Multiple sequence alignment - TraesCS7D01G524300

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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 TraesCS7D01G524300 chr7D 100.000 4187 0 0 1 4187 620259464 620255278 0.000000e+00 7733.0
1 TraesCS7D01G524300 chr7B 89.846 2334 165 43 808 3119 716025220 716022937 0.000000e+00 2931.0
2 TraesCS7D01G524300 chr7B 85.684 475 42 15 43 505 716031075 716030615 1.050000e-130 477.0
3 TraesCS7D01G524300 chr7B 88.421 95 8 3 875 967 716031240 716031147 1.230000e-20 111.0
4 TraesCS7D01G524300 chr7B 87.129 101 6 2 503 597 716030505 716030406 1.590000e-19 108.0
5 TraesCS7D01G524300 chr7B 97.727 44 1 0 600 643 716025422 716025379 4.490000e-10 76.8
6 TraesCS7D01G524300 chr7A 89.258 2439 119 60 706 3102 714660294 714662631 0.000000e+00 2920.0
7 TraesCS7D01G524300 chr7A 89.338 619 57 5 3578 4187 714663119 714663737 0.000000e+00 769.0
8 TraesCS7D01G524300 chr7A 92.887 478 21 8 3128 3594 714662715 714663190 0.000000e+00 682.0
9 TraesCS7D01G524300 chr7A 81.622 740 59 40 2 693 714659514 714660224 3.680000e-150 542.0
10 TraesCS7D01G524300 chr1A 83.769 536 75 8 3659 4187 364030565 364031095 8.080000e-137 497.0
11 TraesCS7D01G524300 chr5B 83.677 533 78 7 3659 4185 451150939 451150410 1.050000e-135 494.0
12 TraesCS7D01G524300 chr5B 92.632 95 7 0 1365 1459 517868648 517868554 2.030000e-28 137.0
13 TraesCS7D01G524300 chr5A 84.078 515 74 4 3661 4169 478801917 478801405 1.350000e-134 490.0
14 TraesCS7D01G524300 chr5A 92.632 95 7 0 1365 1459 544568346 544568252 2.030000e-28 137.0
15 TraesCS7D01G524300 chr2D 80.916 524 80 12 3677 4187 201395386 201394870 3.030000e-106 396.0
16 TraesCS7D01G524300 chr2D 82.993 441 65 5 3659 4092 602662664 602663101 1.410000e-104 390.0
17 TraesCS7D01G524300 chr2D 83.051 118 12 6 3312 3429 629379227 629379336 2.660000e-17 100.0
18 TraesCS7D01G524300 chr6D 80.374 535 92 10 3659 4185 7443351 7442822 1.090000e-105 394.0
19 TraesCS7D01G524300 chr2B 82.774 447 66 7 3667 4106 485886746 485887188 5.080000e-104 388.0
20 TraesCS7D01G524300 chr5D 84.439 392 55 4 3659 4045 215464262 215464652 8.490000e-102 381.0


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 TraesCS7D01G524300 chr7D 620255278 620259464 4186 True 7733.00 7733 100.00000 1 4187 1 chr7D.!!$R1 4186
1 TraesCS7D01G524300 chr7B 716022937 716025422 2485 True 1503.90 2931 93.78650 600 3119 2 chr7B.!!$R1 2519
2 TraesCS7D01G524300 chr7B 716030406 716031240 834 True 232.00 477 87.07800 43 967 3 chr7B.!!$R2 924
3 TraesCS7D01G524300 chr7A 714659514 714663737 4223 False 1228.25 2920 88.27625 2 4187 4 chr7A.!!$F1 4185
4 TraesCS7D01G524300 chr1A 364030565 364031095 530 False 497.00 497 83.76900 3659 4187 1 chr1A.!!$F1 528
5 TraesCS7D01G524300 chr5B 451150410 451150939 529 True 494.00 494 83.67700 3659 4185 1 chr5B.!!$R1 526
6 TraesCS7D01G524300 chr5A 478801405 478801917 512 True 490.00 490 84.07800 3661 4169 1 chr5A.!!$R1 508
7 TraesCS7D01G524300 chr2D 201394870 201395386 516 True 396.00 396 80.91600 3677 4187 1 chr2D.!!$R1 510
8 TraesCS7D01G524300 chr6D 7442822 7443351 529 True 394.00 394 80.37400 3659 4185 1 chr6D.!!$R1 526

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
515 801 0.399949 ACCCTCTGTCTGTCCAACCA 60.400 55.0 0.0 0.00 0.0 3.67 F
2020 2421 0.873743 GCGCTCCATCACTAGCAGAC 60.874 60.0 0.0 0.00 38.7 3.51 F
2688 3101 0.249489 GCACCAGTTCGACTGTGAGT 60.249 55.0 12.1 3.25 44.5 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2069 2471 0.384669 GTCGAGCCGTACCTAGCATT 59.615 55.0 0.00 0.00 0.0 3.56 R
2959 3387 0.035317 AAGCAACAGCGACATGGAGA 59.965 50.0 0.00 0.00 0.0 3.71 R
3604 4108 0.104855 GCTCAGATGCACCGGTATGA 59.895 55.0 6.87 6.12 0.0 2.15 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
52 54 8.281531 TGTGATGGAATAAATGTCCTATTTCCT 58.718 33.333 0.00 0.00 36.03 3.36
57 59 8.660435 TGGAATAAATGTCCTATTTCCTCTAGG 58.340 37.037 0.00 0.00 37.66 3.02
84 203 5.446260 AAAACCCAACTATTACCGGATCT 57.554 39.130 9.46 0.00 0.00 2.75
91 210 6.018507 CCCAACTATTACCGGATCTTTAAACG 60.019 42.308 9.46 0.00 0.00 3.60
93 212 7.064966 CCAACTATTACCGGATCTTTAAACGTT 59.935 37.037 9.46 0.00 0.00 3.99
118 245 1.055849 TGGGTGCCATCTATACGCAT 58.944 50.000 0.00 0.00 34.51 4.73
127 254 7.254455 GGTGCCATCTATACGCATTACATTATC 60.254 40.741 0.00 0.00 34.51 1.75
128 255 6.761242 TGCCATCTATACGCATTACATTATCC 59.239 38.462 0.00 0.00 0.00 2.59
133 260 5.856126 ATACGCATTACATTATCCAACGG 57.144 39.130 0.00 0.00 0.00 4.44
135 262 3.807622 ACGCATTACATTATCCAACGGAG 59.192 43.478 0.00 0.00 34.05 4.63
218 355 7.016170 TCAGAGATCATACTACTCTCTAGCACT 59.984 40.741 0.00 0.00 42.92 4.40
219 356 8.311109 CAGAGATCATACTACTCTCTAGCACTA 58.689 40.741 0.00 0.00 42.92 2.74
220 357 8.531982 AGAGATCATACTACTCTCTAGCACTAG 58.468 40.741 0.00 0.00 42.96 2.57
252 391 4.641645 CAGGTGCTTGGCCGGTGA 62.642 66.667 1.90 0.00 0.00 4.02
253 392 4.335647 AGGTGCTTGGCCGGTGAG 62.336 66.667 1.90 0.00 0.00 3.51
271 410 3.496130 GTGAGAATGTCCATTATCCTGCG 59.504 47.826 11.04 0.00 38.03 5.18
435 598 1.606668 TGTTTTCCATGGTCAACTCGC 59.393 47.619 21.78 5.58 0.00 5.03
443 606 0.888619 TGGTCAACTCGCCTGTCTAG 59.111 55.000 0.00 0.00 0.00 2.43
444 607 0.889306 GGTCAACTCGCCTGTCTAGT 59.111 55.000 0.00 0.00 0.00 2.57
445 608 1.135344 GGTCAACTCGCCTGTCTAGTC 60.135 57.143 0.00 0.00 0.00 2.59
446 609 1.813786 GTCAACTCGCCTGTCTAGTCT 59.186 52.381 0.00 0.00 0.00 3.24
447 610 3.008330 GTCAACTCGCCTGTCTAGTCTA 58.992 50.000 0.00 0.00 0.00 2.59
477 645 5.927954 TCAAATCATTTCTTTTTGGCTGC 57.072 34.783 0.00 0.00 32.52 5.25
491 663 1.341285 TGGCTGCAACAAGGATGCTAT 60.341 47.619 0.50 0.00 44.14 2.97
495 667 4.070716 GCTGCAACAAGGATGCTATCTAT 58.929 43.478 0.00 0.00 44.14 1.98
497 669 5.121454 GCTGCAACAAGGATGCTATCTATAC 59.879 44.000 0.00 0.00 44.14 1.47
515 801 0.399949 ACCCTCTGTCTGTCCAACCA 60.400 55.000 0.00 0.00 0.00 3.67
524 810 2.808543 GTCTGTCCAACCAGTTGACATC 59.191 50.000 12.06 7.15 42.93 3.06
576 875 2.707791 CCTCTCCCATGGCTAGATTTCA 59.292 50.000 6.09 0.00 0.00 2.69
598 897 6.370453 TCACTCTGCCCATTACATAGTACTA 58.630 40.000 4.77 4.77 0.00 1.82
652 960 7.946207 TCACAACAAATTTACATTGCCTCTTA 58.054 30.769 8.26 0.00 0.00 2.10
668 976 6.523840 TGCCTCTTATGCAAAACAAAGAAAT 58.476 32.000 0.00 0.00 35.40 2.17
671 979 6.930722 CCTCTTATGCAAAACAAAGAAATGGT 59.069 34.615 0.00 0.00 30.33 3.55
693 1001 6.095160 TGGTCCTGCTACGTTTTTCTTTAAAA 59.905 34.615 0.00 0.00 33.41 1.52
694 1002 6.974048 GGTCCTGCTACGTTTTTCTTTAAAAA 59.026 34.615 0.00 0.00 41.21 1.94
753 1122 2.445155 GGCCATCCCCAACCAACT 59.555 61.111 0.00 0.00 0.00 3.16
754 1123 1.682344 GGCCATCCCCAACCAACTC 60.682 63.158 0.00 0.00 0.00 3.01
755 1124 1.682344 GCCATCCCCAACCAACTCC 60.682 63.158 0.00 0.00 0.00 3.85
756 1125 1.000359 CCATCCCCAACCAACTCCC 60.000 63.158 0.00 0.00 0.00 4.30
757 1126 1.000359 CATCCCCAACCAACTCCCC 60.000 63.158 0.00 0.00 0.00 4.81
758 1127 2.612493 ATCCCCAACCAACTCCCCG 61.612 63.158 0.00 0.00 0.00 5.73
784 1153 3.108144 CAAAGGCACAAAAGTCAAGTCG 58.892 45.455 0.00 0.00 0.00 4.18
793 1162 2.751166 AAGTCAAGTCGTCTCATGGG 57.249 50.000 0.00 0.00 0.00 4.00
797 1166 2.996621 GTCAAGTCGTCTCATGGGAAAG 59.003 50.000 0.00 0.00 0.00 2.62
798 1167 2.897326 TCAAGTCGTCTCATGGGAAAGA 59.103 45.455 0.00 0.00 0.00 2.52
801 1170 4.351874 AGTCGTCTCATGGGAAAGAAAA 57.648 40.909 0.00 0.00 0.00 2.29
802 1171 4.714632 AGTCGTCTCATGGGAAAGAAAAA 58.285 39.130 0.00 0.00 0.00 1.94
1002 1388 3.307906 CCAACCGTCCTCCGTCCA 61.308 66.667 0.00 0.00 33.66 4.02
1014 1400 2.046314 CGTCCAATTGCCGTCCCT 60.046 61.111 0.00 0.00 0.00 4.20
1015 1401 2.398554 CGTCCAATTGCCGTCCCTG 61.399 63.158 0.00 0.00 0.00 4.45
1016 1402 2.361104 TCCAATTGCCGTCCCTGC 60.361 61.111 0.00 0.00 0.00 4.85
1017 1403 2.676121 CCAATTGCCGTCCCTGCA 60.676 61.111 0.00 0.00 36.84 4.41
1149 1544 3.228017 TTCGACCTGCACCACCGA 61.228 61.111 0.00 0.00 0.00 4.69
1416 1811 3.670377 GCAACGTTCCTGGTGGCC 61.670 66.667 0.00 0.00 0.00 5.36
1706 2101 4.767255 CCACCTCAGCCGGCAGAC 62.767 72.222 31.54 0.00 0.00 3.51
1707 2102 3.699894 CACCTCAGCCGGCAGACT 61.700 66.667 31.54 8.93 0.00 3.24
1709 2104 4.463879 CCTCAGCCGGCAGACTGG 62.464 72.222 31.54 20.55 46.21 4.00
1963 2364 3.691342 CCGAGACGCCCTTCACCA 61.691 66.667 0.00 0.00 0.00 4.17
1990 2391 5.589192 GGAACACGCAGTAAGTATAGTCAT 58.411 41.667 0.00 0.00 41.61 3.06
2019 2420 1.439228 GCGCTCCATCACTAGCAGA 59.561 57.895 0.00 0.00 38.70 4.26
2020 2421 0.873743 GCGCTCCATCACTAGCAGAC 60.874 60.000 0.00 0.00 38.70 3.51
2024 2425 2.106566 CTCCATCACTAGCAGACCACT 58.893 52.381 0.00 0.00 0.00 4.00
2049 2450 3.664869 TGGGCCCCACATATCAGTA 57.335 52.632 22.27 0.00 0.00 2.74
2050 2451 2.132303 TGGGCCCCACATATCAGTAT 57.868 50.000 22.27 0.00 0.00 2.12
2052 2453 1.614317 GGGCCCCACATATCAGTATGC 60.614 57.143 12.23 0.00 41.15 3.14
2064 2466 6.763135 ACATATCAGTATGCGTGAAAAGTCAT 59.237 34.615 0.00 0.00 41.15 3.06
2066 2468 6.834959 ATCAGTATGCGTGAAAAGTCATAG 57.165 37.500 0.00 0.00 33.46 2.23
2067 2469 4.566759 TCAGTATGCGTGAAAAGTCATAGC 59.433 41.667 0.00 0.00 39.36 2.97
2068 2470 4.568359 CAGTATGCGTGAAAAGTCATAGCT 59.432 41.667 0.00 0.00 39.53 3.32
2069 2471 5.748630 CAGTATGCGTGAAAAGTCATAGCTA 59.251 40.000 0.00 0.00 39.53 3.32
2071 2473 6.986817 AGTATGCGTGAAAAGTCATAGCTAAT 59.013 34.615 0.00 0.00 39.53 1.73
2072 2474 5.469373 TGCGTGAAAAGTCATAGCTAATG 57.531 39.130 0.00 0.00 39.53 1.90
2073 2475 4.201812 TGCGTGAAAAGTCATAGCTAATGC 60.202 41.667 0.00 0.00 39.53 3.56
2307 2712 4.570874 GCGCCTCCATCCCCTTCC 62.571 72.222 0.00 0.00 0.00 3.46
2487 2892 2.363807 GTGCTCCAGAACGACATCG 58.636 57.895 0.00 0.00 46.33 3.84
2516 2921 3.968568 ATCGGCCGTACGCGCATA 61.969 61.111 27.15 14.46 38.94 3.14
2517 2922 4.910722 TCGGCCGTACGCGCATAC 62.911 66.667 27.15 5.70 38.94 2.39
2518 2923 4.918129 CGGCCGTACGCGCATACT 62.918 66.667 19.50 0.00 38.94 2.12
2519 2924 3.327754 GGCCGTACGCGCATACTG 61.328 66.667 23.71 6.37 38.94 2.74
2520 2925 2.278336 GCCGTACGCGCATACTGA 60.278 61.111 19.50 0.00 36.67 3.41
2521 2926 1.660575 GCCGTACGCGCATACTGAT 60.661 57.895 19.50 0.00 36.67 2.90
2522 2927 0.386352 GCCGTACGCGCATACTGATA 60.386 55.000 19.50 0.00 36.67 2.15
2523 2928 1.324718 CCGTACGCGCATACTGATAC 58.675 55.000 12.25 0.00 36.67 2.24
2524 2929 1.334329 CCGTACGCGCATACTGATACA 60.334 52.381 12.25 0.00 36.67 2.29
2525 2930 1.707117 CGTACGCGCATACTGATACAC 59.293 52.381 12.25 0.00 0.00 2.90
2526 2931 2.723209 GTACGCGCATACTGATACACA 58.277 47.619 5.73 0.00 0.00 3.72
2527 2932 1.556564 ACGCGCATACTGATACACAC 58.443 50.000 5.73 0.00 0.00 3.82
2528 2933 1.134367 ACGCGCATACTGATACACACT 59.866 47.619 5.73 0.00 0.00 3.55
2529 2934 1.518515 CGCGCATACTGATACACACTG 59.481 52.381 8.75 0.00 0.00 3.66
2530 2935 1.258982 GCGCATACTGATACACACTGC 59.741 52.381 0.30 0.00 0.00 4.40
2531 2936 2.814269 CGCATACTGATACACACTGCT 58.186 47.619 0.00 0.00 0.00 4.24
2532 2937 3.795488 GCGCATACTGATACACACTGCTA 60.795 47.826 0.30 0.00 0.00 3.49
2533 2938 3.731216 CGCATACTGATACACACTGCTAC 59.269 47.826 0.00 0.00 0.00 3.58
2534 2939 4.498177 CGCATACTGATACACACTGCTACT 60.498 45.833 0.00 0.00 0.00 2.57
2535 2940 4.742167 GCATACTGATACACACTGCTACTG 59.258 45.833 0.00 0.00 0.00 2.74
2546 2951 3.891977 ACACTGCTACTGTCTTCTCTTCA 59.108 43.478 0.00 0.00 0.00 3.02
2548 2953 3.056891 ACTGCTACTGTCTTCTCTTCAGC 60.057 47.826 0.00 0.00 33.12 4.26
2555 2960 5.406649 ACTGTCTTCTCTTCAGCTAATTCG 58.593 41.667 0.00 0.00 33.12 3.34
2558 2963 4.497608 GTCTTCTCTTCAGCTAATTCGTCG 59.502 45.833 0.00 0.00 0.00 5.12
2598 3011 6.673154 TTGCTGATTACTTCATCACTGATG 57.327 37.500 12.25 12.25 41.00 3.07
2685 3098 1.224069 CTGGCACCAGTTCGACTGTG 61.224 60.000 8.61 11.08 44.50 3.66
2688 3101 0.249489 GCACCAGTTCGACTGTGAGT 60.249 55.000 12.10 3.25 44.50 3.41
2691 3104 1.754803 ACCAGTTCGACTGTGAGTTCA 59.245 47.619 12.10 0.00 44.50 3.18
2692 3105 2.365617 ACCAGTTCGACTGTGAGTTCAT 59.634 45.455 12.10 0.00 44.50 2.57
2693 3106 2.989840 CCAGTTCGACTGTGAGTTCATC 59.010 50.000 12.10 0.00 44.50 2.92
2694 3107 2.658802 CAGTTCGACTGTGAGTTCATCG 59.341 50.000 6.79 0.00 41.19 3.84
2712 3125 4.590222 TCATCGATCATCATTCTCCCTGAA 59.410 41.667 0.00 0.00 39.24 3.02
2713 3126 5.247792 TCATCGATCATCATTCTCCCTGAAT 59.752 40.000 0.00 0.00 45.52 2.57
2714 3127 5.557576 TCGATCATCATTCTCCCTGAATT 57.442 39.130 0.00 0.00 43.00 2.17
2715 3128 5.303165 TCGATCATCATTCTCCCTGAATTG 58.697 41.667 0.00 0.00 43.00 2.32
2716 3129 5.061853 CGATCATCATTCTCCCTGAATTGT 58.938 41.667 0.00 0.00 43.00 2.71
2717 3130 6.041979 TCGATCATCATTCTCCCTGAATTGTA 59.958 38.462 0.00 0.00 43.00 2.41
2718 3131 6.707608 CGATCATCATTCTCCCTGAATTGTAA 59.292 38.462 0.00 0.00 43.00 2.41
2719 3132 7.389884 CGATCATCATTCTCCCTGAATTGTAAT 59.610 37.037 0.00 0.00 43.00 1.89
2720 3133 9.730705 GATCATCATTCTCCCTGAATTGTAATA 57.269 33.333 0.00 0.00 43.00 0.98
2759 3174 8.738645 ACCTGATGAAAGATTTTCATACTACC 57.261 34.615 14.92 5.50 39.08 3.18
2760 3175 8.328758 ACCTGATGAAAGATTTTCATACTACCA 58.671 33.333 14.92 8.92 39.08 3.25
2761 3176 9.177608 CCTGATGAAAGATTTTCATACTACCAA 57.822 33.333 14.92 0.00 39.08 3.67
2815 3234 2.036733 CAGGTTACAAGGACGTGGAGAA 59.963 50.000 0.00 0.00 31.26 2.87
2821 3240 1.545706 AAGGACGTGGAGAAGGAGGC 61.546 60.000 0.00 0.00 0.00 4.70
2875 3294 2.582498 GCCGACGACCCGAATCAG 60.582 66.667 0.00 0.00 0.00 2.90
2959 3387 2.985456 CAGCCGCCTCTCCTTCTT 59.015 61.111 0.00 0.00 0.00 2.52
2961 3389 1.305718 AGCCGCCTCTCCTTCTTCT 60.306 57.895 0.00 0.00 0.00 2.85
2962 3390 1.142965 GCCGCCTCTCCTTCTTCTC 59.857 63.158 0.00 0.00 0.00 2.87
2963 3391 1.819905 CCGCCTCTCCTTCTTCTCC 59.180 63.158 0.00 0.00 0.00 3.71
2964 3392 0.972983 CCGCCTCTCCTTCTTCTCCA 60.973 60.000 0.00 0.00 0.00 3.86
2967 3395 1.836802 GCCTCTCCTTCTTCTCCATGT 59.163 52.381 0.00 0.00 0.00 3.21
2973 3401 1.066573 CCTTCTTCTCCATGTCGCTGT 60.067 52.381 0.00 0.00 0.00 4.40
2982 3410 0.957395 CATGTCGCTGTTGCTTCCCT 60.957 55.000 0.00 0.00 36.97 4.20
3031 3459 4.508128 TCATCGGCGCGGGAGAAC 62.508 66.667 15.48 0.00 0.00 3.01
3051 3479 6.978338 AGAACCGGTGTACATACATACATAG 58.022 40.000 8.52 0.00 37.40 2.23
3052 3480 6.548622 AGAACCGGTGTACATACATACATAGT 59.451 38.462 8.52 0.00 37.40 2.12
3053 3481 7.720957 AGAACCGGTGTACATACATACATAGTA 59.279 37.037 8.52 0.00 37.40 1.82
3058 3486 8.961092 CGGTGTACATACATACATAGTACAAAC 58.039 37.037 0.00 0.00 44.37 2.93
3107 3579 7.469537 ACACATTCATATACTAGCTAGGTCC 57.530 40.000 24.35 0.00 0.00 4.46
3119 3591 9.998752 ATACTAGCTAGGTCCATCATTTATAGT 57.001 33.333 24.35 2.50 0.00 2.12
3121 3593 8.589338 ACTAGCTAGGTCCATCATTTATAGTTG 58.411 37.037 24.35 0.00 0.00 3.16
3122 3594 7.618019 AGCTAGGTCCATCATTTATAGTTGA 57.382 36.000 0.00 0.00 0.00 3.18
3123 3595 8.212259 AGCTAGGTCCATCATTTATAGTTGAT 57.788 34.615 0.00 0.00 32.87 2.57
3124 3596 8.664079 AGCTAGGTCCATCATTTATAGTTGATT 58.336 33.333 0.00 0.00 30.24 2.57
3125 3597 8.940952 GCTAGGTCCATCATTTATAGTTGATTC 58.059 37.037 0.00 0.00 30.24 2.52
3205 3699 4.065088 TGCACTCCTTCTGTGTACAAATC 58.935 43.478 0.00 0.00 37.70 2.17
3210 3704 4.894784 TCCTTCTGTGTACAAATCTCACC 58.105 43.478 0.00 0.00 0.00 4.02
3243 3743 4.235372 TGAGGGGAAATCTAGGAATCTCC 58.765 47.826 0.00 0.00 36.58 3.71
3245 3745 4.646157 AGGGGAAATCTAGGAATCTCCAA 58.354 43.478 10.03 0.00 39.61 3.53
3252 3752 7.148171 GGAAATCTAGGAATCTCCAAAGTGTTG 60.148 40.741 0.00 0.00 39.61 3.33
3257 3757 5.066593 AGGAATCTCCAAAGTGTTGTTCTC 58.933 41.667 0.00 0.00 39.61 2.87
3258 3758 4.821805 GGAATCTCCAAAGTGTTGTTCTCA 59.178 41.667 0.00 0.00 36.28 3.27
3263 3766 3.138283 TCCAAAGTGTTGTTCTCATCCCT 59.862 43.478 0.00 0.00 32.40 4.20
3265 3768 4.697352 CCAAAGTGTTGTTCTCATCCCTAG 59.303 45.833 0.00 0.00 32.40 3.02
3377 3881 4.695396 AGTGTTTCATCTGCATGCAAAAA 58.305 34.783 22.88 15.77 0.00 1.94
3409 3913 3.795688 ATGACATTTGTGGAGGTCTGT 57.204 42.857 0.00 0.00 0.00 3.41
3410 3914 2.849942 TGACATTTGTGGAGGTCTGTG 58.150 47.619 0.00 0.00 0.00 3.66
3415 3919 4.097892 ACATTTGTGGAGGTCTGTGAAAAC 59.902 41.667 0.00 0.00 0.00 2.43
3437 3941 7.989416 AACAAATTGATGCTCCAAAATGATT 57.011 28.000 0.00 0.00 0.00 2.57
3479 3983 6.764308 ACGAATGTCATTCCATCAGAAAAT 57.236 33.333 17.95 0.00 38.21 1.82
3480 3984 7.161773 ACGAATGTCATTCCATCAGAAAATT 57.838 32.000 17.95 0.00 38.21 1.82
3481 3985 7.605449 ACGAATGTCATTCCATCAGAAAATTT 58.395 30.769 17.95 0.00 38.21 1.82
3527 4031 9.452287 TCATCAATGTTTATCACAAAGAGATCA 57.548 29.630 0.00 0.00 39.50 2.92
3577 4081 2.099062 GGTGCATTTGAGCTCGCG 59.901 61.111 9.64 0.00 34.99 5.87
3585 4089 0.528017 TTTGAGCTCGCGATCAGACT 59.472 50.000 10.36 1.97 36.82 3.24
3586 4090 0.528017 TTGAGCTCGCGATCAGACTT 59.472 50.000 10.36 0.00 36.82 3.01
3617 4121 4.532490 CCGTTCATACCGGTGCAT 57.468 55.556 19.93 0.00 40.59 3.96
3618 4122 2.307363 CCGTTCATACCGGTGCATC 58.693 57.895 19.93 2.93 40.59 3.91
3619 4123 0.179084 CCGTTCATACCGGTGCATCT 60.179 55.000 19.93 0.00 40.59 2.90
3620 4124 0.930310 CGTTCATACCGGTGCATCTG 59.070 55.000 19.93 6.97 0.00 2.90
3621 4125 1.470805 CGTTCATACCGGTGCATCTGA 60.471 52.381 19.93 9.30 0.00 3.27
3622 4126 2.205074 GTTCATACCGGTGCATCTGAG 58.795 52.381 19.93 0.00 0.00 3.35
3623 4127 0.104855 TCATACCGGTGCATCTGAGC 59.895 55.000 19.93 0.00 0.00 4.26
3624 4128 0.105593 CATACCGGTGCATCTGAGCT 59.894 55.000 19.93 0.00 34.99 4.09
3625 4129 0.390860 ATACCGGTGCATCTGAGCTC 59.609 55.000 19.93 6.82 34.99 4.09
3626 4130 2.004808 TACCGGTGCATCTGAGCTCG 62.005 60.000 19.93 4.19 34.99 5.03
3627 4131 3.260483 CGGTGCATCTGAGCTCGC 61.260 66.667 9.64 6.81 34.99 5.03
3628 4132 3.260483 GGTGCATCTGAGCTCGCG 61.260 66.667 9.64 0.00 34.99 5.87
3629 4133 2.202663 GTGCATCTGAGCTCGCGA 60.203 61.111 9.26 9.26 34.99 5.87
3630 4134 1.591059 GTGCATCTGAGCTCGCGAT 60.591 57.895 10.36 10.65 34.99 4.58
3631 4135 1.299697 TGCATCTGAGCTCGCGATC 60.300 57.895 10.36 5.22 34.99 3.69
3632 4136 1.299697 GCATCTGAGCTCGCGATCA 60.300 57.895 10.36 11.13 33.90 2.92
3636 4140 3.590824 TGAGCTCGCGATCAGACA 58.409 55.556 10.36 4.82 30.90 3.41
3637 4141 2.110296 TGAGCTCGCGATCAGACAT 58.890 52.632 10.36 0.00 30.90 3.06
3638 4142 0.457443 TGAGCTCGCGATCAGACATT 59.543 50.000 10.36 0.00 30.90 2.71
3639 4143 1.134995 TGAGCTCGCGATCAGACATTT 60.135 47.619 10.36 0.00 30.90 2.32
3640 4144 2.099098 TGAGCTCGCGATCAGACATTTA 59.901 45.455 10.36 0.00 30.90 1.40
3641 4145 3.243535 TGAGCTCGCGATCAGACATTTAT 60.244 43.478 10.36 0.00 30.90 1.40
3642 4146 3.722147 AGCTCGCGATCAGACATTTATT 58.278 40.909 10.36 0.00 0.00 1.40
3643 4147 4.122776 AGCTCGCGATCAGACATTTATTT 58.877 39.130 10.36 0.00 0.00 1.40
3672 4176 2.774439 TTTTCTGGAGCGTGCTTTTC 57.226 45.000 0.00 0.00 0.00 2.29
3687 4191 3.066621 TGCTTTTCGTGTGCTTCAATCTT 59.933 39.130 0.00 0.00 0.00 2.40
3708 4213 3.296854 TGATAGGCCATAGTTCGACACT 58.703 45.455 5.01 5.74 39.87 3.55
3720 4225 0.030773 TCGACACTCTGCACTGACAC 59.969 55.000 0.00 0.00 0.00 3.67
3729 4234 2.357517 CACTGACACGGAGCACCC 60.358 66.667 0.00 0.00 0.00 4.61
3757 4262 4.326826 CTTTTGGAGGTGATGACTGCTTA 58.673 43.478 0.00 0.00 0.00 3.09
3786 4297 1.298859 GCACAACCGTGGAGGATGAC 61.299 60.000 1.45 0.00 44.72 3.06
3798 4309 2.477825 GAGGATGACCGTGATGACATG 58.522 52.381 0.00 0.00 41.83 3.21
3824 4335 1.735571 CGACCAAGGGTTCCAATTACG 59.264 52.381 0.00 0.00 35.25 3.18
3883 4395 2.820787 ACGTTTGAACAGTTCACCCAAA 59.179 40.909 15.93 4.82 39.87 3.28
3963 4475 1.140312 ACATGTGGACTCACCTTGGT 58.860 50.000 0.00 0.00 42.98 3.67
4008 4522 7.537715 TCATTTTCTTTTGATGTATGCGTGAT 58.462 30.769 0.00 0.00 0.00 3.06
4093 4607 7.328277 TGGTACTATGTGATTTATTTGGTGC 57.672 36.000 0.00 0.00 0.00 5.01
4150 4666 0.945099 TGTTTACATTTGCACGCCGA 59.055 45.000 0.00 0.00 0.00 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.220602 GGGTTACAATCAAGAGGCACAAAT 59.779 41.667 0.00 0.00 0.00 2.32
3 4 2.107378 TGGGTTACAATCAAGAGGCACA 59.893 45.455 0.00 0.00 0.00 4.57
61 180 5.823312 AGATCCGGTAATAGTTGGGTTTTT 58.177 37.500 0.00 0.00 0.00 1.94
72 191 7.775120 AGAGAACGTTTAAAGATCCGGTAATA 58.225 34.615 0.46 0.00 0.00 0.98
76 195 4.532314 AGAGAACGTTTAAAGATCCGGT 57.468 40.909 0.46 0.00 0.00 5.28
78 197 5.462398 CCCATAGAGAACGTTTAAAGATCCG 59.538 44.000 0.46 0.00 0.00 4.18
84 203 4.004982 GGCACCCATAGAGAACGTTTAAA 58.995 43.478 0.46 0.00 0.00 1.52
91 210 4.899352 ATAGATGGCACCCATAGAGAAC 57.101 45.455 0.00 0.00 45.26 3.01
93 212 4.017126 CGTATAGATGGCACCCATAGAGA 58.983 47.826 0.00 0.00 45.26 3.10
118 245 6.604396 TGTACTCTCTCCGTTGGATAATGTAA 59.396 38.462 0.00 0.00 0.00 2.41
127 254 3.288964 ACCTATGTACTCTCTCCGTTGG 58.711 50.000 0.00 0.00 0.00 3.77
128 255 4.202030 GGAACCTATGTACTCTCTCCGTTG 60.202 50.000 0.00 0.00 0.00 4.10
133 260 8.050778 CATAGATGGAACCTATGTACTCTCTC 57.949 42.308 0.00 0.00 38.91 3.20
184 311 9.420118 AGAGTAGTATGATCTCTGAAAAGATGT 57.580 33.333 0.00 0.00 36.13 3.06
185 312 9.897744 GAGAGTAGTATGATCTCTGAAAAGATG 57.102 37.037 0.00 0.00 38.45 2.90
218 355 3.132289 CACCTGATTTACTTCGGCCTCTA 59.868 47.826 0.00 0.00 0.00 2.43
219 356 2.093447 CACCTGATTTACTTCGGCCTCT 60.093 50.000 0.00 0.00 0.00 3.69
220 357 2.280628 CACCTGATTTACTTCGGCCTC 58.719 52.381 0.00 0.00 0.00 4.70
227 366 2.171003 GGCCAAGCACCTGATTTACTT 58.829 47.619 0.00 0.00 0.00 2.24
252 391 2.105477 AGCGCAGGATAATGGACATTCT 59.895 45.455 11.47 0.00 32.50 2.40
253 392 2.225019 CAGCGCAGGATAATGGACATTC 59.775 50.000 11.47 0.00 32.50 2.67
271 410 3.622756 CCTCGTGATCGATGCAGC 58.377 61.111 0.54 0.00 45.21 5.25
288 431 2.550101 GCTCCTTGATCGGCCATGC 61.550 63.158 2.24 0.00 0.00 4.06
290 433 2.512896 GGCTCCTTGATCGGCCAT 59.487 61.111 2.24 0.00 43.59 4.40
370 530 9.461312 AGCAATCCAACAAAAATAGTGTATCTA 57.539 29.630 0.00 0.00 0.00 1.98
381 541 6.093495 CGATCTAGGTAGCAATCCAACAAAAA 59.907 38.462 0.00 0.00 0.00 1.94
391 551 0.977395 GGCCCGATCTAGGTAGCAAT 59.023 55.000 0.00 0.00 0.00 3.56
435 598 6.869315 TTGATCGAATCTAGACTAGACAGG 57.131 41.667 14.47 6.73 37.69 4.00
447 610 9.362539 CCAAAAAGAAATGATTTGATCGAATCT 57.637 29.630 28.18 14.21 36.41 2.40
477 645 6.212388 AGAGGGTATAGATAGCATCCTTGTTG 59.788 42.308 9.16 0.00 41.04 3.33
491 663 4.279145 GTTGGACAGACAGAGGGTATAGA 58.721 47.826 0.00 0.00 0.00 1.98
495 667 1.132977 TGGTTGGACAGACAGAGGGTA 60.133 52.381 0.00 0.00 0.00 3.69
497 669 0.322975 CTGGTTGGACAGACAGAGGG 59.677 60.000 0.00 0.00 40.97 4.30
515 801 3.587797 AATCGTGTACGGATGTCAACT 57.412 42.857 4.44 0.00 40.29 3.16
576 875 5.241064 CGTAGTACTATGTAATGGGCAGAGT 59.759 44.000 13.15 0.00 40.80 3.24
613 921 2.289631 TGTTGTGAGCTCATCGTGGAAT 60.290 45.455 21.47 0.00 0.00 3.01
652 960 5.058490 CAGGACCATTTCTTTGTTTTGCAT 58.942 37.500 0.00 0.00 0.00 3.96
657 965 4.023193 CGTAGCAGGACCATTTCTTTGTTT 60.023 41.667 0.00 0.00 0.00 2.83
668 976 2.922740 AGAAAAACGTAGCAGGACCA 57.077 45.000 0.00 0.00 0.00 4.02
693 1001 5.049543 CCATCCATTGTTGAACGCAATTTTT 60.050 36.000 0.00 0.00 36.22 1.94
694 1002 4.451774 CCATCCATTGTTGAACGCAATTTT 59.548 37.500 0.00 0.00 36.22 1.82
695 1003 3.995705 CCATCCATTGTTGAACGCAATTT 59.004 39.130 0.00 0.00 36.22 1.82
696 1004 3.257873 TCCATCCATTGTTGAACGCAATT 59.742 39.130 0.00 0.00 36.22 2.32
697 1005 2.824936 TCCATCCATTGTTGAACGCAAT 59.175 40.909 0.00 0.00 36.22 3.56
702 1010 2.811431 TGACGTCCATCCATTGTTGAAC 59.189 45.455 14.12 0.00 0.00 3.18
704 1012 2.422597 GTGACGTCCATCCATTGTTGA 58.577 47.619 14.12 0.00 0.00 3.18
715 1084 3.676605 ATCACCGCGTGACGTCCA 61.677 61.111 14.12 0.00 45.65 4.02
748 1117 3.801068 TTTGTGGCCGGGGAGTTGG 62.801 63.158 2.18 0.00 0.00 3.77
749 1118 2.203422 TTTGTGGCCGGGGAGTTG 60.203 61.111 2.18 0.00 0.00 3.16
750 1119 2.115266 CTTTGTGGCCGGGGAGTT 59.885 61.111 2.18 0.00 0.00 3.01
751 1120 3.966543 CCTTTGTGGCCGGGGAGT 61.967 66.667 2.18 0.00 0.00 3.85
769 1138 4.319046 CCATGAGACGACTTGACTTTTGTG 60.319 45.833 0.00 0.00 0.00 3.33
801 1170 4.645136 GGGAACTCCTCAAGTGTTTCTTTT 59.355 41.667 0.00 0.00 38.58 2.27
802 1171 4.207955 GGGAACTCCTCAAGTGTTTCTTT 58.792 43.478 0.00 0.00 38.58 2.52
804 1173 2.224305 CGGGAACTCCTCAAGTGTTTCT 60.224 50.000 0.00 0.00 38.58 2.52
806 1175 1.202770 CCGGGAACTCCTCAAGTGTTT 60.203 52.381 0.00 0.00 38.58 2.83
883 1266 3.326578 CGGTGGGTGGTGGATGGA 61.327 66.667 0.00 0.00 0.00 3.41
884 1267 3.204467 AACGGTGGGTGGTGGATGG 62.204 63.158 0.00 0.00 0.00 3.51
885 1268 1.971167 CAACGGTGGGTGGTGGATG 60.971 63.158 0.00 0.00 0.00 3.51
886 1269 2.150719 TCAACGGTGGGTGGTGGAT 61.151 57.895 0.00 0.00 0.00 3.41
1014 1400 3.680786 AGAGTAGGCGTGCGTGCA 61.681 61.111 5.50 0.00 36.28 4.57
1015 1401 3.181967 CAGAGTAGGCGTGCGTGC 61.182 66.667 0.00 0.00 0.00 5.34
1016 1402 3.181967 GCAGAGTAGGCGTGCGTG 61.182 66.667 0.00 0.00 0.00 5.34
1017 1403 4.436998 GGCAGAGTAGGCGTGCGT 62.437 66.667 0.00 0.00 38.13 5.24
1053 1442 2.202492 GCGACGAGCGACAGACAT 60.202 61.111 0.00 0.00 44.57 3.06
1149 1544 3.461773 CTCACCACGGGCGAGGAT 61.462 66.667 0.00 0.00 0.00 3.24
1311 1706 4.704833 GCGAAGGTGAGCAGCCCA 62.705 66.667 0.00 0.00 0.00 5.36
1401 1796 3.175710 AGGGCCACCAGGAACGTT 61.176 61.111 6.18 0.00 40.13 3.99
1644 2039 2.737376 GAGGACGTGTTGGCGGAC 60.737 66.667 0.00 0.00 35.98 4.79
1713 2108 1.372499 CTTCACCGCCGTCGAAAGA 60.372 57.895 0.00 0.00 38.10 2.52
1714 2109 2.380410 CCTTCACCGCCGTCGAAAG 61.380 63.158 0.00 0.00 38.10 2.62
1715 2110 2.356553 CCTTCACCGCCGTCGAAA 60.357 61.111 0.00 0.00 38.10 3.46
1866 2267 0.976641 ACATGGAGAAGCTGTCGGAA 59.023 50.000 0.00 0.00 0.00 4.30
1963 2364 0.606604 ACTTACTGCGTGTTCCGGAT 59.393 50.000 4.15 0.00 35.87 4.18
1990 2391 2.171659 TGATGGAGCGCCTAATTACCAA 59.828 45.455 8.34 0.00 34.31 3.67
2043 2444 5.235186 GCTATGACTTTTCACGCATACTGAT 59.765 40.000 0.00 0.00 33.38 2.90
2049 2450 5.504665 GCATTAGCTATGACTTTTCACGCAT 60.505 40.000 0.00 0.00 36.26 4.73
2050 2451 4.201812 GCATTAGCTATGACTTTTCACGCA 60.202 41.667 0.00 0.00 36.26 5.24
2066 2468 1.666311 CGAGCCGTACCTAGCATTAGC 60.666 57.143 0.66 0.00 42.56 3.09
2067 2469 1.878088 TCGAGCCGTACCTAGCATTAG 59.122 52.381 0.66 0.00 0.00 1.73
2068 2470 1.605710 GTCGAGCCGTACCTAGCATTA 59.394 52.381 0.00 0.00 0.00 1.90
2069 2471 0.384669 GTCGAGCCGTACCTAGCATT 59.615 55.000 0.00 0.00 0.00 3.56
2071 2473 1.077930 AGTCGAGCCGTACCTAGCA 60.078 57.895 0.00 0.00 0.00 3.49
2072 2474 1.094073 TCAGTCGAGCCGTACCTAGC 61.094 60.000 0.00 0.00 0.00 3.42
2073 2475 1.532007 GATCAGTCGAGCCGTACCTAG 59.468 57.143 0.00 0.00 0.00 3.02
2074 2476 1.590932 GATCAGTCGAGCCGTACCTA 58.409 55.000 0.00 0.00 0.00 3.08
2150 2555 2.285743 AGCTCCTTCCCCTCCACC 60.286 66.667 0.00 0.00 0.00 4.61
2213 2618 2.183555 GCCGGGTCGTTGAGGTAG 59.816 66.667 2.18 0.00 0.00 3.18
2307 2712 0.460987 GCCAGCTGGTAGCAGTACTG 60.461 60.000 32.81 18.93 45.56 2.74
2475 2880 0.525455 TCGATGGCGATGTCGTTCTG 60.525 55.000 4.20 0.00 42.51 3.02
2515 2920 5.254115 AGACAGTAGCAGTGTGTATCAGTA 58.746 41.667 1.98 0.00 30.64 2.74
2516 2921 4.082845 AGACAGTAGCAGTGTGTATCAGT 58.917 43.478 1.98 0.00 30.64 3.41
2517 2922 4.710423 AGACAGTAGCAGTGTGTATCAG 57.290 45.455 1.98 0.00 30.64 2.90
2518 2923 4.767409 AGAAGACAGTAGCAGTGTGTATCA 59.233 41.667 1.98 0.00 30.64 2.15
2519 2924 5.124776 AGAGAAGACAGTAGCAGTGTGTATC 59.875 44.000 1.98 1.81 30.64 2.24
2520 2925 5.013547 AGAGAAGACAGTAGCAGTGTGTAT 58.986 41.667 1.98 0.00 30.64 2.29
2521 2926 4.399219 AGAGAAGACAGTAGCAGTGTGTA 58.601 43.478 1.98 0.00 30.64 2.90
2522 2927 3.226777 AGAGAAGACAGTAGCAGTGTGT 58.773 45.455 1.98 0.00 30.64 3.72
2523 2928 3.932545 AGAGAAGACAGTAGCAGTGTG 57.067 47.619 1.98 0.00 30.64 3.82
2524 2929 3.891977 TGAAGAGAAGACAGTAGCAGTGT 59.108 43.478 0.00 0.00 33.77 3.55
2525 2930 4.484236 CTGAAGAGAAGACAGTAGCAGTG 58.516 47.826 0.00 0.00 0.00 3.66
2526 2931 3.056891 GCTGAAGAGAAGACAGTAGCAGT 60.057 47.826 0.00 0.00 34.60 4.40
2527 2932 3.193267 AGCTGAAGAGAAGACAGTAGCAG 59.807 47.826 0.00 0.00 34.60 4.24
2528 2933 3.161067 AGCTGAAGAGAAGACAGTAGCA 58.839 45.455 0.00 0.00 34.60 3.49
2529 2934 3.866883 AGCTGAAGAGAAGACAGTAGC 57.133 47.619 0.00 0.00 34.60 3.58
2530 2935 6.690957 CGAATTAGCTGAAGAGAAGACAGTAG 59.309 42.308 0.00 0.00 34.60 2.57
2531 2936 6.151312 ACGAATTAGCTGAAGAGAAGACAGTA 59.849 38.462 0.00 0.00 34.60 2.74
2532 2937 5.047660 ACGAATTAGCTGAAGAGAAGACAGT 60.048 40.000 0.00 0.00 34.60 3.55
2533 2938 5.406649 ACGAATTAGCTGAAGAGAAGACAG 58.593 41.667 0.00 0.00 35.14 3.51
2534 2939 5.392767 ACGAATTAGCTGAAGAGAAGACA 57.607 39.130 0.00 0.00 0.00 3.41
2535 2940 4.497608 CGACGAATTAGCTGAAGAGAAGAC 59.502 45.833 0.00 0.00 0.00 3.01
2546 2951 2.728922 GGAACGATCGACGAATTAGCT 58.271 47.619 24.34 0.00 45.77 3.32
2598 3011 4.430137 TGAAGTTCTCTGCATGCATTTC 57.570 40.909 22.97 16.76 0.00 2.17
2600 3013 4.371855 CATGAAGTTCTCTGCATGCATT 57.628 40.909 22.97 11.55 46.69 3.56
2685 3098 4.928615 GGGAGAATGATGATCGATGAACTC 59.071 45.833 0.54 2.11 0.00 3.01
2688 3101 4.590222 TCAGGGAGAATGATGATCGATGAA 59.410 41.667 0.54 0.00 0.00 2.57
2691 3104 5.758790 ATTCAGGGAGAATGATGATCGAT 57.241 39.130 0.00 0.00 45.11 3.59
2692 3105 5.163269 ACAATTCAGGGAGAATGATGATCGA 60.163 40.000 0.00 0.00 46.09 3.59
2693 3106 5.061853 ACAATTCAGGGAGAATGATGATCG 58.938 41.667 0.00 0.00 46.09 3.69
2694 3107 8.632906 ATTACAATTCAGGGAGAATGATGATC 57.367 34.615 0.00 0.00 46.09 2.92
2750 3165 8.046708 ACAGTTAAGCAATGATTGGTAGTATGA 58.953 33.333 10.55 0.00 41.14 2.15
2758 3173 3.763360 TGGGACAGTTAAGCAATGATTGG 59.237 43.478 7.35 0.00 0.00 3.16
2759 3174 5.047802 AGTTGGGACAGTTAAGCAATGATTG 60.048 40.000 0.00 0.00 42.39 2.67
2760 3175 5.079643 AGTTGGGACAGTTAAGCAATGATT 58.920 37.500 0.00 0.00 42.39 2.57
2761 3176 4.666512 AGTTGGGACAGTTAAGCAATGAT 58.333 39.130 0.00 0.00 42.39 2.45
2762 3177 4.098914 AGTTGGGACAGTTAAGCAATGA 57.901 40.909 0.00 0.00 42.39 2.57
2763 3178 5.957842 TTAGTTGGGACAGTTAAGCAATG 57.042 39.130 0.00 0.00 42.39 2.82
2764 3179 7.539034 AATTTAGTTGGGACAGTTAAGCAAT 57.461 32.000 0.00 0.00 42.39 3.56
2771 3190 5.830991 TGCAGTTAATTTAGTTGGGACAGTT 59.169 36.000 0.00 0.00 42.39 3.16
2870 3289 4.845580 CTCTGCCGCGGCCTGATT 62.846 66.667 44.42 0.00 41.09 2.57
2959 3387 0.035317 AAGCAACAGCGACATGGAGA 59.965 50.000 0.00 0.00 0.00 3.71
2961 3389 0.955428 GGAAGCAACAGCGACATGGA 60.955 55.000 0.00 0.00 0.00 3.41
2962 3390 1.503542 GGAAGCAACAGCGACATGG 59.496 57.895 0.00 0.00 0.00 3.66
2963 3391 0.957395 AGGGAAGCAACAGCGACATG 60.957 55.000 0.00 0.00 0.00 3.21
2964 3392 0.250901 AAGGGAAGCAACAGCGACAT 60.251 50.000 0.00 0.00 0.00 3.06
2967 3395 2.260869 GCAAGGGAAGCAACAGCGA 61.261 57.895 0.00 0.00 0.00 4.93
2973 3401 1.904865 CAGCCAGCAAGGGAAGCAA 60.905 57.895 0.00 0.00 38.09 3.91
3000 3428 1.966354 CCGATGAGATCAGACCATGGA 59.034 52.381 21.47 0.00 0.00 3.41
3003 3431 0.316522 CGCCGATGAGATCAGACCAT 59.683 55.000 0.00 0.00 0.00 3.55
3031 3459 7.205737 TGTACTATGTATGTATGTACACCGG 57.794 40.000 0.00 0.00 38.62 5.28
3086 3522 8.298729 TGATGGACCTAGCTAGTATATGAATG 57.701 38.462 19.31 3.41 0.00 2.67
3107 3579 8.295288 GGGCTTCTGAATCAACTATAAATGATG 58.705 37.037 0.00 0.00 36.44 3.07
3119 3591 3.159213 ACACATGGGCTTCTGAATCAA 57.841 42.857 0.00 0.00 0.00 2.57
3121 3593 3.609853 TGTACACATGGGCTTCTGAATC 58.390 45.455 0.00 0.00 0.00 2.52
3122 3594 3.719268 TGTACACATGGGCTTCTGAAT 57.281 42.857 0.00 0.00 0.00 2.57
3123 3595 3.719268 ATGTACACATGGGCTTCTGAA 57.281 42.857 0.00 0.00 34.83 3.02
3149 3643 1.741528 TTCGCATCTGCATGTGACAT 58.258 45.000 3.08 0.00 46.95 3.06
3205 3699 3.321968 CCCCTCAAAAAGAAAAGGGTGAG 59.678 47.826 5.62 0.00 46.02 3.51
3210 3704 6.425210 AGATTTCCCCTCAAAAAGAAAAGG 57.575 37.500 0.00 0.00 32.41 3.11
3229 3729 6.784031 ACAACACTTTGGAGATTCCTAGATT 58.216 36.000 0.00 0.00 37.46 2.40
3243 3743 4.154918 GCTAGGGATGAGAACAACACTTTG 59.845 45.833 0.00 0.00 34.49 2.77
3245 3745 3.584848 AGCTAGGGATGAGAACAACACTT 59.415 43.478 0.00 0.00 34.49 3.16
3252 3752 3.726607 CATGTGAGCTAGGGATGAGAAC 58.273 50.000 0.00 0.00 0.00 3.01
3257 3757 2.336945 TTGCATGTGAGCTAGGGATG 57.663 50.000 0.00 0.00 34.99 3.51
3258 3758 2.648059 GTTTGCATGTGAGCTAGGGAT 58.352 47.619 0.00 0.00 34.99 3.85
3263 3766 0.036164 ACCCGTTTGCATGTGAGCTA 59.964 50.000 0.00 0.00 34.99 3.32
3265 3768 1.081242 CACCCGTTTGCATGTGAGC 60.081 57.895 0.00 0.00 0.00 4.26
3359 3863 4.989797 ACGAATTTTTGCATGCAGATGAAA 59.010 33.333 21.50 18.76 0.00 2.69
3377 3881 5.393352 CCACAAATGTCATTCCATCACGAAT 60.393 40.000 0.00 0.00 32.58 3.34
3409 3913 7.498239 TCATTTTGGAGCATCAATTTGTTTTCA 59.502 29.630 0.00 0.00 36.25 2.69
3410 3914 7.863666 TCATTTTGGAGCATCAATTTGTTTTC 58.136 30.769 0.00 0.00 36.25 2.29
3415 3919 9.104965 ACATAATCATTTTGGAGCATCAATTTG 57.895 29.630 0.00 0.00 36.25 2.32
3437 3941 6.928979 TTCGTTGAGAACAGGAAAAACATA 57.071 33.333 0.00 0.00 33.14 2.29
3479 3983 9.202273 GATGATTGTTTTACCAGCATACAAAAA 57.798 29.630 0.00 0.00 33.04 1.94
3480 3984 8.363390 TGATGATTGTTTTACCAGCATACAAAA 58.637 29.630 0.00 0.00 33.04 2.44
3481 3985 7.890515 TGATGATTGTTTTACCAGCATACAAA 58.109 30.769 0.00 0.00 33.04 2.83
3487 3991 6.343716 ACATTGATGATTGTTTTACCAGCA 57.656 33.333 0.00 0.00 0.00 4.41
3527 4031 9.607988 AACGGTAAAATCCAAAAAGAAAAATCT 57.392 25.926 0.00 0.00 0.00 2.40
3559 4063 2.486966 GCGAGCTCAAATGCACCC 59.513 61.111 15.40 0.00 34.99 4.61
3601 4105 0.930310 CAGATGCACCGGTATGAACG 59.070 55.000 6.87 0.00 0.00 3.95
3602 4106 2.205074 CTCAGATGCACCGGTATGAAC 58.795 52.381 6.87 0.00 0.00 3.18
3603 4107 1.473257 GCTCAGATGCACCGGTATGAA 60.473 52.381 6.87 0.00 0.00 2.57
3604 4108 0.104855 GCTCAGATGCACCGGTATGA 59.895 55.000 6.87 6.12 0.00 2.15
3605 4109 0.105593 AGCTCAGATGCACCGGTATG 59.894 55.000 6.87 0.00 34.99 2.39
3606 4110 0.390860 GAGCTCAGATGCACCGGTAT 59.609 55.000 6.87 0.00 34.99 2.73
3607 4111 1.816537 GAGCTCAGATGCACCGGTA 59.183 57.895 6.87 0.00 34.99 4.02
3608 4112 2.581354 GAGCTCAGATGCACCGGT 59.419 61.111 9.40 0.00 34.99 5.28
3609 4113 2.584418 CGAGCTCAGATGCACCGG 60.584 66.667 15.40 0.00 34.99 5.28
3610 4114 3.260483 GCGAGCTCAGATGCACCG 61.260 66.667 15.40 0.00 35.53 4.94
3611 4115 2.967929 ATCGCGAGCTCAGATGCACC 62.968 60.000 16.66 0.00 34.99 5.01
3612 4116 1.547292 GATCGCGAGCTCAGATGCAC 61.547 60.000 18.63 8.04 34.99 4.57
3613 4117 1.299697 GATCGCGAGCTCAGATGCA 60.300 57.895 18.63 0.00 34.99 3.96
3614 4118 1.299697 TGATCGCGAGCTCAGATGC 60.300 57.895 26.10 12.71 31.77 3.91
3619 4123 0.457443 AATGTCTGATCGCGAGCTCA 59.543 50.000 26.10 18.40 34.69 4.26
3620 4124 1.565305 AAATGTCTGATCGCGAGCTC 58.435 50.000 26.10 14.41 0.00 4.09
3621 4125 2.871182 TAAATGTCTGATCGCGAGCT 57.129 45.000 26.10 3.31 0.00 4.09
3622 4126 4.458951 AAATAAATGTCTGATCGCGAGC 57.541 40.909 19.12 19.12 0.00 5.03
3623 4127 5.006649 TCCAAAATAAATGTCTGATCGCGAG 59.993 40.000 16.66 0.16 0.00 5.03
3624 4128 4.873259 TCCAAAATAAATGTCTGATCGCGA 59.127 37.500 13.09 13.09 0.00 5.87
3625 4129 5.155509 TCCAAAATAAATGTCTGATCGCG 57.844 39.130 0.00 0.00 0.00 5.87
3626 4130 7.992180 AAATCCAAAATAAATGTCTGATCGC 57.008 32.000 0.00 0.00 0.00 4.58
3654 4158 0.586319 CGAAAAGCACGCTCCAGAAA 59.414 50.000 0.00 0.00 0.00 2.52
3672 4176 3.242543 GCCTATCAAGATTGAAGCACACG 60.243 47.826 0.00 0.00 41.13 4.49
3687 4191 3.296854 AGTGTCGAACTATGGCCTATCA 58.703 45.455 3.32 0.00 37.36 2.15
3708 4213 2.340078 GCTCCGTGTCAGTGCAGA 59.660 61.111 0.00 0.00 0.00 4.26
3720 4225 1.455383 AAAAGCTTGTGGGTGCTCCG 61.455 55.000 0.00 0.00 38.75 4.63
3729 4234 2.886523 TCATCACCTCCAAAAGCTTGTG 59.113 45.455 9.89 9.89 0.00 3.33
3757 4262 1.469703 CACGGTTGTGCATGATCACAT 59.530 47.619 0.00 0.00 45.26 3.21
3786 4297 3.300857 GTCGTAGATCATGTCATCACGG 58.699 50.000 13.83 0.00 40.67 4.94
3798 4309 1.829222 TGGAACCCTTGGTCGTAGATC 59.171 52.381 0.00 0.00 40.67 2.75
3824 4335 1.047801 AGGCACAACAATTTCACCCC 58.952 50.000 0.00 0.00 0.00 4.95
3853 4364 1.331138 CTGTTCAAACGTTGCCGGTTA 59.669 47.619 0.00 0.00 43.47 2.85
3883 4395 5.286438 CCAATCACGCATTTCATGATGAAT 58.714 37.500 8.90 0.00 36.11 2.57
4134 4650 1.996898 CTAGTCGGCGTGCAAATGTAA 59.003 47.619 6.85 0.00 0.00 2.41
4150 4666 2.666098 ATTTGGTCCGCCGGCTAGT 61.666 57.895 26.68 0.00 37.67 2.57


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

AutoCloner maintained by Alex Coulton.