Multiple sequence alignment - TraesCS4D01G265000

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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 TraesCS4D01G265000 chr4D 100.000 3858 0 0 1 3858 435210354 435206497 0.000000e+00 7125.0
1 TraesCS4D01G265000 chr4D 83.186 452 65 9 1043 1486 435411092 435410644 1.670000e-108 403.0
2 TraesCS4D01G265000 chr4D 99.099 111 1 0 3748 3858 435205132 435205242 2.350000e-47 200.0
3 TraesCS4D01G265000 chr4B 90.024 1664 77 35 1614 3232 536118676 536120295 0.000000e+00 2071.0
4 TraesCS4D01G265000 chr4B 94.470 651 31 3 979 1627 536117995 536118642 0.000000e+00 998.0
5 TraesCS4D01G265000 chr4B 92.877 702 22 10 2964 3651 535351534 535350847 0.000000e+00 994.0
6 TraesCS4D01G265000 chr4B 83.778 450 64 6 1044 1486 536412533 536412086 5.960000e-113 418.0
7 TraesCS4D01G265000 chr4B 84.483 348 36 11 2658 2989 535351890 535351545 1.030000e-85 327.0
8 TraesCS4D01G265000 chr4B 89.011 273 8 3 719 975 536117690 536117956 6.220000e-83 318.0
9 TraesCS4D01G265000 chr4B 94.554 202 6 2 1 202 536114906 536115102 1.350000e-79 307.0
10 TraesCS4D01G265000 chr4B 92.793 111 7 1 3637 3747 535349233 535349124 3.990000e-35 159.0
11 TraesCS4D01G265000 chr4B 86.735 98 6 4 3268 3364 536120611 536120702 6.820000e-18 102.0
12 TraesCS4D01G265000 chr4B 86.957 69 7 1 3679 3747 535334017 535333951 4.130000e-10 76.8
13 TraesCS4D01G265000 chr4A 89.286 1260 63 28 415 1627 36614733 36613499 0.000000e+00 1513.0
14 TraesCS4D01G265000 chr4A 88.910 1037 69 28 2230 3235 36612785 36611764 0.000000e+00 1236.0
15 TraesCS4D01G265000 chr4A 89.977 439 23 13 1779 2215 36613256 36612837 7.290000e-152 547.0
16 TraesCS4D01G265000 chr4A 86.000 400 51 4 1090 1485 36795261 36794863 1.280000e-114 424.0
17 TraesCS4D01G265000 chr4A 82.942 469 70 6 1055 1515 36671363 36670897 7.710000e-112 414.0
18 TraesCS4D01G265000 chr4A 84.937 239 20 6 1614 1842 36613483 36613251 1.080000e-55 228.0
19 TraesCS4D01G265000 chr4A 89.326 178 6 6 1 169 36620964 36620791 1.090000e-50 211.0
20 TraesCS4D01G265000 chr4A 84.733 131 8 6 3240 3364 36610903 36610779 1.880000e-23 121.0
21 TraesCS4D01G265000 chr4A 93.421 76 4 1 3386 3461 36610342 36610268 1.130000e-20 111.0
22 TraesCS4D01G265000 chrUn 99.107 112 1 0 3747 3858 45272857 45272968 6.540000e-48 202.0
23 TraesCS4D01G265000 chrUn 99.099 111 1 0 3748 3858 90817817 90817927 2.350000e-47 200.0
24 TraesCS4D01G265000 chrUn 98.214 112 2 0 3747 3858 391516318 391516207 3.040000e-46 196.0
25 TraesCS4D01G265000 chrUn 97.321 112 3 0 3747 3858 391511419 391511308 1.410000e-44 191.0
26 TraesCS4D01G265000 chrUn 87.129 101 10 3 248 347 314370573 314370671 1.130000e-20 111.0
27 TraesCS4D01G265000 chr7D 98.198 111 2 0 3748 3858 563446179 563446289 1.090000e-45 195.0
28 TraesCS4D01G265000 chr2D 97.297 111 2 1 3748 3858 452374760 452374869 1.830000e-43 187.0
29 TraesCS4D01G265000 chr2D 83.333 102 14 3 248 348 609331910 609331811 1.480000e-14 91.6
30 TraesCS4D01G265000 chr3D 95.495 111 5 0 3748 3858 268048430 268048540 1.100000e-40 178.0
31 TraesCS4D01G265000 chr3D 95.495 111 5 0 3748 3858 606087187 606087297 1.100000e-40 178.0
32 TraesCS4D01G265000 chr3D 91.837 98 7 1 248 345 532994177 532994081 6.720000e-28 135.0
33 TraesCS4D01G265000 chr3B 86.792 106 12 2 248 352 557174633 557174737 2.440000e-22 117.0
34 TraesCS4D01G265000 chr1B 84.762 105 15 1 248 352 175415469 175415572 1.900000e-18 104.0
35 TraesCS4D01G265000 chr6D 85.149 101 14 1 248 348 345760562 345760463 6.820000e-18 102.0
36 TraesCS4D01G265000 chr7A 84.314 102 15 1 247 348 556577123 556577023 8.820000e-17 99.0
37 TraesCS4D01G265000 chr3A 84.000 100 15 1 248 347 1704500 1704402 1.140000e-15 95.3
38 TraesCS4D01G265000 chr6B 83.000 100 16 1 248 347 239733724 239733822 5.310000e-14 89.8


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 TraesCS4D01G265000 chr4D 435206497 435210354 3857 True 7125.000000 7125 100.0000 1 3858 1 chr4D.!!$R1 3857
1 TraesCS4D01G265000 chr4B 536114906 536120702 5796 False 759.200000 2071 90.9588 1 3364 5 chr4B.!!$F1 3363
2 TraesCS4D01G265000 chr4B 535349124 535351890 2766 True 493.333333 994 90.0510 2658 3747 3 chr4B.!!$R3 1089
3 TraesCS4D01G265000 chr4A 36610268 36614733 4465 True 626.000000 1513 88.5440 415 3461 6 chr4A.!!$R4 3046

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
203 204 0.028902 CACGACCATCGATGACGCTA 59.971 55.0 29.71 0.0 43.74 4.26 F
598 2792 0.034960 GCCCTCTTTCTCAACTCCCC 60.035 60.0 0.00 0.0 0.00 4.81 F
1719 4049 0.302890 CAATGCTCGATTCGCTGTCC 59.697 55.0 0.00 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1973 4366 0.321346 TCAAGGAACGCATGAGCAGA 59.679 50.0 0.0 0.0 42.27 4.26 R
1974 4367 0.445436 GTCAAGGAACGCATGAGCAG 59.555 55.0 0.0 0.0 42.27 4.24 R
3277 6656 0.179032 TGAAGCTGCCAAACGGAAGA 60.179 50.0 0.0 0.0 29.05 2.87 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
77 78 0.682209 GACTAGGCCACGACCCACTA 60.682 60.000 5.01 0.00 0.00 2.74
122 123 2.259818 CCTTGTCGCGCTCTGTCT 59.740 61.111 5.56 0.00 0.00 3.41
123 124 2.091112 CCTTGTCGCGCTCTGTCTG 61.091 63.158 5.56 0.00 0.00 3.51
124 125 1.372251 CTTGTCGCGCTCTGTCTGT 60.372 57.895 5.56 0.00 0.00 3.41
125 126 1.340657 CTTGTCGCGCTCTGTCTGTC 61.341 60.000 5.56 0.00 0.00 3.51
140 141 1.001633 TCTGTCAGGCGAACCCTTTAC 59.998 52.381 0.00 0.00 43.06 2.01
202 203 1.226688 CACGACCATCGATGACGCT 60.227 57.895 29.71 20.05 43.74 5.07
203 204 0.028902 CACGACCATCGATGACGCTA 59.971 55.000 29.71 0.00 43.74 4.26
204 205 0.308068 ACGACCATCGATGACGCTAG 59.692 55.000 29.71 16.43 43.74 3.42
205 206 0.308068 CGACCATCGATGACGCTAGT 59.692 55.000 26.86 14.24 43.74 2.57
216 217 7.902387 TCGATGACGCTAGTAGATTATTAGT 57.098 36.000 0.00 0.00 39.58 2.24
218 219 9.085250 TCGATGACGCTAGTAGATTATTAGTAG 57.915 37.037 0.00 0.00 39.58 2.57
261 302 4.495690 AAAAAGCTACTCCCTCCATCTC 57.504 45.455 0.00 0.00 0.00 2.75
262 303 2.856760 AAGCTACTCCCTCCATCTCA 57.143 50.000 0.00 0.00 0.00 3.27
263 304 2.856760 AGCTACTCCCTCCATCTCAA 57.143 50.000 0.00 0.00 0.00 3.02
264 305 3.121929 AGCTACTCCCTCCATCTCAAA 57.878 47.619 0.00 0.00 0.00 2.69
266 307 4.043596 AGCTACTCCCTCCATCTCAAAAT 58.956 43.478 0.00 0.00 0.00 1.82
267 308 5.219739 AGCTACTCCCTCCATCTCAAAATA 58.780 41.667 0.00 0.00 0.00 1.40
270 311 7.001073 GCTACTCCCTCCATCTCAAAATAAAT 58.999 38.462 0.00 0.00 0.00 1.40
274 445 7.675619 ACTCCCTCCATCTCAAAATAAATGTTT 59.324 33.333 0.00 0.00 0.00 2.83
336 1989 7.193595 AGTTTGAAACACTTATTTTGAGACGG 58.806 34.615 11.02 0.00 0.00 4.79
338 1991 6.539649 TGAAACACTTATTTTGAGACGGAG 57.460 37.500 0.00 0.00 0.00 4.63
341 1994 3.581332 ACACTTATTTTGAGACGGAGGGA 59.419 43.478 0.00 0.00 0.00 4.20
342 1995 4.184629 CACTTATTTTGAGACGGAGGGAG 58.815 47.826 0.00 0.00 0.00 4.30
343 1996 3.838903 ACTTATTTTGAGACGGAGGGAGT 59.161 43.478 0.00 0.00 0.00 3.85
344 1997 5.021458 ACTTATTTTGAGACGGAGGGAGTA 58.979 41.667 0.00 0.00 0.00 2.59
345 1998 3.889520 ATTTTGAGACGGAGGGAGTAC 57.110 47.619 0.00 0.00 0.00 2.73
346 1999 2.599408 TTTGAGACGGAGGGAGTACT 57.401 50.000 0.00 0.00 0.00 2.73
347 2000 3.726557 TTTGAGACGGAGGGAGTACTA 57.273 47.619 0.00 0.00 0.00 1.82
348 2001 3.726557 TTGAGACGGAGGGAGTACTAA 57.273 47.619 0.00 0.00 0.00 2.24
349 2002 3.947612 TGAGACGGAGGGAGTACTAAT 57.052 47.619 0.00 0.00 0.00 1.73
350 2003 4.246712 TGAGACGGAGGGAGTACTAATT 57.753 45.455 0.00 0.00 0.00 1.40
351 2004 5.378230 TGAGACGGAGGGAGTACTAATTA 57.622 43.478 0.00 0.00 0.00 1.40
352 2005 5.759059 TGAGACGGAGGGAGTACTAATTAA 58.241 41.667 0.00 0.00 0.00 1.40
354 2007 6.489361 TGAGACGGAGGGAGTACTAATTAATC 59.511 42.308 0.00 0.00 0.00 1.75
355 2008 6.612741 AGACGGAGGGAGTACTAATTAATCT 58.387 40.000 0.00 0.00 0.00 2.40
356 2009 6.716173 AGACGGAGGGAGTACTAATTAATCTC 59.284 42.308 0.00 0.00 0.00 2.75
357 2010 5.472820 ACGGAGGGAGTACTAATTAATCTCG 59.527 44.000 0.00 0.00 29.99 4.04
359 2012 5.477637 GGAGGGAGTACTAATTAATCTCGCT 59.522 44.000 20.12 20.12 45.95 4.93
360 2013 6.658391 GGAGGGAGTACTAATTAATCTCGCTA 59.342 42.308 20.08 0.00 44.30 4.26
361 2014 7.176340 GGAGGGAGTACTAATTAATCTCGCTAA 59.824 40.741 20.08 0.00 44.30 3.09
362 2015 8.474710 AGGGAGTACTAATTAATCTCGCTAAA 57.525 34.615 19.33 0.00 43.17 1.85
364 2017 9.708092 GGGAGTACTAATTAATCTCGCTAAAAT 57.292 33.333 0.00 0.00 35.96 1.82
367 2020 8.989980 AGTACTAATTAATCTCGCTAAAATGCC 58.010 33.333 0.00 0.00 0.00 4.40
369 2022 4.749245 ATTAATCTCGCTAAAATGCCCG 57.251 40.909 0.00 0.00 0.00 6.13
371 2024 2.902705 ATCTCGCTAAAATGCCCGTA 57.097 45.000 0.00 0.00 0.00 4.02
372 2025 1.930567 TCTCGCTAAAATGCCCGTAC 58.069 50.000 0.00 0.00 0.00 3.67
373 2026 0.935196 CTCGCTAAAATGCCCGTACC 59.065 55.000 0.00 0.00 0.00 3.34
374 2027 0.806884 TCGCTAAAATGCCCGTACCG 60.807 55.000 0.00 0.00 0.00 4.02
386 2039 3.131326 CGTACCGGAAATCACAGCA 57.869 52.632 9.46 0.00 0.00 4.41
387 2040 1.434555 CGTACCGGAAATCACAGCAA 58.565 50.000 9.46 0.00 0.00 3.91
388 2041 2.006888 CGTACCGGAAATCACAGCAAT 58.993 47.619 9.46 0.00 0.00 3.56
389 2042 2.223021 CGTACCGGAAATCACAGCAATG 60.223 50.000 9.46 0.00 0.00 2.82
390 2043 1.176527 ACCGGAAATCACAGCAATGG 58.823 50.000 9.46 0.00 0.00 3.16
391 2044 1.271871 ACCGGAAATCACAGCAATGGA 60.272 47.619 9.46 0.00 0.00 3.41
392 2045 1.818060 CCGGAAATCACAGCAATGGAA 59.182 47.619 0.00 0.00 0.00 3.53
393 2046 2.415893 CCGGAAATCACAGCAATGGAAC 60.416 50.000 0.00 0.00 0.00 3.62
407 2312 2.552093 TGGAACAACCCCCTCAAAAA 57.448 45.000 0.00 0.00 38.00 1.94
470 2659 1.340502 TGAATCCCTTTGCACGGCATA 60.341 47.619 0.00 0.00 38.76 3.14
487 2676 2.286595 GCATAGCATCGGTGTGATTGTG 60.287 50.000 0.00 0.00 34.13 3.33
498 2687 3.316308 GGTGTGATTGTGGCATCTATTCC 59.684 47.826 0.00 0.00 0.00 3.01
510 2699 5.538813 TGGCATCTATTCCTTCGTACTACAT 59.461 40.000 0.00 0.00 0.00 2.29
513 2702 6.447162 CATCTATTCCTTCGTACTACATGCA 58.553 40.000 0.00 0.00 0.00 3.96
558 2747 2.171940 CTTCGCAAGCTCACGCAC 59.828 61.111 3.59 0.00 39.10 5.34
573 2767 2.537560 GCACGCTGCCGAATATGCT 61.538 57.895 0.00 0.00 37.42 3.79
581 2775 1.008538 CCGAATATGCTTTGCCGCC 60.009 57.895 0.00 0.00 0.00 6.13
598 2792 0.034960 GCCCTCTTTCTCAACTCCCC 60.035 60.000 0.00 0.00 0.00 4.81
610 2805 9.559732 CTTTCTCAACTCCCCAAAAATAAAAAT 57.440 29.630 0.00 0.00 0.00 1.82
697 2893 4.142004 GGCCTAGAACTTTCAACGGAGATA 60.142 45.833 0.00 0.00 0.00 1.98
707 2903 7.556844 ACTTTCAACGGAGATATGAACTGTAT 58.443 34.615 0.00 0.00 33.13 2.29
708 2904 7.707035 ACTTTCAACGGAGATATGAACTGTATC 59.293 37.037 0.00 0.00 33.13 2.24
709 2905 6.961360 TCAACGGAGATATGAACTGTATCT 57.039 37.500 0.00 0.00 40.61 1.98
787 2987 1.737838 TTATCGTTCAGCAGCCAAGG 58.262 50.000 0.00 0.00 0.00 3.61
799 2999 0.907230 AGCCAAGGAGACTCTGTCCC 60.907 60.000 1.74 0.00 42.68 4.46
926 3152 3.721706 CCACCACCAGCTCCCTCC 61.722 72.222 0.00 0.00 0.00 4.30
1282 3546 4.368808 CCGGCAGCAACGTGTTCG 62.369 66.667 0.00 0.00 43.34 3.95
1329 3593 1.742880 CGTGCTCACCACCATCCTG 60.743 63.158 0.00 0.00 41.53 3.86
1334 3598 0.539051 CTCACCACCATCCTGAGGAC 59.461 60.000 1.77 0.00 32.98 3.85
1516 3780 4.944372 GTATCTCGCCGCACCCCG 62.944 72.222 0.00 0.00 0.00 5.73
1531 3795 2.108362 CCGTATCGGGGCAGAACC 59.892 66.667 0.00 0.00 44.15 3.62
1541 3805 2.435059 GCAGAACCTCCAGTCCGC 60.435 66.667 0.00 0.00 0.00 5.54
1547 3811 3.003173 CCTCCAGTCCGCCCAGAA 61.003 66.667 0.00 0.00 0.00 3.02
1548 3812 2.266055 CTCCAGTCCGCCCAGAAC 59.734 66.667 0.00 0.00 0.00 3.01
1719 4049 0.302890 CAATGCTCGATTCGCTGTCC 59.697 55.000 0.00 0.00 0.00 4.02
1739 4074 6.976088 TGTCCAATTGTTTACATGTTAGGTG 58.024 36.000 2.30 0.00 0.00 4.00
1821 4207 9.807649 ATTTCAGACCATAAAAATTCAGCATAC 57.192 29.630 0.00 0.00 0.00 2.39
1893 4279 4.381612 CGTGACATGTAAAGAAGGCCTAGA 60.382 45.833 5.16 0.00 0.00 2.43
1902 4288 8.055279 TGTAAAGAAGGCCTAGAATTTCAATG 57.945 34.615 5.16 0.00 0.00 2.82
1926 4317 1.062587 CGATTTGATGGGTTCAGCGAC 59.937 52.381 0.00 0.00 35.27 5.19
1962 4355 3.074538 AGTGATAGGGATGGCCATAAACC 59.925 47.826 20.84 20.68 33.56 3.27
1966 4359 6.157994 GTGATAGGGATGGCCATAAACCTATA 59.842 42.308 34.18 25.22 40.39 1.31
1969 4362 3.591977 GGGATGGCCATAAACCTATACCT 59.408 47.826 20.84 0.00 35.15 3.08
1970 4363 4.324331 GGGATGGCCATAAACCTATACCTC 60.324 50.000 20.84 1.29 35.15 3.85
1971 4364 4.504858 GATGGCCATAAACCTATACCTCG 58.495 47.826 20.84 0.00 0.00 4.63
1973 4366 3.712733 TGGCCATAAACCTATACCTCGTT 59.287 43.478 0.00 0.00 0.00 3.85
1974 4367 4.202284 TGGCCATAAACCTATACCTCGTTC 60.202 45.833 0.00 0.00 0.00 3.95
2039 4432 1.198637 GAAGCAACAAGTAGCCTGCTG 59.801 52.381 0.97 0.00 44.18 4.41
2099 4492 3.139397 TCACCACCCCAACTTGATTTACT 59.861 43.478 0.00 0.00 0.00 2.24
2100 4493 4.351407 TCACCACCCCAACTTGATTTACTA 59.649 41.667 0.00 0.00 0.00 1.82
2101 4494 4.700213 CACCACCCCAACTTGATTTACTAG 59.300 45.833 0.00 0.00 0.00 2.57
2102 4495 4.352893 ACCACCCCAACTTGATTTACTAGT 59.647 41.667 0.00 0.00 36.26 2.57
2103 4496 5.548836 ACCACCCCAACTTGATTTACTAGTA 59.451 40.000 0.00 0.00 33.88 1.82
2104 4497 5.878669 CCACCCCAACTTGATTTACTAGTAC 59.121 44.000 0.91 0.00 33.88 2.73
2105 4498 6.296259 CCACCCCAACTTGATTTACTAGTACT 60.296 42.308 0.91 0.00 33.88 2.73
2106 4499 7.093201 CCACCCCAACTTGATTTACTAGTACTA 60.093 40.741 0.91 1.89 33.88 1.82
2107 4500 7.980099 CACCCCAACTTGATTTACTAGTACTAG 59.020 40.741 25.30 25.30 39.04 2.57
2169 4573 5.248640 CCTACAACTGTTCAATCATGGACT 58.751 41.667 0.00 0.00 35.92 3.85
2220 4624 8.988064 TTGCAAGTAGAAGAGTAATTCACTAG 57.012 34.615 0.00 0.00 37.72 2.57
2257 4698 8.742777 CCAATGTTCCTCTTCTTGATTGAATTA 58.257 33.333 0.00 0.00 0.00 1.40
2396 4842 1.919956 CTACCTCCGCGTGTTCGAGT 61.920 60.000 4.92 0.00 39.71 4.18
2398 4844 2.504244 CTCCGCGTGTTCGAGTCC 60.504 66.667 4.92 0.00 39.71 3.85
2517 4963 0.909610 TCCAAGGGCCTCACCTACAG 60.910 60.000 6.46 0.00 40.87 2.74
2590 5036 4.087892 GCGCTCTTCCTCAGGCCA 62.088 66.667 5.01 0.00 0.00 5.36
2614 5060 2.806244 CAAGAAGAACAAGTACCGGGTG 59.194 50.000 10.66 0.11 0.00 4.61
2707 5153 0.321564 TCAACATCCTCAAGCCGGTG 60.322 55.000 1.90 0.00 0.00 4.94
2797 5243 3.083997 ACCTGGGCCATCGTCCTC 61.084 66.667 6.72 0.00 0.00 3.71
2902 5354 2.716988 GCAGTTTTGATGCTGCGAC 58.283 52.632 0.70 0.00 46.67 5.19
2908 5360 0.660488 TTTGATGCTGCGACGTGTTT 59.340 45.000 0.00 0.00 0.00 2.83
2909 5361 0.041400 TTGATGCTGCGACGTGTTTG 60.041 50.000 0.00 0.00 0.00 2.93
2910 5362 0.878086 TGATGCTGCGACGTGTTTGA 60.878 50.000 0.00 0.00 0.00 2.69
2911 5363 0.179240 GATGCTGCGACGTGTTTGAG 60.179 55.000 0.00 0.00 0.00 3.02
2912 5364 2.127609 GCTGCGACGTGTTTGAGC 60.128 61.111 0.00 0.00 0.00 4.26
2913 5365 2.168621 CTGCGACGTGTTTGAGCG 59.831 61.111 0.00 0.00 0.00 5.03
2914 5366 2.278923 TGCGACGTGTTTGAGCGA 60.279 55.556 0.00 0.00 0.00 4.93
2915 5367 1.617755 CTGCGACGTGTTTGAGCGAT 61.618 55.000 0.00 0.00 0.00 4.58
2916 5368 1.225475 GCGACGTGTTTGAGCGATG 60.225 57.895 0.00 0.00 0.00 3.84
2917 5369 1.614227 GCGACGTGTTTGAGCGATGA 61.614 55.000 0.00 0.00 0.00 2.92
2918 5370 0.781787 CGACGTGTTTGAGCGATGAA 59.218 50.000 0.00 0.00 0.00 2.57
2919 5371 1.460267 CGACGTGTTTGAGCGATGAAC 60.460 52.381 0.00 0.00 0.00 3.18
2937 5400 7.218963 GCGATGAACTCCATGTTTTTATCTTTC 59.781 37.037 0.00 0.00 39.30 2.62
2938 5401 7.426456 CGATGAACTCCATGTTTTTATCTTTCG 59.574 37.037 0.00 0.00 39.30 3.46
2939 5402 7.504924 TGAACTCCATGTTTTTATCTTTCGT 57.495 32.000 0.00 0.00 39.30 3.85
2940 5403 8.610248 TGAACTCCATGTTTTTATCTTTCGTA 57.390 30.769 0.00 0.00 39.30 3.43
2941 5404 9.226606 TGAACTCCATGTTTTTATCTTTCGTAT 57.773 29.630 0.00 0.00 39.30 3.06
2943 5406 9.840427 AACTCCATGTTTTTATCTTTCGTATTG 57.160 29.630 0.00 0.00 34.84 1.90
2968 5474 8.589338 TGCTTCTTCTGTAGTAGATCTTTCTTT 58.411 33.333 0.00 0.00 34.80 2.52
2995 5501 1.878953 TCTTCGACTTCTTTGGTGGC 58.121 50.000 0.00 0.00 0.00 5.01
3034 5546 8.363390 TCTTTCTTCGAGCTGATGTATGATTAT 58.637 33.333 0.00 0.00 0.00 1.28
3235 5758 0.163788 GGCGTCAACGTCATCAACTG 59.836 55.000 1.69 0.00 44.43 3.16
3272 6651 2.614229 GGACCCTCTCTTCTTGTCTTGC 60.614 54.545 0.00 0.00 0.00 4.01
3276 6655 3.072944 CCTCTCTTCTTGTCTTGCCTTG 58.927 50.000 0.00 0.00 0.00 3.61
3277 6656 3.495806 CCTCTCTTCTTGTCTTGCCTTGT 60.496 47.826 0.00 0.00 0.00 3.16
3278 6657 3.733337 TCTCTTCTTGTCTTGCCTTGTC 58.267 45.455 0.00 0.00 0.00 3.18
3279 6658 3.389329 TCTCTTCTTGTCTTGCCTTGTCT 59.611 43.478 0.00 0.00 0.00 3.41
3280 6659 4.133078 CTCTTCTTGTCTTGCCTTGTCTT 58.867 43.478 0.00 0.00 0.00 3.01
3288 6669 1.001378 CTTGCCTTGTCTTCCGTTTGG 60.001 52.381 0.00 0.00 0.00 3.28
3364 6760 2.721797 CGCGAAAACGATGGTTCAAGAG 60.722 50.000 0.00 0.00 34.62 2.85
3365 6761 2.223377 GCGAAAACGATGGTTCAAGAGT 59.777 45.455 0.00 0.00 34.62 3.24
3368 6764 4.025229 CGAAAACGATGGTTCAAGAGTTCA 60.025 41.667 0.00 0.00 34.62 3.18
3369 6765 5.424121 AAAACGATGGTTCAAGAGTTCAG 57.576 39.130 0.00 0.00 34.62 3.02
3370 6766 4.336889 AACGATGGTTCAAGAGTTCAGA 57.663 40.909 0.00 0.00 0.00 3.27
3371 6767 4.336889 ACGATGGTTCAAGAGTTCAGAA 57.663 40.909 0.00 0.00 0.00 3.02
3670 9110 0.529773 GGTCGCCATGTAATCGAGCA 60.530 55.000 15.90 0.00 46.16 4.26
3672 9112 0.875908 TCGCCATGTAATCGAGCAGC 60.876 55.000 0.00 0.00 0.00 5.25
3702 9142 0.512952 CACGACGAAGAAAAGCCCAG 59.487 55.000 0.00 0.00 0.00 4.45
3708 9148 0.884514 GAAGAAAAGCCCAGCAGTCC 59.115 55.000 0.00 0.00 0.00 3.85
3709 9149 0.480252 AAGAAAAGCCCAGCAGTCCT 59.520 50.000 0.00 0.00 0.00 3.85
3738 9178 4.088823 AGCTCATCAAAAACTTGATCGC 57.911 40.909 9.16 9.16 39.47 4.58
3740 9180 3.419915 CTCATCAAAAACTTGATCGCCG 58.580 45.455 0.00 0.00 39.47 6.46
3747 9187 0.459237 AACTTGATCGCCGCTCTCTG 60.459 55.000 0.00 0.00 0.00 3.35
3748 9188 1.315981 ACTTGATCGCCGCTCTCTGA 61.316 55.000 0.00 0.00 0.00 3.27
3749 9189 0.594540 CTTGATCGCCGCTCTCTGAG 60.595 60.000 0.00 0.00 0.00 3.35
3750 9190 1.315981 TTGATCGCCGCTCTCTGAGT 61.316 55.000 4.32 0.00 31.39 3.41
3751 9191 0.463833 TGATCGCCGCTCTCTGAGTA 60.464 55.000 4.32 0.00 31.39 2.59
3752 9192 0.663688 GATCGCCGCTCTCTGAGTAA 59.336 55.000 4.32 0.00 31.39 2.24
3753 9193 1.065701 GATCGCCGCTCTCTGAGTAAA 59.934 52.381 4.32 0.00 31.39 2.01
3754 9194 1.103803 TCGCCGCTCTCTGAGTAAAT 58.896 50.000 4.32 0.00 31.39 1.40
3755 9195 2.294979 TCGCCGCTCTCTGAGTAAATA 58.705 47.619 4.32 0.00 31.39 1.40
3756 9196 2.290916 TCGCCGCTCTCTGAGTAAATAG 59.709 50.000 4.32 0.00 31.39 1.73
3757 9197 2.399448 GCCGCTCTCTGAGTAAATAGC 58.601 52.381 4.32 5.00 31.39 2.97
3758 9198 2.223829 GCCGCTCTCTGAGTAAATAGCA 60.224 50.000 13.57 0.00 31.39 3.49
3759 9199 3.553922 GCCGCTCTCTGAGTAAATAGCAT 60.554 47.826 13.57 0.00 31.39 3.79
3760 9200 4.321304 GCCGCTCTCTGAGTAAATAGCATA 60.321 45.833 13.57 0.00 31.39 3.14
3761 9201 5.773575 CCGCTCTCTGAGTAAATAGCATAA 58.226 41.667 13.57 0.00 31.39 1.90
3762 9202 6.216569 CCGCTCTCTGAGTAAATAGCATAAA 58.783 40.000 13.57 0.00 31.39 1.40
3763 9203 6.701841 CCGCTCTCTGAGTAAATAGCATAAAA 59.298 38.462 13.57 0.00 31.39 1.52
3764 9204 7.306866 CCGCTCTCTGAGTAAATAGCATAAAAC 60.307 40.741 13.57 0.00 31.39 2.43
3765 9205 7.436673 CGCTCTCTGAGTAAATAGCATAAAACT 59.563 37.037 13.57 0.00 31.39 2.66
3766 9206 9.751542 GCTCTCTGAGTAAATAGCATAAAACTA 57.248 33.333 4.32 0.00 31.39 2.24
3769 9209 9.817809 CTCTGAGTAAATAGCATAAAACTACCA 57.182 33.333 0.00 0.00 0.00 3.25
3770 9210 9.595823 TCTGAGTAAATAGCATAAAACTACCAC 57.404 33.333 0.00 0.00 0.00 4.16
3771 9211 9.601217 CTGAGTAAATAGCATAAAACTACCACT 57.399 33.333 0.00 0.00 0.00 4.00
3772 9212 9.953565 TGAGTAAATAGCATAAAACTACCACTT 57.046 29.630 0.00 0.00 0.00 3.16
3777 9217 7.916914 ATAGCATAAAACTACCACTTTTCGT 57.083 32.000 0.00 0.00 0.00 3.85
3778 9218 6.237313 AGCATAAAACTACCACTTTTCGTC 57.763 37.500 0.00 0.00 0.00 4.20
3779 9219 5.180680 AGCATAAAACTACCACTTTTCGTCC 59.819 40.000 0.00 0.00 0.00 4.79
3780 9220 5.180680 GCATAAAACTACCACTTTTCGTCCT 59.819 40.000 0.00 0.00 0.00 3.85
3781 9221 6.369615 GCATAAAACTACCACTTTTCGTCCTA 59.630 38.462 0.00 0.00 0.00 2.94
3782 9222 7.065443 GCATAAAACTACCACTTTTCGTCCTAT 59.935 37.037 0.00 0.00 0.00 2.57
3783 9223 8.943002 CATAAAACTACCACTTTTCGTCCTATT 58.057 33.333 0.00 0.00 0.00 1.73
3784 9224 6.796705 AAACTACCACTTTTCGTCCTATTG 57.203 37.500 0.00 0.00 0.00 1.90
3785 9225 5.479124 ACTACCACTTTTCGTCCTATTGT 57.521 39.130 0.00 0.00 0.00 2.71
3786 9226 5.861727 ACTACCACTTTTCGTCCTATTGTT 58.138 37.500 0.00 0.00 0.00 2.83
3787 9227 5.930569 ACTACCACTTTTCGTCCTATTGTTC 59.069 40.000 0.00 0.00 0.00 3.18
3788 9228 4.070009 ACCACTTTTCGTCCTATTGTTCC 58.930 43.478 0.00 0.00 0.00 3.62
3789 9229 4.069304 CCACTTTTCGTCCTATTGTTCCA 58.931 43.478 0.00 0.00 0.00 3.53
3790 9230 4.517453 CCACTTTTCGTCCTATTGTTCCAA 59.483 41.667 0.00 0.00 0.00 3.53
3791 9231 5.009210 CCACTTTTCGTCCTATTGTTCCAAA 59.991 40.000 0.00 0.00 0.00 3.28
3792 9232 6.460399 CCACTTTTCGTCCTATTGTTCCAAAA 60.460 38.462 0.00 0.00 0.00 2.44
3793 9233 6.975772 CACTTTTCGTCCTATTGTTCCAAAAA 59.024 34.615 0.00 0.00 0.00 1.94
3815 9255 8.608844 AAAAACTACCACATTTTTGTTTGTGA 57.391 26.923 4.70 0.00 44.74 3.58
3816 9256 7.589574 AAACTACCACATTTTTGTTTGTGAC 57.410 32.000 4.70 0.00 44.74 3.67
3817 9257 6.524101 ACTACCACATTTTTGTTTGTGACT 57.476 33.333 4.70 0.00 44.74 3.41
3818 9258 6.329496 ACTACCACATTTTTGTTTGTGACTG 58.671 36.000 4.70 0.00 44.74 3.51
3819 9259 5.398603 ACCACATTTTTGTTTGTGACTGA 57.601 34.783 4.70 0.00 44.74 3.41
3820 9260 5.976458 ACCACATTTTTGTTTGTGACTGAT 58.024 33.333 4.70 0.00 44.74 2.90
3821 9261 7.106439 ACCACATTTTTGTTTGTGACTGATA 57.894 32.000 4.70 0.00 44.74 2.15
3822 9262 7.551585 ACCACATTTTTGTTTGTGACTGATAA 58.448 30.769 4.70 0.00 44.74 1.75
3823 9263 7.491048 ACCACATTTTTGTTTGTGACTGATAAC 59.509 33.333 4.70 0.00 44.74 1.89
3824 9264 7.706179 CCACATTTTTGTTTGTGACTGATAACT 59.294 33.333 4.70 0.00 44.74 2.24
3825 9265 9.729023 CACATTTTTGTTTGTGACTGATAACTA 57.271 29.630 0.00 0.00 44.74 2.24
3826 9266 9.730420 ACATTTTTGTTTGTGACTGATAACTAC 57.270 29.630 0.00 0.00 0.00 2.73
3827 9267 9.180678 CATTTTTGTTTGTGACTGATAACTACC 57.819 33.333 0.00 0.00 0.00 3.18
3828 9268 7.867305 TTTTGTTTGTGACTGATAACTACCA 57.133 32.000 0.00 0.00 0.00 3.25
3829 9269 7.490962 TTTGTTTGTGACTGATAACTACCAG 57.509 36.000 0.00 0.00 36.53 4.00
3830 9270 6.413783 TGTTTGTGACTGATAACTACCAGA 57.586 37.500 0.00 0.00 34.65 3.86
3831 9271 6.822442 TGTTTGTGACTGATAACTACCAGAA 58.178 36.000 0.00 0.00 34.65 3.02
3832 9272 7.450074 TGTTTGTGACTGATAACTACCAGAAT 58.550 34.615 0.00 0.00 34.65 2.40
3833 9273 7.936847 TGTTTGTGACTGATAACTACCAGAATT 59.063 33.333 0.00 0.00 34.65 2.17
3834 9274 7.905604 TTGTGACTGATAACTACCAGAATTG 57.094 36.000 0.00 0.00 34.65 2.32
3848 9288 4.147219 CAGAATTGGAGTCGGTTGTTTC 57.853 45.455 0.00 0.00 0.00 2.78
3849 9289 3.563808 CAGAATTGGAGTCGGTTGTTTCA 59.436 43.478 0.00 0.00 0.00 2.69
3850 9290 4.036262 CAGAATTGGAGTCGGTTGTTTCAA 59.964 41.667 0.00 0.00 0.00 2.69
3851 9291 4.642885 AGAATTGGAGTCGGTTGTTTCAAA 59.357 37.500 0.00 0.00 0.00 2.69
3852 9292 4.993029 ATTGGAGTCGGTTGTTTCAAAA 57.007 36.364 0.00 0.00 0.00 2.44
3853 9293 4.785511 TTGGAGTCGGTTGTTTCAAAAA 57.214 36.364 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 2.032681 GCCGAGTTGCCAGGAGTT 59.967 61.111 0.00 0.00 0.00 3.01
77 78 2.223409 GCCTCGAACTTTTTCCACGTTT 60.223 45.455 0.00 0.00 0.00 3.60
122 123 0.320073 CGTAAAGGGTTCGCCTGACA 60.320 55.000 0.00 0.00 37.45 3.58
123 124 1.632948 GCGTAAAGGGTTCGCCTGAC 61.633 60.000 0.00 0.00 43.41 3.51
124 125 1.375013 GCGTAAAGGGTTCGCCTGA 60.375 57.895 0.00 0.00 43.41 3.86
125 126 3.174788 GCGTAAAGGGTTCGCCTG 58.825 61.111 0.00 0.00 43.41 4.85
140 141 3.818787 GCTGGAGCATGTTGGGCG 61.819 66.667 0.00 0.00 41.59 6.13
243 284 2.856760 TGAGATGGAGGGAGTAGCTT 57.143 50.000 0.00 0.00 0.00 3.74
244 285 2.856760 TTGAGATGGAGGGAGTAGCT 57.143 50.000 0.00 0.00 0.00 3.32
246 287 7.995488 ACATTTATTTTGAGATGGAGGGAGTAG 59.005 37.037 0.00 0.00 0.00 2.57
247 288 7.872138 ACATTTATTTTGAGATGGAGGGAGTA 58.128 34.615 0.00 0.00 0.00 2.59
309 1962 9.710979 CGTCTCAAAATAAGTGTTTCAAACTTA 57.289 29.630 1.10 0.00 42.63 2.24
310 1963 7.700656 CCGTCTCAAAATAAGTGTTTCAAACTT 59.299 33.333 1.10 0.00 40.82 2.66
312 1965 7.190871 TCCGTCTCAAAATAAGTGTTTCAAAC 58.809 34.615 0.00 0.00 0.00 2.93
314 1967 6.017440 CCTCCGTCTCAAAATAAGTGTTTCAA 60.017 38.462 0.00 0.00 0.00 2.69
316 1969 5.106673 CCCTCCGTCTCAAAATAAGTGTTTC 60.107 44.000 0.00 0.00 0.00 2.78
323 1976 5.021458 AGTACTCCCTCCGTCTCAAAATAA 58.979 41.667 0.00 0.00 0.00 1.40
324 1977 4.607239 AGTACTCCCTCCGTCTCAAAATA 58.393 43.478 0.00 0.00 0.00 1.40
327 1980 2.599408 AGTACTCCCTCCGTCTCAAA 57.401 50.000 0.00 0.00 0.00 2.69
329 1982 3.947612 ATTAGTACTCCCTCCGTCTCA 57.052 47.619 0.00 0.00 0.00 3.27
332 1985 6.348376 CGAGATTAATTAGTACTCCCTCCGTC 60.348 46.154 0.00 0.00 0.00 4.79
334 1987 5.619533 GCGAGATTAATTAGTACTCCCTCCG 60.620 48.000 0.00 0.00 0.00 4.63
336 1989 6.578163 AGCGAGATTAATTAGTACTCCCTC 57.422 41.667 0.00 0.00 0.00 4.30
338 1991 9.708092 ATTTTAGCGAGATTAATTAGTACTCCC 57.292 33.333 0.00 0.00 0.00 4.30
341 1994 8.989980 GGCATTTTAGCGAGATTAATTAGTACT 58.010 33.333 0.00 0.00 34.64 2.73
342 1995 8.228464 GGGCATTTTAGCGAGATTAATTAGTAC 58.772 37.037 0.00 0.00 34.64 2.73
343 1996 7.117236 CGGGCATTTTAGCGAGATTAATTAGTA 59.883 37.037 0.00 0.00 34.64 1.82
344 1997 6.073222 CGGGCATTTTAGCGAGATTAATTAGT 60.073 38.462 0.00 0.00 34.64 2.24
345 1998 6.073222 ACGGGCATTTTAGCGAGATTAATTAG 60.073 38.462 0.00 0.00 34.64 1.73
346 1999 5.761234 ACGGGCATTTTAGCGAGATTAATTA 59.239 36.000 0.00 0.00 34.64 1.40
347 2000 4.578928 ACGGGCATTTTAGCGAGATTAATT 59.421 37.500 0.00 0.00 34.64 1.40
348 2001 4.134563 ACGGGCATTTTAGCGAGATTAAT 58.865 39.130 0.00 0.00 34.64 1.40
349 2002 3.537580 ACGGGCATTTTAGCGAGATTAA 58.462 40.909 0.00 0.00 34.64 1.40
350 2003 3.188159 ACGGGCATTTTAGCGAGATTA 57.812 42.857 0.00 0.00 34.64 1.75
351 2004 2.038387 ACGGGCATTTTAGCGAGATT 57.962 45.000 0.00 0.00 34.64 2.40
352 2005 2.480845 GTACGGGCATTTTAGCGAGAT 58.519 47.619 0.00 0.00 34.64 2.75
354 2007 0.935196 GGTACGGGCATTTTAGCGAG 59.065 55.000 0.00 0.00 34.64 5.03
355 2008 3.068574 GGTACGGGCATTTTAGCGA 57.931 52.632 0.00 0.00 34.64 4.93
369 2022 2.097466 CCATTGCTGTGATTTCCGGTAC 59.903 50.000 0.00 0.00 0.00 3.34
371 2024 1.176527 CCATTGCTGTGATTTCCGGT 58.823 50.000 0.00 0.00 0.00 5.28
372 2025 1.462616 TCCATTGCTGTGATTTCCGG 58.537 50.000 0.00 0.00 0.00 5.14
373 2026 2.228582 TGTTCCATTGCTGTGATTTCCG 59.771 45.455 0.00 0.00 0.00 4.30
374 2027 3.940209 TGTTCCATTGCTGTGATTTCC 57.060 42.857 0.00 0.00 0.00 3.13
375 2028 3.989817 GGTTGTTCCATTGCTGTGATTTC 59.010 43.478 0.00 0.00 35.97 2.17
376 2029 3.244181 GGGTTGTTCCATTGCTGTGATTT 60.244 43.478 0.00 0.00 38.11 2.17
377 2030 2.299867 GGGTTGTTCCATTGCTGTGATT 59.700 45.455 0.00 0.00 38.11 2.57
378 2031 1.895131 GGGTTGTTCCATTGCTGTGAT 59.105 47.619 0.00 0.00 38.11 3.06
380 2033 0.318120 GGGGTTGTTCCATTGCTGTG 59.682 55.000 0.00 0.00 38.11 3.66
381 2034 0.831711 GGGGGTTGTTCCATTGCTGT 60.832 55.000 0.00 0.00 38.11 4.40
382 2035 0.542702 AGGGGGTTGTTCCATTGCTG 60.543 55.000 0.00 0.00 38.11 4.41
383 2036 0.251787 GAGGGGGTTGTTCCATTGCT 60.252 55.000 0.00 0.00 38.11 3.91
385 2038 2.008242 TTGAGGGGGTTGTTCCATTG 57.992 50.000 0.00 0.00 38.11 2.82
386 2039 2.785357 TTTGAGGGGGTTGTTCCATT 57.215 45.000 0.00 0.00 38.11 3.16
387 2040 2.785357 TTTTGAGGGGGTTGTTCCAT 57.215 45.000 0.00 0.00 38.11 3.41
388 2041 2.552093 TTTTTGAGGGGGTTGTTCCA 57.448 45.000 0.00 0.00 38.11 3.53
405 2310 4.881273 GGTTGTTCCATTGCTTTTCCTTTT 59.119 37.500 0.00 0.00 35.97 2.27
407 2312 3.454082 TGGTTGTTCCATTGCTTTTCCTT 59.546 39.130 0.00 0.00 41.93 3.36
470 2659 1.308069 GCCACAATCACACCGATGCT 61.308 55.000 0.00 0.00 33.40 3.79
487 2676 5.449107 TGTAGTACGAAGGAATAGATGCC 57.551 43.478 0.00 0.00 0.00 4.40
498 2687 5.276395 CGAAAGGATTGCATGTAGTACGAAG 60.276 44.000 0.00 0.00 0.00 3.79
510 2699 0.250684 TCCAGCACGAAAGGATTGCA 60.251 50.000 0.00 0.00 38.81 4.08
513 2702 2.154462 CTGTTCCAGCACGAAAGGATT 58.846 47.619 0.00 0.00 0.00 3.01
555 2744 2.051804 AAGCATATTCGGCAGCGTGC 62.052 55.000 1.92 1.92 44.08 5.34
556 2745 0.378257 AAAGCATATTCGGCAGCGTG 59.622 50.000 0.00 0.00 0.00 5.34
557 2746 0.378257 CAAAGCATATTCGGCAGCGT 59.622 50.000 0.00 0.00 0.00 5.07
558 2747 0.931662 GCAAAGCATATTCGGCAGCG 60.932 55.000 0.00 0.00 0.00 5.18
573 2767 0.179004 TTGAGAAAGAGGGCGGCAAA 60.179 50.000 12.47 0.00 0.00 3.68
581 2775 3.508845 TTTGGGGAGTTGAGAAAGAGG 57.491 47.619 0.00 0.00 0.00 3.69
610 2805 3.916405 GCAAAGCGCAAACTGTTTTTA 57.084 38.095 11.47 0.00 41.79 1.52
751 2947 4.100529 CGATAAACCTTCGCTCGTCTAAA 58.899 43.478 0.00 0.00 0.00 1.85
752 2948 3.127548 ACGATAAACCTTCGCTCGTCTAA 59.872 43.478 0.00 0.00 38.05 2.10
753 2949 2.679837 ACGATAAACCTTCGCTCGTCTA 59.320 45.455 0.00 0.00 38.05 2.59
761 2961 2.222819 GCTGCTGAACGATAAACCTTCG 60.223 50.000 0.00 0.00 42.20 3.79
787 2987 2.419739 GCGGGAGGGACAGAGTCTC 61.420 68.421 0.00 0.00 32.35 3.36
926 3152 3.775654 GGAGGAGGTGGTGGAGCG 61.776 72.222 0.00 0.00 0.00 5.03
965 3191 1.614824 AGAGCAGGAGGTTGGAGGG 60.615 63.158 0.00 0.00 0.00 4.30
1516 3780 1.335132 TGGAGGTTCTGCCCCGATAC 61.335 60.000 0.00 0.00 38.26 2.24
1526 3790 3.003763 GGGCGGACTGGAGGTTCT 61.004 66.667 0.00 0.00 0.00 3.01
1531 3795 2.266055 GTTCTGGGCGGACTGGAG 59.734 66.667 0.00 0.00 0.00 3.86
1541 3805 0.533032 GAGGAAGTCGAGGTTCTGGG 59.467 60.000 7.26 0.00 0.00 4.45
1547 3811 1.378778 CCGGAGAGGAAGTCGAGGT 60.379 63.158 0.00 0.00 45.00 3.85
1548 3812 2.776913 GCCGGAGAGGAAGTCGAGG 61.777 68.421 5.05 0.00 45.00 4.63
1605 3869 4.142790 TGGAGACAGAGAGACTTACGTTT 58.857 43.478 0.00 0.00 35.01 3.60
1739 4074 6.166279 TCCGATTGATGGCTTATGATAACTC 58.834 40.000 0.00 0.00 0.00 3.01
1820 4206 9.173021 CTCTCGATCATTATCTCCAACTATAGT 57.827 37.037 0.00 0.00 0.00 2.12
1821 4207 8.128582 GCTCTCGATCATTATCTCCAACTATAG 58.871 40.741 0.00 0.00 0.00 1.31
1893 4279 8.010733 ACCCATCAAATCGTATCATTGAAATT 57.989 30.769 0.00 0.00 36.72 1.82
1902 4288 3.059597 CGCTGAACCCATCAAATCGTATC 60.060 47.826 0.00 0.00 37.67 2.24
1926 4317 4.465660 CCCTATCACTATCAGTGGATCAGG 59.534 50.000 6.48 7.60 45.94 3.86
1962 4355 3.312828 GCATGAGCAGAACGAGGTATAG 58.687 50.000 0.00 0.00 41.58 1.31
1966 4359 1.446792 CGCATGAGCAGAACGAGGT 60.447 57.895 0.00 0.00 42.27 3.85
1969 4362 1.014044 GGAACGCATGAGCAGAACGA 61.014 55.000 0.00 0.00 42.27 3.85
1970 4363 1.016130 AGGAACGCATGAGCAGAACG 61.016 55.000 0.00 0.00 42.27 3.95
1971 4364 1.135859 CAAGGAACGCATGAGCAGAAC 60.136 52.381 0.00 0.00 42.27 3.01
1973 4366 0.321346 TCAAGGAACGCATGAGCAGA 59.679 50.000 0.00 0.00 42.27 4.26
1974 4367 0.445436 GTCAAGGAACGCATGAGCAG 59.555 55.000 0.00 0.00 42.27 4.24
2137 4541 0.974383 ACAGTTGTAGGCGGCTAACT 59.026 50.000 21.51 19.80 33.94 2.24
2192 4596 6.963805 GTGAATTACTCTTCTACTTGCAATGC 59.036 38.462 0.00 0.00 0.00 3.56
2517 4963 4.101790 CGATGTTGCGGTGGGTGC 62.102 66.667 0.00 0.00 0.00 5.01
2590 5036 3.244112 CCCGGTACTTGTTCTTCTTGTCT 60.244 47.826 0.00 0.00 0.00 3.41
2614 5060 1.557832 TGGTGGTAGGCATTCCAGTAC 59.442 52.381 0.00 0.00 34.16 2.73
2623 5069 2.203728 ACGGAGTGGTGGTAGGCA 60.204 61.111 0.00 0.00 42.51 4.75
2707 5153 2.182030 CTCGTCTTCCAGCCCGTC 59.818 66.667 0.00 0.00 0.00 4.79
2902 5354 1.126846 GGAGTTCATCGCTCAAACACG 59.873 52.381 0.00 0.00 34.83 4.49
2908 5360 2.768253 AACATGGAGTTCATCGCTCA 57.232 45.000 0.00 0.00 34.74 4.26
2909 5361 4.425577 AAAAACATGGAGTTCATCGCTC 57.574 40.909 0.00 0.00 40.26 5.03
2910 5362 5.882557 AGATAAAAACATGGAGTTCATCGCT 59.117 36.000 0.00 0.00 40.26 4.93
2911 5363 6.124088 AGATAAAAACATGGAGTTCATCGC 57.876 37.500 0.00 0.00 40.26 4.58
2912 5364 7.426456 CGAAAGATAAAAACATGGAGTTCATCG 59.574 37.037 0.00 0.00 40.26 3.84
2913 5365 8.237267 ACGAAAGATAAAAACATGGAGTTCATC 58.763 33.333 0.00 0.00 40.26 2.92
2914 5366 8.110860 ACGAAAGATAAAAACATGGAGTTCAT 57.889 30.769 0.00 0.00 40.26 2.57
2915 5367 7.504924 ACGAAAGATAAAAACATGGAGTTCA 57.495 32.000 0.00 0.00 40.26 3.18
2917 5369 9.840427 CAATACGAAAGATAAAAACATGGAGTT 57.160 29.630 0.00 0.00 43.89 3.01
2918 5370 7.968405 GCAATACGAAAGATAAAAACATGGAGT 59.032 33.333 0.00 0.00 0.00 3.85
2919 5371 8.184192 AGCAATACGAAAGATAAAAACATGGAG 58.816 33.333 0.00 0.00 0.00 3.86
2937 5400 7.644490 AGATCTACTACAGAAGAAGCAATACG 58.356 38.462 0.00 0.00 36.67 3.06
2938 5401 9.810545 AAAGATCTACTACAGAAGAAGCAATAC 57.189 33.333 0.00 0.00 36.67 1.89
2940 5403 8.757877 AGAAAGATCTACTACAGAAGAAGCAAT 58.242 33.333 0.00 0.00 36.67 3.56
2941 5404 8.128322 AGAAAGATCTACTACAGAAGAAGCAA 57.872 34.615 0.00 0.00 36.67 3.91
2942 5405 7.710676 AGAAAGATCTACTACAGAAGAAGCA 57.289 36.000 0.00 0.00 36.67 3.91
2943 5406 8.996024 AAAGAAAGATCTACTACAGAAGAAGC 57.004 34.615 0.00 0.00 36.67 3.86
2968 5474 6.037172 CACCAAAGAAGTCGAAGAAGAAGAAA 59.963 38.462 0.00 0.00 39.69 2.52
2995 5501 7.225538 AGCTCGAAGAAAGAATGTATACAATGG 59.774 37.037 10.14 0.00 34.09 3.16
3235 5758 2.607038 GGGTCCTCATTTTTGTTGCGTC 60.607 50.000 0.00 0.00 0.00 5.19
3272 6651 0.593128 CTGCCAAACGGAAGACAAGG 59.407 55.000 0.00 0.00 29.05 3.61
3276 6655 0.238553 GAAGCTGCCAAACGGAAGAC 59.761 55.000 0.00 0.00 29.05 3.01
3277 6656 0.179032 TGAAGCTGCCAAACGGAAGA 60.179 50.000 0.00 0.00 29.05 2.87
3278 6657 0.883833 ATGAAGCTGCCAAACGGAAG 59.116 50.000 0.00 0.00 31.28 3.46
3279 6658 2.192664 TATGAAGCTGCCAAACGGAA 57.807 45.000 0.00 0.00 0.00 4.30
3280 6659 1.810151 GTTATGAAGCTGCCAAACGGA 59.190 47.619 0.00 0.00 0.00 4.69
3288 6669 3.406764 CCCTATGAGGTTATGAAGCTGC 58.593 50.000 0.00 0.00 39.77 5.25
3326 6722 1.664321 GCGATCCCCACACTCTACGT 61.664 60.000 0.00 0.00 0.00 3.57
3327 6723 1.065928 GCGATCCCCACACTCTACG 59.934 63.158 0.00 0.00 0.00 3.51
3328 6724 1.065928 CGCGATCCCCACACTCTAC 59.934 63.158 0.00 0.00 0.00 2.59
3329 6725 0.681887 TTCGCGATCCCCACACTCTA 60.682 55.000 10.88 0.00 0.00 2.43
3364 6760 1.615502 GCCTCGAGTACGTTCTGAAC 58.384 55.000 12.31 10.48 40.69 3.18
3365 6761 0.524862 GGCCTCGAGTACGTTCTGAA 59.475 55.000 12.31 0.00 40.69 3.02
3368 6764 0.611340 AAGGGCCTCGAGTACGTTCT 60.611 55.000 6.46 0.00 40.69 3.01
3369 6765 1.065251 CTAAGGGCCTCGAGTACGTTC 59.935 57.143 6.46 0.00 40.69 3.95
3370 6766 1.101331 CTAAGGGCCTCGAGTACGTT 58.899 55.000 6.46 13.09 40.69 3.99
3371 6767 0.254178 TCTAAGGGCCTCGAGTACGT 59.746 55.000 6.46 2.30 40.69 3.57
3518 7330 7.297936 ACCCGATGTCATGACTAATTACATA 57.702 36.000 25.55 3.32 34.02 2.29
3614 7426 1.968493 TGCCATACGTTCTCCTATCCC 59.032 52.381 0.00 0.00 0.00 3.85
3708 9148 4.215827 AGTTTTTGATGAGCTCTCTTGCAG 59.784 41.667 16.19 0.00 34.99 4.41
3709 9149 4.139786 AGTTTTTGATGAGCTCTCTTGCA 58.860 39.130 16.19 3.04 34.99 4.08
3738 9178 3.717400 TGCTATTTACTCAGAGAGCGG 57.283 47.619 3.79 0.00 32.04 5.52
3740 9180 8.655651 AGTTTTATGCTATTTACTCAGAGAGC 57.344 34.615 3.79 2.60 32.04 4.09
3751 9191 8.789762 ACGAAAAGTGGTAGTTTTATGCTATTT 58.210 29.630 0.00 0.00 31.40 1.40
3752 9192 8.331730 ACGAAAAGTGGTAGTTTTATGCTATT 57.668 30.769 0.00 0.00 31.40 1.73
3753 9193 7.065443 GGACGAAAAGTGGTAGTTTTATGCTAT 59.935 37.037 0.00 0.00 31.40 2.97
3754 9194 6.369615 GGACGAAAAGTGGTAGTTTTATGCTA 59.630 38.462 0.00 0.00 31.40 3.49
3755 9195 5.180680 GGACGAAAAGTGGTAGTTTTATGCT 59.819 40.000 0.00 0.00 31.40 3.79
3756 9196 5.180680 AGGACGAAAAGTGGTAGTTTTATGC 59.819 40.000 0.00 0.00 31.40 3.14
3757 9197 6.796705 AGGACGAAAAGTGGTAGTTTTATG 57.203 37.500 0.00 0.00 31.40 1.90
3758 9198 8.943002 CAATAGGACGAAAAGTGGTAGTTTTAT 58.057 33.333 0.00 0.00 31.40 1.40
3759 9199 7.933033 ACAATAGGACGAAAAGTGGTAGTTTTA 59.067 33.333 0.00 0.00 31.40 1.52
3760 9200 6.769341 ACAATAGGACGAAAAGTGGTAGTTTT 59.231 34.615 0.00 0.00 33.74 2.43
3761 9201 6.293698 ACAATAGGACGAAAAGTGGTAGTTT 58.706 36.000 0.00 0.00 0.00 2.66
3762 9202 5.861727 ACAATAGGACGAAAAGTGGTAGTT 58.138 37.500 0.00 0.00 0.00 2.24
3763 9203 5.479124 ACAATAGGACGAAAAGTGGTAGT 57.521 39.130 0.00 0.00 0.00 2.73
3764 9204 5.350640 GGAACAATAGGACGAAAAGTGGTAG 59.649 44.000 0.00 0.00 0.00 3.18
3765 9205 5.221682 TGGAACAATAGGACGAAAAGTGGTA 60.222 40.000 0.00 0.00 31.92 3.25
3766 9206 4.070009 GGAACAATAGGACGAAAAGTGGT 58.930 43.478 0.00 0.00 0.00 4.16
3767 9207 4.069304 TGGAACAATAGGACGAAAAGTGG 58.931 43.478 0.00 0.00 31.92 4.00
3790 9230 8.499967 GTCACAAACAAAAATGTGGTAGTTTTT 58.500 29.630 6.11 0.00 45.41 1.94
3791 9231 7.875554 AGTCACAAACAAAAATGTGGTAGTTTT 59.124 29.630 6.11 0.00 45.41 2.43
3792 9232 7.330700 CAGTCACAAACAAAAATGTGGTAGTTT 59.669 33.333 6.11 0.00 45.41 2.66
3793 9233 6.811170 CAGTCACAAACAAAAATGTGGTAGTT 59.189 34.615 6.11 0.00 45.41 2.24
3794 9234 6.151985 TCAGTCACAAACAAAAATGTGGTAGT 59.848 34.615 6.11 0.00 45.41 2.73
3795 9235 6.559810 TCAGTCACAAACAAAAATGTGGTAG 58.440 36.000 6.11 0.00 45.41 3.18
3796 9236 6.516739 TCAGTCACAAACAAAAATGTGGTA 57.483 33.333 6.11 0.00 45.41 3.25
3797 9237 5.398603 TCAGTCACAAACAAAAATGTGGT 57.601 34.783 6.11 0.00 45.41 4.16
3798 9238 7.706179 AGTTATCAGTCACAAACAAAAATGTGG 59.294 33.333 6.11 0.00 45.41 4.17
3799 9239 8.633075 AGTTATCAGTCACAAACAAAAATGTG 57.367 30.769 0.00 0.00 46.44 3.21
3800 9240 9.730420 GTAGTTATCAGTCACAAACAAAAATGT 57.270 29.630 0.00 0.00 0.00 2.71
3801 9241 9.180678 GGTAGTTATCAGTCACAAACAAAAATG 57.819 33.333 0.00 0.00 0.00 2.32
3802 9242 8.908903 TGGTAGTTATCAGTCACAAACAAAAAT 58.091 29.630 0.00 0.00 0.00 1.82
3803 9243 8.282455 TGGTAGTTATCAGTCACAAACAAAAA 57.718 30.769 0.00 0.00 0.00 1.94
3804 9244 7.771361 TCTGGTAGTTATCAGTCACAAACAAAA 59.229 33.333 0.00 0.00 35.90 2.44
3805 9245 7.276658 TCTGGTAGTTATCAGTCACAAACAAA 58.723 34.615 0.00 0.00 35.90 2.83
3806 9246 6.822442 TCTGGTAGTTATCAGTCACAAACAA 58.178 36.000 0.00 0.00 35.90 2.83
3807 9247 6.413783 TCTGGTAGTTATCAGTCACAAACA 57.586 37.500 0.00 0.00 35.90 2.83
3808 9248 7.907214 ATTCTGGTAGTTATCAGTCACAAAC 57.093 36.000 0.00 0.00 35.90 2.93
3809 9249 7.390440 CCAATTCTGGTAGTTATCAGTCACAAA 59.610 37.037 0.00 0.00 38.00 2.83
3810 9250 6.878923 CCAATTCTGGTAGTTATCAGTCACAA 59.121 38.462 0.00 0.00 38.00 3.33
3811 9251 6.212589 TCCAATTCTGGTAGTTATCAGTCACA 59.787 38.462 0.00 0.00 43.97 3.58
3812 9252 6.640518 TCCAATTCTGGTAGTTATCAGTCAC 58.359 40.000 0.00 0.00 43.97 3.67
3813 9253 6.440647 ACTCCAATTCTGGTAGTTATCAGTCA 59.559 38.462 0.00 0.00 43.97 3.41
3814 9254 6.879400 ACTCCAATTCTGGTAGTTATCAGTC 58.121 40.000 0.00 0.00 43.97 3.51
3815 9255 6.405953 CGACTCCAATTCTGGTAGTTATCAGT 60.406 42.308 0.00 0.00 43.97 3.41
3816 9256 5.980116 CGACTCCAATTCTGGTAGTTATCAG 59.020 44.000 0.00 0.00 43.97 2.90
3817 9257 5.163447 CCGACTCCAATTCTGGTAGTTATCA 60.163 44.000 0.00 0.00 43.97 2.15
3818 9258 5.163437 ACCGACTCCAATTCTGGTAGTTATC 60.163 44.000 0.00 0.00 43.97 1.75
3819 9259 4.715297 ACCGACTCCAATTCTGGTAGTTAT 59.285 41.667 0.00 0.00 43.97 1.89
3820 9260 4.091549 ACCGACTCCAATTCTGGTAGTTA 58.908 43.478 0.00 0.00 43.97 2.24
3821 9261 2.904434 ACCGACTCCAATTCTGGTAGTT 59.096 45.455 0.00 0.00 43.97 2.24
3822 9262 2.537143 ACCGACTCCAATTCTGGTAGT 58.463 47.619 0.00 0.00 43.97 2.73
3823 9263 3.262420 CAACCGACTCCAATTCTGGTAG 58.738 50.000 0.00 0.00 43.97 3.18
3824 9264 2.635915 ACAACCGACTCCAATTCTGGTA 59.364 45.455 0.00 0.00 43.97 3.25
3825 9265 1.420138 ACAACCGACTCCAATTCTGGT 59.580 47.619 0.00 0.00 43.97 4.00
3826 9266 2.185004 ACAACCGACTCCAATTCTGG 57.815 50.000 0.00 0.00 45.08 3.86
3827 9267 3.563808 TGAAACAACCGACTCCAATTCTG 59.436 43.478 0.00 0.00 0.00 3.02
3828 9268 3.815809 TGAAACAACCGACTCCAATTCT 58.184 40.909 0.00 0.00 0.00 2.40
3829 9269 4.561735 TTGAAACAACCGACTCCAATTC 57.438 40.909 0.00 0.00 0.00 2.17
3830 9270 4.993029 TTTGAAACAACCGACTCCAATT 57.007 36.364 0.00 0.00 0.00 2.32
3831 9271 4.993029 TTTTGAAACAACCGACTCCAAT 57.007 36.364 0.00 0.00 0.00 3.16
3832 9272 4.785511 TTTTTGAAACAACCGACTCCAA 57.214 36.364 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.