Multiple sequence alignment - TraesCS3D01G420700

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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 TraesCS3D01G420700 chr3D 100.000 3195 0 0 1 3195 532954970 532958164 0.000000e+00 5901.0
1 TraesCS3D01G420700 chr3D 87.958 1445 132 24 1678 3097 533380012 533381439 0.000000e+00 1666.0
2 TraesCS3D01G420700 chr3D 87.708 1440 134 30 1678 3097 533338575 533339991 0.000000e+00 1639.0
3 TraesCS3D01G420700 chr3D 87.965 1371 125 19 1744 3097 533398119 533399466 0.000000e+00 1581.0
4 TraesCS3D01G420700 chr3D 79.769 519 88 13 1699 2211 533674607 533675114 8.430000e-96 361.0
5 TraesCS3D01G420700 chr3D 78.125 512 92 13 1699 2204 533670034 533670531 1.110000e-79 307.0
6 TraesCS3D01G420700 chr3D 87.027 185 23 1 2914 3097 533402345 533402529 1.160000e-49 207.0
7 TraesCS3D01G420700 chr3D 74.537 432 87 19 992 1412 533676743 533677162 1.970000e-37 167.0
8 TraesCS3D01G420700 chr3D 97.500 80 2 0 495 574 532955394 532955473 1.550000e-28 137.0
9 TraesCS3D01G420700 chr3D 97.500 80 2 0 425 504 532955464 532955543 1.550000e-28 137.0
10 TraesCS3D01G420700 chr3D 100.000 29 0 0 3167 3195 532975865 532975893 2.000000e-03 54.7
11 TraesCS3D01G420700 chr3D 100.000 29 0 0 3167 3195 533384331 533384359 2.000000e-03 54.7
12 TraesCS3D01G420700 chr3D 100.000 29 0 0 3167 3195 533387326 533387354 2.000000e-03 54.7
13 TraesCS3D01G420700 chr3D 100.000 29 0 0 3167 3195 533400786 533400814 2.000000e-03 54.7
14 TraesCS3D01G420700 chr3B 90.760 2630 163 28 519 3116 705153283 705155864 0.000000e+00 3437.0
15 TraesCS3D01G420700 chr3B 79.623 530 75 18 1924 2440 705454570 705455079 1.820000e-92 350.0
16 TraesCS3D01G420700 chr3B 75.929 565 102 28 861 1406 705546821 705547370 3.160000e-65 259.0
17 TraesCS3D01G420700 chr3B 75.971 412 64 21 1446 1834 705454134 705454533 2.530000e-41 180.0
18 TraesCS3D01G420700 chr3B 94.030 67 2 2 245 311 705153111 705153175 2.030000e-17 100.0
19 TraesCS3D01G420700 chr3A 93.599 1531 93 3 1668 3195 669046188 669047716 0.000000e+00 2279.0
20 TraesCS3D01G420700 chr3A 95.826 1078 38 3 738 1809 668701850 668702926 0.000000e+00 1735.0
21 TraesCS3D01G420700 chr3A 87.620 1349 135 18 1765 3097 668878101 668879433 0.000000e+00 1537.0
22 TraesCS3D01G420700 chr3A 95.696 790 31 1 1668 2454 668857795 668858584 0.000000e+00 1267.0
23 TraesCS3D01G420700 chr3A 93.832 762 40 6 2436 3195 668703887 668704643 0.000000e+00 1140.0
24 TraesCS3D01G420700 chr3A 96.730 581 19 0 1852 2432 668702924 668703504 0.000000e+00 968.0
25 TraesCS3D01G420700 chr3A 92.656 640 39 2 2560 3195 668858591 668859226 0.000000e+00 915.0
26 TraesCS3D01G420700 chr3A 78.780 410 75 9 1003 1406 669524685 669525088 6.800000e-67 265.0
27 TraesCS3D01G420700 chr3A 77.833 406 57 20 1442 1827 669180881 669181273 1.490000e-53 220.0
28 TraesCS3D01G420700 chr3A 73.148 432 94 18 992 1412 669566549 669566969 5.560000e-28 135.0
29 TraesCS3D01G420700 chr3A 91.011 89 8 0 3009 3097 668706631 668706719 1.560000e-23 121.0
30 TraesCS3D01G420700 chr3A 100.000 29 0 0 3167 3195 668862413 668862441 2.000000e-03 54.7
31 TraesCS3D01G420700 chr6D 91.051 257 22 1 1 256 153862430 153862686 2.360000e-91 346.0
32 TraesCS3D01G420700 chr6D 89.961 259 23 3 1 257 219785072 219784815 6.610000e-87 331.0
33 TraesCS3D01G420700 chr7D 90.347 259 20 5 1 257 520336374 520336119 5.110000e-88 335.0
34 TraesCS3D01G420700 chrUn 89.961 259 24 2 1 258 108525931 108525674 1.840000e-87 333.0
35 TraesCS3D01G420700 chrUn 89.535 258 25 2 1 257 257248194 257247938 3.070000e-85 326.0
36 TraesCS3D01G420700 chrUn 89.535 258 25 2 1 257 364453888 364454144 3.070000e-85 326.0
37 TraesCS3D01G420700 chr5D 89.922 258 25 1 1 257 291919079 291919336 6.610000e-87 331.0
38 TraesCS3D01G420700 chr5D 89.883 257 23 3 1 256 4057905 4057651 8.550000e-86 327.0
39 TraesCS3D01G420700 chr2D 89.804 255 25 1 1 254 291845560 291845814 3.070000e-85 326.0
40 TraesCS3D01G420700 chr1A 89.189 74 8 0 3095 3168 161615685 161615612 3.390000e-15 93.5
41 TraesCS3D01G420700 chr7B 88.889 72 8 0 3095 3166 22661662 22661733 4.390000e-14 89.8
42 TraesCS3D01G420700 chr7B 86.842 76 9 1 3095 3170 22945782 22945856 2.040000e-12 84.2
43 TraesCS3D01G420700 chr1D 96.364 55 1 1 2464 2517 313564508 313564454 4.390000e-14 89.8
44 TraesCS3D01G420700 chr1B 88.889 72 8 0 3095 3166 319917654 319917725 4.390000e-14 89.8
45 TraesCS3D01G420700 chr6B 87.838 74 9 0 3094 3167 493338033 493337960 1.580000e-13 87.9
46 TraesCS3D01G420700 chr6A 87.671 73 9 0 3095 3167 604524069 604524141 5.680000e-13 86.1
47 TraesCS3D01G420700 chr6A 91.111 45 4 0 2739 2783 27079003 27078959 9.570000e-06 62.1
48 TraesCS3D01G420700 chr7A 94.444 54 3 0 2462 2515 204173373 204173426 2.040000e-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 TraesCS3D01G420700 chr3D 532954970 532958164 3194 False 2058.333333 5901 98.333333 1 3195 3 chr3D.!!$F4 3194
1 TraesCS3D01G420700 chr3D 533338575 533339991 1416 False 1639.000000 1639 87.708000 1678 3097 1 chr3D.!!$F2 1419
2 TraesCS3D01G420700 chr3D 533398119 533402529 4410 False 614.233333 1581 91.664000 1744 3195 3 chr3D.!!$F6 1451
3 TraesCS3D01G420700 chr3D 533380012 533387354 7342 False 591.800000 1666 95.986000 1678 3195 3 chr3D.!!$F5 1517
4 TraesCS3D01G420700 chr3D 533674607 533677162 2555 False 264.000000 361 77.153000 992 2211 2 chr3D.!!$F7 1219
5 TraesCS3D01G420700 chr3B 705153111 705155864 2753 False 1768.500000 3437 92.395000 245 3116 2 chr3B.!!$F2 2871
6 TraesCS3D01G420700 chr3B 705454134 705455079 945 False 265.000000 350 77.797000 1446 2440 2 chr3B.!!$F3 994
7 TraesCS3D01G420700 chr3B 705546821 705547370 549 False 259.000000 259 75.929000 861 1406 1 chr3B.!!$F1 545
8 TraesCS3D01G420700 chr3A 669046188 669047716 1528 False 2279.000000 2279 93.599000 1668 3195 1 chr3A.!!$F2 1527
9 TraesCS3D01G420700 chr3A 668878101 668879433 1332 False 1537.000000 1537 87.620000 1765 3097 1 chr3A.!!$F1 1332
10 TraesCS3D01G420700 chr3A 668701850 668706719 4869 False 991.000000 1735 94.349750 738 3195 4 chr3A.!!$F6 2457
11 TraesCS3D01G420700 chr3A 668857795 668862441 4646 False 745.566667 1267 96.117333 1668 3195 3 chr3A.!!$F7 1527

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
379 409 0.243907 TCAGTGGCTTCAGCGAGTAC 59.756 55.0 0.0 0.0 43.26 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2216 2344 0.107993 ATGTCGATGCTCCACCACAG 60.108 55.0 0.0 0.0 0.0 3.66 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
17 18 2.683933 AACCGAGGCGATGAGGGT 60.684 61.111 0.00 0.00 0.00 4.34
18 19 3.019003 AACCGAGGCGATGAGGGTG 62.019 63.158 0.00 0.00 0.00 4.61
19 20 3.147595 CCGAGGCGATGAGGGTGA 61.148 66.667 0.00 0.00 0.00 4.02
20 21 2.105128 CGAGGCGATGAGGGTGAC 59.895 66.667 0.00 0.00 0.00 3.67
21 22 2.105128 GAGGCGATGAGGGTGACG 59.895 66.667 0.00 0.00 0.00 4.35
22 23 2.362503 AGGCGATGAGGGTGACGA 60.363 61.111 0.00 0.00 0.00 4.20
23 24 1.945354 GAGGCGATGAGGGTGACGAA 61.945 60.000 0.00 0.00 0.00 3.85
24 25 1.519455 GGCGATGAGGGTGACGAAG 60.519 63.158 0.00 0.00 0.00 3.79
25 26 2.167861 GCGATGAGGGTGACGAAGC 61.168 63.158 0.00 0.00 0.00 3.86
26 27 1.874019 CGATGAGGGTGACGAAGCG 60.874 63.158 0.00 0.00 0.00 4.68
27 28 1.519455 GATGAGGGTGACGAAGCGG 60.519 63.158 0.00 0.00 0.00 5.52
28 29 2.227089 GATGAGGGTGACGAAGCGGT 62.227 60.000 0.00 0.00 0.00 5.68
29 30 2.432628 GAGGGTGACGAAGCGGTG 60.433 66.667 0.00 0.00 0.00 4.94
30 31 3.222354 GAGGGTGACGAAGCGGTGT 62.222 63.158 0.00 0.00 0.00 4.16
31 32 2.737376 GGGTGACGAAGCGGTGTC 60.737 66.667 0.00 0.00 35.67 3.67
32 33 2.338984 GGTGACGAAGCGGTGTCT 59.661 61.111 6.64 0.00 36.10 3.41
33 34 1.733399 GGTGACGAAGCGGTGTCTC 60.733 63.158 6.64 3.30 36.10 3.36
34 35 2.081212 GTGACGAAGCGGTGTCTCG 61.081 63.158 5.70 5.70 36.10 4.04
42 43 2.202362 CGGTGTCTCGCTGACTCG 60.202 66.667 9.20 9.00 45.54 4.18
43 44 2.179517 GGTGTCTCGCTGACTCGG 59.820 66.667 9.20 0.00 45.54 4.63
44 45 2.505118 GTGTCTCGCTGACTCGGC 60.505 66.667 0.00 0.00 45.54 5.54
72 73 3.097114 GCTTTCGCGCCAAAACCG 61.097 61.111 0.00 0.00 0.00 4.44
73 74 2.330041 CTTTCGCGCCAAAACCGT 59.670 55.556 0.00 0.00 0.00 4.83
74 75 1.298788 CTTTCGCGCCAAAACCGTT 60.299 52.632 0.00 0.00 0.00 4.44
75 76 1.266124 CTTTCGCGCCAAAACCGTTC 61.266 55.000 0.00 0.00 0.00 3.95
76 77 2.968330 TTTCGCGCCAAAACCGTTCG 62.968 55.000 0.00 0.00 0.00 3.95
79 80 4.693525 CGCCAAAACCGTTCGCCC 62.694 66.667 0.00 0.00 0.00 6.13
80 81 4.351938 GCCAAAACCGTTCGCCCC 62.352 66.667 0.00 0.00 0.00 5.80
81 82 4.032987 CCAAAACCGTTCGCCCCG 62.033 66.667 0.00 0.00 0.00 5.73
150 151 3.047735 CCAGTTTCGGCCCAAACC 58.952 61.111 20.72 5.05 37.01 3.27
159 160 2.417936 GCCCAAACCGGCGAAAAA 59.582 55.556 9.30 0.00 39.64 1.94
160 161 1.952133 GCCCAAACCGGCGAAAAAC 60.952 57.895 9.30 0.00 39.64 2.43
161 162 1.659026 CCCAAACCGGCGAAAAACG 60.659 57.895 9.30 0.00 45.66 3.60
166 167 4.097863 CCGGCGAAAAACGGGCTC 62.098 66.667 9.30 0.00 46.08 4.70
167 168 3.047877 CGGCGAAAAACGGGCTCT 61.048 61.111 0.00 0.00 42.83 4.09
168 169 2.613506 CGGCGAAAAACGGGCTCTT 61.614 57.895 0.00 0.00 42.83 2.85
169 170 1.081442 GGCGAAAAACGGGCTCTTG 60.081 57.895 0.00 0.00 42.83 3.02
170 171 1.081442 GCGAAAAACGGGCTCTTGG 60.081 57.895 0.00 0.00 42.83 3.61
171 172 1.579429 CGAAAAACGGGCTCTTGGG 59.421 57.895 0.00 0.00 38.46 4.12
172 173 0.887387 CGAAAAACGGGCTCTTGGGA 60.887 55.000 0.00 0.00 38.46 4.37
173 174 0.596577 GAAAAACGGGCTCTTGGGAC 59.403 55.000 0.00 0.00 0.00 4.46
174 175 1.170290 AAAAACGGGCTCTTGGGACG 61.170 55.000 0.00 0.00 0.00 4.79
175 176 4.699522 AACGGGCTCTTGGGACGC 62.700 66.667 0.00 0.00 0.00 5.19
179 180 4.070552 GGCTCTTGGGACGCGACT 62.071 66.667 15.93 0.00 0.00 4.18
180 181 2.811317 GCTCTTGGGACGCGACTG 60.811 66.667 15.93 0.00 0.00 3.51
181 182 2.125912 CTCTTGGGACGCGACTGG 60.126 66.667 15.93 0.00 0.00 4.00
182 183 3.649277 CTCTTGGGACGCGACTGGG 62.649 68.421 15.93 0.00 0.00 4.45
188 189 4.814294 GACGCGACTGGGCCGATT 62.814 66.667 15.93 0.00 0.00 3.34
189 190 4.388499 ACGCGACTGGGCCGATTT 62.388 61.111 15.93 0.00 0.00 2.17
190 191 3.124921 CGCGACTGGGCCGATTTT 61.125 61.111 0.00 0.00 0.00 1.82
191 192 2.686816 CGCGACTGGGCCGATTTTT 61.687 57.895 0.00 0.00 0.00 1.94
192 193 1.154035 GCGACTGGGCCGATTTTTG 60.154 57.895 0.00 0.00 0.00 2.44
193 194 1.506262 CGACTGGGCCGATTTTTGG 59.494 57.895 0.00 0.00 0.00 3.28
194 195 1.890174 GACTGGGCCGATTTTTGGG 59.110 57.895 0.00 0.00 0.00 4.12
200 201 3.436055 CCGATTTTTGGGCGCCGA 61.436 61.111 22.54 15.52 0.00 5.54
201 202 2.202427 CGATTTTTGGGCGCCGAC 60.202 61.111 22.54 8.26 0.00 4.79
202 203 2.202427 GATTTTTGGGCGCCGACG 60.202 61.111 22.54 0.00 44.07 5.12
212 213 2.276430 CGCCGACGCCGAAAATTC 60.276 61.111 0.00 0.00 38.22 2.17
223 224 1.009829 CGAAAATTCGCCTGGAGAGG 58.990 55.000 0.00 0.00 44.26 3.69
224 225 1.383523 GAAAATTCGCCTGGAGAGGG 58.616 55.000 0.00 0.00 40.19 4.30
225 226 0.681243 AAAATTCGCCTGGAGAGGGC 60.681 55.000 0.00 0.00 45.57 5.19
226 227 2.558380 AAATTCGCCTGGAGAGGGCC 62.558 60.000 0.00 0.00 46.24 5.80
227 228 4.722535 TTCGCCTGGAGAGGGCCT 62.723 66.667 5.25 5.25 46.24 5.19
230 231 3.334054 GCCTGGAGAGGGCCTGTT 61.334 66.667 12.95 0.00 43.49 3.16
231 232 2.673523 CCTGGAGAGGGCCTGTTG 59.326 66.667 12.95 1.10 35.40 3.33
232 233 2.673523 CTGGAGAGGGCCTGTTGG 59.326 66.667 12.95 0.00 0.00 3.77
233 234 2.935481 TGGAGAGGGCCTGTTGGG 60.935 66.667 12.95 0.00 38.36 4.12
234 235 3.732849 GGAGAGGGCCTGTTGGGG 61.733 72.222 12.95 0.00 35.12 4.96
235 236 3.732849 GAGAGGGCCTGTTGGGGG 61.733 72.222 12.95 0.00 35.12 5.40
311 312 5.978934 TTAGTTGACCACTTCGAGAAAAC 57.021 39.130 0.00 0.00 36.88 2.43
313 314 4.514401 AGTTGACCACTTCGAGAAAACTT 58.486 39.130 0.00 0.00 27.32 2.66
314 315 4.332819 AGTTGACCACTTCGAGAAAACTTG 59.667 41.667 0.00 0.00 27.32 3.16
315 316 3.202906 TGACCACTTCGAGAAAACTTGG 58.797 45.455 0.00 0.00 0.00 3.61
316 317 2.548480 GACCACTTCGAGAAAACTTGGG 59.452 50.000 0.00 0.00 0.00 4.12
318 319 3.211045 CCACTTCGAGAAAACTTGGGAA 58.789 45.455 0.00 0.00 0.00 3.97
319 320 3.251004 CCACTTCGAGAAAACTTGGGAAG 59.749 47.826 0.00 0.00 37.49 3.46
320 321 3.877508 CACTTCGAGAAAACTTGGGAAGT 59.122 43.478 0.00 0.00 43.34 3.01
321 322 5.054477 CACTTCGAGAAAACTTGGGAAGTA 58.946 41.667 4.17 0.00 41.35 2.24
322 323 5.050295 CACTTCGAGAAAACTTGGGAAGTAC 60.050 44.000 4.17 0.00 41.35 2.73
345 375 6.056884 ACTAGTAATAGTACTCGCTGAAGCT 58.943 40.000 6.05 0.00 41.06 3.74
355 385 0.596083 CGCTGAAGCTACTGATCGGG 60.596 60.000 6.47 0.00 39.32 5.14
356 386 0.249657 GCTGAAGCTACTGATCGGGG 60.250 60.000 6.47 0.00 38.21 5.73
359 389 2.693591 CTGAAGCTACTGATCGGGGTTA 59.306 50.000 6.47 0.00 0.00 2.85
361 391 3.321111 TGAAGCTACTGATCGGGGTTATC 59.679 47.826 6.47 0.00 0.00 1.75
362 392 2.958818 AGCTACTGATCGGGGTTATCA 58.041 47.619 6.47 0.00 32.56 2.15
367 397 0.468226 TGATCGGGGTTATCAGTGGC 59.532 55.000 0.00 0.00 0.00 5.01
368 398 0.759346 GATCGGGGTTATCAGTGGCT 59.241 55.000 0.00 0.00 0.00 4.75
369 399 1.141053 GATCGGGGTTATCAGTGGCTT 59.859 52.381 0.00 0.00 0.00 4.35
370 400 0.539986 TCGGGGTTATCAGTGGCTTC 59.460 55.000 0.00 0.00 0.00 3.86
373 403 1.383523 GGGTTATCAGTGGCTTCAGC 58.616 55.000 0.00 0.00 41.14 4.26
374 404 1.009829 GGTTATCAGTGGCTTCAGCG 58.990 55.000 0.00 0.00 43.26 5.18
375 405 1.405526 GGTTATCAGTGGCTTCAGCGA 60.406 52.381 0.00 0.00 43.26 4.93
376 406 1.929836 GTTATCAGTGGCTTCAGCGAG 59.070 52.381 0.00 0.00 43.26 5.03
377 407 1.186200 TATCAGTGGCTTCAGCGAGT 58.814 50.000 0.00 0.00 43.26 4.18
378 408 1.186200 ATCAGTGGCTTCAGCGAGTA 58.814 50.000 0.00 0.00 43.26 2.59
379 409 0.243907 TCAGTGGCTTCAGCGAGTAC 59.756 55.000 0.00 0.00 43.26 2.73
381 411 1.472878 CAGTGGCTTCAGCGAGTACTA 59.527 52.381 0.00 0.00 43.26 1.82
382 412 2.099921 CAGTGGCTTCAGCGAGTACTAT 59.900 50.000 0.00 0.00 43.26 2.12
384 414 3.952323 AGTGGCTTCAGCGAGTACTATTA 59.048 43.478 0.00 0.00 43.26 0.98
385 415 4.043073 GTGGCTTCAGCGAGTACTATTAC 58.957 47.826 0.00 0.00 43.26 1.89
388 418 5.238868 TGGCTTCAGCGAGTACTATTACTAG 59.761 44.000 0.00 0.00 43.26 2.57
389 419 5.239087 GGCTTCAGCGAGTACTATTACTAGT 59.761 44.000 0.00 0.00 43.26 2.57
390 420 6.426328 GGCTTCAGCGAGTACTATTACTAGTA 59.574 42.308 0.00 0.00 43.26 1.82
391 421 7.041508 GGCTTCAGCGAGTACTATTACTAGTAA 60.042 40.741 17.41 17.41 40.64 2.24
392 422 8.505625 GCTTCAGCGAGTACTATTACTAGTAAT 58.494 37.037 26.90 26.90 41.09 1.89
395 425 8.997323 TCAGCGAGTACTATTACTAGTAATTCC 58.003 37.037 28.42 15.74 41.09 3.01
396 426 8.235905 CAGCGAGTACTATTACTAGTAATTCCC 58.764 40.741 28.42 14.44 41.09 3.97
397 427 7.941238 AGCGAGTACTATTACTAGTAATTCCCA 59.059 37.037 28.42 13.05 41.09 4.37
398 428 8.571336 GCGAGTACTATTACTAGTAATTCCCAA 58.429 37.037 28.42 12.72 41.09 4.12
406 436 8.953368 ATTACTAGTAATTCCCAAGTTTACCG 57.047 34.615 20.27 0.00 32.21 4.02
407 437 6.364568 ACTAGTAATTCCCAAGTTTACCGT 57.635 37.500 0.00 0.00 0.00 4.83
408 438 7.480760 ACTAGTAATTCCCAAGTTTACCGTA 57.519 36.000 0.00 0.00 0.00 4.02
409 439 7.550712 ACTAGTAATTCCCAAGTTTACCGTAG 58.449 38.462 0.00 0.00 0.00 3.51
425 455 2.344025 CGTAGGGTCAAGTTTAGTGCC 58.656 52.381 0.00 0.00 0.00 5.01
426 456 2.289195 CGTAGGGTCAAGTTTAGTGCCA 60.289 50.000 0.00 0.00 0.00 4.92
427 457 3.746940 GTAGGGTCAAGTTTAGTGCCAA 58.253 45.455 0.00 0.00 0.00 4.52
428 458 3.306472 AGGGTCAAGTTTAGTGCCAAA 57.694 42.857 0.00 0.00 0.00 3.28
429 459 3.637769 AGGGTCAAGTTTAGTGCCAAAA 58.362 40.909 0.00 0.00 0.00 2.44
430 460 4.027437 AGGGTCAAGTTTAGTGCCAAAAA 58.973 39.130 0.00 0.00 0.00 1.94
431 461 4.653801 AGGGTCAAGTTTAGTGCCAAAAAT 59.346 37.500 0.00 0.00 0.00 1.82
432 462 5.130311 AGGGTCAAGTTTAGTGCCAAAAATT 59.870 36.000 0.00 0.00 0.00 1.82
433 463 6.325286 AGGGTCAAGTTTAGTGCCAAAAATTA 59.675 34.615 0.00 0.00 0.00 1.40
434 464 6.987404 GGGTCAAGTTTAGTGCCAAAAATTAA 59.013 34.615 0.00 0.00 0.00 1.40
435 465 7.496263 GGGTCAAGTTTAGTGCCAAAAATTAAA 59.504 33.333 0.00 0.00 0.00 1.52
436 466 9.051679 GGTCAAGTTTAGTGCCAAAAATTAAAT 57.948 29.630 0.00 0.00 0.00 1.40
441 471 9.752961 AGTTTAGTGCCAAAAATTAAATAACGT 57.247 25.926 0.00 0.00 0.00 3.99
442 472 9.998381 GTTTAGTGCCAAAAATTAAATAACGTC 57.002 29.630 0.00 0.00 0.00 4.34
443 473 9.745880 TTTAGTGCCAAAAATTAAATAACGTCA 57.254 25.926 0.00 0.00 0.00 4.35
444 474 9.915629 TTAGTGCCAAAAATTAAATAACGTCAT 57.084 25.926 0.00 0.00 0.00 3.06
445 475 8.238481 AGTGCCAAAAATTAAATAACGTCATG 57.762 30.769 0.00 0.00 0.00 3.07
446 476 7.870445 AGTGCCAAAAATTAAATAACGTCATGT 59.130 29.630 0.00 0.00 0.00 3.21
447 477 8.491950 GTGCCAAAAATTAAATAACGTCATGTT 58.508 29.630 0.00 0.00 44.78 2.71
461 491 3.859961 CGTCATGTTTACTAGACAGCAGG 59.140 47.826 0.00 0.00 0.00 4.85
472 502 3.127425 AGACAGCAGGGTCAAGTTTAC 57.873 47.619 6.06 0.00 40.29 2.01
473 503 2.706190 AGACAGCAGGGTCAAGTTTACT 59.294 45.455 6.06 0.00 40.29 2.24
474 504 2.808543 GACAGCAGGGTCAAGTTTACTG 59.191 50.000 0.00 0.00 37.73 2.74
476 506 0.881796 GCAGGGTCAAGTTTACTGCC 59.118 55.000 0.00 0.00 46.47 4.85
478 508 2.795329 CAGGGTCAAGTTTACTGCCAT 58.205 47.619 0.00 0.00 0.00 4.40
489 519 7.388224 TCAAGTTTACTGCCATGACGTTATTTA 59.612 33.333 0.00 0.00 0.00 1.40
490 520 7.675962 AGTTTACTGCCATGACGTTATTTAA 57.324 32.000 0.00 0.00 0.00 1.52
491 521 8.276252 AGTTTACTGCCATGACGTTATTTAAT 57.724 30.769 0.00 0.00 0.00 1.40
492 522 8.736244 AGTTTACTGCCATGACGTTATTTAATT 58.264 29.630 0.00 0.00 0.00 1.40
493 523 9.006215 GTTTACTGCCATGACGTTATTTAATTC 57.994 33.333 0.00 0.00 0.00 2.17
494 524 6.131544 ACTGCCATGACGTTATTTAATTCC 57.868 37.500 0.00 0.00 0.00 3.01
495 525 5.067283 ACTGCCATGACGTTATTTAATTCCC 59.933 40.000 0.00 0.00 0.00 3.97
496 526 4.950475 TGCCATGACGTTATTTAATTCCCA 59.050 37.500 0.00 0.00 0.00 4.37
497 527 5.419155 TGCCATGACGTTATTTAATTCCCAA 59.581 36.000 0.00 0.00 0.00 4.12
498 528 6.071334 TGCCATGACGTTATTTAATTCCCAAA 60.071 34.615 0.00 0.00 0.00 3.28
499 529 6.814146 GCCATGACGTTATTTAATTCCCAAAA 59.186 34.615 0.00 0.00 0.00 2.44
500 530 7.332182 GCCATGACGTTATTTAATTCCCAAAAA 59.668 33.333 0.00 0.00 0.00 1.94
501 531 9.377312 CCATGACGTTATTTAATTCCCAAAAAT 57.623 29.630 0.00 0.00 0.00 1.82
513 543 9.982651 TTAATTCCCAAAAATTAAATCACGTCA 57.017 25.926 0.00 0.00 37.86 4.35
515 545 7.881643 TTCCCAAAAATTAAATCACGTCATG 57.118 32.000 0.00 0.00 0.00 3.07
516 546 6.987386 TCCCAAAAATTAAATCACGTCATGT 58.013 32.000 0.00 0.00 0.00 3.21
517 547 7.437748 TCCCAAAAATTAAATCACGTCATGTT 58.562 30.769 0.00 0.00 0.00 2.71
518 548 7.928706 TCCCAAAAATTAAATCACGTCATGTTT 59.071 29.630 0.00 0.00 0.00 2.83
519 549 9.197694 CCCAAAAATTAAATCACGTCATGTTTA 57.802 29.630 0.00 0.00 0.00 2.01
526 556 9.647797 ATTAAATCACGTCATGTTTACTAGACA 57.352 29.630 0.00 0.00 0.00 3.41
527 557 7.956420 AAATCACGTCATGTTTACTAGACAA 57.044 32.000 0.00 0.00 0.00 3.18
528 558 6.946229 ATCACGTCATGTTTACTAGACAAC 57.054 37.500 0.00 0.00 0.00 3.32
529 559 5.834169 TCACGTCATGTTTACTAGACAACA 58.166 37.500 12.04 12.04 37.31 3.33
530 560 5.918576 TCACGTCATGTTTACTAGACAACAG 59.081 40.000 14.15 8.59 36.36 3.16
531 561 5.118664 CACGTCATGTTTACTAGACAACAGG 59.881 44.000 13.69 13.69 36.36 4.00
532 562 4.625742 CGTCATGTTTACTAGACAACAGGG 59.374 45.833 17.39 11.94 36.36 4.45
533 563 5.548406 GTCATGTTTACTAGACAACAGGGT 58.452 41.667 17.39 2.37 36.36 4.34
534 564 5.638234 GTCATGTTTACTAGACAACAGGGTC 59.362 44.000 17.39 10.81 36.36 4.46
535 565 5.305902 TCATGTTTACTAGACAACAGGGTCA 59.694 40.000 17.39 3.08 40.29 4.02
536 566 5.617528 TGTTTACTAGACAACAGGGTCAA 57.382 39.130 0.00 0.00 40.29 3.18
537 567 5.607477 TGTTTACTAGACAACAGGGTCAAG 58.393 41.667 0.00 0.00 40.29 3.02
538 568 5.129815 TGTTTACTAGACAACAGGGTCAAGT 59.870 40.000 0.00 0.00 40.29 3.16
539 569 5.881923 TTACTAGACAACAGGGTCAAGTT 57.118 39.130 0.00 0.00 40.29 2.66
540 570 4.772886 ACTAGACAACAGGGTCAAGTTT 57.227 40.909 0.00 0.00 40.29 2.66
541 571 5.881923 ACTAGACAACAGGGTCAAGTTTA 57.118 39.130 0.00 0.00 40.29 2.01
542 572 5.608449 ACTAGACAACAGGGTCAAGTTTAC 58.392 41.667 0.00 0.00 40.29 2.01
543 573 4.772886 AGACAACAGGGTCAAGTTTACT 57.227 40.909 0.00 0.00 40.29 2.24
544 574 4.451900 AGACAACAGGGTCAAGTTTACTG 58.548 43.478 0.00 0.00 40.29 2.74
545 575 2.949644 ACAACAGGGTCAAGTTTACTGC 59.050 45.455 0.00 0.00 32.60 4.40
546 576 2.271944 ACAGGGTCAAGTTTACTGCC 57.728 50.000 0.00 0.00 32.60 4.85
547 577 1.493022 ACAGGGTCAAGTTTACTGCCA 59.507 47.619 0.00 0.00 32.60 4.92
548 578 2.108250 ACAGGGTCAAGTTTACTGCCAT 59.892 45.455 0.00 0.00 32.60 4.40
549 579 2.489329 CAGGGTCAAGTTTACTGCCATG 59.511 50.000 0.00 0.00 0.00 3.66
550 580 2.375174 AGGGTCAAGTTTACTGCCATGA 59.625 45.455 0.00 0.00 0.00 3.07
551 581 2.488153 GGGTCAAGTTTACTGCCATGAC 59.512 50.000 0.00 4.58 37.14 3.06
552 582 2.159627 GGTCAAGTTTACTGCCATGACG 59.840 50.000 0.00 0.00 38.39 4.35
553 583 2.806244 GTCAAGTTTACTGCCATGACGT 59.194 45.455 0.00 0.00 0.00 4.34
554 584 3.250040 GTCAAGTTTACTGCCATGACGTT 59.750 43.478 0.00 0.00 0.00 3.99
555 585 4.449743 GTCAAGTTTACTGCCATGACGTTA 59.550 41.667 0.00 0.00 0.00 3.18
556 586 5.121768 GTCAAGTTTACTGCCATGACGTTAT 59.878 40.000 0.00 0.00 0.00 1.89
557 587 5.703592 TCAAGTTTACTGCCATGACGTTATT 59.296 36.000 0.00 0.00 0.00 1.40
558 588 6.205853 TCAAGTTTACTGCCATGACGTTATTT 59.794 34.615 0.00 0.00 0.00 1.40
559 589 7.388224 TCAAGTTTACTGCCATGACGTTATTTA 59.612 33.333 0.00 0.00 0.00 1.40
566 596 4.950475 TGCCATGACGTTATTTAATTCCCA 59.050 37.500 0.00 0.00 0.00 4.37
568 598 6.071334 TGCCATGACGTTATTTAATTCCCAAA 60.071 34.615 0.00 0.00 0.00 3.28
583 613 9.579932 TTAATTCCCAAAAATTATTGGCAAAGT 57.420 25.926 3.01 0.00 46.97 2.66
588 618 7.723172 TCCCAAAAATTATTGGCAAAGTTGATT 59.277 29.630 3.01 0.00 46.97 2.57
621 657 5.212532 AGACTATCAAAGCTAGCTGATGG 57.787 43.478 20.16 20.97 36.79 3.51
661 698 4.946160 TTTGGAAATCTGGGGATACAGT 57.054 40.909 0.00 0.00 39.48 3.55
686 727 7.894376 TGAGTCCTTTTGTTATTAGTTACCG 57.106 36.000 0.00 0.00 0.00 4.02
733 774 9.722184 AGTTGATGGTCTGAATCTGATATAATG 57.278 33.333 0.00 0.00 0.00 1.90
735 776 9.498176 TTGATGGTCTGAATCTGATATAATGTG 57.502 33.333 0.00 0.00 0.00 3.21
794 835 3.752412 TGCTCTTGAATTCGCAGATTG 57.248 42.857 7.44 0.31 35.04 2.67
917 958 6.205658 ACAAGGTCTTGCTCTATTTTCTGTTC 59.794 38.462 10.31 0.00 44.03 3.18
980 1021 7.655328 TCATTTCCGAGCAAAAATAATGTTTGT 59.345 29.630 2.66 0.00 38.09 2.83
1005 1054 2.776536 CTCCTCCTTTGGACAGATGGAT 59.223 50.000 0.00 0.00 31.94 3.41
1565 1619 8.719645 TCTTAATTTCCATTCTTTTTCTGGGA 57.280 30.769 0.00 0.00 0.00 4.37
1809 1930 1.206132 CTACACAACATGGTCGGCCTA 59.794 52.381 7.97 0.00 35.27 3.93
1810 1931 0.036388 ACACAACATGGTCGGCCTAG 60.036 55.000 7.97 1.44 35.27 3.02
1811 1932 0.249120 CACAACATGGTCGGCCTAGA 59.751 55.000 7.97 0.00 35.27 2.43
1812 1933 0.537188 ACAACATGGTCGGCCTAGAG 59.463 55.000 7.97 0.00 35.27 2.43
1813 1934 0.811616 CAACATGGTCGGCCTAGAGC 60.812 60.000 7.97 1.41 42.60 4.09
1814 1935 2.028190 CATGGTCGGCCTAGAGCG 59.972 66.667 7.97 0.00 45.17 5.03
1815 1936 2.442272 ATGGTCGGCCTAGAGCGT 60.442 61.111 7.97 0.00 45.17 5.07
1816 1937 2.491022 ATGGTCGGCCTAGAGCGTC 61.491 63.158 7.97 0.00 45.17 5.19
1817 1938 3.902086 GGTCGGCCTAGAGCGTCC 61.902 72.222 0.00 0.00 45.17 4.79
1818 1939 3.138798 GTCGGCCTAGAGCGTCCA 61.139 66.667 0.00 0.00 45.17 4.02
1819 1940 2.361992 TCGGCCTAGAGCGTCCAA 60.362 61.111 0.00 0.00 45.17 3.53
1820 1941 2.202756 CGGCCTAGAGCGTCCAAC 60.203 66.667 0.00 0.00 45.17 3.77
1821 1942 2.202756 GGCCTAGAGCGTCCAACG 60.203 66.667 0.00 0.00 45.17 4.10
1822 1943 2.707849 GGCCTAGAGCGTCCAACGA 61.708 63.158 3.28 0.00 46.05 3.85
1823 1944 1.516603 GCCTAGAGCGTCCAACGAC 60.517 63.158 3.28 0.00 46.05 4.34
1824 1945 1.880894 CCTAGAGCGTCCAACGACA 59.119 57.895 3.28 0.00 46.05 4.35
1825 1946 0.242825 CCTAGAGCGTCCAACGACAA 59.757 55.000 3.28 0.00 46.05 3.18
1826 1947 1.337821 CTAGAGCGTCCAACGACAAC 58.662 55.000 3.28 0.00 46.05 3.32
1827 1948 0.038892 TAGAGCGTCCAACGACAACC 60.039 55.000 3.28 0.00 46.05 3.77
1828 1949 1.300697 GAGCGTCCAACGACAACCT 60.301 57.895 3.28 0.00 46.05 3.50
1829 1950 1.282930 GAGCGTCCAACGACAACCTC 61.283 60.000 3.28 0.00 46.05 3.85
1954 2075 9.813826 ACTATATTCCTAATGCTTGGCTAAAAT 57.186 29.630 0.00 0.00 0.00 1.82
2214 2342 3.118298 TGAAATGATCCAGCCATTCGAGA 60.118 43.478 0.00 0.00 33.51 4.04
2215 2343 2.835580 ATGATCCAGCCATTCGAGAG 57.164 50.000 0.00 0.00 0.00 3.20
2216 2344 0.105593 TGATCCAGCCATTCGAGAGC 59.894 55.000 0.00 0.00 0.00 4.09
2571 3876 3.374988 TGTGTTTGTGCAGTCAAGAAGAG 59.625 43.478 0.00 0.00 0.00 2.85
2574 3879 4.094887 TGTTTGTGCAGTCAAGAAGAGTTC 59.905 41.667 0.00 0.00 0.00 3.01
2647 3953 5.699458 CCTTGAGATTGTTTACCTTACGTGT 59.301 40.000 0.00 0.00 0.00 4.49
2648 3954 6.347402 CCTTGAGATTGTTTACCTTACGTGTG 60.347 42.308 0.00 0.00 0.00 3.82
2727 4039 8.718102 AGTAATGTTTTTACACGCAGATCTAT 57.282 30.769 0.00 0.00 0.00 1.98
2777 4091 0.606096 AAAATTGGTTACCAGGCGGC 59.394 50.000 3.65 0.00 33.81 6.53
2812 4130 4.094887 CCAGTACCTCATGAAAAATCACCG 59.905 45.833 0.00 0.00 0.00 4.94
2841 4159 5.640783 GGGCAAGAAATCCTGAATTTTTGAG 59.359 40.000 3.24 0.00 37.70 3.02
2946 4279 0.178975 AAAAATCTCGGTGCCCCACA 60.179 50.000 0.00 0.00 35.86 4.17
3104 4625 4.358851 CAAAATTGCGACCTCTTTCAACA 58.641 39.130 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.683933 ACCCTCATCGCCTCGGTT 60.684 61.111 0.00 0.00 0.00 4.44
3 4 2.105128 GTCACCCTCATCGCCTCG 59.895 66.667 0.00 0.00 0.00 4.63
4 5 1.945354 TTCGTCACCCTCATCGCCTC 61.945 60.000 0.00 0.00 0.00 4.70
5 6 1.949847 CTTCGTCACCCTCATCGCCT 61.950 60.000 0.00 0.00 0.00 5.52
6 7 1.519455 CTTCGTCACCCTCATCGCC 60.519 63.158 0.00 0.00 0.00 5.54
7 8 2.167861 GCTTCGTCACCCTCATCGC 61.168 63.158 0.00 0.00 0.00 4.58
8 9 1.874019 CGCTTCGTCACCCTCATCG 60.874 63.158 0.00 0.00 0.00 3.84
9 10 1.519455 CCGCTTCGTCACCCTCATC 60.519 63.158 0.00 0.00 0.00 2.92
10 11 2.283529 ACCGCTTCGTCACCCTCAT 61.284 57.895 0.00 0.00 0.00 2.90
11 12 2.915659 ACCGCTTCGTCACCCTCA 60.916 61.111 0.00 0.00 0.00 3.86
12 13 2.432628 CACCGCTTCGTCACCCTC 60.433 66.667 0.00 0.00 0.00 4.30
13 14 3.222354 GACACCGCTTCGTCACCCT 62.222 63.158 0.00 0.00 32.24 4.34
14 15 2.737376 GACACCGCTTCGTCACCC 60.737 66.667 0.00 0.00 32.24 4.61
15 16 1.733399 GAGACACCGCTTCGTCACC 60.733 63.158 0.00 0.00 34.48 4.02
16 17 2.081212 CGAGACACCGCTTCGTCAC 61.081 63.158 0.00 0.00 34.48 3.67
17 18 2.254350 CGAGACACCGCTTCGTCA 59.746 61.111 0.00 0.00 34.48 4.35
56 57 1.266124 GAACGGTTTTGGCGCGAAAG 61.266 55.000 17.08 9.09 0.00 2.62
57 58 1.298488 GAACGGTTTTGGCGCGAAA 60.298 52.632 13.91 13.91 0.00 3.46
58 59 2.328639 GAACGGTTTTGGCGCGAA 59.671 55.556 12.10 0.00 0.00 4.70
59 60 4.003011 CGAACGGTTTTGGCGCGA 62.003 61.111 12.10 0.00 0.00 5.87
62 63 4.693525 GGGCGAACGGTTTTGGCG 62.694 66.667 12.22 5.27 41.72 5.69
63 64 4.351938 GGGGCGAACGGTTTTGGC 62.352 66.667 10.73 10.73 40.35 4.52
64 65 4.032987 CGGGGCGAACGGTTTTGG 62.033 66.667 0.00 0.00 0.00 3.28
65 66 4.032987 CCGGGGCGAACGGTTTTG 62.033 66.667 0.00 0.00 46.03 2.44
133 134 3.047735 GGTTTGGGCCGAAACTGG 58.952 61.111 33.51 0.00 36.30 4.00
143 144 1.659026 CGTTTTTCGCCGGTTTGGG 60.659 57.895 1.90 0.00 38.63 4.12
144 145 1.659026 CCGTTTTTCGCCGGTTTGG 60.659 57.895 1.90 0.00 39.38 3.28
145 146 1.659026 CCCGTTTTTCGCCGGTTTG 60.659 57.895 1.90 0.00 42.67 2.93
146 147 2.723116 CCCGTTTTTCGCCGGTTT 59.277 55.556 1.90 0.00 42.67 3.27
147 148 3.968568 GCCCGTTTTTCGCCGGTT 61.969 61.111 1.90 0.00 42.67 4.44
148 149 4.941309 AGCCCGTTTTTCGCCGGT 62.941 61.111 1.90 0.00 42.67 5.28
149 150 4.097863 GAGCCCGTTTTTCGCCGG 62.098 66.667 0.00 0.00 43.82 6.13
150 151 2.613506 AAGAGCCCGTTTTTCGCCG 61.614 57.895 0.00 0.00 38.35 6.46
151 152 1.081442 CAAGAGCCCGTTTTTCGCC 60.081 57.895 0.00 0.00 38.35 5.54
152 153 1.081442 CCAAGAGCCCGTTTTTCGC 60.081 57.895 0.00 0.00 38.35 4.70
153 154 0.887387 TCCCAAGAGCCCGTTTTTCG 60.887 55.000 0.00 0.00 39.52 3.46
154 155 0.596577 GTCCCAAGAGCCCGTTTTTC 59.403 55.000 0.00 0.00 0.00 2.29
155 156 1.170290 CGTCCCAAGAGCCCGTTTTT 61.170 55.000 0.00 0.00 0.00 1.94
156 157 1.599797 CGTCCCAAGAGCCCGTTTT 60.600 57.895 0.00 0.00 0.00 2.43
157 158 2.032071 CGTCCCAAGAGCCCGTTT 59.968 61.111 0.00 0.00 0.00 3.60
158 159 4.699522 GCGTCCCAAGAGCCCGTT 62.700 66.667 0.00 0.00 0.00 4.44
162 163 4.070552 AGTCGCGTCCCAAGAGCC 62.071 66.667 5.77 0.00 0.00 4.70
163 164 2.811317 CAGTCGCGTCCCAAGAGC 60.811 66.667 5.77 0.00 0.00 4.09
164 165 2.125912 CCAGTCGCGTCCCAAGAG 60.126 66.667 5.77 0.00 0.00 2.85
165 166 3.691342 CCCAGTCGCGTCCCAAGA 61.691 66.667 5.77 0.00 0.00 3.02
171 172 4.814294 AATCGGCCCAGTCGCGTC 62.814 66.667 5.77 0.00 0.00 5.19
172 173 3.894547 AAAATCGGCCCAGTCGCGT 62.895 57.895 5.77 0.00 0.00 6.01
173 174 2.686816 AAAAATCGGCCCAGTCGCG 61.687 57.895 0.00 0.00 0.00 5.87
174 175 1.154035 CAAAAATCGGCCCAGTCGC 60.154 57.895 0.00 0.00 0.00 5.19
175 176 1.506262 CCAAAAATCGGCCCAGTCG 59.494 57.895 0.00 0.00 0.00 4.18
176 177 1.890174 CCCAAAAATCGGCCCAGTC 59.110 57.895 0.00 0.00 0.00 3.51
177 178 2.282783 GCCCAAAAATCGGCCCAGT 61.283 57.895 0.00 0.00 39.39 4.00
178 179 2.578664 GCCCAAAAATCGGCCCAG 59.421 61.111 0.00 0.00 39.39 4.45
179 180 3.377759 CGCCCAAAAATCGGCCCA 61.378 61.111 0.00 0.00 42.53 5.36
180 181 4.812476 GCGCCCAAAAATCGGCCC 62.812 66.667 0.00 0.00 42.53 5.80
181 182 4.812476 GGCGCCCAAAAATCGGCC 62.812 66.667 18.11 0.00 42.53 6.13
183 184 3.436055 TCGGCGCCCAAAAATCGG 61.436 61.111 23.46 2.86 0.00 4.18
184 185 2.202427 GTCGGCGCCCAAAAATCG 60.202 61.111 23.46 6.46 0.00 3.34
185 186 2.202427 CGTCGGCGCCCAAAAATC 60.202 61.111 23.46 2.52 0.00 2.17
196 197 2.276430 CGAATTTTCGGCGTCGGC 60.276 61.111 10.62 9.07 46.30 5.54
205 206 1.383523 CCCTCTCCAGGCGAATTTTC 58.616 55.000 0.00 0.00 38.72 2.29
206 207 0.681243 GCCCTCTCCAGGCGAATTTT 60.681 55.000 0.00 0.00 41.41 1.82
207 208 1.077429 GCCCTCTCCAGGCGAATTT 60.077 57.895 0.00 0.00 41.41 1.82
208 209 2.592308 GCCCTCTCCAGGCGAATT 59.408 61.111 0.00 0.00 41.41 2.17
214 215 2.673523 CAACAGGCCCTCTCCAGG 59.326 66.667 0.00 0.00 39.98 4.45
215 216 2.673523 CCAACAGGCCCTCTCCAG 59.326 66.667 0.00 0.00 0.00 3.86
216 217 2.935481 CCCAACAGGCCCTCTCCA 60.935 66.667 0.00 0.00 0.00 3.86
217 218 3.732849 CCCCAACAGGCCCTCTCC 61.733 72.222 0.00 0.00 0.00 3.71
218 219 3.732849 CCCCCAACAGGCCCTCTC 61.733 72.222 0.00 0.00 0.00 3.20
226 227 4.408821 TAGCTGCGCCCCCAACAG 62.409 66.667 4.18 0.00 34.48 3.16
227 228 4.408821 CTAGCTGCGCCCCCAACA 62.409 66.667 4.18 0.00 0.00 3.33
228 229 4.096003 TCTAGCTGCGCCCCCAAC 62.096 66.667 4.18 0.00 0.00 3.77
229 230 3.785859 CTCTAGCTGCGCCCCCAA 61.786 66.667 4.18 0.00 0.00 4.12
230 231 4.777854 TCTCTAGCTGCGCCCCCA 62.778 66.667 4.18 0.00 0.00 4.96
231 232 3.237741 ATCTCTAGCTGCGCCCCC 61.238 66.667 4.18 0.00 0.00 5.40
232 233 2.030262 CATCTCTAGCTGCGCCCC 59.970 66.667 4.18 0.00 0.00 5.80
233 234 2.664518 GCATCTCTAGCTGCGCCC 60.665 66.667 4.18 0.00 0.00 6.13
234 235 1.664333 GAGCATCTCTAGCTGCGCC 60.664 63.158 4.18 0.00 43.58 6.53
235 236 3.935196 GAGCATCTCTAGCTGCGC 58.065 61.111 0.00 0.00 43.58 6.09
249 250 3.657956 AGCGATGAGTGCTTAGAGC 57.342 52.632 0.00 0.00 40.48 4.09
294 295 3.202906 CCAAGTTTTCTCGAAGTGGTCA 58.797 45.455 0.00 0.00 0.00 4.02
320 321 7.418840 GCTTCAGCGAGTACTATTACTAGTA 57.581 40.000 0.00 0.00 38.77 1.82
321 322 6.303021 GCTTCAGCGAGTACTATTACTAGT 57.697 41.667 0.00 0.00 38.77 2.57
355 385 1.009829 CGCTGAAGCCACTGATAACC 58.990 55.000 0.00 0.00 37.91 2.85
356 386 1.929836 CTCGCTGAAGCCACTGATAAC 59.070 52.381 0.00 0.00 37.91 1.89
359 389 1.134965 GTACTCGCTGAAGCCACTGAT 60.135 52.381 0.00 0.00 37.91 2.90
361 391 0.244994 AGTACTCGCTGAAGCCACTG 59.755 55.000 0.00 0.00 37.91 3.66
362 392 1.835494 TAGTACTCGCTGAAGCCACT 58.165 50.000 0.00 0.00 37.91 4.00
363 393 2.873133 ATAGTACTCGCTGAAGCCAC 57.127 50.000 0.00 0.00 37.91 5.01
364 394 3.952323 AGTAATAGTACTCGCTGAAGCCA 59.048 43.478 0.00 0.00 35.55 4.75
365 395 4.571372 AGTAATAGTACTCGCTGAAGCC 57.429 45.455 0.00 0.00 35.55 4.35
369 399 8.997323 GGAATTACTAGTAATAGTACTCGCTGA 58.003 37.037 24.86 0.00 41.06 4.26
370 400 8.235905 GGGAATTACTAGTAATAGTACTCGCTG 58.764 40.741 24.86 0.00 41.06 5.18
381 411 8.542926 ACGGTAAACTTGGGAATTACTAGTAAT 58.457 33.333 20.27 20.27 37.36 1.89
382 412 7.906327 ACGGTAAACTTGGGAATTACTAGTAA 58.094 34.615 17.41 17.41 31.73 2.24
384 414 6.364568 ACGGTAAACTTGGGAATTACTAGT 57.635 37.500 0.00 0.00 31.73 2.57
385 415 6.982724 CCTACGGTAAACTTGGGAATTACTAG 59.017 42.308 0.00 0.00 31.73 2.57
388 418 4.877823 CCCTACGGTAAACTTGGGAATTAC 59.122 45.833 3.88 0.00 36.90 1.89
389 419 4.535692 ACCCTACGGTAAACTTGGGAATTA 59.464 41.667 14.43 0.00 42.18 1.40
390 420 3.331591 ACCCTACGGTAAACTTGGGAATT 59.668 43.478 14.43 0.00 42.18 2.17
391 421 2.914941 ACCCTACGGTAAACTTGGGAAT 59.085 45.455 14.43 0.00 42.18 3.01
392 422 2.302733 GACCCTACGGTAAACTTGGGAA 59.697 50.000 14.43 0.00 44.88 3.97
393 423 1.901833 GACCCTACGGTAAACTTGGGA 59.098 52.381 14.43 0.00 44.88 4.37
394 424 1.624813 TGACCCTACGGTAAACTTGGG 59.375 52.381 7.65 7.65 44.88 4.12
395 425 3.244318 ACTTGACCCTACGGTAAACTTGG 60.244 47.826 0.00 0.00 44.88 3.61
396 426 3.999046 ACTTGACCCTACGGTAAACTTG 58.001 45.455 0.00 0.00 44.88 3.16
397 427 4.694760 AACTTGACCCTACGGTAAACTT 57.305 40.909 0.00 0.00 44.88 2.66
398 428 4.694760 AAACTTGACCCTACGGTAAACT 57.305 40.909 0.00 0.00 44.88 2.66
399 429 5.406477 CACTAAACTTGACCCTACGGTAAAC 59.594 44.000 0.00 0.00 44.88 2.01
400 430 5.540911 CACTAAACTTGACCCTACGGTAAA 58.459 41.667 0.00 0.00 44.88 2.01
401 431 4.561326 GCACTAAACTTGACCCTACGGTAA 60.561 45.833 0.00 0.00 44.88 2.85
402 432 3.056607 GCACTAAACTTGACCCTACGGTA 60.057 47.826 0.00 0.00 44.88 4.02
404 434 2.344025 GCACTAAACTTGACCCTACGG 58.656 52.381 0.00 0.00 0.00 4.02
405 435 2.289195 TGGCACTAAACTTGACCCTACG 60.289 50.000 0.00 0.00 0.00 3.51
406 436 3.412237 TGGCACTAAACTTGACCCTAC 57.588 47.619 0.00 0.00 0.00 3.18
407 437 4.440826 TTTGGCACTAAACTTGACCCTA 57.559 40.909 0.00 0.00 0.00 3.53
408 438 3.306472 TTTGGCACTAAACTTGACCCT 57.694 42.857 0.00 0.00 0.00 4.34
409 439 4.394439 TTTTTGGCACTAAACTTGACCC 57.606 40.909 0.00 0.00 0.00 4.46
410 440 8.426881 TTTAATTTTTGGCACTAAACTTGACC 57.573 30.769 0.00 0.00 0.00 4.02
415 445 9.752961 ACGTTATTTAATTTTTGGCACTAAACT 57.247 25.926 0.00 0.00 0.00 2.66
416 446 9.998381 GACGTTATTTAATTTTTGGCACTAAAC 57.002 29.630 0.00 0.00 0.00 2.01
417 447 9.745880 TGACGTTATTTAATTTTTGGCACTAAA 57.254 25.926 0.00 0.00 0.00 1.85
418 448 9.915629 ATGACGTTATTTAATTTTTGGCACTAA 57.084 25.926 0.00 0.00 0.00 2.24
419 449 9.347934 CATGACGTTATTTAATTTTTGGCACTA 57.652 29.630 0.00 0.00 0.00 2.74
420 450 7.870445 ACATGACGTTATTTAATTTTTGGCACT 59.130 29.630 0.00 0.00 0.00 4.40
421 451 8.013236 ACATGACGTTATTTAATTTTTGGCAC 57.987 30.769 0.00 0.00 0.00 5.01
422 452 8.594881 AACATGACGTTATTTAATTTTTGGCA 57.405 26.923 0.00 0.00 35.52 4.92
432 462 9.079833 GCTGTCTAGTAAACATGACGTTATTTA 57.920 33.333 0.00 0.00 36.59 1.40
433 463 7.601130 TGCTGTCTAGTAAACATGACGTTATTT 59.399 33.333 0.00 0.00 36.59 1.40
434 464 7.094631 TGCTGTCTAGTAAACATGACGTTATT 58.905 34.615 0.00 0.00 36.59 1.40
435 465 6.627243 TGCTGTCTAGTAAACATGACGTTAT 58.373 36.000 0.00 0.00 36.59 1.89
436 466 6.016213 TGCTGTCTAGTAAACATGACGTTA 57.984 37.500 0.00 0.00 36.59 3.18
437 467 4.878439 TGCTGTCTAGTAAACATGACGTT 58.122 39.130 0.00 0.00 40.50 3.99
438 468 4.486090 CTGCTGTCTAGTAAACATGACGT 58.514 43.478 0.00 0.00 32.64 4.34
439 469 3.859961 CCTGCTGTCTAGTAAACATGACG 59.140 47.826 0.00 0.00 32.64 4.35
440 470 4.184629 CCCTGCTGTCTAGTAAACATGAC 58.815 47.826 0.00 0.00 0.00 3.06
441 471 3.838317 ACCCTGCTGTCTAGTAAACATGA 59.162 43.478 0.00 0.00 0.00 3.07
442 472 4.184629 GACCCTGCTGTCTAGTAAACATG 58.815 47.826 0.00 0.00 32.39 3.21
443 473 3.838317 TGACCCTGCTGTCTAGTAAACAT 59.162 43.478 0.00 0.00 36.21 2.71
444 474 3.236047 TGACCCTGCTGTCTAGTAAACA 58.764 45.455 0.00 0.00 36.21 2.83
445 475 3.955650 TGACCCTGCTGTCTAGTAAAC 57.044 47.619 0.00 0.00 36.21 2.01
446 476 3.901844 ACTTGACCCTGCTGTCTAGTAAA 59.098 43.478 13.56 0.00 45.28 2.01
447 477 3.507411 ACTTGACCCTGCTGTCTAGTAA 58.493 45.455 13.56 0.00 45.28 2.24
453 483 2.808543 CAGTAAACTTGACCCTGCTGTC 59.191 50.000 0.00 0.00 35.77 3.51
461 491 2.159627 CGTCATGGCAGTAAACTTGACC 59.840 50.000 8.96 0.00 38.06 4.02
472 502 5.067153 TGGGAATTAAATAACGTCATGGCAG 59.933 40.000 0.00 0.00 0.00 4.85
473 503 4.950475 TGGGAATTAAATAACGTCATGGCA 59.050 37.500 0.00 0.00 0.00 4.92
474 504 5.508200 TGGGAATTAAATAACGTCATGGC 57.492 39.130 0.00 0.00 0.00 4.40
489 519 8.934825 CATGACGTGATTTAATTTTTGGGAATT 58.065 29.630 0.00 0.00 33.95 2.17
490 520 8.093927 ACATGACGTGATTTAATTTTTGGGAAT 58.906 29.630 0.00 0.00 0.00 3.01
491 521 7.437748 ACATGACGTGATTTAATTTTTGGGAA 58.562 30.769 0.00 0.00 0.00 3.97
492 522 6.987386 ACATGACGTGATTTAATTTTTGGGA 58.013 32.000 0.00 0.00 0.00 4.37
493 523 7.650834 AACATGACGTGATTTAATTTTTGGG 57.349 32.000 0.00 0.00 0.00 4.12
500 530 9.647797 TGTCTAGTAAACATGACGTGATTTAAT 57.352 29.630 0.00 5.15 32.64 1.40
501 531 9.478768 TTGTCTAGTAAACATGACGTGATTTAA 57.521 29.630 0.00 0.00 32.64 1.52
502 532 8.918658 GTTGTCTAGTAAACATGACGTGATTTA 58.081 33.333 0.00 0.79 32.64 1.40
503 533 7.439955 TGTTGTCTAGTAAACATGACGTGATTT 59.560 33.333 0.00 1.69 31.52 2.17
504 534 6.926826 TGTTGTCTAGTAAACATGACGTGATT 59.073 34.615 0.00 0.00 31.52 2.57
505 535 6.452242 TGTTGTCTAGTAAACATGACGTGAT 58.548 36.000 0.00 0.00 31.52 3.06
506 536 5.834169 TGTTGTCTAGTAAACATGACGTGA 58.166 37.500 0.00 0.00 31.52 4.35
507 537 5.118664 CCTGTTGTCTAGTAAACATGACGTG 59.881 44.000 0.00 0.00 35.82 4.49
508 538 5.227908 CCTGTTGTCTAGTAAACATGACGT 58.772 41.667 0.00 0.00 35.82 4.34
509 539 4.625742 CCCTGTTGTCTAGTAAACATGACG 59.374 45.833 0.00 3.32 35.82 4.35
510 540 5.548406 ACCCTGTTGTCTAGTAAACATGAC 58.452 41.667 0.00 0.00 35.82 3.06
511 541 5.305902 TGACCCTGTTGTCTAGTAAACATGA 59.694 40.000 0.00 0.00 35.82 3.07
512 542 5.547465 TGACCCTGTTGTCTAGTAAACATG 58.453 41.667 11.61 9.61 35.82 3.21
513 543 5.818678 TGACCCTGTTGTCTAGTAAACAT 57.181 39.130 11.61 0.93 35.82 2.71
514 544 5.129815 ACTTGACCCTGTTGTCTAGTAAACA 59.870 40.000 6.51 10.96 45.28 2.83
515 545 5.608449 ACTTGACCCTGTTGTCTAGTAAAC 58.392 41.667 6.51 0.00 45.28 2.01
516 546 5.881923 ACTTGACCCTGTTGTCTAGTAAA 57.118 39.130 6.51 0.00 45.28 2.01
517 547 5.881923 AACTTGACCCTGTTGTCTAGTAA 57.118 39.130 8.30 0.00 46.00 2.24
518 548 5.881923 AAACTTGACCCTGTTGTCTAGTA 57.118 39.130 8.30 0.00 46.00 1.82
520 550 5.696724 CAGTAAACTTGACCCTGTTGTCTAG 59.303 44.000 0.00 0.00 41.77 2.43
521 551 5.607477 CAGTAAACTTGACCCTGTTGTCTA 58.393 41.667 0.00 0.00 36.21 2.59
522 552 4.451900 CAGTAAACTTGACCCTGTTGTCT 58.548 43.478 0.00 0.00 36.21 3.41
523 553 3.003378 GCAGTAAACTTGACCCTGTTGTC 59.997 47.826 0.00 0.00 35.77 3.18
524 554 2.949644 GCAGTAAACTTGACCCTGTTGT 59.050 45.455 0.00 0.00 0.00 3.32
525 555 2.293399 GGCAGTAAACTTGACCCTGTTG 59.707 50.000 0.00 0.00 0.00 3.33
526 556 2.092103 TGGCAGTAAACTTGACCCTGTT 60.092 45.455 0.00 0.00 0.00 3.16
527 557 1.493022 TGGCAGTAAACTTGACCCTGT 59.507 47.619 0.00 0.00 0.00 4.00
528 558 2.270352 TGGCAGTAAACTTGACCCTG 57.730 50.000 0.00 0.00 0.00 4.45
529 559 2.375174 TCATGGCAGTAAACTTGACCCT 59.625 45.455 0.00 0.00 0.00 4.34
530 560 2.488153 GTCATGGCAGTAAACTTGACCC 59.512 50.000 4.23 0.00 36.39 4.46
531 561 2.159627 CGTCATGGCAGTAAACTTGACC 59.840 50.000 8.96 0.00 38.06 4.02
532 562 2.806244 ACGTCATGGCAGTAAACTTGAC 59.194 45.455 0.00 5.32 37.99 3.18
533 563 3.120321 ACGTCATGGCAGTAAACTTGA 57.880 42.857 0.00 0.00 0.00 3.02
534 564 3.896648 AACGTCATGGCAGTAAACTTG 57.103 42.857 0.00 0.00 0.00 3.16
535 565 6.569179 AAATAACGTCATGGCAGTAAACTT 57.431 33.333 0.00 0.00 0.00 2.66
536 566 7.675962 TTAAATAACGTCATGGCAGTAAACT 57.324 32.000 0.00 0.00 0.00 2.66
537 567 8.905103 AATTAAATAACGTCATGGCAGTAAAC 57.095 30.769 0.00 0.00 0.00 2.01
538 568 8.185505 GGAATTAAATAACGTCATGGCAGTAAA 58.814 33.333 0.00 0.00 0.00 2.01
539 569 7.201750 GGGAATTAAATAACGTCATGGCAGTAA 60.202 37.037 0.00 0.00 0.00 2.24
540 570 6.261381 GGGAATTAAATAACGTCATGGCAGTA 59.739 38.462 0.00 0.00 0.00 2.74
541 571 5.067283 GGGAATTAAATAACGTCATGGCAGT 59.933 40.000 0.00 0.00 0.00 4.40
542 572 5.067153 TGGGAATTAAATAACGTCATGGCAG 59.933 40.000 0.00 0.00 0.00 4.85
543 573 4.950475 TGGGAATTAAATAACGTCATGGCA 59.050 37.500 0.00 0.00 0.00 4.92
544 574 5.508200 TGGGAATTAAATAACGTCATGGC 57.492 39.130 0.00 0.00 0.00 4.40
545 575 8.764524 TTTTTGGGAATTAAATAACGTCATGG 57.235 30.769 0.00 0.00 0.00 3.66
596 626 7.035004 CCATCAGCTAGCTTTGATAGTCTATC 58.965 42.308 16.46 12.29 32.96 2.08
624 660 8.585018 AGATTTCCAAAATTTATATAAGGCGGG 58.415 33.333 0.00 0.00 0.00 6.13
637 674 6.263754 ACTGTATCCCCAGATTTCCAAAATT 58.736 36.000 0.00 0.00 36.30 1.82
657 694 8.747538 AACTAATAACAAAAGGACTCAACTGT 57.252 30.769 0.00 0.00 0.00 3.55
661 698 7.095102 GCGGTAACTAATAACAAAAGGACTCAA 60.095 37.037 0.00 0.00 0.00 3.02
686 727 8.431593 TCAACTTTGATTGCGTAAATAAATTGC 58.568 29.630 0.00 0.00 31.01 3.56
699 740 4.771590 TCAGACCATCAACTTTGATTGC 57.228 40.909 1.52 0.00 45.13 3.56
733 774 1.235724 GTCCCGCAATAATAGCCCAC 58.764 55.000 0.00 0.00 0.00 4.61
735 776 2.200373 ATGTCCCGCAATAATAGCCC 57.800 50.000 0.00 0.00 0.00 5.19
794 835 6.128795 GCAATGGTCTCGTTTCTATATACTGC 60.129 42.308 0.00 0.00 0.00 4.40
917 958 9.104965 TCGAAACCAATCTACATATACAAAAGG 57.895 33.333 0.00 0.00 0.00 3.11
980 1021 2.689658 TCTGTCCAAAGGAGGAGACAA 58.310 47.619 0.00 0.00 38.68 3.18
1005 1054 3.191791 GCCCTTTCGCCATTTTGTAGTAA 59.808 43.478 0.00 0.00 0.00 2.24
1216 1268 2.045926 GCCGGCACCAGATGAAGT 60.046 61.111 24.80 0.00 0.00 3.01
1277 1329 9.185680 TGAGCACACTATCAGTAAAACTATCTA 57.814 33.333 0.00 0.00 0.00 1.98
1565 1619 8.820933 CACATTTCGAACTGATACTATGTCATT 58.179 33.333 20.86 0.00 0.00 2.57
1809 1930 1.300697 GGTTGTCGTTGGACGCTCT 60.301 57.895 0.00 0.00 46.49 4.09
1810 1931 1.282930 GAGGTTGTCGTTGGACGCTC 61.283 60.000 0.00 0.00 46.49 5.03
1811 1932 1.300697 GAGGTTGTCGTTGGACGCT 60.301 57.895 0.00 0.00 46.49 5.07
1812 1933 2.654912 CGAGGTTGTCGTTGGACGC 61.655 63.158 0.00 0.00 46.49 5.19
1813 1934 3.534160 CGAGGTTGTCGTTGGACG 58.466 61.111 0.00 0.00 46.49 4.79
1821 1942 7.061557 GTCTACTGTGTTTATTACGAGGTTGTC 59.938 40.741 0.00 0.00 0.00 3.18
1822 1943 6.865205 GTCTACTGTGTTTATTACGAGGTTGT 59.135 38.462 0.00 0.00 0.00 3.32
1823 1944 6.864685 TGTCTACTGTGTTTATTACGAGGTTG 59.135 38.462 0.00 0.00 0.00 3.77
1824 1945 6.865205 GTGTCTACTGTGTTTATTACGAGGTT 59.135 38.462 0.00 0.00 0.00 3.50
1825 1946 6.016024 TGTGTCTACTGTGTTTATTACGAGGT 60.016 38.462 0.00 0.00 0.00 3.85
1826 1947 6.307318 GTGTGTCTACTGTGTTTATTACGAGG 59.693 42.308 0.00 0.00 0.00 4.63
1827 1948 6.307318 GGTGTGTCTACTGTGTTTATTACGAG 59.693 42.308 0.00 0.00 0.00 4.18
1828 1949 6.016024 AGGTGTGTCTACTGTGTTTATTACGA 60.016 38.462 0.00 0.00 0.00 3.43
1829 1950 6.089016 CAGGTGTGTCTACTGTGTTTATTACG 59.911 42.308 0.00 0.00 0.00 3.18
1954 2075 3.357203 CTGAGTCACCTTAGGCTGTAGA 58.643 50.000 0.00 0.00 0.00 2.59
2214 2342 2.267006 CGATGCTCCACCACAGCT 59.733 61.111 0.00 0.00 37.79 4.24
2215 2343 2.103042 GTCGATGCTCCACCACAGC 61.103 63.158 0.00 0.00 37.40 4.40
2216 2344 0.107993 ATGTCGATGCTCCACCACAG 60.108 55.000 0.00 0.00 0.00 3.66
2571 3876 0.030235 GGGACAACACAAAGCCGAAC 59.970 55.000 0.00 0.00 0.00 3.95
2574 3879 0.535102 AGAGGGACAACACAAAGCCG 60.535 55.000 0.00 0.00 0.00 5.52
2648 3954 1.938625 ACAAATGTGCAAGCCAACAC 58.061 45.000 0.00 0.00 37.31 3.32
2727 4039 1.144913 ACCCAAAACCTTAGCAGCAGA 59.855 47.619 0.00 0.00 0.00 4.26
2777 4091 0.808755 GGTACTGGGATTTGCGGTTG 59.191 55.000 0.00 0.00 0.00 3.77
2812 4130 1.065709 TCAGGATTTCTTGCCCGGTAC 60.066 52.381 0.00 0.00 0.00 3.34
2898 4229 5.761234 ACCGCAGTAACAGAAAAATACAAGA 59.239 36.000 0.00 0.00 0.00 3.02
2946 4279 4.464947 GATCCCGGATGAAAAGAAATCCT 58.535 43.478 4.08 0.00 40.28 3.24
3104 4625 2.110967 GTGATGCACCGCAGCTCAT 61.111 57.895 5.76 0.00 45.80 2.90


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

AutoCloner maintained by Alex Coulton.