Multiple sequence alignment - TraesCS1A01G112100

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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 TraesCS1A01G112100 chr1A 100.000 5263 0 0 1 5263 113862478 113857216 0.000000e+00 9720
1 TraesCS1A01G112100 chr1D 93.067 4630 188 38 1 4536 109977266 109972676 0.000000e+00 6649
2 TraesCS1A01G112100 chr1D 96.923 260 8 0 4574 4833 109972678 109972419 2.250000e-118 436
3 TraesCS1A01G112100 chr1D 96.341 82 3 0 4826 4907 109972398 109972317 9.190000e-28 135
4 TraesCS1A01G112100 chr1B 92.365 4034 202 43 1 3946 166595941 166591926 0.000000e+00 5646
5 TraesCS1A01G112100 chr1B 91.141 587 25 10 4266 4833 166591379 166590801 0.000000e+00 771
6 TraesCS1A01G112100 chr1B 93.824 340 16 4 3946 4283 166591893 166591557 1.690000e-139 507
7 TraesCS1A01G112100 chr6B 99.155 355 3 0 4909 5263 687907284 687906930 1.600000e-179 640
8 TraesCS1A01G112100 chr2B 98.619 362 3 2 4902 5263 141550431 141550790 1.600000e-179 640
9 TraesCS1A01G112100 chr7B 99.155 355 1 1 4909 5263 662825654 662825302 5.750000e-179 638
10 TraesCS1A01G112100 chr5B 98.883 358 2 1 4906 5263 423669816 423670171 5.750000e-179 638
11 TraesCS1A01G112100 chr5B 98.873 355 2 1 4909 5263 423686617 423686969 2.670000e-177 632
12 TraesCS1A01G112100 chr5B 98.873 355 2 1 4909 5263 430228624 430228272 2.670000e-177 632
13 TraesCS1A01G112100 chr5A 99.155 355 1 1 4909 5263 688028822 688029174 5.750000e-179 638
14 TraesCS1A01G112100 chr3A 98.883 358 2 1 4906 5263 494878983 494879338 5.750000e-179 638
15 TraesCS1A01G112100 chr3A 89.286 140 15 0 1324 1463 63065925 63066064 5.420000e-40 176
16 TraesCS1A01G112100 chr3A 77.303 304 58 10 2580 2873 63067031 63067333 9.060000e-38 169
17 TraesCS1A01G112100 chr4B 98.343 362 3 2 4902 5263 337992190 337992548 2.670000e-177 632
18 TraesCS1A01G112100 chr7A 93.469 245 16 0 4064 4308 149286837 149286593 1.080000e-96 364
19 TraesCS1A01G112100 chr7A 96.203 79 3 0 4296 4374 149285001 149284923 4.280000e-26 130
20 TraesCS1A01G112100 chr3B 79.208 303 51 9 2580 2873 79121444 79121743 3.210000e-47 200
21 TraesCS1A01G112100 chr3B 89.286 140 15 0 1324 1463 79120327 79120466 5.420000e-40 176
22 TraesCS1A01G112100 chr3D 78.808 302 53 9 2580 2873 49639510 49639808 5.380000e-45 193
23 TraesCS1A01G112100 chr3D 89.286 140 15 0 1324 1463 49638360 49638499 5.420000e-40 176


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 TraesCS1A01G112100 chr1A 113857216 113862478 5262 True 9720.000000 9720 100.000000 1 5263 1 chr1A.!!$R1 5262
1 TraesCS1A01G112100 chr1D 109972317 109977266 4949 True 2406.666667 6649 95.443667 1 4907 3 chr1D.!!$R1 4906
2 TraesCS1A01G112100 chr1B 166590801 166595941 5140 True 2308.000000 5646 92.443333 1 4833 3 chr1B.!!$R1 4832
3 TraesCS1A01G112100 chr7A 149284923 149286837 1914 True 247.000000 364 94.836000 4064 4374 2 chr7A.!!$R1 310

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
141 146 0.107703 TGCCAGATTCCACCATCGTC 60.108 55.0 0.00 0.0 0.00 4.20 F
379 384 0.109342 GAATGATGGCGGGATCCAGT 59.891 55.0 15.23 0.0 39.89 4.00 F
967 1007 0.179100 CGAGGCGGCCATCCATATAG 60.179 60.0 23.09 0.0 0.00 1.31 F
1578 1620 0.534877 TCTTCGGTTGTGCACATGCT 60.535 50.0 22.39 0.0 42.66 3.79 F
2836 2941 0.749454 CCATACTGTCCTTGCTGGCC 60.749 60.0 0.00 0.0 35.26 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1558 1600 0.310543 GCATGTGCACAACCGAAGAA 59.689 50.000 25.72 0.00 41.59 2.52 R
1811 1876 1.003580 CCAGGACATGCTACACAACCT 59.996 52.381 0.00 0.00 32.91 3.50 R
1874 1939 1.563111 CAGGCAGCACAAACAAACAG 58.437 50.000 0.00 0.00 0.00 3.16 R
3237 3344 1.113788 AGTTTGCCAAAGCTGCTTCA 58.886 45.000 16.28 6.76 40.80 3.02 R
4679 6657 0.260230 TTTCCACAAGGGGCTGTTGA 59.740 50.000 6.41 0.00 37.22 3.18 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
21 23 2.436911 ACCCGGTTTGTTCTTCTACAGT 59.563 45.455 0.00 0.00 0.00 3.55
31 33 9.269453 GTTTGTTCTTCTACAGTTGTAGGTTAT 57.731 33.333 16.86 0.00 46.01 1.89
35 37 9.356433 GTTCTTCTACAGTTGTAGGTTATCTTC 57.644 37.037 16.86 1.30 46.01 2.87
49 51 9.807649 GTAGGTTATCTTCGTTGGTAGATTTTA 57.192 33.333 0.00 0.00 33.09 1.52
53 55 9.845305 GTTATCTTCGTTGGTAGATTTTAATCG 57.155 33.333 0.00 0.00 40.35 3.34
68 70 2.403252 AATCGGTTCATCTTCGGCTT 57.597 45.000 0.00 0.00 0.00 4.35
82 84 0.172578 CGGCTTCGGTAGTGATGACA 59.827 55.000 0.00 0.00 0.00 3.58
88 90 1.964933 TCGGTAGTGATGACAACACCA 59.035 47.619 11.83 0.00 38.82 4.17
94 99 2.151202 GTGATGACAACACCACCGAAT 58.849 47.619 4.56 0.00 34.66 3.34
95 100 3.007506 AGTGATGACAACACCACCGAATA 59.992 43.478 11.83 0.00 41.18 1.75
96 101 3.749088 GTGATGACAACACCACCGAATAA 59.251 43.478 4.56 0.00 34.66 1.40
114 119 5.065218 CGAATAAGGTGTCTCCAAATCCTTG 59.935 44.000 0.00 0.00 38.68 3.61
124 129 2.562298 TCCAAATCCTTGACCAACATGC 59.438 45.455 0.00 0.00 34.14 4.06
141 146 0.107703 TGCCAGATTCCACCATCGTC 60.108 55.000 0.00 0.00 0.00 4.20
156 161 2.119671 TCGTCGACGAATCCATGATG 57.880 50.000 36.25 5.24 46.30 3.07
157 162 1.673920 TCGTCGACGAATCCATGATGA 59.326 47.619 36.25 10.84 46.30 2.92
162 167 4.271049 GTCGACGAATCCATGATGATGTTT 59.729 41.667 0.00 0.00 0.00 2.83
188 193 4.612412 GGGGTCAACGTGGCGACA 62.612 66.667 13.18 0.00 33.66 4.35
190 195 2.028484 GGTCAACGTGGCGACAGA 59.972 61.111 13.18 0.00 44.46 3.41
209 214 5.729510 ACAGAGATGACCTAGAGCTTTTTC 58.270 41.667 0.00 0.00 0.00 2.29
214 219 3.248024 TGACCTAGAGCTTTTTCCTCCA 58.752 45.455 0.00 0.00 0.00 3.86
215 220 3.650942 TGACCTAGAGCTTTTTCCTCCAA 59.349 43.478 0.00 0.00 0.00 3.53
220 225 1.197949 GAGCTTTTTCCTCCAACTCGC 59.802 52.381 0.00 0.00 0.00 5.03
221 226 0.241213 GCTTTTTCCTCCAACTCGCC 59.759 55.000 0.00 0.00 0.00 5.54
223 228 2.874457 GCTTTTTCCTCCAACTCGCCTA 60.874 50.000 0.00 0.00 0.00 3.93
242 247 4.519730 GCCTATCGAGGTAATGTGTACTCT 59.480 45.833 0.00 0.00 45.78 3.24
354 359 0.468226 TGCTCTCGTGAAGGGTTTGT 59.532 50.000 0.00 0.00 0.00 2.83
363 368 1.219213 TGAAGGGTTTGTGGGTGGAAT 59.781 47.619 0.00 0.00 0.00 3.01
369 374 1.066929 GTTTGTGGGTGGAATGATGGC 60.067 52.381 0.00 0.00 0.00 4.40
372 377 2.519302 GGGTGGAATGATGGCGGG 60.519 66.667 0.00 0.00 0.00 6.13
373 378 2.595095 GGTGGAATGATGGCGGGA 59.405 61.111 0.00 0.00 0.00 5.14
376 381 0.890996 GTGGAATGATGGCGGGATCC 60.891 60.000 1.92 1.92 0.00 3.36
377 382 1.351850 TGGAATGATGGCGGGATCCA 61.352 55.000 15.23 0.00 40.97 3.41
378 383 0.607489 GGAATGATGGCGGGATCCAG 60.607 60.000 15.23 11.38 39.89 3.86
379 384 0.109342 GAATGATGGCGGGATCCAGT 59.891 55.000 15.23 0.00 39.89 4.00
381 386 2.060567 ATGATGGCGGGATCCAGTGG 62.061 60.000 15.23 1.40 39.89 4.00
382 387 2.692368 ATGGCGGGATCCAGTGGT 60.692 61.111 15.23 0.00 39.89 4.16
383 388 2.666596 GATGGCGGGATCCAGTGGTC 62.667 65.000 15.23 6.15 39.89 4.02
400 406 1.080093 TCCCTCGACGACATTGTGC 60.080 57.895 0.00 0.00 0.00 4.57
403 409 2.431771 TCGACGACATTGTGCGGG 60.432 61.111 0.00 0.00 0.00 6.13
409 415 1.303317 GACATTGTGCGGGGAAGGT 60.303 57.895 0.00 0.00 0.00 3.50
417 423 1.831286 GCGGGGAAGGTAGATCCGA 60.831 63.158 4.15 0.00 42.94 4.55
422 428 1.619332 GGGAAGGTAGATCCGATGGAC 59.381 57.143 0.00 0.00 41.99 4.02
503 517 6.596888 TCTTCATCGATTCTCAAAGCTTTGAT 59.403 34.615 35.40 24.25 45.26 2.57
507 521 4.996758 TCGATTCTCAAAGCTTTGATGTGA 59.003 37.500 35.40 27.20 45.26 3.58
508 522 5.084722 CGATTCTCAAAGCTTTGATGTGAC 58.915 41.667 35.40 24.26 45.26 3.67
509 523 4.472691 TTCTCAAAGCTTTGATGTGACG 57.527 40.909 35.40 24.40 45.26 4.35
510 524 2.807967 TCTCAAAGCTTTGATGTGACGG 59.192 45.455 35.40 23.78 45.26 4.79
511 525 2.807967 CTCAAAGCTTTGATGTGACGGA 59.192 45.455 35.40 15.09 45.26 4.69
512 526 2.807967 TCAAAGCTTTGATGTGACGGAG 59.192 45.455 32.86 7.96 41.88 4.63
530 544 1.166531 AGCACCGACAGTTCTTTGGC 61.167 55.000 0.00 0.00 0.00 4.52
533 547 0.468226 ACCGACAGTTCTTTGGCTGA 59.532 50.000 0.00 0.00 36.62 4.26
551 565 3.848726 CTGAAGGAGCTTGTCTCTTCTC 58.151 50.000 12.43 0.00 41.60 2.87
608 628 1.228552 CCCCAGGGACCTTGTTGTG 60.229 63.158 7.25 0.00 37.50 3.33
656 676 1.302752 TCTGTGCCAGGACATGTGC 60.303 57.895 9.70 9.70 31.51 4.57
686 706 3.181517 CGTCGGTTCGAGTATGTTCTACA 60.182 47.826 0.00 0.00 36.23 2.74
690 710 4.683832 GGTTCGAGTATGTTCTACAGCAT 58.316 43.478 0.00 0.00 0.00 3.79
709 729 4.067016 CGTGGCGCGTGTTGTACC 62.067 66.667 13.13 0.00 35.54 3.34
711 731 2.109387 TGGCGCGTGTTGTACCTT 59.891 55.556 8.43 0.00 0.00 3.50
825 865 2.398754 TGAGACAAGAGGAAGGTGGA 57.601 50.000 0.00 0.00 0.00 4.02
934 974 3.420839 AATTGCCGCTTCCTTTAATCG 57.579 42.857 0.00 0.00 0.00 3.34
967 1007 0.179100 CGAGGCGGCCATCCATATAG 60.179 60.000 23.09 0.00 0.00 1.31
1144 1184 4.873129 CCCAGATCCACCGACGCG 62.873 72.222 3.53 3.53 0.00 6.01
1172 1213 0.615544 TATGTTTCGACCCCTCCCGT 60.616 55.000 0.00 0.00 0.00 5.28
1282 1323 1.908483 GGTCTGATCGGGAAGGCTT 59.092 57.895 0.00 0.00 0.00 4.35
1451 1492 1.219393 CTCCCTCGGCTTCACCTTC 59.781 63.158 0.00 0.00 35.61 3.46
1502 1543 3.432252 CCAGCTTCTTGATTCGTTACGTT 59.568 43.478 4.24 0.00 0.00 3.99
1558 1600 1.605753 TCTATCTATGCGTGCTCCGT 58.394 50.000 0.00 0.00 39.32 4.69
1563 1605 0.924090 CTATGCGTGCTCCGTTCTTC 59.076 55.000 0.00 0.00 39.32 2.87
1578 1620 0.534877 TCTTCGGTTGTGCACATGCT 60.535 50.000 22.39 0.00 42.66 3.79
1604 1646 6.511767 CGGTTCAGATTATTAACACCAGATGC 60.512 42.308 0.00 0.00 0.00 3.91
1656 1711 9.691362 ATTGAATTTGGTGTGTTTGATAACTAC 57.309 29.630 0.00 0.00 35.24 2.73
1657 1712 8.458573 TGAATTTGGTGTGTTTGATAACTACT 57.541 30.769 0.00 0.00 35.24 2.57
1658 1713 8.349245 TGAATTTGGTGTGTTTGATAACTACTG 58.651 33.333 0.00 0.00 35.24 2.74
1659 1714 7.817418 ATTTGGTGTGTTTGATAACTACTGT 57.183 32.000 0.00 0.00 35.24 3.55
1660 1715 8.911918 ATTTGGTGTGTTTGATAACTACTGTA 57.088 30.769 0.00 0.00 35.24 2.74
1781 1836 9.989394 GTGAAAGCTTTGATTATTTTTCGTAAC 57.011 29.630 18.30 0.00 0.00 2.50
1874 1939 5.278758 GCTTGACAGATGGGAGTAGTATCTC 60.279 48.000 0.00 0.00 0.00 2.75
1919 1984 7.201556 GGAGTGTATGTACATGTGATGTTCAAG 60.202 40.741 18.81 0.00 42.48 3.02
1982 2074 5.556355 TCTGAATGTTGCTTATGCTGAAG 57.444 39.130 1.96 0.00 40.48 3.02
2012 2104 9.770097 GAATGAGAATATGAGATACCAGTGAAA 57.230 33.333 0.00 0.00 0.00 2.69
2108 2200 2.486982 CACTTTCTGCTCCCTTCATGTG 59.513 50.000 0.00 0.00 0.00 3.21
2297 2389 2.835156 TCGTACCATTGTCAGGATTCCA 59.165 45.455 5.29 0.00 0.00 3.53
2338 2430 7.334421 CAGTTCTGCACTTACTACATTTGGTAT 59.666 37.037 0.00 0.00 30.92 2.73
2392 2489 6.529463 TGTAACAAACTTTACTTCCGCTAC 57.471 37.500 0.00 0.00 33.73 3.58
2564 2666 4.576463 GCACTAATCAATCCACCTAACTGG 59.424 45.833 0.00 0.00 42.93 4.00
2786 2891 2.115911 GGTGTCGGTGTTGCAACCA 61.116 57.895 26.14 13.69 40.53 3.67
2836 2941 0.749454 CCATACTGTCCTTGCTGGCC 60.749 60.000 0.00 0.00 35.26 5.36
2905 3010 1.713597 GCCTTTTCTTGGCCAAATCG 58.286 50.000 20.91 8.35 44.32 3.34
2992 3098 2.287915 GCACTTGACGTGATGACTGTTT 59.712 45.455 0.00 0.00 46.81 2.83
3022 3128 8.186821 ACTACTCTGTTACATTCACGTATTACC 58.813 37.037 0.00 0.00 0.00 2.85
3026 3133 4.863689 TGTTACATTCACGTATTACCACCG 59.136 41.667 0.00 0.00 0.00 4.94
3031 3138 5.239087 ACATTCACGTATTACCACCGTTTTT 59.761 36.000 0.00 0.00 31.46 1.94
3034 3141 4.574013 TCACGTATTACCACCGTTTTTGTT 59.426 37.500 0.00 0.00 31.46 2.83
3042 3149 2.255316 CACCGTTTTTGTTGTGTGGTC 58.745 47.619 0.00 0.00 0.00 4.02
3201 3308 4.773013 TCCTGACTAACCAAAACGTCTTT 58.227 39.130 0.00 0.00 0.00 2.52
3237 3344 5.637810 CACATCTAACGTTGTGGTAAGTCAT 59.362 40.000 11.99 0.00 39.61 3.06
3300 3407 5.163205 TGTTTCTGATTCTCCTCTTGTTCCA 60.163 40.000 0.00 0.00 0.00 3.53
3439 3546 0.803117 GCCTAGTTTTGACCTTCGGC 59.197 55.000 0.00 0.00 0.00 5.54
3460 3567 2.900122 ACGTTTTGCTTCATGATCCG 57.100 45.000 0.00 0.00 0.00 4.18
3534 3641 9.413048 GGTACTATATTCATACTTCTGCTCAAC 57.587 37.037 0.00 0.00 0.00 3.18
3697 3804 9.654663 GTTTATAAATCCCTATGCGTTCTCTAT 57.345 33.333 0.31 0.00 0.00 1.98
3747 3854 5.413833 GCACCTTTGATCTCTGATTCTTTGA 59.586 40.000 0.00 0.00 0.00 2.69
3831 3938 2.863809 ACTCAAGGGCGTGAGAATTTT 58.136 42.857 19.99 0.00 46.76 1.82
3994 4156 3.855689 ACCTTCCAAAATTGCAGATCG 57.144 42.857 0.00 0.00 0.00 3.69
4067 4229 6.706270 TCCAAATCTTCTCACTGTAACTTCAC 59.294 38.462 0.00 0.00 0.00 3.18
4374 6335 3.251487 GTGTACACGGTGCCTGTTTTTAT 59.749 43.478 10.84 0.00 0.00 1.40
4375 6336 4.451774 GTGTACACGGTGCCTGTTTTTATA 59.548 41.667 10.84 0.00 0.00 0.98
4434 6405 8.213518 ACATTGAAATCACACAGGTCATATAC 57.786 34.615 0.00 0.00 0.00 1.47
4486 6457 8.292448 CACATACTTCAGTTTGCTAAATGTTCT 58.708 33.333 8.12 0.00 31.55 3.01
4542 6513 5.933790 TCATTTAACTCGCCATGTTGTAAC 58.066 37.500 0.00 0.00 0.00 2.50
4554 6525 3.530265 TGTTGTAACTGTCAGTTCCGT 57.470 42.857 21.40 0.58 39.51 4.69
4563 6534 3.002791 CTGTCAGTTCCGTACAATGCAT 58.997 45.455 0.00 0.00 0.00 3.96
4570 6541 2.217750 TCCGTACAATGCATGCATACC 58.782 47.619 32.36 18.43 35.31 2.73
4691 6669 3.279434 GTCGATAATTCAACAGCCCCTT 58.721 45.455 0.00 0.00 0.00 3.95
4693 6671 3.016736 CGATAATTCAACAGCCCCTTGT 58.983 45.455 0.00 0.00 0.00 3.16
4847 6854 4.248174 TGAAAGGATATCAATGGGCACA 57.752 40.909 4.83 0.00 0.00 4.57
4852 6859 2.358898 GGATATCAATGGGCACACACAC 59.641 50.000 4.83 0.00 0.00 3.82
4864 6871 3.175929 GCACACACACAACTAAACAACC 58.824 45.455 0.00 0.00 0.00 3.77
4907 6914 5.597806 CGGTGTCCAGATAAGTTAAGCATA 58.402 41.667 0.00 0.00 0.00 3.14
4908 6915 6.223852 CGGTGTCCAGATAAGTTAAGCATAT 58.776 40.000 0.00 0.00 0.00 1.78
4909 6916 6.146184 CGGTGTCCAGATAAGTTAAGCATATG 59.854 42.308 0.00 0.00 0.00 1.78
4910 6917 7.217200 GGTGTCCAGATAAGTTAAGCATATGA 58.783 38.462 6.97 0.00 0.00 2.15
4911 6918 7.171678 GGTGTCCAGATAAGTTAAGCATATGAC 59.828 40.741 6.97 0.00 0.00 3.06
4912 6919 6.923508 TGTCCAGATAAGTTAAGCATATGACG 59.076 38.462 6.97 0.00 0.00 4.35
4913 6920 5.926542 TCCAGATAAGTTAAGCATATGACGC 59.073 40.000 6.97 0.00 0.00 5.19
4914 6921 5.120830 CCAGATAAGTTAAGCATATGACGCC 59.879 44.000 6.97 0.00 0.00 5.68
4915 6922 5.120830 CAGATAAGTTAAGCATATGACGCCC 59.879 44.000 6.97 0.00 0.00 6.13
4916 6923 1.865865 AGTTAAGCATATGACGCCCG 58.134 50.000 6.97 0.00 0.00 6.13
4917 6924 0.865769 GTTAAGCATATGACGCCCGG 59.134 55.000 6.97 0.00 0.00 5.73
4918 6925 0.753867 TTAAGCATATGACGCCCGGA 59.246 50.000 0.73 0.00 0.00 5.14
4919 6926 0.973632 TAAGCATATGACGCCCGGAT 59.026 50.000 0.73 0.00 0.00 4.18
4920 6927 0.973632 AAGCATATGACGCCCGGATA 59.026 50.000 0.73 0.00 0.00 2.59
4921 6928 0.973632 AGCATATGACGCCCGGATAA 59.026 50.000 0.73 0.00 0.00 1.75
4922 6929 1.555075 AGCATATGACGCCCGGATAAT 59.445 47.619 0.73 0.00 0.00 1.28
4923 6930 1.933853 GCATATGACGCCCGGATAATC 59.066 52.381 0.73 0.00 0.00 1.75
4924 6931 2.676750 GCATATGACGCCCGGATAATCA 60.677 50.000 0.73 0.90 0.00 2.57
4925 6932 3.595173 CATATGACGCCCGGATAATCAA 58.405 45.455 0.73 0.00 0.00 2.57
4926 6933 2.169832 ATGACGCCCGGATAATCAAG 57.830 50.000 0.73 0.00 0.00 3.02
4927 6934 0.531974 TGACGCCCGGATAATCAAGC 60.532 55.000 0.73 0.00 0.00 4.01
4928 6935 0.249911 GACGCCCGGATAATCAAGCT 60.250 55.000 0.73 0.00 0.00 3.74
4929 6936 1.000506 GACGCCCGGATAATCAAGCTA 59.999 52.381 0.73 0.00 0.00 3.32
4930 6937 1.270147 ACGCCCGGATAATCAAGCTAC 60.270 52.381 0.73 0.00 0.00 3.58
4931 6938 1.270094 CGCCCGGATAATCAAGCTACA 60.270 52.381 0.73 0.00 0.00 2.74
4932 6939 2.417719 GCCCGGATAATCAAGCTACAG 58.582 52.381 0.73 0.00 0.00 2.74
4933 6940 2.224305 GCCCGGATAATCAAGCTACAGT 60.224 50.000 0.73 0.00 0.00 3.55
4934 6941 3.006537 GCCCGGATAATCAAGCTACAGTA 59.993 47.826 0.73 0.00 0.00 2.74
4935 6942 4.502604 GCCCGGATAATCAAGCTACAGTAA 60.503 45.833 0.73 0.00 0.00 2.24
4936 6943 4.989168 CCCGGATAATCAAGCTACAGTAAC 59.011 45.833 0.73 0.00 0.00 2.50
4937 6944 4.989168 CCGGATAATCAAGCTACAGTAACC 59.011 45.833 0.00 0.00 0.00 2.85
4938 6945 5.221461 CCGGATAATCAAGCTACAGTAACCT 60.221 44.000 0.00 0.00 0.00 3.50
4939 6946 5.921408 CGGATAATCAAGCTACAGTAACCTC 59.079 44.000 0.00 0.00 0.00 3.85
4940 6947 6.239064 CGGATAATCAAGCTACAGTAACCTCT 60.239 42.308 0.00 0.00 0.00 3.69
4941 6948 6.926272 GGATAATCAAGCTACAGTAACCTCTG 59.074 42.308 0.00 0.00 40.80 3.35
4942 6949 3.594603 TCAAGCTACAGTAACCTCTGC 57.405 47.619 0.00 0.00 38.84 4.26
4943 6950 3.165875 TCAAGCTACAGTAACCTCTGCT 58.834 45.455 0.00 0.00 38.84 4.24
4944 6951 4.341487 TCAAGCTACAGTAACCTCTGCTA 58.659 43.478 0.00 0.00 38.84 3.49
4945 6952 4.770531 TCAAGCTACAGTAACCTCTGCTAA 59.229 41.667 0.00 0.00 38.84 3.09
4946 6953 5.422331 TCAAGCTACAGTAACCTCTGCTAAT 59.578 40.000 0.00 0.00 38.84 1.73
4947 6954 5.269505 AGCTACAGTAACCTCTGCTAATG 57.730 43.478 0.00 0.00 38.84 1.90
4948 6955 4.956700 AGCTACAGTAACCTCTGCTAATGA 59.043 41.667 0.00 0.00 38.84 2.57
4949 6956 5.600484 AGCTACAGTAACCTCTGCTAATGAT 59.400 40.000 0.00 0.00 38.84 2.45
4950 6957 5.694006 GCTACAGTAACCTCTGCTAATGATG 59.306 44.000 0.00 0.00 38.84 3.07
4951 6958 4.446371 ACAGTAACCTCTGCTAATGATGC 58.554 43.478 0.00 0.00 38.84 3.91
4952 6959 3.812053 CAGTAACCTCTGCTAATGATGCC 59.188 47.826 0.00 0.00 0.00 4.40
4953 6960 3.713764 AGTAACCTCTGCTAATGATGCCT 59.286 43.478 0.00 0.00 0.00 4.75
4954 6961 2.926778 ACCTCTGCTAATGATGCCTC 57.073 50.000 0.00 0.00 0.00 4.70
4955 6962 2.121948 ACCTCTGCTAATGATGCCTCA 58.878 47.619 0.00 0.00 35.41 3.86
4956 6963 2.709934 ACCTCTGCTAATGATGCCTCAT 59.290 45.455 0.00 0.00 44.14 2.90
4957 6964 3.244491 ACCTCTGCTAATGATGCCTCATC 60.244 47.826 4.86 0.13 41.34 2.92
4965 6972 1.576577 TGATGCCTCATCACCACTCT 58.423 50.000 5.48 0.00 44.60 3.24
4966 6973 1.911357 TGATGCCTCATCACCACTCTT 59.089 47.619 5.48 0.00 44.60 2.85
4967 6974 3.106827 TGATGCCTCATCACCACTCTTA 58.893 45.455 5.48 0.00 44.60 2.10
4968 6975 3.118629 TGATGCCTCATCACCACTCTTAC 60.119 47.826 5.48 0.00 44.60 2.34
4969 6976 2.540383 TGCCTCATCACCACTCTTACT 58.460 47.619 0.00 0.00 0.00 2.24
4970 6977 2.234661 TGCCTCATCACCACTCTTACTG 59.765 50.000 0.00 0.00 0.00 2.74
4971 6978 2.234908 GCCTCATCACCACTCTTACTGT 59.765 50.000 0.00 0.00 0.00 3.55
4972 6979 3.307059 GCCTCATCACCACTCTTACTGTT 60.307 47.826 0.00 0.00 0.00 3.16
4973 6980 4.248859 CCTCATCACCACTCTTACTGTTG 58.751 47.826 0.00 0.00 0.00 3.33
4974 6981 4.262635 CCTCATCACCACTCTTACTGTTGT 60.263 45.833 0.00 0.00 0.00 3.32
4975 6982 5.047306 CCTCATCACCACTCTTACTGTTGTA 60.047 44.000 0.00 0.00 0.00 2.41
4976 6983 6.413783 TCATCACCACTCTTACTGTTGTAA 57.586 37.500 0.00 0.00 37.16 2.41
4977 6984 6.822442 TCATCACCACTCTTACTGTTGTAAA 58.178 36.000 0.00 0.00 38.09 2.01
4991 6998 3.924610 GTTGTAAACCTCGCGATGATTC 58.075 45.455 18.54 7.44 42.21 2.52
4992 6999 3.239587 TGTAAACCTCGCGATGATTCA 57.760 42.857 18.54 9.64 0.00 2.57
4993 7000 3.591023 TGTAAACCTCGCGATGATTCAA 58.409 40.909 18.54 2.10 0.00 2.69
4994 7001 4.188462 TGTAAACCTCGCGATGATTCAAT 58.812 39.130 18.54 0.00 0.00 2.57
4995 7002 3.951979 AAACCTCGCGATGATTCAATC 57.048 42.857 18.54 0.00 0.00 2.67
4996 7003 1.871080 ACCTCGCGATGATTCAATCC 58.129 50.000 18.54 0.00 0.00 3.01
4997 7004 1.151668 CCTCGCGATGATTCAATCCC 58.848 55.000 10.36 0.00 0.00 3.85
4998 7005 0.786581 CTCGCGATGATTCAATCCCG 59.213 55.000 10.36 0.03 30.80 5.14
4999 7006 0.104120 TCGCGATGATTCAATCCCGT 59.896 50.000 3.71 0.00 31.41 5.28
5000 7007 0.937304 CGCGATGATTCAATCCCGTT 59.063 50.000 0.00 0.00 0.00 4.44
5001 7008 1.070577 CGCGATGATTCAATCCCGTTC 60.071 52.381 0.00 0.00 0.00 3.95
5002 7009 1.070577 GCGATGATTCAATCCCGTTCG 60.071 52.381 9.95 7.58 0.00 3.95
5003 7010 2.469826 CGATGATTCAATCCCGTTCGA 58.530 47.619 0.00 0.00 0.00 3.71
5004 7011 2.863740 CGATGATTCAATCCCGTTCGAA 59.136 45.455 0.00 0.00 0.00 3.71
5005 7012 3.494626 CGATGATTCAATCCCGTTCGAAT 59.505 43.478 0.00 0.00 0.00 3.34
5006 7013 4.024893 CGATGATTCAATCCCGTTCGAATT 60.025 41.667 0.00 0.00 0.00 2.17
5007 7014 4.875544 TGATTCAATCCCGTTCGAATTC 57.124 40.909 0.00 0.00 0.00 2.17
5008 7015 4.257731 TGATTCAATCCCGTTCGAATTCA 58.742 39.130 0.00 0.00 0.00 2.57
5009 7016 4.697828 TGATTCAATCCCGTTCGAATTCAA 59.302 37.500 0.00 0.00 0.00 2.69
5010 7017 5.182190 TGATTCAATCCCGTTCGAATTCAAA 59.818 36.000 0.00 0.00 0.00 2.69
5011 7018 5.637006 TTCAATCCCGTTCGAATTCAAAT 57.363 34.783 0.00 0.00 0.00 2.32
5012 7019 5.637006 TCAATCCCGTTCGAATTCAAATT 57.363 34.783 0.00 0.00 0.00 1.82
5013 7020 6.019779 TCAATCCCGTTCGAATTCAAATTT 57.980 33.333 0.00 0.00 0.00 1.82
5014 7021 6.090129 TCAATCCCGTTCGAATTCAAATTTC 58.910 36.000 0.00 0.00 0.00 2.17
5015 7022 5.637006 ATCCCGTTCGAATTCAAATTTCA 57.363 34.783 0.00 0.00 0.00 2.69
5016 7023 5.440234 TCCCGTTCGAATTCAAATTTCAA 57.560 34.783 0.00 0.00 0.00 2.69
5017 7024 5.833082 TCCCGTTCGAATTCAAATTTCAAA 58.167 33.333 0.00 0.00 0.00 2.69
5018 7025 6.273825 TCCCGTTCGAATTCAAATTTCAAAA 58.726 32.000 0.00 0.00 0.00 2.44
5019 7026 6.926272 TCCCGTTCGAATTCAAATTTCAAAAT 59.074 30.769 0.00 0.00 0.00 1.82
5020 7027 7.115663 TCCCGTTCGAATTCAAATTTCAAAATC 59.884 33.333 0.00 0.00 0.00 2.17
5021 7028 7.095857 CCCGTTCGAATTCAAATTTCAAAATCA 60.096 33.333 0.00 0.00 0.00 2.57
5022 7029 8.272176 CCGTTCGAATTCAAATTTCAAAATCAA 58.728 29.630 0.00 0.00 0.00 2.57
5023 7030 9.630310 CGTTCGAATTCAAATTTCAAAATCAAA 57.370 25.926 0.00 0.00 0.00 2.69
5025 7032 9.649024 TTCGAATTCAAATTTCAAAATCAAAGC 57.351 25.926 6.22 0.00 0.00 3.51
5026 7033 8.824781 TCGAATTCAAATTTCAAAATCAAAGCA 58.175 25.926 6.22 0.00 0.00 3.91
5027 7034 9.435802 CGAATTCAAATTTCAAAATCAAAGCAA 57.564 25.926 6.22 0.00 0.00 3.91
5031 7038 9.903682 TTCAAATTTCAAAATCAAAGCAAACAA 57.096 22.222 0.00 0.00 0.00 2.83
5074 7081 1.880027 ACAAAAGTGTTCGGGAGATGC 59.120 47.619 0.00 0.00 39.57 3.91
5075 7082 1.200020 CAAAAGTGTTCGGGAGATGCC 59.800 52.381 0.00 0.00 39.57 4.40
5076 7083 0.400213 AAAGTGTTCGGGAGATGCCA 59.600 50.000 0.00 0.00 39.57 4.92
5077 7084 0.620556 AAGTGTTCGGGAGATGCCAT 59.379 50.000 0.00 0.00 39.57 4.40
5078 7085 1.496060 AGTGTTCGGGAGATGCCATA 58.504 50.000 0.00 0.00 39.57 2.74
5079 7086 2.050144 AGTGTTCGGGAGATGCCATAT 58.950 47.619 0.00 0.00 39.57 1.78
5080 7087 2.439507 AGTGTTCGGGAGATGCCATATT 59.560 45.455 0.00 0.00 39.57 1.28
5081 7088 3.117888 AGTGTTCGGGAGATGCCATATTT 60.118 43.478 0.00 0.00 39.57 1.40
5082 7089 3.632145 GTGTTCGGGAGATGCCATATTTT 59.368 43.478 0.00 0.00 39.57 1.82
5083 7090 4.819630 GTGTTCGGGAGATGCCATATTTTA 59.180 41.667 0.00 0.00 39.57 1.52
5084 7091 4.819630 TGTTCGGGAGATGCCATATTTTAC 59.180 41.667 0.00 0.00 39.57 2.01
5085 7092 4.698201 TCGGGAGATGCCATATTTTACA 57.302 40.909 0.00 0.00 38.95 2.41
5086 7093 5.241403 TCGGGAGATGCCATATTTTACAT 57.759 39.130 0.00 0.00 38.95 2.29
5087 7094 6.367374 TCGGGAGATGCCATATTTTACATA 57.633 37.500 0.00 0.00 38.95 2.29
5088 7095 6.774673 TCGGGAGATGCCATATTTTACATAA 58.225 36.000 0.00 0.00 38.95 1.90
5089 7096 6.878923 TCGGGAGATGCCATATTTTACATAAG 59.121 38.462 0.00 0.00 38.95 1.73
5090 7097 6.655003 CGGGAGATGCCATATTTTACATAAGT 59.345 38.462 0.00 0.00 38.95 2.24
5091 7098 7.148407 CGGGAGATGCCATATTTTACATAAGTC 60.148 40.741 0.00 0.00 38.95 3.01
5092 7099 7.665559 GGGAGATGCCATATTTTACATAAGTCA 59.334 37.037 0.00 0.00 38.95 3.41
5093 7100 9.066892 GGAGATGCCATATTTTACATAAGTCAA 57.933 33.333 0.00 0.00 36.34 3.18
5205 7212 8.317891 ACTAACAAAACAAAACAAAAAGAGGG 57.682 30.769 0.00 0.00 0.00 4.30
5206 7213 8.151596 ACTAACAAAACAAAACAAAAAGAGGGA 58.848 29.630 0.00 0.00 0.00 4.20
5207 7214 7.809546 AACAAAACAAAACAAAAAGAGGGAA 57.190 28.000 0.00 0.00 0.00 3.97
5208 7215 7.197071 ACAAAACAAAACAAAAAGAGGGAAC 57.803 32.000 0.00 0.00 0.00 3.62
5226 7233 4.798682 CCCCTCCCACGGCCTACT 62.799 72.222 0.00 0.00 0.00 2.57
5227 7234 3.470888 CCCTCCCACGGCCTACTG 61.471 72.222 0.00 0.00 0.00 2.74
5228 7235 3.470888 CCTCCCACGGCCTACTGG 61.471 72.222 0.00 2.23 0.00 4.00
5246 7253 3.809013 CCTAGTTGGCCGGCCCAT 61.809 66.667 41.75 28.54 44.89 4.00
5247 7254 2.275418 CTAGTTGGCCGGCCCATT 59.725 61.111 41.75 30.12 44.89 3.16
5248 7255 1.823899 CTAGTTGGCCGGCCCATTC 60.824 63.158 41.75 26.88 44.89 2.67
5249 7256 3.690685 TAGTTGGCCGGCCCATTCG 62.691 63.158 41.75 0.00 44.89 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 20 5.235516 ACCAACGAAGATAACCTACAACTG 58.764 41.667 0.00 0.00 0.00 3.16
21 23 6.839124 TCTACCAACGAAGATAACCTACAA 57.161 37.500 0.00 0.00 0.00 2.41
31 33 6.400568 ACCGATTAAAATCTACCAACGAAGA 58.599 36.000 0.00 0.00 33.24 2.87
35 37 6.411630 TGAACCGATTAAAATCTACCAACG 57.588 37.500 1.52 0.00 33.24 4.10
49 51 2.280628 GAAGCCGAAGATGAACCGATT 58.719 47.619 0.00 0.00 0.00 3.34
53 55 0.391263 ACCGAAGCCGAAGATGAACC 60.391 55.000 0.00 0.00 38.22 3.62
68 70 1.964933 TGGTGTTGTCATCACTACCGA 59.035 47.619 12.61 0.00 34.50 4.69
88 90 4.514401 GATTTGGAGACACCTTATTCGGT 58.486 43.478 0.00 0.00 42.67 4.69
94 99 4.263331 GGTCAAGGATTTGGAGACACCTTA 60.263 45.833 0.00 0.00 41.09 2.69
95 100 3.498661 GGTCAAGGATTTGGAGACACCTT 60.499 47.826 0.00 0.00 43.10 3.50
96 101 2.040412 GGTCAAGGATTTGGAGACACCT 59.960 50.000 0.00 0.00 42.67 4.00
114 119 1.474077 GTGGAATCTGGCATGTTGGTC 59.526 52.381 0.00 0.00 0.00 4.02
124 129 0.459899 TCGACGATGGTGGAATCTGG 59.540 55.000 0.00 0.00 0.00 3.86
141 146 4.509230 AGAAACATCATCATGGATTCGTCG 59.491 41.667 0.00 0.00 36.12 5.12
146 151 5.039920 TCGGAGAAACATCATCATGGATT 57.960 39.130 0.00 0.00 33.82 3.01
156 161 1.137282 GACCCCTCTCGGAGAAACATC 59.863 57.143 9.32 1.74 34.09 3.06
157 162 1.196012 GACCCCTCTCGGAGAAACAT 58.804 55.000 9.32 0.00 34.09 2.71
162 167 1.677966 CGTTGACCCCTCTCGGAGA 60.678 63.158 7.60 7.60 0.00 3.71
188 193 5.029474 AGGAAAAAGCTCTAGGTCATCTCT 58.971 41.667 0.00 0.00 0.00 3.10
190 195 4.163268 GGAGGAAAAAGCTCTAGGTCATCT 59.837 45.833 0.00 0.00 0.00 2.90
209 214 2.415825 TCGATAGGCGAGTTGGAGG 58.584 57.895 0.00 0.00 45.59 4.30
221 226 7.441760 ACACTAGAGTACACATTACCTCGATAG 59.558 40.741 0.00 0.00 0.00 2.08
223 228 6.120905 ACACTAGAGTACACATTACCTCGAT 58.879 40.000 0.00 0.00 0.00 3.59
242 247 1.684450 TGAAGCTCCACAACGACACTA 59.316 47.619 0.00 0.00 0.00 2.74
302 307 1.832883 TGTAAGCCAACATTGCCGAT 58.167 45.000 0.00 0.00 0.00 4.18
354 359 2.275089 CCGCCATCATTCCACCCA 59.725 61.111 0.00 0.00 0.00 4.51
363 368 2.745308 CCACTGGATCCCGCCATCA 61.745 63.158 9.90 0.00 37.30 3.07
372 377 1.817209 GTCGAGGGACCACTGGATC 59.183 63.158 0.71 0.00 37.19 3.36
373 378 2.052690 CGTCGAGGGACCACTGGAT 61.053 63.158 0.71 0.00 40.17 3.41
376 381 1.595993 ATGTCGTCGAGGGACCACTG 61.596 60.000 12.56 0.00 40.17 3.66
377 382 0.898789 AATGTCGTCGAGGGACCACT 60.899 55.000 12.56 0.00 40.17 4.00
378 383 0.736325 CAATGTCGTCGAGGGACCAC 60.736 60.000 12.56 1.67 40.17 4.16
379 384 1.183030 ACAATGTCGTCGAGGGACCA 61.183 55.000 12.56 5.15 40.17 4.02
381 386 1.352156 GCACAATGTCGTCGAGGGAC 61.352 60.000 5.12 7.40 39.89 4.46
382 387 1.080093 GCACAATGTCGTCGAGGGA 60.080 57.895 5.12 0.00 0.00 4.20
383 388 2.444624 CGCACAATGTCGTCGAGGG 61.445 63.158 5.12 0.00 0.00 4.30
400 406 0.603569 CATCGGATCTACCTTCCCCG 59.396 60.000 0.00 0.00 41.36 5.73
403 409 1.269998 CGTCCATCGGATCTACCTTCC 59.730 57.143 0.00 0.00 32.73 3.46
417 423 0.690077 GTCCTAGGAACCCCGTCCAT 60.690 60.000 14.65 0.00 40.48 3.41
422 428 1.679977 TGTCGTCCTAGGAACCCCG 60.680 63.158 14.65 13.16 37.58 5.73
472 480 7.604164 AGCTTTGAGAATCGATGAAGAAAACTA 59.396 33.333 0.00 0.00 38.61 2.24
509 523 0.868406 CAAAGAACTGTCGGTGCTCC 59.132 55.000 0.00 0.00 31.23 4.70
510 524 0.868406 CCAAAGAACTGTCGGTGCTC 59.132 55.000 0.00 0.00 31.23 4.26
511 525 1.166531 GCCAAAGAACTGTCGGTGCT 61.167 55.000 0.00 0.00 34.69 4.40
512 526 1.166531 AGCCAAAGAACTGTCGGTGC 61.167 55.000 0.00 0.00 0.00 5.01
530 544 3.368323 GGAGAAGAGACAAGCTCCTTCAG 60.368 52.174 0.00 0.00 45.10 3.02
533 547 1.905894 GGGAGAAGAGACAAGCTCCTT 59.094 52.381 0.00 0.00 45.10 3.36
551 565 2.125147 TTCATCGCCGCTGAAGGG 60.125 61.111 0.00 0.00 0.00 3.95
588 602 1.380302 CAACAAGGTCCCTGGGGAG 59.620 63.158 14.00 0.00 46.16 4.30
589 603 1.386772 ACAACAAGGTCCCTGGGGA 60.387 57.895 14.00 3.92 42.90 4.81
608 628 9.690434 GAAACACATCTCACGTAATAGAAAATC 57.310 33.333 0.00 0.00 0.00 2.17
656 676 3.823330 CGAACCGACGAGAGGGGG 61.823 72.222 0.00 0.00 33.66 5.40
709 729 3.612423 TGTACATTCAATCGAGCGTCAAG 59.388 43.478 0.00 0.00 0.00 3.02
711 731 2.921121 GTGTACATTCAATCGAGCGTCA 59.079 45.455 0.00 0.00 0.00 4.35
776 816 5.936956 CCAAATTTGCCTTTTTGTAGCCATA 59.063 36.000 12.92 0.00 32.23 2.74
779 819 3.058293 GCCAAATTTGCCTTTTTGTAGCC 60.058 43.478 12.92 0.00 32.23 3.93
780 820 3.563390 TGCCAAATTTGCCTTTTTGTAGC 59.437 39.130 12.92 7.15 32.23 3.58
807 847 1.276705 GGTCCACCTTCCTCTTGTCTC 59.723 57.143 0.00 0.00 0.00 3.36
825 865 5.669164 TTGCTAAAAACTTCAAACAGGGT 57.331 34.783 0.00 0.00 0.00 4.34
902 942 2.021457 GCGGCAATTAGGTATGGTTGT 58.979 47.619 0.00 0.00 0.00 3.32
911 951 4.554723 CGATTAAAGGAAGCGGCAATTAGG 60.555 45.833 1.45 0.00 43.21 2.69
934 974 1.519455 CCTCGTCGGTGAGATTGGC 60.519 63.158 6.42 0.00 38.28 4.52
967 1007 1.687660 GGGAGGGAGACGAGGTATTTC 59.312 57.143 0.00 0.00 0.00 2.17
1144 1184 4.568876 CGAAACATACCGCGCGCC 62.569 66.667 27.36 8.11 0.00 6.53
1172 1213 1.667830 CGCTCTGCCAAGAAACGGA 60.668 57.895 0.00 0.00 31.57 4.69
1262 1303 2.423898 GCCTTCCCGATCAGACCGA 61.424 63.158 0.00 0.00 0.00 4.69
1264 1305 0.462759 CAAGCCTTCCCGATCAGACC 60.463 60.000 0.00 0.00 0.00 3.85
1451 1492 4.810790 AGAAACAGTTAGATCTCACACCG 58.189 43.478 9.64 0.60 0.00 4.94
1502 1543 1.492319 GCACCAAGCACGAACACGTA 61.492 55.000 0.00 0.00 44.79 3.57
1558 1600 0.310543 GCATGTGCACAACCGAAGAA 59.689 50.000 25.72 0.00 41.59 2.52
1563 1605 2.174107 CGAGCATGTGCACAACCG 59.826 61.111 25.72 19.31 45.16 4.44
1578 1620 6.288941 TCTGGTGTTAATAATCTGAACCGA 57.711 37.500 0.00 0.00 0.00 4.69
1656 1711 6.453003 GCTGCGACGAATCACAATATATACAG 60.453 42.308 0.00 0.00 0.00 2.74
1657 1712 5.344933 GCTGCGACGAATCACAATATATACA 59.655 40.000 0.00 0.00 0.00 2.29
1658 1713 5.344933 TGCTGCGACGAATCACAATATATAC 59.655 40.000 0.00 0.00 0.00 1.47
1659 1714 5.465935 TGCTGCGACGAATCACAATATATA 58.534 37.500 0.00 0.00 0.00 0.86
1660 1715 4.306600 TGCTGCGACGAATCACAATATAT 58.693 39.130 0.00 0.00 0.00 0.86
1781 1836 2.248487 GGTAGCTACACAACTCGTTCG 58.752 52.381 24.75 0.00 0.00 3.95
1811 1876 1.003580 CCAGGACATGCTACACAACCT 59.996 52.381 0.00 0.00 32.91 3.50
1874 1939 1.563111 CAGGCAGCACAAACAAACAG 58.437 50.000 0.00 0.00 0.00 3.16
1919 1984 5.500645 ACCAAGTCAAAGCTAACAAGTTC 57.499 39.130 0.00 0.00 0.00 3.01
1982 2074 8.584157 ACTGGTATCTCATATTCTCATTCACTC 58.416 37.037 0.00 0.00 0.00 3.51
2033 2125 3.379240 TGCAAAACACAATTCCATGTCG 58.621 40.909 0.00 0.00 0.00 4.35
2108 2200 4.394920 TCGAAAAACTTCATCCATAGTGCC 59.605 41.667 0.00 0.00 0.00 5.01
2271 2363 6.462487 GGAATCCTGACAATGGTACGAGAATA 60.462 42.308 0.00 0.00 0.00 1.75
2285 2377 7.861629 AGTGAATTAACTATGGAATCCTGACA 58.138 34.615 0.00 0.00 0.00 3.58
2297 2389 6.595716 GTGCAGAACTGGAGTGAATTAACTAT 59.404 38.462 0.00 0.00 0.00 2.12
2392 2489 3.056952 AGTAACTATTGTCGTACCGCG 57.943 47.619 0.00 0.00 43.01 6.46
2564 2666 4.213482 AGACGTAAAAGGACAATTCAGCAC 59.787 41.667 0.00 0.00 0.00 4.40
2786 2891 4.219944 AGCATTGAGTTGCAAATCAGTCAT 59.780 37.500 26.36 16.38 45.23 3.06
2836 2941 2.541346 AGCGATGCAAGTCGTGATAATG 59.459 45.455 11.09 0.00 43.27 1.90
2897 3002 2.270923 GCCAGGAAATTTCGATTTGGC 58.729 47.619 25.31 25.31 0.00 4.52
2898 3003 3.591196 TGCCAGGAAATTTCGATTTGG 57.409 42.857 18.05 18.05 0.00 3.28
3022 3128 2.094957 AGACCACACAACAAAAACGGTG 60.095 45.455 0.00 0.00 37.29 4.94
3026 3133 5.705902 ACTACAAGACCACACAACAAAAAC 58.294 37.500 0.00 0.00 0.00 2.43
3031 3138 2.769663 AGGACTACAAGACCACACAACA 59.230 45.455 0.00 0.00 32.35 3.33
3034 3141 4.202284 GGTTAAGGACTACAAGACCACACA 60.202 45.833 0.00 0.00 32.35 3.72
3042 3149 4.222145 TGGTAGCTGGTTAAGGACTACAAG 59.778 45.833 0.00 0.00 35.91 3.16
3201 3308 6.795098 ACGTTAGATGTGTAATTGAAAGCA 57.205 33.333 0.00 0.00 0.00 3.91
3237 3344 1.113788 AGTTTGCCAAAGCTGCTTCA 58.886 45.000 16.28 6.76 40.80 3.02
3300 3407 4.036734 ACAAGACGATGAAAAACTGCACAT 59.963 37.500 0.00 0.00 0.00 3.21
3439 3546 3.370978 ACGGATCATGAAGCAAAACGTAG 59.629 43.478 0.00 0.00 0.00 3.51
3460 3567 5.392057 GCCAAGTATGTTTCTCCAGCTAAAC 60.392 44.000 3.35 3.35 36.38 2.01
3688 3795 7.525688 TCTTTTGACTGCAATATAGAGAACG 57.474 36.000 0.00 0.00 33.25 3.95
3697 3804 5.689383 GTCACCTTCTTTTGACTGCAATA 57.311 39.130 0.00 0.00 39.30 1.90
3747 3854 3.960102 TCACCTCCATTTTCAACTTTGCT 59.040 39.130 0.00 0.00 0.00 3.91
3825 3932 3.062234 CCGCCGTCTAAGAGACAAAATTC 59.938 47.826 7.36 0.00 45.30 2.17
3831 3938 0.738975 CATCCGCCGTCTAAGAGACA 59.261 55.000 7.36 0.00 45.30 3.41
3994 4156 9.149225 CAATATCTGCTATCTAGTTTCATGGTC 57.851 37.037 0.00 0.00 0.00 4.02
4067 4229 1.961277 GCAGACCAGTGTCCCAACG 60.961 63.158 0.00 0.00 42.81 4.10
4434 6405 5.182001 AGTTGCTAGCTCATTACAGTTTTGG 59.818 40.000 17.23 0.00 0.00 3.28
4512 6483 3.797039 TGGCGAGTTAAATGAGAGATGG 58.203 45.455 0.00 0.00 0.00 3.51
4542 6513 2.412870 TGCATTGTACGGAACTGACAG 58.587 47.619 0.00 0.00 0.00 3.51
4554 6525 4.946445 CCATTTGGTATGCATGCATTGTA 58.054 39.130 36.23 17.76 37.82 2.41
4570 6541 2.621055 TGAAGAACCGGTGAACCATTTG 59.379 45.455 8.52 0.00 35.14 2.32
4679 6657 0.260230 TTTCCACAAGGGGCTGTTGA 59.740 50.000 6.41 0.00 37.22 3.18
4691 6669 3.576078 AGGTTGAGTGATGTTTCCACA 57.424 42.857 0.00 0.00 37.01 4.17
4693 6671 3.068024 GCAAAGGTTGAGTGATGTTTCCA 59.932 43.478 0.00 0.00 0.00 3.53
4847 6854 4.777463 AGCTAGGTTGTTTAGTTGTGTGT 58.223 39.130 0.00 0.00 0.00 3.72
4852 6859 8.870879 GTCATAGTTAGCTAGGTTGTTTAGTTG 58.129 37.037 0.00 0.00 31.54 3.16
4864 6871 5.915758 CACCGCTTTAGTCATAGTTAGCTAG 59.084 44.000 0.00 0.00 0.00 3.42
4907 6914 1.878102 GCTTGATTATCCGGGCGTCAT 60.878 52.381 0.00 0.00 0.00 3.06
4908 6915 0.531974 GCTTGATTATCCGGGCGTCA 60.532 55.000 0.00 0.00 0.00 4.35
4909 6916 0.249911 AGCTTGATTATCCGGGCGTC 60.250 55.000 0.00 0.00 0.00 5.19
4910 6917 1.045407 TAGCTTGATTATCCGGGCGT 58.955 50.000 0.00 0.00 0.00 5.68
4911 6918 1.270094 TGTAGCTTGATTATCCGGGCG 60.270 52.381 0.00 0.00 0.00 6.13
4912 6919 2.224305 ACTGTAGCTTGATTATCCGGGC 60.224 50.000 0.00 0.00 0.00 6.13
4913 6920 3.753294 ACTGTAGCTTGATTATCCGGG 57.247 47.619 0.00 0.00 0.00 5.73
4914 6921 4.989168 GGTTACTGTAGCTTGATTATCCGG 59.011 45.833 0.00 0.00 0.00 5.14
4915 6922 5.844004 AGGTTACTGTAGCTTGATTATCCG 58.156 41.667 0.00 0.00 0.00 4.18
4916 6923 6.926272 CAGAGGTTACTGTAGCTTGATTATCC 59.074 42.308 0.00 0.00 33.73 2.59
4917 6924 6.422400 GCAGAGGTTACTGTAGCTTGATTATC 59.578 42.308 0.00 0.00 39.73 1.75
4918 6925 6.098982 AGCAGAGGTTACTGTAGCTTGATTAT 59.901 38.462 0.00 0.00 39.73 1.28
4919 6926 5.422331 AGCAGAGGTTACTGTAGCTTGATTA 59.578 40.000 0.00 0.00 39.73 1.75
4920 6927 4.223923 AGCAGAGGTTACTGTAGCTTGATT 59.776 41.667 0.00 0.00 39.73 2.57
4921 6928 3.772025 AGCAGAGGTTACTGTAGCTTGAT 59.228 43.478 0.00 0.00 39.73 2.57
4922 6929 3.165875 AGCAGAGGTTACTGTAGCTTGA 58.834 45.455 0.00 0.00 39.73 3.02
4923 6930 3.601443 AGCAGAGGTTACTGTAGCTTG 57.399 47.619 0.00 0.74 39.73 4.01
4924 6931 5.422331 TCATTAGCAGAGGTTACTGTAGCTT 59.578 40.000 0.00 0.00 39.73 3.74
4925 6932 4.956700 TCATTAGCAGAGGTTACTGTAGCT 59.043 41.667 1.71 0.00 39.73 3.32
4926 6933 5.263968 TCATTAGCAGAGGTTACTGTAGC 57.736 43.478 0.00 0.00 39.73 3.58
4927 6934 5.694006 GCATCATTAGCAGAGGTTACTGTAG 59.306 44.000 0.00 0.00 39.73 2.74
4928 6935 5.453339 GGCATCATTAGCAGAGGTTACTGTA 60.453 44.000 0.00 0.00 39.73 2.74
4929 6936 4.446371 GCATCATTAGCAGAGGTTACTGT 58.554 43.478 0.00 0.00 39.73 3.55
4930 6937 3.812053 GGCATCATTAGCAGAGGTTACTG 59.188 47.826 0.00 0.00 40.43 2.74
4931 6938 3.713764 AGGCATCATTAGCAGAGGTTACT 59.286 43.478 0.00 0.00 0.00 2.24
4932 6939 4.061596 GAGGCATCATTAGCAGAGGTTAC 58.938 47.826 0.00 0.00 0.00 2.50
4933 6940 3.711190 TGAGGCATCATTAGCAGAGGTTA 59.289 43.478 0.00 0.00 0.00 2.85
4934 6941 2.507058 TGAGGCATCATTAGCAGAGGTT 59.493 45.455 0.00 0.00 0.00 3.50
4935 6942 2.121948 TGAGGCATCATTAGCAGAGGT 58.878 47.619 0.00 0.00 0.00 3.85
4936 6943 2.924757 TGAGGCATCATTAGCAGAGG 57.075 50.000 0.00 0.00 0.00 3.69
4937 6944 4.004196 TGATGAGGCATCATTAGCAGAG 57.996 45.455 16.04 0.00 46.39 3.35
4946 6953 1.576577 AGAGTGGTGATGAGGCATCA 58.423 50.000 2.36 2.36 46.84 3.07
4947 6954 2.706339 AAGAGTGGTGATGAGGCATC 57.294 50.000 0.00 0.00 40.88 3.91
4948 6955 3.110705 AGTAAGAGTGGTGATGAGGCAT 58.889 45.455 0.00 0.00 0.00 4.40
4949 6956 2.234661 CAGTAAGAGTGGTGATGAGGCA 59.765 50.000 0.00 0.00 0.00 4.75
4950 6957 2.234908 ACAGTAAGAGTGGTGATGAGGC 59.765 50.000 0.00 0.00 0.00 4.70
4951 6958 4.248859 CAACAGTAAGAGTGGTGATGAGG 58.751 47.826 0.00 0.00 38.50 3.86
4952 6959 4.887748 ACAACAGTAAGAGTGGTGATGAG 58.112 43.478 6.35 0.00 38.50 2.90
4953 6960 4.955811 ACAACAGTAAGAGTGGTGATGA 57.044 40.909 6.35 0.00 38.50 2.92
4954 6961 6.073222 GGTTTACAACAGTAAGAGTGGTGATG 60.073 42.308 6.35 0.00 38.50 3.07
4955 6962 5.995897 GGTTTACAACAGTAAGAGTGGTGAT 59.004 40.000 6.35 0.00 38.50 3.06
4956 6963 5.129815 AGGTTTACAACAGTAAGAGTGGTGA 59.870 40.000 6.35 0.00 38.50 4.02
4957 6964 5.365619 AGGTTTACAACAGTAAGAGTGGTG 58.634 41.667 0.00 0.00 41.88 4.17
4958 6965 5.608449 GAGGTTTACAACAGTAAGAGTGGT 58.392 41.667 0.00 0.00 0.00 4.16
4959 6966 4.684703 CGAGGTTTACAACAGTAAGAGTGG 59.315 45.833 0.00 0.00 0.00 4.00
4960 6967 4.150098 GCGAGGTTTACAACAGTAAGAGTG 59.850 45.833 0.00 0.00 0.00 3.51
4961 6968 4.304939 GCGAGGTTTACAACAGTAAGAGT 58.695 43.478 0.00 0.00 0.00 3.24
4962 6969 3.364023 CGCGAGGTTTACAACAGTAAGAG 59.636 47.826 0.00 0.00 0.00 2.85
4963 6970 3.004629 TCGCGAGGTTTACAACAGTAAGA 59.995 43.478 3.71 0.00 0.00 2.10
4964 6971 3.311106 TCGCGAGGTTTACAACAGTAAG 58.689 45.455 3.71 0.00 0.00 2.34
4965 6972 3.367992 TCGCGAGGTTTACAACAGTAA 57.632 42.857 3.71 0.00 0.00 2.24
4966 6973 3.057386 TCATCGCGAGGTTTACAACAGTA 60.057 43.478 21.22 0.00 0.00 2.74
4967 6974 2.066262 CATCGCGAGGTTTACAACAGT 58.934 47.619 16.66 0.00 0.00 3.55
4968 6975 2.333926 TCATCGCGAGGTTTACAACAG 58.666 47.619 21.22 0.00 0.00 3.16
4969 6976 2.442212 TCATCGCGAGGTTTACAACA 57.558 45.000 21.22 0.00 0.00 3.33
4970 6977 3.369756 TGAATCATCGCGAGGTTTACAAC 59.630 43.478 21.22 7.27 0.00 3.32
4971 6978 3.591023 TGAATCATCGCGAGGTTTACAA 58.409 40.909 21.22 0.00 0.00 2.41
4972 6979 3.239587 TGAATCATCGCGAGGTTTACA 57.760 42.857 21.22 14.56 0.00 2.41
4973 6980 4.318831 GGATTGAATCATCGCGAGGTTTAC 60.319 45.833 21.22 12.41 0.00 2.01
4974 6981 3.807622 GGATTGAATCATCGCGAGGTTTA 59.192 43.478 21.22 8.36 0.00 2.01
4975 6982 2.614057 GGATTGAATCATCGCGAGGTTT 59.386 45.455 21.22 18.50 0.00 3.27
4976 6983 2.213499 GGATTGAATCATCGCGAGGTT 58.787 47.619 21.22 13.85 0.00 3.50
4977 6984 1.541233 GGGATTGAATCATCGCGAGGT 60.541 52.381 21.22 1.34 0.00 3.85
4978 6985 1.151668 GGGATTGAATCATCGCGAGG 58.848 55.000 15.81 15.81 0.00 4.63
4982 6989 1.070577 CGAACGGGATTGAATCATCGC 60.071 52.381 16.12 4.71 33.09 4.58
4983 6990 2.469826 TCGAACGGGATTGAATCATCG 58.530 47.619 15.10 15.10 34.96 3.84
4984 6991 5.007626 TGAATTCGAACGGGATTGAATCATC 59.992 40.000 7.56 0.00 31.06 2.92
4985 6992 4.881273 TGAATTCGAACGGGATTGAATCAT 59.119 37.500 7.56 0.00 31.06 2.45
4986 6993 4.257731 TGAATTCGAACGGGATTGAATCA 58.742 39.130 7.56 0.00 31.06 2.57
4987 6994 4.875544 TGAATTCGAACGGGATTGAATC 57.124 40.909 0.00 0.00 31.06 2.52
4988 6995 5.637006 TTTGAATTCGAACGGGATTGAAT 57.363 34.783 0.00 0.00 32.69 2.57
4989 6996 5.637006 ATTTGAATTCGAACGGGATTGAA 57.363 34.783 10.38 0.00 0.00 2.69
4990 6997 5.637006 AATTTGAATTCGAACGGGATTGA 57.363 34.783 10.38 0.00 0.00 2.57
4991 6998 5.861251 TGAAATTTGAATTCGAACGGGATTG 59.139 36.000 10.38 0.00 0.00 2.67
4992 6999 6.019779 TGAAATTTGAATTCGAACGGGATT 57.980 33.333 10.38 0.00 0.00 3.01
4993 7000 5.637006 TGAAATTTGAATTCGAACGGGAT 57.363 34.783 10.38 0.00 0.00 3.85
4994 7001 5.440234 TTGAAATTTGAATTCGAACGGGA 57.560 34.783 10.38 0.00 0.00 5.14
4995 7002 6.517914 TTTTGAAATTTGAATTCGAACGGG 57.482 33.333 10.38 0.00 31.53 5.28
4996 7003 7.782242 TGATTTTGAAATTTGAATTCGAACGG 58.218 30.769 10.38 0.00 31.53 4.44
4997 7004 9.630310 TTTGATTTTGAAATTTGAATTCGAACG 57.370 25.926 10.38 0.00 31.53 3.95
4999 7006 9.649024 GCTTTGATTTTGAAATTTGAATTCGAA 57.351 25.926 10.57 10.57 0.00 3.71
5000 7007 8.824781 TGCTTTGATTTTGAAATTTGAATTCGA 58.175 25.926 0.00 0.00 0.00 3.71
5001 7008 8.990722 TGCTTTGATTTTGAAATTTGAATTCG 57.009 26.923 0.00 0.00 0.00 3.34
5005 7012 9.903682 TTGTTTGCTTTGATTTTGAAATTTGAA 57.096 22.222 0.00 0.00 0.00 2.69
5041 7048 9.813080 CCGAACACTTTTGTTTTAAATTTTGAA 57.187 25.926 0.00 0.00 46.43 2.69
5042 7049 8.443937 CCCGAACACTTTTGTTTTAAATTTTGA 58.556 29.630 0.00 0.00 46.43 2.69
5043 7050 8.443937 TCCCGAACACTTTTGTTTTAAATTTTG 58.556 29.630 0.00 0.00 46.43 2.44
5044 7051 8.549338 TCCCGAACACTTTTGTTTTAAATTTT 57.451 26.923 0.00 0.00 46.43 1.82
5045 7052 8.035984 TCTCCCGAACACTTTTGTTTTAAATTT 58.964 29.630 0.00 0.00 46.43 1.82
5046 7053 7.548967 TCTCCCGAACACTTTTGTTTTAAATT 58.451 30.769 0.00 0.00 46.43 1.82
5047 7054 7.102847 TCTCCCGAACACTTTTGTTTTAAAT 57.897 32.000 0.00 0.00 46.43 1.40
5048 7055 6.512342 TCTCCCGAACACTTTTGTTTTAAA 57.488 33.333 0.00 0.00 46.43 1.52
5049 7056 6.500041 CATCTCCCGAACACTTTTGTTTTAA 58.500 36.000 0.00 0.00 46.43 1.52
5050 7057 5.506649 GCATCTCCCGAACACTTTTGTTTTA 60.507 40.000 0.00 0.00 46.43 1.52
5051 7058 4.736464 GCATCTCCCGAACACTTTTGTTTT 60.736 41.667 0.00 0.00 46.43 2.43
5052 7059 3.243401 GCATCTCCCGAACACTTTTGTTT 60.243 43.478 0.00 0.00 46.43 2.83
5054 7061 1.880027 GCATCTCCCGAACACTTTTGT 59.120 47.619 0.00 0.00 37.67 2.83
5055 7062 1.200020 GGCATCTCCCGAACACTTTTG 59.800 52.381 0.00 0.00 0.00 2.44
5056 7063 1.202879 TGGCATCTCCCGAACACTTTT 60.203 47.619 0.00 0.00 0.00 2.27
5057 7064 0.400213 TGGCATCTCCCGAACACTTT 59.600 50.000 0.00 0.00 0.00 2.66
5058 7065 0.620556 ATGGCATCTCCCGAACACTT 59.379 50.000 0.00 0.00 0.00 3.16
5059 7066 1.496060 TATGGCATCTCCCGAACACT 58.504 50.000 1.65 0.00 0.00 3.55
5060 7067 2.550830 ATATGGCATCTCCCGAACAC 57.449 50.000 1.65 0.00 0.00 3.32
5061 7068 3.576078 AAATATGGCATCTCCCGAACA 57.424 42.857 1.65 0.00 0.00 3.18
5062 7069 4.819630 TGTAAAATATGGCATCTCCCGAAC 59.180 41.667 1.65 0.00 0.00 3.95
5063 7070 5.042463 TGTAAAATATGGCATCTCCCGAA 57.958 39.130 1.65 0.00 0.00 4.30
5064 7071 4.698201 TGTAAAATATGGCATCTCCCGA 57.302 40.909 1.65 0.00 0.00 5.14
5065 7072 6.655003 ACTTATGTAAAATATGGCATCTCCCG 59.345 38.462 1.65 0.00 0.00 5.14
5066 7073 7.665559 TGACTTATGTAAAATATGGCATCTCCC 59.334 37.037 1.65 0.00 0.00 4.30
5067 7074 8.621532 TGACTTATGTAAAATATGGCATCTCC 57.378 34.615 1.65 0.00 0.00 3.71
5179 7186 8.779303 CCCTCTTTTTGTTTTGTTTTGTTAGTT 58.221 29.630 0.00 0.00 0.00 2.24
5180 7187 8.151596 TCCCTCTTTTTGTTTTGTTTTGTTAGT 58.848 29.630 0.00 0.00 0.00 2.24
5181 7188 8.541133 TCCCTCTTTTTGTTTTGTTTTGTTAG 57.459 30.769 0.00 0.00 0.00 2.34
5182 7189 8.775527 GTTCCCTCTTTTTGTTTTGTTTTGTTA 58.224 29.630 0.00 0.00 0.00 2.41
5183 7190 7.255312 GGTTCCCTCTTTTTGTTTTGTTTTGTT 60.255 33.333 0.00 0.00 0.00 2.83
5184 7191 6.205853 GGTTCCCTCTTTTTGTTTTGTTTTGT 59.794 34.615 0.00 0.00 0.00 2.83
5185 7192 6.348950 GGGTTCCCTCTTTTTGTTTTGTTTTG 60.349 38.462 0.00 0.00 0.00 2.44
5186 7193 5.708230 GGGTTCCCTCTTTTTGTTTTGTTTT 59.292 36.000 0.00 0.00 0.00 2.43
5187 7194 5.250200 GGGTTCCCTCTTTTTGTTTTGTTT 58.750 37.500 0.00 0.00 0.00 2.83
5188 7195 4.323945 GGGGTTCCCTCTTTTTGTTTTGTT 60.324 41.667 7.87 0.00 41.34 2.83
5189 7196 3.199071 GGGGTTCCCTCTTTTTGTTTTGT 59.801 43.478 7.87 0.00 41.34 2.83
5190 7197 3.804036 GGGGTTCCCTCTTTTTGTTTTG 58.196 45.455 7.87 0.00 41.34 2.44
5209 7216 4.798682 AGTAGGCCGTGGGAGGGG 62.799 72.222 0.00 0.00 0.00 4.79
5210 7217 3.470888 CAGTAGGCCGTGGGAGGG 61.471 72.222 0.00 0.00 0.00 4.30
5211 7218 3.470888 CCAGTAGGCCGTGGGAGG 61.471 72.222 12.74 1.31 0.00 4.30
5229 7236 3.358932 AATGGGCCGGCCAACTAGG 62.359 63.158 44.46 0.00 41.84 3.02
5230 7237 1.823899 GAATGGGCCGGCCAACTAG 60.824 63.158 44.46 0.00 37.98 2.57
5231 7238 2.274104 GAATGGGCCGGCCAACTA 59.726 61.111 44.46 27.85 37.98 2.24


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

AutoCloner maintained by Alex Coulton.