Multiple sequence alignment - TraesCS5B01G105100

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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 TraesCS5B01G105100 chr5B 100.000 3356 0 0 1 3356 140823078 140826433 0.000000e+00 6198.0
1 TraesCS5B01G105100 chr5D 94.513 2661 100 22 58 2715 127885219 127887836 0.000000e+00 4063.0
2 TraesCS5B01G105100 chr5D 89.200 250 14 3 2702 2951 127921911 127922147 1.960000e-77 300.0
3 TraesCS5B01G105100 chr5D 92.179 179 14 0 3178 3356 127941019 127941197 1.550000e-63 254.0
4 TraesCS5B01G105100 chr5D 91.503 153 11 2 3035 3185 127922380 127922532 3.390000e-50 209.0
5 TraesCS5B01G105100 chr1B 73.387 1116 259 31 1229 2316 46829698 46828593 6.790000e-102 381.0
6 TraesCS5B01G105100 chr1B 73.359 1051 249 22 1229 2256 4518368 4517326 8.850000e-96 361.0
7 TraesCS5B01G105100 chr1B 72.646 1115 269 28 1229 2316 46692577 46693682 1.490000e-88 337.0
8 TraesCS5B01G105100 chr6A 73.694 1053 239 30 1229 2253 613494252 613495294 3.160000e-100 375.0
9 TraesCS5B01G105100 chr6A 75.185 270 56 9 963 1225 64066097 64065832 2.120000e-22 117.0
10 TraesCS5B01G105100 chr3B 79.111 225 47 0 989 1213 72922434 72922658 4.480000e-34 156.0
11 TraesCS5B01G105100 chr3B 95.082 61 2 1 1 61 614194062 614194121 9.910000e-16 95.3
12 TraesCS5B01G105100 chr3D 78.166 229 49 1 985 1213 46524963 46525190 9.700000e-31 145.0
13 TraesCS5B01G105100 chr3A 78.355 231 45 5 985 1213 57904708 57904935 9.700000e-31 145.0
14 TraesCS5B01G105100 chr7D 75.833 240 51 6 984 1219 548231383 548231619 7.610000e-22 115.0
15 TraesCS5B01G105100 chr7B 75.833 240 51 6 984 1219 591461931 591462167 7.610000e-22 115.0
16 TraesCS5B01G105100 chr7B 96.610 59 1 1 1 59 529726287 529726344 2.760000e-16 97.1
17 TraesCS5B01G105100 chr7B 93.750 64 3 1 1 63 651484086 651484023 9.910000e-16 95.3
18 TraesCS5B01G105100 chr7A 75.833 240 51 6 984 1219 631984725 631984961 7.610000e-22 115.0
19 TraesCS5B01G105100 chr7A 98.214 56 1 0 1 56 575223087 575223142 7.660000e-17 99.0
20 TraesCS5B01G105100 chr6B 75.806 248 49 11 984 1225 120132606 120132364 7.610000e-22 115.0
21 TraesCS5B01G105100 chr6B 87.500 80 6 3 1 80 63664864 63664789 4.610000e-14 89.8
22 TraesCS5B01G105100 chr5A 98.246 57 1 0 1 57 194712555 194712499 2.130000e-17 100.0
23 TraesCS5B01G105100 chr2A 95.082 61 2 1 1 61 117757296 117757237 9.910000e-16 95.3
24 TraesCS5B01G105100 chr2A 96.429 56 2 0 1 56 423177285 423177340 3.570000e-15 93.5
25 TraesCS5B01G105100 chr4B 95.000 60 2 1 1 60 660113696 660113754 3.570000e-15 93.5


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 TraesCS5B01G105100 chr5B 140823078 140826433 3355 False 6198.0 6198 100.0000 1 3356 1 chr5B.!!$F1 3355
1 TraesCS5B01G105100 chr5D 127885219 127887836 2617 False 4063.0 4063 94.5130 58 2715 1 chr5D.!!$F1 2657
2 TraesCS5B01G105100 chr5D 127921911 127922532 621 False 254.5 300 90.3515 2702 3185 2 chr5D.!!$F3 483
3 TraesCS5B01G105100 chr1B 46828593 46829698 1105 True 381.0 381 73.3870 1229 2316 1 chr1B.!!$R2 1087
4 TraesCS5B01G105100 chr1B 4517326 4518368 1042 True 361.0 361 73.3590 1229 2256 1 chr1B.!!$R1 1027
5 TraesCS5B01G105100 chr1B 46692577 46693682 1105 False 337.0 337 72.6460 1229 2316 1 chr1B.!!$F1 1087
6 TraesCS5B01G105100 chr6A 613494252 613495294 1042 False 375.0 375 73.6940 1229 2253 1 chr6A.!!$F1 1024

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
507 508 0.035317 TAGGTGTGCAGCCTTGTCTG 59.965 55.0 14.18 0.0 37.54 3.51 F
1836 1855 0.253044 TGCCTCCTCAGTATGTTGCC 59.747 55.0 0.00 0.0 37.40 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2259 2281 1.094073 GCGGAGAGATGCAAGCACAT 61.094 55.0 0.0 0.0 0.00 3.21 R
3331 3581 0.383231 GCCCAGTGCATAGCATTCAC 59.617 55.0 0.0 0.0 41.91 3.18 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
17 18 4.035843 ATCAGGACGGGTCTCACC 57.964 61.111 0.00 0.00 37.60 4.02
18 19 1.388531 ATCAGGACGGGTCTCACCT 59.611 57.895 0.00 0.00 38.64 4.00
31 32 6.672266 GGGTCTCACCTGATTTATATGAGA 57.328 41.667 0.00 0.00 42.63 3.27
35 36 7.295322 TCTCACCTGATTTATATGAGACCTG 57.705 40.000 0.00 0.00 40.59 4.00
36 37 6.268617 TCTCACCTGATTTATATGAGACCTGG 59.731 42.308 0.00 0.00 40.59 4.45
37 38 5.905331 TCACCTGATTTATATGAGACCTGGT 59.095 40.000 0.00 0.00 0.00 4.00
38 39 6.042093 TCACCTGATTTATATGAGACCTGGTC 59.958 42.308 19.20 19.20 0.00 4.02
39 40 6.042552 CACCTGATTTATATGAGACCTGGTCT 59.957 42.308 28.70 28.70 46.42 3.85
91 92 2.422597 GACCCAACACGTGATTGATGA 58.577 47.619 25.01 0.00 0.00 2.92
94 95 2.416547 CCCAACACGTGATTGATGACTC 59.583 50.000 25.01 0.00 0.00 3.36
201 202 9.433317 CAAACGCATTTAAAGTCATATCGTATT 57.567 29.630 0.00 0.00 0.00 1.89
279 280 4.748798 CAGCCCCCAGTCCCCTCT 62.749 72.222 0.00 0.00 0.00 3.69
285 286 1.538876 CCCAGTCCCCTCTCAACCA 60.539 63.158 0.00 0.00 0.00 3.67
315 316 2.281070 AAGTCCACAGCTGGCGTG 60.281 61.111 19.93 7.28 37.49 5.34
344 345 3.438216 TCACCAATCCAAGATCAAGCA 57.562 42.857 0.00 0.00 0.00 3.91
378 379 1.748500 GCCTGGCTTCTCTTGCTCC 60.749 63.158 12.43 0.00 0.00 4.70
380 381 1.593787 CTGGCTTCTCTTGCTCCGA 59.406 57.895 0.00 0.00 0.00 4.55
381 382 0.177604 CTGGCTTCTCTTGCTCCGAT 59.822 55.000 0.00 0.00 0.00 4.18
389 390 5.125417 GCTTCTCTTGCTCCGATAGATCTAT 59.875 44.000 15.26 15.26 39.76 1.98
390 391 6.350110 GCTTCTCTTGCTCCGATAGATCTATT 60.350 42.308 16.37 0.85 39.76 1.73
395 396 5.791336 TGCTCCGATAGATCTATTGTTGT 57.209 39.130 23.05 0.55 39.76 3.32
398 399 5.563085 GCTCCGATAGATCTATTGTTGTCGT 60.563 44.000 23.05 0.00 39.76 4.34
411 412 2.814919 TGTTGTCGTCTCTCCTTCTCTC 59.185 50.000 0.00 0.00 0.00 3.20
414 415 2.838813 TGTCGTCTCTCCTTCTCTCCTA 59.161 50.000 0.00 0.00 0.00 2.94
428 429 1.074872 CTCCTACCGTCGCGTTTTCC 61.075 60.000 5.77 0.00 0.00 3.13
429 430 1.373246 CCTACCGTCGCGTTTTCCA 60.373 57.895 5.77 0.00 0.00 3.53
430 431 0.945265 CCTACCGTCGCGTTTTCCAA 60.945 55.000 5.77 0.00 0.00 3.53
435 436 1.323791 CGTCGCGTTTTCCAAATTCC 58.676 50.000 5.77 0.00 0.00 3.01
446 447 7.427214 CGTTTTCCAAATTCCAGGTACTAAAA 58.573 34.615 0.00 0.00 36.02 1.52
447 448 7.921745 CGTTTTCCAAATTCCAGGTACTAAAAA 59.078 33.333 0.00 0.00 36.02 1.94
507 508 0.035317 TAGGTGTGCAGCCTTGTCTG 59.965 55.000 14.18 0.00 37.54 3.51
535 536 5.127194 TCCTCTCTCTATATCTCTCGCTCTC 59.873 48.000 0.00 0.00 0.00 3.20
596 597 2.747686 CCGGCCGGTAATATGCCT 59.252 61.111 36.64 0.00 43.12 4.75
644 645 3.118531 ACCAGACCTCATATTGCCTTCT 58.881 45.455 0.00 0.00 0.00 2.85
680 681 9.469807 ACTTAATTAAGTGCTTCTAGATCATCG 57.530 33.333 26.30 0.00 44.30 3.84
690 691 5.515982 GCTTCTAGATCATCGCATCAGTATG 59.484 44.000 0.00 0.00 36.09 2.39
691 692 6.581171 TTCTAGATCATCGCATCAGTATGT 57.419 37.500 0.00 0.00 37.40 2.29
692 693 6.188400 TCTAGATCATCGCATCAGTATGTC 57.812 41.667 0.00 0.00 37.40 3.06
693 694 5.942826 TCTAGATCATCGCATCAGTATGTCT 59.057 40.000 0.00 0.00 37.40 3.41
694 695 4.807443 AGATCATCGCATCAGTATGTCTG 58.193 43.478 0.00 0.00 44.85 3.51
695 696 3.375782 TCATCGCATCAGTATGTCTGG 57.624 47.619 0.00 0.00 43.76 3.86
696 697 2.036346 TCATCGCATCAGTATGTCTGGG 59.964 50.000 0.00 0.00 43.76 4.45
697 698 1.775385 TCGCATCAGTATGTCTGGGA 58.225 50.000 0.00 0.00 43.76 4.37
698 699 2.319844 TCGCATCAGTATGTCTGGGAT 58.680 47.619 0.00 0.00 43.76 3.85
699 700 2.297315 TCGCATCAGTATGTCTGGGATC 59.703 50.000 0.00 0.00 43.76 3.36
700 701 2.036346 CGCATCAGTATGTCTGGGATCA 59.964 50.000 0.00 0.00 43.76 2.92
701 702 3.306571 CGCATCAGTATGTCTGGGATCAT 60.307 47.826 0.00 0.00 43.76 2.45
702 703 4.252073 GCATCAGTATGTCTGGGATCATC 58.748 47.826 0.00 0.00 43.76 2.92
721 722 7.042658 GGATCATCGTTATCTTAGTGAACAACC 60.043 40.741 0.00 0.00 0.00 3.77
740 741 1.325476 CCCATTCTTTCTGGCCCAGC 61.325 60.000 5.66 0.00 32.08 4.85
761 763 6.040166 CCAGCTGCCTTTGAATATGTAAGATT 59.960 38.462 8.66 0.00 0.00 2.40
807 809 7.717875 ACAAACTTGTGGCAGTTCTAGTTTATA 59.282 33.333 12.96 0.00 40.49 0.98
836 840 7.615582 TGTAGATTAGCTGGAGTGATTTTTG 57.384 36.000 0.00 0.00 0.00 2.44
869 873 9.388506 AGATTAGAACATAGATTTTCACCAGTG 57.611 33.333 0.00 0.00 0.00 3.66
950 954 8.761575 TTTCATTAATTTCATTCCAGCACTTC 57.238 30.769 0.00 0.00 0.00 3.01
955 959 3.410631 TTCATTCCAGCACTTCGGTTA 57.589 42.857 0.00 0.00 0.00 2.85
1011 1015 2.686235 CATTGCTCGATGGAGGATCTC 58.314 52.381 6.88 0.00 40.57 2.75
1059 1063 2.420687 CCAGAGGATTACCAGGACAAGC 60.421 54.545 0.00 0.00 38.94 4.01
1100 1104 2.080693 TGTGTCAAAAAGTCTGTGCGT 58.919 42.857 0.00 0.00 0.00 5.24
1101 1105 2.095213 TGTGTCAAAAAGTCTGTGCGTC 59.905 45.455 0.00 0.00 0.00 5.19
1130 1134 2.104792 CGAATCAAAGGGCCTCTATCCA 59.895 50.000 6.46 0.00 0.00 3.41
1200 1204 2.627945 TCCCGATTCTCCAATTTGTCG 58.372 47.619 0.00 0.00 0.00 4.35
1225 1229 5.576447 AATGGAAATCAATTACACCGGTC 57.424 39.130 2.59 0.00 33.69 4.79
1299 1303 5.088739 GCCAATTGTAAGAAGTTGATGTCG 58.911 41.667 4.43 0.00 0.00 4.35
1836 1855 0.253044 TGCCTCCTCAGTATGTTGCC 59.747 55.000 0.00 0.00 37.40 4.52
2124 2146 3.818586 GGTGAACGATCGGGTAACA 57.181 52.632 20.98 8.74 39.74 2.41
2217 2239 3.126831 GACTGATGCTGGATTAACCGAG 58.873 50.000 0.00 0.00 42.61 4.63
2259 2281 4.218312 TGGATTCTCTGATCATCGAAGGA 58.782 43.478 0.00 0.00 0.00 3.36
2336 2358 0.035881 CTGGAGTCAGCAAGCAGGAA 59.964 55.000 0.00 0.00 33.86 3.36
2352 2374 3.380637 GCAGGAACCGTCTCAGTAGAATA 59.619 47.826 0.00 0.00 32.16 1.75
2379 2401 8.565896 AAACATAATGCTGTTGATCAAGTAGA 57.434 30.769 18.95 8.26 39.25 2.59
2407 2429 5.708230 AGTTATTTTCGGTTGTGCCTCATTA 59.292 36.000 0.00 0.00 34.25 1.90
2421 2443 2.477825 CTCATTAGTGGATGTCGCTGG 58.522 52.381 0.00 0.00 37.42 4.85
2423 2445 0.530650 ATTAGTGGATGTCGCTGGCG 60.531 55.000 8.80 8.80 37.42 5.69
2438 2460 1.220749 GGCGTTGACCCTGCTATCA 59.779 57.895 0.00 0.00 0.00 2.15
2453 2475 7.014038 ACCCTGCTATCATTTTCATCATTTCTC 59.986 37.037 0.00 0.00 0.00 2.87
2473 2495 4.021104 TCTCAGAACCTGTGTCTAATGGTG 60.021 45.833 0.00 0.00 32.53 4.17
2490 2512 3.843422 TGGTGAACTTTGGATCCAATGT 58.157 40.909 30.69 30.69 43.20 2.71
2493 2515 2.562298 TGAACTTTGGATCCAATGTGGC 59.438 45.455 34.44 29.09 41.41 5.01
2502 2524 2.198827 TCCAATGTGGCGAATGAAGT 57.801 45.000 0.00 0.00 37.47 3.01
2538 2560 5.242393 TCTGTTACTGGTGTACTGAACCTAC 59.758 44.000 2.84 0.00 38.60 3.18
2547 2569 5.350640 GGTGTACTGAACCTACTTATGTTGC 59.649 44.000 0.00 0.00 34.66 4.17
2555 2577 4.010349 ACCTACTTATGTTGCTTTGCTCC 58.990 43.478 0.00 0.00 0.00 4.70
2578 2600 5.529060 CCTGTAGCTTAATTTCTCCATGTCC 59.471 44.000 0.00 0.00 0.00 4.02
2601 2623 5.745294 CCGCCATCTTGAAAATTGTCATAAG 59.255 40.000 0.00 0.00 0.00 1.73
2638 2660 5.659440 AACATTTCAGGTGTTCAACTTGT 57.341 34.783 0.00 0.00 37.18 3.16
2687 2709 5.627499 ATGTGGTGTATGAACATGACAAC 57.373 39.130 0.00 0.00 38.08 3.32
2692 2714 5.008514 TGGTGTATGAACATGACAACTTGTG 59.991 40.000 0.00 0.00 38.08 3.33
2706 2728 5.457140 ACAACTTGTGTGTTATTATTGCCG 58.543 37.500 0.00 0.00 39.72 5.69
2728 2750 8.239314 TGCCGTTATATTGTACTAGTAGCATAC 58.761 37.037 1.87 0.00 43.47 2.39
2834 2856 6.764308 ATGTAAGTGTCATCCCAAAAGATG 57.236 37.500 0.00 0.00 44.21 2.90
2836 2858 6.774673 TGTAAGTGTCATCCCAAAAGATGTA 58.225 36.000 1.78 0.00 43.46 2.29
2914 2936 2.733552 CGCTCCATCATAGTTTGGATCG 59.266 50.000 1.46 1.46 42.85 3.69
2927 2949 3.485463 TTGGATCGTTTTGGAGTCTGT 57.515 42.857 0.00 0.00 0.00 3.41
2942 2964 2.568062 AGTCTGTCGAGGTGAGAGTCTA 59.432 50.000 0.00 0.00 39.02 2.59
2956 3204 5.016831 TGAGAGTCTACCATATGTGTGTGT 58.983 41.667 1.24 0.00 0.00 3.72
2957 3205 5.105756 TGAGAGTCTACCATATGTGTGTGTG 60.106 44.000 1.24 0.00 0.00 3.82
2958 3206 4.772624 AGAGTCTACCATATGTGTGTGTGT 59.227 41.667 1.24 0.00 0.00 3.72
2959 3207 4.820897 AGTCTACCATATGTGTGTGTGTG 58.179 43.478 1.24 0.00 0.00 3.82
2960 3208 4.283467 AGTCTACCATATGTGTGTGTGTGT 59.717 41.667 1.24 0.00 0.00 3.72
2961 3209 4.388773 GTCTACCATATGTGTGTGTGTGTG 59.611 45.833 1.24 0.00 0.00 3.82
2962 3210 3.207265 ACCATATGTGTGTGTGTGTGT 57.793 42.857 1.24 0.00 0.00 3.72
2963 3211 2.877786 ACCATATGTGTGTGTGTGTGTG 59.122 45.455 1.24 0.00 0.00 3.82
2964 3212 2.877786 CCATATGTGTGTGTGTGTGTGT 59.122 45.455 1.24 0.00 0.00 3.72
2965 3213 3.303924 CCATATGTGTGTGTGTGTGTGTG 60.304 47.826 1.24 0.00 0.00 3.82
2966 3214 1.819928 ATGTGTGTGTGTGTGTGTGT 58.180 45.000 0.00 0.00 0.00 3.72
2967 3215 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2968 3216 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2969 3217 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2970 3218 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2971 3219 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2972 3220 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2973 3221 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2974 3222 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2975 3223 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2976 3224 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2977 3225 1.265635 GTGTGTGTGTGTGTGTGTGTT 59.734 47.619 0.00 0.00 0.00 3.32
2978 3226 1.950216 TGTGTGTGTGTGTGTGTGTTT 59.050 42.857 0.00 0.00 0.00 2.83
2979 3227 2.287248 TGTGTGTGTGTGTGTGTGTTTG 60.287 45.455 0.00 0.00 0.00 2.93
2980 3228 1.950216 TGTGTGTGTGTGTGTGTTTGT 59.050 42.857 0.00 0.00 0.00 2.83
2981 3229 2.359214 TGTGTGTGTGTGTGTGTTTGTT 59.641 40.909 0.00 0.00 0.00 2.83
2982 3230 3.181486 TGTGTGTGTGTGTGTGTTTGTTT 60.181 39.130 0.00 0.00 0.00 2.83
2983 3231 3.799420 GTGTGTGTGTGTGTGTTTGTTTT 59.201 39.130 0.00 0.00 0.00 2.43
2984 3232 4.045104 TGTGTGTGTGTGTGTTTGTTTTC 58.955 39.130 0.00 0.00 0.00 2.29
2985 3233 4.045104 GTGTGTGTGTGTGTTTGTTTTCA 58.955 39.130 0.00 0.00 0.00 2.69
2986 3234 4.045104 TGTGTGTGTGTGTTTGTTTTCAC 58.955 39.130 0.00 0.00 35.43 3.18
2987 3235 4.045104 GTGTGTGTGTGTTTGTTTTCACA 58.955 39.130 0.00 0.00 41.37 3.58
2993 3241 4.336889 TGTGTTTGTTTTCACACCCAAA 57.663 36.364 0.20 0.00 39.23 3.28
2994 3242 4.899502 TGTGTTTGTTTTCACACCCAAAT 58.100 34.783 0.20 0.00 39.23 2.32
2995 3243 4.692625 TGTGTTTGTTTTCACACCCAAATG 59.307 37.500 0.20 0.00 39.23 2.32
2996 3244 4.094146 GTGTTTGTTTTCACACCCAAATGG 59.906 41.667 0.00 0.00 41.37 3.16
3014 3262 8.520351 CCCAAATGGTACTTCTAAACTTTTAGG 58.480 37.037 8.54 0.00 40.35 2.69
3015 3263 8.520351 CCAAATGGTACTTCTAAACTTTTAGGG 58.480 37.037 8.54 5.42 40.35 3.53
3016 3264 8.520351 CAAATGGTACTTCTAAACTTTTAGGGG 58.480 37.037 8.54 5.15 40.35 4.79
3017 3265 6.130692 TGGTACTTCTAAACTTTTAGGGGG 57.869 41.667 8.54 3.21 40.35 5.40
3018 3266 5.851138 TGGTACTTCTAAACTTTTAGGGGGA 59.149 40.000 8.54 0.00 40.35 4.81
3019 3267 6.332369 TGGTACTTCTAAACTTTTAGGGGGAA 59.668 38.462 8.54 0.00 40.35 3.97
3020 3268 7.147159 TGGTACTTCTAAACTTTTAGGGGGAAA 60.147 37.037 8.54 0.00 40.35 3.13
3021 3269 7.392673 GGTACTTCTAAACTTTTAGGGGGAAAG 59.607 40.741 8.54 7.07 40.35 2.62
3022 3270 5.773680 ACTTCTAAACTTTTAGGGGGAAAGC 59.226 40.000 8.54 0.00 40.35 3.51
3023 3271 5.327737 TCTAAACTTTTAGGGGGAAAGCA 57.672 39.130 8.54 0.00 40.35 3.91
3024 3272 5.707495 TCTAAACTTTTAGGGGGAAAGCAA 58.293 37.500 8.54 0.00 40.35 3.91
3025 3273 4.955811 AAACTTTTAGGGGGAAAGCAAG 57.044 40.909 0.00 0.00 37.57 4.01
3026 3274 2.248248 ACTTTTAGGGGGAAAGCAAGC 58.752 47.619 0.00 0.00 37.57 4.01
3027 3275 2.247358 CTTTTAGGGGGAAAGCAAGCA 58.753 47.619 0.00 0.00 0.00 3.91
3028 3276 2.390225 TTTAGGGGGAAAGCAAGCAA 57.610 45.000 0.00 0.00 0.00 3.91
3029 3277 2.390225 TTAGGGGGAAAGCAAGCAAA 57.610 45.000 0.00 0.00 0.00 3.68
3030 3278 2.390225 TAGGGGGAAAGCAAGCAAAA 57.610 45.000 0.00 0.00 0.00 2.44
3031 3279 1.506025 AGGGGGAAAGCAAGCAAAAA 58.494 45.000 0.00 0.00 0.00 1.94
3058 3307 5.866335 AAAACAAGTCGACAACAAGTGTA 57.134 34.783 19.50 0.00 41.96 2.90
3067 3316 4.936411 TCGACAACAAGTGTAACCTTCAAA 59.064 37.500 0.00 0.00 41.96 2.69
3085 3334 6.586082 CCTTCAAATGGTACACTTAACATTGC 59.414 38.462 0.00 0.00 43.63 3.56
3098 3347 2.969443 ACATTGCTTTTTCCTCGACG 57.031 45.000 0.00 0.00 0.00 5.12
3113 3362 0.872021 CGACGAAGCACTGCTATCCC 60.872 60.000 3.33 0.00 38.25 3.85
3134 3383 1.994779 GTTCCGCATGAAAATTGGCAG 59.005 47.619 0.00 0.00 33.94 4.85
3136 3385 0.531657 CCGCATGAAAATTGGCAGGA 59.468 50.000 0.00 0.00 0.00 3.86
3137 3386 1.632422 CGCATGAAAATTGGCAGGAC 58.368 50.000 0.00 0.00 0.00 3.85
3152 3402 3.000727 GCAGGACGCTTGTTACACTAAT 58.999 45.455 0.00 0.00 37.77 1.73
3155 3405 4.264614 CAGGACGCTTGTTACACTAATACG 59.735 45.833 0.00 0.00 0.00 3.06
3205 3455 9.911138 TTTTTAGAACTTACTTTCCGTTTGTTT 57.089 25.926 0.00 0.00 0.00 2.83
3206 3456 9.911138 TTTTAGAACTTACTTTCCGTTTGTTTT 57.089 25.926 0.00 0.00 0.00 2.43
3207 3457 9.911138 TTTAGAACTTACTTTCCGTTTGTTTTT 57.089 25.926 0.00 0.00 0.00 1.94
3212 3462 9.642327 AACTTACTTTCCGTTTGTTTTTAATGT 57.358 25.926 0.00 0.00 0.00 2.71
3217 3467 9.589111 ACTTTCCGTTTGTTTTTAATGTATTGT 57.411 25.926 0.00 0.00 0.00 2.71
3220 3470 9.582431 TTCCGTTTGTTTTTAATGTATTGTTCA 57.418 25.926 0.00 0.00 0.00 3.18
3221 3471 9.021863 TCCGTTTGTTTTTAATGTATTGTTCAC 57.978 29.630 0.00 0.00 0.00 3.18
3222 3472 8.270111 CCGTTTGTTTTTAATGTATTGTTCACC 58.730 33.333 0.00 0.00 0.00 4.02
3223 3473 7.993792 CGTTTGTTTTTAATGTATTGTTCACCG 59.006 33.333 0.00 0.00 0.00 4.94
3224 3474 8.809478 GTTTGTTTTTAATGTATTGTTCACCGT 58.191 29.630 0.00 0.00 0.00 4.83
3230 3480 9.828852 TTTTAATGTATTGTTCACCGTAATGTC 57.171 29.630 0.00 0.00 0.00 3.06
3231 3481 5.712217 ATGTATTGTTCACCGTAATGTCG 57.288 39.130 0.00 0.00 0.00 4.35
3232 3482 4.807443 TGTATTGTTCACCGTAATGTCGA 58.193 39.130 0.00 0.00 0.00 4.20
3233 3483 5.412640 TGTATTGTTCACCGTAATGTCGAT 58.587 37.500 0.00 0.00 0.00 3.59
3234 3484 5.870433 TGTATTGTTCACCGTAATGTCGATT 59.130 36.000 0.00 0.00 0.00 3.34
3235 3485 7.034397 TGTATTGTTCACCGTAATGTCGATTA 58.966 34.615 0.00 0.00 0.00 1.75
3236 3486 6.583912 ATTGTTCACCGTAATGTCGATTAG 57.416 37.500 0.00 0.00 0.00 1.73
3237 3487 3.861113 TGTTCACCGTAATGTCGATTAGC 59.139 43.478 0.00 0.00 0.00 3.09
3238 3488 2.723209 TCACCGTAATGTCGATTAGCG 58.277 47.619 0.00 0.00 42.69 4.26
3269 3519 9.764363 TTTCATACATAATTAGTAGCAGAGGTG 57.236 33.333 0.00 0.00 0.00 4.00
3270 3520 8.478775 TCATACATAATTAGTAGCAGAGGTGT 57.521 34.615 0.00 0.00 0.00 4.16
3271 3521 8.924303 TCATACATAATTAGTAGCAGAGGTGTT 58.076 33.333 0.00 0.00 0.00 3.32
3272 3522 8.982685 CATACATAATTAGTAGCAGAGGTGTTG 58.017 37.037 0.00 0.00 0.00 3.33
3273 3523 7.182817 ACATAATTAGTAGCAGAGGTGTTGA 57.817 36.000 0.00 0.00 0.00 3.18
3274 3524 7.620880 ACATAATTAGTAGCAGAGGTGTTGAA 58.379 34.615 0.00 0.00 0.00 2.69
3275 3525 8.100791 ACATAATTAGTAGCAGAGGTGTTGAAA 58.899 33.333 0.00 0.00 0.00 2.69
3276 3526 8.946085 CATAATTAGTAGCAGAGGTGTTGAAAA 58.054 33.333 0.00 0.00 0.00 2.29
3277 3527 9.686683 ATAATTAGTAGCAGAGGTGTTGAAAAT 57.313 29.630 0.00 0.00 0.00 1.82
3278 3528 8.409358 AATTAGTAGCAGAGGTGTTGAAAATT 57.591 30.769 0.00 0.00 0.00 1.82
3279 3529 7.817418 TTAGTAGCAGAGGTGTTGAAAATTT 57.183 32.000 0.00 0.00 0.00 1.82
3280 3530 6.076981 AGTAGCAGAGGTGTTGAAAATTTG 57.923 37.500 0.00 0.00 0.00 2.32
3281 3531 3.721035 AGCAGAGGTGTTGAAAATTTGC 58.279 40.909 0.00 0.00 0.00 3.68
3282 3532 2.802247 GCAGAGGTGTTGAAAATTTGCC 59.198 45.455 0.00 0.00 0.00 4.52
3283 3533 3.493176 GCAGAGGTGTTGAAAATTTGCCT 60.493 43.478 0.00 0.00 0.00 4.75
3284 3534 4.696455 CAGAGGTGTTGAAAATTTGCCTT 58.304 39.130 0.00 0.00 0.00 4.35
3285 3535 5.738783 GCAGAGGTGTTGAAAATTTGCCTTA 60.739 40.000 0.00 0.00 0.00 2.69
3286 3536 5.691754 CAGAGGTGTTGAAAATTTGCCTTAC 59.308 40.000 0.00 0.00 0.00 2.34
3287 3537 5.362430 AGAGGTGTTGAAAATTTGCCTTACA 59.638 36.000 0.00 0.00 0.00 2.41
3288 3538 5.983540 AGGTGTTGAAAATTTGCCTTACAA 58.016 33.333 0.00 0.00 36.13 2.41
3300 3550 5.499139 TTGCCTTACAAATATGTAGCAGC 57.501 39.130 4.01 0.00 41.43 5.25
3301 3551 4.780815 TGCCTTACAAATATGTAGCAGCT 58.219 39.130 0.00 0.00 42.72 4.24
3302 3552 5.924356 TGCCTTACAAATATGTAGCAGCTA 58.076 37.500 0.00 0.00 42.72 3.32
3303 3553 6.533730 TGCCTTACAAATATGTAGCAGCTAT 58.466 36.000 5.14 0.00 42.72 2.97
3304 3554 7.676004 TGCCTTACAAATATGTAGCAGCTATA 58.324 34.615 5.14 2.83 42.72 1.31
3305 3555 7.819415 TGCCTTACAAATATGTAGCAGCTATAG 59.181 37.037 5.14 0.00 42.72 1.31
3306 3556 7.201565 GCCTTACAAATATGTAGCAGCTATAGC 60.202 40.741 17.33 17.33 42.72 2.97
3307 3557 7.278868 CCTTACAAATATGTAGCAGCTATAGCC 59.721 40.741 21.17 6.99 42.72 3.93
3308 3558 6.365970 ACAAATATGTAGCAGCTATAGCCT 57.634 37.500 21.17 14.08 39.03 4.58
3309 3559 6.169094 ACAAATATGTAGCAGCTATAGCCTG 58.831 40.000 21.17 17.90 39.03 4.85
3310 3560 2.758736 ATGTAGCAGCTATAGCCTGC 57.241 50.000 27.66 27.66 43.38 4.85
3311 3561 1.413118 TGTAGCAGCTATAGCCTGCA 58.587 50.000 32.12 24.47 43.00 4.41
3312 3562 1.973515 TGTAGCAGCTATAGCCTGCAT 59.026 47.619 32.12 24.05 43.00 3.96
3313 3563 2.369860 TGTAGCAGCTATAGCCTGCATT 59.630 45.455 32.12 22.44 43.00 3.56
3314 3564 2.653234 AGCAGCTATAGCCTGCATTT 57.347 45.000 32.12 19.42 43.00 2.32
3315 3565 2.941480 AGCAGCTATAGCCTGCATTTT 58.059 42.857 32.12 19.18 43.00 1.82
3316 3566 2.621998 AGCAGCTATAGCCTGCATTTTG 59.378 45.455 32.12 20.19 43.00 2.44
3317 3567 2.861360 GCAGCTATAGCCTGCATTTTGC 60.861 50.000 28.88 22.13 42.71 3.68
3319 3569 2.360165 AGCTATAGCCTGCATTTTGCAC 59.640 45.455 21.17 0.00 45.41 4.57
3320 3570 4.804133 AGCTATAGCCTGCATTTTGCACC 61.804 47.826 21.17 0.00 45.41 5.01
3326 3576 3.062639 GCATTTTGCACCCCAGCT 58.937 55.556 0.00 0.00 44.26 4.24
3327 3577 1.375013 GCATTTTGCACCCCAGCTG 60.375 57.895 6.78 6.78 44.26 4.24
3328 3578 1.818959 GCATTTTGCACCCCAGCTGA 61.819 55.000 17.39 0.00 44.26 4.26
3329 3579 0.899720 CATTTTGCACCCCAGCTGAT 59.100 50.000 17.39 0.00 34.99 2.90
3330 3580 0.899720 ATTTTGCACCCCAGCTGATG 59.100 50.000 17.39 11.61 34.99 3.07
3339 3589 3.186345 CCAGCTGATGGTGAATGCT 57.814 52.632 17.39 0.00 44.91 3.79
3340 3590 2.336945 CCAGCTGATGGTGAATGCTA 57.663 50.000 17.39 0.00 44.91 3.49
3341 3591 2.860009 CCAGCTGATGGTGAATGCTAT 58.140 47.619 17.39 0.00 44.91 2.97
3342 3592 2.552743 CCAGCTGATGGTGAATGCTATG 59.447 50.000 17.39 0.00 44.91 2.23
3343 3593 2.031069 CAGCTGATGGTGAATGCTATGC 60.031 50.000 8.42 0.00 43.76 3.14
3344 3594 1.951602 GCTGATGGTGAATGCTATGCA 59.048 47.619 0.00 0.00 44.86 3.96
3345 3595 2.287427 GCTGATGGTGAATGCTATGCAC 60.287 50.000 0.00 0.00 43.04 4.57
3346 3596 3.211865 CTGATGGTGAATGCTATGCACT 58.788 45.455 0.00 0.00 43.04 4.40
3347 3597 2.946990 TGATGGTGAATGCTATGCACTG 59.053 45.455 0.00 0.00 43.04 3.66
3348 3598 1.753930 TGGTGAATGCTATGCACTGG 58.246 50.000 0.00 0.00 43.04 4.00
3349 3599 1.027357 GGTGAATGCTATGCACTGGG 58.973 55.000 0.00 0.00 43.04 4.45
3350 3600 0.383231 GTGAATGCTATGCACTGGGC 59.617 55.000 0.00 0.00 43.04 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.388531 AGGTGAGACCCGTCCTGAT 59.611 57.895 0.00 0.00 39.75 2.90
2 3 0.972983 ATCAGGTGAGACCCGTCCTG 60.973 60.000 0.00 0.00 46.00 3.86
3 4 0.252284 AATCAGGTGAGACCCGTCCT 60.252 55.000 0.00 0.00 39.75 3.85
4 5 0.613777 AAATCAGGTGAGACCCGTCC 59.386 55.000 0.00 0.00 39.75 4.79
5 6 3.821421 ATAAATCAGGTGAGACCCGTC 57.179 47.619 0.00 0.00 39.75 4.79
6 7 4.899457 TCATATAAATCAGGTGAGACCCGT 59.101 41.667 0.00 0.00 39.75 5.28
7 8 5.243954 TCTCATATAAATCAGGTGAGACCCG 59.756 44.000 0.00 0.00 40.06 5.28
8 9 6.672266 TCTCATATAAATCAGGTGAGACCC 57.328 41.667 0.00 0.00 40.06 4.46
11 12 6.268617 CCAGGTCTCATATAAATCAGGTGAGA 59.731 42.308 0.00 0.00 41.99 3.27
12 13 6.042552 ACCAGGTCTCATATAAATCAGGTGAG 59.957 42.308 0.00 0.00 38.07 3.51
13 14 5.905331 ACCAGGTCTCATATAAATCAGGTGA 59.095 40.000 0.00 0.00 0.00 4.02
14 15 6.042552 AGACCAGGTCTCATATAAATCAGGTG 59.957 42.308 17.31 0.00 38.71 4.00
15 16 6.146760 AGACCAGGTCTCATATAAATCAGGT 58.853 40.000 17.31 0.00 38.71 4.00
16 17 6.678568 AGACCAGGTCTCATATAAATCAGG 57.321 41.667 17.31 0.00 38.71 3.86
91 92 2.660236 GACGTAAACGATTCTTGCGAGT 59.340 45.455 9.86 0.00 43.02 4.18
94 95 3.634730 ATGACGTAAACGATTCTTGCG 57.365 42.857 9.86 0.00 43.02 4.85
157 158 7.306213 TGCGTTTGATTTCGATAAATACCAAA 58.694 30.769 0.00 0.00 35.41 3.28
169 170 6.667981 TGACTTTAAATGCGTTTGATTTCG 57.332 33.333 14.25 0.00 0.00 3.46
224 225 8.713971 CCTGGCCATTCAGTTATATATATGGTA 58.286 37.037 5.51 2.34 35.94 3.25
225 226 7.577303 CCTGGCCATTCAGTTATATATATGGT 58.423 38.462 5.51 0.00 35.94 3.55
226 227 6.488006 GCCTGGCCATTCAGTTATATATATGG 59.512 42.308 5.51 0.00 36.47 2.74
227 228 7.285566 AGCCTGGCCATTCAGTTATATATATG 58.714 38.462 16.57 0.00 33.14 1.78
228 229 7.457380 AGCCTGGCCATTCAGTTATATATAT 57.543 36.000 16.57 0.00 33.14 0.86
229 230 6.891306 AGCCTGGCCATTCAGTTATATATA 57.109 37.500 16.57 0.00 33.14 0.86
230 231 5.786121 AGCCTGGCCATTCAGTTATATAT 57.214 39.130 16.57 0.00 33.14 0.86
231 232 5.045869 GGTAGCCTGGCCATTCAGTTATATA 60.046 44.000 16.57 0.00 33.14 0.86
248 249 3.335711 GCTGGGGAATGGTAGCCT 58.664 61.111 0.00 0.00 0.00 4.58
279 280 1.613630 GGCTCCCCTCTCTGGTTGA 60.614 63.158 0.00 0.00 0.00 3.18
285 286 1.306568 GGACTTGGCTCCCCTCTCT 60.307 63.158 0.00 0.00 0.00 3.10
359 360 2.046507 AGCAAGAGAAGCCAGGCG 60.047 61.111 5.55 0.00 0.00 5.52
363 364 1.410517 CTATCGGAGCAAGAGAAGCCA 59.589 52.381 0.00 0.00 0.00 4.75
365 366 3.255642 AGATCTATCGGAGCAAGAGAAGC 59.744 47.826 0.00 0.00 31.91 3.86
372 373 6.161855 ACAACAATAGATCTATCGGAGCAA 57.838 37.500 15.62 0.00 31.91 3.91
378 379 6.893759 AGAGACGACAACAATAGATCTATCG 58.106 40.000 15.62 15.83 0.00 2.92
380 381 7.001674 AGGAGAGACGACAACAATAGATCTAT 58.998 38.462 9.57 9.57 0.00 1.98
381 382 6.358178 AGGAGAGACGACAACAATAGATCTA 58.642 40.000 4.57 4.57 0.00 1.98
389 390 3.223435 AGAGAAGGAGAGACGACAACAA 58.777 45.455 0.00 0.00 0.00 2.83
390 391 2.814919 GAGAGAAGGAGAGACGACAACA 59.185 50.000 0.00 0.00 0.00 3.33
395 396 2.171027 GGTAGGAGAGAAGGAGAGACGA 59.829 54.545 0.00 0.00 0.00 4.20
398 399 2.171027 GACGGTAGGAGAGAAGGAGAGA 59.829 54.545 0.00 0.00 0.00 3.10
411 412 0.945265 TTGGAAAACGCGACGGTAGG 60.945 55.000 15.93 0.00 0.00 3.18
414 415 0.664224 AATTTGGAAAACGCGACGGT 59.336 45.000 15.93 0.00 0.00 4.83
446 447 4.096984 CACAGAAGGACAAGAGTTGCTTTT 59.903 41.667 0.00 0.00 33.60 2.27
447 448 3.629398 CACAGAAGGACAAGAGTTGCTTT 59.371 43.478 0.00 0.00 33.60 3.51
498 499 2.250741 GAGAGGAGGGCAGACAAGGC 62.251 65.000 0.00 0.00 0.00 4.35
507 508 4.683400 CGAGAGATATAGAGAGAGGAGGGC 60.683 54.167 0.00 0.00 0.00 5.19
512 513 5.127845 AGAGAGCGAGAGATATAGAGAGAGG 59.872 48.000 0.00 0.00 0.00 3.69
596 597 1.304254 TGCTTCAACGTTGCAGCTTA 58.696 45.000 39.03 25.33 45.63 3.09
620 621 5.191722 AGAAGGCAATATGAGGTCTGGTTAA 59.808 40.000 0.00 0.00 0.00 2.01
690 691 6.016192 TCACTAAGATAACGATGATCCCAGAC 60.016 42.308 0.00 0.00 0.00 3.51
691 692 6.068670 TCACTAAGATAACGATGATCCCAGA 58.931 40.000 0.00 0.00 0.00 3.86
692 693 6.332735 TCACTAAGATAACGATGATCCCAG 57.667 41.667 0.00 0.00 0.00 4.45
693 694 6.097696 TGTTCACTAAGATAACGATGATCCCA 59.902 38.462 0.00 0.00 0.00 4.37
694 695 6.513180 TGTTCACTAAGATAACGATGATCCC 58.487 40.000 0.00 0.00 0.00 3.85
695 696 7.042658 GGTTGTTCACTAAGATAACGATGATCC 60.043 40.741 0.00 0.00 0.00 3.36
696 697 7.042658 GGGTTGTTCACTAAGATAACGATGATC 60.043 40.741 0.00 0.00 0.00 2.92
697 698 6.761714 GGGTTGTTCACTAAGATAACGATGAT 59.238 38.462 0.00 0.00 0.00 2.45
698 699 6.103997 GGGTTGTTCACTAAGATAACGATGA 58.896 40.000 0.00 0.00 0.00 2.92
699 700 5.293569 GGGGTTGTTCACTAAGATAACGATG 59.706 44.000 0.00 0.00 0.00 3.84
700 701 5.046159 TGGGGTTGTTCACTAAGATAACGAT 60.046 40.000 0.00 0.00 0.00 3.73
701 702 4.283978 TGGGGTTGTTCACTAAGATAACGA 59.716 41.667 0.00 0.00 0.00 3.85
702 703 4.571919 TGGGGTTGTTCACTAAGATAACG 58.428 43.478 0.00 0.00 0.00 3.18
721 722 1.325476 GCTGGGCCAGAAAGAATGGG 61.325 60.000 37.07 7.79 38.33 4.00
740 741 8.072567 GCACTAATCTTACATATTCAAAGGCAG 58.927 37.037 0.00 0.00 0.00 4.85
746 747 9.448438 ACTGTTGCACTAATCTTACATATTCAA 57.552 29.630 0.00 0.00 0.00 2.69
761 763 4.765273 TGTGAGAGAAAACTGTTGCACTA 58.235 39.130 0.00 0.00 0.00 2.74
807 809 6.798427 TCACTCCAGCTAATCTACAAAGAT 57.202 37.500 0.00 0.00 44.67 2.40
869 873 5.851177 CACCAATGTTAATCACGAAGAACAC 59.149 40.000 0.00 0.00 34.80 3.32
955 959 0.693049 AATCTCAAGGTTCAGCGGGT 59.307 50.000 0.00 0.00 0.00 5.28
1011 1015 4.162690 GCCTGCAGTACCTCCGGG 62.163 72.222 13.81 0.00 38.88 5.73
1025 1029 0.539051 CCTCTGGACGATTTCTGCCT 59.461 55.000 0.00 0.00 0.00 4.75
1059 1063 5.064452 CACAAGGGAAAGAGAATTCAGATCG 59.936 44.000 8.44 0.00 0.00 3.69
1100 1104 1.438651 CCTTTGATTCGCCTCAACGA 58.561 50.000 0.00 0.00 41.04 3.85
1101 1105 0.447801 CCCTTTGATTCGCCTCAACG 59.552 55.000 0.00 0.00 34.96 4.10
1130 1134 4.217118 CAGAAAACAAGCTGCATCCTAAGT 59.783 41.667 1.02 0.00 0.00 2.24
1200 1204 6.394809 ACCGGTGTAATTGATTTCCATTTTC 58.605 36.000 6.12 0.00 0.00 2.29
1225 1229 5.702670 TGTATGAGAAGAAGCTCAAGGTTTG 59.297 40.000 0.00 0.00 46.94 2.93
1299 1303 4.252971 TGGTACAGAGTTTAGTGTGAGC 57.747 45.455 0.00 0.00 0.00 4.26
1830 1849 4.218200 AGAAAATCATTGTCATCGGCAACA 59.782 37.500 0.00 0.00 0.00 3.33
1836 1855 9.438291 GGTATGTAAAGAAAATCATTGTCATCG 57.562 33.333 0.00 0.00 0.00 3.84
1983 2005 6.102663 ACAAGACTGAATGAGAATCCTAACG 58.897 40.000 0.00 0.00 0.00 3.18
2117 2139 1.972872 CATCCCAGCATCTGTTACCC 58.027 55.000 0.00 0.00 0.00 3.69
2157 2179 1.342819 AGTGTCAGACTCCTCAAGCAC 59.657 52.381 1.31 0.00 0.00 4.40
2217 2239 3.189287 CCAACTTCTGTGAATGTACCAGC 59.811 47.826 0.00 0.00 0.00 4.85
2259 2281 1.094073 GCGGAGAGATGCAAGCACAT 61.094 55.000 0.00 0.00 0.00 3.21
2379 2401 6.207810 TGAGGCACAACCGAAAATAACTTTAT 59.792 34.615 0.00 0.00 46.52 1.40
2407 2429 3.240134 AACGCCAGCGACATCCACT 62.240 57.895 20.32 0.00 42.83 4.00
2421 2443 1.668419 AATGATAGCAGGGTCAACGC 58.332 50.000 0.00 0.00 0.00 4.84
2423 2445 5.357878 TGATGAAAATGATAGCAGGGTCAAC 59.642 40.000 0.00 0.00 0.00 3.18
2438 2460 7.232127 ACACAGGTTCTGAGAAATGATGAAAAT 59.768 33.333 13.66 0.00 35.18 1.82
2453 2475 4.271696 TCACCATTAGACACAGGTTCTG 57.728 45.455 0.00 0.00 37.52 3.02
2473 2495 2.415893 CGCCACATTGGATCCAAAGTTC 60.416 50.000 28.28 21.45 40.96 3.01
2490 2512 6.744112 ACAATTTTAAAGACTTCATTCGCCA 58.256 32.000 0.00 0.00 0.00 5.69
2493 2515 9.450807 AACAGACAATTTTAAAGACTTCATTCG 57.549 29.630 0.00 0.00 0.00 3.34
2502 2524 8.514330 ACACCAGTAACAGACAATTTTAAAGA 57.486 30.769 0.00 0.00 0.00 2.52
2538 2560 5.227238 CTACAGGAGCAAAGCAACATAAG 57.773 43.478 0.00 0.00 0.00 1.73
2555 2577 5.235186 CGGACATGGAGAAATTAAGCTACAG 59.765 44.000 0.00 0.00 0.00 2.74
2562 2584 3.358111 TGGCGGACATGGAGAAATTAA 57.642 42.857 0.00 0.00 0.00 1.40
2578 2600 6.324819 ACTTATGACAATTTTCAAGATGGCG 58.675 36.000 0.00 0.00 0.00 5.69
2601 2623 6.863126 CCTGAAATGTTTATCTTGTGGTTGAC 59.137 38.462 0.00 0.00 0.00 3.18
2638 2660 2.736347 GAGAGGCACTGTTAGGACCTA 58.264 52.381 0.00 0.00 41.55 3.08
2687 2709 9.944663 AATATAACGGCAATAATAACACACAAG 57.055 29.630 0.00 0.00 0.00 3.16
2728 2750 4.121317 TGGTAACACCACAACTTCGTAAG 58.879 43.478 0.00 0.00 44.79 2.34
2760 2782 2.887152 GCATGGGTTCAATGATCCCTAC 59.113 50.000 25.07 13.54 41.02 3.18
2812 2834 5.630121 ACATCTTTTGGGATGACACTTACA 58.370 37.500 10.81 0.00 44.01 2.41
2813 2835 6.093633 GGTACATCTTTTGGGATGACACTTAC 59.906 42.308 10.81 3.54 44.01 2.34
2814 2836 6.177610 GGTACATCTTTTGGGATGACACTTA 58.822 40.000 10.81 0.00 44.01 2.24
2815 2837 5.010282 GGTACATCTTTTGGGATGACACTT 58.990 41.667 10.81 0.00 44.01 3.16
2816 2838 4.042809 TGGTACATCTTTTGGGATGACACT 59.957 41.667 10.81 0.00 44.01 3.55
2834 2856 7.883311 ACATTATGGAGGCTACAAATATGGTAC 59.117 37.037 2.08 0.00 0.00 3.34
2836 2858 6.852404 ACATTATGGAGGCTACAAATATGGT 58.148 36.000 2.08 0.00 0.00 3.55
2881 2903 7.841956 ACTATGATGGAGCGCTTATAAGTTAT 58.158 34.615 13.26 0.17 0.00 1.89
2882 2904 7.228314 ACTATGATGGAGCGCTTATAAGTTA 57.772 36.000 13.26 0.00 0.00 2.24
2883 2905 6.102897 ACTATGATGGAGCGCTTATAAGTT 57.897 37.500 13.26 0.00 0.00 2.66
2884 2906 5.730296 ACTATGATGGAGCGCTTATAAGT 57.270 39.130 13.26 10.81 0.00 2.24
2885 2907 6.128445 CCAAACTATGATGGAGCGCTTATAAG 60.128 42.308 13.26 8.20 39.12 1.73
2886 2908 5.700832 CCAAACTATGATGGAGCGCTTATAA 59.299 40.000 13.26 2.87 39.12 0.98
2887 2909 5.011635 TCCAAACTATGATGGAGCGCTTATA 59.988 40.000 13.26 0.64 40.74 0.98
2888 2910 4.067896 CCAAACTATGATGGAGCGCTTAT 58.932 43.478 13.26 9.90 39.12 1.73
2891 2913 1.486310 TCCAAACTATGATGGAGCGCT 59.514 47.619 11.27 11.27 40.74 5.92
2901 2923 5.643777 AGACTCCAAAACGATCCAAACTATG 59.356 40.000 0.00 0.00 0.00 2.23
2914 2936 2.135933 CACCTCGACAGACTCCAAAAC 58.864 52.381 0.00 0.00 0.00 2.43
2927 2949 4.141459 ACATATGGTAGACTCTCACCTCGA 60.141 45.833 7.80 0.00 35.73 4.04
2942 2964 2.877786 CACACACACACACACATATGGT 59.122 45.455 7.80 0.00 0.00 3.55
2956 3204 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2957 3205 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2958 3206 1.598882 AACACACACACACACACACA 58.401 45.000 0.00 0.00 0.00 3.72
2959 3207 2.287308 ACAAACACACACACACACACAC 60.287 45.455 0.00 0.00 0.00 3.82
2960 3208 1.950216 ACAAACACACACACACACACA 59.050 42.857 0.00 0.00 0.00 3.72
2961 3209 2.697431 ACAAACACACACACACACAC 57.303 45.000 0.00 0.00 0.00 3.82
2962 3210 3.717400 AAACAAACACACACACACACA 57.283 38.095 0.00 0.00 0.00 3.72
2963 3211 4.045104 TGAAAACAAACACACACACACAC 58.955 39.130 0.00 0.00 0.00 3.82
2964 3212 4.045104 GTGAAAACAAACACACACACACA 58.955 39.130 0.00 0.00 37.05 3.72
2965 3213 4.045104 TGTGAAAACAAACACACACACAC 58.955 39.130 0.00 0.00 41.19 3.82
2966 3214 4.307443 TGTGAAAACAAACACACACACA 57.693 36.364 0.00 0.00 41.19 3.72
2972 3220 4.336889 TTTGGGTGTGAAAACAAACACA 57.663 36.364 8.08 0.00 46.83 3.72
2973 3221 4.094146 CCATTTGGGTGTGAAAACAAACAC 59.906 41.667 0.00 0.00 44.79 3.32
2974 3222 4.256920 CCATTTGGGTGTGAAAACAAACA 58.743 39.130 0.00 0.00 35.87 2.83
2975 3223 4.873768 CCATTTGGGTGTGAAAACAAAC 57.126 40.909 0.00 0.00 35.87 2.93
2987 3235 9.074576 CTAAAAGTTTAGAAGTACCATTTGGGT 57.925 33.333 5.06 0.00 46.34 4.51
2988 3236 8.520351 CCTAAAAGTTTAGAAGTACCATTTGGG 58.480 37.037 11.57 0.00 42.05 4.12
2989 3237 8.520351 CCCTAAAAGTTTAGAAGTACCATTTGG 58.480 37.037 11.57 0.00 42.05 3.28
2990 3238 8.520351 CCCCTAAAAGTTTAGAAGTACCATTTG 58.480 37.037 11.57 0.00 42.05 2.32
2991 3239 7.672660 CCCCCTAAAAGTTTAGAAGTACCATTT 59.327 37.037 11.57 0.00 42.05 2.32
2992 3240 7.018851 TCCCCCTAAAAGTTTAGAAGTACCATT 59.981 37.037 11.57 0.00 42.05 3.16
2993 3241 6.506413 TCCCCCTAAAAGTTTAGAAGTACCAT 59.494 38.462 11.57 0.00 42.05 3.55
2994 3242 5.851138 TCCCCCTAAAAGTTTAGAAGTACCA 59.149 40.000 11.57 0.00 42.05 3.25
2995 3243 6.378661 TCCCCCTAAAAGTTTAGAAGTACC 57.621 41.667 11.57 0.00 42.05 3.34
2996 3244 7.094463 GCTTTCCCCCTAAAAGTTTAGAAGTAC 60.094 40.741 11.57 0.00 42.05 2.73
2997 3245 6.944290 GCTTTCCCCCTAAAAGTTTAGAAGTA 59.056 38.462 11.57 0.00 42.05 2.24
2998 3246 5.773680 GCTTTCCCCCTAAAAGTTTAGAAGT 59.226 40.000 11.57 0.00 42.05 3.01
2999 3247 5.773176 TGCTTTCCCCCTAAAAGTTTAGAAG 59.227 40.000 11.57 8.08 42.05 2.85
3000 3248 5.707495 TGCTTTCCCCCTAAAAGTTTAGAA 58.293 37.500 11.57 0.00 42.05 2.10
3001 3249 5.327737 TGCTTTCCCCCTAAAAGTTTAGA 57.672 39.130 11.57 0.00 42.05 2.10
3002 3250 5.566826 GCTTGCTTTCCCCCTAAAAGTTTAG 60.567 44.000 4.16 4.16 39.80 1.85
3003 3251 4.282449 GCTTGCTTTCCCCCTAAAAGTTTA 59.718 41.667 0.00 0.00 36.36 2.01
3004 3252 3.071023 GCTTGCTTTCCCCCTAAAAGTTT 59.929 43.478 0.00 0.00 36.36 2.66
3005 3253 2.632996 GCTTGCTTTCCCCCTAAAAGTT 59.367 45.455 0.00 0.00 36.36 2.66
3006 3254 2.248248 GCTTGCTTTCCCCCTAAAAGT 58.752 47.619 0.00 0.00 36.36 2.66
3007 3255 2.247358 TGCTTGCTTTCCCCCTAAAAG 58.753 47.619 0.00 0.00 36.91 2.27
3008 3256 2.390225 TGCTTGCTTTCCCCCTAAAA 57.610 45.000 0.00 0.00 0.00 1.52
3009 3257 2.390225 TTGCTTGCTTTCCCCCTAAA 57.610 45.000 0.00 0.00 0.00 1.85
3010 3258 2.390225 TTTGCTTGCTTTCCCCCTAA 57.610 45.000 0.00 0.00 0.00 2.69
3011 3259 2.390225 TTTTGCTTGCTTTCCCCCTA 57.610 45.000 0.00 0.00 0.00 3.53
3012 3260 1.506025 TTTTTGCTTGCTTTCCCCCT 58.494 45.000 0.00 0.00 0.00 4.79
3046 3294 5.977129 CCATTTGAAGGTTACACTTGTTGTC 59.023 40.000 0.00 0.00 39.91 3.18
3054 3303 6.628919 AAGTGTACCATTTGAAGGTTACAC 57.371 37.500 7.77 7.77 40.25 2.90
3058 3307 7.833285 ATGTTAAGTGTACCATTTGAAGGTT 57.167 32.000 0.00 0.00 40.54 3.50
3067 3316 7.015195 AGGAAAAAGCAATGTTAAGTGTACCAT 59.985 33.333 0.00 0.00 0.00 3.55
3085 3334 2.096713 CAGTGCTTCGTCGAGGAAAAAG 60.097 50.000 19.96 10.79 0.00 2.27
3098 3347 1.291132 GAACGGGATAGCAGTGCTTC 58.709 55.000 25.23 18.88 40.44 3.86
3134 3383 4.414852 TCGTATTAGTGTAACAAGCGTCC 58.585 43.478 0.00 0.00 41.43 4.79
3136 3385 5.221880 TGTTCGTATTAGTGTAACAAGCGT 58.778 37.500 0.00 0.00 41.43 5.07
3137 3386 5.750484 TGTTCGTATTAGTGTAACAAGCG 57.250 39.130 0.00 0.00 41.43 4.68
3186 3436 9.642327 ACATTAAAAACAAACGGAAAGTAAGTT 57.358 25.926 0.00 0.00 33.30 2.66
3191 3441 9.589111 ACAATACATTAAAAACAAACGGAAAGT 57.411 25.926 0.00 0.00 0.00 2.66
3194 3444 9.582431 TGAACAATACATTAAAAACAAACGGAA 57.418 25.926 0.00 0.00 0.00 4.30
3195 3445 9.021863 GTGAACAATACATTAAAAACAAACGGA 57.978 29.630 0.00 0.00 0.00 4.69
3196 3446 8.270111 GGTGAACAATACATTAAAAACAAACGG 58.730 33.333 0.00 0.00 0.00 4.44
3197 3447 7.993792 CGGTGAACAATACATTAAAAACAAACG 59.006 33.333 0.00 0.00 0.00 3.60
3198 3448 8.809478 ACGGTGAACAATACATTAAAAACAAAC 58.191 29.630 0.00 0.00 0.00 2.93
3199 3449 8.928270 ACGGTGAACAATACATTAAAAACAAA 57.072 26.923 0.00 0.00 0.00 2.83
3204 3454 9.828852 GACATTACGGTGAACAATACATTAAAA 57.171 29.630 0.00 0.00 0.00 1.52
3205 3455 8.169910 CGACATTACGGTGAACAATACATTAAA 58.830 33.333 0.00 0.00 0.00 1.52
3206 3456 7.544915 TCGACATTACGGTGAACAATACATTAA 59.455 33.333 0.00 0.00 0.00 1.40
3207 3457 7.034397 TCGACATTACGGTGAACAATACATTA 58.966 34.615 0.00 0.00 0.00 1.90
3208 3458 5.870433 TCGACATTACGGTGAACAATACATT 59.130 36.000 0.00 0.00 0.00 2.71
3209 3459 5.412640 TCGACATTACGGTGAACAATACAT 58.587 37.500 0.00 0.00 0.00 2.29
3210 3460 4.807443 TCGACATTACGGTGAACAATACA 58.193 39.130 0.00 0.00 0.00 2.29
3211 3461 5.961395 ATCGACATTACGGTGAACAATAC 57.039 39.130 0.00 0.00 0.00 1.89
3212 3462 6.199531 GCTAATCGACATTACGGTGAACAATA 59.800 38.462 0.00 0.00 0.00 1.90
3213 3463 5.006358 GCTAATCGACATTACGGTGAACAAT 59.994 40.000 0.00 0.00 0.00 2.71
3214 3464 4.327898 GCTAATCGACATTACGGTGAACAA 59.672 41.667 0.00 0.00 0.00 2.83
3215 3465 3.861113 GCTAATCGACATTACGGTGAACA 59.139 43.478 0.00 0.00 0.00 3.18
3216 3466 3.061403 CGCTAATCGACATTACGGTGAAC 60.061 47.826 0.00 0.00 41.67 3.18
3217 3467 3.110358 CGCTAATCGACATTACGGTGAA 58.890 45.455 0.00 0.00 41.67 3.18
3218 3468 2.355444 TCGCTAATCGACATTACGGTGA 59.645 45.455 0.00 0.00 43.16 4.02
3219 3469 2.723209 TCGCTAATCGACATTACGGTG 58.277 47.619 0.00 0.00 43.16 4.94
3243 3493 9.764363 CACCTCTGCTACTAATTATGTATGAAA 57.236 33.333 0.00 0.00 0.00 2.69
3244 3494 8.924303 ACACCTCTGCTACTAATTATGTATGAA 58.076 33.333 0.00 0.00 0.00 2.57
3245 3495 8.478775 ACACCTCTGCTACTAATTATGTATGA 57.521 34.615 0.00 0.00 0.00 2.15
3246 3496 8.982685 CAACACCTCTGCTACTAATTATGTATG 58.017 37.037 0.00 0.00 0.00 2.39
3247 3497 8.924303 TCAACACCTCTGCTACTAATTATGTAT 58.076 33.333 0.00 0.00 0.00 2.29
3248 3498 8.301252 TCAACACCTCTGCTACTAATTATGTA 57.699 34.615 0.00 0.00 0.00 2.29
3249 3499 7.182817 TCAACACCTCTGCTACTAATTATGT 57.817 36.000 0.00 0.00 0.00 2.29
3250 3500 8.492673 TTTCAACACCTCTGCTACTAATTATG 57.507 34.615 0.00 0.00 0.00 1.90
3251 3501 9.686683 ATTTTCAACACCTCTGCTACTAATTAT 57.313 29.630 0.00 0.00 0.00 1.28
3252 3502 9.515226 AATTTTCAACACCTCTGCTACTAATTA 57.485 29.630 0.00 0.00 0.00 1.40
3253 3503 8.409358 AATTTTCAACACCTCTGCTACTAATT 57.591 30.769 0.00 0.00 0.00 1.40
3254 3504 8.299570 CAAATTTTCAACACCTCTGCTACTAAT 58.700 33.333 0.00 0.00 0.00 1.73
3255 3505 7.648142 CAAATTTTCAACACCTCTGCTACTAA 58.352 34.615 0.00 0.00 0.00 2.24
3256 3506 6.293955 GCAAATTTTCAACACCTCTGCTACTA 60.294 38.462 0.00 0.00 0.00 1.82
3257 3507 5.507985 GCAAATTTTCAACACCTCTGCTACT 60.508 40.000 0.00 0.00 0.00 2.57
3258 3508 4.681483 GCAAATTTTCAACACCTCTGCTAC 59.319 41.667 0.00 0.00 0.00 3.58
3259 3509 4.261994 GGCAAATTTTCAACACCTCTGCTA 60.262 41.667 0.00 0.00 0.00 3.49
3260 3510 3.493176 GGCAAATTTTCAACACCTCTGCT 60.493 43.478 0.00 0.00 0.00 4.24
3261 3511 2.802247 GGCAAATTTTCAACACCTCTGC 59.198 45.455 0.00 0.00 0.00 4.26
3262 3512 4.326504 AGGCAAATTTTCAACACCTCTG 57.673 40.909 0.00 0.00 0.00 3.35
3263 3513 5.362430 TGTAAGGCAAATTTTCAACACCTCT 59.638 36.000 0.00 0.00 0.00 3.69
3264 3514 5.596845 TGTAAGGCAAATTTTCAACACCTC 58.403 37.500 0.00 0.00 0.00 3.85
3265 3515 5.606348 TGTAAGGCAAATTTTCAACACCT 57.394 34.783 0.00 0.00 0.00 4.00
3266 3516 6.670077 TTTGTAAGGCAAATTTTCAACACC 57.330 33.333 0.00 0.00 41.68 4.16
3278 3528 5.192927 AGCTGCTACATATTTGTAAGGCAA 58.807 37.500 0.00 0.00 38.37 4.52
3279 3529 4.780815 AGCTGCTACATATTTGTAAGGCA 58.219 39.130 0.00 9.01 37.86 4.75
3280 3530 7.201565 GCTATAGCTGCTACATATTTGTAAGGC 60.202 40.741 17.75 0.11 36.65 4.35
3281 3531 7.278868 GGCTATAGCTGCTACATATTTGTAAGG 59.721 40.741 23.53 0.00 38.29 2.69
3282 3532 8.037758 AGGCTATAGCTGCTACATATTTGTAAG 58.962 37.037 23.53 0.00 38.29 2.34
3283 3533 7.819415 CAGGCTATAGCTGCTACATATTTGTAA 59.181 37.037 23.53 0.00 38.29 2.41
3284 3534 7.323420 CAGGCTATAGCTGCTACATATTTGTA 58.677 38.462 23.53 0.00 41.70 2.41
3285 3535 6.169094 CAGGCTATAGCTGCTACATATTTGT 58.831 40.000 23.53 0.00 41.70 2.83
3286 3536 5.064452 GCAGGCTATAGCTGCTACATATTTG 59.936 44.000 27.64 7.83 39.95 2.32
3287 3537 5.181748 GCAGGCTATAGCTGCTACATATTT 58.818 41.667 27.64 0.00 39.95 1.40
3288 3538 4.223700 TGCAGGCTATAGCTGCTACATATT 59.776 41.667 31.17 0.00 41.95 1.28
3289 3539 3.771479 TGCAGGCTATAGCTGCTACATAT 59.229 43.478 31.17 0.00 41.95 1.78
3290 3540 3.165071 TGCAGGCTATAGCTGCTACATA 58.835 45.455 31.17 18.49 41.95 2.29
3291 3541 1.973515 TGCAGGCTATAGCTGCTACAT 59.026 47.619 31.17 0.33 41.95 2.29
3292 3542 1.413118 TGCAGGCTATAGCTGCTACA 58.587 50.000 31.17 18.95 41.95 2.74
3293 3543 2.758736 ATGCAGGCTATAGCTGCTAC 57.241 50.000 31.17 17.20 41.95 3.58
3294 3544 3.777106 AAATGCAGGCTATAGCTGCTA 57.223 42.857 31.17 23.34 41.95 3.49
3295 3545 2.621998 CAAAATGCAGGCTATAGCTGCT 59.378 45.455 31.17 18.93 41.95 4.24
3296 3546 2.861360 GCAAAATGCAGGCTATAGCTGC 60.861 50.000 27.94 27.94 44.26 5.25
3297 3547 3.009301 GCAAAATGCAGGCTATAGCTG 57.991 47.619 23.53 18.99 44.26 4.24
3309 3559 1.375013 CAGCTGGGGTGCAAAATGC 60.375 57.895 5.57 0.00 45.29 3.56
3310 3560 0.899720 ATCAGCTGGGGTGCAAAATG 59.100 50.000 15.13 0.00 34.99 2.32
3311 3561 0.899720 CATCAGCTGGGGTGCAAAAT 59.100 50.000 15.13 0.00 34.99 1.82
3312 3562 1.186917 CCATCAGCTGGGGTGCAAAA 61.187 55.000 15.13 0.00 41.82 2.44
3313 3563 1.607178 CCATCAGCTGGGGTGCAAA 60.607 57.895 15.13 0.00 41.82 3.68
3314 3564 2.036098 CCATCAGCTGGGGTGCAA 59.964 61.111 15.13 0.00 41.82 4.08
3322 3572 2.031069 GCATAGCATTCACCATCAGCTG 60.031 50.000 7.63 7.63 36.80 4.24
3323 3573 2.228059 GCATAGCATTCACCATCAGCT 58.772 47.619 0.00 0.00 39.22 4.24
3324 3574 1.951602 TGCATAGCATTCACCATCAGC 59.048 47.619 0.00 0.00 31.71 4.26
3325 3575 3.003378 CAGTGCATAGCATTCACCATCAG 59.997 47.826 0.00 0.00 41.91 2.90
3326 3576 2.946990 CAGTGCATAGCATTCACCATCA 59.053 45.455 0.00 0.00 41.91 3.07
3327 3577 2.292569 CCAGTGCATAGCATTCACCATC 59.707 50.000 0.00 0.00 41.91 3.51
3328 3578 2.304092 CCAGTGCATAGCATTCACCAT 58.696 47.619 0.00 0.00 41.91 3.55
3329 3579 1.682702 CCCAGTGCATAGCATTCACCA 60.683 52.381 0.00 0.00 41.91 4.17
3330 3580 1.027357 CCCAGTGCATAGCATTCACC 58.973 55.000 0.00 0.00 41.91 4.02
3331 3581 0.383231 GCCCAGTGCATAGCATTCAC 59.617 55.000 0.00 0.00 41.91 3.18
3332 3582 2.797837 GCCCAGTGCATAGCATTCA 58.202 52.632 0.00 0.00 41.91 2.57


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

AutoCloner maintained by Alex Coulton.