Multiple sequence alignment - TraesCS7D01G449900

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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 TraesCS7D01G449900 chr7D 100.000 7060 0 0 1 7060 568955531 568948472 0.000000e+00 13038.0
1 TraesCS7D01G449900 chr7D 90.693 462 31 7 2214 2665 548771460 548771919 7.830000e-169 604.0
2 TraesCS7D01G449900 chr7B 93.610 2817 113 35 3807 6585 625298893 625296106 0.000000e+00 4143.0
3 TraesCS7D01G449900 chr7B 90.143 2313 110 43 2 2260 625302660 625300412 0.000000e+00 2900.0
4 TraesCS7D01G449900 chr7B 91.039 1473 86 26 2254 3702 625300386 625298936 0.000000e+00 1947.0
5 TraesCS7D01G449900 chr7B 94.196 224 11 2 2214 2437 592343187 592343408 2.440000e-89 340.0
6 TraesCS7D01G449900 chr7B 80.399 301 26 14 6634 6914 625296104 625295817 1.550000e-46 198.0
7 TraesCS7D01G449900 chr7A 91.773 3063 124 57 3744 6756 657718776 657715792 0.000000e+00 4143.0
8 TraesCS7D01G449900 chr7A 89.071 2324 128 52 7 2259 657722572 657720304 0.000000e+00 2769.0
9 TraesCS7D01G449900 chr7A 96.342 1449 47 4 2258 3703 657720222 657718777 0.000000e+00 2377.0
10 TraesCS7D01G449900 chr7A 92.411 224 11 2 2214 2437 632546248 632546465 1.480000e-81 315.0
11 TraesCS7D01G449900 chr7A 91.429 210 13 3 2463 2668 632546463 632546671 4.170000e-72 283.0
12 TraesCS7D01G449900 chr7A 80.068 296 33 15 6789 7060 657715795 657715502 5.590000e-46 196.0
13 TraesCS7D01G449900 chr4A 93.103 754 47 2 3807 4560 639045925 639046673 0.000000e+00 1099.0
14 TraesCS7D01G449900 chr4A 88.158 228 22 4 3476 3702 639045659 639045882 4.200000e-67 267.0
15 TraesCS7D01G449900 chr6D 75.800 719 134 32 1996 2690 91518042 91518744 1.900000e-85 327.0
16 TraesCS7D01G449900 chr6D 79.581 382 66 9 3042 3422 91519120 91519490 5.430000e-66 263.0
17 TraesCS7D01G449900 chr6B 75.419 716 140 30 1996 2690 175339004 175339704 1.480000e-81 315.0
18 TraesCS7D01G449900 chr6B 79.790 381 67 8 3042 3422 175340080 175340450 1.170000e-67 268.0
19 TraesCS7D01G449900 chr6B 97.143 35 1 0 274 308 175337544 175337578 7.650000e-05 60.2
20 TraesCS7D01G449900 chr6A 79.843 382 65 9 3042 3422 109985282 109985652 1.170000e-67 268.0
21 TraesCS7D01G449900 chr6A 85.938 64 6 3 245 308 109982715 109982775 1.640000e-06 65.8
22 TraesCS7D01G449900 chr5B 81.407 199 37 0 5563 5761 44781737 44781935 5.670000e-36 163.0
23 TraesCS7D01G449900 chr5A 81.407 199 37 0 5563 5761 35632169 35632367 5.670000e-36 163.0
24 TraesCS7D01G449900 chr5A 94.286 35 2 0 3708 3742 522609295 522609261 4.000000e-03 54.7
25 TraesCS7D01G449900 chr5D 80.905 199 38 0 5563 5761 44912591 44912789 2.640000e-34 158.0
26 TraesCS7D01G449900 chr2D 84.848 99 13 2 5663 5760 624367328 624367425 1.620000e-16 99.0
27 TraesCS7D01G449900 chr2B 84.848 99 13 2 5663 5760 766566852 766566949 1.620000e-16 99.0
28 TraesCS7D01G449900 chr2A 84.848 99 13 2 5663 5760 755774288 755774385 1.620000e-16 99.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G449900 chr7D 568948472 568955531 7059 True 13038.00 13038 100.000000 1 7060 1 chr7D.!!$R1 7059
1 TraesCS7D01G449900 chr7B 625295817 625302660 6843 True 2297.00 4143 88.797750 2 6914 4 chr7B.!!$R1 6912
2 TraesCS7D01G449900 chr7A 657715502 657722572 7070 True 2371.25 4143 89.313500 7 7060 4 chr7A.!!$R1 7053
3 TraesCS7D01G449900 chr4A 639045659 639046673 1014 False 683.00 1099 90.630500 3476 4560 2 chr4A.!!$F1 1084
4 TraesCS7D01G449900 chr6D 91518042 91519490 1448 False 295.00 327 77.690500 1996 3422 2 chr6D.!!$F1 1426
5 TraesCS7D01G449900 chr6B 175337544 175340450 2906 False 214.40 315 84.117333 274 3422 3 chr6B.!!$F1 3148


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
407 490 0.179018 AAGCAAAGCCAGTCCGAAGT 60.179 50.000 0.00 0.00 0.00 3.01 F
1326 1577 0.392461 TAGGGGTTGCTGCAATCGAC 60.392 55.000 19.11 13.85 0.00 4.20 F
1703 2027 1.311859 CTGACAAGCCTTCTGCACAA 58.688 50.000 0.00 0.00 44.83 3.33 F
2690 3237 1.542472 TCACATCTTTCGCGGTGAGTA 59.458 47.619 6.13 0.00 35.51 2.59 F
3715 4358 1.067212 CCATGTACTCCCTCTGTACGC 59.933 57.143 0.00 0.00 42.09 4.42 F
4464 5109 0.179034 CTATCCAAGGCCAGGCTCAC 60.179 60.000 12.43 0.00 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1857 2182 0.538287 AAGTTCCTTGCACTGGAGGC 60.538 55.000 7.57 5.85 34.76 4.70 R
3239 3876 3.006217 AGCATTCAGAAAGGAAAAGCACC 59.994 43.478 0.00 0.00 35.56 5.01 R
3700 4343 2.803030 AAGAGCGTACAGAGGGAGTA 57.197 50.000 0.00 0.00 0.00 2.59 R
3886 4531 0.258774 AAAGTGACACCCTTGGCTGT 59.741 50.000 0.84 0.00 0.00 4.40 R
4899 5544 0.253044 ATAGCTGTTCCATGTGCGGT 59.747 50.000 0.00 0.00 0.00 5.68 R
6063 6747 0.036010 CCTCGCCTCAGAACACCATT 60.036 55.000 0.00 0.00 0.00 3.16 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
42 43 3.498397 GGAAACGTTCACATCACTCACAT 59.502 43.478 0.00 0.00 0.00 3.21
48 49 3.531934 TCACATCACTCACATAGGCAG 57.468 47.619 0.00 0.00 0.00 4.85
56 57 4.489771 ACATAGGCAGGCGGGCAC 62.490 66.667 14.36 0.00 46.44 5.01
64 65 3.387091 AGGCGGGCACATCGTACA 61.387 61.111 3.78 0.00 0.00 2.90
84 85 1.336887 ACGTACATGCAGAGAACGCTT 60.337 47.619 11.96 0.00 37.07 4.68
85 86 2.094906 ACGTACATGCAGAGAACGCTTA 60.095 45.455 11.96 0.00 37.07 3.09
134 135 4.819761 GCATGAGCGGACGCCTCA 62.820 66.667 13.63 15.48 43.17 3.86
135 136 2.107750 CATGAGCGGACGCCTCAT 59.892 61.111 13.63 16.88 43.17 2.90
136 137 1.953138 CATGAGCGGACGCCTCATC 60.953 63.158 20.49 11.10 43.17 2.92
152 168 5.008019 CGCCTCATCACACTGCTATAAAAAT 59.992 40.000 0.00 0.00 0.00 1.82
153 169 6.202762 CGCCTCATCACACTGCTATAAAAATA 59.797 38.462 0.00 0.00 0.00 1.40
154 170 7.355778 GCCTCATCACACTGCTATAAAAATAC 58.644 38.462 0.00 0.00 0.00 1.89
155 171 7.012327 GCCTCATCACACTGCTATAAAAATACA 59.988 37.037 0.00 0.00 0.00 2.29
156 172 8.554528 CCTCATCACACTGCTATAAAAATACAG 58.445 37.037 0.00 0.00 0.00 2.74
256 299 6.431543 ACACGATTTTACAAGAGAGAGAGAGA 59.568 38.462 0.00 0.00 0.00 3.10
262 305 0.261696 AAGAGAGAGAGAGAGGGGCC 59.738 60.000 0.00 0.00 0.00 5.80
264 307 2.520741 GAGAGAGAGAGGGGCCGG 60.521 72.222 0.00 0.00 0.00 6.13
311 354 4.330944 GGTTAAAACCCCAAGAACAAGG 57.669 45.455 0.02 0.00 43.43 3.61
400 483 1.413812 CCCAAGAAAAGCAAAGCCAGT 59.586 47.619 0.00 0.00 0.00 4.00
405 488 1.336755 GAAAAGCAAAGCCAGTCCGAA 59.663 47.619 0.00 0.00 0.00 4.30
407 490 0.179018 AAGCAAAGCCAGTCCGAAGT 60.179 50.000 0.00 0.00 0.00 3.01
588 736 1.746220 CTCCTCGGATCGACTGTTTCT 59.254 52.381 0.00 0.00 0.00 2.52
599 747 3.302347 CTGTTTCTCGGCTCCGGCT 62.302 63.158 8.59 0.00 40.25 5.52
714 953 0.551624 TTTCCCGGGGAGGAAGGATT 60.552 55.000 23.50 0.00 46.44 3.01
747 986 4.021925 GCACGGCAGAAGGGGTCT 62.022 66.667 0.00 0.00 36.88 3.85
748 987 2.656069 GCACGGCAGAAGGGGTCTA 61.656 63.158 0.00 0.00 33.56 2.59
752 991 1.677637 CGGCAGAAGGGGTCTACTCC 61.678 65.000 0.00 0.00 33.56 3.85
753 992 1.338890 GGCAGAAGGGGTCTACTCCC 61.339 65.000 0.00 0.00 46.31 4.30
763 1002 0.398806 GTCTACTCCCCTCCCTTCCC 60.399 65.000 0.00 0.00 0.00 3.97
764 1003 1.457831 CTACTCCCCTCCCTTCCCG 60.458 68.421 0.00 0.00 0.00 5.14
778 1017 0.842905 TTCCCGTCCCTTCCATTCCA 60.843 55.000 0.00 0.00 0.00 3.53
904 1148 3.157949 CTCCGCTCTCCCCTTCCC 61.158 72.222 0.00 0.00 0.00 3.97
905 1149 3.684628 TCCGCTCTCCCCTTCCCT 61.685 66.667 0.00 0.00 0.00 4.20
906 1150 2.689034 CCGCTCTCCCCTTCCCTT 60.689 66.667 0.00 0.00 0.00 3.95
907 1151 2.736826 CCGCTCTCCCCTTCCCTTC 61.737 68.421 0.00 0.00 0.00 3.46
1179 1426 3.006967 AGTTTGTGGGACTAGCAGTACTG 59.993 47.826 18.93 18.93 0.00 2.74
1226 1477 0.811915 TTTCCTCGGAAGCTCTCTCG 59.188 55.000 0.00 0.00 35.38 4.04
1326 1577 0.392461 TAGGGGTTGCTGCAATCGAC 60.392 55.000 19.11 13.85 0.00 4.20
1394 1645 4.624024 TGCGAAATTTCAGTTCGGTACTAG 59.376 41.667 17.99 0.00 46.17 2.57
1396 1647 5.801947 GCGAAATTTCAGTTCGGTACTAGTA 59.198 40.000 17.99 0.00 46.17 1.82
1397 1648 6.308766 GCGAAATTTCAGTTCGGTACTAGTAA 59.691 38.462 17.99 0.00 46.17 2.24
1398 1649 7.148755 GCGAAATTTCAGTTCGGTACTAGTAAA 60.149 37.037 17.99 0.00 46.17 2.01
1399 1650 8.866956 CGAAATTTCAGTTCGGTACTAGTAAAT 58.133 33.333 17.99 0.00 43.19 1.40
1471 1723 7.917505 CCAATTTCCTGCTCTATGTGTTAATTC 59.082 37.037 0.00 0.00 0.00 2.17
1613 1926 4.201950 CGCCCACCTTCTTGAATAATCTTG 60.202 45.833 0.00 0.00 0.00 3.02
1643 1959 7.281774 CCAGCATATGAATTCAGAGTTGTTACT 59.718 37.037 14.54 0.00 37.31 2.24
1645 1961 7.826252 AGCATATGAATTCAGAGTTGTTACTGT 59.174 33.333 14.54 0.00 33.84 3.55
1647 1963 8.607459 CATATGAATTCAGAGTTGTTACTGTCC 58.393 37.037 14.54 0.00 33.84 4.02
1648 1964 5.305585 TGAATTCAGAGTTGTTACTGTCCC 58.694 41.667 3.38 0.00 33.84 4.46
1649 1965 5.071788 TGAATTCAGAGTTGTTACTGTCCCT 59.928 40.000 3.38 0.00 33.84 4.20
1683 2000 8.745837 GCCATCATTATCTGTTAAAAATCAACG 58.254 33.333 0.00 0.00 0.00 4.10
1700 2024 4.069869 GCTGACAAGCCTTCTGCA 57.930 55.556 0.00 0.00 44.22 4.41
1703 2027 1.311859 CTGACAAGCCTTCTGCACAA 58.688 50.000 0.00 0.00 44.83 3.33
1753 2078 1.879380 CACAAGTGCCTGAATTCGGAA 59.121 47.619 16.17 4.42 0.00 4.30
1856 2181 2.036346 GAGCAGGTTGGTGCAAAATTCT 59.964 45.455 0.00 0.00 46.60 2.40
1857 2182 2.137523 GCAGGTTGGTGCAAAATTCTG 58.862 47.619 0.00 0.58 43.41 3.02
1902 2227 4.007581 TGATCCTGAATCCTAACCTCCA 57.992 45.455 0.00 0.00 33.01 3.86
2149 2602 5.878406 ACCAGCTAAGTAATATCACTGCT 57.122 39.130 0.00 0.00 30.26 4.24
2178 2631 7.462109 TCTTTTCGTTTGATCATTGGTTTTG 57.538 32.000 0.00 0.00 0.00 2.44
2690 3237 1.542472 TCACATCTTTCGCGGTGAGTA 59.458 47.619 6.13 0.00 35.51 2.59
2813 3364 8.298140 TCTTAAGAGTTAAGAGAACGAAGAAGG 58.702 37.037 0.00 0.00 44.85 3.46
3006 3591 4.460263 TGTCTACTCCAGCACACAAATTT 58.540 39.130 0.00 0.00 0.00 1.82
3040 3677 8.093927 TCAAATTTGTGTATCCCCTTGAATTTC 58.906 33.333 17.47 0.00 0.00 2.17
3250 3887 3.971245 TGTTTGTTTGGTGCTTTTCCT 57.029 38.095 0.00 0.00 0.00 3.36
3645 4288 8.441572 TGTAAAGGTATATTTATGGGCTAGCAA 58.558 33.333 18.24 4.19 0.00 3.91
3648 4291 7.944729 AGGTATATTTATGGGCTAGCAATTG 57.055 36.000 18.24 0.00 0.00 2.32
3700 4343 2.264005 TCGCCTGTTGTTTACCATGT 57.736 45.000 0.00 0.00 0.00 3.21
3703 4346 3.071479 CGCCTGTTGTTTACCATGTACT 58.929 45.455 0.00 0.00 0.00 2.73
3704 4347 3.124636 CGCCTGTTGTTTACCATGTACTC 59.875 47.826 0.00 0.00 0.00 2.59
3705 4348 3.439129 GCCTGTTGTTTACCATGTACTCC 59.561 47.826 0.00 0.00 0.00 3.85
3706 4349 4.007659 CCTGTTGTTTACCATGTACTCCC 58.992 47.826 0.00 0.00 0.00 4.30
3707 4350 4.263331 CCTGTTGTTTACCATGTACTCCCT 60.263 45.833 0.00 0.00 0.00 4.20
3708 4351 4.901868 TGTTGTTTACCATGTACTCCCTC 58.098 43.478 0.00 0.00 0.00 4.30
3709 4352 4.595781 TGTTGTTTACCATGTACTCCCTCT 59.404 41.667 0.00 0.00 0.00 3.69
3710 4353 4.819105 TGTTTACCATGTACTCCCTCTG 57.181 45.455 0.00 0.00 0.00 3.35
3711 4354 4.164981 TGTTTACCATGTACTCCCTCTGT 58.835 43.478 0.00 0.00 0.00 3.41
3712 4355 5.335261 TGTTTACCATGTACTCCCTCTGTA 58.665 41.667 0.00 0.00 0.00 2.74
3713 4356 5.186409 TGTTTACCATGTACTCCCTCTGTAC 59.814 44.000 0.00 0.00 40.27 2.90
3714 4357 2.376109 ACCATGTACTCCCTCTGTACG 58.624 52.381 0.00 0.00 42.09 3.67
3715 4358 1.067212 CCATGTACTCCCTCTGTACGC 59.933 57.143 0.00 0.00 42.09 4.42
3716 4359 2.025155 CATGTACTCCCTCTGTACGCT 58.975 52.381 0.00 0.00 42.09 5.07
3717 4360 1.747709 TGTACTCCCTCTGTACGCTC 58.252 55.000 0.00 0.00 42.09 5.03
3718 4361 1.281287 TGTACTCCCTCTGTACGCTCT 59.719 52.381 0.00 0.00 42.09 4.09
3719 4362 2.290768 TGTACTCCCTCTGTACGCTCTT 60.291 50.000 0.00 0.00 42.09 2.85
3720 4363 2.803030 ACTCCCTCTGTACGCTCTTA 57.197 50.000 0.00 0.00 0.00 2.10
3721 4364 3.300239 ACTCCCTCTGTACGCTCTTAT 57.700 47.619 0.00 0.00 0.00 1.73
3722 4365 4.434545 ACTCCCTCTGTACGCTCTTATA 57.565 45.455 0.00 0.00 0.00 0.98
3723 4366 4.391155 ACTCCCTCTGTACGCTCTTATAG 58.609 47.826 0.00 0.00 0.00 1.31
3724 4367 4.141436 ACTCCCTCTGTACGCTCTTATAGT 60.141 45.833 0.00 0.00 0.00 2.12
3725 4368 4.789807 TCCCTCTGTACGCTCTTATAGTT 58.210 43.478 0.00 0.00 0.00 2.24
3726 4369 4.820716 TCCCTCTGTACGCTCTTATAGTTC 59.179 45.833 0.00 0.00 0.00 3.01
3727 4370 4.822896 CCCTCTGTACGCTCTTATAGTTCT 59.177 45.833 0.00 0.00 0.00 3.01
3728 4371 5.299782 CCCTCTGTACGCTCTTATAGTTCTT 59.700 44.000 0.00 0.00 0.00 2.52
3729 4372 6.183360 CCCTCTGTACGCTCTTATAGTTCTTT 60.183 42.308 0.00 0.00 0.00 2.52
3730 4373 7.013083 CCCTCTGTACGCTCTTATAGTTCTTTA 59.987 40.741 0.00 0.00 0.00 1.85
3731 4374 7.856894 CCTCTGTACGCTCTTATAGTTCTTTAC 59.143 40.741 0.00 0.00 0.00 2.01
3732 4375 7.404985 TCTGTACGCTCTTATAGTTCTTTACG 58.595 38.462 0.00 0.00 0.00 3.18
3733 4376 6.489675 TGTACGCTCTTATAGTTCTTTACGG 58.510 40.000 0.00 0.00 0.00 4.02
3734 4377 5.824904 ACGCTCTTATAGTTCTTTACGGA 57.175 39.130 0.00 0.00 0.00 4.69
3735 4378 5.819059 ACGCTCTTATAGTTCTTTACGGAG 58.181 41.667 0.00 0.00 0.00 4.63
3736 4379 5.213675 CGCTCTTATAGTTCTTTACGGAGG 58.786 45.833 0.00 0.00 0.00 4.30
3737 4380 5.530712 GCTCTTATAGTTCTTTACGGAGGG 58.469 45.833 0.00 0.00 0.00 4.30
3738 4381 5.301298 GCTCTTATAGTTCTTTACGGAGGGA 59.699 44.000 0.00 0.00 0.00 4.20
3739 4382 6.515365 GCTCTTATAGTTCTTTACGGAGGGAG 60.515 46.154 0.00 0.00 0.00 4.30
3740 4383 6.430007 TCTTATAGTTCTTTACGGAGGGAGT 58.570 40.000 0.00 0.00 0.00 3.85
3741 4384 7.577303 TCTTATAGTTCTTTACGGAGGGAGTA 58.423 38.462 0.00 0.00 0.00 2.59
3742 4385 8.223330 TCTTATAGTTCTTTACGGAGGGAGTAT 58.777 37.037 0.00 0.00 0.00 2.12
3771 4416 7.487829 TGCAAAGTTTTTGTTAGACAAGATGAC 59.512 33.333 3.77 0.00 39.53 3.06
3793 4438 7.382110 TGACTTCCTATAGATATTGCTTGCTC 58.618 38.462 0.00 0.00 0.00 4.26
3800 4445 8.934825 CCTATAGATATTGCTTGCTCTTTCTTC 58.065 37.037 0.00 0.00 0.00 2.87
3886 4531 3.168292 TGAATCAACTGCTGGAGAGAGA 58.832 45.455 2.24 0.00 0.00 3.10
4090 4735 8.979574 GTATGCTTTCAGTATGGAGTGTTATAC 58.020 37.037 0.00 0.00 36.16 1.47
4122 4767 4.771054 TCTCTTTCTGTAGGTGGTAAGGAC 59.229 45.833 0.00 0.00 0.00 3.85
4173 4818 1.440145 GAGATAGCGCAAACCCTGGC 61.440 60.000 11.47 0.00 0.00 4.85
4242 4887 2.034879 AAGGCTGGATGCGTCGTTG 61.035 57.895 0.00 0.00 44.05 4.10
4311 4956 2.224867 CCAGGACCCAACAAAGATGTCT 60.225 50.000 0.00 0.00 39.40 3.41
4377 5022 2.568935 CTACGCCGCTTCTGCAAAGC 62.569 60.000 18.09 18.09 39.64 3.51
4446 5091 2.964464 TCAAAACATGAATGGCACCACT 59.036 40.909 0.00 0.00 34.30 4.00
4464 5109 0.179034 CTATCCAAGGCCAGGCTCAC 60.179 60.000 12.43 0.00 0.00 3.51
4494 5139 0.463654 TTCAACAGCAGCTCCAACGT 60.464 50.000 0.00 0.00 0.00 3.99
4624 5269 4.884164 AGAAGAATATGGCAAACTACCAGC 59.116 41.667 0.00 0.00 41.46 4.85
4659 5304 1.079256 CTCCCCAGGTCCTCAGTCA 59.921 63.158 0.00 0.00 0.00 3.41
4662 5307 0.326048 CCCCAGGTCCTCAGTCATCT 60.326 60.000 0.00 0.00 0.00 2.90
4666 5311 1.755959 CAGGTCCTCAGTCATCTCCTG 59.244 57.143 0.00 0.00 35.72 3.86
4699 5344 2.556287 CCTCACCGTTTTCGCAGC 59.444 61.111 0.00 0.00 42.58 5.25
4767 5412 1.480312 GCCCCCACCATGCATAATACA 60.480 52.381 0.00 0.00 0.00 2.29
4803 5448 4.040339 TCATCAGAAACAGCTTCACACCTA 59.960 41.667 0.00 0.00 36.40 3.08
4896 5541 0.251832 TTCCTTCTCGGCCTCAGTCT 60.252 55.000 0.00 0.00 0.00 3.24
4899 5544 1.464734 CTTCTCGGCCTCAGTCTACA 58.535 55.000 0.00 0.00 0.00 2.74
4900 5545 1.133407 CTTCTCGGCCTCAGTCTACAC 59.867 57.143 0.00 0.00 0.00 2.90
4932 5577 1.278985 CAGCTATCCTCAACACCACCA 59.721 52.381 0.00 0.00 0.00 4.17
5013 5658 2.045524 GATGGGAGCTCTGATCCTCAA 58.954 52.381 14.64 0.00 37.01 3.02
5016 5661 2.026822 TGGGAGCTCTGATCCTCAAAAC 60.027 50.000 14.64 0.00 37.01 2.43
5166 5811 5.407407 TCTCCTTGGATCAGACACTAAAC 57.593 43.478 0.00 0.00 0.00 2.01
5269 5914 2.221981 GTGAAGGTGAGTTGCTTTCTCG 59.778 50.000 0.00 0.00 34.99 4.04
5273 5918 3.851098 AGGTGAGTTGCTTTCTCGATAC 58.149 45.455 0.00 0.00 34.99 2.24
5278 5923 3.243336 AGTTGCTTTCTCGATACGACAC 58.757 45.455 0.00 0.00 0.00 3.67
5279 5924 2.984471 GTTGCTTTCTCGATACGACACA 59.016 45.455 0.00 0.00 0.00 3.72
5299 5944 5.473504 ACACACAATCATGTTACTTCTTCCC 59.526 40.000 0.00 0.00 37.82 3.97
5322 5967 6.238484 CCCTGAAACTATCTTGCTTATTTCCG 60.238 42.308 0.00 0.00 0.00 4.30
5372 6040 0.949105 AGCTACTGTCCGTTTTGCCG 60.949 55.000 0.00 0.00 0.00 5.69
5378 6046 1.535462 CTGTCCGTTTTGCCGATTTCT 59.465 47.619 0.00 0.00 0.00 2.52
5423 6099 6.508777 TGCCTTAAAATTGGTAGAAACACAC 58.491 36.000 0.00 0.00 0.00 3.82
5427 6103 5.529581 AAAATTGGTAGAAACACACCTGG 57.470 39.130 0.00 0.00 35.73 4.45
5500 6177 9.896645 AGATGCAAGAAAAAGAATACTCTGATA 57.103 29.630 0.00 0.00 30.03 2.15
5537 6215 4.219507 TCCATTACCGCATTTGATGTGTTT 59.780 37.500 1.39 0.00 39.07 2.83
5638 6318 3.950395 ACTACCATGAACTACGTAGGGAC 59.050 47.826 25.63 15.97 33.91 4.46
5790 6470 0.249073 CCCCGACGATGATCTGTGTC 60.249 60.000 0.00 0.00 0.00 3.67
5801 6481 6.019762 CGATGATCTGTGTCACTTCATTTTG 58.980 40.000 13.97 7.33 0.00 2.44
5829 6509 1.705256 TCTTTAACAGTAGTGCCGCG 58.295 50.000 0.00 0.00 0.00 6.46
5849 6530 0.035630 CCTTCCAACTCTGCAGGGAG 60.036 60.000 23.49 11.34 39.09 4.30
5927 6608 4.044439 AAGCAGGGCCTGGAGCTG 62.044 66.667 33.43 9.87 43.05 4.24
6065 6749 5.122512 TCGAAGTCGAGTTCTGAAGAAAT 57.877 39.130 26.13 0.00 44.22 2.17
6068 6752 4.608948 AGTCGAGTTCTGAAGAAATGGT 57.391 40.909 0.00 0.00 35.58 3.55
6074 6758 5.333645 CGAGTTCTGAAGAAATGGTGTTCTG 60.334 44.000 0.00 0.00 37.90 3.02
6075 6759 5.684704 AGTTCTGAAGAAATGGTGTTCTGA 58.315 37.500 0.00 0.00 37.90 3.27
6076 6760 5.762218 AGTTCTGAAGAAATGGTGTTCTGAG 59.238 40.000 0.00 0.00 38.27 3.35
6162 6846 3.354467 TCTCTCCTAGTTTTCGAGACCC 58.646 50.000 0.00 0.00 0.00 4.46
6338 7030 6.378564 TCTCTTCTGTGGAATACTCCTACTTG 59.621 42.308 0.00 0.00 42.94 3.16
6376 7068 4.953940 AGGCTCTCTAGTCATCAATTCC 57.046 45.455 0.00 0.00 0.00 3.01
6391 7083 0.591170 ATTCCCTTGTCGTTGTTGCG 59.409 50.000 0.00 0.00 0.00 4.85
6392 7084 0.462225 TTCCCTTGTCGTTGTTGCGA 60.462 50.000 0.00 0.00 38.68 5.10
6399 7112 0.725784 GTCGTTGTTGCGATTGCCTG 60.726 55.000 1.50 0.00 43.07 4.85
6410 7123 2.730090 GCGATTGCCTGTCTTGTTCATG 60.730 50.000 0.00 0.00 33.98 3.07
6458 7171 2.112190 TCCACATGCATCAATGGCAAT 58.888 42.857 13.99 0.00 45.60 3.56
6467 7180 3.243301 GCATCAATGGCAATACACCAGAG 60.243 47.826 0.00 0.00 41.46 3.35
6505 7223 3.552875 CATTGATCTTCATGGCCTCACT 58.447 45.455 3.32 0.00 0.00 3.41
6506 7224 3.726557 TTGATCTTCATGGCCTCACTT 57.273 42.857 3.32 0.00 0.00 3.16
6507 7225 3.272574 TGATCTTCATGGCCTCACTTC 57.727 47.619 3.32 0.00 0.00 3.01
6508 7226 2.092753 TGATCTTCATGGCCTCACTTCC 60.093 50.000 3.32 0.00 0.00 3.46
6509 7227 1.361204 TCTTCATGGCCTCACTTCCA 58.639 50.000 3.32 0.00 36.70 3.53
6510 7228 1.280133 TCTTCATGGCCTCACTTCCAG 59.720 52.381 3.32 0.00 35.57 3.86
6585 7303 2.439409 CAATCAGAAGTGGCATGTCCA 58.561 47.619 4.93 4.93 44.18 4.02
6613 7331 5.909621 TTACCTGTAGATGTAGAAACGCT 57.090 39.130 0.00 0.00 0.00 5.07
6618 7336 5.386958 TGTAGATGTAGAAACGCTCTGTT 57.613 39.130 0.00 0.00 44.59 3.16
6629 7347 1.072159 GCTCTGTTGTGCAGGACCT 59.928 57.895 0.00 0.00 45.08 3.85
6631 7349 1.233019 CTCTGTTGTGCAGGACCTTG 58.767 55.000 0.00 0.00 45.08 3.61
6632 7350 0.179020 TCTGTTGTGCAGGACCTTGG 60.179 55.000 0.00 0.00 45.08 3.61
6705 7428 4.577096 TGGGGGAAGAGGAATGTATGTAT 58.423 43.478 0.00 0.00 0.00 2.29
6706 7429 4.350816 TGGGGGAAGAGGAATGTATGTATG 59.649 45.833 0.00 0.00 0.00 2.39
6707 7430 4.351111 GGGGGAAGAGGAATGTATGTATGT 59.649 45.833 0.00 0.00 0.00 2.29
6708 7431 5.546499 GGGGGAAGAGGAATGTATGTATGTA 59.454 44.000 0.00 0.00 0.00 2.29
6760 7489 2.278466 TTTGGCTTTGCACGCGTG 60.278 55.556 34.01 34.01 0.00 5.34
6821 7550 0.691078 GAGGGCTACAGGTCCCATCA 60.691 60.000 0.00 0.00 45.07 3.07
6825 7554 1.490574 GCTACAGGTCCCATCAGACT 58.509 55.000 0.00 0.00 36.95 3.24
6846 7582 0.706433 ACTCATCCCCTTGTGCCAAT 59.294 50.000 0.00 0.00 0.00 3.16
6847 7583 1.077663 ACTCATCCCCTTGTGCCAATT 59.922 47.619 0.00 0.00 0.00 2.32
6848 7584 1.479323 CTCATCCCCTTGTGCCAATTG 59.521 52.381 0.00 0.00 0.00 2.32
6850 7586 1.606885 ATCCCCTTGTGCCAATTGCG 61.607 55.000 0.00 0.00 45.60 4.85
6854 7590 1.559149 CCTTGTGCCAATTGCGTTGC 61.559 55.000 0.00 0.00 45.60 4.17
6855 7591 0.875040 CTTGTGCCAATTGCGTTGCA 60.875 50.000 0.00 1.11 45.60 4.08
6918 7657 2.625695 TGGATGATGTGATGCGATGT 57.374 45.000 0.00 0.00 0.00 3.06
6919 7658 2.215196 TGGATGATGTGATGCGATGTG 58.785 47.619 0.00 0.00 0.00 3.21
6920 7659 2.158928 TGGATGATGTGATGCGATGTGA 60.159 45.455 0.00 0.00 0.00 3.58
6921 7660 3.072211 GGATGATGTGATGCGATGTGAT 58.928 45.455 0.00 0.00 0.00 3.06
6922 7661 3.120304 GGATGATGTGATGCGATGTGATG 60.120 47.826 0.00 0.00 0.00 3.07
6923 7662 2.908916 TGATGTGATGCGATGTGATGT 58.091 42.857 0.00 0.00 0.00 3.06
6924 7663 2.610374 TGATGTGATGCGATGTGATGTG 59.390 45.455 0.00 0.00 0.00 3.21
6925 7664 2.383368 TGTGATGCGATGTGATGTGA 57.617 45.000 0.00 0.00 0.00 3.58
6927 7666 2.610374 TGTGATGCGATGTGATGTGATG 59.390 45.455 0.00 0.00 0.00 3.07
6929 7668 0.949397 ATGCGATGTGATGTGATGCC 59.051 50.000 0.00 0.00 0.00 4.40
6930 7669 1.096967 TGCGATGTGATGTGATGCCC 61.097 55.000 0.00 0.00 0.00 5.36
6942 7683 0.402419 TGATGCCCCTCCATCCATCT 60.402 55.000 0.00 0.00 40.66 2.90
6943 7684 0.037877 GATGCCCCTCCATCCATCTG 59.962 60.000 0.00 0.00 36.46 2.90
6956 7697 0.531532 CCATCTGTCCATCACGCTCC 60.532 60.000 0.00 0.00 0.00 4.70
6959 7700 0.977627 TCTGTCCATCACGCTCCCAT 60.978 55.000 0.00 0.00 0.00 4.00
6970 7711 0.940126 CGCTCCCATCCATTTCTTCG 59.060 55.000 0.00 0.00 0.00 3.79
6971 7712 1.743772 CGCTCCCATCCATTTCTTCGT 60.744 52.381 0.00 0.00 0.00 3.85
6973 7714 2.292267 CTCCCATCCATTTCTTCGTGG 58.708 52.381 0.00 0.00 36.82 4.94
6974 7715 1.633432 TCCCATCCATTTCTTCGTGGT 59.367 47.619 0.00 0.00 36.84 4.16
6975 7716 1.745087 CCCATCCATTTCTTCGTGGTG 59.255 52.381 0.00 0.00 36.84 4.17
6976 7717 1.133025 CCATCCATTTCTTCGTGGTGC 59.867 52.381 0.00 0.00 36.84 5.01
6977 7718 2.086869 CATCCATTTCTTCGTGGTGCT 58.913 47.619 0.00 0.00 36.84 4.40
6978 7719 1.808411 TCCATTTCTTCGTGGTGCTC 58.192 50.000 0.00 0.00 36.84 4.26
6979 7720 0.804989 CCATTTCTTCGTGGTGCTCC 59.195 55.000 0.00 0.00 0.00 4.70
6980 7721 0.804989 CATTTCTTCGTGGTGCTCCC 59.195 55.000 1.59 0.00 0.00 4.30
6981 7722 0.673644 ATTTCTTCGTGGTGCTCCCG 60.674 55.000 1.59 5.90 35.15 5.14
6986 7744 3.770040 CGTGGTGCTCCCGATCCA 61.770 66.667 1.59 0.00 35.15 3.41
6987 7745 2.911143 GTGGTGCTCCCGATCCAT 59.089 61.111 1.59 0.00 35.15 3.41
6998 7756 1.362224 CCGATCCATTCCCCAGGTAT 58.638 55.000 0.00 0.00 0.00 2.73
7006 7764 1.324740 TTCCCCAGGTATCCGTCACG 61.325 60.000 0.00 0.00 0.00 4.35
7012 7770 1.660575 GGTATCCGTCACGCCATCG 60.661 63.158 0.00 0.00 42.43 3.84
7016 7774 4.129737 CCGTCACGCCATCGGTCT 62.130 66.667 0.00 0.00 40.69 3.85
7020 7778 0.669077 GTCACGCCATCGGTCTATCT 59.331 55.000 0.00 0.00 40.69 1.98
7028 7786 3.957497 GCCATCGGTCTATCTATCCATCT 59.043 47.826 0.00 0.00 0.00 2.90
7032 7790 6.148645 CCATCGGTCTATCTATCCATCTATCG 59.851 46.154 0.00 0.00 0.00 2.92
7050 7808 3.790437 CCCACCTGGCTCGATGCT 61.790 66.667 0.00 0.00 42.39 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.359602 CCCAGTGGAGTGCTGCTG 60.360 66.667 11.95 1.12 32.93 4.41
15 16 1.271163 TGATGTGAACGTTTCCTCCCC 60.271 52.381 0.46 0.00 0.00 4.81
42 43 4.175337 GATGTGCCCGCCTGCCTA 62.175 66.667 0.00 0.00 0.00 3.93
48 49 3.192922 GTGTACGATGTGCCCGCC 61.193 66.667 0.00 0.00 0.00 6.13
56 57 2.783832 CTCTGCATGTACGTGTACGATG 59.216 50.000 16.28 5.89 43.02 3.84
64 65 0.243907 AGCGTTCTCTGCATGTACGT 59.756 50.000 15.94 0.00 34.89 3.57
84 85 0.396060 TGTGGCATGTGCAGTGAGTA 59.604 50.000 7.36 0.00 44.36 2.59
85 86 1.148949 TGTGGCATGTGCAGTGAGT 59.851 52.632 7.36 0.00 44.36 3.41
125 126 2.103042 GCAGTGTGATGAGGCGTCC 61.103 63.158 3.56 0.00 0.00 4.79
126 127 0.173481 TAGCAGTGTGATGAGGCGTC 59.827 55.000 0.00 0.00 0.00 5.19
130 131 8.437360 TGTATTTTTATAGCAGTGTGATGAGG 57.563 34.615 0.00 0.00 0.00 3.86
131 132 9.102757 ACTGTATTTTTATAGCAGTGTGATGAG 57.897 33.333 0.00 0.00 38.74 2.90
134 135 9.326413 GGTACTGTATTTTTATAGCAGTGTGAT 57.674 33.333 0.00 0.00 40.18 3.06
135 136 8.537016 AGGTACTGTATTTTTATAGCAGTGTGA 58.463 33.333 0.00 0.00 40.18 3.58
136 137 8.718102 AGGTACTGTATTTTTATAGCAGTGTG 57.282 34.615 0.00 0.00 40.18 3.82
244 287 1.930520 GGCCCCTCTCTCTCTCTCT 59.069 63.158 0.00 0.00 0.00 3.10
262 305 4.467084 TGCTAGCCGCTTTCCCCG 62.467 66.667 13.29 0.00 40.11 5.73
264 307 2.824489 GGTGCTAGCCGCTTTCCC 60.824 66.667 13.29 0.00 40.11 3.97
326 369 2.669849 CTTGCTCTGGCTCTGGCT 59.330 61.111 0.00 0.00 39.59 4.75
400 483 1.202710 TGGTTGCTTGCTTACTTCGGA 60.203 47.619 0.00 0.00 0.00 4.55
745 984 1.946063 CGGGAAGGGAGGGGAGTAGA 61.946 65.000 0.00 0.00 0.00 2.59
746 985 1.457831 CGGGAAGGGAGGGGAGTAG 60.458 68.421 0.00 0.00 0.00 2.57
747 986 2.234246 GACGGGAAGGGAGGGGAGTA 62.234 65.000 0.00 0.00 0.00 2.59
748 987 3.612607 ACGGGAAGGGAGGGGAGT 61.613 66.667 0.00 0.00 0.00 3.85
752 991 3.945064 AAGGGACGGGAAGGGAGGG 62.945 68.421 0.00 0.00 0.00 4.30
753 992 2.285442 AAGGGACGGGAAGGGAGG 60.285 66.667 0.00 0.00 0.00 4.30
763 1002 1.064758 TGGAATGGAATGGAAGGGACG 60.065 52.381 0.00 0.00 0.00 4.79
764 1003 2.826674 TGGAATGGAATGGAAGGGAC 57.173 50.000 0.00 0.00 0.00 4.46
768 1007 3.640029 CAGGGAATGGAATGGAATGGAAG 59.360 47.826 0.00 0.00 0.00 3.46
904 1148 3.798511 GGAGGCGGGGGAAGGAAG 61.799 72.222 0.00 0.00 0.00 3.46
1179 1426 0.663153 AGCACAAACGAGAACAAGGC 59.337 50.000 0.00 0.00 0.00 4.35
1181 1428 3.100817 CACAAGCACAAACGAGAACAAG 58.899 45.455 0.00 0.00 0.00 3.16
1183 1433 2.351455 TCACAAGCACAAACGAGAACA 58.649 42.857 0.00 0.00 0.00 3.18
1185 1435 4.630894 AAATCACAAGCACAAACGAGAA 57.369 36.364 0.00 0.00 0.00 2.87
1217 1468 1.686355 ATCAATCCGTCGAGAGAGCT 58.314 50.000 0.00 0.00 43.49 4.09
1326 1577 6.441274 ACACACAAGAAGCATTTTCATGTAG 58.559 36.000 0.00 0.00 30.40 2.74
1405 1657 8.641498 AGATTACACAACTGAAATTCCATTCT 57.359 30.769 0.00 0.00 0.00 2.40
1425 1677 3.907474 TGGATGGGAAATAGGCGAGATTA 59.093 43.478 0.00 0.00 0.00 1.75
1613 1926 5.609423 ACTCTGAATTCATATGCTGGTCTC 58.391 41.667 8.96 0.00 0.00 3.36
1643 1959 3.533238 TGGCTCTAGGGAGGGACA 58.467 61.111 0.00 0.00 39.74 4.02
1645 1961 0.870313 ATGATGGCTCTAGGGAGGGA 59.130 55.000 0.00 0.00 39.80 4.20
1647 1963 4.161942 CAGATAATGATGGCTCTAGGGAGG 59.838 50.000 0.00 0.00 39.80 4.30
1648 1964 4.776837 ACAGATAATGATGGCTCTAGGGAG 59.223 45.833 0.00 0.00 42.18 4.30
1649 1965 4.756564 ACAGATAATGATGGCTCTAGGGA 58.243 43.478 0.00 0.00 0.00 4.20
1683 2000 1.168407 TGTGCAGAAGGCTTGTCAGC 61.168 55.000 3.46 1.56 46.52 4.26
1700 2024 5.640357 CAGCTGTAATGGCAAAATCATTTGT 59.360 36.000 5.25 0.00 46.19 2.83
1703 2027 4.081309 AGCAGCTGTAATGGCAAAATCATT 60.081 37.500 16.64 0.00 38.29 2.57
1856 2181 1.228245 GTTCCTTGCACTGGAGGCA 60.228 57.895 7.57 0.00 40.00 4.75
1857 2182 0.538287 AAGTTCCTTGCACTGGAGGC 60.538 55.000 7.57 5.85 34.76 4.70
1942 2269 5.108385 ACATAGACAAAGAAAGCAAACGG 57.892 39.130 0.00 0.00 0.00 4.44
1984 2436 1.337823 GCGGCTACCTGAGACAGAAAA 60.338 52.381 0.00 0.00 32.44 2.29
2149 2602 8.786826 ACCAATGATCAAACGAAAAGATACTA 57.213 30.769 0.00 0.00 0.00 1.82
2160 2613 8.643752 GGTAATAACAAAACCAATGATCAAACG 58.356 33.333 0.00 0.00 33.28 3.60
2178 2631 3.248602 CGCATCAGCCTGAAGGTAATAAC 59.751 47.826 0.00 0.00 37.52 1.89
2715 3262 5.988287 ACATTGTTCCCTGACACAATTTTT 58.012 33.333 0.00 0.00 40.85 1.94
2720 3268 3.289407 TGACATTGTTCCCTGACACAA 57.711 42.857 0.00 0.00 37.31 3.33
2748 3296 5.416013 GGGGAAATTGAGTAAACAGAAGGAG 59.584 44.000 0.00 0.00 0.00 3.69
2813 3364 7.327032 CCTGCAAAATAAGAGCTTTTCAGTAAC 59.673 37.037 0.00 0.00 0.00 2.50
3006 3591 6.295575 GGGGATACACAAATTTGACCAATGAA 60.296 38.462 24.64 1.92 42.67 2.57
3040 3677 3.087031 AGCTGATTGTTGTCATTCCTGG 58.913 45.455 0.00 0.00 0.00 4.45
3229 3866 4.486125 AGGAAAAGCACCAAACAAACAT 57.514 36.364 0.00 0.00 0.00 2.71
3238 3875 3.243839 GCATTCAGAAAGGAAAAGCACCA 60.244 43.478 0.00 0.00 34.20 4.17
3239 3876 3.006217 AGCATTCAGAAAGGAAAAGCACC 59.994 43.478 0.00 0.00 35.56 5.01
3446 4083 7.452880 TGCTGCAACTTGTCTAGAATAAAAT 57.547 32.000 0.00 0.00 0.00 1.82
3645 4288 4.666512 ACTTGACTGGAGGCAATAACAAT 58.333 39.130 0.00 0.00 0.00 2.71
3648 4291 3.686726 CAGACTTGACTGGAGGCAATAAC 59.313 47.826 0.00 0.00 34.64 1.89
3700 4343 2.803030 AAGAGCGTACAGAGGGAGTA 57.197 50.000 0.00 0.00 0.00 2.59
3703 4346 4.434545 ACTATAAGAGCGTACAGAGGGA 57.565 45.455 0.00 0.00 0.00 4.20
3704 4347 4.822896 AGAACTATAAGAGCGTACAGAGGG 59.177 45.833 0.00 0.00 0.00 4.30
3705 4348 6.380095 AAGAACTATAAGAGCGTACAGAGG 57.620 41.667 0.00 0.00 0.00 3.69
3706 4349 7.583401 CGTAAAGAACTATAAGAGCGTACAGAG 59.417 40.741 0.00 0.00 0.00 3.35
3707 4350 7.404985 CGTAAAGAACTATAAGAGCGTACAGA 58.595 38.462 0.00 0.00 0.00 3.41
3708 4351 6.632035 CCGTAAAGAACTATAAGAGCGTACAG 59.368 42.308 0.00 0.00 0.00 2.74
3709 4352 6.316140 TCCGTAAAGAACTATAAGAGCGTACA 59.684 38.462 0.00 0.00 0.00 2.90
3710 4353 6.719365 TCCGTAAAGAACTATAAGAGCGTAC 58.281 40.000 0.00 0.00 0.00 3.67
3711 4354 6.017605 CCTCCGTAAAGAACTATAAGAGCGTA 60.018 42.308 0.00 0.00 0.00 4.42
3712 4355 5.221009 CCTCCGTAAAGAACTATAAGAGCGT 60.221 44.000 0.00 0.00 0.00 5.07
3713 4356 5.213675 CCTCCGTAAAGAACTATAAGAGCG 58.786 45.833 0.00 0.00 0.00 5.03
3714 4357 5.301298 TCCCTCCGTAAAGAACTATAAGAGC 59.699 44.000 0.00 0.00 0.00 4.09
3715 4358 6.546772 ACTCCCTCCGTAAAGAACTATAAGAG 59.453 42.308 0.00 0.00 0.00 2.85
3716 4359 6.430007 ACTCCCTCCGTAAAGAACTATAAGA 58.570 40.000 0.00 0.00 0.00 2.10
3717 4360 6.712179 ACTCCCTCCGTAAAGAACTATAAG 57.288 41.667 0.00 0.00 0.00 1.73
3718 4361 8.000709 TGATACTCCCTCCGTAAAGAACTATAA 58.999 37.037 0.00 0.00 0.00 0.98
3719 4362 7.520798 TGATACTCCCTCCGTAAAGAACTATA 58.479 38.462 0.00 0.00 0.00 1.31
3720 4363 6.371278 TGATACTCCCTCCGTAAAGAACTAT 58.629 40.000 0.00 0.00 0.00 2.12
3721 4364 5.759059 TGATACTCCCTCCGTAAAGAACTA 58.241 41.667 0.00 0.00 0.00 2.24
3722 4365 4.607239 TGATACTCCCTCCGTAAAGAACT 58.393 43.478 0.00 0.00 0.00 3.01
3723 4366 4.996788 TGATACTCCCTCCGTAAAGAAC 57.003 45.455 0.00 0.00 0.00 3.01
3724 4367 4.202223 GCATGATACTCCCTCCGTAAAGAA 60.202 45.833 0.00 0.00 0.00 2.52
3725 4368 3.321111 GCATGATACTCCCTCCGTAAAGA 59.679 47.826 0.00 0.00 0.00 2.52
3726 4369 3.069586 TGCATGATACTCCCTCCGTAAAG 59.930 47.826 0.00 0.00 0.00 1.85
3727 4370 3.035363 TGCATGATACTCCCTCCGTAAA 58.965 45.455 0.00 0.00 0.00 2.01
3728 4371 2.673258 TGCATGATACTCCCTCCGTAA 58.327 47.619 0.00 0.00 0.00 3.18
3729 4372 2.375014 TGCATGATACTCCCTCCGTA 57.625 50.000 0.00 0.00 0.00 4.02
3730 4373 1.496060 TTGCATGATACTCCCTCCGT 58.504 50.000 0.00 0.00 0.00 4.69
3731 4374 2.158900 ACTTTGCATGATACTCCCTCCG 60.159 50.000 0.00 0.00 0.00 4.63
3732 4375 3.567478 ACTTTGCATGATACTCCCTCC 57.433 47.619 0.00 0.00 0.00 4.30
3733 4376 5.904362 AAAACTTTGCATGATACTCCCTC 57.096 39.130 0.00 0.00 0.00 4.30
3734 4377 5.539955 ACAAAAACTTTGCATGATACTCCCT 59.460 36.000 0.00 0.00 0.00 4.20
3735 4378 5.783111 ACAAAAACTTTGCATGATACTCCC 58.217 37.500 0.00 0.00 0.00 4.30
3736 4379 8.296713 TCTAACAAAAACTTTGCATGATACTCC 58.703 33.333 0.00 0.00 0.00 3.85
3737 4380 9.118236 GTCTAACAAAAACTTTGCATGATACTC 57.882 33.333 0.00 0.00 0.00 2.59
3738 4381 8.629158 TGTCTAACAAAAACTTTGCATGATACT 58.371 29.630 0.00 0.00 0.00 2.12
3739 4382 8.795786 TGTCTAACAAAAACTTTGCATGATAC 57.204 30.769 0.00 0.00 0.00 2.24
3740 4383 9.462174 CTTGTCTAACAAAAACTTTGCATGATA 57.538 29.630 0.00 0.00 37.69 2.15
3741 4384 8.196771 TCTTGTCTAACAAAAACTTTGCATGAT 58.803 29.630 0.00 0.00 37.69 2.45
3742 4385 7.542890 TCTTGTCTAACAAAAACTTTGCATGA 58.457 30.769 0.00 0.00 37.69 3.07
3771 4416 8.845413 AAAGAGCAAGCAATATCTATAGGAAG 57.155 34.615 0.00 0.00 0.00 3.46
3793 4438 3.724374 TGTGAGGTTGGTACGAAGAAAG 58.276 45.455 0.00 0.00 0.00 2.62
3800 4445 2.735134 GCTAAACTGTGAGGTTGGTACG 59.265 50.000 0.00 0.00 0.00 3.67
3886 4531 0.258774 AAAGTGACACCCTTGGCTGT 59.741 50.000 0.84 0.00 0.00 4.40
4090 4735 8.865090 ACCACCTACAGAAAGAGATAGATAATG 58.135 37.037 0.00 0.00 0.00 1.90
4173 4818 1.394917 CCGAAATTCAGCGACTGGAAG 59.605 52.381 6.95 0.00 42.29 3.46
4242 4887 0.321671 TGTCAGGCTGTAGACCAAGC 59.678 55.000 15.27 0.00 33.89 4.01
4311 4956 0.605319 GGAACTGCAACATCGTGGGA 60.605 55.000 0.00 0.00 0.00 4.37
4446 5091 0.621571 AGTGAGCCTGGCCTTGGATA 60.622 55.000 16.57 2.04 0.00 2.59
4464 5109 3.065655 CTGCTGTTGAAGGAACTCAGAG 58.934 50.000 0.00 0.00 38.49 3.35
4494 5139 1.202915 TGCTCATTGAAGGACTGGCAA 60.203 47.619 0.00 0.00 0.00 4.52
4624 5269 3.495806 GGGGAGAGTTGAGAATATGCTGG 60.496 52.174 0.00 0.00 0.00 4.85
4680 5325 1.961277 CTGCGAAAACGGTGAGGCT 60.961 57.895 0.00 0.00 0.00 4.58
4685 5330 2.175184 CTGAGGCTGCGAAAACGGTG 62.175 60.000 0.00 0.00 0.00 4.94
4699 5344 1.433534 GTGTCCGAAAAGCTCTGAGG 58.566 55.000 6.83 0.00 0.00 3.86
4753 5398 2.899256 GCCCCAATGTATTATGCATGGT 59.101 45.455 10.16 0.00 0.00 3.55
4767 5412 1.854939 TCTGATGAGAATGGCCCCAAT 59.145 47.619 0.00 0.00 0.00 3.16
4803 5448 2.418746 CGCAGTAGGCCTTGACATACTT 60.419 50.000 12.58 0.00 35.10 2.24
4896 5541 0.953471 GCTGTTCCATGTGCGGTGTA 60.953 55.000 0.00 0.00 0.00 2.90
4899 5544 0.253044 ATAGCTGTTCCATGTGCGGT 59.747 50.000 0.00 0.00 0.00 5.68
4900 5545 0.940126 GATAGCTGTTCCATGTGCGG 59.060 55.000 0.00 0.00 0.00 5.69
5013 5658 1.679153 ACGCCGAACAAAAGATGGTTT 59.321 42.857 0.00 0.00 0.00 3.27
5016 5661 3.546002 TTAACGCCGAACAAAAGATGG 57.454 42.857 0.00 0.00 0.00 3.51
5166 5811 2.943690 CTCATCCAAGCATCCTGAACTG 59.056 50.000 0.00 0.00 0.00 3.16
5260 5905 2.030628 TGTGTGTCGTATCGAGAAAGCA 60.031 45.455 0.00 0.00 36.23 3.91
5269 5914 6.887376 AGTAACATGATTGTGTGTCGTATC 57.113 37.500 0.00 0.00 35.83 2.24
5273 5918 5.845985 AGAAGTAACATGATTGTGTGTCG 57.154 39.130 0.00 0.00 35.83 4.35
5278 5923 5.939883 TCAGGGAAGAAGTAACATGATTGTG 59.060 40.000 0.00 0.00 35.83 3.33
5279 5924 6.126863 TCAGGGAAGAAGTAACATGATTGT 57.873 37.500 0.00 0.00 37.82 2.71
5299 5944 7.064609 TCACGGAAATAAGCAAGATAGTTTCAG 59.935 37.037 0.00 0.00 0.00 3.02
5322 5967 8.850454 TTGTTAAAGAAGCAACATAGTTTCAC 57.150 30.769 0.00 0.00 34.78 3.18
5357 6025 1.265905 GAAATCGGCAAAACGGACAGT 59.734 47.619 0.00 0.00 0.00 3.55
5363 6031 3.268013 AGTCAAGAAATCGGCAAAACG 57.732 42.857 0.00 0.00 0.00 3.60
5378 6046 7.568349 AGGCATGTCTTTCTATTGATAGTCAA 58.432 34.615 0.00 0.00 41.09 3.18
5423 6099 6.575162 AAGTTGAGTAAAAATAGCACCAGG 57.425 37.500 0.00 0.00 0.00 4.45
5427 6103 7.114953 GCTCCAAAAGTTGAGTAAAAATAGCAC 59.885 37.037 0.00 0.00 0.00 4.40
5500 6177 6.103330 GCGGTAATGGACAATTTACCAAAAT 58.897 36.000 12.71 0.00 39.69 1.82
5548 6228 5.163302 TGTAAACCTGTTTGATGTTCACG 57.837 39.130 5.55 0.00 34.23 4.35
5584 6264 2.158957 GGTGATATCAAGCGACCTTCCA 60.159 50.000 7.07 0.00 0.00 3.53
5638 6318 2.519302 CCAAATAGGCGCCCCAGG 60.519 66.667 26.15 14.79 0.00 4.45
5790 6470 4.304110 AGAACAGCATGCAAAATGAAGTG 58.696 39.130 21.98 8.37 42.53 3.16
5829 6509 1.676967 CCCTGCAGAGTTGGAAGGC 60.677 63.158 17.39 0.00 0.00 4.35
5840 6521 0.249868 TGTTCACGAACTCCCTGCAG 60.250 55.000 6.78 6.78 41.67 4.41
5849 6530 0.874607 AGGACACGCTGTTCACGAAC 60.875 55.000 2.89 2.89 41.50 3.95
6063 6747 0.036010 CCTCGCCTCAGAACACCATT 60.036 55.000 0.00 0.00 0.00 3.16
6065 6749 3.059982 CCTCGCCTCAGAACACCA 58.940 61.111 0.00 0.00 0.00 4.17
6068 6752 2.492449 CTTCGCCTCGCCTCAGAACA 62.492 60.000 0.00 0.00 0.00 3.18
6137 6821 5.404096 GTCTCGAAAACTAGGAGAGAAAGG 58.596 45.833 0.00 0.00 39.33 3.11
6162 6846 1.172180 TGCTTGCTTTCCAGTTCCGG 61.172 55.000 0.00 0.00 0.00 5.14
6338 7030 4.061596 GAGCCTACATTCACAGGATTAGC 58.938 47.826 0.00 0.00 33.42 3.09
6376 7068 1.673760 CAATCGCAACAACGACAAGG 58.326 50.000 0.00 0.00 46.28 3.61
6391 7083 4.217118 AGAACATGAACAAGACAGGCAATC 59.783 41.667 0.00 0.00 0.00 2.67
6392 7084 4.022589 CAGAACATGAACAAGACAGGCAAT 60.023 41.667 0.00 0.00 0.00 3.56
6399 7112 4.913924 GTCAATGCAGAACATGAACAAGAC 59.086 41.667 0.00 0.20 39.60 3.01
6458 7171 6.430308 CACTCTACTAACTGAACTCTGGTGTA 59.570 42.308 0.00 0.00 0.00 2.90
6467 7180 7.038659 AGATCAATGCACTCTACTAACTGAAC 58.961 38.462 0.00 0.00 0.00 3.18
6505 7223 3.055819 GTGCTACTCATCTGGAACTGGAA 60.056 47.826 0.00 0.00 0.00 3.53
6506 7224 2.497675 GTGCTACTCATCTGGAACTGGA 59.502 50.000 0.00 0.00 0.00 3.86
6507 7225 2.419297 GGTGCTACTCATCTGGAACTGG 60.419 54.545 0.00 0.00 0.00 4.00
6508 7226 2.419297 GGGTGCTACTCATCTGGAACTG 60.419 54.545 0.00 0.00 0.00 3.16
6509 7227 1.834263 GGGTGCTACTCATCTGGAACT 59.166 52.381 0.00 0.00 0.00 3.01
6510 7228 1.834263 AGGGTGCTACTCATCTGGAAC 59.166 52.381 0.00 0.00 0.00 3.62
6566 7284 2.885135 TGGACATGCCACTTCTGATT 57.115 45.000 4.93 0.00 43.33 2.57
6587 7305 8.472413 AGCGTTTCTACATCTACAGGTAAATAA 58.528 33.333 0.00 0.00 0.00 1.40
6588 7306 8.004087 AGCGTTTCTACATCTACAGGTAAATA 57.996 34.615 0.00 0.00 0.00 1.40
6589 7307 6.875076 AGCGTTTCTACATCTACAGGTAAAT 58.125 36.000 0.00 0.00 0.00 1.40
6590 7308 6.152323 AGAGCGTTTCTACATCTACAGGTAAA 59.848 38.462 0.00 0.00 33.23 2.01
6591 7309 5.651139 AGAGCGTTTCTACATCTACAGGTAA 59.349 40.000 0.00 0.00 33.23 2.85
6595 7313 4.987832 ACAGAGCGTTTCTACATCTACAG 58.012 43.478 0.00 0.00 33.83 2.74
6613 7331 4.707776 GACCAAGGTCCTGCACAACAGA 62.708 54.545 8.06 0.00 46.81 3.41
6705 7428 0.623031 TGATGGGGTGGATGCCTACA 60.623 55.000 0.00 0.00 0.00 2.74
6706 7429 0.773644 ATGATGGGGTGGATGCCTAC 59.226 55.000 0.00 0.00 0.00 3.18
6707 7430 1.425066 GAATGATGGGGTGGATGCCTA 59.575 52.381 0.00 0.00 0.00 3.93
6708 7431 0.186873 GAATGATGGGGTGGATGCCT 59.813 55.000 0.00 0.00 0.00 4.75
6773 7502 4.383861 TGCCGCTCTGCTCTGGTG 62.384 66.667 0.00 0.00 0.00 4.17
6774 7503 4.385405 GTGCCGCTCTGCTCTGGT 62.385 66.667 0.00 0.00 0.00 4.00
6821 7550 1.905215 CACAAGGGGATGAGTGAGTCT 59.095 52.381 0.00 0.00 33.99 3.24
6825 7554 1.133181 TGGCACAAGGGGATGAGTGA 61.133 55.000 0.00 0.00 33.99 3.41
6847 7583 0.179059 TCCTCAGTCTTTGCAACGCA 60.179 50.000 0.00 0.00 36.47 5.24
6848 7584 1.160137 ATCCTCAGTCTTTGCAACGC 58.840 50.000 0.00 0.00 0.00 4.84
6850 7586 4.759183 AGAGAAATCCTCAGTCTTTGCAAC 59.241 41.667 0.00 0.00 44.40 4.17
6854 7590 7.502120 TCAAAAGAGAAATCCTCAGTCTTTG 57.498 36.000 0.00 0.00 44.40 2.77
6855 7591 8.525290 TTTCAAAAGAGAAATCCTCAGTCTTT 57.475 30.769 0.00 0.00 44.40 2.52
6859 7595 9.018582 CCTAATTTCAAAAGAGAAATCCTCAGT 57.981 33.333 2.78 0.00 44.96 3.41
6860 7596 9.236006 TCCTAATTTCAAAAGAGAAATCCTCAG 57.764 33.333 2.78 0.22 44.96 3.35
6861 7597 9.236006 CTCCTAATTTCAAAAGAGAAATCCTCA 57.764 33.333 2.78 0.00 44.96 3.86
6862 7598 9.454859 TCTCCTAATTTCAAAAGAGAAATCCTC 57.545 33.333 2.78 0.00 44.96 3.71
6863 7599 9.813826 TTCTCCTAATTTCAAAAGAGAAATCCT 57.186 29.630 2.78 0.00 44.96 3.24
6890 7629 5.311265 GCATCACATCATCCATCTTTCCTA 58.689 41.667 0.00 0.00 0.00 2.94
6918 7657 0.475475 GATGGAGGGGCATCACATCA 59.525 55.000 0.00 0.00 38.20 3.07
6919 7658 0.251077 GGATGGAGGGGCATCACATC 60.251 60.000 0.00 0.00 37.73 3.06
6920 7659 0.995132 TGGATGGAGGGGCATCACAT 60.995 55.000 0.00 0.00 0.00 3.21
6921 7660 0.995132 ATGGATGGAGGGGCATCACA 60.995 55.000 0.00 0.00 0.00 3.58
6922 7661 0.251077 GATGGATGGAGGGGCATCAC 60.251 60.000 0.00 0.00 0.00 3.06
6923 7662 0.402419 AGATGGATGGAGGGGCATCA 60.402 55.000 0.00 0.00 0.00 3.07
6924 7663 0.037877 CAGATGGATGGAGGGGCATC 59.962 60.000 0.00 0.00 0.00 3.91
6925 7664 0.700269 ACAGATGGATGGAGGGGCAT 60.700 55.000 0.00 0.00 0.00 4.40
6927 7666 1.453669 GACAGATGGATGGAGGGGC 59.546 63.158 0.00 0.00 0.00 5.80
6929 7668 1.350351 GATGGACAGATGGATGGAGGG 59.650 57.143 0.00 0.00 0.00 4.30
6930 7669 2.052468 TGATGGACAGATGGATGGAGG 58.948 52.381 0.00 0.00 0.00 4.30
6942 7683 1.522092 GATGGGAGCGTGATGGACA 59.478 57.895 0.00 0.00 0.00 4.02
6943 7684 1.227674 GGATGGGAGCGTGATGGAC 60.228 63.158 0.00 0.00 0.00 4.02
6956 7697 1.133025 GCACCACGAAGAAATGGATGG 59.867 52.381 0.00 0.00 39.46 3.51
6959 7700 1.610624 GGAGCACCACGAAGAAATGGA 60.611 52.381 0.00 0.00 39.46 3.41
6970 7711 0.815615 GAATGGATCGGGAGCACCAC 60.816 60.000 1.58 0.00 40.22 4.16
6971 7712 1.526887 GAATGGATCGGGAGCACCA 59.473 57.895 1.58 0.00 40.22 4.17
6973 7714 1.227973 GGGAATGGATCGGGAGCAC 60.228 63.158 0.00 0.00 0.00 4.40
6974 7715 2.452064 GGGGAATGGATCGGGAGCA 61.452 63.158 0.00 0.00 0.00 4.26
6975 7716 2.403132 CTGGGGAATGGATCGGGAGC 62.403 65.000 0.00 0.00 0.00 4.70
6976 7717 1.757306 CTGGGGAATGGATCGGGAG 59.243 63.158 0.00 0.00 0.00 4.30
6977 7718 1.770110 CCTGGGGAATGGATCGGGA 60.770 63.158 0.00 0.00 0.00 5.14
6978 7719 0.766674 TACCTGGGGAATGGATCGGG 60.767 60.000 0.00 0.00 0.00 5.14
6979 7720 1.279271 GATACCTGGGGAATGGATCGG 59.721 57.143 0.00 0.00 0.00 4.18
6980 7721 1.279271 GGATACCTGGGGAATGGATCG 59.721 57.143 0.00 0.00 0.00 3.69
6981 7722 1.279271 CGGATACCTGGGGAATGGATC 59.721 57.143 0.00 0.00 0.00 3.36
6986 7744 1.129058 GTGACGGATACCTGGGGAAT 58.871 55.000 0.00 0.00 0.00 3.01
6987 7745 1.324740 CGTGACGGATACCTGGGGAA 61.325 60.000 0.00 0.00 0.00 3.97
7006 7764 3.957497 AGATGGATAGATAGACCGATGGC 59.043 47.826 0.00 0.00 0.00 4.40
7012 7770 4.521256 GGGCGATAGATGGATAGATAGACC 59.479 50.000 0.00 0.00 39.76 3.85
7016 7774 4.079154 AGGTGGGCGATAGATGGATAGATA 60.079 45.833 0.00 0.00 39.76 1.98
7020 7778 2.179427 CAGGTGGGCGATAGATGGATA 58.821 52.381 0.00 0.00 39.76 2.59



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

AutoCloner maintained by Alex Coulton.