Multiple sequence alignment - TraesCS4A01G248100

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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 TraesCS4A01G248100 chr4A 100.000 5591 0 0 1 5591 558844272 558849862 0.000000e+00 10325.0
1 TraesCS4A01G248100 chr4A 95.652 46 1 1 4257 4302 613402935 613402979 7.770000e-09 73.1
2 TraesCS4A01G248100 chr4B 92.479 3364 138 53 2089 5384 59600829 59597513 0.000000e+00 4704.0
3 TraesCS4A01G248100 chr4B 89.833 1377 81 24 666 2007 59602180 59600828 0.000000e+00 1712.0
4 TraesCS4A01G248100 chr4B 91.716 676 45 4 1 668 631604702 631605374 0.000000e+00 928.0
5 TraesCS4A01G248100 chr4B 91.346 104 7 2 2006 2109 106975942 106975841 2.100000e-29 141.0
6 TraesCS4A01G248100 chr4B 95.745 47 2 0 4250 4296 282886929 282886975 6.010000e-10 76.8
7 TraesCS4A01G248100 chr4D 95.210 2067 80 11 2205 4256 40798945 40796883 0.000000e+00 3251.0
8 TraesCS4A01G248100 chr4D 90.244 1189 57 22 4267 5431 40796812 40795659 0.000000e+00 1498.0
9 TraesCS4A01G248100 chr4D 89.111 1249 62 21 809 2007 40801290 40800066 0.000000e+00 1485.0
10 TraesCS4A01G248100 chr4D 98.387 124 2 0 2089 2212 40800067 40799944 9.430000e-53 219.0
11 TraesCS4A01G248100 chr4D 85.714 161 16 5 667 826 40801745 40801591 4.480000e-36 163.0
12 TraesCS4A01G248100 chr4D 92.958 71 5 0 5521 5591 40794486 40794416 2.760000e-18 104.0
13 TraesCS4A01G248100 chr4D 97.500 40 1 0 4257 4296 259809046 259809085 1.010000e-07 69.4
14 TraesCS4A01G248100 chr2A 93.047 676 38 4 1 668 487373808 487374482 0.000000e+00 979.0
15 TraesCS4A01G248100 chr3B 93.688 507 31 1 2089 2595 15735436 15735941 0.000000e+00 758.0
16 TraesCS4A01G248100 chr3B 85.356 478 39 7 1561 2007 15734960 15735437 3.050000e-127 466.0
17 TraesCS4A01G248100 chr3B 90.683 322 29 1 1267 1588 15733650 15733970 1.440000e-115 427.0
18 TraesCS4A01G248100 chr3B 87.500 120 7 2 2850 2969 764158291 764158180 1.260000e-26 132.0
19 TraesCS4A01G248100 chr1D 86.739 641 81 3 1 638 442697042 442696403 0.000000e+00 710.0
20 TraesCS4A01G248100 chr1D 92.079 101 4 3 1996 2096 97862652 97862748 7.550000e-29 139.0
21 TraesCS4A01G248100 chr1D 90.291 103 8 2 2002 2103 93124787 93124888 3.510000e-27 134.0
22 TraesCS4A01G248100 chr1D 100.000 41 0 0 4256 4296 22785253 22785293 6.010000e-10 76.8
23 TraesCS4A01G248100 chr1D 95.745 47 2 0 4250 4296 338394515 338394561 6.010000e-10 76.8
24 TraesCS4A01G248100 chr1D 90.566 53 4 1 4250 4301 311688874 311688926 1.010000e-07 69.4
25 TraesCS4A01G248100 chr1B 86.364 638 87 0 1 638 306979875 306980512 0.000000e+00 697.0
26 TraesCS4A01G248100 chr7D 86.271 641 85 3 1 639 610713668 610714307 0.000000e+00 693.0
27 TraesCS4A01G248100 chr7D 92.784 97 6 1 1995 2091 426558889 426558984 7.550000e-29 139.0
28 TraesCS4A01G248100 chr7D 97.500 40 1 0 4257 4296 264488528 264488567 1.010000e-07 69.4
29 TraesCS4A01G248100 chr6D 86.293 642 83 5 1 639 368120493 368121132 0.000000e+00 693.0
30 TraesCS4A01G248100 chrUn 86.094 640 85 3 1 638 79604483 79605120 0.000000e+00 686.0
31 TraesCS4A01G248100 chrUn 86.094 640 85 3 1 638 289417288 289417925 0.000000e+00 686.0
32 TraesCS4A01G248100 chrUn 97.436 39 1 0 4257 4295 48487596 48487558 3.610000e-07 67.6
33 TraesCS4A01G248100 chrUn 97.436 39 1 0 4257 4295 348790594 348790632 3.610000e-07 67.6
34 TraesCS4A01G248100 chrUn 97.436 39 1 0 4257 4295 412939441 412939403 3.610000e-07 67.6
35 TraesCS4A01G248100 chrUn 97.436 39 1 0 4257 4295 463220519 463220557 3.610000e-07 67.6
36 TraesCS4A01G248100 chrUn 100.000 31 0 0 4266 4296 35341710 35341740 2.180000e-04 58.4
37 TraesCS4A01G248100 chr3D 86.072 639 87 2 1 638 277229381 277230018 0.000000e+00 686.0
38 TraesCS4A01G248100 chr3D 93.000 100 6 1 1992 2091 570848655 570848753 1.620000e-30 145.0
39 TraesCS4A01G248100 chr3D 91.000 100 7 2 2006 2105 54370497 54370400 3.510000e-27 134.0
40 TraesCS4A01G248100 chr2D 93.617 94 5 1 1998 2091 203023994 203023902 7.550000e-29 139.0
41 TraesCS4A01G248100 chr5D 91.919 99 6 2 1994 2091 109535636 109535539 2.720000e-28 137.0
42 TraesCS4A01G248100 chr5D 92.708 96 6 1 2006 2101 240428042 240428136 2.720000e-28 137.0
43 TraesCS4A01G248100 chr5D 95.745 47 2 0 4250 4296 318879379 318879333 6.010000e-10 76.8
44 TraesCS4A01G248100 chr5B 85.938 128 10 2 2842 2969 126395453 126395334 4.550000e-26 130.0
45 TraesCS4A01G248100 chr5B 96.610 59 1 1 4238 4296 694157946 694157889 4.610000e-16 97.1
46 TraesCS4A01G248100 chr5B 88.710 62 4 3 4256 4317 612631870 612631928 7.770000e-09 73.1
47 TraesCS4A01G248100 chr6B 95.745 47 2 0 4250 4296 571737285 571737239 6.010000e-10 76.8
48 TraesCS4A01G248100 chr2B 95.745 47 2 0 4250 4296 225436033 225436079 6.010000e-10 76.8
49 TraesCS4A01G248100 chr1A 91.228 57 4 1 2913 2969 565738565 565738620 6.010000e-10 76.8
50 TraesCS4A01G248100 chr1A 93.182 44 3 0 4250 4293 119144537 119144580 1.300000e-06 65.8
51 TraesCS4A01G248100 chr3A 82.278 79 4 8 4225 4296 581374695 581374770 6.050000e-05 60.2


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G248100 chr4A 558844272 558849862 5590 False 10325.000000 10325 100.000000 1 5591 1 chr4A.!!$F1 5590
1 TraesCS4A01G248100 chr4B 59597513 59602180 4667 True 3208.000000 4704 91.156000 666 5384 2 chr4B.!!$R2 4718
2 TraesCS4A01G248100 chr4B 631604702 631605374 672 False 928.000000 928 91.716000 1 668 1 chr4B.!!$F2 667
3 TraesCS4A01G248100 chr4D 40794416 40801745 7329 True 1120.000000 3251 91.937333 667 5591 6 chr4D.!!$R1 4924
4 TraesCS4A01G248100 chr2A 487373808 487374482 674 False 979.000000 979 93.047000 1 668 1 chr2A.!!$F1 667
5 TraesCS4A01G248100 chr3B 15733650 15735941 2291 False 550.333333 758 89.909000 1267 2595 3 chr3B.!!$F1 1328
6 TraesCS4A01G248100 chr1D 442696403 442697042 639 True 710.000000 710 86.739000 1 638 1 chr1D.!!$R1 637
7 TraesCS4A01G248100 chr1B 306979875 306980512 637 False 697.000000 697 86.364000 1 638 1 chr1B.!!$F1 637
8 TraesCS4A01G248100 chr7D 610713668 610714307 639 False 693.000000 693 86.271000 1 639 1 chr7D.!!$F3 638
9 TraesCS4A01G248100 chr6D 368120493 368121132 639 False 693.000000 693 86.293000 1 639 1 chr6D.!!$F1 638
10 TraesCS4A01G248100 chrUn 79604483 79605120 637 False 686.000000 686 86.094000 1 638 1 chrUn.!!$F2 637
11 TraesCS4A01G248100 chrUn 289417288 289417925 637 False 686.000000 686 86.094000 1 638 1 chrUn.!!$F3 637
12 TraesCS4A01G248100 chr3D 277229381 277230018 637 False 686.000000 686 86.072000 1 638 1 chr3D.!!$F1 637

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
309 310 0.238289 GCGGACCATCATATTTGGCG 59.762 55.000 1.98 0.85 37.81 5.69 F
1197 1526 0.250338 GCCTCAACCCTGACGACTTT 60.250 55.000 0.00 0.00 0.00 2.66 F
1233 1562 1.076705 GGATCCCAGGGTTTGCTCC 60.077 63.158 5.01 1.93 0.00 4.70 F
1450 1788 1.098050 TAACCGCGTCCTAGGTTCTC 58.902 55.000 9.08 0.00 46.87 2.87 F
2381 4818 1.915489 AGCATGTCCTTGTGATGGGTA 59.085 47.619 0.00 0.00 0.00 3.69 F
2809 5246 0.037734 GTTCACAGGTTTCCCCGGAT 59.962 55.000 0.73 0.00 38.74 4.18 F
4089 6548 0.621082 CTTTCTGACCTTCCCTCCCC 59.379 60.000 0.00 0.00 0.00 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2076 3502 0.033306 AGAACCTACTCCCTCCGTCC 60.033 60.000 0.00 0.00 0.00 4.79 R
2078 3504 0.408700 ACAGAACCTACTCCCTCCGT 59.591 55.000 0.00 0.00 0.00 4.69 R
2687 5124 1.228063 AACCACCAGCTGACTGCAG 60.228 57.895 17.39 13.48 45.94 4.41 R
2802 5239 1.479323 TGTTTCGACTAAGATCCGGGG 59.521 52.381 0.00 0.00 0.00 5.73 R
3711 6158 2.668457 GTCAACGTGTCAATCTGCTAGG 59.332 50.000 0.00 0.00 0.00 3.02 R
4524 7045 0.598065 AAATCAGCAGGTTTGTCCGC 59.402 50.000 0.00 0.00 41.99 5.54 R
5333 7899 0.103572 GCGACGCAAGGAATAGGGTA 59.896 55.000 16.42 0.00 46.39 3.69 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
30 31 7.116075 TCAGCCTAGGAAATTGCTACAAAATA 58.884 34.615 14.75 0.00 31.69 1.40
58 59 2.612567 TTCGCGCACACAATCACCC 61.613 57.895 8.75 0.00 0.00 4.61
92 93 2.022718 AGCCAAGTCTGAGAGACCTT 57.977 50.000 0.01 0.00 46.18 3.50
95 96 2.224402 GCCAAGTCTGAGAGACCTTTGT 60.224 50.000 0.01 0.00 46.18 2.83
115 116 7.659390 CCTTTGTTATTCCAAAACATGCCTTTA 59.341 33.333 0.00 0.00 36.75 1.85
135 136 1.189524 ATGTGGAAACTCGGGTCGGA 61.190 55.000 0.00 0.00 0.00 4.55
148 149 0.253327 GGTCGGAATGGAGCCTTTCT 59.747 55.000 12.97 0.00 32.71 2.52
160 161 0.967887 GCCTTTCTCCTTCTTGGGCC 60.968 60.000 0.00 0.00 36.20 5.80
201 202 7.745620 AGAGGAATGTGATTTAGTTTTTCGT 57.254 32.000 0.00 0.00 0.00 3.85
309 310 0.238289 GCGGACCATCATATTTGGCG 59.762 55.000 1.98 0.85 37.81 5.69
317 318 1.745232 TCATATTTGGCGTCCGCTTT 58.255 45.000 11.82 0.00 41.60 3.51
410 411 7.460214 TCTCCATATGTTTAAGTACCCCAAT 57.540 36.000 1.24 0.00 0.00 3.16
668 677 4.095932 CAGATATAGCACCTATCGGCGTTA 59.904 45.833 6.85 1.39 32.07 3.18
669 678 4.335874 AGATATAGCACCTATCGGCGTTAG 59.664 45.833 16.16 16.16 32.07 2.34
670 679 1.683943 TAGCACCTATCGGCGTTAGT 58.316 50.000 20.12 8.61 34.54 2.24
671 680 0.822164 AGCACCTATCGGCGTTAGTT 59.178 50.000 20.12 6.72 34.54 2.24
672 681 1.202382 AGCACCTATCGGCGTTAGTTC 60.202 52.381 20.12 10.67 34.54 3.01
673 682 1.202382 GCACCTATCGGCGTTAGTTCT 60.202 52.381 20.12 3.55 0.00 3.01
674 683 2.737679 GCACCTATCGGCGTTAGTTCTT 60.738 50.000 20.12 3.03 0.00 2.52
675 684 3.489738 GCACCTATCGGCGTTAGTTCTTA 60.490 47.826 20.12 0.00 0.00 2.10
750 759 8.986477 ATATTTCAACTAATTCCTGCAACAAC 57.014 30.769 0.00 0.00 0.00 3.32
753 762 5.057819 TCAACTAATTCCTGCAACAACGTA 58.942 37.500 0.00 0.00 0.00 3.57
761 770 0.599728 TGCAACAACGTACGGGGTAC 60.600 55.000 21.06 12.55 35.86 3.34
850 1177 8.783833 TGATGCAATTTCCTCTCTATATAAGC 57.216 34.615 0.00 0.00 0.00 3.09
863 1191 8.311395 TCTCTATATAAGCCCCTGAATATGTG 57.689 38.462 0.00 0.00 0.00 3.21
1197 1526 0.250338 GCCTCAACCCTGACGACTTT 60.250 55.000 0.00 0.00 0.00 2.66
1233 1562 1.076705 GGATCCCAGGGTTTGCTCC 60.077 63.158 5.01 1.93 0.00 4.70
1265 1594 2.256174 TGTGCTCTCGTTGTATTACGC 58.744 47.619 0.00 0.00 41.16 4.42
1335 1670 2.835895 GAGGAGGGAGAGGCGGAC 60.836 72.222 0.00 0.00 0.00 4.79
1450 1788 1.098050 TAACCGCGTCCTAGGTTCTC 58.902 55.000 9.08 0.00 46.87 2.87
1507 1845 2.177531 CATGCTTGTGGAGTGCGC 59.822 61.111 0.00 0.00 0.00 6.09
1527 1865 3.091417 GCTCGTACATTCATGCGTTTTC 58.909 45.455 0.00 0.00 0.00 2.29
1528 1866 3.424302 GCTCGTACATTCATGCGTTTTCA 60.424 43.478 0.00 0.00 0.00 2.69
1529 1867 4.320667 TCGTACATTCATGCGTTTTCAG 57.679 40.909 0.00 0.00 0.00 3.02
1530 1868 3.743911 TCGTACATTCATGCGTTTTCAGT 59.256 39.130 0.00 0.00 0.00 3.41
1531 1869 4.924462 TCGTACATTCATGCGTTTTCAGTA 59.076 37.500 0.00 0.00 0.00 2.74
1532 1870 5.405873 TCGTACATTCATGCGTTTTCAGTAA 59.594 36.000 0.00 0.00 0.00 2.24
1533 1871 6.073711 TCGTACATTCATGCGTTTTCAGTAAA 60.074 34.615 0.00 0.00 0.00 2.01
1534 1872 6.575572 CGTACATTCATGCGTTTTCAGTAAAA 59.424 34.615 0.00 0.00 32.15 1.52
1683 3084 2.376518 CCACTGCTTGGGGGACATATAT 59.623 50.000 0.00 0.00 42.54 0.86
1684 3085 3.181429 CCACTGCTTGGGGGACATATATT 60.181 47.826 0.00 0.00 42.54 1.28
1847 3269 7.752239 GCGAATCATTTATGATGGGTTTATCTG 59.248 37.037 6.01 0.00 46.22 2.90
1863 3285 6.183360 GGTTTATCTGTAAACTATGCAAGCGT 60.183 38.462 9.96 0.00 45.73 5.07
1972 3397 8.270030 AGTTGAATCCAGATATGAATGTTGAGA 58.730 33.333 0.00 0.00 0.00 3.27
2005 3431 5.868801 GCCATGTTGTTGCTACAAATATGTT 59.131 36.000 24.05 6.07 45.33 2.71
2006 3432 7.032580 GCCATGTTGTTGCTACAAATATGTTA 58.967 34.615 24.05 7.73 45.33 2.41
2007 3433 7.009174 GCCATGTTGTTGCTACAAATATGTTAC 59.991 37.037 24.05 15.82 45.33 2.50
2008 3434 8.243426 CCATGTTGTTGCTACAAATATGTTACT 58.757 33.333 24.05 2.57 45.33 2.24
2009 3435 9.277565 CATGTTGTTGCTACAAATATGTTACTC 57.722 33.333 15.28 0.30 45.33 2.59
2010 3436 7.812648 TGTTGTTGCTACAAATATGTTACTCC 58.187 34.615 15.28 0.00 45.33 3.85
2011 3437 6.995511 TGTTGCTACAAATATGTTACTCCC 57.004 37.500 0.00 0.00 41.05 4.30
2012 3438 6.717289 TGTTGCTACAAATATGTTACTCCCT 58.283 36.000 0.00 0.00 41.05 4.20
2013 3439 6.821665 TGTTGCTACAAATATGTTACTCCCTC 59.178 38.462 0.00 0.00 41.05 4.30
2014 3440 5.925509 TGCTACAAATATGTTACTCCCTCC 58.074 41.667 0.00 0.00 41.05 4.30
2015 3441 5.427157 TGCTACAAATATGTTACTCCCTCCA 59.573 40.000 0.00 0.00 41.05 3.86
2016 3442 6.101150 TGCTACAAATATGTTACTCCCTCCAT 59.899 38.462 0.00 0.00 41.05 3.41
2017 3443 6.651225 GCTACAAATATGTTACTCCCTCCATC 59.349 42.308 0.00 0.00 41.05 3.51
2018 3444 5.941788 ACAAATATGTTACTCCCTCCATCC 58.058 41.667 0.00 0.00 35.91 3.51
2019 3445 5.163088 ACAAATATGTTACTCCCTCCATCCC 60.163 44.000 0.00 0.00 35.91 3.85
2020 3446 2.587060 ATGTTACTCCCTCCATCCCA 57.413 50.000 0.00 0.00 0.00 4.37
2021 3447 2.587060 TGTTACTCCCTCCATCCCAT 57.413 50.000 0.00 0.00 0.00 4.00
2022 3448 3.717507 TGTTACTCCCTCCATCCCATA 57.282 47.619 0.00 0.00 0.00 2.74
2023 3449 4.015617 TGTTACTCCCTCCATCCCATAA 57.984 45.455 0.00 0.00 0.00 1.90
2024 3450 4.577096 TGTTACTCCCTCCATCCCATAAT 58.423 43.478 0.00 0.00 0.00 1.28
2025 3451 5.733000 TGTTACTCCCTCCATCCCATAATA 58.267 41.667 0.00 0.00 0.00 0.98
2026 3452 6.339220 TGTTACTCCCTCCATCCCATAATAT 58.661 40.000 0.00 0.00 0.00 1.28
2027 3453 7.492552 TGTTACTCCCTCCATCCCATAATATA 58.507 38.462 0.00 0.00 0.00 0.86
2028 3454 7.964867 TGTTACTCCCTCCATCCCATAATATAA 59.035 37.037 0.00 0.00 0.00 0.98
2029 3455 8.487028 GTTACTCCCTCCATCCCATAATATAAG 58.513 40.741 0.00 0.00 0.00 1.73
2030 3456 6.826727 ACTCCCTCCATCCCATAATATAAGA 58.173 40.000 0.00 0.00 0.00 2.10
2031 3457 6.905776 ACTCCCTCCATCCCATAATATAAGAG 59.094 42.308 0.00 0.00 0.00 2.85
2032 3458 5.667626 TCCCTCCATCCCATAATATAAGAGC 59.332 44.000 0.00 0.00 0.00 4.09
2033 3459 5.453903 CCCTCCATCCCATAATATAAGAGCG 60.454 48.000 0.00 0.00 0.00 5.03
2034 3460 5.129485 CCTCCATCCCATAATATAAGAGCGT 59.871 44.000 0.00 0.00 0.00 5.07
2035 3461 6.352222 CCTCCATCCCATAATATAAGAGCGTT 60.352 42.308 0.00 0.00 0.00 4.84
2036 3462 7.016153 TCCATCCCATAATATAAGAGCGTTT 57.984 36.000 0.00 0.00 0.00 3.60
2037 3463 7.458397 TCCATCCCATAATATAAGAGCGTTTT 58.542 34.615 0.00 0.00 0.00 2.43
2038 3464 8.598916 TCCATCCCATAATATAAGAGCGTTTTA 58.401 33.333 0.00 0.00 0.00 1.52
2039 3465 8.883731 CCATCCCATAATATAAGAGCGTTTTAG 58.116 37.037 0.00 0.00 0.00 1.85
2040 3466 9.653287 CATCCCATAATATAAGAGCGTTTTAGA 57.347 33.333 0.00 0.00 0.00 2.10
2041 3467 9.654663 ATCCCATAATATAAGAGCGTTTTAGAC 57.345 33.333 0.00 0.00 0.00 2.59
2042 3468 8.644216 TCCCATAATATAAGAGCGTTTTAGACA 58.356 33.333 0.00 0.00 0.00 3.41
2043 3469 8.709646 CCCATAATATAAGAGCGTTTTAGACAC 58.290 37.037 0.00 0.00 0.00 3.67
2044 3470 8.709646 CCATAATATAAGAGCGTTTTAGACACC 58.290 37.037 0.00 0.00 0.00 4.16
2045 3471 9.256477 CATAATATAAGAGCGTTTTAGACACCA 57.744 33.333 0.00 0.00 0.00 4.17
2046 3472 7.772332 AATATAAGAGCGTTTTAGACACCAG 57.228 36.000 0.00 0.00 0.00 4.00
2047 3473 3.470645 AAGAGCGTTTTAGACACCAGT 57.529 42.857 0.00 0.00 0.00 4.00
2048 3474 2.755650 AGAGCGTTTTAGACACCAGTG 58.244 47.619 0.00 0.00 0.00 3.66
2050 3476 3.319972 AGAGCGTTTTAGACACCAGTGTA 59.680 43.478 2.85 0.00 45.05 2.90
2051 3477 3.650139 AGCGTTTTAGACACCAGTGTAG 58.350 45.455 2.85 0.00 45.05 2.74
2052 3478 3.069158 AGCGTTTTAGACACCAGTGTAGT 59.931 43.478 2.85 0.00 45.05 2.73
2053 3479 3.183775 GCGTTTTAGACACCAGTGTAGTG 59.816 47.826 2.85 0.00 45.05 2.74
2062 3488 5.499139 ACACCAGTGTAGTGTCAAAAATG 57.501 39.130 0.54 0.00 45.13 2.32
2063 3489 4.202010 ACACCAGTGTAGTGTCAAAAATGC 60.202 41.667 0.54 0.00 45.13 3.56
2064 3490 4.036734 CACCAGTGTAGTGTCAAAAATGCT 59.963 41.667 0.00 0.00 0.00 3.79
2065 3491 4.275936 ACCAGTGTAGTGTCAAAAATGCTC 59.724 41.667 0.00 0.00 0.00 4.26
2066 3492 4.516698 CCAGTGTAGTGTCAAAAATGCTCT 59.483 41.667 0.00 0.00 0.00 4.09
2067 3493 5.009010 CCAGTGTAGTGTCAAAAATGCTCTT 59.991 40.000 0.00 0.00 0.00 2.85
2068 3494 6.204688 CCAGTGTAGTGTCAAAAATGCTCTTA 59.795 38.462 0.00 0.00 0.00 2.10
2069 3495 7.094634 CCAGTGTAGTGTCAAAAATGCTCTTAT 60.095 37.037 0.00 0.00 0.00 1.73
2070 3496 8.935844 CAGTGTAGTGTCAAAAATGCTCTTATA 58.064 33.333 0.00 0.00 0.00 0.98
2071 3497 9.672673 AGTGTAGTGTCAAAAATGCTCTTATAT 57.327 29.630 0.00 0.00 0.00 0.86
2077 3503 9.683069 GTGTCAAAAATGCTCTTATATTATGGG 57.317 33.333 0.00 0.00 0.00 4.00
2078 3504 9.639563 TGTCAAAAATGCTCTTATATTATGGGA 57.360 29.630 0.00 0.00 0.00 4.37
2079 3505 9.899226 GTCAAAAATGCTCTTATATTATGGGAC 57.101 33.333 0.00 0.00 0.00 4.46
2080 3506 8.783093 TCAAAAATGCTCTTATATTATGGGACG 58.217 33.333 0.00 0.00 0.00 4.79
2081 3507 7.687941 AAAATGCTCTTATATTATGGGACGG 57.312 36.000 0.00 0.00 0.00 4.79
2082 3508 6.620877 AATGCTCTTATATTATGGGACGGA 57.379 37.500 0.00 0.00 0.00 4.69
2083 3509 5.661056 TGCTCTTATATTATGGGACGGAG 57.339 43.478 0.00 0.00 0.00 4.63
2084 3510 4.466370 TGCTCTTATATTATGGGACGGAGG 59.534 45.833 0.00 0.00 0.00 4.30
2085 3511 4.141914 GCTCTTATATTATGGGACGGAGGG 60.142 50.000 0.00 0.00 0.00 4.30
2086 3512 5.269991 CTCTTATATTATGGGACGGAGGGA 58.730 45.833 0.00 0.00 0.00 4.20
2087 3513 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
2140 3566 4.898320 TGCAACTTCTGAGAAAGAGCATA 58.102 39.130 9.93 0.00 36.59 3.14
2240 4672 2.289444 TGCACTACCTGTTGCCTACTTC 60.289 50.000 0.00 0.00 0.00 3.01
2312 4744 4.593597 AACCAAATCGTATGCTAACGTG 57.406 40.909 10.46 3.34 43.31 4.49
2381 4818 1.915489 AGCATGTCCTTGTGATGGGTA 59.085 47.619 0.00 0.00 0.00 3.69
2415 4852 5.512788 GGATATTTGCACGAACTTGTTCATG 59.487 40.000 13.05 9.32 0.00 3.07
2422 4859 3.483196 CACGAACTTGTTCATGCACTTTG 59.517 43.478 13.05 0.00 0.00 2.77
2431 4868 2.591923 TCATGCACTTTGGCCTACAAA 58.408 42.857 3.32 0.00 46.34 2.83
2449 4886 9.685828 GCCTACAAATCTCTCTAAGTAATGTAG 57.314 37.037 0.00 0.00 36.33 2.74
2549 4986 9.482627 CTACTATCACCAAAAGATAGGAATGTC 57.517 37.037 13.05 0.00 45.84 3.06
2687 5124 4.782019 TTGTTGGTTGTTGGCTATGATC 57.218 40.909 0.00 0.00 0.00 2.92
2802 5239 0.868406 CGAGGCTGTTCACAGGTTTC 59.132 55.000 9.01 0.00 43.94 2.78
2809 5246 0.037734 GTTCACAGGTTTCCCCGGAT 59.962 55.000 0.73 0.00 38.74 4.18
2882 5319 7.782049 TCCTAGATCAAGTTGTAGTGTATTGG 58.218 38.462 2.11 0.00 0.00 3.16
2955 5392 5.952526 TGAGCATCCATTTATGTGCTATG 57.047 39.130 7.55 0.00 46.98 2.23
2956 5393 5.379187 TGAGCATCCATTTATGTGCTATGT 58.621 37.500 7.55 0.00 46.98 2.29
2957 5394 5.239963 TGAGCATCCATTTATGTGCTATGTG 59.760 40.000 7.55 0.00 46.98 3.21
3072 5517 3.620488 TGCTAGAAATCAACATGGTCCC 58.380 45.455 0.00 0.00 0.00 4.46
3134 5579 8.827832 TTGTATCTCAATTCAGATGGGAAAAT 57.172 30.769 1.51 0.00 34.75 1.82
3135 5580 8.229253 TGTATCTCAATTCAGATGGGAAAATG 57.771 34.615 1.51 0.00 34.75 2.32
3250 5695 4.277672 ACTGAATGCATGCCTATCATTCAC 59.722 41.667 20.47 3.78 46.25 3.18
3261 5706 7.677454 TGCCTATCATTCACTAATTATGCAG 57.323 36.000 0.00 0.00 0.00 4.41
3280 5725 3.620966 GCAGGAGAGCACAAACCTATTCT 60.621 47.826 0.00 0.00 0.00 2.40
3373 5818 9.760077 CTTTTGAGGTTAGAGACAAAAGTAGTA 57.240 33.333 17.40 0.00 46.25 1.82
3427 5872 4.034394 ACAATGTGATTCATCCGTTCATCG 59.966 41.667 0.00 0.00 35.48 3.84
3437 5882 5.583495 TCATCCGTTCATCGTTTTGTTTTT 58.417 33.333 0.00 0.00 37.94 1.94
3494 5940 6.599638 CCTTGGGTTATTTCTGAGGTTCTTAG 59.400 42.308 0.00 0.00 0.00 2.18
3531 5977 7.907389 ACTGTACTGGATTTCTTGATACTTCA 58.093 34.615 4.66 0.00 0.00 3.02
3599 6045 9.474920 TGAAAAATCTAAAGGTATGCTTTTGTG 57.525 29.630 1.08 0.00 0.00 3.33
3647 6094 7.686434 AGCTTAAGTTAAGGAGGTGAACAATA 58.314 34.615 21.36 0.00 36.31 1.90
3666 6113 9.243637 GAACAATAAGACAATTGCAAGTAAACA 57.756 29.630 4.94 0.00 39.93 2.83
3743 6196 4.637276 TGACACGTTGACATCCTTGTTAT 58.363 39.130 0.00 0.00 35.79 1.89
3860 6313 7.236487 ACAGTTCATGTACGTGTTGTTACGC 62.236 44.000 14.63 0.00 41.60 4.42
3869 6322 4.524933 CGTGTTGTTACGCAATAAAAGC 57.475 40.909 0.00 0.00 39.55 3.51
3914 6367 2.812591 CTGTGCAGAAAACATCAGAGCT 59.187 45.455 0.00 0.00 0.00 4.09
3952 6408 8.798859 ATACATTTTCTGCAAGATAGAACTGT 57.201 30.769 0.00 0.00 46.36 3.55
4019 6478 4.323417 TGTGTGAGGTAAATCGCTGAAAT 58.677 39.130 0.00 0.00 0.00 2.17
4047 6506 5.392767 TTGGCTTATTTGAACGGCAATTA 57.607 34.783 0.00 0.00 37.07 1.40
4089 6548 0.621082 CTTTCTGACCTTCCCTCCCC 59.379 60.000 0.00 0.00 0.00 4.81
4236 6695 5.701290 AGCTCTGCGTTCTTTGTAAATAGTT 59.299 36.000 0.00 0.00 0.00 2.24
4245 6704 7.063544 CGTTCTTTGTAAATAGTTCTCCCTCTG 59.936 40.741 0.00 0.00 0.00 3.35
4255 6758 9.765295 AAATAGTTCTCCCTCTGTAAACTACTA 57.235 33.333 0.00 0.00 35.81 1.82
4300 6821 5.578005 TTAGTTTACAGAGGGAGTGATCG 57.422 43.478 0.00 0.00 0.00 3.69
4334 6855 6.038161 TGGTTCTTTATGCATATTTCTGACCG 59.962 38.462 7.36 0.00 0.00 4.79
4348 6869 4.563337 TCTGACCGTGGTATATTTCTCG 57.437 45.455 0.00 0.00 0.00 4.04
4443 6964 6.746120 TCTTACACTTTACTCCACTCAAGTC 58.254 40.000 0.00 0.00 0.00 3.01
4524 7045 2.859165 TAGCTGACAGGAAGTTTGGG 57.141 50.000 4.26 0.00 0.00 4.12
4551 7072 0.466189 ACCTGCTGATTTATGGGCCG 60.466 55.000 0.00 0.00 0.00 6.13
4610 7131 4.139510 TGTGCAACACTGACGCAT 57.860 50.000 0.00 0.00 45.67 4.73
4655 7178 8.147704 TCTTGTTTTATTTCCAAGTCCAATTCC 58.852 33.333 0.00 0.00 37.45 3.01
4671 7194 4.141620 CCAATTCCTCACCAGCAGTAGTAT 60.142 45.833 0.00 0.00 0.00 2.12
4694 7217 9.186323 GTATACTAACATACATGCTCTTCAGTG 57.814 37.037 0.00 0.00 32.61 3.66
4721 7244 1.454201 TGCAGACCAGTACTCTCTCG 58.546 55.000 0.00 0.00 0.00 4.04
4752 7280 6.037720 CCGTATATTATGAACAACACCAAGCA 59.962 38.462 0.00 0.00 0.00 3.91
4992 7534 4.446413 CGTCCGGTAGGGGCACAC 62.446 72.222 0.00 0.00 42.07 3.82
4993 7535 4.091939 GTCCGGTAGGGGCACACC 62.092 72.222 0.00 0.00 41.38 4.16
5030 7577 0.991920 ACACCCCCTGTACCTTGATG 59.008 55.000 0.00 0.00 0.00 3.07
5114 7663 1.158434 GTTTATTTCCACCGTGCGGA 58.842 50.000 18.16 0.00 38.96 5.54
5165 7723 0.736325 CCGTTTAGGCTCAGACGTGG 60.736 60.000 13.62 0.00 33.95 4.94
5214 7780 0.975887 GCCTGGCCAATGAAGGAAAA 59.024 50.000 7.01 0.00 32.43 2.29
5238 7804 2.029380 AGTTGGCCTTTTGTATTTCGCC 60.029 45.455 3.32 0.00 36.91 5.54
5318 7884 4.961511 TGTGCCAGTGCGACCGTC 62.962 66.667 0.00 0.00 41.78 4.79
5386 7953 1.019673 GGATTGTGCGTGCATGATCT 58.980 50.000 10.93 0.00 0.00 2.75
5406 7973 1.371337 GCGCTGGAGTTGCATGATCA 61.371 55.000 0.00 0.00 0.00 2.92
5408 7975 0.737219 GCTGGAGTTGCATGATCACC 59.263 55.000 0.00 0.00 0.00 4.02
5409 7976 1.681166 GCTGGAGTTGCATGATCACCT 60.681 52.381 0.00 0.00 0.00 4.00
5444 8019 0.333993 TTGGTAGGGTCGCCTCTACT 59.666 55.000 3.15 0.00 36.86 2.57
5556 9224 3.963129 TGGTATCTCCCAAAACCATGTC 58.037 45.455 0.00 0.00 37.09 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.568072 TTGTAGCAATTTCCTAGGCTGA 57.432 40.909 2.96 0.00 37.17 4.26
12 13 6.571537 CGGGTTGTATTTTGTAGCAATTTCCT 60.572 38.462 0.00 0.00 0.00 3.36
22 23 3.059051 GCGAACACGGGTTGTATTTTGTA 60.059 43.478 8.36 0.00 37.51 2.41
58 59 5.049680 AGACTTGGCTAAACATAAACACGTG 60.050 40.000 15.48 15.48 0.00 4.49
92 93 8.997323 CATTAAAGGCATGTTTTGGAATAACAA 58.003 29.630 0.00 0.00 38.82 2.83
95 96 7.605691 CCACATTAAAGGCATGTTTTGGAATAA 59.394 33.333 0.00 0.00 32.25 1.40
115 116 0.321298 CCGACCCGAGTTTCCACATT 60.321 55.000 0.00 0.00 0.00 2.71
148 149 1.036707 CAAAAACGGCCCAAGAAGGA 58.963 50.000 0.00 0.00 41.22 3.36
160 161 9.083080 ACATTCCTCTAAAAAGAAACAAAAACG 57.917 29.630 0.00 0.00 0.00 3.60
201 202 1.852942 GTGACTTCACAGCGTCTTCA 58.147 50.000 4.43 0.00 45.75 3.02
309 310 2.989840 CGAGGATGATGATAAAGCGGAC 59.010 50.000 0.00 0.00 0.00 4.79
317 318 3.195610 CCCCGAAATCGAGGATGATGATA 59.804 47.826 4.04 0.00 39.83 2.15
469 470 7.946207 TCTTTCTCAGATACTCGCATTTCTAT 58.054 34.615 0.00 0.00 0.00 1.98
750 759 1.972872 ACTAGATGGTACCCCGTACG 58.027 55.000 10.07 8.69 39.64 3.67
753 762 3.053395 TCACTAACTAGATGGTACCCCGT 60.053 47.826 10.07 0.00 0.00 5.28
761 770 7.338710 TCTGGGAATTTTCACTAACTAGATGG 58.661 38.462 0.00 0.00 0.00 3.51
850 1177 3.955471 ACACAGTTCACATATTCAGGGG 58.045 45.455 0.00 0.00 0.00 4.79
863 1191 3.062042 ACGGTTCGGATAAACACAGTTC 58.938 45.455 0.00 0.00 0.00 3.01
1173 1502 1.675219 GTCAGGGTTGAGGCCGTAA 59.325 57.895 0.00 0.00 32.98 3.18
1197 1526 2.903357 GGCTCGGCATCTTCCTCA 59.097 61.111 0.00 0.00 0.00 3.86
1233 1562 0.036010 AGAGCACAAAGGGGTCGATG 60.036 55.000 0.00 0.00 37.81 3.84
1450 1788 4.034394 CACTGGGAACATCATACACGAATG 59.966 45.833 0.00 0.00 41.51 2.67
1507 1845 4.143115 ACTGAAAACGCATGAATGTACGAG 60.143 41.667 0.00 0.00 0.00 4.18
1527 1865 5.941948 AAGACCGGATTGAAGTTTTACTG 57.058 39.130 9.46 0.00 0.00 2.74
1528 1866 7.336176 GGATTAAGACCGGATTGAAGTTTTACT 59.664 37.037 9.46 0.00 0.00 2.24
1529 1867 7.336176 AGGATTAAGACCGGATTGAAGTTTTAC 59.664 37.037 9.46 0.00 0.00 2.01
1530 1868 7.335924 CAGGATTAAGACCGGATTGAAGTTTTA 59.664 37.037 9.46 0.00 0.00 1.52
1531 1869 6.151144 CAGGATTAAGACCGGATTGAAGTTTT 59.849 38.462 9.46 0.00 0.00 2.43
1532 1870 5.648092 CAGGATTAAGACCGGATTGAAGTTT 59.352 40.000 9.46 0.00 0.00 2.66
1533 1871 5.186198 CAGGATTAAGACCGGATTGAAGTT 58.814 41.667 9.46 0.00 0.00 2.66
1534 1872 4.384208 CCAGGATTAAGACCGGATTGAAGT 60.384 45.833 9.46 0.00 0.00 3.01
1535 1873 4.130118 CCAGGATTAAGACCGGATTGAAG 58.870 47.826 9.46 0.00 0.00 3.02
1536 1874 3.521937 ACCAGGATTAAGACCGGATTGAA 59.478 43.478 9.46 0.00 0.00 2.69
1537 1875 3.112263 ACCAGGATTAAGACCGGATTGA 58.888 45.455 9.46 0.00 0.00 2.57
1538 1876 3.560636 ACCAGGATTAAGACCGGATTG 57.439 47.619 9.46 0.00 0.00 2.67
1539 1877 3.390311 GGTACCAGGATTAAGACCGGATT 59.610 47.826 9.46 4.99 0.00 3.01
1540 1878 2.970640 GGTACCAGGATTAAGACCGGAT 59.029 50.000 9.46 0.00 0.00 4.18
1541 1879 2.023695 AGGTACCAGGATTAAGACCGGA 60.024 50.000 15.94 0.00 32.04 5.14
1542 1880 2.395619 AGGTACCAGGATTAAGACCGG 58.604 52.381 15.94 0.00 32.04 5.28
1543 1881 3.705072 AGAAGGTACCAGGATTAAGACCG 59.295 47.826 15.94 0.00 32.04 4.79
1683 3084 5.359576 ACACCACTACAATTCTGAAGCAAAA 59.640 36.000 0.00 0.00 0.00 2.44
1684 3085 4.887071 ACACCACTACAATTCTGAAGCAAA 59.113 37.500 0.00 0.00 0.00 3.68
1729 3130 5.983118 GGCAAAGCAACACTTACATAAAACT 59.017 36.000 0.00 0.00 37.75 2.66
1847 3269 4.156182 GGTTTGACGCTTGCATAGTTTAC 58.844 43.478 0.00 0.00 0.00 2.01
1852 3274 3.623060 AGTATGGTTTGACGCTTGCATAG 59.377 43.478 0.00 0.00 0.00 2.23
1885 3310 6.163476 TGATATATACCGTGCATTCCAAGAC 58.837 40.000 0.00 0.00 0.00 3.01
1972 3397 1.271379 CAACAACATGGCTGCATCAGT 59.729 47.619 0.50 0.00 33.43 3.41
2005 3431 7.961940 TCTTATATTATGGGATGGAGGGAGTA 58.038 38.462 0.00 0.00 0.00 2.59
2006 3432 6.826727 TCTTATATTATGGGATGGAGGGAGT 58.173 40.000 0.00 0.00 0.00 3.85
2007 3433 6.183361 GCTCTTATATTATGGGATGGAGGGAG 60.183 46.154 0.00 0.00 0.00 4.30
2008 3434 5.667626 GCTCTTATATTATGGGATGGAGGGA 59.332 44.000 0.00 0.00 0.00 4.20
2009 3435 5.453903 CGCTCTTATATTATGGGATGGAGGG 60.454 48.000 0.00 0.00 0.00 4.30
2010 3436 5.129485 ACGCTCTTATATTATGGGATGGAGG 59.871 44.000 0.00 0.00 0.00 4.30
2011 3437 6.227298 ACGCTCTTATATTATGGGATGGAG 57.773 41.667 0.00 0.00 0.00 3.86
2012 3438 6.620877 AACGCTCTTATATTATGGGATGGA 57.379 37.500 0.00 0.00 0.00 3.41
2013 3439 7.687941 AAAACGCTCTTATATTATGGGATGG 57.312 36.000 0.00 0.00 0.00 3.51
2014 3440 9.653287 TCTAAAACGCTCTTATATTATGGGATG 57.347 33.333 0.00 0.00 0.00 3.51
2015 3441 9.654663 GTCTAAAACGCTCTTATATTATGGGAT 57.345 33.333 0.00 0.00 0.00 3.85
2016 3442 8.644216 TGTCTAAAACGCTCTTATATTATGGGA 58.356 33.333 0.00 0.00 0.00 4.37
2017 3443 8.709646 GTGTCTAAAACGCTCTTATATTATGGG 58.290 37.037 0.00 0.00 35.42 4.00
2018 3444 8.709646 GGTGTCTAAAACGCTCTTATATTATGG 58.290 37.037 0.00 0.00 38.49 2.74
2019 3445 9.256477 TGGTGTCTAAAACGCTCTTATATTATG 57.744 33.333 0.00 0.00 38.49 1.90
2020 3446 9.477484 CTGGTGTCTAAAACGCTCTTATATTAT 57.523 33.333 0.00 0.00 38.49 1.28
2021 3447 8.472413 ACTGGTGTCTAAAACGCTCTTATATTA 58.528 33.333 0.00 0.00 38.49 0.98
2022 3448 7.277981 CACTGGTGTCTAAAACGCTCTTATATT 59.722 37.037 0.00 0.00 38.49 1.28
2023 3449 6.757010 CACTGGTGTCTAAAACGCTCTTATAT 59.243 38.462 0.00 0.00 38.49 0.86
2024 3450 6.097356 CACTGGTGTCTAAAACGCTCTTATA 58.903 40.000 0.00 0.00 38.49 0.98
2025 3451 4.929808 CACTGGTGTCTAAAACGCTCTTAT 59.070 41.667 0.00 0.00 38.49 1.73
2026 3452 4.202182 ACACTGGTGTCTAAAACGCTCTTA 60.202 41.667 0.01 0.00 40.24 2.10
2027 3453 3.131396 CACTGGTGTCTAAAACGCTCTT 58.869 45.455 0.00 0.00 38.49 2.85
2028 3454 2.102588 ACACTGGTGTCTAAAACGCTCT 59.897 45.455 0.01 0.00 40.24 4.09
2029 3455 2.480845 ACACTGGTGTCTAAAACGCTC 58.519 47.619 0.01 0.00 40.24 5.03
2030 3456 2.614829 ACACTGGTGTCTAAAACGCT 57.385 45.000 0.01 0.00 40.24 5.07
2031 3457 3.183775 CACTACACTGGTGTCTAAAACGC 59.816 47.826 9.77 0.00 43.74 4.84
2032 3458 4.365723 ACACTACACTGGTGTCTAAAACG 58.634 43.478 9.77 0.00 43.35 3.60
2041 3467 4.036734 AGCATTTTTGACACTACACTGGTG 59.963 41.667 0.00 0.00 40.19 4.17
2042 3468 4.207165 AGCATTTTTGACACTACACTGGT 58.793 39.130 0.00 0.00 0.00 4.00
2043 3469 4.516698 AGAGCATTTTTGACACTACACTGG 59.483 41.667 0.00 0.00 0.00 4.00
2044 3470 5.679734 AGAGCATTTTTGACACTACACTG 57.320 39.130 0.00 0.00 0.00 3.66
2045 3471 7.986085 ATAAGAGCATTTTTGACACTACACT 57.014 32.000 0.00 0.00 0.00 3.55
2051 3477 9.683069 CCCATAATATAAGAGCATTTTTGACAC 57.317 33.333 0.00 0.00 0.00 3.67
2052 3478 9.639563 TCCCATAATATAAGAGCATTTTTGACA 57.360 29.630 0.00 0.00 0.00 3.58
2053 3479 9.899226 GTCCCATAATATAAGAGCATTTTTGAC 57.101 33.333 0.00 0.00 0.00 3.18
2054 3480 8.783093 CGTCCCATAATATAAGAGCATTTTTGA 58.217 33.333 0.00 0.00 0.00 2.69
2055 3481 8.023128 CCGTCCCATAATATAAGAGCATTTTTG 58.977 37.037 0.00 0.00 0.00 2.44
2056 3482 7.942341 TCCGTCCCATAATATAAGAGCATTTTT 59.058 33.333 0.00 0.00 0.00 1.94
2057 3483 7.458397 TCCGTCCCATAATATAAGAGCATTTT 58.542 34.615 0.00 0.00 0.00 1.82
2058 3484 7.016153 TCCGTCCCATAATATAAGAGCATTT 57.984 36.000 0.00 0.00 0.00 2.32
2059 3485 6.352222 CCTCCGTCCCATAATATAAGAGCATT 60.352 42.308 0.00 0.00 0.00 3.56
2060 3486 5.129485 CCTCCGTCCCATAATATAAGAGCAT 59.871 44.000 0.00 0.00 0.00 3.79
2061 3487 4.466370 CCTCCGTCCCATAATATAAGAGCA 59.534 45.833 0.00 0.00 0.00 4.26
2062 3488 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
2063 3489 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
2064 3490 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
2065 3491 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
2066 3492 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
2067 3493 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
2068 3494 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
2069 3495 3.245514 CCTACTCCCTCCGTCCCATAATA 60.246 52.174 0.00 0.00 0.00 0.98
2070 3496 2.492940 CCTACTCCCTCCGTCCCATAAT 60.493 54.545 0.00 0.00 0.00 1.28
2071 3497 1.133262 CCTACTCCCTCCGTCCCATAA 60.133 57.143 0.00 0.00 0.00 1.90
2072 3498 0.481567 CCTACTCCCTCCGTCCCATA 59.518 60.000 0.00 0.00 0.00 2.74
2073 3499 1.233369 CCTACTCCCTCCGTCCCAT 59.767 63.158 0.00 0.00 0.00 4.00
2074 3500 1.807771 AACCTACTCCCTCCGTCCCA 61.808 60.000 0.00 0.00 0.00 4.37
2075 3501 1.001376 AACCTACTCCCTCCGTCCC 59.999 63.158 0.00 0.00 0.00 4.46
2076 3502 0.033306 AGAACCTACTCCCTCCGTCC 60.033 60.000 0.00 0.00 0.00 4.79
2077 3503 1.104630 CAGAACCTACTCCCTCCGTC 58.895 60.000 0.00 0.00 0.00 4.79
2078 3504 0.408700 ACAGAACCTACTCCCTCCGT 59.591 55.000 0.00 0.00 0.00 4.69
2079 3505 2.431954 TACAGAACCTACTCCCTCCG 57.568 55.000 0.00 0.00 0.00 4.63
2080 3506 4.715297 TCATTTACAGAACCTACTCCCTCC 59.285 45.833 0.00 0.00 0.00 4.30
2081 3507 5.934402 TCATTTACAGAACCTACTCCCTC 57.066 43.478 0.00 0.00 0.00 4.30
2082 3508 6.697641 TTTCATTTACAGAACCTACTCCCT 57.302 37.500 0.00 0.00 0.00 4.20
2083 3509 7.110155 TGATTTCATTTACAGAACCTACTCCC 58.890 38.462 0.00 0.00 0.00 4.30
2084 3510 8.561738 TTGATTTCATTTACAGAACCTACTCC 57.438 34.615 0.00 0.00 0.00 3.85
2085 3511 9.220767 ACTTGATTTCATTTACAGAACCTACTC 57.779 33.333 0.00 0.00 0.00 2.59
2140 3566 4.240881 ACCCATGCATATGAACAAGAGT 57.759 40.909 6.97 0.00 36.36 3.24
2240 4672 3.999663 CACCTGCCTTTCTTACAGAAGAG 59.000 47.826 0.00 0.00 42.66 2.85
2415 4852 3.084786 AGAGATTTGTAGGCCAAAGTGC 58.915 45.455 5.01 0.00 45.79 4.40
2422 4859 7.501844 ACATTACTTAGAGAGATTTGTAGGCC 58.498 38.462 0.00 0.00 0.00 5.19
2431 4868 6.514212 CGCAGTGCTACATTACTTAGAGAGAT 60.514 42.308 14.33 0.00 0.00 2.75
2441 4878 5.479716 AAAATACCGCAGTGCTACATTAC 57.520 39.130 14.33 0.00 0.00 1.89
2449 4886 5.229921 TCAATCTAAAAATACCGCAGTGC 57.770 39.130 4.58 4.58 0.00 4.40
2687 5124 1.228063 AACCACCAGCTGACTGCAG 60.228 57.895 17.39 13.48 45.94 4.41
2802 5239 1.479323 TGTTTCGACTAAGATCCGGGG 59.521 52.381 0.00 0.00 0.00 5.73
3072 5517 6.798315 AATGATTCATTCTCTTCATAGCCG 57.202 37.500 6.06 0.00 26.27 5.52
3100 5545 7.576403 TCTGAATTGAGATACAAATGGGATGA 58.424 34.615 0.00 0.00 42.03 2.92
3134 5579 6.238566 GCAAAGCTAGATTCAGCATCATAACA 60.239 38.462 11.77 0.00 44.35 2.41
3135 5580 6.141462 GCAAAGCTAGATTCAGCATCATAAC 58.859 40.000 11.77 0.00 44.35 1.89
3250 5695 5.220931 GGTTTGTGCTCTCCTGCATAATTAG 60.221 44.000 0.00 0.00 45.23 1.73
3261 5706 4.207891 TCAGAATAGGTTTGTGCTCTCC 57.792 45.455 0.00 0.00 0.00 3.71
3404 5849 4.034394 CGATGAACGGATGAATCACATTGT 59.966 41.667 0.00 0.00 39.56 2.71
3405 5850 4.521010 CGATGAACGGATGAATCACATTG 58.479 43.478 0.00 0.00 39.56 2.82
3437 5882 5.596361 TCAACAAAATGTGCCTAGAGGAAAA 59.404 36.000 0.00 0.00 37.39 2.29
3444 5890 4.278170 TCCAACTCAACAAAATGTGCCTAG 59.722 41.667 0.00 0.00 0.00 3.02
3450 5896 3.642141 AGGGTCCAACTCAACAAAATGT 58.358 40.909 0.00 0.00 0.00 2.71
3494 5940 4.279145 TCCAGTACAGTCCAGATTAGGTC 58.721 47.826 0.00 0.00 0.00 3.85
3531 5977 3.717707 GACACGGAGCATATGTATGTGT 58.282 45.455 18.44 18.44 36.11 3.72
3599 6045 4.432712 AGTGATGTTGTGCTTCCAAAAAC 58.567 39.130 0.00 0.00 0.00 2.43
3647 6094 6.872920 TCCTTTGTTTACTTGCAATTGTCTT 58.127 32.000 7.40 0.00 0.00 3.01
3666 6113 9.859152 CCTTCATAGAATATCTTTTCCTCCTTT 57.141 33.333 0.00 0.00 0.00 3.11
3711 6158 2.668457 GTCAACGTGTCAATCTGCTAGG 59.332 50.000 0.00 0.00 0.00 3.02
3743 6196 6.572167 TTCATTAACACATGAACTGCATCA 57.428 33.333 0.00 0.00 38.09 3.07
3785 6238 7.718272 TTGTTTCAAATACTACTTGTACGCT 57.282 32.000 0.00 0.00 33.45 5.07
3869 6322 5.106791 GCTGCACTTCTGGCATATATTACTG 60.107 44.000 0.00 0.00 41.06 2.74
3914 6367 7.443879 TGCAGAAAATGTATCACAAGTCTACAA 59.556 33.333 0.00 0.00 0.00 2.41
3952 6408 8.116669 ACTATGCTGCCTAAAGTATAGGAGATA 58.883 37.037 12.09 0.00 43.36 1.98
4019 6478 5.184096 TGCCGTTCAAATAAGCCAAATCTTA 59.816 36.000 0.00 0.00 33.56 2.10
4236 6695 8.098963 TCACTATAGTAGTTTACAGAGGGAGA 57.901 38.462 4.74 0.00 36.76 3.71
4296 6817 6.741358 GCATAAAGAACCAAACAGTTACGATC 59.259 38.462 0.00 0.00 0.00 3.69
4300 6821 9.855021 AATATGCATAAAGAACCAAACAGTTAC 57.145 29.630 11.13 0.00 0.00 2.50
4334 6855 6.572167 ACTAGCTACCGAGAAATATACCAC 57.428 41.667 0.00 0.00 0.00 4.16
4348 6869 3.363627 AGTGGGTACTCAACTAGCTACC 58.636 50.000 0.00 0.00 34.05 3.18
4370 6891 5.735354 GCAGGATTCAGGCATATCTGTTTTG 60.735 44.000 0.00 0.00 36.25 2.44
4443 6964 1.275291 TCCAGAAAGCCTTACGTCAGG 59.725 52.381 11.62 11.62 36.95 3.86
4524 7045 0.598065 AAATCAGCAGGTTTGTCCGC 59.402 50.000 0.00 0.00 41.99 5.54
4551 7072 4.517075 CCTTTCTTTTTCTCTGACCAGGTC 59.483 45.833 13.35 13.35 0.00 3.85
4610 7131 3.023119 AGATCACCTTGTGTGCAAAACA 58.977 40.909 0.00 0.00 45.03 2.83
4638 7159 4.089361 GGTGAGGAATTGGACTTGGAAAT 58.911 43.478 0.00 0.00 0.00 2.17
4645 7168 1.004044 CTGCTGGTGAGGAATTGGACT 59.996 52.381 0.00 0.00 0.00 3.85
4655 7178 6.694877 TGTTAGTATACTACTGCTGGTGAG 57.305 41.667 12.25 0.00 39.81 3.51
4671 7194 6.042777 GCACTGAAGAGCATGTATGTTAGTA 58.957 40.000 0.00 0.00 0.00 1.82
4683 7206 1.614903 CAAAATGGGCACTGAAGAGCA 59.385 47.619 2.21 0.00 33.19 4.26
4694 7217 1.202348 GTACTGGTCTGCAAAATGGGC 59.798 52.381 0.00 0.00 0.00 5.36
4721 7244 7.042254 GGTGTTGTTCATAATATACGGTCTTCC 60.042 40.741 0.00 0.00 0.00 3.46
4752 7280 3.030652 CACCGAAGCGCCAACTTT 58.969 55.556 2.29 0.00 0.00 2.66
4802 7330 1.065709 GCCGGTAGGAAATTCACAGGA 60.066 52.381 1.90 0.00 41.02 3.86
4993 7535 2.193127 TGTACATCAAGGTACAGGGGG 58.807 52.381 3.70 0.00 46.32 5.40
4999 7541 2.093128 CAGGGGGTGTACATCAAGGTAC 60.093 54.545 8.70 0.00 43.08 3.34
5000 7542 2.193127 CAGGGGGTGTACATCAAGGTA 58.807 52.381 8.70 0.00 0.00 3.08
5001 7543 0.991920 CAGGGGGTGTACATCAAGGT 59.008 55.000 8.70 0.00 0.00 3.50
5002 7544 0.991920 ACAGGGGGTGTACATCAAGG 59.008 55.000 8.70 0.00 37.75 3.61
5010 7552 2.193127 CATCAAGGTACAGGGGGTGTA 58.807 52.381 0.00 0.00 40.94 2.90
5124 7673 1.484240 ACAGATAAGAGTCAGCCTGCC 59.516 52.381 0.00 0.00 0.00 4.85
5165 7723 6.428465 TGATCATTCTACGGAGAGATACAGAC 59.572 42.308 0.00 0.00 31.77 3.51
5214 7780 4.618227 GCGAAATACAAAAGGCCAACTCAT 60.618 41.667 5.01 0.00 0.00 2.90
5333 7899 0.103572 GCGACGCAAGGAATAGGGTA 59.896 55.000 16.42 0.00 46.39 3.69
5386 7953 1.371337 GATCATGCAACTCCAGCGCA 61.371 55.000 11.47 0.00 40.50 6.09
5406 7973 3.244665 CCAACTCCCTTTTAACGGTAGGT 60.245 47.826 0.00 0.00 0.00 3.08
5408 7975 4.011966 ACCAACTCCCTTTTAACGGTAG 57.988 45.455 0.00 0.00 0.00 3.18
5409 7976 4.020307 CCTACCAACTCCCTTTTAACGGTA 60.020 45.833 0.00 0.00 0.00 4.02
5540 9208 2.238521 GCAAGACATGGTTTTGGGAGA 58.761 47.619 0.00 0.00 29.93 3.71
5541 9209 1.068333 CGCAAGACATGGTTTTGGGAG 60.068 52.381 13.98 0.00 40.93 4.30
5543 9211 0.673437 ACGCAAGACATGGTTTTGGG 59.327 50.000 16.20 16.20 42.89 4.12
5556 9224 7.167302 TGTTTGATTTGATTGAGTTAACGCAAG 59.833 33.333 25.39 0.00 38.93 4.01


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

AutoCloner maintained by Alex Coulton.