Multiple sequence alignment - TraesCS2D01G500000

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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 TraesCS2D01G500000 chr2D 100.000 3643 0 0 1 3643 594579307 594575665 0.000000e+00 6728.0
1 TraesCS2D01G500000 chr2D 87.374 198 23 2 2039 2235 424035669 424035473 3.660000e-55 226.0
2 TraesCS2D01G500000 chr2D 78.983 295 56 6 1957 2248 574656751 574657042 2.870000e-46 196.0
3 TraesCS2D01G500000 chr2D 79.191 173 26 9 1058 1225 445059654 445059821 1.070000e-20 111.0
4 TraesCS2D01G500000 chr2B 92.308 2223 115 32 560 2744 722327050 722324846 0.000000e+00 3107.0
5 TraesCS2D01G500000 chr2B 86.940 536 37 16 3061 3580 722323583 722323065 4.080000e-159 571.0
6 TraesCS2D01G500000 chr2B 95.872 218 8 1 265 482 627324172 627323956 5.790000e-93 351.0
7 TraesCS2D01G500000 chr2B 95.475 221 9 1 264 484 627324437 627324218 5.790000e-93 351.0
8 TraesCS2D01G500000 chr2B 79.202 351 63 9 1948 2293 690931051 690931396 6.080000e-58 235.0
9 TraesCS2D01G500000 chr2B 89.000 100 9 1 163 262 722327257 722327160 4.940000e-24 122.0
10 TraesCS2D01G500000 chr2B 80.741 135 15 5 2821 2955 722324611 722324488 1.080000e-15 95.3
11 TraesCS2D01G500000 chr2B 80.645 93 18 0 1686 1778 523233651 523233743 5.050000e-09 73.1
12 TraesCS2D01G500000 chr2A 90.416 2233 102 41 482 2643 729191004 729188813 0.000000e+00 2835.0
13 TraesCS2D01G500000 chr2A 95.434 219 10 0 263 481 631666498 631666716 2.080000e-92 350.0
14 TraesCS2D01G500000 chr2A 88.258 264 29 2 1 264 729191261 729191000 7.590000e-82 315.0
15 TraesCS2D01G500000 chr2A 87.879 198 22 2 2039 2235 564106465 564106661 7.870000e-57 231.0
16 TraesCS2D01G500000 chr2A 78.788 297 54 8 1955 2248 713016548 713016838 1.340000e-44 191.0
17 TraesCS2D01G500000 chr7B 96.774 217 7 0 265 481 603660508 603660724 2.670000e-96 363.0
18 TraesCS2D01G500000 chr7B 95.392 217 10 0 265 481 694806628 694806844 2.690000e-91 346.0
19 TraesCS2D01G500000 chr7D 95.475 221 10 0 265 485 24496972 24496752 1.610000e-93 353.0
20 TraesCS2D01G500000 chr7D 94.196 224 13 0 261 484 24497828 24497605 3.480000e-90 342.0
21 TraesCS2D01G500000 chr7D 79.931 289 48 9 2005 2288 141562156 141562439 1.710000e-48 204.0
22 TraesCS2D01G500000 chr7D 80.645 93 11 4 23 114 549680520 549680434 8.440000e-07 65.8
23 TraesCS2D01G500000 chr5D 95.853 217 9 0 265 481 361214085 361214301 5.790000e-93 351.0
24 TraesCS2D01G500000 chr3B 95.000 220 11 0 265 484 814900245 814900026 2.690000e-91 346.0
25 TraesCS2D01G500000 chr3B 80.233 172 24 10 1095 1261 680477773 680477607 1.780000e-23 121.0
26 TraesCS2D01G500000 chr3B 80.000 170 28 6 1095 1261 680732604 680732438 1.780000e-23 121.0
27 TraesCS2D01G500000 chr3B 79.070 172 26 10 1095 1261 680676735 680676569 3.850000e-20 110.0
28 TraesCS2D01G500000 chr7A 80.612 294 46 10 2005 2292 144170867 144170579 2.200000e-52 217.0
29 TraesCS2D01G500000 chr6B 93.939 99 6 0 3414 3512 684432611 684432513 2.270000e-32 150.0
30 TraesCS2D01G500000 chr6B 77.434 226 35 12 1545 1759 561834752 561834972 1.780000e-23 121.0
31 TraesCS2D01G500000 chr1B 94.737 95 5 0 3417 3511 328153376 328153282 8.150000e-32 148.0
32 TraesCS2D01G500000 chr1B 92.929 99 6 1 3414 3512 342365336 342365433 3.790000e-30 143.0
33 TraesCS2D01G500000 chr5B 92.929 99 7 0 3414 3512 190125455 190125553 1.050000e-30 145.0
34 TraesCS2D01G500000 chr5A 93.750 96 6 0 3417 3512 439372511 439372416 1.050000e-30 145.0
35 TraesCS2D01G500000 chr5A 92.929 99 6 1 3414 3512 232839572 232839669 3.790000e-30 143.0
36 TraesCS2D01G500000 chr3A 92.929 99 7 0 3414 3512 45171872 45171774 1.050000e-30 145.0
37 TraesCS2D01G500000 chr3A 81.287 171 24 8 1095 1261 651648985 651649151 8.210000e-27 132.0
38 TraesCS2D01G500000 chr3A 80.000 170 28 6 1095 1261 651996523 651996689 1.780000e-23 121.0
39 TraesCS2D01G500000 chr1D 91.429 105 9 0 3417 3521 228830142 228830038 1.050000e-30 145.0
40 TraesCS2D01G500000 chr6A 77.477 222 42 6 1545 1759 516675761 516675981 3.820000e-25 126.0
41 TraesCS2D01G500000 chr3D 80.588 170 27 6 1095 1261 516671493 516671659 3.820000e-25 126.0
42 TraesCS2D01G500000 chr6D 83.582 134 21 1 1627 1759 375291976 375292109 1.370000e-24 124.0
43 TraesCS2D01G500000 chr4B 89.474 76 8 0 1696 1771 106492290 106492215 2.990000e-16 97.1
44 TraesCS2D01G500000 chr4D 88.158 76 9 0 1696 1771 74159564 74159489 1.390000e-14 91.6
45 TraesCS2D01G500000 chr4A 92.188 64 5 0 1696 1759 513805008 513805071 1.390000e-14 91.6


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 TraesCS2D01G500000 chr2D 594575665 594579307 3642 True 6728.000 6728 100.00000 1 3643 1 chr2D.!!$R2 3642
1 TraesCS2D01G500000 chr2B 722323065 722327257 4192 True 973.825 3107 87.24725 163 3580 4 chr2B.!!$R2 3417
2 TraesCS2D01G500000 chr2A 729188813 729191261 2448 True 1575.000 2835 89.33700 1 2643 2 chr2A.!!$R1 2642
3 TraesCS2D01G500000 chr7D 24496752 24497828 1076 True 347.500 353 94.83550 261 485 2 chr7D.!!$R2 224

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
56 57 0.250901 TCAGCCTCAAGGGAGCAAAC 60.251 55.0 0.0 0.0 39.96 2.93 F
58 59 0.480252 AGCCTCAAGGGAGCAAACTT 59.520 50.0 0.0 0.0 39.96 2.66 F
607 1503 0.604578 TTAGTACACCAGGACACGCC 59.395 55.0 0.0 0.0 0.00 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1973 2934 0.248784 GCACGATGGAGTACGGGTAC 60.249 60.000 0.70 0.7 35.25 3.34 R
2417 3378 1.345415 TCGTTGAAGTAGGGGAACACC 59.655 52.381 0.00 0.0 39.11 4.16 R
2643 3604 0.030369 GGTGTGGCCTACGATACGAG 59.970 60.000 3.32 0.0 0.00 4.18 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 1.871080 CATAACTCGATGCCACCTCC 58.129 55.000 0.00 0.00 0.00 4.30
33 34 1.496060 TAACTCGATGCCACCTCCAT 58.504 50.000 0.00 0.00 0.00 3.41
39 40 2.274948 GATGCCACCTCCATGCCTCA 62.275 60.000 0.00 0.00 0.00 3.86
46 47 1.605992 CTCCATGCCTCAGCCTCAA 59.394 57.895 0.00 0.00 38.69 3.02
56 57 0.250901 TCAGCCTCAAGGGAGCAAAC 60.251 55.000 0.00 0.00 39.96 2.93
58 59 0.480252 AGCCTCAAGGGAGCAAACTT 59.520 50.000 0.00 0.00 39.96 2.66
61 62 2.103094 GCCTCAAGGGAGCAAACTTTTT 59.897 45.455 0.00 0.00 39.96 1.94
71 72 5.163864 GGGAGCAAACTTTTTGAAACACAAG 60.164 40.000 2.80 0.00 39.77 3.16
102 103 3.695830 ATAGAAGCAACAGACGGGAAA 57.304 42.857 0.00 0.00 0.00 3.13
105 106 2.151202 GAAGCAACAGACGGGAAATCA 58.849 47.619 0.00 0.00 0.00 2.57
121 122 5.240891 GGAAATCATCGATGCAGATTAGGA 58.759 41.667 20.81 0.02 32.11 2.94
122 123 5.879223 GGAAATCATCGATGCAGATTAGGAT 59.121 40.000 20.81 2.62 32.11 3.24
127 128 2.094700 TCGATGCAGATTAGGATACGCC 60.095 50.000 0.00 0.00 46.39 5.68
131 132 0.732880 CAGATTAGGATACGCCGCCG 60.733 60.000 0.00 0.00 43.43 6.46
152 153 1.894756 CGCCCCGGAGAAAACAACA 60.895 57.895 0.73 0.00 0.00 3.33
176 177 0.687354 TGAGGACCTGCAGAAACTCC 59.313 55.000 17.39 12.86 0.00 3.85
229 230 2.557924 TCTCTTTTACACGCCGTCCTTA 59.442 45.455 0.00 0.00 0.00 2.69
238 239 3.315749 ACACGCCGTCCTTATTTTTCAAA 59.684 39.130 0.00 0.00 0.00 2.69
320 1173 4.296056 ACTTTAGTCCCACCTCGGATATT 58.704 43.478 0.00 0.00 36.56 1.28
379 1232 3.259625 ACACTCCTTTCAGGCTAGTCTTC 59.740 47.826 0.00 0.00 34.61 2.87
386 1239 2.392662 TCAGGCTAGTCTTCTGGGATG 58.607 52.381 0.00 0.00 0.00 3.51
449 1302 1.329599 GAAACGTCCGAACATATGCCC 59.670 52.381 1.58 0.00 0.00 5.36
481 1334 2.125106 GGCCTGGGACGCTAACAG 60.125 66.667 0.00 0.00 0.00 3.16
485 1338 1.134491 GCCTGGGACGCTAACAGTTAT 60.134 52.381 0.00 0.00 0.00 1.89
486 1339 2.101917 GCCTGGGACGCTAACAGTTATA 59.898 50.000 0.00 0.00 0.00 0.98
487 1340 3.244112 GCCTGGGACGCTAACAGTTATAT 60.244 47.826 0.00 0.00 0.00 0.86
532 1406 6.314400 ACCATGCATTGTAAATTTCATTCAGC 59.686 34.615 0.69 0.00 0.00 4.26
534 1408 6.954616 TGCATTGTAAATTTCATTCAGCTG 57.045 33.333 7.63 7.63 0.00 4.24
597 1493 5.266733 TGACCGTGGATATTTAGTACACC 57.733 43.478 0.00 0.00 0.00 4.16
607 1503 0.604578 TTAGTACACCAGGACACGCC 59.395 55.000 0.00 0.00 0.00 5.68
671 1567 5.147767 TCCGATGATCCCAGAAATCTCTAA 58.852 41.667 0.00 0.00 0.00 2.10
685 1581 4.662468 ATCTCTAAGATGTGACGTGCAT 57.338 40.909 0.00 0.00 32.80 3.96
690 1586 6.015940 TCTCTAAGATGTGACGTGCATATGAT 60.016 38.462 6.97 0.00 0.00 2.45
691 1587 6.152379 TCTAAGATGTGACGTGCATATGATC 58.848 40.000 6.97 0.00 0.00 2.92
696 1592 2.423926 GACGTGCATATGATCGTCCT 57.576 50.000 27.18 9.96 44.18 3.85
698 1594 2.472861 GACGTGCATATGATCGTCCTTG 59.527 50.000 27.18 5.12 44.18 3.61
700 1596 2.803133 CGTGCATATGATCGTCCTTGGT 60.803 50.000 6.97 0.00 0.00 3.67
727 1640 1.378514 CGGCCATTTGGTACAGGCT 60.379 57.895 2.24 0.00 45.15 4.58
732 1645 2.238521 CCATTTGGTACAGGCTGTTGT 58.761 47.619 27.24 3.97 42.39 3.32
822 1750 2.037772 GTCCAAAGACTCTGAGCAGGAA 59.962 50.000 4.19 0.00 40.10 3.36
838 1766 1.007154 GAAGGACGCGGCTCTATCC 60.007 63.158 13.91 7.63 0.00 2.59
893 1825 1.797537 GGTGACGCCACGTACGTAC 60.798 63.158 22.34 15.90 45.24 3.67
905 1837 1.135689 CGTACGTACACCGGCTAGTTT 60.136 52.381 24.50 0.00 42.24 2.66
919 1851 4.038763 CGGCTAGTTTGGAGTATATCACCA 59.961 45.833 0.00 0.00 35.11 4.17
942 1874 2.349886 GCATCTCGTCAGATTGGTCAAC 59.650 50.000 0.00 0.00 37.25 3.18
943 1875 3.854666 CATCTCGTCAGATTGGTCAACT 58.145 45.455 0.00 0.00 37.25 3.16
1128 2072 2.813179 GCACATCATCACCGGCGTC 61.813 63.158 6.01 0.00 0.00 5.19
1257 2201 3.082579 GCTCTCCCACTGCTACCGG 62.083 68.421 0.00 0.00 0.00 5.28
1259 2203 1.668101 CTCTCCCACTGCTACCGGTC 61.668 65.000 12.40 0.00 0.00 4.79
1260 2204 2.682494 TCCCACTGCTACCGGTCC 60.682 66.667 12.40 3.85 0.00 4.46
1261 2205 3.782443 CCCACTGCTACCGGTCCC 61.782 72.222 12.40 3.40 0.00 4.46
1262 2206 3.782443 CCACTGCTACCGGTCCCC 61.782 72.222 12.40 0.28 0.00 4.81
1263 2207 3.782443 CACTGCTACCGGTCCCCC 61.782 72.222 12.40 0.00 0.00 5.40
1372 2325 4.069232 TCCTCGGCAGGAAGCACG 62.069 66.667 3.59 0.00 46.84 5.34
1464 2417 0.673644 CCTGCCTCGGGTAAACACTG 60.674 60.000 0.00 0.00 0.00 3.66
1494 2452 2.428890 AGAGCTCGATCGATTTGTTCCT 59.571 45.455 19.78 6.40 0.00 3.36
1495 2453 3.118956 AGAGCTCGATCGATTTGTTCCTT 60.119 43.478 19.78 0.00 0.00 3.36
1496 2454 3.190874 AGCTCGATCGATTTGTTCCTTC 58.809 45.455 19.78 0.00 0.00 3.46
1497 2455 3.118956 AGCTCGATCGATTTGTTCCTTCT 60.119 43.478 19.78 0.00 0.00 2.85
1526 2484 1.215382 CCTCGTCGTTGCTGATGGA 59.785 57.895 0.00 0.00 0.00 3.41
1794 2752 9.463902 ACCATAGGTATATACAGTACATCAGAC 57.536 37.037 14.70 0.00 32.11 3.51
1856 2817 5.537188 AGTCTGAATCTGACACTGAAACTC 58.463 41.667 19.80 0.00 35.30 3.01
2321 3282 4.367023 GTGTGCCGGACCTACGCA 62.367 66.667 5.05 0.00 0.00 5.24
2643 3604 1.681486 AAAGAGGCTCGGCTCCTAGC 61.681 60.000 15.79 4.03 41.46 3.42
2644 3605 2.520741 GAGGCTCGGCTCCTAGCT 60.521 66.667 11.49 0.00 41.99 3.32
2645 3606 2.520741 AGGCTCGGCTCCTAGCTC 60.521 66.667 11.49 3.42 41.99 4.09
2646 3607 3.972276 GGCTCGGCTCCTAGCTCG 61.972 72.222 11.49 2.10 41.99 5.03
2649 3610 1.238625 GCTCGGCTCCTAGCTCGTAT 61.239 60.000 5.30 0.00 41.99 3.06
2650 3611 0.800012 CTCGGCTCCTAGCTCGTATC 59.200 60.000 0.00 0.00 41.99 2.24
2651 3612 0.949588 TCGGCTCCTAGCTCGTATCG 60.950 60.000 0.00 0.00 41.99 2.92
2652 3613 1.229315 CGGCTCCTAGCTCGTATCGT 61.229 60.000 0.00 0.00 41.99 3.73
2654 3615 1.733360 GGCTCCTAGCTCGTATCGTAG 59.267 57.143 0.00 0.00 41.99 3.51
2655 3616 1.733360 GCTCCTAGCTCGTATCGTAGG 59.267 57.143 0.00 0.00 38.45 3.18
2656 3617 1.733360 CTCCTAGCTCGTATCGTAGGC 59.267 57.143 0.00 0.00 33.32 3.93
2657 3618 0.803740 CCTAGCTCGTATCGTAGGCC 59.196 60.000 0.00 0.00 0.00 5.19
2658 3619 1.520494 CTAGCTCGTATCGTAGGCCA 58.480 55.000 5.01 0.00 0.00 5.36
2659 3620 1.197264 CTAGCTCGTATCGTAGGCCAC 59.803 57.143 5.01 0.00 0.00 5.01
2660 3621 0.750546 AGCTCGTATCGTAGGCCACA 60.751 55.000 5.01 0.00 0.00 4.17
2661 3622 0.594284 GCTCGTATCGTAGGCCACAC 60.594 60.000 5.01 0.49 0.00 3.82
2663 3624 1.298863 CGTATCGTAGGCCACACCG 60.299 63.158 5.01 0.57 46.52 4.94
2664 3625 1.590792 GTATCGTAGGCCACACCGC 60.591 63.158 5.01 0.00 46.52 5.68
2678 3639 4.697756 CCGCCACACACCGACCAT 62.698 66.667 0.00 0.00 0.00 3.55
2698 3659 7.101652 ACCATTGTTTGTTGTTGTACATGTA 57.898 32.000 0.08 0.08 0.00 2.29
2699 3660 6.975772 ACCATTGTTTGTTGTTGTACATGTAC 59.024 34.615 25.99 25.99 36.63 2.90
2703 3664 6.787225 TGTTTGTTGTTGTACATGTACTTCC 58.213 36.000 30.69 20.13 37.00 3.46
2704 3665 6.374613 TGTTTGTTGTTGTACATGTACTTCCA 59.625 34.615 30.69 22.00 37.00 3.53
2706 3667 7.575414 TTGTTGTTGTACATGTACTTCCATT 57.425 32.000 30.69 0.00 37.00 3.16
2707 3668 6.964908 TGTTGTTGTACATGTACTTCCATTG 58.035 36.000 30.69 0.00 37.00 2.82
2708 3669 6.016693 TGTTGTTGTACATGTACTTCCATTGG 60.017 38.462 30.69 0.00 37.00 3.16
2709 3670 4.457603 TGTTGTACATGTACTTCCATTGGC 59.542 41.667 30.69 13.68 37.00 4.52
2735 3697 5.467063 AGCTAGCACTTTAGAAACTGTTCAC 59.533 40.000 18.83 0.00 36.09 3.18
2741 3703 7.011482 AGCACTTTAGAAACTGTTCACTTGTAG 59.989 37.037 0.00 0.00 36.09 2.74
2743 3705 7.494625 CACTTTAGAAACTGTTCACTTGTAGGA 59.505 37.037 0.00 0.00 36.09 2.94
2744 3706 7.711339 ACTTTAGAAACTGTTCACTTGTAGGAG 59.289 37.037 0.00 0.00 36.09 3.69
2745 3707 5.615925 AGAAACTGTTCACTTGTAGGAGT 57.384 39.130 0.00 0.00 36.09 3.85
2746 3708 6.726490 AGAAACTGTTCACTTGTAGGAGTA 57.274 37.500 0.00 0.00 36.09 2.59
2747 3709 6.514063 AGAAACTGTTCACTTGTAGGAGTAC 58.486 40.000 0.00 0.00 36.09 2.73
2748 3710 6.324254 AGAAACTGTTCACTTGTAGGAGTACT 59.676 38.462 0.00 0.00 36.09 2.73
2749 3711 6.481434 AACTGTTCACTTGTAGGAGTACTT 57.519 37.500 0.00 0.00 0.00 2.24
2750 3712 7.592885 AACTGTTCACTTGTAGGAGTACTTA 57.407 36.000 0.00 0.00 0.00 2.24
2751 3713 6.979465 ACTGTTCACTTGTAGGAGTACTTAC 58.021 40.000 0.00 0.00 0.00 2.34
2752 3714 6.548622 ACTGTTCACTTGTAGGAGTACTTACA 59.451 38.462 0.00 0.00 36.93 2.41
2756 3718 9.269453 GTTCACTTGTAGGAGTACTTACAAAAT 57.731 33.333 16.94 8.80 44.00 1.82
2770 3732 6.270064 ACTTACAAAATTTGTTCGGTTCCTG 58.730 36.000 16.99 0.80 42.22 3.86
2773 3736 4.339814 ACAAAATTTGTTCGGTTCCTGCTA 59.660 37.500 5.41 0.00 42.22 3.49
2779 3742 1.823610 GTTCGGTTCCTGCTACTAGGT 59.176 52.381 0.00 0.00 38.99 3.08
2780 3743 2.226962 TCGGTTCCTGCTACTAGGTT 57.773 50.000 0.00 0.00 38.99 3.50
2791 3754 4.320870 TGCTACTAGGTTGTACTTTTGGC 58.679 43.478 0.00 0.00 0.00 4.52
2795 3758 1.995376 AGGTTGTACTTTTGGCTGGG 58.005 50.000 0.00 0.00 0.00 4.45
2802 3765 4.538738 TGTACTTTTGGCTGGGTTTTACT 58.461 39.130 0.00 0.00 0.00 2.24
2804 3767 6.308566 TGTACTTTTGGCTGGGTTTTACTAT 58.691 36.000 0.00 0.00 0.00 2.12
2805 3768 5.722021 ACTTTTGGCTGGGTTTTACTATG 57.278 39.130 0.00 0.00 0.00 2.23
2806 3769 4.526650 ACTTTTGGCTGGGTTTTACTATGG 59.473 41.667 0.00 0.00 0.00 2.74
2808 3771 4.931027 TTGGCTGGGTTTTACTATGGTA 57.069 40.909 0.00 0.00 0.00 3.25
2809 3772 5.459982 TTGGCTGGGTTTTACTATGGTAT 57.540 39.130 0.00 0.00 0.00 2.73
2811 3774 5.197451 TGGCTGGGTTTTACTATGGTATTG 58.803 41.667 0.00 0.00 0.00 1.90
2812 3775 5.198207 GGCTGGGTTTTACTATGGTATTGT 58.802 41.667 0.00 0.00 0.00 2.71
2813 3776 5.655090 GGCTGGGTTTTACTATGGTATTGTT 59.345 40.000 0.00 0.00 0.00 2.83
2814 3777 6.405397 GGCTGGGTTTTACTATGGTATTGTTG 60.405 42.308 0.00 0.00 0.00 3.33
2815 3778 6.152154 GCTGGGTTTTACTATGGTATTGTTGT 59.848 38.462 0.00 0.00 0.00 3.32
2816 3779 7.337436 GCTGGGTTTTACTATGGTATTGTTGTA 59.663 37.037 0.00 0.00 0.00 2.41
2817 3780 8.564509 TGGGTTTTACTATGGTATTGTTGTAC 57.435 34.615 0.00 0.00 0.00 2.90
2818 3781 8.384718 TGGGTTTTACTATGGTATTGTTGTACT 58.615 33.333 0.00 0.00 0.00 2.73
2819 3782 8.671028 GGGTTTTACTATGGTATTGTTGTACTG 58.329 37.037 0.00 0.00 0.00 2.74
2820 3783 9.223099 GGTTTTACTATGGTATTGTTGTACTGT 57.777 33.333 0.00 0.00 0.00 3.55
2827 3790 7.997107 ATGGTATTGTTGTACTGTACATACG 57.003 36.000 20.31 0.00 38.68 3.06
2843 3973 4.541482 CGCACGCCATCACCATGC 62.541 66.667 0.00 0.00 0.00 4.06
2885 4019 4.612536 GCATGTATGGCACGCCGC 62.613 66.667 3.13 0.00 39.42 6.53
2886 4020 4.297891 CATGTATGGCACGCCGCG 62.298 66.667 12.14 12.14 43.84 6.46
2889 4023 3.795342 GTATGGCACGCCGCGTTT 61.795 61.111 17.45 4.21 43.84 3.60
2890 4024 3.492545 TATGGCACGCCGCGTTTC 61.493 61.111 17.45 11.77 43.84 2.78
2898 4032 4.322385 GCCGCGTTTCGTGCCTTT 62.322 61.111 4.92 0.00 35.94 3.11
2899 4033 2.127383 CCGCGTTTCGTGCCTTTC 60.127 61.111 4.92 0.00 35.94 2.62
2900 4034 2.127383 CGCGTTTCGTGCCTTTCC 60.127 61.111 0.00 0.00 0.00 3.13
2901 4035 2.254350 GCGTTTCGTGCCTTTCCC 59.746 61.111 0.00 0.00 0.00 3.97
2902 4036 2.951458 CGTTTCGTGCCTTTCCCC 59.049 61.111 0.00 0.00 0.00 4.81
2903 4037 2.622962 CGTTTCGTGCCTTTCCCCC 61.623 63.158 0.00 0.00 0.00 5.40
2904 4038 1.529713 GTTTCGTGCCTTTCCCCCA 60.530 57.895 0.00 0.00 0.00 4.96
2917 4051 3.805928 CCCCATCGGGCTAGCATA 58.194 61.111 18.24 0.70 44.50 3.14
2958 4736 9.155053 CATTTGTCTTTTCTCAAAACTACGTAC 57.845 33.333 0.00 0.00 37.16 3.67
2962 4740 8.408601 TGTCTTTTCTCAAAACTACGTACTAGT 58.591 33.333 0.00 0.00 37.28 2.57
3032 4810 4.481368 ACATTAACCATGTAAGCGGAGA 57.519 40.909 0.00 0.00 45.00 3.71
3041 4819 4.038042 CCATGTAAGCGGAGACTAGAATCA 59.962 45.833 0.00 0.00 0.00 2.57
3049 4827 1.691434 GAGACTAGAATCAGGCAGGGG 59.309 57.143 0.00 0.00 0.00 4.79
3053 4831 1.056700 TAGAATCAGGCAGGGGCTCC 61.057 60.000 0.00 0.00 40.87 4.70
3056 4834 1.513087 AATCAGGCAGGGGCTCCTTT 61.513 55.000 0.00 0.00 42.67 3.11
3066 5005 0.881796 GGGCTCCTTTTGCAGTACAC 59.118 55.000 0.00 0.00 0.00 2.90
3081 5020 5.163311 TGCAGTACACCATAGTCAATATGCT 60.163 40.000 0.00 0.00 40.10 3.79
3103 5042 4.942761 AAGACAAACAAGTCATGCCATT 57.057 36.364 0.00 0.00 40.98 3.16
3108 5052 7.271511 AGACAAACAAGTCATGCCATTAAAAA 58.728 30.769 0.00 0.00 40.98 1.94
3121 5065 9.384682 CATGCCATTAAAAATGACAAAGTTTTC 57.615 29.630 1.23 0.00 0.00 2.29
3124 5068 7.068955 CCATTAAAAATGACAAAGTTTTCGCC 58.931 34.615 1.23 0.00 0.00 5.54
3127 5071 2.793278 ATGACAAAGTTTTCGCCACC 57.207 45.000 0.00 0.00 0.00 4.61
3146 5090 2.101582 ACCCACATCTCGCTATCTTGTC 59.898 50.000 0.00 0.00 0.00 3.18
3147 5091 2.101415 CCCACATCTCGCTATCTTGTCA 59.899 50.000 0.00 0.00 0.00 3.58
3157 5101 7.466805 TCTCGCTATCTTGTCAAATTGAATTG 58.533 34.615 0.00 0.00 0.00 2.32
3203 5147 1.538687 GCTCCAACCCAAGCAATGCT 61.539 55.000 0.00 0.00 42.56 3.79
3213 5157 2.159282 CCAAGCAATGCTCAATCACTCC 60.159 50.000 8.71 0.00 38.25 3.85
3214 5158 2.490509 CAAGCAATGCTCAATCACTCCA 59.509 45.455 8.71 0.00 38.25 3.86
3215 5159 2.366533 AGCAATGCTCAATCACTCCAG 58.633 47.619 0.00 0.00 30.62 3.86
3216 5160 1.202268 GCAATGCTCAATCACTCCAGC 60.202 52.381 0.00 0.00 0.00 4.85
3217 5161 2.089201 CAATGCTCAATCACTCCAGCA 58.911 47.619 0.00 0.00 45.65 4.41
3218 5162 2.490509 CAATGCTCAATCACTCCAGCAA 59.509 45.455 0.00 0.00 44.78 3.91
3219 5163 1.527034 TGCTCAATCACTCCAGCAAC 58.473 50.000 0.00 0.00 38.93 4.17
3220 5164 0.445436 GCTCAATCACTCCAGCAACG 59.555 55.000 0.00 0.00 0.00 4.10
3263 5208 3.117512 CCTAGGGCTACCATCCAAACATT 60.118 47.826 0.00 0.00 40.13 2.71
3283 5228 1.028905 CCCGCAAGAAACCAGTCAAA 58.971 50.000 0.00 0.00 43.02 2.69
3284 5229 1.407258 CCCGCAAGAAACCAGTCAAAA 59.593 47.619 0.00 0.00 43.02 2.44
3285 5230 2.459934 CCGCAAGAAACCAGTCAAAAC 58.540 47.619 0.00 0.00 43.02 2.43
3330 5275 7.253905 TGTATTACTCAAACTTAAGCCCTCT 57.746 36.000 1.29 0.00 0.00 3.69
3357 5302 2.279918 GCACACGTGACCTCCGTT 60.280 61.111 25.01 0.00 36.17 4.44
3358 5303 2.594962 GCACACGTGACCTCCGTTG 61.595 63.158 25.01 8.43 36.17 4.10
3378 5331 1.065551 GCCCTATGCAAACAATCGACC 59.934 52.381 0.00 0.00 40.77 4.79
3395 5348 1.459592 GACCAAATGTGTCGAGAACCG 59.540 52.381 0.00 0.00 40.25 4.44
3412 5366 1.069668 ACCGGTCAACTCCAACTACAC 59.930 52.381 0.00 0.00 0.00 2.90
3435 5389 7.116376 ACACTACTTTGACACTATTCACATTCG 59.884 37.037 0.00 0.00 0.00 3.34
3440 5394 8.567948 ACTTTGACACTATTCACATTCGATTTT 58.432 29.630 0.00 0.00 0.00 1.82
3441 5395 8.726650 TTTGACACTATTCACATTCGATTTTG 57.273 30.769 0.00 0.00 0.00 2.44
3442 5396 7.433708 TGACACTATTCACATTCGATTTTGT 57.566 32.000 0.00 0.00 0.00 2.83
3443 5397 7.518161 TGACACTATTCACATTCGATTTTGTC 58.482 34.615 0.00 0.00 0.00 3.18
3444 5398 7.387673 TGACACTATTCACATTCGATTTTGTCT 59.612 33.333 0.00 0.00 31.76 3.41
3445 5399 8.099364 ACACTATTCACATTCGATTTTGTCTT 57.901 30.769 0.00 0.00 0.00 3.01
3446 5400 8.567948 ACACTATTCACATTCGATTTTGTCTTT 58.432 29.630 0.00 0.00 0.00 2.52
3512 5466 8.755696 TTTTGAGGTTGTATATCAAACATTGC 57.244 30.769 0.00 0.00 45.36 3.56
3531 5485 0.320374 CTTAGTGCCCGACTCCAACA 59.680 55.000 0.00 0.00 35.96 3.33
3538 5492 1.734477 CCGACTCCAACAGCACTCG 60.734 63.158 0.00 0.00 0.00 4.18
3540 5494 2.029844 GACTCCAACAGCACTCGCC 61.030 63.158 0.00 0.00 39.83 5.54
3544 5498 2.249309 CAACAGCACTCGCCAACG 59.751 61.111 0.00 0.00 39.83 4.10
3568 5522 2.653890 GCATACACACACAACTGCAAG 58.346 47.619 0.00 0.00 42.29 4.01
3570 5524 1.674359 TACACACACAACTGCAAGGG 58.326 50.000 0.00 0.00 39.30 3.95
3572 5526 1.037030 CACACACAACTGCAAGGGGT 61.037 55.000 0.00 0.00 39.30 4.95
3573 5527 0.548989 ACACACAACTGCAAGGGGTA 59.451 50.000 0.00 0.00 39.30 3.69
3574 5528 0.951558 CACACAACTGCAAGGGGTAC 59.048 55.000 0.00 0.00 39.30 3.34
3575 5529 0.843984 ACACAACTGCAAGGGGTACT 59.156 50.000 0.00 0.00 39.30 2.73
3576 5530 1.238439 CACAACTGCAAGGGGTACTG 58.762 55.000 0.00 0.00 39.30 2.74
3577 5531 0.537371 ACAACTGCAAGGGGTACTGC 60.537 55.000 0.00 0.00 39.30 4.40
3578 5532 0.537143 CAACTGCAAGGGGTACTGCA 60.537 55.000 7.24 7.24 39.30 4.41
3580 5534 0.250901 ACTGCAAGGGGTACTGCAAG 60.251 55.000 8.63 6.05 39.30 4.01
3581 5535 0.962356 CTGCAAGGGGTACTGCAAGG 60.962 60.000 8.63 0.00 39.30 3.61
3582 5536 1.678970 GCAAGGGGTACTGCAAGGG 60.679 63.158 0.27 0.00 39.30 3.95
3583 5537 1.000896 CAAGGGGTACTGCAAGGGG 60.001 63.158 0.00 0.00 39.30 4.79
3584 5538 2.919096 AAGGGGTACTGCAAGGGGC 61.919 63.158 0.00 0.00 45.13 5.80
3585 5539 3.339093 GGGGTACTGCAAGGGGCT 61.339 66.667 0.00 0.00 45.15 5.19
3586 5540 2.044946 GGGTACTGCAAGGGGCTG 60.045 66.667 0.00 0.00 45.15 4.85
3591 5545 2.752358 CTGCAAGGGGCTGTGAGA 59.248 61.111 0.00 0.00 45.15 3.27
3592 5546 1.302285 CTGCAAGGGGCTGTGAGAT 59.698 57.895 0.00 0.00 45.15 2.75
3593 5547 0.323178 CTGCAAGGGGCTGTGAGATT 60.323 55.000 0.00 0.00 45.15 2.40
3594 5548 0.112995 TGCAAGGGGCTGTGAGATTT 59.887 50.000 0.00 0.00 45.15 2.17
3595 5549 1.354031 TGCAAGGGGCTGTGAGATTTA 59.646 47.619 0.00 0.00 45.15 1.40
3596 5550 2.025037 TGCAAGGGGCTGTGAGATTTAT 60.025 45.455 0.00 0.00 45.15 1.40
3597 5551 2.360165 GCAAGGGGCTGTGAGATTTATG 59.640 50.000 0.00 0.00 40.25 1.90
3598 5552 2.355010 AGGGGCTGTGAGATTTATGC 57.645 50.000 0.00 0.00 0.00 3.14
3599 5553 0.947244 GGGGCTGTGAGATTTATGCG 59.053 55.000 0.00 0.00 0.00 4.73
3600 5554 1.668419 GGGCTGTGAGATTTATGCGT 58.332 50.000 0.00 0.00 0.00 5.24
3601 5555 1.331756 GGGCTGTGAGATTTATGCGTG 59.668 52.381 0.00 0.00 0.00 5.34
3602 5556 1.268234 GGCTGTGAGATTTATGCGTGC 60.268 52.381 0.00 0.00 0.00 5.34
3603 5557 1.667724 GCTGTGAGATTTATGCGTGCT 59.332 47.619 0.00 0.00 0.00 4.40
3604 5558 2.866156 GCTGTGAGATTTATGCGTGCTA 59.134 45.455 0.00 0.00 0.00 3.49
3605 5559 3.496130 GCTGTGAGATTTATGCGTGCTAT 59.504 43.478 0.00 0.00 0.00 2.97
3606 5560 4.610007 GCTGTGAGATTTATGCGTGCTATG 60.610 45.833 0.00 0.00 0.00 2.23
3607 5561 4.441792 TGTGAGATTTATGCGTGCTATGT 58.558 39.130 0.00 0.00 0.00 2.29
3608 5562 4.875536 TGTGAGATTTATGCGTGCTATGTT 59.124 37.500 0.00 0.00 0.00 2.71
3609 5563 5.006649 TGTGAGATTTATGCGTGCTATGTTC 59.993 40.000 0.00 0.00 0.00 3.18
3610 5564 4.209080 TGAGATTTATGCGTGCTATGTTCG 59.791 41.667 0.00 0.00 0.00 3.95
3611 5565 4.119862 AGATTTATGCGTGCTATGTTCGT 58.880 39.130 0.00 0.00 0.00 3.85
3612 5566 3.649870 TTTATGCGTGCTATGTTCGTG 57.350 42.857 0.00 0.00 0.00 4.35
3613 5567 2.287393 TATGCGTGCTATGTTCGTGT 57.713 45.000 0.00 0.00 0.00 4.49
3614 5568 2.287393 ATGCGTGCTATGTTCGTGTA 57.713 45.000 0.00 0.00 0.00 2.90
3615 5569 1.342555 TGCGTGCTATGTTCGTGTAC 58.657 50.000 0.00 0.00 0.00 2.90
3616 5570 1.068125 TGCGTGCTATGTTCGTGTACT 60.068 47.619 0.00 0.00 0.00 2.73
3617 5571 1.320555 GCGTGCTATGTTCGTGTACTG 59.679 52.381 0.00 0.00 0.00 2.74
3618 5572 1.320555 CGTGCTATGTTCGTGTACTGC 59.679 52.381 0.00 0.00 0.00 4.40
3619 5573 1.320555 GTGCTATGTTCGTGTACTGCG 59.679 52.381 0.00 0.00 0.00 5.18
3620 5574 0.921347 GCTATGTTCGTGTACTGCGG 59.079 55.000 9.73 0.00 0.00 5.69
3621 5575 1.734707 GCTATGTTCGTGTACTGCGGT 60.735 52.381 2.42 2.42 0.00 5.68
3622 5576 2.602878 CTATGTTCGTGTACTGCGGTT 58.397 47.619 1.99 0.00 0.00 4.44
3623 5577 1.144969 ATGTTCGTGTACTGCGGTTG 58.855 50.000 1.99 0.00 0.00 3.77
3624 5578 1.203313 GTTCGTGTACTGCGGTTGC 59.797 57.895 1.99 0.00 43.20 4.17
3639 5593 2.823114 TGCGGAGGACGGAAACAA 59.177 55.556 0.00 0.00 41.04 2.83
3640 5594 1.301401 TGCGGAGGACGGAAACAAG 60.301 57.895 0.00 0.00 41.04 3.16
3641 5595 2.033194 GCGGAGGACGGAAACAAGG 61.033 63.158 0.00 0.00 44.51 3.61
3642 5596 1.669440 CGGAGGACGGAAACAAGGA 59.331 57.895 0.00 0.00 39.42 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 1.527844 GAGGCATGGAGGTGGCATC 60.528 63.158 0.00 0.00 46.19 3.91
23 24 2.124403 CTGAGGCATGGAGGTGGC 60.124 66.667 0.00 0.00 44.31 5.01
26 27 2.285969 AGGCTGAGGCATGGAGGT 60.286 61.111 9.23 0.00 40.87 3.85
31 32 1.453379 CCCTTGAGGCTGAGGCATG 60.453 63.158 9.23 0.00 40.87 4.06
33 34 2.203983 TCCCTTGAGGCTGAGGCA 60.204 61.111 9.23 0.00 40.87 4.75
39 40 0.480252 AAGTTTGCTCCCTTGAGGCT 59.520 50.000 0.00 0.00 39.14 4.58
46 47 4.020662 TGTGTTTCAAAAAGTTTGCTCCCT 60.021 37.500 0.00 0.00 0.00 4.20
71 72 3.753272 TGTTGCTTCTATTCCACAAGCTC 59.247 43.478 4.65 0.00 42.60 4.09
79 80 2.093658 TCCCGTCTGTTGCTTCTATTCC 60.094 50.000 0.00 0.00 0.00 3.01
88 89 1.062587 CGATGATTTCCCGTCTGTTGC 59.937 52.381 0.00 0.00 0.00 4.17
91 92 2.826428 CATCGATGATTTCCCGTCTGT 58.174 47.619 21.02 0.00 0.00 3.41
102 103 5.586339 CGTATCCTAATCTGCATCGATGAT 58.414 41.667 29.20 10.85 0.00 2.45
105 106 3.429547 GGCGTATCCTAATCTGCATCGAT 60.430 47.826 0.00 0.00 0.00 3.59
140 141 2.484264 CCTCATCGGTGTTGTTTTCTCC 59.516 50.000 0.00 0.00 0.00 3.71
148 149 1.021390 GCAGGTCCTCATCGGTGTTG 61.021 60.000 0.00 0.00 0.00 3.33
152 153 0.904865 TTCTGCAGGTCCTCATCGGT 60.905 55.000 15.13 0.00 0.00 4.69
251 252 6.918569 AGCGTCTCTGACAATAACACATATAC 59.081 38.462 0.00 0.00 32.09 1.47
320 1173 3.289211 TGGTCCTAGCCCCCTCCA 61.289 66.667 0.00 0.00 0.00 3.86
326 1179 2.638363 CCTTATAAGGTGGTCCTAGCCC 59.362 54.545 21.62 0.00 44.35 5.19
367 1220 2.114616 ACATCCCAGAAGACTAGCCTG 58.885 52.381 0.00 0.00 0.00 4.85
379 1232 1.207791 AAGAGCCCACTACATCCCAG 58.792 55.000 0.00 0.00 0.00 4.45
437 1290 0.937304 CAACCTCGGGCATATGTTCG 59.063 55.000 4.29 8.79 0.00 3.95
449 1302 4.785453 GCCCAGCTCCCAACCTCG 62.785 72.222 0.00 0.00 0.00 4.63
505 1358 6.092396 TGAATGAAATTTACAATGCATGGTGC 59.908 34.615 17.42 0.31 39.74 5.01
506 1359 7.598189 TGAATGAAATTTACAATGCATGGTG 57.402 32.000 17.42 6.92 36.07 4.17
508 1361 6.537301 AGCTGAATGAAATTTACAATGCATGG 59.463 34.615 0.00 0.00 36.07 3.66
512 1365 5.349270 TGCAGCTGAATGAAATTTACAATGC 59.651 36.000 20.43 0.00 36.07 3.56
526 1400 5.581126 TTTTATCGGATTTGCAGCTGAAT 57.419 34.783 20.43 9.35 0.00 2.57
532 1406 4.201910 ACGGTCATTTTATCGGATTTGCAG 60.202 41.667 0.00 0.00 0.00 4.41
534 1408 4.035017 CACGGTCATTTTATCGGATTTGC 58.965 43.478 0.00 0.00 0.00 3.68
567 1445 8.603242 ACTAAATATCCACGGTCATATTTGTC 57.397 34.615 17.33 0.00 36.36 3.18
568 1446 9.485206 GTACTAAATATCCACGGTCATATTTGT 57.515 33.333 17.33 15.39 36.36 2.83
597 1493 2.187946 GAGATGGGGCGTGTCCTG 59.812 66.667 0.00 0.00 34.39 3.86
607 1503 1.907936 GGGGAGATGATGAGAGATGGG 59.092 57.143 0.00 0.00 0.00 4.00
671 1567 3.243535 ACGATCATATGCACGTCACATCT 60.244 43.478 16.81 0.00 33.80 2.90
685 1581 9.227777 CCGATATATATACCAAGGACGATCATA 57.772 37.037 0.00 0.00 0.00 2.15
690 1586 4.581824 GGCCGATATATATACCAAGGACGA 59.418 45.833 0.00 0.00 0.00 4.20
691 1587 4.340097 TGGCCGATATATATACCAAGGACG 59.660 45.833 0.00 0.82 0.00 4.79
694 1590 6.486657 CCAAATGGCCGATATATATACCAAGG 59.513 42.308 13.00 11.64 0.00 3.61
695 1591 7.054124 ACCAAATGGCCGATATATATACCAAG 58.946 38.462 13.00 8.13 39.32 3.61
696 1592 6.964464 ACCAAATGGCCGATATATATACCAA 58.036 36.000 13.00 1.85 39.32 3.67
698 1594 7.502696 TGTACCAAATGGCCGATATATATACC 58.497 38.462 0.00 0.00 39.32 2.73
700 1596 7.688328 GCCTGTACCAAATGGCCGATATATATA 60.688 40.741 0.00 0.00 39.49 0.86
727 1640 3.069980 GCCCAACAACCGCACAACA 62.070 57.895 0.00 0.00 0.00 3.33
732 1645 2.811101 CAAAGCCCAACAACCGCA 59.189 55.556 0.00 0.00 0.00 5.69
759 1672 1.618837 TCTTCTCCCGTCTTCTTGTGG 59.381 52.381 0.00 0.00 0.00 4.17
768 1681 2.000447 CGGTCATTTTCTTCTCCCGTC 59.000 52.381 0.00 0.00 0.00 4.79
822 1750 2.913060 GGGATAGAGCCGCGTCCT 60.913 66.667 4.92 0.00 0.00 3.85
838 1766 1.396996 CAGAGTTGAAAATACCGGCGG 59.603 52.381 27.06 27.06 0.00 6.13
893 1825 2.981859 ATACTCCAAACTAGCCGGTG 57.018 50.000 1.90 0.00 0.00 4.94
905 1837 3.230976 AGATGCGTGGTGATATACTCCA 58.769 45.455 0.00 0.00 39.44 3.86
942 1874 0.322997 ACACAGGGGAGTCGAGAGAG 60.323 60.000 0.00 0.00 43.49 3.20
943 1875 0.609406 CACACAGGGGAGTCGAGAGA 60.609 60.000 0.00 0.00 38.16 3.10
1464 2417 0.723981 GATCGAGCTCTGGTTTGTGC 59.276 55.000 12.85 0.00 0.00 4.57
1494 2452 2.029290 CGACGAGGAAGGAAGGAAAGAA 60.029 50.000 0.00 0.00 0.00 2.52
1495 2453 1.544691 CGACGAGGAAGGAAGGAAAGA 59.455 52.381 0.00 0.00 0.00 2.52
1496 2454 1.272769 ACGACGAGGAAGGAAGGAAAG 59.727 52.381 0.00 0.00 0.00 2.62
1497 2455 1.335145 ACGACGAGGAAGGAAGGAAA 58.665 50.000 0.00 0.00 0.00 3.13
1831 2792 5.757320 AGTTTCAGTGTCAGATTCAGACTTG 59.243 40.000 10.14 8.63 36.94 3.16
1973 2934 0.248784 GCACGATGGAGTACGGGTAC 60.249 60.000 0.70 0.70 35.25 3.34
2417 3378 1.345415 TCGTTGAAGTAGGGGAACACC 59.655 52.381 0.00 0.00 39.11 4.16
2594 3555 3.989698 CTGGACGCAGCCGACGAAT 62.990 63.158 0.00 0.00 38.29 3.34
2643 3604 0.030369 GGTGTGGCCTACGATACGAG 59.970 60.000 3.32 0.00 0.00 4.18
2644 3605 1.717791 CGGTGTGGCCTACGATACGA 61.718 60.000 3.32 0.00 34.25 3.43
2645 3606 1.298863 CGGTGTGGCCTACGATACG 60.299 63.158 3.32 0.00 34.25 3.06
2646 3607 1.590792 GCGGTGTGGCCTACGATAC 60.591 63.158 3.32 0.00 34.25 2.24
2657 3618 4.901123 TCGGTGTGTGGCGGTGTG 62.901 66.667 0.00 0.00 0.00 3.82
2658 3619 4.903010 GTCGGTGTGTGGCGGTGT 62.903 66.667 0.00 0.00 0.00 4.16
2661 3622 4.697756 ATGGTCGGTGTGTGGCGG 62.698 66.667 0.00 0.00 0.00 6.13
2663 3624 1.452145 AACAATGGTCGGTGTGTGGC 61.452 55.000 0.00 0.00 0.00 5.01
2664 3625 1.028905 AAACAATGGTCGGTGTGTGG 58.971 50.000 0.00 0.00 0.00 4.17
2666 3627 1.757682 ACAAACAATGGTCGGTGTGT 58.242 45.000 0.00 0.00 30.72 3.72
2667 3628 2.159310 ACAACAAACAATGGTCGGTGTG 60.159 45.455 0.00 0.00 0.00 3.82
2668 3629 2.096248 ACAACAAACAATGGTCGGTGT 58.904 42.857 0.00 0.00 0.00 4.16
2669 3630 2.857152 CAACAACAAACAATGGTCGGTG 59.143 45.455 0.00 0.00 0.00 4.94
2670 3631 2.494073 ACAACAACAAACAATGGTCGGT 59.506 40.909 0.00 0.00 0.00 4.69
2671 3632 3.157932 ACAACAACAAACAATGGTCGG 57.842 42.857 0.00 0.00 0.00 4.79
2672 3633 4.663166 TGTACAACAACAAACAATGGTCG 58.337 39.130 0.00 0.00 0.00 4.79
2678 3639 7.094334 TGGAAGTACATGTACAACAACAAACAA 60.094 33.333 32.02 8.06 38.48 2.83
2698 3659 2.629336 GCTAGCTAGCCAATGGAAGT 57.371 50.000 31.67 0.00 43.39 3.01
2708 3669 8.477604 TGAACAGTTTCTAAAGTGCTAGCTAGC 61.478 40.741 34.20 34.20 41.85 3.42
2709 3670 6.868864 TGAACAGTTTCTAAAGTGCTAGCTAG 59.131 38.462 16.84 16.84 41.85 3.42
2718 3679 7.562135 TCCTACAAGTGAACAGTTTCTAAAGT 58.438 34.615 0.00 0.00 32.36 2.66
2723 3685 5.615925 ACTCCTACAAGTGAACAGTTTCT 57.384 39.130 0.00 0.00 32.36 2.52
2727 3689 6.548622 TGTAAGTACTCCTACAAGTGAACAGT 59.451 38.462 5.17 0.00 0.00 3.55
2732 3694 9.841295 AAATTTTGTAAGTACTCCTACAAGTGA 57.159 29.630 16.04 9.74 34.46 3.41
2741 3703 6.962686 ACCGAACAAATTTTGTAAGTACTCC 58.037 36.000 14.81 0.00 44.59 3.85
2743 3705 7.283807 AGGAACCGAACAAATTTTGTAAGTACT 59.716 33.333 14.81 10.94 44.59 2.73
2744 3706 7.377662 CAGGAACCGAACAAATTTTGTAAGTAC 59.622 37.037 14.81 9.32 44.59 2.73
2745 3707 7.419204 CAGGAACCGAACAAATTTTGTAAGTA 58.581 34.615 14.81 0.00 44.59 2.24
2746 3708 6.270064 CAGGAACCGAACAAATTTTGTAAGT 58.730 36.000 14.81 9.82 44.59 2.24
2747 3709 5.174943 GCAGGAACCGAACAAATTTTGTAAG 59.825 40.000 14.81 11.38 44.59 2.34
2748 3710 5.044558 GCAGGAACCGAACAAATTTTGTAA 58.955 37.500 14.81 0.00 44.59 2.41
2749 3711 4.339814 AGCAGGAACCGAACAAATTTTGTA 59.660 37.500 14.81 0.00 44.59 2.41
2751 3713 3.716601 AGCAGGAACCGAACAAATTTTG 58.283 40.909 7.59 7.59 0.00 2.44
2752 3714 4.583073 AGTAGCAGGAACCGAACAAATTTT 59.417 37.500 0.00 0.00 0.00 1.82
2756 3718 2.922740 AGTAGCAGGAACCGAACAAA 57.077 45.000 0.00 0.00 0.00 2.83
2762 3724 1.549170 ACAACCTAGTAGCAGGAACCG 59.451 52.381 0.00 0.00 39.18 4.44
2770 3732 4.392138 CAGCCAAAAGTACAACCTAGTAGC 59.608 45.833 0.00 0.00 0.00 3.58
2773 3736 3.497942 CCCAGCCAAAAGTACAACCTAGT 60.498 47.826 0.00 0.00 0.00 2.57
2779 3742 4.957327 AGTAAAACCCAGCCAAAAGTACAA 59.043 37.500 0.00 0.00 0.00 2.41
2780 3743 4.538738 AGTAAAACCCAGCCAAAAGTACA 58.461 39.130 0.00 0.00 0.00 2.90
2791 3754 7.696992 ACAACAATACCATAGTAAAACCCAG 57.303 36.000 0.00 0.00 30.59 4.45
2802 3765 7.648908 GCGTATGTACAGTACAACAATACCATA 59.351 37.037 17.43 0.00 42.76 2.74
2804 3767 5.806502 GCGTATGTACAGTACAACAATACCA 59.193 40.000 17.43 0.00 42.76 3.25
2805 3768 5.806502 TGCGTATGTACAGTACAACAATACC 59.193 40.000 17.43 9.52 42.76 2.73
2806 3769 6.505265 CGTGCGTATGTACAGTACAACAATAC 60.505 42.308 17.43 13.29 42.76 1.89
2808 3771 4.325204 CGTGCGTATGTACAGTACAACAAT 59.675 41.667 17.43 3.76 42.76 2.71
2809 3772 3.669588 CGTGCGTATGTACAGTACAACAA 59.330 43.478 17.43 3.84 42.76 2.83
2811 3774 2.027214 GCGTGCGTATGTACAGTACAAC 59.973 50.000 17.43 14.41 42.76 3.32
2812 3775 2.252747 GCGTGCGTATGTACAGTACAA 58.747 47.619 17.43 4.72 42.76 2.41
2813 3776 1.467883 GGCGTGCGTATGTACAGTACA 60.468 52.381 15.90 15.90 43.80 2.90
2814 3777 1.194495 GGCGTGCGTATGTACAGTAC 58.806 55.000 0.33 3.49 0.00 2.73
2815 3778 0.810016 TGGCGTGCGTATGTACAGTA 59.190 50.000 0.33 0.00 0.00 2.74
2816 3779 0.174845 ATGGCGTGCGTATGTACAGT 59.825 50.000 0.33 0.00 0.00 3.55
2817 3780 0.852777 GATGGCGTGCGTATGTACAG 59.147 55.000 0.33 0.00 0.00 2.74
2818 3781 0.173708 TGATGGCGTGCGTATGTACA 59.826 50.000 0.00 0.00 0.00 2.90
2819 3782 0.575390 GTGATGGCGTGCGTATGTAC 59.425 55.000 0.00 0.00 0.00 2.90
2820 3783 0.528901 GGTGATGGCGTGCGTATGTA 60.529 55.000 0.00 0.00 0.00 2.29
2821 3784 1.813753 GGTGATGGCGTGCGTATGT 60.814 57.895 0.00 0.00 0.00 2.29
2822 3785 1.159713 ATGGTGATGGCGTGCGTATG 61.160 55.000 0.00 0.00 0.00 2.39
2824 3787 1.813337 CATGGTGATGGCGTGCGTA 60.813 57.895 0.00 0.00 0.00 4.42
2826 3789 4.541482 GCATGGTGATGGCGTGCG 62.541 66.667 0.00 0.00 0.00 5.34
2827 3790 4.197498 GGCATGGTGATGGCGTGC 62.197 66.667 0.00 0.00 44.46 5.34
2843 3973 1.396653 GCCATGGAGATTGGTTGAGG 58.603 55.000 18.40 0.00 36.57 3.86
2872 4006 3.711997 GAAACGCGGCGTGCCATAC 62.712 63.158 30.10 12.54 39.99 2.39
2885 4019 2.622962 GGGGGAAAGGCACGAAACG 61.623 63.158 0.00 0.00 0.00 3.60
2886 4020 0.898326 ATGGGGGAAAGGCACGAAAC 60.898 55.000 0.00 0.00 0.00 2.78
2888 4022 1.001393 GATGGGGGAAAGGCACGAA 60.001 57.895 0.00 0.00 0.00 3.85
2889 4023 2.674754 GATGGGGGAAAGGCACGA 59.325 61.111 0.00 0.00 0.00 4.35
2890 4024 2.824041 CGATGGGGGAAAGGCACG 60.824 66.667 0.00 0.00 0.00 5.34
2891 4025 2.440247 CCGATGGGGGAAAGGCAC 60.440 66.667 0.00 0.00 0.00 5.01
2901 4035 1.078848 GCTATGCTAGCCCGATGGG 60.079 63.158 13.29 0.00 45.95 4.00
2902 4036 4.606071 GCTATGCTAGCCCGATGG 57.394 61.111 13.29 2.24 45.95 3.51
2916 4050 8.627208 AAGACAAATGAAAGATTCTTGAGCTA 57.373 30.769 0.00 0.00 0.00 3.32
2917 4051 7.521871 AAGACAAATGAAAGATTCTTGAGCT 57.478 32.000 0.00 0.00 0.00 4.09
2920 4054 9.956720 GAGAAAAGACAAATGAAAGATTCTTGA 57.043 29.630 0.00 0.00 0.00 3.02
2931 4065 7.981142 ACGTAGTTTTGAGAAAAGACAAATGA 58.019 30.769 0.00 0.00 37.78 2.57
3032 4810 0.327000 AGCCCCTGCCTGATTCTAGT 60.327 55.000 0.00 0.00 38.69 2.57
3041 4819 2.442413 CAAAAGGAGCCCCTGCCT 59.558 61.111 0.00 0.00 43.48 4.75
3049 4827 1.604604 TGGTGTACTGCAAAAGGAGC 58.395 50.000 0.00 0.00 0.00 4.70
3053 4831 5.940192 TTGACTATGGTGTACTGCAAAAG 57.060 39.130 0.00 0.00 0.00 2.27
3056 4834 5.527214 GCATATTGACTATGGTGTACTGCAA 59.473 40.000 0.00 0.00 38.14 4.08
3066 5005 8.437360 TGTTTGTCTTAGCATATTGACTATGG 57.563 34.615 0.00 0.00 38.14 2.74
3081 5020 7.517614 TTAATGGCATGACTTGTTTGTCTTA 57.482 32.000 0.00 0.00 37.79 2.10
3103 5042 5.520649 GGTGGCGAAAACTTTGTCATTTTTA 59.479 36.000 0.00 0.00 0.00 1.52
3108 5052 1.339929 GGGTGGCGAAAACTTTGTCAT 59.660 47.619 0.00 0.00 0.00 3.06
3121 5065 2.369257 ATAGCGAGATGTGGGTGGCG 62.369 60.000 0.00 0.00 0.00 5.69
3124 5068 2.159043 ACAAGATAGCGAGATGTGGGTG 60.159 50.000 0.00 0.00 0.00 4.61
3127 5071 3.443099 TGACAAGATAGCGAGATGTGG 57.557 47.619 0.00 0.00 0.00 4.17
3146 5090 9.820229 CATTCACAGGATTTTCAATTCAATTTG 57.180 29.630 0.00 0.00 0.00 2.32
3147 5091 8.508875 GCATTCACAGGATTTTCAATTCAATTT 58.491 29.630 0.00 0.00 0.00 1.82
3157 5101 5.481105 TCATTTGGCATTCACAGGATTTTC 58.519 37.500 0.00 0.00 0.00 2.29
3185 5129 0.529378 GAGCATTGCTTGGGTTGGAG 59.471 55.000 13.35 0.00 39.88 3.86
3197 5141 2.089201 TGCTGGAGTGATTGAGCATTG 58.911 47.619 0.00 0.00 36.54 2.82
3203 5147 0.955428 GGCGTTGCTGGAGTGATTGA 60.955 55.000 0.00 0.00 0.00 2.57
3263 5208 0.181587 TTGACTGGTTTCTTGCGGGA 59.818 50.000 0.00 0.00 0.00 5.14
3304 5249 8.161425 AGAGGGCTTAAGTTTGAGTAATACAAA 58.839 33.333 4.02 0.00 35.34 2.83
3358 5303 1.065551 GGTCGATTGTTTGCATAGGGC 59.934 52.381 0.00 0.00 45.13 5.19
3378 5331 1.459592 GACCGGTTCTCGACACATTTG 59.540 52.381 9.42 0.00 42.43 2.32
3388 5341 1.070289 AGTTGGAGTTGACCGGTTCTC 59.930 52.381 9.42 16.65 0.00 2.87
3389 5342 1.129058 AGTTGGAGTTGACCGGTTCT 58.871 50.000 9.42 8.17 0.00 3.01
3390 5343 2.224113 TGTAGTTGGAGTTGACCGGTTC 60.224 50.000 9.42 0.91 0.00 3.62
3391 5344 1.764134 TGTAGTTGGAGTTGACCGGTT 59.236 47.619 9.42 0.00 0.00 4.44
3393 5346 1.343465 AGTGTAGTTGGAGTTGACCGG 59.657 52.381 0.00 0.00 0.00 5.28
3395 5348 4.868314 AGTAGTGTAGTTGGAGTTGACC 57.132 45.455 0.00 0.00 0.00 4.02
3412 5366 7.812309 TCGAATGTGAATAGTGTCAAAGTAG 57.188 36.000 0.00 0.00 0.00 2.57
3486 5440 9.202273 GCAATGTTTGATATACAACCTCAAAAA 57.798 29.630 1.07 0.00 39.74 1.94
3512 5466 0.320374 TGTTGGAGTCGGGCACTAAG 59.680 55.000 0.00 0.00 34.41 2.18
3540 5494 2.570581 GTGTGTATGCGCGCGTTG 60.571 61.111 32.97 3.57 0.00 4.10
3544 5498 1.792057 GTTGTGTGTGTATGCGCGC 60.792 57.895 27.26 27.26 36.27 6.86
3546 5500 0.725784 GCAGTTGTGTGTGTATGCGC 60.726 55.000 0.00 0.00 0.00 6.09
3548 5502 2.605338 CCTTGCAGTTGTGTGTGTATGC 60.605 50.000 0.00 0.00 0.00 3.14
3568 5522 3.339093 AGCCCCTTGCAGTACCCC 61.339 66.667 0.00 0.00 44.83 4.95
3570 5524 1.675641 CACAGCCCCTTGCAGTACC 60.676 63.158 0.00 0.00 44.83 3.34
3572 5526 0.835971 TCTCACAGCCCCTTGCAGTA 60.836 55.000 0.00 0.00 44.83 2.74
3573 5527 1.495579 ATCTCACAGCCCCTTGCAGT 61.496 55.000 0.00 0.00 44.83 4.40
3574 5528 0.323178 AATCTCACAGCCCCTTGCAG 60.323 55.000 0.00 0.00 44.83 4.41
3575 5529 0.112995 AAATCTCACAGCCCCTTGCA 59.887 50.000 0.00 0.00 44.83 4.08
3576 5530 2.128771 TAAATCTCACAGCCCCTTGC 57.871 50.000 0.00 0.00 41.71 4.01
3577 5531 2.360165 GCATAAATCTCACAGCCCCTTG 59.640 50.000 0.00 0.00 0.00 3.61
3578 5532 2.659428 GCATAAATCTCACAGCCCCTT 58.341 47.619 0.00 0.00 0.00 3.95
3580 5534 0.947244 CGCATAAATCTCACAGCCCC 59.053 55.000 0.00 0.00 0.00 5.80
3581 5535 1.331756 CACGCATAAATCTCACAGCCC 59.668 52.381 0.00 0.00 0.00 5.19
3582 5536 1.268234 GCACGCATAAATCTCACAGCC 60.268 52.381 0.00 0.00 0.00 4.85
3583 5537 1.667724 AGCACGCATAAATCTCACAGC 59.332 47.619 0.00 0.00 0.00 4.40
3584 5538 4.509230 ACATAGCACGCATAAATCTCACAG 59.491 41.667 0.00 0.00 0.00 3.66
3585 5539 4.441792 ACATAGCACGCATAAATCTCACA 58.558 39.130 0.00 0.00 0.00 3.58
3586 5540 5.409643 AACATAGCACGCATAAATCTCAC 57.590 39.130 0.00 0.00 0.00 3.51
3587 5541 4.209080 CGAACATAGCACGCATAAATCTCA 59.791 41.667 0.00 0.00 0.00 3.27
3588 5542 4.209288 ACGAACATAGCACGCATAAATCTC 59.791 41.667 0.00 0.00 0.00 2.75
3589 5543 4.025730 CACGAACATAGCACGCATAAATCT 60.026 41.667 0.00 0.00 0.00 2.40
3590 5544 4.203828 CACGAACATAGCACGCATAAATC 58.796 43.478 0.00 0.00 0.00 2.17
3591 5545 3.621268 ACACGAACATAGCACGCATAAAT 59.379 39.130 0.00 0.00 0.00 1.40
3592 5546 2.997303 ACACGAACATAGCACGCATAAA 59.003 40.909 0.00 0.00 0.00 1.40
3593 5547 2.612604 ACACGAACATAGCACGCATAA 58.387 42.857 0.00 0.00 0.00 1.90
3594 5548 2.287393 ACACGAACATAGCACGCATA 57.713 45.000 0.00 0.00 0.00 3.14
3595 5549 1.924524 GTACACGAACATAGCACGCAT 59.075 47.619 0.00 0.00 0.00 4.73
3596 5550 1.068125 AGTACACGAACATAGCACGCA 60.068 47.619 0.00 0.00 0.00 5.24
3597 5551 1.320555 CAGTACACGAACATAGCACGC 59.679 52.381 0.00 0.00 0.00 5.34
3598 5552 1.320555 GCAGTACACGAACATAGCACG 59.679 52.381 0.00 0.00 0.00 5.34
3599 5553 1.320555 CGCAGTACACGAACATAGCAC 59.679 52.381 2.41 0.00 0.00 4.40
3600 5554 1.624487 CGCAGTACACGAACATAGCA 58.376 50.000 2.41 0.00 0.00 3.49
3601 5555 0.921347 CCGCAGTACACGAACATAGC 59.079 55.000 9.60 0.00 0.00 2.97
3602 5556 2.273370 ACCGCAGTACACGAACATAG 57.727 50.000 9.60 0.00 0.00 2.23
3603 5557 2.330286 CAACCGCAGTACACGAACATA 58.670 47.619 9.60 0.00 0.00 2.29
3604 5558 1.144969 CAACCGCAGTACACGAACAT 58.855 50.000 9.60 0.00 0.00 2.71
3605 5559 1.492319 GCAACCGCAGTACACGAACA 61.492 55.000 9.60 0.00 38.36 3.18
3606 5560 1.203313 GCAACCGCAGTACACGAAC 59.797 57.895 9.60 0.00 38.36 3.95
3607 5561 2.304401 CGCAACCGCAGTACACGAA 61.304 57.895 9.60 0.00 38.40 3.85
3608 5562 2.731721 CGCAACCGCAGTACACGA 60.732 61.111 9.60 0.00 38.40 4.35
3609 5563 3.773630 CCGCAACCGCAGTACACG 61.774 66.667 0.00 0.00 38.40 4.49
3610 5564 2.356553 TCCGCAACCGCAGTACAC 60.357 61.111 0.00 0.00 38.40 2.90
3611 5565 2.048597 CTCCGCAACCGCAGTACA 60.049 61.111 0.00 0.00 38.40 2.90
3612 5566 2.813908 CCTCCGCAACCGCAGTAC 60.814 66.667 0.00 0.00 38.40 2.73
3613 5567 2.992689 TCCTCCGCAACCGCAGTA 60.993 61.111 0.00 0.00 38.40 2.74
3614 5568 4.681978 GTCCTCCGCAACCGCAGT 62.682 66.667 0.00 0.00 38.40 4.40
3618 5572 3.869473 TTTCCGTCCTCCGCAACCG 62.869 63.158 0.00 0.00 34.38 4.44
3619 5573 2.031465 TTTCCGTCCTCCGCAACC 59.969 61.111 0.00 0.00 34.38 3.77
3620 5574 1.161563 TTGTTTCCGTCCTCCGCAAC 61.162 55.000 0.00 0.00 34.38 4.17
3621 5575 0.882927 CTTGTTTCCGTCCTCCGCAA 60.883 55.000 0.00 0.00 34.38 4.85
3622 5576 1.301401 CTTGTTTCCGTCCTCCGCA 60.301 57.895 0.00 0.00 34.38 5.69
3623 5577 2.033194 CCTTGTTTCCGTCCTCCGC 61.033 63.158 0.00 0.00 34.38 5.54
3624 5578 1.669440 TCCTTGTTTCCGTCCTCCG 59.331 57.895 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.