Multiple sequence alignment - TraesCS2D01G337900

Loading Multiple Alignment...

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 TraesCS2D01G337900 chr2D 100.000 4109 0 0 1 4109 431516194 431512086 0.000000e+00 7589.0
1 TraesCS2D01G337900 chr2D 92.683 41 1 2 4071 4109 33991685 33991645 1.600000e-04 58.4
2 TraesCS2D01G337900 chr2D 96.875 32 1 0 4078 4109 606579589 606579620 2.000000e-03 54.7
3 TraesCS2D01G337900 chr2A 95.187 3387 121 21 1 3362 554823018 554826387 0.000000e+00 5313.0
4 TraesCS2D01G337900 chr2A 90.184 326 22 4 3761 4079 554826585 554826907 2.280000e-112 416.0
5 TraesCS2D01G337900 chr2A 95.455 88 3 1 3652 3739 554826378 554826464 5.540000e-29 139.0
6 TraesCS2D01G337900 chr2A 94.643 56 3 0 3707 3762 554826462 554826517 2.030000e-13 87.9
7 TraesCS2D01G337900 chr2B 95.114 3377 143 13 1 3362 510401060 510397691 0.000000e+00 5302.0
8 TraesCS2D01G337900 chr2B 90.719 334 16 7 3760 4079 510397523 510397191 8.160000e-117 431.0
9 TraesCS2D01G337900 chr2B 97.297 111 3 0 3652 3762 510397700 510397590 5.420000e-44 189.0
10 TraesCS2D01G337900 chr2B 92.683 41 1 2 4071 4109 504788994 504788954 1.600000e-04 58.4
11 TraesCS2D01G337900 chr3D 88.433 268 29 2 3381 3647 563998313 563998579 5.120000e-84 322.0
12 TraesCS2D01G337900 chr3D 80.597 268 50 2 3381 3647 105454987 105455253 5.380000e-49 206.0
13 TraesCS2D01G337900 chr5B 87.313 268 31 3 3381 3647 216854624 216854359 1.860000e-78 303.0
14 TraesCS2D01G337900 chr3B 91.667 48 3 1 3572 3619 598193042 598193088 9.530000e-07 65.8
15 TraesCS2D01G337900 chr7B 92.683 41 1 2 4071 4109 336915580 336915540 1.600000e-04 58.4
16 TraesCS2D01G337900 chr5D 92.683 41 1 2 4071 4109 354714751 354714791 1.600000e-04 58.4
17 TraesCS2D01G337900 chr7D 100.000 30 0 0 4080 4109 517334973 517334944 5.740000e-04 56.5


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 TraesCS2D01G337900 chr2D 431512086 431516194 4108 True 7589.000 7589 100.000000 1 4109 1 chr2D.!!$R2 4108
1 TraesCS2D01G337900 chr2A 554823018 554826907 3889 False 1488.975 5313 93.867250 1 4079 4 chr2A.!!$F1 4078
2 TraesCS2D01G337900 chr2B 510397191 510401060 3869 True 1974.000 5302 94.376667 1 4079 3 chr2B.!!$R2 4078

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
325 332 0.596083 CTAGAACAGCGCAGGGATCG 60.596 60.0 11.47 0.0 0.0 3.69 F
2013 2031 0.392193 CCATGGTCAGTGTGCTCTCC 60.392 60.0 2.57 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2247 2265 0.459489 GCATGGACGAGAAGAGCTCT 59.541 55.0 11.45 11.45 41.66 4.09 R
3540 3574 0.035056 CCCTGGTTCATGTCCTGGTC 60.035 60.0 22.62 0.00 40.81 4.02 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 4.193090 ACATACGGTGTTGTGAAGTTCAA 58.807 39.130 7.25 0.00 38.01 2.69
71 73 9.661187 CTCTAGCAGCAACAAATATATTCAAAG 57.339 33.333 0.00 0.00 0.00 2.77
142 144 9.590451 AGACATATTCAATTTTGGCATAACTTG 57.410 29.630 0.00 0.00 0.00 3.16
144 146 9.941325 ACATATTCAATTTTGGCATAACTTGAA 57.059 25.926 19.46 19.46 37.12 2.69
146 148 7.671495 ATTCAATTTTGGCATAACTTGAACC 57.329 32.000 19.52 0.00 35.97 3.62
148 150 6.825610 TCAATTTTGGCATAACTTGAACCTT 58.174 32.000 10.43 0.00 0.00 3.50
149 151 7.957002 TCAATTTTGGCATAACTTGAACCTTA 58.043 30.769 10.43 0.00 0.00 2.69
150 152 8.592809 TCAATTTTGGCATAACTTGAACCTTAT 58.407 29.630 10.43 0.00 0.00 1.73
151 153 9.868277 CAATTTTGGCATAACTTGAACCTTATA 57.132 29.630 0.00 0.00 0.00 0.98
152 154 9.869757 AATTTTGGCATAACTTGAACCTTATAC 57.130 29.630 0.00 0.00 0.00 1.47
153 155 8.644374 TTTTGGCATAACTTGAACCTTATACT 57.356 30.769 0.00 0.00 0.00 2.12
168 170 9.090692 GAACCTTATACTAATTCGCAACACTAA 57.909 33.333 0.00 0.00 0.00 2.24
178 180 2.353269 TCGCAACACTAACAACACTTGG 59.647 45.455 0.00 0.00 34.12 3.61
273 280 9.362539 CTTGCACTTTTGAATAGCTAAATGAAT 57.637 29.630 0.00 0.00 0.00 2.57
314 321 5.119279 CGACATCAAGTCCAAACTAGAACAG 59.881 44.000 0.00 0.00 44.66 3.16
321 328 0.798776 CAAACTAGAACAGCGCAGGG 59.201 55.000 11.47 0.14 0.00 4.45
325 332 0.596083 CTAGAACAGCGCAGGGATCG 60.596 60.000 11.47 0.00 0.00 3.69
345 352 6.418819 GGATCGGAATAAACAAATGCAATCTG 59.581 38.462 0.00 0.00 0.00 2.90
366 377 1.847088 GGCTTCTCAGGGGATAACCTT 59.153 52.381 0.00 0.00 39.34 3.50
380 391 6.381707 GGGGATAACCTTGGTTATTTAAAGCA 59.618 38.462 21.62 0.00 40.03 3.91
773 784 2.821688 CGGACGCTAGGAGGACGAC 61.822 68.421 0.00 0.00 0.00 4.34
805 816 1.599606 GAGCAGCCGAGTTGGAGAGA 61.600 60.000 0.00 0.00 42.00 3.10
952 970 4.151883 TGGATAAGCAAAGAAAGGCAAGT 58.848 39.130 0.00 0.00 0.00 3.16
1113 1131 4.687215 GTGCCTCAGCTCCACGCA 62.687 66.667 0.00 0.00 42.61 5.24
1275 1293 3.950254 CTCTCCGCGCGGTCGTAT 61.950 66.667 44.16 0.00 38.14 3.06
1294 1312 4.321750 CGTATAACATCCTTATCCGTGCCT 60.322 45.833 0.00 0.00 0.00 4.75
1392 1410 2.436646 CCCGACCAGCACACCATC 60.437 66.667 0.00 0.00 0.00 3.51
1437 1455 3.525537 CAGGATATATGCCTTGGCTACG 58.474 50.000 13.18 0.00 32.12 3.51
1611 1629 0.826715 ATGCGATGATAGCGGGCTAT 59.173 50.000 12.74 12.74 41.48 2.97
1757 1775 4.207281 CGGCGAGCGGATTGGAGA 62.207 66.667 0.00 0.00 0.00 3.71
1872 1890 3.698040 GGAGATTGTTTGACAGGATGCAT 59.302 43.478 0.00 0.00 42.53 3.96
1957 1975 5.294306 CGAGAGGCACTTGCTATTTTCAATA 59.706 40.000 0.38 0.00 41.55 1.90
2013 2031 0.392193 CCATGGTCAGTGTGCTCTCC 60.392 60.000 2.57 0.00 0.00 3.71
2054 2072 3.842925 TTGAGACGGGCAAGTGGGC 62.843 63.158 0.00 0.00 42.44 5.36
2244 2262 1.188219 ACGGAAGAGGCAGAGAAGCA 61.188 55.000 0.00 0.00 35.83 3.91
2247 2265 1.827969 GGAAGAGGCAGAGAAGCACTA 59.172 52.381 0.00 0.00 35.83 2.74
2259 2277 2.682856 AGAAGCACTAGAGCTCTTCTCG 59.317 50.000 23.84 10.68 45.89 4.04
2351 2369 1.902508 CTGCTTAGTTGAGGAGGGTCA 59.097 52.381 0.00 0.00 32.11 4.02
2462 2480 1.368345 TTGATTGATGAGGCGCACCG 61.368 55.000 10.83 0.00 42.76 4.94
2481 2499 2.742053 CCGGTTTATCAGGAATATGCCG 59.258 50.000 0.00 0.00 37.30 5.69
2760 2778 4.142609 TGAGTTCTTTGCTGAAGACAGT 57.857 40.909 3.09 0.06 43.90 3.55
2772 2790 0.991355 AAGACAGTGACCACCCCCAA 60.991 55.000 0.00 0.00 0.00 4.12
2940 2958 1.522668 CGTTTGGCCTGATGAAGTCA 58.477 50.000 3.32 0.00 35.05 3.41
3181 3205 1.539560 GCACACCTGAGCCAGAGAGA 61.540 60.000 4.00 0.00 32.44 3.10
3270 3304 8.279103 GGTATTAAGATCAAGAGCAAATTCTCG 58.721 37.037 0.00 0.00 38.12 4.04
3304 3338 2.349886 GCTTGGTTAGCTCAGACATTCG 59.650 50.000 0.00 0.00 46.77 3.34
3352 3386 3.782656 ACCGGAGTTGGTTAATCTGTT 57.217 42.857 9.46 0.00 39.99 3.16
3353 3387 4.094830 ACCGGAGTTGGTTAATCTGTTT 57.905 40.909 9.46 0.00 39.99 2.83
3354 3388 4.070009 ACCGGAGTTGGTTAATCTGTTTC 58.930 43.478 9.46 0.00 39.99 2.78
3355 3389 3.439129 CCGGAGTTGGTTAATCTGTTTCC 59.561 47.826 0.00 0.00 0.00 3.13
3356 3390 3.439129 CGGAGTTGGTTAATCTGTTTCCC 59.561 47.826 0.00 0.00 0.00 3.97
3357 3391 3.762288 GGAGTTGGTTAATCTGTTTCCCC 59.238 47.826 0.00 0.00 0.00 4.81
3358 3392 4.508584 GGAGTTGGTTAATCTGTTTCCCCT 60.509 45.833 0.00 0.00 0.00 4.79
3359 3393 5.074746 AGTTGGTTAATCTGTTTCCCCTT 57.925 39.130 0.00 0.00 0.00 3.95
3360 3394 5.464069 AGTTGGTTAATCTGTTTCCCCTTT 58.536 37.500 0.00 0.00 0.00 3.11
3361 3395 5.903010 AGTTGGTTAATCTGTTTCCCCTTTT 59.097 36.000 0.00 0.00 0.00 2.27
3362 3396 6.385759 AGTTGGTTAATCTGTTTCCCCTTTTT 59.614 34.615 0.00 0.00 0.00 1.94
3363 3397 6.413783 TGGTTAATCTGTTTCCCCTTTTTC 57.586 37.500 0.00 0.00 0.00 2.29
3364 3398 6.140377 TGGTTAATCTGTTTCCCCTTTTTCT 58.860 36.000 0.00 0.00 0.00 2.52
3365 3399 6.613679 TGGTTAATCTGTTTCCCCTTTTTCTT 59.386 34.615 0.00 0.00 0.00 2.52
3366 3400 7.126573 TGGTTAATCTGTTTCCCCTTTTTCTTT 59.873 33.333 0.00 0.00 0.00 2.52
3367 3401 7.990886 GGTTAATCTGTTTCCCCTTTTTCTTTT 59.009 33.333 0.00 0.00 0.00 2.27
3368 3402 9.042008 GTTAATCTGTTTCCCCTTTTTCTTTTC 57.958 33.333 0.00 0.00 0.00 2.29
3369 3403 5.257082 TCTGTTTCCCCTTTTTCTTTTCG 57.743 39.130 0.00 0.00 0.00 3.46
3370 3404 4.951094 TCTGTTTCCCCTTTTTCTTTTCGA 59.049 37.500 0.00 0.00 0.00 3.71
3371 3405 5.067283 TCTGTTTCCCCTTTTTCTTTTCGAG 59.933 40.000 0.00 0.00 0.00 4.04
3372 3406 4.951094 TGTTTCCCCTTTTTCTTTTCGAGA 59.049 37.500 0.00 0.00 0.00 4.04
3373 3407 5.419471 TGTTTCCCCTTTTTCTTTTCGAGAA 59.581 36.000 0.00 0.00 42.56 2.87
3383 3417 5.864830 TTCTTTTCGAGAAAACGCAATTG 57.135 34.783 6.89 0.00 41.34 2.32
3384 3418 3.728718 TCTTTTCGAGAAAACGCAATTGC 59.271 39.130 20.76 20.76 35.57 3.56
3385 3419 2.765108 TTCGAGAAAACGCAATTGCA 57.235 40.000 28.77 4.20 42.21 4.08
3386 3420 2.987413 TCGAGAAAACGCAATTGCAT 57.013 40.000 28.77 12.92 42.21 3.96
3387 3421 3.281341 TCGAGAAAACGCAATTGCATT 57.719 38.095 28.77 18.77 42.21 3.56
3388 3422 2.979151 TCGAGAAAACGCAATTGCATTG 59.021 40.909 28.77 15.76 42.21 2.82
3389 3423 2.979151 CGAGAAAACGCAATTGCATTGA 59.021 40.909 28.77 0.00 42.83 2.57
3390 3424 3.058520 CGAGAAAACGCAATTGCATTGAG 59.941 43.478 28.77 15.04 42.83 3.02
3391 3425 4.229096 GAGAAAACGCAATTGCATTGAGA 58.771 39.130 28.77 0.00 41.74 3.27
3392 3426 4.619973 AGAAAACGCAATTGCATTGAGAA 58.380 34.783 28.77 0.00 41.74 2.87
3393 3427 4.682860 AGAAAACGCAATTGCATTGAGAAG 59.317 37.500 28.77 12.93 41.74 2.85
3394 3428 2.642139 ACGCAATTGCATTGAGAAGG 57.358 45.000 28.77 12.24 41.74 3.46
3395 3429 1.888512 ACGCAATTGCATTGAGAAGGT 59.111 42.857 28.77 12.87 41.74 3.50
3396 3430 3.081061 ACGCAATTGCATTGAGAAGGTA 58.919 40.909 28.77 0.00 41.74 3.08
3397 3431 3.127548 ACGCAATTGCATTGAGAAGGTAG 59.872 43.478 28.77 10.86 41.74 3.18
3398 3432 3.374988 CGCAATTGCATTGAGAAGGTAGA 59.625 43.478 28.77 0.00 41.74 2.59
3399 3433 4.495349 CGCAATTGCATTGAGAAGGTAGAG 60.495 45.833 28.77 3.99 41.74 2.43
3400 3434 4.397417 GCAATTGCATTGAGAAGGTAGAGT 59.603 41.667 25.36 0.00 42.83 3.24
3401 3435 5.105997 GCAATTGCATTGAGAAGGTAGAGTT 60.106 40.000 25.36 0.00 42.83 3.01
3402 3436 6.571150 GCAATTGCATTGAGAAGGTAGAGTTT 60.571 38.462 25.36 0.00 42.83 2.66
3403 3437 5.947228 TTGCATTGAGAAGGTAGAGTTTG 57.053 39.130 0.00 0.00 0.00 2.93
3404 3438 4.326826 TGCATTGAGAAGGTAGAGTTTGG 58.673 43.478 0.00 0.00 0.00 3.28
3405 3439 4.041567 TGCATTGAGAAGGTAGAGTTTGGA 59.958 41.667 0.00 0.00 0.00 3.53
3406 3440 5.189180 GCATTGAGAAGGTAGAGTTTGGAT 58.811 41.667 0.00 0.00 0.00 3.41
3407 3441 6.070251 TGCATTGAGAAGGTAGAGTTTGGATA 60.070 38.462 0.00 0.00 0.00 2.59
3408 3442 6.258947 GCATTGAGAAGGTAGAGTTTGGATAC 59.741 42.308 0.00 0.00 0.00 2.24
3422 3456 3.885976 TGGATACAGTCCTCCTAGGAG 57.114 52.381 29.27 29.27 44.59 3.69
3433 3467 3.383698 CTCCTAGGAGGTCAGGTACAA 57.616 52.381 28.68 0.00 38.51 2.41
3434 3468 3.709587 CTCCTAGGAGGTCAGGTACAAA 58.290 50.000 28.68 0.00 38.51 2.83
3435 3469 4.290942 CTCCTAGGAGGTCAGGTACAAAT 58.709 47.826 28.68 0.00 38.51 2.32
3436 3470 4.030913 TCCTAGGAGGTCAGGTACAAATG 58.969 47.826 7.62 0.00 36.53 2.32
3437 3471 4.030913 CCTAGGAGGTCAGGTACAAATGA 58.969 47.826 1.05 0.00 0.00 2.57
3438 3472 4.469945 CCTAGGAGGTCAGGTACAAATGAA 59.530 45.833 1.05 0.00 0.00 2.57
3439 3473 4.559862 AGGAGGTCAGGTACAAATGAAG 57.440 45.455 0.00 0.00 0.00 3.02
3440 3474 4.168101 AGGAGGTCAGGTACAAATGAAGA 58.832 43.478 0.00 0.00 0.00 2.87
3441 3475 4.597507 AGGAGGTCAGGTACAAATGAAGAA 59.402 41.667 0.00 0.00 0.00 2.52
3442 3476 4.695928 GGAGGTCAGGTACAAATGAAGAAC 59.304 45.833 0.00 0.00 0.00 3.01
3443 3477 5.304686 AGGTCAGGTACAAATGAAGAACA 57.695 39.130 0.00 0.00 0.00 3.18
3444 3478 5.308825 AGGTCAGGTACAAATGAAGAACAG 58.691 41.667 0.00 0.00 0.00 3.16
3445 3479 5.063880 GGTCAGGTACAAATGAAGAACAGT 58.936 41.667 0.00 0.00 0.00 3.55
3446 3480 5.049405 GGTCAGGTACAAATGAAGAACAGTG 60.049 44.000 0.00 0.00 0.00 3.66
3447 3481 5.758296 GTCAGGTACAAATGAAGAACAGTGA 59.242 40.000 0.00 0.00 0.00 3.41
3448 3482 6.260050 GTCAGGTACAAATGAAGAACAGTGAA 59.740 38.462 0.00 0.00 0.00 3.18
3449 3483 6.826231 TCAGGTACAAATGAAGAACAGTGAAA 59.174 34.615 0.00 0.00 0.00 2.69
3450 3484 6.912591 CAGGTACAAATGAAGAACAGTGAAAC 59.087 38.462 0.00 0.00 0.00 2.78
3466 3500 3.930848 GTGAAACTAATACACGTCCCAGG 59.069 47.826 0.00 0.00 0.00 4.45
3467 3501 3.579586 TGAAACTAATACACGTCCCAGGT 59.420 43.478 0.00 0.00 0.00 4.00
3468 3502 3.604875 AACTAATACACGTCCCAGGTG 57.395 47.619 0.00 0.00 39.65 4.00
3469 3503 1.829222 ACTAATACACGTCCCAGGTGG 59.171 52.381 0.00 0.00 38.22 4.61
3470 3504 2.104967 CTAATACACGTCCCAGGTGGA 58.895 52.381 0.00 0.00 42.41 4.02
3480 3514 4.704833 CAGGTGGACGGCAGGGTG 62.705 72.222 0.00 0.00 0.00 4.61
3481 3515 4.954118 AGGTGGACGGCAGGGTGA 62.954 66.667 0.00 0.00 0.00 4.02
3482 3516 4.699522 GGTGGACGGCAGGGTGAC 62.700 72.222 0.00 0.00 0.00 3.67
3488 3522 2.738521 CGGCAGGGTGACGTGAAG 60.739 66.667 0.00 0.00 45.41 3.02
3492 3526 2.847234 AGGGTGACGTGAAGGCCA 60.847 61.111 5.01 0.00 0.00 5.36
3493 3527 2.112297 GGGTGACGTGAAGGCCAA 59.888 61.111 5.01 0.00 0.00 4.52
3494 3528 1.966451 GGGTGACGTGAAGGCCAAG 60.966 63.158 5.01 0.00 0.00 3.61
3495 3529 1.966451 GGTGACGTGAAGGCCAAGG 60.966 63.158 5.01 0.00 0.00 3.61
3496 3530 1.966451 GTGACGTGAAGGCCAAGGG 60.966 63.158 5.01 0.00 0.00 3.95
3514 3548 4.320456 CACCAGCTCGTGCCCACT 62.320 66.667 5.73 0.00 40.80 4.00
3515 3549 4.320456 ACCAGCTCGTGCCCACTG 62.320 66.667 5.73 0.00 40.80 3.66
3517 3551 4.694233 CAGCTCGTGCCCACTGCT 62.694 66.667 5.73 9.03 42.00 4.24
3518 3552 4.385405 AGCTCGTGCCCACTGCTC 62.385 66.667 5.73 0.00 42.00 4.26
3524 3558 4.704833 TGCCCACTGCTCGGCTTC 62.705 66.667 0.00 0.00 45.90 3.86
3525 3559 4.704833 GCCCACTGCTCGGCTTCA 62.705 66.667 0.00 0.00 42.21 3.02
3526 3560 2.270205 CCCACTGCTCGGCTTCAT 59.730 61.111 0.00 0.00 0.00 2.57
3527 3561 1.817099 CCCACTGCTCGGCTTCATC 60.817 63.158 0.00 0.00 0.00 2.92
3528 3562 1.817099 CCACTGCTCGGCTTCATCC 60.817 63.158 0.00 0.00 0.00 3.51
3529 3563 1.220206 CACTGCTCGGCTTCATCCT 59.780 57.895 0.00 0.00 0.00 3.24
3530 3564 0.392193 CACTGCTCGGCTTCATCCTT 60.392 55.000 0.00 0.00 0.00 3.36
3531 3565 0.392193 ACTGCTCGGCTTCATCCTTG 60.392 55.000 0.00 0.00 0.00 3.61
3532 3566 0.107993 CTGCTCGGCTTCATCCTTGA 60.108 55.000 0.00 0.00 0.00 3.02
3533 3567 0.543277 TGCTCGGCTTCATCCTTGAT 59.457 50.000 0.00 0.00 0.00 2.57
3534 3568 1.224965 GCTCGGCTTCATCCTTGATC 58.775 55.000 0.00 0.00 0.00 2.92
3535 3569 1.202627 GCTCGGCTTCATCCTTGATCT 60.203 52.381 0.00 0.00 0.00 2.75
3536 3570 2.744494 GCTCGGCTTCATCCTTGATCTT 60.744 50.000 0.00 0.00 0.00 2.40
3537 3571 3.539604 CTCGGCTTCATCCTTGATCTTT 58.460 45.455 0.00 0.00 0.00 2.52
3538 3572 3.273434 TCGGCTTCATCCTTGATCTTTG 58.727 45.455 0.00 0.00 0.00 2.77
3539 3573 3.055167 TCGGCTTCATCCTTGATCTTTGA 60.055 43.478 0.00 0.00 0.00 2.69
3540 3574 3.311871 CGGCTTCATCCTTGATCTTTGAG 59.688 47.826 0.00 0.00 0.00 3.02
3541 3575 4.521146 GGCTTCATCCTTGATCTTTGAGA 58.479 43.478 0.00 0.00 0.00 3.27
3542 3576 4.335037 GGCTTCATCCTTGATCTTTGAGAC 59.665 45.833 0.00 0.00 0.00 3.36
3543 3577 4.335037 GCTTCATCCTTGATCTTTGAGACC 59.665 45.833 0.00 0.00 0.00 3.85
3544 3578 5.494724 CTTCATCCTTGATCTTTGAGACCA 58.505 41.667 0.00 0.00 0.00 4.02
3545 3579 5.095145 TCATCCTTGATCTTTGAGACCAG 57.905 43.478 0.00 0.00 0.00 4.00
3546 3580 3.988976 TCCTTGATCTTTGAGACCAGG 57.011 47.619 0.00 0.00 0.00 4.45
3547 3581 3.520696 TCCTTGATCTTTGAGACCAGGA 58.479 45.455 0.00 0.00 0.00 3.86
3548 3582 3.261897 TCCTTGATCTTTGAGACCAGGAC 59.738 47.826 0.00 0.00 0.00 3.85
3549 3583 3.008375 CCTTGATCTTTGAGACCAGGACA 59.992 47.826 0.00 0.00 0.00 4.02
3550 3584 4.324099 CCTTGATCTTTGAGACCAGGACAT 60.324 45.833 0.00 0.00 0.00 3.06
3551 3585 4.212143 TGATCTTTGAGACCAGGACATG 57.788 45.455 0.00 0.00 0.00 3.21
3552 3586 3.840078 TGATCTTTGAGACCAGGACATGA 59.160 43.478 0.00 0.00 0.00 3.07
3553 3587 4.286808 TGATCTTTGAGACCAGGACATGAA 59.713 41.667 0.00 0.00 0.00 2.57
3554 3588 4.008074 TCTTTGAGACCAGGACATGAAC 57.992 45.455 0.00 0.00 0.00 3.18
3555 3589 2.859165 TTGAGACCAGGACATGAACC 57.141 50.000 0.00 2.33 0.00 3.62
3556 3590 1.728323 TGAGACCAGGACATGAACCA 58.272 50.000 0.00 0.00 0.00 3.67
3557 3591 1.625315 TGAGACCAGGACATGAACCAG 59.375 52.381 0.00 0.00 0.00 4.00
3558 3592 0.987294 AGACCAGGACATGAACCAGG 59.013 55.000 17.80 17.80 39.50 4.45
3559 3593 0.035056 GACCAGGACATGAACCAGGG 60.035 60.000 21.17 18.56 38.21 4.45
3560 3594 1.304282 CCAGGACATGAACCAGGGG 59.696 63.158 0.00 2.65 31.66 4.79
3561 3595 1.379044 CAGGACATGAACCAGGGGC 60.379 63.158 0.00 0.00 0.00 5.80
3562 3596 1.542375 AGGACATGAACCAGGGGCT 60.542 57.895 0.00 0.00 0.00 5.19
3563 3597 1.379044 GGACATGAACCAGGGGCTG 60.379 63.158 0.00 0.00 0.00 4.85
3577 3611 2.184322 GCTGGACGCCATCGAAGA 59.816 61.111 0.00 0.00 45.75 2.87
3578 3612 1.227380 GCTGGACGCCATCGAAGAT 60.227 57.895 0.00 0.00 45.12 2.40
3579 3613 1.493950 GCTGGACGCCATCGAAGATG 61.494 60.000 3.21 3.21 45.12 2.90
3580 3614 1.493950 CTGGACGCCATCGAAGATGC 61.494 60.000 4.60 0.67 45.12 3.91
3581 3615 1.521457 GGACGCCATCGAAGATGCA 60.521 57.895 4.60 0.00 45.12 3.96
3582 3616 1.638467 GACGCCATCGAAGATGCAC 59.362 57.895 4.60 0.00 45.12 4.57
3583 3617 0.807667 GACGCCATCGAAGATGCACT 60.808 55.000 4.60 0.00 45.12 4.40
3584 3618 0.807667 ACGCCATCGAAGATGCACTC 60.808 55.000 4.60 0.00 45.12 3.51
3585 3619 1.815212 CGCCATCGAAGATGCACTCG 61.815 60.000 8.07 8.07 45.12 4.18
3586 3620 0.807667 GCCATCGAAGATGCACTCGT 60.808 55.000 12.73 0.51 45.12 4.18
3587 3621 1.645034 CCATCGAAGATGCACTCGTT 58.355 50.000 12.73 4.13 45.12 3.85
3588 3622 1.325640 CCATCGAAGATGCACTCGTTG 59.674 52.381 12.73 13.62 45.12 4.10
3589 3623 1.002366 ATCGAAGATGCACTCGTTGC 58.998 50.000 12.73 5.01 46.73 4.17
3596 3630 4.017877 GCACTCGTTGCGCTGCTT 62.018 61.111 9.73 0.00 42.79 3.91
3597 3631 2.171940 CACTCGTTGCGCTGCTTC 59.828 61.111 9.73 0.00 0.00 3.86
3598 3632 3.044305 ACTCGTTGCGCTGCTTCC 61.044 61.111 9.73 0.00 0.00 3.46
3599 3633 3.043713 CTCGTTGCGCTGCTTCCA 61.044 61.111 9.73 0.00 0.00 3.53
3600 3634 3.020026 CTCGTTGCGCTGCTTCCAG 62.020 63.158 9.73 0.00 42.13 3.86
3601 3635 3.043713 CGTTGCGCTGCTTCCAGA 61.044 61.111 9.73 0.00 41.77 3.86
3602 3636 2.393768 CGTTGCGCTGCTTCCAGAT 61.394 57.895 9.73 0.00 41.77 2.90
3603 3637 1.427020 GTTGCGCTGCTTCCAGATC 59.573 57.895 9.73 0.00 41.77 2.75
3604 3638 1.003476 TTGCGCTGCTTCCAGATCA 60.003 52.632 9.73 0.00 41.77 2.92
3605 3639 0.393402 TTGCGCTGCTTCCAGATCAT 60.393 50.000 9.73 0.00 41.77 2.45
3606 3640 0.812811 TGCGCTGCTTCCAGATCATC 60.813 55.000 9.73 0.00 41.77 2.92
3607 3641 1.505477 GCGCTGCTTCCAGATCATCC 61.505 60.000 0.00 0.00 41.77 3.51
3608 3642 0.179065 CGCTGCTTCCAGATCATCCA 60.179 55.000 0.00 0.00 41.77 3.41
3609 3643 1.542767 CGCTGCTTCCAGATCATCCAT 60.543 52.381 0.00 0.00 41.77 3.41
3610 3644 1.880675 GCTGCTTCCAGATCATCCATG 59.119 52.381 0.00 0.00 41.77 3.66
3611 3645 2.505405 CTGCTTCCAGATCATCCATGG 58.495 52.381 4.97 4.97 41.77 3.66
3612 3646 1.848388 TGCTTCCAGATCATCCATGGT 59.152 47.619 12.58 0.00 35.51 3.55
3613 3647 2.228059 GCTTCCAGATCATCCATGGTG 58.772 52.381 12.58 9.69 35.51 4.17
3614 3648 2.422519 GCTTCCAGATCATCCATGGTGT 60.423 50.000 12.58 0.00 35.51 4.16
3615 3649 3.474600 CTTCCAGATCATCCATGGTGTC 58.525 50.000 12.58 6.03 35.51 3.67
3616 3650 2.480390 TCCAGATCATCCATGGTGTCA 58.520 47.619 12.58 0.00 35.51 3.58
3617 3651 2.845586 TCCAGATCATCCATGGTGTCAA 59.154 45.455 12.58 0.00 35.51 3.18
3618 3652 3.118149 TCCAGATCATCCATGGTGTCAAG 60.118 47.826 12.58 3.50 35.51 3.02
3619 3653 3.118149 CCAGATCATCCATGGTGTCAAGA 60.118 47.826 12.58 2.56 0.00 3.02
3620 3654 4.127907 CAGATCATCCATGGTGTCAAGAG 58.872 47.826 12.58 0.00 0.00 2.85
3621 3655 3.136077 AGATCATCCATGGTGTCAAGAGG 59.864 47.826 12.58 0.00 0.00 3.69
3622 3656 1.561076 TCATCCATGGTGTCAAGAGGG 59.439 52.381 12.58 0.00 0.00 4.30
3623 3657 0.257039 ATCCATGGTGTCAAGAGGGC 59.743 55.000 12.58 0.00 0.00 5.19
3624 3658 1.133181 TCCATGGTGTCAAGAGGGCA 61.133 55.000 12.58 0.00 0.00 5.36
3625 3659 0.679002 CCATGGTGTCAAGAGGGCAG 60.679 60.000 2.57 0.00 0.00 4.85
3626 3660 0.037303 CATGGTGTCAAGAGGGCAGT 59.963 55.000 0.00 0.00 0.00 4.40
3627 3661 0.037303 ATGGTGTCAAGAGGGCAGTG 59.963 55.000 0.00 0.00 0.00 3.66
3628 3662 1.302832 GGTGTCAAGAGGGCAGTGG 60.303 63.158 0.00 0.00 0.00 4.00
3629 3663 1.754745 GTGTCAAGAGGGCAGTGGA 59.245 57.895 0.00 0.00 0.00 4.02
3630 3664 0.321122 GTGTCAAGAGGGCAGTGGAG 60.321 60.000 0.00 0.00 0.00 3.86
3631 3665 1.298014 GTCAAGAGGGCAGTGGAGG 59.702 63.158 0.00 0.00 0.00 4.30
3632 3666 2.045536 CAAGAGGGCAGTGGAGGC 60.046 66.667 0.00 0.00 0.00 4.70
3633 3667 2.204059 AAGAGGGCAGTGGAGGCT 60.204 61.111 0.00 0.00 0.00 4.58
3634 3668 1.081092 AAGAGGGCAGTGGAGGCTA 59.919 57.895 0.00 0.00 0.00 3.93
3635 3669 0.980231 AAGAGGGCAGTGGAGGCTAG 60.980 60.000 0.00 0.00 0.00 3.42
3636 3670 2.366167 AGGGCAGTGGAGGCTAGG 60.366 66.667 0.00 0.00 0.00 3.02
3637 3671 4.182433 GGGCAGTGGAGGCTAGGC 62.182 72.222 8.55 8.55 0.00 3.93
3647 3681 2.203029 GGCTAGGCCCTTACGCAC 60.203 66.667 4.61 0.00 44.06 5.34
3648 3682 2.203029 GCTAGGCCCTTACGCACC 60.203 66.667 0.00 0.00 0.00 5.01
3649 3683 2.504519 CTAGGCCCTTACGCACCC 59.495 66.667 0.00 0.00 0.00 4.61
3650 3684 3.441011 CTAGGCCCTTACGCACCCG 62.441 68.421 0.00 0.00 41.14 5.28
3661 3695 1.737201 CGCACCCGTTTCCCTTTTT 59.263 52.632 0.00 0.00 0.00 1.94
3713 3747 7.921786 TTTTCTCCTTACCTCATGTAACATG 57.078 36.000 0.00 0.00 34.50 3.21
3751 3814 7.854557 AAATTTACCGTAGAACTATTGTCCC 57.145 36.000 0.00 0.00 0.00 4.46
3779 3911 2.296190 TGCGAGAACTGTGAGTGTGTAT 59.704 45.455 0.00 0.00 0.00 2.29
3797 3929 6.459923 TGTGTATAGACTGCACATTGTTGTA 58.540 36.000 1.30 0.00 44.30 2.41
3868 4007 3.684103 TGTAAAGAAACTGTGTTGCGG 57.316 42.857 0.00 0.00 0.00 5.69
3897 4037 9.745880 ATATAAAATTTCAAATGCAGAGCAGAG 57.254 29.630 0.00 0.00 43.65 3.35
4035 4187 3.200294 TGCGCACATGTCTAATTTGTG 57.800 42.857 5.66 3.33 42.80 3.33
4079 4231 2.371841 TGTAATCCCGGCTGCTGATATT 59.628 45.455 10.70 11.10 0.00 1.28
4080 4232 1.901591 AATCCCGGCTGCTGATATTG 58.098 50.000 10.70 0.00 0.00 1.90
4081 4233 0.767375 ATCCCGGCTGCTGATATTGT 59.233 50.000 10.70 0.00 0.00 2.71
4082 4234 0.546122 TCCCGGCTGCTGATATTGTT 59.454 50.000 10.70 0.00 0.00 2.83
4083 4235 0.947244 CCCGGCTGCTGATATTGTTC 59.053 55.000 10.70 0.00 0.00 3.18
4084 4236 0.947244 CCGGCTGCTGATATTGTTCC 59.053 55.000 10.70 0.00 0.00 3.62
4085 4237 0.583438 CGGCTGCTGATATTGTTCCG 59.417 55.000 1.17 0.00 0.00 4.30
4086 4238 0.308993 GGCTGCTGATATTGTTCCGC 59.691 55.000 0.00 0.00 0.00 5.54
4087 4239 1.016627 GCTGCTGATATTGTTCCGCA 58.983 50.000 0.00 0.00 35.08 5.69
4088 4240 1.401552 GCTGCTGATATTGTTCCGCAA 59.598 47.619 0.00 0.00 41.89 4.85
4089 4241 2.792542 GCTGCTGATATTGTTCCGCAAC 60.793 50.000 0.00 0.00 40.28 4.17
4090 4242 2.679837 CTGCTGATATTGTTCCGCAACT 59.320 45.455 0.00 0.00 40.28 3.16
4091 4243 2.677836 TGCTGATATTGTTCCGCAACTC 59.322 45.455 0.00 0.00 40.28 3.01
4092 4244 2.032178 GCTGATATTGTTCCGCAACTCC 59.968 50.000 0.00 0.00 40.28 3.85
4093 4245 2.276201 TGATATTGTTCCGCAACTCCG 58.724 47.619 0.00 0.00 40.28 4.63
4094 4246 1.003866 GATATTGTTCCGCAACTCCGC 60.004 52.381 0.00 0.00 40.28 5.54
4095 4247 1.022451 TATTGTTCCGCAACTCCGCC 61.022 55.000 0.00 0.00 40.28 6.13
4103 4255 3.423154 CAACTCCGCCGGCAAGTC 61.423 66.667 28.98 0.00 0.00 3.01
4104 4256 4.699522 AACTCCGCCGGCAAGTCC 62.700 66.667 28.98 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 3.960571 AGAGTGCCAATTAGCAGTGAAT 58.039 40.909 11.08 0.00 46.36 2.57
39 40 0.108396 TGTTGCTGCTAGAGTGCCAA 59.892 50.000 0.00 0.00 0.00 4.52
142 144 7.535489 AGTGTTGCGAATTAGTATAAGGTTC 57.465 36.000 0.00 0.00 0.00 3.62
144 146 8.036575 TGTTAGTGTTGCGAATTAGTATAAGGT 58.963 33.333 0.00 0.00 0.00 3.50
146 148 9.685005 GTTGTTAGTGTTGCGAATTAGTATAAG 57.315 33.333 0.00 0.00 0.00 1.73
148 150 8.649841 GTGTTGTTAGTGTTGCGAATTAGTATA 58.350 33.333 0.00 0.00 0.00 1.47
149 151 7.386848 AGTGTTGTTAGTGTTGCGAATTAGTAT 59.613 33.333 0.00 0.00 0.00 2.12
150 152 6.702723 AGTGTTGTTAGTGTTGCGAATTAGTA 59.297 34.615 0.00 0.00 0.00 1.82
151 153 5.526111 AGTGTTGTTAGTGTTGCGAATTAGT 59.474 36.000 0.00 0.00 0.00 2.24
152 154 5.985781 AGTGTTGTTAGTGTTGCGAATTAG 58.014 37.500 0.00 0.00 0.00 1.73
153 155 5.994887 AGTGTTGTTAGTGTTGCGAATTA 57.005 34.783 0.00 0.00 0.00 1.40
168 170 3.197549 ACCAAAGAATTGCCAAGTGTTGT 59.802 39.130 0.00 0.00 35.10 3.32
178 180 6.759497 ATCTTACTACCACCAAAGAATTGC 57.241 37.500 0.00 0.00 35.10 3.56
276 283 7.280205 GGACTTGATGTCGGTATTAATCAAACT 59.720 37.037 0.00 0.00 46.24 2.66
314 321 0.586802 GTTTATTCCGATCCCTGCGC 59.413 55.000 0.00 0.00 0.00 6.09
321 328 6.418819 CCAGATTGCATTTGTTTATTCCGATC 59.581 38.462 0.00 0.00 0.00 3.69
325 332 4.571984 GCCCAGATTGCATTTGTTTATTCC 59.428 41.667 0.00 0.00 0.00 3.01
345 352 0.474614 GGTTATCCCCTGAGAAGCCC 59.525 60.000 0.00 0.00 34.87 5.19
366 377 7.362574 GGTTGCTATCAGTGCTTTAAATAACCA 60.363 37.037 0.00 0.00 33.43 3.67
380 391 1.838077 GGGTAGGTGGTTGCTATCAGT 59.162 52.381 0.00 0.00 0.00 3.41
561 572 2.828549 GCGGCGATGGGGTTCAAT 60.829 61.111 12.98 0.00 0.00 2.57
793 804 2.289072 TGGCTTCTTTCTCTCCAACTCG 60.289 50.000 0.00 0.00 0.00 4.18
805 816 4.956075 CCCAGTAATTACCATGGCTTCTTT 59.044 41.667 13.04 1.44 0.00 2.52
913 931 1.651240 CCAAGCAGCAACCGATCTGG 61.651 60.000 0.00 2.55 46.41 3.86
915 933 0.254178 ATCCAAGCAGCAACCGATCT 59.746 50.000 0.00 0.00 0.00 2.75
957 975 1.926511 CTTAAGCGCACCAGGCCAAG 61.927 60.000 11.47 0.00 40.31 3.61
1113 1131 1.910772 ACCGGACTTGAGCAGAGCT 60.911 57.895 9.46 0.00 43.88 4.09
1275 1293 3.709653 AGAAGGCACGGATAAGGATGTTA 59.290 43.478 0.00 0.00 0.00 2.41
1392 1410 1.990563 CAGGACTTTACGGTGTTAGCG 59.009 52.381 0.00 0.00 45.69 4.26
1566 1584 2.510382 TGTAACCACACCCTTTTCCTCA 59.490 45.455 0.00 0.00 0.00 3.86
1611 1629 4.350816 TCCTTCCAGTCTCCATTCTTGAAA 59.649 41.667 0.00 0.00 0.00 2.69
1757 1775 3.066208 TCCCCTTCTCCTCTGCATAAT 57.934 47.619 0.00 0.00 0.00 1.28
1834 1852 0.652592 CTCCGCGCCTTATCAAGTTG 59.347 55.000 0.00 0.00 0.00 3.16
1872 1890 2.034999 GCAACCACATCCCGGGAA 59.965 61.111 30.84 11.68 0.00 3.97
1957 1975 0.978146 ACCTCGGTAGCCTGCATCTT 60.978 55.000 0.00 0.00 0.00 2.40
2054 2072 5.334414 GCCTTTCTCCTTATGTATGAATGCG 60.334 44.000 0.00 0.00 0.00 4.73
2082 2100 1.346722 CCGAGAACAACTGTAAGGGGT 59.653 52.381 0.00 0.00 39.30 4.95
2176 2194 2.571653 TCCACGTCCAAGAATTCCTCAT 59.428 45.455 0.65 0.00 0.00 2.90
2244 2262 2.791347 TGGACGAGAAGAGCTCTAGT 57.209 50.000 18.59 14.59 42.16 2.57
2247 2265 0.459489 GCATGGACGAGAAGAGCTCT 59.541 55.000 11.45 11.45 41.66 4.09
2259 2277 4.424711 TTGGCCTCCCGCATGGAC 62.425 66.667 3.32 0.00 38.61 4.02
2351 2369 4.134563 GGTCATACTATCAAAATGCCGGT 58.865 43.478 1.90 0.00 0.00 5.28
2462 2480 5.705441 TCAATCGGCATATTCCTGATAAACC 59.295 40.000 0.00 0.00 0.00 3.27
2481 2499 3.057033 AGACAACTGCATTTGGCTCAATC 60.057 43.478 18.82 6.97 41.29 2.67
2652 2670 1.762370 TCCTTCCGAATCATAGCTGCA 59.238 47.619 1.02 0.00 0.00 4.41
2760 2778 2.297895 CCTCGATTGGGGGTGGTCA 61.298 63.158 0.00 0.00 0.00 4.02
2772 2790 6.379703 CCACTTTCTCATATATCTCCCTCGAT 59.620 42.308 0.00 0.00 0.00 3.59
2998 3016 1.696832 GAGATCAACTTCGTGGCGGC 61.697 60.000 0.00 0.00 0.00 6.53
3119 3137 3.632145 AGAGAAAAACCTTGACGCACATT 59.368 39.130 0.00 0.00 0.00 2.71
3120 3138 3.214328 AGAGAAAAACCTTGACGCACAT 58.786 40.909 0.00 0.00 0.00 3.21
3270 3304 0.538287 ACCAAGCCTGAAACTCTGCC 60.538 55.000 0.00 0.00 0.00 4.85
3360 3394 7.600640 TGCAATTGCGTTTTCTCGAAAAGAAA 61.601 34.615 24.58 0.00 46.58 2.52
3361 3395 4.206200 GCAATTGCGTTTTCTCGAAAAGAA 59.794 37.500 15.87 0.82 42.35 2.52
3362 3396 3.728718 GCAATTGCGTTTTCTCGAAAAGA 59.271 39.130 15.87 0.00 40.53 2.52
3363 3397 3.485378 TGCAATTGCGTTTTCTCGAAAAG 59.515 39.130 24.58 2.34 45.83 2.27
3364 3398 3.439293 TGCAATTGCGTTTTCTCGAAAA 58.561 36.364 24.58 0.00 45.83 2.29
3365 3399 3.071786 TGCAATTGCGTTTTCTCGAAA 57.928 38.095 24.58 0.12 45.83 3.46
3366 3400 2.765108 TGCAATTGCGTTTTCTCGAA 57.235 40.000 24.58 0.67 45.83 3.71
3367 3401 2.987413 ATGCAATTGCGTTTTCTCGA 57.013 40.000 24.58 4.86 45.83 4.04
3379 3413 6.071728 CCAAACTCTACCTTCTCAATGCAATT 60.072 38.462 0.00 0.00 36.63 2.32
3380 3414 5.416952 CCAAACTCTACCTTCTCAATGCAAT 59.583 40.000 0.00 0.00 0.00 3.56
3381 3415 4.761739 CCAAACTCTACCTTCTCAATGCAA 59.238 41.667 0.00 0.00 0.00 4.08
3382 3416 4.041567 TCCAAACTCTACCTTCTCAATGCA 59.958 41.667 0.00 0.00 0.00 3.96
3383 3417 4.579869 TCCAAACTCTACCTTCTCAATGC 58.420 43.478 0.00 0.00 0.00 3.56
3384 3418 7.331026 TGTATCCAAACTCTACCTTCTCAATG 58.669 38.462 0.00 0.00 0.00 2.82
3385 3419 7.181125 ACTGTATCCAAACTCTACCTTCTCAAT 59.819 37.037 0.00 0.00 0.00 2.57
3386 3420 6.497259 ACTGTATCCAAACTCTACCTTCTCAA 59.503 38.462 0.00 0.00 0.00 3.02
3387 3421 6.017192 ACTGTATCCAAACTCTACCTTCTCA 58.983 40.000 0.00 0.00 0.00 3.27
3388 3422 6.532988 ACTGTATCCAAACTCTACCTTCTC 57.467 41.667 0.00 0.00 0.00 2.87
3389 3423 6.532988 GACTGTATCCAAACTCTACCTTCT 57.467 41.667 0.00 0.00 0.00 2.85
3413 3447 3.383698 TTGTACCTGACCTCCTAGGAG 57.616 52.381 29.27 29.27 37.67 3.69
3414 3448 3.839323 TTTGTACCTGACCTCCTAGGA 57.161 47.619 11.98 11.98 37.67 2.94
3415 3449 4.030913 TCATTTGTACCTGACCTCCTAGG 58.969 47.826 0.82 0.82 42.49 3.02
3416 3450 5.422331 TCTTCATTTGTACCTGACCTCCTAG 59.578 44.000 0.00 0.00 0.00 3.02
3417 3451 5.338632 TCTTCATTTGTACCTGACCTCCTA 58.661 41.667 0.00 0.00 0.00 2.94
3418 3452 4.168101 TCTTCATTTGTACCTGACCTCCT 58.832 43.478 0.00 0.00 0.00 3.69
3419 3453 4.553330 TCTTCATTTGTACCTGACCTCC 57.447 45.455 0.00 0.00 0.00 4.30
3420 3454 5.305585 TGTTCTTCATTTGTACCTGACCTC 58.694 41.667 0.00 0.00 0.00 3.85
3421 3455 5.163195 ACTGTTCTTCATTTGTACCTGACCT 60.163 40.000 0.00 0.00 0.00 3.85
3422 3456 5.049405 CACTGTTCTTCATTTGTACCTGACC 60.049 44.000 0.00 0.00 0.00 4.02
3423 3457 5.758296 TCACTGTTCTTCATTTGTACCTGAC 59.242 40.000 0.00 0.00 0.00 3.51
3424 3458 5.924356 TCACTGTTCTTCATTTGTACCTGA 58.076 37.500 0.00 0.00 0.00 3.86
3425 3459 6.618287 TTCACTGTTCTTCATTTGTACCTG 57.382 37.500 0.00 0.00 0.00 4.00
3426 3460 6.828785 AGTTTCACTGTTCTTCATTTGTACCT 59.171 34.615 0.00 0.00 0.00 3.08
3427 3461 7.027778 AGTTTCACTGTTCTTCATTTGTACC 57.972 36.000 0.00 0.00 0.00 3.34
3433 3467 8.495949 CGTGTATTAGTTTCACTGTTCTTCATT 58.504 33.333 0.00 0.00 0.00 2.57
3434 3468 7.656137 ACGTGTATTAGTTTCACTGTTCTTCAT 59.344 33.333 0.00 0.00 0.00 2.57
3435 3469 6.982141 ACGTGTATTAGTTTCACTGTTCTTCA 59.018 34.615 0.00 0.00 0.00 3.02
3436 3470 7.359014 GGACGTGTATTAGTTTCACTGTTCTTC 60.359 40.741 0.00 0.00 0.00 2.87
3437 3471 6.423001 GGACGTGTATTAGTTTCACTGTTCTT 59.577 38.462 0.00 0.00 0.00 2.52
3438 3472 5.924825 GGACGTGTATTAGTTTCACTGTTCT 59.075 40.000 0.00 0.00 0.00 3.01
3439 3473 5.119743 GGGACGTGTATTAGTTTCACTGTTC 59.880 44.000 0.00 0.00 0.00 3.18
3440 3474 4.992951 GGGACGTGTATTAGTTTCACTGTT 59.007 41.667 0.00 0.00 0.00 3.16
3441 3475 4.039488 TGGGACGTGTATTAGTTTCACTGT 59.961 41.667 0.00 0.00 0.00 3.55
3442 3476 4.562082 TGGGACGTGTATTAGTTTCACTG 58.438 43.478 0.00 0.00 0.00 3.66
3443 3477 4.322499 CCTGGGACGTGTATTAGTTTCACT 60.322 45.833 0.00 0.00 0.00 3.41
3444 3478 3.930848 CCTGGGACGTGTATTAGTTTCAC 59.069 47.826 0.00 0.00 0.00 3.18
3445 3479 3.579586 ACCTGGGACGTGTATTAGTTTCA 59.420 43.478 0.00 0.00 0.00 2.69
3446 3480 3.930848 CACCTGGGACGTGTATTAGTTTC 59.069 47.826 0.00 0.00 0.00 2.78
3447 3481 3.307199 CCACCTGGGACGTGTATTAGTTT 60.307 47.826 0.00 0.00 40.01 2.66
3448 3482 2.235402 CCACCTGGGACGTGTATTAGTT 59.765 50.000 0.00 0.00 40.01 2.24
3449 3483 1.829222 CCACCTGGGACGTGTATTAGT 59.171 52.381 0.00 0.00 40.01 2.24
3450 3484 2.104967 TCCACCTGGGACGTGTATTAG 58.895 52.381 0.00 0.00 42.15 1.73
3451 3485 2.234896 TCCACCTGGGACGTGTATTA 57.765 50.000 0.00 0.00 42.15 0.98
3452 3486 3.076350 TCCACCTGGGACGTGTATT 57.924 52.632 0.00 0.00 42.15 1.89
3453 3487 4.878987 TCCACCTGGGACGTGTAT 57.121 55.556 0.00 0.00 42.15 2.29
3463 3497 4.704833 CACCCTGCCGTCCACCTG 62.705 72.222 0.00 0.00 0.00 4.00
3464 3498 4.954118 TCACCCTGCCGTCCACCT 62.954 66.667 0.00 0.00 0.00 4.00
3465 3499 4.699522 GTCACCCTGCCGTCCACC 62.700 72.222 0.00 0.00 0.00 4.61
3469 3503 3.509137 TTCACGTCACCCTGCCGTC 62.509 63.158 0.00 0.00 31.46 4.79
3470 3504 3.515316 CTTCACGTCACCCTGCCGT 62.515 63.158 0.00 0.00 34.71 5.68
3471 3505 2.738521 CTTCACGTCACCCTGCCG 60.739 66.667 0.00 0.00 0.00 5.69
3472 3506 2.358737 CCTTCACGTCACCCTGCC 60.359 66.667 0.00 0.00 0.00 4.85
3473 3507 3.050275 GCCTTCACGTCACCCTGC 61.050 66.667 0.00 0.00 0.00 4.85
3474 3508 2.358737 GGCCTTCACGTCACCCTG 60.359 66.667 0.00 0.00 0.00 4.45
3475 3509 2.397413 CTTGGCCTTCACGTCACCCT 62.397 60.000 3.32 0.00 0.00 4.34
3476 3510 1.966451 CTTGGCCTTCACGTCACCC 60.966 63.158 3.32 0.00 0.00 4.61
3477 3511 1.966451 CCTTGGCCTTCACGTCACC 60.966 63.158 3.32 0.00 0.00 4.02
3478 3512 1.966451 CCCTTGGCCTTCACGTCAC 60.966 63.158 3.32 0.00 0.00 3.67
3479 3513 2.429930 CCCTTGGCCTTCACGTCA 59.570 61.111 3.32 0.00 0.00 4.35
3480 3514 3.056328 GCCCTTGGCCTTCACGTC 61.056 66.667 3.32 0.00 44.06 4.34
3490 3524 4.335647 ACGAGCTGGTGCCCTTGG 62.336 66.667 0.00 0.00 40.80 3.61
3491 3525 3.052082 CACGAGCTGGTGCCCTTG 61.052 66.667 16.26 0.00 40.80 3.61
3497 3531 4.320456 AGTGGGCACGAGCTGGTG 62.320 66.667 23.11 23.11 41.70 4.17
3498 3532 4.320456 CAGTGGGCACGAGCTGGT 62.320 66.667 4.48 0.00 41.70 4.00
3509 3543 1.817099 GATGAAGCCGAGCAGTGGG 60.817 63.158 0.00 0.00 0.00 4.61
3510 3544 1.817099 GGATGAAGCCGAGCAGTGG 60.817 63.158 0.00 0.00 0.00 4.00
3511 3545 0.392193 AAGGATGAAGCCGAGCAGTG 60.392 55.000 0.00 0.00 0.00 3.66
3512 3546 0.392193 CAAGGATGAAGCCGAGCAGT 60.392 55.000 0.00 0.00 0.00 4.40
3513 3547 0.107993 TCAAGGATGAAGCCGAGCAG 60.108 55.000 0.00 0.00 30.99 4.24
3514 3548 0.543277 ATCAAGGATGAAGCCGAGCA 59.457 50.000 0.00 0.00 39.49 4.26
3515 3549 1.202627 AGATCAAGGATGAAGCCGAGC 60.203 52.381 0.00 0.00 39.49 5.03
3516 3550 2.906691 AGATCAAGGATGAAGCCGAG 57.093 50.000 0.00 0.00 39.49 4.63
3517 3551 3.055167 TCAAAGATCAAGGATGAAGCCGA 60.055 43.478 0.00 0.00 39.49 5.54
3518 3552 3.273434 TCAAAGATCAAGGATGAAGCCG 58.727 45.455 0.00 0.00 39.49 5.52
3519 3553 4.335037 GTCTCAAAGATCAAGGATGAAGCC 59.665 45.833 0.00 0.00 39.49 4.35
3520 3554 4.335037 GGTCTCAAAGATCAAGGATGAAGC 59.665 45.833 0.00 0.00 39.49 3.86
3521 3555 5.494724 TGGTCTCAAAGATCAAGGATGAAG 58.505 41.667 0.00 0.00 39.49 3.02
3522 3556 5.494724 CTGGTCTCAAAGATCAAGGATGAA 58.505 41.667 0.00 0.00 34.46 2.57
3523 3557 4.080695 CCTGGTCTCAAAGATCAAGGATGA 60.081 45.833 0.00 0.00 34.46 2.92
3524 3558 4.080695 TCCTGGTCTCAAAGATCAAGGATG 60.081 45.833 0.00 0.00 34.46 3.51
3525 3559 4.080638 GTCCTGGTCTCAAAGATCAAGGAT 60.081 45.833 9.89 0.00 34.46 3.24
3526 3560 3.261897 GTCCTGGTCTCAAAGATCAAGGA 59.738 47.826 0.00 5.04 34.46 3.36
3527 3561 3.008375 TGTCCTGGTCTCAAAGATCAAGG 59.992 47.826 0.00 0.00 34.46 3.61
3528 3562 4.277515 TGTCCTGGTCTCAAAGATCAAG 57.722 45.455 0.00 0.00 34.46 3.02
3529 3563 4.286808 TCATGTCCTGGTCTCAAAGATCAA 59.713 41.667 0.00 0.00 34.46 2.57
3530 3564 3.840078 TCATGTCCTGGTCTCAAAGATCA 59.160 43.478 0.00 0.00 33.63 2.92
3531 3565 4.478206 TCATGTCCTGGTCTCAAAGATC 57.522 45.455 0.00 0.00 0.00 2.75
3532 3566 4.566488 GGTTCATGTCCTGGTCTCAAAGAT 60.566 45.833 0.00 0.00 0.00 2.40
3533 3567 3.244561 GGTTCATGTCCTGGTCTCAAAGA 60.245 47.826 0.00 0.00 0.00 2.52
3534 3568 3.077359 GGTTCATGTCCTGGTCTCAAAG 58.923 50.000 0.00 0.00 0.00 2.77
3535 3569 2.441375 TGGTTCATGTCCTGGTCTCAAA 59.559 45.455 10.06 0.00 0.00 2.69
3536 3570 2.038952 CTGGTTCATGTCCTGGTCTCAA 59.961 50.000 10.06 0.00 0.00 3.02
3537 3571 1.625315 CTGGTTCATGTCCTGGTCTCA 59.375 52.381 10.06 0.00 0.00 3.27
3538 3572 1.065854 CCTGGTTCATGTCCTGGTCTC 60.066 57.143 19.18 0.00 38.64 3.36
3539 3573 0.987294 CCTGGTTCATGTCCTGGTCT 59.013 55.000 19.18 0.00 38.64 3.85
3540 3574 0.035056 CCCTGGTTCATGTCCTGGTC 60.035 60.000 22.62 0.00 40.81 4.02
3541 3575 1.500783 CCCCTGGTTCATGTCCTGGT 61.501 60.000 22.62 0.00 40.81 4.00
3542 3576 1.304282 CCCCTGGTTCATGTCCTGG 59.696 63.158 19.93 19.93 41.66 4.45
3543 3577 1.379044 GCCCCTGGTTCATGTCCTG 60.379 63.158 10.06 9.31 0.00 3.86
3544 3578 1.542375 AGCCCCTGGTTCATGTCCT 60.542 57.895 10.06 0.00 0.00 3.85
3545 3579 1.379044 CAGCCCCTGGTTCATGTCC 60.379 63.158 0.00 0.00 0.00 4.02
3546 3580 1.379044 CCAGCCCCTGGTTCATGTC 60.379 63.158 3.09 0.00 45.82 3.06
3547 3581 2.765969 CCAGCCCCTGGTTCATGT 59.234 61.111 3.09 0.00 45.82 3.21
3561 3595 1.493950 GCATCTTCGATGGCGTCCAG 61.494 60.000 0.14 0.00 36.75 3.86
3562 3596 1.521457 GCATCTTCGATGGCGTCCA 60.521 57.895 0.14 1.01 38.19 4.02
3563 3597 1.521457 TGCATCTTCGATGGCGTCC 60.521 57.895 0.14 0.00 38.98 4.79
3564 3598 0.807667 AGTGCATCTTCGATGGCGTC 60.808 55.000 6.04 0.00 38.98 5.19
3565 3599 0.807667 GAGTGCATCTTCGATGGCGT 60.808 55.000 6.04 0.00 38.98 5.68
3566 3600 1.815212 CGAGTGCATCTTCGATGGCG 61.815 60.000 11.35 0.00 39.35 5.69
3567 3601 0.807667 ACGAGTGCATCTTCGATGGC 60.808 55.000 20.27 0.00 0.00 4.40
3568 3602 1.325640 CAACGAGTGCATCTTCGATGG 59.674 52.381 20.27 8.70 0.00 3.51
3569 3603 2.708548 CAACGAGTGCATCTTCGATG 57.291 50.000 20.27 15.87 0.00 3.84
3580 3614 2.171940 GAAGCAGCGCAACGAGTG 59.828 61.111 11.47 0.00 0.00 3.51
3581 3615 3.044305 GGAAGCAGCGCAACGAGT 61.044 61.111 11.47 0.00 0.00 4.18
3582 3616 3.020026 CTGGAAGCAGCGCAACGAG 62.020 63.158 11.47 0.00 0.00 4.18
3583 3617 2.786539 ATCTGGAAGCAGCGCAACGA 62.787 55.000 11.47 0.00 0.00 3.85
3584 3618 2.301902 GATCTGGAAGCAGCGCAACG 62.302 60.000 11.47 0.00 0.00 4.10
3585 3619 1.300971 TGATCTGGAAGCAGCGCAAC 61.301 55.000 11.47 0.00 0.00 4.17
3586 3620 0.393402 ATGATCTGGAAGCAGCGCAA 60.393 50.000 11.47 0.00 0.00 4.85
3587 3621 0.812811 GATGATCTGGAAGCAGCGCA 60.813 55.000 11.47 0.00 0.00 6.09
3588 3622 1.505477 GGATGATCTGGAAGCAGCGC 61.505 60.000 0.00 0.00 0.00 5.92
3589 3623 0.179065 TGGATGATCTGGAAGCAGCG 60.179 55.000 0.00 0.00 0.00 5.18
3590 3624 1.880675 CATGGATGATCTGGAAGCAGC 59.119 52.381 0.00 0.00 0.00 5.25
3591 3625 2.158652 ACCATGGATGATCTGGAAGCAG 60.159 50.000 21.47 0.00 34.08 4.24
3592 3626 1.848388 ACCATGGATGATCTGGAAGCA 59.152 47.619 21.47 0.00 34.08 3.91
3593 3627 2.228059 CACCATGGATGATCTGGAAGC 58.772 52.381 21.47 0.00 34.08 3.86
3594 3628 3.118149 TGACACCATGGATGATCTGGAAG 60.118 47.826 21.47 3.03 34.08 3.46
3595 3629 2.845586 TGACACCATGGATGATCTGGAA 59.154 45.455 21.47 0.00 34.08 3.53
3596 3630 2.480390 TGACACCATGGATGATCTGGA 58.520 47.619 21.47 0.00 34.08 3.86
3597 3631 3.118149 TCTTGACACCATGGATGATCTGG 60.118 47.826 21.47 0.00 36.09 3.86
3598 3632 4.127907 CTCTTGACACCATGGATGATCTG 58.872 47.826 21.47 7.57 0.00 2.90
3599 3633 3.136077 CCTCTTGACACCATGGATGATCT 59.864 47.826 21.47 0.00 0.00 2.75
3600 3634 3.474600 CCTCTTGACACCATGGATGATC 58.525 50.000 21.47 10.31 0.00 2.92
3601 3635 2.174210 CCCTCTTGACACCATGGATGAT 59.826 50.000 21.47 0.00 0.00 2.45
3602 3636 1.561076 CCCTCTTGACACCATGGATGA 59.439 52.381 21.47 2.60 0.00 2.92
3603 3637 2.020694 GCCCTCTTGACACCATGGATG 61.021 57.143 21.47 15.31 0.00 3.51
3604 3638 0.257039 GCCCTCTTGACACCATGGAT 59.743 55.000 21.47 5.75 0.00 3.41
3605 3639 1.133181 TGCCCTCTTGACACCATGGA 61.133 55.000 21.47 0.00 0.00 3.41
3606 3640 0.679002 CTGCCCTCTTGACACCATGG 60.679 60.000 11.19 11.19 0.00 3.66
3607 3641 0.037303 ACTGCCCTCTTGACACCATG 59.963 55.000 0.00 0.00 0.00 3.66
3608 3642 0.037303 CACTGCCCTCTTGACACCAT 59.963 55.000 0.00 0.00 0.00 3.55
3609 3643 1.451504 CACTGCCCTCTTGACACCA 59.548 57.895 0.00 0.00 0.00 4.17
3610 3644 1.302832 CCACTGCCCTCTTGACACC 60.303 63.158 0.00 0.00 0.00 4.16
3611 3645 0.321122 CTCCACTGCCCTCTTGACAC 60.321 60.000 0.00 0.00 0.00 3.67
3612 3646 1.483595 CCTCCACTGCCCTCTTGACA 61.484 60.000 0.00 0.00 0.00 3.58
3613 3647 1.298014 CCTCCACTGCCCTCTTGAC 59.702 63.158 0.00 0.00 0.00 3.18
3614 3648 2.596851 GCCTCCACTGCCCTCTTGA 61.597 63.158 0.00 0.00 0.00 3.02
3615 3649 1.267574 TAGCCTCCACTGCCCTCTTG 61.268 60.000 0.00 0.00 0.00 3.02
3616 3650 0.980231 CTAGCCTCCACTGCCCTCTT 60.980 60.000 0.00 0.00 0.00 2.85
3617 3651 1.382420 CTAGCCTCCACTGCCCTCT 60.382 63.158 0.00 0.00 0.00 3.69
3618 3652 2.439104 CCTAGCCTCCACTGCCCTC 61.439 68.421 0.00 0.00 0.00 4.30
3619 3653 2.366167 CCTAGCCTCCACTGCCCT 60.366 66.667 0.00 0.00 0.00 5.19
3620 3654 4.182433 GCCTAGCCTCCACTGCCC 62.182 72.222 0.00 0.00 0.00 5.36
3621 3655 4.182433 GGCCTAGCCTCCACTGCC 62.182 72.222 0.00 0.00 46.69 4.85
3631 3665 2.203029 GGTGCGTAAGGGCCTAGC 60.203 66.667 6.41 14.15 38.28 3.42
3632 3666 2.504519 GGGTGCGTAAGGGCCTAG 59.495 66.667 6.41 2.34 38.28 3.02
3633 3667 3.463585 CGGGTGCGTAAGGGCCTA 61.464 66.667 6.41 0.00 38.28 3.93
3635 3669 4.710167 AACGGGTGCGTAAGGGCC 62.710 66.667 0.00 0.00 38.28 5.80
3636 3670 2.670592 AAACGGGTGCGTAAGGGC 60.671 61.111 0.00 0.00 38.28 5.19
3637 3671 2.036571 GGAAACGGGTGCGTAAGGG 61.037 63.158 0.00 0.00 38.28 3.95
3638 3672 2.036571 GGGAAACGGGTGCGTAAGG 61.037 63.158 0.00 0.00 38.28 2.69
3639 3673 0.604511 AAGGGAAACGGGTGCGTAAG 60.605 55.000 0.00 0.00 43.44 2.34
3640 3674 0.179023 AAAGGGAAACGGGTGCGTAA 60.179 50.000 0.00 0.00 0.00 3.18
3641 3675 0.179023 AAAAGGGAAACGGGTGCGTA 60.179 50.000 0.00 0.00 0.00 4.42
3642 3676 1.038681 AAAAAGGGAAACGGGTGCGT 61.039 50.000 0.00 0.00 0.00 5.24
3643 3677 1.737201 AAAAAGGGAAACGGGTGCG 59.263 52.632 0.00 0.00 0.00 5.34
3661 3695 9.449719 GAAGAAAACTACAAAGATCCTATCCAA 57.550 33.333 0.00 0.00 0.00 3.53
3751 3814 1.591594 ACAGTTCTCGCACACCGTG 60.592 57.895 0.00 0.00 38.35 4.94
3793 3925 6.072452 TCGTTTGGTATTCATGCAATGTACAA 60.072 34.615 0.00 0.00 46.80 2.41
3797 3929 4.142403 CCTCGTTTGGTATTCATGCAATGT 60.142 41.667 0.00 0.00 46.80 2.71
3863 4002 9.371136 TGCATTTGAAATTTTATATAACCGCAA 57.629 25.926 0.00 0.00 0.00 4.85
3896 4036 4.038402 CCAAGACAATGAAAGGAAACTGCT 59.962 41.667 0.00 0.00 42.68 4.24
3897 4037 4.301628 CCAAGACAATGAAAGGAAACTGC 58.698 43.478 0.00 0.00 42.68 4.40
3999 4146 3.084579 CATCCACGCGTCAGCTTC 58.915 61.111 9.86 0.00 42.32 3.86
4086 4238 3.423154 GACTTGCCGGCGGAGTTG 61.423 66.667 33.44 17.92 0.00 3.16
4087 4239 4.699522 GGACTTGCCGGCGGAGTT 62.700 66.667 33.44 16.84 0.00 3.01


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

AutoCloner maintained by Alex Coulton.