Multiple sequence alignment - TraesCS6D01G154200

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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 TraesCS6D01G154200 chr6D 100.000 6624 0 0 1 6624 129159150 129152527 0.000000e+00 12233.0
1 TraesCS6D01G154200 chr6D 99.048 105 1 0 2541 2645 129156506 129156610 8.770000e-44 189.0
2 TraesCS6D01G154200 chr6A 96.789 2803 80 6 2644 5437 166502667 166505468 0.000000e+00 4669.0
3 TraesCS6D01G154200 chr6A 93.863 2102 63 28 492 2543 166500584 166502669 0.000000e+00 3107.0
4 TraesCS6D01G154200 chr6A 92.541 1153 54 13 5501 6624 166505462 166506611 0.000000e+00 1624.0
5 TraesCS6D01G154200 chr6A 88.942 208 8 7 230 428 166500366 166500567 6.640000e-60 243.0
6 TraesCS6D01G154200 chr6A 89.677 155 10 1 70 224 166499910 166500058 6.780000e-45 193.0
7 TraesCS6D01G154200 chr6A 95.614 114 2 3 2533 2646 61597789 61597899 5.280000e-41 180.0
8 TraesCS6D01G154200 chr6A 97.143 105 1 2 2541 2645 61597898 61597796 6.830000e-40 176.0
9 TraesCS6D01G154200 chr6B 91.548 2248 90 30 314 2484 227277014 227274790 0.000000e+00 3007.0
10 TraesCS6D01G154200 chr6B 91.985 1884 91 24 4724 6577 227272028 227270175 0.000000e+00 2588.0
11 TraesCS6D01G154200 chr6B 92.982 1311 77 9 2644 3950 227274425 227273126 0.000000e+00 1897.0
12 TraesCS6D01G154200 chr6B 92.244 722 44 6 3954 4673 227272746 227272035 0.000000e+00 1013.0
13 TraesCS6D01G154200 chr6B 88.571 70 7 1 18 87 63610477 63610545 4.260000e-12 84.2
14 TraesCS6D01G154200 chr6B 92.593 54 3 1 33 86 697570138 697570190 7.120000e-10 76.8
15 TraesCS6D01G154200 chr7D 92.395 618 39 5 3770 4387 563444002 563444611 0.000000e+00 874.0
16 TraesCS6D01G154200 chr1A 97.248 109 2 1 2538 2645 202090615 202090507 4.080000e-42 183.0
17 TraesCS6D01G154200 chr1A 97.170 106 2 1 2541 2645 202090507 202090612 1.900000e-40 178.0
18 TraesCS6D01G154200 chr7B 97.143 105 2 1 2541 2645 377026905 377026802 6.830000e-40 176.0
19 TraesCS6D01G154200 chr7B 93.333 120 5 3 2526 2645 377026789 377026905 2.460000e-39 174.0
20 TraesCS6D01G154200 chr3B 96.262 107 3 1 2541 2646 283473982 283474088 2.460000e-39 174.0
21 TraesCS6D01G154200 chr3D 94.690 113 2 3 2537 2645 1921175 1921287 8.830000e-39 172.0
22 TraesCS6D01G154200 chr3D 89.831 59 6 0 17 75 34691773 34691715 7.120000e-10 76.8
23 TraesCS6D01G154200 chr3D 81.707 82 14 1 4 84 6993402 6993321 4.290000e-07 67.6
24 TraesCS6D01G154200 chr7A 76.087 230 42 7 1661 1879 585061831 585062058 2.530000e-19 108.0
25 TraesCS6D01G154200 chr7A 83.951 81 12 1 4 83 129617450 129617370 7.120000e-10 76.8
26 TraesCS6D01G154200 chr7A 88.710 62 7 0 21 82 669653612 669653551 7.120000e-10 76.8
27 TraesCS6D01G154200 chr2A 90.769 65 6 0 18 82 761175399 761175463 3.290000e-13 87.9
28 TraesCS6D01G154200 chr1B 88.060 67 8 0 18 84 395973292 395973358 5.510000e-11 80.5
29 TraesCS6D01G154200 chr5A 87.879 66 7 1 19 84 708131468 708131532 7.120000e-10 76.8
30 TraesCS6D01G154200 chr4B 100.000 30 0 0 3826 3855 140925206 140925235 1.000000e-03 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 TraesCS6D01G154200 chr6D 129152527 129159150 6623 True 12233.00 12233 100.00000 1 6624 1 chr6D.!!$R1 6623
1 TraesCS6D01G154200 chr6A 166499910 166506611 6701 False 1967.20 4669 92.36240 70 6624 5 chr6A.!!$F2 6554
2 TraesCS6D01G154200 chr6B 227270175 227277014 6839 True 2126.25 3007 92.18975 314 6577 4 chr6B.!!$R1 6263
3 TraesCS6D01G154200 chr7D 563444002 563444611 609 False 874.00 874 92.39500 3770 4387 1 chr7D.!!$F1 617

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
108 109 0.389025 CGGGGATGGGCTAAAAATGC 59.611 55.000 0.00 0.0 0.00 3.56 F
789 1122 0.523072 CGGCCAAAATCACCACTCAG 59.477 55.000 2.24 0.0 0.00 3.35 F
1961 2341 0.320771 ATCCGTGTCCTGTGTTCTGC 60.321 55.000 0.00 0.0 0.00 4.26 F
3266 3978 0.337773 TCCTCTGACCTCCTCATGCT 59.662 55.000 0.00 0.0 0.00 3.79 F
4431 5528 1.005867 CCAGTGGCGCAAAAGCAAT 60.006 52.632 10.83 0.0 39.27 3.56 F
5101 6204 0.106708 TGTCAAGCTCAAACGGCTCT 59.893 50.000 0.00 0.0 39.30 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1751 2128 0.391228 TCTGGCAGTCGTTTAGCACA 59.609 50.0 15.27 0.0 0.00 4.57 R
2627 3336 0.906282 GGTACTCCCTCCGTCCCAAA 60.906 60.0 0.00 0.0 0.00 3.28 R
3329 4041 0.879090 TGATGCAGCTTCACTTGCAG 59.121 50.0 2.53 0.0 36.37 4.41 R
4669 5766 0.179189 GCATATATTTCGGCGGCAGC 60.179 55.0 10.53 0.0 44.18 5.25 R
5368 6471 0.261696 AGAAGCACCCTGGTTTGGTT 59.738 50.0 9.10 9.1 38.31 3.67 R
6119 7225 0.625849 ATTTGTGGTCAGGCCCCTAG 59.374 55.0 0.00 0.0 36.04 3.02 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
32 33 8.371571 TCTGCTGATGTAGGATAATATCATGT 57.628 34.615 2.41 0.00 29.64 3.21
33 34 8.819845 TCTGCTGATGTAGGATAATATCATGTT 58.180 33.333 2.41 0.00 29.64 2.71
44 45 9.331466 AGGATAATATCATGTTAGATGTGAGGT 57.669 33.333 2.41 0.00 0.00 3.85
53 54 9.367160 TCATGTTAGATGTGAGGTATTATCTCA 57.633 33.333 2.40 2.40 38.75 3.27
92 93 2.621526 GACAGGCCCATTAAATTACGGG 59.378 50.000 0.00 2.97 42.03 5.28
102 103 4.792513 TTAAATTACGGGGATGGGCTAA 57.207 40.909 0.00 0.00 0.00 3.09
108 109 0.389025 CGGGGATGGGCTAAAAATGC 59.611 55.000 0.00 0.00 0.00 3.56
125 126 1.377690 TGCCCTTAAGGTCCATTCCA 58.622 50.000 20.22 3.13 38.26 3.53
129 130 3.096852 CCCTTAAGGTCCATTCCAAACC 58.903 50.000 20.22 0.00 0.00 3.27
163 164 0.526211 GCCTGGTCGGTTGGAAATTC 59.474 55.000 0.00 0.00 34.25 2.17
171 172 1.127951 CGGTTGGAAATTCGAGAACGG 59.872 52.381 0.00 0.00 40.21 4.44
220 221 2.411701 TCGTGTGCCGATCGATCC 59.588 61.111 18.66 7.25 41.60 3.36
224 225 1.488527 GTGTGCCGATCGATCCTAAC 58.511 55.000 18.66 14.33 0.00 2.34
225 226 1.067212 GTGTGCCGATCGATCCTAACT 59.933 52.381 18.66 0.00 0.00 2.24
264 567 1.437573 CGGCGAGCTGAGGTCATAA 59.562 57.895 12.54 0.00 0.00 1.90
276 579 5.448360 GCTGAGGTCATAAACAAAGATGCTC 60.448 44.000 0.00 0.00 0.00 4.26
328 631 5.334105 GCATCTATAATGGTAAACGGCAGTG 60.334 44.000 0.00 0.00 0.00 3.66
382 695 2.289532 ACTCTGGTCTGGGCTCAGC 61.290 63.158 9.36 3.86 40.69 4.26
411 724 8.401709 GGAAATCCAAGAACAGAAATAGATGAC 58.598 37.037 0.00 0.00 35.64 3.06
447 772 2.872925 CGTCCGTCTTGTACCGCG 60.873 66.667 0.00 0.00 0.00 6.46
483 808 1.084370 GCTGAGGTACACATGGACGC 61.084 60.000 0.00 0.00 0.00 5.19
484 809 0.802222 CTGAGGTACACATGGACGCG 60.802 60.000 3.53 3.53 0.00 6.01
485 810 2.125673 AGGTACACATGGACGCGC 60.126 61.111 5.73 0.00 0.00 6.86
486 811 3.192922 GGTACACATGGACGCGCC 61.193 66.667 5.73 9.63 37.10 6.53
750 1083 6.325596 CCCCGATTTTTCTCAGAAAAGAATC 58.674 40.000 12.35 12.19 35.30 2.52
789 1122 0.523072 CGGCCAAAATCACCACTCAG 59.477 55.000 2.24 0.00 0.00 3.35
929 1295 4.471386 GCTCTCCTTCCCCTATATTATGCA 59.529 45.833 0.00 0.00 0.00 3.96
1688 2065 2.656646 CACTACCTGAGCGCCACA 59.343 61.111 2.29 3.92 0.00 4.17
1751 2128 1.088340 AGATGTCGTCCGTCGTCGAT 61.088 55.000 2.98 0.00 40.80 3.59
1896 2273 8.487028 AGGTATACAATCTTTTACTCCTCCTTG 58.513 37.037 5.01 0.00 0.00 3.61
1923 2303 3.192001 ACATGTGGATCATTGTGTTGAGC 59.808 43.478 0.00 0.00 34.09 4.26
1952 2332 0.460311 GATTCCGTGATCCGTGTCCT 59.540 55.000 0.00 0.00 33.66 3.85
1961 2341 0.320771 ATCCGTGTCCTGTGTTCTGC 60.321 55.000 0.00 0.00 0.00 4.26
1970 2363 2.560981 TCCTGTGTTCTGCGTGATTCTA 59.439 45.455 0.00 0.00 0.00 2.10
2030 2425 4.708177 TGTAGATTATGCAAGGGCTTCTC 58.292 43.478 0.00 0.00 41.91 2.87
2249 2644 6.539649 TGTGTAGTTTGTCATCTGCTTTAC 57.460 37.500 0.00 0.00 0.00 2.01
2250 2645 6.288294 TGTGTAGTTTGTCATCTGCTTTACT 58.712 36.000 0.00 0.00 0.00 2.24
2251 2646 7.438564 TGTGTAGTTTGTCATCTGCTTTACTA 58.561 34.615 0.00 0.00 0.00 1.82
2252 2647 7.384115 TGTGTAGTTTGTCATCTGCTTTACTAC 59.616 37.037 0.00 0.00 37.99 2.73
2423 2818 2.830923 CCTAGCCCTGACTCCTATGATG 59.169 54.545 0.00 0.00 0.00 3.07
2550 3259 5.954296 TTCGTTTCTATATACTCCCTCCG 57.046 43.478 0.00 0.00 0.00 4.63
2551 3260 4.978099 TCGTTTCTATATACTCCCTCCGT 58.022 43.478 0.00 0.00 0.00 4.69
2552 3261 4.999950 TCGTTTCTATATACTCCCTCCGTC 59.000 45.833 0.00 0.00 0.00 4.79
2553 3262 4.155644 CGTTTCTATATACTCCCTCCGTCC 59.844 50.000 0.00 0.00 0.00 4.79
2554 3263 4.313020 TTCTATATACTCCCTCCGTCCC 57.687 50.000 0.00 0.00 0.00 4.46
2555 3264 3.262842 TCTATATACTCCCTCCGTCCCA 58.737 50.000 0.00 0.00 0.00 4.37
2556 3265 3.659195 TCTATATACTCCCTCCGTCCCAA 59.341 47.826 0.00 0.00 0.00 4.12
2557 3266 2.852714 TATACTCCCTCCGTCCCAAA 57.147 50.000 0.00 0.00 0.00 3.28
2558 3267 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
2559 3268 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
2560 3269 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
2561 3270 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
2562 3271 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
2563 3272 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
2564 3273 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
2565 3274 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
2566 3275 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
2567 3276 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
2568 3277 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
2569 3278 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
2570 3279 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
2571 3280 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
2572 3281 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
2573 3282 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
2574 3283 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
2575 3284 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
2576 3285 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
2577 3286 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
2578 3287 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
2586 3295 8.622157 TCTTGTCTTAGATTTGTCTAGATACGG 58.378 37.037 0.00 0.00 0.00 4.02
2587 3296 8.515695 TTGTCTTAGATTTGTCTAGATACGGA 57.484 34.615 0.00 0.00 0.00 4.69
2588 3297 8.693120 TGTCTTAGATTTGTCTAGATACGGAT 57.307 34.615 0.00 0.00 0.00 4.18
2589 3298 8.568794 TGTCTTAGATTTGTCTAGATACGGATG 58.431 37.037 0.00 0.00 0.00 3.51
2590 3299 8.569641 GTCTTAGATTTGTCTAGATACGGATGT 58.430 37.037 0.00 0.00 0.00 3.06
2591 3300 9.788889 TCTTAGATTTGTCTAGATACGGATGTA 57.211 33.333 0.00 0.00 34.45 2.29
2592 3301 9.828852 CTTAGATTTGTCTAGATACGGATGTAC 57.171 37.037 0.00 0.00 32.26 2.90
2593 3302 9.570468 TTAGATTTGTCTAGATACGGATGTACT 57.430 33.333 0.00 0.00 32.26 2.73
2595 3304 9.001542 AGATTTGTCTAGATACGGATGTACTAC 57.998 37.037 0.00 0.00 32.26 2.73
2596 3305 8.687292 ATTTGTCTAGATACGGATGTACTACA 57.313 34.615 0.00 0.00 32.26 2.74
2597 3306 8.687292 TTTGTCTAGATACGGATGTACTACAT 57.313 34.615 1.01 1.01 42.43 2.29
2610 3319 7.902387 GATGTACTACATCCGTATCTAGACA 57.098 40.000 15.79 0.00 46.99 3.41
2611 3320 8.320396 GATGTACTACATCCGTATCTAGACAA 57.680 38.462 15.79 0.00 46.99 3.18
2612 3321 8.687292 ATGTACTACATCCGTATCTAGACAAA 57.313 34.615 0.00 0.00 32.38 2.83
2613 3322 8.687292 TGTACTACATCCGTATCTAGACAAAT 57.313 34.615 0.00 0.00 0.00 2.32
2614 3323 8.781196 TGTACTACATCCGTATCTAGACAAATC 58.219 37.037 0.00 0.00 0.00 2.17
2615 3324 9.001542 GTACTACATCCGTATCTAGACAAATCT 57.998 37.037 0.00 0.00 39.15 2.40
2617 3326 9.570468 ACTACATCCGTATCTAGACAAATCTAA 57.430 33.333 0.00 0.00 36.98 2.10
2619 3328 8.693120 ACATCCGTATCTAGACAAATCTAAGA 57.307 34.615 0.00 0.00 36.98 2.10
2620 3329 8.569641 ACATCCGTATCTAGACAAATCTAAGAC 58.430 37.037 0.00 0.00 36.98 3.01
2621 3330 8.568794 CATCCGTATCTAGACAAATCTAAGACA 58.431 37.037 0.00 0.00 36.98 3.41
2622 3331 8.515695 TCCGTATCTAGACAAATCTAAGACAA 57.484 34.615 0.00 0.00 36.98 3.18
2623 3332 8.622157 TCCGTATCTAGACAAATCTAAGACAAG 58.378 37.037 0.00 0.00 36.98 3.16
2624 3333 8.622157 CCGTATCTAGACAAATCTAAGACAAGA 58.378 37.037 0.00 0.00 36.98 3.02
2632 3341 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
2633 3342 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
2634 3343 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
2635 3344 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
2636 3345 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
2637 3346 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
2638 3347 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
2639 3348 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
2640 3349 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
2641 3350 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
2642 3351 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
2661 3370 9.281371 GGAGGGAGTACCAAATACAATATAAAC 57.719 37.037 0.00 0.00 43.89 2.01
3020 3731 7.671302 TCAGATTACCATATTGGCTACTCTTC 58.329 38.462 0.00 0.00 42.67 2.87
3031 3742 4.389374 TGGCTACTCTTCCAAACAGAAAG 58.611 43.478 0.00 0.00 0.00 2.62
3050 3761 7.093814 ACAGAAAGCATTGGCATTAGTATTTCA 60.094 33.333 0.00 0.00 44.61 2.69
3059 3770 8.718102 TTGGCATTAGTATTTCACTTCTAGTC 57.282 34.615 0.00 0.00 38.80 2.59
3137 3848 1.239347 GTCTGGGGCAAAGAAGACAC 58.761 55.000 0.00 0.00 39.09 3.67
3157 3868 7.096551 AGACACTTAATGCAAAAACTGTGTTT 58.903 30.769 12.37 0.00 37.50 2.83
3249 3961 6.237835 GCTGCTTTGTTTACTTCAGTTTTTCC 60.238 38.462 0.00 0.00 0.00 3.13
3266 3978 0.337773 TCCTCTGACCTCCTCATGCT 59.662 55.000 0.00 0.00 0.00 3.79
3302 4014 7.867305 TTGGTATTTTACTGAAGTTGTGTCA 57.133 32.000 0.00 0.00 0.00 3.58
3329 4041 5.770162 TCCTTCTTTTCTCATTTTGACTCCC 59.230 40.000 0.00 0.00 0.00 4.30
3364 4076 2.285834 GCATCAAAGCTGACCGTAATCG 60.286 50.000 0.00 0.00 33.30 3.34
3858 4576 1.053424 ACCTGGACGGTCTAAAGCAA 58.947 50.000 8.23 0.00 44.93 3.91
3966 5060 7.279615 TGTTTACTACTGTATATGGCATTGCT 58.720 34.615 4.78 0.00 0.00 3.91
4005 5099 2.517959 AGCAACTGCAGCATTTTCCTA 58.482 42.857 15.27 0.00 45.16 2.94
4078 5173 4.510038 AAGTCATTGTGAATGTTCTGCC 57.490 40.909 0.00 0.00 39.87 4.85
4189 5284 6.714810 TCATTCAGTACATACCAAGCACTTTT 59.285 34.615 0.00 0.00 0.00 2.27
4431 5528 1.005867 CCAGTGGCGCAAAAGCAAT 60.006 52.632 10.83 0.00 39.27 3.56
4510 5607 2.858745 ACCATTTCAACTACAGCCGTT 58.141 42.857 0.00 0.00 0.00 4.44
4518 5615 5.365403 TCAACTACAGCCGTTAATTTTGG 57.635 39.130 0.00 0.00 0.00 3.28
4536 5633 4.864704 TTGGGGAAGCAAGTGTTTTATC 57.135 40.909 0.00 0.00 0.00 1.75
4674 5771 4.516321 ACAATTTTGGAAATTTCAGCTGCC 59.484 37.500 19.49 3.60 0.00 4.85
4721 5818 6.531503 TCTAAGCTTGAAGTAGCACATAGT 57.468 37.500 9.86 0.00 43.68 2.12
4722 5819 6.936279 TCTAAGCTTGAAGTAGCACATAGTT 58.064 36.000 9.86 0.00 43.68 2.24
4732 5829 9.062524 TGAAGTAGCACATAGTTAATTTGTTGT 57.937 29.630 0.00 0.00 0.00 3.32
4899 6002 4.901250 TCATAACTATGCCTCAGATGACCA 59.099 41.667 0.00 0.00 33.76 4.02
4992 6095 0.313672 GATGCAAAAACCGGCAGTGA 59.686 50.000 0.00 0.00 44.24 3.41
5032 6135 2.009774 GCAGTACCTTCATCGCACAAT 58.990 47.619 0.00 0.00 0.00 2.71
5070 6173 3.743521 TCACACAAGAATCAAGTGGGAG 58.256 45.455 6.04 0.00 40.49 4.30
5101 6204 0.106708 TGTCAAGCTCAAACGGCTCT 59.893 50.000 0.00 0.00 39.30 4.09
5187 6290 0.463295 CATCCTCAGGACGCAGCAAT 60.463 55.000 0.00 0.00 32.98 3.56
5206 6309 2.268920 CTGCATGGCACCTACGGT 59.731 61.111 0.00 0.00 35.62 4.83
5368 6471 2.178521 GTTTCGCTCGAGCTCGGA 59.821 61.111 33.98 21.35 40.29 4.55
5431 6534 1.000896 CGGGGCAAAGATCCAGGTT 60.001 57.895 0.00 0.00 0.00 3.50
5522 6625 1.599047 CTGAGGCAGTACCACCCAG 59.401 63.158 0.00 2.96 43.14 4.45
5572 6675 1.128188 ACTTCCTCCTGGAGCCGTTT 61.128 55.000 18.51 0.00 44.24 3.60
5752 6855 7.496529 TGAGTTTGTTTCTTCTGGAATACTG 57.503 36.000 0.00 0.00 33.53 2.74
5757 6860 7.496529 TTGTTTCTTCTGGAATACTGTGAAG 57.503 36.000 0.00 0.00 36.44 3.02
5834 6938 9.900264 GTTGTGTGAATTTTATTGTTTTCAGAC 57.100 29.630 5.22 5.22 40.68 3.51
5867 6973 6.971756 CCACGATGTGCATATATGTTGAAAAA 59.028 34.615 14.14 0.00 31.34 1.94
5872 6978 7.758613 TGTGCATATATGTTGAAAAATGCTG 57.241 32.000 14.14 0.00 40.22 4.41
6117 7223 4.993905 AGTTGATCAATGTGCACATCATG 58.006 39.130 31.45 25.52 35.10 3.07
6119 7225 4.625972 TGATCAATGTGCACATCATGTC 57.374 40.909 31.45 24.07 35.10 3.06
6153 7263 6.091986 TGACCACAAATCAAGCAAAAGAAAAC 59.908 34.615 0.00 0.00 0.00 2.43
6262 7375 3.576118 CCCATGTGTTGTAATTGTTCCCA 59.424 43.478 0.00 0.00 0.00 4.37
6305 7436 5.386323 GCGAAATGAATAAAATCCGCATTCG 60.386 40.000 0.00 0.00 40.88 3.34
6315 7446 1.946745 TCCGCATTCGCAATCATACA 58.053 45.000 0.00 0.00 38.40 2.29
6351 7482 7.582667 TTTAAACTTCAGCTTTTCTAAGGCT 57.417 32.000 0.00 0.00 31.76 4.58
6352 7483 8.685838 TTTAAACTTCAGCTTTTCTAAGGCTA 57.314 30.769 0.00 0.00 31.76 3.93
6353 7484 6.809630 AAACTTCAGCTTTTCTAAGGCTAG 57.190 37.500 0.00 0.00 31.76 3.42
6396 7528 4.022849 CCACAAGGACTCCATTCTTTTCAC 60.023 45.833 0.00 0.00 36.89 3.18
6405 7537 5.015178 ACTCCATTCTTTTCACCCTGGATTA 59.985 40.000 0.00 0.00 32.66 1.75
6468 7603 9.811995 TGACATATAAGAACTGTAACCATGTAC 57.188 33.333 0.00 0.00 0.00 2.90
6482 7619 1.596260 CATGTACGCCATTGCTCTCAG 59.404 52.381 0.00 0.00 34.43 3.35
6483 7620 0.740868 TGTACGCCATTGCTCTCAGC 60.741 55.000 0.00 0.00 42.82 4.26
6526 7663 5.470845 GAGAACCATAACCATGTTTCTCG 57.529 43.478 8.53 0.00 45.20 4.04
6535 7672 3.214328 ACCATGTTTCTCGTTGCTCTTT 58.786 40.909 0.00 0.00 0.00 2.52
6607 7745 6.375736 TCCAAACTAACAACAATGAGAACACA 59.624 34.615 0.00 0.00 0.00 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 8.990203 ACATGATATTATCCTACATCAGCAGAT 58.010 33.333 0.00 0.00 31.35 2.90
7 8 8.371571 ACATGATATTATCCTACATCAGCAGA 57.628 34.615 0.00 0.00 31.35 4.26
18 19 9.331466 ACCTCACATCTAACATGATATTATCCT 57.669 33.333 0.00 0.00 0.00 3.24
27 28 9.367160 TGAGATAATACCTCACATCTAACATGA 57.633 33.333 0.00 0.00 35.89 3.07
54 55 6.820656 GGGCCTGTCTATATCACATTTAGATG 59.179 42.308 0.84 0.00 39.25 2.90
55 56 6.501805 TGGGCCTGTCTATATCACATTTAGAT 59.498 38.462 4.53 0.00 0.00 1.98
56 57 5.843969 TGGGCCTGTCTATATCACATTTAGA 59.156 40.000 4.53 0.00 0.00 2.10
57 58 6.114187 TGGGCCTGTCTATATCACATTTAG 57.886 41.667 4.53 0.00 0.00 1.85
58 59 6.702449 ATGGGCCTGTCTATATCACATTTA 57.298 37.500 4.53 0.00 0.00 1.40
59 60 5.589367 ATGGGCCTGTCTATATCACATTT 57.411 39.130 4.53 0.00 0.00 2.32
60 61 5.589367 AATGGGCCTGTCTATATCACATT 57.411 39.130 4.53 0.00 0.00 2.71
61 62 6.702449 TTAATGGGCCTGTCTATATCACAT 57.298 37.500 4.53 0.00 0.00 3.21
62 63 6.508030 TTTAATGGGCCTGTCTATATCACA 57.492 37.500 4.53 0.00 0.00 3.58
63 64 8.947115 GTAATTTAATGGGCCTGTCTATATCAC 58.053 37.037 4.53 0.00 0.00 3.06
64 65 7.822334 CGTAATTTAATGGGCCTGTCTATATCA 59.178 37.037 4.53 0.00 0.00 2.15
65 66 7.280205 CCGTAATTTAATGGGCCTGTCTATATC 59.720 40.741 4.53 0.00 0.00 1.63
66 67 7.110155 CCGTAATTTAATGGGCCTGTCTATAT 58.890 38.462 4.53 0.00 0.00 0.86
67 68 6.469410 CCGTAATTTAATGGGCCTGTCTATA 58.531 40.000 4.53 0.00 0.00 1.31
68 69 5.313712 CCGTAATTTAATGGGCCTGTCTAT 58.686 41.667 4.53 0.00 0.00 1.98
76 77 2.560981 CCATCCCCGTAATTTAATGGGC 59.439 50.000 8.78 0.00 43.49 5.36
108 109 3.096852 GGTTTGGAATGGACCTTAAGGG 58.903 50.000 25.31 7.85 40.27 3.95
111 112 3.791953 TCGGTTTGGAATGGACCTTAA 57.208 42.857 0.00 0.00 0.00 1.85
112 113 3.073356 ACTTCGGTTTGGAATGGACCTTA 59.927 43.478 0.00 0.00 0.00 2.69
113 114 2.158519 ACTTCGGTTTGGAATGGACCTT 60.159 45.455 0.00 0.00 0.00 3.50
114 115 1.423921 ACTTCGGTTTGGAATGGACCT 59.576 47.619 0.00 0.00 0.00 3.85
115 116 1.905637 ACTTCGGTTTGGAATGGACC 58.094 50.000 0.00 0.00 0.00 4.46
125 126 2.223947 GGCATGAACCAAACTTCGGTTT 60.224 45.455 0.00 0.00 46.80 3.27
129 130 1.068333 CCAGGCATGAACCAAACTTCG 60.068 52.381 0.00 0.00 0.00 3.79
163 164 1.804326 ACCGCGATTTCCGTTCTCG 60.804 57.895 8.23 0.00 41.15 4.04
171 172 1.062525 GCATCCACACCGCGATTTC 59.937 57.895 8.23 0.00 0.00 2.17
220 221 2.893637 AGCTCGTATGGTTGCAGTTAG 58.106 47.619 0.00 0.00 0.00 2.34
224 225 2.586258 ACTAGCTCGTATGGTTGCAG 57.414 50.000 0.00 0.00 0.00 4.41
225 226 2.418197 GGAACTAGCTCGTATGGTTGCA 60.418 50.000 0.00 0.00 31.31 4.08
525 850 5.759506 AACGATGTGATCTAGGAGTAGTG 57.240 43.478 0.00 0.00 0.00 2.74
728 1061 6.325596 GGGATTCTTTTCTGAGAAAAATCGG 58.674 40.000 19.62 9.48 38.98 4.18
915 1271 1.134098 CCCGGCTGCATAATATAGGGG 60.134 57.143 0.50 0.00 34.19 4.79
1190 1561 4.687215 TGAGGTGCTGCTCGTGGC 62.687 66.667 0.00 0.00 42.22 5.01
1688 2065 2.270205 CTCGCCCACATCTTGGCT 59.730 61.111 0.00 0.00 45.37 4.75
1751 2128 0.391228 TCTGGCAGTCGTTTAGCACA 59.609 50.000 15.27 0.00 0.00 4.57
1896 2273 5.125100 ACACAATGATCCACATGTTGTTC 57.875 39.130 0.00 0.00 39.39 3.18
1923 2303 2.967599 TCACGGAATCCAGATCACAG 57.032 50.000 0.00 0.00 0.00 3.66
1948 2328 1.461127 GAATCACGCAGAACACAGGAC 59.539 52.381 0.00 0.00 0.00 3.85
1952 2332 8.710835 TTTATTATAGAATCACGCAGAACACA 57.289 30.769 0.00 0.00 0.00 3.72
1970 2363 6.489675 CAGACGCAGCAAGACAATTTATTAT 58.510 36.000 0.00 0.00 0.00 1.28
2003 2398 3.433598 GCCCTTGCATAATCTACAGACCA 60.434 47.826 0.00 0.00 37.47 4.02
2005 2400 4.078639 AGCCCTTGCATAATCTACAGAC 57.921 45.455 0.00 0.00 41.13 3.51
2007 2402 4.712476 AGAAGCCCTTGCATAATCTACAG 58.288 43.478 0.00 0.00 41.13 2.74
2030 2425 2.623416 TCCAGCCACTGTATACTGATCG 59.377 50.000 15.84 4.66 31.67 3.69
2275 2670 5.703130 AGAAATAAGCAACTCTGAACTCCAC 59.297 40.000 0.00 0.00 0.00 4.02
2423 2818 4.461405 GCATTACGTGATGATGCTGAATC 58.539 43.478 23.11 0.00 44.85 2.52
2540 3249 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
2541 3250 1.004394 GAATTTTGGGACGGAGGGAGT 59.996 52.381 0.00 0.00 0.00 3.85
2542 3251 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
2543 3252 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
2544 3253 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
2545 3254 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
2546 3255 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
2547 3256 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
2548 3257 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
2549 3258 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
2550 3259 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
2551 3260 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
2552 3261 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
2560 3269 8.622157 CCGTATCTAGACAAATCTAAGACAAGA 58.378 37.037 0.00 0.00 36.98 3.02
2561 3270 8.622157 TCCGTATCTAGACAAATCTAAGACAAG 58.378 37.037 0.00 0.00 36.98 3.16
2562 3271 8.515695 TCCGTATCTAGACAAATCTAAGACAA 57.484 34.615 0.00 0.00 36.98 3.18
2563 3272 8.568794 CATCCGTATCTAGACAAATCTAAGACA 58.431 37.037 0.00 0.00 36.98 3.41
2564 3273 8.569641 ACATCCGTATCTAGACAAATCTAAGAC 58.430 37.037 0.00 0.00 36.98 3.01
2565 3274 8.693120 ACATCCGTATCTAGACAAATCTAAGA 57.307 34.615 0.00 0.00 36.98 2.10
2566 3275 9.828852 GTACATCCGTATCTAGACAAATCTAAG 57.171 37.037 0.00 0.00 36.98 2.18
2567 3276 9.570468 AGTACATCCGTATCTAGACAAATCTAA 57.430 33.333 0.00 0.00 36.98 2.10
2569 3278 9.001542 GTAGTACATCCGTATCTAGACAAATCT 57.998 37.037 0.00 0.00 39.15 2.40
2570 3279 8.781196 TGTAGTACATCCGTATCTAGACAAATC 58.219 37.037 0.00 0.00 0.00 2.17
2571 3280 8.687292 TGTAGTACATCCGTATCTAGACAAAT 57.313 34.615 0.00 0.00 0.00 2.32
2572 3281 8.687292 ATGTAGTACATCCGTATCTAGACAAA 57.313 34.615 10.10 0.00 32.38 2.83
2573 3282 8.320396 GATGTAGTACATCCGTATCTAGACAA 57.680 38.462 26.53 0.00 46.99 3.18
2574 3283 7.902387 GATGTAGTACATCCGTATCTAGACA 57.098 40.000 26.53 0.00 46.99 3.41
2587 3296 8.687292 TTTGTCTAGATACGGATGTAGTACAT 57.313 34.615 15.73 15.73 42.43 2.29
2588 3297 8.687292 ATTTGTCTAGATACGGATGTAGTACA 57.313 34.615 11.34 5.24 32.08 2.90
2589 3298 9.001542 AGATTTGTCTAGATACGGATGTAGTAC 57.998 37.037 11.34 8.92 32.08 2.73
2591 3300 9.570468 TTAGATTTGTCTAGATACGGATGTAGT 57.430 33.333 11.34 0.00 32.08 2.73
2593 3302 9.788889 TCTTAGATTTGTCTAGATACGGATGTA 57.211 33.333 0.00 0.00 34.45 2.29
2594 3303 8.569641 GTCTTAGATTTGTCTAGATACGGATGT 58.430 37.037 0.00 0.00 0.00 3.06
2595 3304 8.568794 TGTCTTAGATTTGTCTAGATACGGATG 58.431 37.037 0.00 0.00 0.00 3.51
2596 3305 8.693120 TGTCTTAGATTTGTCTAGATACGGAT 57.307 34.615 0.00 0.00 0.00 4.18
2597 3306 8.515695 TTGTCTTAGATTTGTCTAGATACGGA 57.484 34.615 0.00 0.00 0.00 4.69
2598 3307 8.622157 TCTTGTCTTAGATTTGTCTAGATACGG 58.378 37.037 0.00 0.00 0.00 4.02
2606 3315 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
2607 3316 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
2608 3317 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
2609 3318 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
2610 3319 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
2611 3320 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
2612 3321 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
2613 3322 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
2614 3323 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
2615 3324 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
2616 3325 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
2617 3326 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
2618 3327 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
2619 3328 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
2620 3329 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
2621 3330 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
2622 3331 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
2623 3332 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
2624 3333 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
2625 3334 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
2626 3335 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
2627 3336 0.906282 GGTACTCCCTCCGTCCCAAA 60.906 60.000 0.00 0.00 0.00 3.28
2628 3337 1.305549 GGTACTCCCTCCGTCCCAA 60.306 63.158 0.00 0.00 0.00 4.12
2629 3338 2.096707 TTGGTACTCCCTCCGTCCCA 62.097 60.000 0.00 0.00 0.00 4.37
2630 3339 0.906282 TTTGGTACTCCCTCCGTCCC 60.906 60.000 0.00 0.00 0.00 4.46
2631 3340 1.201424 ATTTGGTACTCCCTCCGTCC 58.799 55.000 0.00 0.00 0.00 4.79
2632 3341 2.762327 TGTATTTGGTACTCCCTCCGTC 59.238 50.000 0.00 0.00 34.27 4.79
2633 3342 2.823959 TGTATTTGGTACTCCCTCCGT 58.176 47.619 0.00 0.00 34.27 4.69
2634 3343 3.899052 TTGTATTTGGTACTCCCTCCG 57.101 47.619 0.00 0.00 34.27 4.63
2635 3344 9.281371 GTTTATATTGTATTTGGTACTCCCTCC 57.719 37.037 0.00 0.00 34.27 4.30
2661 3370 8.331022 GCACATTCAATTGTAGTAGTGACATAG 58.669 37.037 16.96 0.00 0.00 2.23
3020 3731 2.529780 TGCCAATGCTTTCTGTTTGG 57.470 45.000 0.00 0.00 41.26 3.28
3031 3742 6.799512 AGAAGTGAAATACTAATGCCAATGC 58.200 36.000 0.00 0.00 39.18 3.56
3050 3761 4.528596 TGCTGAAAAGCCTAGACTAGAAGT 59.471 41.667 11.27 0.00 0.00 3.01
3059 3770 5.841957 ACCAATATTGCTGAAAAGCCTAG 57.158 39.130 10.11 0.00 0.00 3.02
3137 3848 7.904461 CCAAGAAAACACAGTTTTTGCATTAAG 59.096 33.333 9.00 0.00 0.00 1.85
3157 3868 4.321601 CCGCACCAAAAATGATACCAAGAA 60.322 41.667 0.00 0.00 0.00 2.52
3249 3961 1.482954 TCAGCATGAGGAGGTCAGAG 58.517 55.000 0.00 0.00 42.56 3.35
3266 3978 9.513906 TCAGTAAAATACCAATCACAATCTTCA 57.486 29.630 0.00 0.00 0.00 3.02
3302 4014 7.013750 GGAGTCAAAATGAGAAAAGAAGGAAGT 59.986 37.037 0.00 0.00 0.00 3.01
3329 4041 0.879090 TGATGCAGCTTCACTTGCAG 59.121 50.000 2.53 0.00 36.37 4.41
3364 4076 5.695816 TGCAATTTGCTGTTTCAGGAATTAC 59.304 36.000 21.19 0.00 45.31 1.89
3858 4576 4.729868 GTTCCCCAACCATGATAGCTTAT 58.270 43.478 0.00 0.00 0.00 1.73
3925 4643 4.527038 AGTAAACAGTACTCAGCAGGCTTA 59.473 41.667 0.00 0.00 0.00 3.09
3966 5060 7.760794 CAGTTGCTTGATTTTAATATGAAGGCA 59.239 33.333 7.10 3.83 0.00 4.75
4022 5116 6.481434 ACTACAACCTTCACAACTTAGAGT 57.519 37.500 0.00 0.00 0.00 3.24
4061 5156 3.430895 GCAAAGGCAGAACATTCACAATG 59.569 43.478 0.00 0.00 41.47 2.82
4078 5173 5.738208 GGATTCTATCCCTGCAAATGCAAAG 60.738 44.000 9.65 3.96 45.21 2.77
4189 5284 1.497286 ACCCCAGCTGTTTTCCAGTTA 59.503 47.619 13.81 0.00 43.55 2.24
4431 5528 9.709495 CTGATCCCAAATCTTTGTCATTTAAAA 57.291 29.630 0.00 0.00 36.45 1.52
4510 5607 5.622346 AAACACTTGCTTCCCCAAAATTA 57.378 34.783 0.00 0.00 0.00 1.40
4518 5615 5.649831 AGATCAGATAAAACACTTGCTTCCC 59.350 40.000 0.00 0.00 0.00 3.97
4536 5633 2.947652 CCTGCCCACACAATAAGATCAG 59.052 50.000 0.00 0.00 0.00 2.90
4669 5766 0.179189 GCATATATTTCGGCGGCAGC 60.179 55.000 10.53 0.00 44.18 5.25
4674 5771 8.929746 AGATATATCAATGCATATATTTCGGCG 58.070 33.333 15.08 0.00 33.70 6.46
4732 5829 9.247126 CAAATTATTGTGTCTGAATTGTGAACA 57.753 29.630 0.00 0.00 0.00 3.18
4874 5977 5.698545 GGTCATCTGAGGCATAGTTATGAAC 59.301 44.000 3.38 0.00 35.75 3.18
4899 6002 1.342819 GAAGAGATGCATACTCCGGCT 59.657 52.381 17.31 2.68 35.27 5.52
4992 6095 3.244665 TGCAGTGATCCAGTCTGAAACAT 60.245 43.478 0.00 0.00 0.00 2.71
5032 6135 2.104622 TGTGAAGGTCATCAGCTGTGAA 59.895 45.455 14.67 0.00 35.88 3.18
5101 6204 0.874390 GCCGTTCTTGCATTGTCAGA 59.126 50.000 0.00 0.00 0.00 3.27
5206 6309 0.550914 AGGTGTCTTTCAGGGTTGCA 59.449 50.000 0.00 0.00 0.00 4.08
5210 6313 1.417890 CACAGAGGTGTCTTTCAGGGT 59.582 52.381 0.00 0.00 40.24 4.34
5273 6376 1.227853 GTGCGGACAAGGTGAGGTT 60.228 57.895 0.63 0.00 0.00 3.50
5368 6471 0.261696 AGAAGCACCCTGGTTTGGTT 59.738 50.000 9.10 9.10 38.31 3.67
5417 6520 1.403323 GCAGCTAACCTGGATCTTTGC 59.597 52.381 0.00 1.01 42.03 3.68
5431 6534 1.970640 TGGACAGAACTCTTGCAGCTA 59.029 47.619 0.00 0.00 0.00 3.32
5522 6625 1.359459 CCCTTGGCGACGAAGCTTAC 61.359 60.000 0.00 0.00 37.29 2.34
5572 6675 1.568504 ATTCGTCCCTCAGGCTGTAA 58.431 50.000 15.27 0.00 0.00 2.41
5834 6938 0.306228 TGCACATCGTGGTTTGTTCG 59.694 50.000 0.00 0.00 33.64 3.95
5867 6973 3.826157 TGCAGTTAACCTTTTAGCAGCAT 59.174 39.130 0.88 0.00 36.46 3.79
5872 6978 5.183140 TGAAGGATGCAGTTAACCTTTTAGC 59.817 40.000 0.88 0.00 41.90 3.09
5926 7032 5.366768 TGCTACTTGCCCTGATTACTTATCT 59.633 40.000 0.00 0.00 42.00 1.98
6117 7223 1.198759 TTGTGGTCAGGCCCCTAGAC 61.199 60.000 0.00 2.55 36.04 2.59
6119 7225 0.625849 ATTTGTGGTCAGGCCCCTAG 59.374 55.000 0.00 0.00 36.04 3.02
6262 7375 1.066605 GCTTGCGCATTCTGATCCAAT 59.933 47.619 12.75 0.00 35.78 3.16
6305 7436 6.630444 AATCAGGATTCAGTGTATGATTGC 57.370 37.500 0.00 0.00 37.89 3.56
6315 7446 6.944862 AGCTGAAGTTTAAATCAGGATTCAGT 59.055 34.615 16.74 7.56 42.49 3.41
6351 7482 6.385649 GGTTGATCACCAGTTGAAAAACTA 57.614 37.500 0.00 0.00 46.42 2.24
6352 7483 5.262588 GGTTGATCACCAGTTGAAAAACT 57.737 39.130 0.00 0.00 46.42 2.66
6381 7513 2.716424 TCCAGGGTGAAAAGAATGGAGT 59.284 45.455 0.00 0.00 33.11 3.85
6405 7537 9.668497 CTGATGATATGTGGATTATGATGAAGT 57.332 33.333 0.00 0.00 0.00 3.01
6482 7619 8.406172 TCTCAAGTTTTAGTTTGAAAACATGC 57.594 30.769 12.74 0.00 46.98 4.06
6484 7621 9.366216 GGTTCTCAAGTTTTAGTTTGAAAACAT 57.634 29.630 12.74 0.16 46.98 2.71
6486 7623 8.751302 TGGTTCTCAAGTTTTAGTTTGAAAAC 57.249 30.769 4.04 4.04 45.60 2.43
6490 7627 8.626526 GGTTATGGTTCTCAAGTTTTAGTTTGA 58.373 33.333 0.00 0.00 32.75 2.69
6491 7628 8.410141 TGGTTATGGTTCTCAAGTTTTAGTTTG 58.590 33.333 0.00 0.00 0.00 2.93
6492 7629 8.528044 TGGTTATGGTTCTCAAGTTTTAGTTT 57.472 30.769 0.00 0.00 0.00 2.66
6526 7663 9.807649 AAATATACATCCAAATCAAAGAGCAAC 57.192 29.630 0.00 0.00 0.00 4.17
6535 7672 6.427853 CCGCTCTCAAATATACATCCAAATCA 59.572 38.462 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.