Multiple sequence alignment - TraesCS1B01G090800

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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 TraesCS1B01G090800 chr1B 100.000 3243 0 0 1 3243 91887007 91883765 0.000000e+00 5989
1 TraesCS1B01G090800 chr1B 95.439 285 12 1 1 285 633228545 633228262 1.370000e-123 453
2 TraesCS1B01G090800 chr4B 94.629 2197 89 12 285 2475 221191823 221193996 0.000000e+00 3376
3 TraesCS1B01G090800 chr4B 91.431 2334 139 29 285 2616 361733591 361731317 0.000000e+00 3145
4 TraesCS1B01G090800 chr4B 93.264 193 13 0 285 477 564156549 564156741 5.300000e-73 285
5 TraesCS1B01G090800 chr6D 93.942 2146 116 7 474 2616 59751320 59749186 0.000000e+00 3230
6 TraesCS1B01G090800 chr6D 92.894 2153 124 15 474 2623 352345989 352348115 0.000000e+00 3101
7 TraesCS1B01G090800 chr6D 93.472 1930 111 8 690 2616 173910679 173912596 0.000000e+00 2852
8 TraesCS1B01G090800 chr6D 93.347 1413 68 5 1221 2616 263997311 263995908 0.000000e+00 2065
9 TraesCS1B01G090800 chr5D 93.250 2148 117 10 474 2616 61458853 61460977 0.000000e+00 3138
10 TraesCS1B01G090800 chr2A 92.115 2194 112 16 285 2475 492833717 492835852 0.000000e+00 3037
11 TraesCS1B01G090800 chr2A 95.455 286 12 1 1 286 12333055 12333339 3.810000e-124 455
12 TraesCS1B01G090800 chr5B 92.829 1785 85 16 285 2068 706040033 706041775 0.000000e+00 2547
13 TraesCS1B01G090800 chr5B 96.491 285 9 1 1 285 684004183 684004466 1.360000e-128 470
14 TraesCS1B01G090800 chr3B 92.595 1634 82 14 285 1918 124768806 124767212 0.000000e+00 2311
15 TraesCS1B01G090800 chr3B 93.145 1342 77 9 1285 2616 254908594 254907258 0.000000e+00 1954
16 TraesCS1B01G090800 chr2D 94.076 1401 70 6 1218 2616 540174496 540175885 0.000000e+00 2115
17 TraesCS1B01G090800 chr7D 93.867 1337 73 4 1285 2616 46098300 46096968 0.000000e+00 2006
18 TraesCS1B01G090800 chr4A 92.308 1417 70 11 285 1701 90386630 90385253 0.000000e+00 1977
19 TraesCS1B01G090800 chr4A 95.455 286 13 0 1 286 709718170 709718455 1.060000e-124 457
20 TraesCS1B01G090800 chr4A 95.439 285 12 1 1 285 715001406 715001123 1.370000e-123 453
21 TraesCS1B01G090800 chr4D 93.090 796 50 3 475 1269 313007166 313007957 0.000000e+00 1160
22 TraesCS1B01G090800 chr1A 91.950 646 34 8 2612 3243 56325236 56325877 0.000000e+00 889
23 TraesCS1B01G090800 chr1A 89.308 636 54 11 2612 3243 56364382 56365007 0.000000e+00 785
24 TraesCS1B01G090800 chr1A 80.338 651 80 23 2637 3243 54457015 54457661 1.770000e-122 449
25 TraesCS1B01G090800 chr1A 80.495 646 76 20 2640 3242 56366864 56367502 1.770000e-122 449
26 TraesCS1B01G090800 chr1D 94.444 396 19 2 2612 3007 56896285 56895893 9.950000e-170 606
27 TraesCS1B01G090800 chr1D 82.298 644 66 18 2642 3243 56612182 56611545 6.200000e-142 514
28 TraesCS1B01G090800 chr1D 79.128 642 87 18 2643 3241 56619629 56618992 1.810000e-107 399
29 TraesCS1B01G090800 chr1D 80.102 588 70 21 2699 3243 56532706 56532123 8.430000e-106 394
30 TraesCS1B01G090800 chr1D 88.235 255 16 4 3003 3243 56880468 56880214 3.160000e-75 292
31 TraesCS1B01G090800 chr1D 85.606 132 18 1 2711 2842 56433120 56432990 1.570000e-28 137
32 TraesCS1B01G090800 chr6B 96.167 287 9 2 1 285 463556785 463557071 4.900000e-128 468
33 TraesCS1B01G090800 chr7B 95.439 285 11 2 2 285 21718325 21718042 1.370000e-123 453
34 TraesCS1B01G090800 chr7B 93.137 306 17 4 1 304 728874013 728874316 2.300000e-121 446
35 TraesCS1B01G090800 chr3A 93.137 306 16 5 1 304 662833585 662833283 8.260000e-121 444
36 TraesCS1B01G090800 chr3D 92.746 193 14 0 285 477 562561749 562561941 2.460000e-71 279


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 TraesCS1B01G090800 chr1B 91883765 91887007 3242 True 5989 5989 100.0000 1 3243 1 chr1B.!!$R1 3242
1 TraesCS1B01G090800 chr4B 221191823 221193996 2173 False 3376 3376 94.6290 285 2475 1 chr4B.!!$F1 2190
2 TraesCS1B01G090800 chr4B 361731317 361733591 2274 True 3145 3145 91.4310 285 2616 1 chr4B.!!$R1 2331
3 TraesCS1B01G090800 chr6D 59749186 59751320 2134 True 3230 3230 93.9420 474 2616 1 chr6D.!!$R1 2142
4 TraesCS1B01G090800 chr6D 352345989 352348115 2126 False 3101 3101 92.8940 474 2623 1 chr6D.!!$F2 2149
5 TraesCS1B01G090800 chr6D 173910679 173912596 1917 False 2852 2852 93.4720 690 2616 1 chr6D.!!$F1 1926
6 TraesCS1B01G090800 chr6D 263995908 263997311 1403 True 2065 2065 93.3470 1221 2616 1 chr6D.!!$R2 1395
7 TraesCS1B01G090800 chr5D 61458853 61460977 2124 False 3138 3138 93.2500 474 2616 1 chr5D.!!$F1 2142
8 TraesCS1B01G090800 chr2A 492833717 492835852 2135 False 3037 3037 92.1150 285 2475 1 chr2A.!!$F2 2190
9 TraesCS1B01G090800 chr5B 706040033 706041775 1742 False 2547 2547 92.8290 285 2068 1 chr5B.!!$F2 1783
10 TraesCS1B01G090800 chr3B 124767212 124768806 1594 True 2311 2311 92.5950 285 1918 1 chr3B.!!$R1 1633
11 TraesCS1B01G090800 chr3B 254907258 254908594 1336 True 1954 1954 93.1450 1285 2616 1 chr3B.!!$R2 1331
12 TraesCS1B01G090800 chr2D 540174496 540175885 1389 False 2115 2115 94.0760 1218 2616 1 chr2D.!!$F1 1398
13 TraesCS1B01G090800 chr7D 46096968 46098300 1332 True 2006 2006 93.8670 1285 2616 1 chr7D.!!$R1 1331
14 TraesCS1B01G090800 chr4A 90385253 90386630 1377 True 1977 1977 92.3080 285 1701 1 chr4A.!!$R1 1416
15 TraesCS1B01G090800 chr4D 313007166 313007957 791 False 1160 1160 93.0900 475 1269 1 chr4D.!!$F1 794
16 TraesCS1B01G090800 chr1A 56325236 56325877 641 False 889 889 91.9500 2612 3243 1 chr1A.!!$F2 631
17 TraesCS1B01G090800 chr1A 56364382 56367502 3120 False 617 785 84.9015 2612 3243 2 chr1A.!!$F3 631
18 TraesCS1B01G090800 chr1A 54457015 54457661 646 False 449 449 80.3380 2637 3243 1 chr1A.!!$F1 606
19 TraesCS1B01G090800 chr1D 56611545 56612182 637 True 514 514 82.2980 2642 3243 1 chr1D.!!$R3 601
20 TraesCS1B01G090800 chr1D 56618992 56619629 637 True 399 399 79.1280 2643 3241 1 chr1D.!!$R4 598
21 TraesCS1B01G090800 chr1D 56532123 56532706 583 True 394 394 80.1020 2699 3243 1 chr1D.!!$R2 544

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
47 48 0.107268 TTCTGTGCAGCTCTCAGCAA 59.893 50.0 0.00 0.00 45.56 3.91 F
48 49 0.107268 TCTGTGCAGCTCTCAGCAAA 59.893 50.0 0.00 0.00 45.56 3.68 F
664 665 0.248458 CAACTTTGCGGTGTCCACAC 60.248 55.0 0.85 0.85 45.72 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1045 1049 0.322816 AGCCGCACCATGATCTTGTT 60.323 50.0 7.73 0.0 0.00 2.83 R
1055 1059 0.884704 GAGTTTCTTGAGCCGCACCA 60.885 55.0 0.00 0.0 0.00 4.17 R
2595 2641 0.032678 CTAGATGACCCGATTGCGCT 59.967 55.0 9.73 0.0 35.83 5.92 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 4.385358 ACGCTCCAATTTTCAAAACACT 57.615 36.364 0.00 0.00 0.00 3.55
23 24 4.754322 ACGCTCCAATTTTCAAAACACTT 58.246 34.783 0.00 0.00 0.00 3.16
24 25 4.566360 ACGCTCCAATTTTCAAAACACTTG 59.434 37.500 0.00 0.00 0.00 3.16
25 26 4.025813 CGCTCCAATTTTCAAAACACTTGG 60.026 41.667 7.23 7.23 35.54 3.61
26 27 5.115480 GCTCCAATTTTCAAAACACTTGGA 58.885 37.500 13.46 13.46 39.72 3.53
27 28 5.006649 GCTCCAATTTTCAAAACACTTGGAC 59.993 40.000 11.02 6.49 37.74 4.02
28 29 6.293004 TCCAATTTTCAAAACACTTGGACT 57.707 33.333 11.02 0.00 37.74 3.85
29 30 6.706295 TCCAATTTTCAAAACACTTGGACTT 58.294 32.000 11.02 0.00 37.74 3.01
30 31 6.816140 TCCAATTTTCAAAACACTTGGACTTC 59.184 34.615 11.02 0.00 37.74 3.01
31 32 6.818142 CCAATTTTCAAAACACTTGGACTTCT 59.182 34.615 7.67 0.00 36.14 2.85
32 33 7.201548 CCAATTTTCAAAACACTTGGACTTCTG 60.202 37.037 7.67 0.00 36.14 3.02
33 34 5.975693 TTTCAAAACACTTGGACTTCTGT 57.024 34.783 0.00 0.00 0.00 3.41
34 35 4.963276 TCAAAACACTTGGACTTCTGTG 57.037 40.909 0.00 0.00 36.59 3.66
35 36 3.128589 TCAAAACACTTGGACTTCTGTGC 59.871 43.478 0.00 0.00 34.14 4.57
36 37 2.418368 AACACTTGGACTTCTGTGCA 57.582 45.000 0.00 0.00 42.73 4.57
37 38 1.959042 ACACTTGGACTTCTGTGCAG 58.041 50.000 0.00 0.00 44.96 4.41
38 39 0.590195 CACTTGGACTTCTGTGCAGC 59.410 55.000 0.00 0.00 44.96 5.25
39 40 0.471617 ACTTGGACTTCTGTGCAGCT 59.528 50.000 0.00 0.00 44.96 4.24
40 41 1.155042 CTTGGACTTCTGTGCAGCTC 58.845 55.000 0.00 0.00 44.96 4.09
41 42 0.761187 TTGGACTTCTGTGCAGCTCT 59.239 50.000 0.00 0.00 44.96 4.09
42 43 0.319728 TGGACTTCTGTGCAGCTCTC 59.680 55.000 0.00 0.00 39.59 3.20
43 44 0.319728 GGACTTCTGTGCAGCTCTCA 59.680 55.000 0.00 0.00 34.50 3.27
44 45 1.672441 GGACTTCTGTGCAGCTCTCAG 60.672 57.143 0.00 0.28 37.58 3.35
45 46 0.320596 ACTTCTGTGCAGCTCTCAGC 60.321 55.000 0.00 0.00 42.84 4.26
46 47 0.320508 CTTCTGTGCAGCTCTCAGCA 60.321 55.000 0.00 2.10 45.56 4.41
47 48 0.107268 TTCTGTGCAGCTCTCAGCAA 59.893 50.000 0.00 0.00 45.56 3.91
48 49 0.107268 TCTGTGCAGCTCTCAGCAAA 59.893 50.000 0.00 0.00 45.56 3.68
49 50 0.949397 CTGTGCAGCTCTCAGCAAAA 59.051 50.000 0.00 0.00 45.56 2.44
50 51 1.335810 CTGTGCAGCTCTCAGCAAAAA 59.664 47.619 0.00 0.00 45.56 1.94
69 70 3.771577 AAAGACAAATCGGAGGTCTGT 57.228 42.857 9.58 3.24 40.80 3.41
70 71 4.884668 AAAGACAAATCGGAGGTCTGTA 57.115 40.909 9.58 0.00 40.80 2.74
71 72 4.884668 AAGACAAATCGGAGGTCTGTAA 57.115 40.909 9.58 0.00 40.80 2.41
72 73 4.884668 AGACAAATCGGAGGTCTGTAAA 57.115 40.909 8.42 0.00 40.21 2.01
73 74 5.223449 AGACAAATCGGAGGTCTGTAAAA 57.777 39.130 8.42 0.00 40.21 1.52
74 75 5.617252 AGACAAATCGGAGGTCTGTAAAAA 58.383 37.500 8.42 0.00 40.21 1.94
75 76 6.238648 AGACAAATCGGAGGTCTGTAAAAAT 58.761 36.000 8.42 0.00 40.21 1.82
76 77 7.391620 AGACAAATCGGAGGTCTGTAAAAATA 58.608 34.615 8.42 0.00 40.21 1.40
77 78 8.047310 AGACAAATCGGAGGTCTGTAAAAATAT 58.953 33.333 8.42 0.00 40.21 1.28
78 79 7.985476 ACAAATCGGAGGTCTGTAAAAATATG 58.015 34.615 0.00 0.00 0.00 1.78
79 80 7.610305 ACAAATCGGAGGTCTGTAAAAATATGT 59.390 33.333 0.00 0.00 0.00 2.29
80 81 9.104965 CAAATCGGAGGTCTGTAAAAATATGTA 57.895 33.333 0.00 0.00 0.00 2.29
81 82 8.658499 AATCGGAGGTCTGTAAAAATATGTAC 57.342 34.615 0.00 0.00 0.00 2.90
82 83 7.414222 TCGGAGGTCTGTAAAAATATGTACT 57.586 36.000 0.00 0.00 0.00 2.73
83 84 7.262772 TCGGAGGTCTGTAAAAATATGTACTG 58.737 38.462 0.00 0.00 0.00 2.74
84 85 7.039882 CGGAGGTCTGTAAAAATATGTACTGT 58.960 38.462 0.00 0.00 0.00 3.55
85 86 7.548075 CGGAGGTCTGTAAAAATATGTACTGTT 59.452 37.037 0.00 0.00 0.00 3.16
86 87 8.880750 GGAGGTCTGTAAAAATATGTACTGTTC 58.119 37.037 0.00 0.00 0.00 3.18
87 88 9.431887 GAGGTCTGTAAAAATATGTACTGTTCA 57.568 33.333 0.00 0.00 0.00 3.18
88 89 9.959721 AGGTCTGTAAAAATATGTACTGTTCAT 57.040 29.630 5.26 5.26 0.00 2.57
101 102 7.476540 TGTACTGTTCATATACTGTTCTGGT 57.523 36.000 0.00 0.00 33.15 4.00
102 103 7.544622 TGTACTGTTCATATACTGTTCTGGTC 58.455 38.462 0.00 0.00 33.15 4.02
103 104 6.859112 ACTGTTCATATACTGTTCTGGTCT 57.141 37.500 0.00 0.00 0.00 3.85
104 105 6.634805 ACTGTTCATATACTGTTCTGGTCTG 58.365 40.000 0.00 0.00 0.00 3.51
105 106 6.437477 ACTGTTCATATACTGTTCTGGTCTGA 59.563 38.462 0.00 0.00 0.00 3.27
106 107 7.124901 ACTGTTCATATACTGTTCTGGTCTGAT 59.875 37.037 0.00 0.00 0.00 2.90
107 108 7.851228 TGTTCATATACTGTTCTGGTCTGATT 58.149 34.615 0.00 0.00 0.00 2.57
108 109 8.321353 TGTTCATATACTGTTCTGGTCTGATTT 58.679 33.333 0.00 0.00 0.00 2.17
109 110 8.607459 GTTCATATACTGTTCTGGTCTGATTTG 58.393 37.037 0.00 0.00 0.00 2.32
110 111 7.851228 TCATATACTGTTCTGGTCTGATTTGT 58.149 34.615 0.00 0.00 0.00 2.83
111 112 7.981789 TCATATACTGTTCTGGTCTGATTTGTC 59.018 37.037 0.00 0.00 0.00 3.18
112 113 4.696479 ACTGTTCTGGTCTGATTTGTCT 57.304 40.909 0.00 0.00 0.00 3.41
113 114 5.041191 ACTGTTCTGGTCTGATTTGTCTT 57.959 39.130 0.00 0.00 0.00 3.01
114 115 5.440610 ACTGTTCTGGTCTGATTTGTCTTT 58.559 37.500 0.00 0.00 0.00 2.52
115 116 5.888161 ACTGTTCTGGTCTGATTTGTCTTTT 59.112 36.000 0.00 0.00 0.00 2.27
116 117 6.378280 ACTGTTCTGGTCTGATTTGTCTTTTT 59.622 34.615 0.00 0.00 0.00 1.94
130 131 4.155950 TTTTTGCCGAGAGCTGCA 57.844 50.000 1.02 0.00 44.23 4.41
131 132 1.654220 TTTTTGCCGAGAGCTGCAC 59.346 52.632 1.02 0.00 44.23 4.57
132 133 1.100463 TTTTTGCCGAGAGCTGCACA 61.100 50.000 1.02 0.00 44.23 4.57
133 134 1.509644 TTTTGCCGAGAGCTGCACAG 61.510 55.000 1.02 0.00 44.23 3.66
134 135 2.381838 TTTGCCGAGAGCTGCACAGA 62.382 55.000 1.02 0.00 44.23 3.41
135 136 2.047844 GCCGAGAGCTGCACAGAA 60.048 61.111 1.02 0.00 38.99 3.02
136 137 2.099431 GCCGAGAGCTGCACAGAAG 61.099 63.158 1.02 0.00 38.99 2.85
137 138 1.291588 CCGAGAGCTGCACAGAAGT 59.708 57.895 1.02 0.00 0.00 3.01
138 139 0.735632 CCGAGAGCTGCACAGAAGTC 60.736 60.000 1.02 0.00 0.00 3.01
139 140 0.735632 CGAGAGCTGCACAGAAGTCC 60.736 60.000 1.02 0.00 0.00 3.85
140 141 0.319728 GAGAGCTGCACAGAAGTCCA 59.680 55.000 1.02 0.00 0.00 4.02
141 142 0.761187 AGAGCTGCACAGAAGTCCAA 59.239 50.000 1.02 0.00 0.00 3.53
142 143 1.141657 AGAGCTGCACAGAAGTCCAAA 59.858 47.619 1.02 0.00 0.00 3.28
143 144 2.157738 GAGCTGCACAGAAGTCCAAAT 58.842 47.619 1.02 0.00 0.00 2.32
144 145 1.884579 AGCTGCACAGAAGTCCAAATG 59.115 47.619 1.02 0.00 0.00 2.32
145 146 1.610522 GCTGCACAGAAGTCCAAATGT 59.389 47.619 0.81 0.00 0.00 2.71
146 147 2.035066 GCTGCACAGAAGTCCAAATGTT 59.965 45.455 0.81 0.00 0.00 2.71
147 148 3.491447 GCTGCACAGAAGTCCAAATGTTT 60.491 43.478 0.81 0.00 0.00 2.83
148 149 4.685924 CTGCACAGAAGTCCAAATGTTTT 58.314 39.130 0.00 0.00 0.00 2.43
149 150 5.735922 GCTGCACAGAAGTCCAAATGTTTTA 60.736 40.000 0.81 0.00 0.00 1.52
150 151 6.214191 TGCACAGAAGTCCAAATGTTTTAA 57.786 33.333 0.00 0.00 0.00 1.52
151 152 6.634805 TGCACAGAAGTCCAAATGTTTTAAA 58.365 32.000 0.00 0.00 0.00 1.52
152 153 7.099764 TGCACAGAAGTCCAAATGTTTTAAAA 58.900 30.769 0.00 0.00 0.00 1.52
153 154 7.604164 TGCACAGAAGTCCAAATGTTTTAAAAA 59.396 29.630 1.31 0.00 0.00 1.94
154 155 8.611757 GCACAGAAGTCCAAATGTTTTAAAAAT 58.388 29.630 1.31 0.00 0.00 1.82
157 158 9.934190 CAGAAGTCCAAATGTTTTAAAAATTGG 57.066 29.630 23.03 23.03 38.88 3.16
158 159 9.898152 AGAAGTCCAAATGTTTTAAAAATTGGA 57.102 25.926 25.41 25.41 42.84 3.53
160 161 8.153479 AGTCCAAATGTTTTAAAAATTGGAGC 57.847 30.769 27.64 23.28 44.92 4.70
161 162 7.042119 AGTCCAAATGTTTTAAAAATTGGAGCG 60.042 33.333 27.64 12.75 44.92 5.03
162 163 6.763610 TCCAAATGTTTTAAAAATTGGAGCGT 59.236 30.769 25.41 5.95 40.87 5.07
163 164 7.926555 TCCAAATGTTTTAAAAATTGGAGCGTA 59.073 29.630 25.41 13.21 40.87 4.42
164 165 8.220434 CCAAATGTTTTAAAAATTGGAGCGTAG 58.780 33.333 23.90 6.76 39.69 3.51
180 181 2.697363 CGTAGCTCACGCATCAAATTG 58.303 47.619 0.00 0.00 45.03 2.32
181 182 2.094258 CGTAGCTCACGCATCAAATTGT 59.906 45.455 0.00 0.00 45.03 2.71
182 183 2.907910 AGCTCACGCATCAAATTGTC 57.092 45.000 0.00 0.00 39.10 3.18
183 184 2.430465 AGCTCACGCATCAAATTGTCT 58.570 42.857 0.00 0.00 39.10 3.41
184 185 3.599343 AGCTCACGCATCAAATTGTCTA 58.401 40.909 0.00 0.00 39.10 2.59
185 186 3.372206 AGCTCACGCATCAAATTGTCTAC 59.628 43.478 0.00 0.00 39.10 2.59
186 187 3.485877 GCTCACGCATCAAATTGTCTACC 60.486 47.826 0.00 0.00 35.78 3.18
187 188 3.669536 TCACGCATCAAATTGTCTACCA 58.330 40.909 0.00 0.00 0.00 3.25
188 189 3.435327 TCACGCATCAAATTGTCTACCAC 59.565 43.478 0.00 0.00 0.00 4.16
189 190 2.747446 ACGCATCAAATTGTCTACCACC 59.253 45.455 0.00 0.00 0.00 4.61
190 191 2.097466 CGCATCAAATTGTCTACCACCC 59.903 50.000 0.00 0.00 0.00 4.61
191 192 3.088532 GCATCAAATTGTCTACCACCCA 58.911 45.455 0.00 0.00 0.00 4.51
192 193 3.509575 GCATCAAATTGTCTACCACCCAA 59.490 43.478 0.00 0.00 0.00 4.12
193 194 4.021544 GCATCAAATTGTCTACCACCCAAA 60.022 41.667 0.00 0.00 0.00 3.28
194 195 5.337491 GCATCAAATTGTCTACCACCCAAAT 60.337 40.000 0.00 0.00 0.00 2.32
195 196 6.127479 GCATCAAATTGTCTACCACCCAAATA 60.127 38.462 0.00 0.00 0.00 1.40
196 197 7.417797 GCATCAAATTGTCTACCACCCAAATAT 60.418 37.037 0.00 0.00 0.00 1.28
197 198 8.477256 CATCAAATTGTCTACCACCCAAATATT 58.523 33.333 0.00 0.00 0.00 1.28
198 199 8.429237 TCAAATTGTCTACCACCCAAATATTT 57.571 30.769 0.00 0.00 0.00 1.40
199 200 8.875168 TCAAATTGTCTACCACCCAAATATTTT 58.125 29.630 0.00 0.00 0.00 1.82
200 201 9.500785 CAAATTGTCTACCACCCAAATATTTTT 57.499 29.630 0.00 0.00 0.00 1.94
256 257 3.849064 TTTTTGACCGGGTGCAGG 58.151 55.556 3.30 0.00 0.00 4.85
257 258 1.076632 TTTTTGACCGGGTGCAGGT 60.077 52.632 3.30 0.00 46.16 4.00
258 259 1.388065 TTTTTGACCGGGTGCAGGTG 61.388 55.000 3.30 0.00 43.01 4.00
259 260 4.947147 TTGACCGGGTGCAGGTGC 62.947 66.667 3.30 0.00 43.01 5.01
282 283 4.379143 GGCACCGAAACGCCGTTC 62.379 66.667 1.60 0.00 38.82 3.95
283 284 3.343421 GCACCGAAACGCCGTTCT 61.343 61.111 1.60 0.00 0.00 3.01
409 410 7.566760 ACGATTAACAATTTCATGGCTATCA 57.433 32.000 0.00 0.00 0.00 2.15
427 428 6.371548 GGCTATCATGTGTAAGAAACAGACAA 59.628 38.462 0.00 0.00 39.29 3.18
481 482 0.606401 CCTGTTGGCCGAGTGATGTT 60.606 55.000 0.00 0.00 0.00 2.71
628 629 6.474140 TCTTCTACAAGGTTGTTGTCTGTA 57.526 37.500 0.00 0.00 42.35 2.74
661 662 1.234821 GATCAACTTTGCGGTGTCCA 58.765 50.000 0.00 0.00 0.00 4.02
664 665 0.248458 CAACTTTGCGGTGTCCACAC 60.248 55.000 0.85 0.85 45.72 3.82
732 733 3.542712 AGCACACTTAAGAAACATGCG 57.457 42.857 10.09 0.00 36.71 4.73
734 735 2.233355 CACACTTAAGAAACATGCGCG 58.767 47.619 10.09 0.00 0.00 6.86
834 835 4.124238 GCAGCATGGCATTCATAATGTTT 58.876 39.130 0.00 0.00 37.67 2.83
953 954 5.091261 TGTACAAACAGGCAAAACCATTT 57.909 34.783 0.00 0.00 43.14 2.32
975 976 2.159156 CCTGTTTGGATGATGCACATGG 60.159 50.000 6.52 0.00 39.56 3.66
1055 1059 2.485426 CGGTGCACTTCAACAAGATCAT 59.515 45.455 17.98 0.00 33.34 2.45
1102 1106 1.336887 GGCACTTCGACAAGAGCACTA 60.337 52.381 8.48 0.00 45.33 2.74
1241 1246 1.053264 CCCAGCCTGACTATGCCTCT 61.053 60.000 0.00 0.00 0.00 3.69
1275 1280 4.041691 TCTTTCGATTTGTCTCTCCCCTTT 59.958 41.667 0.00 0.00 0.00 3.11
1276 1281 4.367039 TTCGATTTGTCTCTCCCCTTTT 57.633 40.909 0.00 0.00 0.00 2.27
1277 1282 3.674997 TCGATTTGTCTCTCCCCTTTTG 58.325 45.455 0.00 0.00 0.00 2.44
1278 1283 2.749621 CGATTTGTCTCTCCCCTTTTGG 59.250 50.000 0.00 0.00 39.97 3.28
1279 1284 3.767711 GATTTGTCTCTCCCCTTTTGGT 58.232 45.455 0.00 0.00 38.10 3.67
1280 1285 3.680777 TTTGTCTCTCCCCTTTTGGTT 57.319 42.857 0.00 0.00 38.10 3.67
1283 1288 1.071857 GTCTCTCCCCTTTTGGTTCGT 59.928 52.381 0.00 0.00 38.10 3.85
1328 1334 2.022129 CCGTGTTCGTGTCTCCTGC 61.022 63.158 0.00 0.00 35.01 4.85
1342 1348 0.613572 TCCTGCCCTGACGTATGTGA 60.614 55.000 0.00 0.00 0.00 3.58
1423 1444 0.608130 AATAGTCTGTGTGGCGCTCA 59.392 50.000 7.64 4.33 0.00 4.26
1495 1516 6.830838 ACTTCTGTCATTTTCTTTGGTCTCTT 59.169 34.615 0.00 0.00 0.00 2.85
1835 1861 4.943705 GGTGTGACATGATTGGTAACTGAT 59.056 41.667 0.00 0.00 37.61 2.90
1960 1988 4.466827 ACAGTTATTTTGAAACGGAGGGT 58.533 39.130 0.00 0.00 32.00 4.34
1967 1995 8.680001 GTTATTTTGAAACGGAGGGTGTATTAT 58.320 33.333 0.00 0.00 0.00 1.28
2056 2084 4.419522 AGCTTGCCGTTGTTACAAATAG 57.580 40.909 0.00 0.00 0.00 1.73
2212 2255 7.707624 ATTCTAAACATGTTCCATGTGACAT 57.292 32.000 12.39 0.00 36.97 3.06
2222 2265 8.785946 CATGTTCCATGTGACATAAATAGCATA 58.214 33.333 0.00 0.00 34.88 3.14
2329 2373 3.214328 GCTTGGAACTCTCCTTGTGAAA 58.786 45.455 0.00 0.00 42.94 2.69
2382 2426 8.947115 GCCTCTTTAGTTGTAATTGTGATACTT 58.053 33.333 0.00 0.00 0.00 2.24
2414 2460 5.701290 GCAAGTAAACACTCCTGTGATACTT 59.299 40.000 17.32 17.32 46.97 2.24
2447 2493 9.268268 CTAAAATGTTGGTTGTTAGTACAGAGA 57.732 33.333 0.00 0.00 35.28 3.10
2650 2696 5.163237 ACCGATTAATTGGGCATAGTACTGT 60.163 40.000 23.25 0.00 35.53 3.55
2764 2810 4.623647 GCAATGACCATGTGCCCTATTTTT 60.624 41.667 0.00 0.00 31.94 1.94
2777 2823 4.320494 GCCCTATTTTTACATCATCGGCTG 60.320 45.833 0.00 0.00 0.00 4.85
2879 5400 5.036117 TGGAGATGCTTTAATACCAGGAC 57.964 43.478 0.00 0.00 0.00 3.85
2914 5435 3.682292 CTACCTTGAGCCCCCACGC 62.682 68.421 0.00 0.00 0.00 5.34
2953 5475 6.608002 ACCTGAGACTGTTAGGACTAATAAGG 59.392 42.308 11.91 0.00 35.55 2.69
3013 5536 0.179018 GTGGCAACTGTTGAGAGGGT 60.179 55.000 23.81 0.00 37.61 4.34
3109 5632 1.690633 CTTGGCAGCCTCCCTCCTA 60.691 63.158 14.15 0.00 0.00 2.94
3113 5636 0.109532 GGCAGCCTCCCTCCTATTTC 59.890 60.000 3.29 0.00 0.00 2.17
3116 5640 0.031010 AGCCTCCCTCCTATTTCGGT 60.031 55.000 0.00 0.00 0.00 4.69
3128 5666 7.417612 CCTCCTATTTCGGTGATGTTTAATTG 58.582 38.462 0.00 0.00 0.00 2.32
3135 5673 6.862711 TCGGTGATGTTTAATTGTGTGTAA 57.137 33.333 0.00 0.00 0.00 2.41
3150 5688 7.979115 TTGTGTGTAATTCAAACTGTTTAGC 57.021 32.000 5.31 0.00 35.43 3.09
3166 5705 7.430441 ACTGTTTAGCGTGTATTTTGGATTTT 58.570 30.769 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.508200 AGTGTTTTGAAAATTGGAGCGTA 57.492 34.783 0.00 0.00 0.00 4.42
1 2 4.385358 AGTGTTTTGAAAATTGGAGCGT 57.615 36.364 0.00 0.00 0.00 5.07
2 3 4.025813 CCAAGTGTTTTGAAAATTGGAGCG 60.026 41.667 13.56 0.00 39.63 5.03
3 4 5.006649 GTCCAAGTGTTTTGAAAATTGGAGC 59.993 40.000 19.15 12.74 44.96 4.70
4 5 6.340522 AGTCCAAGTGTTTTGAAAATTGGAG 58.659 36.000 19.15 1.41 44.96 3.86
5 6 6.293004 AGTCCAAGTGTTTTGAAAATTGGA 57.707 33.333 16.22 16.22 42.84 3.53
6 7 6.818142 AGAAGTCCAAGTGTTTTGAAAATTGG 59.182 34.615 12.90 12.90 38.81 3.16
7 8 7.331687 ACAGAAGTCCAAGTGTTTTGAAAATTG 59.668 33.333 0.00 0.00 0.00 2.32
8 9 7.331687 CACAGAAGTCCAAGTGTTTTGAAAATT 59.668 33.333 0.00 0.00 0.00 1.82
9 10 6.813152 CACAGAAGTCCAAGTGTTTTGAAAAT 59.187 34.615 0.00 0.00 0.00 1.82
10 11 6.155827 CACAGAAGTCCAAGTGTTTTGAAAA 58.844 36.000 0.00 0.00 0.00 2.29
11 12 5.708948 CACAGAAGTCCAAGTGTTTTGAAA 58.291 37.500 0.00 0.00 0.00 2.69
12 13 4.380444 GCACAGAAGTCCAAGTGTTTTGAA 60.380 41.667 0.00 0.00 34.59 2.69
13 14 3.128589 GCACAGAAGTCCAAGTGTTTTGA 59.871 43.478 0.00 0.00 34.59 2.69
14 15 3.119531 TGCACAGAAGTCCAAGTGTTTTG 60.120 43.478 0.00 0.00 34.59 2.44
15 16 3.088532 TGCACAGAAGTCCAAGTGTTTT 58.911 40.909 0.00 0.00 34.59 2.43
16 17 2.684881 CTGCACAGAAGTCCAAGTGTTT 59.315 45.455 0.00 0.00 34.59 2.83
17 18 2.292267 CTGCACAGAAGTCCAAGTGTT 58.708 47.619 0.00 0.00 34.59 3.32
18 19 1.959042 CTGCACAGAAGTCCAAGTGT 58.041 50.000 0.00 0.00 34.59 3.55
19 20 0.590195 GCTGCACAGAAGTCCAAGTG 59.410 55.000 0.81 0.00 35.19 3.16
20 21 0.471617 AGCTGCACAGAAGTCCAAGT 59.528 50.000 1.02 0.00 0.00 3.16
21 22 1.155042 GAGCTGCACAGAAGTCCAAG 58.845 55.000 1.02 0.00 0.00 3.61
22 23 0.761187 AGAGCTGCACAGAAGTCCAA 59.239 50.000 1.02 0.00 0.00 3.53
23 24 0.319728 GAGAGCTGCACAGAAGTCCA 59.680 55.000 1.02 0.00 0.00 4.02
24 25 0.319728 TGAGAGCTGCACAGAAGTCC 59.680 55.000 1.02 0.00 0.00 3.85
25 26 1.712401 CTGAGAGCTGCACAGAAGTC 58.288 55.000 13.36 0.00 37.38 3.01
26 27 0.320596 GCTGAGAGCTGCACAGAAGT 60.321 55.000 19.67 0.00 38.45 3.01
27 28 0.320508 TGCTGAGAGCTGCACAGAAG 60.321 55.000 19.67 7.28 42.93 2.85
28 29 0.107268 TTGCTGAGAGCTGCACAGAA 59.893 50.000 19.67 10.58 46.64 3.02
29 30 0.107268 TTTGCTGAGAGCTGCACAGA 59.893 50.000 19.67 7.28 46.64 3.41
30 31 0.949397 TTTTGCTGAGAGCTGCACAG 59.051 50.000 1.02 9.52 46.64 3.66
31 32 1.391577 TTTTTGCTGAGAGCTGCACA 58.608 45.000 1.02 0.00 46.64 4.57
47 48 4.461198 ACAGACCTCCGATTTGTCTTTTT 58.539 39.130 0.00 0.00 37.25 1.94
48 49 4.086706 ACAGACCTCCGATTTGTCTTTT 57.913 40.909 0.00 0.00 37.25 2.27
49 50 3.771577 ACAGACCTCCGATTTGTCTTT 57.228 42.857 0.00 0.00 37.25 2.52
50 51 4.884668 TTACAGACCTCCGATTTGTCTT 57.115 40.909 0.00 0.00 37.25 3.01
51 52 4.884668 TTTACAGACCTCCGATTTGTCT 57.115 40.909 0.00 0.00 39.86 3.41
52 53 5.934935 TTTTTACAGACCTCCGATTTGTC 57.065 39.130 0.00 0.00 0.00 3.18
53 54 7.610305 ACATATTTTTACAGACCTCCGATTTGT 59.390 33.333 0.00 0.00 0.00 2.83
54 55 7.985476 ACATATTTTTACAGACCTCCGATTTG 58.015 34.615 0.00 0.00 0.00 2.32
55 56 9.106070 GTACATATTTTTACAGACCTCCGATTT 57.894 33.333 0.00 0.00 0.00 2.17
56 57 8.483758 AGTACATATTTTTACAGACCTCCGATT 58.516 33.333 0.00 0.00 0.00 3.34
57 58 7.926555 CAGTACATATTTTTACAGACCTCCGAT 59.073 37.037 0.00 0.00 0.00 4.18
58 59 7.093640 ACAGTACATATTTTTACAGACCTCCGA 60.094 37.037 0.00 0.00 0.00 4.55
59 60 7.039882 ACAGTACATATTTTTACAGACCTCCG 58.960 38.462 0.00 0.00 0.00 4.63
60 61 8.788325 AACAGTACATATTTTTACAGACCTCC 57.212 34.615 0.00 0.00 0.00 4.30
61 62 9.431887 TGAACAGTACATATTTTTACAGACCTC 57.568 33.333 0.00 0.00 0.00 3.85
62 63 9.959721 ATGAACAGTACATATTTTTACAGACCT 57.040 29.630 0.00 0.00 0.00 3.85
75 76 9.197306 ACCAGAACAGTATATGAACAGTACATA 57.803 33.333 0.00 0.00 35.23 2.29
76 77 8.079211 ACCAGAACAGTATATGAACAGTACAT 57.921 34.615 0.00 0.00 0.00 2.29
77 78 7.396339 AGACCAGAACAGTATATGAACAGTACA 59.604 37.037 0.00 0.00 0.00 2.90
78 79 7.702772 CAGACCAGAACAGTATATGAACAGTAC 59.297 40.741 0.00 0.00 0.00 2.73
79 80 7.614192 TCAGACCAGAACAGTATATGAACAGTA 59.386 37.037 0.00 0.00 0.00 2.74
80 81 6.437477 TCAGACCAGAACAGTATATGAACAGT 59.563 38.462 0.00 0.00 0.00 3.55
81 82 6.867550 TCAGACCAGAACAGTATATGAACAG 58.132 40.000 0.00 0.00 0.00 3.16
82 83 6.850752 TCAGACCAGAACAGTATATGAACA 57.149 37.500 0.00 0.00 0.00 3.18
83 84 8.607459 CAAATCAGACCAGAACAGTATATGAAC 58.393 37.037 0.00 0.00 0.00 3.18
84 85 8.321353 ACAAATCAGACCAGAACAGTATATGAA 58.679 33.333 0.00 0.00 0.00 2.57
85 86 7.851228 ACAAATCAGACCAGAACAGTATATGA 58.149 34.615 0.00 0.00 0.00 2.15
86 87 7.984050 AGACAAATCAGACCAGAACAGTATATG 59.016 37.037 0.00 0.00 0.00 1.78
87 88 8.083828 AGACAAATCAGACCAGAACAGTATAT 57.916 34.615 0.00 0.00 0.00 0.86
88 89 7.482169 AGACAAATCAGACCAGAACAGTATA 57.518 36.000 0.00 0.00 0.00 1.47
89 90 6.365970 AGACAAATCAGACCAGAACAGTAT 57.634 37.500 0.00 0.00 0.00 2.12
90 91 5.808366 AGACAAATCAGACCAGAACAGTA 57.192 39.130 0.00 0.00 0.00 2.74
91 92 4.696479 AGACAAATCAGACCAGAACAGT 57.304 40.909 0.00 0.00 0.00 3.55
92 93 6.382869 AAAAGACAAATCAGACCAGAACAG 57.617 37.500 0.00 0.00 0.00 3.16
93 94 6.773976 AAAAAGACAAATCAGACCAGAACA 57.226 33.333 0.00 0.00 0.00 3.18
113 114 1.100463 TGTGCAGCTCTCGGCAAAAA 61.100 50.000 0.00 0.00 44.54 1.94
114 115 1.509644 CTGTGCAGCTCTCGGCAAAA 61.510 55.000 0.00 0.00 44.54 2.44
115 116 1.962822 CTGTGCAGCTCTCGGCAAA 60.963 57.895 0.00 0.00 44.54 3.68
116 117 2.357881 CTGTGCAGCTCTCGGCAA 60.358 61.111 0.00 0.00 44.54 4.52
117 118 2.776670 CTTCTGTGCAGCTCTCGGCA 62.777 60.000 0.00 0.00 44.79 5.69
118 119 2.047844 TTCTGTGCAGCTCTCGGC 60.048 61.111 0.00 0.00 42.19 5.54
119 120 0.735632 GACTTCTGTGCAGCTCTCGG 60.736 60.000 0.00 0.00 0.00 4.63
120 121 0.735632 GGACTTCTGTGCAGCTCTCG 60.736 60.000 0.00 0.00 34.50 4.04
121 122 0.319728 TGGACTTCTGTGCAGCTCTC 59.680 55.000 0.00 0.00 39.59 3.20
122 123 0.761187 TTGGACTTCTGTGCAGCTCT 59.239 50.000 0.00 0.00 44.96 4.09
123 124 1.597742 TTTGGACTTCTGTGCAGCTC 58.402 50.000 0.00 0.00 44.96 4.09
124 125 1.884579 CATTTGGACTTCTGTGCAGCT 59.115 47.619 0.00 0.00 44.96 4.24
125 126 1.610522 ACATTTGGACTTCTGTGCAGC 59.389 47.619 0.00 0.00 44.96 5.25
126 127 3.996150 AACATTTGGACTTCTGTGCAG 57.004 42.857 0.00 0.00 44.96 4.41
127 128 4.734398 AAAACATTTGGACTTCTGTGCA 57.266 36.364 0.00 0.00 42.73 4.57
128 129 7.532682 TTTTAAAACATTTGGACTTCTGTGC 57.467 32.000 0.00 0.00 34.96 4.57
131 132 9.934190 CCAATTTTTAAAACATTTGGACTTCTG 57.066 29.630 21.26 5.42 36.55 3.02
132 133 9.898152 TCCAATTTTTAAAACATTTGGACTTCT 57.102 25.926 22.95 0.00 38.10 2.85
134 135 8.620416 GCTCCAATTTTTAAAACATTTGGACTT 58.380 29.630 22.95 0.00 38.10 3.01
135 136 7.042119 CGCTCCAATTTTTAAAACATTTGGACT 60.042 33.333 22.95 0.00 38.10 3.85
136 137 7.068955 CGCTCCAATTTTTAAAACATTTGGAC 58.931 34.615 22.95 19.49 38.10 4.02
137 138 6.763610 ACGCTCCAATTTTTAAAACATTTGGA 59.236 30.769 24.10 24.10 40.08 3.53
138 139 6.953843 ACGCTCCAATTTTTAAAACATTTGG 58.046 32.000 20.46 20.46 35.93 3.28
139 140 7.739911 GCTACGCTCCAATTTTTAAAACATTTG 59.260 33.333 0.00 5.50 0.00 2.32
140 141 7.655732 AGCTACGCTCCAATTTTTAAAACATTT 59.344 29.630 0.00 0.00 30.62 2.32
141 142 7.151976 AGCTACGCTCCAATTTTTAAAACATT 58.848 30.769 0.00 1.97 30.62 2.71
142 143 6.687604 AGCTACGCTCCAATTTTTAAAACAT 58.312 32.000 0.00 0.00 30.62 2.71
143 144 6.079424 AGCTACGCTCCAATTTTTAAAACA 57.921 33.333 0.00 0.00 30.62 2.83
165 166 3.684305 TGGTAGACAATTTGATGCGTGAG 59.316 43.478 2.79 0.00 0.00 3.51
166 167 3.435327 GTGGTAGACAATTTGATGCGTGA 59.565 43.478 2.79 0.00 0.00 4.35
167 168 3.426159 GGTGGTAGACAATTTGATGCGTG 60.426 47.826 2.79 0.00 0.00 5.34
168 169 2.747446 GGTGGTAGACAATTTGATGCGT 59.253 45.455 2.79 0.00 0.00 5.24
169 170 2.097466 GGGTGGTAGACAATTTGATGCG 59.903 50.000 2.79 0.00 0.00 4.73
170 171 3.088532 TGGGTGGTAGACAATTTGATGC 58.911 45.455 2.79 0.00 0.00 3.91
171 172 5.720371 TTTGGGTGGTAGACAATTTGATG 57.280 39.130 2.79 0.00 0.00 3.07
172 173 8.608185 AATATTTGGGTGGTAGACAATTTGAT 57.392 30.769 2.79 0.00 0.00 2.57
173 174 8.429237 AAATATTTGGGTGGTAGACAATTTGA 57.571 30.769 2.79 0.00 0.00 2.69
174 175 9.500785 AAAAATATTTGGGTGGTAGACAATTTG 57.499 29.630 0.39 0.00 0.00 2.32
239 240 1.076632 ACCTGCACCCGGTCAAAAA 60.077 52.632 0.00 0.00 0.00 1.94
240 241 1.826054 CACCTGCACCCGGTCAAAA 60.826 57.895 0.00 0.00 30.82 2.44
241 242 2.203280 CACCTGCACCCGGTCAAA 60.203 61.111 0.00 0.00 30.82 2.69
242 243 4.947147 GCACCTGCACCCGGTCAA 62.947 66.667 0.00 0.00 41.59 3.18
266 267 3.291167 GAGAACGGCGTTTCGGTGC 62.291 63.158 27.48 12.66 0.00 5.01
267 268 1.219522 AAGAGAACGGCGTTTCGGTG 61.220 55.000 27.48 0.00 0.00 4.94
268 269 0.531311 AAAGAGAACGGCGTTTCGGT 60.531 50.000 27.48 11.90 0.00 4.69
269 270 0.584876 AAAAGAGAACGGCGTTTCGG 59.415 50.000 27.48 0.00 0.00 4.30
270 271 2.378507 AAAAAGAGAACGGCGTTTCG 57.621 45.000 27.48 0.00 0.00 3.46
271 272 4.199840 TGTAAAAAGAGAACGGCGTTTC 57.800 40.909 27.48 22.85 0.00 2.78
272 273 4.823790 ATGTAAAAAGAGAACGGCGTTT 57.176 36.364 27.48 16.17 0.00 3.60
273 274 4.533222 CAATGTAAAAAGAGAACGGCGTT 58.467 39.130 27.15 27.15 0.00 4.84
274 275 3.608474 GCAATGTAAAAAGAGAACGGCGT 60.608 43.478 6.77 6.77 0.00 5.68
275 276 2.908626 GCAATGTAAAAAGAGAACGGCG 59.091 45.455 4.80 4.80 0.00 6.46
276 277 4.160736 AGCAATGTAAAAAGAGAACGGC 57.839 40.909 0.00 0.00 0.00 5.68
277 278 8.742554 AAATAAGCAATGTAAAAAGAGAACGG 57.257 30.769 0.00 0.00 0.00 4.44
409 410 5.220777 CCAACGTTGTCTGTTTCTTACACAT 60.221 40.000 25.63 0.00 32.10 3.21
481 482 7.112122 ACAATAAGCATCTTCACAATAGGACA 58.888 34.615 0.00 0.00 0.00 4.02
628 629 7.657761 CGCAAAGTTGATCCTATCCTAATAGTT 59.342 37.037 0.00 0.00 34.20 2.24
661 662 0.393077 AGCTTGACTTGTAGCGGTGT 59.607 50.000 0.00 0.00 42.18 4.16
664 665 4.933330 TCTATTAGCTTGACTTGTAGCGG 58.067 43.478 0.00 0.00 42.18 5.52
732 733 3.555168 CCATAGGATCTAAAGACACCCGC 60.555 52.174 0.00 0.00 0.00 6.13
734 735 4.262678 GCTCCATAGGATCTAAAGACACCC 60.263 50.000 0.00 0.00 0.00 4.61
787 788 5.341872 TTTGTAATGGCAATGATCCAAGG 57.658 39.130 0.00 0.00 37.13 3.61
975 976 7.194962 TCACCGAAAACTAACAAAAACATACC 58.805 34.615 0.00 0.00 0.00 2.73
1045 1049 0.322816 AGCCGCACCATGATCTTGTT 60.323 50.000 7.73 0.00 0.00 2.83
1055 1059 0.884704 GAGTTTCTTGAGCCGCACCA 60.885 55.000 0.00 0.00 0.00 4.17
1328 1334 1.272490 ACACACTCACATACGTCAGGG 59.728 52.381 0.00 0.00 0.00 4.45
1342 1348 1.959042 CTGCAGAAGAACCACACACT 58.041 50.000 8.42 0.00 0.00 3.55
1495 1516 8.774546 TCAGCCCATATCACCATTTATTTTTA 57.225 30.769 0.00 0.00 0.00 1.52
1871 1897 8.887264 TTTTAGACCATGGTACCACATAAATT 57.113 30.769 19.80 0.00 0.00 1.82
1935 1963 5.240844 CCCTCCGTTTCAAAATAACTGTCTT 59.759 40.000 0.00 0.00 0.00 3.01
2005 2033 5.125100 TGCAAAATGATCACTCTGAAACC 57.875 39.130 0.00 0.00 0.00 3.27
2056 2084 5.066505 AGTGAATTGAGGACAACAGAACAAC 59.933 40.000 0.00 0.00 38.90 3.32
2270 2314 0.173029 AGCTCTGCACATGACTCTCG 59.827 55.000 0.00 0.00 0.00 4.04
2274 2318 0.249676 CTCCAGCTCTGCACATGACT 59.750 55.000 0.00 0.00 0.00 3.41
2329 2373 1.123861 TCACTGCTGTCCTTGAGCCT 61.124 55.000 0.00 0.00 35.43 4.58
2382 2426 4.065088 GGAGTGTTTACTTGCACATCAGA 58.935 43.478 0.00 0.00 37.25 3.27
2414 2460 5.590530 ACAACCAACATTTTAGCACAAGA 57.409 34.783 0.00 0.00 0.00 3.02
2447 2493 6.153340 CCAAGAGAACCAAATAATGTCACCAT 59.847 38.462 0.00 0.00 0.00 3.55
2595 2641 0.032678 CTAGATGACCCGATTGCGCT 59.967 55.000 9.73 0.00 35.83 5.92
2602 2648 4.164796 TGTTAGGTAGACTAGATGACCCGA 59.835 45.833 0.00 0.00 32.16 5.14
2650 2696 6.813649 ACACTACGAAAGTACTACGATAGACA 59.186 38.462 22.78 5.83 46.88 3.41
2764 2810 0.179076 CTGCCACAGCCGATGATGTA 60.179 55.000 0.00 0.00 39.58 2.29
2914 5435 1.662629 CTCAGGTTCGCTACTTGCATG 59.337 52.381 0.00 0.00 43.06 4.06
2915 5436 1.550524 TCTCAGGTTCGCTACTTGCAT 59.449 47.619 0.00 0.00 43.06 3.96
2931 5452 8.660295 TTTCCTTATTAGTCCTAACAGTCTCA 57.340 34.615 0.00 0.00 0.00 3.27
3109 5632 6.744112 ACACACAATTAAACATCACCGAAAT 58.256 32.000 0.00 0.00 0.00 2.17
3113 5636 7.805542 TGAATTACACACAATTAAACATCACCG 59.194 33.333 0.00 0.00 0.00 4.94
3128 5666 6.140108 CACGCTAAACAGTTTGAATTACACAC 59.860 38.462 8.93 0.00 0.00 3.82
3135 5673 7.381139 CCAAAATACACGCTAAACAGTTTGAAT 59.619 33.333 8.93 0.00 0.00 2.57
3144 5682 8.856247 CCTTAAAATCCAAAATACACGCTAAAC 58.144 33.333 0.00 0.00 0.00 2.01
3150 5688 8.804688 TTGAACCTTAAAATCCAAAATACACG 57.195 30.769 0.00 0.00 0.00 4.49


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

AutoCloner maintained by Alex Coulton.