Multiple sequence alignment - TraesCS1D01G126500

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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 TraesCS1D01G126500 chr1D 100.000 4657 0 0 1 4657 137970724 137966068 0.000000e+00 8600
1 TraesCS1D01G126500 chr1D 97.115 312 9 0 4055 4366 137961589 137961278 1.150000e-145 527
2 TraesCS1D01G126500 chr1D 98.347 242 4 0 3658 3899 203950132 203949891 4.310000e-115 425
3 TraesCS1D01G126500 chr1D 98.340 241 4 0 3658 3898 16232233 16231993 1.550000e-114 424
4 TraesCS1D01G126500 chr1D 73.122 852 206 19 2394 3235 482233324 482234162 2.740000e-72 283
5 TraesCS1D01G126500 chr1A 95.969 2208 57 13 1474 3659 154699684 154701881 0.000000e+00 3555
6 TraesCS1D01G126500 chr1A 88.469 529 33 10 884 1395 154699142 154699659 8.560000e-172 614
7 TraesCS1D01G126500 chr1A 86.667 585 22 20 1 537 154691477 154692053 8.620000e-167 597
8 TraesCS1D01G126500 chr1A 85.075 536 63 14 4100 4624 50989306 50989835 8.870000e-147 531
9 TraesCS1D01G126500 chr1A 84.014 563 77 12 4100 4657 505197311 505197865 3.190000e-146 529
10 TraesCS1D01G126500 chr1A 90.786 369 18 4 517 879 154698603 154698961 3.260000e-131 479
11 TraesCS1D01G126500 chr1A 96.855 159 5 0 3896 4054 154701879 154702037 2.760000e-67 267
12 TraesCS1D01G126500 chr1A 74.749 598 138 13 2640 3232 578356175 578355586 5.980000e-64 255
13 TraesCS1D01G126500 chr1B 95.675 1318 36 9 2348 3659 212410429 212409127 0.000000e+00 2098
14 TraesCS1D01G126500 chr1B 89.277 1287 82 19 1 1259 212415955 212414697 0.000000e+00 1561
15 TraesCS1D01G126500 chr1B 97.460 630 7 2 1669 2294 212411084 212410460 0.000000e+00 1066
16 TraesCS1D01G126500 chr1B 96.394 416 14 1 1258 1672 212414429 212414014 0.000000e+00 684
17 TraesCS1D01G126500 chr1B 89.241 158 7 2 3897 4054 212409128 212408981 6.150000e-44 189
18 TraesCS1D01G126500 chr6D 95.869 581 24 0 4055 4635 454003391 454003971 0.000000e+00 941
19 TraesCS1D01G126500 chr5A 89.716 564 48 6 4100 4656 406673809 406674369 0.000000e+00 712
20 TraesCS1D01G126500 chr5B 89.698 563 49 6 4101 4656 214937370 214937930 0.000000e+00 710
21 TraesCS1D01G126500 chr3B 81.830 776 135 6 2394 3166 183083329 183084101 0.000000e+00 647
22 TraesCS1D01G126500 chr3B 78.553 788 143 21 2382 3158 410774983 410774211 3.240000e-136 496
23 TraesCS1D01G126500 chr3D 81.725 777 134 8 2394 3166 129025158 129025930 3.930000e-180 641
24 TraesCS1D01G126500 chr3D 79.028 782 139 20 2388 3158 310683026 310683793 3.210000e-141 512
25 TraesCS1D01G126500 chr3D 98.374 246 4 0 3657 3902 129016825 129016580 2.570000e-117 433
26 TraesCS1D01G126500 chr3D 98.755 241 3 0 3658 3898 94886843 94886603 3.330000e-116 429
27 TraesCS1D01G126500 chr3D 98.367 245 3 1 3658 3901 327381717 327381961 3.330000e-116 429
28 TraesCS1D01G126500 chr3D 97.571 247 6 0 3657 3903 358171040 358171286 1.550000e-114 424
29 TraesCS1D01G126500 chr3A 81.234 778 136 10 2394 3166 140806702 140805930 1.840000e-173 619
30 TraesCS1D01G126500 chr3A 78.306 779 144 21 2391 3158 421720853 421720089 3.260000e-131 479
31 TraesCS1D01G126500 chr7D 83.876 614 77 21 4055 4656 624912959 624912356 2.430000e-157 566
32 TraesCS1D01G126500 chr4A 83.197 613 86 15 4055 4657 7337557 7338162 3.170000e-151 545
33 TraesCS1D01G126500 chr2D 84.530 543 62 16 4128 4656 331181723 331182257 6.910000e-143 518
34 TraesCS1D01G126500 chr2A 83.363 565 81 13 4100 4656 663481452 663480893 1.160000e-140 510
35 TraesCS1D01G126500 chr5D 98.361 244 4 0 3658 3901 312074584 312074341 3.330000e-116 429
36 TraesCS1D01G126500 chr4D 97.967 246 4 1 3658 3902 226543479 226543724 4.310000e-115 425
37 TraesCS1D01G126500 chr4D 97.581 248 5 1 3658 3905 48534596 48534350 1.550000e-114 424


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 TraesCS1D01G126500 chr1D 137966068 137970724 4656 True 8600.00 8600 100.00000 1 4657 1 chr1D.!!$R3 4656
1 TraesCS1D01G126500 chr1D 482233324 482234162 838 False 283.00 283 73.12200 2394 3235 1 chr1D.!!$F1 841
2 TraesCS1D01G126500 chr1A 154698603 154702037 3434 False 1228.75 3555 93.01975 517 4054 4 chr1A.!!$F4 3537
3 TraesCS1D01G126500 chr1A 154691477 154692053 576 False 597.00 597 86.66700 1 537 1 chr1A.!!$F2 536
4 TraesCS1D01G126500 chr1A 50989306 50989835 529 False 531.00 531 85.07500 4100 4624 1 chr1A.!!$F1 524
5 TraesCS1D01G126500 chr1A 505197311 505197865 554 False 529.00 529 84.01400 4100 4657 1 chr1A.!!$F3 557
6 TraesCS1D01G126500 chr1A 578355586 578356175 589 True 255.00 255 74.74900 2640 3232 1 chr1A.!!$R1 592
7 TraesCS1D01G126500 chr1B 212408981 212415955 6974 True 1119.60 2098 93.60940 1 4054 5 chr1B.!!$R1 4053
8 TraesCS1D01G126500 chr6D 454003391 454003971 580 False 941.00 941 95.86900 4055 4635 1 chr6D.!!$F1 580
9 TraesCS1D01G126500 chr5A 406673809 406674369 560 False 712.00 712 89.71600 4100 4656 1 chr5A.!!$F1 556
10 TraesCS1D01G126500 chr5B 214937370 214937930 560 False 710.00 710 89.69800 4101 4656 1 chr5B.!!$F1 555
11 TraesCS1D01G126500 chr3B 183083329 183084101 772 False 647.00 647 81.83000 2394 3166 1 chr3B.!!$F1 772
12 TraesCS1D01G126500 chr3B 410774211 410774983 772 True 496.00 496 78.55300 2382 3158 1 chr3B.!!$R1 776
13 TraesCS1D01G126500 chr3D 129025158 129025930 772 False 641.00 641 81.72500 2394 3166 1 chr3D.!!$F1 772
14 TraesCS1D01G126500 chr3D 310683026 310683793 767 False 512.00 512 79.02800 2388 3158 1 chr3D.!!$F2 770
15 TraesCS1D01G126500 chr3A 140805930 140806702 772 True 619.00 619 81.23400 2394 3166 1 chr3A.!!$R1 772
16 TraesCS1D01G126500 chr3A 421720089 421720853 764 True 479.00 479 78.30600 2391 3158 1 chr3A.!!$R2 767
17 TraesCS1D01G126500 chr7D 624912356 624912959 603 True 566.00 566 83.87600 4055 4656 1 chr7D.!!$R1 601
18 TraesCS1D01G126500 chr4A 7337557 7338162 605 False 545.00 545 83.19700 4055 4657 1 chr4A.!!$F1 602
19 TraesCS1D01G126500 chr2D 331181723 331182257 534 False 518.00 518 84.53000 4128 4656 1 chr2D.!!$F1 528
20 TraesCS1D01G126500 chr2A 663480893 663481452 559 True 510.00 510 83.36300 4100 4656 1 chr2A.!!$R1 556

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
79 92 0.395311 TCCTCCTGTACCTACGGCTG 60.395 60.000 0.00 0.0 0.0 4.85 F
1202 1460 0.459489 TGCTCAACAACTTGGTTGCC 59.541 50.000 9.89 0.0 46.2 4.52 F
1545 2076 0.740149 CAACACAAGCAGCAAGACCA 59.260 50.000 0.00 0.0 0.0 4.02 F
2482 5954 1.514087 GTTCGGTATGTGCCTCGGA 59.486 57.895 0.00 0.0 0.0 4.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1699 5163 0.240945 ATTTCTTTTCAGCCGTGCCG 59.759 50.000 0.00 0.0 0.00 5.69 R
3198 6673 1.299850 CACCACGACAGCGAGAACA 60.300 57.895 0.00 0.0 41.64 3.18 R
3378 6853 0.466739 GTTGGGGAAAAGGTCGTGGT 60.467 55.000 0.00 0.0 0.00 4.16 R
3865 7354 0.040425 CCAAAATATAGTGCGCCCGC 60.040 55.000 4.18 5.6 42.35 6.13 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
24 25 5.339008 ACGGCTGATCTTTGTAATGTCTA 57.661 39.130 0.00 0.00 0.00 2.59
32 33 8.539117 TGATCTTTGTAATGTCTATCTCCAGA 57.461 34.615 0.00 0.00 0.00 3.86
67 80 1.486997 ATGCCCGATCCATCCTCCTG 61.487 60.000 0.00 0.00 0.00 3.86
79 92 0.395311 TCCTCCTGTACCTACGGCTG 60.395 60.000 0.00 0.00 0.00 4.85
123 151 2.159142 ACGGCCCTGATTTTACTACTCG 60.159 50.000 0.00 0.00 0.00 4.18
124 152 2.159142 CGGCCCTGATTTTACTACTCGT 60.159 50.000 0.00 0.00 0.00 4.18
243 272 9.671521 CTATTTTAGATTGTGAAACTTACGACG 57.328 33.333 0.00 0.00 38.04 5.12
284 313 2.934932 TGCAGGCCTGATGTGGGA 60.935 61.111 37.21 6.23 0.00 4.37
350 390 4.846779 TTTTCCAAACAAGAGGAATCGG 57.153 40.909 0.00 0.00 43.02 4.18
351 391 3.502123 TTCCAAACAAGAGGAATCGGT 57.498 42.857 0.00 0.00 38.91 4.69
413 454 5.552870 ATCCACCTAATAGCTTGAACGAT 57.447 39.130 0.00 0.00 0.00 3.73
434 483 3.866651 TCATCTTGCTACTCCTGAAAGC 58.133 45.455 0.00 0.00 36.77 3.51
461 510 3.544684 TCCAGCAGTAATGCCATACTTG 58.455 45.455 12.26 2.07 33.90 3.16
464 513 4.581824 CCAGCAGTAATGCCATACTTGAAT 59.418 41.667 12.26 0.00 33.90 2.57
491 540 6.997239 TCATTCATTCATGGAAAGAGTCTG 57.003 37.500 0.00 0.00 0.00 3.51
499 551 5.620206 TCATGGAAAGAGTCTGCTTACAAA 58.380 37.500 0.00 0.00 0.00 2.83
507 559 1.996191 GTCTGCTTACAAAGAGGAGCG 59.004 52.381 0.00 0.00 37.94 5.03
510 562 1.066858 TGCTTACAAAGAGGAGCGAGG 60.067 52.381 0.00 0.00 37.94 4.63
572 625 1.161563 ACCCCAAACGCACGTTACTG 61.162 55.000 9.08 4.83 37.35 2.74
608 661 0.663153 AACGTTGCTGAAACTCCTGC 59.337 50.000 0.00 0.00 36.56 4.85
612 665 2.479389 CGTTGCTGAAACTCCTGCAAAA 60.479 45.455 9.19 0.00 47.00 2.44
652 705 3.365265 CACACTTTGGGCGCCTCC 61.365 66.667 28.56 11.61 0.00 4.30
739 797 0.867753 CTCGTGTAGCGTCATGGAGC 60.868 60.000 5.37 5.37 42.13 4.70
780 844 0.882042 ACAGCTTGCTCTCACAACCG 60.882 55.000 0.00 0.00 0.00 4.44
817 881 2.706636 CACAACTGTCAGGTGGTGG 58.293 57.895 21.79 7.38 37.20 4.61
881 950 3.801114 TTCCGAGGATGACACATACAG 57.199 47.619 0.00 0.00 0.00 2.74
970 1215 1.135915 GCCAGTCATCGACTCATCACT 59.864 52.381 0.00 0.00 41.37 3.41
1020 1265 0.591170 AGCCAAACACAAATCGTCGG 59.409 50.000 0.00 0.00 0.00 4.79
1184 1442 2.735762 GCCCAGAAGCGTCTAGTAGTTG 60.736 54.545 0.57 0.00 30.85 3.16
1202 1460 0.459489 TGCTCAACAACTTGGTTGCC 59.541 50.000 9.89 0.00 46.20 4.52
1204 1462 1.536709 GCTCAACAACTTGGTTGCCAG 60.537 52.381 9.89 5.30 46.20 4.85
1206 1464 2.166254 CTCAACAACTTGGTTGCCAGTT 59.834 45.455 9.89 0.00 46.20 3.16
1230 1488 4.706842 TTCTTAGTTTCTCCAGGCAAGT 57.293 40.909 0.00 0.00 0.00 3.16
1377 1908 6.565247 GCAGAAAAACATTGATTTGCTCTTGG 60.565 38.462 0.00 0.00 0.00 3.61
1378 1909 5.467735 AGAAAAACATTGATTTGCTCTTGGC 59.532 36.000 0.00 0.00 42.22 4.52
1414 1945 6.931840 GTGACTCCTAATTTGTTTCACTCTCT 59.068 38.462 0.00 0.00 31.25 3.10
1422 1953 9.950680 CTAATTTGTTTCACTCTCTAGCAAAAA 57.049 29.630 0.00 0.00 0.00 1.94
1514 2045 2.487428 CAGGTCTCGTCTGAGCGG 59.513 66.667 0.00 0.00 42.26 5.52
1545 2076 0.740149 CAACACAAGCAGCAAGACCA 59.260 50.000 0.00 0.00 0.00 4.02
1549 2080 2.670934 AAGCAGCAAGACCAGCGG 60.671 61.111 0.00 0.00 37.01 5.52
1550 2081 3.482232 AAGCAGCAAGACCAGCGGT 62.482 57.895 0.00 0.00 39.44 5.68
1680 5144 2.344203 CGGGTGAGTCTTCCGCTCT 61.344 63.158 10.77 0.00 37.25 4.09
1878 5346 1.589993 CGTGTCTATCAGCCTGCCG 60.590 63.158 0.00 0.00 0.00 5.69
2319 5787 6.584563 CACTACTTCTTCTTCTTCTTCTTCGG 59.415 42.308 0.00 0.00 0.00 4.30
2343 5811 3.681417 CGGTCGATCACATTATCATGCAT 59.319 43.478 0.00 0.00 33.05 3.96
2441 5913 3.307379 GACAAGAAGTGGCCGTTCT 57.693 52.632 13.25 13.25 35.71 3.01
2482 5954 1.514087 GTTCGGTATGTGCCTCGGA 59.486 57.895 0.00 0.00 0.00 4.55
3198 6673 4.982241 TCAACTTCTTCAGAGGGTTCAT 57.018 40.909 0.00 0.00 0.00 2.57
3316 6791 4.320456 CTGTGCGTGGGGCTGTCT 62.320 66.667 0.00 0.00 44.05 3.41
3378 6853 2.281208 GGTGCACGCCTTGGTGTA 60.281 61.111 11.45 0.00 40.08 2.90
3549 7030 1.093159 GAAGCTTGATGGAGTGGCTG 58.907 55.000 2.10 0.00 33.30 4.85
3595 7076 0.817013 AAATGATGGCGCCAACGATT 59.183 45.000 36.33 26.26 43.93 3.34
3596 7077 0.101040 AATGATGGCGCCAACGATTG 59.899 50.000 36.33 0.00 43.93 2.67
3640 7129 6.441093 AGGATACGATCGTACTGTACAAAA 57.559 37.500 28.96 6.30 46.39 2.44
3641 7130 6.855836 AGGATACGATCGTACTGTACAAAAA 58.144 36.000 28.96 5.74 46.39 1.94
3656 7145 2.296658 AAAAAGTTTGCTTGCGCGG 58.703 47.368 8.83 0.00 39.65 6.46
3657 7146 0.459411 AAAAAGTTTGCTTGCGCGGT 60.459 45.000 8.83 0.00 39.65 5.68
3658 7147 0.382515 AAAAGTTTGCTTGCGCGGTA 59.617 45.000 8.83 0.00 39.65 4.02
3659 7148 0.317519 AAAGTTTGCTTGCGCGGTAC 60.318 50.000 8.83 0.00 39.65 3.34
3660 7149 1.164041 AAGTTTGCTTGCGCGGTACT 61.164 50.000 8.83 0.00 39.65 2.73
3661 7150 1.154469 GTTTGCTTGCGCGGTACTC 60.154 57.895 8.83 0.00 39.65 2.59
3662 7151 2.322081 TTTGCTTGCGCGGTACTCC 61.322 57.895 8.83 0.00 39.65 3.85
3663 7152 4.752879 TGCTTGCGCGGTACTCCC 62.753 66.667 8.83 0.00 39.65 4.30
3664 7153 4.452733 GCTTGCGCGGTACTCCCT 62.453 66.667 8.83 0.00 0.00 4.20
3665 7154 2.202756 CTTGCGCGGTACTCCCTC 60.203 66.667 8.83 0.00 0.00 4.30
3666 7155 3.718210 CTTGCGCGGTACTCCCTCC 62.718 68.421 8.83 0.00 0.00 4.30
3668 7157 3.537874 GCGCGGTACTCCCTCCAT 61.538 66.667 8.83 0.00 0.00 3.41
3669 7158 3.090219 GCGCGGTACTCCCTCCATT 62.090 63.158 8.83 0.00 0.00 3.16
3670 7159 1.067582 CGCGGTACTCCCTCCATTC 59.932 63.158 0.00 0.00 0.00 2.67
3671 7160 1.446366 GCGGTACTCCCTCCATTCC 59.554 63.158 0.00 0.00 0.00 3.01
3672 7161 1.335132 GCGGTACTCCCTCCATTCCA 61.335 60.000 0.00 0.00 0.00 3.53
3673 7162 0.464452 CGGTACTCCCTCCATTCCAC 59.536 60.000 0.00 0.00 0.00 4.02
3674 7163 1.580059 GGTACTCCCTCCATTCCACA 58.420 55.000 0.00 0.00 0.00 4.17
3675 7164 1.913419 GGTACTCCCTCCATTCCACAA 59.087 52.381 0.00 0.00 0.00 3.33
3676 7165 2.509964 GGTACTCCCTCCATTCCACAAT 59.490 50.000 0.00 0.00 0.00 2.71
3677 7166 2.814805 ACTCCCTCCATTCCACAATG 57.185 50.000 0.00 0.00 39.45 2.82
3678 7167 1.995542 ACTCCCTCCATTCCACAATGT 59.004 47.619 0.00 0.00 38.22 2.71
3679 7168 3.189606 ACTCCCTCCATTCCACAATGTA 58.810 45.455 0.00 0.00 38.22 2.29
3680 7169 3.200825 ACTCCCTCCATTCCACAATGTAG 59.799 47.826 0.00 0.00 38.22 2.74
3681 7170 3.189606 TCCCTCCATTCCACAATGTAGT 58.810 45.455 0.00 0.00 38.22 2.73
3682 7171 3.054434 TCCCTCCATTCCACAATGTAGTG 60.054 47.826 0.00 0.00 38.22 2.74
3683 7172 2.684881 CCTCCATTCCACAATGTAGTGC 59.315 50.000 0.00 0.00 38.22 4.40
3684 7173 3.614092 CTCCATTCCACAATGTAGTGCT 58.386 45.455 0.00 0.00 38.22 4.40
3685 7174 4.012374 CTCCATTCCACAATGTAGTGCTT 58.988 43.478 0.00 0.00 38.22 3.91
3686 7175 3.758023 TCCATTCCACAATGTAGTGCTTG 59.242 43.478 0.00 0.00 38.22 4.01
3687 7176 3.504863 CATTCCACAATGTAGTGCTTGC 58.495 45.455 0.00 0.00 38.18 4.01
3688 7177 2.566833 TCCACAATGTAGTGCTTGCT 57.433 45.000 0.00 0.00 38.18 3.91
3689 7178 2.426522 TCCACAATGTAGTGCTTGCTC 58.573 47.619 0.00 0.00 38.18 4.26
3690 7179 2.038952 TCCACAATGTAGTGCTTGCTCT 59.961 45.455 2.77 2.77 38.18 4.09
3691 7180 3.260632 TCCACAATGTAGTGCTTGCTCTA 59.739 43.478 0.91 0.91 38.18 2.43
3692 7181 4.080919 TCCACAATGTAGTGCTTGCTCTAT 60.081 41.667 7.51 0.00 38.18 1.98
3693 7182 4.272018 CCACAATGTAGTGCTTGCTCTATC 59.728 45.833 7.51 3.65 38.18 2.08
3694 7183 5.114780 CACAATGTAGTGCTTGCTCTATCT 58.885 41.667 7.51 0.00 32.04 1.98
3695 7184 5.233902 CACAATGTAGTGCTTGCTCTATCTC 59.766 44.000 7.51 0.00 32.04 2.75
3696 7185 4.599047 ATGTAGTGCTTGCTCTATCTCC 57.401 45.455 7.51 0.00 0.00 3.71
3697 7186 2.359214 TGTAGTGCTTGCTCTATCTCCG 59.641 50.000 7.51 0.00 0.00 4.63
3698 7187 1.479709 AGTGCTTGCTCTATCTCCGT 58.520 50.000 0.00 0.00 0.00 4.69
3699 7188 1.135915 AGTGCTTGCTCTATCTCCGTG 59.864 52.381 0.00 0.00 0.00 4.94
3700 7189 0.179100 TGCTTGCTCTATCTCCGTGC 60.179 55.000 0.00 0.00 0.00 5.34
3701 7190 0.103937 GCTTGCTCTATCTCCGTGCT 59.896 55.000 0.00 0.00 0.00 4.40
3702 7191 1.472376 GCTTGCTCTATCTCCGTGCTT 60.472 52.381 0.00 0.00 0.00 3.91
3703 7192 2.468831 CTTGCTCTATCTCCGTGCTTC 58.531 52.381 0.00 0.00 0.00 3.86
3704 7193 1.474330 TGCTCTATCTCCGTGCTTCA 58.526 50.000 0.00 0.00 0.00 3.02
3705 7194 1.824852 TGCTCTATCTCCGTGCTTCAA 59.175 47.619 0.00 0.00 0.00 2.69
3706 7195 2.197577 GCTCTATCTCCGTGCTTCAAC 58.802 52.381 0.00 0.00 0.00 3.18
3707 7196 2.159170 GCTCTATCTCCGTGCTTCAACT 60.159 50.000 0.00 0.00 0.00 3.16
3708 7197 3.677424 GCTCTATCTCCGTGCTTCAACTT 60.677 47.826 0.00 0.00 0.00 2.66
3709 7198 4.499183 CTCTATCTCCGTGCTTCAACTTT 58.501 43.478 0.00 0.00 0.00 2.66
3710 7199 4.245660 TCTATCTCCGTGCTTCAACTTTG 58.754 43.478 0.00 0.00 0.00 2.77
3711 7200 2.613026 TCTCCGTGCTTCAACTTTGA 57.387 45.000 0.00 0.00 34.92 2.69
3712 7201 2.210116 TCTCCGTGCTTCAACTTTGAC 58.790 47.619 0.00 0.00 36.83 3.18
3713 7202 1.264288 CTCCGTGCTTCAACTTTGACC 59.736 52.381 0.00 0.00 36.83 4.02
3714 7203 0.041312 CCGTGCTTCAACTTTGACCG 60.041 55.000 0.00 0.00 36.83 4.79
3715 7204 0.655733 CGTGCTTCAACTTTGACCGT 59.344 50.000 0.00 0.00 36.83 4.83
3716 7205 1.862201 CGTGCTTCAACTTTGACCGTA 59.138 47.619 0.00 0.00 36.83 4.02
3717 7206 2.285756 CGTGCTTCAACTTTGACCGTAA 59.714 45.455 0.00 0.00 36.83 3.18
3718 7207 3.242478 CGTGCTTCAACTTTGACCGTAAA 60.242 43.478 0.00 0.00 36.83 2.01
3719 7208 4.553938 CGTGCTTCAACTTTGACCGTAAAT 60.554 41.667 0.00 0.00 36.83 1.40
3720 7209 5.278604 GTGCTTCAACTTTGACCGTAAATT 58.721 37.500 0.00 0.00 36.83 1.82
3721 7210 5.746721 GTGCTTCAACTTTGACCGTAAATTT 59.253 36.000 0.00 0.00 36.83 1.82
3722 7211 6.913673 GTGCTTCAACTTTGACCGTAAATTTA 59.086 34.615 0.00 0.00 36.83 1.40
3723 7212 7.432838 GTGCTTCAACTTTGACCGTAAATTTAA 59.567 33.333 0.00 0.00 36.83 1.52
3724 7213 7.432838 TGCTTCAACTTTGACCGTAAATTTAAC 59.567 33.333 0.00 0.00 36.83 2.01
3725 7214 7.646526 GCTTCAACTTTGACCGTAAATTTAACT 59.353 33.333 0.00 0.00 36.83 2.24
3727 7216 9.934190 TTCAACTTTGACCGTAAATTTAACTAC 57.066 29.630 0.00 0.00 36.83 2.73
3728 7217 8.558700 TCAACTTTGACCGTAAATTTAACTACC 58.441 33.333 0.00 0.00 31.01 3.18
3729 7218 8.344098 CAACTTTGACCGTAAATTTAACTACCA 58.656 33.333 0.00 0.00 0.00 3.25
3730 7219 8.449251 ACTTTGACCGTAAATTTAACTACCAA 57.551 30.769 0.00 0.00 0.00 3.67
3731 7220 8.562052 ACTTTGACCGTAAATTTAACTACCAAG 58.438 33.333 0.00 2.45 0.00 3.61
3732 7221 8.674263 TTTGACCGTAAATTTAACTACCAAGA 57.326 30.769 0.00 0.00 0.00 3.02
3733 7222 7.656707 TGACCGTAAATTTAACTACCAAGAC 57.343 36.000 0.00 0.00 0.00 3.01
3734 7223 6.650390 TGACCGTAAATTTAACTACCAAGACC 59.350 38.462 0.00 0.00 0.00 3.85
3735 7224 5.639082 ACCGTAAATTTAACTACCAAGACCG 59.361 40.000 0.00 0.00 0.00 4.79
3736 7225 5.868801 CCGTAAATTTAACTACCAAGACCGA 59.131 40.000 0.00 0.00 0.00 4.69
3737 7226 6.536224 CCGTAAATTTAACTACCAAGACCGAT 59.464 38.462 0.00 0.00 0.00 4.18
3738 7227 7.064966 CCGTAAATTTAACTACCAAGACCGATT 59.935 37.037 0.00 0.00 0.00 3.34
3739 7228 7.901377 CGTAAATTTAACTACCAAGACCGATTG 59.099 37.037 0.00 0.00 0.00 2.67
3740 7229 5.813080 ATTTAACTACCAAGACCGATTGC 57.187 39.130 0.00 0.00 0.00 3.56
3741 7230 1.722011 AACTACCAAGACCGATTGCG 58.278 50.000 0.00 0.00 37.24 4.85
3769 7258 9.965824 CGGGAGCAAAAATTATATTAGTGAATT 57.034 29.630 0.00 0.00 0.00 2.17
3818 7307 2.517402 TTTTTCACCCGCCGCAGT 60.517 55.556 0.00 0.00 0.00 4.40
3819 7308 2.548295 TTTTTCACCCGCCGCAGTC 61.548 57.895 0.00 0.00 0.00 3.51
3830 7319 2.870161 CGCAGTCGGTCTCGTTCG 60.870 66.667 0.00 0.00 37.69 3.95
3831 7320 2.254651 GCAGTCGGTCTCGTTCGT 59.745 61.111 0.00 0.00 37.69 3.85
3832 7321 1.371389 GCAGTCGGTCTCGTTCGTT 60.371 57.895 0.00 0.00 37.69 3.85
3833 7322 0.110056 GCAGTCGGTCTCGTTCGTTA 60.110 55.000 0.00 0.00 37.69 3.18
3834 7323 1.664016 GCAGTCGGTCTCGTTCGTTAA 60.664 52.381 0.00 0.00 37.69 2.01
3835 7324 2.653890 CAGTCGGTCTCGTTCGTTAAA 58.346 47.619 0.00 0.00 37.69 1.52
3836 7325 3.240069 CAGTCGGTCTCGTTCGTTAAAT 58.760 45.455 0.00 0.00 37.69 1.40
3837 7326 3.671928 CAGTCGGTCTCGTTCGTTAAATT 59.328 43.478 0.00 0.00 37.69 1.82
3838 7327 4.149396 CAGTCGGTCTCGTTCGTTAAATTT 59.851 41.667 0.00 0.00 37.69 1.82
3839 7328 5.343058 CAGTCGGTCTCGTTCGTTAAATTTA 59.657 40.000 0.00 0.00 37.69 1.40
3840 7329 6.034256 CAGTCGGTCTCGTTCGTTAAATTTAT 59.966 38.462 0.00 0.00 37.69 1.40
3841 7330 6.034256 AGTCGGTCTCGTTCGTTAAATTTATG 59.966 38.462 0.00 0.00 37.69 1.90
3842 7331 5.289193 TCGGTCTCGTTCGTTAAATTTATGG 59.711 40.000 0.00 0.00 37.69 2.74
3843 7332 5.062558 CGGTCTCGTTCGTTAAATTTATGGT 59.937 40.000 0.00 0.00 0.00 3.55
3844 7333 6.472680 GGTCTCGTTCGTTAAATTTATGGTC 58.527 40.000 0.00 0.00 0.00 4.02
3845 7334 6.091169 GGTCTCGTTCGTTAAATTTATGGTCA 59.909 38.462 0.00 0.00 0.00 4.02
3846 7335 7.360269 GGTCTCGTTCGTTAAATTTATGGTCAA 60.360 37.037 0.00 0.00 0.00 3.18
3847 7336 8.011106 GTCTCGTTCGTTAAATTTATGGTCAAA 58.989 33.333 0.00 0.00 0.00 2.69
3848 7337 8.225107 TCTCGTTCGTTAAATTTATGGTCAAAG 58.775 33.333 0.00 0.00 0.00 2.77
3849 7338 7.863666 TCGTTCGTTAAATTTATGGTCAAAGT 58.136 30.769 0.00 0.00 0.00 2.66
3850 7339 8.344098 TCGTTCGTTAAATTTATGGTCAAAGTT 58.656 29.630 0.00 0.00 31.36 2.66
3851 7340 8.624028 CGTTCGTTAAATTTATGGTCAAAGTTC 58.376 33.333 0.00 0.00 29.44 3.01
3852 7341 8.624028 GTTCGTTAAATTTATGGTCAAAGTTCG 58.376 33.333 0.00 0.00 29.44 3.95
3853 7342 8.085720 TCGTTAAATTTATGGTCAAAGTTCGA 57.914 30.769 0.00 0.00 29.44 3.71
3854 7343 8.011106 TCGTTAAATTTATGGTCAAAGTTCGAC 58.989 33.333 0.00 0.00 29.44 4.20
3860 7349 2.823628 GTCAAAGTTCGACCTCGGG 58.176 57.895 0.00 0.00 40.29 5.14
3861 7350 0.316204 GTCAAAGTTCGACCTCGGGA 59.684 55.000 0.00 0.00 40.29 5.14
3862 7351 1.042229 TCAAAGTTCGACCTCGGGAA 58.958 50.000 0.00 0.00 40.29 3.97
3863 7352 1.413445 TCAAAGTTCGACCTCGGGAAA 59.587 47.619 0.00 0.00 40.29 3.13
3864 7353 1.529865 CAAAGTTCGACCTCGGGAAAC 59.470 52.381 0.00 0.00 40.29 2.78
3865 7354 0.319297 AAGTTCGACCTCGGGAAACG 60.319 55.000 0.00 0.00 46.11 3.60
3866 7355 2.048877 TTCGACCTCGGGAAACGC 60.049 61.111 0.00 0.00 43.86 4.84
3867 7356 3.902162 TTCGACCTCGGGAAACGCG 62.902 63.158 3.53 3.53 43.86 6.01
3877 7366 3.192922 GAAACGCGGGCGCACTAT 61.193 61.111 12.47 0.00 44.19 2.12
3878 7367 1.879430 GAAACGCGGGCGCACTATA 60.879 57.895 12.47 0.00 44.19 1.31
3879 7368 1.219522 GAAACGCGGGCGCACTATAT 61.220 55.000 12.47 0.00 44.19 0.86
3880 7369 0.812412 AAACGCGGGCGCACTATATT 60.812 50.000 12.47 0.00 44.19 1.28
3881 7370 0.812412 AACGCGGGCGCACTATATTT 60.812 50.000 12.47 0.00 44.19 1.40
3882 7371 0.812412 ACGCGGGCGCACTATATTTT 60.812 50.000 12.47 0.00 44.19 1.82
3883 7372 0.384230 CGCGGGCGCACTATATTTTG 60.384 55.000 8.62 0.00 42.06 2.44
3884 7373 0.040425 GCGGGCGCACTATATTTTGG 60.040 55.000 8.62 0.00 41.49 3.28
3885 7374 1.588674 CGGGCGCACTATATTTTGGA 58.411 50.000 8.62 0.00 0.00 3.53
3886 7375 1.944024 CGGGCGCACTATATTTTGGAA 59.056 47.619 8.62 0.00 0.00 3.53
3887 7376 2.552315 CGGGCGCACTATATTTTGGAAT 59.448 45.455 8.62 0.00 0.00 3.01
3888 7377 3.609175 CGGGCGCACTATATTTTGGAATG 60.609 47.826 8.62 0.00 0.00 2.67
3889 7378 3.305335 GGGCGCACTATATTTTGGAATGG 60.305 47.826 10.83 0.00 0.00 3.16
3890 7379 3.568007 GGCGCACTATATTTTGGAATGGA 59.432 43.478 10.83 0.00 0.00 3.41
3891 7380 4.320494 GGCGCACTATATTTTGGAATGGAG 60.320 45.833 10.83 0.00 0.00 3.86
3892 7381 4.320494 GCGCACTATATTTTGGAATGGAGG 60.320 45.833 0.30 0.00 0.00 4.30
3893 7382 4.216257 CGCACTATATTTTGGAATGGAGGG 59.784 45.833 0.00 0.00 0.00 4.30
3894 7383 5.385198 GCACTATATTTTGGAATGGAGGGA 58.615 41.667 0.00 0.00 0.00 4.20
3942 7431 2.662700 GATAGTCACCGGCGTAGAATG 58.337 52.381 6.01 0.00 0.00 2.67
3973 7462 6.721208 AGAAGGTCTATTTGGAATTTGCAAGA 59.279 34.615 0.00 0.00 0.00 3.02
4028 7517 1.257743 TACGACCTCTGCTCTGCTTT 58.742 50.000 0.00 0.00 0.00 3.51
4065 7554 1.523154 GCGTCCATTGTCAAGGCCAA 61.523 55.000 5.01 0.00 0.00 4.52
4097 7586 4.085876 CCACACCAGGCAAGGAAG 57.914 61.111 2.81 0.00 0.00 3.46
4298 7807 7.406553 CAATTCGTGTATCCGTGATTGTAATT 58.593 34.615 0.00 0.00 32.85 1.40
4372 7885 4.130118 CTGGGTTGCTTACATCTGGTATC 58.870 47.826 0.00 0.00 0.00 2.24
4404 7917 2.584064 CACACCCTGGCGCATCTA 59.416 61.111 10.83 0.00 0.00 1.98
4592 8105 1.078848 GGCGTGTGGATCAGCTCTT 60.079 57.895 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 6.054295 GCTTGACATTCTGGAGATAGACATT 58.946 40.000 0.00 0.00 0.00 2.71
24 25 4.268359 GAAAGGCTTGACATTCTGGAGAT 58.732 43.478 0.00 0.00 0.00 2.75
32 33 1.551883 GGCATGGAAAGGCTTGACATT 59.448 47.619 12.58 0.00 0.00 2.71
79 92 1.676014 CCATCGTCTTGACAAGGGACC 60.676 57.143 15.13 1.03 0.00 4.46
117 145 1.740585 CAGAGTCCAGGACACGAGTAG 59.259 57.143 22.31 2.77 34.60 2.57
123 151 3.685139 TCAAATCAGAGTCCAGGACAC 57.315 47.619 22.31 15.68 34.60 3.67
124 152 3.648067 ACTTCAAATCAGAGTCCAGGACA 59.352 43.478 22.31 0.55 34.60 4.02
188 217 3.521796 GGAGCAATTCCAGGCCGC 61.522 66.667 0.00 0.00 46.01 6.53
238 267 4.082949 TGTTGAATCATCAGTAGTCGTCGT 60.083 41.667 0.00 0.00 36.78 4.34
241 270 4.621460 CGTTGTTGAATCATCAGTAGTCGT 59.379 41.667 0.00 0.00 36.78 4.34
242 271 4.621460 ACGTTGTTGAATCATCAGTAGTCG 59.379 41.667 0.00 0.00 36.78 4.18
243 272 5.864474 AGACGTTGTTGAATCATCAGTAGTC 59.136 40.000 13.08 13.08 36.78 2.59
284 313 2.290577 GGATTCTGCTGAACAACCCTCT 60.291 50.000 8.32 0.00 34.71 3.69
349 389 2.100418 GTGACCTCTAATCGTACCCACC 59.900 54.545 0.00 0.00 0.00 4.61
350 390 3.022406 AGTGACCTCTAATCGTACCCAC 58.978 50.000 0.00 0.00 0.00 4.61
351 391 3.021695 CAGTGACCTCTAATCGTACCCA 58.978 50.000 0.00 0.00 0.00 4.51
413 454 3.677148 CGCTTTCAGGAGTAGCAAGATGA 60.677 47.826 0.00 0.00 34.62 2.92
434 483 1.756375 GCATTACTGCTGGAGCGTCG 61.756 60.000 0.00 0.00 45.32 5.12
464 513 7.449395 AGACTCTTTCCATGAATGAATGAAACA 59.551 33.333 0.00 0.00 0.00 2.83
491 540 1.204941 TCCTCGCTCCTCTTTGTAAGC 59.795 52.381 0.00 0.00 0.00 3.09
499 551 0.260230 TTCCTCATCCTCGCTCCTCT 59.740 55.000 0.00 0.00 0.00 3.69
507 559 7.645058 TGGTTATTTCATTTTCCTCATCCTC 57.355 36.000 0.00 0.00 0.00 3.71
510 562 9.358872 GAAGTTGGTTATTTCATTTTCCTCATC 57.641 33.333 0.00 0.00 0.00 2.92
572 625 0.438830 GTTCTGACGCGGATGACAAC 59.561 55.000 12.47 1.43 0.00 3.32
595 648 2.735823 CACTTTTGCAGGAGTTTCAGC 58.264 47.619 1.67 0.00 0.00 4.26
652 705 2.469274 TCTTGGCAGCTCTCTGAAAG 57.531 50.000 0.00 0.26 42.95 2.62
697 751 5.357878 AGAGCTTCACACAATTCTTCACAAA 59.642 36.000 0.00 0.00 0.00 2.83
780 844 3.568007 TGTGGATGCTACTGAAACAAACC 59.432 43.478 0.00 0.00 0.00 3.27
817 881 4.137872 TGGCTGGGTACTACGCGC 62.138 66.667 5.73 0.00 33.25 6.86
970 1215 2.156117 GCAAATGCGCCGTTCGTATATA 59.844 45.455 4.18 0.00 42.62 0.86
1184 1442 0.459489 TGGCAACCAAGTTGTTGAGC 59.541 50.000 17.11 9.31 46.77 4.26
1206 1464 5.891551 ACTTGCCTGGAGAAACTAAGAAAAA 59.108 36.000 0.00 0.00 0.00 1.94
1210 1468 3.646162 TGACTTGCCTGGAGAAACTAAGA 59.354 43.478 0.00 0.00 0.00 2.10
1211 1469 3.999663 CTGACTTGCCTGGAGAAACTAAG 59.000 47.826 0.00 0.00 0.00 2.18
1214 1472 2.050144 TCTGACTTGCCTGGAGAAACT 58.950 47.619 0.00 0.00 0.00 2.66
1216 1474 2.811873 GCTTCTGACTTGCCTGGAGAAA 60.812 50.000 0.00 0.00 0.00 2.52
1217 1475 1.271054 GCTTCTGACTTGCCTGGAGAA 60.271 52.381 0.00 0.00 0.00 2.87
1219 1477 0.324285 AGCTTCTGACTTGCCTGGAG 59.676 55.000 0.00 0.00 0.00 3.86
1221 1479 0.324285 AGAGCTTCTGACTTGCCTGG 59.676 55.000 0.00 0.00 0.00 4.45
1222 1480 2.615869 GTAGAGCTTCTGACTTGCCTG 58.384 52.381 0.00 0.00 0.00 4.85
1230 1488 5.344743 AATGAAATCGGTAGAGCTTCTGA 57.655 39.130 0.00 0.00 0.00 3.27
1377 1908 1.168714 GGAGTCACCATCCAAACTGC 58.831 55.000 0.00 0.00 36.79 4.40
1378 1909 2.867109 AGGAGTCACCATCCAAACTG 57.133 50.000 0.00 0.00 42.04 3.16
1549 2080 4.436998 CGAGGAGGGACGGCACAC 62.437 72.222 0.00 0.00 0.00 3.82
1680 5144 3.434319 GCCGTGGTCCGTACGAGA 61.434 66.667 18.76 9.65 43.82 4.04
1696 5160 3.879351 CTTTTCAGCCGTGCCGTGC 62.879 63.158 0.00 0.00 0.00 5.34
1697 5161 1.781025 TTCTTTTCAGCCGTGCCGTG 61.781 55.000 0.00 0.00 0.00 4.94
1698 5162 1.098712 TTTCTTTTCAGCCGTGCCGT 61.099 50.000 0.00 0.00 0.00 5.68
1699 5163 0.240945 ATTTCTTTTCAGCCGTGCCG 59.759 50.000 0.00 0.00 0.00 5.69
1700 5164 1.669795 CCATTTCTTTTCAGCCGTGCC 60.670 52.381 0.00 0.00 0.00 5.01
2319 5787 3.121944 GCATGATAATGTGATCGACCGAC 59.878 47.826 0.00 0.00 0.00 4.79
2343 5811 1.416401 GACTCGAATGGGAGGGCAATA 59.584 52.381 0.00 0.00 38.39 1.90
2482 5954 3.382803 GATCGCCTGGCTGCTCACT 62.383 63.158 17.92 0.00 0.00 3.41
3198 6673 1.299850 CACCACGACAGCGAGAACA 60.300 57.895 0.00 0.00 41.64 3.18
3316 6791 4.687215 GTGAGCGTGGCCAGCAGA 62.687 66.667 23.46 10.60 37.01 4.26
3378 6853 0.466739 GTTGGGGAAAAGGTCGTGGT 60.467 55.000 0.00 0.00 0.00 4.16
3549 7030 3.061563 TCCACGCAAATAATATATCGCGC 59.938 43.478 0.00 0.00 46.16 6.86
3599 7080 3.338275 TATCCCACCAAGTGCCCGC 62.338 63.158 0.00 0.00 31.34 6.13
3656 7145 3.054361 ACATTGTGGAATGGAGGGAGTAC 60.054 47.826 0.00 0.00 43.00 2.73
3657 7146 3.189606 ACATTGTGGAATGGAGGGAGTA 58.810 45.455 0.00 0.00 43.00 2.59
3658 7147 1.995542 ACATTGTGGAATGGAGGGAGT 59.004 47.619 0.00 0.00 43.00 3.85
3659 7148 2.814805 ACATTGTGGAATGGAGGGAG 57.185 50.000 0.00 0.00 43.00 4.30
3660 7149 3.931907 CTACATTGTGGAATGGAGGGA 57.068 47.619 0.00 0.00 44.23 4.20
3664 7153 3.719268 AGCACTACATTGTGGAATGGA 57.281 42.857 7.20 0.00 43.00 3.41
3665 7154 3.674138 GCAAGCACTACATTGTGGAATGG 60.674 47.826 7.20 0.00 43.00 3.16
3666 7155 3.192001 AGCAAGCACTACATTGTGGAATG 59.808 43.478 7.20 0.00 44.11 2.67
3667 7156 3.424703 AGCAAGCACTACATTGTGGAAT 58.575 40.909 7.20 0.00 38.31 3.01
3668 7157 2.813754 GAGCAAGCACTACATTGTGGAA 59.186 45.455 7.20 0.00 38.31 3.53
3669 7158 2.038952 AGAGCAAGCACTACATTGTGGA 59.961 45.455 7.20 0.00 38.31 4.02
3670 7159 2.430465 AGAGCAAGCACTACATTGTGG 58.570 47.619 0.00 0.00 38.31 4.17
3671 7160 5.114780 AGATAGAGCAAGCACTACATTGTG 58.885 41.667 0.00 0.00 40.62 3.33
3672 7161 5.350504 AGATAGAGCAAGCACTACATTGT 57.649 39.130 1.36 0.00 0.00 2.71
3673 7162 4.749099 GGAGATAGAGCAAGCACTACATTG 59.251 45.833 1.36 0.00 0.00 2.82
3674 7163 4.500545 CGGAGATAGAGCAAGCACTACATT 60.501 45.833 1.36 0.00 0.00 2.71
3675 7164 3.005261 CGGAGATAGAGCAAGCACTACAT 59.995 47.826 1.36 0.00 0.00 2.29
3676 7165 2.359214 CGGAGATAGAGCAAGCACTACA 59.641 50.000 1.36 0.00 0.00 2.74
3677 7166 2.359531 ACGGAGATAGAGCAAGCACTAC 59.640 50.000 1.36 0.00 0.00 2.73
3678 7167 2.359214 CACGGAGATAGAGCAAGCACTA 59.641 50.000 1.83 1.83 0.00 2.74
3679 7168 1.135915 CACGGAGATAGAGCAAGCACT 59.864 52.381 0.00 0.00 0.00 4.40
3680 7169 1.565305 CACGGAGATAGAGCAAGCAC 58.435 55.000 0.00 0.00 0.00 4.40
3681 7170 0.179100 GCACGGAGATAGAGCAAGCA 60.179 55.000 0.00 0.00 0.00 3.91
3682 7171 0.103937 AGCACGGAGATAGAGCAAGC 59.896 55.000 0.00 0.00 0.00 4.01
3683 7172 2.159184 TGAAGCACGGAGATAGAGCAAG 60.159 50.000 0.00 0.00 0.00 4.01
3684 7173 1.824852 TGAAGCACGGAGATAGAGCAA 59.175 47.619 0.00 0.00 0.00 3.91
3685 7174 1.474330 TGAAGCACGGAGATAGAGCA 58.526 50.000 0.00 0.00 0.00 4.26
3686 7175 2.159170 AGTTGAAGCACGGAGATAGAGC 60.159 50.000 0.00 0.00 0.00 4.09
3687 7176 3.791973 AGTTGAAGCACGGAGATAGAG 57.208 47.619 0.00 0.00 0.00 2.43
3688 7177 4.021456 TCAAAGTTGAAGCACGGAGATAGA 60.021 41.667 0.00 0.00 33.55 1.98
3689 7178 4.092091 GTCAAAGTTGAAGCACGGAGATAG 59.908 45.833 0.00 0.00 39.21 2.08
3690 7179 3.994392 GTCAAAGTTGAAGCACGGAGATA 59.006 43.478 0.00 0.00 39.21 1.98
3691 7180 2.808543 GTCAAAGTTGAAGCACGGAGAT 59.191 45.455 0.00 0.00 39.21 2.75
3692 7181 2.210116 GTCAAAGTTGAAGCACGGAGA 58.790 47.619 0.00 0.00 39.21 3.71
3693 7182 1.264288 GGTCAAAGTTGAAGCACGGAG 59.736 52.381 0.00 0.00 39.21 4.63
3694 7183 1.305201 GGTCAAAGTTGAAGCACGGA 58.695 50.000 0.00 0.00 39.21 4.69
3695 7184 0.041312 CGGTCAAAGTTGAAGCACGG 60.041 55.000 0.00 0.00 39.21 4.94
3696 7185 0.655733 ACGGTCAAAGTTGAAGCACG 59.344 50.000 0.00 2.00 39.21 5.34
3697 7186 3.955771 TTACGGTCAAAGTTGAAGCAC 57.044 42.857 0.00 0.00 39.21 4.40
3698 7187 5.508200 AATTTACGGTCAAAGTTGAAGCA 57.492 34.783 0.00 0.00 39.21 3.91
3699 7188 7.646526 AGTTAAATTTACGGTCAAAGTTGAAGC 59.353 33.333 0.00 0.00 39.21 3.86
3701 7190 9.934190 GTAGTTAAATTTACGGTCAAAGTTGAA 57.066 29.630 0.00 0.00 39.21 2.69
3702 7191 8.558700 GGTAGTTAAATTTACGGTCAAAGTTGA 58.441 33.333 0.00 0.00 34.20 3.18
3703 7192 8.344098 TGGTAGTTAAATTTACGGTCAAAGTTG 58.656 33.333 0.00 0.00 29.44 3.16
3704 7193 8.449251 TGGTAGTTAAATTTACGGTCAAAGTT 57.551 30.769 0.00 0.00 31.36 2.66
3705 7194 8.449251 TTGGTAGTTAAATTTACGGTCAAAGT 57.551 30.769 0.00 0.00 0.00 2.66
3706 7195 8.776470 TCTTGGTAGTTAAATTTACGGTCAAAG 58.224 33.333 0.00 0.00 0.00 2.77
3707 7196 8.558700 GTCTTGGTAGTTAAATTTACGGTCAAA 58.441 33.333 0.00 0.00 0.00 2.69
3708 7197 7.173047 GGTCTTGGTAGTTAAATTTACGGTCAA 59.827 37.037 0.00 0.00 0.00 3.18
3709 7198 6.650390 GGTCTTGGTAGTTAAATTTACGGTCA 59.350 38.462 0.00 0.00 0.00 4.02
3710 7199 6.183360 CGGTCTTGGTAGTTAAATTTACGGTC 60.183 42.308 0.00 0.00 0.00 4.79
3711 7200 5.639082 CGGTCTTGGTAGTTAAATTTACGGT 59.361 40.000 0.00 0.00 0.00 4.83
3712 7201 5.868801 TCGGTCTTGGTAGTTAAATTTACGG 59.131 40.000 0.00 0.00 0.00 4.02
3713 7202 6.949578 TCGGTCTTGGTAGTTAAATTTACG 57.050 37.500 0.00 0.00 0.00 3.18
3714 7203 7.695201 GCAATCGGTCTTGGTAGTTAAATTTAC 59.305 37.037 0.00 0.00 0.00 2.01
3715 7204 7.413219 CGCAATCGGTCTTGGTAGTTAAATTTA 60.413 37.037 0.00 0.00 0.00 1.40
3716 7205 6.617879 GCAATCGGTCTTGGTAGTTAAATTT 58.382 36.000 0.00 0.00 0.00 1.82
3717 7206 5.163794 CGCAATCGGTCTTGGTAGTTAAATT 60.164 40.000 0.00 0.00 0.00 1.82
3718 7207 4.331717 CGCAATCGGTCTTGGTAGTTAAAT 59.668 41.667 0.00 0.00 0.00 1.40
3719 7208 3.680937 CGCAATCGGTCTTGGTAGTTAAA 59.319 43.478 0.00 0.00 0.00 1.52
3720 7209 3.255725 CGCAATCGGTCTTGGTAGTTAA 58.744 45.455 0.00 0.00 0.00 2.01
3721 7210 2.883574 CGCAATCGGTCTTGGTAGTTA 58.116 47.619 0.00 0.00 0.00 2.24
3722 7211 1.722011 CGCAATCGGTCTTGGTAGTT 58.278 50.000 0.00 0.00 0.00 2.24
3723 7212 3.436001 CGCAATCGGTCTTGGTAGT 57.564 52.632 0.00 0.00 0.00 2.73
3735 7224 2.485188 TTTTTGCTCCCGCCGCAATC 62.485 55.000 5.33 0.00 45.67 2.67
3736 7225 1.887344 ATTTTTGCTCCCGCCGCAAT 61.887 50.000 5.33 0.00 45.67 3.56
3737 7226 2.093537 AATTTTTGCTCCCGCCGCAA 62.094 50.000 0.00 0.00 44.83 4.85
3738 7227 1.244697 TAATTTTTGCTCCCGCCGCA 61.245 50.000 0.00 0.00 35.22 5.69
3739 7228 0.102300 ATAATTTTTGCTCCCGCCGC 59.898 50.000 0.00 0.00 34.43 6.53
3740 7229 3.915437 ATATAATTTTTGCTCCCGCCG 57.085 42.857 0.00 0.00 34.43 6.46
3741 7230 6.016610 TCACTAATATAATTTTTGCTCCCGCC 60.017 38.462 0.00 0.00 34.43 6.13
3742 7231 6.966021 TCACTAATATAATTTTTGCTCCCGC 58.034 36.000 0.00 0.00 0.00 6.13
3743 7232 9.965824 AATTCACTAATATAATTTTTGCTCCCG 57.034 29.630 0.00 0.00 0.00 5.14
3801 7290 2.517402 ACTGCGGCGGGTGAAAAA 60.517 55.556 14.26 0.00 0.00 1.94
3802 7291 2.975799 GACTGCGGCGGGTGAAAA 60.976 61.111 14.26 0.00 0.00 2.29
3813 7302 2.870161 CGAACGAGACCGACTGCG 60.870 66.667 0.00 0.00 39.50 5.18
3814 7303 0.110056 TAACGAACGAGACCGACTGC 60.110 55.000 0.14 0.00 39.50 4.40
3815 7304 2.320805 TTAACGAACGAGACCGACTG 57.679 50.000 0.14 0.00 39.50 3.51
3816 7305 3.565905 ATTTAACGAACGAGACCGACT 57.434 42.857 0.14 0.00 39.50 4.18
3817 7306 4.635961 AAATTTAACGAACGAGACCGAC 57.364 40.909 0.14 0.00 39.50 4.79
3818 7307 5.289193 CCATAAATTTAACGAACGAGACCGA 59.711 40.000 1.21 0.00 39.50 4.69
3819 7308 5.062558 ACCATAAATTTAACGAACGAGACCG 59.937 40.000 1.21 0.00 42.50 4.79
3820 7309 6.091169 TGACCATAAATTTAACGAACGAGACC 59.909 38.462 1.21 0.00 0.00 3.85
3821 7310 7.052565 TGACCATAAATTTAACGAACGAGAC 57.947 36.000 1.21 0.00 0.00 3.36
3822 7311 7.655236 TTGACCATAAATTTAACGAACGAGA 57.345 32.000 1.21 0.00 0.00 4.04
3823 7312 8.013378 ACTTTGACCATAAATTTAACGAACGAG 58.987 33.333 1.21 0.01 0.00 4.18
3824 7313 7.863666 ACTTTGACCATAAATTTAACGAACGA 58.136 30.769 1.21 0.00 0.00 3.85
3825 7314 8.496872 AACTTTGACCATAAATTTAACGAACG 57.503 30.769 1.21 0.00 0.00 3.95
3826 7315 8.624028 CGAACTTTGACCATAAATTTAACGAAC 58.376 33.333 1.21 0.00 0.00 3.95
3827 7316 8.557864 TCGAACTTTGACCATAAATTTAACGAA 58.442 29.630 1.21 1.12 0.00 3.85
3828 7317 8.011106 GTCGAACTTTGACCATAAATTTAACGA 58.989 33.333 1.21 0.00 0.00 3.85
3829 7318 8.142348 GTCGAACTTTGACCATAAATTTAACG 57.858 34.615 1.21 0.00 0.00 3.18
3842 7331 0.316204 TCCCGAGGTCGAACTTTGAC 59.684 55.000 3.47 0.86 43.02 3.18
3843 7332 1.042229 TTCCCGAGGTCGAACTTTGA 58.958 50.000 3.47 0.00 43.02 2.69
3844 7333 1.529865 GTTTCCCGAGGTCGAACTTTG 59.470 52.381 3.47 0.00 43.02 2.77
3845 7334 1.870993 CGTTTCCCGAGGTCGAACTTT 60.871 52.381 3.47 0.00 43.02 2.66
3846 7335 0.319297 CGTTTCCCGAGGTCGAACTT 60.319 55.000 3.47 0.00 43.02 2.66
3847 7336 1.288127 CGTTTCCCGAGGTCGAACT 59.712 57.895 0.34 0.34 43.02 3.01
3848 7337 2.378084 GCGTTTCCCGAGGTCGAAC 61.378 63.158 0.00 0.00 43.02 3.95
3849 7338 2.048877 GCGTTTCCCGAGGTCGAA 60.049 61.111 0.00 0.00 43.02 3.71
3850 7339 4.409218 CGCGTTTCCCGAGGTCGA 62.409 66.667 0.00 0.00 43.02 4.20
3860 7349 1.219522 ATATAGTGCGCCCGCGTTTC 61.220 55.000 4.18 2.02 45.51 2.78
3861 7350 0.812412 AATATAGTGCGCCCGCGTTT 60.812 50.000 4.18 0.00 45.51 3.60
3862 7351 0.812412 AAATATAGTGCGCCCGCGTT 60.812 50.000 4.18 1.35 45.51 4.84
3863 7352 0.812412 AAAATATAGTGCGCCCGCGT 60.812 50.000 4.18 0.52 45.51 6.01
3864 7353 0.384230 CAAAATATAGTGCGCCCGCG 60.384 55.000 4.18 4.36 45.51 6.46
3865 7354 0.040425 CCAAAATATAGTGCGCCCGC 60.040 55.000 4.18 5.60 42.35 6.13
3866 7355 1.588674 TCCAAAATATAGTGCGCCCG 58.411 50.000 4.18 0.00 0.00 6.13
3867 7356 3.305335 CCATTCCAAAATATAGTGCGCCC 60.305 47.826 4.18 0.00 0.00 6.13
3868 7357 3.568007 TCCATTCCAAAATATAGTGCGCC 59.432 43.478 4.18 0.00 0.00 6.53
3869 7358 4.320494 CCTCCATTCCAAAATATAGTGCGC 60.320 45.833 0.00 0.00 0.00 6.09
3870 7359 4.216257 CCCTCCATTCCAAAATATAGTGCG 59.784 45.833 0.00 0.00 0.00 5.34
3871 7360 5.385198 TCCCTCCATTCCAAAATATAGTGC 58.615 41.667 0.00 0.00 0.00 4.40
3872 7361 6.605119 ACTCCCTCCATTCCAAAATATAGTG 58.395 40.000 0.00 0.00 0.00 2.74
3873 7362 6.848562 ACTCCCTCCATTCCAAAATATAGT 57.151 37.500 0.00 0.00 0.00 2.12
3874 7363 7.978925 ACTACTCCCTCCATTCCAAAATATAG 58.021 38.462 0.00 0.00 0.00 1.31
3875 7364 7.947782 ACTACTCCCTCCATTCCAAAATATA 57.052 36.000 0.00 0.00 0.00 0.86
3876 7365 6.848562 ACTACTCCCTCCATTCCAAAATAT 57.151 37.500 0.00 0.00 0.00 1.28
3877 7366 7.758820 TTACTACTCCCTCCATTCCAAAATA 57.241 36.000 0.00 0.00 0.00 1.40
3878 7367 6.652205 TTACTACTCCCTCCATTCCAAAAT 57.348 37.500 0.00 0.00 0.00 1.82
3879 7368 6.457159 TTTACTACTCCCTCCATTCCAAAA 57.543 37.500 0.00 0.00 0.00 2.44
3880 7369 6.243148 GTTTTACTACTCCCTCCATTCCAAA 58.757 40.000 0.00 0.00 0.00 3.28
3881 7370 5.570034 CGTTTTACTACTCCCTCCATTCCAA 60.570 44.000 0.00 0.00 0.00 3.53
3882 7371 4.081309 CGTTTTACTACTCCCTCCATTCCA 60.081 45.833 0.00 0.00 0.00 3.53
3883 7372 4.439968 CGTTTTACTACTCCCTCCATTCC 58.560 47.826 0.00 0.00 0.00 3.01
3884 7373 4.161001 TCCGTTTTACTACTCCCTCCATTC 59.839 45.833 0.00 0.00 0.00 2.67
3885 7374 4.098894 TCCGTTTTACTACTCCCTCCATT 58.901 43.478 0.00 0.00 0.00 3.16
3886 7375 3.705072 CTCCGTTTTACTACTCCCTCCAT 59.295 47.826 0.00 0.00 0.00 3.41
3887 7376 3.094572 CTCCGTTTTACTACTCCCTCCA 58.905 50.000 0.00 0.00 0.00 3.86
3888 7377 3.359950 TCTCCGTTTTACTACTCCCTCC 58.640 50.000 0.00 0.00 0.00 4.30
3889 7378 3.380954 CCTCTCCGTTTTACTACTCCCTC 59.619 52.174 0.00 0.00 0.00 4.30
3890 7379 3.011032 TCCTCTCCGTTTTACTACTCCCT 59.989 47.826 0.00 0.00 0.00 4.20
3891 7380 3.359950 TCCTCTCCGTTTTACTACTCCC 58.640 50.000 0.00 0.00 0.00 4.30
3892 7381 3.181488 GCTCCTCTCCGTTTTACTACTCC 60.181 52.174 0.00 0.00 0.00 3.85
3893 7382 3.695556 AGCTCCTCTCCGTTTTACTACTC 59.304 47.826 0.00 0.00 0.00 2.59
3894 7383 3.444388 CAGCTCCTCTCCGTTTTACTACT 59.556 47.826 0.00 0.00 0.00 2.57
3935 7424 8.394121 CAAATAGACCTTCTTTGCTCATTCTAC 58.606 37.037 0.00 0.00 0.00 2.59
3942 7431 6.765915 ATTCCAAATAGACCTTCTTTGCTC 57.234 37.500 0.00 0.00 0.00 4.26
3973 7462 1.978580 ACGGAGGTTTCCAGTGAGATT 59.021 47.619 0.00 0.00 44.26 2.40
4028 7517 1.063912 CGCTATTTGCTCATTTCGGCA 59.936 47.619 0.00 0.00 40.11 5.69
4065 7554 4.710167 TGGCTGCAGCGCTGACAT 62.710 61.111 40.21 0.00 40.46 3.06
4181 7677 3.455327 GGTGGAATCGCCTTAAGTAGTC 58.545 50.000 0.97 0.00 40.31 2.59
4198 7694 1.895020 TACCTAGCGCTTGTGGGTGG 61.895 60.000 18.68 9.39 0.00 4.61
4298 7807 3.055458 TCACGAATCTGGTGGCAATTAGA 60.055 43.478 0.00 0.00 36.09 2.10
4372 7885 0.465097 GTGTGGATCCATGGCTCTGG 60.465 60.000 19.62 0.78 37.66 3.86
4404 7917 5.163854 CGATTTCTGTAGCCTTGTTTCGATT 60.164 40.000 0.00 0.00 0.00 3.34


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

AutoCloner maintained by Alex Coulton.