Multiple sequence alignment - TraesCS4D01G324000

Loading Multiple Alignment...

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 TraesCS4D01G324000 chr4D 100.000 3128 0 0 1 3128 484886606 484889733 0.000000e+00 5777.0
1 TraesCS4D01G324000 chr4D 88.063 511 40 9 1637 2128 484840755 484841263 1.250000e-163 586.0
2 TraesCS4D01G324000 chr4D 88.378 413 45 2 1733 2145 484809276 484809685 7.790000e-136 494.0
3 TraesCS4D01G324000 chr4D 90.986 355 30 2 1228 1582 484808865 484809217 7.850000e-131 477.0
4 TraesCS4D01G324000 chr4D 92.470 332 25 0 1228 1559 484840417 484840748 2.820000e-130 475.0
5 TraesCS4D01G324000 chr4D 84.937 239 33 3 1366 1602 484770825 484771062 4.030000e-59 239.0
6 TraesCS4D01G324000 chr4D 92.254 142 10 1 1011 1152 484770312 484770452 1.900000e-47 200.0
7 TraesCS4D01G324000 chr5A 89.516 2747 155 53 2 2670 666037986 666040677 0.000000e+00 3354.0
8 TraesCS4D01G324000 chr5A 86.914 512 45 10 1637 2128 665983201 665983710 3.520000e-154 555.0
9 TraesCS4D01G324000 chr5A 90.073 413 41 0 1733 2145 665892411 665892823 1.280000e-148 536.0
10 TraesCS4D01G324000 chr5A 91.049 391 35 0 1733 2123 665978102 665978492 2.140000e-146 529.0
11 TraesCS4D01G324000 chr5A 82.877 584 60 28 989 1561 665982642 665983196 3.630000e-134 488.0
12 TraesCS4D01G324000 chr5A 91.525 354 29 1 1228 1581 665892000 665892352 1.300000e-133 486.0
13 TraesCS4D01G324000 chr5A 92.515 334 25 0 1228 1561 665970017 665970350 2.180000e-131 479.0
14 TraesCS4D01G324000 chr5A 85.625 160 13 5 1011 1170 665816200 665816349 3.230000e-35 159.0
15 TraesCS4D01G324000 chr5A 79.817 218 12 13 2941 3126 666040808 666041025 2.530000e-26 130.0
16 TraesCS4D01G324000 chr5A 94.000 50 3 0 2321 2370 665983720 665983769 3.350000e-10 76.8
17 TraesCS4D01G324000 chr4B 89.645 2115 113 41 600 2670 618157987 618160039 0.000000e+00 2595.0
18 TraesCS4D01G324000 chr4B 92.010 413 33 0 1733 2145 618075206 618075618 5.820000e-162 580.0
19 TraesCS4D01G324000 chr4B 93.694 333 21 0 1228 1560 618074755 618075087 1.680000e-137 499.0
20 TraesCS4D01G324000 chr4B 85.401 411 34 7 176 578 618131567 618131959 1.350000e-108 403.0
21 TraesCS4D01G324000 chr4B 87.500 256 29 3 1873 2128 617766467 617766719 3.050000e-75 292.0
22 TraesCS4D01G324000 chr4B 86.875 160 11 6 1011 1170 617765315 617765464 1.490000e-38 171.0
23 TraesCS4D01G324000 chr4B 88.281 128 13 2 2941 3066 618160165 618160292 5.400000e-33 152.0
24 TraesCS4D01G324000 chr4B 85.517 145 16 4 1232 1373 617765533 617765675 2.510000e-31 147.0
25 TraesCS4D01G324000 chr4B 100.000 33 0 0 3073 3105 618160314 618160346 9.370000e-06 62.1
26 TraesCS4D01G324000 chr7D 83.333 186 24 5 315 499 614693362 614693183 6.940000e-37 165.0
27 TraesCS4D01G324000 chr3A 86.207 87 11 1 2760 2846 382257234 382257149 3.320000e-15 93.5
28 TraesCS4D01G324000 chr2B 86.364 88 8 3 2760 2846 236717891 236717975 3.320000e-15 93.5
29 TraesCS4D01G324000 chr7B 78.417 139 24 6 1748 1882 725812785 725812649 5.560000e-13 86.1
30 TraesCS4D01G324000 chr2A 83.908 87 13 1 2760 2846 234466530 234466445 7.190000e-12 82.4
31 TraesCS4D01G324000 chr7A 97.778 45 1 0 2801 2845 3058706 3058662 9.300000e-11 78.7
32 TraesCS4D01G324000 chr7A 82.558 86 14 1 2760 2845 664207806 664207890 1.200000e-09 75.0
33 TraesCS4D01G324000 chr2D 82.418 91 13 3 2757 2846 274083322 274083410 3.350000e-10 76.8
34 TraesCS4D01G324000 chr2D 100.000 34 0 0 2812 2845 528997968 528998001 2.600000e-06 63.9
35 TraesCS4D01G324000 chr6B 100.000 33 0 0 2813 2845 21037417 21037385 9.370000e-06 62.1
36 TraesCS4D01G324000 chr3D 100.000 30 0 0 2816 2845 59258683 59258654 4.360000e-04 56.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G324000 chr4D 484886606 484889733 3127 False 5777.000000 5777 100.000000 1 3128 1 chr4D.!!$F1 3127
1 TraesCS4D01G324000 chr4D 484840417 484841263 846 False 530.500000 586 90.266500 1228 2128 2 chr4D.!!$F4 900
2 TraesCS4D01G324000 chr4D 484808865 484809685 820 False 485.500000 494 89.682000 1228 2145 2 chr4D.!!$F3 917
3 TraesCS4D01G324000 chr4D 484770312 484771062 750 False 219.500000 239 88.595500 1011 1602 2 chr4D.!!$F2 591
4 TraesCS4D01G324000 chr5A 666037986 666041025 3039 False 1742.000000 3354 84.666500 2 3126 2 chr5A.!!$F6 3124
5 TraesCS4D01G324000 chr5A 665892000 665892823 823 False 511.000000 536 90.799000 1228 2145 2 chr5A.!!$F4 917
6 TraesCS4D01G324000 chr5A 665982642 665983769 1127 False 373.266667 555 87.930333 989 2370 3 chr5A.!!$F5 1381
7 TraesCS4D01G324000 chr4B 618157987 618160346 2359 False 936.366667 2595 92.642000 600 3105 3 chr4B.!!$F4 2505
8 TraesCS4D01G324000 chr4B 618074755 618075618 863 False 539.500000 580 92.852000 1228 2145 2 chr4B.!!$F3 917
9 TraesCS4D01G324000 chr4B 617765315 617766719 1404 False 203.333333 292 86.630667 1011 2128 3 chr4B.!!$F2 1117

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
948 973 0.184933 CCTCCTCCTCCGTCTCTCAT 59.815 60.000 0.0 0.0 0.0 2.9 F
1699 1973 1.000283 CTCCAGTTGTCTCGAAGCTGT 60.000 52.381 0.0 0.0 0.0 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1749 2050 0.037326 TCTTGCCCTTGTACTCGCAG 60.037 55.0 0.0 0.0 31.86 5.18 R
2566 2998 0.039618 AATCTCGCCACCAACCCATT 59.960 50.0 0.0 0.0 0.00 3.16 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
56 57 5.354234 CGTTTGTAGAGCTTGGGATTTGTAT 59.646 40.000 0.00 0.00 0.00 2.29
58 59 5.692115 TGTAGAGCTTGGGATTTGTATGA 57.308 39.130 0.00 0.00 0.00 2.15
86 97 1.608590 CCTTGCCGATCTCTCTCTCTC 59.391 57.143 0.00 0.00 0.00 3.20
88 99 2.254546 TGCCGATCTCTCTCTCTCTC 57.745 55.000 0.00 0.00 0.00 3.20
90 101 2.224281 TGCCGATCTCTCTCTCTCTCTC 60.224 54.545 0.00 0.00 0.00 3.20
92 103 3.862642 GCCGATCTCTCTCTCTCTCTCTC 60.863 56.522 0.00 0.00 0.00 3.20
94 105 4.321601 CCGATCTCTCTCTCTCTCTCTCTC 60.322 54.167 0.00 0.00 0.00 3.20
102 113 4.949238 TCTCTCTCTCTCTCTCAATGTTGG 59.051 45.833 0.00 0.00 0.00 3.77
113 124 1.680735 TCAATGTTGGTTGTGTGCCTC 59.319 47.619 0.00 0.00 0.00 4.70
114 125 1.039856 AATGTTGGTTGTGTGCCTCC 58.960 50.000 0.00 0.00 0.00 4.30
116 127 0.465460 TGTTGGTTGTGTGCCTCCTC 60.465 55.000 0.00 0.00 0.00 3.71
123 134 1.448540 GTGTGCCTCCTCGTCATGG 60.449 63.158 0.00 0.00 0.00 3.66
152 163 4.043750 CAGGTGTGTGCTTATTGTGTTTG 58.956 43.478 0.00 0.00 0.00 2.93
187 198 9.860898 GGATGCTTCAGTTTGAGTTAATAAAAT 57.139 29.630 1.64 0.00 0.00 1.82
266 277 2.629017 ATTCAATGCTCCCAACCCTT 57.371 45.000 0.00 0.00 0.00 3.95
306 317 9.663904 CTTCAATGTCTAAAAGTCAAATTCGAA 57.336 29.630 0.00 0.00 0.00 3.71
317 328 8.485976 AAAGTCAAATTCGAATGTTCCAAAAA 57.514 26.923 12.25 0.00 0.00 1.94
405 416 8.149973 TCCAAACTTGAAATACACACTTAGAC 57.850 34.615 0.00 0.00 0.00 2.59
466 477 6.321181 TCACAGGAAGACAAAAGCTAAAATGT 59.679 34.615 0.00 0.00 0.00 2.71
490 501 7.928167 TGTCGCTATTCACATAATGATTTCTCT 59.072 33.333 0.00 0.00 37.11 3.10
491 502 8.768955 GTCGCTATTCACATAATGATTTCTCTT 58.231 33.333 0.00 0.00 37.11 2.85
492 503 9.330063 TCGCTATTCACATAATGATTTCTCTTT 57.670 29.630 0.00 0.00 37.11 2.52
493 504 9.941664 CGCTATTCACATAATGATTTCTCTTTT 57.058 29.630 0.00 0.00 37.11 2.27
524 535 8.347004 TGTTTCTCATGGCATATTTCAAGTTA 57.653 30.769 0.00 0.00 0.00 2.24
527 538 6.064060 TCTCATGGCATATTTCAAGTTAGGG 58.936 40.000 0.00 0.00 0.00 3.53
534 545 6.377146 GGCATATTTCAAGTTAGGGTCTGAAA 59.623 38.462 0.00 0.00 0.00 2.69
553 568 7.284489 GTCTGAAATTTATAGGGGTTGCACATA 59.716 37.037 0.00 0.00 0.00 2.29
559 574 4.796110 ATAGGGGTTGCACATATCTTGT 57.204 40.909 0.00 0.00 39.91 3.16
639 660 6.348498 GCATTTGGGAGCACCTTAATATTTT 58.652 36.000 0.00 0.00 41.11 1.82
640 661 6.823182 GCATTTGGGAGCACCTTAATATTTTT 59.177 34.615 0.00 0.00 41.11 1.94
683 704 4.082125 CTGTTTTGCAGGGATTAGGTTCT 58.918 43.478 0.00 0.00 41.42 3.01
785 810 7.177041 ACAAAACCAAAACAAGTAGTCCTAACA 59.823 33.333 0.00 0.00 0.00 2.41
822 847 2.132762 GTGTTAACACGAGGACTGTGG 58.867 52.381 22.16 0.00 41.64 4.17
825 850 2.798847 GTTAACACGAGGACTGTGGTTC 59.201 50.000 0.00 0.00 41.64 3.62
827 852 1.991121 ACACGAGGACTGTGGTTCTA 58.009 50.000 0.00 0.00 41.64 2.10
841 866 3.068307 GTGGTTCTAGTGTGTGTGAGAGT 59.932 47.826 0.00 0.00 0.00 3.24
946 971 0.476771 ATCCTCCTCCTCCGTCTCTC 59.523 60.000 0.00 0.00 0.00 3.20
948 973 0.184933 CCTCCTCCTCCGTCTCTCAT 59.815 60.000 0.00 0.00 0.00 2.90
1042 1073 2.038007 TTCTGCTCCCGCTCCTCT 59.962 61.111 0.00 0.00 36.97 3.69
1563 1796 3.545624 CGTCGAGTACAAGAGGTAATCCG 60.546 52.174 0.00 0.00 42.58 4.18
1564 1797 3.376546 GTCGAGTACAAGAGGTAATCCGT 59.623 47.826 0.00 0.00 42.58 4.69
1584 1828 2.101233 GCGCCCCTCTCGTTTTCTC 61.101 63.158 0.00 0.00 0.00 2.87
1699 1973 1.000283 CTCCAGTTGTCTCGAAGCTGT 60.000 52.381 0.00 0.00 0.00 4.40
1782 2083 1.373497 CAAGAACCTCTCGCTGCGT 60.373 57.895 22.48 0.24 0.00 5.24
1848 2149 4.715130 TACCAGGGCGGCCAGACT 62.715 66.667 31.59 12.91 39.03 3.24
2130 2531 2.217038 GCAGGAGTGGAGGTGACCA 61.217 63.158 3.63 0.00 37.63 4.02
2184 2589 1.401905 CTAAGCTCCAAAATCGTGGCC 59.598 52.381 0.00 0.00 38.68 5.36
2220 2625 1.679305 TCAGAGGCTCCTCGTCACC 60.679 63.158 11.71 0.00 46.90 4.02
2225 2630 4.803426 GCTCCTCGTCACCGCTGG 62.803 72.222 0.00 0.00 0.00 4.85
2257 2662 1.117150 CTGGGCATGGAATTGGAAGG 58.883 55.000 0.00 0.00 0.00 3.46
2258 2663 0.709397 TGGGCATGGAATTGGAAGGA 59.291 50.000 0.00 0.00 0.00 3.36
2259 2664 1.291637 TGGGCATGGAATTGGAAGGAT 59.708 47.619 0.00 0.00 0.00 3.24
2260 2665 2.517553 TGGGCATGGAATTGGAAGGATA 59.482 45.455 0.00 0.00 0.00 2.59
2318 2727 2.280628 CCTCGTTGCTTATCCAACTCC 58.719 52.381 3.89 0.00 42.17 3.85
2393 2805 3.871594 AGTAGCAACCATGAAGCGATAAC 59.128 43.478 0.00 0.00 0.00 1.89
2404 2816 1.659644 GCGATAACGGGTAGCGGAC 60.660 63.158 12.99 0.00 41.93 4.79
2431 2843 4.115199 GCCGTGGCCTGAATCCCT 62.115 66.667 3.32 0.00 34.56 4.20
2468 2883 1.512926 CGGTGACTTTTCTCAGTGGG 58.487 55.000 0.00 0.00 0.00 4.61
2471 2886 3.665190 GGTGACTTTTCTCAGTGGGTAG 58.335 50.000 0.00 0.00 0.00 3.18
2519 2934 3.050275 GCTCCGTTGCTTTCGGCT 61.050 61.111 9.25 0.00 46.49 5.52
2520 2935 3.028366 GCTCCGTTGCTTTCGGCTC 62.028 63.158 9.25 1.86 46.49 4.70
2521 2936 2.730672 CTCCGTTGCTTTCGGCTCG 61.731 63.158 9.25 0.00 46.49 5.03
2522 2937 2.736995 CCGTTGCTTTCGGCTCGA 60.737 61.111 2.44 0.00 41.48 4.04
2525 2956 1.425428 GTTGCTTTCGGCTCGATGG 59.575 57.895 0.00 0.00 42.39 3.51
2565 2997 3.479269 GCCGAGCTCGACCGTTTG 61.479 66.667 36.59 18.84 43.02 2.93
2566 2998 2.257371 CCGAGCTCGACCGTTTGA 59.743 61.111 36.59 0.00 43.02 2.69
2567 2999 1.372499 CCGAGCTCGACCGTTTGAA 60.372 57.895 36.59 0.00 43.02 2.69
2569 3001 0.366871 CGAGCTCGACCGTTTGAATG 59.633 55.000 32.06 0.00 43.02 2.67
2592 3033 4.215613 GGGTTGGTGGCGAGATTAATAATC 59.784 45.833 4.89 4.89 38.20 1.75
2610 3051 1.008194 CTGTTGGACGACGGACGAA 60.008 57.895 6.90 0.00 45.77 3.85
2611 3052 0.595567 CTGTTGGACGACGGACGAAA 60.596 55.000 6.90 0.00 45.77 3.46
2612 3053 0.871163 TGTTGGACGACGGACGAAAC 60.871 55.000 6.90 8.44 45.77 2.78
2613 3054 1.658102 TTGGACGACGGACGAAACG 60.658 57.895 6.90 4.17 45.77 3.60
2614 3055 2.057654 TTGGACGACGGACGAAACGA 62.058 55.000 6.90 0.00 45.77 3.85
2647 3088 3.588842 TGGTCTTCCAGGATTCACTGAAT 59.411 43.478 3.80 3.80 40.97 2.57
2651 3092 4.779489 TCTTCCAGGATTCACTGAATGAGA 59.221 41.667 9.08 0.00 40.97 3.27
2652 3093 4.478206 TCCAGGATTCACTGAATGAGAC 57.522 45.455 9.08 0.00 40.97 3.36
2666 3107 5.800296 TGAATGAGACGGTCAGGAAATTAA 58.200 37.500 11.27 0.00 39.07 1.40
2669 3110 3.055385 TGAGACGGTCAGGAAATTAAGGG 60.055 47.826 11.27 0.00 0.00 3.95
2670 3111 2.014857 GACGGTCAGGAAATTAAGGGC 58.985 52.381 2.62 0.00 0.00 5.19
2671 3112 1.014352 CGGTCAGGAAATTAAGGGCG 58.986 55.000 0.00 0.00 0.00 6.13
2674 3115 3.203716 GGTCAGGAAATTAAGGGCGTAG 58.796 50.000 0.00 0.00 0.00 3.51
2675 3116 3.370209 GGTCAGGAAATTAAGGGCGTAGT 60.370 47.826 0.00 0.00 0.00 2.73
2676 3117 3.621715 GTCAGGAAATTAAGGGCGTAGTG 59.378 47.826 0.00 0.00 0.00 2.74
2677 3118 2.354821 CAGGAAATTAAGGGCGTAGTGC 59.645 50.000 0.00 0.00 45.38 4.40
2688 3129 3.134081 AGGGCGTAGTGCAATACAATACT 59.866 43.478 22.73 12.24 45.47 2.12
2689 3130 3.247648 GGGCGTAGTGCAATACAATACTG 59.752 47.826 22.73 7.57 45.47 2.74
2690 3131 3.869246 GGCGTAGTGCAATACAATACTGT 59.131 43.478 22.73 0.00 45.47 3.55
2691 3132 5.045215 GGCGTAGTGCAATACAATACTGTA 58.955 41.667 22.73 0.00 45.47 2.74
2692 3133 5.521010 GGCGTAGTGCAATACAATACTGTAA 59.479 40.000 22.73 0.00 45.47 2.41
2693 3134 6.202188 GGCGTAGTGCAATACAATACTGTAAT 59.798 38.462 22.73 0.00 45.47 1.89
2694 3135 7.281484 GCGTAGTGCAATACAATACTGTAATC 58.719 38.462 22.73 0.00 45.47 1.75
2695 3136 7.042992 GCGTAGTGCAATACAATACTGTAATCA 60.043 37.037 22.73 0.00 45.47 2.57
2696 3137 8.480066 CGTAGTGCAATACAATACTGTAATCAG 58.520 37.037 22.73 0.00 45.47 2.90
2697 3138 7.792374 AGTGCAATACAATACTGTAATCAGG 57.208 36.000 0.00 0.00 45.14 3.86
2698 3139 7.564793 AGTGCAATACAATACTGTAATCAGGA 58.435 34.615 0.00 0.00 45.14 3.86
2699 3140 7.712639 AGTGCAATACAATACTGTAATCAGGAG 59.287 37.037 0.00 0.00 45.14 3.69
2700 3141 7.495934 GTGCAATACAATACTGTAATCAGGAGT 59.504 37.037 0.00 0.00 45.14 3.85
2701 3142 8.700973 TGCAATACAATACTGTAATCAGGAGTA 58.299 33.333 0.00 0.00 45.14 2.59
2702 3143 9.197694 GCAATACAATACTGTAATCAGGAGTAG 57.802 37.037 0.00 0.00 45.14 2.57
2707 3148 7.982354 ACAATACTGTAATCAGGAGTAGAAAGC 59.018 37.037 0.00 0.00 45.14 3.51
2708 3149 7.661536 ATACTGTAATCAGGAGTAGAAAGCA 57.338 36.000 0.00 0.00 45.14 3.91
2709 3150 5.725362 ACTGTAATCAGGAGTAGAAAGCAC 58.275 41.667 0.47 0.00 45.14 4.40
2710 3151 4.744570 TGTAATCAGGAGTAGAAAGCACG 58.255 43.478 0.00 0.00 0.00 5.34
2711 3152 3.963428 AATCAGGAGTAGAAAGCACGT 57.037 42.857 0.00 0.00 0.00 4.49
2712 3153 3.512033 ATCAGGAGTAGAAAGCACGTC 57.488 47.619 0.00 0.00 0.00 4.34
2713 3154 1.199327 TCAGGAGTAGAAAGCACGTCG 59.801 52.381 0.00 0.00 0.00 5.12
2719 3160 3.909430 AGTAGAAAGCACGTCGAATTCA 58.091 40.909 6.22 0.00 0.00 2.57
2745 3186 2.431782 TGTATGCACTGAGCTGAGCATA 59.568 45.455 7.39 10.71 45.09 3.14
2746 3187 1.950828 ATGCACTGAGCTGAGCATAC 58.049 50.000 7.39 0.00 45.09 2.39
2747 3188 0.609662 TGCACTGAGCTGAGCATACA 59.390 50.000 7.39 2.96 45.94 2.29
2748 3189 1.208776 TGCACTGAGCTGAGCATACAT 59.791 47.619 7.39 0.00 45.94 2.29
2749 3190 1.598132 GCACTGAGCTGAGCATACATG 59.402 52.381 7.39 0.00 41.15 3.21
2750 3191 2.740904 GCACTGAGCTGAGCATACATGA 60.741 50.000 7.39 0.00 41.15 3.07
2751 3192 3.729966 CACTGAGCTGAGCATACATGAT 58.270 45.455 7.39 0.00 0.00 2.45
2752 3193 4.127907 CACTGAGCTGAGCATACATGATT 58.872 43.478 7.39 0.00 0.00 2.57
2753 3194 4.024809 CACTGAGCTGAGCATACATGATTG 60.025 45.833 7.39 0.00 0.00 2.67
2754 3195 3.473625 TGAGCTGAGCATACATGATTGG 58.526 45.455 7.39 0.00 0.00 3.16
2755 3196 3.118149 TGAGCTGAGCATACATGATTGGT 60.118 43.478 7.39 1.44 0.00 3.67
2756 3197 3.211865 AGCTGAGCATACATGATTGGTG 58.788 45.455 7.39 0.00 0.00 4.17
2757 3198 3.118149 AGCTGAGCATACATGATTGGTGA 60.118 43.478 7.39 0.00 0.00 4.02
2758 3199 3.819337 GCTGAGCATACATGATTGGTGAT 59.181 43.478 0.00 0.00 0.00 3.06
2759 3200 4.277672 GCTGAGCATACATGATTGGTGATT 59.722 41.667 0.00 0.00 0.00 2.57
2760 3201 5.471116 GCTGAGCATACATGATTGGTGATTA 59.529 40.000 0.00 0.00 0.00 1.75
2761 3202 6.567321 GCTGAGCATACATGATTGGTGATTAC 60.567 42.308 0.00 0.00 0.00 1.89
2762 3203 6.594744 TGAGCATACATGATTGGTGATTACT 58.405 36.000 0.00 0.00 0.00 2.24
2763 3204 6.707608 TGAGCATACATGATTGGTGATTACTC 59.292 38.462 0.00 0.00 0.00 2.59
2764 3205 6.000219 AGCATACATGATTGGTGATTACTCC 59.000 40.000 0.00 0.00 0.00 3.85
2765 3206 6.000219 GCATACATGATTGGTGATTACTCCT 59.000 40.000 0.00 0.00 0.00 3.69
2766 3207 6.488006 GCATACATGATTGGTGATTACTCCTT 59.512 38.462 0.00 0.00 0.00 3.36
2767 3208 7.308229 GCATACATGATTGGTGATTACTCCTTC 60.308 40.741 0.00 0.00 0.00 3.46
2768 3209 5.118990 ACATGATTGGTGATTACTCCTTCG 58.881 41.667 0.00 0.00 0.00 3.79
2769 3210 4.137116 TGATTGGTGATTACTCCTTCGG 57.863 45.455 0.00 0.00 0.00 4.30
2770 3211 3.517901 TGATTGGTGATTACTCCTTCGGT 59.482 43.478 0.00 0.00 0.00 4.69
2771 3212 3.604875 TTGGTGATTACTCCTTCGGTC 57.395 47.619 0.00 0.00 0.00 4.79
2772 3213 2.816411 TGGTGATTACTCCTTCGGTCT 58.184 47.619 0.00 0.00 0.00 3.85
2773 3214 2.758979 TGGTGATTACTCCTTCGGTCTC 59.241 50.000 0.00 0.00 0.00 3.36
2774 3215 2.758979 GGTGATTACTCCTTCGGTCTCA 59.241 50.000 0.00 0.00 0.00 3.27
2775 3216 3.385111 GGTGATTACTCCTTCGGTCTCAT 59.615 47.826 0.00 0.00 0.00 2.90
2776 3217 4.583489 GGTGATTACTCCTTCGGTCTCATA 59.417 45.833 0.00 0.00 0.00 2.15
2777 3218 5.068723 GGTGATTACTCCTTCGGTCTCATAA 59.931 44.000 0.00 0.00 0.00 1.90
2778 3219 6.239345 GGTGATTACTCCTTCGGTCTCATAAT 60.239 42.308 0.00 0.00 0.00 1.28
2779 3220 6.642950 GTGATTACTCCTTCGGTCTCATAATG 59.357 42.308 0.00 0.00 0.00 1.90
2780 3221 3.460857 ACTCCTTCGGTCTCATAATGC 57.539 47.619 0.00 0.00 0.00 3.56
2781 3222 2.766263 ACTCCTTCGGTCTCATAATGCA 59.234 45.455 0.00 0.00 0.00 3.96
2782 3223 3.197766 ACTCCTTCGGTCTCATAATGCAA 59.802 43.478 0.00 0.00 0.00 4.08
2783 3224 3.797039 TCCTTCGGTCTCATAATGCAAG 58.203 45.455 0.00 0.00 0.00 4.01
2784 3225 2.874701 CCTTCGGTCTCATAATGCAAGG 59.125 50.000 0.00 0.00 0.00 3.61
2785 3226 1.953559 TCGGTCTCATAATGCAAGGC 58.046 50.000 0.00 0.00 0.00 4.35
2786 3227 1.209261 TCGGTCTCATAATGCAAGGCA 59.791 47.619 0.00 0.00 44.86 4.75
2838 3279 8.888579 AAAACATCTTACATTATAGGACGGAG 57.111 34.615 0.00 0.00 0.00 4.63
2839 3280 6.591750 ACATCTTACATTATAGGACGGAGG 57.408 41.667 0.00 0.00 0.00 4.30
2840 3281 5.480772 ACATCTTACATTATAGGACGGAGGG 59.519 44.000 0.00 0.00 0.00 4.30
2841 3282 5.329191 TCTTACATTATAGGACGGAGGGA 57.671 43.478 0.00 0.00 0.00 4.20
2842 3283 5.322754 TCTTACATTATAGGACGGAGGGAG 58.677 45.833 0.00 0.00 0.00 4.30
2843 3284 3.614568 ACATTATAGGACGGAGGGAGT 57.385 47.619 0.00 0.00 0.00 3.85
2846 3287 3.803186 TTATAGGACGGAGGGAGTAGG 57.197 52.381 0.00 0.00 0.00 3.18
2848 3289 0.842635 TAGGACGGAGGGAGTAGGTC 59.157 60.000 0.00 0.00 0.00 3.85
2851 3292 0.179000 GACGGAGGGAGTAGGTCGTA 59.821 60.000 0.00 0.00 0.00 3.43
2852 3293 0.179936 ACGGAGGGAGTAGGTCGTAG 59.820 60.000 0.00 0.00 0.00 3.51
2855 3296 1.310904 GAGGGAGTAGGTCGTAGCTG 58.689 60.000 0.00 0.00 0.00 4.24
2871 3312 2.748251 TGGGTGCGCCATAAACGG 60.748 61.111 19.98 0.00 36.17 4.44
2885 3326 0.322816 AAACGGCAGCCACTCATCAT 60.323 50.000 13.30 0.00 0.00 2.45
2886 3327 0.745845 AACGGCAGCCACTCATCATC 60.746 55.000 13.30 0.00 0.00 2.92
2895 3339 1.395954 CCACTCATCATCAGTGCAACG 59.604 52.381 0.00 0.00 45.86 4.10
2913 3368 0.105039 CGGCAACCATCTACTCCTCC 59.895 60.000 0.00 0.00 0.00 4.30
2914 3369 1.204146 GGCAACCATCTACTCCTCCA 58.796 55.000 0.00 0.00 0.00 3.86
2917 3372 1.139853 CAACCATCTACTCCTCCAGGC 59.860 57.143 0.00 0.00 34.44 4.85
2918 3373 0.399233 ACCATCTACTCCTCCAGGCC 60.399 60.000 0.00 0.00 34.44 5.19
2919 3374 0.105246 CCATCTACTCCTCCAGGCCT 60.105 60.000 0.00 0.00 34.44 5.19
2920 3375 1.337118 CATCTACTCCTCCAGGCCTC 58.663 60.000 0.00 0.00 34.44 4.70
2921 3376 0.937441 ATCTACTCCTCCAGGCCTCA 59.063 55.000 0.00 0.00 34.44 3.86
2922 3377 0.033011 TCTACTCCTCCAGGCCTCAC 60.033 60.000 0.00 0.00 34.44 3.51
2923 3378 1.379977 TACTCCTCCAGGCCTCACG 60.380 63.158 0.00 0.00 34.44 4.35
2924 3379 1.859841 TACTCCTCCAGGCCTCACGA 61.860 60.000 0.00 0.00 34.44 4.35
2925 3380 1.984570 CTCCTCCAGGCCTCACGAA 60.985 63.158 0.00 0.00 34.44 3.85
2926 3381 1.535444 TCCTCCAGGCCTCACGAAA 60.535 57.895 0.00 0.00 34.44 3.46
2927 3382 1.376037 CCTCCAGGCCTCACGAAAC 60.376 63.158 0.00 0.00 0.00 2.78
2928 3383 1.376037 CTCCAGGCCTCACGAAACC 60.376 63.158 0.00 0.00 0.00 3.27
2929 3384 2.111999 CTCCAGGCCTCACGAAACCA 62.112 60.000 0.00 0.00 0.00 3.67
2930 3385 1.002134 CCAGGCCTCACGAAACCAT 60.002 57.895 0.00 0.00 0.00 3.55
2931 3386 0.609131 CCAGGCCTCACGAAACCATT 60.609 55.000 0.00 0.00 0.00 3.16
2932 3387 0.523072 CAGGCCTCACGAAACCATTG 59.477 55.000 0.00 0.00 0.00 2.82
2933 3388 1.212751 GGCCTCACGAAACCATTGC 59.787 57.895 0.00 0.00 0.00 3.56
2934 3389 1.244019 GGCCTCACGAAACCATTGCT 61.244 55.000 0.00 0.00 0.00 3.91
2935 3390 0.598065 GCCTCACGAAACCATTGCTT 59.402 50.000 0.00 0.00 0.00 3.91
2936 3391 1.666888 GCCTCACGAAACCATTGCTTG 60.667 52.381 0.00 0.00 0.00 4.01
2937 3392 1.608590 CCTCACGAAACCATTGCTTGT 59.391 47.619 0.00 0.00 0.00 3.16
2938 3393 2.350772 CCTCACGAAACCATTGCTTGTC 60.351 50.000 0.00 0.00 0.00 3.18
2939 3394 2.290367 CTCACGAAACCATTGCTTGTCA 59.710 45.455 0.00 0.00 0.00 3.58
2956 3411 5.008019 GCTTGTCAATGATGATAACGATGGT 59.992 40.000 0.00 0.00 38.01 3.55
2964 3419 3.801114 TGATAACGATGGTCAGTGGAG 57.199 47.619 0.00 0.00 0.00 3.86
2970 3425 1.478510 CGATGGTCAGTGGAGCTAGTT 59.521 52.381 0.00 0.00 42.05 2.24
2975 3430 2.408050 GTCAGTGGAGCTAGTTGTGTG 58.592 52.381 0.00 0.00 0.00 3.82
2977 3432 2.035961 TCAGTGGAGCTAGTTGTGTGTC 59.964 50.000 0.00 0.00 0.00 3.67
2981 3439 3.256136 GTGGAGCTAGTTGTGTGTCTACT 59.744 47.826 0.00 0.00 36.28 2.57
2992 3450 2.614057 GTGTGTCTACTGGCCAATATGC 59.386 50.000 7.01 0.00 0.00 3.14
3029 3496 0.104304 GAAAGCCGGCCGAGATTCTA 59.896 55.000 30.73 0.00 0.00 2.10
3062 3529 3.991051 CGTCTGTCCGCCACCACT 61.991 66.667 0.00 0.00 0.00 4.00
3066 3533 4.293648 TGTCCGCCACCACTCACG 62.294 66.667 0.00 0.00 0.00 4.35
3127 3614 1.000060 TGCTCAAAATTCAGGCACAGC 60.000 47.619 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 2.288825 CCAAGCTCTACAAACGTGAGGA 60.289 50.000 0.00 0.00 0.00 3.71
28 29 2.069273 CCCAAGCTCTACAAACGTGAG 58.931 52.381 0.00 0.00 0.00 3.51
29 30 1.689813 TCCCAAGCTCTACAAACGTGA 59.310 47.619 0.00 0.00 0.00 4.35
30 31 2.163818 TCCCAAGCTCTACAAACGTG 57.836 50.000 0.00 0.00 0.00 4.49
31 32 3.418684 AATCCCAAGCTCTACAAACGT 57.581 42.857 0.00 0.00 0.00 3.99
32 33 3.502211 ACAAATCCCAAGCTCTACAAACG 59.498 43.478 0.00 0.00 0.00 3.60
33 34 6.374333 TCATACAAATCCCAAGCTCTACAAAC 59.626 38.462 0.00 0.00 0.00 2.93
35 36 5.880332 GTCATACAAATCCCAAGCTCTACAA 59.120 40.000 0.00 0.00 0.00 2.41
36 37 5.189736 AGTCATACAAATCCCAAGCTCTACA 59.810 40.000 0.00 0.00 0.00 2.74
37 38 5.675538 AGTCATACAAATCCCAAGCTCTAC 58.324 41.667 0.00 0.00 0.00 2.59
38 39 5.957771 AGTCATACAAATCCCAAGCTCTA 57.042 39.130 0.00 0.00 0.00 2.43
86 97 4.212847 CACACAACCAACATTGAGAGAGAG 59.787 45.833 0.00 0.00 33.57 3.20
88 99 3.304257 GCACACAACCAACATTGAGAGAG 60.304 47.826 0.00 0.00 33.57 3.20
90 101 2.287788 GGCACACAACCAACATTGAGAG 60.288 50.000 0.00 0.00 33.57 3.20
92 103 1.682854 AGGCACACAACCAACATTGAG 59.317 47.619 0.00 0.00 33.57 3.02
94 105 1.269726 GGAGGCACACAACCAACATTG 60.270 52.381 0.00 0.00 35.59 2.82
102 113 0.320771 ATGACGAGGAGGCACACAAC 60.321 55.000 0.00 0.00 43.31 3.32
113 124 2.025767 CTGGCCTCTCCATGACGAGG 62.026 65.000 19.95 19.95 45.50 4.63
114 125 1.440893 CTGGCCTCTCCATGACGAG 59.559 63.158 3.32 0.00 45.50 4.18
116 127 2.362369 ACCTGGCCTCTCCATGACG 61.362 63.158 3.32 0.00 45.50 4.35
123 134 2.359230 GCACACACCTGGCCTCTC 60.359 66.667 3.32 0.00 0.00 3.20
126 137 0.405585 AATAAGCACACACCTGGCCT 59.594 50.000 3.32 0.00 0.00 5.19
129 140 2.229792 ACACAATAAGCACACACCTGG 58.770 47.619 0.00 0.00 0.00 4.45
131 142 3.490761 GCAAACACAATAAGCACACACCT 60.491 43.478 0.00 0.00 0.00 4.00
203 214 8.877864 ATTACCAGAAATGTTGGACTTGATTA 57.122 30.769 0.00 0.00 39.08 1.75
220 231 7.303182 TCTCTCTTTGAGACAAATTACCAGA 57.697 36.000 0.00 0.00 46.03 3.86
266 277 2.741759 TTGAAGCATGAGAGCACGTA 57.258 45.000 0.00 0.00 36.85 3.57
361 372 7.391833 AGTTTGGATCTGAATTTTGTAGAGGTC 59.608 37.037 0.00 0.00 0.00 3.85
371 382 9.696917 GTGTATTTCAAGTTTGGATCTGAATTT 57.303 29.630 0.00 0.00 0.00 1.82
428 439 8.918202 TGTCTTCCTGTGACACTATTTATTTT 57.082 30.769 7.20 0.00 39.23 1.82
429 440 8.918202 TTGTCTTCCTGTGACACTATTTATTT 57.082 30.769 7.20 0.00 43.13 1.40
430 441 8.918202 TTTGTCTTCCTGTGACACTATTTATT 57.082 30.769 7.20 0.00 43.13 1.40
431 442 8.918202 TTTTGTCTTCCTGTGACACTATTTAT 57.082 30.769 7.20 0.00 43.13 1.40
432 443 7.041372 GCTTTTGTCTTCCTGTGACACTATTTA 60.041 37.037 7.20 0.00 43.13 1.40
445 456 5.562890 GCGACATTTTAGCTTTTGTCTTCCT 60.563 40.000 0.00 0.00 37.04 3.36
466 477 8.893219 AAGAGAAATCATTATGTGAATAGCGA 57.107 30.769 0.00 0.00 40.97 4.93
524 535 5.766590 CAACCCCTATAAATTTCAGACCCT 58.233 41.667 0.00 0.00 0.00 4.34
527 538 5.417580 TGTGCAACCCCTATAAATTTCAGAC 59.582 40.000 0.00 0.00 34.36 3.51
534 545 7.297614 ACAAGATATGTGCAACCCCTATAAAT 58.702 34.615 0.00 0.00 41.93 1.40
538 549 4.796110 ACAAGATATGTGCAACCCCTAT 57.204 40.909 0.00 0.00 41.93 2.57
597 612 9.061435 CCCAAATGCCTAAAAAGTGAATTTTAA 57.939 29.630 0.00 0.00 40.27 1.52
605 620 3.006752 TGCTCCCAAATGCCTAAAAAGTG 59.993 43.478 0.00 0.00 0.00 3.16
639 660 3.222603 GGAGCTTTGAGACAGGGAAAAA 58.777 45.455 0.00 0.00 0.00 1.94
640 661 2.489073 GGGAGCTTTGAGACAGGGAAAA 60.489 50.000 0.00 0.00 0.00 2.29
683 704 8.048514 ACACAGGGAGTACTACTTTGTTAAAAA 58.951 33.333 4.77 0.00 0.00 1.94
819 844 3.068307 ACTCTCACACACACTAGAACCAC 59.932 47.826 0.00 0.00 0.00 4.16
820 845 3.296854 ACTCTCACACACACTAGAACCA 58.703 45.455 0.00 0.00 0.00 3.67
822 847 4.504461 CACAACTCTCACACACACTAGAAC 59.496 45.833 0.00 0.00 0.00 3.01
825 850 4.307443 TCACAACTCTCACACACACTAG 57.693 45.455 0.00 0.00 0.00 2.57
827 852 3.055819 AGTTCACAACTCTCACACACACT 60.056 43.478 0.00 0.00 37.02 3.55
841 866 4.631377 CACAGAAACTGACAGAGTTCACAA 59.369 41.667 10.08 0.00 44.68 3.33
937 962 3.636153 TGAGAGAAGATGAGAGACGGA 57.364 47.619 0.00 0.00 0.00 4.69
939 964 4.963276 AGTTGAGAGAAGATGAGAGACG 57.037 45.455 0.00 0.00 0.00 4.18
946 971 4.153835 GTGGCTTCAAGTTGAGAGAAGATG 59.846 45.833 5.56 0.00 40.85 2.90
948 973 3.389329 AGTGGCTTCAAGTTGAGAGAAGA 59.611 43.478 5.56 0.00 40.85 2.87
1042 1073 0.415429 AGGGAGCAGAGGAAGAGGAA 59.585 55.000 0.00 0.00 0.00 3.36
1106 1137 1.437986 GAGGTGTAGTAGGCGGCTG 59.562 63.158 23.55 0.00 0.00 4.85
1563 1796 4.736896 AAACGAGAGGGGCGCGAC 62.737 66.667 12.10 6.99 42.77 5.19
1564 1797 3.927163 GAAAACGAGAGGGGCGCGA 62.927 63.158 12.10 0.00 42.77 5.87
1577 1814 2.727777 GCGGTTGGTGAAAGAGAAAAC 58.272 47.619 0.00 0.00 0.00 2.43
1666 1932 2.146920 ACTGGAGTCCTGTACTAGGC 57.853 55.000 19.33 3.35 46.87 3.93
1668 1934 4.337145 AGACAACTGGAGTCCTGTACTAG 58.663 47.826 20.82 13.57 39.07 2.57
1699 1973 5.186198 GTGAGCCTAGCTTCCAAATTCTAA 58.814 41.667 0.00 0.00 39.88 2.10
1749 2050 0.037326 TCTTGCCCTTGTACTCGCAG 60.037 55.000 0.00 0.00 31.86 5.18
1782 2083 3.385384 CGGCTCCTCTGCTCCACA 61.385 66.667 0.00 0.00 0.00 4.17
1848 2149 3.424859 TCGACCGCGACGATGTCA 61.425 61.111 20.19 2.91 42.51 3.58
2072 2473 2.796483 TTCTTGGGCGATGTCGGTGG 62.796 60.000 4.44 0.00 40.23 4.61
2145 2546 1.077858 CTCCTCCTCTTGGCTTGCC 60.078 63.158 4.43 4.43 0.00 4.52
2196 2601 1.216710 GAGGAGCCTCTGACCGTTG 59.783 63.158 9.28 0.00 39.80 4.10
2229 2634 2.703798 CCATGCCCAGCCGAAACTG 61.704 63.158 0.00 0.00 37.42 3.16
2231 2636 1.322538 ATTCCATGCCCAGCCGAAAC 61.323 55.000 0.00 0.00 0.00 2.78
2257 2662 8.937884 TGCGTCAGTTACTAATCTCTATCTATC 58.062 37.037 0.00 0.00 0.00 2.08
2258 2663 8.850007 TGCGTCAGTTACTAATCTCTATCTAT 57.150 34.615 0.00 0.00 0.00 1.98
2259 2664 7.095144 GCTGCGTCAGTTACTAATCTCTATCTA 60.095 40.741 8.32 0.00 33.43 1.98
2260 2665 6.293735 GCTGCGTCAGTTACTAATCTCTATCT 60.294 42.308 8.32 0.00 33.43 1.98
2318 2727 2.670229 GCTCATGCATGTTTGTCCACAG 60.670 50.000 25.43 13.29 39.41 3.66
2431 2843 4.827835 TCACCGGATTTTGTATTTTGTCCA 59.172 37.500 9.46 0.00 0.00 4.02
2489 2904 2.825836 GGAGCATGAACCCTGCGG 60.826 66.667 0.00 0.00 44.38 5.69
2496 2911 1.725931 CGAAAGCAACGGAGCATGAAC 60.726 52.381 0.00 0.00 36.85 3.18
2519 2934 4.083057 TGAATGAAAATCGTTTGCCATCGA 60.083 37.500 0.00 0.00 40.28 3.59
2520 2935 4.165036 TGAATGAAAATCGTTTGCCATCG 58.835 39.130 0.00 0.00 0.00 3.84
2521 2936 5.005971 CCATGAATGAAAATCGTTTGCCATC 59.994 40.000 0.00 0.00 0.00 3.51
2522 2937 4.871557 CCATGAATGAAAATCGTTTGCCAT 59.128 37.500 0.00 0.00 0.00 4.40
2525 2956 3.062504 GCCCATGAATGAAAATCGTTTGC 59.937 43.478 0.00 0.00 0.00 3.68
2559 2991 0.316841 CCACCAACCCATTCAAACGG 59.683 55.000 0.00 0.00 0.00 4.44
2563 2995 0.893270 CTCGCCACCAACCCATTCAA 60.893 55.000 0.00 0.00 0.00 2.69
2564 2996 1.303236 CTCGCCACCAACCCATTCA 60.303 57.895 0.00 0.00 0.00 2.57
2565 2997 0.394352 ATCTCGCCACCAACCCATTC 60.394 55.000 0.00 0.00 0.00 2.67
2566 2998 0.039618 AATCTCGCCACCAACCCATT 59.960 50.000 0.00 0.00 0.00 3.16
2567 2999 0.916086 TAATCTCGCCACCAACCCAT 59.084 50.000 0.00 0.00 0.00 4.00
2569 3001 2.052782 ATTAATCTCGCCACCAACCC 57.947 50.000 0.00 0.00 0.00 4.11
2592 3033 0.595567 TTTCGTCCGTCGTCCAACAG 60.596 55.000 0.00 0.00 40.80 3.16
2610 3051 1.612463 AGACCAGCGACTAGTTTCGTT 59.388 47.619 0.00 0.00 41.26 3.85
2611 3052 1.245732 AGACCAGCGACTAGTTTCGT 58.754 50.000 0.00 0.00 41.26 3.85
2612 3053 2.251893 GAAGACCAGCGACTAGTTTCG 58.748 52.381 0.00 0.00 42.15 3.46
2613 3054 2.029290 TGGAAGACCAGCGACTAGTTTC 60.029 50.000 0.00 0.00 41.77 2.78
2614 3055 1.968493 TGGAAGACCAGCGACTAGTTT 59.032 47.619 0.00 0.00 41.77 2.66
2647 3088 3.055385 CCCTTAATTTCCTGACCGTCTCA 60.055 47.826 0.00 0.00 0.00 3.27
2651 3092 1.677820 CGCCCTTAATTTCCTGACCGT 60.678 52.381 0.00 0.00 0.00 4.83
2652 3093 1.014352 CGCCCTTAATTTCCTGACCG 58.986 55.000 0.00 0.00 0.00 4.79
2666 3107 2.710096 ATTGTATTGCACTACGCCCT 57.290 45.000 9.39 0.00 41.33 5.19
2669 3110 6.578020 TTACAGTATTGTATTGCACTACGC 57.422 37.500 9.39 1.09 39.43 4.42
2670 3111 8.347729 TGATTACAGTATTGTATTGCACTACG 57.652 34.615 9.39 0.00 39.43 3.51
2671 3112 8.765219 CCTGATTACAGTATTGTATTGCACTAC 58.235 37.037 7.25 7.25 42.05 2.73
2674 3115 7.495934 ACTCCTGATTACAGTATTGTATTGCAC 59.504 37.037 0.00 0.00 42.05 4.57
2675 3116 7.564793 ACTCCTGATTACAGTATTGTATTGCA 58.435 34.615 0.00 0.00 42.05 4.08
2676 3117 9.197694 CTACTCCTGATTACAGTATTGTATTGC 57.802 37.037 0.00 0.00 42.05 3.56
2681 3122 7.982354 GCTTTCTACTCCTGATTACAGTATTGT 59.018 37.037 0.00 0.00 42.05 2.71
2682 3123 7.981789 TGCTTTCTACTCCTGATTACAGTATTG 59.018 37.037 0.00 0.00 42.05 1.90
2683 3124 7.982354 GTGCTTTCTACTCCTGATTACAGTATT 59.018 37.037 0.00 0.00 42.05 1.89
2685 3126 6.404403 CGTGCTTTCTACTCCTGATTACAGTA 60.404 42.308 0.00 0.00 42.05 2.74
2687 3128 4.800993 CGTGCTTTCTACTCCTGATTACAG 59.199 45.833 0.00 0.00 43.12 2.74
2688 3129 4.219944 ACGTGCTTTCTACTCCTGATTACA 59.780 41.667 0.00 0.00 0.00 2.41
2689 3130 4.745649 ACGTGCTTTCTACTCCTGATTAC 58.254 43.478 0.00 0.00 0.00 1.89
2690 3131 4.438336 CGACGTGCTTTCTACTCCTGATTA 60.438 45.833 0.00 0.00 0.00 1.75
2691 3132 3.673594 CGACGTGCTTTCTACTCCTGATT 60.674 47.826 0.00 0.00 0.00 2.57
2692 3133 2.159366 CGACGTGCTTTCTACTCCTGAT 60.159 50.000 0.00 0.00 0.00 2.90
2693 3134 1.199327 CGACGTGCTTTCTACTCCTGA 59.801 52.381 0.00 0.00 0.00 3.86
2694 3135 1.199327 TCGACGTGCTTTCTACTCCTG 59.801 52.381 0.00 0.00 0.00 3.86
2695 3136 1.531423 TCGACGTGCTTTCTACTCCT 58.469 50.000 0.00 0.00 0.00 3.69
2696 3137 2.342910 TTCGACGTGCTTTCTACTCC 57.657 50.000 0.00 0.00 0.00 3.85
2697 3138 3.918591 TGAATTCGACGTGCTTTCTACTC 59.081 43.478 0.00 0.00 0.00 2.59
2698 3139 3.909430 TGAATTCGACGTGCTTTCTACT 58.091 40.909 0.00 0.00 0.00 2.57
2699 3140 3.918591 TCTGAATTCGACGTGCTTTCTAC 59.081 43.478 0.00 0.00 0.00 2.59
2700 3141 3.918591 GTCTGAATTCGACGTGCTTTCTA 59.081 43.478 12.42 0.00 0.00 2.10
2701 3142 2.731976 GTCTGAATTCGACGTGCTTTCT 59.268 45.455 12.42 0.00 0.00 2.52
2702 3143 2.475111 TGTCTGAATTCGACGTGCTTTC 59.525 45.455 18.74 0.00 34.17 2.62
2703 3144 2.479837 TGTCTGAATTCGACGTGCTTT 58.520 42.857 18.74 0.00 34.17 3.51
2704 3145 2.148916 TGTCTGAATTCGACGTGCTT 57.851 45.000 18.74 0.00 34.17 3.91
2705 3146 1.995484 CATGTCTGAATTCGACGTGCT 59.005 47.619 25.39 11.16 40.33 4.40
2706 3147 1.726791 ACATGTCTGAATTCGACGTGC 59.273 47.619 30.70 12.15 46.98 5.34
2708 3149 3.551890 GCATACATGTCTGAATTCGACGT 59.448 43.478 14.90 16.95 34.17 4.34
2709 3150 3.551485 TGCATACATGTCTGAATTCGACG 59.449 43.478 14.90 11.75 34.17 5.12
2710 3151 4.568359 AGTGCATACATGTCTGAATTCGAC 59.432 41.667 14.90 17.82 0.00 4.20
2711 3152 4.567959 CAGTGCATACATGTCTGAATTCGA 59.432 41.667 14.90 0.00 35.55 3.71
2712 3153 4.567959 TCAGTGCATACATGTCTGAATTCG 59.432 41.667 14.90 0.00 37.66 3.34
2713 3154 5.503683 GCTCAGTGCATACATGTCTGAATTC 60.504 44.000 14.90 0.00 38.88 2.17
2719 3160 2.498885 TCAGCTCAGTGCATACATGTCT 59.501 45.455 0.00 0.00 45.94 3.41
2744 3185 6.280643 CGAAGGAGTAATCACCAATCATGTA 58.719 40.000 0.00 0.00 0.00 2.29
2745 3186 5.118990 CGAAGGAGTAATCACCAATCATGT 58.881 41.667 0.00 0.00 0.00 3.21
2746 3187 5.663795 CGAAGGAGTAATCACCAATCATG 57.336 43.478 0.00 0.00 0.00 3.07
2764 3205 2.289002 GCCTTGCATTATGAGACCGAAG 59.711 50.000 0.00 0.00 0.00 3.79
2765 3206 2.288666 GCCTTGCATTATGAGACCGAA 58.711 47.619 0.00 0.00 0.00 4.30
2766 3207 1.209261 TGCCTTGCATTATGAGACCGA 59.791 47.619 0.00 0.00 31.71 4.69
2767 3208 1.667236 TGCCTTGCATTATGAGACCG 58.333 50.000 0.00 0.00 31.71 4.79
2812 3253 9.326413 CTCCGTCCTATAATGTAAGATGTTTTT 57.674 33.333 0.00 0.00 0.00 1.94
2813 3254 7.931948 CCTCCGTCCTATAATGTAAGATGTTTT 59.068 37.037 0.00 0.00 0.00 2.43
2814 3255 7.442656 CCTCCGTCCTATAATGTAAGATGTTT 58.557 38.462 0.00 0.00 0.00 2.83
2815 3256 6.014499 CCCTCCGTCCTATAATGTAAGATGTT 60.014 42.308 0.00 0.00 0.00 2.71
2816 3257 5.480772 CCCTCCGTCCTATAATGTAAGATGT 59.519 44.000 0.00 0.00 0.00 3.06
2817 3258 5.715279 TCCCTCCGTCCTATAATGTAAGATG 59.285 44.000 0.00 0.00 0.00 2.90
2818 3259 5.900437 TCCCTCCGTCCTATAATGTAAGAT 58.100 41.667 0.00 0.00 0.00 2.40
2819 3260 5.163012 ACTCCCTCCGTCCTATAATGTAAGA 60.163 44.000 0.00 0.00 0.00 2.10
2820 3261 5.078256 ACTCCCTCCGTCCTATAATGTAAG 58.922 45.833 0.00 0.00 0.00 2.34
2821 3262 5.070823 ACTCCCTCCGTCCTATAATGTAA 57.929 43.478 0.00 0.00 0.00 2.41
2822 3263 4.736611 ACTCCCTCCGTCCTATAATGTA 57.263 45.455 0.00 0.00 0.00 2.29
2823 3264 3.614568 ACTCCCTCCGTCCTATAATGT 57.385 47.619 0.00 0.00 0.00 2.71
2824 3265 4.017808 CCTACTCCCTCCGTCCTATAATG 58.982 52.174 0.00 0.00 0.00 1.90
2825 3266 3.661654 ACCTACTCCCTCCGTCCTATAAT 59.338 47.826 0.00 0.00 0.00 1.28
2826 3267 3.059097 ACCTACTCCCTCCGTCCTATAA 58.941 50.000 0.00 0.00 0.00 0.98
2827 3268 2.641815 GACCTACTCCCTCCGTCCTATA 59.358 54.545 0.00 0.00 0.00 1.31
2828 3269 1.424684 GACCTACTCCCTCCGTCCTAT 59.575 57.143 0.00 0.00 0.00 2.57
2829 3270 0.842635 GACCTACTCCCTCCGTCCTA 59.157 60.000 0.00 0.00 0.00 2.94
2830 3271 1.614160 GACCTACTCCCTCCGTCCT 59.386 63.158 0.00 0.00 0.00 3.85
2831 3272 1.823041 CGACCTACTCCCTCCGTCC 60.823 68.421 0.00 0.00 0.00 4.79
2832 3273 0.179000 TACGACCTACTCCCTCCGTC 59.821 60.000 0.00 0.00 0.00 4.79
2833 3274 0.179936 CTACGACCTACTCCCTCCGT 59.820 60.000 0.00 0.00 0.00 4.69
2834 3275 1.165284 GCTACGACCTACTCCCTCCG 61.165 65.000 0.00 0.00 0.00 4.63
2835 3276 0.183252 AGCTACGACCTACTCCCTCC 59.817 60.000 0.00 0.00 0.00 4.30
2836 3277 1.310904 CAGCTACGACCTACTCCCTC 58.689 60.000 0.00 0.00 0.00 4.30
2837 3278 0.106619 CCAGCTACGACCTACTCCCT 60.107 60.000 0.00 0.00 0.00 4.20
2838 3279 1.108132 CCCAGCTACGACCTACTCCC 61.108 65.000 0.00 0.00 0.00 4.30
2839 3280 0.395448 ACCCAGCTACGACCTACTCC 60.395 60.000 0.00 0.00 0.00 3.85
2840 3281 0.739561 CACCCAGCTACGACCTACTC 59.260 60.000 0.00 0.00 0.00 2.59
2841 3282 1.321074 GCACCCAGCTACGACCTACT 61.321 60.000 0.00 0.00 41.15 2.57
2842 3283 1.141234 GCACCCAGCTACGACCTAC 59.859 63.158 0.00 0.00 41.15 3.18
2843 3284 2.412323 CGCACCCAGCTACGACCTA 61.412 63.158 0.00 0.00 42.61 3.08
2855 3296 4.187810 GCCGTTTATGGCGCACCC 62.188 66.667 10.83 0.00 46.75 4.61
2866 3307 0.322816 ATGATGAGTGGCTGCCGTTT 60.323 50.000 14.98 1.20 0.00 3.60
2871 3312 1.015109 CACTGATGATGAGTGGCTGC 58.985 55.000 4.00 0.00 37.72 5.25
2872 3313 1.015109 GCACTGATGATGAGTGGCTG 58.985 55.000 13.72 0.00 41.08 4.85
2895 3339 1.139853 CTGGAGGAGTAGATGGTTGCC 59.860 57.143 0.00 0.00 0.00 4.52
2913 3368 0.523072 CAATGGTTTCGTGAGGCCTG 59.477 55.000 12.00 0.00 0.00 4.85
2914 3369 1.244019 GCAATGGTTTCGTGAGGCCT 61.244 55.000 3.86 3.86 0.00 5.19
2917 3372 1.608590 ACAAGCAATGGTTTCGTGAGG 59.391 47.619 0.00 0.00 0.00 3.86
2918 3373 2.290367 TGACAAGCAATGGTTTCGTGAG 59.710 45.455 0.00 0.00 0.00 3.51
2919 3374 2.293170 TGACAAGCAATGGTTTCGTGA 58.707 42.857 0.00 0.00 0.00 4.35
2920 3375 2.772568 TGACAAGCAATGGTTTCGTG 57.227 45.000 0.00 0.00 0.00 4.35
2930 3385 6.458615 CCATCGTTATCATCATTGACAAGCAA 60.459 38.462 0.00 0.00 41.53 3.91
2931 3386 5.007921 CCATCGTTATCATCATTGACAAGCA 59.992 40.000 0.00 0.00 33.85 3.91
2932 3387 5.008019 ACCATCGTTATCATCATTGACAAGC 59.992 40.000 0.00 0.00 33.85 4.01
2933 3388 6.258507 TGACCATCGTTATCATCATTGACAAG 59.741 38.462 0.00 0.00 33.85 3.16
2934 3389 6.112058 TGACCATCGTTATCATCATTGACAA 58.888 36.000 0.00 0.00 33.85 3.18
2935 3390 5.669477 TGACCATCGTTATCATCATTGACA 58.331 37.500 0.00 0.00 33.85 3.58
2936 3391 5.755375 ACTGACCATCGTTATCATCATTGAC 59.245 40.000 0.00 0.00 33.85 3.18
2937 3392 5.754890 CACTGACCATCGTTATCATCATTGA 59.245 40.000 0.00 0.00 36.00 2.57
2938 3393 5.049886 CCACTGACCATCGTTATCATCATTG 60.050 44.000 0.00 0.00 0.00 2.82
2939 3394 5.059161 CCACTGACCATCGTTATCATCATT 58.941 41.667 0.00 0.00 0.00 2.57
2950 3405 1.107114 ACTAGCTCCACTGACCATCG 58.893 55.000 0.00 0.00 0.00 3.84
2956 3411 2.035961 GACACACAACTAGCTCCACTGA 59.964 50.000 0.00 0.00 0.00 3.41
2964 3419 2.338500 GCCAGTAGACACACAACTAGC 58.662 52.381 0.00 0.00 0.00 3.42
2970 3425 3.872696 CATATTGGCCAGTAGACACACA 58.127 45.455 13.92 0.00 0.00 3.72
2975 3430 2.158755 ACCTGCATATTGGCCAGTAGAC 60.159 50.000 13.92 8.49 0.00 2.59
2977 3432 2.224606 CACCTGCATATTGGCCAGTAG 58.775 52.381 13.92 7.42 0.00 2.57
2981 3439 0.683828 CACCACCTGCATATTGGCCA 60.684 55.000 0.00 0.00 33.25 5.36
3029 3496 2.258591 CGTACAGTGCACTCCGCT 59.741 61.111 18.64 2.10 43.06 5.52
3062 3529 2.157305 ATTTACACGGGTCGGCGTGA 62.157 55.000 6.85 0.00 39.18 4.35
3066 3533 1.869132 GGATAATTTACACGGGTCGGC 59.131 52.381 0.00 0.00 0.00 5.54
3069 3536 3.880490 TGCATGGATAATTTACACGGGTC 59.120 43.478 0.00 0.00 0.00 4.46
3070 3537 3.892284 TGCATGGATAATTTACACGGGT 58.108 40.909 0.00 0.00 0.00 5.28
3071 3538 4.909696 TTGCATGGATAATTTACACGGG 57.090 40.909 0.00 0.00 0.00 5.28


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

AutoCloner maintained by Alex Coulton.