Multiple sequence alignment - TraesCS3A01G172500

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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 TraesCS3A01G172500 chr3A 100.000 5040 0 0 1 5040 187254027 187259066 0.000000e+00 9308
1 TraesCS3A01G172500 chr3A 98.903 1276 14 0 3765 5040 187265950 187267225 0.000000e+00 2279
2 TraesCS3A01G172500 chr3A 97.897 1284 23 4 3759 5040 398373562 398372281 0.000000e+00 2218
3 TraesCS3A01G172500 chr3A 96.244 426 14 1 3341 3764 102383059 102383484 0.000000e+00 697
4 TraesCS3A01G172500 chr3D 95.574 3389 87 37 1 3339 160704868 160708243 0.000000e+00 5369
5 TraesCS3A01G172500 chr3B 95.852 1567 56 3 1773 3339 237494839 237496396 0.000000e+00 2525
6 TraesCS3A01G172500 chr3B 98.045 1279 23 2 3764 5040 54741692 54742970 0.000000e+00 2222
7 TraesCS3A01G172500 chr3B 91.473 1032 57 16 531 1561 237493643 237494644 0.000000e+00 1389
8 TraesCS3A01G172500 chr5B 98.199 1277 22 1 3765 5040 667596994 667598270 0.000000e+00 2230
9 TraesCS3A01G172500 chr5B 98.121 1277 22 2 3765 5040 439111637 439112912 0.000000e+00 2224
10 TraesCS3A01G172500 chr5B 80.660 212 39 2 1165 1375 572142062 572142272 4.040000e-36 163
11 TraesCS3A01G172500 chr6B 98.121 1277 21 3 3765 5040 161315178 161313904 0.000000e+00 2222
12 TraesCS3A01G172500 chr6B 96.714 426 12 1 3341 3764 245972418 245971993 0.000000e+00 708
13 TraesCS3A01G172500 chr6B 96.479 426 13 1 3341 3764 700666139 700665714 0.000000e+00 702
14 TraesCS3A01G172500 chr4A 98.044 1278 22 3 3765 5040 370458434 370459710 0.000000e+00 2218
15 TraesCS3A01G172500 chr1B 97.966 1278 25 1 3764 5040 366386205 366384928 0.000000e+00 2215
16 TraesCS3A01G172500 chr1B 96.296 432 14 1 3335 3764 564293935 564294366 0.000000e+00 708
17 TraesCS3A01G172500 chr2B 97.819 1284 25 3 3758 5040 588720213 588718932 0.000000e+00 2213
18 TraesCS3A01G172500 chr2B 97.183 426 10 1 3341 3764 581792934 581793359 0.000000e+00 719
19 TraesCS3A01G172500 chr7B 96.714 426 12 1 3341 3764 371217215 371216790 0.000000e+00 708
20 TraesCS3A01G172500 chr7B 96.270 429 14 1 3338 3764 649855234 649855662 0.000000e+00 702
21 TraesCS3A01G172500 chrUn 96.479 426 13 1 3341 3764 38531881 38532306 0.000000e+00 702
22 TraesCS3A01G172500 chr4B 96.037 429 15 1 3338 3764 2511427 2511855 0.000000e+00 697
23 TraesCS3A01G172500 chr5D 80.465 215 34 7 1165 1375 464916839 464917049 1.880000e-34 158
24 TraesCS3A01G172500 chr5A 80.000 215 35 7 1165 1375 585234591 585234801 8.740000e-33 152


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 TraesCS3A01G172500 chr3A 187254027 187259066 5039 False 9308 9308 100.0000 1 5040 1 chr3A.!!$F2 5039
1 TraesCS3A01G172500 chr3A 187265950 187267225 1275 False 2279 2279 98.9030 3765 5040 1 chr3A.!!$F3 1275
2 TraesCS3A01G172500 chr3A 398372281 398373562 1281 True 2218 2218 97.8970 3759 5040 1 chr3A.!!$R1 1281
3 TraesCS3A01G172500 chr3D 160704868 160708243 3375 False 5369 5369 95.5740 1 3339 1 chr3D.!!$F1 3338
4 TraesCS3A01G172500 chr3B 54741692 54742970 1278 False 2222 2222 98.0450 3764 5040 1 chr3B.!!$F1 1276
5 TraesCS3A01G172500 chr3B 237493643 237496396 2753 False 1957 2525 93.6625 531 3339 2 chr3B.!!$F2 2808
6 TraesCS3A01G172500 chr5B 667596994 667598270 1276 False 2230 2230 98.1990 3765 5040 1 chr5B.!!$F3 1275
7 TraesCS3A01G172500 chr5B 439111637 439112912 1275 False 2224 2224 98.1210 3765 5040 1 chr5B.!!$F1 1275
8 TraesCS3A01G172500 chr6B 161313904 161315178 1274 True 2222 2222 98.1210 3765 5040 1 chr6B.!!$R1 1275
9 TraesCS3A01G172500 chr4A 370458434 370459710 1276 False 2218 2218 98.0440 3765 5040 1 chr4A.!!$F1 1275
10 TraesCS3A01G172500 chr1B 366384928 366386205 1277 True 2215 2215 97.9660 3764 5040 1 chr1B.!!$R1 1276
11 TraesCS3A01G172500 chr2B 588718932 588720213 1281 True 2213 2213 97.8190 3758 5040 1 chr2B.!!$R1 1282

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
568 578 0.036306 CCGTGGGGTTAGCTTTGACT 59.964 55.0 0.00 0.0 0.00 3.41 F
783 796 0.036952 TGCTCCTTCACACTGCTAGC 60.037 55.0 8.10 8.1 0.00 3.42 F
784 797 0.248843 GCTCCTTCACACTGCTAGCT 59.751 55.0 17.23 0.0 0.00 3.32 F
1600 1623 0.318614 GGAGCTCGCTCACATCTAGC 60.319 60.0 19.44 0.0 44.40 3.42 F
3455 3521 0.178873 AGGGTTGAGCCAGTTCCCTA 60.179 55.0 1.66 0.0 45.56 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2277 2343 0.798776 AGAAATGCACGGCGAAGAAG 59.201 50.000 16.62 0.00 0.00 2.85 R
2666 2732 1.153686 GGCGTAGGGGTTCTCGAAC 60.154 63.158 1.22 1.22 40.45 3.95 R
2927 2993 2.708865 GCGCGCTATCATTGTGCA 59.291 55.556 26.67 0.00 40.54 4.57 R
3691 3757 0.099791 CGACGAGGAGAAGAAGGAGC 59.900 60.000 0.00 0.00 0.00 4.70 R
4563 4630 0.176680 ATGCAGACATGACCGAGACC 59.823 55.000 0.00 0.00 34.35 3.85 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
18 19 1.067582 GATGTTAGGGGCGGTCGAG 59.932 63.158 0.00 0.00 0.00 4.04
37 39 0.246910 GAAGGGGAGACGAGTTGGAC 59.753 60.000 0.00 0.00 0.00 4.02
50 52 1.377202 TTGGACGATGGGAGCTTGC 60.377 57.895 0.00 0.00 0.00 4.01
85 87 3.160047 CCTCCCTGCTCCTGCGAT 61.160 66.667 0.00 0.00 43.34 4.58
137 139 2.856988 GGTGGGTGGGACTTGGGA 60.857 66.667 0.00 0.00 0.00 4.37
259 265 2.104967 TCGCGGAAGGAGATAAAAGGA 58.895 47.619 6.13 0.00 0.00 3.36
267 273 6.823689 CGGAAGGAGATAAAAGGATTGAGAAA 59.176 38.462 0.00 0.00 0.00 2.52
291 297 5.011023 ACCTCCTCAAACTGCTTAATTTTGG 59.989 40.000 0.00 0.00 31.19 3.28
328 334 3.366052 TTGAGGAGCAACCCCTATTTC 57.634 47.619 0.00 0.00 40.05 2.17
367 373 5.472137 CGGTTTTGAGGGAAGATCTACAAAA 59.528 40.000 0.00 7.87 35.75 2.44
425 431 5.080337 GGAAAGAAGATTTGAGGAAAGGGT 58.920 41.667 0.00 0.00 0.00 4.34
452 458 5.923204 AGATGCTCTTACTGAAAATCGGAT 58.077 37.500 0.00 0.00 0.00 4.18
470 476 4.065088 CGGATAACCCACTTATCATGGTG 58.935 47.826 0.00 0.00 41.91 4.17
554 564 1.384989 ATGCGTCTAGGAGACCGTGG 61.385 60.000 1.13 0.00 42.12 4.94
568 578 0.036306 CCGTGGGGTTAGCTTTGACT 59.964 55.000 0.00 0.00 0.00 3.41
659 669 6.036408 ACAAAAGCTCTTGAACAAAGCAAATC 59.964 34.615 6.82 0.00 38.51 2.17
702 713 6.970043 GTGCGTGAAATTTTATAACTGCCATA 59.030 34.615 0.00 0.00 0.00 2.74
751 762 0.107897 AAGTATGCACGGATGGCGAA 60.108 50.000 0.00 0.00 0.00 4.70
782 795 1.274728 AGTGCTCCTTCACACTGCTAG 59.725 52.381 0.00 0.00 45.19 3.42
783 796 0.036952 TGCTCCTTCACACTGCTAGC 60.037 55.000 8.10 8.10 0.00 3.42
784 797 0.248843 GCTCCTTCACACTGCTAGCT 59.751 55.000 17.23 0.00 0.00 3.32
785 798 1.478510 GCTCCTTCACACTGCTAGCTA 59.521 52.381 17.23 1.31 0.00 3.32
786 799 2.737039 GCTCCTTCACACTGCTAGCTAC 60.737 54.545 17.23 0.00 0.00 3.58
787 800 1.472878 TCCTTCACACTGCTAGCTACG 59.527 52.381 17.23 6.98 0.00 3.51
788 801 1.202582 CCTTCACACTGCTAGCTACGT 59.797 52.381 17.23 7.64 0.00 3.57
789 802 2.422479 CCTTCACACTGCTAGCTACGTA 59.578 50.000 17.23 0.00 0.00 3.57
790 803 3.427243 CTTCACACTGCTAGCTACGTAC 58.573 50.000 17.23 0.00 0.00 3.67
791 804 2.429478 TCACACTGCTAGCTACGTACA 58.571 47.619 17.23 0.00 0.00 2.90
792 805 2.815503 TCACACTGCTAGCTACGTACAA 59.184 45.455 17.23 0.00 0.00 2.41
793 806 2.915463 CACACTGCTAGCTACGTACAAC 59.085 50.000 17.23 0.00 0.00 3.32
794 807 2.555325 ACACTGCTAGCTACGTACAACA 59.445 45.455 17.23 0.00 0.00 3.33
795 808 3.192844 ACACTGCTAGCTACGTACAACAT 59.807 43.478 17.23 0.00 0.00 2.71
796 809 4.397103 ACACTGCTAGCTACGTACAACATA 59.603 41.667 17.23 0.00 0.00 2.29
797 810 4.970611 CACTGCTAGCTACGTACAACATAG 59.029 45.833 17.23 2.24 0.00 2.23
798 811 4.639310 ACTGCTAGCTACGTACAACATAGT 59.361 41.667 17.23 2.92 0.00 2.12
799 812 5.819379 ACTGCTAGCTACGTACAACATAGTA 59.181 40.000 17.23 0.00 0.00 1.82
800 813 6.052840 TGCTAGCTACGTACAACATAGTAC 57.947 41.667 17.23 0.00 40.68 2.73
801 814 5.819379 TGCTAGCTACGTACAACATAGTACT 59.181 40.000 17.23 0.00 41.65 2.73
813 826 9.825972 GTACAACATAGTACTCGTACAACTTTA 57.174 33.333 0.00 0.00 40.85 1.85
817 830 3.826466 AGTACTCGTACAACTTTACGCC 58.174 45.455 9.62 0.00 43.72 5.68
822 835 1.136446 CGTACAACTTTACGCCTGCAC 60.136 52.381 0.00 0.00 38.54 4.57
839 852 2.210013 ACTGGCAGGTCGAGAAGCA 61.210 57.895 20.34 0.00 0.00 3.91
840 853 1.739562 CTGGCAGGTCGAGAAGCAC 60.740 63.158 6.61 0.00 0.00 4.40
965 988 1.192146 TACAAGGACCCGAAGCAGCT 61.192 55.000 0.00 0.00 0.00 4.24
1123 1146 3.715495 TGCATTTCACGTGCATTTTTCT 58.285 36.364 11.67 0.00 46.76 2.52
1128 1151 5.759506 TTTCACGTGCATTTTTCTTAGGA 57.240 34.783 11.67 0.00 0.00 2.94
1599 1622 1.266718 GAGGAGCTCGCTCACATCTAG 59.733 57.143 19.44 0.00 44.40 2.43
1600 1623 0.318614 GGAGCTCGCTCACATCTAGC 60.319 60.000 19.44 0.00 44.40 3.42
1866 1932 3.196913 TACGTGTTCGCTCCGTGCA 62.197 57.895 0.00 0.00 43.06 4.57
1962 2028 2.430610 GCCTCCGTCATCTCTGGCT 61.431 63.158 0.00 0.00 37.58 4.75
2174 2240 4.742201 CAGGGCGTCTCCACCGTG 62.742 72.222 0.00 0.00 35.69 4.94
2277 2343 1.001158 GATTCAGGGTCTCCGATCGAC 60.001 57.143 18.66 6.80 38.33 4.20
2666 2732 2.154462 GTCAAGTTCACCATGGGTCTG 58.846 52.381 18.09 5.51 31.02 3.51
2927 2993 1.061546 ACAACCTCACCACCGGTAAT 58.938 50.000 6.87 0.00 32.11 1.89
2934 3000 1.173043 CACCACCGGTAATGCACAAT 58.827 50.000 6.87 0.00 32.11 2.71
3270 3336 4.752879 GGCAGGCCGCTTGTCGTA 62.753 66.667 17.07 0.00 41.91 3.43
3341 3407 3.489513 GGAGGGGCAGGGCGTATT 61.490 66.667 0.00 0.00 0.00 1.89
3342 3408 2.144738 GGAGGGGCAGGGCGTATTA 61.145 63.158 0.00 0.00 0.00 0.98
3343 3409 1.371558 GAGGGGCAGGGCGTATTAG 59.628 63.158 0.00 0.00 0.00 1.73
3344 3410 1.074775 AGGGGCAGGGCGTATTAGA 60.075 57.895 0.00 0.00 0.00 2.10
3345 3411 1.070957 GGGGCAGGGCGTATTAGAC 59.929 63.158 0.00 0.00 0.00 2.59
3346 3412 1.408453 GGGGCAGGGCGTATTAGACT 61.408 60.000 0.00 0.00 0.00 3.24
3347 3413 0.249911 GGGCAGGGCGTATTAGACTG 60.250 60.000 0.00 0.00 0.00 3.51
3348 3414 0.464452 GGCAGGGCGTATTAGACTGT 59.536 55.000 0.00 0.00 0.00 3.55
3349 3415 1.684983 GGCAGGGCGTATTAGACTGTA 59.315 52.381 0.00 0.00 0.00 2.74
3350 3416 2.299297 GGCAGGGCGTATTAGACTGTAT 59.701 50.000 0.00 0.00 0.00 2.29
3351 3417 3.508793 GGCAGGGCGTATTAGACTGTATA 59.491 47.826 0.00 0.00 0.00 1.47
3352 3418 4.380655 GGCAGGGCGTATTAGACTGTATAG 60.381 50.000 0.00 0.00 0.00 1.31
3353 3419 4.734917 CAGGGCGTATTAGACTGTATAGC 58.265 47.826 0.00 0.00 0.00 2.97
3354 3420 4.459685 CAGGGCGTATTAGACTGTATAGCT 59.540 45.833 0.00 0.00 0.00 3.32
3355 3421 4.701171 AGGGCGTATTAGACTGTATAGCTC 59.299 45.833 0.00 0.00 0.00 4.09
3356 3422 4.142425 GGGCGTATTAGACTGTATAGCTCC 60.142 50.000 0.00 0.00 0.00 4.70
3357 3423 4.701171 GGCGTATTAGACTGTATAGCTCCT 59.299 45.833 0.00 0.00 0.00 3.69
3358 3424 5.392165 GGCGTATTAGACTGTATAGCTCCTG 60.392 48.000 0.00 0.00 0.00 3.86
3359 3425 5.181622 GCGTATTAGACTGTATAGCTCCTGT 59.818 44.000 0.00 0.00 0.00 4.00
3360 3426 6.370994 GCGTATTAGACTGTATAGCTCCTGTA 59.629 42.308 0.00 0.00 0.00 2.74
3361 3427 7.066043 GCGTATTAGACTGTATAGCTCCTGTAT 59.934 40.741 0.00 0.00 0.00 2.29
3362 3428 9.597170 CGTATTAGACTGTATAGCTCCTGTATA 57.403 37.037 0.00 0.00 0.00 1.47
3365 3431 9.983024 ATTAGACTGTATAGCTCCTGTATATGT 57.017 33.333 0.00 0.00 0.00 2.29
3366 3432 7.695480 AGACTGTATAGCTCCTGTATATGTG 57.305 40.000 0.00 0.00 0.00 3.21
3367 3433 7.235079 AGACTGTATAGCTCCTGTATATGTGT 58.765 38.462 0.00 0.00 0.00 3.72
3368 3434 8.383947 AGACTGTATAGCTCCTGTATATGTGTA 58.616 37.037 0.00 0.00 0.00 2.90
3369 3435 8.338072 ACTGTATAGCTCCTGTATATGTGTAC 57.662 38.462 0.00 0.00 0.00 2.90
3370 3436 7.119407 ACTGTATAGCTCCTGTATATGTGTACG 59.881 40.741 0.00 0.00 0.00 3.67
3371 3437 6.938596 TGTATAGCTCCTGTATATGTGTACGT 59.061 38.462 0.00 0.00 0.00 3.57
3372 3438 8.096414 TGTATAGCTCCTGTATATGTGTACGTA 58.904 37.037 0.00 0.00 0.00 3.57
3373 3439 9.107177 GTATAGCTCCTGTATATGTGTACGTAT 57.893 37.037 0.00 2.63 33.10 3.06
3375 3441 9.848710 ATAGCTCCTGTATATGTGTACGTATAT 57.151 33.333 0.00 0.00 34.10 0.86
3376 3442 7.986562 AGCTCCTGTATATGTGTACGTATATG 58.013 38.462 0.00 0.00 34.10 1.78
3377 3443 7.827729 AGCTCCTGTATATGTGTACGTATATGA 59.172 37.037 0.00 4.93 34.10 2.15
3378 3444 8.456471 GCTCCTGTATATGTGTACGTATATGAA 58.544 37.037 0.00 0.00 34.10 2.57
3402 3468 2.845967 CGTACGATGTAACGTTGTACCC 59.154 50.000 10.44 0.00 44.14 3.69
3403 3469 3.426159 CGTACGATGTAACGTTGTACCCT 60.426 47.826 10.44 0.00 44.14 4.34
3404 3470 3.665745 ACGATGTAACGTTGTACCCTT 57.334 42.857 11.99 0.00 44.14 3.95
3405 3471 3.319755 ACGATGTAACGTTGTACCCTTG 58.680 45.455 11.99 0.00 44.14 3.61
3406 3472 3.243839 ACGATGTAACGTTGTACCCTTGT 60.244 43.478 11.99 0.09 44.14 3.16
3407 3473 3.742369 CGATGTAACGTTGTACCCTTGTT 59.258 43.478 11.99 0.00 0.00 2.83
3408 3474 4.922692 CGATGTAACGTTGTACCCTTGTTA 59.077 41.667 11.99 0.00 0.00 2.41
3409 3475 5.577945 CGATGTAACGTTGTACCCTTGTTAT 59.422 40.000 11.99 0.00 0.00 1.89
3410 3476 6.751425 CGATGTAACGTTGTACCCTTGTTATA 59.249 38.462 11.99 0.00 0.00 0.98
3411 3477 7.436080 CGATGTAACGTTGTACCCTTGTTATAT 59.564 37.037 11.99 0.00 32.06 0.86
3412 3478 9.748708 GATGTAACGTTGTACCCTTGTTATATA 57.251 33.333 11.99 0.00 30.34 0.86
3437 3503 8.846423 ATATATGAGATAGACCACCCCTAAAG 57.154 38.462 0.00 0.00 0.00 1.85
3438 3504 3.654273 TGAGATAGACCACCCCTAAAGG 58.346 50.000 0.00 0.00 0.00 3.11
3450 3516 2.586648 CCTAAAGGGTTGAGCCAGTT 57.413 50.000 1.66 0.00 39.65 3.16
3451 3517 2.437413 CCTAAAGGGTTGAGCCAGTTC 58.563 52.381 1.66 0.00 39.65 3.01
3452 3518 2.437413 CTAAAGGGTTGAGCCAGTTCC 58.563 52.381 1.66 0.00 39.65 3.62
3453 3519 0.178961 AAAGGGTTGAGCCAGTTCCC 60.179 55.000 1.66 0.00 39.65 3.97
3454 3520 1.464198 AGGGTTGAGCCAGTTCCCT 60.464 57.895 1.66 0.00 43.03 4.20
3455 3521 0.178873 AGGGTTGAGCCAGTTCCCTA 60.179 55.000 1.66 0.00 45.56 3.53
3456 3522 0.696501 GGGTTGAGCCAGTTCCCTAA 59.303 55.000 0.00 0.00 39.65 2.69
3457 3523 1.074889 GGGTTGAGCCAGTTCCCTAAA 59.925 52.381 0.00 0.00 39.65 1.85
3458 3524 2.160205 GGTTGAGCCAGTTCCCTAAAC 58.840 52.381 0.00 0.00 38.21 2.01
3459 3525 2.160205 GTTGAGCCAGTTCCCTAAACC 58.840 52.381 0.00 0.00 38.76 3.27
3460 3526 1.742308 TGAGCCAGTTCCCTAAACCT 58.258 50.000 0.00 0.00 38.76 3.50
3461 3527 2.910544 TGAGCCAGTTCCCTAAACCTA 58.089 47.619 0.00 0.00 38.76 3.08
3462 3528 2.570302 TGAGCCAGTTCCCTAAACCTAC 59.430 50.000 0.00 0.00 38.76 3.18
3463 3529 2.838813 GAGCCAGTTCCCTAAACCTACT 59.161 50.000 0.00 0.00 38.76 2.57
3464 3530 2.572104 AGCCAGTTCCCTAAACCTACTG 59.428 50.000 0.00 0.00 38.76 2.74
3465 3531 2.305052 GCCAGTTCCCTAAACCTACTGT 59.695 50.000 0.00 0.00 38.76 3.55
3466 3532 3.619242 GCCAGTTCCCTAAACCTACTGTC 60.619 52.174 0.00 0.00 38.76 3.51
3467 3533 3.838903 CCAGTTCCCTAAACCTACTGTCT 59.161 47.826 0.00 0.00 38.76 3.41
3468 3534 4.286291 CCAGTTCCCTAAACCTACTGTCTT 59.714 45.833 0.00 0.00 38.76 3.01
3469 3535 5.482878 CCAGTTCCCTAAACCTACTGTCTTA 59.517 44.000 0.00 0.00 38.76 2.10
3470 3536 6.396450 CAGTTCCCTAAACCTACTGTCTTAC 58.604 44.000 0.00 0.00 38.76 2.34
3471 3537 5.184671 AGTTCCCTAAACCTACTGTCTTACG 59.815 44.000 0.00 0.00 38.76 3.18
3472 3538 4.666512 TCCCTAAACCTACTGTCTTACGT 58.333 43.478 0.00 0.00 0.00 3.57
3473 3539 4.460382 TCCCTAAACCTACTGTCTTACGTG 59.540 45.833 0.00 0.00 0.00 4.49
3474 3540 4.381292 CCCTAAACCTACTGTCTTACGTGG 60.381 50.000 0.00 0.00 0.00 4.94
3475 3541 4.219288 CCTAAACCTACTGTCTTACGTGGT 59.781 45.833 0.00 0.00 0.00 4.16
3476 3542 5.415701 CCTAAACCTACTGTCTTACGTGGTA 59.584 44.000 0.00 0.00 0.00 3.25
3477 3543 5.990120 AAACCTACTGTCTTACGTGGTAT 57.010 39.130 0.00 0.00 0.00 2.73
3478 3544 5.990120 AACCTACTGTCTTACGTGGTATT 57.010 39.130 0.00 0.00 0.00 1.89
3479 3545 7.466746 AAACCTACTGTCTTACGTGGTATTA 57.533 36.000 0.00 0.00 0.00 0.98
3480 3546 7.466746 AACCTACTGTCTTACGTGGTATTAA 57.533 36.000 0.00 0.00 0.00 1.40
3481 3547 7.466746 ACCTACTGTCTTACGTGGTATTAAA 57.533 36.000 0.00 0.00 0.00 1.52
3482 3548 8.071177 ACCTACTGTCTTACGTGGTATTAAAT 57.929 34.615 0.00 0.00 0.00 1.40
3483 3549 8.534496 ACCTACTGTCTTACGTGGTATTAAATT 58.466 33.333 0.00 0.00 0.00 1.82
3486 3552 8.937634 ACTGTCTTACGTGGTATTAAATTAGG 57.062 34.615 0.00 0.00 0.00 2.69
3487 3553 8.534496 ACTGTCTTACGTGGTATTAAATTAGGT 58.466 33.333 0.00 0.00 0.00 3.08
3488 3554 8.931385 TGTCTTACGTGGTATTAAATTAGGTC 57.069 34.615 0.00 0.00 0.00 3.85
3489 3555 8.752187 TGTCTTACGTGGTATTAAATTAGGTCT 58.248 33.333 0.00 0.00 0.00 3.85
3492 3558 9.173939 CTTACGTGGTATTAAATTAGGTCTACG 57.826 37.037 0.00 0.00 35.26 3.51
3493 3559 5.979517 ACGTGGTATTAAATTAGGTCTACGC 59.020 40.000 0.00 0.00 33.17 4.42
3494 3560 6.183360 ACGTGGTATTAAATTAGGTCTACGCT 60.183 38.462 0.00 0.00 33.17 5.07
3495 3561 6.698766 CGTGGTATTAAATTAGGTCTACGCTT 59.301 38.462 0.00 0.00 0.00 4.68
3496 3562 7.096312 CGTGGTATTAAATTAGGTCTACGCTTC 60.096 40.741 0.00 0.00 0.00 3.86
3497 3563 7.170489 GTGGTATTAAATTAGGTCTACGCTTCC 59.830 40.741 0.00 0.00 0.00 3.46
3498 3564 6.364435 GGTATTAAATTAGGTCTACGCTTCCG 59.636 42.308 0.00 0.00 41.14 4.30
3499 3565 2.220479 AATTAGGTCTACGCTTCCGC 57.780 50.000 0.00 0.00 38.22 5.54
3500 3566 1.400737 ATTAGGTCTACGCTTCCGCT 58.599 50.000 0.00 0.00 38.22 5.52
3501 3567 2.042686 TTAGGTCTACGCTTCCGCTA 57.957 50.000 0.00 0.00 38.22 4.26
3502 3568 1.303309 TAGGTCTACGCTTCCGCTAC 58.697 55.000 0.00 0.00 38.22 3.58
3503 3569 0.679002 AGGTCTACGCTTCCGCTACA 60.679 55.000 0.00 0.00 38.22 2.74
3504 3570 0.525029 GGTCTACGCTTCCGCTACAC 60.525 60.000 0.00 0.00 38.22 2.90
3505 3571 0.525029 GTCTACGCTTCCGCTACACC 60.525 60.000 0.00 0.00 38.22 4.16
3506 3572 1.226888 CTACGCTTCCGCTACACCC 60.227 63.158 0.00 0.00 38.22 4.61
3507 3573 2.624437 CTACGCTTCCGCTACACCCC 62.624 65.000 0.00 0.00 38.22 4.95
3508 3574 4.077184 CGCTTCCGCTACACCCCA 62.077 66.667 0.00 0.00 0.00 4.96
3509 3575 2.349755 GCTTCCGCTACACCCCAA 59.650 61.111 0.00 0.00 0.00 4.12
3510 3576 1.745489 GCTTCCGCTACACCCCAAG 60.745 63.158 0.00 0.00 0.00 3.61
3511 3577 1.745489 CTTCCGCTACACCCCAAGC 60.745 63.158 0.00 0.00 35.33 4.01
3512 3578 3.262448 TTCCGCTACACCCCAAGCC 62.262 63.158 0.00 0.00 35.22 4.35
3547 3613 4.847516 CGCCGTCGCCATCTTCGA 62.848 66.667 0.00 0.00 0.00 3.71
3548 3614 2.279517 GCCGTCGCCATCTTCGAT 60.280 61.111 0.00 0.00 38.29 3.59
3549 3615 2.303676 GCCGTCGCCATCTTCGATC 61.304 63.158 0.00 0.00 38.29 3.69
3550 3616 2.011349 CCGTCGCCATCTTCGATCG 61.011 63.158 9.36 9.36 38.29 3.69
3551 3617 2.639926 CGTCGCCATCTTCGATCGC 61.640 63.158 11.09 0.00 38.29 4.58
3552 3618 2.353492 TCGCCATCTTCGATCGCG 60.353 61.111 11.09 0.00 44.00 5.87
3553 3619 4.051963 CGCCATCTTCGATCGCGC 62.052 66.667 11.09 0.00 36.02 6.86
3554 3620 3.706668 GCCATCTTCGATCGCGCC 61.707 66.667 11.09 0.00 37.46 6.53
3555 3621 2.279451 CCATCTTCGATCGCGCCA 60.279 61.111 11.09 0.00 37.46 5.69
3556 3622 2.589492 CCATCTTCGATCGCGCCAC 61.589 63.158 11.09 0.00 37.46 5.01
3557 3623 2.279517 ATCTTCGATCGCGCCACC 60.280 61.111 11.09 0.00 37.46 4.61
3558 3624 4.847516 TCTTCGATCGCGCCACCG 62.848 66.667 11.09 2.28 37.46 4.94
3573 3639 4.175337 CCGCCACCATGTCGGGAT 62.175 66.667 0.00 0.00 40.22 3.85
3574 3640 2.588877 CGCCACCATGTCGGGATC 60.589 66.667 0.00 0.00 40.22 3.36
3575 3641 2.203209 GCCACCATGTCGGGATCC 60.203 66.667 1.92 1.92 40.22 3.36
3604 3670 2.759973 CTCCTCCACGGCCAGCTA 60.760 66.667 2.24 0.00 0.00 3.32
3605 3671 3.075005 TCCTCCACGGCCAGCTAC 61.075 66.667 2.24 0.00 0.00 3.58
3606 3672 4.162690 CCTCCACGGCCAGCTACC 62.163 72.222 2.24 0.00 0.00 3.18
3607 3673 3.077556 CTCCACGGCCAGCTACCT 61.078 66.667 2.24 0.00 0.00 3.08
3608 3674 3.376935 CTCCACGGCCAGCTACCTG 62.377 68.421 2.24 0.00 38.85 4.00
3616 3682 4.537433 CAGCTACCTGCCGGCCTC 62.537 72.222 26.77 6.27 44.23 4.70
3672 3738 4.069232 CGGCTGCTTCACTCCCGA 62.069 66.667 0.00 0.00 41.34 5.14
3673 3739 2.586792 GGCTGCTTCACTCCCGAT 59.413 61.111 0.00 0.00 0.00 4.18
3674 3740 1.522580 GGCTGCTTCACTCCCGATC 60.523 63.158 0.00 0.00 0.00 3.69
3675 3741 1.880340 GCTGCTTCACTCCCGATCG 60.880 63.158 8.51 8.51 0.00 3.69
3676 3742 1.227089 CTGCTTCACTCCCGATCGG 60.227 63.158 27.65 27.65 0.00 4.18
3702 3768 2.574399 GCGTCGGCTCCTTCTTCT 59.426 61.111 0.00 0.00 35.83 2.85
3703 3769 1.517475 GCGTCGGCTCCTTCTTCTC 60.517 63.158 0.00 0.00 35.83 2.87
3704 3770 1.139947 CGTCGGCTCCTTCTTCTCC 59.860 63.158 0.00 0.00 0.00 3.71
3705 3771 1.316706 CGTCGGCTCCTTCTTCTCCT 61.317 60.000 0.00 0.00 0.00 3.69
3706 3772 0.458260 GTCGGCTCCTTCTTCTCCTC 59.542 60.000 0.00 0.00 0.00 3.71
3707 3773 1.032657 TCGGCTCCTTCTTCTCCTCG 61.033 60.000 0.00 0.00 0.00 4.63
3708 3774 1.316706 CGGCTCCTTCTTCTCCTCGT 61.317 60.000 0.00 0.00 0.00 4.18
3709 3775 0.458260 GGCTCCTTCTTCTCCTCGTC 59.542 60.000 0.00 0.00 0.00 4.20
3710 3776 0.099791 GCTCCTTCTTCTCCTCGTCG 59.900 60.000 0.00 0.00 0.00 5.12
3711 3777 0.099791 CTCCTTCTTCTCCTCGTCGC 59.900 60.000 0.00 0.00 0.00 5.19
3712 3778 1.139947 CCTTCTTCTCCTCGTCGCC 59.860 63.158 0.00 0.00 0.00 5.54
3713 3779 1.226435 CTTCTTCTCCTCGTCGCCG 60.226 63.158 0.00 0.00 0.00 6.46
3714 3780 2.600122 CTTCTTCTCCTCGTCGCCGG 62.600 65.000 0.00 0.00 33.95 6.13
3715 3781 4.194720 CTTCTCCTCGTCGCCGGG 62.195 72.222 2.18 0.00 33.95 5.73
3716 3782 4.728110 TTCTCCTCGTCGCCGGGA 62.728 66.667 2.18 0.00 36.35 5.14
3717 3783 4.728110 TCTCCTCGTCGCCGGGAA 62.728 66.667 2.18 0.00 36.35 3.97
3718 3784 4.493747 CTCCTCGTCGCCGGGAAC 62.494 72.222 2.18 0.00 36.35 3.62
3738 3804 4.988598 CGCTGGTGGTCCGCACTT 62.989 66.667 4.48 0.00 36.30 3.16
3739 3805 3.050275 GCTGGTGGTCCGCACTTC 61.050 66.667 4.48 0.00 36.30 3.01
3740 3806 2.358737 CTGGTGGTCCGCACTTCC 60.359 66.667 4.48 0.00 36.30 3.46
3741 3807 3.164977 TGGTGGTCCGCACTTCCA 61.165 61.111 4.48 0.00 36.30 3.53
3742 3808 2.358737 GGTGGTCCGCACTTCCAG 60.359 66.667 4.48 0.00 31.54 3.86
3743 3809 3.050275 GTGGTCCGCACTTCCAGC 61.050 66.667 0.00 0.00 31.54 4.85
3751 3817 3.414700 CACTTCCAGCGCCACGAC 61.415 66.667 2.29 0.00 0.00 4.34
3761 3827 4.773117 GCCACGACGGACGACTCC 62.773 72.222 6.90 0.00 45.77 3.85
3762 3828 4.112341 CCACGACGGACGACTCCC 62.112 72.222 6.90 0.00 45.77 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 0.171455 CAACTCGTCTCCCCTTCTCG 59.829 60.000 0.00 0.00 0.00 4.04
18 19 0.246910 GTCCAACTCGTCTCCCCTTC 59.753 60.000 0.00 0.00 0.00 3.46
71 73 1.147824 ATTCATCGCAGGAGCAGGG 59.852 57.895 0.00 0.00 42.27 4.45
122 124 3.246112 CGTCCCAAGTCCCACCCA 61.246 66.667 0.00 0.00 0.00 4.51
211 217 2.543037 ACCTTTGACAAAACCCCACT 57.457 45.000 1.62 0.00 0.00 4.00
259 265 3.823304 GCAGTTTGAGGAGGTTTCTCAAT 59.177 43.478 7.25 0.00 46.54 2.57
267 273 5.011023 CCAAAATTAAGCAGTTTGAGGAGGT 59.989 40.000 0.00 0.00 34.80 3.85
291 297 3.149981 CTCAAAACACCTCCTTCCTTCC 58.850 50.000 0.00 0.00 0.00 3.46
328 334 6.114221 TCAAAACCGTTAACTTCTCACAAG 57.886 37.500 3.71 0.00 0.00 3.16
385 391 5.468658 TCTTTCCACCCCCTGAAAATTTTA 58.531 37.500 2.75 0.00 30.65 1.52
452 458 4.269183 CTTGCACCATGATAAGTGGGTTA 58.731 43.478 0.00 0.00 41.14 2.85
554 564 3.895656 AGGGAAAAAGTCAAAGCTAACCC 59.104 43.478 0.00 0.00 0.00 4.11
568 578 5.505780 TCAGTGTGAAAGAAGAGGGAAAAA 58.494 37.500 0.00 0.00 0.00 1.94
751 762 0.990374 AGGAGCACTCTGCCTTTCAT 59.010 50.000 0.00 0.00 46.52 2.57
782 795 5.149054 ACGAGTACTATGTTGTACGTAGC 57.851 43.478 0.00 0.00 45.23 3.58
783 796 7.221828 TGTACGAGTACTATGTTGTACGTAG 57.778 40.000 13.67 4.87 45.23 3.51
784 797 7.330946 AGTTGTACGAGTACTATGTTGTACGTA 59.669 37.037 13.67 0.00 45.23 3.57
785 798 6.147821 AGTTGTACGAGTACTATGTTGTACGT 59.852 38.462 13.67 0.94 45.23 3.57
786 799 6.537566 AGTTGTACGAGTACTATGTTGTACG 58.462 40.000 13.67 0.00 45.23 3.67
787 800 8.733857 AAAGTTGTACGAGTACTATGTTGTAC 57.266 34.615 13.67 5.30 42.09 2.90
788 801 9.825972 GTAAAGTTGTACGAGTACTATGTTGTA 57.174 33.333 13.67 0.00 37.00 2.41
789 802 8.733857 GTAAAGTTGTACGAGTACTATGTTGT 57.266 34.615 13.67 0.00 37.00 3.32
822 835 1.739562 GTGCTTCTCGACCTGCCAG 60.740 63.158 0.00 0.00 0.00 4.85
832 845 2.125350 CCAGCTCGGGTGCTTCTC 60.125 66.667 0.00 0.00 41.98 2.87
965 988 1.078918 CTGATCCGCCTGTTGAGCA 60.079 57.895 0.00 0.00 0.00 4.26
1123 1146 6.457663 CCGTTGATAAATTGAACGCATCCTAA 60.458 38.462 0.00 0.00 40.84 2.69
1128 1151 3.434637 GCCGTTGATAAATTGAACGCAT 58.565 40.909 0.00 0.00 40.84 4.73
1588 1611 3.312973 ACGTAGTAGTGCTAGATGTGAGC 59.687 47.826 0.00 0.00 41.94 4.26
1599 1622 1.136336 GCAAGTGCAACGTAGTAGTGC 60.136 52.381 2.20 2.20 45.00 4.40
1600 1623 2.856091 GCAAGTGCAACGTAGTAGTG 57.144 50.000 0.00 0.00 45.00 2.74
1866 1932 4.722700 GTCCCTGCACACCGCCAT 62.723 66.667 0.00 0.00 41.33 4.40
1962 2028 3.154473 CGGGATCTCGCCCTGGAA 61.154 66.667 0.00 0.00 46.44 3.53
2174 2240 1.138661 CAGCTGGAGAAGGAGACCATC 59.861 57.143 5.57 0.00 33.08 3.51
2277 2343 0.798776 AGAAATGCACGGCGAAGAAG 59.201 50.000 16.62 0.00 0.00 2.85
2666 2732 1.153686 GGCGTAGGGGTTCTCGAAC 60.154 63.158 1.22 1.22 40.45 3.95
2927 2993 2.708865 GCGCGCTATCATTGTGCA 59.291 55.556 26.67 0.00 40.54 4.57
3018 3084 2.410469 GCGTGCTTGATGCCATCC 59.590 61.111 1.49 0.00 42.00 3.51
3270 3336 2.494918 GCGTCCATGTACGGCTCT 59.505 61.111 12.99 0.00 43.06 4.09
3339 3405 9.983024 ACATATACAGGAGCTATACAGTCTAAT 57.017 33.333 0.00 0.00 0.00 1.73
3340 3406 9.232473 CACATATACAGGAGCTATACAGTCTAA 57.768 37.037 0.00 0.00 0.00 2.10
3341 3407 8.383947 ACACATATACAGGAGCTATACAGTCTA 58.616 37.037 0.00 0.00 0.00 2.59
3342 3408 7.235079 ACACATATACAGGAGCTATACAGTCT 58.765 38.462 0.00 0.00 0.00 3.24
3343 3409 7.455641 ACACATATACAGGAGCTATACAGTC 57.544 40.000 0.00 0.00 0.00 3.51
3344 3410 7.119407 CGTACACATATACAGGAGCTATACAGT 59.881 40.741 0.00 0.00 0.00 3.55
3345 3411 7.119407 ACGTACACATATACAGGAGCTATACAG 59.881 40.741 0.00 0.00 0.00 2.74
3346 3412 6.938596 ACGTACACATATACAGGAGCTATACA 59.061 38.462 0.00 0.00 0.00 2.29
3347 3413 7.375106 ACGTACACATATACAGGAGCTATAC 57.625 40.000 0.00 0.00 0.00 1.47
3349 3415 9.848710 ATATACGTACACATATACAGGAGCTAT 57.151 33.333 0.00 0.00 0.00 2.97
3350 3416 9.106070 CATATACGTACACATATACAGGAGCTA 57.894 37.037 0.00 0.00 0.00 3.32
3351 3417 7.827729 TCATATACGTACACATATACAGGAGCT 59.172 37.037 0.00 0.00 0.00 4.09
3352 3418 7.982224 TCATATACGTACACATATACAGGAGC 58.018 38.462 0.00 0.00 0.00 4.70
3381 3447 2.845967 GGGTACAACGTTACATCGTACG 59.154 50.000 9.53 9.53 43.38 3.67
3382 3448 4.096732 AGGGTACAACGTTACATCGTAC 57.903 45.455 14.31 14.31 43.38 3.67
3383 3449 4.022416 ACAAGGGTACAACGTTACATCGTA 60.022 41.667 0.00 0.00 43.38 3.43
3384 3450 3.243839 ACAAGGGTACAACGTTACATCGT 60.244 43.478 0.00 0.00 46.19 3.73
3385 3451 3.319755 ACAAGGGTACAACGTTACATCG 58.680 45.455 0.00 0.00 0.00 3.84
3386 3452 6.973229 ATAACAAGGGTACAACGTTACATC 57.027 37.500 0.00 0.00 0.00 3.06
3411 3477 9.937876 CTTTAGGGGTGGTCTATCTCATATATA 57.062 37.037 0.00 0.00 0.00 0.86
3412 3478 7.846823 CCTTTAGGGGTGGTCTATCTCATATAT 59.153 40.741 0.00 0.00 0.00 0.86
3413 3479 7.189794 CCTTTAGGGGTGGTCTATCTCATATA 58.810 42.308 0.00 0.00 0.00 0.86
3414 3480 6.026186 CCTTTAGGGGTGGTCTATCTCATAT 58.974 44.000 0.00 0.00 0.00 1.78
3415 3481 5.403512 CCTTTAGGGGTGGTCTATCTCATA 58.596 45.833 0.00 0.00 0.00 2.15
3416 3482 4.235372 CCTTTAGGGGTGGTCTATCTCAT 58.765 47.826 0.00 0.00 0.00 2.90
3417 3483 3.654273 CCTTTAGGGGTGGTCTATCTCA 58.346 50.000 0.00 0.00 0.00 3.27
3431 3497 2.437413 GAACTGGCTCAACCCTTTAGG 58.563 52.381 0.00 0.00 43.78 2.69
3432 3498 2.437413 GGAACTGGCTCAACCCTTTAG 58.563 52.381 0.00 0.00 37.83 1.85
3433 3499 1.074889 GGGAACTGGCTCAACCCTTTA 59.925 52.381 0.00 0.00 37.83 1.85
3434 3500 0.178961 GGGAACTGGCTCAACCCTTT 60.179 55.000 0.00 0.00 37.83 3.11
3435 3501 1.460699 GGGAACTGGCTCAACCCTT 59.539 57.895 0.00 0.00 37.83 3.95
3436 3502 1.464198 AGGGAACTGGCTCAACCCT 60.464 57.895 0.00 0.00 45.06 4.34
3437 3503 0.696501 TTAGGGAACTGGCTCAACCC 59.303 55.000 0.00 0.00 43.88 4.11
3438 3504 2.160205 GTTTAGGGAACTGGCTCAACC 58.840 52.381 0.00 0.00 43.88 3.77
3439 3505 2.160205 GGTTTAGGGAACTGGCTCAAC 58.840 52.381 0.00 0.00 43.88 3.18
3440 3506 2.062636 AGGTTTAGGGAACTGGCTCAA 58.937 47.619 0.00 0.00 43.88 3.02
3441 3507 1.742308 AGGTTTAGGGAACTGGCTCA 58.258 50.000 0.00 0.00 43.88 4.26
3442 3508 2.838813 AGTAGGTTTAGGGAACTGGCTC 59.161 50.000 0.00 0.00 43.88 4.70
3443 3509 2.572104 CAGTAGGTTTAGGGAACTGGCT 59.428 50.000 0.00 0.00 43.88 4.75
3444 3510 2.305052 ACAGTAGGTTTAGGGAACTGGC 59.695 50.000 5.83 0.00 43.88 4.85
3445 3511 3.838903 AGACAGTAGGTTTAGGGAACTGG 59.161 47.826 5.83 0.00 43.88 4.00
3446 3512 5.485209 AAGACAGTAGGTTTAGGGAACTG 57.515 43.478 0.00 0.00 43.88 3.16
3447 3513 5.184671 CGTAAGACAGTAGGTTTAGGGAACT 59.815 44.000 0.00 0.00 43.44 3.01
3448 3514 5.047731 ACGTAAGACAGTAGGTTTAGGGAAC 60.048 44.000 0.00 0.00 43.62 3.62
3449 3515 5.047802 CACGTAAGACAGTAGGTTTAGGGAA 60.048 44.000 0.00 0.00 43.62 3.97
3450 3516 4.460382 CACGTAAGACAGTAGGTTTAGGGA 59.540 45.833 0.00 0.00 43.62 4.20
3451 3517 4.381292 CCACGTAAGACAGTAGGTTTAGGG 60.381 50.000 0.00 0.00 43.62 3.53
3452 3518 4.219288 ACCACGTAAGACAGTAGGTTTAGG 59.781 45.833 0.00 0.00 43.62 2.69
3453 3519 5.382618 ACCACGTAAGACAGTAGGTTTAG 57.617 43.478 0.00 0.00 43.62 1.85
3454 3520 7.466746 AATACCACGTAAGACAGTAGGTTTA 57.533 36.000 0.00 0.00 43.62 2.01
3455 3521 5.990120 ATACCACGTAAGACAGTAGGTTT 57.010 39.130 0.00 0.00 43.62 3.27
3456 3522 5.990120 AATACCACGTAAGACAGTAGGTT 57.010 39.130 0.00 0.00 43.62 3.50
3457 3523 7.466746 TTTAATACCACGTAAGACAGTAGGT 57.533 36.000 0.00 0.00 43.62 3.08
3458 3524 8.937634 AATTTAATACCACGTAAGACAGTAGG 57.062 34.615 0.00 0.00 43.62 3.18
3461 3527 8.534496 ACCTAATTTAATACCACGTAAGACAGT 58.466 33.333 0.00 0.00 43.62 3.55
3462 3528 8.937634 ACCTAATTTAATACCACGTAAGACAG 57.062 34.615 0.00 0.00 43.62 3.51
3463 3529 8.752187 AGACCTAATTTAATACCACGTAAGACA 58.248 33.333 0.00 0.00 43.62 3.41
3467 3533 7.647715 GCGTAGACCTAATTTAATACCACGTAA 59.352 37.037 0.00 0.00 0.00 3.18
3468 3534 7.013274 AGCGTAGACCTAATTTAATACCACGTA 59.987 37.037 0.00 0.00 0.00 3.57
3469 3535 5.979517 GCGTAGACCTAATTTAATACCACGT 59.020 40.000 0.00 0.00 0.00 4.49
3470 3536 6.211515 AGCGTAGACCTAATTTAATACCACG 58.788 40.000 0.00 0.00 0.00 4.94
3471 3537 7.170489 GGAAGCGTAGACCTAATTTAATACCAC 59.830 40.741 0.00 0.00 0.00 4.16
3472 3538 7.212274 GGAAGCGTAGACCTAATTTAATACCA 58.788 38.462 0.00 0.00 0.00 3.25
3473 3539 6.364435 CGGAAGCGTAGACCTAATTTAATACC 59.636 42.308 0.00 0.00 0.00 2.73
3474 3540 7.330720 CGGAAGCGTAGACCTAATTTAATAC 57.669 40.000 0.00 0.00 0.00 1.89
3493 3559 1.745489 GCTTGGGGTGTAGCGGAAG 60.745 63.158 0.00 0.00 0.00 3.46
3494 3560 2.349755 GCTTGGGGTGTAGCGGAA 59.650 61.111 0.00 0.00 0.00 4.30
3495 3561 3.712907 GGCTTGGGGTGTAGCGGA 61.713 66.667 0.00 0.00 38.28 5.54
3530 3596 4.847516 TCGAAGATGGCGACGGCG 62.848 66.667 17.16 6.12 41.24 6.46
3531 3597 2.279517 ATCGAAGATGGCGACGGC 60.280 61.111 15.43 15.43 45.12 5.68
3532 3598 2.011349 CGATCGAAGATGGCGACGG 61.011 63.158 10.26 0.00 45.12 4.79
3533 3599 2.639926 GCGATCGAAGATGGCGACG 61.640 63.158 21.57 0.00 45.12 5.12
3534 3600 2.639926 CGCGATCGAAGATGGCGAC 61.640 63.158 26.88 0.00 46.56 5.19
3535 3601 2.353492 CGCGATCGAAGATGGCGA 60.353 61.111 26.88 4.19 46.56 5.54
3536 3602 4.051963 GCGCGATCGAAGATGGCG 62.052 66.667 26.70 26.70 46.41 5.69
3537 3603 3.706668 GGCGCGATCGAAGATGGC 61.707 66.667 21.57 10.62 45.12 4.40
3538 3604 2.279451 TGGCGCGATCGAAGATGG 60.279 61.111 21.57 0.85 45.12 3.51
3539 3605 2.589492 GGTGGCGCGATCGAAGATG 61.589 63.158 21.57 3.32 45.12 2.90
3540 3606 2.279517 GGTGGCGCGATCGAAGAT 60.280 61.111 21.57 0.00 45.12 2.40
3541 3607 4.847516 CGGTGGCGCGATCGAAGA 62.848 66.667 21.12 0.00 45.75 2.87
3558 3624 2.203209 GGATCCCGACATGGTGGC 60.203 66.667 0.00 0.00 35.15 5.01
3587 3653 2.759973 TAGCTGGCCGTGGAGGAG 60.760 66.667 0.00 0.00 45.00 3.69
3588 3654 3.075005 GTAGCTGGCCGTGGAGGA 61.075 66.667 0.00 0.00 45.00 3.71
3589 3655 4.162690 GGTAGCTGGCCGTGGAGG 62.163 72.222 0.00 0.00 44.97 4.30
3590 3656 3.077556 AGGTAGCTGGCCGTGGAG 61.078 66.667 0.00 0.00 0.00 3.86
3591 3657 3.390521 CAGGTAGCTGGCCGTGGA 61.391 66.667 14.29 0.00 0.00 4.02
3655 3721 3.376935 ATCGGGAGTGAAGCAGCCG 62.377 63.158 0.00 0.00 0.00 5.52
3656 3722 1.522580 GATCGGGAGTGAAGCAGCC 60.523 63.158 0.00 0.00 0.00 4.85
3657 3723 1.880340 CGATCGGGAGTGAAGCAGC 60.880 63.158 7.38 0.00 0.00 5.25
3658 3724 1.227089 CCGATCGGGAGTGAAGCAG 60.227 63.158 26.95 0.00 38.47 4.24
3659 3725 2.892640 CCGATCGGGAGTGAAGCA 59.107 61.111 26.95 0.00 38.47 3.91
3669 3735 3.967335 GCTCCTCGTCCCGATCGG 61.967 72.222 27.65 27.65 34.61 4.18
3670 3736 4.315122 CGCTCCTCGTCCCGATCG 62.315 72.222 8.51 8.51 34.61 3.69
3685 3751 1.517475 GAGAAGAAGGAGCCGACGC 60.517 63.158 0.00 0.00 0.00 5.19
3686 3752 1.139947 GGAGAAGAAGGAGCCGACG 59.860 63.158 0.00 0.00 0.00 5.12
3687 3753 0.458260 GAGGAGAAGAAGGAGCCGAC 59.542 60.000 0.00 0.00 0.00 4.79
3688 3754 1.032657 CGAGGAGAAGAAGGAGCCGA 61.033 60.000 0.00 0.00 0.00 5.54
3689 3755 1.316706 ACGAGGAGAAGAAGGAGCCG 61.317 60.000 0.00 0.00 0.00 5.52
3690 3756 0.458260 GACGAGGAGAAGAAGGAGCC 59.542 60.000 0.00 0.00 0.00 4.70
3691 3757 0.099791 CGACGAGGAGAAGAAGGAGC 59.900 60.000 0.00 0.00 0.00 4.70
3692 3758 0.099791 GCGACGAGGAGAAGAAGGAG 59.900 60.000 0.00 0.00 0.00 3.69
3693 3759 1.313812 GGCGACGAGGAGAAGAAGGA 61.314 60.000 0.00 0.00 0.00 3.36
3694 3760 1.139947 GGCGACGAGGAGAAGAAGG 59.860 63.158 0.00 0.00 0.00 3.46
3695 3761 4.796225 GGCGACGAGGAGAAGAAG 57.204 61.111 0.00 0.00 0.00 2.85
3721 3787 4.988598 AAGTGCGGACCACCAGCG 62.989 66.667 2.38 0.00 45.83 5.18
3722 3788 3.050275 GAAGTGCGGACCACCAGC 61.050 66.667 2.38 0.00 45.83 4.85
3723 3789 2.358737 GGAAGTGCGGACCACCAG 60.359 66.667 2.38 0.00 45.83 4.00
3724 3790 3.164977 TGGAAGTGCGGACCACCA 61.165 61.111 16.23 16.23 45.83 4.17
3725 3791 2.358737 CTGGAAGTGCGGACCACC 60.359 66.667 2.38 8.33 45.83 4.61
3726 3792 3.050275 GCTGGAAGTGCGGACCAC 61.050 66.667 2.38 0.00 45.01 4.16
3744 3810 4.773117 GGAGTCGTCCGTCGTGGC 62.773 72.222 0.00 0.00 40.80 5.01
3745 3811 4.112341 GGGAGTCGTCCGTCGTGG 62.112 72.222 0.00 0.00 45.05 4.94
3746 3812 2.623915 AAGGGAGTCGTCCGTCGTG 61.624 63.158 0.00 0.00 45.05 4.35
3747 3813 2.282040 AAGGGAGTCGTCCGTCGT 60.282 61.111 0.00 0.00 45.05 4.34
3748 3814 2.138656 AACAAGGGAGTCGTCCGTCG 62.139 60.000 0.00 0.00 45.05 5.12
3749 3815 0.666577 CAACAAGGGAGTCGTCCGTC 60.667 60.000 0.00 0.00 45.05 4.79
3750 3816 1.366366 CAACAAGGGAGTCGTCCGT 59.634 57.895 0.00 0.00 45.05 4.69
3751 3817 1.374252 CCAACAAGGGAGTCGTCCG 60.374 63.158 0.00 0.00 45.05 4.79
3752 3818 0.395312 TTCCAACAAGGGAGTCGTCC 59.605 55.000 0.00 0.00 43.05 4.79
3753 3819 2.249844 TTTCCAACAAGGGAGTCGTC 57.750 50.000 0.00 0.00 38.42 4.20
3754 3820 2.951229 ATTTCCAACAAGGGAGTCGT 57.049 45.000 0.00 0.00 38.42 4.34
3755 3821 3.065371 GCATATTTCCAACAAGGGAGTCG 59.935 47.826 0.00 0.00 38.42 4.18
3756 3822 3.381590 GGCATATTTCCAACAAGGGAGTC 59.618 47.826 0.00 0.00 38.42 3.36
3757 3823 3.365472 GGCATATTTCCAACAAGGGAGT 58.635 45.455 0.00 0.00 38.42 3.85
3758 3824 2.695147 GGGCATATTTCCAACAAGGGAG 59.305 50.000 0.00 0.00 38.42 4.30
3759 3825 2.314549 AGGGCATATTTCCAACAAGGGA 59.685 45.455 0.00 0.00 38.24 4.20
3760 3826 2.750814 AGGGCATATTTCCAACAAGGG 58.249 47.619 0.00 0.00 38.24 3.95
3761 3827 4.792068 TCTAGGGCATATTTCCAACAAGG 58.208 43.478 0.00 0.00 39.47 3.61
3762 3828 4.823989 CCTCTAGGGCATATTTCCAACAAG 59.176 45.833 0.00 0.00 0.00 3.16
3891 3957 4.384208 GCTCACTAGGGACATATTGTGGTT 60.384 45.833 0.00 0.00 0.00 3.67
4409 4476 4.334481 CGGTATTTTACTTGCCCGAGATTT 59.666 41.667 0.00 0.00 37.66 2.17
4563 4630 0.176680 ATGCAGACATGACCGAGACC 59.823 55.000 0.00 0.00 34.35 3.85


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

AutoCloner maintained by Alex Coulton.