Multiple sequence alignment - TraesCS7D01G150300

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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 TraesCS7D01G150300 chr7D 100.000 3243 0 0 1 3243 99619245 99616003 0.000000e+00 5989.0
1 TraesCS7D01G150300 chr7D 90.840 393 33 2 2525 2917 230975906 230975517 1.030000e-144 523.0
2 TraesCS7D01G150300 chr7D 84.615 299 36 8 2953 3243 600897211 600897507 4.090000e-74 289.0
3 TraesCS7D01G150300 chr7B 95.980 1194 31 10 878 2054 54789153 54787960 0.000000e+00 1923.0
4 TraesCS7D01G150300 chr7B 94.769 497 18 6 126 617 54790174 54789681 0.000000e+00 767.0
5 TraesCS7D01G150300 chr7B 90.331 393 35 3 2527 2917 615788568 615788177 2.230000e-141 512.0
6 TraesCS7D01G150300 chr7B 90.066 302 19 2 2203 2504 54787772 54787482 6.570000e-102 381.0
7 TraesCS7D01G150300 chr7B 94.215 121 3 2 2088 2208 54787962 54787846 7.150000e-42 182.0
8 TraesCS7D01G150300 chr7B 95.536 112 5 0 1 112 54790268 54790157 2.570000e-41 180.0
9 TraesCS7D01G150300 chr7B 97.143 35 1 0 2921 2955 54787475 54787441 3.490000e-05 60.2
10 TraesCS7D01G150300 chr7A 91.108 686 41 8 883 1563 102040433 102041103 0.000000e+00 911.0
11 TraesCS7D01G150300 chr7A 94.407 590 26 4 1595 2181 102041546 102042131 0.000000e+00 900.0
12 TraesCS7D01G150300 chr7A 89.559 431 40 3 126 551 102039685 102040115 2.850000e-150 542.0
13 TraesCS7D01G150300 chr7A 90.979 388 35 0 2530 2917 674358482 674358095 1.030000e-144 523.0
14 TraesCS7D01G150300 chr7A 90.979 388 35 0 2530 2917 674407063 674406676 1.030000e-144 523.0
15 TraesCS7D01G150300 chr7A 88.933 253 28 0 612 864 329488277 329488529 2.430000e-81 313.0
16 TraesCS7D01G150300 chr7A 83.557 298 40 8 2953 3243 692893166 692893461 1.480000e-68 270.0
17 TraesCS7D01G150300 chr3D 91.603 393 27 5 2527 2918 590229124 590228737 3.680000e-149 538.0
18 TraesCS7D01G150300 chr3D 91.260 389 31 3 2527 2915 590228732 590228347 7.970000e-146 527.0
19 TraesCS7D01G150300 chr3D 85.556 270 28 6 2983 3243 510649717 510649450 4.120000e-69 272.0
20 TraesCS7D01G150300 chr2A 89.756 410 37 5 2521 2927 764335452 764335859 1.330000e-143 520.0
21 TraesCS7D01G150300 chr5B 90.380 395 31 7 2525 2918 710240920 710240532 2.230000e-141 512.0
22 TraesCS7D01G150300 chr2D 90.561 392 29 6 2529 2917 8142766 8142380 2.230000e-141 512.0
23 TraesCS7D01G150300 chr2D 87.547 265 33 0 615 879 455942225 455942489 1.130000e-79 307.0
24 TraesCS7D01G150300 chr1B 89.062 256 28 0 615 870 442201897 442201642 5.220000e-83 318.0
25 TraesCS7D01G150300 chr5D 88.889 252 28 0 615 866 538762370 538762621 8.740000e-81 311.0
26 TraesCS7D01G150300 chr4A 87.879 264 28 3 615 876 674617054 674616793 1.130000e-79 307.0
27 TraesCS7D01G150300 chr4A 82.657 271 27 12 2990 3243 514414830 514415097 4.210000e-54 222.0
28 TraesCS7D01G150300 chr5A 87.739 261 31 1 610 870 512225987 512225728 1.460000e-78 303.0
29 TraesCS7D01G150300 chr5A 88.031 259 28 3 614 870 659829026 659828769 1.460000e-78 303.0
30 TraesCS7D01G150300 chr5A 87.170 265 34 0 615 879 483514744 483514480 5.260000e-78 302.0
31 TraesCS7D01G150300 chr6A 88.142 253 30 0 612 864 76765364 76765616 5.260000e-78 302.0
32 TraesCS7D01G150300 chr6A 85.235 298 33 8 2953 3243 25769413 25769120 2.450000e-76 296.0
33 TraesCS7D01G150300 chrUn 87.356 261 26 5 2990 3243 61742339 61742599 3.160000e-75 292.0
34 TraesCS7D01G150300 chrUn 85.570 298 22 7 2953 3243 94877028 94876745 3.160000e-75 292.0
35 TraesCS7D01G150300 chrUn 82.824 262 28 9 2993 3238 254958174 254957914 5.450000e-53 219.0
36 TraesCS7D01G150300 chr4D 85.235 298 26 6 2953 3243 499898202 499897916 1.140000e-74 291.0
37 TraesCS7D01G150300 chr6B 81.132 265 36 8 2990 3243 716432815 716433076 1.970000e-47 200.0
38 TraesCS7D01G150300 chr3A 85.227 176 18 5 3073 3243 26671807 26671979 1.200000e-39 174.0
39 TraesCS7D01G150300 chr1D 93.220 118 7 1 2951 3068 383154936 383155052 4.300000e-39 172.0


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 TraesCS7D01G150300 chr7D 99616003 99619245 3242 True 5989.000000 5989 100.000000 1 3243 1 chr7D.!!$R1 3242
1 TraesCS7D01G150300 chr7B 54787441 54790268 2827 True 582.200000 1923 94.618167 1 2955 6 chr7B.!!$R2 2954
2 TraesCS7D01G150300 chr7A 102039685 102042131 2446 False 784.333333 911 91.691333 126 2181 3 chr7A.!!$F3 2055
3 TraesCS7D01G150300 chr3D 590228347 590229124 777 True 532.500000 538 91.431500 2527 2918 2 chr3D.!!$R2 391

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
499 505 0.249398 AGCCTTGGATCACGTACACC 59.751 55.0 0.0 0.0 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2462 3401 0.101939 CTCGTAAACCTAGCCGTCCC 59.898 60.0 0.0 0.0 0.0 4.46 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
27 28 1.448985 AGAATCTTTAAAGGCGCGCA 58.551 45.000 34.42 9.57 0.00 6.09
55 56 1.603455 CACACGCCACCCCATCTTT 60.603 57.895 0.00 0.00 0.00 2.52
74 75 8.897752 CCATCTTTATTCCTTTAGGTCTCTTTG 58.102 37.037 0.00 0.00 36.34 2.77
112 113 6.767902 TGCGCCTAATATTCTCTGATTCTTTT 59.232 34.615 4.18 0.00 0.00 2.27
113 114 7.283127 TGCGCCTAATATTCTCTGATTCTTTTT 59.717 33.333 4.18 0.00 0.00 1.94
154 155 4.012374 TCTGATTCTTTGATGGAGCCAAC 58.988 43.478 0.00 0.00 0.00 3.77
242 243 3.976758 TGCTGCAGATGTGAGCAC 58.023 55.556 20.43 0.00 37.81 4.40
342 344 4.023021 CCCCAAGAAAAATGCATTGTTTGG 60.023 41.667 19.98 19.98 0.00 3.28
411 414 2.161808 ACGTAGTAGTAGCAGTGTGCAG 59.838 50.000 1.08 0.00 43.87 4.41
474 480 1.134946 AGCATTATTCTTTGCCGCCAC 59.865 47.619 0.00 0.00 39.72 5.01
499 505 0.249398 AGCCTTGGATCACGTACACC 59.751 55.000 0.00 0.00 0.00 4.16
534 542 4.080863 ACCTTCCGAGCATCTATTCTTTGT 60.081 41.667 0.00 0.00 0.00 2.83
568 576 9.466497 ACAGTGATGGAATATAAGTGAATTGTT 57.534 29.630 0.00 0.00 0.00 2.83
622 630 9.536510 GAGTTGAAGATATATAGGTACTCCCTT 57.463 37.037 0.00 0.00 42.73 3.95
624 632 8.460428 GTTGAAGATATATAGGTACTCCCTTCG 58.540 40.741 0.00 0.00 42.73 3.79
625 633 7.696981 TGAAGATATATAGGTACTCCCTTCGT 58.303 38.462 0.00 0.00 42.73 3.85
626 634 8.168725 TGAAGATATATAGGTACTCCCTTCGTT 58.831 37.037 0.00 0.00 42.73 3.85
628 636 8.953223 AGATATATAGGTACTCCCTTCGTTTT 57.047 34.615 0.00 0.00 42.73 2.43
629 637 9.377238 AGATATATAGGTACTCCCTTCGTTTTT 57.623 33.333 0.00 0.00 42.73 1.94
635 643 9.828039 ATAGGTACTCCCTTCGTTTTTATTTAG 57.172 33.333 0.00 0.00 42.73 1.85
637 645 7.821359 AGGTACTCCCTTCGTTTTTATTTAGTC 59.179 37.037 0.00 0.00 42.73 2.59
640 648 4.392754 TCCCTTCGTTTTTATTTAGTCCGC 59.607 41.667 0.00 0.00 0.00 5.54
643 651 5.062058 CCTTCGTTTTTATTTAGTCCGCGTA 59.938 40.000 4.92 0.00 0.00 4.42
649 657 7.254084 CGTTTTTATTTAGTCCGCGTATTAGGT 60.254 37.037 4.92 0.00 0.00 3.08
652 660 4.717233 TTTAGTCCGCGTATTAGGTTCA 57.283 40.909 4.92 0.00 0.00 3.18
653 661 2.865343 AGTCCGCGTATTAGGTTCAG 57.135 50.000 4.92 0.00 0.00 3.02
654 662 2.097825 AGTCCGCGTATTAGGTTCAGT 58.902 47.619 4.92 0.00 0.00 3.41
655 663 2.098770 AGTCCGCGTATTAGGTTCAGTC 59.901 50.000 4.92 0.00 0.00 3.51
660 668 3.924686 CGCGTATTAGGTTCAGTCAAAGT 59.075 43.478 0.00 0.00 0.00 2.66
662 670 4.927425 GCGTATTAGGTTCAGTCAAAGTCA 59.073 41.667 0.00 0.00 0.00 3.41
664 672 6.073440 GCGTATTAGGTTCAGTCAAAGTCAAA 60.073 38.462 0.00 0.00 0.00 2.69
665 673 7.288672 CGTATTAGGTTCAGTCAAAGTCAAAC 58.711 38.462 0.00 0.00 0.00 2.93
666 674 7.170998 CGTATTAGGTTCAGTCAAAGTCAAACT 59.829 37.037 0.00 0.00 0.00 2.66
667 675 7.881775 ATTAGGTTCAGTCAAAGTCAAACTT 57.118 32.000 0.00 0.00 40.80 2.66
682 690 5.988561 AGTCAAACTTTGCAAACTTTGACAA 59.011 32.000 40.86 24.95 44.72 3.18
683 691 6.481644 AGTCAAACTTTGCAAACTTTGACAAA 59.518 30.769 40.86 24.73 44.72 2.83
684 692 7.011857 AGTCAAACTTTGCAAACTTTGACAAAA 59.988 29.630 40.86 24.50 44.72 2.44
685 693 7.802720 GTCAAACTTTGCAAACTTTGACAAAAT 59.197 29.630 38.57 13.49 43.43 1.82
687 695 8.629132 CAAACTTTGCAAACTTTGACAAAATTC 58.371 29.630 26.92 0.00 36.76 2.17
688 696 6.533185 ACTTTGCAAACTTTGACAAAATTCG 58.467 32.000 8.05 11.85 36.76 3.34
690 698 7.329717 ACTTTGCAAACTTTGACAAAATTCGTA 59.670 29.630 8.05 0.00 36.76 3.43
691 699 7.582435 TTGCAAACTTTGACAAAATTCGTAA 57.418 28.000 5.65 0.00 0.00 3.18
692 700 7.215696 TGCAAACTTTGACAAAATTCGTAAG 57.784 32.000 5.65 0.00 0.00 2.34
693 701 6.120157 GCAAACTTTGACAAAATTCGTAAGC 58.880 36.000 5.65 1.60 37.18 3.09
695 703 7.670916 CAAACTTTGACAAAATTCGTAAGCAA 58.329 30.769 1.62 0.00 37.18 3.91
696 704 7.820044 AACTTTGACAAAATTCGTAAGCAAA 57.180 28.000 1.62 0.00 37.18 3.68
703 711 9.684448 TGACAAAATTCGTAAGCAAAAATATCA 57.316 25.926 0.00 0.00 37.18 2.15
708 716 9.906660 AAATTCGTAAGCAAAAATATCAACAGA 57.093 25.926 0.00 0.00 37.18 3.41
711 719 9.982291 TTCGTAAGCAAAAATATCAACAGATAC 57.018 29.630 0.00 0.00 37.18 2.24
712 720 9.157104 TCGTAAGCAAAAATATCAACAGATACA 57.843 29.630 0.00 0.00 37.18 2.29
839 1228 9.093970 ACTTTACAAAGTTTGATTTTAGGCAAC 57.906 29.630 22.23 0.00 46.52 4.17
843 1232 7.777095 ACAAAGTTTGATTTTAGGCAACACTA 58.223 30.769 22.23 0.00 41.41 2.74
844 1233 8.254508 ACAAAGTTTGATTTTAGGCAACACTAA 58.745 29.630 22.23 0.00 41.41 2.24
901 1328 6.402456 ACAACTTAATATAGAGGGACGTCC 57.598 41.667 27.04 27.04 0.00 4.79
936 1363 0.804989 CCCGCAAGACTAAGCTTTGG 59.195 55.000 3.20 0.38 43.02 3.28
1024 1452 2.512692 TAATGCCATCACCTTGCACT 57.487 45.000 0.00 0.00 37.92 4.40
1121 1549 3.050275 GTGGTTCTGGTGGAGCGC 61.050 66.667 0.00 0.00 0.00 5.92
1433 1866 1.132453 TCGACTATGTGTTCGGCAGAG 59.868 52.381 0.00 0.00 0.00 3.35
1473 1906 0.676736 CAGGATAGCTCTCCCGGAAC 59.323 60.000 14.26 0.00 35.79 3.62
1509 1942 5.771666 TCAAAGATATGGAGGAATGGCAATC 59.228 40.000 0.00 0.00 0.00 2.67
1571 2415 0.391263 GTACCTAACCTTGCAGCGCT 60.391 55.000 2.64 2.64 0.00 5.92
1572 2416 1.134907 GTACCTAACCTTGCAGCGCTA 60.135 52.381 10.99 0.00 0.00 4.26
1573 2417 0.108138 ACCTAACCTTGCAGCGCTAG 60.108 55.000 10.99 3.61 0.00 3.42
1574 2418 1.432270 CCTAACCTTGCAGCGCTAGC 61.432 60.000 10.99 17.19 45.58 3.42
1589 2444 3.854240 GCGCTAGCTTTTCAAATTCCTTC 59.146 43.478 13.93 0.00 41.01 3.46
1630 2486 1.067364 GGGACTCGACCTTTAGCTAGC 59.933 57.143 6.62 6.62 0.00 3.42
2030 2890 7.404139 ACTAGTACTCAATGTTTTTCGTGTC 57.596 36.000 0.00 0.00 0.00 3.67
2065 2925 1.359848 GCCTTCATATACGCATCGGG 58.640 55.000 0.00 0.00 0.00 5.14
2083 2943 0.179073 GGAGTGCGAGGTACATGCAT 60.179 55.000 8.80 0.00 42.21 3.96
2104 2964 4.033702 CATGTGCATGCTACAGAACTACTG 59.966 45.833 20.33 10.39 40.88 2.74
2183 3046 9.070210 AGATGTACTACTCCATGGACCTATATA 57.930 37.037 11.44 0.49 0.00 0.86
2184 3047 9.869667 GATGTACTACTCCATGGACCTATATAT 57.130 37.037 11.44 5.43 0.00 0.86
2190 3053 5.215069 CTCCATGGACCTATATATGCTCCT 58.785 45.833 11.44 0.00 0.00 3.69
2204 3067 3.690475 TGCTCCTGCATGGTATATGAG 57.310 47.619 0.00 0.00 45.31 2.90
2205 3068 2.289882 TGCTCCTGCATGGTATATGAGC 60.290 50.000 0.00 0.00 45.31 4.26
2376 3315 4.128925 TGCTACACAGATCAATCAGACC 57.871 45.455 0.00 0.00 0.00 3.85
2380 3319 2.093973 ACACAGATCAATCAGACCGGTC 60.094 50.000 27.67 27.67 0.00 4.79
2386 3325 0.107508 CAATCAGACCGGTCCAGCAT 60.108 55.000 30.82 14.42 0.00 3.79
2388 3327 1.690219 ATCAGACCGGTCCAGCATCC 61.690 60.000 30.82 4.01 0.00 3.51
2432 3371 1.847818 TAGCCCAAATCGATCGTTCG 58.152 50.000 15.94 9.59 46.87 3.95
2451 3390 4.585955 TCGAGAAGATAACTACCATGCC 57.414 45.455 0.00 0.00 0.00 4.40
2455 3394 5.455056 AGAAGATAACTACCATGCCTACG 57.545 43.478 0.00 0.00 0.00 3.51
2462 3401 0.756294 TACCATGCCTACGTGATGGG 59.244 55.000 17.09 8.01 40.96 4.00
2504 3443 4.813697 GCAAACCAGCAAAAAGATAACCAA 59.186 37.500 0.00 0.00 0.00 3.67
2505 3444 5.277297 GCAAACCAGCAAAAAGATAACCAAC 60.277 40.000 0.00 0.00 0.00 3.77
2506 3445 4.237349 ACCAGCAAAAAGATAACCAACG 57.763 40.909 0.00 0.00 0.00 4.10
2507 3446 2.986479 CCAGCAAAAAGATAACCAACGC 59.014 45.455 0.00 0.00 0.00 4.84
2508 3447 3.551863 CCAGCAAAAAGATAACCAACGCA 60.552 43.478 0.00 0.00 0.00 5.24
2509 3448 3.425193 CAGCAAAAAGATAACCAACGCAC 59.575 43.478 0.00 0.00 0.00 5.34
2510 3449 3.317993 AGCAAAAAGATAACCAACGCACT 59.682 39.130 0.00 0.00 0.00 4.40
2511 3450 4.048504 GCAAAAAGATAACCAACGCACTT 58.951 39.130 0.00 0.00 0.00 3.16
2512 3451 5.009210 AGCAAAAAGATAACCAACGCACTTA 59.991 36.000 0.00 0.00 0.00 2.24
2513 3452 5.116528 GCAAAAAGATAACCAACGCACTTAC 59.883 40.000 0.00 0.00 0.00 2.34
2514 3453 6.202937 CAAAAAGATAACCAACGCACTTACA 58.797 36.000 0.00 0.00 0.00 2.41
2515 3454 6.380095 AAAAGATAACCAACGCACTTACAA 57.620 33.333 0.00 0.00 0.00 2.41
2516 3455 6.569179 AAAGATAACCAACGCACTTACAAT 57.431 33.333 0.00 0.00 0.00 2.71
2517 3456 5.545658 AGATAACCAACGCACTTACAATG 57.454 39.130 0.00 0.00 0.00 2.82
2518 3457 5.242434 AGATAACCAACGCACTTACAATGA 58.758 37.500 0.00 0.00 0.00 2.57
2519 3458 3.619233 AACCAACGCACTTACAATGAC 57.381 42.857 0.00 0.00 0.00 3.06
2520 3459 1.529438 ACCAACGCACTTACAATGACG 59.471 47.619 0.00 0.00 0.00 4.35
2521 3460 1.795872 CCAACGCACTTACAATGACGA 59.204 47.619 0.00 0.00 0.00 4.20
2522 3461 2.222213 CCAACGCACTTACAATGACGAA 59.778 45.455 0.00 0.00 0.00 3.85
2523 3462 3.469629 CAACGCACTTACAATGACGAAG 58.530 45.455 0.00 0.00 0.00 3.79
2524 3463 3.021269 ACGCACTTACAATGACGAAGA 57.979 42.857 0.00 0.00 0.00 2.87
2525 3464 2.729882 ACGCACTTACAATGACGAAGAC 59.270 45.455 0.00 0.00 0.00 3.01
2575 3514 0.385473 CGTTCCTGCACGCGAAAAAT 60.385 50.000 15.93 0.00 32.43 1.82
2622 3561 8.948631 TTCTAAACAAAAATTTGGCACATACA 57.051 26.923 10.38 0.00 42.34 2.29
2643 3582 4.991056 ACATCTCGACATTATATGTGTGCC 59.009 41.667 0.00 0.00 45.03 5.01
2678 3617 5.399013 GGAGAAAACCGACATATTTTGTGG 58.601 41.667 0.00 0.00 39.18 4.17
2722 3662 7.049754 AAGGATGTCTTGTGAAAAGCATTTTT 58.950 30.769 0.00 0.00 40.56 1.94
2761 3701 3.513462 TTTTCACACGCGACACATAAG 57.487 42.857 15.93 0.00 0.00 1.73
2764 3704 1.790043 TCACACGCGACACATAAGTTG 59.210 47.619 15.93 0.00 0.00 3.16
2775 3715 4.839796 ACACATAAGTTGTCGGTTTTTCG 58.160 39.130 0.00 0.00 36.00 3.46
2776 3716 4.333372 ACACATAAGTTGTCGGTTTTTCGT 59.667 37.500 0.00 0.00 36.00 3.85
2779 3719 3.668596 AAGTTGTCGGTTTTTCGTGAG 57.331 42.857 0.00 0.00 0.00 3.51
2782 3722 1.202203 TGTCGGTTTTTCGTGAGACG 58.798 50.000 0.00 0.00 44.19 4.18
2835 3775 4.754322 ACGAGCCAAGTTTTTGTTTGAAT 58.246 34.783 0.00 0.00 32.21 2.57
2887 3827 2.488153 ACATTTTAAGAACCAGGAGCGC 59.512 45.455 0.00 0.00 0.00 5.92
2889 3829 1.296056 TTTAAGAACCAGGAGCGCGC 61.296 55.000 26.66 26.66 0.00 6.86
2918 3858 2.966309 GCCAAAACGCCACTCTCGG 61.966 63.158 0.00 0.00 0.00 4.63
2952 3892 4.992381 AGTTTACGAGCAAACTAGCAAG 57.008 40.909 11.10 0.00 44.83 4.01
2955 3895 0.685097 ACGAGCAAACTAGCAAGGGA 59.315 50.000 0.00 0.00 36.85 4.20
2956 3896 1.071699 ACGAGCAAACTAGCAAGGGAA 59.928 47.619 0.00 0.00 36.85 3.97
2957 3897 2.151202 CGAGCAAACTAGCAAGGGAAA 58.849 47.619 0.00 0.00 36.85 3.13
2958 3898 2.160417 CGAGCAAACTAGCAAGGGAAAG 59.840 50.000 0.00 0.00 36.85 2.62
2959 3899 3.149981 GAGCAAACTAGCAAGGGAAAGT 58.850 45.455 0.00 0.00 36.85 2.66
2960 3900 4.324267 GAGCAAACTAGCAAGGGAAAGTA 58.676 43.478 0.00 0.00 36.85 2.24
2961 3901 4.327680 AGCAAACTAGCAAGGGAAAGTAG 58.672 43.478 0.00 0.00 36.85 2.57
2964 3904 3.983044 ACTAGCAAGGGAAAGTAGTGG 57.017 47.619 0.00 0.00 0.00 4.00
2965 3905 2.027100 ACTAGCAAGGGAAAGTAGTGGC 60.027 50.000 0.00 0.00 0.00 5.01
2966 3906 1.068121 AGCAAGGGAAAGTAGTGGCT 58.932 50.000 0.00 0.00 0.00 4.75
2967 3907 1.168714 GCAAGGGAAAGTAGTGGCTG 58.831 55.000 0.00 0.00 0.00 4.85
2970 3910 2.814336 CAAGGGAAAGTAGTGGCTGAAC 59.186 50.000 0.00 0.00 0.00 3.18
2971 3911 1.351350 AGGGAAAGTAGTGGCTGAACC 59.649 52.381 0.00 0.00 39.84 3.62
2972 3912 1.613520 GGGAAAGTAGTGGCTGAACCC 60.614 57.143 0.00 0.00 37.83 4.11
2973 3913 1.613520 GGAAAGTAGTGGCTGAACCCC 60.614 57.143 0.00 0.00 37.83 4.95
2976 3916 0.912486 AGTAGTGGCTGAACCCCATC 59.088 55.000 0.00 0.00 37.83 3.51
2977 3917 0.912486 GTAGTGGCTGAACCCCATCT 59.088 55.000 0.00 0.00 37.83 2.90
2978 3918 1.134371 GTAGTGGCTGAACCCCATCTC 60.134 57.143 0.00 0.00 37.83 2.75
2979 3919 1.450312 GTGGCTGAACCCCATCTCG 60.450 63.158 0.00 0.00 37.83 4.04
2980 3920 2.190578 GGCTGAACCCCATCTCGG 59.809 66.667 0.00 0.00 0.00 4.63
2981 3921 2.670148 GGCTGAACCCCATCTCGGT 61.670 63.158 0.00 0.00 34.07 4.69
2982 3922 1.450312 GCTGAACCCCATCTCGGTG 60.450 63.158 0.00 0.00 32.55 4.94
2983 3923 1.450312 CTGAACCCCATCTCGGTGC 60.450 63.158 0.00 0.00 32.55 5.01
2984 3924 2.184020 CTGAACCCCATCTCGGTGCA 62.184 60.000 0.00 0.00 36.51 4.57
2985 3925 1.745489 GAACCCCATCTCGGTGCAC 60.745 63.158 8.80 8.80 32.55 4.57
2986 3926 2.463589 GAACCCCATCTCGGTGCACA 62.464 60.000 20.43 0.00 32.55 4.57
2987 3927 2.436646 CCCCATCTCGGTGCACAC 60.437 66.667 20.43 7.22 0.00 3.82
2988 3928 2.347114 CCCATCTCGGTGCACACA 59.653 61.111 20.43 2.66 0.00 3.72
2989 3929 2.034879 CCCATCTCGGTGCACACAC 61.035 63.158 20.43 0.00 46.66 3.82
2999 3939 2.977456 GCACACACGATGCACCCA 60.977 61.111 0.00 0.00 42.88 4.51
3000 3940 2.945984 CACACACGATGCACCCAC 59.054 61.111 0.00 0.00 0.00 4.61
3001 3941 2.664851 ACACACGATGCACCCACG 60.665 61.111 0.00 0.00 0.00 4.94
3002 3942 4.088762 CACACGATGCACCCACGC 62.089 66.667 0.00 0.00 0.00 5.34
3004 3944 3.353029 CACGATGCACCCACGCAA 61.353 61.111 0.00 0.00 46.87 4.85
3005 3945 3.049674 ACGATGCACCCACGCAAG 61.050 61.111 0.00 0.00 46.87 4.01
3006 3946 2.741985 CGATGCACCCACGCAAGA 60.742 61.111 0.00 0.00 46.87 3.02
3007 3947 2.324330 CGATGCACCCACGCAAGAA 61.324 57.895 0.00 0.00 46.87 2.52
3008 3948 1.851021 CGATGCACCCACGCAAGAAA 61.851 55.000 0.00 0.00 46.87 2.52
3009 3949 0.313672 GATGCACCCACGCAAGAAAA 59.686 50.000 0.00 0.00 46.87 2.29
3010 3950 0.031994 ATGCACCCACGCAAGAAAAC 59.968 50.000 0.00 0.00 46.87 2.43
3011 3951 1.315981 TGCACCCACGCAAGAAAACA 61.316 50.000 0.00 0.00 39.45 2.83
3012 3952 0.031994 GCACCCACGCAAGAAAACAT 59.968 50.000 0.00 0.00 43.62 2.71
3013 3953 1.268352 GCACCCACGCAAGAAAACATA 59.732 47.619 0.00 0.00 43.62 2.29
3014 3954 2.920647 GCACCCACGCAAGAAAACATAC 60.921 50.000 0.00 0.00 43.62 2.39
3015 3955 1.883926 ACCCACGCAAGAAAACATACC 59.116 47.619 0.00 0.00 43.62 2.73
3016 3956 1.883275 CCCACGCAAGAAAACATACCA 59.117 47.619 0.00 0.00 43.62 3.25
3017 3957 2.294791 CCCACGCAAGAAAACATACCAA 59.705 45.455 0.00 0.00 43.62 3.67
3018 3958 3.243569 CCCACGCAAGAAAACATACCAAA 60.244 43.478 0.00 0.00 43.62 3.28
3019 3959 4.363999 CCACGCAAGAAAACATACCAAAA 58.636 39.130 0.00 0.00 43.62 2.44
3020 3960 4.208253 CCACGCAAGAAAACATACCAAAAC 59.792 41.667 0.00 0.00 43.62 2.43
3021 3961 4.800993 CACGCAAGAAAACATACCAAAACA 59.199 37.500 0.00 0.00 43.62 2.83
3022 3962 5.461737 CACGCAAGAAAACATACCAAAACAT 59.538 36.000 0.00 0.00 43.62 2.71
3023 3963 6.019156 CACGCAAGAAAACATACCAAAACATT 60.019 34.615 0.00 0.00 43.62 2.71
3024 3964 6.536941 ACGCAAGAAAACATACCAAAACATTT 59.463 30.769 0.00 0.00 43.62 2.32
3025 3965 7.065204 ACGCAAGAAAACATACCAAAACATTTT 59.935 29.630 0.00 0.00 43.62 1.82
3026 3966 7.372918 CGCAAGAAAACATACCAAAACATTTTG 59.627 33.333 9.66 9.66 43.28 2.44
3056 3996 8.945481 AAACTGAAACATTGTGAAAATGATCA 57.055 26.923 1.66 0.00 0.00 2.92
3057 3997 9.550406 AAACTGAAACATTGTGAAAATGATCAT 57.450 25.926 1.18 1.18 31.85 2.45
3058 3998 9.550406 AACTGAAACATTGTGAAAATGATCATT 57.450 25.926 15.36 15.36 31.85 2.57
3069 4009 9.978044 TGTGAAAATGATCATTAACAAATGTCA 57.022 25.926 21.00 13.47 0.00 3.58
3073 4013 8.991243 AAATGATCATTAACAAATGTCAGTGG 57.009 30.769 21.00 0.00 0.00 4.00
3074 4014 5.953183 TGATCATTAACAAATGTCAGTGGC 58.047 37.500 0.00 0.00 0.00 5.01
3075 4015 5.711506 TGATCATTAACAAATGTCAGTGGCT 59.288 36.000 0.00 0.00 0.00 4.75
3076 4016 6.209192 TGATCATTAACAAATGTCAGTGGCTT 59.791 34.615 0.00 0.00 0.00 4.35
3077 4017 5.771469 TCATTAACAAATGTCAGTGGCTTG 58.229 37.500 0.00 0.00 0.00 4.01
3078 4018 2.514205 AACAAATGTCAGTGGCTTGC 57.486 45.000 0.00 0.00 0.00 4.01
3079 4019 0.675633 ACAAATGTCAGTGGCTTGCC 59.324 50.000 4.43 4.43 0.00 4.52
3080 4020 0.675083 CAAATGTCAGTGGCTTGCCA 59.325 50.000 10.65 10.65 0.00 4.92
3081 4021 1.068895 CAAATGTCAGTGGCTTGCCAA 59.931 47.619 16.55 0.28 0.00 4.52
3082 4022 0.963962 AATGTCAGTGGCTTGCCAAG 59.036 50.000 16.55 11.89 0.00 3.61
3083 4023 0.178981 ATGTCAGTGGCTTGCCAAGT 60.179 50.000 16.55 3.91 0.00 3.16
3084 4024 0.395586 TGTCAGTGGCTTGCCAAGTT 60.396 50.000 16.55 2.46 0.00 2.66
3085 4025 0.746659 GTCAGTGGCTTGCCAAGTTT 59.253 50.000 16.55 0.00 0.00 2.66
3086 4026 0.746063 TCAGTGGCTTGCCAAGTTTG 59.254 50.000 16.55 11.97 0.00 2.93
3099 4039 3.716601 CCAAGTTTGGTGGTCAAATGAC 58.283 45.455 4.96 4.96 45.79 3.06
3100 4040 3.131933 CCAAGTTTGGTGGTCAAATGACA 59.868 43.478 14.93 0.00 45.79 3.58
3101 4041 4.202243 CCAAGTTTGGTGGTCAAATGACAT 60.202 41.667 14.93 0.00 45.79 3.06
3102 4042 4.853924 AGTTTGGTGGTCAAATGACATC 57.146 40.909 14.93 7.15 45.79 3.06
3103 4043 4.214310 AGTTTGGTGGTCAAATGACATCA 58.786 39.130 14.93 7.13 45.79 3.07
3104 4044 4.279169 AGTTTGGTGGTCAAATGACATCAG 59.721 41.667 14.93 0.00 45.79 2.90
3105 4045 3.786368 TGGTGGTCAAATGACATCAGA 57.214 42.857 14.93 0.00 46.47 3.27
3106 4046 3.678289 TGGTGGTCAAATGACATCAGAG 58.322 45.455 14.93 0.00 46.47 3.35
3107 4047 3.012518 GGTGGTCAAATGACATCAGAGG 58.987 50.000 14.93 0.00 46.47 3.69
3108 4048 3.012518 GTGGTCAAATGACATCAGAGGG 58.987 50.000 14.93 0.00 46.47 4.30
3109 4049 2.025981 TGGTCAAATGACATCAGAGGGG 60.026 50.000 14.93 0.00 46.47 4.79
3110 4050 2.239654 GGTCAAATGACATCAGAGGGGA 59.760 50.000 14.93 0.00 46.47 4.81
3111 4051 3.308402 GGTCAAATGACATCAGAGGGGAA 60.308 47.826 14.93 0.00 46.47 3.97
3112 4052 3.691609 GTCAAATGACATCAGAGGGGAAC 59.308 47.826 8.63 0.00 44.18 3.62
3113 4053 3.588842 TCAAATGACATCAGAGGGGAACT 59.411 43.478 0.00 0.00 0.00 3.01
3116 4056 3.184382 TGACATCAGAGGGGAACTGTA 57.816 47.619 0.00 0.00 36.81 2.74
3154 4094 8.785329 AATTACAAATTTTGGTCAAACAGTGT 57.215 26.923 13.42 0.00 34.12 3.55
3155 4095 9.877178 AATTACAAATTTTGGTCAAACAGTGTA 57.123 25.926 13.42 2.93 34.12 2.90
3157 4097 7.769272 ACAAATTTTGGTCAAACAGTGTATG 57.231 32.000 13.42 0.00 34.12 2.39
3158 4098 7.327214 ACAAATTTTGGTCAAACAGTGTATGT 58.673 30.769 13.42 0.00 38.36 2.29
3159 4099 8.470805 ACAAATTTTGGTCAAACAGTGTATGTA 58.529 29.630 13.42 0.00 36.53 2.29
3164 4104 8.864069 TTTGGTCAAACAGTGTATGTATTTTG 57.136 30.769 0.00 0.00 43.00 2.44
3165 4105 7.809546 TGGTCAAACAGTGTATGTATTTTGA 57.190 32.000 0.00 0.00 43.00 2.69
3166 4106 7.870826 TGGTCAAACAGTGTATGTATTTTGAG 58.129 34.615 0.00 0.00 43.00 3.02
3167 4107 7.500892 TGGTCAAACAGTGTATGTATTTTGAGT 59.499 33.333 0.00 0.00 43.00 3.41
3168 4108 8.995220 GGTCAAACAGTGTATGTATTTTGAGTA 58.005 33.333 0.00 0.00 43.00 2.59
3204 4235 9.911788 TTTTTATAGAGCTCCTCAAATCTCATT 57.088 29.630 10.93 0.00 32.06 2.57
3225 4256 5.421212 TTTGACCATCAAAATTTGCAAGC 57.579 34.783 0.00 0.00 42.72 4.01
3226 4257 3.401182 TGACCATCAAAATTTGCAAGCC 58.599 40.909 0.00 0.00 0.00 4.35
3227 4258 2.412770 GACCATCAAAATTTGCAAGCCG 59.587 45.455 0.00 0.00 0.00 5.52
3228 4259 1.129064 CCATCAAAATTTGCAAGCCGC 59.871 47.619 0.00 0.00 42.89 6.53
3229 4260 2.070783 CATCAAAATTTGCAAGCCGCT 58.929 42.857 0.00 0.00 43.06 5.52
3230 4261 1.782044 TCAAAATTTGCAAGCCGCTC 58.218 45.000 0.00 0.00 43.06 5.03
3232 4263 2.556189 TCAAAATTTGCAAGCCGCTCTA 59.444 40.909 0.00 0.00 43.06 2.43
3233 4264 3.005261 TCAAAATTTGCAAGCCGCTCTAA 59.995 39.130 0.00 0.00 43.06 2.10
3234 4265 2.636768 AATTTGCAAGCCGCTCTAAC 57.363 45.000 0.00 0.00 43.06 2.34
3235 4266 1.533625 ATTTGCAAGCCGCTCTAACA 58.466 45.000 0.00 0.00 43.06 2.41
3236 4267 1.533625 TTTGCAAGCCGCTCTAACAT 58.466 45.000 0.00 0.00 43.06 2.71
3237 4268 1.533625 TTGCAAGCCGCTCTAACATT 58.466 45.000 0.00 0.00 43.06 2.71
3239 4270 1.199789 TGCAAGCCGCTCTAACATTTG 59.800 47.619 0.00 0.00 43.06 2.32
3241 4272 2.351738 GCAAGCCGCTCTAACATTTGTT 60.352 45.455 0.00 1.08 38.70 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.350498 GTGCGCGCCTTTAAAGATTCTA 59.650 45.455 30.77 0.16 0.00 2.10
8 9 1.130561 GTGCGCGCCTTTAAAGATTCT 59.869 47.619 30.77 0.00 0.00 2.40
27 28 4.868116 GGCGTGTGGGGTGTGTGT 62.868 66.667 0.00 0.00 0.00 3.72
55 56 7.016153 TCAAGCAAAGAGACCTAAAGGAATA 57.984 36.000 2.23 0.00 38.94 1.75
113 114 9.950680 GAATCAGAGAATATTTATCCGCAAAAA 57.049 29.630 0.00 0.00 0.00 1.94
114 115 9.342308 AGAATCAGAGAATATTTATCCGCAAAA 57.658 29.630 0.00 0.00 0.00 2.44
115 116 8.908786 AGAATCAGAGAATATTTATCCGCAAA 57.091 30.769 0.00 0.00 0.00 3.68
116 117 8.908786 AAGAATCAGAGAATATTTATCCGCAA 57.091 30.769 0.00 0.00 0.00 4.85
117 118 8.777413 CAAAGAATCAGAGAATATTTATCCGCA 58.223 33.333 0.00 0.00 0.00 5.69
118 119 8.993121 TCAAAGAATCAGAGAATATTTATCCGC 58.007 33.333 0.00 0.00 0.00 5.54
124 125 8.848182 GCTCCATCAAAGAATCAGAGAATATTT 58.152 33.333 0.00 0.00 0.00 1.40
133 134 4.015084 AGTTGGCTCCATCAAAGAATCAG 58.985 43.478 0.42 0.00 0.00 2.90
154 155 0.454957 CCTGCGGTGCAAATTCGAAG 60.455 55.000 3.35 0.00 38.41 3.79
175 176 4.750098 CGTTATCTTTCCATTGGATAGCGT 59.250 41.667 15.98 10.63 39.74 5.07
242 243 5.419788 TGTCAGAATCCAATCAAATTCCAGG 59.580 40.000 0.00 0.00 33.29 4.45
342 344 9.167311 ACTGATCTAGATGTTGGTTTCATTTAC 57.833 33.333 10.74 0.00 0.00 2.01
474 480 1.642037 CGTGATCCAAGGCTGCTGTG 61.642 60.000 0.00 0.00 0.00 3.66
510 518 5.128827 ACAAAGAATAGATGCTCGGAAGGTA 59.871 40.000 0.00 0.00 0.00 3.08
534 542 1.763546 TTCCATCACTGTGCGTGGGA 61.764 55.000 22.99 16.44 43.94 4.37
617 625 4.392754 GCGGACTAAATAAAAACGAAGGGA 59.607 41.667 0.00 0.00 0.00 4.20
618 626 4.655027 GCGGACTAAATAAAAACGAAGGG 58.345 43.478 0.00 0.00 0.00 3.95
619 627 4.143052 ACGCGGACTAAATAAAAACGAAGG 60.143 41.667 12.47 0.00 0.00 3.46
622 630 6.645700 AATACGCGGACTAAATAAAAACGA 57.354 33.333 12.47 0.00 0.00 3.85
624 632 7.909267 ACCTAATACGCGGACTAAATAAAAAC 58.091 34.615 12.47 0.00 0.00 2.43
625 633 8.491331 AACCTAATACGCGGACTAAATAAAAA 57.509 30.769 12.47 0.00 0.00 1.94
626 634 7.763528 TGAACCTAATACGCGGACTAAATAAAA 59.236 33.333 12.47 0.00 0.00 1.52
628 636 6.804677 TGAACCTAATACGCGGACTAAATAA 58.195 36.000 12.47 0.00 0.00 1.40
629 637 6.039717 ACTGAACCTAATACGCGGACTAAATA 59.960 38.462 12.47 0.00 0.00 1.40
632 640 3.696051 ACTGAACCTAATACGCGGACTAA 59.304 43.478 12.47 0.00 0.00 2.24
634 642 2.097825 ACTGAACCTAATACGCGGACT 58.902 47.619 12.47 0.00 0.00 3.85
635 643 2.159338 TGACTGAACCTAATACGCGGAC 60.159 50.000 12.47 0.00 0.00 4.79
637 645 2.572191 TGACTGAACCTAATACGCGG 57.428 50.000 12.47 0.00 0.00 6.46
640 648 7.170998 AGTTTGACTTTGACTGAACCTAATACG 59.829 37.037 0.00 0.00 0.00 3.06
643 651 7.881775 AAGTTTGACTTTGACTGAACCTAAT 57.118 32.000 0.00 0.00 34.11 1.73
662 670 7.533561 CGAATTTTGTCAAAGTTTGCAAAGTTT 59.466 29.630 30.47 30.47 41.01 2.66
664 672 6.147000 ACGAATTTTGTCAAAGTTTGCAAAGT 59.853 30.769 24.12 21.38 37.67 2.66
665 673 6.533185 ACGAATTTTGTCAAAGTTTGCAAAG 58.467 32.000 24.12 18.90 37.67 2.77
666 674 6.473397 ACGAATTTTGTCAAAGTTTGCAAA 57.527 29.167 22.83 22.83 36.02 3.68
667 675 7.582435 TTACGAATTTTGTCAAAGTTTGCAA 57.418 28.000 16.72 14.28 0.00 4.08
677 685 9.684448 TGATATTTTTGCTTACGAATTTTGTCA 57.316 25.926 0.00 0.00 0.00 3.58
682 690 9.906660 TCTGTTGATATTTTTGCTTACGAATTT 57.093 25.926 0.00 0.00 0.00 1.82
685 693 9.982291 GTATCTGTTGATATTTTTGCTTACGAA 57.018 29.630 0.00 0.00 37.48 3.85
687 695 9.767684 TTGTATCTGTTGATATTTTTGCTTACG 57.232 29.630 0.00 0.00 37.48 3.18
814 888 9.092876 TGTTGCCTAAAATCAAACTTTGTAAAG 57.907 29.630 2.94 2.94 41.73 1.85
815 889 8.874816 GTGTTGCCTAAAATCAAACTTTGTAAA 58.125 29.630 1.44 0.00 0.00 2.01
816 890 8.254508 AGTGTTGCCTAAAATCAAACTTTGTAA 58.745 29.630 1.44 0.00 0.00 2.41
817 891 7.777095 AGTGTTGCCTAAAATCAAACTTTGTA 58.223 30.769 1.44 0.00 0.00 2.41
818 892 6.639563 AGTGTTGCCTAAAATCAAACTTTGT 58.360 32.000 1.44 0.00 0.00 2.83
819 893 8.641499 TTAGTGTTGCCTAAAATCAAACTTTG 57.359 30.769 0.00 0.00 0.00 2.77
873 1262 9.578576 ACGTCCCTCTATATTAAGTTGTATGTA 57.421 33.333 0.00 0.00 0.00 2.29
874 1263 8.474710 ACGTCCCTCTATATTAAGTTGTATGT 57.525 34.615 0.00 0.00 0.00 2.29
875 1264 8.027771 GGACGTCCCTCTATATTAAGTTGTATG 58.972 40.741 24.75 0.00 0.00 2.39
876 1265 7.727186 TGGACGTCCCTCTATATTAAGTTGTAT 59.273 37.037 31.19 0.00 35.38 2.29
901 1328 2.181021 GGTCTCGTGTACGCCCTG 59.819 66.667 0.00 0.00 39.60 4.45
936 1363 1.268743 GCGGCAAAGAATATGTGCTCC 60.269 52.381 0.00 0.00 38.36 4.70
1024 1452 3.082548 CTCGTGAGGAAGGAGTAAGACA 58.917 50.000 0.00 0.00 36.28 3.41
1121 1549 2.622011 TTAGTTTTGCGCCAGCCGG 61.622 57.895 4.18 0.00 44.33 6.13
1133 1561 3.315191 GGCATGCATACCATCGTTAGTTT 59.685 43.478 21.36 0.00 29.71 2.66
1316 1749 9.676861 GGAAGTGGGTATAGTTAAAATTACAGT 57.323 33.333 0.00 0.00 0.00 3.55
1433 1866 1.005097 AGGGGGTTCGGTTAATGGTTC 59.995 52.381 0.00 0.00 0.00 3.62
1473 1906 6.685657 TCCATATCTTTGATCGAGATCACAG 58.314 40.000 18.26 18.26 46.49 3.66
1498 1931 1.226660 CCAACGCGATTGCCATTCC 60.227 57.895 15.93 0.00 36.93 3.01
1509 1942 1.154225 GCAGAATTGTCCCAACGCG 60.154 57.895 3.53 3.53 0.00 6.01
1611 2467 1.749634 TGCTAGCTAAAGGTCGAGTCC 59.250 52.381 17.23 0.00 0.00 3.85
2065 2925 0.933097 CATGCATGTACCTCGCACTC 59.067 55.000 18.91 0.00 38.73 3.51
2083 2943 3.588955 CAGTAGTTCTGTAGCATGCACA 58.411 45.455 21.98 19.49 39.17 4.57
2104 2964 5.308825 ACCATGCTTATTCCAGCTACATAC 58.691 41.667 0.00 0.00 40.79 2.39
2190 3053 9.440773 CTAAAATTCTAGCTCATATACCATGCA 57.559 33.333 0.00 0.00 0.00 3.96
2272 3211 7.704472 CCTAAATTTGCGCCAACAGATAATTAA 59.296 33.333 4.18 0.00 0.00 1.40
2275 3214 5.451798 CCCTAAATTTGCGCCAACAGATAAT 60.452 40.000 4.18 0.00 0.00 1.28
2349 3288 5.654497 TGATTGATCTGTGTAGCAGTACTG 58.346 41.667 18.93 18.93 45.23 2.74
2366 3305 1.191489 TGCTGGACCGGTCTGATTGA 61.191 55.000 32.52 10.58 0.00 2.57
2369 3308 1.690219 GGATGCTGGACCGGTCTGAT 61.690 60.000 32.52 18.82 0.00 2.90
2374 3313 3.402681 CTGGGATGCTGGACCGGT 61.403 66.667 6.92 6.92 0.00 5.28
2376 3315 0.179073 CTAACTGGGATGCTGGACCG 60.179 60.000 0.00 0.00 0.00 4.79
2380 3319 0.179073 CGGTCTAACTGGGATGCTGG 60.179 60.000 0.00 0.00 0.00 4.85
2432 3371 5.009811 ACGTAGGCATGGTAGTTATCTTCTC 59.990 44.000 0.00 0.00 0.00 2.87
2436 3375 4.212716 TCACGTAGGCATGGTAGTTATCT 58.787 43.478 0.00 0.00 0.00 1.98
2451 3390 2.812499 CCGTCCCCCATCACGTAG 59.188 66.667 0.00 0.00 34.06 3.51
2455 3394 2.808206 CCTAGCCGTCCCCCATCAC 61.808 68.421 0.00 0.00 0.00 3.06
2462 3401 0.101939 CTCGTAAACCTAGCCGTCCC 59.898 60.000 0.00 0.00 0.00 4.46
2504 3443 2.729882 GTCTTCGTCATTGTAAGTGCGT 59.270 45.455 0.00 0.00 0.00 5.24
2505 3444 2.092211 GGTCTTCGTCATTGTAAGTGCG 59.908 50.000 0.00 0.00 0.00 5.34
2506 3445 2.092211 CGGTCTTCGTCATTGTAAGTGC 59.908 50.000 0.00 0.00 0.00 4.40
2507 3446 2.666508 CCGGTCTTCGTCATTGTAAGTG 59.333 50.000 0.00 0.00 37.11 3.16
2508 3447 2.559668 TCCGGTCTTCGTCATTGTAAGT 59.440 45.455 0.00 0.00 37.11 2.24
2509 3448 3.226346 TCCGGTCTTCGTCATTGTAAG 57.774 47.619 0.00 0.00 37.11 2.34
2510 3449 3.663995 TTCCGGTCTTCGTCATTGTAA 57.336 42.857 0.00 0.00 37.11 2.41
2511 3450 3.663995 TTTCCGGTCTTCGTCATTGTA 57.336 42.857 0.00 0.00 37.11 2.41
2512 3451 2.536761 TTTCCGGTCTTCGTCATTGT 57.463 45.000 0.00 0.00 37.11 2.71
2513 3452 2.351726 GGATTTCCGGTCTTCGTCATTG 59.648 50.000 0.00 0.00 37.11 2.82
2514 3453 2.629051 GGATTTCCGGTCTTCGTCATT 58.371 47.619 0.00 0.00 37.11 2.57
2515 3454 2.311124 GGATTTCCGGTCTTCGTCAT 57.689 50.000 0.00 0.00 37.11 3.06
2516 3455 3.826637 GGATTTCCGGTCTTCGTCA 57.173 52.632 0.00 0.00 37.11 4.35
2557 3496 2.604969 TATTTTTCGCGTGCAGGAAC 57.395 45.000 11.29 0.00 0.00 3.62
2558 3497 5.493133 AATATATTTTTCGCGTGCAGGAA 57.507 34.783 11.29 0.25 0.00 3.36
2599 3538 9.206870 AGATGTATGTGCCAAATTTTTGTTTAG 57.793 29.630 2.63 0.00 36.45 1.85
2600 3539 9.202273 GAGATGTATGTGCCAAATTTTTGTTTA 57.798 29.630 2.63 0.00 36.45 2.01
2603 3542 5.863397 CGAGATGTATGTGCCAAATTTTTGT 59.137 36.000 2.63 0.00 36.45 2.83
2604 3543 6.033831 GTCGAGATGTATGTGCCAAATTTTTG 59.966 38.462 0.00 0.00 37.90 2.44
2614 3553 7.329471 ACACATATAATGTCGAGATGTATGTGC 59.671 37.037 33.20 7.87 45.72 4.57
2616 3555 7.329471 GCACACATATAATGTCGAGATGTATGT 59.671 37.037 19.57 19.57 42.70 2.29
2622 3561 4.569943 GGGCACACATATAATGTCGAGAT 58.430 43.478 0.00 0.00 42.70 2.75
2761 3701 2.595881 CGTCTCACGAAAAACCGACAAC 60.596 50.000 0.00 0.00 46.05 3.32
2764 3704 3.991924 CGTCTCACGAAAAACCGAC 57.008 52.632 0.00 0.00 46.05 4.79
2775 3715 1.852942 TGCTCACAAAGTCGTCTCAC 58.147 50.000 0.00 0.00 0.00 3.51
2776 3716 2.224042 ACATGCTCACAAAGTCGTCTCA 60.224 45.455 0.00 0.00 0.00 3.27
2779 3719 3.057019 TGTACATGCTCACAAAGTCGTC 58.943 45.455 0.00 0.00 0.00 4.20
2782 3722 6.255670 TCGATATTGTACATGCTCACAAAGTC 59.744 38.462 10.93 10.56 38.11 3.01
2889 3829 3.283684 TTTTGGCACGTGGGAGCG 61.284 61.111 18.88 0.00 37.94 5.03
2918 3858 2.159653 TCGTAAACTAGTCGGTCTTCGC 60.160 50.000 0.00 0.00 39.05 4.70
2952 3892 1.613520 GGGTTCAGCCACTACTTTCCC 60.614 57.143 0.00 0.00 39.65 3.97
2955 3895 1.145571 TGGGGTTCAGCCACTACTTT 58.854 50.000 0.00 0.00 42.62 2.66
2956 3896 1.282157 GATGGGGTTCAGCCACTACTT 59.718 52.381 0.00 0.00 42.62 2.24
2957 3897 0.912486 GATGGGGTTCAGCCACTACT 59.088 55.000 0.00 0.00 42.62 2.57
2958 3898 0.912486 AGATGGGGTTCAGCCACTAC 59.088 55.000 0.00 0.00 42.62 2.73
2959 3899 1.204146 GAGATGGGGTTCAGCCACTA 58.796 55.000 0.00 0.00 42.62 2.74
2960 3900 1.903877 CGAGATGGGGTTCAGCCACT 61.904 60.000 0.00 0.00 42.62 4.00
2961 3901 1.450312 CGAGATGGGGTTCAGCCAC 60.450 63.158 0.00 0.00 42.43 5.01
2964 3904 1.450312 CACCGAGATGGGGTTCAGC 60.450 63.158 0.00 0.00 44.64 4.26
2965 3905 1.450312 GCACCGAGATGGGGTTCAG 60.450 63.158 0.00 0.00 46.09 3.02
2966 3906 2.220586 TGCACCGAGATGGGGTTCA 61.221 57.895 0.00 0.00 46.09 3.18
2967 3907 1.745489 GTGCACCGAGATGGGGTTC 60.745 63.158 5.22 0.00 46.09 3.62
2971 3911 2.034879 GTGTGTGCACCGAGATGGG 61.035 63.158 15.69 0.00 44.64 4.00
2972 3912 2.382746 CGTGTGTGCACCGAGATGG 61.383 63.158 15.69 0.00 42.39 3.51
2973 3913 0.737367 ATCGTGTGTGCACCGAGATG 60.737 55.000 15.69 0.43 42.39 2.90
2976 3916 3.015293 GCATCGTGTGTGCACCGAG 62.015 63.158 15.69 10.76 42.39 4.63
2977 3917 3.041351 GCATCGTGTGTGCACCGA 61.041 61.111 15.69 16.47 42.39 4.69
2978 3918 3.345011 TGCATCGTGTGTGCACCG 61.345 61.111 15.69 11.12 46.76 4.94
2982 3922 2.977456 TGGGTGCATCGTGTGTGC 60.977 61.111 0.00 0.00 42.81 4.57
2983 3923 2.945984 GTGGGTGCATCGTGTGTG 59.054 61.111 0.00 0.00 0.00 3.82
2984 3924 2.664851 CGTGGGTGCATCGTGTGT 60.665 61.111 0.00 0.00 0.00 3.72
2985 3925 4.088762 GCGTGGGTGCATCGTGTG 62.089 66.667 0.00 0.00 34.15 3.82
2986 3926 4.617520 TGCGTGGGTGCATCGTGT 62.618 61.111 0.00 0.00 40.62 4.49
2987 3927 3.313007 CTTGCGTGGGTGCATCGTG 62.313 63.158 0.00 0.00 45.78 4.35
2988 3928 3.049674 CTTGCGTGGGTGCATCGT 61.050 61.111 0.00 0.00 45.78 3.73
2989 3929 1.851021 TTTCTTGCGTGGGTGCATCG 61.851 55.000 0.00 0.00 45.78 3.84
2990 3930 0.313672 TTTTCTTGCGTGGGTGCATC 59.686 50.000 0.00 0.00 45.78 3.91
2991 3931 0.031994 GTTTTCTTGCGTGGGTGCAT 59.968 50.000 0.00 0.00 45.78 3.96
2992 3932 1.315981 TGTTTTCTTGCGTGGGTGCA 61.316 50.000 0.00 0.00 44.61 4.57
2993 3933 0.031994 ATGTTTTCTTGCGTGGGTGC 59.968 50.000 0.00 0.00 0.00 5.01
2994 3934 2.351350 GGTATGTTTTCTTGCGTGGGTG 60.351 50.000 0.00 0.00 0.00 4.61
2995 3935 1.883926 GGTATGTTTTCTTGCGTGGGT 59.116 47.619 0.00 0.00 0.00 4.51
2996 3936 1.883275 TGGTATGTTTTCTTGCGTGGG 59.117 47.619 0.00 0.00 0.00 4.61
2997 3937 3.634568 TTGGTATGTTTTCTTGCGTGG 57.365 42.857 0.00 0.00 0.00 4.94
2998 3938 4.800993 TGTTTTGGTATGTTTTCTTGCGTG 59.199 37.500 0.00 0.00 0.00 5.34
2999 3939 5.000012 TGTTTTGGTATGTTTTCTTGCGT 58.000 34.783 0.00 0.00 0.00 5.24
3000 3940 6.523676 AATGTTTTGGTATGTTTTCTTGCG 57.476 33.333 0.00 0.00 0.00 4.85
3001 3941 8.394121 TCAAAATGTTTTGGTATGTTTTCTTGC 58.606 29.630 15.84 0.00 45.68 4.01
3030 3970 9.381033 TGATCATTTTCACAATGTTTCAGTTTT 57.619 25.926 0.00 0.00 0.00 2.43
3031 3971 8.945481 TGATCATTTTCACAATGTTTCAGTTT 57.055 26.923 0.00 0.00 0.00 2.66
3032 3972 9.550406 AATGATCATTTTCACAATGTTTCAGTT 57.450 25.926 15.36 0.00 30.66 3.16
3043 3983 9.978044 TGACATTTGTTAATGATCATTTTCACA 57.022 25.926 25.26 20.60 43.12 3.58
3047 3987 9.426837 CCACTGACATTTGTTAATGATCATTTT 57.573 29.630 25.26 6.52 43.12 1.82
3048 3988 7.546667 GCCACTGACATTTGTTAATGATCATTT 59.453 33.333 25.26 10.37 43.12 2.32
3049 3989 7.037438 GCCACTGACATTTGTTAATGATCATT 58.963 34.615 23.75 23.75 43.12 2.57
3050 3990 6.379133 AGCCACTGACATTTGTTAATGATCAT 59.621 34.615 1.18 1.18 43.12 2.45
3051 3991 5.711506 AGCCACTGACATTTGTTAATGATCA 59.288 36.000 0.00 0.00 43.12 2.92
3052 3992 6.199937 AGCCACTGACATTTGTTAATGATC 57.800 37.500 4.99 0.00 43.12 2.92
3053 3993 6.392354 CAAGCCACTGACATTTGTTAATGAT 58.608 36.000 4.99 0.00 43.12 2.45
3054 3994 5.771469 CAAGCCACTGACATTTGTTAATGA 58.229 37.500 4.99 0.00 43.12 2.57
3055 3995 4.386652 GCAAGCCACTGACATTTGTTAATG 59.613 41.667 0.00 0.00 45.39 1.90
3056 3996 4.559153 GCAAGCCACTGACATTTGTTAAT 58.441 39.130 0.00 0.00 0.00 1.40
3057 3997 3.243704 GGCAAGCCACTGACATTTGTTAA 60.244 43.478 6.14 0.00 35.81 2.01
3058 3998 2.295909 GGCAAGCCACTGACATTTGTTA 59.704 45.455 6.14 0.00 35.81 2.41
3059 3999 1.069049 GGCAAGCCACTGACATTTGTT 59.931 47.619 6.14 0.00 35.81 2.83
3060 4000 0.675633 GGCAAGCCACTGACATTTGT 59.324 50.000 6.14 0.00 35.81 2.83
3061 4001 0.675083 TGGCAAGCCACTGACATTTG 59.325 50.000 10.24 0.00 41.89 2.32
3062 4002 3.130264 TGGCAAGCCACTGACATTT 57.870 47.368 10.24 0.00 41.89 2.32
3063 4003 4.927557 TGGCAAGCCACTGACATT 57.072 50.000 10.24 0.00 41.89 2.71
3075 4015 7.866003 GTCATTTGACCACCAAACTTGGCAA 62.866 44.000 8.44 0.00 46.41 4.52
3076 4016 6.476731 GTCATTTGACCACCAAACTTGGCA 62.477 45.833 8.44 0.00 46.41 4.92
3077 4017 4.045049 GTCATTTGACCACCAAACTTGGC 61.045 47.826 8.44 0.00 46.41 4.52
3078 4018 3.131933 TGTCATTTGACCACCAAACTTGG 59.868 43.478 6.95 6.95 46.41 3.61
3079 4019 4.383850 TGTCATTTGACCACCAAACTTG 57.616 40.909 8.16 0.00 46.41 3.16
3080 4020 4.648762 TGATGTCATTTGACCACCAAACTT 59.351 37.500 8.16 0.00 46.41 2.66
3081 4021 4.214310 TGATGTCATTTGACCACCAAACT 58.786 39.130 8.16 0.00 46.41 2.66
3082 4022 4.278170 TCTGATGTCATTTGACCACCAAAC 59.722 41.667 8.16 0.00 46.41 2.93
3084 4024 4.074259 CTCTGATGTCATTTGACCACCAA 58.926 43.478 8.16 0.00 44.15 3.67
3085 4025 3.559811 CCTCTGATGTCATTTGACCACCA 60.560 47.826 8.16 3.23 44.15 4.17
3086 4026 3.012518 CCTCTGATGTCATTTGACCACC 58.987 50.000 8.16 0.00 44.15 4.61
3087 4027 3.012518 CCCTCTGATGTCATTTGACCAC 58.987 50.000 8.16 3.41 44.15 4.16
3088 4028 2.025981 CCCCTCTGATGTCATTTGACCA 60.026 50.000 8.16 0.00 44.15 4.02
3089 4029 2.239654 TCCCCTCTGATGTCATTTGACC 59.760 50.000 8.16 0.00 44.15 4.02
3090 4030 3.634397 TCCCCTCTGATGTCATTTGAC 57.366 47.619 3.72 3.72 44.97 3.18
3091 4031 3.588842 AGTTCCCCTCTGATGTCATTTGA 59.411 43.478 0.00 0.00 0.00 2.69
3092 4032 3.693085 CAGTTCCCCTCTGATGTCATTTG 59.307 47.826 0.00 0.00 35.20 2.32
3093 4033 3.331889 ACAGTTCCCCTCTGATGTCATTT 59.668 43.478 0.00 0.00 36.81 2.32
3094 4034 2.915604 ACAGTTCCCCTCTGATGTCATT 59.084 45.455 0.00 0.00 36.81 2.57
3095 4035 2.555664 ACAGTTCCCCTCTGATGTCAT 58.444 47.619 0.00 0.00 36.81 3.06
3096 4036 2.030027 ACAGTTCCCCTCTGATGTCA 57.970 50.000 0.00 0.00 36.81 3.58
3097 4037 3.706594 TCATACAGTTCCCCTCTGATGTC 59.293 47.826 0.00 0.00 36.81 3.06
3098 4038 3.724478 TCATACAGTTCCCCTCTGATGT 58.276 45.455 0.00 0.00 36.81 3.06
3099 4039 4.760530 TTCATACAGTTCCCCTCTGATG 57.239 45.455 0.00 0.00 36.81 3.07
3100 4040 5.779241 TTTTCATACAGTTCCCCTCTGAT 57.221 39.130 0.00 0.00 36.81 2.90
3101 4041 5.576563 TTTTTCATACAGTTCCCCTCTGA 57.423 39.130 0.00 0.00 36.81 3.27
3128 4068 9.225436 ACACTGTTTGACCAAAATTTGTAATTT 57.775 25.926 4.92 0.00 31.33 1.82
3131 4071 9.307121 CATACACTGTTTGACCAAAATTTGTAA 57.693 29.630 4.92 0.00 30.49 2.41
3132 4072 8.470805 ACATACACTGTTTGACCAAAATTTGTA 58.529 29.630 4.92 10.85 32.90 2.41
3134 4074 7.769272 ACATACACTGTTTGACCAAAATTTG 57.231 32.000 6.62 0.00 32.90 2.32
3141 4081 7.500892 ACTCAAAATACATACACTGTTTGACCA 59.499 33.333 6.62 0.00 39.39 4.02
3194 4225 9.820229 CAAATTTTGATGGTCAAATGAGATTTG 57.180 29.630 17.10 17.10 44.75 2.32
3197 4228 7.162761 TGCAAATTTTGATGGTCAAATGAGAT 58.837 30.769 13.26 0.00 44.75 2.75
3199 4230 6.788684 TGCAAATTTTGATGGTCAAATGAG 57.211 33.333 13.26 0.08 44.75 2.90
3200 4231 6.293516 GCTTGCAAATTTTGATGGTCAAATGA 60.294 34.615 13.26 0.00 44.75 2.57
3201 4232 5.854338 GCTTGCAAATTTTGATGGTCAAATG 59.146 36.000 13.26 3.74 44.75 2.32
3202 4233 5.048573 GGCTTGCAAATTTTGATGGTCAAAT 60.049 36.000 13.26 0.00 44.75 2.32
3203 4234 4.275443 GGCTTGCAAATTTTGATGGTCAAA 59.725 37.500 13.26 1.24 43.84 2.69
3204 4235 3.814283 GGCTTGCAAATTTTGATGGTCAA 59.186 39.130 13.26 6.21 34.03 3.18
3206 4237 2.412770 CGGCTTGCAAATTTTGATGGTC 59.587 45.455 13.26 2.51 0.00 4.02
3207 4238 2.415776 CGGCTTGCAAATTTTGATGGT 58.584 42.857 13.26 0.00 0.00 3.55
3208 4239 1.129064 GCGGCTTGCAAATTTTGATGG 59.871 47.619 13.26 2.97 45.45 3.51
3209 4240 2.513964 GCGGCTTGCAAATTTTGATG 57.486 45.000 13.26 3.28 45.45 3.07
3217 4248 7.683161 AACAAATGTTAGAGCGGCTTGCAAA 62.683 40.000 2.97 0.00 40.76 3.68
3218 4249 6.288084 AACAAATGTTAGAGCGGCTTGCAA 62.288 41.667 2.97 0.00 40.76 4.08
3219 4250 4.859326 AACAAATGTTAGAGCGGCTTGCA 61.859 43.478 2.97 1.57 40.76 4.08
3220 4251 1.200020 ACAAATGTTAGAGCGGCTTGC 59.800 47.619 2.97 0.00 46.98 4.01
3221 4252 3.236816 CAACAAATGTTAGAGCGGCTTG 58.763 45.455 2.97 0.00 36.32 4.01
3222 4253 3.559238 CAACAAATGTTAGAGCGGCTT 57.441 42.857 2.97 0.00 36.32 4.35


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

AutoCloner maintained by Alex Coulton.