Multiple sequence alignment - TraesCS7A01G549700

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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 TraesCS7A01G549700 chr7A 100.000 4246 0 0 1 4246 723956332 723960577 0.000000e+00 7841.0
1 TraesCS7A01G549700 chr7A 81.818 836 120 18 3 825 723862220 723863036 0.000000e+00 673.0
2 TraesCS7A01G549700 chr7A 87.755 588 52 11 829 1403 723915096 723915676 0.000000e+00 669.0
3 TraesCS7A01G549700 chr7B 91.146 3806 274 35 3 3779 730021831 730025602 0.000000e+00 5103.0
4 TraesCS7A01G549700 chr7B 85.799 1514 174 24 3 1495 729677973 729679466 0.000000e+00 1567.0
5 TraesCS7A01G549700 chr7B 90.877 285 24 2 3960 4244 730034641 730034923 8.620000e-102 381.0
6 TraesCS7A01G549700 chr7B 88.000 75 7 2 678 750 713272708 713272782 2.100000e-13 87.9
7 TraesCS7A01G549700 chr7D 91.873 3064 191 29 746 3787 628131322 628134349 0.000000e+00 4226.0
8 TraesCS7A01G549700 chr7D 84.463 708 92 10 3 700 628130626 628131325 0.000000e+00 682.0
9 TraesCS7A01G549700 chr7D 91.710 193 15 1 3938 4129 628135146 628135338 2.520000e-67 267.0
10 TraesCS7A01G549700 chr7D 88.770 187 20 1 3 189 627895337 627895522 1.190000e-55 228.0
11 TraesCS7A01G549700 chr7D 89.831 177 17 1 3 179 627778757 627778932 4.270000e-55 226.0
12 TraesCS7A01G549700 chr7D 89.831 177 17 1 3 179 627989525 627989700 4.270000e-55 226.0
13 TraesCS7A01G549700 chr7D 89.266 177 18 1 3 179 627719876 627720051 1.990000e-53 220.0
14 TraesCS7A01G549700 chr7D 89.266 177 17 2 3 179 627834485 627834659 1.990000e-53 220.0
15 TraesCS7A01G549700 chrUn 100.000 394 0 0 1991 2384 479428876 479429269 0.000000e+00 728.0
16 TraesCS7A01G549700 chr6B 79.870 308 45 8 3950 4244 493320830 493321133 4.300000e-50 209.0
17 TraesCS7A01G549700 chr6A 77.564 312 54 11 3946 4244 468259782 468260090 1.570000e-39 174.0
18 TraesCS7A01G549700 chr1B 75.467 375 70 19 402 770 633266211 633265853 3.400000e-36 163.0
19 TraesCS7A01G549700 chr1B 79.720 143 25 3 641 783 625278371 625278233 2.700000e-17 100.0
20 TraesCS7A01G549700 chr2B 78.970 233 45 4 531 762 636118420 636118191 5.680000e-34 156.0
21 TraesCS7A01G549700 chr3A 72.515 342 81 12 385 721 605181130 605180797 9.720000e-17 99.0
22 TraesCS7A01G549700 chr3B 88.095 84 7 2 687 770 726599541 726599621 3.490000e-16 97.1
23 TraesCS7A01G549700 chr4D 73.551 276 56 15 483 753 417418720 417418983 5.850000e-14 89.8
24 TraesCS7A01G549700 chr4D 92.593 54 4 0 2027 2080 97381287 97381340 1.270000e-10 78.7
25 TraesCS7A01G549700 chr5D 100.000 28 0 0 725 752 456729413 456729440 8.000000e-03 52.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G549700 chr7A 723956332 723960577 4245 False 7841 7841 100.000000 1 4246 1 chr7A.!!$F3 4245
1 TraesCS7A01G549700 chr7A 723862220 723863036 816 False 673 673 81.818000 3 825 1 chr7A.!!$F1 822
2 TraesCS7A01G549700 chr7A 723915096 723915676 580 False 669 669 87.755000 829 1403 1 chr7A.!!$F2 574
3 TraesCS7A01G549700 chr7B 730021831 730025602 3771 False 5103 5103 91.146000 3 3779 1 chr7B.!!$F3 3776
4 TraesCS7A01G549700 chr7B 729677973 729679466 1493 False 1567 1567 85.799000 3 1495 1 chr7B.!!$F2 1492
5 TraesCS7A01G549700 chr7D 628130626 628135338 4712 False 1725 4226 89.348667 3 4129 3 chr7D.!!$F6 4126

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
676 693 0.388649 TCTTCAGCTCGCTTCGGTTC 60.389 55.000 0.00 0.0 0.00 3.62 F
1924 1982 1.063174 GCACAAAGCAGATCATCGACC 59.937 52.381 0.00 0.0 44.79 4.79 F
2612 2676 0.318699 CGTCGTTGCTCAACCTCTCA 60.319 55.000 7.12 0.0 38.03 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1944 2002 0.175760 TCTCGTCTATGCCAGCAACC 59.824 55.0 0.00 0.0 0.00 3.77 R
2906 2970 0.162507 CGAGAGTTTTGAGCAGCACG 59.837 55.0 0.00 0.0 0.00 5.34 R
4139 4903 0.034283 TGCATCCTAGTTGCATGGCA 60.034 50.0 12.23 0.0 44.73 4.92 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
54 55 9.787435 AAGATATTATTTACCGAAACCATAGCA 57.213 29.630 0.00 0.00 0.00 3.49
128 129 5.313712 CCAACCTAGTCAAAAGGTGTACAT 58.686 41.667 0.00 0.00 46.85 2.29
132 133 5.544948 ACCTAGTCAAAAGGTGTACATGGTA 59.455 40.000 0.00 0.00 45.78 3.25
179 180 4.172346 CGTACGAACGGCATCCAA 57.828 55.556 10.44 0.00 45.50 3.53
182 183 0.671163 GTACGAACGGCATCCAACCA 60.671 55.000 0.00 0.00 0.00 3.67
218 219 1.197036 CTGTCTGCGTCGTCTTCTGTA 59.803 52.381 0.00 0.00 0.00 2.74
220 221 1.977412 GTCTGCGTCGTCTTCTGTAAC 59.023 52.381 0.00 0.00 0.00 2.50
228 229 3.760684 GTCGTCTTCTGTAACCTTAGGGA 59.239 47.826 2.32 0.00 36.25 4.20
235 236 4.499472 TCTGTAACCTTAGGGATATGGGG 58.501 47.826 2.32 0.00 36.25 4.96
237 238 2.931481 AACCTTAGGGATATGGGGGT 57.069 50.000 2.32 0.00 36.25 4.95
243 244 0.651124 AGGGATATGGGGGTGTGGTA 59.349 55.000 0.00 0.00 0.00 3.25
247 248 3.505278 GGGATATGGGGGTGTGGTAGATA 60.505 52.174 0.00 0.00 0.00 1.98
280 281 2.095415 CGACGGGAGGGATTTGTTTTTC 60.095 50.000 0.00 0.00 0.00 2.29
322 325 2.922740 AGAGTTTGTGTCCCGCTTAA 57.077 45.000 0.00 0.00 0.00 1.85
327 330 2.614983 GTTTGTGTCCCGCTTAAAGACA 59.385 45.455 0.00 0.00 38.17 3.41
361 364 1.996191 GCGGCTCTCGAATATGGAATC 59.004 52.381 0.00 0.00 42.43 2.52
363 366 3.653344 CGGCTCTCGAATATGGAATCAA 58.347 45.455 0.00 0.00 42.43 2.57
375 378 1.742831 TGGAATCAAATTCTTCCCGCG 59.257 47.619 0.00 0.00 40.22 6.46
392 405 0.594796 GCGTTTTGGTGGTGCTTCTG 60.595 55.000 0.00 0.00 0.00 3.02
394 407 1.111277 GTTTTGGTGGTGCTTCTGGT 58.889 50.000 0.00 0.00 0.00 4.00
399 412 0.955919 GGTGGTGCTTCTGGTGTAGC 60.956 60.000 0.00 0.00 37.16 3.58
424 437 1.002792 GGGCGTGTGAAAGTTTGTCTC 60.003 52.381 0.00 0.00 0.00 3.36
426 439 1.668751 GCGTGTGAAAGTTTGTCTCCA 59.331 47.619 0.00 0.00 0.00 3.86
428 441 2.286418 CGTGTGAAAGTTTGTCTCCAGC 60.286 50.000 0.00 0.00 0.00 4.85
515 532 3.767131 TGTGTCGAGAGGTTGGATATTCA 59.233 43.478 0.00 0.00 0.00 2.57
522 539 5.048643 CGAGAGGTTGGATATTCACGTCTAT 60.049 44.000 8.07 0.00 0.00 1.98
579 596 4.035208 GTGCGTTGATCCTATAAGGGTTTG 59.965 45.833 0.00 0.00 35.59 2.93
597 614 1.375523 GGCACAACGACTTCCCGAT 60.376 57.895 0.00 0.00 0.00 4.18
638 655 3.374764 TGCCTAGCATTAGTGAAGGAGA 58.625 45.455 10.19 0.00 33.91 3.71
639 656 3.774766 TGCCTAGCATTAGTGAAGGAGAA 59.225 43.478 10.19 0.00 33.91 2.87
648 665 1.895798 AGTGAAGGAGAAGCGATGACA 59.104 47.619 0.00 0.00 0.00 3.58
650 667 2.413453 GTGAAGGAGAAGCGATGACAAC 59.587 50.000 0.00 0.00 0.00 3.32
662 679 2.357034 GACAACGGCGCCTCTTCA 60.357 61.111 26.68 0.00 0.00 3.02
666 683 3.941657 AACGGCGCCTCTTCAGCTC 62.942 63.158 26.68 0.00 0.00 4.09
676 693 0.388649 TCTTCAGCTCGCTTCGGTTC 60.389 55.000 0.00 0.00 0.00 3.62
688 705 4.501559 TCGCTTCGGTTCTTATAATTGTCG 59.498 41.667 0.00 0.00 0.00 4.35
702 719 2.149803 TTGTCGCTAGGTGGTCCACG 62.150 60.000 15.93 4.19 34.83 4.94
708 725 1.471676 GCTAGGTGGTCCACGAATCTG 60.472 57.143 15.93 4.20 34.83 2.90
770 791 8.179148 GTCATGATGGATAATGACGAATAGAC 57.821 38.462 0.00 0.00 42.24 2.59
771 792 7.814587 GTCATGATGGATAATGACGAATAGACA 59.185 37.037 0.00 0.00 42.24 3.41
785 806 6.296803 ACGAATAGACAAGAAAGTTTTCCCT 58.703 36.000 0.00 0.00 37.92 4.20
786 807 7.447594 ACGAATAGACAAGAAAGTTTTCCCTA 58.552 34.615 0.00 0.40 37.92 3.53
787 808 7.603024 ACGAATAGACAAGAAAGTTTTCCCTAG 59.397 37.037 0.00 0.00 37.92 3.02
788 809 7.064728 CGAATAGACAAGAAAGTTTTCCCTAGG 59.935 40.741 0.06 0.06 37.92 3.02
789 810 5.906772 AGACAAGAAAGTTTTCCCTAGGA 57.093 39.130 11.48 0.00 37.92 2.94
803 831 5.500546 TCCCTAGGAAAGAAAGAAAGACC 57.499 43.478 11.48 0.00 0.00 3.85
864 896 5.795441 CGTTTGCTATTTTTGAAGCCTACTC 59.205 40.000 0.00 0.00 37.97 2.59
882 914 2.039084 ACTCGTTCCTGGAATTCAGCTT 59.961 45.455 13.07 0.00 42.05 3.74
933 966 3.626924 CTATTCCCTCCGCCCCCG 61.627 72.222 0.00 0.00 0.00 5.73
978 1011 3.453070 CTCGCCAAGCTAGCCTCCC 62.453 68.421 12.13 0.00 0.00 4.30
1403 1459 4.693566 TCTCTTGCCGTCAACGAATTAATT 59.306 37.500 0.00 0.00 43.02 1.40
1404 1460 5.870433 TCTCTTGCCGTCAACGAATTAATTA 59.130 36.000 3.71 0.00 43.02 1.40
1405 1461 6.369340 TCTCTTGCCGTCAACGAATTAATTAA 59.631 34.615 3.71 0.00 43.02 1.40
1423 1479 5.734855 ATTAACGGGATTTCTGATTCGTG 57.265 39.130 0.00 0.00 0.00 4.35
1433 1489 1.879380 TCTGATTCGTGGCTGGTTTTG 59.121 47.619 0.00 0.00 0.00 2.44
1479 1535 4.021925 GTGCAGGGGAGCTTCCGT 62.022 66.667 4.51 1.54 37.43 4.69
1488 1544 1.153628 GAGCTTCCGTGCCGTGTAT 60.154 57.895 0.00 0.00 0.00 2.29
1501 1557 2.535984 GCCGTGTATGAGAAGATCAACG 59.464 50.000 0.00 0.00 42.53 4.10
1502 1558 3.770666 CCGTGTATGAGAAGATCAACGT 58.229 45.455 0.00 0.00 42.53 3.99
1503 1559 3.791887 CCGTGTATGAGAAGATCAACGTC 59.208 47.826 0.00 0.00 42.53 4.34
1506 1562 1.550065 ATGAGAAGATCAACGTCGCG 58.450 50.000 0.00 0.00 42.53 5.87
1620 1678 3.681417 GCCTCCAAGAAATCAAATTGTGC 59.319 43.478 0.00 0.00 0.00 4.57
1653 1711 5.994250 TGCTGCCTCTGATCTAACTAAAAT 58.006 37.500 0.00 0.00 0.00 1.82
1802 1860 1.305297 ACAGGGTCATCCTCGAGCA 60.305 57.895 6.99 0.00 46.12 4.26
1887 1945 1.656652 AGCTAATCAACGAGCGCAAT 58.343 45.000 11.47 0.00 43.72 3.56
1923 1981 2.448726 GCACAAAGCAGATCATCGAC 57.551 50.000 0.00 0.00 44.79 4.20
1924 1982 1.063174 GCACAAAGCAGATCATCGACC 59.937 52.381 0.00 0.00 44.79 4.79
1930 1988 1.686052 AGCAGATCATCGACCTTCTCC 59.314 52.381 0.00 0.00 0.00 3.71
2392 2456 2.689658 TCCTGTTGAGGAGGAAGTGAA 58.310 47.619 0.00 0.00 44.13 3.18
2399 2463 5.309543 TGTTGAGGAGGAAGTGAATAAGGAA 59.690 40.000 0.00 0.00 0.00 3.36
2402 2466 6.261435 TGAGGAGGAAGTGAATAAGGAAGTA 58.739 40.000 0.00 0.00 0.00 2.24
2477 2541 3.577313 GCCGCCAAGAAGATCCGC 61.577 66.667 0.00 0.00 0.00 5.54
2498 2562 1.746991 GCTTTCCAAGGAGAGCCCG 60.747 63.158 18.18 0.00 43.78 6.13
2517 2581 1.591703 GAGGACCGCACACTCATCA 59.408 57.895 0.00 0.00 0.00 3.07
2518 2582 0.737715 GAGGACCGCACACTCATCAC 60.738 60.000 0.00 0.00 0.00 3.06
2527 2591 2.410939 CACACTCATCACTGACAGTGG 58.589 52.381 30.39 18.83 45.94 4.00
2528 2592 2.036346 CACACTCATCACTGACAGTGGA 59.964 50.000 30.39 20.84 45.94 4.02
2564 2628 3.009115 GGCCTCCTGCAGTACCCA 61.009 66.667 13.81 0.00 43.89 4.51
2570 2634 1.347707 CTCCTGCAGTACCCAGACAAA 59.652 52.381 13.81 0.00 32.03 2.83
2585 2649 4.768968 CCAGACAAAAAGATCCAGGACAAT 59.231 41.667 0.00 0.00 0.00 2.71
2612 2676 0.318699 CGTCGTTGCTCAACCTCTCA 60.319 55.000 7.12 0.00 38.03 3.27
2645 2709 3.703556 TCAACAAGGTCTTGATTGCCAAA 59.296 39.130 16.55 1.31 42.93 3.28
2651 2715 2.833943 GGTCTTGATTGCCAAAGGGAAT 59.166 45.455 2.24 2.24 46.17 3.01
2741 2805 2.795329 CTGTTTAGCCTGTCCATGGTT 58.205 47.619 12.58 0.00 0.00 3.67
2888 2952 5.010282 CACCAGAACAAGTTAAGGGCTATT 58.990 41.667 7.70 0.00 0.00 1.73
2906 2970 2.514824 GAGGCTGGCATCGTTCCC 60.515 66.667 3.38 0.00 0.00 3.97
2920 2984 0.317854 GTTCCCGTGCTGCTCAAAAC 60.318 55.000 0.00 0.00 0.00 2.43
2936 3000 3.927758 TCAAAACTCTCGACAACACGAAA 59.072 39.130 0.00 0.00 41.67 3.46
2990 3054 1.672356 CCTGCTTGGGTCCAACTCG 60.672 63.158 0.00 0.00 0.00 4.18
3026 3090 0.959553 TCGGAACAGAGAGCTTCGTT 59.040 50.000 0.00 0.00 0.00 3.85
3080 3144 1.679139 CCAAGAACAAGGAGTGTGCA 58.321 50.000 0.00 0.00 40.60 4.57
3095 3159 4.718961 AGTGTGCACTTTCTGTTATCCTT 58.281 39.130 19.41 0.00 38.83 3.36
3167 3231 1.226802 CCACGAGCATCTCACGGAG 60.227 63.158 0.00 0.00 32.98 4.63
3236 3300 0.183492 TTCAGCTTGCCCAGAAGTGT 59.817 50.000 0.00 0.00 0.00 3.55
3257 3321 8.690680 AGTGTGAATCGTAGAAGAAGAATTAC 57.309 34.615 0.00 0.00 43.58 1.89
3259 3323 6.750501 TGTGAATCGTAGAAGAAGAATTACGG 59.249 38.462 3.49 0.00 43.58 4.02
3266 3330 5.723672 AGAAGAAGAATTACGGACTGTGA 57.276 39.130 0.00 0.00 0.00 3.58
3271 3335 7.133891 AGAAGAATTACGGACTGTGAAATTG 57.866 36.000 0.00 0.00 0.00 2.32
3278 3342 2.807967 CGGACTGTGAAATTGAAGCTCA 59.192 45.455 0.00 0.00 0.00 4.26
3467 3544 7.972277 ACAGTTCATATTGTTCATTGATTGAGC 59.028 33.333 0.00 0.00 35.27 4.26
3472 3549 4.933505 TTGTTCATTGATTGAGCAACCA 57.066 36.364 3.10 0.00 46.62 3.67
3479 3556 4.836125 TTGATTGAGCAACCAGAAGAAC 57.164 40.909 0.00 0.00 0.00 3.01
3593 3670 3.378427 GGTGTGTTGATATTTCTCAGGGC 59.622 47.826 0.00 0.00 0.00 5.19
3594 3671 3.378427 GTGTGTTGATATTTCTCAGGGCC 59.622 47.826 0.00 0.00 0.00 5.80
3595 3672 2.614057 GTGTTGATATTTCTCAGGGCCG 59.386 50.000 0.00 0.00 0.00 6.13
3596 3673 2.222027 GTTGATATTTCTCAGGGCCGG 58.778 52.381 0.00 0.00 0.00 6.13
3636 3713 3.564225 ACTGAATTTTTGTCCGGACAGTC 59.436 43.478 34.25 25.34 42.94 3.51
3658 3738 4.454504 TCGACTCAGCCAAACCTATTTTTC 59.545 41.667 0.00 0.00 0.00 2.29
3696 3777 3.974871 TTTGTTGCTTTAGGGTCGAAC 57.025 42.857 0.00 0.00 0.00 3.95
3807 3905 0.464554 GCTTACCTGTGATGGCCCTC 60.465 60.000 0.00 0.00 0.00 4.30
3815 3913 3.562176 CCTGTGATGGCCCTCTTTTACTT 60.562 47.826 9.61 0.00 0.00 2.24
3816 3914 4.082125 CTGTGATGGCCCTCTTTTACTTT 58.918 43.478 9.61 0.00 0.00 2.66
3817 3915 3.826157 TGTGATGGCCCTCTTTTACTTTG 59.174 43.478 9.61 0.00 0.00 2.77
3818 3916 3.826729 GTGATGGCCCTCTTTTACTTTGT 59.173 43.478 9.61 0.00 0.00 2.83
3819 3917 3.826157 TGATGGCCCTCTTTTACTTTGTG 59.174 43.478 9.61 0.00 0.00 3.33
3820 3918 3.306472 TGGCCCTCTTTTACTTTGTGT 57.694 42.857 0.00 0.00 0.00 3.72
3821 3919 3.637769 TGGCCCTCTTTTACTTTGTGTT 58.362 40.909 0.00 0.00 0.00 3.32
3822 3920 4.794334 TGGCCCTCTTTTACTTTGTGTTA 58.206 39.130 0.00 0.00 0.00 2.41
3823 3921 4.581409 TGGCCCTCTTTTACTTTGTGTTAC 59.419 41.667 0.00 0.00 0.00 2.50
3824 3922 4.825634 GGCCCTCTTTTACTTTGTGTTACT 59.174 41.667 0.00 0.00 0.00 2.24
3825 3923 5.301045 GGCCCTCTTTTACTTTGTGTTACTT 59.699 40.000 0.00 0.00 0.00 2.24
3826 3924 6.206498 GCCCTCTTTTACTTTGTGTTACTTG 58.794 40.000 0.00 0.00 0.00 3.16
3827 3925 6.734871 GCCCTCTTTTACTTTGTGTTACTTGG 60.735 42.308 0.00 0.00 0.00 3.61
3828 3926 6.544564 CCCTCTTTTACTTTGTGTTACTTGGA 59.455 38.462 0.00 0.00 0.00 3.53
3829 3927 7.067737 CCCTCTTTTACTTTGTGTTACTTGGAA 59.932 37.037 0.00 0.00 0.00 3.53
3830 3928 8.463607 CCTCTTTTACTTTGTGTTACTTGGAAA 58.536 33.333 0.00 0.00 0.00 3.13
3838 3936 9.758651 ACTTTGTGTTACTTGGAAATTAAATCC 57.241 29.630 4.16 4.16 37.48 3.01
3839 3937 9.203421 CTTTGTGTTACTTGGAAATTAAATCCC 57.797 33.333 7.89 0.00 36.04 3.85
3840 3938 7.841282 TGTGTTACTTGGAAATTAAATCCCA 57.159 32.000 7.89 0.00 36.04 4.37
3841 3939 7.662897 TGTGTTACTTGGAAATTAAATCCCAC 58.337 34.615 7.89 7.81 36.04 4.61
3842 3940 7.287927 TGTGTTACTTGGAAATTAAATCCCACA 59.712 33.333 7.89 9.69 36.04 4.17
3843 3941 8.145122 GTGTTACTTGGAAATTAAATCCCACAA 58.855 33.333 7.89 0.00 36.04 3.33
3844 3942 8.705594 TGTTACTTGGAAATTAAATCCCACAAA 58.294 29.630 7.89 0.00 36.04 2.83
3845 3943 9.719355 GTTACTTGGAAATTAAATCCCACAAAT 57.281 29.630 7.89 0.00 36.04 2.32
3848 3946 9.639563 ACTTGGAAATTAAATCCCACAAATTTT 57.360 25.926 7.89 0.00 36.04 1.82
3909 4007 2.450609 ACGCCCAACAACTGTACTAG 57.549 50.000 0.00 0.00 0.00 2.57
3934 4032 4.394300 ACACATCTTCTTGAGCATAAGCAC 59.606 41.667 0.00 0.00 45.49 4.40
3939 4702 4.874396 TCTTCTTGAGCATAAGCACATCTG 59.126 41.667 0.00 0.00 45.49 2.90
3947 4710 2.967459 TAAGCACATCTGCAACGTTG 57.033 45.000 23.90 23.90 46.97 4.10
3977 4740 6.801539 TGTTTGCTCTATTTCACGATCTTT 57.198 33.333 0.00 0.00 0.00 2.52
3997 4760 8.679288 ATCTTTACAAATTCAAAATCTGAGCG 57.321 30.769 0.00 0.00 34.81 5.03
4036 4799 6.333416 TCGCATATAGAGGAGATAATGTTGC 58.667 40.000 0.00 0.00 0.00 4.17
4046 4810 4.438744 GGAGATAATGTTGCGGGTTGAAAG 60.439 45.833 0.00 0.00 0.00 2.62
4084 4848 3.637998 AATCTTGCAACAACTCAGCTG 57.362 42.857 7.63 7.63 0.00 4.24
4087 4851 1.002033 CTTGCAACAACTCAGCTGACC 60.002 52.381 13.74 0.00 0.00 4.02
4115 4879 4.187694 GACAACAGGAAGACCTCATGATC 58.812 47.826 0.00 0.00 45.94 2.92
4116 4880 3.193263 CAACAGGAAGACCTCATGATCG 58.807 50.000 0.00 0.00 45.94 3.69
4129 4893 4.153655 CCTCATGATCGATATTGTGCAAGG 59.846 45.833 0.00 0.00 0.00 3.61
4130 4894 4.959723 TCATGATCGATATTGTGCAAGGA 58.040 39.130 0.00 0.00 0.00 3.36
4131 4895 4.992951 TCATGATCGATATTGTGCAAGGAG 59.007 41.667 0.00 0.00 0.00 3.69
4132 4896 4.406648 TGATCGATATTGTGCAAGGAGT 57.593 40.909 0.00 0.00 0.00 3.85
4133 4897 4.122046 TGATCGATATTGTGCAAGGAGTG 58.878 43.478 0.00 0.00 0.00 3.51
4134 4898 2.905075 TCGATATTGTGCAAGGAGTGG 58.095 47.619 0.00 0.00 0.00 4.00
4135 4899 1.942657 CGATATTGTGCAAGGAGTGGG 59.057 52.381 0.00 0.00 0.00 4.61
4136 4900 2.301346 GATATTGTGCAAGGAGTGGGG 58.699 52.381 0.00 0.00 0.00 4.96
4137 4901 1.367346 TATTGTGCAAGGAGTGGGGA 58.633 50.000 0.00 0.00 0.00 4.81
4138 4902 0.706433 ATTGTGCAAGGAGTGGGGAT 59.294 50.000 0.00 0.00 0.00 3.85
4139 4903 0.482446 TTGTGCAAGGAGTGGGGATT 59.518 50.000 0.00 0.00 0.00 3.01
4140 4904 0.251297 TGTGCAAGGAGTGGGGATTG 60.251 55.000 0.00 0.00 0.00 2.67
4141 4905 1.304381 TGCAAGGAGTGGGGATTGC 60.304 57.895 1.96 1.96 36.11 3.56
4142 4906 2.054453 GCAAGGAGTGGGGATTGCC 61.054 63.158 0.00 0.00 0.00 4.52
4143 4907 1.383799 CAAGGAGTGGGGATTGCCA 59.616 57.895 0.00 0.00 35.15 4.92
4144 4908 0.032813 CAAGGAGTGGGGATTGCCAT 60.033 55.000 0.00 0.00 35.15 4.40
4145 4909 0.032813 AAGGAGTGGGGATTGCCATG 60.033 55.000 0.00 0.00 35.15 3.66
4146 4910 2.129785 GGAGTGGGGATTGCCATGC 61.130 63.158 0.00 0.00 35.15 4.06
4147 4911 1.380246 GAGTGGGGATTGCCATGCA 60.380 57.895 0.00 0.00 36.47 3.96
4157 4921 1.105457 TTGCCATGCAACTAGGATGC 58.895 50.000 14.02 14.02 43.99 3.91
4164 4928 2.099141 GCAACTAGGATGCACACAGA 57.901 50.000 15.52 0.00 43.29 3.41
4165 4929 2.636830 GCAACTAGGATGCACACAGAT 58.363 47.619 15.52 0.00 43.29 2.90
4166 4930 2.611292 GCAACTAGGATGCACACAGATC 59.389 50.000 15.52 0.00 43.29 2.75
4167 4931 3.865446 CAACTAGGATGCACACAGATCA 58.135 45.455 0.00 0.00 0.00 2.92
4168 4932 4.256110 CAACTAGGATGCACACAGATCAA 58.744 43.478 0.00 0.00 0.00 2.57
4169 4933 4.767578 ACTAGGATGCACACAGATCAAT 57.232 40.909 0.00 0.00 0.00 2.57
4170 4934 5.876651 ACTAGGATGCACACAGATCAATA 57.123 39.130 0.00 0.00 0.00 1.90
4171 4935 6.430962 ACTAGGATGCACACAGATCAATAT 57.569 37.500 0.00 0.00 0.00 1.28
4172 4936 6.228995 ACTAGGATGCACACAGATCAATATG 58.771 40.000 0.00 0.00 0.00 1.78
4173 4937 4.395625 AGGATGCACACAGATCAATATGG 58.604 43.478 0.00 0.00 0.00 2.74
4174 4938 3.057736 GGATGCACACAGATCAATATGGC 60.058 47.826 0.00 0.00 0.00 4.40
4175 4939 3.002038 TGCACACAGATCAATATGGCA 57.998 42.857 0.00 0.00 0.00 4.92
4176 4940 3.354467 TGCACACAGATCAATATGGCAA 58.646 40.909 0.00 0.00 0.00 4.52
4177 4941 3.955551 TGCACACAGATCAATATGGCAAT 59.044 39.130 0.00 0.00 0.00 3.56
4178 4942 4.202070 TGCACACAGATCAATATGGCAATG 60.202 41.667 0.00 0.00 0.00 2.82
4179 4943 4.037089 GCACACAGATCAATATGGCAATGA 59.963 41.667 0.00 0.00 0.00 2.57
4180 4944 5.450826 GCACACAGATCAATATGGCAATGAA 60.451 40.000 0.00 0.00 0.00 2.57
4181 4945 6.566141 CACACAGATCAATATGGCAATGAAA 58.434 36.000 0.00 0.00 0.00 2.69
4182 4946 6.695713 CACACAGATCAATATGGCAATGAAAG 59.304 38.462 0.00 0.00 0.00 2.62
4183 4947 5.690409 CACAGATCAATATGGCAATGAAAGC 59.310 40.000 0.00 0.00 0.00 3.51
4184 4948 5.597182 ACAGATCAATATGGCAATGAAAGCT 59.403 36.000 0.00 0.00 0.00 3.74
4185 4949 6.150318 CAGATCAATATGGCAATGAAAGCTC 58.850 40.000 0.00 0.00 0.00 4.09
4186 4950 6.016192 CAGATCAATATGGCAATGAAAGCTCT 60.016 38.462 0.00 0.00 0.00 4.09
4187 4951 5.762825 TCAATATGGCAATGAAAGCTCTC 57.237 39.130 0.00 0.00 0.00 3.20
4188 4952 4.581824 TCAATATGGCAATGAAAGCTCTCC 59.418 41.667 0.00 0.00 0.00 3.71
4189 4953 2.822707 ATGGCAATGAAAGCTCTCCT 57.177 45.000 0.00 0.00 0.00 3.69
4190 4954 3.939740 ATGGCAATGAAAGCTCTCCTA 57.060 42.857 0.00 0.00 0.00 2.94
4191 4955 2.991250 TGGCAATGAAAGCTCTCCTAC 58.009 47.619 0.00 0.00 0.00 3.18
4192 4956 1.936547 GGCAATGAAAGCTCTCCTACG 59.063 52.381 0.00 0.00 0.00 3.51
4193 4957 1.936547 GCAATGAAAGCTCTCCTACGG 59.063 52.381 0.00 0.00 0.00 4.02
4194 4958 2.418746 GCAATGAAAGCTCTCCTACGGA 60.419 50.000 0.00 0.00 0.00 4.69
4195 4959 3.190874 CAATGAAAGCTCTCCTACGGAC 58.809 50.000 0.00 0.00 0.00 4.79
4196 4960 2.217510 TGAAAGCTCTCCTACGGACT 57.782 50.000 0.00 0.00 0.00 3.85
4197 4961 3.361281 TGAAAGCTCTCCTACGGACTA 57.639 47.619 0.00 0.00 0.00 2.59
4198 4962 3.693807 TGAAAGCTCTCCTACGGACTAA 58.306 45.455 0.00 0.00 0.00 2.24
4199 4963 4.279145 TGAAAGCTCTCCTACGGACTAAT 58.721 43.478 0.00 0.00 0.00 1.73
4200 4964 4.098044 TGAAAGCTCTCCTACGGACTAATG 59.902 45.833 0.00 0.00 0.00 1.90
4201 4965 1.957877 AGCTCTCCTACGGACTAATGC 59.042 52.381 0.00 0.00 0.00 3.56
4202 4966 1.335142 GCTCTCCTACGGACTAATGCG 60.335 57.143 0.00 0.00 46.59 4.73
4203 4967 1.267261 CTCTCCTACGGACTAATGCGG 59.733 57.143 0.00 0.00 45.25 5.69
4204 4968 0.314302 CTCCTACGGACTAATGCGGG 59.686 60.000 0.00 0.00 45.25 6.13
4205 4969 0.396139 TCCTACGGACTAATGCGGGT 60.396 55.000 0.00 0.00 45.25 5.28
4206 4970 1.133823 TCCTACGGACTAATGCGGGTA 60.134 52.381 0.00 0.00 45.25 3.69
4207 4971 1.000938 CCTACGGACTAATGCGGGTAC 60.001 57.143 0.00 0.00 45.25 3.34
4208 4972 1.677576 CTACGGACTAATGCGGGTACA 59.322 52.381 0.00 0.00 45.25 2.90
4209 4973 1.117150 ACGGACTAATGCGGGTACAT 58.883 50.000 0.00 0.00 45.25 2.29
4210 4974 1.068127 ACGGACTAATGCGGGTACATC 59.932 52.381 0.00 0.00 45.25 3.06
4211 4975 1.067974 CGGACTAATGCGGGTACATCA 59.932 52.381 0.00 0.00 35.75 3.07
4212 4976 2.755650 GGACTAATGCGGGTACATCAG 58.244 52.381 0.00 0.00 0.00 2.90
4213 4977 2.135933 GACTAATGCGGGTACATCAGC 58.864 52.381 0.00 0.00 0.00 4.26
4214 4978 1.762957 ACTAATGCGGGTACATCAGCT 59.237 47.619 0.00 0.00 0.00 4.24
4215 4979 2.170607 ACTAATGCGGGTACATCAGCTT 59.829 45.455 0.00 0.00 0.00 3.74
4216 4980 1.382522 AATGCGGGTACATCAGCTTG 58.617 50.000 0.00 0.00 0.00 4.01
4217 4981 1.097547 ATGCGGGTACATCAGCTTGC 61.098 55.000 0.00 0.00 0.00 4.01
4218 4982 2.472909 GCGGGTACATCAGCTTGCC 61.473 63.158 0.00 0.00 0.00 4.52
4219 4983 1.221840 CGGGTACATCAGCTTGCCT 59.778 57.895 0.00 0.00 0.00 4.75
4220 4984 0.811616 CGGGTACATCAGCTTGCCTC 60.812 60.000 0.00 0.00 0.00 4.70
4221 4985 0.543749 GGGTACATCAGCTTGCCTCT 59.456 55.000 0.00 0.00 0.00 3.69
4222 4986 1.065126 GGGTACATCAGCTTGCCTCTT 60.065 52.381 0.00 0.00 0.00 2.85
4223 4987 2.284190 GGTACATCAGCTTGCCTCTTC 58.716 52.381 0.00 0.00 0.00 2.87
4224 4988 2.355108 GGTACATCAGCTTGCCTCTTCA 60.355 50.000 0.00 0.00 0.00 3.02
4225 4989 2.803030 ACATCAGCTTGCCTCTTCAT 57.197 45.000 0.00 0.00 0.00 2.57
4226 4990 2.366533 ACATCAGCTTGCCTCTTCATG 58.633 47.619 0.00 0.00 0.00 3.07
4227 4991 2.026542 ACATCAGCTTGCCTCTTCATGA 60.027 45.455 0.00 0.00 0.00 3.07
4228 4992 2.865119 TCAGCTTGCCTCTTCATGAA 57.135 45.000 8.12 8.12 0.00 2.57
4229 4993 2.708051 TCAGCTTGCCTCTTCATGAAG 58.292 47.619 26.56 26.56 39.71 3.02
4230 4994 2.303890 TCAGCTTGCCTCTTCATGAAGA 59.696 45.455 31.10 31.10 44.47 2.87
4231 4995 2.419324 CAGCTTGCCTCTTCATGAAGAC 59.581 50.000 30.05 22.32 42.06 3.01
4232 4996 1.742268 GCTTGCCTCTTCATGAAGACC 59.258 52.381 30.05 23.29 42.06 3.85
4233 4997 2.617532 GCTTGCCTCTTCATGAAGACCT 60.618 50.000 30.05 0.00 42.06 3.85
4234 4998 3.369892 GCTTGCCTCTTCATGAAGACCTA 60.370 47.826 30.05 19.53 42.06 3.08
4235 4999 4.440880 CTTGCCTCTTCATGAAGACCTAG 58.559 47.826 30.05 23.42 42.06 3.02
4236 5000 3.713003 TGCCTCTTCATGAAGACCTAGA 58.287 45.455 30.05 12.49 42.06 2.43
4237 5001 4.293494 TGCCTCTTCATGAAGACCTAGAT 58.707 43.478 30.05 0.00 42.06 1.98
4238 5002 4.343526 TGCCTCTTCATGAAGACCTAGATC 59.656 45.833 30.05 16.51 42.06 2.75
4239 5003 4.588528 GCCTCTTCATGAAGACCTAGATCT 59.411 45.833 30.05 0.00 42.06 2.75
4240 5004 5.278957 GCCTCTTCATGAAGACCTAGATCTC 60.279 48.000 30.05 10.36 42.06 2.75
4241 5005 5.832595 CCTCTTCATGAAGACCTAGATCTCA 59.167 44.000 30.05 9.07 42.06 3.27
4242 5006 6.494491 CCTCTTCATGAAGACCTAGATCTCAT 59.506 42.308 30.05 0.00 42.06 2.90
4243 5007 7.015487 CCTCTTCATGAAGACCTAGATCTCATT 59.985 40.741 30.05 0.00 42.06 2.57
4244 5008 9.076781 CTCTTCATGAAGACCTAGATCTCATTA 57.923 37.037 30.05 7.90 42.06 1.90
4245 5009 9.599056 TCTTCATGAAGACCTAGATCTCATTAT 57.401 33.333 30.05 0.00 42.06 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 4.439289 GGCAAATGTCTCTGCTATGGTTTC 60.439 45.833 0.00 0.00 38.65 2.78
54 55 2.905415 TCATTGGGGCAAATGTCTCT 57.095 45.000 10.72 0.00 38.46 3.10
82 83 3.502123 AGGGGTTCGACTTTTCATCAA 57.498 42.857 0.00 0.00 0.00 2.57
132 133 1.757306 CCTAGAGGCGCAATGGGAT 59.243 57.895 10.83 0.00 0.00 3.85
137 138 2.551071 GCTATTTCCCTAGAGGCGCAAT 60.551 50.000 10.83 0.00 34.51 3.56
138 139 1.202651 GCTATTTCCCTAGAGGCGCAA 60.203 52.381 10.83 0.00 34.51 4.85
139 140 0.393077 GCTATTTCCCTAGAGGCGCA 59.607 55.000 10.83 0.00 34.51 6.09
173 174 1.423845 GCGCTAACGTGGTTGGATG 59.576 57.895 0.00 0.00 42.83 3.51
195 196 3.575351 AAGACGACGCAGACAGGGC 62.575 63.158 0.00 0.00 0.00 5.19
206 207 3.760684 TCCCTAAGGTTACAGAAGACGAC 59.239 47.826 0.00 0.00 0.00 4.34
218 219 2.294948 ACACCCCCATATCCCTAAGGTT 60.295 50.000 0.00 0.00 0.00 3.50
220 221 1.705186 CACACCCCCATATCCCTAAGG 59.295 57.143 0.00 0.00 0.00 2.69
228 229 3.527937 GGTATCTACCACACCCCCATAT 58.472 50.000 1.40 0.00 45.73 1.78
235 236 1.444672 GGCCGGTATCTACCACACC 59.555 63.158 1.90 1.26 46.80 4.16
237 238 0.325860 AAGGGCCGGTATCTACCACA 60.326 55.000 1.90 0.00 46.80 4.17
261 262 3.238788 AGAAAAACAAATCCCTCCCGT 57.761 42.857 0.00 0.00 0.00 5.28
305 308 2.876550 GTCTTTAAGCGGGACACAAACT 59.123 45.455 0.00 0.00 0.00 2.66
316 319 0.165944 CACCGCCTTGTCTTTAAGCG 59.834 55.000 0.00 0.00 0.00 4.68
340 343 0.033504 TTCCATATTCGAGAGCCGCC 59.966 55.000 0.00 0.00 38.37 6.13
341 344 1.996191 GATTCCATATTCGAGAGCCGC 59.004 52.381 0.00 0.00 38.37 6.53
343 346 6.429385 AGAATTTGATTCCATATTCGAGAGCC 59.571 38.462 0.00 0.00 42.07 4.70
344 347 7.432350 AGAATTTGATTCCATATTCGAGAGC 57.568 36.000 0.00 0.00 42.07 4.09
345 348 8.502387 GGAAGAATTTGATTCCATATTCGAGAG 58.498 37.037 11.24 0.00 43.75 3.20
346 349 7.445402 GGGAAGAATTTGATTCCATATTCGAGA 59.555 37.037 15.73 0.00 45.70 4.04
347 350 7.571983 CGGGAAGAATTTGATTCCATATTCGAG 60.572 40.741 15.73 0.00 45.70 4.04
348 351 6.204688 CGGGAAGAATTTGATTCCATATTCGA 59.795 38.462 15.73 0.00 45.70 3.71
349 352 6.373779 CGGGAAGAATTTGATTCCATATTCG 58.626 40.000 15.73 8.66 45.70 3.34
353 356 3.563808 CGCGGGAAGAATTTGATTCCATA 59.436 43.478 15.73 0.00 45.70 2.74
361 364 2.058057 CCAAAACGCGGGAAGAATTTG 58.942 47.619 12.47 9.54 0.00 2.32
363 366 1.000717 CACCAAAACGCGGGAAGAATT 60.001 47.619 12.47 0.00 0.00 2.17
375 378 1.111277 ACCAGAAGCACCACCAAAAC 58.889 50.000 0.00 0.00 0.00 2.43
392 405 3.391382 ACGCCCTCCAGCTACACC 61.391 66.667 0.00 0.00 0.00 4.16
394 407 2.603473 ACACGCCCTCCAGCTACA 60.603 61.111 0.00 0.00 0.00 2.74
399 412 0.535102 AACTTTCACACGCCCTCCAG 60.535 55.000 0.00 0.00 0.00 3.86
428 441 4.315122 CGACTCCCGCGAGATCCG 62.315 72.222 8.23 2.02 38.52 4.18
452 465 4.927267 TGTGGATCCACCTAAGACAAAT 57.073 40.909 36.27 0.00 45.63 2.32
501 518 4.686554 GCATAGACGTGAATATCCAACCTC 59.313 45.833 0.00 0.00 0.00 3.85
515 532 4.142816 GCTGTTGAAAAGATGCATAGACGT 60.143 41.667 0.00 0.00 0.00 4.34
522 539 0.039256 GCCGCTGTTGAAAAGATGCA 60.039 50.000 0.00 0.00 0.00 3.96
551 568 4.035208 CCTTATAGGATCAACGCACCAAAC 59.965 45.833 0.00 0.00 37.67 2.93
579 596 0.953960 AATCGGGAAGTCGTTGTGCC 60.954 55.000 0.00 0.00 0.00 5.01
621 638 3.699538 TCGCTTCTCCTTCACTAATGCTA 59.300 43.478 0.00 0.00 0.00 3.49
627 644 3.089284 TGTCATCGCTTCTCCTTCACTA 58.911 45.455 0.00 0.00 0.00 2.74
638 655 3.788766 GCGCCGTTGTCATCGCTT 61.789 61.111 0.00 0.00 43.70 4.68
648 665 3.941657 GAGCTGAAGAGGCGCCGTT 62.942 63.158 23.20 19.19 34.52 4.44
656 673 0.389166 AACCGAAGCGAGCTGAAGAG 60.389 55.000 0.00 0.00 0.00 2.85
662 679 3.795623 TTATAAGAACCGAAGCGAGCT 57.204 42.857 0.00 0.00 0.00 4.09
666 683 4.748023 CGACAATTATAAGAACCGAAGCG 58.252 43.478 0.00 0.00 0.00 4.68
668 685 5.968387 AGCGACAATTATAAGAACCGAAG 57.032 39.130 0.00 0.00 0.00 3.79
676 693 4.989168 GGACCACCTAGCGACAATTATAAG 59.011 45.833 0.00 0.00 0.00 1.73
688 705 0.824759 AGATTCGTGGACCACCTAGC 59.175 55.000 19.11 9.66 37.04 3.42
728 745 8.676401 CCATCATGACAGTACAATGAACATAAA 58.324 33.333 0.00 0.00 0.00 1.40
730 747 7.563906 TCCATCATGACAGTACAATGAACATA 58.436 34.615 0.00 0.00 0.00 2.29
733 750 6.932356 ATCCATCATGACAGTACAATGAAC 57.068 37.500 0.00 0.00 0.00 3.18
748 765 8.588472 TCTTGTCTATTCGTCATTATCCATCAT 58.412 33.333 0.00 0.00 0.00 2.45
753 774 8.649973 ACTTTCTTGTCTATTCGTCATTATCC 57.350 34.615 0.00 0.00 0.00 2.59
762 783 6.803154 AGGGAAAACTTTCTTGTCTATTCG 57.197 37.500 2.41 0.00 37.35 3.34
785 806 5.535030 GGCAAAGGTCTTTCTTTCTTTCCTA 59.465 40.000 0.00 0.00 35.04 2.94
786 807 4.342378 GGCAAAGGTCTTTCTTTCTTTCCT 59.658 41.667 0.00 0.00 35.04 3.36
787 808 4.501571 GGGCAAAGGTCTTTCTTTCTTTCC 60.502 45.833 0.00 0.00 35.04 3.13
788 809 4.501571 GGGGCAAAGGTCTTTCTTTCTTTC 60.502 45.833 0.00 0.00 35.04 2.62
789 810 3.388024 GGGGCAAAGGTCTTTCTTTCTTT 59.612 43.478 0.00 0.00 35.04 2.52
796 824 3.132824 CCATATTGGGGCAAAGGTCTTTC 59.867 47.826 0.00 0.00 32.67 2.62
825 853 4.824515 ACGGGAGAGGCGAGGAGG 62.825 72.222 0.00 0.00 0.00 4.30
834 862 5.371115 TTCAAAAATAGCAAACGGGAGAG 57.629 39.130 0.00 0.00 0.00 3.20
864 896 1.470098 CCAAGCTGAATTCCAGGAACG 59.530 52.381 3.18 0.00 43.13 3.95
882 914 2.994417 GATGGTTTTGGCGGGCCA 60.994 61.111 8.62 8.62 45.63 5.36
978 1011 0.238817 GTAGGCAGATACGGAGAGCG 59.761 60.000 0.00 0.00 0.00 5.03
1403 1459 3.527533 CCACGAATCAGAAATCCCGTTA 58.472 45.455 0.00 0.00 0.00 3.18
1404 1460 2.356135 CCACGAATCAGAAATCCCGTT 58.644 47.619 0.00 0.00 0.00 4.44
1405 1461 2.012051 GCCACGAATCAGAAATCCCGT 61.012 52.381 0.00 0.00 0.00 5.28
1423 1479 1.212751 GCGACCATCAAAACCAGCC 59.787 57.895 0.00 0.00 0.00 4.85
1479 1535 3.521560 GTTGATCTTCTCATACACGGCA 58.478 45.455 0.00 0.00 32.72 5.69
1488 1544 0.240145 ACGCGACGTTGATCTTCTCA 59.760 50.000 15.93 0.00 36.35 3.27
1501 1557 4.147322 CATGCCGTCCAACGCGAC 62.147 66.667 15.93 0.00 40.91 5.19
1506 1562 2.112815 GTAGGGCATGCCGTCCAAC 61.113 63.158 33.79 22.80 44.49 3.77
1620 1678 3.538591 TCAGAGGCAGCATTAACAGATG 58.461 45.455 0.00 0.00 0.00 2.90
1653 1711 2.832661 ACCTGCACGCTTTTGCCA 60.833 55.556 0.01 0.00 42.25 4.92
1887 1945 2.752358 CTCTCAGGTTGCTGCCCA 59.248 61.111 0.00 0.00 0.00 5.36
1923 1981 1.349026 TCCTTGAGCTTGTGGAGAAGG 59.651 52.381 0.00 0.00 32.74 3.46
1924 1982 2.614987 CCTCCTTGAGCTTGTGGAGAAG 60.615 54.545 23.03 9.94 46.53 2.85
1930 1988 0.595095 GCAACCTCCTTGAGCTTGTG 59.405 55.000 0.00 0.00 30.50 3.33
1944 2002 0.175760 TCTCGTCTATGCCAGCAACC 59.824 55.000 0.00 0.00 0.00 3.77
2392 2456 4.543689 TGACGGGATGAGTACTTCCTTAT 58.456 43.478 12.38 0.45 39.41 1.73
2399 2463 2.168521 CACCAATGACGGGATGAGTACT 59.831 50.000 0.00 0.00 0.00 2.73
2402 2466 1.275666 TCACCAATGACGGGATGAGT 58.724 50.000 0.00 0.00 0.00 3.41
2477 2541 1.301677 GGCTCTCCTTGGAAAGCGTG 61.302 60.000 8.66 0.00 44.44 5.34
2498 2562 1.153549 GATGAGTGTGCGGTCCTCC 60.154 63.158 0.00 0.00 0.00 4.30
2517 2581 1.593787 CGATGCCTCCACTGTCAGT 59.406 57.895 0.00 0.00 0.00 3.41
2518 2582 1.812922 GCGATGCCTCCACTGTCAG 60.813 63.158 0.00 0.00 0.00 3.51
2564 2628 4.219288 GCATTGTCCTGGATCTTTTTGTCT 59.781 41.667 0.00 0.00 0.00 3.41
2570 2634 1.004745 ACCGCATTGTCCTGGATCTTT 59.995 47.619 0.00 0.00 0.00 2.52
2585 2649 4.578898 AGCAACGACGTGACCGCA 62.579 61.111 0.00 0.00 37.70 5.69
2612 2676 1.343465 ACCTTGTTGACCTCGTCGATT 59.657 47.619 0.00 0.00 34.95 3.34
2623 2687 2.942804 TGGCAATCAAGACCTTGTTGA 58.057 42.857 19.41 5.64 41.16 3.18
2651 2715 1.420891 TCGATGATCAATGGGATGGCA 59.579 47.619 0.00 0.00 36.00 4.92
2741 2805 1.070786 GGCCACCTTGTTCTCGTCA 59.929 57.895 0.00 0.00 0.00 4.35
2888 2952 2.268920 GGAACGATGCCAGCCTCA 59.731 61.111 0.00 0.00 0.00 3.86
2906 2970 0.162507 CGAGAGTTTTGAGCAGCACG 59.837 55.000 0.00 0.00 0.00 5.34
2920 2984 2.218759 CCAAGTTTCGTGTTGTCGAGAG 59.781 50.000 0.00 0.00 40.86 3.20
2936 3000 1.843368 CCTCATCAACCATGCCAAGT 58.157 50.000 0.00 0.00 31.70 3.16
2990 3054 2.823829 GATCGTTCCACGGCATGCC 61.824 63.158 27.67 27.67 42.81 4.40
3011 3075 3.019933 GTCTCAACGAAGCTCTCTGTT 57.980 47.619 0.00 0.00 0.00 3.16
3080 3144 5.006386 CCAAGCTCAAGGATAACAGAAAGT 58.994 41.667 0.00 0.00 0.00 2.66
3095 3159 4.096833 GCATTATTGTGTGATCCAAGCTCA 59.903 41.667 0.00 0.00 0.00 4.26
3188 3252 1.644509 TTGCCTTCCTCTGTGCTCTA 58.355 50.000 0.00 0.00 0.00 2.43
3236 3300 6.971184 GTCCGTAATTCTTCTTCTACGATTCA 59.029 38.462 2.28 0.00 39.52 2.57
3257 3321 2.807967 TGAGCTTCAATTTCACAGTCCG 59.192 45.455 0.00 0.00 0.00 4.79
3259 3323 4.083590 GGAGTGAGCTTCAATTTCACAGTC 60.084 45.833 9.31 0.00 42.75 3.51
3266 3330 7.148171 GCTTTAGTATGGAGTGAGCTTCAATTT 60.148 37.037 0.00 0.00 33.19 1.82
3271 3335 4.759782 TGCTTTAGTATGGAGTGAGCTTC 58.240 43.478 0.00 0.00 0.00 3.86
3278 3342 6.572314 GCAAAACCATTGCTTTAGTATGGAGT 60.572 38.462 15.38 5.01 41.05 3.85
3333 3409 4.275196 CCATCAGTCCACATTGCTCTTATG 59.725 45.833 0.00 0.00 0.00 1.90
3347 3423 6.166984 TGTAGATTCTCATTCCATCAGTCC 57.833 41.667 0.00 0.00 0.00 3.85
3447 3524 7.036829 TGGTTGCTCAATCAATGAACAATATG 58.963 34.615 0.00 0.00 43.80 1.78
3467 3544 4.991056 TCATTTCTCTCGTTCTTCTGGTTG 59.009 41.667 0.00 0.00 0.00 3.77
3471 3548 5.473931 TCCTTCATTTCTCTCGTTCTTCTG 58.526 41.667 0.00 0.00 0.00 3.02
3472 3549 5.478679 TCTCCTTCATTTCTCTCGTTCTTCT 59.521 40.000 0.00 0.00 0.00 2.85
3479 3556 8.335532 AGAGTATATCTCCTTCATTTCTCTCG 57.664 38.462 0.00 0.00 43.71 4.04
3565 3642 7.040478 CCTGAGAAATATCAACACACCTTTCAA 60.040 37.037 0.00 0.00 0.00 2.69
3593 3670 6.872020 TCAGTAGTTTCAGAATTACTTTCCGG 59.128 38.462 0.00 0.00 36.50 5.14
3594 3671 7.884816 TCAGTAGTTTCAGAATTACTTTCCG 57.115 36.000 5.51 0.00 36.50 4.30
3624 3701 1.228033 TGAGTCGACTGTCCGGACA 60.228 57.895 34.13 34.13 39.32 4.02
3636 3713 4.379499 GGAAAAATAGGTTTGGCTGAGTCG 60.379 45.833 0.00 0.00 0.00 4.18
3688 3769 0.804989 CTGAAATGCCAGTTCGACCC 59.195 55.000 0.00 0.00 0.00 4.46
3696 3777 3.573967 AGTAAACCAACCTGAAATGCCAG 59.426 43.478 0.00 0.00 0.00 4.85
3780 3861 0.616395 TCACAGGTAAGCATCCGGGA 60.616 55.000 0.00 0.00 0.00 5.14
3783 3864 1.586422 CCATCACAGGTAAGCATCCG 58.414 55.000 0.00 0.00 0.00 4.18
3793 3891 2.025887 AGTAAAAGAGGGCCATCACAGG 60.026 50.000 21.34 0.00 0.00 4.00
3815 3913 8.145122 GTGGGATTTAATTTCCAAGTAACACAA 58.855 33.333 0.00 0.00 34.77 3.33
3816 3914 7.287927 TGTGGGATTTAATTTCCAAGTAACACA 59.712 33.333 0.00 4.38 34.77 3.72
3817 3915 7.662897 TGTGGGATTTAATTTCCAAGTAACAC 58.337 34.615 0.00 2.25 34.77 3.32
3818 3916 7.841282 TGTGGGATTTAATTTCCAAGTAACA 57.159 32.000 0.00 0.00 34.77 2.41
3819 3917 9.719355 ATTTGTGGGATTTAATTTCCAAGTAAC 57.281 29.630 0.00 0.00 34.77 2.50
3822 3920 9.639563 AAAATTTGTGGGATTTAATTTCCAAGT 57.360 25.926 0.00 0.00 34.77 3.16
3832 3930 8.311109 GCTTCCTTCTAAAATTTGTGGGATTTA 58.689 33.333 0.00 0.00 0.00 1.40
3833 3931 7.016563 AGCTTCCTTCTAAAATTTGTGGGATTT 59.983 33.333 0.00 0.00 0.00 2.17
3834 3932 6.498303 AGCTTCCTTCTAAAATTTGTGGGATT 59.502 34.615 0.00 0.00 0.00 3.01
3835 3933 6.019108 AGCTTCCTTCTAAAATTTGTGGGAT 58.981 36.000 0.00 0.00 0.00 3.85
3836 3934 5.393866 AGCTTCCTTCTAAAATTTGTGGGA 58.606 37.500 0.00 0.00 0.00 4.37
3837 3935 5.728637 AGCTTCCTTCTAAAATTTGTGGG 57.271 39.130 0.00 0.00 0.00 4.61
3838 3936 6.159293 GGAAGCTTCCTTCTAAAATTTGTGG 58.841 40.000 33.98 0.00 45.44 4.17
3891 3989 1.076332 GCTAGTACAGTTGTTGGGCG 58.924 55.000 0.00 0.00 0.00 6.13
3909 4007 4.730035 GCTTATGCTCAAGAAGATGTGTGC 60.730 45.833 2.50 0.00 35.38 4.57
3934 4032 3.611986 ACAAACAAACAACGTTGCAGATG 59.388 39.130 27.61 21.14 31.29 2.90
3939 4702 2.899439 GCAAACAAACAAACAACGTTGC 59.101 40.909 27.61 6.22 31.29 4.17
3947 4710 6.470877 TCGTGAAATAGAGCAAACAAACAAAC 59.529 34.615 0.00 0.00 0.00 2.93
3977 4740 7.021196 GCTTACGCTCAGATTTTGAATTTGTA 58.979 34.615 0.00 0.00 34.81 2.41
3997 4760 5.914085 ATATGCGAGAAACTCATGCTTAC 57.086 39.130 0.00 0.00 0.00 2.34
4002 4765 6.018589 TCCTCTATATGCGAGAAACTCATG 57.981 41.667 5.66 0.00 0.00 3.07
4011 4774 6.475076 GCAACATTATCTCCTCTATATGCGAG 59.525 42.308 0.00 0.00 0.00 5.03
4013 4776 5.230936 CGCAACATTATCTCCTCTATATGCG 59.769 44.000 0.00 0.00 44.27 4.73
4014 4777 5.521735 CCGCAACATTATCTCCTCTATATGC 59.478 44.000 0.00 0.00 0.00 3.14
4036 4799 4.739195 TGTTTTTCACTTCTTTCAACCCG 58.261 39.130 0.00 0.00 0.00 5.28
4070 4834 1.242076 ATGGTCAGCTGAGTTGTTGC 58.758 50.000 18.89 2.83 0.00 4.17
4084 4848 4.254492 GTCTTCCTGTTGTCCTAATGGTC 58.746 47.826 0.00 0.00 34.23 4.02
4087 4851 4.020218 TGAGGTCTTCCTGTTGTCCTAATG 60.020 45.833 0.00 0.00 45.24 1.90
4115 4879 1.942657 CCCACTCCTTGCACAATATCG 59.057 52.381 0.00 0.00 0.00 2.92
4116 4880 2.092429 TCCCCACTCCTTGCACAATATC 60.092 50.000 0.00 0.00 0.00 1.63
4129 4893 0.971959 TTGCATGGCAATCCCCACTC 60.972 55.000 0.00 0.00 43.99 3.51
4130 4894 1.078891 TTGCATGGCAATCCCCACT 59.921 52.632 0.00 0.00 43.99 4.00
4131 4895 3.710926 TTGCATGGCAATCCCCAC 58.289 55.556 0.00 0.00 43.99 4.61
4138 4902 1.105457 GCATCCTAGTTGCATGGCAA 58.895 50.000 9.40 0.00 46.80 4.52
4139 4903 0.034283 TGCATCCTAGTTGCATGGCA 60.034 50.000 12.23 0.00 44.73 4.92
4140 4904 2.797837 TGCATCCTAGTTGCATGGC 58.202 52.632 12.23 0.00 44.73 4.40
4145 4909 2.099141 TCTGTGTGCATCCTAGTTGC 57.901 50.000 7.73 7.73 40.55 4.17
4146 4910 3.865446 TGATCTGTGTGCATCCTAGTTG 58.135 45.455 0.00 0.00 0.00 3.16
4147 4911 4.558226 TTGATCTGTGTGCATCCTAGTT 57.442 40.909 0.00 0.00 0.00 2.24
4148 4912 4.767578 ATTGATCTGTGTGCATCCTAGT 57.232 40.909 0.00 0.00 0.00 2.57
4149 4913 5.642491 CCATATTGATCTGTGTGCATCCTAG 59.358 44.000 0.00 0.00 0.00 3.02
4150 4914 5.554070 CCATATTGATCTGTGTGCATCCTA 58.446 41.667 0.00 0.00 0.00 2.94
4151 4915 4.395625 CCATATTGATCTGTGTGCATCCT 58.604 43.478 0.00 0.00 0.00 3.24
4152 4916 3.057736 GCCATATTGATCTGTGTGCATCC 60.058 47.826 0.00 0.00 0.00 3.51
4153 4917 3.566742 TGCCATATTGATCTGTGTGCATC 59.433 43.478 0.00 0.00 0.00 3.91
4154 4918 3.558033 TGCCATATTGATCTGTGTGCAT 58.442 40.909 0.00 0.00 0.00 3.96
4155 4919 3.002038 TGCCATATTGATCTGTGTGCA 57.998 42.857 0.00 0.00 0.00 4.57
4156 4920 4.037089 TCATTGCCATATTGATCTGTGTGC 59.963 41.667 0.00 0.00 0.00 4.57
4157 4921 5.761165 TCATTGCCATATTGATCTGTGTG 57.239 39.130 0.00 0.00 0.00 3.82
4158 4922 6.682113 GCTTTCATTGCCATATTGATCTGTGT 60.682 38.462 0.00 0.00 0.00 3.72
4159 4923 5.690409 GCTTTCATTGCCATATTGATCTGTG 59.310 40.000 0.00 0.00 0.00 3.66
4160 4924 5.597182 AGCTTTCATTGCCATATTGATCTGT 59.403 36.000 0.00 0.00 0.00 3.41
4161 4925 6.016192 AGAGCTTTCATTGCCATATTGATCTG 60.016 38.462 0.00 0.00 0.00 2.90
4162 4926 6.069331 AGAGCTTTCATTGCCATATTGATCT 58.931 36.000 0.00 0.00 0.00 2.75
4163 4927 6.328641 AGAGCTTTCATTGCCATATTGATC 57.671 37.500 0.00 0.00 0.00 2.92
4164 4928 5.243283 GGAGAGCTTTCATTGCCATATTGAT 59.757 40.000 6.59 0.00 0.00 2.57
4165 4929 4.581824 GGAGAGCTTTCATTGCCATATTGA 59.418 41.667 6.59 0.00 0.00 2.57
4166 4930 4.583489 AGGAGAGCTTTCATTGCCATATTG 59.417 41.667 6.59 0.00 0.00 1.90
4167 4931 4.801164 AGGAGAGCTTTCATTGCCATATT 58.199 39.130 6.59 0.00 0.00 1.28
4168 4932 4.450305 AGGAGAGCTTTCATTGCCATAT 57.550 40.909 6.59 0.00 0.00 1.78
4169 4933 3.939740 AGGAGAGCTTTCATTGCCATA 57.060 42.857 6.59 0.00 0.00 2.74
4170 4934 2.822707 AGGAGAGCTTTCATTGCCAT 57.177 45.000 6.59 0.00 0.00 4.40
4171 4935 2.677902 CGTAGGAGAGCTTTCATTGCCA 60.678 50.000 6.59 0.00 0.00 4.92
4172 4936 1.936547 CGTAGGAGAGCTTTCATTGCC 59.063 52.381 6.59 0.00 0.00 4.52
4188 4952 1.677576 TGTACCCGCATTAGTCCGTAG 59.322 52.381 0.00 0.00 0.00 3.51
4189 4953 1.761449 TGTACCCGCATTAGTCCGTA 58.239 50.000 0.00 0.00 0.00 4.02
4190 4954 1.068127 GATGTACCCGCATTAGTCCGT 59.932 52.381 0.00 0.00 0.00 4.69
4191 4955 1.067974 TGATGTACCCGCATTAGTCCG 59.932 52.381 0.00 0.00 0.00 4.79
4192 4956 2.755650 CTGATGTACCCGCATTAGTCC 58.244 52.381 0.00 0.00 30.68 3.85
4193 4957 2.135933 GCTGATGTACCCGCATTAGTC 58.864 52.381 0.00 0.00 35.64 2.59
4194 4958 1.762957 AGCTGATGTACCCGCATTAGT 59.237 47.619 0.00 0.00 35.64 2.24
4195 4959 2.533266 AGCTGATGTACCCGCATTAG 57.467 50.000 0.00 0.00 36.10 1.73
4196 4960 2.560504 CAAGCTGATGTACCCGCATTA 58.439 47.619 0.00 0.00 0.00 1.90
4197 4961 1.382522 CAAGCTGATGTACCCGCATT 58.617 50.000 0.00 0.00 0.00 3.56
4198 4962 1.097547 GCAAGCTGATGTACCCGCAT 61.098 55.000 0.00 0.00 0.00 4.73
4199 4963 1.745115 GCAAGCTGATGTACCCGCA 60.745 57.895 0.00 0.00 0.00 5.69
4200 4964 2.472909 GGCAAGCTGATGTACCCGC 61.473 63.158 0.00 0.00 0.00 6.13
4201 4965 0.811616 GAGGCAAGCTGATGTACCCG 60.812 60.000 0.00 0.00 0.00 5.28
4202 4966 0.543749 AGAGGCAAGCTGATGTACCC 59.456 55.000 0.00 0.00 0.00 3.69
4203 4967 2.284190 GAAGAGGCAAGCTGATGTACC 58.716 52.381 0.00 0.00 0.00 3.34
4204 4968 2.977914 TGAAGAGGCAAGCTGATGTAC 58.022 47.619 0.00 0.00 0.00 2.90
4205 4969 3.198417 TCATGAAGAGGCAAGCTGATGTA 59.802 43.478 0.00 0.00 0.00 2.29
4206 4970 2.026542 TCATGAAGAGGCAAGCTGATGT 60.027 45.455 0.00 0.00 0.00 3.06
4207 4971 2.640184 TCATGAAGAGGCAAGCTGATG 58.360 47.619 0.00 0.00 0.00 3.07
4208 4972 3.054582 TCTTCATGAAGAGGCAAGCTGAT 60.055 43.478 30.05 0.00 42.06 2.90
4209 4973 2.303890 TCTTCATGAAGAGGCAAGCTGA 59.696 45.455 30.05 8.16 42.06 4.26
4210 4974 2.419324 GTCTTCATGAAGAGGCAAGCTG 59.581 50.000 33.35 7.91 46.93 4.24
4211 4975 2.617532 GGTCTTCATGAAGAGGCAAGCT 60.618 50.000 33.35 0.00 46.93 3.74
4212 4976 1.742268 GGTCTTCATGAAGAGGCAAGC 59.258 52.381 33.35 21.54 46.93 4.01
4213 4977 3.347077 AGGTCTTCATGAAGAGGCAAG 57.653 47.619 33.35 10.00 46.93 4.01
4214 4978 4.096681 TCTAGGTCTTCATGAAGAGGCAA 58.903 43.478 33.35 19.57 46.93 4.52
4215 4979 3.713003 TCTAGGTCTTCATGAAGAGGCA 58.287 45.455 33.35 20.81 46.93 4.75
4216 4980 4.588528 AGATCTAGGTCTTCATGAAGAGGC 59.411 45.833 33.35 23.44 46.93 4.70
4217 4981 5.832595 TGAGATCTAGGTCTTCATGAAGAGG 59.167 44.000 33.35 23.06 46.93 3.69
4218 4982 6.957920 TGAGATCTAGGTCTTCATGAAGAG 57.042 41.667 33.35 22.83 46.93 2.85
4219 4983 7.911130 AATGAGATCTAGGTCTTCATGAAGA 57.089 36.000 30.05 30.05 44.47 2.87


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

AutoCloner maintained by Alex Coulton.