Multiple sequence alignment - TraesCS2B01G615800

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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 TraesCS2B01G615800 chr2B 100.000 3332 0 0 1 3332 793507324 793503993 0.000000e+00 6154.0
1 TraesCS2B01G615800 chr2B 84.570 1024 133 19 1126 2141 793518189 793517183 0.000000e+00 992.0
2 TraesCS2B01G615800 chr2B 78.446 914 180 14 1207 2116 793456450 793457350 6.200000e-162 580.0
3 TraesCS2B01G615800 chr2B 78.726 879 169 14 1207 2079 793446972 793446106 3.730000e-159 571.0
4 TraesCS2B01G615800 chr2B 90.566 106 8 2 3227 3332 143132361 143132464 4.480000e-29 139.0
5 TraesCS2B01G615800 chr2B 87.037 108 6 2 2416 2522 793508734 793508834 7.550000e-22 115.0
6 TraesCS2B01G615800 chr2B 84.158 101 12 4 74 170 265432120 265432020 9.840000e-16 95.3
7 TraesCS2B01G615800 chr2B 84.158 101 12 4 74 170 521974986 521974886 9.840000e-16 95.3
8 TraesCS2B01G615800 chr2B 94.340 53 3 0 203 255 248152481 248152533 7.660000e-12 82.4
9 TraesCS2B01G615800 chr2B 100.000 32 0 0 2123 2154 793505151 793505120 3.590000e-05 60.2
10 TraesCS2B01G615800 chr2B 100.000 32 0 0 2174 2205 793505202 793505171 3.590000e-05 60.2
11 TraesCS2B01G615800 chr2A 89.884 1641 88 41 766 2390 768267357 768265779 0.000000e+00 2039.0
12 TraesCS2B01G615800 chr2A 83.462 1167 155 26 995 2150 768256845 768257984 0.000000e+00 1051.0
13 TraesCS2B01G615800 chr2A 78.993 914 175 14 1207 2116 768306703 768305803 2.840000e-170 608.0
14 TraesCS2B01G615800 chr2A 91.509 106 7 2 3227 3332 90068094 90068197 9.630000e-31 145.0
15 TraesCS2B01G615800 chr2A 90.566 106 8 2 3227 3332 90217739 90217842 4.480000e-29 139.0
16 TraesCS2B01G615800 chr2A 94.444 90 5 0 3243 3332 120724850 120724761 4.480000e-29 139.0
17 TraesCS2B01G615800 chr2A 94.444 90 5 0 3243 3332 120738584 120738495 4.480000e-29 139.0
18 TraesCS2B01G615800 chr2A 94.444 90 5 0 3243 3332 120754461 120754372 4.480000e-29 139.0
19 TraesCS2B01G615800 chr2A 73.700 327 66 18 1205 1522 769020445 769020760 3.510000e-20 110.0
20 TraesCS2B01G615800 chr2A 83.654 104 13 4 71 170 758586624 758586727 9.840000e-16 95.3
21 TraesCS2B01G615800 chr2A 94.915 59 3 0 10 68 695477021 695477079 3.540000e-15 93.5
22 TraesCS2B01G615800 chr2A 84.043 94 9 2 2518 2605 768265541 768265448 5.920000e-13 86.1
23 TraesCS2B01G615800 chr2D 91.133 1500 68 29 660 2153 643434747 643436187 0.000000e+00 1973.0
24 TraesCS2B01G615800 chr2D 83.216 1132 150 26 1026 2141 643330240 643331347 0.000000e+00 1002.0
25 TraesCS2B01G615800 chr2D 88.745 542 24 15 2174 2705 643436157 643436671 2.180000e-176 628.0
26 TraesCS2B01G615800 chr2D 78.804 920 166 22 1207 2116 643640466 643641366 2.860000e-165 592.0
27 TraesCS2B01G615800 chr2D 78.105 918 176 20 1207 2116 643468533 643467633 2.900000e-155 558.0
28 TraesCS2B01G615800 chr2D 82.400 625 48 24 71 678 643434152 643434731 3.860000e-134 488.0
29 TraesCS2B01G615800 chr2D 87.941 340 27 4 2711 3038 114665298 114664961 4.030000e-104 388.0
30 TraesCS2B01G615800 chr2D 92.265 181 9 5 3030 3207 114664903 114664725 5.520000e-63 252.0
31 TraesCS2B01G615800 chr2D 94.444 90 5 0 3243 3332 118846178 118846089 4.480000e-29 139.0
32 TraesCS2B01G615800 chr2D 72.467 523 111 27 1209 1720 644016477 644016977 1.610000e-28 137.0
33 TraesCS2B01G615800 chr2D 84.694 98 11 4 77 170 61976423 61976326 9.840000e-16 95.3
34 TraesCS2B01G615800 chr2D 82.857 105 14 4 70 170 428554995 428554891 1.270000e-14 91.6
35 TraesCS2B01G615800 chr2D 76.224 143 30 4 1206 1346 643901181 643901321 4.610000e-09 73.1
36 TraesCS2B01G615800 chr2D 87.755 49 4 2 1464 1511 60108291 60108244 4.640000e-04 56.5
37 TraesCS2B01G615800 chr3D 88.715 1276 96 21 911 2179 532205977 532204743 0.000000e+00 1515.0
38 TraesCS2B01G615800 chr3D 90.462 325 27 3 2714 3037 23255395 23255074 3.070000e-115 425.0
39 TraesCS2B01G615800 chr3D 96.070 229 8 1 3097 3324 23255077 23254849 4.060000e-99 372.0
40 TraesCS2B01G615800 chr3D 94.521 73 3 1 3052 3124 434960315 434960386 9.770000e-21 111.0
41 TraesCS2B01G615800 chr3D 74.661 221 43 10 1303 1512 600632497 600632715 5.920000e-13 86.1
42 TraesCS2B01G615800 chr3A 89.280 1194 95 17 995 2179 667495354 667494185 0.000000e+00 1465.0
43 TraesCS2B01G615800 chr3A 92.754 69 5 0 10 78 16144097 16144029 2.120000e-17 100.0
44 TraesCS2B01G615800 chr3A 92.424 66 5 0 10 75 79382824 79382759 9.840000e-16 95.3
45 TraesCS2B01G615800 chr3A 84.158 101 12 4 74 170 238686321 238686221 9.840000e-16 95.3
46 TraesCS2B01G615800 chr3A 71.947 303 66 14 1303 1591 730656600 730656303 1.660000e-08 71.3
47 TraesCS2B01G615800 chr3B 87.628 1172 111 13 1002 2167 704479317 704478174 0.000000e+00 1330.0
48 TraesCS2B01G615800 chr3B 91.652 563 38 4 1619 2180 704406969 704406415 0.000000e+00 771.0
49 TraesCS2B01G615800 chr3B 88.211 475 34 11 911 1378 704409012 704408553 6.280000e-152 547.0
50 TraesCS2B01G615800 chr3B 88.959 317 26 6 2708 3018 744558858 744559171 1.880000e-102 383.0
51 TraesCS2B01G615800 chr3B 92.308 169 11 2 3047 3214 746988426 746988259 4.300000e-59 239.0
52 TraesCS2B01G615800 chr3B 90.659 182 12 5 3030 3208 744559228 744559407 1.550000e-58 237.0
53 TraesCS2B01G615800 chr3B 83.886 211 32 2 2724 2934 613754747 613754539 2.030000e-47 200.0
54 TraesCS2B01G615800 chr3B 93.151 73 4 1 3052 3124 571022908 571022979 4.550000e-19 106.0
55 TraesCS2B01G615800 chr3B 93.939 66 4 0 10 75 209723725 209723790 2.120000e-17 100.0
56 TraesCS2B01G615800 chr3B 83.654 104 13 4 71 170 269252036 269252139 9.840000e-16 95.3
57 TraesCS2B01G615800 chr3B 73.630 292 58 14 1303 1580 807976135 807976421 9.840000e-16 95.3
58 TraesCS2B01G615800 chr7B 90.690 623 49 6 2711 3332 506595488 506596102 0.000000e+00 821.0
59 TraesCS2B01G615800 chr7B 84.615 104 12 4 71 170 483864921 483865024 2.120000e-17 100.0
60 TraesCS2B01G615800 chr4B 89.406 623 50 4 2711 3332 88931661 88932268 0.000000e+00 771.0
61 TraesCS2B01G615800 chr1D 90.385 364 17 3 2849 3211 475243119 475243465 2.340000e-126 462.0
62 TraesCS2B01G615800 chr4D 87.444 223 24 4 2710 2931 273913603 273913822 1.530000e-63 254.0
63 TraesCS2B01G615800 chr6A 86.222 225 27 4 2711 2934 143010292 143010071 1.190000e-59 241.0
64 TraesCS2B01G615800 chr6A 88.095 168 19 1 3048 3214 143008802 143008635 7.290000e-47 198.0
65 TraesCS2B01G615800 chr7A 85.333 225 29 4 2711 2934 563213176 563212955 2.590000e-56 230.0
66 TraesCS2B01G615800 chrUn 93.333 90 4 2 3126 3214 1831693 1831781 7.500000e-27 132.0
67 TraesCS2B01G615800 chr6B 96.667 60 2 0 10 69 574032306 574032365 2.120000e-17 100.0
68 TraesCS2B01G615800 chr6D 89.474 76 6 2 4 78 266382191 266382265 9.840000e-16 95.3
69 TraesCS2B01G615800 chr6D 82.407 108 14 5 74 177 141974442 141974336 4.580000e-14 89.8
70 TraesCS2B01G615800 chr5B 93.750 64 3 1 10 73 454295435 454295373 9.840000e-16 95.3
71 TraesCS2B01G615800 chr1B 92.424 66 5 0 4 69 231057989 231058054 9.840000e-16 95.3
72 TraesCS2B01G615800 chr1B 88.312 77 7 2 4 79 535878716 535878641 1.270000e-14 91.6


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 TraesCS2B01G615800 chr2B 793503993 793507324 3331 True 2091.466667 6154 100.0000 1 3332 3 chr2B.!!$R5 3331
1 TraesCS2B01G615800 chr2B 793517183 793518189 1006 True 992.000000 992 84.5700 1126 2141 1 chr2B.!!$R4 1015
2 TraesCS2B01G615800 chr2B 793456450 793457350 900 False 580.000000 580 78.4460 1207 2116 1 chr2B.!!$F3 909
3 TraesCS2B01G615800 chr2B 793446106 793446972 866 True 571.000000 571 78.7260 1207 2079 1 chr2B.!!$R3 872
4 TraesCS2B01G615800 chr2A 768265448 768267357 1909 True 1062.550000 2039 86.9635 766 2605 2 chr2A.!!$R5 1839
5 TraesCS2B01G615800 chr2A 768256845 768257984 1139 False 1051.000000 1051 83.4620 995 2150 1 chr2A.!!$F5 1155
6 TraesCS2B01G615800 chr2A 768305803 768306703 900 True 608.000000 608 78.9930 1207 2116 1 chr2A.!!$R4 909
7 TraesCS2B01G615800 chr2D 643434152 643436671 2519 False 1029.666667 1973 87.4260 71 2705 3 chr2D.!!$F5 2634
8 TraesCS2B01G615800 chr2D 643330240 643331347 1107 False 1002.000000 1002 83.2160 1026 2141 1 chr2D.!!$F1 1115
9 TraesCS2B01G615800 chr2D 643640466 643641366 900 False 592.000000 592 78.8040 1207 2116 1 chr2D.!!$F2 909
10 TraesCS2B01G615800 chr2D 643467633 643468533 900 True 558.000000 558 78.1050 1207 2116 1 chr2D.!!$R5 909
11 TraesCS2B01G615800 chr2D 114664725 114665298 573 True 320.000000 388 90.1030 2711 3207 2 chr2D.!!$R6 496
12 TraesCS2B01G615800 chr3D 532204743 532205977 1234 True 1515.000000 1515 88.7150 911 2179 1 chr3D.!!$R1 1268
13 TraesCS2B01G615800 chr3D 23254849 23255395 546 True 398.500000 425 93.2660 2714 3324 2 chr3D.!!$R2 610
14 TraesCS2B01G615800 chr3A 667494185 667495354 1169 True 1465.000000 1465 89.2800 995 2179 1 chr3A.!!$R4 1184
15 TraesCS2B01G615800 chr3B 704478174 704479317 1143 True 1330.000000 1330 87.6280 1002 2167 1 chr3B.!!$R2 1165
16 TraesCS2B01G615800 chr3B 704406415 704409012 2597 True 659.000000 771 89.9315 911 2180 2 chr3B.!!$R4 1269
17 TraesCS2B01G615800 chr3B 744558858 744559407 549 False 310.000000 383 89.8090 2708 3208 2 chr3B.!!$F5 500
18 TraesCS2B01G615800 chr7B 506595488 506596102 614 False 821.000000 821 90.6900 2711 3332 1 chr7B.!!$F2 621
19 TraesCS2B01G615800 chr4B 88931661 88932268 607 False 771.000000 771 89.4060 2711 3332 1 chr4B.!!$F1 621
20 TraesCS2B01G615800 chr6A 143008635 143010292 1657 True 219.500000 241 87.1585 2711 3214 2 chr6A.!!$R1 503

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
514 527 0.032515 TAGCCAGTAGCCAGTAGCCA 60.033 55.0 0.0 0.0 45.47 4.75 F
944 1001 0.175760 TGCGTGATCTAAGCCAGGAC 59.824 55.0 0.0 0.0 32.37 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2189 3736 0.100682 CGACGACCGAACCATCAGAT 59.899 55.0 0.0 0.0 41.76 2.90 R
2642 4329 0.035439 CCACCCAGTGACCCACATAC 60.035 60.0 0.0 0.0 36.74 2.39 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
29 30 8.697292 AGACTCATTTTAGTTCTAGATACACCC 58.303 37.037 0.00 0.00 0.00 4.61
30 31 8.375493 ACTCATTTTAGTTCTAGATACACCCA 57.625 34.615 0.00 0.00 0.00 4.51
31 32 8.993424 ACTCATTTTAGTTCTAGATACACCCAT 58.007 33.333 0.00 0.00 0.00 4.00
32 33 9.838339 CTCATTTTAGTTCTAGATACACCCATT 57.162 33.333 0.00 0.00 0.00 3.16
46 47 9.699410 AGATACACCCATTTTTATTCATTCTGA 57.301 29.630 0.00 0.00 0.00 3.27
49 50 8.365060 ACACCCATTTTTATTCATTCTGATGA 57.635 30.769 0.00 0.00 40.46 2.92
50 51 8.253113 ACACCCATTTTTATTCATTCTGATGAC 58.747 33.333 0.00 0.00 41.84 3.06
51 52 8.252417 CACCCATTTTTATTCATTCTGATGACA 58.748 33.333 0.00 0.00 41.84 3.58
52 53 8.814931 ACCCATTTTTATTCATTCTGATGACAA 58.185 29.630 0.00 0.00 41.84 3.18
53 54 9.309516 CCCATTTTTATTCATTCTGATGACAAG 57.690 33.333 0.00 0.00 41.84 3.16
54 55 9.865321 CCATTTTTATTCATTCTGATGACAAGT 57.135 29.630 0.00 0.00 41.84 3.16
62 63 7.307493 TCATTCTGATGACAAGTATTTTCGG 57.693 36.000 0.00 0.00 37.37 4.30
63 64 7.102993 TCATTCTGATGACAAGTATTTTCGGA 58.897 34.615 0.00 0.00 37.37 4.55
64 65 6.721571 TTCTGATGACAAGTATTTTCGGAC 57.278 37.500 0.00 0.00 0.00 4.79
65 66 4.862574 TCTGATGACAAGTATTTTCGGACG 59.137 41.667 0.00 0.00 0.00 4.79
66 67 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
67 68 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
68 69 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
69 70 3.256383 TGACAAGTATTTTCGGACGGAGA 59.744 43.478 0.00 0.00 0.00 3.71
70 71 3.846360 ACAAGTATTTTCGGACGGAGAG 58.154 45.455 0.00 0.00 0.00 3.20
71 72 3.508793 ACAAGTATTTTCGGACGGAGAGA 59.491 43.478 0.00 0.00 0.00 3.10
72 73 4.021719 ACAAGTATTTTCGGACGGAGAGAA 60.022 41.667 0.00 0.00 0.00 2.87
73 74 5.109903 CAAGTATTTTCGGACGGAGAGAAT 58.890 41.667 0.00 0.00 0.00 2.40
74 75 6.127535 ACAAGTATTTTCGGACGGAGAGAATA 60.128 38.462 0.00 0.00 0.00 1.75
75 76 5.829829 AGTATTTTCGGACGGAGAGAATAC 58.170 41.667 15.76 15.76 41.79 1.89
76 77 4.730949 ATTTTCGGACGGAGAGAATACA 57.269 40.909 0.00 0.00 0.00 2.29
77 78 4.730949 TTTTCGGACGGAGAGAATACAT 57.269 40.909 0.00 0.00 0.00 2.29
78 79 5.840243 TTTTCGGACGGAGAGAATACATA 57.160 39.130 0.00 0.00 0.00 2.29
79 80 4.825546 TTCGGACGGAGAGAATACATAC 57.174 45.455 0.00 0.00 0.00 2.39
80 81 2.804527 TCGGACGGAGAGAATACATACG 59.195 50.000 0.00 0.00 0.00 3.06
81 82 2.804527 CGGACGGAGAGAATACATACGA 59.195 50.000 0.00 0.00 0.00 3.43
85 86 3.227147 CGGAGAGAATACATACGAAGCG 58.773 50.000 0.00 0.00 0.00 4.68
90 91 4.733887 AGAGAATACATACGAAGCGAAACG 59.266 41.667 0.00 0.00 0.00 3.60
91 92 4.665212 AGAATACATACGAAGCGAAACGA 58.335 39.130 0.00 0.00 0.00 3.85
94 95 3.476295 ACATACGAAGCGAAACGAGTA 57.524 42.857 0.00 0.00 0.00 2.59
213 217 6.946229 ACGGCTAGATACAATATAAAAGCG 57.054 37.500 0.00 0.00 0.00 4.68
300 309 1.299926 GCCTACGCCCATACTCGTG 60.300 63.158 0.00 0.00 39.46 4.35
301 310 2.012902 GCCTACGCCCATACTCGTGT 62.013 60.000 0.00 0.00 39.46 4.49
307 316 1.269778 CGCCCATACTCGTGTCATGAT 60.270 52.381 0.00 0.00 0.00 2.45
309 318 2.868044 GCCCATACTCGTGTCATGATCC 60.868 54.545 0.00 0.00 0.00 3.36
310 319 2.630098 CCCATACTCGTGTCATGATCCT 59.370 50.000 0.00 0.00 0.00 3.24
315 324 0.897621 TCGTGTCATGATCCTGCACT 59.102 50.000 16.85 0.00 0.00 4.40
316 325 1.004595 CGTGTCATGATCCTGCACTG 58.995 55.000 16.85 10.53 0.00 3.66
372 384 7.255035 GCAATACTAGTACTATTCGACCTGTCA 60.255 40.741 4.31 0.00 0.00 3.58
407 420 6.072948 ACGTGTCCAAATCATTGACGAAATTA 60.073 34.615 0.00 0.00 36.78 1.40
418 431 8.426881 TCATTGACGAAATTAACGGATTGATA 57.573 30.769 9.19 0.00 34.93 2.15
423 436 5.756833 ACGAAATTAACGGATTGATAGGGAC 59.243 40.000 9.19 0.00 34.93 4.46
428 441 1.768275 ACGGATTGATAGGGACATGCA 59.232 47.619 0.00 0.00 0.00 3.96
437 450 5.754782 TGATAGGGACATGCACTGTTTAAT 58.245 37.500 0.00 0.00 38.54 1.40
439 452 3.091545 AGGGACATGCACTGTTTAATGG 58.908 45.455 0.00 0.00 38.54 3.16
440 453 2.417243 GGGACATGCACTGTTTAATGGC 60.417 50.000 0.00 0.00 38.54 4.40
441 454 2.493278 GGACATGCACTGTTTAATGGCT 59.507 45.455 0.00 0.00 38.54 4.75
442 455 3.056607 GGACATGCACTGTTTAATGGCTT 60.057 43.478 0.00 0.00 38.54 4.35
462 475 4.919754 GCTTGATTGATGTGTCCAAGTTTC 59.080 41.667 0.00 0.00 37.23 2.78
474 487 5.805486 GTGTCCAAGTTTCCAAAGACTTTTC 59.195 40.000 0.00 0.00 34.04 2.29
475 488 5.714806 TGTCCAAGTTTCCAAAGACTTTTCT 59.285 36.000 0.00 0.00 34.04 2.52
477 490 7.394923 TGTCCAAGTTTCCAAAGACTTTTCTTA 59.605 33.333 0.00 0.00 41.56 2.10
478 491 7.915923 GTCCAAGTTTCCAAAGACTTTTCTTAG 59.084 37.037 0.00 0.00 41.56 2.18
479 492 7.068226 TCCAAGTTTCCAAAGACTTTTCTTAGG 59.932 37.037 0.00 0.00 41.56 2.69
482 495 5.656549 TTCCAAAGACTTTTCTTAGGGGA 57.343 39.130 0.00 0.00 41.56 4.81
484 497 5.631119 TCCAAAGACTTTTCTTAGGGGAAG 58.369 41.667 0.00 0.00 41.56 3.46
485 498 4.218635 CCAAAGACTTTTCTTAGGGGAAGC 59.781 45.833 0.00 0.00 41.56 3.86
486 499 4.724279 AAGACTTTTCTTAGGGGAAGCA 57.276 40.909 0.00 0.00 40.54 3.91
487 500 4.293662 AGACTTTTCTTAGGGGAAGCAG 57.706 45.455 0.00 0.00 34.87 4.24
488 501 3.653352 AGACTTTTCTTAGGGGAAGCAGT 59.347 43.478 0.00 0.00 34.87 4.40
489 502 4.844655 AGACTTTTCTTAGGGGAAGCAGTA 59.155 41.667 0.00 0.00 34.87 2.74
490 503 5.046231 AGACTTTTCTTAGGGGAAGCAGTAG 60.046 44.000 0.00 0.00 34.87 2.57
491 504 3.629142 TTTCTTAGGGGAAGCAGTAGC 57.371 47.619 0.00 0.00 42.56 3.58
492 505 1.497161 TCTTAGGGGAAGCAGTAGCC 58.503 55.000 0.00 0.00 43.56 3.93
493 506 1.204146 CTTAGGGGAAGCAGTAGCCA 58.796 55.000 0.00 0.00 43.56 4.75
494 507 1.559682 CTTAGGGGAAGCAGTAGCCAA 59.440 52.381 0.00 0.00 43.56 4.52
495 508 1.893315 TAGGGGAAGCAGTAGCCAAT 58.107 50.000 0.00 0.00 43.56 3.16
496 509 1.893315 AGGGGAAGCAGTAGCCAATA 58.107 50.000 0.00 0.00 43.56 1.90
497 510 1.771255 AGGGGAAGCAGTAGCCAATAG 59.229 52.381 0.00 0.00 43.56 1.73
498 511 1.598882 GGGAAGCAGTAGCCAATAGC 58.401 55.000 0.00 0.00 43.56 2.97
499 512 1.598882 GGAAGCAGTAGCCAATAGCC 58.401 55.000 0.00 0.00 45.47 3.93
500 513 1.134098 GGAAGCAGTAGCCAATAGCCA 60.134 52.381 0.00 0.00 45.47 4.75
501 514 2.216898 GAAGCAGTAGCCAATAGCCAG 58.783 52.381 0.00 0.00 45.47 4.85
502 515 1.207791 AGCAGTAGCCAATAGCCAGT 58.792 50.000 0.00 0.00 45.47 4.00
503 516 2.398588 AGCAGTAGCCAATAGCCAGTA 58.601 47.619 0.00 0.00 45.47 2.74
504 517 2.366916 AGCAGTAGCCAATAGCCAGTAG 59.633 50.000 0.00 0.00 45.47 2.57
505 518 2.760374 CAGTAGCCAATAGCCAGTAGC 58.240 52.381 0.00 0.00 45.47 3.58
514 527 0.032515 TAGCCAGTAGCCAGTAGCCA 60.033 55.000 0.00 0.00 45.47 4.75
573 586 6.015095 GGAAATCAGATGTTTTCCTTTCCACT 60.015 38.462 20.71 0.00 44.53 4.00
584 597 5.359194 TTCCTTTCCACTGGCTATCTTAG 57.641 43.478 0.00 0.00 0.00 2.18
585 598 4.362677 TCCTTTCCACTGGCTATCTTAGT 58.637 43.478 0.00 0.00 0.00 2.24
586 599 4.406003 TCCTTTCCACTGGCTATCTTAGTC 59.594 45.833 0.00 0.00 0.00 2.59
587 600 4.407296 CCTTTCCACTGGCTATCTTAGTCT 59.593 45.833 0.00 0.00 0.00 3.24
588 601 5.104735 CCTTTCCACTGGCTATCTTAGTCTT 60.105 44.000 0.00 0.00 0.00 3.01
589 602 6.098409 CCTTTCCACTGGCTATCTTAGTCTTA 59.902 42.308 0.00 0.00 0.00 2.10
630 643 4.520492 ACGAAATCACTTGATCAGGCTTTT 59.480 37.500 4.46 2.68 32.75 2.27
703 750 8.633561 TGTGACACCATGACAAATTGTTATTAA 58.366 29.630 0.00 0.00 0.00 1.40
832 888 1.445095 CTGCTAGCCGCCTTCATCT 59.555 57.895 13.29 0.00 38.05 2.90
839 895 3.350219 AGCCGCCTTCATCTCTTTTTA 57.650 42.857 0.00 0.00 0.00 1.52
840 896 3.686016 AGCCGCCTTCATCTCTTTTTAA 58.314 40.909 0.00 0.00 0.00 1.52
890 946 9.524106 TTCTATATTATTACACCAAGACACGTG 57.476 33.333 15.48 15.48 36.04 4.49
891 947 8.139350 TCTATATTATTACACCAAGACACGTGG 58.861 37.037 21.57 3.65 42.28 4.94
896 952 4.868026 CCAAGACACGTGGTTGGA 57.132 55.556 32.88 0.00 43.01 3.53
897 953 3.088259 CCAAGACACGTGGTTGGAA 57.912 52.632 32.88 0.00 43.01 3.53
898 954 0.661020 CCAAGACACGTGGTTGGAAC 59.339 55.000 32.88 12.46 43.01 3.62
940 997 0.323302 TTGGTGCGTGATCTAAGCCA 59.677 50.000 0.00 0.00 32.37 4.75
944 1001 0.175760 TGCGTGATCTAAGCCAGGAC 59.824 55.000 0.00 0.00 32.37 3.85
947 1004 1.751351 CGTGATCTAAGCCAGGACTGA 59.249 52.381 0.00 0.00 0.00 3.41
993 1058 1.067821 TCACCCGGTTTTGTTGATTGC 59.932 47.619 0.00 0.00 0.00 3.56
1046 1112 1.676967 GAGGAAGCCACAAGCCCAG 60.677 63.158 0.00 0.00 45.47 4.45
1047 1113 2.116125 GGAAGCCACAAGCCCAGT 59.884 61.111 0.00 0.00 45.47 4.00
1048 1114 1.973812 GGAAGCCACAAGCCCAGTC 60.974 63.158 0.00 0.00 45.47 3.51
1049 1115 1.228245 GAAGCCACAAGCCCAGTCA 60.228 57.895 0.00 0.00 45.47 3.41
1083 1154 2.817396 GCTCAAGCTCCGCAGTCC 60.817 66.667 0.00 0.00 38.21 3.85
1084 1155 2.507992 CTCAAGCTCCGCAGTCCG 60.508 66.667 0.00 0.00 0.00 4.79
1085 1156 4.742201 TCAAGCTCCGCAGTCCGC 62.742 66.667 0.00 0.00 35.03 5.54
1108 1186 0.958822 AAAGAAACCATGGCGACCAC 59.041 50.000 13.04 0.00 35.80 4.16
1124 1202 1.078848 CACCAGCCCAGCAGTAGTC 60.079 63.158 0.00 0.00 0.00 2.59
1197 1275 4.052229 CCGTCTTCACCGGCGACT 62.052 66.667 9.30 0.00 38.85 4.18
2171 3718 2.597305 GGTCAAGTACGTGCGTAAGATG 59.403 50.000 6.00 6.26 43.02 2.90
2172 3719 2.597305 GTCAAGTACGTGCGTAAGATGG 59.403 50.000 6.00 0.00 43.02 3.51
2173 3720 2.229543 TCAAGTACGTGCGTAAGATGGT 59.770 45.455 6.00 0.00 43.02 3.55
2174 3721 2.556534 AGTACGTGCGTAAGATGGTC 57.443 50.000 6.00 0.00 43.02 4.02
2175 3722 1.186030 GTACGTGCGTAAGATGGTCG 58.814 55.000 6.00 0.00 43.02 4.79
2179 3726 3.627218 GCGTAAGATGGTCGCCGC 61.627 66.667 0.00 0.00 43.41 6.53
2180 3727 2.960129 CGTAAGATGGTCGCCGCC 60.960 66.667 0.00 0.00 43.02 6.13
2181 3728 2.499685 GTAAGATGGTCGCCGCCT 59.500 61.111 0.00 0.00 0.00 5.52
2182 3729 1.591863 GTAAGATGGTCGCCGCCTC 60.592 63.158 0.00 0.00 0.00 4.70
2183 3730 2.792947 TAAGATGGTCGCCGCCTCC 61.793 63.158 0.00 0.00 0.00 4.30
2192 3739 4.537433 GCCGCCTCCGCTTGATCT 62.537 66.667 0.00 0.00 0.00 2.75
2193 3740 2.587194 CCGCCTCCGCTTGATCTG 60.587 66.667 0.00 0.00 0.00 2.90
2194 3741 2.496341 CGCCTCCGCTTGATCTGA 59.504 61.111 0.00 0.00 0.00 3.27
2195 3742 1.068753 CGCCTCCGCTTGATCTGAT 59.931 57.895 0.00 0.00 0.00 2.90
2196 3743 1.220169 CGCCTCCGCTTGATCTGATG 61.220 60.000 0.00 0.00 0.00 3.07
2197 3744 0.883814 GCCTCCGCTTGATCTGATGG 60.884 60.000 0.00 0.00 0.00 3.51
2198 3745 0.467384 CCTCCGCTTGATCTGATGGT 59.533 55.000 0.00 0.00 0.00 3.55
2199 3746 1.134280 CCTCCGCTTGATCTGATGGTT 60.134 52.381 0.00 0.00 0.00 3.67
2200 3747 2.208431 CTCCGCTTGATCTGATGGTTC 58.792 52.381 0.00 0.00 0.00 3.62
2214 3761 2.355481 GTTCGGTCGTCGGCAAGT 60.355 61.111 0.00 0.00 39.77 3.16
2222 3769 1.065928 CGTCGGCAAGTAGGCTAGG 59.934 63.158 0.00 0.00 41.46 3.02
2243 3794 1.959226 CCCGTGCGTTGTGTTAGCT 60.959 57.895 0.00 0.00 0.00 3.32
2341 3900 7.592938 CAATGTTGGTGTAGCAATAAAGAGAA 58.407 34.615 0.00 0.00 0.00 2.87
2344 3903 6.770785 TGTTGGTGTAGCAATAAAGAGAAAGT 59.229 34.615 0.00 0.00 0.00 2.66
2362 3921 0.515564 GTGGTTTGGATCGTCGTTGG 59.484 55.000 0.00 0.00 0.00 3.77
2379 3943 3.433615 CGTTGGATCTTGAGTTCTTGACC 59.566 47.826 0.00 0.00 0.00 4.02
2409 4051 6.931838 TGTCAATTAGTCTCGACACCTATTT 58.068 36.000 0.00 0.00 33.61 1.40
2410 4052 8.058667 TGTCAATTAGTCTCGACACCTATTTA 57.941 34.615 0.00 0.00 33.61 1.40
2411 4053 8.692710 TGTCAATTAGTCTCGACACCTATTTAT 58.307 33.333 0.00 0.00 33.61 1.40
2412 4054 8.969267 GTCAATTAGTCTCGACACCTATTTATG 58.031 37.037 0.00 0.00 0.00 1.90
2413 4055 8.692710 TCAATTAGTCTCGACACCTATTTATGT 58.307 33.333 0.00 0.00 0.00 2.29
2414 4056 9.961265 CAATTAGTCTCGACACCTATTTATGTA 57.039 33.333 0.00 0.00 0.00 2.29
2436 4078 7.025365 TGTAGTACGTATTGATGGCGATAATC 58.975 38.462 0.00 0.00 0.00 1.75
2549 4236 3.391506 ACTGGTACTGGAAAACCGTAC 57.608 47.619 0.00 0.00 38.70 3.67
2584 4271 1.135315 CGATGCAAGTTGGCGGAAG 59.865 57.895 4.75 0.00 36.28 3.46
2598 4285 4.570874 GAAGCCGGGGGAGATGCC 62.571 72.222 2.18 0.00 0.00 4.40
2606 4293 3.415087 GGGAGATGCCTGCCTGGT 61.415 66.667 0.00 0.00 46.25 4.00
2607 4294 2.124403 GGAGATGCCTGCCTGGTG 60.124 66.667 0.00 0.00 38.35 4.17
2608 4295 2.827642 GAGATGCCTGCCTGGTGC 60.828 66.667 0.00 0.00 41.77 5.01
2609 4296 4.790962 AGATGCCTGCCTGGTGCG 62.791 66.667 0.00 0.00 45.60 5.34
2631 4318 0.390603 TCCGGCATAAACACCGTGAG 60.391 55.000 5.28 0.00 0.00 3.51
2642 4329 2.079158 ACACCGTGAGCAATCAATCAG 58.921 47.619 5.28 0.00 0.00 2.90
2645 4332 3.873361 CACCGTGAGCAATCAATCAGTAT 59.127 43.478 0.00 0.00 0.00 2.12
2646 4333 3.873361 ACCGTGAGCAATCAATCAGTATG 59.127 43.478 0.00 0.00 37.54 2.39
2683 4370 1.671742 GTGCAAGGAGGAGAACCGA 59.328 57.895 0.00 0.00 41.83 4.69
2705 4392 3.120105 CAGCCCAGCTCGATCGTA 58.880 61.111 15.94 0.90 36.40 3.43
2706 4393 1.662608 CAGCCCAGCTCGATCGTAT 59.337 57.895 15.94 0.00 36.40 3.06
2707 4394 0.665670 CAGCCCAGCTCGATCGTATG 60.666 60.000 15.94 11.83 36.40 2.39
2708 4395 2.024319 GCCCAGCTCGATCGTATGC 61.024 63.158 15.94 16.96 0.00 3.14
2709 4396 1.363807 CCCAGCTCGATCGTATGCA 59.636 57.895 23.53 0.00 0.00 3.96
2774 4463 2.350772 GCAACATCGTTTTGGACCTCAG 60.351 50.000 0.00 0.00 0.00 3.35
2775 4464 2.878406 CAACATCGTTTTGGACCTCAGT 59.122 45.455 0.00 0.00 0.00 3.41
2809 4498 0.673333 CGCATACACTGTTGAGCCCA 60.673 55.000 0.00 0.00 0.00 5.36
2814 4503 2.185004 ACACTGTTGAGCCCACATAC 57.815 50.000 0.00 0.00 0.00 2.39
2824 4513 0.743345 GCCCACATACCACGGTTCTC 60.743 60.000 0.00 0.00 0.00 2.87
2832 4521 1.981256 ACCACGGTTCTCAAAGCATT 58.019 45.000 0.00 0.00 33.03 3.56
2842 4531 3.759581 TCTCAAAGCATTCTTGAGCCTT 58.240 40.909 7.54 0.00 32.48 4.35
2845 4534 1.920610 AAGCATTCTTGAGCCTTGCT 58.079 45.000 0.00 0.00 45.06 3.91
2940 4638 2.479730 CCTCTGGAGACGTGTTAATCCG 60.480 54.545 0.00 0.00 34.39 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 8.475639 TGGGTGTATCTAGAACTAAAATGAGTC 58.524 37.037 0.00 0.00 0.00 3.36
20 21 9.699410 TCAGAATGAATAAAAATGGGTGTATCT 57.301 29.630 0.00 0.00 45.97 1.98
39 40 7.182761 GTCCGAAAATACTTGTCATCAGAATG 58.817 38.462 0.00 0.00 37.54 2.67
40 41 6.036083 CGTCCGAAAATACTTGTCATCAGAAT 59.964 38.462 0.00 0.00 0.00 2.40
41 42 5.347635 CGTCCGAAAATACTTGTCATCAGAA 59.652 40.000 0.00 0.00 0.00 3.02
42 43 4.862574 CGTCCGAAAATACTTGTCATCAGA 59.137 41.667 0.00 0.00 0.00 3.27
43 44 4.032900 CCGTCCGAAAATACTTGTCATCAG 59.967 45.833 0.00 0.00 0.00 2.90
44 45 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
45 46 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
46 47 4.081862 TCTCCGTCCGAAAATACTTGTCAT 60.082 41.667 0.00 0.00 0.00 3.06
47 48 3.256383 TCTCCGTCCGAAAATACTTGTCA 59.744 43.478 0.00 0.00 0.00 3.58
48 49 3.841643 TCTCCGTCCGAAAATACTTGTC 58.158 45.455 0.00 0.00 0.00 3.18
49 50 3.508793 TCTCTCCGTCCGAAAATACTTGT 59.491 43.478 0.00 0.00 0.00 3.16
50 51 4.106029 TCTCTCCGTCCGAAAATACTTG 57.894 45.455 0.00 0.00 0.00 3.16
51 52 4.796038 TTCTCTCCGTCCGAAAATACTT 57.204 40.909 0.00 0.00 0.00 2.24
52 53 5.359009 TGTATTCTCTCCGTCCGAAAATACT 59.641 40.000 0.00 0.00 32.19 2.12
53 54 5.585390 TGTATTCTCTCCGTCCGAAAATAC 58.415 41.667 0.00 0.00 0.00 1.89
54 55 5.840243 TGTATTCTCTCCGTCCGAAAATA 57.160 39.130 0.00 0.00 0.00 1.40
55 56 4.730949 TGTATTCTCTCCGTCCGAAAAT 57.269 40.909 0.00 0.00 0.00 1.82
56 57 4.730949 ATGTATTCTCTCCGTCCGAAAA 57.269 40.909 0.00 0.00 0.00 2.29
57 58 4.260907 CGTATGTATTCTCTCCGTCCGAAA 60.261 45.833 0.00 0.00 0.00 3.46
58 59 3.249320 CGTATGTATTCTCTCCGTCCGAA 59.751 47.826 0.00 0.00 0.00 4.30
59 60 2.804527 CGTATGTATTCTCTCCGTCCGA 59.195 50.000 0.00 0.00 0.00 4.55
60 61 2.804527 TCGTATGTATTCTCTCCGTCCG 59.195 50.000 0.00 0.00 0.00 4.79
61 62 4.785417 CTTCGTATGTATTCTCTCCGTCC 58.215 47.826 0.00 0.00 0.00 4.79
62 63 4.220572 GCTTCGTATGTATTCTCTCCGTC 58.779 47.826 0.00 0.00 0.00 4.79
63 64 3.303857 CGCTTCGTATGTATTCTCTCCGT 60.304 47.826 0.00 0.00 0.00 4.69
64 65 3.059120 TCGCTTCGTATGTATTCTCTCCG 60.059 47.826 0.00 0.00 0.00 4.63
65 66 4.485024 TCGCTTCGTATGTATTCTCTCC 57.515 45.455 0.00 0.00 0.00 3.71
66 67 5.108705 CGTTTCGCTTCGTATGTATTCTCTC 60.109 44.000 0.00 0.00 0.00 3.20
67 68 4.733887 CGTTTCGCTTCGTATGTATTCTCT 59.266 41.667 0.00 0.00 0.00 3.10
68 69 4.731961 TCGTTTCGCTTCGTATGTATTCTC 59.268 41.667 0.00 0.00 0.00 2.87
69 70 4.665212 TCGTTTCGCTTCGTATGTATTCT 58.335 39.130 0.00 0.00 0.00 2.40
70 71 4.498323 ACTCGTTTCGCTTCGTATGTATTC 59.502 41.667 0.00 0.00 0.00 1.75
71 72 4.418392 ACTCGTTTCGCTTCGTATGTATT 58.582 39.130 0.00 0.00 0.00 1.89
72 73 4.025015 ACTCGTTTCGCTTCGTATGTAT 57.975 40.909 0.00 0.00 0.00 2.29
73 74 3.476295 ACTCGTTTCGCTTCGTATGTA 57.524 42.857 0.00 0.00 0.00 2.29
74 75 2.342910 ACTCGTTTCGCTTCGTATGT 57.657 45.000 0.00 0.00 0.00 2.29
75 76 4.811158 TTTACTCGTTTCGCTTCGTATG 57.189 40.909 0.00 0.00 0.00 2.39
76 77 5.338365 AGATTTACTCGTTTCGCTTCGTAT 58.662 37.500 0.00 0.00 0.00 3.06
77 78 4.726416 AGATTTACTCGTTTCGCTTCGTA 58.274 39.130 0.00 0.00 0.00 3.43
78 79 3.572584 AGATTTACTCGTTTCGCTTCGT 58.427 40.909 0.00 0.00 0.00 3.85
79 80 4.556135 TGTAGATTTACTCGTTTCGCTTCG 59.444 41.667 0.00 0.00 0.00 3.79
80 81 5.572126 AGTGTAGATTTACTCGTTTCGCTTC 59.428 40.000 0.00 0.00 0.00 3.86
81 82 5.467705 AGTGTAGATTTACTCGTTTCGCTT 58.532 37.500 0.00 0.00 0.00 4.68
85 86 9.623350 AGTTTAGAGTGTAGATTTACTCGTTTC 57.377 33.333 0.00 0.00 46.05 2.78
170 174 7.280356 AGCCGTTAGAATGTTAAATCCTATGT 58.720 34.615 0.00 0.00 0.00 2.29
171 175 7.730364 AGCCGTTAGAATGTTAAATCCTATG 57.270 36.000 0.00 0.00 0.00 2.23
173 177 8.241497 TCTAGCCGTTAGAATGTTAAATCCTA 57.759 34.615 0.00 0.00 35.46 2.94
174 178 7.120923 TCTAGCCGTTAGAATGTTAAATCCT 57.879 36.000 0.00 0.00 35.46 3.24
177 181 9.826574 TTGTATCTAGCCGTTAGAATGTTAAAT 57.173 29.630 0.00 0.00 41.59 1.40
186 190 9.635520 GCTTTTATATTGTATCTAGCCGTTAGA 57.364 33.333 0.00 0.00 42.44 2.10
187 191 8.584600 CGCTTTTATATTGTATCTAGCCGTTAG 58.415 37.037 0.00 0.00 0.00 2.34
192 196 8.861101 CACTACGCTTTTATATTGTATCTAGCC 58.139 37.037 0.00 0.00 0.00 3.93
209 213 6.518208 AAGAGTCTTTAGATCACTACGCTT 57.482 37.500 0.00 0.00 0.00 4.68
244 252 7.093068 TGGCAGAACAATATTGTACTTCCTCTA 60.093 37.037 21.07 5.87 41.31 2.43
246 254 5.880332 TGGCAGAACAATATTGTACTTCCTC 59.120 40.000 21.07 13.43 41.31 3.71
300 309 2.169352 AGGTACAGTGCAGGATCATGAC 59.831 50.000 12.39 6.69 0.00 3.06
301 310 2.470990 AGGTACAGTGCAGGATCATGA 58.529 47.619 12.39 0.00 0.00 3.07
307 316 2.288825 CGAGAAAAGGTACAGTGCAGGA 60.289 50.000 0.00 0.00 0.00 3.86
309 318 2.731976 GTCGAGAAAAGGTACAGTGCAG 59.268 50.000 0.00 0.00 0.00 4.41
310 319 2.364324 AGTCGAGAAAAGGTACAGTGCA 59.636 45.455 0.00 0.00 0.00 4.57
315 324 3.192844 CAGGCTAGTCGAGAAAAGGTACA 59.807 47.826 0.00 0.00 0.00 2.90
316 325 3.442977 TCAGGCTAGTCGAGAAAAGGTAC 59.557 47.826 0.00 0.00 0.00 3.34
407 420 2.172505 TGCATGTCCCTATCAATCCGTT 59.827 45.455 0.00 0.00 0.00 4.44
418 431 3.091545 CCATTAAACAGTGCATGTCCCT 58.908 45.455 0.00 0.00 43.00 4.20
423 436 4.177165 TCAAGCCATTAAACAGTGCATG 57.823 40.909 0.00 0.00 0.00 4.06
428 441 6.015180 ACACATCAATCAAGCCATTAAACAGT 60.015 34.615 0.00 0.00 0.00 3.55
437 450 2.583024 TGGACACATCAATCAAGCCA 57.417 45.000 0.00 0.00 0.00 4.75
439 452 4.510038 AACTTGGACACATCAATCAAGC 57.490 40.909 0.00 0.00 38.56 4.01
440 453 5.009911 TGGAAACTTGGACACATCAATCAAG 59.990 40.000 0.00 0.00 40.21 3.02
441 454 4.892345 TGGAAACTTGGACACATCAATCAA 59.108 37.500 0.00 0.00 0.00 2.57
442 455 4.468713 TGGAAACTTGGACACATCAATCA 58.531 39.130 0.00 0.00 0.00 2.57
474 487 1.204146 TGGCTACTGCTTCCCCTAAG 58.796 55.000 0.00 0.00 39.59 2.18
475 488 1.663911 TTGGCTACTGCTTCCCCTAA 58.336 50.000 0.00 0.00 39.59 2.69
477 490 1.771255 CTATTGGCTACTGCTTCCCCT 59.229 52.381 0.00 0.00 39.59 4.79
478 491 1.815795 GCTATTGGCTACTGCTTCCCC 60.816 57.143 0.00 0.00 39.59 4.81
479 492 1.598882 GCTATTGGCTACTGCTTCCC 58.401 55.000 0.00 0.00 39.59 3.97
482 495 1.561542 ACTGGCTATTGGCTACTGCTT 59.438 47.619 1.98 0.00 41.46 3.91
484 497 2.760374 CTACTGGCTATTGGCTACTGC 58.240 52.381 1.98 0.00 41.46 4.40
485 498 2.548920 GGCTACTGGCTATTGGCTACTG 60.549 54.545 1.98 0.00 41.46 2.74
486 499 1.694696 GGCTACTGGCTATTGGCTACT 59.305 52.381 1.98 0.00 41.46 2.57
487 500 1.416401 TGGCTACTGGCTATTGGCTAC 59.584 52.381 1.98 0.00 41.46 3.58
488 501 1.694150 CTGGCTACTGGCTATTGGCTA 59.306 52.381 1.98 0.00 41.46 3.93
489 502 0.471617 CTGGCTACTGGCTATTGGCT 59.528 55.000 1.98 0.00 41.46 4.75
490 503 0.181350 ACTGGCTACTGGCTATTGGC 59.819 55.000 0.00 0.00 41.46 4.52
491 504 2.548920 GCTACTGGCTACTGGCTATTGG 60.549 54.545 0.00 0.00 41.46 3.16
492 505 2.548920 GGCTACTGGCTACTGGCTATTG 60.549 54.545 0.00 0.00 41.46 1.90
493 506 1.694696 GGCTACTGGCTACTGGCTATT 59.305 52.381 0.00 0.00 41.46 1.73
494 507 1.343069 GGCTACTGGCTACTGGCTAT 58.657 55.000 0.00 0.00 41.46 2.97
495 508 0.032515 TGGCTACTGGCTACTGGCTA 60.033 55.000 0.00 0.00 41.46 3.93
496 509 1.306141 TGGCTACTGGCTACTGGCT 60.306 57.895 0.00 0.00 41.46 4.75
497 510 1.144936 CTGGCTACTGGCTACTGGC 59.855 63.158 0.00 0.00 41.46 4.85
498 511 1.683917 CTACTGGCTACTGGCTACTGG 59.316 57.143 0.00 0.00 41.46 4.00
499 512 1.683917 CCTACTGGCTACTGGCTACTG 59.316 57.143 0.00 0.00 41.46 2.74
500 513 1.288335 ACCTACTGGCTACTGGCTACT 59.712 52.381 0.00 0.00 41.46 2.57
501 514 1.409427 CACCTACTGGCTACTGGCTAC 59.591 57.143 0.00 0.00 41.46 3.58
502 515 1.776662 CACCTACTGGCTACTGGCTA 58.223 55.000 0.00 0.00 41.46 3.93
503 516 1.617947 GCACCTACTGGCTACTGGCT 61.618 60.000 0.00 0.00 41.46 4.75
504 517 1.153349 GCACCTACTGGCTACTGGC 60.153 63.158 0.00 0.00 40.90 4.85
505 518 0.461961 GAGCACCTACTGGCTACTGG 59.538 60.000 0.00 0.00 41.22 4.00
514 527 1.202806 TGCAAAAGCAGAGCACCTACT 60.203 47.619 0.00 0.00 32.55 2.57
573 586 5.450453 AGCTGAGTAAGACTAAGATAGCCA 58.550 41.667 0.00 0.00 27.25 4.75
608 621 4.691860 AAAGCCTGATCAAGTGATTTCG 57.308 40.909 0.00 0.00 34.37 3.46
638 651 9.905713 ACTAAGCCTGATCAAGTGATTTATTTA 57.094 29.630 0.00 0.00 34.37 1.40
642 655 6.070251 TCCACTAAGCCTGATCAAGTGATTTA 60.070 38.462 20.97 5.74 39.93 1.40
678 691 9.638239 ATTAATAACAATTTGTCATGGTGTCAC 57.362 29.630 1.83 0.00 0.00 3.67
703 750 5.755375 CGACTATGTGCTGTTATTTCTGGAT 59.245 40.000 0.00 0.00 0.00 3.41
839 895 8.753497 AATGGAAAGTTTTTCTACAGAGAGTT 57.247 30.769 2.03 0.00 31.77 3.01
840 896 8.753497 AAATGGAAAGTTTTTCTACAGAGAGT 57.247 30.769 2.03 0.00 31.77 3.24
873 929 2.922740 ACCACGTGTCTTGGTGTAAT 57.077 45.000 15.65 0.00 46.09 1.89
887 943 0.951558 CCTTCCAAGTTCCAACCACG 59.048 55.000 0.00 0.00 0.00 4.94
888 944 1.133606 TCCCTTCCAAGTTCCAACCAC 60.134 52.381 0.00 0.00 0.00 4.16
889 945 1.227249 TCCCTTCCAAGTTCCAACCA 58.773 50.000 0.00 0.00 0.00 3.67
890 946 2.171003 CATCCCTTCCAAGTTCCAACC 58.829 52.381 0.00 0.00 0.00 3.77
891 947 3.154827 TCATCCCTTCCAAGTTCCAAC 57.845 47.619 0.00 0.00 0.00 3.77
892 948 3.893753 TTCATCCCTTCCAAGTTCCAA 57.106 42.857 0.00 0.00 0.00 3.53
896 952 3.879321 GCTCCATTCATCCCTTCCAAGTT 60.879 47.826 0.00 0.00 0.00 2.66
897 953 2.357569 GCTCCATTCATCCCTTCCAAGT 60.358 50.000 0.00 0.00 0.00 3.16
898 954 2.305009 GCTCCATTCATCCCTTCCAAG 58.695 52.381 0.00 0.00 0.00 3.61
940 997 0.674895 GAAACAGCGGCATCAGTCCT 60.675 55.000 1.45 0.00 0.00 3.85
944 1001 0.647410 CGTAGAAACAGCGGCATCAG 59.353 55.000 1.45 0.00 0.00 2.90
947 1004 1.079127 AGCGTAGAAACAGCGGCAT 60.079 52.632 1.45 0.00 35.78 4.40
993 1058 4.944930 TGGGTGTCATTTTATAACGGGAAG 59.055 41.667 0.00 0.00 0.00 3.46
1046 1112 2.414825 GCTGAAGCTAGCTTGACTTGAC 59.585 50.000 33.91 17.61 40.52 3.18
1047 1113 2.693069 GCTGAAGCTAGCTTGACTTGA 58.307 47.619 33.91 3.28 40.52 3.02
1080 1151 0.958822 ATGGTTTCTTTGGTGCGGAC 59.041 50.000 0.00 0.00 0.00 4.79
1081 1152 0.958091 CATGGTTTCTTTGGTGCGGA 59.042 50.000 0.00 0.00 0.00 5.54
1082 1153 0.038343 CCATGGTTTCTTTGGTGCGG 60.038 55.000 2.57 0.00 0.00 5.69
1083 1154 0.667184 GCCATGGTTTCTTTGGTGCG 60.667 55.000 14.67 0.00 32.90 5.34
1084 1155 0.667184 CGCCATGGTTTCTTTGGTGC 60.667 55.000 14.67 0.00 34.55 5.01
1085 1156 0.958091 TCGCCATGGTTTCTTTGGTG 59.042 50.000 14.67 0.00 41.38 4.17
1086 1157 0.958822 GTCGCCATGGTTTCTTTGGT 59.041 50.000 14.67 0.00 32.90 3.67
1108 1186 1.992277 AGGACTACTGCTGGGCTGG 60.992 63.158 0.00 0.00 0.00 4.85
1247 1331 4.436998 GCCTCCACGGACGACCAG 62.437 72.222 4.48 0.00 35.59 4.00
1385 1909 3.319198 GTGAGGTTGGGGCCGAGA 61.319 66.667 0.00 0.00 0.00 4.04
2175 3722 4.537433 AGATCAAGCGGAGGCGGC 62.537 66.667 0.00 0.00 46.35 6.53
2176 3723 2.374830 ATCAGATCAAGCGGAGGCGG 62.375 60.000 0.00 0.00 46.35 6.13
2177 3724 1.068753 ATCAGATCAAGCGGAGGCG 59.931 57.895 0.00 0.00 46.35 5.52
2178 3725 0.883814 CCATCAGATCAAGCGGAGGC 60.884 60.000 0.00 0.00 40.37 4.70
2179 3726 0.467384 ACCATCAGATCAAGCGGAGG 59.533 55.000 0.00 0.00 0.00 4.30
2180 3727 2.208431 GAACCATCAGATCAAGCGGAG 58.792 52.381 0.00 0.00 0.00 4.63
2181 3728 1.471501 CGAACCATCAGATCAAGCGGA 60.472 52.381 0.00 0.00 0.00 5.54
2182 3729 0.933097 CGAACCATCAGATCAAGCGG 59.067 55.000 0.00 0.00 0.00 5.52
2183 3730 0.933097 CCGAACCATCAGATCAAGCG 59.067 55.000 0.00 0.00 0.00 4.68
2184 3731 1.936547 GACCGAACCATCAGATCAAGC 59.063 52.381 0.00 0.00 0.00 4.01
2185 3732 2.196749 CGACCGAACCATCAGATCAAG 58.803 52.381 0.00 0.00 0.00 3.02
2186 3733 1.548719 ACGACCGAACCATCAGATCAA 59.451 47.619 0.00 0.00 0.00 2.57
2187 3734 1.134367 GACGACCGAACCATCAGATCA 59.866 52.381 0.00 0.00 0.00 2.92
2188 3735 1.841450 GACGACCGAACCATCAGATC 58.159 55.000 0.00 0.00 0.00 2.75
2189 3736 0.100682 CGACGACCGAACCATCAGAT 59.899 55.000 0.00 0.00 41.76 2.90
2190 3737 1.504900 CGACGACCGAACCATCAGA 59.495 57.895 0.00 0.00 41.76 3.27
2191 3738 1.516386 CCGACGACCGAACCATCAG 60.516 63.158 0.00 0.00 41.76 2.90
2192 3739 2.569657 CCGACGACCGAACCATCA 59.430 61.111 0.00 0.00 41.76 3.07
2193 3740 2.884207 GCCGACGACCGAACCATC 60.884 66.667 0.00 0.00 41.76 3.51
2194 3741 3.229156 TTGCCGACGACCGAACCAT 62.229 57.895 0.00 0.00 41.76 3.55
2195 3742 3.851845 CTTGCCGACGACCGAACCA 62.852 63.158 0.00 0.00 41.76 3.67
2196 3743 2.476534 TACTTGCCGACGACCGAACC 62.477 60.000 0.00 0.00 41.76 3.62
2197 3744 1.069378 CTACTTGCCGACGACCGAAC 61.069 60.000 0.00 0.00 41.76 3.95
2198 3745 1.210931 CTACTTGCCGACGACCGAA 59.789 57.895 0.00 0.00 41.76 4.30
2199 3746 2.693762 CCTACTTGCCGACGACCGA 61.694 63.158 0.00 0.00 41.76 4.69
2200 3747 2.202570 CCTACTTGCCGACGACCG 60.203 66.667 0.00 0.00 38.18 4.79
2222 3769 2.438385 CTAACACAACGCACGGGCAC 62.438 60.000 11.77 0.00 41.24 5.01
2341 3900 1.871039 CAACGACGATCCAAACCACTT 59.129 47.619 0.00 0.00 0.00 3.16
2344 3903 0.393448 TCCAACGACGATCCAAACCA 59.607 50.000 0.00 0.00 0.00 3.67
2362 3921 6.876257 ACATAGTTGGTCAAGAACTCAAGATC 59.124 38.462 0.00 0.00 35.30 2.75
2379 3943 6.253727 GGTGTCGAGACTAATTGACATAGTTG 59.746 42.308 12.92 0.00 43.70 3.16
2398 4040 9.110617 CAATACGTACTACATAAATAGGTGTCG 57.889 37.037 0.00 0.00 0.00 4.35
2409 4051 5.945466 TCGCCATCAATACGTACTACATA 57.055 39.130 0.00 0.00 0.00 2.29
2410 4052 4.841443 TCGCCATCAATACGTACTACAT 57.159 40.909 0.00 0.00 0.00 2.29
2411 4053 4.841443 ATCGCCATCAATACGTACTACA 57.159 40.909 0.00 0.00 0.00 2.74
2412 4054 6.194142 CGATTATCGCCATCAATACGTACTAC 59.806 42.308 0.46 0.00 31.14 2.73
2413 4055 6.128200 ACGATTATCGCCATCAATACGTACTA 60.128 38.462 14.97 0.00 45.12 1.82
2414 4056 5.093457 CGATTATCGCCATCAATACGTACT 58.907 41.667 0.46 0.00 31.14 2.73
2549 4236 0.813184 TCGTACTTTGCGGGTCTAGG 59.187 55.000 0.00 0.00 0.00 3.02
2591 4278 2.827642 GCACCAGGCAGGCATCTC 60.828 66.667 0.00 0.00 43.14 2.75
2602 4289 3.657448 TATGCCGGACACGCACCAG 62.657 63.158 5.05 0.00 39.22 4.00
2605 4292 1.133869 GTTTATGCCGGACACGCAC 59.866 57.895 5.05 0.00 39.22 5.34
2606 4293 1.301795 TGTTTATGCCGGACACGCA 60.302 52.632 5.05 0.00 39.22 5.24
2607 4294 1.133869 GTGTTTATGCCGGACACGC 59.866 57.895 5.05 0.00 39.22 5.34
2608 4295 1.791662 GGTGTTTATGCCGGACACG 59.208 57.895 5.05 0.00 43.41 4.49
2609 4296 1.791662 CGGTGTTTATGCCGGACAC 59.208 57.895 5.05 10.61 43.85 3.67
2610 4297 4.287580 CGGTGTTTATGCCGGACA 57.712 55.556 5.05 2.56 43.85 4.02
2615 4302 0.878416 TTGCTCACGGTGTTTATGCC 59.122 50.000 8.17 0.00 0.00 4.40
2616 4303 2.161410 TGATTGCTCACGGTGTTTATGC 59.839 45.455 8.17 6.89 0.00 3.14
2617 4304 4.418013 TTGATTGCTCACGGTGTTTATG 57.582 40.909 8.17 0.00 0.00 1.90
2618 4305 4.699735 TGATTGATTGCTCACGGTGTTTAT 59.300 37.500 8.17 0.00 0.00 1.40
2619 4306 4.068599 TGATTGATTGCTCACGGTGTTTA 58.931 39.130 8.17 0.00 0.00 2.01
2631 4318 3.947196 TGACCCACATACTGATTGATTGC 59.053 43.478 0.00 0.00 0.00 3.56
2642 4329 0.035439 CCACCCAGTGACCCACATAC 60.035 60.000 0.00 0.00 36.74 2.39
2645 4332 3.884774 GCCACCCAGTGACCCACA 61.885 66.667 0.00 0.00 36.74 4.17
2646 4333 3.884774 TGCCACCCAGTGACCCAC 61.885 66.667 0.00 0.00 35.23 4.61
2683 4370 2.866085 GATCGAGCTGGGCTGCACTT 62.866 60.000 2.50 0.00 39.88 3.16
2705 4392 0.823356 AGCCAACCAAACTCGTGCAT 60.823 50.000 0.00 0.00 0.00 3.96
2706 4393 1.453015 AGCCAACCAAACTCGTGCA 60.453 52.632 0.00 0.00 0.00 4.57
2707 4394 1.008538 CAGCCAACCAAACTCGTGC 60.009 57.895 0.00 0.00 0.00 5.34
2708 4395 1.008538 GCAGCCAACCAAACTCGTG 60.009 57.895 0.00 0.00 0.00 4.35
2709 4396 0.823356 ATGCAGCCAACCAAACTCGT 60.823 50.000 0.00 0.00 0.00 4.18
2756 4445 2.158813 ACACTGAGGTCCAAAACGATGT 60.159 45.455 0.00 0.00 0.00 3.06
2761 4450 4.173256 CAAACAACACTGAGGTCCAAAAC 58.827 43.478 0.00 0.00 0.00 2.43
2774 4463 0.171455 TGCGGACAACCAAACAACAC 59.829 50.000 0.00 0.00 35.59 3.32
2775 4464 1.107114 ATGCGGACAACCAAACAACA 58.893 45.000 0.00 0.00 35.59 3.33
2809 4498 2.224426 TGCTTTGAGAACCGTGGTATGT 60.224 45.455 0.00 0.00 0.00 2.29
2814 4503 2.154462 AGAATGCTTTGAGAACCGTGG 58.846 47.619 0.00 0.00 0.00 4.94
2824 4513 2.029290 AGCAAGGCTCAAGAATGCTTTG 60.029 45.455 3.35 5.63 44.43 2.77
2842 4531 2.281484 GGCTGTTCCCAACGAGCA 60.281 61.111 0.00 0.00 37.31 4.26
2845 4534 0.672401 GATTCGGCTGTTCCCAACGA 60.672 55.000 0.00 0.00 0.00 3.85
2919 4608 2.479730 CGGATTAACACGTCTCCAGAGG 60.480 54.545 0.00 0.00 36.14 3.69
2940 4638 6.463755 GGGGATTGAGGATTAGAAAGAGAGAC 60.464 46.154 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.