTTTCC 58.758 40.000 9.43 0.00 36.85 3.13
4314 4893 5.123027 CCAAAAGAAGAGAGATCCTTTTCCG 59.877 44.000 9.43 0.00 36.85 4.30
4315 4894 3.535280 AGAAGAGAGATCCTTTTCCGC 57.465 47.619 9.43 0.00 36.85 5.54
4316 4895 2.834549 AGAAGAGAGATCCTTTTCCGCA 59.165 45.455 9.43 0.00 36.85 5.69
4317 4896 3.261897 AGAAGAGAGATCCTTTTCCGCAA 59.738 43.478 9.43 0.00 36.85 4.85
4318 4897 3.703001 AGAGAGATCCTTTTCCGCAAA 57.297 42.857 0.00 0.00 0.00 3.68
4319 4898 4.021102 AGAGAGATCCTTTTCCGCAAAA 57.979 40.909 0.00 0.00 0.00 2.44
4320 4899 4.398319 AGAGAGATCCTTTTCCGCAAAAA 58.602 39.130 0.00 0.00 35.56 1.94
4372 4951 4.140924 ACTGAAAACTGAAAAGGGAGGGAT 60.141 41.667 0.00 0.00 0.00 3.85
4404 4983 0.988832 ATCCACCGAAAAGGGTAGCA 59.011 50.000 0.00 0.00 46.96 3.49
4443 5022 7.973048 ATTAAGTGTAGATGTCCCTTACTGA 57.027 36.000 0.00 0.00 0.00 3.41
4444 5023 5.662674 AAGTGTAGATGTCCCTTACTGAC 57.337 43.478 0.00 0.00 0.00 3.51
4650 5229 3.430513 GCAGACTGATCTCTTGCTCATCA 60.431 47.826 6.65 0.00 30.42 3.07
4686 5265 1.154205 CGCGGGGCTGTAGATTCTTG 61.154 60.000 0.00 0.00 0.00 3.02
4782 5363 2.968574 ACATCAGTCAGAGTCAAGGTGT 59.031 45.455 0.00 0.00 0.00 4.16
4951 5552 3.820467 TGTAAAGGAAGTCTTGTGCATGG 59.180 43.478 0.00 0.00 35.55 3.66
4992 5620 3.883744 CTCCCACGGACAGGTGCAC 62.884 68.421 8.80 8.80 36.59 4.57
5013 5642 5.042593 CACTTGATGCTTGTGCTGTAAAAA 58.957 37.500 0.00 0.00 40.48 1.94
5016 5645 5.710513 TGATGCTTGTGCTGTAAAAATCT 57.289 34.783 0.00 0.00 40.48 2.40
5026 5655 4.245660 GCTGTAAAAATCTGCCCTTTTCC 58.754 43.478 0.00 0.00 0.00 3.13
5031 5660 2.222227 AATCTGCCCTTTTCCTGTCC 57.778 50.000 0.00 0.00 0.00 4.02
5034 5663 1.073923 TCTGCCCTTTTCCTGTCCTTC 59.926 52.381 0.00 0.00 0.00 3.46
5040 5669 4.202357 GCCCTTTTCCTGTCCTTCAAAATT 60.202 41.667 0.00 0.00 0.00 1.82
5047 5676 6.790285 TCCTGTCCTTCAAAATTTACGTAC 57.210 37.500 0.00 0.00 0.00 3.67
5048 5677 6.289834 TCCTGTCCTTCAAAATTTACGTACA 58.710 36.000 0.00 0.00 0.00 2.90
5049 5678 6.938030 TCCTGTCCTTCAAAATTTACGTACAT 59.062 34.615 0.00 0.00 0.00 2.29
5050 5679 7.021196 CCTGTCCTTCAAAATTTACGTACATG 58.979 38.462 0.00 0.00 0.00 3.21
5160 5794 4.153958 TGCCACAATTATGAAACGTCAC 57.846 40.909 0.00 0.00 36.31 3.67
5163 5797 3.160545 CACAATTATGAAACGTCACGGC 58.839 45.455 0.35 0.00 36.31 5.68
5233 5867 0.832135 TATGGACGAGGATCCCCTGC 60.832 60.000 8.55 0.00 44.53 4.85
5234 5868 3.551407 GGACGAGGATCCCCTGCC 61.551 72.222 8.55 1.52 44.53 4.85
5250 5892 3.414700 CCGTTCGCTGGCTGACAC 61.415 66.667 0.00 0.00 0.00 3.67
5281 5923 3.249687 GGAACCTGACCCACATGTC 57.750 57.895 0.00 0.00 35.77 3.06
5282 5924 0.400213 GGAACCTGACCCACATGTCA 59.600 55.000 0.00 0.00 42.75 3.58
5291 5933 4.498346 CACATGTCAGTGGCCCAA 57.502 55.556 0.00 0.00 35.88 4.12
5344 6102 5.455392 CAGCAGTCTAGGTTTGTTCAATTG 58.545 41.667 0.00 0.00 0.00 2.32
5360 6118 6.013898 TGTTCAATTGGGATTTTTGGCTATCA 60.014 34.615 5.42 0.00 0.00 2.15
5369 6127 2.708216 TTTGGCTATCATGGCTTCGA 57.292 45.000 0.00 0.00 0.00 3.71
5374 6132 2.609244 GGCTATCATGGCTTCGACTCTC 60.609 54.545 0.00 0.00 0.00 3.20
5413 6171 5.067936 GGTTTCTCTAGATCATCCTTCGACA 59.932 44.000 0.00 0.00 0.00 4.35
5437 6197 3.880047 AATAGTTTGATCGGGTCGACA 57.120 42.857 18.91 0.00 39.18 4.35
5486 6246 4.202070 GGATCTAGAAGGTAGTGTCTGCAC 60.202 50.000 0.00 0.00 45.57 4.57
5524 6284 3.324099 CTAGGTGAGCGCGTCGTGT 62.324 63.158 8.43 0.00 0.00 4.49
5585 6345 3.449632 GTCTTCGTCATTCTTAGCCCTC 58.550 50.000 0.00 0.00 0.00 4.30
5586 6346 3.131400 GTCTTCGTCATTCTTAGCCCTCT 59.869 47.826 0.00 0.00 0.00 3.69
5591 6351 3.491792 CGTCATTCTTAGCCCTCTTCCTC 60.492 52.174 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 82 9.448438 TGTGCTAGTCTGTTTTCAAATATATGT 57.552 29.630 0.00 0.00 0.00 2.29
82 83 9.708222 GTGTGCTAGTCTGTTTTCAAATATATG 57.292 33.333 0.00 0.00 0.00 1.78
83 84 9.448438 TGTGTGCTAGTCTGTTTTCAAATATAT 57.552 29.630 0.00 0.00 0.00 0.86
84 85 8.840833 TGTGTGCTAGTCTGTTTTCAAATATA 57.159 30.769 0.00 0.00 0.00 0.86
85 86 7.744087 TGTGTGCTAGTCTGTTTTCAAATAT 57.256 32.000 0.00 0.00 0.00 1.28
86 87 7.744087 ATGTGTGCTAGTCTGTTTTCAAATA 57.256 32.000 0.00 0.00 0.00 1.40
87 88 6.639632 ATGTGTGCTAGTCTGTTTTCAAAT 57.360 33.333 0.00 0.00 0.00 2.32
88 89 6.449635 AATGTGTGCTAGTCTGTTTTCAAA 57.550 33.333 0.00 0.00 0.00 2.69
89 90 7.561021 TTAATGTGTGCTAGTCTGTTTTCAA 57.439 32.000 0.00 0.00 0.00 2.69
90 91 7.561021 TTTAATGTGTGCTAGTCTGTTTTCA 57.439 32.000 0.00 0.00 0.00 2.69
91 92 8.850454 TTTTTAATGTGTGCTAGTCTGTTTTC 57.150 30.769 0.00 0.00 0.00 2.29
133 134 8.764287 CGTACACATGATTGATGCTTATCTAAA 58.236 33.333 0.00 0.00 35.15 1.85
134 135 8.141268 TCGTACACATGATTGATGCTTATCTAA 58.859 33.333 0.00 0.00 35.15 2.10
135 136 7.657336 TCGTACACATGATTGATGCTTATCTA 58.343 34.615 0.00 0.00 35.15 1.98
136 137 6.515832 TCGTACACATGATTGATGCTTATCT 58.484 36.000 0.00 0.00 35.15 1.98
137 138 6.769608 TCGTACACATGATTGATGCTTATC 57.230 37.500 0.00 0.00 35.15 1.75
138 139 7.552458 TTTCGTACACATGATTGATGCTTAT 57.448 32.000 0.00 0.00 35.15 1.73
139 140 6.976636 TTTCGTACACATGATTGATGCTTA 57.023 33.333 0.00 0.00 35.15 3.09
140 141 5.878332 TTTCGTACACATGATTGATGCTT 57.122 34.783 0.00 0.00 35.15 3.91
141 142 7.734924 ATATTTCGTACACATGATTGATGCT 57.265 32.000 0.00 0.00 35.15 3.79
381 391 5.364446 ACCGGTTTTCTTTGGGTTTTAATCT 59.636 36.000 0.00 0.00 0.00 2.40
385 395 3.430513 GCACCGGTTTTCTTTGGGTTTTA 60.431 43.478 2.97 0.00 0.00 1.52
439 460 1.602377 CGCCCGAGTTTTTCTTCTGTT 59.398 47.619 0.00 0.00 0.00 3.16
440 461 1.226746 CGCCCGAGTTTTTCTTCTGT 58.773 50.000 0.00 0.00 0.00 3.41
441 462 0.517316 CCGCCCGAGTTTTTCTTCTG 59.483 55.000 0.00 0.00 0.00 3.02
442 463 0.395312 TCCGCCCGAGTTTTTCTTCT 59.605 50.000 0.00 0.00 0.00 2.85
443 464 1.397343 GATCCGCCCGAGTTTTTCTTC 59.603 52.381 0.00 0.00 0.00 2.87
444 465 1.450025 GATCCGCCCGAGTTTTTCTT 58.550 50.000 0.00 0.00 0.00 2.52
445 466 0.392595 GGATCCGCCCGAGTTTTTCT 60.393 55.000 0.00 0.00 0.00 2.52
446 467 0.675522 TGGATCCGCCCGAGTTTTTC 60.676 55.000 7.39 0.00 34.97 2.29
447 468 0.034477 ATGGATCCGCCCGAGTTTTT 60.034 50.000 7.39 0.00 34.97 1.94
448 469 0.748005 CATGGATCCGCCCGAGTTTT 60.748 55.000 7.39 0.00 34.97 2.43
449 470 1.153168 CATGGATCCGCCCGAGTTT 60.153 57.895 7.39 0.00 34.97 2.66
450 471 1.622607 TTCATGGATCCGCCCGAGTT 61.623 55.000 7.39 0.00 34.97 3.01
451 472 1.622607 TTTCATGGATCCGCCCGAGT 61.623 55.000 7.39 0.00 34.97 4.18
462 483 5.239306 CAGCACTGTAGTTTCTTTTCATGGA 59.761 40.000 0.00 0.00 0.00 3.41
463 484 5.455392 CAGCACTGTAGTTTCTTTTCATGG 58.545 41.667 0.00 0.00 0.00 3.66
466 487 4.574828 GTCCAGCACTGTAGTTTCTTTTCA 59.425 41.667 0.00 0.00 0.00 2.69
467 488 4.574828 TGTCCAGCACTGTAGTTTCTTTTC 59.425 41.667 0.00 0.00 0.00 2.29
472 511 2.417719 CCTGTCCAGCACTGTAGTTTC 58.582 52.381 0.00 0.00 0.00 2.78
478 517 2.109517 CTGAGCCTGTCCAGCACTGT 62.110 60.000 0.00 0.00 0.00 3.55
506 545 1.269726 TGACTTAACCCCGTCACGTTC 60.270 52.381 0.00 0.00 35.40 3.95
555 595 2.281276 GAGGACGGGCCGTTTGTT 60.281 61.111 34.58 18.45 41.37 2.83
556 596 2.890766 ATGAGGACGGGCCGTTTGT 61.891 57.895 34.58 20.45 41.37 2.83
557 597 2.046314 ATGAGGACGGGCCGTTTG 60.046 61.111 34.58 3.27 41.37 2.93
558 598 1.910580 ATCATGAGGACGGGCCGTTT 61.911 55.000 34.58 24.20 41.37 3.60
559 599 2.367202 ATCATGAGGACGGGCCGTT 61.367 57.895 34.58 19.35 41.37 4.44
604 658 1.139853 GAGCGATGACTTTGGAGGGAT 59.860 52.381 0.00 0.00 0.00 3.85
605 659 0.537188 GAGCGATGACTTTGGAGGGA 59.463 55.000 0.00 0.00 0.00 4.20
611 665 1.746727 CGAGGCGAGCGATGACTTTG 61.747 60.000 0.00 0.00 0.00 2.77
759 827 2.821437 TCTACTTTGAGAGTGGGGGAG 58.179 52.381 0.00 0.00 39.48 4.30
790 858 2.370849 GGAAGAAGTGGTTCCACTACCA 59.629 50.000 22.46 0.00 45.37 3.25
809 880 3.706373 GCTCTGCTTGGACGGGGA 61.706 66.667 0.00 0.00 0.00 4.81
827 898 2.802740 CTTTTCCGCTTGCTTCGCCC 62.803 60.000 0.00 0.00 0.00 6.13
935 1006 3.074412 CTCTCTCTCTCTCTAATCCGCC 58.926 54.545 0.00 0.00 0.00 6.13
936 1007 3.997021 CTCTCTCTCTCTCTCTAATCCGC 59.003 52.174 0.00 0.00 0.00 5.54
937 1008 5.243954 TCTCTCTCTCTCTCTCTCTAATCCG 59.756 48.000 0.00 0.00 0.00 4.18
984 1056 3.671411 ATCGCCTACGCCTAGCCG 61.671 66.667 0.00 0.00 39.84 5.52
985 1057 2.049063 CATCGCCTACGCCTAGCC 60.049 66.667 0.00 0.00 39.84 3.93
986 1058 2.049063 CCATCGCCTACGCCTAGC 60.049 66.667 0.00 0.00 39.84 3.42
987 1059 2.049063 GCCATCGCCTACGCCTAG 60.049 66.667 0.00 0.00 39.84 3.02
988 1060 3.973516 CGCCATCGCCTACGCCTA 61.974 66.667 0.00 0.00 39.84 3.93
1093 1171 3.717294 CTGGTAAGGGCTGGCCGT 61.717 66.667 15.17 14.49 36.85 5.68
1149 1227 4.247380 CAGGCCGATGGGGAGAGC 62.247 72.222 0.00 0.00 38.47 4.09
1214 1293 2.035312 AAGCAAGAGCAGCAGGGG 59.965 61.111 0.00 0.00 45.49 4.79
1234 1313 2.359967 GGGACTCGGAGTTCCCCAG 61.360 68.421 22.87 0.00 37.96 4.45
1235 1314 2.284405 GGGACTCGGAGTTCCCCA 60.284 66.667 22.87 0.00 37.96 4.96
1258 1337 2.741985 CCGATTCCAGCACACGCA 60.742 61.111 0.00 0.00 42.27 5.24
1293 1372 2.593148 TGTGGCACGCGAACCAAT 60.593 55.556 22.78 0.00 45.01 3.16
1321 1400 4.832266 CAGAGATCCTAATCTACCAGCACT 59.168 45.833 0.00 0.00 42.46 4.40
1329 1408 3.827302 GGTTCGCCAGAGATCCTAATCTA 59.173 47.826 0.00 0.00 38.64 1.98
1438 1743 0.751643 AGCACCCAGTTGGAACACAC 60.752 55.000 0.00 0.00 39.29 3.82
1446 1754 2.872557 CATCGCAGCACCCAGTTG 59.127 61.111 0.00 0.00 0.00 3.16
1447 1755 3.058160 GCATCGCAGCACCCAGTT 61.058 61.111 0.00 0.00 0.00 3.16
1449 1757 3.506096 CAGCATCGCAGCACCCAG 61.506 66.667 0.00 0.00 36.85 4.45
1453 1761 2.470362 ATGAGCAGCATCGCAGCAC 61.470 57.895 6.13 0.14 43.44 4.40
1455 1763 2.328289 CATGAGCAGCATCGCAGC 59.672 61.111 0.00 0.00 41.34 5.25
1456 1764 2.328289 GCATGAGCAGCATCGCAG 59.672 61.111 0.00 0.00 41.58 5.18
1457 1765 2.904470 TACGCATGAGCAGCATCGCA 62.904 55.000 0.00 0.00 42.27 5.10
1458 1766 2.155636 CTACGCATGAGCAGCATCGC 62.156 60.000 0.00 0.00 42.27 4.58
1473 1853 3.308866 GGATTCGTTCCACCAATTCTACG 59.691 47.826 2.81 0.00 44.74 3.51
1485 1868 1.014352 CAACCATCCGGATTCGTTCC 58.986 55.000 16.19 0.00 41.59 3.62
1509 1898 4.102524 TGCAGTCTTATATACCAACCCCAG 59.897 45.833 0.00 0.00 0.00 4.45
1533 1922 5.868801 CACATTTAAAACACCTGGCAATAGG 59.131 40.000 0.00 0.00 43.71 2.57
1534 1923 5.348451 GCACATTTAAAACACCTGGCAATAG 59.652 40.000 0.00 0.00 0.00 1.73
1536 1925 4.064388 GCACATTTAAAACACCTGGCAAT 58.936 39.130 0.00 0.00 0.00 3.56
1537 1926 3.118629 TGCACATTTAAAACACCTGGCAA 60.119 39.130 0.00 0.00 0.00 4.52
1538 1927 2.432146 TGCACATTTAAAACACCTGGCA 59.568 40.909 0.00 0.00 0.00 4.92
1539 1928 3.104843 TGCACATTTAAAACACCTGGC 57.895 42.857 0.00 0.00 0.00 4.85
1541 1930 4.856487 CGGTATGCACATTTAAAACACCTG 59.144 41.667 0.00 0.00 0.00 4.00
1542 1931 4.762765 TCGGTATGCACATTTAAAACACCT 59.237 37.500 0.00 0.00 0.00 4.00
1552 1941 2.358898 GCCTCATTTCGGTATGCACATT 59.641 45.455 0.00 0.00 0.00 2.71
1560 1949 1.813753 GCGCTGCCTCATTTCGGTA 60.814 57.895 0.00 0.00 0.00 4.02
1576 1965 1.280746 CAACCACTTGAGCACTGCG 59.719 57.895 0.00 0.00 0.00 5.18
1598 1987 1.021390 CACTCAAGTAGGCCGCCAAG 61.021 60.000 13.15 1.61 0.00 3.61
1619 2008 1.398692 ACGCCAACAAAGTCATGGTT 58.601 45.000 0.00 0.00 36.57 3.67
1637 2026 4.319984 CCAAAACTCTACGGGCAAACTAAC 60.320 45.833 0.00 0.00 0.00 2.34
1654 2043 5.067023 TCAAAATTTGTGCAATCCCCAAAAC 59.933 36.000 5.56 0.00 32.39 2.43
1701 2090 5.164233 GTCGTCAGAGAATTGAGAATGTCA 58.836 41.667 0.00 0.00 0.00 3.58
1703 2092 5.139435 TGTCGTCAGAGAATTGAGAATGT 57.861 39.130 0.00 0.00 0.00 2.71
1721 2110 2.286595 GCCATACTGAATGTGCATGTCG 60.287 50.000 0.00 0.00 34.05 4.35
1724 2113 4.132336 AGTAGCCATACTGAATGTGCATG 58.868 43.478 0.00 0.00 40.84 4.06
1801 2196 9.107177 CAGTTTAAGATGCAGATGATAGAGTTT 57.893 33.333 0.00 0.00 0.00 2.66
1807 2202 9.060347 GGAAATCAGTTTAAGATGCAGATGATA 57.940 33.333 0.00 0.00 0.00 2.15
1863 2260 5.076873 ACAAGCACATAAACTGGTATTGGT 58.923 37.500 0.00 0.00 0.00 3.67
1870 2267 8.437360 TCATTCTATACAAGCACATAAACTGG 57.563 34.615 0.00 0.00 0.00 4.00
1949 2377 9.042008 CAATACGTGTTTTAAGCTATCCTGTAT 57.958 33.333 0.00 0.00 0.00 2.29
1998 2426 5.699839 AGAAACATGCAACGAGTTATTTCC 58.300 37.500 0.00 0.00 0.00 3.13
1999 2427 8.227791 TCTTAGAAACATGCAACGAGTTATTTC 58.772 33.333 0.00 0.00 0.00 2.17
2015 2445 6.071560 TCGGTGCTAATCTTCTCTTAGAAACA 60.072 38.462 0.00 0.00 33.19 2.83
2029 2459 5.452777 GCTATTGGAATTTCGGTGCTAATC 58.547 41.667 0.00 0.00 0.00 1.75
2034 2464 1.268539 CGGCTATTGGAATTTCGGTGC 60.269 52.381 0.00 0.00 0.00 5.01
2044 2474 4.099266 CCCAAAATGAAATCGGCTATTGGA 59.901 41.667 0.00 0.00 38.64 3.53
2049 2479 3.130340 GCTTCCCAAAATGAAATCGGCTA 59.870 43.478 0.00 0.00 0.00 3.93
2093 2625 8.502738 AGTTTGTGAAGATAACCCCATATGTAT 58.497 33.333 1.24 0.00 0.00 2.29
2104 2636 4.302559 AGGGGGAGTTTGTGAAGATAAC 57.697 45.455 0.00 0.00 0.00 1.89
2129 2661 5.428253 TCACCATCAGTCTATAAGCCAAAC 58.572 41.667 0.00 0.00 0.00 2.93
2131 2663 5.692115 TTCACCATCAGTCTATAAGCCAA 57.308 39.130 0.00 0.00 0.00 4.52
2148 2680 8.514594 TGTCAGAATAAGATGAATGTTTTCACC 58.485 33.333 0.00 0.00 44.36 4.02
2187 2719 6.871492 TGATGCTAGAACAGAAAAATGTCGTA 59.129 34.615 0.00 0.00 31.50 3.43
2190 2722 9.713740 CTTATGATGCTAGAACAGAAAAATGTC 57.286 33.333 0.00 0.00 31.50 3.06
2199 2731 7.307278 GCAGATTCACTTATGATGCTAGAACAG 60.307 40.741 0.00 0.00 36.06 3.16
2201 2733 6.705381 AGCAGATTCACTTATGATGCTAGAAC 59.295 38.462 0.00 0.00 43.64 3.01
2222 2754 5.303165 TGCCATCTTGTCTGATAATAGCAG 58.697 41.667 0.00 0.00 34.71 4.24
2257 2789 6.905027 AGGGACTAATGCAAGTCAGCAGTG 62.905 50.000 17.98 0.00 46.40 3.66
2263 2795 2.113860 GCAGGGACTAATGCAAGTCA 57.886 50.000 17.98 0.00 46.40 3.41
2281 2813 7.869800 ACTCATATCTAGCTTAAAGCAAATGC 58.130 34.615 0.00 0.00 45.56 3.56
2338 2878 7.655328 CAGAAACCCATATCTCTAACAGATGTC 59.345 40.741 0.00 0.00 42.37 3.06
2365 2905 7.230027 TGCAAATGATTCCCCAAAAGTTATTT 58.770 30.769 0.00 0.00 0.00 1.40
2421 2961 2.159198 GGAGCAAACATGGTGCATTAGG 60.159 50.000 21.45 0.00 44.74 2.69
2485 3039 9.752961 GGTAAAAAGTTTGCTATCCTTTAAACA 57.247 29.630 0.00 0.00 35.93 2.83
2486 3040 9.752961 TGGTAAAAAGTTTGCTATCCTTTAAAC 57.247 29.630 0.00 0.00 34.21 2.01
2504 3058 1.730064 GCTGTCGCGAGATGGTAAAAA 59.270 47.619 10.24 0.00 45.19 1.94
2536 3090 6.699575 AGTCAGTAATGGGATTTTGTATGC 57.300 37.500 0.00 0.00 0.00 3.14
2555 3116 3.502191 AAAACAAAAGCAGCGAAGTCA 57.498 38.095 0.00 0.00 0.00 3.41
2570 3131 9.349713 ACATTAGTGAAGTGGAATCTTAAAACA 57.650 29.630 0.00 0.00 0.00 2.83
2600 3161 3.055819 TGGCACCTGAAGAAGTAGTGATC 60.056 47.826 0.00 0.00 0.00 2.92
2602 3163 2.037251 GTGGCACCTGAAGAAGTAGTGA 59.963 50.000 6.29 0.00 0.00 3.41
2778 3339 2.592993 CGGGTGGGAAGAAGCCTGA 61.593 63.158 0.00 0.00 32.85 3.86
2814 3375 1.794222 CGGAATGAAGTGGGCGAAC 59.206 57.895 0.00 0.00 0.00 3.95
2973 3534 2.100631 GGCTTCACCATCACCGACG 61.101 63.158 0.00 0.00 38.86 5.12
3036 3597 0.840617 TGGCCCAACAACTGTACAGA 59.159 50.000 29.30 0.00 0.00 3.41
3075 3636 3.849953 GAAAGTACTGCGGCGGCG 61.850 66.667 28.70 28.70 44.10 6.46
3129 3690 4.020662 ACAACAAAAAGAACCAGGCAAGAA 60.021 37.500 0.00 0.00 0.00 2.52
3264 3825 3.057526 CCTGCATTGTCCATGATATGCTG 60.058 47.826 16.56 15.68 42.85 4.41
3573 4134 0.893270 CGACATGGACAAAGCCCCAA 60.893 55.000 0.00 0.00 35.85 4.12
3687 4248 2.810400 CGAAAGGAAGCAGAAGGAACCA 60.810 50.000 0.00 0.00 0.00 3.67
3724 4285 1.187567 GCAACCAATGAGGCCAAGGT 61.188 55.000 5.01 1.62 43.14 3.50
3756 4317 1.661463 GATCCCTATCCATGGCCAGA 58.339 55.000 13.05 3.90 0.00 3.86
3864 4425 9.174166 ACTAACGCTGATAAACATAGGAAAAAT 57.826 29.630 0.00 0.00 0.00 1.82
3873 4434 5.932303 AGTTGTCACTAACGCTGATAAACAT 59.068 36.000 0.00 0.00 35.73 2.71
3885 4446 6.787085 ATGCAGACTTAAGTTGTCACTAAC 57.213 37.500 10.02 0.00 36.94 2.34
3933 4494 7.692291 CACTAATAGACGGTATGCTTTTTGTTG 59.308 37.037 0.00 0.00 0.00 3.33
3936 4507 7.534085 TCACTAATAGACGGTATGCTTTTTG 57.466 36.000 0.00 0.00 0.00 2.44
3945 4516 2.951642 CCGGGTTCACTAATAGACGGTA 59.048 50.000 0.00 0.00 35.67 4.02
3948 4519 3.119388 TCAACCGGGTTCACTAATAGACG 60.119 47.826 10.04 0.00 0.00 4.18
3956 4527 6.413783 AAAATAAATTCAACCGGGTTCACT 57.586 33.333 10.04 0.00 0.00 3.41
3964 4535 9.573133 AGCAGAAGATTAAAATAAATTCAACCG 57.427 29.630 0.00 0.00 0.00 4.44
3975 4546 8.627208 TCTTCTTGTCAGCAGAAGATTAAAAT 57.373 30.769 11.41 0.00 41.87 1.82
3978 4549 7.957676 AGCTTCTTCTTGTCAGCAGAAGATTAA 60.958 37.037 14.83 3.55 43.78 1.40
3989 4560 3.743396 GTGTGGTAGCTTCTTCTTGTCAG 59.257 47.826 0.00 0.00 0.00 3.51
3998 4569 1.001406 GCAGACAGTGTGGTAGCTTCT 59.999 52.381 0.00 0.00 0.00 2.85
4001 4572 0.034059 GTGCAGACAGTGTGGTAGCT 59.966 55.000 0.00 0.00 0.00 3.32
4003 4574 0.392706 TGGTGCAGACAGTGTGGTAG 59.607 55.000 0.00 0.00 0.00 3.18
4006 4577 1.146930 ACTGGTGCAGACAGTGTGG 59.853 57.895 19.91 0.00 46.67 4.17
4052 4623 9.961265 AACAGGTTTATGCTACTTCTTTAAAAC 57.039 29.630 0.00 0.00 0.00 2.43
4099 4672 5.654497 ACTACCTAAAACGTAGTGGCATAC 58.346 41.667 0.00 0.00 45.00 2.39
4102 4675 4.039004 TCAACTACCTAAAACGTAGTGGCA 59.961 41.667 1.64 0.00 45.00 4.92
4103 4676 4.559153 TCAACTACCTAAAACGTAGTGGC 58.441 43.478 1.64 0.00 45.00 5.01
4104 4677 5.776744 ACTCAACTACCTAAAACGTAGTGG 58.223 41.667 1.64 0.00 45.00 4.00
4105 4678 5.860716 GGACTCAACTACCTAAAACGTAGTG 59.139 44.000 1.64 0.00 45.00 2.74
4107 4680 6.017400 TGGACTCAACTACCTAAAACGTAG 57.983 41.667 0.00 0.00 39.32 3.51
4108 4681 6.594788 ATGGACTCAACTACCTAAAACGTA 57.405 37.500 0.00 0.00 0.00 3.57
4111 4690 6.035758 CGCTTATGGACTCAACTACCTAAAAC 59.964 42.308 0.00 0.00 0.00 2.43
4125 4704 1.276421 AGCTTGTGACGCTTATGGACT 59.724 47.619 0.00 0.00 32.98 3.85
4136 4715 4.022242 TCTCTGTACCAACTAGCTTGTGAC 60.022 45.833 0.36 0.00 0.00 3.67
4285 4864 9.987726 AAAAGGATCTCTCTTCTTTTGGATAAT 57.012 29.630 4.85 0.00 37.83 1.28
4290 4869 5.123027 CGGAAAAGGATCTCTCTTCTTTTGG 59.877 44.000 9.08 0.46 38.88 3.28
4291 4870 5.391416 GCGGAAAAGGATCTCTCTTCTTTTG 60.391 44.000 9.08 0.22 38.88 2.44
4292 4871 4.697828 GCGGAAAAGGATCTCTCTTCTTTT 59.302 41.667 5.22 5.22 40.69 2.27
4293 4872 4.257731 GCGGAAAAGGATCTCTCTTCTTT 58.742 43.478 0.00 0.00 0.00 2.52
4296 4875 3.252974 TGCGGAAAAGGATCTCTCTTC 57.747 47.619 0.00 0.00 0.00 2.87
4297 4876 3.703001 TTGCGGAAAAGGATCTCTCTT 57.297 42.857 0.00 0.00 0.00 2.85
4298 4877 3.703001 TTTGCGGAAAAGGATCTCTCT 57.297 42.857 0.00 0.00 0.00 3.10
4299 4878 4.766404 TTTTTGCGGAAAAGGATCTCTC 57.234 40.909 14.59 0.00 32.44 3.20
4317 4896 8.659527 AGGATCTCTCTTCTTCTTCTTCTTTTT 58.340 33.333 0.00 0.00 0.00 1.94
4318 4897 8.206126 AGGATCTCTCTTCTTCTTCTTCTTTT 57.794 34.615 0.00 0.00 0.00 2.27
4319 4898 7.797121 AGGATCTCTCTTCTTCTTCTTCTTT 57.203 36.000 0.00 0.00 0.00 2.52
4320 4899 7.235399 ACAAGGATCTCTCTTCTTCTTCTTCTT 59.765 37.037 0.00 0.00 0.00 2.52
4321 4900 6.725834 ACAAGGATCTCTCTTCTTCTTCTTCT 59.274 38.462 0.00 0.00 0.00 2.85
4322 4901 6.935167 ACAAGGATCTCTCTTCTTCTTCTTC 58.065 40.000 0.00 0.00 0.00 2.87
4323 4902 6.070824 GGACAAGGATCTCTCTTCTTCTTCTT 60.071 42.308 0.00 0.00 0.00 2.52
4324 4903 5.422012 GGACAAGGATCTCTCTTCTTCTTCT 59.578 44.000 0.00 0.00 0.00 2.85
4325 4904 5.186797 TGGACAAGGATCTCTCTTCTTCTTC 59.813 44.000 0.00 0.00 0.00 2.87
4326 4905 5.046663 GTGGACAAGGATCTCTCTTCTTCTT 60.047 44.000 0.00 0.00 0.00 2.52
4327 4906 4.466015 GTGGACAAGGATCTCTCTTCTTCT 59.534 45.833 0.00 0.00 0.00 2.85
4328 4907 4.466015 AGTGGACAAGGATCTCTCTTCTTC 59.534 45.833 0.00 0.00 0.00 2.87
4341 4920 4.981806 TTTCAGTTTTCAGTGGACAAGG 57.018 40.909 0.00 0.00 0.00 3.61
4372 4951 9.550406 CCTTTTCGGTGGATAAATAACAGTATA 57.450 33.333 0.00 0.00 0.00 1.47
4441 5020 1.899814 ACCGGAAGCATAGAACAGTCA 59.100 47.619 9.46 0.00 0.00 3.41
4442 5021 2.674796 ACCGGAAGCATAGAACAGTC 57.325 50.000 9.46 0.00 0.00 3.51
4443 5022 3.418684 AAACCGGAAGCATAGAACAGT 57.581 42.857 9.46 0.00 0.00 3.55
4444 5023 5.116180 TCATAAACCGGAAGCATAGAACAG 58.884 41.667 9.46 0.00 0.00 3.16
4650 5229 2.839098 GGGGGATCGCACATGGAT 59.161 61.111 12.32 0.00 0.00 3.41
4676 5255 8.883954 TCATGAATGTGATCTCAAGAATCTAC 57.116 34.615 0.90 0.00 0.00 2.59
4710 5289 9.683069 GAAAGCTGACTAAATCAATTGAAGAAA 57.317 29.630 13.09 0.00 36.69 2.52
4747 5326 5.858381 TGACTGATGTCTTGCTTCTAAGTT 58.142 37.500 0.00 0.00 43.29 2.66
4776 5357 5.255687 TCTGAATCATATGCACAACACCTT 58.744 37.500 0.00 0.00 0.00 3.50
4782 5363 6.231258 AGAGTCTCTGAATCATATGCACAA 57.769 37.500 0.18 0.00 0.00 3.33
4951 5552 4.622740 GGCAGCAATTCTGTAAATGTGTTC 59.377 41.667 0.00 0.00 44.66 3.18
4992 5620 6.089016 CAGATTTTTACAGCACAAGCATCAAG 59.911 38.462 0.00 0.00 45.49 3.02
5013 5642 1.376649 AGGACAGGAAAAGGGCAGAT 58.623 50.000 0.00 0.00 0.00 2.90
5016 5645 0.850100 TGAAGGACAGGAAAAGGGCA 59.150 50.000 0.00 0.00 0.00 5.36
5026 5655 6.523201 GCATGTACGTAAATTTTGAAGGACAG 59.477 38.462 0.00 0.00 0.00 3.51
5031 5660 6.086222 AGCTGCATGTACGTAAATTTTGAAG 58.914 36.000 1.02 0.00 0.00 3.02
5034 5663 5.389778 TGAGCTGCATGTACGTAAATTTTG 58.610 37.500 1.02 0.00 0.00 2.44
5040 5669 3.920446 TCTTTGAGCTGCATGTACGTAA 58.080 40.909 1.02 0.00 0.00 3.18
5047 5676 1.065701 GCATCCTCTTTGAGCTGCATG 59.934 52.381 1.02 0.00 37.04 4.06
5048 5677 1.390565 GCATCCTCTTTGAGCTGCAT 58.609 50.000 1.02 0.00 37.04 3.96
5049 5678 0.679002 GGCATCCTCTTTGAGCTGCA 60.679 55.000 16.37 0.00 38.02 4.41
5050 5679 0.394080 AGGCATCCTCTTTGAGCTGC 60.394 55.000 0.00 10.06 36.65 5.25
5233 5867 3.414700 GTGTCAGCCAGCGAACGG 61.415 66.667 0.00 0.00 0.00 4.44
5234 5868 3.767230 CGTGTCAGCCAGCGAACG 61.767 66.667 0.00 0.00 0.00 3.95
5276 5918 2.334946 CCGTTGGGCCACTGACATG 61.335 63.158 5.23 0.00 0.00 3.21
5277 5919 1.852157 ATCCGTTGGGCCACTGACAT 61.852 55.000 5.23 0.00 0.00 3.06
5278 5920 2.463589 GATCCGTTGGGCCACTGACA 62.464 60.000 5.23 0.00 0.00 3.58
5280 5922 2.668632 GATCCGTTGGGCCACTGA 59.331 61.111 5.23 3.03 0.00 3.41
5281 5923 2.438434 GGATCCGTTGGGCCACTG 60.438 66.667 5.23 0.30 0.00 3.66
5282 5924 4.096003 CGGATCCGTTGGGCCACT 62.096 66.667 26.35 0.00 34.35 4.00
5344 6102 2.967887 AGCCATGATAGCCAAAAATCCC 59.032 45.455 0.00 0.00 0.00 3.85
5360 6118 1.251527 ACCGTGAGAGTCGAAGCCAT 61.252 55.000 0.00 0.00 0.00 4.40
5369 6127 2.163815 CCTTATTCGTCACCGTGAGAGT 59.836 50.000 0.08 2.00 35.01 3.24
5374 6132 3.323243 AGAAACCTTATTCGTCACCGTG 58.677 45.455 0.00 0.00 34.46 4.94
5413 6171 3.119388 TCGACCCGATCAAACTATTTCGT 60.119 43.478 0.00 0.00 0.00 3.85
5454 6214 4.287766 ACCTTCTAGATCCAACACCAAC 57.712 45.455 0.00 0.00 0.00 3.77
5486 6246 5.986135 CCTAGATTTGAAAGAGTCCATACGG 59.014 44.000 0.00 0.00 0.00 4.02
5524 6284 1.003839 GGACCTTGACGCCATGACA 60.004 57.895 0.00 0.00 0.00 3.58
5585 6345 3.211045 CCTAGAGAAGAGGACGAGGAAG 58.789 54.545 0.00 0.00 35.99 3.46
5586 6346 2.092321 CCCTAGAGAAGAGGACGAGGAA 60.092 54.545 0.00 0.00 35.99 3.36
5591 6351 0.464013 TCGCCCTAGAGAAGAGGACG 60.464 60.000 0.00 0.00 35.99 4.79


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

AutoCloner maintained by Alex Coulton.