Multiple sequence alignment - TraesCS5D01G156000

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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 TraesCS5D01G156000 chr5D 100.000 4354 0 0 1 4354 244370048 244365695 0.000000e+00 8041.0
1 TraesCS5D01G156000 chr5D 96.850 127 4 0 276 402 7945908 7945782 3.410000e-51 213.0
2 TraesCS5D01G156000 chr5B 94.395 2837 104 17 418 3214 277638064 277635243 0.000000e+00 4307.0
3 TraesCS5D01G156000 chr5B 93.497 1138 52 16 3205 4324 277632871 277631738 0.000000e+00 1672.0
4 TraesCS5D01G156000 chr5B 93.023 215 9 4 67 277 277638286 277638074 4.230000e-80 309.0
5 TraesCS5D01G156000 chr5B 87.838 74 6 3 2 72 8543989 8543916 2.790000e-12 84.2
6 TraesCS5D01G156000 chr5A 93.631 2842 124 32 418 3214 328718878 328716049 0.000000e+00 4193.0
7 TraesCS5D01G156000 chr5A 94.670 863 37 7 3469 4324 328715228 328714368 0.000000e+00 1330.0
8 TraesCS5D01G156000 chr5A 97.949 195 3 1 3206 3399 328715420 328715226 1.940000e-88 337.0
9 TraesCS5D01G156000 chr5A 92.273 220 7 7 67 277 328719106 328718888 1.970000e-78 303.0
10 TraesCS5D01G156000 chr5A 95.276 127 6 0 276 402 439864776 439864650 7.380000e-48 202.0
11 TraesCS5D01G156000 chr5A 94.030 134 7 1 270 403 523741601 523741469 7.380000e-48 202.0
12 TraesCS5D01G156000 chr5A 90.141 71 4 3 1 69 436259241 436259172 6.000000e-14 89.8
13 TraesCS5D01G156000 chr5A 87.671 73 8 1 1 72 44998139 44998067 2.790000e-12 84.2
14 TraesCS5D01G156000 chrUn 97.692 130 3 0 273 402 108296189 108296318 1.580000e-54 224.0
15 TraesCS5D01G156000 chr4D 96.947 131 4 0 272 402 8137598 8137728 2.040000e-53 220.0
16 TraesCS5D01G156000 chr4D 94.074 135 7 1 268 402 329006000 329006133 2.050000e-48 204.0
17 TraesCS5D01G156000 chr4D 90.000 70 6 1 1 69 414221178 414221109 6.000000e-14 89.8
18 TraesCS5D01G156000 chr4D 88.406 69 6 2 1 69 213840211 213840277 1.000000e-11 82.4
19 TraesCS5D01G156000 chr6D 96.094 128 5 0 275 402 87124599 87124472 4.410000e-50 209.0
20 TraesCS5D01G156000 chr4A 93.571 140 8 1 264 403 520182070 520181932 1.590000e-49 207.0
21 TraesCS5D01G156000 chr7B 92.254 142 10 1 261 402 108491014 108491154 2.660000e-47 200.0
22 TraesCS5D01G156000 chr3B 92.806 139 8 2 275 412 583843955 583843818 2.660000e-47 200.0
23 TraesCS5D01G156000 chr3B 88.732 71 5 2 1 69 826092920 826092989 2.790000e-12 84.2
24 TraesCS5D01G156000 chr3A 91.304 69 6 0 1 69 265542776 265542708 1.290000e-15 95.3
25 TraesCS5D01G156000 chr1B 88.571 70 7 1 1 69 476018860 476018791 2.790000e-12 84.2
26 TraesCS5D01G156000 chr1B 92.683 41 2 1 4315 4354 679695854 679695814 1.690000e-04 58.4
27 TraesCS5D01G156000 chr2D 88.406 69 7 1 2 69 517098560 517098628 1.000000e-11 82.4


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 TraesCS5D01G156000 chr5D 244365695 244370048 4353 True 8041.00 8041 100.000000 1 4354 1 chr5D.!!$R2 4353
1 TraesCS5D01G156000 chr5B 277631738 277638286 6548 True 2096.00 4307 93.638333 67 4324 3 chr5B.!!$R2 4257
2 TraesCS5D01G156000 chr5A 328714368 328719106 4738 True 1540.75 4193 94.630750 67 4324 4 chr5A.!!$R5 4257

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
294 306 0.032813 TACTCCCTCCGTCCCGAAAT 60.033 55.0 0.00 0.00 0.00 2.17 F
295 307 0.032813 ACTCCCTCCGTCCCGAAATA 60.033 55.0 0.00 0.00 0.00 1.40 F
401 413 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.0 13.64 0.00 46.06 2.59 F
402 414 0.032813 TTTCCGGACGGAGGGAGTAT 60.033 55.0 13.64 0.00 46.06 2.12 F
530 542 0.319555 CTGAGCCGAGAAAACCGTCA 60.320 55.0 0.00 0.00 0.00 4.35 F
2486 2552 0.032117 TGGGCCTAGAGCTGCTCTTA 60.032 55.0 34.42 19.55 41.50 2.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1344 1383 0.465460 TTTTGGACAAGGAGCACGCT 60.465 50.000 0.00 0.0 0.00 5.07 R
1354 1393 1.614850 GGGCGATAGGGTTTTGGACAA 60.615 52.381 0.00 0.0 0.00 3.18 R
2384 2432 1.760192 ATCAAGCATCTTGGTGGAGC 58.240 50.000 6.71 0.0 30.47 4.70 R
2462 2528 1.006400 AGCAGCTCTAGGCCCAAATTT 59.994 47.619 0.00 0.0 43.05 1.82 R
2547 2613 0.462759 GCCCTCCAAATCTCAGGACG 60.463 60.000 0.00 0.0 0.00 4.79 R
4189 6675 0.034863 TGATTTTACGAGGGCCACCC 60.035 55.000 6.18 0.0 45.90 4.61 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
33 34 5.638596 TCGTTTAGATCACTACTTGCTGA 57.361 39.130 0.00 0.00 0.00 4.26
34 35 6.208988 TCGTTTAGATCACTACTTGCTGAT 57.791 37.500 0.00 0.00 0.00 2.90
35 36 6.266323 TCGTTTAGATCACTACTTGCTGATC 58.734 40.000 0.00 3.76 42.16 2.92
41 42 6.503616 GATCACTACTTGCTGATCTAAACG 57.496 41.667 4.57 0.00 39.76 3.60
42 43 4.174009 TCACTACTTGCTGATCTAAACGC 58.826 43.478 0.00 0.00 0.00 4.84
43 44 4.082190 TCACTACTTGCTGATCTAAACGCT 60.082 41.667 0.00 0.00 0.00 5.07
44 45 4.266502 CACTACTTGCTGATCTAAACGCTC 59.733 45.833 0.00 0.00 0.00 5.03
45 46 3.601443 ACTTGCTGATCTAAACGCTCT 57.399 42.857 0.00 0.00 0.00 4.09
46 47 3.931578 ACTTGCTGATCTAAACGCTCTT 58.068 40.909 0.00 0.00 0.00 2.85
47 48 5.073311 ACTTGCTGATCTAAACGCTCTTA 57.927 39.130 0.00 0.00 0.00 2.10
48 49 5.665459 ACTTGCTGATCTAAACGCTCTTAT 58.335 37.500 0.00 0.00 0.00 1.73
49 50 6.806751 ACTTGCTGATCTAAACGCTCTTATA 58.193 36.000 0.00 0.00 0.00 0.98
50 51 7.437748 ACTTGCTGATCTAAACGCTCTTATAT 58.562 34.615 0.00 0.00 0.00 0.86
51 52 7.928706 ACTTGCTGATCTAAACGCTCTTATATT 59.071 33.333 0.00 0.00 0.00 1.28
52 53 8.662781 TTGCTGATCTAAACGCTCTTATATTT 57.337 30.769 0.00 0.00 0.00 1.40
53 54 8.299262 TGCTGATCTAAACGCTCTTATATTTC 57.701 34.615 0.00 0.00 0.00 2.17
54 55 8.144478 TGCTGATCTAAACGCTCTTATATTTCT 58.856 33.333 0.00 0.00 0.00 2.52
55 56 8.983724 GCTGATCTAAACGCTCTTATATTTCTT 58.016 33.333 0.00 0.00 0.00 2.52
58 59 9.587461 GATCTAAACGCTCTTATATTTCTTTGC 57.413 33.333 0.00 0.00 0.00 3.68
59 60 8.487313 TCTAAACGCTCTTATATTTCTTTGCA 57.513 30.769 0.00 0.00 0.00 4.08
60 61 8.941977 TCTAAACGCTCTTATATTTCTTTGCAA 58.058 29.630 0.00 0.00 0.00 4.08
61 62 9.214953 CTAAACGCTCTTATATTTCTTTGCAAG 57.785 33.333 0.00 0.00 0.00 4.01
62 63 6.124088 ACGCTCTTATATTTCTTTGCAAGG 57.876 37.500 1.35 1.35 0.00 3.61
63 64 5.066505 ACGCTCTTATATTTCTTTGCAAGGG 59.933 40.000 8.88 2.01 0.00 3.95
64 65 5.506317 CGCTCTTATATTTCTTTGCAAGGGG 60.506 44.000 8.88 0.00 0.00 4.79
65 66 5.594317 GCTCTTATATTTCTTTGCAAGGGGA 59.406 40.000 8.88 1.95 0.00 4.81
66 67 6.238869 GCTCTTATATTTCTTTGCAAGGGGAG 60.239 42.308 8.88 0.00 0.00 4.30
67 68 6.731467 TCTTATATTTCTTTGCAAGGGGAGT 58.269 36.000 8.88 0.00 0.00 3.85
68 69 7.867921 TCTTATATTTCTTTGCAAGGGGAGTA 58.132 34.615 8.88 0.40 0.00 2.59
69 70 7.993183 TCTTATATTTCTTTGCAAGGGGAGTAG 59.007 37.037 8.88 0.00 0.00 2.57
70 71 3.876309 TTTCTTTGCAAGGGGAGTAGT 57.124 42.857 8.88 0.00 0.00 2.73
87 88 5.179555 GGAGTAGTTCTCAGAAAAATTGCGT 59.820 40.000 0.00 0.00 44.40 5.24
95 96 6.680810 TCTCAGAAAAATTGCGTTGATCAAT 58.319 32.000 12.12 0.00 35.83 2.57
107 108 4.744631 GCGTTGATCAATTGTTGAAACCTT 59.255 37.500 12.12 0.00 43.95 3.50
181 182 4.636206 GGTGAATACAGGGATGAAGTCAAC 59.364 45.833 0.00 0.00 0.00 3.18
277 289 9.377312 CCGAACCTATACCTACTATCTAAGTAC 57.623 40.741 0.00 0.00 39.80 2.73
281 293 9.056799 ACCTATACCTACTATCTAAGTACTCCC 57.943 40.741 0.00 0.00 39.80 4.30
282 294 9.282905 CCTATACCTACTATCTAAGTACTCCCT 57.717 40.741 0.00 0.00 39.80 4.20
284 296 6.452757 ACCTACTATCTAAGTACTCCCTCC 57.547 45.833 0.00 0.00 39.80 4.30
285 297 5.012975 ACCTACTATCTAAGTACTCCCTCCG 59.987 48.000 0.00 0.00 39.80 4.63
286 298 5.012975 CCTACTATCTAAGTACTCCCTCCGT 59.987 48.000 0.00 0.00 39.80 4.69
287 299 4.971939 ACTATCTAAGTACTCCCTCCGTC 58.028 47.826 0.00 0.00 36.36 4.79
288 300 2.725221 TCTAAGTACTCCCTCCGTCC 57.275 55.000 0.00 0.00 0.00 4.79
289 301 1.213926 TCTAAGTACTCCCTCCGTCCC 59.786 57.143 0.00 0.00 0.00 4.46
290 302 0.107017 TAAGTACTCCCTCCGTCCCG 60.107 60.000 0.00 0.00 0.00 5.14
291 303 1.856539 AAGTACTCCCTCCGTCCCGA 61.857 60.000 0.00 0.00 0.00 5.14
292 304 1.379044 GTACTCCCTCCGTCCCGAA 60.379 63.158 0.00 0.00 0.00 4.30
293 305 0.967380 GTACTCCCTCCGTCCCGAAA 60.967 60.000 0.00 0.00 0.00 3.46
294 306 0.032813 TACTCCCTCCGTCCCGAAAT 60.033 55.000 0.00 0.00 0.00 2.17
295 307 0.032813 ACTCCCTCCGTCCCGAAATA 60.033 55.000 0.00 0.00 0.00 1.40
296 308 0.388294 CTCCCTCCGTCCCGAAATAC 59.612 60.000 0.00 0.00 0.00 1.89
297 309 0.032813 TCCCTCCGTCCCGAAATACT 60.033 55.000 0.00 0.00 0.00 2.12
298 310 0.828677 CCCTCCGTCCCGAAATACTT 59.171 55.000 0.00 0.00 0.00 2.24
299 311 1.472728 CCCTCCGTCCCGAAATACTTG 60.473 57.143 0.00 0.00 0.00 3.16
300 312 1.206371 CCTCCGTCCCGAAATACTTGT 59.794 52.381 0.00 0.00 0.00 3.16
301 313 2.537401 CTCCGTCCCGAAATACTTGTC 58.463 52.381 0.00 0.00 0.00 3.18
302 314 1.894466 TCCGTCCCGAAATACTTGTCA 59.106 47.619 0.00 0.00 0.00 3.58
303 315 2.498481 TCCGTCCCGAAATACTTGTCAT 59.502 45.455 0.00 0.00 0.00 3.06
304 316 2.864343 CCGTCCCGAAATACTTGTCATC 59.136 50.000 0.00 0.00 0.00 2.92
305 317 3.517602 CGTCCCGAAATACTTGTCATCA 58.482 45.455 0.00 0.00 0.00 3.07
306 318 3.930229 CGTCCCGAAATACTTGTCATCAA 59.070 43.478 0.00 0.00 0.00 2.57
307 319 4.390603 CGTCCCGAAATACTTGTCATCAAA 59.609 41.667 0.00 0.00 32.87 2.69
308 320 5.106869 CGTCCCGAAATACTTGTCATCAAAA 60.107 40.000 0.00 0.00 32.87 2.44
309 321 6.403200 CGTCCCGAAATACTTGTCATCAAAAT 60.403 38.462 0.00 0.00 32.87 1.82
310 322 6.747280 GTCCCGAAATACTTGTCATCAAAATG 59.253 38.462 0.00 0.00 32.87 2.32
311 323 6.035843 CCCGAAATACTTGTCATCAAAATGG 58.964 40.000 0.00 0.00 33.42 3.16
312 324 6.127758 CCCGAAATACTTGTCATCAAAATGGA 60.128 38.462 0.00 0.00 33.42 3.41
313 325 6.747280 CCGAAATACTTGTCATCAAAATGGAC 59.253 38.462 0.00 0.00 33.42 4.02
314 326 7.304735 CGAAATACTTGTCATCAAAATGGACA 58.695 34.615 0.00 0.00 33.42 4.02
315 327 7.807433 CGAAATACTTGTCATCAAAATGGACAA 59.193 33.333 0.00 0.00 34.59 3.18
316 328 9.474920 GAAATACTTGTCATCAAAATGGACAAA 57.525 29.630 7.70 0.00 34.98 2.83
317 329 9.829507 AAATACTTGTCATCAAAATGGACAAAA 57.170 25.926 7.70 0.84 34.98 2.44
318 330 9.829507 AATACTTGTCATCAAAATGGACAAAAA 57.170 25.926 7.70 0.55 34.98 1.94
367 379 9.607333 ATGTCTAGATACATCTCCTTTTATCCA 57.393 33.333 0.00 0.00 35.08 3.41
368 380 9.607333 TGTCTAGATACATCTCCTTTTATCCAT 57.393 33.333 0.00 0.00 38.32 3.41
376 388 8.827832 ACATCTCCTTTTATCCATTTTGATGA 57.172 30.769 0.00 0.00 33.85 2.92
377 389 8.689972 ACATCTCCTTTTATCCATTTTGATGAC 58.310 33.333 0.00 0.00 33.85 3.06
378 390 8.689061 CATCTCCTTTTATCCATTTTGATGACA 58.311 33.333 0.00 0.00 32.05 3.58
379 391 8.648698 TCTCCTTTTATCCATTTTGATGACAA 57.351 30.769 0.00 0.00 0.00 3.18
380 392 8.742777 TCTCCTTTTATCCATTTTGATGACAAG 58.257 33.333 0.00 0.00 37.32 3.16
381 393 8.421249 TCCTTTTATCCATTTTGATGACAAGT 57.579 30.769 0.00 0.00 37.32 3.16
382 394 9.527157 TCCTTTTATCCATTTTGATGACAAGTA 57.473 29.630 0.00 0.00 37.32 2.24
388 400 6.851609 TCCATTTTGATGACAAGTATTTCCG 58.148 36.000 0.00 0.00 37.32 4.30
389 401 6.035843 CCATTTTGATGACAAGTATTTCCGG 58.964 40.000 0.00 0.00 37.32 5.14
390 402 6.127758 CCATTTTGATGACAAGTATTTCCGGA 60.128 38.462 0.00 0.00 37.32 5.14
391 403 5.873179 TTTGATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
392 404 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
393 405 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
394 406 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
395 407 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
396 408 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
397 409 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
398 410 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
399 411 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
400 412 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
401 413 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
402 414 0.032813 TTTCCGGACGGAGGGAGTAT 60.033 55.000 13.64 0.00 46.06 2.12
403 415 0.466922 TTCCGGACGGAGGGAGTATC 60.467 60.000 13.64 0.00 46.06 2.24
404 416 1.150992 CCGGACGGAGGGAGTATCT 59.849 63.158 4.40 0.00 37.50 1.98
405 417 0.890090 CCGGACGGAGGGAGTATCTC 60.890 65.000 4.40 0.00 37.50 2.75
415 427 3.934457 GGGAGTATCTCTCTAAGCTGC 57.066 52.381 0.00 0.00 42.40 5.25
416 428 3.496331 GGGAGTATCTCTCTAAGCTGCT 58.504 50.000 0.00 0.00 42.40 4.24
515 527 1.077858 GAAGCCCTTGCCTCCTGAG 60.078 63.158 0.00 0.00 38.69 3.35
530 542 0.319555 CTGAGCCGAGAAAACCGTCA 60.320 55.000 0.00 0.00 0.00 4.35
531 543 0.320374 TGAGCCGAGAAAACCGTCAT 59.680 50.000 0.00 0.00 0.00 3.06
621 634 6.096036 TGAAACTGAACTGAATTGCGAAAAA 58.904 32.000 0.00 0.00 0.00 1.94
667 680 6.551736 ACATTTGATTTGTTACCGTATGCTC 58.448 36.000 0.00 0.00 0.00 4.26
674 695 4.664150 TGTTACCGTATGCTCATGATCA 57.336 40.909 1.00 1.00 0.00 2.92
706 727 2.159310 TCGTTTGCCTTCCTGTTGTTTG 60.159 45.455 0.00 0.00 0.00 2.93
750 771 1.486310 ACACAGCAAGAGAACACCAGA 59.514 47.619 0.00 0.00 0.00 3.86
904 927 5.195848 ACTAGAACTGTAGAAGTAGGGCT 57.804 43.478 0.00 0.00 38.56 5.19
905 928 4.951094 ACTAGAACTGTAGAAGTAGGGCTG 59.049 45.833 0.00 0.00 38.56 4.85
906 929 3.100671 AGAACTGTAGAAGTAGGGCTGG 58.899 50.000 0.00 0.00 38.56 4.85
907 930 1.196012 ACTGTAGAAGTAGGGCTGGC 58.804 55.000 0.00 0.00 37.36 4.85
918 952 2.980233 GGCTGGCGTGCAGAAAGT 60.980 61.111 4.78 0.00 34.04 2.66
950 989 4.705507 AGATAGTAAAGAGGACGTGCAGAA 59.294 41.667 10.52 0.00 0.00 3.02
979 1018 0.382873 TTACACGTCCCCATCGATCG 59.617 55.000 9.36 9.36 0.00 3.69
984 1023 1.367471 GTCCCCATCGATCGCATCA 59.633 57.895 11.09 0.00 0.00 3.07
987 1026 0.321034 CCCCATCGATCGCATCACAT 60.321 55.000 11.09 0.00 0.00 3.21
989 1028 1.073964 CCATCGATCGCATCACATCC 58.926 55.000 11.09 0.00 0.00 3.51
991 1030 0.681175 ATCGATCGCATCACATCCCA 59.319 50.000 11.09 0.00 0.00 4.37
1155 1194 0.465824 CCACCCTCTCCGACTACGAT 60.466 60.000 0.00 0.00 42.66 3.73
1403 1442 1.299773 CGCTCCTCTTCATCCTCGC 60.300 63.158 0.00 0.00 0.00 5.03
1585 1624 4.451150 TGCAGACTAAGCCGCCGG 62.451 66.667 0.00 0.00 0.00 6.13
1670 1709 4.293671 CGGGTTTGGGCTGGGGAA 62.294 66.667 0.00 0.00 0.00 3.97
1809 1848 0.468226 TGCTCGACCAGGTTGTCTTT 59.532 50.000 6.73 0.00 32.97 2.52
1823 1862 4.096984 GGTTGTCTTTTCATCCTGCCTATG 59.903 45.833 0.00 0.00 0.00 2.23
1827 1866 5.128919 GTCTTTTCATCCTGCCTATGATGT 58.871 41.667 0.00 0.00 39.47 3.06
1836 1875 5.428253 TCCTGCCTATGATGTTGTTCTTAC 58.572 41.667 0.00 0.00 0.00 2.34
1844 1883 8.607459 CCTATGATGTTGTTCTTACAGTGATTC 58.393 37.037 0.00 0.00 35.28 2.52
1850 1889 3.684305 TGTTCTTACAGTGATTCCATGCG 59.316 43.478 0.00 0.00 0.00 4.73
1971 2012 6.582672 GGAGCTACATCTTGCAAAGTTTTAAC 59.417 38.462 0.00 0.00 46.34 2.01
2073 2116 3.066760 GCAAGGGTGGTAGTTATTCATGC 59.933 47.826 0.00 0.00 0.00 4.06
2098 2146 4.011023 ACGCAGAGTAGTGTGTAGAGAAT 58.989 43.478 0.00 0.00 39.40 2.40
2127 2175 6.600822 TCATTCTGGTCAAGATTTGATTCTCC 59.399 38.462 0.00 0.00 42.47 3.71
2172 2220 6.154363 TCGTGTAGATTATGCATGGGATATGA 59.846 38.462 10.16 0.00 31.89 2.15
2384 2432 9.695526 CTCAGTCTATCTCCTATTTCAATCTTG 57.304 37.037 0.00 0.00 0.00 3.02
2486 2552 0.032117 TGGGCCTAGAGCTGCTCTTA 60.032 55.000 34.42 19.55 41.50 2.10
2547 2613 1.410004 GGTTTATAAAGCCAGGGCCC 58.590 55.000 16.46 16.46 43.17 5.80
2843 2911 9.932207 TTTTCTGTGAAAATGCAAATCAGATAT 57.068 25.926 0.00 0.00 31.99 1.63
2982 3056 1.813896 CCATGCGCAGTTTTCGTATG 58.186 50.000 18.32 5.46 45.26 2.39
3003 3077 2.520458 CTGGCAAACTCACCCCCA 59.480 61.111 0.00 0.00 0.00 4.96
3326 5789 1.451936 GAACCTGGTGCTGAGGTGT 59.548 57.895 0.00 0.00 43.42 4.16
3424 5902 6.858478 GGACTCTTGTAAAACTTGCTTCAATC 59.142 38.462 0.00 0.00 0.00 2.67
3425 5903 7.333528 ACTCTTGTAAAACTTGCTTCAATCA 57.666 32.000 0.00 0.00 0.00 2.57
3426 5904 7.771183 ACTCTTGTAAAACTTGCTTCAATCAA 58.229 30.769 0.00 0.00 0.00 2.57
3427 5905 8.416329 ACTCTTGTAAAACTTGCTTCAATCAAT 58.584 29.630 0.00 0.00 0.00 2.57
3478 5956 7.599630 ACTCTTTTGTAGTTTTGTTACGACA 57.400 32.000 0.00 0.00 32.85 4.35
3620 6101 2.270923 TCGAGATTCCAGCACATTTCG 58.729 47.619 0.00 0.00 0.00 3.46
3658 6139 3.498082 CAACTATTTGGTACTTTGCCGC 58.502 45.455 0.00 0.00 0.00 6.53
3677 6158 1.286880 CGCAAGGAGCAACTTTGGG 59.713 57.895 7.92 7.92 46.13 4.12
3680 6161 1.533994 AAGGAGCAACTTTGGGCCC 60.534 57.895 17.59 17.59 0.00 5.80
3687 6168 0.808755 CAACTTTGGGCCCGATGTAC 59.191 55.000 26.87 0.00 0.00 2.90
3690 6171 1.910671 ACTTTGGGCCCGATGTACTTA 59.089 47.619 25.77 2.92 0.00 2.24
3707 6188 6.734137 TGTACTTAAACCTGAAATGTTGCTG 58.266 36.000 0.00 0.00 0.00 4.41
3775 6258 4.275936 GCCTATGTTGACTTGTGTTTCACT 59.724 41.667 1.72 0.00 35.11 3.41
3785 6268 6.535150 TGACTTGTGTTTCACTTAACTCTCTG 59.465 38.462 1.72 0.00 35.11 3.35
3812 6295 4.833380 AGTGTGTATATGCTCCGGAATACT 59.167 41.667 19.75 8.38 0.00 2.12
3820 6303 2.516448 TCCGGAATACTGGAGCAGG 58.484 57.895 0.00 0.00 45.56 4.85
3952 6436 0.040067 GCTTGCCGTTCAGAAACTGG 60.040 55.000 0.00 0.00 34.34 4.00
4052 6537 4.738740 CGGACTGAGTCGTAATGTATTTCC 59.261 45.833 6.50 0.00 32.65 3.13
4061 6546 6.153000 AGTCGTAATGTATTTCCTCAGACACT 59.847 38.462 0.00 0.00 0.00 3.55
4137 6623 9.992910 ATTTGTTGATTTTTCTTTTCTTTCTGC 57.007 25.926 0.00 0.00 0.00 4.26
4189 6675 1.071699 TCCACCGTTTCCTTCTTCAGG 59.928 52.381 0.00 0.00 45.64 3.86
4201 6687 4.974438 TTCAGGGGTGGCCCTCGT 62.974 66.667 0.00 0.00 44.66 4.18
4324 6810 5.857822 AGATTGGCTGACTTTAACGTAAC 57.142 39.130 0.00 0.00 0.00 2.50
4325 6811 5.302360 AGATTGGCTGACTTTAACGTAACA 58.698 37.500 0.00 0.00 0.00 2.41
4326 6812 4.799419 TTGGCTGACTTTAACGTAACAC 57.201 40.909 0.00 0.00 0.00 3.32
4327 6813 4.062677 TGGCTGACTTTAACGTAACACT 57.937 40.909 0.00 0.00 0.00 3.55
4328 6814 5.199024 TGGCTGACTTTAACGTAACACTA 57.801 39.130 0.00 0.00 0.00 2.74
4329 6815 5.224888 TGGCTGACTTTAACGTAACACTAG 58.775 41.667 0.00 0.00 0.00 2.57
4330 6816 4.091075 GGCTGACTTTAACGTAACACTAGC 59.909 45.833 0.00 0.00 0.00 3.42
4331 6817 4.682860 GCTGACTTTAACGTAACACTAGCA 59.317 41.667 0.00 0.00 0.00 3.49
4332 6818 5.176223 GCTGACTTTAACGTAACACTAGCAA 59.824 40.000 0.00 0.00 0.00 3.91
4333 6819 6.292488 GCTGACTTTAACGTAACACTAGCAAA 60.292 38.462 0.00 0.00 0.00 3.68
4334 6820 7.169035 TGACTTTAACGTAACACTAGCAAAG 57.831 36.000 0.00 0.00 0.00 2.77
4335 6821 6.979817 TGACTTTAACGTAACACTAGCAAAGA 59.020 34.615 0.00 0.00 0.00 2.52
4336 6822 7.654520 TGACTTTAACGTAACACTAGCAAAGAT 59.345 33.333 0.00 0.00 0.00 2.40
4337 6823 7.793902 ACTTTAACGTAACACTAGCAAAGATG 58.206 34.615 0.00 0.00 0.00 2.90
4348 6834 3.038946 CAAAGATGCCCATGCGTTG 57.961 52.632 0.00 0.00 41.78 4.10
4349 6835 1.079875 CAAAGATGCCCATGCGTTGC 61.080 55.000 0.00 0.00 41.78 4.17
4350 6836 1.534336 AAAGATGCCCATGCGTTGCA 61.534 50.000 2.57 2.57 44.86 4.08
4351 6837 1.534336 AAGATGCCCATGCGTTGCAA 61.534 50.000 0.00 0.00 43.62 4.08
4352 6838 1.806758 GATGCCCATGCGTTGCAAC 60.807 57.895 19.89 19.89 43.62 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 6.208988 TCAGCAAGTAGTGATCTAAACGAT 57.791 37.500 0.00 0.00 34.25 3.73
11 12 5.638596 TCAGCAAGTAGTGATCTAAACGA 57.361 39.130 0.00 0.00 0.00 3.85
12 13 6.503616 GATCAGCAAGTAGTGATCTAAACG 57.496 41.667 5.29 0.00 43.88 3.60
18 19 5.051374 GCGTTTAGATCAGCAAGTAGTGATC 60.051 44.000 4.48 4.48 46.45 2.92
19 20 4.806247 GCGTTTAGATCAGCAAGTAGTGAT 59.194 41.667 0.00 0.00 36.07 3.06
20 21 4.082190 AGCGTTTAGATCAGCAAGTAGTGA 60.082 41.667 0.00 0.00 0.00 3.41
21 22 4.177026 AGCGTTTAGATCAGCAAGTAGTG 58.823 43.478 0.00 0.00 0.00 2.74
22 23 4.158764 AGAGCGTTTAGATCAGCAAGTAGT 59.841 41.667 0.00 0.00 37.82 2.73
23 24 4.677584 AGAGCGTTTAGATCAGCAAGTAG 58.322 43.478 0.00 0.00 37.82 2.57
24 25 4.720649 AGAGCGTTTAGATCAGCAAGTA 57.279 40.909 0.00 0.00 37.82 2.24
25 26 3.601443 AGAGCGTTTAGATCAGCAAGT 57.399 42.857 0.00 0.00 37.82 3.16
26 27 7.881643 ATATAAGAGCGTTTAGATCAGCAAG 57.118 36.000 0.00 0.00 37.82 4.01
27 28 8.662781 AAATATAAGAGCGTTTAGATCAGCAA 57.337 30.769 0.00 0.00 37.82 3.91
28 29 8.144478 AGAAATATAAGAGCGTTTAGATCAGCA 58.856 33.333 0.00 0.00 37.82 4.41
29 30 8.527567 AGAAATATAAGAGCGTTTAGATCAGC 57.472 34.615 0.00 0.00 37.82 4.26
32 33 9.587461 GCAAAGAAATATAAGAGCGTTTAGATC 57.413 33.333 0.00 0.00 35.01 2.75
33 34 9.109393 TGCAAAGAAATATAAGAGCGTTTAGAT 57.891 29.630 0.00 0.00 0.00 1.98
34 35 8.487313 TGCAAAGAAATATAAGAGCGTTTAGA 57.513 30.769 0.00 0.00 0.00 2.10
48 49 8.013004 GAGAACTACTCCCCTTGCAAAGAAATA 61.013 40.741 0.00 0.00 42.26 1.40
49 50 7.248681 GAGAACTACTCCCCTTGCAAAGAAAT 61.249 42.308 0.00 0.00 42.26 2.17
50 51 5.977209 GAGAACTACTCCCCTTGCAAAGAAA 60.977 44.000 0.00 0.00 42.26 2.52
51 52 4.505039 GAGAACTACTCCCCTTGCAAAGAA 60.505 45.833 0.00 0.00 42.26 2.52
52 53 3.008049 GAGAACTACTCCCCTTGCAAAGA 59.992 47.826 0.00 0.00 42.26 2.52
53 54 3.244561 TGAGAACTACTCCCCTTGCAAAG 60.245 47.826 0.00 0.00 44.34 2.77
54 55 2.708861 TGAGAACTACTCCCCTTGCAAA 59.291 45.455 0.00 0.00 44.34 3.68
55 56 2.303022 CTGAGAACTACTCCCCTTGCAA 59.697 50.000 0.00 0.00 44.34 4.08
56 57 1.902508 CTGAGAACTACTCCCCTTGCA 59.097 52.381 0.00 0.00 44.34 4.08
57 58 2.180276 TCTGAGAACTACTCCCCTTGC 58.820 52.381 0.00 0.00 44.34 4.01
58 59 4.891992 TTTCTGAGAACTACTCCCCTTG 57.108 45.455 0.00 0.00 44.34 3.61
59 60 5.906772 TTTTTCTGAGAACTACTCCCCTT 57.093 39.130 0.00 0.00 44.34 3.95
60 61 6.241645 CAATTTTTCTGAGAACTACTCCCCT 58.758 40.000 0.00 0.00 44.34 4.79
61 62 5.106118 GCAATTTTTCTGAGAACTACTCCCC 60.106 44.000 0.00 0.00 44.34 4.81
62 63 5.390991 CGCAATTTTTCTGAGAACTACTCCC 60.391 44.000 0.00 0.00 44.34 4.30
63 64 5.179555 ACGCAATTTTTCTGAGAACTACTCC 59.820 40.000 0.00 0.00 44.34 3.85
64 65 6.229561 ACGCAATTTTTCTGAGAACTACTC 57.770 37.500 0.00 0.00 45.11 2.59
65 66 6.260050 TCAACGCAATTTTTCTGAGAACTACT 59.740 34.615 0.00 0.00 0.00 2.57
66 67 6.427150 TCAACGCAATTTTTCTGAGAACTAC 58.573 36.000 0.00 0.00 0.00 2.73
67 68 6.612247 TCAACGCAATTTTTCTGAGAACTA 57.388 33.333 0.00 0.00 0.00 2.24
68 69 5.499139 TCAACGCAATTTTTCTGAGAACT 57.501 34.783 0.00 0.00 0.00 3.01
69 70 5.914635 TGATCAACGCAATTTTTCTGAGAAC 59.085 36.000 0.00 0.00 0.00 3.01
70 71 6.070897 TGATCAACGCAATTTTTCTGAGAA 57.929 33.333 0.00 0.00 0.00 2.87
87 88 7.605691 ACACAAAAGGTTTCAACAATTGATCAA 59.394 29.630 13.59 11.26 39.84 2.57
95 96 5.215252 TCCAACACAAAAGGTTTCAACAA 57.785 34.783 0.00 0.00 0.00 2.83
107 108 3.573538 CCTGACAATCCATCCAACACAAA 59.426 43.478 0.00 0.00 0.00 2.83
282 294 8.687116 TTTGATGACAAGTATTTCGGGACGGA 62.687 42.308 0.00 0.00 44.62 4.69
283 295 6.592789 TTTGATGACAAGTATTTCGGGACGG 61.593 44.000 0.00 0.00 44.62 4.79
284 296 4.390603 TTTGATGACAAGTATTTCGGGACG 59.609 41.667 0.00 0.00 45.38 4.79
285 297 5.873179 TTTGATGACAAGTATTTCGGGAC 57.127 39.130 0.00 0.00 37.32 4.46
286 298 6.127758 CCATTTTGATGACAAGTATTTCGGGA 60.128 38.462 0.00 0.00 37.32 5.14
287 299 6.035843 CCATTTTGATGACAAGTATTTCGGG 58.964 40.000 0.00 0.00 37.32 5.14
288 300 6.747280 GTCCATTTTGATGACAAGTATTTCGG 59.253 38.462 0.00 0.00 37.32 4.30
289 301 7.304735 TGTCCATTTTGATGACAAGTATTTCG 58.695 34.615 0.00 0.00 37.32 3.46
290 302 9.474920 TTTGTCCATTTTGATGACAAGTATTTC 57.525 29.630 0.00 0.00 37.13 2.17
291 303 9.829507 TTTTGTCCATTTTGATGACAAGTATTT 57.170 25.926 0.00 0.00 37.13 1.40
292 304 9.829507 TTTTTGTCCATTTTGATGACAAGTATT 57.170 25.926 0.00 0.00 37.13 1.89
341 353 9.607333 TGGATAAAAGGAGATGTATCTAGACAT 57.393 33.333 0.00 0.00 42.82 3.06
342 354 9.607333 ATGGATAAAAGGAGATGTATCTAGACA 57.393 33.333 0.00 0.00 37.25 3.41
350 362 9.919416 TCATCAAAATGGATAAAAGGAGATGTA 57.081 29.630 0.00 0.00 33.42 2.29
351 363 8.689972 GTCATCAAAATGGATAAAAGGAGATGT 58.310 33.333 0.00 0.00 33.42 3.06
352 364 8.689061 TGTCATCAAAATGGATAAAAGGAGATG 58.311 33.333 0.00 0.00 33.42 2.90
353 365 8.827832 TGTCATCAAAATGGATAAAAGGAGAT 57.172 30.769 0.00 0.00 33.42 2.75
354 366 8.648698 TTGTCATCAAAATGGATAAAAGGAGA 57.351 30.769 0.00 0.00 33.42 3.71
355 367 8.526147 ACTTGTCATCAAAATGGATAAAAGGAG 58.474 33.333 0.00 0.00 33.42 3.69
356 368 8.421249 ACTTGTCATCAAAATGGATAAAAGGA 57.579 30.769 0.00 0.00 33.42 3.36
362 374 8.620416 CGGAAATACTTGTCATCAAAATGGATA 58.380 33.333 0.00 0.00 33.42 2.59
363 375 7.416664 CCGGAAATACTTGTCATCAAAATGGAT 60.417 37.037 0.00 0.00 33.42 3.41
364 376 6.127758 CCGGAAATACTTGTCATCAAAATGGA 60.128 38.462 0.00 0.00 33.42 3.41
365 377 6.035843 CCGGAAATACTTGTCATCAAAATGG 58.964 40.000 0.00 0.00 33.42 3.16
366 378 6.747280 GTCCGGAAATACTTGTCATCAAAATG 59.253 38.462 5.23 0.00 32.87 2.32
367 379 6.403200 CGTCCGGAAATACTTGTCATCAAAAT 60.403 38.462 5.23 0.00 32.87 1.82
368 380 5.106869 CGTCCGGAAATACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
369 381 4.390603 CGTCCGGAAATACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
370 382 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
371 383 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
372 384 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
373 385 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
374 386 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
375 387 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
376 388 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
377 389 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
378 390 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
379 391 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
380 392 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
381 393 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
382 394 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
383 395 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
384 396 0.466922 GATACTCCCTCCGTCCGGAA 60.467 60.000 5.23 0.00 44.66 4.30
385 397 1.150081 GATACTCCCTCCGTCCGGA 59.850 63.158 0.00 0.00 42.90 5.14
386 398 0.890090 GAGATACTCCCTCCGTCCGG 60.890 65.000 0.00 0.00 0.00 5.14
387 399 0.108963 AGAGATACTCCCTCCGTCCG 59.891 60.000 0.00 0.00 0.00 4.79
388 400 1.422402 AGAGAGATACTCCCTCCGTCC 59.578 57.143 0.00 0.00 45.96 4.79
389 401 2.943036 AGAGAGATACTCCCTCCGTC 57.057 55.000 0.00 0.00 45.96 4.79
390 402 3.497227 GCTTAGAGAGATACTCCCTCCGT 60.497 52.174 0.00 0.00 45.96 4.69
391 403 3.078837 GCTTAGAGAGATACTCCCTCCG 58.921 54.545 0.00 0.00 45.96 4.63
392 404 4.079253 CAGCTTAGAGAGATACTCCCTCC 58.921 52.174 0.00 0.00 45.96 4.30
393 405 3.506067 GCAGCTTAGAGAGATACTCCCTC 59.494 52.174 0.00 0.00 45.96 4.30
394 406 3.140144 AGCAGCTTAGAGAGATACTCCCT 59.860 47.826 0.00 0.00 45.96 4.20
395 407 3.255642 CAGCAGCTTAGAGAGATACTCCC 59.744 52.174 0.00 0.00 45.96 4.30
396 408 3.305335 GCAGCAGCTTAGAGAGATACTCC 60.305 52.174 0.00 0.00 41.09 3.85
397 409 3.900941 GCAGCAGCTTAGAGAGATACTC 58.099 50.000 0.00 0.00 40.78 2.59
415 427 1.710103 CTCATCAGCAGCAGCAGCAG 61.710 60.000 12.92 3.97 45.49 4.24
416 428 1.745489 CTCATCAGCAGCAGCAGCA 60.745 57.895 12.92 0.00 45.49 4.41
515 527 0.734942 TCGATGACGGTTTTCTCGGC 60.735 55.000 0.00 0.00 40.21 5.54
530 542 3.594603 ACGAGAAATTGGACAGTCGAT 57.405 42.857 0.00 0.00 0.00 3.59
531 543 3.380479 AACGAGAAATTGGACAGTCGA 57.620 42.857 0.00 0.00 0.00 4.20
579 592 5.630680 AGTTTCAAATTAGATGTTTGCTGCG 59.369 36.000 0.00 0.00 36.69 5.18
593 606 6.272318 TCGCAATTCAGTTCAGTTTCAAATT 58.728 32.000 0.00 0.00 0.00 1.82
612 625 2.011222 AGTTCGTGTCCTTTTTCGCAA 58.989 42.857 0.00 0.00 0.00 4.85
621 634 3.548770 TCGTCCATATAGTTCGTGTCCT 58.451 45.455 0.00 0.00 0.00 3.85
657 670 5.277490 CGAAAAATGATCATGAGCATACGGT 60.277 40.000 25.67 12.10 36.27 4.83
667 680 4.007282 ACGACAGCGAAAAATGATCATG 57.993 40.909 9.46 0.00 41.64 3.07
674 695 1.336755 AGGCAAACGACAGCGAAAAAT 59.663 42.857 0.00 0.00 41.64 1.82
750 771 0.107165 GCCGGGCCTGAATCTAAACT 60.107 55.000 15.09 0.00 0.00 2.66
904 927 1.453015 AACCACTTTCTGCACGCCA 60.453 52.632 0.00 0.00 0.00 5.69
905 928 1.008538 CAACCACTTTCTGCACGCC 60.009 57.895 0.00 0.00 0.00 5.68
906 929 0.100503 AACAACCACTTTCTGCACGC 59.899 50.000 0.00 0.00 0.00 5.34
907 930 1.400142 TCAACAACCACTTTCTGCACG 59.600 47.619 0.00 0.00 0.00 5.34
918 952 6.571731 CGTCCTCTTTACTATCTCAACAACCA 60.572 42.308 0.00 0.00 0.00 3.67
950 989 2.498885 GGGGACGTGTAAAGGTCAGTAT 59.501 50.000 7.98 0.00 34.87 2.12
979 1018 1.322538 GGTGGGTTGGGATGTGATGC 61.323 60.000 0.00 0.00 0.00 3.91
984 1023 1.302949 CATCGGTGGGTTGGGATGT 59.697 57.895 0.00 0.00 33.36 3.06
987 1026 4.041762 GCCATCGGTGGGTTGGGA 62.042 66.667 18.38 0.00 46.14 4.37
991 1030 4.404098 GACGGCCATCGGTGGGTT 62.404 66.667 18.38 0.00 46.14 4.11
1171 1210 0.035439 GAGATGAAAAGGCACGGGGA 60.035 55.000 0.00 0.00 0.00 4.81
1344 1383 0.465460 TTTTGGACAAGGAGCACGCT 60.465 50.000 0.00 0.00 0.00 5.07
1354 1393 1.614850 GGGCGATAGGGTTTTGGACAA 60.615 52.381 0.00 0.00 0.00 3.18
1670 1709 3.317571 AGACGAGCCCTTGCAGCT 61.318 61.111 0.00 0.00 45.23 4.24
1809 1848 4.508551 ACAACATCATAGGCAGGATGAA 57.491 40.909 16.52 0.00 44.01 2.57
1823 1862 6.801539 TGGAATCACTGTAAGAACAACATC 57.198 37.500 0.00 0.00 37.43 3.06
1827 1866 4.154015 CGCATGGAATCACTGTAAGAACAA 59.846 41.667 0.00 0.00 37.43 2.83
1850 1889 4.670621 CGCAATAACTCGTAAATGCATTCC 59.329 41.667 13.38 5.71 31.36 3.01
1866 1905 3.376859 CCACTAGATGGTTTGCGCAATAA 59.623 43.478 25.64 12.93 44.46 1.40
2098 2146 8.868522 AATCAAATCTTGACCAGAATGACTAA 57.131 30.769 0.00 0.00 43.48 2.24
2115 2163 7.149569 TGTTGTGATGAAGGAGAATCAAATC 57.850 36.000 0.00 0.00 34.70 2.17
2127 2175 3.185188 CGAGTGAACCTGTTGTGATGAAG 59.815 47.826 0.00 0.00 0.00 3.02
2384 2432 1.760192 ATCAAGCATCTTGGTGGAGC 58.240 50.000 6.71 0.00 30.47 4.70
2462 2528 1.006400 AGCAGCTCTAGGCCCAAATTT 59.994 47.619 0.00 0.00 43.05 1.82
2486 2552 1.273327 CCGCCTTTTCTTGCCTTGAAT 59.727 47.619 0.00 0.00 0.00 2.57
2547 2613 0.462759 GCCCTCCAAATCTCAGGACG 60.463 60.000 0.00 0.00 0.00 4.79
2711 2779 6.695429 TCAATACATTTAAAATGTGGCAGCA 58.305 32.000 0.00 0.00 33.76 4.41
2885 2954 6.238869 GGCCTTTCCAGATTTGTATTCTCATC 60.239 42.308 0.00 0.00 34.01 2.92
2903 2973 2.350102 CGGTTTCGTGTAAAGGCCTTTC 60.350 50.000 33.64 23.47 34.23 2.62
2907 2977 1.228533 TTCGGTTTCGTGTAAAGGCC 58.771 50.000 0.00 0.00 37.69 5.19
2982 3056 0.960861 GGGGTGAGTTTGCCAGCTAC 60.961 60.000 0.00 0.00 33.02 3.58
3003 3077 8.497745 ACCATGATAATACACATCCTCTCTTTT 58.502 33.333 0.00 0.00 0.00 2.27
3150 3224 3.309600 AAGCCCGGTGTAGTAGATAGT 57.690 47.619 0.00 0.00 0.00 2.12
3204 3278 2.305009 CAAATCCTCTCATGCCCCTTC 58.695 52.381 0.00 0.00 0.00 3.46
3326 5789 0.320421 GTTGCAGTCCCGCTGTCTTA 60.320 55.000 0.00 0.00 46.64 2.10
3424 5902 1.678123 CCCTCAGGAGCACAGACATTG 60.678 57.143 0.00 0.00 33.47 2.82
3425 5903 0.617413 CCCTCAGGAGCACAGACATT 59.383 55.000 0.00 0.00 33.47 2.71
3426 5904 0.546267 ACCCTCAGGAGCACAGACAT 60.546 55.000 0.00 0.00 36.73 3.06
3427 5905 0.764369 AACCCTCAGGAGCACAGACA 60.764 55.000 0.00 0.00 36.73 3.41
3478 5956 8.405418 TGAGTCAACTACTGTAACAGAAGTAT 57.595 34.615 0.00 0.00 39.07 2.12
3578 6058 4.729868 AGACTGCAATTTTACCAGTTCCT 58.270 39.130 0.00 0.00 39.72 3.36
3620 6101 1.390463 GTTGCAGAACTAGCACGCTAC 59.610 52.381 0.00 0.00 42.54 3.58
3658 6139 1.286880 CCAAAGTTGCTCCTTGCGG 59.713 57.895 0.00 0.00 46.63 5.69
3677 6158 3.255969 TCAGGTTTAAGTACATCGGGC 57.744 47.619 0.00 0.00 0.00 6.13
3680 6161 6.523201 GCAACATTTCAGGTTTAAGTACATCG 59.477 38.462 0.00 0.00 0.00 3.84
3687 6168 5.591099 ACACAGCAACATTTCAGGTTTAAG 58.409 37.500 0.00 0.00 0.00 1.85
3690 6171 4.183101 CAACACAGCAACATTTCAGGTTT 58.817 39.130 0.00 0.00 0.00 3.27
3707 6188 1.535462 AGAATACACAAGCGCCAACAC 59.465 47.619 2.29 0.00 0.00 3.32
3775 6258 3.819564 ACACACTGCACAGAGAGTTAA 57.180 42.857 4.31 0.00 0.00 2.01
3785 6268 1.860950 CGGAGCATATACACACTGCAC 59.139 52.381 0.00 0.00 38.37 4.57
3820 6303 1.617947 AATCCCTGACTGGAGACGCC 61.618 60.000 0.00 0.00 37.96 5.68
3952 6436 2.028043 GCACTTTGCCAGCACCAC 59.972 61.111 0.00 0.00 37.42 4.16
4052 6537 9.371136 ACATAATGTTGTTATGTAGTGTCTGAG 57.629 33.333 10.71 0.00 42.06 3.35
4134 6620 4.761235 AGTCAACAAATCATCAGTGCAG 57.239 40.909 0.00 0.00 0.00 4.41
4137 6623 5.217393 CCACAAGTCAACAAATCATCAGTG 58.783 41.667 0.00 0.00 0.00 3.66
4189 6675 0.034863 TGATTTTACGAGGGCCACCC 60.035 55.000 6.18 0.00 45.90 4.61
4201 6687 6.795144 ATCACCATCAATTGCCTGATTTTA 57.205 33.333 0.00 0.00 33.66 1.52
4330 6816 1.079875 GCAACGCATGGGCATCTTTG 61.080 55.000 10.10 7.60 41.24 2.77
4331 6817 1.216178 GCAACGCATGGGCATCTTT 59.784 52.632 10.10 0.00 41.24 2.52
4332 6818 1.534336 TTGCAACGCATGGGCATCTT 61.534 50.000 10.10 0.00 38.76 2.40
4333 6819 1.978080 TTGCAACGCATGGGCATCT 60.978 52.632 10.10 0.00 38.76 2.90
4334 6820 1.806758 GTTGCAACGCATGGGCATC 60.807 57.895 14.90 0.00 38.76 3.91
4335 6821 2.262292 GTTGCAACGCATGGGCAT 59.738 55.556 14.90 0.00 38.76 4.40
4336 6822 4.340019 CGTTGCAACGCATGGGCA 62.340 61.111 35.89 0.00 46.06 5.36


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

AutoCloner maintained by Alex Coulton.