Multiple sequence alignment - TraesCS6B01G239400

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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 TraesCS6B01G239400 chr6B 100.000 3735 0 0 1 3735 416103021 416099287 0.000000e+00 6898.0
1 TraesCS6B01G239400 chr6B 81.429 70 11 1 1 68 34208911 34208842 5.210000e-04 56.5
2 TraesCS6B01G239400 chr6D 92.624 3037 133 38 549 3563 267730227 267727260 0.000000e+00 4283.0
3 TraesCS6B01G239400 chr6D 92.676 355 25 1 1 355 267730576 267730223 9.250000e-141 510.0
4 TraesCS6B01G239400 chr6A 93.865 2119 102 13 82 2194 381527275 381525179 0.000000e+00 3168.0
5 TraesCS6B01G239400 chr6A 92.030 527 17 8 2299 2821 381524775 381524270 0.000000e+00 717.0
6 TraesCS6B01G239400 chr6A 83.651 630 68 20 2955 3573 381524192 381523587 9.060000e-156 560.0
7 TraesCS6B01G239400 chr6A 91.566 83 7 0 1 83 381527457 381527375 8.480000e-22 115.0
8 TraesCS6B01G239400 chr7A 77.632 152 24 7 3038 3183 717076208 717076355 2.390000e-12 84.2
9 TraesCS6B01G239400 chr5A 72.253 364 70 29 1320 1669 674576481 674576827 2.390000e-12 84.2
10 TraesCS6B01G239400 chr4D 94.000 50 3 0 1376 1425 403182525 403182574 4.000000e-10 76.8
11 TraesCS6B01G239400 chr4D 95.238 42 1 1 1 42 308057792 308057832 8.660000e-07 65.8
12 TraesCS6B01G239400 chr4D 78.704 108 16 6 1320 1425 494877439 494877541 8.660000e-07 65.8
13 TraesCS6B01G239400 chr4B 100.000 41 0 0 1385 1425 500053200 500053240 4.000000e-10 76.8
14 TraesCS6B01G239400 chr4B 89.796 49 3 2 1379 1426 634981586 634981633 1.120000e-05 62.1
15 TraesCS6B01G239400 chr4B 85.965 57 5 3 1 57 179714429 179714376 1.450000e-04 58.4
16 TraesCS6B01G239400 chr4A 94.000 50 3 0 1376 1425 60730865 60730914 4.000000e-10 76.8
17 TraesCS6B01G239400 chr4A 76.129 155 31 5 1274 1425 60880236 60880387 4.000000e-10 76.8
18 TraesCS6B01G239400 chrUn 73.444 241 46 15 3042 3270 289819911 289820145 1.440000e-09 75.0
19 TraesCS6B01G239400 chr7B 87.500 56 6 1 1 55 629291251 629291306 3.110000e-06 63.9
20 TraesCS6B01G239400 chr3B 94.737 38 2 0 1 38 28289198 28289235 4.030000e-05 60.2
21 TraesCS6B01G239400 chr3A 85.965 57 6 2 1 57 63409172 63409226 4.030000e-05 60.2
22 TraesCS6B01G239400 chr5D 85.246 61 4 4 1 58 520740749 520740807 1.450000e-04 58.4


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 TraesCS6B01G239400 chr6B 416099287 416103021 3734 True 6898.0 6898 100.000 1 3735 1 chr6B.!!$R2 3734
1 TraesCS6B01G239400 chr6D 267727260 267730576 3316 True 2396.5 4283 92.650 1 3563 2 chr6D.!!$R1 3562
2 TraesCS6B01G239400 chr6A 381523587 381527457 3870 True 1140.0 3168 90.278 1 3573 4 chr6A.!!$R1 3572

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
283 385 0.386476 CAATGTGTGGCAGTGCAAGT 59.614 50.000 18.61 0.0 36.35 3.16 F
362 464 0.389948 GGCGGGCGTAGGAGAATATG 60.390 60.000 0.00 0.0 0.00 1.78 F
1995 2103 1.066502 GTCTGGTTCTTCTGGCTCCTC 60.067 57.143 0.00 0.0 0.00 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2238 2346 0.915364 GGAACTCCAGGCAATCCTCT 59.085 55.000 0.0 0.0 41.93 3.69 R
2281 2389 3.070576 GCCGCCAGCAAAATCCCT 61.071 61.111 0.0 0.0 42.97 4.20 R
3667 4094 0.033781 CCACAAGGCACCAAACCATG 59.966 55.000 0.0 0.0 32.18 3.66 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 4.392940 CCTCTAGGGCATATTTCCAACAG 58.607 47.826 0.00 0.00 0.00 3.16
68 69 0.591170 CCGATGCAGTTTCCGTTGTT 59.409 50.000 0.00 0.00 0.00 2.83
74 75 0.666374 CAGTTTCCGTTGTTGTCCCC 59.334 55.000 0.00 0.00 0.00 4.81
84 186 2.638363 GTTGTTGTCCCCTCCTCTAGTT 59.362 50.000 0.00 0.00 0.00 2.24
110 212 6.933521 AGATTCAAGTGGATATTGAGATTCGG 59.066 38.462 0.00 0.00 37.91 4.30
189 291 2.866762 GTCATCAATTAGCTCCGACACC 59.133 50.000 0.00 0.00 0.00 4.16
230 332 1.482593 AGTTCTTCCCATAGCTGACGG 59.517 52.381 0.00 0.00 0.00 4.79
280 382 1.202746 TCTACAATGTGTGGCAGTGCA 60.203 47.619 18.61 0.00 46.06 4.57
283 385 0.386476 CAATGTGTGGCAGTGCAAGT 59.614 50.000 18.61 0.00 36.35 3.16
320 422 3.591023 TCCAAACGTCTCGAATATGCAA 58.409 40.909 0.00 0.00 0.00 4.08
322 424 3.124466 CCAAACGTCTCGAATATGCAACA 59.876 43.478 0.00 0.00 0.00 3.33
325 427 3.845178 ACGTCTCGAATATGCAACAGAA 58.155 40.909 0.00 0.00 0.00 3.02
355 457 2.363975 ATTCTTGGCGGGCGTAGGA 61.364 57.895 0.00 0.00 0.00 2.94
358 460 2.998480 TTGGCGGGCGTAGGAGAA 60.998 61.111 0.00 0.00 0.00 2.87
359 461 2.311688 CTTGGCGGGCGTAGGAGAAT 62.312 60.000 0.00 0.00 0.00 2.40
362 464 0.389948 GGCGGGCGTAGGAGAATATG 60.390 60.000 0.00 0.00 0.00 1.78
374 478 3.511934 AGGAGAATATGAGGTGATACCGC 59.488 47.826 0.00 0.00 44.90 5.68
401 505 4.910195 TGTATGCTCCCATCATACCAATC 58.090 43.478 9.73 0.00 43.31 2.67
402 506 2.957402 TGCTCCCATCATACCAATCC 57.043 50.000 0.00 0.00 0.00 3.01
405 509 2.613977 GCTCCCATCATACCAATCCGAG 60.614 54.545 0.00 0.00 0.00 4.63
408 512 3.714280 TCCCATCATACCAATCCGAGAAA 59.286 43.478 0.00 0.00 0.00 2.52
422 527 7.968405 CCAATCCGAGAAAGTAAGTTTAAATGG 59.032 37.037 0.00 0.00 0.00 3.16
476 581 6.018262 TGTTCACAACACATAAGTCTACAAGC 60.018 38.462 0.00 0.00 36.25 4.01
477 582 4.994852 TCACAACACATAAGTCTACAAGCC 59.005 41.667 0.00 0.00 0.00 4.35
479 584 3.629142 ACACATAAGTCTACAAGCCCC 57.371 47.619 0.00 0.00 0.00 5.80
484 589 5.242838 CACATAAGTCTACAAGCCCCAAAAA 59.757 40.000 0.00 0.00 0.00 1.94
501 606 7.040548 GCCCCAAAAATTTCAGATCAAAATTCA 60.041 33.333 15.22 0.00 35.75 2.57
523 628 9.778741 ATTCAGAGTACACATAGAGAAACAAAA 57.221 29.630 0.00 0.00 0.00 2.44
587 692 6.922957 TGTTCATGCTTTTGTCTTTATTGACC 59.077 34.615 0.00 0.00 36.21 4.02
699 804 7.359262 TGTGAACATCCGTAATTGTCTTTAG 57.641 36.000 0.00 0.00 0.00 1.85
829 937 1.398451 GCGGTCACAAACACGATTCAG 60.398 52.381 0.00 0.00 0.00 3.02
907 1015 2.433868 TCGCACACTTCAGTAGTTCC 57.566 50.000 0.00 0.00 33.85 3.62
965 1073 1.256652 CTAACACATCGTCGTCACCG 58.743 55.000 0.00 0.00 0.00 4.94
1179 1287 2.285368 ATCCCCACCCTCTTCGCA 60.285 61.111 0.00 0.00 0.00 5.10
1497 1605 2.675423 ACCGTCGAGCAGCTGGTA 60.675 61.111 20.22 0.27 0.00 3.25
1605 1713 3.422303 GACAACATCTGCGCCGCA 61.422 61.111 12.83 12.83 36.92 5.69
1995 2103 1.066502 GTCTGGTTCTTCTGGCTCCTC 60.067 57.143 0.00 0.00 0.00 3.71
2281 2389 3.329542 GAGCGGTGGATGAAGGGCA 62.330 63.158 0.00 0.00 0.00 5.36
2286 2394 1.649271 GGTGGATGAAGGGCAGGGAT 61.649 60.000 0.00 0.00 0.00 3.85
2333 2740 1.259507 CAAGTACGTGGTGTTCAACGG 59.740 52.381 0.00 0.00 0.00 4.44
2535 2942 1.374885 CGTCCATTGCACCACCGTA 60.375 57.895 0.00 0.00 0.00 4.02
2560 2970 5.456548 TGGTACGTATCAACTTTCAGTCA 57.543 39.130 5.94 0.00 0.00 3.41
2561 2971 6.032956 TGGTACGTATCAACTTTCAGTCAT 57.967 37.500 5.94 0.00 0.00 3.06
2562 2972 6.097356 TGGTACGTATCAACTTTCAGTCATC 58.903 40.000 5.94 0.00 0.00 2.92
2563 2973 6.071560 TGGTACGTATCAACTTTCAGTCATCT 60.072 38.462 5.94 0.00 0.00 2.90
2564 2974 6.472808 GGTACGTATCAACTTTCAGTCATCTC 59.527 42.308 0.00 0.00 0.00 2.75
2565 2975 5.096169 ACGTATCAACTTTCAGTCATCTCG 58.904 41.667 0.00 0.00 0.00 4.04
2566 2976 5.096169 CGTATCAACTTTCAGTCATCTCGT 58.904 41.667 0.00 0.00 0.00 4.18
2567 2977 6.128090 ACGTATCAACTTTCAGTCATCTCGTA 60.128 38.462 0.00 0.00 0.00 3.43
2568 2978 6.913132 CGTATCAACTTTCAGTCATCTCGTAT 59.087 38.462 0.00 0.00 0.00 3.06
2570 2980 7.763172 ATCAACTTTCAGTCATCTCGTATTC 57.237 36.000 0.00 0.00 0.00 1.75
2571 2981 6.925211 TCAACTTTCAGTCATCTCGTATTCT 58.075 36.000 0.00 0.00 0.00 2.40
2573 2983 5.574082 ACTTTCAGTCATCTCGTATTCTCG 58.426 41.667 0.00 0.00 0.00 4.04
2574 2984 5.124138 ACTTTCAGTCATCTCGTATTCTCGT 59.876 40.000 0.00 0.00 0.00 4.18
2575 2985 6.315642 ACTTTCAGTCATCTCGTATTCTCGTA 59.684 38.462 0.00 0.00 0.00 3.43
2576 2986 6.862711 TTCAGTCATCTCGTATTCTCGTAT 57.137 37.500 0.00 0.00 0.00 3.06
2577 2987 6.229561 TCAGTCATCTCGTATTCTCGTATG 57.770 41.667 0.00 0.00 0.00 2.39
2578 2988 5.989777 TCAGTCATCTCGTATTCTCGTATGA 59.010 40.000 0.00 0.00 34.68 2.15
2579 2989 6.146347 TCAGTCATCTCGTATTCTCGTATGAG 59.854 42.308 5.53 5.53 43.99 2.90
2670 3085 2.756760 ACAGCGCAAGAATGATGGAAAT 59.243 40.909 11.47 0.00 43.02 2.17
2713 3128 7.912383 TGAACAGAAGTAAACTTAAAGGAACG 58.088 34.615 0.00 0.00 36.11 3.95
2714 3129 6.856135 ACAGAAGTAAACTTAAAGGAACGG 57.144 37.500 0.00 0.00 36.11 4.44
2715 3130 6.585416 ACAGAAGTAAACTTAAAGGAACGGA 58.415 36.000 0.00 0.00 36.11 4.69
2716 3131 7.049754 ACAGAAGTAAACTTAAAGGAACGGAA 58.950 34.615 0.00 0.00 36.11 4.30
2721 3136 5.447624 AAACTTAAAGGAACGGAATGTGG 57.552 39.130 0.00 0.00 0.00 4.17
2761 3176 2.237393 GTTTCAACCATGCAGGCAAA 57.763 45.000 0.00 0.00 43.14 3.68
2821 3236 8.432805 ACTGCTACATATATTGCCTCTACTTTT 58.567 33.333 0.00 0.00 0.00 2.27
2822 3237 9.277783 CTGCTACATATATTGCCTCTACTTTTT 57.722 33.333 0.00 0.00 0.00 1.94
2866 3281 6.514063 ACTTTATACGTATTTCTCTGCTCCC 58.486 40.000 14.33 0.00 0.00 4.30
2873 3288 0.117140 TTTCTCTGCTCCCCTCTCCA 59.883 55.000 0.00 0.00 0.00 3.86
2877 3292 1.379977 CTGCTCCCCTCTCCACGTA 60.380 63.158 0.00 0.00 0.00 3.57
2891 3306 1.608025 CCACGTATGTGTGCTCCTTGT 60.608 52.381 13.91 0.00 44.92 3.16
2892 3307 1.460743 CACGTATGTGTGCTCCTTGTG 59.539 52.381 6.93 0.00 41.34 3.33
2941 3356 0.996727 GCGTTGTGCATTCCGTCAAC 60.997 55.000 5.73 5.73 45.45 3.18
2943 3358 1.398451 CGTTGTGCATTCCGTCAACTC 60.398 52.381 12.16 0.00 38.25 3.01
2958 3373 4.488879 GTCAACTCGGTTCGGTAAATACT 58.511 43.478 0.00 0.00 0.00 2.12
2979 3394 9.769093 AATACTGTTTCTCGTTAAATATGTTGC 57.231 29.630 0.00 0.00 0.00 4.17
3093 3508 6.566079 ATCATTCACTCCCTCTTTACATCA 57.434 37.500 0.00 0.00 0.00 3.07
3094 3509 6.373005 TCATTCACTCCCTCTTTACATCAA 57.627 37.500 0.00 0.00 0.00 2.57
3095 3510 6.962182 TCATTCACTCCCTCTTTACATCAAT 58.038 36.000 0.00 0.00 0.00 2.57
3096 3511 6.825213 TCATTCACTCCCTCTTTACATCAATG 59.175 38.462 0.00 0.00 0.00 2.82
3097 3512 4.517285 TCACTCCCTCTTTACATCAATGC 58.483 43.478 0.00 0.00 0.00 3.56
3098 3513 4.019411 TCACTCCCTCTTTACATCAATGCA 60.019 41.667 0.00 0.00 0.00 3.96
3099 3514 4.701651 CACTCCCTCTTTACATCAATGCAA 59.298 41.667 0.00 0.00 0.00 4.08
3100 3515 4.702131 ACTCCCTCTTTACATCAATGCAAC 59.298 41.667 0.00 0.00 0.00 4.17
3101 3516 4.016444 TCCCTCTTTACATCAATGCAACC 58.984 43.478 0.00 0.00 0.00 3.77
3102 3517 4.019174 CCCTCTTTACATCAATGCAACCT 58.981 43.478 0.00 0.00 0.00 3.50
3103 3518 5.045213 TCCCTCTTTACATCAATGCAACCTA 60.045 40.000 0.00 0.00 0.00 3.08
3104 3519 5.829924 CCCTCTTTACATCAATGCAACCTAT 59.170 40.000 0.00 0.00 0.00 2.57
3105 3520 6.238842 CCCTCTTTACATCAATGCAACCTATG 60.239 42.308 0.00 0.00 0.00 2.23
3108 3523 8.121305 TCTTTACATCAATGCAACCTATGTTT 57.879 30.769 11.13 0.00 33.15 2.83
3122 3537 9.503427 GCAACCTATGTTTACATCATTTAGTTC 57.497 33.333 0.00 0.00 37.76 3.01
3325 3751 7.982371 ACGTAACTATCTGTATAGCAAACAC 57.018 36.000 0.00 0.00 39.01 3.32
3341 3767 9.979578 ATAGCAAACACAATTCTTAATGAAACA 57.020 25.926 0.00 0.00 38.29 2.83
3389 3815 4.773323 AACTTATTCTGCACCAAAGCTC 57.227 40.909 0.00 0.00 34.99 4.09
3412 3839 7.201496 GCTCAGACAATTTAAAATGAGGCAATG 60.201 37.037 10.23 0.65 35.75 2.82
3414 3841 8.533657 TCAGACAATTTAAAATGAGGCAATGAT 58.466 29.630 10.23 0.00 0.00 2.45
3416 3843 9.807649 AGACAATTTAAAATGAGGCAATGATAC 57.192 29.630 10.23 0.00 0.00 2.24
3444 3871 6.868622 AGTTTTGTTGGTGTATTTGCTAACA 58.131 32.000 0.00 0.00 0.00 2.41
3459 3886 2.223180 GCTAACAAAATAACCTCGGCGG 60.223 50.000 7.21 0.00 39.35 6.13
3532 3959 3.938963 TCCATGGCACTTAAAATCGAGTC 59.061 43.478 6.96 0.00 0.00 3.36
3539 3966 3.678072 CACTTAAAATCGAGTCCGCAAGA 59.322 43.478 0.00 0.00 43.02 3.02
3554 3981 3.000041 CGCAAGACACAAAGTAGGCATA 59.000 45.455 0.00 0.00 43.02 3.14
3555 3982 3.435327 CGCAAGACACAAAGTAGGCATAA 59.565 43.478 0.00 0.00 43.02 1.90
3559 3986 6.308766 GCAAGACACAAAGTAGGCATAAAATG 59.691 38.462 0.00 0.00 0.00 2.32
3584 4011 3.272017 CCCCCACCAGGAAAACCT 58.728 61.111 0.00 0.00 38.24 3.50
3585 4012 2.481890 CCCCCACCAGGAAAACCTA 58.518 57.895 0.00 0.00 38.24 3.08
3586 4013 1.007607 CCCCCACCAGGAAAACCTAT 58.992 55.000 0.00 0.00 38.24 2.57
3587 4014 2.210644 CCCCCACCAGGAAAACCTATA 58.789 52.381 0.00 0.00 38.24 1.31
3588 4015 2.789399 CCCCCACCAGGAAAACCTATAT 59.211 50.000 0.00 0.00 38.24 0.86
3589 4016 3.181433 CCCCCACCAGGAAAACCTATATC 60.181 52.174 0.00 0.00 38.24 1.63
3590 4017 3.496160 CCCCACCAGGAAAACCTATATCG 60.496 52.174 0.00 0.00 38.24 2.92
3591 4018 3.139077 CCACCAGGAAAACCTATATCGC 58.861 50.000 0.00 0.00 36.89 4.58
3592 4019 3.139077 CACCAGGAAAACCTATATCGCC 58.861 50.000 0.00 0.00 0.00 5.54
3593 4020 3.046374 ACCAGGAAAACCTATATCGCCT 58.954 45.455 0.00 0.00 0.00 5.52
3594 4021 3.071167 ACCAGGAAAACCTATATCGCCTC 59.929 47.826 0.00 0.00 0.00 4.70
3595 4022 3.557264 CCAGGAAAACCTATATCGCCTCC 60.557 52.174 0.00 0.00 0.00 4.30
3596 4023 3.325135 CAGGAAAACCTATATCGCCTCCT 59.675 47.826 0.00 0.00 32.19 3.69
3597 4024 3.579151 AGGAAAACCTATATCGCCTCCTC 59.421 47.826 0.00 0.00 0.00 3.71
3598 4025 3.576648 GAAAACCTATATCGCCTCCTCG 58.423 50.000 0.00 0.00 0.00 4.63
3599 4026 0.889306 AACCTATATCGCCTCCTCGC 59.111 55.000 0.00 0.00 0.00 5.03
3600 4027 0.966370 ACCTATATCGCCTCCTCGCC 60.966 60.000 0.00 0.00 0.00 5.54
3601 4028 0.681564 CCTATATCGCCTCCTCGCCT 60.682 60.000 0.00 0.00 0.00 5.52
3602 4029 0.736053 CTATATCGCCTCCTCGCCTC 59.264 60.000 0.00 0.00 0.00 4.70
3603 4030 0.328592 TATATCGCCTCCTCGCCTCT 59.671 55.000 0.00 0.00 0.00 3.69
3604 4031 0.963355 ATATCGCCTCCTCGCCTCTC 60.963 60.000 0.00 0.00 0.00 3.20
3605 4032 2.339275 TATCGCCTCCTCGCCTCTCA 62.339 60.000 0.00 0.00 0.00 3.27
3606 4033 4.200283 CGCCTCCTCGCCTCTCAC 62.200 72.222 0.00 0.00 0.00 3.51
3607 4034 3.844090 GCCTCCTCGCCTCTCACC 61.844 72.222 0.00 0.00 0.00 4.02
3608 4035 2.363018 CCTCCTCGCCTCTCACCA 60.363 66.667 0.00 0.00 0.00 4.17
3609 4036 2.716017 CCTCCTCGCCTCTCACCAC 61.716 68.421 0.00 0.00 0.00 4.16
3610 4037 1.680651 CTCCTCGCCTCTCACCACT 60.681 63.158 0.00 0.00 0.00 4.00
3611 4038 0.394488 CTCCTCGCCTCTCACCACTA 60.394 60.000 0.00 0.00 0.00 2.74
3612 4039 0.394488 TCCTCGCCTCTCACCACTAG 60.394 60.000 0.00 0.00 0.00 2.57
3613 4040 1.388065 CCTCGCCTCTCACCACTAGG 61.388 65.000 0.00 0.00 42.21 3.02
3614 4041 1.379977 TCGCCTCTCACCACTAGGG 60.380 63.158 0.00 0.00 44.81 3.53
3624 4051 2.932663 CCACTAGGGTGTGCTGTTG 58.067 57.895 0.00 0.00 41.53 3.33
3625 4052 0.606401 CCACTAGGGTGTGCTGTTGG 60.606 60.000 0.00 0.00 41.53 3.77
3626 4053 0.606401 CACTAGGGTGTGCTGTTGGG 60.606 60.000 0.00 0.00 38.54 4.12
3627 4054 1.675641 CTAGGGTGTGCTGTTGGGC 60.676 63.158 0.00 0.00 0.00 5.36
3628 4055 2.410322 CTAGGGTGTGCTGTTGGGCA 62.410 60.000 0.00 0.00 40.15 5.36
3629 4056 2.000825 TAGGGTGTGCTGTTGGGCAA 62.001 55.000 0.00 0.00 44.18 4.52
3630 4057 2.430610 GGGTGTGCTGTTGGGCAAA 61.431 57.895 0.00 0.00 44.18 3.68
3631 4058 1.067916 GGTGTGCTGTTGGGCAAAG 59.932 57.895 0.00 0.00 44.18 2.77
3632 4059 1.592400 GTGTGCTGTTGGGCAAAGC 60.592 57.895 0.00 0.00 44.18 3.51
3644 4071 3.793144 CAAAGCCGAGGCAGCGTC 61.793 66.667 17.18 4.93 44.88 5.19
3651 4078 4.415332 GAGGCAGCGTCGACGGAA 62.415 66.667 36.13 0.00 40.23 4.30
3652 4079 4.421479 AGGCAGCGTCGACGGAAG 62.421 66.667 36.13 11.87 40.23 3.46
3658 4085 3.744719 CGTCGACGGAAGCAGGGA 61.745 66.667 29.70 0.00 35.37 4.20
3659 4086 2.182030 GTCGACGGAAGCAGGGAG 59.818 66.667 0.00 0.00 0.00 4.30
3660 4087 3.068691 TCGACGGAAGCAGGGAGG 61.069 66.667 0.00 0.00 0.00 4.30
3661 4088 3.382832 CGACGGAAGCAGGGAGGT 61.383 66.667 0.00 0.00 0.00 3.85
3662 4089 2.050350 CGACGGAAGCAGGGAGGTA 61.050 63.158 0.00 0.00 0.00 3.08
3663 4090 1.392710 CGACGGAAGCAGGGAGGTAT 61.393 60.000 0.00 0.00 0.00 2.73
3664 4091 0.831307 GACGGAAGCAGGGAGGTATT 59.169 55.000 0.00 0.00 0.00 1.89
3665 4092 0.831307 ACGGAAGCAGGGAGGTATTC 59.169 55.000 0.00 0.00 0.00 1.75
3666 4093 1.123928 CGGAAGCAGGGAGGTATTCT 58.876 55.000 0.00 0.00 0.00 2.40
3667 4094 1.069358 CGGAAGCAGGGAGGTATTCTC 59.931 57.143 0.00 0.00 41.71 2.87
3668 4095 2.119495 GGAAGCAGGGAGGTATTCTCA 58.881 52.381 0.00 0.00 44.19 3.27
3669 4096 2.708325 GGAAGCAGGGAGGTATTCTCAT 59.292 50.000 0.00 0.00 44.19 2.90
3670 4097 3.495806 GGAAGCAGGGAGGTATTCTCATG 60.496 52.174 0.00 0.00 44.19 3.07
3671 4098 2.053244 AGCAGGGAGGTATTCTCATGG 58.947 52.381 0.00 0.00 44.19 3.66
3672 4099 1.771255 GCAGGGAGGTATTCTCATGGT 59.229 52.381 0.00 0.00 44.19 3.55
3673 4100 2.173569 GCAGGGAGGTATTCTCATGGTT 59.826 50.000 0.00 0.00 44.19 3.67
3674 4101 3.372025 GCAGGGAGGTATTCTCATGGTTT 60.372 47.826 0.00 0.00 44.19 3.27
3675 4102 4.202441 CAGGGAGGTATTCTCATGGTTTG 58.798 47.826 0.00 0.00 44.19 2.93
3676 4103 3.203040 AGGGAGGTATTCTCATGGTTTGG 59.797 47.826 0.00 0.00 44.19 3.28
3677 4104 3.053619 GGGAGGTATTCTCATGGTTTGGT 60.054 47.826 0.00 0.00 44.19 3.67
3678 4105 3.947834 GGAGGTATTCTCATGGTTTGGTG 59.052 47.826 0.00 0.00 44.19 4.17
3679 4106 3.356290 AGGTATTCTCATGGTTTGGTGC 58.644 45.455 0.00 0.00 0.00 5.01
3680 4107 2.427095 GGTATTCTCATGGTTTGGTGCC 59.573 50.000 0.00 0.00 0.00 5.01
3681 4108 2.610438 ATTCTCATGGTTTGGTGCCT 57.390 45.000 0.00 0.00 0.00 4.75
3682 4109 2.380064 TTCTCATGGTTTGGTGCCTT 57.620 45.000 0.00 0.00 0.00 4.35
3683 4110 1.619654 TCTCATGGTTTGGTGCCTTG 58.380 50.000 0.00 0.00 33.86 3.61
3684 4111 1.133513 TCTCATGGTTTGGTGCCTTGT 60.134 47.619 0.00 0.00 34.13 3.16
3685 4112 1.000060 CTCATGGTTTGGTGCCTTGTG 60.000 52.381 0.00 0.00 34.13 3.33
3686 4113 0.033781 CATGGTTTGGTGCCTTGTGG 59.966 55.000 0.00 0.00 0.00 4.17
3687 4114 1.120795 ATGGTTTGGTGCCTTGTGGG 61.121 55.000 0.00 0.00 38.36 4.61
3688 4115 2.506957 GGTTTGGTGCCTTGTGGGG 61.507 63.158 0.00 0.00 35.12 4.96
3689 4116 2.123077 TTTGGTGCCTTGTGGGGG 60.123 61.111 0.00 0.00 35.12 5.40
3690 4117 3.015332 TTTGGTGCCTTGTGGGGGT 62.015 57.895 0.00 0.00 35.12 4.95
3691 4118 3.747521 TTGGTGCCTTGTGGGGGTG 62.748 63.158 0.00 0.00 35.12 4.61
3692 4119 4.994756 GGTGCCTTGTGGGGGTGG 62.995 72.222 0.00 0.00 35.12 4.61
3693 4120 4.218686 GTGCCTTGTGGGGGTGGT 62.219 66.667 0.00 0.00 35.12 4.16
3694 4121 3.897122 TGCCTTGTGGGGGTGGTC 61.897 66.667 0.00 0.00 35.12 4.02
3695 4122 3.580319 GCCTTGTGGGGGTGGTCT 61.580 66.667 0.00 0.00 35.12 3.85
3696 4123 2.436109 CCTTGTGGGGGTGGTCTG 59.564 66.667 0.00 0.00 0.00 3.51
3697 4124 2.436109 CTTGTGGGGGTGGTCTGG 59.564 66.667 0.00 0.00 0.00 3.86
3698 4125 2.369015 TTGTGGGGGTGGTCTGGT 60.369 61.111 0.00 0.00 0.00 4.00
3699 4126 1.073629 TTGTGGGGGTGGTCTGGTA 60.074 57.895 0.00 0.00 0.00 3.25
3700 4127 0.476808 TTGTGGGGGTGGTCTGGTAT 60.477 55.000 0.00 0.00 0.00 2.73
3701 4128 1.204786 TGTGGGGGTGGTCTGGTATG 61.205 60.000 0.00 0.00 0.00 2.39
3702 4129 0.912487 GTGGGGGTGGTCTGGTATGA 60.912 60.000 0.00 0.00 0.00 2.15
3703 4130 0.045623 TGGGGGTGGTCTGGTATGAT 59.954 55.000 0.00 0.00 0.00 2.45
3704 4131 0.474184 GGGGGTGGTCTGGTATGATG 59.526 60.000 0.00 0.00 0.00 3.07
3705 4132 0.474184 GGGGTGGTCTGGTATGATGG 59.526 60.000 0.00 0.00 0.00 3.51
3706 4133 0.474184 GGGTGGTCTGGTATGATGGG 59.526 60.000 0.00 0.00 0.00 4.00
3707 4134 0.474184 GGTGGTCTGGTATGATGGGG 59.526 60.000 0.00 0.00 0.00 4.96
3708 4135 1.507140 GTGGTCTGGTATGATGGGGA 58.493 55.000 0.00 0.00 0.00 4.81
3709 4136 1.843851 GTGGTCTGGTATGATGGGGAA 59.156 52.381 0.00 0.00 0.00 3.97
3710 4137 2.126882 TGGTCTGGTATGATGGGGAAG 58.873 52.381 0.00 0.00 0.00 3.46
3711 4138 1.421646 GGTCTGGTATGATGGGGAAGG 59.578 57.143 0.00 0.00 0.00 3.46
3712 4139 1.140312 TCTGGTATGATGGGGAAGGC 58.860 55.000 0.00 0.00 0.00 4.35
3713 4140 0.111253 CTGGTATGATGGGGAAGGCC 59.889 60.000 0.00 0.00 0.00 5.19
3714 4141 1.073199 GGTATGATGGGGAAGGCCG 59.927 63.158 0.00 0.00 33.83 6.13
3715 4142 1.415672 GGTATGATGGGGAAGGCCGA 61.416 60.000 0.00 0.00 33.83 5.54
3716 4143 0.250338 GTATGATGGGGAAGGCCGAC 60.250 60.000 0.00 0.00 33.83 4.79
3717 4144 0.399949 TATGATGGGGAAGGCCGACT 60.400 55.000 0.00 0.00 33.83 4.18
3718 4145 0.399949 ATGATGGGGAAGGCCGACTA 60.400 55.000 0.00 0.00 33.83 2.59
3719 4146 0.619255 TGATGGGGAAGGCCGACTAA 60.619 55.000 0.00 0.00 33.83 2.24
3720 4147 0.765510 GATGGGGAAGGCCGACTAAT 59.234 55.000 0.00 0.00 33.83 1.73
3721 4148 0.474184 ATGGGGAAGGCCGACTAATG 59.526 55.000 0.00 0.00 33.83 1.90
3722 4149 0.912487 TGGGGAAGGCCGACTAATGT 60.912 55.000 0.00 0.00 33.83 2.71
3723 4150 0.463833 GGGGAAGGCCGACTAATGTG 60.464 60.000 0.00 0.00 33.83 3.21
3724 4151 0.252197 GGGAAGGCCGACTAATGTGT 59.748 55.000 0.00 0.00 33.83 3.72
3725 4152 1.369625 GGAAGGCCGACTAATGTGTG 58.630 55.000 0.00 0.00 0.00 3.82
3726 4153 0.727398 GAAGGCCGACTAATGTGTGC 59.273 55.000 0.00 0.00 0.00 4.57
3727 4154 1.019278 AAGGCCGACTAATGTGTGCG 61.019 55.000 0.00 0.00 0.00 5.34
3728 4155 2.399611 GCCGACTAATGTGTGCGC 59.600 61.111 0.00 0.00 0.00 6.09
3729 4156 2.100631 GCCGACTAATGTGTGCGCT 61.101 57.895 9.73 0.00 0.00 5.92
3730 4157 0.804544 GCCGACTAATGTGTGCGCTA 60.805 55.000 9.73 0.00 0.00 4.26
3731 4158 1.200483 CCGACTAATGTGTGCGCTAG 58.800 55.000 9.73 2.92 0.00 3.42
3732 4159 0.572590 CGACTAATGTGTGCGCTAGC 59.427 55.000 9.73 4.06 45.41 3.42
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 69 4.232122 TGAATCTAACTAGAGGAGGGGACA 59.768 45.833 0.00 0.00 35.50 4.02
74 75 7.595819 ATCCACTTGAATCTAACTAGAGGAG 57.404 40.000 0.00 0.00 34.91 3.69
84 186 8.090831 CCGAATCTCAATATCCACTTGAATCTA 58.909 37.037 0.00 0.00 32.53 1.98
110 212 3.678915 TTTTTCTTCAACCGGACGAAC 57.321 42.857 9.46 0.00 33.94 3.95
205 307 1.440145 GCTATGGGAAGAACTGGCGC 61.440 60.000 0.00 0.00 0.00 6.53
230 332 4.435121 CGTATTTCCTTCACAACCGTTAGC 60.435 45.833 0.00 0.00 0.00 3.09
244 346 6.043243 ACATTGTAGATGGATCCGTATTTCCT 59.957 38.462 6.41 1.74 32.95 3.36
320 422 6.294176 GCCAAGAATGAGTGTTATTGTTCTGT 60.294 38.462 0.00 0.00 30.44 3.41
322 424 5.106555 CGCCAAGAATGAGTGTTATTGTTCT 60.107 40.000 0.00 0.00 30.44 3.01
325 427 3.440173 CCGCCAAGAATGAGTGTTATTGT 59.560 43.478 0.00 0.00 30.44 2.71
355 457 3.006967 GTGGCGGTATCACCTCATATTCT 59.993 47.826 0.00 0.00 35.66 2.40
358 460 2.609747 AGTGGCGGTATCACCTCATAT 58.390 47.619 0.00 0.00 35.66 1.78
359 461 2.082140 AGTGGCGGTATCACCTCATA 57.918 50.000 0.00 0.00 35.66 2.15
362 464 0.249398 ACAAGTGGCGGTATCACCTC 59.751 55.000 0.00 0.00 35.66 3.85
374 478 2.715749 TGATGGGAGCATACAAGTGG 57.284 50.000 0.00 0.00 0.00 4.00
401 505 8.347035 TCAAACCATTTAAACTTACTTTCTCGG 58.653 33.333 0.00 0.00 0.00 4.63
402 506 9.724839 TTCAAACCATTTAAACTTACTTTCTCG 57.275 29.630 0.00 0.00 0.00 4.04
440 545 7.707624 ATGTGTTGTGAACATCCATAATCTT 57.292 32.000 0.00 0.00 44.35 2.40
442 547 8.677300 ACTTATGTGTTGTGAACATCCATAATC 58.323 33.333 10.51 0.00 44.35 1.75
476 581 8.393671 TGAATTTTGATCTGAAATTTTTGGGG 57.606 30.769 16.28 0.00 36.96 4.96
477 582 9.275398 TCTGAATTTTGATCTGAAATTTTTGGG 57.725 29.630 16.28 9.03 36.96 4.12
484 589 9.288576 TGTGTACTCTGAATTTTGATCTGAAAT 57.711 29.630 0.00 0.00 0.00 2.17
523 628 8.141268 ACAATATTCACATTCGGTTTTGTCTTT 58.859 29.630 0.00 0.00 0.00 2.52
546 651 5.449862 GCATGAACAGTGTCAAAACCTACAA 60.450 40.000 0.00 0.00 0.00 2.41
623 728 8.752766 AATCAGATGCAAAATTCAAAGTACAG 57.247 30.769 0.00 0.00 0.00 2.74
829 937 4.659088 TCGTGTACATTCGAGATGAGTTC 58.341 43.478 0.00 0.00 0.00 3.01
965 1073 0.097325 CGTGAGTGAGAGAGTACGGC 59.903 60.000 0.00 0.00 0.00 5.68
1179 1287 2.095364 GTCGTAGATGTTGTCGAGGTGT 60.095 50.000 0.00 0.00 40.67 4.16
1872 1980 2.801631 GGAGGACATGAGGCGGGAG 61.802 68.421 0.00 0.00 0.00 4.30
2238 2346 0.915364 GGAACTCCAGGCAATCCTCT 59.085 55.000 0.00 0.00 41.93 3.69
2244 2352 4.344865 GGGCGGAACTCCAGGCAA 62.345 66.667 13.27 0.00 32.84 4.52
2281 2389 3.070576 GCCGCCAGCAAAATCCCT 61.071 61.111 0.00 0.00 42.97 4.20
2535 2942 4.495422 CTGAAAGTTGATACGTACCAGCT 58.505 43.478 0.00 0.00 0.00 4.24
2560 2970 4.083217 GGTGCTCATACGAGAATACGAGAT 60.083 45.833 0.00 0.00 42.34 2.75
2561 2971 3.250280 GGTGCTCATACGAGAATACGAGA 59.750 47.826 0.00 0.00 42.34 4.04
2562 2972 3.556513 GGTGCTCATACGAGAATACGAG 58.443 50.000 0.00 0.00 42.34 4.18
2563 2973 2.292569 GGGTGCTCATACGAGAATACGA 59.707 50.000 0.00 0.00 42.34 3.43
2564 2974 2.034179 TGGGTGCTCATACGAGAATACG 59.966 50.000 0.00 0.00 42.34 3.06
2565 2975 3.728076 TGGGTGCTCATACGAGAATAC 57.272 47.619 0.00 0.00 42.34 1.89
2566 2976 4.081365 TGTTTGGGTGCTCATACGAGAATA 60.081 41.667 0.00 0.00 42.34 1.75
2567 2977 3.270877 GTTTGGGTGCTCATACGAGAAT 58.729 45.455 0.00 0.00 42.34 2.40
2568 2978 2.037902 TGTTTGGGTGCTCATACGAGAA 59.962 45.455 0.00 0.00 42.34 2.87
2570 2980 2.093306 TGTTTGGGTGCTCATACGAG 57.907 50.000 0.00 0.00 42.66 4.18
2571 2981 2.550606 GTTTGTTTGGGTGCTCATACGA 59.449 45.455 0.00 0.00 0.00 3.43
2573 2983 3.568007 TCAGTTTGTTTGGGTGCTCATAC 59.432 43.478 0.00 0.00 0.00 2.39
2574 2984 3.826524 TCAGTTTGTTTGGGTGCTCATA 58.173 40.909 0.00 0.00 0.00 2.15
2575 2985 2.665165 TCAGTTTGTTTGGGTGCTCAT 58.335 42.857 0.00 0.00 0.00 2.90
2576 2986 2.136298 TCAGTTTGTTTGGGTGCTCA 57.864 45.000 0.00 0.00 0.00 4.26
2577 2987 3.733443 AATCAGTTTGTTTGGGTGCTC 57.267 42.857 0.00 0.00 0.00 4.26
2578 2988 5.304101 TGATAAATCAGTTTGTTTGGGTGCT 59.696 36.000 0.00 0.00 32.11 4.40
2579 2989 5.405269 GTGATAAATCAGTTTGTTTGGGTGC 59.595 40.000 0.00 0.00 37.51 5.01
2621 3031 7.765819 CCATCCCAAAATCAGGAAAATAAACTC 59.234 37.037 0.00 0.00 35.30 3.01
2623 3033 7.619965 TCCATCCCAAAATCAGGAAAATAAAC 58.380 34.615 0.00 0.00 35.30 2.01
2627 3037 5.547276 TGTTCCATCCCAAAATCAGGAAAAT 59.453 36.000 0.00 0.00 36.95 1.82
2670 3085 1.282738 TCAAAGCAGGGCATGATGAGA 59.717 47.619 1.99 0.00 0.00 3.27
2712 3127 3.381590 TCAGAGATCTGTACCACATTCCG 59.618 47.826 0.00 0.00 44.12 4.30
2713 3128 5.344743 TTCAGAGATCTGTACCACATTCC 57.655 43.478 0.00 0.00 44.12 3.01
2714 3129 5.105146 ACCTTCAGAGATCTGTACCACATTC 60.105 44.000 0.00 0.00 44.12 2.67
2715 3130 4.780021 ACCTTCAGAGATCTGTACCACATT 59.220 41.667 0.00 0.00 44.12 2.71
2716 3131 4.357325 ACCTTCAGAGATCTGTACCACAT 58.643 43.478 0.00 0.00 44.12 3.21
2721 3136 3.444388 ACCGAACCTTCAGAGATCTGTAC 59.556 47.826 0.00 0.00 44.12 2.90
2761 3176 3.502920 GTCTCGAACGTCTTGATCACAT 58.497 45.455 0.00 0.00 0.00 3.21
2836 3251 8.351461 GCAGAGAAATACGTATAAAGTAGAGGT 58.649 37.037 8.83 0.00 0.00 3.85
2837 3252 8.569641 AGCAGAGAAATACGTATAAAGTAGAGG 58.430 37.037 8.83 0.00 0.00 3.69
2838 3253 9.601971 GAGCAGAGAAATACGTATAAAGTAGAG 57.398 37.037 8.83 0.00 0.00 2.43
2839 3254 8.566260 GGAGCAGAGAAATACGTATAAAGTAGA 58.434 37.037 8.83 0.00 0.00 2.59
2840 3255 7.808856 GGGAGCAGAGAAATACGTATAAAGTAG 59.191 40.741 8.83 0.00 0.00 2.57
2841 3256 7.255730 GGGGAGCAGAGAAATACGTATAAAGTA 60.256 40.741 8.83 0.00 0.00 2.24
2842 3257 6.462628 GGGGAGCAGAGAAATACGTATAAAGT 60.463 42.308 8.83 0.00 0.00 2.66
2843 3258 5.927115 GGGGAGCAGAGAAATACGTATAAAG 59.073 44.000 8.83 0.00 0.00 1.85
2844 3259 5.601313 AGGGGAGCAGAGAAATACGTATAAA 59.399 40.000 8.83 0.00 0.00 1.40
2845 3260 5.145564 AGGGGAGCAGAGAAATACGTATAA 58.854 41.667 8.83 0.00 0.00 0.98
2846 3261 4.737578 AGGGGAGCAGAGAAATACGTATA 58.262 43.478 8.83 0.00 0.00 1.47
2847 3262 3.574826 GAGGGGAGCAGAGAAATACGTAT 59.425 47.826 1.14 1.14 0.00 3.06
2848 3263 2.957006 GAGGGGAGCAGAGAAATACGTA 59.043 50.000 0.00 0.00 0.00 3.57
2849 3264 1.757699 GAGGGGAGCAGAGAAATACGT 59.242 52.381 0.00 0.00 0.00 3.57
2850 3265 2.035321 GAGAGGGGAGCAGAGAAATACG 59.965 54.545 0.00 0.00 0.00 3.06
2851 3266 2.367241 GGAGAGGGGAGCAGAGAAATAC 59.633 54.545 0.00 0.00 0.00 1.89
2873 3288 1.795768 CACAAGGAGCACACATACGT 58.204 50.000 0.00 0.00 0.00 3.57
2877 3292 1.696063 AAAGCACAAGGAGCACACAT 58.304 45.000 0.00 0.00 0.00 3.21
2911 3326 1.878070 CACAACGCTGCATGTGGAT 59.122 52.632 21.33 0.00 42.46 3.41
2941 3356 5.166398 AGAAACAGTATTTACCGAACCGAG 58.834 41.667 0.00 0.00 0.00 4.63
2943 3358 4.030977 CGAGAAACAGTATTTACCGAACCG 59.969 45.833 0.00 0.00 0.00 4.44
2989 3404 9.902684 TCCAAATCAATACAATATTTGCCAAAT 57.097 25.926 7.93 7.93 38.62 2.32
3027 3442 8.749841 AGCGATGAATAGTCTGTATATCAAAC 57.250 34.615 0.00 0.00 0.00 2.93
3043 3458 0.179073 CTTCACCCCGAGCGATGAAT 60.179 55.000 0.00 0.00 31.00 2.57
3086 3501 8.341892 TGTAAACATAGGTTGCATTGATGTAA 57.658 30.769 0.00 0.00 37.30 2.41
3088 3503 6.832520 TGTAAACATAGGTTGCATTGATGT 57.167 33.333 0.00 0.00 37.30 3.06
3089 3504 7.482474 TGATGTAAACATAGGTTGCATTGATG 58.518 34.615 10.50 0.00 37.30 3.07
3092 3507 8.706492 AAATGATGTAAACATAGGTTGCATTG 57.294 30.769 10.50 0.00 37.30 2.82
3094 3509 9.189156 ACTAAATGATGTAAACATAGGTTGCAT 57.811 29.630 9.39 9.39 37.30 3.96
3095 3510 8.574251 ACTAAATGATGTAAACATAGGTTGCA 57.426 30.769 0.00 0.00 37.30 4.08
3096 3511 9.503427 GAACTAAATGATGTAAACATAGGTTGC 57.497 33.333 0.00 0.00 37.30 4.17
3122 3537 7.812648 TCGTTTGACTCCCAATGTAATAAAAG 58.187 34.615 0.00 0.00 34.23 2.27
3132 3548 4.021102 ACATTCTCGTTTGACTCCCAAT 57.979 40.909 0.00 0.00 34.23 3.16
3263 3689 9.994432 CACTTTGTTAAATTTGGCATAAAAACA 57.006 25.926 0.00 0.00 0.00 2.83
3270 3696 8.674263 TTGATTCACTTTGTTAAATTTGGCAT 57.326 26.923 0.00 0.00 0.00 4.40
3271 3697 8.674263 ATTGATTCACTTTGTTAAATTTGGCA 57.326 26.923 0.00 0.00 0.00 4.92
3281 3707 8.803799 GTTACGTTCAAATTGATTCACTTTGTT 58.196 29.630 21.70 11.84 36.10 2.83
3305 3731 9.672673 AGAATTGTGTTTGCTATACAGATAGTT 57.327 29.630 0.00 0.00 37.87 2.24
3325 3751 9.672086 TTTCTTACGGTGTTTCATTAAGAATTG 57.328 29.630 0.00 0.00 38.14 2.32
3341 3767 2.933928 GCATCCGAGGTTTTCTTACGGT 60.934 50.000 0.00 0.00 43.36 4.83
3389 3815 8.712285 ATCATTGCCTCATTTTAAATTGTCTG 57.288 30.769 9.31 2.53 0.00 3.51
3412 3839 9.620660 CAAATACACCAACAAAACTAAGGTATC 57.379 33.333 0.00 0.00 0.00 2.24
3414 3841 7.285858 AGCAAATACACCAACAAAACTAAGGTA 59.714 33.333 0.00 0.00 0.00 3.08
3416 3843 6.512297 AGCAAATACACCAACAAAACTAAGG 58.488 36.000 0.00 0.00 0.00 2.69
3444 3871 1.002773 AGTGTCCGCCGAGGTTATTTT 59.997 47.619 0.00 0.00 41.99 1.82
3452 3879 2.074547 TTTTCTTAGTGTCCGCCGAG 57.925 50.000 0.00 0.00 0.00 4.63
3492 3919 9.194972 TGCCATGGAAACTAATTATGTTATTGA 57.805 29.630 18.40 0.00 0.00 2.57
3504 3931 6.431543 TCGATTTTAAGTGCCATGGAAACTAA 59.568 34.615 18.40 9.70 0.00 2.24
3505 3932 5.941058 TCGATTTTAAGTGCCATGGAAACTA 59.059 36.000 18.40 3.35 0.00 2.24
3515 3942 1.062148 GCGGACTCGATTTTAAGTGCC 59.938 52.381 0.00 0.00 39.00 5.01
3527 3954 0.508641 CTTTGTGTCTTGCGGACTCG 59.491 55.000 10.27 0.00 44.74 4.18
3532 3959 0.517316 GCCTACTTTGTGTCTTGCGG 59.483 55.000 0.00 0.00 0.00 5.69
3539 3966 4.081697 GGCCATTTTATGCCTACTTTGTGT 60.082 41.667 0.00 0.00 44.46 3.72
3576 4003 3.614390 CGAGGAGGCGATATAGGTTTTCC 60.614 52.174 0.00 0.00 41.05 3.13
3577 4004 3.576648 CGAGGAGGCGATATAGGTTTTC 58.423 50.000 0.00 0.00 0.00 2.29
3578 4005 2.288886 GCGAGGAGGCGATATAGGTTTT 60.289 50.000 0.00 0.00 0.00 2.43
3579 4006 1.272769 GCGAGGAGGCGATATAGGTTT 59.727 52.381 0.00 0.00 0.00 3.27
3580 4007 0.889306 GCGAGGAGGCGATATAGGTT 59.111 55.000 0.00 0.00 0.00 3.50
3581 4008 0.966370 GGCGAGGAGGCGATATAGGT 60.966 60.000 0.00 0.00 35.04 3.08
3582 4009 1.810532 GGCGAGGAGGCGATATAGG 59.189 63.158 0.00 0.00 35.04 2.57
3591 4018 2.363018 TGGTGAGAGGCGAGGAGG 60.363 66.667 0.00 0.00 0.00 4.30
3592 4019 0.394488 TAGTGGTGAGAGGCGAGGAG 60.394 60.000 0.00 0.00 0.00 3.69
3593 4020 0.394488 CTAGTGGTGAGAGGCGAGGA 60.394 60.000 0.00 0.00 0.00 3.71
3594 4021 1.388065 CCTAGTGGTGAGAGGCGAGG 61.388 65.000 0.00 0.00 0.00 4.63
3595 4022 1.388065 CCCTAGTGGTGAGAGGCGAG 61.388 65.000 0.00 0.00 0.00 5.03
3596 4023 1.379977 CCCTAGTGGTGAGAGGCGA 60.380 63.158 0.00 0.00 0.00 5.54
3597 4024 3.211288 CCCTAGTGGTGAGAGGCG 58.789 66.667 0.00 0.00 0.00 5.52
3608 4035 1.761174 CCCAACAGCACACCCTAGT 59.239 57.895 0.00 0.00 0.00 2.57
3609 4036 1.675641 GCCCAACAGCACACCCTAG 60.676 63.158 0.00 0.00 0.00 3.02
3610 4037 2.000825 TTGCCCAACAGCACACCCTA 62.001 55.000 0.00 0.00 43.97 3.53
3611 4038 2.870035 TTTGCCCAACAGCACACCCT 62.870 55.000 0.00 0.00 43.97 4.34
3612 4039 2.367868 CTTTGCCCAACAGCACACCC 62.368 60.000 0.00 0.00 43.97 4.61
3613 4040 1.067916 CTTTGCCCAACAGCACACC 59.932 57.895 0.00 0.00 43.97 4.16
3614 4041 1.592400 GCTTTGCCCAACAGCACAC 60.592 57.895 9.00 0.00 43.97 3.82
3615 4042 2.795110 GGCTTTGCCCAACAGCACA 61.795 57.895 13.25 0.00 43.97 4.57
3616 4043 2.029518 GGCTTTGCCCAACAGCAC 59.970 61.111 13.25 4.27 43.97 4.40
3627 4054 3.793144 GACGCTGCCTCGGCTTTG 61.793 66.667 9.65 1.30 42.51 2.77
3634 4061 4.415332 TTCCGTCGACGCTGCCTC 62.415 66.667 31.73 0.00 38.18 4.70
3635 4062 4.421479 CTTCCGTCGACGCTGCCT 62.421 66.667 31.73 0.00 38.18 4.75
3638 4065 3.175240 CTGCTTCCGTCGACGCTG 61.175 66.667 31.73 22.26 34.45 5.18
3639 4066 4.421479 CCTGCTTCCGTCGACGCT 62.421 66.667 31.73 0.00 34.45 5.07
3641 4068 3.685214 CTCCCTGCTTCCGTCGACG 62.685 68.421 30.33 30.33 39.44 5.12
3642 4069 2.182030 CTCCCTGCTTCCGTCGAC 59.818 66.667 5.18 5.18 0.00 4.20
3643 4070 2.488771 TACCTCCCTGCTTCCGTCGA 62.489 60.000 0.00 0.00 0.00 4.20
3644 4071 1.392710 ATACCTCCCTGCTTCCGTCG 61.393 60.000 0.00 0.00 0.00 5.12
3645 4072 0.831307 AATACCTCCCTGCTTCCGTC 59.169 55.000 0.00 0.00 0.00 4.79
3646 4073 0.831307 GAATACCTCCCTGCTTCCGT 59.169 55.000 0.00 0.00 0.00 4.69
3647 4074 1.069358 GAGAATACCTCCCTGCTTCCG 59.931 57.143 0.00 0.00 35.87 4.30
3648 4075 2.119495 TGAGAATACCTCCCTGCTTCC 58.881 52.381 0.00 0.00 41.25 3.46
3649 4076 3.495806 CCATGAGAATACCTCCCTGCTTC 60.496 52.174 0.00 0.00 41.25 3.86
3650 4077 2.441001 CCATGAGAATACCTCCCTGCTT 59.559 50.000 0.00 0.00 41.25 3.91
3651 4078 2.053244 CCATGAGAATACCTCCCTGCT 58.947 52.381 0.00 0.00 41.25 4.24
3652 4079 1.771255 ACCATGAGAATACCTCCCTGC 59.229 52.381 0.00 0.00 41.25 4.85
3653 4080 4.202441 CAAACCATGAGAATACCTCCCTG 58.798 47.826 0.00 0.00 41.25 4.45
3654 4081 3.203040 CCAAACCATGAGAATACCTCCCT 59.797 47.826 0.00 0.00 41.25 4.20
3655 4082 3.053619 ACCAAACCATGAGAATACCTCCC 60.054 47.826 0.00 0.00 41.25 4.30
3656 4083 3.947834 CACCAAACCATGAGAATACCTCC 59.052 47.826 0.00 0.00 41.25 4.30
3657 4084 3.378427 GCACCAAACCATGAGAATACCTC 59.622 47.826 0.00 0.00 42.30 3.85
3658 4085 3.356290 GCACCAAACCATGAGAATACCT 58.644 45.455 0.00 0.00 0.00 3.08
3659 4086 2.427095 GGCACCAAACCATGAGAATACC 59.573 50.000 0.00 0.00 0.00 2.73
3660 4087 3.356290 AGGCACCAAACCATGAGAATAC 58.644 45.455 0.00 0.00 0.00 1.89
3661 4088 3.737559 AGGCACCAAACCATGAGAATA 57.262 42.857 0.00 0.00 0.00 1.75
3662 4089 2.564062 CAAGGCACCAAACCATGAGAAT 59.436 45.455 0.00 0.00 0.00 2.40
3663 4090 1.962807 CAAGGCACCAAACCATGAGAA 59.037 47.619 0.00 0.00 0.00 2.87
3664 4091 1.133513 ACAAGGCACCAAACCATGAGA 60.134 47.619 0.00 0.00 30.49 3.27
3665 4092 1.000060 CACAAGGCACCAAACCATGAG 60.000 52.381 0.00 0.00 30.49 2.90
3666 4093 1.039068 CACAAGGCACCAAACCATGA 58.961 50.000 0.00 0.00 30.49 3.07
3667 4094 0.033781 CCACAAGGCACCAAACCATG 59.966 55.000 0.00 0.00 32.18 3.66
3668 4095 1.120795 CCCACAAGGCACCAAACCAT 61.121 55.000 0.00 0.00 0.00 3.55
3669 4096 1.760086 CCCACAAGGCACCAAACCA 60.760 57.895 0.00 0.00 0.00 3.67
3670 4097 2.506957 CCCCACAAGGCACCAAACC 61.507 63.158 0.00 0.00 0.00 3.27
3671 4098 2.506957 CCCCCACAAGGCACCAAAC 61.507 63.158 0.00 0.00 0.00 2.93
3672 4099 2.123077 CCCCCACAAGGCACCAAA 60.123 61.111 0.00 0.00 0.00 3.28
3673 4100 3.434179 ACCCCCACAAGGCACCAA 61.434 61.111 0.00 0.00 0.00 3.67
3674 4101 4.217210 CACCCCCACAAGGCACCA 62.217 66.667 0.00 0.00 0.00 4.17
3675 4102 4.994756 CCACCCCCACAAGGCACC 62.995 72.222 0.00 0.00 0.00 5.01
3676 4103 4.218686 ACCACCCCCACAAGGCAC 62.219 66.667 0.00 0.00 0.00 5.01
3677 4104 3.897122 GACCACCCCCACAAGGCA 61.897 66.667 0.00 0.00 0.00 4.75
3678 4105 3.580319 AGACCACCCCCACAAGGC 61.580 66.667 0.00 0.00 0.00 4.35
3679 4106 2.436109 CAGACCACCCCCACAAGG 59.564 66.667 0.00 0.00 0.00 3.61
3680 4107 1.131303 TACCAGACCACCCCCACAAG 61.131 60.000 0.00 0.00 0.00 3.16
3681 4108 0.476808 ATACCAGACCACCCCCACAA 60.477 55.000 0.00 0.00 0.00 3.33
3682 4109 1.162329 ATACCAGACCACCCCCACA 59.838 57.895 0.00 0.00 0.00 4.17
3683 4110 0.912487 TCATACCAGACCACCCCCAC 60.912 60.000 0.00 0.00 0.00 4.61
3684 4111 0.045623 ATCATACCAGACCACCCCCA 59.954 55.000 0.00 0.00 0.00 4.96
3685 4112 0.474184 CATCATACCAGACCACCCCC 59.526 60.000 0.00 0.00 0.00 5.40
3686 4113 0.474184 CCATCATACCAGACCACCCC 59.526 60.000 0.00 0.00 0.00 4.95
3687 4114 0.474184 CCCATCATACCAGACCACCC 59.526 60.000 0.00 0.00 0.00 4.61
3688 4115 0.474184 CCCCATCATACCAGACCACC 59.526 60.000 0.00 0.00 0.00 4.61
3689 4116 1.507140 TCCCCATCATACCAGACCAC 58.493 55.000 0.00 0.00 0.00 4.16
3690 4117 2.126882 CTTCCCCATCATACCAGACCA 58.873 52.381 0.00 0.00 0.00 4.02
3691 4118 1.421646 CCTTCCCCATCATACCAGACC 59.578 57.143 0.00 0.00 0.00 3.85
3692 4119 1.202818 GCCTTCCCCATCATACCAGAC 60.203 57.143 0.00 0.00 0.00 3.51
3693 4120 1.140312 GCCTTCCCCATCATACCAGA 58.860 55.000 0.00 0.00 0.00 3.86
3694 4121 0.111253 GGCCTTCCCCATCATACCAG 59.889 60.000 0.00 0.00 0.00 4.00
3695 4122 1.705002 CGGCCTTCCCCATCATACCA 61.705 60.000 0.00 0.00 0.00 3.25
3696 4123 1.073199 CGGCCTTCCCCATCATACC 59.927 63.158 0.00 0.00 0.00 2.73
3697 4124 0.250338 GTCGGCCTTCCCCATCATAC 60.250 60.000 0.00 0.00 0.00 2.39
3698 4125 0.399949 AGTCGGCCTTCCCCATCATA 60.400 55.000 0.00 0.00 0.00 2.15
3699 4126 0.399949 TAGTCGGCCTTCCCCATCAT 60.400 55.000 0.00 0.00 0.00 2.45
3700 4127 0.619255 TTAGTCGGCCTTCCCCATCA 60.619 55.000 0.00 0.00 0.00 3.07
3701 4128 0.765510 ATTAGTCGGCCTTCCCCATC 59.234 55.000 0.00 0.00 0.00 3.51
3702 4129 0.474184 CATTAGTCGGCCTTCCCCAT 59.526 55.000 0.00 0.00 0.00 4.00
3703 4130 0.912487 ACATTAGTCGGCCTTCCCCA 60.912 55.000 0.00 0.00 0.00 4.96
3704 4131 0.463833 CACATTAGTCGGCCTTCCCC 60.464 60.000 0.00 0.00 0.00 4.81
3705 4132 0.252197 ACACATTAGTCGGCCTTCCC 59.748 55.000 0.00 0.00 0.00 3.97
3706 4133 1.369625 CACACATTAGTCGGCCTTCC 58.630 55.000 0.00 0.00 0.00 3.46
3707 4134 0.727398 GCACACATTAGTCGGCCTTC 59.273 55.000 0.00 0.00 0.00 3.46
3708 4135 1.019278 CGCACACATTAGTCGGCCTT 61.019 55.000 0.00 0.00 0.00 4.35
3709 4136 1.447838 CGCACACATTAGTCGGCCT 60.448 57.895 0.00 0.00 0.00 5.19
3710 4137 3.089784 CGCACACATTAGTCGGCC 58.910 61.111 0.00 0.00 0.00 6.13
3711 4138 0.804544 TAGCGCACACATTAGTCGGC 60.805 55.000 11.47 0.00 0.00 5.54
3712 4139 1.200483 CTAGCGCACACATTAGTCGG 58.800 55.000 11.47 0.00 0.00 4.79
3713 4140 0.572590 GCTAGCGCACACATTAGTCG 59.427 55.000 11.47 0.00 35.78 4.18
3714 4141 0.572590 CGCTAGCGCACACATTAGTC 59.427 55.000 26.07 0.00 35.30 2.59
3715 4142 2.665777 CGCTAGCGCACACATTAGT 58.334 52.632 26.07 0.00 35.30 2.24


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

AutoCloner maintained by Alex Coulton.