Multiple sequence alignment - TraesCS3B01G605000

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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 TraesCS3B01G605000 chr3B 100.000 4109 0 0 1 4109 823555005 823550897 0.000000e+00 7589.0
1 TraesCS3B01G605000 chr3B 82.192 584 84 15 3534 4109 389255394 389254823 6.180000e-133 484.0
2 TraesCS3B01G605000 chr3B 97.959 147 3 0 1 147 151440002 151440148 5.270000e-64 255.0
3 TraesCS3B01G605000 chr3B 90.604 149 14 0 678 826 103746850 103746998 9.010000e-47 198.0
4 TraesCS3B01G605000 chr3B 89.933 149 15 0 678 826 703326745 703326597 4.190000e-45 193.0
5 TraesCS3B01G605000 chr3B 87.879 99 11 1 525 622 802706459 802706361 9.330000e-22 115.0
6 TraesCS3B01G605000 chr3D 95.866 3338 129 8 776 4109 613900090 613903422 0.000000e+00 5391.0
7 TraesCS3B01G605000 chr3D 94.055 471 18 4 145 613 613899600 613900062 0.000000e+00 706.0
8 TraesCS3B01G605000 chr3D 83.592 579 83 7 3535 4109 414780699 414780129 2.170000e-147 532.0
9 TraesCS3B01G605000 chr3D 91.216 148 13 0 679 826 599373775 599373922 6.960000e-48 202.0
10 TraesCS3B01G605000 chr3D 74.105 475 108 6 1034 1493 569208006 569208480 9.070000e-42 182.0
11 TraesCS3B01G605000 chr2A 83.739 781 106 8 859 1635 754609498 754610261 0.000000e+00 719.0
12 TraesCS3B01G605000 chr2A 81.442 749 119 14 1541 2283 754610335 754611069 2.730000e-166 595.0
13 TraesCS3B01G605000 chr2A 86.325 234 25 6 1694 1923 754613863 754614093 8.820000e-62 248.0
14 TraesCS3B01G605000 chr2A 86.471 170 19 3 657 822 763401745 763401914 2.520000e-42 183.0
15 TraesCS3B01G605000 chr2A 92.308 65 5 0 2402 2466 754611173 754611237 4.370000e-15 93.5
16 TraesCS3B01G605000 chr4D 84.629 579 76 9 3535 4109 63901527 63902096 7.710000e-157 564.0
17 TraesCS3B01G605000 chr4D 89.933 149 15 0 678 826 121553860 121553712 4.190000e-45 193.0
18 TraesCS3B01G605000 chr4D 89.262 149 16 0 678 826 293775893 293776041 1.950000e-43 187.0
19 TraesCS3B01G605000 chr4D 89.262 149 16 0 678 826 337478817 337478669 1.950000e-43 187.0
20 TraesCS3B01G605000 chr2B 83.737 578 81 11 3534 4106 256989913 256990482 6.050000e-148 534.0
21 TraesCS3B01G605000 chr2B 98.639 147 2 0 1 147 474549154 474549008 1.130000e-65 261.0
22 TraesCS3B01G605000 chr2B 97.959 147 3 0 1 147 671761434 671761288 5.270000e-64 255.0
23 TraesCS3B01G605000 chr2B 97.279 147 4 0 1 147 234356823 234356677 2.450000e-62 250.0
24 TraesCS3B01G605000 chr2B 75.229 436 104 4 1048 1481 794621579 794622012 1.940000e-48 204.0
25 TraesCS3B01G605000 chr4B 83.652 575 77 9 3539 4109 94526911 94527472 3.640000e-145 525.0
26 TraesCS3B01G605000 chr7B 82.847 583 82 13 3531 4106 254131393 254131964 1.320000e-139 507.0
27 TraesCS3B01G605000 chr7B 98.639 147 2 0 1 147 104267906 104267760 1.130000e-65 261.0
28 TraesCS3B01G605000 chr2D 82.383 579 90 8 3535 4109 6161076 6160506 1.030000e-135 494.0
29 TraesCS3B01G605000 chr2D 79.422 277 57 0 1217 1493 60202665 60202389 3.240000e-46 196.0
30 TraesCS3B01G605000 chr3A 82.383 579 89 10 3535 4109 136414527 136413958 3.690000e-135 492.0
31 TraesCS3B01G605000 chr3A 80.645 496 90 6 1044 1536 706760 707252 3.000000e-101 379.0
32 TraesCS3B01G605000 chr6A 78.244 501 92 15 1046 1536 616033499 616033006 5.160000e-79 305.0
33 TraesCS3B01G605000 chr6B 98.639 147 2 0 1 147 579064822 579064676 1.130000e-65 261.0
34 TraesCS3B01G605000 chr6B 97.279 147 4 0 1 147 15869514 15869660 2.450000e-62 250.0
35 TraesCS3B01G605000 chr6B 91.946 149 12 0 678 826 368464669 368464817 4.160000e-50 209.0
36 TraesCS3B01G605000 chr6B 95.455 44 2 0 631 674 660642448 660642405 2.050000e-08 71.3
37 TraesCS3B01G605000 chr1B 98.621 145 2 0 3 147 526166348 526166204 1.470000e-64 257.0
38 TraesCS3B01G605000 chr4A 97.279 147 4 0 1 147 672244796 672244650 2.450000e-62 250.0
39 TraesCS3B01G605000 chr6D 89.933 149 15 0 678 826 334161344 334161196 4.190000e-45 193.0
40 TraesCS3B01G605000 chr6D 78.700 277 59 0 1217 1493 97569999 97569723 7.010000e-43 185.0
41 TraesCS3B01G605000 chr6D 88.889 90 9 1 524 612 192071552 192071641 4.340000e-20 110.0
42 TraesCS3B01G605000 chr7D 74.273 447 113 2 1031 1476 622271372 622271817 1.950000e-43 187.0
43 TraesCS3B01G605000 chr1D 82.828 99 16 1 527 624 16272679 16272777 2.030000e-13 87.9
44 TraesCS3B01G605000 chr5B 84.706 85 11 2 527 610 518566384 518566301 2.630000e-12 84.2


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 TraesCS3B01G605000 chr3B 823550897 823555005 4108 True 7589.000 7589 100.0000 1 4109 1 chr3B.!!$R4 4108
1 TraesCS3B01G605000 chr3B 389254823 389255394 571 True 484.000 484 82.1920 3534 4109 1 chr3B.!!$R1 575
2 TraesCS3B01G605000 chr3D 613899600 613903422 3822 False 3048.500 5391 94.9605 145 4109 2 chr3D.!!$F3 3964
3 TraesCS3B01G605000 chr3D 414780129 414780699 570 True 532.000 532 83.5920 3535 4109 1 chr3D.!!$R1 574
4 TraesCS3B01G605000 chr2A 754609498 754614093 4595 False 413.875 719 85.9535 859 2466 4 chr2A.!!$F2 1607
5 TraesCS3B01G605000 chr4D 63901527 63902096 569 False 564.000 564 84.6290 3535 4109 1 chr4D.!!$F1 574
6 TraesCS3B01G605000 chr2B 256989913 256990482 569 False 534.000 534 83.7370 3534 4106 1 chr2B.!!$F1 572
7 TraesCS3B01G605000 chr4B 94526911 94527472 561 False 525.000 525 83.6520 3539 4109 1 chr4B.!!$F1 570
8 TraesCS3B01G605000 chr7B 254131393 254131964 571 False 507.000 507 82.8470 3531 4106 1 chr7B.!!$F1 575
9 TraesCS3B01G605000 chr2D 6160506 6161076 570 True 494.000 494 82.3830 3535 4109 1 chr2D.!!$R1 574
10 TraesCS3B01G605000 chr3A 136413958 136414527 569 True 492.000 492 82.3830 3535 4109 1 chr3A.!!$R1 574

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
116 117 0.316204 CGTGGACCGTCTACCAAAGT 59.684 55.0 9.25 0.0 37.94 2.66 F
214 215 0.405198 TGGATCCATTGCGGCCATAT 59.595 50.0 11.44 0.0 33.14 1.78 F
1983 2161 0.103937 ATGTTTTGTTGGGTGGTGCG 59.896 50.0 0.00 0.0 0.00 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1036 1042 1.214992 ACTTGGATCCCCCACCCTTC 61.215 60.000 9.90 0.0 46.62 3.46 R
2066 2244 1.597854 CGAACCACAGGAGCAAGCA 60.598 57.895 0.00 0.0 0.00 3.91 R
3936 4857 1.142262 ACACCCAGTTACCAAGTGACC 59.858 52.381 3.78 0.0 33.58 4.02 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
19 20 1.217882 CCAACCCGAATATGTCTCGC 58.782 55.000 0.00 0.00 34.95 5.03
20 21 1.202533 CCAACCCGAATATGTCTCGCT 60.203 52.381 0.00 0.00 34.95 4.93
21 22 2.035449 CCAACCCGAATATGTCTCGCTA 59.965 50.000 0.00 0.00 34.95 4.26
22 23 3.491964 CCAACCCGAATATGTCTCGCTAA 60.492 47.826 0.00 0.00 34.95 3.09
23 24 3.644884 ACCCGAATATGTCTCGCTAAG 57.355 47.619 0.00 0.00 34.95 2.18
24 25 2.957006 ACCCGAATATGTCTCGCTAAGT 59.043 45.455 0.00 0.00 34.95 2.24
25 26 3.383825 ACCCGAATATGTCTCGCTAAGTT 59.616 43.478 0.00 0.00 34.95 2.66
26 27 4.581824 ACCCGAATATGTCTCGCTAAGTTA 59.418 41.667 0.00 0.00 34.95 2.24
27 28 5.154932 CCCGAATATGTCTCGCTAAGTTAG 58.845 45.833 5.47 5.47 34.95 2.34
28 29 5.154932 CCGAATATGTCTCGCTAAGTTAGG 58.845 45.833 11.84 2.53 34.95 2.69
29 30 4.617645 CGAATATGTCTCGCTAAGTTAGGC 59.382 45.833 11.84 3.58 0.00 3.93
30 31 5.563085 CGAATATGTCTCGCTAAGTTAGGCT 60.563 44.000 11.84 0.00 0.00 4.58
31 32 3.719173 ATGTCTCGCTAAGTTAGGCTC 57.281 47.619 11.84 0.00 0.00 4.70
32 33 2.443416 TGTCTCGCTAAGTTAGGCTCA 58.557 47.619 11.84 0.00 0.00 4.26
33 34 2.823747 TGTCTCGCTAAGTTAGGCTCAA 59.176 45.455 11.84 0.00 0.00 3.02
34 35 3.447586 TGTCTCGCTAAGTTAGGCTCAAT 59.552 43.478 11.84 0.00 0.00 2.57
35 36 4.045783 GTCTCGCTAAGTTAGGCTCAATC 58.954 47.826 11.84 0.00 0.00 2.67
36 37 3.068307 TCTCGCTAAGTTAGGCTCAATCC 59.932 47.826 11.84 0.00 0.00 3.01
37 38 2.102588 TCGCTAAGTTAGGCTCAATCCC 59.897 50.000 11.84 0.00 0.00 3.85
38 39 2.158957 CGCTAAGTTAGGCTCAATCCCA 60.159 50.000 11.84 0.00 0.00 4.37
39 40 3.495100 CGCTAAGTTAGGCTCAATCCCAT 60.495 47.826 11.84 0.00 0.00 4.00
40 41 4.464947 GCTAAGTTAGGCTCAATCCCATT 58.535 43.478 11.84 0.00 0.00 3.16
41 42 5.621193 GCTAAGTTAGGCTCAATCCCATTA 58.379 41.667 11.84 0.00 0.00 1.90
42 43 6.062095 GCTAAGTTAGGCTCAATCCCATTAA 58.938 40.000 11.84 0.00 0.00 1.40
43 44 6.205658 GCTAAGTTAGGCTCAATCCCATTAAG 59.794 42.308 11.84 0.00 0.00 1.85
44 45 4.464947 AGTTAGGCTCAATCCCATTAAGC 58.535 43.478 0.00 0.00 0.00 3.09
48 49 3.655276 GCTCAATCCCATTAAGCCATG 57.345 47.619 0.00 0.00 0.00 3.66
49 50 2.961062 GCTCAATCCCATTAAGCCATGT 59.039 45.455 0.00 0.00 0.00 3.21
50 51 3.005155 GCTCAATCCCATTAAGCCATGTC 59.995 47.826 0.00 0.00 0.00 3.06
51 52 3.565307 TCAATCCCATTAAGCCATGTCC 58.435 45.455 0.00 0.00 0.00 4.02
52 53 2.629617 CAATCCCATTAAGCCATGTCCC 59.370 50.000 0.00 0.00 0.00 4.46
53 54 1.303898 TCCCATTAAGCCATGTCCCA 58.696 50.000 0.00 0.00 0.00 4.37
54 55 1.643286 TCCCATTAAGCCATGTCCCAA 59.357 47.619 0.00 0.00 0.00 4.12
55 56 2.043664 TCCCATTAAGCCATGTCCCAAA 59.956 45.455 0.00 0.00 0.00 3.28
56 57 3.040477 CCCATTAAGCCATGTCCCAAAT 58.960 45.455 0.00 0.00 0.00 2.32
57 58 4.078922 TCCCATTAAGCCATGTCCCAAATA 60.079 41.667 0.00 0.00 0.00 1.40
58 59 4.653341 CCCATTAAGCCATGTCCCAAATAA 59.347 41.667 0.00 0.00 0.00 1.40
59 60 5.453198 CCCATTAAGCCATGTCCCAAATAAC 60.453 44.000 0.00 0.00 0.00 1.89
60 61 4.974368 TTAAGCCATGTCCCAAATAACG 57.026 40.909 0.00 0.00 0.00 3.18
61 62 1.102978 AGCCATGTCCCAAATAACGC 58.897 50.000 0.00 0.00 0.00 4.84
62 63 0.814457 GCCATGTCCCAAATAACGCA 59.186 50.000 0.00 0.00 0.00 5.24
63 64 1.408702 GCCATGTCCCAAATAACGCAT 59.591 47.619 0.00 0.00 0.00 4.73
64 65 2.159114 GCCATGTCCCAAATAACGCATT 60.159 45.455 0.00 0.00 0.00 3.56
65 66 3.067461 GCCATGTCCCAAATAACGCATTA 59.933 43.478 0.00 0.00 0.00 1.90
66 67 4.440802 GCCATGTCCCAAATAACGCATTAA 60.441 41.667 0.00 0.00 0.00 1.40
67 68 5.040635 CCATGTCCCAAATAACGCATTAAC 58.959 41.667 0.00 0.00 0.00 2.01
68 69 5.393569 CCATGTCCCAAATAACGCATTAACA 60.394 40.000 0.00 0.00 0.00 2.41
69 70 5.303747 TGTCCCAAATAACGCATTAACAG 57.696 39.130 0.00 0.00 0.00 3.16
70 71 5.004448 TGTCCCAAATAACGCATTAACAGA 58.996 37.500 0.00 0.00 0.00 3.41
71 72 5.473846 TGTCCCAAATAACGCATTAACAGAA 59.526 36.000 0.00 0.00 0.00 3.02
72 73 6.151985 TGTCCCAAATAACGCATTAACAGAAT 59.848 34.615 0.00 0.00 0.00 2.40
73 74 7.033185 GTCCCAAATAACGCATTAACAGAATT 58.967 34.615 0.00 0.00 0.00 2.17
74 75 7.220108 GTCCCAAATAACGCATTAACAGAATTC 59.780 37.037 0.00 0.00 0.00 2.17
75 76 6.196353 CCCAAATAACGCATTAACAGAATTCG 59.804 38.462 0.00 0.00 0.00 3.34
76 77 6.196353 CCAAATAACGCATTAACAGAATTCGG 59.804 38.462 3.87 3.87 0.00 4.30
77 78 3.757745 AACGCATTAACAGAATTCGGG 57.242 42.857 10.43 4.72 0.00 5.14
78 79 2.014128 ACGCATTAACAGAATTCGGGG 58.986 47.619 10.43 2.26 0.00 5.73
79 80 1.333619 CGCATTAACAGAATTCGGGGG 59.666 52.381 10.43 0.00 0.00 5.40
80 81 2.375146 GCATTAACAGAATTCGGGGGT 58.625 47.619 10.43 0.93 0.00 4.95
81 82 2.758423 GCATTAACAGAATTCGGGGGTT 59.242 45.455 10.43 10.71 0.00 4.11
82 83 3.194755 GCATTAACAGAATTCGGGGGTTT 59.805 43.478 10.43 0.00 0.00 3.27
83 84 4.743493 CATTAACAGAATTCGGGGGTTTG 58.257 43.478 10.43 0.00 0.00 2.93
84 85 2.668144 AACAGAATTCGGGGGTTTGA 57.332 45.000 10.43 0.00 0.00 2.69
85 86 2.899303 ACAGAATTCGGGGGTTTGAT 57.101 45.000 10.43 0.00 0.00 2.57
86 87 4.310022 AACAGAATTCGGGGGTTTGATA 57.690 40.909 10.43 0.00 0.00 2.15
87 88 4.519906 ACAGAATTCGGGGGTTTGATAT 57.480 40.909 10.43 0.00 0.00 1.63
88 89 4.867086 ACAGAATTCGGGGGTTTGATATT 58.133 39.130 10.43 0.00 0.00 1.28
89 90 6.008696 ACAGAATTCGGGGGTTTGATATTA 57.991 37.500 10.43 0.00 0.00 0.98
90 91 6.428295 ACAGAATTCGGGGGTTTGATATTAA 58.572 36.000 10.43 0.00 0.00 1.40
91 92 6.893005 ACAGAATTCGGGGGTTTGATATTAAA 59.107 34.615 10.43 0.00 0.00 1.52
92 93 7.397761 ACAGAATTCGGGGGTTTGATATTAAAA 59.602 33.333 10.43 0.00 0.00 1.52
93 94 7.920682 CAGAATTCGGGGGTTTGATATTAAAAG 59.079 37.037 0.00 0.00 0.00 2.27
94 95 5.585820 TTCGGGGGTTTGATATTAAAAGC 57.414 39.130 0.00 0.64 34.93 3.51
95 96 4.601084 TCGGGGGTTTGATATTAAAAGCA 58.399 39.130 13.01 0.00 36.88 3.91
96 97 5.017490 TCGGGGGTTTGATATTAAAAGCAA 58.983 37.500 13.01 0.00 36.88 3.91
97 98 5.105675 TCGGGGGTTTGATATTAAAAGCAAC 60.106 40.000 13.01 7.41 36.88 4.17
98 99 5.106442 GGGGGTTTGATATTAAAAGCAACG 58.894 41.667 13.01 0.00 36.88 4.10
99 100 5.336929 GGGGGTTTGATATTAAAAGCAACGT 60.337 40.000 13.01 0.00 36.88 3.99
100 101 5.575218 GGGGTTTGATATTAAAAGCAACGTG 59.425 40.000 13.01 0.00 36.88 4.49
101 102 5.575218 GGGTTTGATATTAAAAGCAACGTGG 59.425 40.000 13.01 0.00 36.88 4.94
102 103 6.383415 GGTTTGATATTAAAAGCAACGTGGA 58.617 36.000 0.00 0.00 35.58 4.02
103 104 6.307077 GGTTTGATATTAAAAGCAACGTGGAC 59.693 38.462 0.00 0.00 35.58 4.02
104 105 5.554822 TGATATTAAAAGCAACGTGGACC 57.445 39.130 0.00 0.00 0.00 4.46
105 106 2.981400 ATTAAAAGCAACGTGGACCG 57.019 45.000 0.00 0.00 44.03 4.79
115 116 3.117589 CGTGGACCGTCTACCAAAG 57.882 57.895 9.25 0.00 37.94 2.77
116 117 0.316204 CGTGGACCGTCTACCAAAGT 59.684 55.000 9.25 0.00 37.94 2.66
117 118 1.541147 CGTGGACCGTCTACCAAAGTA 59.459 52.381 9.25 0.00 37.94 2.24
118 119 2.669391 CGTGGACCGTCTACCAAAGTAC 60.669 54.545 9.25 0.00 37.94 2.73
119 120 1.895131 TGGACCGTCTACCAAAGTACC 59.105 52.381 0.00 0.00 32.93 3.34
120 121 2.174360 GGACCGTCTACCAAAGTACCT 58.826 52.381 0.00 0.00 0.00 3.08
121 122 2.564504 GGACCGTCTACCAAAGTACCTT 59.435 50.000 0.00 0.00 0.00 3.50
122 123 3.582780 GACCGTCTACCAAAGTACCTTG 58.417 50.000 0.00 0.00 0.00 3.61
128 129 2.267045 CCAAAGTACCTTGGCCAGC 58.733 57.895 10.29 0.00 39.55 4.85
129 130 1.586154 CCAAAGTACCTTGGCCAGCG 61.586 60.000 10.29 1.95 39.55 5.18
130 131 1.303317 AAAGTACCTTGGCCAGCGG 60.303 57.895 18.71 18.71 0.00 5.52
131 132 2.764637 AAAGTACCTTGGCCAGCGGG 62.765 60.000 22.72 19.69 37.18 6.13
160 161 3.953542 AAAGAGGAACAAAGGAGTGGT 57.046 42.857 0.00 0.00 0.00 4.16
177 178 4.536765 AGTGGTTTTGTCTCAACTCCATT 58.463 39.130 7.60 3.00 0.00 3.16
214 215 0.405198 TGGATCCATTGCGGCCATAT 59.595 50.000 11.44 0.00 33.14 1.78
215 216 1.632920 TGGATCCATTGCGGCCATATA 59.367 47.619 11.44 0.00 33.14 0.86
240 241 3.195825 AGACCTGGTTATGAAGGAGAACG 59.804 47.826 0.00 0.00 37.01 3.95
245 246 3.512329 TGGTTATGAAGGAGAACGCTACA 59.488 43.478 0.00 0.00 0.00 2.74
276 277 1.559368 TTGGATGCACATGGGGAAAG 58.441 50.000 0.00 0.00 0.00 2.62
439 440 2.622436 GGTCCATGCTTCTCACACTAC 58.378 52.381 0.00 0.00 0.00 2.73
445 446 2.337583 TGCTTCTCACACTACGATTGC 58.662 47.619 0.00 0.00 0.00 3.56
476 477 2.371306 CCACCACATGATTCATCAGCA 58.629 47.619 0.00 0.00 40.64 4.41
544 547 2.126882 TGAGGCTGGCCATAGTGTTAT 58.873 47.619 5.51 0.00 38.92 1.89
571 574 3.851458 AGCTGATATCATGCACTTGGA 57.149 42.857 21.46 0.00 0.00 3.53
584 587 2.979813 GCACTTGGAAATAGCAAACACG 59.020 45.455 0.00 0.00 0.00 4.49
613 616 9.793259 AATGTGGTAGAGAATTAAAAAGAGACA 57.207 29.630 0.00 0.00 0.00 3.41
614 617 8.833231 TGTGGTAGAGAATTAAAAAGAGACAG 57.167 34.615 0.00 0.00 0.00 3.51
615 618 7.387948 TGTGGTAGAGAATTAAAAAGAGACAGC 59.612 37.037 0.00 0.00 0.00 4.40
616 619 7.387948 GTGGTAGAGAATTAAAAAGAGACAGCA 59.612 37.037 0.00 0.00 0.00 4.41
617 620 8.103305 TGGTAGAGAATTAAAAAGAGACAGCAT 58.897 33.333 0.00 0.00 0.00 3.79
618 621 8.951243 GGTAGAGAATTAAAAAGAGACAGCATT 58.049 33.333 0.00 0.00 0.00 3.56
621 624 9.950496 AGAGAATTAAAAAGAGACAGCATTAGA 57.050 29.630 0.00 0.00 0.00 2.10
653 656 9.850628 TTTTCATTGATTGCAAATTTTTGTTGA 57.149 22.222 1.71 0.00 40.24 3.18
663 666 8.948631 TGCAAATTTTTGTTGATAACTTACCA 57.051 26.923 5.05 0.00 40.24 3.25
664 667 9.383519 TGCAAATTTTTGTTGATAACTTACCAA 57.616 25.926 5.05 0.00 40.24 3.67
665 668 9.862585 GCAAATTTTTGTTGATAACTTACCAAG 57.137 29.630 5.05 0.00 40.24 3.61
670 673 9.959749 TTTTTGTTGATAACTTACCAAGATGAC 57.040 29.630 0.00 0.00 0.00 3.06
671 674 7.681939 TTGTTGATAACTTACCAAGATGACC 57.318 36.000 0.00 0.00 0.00 4.02
672 675 6.774673 TGTTGATAACTTACCAAGATGACCA 58.225 36.000 0.00 0.00 0.00 4.02
673 676 6.653320 TGTTGATAACTTACCAAGATGACCAC 59.347 38.462 0.00 0.00 0.00 4.16
674 677 6.620877 TGATAACTTACCAAGATGACCACT 57.379 37.500 0.00 0.00 0.00 4.00
675 678 7.016153 TGATAACTTACCAAGATGACCACTT 57.984 36.000 0.00 0.00 0.00 3.16
676 679 6.878923 TGATAACTTACCAAGATGACCACTTG 59.121 38.462 0.00 0.00 42.72 3.16
700 703 8.411991 TGGTAACATTGATAGATACCGTATCA 57.588 34.615 18.67 7.10 46.17 2.15
701 704 9.031537 TGGTAACATTGATAGATACCGTATCAT 57.968 33.333 18.67 10.86 46.17 2.45
729 732 9.838975 TTAAATGTTATGCTACTTTGTGTCATG 57.161 29.630 0.00 0.00 0.00 3.07
730 733 5.295431 TGTTATGCTACTTTGTGTCATGC 57.705 39.130 0.00 0.00 0.00 4.06
731 734 4.759183 TGTTATGCTACTTTGTGTCATGCA 59.241 37.500 0.00 0.00 35.34 3.96
732 735 5.415389 TGTTATGCTACTTTGTGTCATGCAT 59.585 36.000 0.00 0.00 40.50 3.96
733 736 3.835378 TGCTACTTTGTGTCATGCATG 57.165 42.857 21.07 21.07 0.00 4.06
734 737 3.410508 TGCTACTTTGTGTCATGCATGA 58.589 40.909 25.42 25.42 0.00 3.07
793 796 5.326200 ACTGTGCACTATGAAGGTAGTAC 57.674 43.478 19.41 0.00 33.29 2.73
840 843 7.605449 TGGTACTAGTAGTTAATGAACACCAC 58.395 38.462 8.40 0.00 38.10 4.16
842 845 8.960591 GGTACTAGTAGTTAATGAACACCACTA 58.039 37.037 8.40 0.00 38.10 2.74
893 896 2.926329 ACCCCCATTCTTCACAACCTAT 59.074 45.455 0.00 0.00 0.00 2.57
969 972 6.246420 TGTAAGTGTACCTAAAGTCGTCTC 57.754 41.667 0.00 0.00 0.00 3.36
976 979 5.533903 TGTACCTAAAGTCGTCTCTGTCTTT 59.466 40.000 0.00 0.00 34.98 2.52
1024 1030 5.918608 TGGCTGGTGAATTAGAGATACTTC 58.081 41.667 0.00 0.00 0.00 3.01
1036 1042 1.492176 AGATACTTCTGGTGGCATGGG 59.508 52.381 0.00 0.00 0.00 4.00
1132 1138 4.980805 GCCGCAACGACTCCACCA 62.981 66.667 0.00 0.00 0.00 4.17
1230 1236 0.965866 TGAGTAGGTCACCGGAGCAG 60.966 60.000 9.46 0.00 43.97 4.24
1338 1344 2.256072 TATGGCTGCGTCACCTGCAT 62.256 55.000 0.00 0.00 42.32 3.96
1458 1464 1.553704 GTGGTCGGGGTTCTCAAGTAT 59.446 52.381 0.00 0.00 0.00 2.12
1585 1663 0.257039 GGAGGGAGATGGTGTGCAAT 59.743 55.000 0.00 0.00 0.00 3.56
1678 1856 7.997773 GGAAACCAGAAAGACCTACTATTTT 57.002 36.000 0.00 0.00 0.00 1.82
1755 1933 7.273381 CGTTTTGTGAAAATCAATAGGGATCAC 59.727 37.037 0.00 0.00 32.22 3.06
1836 2014 2.680913 GCTGTACACCAAGGCTGCG 61.681 63.158 0.00 0.00 0.00 5.18
1930 2108 6.801539 TGTTCCATAGATCAAGTGACAAAC 57.198 37.500 0.00 0.00 0.00 2.93
1972 2150 5.906113 TGTGGTTGTCACTTATGTTTTGT 57.094 34.783 0.00 0.00 46.20 2.83
1983 2161 0.103937 ATGTTTTGTTGGGTGGTGCG 59.896 50.000 0.00 0.00 0.00 5.34
2010 2188 6.611236 TCATCTTGGAGACCACATCAGTATTA 59.389 38.462 0.00 0.00 30.78 0.98
2066 2244 9.715121 ATTCATGTTAGAAAAGAAATGTGCATT 57.285 25.926 0.00 0.00 0.00 3.56
2275 2453 4.872691 CGCTTCTTATCATTCAGAAGGTGT 59.127 41.667 10.21 0.00 44.32 4.16
2350 2558 1.345715 CCGGAATGCCCTAAGGAGGT 61.346 60.000 0.00 0.00 41.95 3.85
2362 2570 4.223953 CCTAAGGAGGTATAGTGCCTTGA 58.776 47.826 0.00 0.00 40.71 3.02
2420 2628 5.690865 TGTATTATTGGACCTGGAATGGAC 58.309 41.667 0.00 0.00 0.00 4.02
2496 2704 3.197790 CTCGGCTGGTTGGATGCG 61.198 66.667 0.00 0.00 0.00 4.73
2500 2708 1.377202 GGCTGGTTGGATGCGAAGA 60.377 57.895 0.00 0.00 0.00 2.87
2564 2772 1.256812 AATCTTTTCCTGGCAACCGG 58.743 50.000 0.00 0.00 0.00 5.28
2662 2870 7.603180 AGGTATGTTCAACTCTGCTATGATA 57.397 36.000 0.00 0.00 0.00 2.15
2680 2888 8.954350 GCTATGATATGATAAATTGCTTGGAGT 58.046 33.333 0.00 0.00 0.00 3.85
2982 3193 4.054085 CACCTGAGCAGTGGTGTG 57.946 61.111 0.00 0.00 46.18 3.82
3068 3282 2.272146 GTCCCATGCACCGGACAT 59.728 61.111 23.14 8.93 46.59 3.06
3241 3938 4.092383 GTCCATGAATCATTTGCTTGTTGC 59.908 41.667 0.00 0.00 43.25 4.17
3316 4015 0.818445 TCTACGCCGGAGAGTCATCC 60.818 60.000 13.83 0.00 35.88 3.51
3339 4038 7.644062 TCCATAATTCCATTTTGTACCTGGTA 58.356 34.615 1.49 1.49 0.00 3.25
3346 4045 5.044476 TCCATTTTGTACCTGGTACCATCAT 60.044 40.000 29.04 15.51 38.14 2.45
3359 4058 2.381911 ACCATCATGGGCTTCATTGTC 58.618 47.619 9.04 0.00 43.37 3.18
3488 4187 2.890474 GATTCGTCGTGCCGGCAT 60.890 61.111 35.23 15.50 0.00 4.40
3502 4201 5.277586 CGTGCCGGCATTATGTTCTTTATTA 60.278 40.000 35.23 0.00 0.00 0.98
3529 4229 9.069082 TCCTTTGATTATTTTCACCGTTAGAAA 57.931 29.630 0.00 0.00 33.48 2.52
3541 4241 9.672086 TTTCACCGTTAGAAAATAATGTTGAAG 57.328 29.630 0.00 0.00 30.41 3.02
3602 4302 8.149647 TCAAATTTTCCTGTTCATGCTAAATGT 58.850 29.630 0.00 0.00 0.00 2.71
3643 4344 9.726232 CATGTTATCATTGTATTGACCAGAAAG 57.274 33.333 0.00 0.00 31.15 2.62
3750 4488 6.942976 ACGGTTTCCTAAAGATAGACATGAA 58.057 36.000 0.00 0.00 0.00 2.57
3944 4865 3.750371 TGTGGGTATCAAAGGTCACTTG 58.250 45.455 0.00 0.00 36.93 3.16
3964 4885 6.487331 CACTTGGTAACTGGGTGTACATAAAA 59.513 38.462 0.00 0.00 37.61 1.52
3967 4888 6.603224 TGGTAACTGGGTGTACATAAAAGTT 58.397 36.000 15.78 15.78 37.61 2.66
3975 4896 7.737869 TGGGTGTACATAAAAGTTCTCTACAA 58.262 34.615 0.00 0.00 0.00 2.41
3988 4909 7.463961 AGTTCTCTACAAGTATCTCGGAAAA 57.536 36.000 0.00 0.00 0.00 2.29
4035 5255 3.265791 GAGTGAGATTTGTCGCTCCATT 58.734 45.455 6.95 0.00 44.89 3.16
4040 5260 3.411446 AGATTTGTCGCTCCATTTGACA 58.589 40.909 0.00 0.00 40.62 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.202533 AGCGAGACATATTCGGGTTGG 60.203 52.381 0.00 0.00 38.45 3.77
1 2 2.225068 AGCGAGACATATTCGGGTTG 57.775 50.000 0.00 0.00 38.45 3.77
5 6 5.154932 CCTAACTTAGCGAGACATATTCGG 58.845 45.833 0.00 0.00 38.45 4.30
6 7 4.617645 GCCTAACTTAGCGAGACATATTCG 59.382 45.833 0.00 0.00 40.85 3.34
7 8 5.774630 AGCCTAACTTAGCGAGACATATTC 58.225 41.667 0.00 0.00 0.00 1.75
8 9 5.302059 TGAGCCTAACTTAGCGAGACATATT 59.698 40.000 0.00 0.00 0.00 1.28
9 10 4.827835 TGAGCCTAACTTAGCGAGACATAT 59.172 41.667 0.00 0.00 0.00 1.78
10 11 4.204799 TGAGCCTAACTTAGCGAGACATA 58.795 43.478 0.00 0.00 0.00 2.29
11 12 3.024547 TGAGCCTAACTTAGCGAGACAT 58.975 45.455 0.00 0.00 0.00 3.06
12 13 2.443416 TGAGCCTAACTTAGCGAGACA 58.557 47.619 0.00 0.00 0.00 3.41
13 14 3.505464 TTGAGCCTAACTTAGCGAGAC 57.495 47.619 0.00 0.00 0.00 3.36
14 15 3.068307 GGATTGAGCCTAACTTAGCGAGA 59.932 47.826 0.00 0.00 0.00 4.04
15 16 3.385577 GGATTGAGCCTAACTTAGCGAG 58.614 50.000 0.00 0.00 0.00 5.03
16 17 2.102588 GGGATTGAGCCTAACTTAGCGA 59.897 50.000 0.00 0.00 0.00 4.93
17 18 2.158957 TGGGATTGAGCCTAACTTAGCG 60.159 50.000 0.00 0.00 0.00 4.26
18 19 3.560636 TGGGATTGAGCCTAACTTAGC 57.439 47.619 0.00 0.00 0.00 3.09
19 20 6.205658 GCTTAATGGGATTGAGCCTAACTTAG 59.794 42.308 2.47 0.00 43.65 2.18
20 21 6.062095 GCTTAATGGGATTGAGCCTAACTTA 58.938 40.000 2.47 0.00 43.65 2.24
21 22 4.889995 GCTTAATGGGATTGAGCCTAACTT 59.110 41.667 2.47 0.00 43.65 2.66
22 23 4.464947 GCTTAATGGGATTGAGCCTAACT 58.535 43.478 2.47 0.00 43.65 2.24
23 24 4.837896 GCTTAATGGGATTGAGCCTAAC 57.162 45.455 2.47 0.00 43.65 2.34
29 30 3.571401 GGACATGGCTTAATGGGATTGAG 59.429 47.826 0.00 0.00 31.46 3.02
30 31 3.565307 GGACATGGCTTAATGGGATTGA 58.435 45.455 0.00 0.00 31.46 2.57
31 32 2.629617 GGGACATGGCTTAATGGGATTG 59.370 50.000 0.00 0.00 31.46 2.67
32 33 2.247111 TGGGACATGGCTTAATGGGATT 59.753 45.455 0.00 0.00 31.46 3.01
33 34 1.858910 TGGGACATGGCTTAATGGGAT 59.141 47.619 0.00 0.00 31.46 3.85
34 35 1.303898 TGGGACATGGCTTAATGGGA 58.696 50.000 0.00 0.00 31.46 4.37
35 36 2.157640 TTGGGACATGGCTTAATGGG 57.842 50.000 0.00 0.00 39.30 4.00
36 37 5.600696 GTTATTTGGGACATGGCTTAATGG 58.399 41.667 0.00 0.00 39.30 3.16
37 38 5.280945 CGTTATTTGGGACATGGCTTAATG 58.719 41.667 0.00 0.00 39.30 1.90
38 39 4.202111 GCGTTATTTGGGACATGGCTTAAT 60.202 41.667 0.00 0.00 39.30 1.40
39 40 3.129638 GCGTTATTTGGGACATGGCTTAA 59.870 43.478 0.00 0.00 39.30 1.85
40 41 2.685897 GCGTTATTTGGGACATGGCTTA 59.314 45.455 0.00 0.00 39.30 3.09
41 42 1.476488 GCGTTATTTGGGACATGGCTT 59.524 47.619 0.00 0.00 39.30 4.35
42 43 1.102978 GCGTTATTTGGGACATGGCT 58.897 50.000 0.00 0.00 39.30 4.75
43 44 0.814457 TGCGTTATTTGGGACATGGC 59.186 50.000 0.00 0.00 39.30 4.40
44 45 3.799281 AATGCGTTATTTGGGACATGG 57.201 42.857 0.00 0.00 39.30 3.66
45 46 5.645624 TGTTAATGCGTTATTTGGGACATG 58.354 37.500 0.00 0.00 39.30 3.21
46 47 5.650266 TCTGTTAATGCGTTATTTGGGACAT 59.350 36.000 0.00 0.00 39.30 3.06
47 48 5.004448 TCTGTTAATGCGTTATTTGGGACA 58.996 37.500 0.00 0.00 0.00 4.02
48 49 5.554822 TCTGTTAATGCGTTATTTGGGAC 57.445 39.130 0.00 0.00 0.00 4.46
49 50 6.767524 ATTCTGTTAATGCGTTATTTGGGA 57.232 33.333 0.00 0.00 0.00 4.37
50 51 6.196353 CGAATTCTGTTAATGCGTTATTTGGG 59.804 38.462 3.52 0.00 0.00 4.12
51 52 6.196353 CCGAATTCTGTTAATGCGTTATTTGG 59.804 38.462 3.52 0.82 0.00 3.28
52 53 6.196353 CCCGAATTCTGTTAATGCGTTATTTG 59.804 38.462 3.52 0.00 0.00 2.32
53 54 6.262601 CCCGAATTCTGTTAATGCGTTATTT 58.737 36.000 3.52 0.00 0.00 1.40
54 55 5.220970 CCCCGAATTCTGTTAATGCGTTATT 60.221 40.000 3.52 0.00 0.00 1.40
55 56 4.274950 CCCCGAATTCTGTTAATGCGTTAT 59.725 41.667 3.52 0.00 0.00 1.89
56 57 3.623960 CCCCGAATTCTGTTAATGCGTTA 59.376 43.478 3.52 0.00 0.00 3.18
57 58 2.422127 CCCCGAATTCTGTTAATGCGTT 59.578 45.455 3.52 0.00 0.00 4.84
58 59 2.014128 CCCCGAATTCTGTTAATGCGT 58.986 47.619 3.52 0.00 0.00 5.24
59 60 1.333619 CCCCCGAATTCTGTTAATGCG 59.666 52.381 3.52 0.00 0.00 4.73
60 61 2.375146 ACCCCCGAATTCTGTTAATGC 58.625 47.619 3.52 0.00 0.00 3.56
61 62 4.461081 TCAAACCCCCGAATTCTGTTAATG 59.539 41.667 3.52 0.00 0.00 1.90
62 63 4.668636 TCAAACCCCCGAATTCTGTTAAT 58.331 39.130 3.52 0.00 0.00 1.40
63 64 4.101645 TCAAACCCCCGAATTCTGTTAA 57.898 40.909 3.52 0.00 0.00 2.01
64 65 3.791953 TCAAACCCCCGAATTCTGTTA 57.208 42.857 3.52 0.00 0.00 2.41
65 66 2.668144 TCAAACCCCCGAATTCTGTT 57.332 45.000 3.52 0.00 0.00 3.16
66 67 2.899303 ATCAAACCCCCGAATTCTGT 57.101 45.000 3.52 0.00 0.00 3.41
67 68 6.952773 TTAATATCAAACCCCCGAATTCTG 57.047 37.500 3.52 0.00 0.00 3.02
68 69 7.417456 GCTTTTAATATCAAACCCCCGAATTCT 60.417 37.037 3.52 0.00 0.00 2.40
69 70 6.700081 GCTTTTAATATCAAACCCCCGAATTC 59.300 38.462 0.00 0.00 0.00 2.17
70 71 6.155393 TGCTTTTAATATCAAACCCCCGAATT 59.845 34.615 0.00 0.00 0.00 2.17
71 72 5.659079 TGCTTTTAATATCAAACCCCCGAAT 59.341 36.000 0.00 0.00 0.00 3.34
72 73 5.017490 TGCTTTTAATATCAAACCCCCGAA 58.983 37.500 0.00 0.00 0.00 4.30
73 74 4.601084 TGCTTTTAATATCAAACCCCCGA 58.399 39.130 0.00 0.00 0.00 5.14
74 75 4.993029 TGCTTTTAATATCAAACCCCCG 57.007 40.909 0.00 0.00 0.00 5.73
75 76 5.106442 CGTTGCTTTTAATATCAAACCCCC 58.894 41.667 0.00 0.00 0.00 5.40
76 77 5.575218 CACGTTGCTTTTAATATCAAACCCC 59.425 40.000 0.00 0.00 0.00 4.95
77 78 5.575218 CCACGTTGCTTTTAATATCAAACCC 59.425 40.000 0.00 0.00 0.00 4.11
78 79 6.307077 GTCCACGTTGCTTTTAATATCAAACC 59.693 38.462 0.00 0.00 0.00 3.27
79 80 6.307077 GGTCCACGTTGCTTTTAATATCAAAC 59.693 38.462 0.00 0.00 0.00 2.93
80 81 6.383415 GGTCCACGTTGCTTTTAATATCAAA 58.617 36.000 0.00 0.00 0.00 2.69
81 82 5.391097 CGGTCCACGTTGCTTTTAATATCAA 60.391 40.000 0.00 0.00 37.93 2.57
82 83 4.093703 CGGTCCACGTTGCTTTTAATATCA 59.906 41.667 0.00 0.00 37.93 2.15
83 84 4.584394 CGGTCCACGTTGCTTTTAATATC 58.416 43.478 0.00 0.00 37.93 1.63
84 85 4.609691 CGGTCCACGTTGCTTTTAATAT 57.390 40.909 0.00 0.00 37.93 1.28
86 87 2.981400 CGGTCCACGTTGCTTTTAAT 57.019 45.000 0.00 0.00 37.93 1.40
98 99 2.353109 GGTACTTTGGTAGACGGTCCAC 60.353 54.545 4.14 0.68 33.12 4.02
99 100 1.895131 GGTACTTTGGTAGACGGTCCA 59.105 52.381 4.14 0.00 0.00 4.02
100 101 2.174360 AGGTACTTTGGTAGACGGTCC 58.826 52.381 4.14 0.00 27.25 4.46
138 139 4.610333 ACCACTCCTTTGTTCCTCTTTTT 58.390 39.130 0.00 0.00 0.00 1.94
139 140 4.251103 ACCACTCCTTTGTTCCTCTTTT 57.749 40.909 0.00 0.00 0.00 2.27
140 141 3.953542 ACCACTCCTTTGTTCCTCTTT 57.046 42.857 0.00 0.00 0.00 2.52
141 142 3.953542 AACCACTCCTTTGTTCCTCTT 57.046 42.857 0.00 0.00 0.00 2.85
142 143 3.953542 AAACCACTCCTTTGTTCCTCT 57.046 42.857 0.00 0.00 0.00 3.69
143 144 3.699538 ACAAAACCACTCCTTTGTTCCTC 59.300 43.478 0.00 0.00 41.77 3.71
160 161 5.415701 GGAGCATAATGGAGTTGAGACAAAA 59.584 40.000 0.00 0.00 0.00 2.44
177 178 7.134842 TGGATCCATAGATCTATTGGAGCATA 58.865 38.462 29.79 22.11 46.96 3.14
214 215 6.337185 TCTCCTTCATAACCAGGTCTACTA 57.663 41.667 0.00 0.00 0.00 1.82
215 216 5.208294 TCTCCTTCATAACCAGGTCTACT 57.792 43.478 0.00 0.00 0.00 2.57
240 241 5.335127 CATCCAAACATGTTTAGCTGTAGC 58.665 41.667 22.87 0.00 42.49 3.58
245 246 3.573538 TGTGCATCCAAACATGTTTAGCT 59.426 39.130 22.87 5.38 0.00 3.32
276 277 1.804748 CTTTGGGCTAACGTGGAAGAC 59.195 52.381 0.00 0.00 0.00 3.01
354 355 0.757561 GCCTAGGAGGGGTCAGAGAC 60.758 65.000 14.75 0.00 35.37 3.36
439 440 4.465512 GGCAGGTGCACGCAATCG 62.466 66.667 16.93 1.07 44.36 3.34
451 452 0.323633 TGAATCATGTGGTGGGCAGG 60.324 55.000 0.00 0.00 0.00 4.85
501 502 1.893544 CATTGCCCTGCTAGATGGAG 58.106 55.000 0.00 0.00 0.00 3.86
502 503 0.179009 GCATTGCCCTGCTAGATGGA 60.179 55.000 0.00 0.00 39.12 3.41
504 505 2.338381 GGCATTGCCCTGCTAGATG 58.662 57.895 17.28 0.00 44.06 2.90
505 506 4.916358 GGCATTGCCCTGCTAGAT 57.084 55.556 17.28 0.00 44.06 1.98
524 527 1.578897 TAACACTATGGCCAGCCTCA 58.421 50.000 13.05 0.00 36.94 3.86
544 547 7.605309 CCAAGTGCATGATATCAGCTAAGATAA 59.395 37.037 20.51 4.04 34.42 1.75
571 574 4.217550 ACCACATTAGCGTGTTTGCTATTT 59.782 37.500 0.00 0.00 46.19 1.40
587 590 9.793259 TGTCTCTTTTTAATTCTCTACCACATT 57.207 29.630 0.00 0.00 0.00 2.71
588 591 9.442047 CTGTCTCTTTTTAATTCTCTACCACAT 57.558 33.333 0.00 0.00 0.00 3.21
589 592 7.387948 GCTGTCTCTTTTTAATTCTCTACCACA 59.612 37.037 0.00 0.00 0.00 4.17
590 593 7.387948 TGCTGTCTCTTTTTAATTCTCTACCAC 59.612 37.037 0.00 0.00 0.00 4.16
591 594 7.450074 TGCTGTCTCTTTTTAATTCTCTACCA 58.550 34.615 0.00 0.00 0.00 3.25
592 595 7.907214 TGCTGTCTCTTTTTAATTCTCTACC 57.093 36.000 0.00 0.00 0.00 3.18
627 630 9.850628 TCAACAAAAATTTGCAATCAATGAAAA 57.149 22.222 0.00 0.00 40.89 2.29
638 641 8.948631 TGGTAAGTTATCAACAAAAATTTGCA 57.051 26.923 5.82 0.00 41.79 4.08
639 642 9.862585 CTTGGTAAGTTATCAACAAAAATTTGC 57.137 29.630 4.40 0.00 41.79 3.68
644 647 9.959749 GTCATCTTGGTAAGTTATCAACAAAAA 57.040 29.630 4.40 0.00 0.00 1.94
645 648 8.573035 GGTCATCTTGGTAAGTTATCAACAAAA 58.427 33.333 4.40 0.00 0.00 2.44
646 649 7.721842 TGGTCATCTTGGTAAGTTATCAACAAA 59.278 33.333 4.40 0.00 0.00 2.83
647 650 7.174253 GTGGTCATCTTGGTAAGTTATCAACAA 59.826 37.037 4.40 0.00 0.00 2.83
648 651 6.653320 GTGGTCATCTTGGTAAGTTATCAACA 59.347 38.462 4.40 0.00 0.00 3.33
649 652 6.879458 AGTGGTCATCTTGGTAAGTTATCAAC 59.121 38.462 4.40 0.00 0.00 3.18
650 653 7.016153 AGTGGTCATCTTGGTAAGTTATCAA 57.984 36.000 8.29 8.29 0.00 2.57
651 654 6.620877 AGTGGTCATCTTGGTAAGTTATCA 57.379 37.500 0.00 0.00 0.00 2.15
652 655 7.308782 CAAGTGGTCATCTTGGTAAGTTATC 57.691 40.000 0.00 0.00 38.70 1.75
670 673 6.423905 CGGTATCTATCAATGTTACCAAGTGG 59.576 42.308 0.00 0.00 42.17 4.00
671 674 6.984474 ACGGTATCTATCAATGTTACCAAGTG 59.016 38.462 0.00 0.00 33.43 3.16
672 675 7.120923 ACGGTATCTATCAATGTTACCAAGT 57.879 36.000 0.00 0.00 33.43 3.16
673 676 9.355215 GATACGGTATCTATCAATGTTACCAAG 57.645 37.037 18.61 0.00 33.43 3.61
674 677 8.862085 TGATACGGTATCTATCAATGTTACCAA 58.138 33.333 24.27 0.78 36.17 3.67
675 678 8.411991 TGATACGGTATCTATCAATGTTACCA 57.588 34.615 24.27 1.92 36.17 3.25
703 706 9.838975 CATGACACAAAGTAGCATAACATTTAA 57.161 29.630 0.00 0.00 0.00 1.52
704 707 7.967854 GCATGACACAAAGTAGCATAACATTTA 59.032 33.333 0.00 0.00 0.00 1.40
705 708 6.808212 GCATGACACAAAGTAGCATAACATTT 59.192 34.615 0.00 0.00 0.00 2.32
706 709 6.072008 TGCATGACACAAAGTAGCATAACATT 60.072 34.615 0.00 0.00 30.65 2.71
707 710 5.415389 TGCATGACACAAAGTAGCATAACAT 59.585 36.000 0.00 0.00 30.65 2.71
708 711 4.759183 TGCATGACACAAAGTAGCATAACA 59.241 37.500 0.00 0.00 30.65 2.41
709 712 5.295431 TGCATGACACAAAGTAGCATAAC 57.705 39.130 0.00 0.00 30.65 1.89
710 713 5.647225 TCATGCATGACACAAAGTAGCATAA 59.353 36.000 25.42 0.00 39.67 1.90
711 714 5.184711 TCATGCATGACACAAAGTAGCATA 58.815 37.500 25.42 0.00 39.67 3.14
712 715 4.011698 TCATGCATGACACAAAGTAGCAT 58.988 39.130 25.42 0.00 41.24 3.79
713 716 3.410508 TCATGCATGACACAAAGTAGCA 58.589 40.909 25.42 0.00 37.13 3.49
752 755 9.933723 TGCACAGTATCGTAGAGTAGTATTATA 57.066 33.333 0.00 0.00 43.63 0.98
753 756 8.719648 GTGCACAGTATCGTAGAGTAGTATTAT 58.280 37.037 13.17 0.00 43.63 1.28
754 757 7.930325 AGTGCACAGTATCGTAGAGTAGTATTA 59.070 37.037 21.04 0.00 43.63 0.98
755 758 6.766944 AGTGCACAGTATCGTAGAGTAGTATT 59.233 38.462 21.04 0.00 43.63 1.89
756 759 6.289834 AGTGCACAGTATCGTAGAGTAGTAT 58.710 40.000 21.04 0.00 43.63 2.12
757 760 5.668471 AGTGCACAGTATCGTAGAGTAGTA 58.332 41.667 21.04 0.00 43.63 1.82
758 761 4.515361 AGTGCACAGTATCGTAGAGTAGT 58.485 43.478 21.04 0.00 43.63 2.73
759 762 6.424207 TCATAGTGCACAGTATCGTAGAGTAG 59.576 42.308 21.04 0.00 43.63 2.57
760 763 6.285990 TCATAGTGCACAGTATCGTAGAGTA 58.714 40.000 21.04 0.00 43.63 2.59
761 764 5.123936 TCATAGTGCACAGTATCGTAGAGT 58.876 41.667 21.04 0.00 43.63 3.24
762 765 5.674933 TCATAGTGCACAGTATCGTAGAG 57.325 43.478 21.04 0.00 43.63 2.43
763 766 5.008712 CCTTCATAGTGCACAGTATCGTAGA 59.991 44.000 21.04 0.14 45.75 2.59
764 767 5.215903 CCTTCATAGTGCACAGTATCGTAG 58.784 45.833 21.04 5.53 0.00 3.51
765 768 4.643334 ACCTTCATAGTGCACAGTATCGTA 59.357 41.667 21.04 0.33 0.00 3.43
766 769 3.447586 ACCTTCATAGTGCACAGTATCGT 59.552 43.478 21.04 3.60 0.00 3.73
767 770 4.046938 ACCTTCATAGTGCACAGTATCG 57.953 45.455 21.04 2.93 0.00 2.92
768 771 6.150396 ACTACCTTCATAGTGCACAGTATC 57.850 41.667 21.04 0.00 34.02 2.24
769 772 6.040616 GGTACTACCTTCATAGTGCACAGTAT 59.959 42.308 21.04 6.18 38.96 2.12
770 773 5.359009 GGTACTACCTTCATAGTGCACAGTA 59.641 44.000 21.04 11.36 38.96 2.74
771 774 4.159879 GGTACTACCTTCATAGTGCACAGT 59.840 45.833 21.04 12.40 38.96 3.55
772 775 4.159693 TGGTACTACCTTCATAGTGCACAG 59.840 45.833 21.04 6.90 38.96 3.66
773 776 4.090819 TGGTACTACCTTCATAGTGCACA 58.909 43.478 21.04 5.47 38.96 4.57
774 777 4.730949 TGGTACTACCTTCATAGTGCAC 57.269 45.455 9.40 9.40 38.96 4.57
969 972 6.748333 TTTCTCTGCCATAATCAAAGACAG 57.252 37.500 0.00 0.00 0.00 3.51
1012 1015 4.101585 CCATGCCACCAGAAGTATCTCTAA 59.898 45.833 0.00 0.00 32.03 2.10
1024 1030 2.043652 CCCTTCCCATGCCACCAG 60.044 66.667 0.00 0.00 0.00 4.00
1036 1042 1.214992 ACTTGGATCCCCCACCCTTC 61.215 60.000 9.90 0.00 46.62 3.46
1132 1138 7.231925 TGCTGACCATATGATGAATTTAAGCAT 59.768 33.333 3.65 0.00 30.10 3.79
1458 1464 2.501723 GAGTGCCCATACTCTTTCCTCA 59.498 50.000 0.00 0.00 42.93 3.86
1553 1631 4.335647 CCTCCGGCACCAACTGCT 62.336 66.667 0.00 0.00 46.25 4.24
1585 1663 4.615901 CGGTGCCAACTGCTGATA 57.384 55.556 0.00 0.00 42.00 2.15
1625 1799 2.328099 CCGTCTGAAGCCAACTGCC 61.328 63.158 0.00 0.00 42.71 4.85
1678 1856 3.880490 ACGTCCAACAATGTGAAAGCTAA 59.120 39.130 0.00 0.00 0.00 3.09
1755 1933 2.543777 TCTCCCGTCCTTCAAAACTG 57.456 50.000 0.00 0.00 0.00 3.16
1930 2108 6.609237 CACATCTATTCTGTGGTAACCATG 57.391 41.667 0.00 0.00 40.23 3.66
1972 2150 2.033448 GATGACCGCACCACCCAA 59.967 61.111 0.00 0.00 0.00 4.12
2010 2188 2.436417 CATTTGGAGAACATGGTCCGT 58.564 47.619 7.26 0.00 35.37 4.69
2066 2244 1.597854 CGAACCACAGGAGCAAGCA 60.598 57.895 0.00 0.00 0.00 3.91
2255 2433 8.567948 GTTTCAACACCTTCTGAATGATAAGAA 58.432 33.333 0.00 0.00 31.85 2.52
2256 2434 7.939039 AGTTTCAACACCTTCTGAATGATAAGA 59.061 33.333 0.00 0.00 31.85 2.10
2294 2472 0.247460 GTCAAATTGGCTTGGCTCCC 59.753 55.000 0.00 0.00 0.00 4.30
2299 2477 2.299582 TGGTGATGTCAAATTGGCTTGG 59.700 45.455 0.00 0.00 0.00 3.61
2350 2558 5.147767 TCCATTAGAGCTCAAGGCACTATA 58.852 41.667 17.77 0.00 42.07 1.31
2362 2570 4.166725 TCCATGTTCCATTCCATTAGAGCT 59.833 41.667 0.00 0.00 0.00 4.09
2420 2628 0.987294 ATCCAGGTCCAACTCCACAG 59.013 55.000 0.00 0.00 0.00 3.66
2496 2704 3.498397 CACGCCATACCACCATTATCTTC 59.502 47.826 0.00 0.00 0.00 2.87
2500 2708 2.224523 CCTCACGCCATACCACCATTAT 60.225 50.000 0.00 0.00 0.00 1.28
2564 2772 4.355543 AACATGTAATTGGACATCGCAC 57.644 40.909 0.00 0.00 37.99 5.34
2662 2870 5.296780 CGGTGTACTCCAAGCAATTTATCAT 59.703 40.000 14.09 0.00 0.00 2.45
2680 2888 2.679639 GCAGATCACAATTCCCGGTGTA 60.680 50.000 0.00 0.00 36.43 2.90
2770 2981 7.981789 TCTGTCCAATATAAGATTGACACTGAC 59.018 37.037 0.00 0.00 0.00 3.51
2982 3193 3.217626 GGAAATGGTGGTCATGATCTCC 58.782 50.000 18.38 18.38 35.99 3.71
3068 3282 1.834378 CCTCTAGGAGCCGCATGGA 60.834 63.158 0.00 0.00 35.31 3.41
3094 3308 9.621629 ACATCAGTATAATTAAACATTTCCGGA 57.378 29.630 0.00 0.00 0.00 5.14
3241 3938 8.218441 CACAACAAGCAAATGATTGATACTTTG 58.782 33.333 17.36 12.53 43.50 2.77
3246 3943 6.343716 ACCACAACAAGCAAATGATTGATA 57.656 33.333 17.36 0.00 43.50 2.15
3316 4015 7.340743 TGGTACCAGGTACAAAATGGAATTATG 59.659 37.037 27.85 0.00 40.41 1.90
3339 4038 2.024655 AGACAATGAAGCCCATGATGGT 60.025 45.455 11.09 0.00 35.17 3.55
3346 4045 2.037901 TGCAAAAGACAATGAAGCCCA 58.962 42.857 0.00 0.00 0.00 5.36
3359 4058 7.769272 TTAACAACTTGAGGAAATGCAAAAG 57.231 32.000 0.00 0.00 0.00 2.27
3479 4178 2.939460 AAAGAACATAATGCCGGCAC 57.061 45.000 35.50 17.81 0.00 5.01
3502 4201 8.801882 TCTAACGGTGAAAATAATCAAAGGAT 57.198 30.769 0.00 0.00 34.43 3.24
3529 4229 8.105829 CCTCTAGGGCATATCTTCAACATTATT 58.894 37.037 0.00 0.00 0.00 1.40
3531 4231 7.009179 CCTCTAGGGCATATCTTCAACATTA 57.991 40.000 0.00 0.00 0.00 1.90
3579 4279 7.669427 TGACATTTAGCATGAACAGGAAAATT 58.331 30.769 0.00 0.00 0.00 1.82
3584 4284 5.711506 ACATTGACATTTAGCATGAACAGGA 59.288 36.000 0.00 0.00 0.00 3.86
3686 4424 5.163280 ACGAGTTAGTCTAGTAGAGGCTCAT 60.163 44.000 18.26 4.69 40.19 2.90
3868 4781 7.876068 ACAATCTCACGTCTAAGGAACAAATAA 59.124 33.333 0.00 0.00 0.00 1.40
3936 4857 1.142262 ACACCCAGTTACCAAGTGACC 59.858 52.381 3.78 0.00 33.58 4.02
3944 4865 6.938596 AGAACTTTTATGTACACCCAGTTACC 59.061 38.462 0.00 0.00 0.00 2.85
3964 4885 7.177041 ACTTTTCCGAGATACTTGTAGAGAACT 59.823 37.037 0.00 0.00 0.00 3.01
3967 4888 6.433404 ACACTTTTCCGAGATACTTGTAGAGA 59.567 38.462 0.00 0.00 0.00 3.10
3975 4896 5.238650 CCAACAAACACTTTTCCGAGATACT 59.761 40.000 0.00 0.00 0.00 2.12
3988 4909 2.375174 TCCATCTAGCCCAACAAACACT 59.625 45.455 0.00 0.00 0.00 3.55
4035 5255 3.541632 GCCCGGAGAATATCTTTGTCAA 58.458 45.455 0.73 0.00 0.00 3.18
4040 5260 1.143073 GTGGGCCCGGAGAATATCTTT 59.857 52.381 19.37 0.00 0.00 2.52
4041 5261 0.765510 GTGGGCCCGGAGAATATCTT 59.234 55.000 19.37 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.