Multiple sequence alignment - TraesCS5A01G428900

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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 TraesCS5A01G428900 chr5A 100.000 5028 0 0 1 5028 613539046 613544073 0.000000e+00 9286.0
1 TraesCS5A01G428900 chr5D 93.131 3625 180 32 700 4311 491095347 491098915 0.000000e+00 5251.0
2 TraesCS5A01G428900 chr5D 93.880 719 37 5 4310 5028 491098945 491099656 0.000000e+00 1077.0
3 TraesCS5A01G428900 chr5D 82.822 489 39 17 143 607 491094770 491095237 3.650000e-106 396.0
4 TraesCS5A01G428900 chr5B 92.535 3523 177 45 700 4215 605822079 605825522 0.000000e+00 4970.0
5 TraesCS5A01G428900 chr5B 91.472 598 28 6 4315 4912 605825767 605826341 0.000000e+00 800.0
6 TraesCS5A01G428900 chr5B 87.477 535 39 16 89 607 605821452 605821974 4.330000e-165 592.0
7 TraesCS5A01G428900 chr5B 96.296 108 4 0 4914 5021 605826427 605826534 1.440000e-40 178.0
8 TraesCS5A01G428900 chr5B 92.000 50 3 1 4186 4234 605825527 605825576 9.030000e-08 69.4
9 TraesCS5A01G428900 chr6D 82.107 693 109 11 2787 3475 358395810 358396491 3.370000e-161 579.0
10 TraesCS5A01G428900 chr6D 88.889 144 15 1 2571 2714 358394763 358394905 5.170000e-40 176.0
11 TraesCS5A01G428900 chr2B 75.989 1112 216 35 1071 2149 368339437 368338344 1.240000e-145 527.0
12 TraesCS5A01G428900 chr2D 75.725 1104 212 37 1071 2149 291955988 291954916 2.090000e-138 503.0
13 TraesCS5A01G428900 chr2D 94.444 36 2 0 1 36 638389349 638389314 7.030000e-04 56.5
14 TraesCS5A01G428900 chr2A 75.435 1091 220 32 1077 2149 342546421 342545361 2.100000e-133 486.0
15 TraesCS5A01G428900 chr7D 93.750 48 3 0 1 48 77854341 77854388 6.980000e-09 73.1
16 TraesCS5A01G428900 chr7B 91.837 49 4 0 1 49 293987215 293987167 9.030000e-08 69.4
17 TraesCS5A01G428900 chr4D 91.667 48 4 0 1 48 279213615 279213662 3.250000e-07 67.6
18 TraesCS5A01G428900 chr1D 91.667 48 4 0 1 48 219260227 219260274 3.250000e-07 67.6
19 TraesCS5A01G428900 chr7A 89.796 49 5 0 1 49 379925842 379925794 4.200000e-06 63.9
20 TraesCS5A01G428900 chr4B 89.583 48 5 0 1 48 446735049 446735002 1.510000e-05 62.1
21 TraesCS5A01G428900 chr1B 94.595 37 2 0 1 37 319139270 319139234 1.960000e-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 TraesCS5A01G428900 chr5A 613539046 613544073 5027 False 9286.000000 9286 100.000000 1 5028 1 chr5A.!!$F1 5027
1 TraesCS5A01G428900 chr5D 491094770 491099656 4886 False 2241.333333 5251 89.944333 143 5028 3 chr5D.!!$F1 4885
2 TraesCS5A01G428900 chr5B 605821452 605826534 5082 False 1321.880000 4970 91.956000 89 5021 5 chr5B.!!$F1 4932
3 TraesCS5A01G428900 chr6D 358394763 358396491 1728 False 377.500000 579 85.498000 2571 3475 2 chr6D.!!$F1 904
4 TraesCS5A01G428900 chr2B 368338344 368339437 1093 True 527.000000 527 75.989000 1071 2149 1 chr2B.!!$R1 1078
5 TraesCS5A01G428900 chr2D 291954916 291955988 1072 True 503.000000 503 75.725000 1071 2149 1 chr2D.!!$R1 1078
6 TraesCS5A01G428900 chr2A 342545361 342546421 1060 True 486.000000 486 75.435000 1077 2149 1 chr2A.!!$R1 1072

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
630 699 0.035630 AGTCTGGTGCCAGCATCTTC 60.036 55.0 13.12 0.0 43.31 2.87 F
2001 2093 0.037303 ACCTGTCGTCGAACCTCCTA 59.963 55.0 0.00 0.0 0.00 2.94 F
2945 3884 0.100682 ATCTCGACGAATCCACCGTG 59.899 55.0 0.00 0.0 40.67 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2619 2726 1.211703 TCGCCATAAGAATCTTGCCCA 59.788 47.619 5.64 0.0 0.0 5.36 R
3049 3990 0.038166 ACATTCAGGCATTGGACCGT 59.962 50.000 0.00 0.0 0.0 4.83 R
4135 5082 0.460311 CCGTAGTAGTTGGGAGCCTG 59.540 60.000 0.00 0.0 0.0 4.85 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
25 26 8.256611 GACTTGAGACAAAACTTATATGCAGA 57.743 34.615 0.00 0.00 0.00 4.26
26 27 8.034058 ACTTGAGACAAAACTTATATGCAGAC 57.966 34.615 0.00 0.00 0.00 3.51
27 28 7.880195 ACTTGAGACAAAACTTATATGCAGACT 59.120 33.333 0.00 0.00 0.00 3.24
28 29 9.371136 CTTGAGACAAAACTTATATGCAGACTA 57.629 33.333 0.00 0.00 0.00 2.59
29 30 9.890629 TTGAGACAAAACTTATATGCAGACTAT 57.109 29.630 0.00 0.00 0.00 2.12
38 39 8.988064 ACTTATATGCAGACTATAAATGACCG 57.012 34.615 0.00 0.00 0.00 4.79
39 40 8.803235 ACTTATATGCAGACTATAAATGACCGA 58.197 33.333 0.00 0.00 0.00 4.69
40 41 9.639601 CTTATATGCAGACTATAAATGACCGAA 57.360 33.333 0.00 0.00 0.00 4.30
41 42 9.639601 TTATATGCAGACTATAAATGACCGAAG 57.360 33.333 0.00 0.00 0.00 3.79
59 60 5.769484 CGAAGGGAGTATTAGCTTACAGA 57.231 43.478 0.00 0.00 0.00 3.41
60 61 5.764131 CGAAGGGAGTATTAGCTTACAGAG 58.236 45.833 0.00 0.00 0.00 3.35
61 62 5.531659 CGAAGGGAGTATTAGCTTACAGAGA 59.468 44.000 0.00 0.00 0.00 3.10
62 63 6.039493 CGAAGGGAGTATTAGCTTACAGAGAA 59.961 42.308 0.00 0.00 0.00 2.87
63 64 6.969993 AGGGAGTATTAGCTTACAGAGAAG 57.030 41.667 0.00 0.00 0.00 2.85
64 65 6.436890 AGGGAGTATTAGCTTACAGAGAAGT 58.563 40.000 0.00 0.00 0.00 3.01
65 66 7.584532 AGGGAGTATTAGCTTACAGAGAAGTA 58.415 38.462 0.00 0.00 0.00 2.24
66 67 8.060075 AGGGAGTATTAGCTTACAGAGAAGTAA 58.940 37.037 0.00 0.00 33.28 2.24
67 68 8.862085 GGGAGTATTAGCTTACAGAGAAGTAAT 58.138 37.037 0.00 0.00 33.82 1.89
81 82 9.091220 ACAGAGAAGTAATTAGTTTACAGAGGT 57.909 33.333 6.99 0.00 42.30 3.85
93 94 7.242322 AGTTTACAGAGGTAGTAAAAGAGGG 57.758 40.000 0.00 0.00 41.51 4.30
104 105 2.370257 AAAAGAGGGTGGGAGGGGGA 62.370 60.000 0.00 0.00 0.00 4.81
301 303 1.332195 CTCACAGGACACTCACTCCA 58.668 55.000 0.00 0.00 0.00 3.86
322 324 0.762842 TCCACTAGCCACCACAGTGT 60.763 55.000 0.00 0.00 42.88 3.55
325 327 1.618837 CACTAGCCACCACAGTGTACT 59.381 52.381 0.00 0.00 42.88 2.73
337 339 3.717400 CAGTGTACTGTGAGTGTCTGT 57.283 47.619 3.88 0.00 39.09 3.41
339 341 4.537965 CAGTGTACTGTGAGTGTCTGTAC 58.462 47.826 3.88 0.00 39.09 2.90
341 343 3.003068 GTGTACTGTGAGTGTCTGTACGT 59.997 47.826 0.00 0.00 40.52 3.57
342 344 3.628942 TGTACTGTGAGTGTCTGTACGTT 59.371 43.478 0.00 0.00 40.52 3.99
344 346 4.906065 ACTGTGAGTGTCTGTACGTTTA 57.094 40.909 0.00 0.00 0.00 2.01
345 347 4.856664 ACTGTGAGTGTCTGTACGTTTAG 58.143 43.478 0.00 0.00 0.00 1.85
346 348 3.635331 TGTGAGTGTCTGTACGTTTAGC 58.365 45.455 0.00 0.00 0.00 3.09
347 349 2.985139 GTGAGTGTCTGTACGTTTAGCC 59.015 50.000 0.00 0.00 0.00 3.93
348 350 2.624364 TGAGTGTCTGTACGTTTAGCCA 59.376 45.455 0.00 0.00 0.00 4.75
349 351 2.985139 GAGTGTCTGTACGTTTAGCCAC 59.015 50.000 0.00 0.00 0.00 5.01
350 352 2.626743 AGTGTCTGTACGTTTAGCCACT 59.373 45.455 8.91 8.91 0.00 4.00
351 353 2.985139 GTGTCTGTACGTTTAGCCACTC 59.015 50.000 0.00 0.00 0.00 3.51
352 354 2.029649 TGTCTGTACGTTTAGCCACTCC 60.030 50.000 0.00 0.00 0.00 3.85
355 357 1.965643 TGTACGTTTAGCCACTCCACT 59.034 47.619 0.00 0.00 0.00 4.00
361 385 1.103803 TTAGCCACTCCACTAGCTCG 58.896 55.000 0.00 0.00 36.79 5.03
368 392 1.716826 CTCCACTAGCTCGTCGTCCC 61.717 65.000 0.00 0.00 0.00 4.46
380 408 2.819595 CGTCCCGCCCATCACAAG 60.820 66.667 0.00 0.00 0.00 3.16
400 428 0.625849 TTCCCTTGGCCTCTTCCATC 59.374 55.000 3.32 0.00 35.77 3.51
406 434 1.148048 GGCCTCTTCCATCTCTGCC 59.852 63.158 0.00 0.00 0.00 4.85
451 480 7.276953 CGCGAGGTAAAATTCATTTCATTTT 57.723 32.000 0.00 0.00 37.54 1.82
471 500 8.527810 TCATTTTTGTTTAGTTTCCTGTCAAGT 58.472 29.630 0.00 0.00 0.00 3.16
472 501 9.796120 CATTTTTGTTTAGTTTCCTGTCAAGTA 57.204 29.630 0.00 0.00 0.00 2.24
474 503 9.628746 TTTTTGTTTAGTTTCCTGTCAAGTAAC 57.371 29.630 0.00 0.00 0.00 2.50
475 504 6.592798 TGTTTAGTTTCCTGTCAAGTAACG 57.407 37.500 0.00 0.00 0.00 3.18
476 505 6.108015 TGTTTAGTTTCCTGTCAAGTAACGT 58.892 36.000 0.00 0.00 0.00 3.99
527 556 1.060698 GCACGCCGACTCTTGTTTATC 59.939 52.381 0.00 0.00 0.00 1.75
554 583 1.370900 CGCCAGTTGTTGAGCAAGC 60.371 57.895 0.00 0.00 37.83 4.01
560 589 4.142403 GCCAGTTGTTGAGCAAGCATATAA 60.142 41.667 0.00 0.00 37.83 0.98
616 685 5.735922 GCTTCTCTGCTAATGGTCTAGTCTG 60.736 48.000 0.00 0.00 0.00 3.51
630 699 0.035630 AGTCTGGTGCCAGCATCTTC 60.036 55.000 13.12 0.00 43.31 2.87
643 712 1.728971 GCATCTTCGTGACTTGTGAGG 59.271 52.381 0.00 0.00 0.00 3.86
664 733 2.357952 GGACTAATTTGGACGCCATTCC 59.642 50.000 0.00 0.00 31.53 3.01
665 734 3.279434 GACTAATTTGGACGCCATTCCT 58.721 45.455 0.00 0.00 36.51 3.36
667 736 1.094785 AATTTGGACGCCATTCCTCG 58.905 50.000 0.00 0.00 36.51 4.63
673 742 3.257561 CGCCATTCCTCGTCTGCG 61.258 66.667 0.00 0.00 39.92 5.18
676 745 2.456119 CCATTCCTCGTCTGCGCAC 61.456 63.158 5.66 0.00 38.14 5.34
677 746 1.737735 CATTCCTCGTCTGCGCACA 60.738 57.895 5.66 0.00 38.14 4.57
678 747 1.005037 ATTCCTCGTCTGCGCACAA 60.005 52.632 5.66 0.00 38.14 3.33
679 748 1.016130 ATTCCTCGTCTGCGCACAAG 61.016 55.000 5.66 0.00 38.14 3.16
680 749 3.782244 CCTCGTCTGCGCACAAGC 61.782 66.667 5.66 0.00 38.14 4.01
681 750 3.037833 CTCGTCTGCGCACAAGCA 61.038 61.111 5.66 0.00 45.96 3.91
682 751 3.287121 CTCGTCTGCGCACAAGCAC 62.287 63.158 5.66 0.00 42.92 4.40
683 752 3.639008 CGTCTGCGCACAAGCACA 61.639 61.111 5.66 0.00 42.92 4.57
684 753 2.949106 GTCTGCGCACAAGCACAT 59.051 55.556 5.66 0.00 42.92 3.21
685 754 1.283793 GTCTGCGCACAAGCACATT 59.716 52.632 5.66 0.00 42.92 2.71
686 755 1.000233 GTCTGCGCACAAGCACATTG 61.000 55.000 5.66 0.00 42.92 2.82
696 765 3.307339 CAAGCACATTGTTGTTGTTGC 57.693 42.857 0.00 0.00 32.34 4.17
697 766 2.931325 CAAGCACATTGTTGTTGTTGCT 59.069 40.909 0.00 0.00 34.89 3.91
698 767 2.542597 AGCACATTGTTGTTGTTGCTG 58.457 42.857 0.00 0.00 33.37 4.41
735 804 1.665916 CACTCACCAGCACCTGTCG 60.666 63.158 0.00 0.00 0.00 4.35
768 837 3.409856 CGCTTTACATCCAGGCGG 58.590 61.111 0.00 0.00 41.77 6.13
769 838 2.823829 CGCTTTACATCCAGGCGGC 61.824 63.158 0.00 0.00 41.77 6.53
770 839 2.823829 GCTTTACATCCAGGCGGCG 61.824 63.158 0.51 0.51 0.00 6.46
827 897 1.926511 AAAAGCTCCATTCCGCAGCG 61.927 55.000 8.18 8.18 38.26 5.18
919 989 6.477033 GCAGTACACATTCTTAATCTGATCGT 59.523 38.462 0.00 0.00 0.00 3.73
925 995 8.660373 ACACATTCTTAATCTGATCGTCTTTTC 58.340 33.333 0.00 0.00 0.00 2.29
979 1053 0.389948 GGTGTCGCTGAAGGAATCGT 60.390 55.000 0.00 0.00 0.00 3.73
980 1054 0.992802 GTGTCGCTGAAGGAATCGTC 59.007 55.000 0.00 0.00 0.00 4.20
981 1055 0.456142 TGTCGCTGAAGGAATCGTCG 60.456 55.000 0.00 0.00 0.00 5.12
982 1056 0.456312 GTCGCTGAAGGAATCGTCGT 60.456 55.000 0.00 0.00 0.00 4.34
1038 1112 1.833934 CTGCTTGCTGGGGTTGGTT 60.834 57.895 0.00 0.00 0.00 3.67
1047 1121 1.051556 TGGGGTTGGTTTTCTTGGCC 61.052 55.000 0.00 0.00 0.00 5.36
1244 1318 4.700365 CACGCAGCTCCACGTCGA 62.700 66.667 0.00 0.00 41.32 4.20
1296 1382 2.358737 AACTTCTCCCTTGGCGCG 60.359 61.111 0.00 0.00 0.00 6.86
1331 1417 3.465403 CAGGCTCCCCGACCTCAG 61.465 72.222 0.00 0.00 32.56 3.35
1788 1880 4.449391 CGGAACAAGTTCACCGGT 57.551 55.556 0.00 0.00 41.20 5.28
1962 2054 4.329545 GACAAGGTGCCCTGCGGA 62.330 66.667 0.00 0.00 32.13 5.54
2001 2093 0.037303 ACCTGTCGTCGAACCTCCTA 59.963 55.000 0.00 0.00 0.00 2.94
2391 2498 7.009083 CGTATGATCGATCTCTGAATTTCATCC 59.991 40.741 25.02 0.00 0.00 3.51
2477 2584 6.463995 AAAACTCACTAACATTTGCTTCCA 57.536 33.333 0.00 0.00 0.00 3.53
2493 2600 3.622953 GCTTCCATTTTGGCATTTGGGAT 60.623 43.478 10.00 0.00 37.47 3.85
2497 2604 3.307550 CCATTTTGGCATTTGGGATGACA 60.308 43.478 0.00 0.00 34.80 3.58
2661 2768 1.062294 GTACAGCGTCGTCGATCTCTT 59.938 52.381 6.17 0.00 39.71 2.85
2732 2892 6.491394 TGAAATTTTACCACGACTTGTTCTG 58.509 36.000 0.00 0.00 0.00 3.02
2936 3875 3.789756 GCTTTGAATACGATCTCGACGAA 59.210 43.478 6.60 0.00 43.02 3.85
2945 3884 0.100682 ATCTCGACGAATCCACCGTG 59.899 55.000 0.00 0.00 40.67 4.94
3010 3949 0.753262 AGGAGCAGGATTTCGCGTAT 59.247 50.000 5.77 0.24 0.00 3.06
3017 3956 2.670905 CAGGATTTCGCGTATGTTGTCA 59.329 45.455 5.77 0.00 0.00 3.58
3019 3958 2.536928 GGATTTCGCGTATGTTGTCAGC 60.537 50.000 5.77 0.00 0.00 4.26
3030 3969 5.450550 CGTATGTTGTCAGCTCTTATCTCCA 60.451 44.000 0.00 0.00 0.00 3.86
3032 3971 5.426689 TGTTGTCAGCTCTTATCTCCATT 57.573 39.130 0.00 0.00 0.00 3.16
3033 3972 5.809001 TGTTGTCAGCTCTTATCTCCATTT 58.191 37.500 0.00 0.00 0.00 2.32
3060 4001 0.955428 TTGCTCTGACGGTCCAATGC 60.955 55.000 5.55 5.73 0.00 3.56
3075 4016 5.104374 GTCCAATGCCTGAATGTTATGTTG 58.896 41.667 0.00 0.00 0.00 3.33
3077 4018 4.382254 CCAATGCCTGAATGTTATGTTGCT 60.382 41.667 0.00 0.00 0.00 3.91
3081 4022 3.368843 GCCTGAATGTTATGTTGCTTTGC 59.631 43.478 0.00 0.00 0.00 3.68
3093 4034 3.056962 TGTTGCTTTGCTTGAACTGTTCA 60.057 39.130 18.69 18.69 38.04 3.18
3108 4049 6.409234 TGAACTGTTCATTACCAGAAGGAACT 60.409 38.462 18.69 0.00 38.82 3.01
3144 4085 0.474466 CCTGGGGGCAGAGGATATCA 60.474 60.000 4.83 0.00 0.00 2.15
3204 4145 1.974236 GGAGGGATCATACCTGGTCTG 59.026 57.143 0.63 3.82 38.79 3.51
3207 4148 3.456277 GAGGGATCATACCTGGTCTGTTT 59.544 47.826 0.63 0.00 38.79 2.83
3246 4187 5.227569 TCAGCAACATTCTTCTAGACCAA 57.772 39.130 0.00 0.00 0.00 3.67
3276 4217 2.262572 CCAAAATCGGCAGCTACAAC 57.737 50.000 0.00 0.00 0.00 3.32
3282 4223 0.739462 TCGGCAGCTACAACATTCCG 60.739 55.000 0.00 0.00 37.00 4.30
3317 4258 3.274288 CTGCAAAACCTGAGGTAGATCC 58.726 50.000 3.68 0.00 33.12 3.36
3324 4265 1.341531 CCTGAGGTAGATCCGCGAAAT 59.658 52.381 8.23 0.00 41.99 2.17
3343 4284 7.042321 CGCGAAATACTAACTTATGGGATGAAA 60.042 37.037 0.00 0.00 0.00 2.69
3344 4285 8.617809 GCGAAATACTAACTTATGGGATGAAAA 58.382 33.333 0.00 0.00 0.00 2.29
3345 4286 9.931210 CGAAATACTAACTTATGGGATGAAAAC 57.069 33.333 0.00 0.00 0.00 2.43
3360 4301 6.749923 GATGAAAACATCCAGCTACTCTTT 57.250 37.500 0.00 0.00 0.00 2.52
3362 4303 5.376625 TGAAAACATCCAGCTACTCTTTGT 58.623 37.500 0.00 0.00 0.00 2.83
3363 4304 6.530120 TGAAAACATCCAGCTACTCTTTGTA 58.470 36.000 0.00 0.00 0.00 2.41
3364 4305 6.995686 TGAAAACATCCAGCTACTCTTTGTAA 59.004 34.615 0.00 0.00 0.00 2.41
3365 4306 7.173218 TGAAAACATCCAGCTACTCTTTGTAAG 59.827 37.037 0.00 0.00 0.00 2.34
3377 4318 6.340962 ACTCTTTGTAAGGTTTTTATGGCC 57.659 37.500 0.00 0.00 0.00 5.36
3400 4341 3.574284 TTGCTGACCAACAATGTATGC 57.426 42.857 0.00 0.00 0.00 3.14
3402 4343 3.156293 TGCTGACCAACAATGTATGCTT 58.844 40.909 0.00 0.00 0.00 3.91
3403 4344 3.057386 TGCTGACCAACAATGTATGCTTG 60.057 43.478 0.00 0.00 0.00 4.01
3405 4346 4.726416 CTGACCAACAATGTATGCTTGTC 58.274 43.478 0.00 0.00 35.84 3.18
3464 4405 5.307196 ACCAAACTGACAGGTATCTACAAGT 59.693 40.000 7.51 0.00 32.92 3.16
3545 4490 1.269448 TCTTTCCTTGTTCCGCAATGC 59.731 47.619 0.00 0.00 36.36 3.56
3546 4491 1.270550 CTTTCCTTGTTCCGCAATGCT 59.729 47.619 2.94 0.00 36.36 3.79
3577 4522 1.148157 CGATGCTCGGCGACAAGATT 61.148 55.000 4.99 0.00 36.00 2.40
3628 4573 0.538287 AGCTTGTGTCTGGAAAGCCC 60.538 55.000 3.16 0.00 45.94 5.19
3652 4597 6.296605 CCATCACATCCATATATGAGGTGGAA 60.297 42.308 14.54 5.15 46.06 3.53
3706 4651 3.380637 ACCTAGTTGTAGATGGTAGTGCG 59.619 47.826 0.00 0.00 0.00 5.34
3734 4679 4.697352 GCAACACAGATACCTGAATCTTGT 59.303 41.667 0.00 0.00 43.02 3.16
3751 4696 0.818852 TGTTTGTGCTGCAGCTGCTA 60.819 50.000 36.61 23.15 42.66 3.49
3802 4747 3.358076 GAGGAGCTTCGTGGACCCG 62.358 68.421 0.00 0.00 0.00 5.28
3841 4786 4.344968 TGTTCAGAAGAATCACTGAGGACA 59.655 41.667 9.27 9.26 42.72 4.02
4060 5005 0.035458 AGCTGTTTCTCCCGTCCAAG 59.965 55.000 0.00 0.00 0.00 3.61
4112 5059 1.376424 AGCTGCCGGTGATGAGTTG 60.376 57.895 1.90 0.00 0.00 3.16
4131 5078 3.087343 TCCTCCAGGATGTGCAGAA 57.913 52.632 0.00 0.00 39.78 3.02
4135 5082 1.471684 CTCCAGGATGTGCAGAAAAGC 59.528 52.381 0.00 0.00 0.00 3.51
4141 5088 0.886563 ATGTGCAGAAAAGCAGGCTC 59.113 50.000 0.00 0.00 46.69 4.70
4152 5099 1.196012 AGCAGGCTCCCAACTACTAC 58.804 55.000 0.00 0.00 0.00 2.73
4159 5106 2.493278 GCTCCCAACTACTACGGTTGTA 59.507 50.000 2.63 2.63 41.47 2.41
4182 5129 5.537300 TTTCTTCTGTCAGTGTAGAGCTT 57.463 39.130 0.00 0.00 0.00 3.74
4184 5131 5.127693 TCTTCTGTCAGTGTAGAGCTTTC 57.872 43.478 0.00 0.00 0.00 2.62
4199 5182 8.695456 TGTAGAGCTTTCTTTTTCCTTTCAATT 58.305 29.630 0.00 0.00 0.00 2.32
4234 5217 2.690497 TCTACCTGAAGCCTTCATCTCG 59.310 50.000 7.75 0.00 39.30 4.04
4242 5225 0.392998 GCCTTCATCTCGGGAGCAAA 60.393 55.000 0.00 0.00 0.00 3.68
4244 5227 2.485479 GCCTTCATCTCGGGAGCAAATA 60.485 50.000 0.00 0.00 0.00 1.40
4252 5235 5.152623 TCTCGGGAGCAAATATTCCTATG 57.847 43.478 0.00 0.00 33.85 2.23
4311 5302 3.500680 GCATCGTTCCTGTTTCTACCAAA 59.499 43.478 0.00 0.00 0.00 3.28
4312 5303 4.023536 GCATCGTTCCTGTTTCTACCAAAA 60.024 41.667 0.00 0.00 0.00 2.44
4338 5455 6.892658 AGCACAAATACCATTTGTAGAACA 57.107 33.333 14.94 0.00 40.30 3.18
4346 5463 4.532834 ACCATTTGTAGAACACACCAAGT 58.467 39.130 0.00 0.00 36.69 3.16
4431 5548 7.201821 GCTATAACATGCCTTAGTTCACCAAAT 60.202 37.037 0.00 0.00 0.00 2.32
4492 5609 3.860930 GACACAACGGCCATGGGGT 62.861 63.158 15.13 0.00 36.17 4.95
4727 5844 2.009774 GACTGCATAGCAAACCACGAT 58.990 47.619 0.00 0.00 38.41 3.73
4790 5907 0.045008 TAACCCATAGCACCCCAGGA 59.955 55.000 0.00 0.00 0.00 3.86
4808 5925 5.510179 CCCAGGACACTACTTTCGAAGTAAA 60.510 44.000 0.00 0.00 42.99 2.01
4809 5926 6.164176 CCAGGACACTACTTTCGAAGTAAAT 58.836 40.000 0.00 0.00 42.99 1.40
4912 6029 2.802816 CAAGCTGTGTCACTGGTAACTC 59.197 50.000 14.00 0.00 37.61 3.01
4966 6167 7.434013 CAGGTGGTTGTTACACAATAAAAGTTC 59.566 37.037 0.00 0.00 40.59 3.01
4992 6193 2.187239 AGATCTGGATCTGGCCTCAA 57.813 50.000 11.74 0.00 45.77 3.02
5015 6216 3.181466 TGACAGTACTGTGCAACTCATGT 60.181 43.478 32.51 4.37 45.05 3.21
5021 6222 3.748083 ACTGTGCAACTCATGTCAATCT 58.252 40.909 0.00 0.00 38.04 2.40
5023 6224 5.494724 ACTGTGCAACTCATGTCAATCTAT 58.505 37.500 0.00 0.00 38.04 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.171840 GTCTGCATATAAGTTTTGTCTCAAGTC 58.828 37.037 0.00 0.00 0.00 3.01
1 2 7.880195 AGTCTGCATATAAGTTTTGTCTCAAGT 59.120 33.333 0.00 0.00 0.00 3.16
2 3 8.261492 AGTCTGCATATAAGTTTTGTCTCAAG 57.739 34.615 0.00 0.00 0.00 3.02
3 4 9.890629 ATAGTCTGCATATAAGTTTTGTCTCAA 57.109 29.630 0.00 0.00 0.00 3.02
12 13 9.424319 CGGTCATTTATAGTCTGCATATAAGTT 57.576 33.333 0.00 0.00 0.00 2.66
13 14 8.803235 TCGGTCATTTATAGTCTGCATATAAGT 58.197 33.333 0.00 0.00 0.00 2.24
14 15 9.639601 TTCGGTCATTTATAGTCTGCATATAAG 57.360 33.333 0.00 0.00 0.00 1.73
15 16 9.639601 CTTCGGTCATTTATAGTCTGCATATAA 57.360 33.333 0.00 0.00 0.00 0.98
16 17 8.251026 CCTTCGGTCATTTATAGTCTGCATATA 58.749 37.037 0.00 0.00 0.00 0.86
17 18 7.099764 CCTTCGGTCATTTATAGTCTGCATAT 58.900 38.462 0.00 0.00 0.00 1.78
18 19 6.455647 CCTTCGGTCATTTATAGTCTGCATA 58.544 40.000 0.00 0.00 0.00 3.14
19 20 5.300752 CCTTCGGTCATTTATAGTCTGCAT 58.699 41.667 0.00 0.00 0.00 3.96
20 21 4.442893 CCCTTCGGTCATTTATAGTCTGCA 60.443 45.833 0.00 0.00 0.00 4.41
21 22 4.058817 CCCTTCGGTCATTTATAGTCTGC 58.941 47.826 0.00 0.00 0.00 4.26
22 23 5.069251 ACTCCCTTCGGTCATTTATAGTCTG 59.931 44.000 0.00 0.00 0.00 3.51
23 24 5.209659 ACTCCCTTCGGTCATTTATAGTCT 58.790 41.667 0.00 0.00 0.00 3.24
24 25 5.532664 ACTCCCTTCGGTCATTTATAGTC 57.467 43.478 0.00 0.00 0.00 2.59
25 26 7.613551 AATACTCCCTTCGGTCATTTATAGT 57.386 36.000 0.00 0.00 0.00 2.12
26 27 7.760340 GCTAATACTCCCTTCGGTCATTTATAG 59.240 40.741 0.00 0.00 0.00 1.31
27 28 7.453752 AGCTAATACTCCCTTCGGTCATTTATA 59.546 37.037 0.00 0.00 0.00 0.98
28 29 6.270231 AGCTAATACTCCCTTCGGTCATTTAT 59.730 38.462 0.00 0.00 0.00 1.40
29 30 5.601313 AGCTAATACTCCCTTCGGTCATTTA 59.399 40.000 0.00 0.00 0.00 1.40
30 31 4.409247 AGCTAATACTCCCTTCGGTCATTT 59.591 41.667 0.00 0.00 0.00 2.32
31 32 3.967987 AGCTAATACTCCCTTCGGTCATT 59.032 43.478 0.00 0.00 0.00 2.57
32 33 3.577919 AGCTAATACTCCCTTCGGTCAT 58.422 45.455 0.00 0.00 0.00 3.06
33 34 3.028094 AGCTAATACTCCCTTCGGTCA 57.972 47.619 0.00 0.00 0.00 4.02
34 35 4.340381 TGTAAGCTAATACTCCCTTCGGTC 59.660 45.833 0.00 0.00 0.00 4.79
35 36 4.284178 TGTAAGCTAATACTCCCTTCGGT 58.716 43.478 0.00 0.00 0.00 4.69
36 37 4.583489 TCTGTAAGCTAATACTCCCTTCGG 59.417 45.833 0.00 0.00 0.00 4.30
37 38 5.531659 TCTCTGTAAGCTAATACTCCCTTCG 59.468 44.000 0.00 0.00 0.00 3.79
38 39 6.963083 TCTCTGTAAGCTAATACTCCCTTC 57.037 41.667 0.00 0.00 0.00 3.46
39 40 6.898521 ACTTCTCTGTAAGCTAATACTCCCTT 59.101 38.462 0.00 0.00 0.00 3.95
40 41 6.436890 ACTTCTCTGTAAGCTAATACTCCCT 58.563 40.000 0.00 0.00 0.00 4.20
41 42 6.718522 ACTTCTCTGTAAGCTAATACTCCC 57.281 41.667 0.00 0.00 0.00 4.30
55 56 9.091220 ACCTCTGTAAACTAATTACTTCTCTGT 57.909 33.333 0.69 0.00 43.60 3.41
67 68 8.810041 CCCTCTTTTACTACCTCTGTAAACTAA 58.190 37.037 0.00 0.00 38.91 2.24
68 69 7.952368 ACCCTCTTTTACTACCTCTGTAAACTA 59.048 37.037 0.00 0.00 38.91 2.24
69 70 6.786461 ACCCTCTTTTACTACCTCTGTAAACT 59.214 38.462 0.00 0.00 38.91 2.66
70 71 6.872547 CACCCTCTTTTACTACCTCTGTAAAC 59.127 42.308 0.00 0.00 38.91 2.01
71 72 6.013984 CCACCCTCTTTTACTACCTCTGTAAA 60.014 42.308 0.00 0.00 37.88 2.01
72 73 5.482878 CCACCCTCTTTTACTACCTCTGTAA 59.517 44.000 0.00 0.00 0.00 2.41
73 74 5.021458 CCACCCTCTTTTACTACCTCTGTA 58.979 45.833 0.00 0.00 0.00 2.74
74 75 3.838903 CCACCCTCTTTTACTACCTCTGT 59.161 47.826 0.00 0.00 0.00 3.41
75 76 3.197983 CCCACCCTCTTTTACTACCTCTG 59.802 52.174 0.00 0.00 0.00 3.35
76 77 3.078612 TCCCACCCTCTTTTACTACCTCT 59.921 47.826 0.00 0.00 0.00 3.69
77 78 3.447950 TCCCACCCTCTTTTACTACCTC 58.552 50.000 0.00 0.00 0.00 3.85
78 79 3.451890 CTCCCACCCTCTTTTACTACCT 58.548 50.000 0.00 0.00 0.00 3.08
79 80 2.504585 CCTCCCACCCTCTTTTACTACC 59.495 54.545 0.00 0.00 0.00 3.18
80 81 2.504585 CCCTCCCACCCTCTTTTACTAC 59.495 54.545 0.00 0.00 0.00 2.73
81 82 2.563596 CCCCTCCCACCCTCTTTTACTA 60.564 54.545 0.00 0.00 0.00 1.82
82 83 1.670059 CCCTCCCACCCTCTTTTACT 58.330 55.000 0.00 0.00 0.00 2.24
83 84 0.624254 CCCCTCCCACCCTCTTTTAC 59.376 60.000 0.00 0.00 0.00 2.01
84 85 0.551624 CCCCCTCCCACCCTCTTTTA 60.552 60.000 0.00 0.00 0.00 1.52
85 86 1.857348 CCCCCTCCCACCCTCTTTT 60.857 63.158 0.00 0.00 0.00 2.27
86 87 2.204306 CCCCCTCCCACCCTCTTT 60.204 66.667 0.00 0.00 0.00 2.52
87 88 2.370257 TTTCCCCCTCCCACCCTCTT 62.370 60.000 0.00 0.00 0.00 2.85
92 93 1.076727 CACTTTTCCCCCTCCCACC 59.923 63.158 0.00 0.00 0.00 4.61
93 94 1.076727 CCACTTTTCCCCCTCCCAC 59.923 63.158 0.00 0.00 0.00 4.61
104 105 1.347707 TCAGTCCGATGCTCCACTTTT 59.652 47.619 0.00 0.00 0.00 2.27
128 129 3.414700 GGCAACGGACGACAGCAG 61.415 66.667 0.00 0.00 0.00 4.24
164 165 3.178540 AACGGACAGGTGGTGCCTC 62.179 63.158 0.00 0.00 46.96 4.70
240 242 3.899981 TTGTAGCTGCTGCGGTGGG 62.900 63.158 13.43 0.00 45.42 4.61
301 303 0.471971 ACTGTGGTGGCTAGTGGAGT 60.472 55.000 0.00 0.00 0.00 3.85
322 324 4.906065 AAACGTACAGACACTCACAGTA 57.094 40.909 0.00 0.00 0.00 2.74
325 327 3.551454 GGCTAAACGTACAGACACTCACA 60.551 47.826 0.00 0.00 0.00 3.58
326 328 2.985139 GGCTAAACGTACAGACACTCAC 59.015 50.000 0.00 0.00 0.00 3.51
327 329 2.624364 TGGCTAAACGTACAGACACTCA 59.376 45.455 0.82 0.00 0.00 3.41
331 333 2.029649 GGAGTGGCTAAACGTACAGACA 60.030 50.000 0.82 0.82 0.00 3.41
337 339 2.165030 GCTAGTGGAGTGGCTAAACGTA 59.835 50.000 0.00 0.00 0.00 3.57
339 341 1.204941 AGCTAGTGGAGTGGCTAAACG 59.795 52.381 0.00 0.00 31.46 3.60
341 343 1.476891 CGAGCTAGTGGAGTGGCTAAA 59.523 52.381 0.00 0.00 33.80 1.85
342 344 1.103803 CGAGCTAGTGGAGTGGCTAA 58.896 55.000 0.00 0.00 33.80 3.09
344 346 1.304547 ACGAGCTAGTGGAGTGGCT 60.305 57.895 0.00 0.00 36.89 4.75
345 347 1.139947 GACGAGCTAGTGGAGTGGC 59.860 63.158 3.45 0.00 0.00 5.01
346 348 1.306642 ACGACGAGCTAGTGGAGTGG 61.307 60.000 15.48 0.19 0.00 4.00
347 349 0.097325 GACGACGAGCTAGTGGAGTG 59.903 60.000 15.48 0.00 0.00 3.51
348 350 1.025647 GGACGACGAGCTAGTGGAGT 61.026 60.000 15.48 7.41 0.00 3.85
349 351 1.716826 GGGACGACGAGCTAGTGGAG 61.717 65.000 15.48 4.35 0.00 3.86
350 352 1.748122 GGGACGACGAGCTAGTGGA 60.748 63.158 15.48 0.00 0.00 4.02
351 353 2.799371 GGGACGACGAGCTAGTGG 59.201 66.667 3.45 5.73 0.00 4.00
368 392 1.002134 AGGGAACTTGTGATGGGCG 60.002 57.895 0.00 0.00 37.44 6.13
380 408 0.332972 ATGGAAGAGGCCAAGGGAAC 59.667 55.000 5.01 0.00 42.16 3.62
451 480 6.594937 ACGTTACTTGACAGGAAACTAAACAA 59.405 34.615 0.00 0.00 40.21 2.83
455 484 5.922544 GCTACGTTACTTGACAGGAAACTAA 59.077 40.000 0.00 0.00 40.21 2.24
457 486 4.038883 AGCTACGTTACTTGACAGGAAACT 59.961 41.667 0.00 0.00 46.44 2.66
471 500 1.134610 GGGCCAAAGCTAGCTACGTTA 60.135 52.381 19.70 0.00 39.73 3.18
472 501 0.392595 GGGCCAAAGCTAGCTACGTT 60.393 55.000 19.70 5.93 39.73 3.99
473 502 1.221021 GGGCCAAAGCTAGCTACGT 59.779 57.895 19.70 3.43 39.73 3.57
474 503 1.523938 GGGGCCAAAGCTAGCTACG 60.524 63.158 19.70 11.98 39.73 3.51
475 504 0.034477 TTGGGGCCAAAGCTAGCTAC 60.034 55.000 19.70 8.02 39.73 3.58
476 505 0.701731 TTTGGGGCCAAAGCTAGCTA 59.298 50.000 19.70 0.00 40.51 3.32
527 556 4.027572 TCAACAACTGGCGAAAAGAAAG 57.972 40.909 0.00 0.00 0.00 2.62
560 589 7.033791 CAGAAAGATTTGCAACAGCATTAGAT 58.966 34.615 0.00 0.00 38.23 1.98
616 685 1.375908 TCACGAAGATGCTGGCACC 60.376 57.895 0.00 0.00 0.00 5.01
630 699 3.594603 ATTAGTCCCTCACAAGTCACG 57.405 47.619 0.00 0.00 0.00 4.35
643 712 2.357952 GGAATGGCGTCCAAATTAGTCC 59.642 50.000 2.68 0.00 36.95 3.85
664 733 3.037833 TGCTTGTGCGCAGACGAG 61.038 61.111 12.22 10.94 43.93 4.18
676 745 2.931325 AGCAACAACAACAATGTGCTTG 59.069 40.909 0.00 0.00 40.46 4.01
677 746 2.931325 CAGCAACAACAACAATGTGCTT 59.069 40.909 0.00 0.00 40.46 3.91
678 747 2.094078 ACAGCAACAACAACAATGTGCT 60.094 40.909 0.00 0.00 40.46 4.40
679 748 2.270047 ACAGCAACAACAACAATGTGC 58.730 42.857 0.00 0.00 40.46 4.57
680 749 3.679025 ACAACAGCAACAACAACAATGTG 59.321 39.130 0.00 0.00 40.46 3.21
681 750 3.924144 ACAACAGCAACAACAACAATGT 58.076 36.364 0.00 0.00 43.14 2.71
682 751 4.152045 ACAACAACAGCAACAACAACAATG 59.848 37.500 0.00 0.00 0.00 2.82
683 752 4.314121 ACAACAACAGCAACAACAACAAT 58.686 34.783 0.00 0.00 0.00 2.71
684 753 3.722147 ACAACAACAGCAACAACAACAA 58.278 36.364 0.00 0.00 0.00 2.83
685 754 3.377346 ACAACAACAGCAACAACAACA 57.623 38.095 0.00 0.00 0.00 3.33
686 755 3.492756 ACAACAACAACAGCAACAACAAC 59.507 39.130 0.00 0.00 0.00 3.32
687 756 3.722147 ACAACAACAACAGCAACAACAA 58.278 36.364 0.00 0.00 0.00 2.83
688 757 3.005261 AGACAACAACAACAGCAACAACA 59.995 39.130 0.00 0.00 0.00 3.33
689 758 3.364621 CAGACAACAACAACAGCAACAAC 59.635 43.478 0.00 0.00 0.00 3.32
690 759 3.573598 CAGACAACAACAACAGCAACAA 58.426 40.909 0.00 0.00 0.00 2.83
691 760 2.094803 CCAGACAACAACAACAGCAACA 60.095 45.455 0.00 0.00 0.00 3.33
692 761 2.094752 ACCAGACAACAACAACAGCAAC 60.095 45.455 0.00 0.00 0.00 4.17
693 762 2.163412 GACCAGACAACAACAACAGCAA 59.837 45.455 0.00 0.00 0.00 3.91
694 763 1.742831 GACCAGACAACAACAACAGCA 59.257 47.619 0.00 0.00 0.00 4.41
695 764 1.742831 TGACCAGACAACAACAACAGC 59.257 47.619 0.00 0.00 0.00 4.40
696 765 2.097466 GGTGACCAGACAACAACAACAG 59.903 50.000 0.00 0.00 0.00 3.16
697 766 2.088423 GGTGACCAGACAACAACAACA 58.912 47.619 0.00 0.00 0.00 3.33
698 767 2.088423 TGGTGACCAGACAACAACAAC 58.912 47.619 0.00 0.00 34.39 3.32
768 837 0.735471 GGAAATTTCAGAGGCCTCGC 59.265 55.000 26.95 5.04 34.09 5.03
769 838 2.012673 CAGGAAATTTCAGAGGCCTCG 58.987 52.381 26.95 20.71 34.09 4.63
770 839 3.078891 ACAGGAAATTTCAGAGGCCTC 57.921 47.619 26.22 26.22 0.00 4.70
836 906 1.202154 GGTGATCGAGGACTGTACGTG 60.202 57.143 0.00 0.00 0.00 4.49
960 1034 0.389948 ACGATTCCTTCAGCGACACC 60.390 55.000 0.00 0.00 0.00 4.16
979 1053 2.257371 CGGCCAAGAAGACGACGA 59.743 61.111 2.24 0.00 0.00 4.20
980 1054 2.809601 CCGGCCAAGAAGACGACG 60.810 66.667 2.24 0.00 0.00 5.12
981 1055 3.119096 GCCGGCCAAGAAGACGAC 61.119 66.667 18.11 0.00 0.00 4.34
982 1056 2.463589 ATTGCCGGCCAAGAAGACGA 62.464 55.000 26.77 0.00 36.76 4.20
1031 1105 0.249280 CACGGCCAAGAAAACCAACC 60.249 55.000 2.24 0.00 0.00 3.77
1038 1112 2.203337 AGCAGCACGGCCAAGAAA 60.203 55.556 2.24 0.00 0.00 2.52
1296 1382 3.044305 GACAGCGTGGTGACCAGC 61.044 66.667 3.58 11.29 32.34 4.85
1369 1455 4.033776 CTCCAGCTTCCCCGGCAA 62.034 66.667 0.00 0.00 0.00 4.52
2458 2565 6.366877 CCAAAATGGAAGCAAATGTTAGTGAG 59.633 38.462 0.00 0.00 40.96 3.51
2477 2584 4.637387 TTGTCATCCCAAATGCCAAAAT 57.363 36.364 0.00 0.00 0.00 1.82
2619 2726 1.211703 TCGCCATAAGAATCTTGCCCA 59.788 47.619 5.64 0.00 0.00 5.36
2732 2892 5.647658 TGAACTCATGGTCATGAACATAACC 59.352 40.000 25.46 13.24 46.10 2.85
2936 3875 0.836400 AGAGTTGGGTCACGGTGGAT 60.836 55.000 8.50 0.00 0.00 3.41
2945 3884 1.254954 ACACGAGGTAGAGTTGGGTC 58.745 55.000 0.00 0.00 0.00 4.46
3010 3949 5.426689 AATGGAGATAAGAGCTGACAACA 57.573 39.130 0.00 0.00 0.00 3.33
3033 3972 3.004315 GGACCGTCAGAGCAATTGAAAAA 59.996 43.478 10.34 0.00 0.00 1.94
3040 3981 1.742761 CATTGGACCGTCAGAGCAAT 58.257 50.000 0.00 0.00 0.00 3.56
3049 3990 0.038166 ACATTCAGGCATTGGACCGT 59.962 50.000 0.00 0.00 0.00 4.83
3051 3992 3.701040 ACATAACATTCAGGCATTGGACC 59.299 43.478 0.00 0.00 0.00 4.46
3060 4001 4.813027 AGCAAAGCAACATAACATTCAGG 58.187 39.130 0.00 0.00 0.00 3.86
3075 4016 4.681483 GGTAATGAACAGTTCAAGCAAAGC 59.319 41.667 19.92 9.41 43.95 3.51
3077 4018 5.592282 TCTGGTAATGAACAGTTCAAGCAAA 59.408 36.000 19.92 4.71 43.95 3.68
3081 4022 5.997746 TCCTTCTGGTAATGAACAGTTCAAG 59.002 40.000 19.92 12.11 37.67 3.02
3093 4034 4.322801 CGTCCTTCAGTTCCTTCTGGTAAT 60.323 45.833 0.00 0.00 36.25 1.89
3108 4049 1.275291 CAGGTAAGCTTCCGTCCTTCA 59.725 52.381 0.00 0.00 0.00 3.02
3171 4112 1.067295 TCCCTCCATGCAAGAACTGT 58.933 50.000 0.00 0.00 0.00 3.55
3246 4187 1.067915 CCGATTTTGGCGACATGGTTT 60.068 47.619 0.00 0.00 42.32 3.27
3276 4217 2.821245 AGCCTCTCCTAGGATCGGAATG 60.821 54.545 23.86 7.90 41.34 2.67
3282 4223 1.418334 TTGCAGCCTCTCCTAGGATC 58.582 55.000 13.12 2.22 41.34 3.36
3317 4258 5.924254 TCATCCCATAAGTTAGTATTTCGCG 59.076 40.000 0.00 0.00 0.00 5.87
3343 4284 5.013183 ACCTTACAAAGAGTAGCTGGATGTT 59.987 40.000 0.00 0.00 33.43 2.71
3344 4285 4.532521 ACCTTACAAAGAGTAGCTGGATGT 59.467 41.667 0.00 0.00 33.43 3.06
3345 4286 5.091261 ACCTTACAAAGAGTAGCTGGATG 57.909 43.478 0.00 0.00 33.43 3.51
3346 4287 5.763876 AACCTTACAAAGAGTAGCTGGAT 57.236 39.130 0.00 0.00 33.43 3.41
3347 4288 5.562298 AAACCTTACAAAGAGTAGCTGGA 57.438 39.130 0.00 0.00 33.43 3.86
3349 4290 8.237267 CCATAAAAACCTTACAAAGAGTAGCTG 58.763 37.037 0.00 0.00 33.43 4.24
3351 4292 7.027760 GCCATAAAAACCTTACAAAGAGTAGC 58.972 38.462 0.00 0.00 33.43 3.58
3352 4293 7.175990 TGGCCATAAAAACCTTACAAAGAGTAG 59.824 37.037 0.00 0.00 33.43 2.57
3353 4294 7.005296 TGGCCATAAAAACCTTACAAAGAGTA 58.995 34.615 0.00 0.00 0.00 2.59
3354 4295 5.836358 TGGCCATAAAAACCTTACAAAGAGT 59.164 36.000 0.00 0.00 0.00 3.24
3355 4296 6.339587 TGGCCATAAAAACCTTACAAAGAG 57.660 37.500 0.00 0.00 0.00 2.85
3357 4298 7.572910 GCAAATGGCCATAAAAACCTTACAAAG 60.573 37.037 21.15 0.00 36.11 2.77
3358 4299 6.205658 GCAAATGGCCATAAAAACCTTACAAA 59.794 34.615 21.15 0.00 36.11 2.83
3360 4301 5.012561 AGCAAATGGCCATAAAAACCTTACA 59.987 36.000 21.15 0.00 46.50 2.41
3362 4303 5.247110 TCAGCAAATGGCCATAAAAACCTTA 59.753 36.000 21.15 0.00 46.50 2.69
3363 4304 4.041444 TCAGCAAATGGCCATAAAAACCTT 59.959 37.500 21.15 4.48 46.50 3.50
3364 4305 3.582208 TCAGCAAATGGCCATAAAAACCT 59.418 39.130 21.15 7.03 46.50 3.50
3365 4306 3.684305 GTCAGCAAATGGCCATAAAAACC 59.316 43.478 21.15 4.70 46.50 3.27
3377 4318 4.327898 GCATACATTGTTGGTCAGCAAATG 59.672 41.667 4.48 0.00 35.25 2.32
3494 4439 2.279935 TTAGTTGTGCCGGTTGGAAT 57.720 45.000 1.90 0.00 37.49 3.01
3497 4442 4.712122 AAATATTAGTTGTGCCGGTTGG 57.288 40.909 1.90 0.00 38.77 3.77
3545 4490 3.593247 GCATCGTGCTGCAAAGTAG 57.407 52.632 2.77 0.74 40.96 2.57
3577 4522 4.849518 TCACCCCGAAATCAAATATGTCA 58.150 39.130 0.00 0.00 0.00 3.58
3628 4573 6.303903 TCCACCTCATATATGGATGTGATG 57.696 41.667 21.51 12.07 37.60 3.07
3706 4651 1.135972 CAGGTATCTGTGTTGCGTTGC 60.136 52.381 0.00 0.00 36.30 4.17
3734 4679 0.524414 CATAGCAGCTGCAGCACAAA 59.476 50.000 38.24 21.85 45.16 2.83
3841 4786 2.040939 CTCAGGCAGATCTCCATGACT 58.959 52.381 0.00 0.00 34.15 3.41
3976 4921 4.410743 GACGACGACACCGGGGAC 62.411 72.222 12.96 1.98 40.78 4.46
4060 5005 1.694133 CCTCCTGGGAGCTGGATGAC 61.694 65.000 10.92 0.00 40.69 3.06
4129 5076 1.813178 GTAGTTGGGAGCCTGCTTTTC 59.187 52.381 0.00 0.00 0.00 2.29
4131 5078 1.068121 AGTAGTTGGGAGCCTGCTTT 58.932 50.000 0.00 0.00 0.00 3.51
4135 5082 0.460311 CCGTAGTAGTTGGGAGCCTG 59.540 60.000 0.00 0.00 0.00 4.85
4152 5099 4.750098 ACACTGACAGAAGAAATACAACCG 59.250 41.667 10.08 0.00 0.00 4.44
4159 5106 5.736951 AGCTCTACACTGACAGAAGAAAT 57.263 39.130 10.08 0.00 0.00 2.17
4182 5129 7.660030 ACAGAGGAATTGAAAGGAAAAAGAA 57.340 32.000 0.00 0.00 0.00 2.52
4184 5131 7.267857 ACAACAGAGGAATTGAAAGGAAAAAG 58.732 34.615 0.00 0.00 0.00 2.27
4199 5182 4.480115 TCAGGTAGAGAAACAACAGAGGA 58.520 43.478 0.00 0.00 0.00 3.71
4270 5253 5.403166 CGATGCTTGCCCAACATTATTATTG 59.597 40.000 0.00 0.00 0.00 1.90
4311 5302 8.512138 GTTCTACAAATGGTATTTGTGCTAGTT 58.488 33.333 23.09 4.19 42.05 2.24
4312 5303 7.663905 TGTTCTACAAATGGTATTTGTGCTAGT 59.336 33.333 23.09 4.75 42.05 2.57
4346 5463 2.032030 GCTGCTTGCGAGTCTTTAAACA 60.032 45.455 2.14 0.00 0.00 2.83
4409 5526 6.601613 CCTATTTGGTGAACTAAGGCATGTTA 59.398 38.462 0.00 0.00 0.00 2.41
4410 5527 5.418840 CCTATTTGGTGAACTAAGGCATGTT 59.581 40.000 0.00 0.00 0.00 2.71
4431 5548 2.623878 TTTTCGGTGCTTGTGACCTA 57.376 45.000 0.00 0.00 0.00 3.08
4456 5573 1.134551 GTCCCTGTGCTTGATCTCCTC 60.135 57.143 0.00 0.00 0.00 3.71
4492 5609 9.032420 GTACCACCGAATTAAAACATTGAAAAA 57.968 29.630 0.00 0.00 0.00 1.94
4714 5831 9.656040 TTTACTTATTTCTATCGTGGTTTGCTA 57.344 29.630 0.00 0.00 0.00 3.49
4748 5865 2.567169 CTGTCCCTGAATCCACACACTA 59.433 50.000 0.00 0.00 0.00 2.74
4779 5896 0.473886 AAGTAGTGTCCTGGGGTGCT 60.474 55.000 0.00 0.00 0.00 4.40
4782 5899 0.974383 CGAAAGTAGTGTCCTGGGGT 59.026 55.000 0.00 0.00 0.00 4.95
4790 5907 6.989659 TCCTCATTTACTTCGAAAGTAGTGT 58.010 36.000 0.00 0.00 44.22 3.55
4822 5939 4.452825 TCCGTTCTGTTGTGGATGTAAAA 58.547 39.130 0.00 0.00 0.00 1.52
4912 6029 6.861065 ATAGGTAACATGCGACCAATAAAG 57.139 37.500 16.73 0.00 38.27 1.85
4966 6167 4.286549 AGGCCAGATCCAGATCTTATTGAG 59.713 45.833 5.01 0.00 45.31 3.02
4992 6193 3.751479 TGAGTTGCACAGTACTGTCAT 57.249 42.857 25.63 12.13 42.83 3.06


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

AutoCloner maintained by Alex Coulton.