Multiple sequence alignment - TraesCS2B01G115300

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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 TraesCS2B01G115300 chr2B 100.000 2729 0 0 1 2729 78812964 78810236 0.000000e+00 5040.0
1 TraesCS2B01G115300 chr2B 82.795 1424 110 54 589 1952 579797291 579795943 0.000000e+00 1147.0
2 TraesCS2B01G115300 chr2B 80.553 1229 118 56 670 1854 78414317 78413166 0.000000e+00 833.0
3 TraesCS2B01G115300 chr2B 80.895 827 79 30 830 1614 78104151 78103362 1.820000e-161 579.0
4 TraesCS2B01G115300 chr2B 80.658 486 65 17 652 1124 579916111 579915642 1.560000e-92 350.0
5 TraesCS2B01G115300 chr2B 85.227 352 34 7 2053 2392 78118397 78118052 2.010000e-91 346.0
6 TraesCS2B01G115300 chr2B 83.029 383 40 13 1984 2343 579795938 579795558 9.430000e-85 324.0
7 TraesCS2B01G115300 chr2B 87.755 245 14 8 6 245 579799872 579799639 3.460000e-69 272.0
8 TraesCS2B01G115300 chr2B 93.714 175 10 1 80 253 78414762 78414588 7.500000e-66 261.0
9 TraesCS2B01G115300 chr2B 78.893 289 31 13 126 398 579918896 579918622 4.670000e-38 169.0
10 TraesCS2B01G115300 chr2B 100.000 32 0 0 1843 1874 78811091 78811122 2.930000e-05 60.2
11 TraesCS2B01G115300 chr2B 97.059 34 1 0 365 398 78414481 78414448 1.060000e-04 58.4
12 TraesCS2B01G115300 chr2A 78.002 1091 135 59 589 1598 52009764 52008698 3.030000e-164 588.0
13 TraesCS2B01G115300 chr2A 84.868 608 49 23 993 1588 52072809 52072233 8.480000e-160 573.0
14 TraesCS2B01G115300 chr2A 84.990 493 50 8 2051 2520 52071895 52071404 1.900000e-131 479.0
15 TraesCS2B01G115300 chr2A 88.462 234 21 5 1732 1960 52072206 52071974 7.440000e-71 278.0
16 TraesCS2B01G115300 chr2A 84.151 265 12 16 1 253 52077475 52077229 2.110000e-56 230.0
17 TraesCS2B01G115300 chr2A 84.186 215 31 2 2518 2729 618953581 618953367 3.560000e-49 206.0
18 TraesCS2B01G115300 chr2A 86.188 181 17 6 74 253 52080865 52080692 3.590000e-44 189.0
19 TraesCS2B01G115300 chr2A 97.059 34 1 0 365 398 52072995 52072962 1.060000e-04 58.4
20 TraesCS2B01G115300 chr2D 88.235 442 38 6 2093 2520 50404446 50404005 1.450000e-142 516.0
21 TraesCS2B01G115300 chr2D 78.161 783 88 39 876 1607 50343291 50342541 3.250000e-114 422.0
22 TraesCS2B01G115300 chr2D 83.434 495 36 24 3 486 50405805 50405346 4.200000e-113 418.0
23 TraesCS2B01G115300 chr2D 83.766 154 12 8 531 682 50405344 50405202 1.700000e-27 134.0
24 TraesCS2B01G115300 chr2D 84.545 110 4 5 589 698 50343601 50343505 2.240000e-16 97.1
25 TraesCS2B01G115300 chr5B 84.422 199 28 3 2531 2728 261896190 261895994 2.770000e-45 193.0
26 TraesCS2B01G115300 chr4B 83.333 198 29 4 2532 2728 440933912 440934106 2.160000e-41 180.0
27 TraesCS2B01G115300 chr5D 82.000 200 30 6 2531 2728 357711266 357711071 6.050000e-37 165.0
28 TraesCS2B01G115300 chr5D 80.488 164 29 2 2175 2335 264021012 264021175 3.690000e-24 122.0
29 TraesCS2B01G115300 chr7D 80.392 204 34 5 2531 2729 398380825 398380623 1.690000e-32 150.0
30 TraesCS2B01G115300 chr6B 80.788 203 27 12 2531 2729 498971181 498970987 6.090000e-32 148.0
31 TraesCS2B01G115300 chr1D 80.296 203 28 12 2531 2729 208067267 208067073 2.830000e-30 143.0
32 TraesCS2B01G115300 chr6D 79.902 204 28 12 2531 2729 13550964 13550769 1.320000e-28 137.0
33 TraesCS2B01G115300 chr4D 79.126 206 25 17 2531 2729 268036103 268036297 2.850000e-25 126.0
34 TraesCS2B01G115300 chr3A 78.922 204 29 13 2531 2729 370701529 370701723 2.850000e-25 126.0
35 TraesCS2B01G115300 chr3A 77.228 202 41 5 2531 2729 269776514 269776713 2.220000e-21 113.0
36 TraesCS2B01G115300 chr4A 77.833 203 33 10 2531 2729 473658427 473658621 6.180000e-22 115.0
37 TraesCS2B01G115300 chr1B 95.349 43 1 1 1844 1886 361006697 361006738 1.750000e-07 67.6


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 TraesCS2B01G115300 chr2B 78810236 78812964 2728 True 5040.000000 5040 100.000000 1 2729 1 chr2B.!!$R3 2728
1 TraesCS2B01G115300 chr2B 579795558 579799872 4314 True 581.000000 1147 84.526333 6 2343 3 chr2B.!!$R5 2337
2 TraesCS2B01G115300 chr2B 78103362 78104151 789 True 579.000000 579 80.895000 830 1614 1 chr2B.!!$R1 784
3 TraesCS2B01G115300 chr2B 78413166 78414762 1596 True 384.133333 833 90.442000 80 1854 3 chr2B.!!$R4 1774
4 TraesCS2B01G115300 chr2B 579915642 579918896 3254 True 259.500000 350 79.775500 126 1124 2 chr2B.!!$R6 998
5 TraesCS2B01G115300 chr2A 52008698 52009764 1066 True 588.000000 588 78.002000 589 1598 1 chr2A.!!$R1 1009
6 TraesCS2B01G115300 chr2A 52071404 52072995 1591 True 347.100000 573 88.844750 365 2520 4 chr2A.!!$R3 2155
7 TraesCS2B01G115300 chr2A 52077229 52080865 3636 True 209.500000 230 85.169500 1 253 2 chr2A.!!$R4 252
8 TraesCS2B01G115300 chr2D 50404005 50405805 1800 True 356.000000 516 85.145000 3 2520 3 chr2D.!!$R2 2517
9 TraesCS2B01G115300 chr2D 50342541 50343601 1060 True 259.550000 422 81.353000 589 1607 2 chr2D.!!$R1 1018

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
745 5427 0.106894 CTCGCTCCCCTATTCCAACC 59.893 60.0 0.0 0.0 0.0 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2551 9548 0.795698 CGCATTGTCGTCAATCACCA 59.204 50.0 4.86 0.0 41.66 4.17 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
33 34 3.490759 CCGTGCACTTGCTAGCGG 61.491 66.667 16.19 14.42 41.62 5.52
47 48 0.254747 TAGCGGTTTCCCATTGGAGG 59.745 55.000 3.62 0.00 43.07 4.30
100 102 2.669229 TGGTGCGACATGTGCAGG 60.669 61.111 19.02 1.70 44.21 4.85
177 182 0.317799 TTGCACGTGGTACCGTACAT 59.682 50.000 18.88 0.00 39.45 2.29
178 183 0.388778 TGCACGTGGTACCGTACATG 60.389 55.000 18.88 0.35 39.45 3.21
179 184 0.388907 GCACGTGGTACCGTACATGT 60.389 55.000 18.88 2.69 39.45 3.21
290 305 3.038280 TGGCATGTGGCACGAAAC 58.962 55.556 13.77 4.25 46.12 2.78
291 306 1.825622 TGGCATGTGGCACGAAACA 60.826 52.632 13.77 6.96 46.12 2.83
292 307 2.069465 TGGCATGTGGCACGAAACAC 62.069 55.000 13.77 1.69 46.12 3.32
529 2674 2.171209 CTGGAGACCATGGACGCACA 62.171 60.000 21.47 12.94 30.82 4.57
532 2677 3.788766 GACCATGGACGCACACGC 61.789 66.667 21.47 0.00 45.53 5.34
543 2688 3.172575 CACACGCGTACGCCTGAG 61.173 66.667 35.04 26.83 45.53 3.35
551 2696 0.523546 CGTACGCCTGAGCTGTGTAG 60.524 60.000 0.52 0.00 36.60 2.74
559 2726 2.625737 CTGAGCTGTGTAGATGGTTGG 58.374 52.381 0.00 0.00 0.00 3.77
742 5424 2.140792 GCCTCGCTCCCCTATTCCA 61.141 63.158 0.00 0.00 0.00 3.53
745 5427 0.106894 CTCGCTCCCCTATTCCAACC 59.893 60.000 0.00 0.00 0.00 3.77
749 5431 0.328548 CTCCCCTATTCCAACCCCCT 60.329 60.000 0.00 0.00 0.00 4.79
757 5439 0.996762 TTCCAACCCCCTCAACACCT 60.997 55.000 0.00 0.00 0.00 4.00
760 5442 0.184933 CAACCCCCTCAACACCTCAA 59.815 55.000 0.00 0.00 0.00 3.02
798 5488 1.445410 GAGACGCACGCACACCATA 60.445 57.895 0.00 0.00 0.00 2.74
800 5490 1.736645 GACGCACGCACACCATACT 60.737 57.895 0.00 0.00 0.00 2.12
801 5491 1.683790 GACGCACGCACACCATACTC 61.684 60.000 0.00 0.00 0.00 2.59
802 5492 1.446099 CGCACGCACACCATACTCT 60.446 57.895 0.00 0.00 0.00 3.24
808 5498 1.204704 CGCACACCATACTCTTCCTCA 59.795 52.381 0.00 0.00 0.00 3.86
872 5641 3.199289 TCACTGATCATCATCTGCCTTGT 59.801 43.478 0.00 0.00 32.45 3.16
931 5725 2.579738 GTGGTTCCTCTCGGCCTC 59.420 66.667 0.00 0.00 0.00 4.70
932 5726 2.683933 TGGTTCCTCTCGGCCTCC 60.684 66.667 0.00 0.00 0.00 4.30
933 5727 2.364448 GGTTCCTCTCGGCCTCCT 60.364 66.667 0.00 0.00 0.00 3.69
934 5728 2.428085 GGTTCCTCTCGGCCTCCTC 61.428 68.421 0.00 0.00 0.00 3.71
935 5729 2.440430 TTCCTCTCGGCCTCCTCG 60.440 66.667 0.00 0.00 0.00 4.63
955 5749 3.152400 CGGGCCGGCCTACTAGTT 61.152 66.667 42.70 0.00 36.10 2.24
1003 5797 0.807496 GTTGCACTTCTCCTCCATGC 59.193 55.000 0.00 0.00 36.81 4.06
1038 5832 2.514592 TACGACTACTCCCCCGCG 60.515 66.667 0.00 0.00 0.00 6.46
1057 5860 2.617538 TCTCCTCCCCGTCCTCCT 60.618 66.667 0.00 0.00 0.00 3.69
1086 5889 1.308326 CTCCTCCTCGTCCCTCCTT 59.692 63.158 0.00 0.00 0.00 3.36
1154 5979 4.208686 GACGGGATCGCTCGCCTT 62.209 66.667 8.28 0.00 43.33 4.35
1405 6449 4.373116 GCGTCCTGCCCTTGTCGA 62.373 66.667 0.00 0.00 37.76 4.20
1430 6492 3.755526 ATGCCGCGCTGCTGGATTA 62.756 57.895 24.31 3.42 0.00 1.75
1523 6600 3.677648 CCACCAACAGCAGCTGGC 61.678 66.667 26.38 7.98 45.30 4.85
1560 6649 2.753043 TACCCGACGCTGGACTCC 60.753 66.667 0.00 0.00 0.00 3.85
1617 6715 2.642183 TAGCCGATCGAGCTCCCCTT 62.642 60.000 27.01 11.09 41.83 3.95
1632 6730 0.897621 CCCTTCCATTTGCCAGGAAC 59.102 55.000 0.00 0.00 38.91 3.62
1713 6817 2.366533 TCGCCTAGACGACAGAAGAAT 58.633 47.619 0.00 0.00 37.09 2.40
1723 6828 7.283625 AGACGACAGAAGAATATAAGCAGAT 57.716 36.000 0.00 0.00 0.00 2.90
1724 6829 8.397575 AGACGACAGAAGAATATAAGCAGATA 57.602 34.615 0.00 0.00 0.00 1.98
1725 6830 8.293867 AGACGACAGAAGAATATAAGCAGATAC 58.706 37.037 0.00 0.00 0.00 2.24
1746 7261 2.225068 AGTTCACCAACACAGACTCG 57.775 50.000 0.00 0.00 34.60 4.18
1833 7647 5.949952 GGGACTGTTTGGATGGTTACTAAAT 59.050 40.000 0.00 0.00 0.00 1.40
1834 7649 6.095021 GGGACTGTTTGGATGGTTACTAAATC 59.905 42.308 0.00 0.00 0.00 2.17
1840 7655 5.936187 TGGATGGTTACTAAATCGTACCA 57.064 39.130 0.00 0.00 0.00 3.25
1907 7735 3.326588 TGAAGGCTTCTTTACCAGCTGTA 59.673 43.478 26.26 2.40 36.20 2.74
1958 7789 0.383949 TCGGCAAGCAAAACCTCAAC 59.616 50.000 0.00 0.00 0.00 3.18
1959 7790 0.597377 CGGCAAGCAAAACCTCAACC 60.597 55.000 0.00 0.00 0.00 3.77
1960 7791 0.249868 GGCAAGCAAAACCTCAACCC 60.250 55.000 0.00 0.00 0.00 4.11
1966 7797 3.103742 AGCAAAACCTCAACCCTTTTCA 58.896 40.909 0.00 0.00 0.00 2.69
1967 7798 3.517500 AGCAAAACCTCAACCCTTTTCAA 59.482 39.130 0.00 0.00 0.00 2.69
1968 7799 4.019771 AGCAAAACCTCAACCCTTTTCAAA 60.020 37.500 0.00 0.00 0.00 2.69
1969 7800 4.697828 GCAAAACCTCAACCCTTTTCAAAA 59.302 37.500 0.00 0.00 0.00 2.44
1994 7825 4.526970 AGAAGAAGAGCAAAACCTCAACA 58.473 39.130 0.00 0.00 34.26 3.33
2018 7849 5.754543 AAAAATTGGCAACCAACATCTTG 57.245 34.783 0.00 0.00 46.95 3.02
2019 7850 2.460757 ATTGGCAACCAACATCTTGC 57.539 45.000 0.00 0.00 46.95 4.01
2020 7851 1.412079 TTGGCAACCAACATCTTGCT 58.588 45.000 0.00 0.00 42.11 3.91
2025 7856 2.554032 GCAACCAACATCTTGCTAGTGT 59.446 45.455 0.00 0.00 39.79 3.55
2077 7946 3.840666 TCCAACTTCTCTAGCAACAGGAT 59.159 43.478 0.00 0.00 0.00 3.24
2087 7956 5.665459 TCTAGCAACAGGATAGAGAAAAGC 58.335 41.667 0.00 0.00 39.49 3.51
2090 7959 3.376546 GCAACAGGATAGAGAAAAGCCAG 59.623 47.826 0.00 0.00 0.00 4.85
2125 8649 8.413309 AGATTCAATTTGATCACAAAAGGAGA 57.587 30.769 0.00 0.00 46.77 3.71
2224 8816 3.202151 TCCCCTTTTAGAGATTCGGCAAT 59.798 43.478 0.00 0.00 0.00 3.56
2233 8825 2.393557 ATTCGGCAATGCGTCGAAT 58.606 47.368 20.62 20.62 44.84 3.34
2263 8856 5.369110 AGATCTTCAGATATGGAGGCTTTGT 59.631 40.000 0.00 0.00 34.37 2.83
2272 8865 4.591321 ATGGAGGCTTTGTTTATCCAGA 57.409 40.909 0.00 0.00 42.99 3.86
2277 8870 5.163612 GGAGGCTTTGTTTATCCAGATTCAC 60.164 44.000 0.00 0.00 0.00 3.18
2279 8872 4.438744 GGCTTTGTTTATCCAGATTCACGG 60.439 45.833 0.00 0.00 0.00 4.94
2284 8877 4.081365 TGTTTATCCAGATTCACGGCACTA 60.081 41.667 0.00 0.00 0.00 2.74
2331 8924 3.792956 GTGTGTGTTCTTGCTGAAATGTG 59.207 43.478 0.00 0.00 36.30 3.21
2379 8972 0.473694 TCTTGGCTCTGGTTCCTCCA 60.474 55.000 0.00 0.00 45.01 3.86
2412 9005 0.620556 AGGGAAATCACACGAGCCAT 59.379 50.000 0.00 0.00 0.00 4.40
2416 9009 2.159517 GGAAATCACACGAGCCATTCAC 60.160 50.000 0.00 0.00 0.00 3.18
2461 9104 2.457743 TACCTGCCCAAATGACGCGT 62.458 55.000 13.85 13.85 0.00 6.01
2467 9110 1.580893 CCAAATGACGCGTGCATCG 60.581 57.895 20.70 13.80 43.12 3.84
2495 9492 3.118665 GGGTTGGTAGCGTAATCCTGTAA 60.119 47.826 0.00 0.00 0.00 2.41
2520 9517 2.165641 CGTGTTGCTGGACATCTACCTA 59.834 50.000 0.00 0.00 0.00 3.08
2521 9518 3.522553 GTGTTGCTGGACATCTACCTAC 58.477 50.000 0.00 0.00 0.00 3.18
2523 9520 3.195610 TGTTGCTGGACATCTACCTACTG 59.804 47.826 0.00 0.00 0.00 2.74
2524 9521 3.101643 TGCTGGACATCTACCTACTGT 57.898 47.619 0.00 0.00 0.00 3.55
2525 9522 3.441101 TGCTGGACATCTACCTACTGTT 58.559 45.455 0.00 0.00 0.00 3.16
2527 9524 4.401519 TGCTGGACATCTACCTACTGTTAC 59.598 45.833 0.00 0.00 0.00 2.50
2529 9526 5.105473 GCTGGACATCTACCTACTGTTACAA 60.105 44.000 0.00 0.00 0.00 2.41
2531 9528 5.776208 TGGACATCTACCTACTGTTACAACA 59.224 40.000 0.00 0.00 37.37 3.33
2532 9529 6.439375 TGGACATCTACCTACTGTTACAACAT 59.561 38.462 0.00 0.00 38.41 2.71
2533 9530 7.616542 TGGACATCTACCTACTGTTACAACATA 59.383 37.037 0.00 0.00 38.41 2.29
2534 9531 8.639761 GGACATCTACCTACTGTTACAACATAT 58.360 37.037 0.00 0.00 38.41 1.78
2541 9538 8.147244 ACCTACTGTTACAACATATTTCTCCT 57.853 34.615 0.00 0.00 38.41 3.69
2546 9543 9.436957 ACTGTTACAACATATTTCTCCTTAGTG 57.563 33.333 0.00 0.00 38.41 2.74
2547 9544 8.786826 TGTTACAACATATTTCTCCTTAGTGG 57.213 34.615 0.00 0.00 33.17 4.00
2548 9545 8.380099 TGTTACAACATATTTCTCCTTAGTGGT 58.620 33.333 0.00 0.00 33.67 4.16
2550 9547 9.802039 TTACAACATATTTCTCCTTAGTGGTTT 57.198 29.630 0.00 0.00 37.07 3.27
2551 9548 8.706322 ACAACATATTTCTCCTTAGTGGTTTT 57.294 30.769 0.00 0.00 37.07 2.43
2553 9550 7.703058 ACATATTTCTCCTTAGTGGTTTTGG 57.297 36.000 0.00 0.00 37.07 3.28
2554 9551 7.238710 ACATATTTCTCCTTAGTGGTTTTGGT 58.761 34.615 0.00 0.00 37.07 3.67
2556 9553 4.781775 TTCTCCTTAGTGGTTTTGGTGA 57.218 40.909 0.00 0.00 37.07 4.02
2557 9554 4.993705 TCTCCTTAGTGGTTTTGGTGAT 57.006 40.909 0.00 0.00 37.07 3.06
2558 9555 5.319043 TCTCCTTAGTGGTTTTGGTGATT 57.681 39.130 0.00 0.00 37.07 2.57
2560 9557 5.055265 TCCTTAGTGGTTTTGGTGATTGA 57.945 39.130 0.00 0.00 37.07 2.57
2565 9562 2.356382 GTGGTTTTGGTGATTGACGACA 59.644 45.455 0.00 0.00 0.00 4.35
2566 9563 3.017442 TGGTTTTGGTGATTGACGACAA 58.983 40.909 2.18 2.18 40.42 3.18
2568 9565 3.980775 GGTTTTGGTGATTGACGACAATG 59.019 43.478 17.59 0.00 45.30 2.82
2569 9566 2.987413 TTGGTGATTGACGACAATGC 57.013 45.000 17.59 9.86 45.30 3.56
2571 9568 1.075542 GGTGATTGACGACAATGCGA 58.924 50.000 17.59 0.00 45.30 5.10
2572 9569 1.665679 GGTGATTGACGACAATGCGAT 59.334 47.619 17.59 0.00 45.30 4.58
2573 9570 2.095853 GGTGATTGACGACAATGCGATT 59.904 45.455 17.59 0.00 45.30 3.34
2574 9571 3.426159 GGTGATTGACGACAATGCGATTT 60.426 43.478 17.59 0.00 45.30 2.17
2575 9572 4.201773 GGTGATTGACGACAATGCGATTTA 60.202 41.667 17.59 0.00 45.30 1.40
2576 9573 4.723862 GTGATTGACGACAATGCGATTTAC 59.276 41.667 17.59 1.83 45.30 2.01
2577 9574 3.362281 TTGACGACAATGCGATTTACG 57.638 42.857 0.00 0.00 45.66 3.18
2578 9575 1.656594 TGACGACAATGCGATTTACGG 59.343 47.619 4.30 0.00 42.83 4.02
2580 9577 1.657094 ACGACAATGCGATTTACGGAC 59.343 47.619 4.30 0.00 46.19 4.79
2582 9579 3.110358 CGACAATGCGATTTACGGACTA 58.890 45.455 0.00 0.00 46.19 2.59
2583 9580 3.548668 CGACAATGCGATTTACGGACTAA 59.451 43.478 0.00 0.00 46.19 2.24
2584 9581 4.208460 CGACAATGCGATTTACGGACTAAT 59.792 41.667 0.00 0.00 46.19 1.73
2585 9582 5.609696 CGACAATGCGATTTACGGACTAATC 60.610 44.000 0.00 0.00 46.19 1.75
2591 9588 3.061403 CGATTTACGGACTAATCGTGTGC 60.061 47.826 6.33 0.00 44.80 4.57
2594 9591 2.380084 ACGGACTAATCGTGTGCATT 57.620 45.000 0.00 0.00 39.55 3.56
2595 9592 2.268298 ACGGACTAATCGTGTGCATTC 58.732 47.619 0.00 0.00 39.55 2.67
2596 9593 2.267426 CGGACTAATCGTGTGCATTCA 58.733 47.619 0.00 0.00 0.00 2.57
2597 9594 2.282555 CGGACTAATCGTGTGCATTCAG 59.717 50.000 0.00 0.00 0.00 3.02
2598 9595 2.030946 GGACTAATCGTGTGCATTCAGC 59.969 50.000 0.00 0.00 45.96 4.26
2616 9613 8.727910 GCATTCAGCATTTCAGATATTCTATCA 58.272 33.333 0.00 0.00 44.79 2.15
2629 9626 9.715123 CAGATATTCTATCATATGACACGAGAC 57.285 37.037 7.78 0.00 0.00 3.36
2630 9627 8.608317 AGATATTCTATCATATGACACGAGACG 58.392 37.037 7.78 0.00 0.00 4.18
2632 9629 6.803154 TTCTATCATATGACACGAGACGAT 57.197 37.500 7.78 0.00 0.00 3.73
2633 9630 6.803154 TCTATCATATGACACGAGACGATT 57.197 37.500 7.78 0.00 0.00 3.34
2634 9631 7.203255 TCTATCATATGACACGAGACGATTT 57.797 36.000 7.78 0.00 0.00 2.17
2635 9632 8.319143 TCTATCATATGACACGAGACGATTTA 57.681 34.615 7.78 0.00 0.00 1.40
2636 9633 8.947115 TCTATCATATGACACGAGACGATTTAT 58.053 33.333 7.78 0.00 0.00 1.40
2637 9634 9.561270 CTATCATATGACACGAGACGATTTATT 57.439 33.333 7.78 0.00 0.00 1.40
2638 9635 7.853377 TCATATGACACGAGACGATTTATTC 57.147 36.000 0.00 0.00 0.00 1.75
2639 9636 6.861572 TCATATGACACGAGACGATTTATTCC 59.138 38.462 0.00 0.00 0.00 3.01
2641 9638 3.121544 GACACGAGACGATTTATTCCCC 58.878 50.000 0.00 0.00 0.00 4.81
2642 9639 2.764572 ACACGAGACGATTTATTCCCCT 59.235 45.455 0.00 0.00 0.00 4.79
2643 9640 3.181478 ACACGAGACGATTTATTCCCCTC 60.181 47.826 0.00 0.00 0.00 4.30
2644 9641 3.028850 ACGAGACGATTTATTCCCCTCA 58.971 45.455 0.00 0.00 0.00 3.86
2645 9642 3.068307 ACGAGACGATTTATTCCCCTCAG 59.932 47.826 0.00 0.00 0.00 3.35
2646 9643 3.068307 CGAGACGATTTATTCCCCTCAGT 59.932 47.826 0.00 0.00 0.00 3.41
2650 9647 5.839063 AGACGATTTATTCCCCTCAGTGATA 59.161 40.000 0.00 0.00 0.00 2.15
2651 9648 6.498651 AGACGATTTATTCCCCTCAGTGATAT 59.501 38.462 0.00 0.00 0.00 1.63
2652 9649 7.674348 AGACGATTTATTCCCCTCAGTGATATA 59.326 37.037 0.00 0.00 0.00 0.86
2653 9650 8.202461 ACGATTTATTCCCCTCAGTGATATAA 57.798 34.615 0.00 0.00 0.00 0.98
2654 9651 8.656806 ACGATTTATTCCCCTCAGTGATATAAA 58.343 33.333 0.00 1.09 0.00 1.40
2655 9652 9.155975 CGATTTATTCCCCTCAGTGATATAAAG 57.844 37.037 0.00 0.00 0.00 1.85
2657 9654 9.799106 ATTTATTCCCCTCAGTGATATAAAGTG 57.201 33.333 0.00 0.00 0.00 3.16
2658 9655 8.561536 TTATTCCCCTCAGTGATATAAAGTGA 57.438 34.615 0.00 0.00 0.00 3.41
2659 9656 6.884472 TTCCCCTCAGTGATATAAAGTGAA 57.116 37.500 0.00 0.00 0.00 3.18
2660 9657 6.485830 TCCCCTCAGTGATATAAAGTGAAG 57.514 41.667 0.00 0.00 0.00 3.02
2661 9658 6.202331 TCCCCTCAGTGATATAAAGTGAAGA 58.798 40.000 0.00 0.00 0.00 2.87
2663 9660 5.980116 CCCTCAGTGATATAAAGTGAAGACG 59.020 44.000 0.00 0.00 0.00 4.18
2664 9661 6.183360 CCCTCAGTGATATAAAGTGAAGACGA 60.183 42.308 0.00 0.00 0.00 4.20
2666 9663 7.923344 CCTCAGTGATATAAAGTGAAGACGATT 59.077 37.037 0.00 0.00 0.00 3.34
2667 9664 9.307121 CTCAGTGATATAAAGTGAAGACGATTT 57.693 33.333 0.00 0.00 0.00 2.17
2668 9665 9.302345 TCAGTGATATAAAGTGAAGACGATTTC 57.698 33.333 0.00 0.00 0.00 2.17
2669 9666 9.307121 CAGTGATATAAAGTGAAGACGATTTCT 57.693 33.333 0.00 0.00 35.32 2.52
2676 9673 6.451064 AAGTGAAGACGATTTCTTTTTGGT 57.549 33.333 0.00 0.00 45.24 3.67
2677 9674 5.821204 AGTGAAGACGATTTCTTTTTGGTG 58.179 37.500 0.00 0.00 45.24 4.17
2678 9675 5.357032 AGTGAAGACGATTTCTTTTTGGTGT 59.643 36.000 0.00 0.00 45.24 4.16
2679 9676 6.033966 GTGAAGACGATTTCTTTTTGGTGTT 58.966 36.000 0.00 0.00 45.24 3.32
2680 9677 6.530181 GTGAAGACGATTTCTTTTTGGTGTTT 59.470 34.615 0.00 0.00 45.24 2.83
2681 9678 6.750039 TGAAGACGATTTCTTTTTGGTGTTTC 59.250 34.615 0.00 0.00 45.24 2.78
2682 9679 6.451064 AGACGATTTCTTTTTGGTGTTTCT 57.549 33.333 0.00 0.00 0.00 2.52
2683 9680 6.863275 AGACGATTTCTTTTTGGTGTTTCTT 58.137 32.000 0.00 0.00 0.00 2.52
2686 9683 8.317891 ACGATTTCTTTTTGGTGTTTCTTTTT 57.682 26.923 0.00 0.00 0.00 1.94
2687 9684 8.440059 ACGATTTCTTTTTGGTGTTTCTTTTTC 58.560 29.630 0.00 0.00 0.00 2.29
2688 9685 8.439286 CGATTTCTTTTTGGTGTTTCTTTTTCA 58.561 29.630 0.00 0.00 0.00 2.69
2690 9687 8.669946 TTTCTTTTTGGTGTTTCTTTTTCAGT 57.330 26.923 0.00 0.00 0.00 3.41
2692 9689 6.648725 TCTTTTTGGTGTTTCTTTTTCAGTGG 59.351 34.615 0.00 0.00 0.00 4.00
2694 9691 5.730296 TTGGTGTTTCTTTTTCAGTGGAA 57.270 34.783 0.00 0.00 0.00 3.53
2695 9692 5.930837 TGGTGTTTCTTTTTCAGTGGAAT 57.069 34.783 0.00 0.00 31.93 3.01
2696 9693 6.293004 TGGTGTTTCTTTTTCAGTGGAATT 57.707 33.333 0.00 0.00 31.93 2.17
2698 9695 6.071108 TGGTGTTTCTTTTTCAGTGGAATTGA 60.071 34.615 0.00 0.00 31.93 2.57
2699 9696 6.816140 GGTGTTTCTTTTTCAGTGGAATTGAA 59.184 34.615 0.00 0.00 41.04 2.69
2700 9697 7.495606 GGTGTTTCTTTTTCAGTGGAATTGAAT 59.504 33.333 0.00 0.00 42.34 2.57
2701 9698 8.542953 GTGTTTCTTTTTCAGTGGAATTGAATC 58.457 33.333 0.00 0.00 42.34 2.52
2702 9699 8.256605 TGTTTCTTTTTCAGTGGAATTGAATCA 58.743 29.630 0.00 0.00 42.34 2.57
2703 9700 9.264719 GTTTCTTTTTCAGTGGAATTGAATCAT 57.735 29.630 0.00 0.00 42.34 2.45
2706 9703 8.742777 TCTTTTTCAGTGGAATTGAATCATAGG 58.257 33.333 0.00 0.00 42.34 2.57
2707 9704 8.648698 TTTTTCAGTGGAATTGAATCATAGGA 57.351 30.769 0.00 0.00 42.34 2.94
2708 9705 8.648698 TTTTCAGTGGAATTGAATCATAGGAA 57.351 30.769 0.00 0.00 42.34 3.36
2709 9706 8.648698 TTTCAGTGGAATTGAATCATAGGAAA 57.351 30.769 0.00 0.00 42.34 3.13
2710 9707 8.648698 TTCAGTGGAATTGAATCATAGGAAAA 57.351 30.769 0.00 0.00 37.66 2.29
2711 9708 8.055279 TCAGTGGAATTGAATCATAGGAAAAC 57.945 34.615 0.00 0.00 25.66 2.43
2712 9709 7.122650 TCAGTGGAATTGAATCATAGGAAAACC 59.877 37.037 0.00 0.00 25.66 3.27
2713 9710 6.095440 AGTGGAATTGAATCATAGGAAAACCG 59.905 38.462 0.00 0.00 0.00 4.44
2714 9711 5.949354 TGGAATTGAATCATAGGAAAACCGT 59.051 36.000 0.00 0.00 0.00 4.83
2715 9712 7.066525 GTGGAATTGAATCATAGGAAAACCGTA 59.933 37.037 0.00 0.00 0.00 4.02
2716 9713 7.066525 TGGAATTGAATCATAGGAAAACCGTAC 59.933 37.037 0.00 0.00 0.00 3.67
2717 9714 7.282450 GGAATTGAATCATAGGAAAACCGTACT 59.718 37.037 0.00 0.00 0.00 2.73
2718 9715 9.321562 GAATTGAATCATAGGAAAACCGTACTA 57.678 33.333 0.00 0.00 0.00 1.82
2719 9716 9.847224 AATTGAATCATAGGAAAACCGTACTAT 57.153 29.630 0.00 0.00 0.00 2.12
2720 9717 9.847224 ATTGAATCATAGGAAAACCGTACTATT 57.153 29.630 0.00 0.00 0.00 1.73
2726 9723 8.636213 TCATAGGAAAACCGTACTATTAAGAGG 58.364 37.037 1.59 0.00 0.00 3.69
2727 9724 6.231258 AGGAAAACCGTACTATTAAGAGGG 57.769 41.667 1.59 0.00 0.00 4.30
2728 9725 5.129980 AGGAAAACCGTACTATTAAGAGGGG 59.870 44.000 1.59 2.69 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.726912 GGACGCACGAACGAACGA 60.727 61.111 16.45 0.00 36.70 3.85
1 2 4.099585 CGGACGCACGAACGAACG 62.100 66.667 8.71 6.65 36.70 3.95
2 3 3.026311 ACGGACGCACGAACGAAC 61.026 61.111 15.27 2.99 37.61 3.95
66 67 2.094099 CACCACACAGCTTTTTGCAAAC 59.906 45.455 12.39 0.16 45.94 2.93
70 71 1.481819 CGCACCACACAGCTTTTTGC 61.482 55.000 0.00 0.00 43.29 3.68
71 72 0.100325 TCGCACCACACAGCTTTTTG 59.900 50.000 0.00 0.00 0.00 2.44
72 73 0.100503 GTCGCACCACACAGCTTTTT 59.899 50.000 0.00 0.00 0.00 1.94
177 182 2.733671 CGTCCGTCTCGCTCGTACA 61.734 63.158 0.00 0.00 0.00 2.90
178 183 2.021106 CGTCCGTCTCGCTCGTAC 59.979 66.667 0.00 0.00 0.00 3.67
179 184 3.190849 CCGTCCGTCTCGCTCGTA 61.191 66.667 0.00 0.00 0.00 3.43
255 270 3.506096 CATGCCGCTGGAGTGCTG 61.506 66.667 0.00 0.00 0.00 4.41
256 271 4.025858 ACATGCCGCTGGAGTGCT 62.026 61.111 0.00 0.00 0.00 4.40
257 272 3.807538 CACATGCCGCTGGAGTGC 61.808 66.667 0.00 0.00 0.00 4.40
258 273 3.129502 CCACATGCCGCTGGAGTG 61.130 66.667 0.00 4.20 0.00 3.51
261 276 4.429522 ATGCCACATGCCGCTGGA 62.430 61.111 4.31 0.00 40.16 3.86
262 277 4.201679 CATGCCACATGCCGCTGG 62.202 66.667 6.21 1.25 40.16 4.85
263 278 3.445687 ACATGCCACATGCCGCTG 61.446 61.111 7.46 4.89 40.16 5.18
280 295 0.464554 TGATGGTGTGTTTCGTGCCA 60.465 50.000 0.00 0.00 0.00 4.92
281 296 0.881118 ATGATGGTGTGTTTCGTGCC 59.119 50.000 0.00 0.00 0.00 5.01
283 298 3.299162 CACAATGATGGTGTGTTTCGTG 58.701 45.455 0.00 0.00 41.22 4.35
284 299 2.287547 GCACAATGATGGTGTGTTTCGT 60.288 45.455 1.36 0.00 46.58 3.85
285 300 2.287487 TGCACAATGATGGTGTGTTTCG 60.287 45.455 1.36 0.00 46.58 3.46
286 301 3.052036 GTGCACAATGATGGTGTGTTTC 58.948 45.455 13.17 0.00 46.58 2.78
289 304 0.961019 GGTGCACAATGATGGTGTGT 59.039 50.000 20.43 0.00 46.58 3.72
291 306 1.865788 GCGGTGCACAATGATGGTGT 61.866 55.000 20.43 0.00 38.51 4.16
292 307 1.153978 GCGGTGCACAATGATGGTG 60.154 57.895 20.43 0.00 39.25 4.17
293 308 1.588824 CTGCGGTGCACAATGATGGT 61.589 55.000 20.43 0.00 33.79 3.55
326 362 1.517257 GCACGTCGCTGCTACTCAT 60.517 57.895 11.08 0.00 37.77 2.90
346 2254 2.106683 CCCCACTTTTCGCTAGCCG 61.107 63.158 9.66 4.62 38.61 5.52
349 2257 0.734889 CATGCCCCACTTTTCGCTAG 59.265 55.000 0.00 0.00 0.00 3.42
499 2644 3.992641 TCTCCAGACCAGGCCCGA 61.993 66.667 0.00 0.00 0.00 5.14
514 2659 2.048222 CGTGTGCGTCCATGGTCT 60.048 61.111 12.58 0.00 0.00 3.85
529 2674 4.778415 CAGCTCAGGCGTACGCGT 62.778 66.667 31.78 29.95 44.37 6.01
532 2677 0.523546 CTACACAGCTCAGGCGTACG 60.524 60.000 11.84 11.84 44.37 3.67
533 2678 0.809385 TCTACACAGCTCAGGCGTAC 59.191 55.000 0.00 0.00 44.37 3.67
534 2679 1.405463 CATCTACACAGCTCAGGCGTA 59.595 52.381 0.00 0.00 44.37 4.42
535 2680 0.174389 CATCTACACAGCTCAGGCGT 59.826 55.000 0.00 0.00 44.37 5.68
538 2683 2.625737 CAACCATCTACACAGCTCAGG 58.374 52.381 0.00 0.00 0.00 3.86
540 2685 1.339055 GCCAACCATCTACACAGCTCA 60.339 52.381 0.00 0.00 0.00 4.26
541 2686 1.065854 AGCCAACCATCTACACAGCTC 60.066 52.381 0.00 0.00 0.00 4.09
543 2688 1.373570 GAGCCAACCATCTACACAGC 58.626 55.000 0.00 0.00 0.00 4.40
544 2689 1.278985 TGGAGCCAACCATCTACACAG 59.721 52.381 0.00 0.00 34.77 3.66
551 2696 1.817099 CGAGCTGGAGCCAACCATC 60.817 63.158 0.00 0.00 43.38 3.51
584 2751 2.046314 CATGTCCCGGTGTCACCC 60.046 66.667 16.60 2.76 33.75 4.61
585 2752 2.746277 GCATGTCCCGGTGTCACC 60.746 66.667 12.40 12.40 34.05 4.02
586 2753 2.746277 GGCATGTCCCGGTGTCAC 60.746 66.667 0.00 0.00 0.00 3.67
587 2754 4.386951 CGGCATGTCCCGGTGTCA 62.387 66.667 0.00 0.00 44.46 3.58
720 5397 2.898472 AATAGGGGAGCGAGGCAGGT 62.898 60.000 0.00 0.00 0.00 4.00
736 5418 1.356398 GGTGTTGAGGGGGTTGGAATA 59.644 52.381 0.00 0.00 0.00 1.75
742 5424 0.185175 GTTGAGGTGTTGAGGGGGTT 59.815 55.000 0.00 0.00 0.00 4.11
745 5427 1.545651 GGAAGTTGAGGTGTTGAGGGG 60.546 57.143 0.00 0.00 0.00 4.79
749 5431 2.158667 GGAAGGGAAGTTGAGGTGTTGA 60.159 50.000 0.00 0.00 0.00 3.18
757 5439 1.477923 CGGTTTGGGAAGGGAAGTTGA 60.478 52.381 0.00 0.00 0.00 3.18
760 5442 1.228459 GCGGTTTGGGAAGGGAAGT 60.228 57.895 0.00 0.00 0.00 3.01
798 5488 2.938428 ACAGGAGGATGAGGAAGAGT 57.062 50.000 0.00 0.00 0.00 3.24
800 5490 4.229812 TGTAGTACAGGAGGATGAGGAAGA 59.770 45.833 0.00 0.00 0.00 2.87
801 5491 4.339814 GTGTAGTACAGGAGGATGAGGAAG 59.660 50.000 2.39 0.00 0.00 3.46
802 5492 4.017407 AGTGTAGTACAGGAGGATGAGGAA 60.017 45.833 2.39 0.00 0.00 3.36
808 5498 2.299521 GCGAGTGTAGTACAGGAGGAT 58.700 52.381 2.39 0.00 0.00 3.24
938 5732 1.829533 TAACTAGTAGGCCGGCCCG 60.830 63.158 41.72 25.45 39.21 6.13
939 5733 0.758310 AGTAACTAGTAGGCCGGCCC 60.758 60.000 41.72 27.43 36.58 5.80
940 5734 1.611006 GTAGTAACTAGTAGGCCGGCC 59.389 57.143 39.29 39.29 0.00 6.13
941 5735 2.033927 GTGTAGTAACTAGTAGGCCGGC 59.966 54.545 21.18 21.18 0.00 6.13
942 5736 2.620585 GGTGTAGTAACTAGTAGGCCGG 59.379 54.545 0.00 0.00 0.00 6.13
943 5737 2.289002 CGGTGTAGTAACTAGTAGGCCG 59.711 54.545 0.00 0.38 0.00 6.13
944 5738 3.313803 GTCGGTGTAGTAACTAGTAGGCC 59.686 52.174 0.00 0.00 0.00 5.19
945 5739 3.001736 CGTCGGTGTAGTAACTAGTAGGC 59.998 52.174 0.00 0.00 0.00 3.93
946 5740 3.001736 GCGTCGGTGTAGTAACTAGTAGG 59.998 52.174 0.00 0.00 0.00 3.18
947 5741 3.001736 GGCGTCGGTGTAGTAACTAGTAG 59.998 52.174 0.00 0.00 0.00 2.57
948 5742 2.936498 GGCGTCGGTGTAGTAACTAGTA 59.064 50.000 0.00 0.00 0.00 1.82
949 5743 1.740025 GGCGTCGGTGTAGTAACTAGT 59.260 52.381 0.00 0.00 0.00 2.57
950 5744 1.267732 CGGCGTCGGTGTAGTAACTAG 60.268 57.143 0.00 0.00 0.00 2.57
951 5745 0.726827 CGGCGTCGGTGTAGTAACTA 59.273 55.000 0.00 0.00 0.00 2.24
952 5746 1.503542 CGGCGTCGGTGTAGTAACT 59.496 57.895 0.00 0.00 0.00 2.24
953 5747 2.154569 GCGGCGTCGGTGTAGTAAC 61.155 63.158 13.05 0.00 36.79 2.50
954 5748 2.179018 GCGGCGTCGGTGTAGTAA 59.821 61.111 13.05 0.00 36.79 2.24
955 5749 3.814268 GGCGGCGTCGGTGTAGTA 61.814 66.667 13.05 0.00 36.79 1.82
985 5779 0.322816 GGCATGGAGGAGAAGTGCAA 60.323 55.000 0.00 0.00 37.53 4.08
1003 5797 1.855360 GTACTCGTACTCGTACTCGGG 59.145 57.143 11.91 0.00 43.99 5.14
1038 5832 2.442458 GAGGACGGGGAGGAGACC 60.442 72.222 0.00 0.00 0.00 3.85
1325 6180 0.606401 CACCATGAGCCGGAAGTTGT 60.606 55.000 5.05 0.00 0.00 3.32
1538 6627 4.063967 CCAGCGTCGGGTAGCACA 62.064 66.667 0.00 0.00 35.48 4.57
1617 6715 2.172900 AGGGTTCCTGGCAAATGGA 58.827 52.632 0.00 0.00 29.57 3.41
1713 6817 8.195436 GTGTTGGTGAACTAGTATCTGCTTATA 58.805 37.037 0.00 0.00 32.79 0.98
1723 6828 4.023450 CGAGTCTGTGTTGGTGAACTAGTA 60.023 45.833 0.00 0.00 32.79 1.82
1724 6829 3.243434 CGAGTCTGTGTTGGTGAACTAGT 60.243 47.826 0.00 0.00 32.79 2.57
1725 6830 3.004419 TCGAGTCTGTGTTGGTGAACTAG 59.996 47.826 0.00 0.00 32.79 2.57
1746 7261 4.820897 TGTCTGAGATAATGTGTGGTGTC 58.179 43.478 0.00 0.00 0.00 3.67
1867 7694 4.222588 CCTTCATCCAAACAAAGGCCAATA 59.777 41.667 5.01 0.00 32.50 1.90
1931 7761 3.367910 GGTTTTGCTTGCCGATGGATTTA 60.368 43.478 0.00 0.00 0.00 1.40
1932 7762 2.612721 GGTTTTGCTTGCCGATGGATTT 60.613 45.455 0.00 0.00 0.00 2.17
1968 7799 6.530019 TGAGGTTTTGCTCTTCTTCTTTTT 57.470 33.333 0.00 0.00 0.00 1.94
1969 7800 6.071391 TGTTGAGGTTTTGCTCTTCTTCTTTT 60.071 34.615 0.00 0.00 0.00 2.27
2013 7844 5.151454 AGCCTAGGATTACACTAGCAAGAT 58.849 41.667 14.75 0.00 37.25 2.40
2018 7849 4.939052 TTGAGCCTAGGATTACACTAGC 57.061 45.455 14.75 0.00 37.25 3.42
2019 7850 6.640518 TGTTTTGAGCCTAGGATTACACTAG 58.359 40.000 14.75 0.00 38.09 2.57
2020 7851 6.614694 TGTTTTGAGCCTAGGATTACACTA 57.385 37.500 14.75 0.00 0.00 2.74
2025 7856 6.430000 GTCTGTTTGTTTTGAGCCTAGGATTA 59.570 38.462 14.75 0.00 0.00 1.75
2077 7946 3.857157 ACAACACCTGGCTTTTCTCTA 57.143 42.857 0.00 0.00 0.00 2.43
2086 7955 3.334583 TGAATCTCTACAACACCTGGC 57.665 47.619 0.00 0.00 0.00 4.85
2087 7956 6.430925 TCAAATTGAATCTCTACAACACCTGG 59.569 38.462 0.00 0.00 0.00 4.45
2090 7959 7.965107 GTGATCAAATTGAATCTCTACAACACC 59.035 37.037 0.00 0.00 0.00 4.16
2204 8796 3.243201 GCATTGCCGAATCTCTAAAAGGG 60.243 47.826 0.00 0.00 0.00 3.95
2224 8816 3.443099 AGATCTGAATCATTCGACGCA 57.557 42.857 0.00 0.00 34.07 5.24
2233 8825 6.295745 GCCTCCATATCTGAAGATCTGAATCA 60.296 42.308 0.00 0.00 36.05 2.57
2263 8856 3.627395 AGTGCCGTGAATCTGGATAAA 57.373 42.857 0.00 0.00 0.00 1.40
2272 8865 2.038557 ACACCTTCTTAGTGCCGTGAAT 59.961 45.455 0.00 0.00 38.87 2.57
2277 8870 4.117685 GGTATTACACCTTCTTAGTGCCG 58.882 47.826 0.00 0.00 44.79 5.69
2331 8924 7.088589 AGGAACAATCTTATAACATGCACAC 57.911 36.000 0.00 0.00 0.00 3.82
2379 8972 9.125026 GTGTGATTTCCCTTGACAGAATATAAT 57.875 33.333 0.00 0.00 0.00 1.28
2412 9005 4.211920 AGATCGGTTTGGGAAAAAGTGAA 58.788 39.130 0.00 0.00 0.00 3.18
2416 9009 3.421844 AGGAGATCGGTTTGGGAAAAAG 58.578 45.455 0.00 0.00 0.00 2.27
2467 9110 2.187896 TACGCTACCAACCCTTGCCC 62.188 60.000 0.00 0.00 0.00 5.36
2475 9118 5.233689 GTCATTACAGGATTACGCTACCAAC 59.766 44.000 0.00 0.00 0.00 3.77
2495 9492 1.002430 AGATGTCCAGCAACACGTCAT 59.998 47.619 0.00 0.00 31.86 3.06
2520 9517 9.436957 CACTAAGGAGAAATATGTTGTAACAGT 57.563 33.333 3.66 0.00 43.04 3.55
2521 9518 8.883731 CCACTAAGGAGAAATATGTTGTAACAG 58.116 37.037 3.66 0.00 40.52 3.16
2523 9520 8.788325 ACCACTAAGGAGAAATATGTTGTAAC 57.212 34.615 0.00 0.00 41.22 2.50
2524 9521 9.802039 AAACCACTAAGGAGAAATATGTTGTAA 57.198 29.630 0.00 0.00 41.22 2.41
2525 9522 9.802039 AAAACCACTAAGGAGAAATATGTTGTA 57.198 29.630 0.00 0.00 41.22 2.41
2527 9524 8.028938 CCAAAACCACTAAGGAGAAATATGTTG 58.971 37.037 0.00 0.00 41.22 3.33
2529 9526 7.176690 CACCAAAACCACTAAGGAGAAATATGT 59.823 37.037 0.00 0.00 41.22 2.29
2531 9528 7.466804 TCACCAAAACCACTAAGGAGAAATAT 58.533 34.615 0.00 0.00 41.22 1.28
2532 9529 6.843752 TCACCAAAACCACTAAGGAGAAATA 58.156 36.000 0.00 0.00 41.22 1.40
2533 9530 5.701224 TCACCAAAACCACTAAGGAGAAAT 58.299 37.500 0.00 0.00 41.22 2.17
2534 9531 5.118729 TCACCAAAACCACTAAGGAGAAA 57.881 39.130 0.00 0.00 41.22 2.52
2536 9533 4.993705 ATCACCAAAACCACTAAGGAGA 57.006 40.909 0.00 0.00 41.22 3.71
2537 9534 5.048713 GTCAATCACCAAAACCACTAAGGAG 60.049 44.000 0.00 0.00 41.22 3.69
2539 9536 4.320202 CGTCAATCACCAAAACCACTAAGG 60.320 45.833 0.00 0.00 45.67 2.69
2541 9538 4.273969 GTCGTCAATCACCAAAACCACTAA 59.726 41.667 0.00 0.00 0.00 2.24
2543 9540 2.616842 GTCGTCAATCACCAAAACCACT 59.383 45.455 0.00 0.00 0.00 4.00
2544 9541 2.356382 TGTCGTCAATCACCAAAACCAC 59.644 45.455 0.00 0.00 0.00 4.16
2545 9542 2.644676 TGTCGTCAATCACCAAAACCA 58.355 42.857 0.00 0.00 0.00 3.67
2546 9543 3.701532 TTGTCGTCAATCACCAAAACC 57.298 42.857 0.00 0.00 0.00 3.27
2547 9544 3.425193 GCATTGTCGTCAATCACCAAAAC 59.575 43.478 4.86 0.00 41.66 2.43
2548 9545 3.637432 GCATTGTCGTCAATCACCAAAA 58.363 40.909 4.86 0.00 41.66 2.44
2550 9547 1.196581 CGCATTGTCGTCAATCACCAA 59.803 47.619 4.86 0.00 41.66 3.67
2551 9548 0.795698 CGCATTGTCGTCAATCACCA 59.204 50.000 4.86 0.00 41.66 4.17
2553 9550 3.389687 AATCGCATTGTCGTCAATCAC 57.610 42.857 4.86 0.64 41.66 3.06
2554 9551 4.491763 CGTAAATCGCATTGTCGTCAATCA 60.492 41.667 4.86 0.00 41.66 2.57
2556 9553 3.242284 CCGTAAATCGCATTGTCGTCAAT 60.242 43.478 1.85 1.85 39.42 2.57
2557 9554 2.092995 CCGTAAATCGCATTGTCGTCAA 59.907 45.455 0.00 0.00 38.35 3.18
2558 9555 1.656594 CCGTAAATCGCATTGTCGTCA 59.343 47.619 0.00 0.00 38.35 4.35
2560 9557 1.657094 GTCCGTAAATCGCATTGTCGT 59.343 47.619 0.00 0.00 38.35 4.34
2565 9562 4.966850 CGATTAGTCCGTAAATCGCATT 57.033 40.909 4.73 0.00 45.33 3.56
2571 9568 3.852286 TGCACACGATTAGTCCGTAAAT 58.148 40.909 0.00 0.00 38.29 1.40
2572 9569 3.300852 TGCACACGATTAGTCCGTAAA 57.699 42.857 0.00 0.00 38.29 2.01
2573 9570 3.513680 ATGCACACGATTAGTCCGTAA 57.486 42.857 0.00 0.00 38.29 3.18
2574 9571 3.119424 TGAATGCACACGATTAGTCCGTA 60.119 43.478 0.00 0.00 38.29 4.02
2575 9572 2.268298 GAATGCACACGATTAGTCCGT 58.732 47.619 0.00 0.00 41.36 4.69
2576 9573 2.267426 TGAATGCACACGATTAGTCCG 58.733 47.619 0.00 0.00 0.00 4.79
2577 9574 2.030946 GCTGAATGCACACGATTAGTCC 59.969 50.000 0.00 0.00 42.31 3.85
2578 9575 3.310303 GCTGAATGCACACGATTAGTC 57.690 47.619 0.00 0.00 42.31 2.59
2602 9599 9.672673 TCTCGTGTCATATGATAGAATATCTGA 57.327 33.333 9.02 0.00 0.00 3.27
2603 9600 9.715123 GTCTCGTGTCATATGATAGAATATCTG 57.285 37.037 9.02 0.00 0.00 2.90
2604 9601 8.608317 CGTCTCGTGTCATATGATAGAATATCT 58.392 37.037 9.02 0.00 0.00 1.98
2605 9602 8.604890 TCGTCTCGTGTCATATGATAGAATATC 58.395 37.037 9.02 0.00 0.00 1.63
2606 9603 8.494016 TCGTCTCGTGTCATATGATAGAATAT 57.506 34.615 9.02 0.00 0.00 1.28
2607 9604 7.900782 TCGTCTCGTGTCATATGATAGAATA 57.099 36.000 9.02 0.28 0.00 1.75
2608 9605 6.803154 TCGTCTCGTGTCATATGATAGAAT 57.197 37.500 9.02 0.00 0.00 2.40
2610 9607 6.803154 AATCGTCTCGTGTCATATGATAGA 57.197 37.500 9.02 7.94 0.00 1.98
2612 9609 9.556030 GAATAAATCGTCTCGTGTCATATGATA 57.444 33.333 9.02 2.88 0.00 2.15
2613 9610 7.542477 GGAATAAATCGTCTCGTGTCATATGAT 59.458 37.037 9.02 0.00 0.00 2.45
2614 9611 6.861572 GGAATAAATCGTCTCGTGTCATATGA 59.138 38.462 0.00 0.00 0.00 2.15
2616 9613 6.157211 GGGAATAAATCGTCTCGTGTCATAT 58.843 40.000 0.00 0.00 0.00 1.78
2617 9614 5.508489 GGGGAATAAATCGTCTCGTGTCATA 60.508 44.000 0.00 0.00 0.00 2.15
2618 9615 4.369182 GGGAATAAATCGTCTCGTGTCAT 58.631 43.478 0.00 0.00 0.00 3.06
2620 9617 3.121544 GGGGAATAAATCGTCTCGTGTC 58.878 50.000 0.00 0.00 0.00 3.67
2621 9618 2.764572 AGGGGAATAAATCGTCTCGTGT 59.235 45.455 0.00 0.00 0.00 4.49
2622 9619 3.181479 TGAGGGGAATAAATCGTCTCGTG 60.181 47.826 0.00 0.00 33.26 4.35
2623 9620 3.028850 TGAGGGGAATAAATCGTCTCGT 58.971 45.455 0.00 0.00 33.26 4.18
2624 9621 3.068307 ACTGAGGGGAATAAATCGTCTCG 59.932 47.826 0.00 0.00 33.26 4.04
2626 9623 4.030913 TCACTGAGGGGAATAAATCGTCT 58.969 43.478 0.00 0.00 0.00 4.18
2627 9624 4.402056 TCACTGAGGGGAATAAATCGTC 57.598 45.455 0.00 0.00 0.00 4.20
2629 9626 9.155975 CTTTATATCACTGAGGGGAATAAATCG 57.844 37.037 3.87 0.00 0.00 3.34
2632 9629 8.998814 TCACTTTATATCACTGAGGGGAATAAA 58.001 33.333 3.53 3.53 0.00 1.40
2633 9630 8.561536 TCACTTTATATCACTGAGGGGAATAA 57.438 34.615 0.00 0.00 0.00 1.40
2634 9631 8.561536 TTCACTTTATATCACTGAGGGGAATA 57.438 34.615 0.00 0.00 0.00 1.75
2635 9632 7.348274 TCTTCACTTTATATCACTGAGGGGAAT 59.652 37.037 0.00 0.00 0.00 3.01
2636 9633 6.672218 TCTTCACTTTATATCACTGAGGGGAA 59.328 38.462 0.00 0.00 0.00 3.97
2637 9634 6.098409 GTCTTCACTTTATATCACTGAGGGGA 59.902 42.308 0.00 0.00 0.00 4.81
2638 9635 6.284459 GTCTTCACTTTATATCACTGAGGGG 58.716 44.000 0.00 0.00 0.00 4.79
2639 9636 5.980116 CGTCTTCACTTTATATCACTGAGGG 59.020 44.000 0.00 0.00 0.00 4.30
2641 9638 8.864069 AATCGTCTTCACTTTATATCACTGAG 57.136 34.615 0.00 0.00 0.00 3.35
2642 9639 9.302345 GAAATCGTCTTCACTTTATATCACTGA 57.698 33.333 0.00 0.00 0.00 3.41
2643 9640 9.307121 AGAAATCGTCTTCACTTTATATCACTG 57.693 33.333 2.86 0.00 29.66 3.66
2644 9641 9.877178 AAGAAATCGTCTTCACTTTATATCACT 57.123 29.630 2.86 0.00 43.49 3.41
2650 9647 8.630037 ACCAAAAAGAAATCGTCTTCACTTTAT 58.370 29.630 0.00 0.00 46.36 1.40
2651 9648 7.913297 CACCAAAAAGAAATCGTCTTCACTTTA 59.087 33.333 0.00 0.00 46.36 1.85
2652 9649 6.751888 CACCAAAAAGAAATCGTCTTCACTTT 59.248 34.615 0.00 0.00 46.36 2.66
2653 9650 6.127730 ACACCAAAAAGAAATCGTCTTCACTT 60.128 34.615 2.86 0.00 46.36 3.16
2654 9651 5.357032 ACACCAAAAAGAAATCGTCTTCACT 59.643 36.000 2.86 0.00 46.36 3.41
2655 9652 5.578776 ACACCAAAAAGAAATCGTCTTCAC 58.421 37.500 2.86 0.00 46.36 3.18
2657 9654 6.972901 AGAAACACCAAAAAGAAATCGTCTTC 59.027 34.615 0.00 0.00 46.36 2.87
2659 9656 6.451064 AGAAACACCAAAAAGAAATCGTCT 57.549 33.333 0.00 0.00 38.69 4.18
2660 9657 7.520119 AAAGAAACACCAAAAAGAAATCGTC 57.480 32.000 0.00 0.00 0.00 4.20
2661 9658 7.899178 AAAAGAAACACCAAAAAGAAATCGT 57.101 28.000 0.00 0.00 0.00 3.73
2663 9660 9.759259 CTGAAAAAGAAACACCAAAAAGAAATC 57.241 29.630 0.00 0.00 0.00 2.17
2664 9661 9.283768 ACTGAAAAAGAAACACCAAAAAGAAAT 57.716 25.926 0.00 0.00 0.00 2.17
2666 9663 7.172361 CCACTGAAAAAGAAACACCAAAAAGAA 59.828 33.333 0.00 0.00 0.00 2.52
2667 9664 6.648725 CCACTGAAAAAGAAACACCAAAAAGA 59.351 34.615 0.00 0.00 0.00 2.52
2668 9665 6.648725 TCCACTGAAAAAGAAACACCAAAAAG 59.351 34.615 0.00 0.00 0.00 2.27
2669 9666 6.525629 TCCACTGAAAAAGAAACACCAAAAA 58.474 32.000 0.00 0.00 0.00 1.94
2670 9667 6.102897 TCCACTGAAAAAGAAACACCAAAA 57.897 33.333 0.00 0.00 0.00 2.44
2671 9668 5.730296 TCCACTGAAAAAGAAACACCAAA 57.270 34.783 0.00 0.00 0.00 3.28
2672 9669 5.730296 TTCCACTGAAAAAGAAACACCAA 57.270 34.783 0.00 0.00 0.00 3.67
2673 9670 5.930837 ATTCCACTGAAAAAGAAACACCA 57.069 34.783 0.00 0.00 33.32 4.17
2674 9671 6.337356 TCAATTCCACTGAAAAAGAAACACC 58.663 36.000 0.00 0.00 33.32 4.16
2676 9673 8.256605 TGATTCAATTCCACTGAAAAAGAAACA 58.743 29.630 0.00 0.00 36.43 2.83
2677 9674 8.647143 TGATTCAATTCCACTGAAAAAGAAAC 57.353 30.769 0.00 0.00 36.43 2.78
2680 9677 8.742777 CCTATGATTCAATTCCACTGAAAAAGA 58.257 33.333 0.00 0.00 36.43 2.52
2681 9678 8.742777 TCCTATGATTCAATTCCACTGAAAAAG 58.257 33.333 0.00 0.00 36.43 2.27
2682 9679 8.648698 TCCTATGATTCAATTCCACTGAAAAA 57.351 30.769 0.00 0.00 36.43 1.94
2683 9680 8.648698 TTCCTATGATTCAATTCCACTGAAAA 57.351 30.769 0.00 0.00 36.43 2.29
2686 9683 7.122650 GGTTTTCCTATGATTCAATTCCACTGA 59.877 37.037 0.00 0.00 36.94 3.41
2687 9684 7.260603 GGTTTTCCTATGATTCAATTCCACTG 58.739 38.462 0.00 0.00 36.94 3.66
2688 9685 6.095440 CGGTTTTCCTATGATTCAATTCCACT 59.905 38.462 0.00 0.00 37.95 4.00
2690 9687 5.949354 ACGGTTTTCCTATGATTCAATTCCA 59.051 36.000 0.00 0.00 37.95 3.53
2692 9689 8.209917 AGTACGGTTTTCCTATGATTCAATTC 57.790 34.615 0.00 0.00 37.95 2.17
2694 9691 9.847224 AATAGTACGGTTTTCCTATGATTCAAT 57.153 29.630 0.00 0.00 37.95 2.57
2700 9697 8.636213 CCTCTTAATAGTACGGTTTTCCTATGA 58.364 37.037 0.00 0.00 37.95 2.15
2701 9698 7.871463 CCCTCTTAATAGTACGGTTTTCCTATG 59.129 40.741 0.00 0.00 37.95 2.23
2702 9699 7.015974 CCCCTCTTAATAGTACGGTTTTCCTAT 59.984 40.741 0.00 0.00 37.95 2.57
2703 9700 6.324770 CCCCTCTTAATAGTACGGTTTTCCTA 59.675 42.308 0.00 0.00 37.95 2.94
2704 9701 5.129980 CCCCTCTTAATAGTACGGTTTTCCT 59.870 44.000 0.00 0.00 37.95 3.36
2705 9702 5.363101 CCCCTCTTAATAGTACGGTTTTCC 58.637 45.833 0.00 0.00 0.00 3.13


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

AutoCloner maintained by Alex Coulton.