Multiple sequence alignment - TraesCS5D01G198600

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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 TraesCS5D01G198600 chr5D 100.000 8293 0 0 1 8293 301571042 301579334 0.000000e+00 15315.0
1 TraesCS5D01G198600 chr5D 92.593 54 2 2 4612 4664 498540011 498539959 8.930000e-10 76.8
2 TraesCS5D01G198600 chr5A 95.473 3733 122 25 815 4514 395919763 395916045 0.000000e+00 5914.0
3 TraesCS5D01G198600 chr5A 94.748 3789 108 22 4547 8293 395916044 395912305 0.000000e+00 5810.0
4 TraesCS5D01G198600 chr5A 93.023 731 37 7 1 725 395920502 395919780 0.000000e+00 1055.0
5 TraesCS5D01G198600 chr5A 90.278 72 7 0 5028 5099 619460453 619460382 2.460000e-15 95.3
6 TraesCS5D01G198600 chr5A 97.368 38 0 1 5778 5815 363848867 363848903 6.950000e-06 63.9
7 TraesCS5D01G198600 chr5B 94.821 3109 105 23 815 3901 344612748 344615822 0.000000e+00 4798.0
8 TraesCS5D01G198600 chr5B 95.380 2489 94 10 5808 8293 344617461 344619931 0.000000e+00 3940.0
9 TraesCS5D01G198600 chr5B 94.286 560 27 1 3899 4453 344615929 344616488 0.000000e+00 852.0
10 TraesCS5D01G198600 chr5B 86.406 743 45 22 1 725 344612027 344612731 0.000000e+00 761.0
11 TraesCS5D01G198600 chr5B 96.419 391 9 3 5100 5485 344616513 344616903 2.520000e-179 640.0
12 TraesCS5D01G198600 chr5B 74.521 365 65 20 3940 4293 695477771 695477424 5.220000e-27 134.0
13 TraesCS5D01G198600 chr5B 90.541 74 6 1 5025 5097 221399673 221399746 6.850000e-16 97.1
14 TraesCS5D01G198600 chrUn 100.000 139 0 0 1 139 476731999 476732137 2.970000e-64 257.0
15 TraesCS5D01G198600 chr6D 78.740 381 67 13 3940 4314 15375651 15376023 8.320000e-60 243.0
16 TraesCS5D01G198600 chr6D 87.342 79 10 0 5025 5103 109734435 109734513 3.190000e-14 91.6
17 TraesCS5D01G198600 chr6D 97.436 39 0 1 5780 5818 249454617 249454580 1.930000e-06 65.8
18 TraesCS5D01G198600 chr6D 97.368 38 0 1 5778 5815 4632423 4632459 6.950000e-06 63.9
19 TraesCS5D01G198600 chr7B 76.127 377 69 17 3942 4314 674689783 674689424 2.380000e-40 178.0
20 TraesCS5D01G198600 chr4A 90.909 132 9 3 4971 5100 80843670 80843540 3.080000e-39 174.0
21 TraesCS5D01G198600 chr4B 90.411 73 7 0 5025 5097 604653785 604653857 6.850000e-16 97.1
22 TraesCS5D01G198600 chr4B 95.556 45 2 0 4609 4653 19670125 19670081 1.150000e-08 73.1
23 TraesCS5D01G198600 chr4B 95.652 46 1 1 4608 4653 236975539 236975495 1.150000e-08 73.1
24 TraesCS5D01G198600 chr3B 91.429 70 6 0 5028 5097 773465438 773465507 6.850000e-16 97.1
25 TraesCS5D01G198600 chr2B 90.411 73 7 0 5028 5100 69970866 69970794 6.850000e-16 97.1
26 TraesCS5D01G198600 chr2B 86.517 89 11 1 5014 5101 402688941 402689029 6.850000e-16 97.1
27 TraesCS5D01G198600 chr2B 92.308 52 4 0 4613 4664 439331602 439331653 3.210000e-09 75.0
28 TraesCS5D01G198600 chr2B 95.556 45 2 0 4609 4653 545551326 545551282 1.150000e-08 73.1
29 TraesCS5D01G198600 chr3A 92.453 53 4 0 4610 4662 124174517 124174569 8.930000e-10 76.8
30 TraesCS5D01G198600 chr3A 97.619 42 1 0 4612 4653 406948336 406948295 1.150000e-08 73.1
31 TraesCS5D01G198600 chr6A 100.000 38 0 0 4613 4650 338169956 338169993 4.150000e-08 71.3
32 TraesCS5D01G198600 chr6B 97.561 41 0 1 5778 5818 337237202 337237163 1.490000e-07 69.4
33 TraesCS5D01G198600 chr6B 97.368 38 0 1 5778 5815 225525502 225525538 6.950000e-06 63.9
34 TraesCS5D01G198600 chr6B 95.122 41 1 1 5778 5818 534953794 534953755 6.950000e-06 63.9
35 TraesCS5D01G198600 chr7D 97.368 38 0 1 5778 5815 120323587 120323623 6.950000e-06 63.9
36 TraesCS5D01G198600 chr3D 97.368 38 0 1 5778 5815 455855412 455855448 6.950000e-06 63.9


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 TraesCS5D01G198600 chr5D 301571042 301579334 8292 False 15315.000000 15315 100.000000 1 8293 1 chr5D.!!$F1 8292
1 TraesCS5D01G198600 chr5A 395912305 395920502 8197 True 4259.666667 5914 94.414667 1 8293 3 chr5A.!!$R2 8292
2 TraesCS5D01G198600 chr5B 344612027 344619931 7904 False 2198.200000 4798 93.462400 1 8293 5 chr5B.!!$F2 8292

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
792 811 0.037419 TAACAAAGCCGTCGTACCCC 60.037 55.000 0.00 0.00 0.00 4.95 F
795 814 0.247185 CAAAGCCGTCGTACCCCTAA 59.753 55.000 0.00 0.00 0.00 2.69 F
1954 1985 0.390078 TTTACCATTCCGCGCTCGAA 60.390 50.000 5.56 7.60 38.10 3.71 F
2117 2148 0.807496 GCAATTGGAGGTCTGAGTGC 59.193 55.000 7.72 0.00 0.00 4.40 F
3046 3089 1.075482 CCAACCTGTGGCTGTGGAT 59.925 57.895 0.00 0.00 41.72 3.41 F
3503 3551 0.168128 GCATTGGACTGTTGTACGCC 59.832 55.000 0.00 0.00 0.00 5.68 F
4282 4444 0.257039 CCTTCAATCCTCACCCCCTG 59.743 60.000 0.00 0.00 0.00 4.45 F
4919 5088 0.321919 ACACAATCGGCTGAGCATGT 60.322 50.000 6.82 3.47 0.00 3.21 F
4920 5089 0.806868 CACAATCGGCTGAGCATGTT 59.193 50.000 6.82 0.00 0.00 2.71 F
5300 5477 2.020131 GCATGTGCCTCATCTTCCG 58.980 57.895 0.00 0.00 34.09 4.30 F
7177 7670 0.034186 ACATGATTCCGTGGTGGCAT 60.034 50.000 0.00 0.00 37.80 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2534 2576 0.031616 ACAAACCAGCAAAGGGGGAA 60.032 50.000 0.00 0.0 0.00 3.97 R
2646 2688 5.412904 CCTGAACAGTAAATGGTTCCTCTTC 59.587 44.000 0.00 0.0 42.04 2.87 R
3484 3532 0.168128 GGCGTACAACAGTCCAATGC 59.832 55.000 0.00 0.0 0.00 3.56 R
3503 3551 3.359654 ACGCAAGAAAACAAAGTTAGCG 58.640 40.909 0.00 0.0 46.98 4.26 R
4222 4384 0.472471 CGTATGGTTAGGGGGCATGT 59.528 55.000 0.00 0.0 0.00 3.21 R
4904 5073 1.134280 AGCTAACATGCTCAGCCGATT 60.134 47.619 9.48 0.0 39.34 3.34 R
5806 6291 2.902705 TCCATAATAGACCGGTGCAC 57.097 50.000 14.63 8.8 0.00 4.57 R
6646 7135 1.234615 ATGTCAAGAACAACCCGGCG 61.235 55.000 0.00 0.0 42.37 6.46 R
6733 7222 3.050089 TCTACCCAAAGAGGTGTTCCAA 58.950 45.455 0.00 0.0 41.42 3.53 R
7179 7672 2.103771 GGCCAGTCTGAAGATAGCATCA 59.896 50.000 0.00 0.0 0.00 3.07 R
8163 8658 9.567776 TTGAACCAAGAATAAGTTTCTGACATA 57.432 29.630 0.00 0.0 0.00 2.29 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
139 140 6.017687 CGTAAGGGTTAACTGTAAAAAGCACT 60.018 38.462 5.42 0.00 0.00 4.40
308 309 3.181452 ACGAACTACCCTTTAGGCAACAA 60.181 43.478 0.00 0.00 40.58 2.83
366 367 0.687354 ATCGGCTGATCCCATGTACC 59.313 55.000 0.90 0.00 0.00 3.34
402 403 1.969064 CGGGATCGGGCAAACACAA 60.969 57.895 0.00 0.00 0.00 3.33
410 411 0.108424 GGGCAAACACAAACAGCACA 60.108 50.000 0.00 0.00 0.00 4.57
416 420 4.419280 CAAACACAAACAGCACATGTACA 58.581 39.130 0.00 0.00 43.00 2.90
423 427 2.086869 ACAGCACATGTACAAGGATGC 58.913 47.619 0.00 7.73 41.60 3.91
443 447 6.093357 GGATGCCAAGAAAGTTTTTGAAACAA 59.907 34.615 6.35 0.00 0.00 2.83
448 452 6.128688 CCAAGAAAGTTTTTGAAACAAAGCGA 60.129 34.615 6.35 0.00 0.00 4.93
455 459 2.910688 TGAAACAAAGCGAGAGAGGT 57.089 45.000 0.00 0.00 0.00 3.85
472 490 5.836898 AGAGAGGTAGAGAGAGAGATTCGTA 59.163 44.000 0.00 0.00 0.00 3.43
561 580 2.444895 AGGGGAGAGATGCGGACC 60.445 66.667 0.00 0.00 0.00 4.46
569 588 3.799755 GATGCGGACCGTGGCAAC 61.800 66.667 16.73 0.00 43.26 4.17
648 667 1.420138 GAATTATTCCTCGGCCCAGGA 59.580 52.381 16.17 16.17 41.16 3.86
650 669 2.409064 TTATTCCTCGGCCCAGGATA 57.591 50.000 20.88 11.41 42.49 2.59
674 693 1.749063 GCCCATGTAAAGCCCACTTAC 59.251 52.381 0.00 0.00 34.05 2.34
695 714 1.244019 GCCTGTTGACCCACATGTCC 61.244 60.000 0.00 0.00 34.25 4.02
698 717 1.001520 CTGTTGACCCACATGTCCGTA 59.998 52.381 0.00 0.00 34.25 4.02
706 725 1.002659 CCACATGTCCGTAAACAGGGA 59.997 52.381 0.00 0.00 35.33 4.20
712 731 3.972133 TGTCCGTAAACAGGGATCTCTA 58.028 45.455 0.00 0.00 34.25 2.43
725 744 3.759618 GGGATCTCTAGACTATTGACCCG 59.240 52.174 0.00 0.00 0.00 5.28
726 745 3.759618 GGATCTCTAGACTATTGACCCGG 59.240 52.174 0.00 0.00 0.00 5.73
729 748 5.063017 TCTCTAGACTATTGACCCGGATT 57.937 43.478 0.73 0.00 0.00 3.01
730 749 5.071370 TCTCTAGACTATTGACCCGGATTC 58.929 45.833 0.73 0.00 0.00 2.52
731 750 5.063017 TCTAGACTATTGACCCGGATTCT 57.937 43.478 0.73 0.00 0.00 2.40
732 751 5.071370 TCTAGACTATTGACCCGGATTCTC 58.929 45.833 0.73 0.00 0.00 2.87
733 752 3.643237 AGACTATTGACCCGGATTCTCA 58.357 45.455 0.73 0.00 0.00 3.27
734 753 4.030913 AGACTATTGACCCGGATTCTCAA 58.969 43.478 0.73 4.59 0.00 3.02
735 754 4.469945 AGACTATTGACCCGGATTCTCAAA 59.530 41.667 0.73 0.00 0.00 2.69
736 755 5.045869 AGACTATTGACCCGGATTCTCAAAA 60.046 40.000 0.73 0.00 0.00 2.44
737 756 5.566469 ACTATTGACCCGGATTCTCAAAAA 58.434 37.500 0.73 0.00 0.00 1.94
776 795 5.508200 TTTTGACCCACATGTCAGTTAAC 57.492 39.130 0.00 0.00 45.37 2.01
777 796 3.847671 TGACCCACATGTCAGTTAACA 57.152 42.857 8.61 0.00 40.22 2.41
778 797 4.157849 TGACCCACATGTCAGTTAACAA 57.842 40.909 8.61 0.00 40.22 2.83
779 798 4.527944 TGACCCACATGTCAGTTAACAAA 58.472 39.130 8.61 0.00 40.22 2.83
780 799 4.578516 TGACCCACATGTCAGTTAACAAAG 59.421 41.667 8.61 0.00 40.22 2.77
781 800 3.317993 ACCCACATGTCAGTTAACAAAGC 59.682 43.478 8.61 0.00 31.81 3.51
782 801 3.305335 CCCACATGTCAGTTAACAAAGCC 60.305 47.826 8.61 0.00 31.81 4.35
783 802 3.554524 CACATGTCAGTTAACAAAGCCG 58.445 45.455 8.61 0.00 31.81 5.52
784 803 3.003275 CACATGTCAGTTAACAAAGCCGT 59.997 43.478 8.61 0.00 31.81 5.68
785 804 3.250040 ACATGTCAGTTAACAAAGCCGTC 59.750 43.478 8.61 0.00 31.81 4.79
786 805 1.862201 TGTCAGTTAACAAAGCCGTCG 59.138 47.619 8.61 0.00 0.00 5.12
787 806 1.862827 GTCAGTTAACAAAGCCGTCGT 59.137 47.619 8.61 0.00 0.00 4.34
788 807 3.052036 GTCAGTTAACAAAGCCGTCGTA 58.948 45.455 8.61 0.00 0.00 3.43
789 808 3.052036 TCAGTTAACAAAGCCGTCGTAC 58.948 45.455 8.61 0.00 0.00 3.67
790 809 2.156310 CAGTTAACAAAGCCGTCGTACC 59.844 50.000 8.61 0.00 0.00 3.34
791 810 1.460743 GTTAACAAAGCCGTCGTACCC 59.539 52.381 0.00 0.00 0.00 3.69
792 811 0.037419 TAACAAAGCCGTCGTACCCC 60.037 55.000 0.00 0.00 0.00 4.95
793 812 1.761500 AACAAAGCCGTCGTACCCCT 61.761 55.000 0.00 0.00 0.00 4.79
794 813 0.899717 ACAAAGCCGTCGTACCCCTA 60.900 55.000 0.00 0.00 0.00 3.53
795 814 0.247185 CAAAGCCGTCGTACCCCTAA 59.753 55.000 0.00 0.00 0.00 2.69
796 815 0.975887 AAAGCCGTCGTACCCCTAAA 59.024 50.000 0.00 0.00 0.00 1.85
797 816 0.975887 AAGCCGTCGTACCCCTAAAA 59.024 50.000 0.00 0.00 0.00 1.52
798 817 0.975887 AGCCGTCGTACCCCTAAAAA 59.024 50.000 0.00 0.00 0.00 1.94
1222 1244 9.276397 GTACGTAAATAAAACCGTAATTGCATT 57.724 29.630 0.00 0.00 37.51 3.56
1241 1263 0.899019 TATGTACTGGTTGCGCCTCA 59.101 50.000 4.18 0.00 38.35 3.86
1261 1283 1.475280 AGCTGTTCGACGTAATGCCTA 59.525 47.619 0.00 0.00 0.00 3.93
1463 1485 1.400530 CCCGTATGACCCTCCACCTC 61.401 65.000 0.00 0.00 0.00 3.85
1468 1490 0.695803 ATGACCCTCCACCTCCATCC 60.696 60.000 0.00 0.00 0.00 3.51
1469 1491 1.003573 GACCCTCCACCTCCATCCT 59.996 63.158 0.00 0.00 0.00 3.24
1471 1493 2.074948 CCCTCCACCTCCATCCTGG 61.075 68.421 0.00 0.00 39.43 4.45
1498 1520 2.672996 CCGGTGGGCTCACTTTGG 60.673 66.667 18.03 12.52 43.17 3.28
1503 1525 1.239347 GTGGGCTCACTTTGGTTCTC 58.761 55.000 10.23 0.00 40.58 2.87
1504 1526 1.140312 TGGGCTCACTTTGGTTCTCT 58.860 50.000 0.00 0.00 0.00 3.10
1517 1539 3.808728 TGGTTCTCTTTTCTCACAGTGG 58.191 45.455 0.00 0.00 0.00 4.00
1522 1551 0.868406 CTTTTCTCACAGTGGTCGGC 59.132 55.000 0.00 0.00 0.00 5.54
1545 1574 3.551485 GTGATGTTGGCTGTTTGTTTGTC 59.449 43.478 0.00 0.00 0.00 3.18
1577 1606 0.963962 CAGGTTTGCATCAAGGCAGT 59.036 50.000 0.00 0.00 45.88 4.40
1922 1953 2.227388 CACACCCTGATGCTTTGTTCTC 59.773 50.000 0.00 0.00 0.00 2.87
1952 1983 0.444651 TTTTTACCATTCCGCGCTCG 59.555 50.000 5.56 0.00 0.00 5.03
1954 1985 0.390078 TTTACCATTCCGCGCTCGAA 60.390 50.000 5.56 7.60 38.10 3.71
2117 2148 0.807496 GCAATTGGAGGTCTGAGTGC 59.193 55.000 7.72 0.00 0.00 4.40
2534 2576 3.068732 GCTGGCTCAGTTTTCTTTCCTTT 59.931 43.478 4.45 0.00 33.43 3.11
2685 2727 4.136796 TGTTCAGGATCTTGAGGTTTGTG 58.863 43.478 7.65 0.00 0.00 3.33
2686 2728 4.137543 GTTCAGGATCTTGAGGTTTGTGT 58.862 43.478 7.65 0.00 0.00 3.72
2700 2742 6.036577 AGGTTTGTGTTCTGAAACAACAAT 57.963 33.333 13.74 1.56 46.56 2.71
2797 2839 7.551585 ACTCAGTGAGATGTAGTAAGGAAATG 58.448 38.462 26.86 0.00 33.32 2.32
2991 3034 3.319137 TGATGGCTCGAGGTAATATGC 57.681 47.619 15.58 0.00 0.00 3.14
3046 3089 1.075482 CCAACCTGTGGCTGTGGAT 59.925 57.895 0.00 0.00 41.72 3.41
3069 3115 3.777106 AAGTCCTGTCATGAGCTCAAA 57.223 42.857 22.50 9.43 0.00 2.69
3079 3125 7.912250 CCTGTCATGAGCTCAAATTTTATGTAC 59.088 37.037 22.50 12.19 0.00 2.90
3144 3190 8.084985 TGTGTTGAGTATACTTGGGATTCATA 57.915 34.615 6.88 0.00 0.00 2.15
3145 3191 8.204160 TGTGTTGAGTATACTTGGGATTCATAG 58.796 37.037 6.88 0.00 0.00 2.23
3311 3357 4.765339 ACTGGAAGGCCTGTTTATTGTAAC 59.235 41.667 5.69 0.00 42.99 2.50
3503 3551 0.168128 GCATTGGACTGTTGTACGCC 59.832 55.000 0.00 0.00 0.00 5.68
3604 3652 9.177608 TCTTATGCTGCTAACTTTTGTATTGAT 57.822 29.630 0.00 0.00 0.00 2.57
3895 3943 6.849588 ACCAATCATTTTGTTGCTTCTTTC 57.150 33.333 0.00 0.00 0.00 2.62
4002 4164 4.403734 TCCAACTCCTTTGTTTGGTATCC 58.596 43.478 0.00 0.00 32.71 2.59
4046 4208 6.743575 AATTGACAGAGAAGTTTATTCCGG 57.256 37.500 0.00 0.00 0.00 5.14
4095 4257 7.254387 GCAAGATTAGACAAGAGATGATGACAC 60.254 40.741 0.00 0.00 0.00 3.67
4142 4304 7.671398 AGATGTCATCACTAAAACAATTCCCTT 59.329 33.333 15.20 0.00 0.00 3.95
4148 4310 7.227049 TCACTAAAACAATTCCCTTCCAATC 57.773 36.000 0.00 0.00 0.00 2.67
4222 4384 6.263842 GTCATGCTTAATCCCTCATCAATTCA 59.736 38.462 0.00 0.00 0.00 2.57
4282 4444 0.257039 CCTTCAATCCTCACCCCCTG 59.743 60.000 0.00 0.00 0.00 4.45
4365 4532 3.190327 TGGATCCACAAAACATAACGCAG 59.810 43.478 11.44 0.00 0.00 5.18
4373 4540 6.861055 CCACAAAACATAACGCAGTCTTAAAT 59.139 34.615 0.00 0.00 45.00 1.40
4505 4672 6.587273 AGGACAACTATTTGATCTCCTTAGC 58.413 40.000 0.00 0.00 33.81 3.09
4514 4681 4.111375 TGATCTCCTTAGCGAACTGTTC 57.889 45.455 10.48 10.48 0.00 3.18
4515 4682 3.509967 TGATCTCCTTAGCGAACTGTTCA 59.490 43.478 19.56 0.00 0.00 3.18
4516 4683 4.021456 TGATCTCCTTAGCGAACTGTTCAA 60.021 41.667 19.56 6.50 0.00 2.69
4517 4684 4.537135 TCTCCTTAGCGAACTGTTCAAT 57.463 40.909 19.56 9.95 0.00 2.57
4518 4685 5.654603 TCTCCTTAGCGAACTGTTCAATA 57.345 39.130 19.56 9.03 0.00 1.90
4519 4686 6.032956 TCTCCTTAGCGAACTGTTCAATAA 57.967 37.500 19.56 15.00 0.00 1.40
4520 4687 6.640518 TCTCCTTAGCGAACTGTTCAATAAT 58.359 36.000 19.56 3.82 0.00 1.28
4521 4688 7.103641 TCTCCTTAGCGAACTGTTCAATAATT 58.896 34.615 19.56 2.02 0.00 1.40
4522 4689 7.606456 TCTCCTTAGCGAACTGTTCAATAATTT 59.394 33.333 19.56 0.79 0.00 1.82
4523 4690 7.748847 TCCTTAGCGAACTGTTCAATAATTTC 58.251 34.615 19.56 0.00 0.00 2.17
4524 4691 7.389330 TCCTTAGCGAACTGTTCAATAATTTCA 59.611 33.333 19.56 1.58 0.00 2.69
4525 4692 8.184192 CCTTAGCGAACTGTTCAATAATTTCAT 58.816 33.333 19.56 0.00 0.00 2.57
4526 4693 8.894409 TTAGCGAACTGTTCAATAATTTCATG 57.106 30.769 19.56 1.09 0.00 3.07
4527 4694 7.144722 AGCGAACTGTTCAATAATTTCATGA 57.855 32.000 19.56 0.00 0.00 3.07
4528 4695 7.023575 AGCGAACTGTTCAATAATTTCATGAC 58.976 34.615 19.56 0.00 0.00 3.06
4529 4696 7.023575 GCGAACTGTTCAATAATTTCATGACT 58.976 34.615 19.56 0.00 0.00 3.41
4530 4697 7.538678 GCGAACTGTTCAATAATTTCATGACTT 59.461 33.333 19.56 0.00 0.00 3.01
4531 4698 9.055248 CGAACTGTTCAATAATTTCATGACTTC 57.945 33.333 19.56 0.00 0.00 3.01
4532 4699 8.955061 AACTGTTCAATAATTTCATGACTTCG 57.045 30.769 0.00 0.00 0.00 3.79
4533 4700 8.099364 ACTGTTCAATAATTTCATGACTTCGT 57.901 30.769 0.00 0.00 0.00 3.85
4534 4701 8.567948 ACTGTTCAATAATTTCATGACTTCGTT 58.432 29.630 0.00 0.00 0.00 3.85
4535 4702 9.398170 CTGTTCAATAATTTCATGACTTCGTTT 57.602 29.630 0.00 0.00 0.00 3.60
4536 4703 9.743057 TGTTCAATAATTTCATGACTTCGTTTT 57.257 25.926 0.00 0.00 0.00 2.43
4539 4706 8.698854 TCAATAATTTCATGACTTCGTTTTTGC 58.301 29.630 0.00 0.00 0.00 3.68
4540 4707 8.486383 CAATAATTTCATGACTTCGTTTTTGCA 58.514 29.630 0.00 0.00 0.00 4.08
4541 4708 6.900568 AATTTCATGACTTCGTTTTTGCAA 57.099 29.167 0.00 0.00 0.00 4.08
4542 4709 5.947503 TTTCATGACTTCGTTTTTGCAAG 57.052 34.783 0.00 0.00 0.00 4.01
4543 4710 4.891627 TCATGACTTCGTTTTTGCAAGA 57.108 36.364 0.00 0.00 0.00 3.02
4544 4711 4.597079 TCATGACTTCGTTTTTGCAAGAC 58.403 39.130 0.00 2.01 0.00 3.01
4545 4712 4.095632 TCATGACTTCGTTTTTGCAAGACA 59.904 37.500 13.35 2.26 0.00 3.41
4565 4732 7.100458 AGACAAAGCAAAACTCTTAACACAT 57.900 32.000 0.00 0.00 0.00 3.21
4583 4750 7.621832 AACACATGTTGACATTGTTATTTCG 57.378 32.000 16.06 0.00 36.63 3.46
4614 4781 9.443283 CTTGCAGCTTTTGATGTTAGATATTAC 57.557 33.333 0.00 0.00 38.25 1.89
4622 4789 8.561536 TTTGATGTTAGATATTACTCCCTCCA 57.438 34.615 0.00 0.00 0.00 3.86
4736 4903 3.791973 GGTGACCATGTGAGACTAGAG 57.208 52.381 0.00 0.00 0.00 2.43
4739 4906 2.035632 GACCATGTGAGACTAGAGGGG 58.964 57.143 0.00 0.00 0.00 4.79
4753 4920 6.494146 AGACTAGAGGGGAAATAGGTAAATCG 59.506 42.308 0.00 0.00 0.00 3.34
4774 4941 1.135960 GGGGATCCTCTTTCTCCTGG 58.864 60.000 12.58 0.00 30.48 4.45
4798 4967 8.647796 TGGTCAGATTACTTCCATAAATATCGT 58.352 33.333 0.00 0.00 0.00 3.73
4815 4984 7.956420 AATATCGTCCTTGCGTTAATATTCA 57.044 32.000 0.00 0.00 0.00 2.57
4823 4992 7.275560 GTCCTTGCGTTAATATTCAAGCAAAAT 59.724 33.333 19.00 0.00 42.80 1.82
4904 5073 5.479375 AGAGGTACCGAGAGAAATTAACACA 59.521 40.000 6.18 0.00 0.00 3.72
4913 5082 5.245531 AGAGAAATTAACACAATCGGCTGA 58.754 37.500 0.00 0.00 0.00 4.26
4919 5088 0.321919 ACACAATCGGCTGAGCATGT 60.322 50.000 6.82 3.47 0.00 3.21
4920 5089 0.806868 CACAATCGGCTGAGCATGTT 59.193 50.000 6.82 0.00 0.00 2.71
4932 5101 3.706698 TGAGCATGTTAGCTACACGATC 58.293 45.455 0.00 0.00 46.75 3.69
4942 5111 7.372714 TGTTAGCTACACGATCTGTTAAAAGA 58.627 34.615 0.00 0.00 33.91 2.52
4947 5117 8.283291 AGCTACACGATCTGTTAAAAGAAAAAG 58.717 33.333 0.00 0.00 33.91 2.27
5005 5175 2.284625 TGGGAGCTGATCGGTGGT 60.285 61.111 2.89 0.00 0.00 4.16
5009 5179 2.607750 AGCTGATCGGTGGTGGGT 60.608 61.111 2.89 0.00 0.00 4.51
5035 5205 6.843069 AAATTGACAACAAAGGCAATACAC 57.157 33.333 0.00 0.00 39.54 2.90
5092 5264 5.163012 ACACCTTATATCTAGGAACGGAGGA 60.163 44.000 10.07 0.00 36.58 3.71
5122 5294 8.353684 AGTATATCACCTCTCAAATACTTGTCG 58.646 37.037 0.00 0.00 33.94 4.35
5146 5318 7.010738 TCGAAGAAAGTAATAAATTACGCCTGG 59.989 37.037 7.11 0.00 45.48 4.45
5147 5319 6.937436 AGAAAGTAATAAATTACGCCTGGG 57.063 37.500 7.11 0.00 45.48 4.45
5229 5402 5.942872 AGTCTTGGAAACTTTATCGCAATG 58.057 37.500 0.00 0.00 0.00 2.82
5300 5477 2.020131 GCATGTGCCTCATCTTCCG 58.980 57.895 0.00 0.00 34.09 4.30
5553 5756 6.757897 ATGATCACAACATGTAATCCGTTT 57.242 33.333 0.00 0.00 0.00 3.60
5699 6184 6.642131 CACATGGTTTGTTTCATACTTTCTGG 59.358 38.462 0.00 0.00 36.00 3.86
5782 6267 4.733725 TCCTTCCCCGGACCCTGG 62.734 72.222 0.73 0.00 0.00 4.45
5815 6300 4.065281 GGAGCTACGTGCACCGGT 62.065 66.667 12.15 0.00 42.21 5.28
5863 6349 9.906660 TTGTAGATGTTTTATCAAACCATTCAC 57.093 29.630 0.20 0.00 41.60 3.18
6106 6592 4.588528 ACACATCATAAAAGGCAGGTGTTT 59.411 37.500 0.00 0.00 34.89 2.83
6178 6664 2.037251 TCACTCCAAAGTACCTGAGCAC 59.963 50.000 0.00 0.00 33.25 4.40
6217 6703 6.092748 AGCCATTACAGTTTAAAATTGAGCG 58.907 36.000 7.70 0.00 0.00 5.03
6240 6726 7.870445 AGCGTTTATTTTGCCAAATAAGAAAGA 59.130 29.630 13.56 0.00 42.95 2.52
6559 7048 3.129462 CAGGAGTCAGATGAGCGAAACTA 59.871 47.826 0.00 0.00 0.00 2.24
6646 7135 6.569179 TGGCTGAAATAGTTGAAAGTAACC 57.431 37.500 0.00 0.00 0.00 2.85
6733 7222 5.843019 TCTTCTCAAGGATAAAACCACCT 57.157 39.130 0.00 0.00 35.36 4.00
6949 7439 7.482474 TGATGACATGGTTATACTTGCATTTG 58.518 34.615 0.00 0.00 0.00 2.32
7177 7670 0.034186 ACATGATTCCGTGGTGGCAT 60.034 50.000 0.00 0.00 37.80 4.40
7179 7672 1.477700 CATGATTCCGTGGTGGCATTT 59.522 47.619 0.00 0.00 37.80 2.32
7201 7694 0.461548 TGCTATCTTCAGACTGGCCG 59.538 55.000 1.81 0.00 0.00 6.13
7213 7706 2.281484 TGGCCGAAACCACTGCTC 60.281 61.111 0.00 0.00 33.75 4.26
7246 7739 1.349688 ACACCGGCTTCAGTTATTCCA 59.650 47.619 0.00 0.00 0.00 3.53
7270 7763 1.067565 GTCTCAATCAGTGACTGCCGA 60.068 52.381 7.93 3.16 37.67 5.54
7327 7820 0.890683 GGTTGTCAGCCATCCCTTTG 59.109 55.000 0.00 0.00 0.00 2.77
7463 7956 7.601886 AGATGATAATTTCGCTATCTCTGTTGG 59.398 37.037 0.00 0.00 0.00 3.77
7565 8058 7.761409 TGCATAGGAGTTCATGTTATTGAAAC 58.239 34.615 0.00 0.00 37.36 2.78
7666 8159 2.859526 GCTTTTAGGAGCTTGGATGC 57.140 50.000 0.00 0.00 39.57 3.91
7826 8319 3.527253 TGGTCCCAGAAACATGGTCATAT 59.473 43.478 0.00 0.00 38.81 1.78
7862 8355 1.282157 GGGGATACACCTGCTTCAACT 59.718 52.381 0.00 0.00 38.98 3.16
7919 8412 0.400213 TAGGCCACTGGACAACCTTG 59.600 55.000 5.01 0.00 37.04 3.61
7970 8463 0.955919 GGTCTTCTTCCCAGCCAACG 60.956 60.000 0.00 0.00 0.00 4.10
8162 8657 4.381079 GGGTTTGGTTTTGCTAATGCGATA 60.381 41.667 0.00 0.00 43.34 2.92
8163 8658 5.348164 GGTTTGGTTTTGCTAATGCGATAT 58.652 37.500 0.00 0.00 43.34 1.63
8275 8770 3.624777 AGTTACCATGGGCATCAAAGAG 58.375 45.455 18.09 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
139 140 3.053095 ACCTCTTGATCTCGGGGTACTTA 60.053 47.826 4.77 0.00 0.00 2.24
366 367 0.453793 CGGGATAGGCTAGATCGCTG 59.546 60.000 11.22 3.50 34.87 5.18
402 403 2.489329 GCATCCTTGTACATGTGCTGTT 59.511 45.455 15.25 0.00 39.39 3.16
410 411 4.666512 ACTTTCTTGGCATCCTTGTACAT 58.333 39.130 0.00 0.00 0.00 2.29
416 420 5.612725 TCAAAAACTTTCTTGGCATCCTT 57.387 34.783 0.00 0.00 0.00 3.36
423 427 6.014898 CGCTTTGTTTCAAAAACTTTCTTGG 58.985 36.000 4.40 0.00 0.00 3.61
443 447 2.769663 TCTCTCTCTACCTCTCTCGCTT 59.230 50.000 0.00 0.00 0.00 4.68
448 452 4.654262 ACGAATCTCTCTCTCTACCTCTCT 59.346 45.833 0.00 0.00 0.00 3.10
455 459 5.361427 CACAGGTACGAATCTCTCTCTCTA 58.639 45.833 0.00 0.00 0.00 2.43
472 490 3.556306 CGACACACCCCCACAGGT 61.556 66.667 0.00 0.00 42.40 4.00
561 580 1.373246 CCAATTGCCAGTTGCCACG 60.373 57.895 0.00 0.00 40.16 4.94
569 588 0.106819 CTCCTCTCCCCAATTGCCAG 60.107 60.000 0.00 0.00 0.00 4.85
571 590 0.106967 GTCTCCTCTCCCCAATTGCC 60.107 60.000 0.00 0.00 0.00 4.52
572 591 0.462759 CGTCTCCTCTCCCCAATTGC 60.463 60.000 0.00 0.00 0.00 3.56
573 592 1.195115 TCGTCTCCTCTCCCCAATTG 58.805 55.000 0.00 0.00 0.00 2.32
574 593 2.182516 ATCGTCTCCTCTCCCCAATT 57.817 50.000 0.00 0.00 0.00 2.32
575 594 2.491825 CCTATCGTCTCCTCTCCCCAAT 60.492 54.545 0.00 0.00 0.00 3.16
576 595 1.133450 CCTATCGTCTCCTCTCCCCAA 60.133 57.143 0.00 0.00 0.00 4.12
577 596 0.478942 CCTATCGTCTCCTCTCCCCA 59.521 60.000 0.00 0.00 0.00 4.96
578 597 0.772384 TCCTATCGTCTCCTCTCCCC 59.228 60.000 0.00 0.00 0.00 4.81
648 667 3.450817 GTGGGCTTTACATGGGCTTTTAT 59.549 43.478 0.00 0.00 0.00 1.40
650 669 1.623311 GTGGGCTTTACATGGGCTTTT 59.377 47.619 0.00 0.00 0.00 2.27
674 693 2.034066 ATGTGGGTCAACAGGCCG 59.966 61.111 0.00 0.00 32.52 6.13
677 696 0.955428 CGGACATGTGGGTCAACAGG 60.955 60.000 1.15 0.00 39.59 4.00
695 714 7.228906 TCAATAGTCTAGAGATCCCTGTTTACG 59.771 40.741 0.00 0.00 0.00 3.18
698 717 6.325286 GGTCAATAGTCTAGAGATCCCTGTTT 59.675 42.308 0.00 0.00 0.00 2.83
706 725 4.726035 TCCGGGTCAATAGTCTAGAGAT 57.274 45.455 0.00 0.00 0.00 2.75
712 731 3.643237 TGAGAATCCGGGTCAATAGTCT 58.357 45.455 0.00 0.00 0.00 3.24
753 772 5.419155 TGTTAACTGACATGTGGGTCAAAAA 59.581 36.000 1.15 0.00 46.36 1.94
754 773 4.950475 TGTTAACTGACATGTGGGTCAAAA 59.050 37.500 1.15 0.00 46.36 2.44
755 774 4.527944 TGTTAACTGACATGTGGGTCAAA 58.472 39.130 1.15 0.00 46.36 2.69
756 775 4.157849 TGTTAACTGACATGTGGGTCAA 57.842 40.909 1.15 0.00 46.36 3.18
757 776 3.847671 TGTTAACTGACATGTGGGTCA 57.152 42.857 1.15 0.00 45.06 4.02
758 777 4.556699 GCTTTGTTAACTGACATGTGGGTC 60.557 45.833 1.15 0.00 38.29 4.46
759 778 3.317993 GCTTTGTTAACTGACATGTGGGT 59.682 43.478 1.15 0.00 0.00 4.51
760 779 3.305335 GGCTTTGTTAACTGACATGTGGG 60.305 47.826 1.15 0.00 0.00 4.61
761 780 3.609175 CGGCTTTGTTAACTGACATGTGG 60.609 47.826 1.15 0.00 0.00 4.17
762 781 3.003275 ACGGCTTTGTTAACTGACATGTG 59.997 43.478 1.15 0.00 0.00 3.21
763 782 3.211045 ACGGCTTTGTTAACTGACATGT 58.789 40.909 7.22 0.00 0.00 3.21
764 783 3.664276 CGACGGCTTTGTTAACTGACATG 60.664 47.826 7.22 0.00 0.00 3.21
765 784 2.478894 CGACGGCTTTGTTAACTGACAT 59.521 45.455 7.22 0.00 0.00 3.06
766 785 1.862201 CGACGGCTTTGTTAACTGACA 59.138 47.619 7.22 0.00 0.00 3.58
767 786 1.862827 ACGACGGCTTTGTTAACTGAC 59.137 47.619 7.22 0.00 0.00 3.51
768 787 2.228138 ACGACGGCTTTGTTAACTGA 57.772 45.000 7.22 0.00 0.00 3.41
769 788 2.156310 GGTACGACGGCTTTGTTAACTG 59.844 50.000 7.22 0.00 0.00 3.16
770 789 2.407090 GGTACGACGGCTTTGTTAACT 58.593 47.619 7.22 0.00 0.00 2.24
771 790 1.460743 GGGTACGACGGCTTTGTTAAC 59.539 52.381 0.00 0.00 0.00 2.01
772 791 1.607767 GGGGTACGACGGCTTTGTTAA 60.608 52.381 0.00 0.00 0.00 2.01
773 792 0.037419 GGGGTACGACGGCTTTGTTA 60.037 55.000 0.00 0.00 0.00 2.41
774 793 1.301953 GGGGTACGACGGCTTTGTT 60.302 57.895 0.00 0.00 0.00 2.83
775 794 0.899717 TAGGGGTACGACGGCTTTGT 60.900 55.000 0.00 0.00 0.00 2.83
776 795 0.247185 TTAGGGGTACGACGGCTTTG 59.753 55.000 0.00 0.00 0.00 2.77
777 796 0.975887 TTTAGGGGTACGACGGCTTT 59.024 50.000 0.00 0.00 0.00 3.51
778 797 0.975887 TTTTAGGGGTACGACGGCTT 59.024 50.000 0.00 0.00 0.00 4.35
779 798 0.975887 TTTTTAGGGGTACGACGGCT 59.024 50.000 0.00 0.00 0.00 5.52
780 799 3.531073 TTTTTAGGGGTACGACGGC 57.469 52.632 0.00 0.00 0.00 5.68
800 819 3.377798 TCCGACGGCTTTGTTAACTTTTT 59.622 39.130 9.66 0.00 0.00 1.94
801 820 2.944349 TCCGACGGCTTTGTTAACTTTT 59.056 40.909 9.66 0.00 0.00 2.27
802 821 2.563702 TCCGACGGCTTTGTTAACTTT 58.436 42.857 9.66 0.00 0.00 2.66
803 822 2.243602 TCCGACGGCTTTGTTAACTT 57.756 45.000 9.66 0.00 0.00 2.66
804 823 2.140717 CTTCCGACGGCTTTGTTAACT 58.859 47.619 9.66 0.00 0.00 2.24
805 824 2.137523 TCTTCCGACGGCTTTGTTAAC 58.862 47.619 9.66 0.00 0.00 2.01
806 825 2.409975 CTCTTCCGACGGCTTTGTTAA 58.590 47.619 9.66 0.00 0.00 2.01
807 826 1.938016 GCTCTTCCGACGGCTTTGTTA 60.938 52.381 9.66 0.00 0.00 2.41
808 827 1.228657 GCTCTTCCGACGGCTTTGTT 61.229 55.000 9.66 0.00 0.00 2.83
1204 1226 9.944663 CAGTACATAATGCAATTACGGTTTTAT 57.055 29.630 0.00 0.00 42.43 1.40
1207 1229 6.376018 ACCAGTACATAATGCAATTACGGTTT 59.624 34.615 0.00 0.00 42.43 3.27
1210 1232 6.198687 CAACCAGTACATAATGCAATTACGG 58.801 40.000 0.00 0.00 42.43 4.02
1222 1244 0.899019 TGAGGCGCAACCAGTACATA 59.101 50.000 10.83 0.00 43.14 2.29
1223 1245 0.391661 CTGAGGCGCAACCAGTACAT 60.392 55.000 10.83 0.00 43.14 2.29
1225 1247 2.391389 GCTGAGGCGCAACCAGTAC 61.391 63.158 10.83 0.00 43.14 2.73
1241 1263 0.246635 AGGCATTACGTCGAACAGCT 59.753 50.000 0.00 0.00 0.00 4.24
1261 1283 1.129058 GGAAGGATCACCACGGGTAT 58.871 55.000 0.00 0.00 38.94 2.73
1480 1502 2.113139 CAAAGTGAGCCCACCGGT 59.887 61.111 0.00 0.00 44.22 5.28
1488 1510 4.576463 TGAGAAAAGAGAACCAAAGTGAGC 59.424 41.667 0.00 0.00 0.00 4.26
1498 1520 3.491267 CGACCACTGTGAGAAAAGAGAAC 59.509 47.826 9.86 0.00 0.00 3.01
1503 1525 0.868406 GCCGACCACTGTGAGAAAAG 59.132 55.000 9.86 0.00 0.00 2.27
1504 1526 0.878523 CGCCGACCACTGTGAGAAAA 60.879 55.000 9.86 0.00 0.00 2.29
1517 1539 2.742372 AGCCAACATCACGCCGAC 60.742 61.111 0.00 0.00 0.00 4.79
1522 1551 2.490328 AACAAACAGCCAACATCACG 57.510 45.000 0.00 0.00 0.00 4.35
1887 1917 7.686859 GCATCAGGGTGTGATAACTCATTACTA 60.687 40.741 0.00 0.00 44.73 1.82
1888 1918 6.586344 CATCAGGGTGTGATAACTCATTACT 58.414 40.000 0.00 0.00 44.73 2.24
1936 1967 0.179094 ATTCGAGCGCGGAATGGTAA 60.179 50.000 23.04 0.00 38.28 2.85
2026 2057 2.478894 AGATCAGCACCAAACGTTAACG 59.521 45.455 25.68 25.68 46.33 3.18
2117 2148 3.778954 AGGAGTTGAGAAGGTTGGAAG 57.221 47.619 0.00 0.00 0.00 3.46
2214 2245 7.652507 GGGTTTCTCGTCTCGATTAATAGAAAT 59.347 37.037 9.42 0.00 34.61 2.17
2534 2576 0.031616 ACAAACCAGCAAAGGGGGAA 60.032 50.000 0.00 0.00 0.00 3.97
2646 2688 5.412904 CCTGAACAGTAAATGGTTCCTCTTC 59.587 44.000 0.00 0.00 42.04 2.87
2685 2727 7.059448 TGCTTTGAAATTGTTGTTTCAGAAC 57.941 32.000 2.80 0.00 45.67 3.01
2686 2728 7.601886 TCTTGCTTTGAAATTGTTGTTTCAGAA 59.398 29.630 2.80 0.00 45.67 3.02
2700 2742 6.959639 ATAAGTCCACTTCTTGCTTTGAAA 57.040 33.333 0.00 0.00 37.40 2.69
2797 2839 5.864418 TTGTATACCTGACTACATGGACC 57.136 43.478 0.00 0.00 0.00 4.46
3046 3089 3.701664 TGAGCTCATGACAGGACTTAGA 58.298 45.455 13.74 0.00 0.00 2.10
3069 3115 5.421693 TGCATTTGAGCAGGGTACATAAAAT 59.578 36.000 0.00 0.00 40.11 1.82
3079 3125 4.824289 AGTAATTTTGCATTTGAGCAGGG 58.176 39.130 0.00 0.00 46.54 4.45
3111 3157 5.165911 AGTATACTCAACACATACGGACG 57.834 43.478 0.00 0.00 31.76 4.79
3144 3190 4.363991 AAATTGAACAGGAGACTCTGCT 57.636 40.909 1.74 0.00 40.21 4.24
3145 3191 6.749923 AATAAATTGAACAGGAGACTCTGC 57.250 37.500 1.74 0.00 40.21 4.26
3311 3357 1.263217 GCCTACCAACAACACAAGTCG 59.737 52.381 0.00 0.00 0.00 4.18
3483 3531 0.179225 GCGTACAACAGTCCAATGCG 60.179 55.000 0.00 0.00 0.00 4.73
3484 3532 0.168128 GGCGTACAACAGTCCAATGC 59.832 55.000 0.00 0.00 0.00 3.56
3503 3551 3.359654 ACGCAAGAAAACAAAGTTAGCG 58.640 40.909 0.00 0.00 46.98 4.26
3604 3652 4.769488 ACTCAAGAGAGATGCACAAGTAGA 59.231 41.667 3.73 0.00 44.98 2.59
4002 4164 3.364460 TCCCACACATAGTTCCCATTG 57.636 47.619 0.00 0.00 0.00 2.82
4011 4173 5.491070 TCTCTGTCAATTTCCCACACATAG 58.509 41.667 0.00 0.00 0.00 2.23
4046 4208 6.320164 TGCACCAATTCCCACTATACAAATAC 59.680 38.462 0.00 0.00 0.00 1.89
4095 4257 5.500234 TCTTAACCCCTTCATCATGACTTG 58.500 41.667 0.00 0.00 0.00 3.16
4142 4304 2.286885 GAGGGGGTGGGGATTGGA 60.287 66.667 0.00 0.00 0.00 3.53
4222 4384 0.472471 CGTATGGTTAGGGGGCATGT 59.528 55.000 0.00 0.00 0.00 3.21
4282 4444 3.359695 TGGTTGGGTGTAATTAGAGCC 57.640 47.619 20.86 20.86 37.61 4.70
4505 4672 8.955061 AAGTCATGAAATTATTGAACAGTTCG 57.045 30.769 8.80 0.00 0.00 3.95
4514 4681 8.486383 TGCAAAAACGAAGTCATGAAATTATTG 58.514 29.630 0.00 0.00 45.00 1.90
4515 4682 8.586570 TGCAAAAACGAAGTCATGAAATTATT 57.413 26.923 0.00 0.00 45.00 1.40
4516 4683 8.586570 TTGCAAAAACGAAGTCATGAAATTAT 57.413 26.923 0.00 0.00 45.00 1.28
4517 4684 7.918033 TCTTGCAAAAACGAAGTCATGAAATTA 59.082 29.630 0.00 0.00 45.00 1.40
4518 4685 6.756074 TCTTGCAAAAACGAAGTCATGAAATT 59.244 30.769 0.00 0.00 45.00 1.82
4519 4686 6.198966 GTCTTGCAAAAACGAAGTCATGAAAT 59.801 34.615 0.00 0.00 45.00 2.17
4520 4687 5.514914 GTCTTGCAAAAACGAAGTCATGAAA 59.485 36.000 0.00 0.00 45.00 2.69
4521 4688 5.034152 GTCTTGCAAAAACGAAGTCATGAA 58.966 37.500 0.00 0.00 45.00 2.57
4522 4689 4.095632 TGTCTTGCAAAAACGAAGTCATGA 59.904 37.500 0.00 0.00 45.00 3.07
4523 4690 4.350346 TGTCTTGCAAAAACGAAGTCATG 58.650 39.130 0.00 0.00 45.00 3.07
4524 4691 4.630894 TGTCTTGCAAAAACGAAGTCAT 57.369 36.364 0.00 0.00 45.00 3.06
4525 4692 4.427096 TTGTCTTGCAAAAACGAAGTCA 57.573 36.364 0.00 0.00 34.43 3.41
4526 4693 4.259411 GCTTTGTCTTGCAAAAACGAAGTC 60.259 41.667 26.85 20.14 45.35 3.01
4527 4694 3.612423 GCTTTGTCTTGCAAAAACGAAGT 59.388 39.130 26.85 0.00 45.35 3.01
4528 4695 3.611986 TGCTTTGTCTTGCAAAAACGAAG 59.388 39.130 24.52 24.52 45.35 3.79
4529 4696 3.579709 TGCTTTGTCTTGCAAAAACGAA 58.420 36.364 0.00 7.30 45.35 3.85
4530 4697 3.223423 TGCTTTGTCTTGCAAAAACGA 57.777 38.095 0.00 0.00 45.35 3.85
4531 4698 3.987807 TTGCTTTGTCTTGCAAAAACG 57.012 38.095 0.00 0.00 45.35 3.60
4536 4703 4.454728 AGAGTTTTGCTTTGTCTTGCAA 57.545 36.364 0.00 0.00 45.83 4.08
4537 4704 4.454728 AAGAGTTTTGCTTTGTCTTGCA 57.545 36.364 0.00 0.00 37.42 4.08
4538 4705 5.804979 TGTTAAGAGTTTTGCTTTGTCTTGC 59.195 36.000 0.00 0.00 0.00 4.01
4539 4706 6.806249 TGTGTTAAGAGTTTTGCTTTGTCTTG 59.194 34.615 0.00 0.00 0.00 3.02
4540 4707 6.919721 TGTGTTAAGAGTTTTGCTTTGTCTT 58.080 32.000 0.00 0.00 0.00 3.01
4541 4708 6.509418 TGTGTTAAGAGTTTTGCTTTGTCT 57.491 33.333 0.00 0.00 0.00 3.41
4542 4709 6.751888 ACATGTGTTAAGAGTTTTGCTTTGTC 59.248 34.615 0.00 0.00 0.00 3.18
4543 4710 6.630071 ACATGTGTTAAGAGTTTTGCTTTGT 58.370 32.000 0.00 0.00 0.00 2.83
4544 4711 7.275341 TCAACATGTGTTAAGAGTTTTGCTTTG 59.725 33.333 0.00 0.00 36.32 2.77
4545 4712 7.275560 GTCAACATGTGTTAAGAGTTTTGCTTT 59.724 33.333 0.00 0.00 36.32 3.51
4565 4732 7.956420 AGAGTACGAAATAACAATGTCAACA 57.044 32.000 0.00 0.00 0.00 3.33
4583 4750 4.756084 ACATCAAAAGCTGCAAGAGTAC 57.244 40.909 1.02 0.00 34.07 2.73
4614 4781 5.042979 ACCCTATATCTAGGAATGGAGGGAG 60.043 48.000 17.15 0.00 46.66 4.30
4655 4822 3.201266 TCCCAGCCCGTGAGTTAATATTT 59.799 43.478 0.00 0.00 0.00 1.40
4669 4836 1.617018 GGAATTTGCCTTCCCAGCCC 61.617 60.000 0.00 0.00 39.06 5.19
4717 4884 2.428890 CCCTCTAGTCTCACATGGTCAC 59.571 54.545 0.00 0.00 0.00 3.67
4718 4885 2.624293 CCCCTCTAGTCTCACATGGTCA 60.624 54.545 0.00 0.00 0.00 4.02
4730 4897 5.543020 CCGATTTACCTATTTCCCCTCTAGT 59.457 44.000 0.00 0.00 0.00 2.57
4736 4903 2.224942 CCCCCGATTTACCTATTTCCCC 60.225 54.545 0.00 0.00 0.00 4.81
4766 4933 4.425772 TGGAAGTAATCTGACCAGGAGAA 58.574 43.478 0.00 0.00 31.31 2.87
4774 4941 9.141400 GGACGATATTTATGGAAGTAATCTGAC 57.859 37.037 0.00 0.00 0.00 3.51
4798 4967 5.888691 TTGCTTGAATATTAACGCAAGGA 57.111 34.783 11.70 8.27 46.39 3.36
4814 4983 8.099364 CCTACATATAGGGTGTATTTTGCTTG 57.901 38.462 0.00 0.00 44.06 4.01
4843 5012 5.157770 TCTTAACAGATCATACCCCCTCT 57.842 43.478 0.00 0.00 0.00 3.69
4904 5073 1.134280 AGCTAACATGCTCAGCCGATT 60.134 47.619 9.48 0.00 39.34 3.34
4913 5082 3.131223 ACAGATCGTGTAGCTAACATGCT 59.869 43.478 0.00 0.00 43.65 3.79
4919 5088 8.821147 TTTCTTTTAACAGATCGTGTAGCTAA 57.179 30.769 0.00 0.00 39.03 3.09
4920 5089 8.821147 TTTTCTTTTAACAGATCGTGTAGCTA 57.179 30.769 0.00 0.00 39.03 3.32
5005 5175 5.119694 GCCTTTGTTGTCAATTTTAACCCA 58.880 37.500 0.00 0.00 33.32 4.51
5009 5179 8.821894 GTGTATTGCCTTTGTTGTCAATTTTAA 58.178 29.630 0.00 0.00 33.32 1.52
5122 5294 7.415229 CCCAGGCGTAATTTATTACTTTCTTC 58.585 38.462 10.07 0.00 40.27 2.87
5229 5402 7.308435 CCATAGTTCCATGTCAAGAAGAAAAC 58.692 38.462 0.00 0.00 0.00 2.43
5553 5756 3.554337 GGAAAGCTTGACGTGAGGAGTTA 60.554 47.826 0.00 0.00 0.00 2.24
5806 6291 2.902705 TCCATAATAGACCGGTGCAC 57.097 50.000 14.63 8.80 0.00 4.57
5863 6349 7.698506 TCAGTATATGGTCCCTAATCTTACG 57.301 40.000 0.00 0.00 0.00 3.18
6075 6561 4.711721 CCTTTTATGATGTGTGTGTGACG 58.288 43.478 0.00 0.00 0.00 4.35
6106 6592 5.133941 CAGCTGGAGTGTAGTAGATTCCTA 58.866 45.833 5.57 0.00 0.00 2.94
6178 6664 9.113838 ACTGTAATGGCTTCTAATCATACTTTG 57.886 33.333 0.00 0.00 0.00 2.77
6240 6726 5.765182 GGCAGGTACTTAATGCAGAACATAT 59.235 40.000 12.53 0.00 41.78 1.78
6331 6817 3.844090 GGAGTCTCAGGGCTCCGC 61.844 72.222 1.47 0.00 41.40 5.54
6646 7135 1.234615 ATGTCAAGAACAACCCGGCG 61.235 55.000 0.00 0.00 42.37 6.46
6733 7222 3.050089 TCTACCCAAAGAGGTGTTCCAA 58.950 45.455 0.00 0.00 41.42 3.53
6933 7423 9.722056 CTTATGTCTTCAAATGCAAGTATAACC 57.278 33.333 0.00 0.00 0.00 2.85
7117 7610 8.982685 CACCAATCTTACTACTTACATGCATAG 58.017 37.037 0.00 0.00 0.00 2.23
7118 7611 7.441157 GCACCAATCTTACTACTTACATGCATA 59.559 37.037 0.00 0.00 0.00 3.14
7119 7612 6.260936 GCACCAATCTTACTACTTACATGCAT 59.739 38.462 0.00 0.00 0.00 3.96
7124 7617 5.748670 TGGCACCAATCTTACTACTTACA 57.251 39.130 0.00 0.00 0.00 2.41
7177 7670 4.194640 GCCAGTCTGAAGATAGCATCAAA 58.805 43.478 0.00 0.00 0.00 2.69
7179 7672 2.103771 GGCCAGTCTGAAGATAGCATCA 59.896 50.000 0.00 0.00 0.00 3.07
7201 7694 2.383527 CGAGGCGAGCAGTGGTTTC 61.384 63.158 0.00 0.00 0.00 2.78
7213 7706 3.474806 GGTGTGTTCATCGAGGCG 58.525 61.111 0.00 0.00 0.00 5.52
7463 7956 0.886490 CACCAGGCACTCCTCAACAC 60.886 60.000 0.00 0.00 41.93 3.32
7565 8058 2.373169 ACATAGGCCATCATGTACCCTG 59.627 50.000 14.08 0.00 33.66 4.45
7666 8159 1.400142 TGTTCAACTCGCAACAAGGTG 59.600 47.619 0.00 0.00 32.52 4.00
7826 8319 2.066592 TCCCCTTTCAATGGGTACACA 58.933 47.619 0.00 0.00 43.09 3.72
7862 8355 4.175337 GCACTGCGGGATGGGCTA 62.175 66.667 0.00 0.00 0.00 3.93
7919 8412 1.290130 TCCTACCCTTGGGTAGAGGAC 59.710 57.143 35.24 0.00 43.04 3.85
7970 8463 1.160329 ACAACAGCTTCGTGCAGGAC 61.160 55.000 8.96 0.00 45.94 3.85
8162 8657 9.739276 TGAACCAAGAATAAGTTTCTGACATAT 57.261 29.630 0.00 0.00 0.00 1.78
8163 8658 9.567776 TTGAACCAAGAATAAGTTTCTGACATA 57.432 29.630 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.