Multiple sequence alignment - TraesCS4A01G009300

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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 TraesCS4A01G009300 chr4A 100.000 2844 0 0 1 2844 5553722 5550879 0.000000e+00 5252.0
1 TraesCS4A01G009300 chr4B 91.230 1756 104 21 9 1743 581067756 581069482 0.000000e+00 2344.0
2 TraesCS4A01G009300 chr4B 94.460 704 33 3 1810 2513 581082216 581082913 0.000000e+00 1079.0
3 TraesCS4A01G009300 chr4B 94.400 250 9 4 1580 1825 581080695 581080943 2.070000e-101 379.0
4 TraesCS4A01G009300 chr4D 87.242 1693 101 31 1 1651 464659370 464660989 0.000000e+00 1823.0
5 TraesCS4A01G009300 chr4D 95.500 400 17 1 2114 2513 464672736 464673134 3.090000e-179 638.0
6 TraesCS4A01G009300 chr4D 89.426 331 33 2 2515 2844 505190219 505190548 1.580000e-112 416.0
7 TraesCS4A01G009300 chr2D 90.937 331 28 2 2515 2844 466686034 466686363 7.230000e-121 444.0
8 TraesCS4A01G009300 chr2D 77.751 418 53 22 1184 1569 544610578 544610987 1.330000e-53 220.0
9 TraesCS4A01G009300 chr7D 90.634 331 29 2 2515 2844 26612431 26612760 3.360000e-119 438.0
10 TraesCS4A01G009300 chr6A 89.881 336 31 3 2511 2844 33289465 33289131 2.020000e-116 429.0
11 TraesCS4A01G009300 chr6A 84.737 190 18 7 1155 1338 503769157 503769341 2.250000e-41 180.0
12 TraesCS4A01G009300 chr6D 90.030 331 31 2 2515 2844 16681973 16681644 7.280000e-116 427.0
13 TraesCS4A01G009300 chr6D 79.286 280 45 9 1191 1465 363063888 363064159 1.740000e-42 183.0
14 TraesCS4A01G009300 chr5D 87.915 331 38 2 2515 2844 430538959 430539288 3.440000e-104 388.0
15 TraesCS4A01G009300 chr3A 86.747 332 42 2 2515 2844 67315864 67316195 4.480000e-98 368.0
16 TraesCS4A01G009300 chr3A 86.018 329 43 3 2518 2844 629175104 629175431 1.620000e-92 350.0
17 TraesCS4A01G009300 chr3A 85.498 331 45 3 2515 2844 366635392 366635720 2.710000e-90 342.0
18 TraesCS4A01G009300 chr2A 79.506 405 57 18 1184 1569 686839337 686839734 6.040000e-67 265.0
19 TraesCS4A01G009300 chr7B 86.404 228 31 0 377 604 567882964 567883191 1.690000e-62 250.0
20 TraesCS4A01G009300 chr7A 85.973 221 31 0 377 597 609336005 609336225 1.320000e-58 237.0
21 TraesCS4A01G009300 chr7A 84.188 234 35 1 377 608 609172472 609172239 2.850000e-55 226.0
22 TraesCS4A01G009300 chr2B 77.482 413 57 19 1184 1566 650164649 650165055 6.170000e-52 215.0
23 TraesCS4A01G009300 chr6B 84.615 195 17 9 1156 1338 545253394 545253587 6.260000e-42 182.0
24 TraesCS4A01G009300 chr3B 83.544 79 11 2 62 138 631579902 631579824 3.930000e-09 73.1


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 TraesCS4A01G009300 chr4A 5550879 5553722 2843 True 5252 5252 100.000 1 2844 1 chr4A.!!$R1 2843
1 TraesCS4A01G009300 chr4B 581067756 581069482 1726 False 2344 2344 91.230 9 1743 1 chr4B.!!$F1 1734
2 TraesCS4A01G009300 chr4B 581080695 581082913 2218 False 729 1079 94.430 1580 2513 2 chr4B.!!$F2 933
3 TraesCS4A01G009300 chr4D 464659370 464660989 1619 False 1823 1823 87.242 1 1651 1 chr4D.!!$F1 1650

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
450 475 0.324738 TTCTGCTCCCTCATCCTCGT 60.325 55.0 0.0 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2112 3460 0.241481 AGCGAAGAACTGTCGGAGTC 59.759 55.0 0.0 0.0 38.93 3.36 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
102 103 2.542205 GCGGTGAGTGTATGCGTGTATA 60.542 50.000 0.00 0.00 0.00 1.47
123 124 1.934589 TTGAGCGCTTGCGTATGTAT 58.065 45.000 13.26 0.00 45.69 2.29
126 127 3.449632 TGAGCGCTTGCGTATGTATTAA 58.550 40.909 13.26 0.00 45.69 1.40
129 130 4.613944 AGCGCTTGCGTATGTATTAAGTA 58.386 39.130 16.38 0.00 45.69 2.24
177 183 8.728088 AATTTGACTTCTAACGCTTACAAATG 57.272 30.769 0.00 0.00 37.00 2.32
225 231 2.550830 TGCTCTTTTCGCTTCCTCTT 57.449 45.000 0.00 0.00 0.00 2.85
446 471 1.144936 CCGTTCTGCTCCCTCATCC 59.855 63.158 0.00 0.00 0.00 3.51
450 475 0.324738 TTCTGCTCCCTCATCCTCGT 60.325 55.000 0.00 0.00 0.00 4.18
500 525 3.329542 TTCCTCGCCATCAGTGCCC 62.330 63.158 0.00 0.00 0.00 5.36
601 634 1.013005 CCTGATGCGCCTGATCGATC 61.013 60.000 18.72 18.72 0.00 3.69
608 641 1.370657 GCCTGATCGATCGACGGAC 60.371 63.158 22.06 12.53 42.82 4.79
620 653 1.003718 GACGGACCAAAGACAGGGG 60.004 63.158 0.00 0.00 0.00 4.79
750 783 2.930682 GAGAGCCGTCAAAACCATACTC 59.069 50.000 0.00 0.00 0.00 2.59
886 932 0.892063 ACCCGCTCTTCTCAACTCTC 59.108 55.000 0.00 0.00 0.00 3.20
985 1034 4.223032 CGTCCTGTATATAAAGGCCTCCAT 59.777 45.833 13.60 4.81 33.25 3.41
1007 1056 0.234625 CGCTAGCAAAAGACGCACAA 59.765 50.000 16.45 0.00 0.00 3.33
1026 1075 0.179018 AACAGACACAACCTGAGGCC 60.179 55.000 0.00 0.00 35.69 5.19
1043 1092 1.539157 GCCAGAGCCTTACTGCTTTT 58.461 50.000 0.00 0.00 42.95 2.27
1045 1094 1.734465 CCAGAGCCTTACTGCTTTTCG 59.266 52.381 0.00 0.00 42.95 3.46
1046 1095 1.129437 CAGAGCCTTACTGCTTTTCGC 59.871 52.381 0.00 0.00 42.95 4.70
1055 1104 0.591170 CTGCTTTTCGCCGAGGAAAA 59.409 50.000 11.39 11.39 42.03 2.29
1070 1119 4.056050 GAGGAAAAGTTAGTCGTCAGCAA 58.944 43.478 0.00 0.00 0.00 3.91
1103 1152 1.007964 CAGCCGCACGAGGAGATAG 60.008 63.158 0.00 0.00 0.00 2.08
1104 1153 1.152943 AGCCGCACGAGGAGATAGA 60.153 57.895 0.00 0.00 0.00 1.98
1105 1154 0.538516 AGCCGCACGAGGAGATAGAT 60.539 55.000 0.00 0.00 0.00 1.98
1106 1155 1.166129 GCCGCACGAGGAGATAGATA 58.834 55.000 0.00 0.00 0.00 1.98
1107 1156 1.131504 GCCGCACGAGGAGATAGATAG 59.868 57.143 0.00 0.00 0.00 2.08
1108 1157 2.701107 CCGCACGAGGAGATAGATAGA 58.299 52.381 0.00 0.00 0.00 1.98
1109 1158 3.275143 CCGCACGAGGAGATAGATAGAT 58.725 50.000 0.00 0.00 0.00 1.98
1110 1159 4.443621 CCGCACGAGGAGATAGATAGATA 58.556 47.826 0.00 0.00 0.00 1.98
1206 1255 1.956043 GGCAACAATGGCGTCAAGA 59.044 52.632 0.00 0.00 42.73 3.02
1364 1416 4.863925 GAGAGGGCGAGCGCTGTC 62.864 72.222 18.48 19.60 40.74 3.51
1373 1425 3.580100 GAGCGCTGTCACTGGAGCA 62.580 63.158 18.48 0.00 34.69 4.26
1470 1522 2.805807 GCCAACGACGGCGATTACC 61.806 63.158 22.49 0.00 43.52 2.85
1628 1685 1.133407 GACTCTCTGGTTACGAGGCAG 59.867 57.143 0.00 0.00 33.01 4.85
1737 1794 3.915437 AGTAAACAACGGGAGCATTTG 57.085 42.857 0.00 0.00 0.00 2.32
1757 1817 4.552166 TGCTTTGCAAGTACTCTGAAAC 57.448 40.909 0.00 0.00 34.76 2.78
1762 1822 3.728845 TGCAAGTACTCTGAAACTGGTC 58.271 45.455 0.00 0.00 0.00 4.02
1800 1861 3.356290 AGATTCCCACATACAGCAAACC 58.644 45.455 0.00 0.00 0.00 3.27
1801 1862 2.666272 TTCCCACATACAGCAAACCA 57.334 45.000 0.00 0.00 0.00 3.67
1803 1864 0.887933 CCCACATACAGCAAACCACC 59.112 55.000 0.00 0.00 0.00 4.61
1804 1865 1.547675 CCCACATACAGCAAACCACCT 60.548 52.381 0.00 0.00 0.00 4.00
1805 1866 1.541147 CCACATACAGCAAACCACCTG 59.459 52.381 0.00 0.00 35.26 4.00
1806 1867 1.068333 CACATACAGCAAACCACCTGC 60.068 52.381 0.00 0.00 40.24 4.85
1807 1868 1.246649 CATACAGCAAACCACCTGCA 58.753 50.000 0.00 0.00 42.48 4.41
1808 1869 1.820519 CATACAGCAAACCACCTGCAT 59.179 47.619 0.00 0.00 42.48 3.96
1850 3198 7.220599 CAAAAGTGTGTCATTTTGTCGAAAT 57.779 32.000 0.00 0.00 40.09 2.17
1886 3234 8.589629 CATAAATCAGTAACATTTTGCTCAAGC 58.410 33.333 0.00 0.00 42.50 4.01
1887 3235 5.972107 ATCAGTAACATTTTGCTCAAGCT 57.028 34.783 3.32 0.00 42.66 3.74
1925 3273 2.418334 GCCTAAGGCGTACTACAGCTTT 60.418 50.000 0.00 5.97 39.62 3.51
1967 3315 6.328641 AGTACAGAAACACTAACACTCGAT 57.671 37.500 0.00 0.00 0.00 3.59
1977 3325 1.577468 AACACTCGATGCGAACAACA 58.423 45.000 0.00 0.00 34.74 3.33
1979 3327 1.526887 ACACTCGATGCGAACAACAAG 59.473 47.619 0.00 0.00 34.74 3.16
1981 3329 0.517132 CTCGATGCGAACAACAAGCG 60.517 55.000 0.00 0.00 34.74 4.68
2040 3388 4.609691 ACGACCAAAACAACAACTACAG 57.390 40.909 0.00 0.00 0.00 2.74
2076 3424 3.399330 CCCTAACTGAACACAACATCGT 58.601 45.455 0.00 0.00 0.00 3.73
2112 3460 0.179134 GACACCTCCGAAGACCATCG 60.179 60.000 0.00 0.00 42.37 3.84
2159 3507 1.064758 GCACCATCCACCCTGAATGTA 60.065 52.381 0.00 0.00 0.00 2.29
2194 3542 3.446442 AAGTTGATGGCAGGACTTGAT 57.554 42.857 10.81 0.00 31.59 2.57
2195 3543 4.574674 AAGTTGATGGCAGGACTTGATA 57.425 40.909 10.81 0.00 31.59 2.15
2230 3578 1.022735 CAGCACCATCATCTCAAGCC 58.977 55.000 0.00 0.00 0.00 4.35
2237 3585 4.040095 CACCATCATCTCAAGCCTCTCATA 59.960 45.833 0.00 0.00 0.00 2.15
2243 3591 6.757237 TCATCTCAAGCCTCTCATAAGAATC 58.243 40.000 0.00 0.00 0.00 2.52
2263 3611 8.000780 AGAATCTGATATTACAAGTTTTGCCC 57.999 34.615 0.00 0.00 0.00 5.36
2292 3640 4.734398 ACCAAGAAATGTGACAAAGCAA 57.266 36.364 0.00 0.00 0.00 3.91
2336 3684 3.876156 GCAGTACCCCTTGGCATTAGAAA 60.876 47.826 0.00 0.00 33.59 2.52
2388 3736 4.523943 TGCATATTATTCTTGGGATGGTGC 59.476 41.667 0.00 0.00 0.00 5.01
2446 3794 2.162408 AGCTAGAAAGAACAATTGGCGC 59.838 45.455 10.83 0.00 0.00 6.53
2505 3853 1.463444 GCACGTAAATCGCCTGACTTT 59.537 47.619 0.00 0.00 44.19 2.66
2508 3856 4.201783 GCACGTAAATCGCCTGACTTTTAT 60.202 41.667 0.00 0.00 44.19 1.40
2513 3861 8.671028 ACGTAAATCGCCTGACTTTTATATTTT 58.329 29.630 0.00 0.00 44.19 1.82
2514 3862 9.155053 CGTAAATCGCCTGACTTTTATATTTTC 57.845 33.333 0.00 0.00 0.00 2.29
2515 3863 9.447040 GTAAATCGCCTGACTTTTATATTTTCC 57.553 33.333 0.00 0.00 0.00 3.13
2516 3864 7.639113 AATCGCCTGACTTTTATATTTTCCA 57.361 32.000 0.00 0.00 0.00 3.53
2517 3865 7.639113 ATCGCCTGACTTTTATATTTTCCAA 57.361 32.000 0.00 0.00 0.00 3.53
2518 3866 7.455641 TCGCCTGACTTTTATATTTTCCAAA 57.544 32.000 0.00 0.00 0.00 3.28
2519 3867 8.062065 TCGCCTGACTTTTATATTTTCCAAAT 57.938 30.769 0.00 0.00 0.00 2.32
2520 3868 9.179909 TCGCCTGACTTTTATATTTTCCAAATA 57.820 29.630 0.00 0.00 0.00 1.40
2521 3869 9.233232 CGCCTGACTTTTATATTTTCCAAATAC 57.767 33.333 0.00 0.00 0.00 1.89
2531 3879 7.673810 ATATTTTCCAAATACTTAAACGCGC 57.326 32.000 5.73 0.00 0.00 6.86
2532 3880 4.485024 TTTCCAAATACTTAAACGCGCA 57.515 36.364 5.73 0.00 0.00 6.09
2533 3881 4.485024 TTCCAAATACTTAAACGCGCAA 57.515 36.364 5.73 0.00 0.00 4.85
2534 3882 3.812656 TCCAAATACTTAAACGCGCAAC 58.187 40.909 5.73 0.00 0.00 4.17
2535 3883 3.499157 TCCAAATACTTAAACGCGCAACT 59.501 39.130 5.73 0.00 0.00 3.16
2536 3884 3.602062 CCAAATACTTAAACGCGCAACTG 59.398 43.478 5.73 0.00 0.00 3.16
2537 3885 2.520686 ATACTTAAACGCGCAACTGC 57.479 45.000 5.73 0.00 37.78 4.40
2547 3895 2.711924 GCAACTGCGCTATCTGGC 59.288 61.111 9.73 0.85 0.00 4.85
2574 3922 2.703409 CGCACACGCAAGCTATCC 59.297 61.111 0.00 0.00 45.62 2.59
2575 3923 2.703409 GCACACGCAAGCTATCCG 59.297 61.111 0.00 0.00 45.62 4.18
2576 3924 1.809619 GCACACGCAAGCTATCCGA 60.810 57.895 7.46 0.00 45.62 4.55
2577 3925 1.154205 GCACACGCAAGCTATCCGAT 61.154 55.000 7.46 0.00 45.62 4.18
2578 3926 0.578683 CACACGCAAGCTATCCGATG 59.421 55.000 7.46 5.16 45.62 3.84
2579 3927 1.154205 ACACGCAAGCTATCCGATGC 61.154 55.000 7.46 1.92 45.62 3.91
2580 3928 0.877649 CACGCAAGCTATCCGATGCT 60.878 55.000 4.44 0.00 45.62 3.79
2585 3933 1.876322 AAGCTATCCGATGCTTGAGC 58.124 50.000 13.79 5.05 46.25 4.26
2601 3949 4.354155 GCACCTGCTACACGACAA 57.646 55.556 0.00 0.00 38.21 3.18
2602 3950 2.153913 GCACCTGCTACACGACAAG 58.846 57.895 0.00 0.00 38.21 3.16
2603 3951 0.319555 GCACCTGCTACACGACAAGA 60.320 55.000 0.00 0.00 38.21 3.02
2604 3952 1.419374 CACCTGCTACACGACAAGAC 58.581 55.000 0.00 0.00 0.00 3.01
2605 3953 1.000163 CACCTGCTACACGACAAGACT 60.000 52.381 0.00 0.00 0.00 3.24
2606 3954 1.000163 ACCTGCTACACGACAAGACTG 60.000 52.381 0.00 0.00 0.00 3.51
2607 3955 1.063806 CTGCTACACGACAAGACTGC 58.936 55.000 0.00 0.00 0.00 4.40
2608 3956 0.673985 TGCTACACGACAAGACTGCT 59.326 50.000 0.00 0.00 0.00 4.24
2609 3957 1.883926 TGCTACACGACAAGACTGCTA 59.116 47.619 0.00 0.00 0.00 3.49
2610 3958 2.295070 TGCTACACGACAAGACTGCTAA 59.705 45.455 0.00 0.00 0.00 3.09
2611 3959 2.917971 GCTACACGACAAGACTGCTAAG 59.082 50.000 0.00 0.00 0.00 2.18
2612 3960 3.366070 GCTACACGACAAGACTGCTAAGA 60.366 47.826 0.00 0.00 0.00 2.10
2613 3961 3.728076 ACACGACAAGACTGCTAAGAA 57.272 42.857 0.00 0.00 0.00 2.52
2614 3962 4.054780 ACACGACAAGACTGCTAAGAAA 57.945 40.909 0.00 0.00 0.00 2.52
2615 3963 4.439057 ACACGACAAGACTGCTAAGAAAA 58.561 39.130 0.00 0.00 0.00 2.29
2616 3964 4.270325 ACACGACAAGACTGCTAAGAAAAC 59.730 41.667 0.00 0.00 0.00 2.43
2617 3965 4.270084 CACGACAAGACTGCTAAGAAAACA 59.730 41.667 0.00 0.00 0.00 2.83
2618 3966 4.873827 ACGACAAGACTGCTAAGAAAACAA 59.126 37.500 0.00 0.00 0.00 2.83
2619 3967 5.198274 CGACAAGACTGCTAAGAAAACAAC 58.802 41.667 0.00 0.00 0.00 3.32
2620 3968 5.006746 CGACAAGACTGCTAAGAAAACAACT 59.993 40.000 0.00 0.00 0.00 3.16
2621 3969 6.456988 CGACAAGACTGCTAAGAAAACAACTT 60.457 38.462 0.00 0.00 0.00 2.66
2622 3970 7.158099 ACAAGACTGCTAAGAAAACAACTTT 57.842 32.000 0.00 0.00 0.00 2.66
2623 3971 7.251281 ACAAGACTGCTAAGAAAACAACTTTC 58.749 34.615 0.00 0.00 43.36 2.62
2632 3980 4.733972 GAAAACAACTTTCTCCTCCTCG 57.266 45.455 0.00 0.00 40.38 4.63
2633 3981 3.840124 AAACAACTTTCTCCTCCTCGT 57.160 42.857 0.00 0.00 0.00 4.18
2634 3982 2.821991 ACAACTTTCTCCTCCTCGTG 57.178 50.000 0.00 0.00 0.00 4.35
2635 3983 2.317040 ACAACTTTCTCCTCCTCGTGA 58.683 47.619 0.00 0.00 0.00 4.35
2636 3984 2.900546 ACAACTTTCTCCTCCTCGTGAT 59.099 45.455 0.00 0.00 0.00 3.06
2637 3985 3.257393 CAACTTTCTCCTCCTCGTGATG 58.743 50.000 0.00 0.00 0.00 3.07
2638 3986 2.530701 ACTTTCTCCTCCTCGTGATGT 58.469 47.619 0.00 0.00 0.00 3.06
2639 3987 3.698289 ACTTTCTCCTCCTCGTGATGTA 58.302 45.455 0.00 0.00 0.00 2.29
2640 3988 3.444388 ACTTTCTCCTCCTCGTGATGTAC 59.556 47.826 0.00 0.00 0.00 2.90
2641 3989 2.054232 TCTCCTCCTCGTGATGTACC 57.946 55.000 0.00 0.00 0.00 3.34
2642 3990 1.564818 TCTCCTCCTCGTGATGTACCT 59.435 52.381 0.00 0.00 0.00 3.08
2643 3991 1.678627 CTCCTCCTCGTGATGTACCTG 59.321 57.143 0.00 0.00 0.00 4.00
2644 3992 1.283905 TCCTCCTCGTGATGTACCTGA 59.716 52.381 0.00 0.00 0.00 3.86
2645 3993 1.405821 CCTCCTCGTGATGTACCTGAC 59.594 57.143 0.00 0.00 0.00 3.51
2646 3994 1.064208 CTCCTCGTGATGTACCTGACG 59.936 57.143 3.89 3.89 0.00 4.35
2647 3995 0.809385 CCTCGTGATGTACCTGACGT 59.191 55.000 9.61 0.00 33.56 4.34
2648 3996 1.201647 CCTCGTGATGTACCTGACGTT 59.798 52.381 9.61 0.00 33.56 3.99
2649 3997 2.251040 CTCGTGATGTACCTGACGTTG 58.749 52.381 9.61 1.95 33.56 4.10
2650 3998 1.610038 TCGTGATGTACCTGACGTTGT 59.390 47.619 9.61 0.00 33.56 3.32
2651 3999 2.034939 TCGTGATGTACCTGACGTTGTT 59.965 45.455 9.61 0.00 33.56 2.83
2652 4000 3.252944 TCGTGATGTACCTGACGTTGTTA 59.747 43.478 9.61 0.00 33.56 2.41
2653 4001 3.606777 CGTGATGTACCTGACGTTGTTAG 59.393 47.826 2.20 0.00 0.00 2.34
2654 4002 3.924686 GTGATGTACCTGACGTTGTTAGG 59.075 47.826 6.25 6.25 43.70 2.69
2659 4007 1.508632 CCTGACGTTGTTAGGTGGTG 58.491 55.000 0.00 0.00 35.04 4.17
2660 4008 1.508632 CTGACGTTGTTAGGTGGTGG 58.491 55.000 0.00 0.00 0.00 4.61
2661 4009 1.069513 CTGACGTTGTTAGGTGGTGGA 59.930 52.381 0.00 0.00 0.00 4.02
2662 4010 1.695242 TGACGTTGTTAGGTGGTGGAT 59.305 47.619 0.00 0.00 0.00 3.41
2663 4011 2.073816 GACGTTGTTAGGTGGTGGATG 58.926 52.381 0.00 0.00 0.00 3.51
2664 4012 1.271163 ACGTTGTTAGGTGGTGGATGG 60.271 52.381 0.00 0.00 0.00 3.51
2665 4013 1.271163 CGTTGTTAGGTGGTGGATGGT 60.271 52.381 0.00 0.00 0.00 3.55
2666 4014 2.433436 GTTGTTAGGTGGTGGATGGTC 58.567 52.381 0.00 0.00 0.00 4.02
2667 4015 1.735926 TGTTAGGTGGTGGATGGTCA 58.264 50.000 0.00 0.00 0.00 4.02
2668 4016 1.349688 TGTTAGGTGGTGGATGGTCAC 59.650 52.381 0.00 0.00 36.95 3.67
2669 4017 1.628846 GTTAGGTGGTGGATGGTCACT 59.371 52.381 0.00 0.00 37.75 3.41
2670 4018 2.835764 GTTAGGTGGTGGATGGTCACTA 59.164 50.000 0.00 0.00 37.75 2.74
2671 4019 2.038863 AGGTGGTGGATGGTCACTAA 57.961 50.000 0.00 0.00 37.75 2.24
2672 4020 1.909302 AGGTGGTGGATGGTCACTAAG 59.091 52.381 0.00 0.00 37.75 2.18
2673 4021 1.065418 GGTGGTGGATGGTCACTAAGG 60.065 57.143 0.00 0.00 37.75 2.69
2674 4022 1.906574 GTGGTGGATGGTCACTAAGGA 59.093 52.381 0.00 0.00 37.75 3.36
2675 4023 2.505819 GTGGTGGATGGTCACTAAGGAT 59.494 50.000 0.00 0.00 37.75 3.24
2676 4024 3.054361 GTGGTGGATGGTCACTAAGGATT 60.054 47.826 0.00 0.00 37.75 3.01
2677 4025 4.163458 GTGGTGGATGGTCACTAAGGATTA 59.837 45.833 0.00 0.00 37.75 1.75
2678 4026 4.163458 TGGTGGATGGTCACTAAGGATTAC 59.837 45.833 0.00 0.00 37.75 1.89
2679 4027 4.444449 GGTGGATGGTCACTAAGGATTACC 60.444 50.000 0.00 0.00 37.75 2.85
2680 4028 4.409247 GTGGATGGTCACTAAGGATTACCT 59.591 45.833 0.00 0.00 40.16 3.08
2681 4029 5.685075 GTGGATGGTCACTAAGGATTACCTG 60.685 48.000 0.00 0.00 39.28 4.00
2692 4040 4.377762 AGGATTACCTGCATGCATATGT 57.622 40.909 22.97 19.92 45.92 2.29
2693 4041 4.733165 AGGATTACCTGCATGCATATGTT 58.267 39.130 22.97 6.56 45.92 2.71
2694 4042 4.521639 AGGATTACCTGCATGCATATGTTG 59.478 41.667 22.97 8.20 45.92 3.33
2695 4043 4.520111 GGATTACCTGCATGCATATGTTGA 59.480 41.667 22.97 11.10 36.65 3.18
2696 4044 5.184479 GGATTACCTGCATGCATATGTTGAT 59.816 40.000 22.97 14.78 36.65 2.57
2697 4045 5.441709 TTACCTGCATGCATATGTTGATG 57.558 39.130 22.97 5.79 36.65 3.07
2698 4046 3.293337 ACCTGCATGCATATGTTGATGT 58.707 40.909 22.97 4.69 36.65 3.06
2699 4047 3.317149 ACCTGCATGCATATGTTGATGTC 59.683 43.478 22.97 2.92 36.65 3.06
2700 4048 3.316868 CCTGCATGCATATGTTGATGTCA 59.683 43.478 22.97 6.54 36.65 3.58
2701 4049 4.022329 CCTGCATGCATATGTTGATGTCAT 60.022 41.667 22.97 0.00 36.65 3.06
2702 4050 5.116069 TGCATGCATATGTTGATGTCATC 57.884 39.130 18.46 5.83 36.65 2.92
2703 4051 4.022676 TGCATGCATATGTTGATGTCATCC 60.023 41.667 18.46 0.00 36.65 3.51
2704 4052 4.617530 GCATGCATATGTTGATGTCATCCC 60.618 45.833 14.21 1.92 36.65 3.85
2705 4053 4.167652 TGCATATGTTGATGTCATCCCA 57.832 40.909 10.36 7.45 0.00 4.37
2706 4054 3.884693 TGCATATGTTGATGTCATCCCAC 59.115 43.478 10.36 7.67 0.00 4.61
2707 4055 3.884693 GCATATGTTGATGTCATCCCACA 59.115 43.478 14.32 14.32 0.00 4.17
2708 4056 4.521639 GCATATGTTGATGTCATCCCACAT 59.478 41.667 22.27 22.27 39.84 3.21
2709 4057 5.010314 GCATATGTTGATGTCATCCCACATT 59.990 40.000 23.18 13.62 37.11 2.71
2710 4058 6.207221 GCATATGTTGATGTCATCCCACATTA 59.793 38.462 23.18 14.30 37.11 1.90
2711 4059 7.094075 GCATATGTTGATGTCATCCCACATTAT 60.094 37.037 23.18 15.32 37.11 1.28
2712 4060 8.799367 CATATGTTGATGTCATCCCACATTATT 58.201 33.333 23.18 12.27 37.11 1.40
2713 4061 7.664552 ATGTTGATGTCATCCCACATTATTT 57.335 32.000 16.72 2.43 37.11 1.40
2714 4062 7.099266 TGTTGATGTCATCCCACATTATTTC 57.901 36.000 10.36 0.00 37.11 2.17
2715 4063 6.183360 TGTTGATGTCATCCCACATTATTTCG 60.183 38.462 10.36 0.00 37.11 3.46
2716 4064 5.436175 TGATGTCATCCCACATTATTTCGT 58.564 37.500 10.36 0.00 37.11 3.85
2717 4065 5.527214 TGATGTCATCCCACATTATTTCGTC 59.473 40.000 10.36 0.00 37.11 4.20
2718 4066 5.097742 TGTCATCCCACATTATTTCGTCT 57.902 39.130 0.00 0.00 0.00 4.18
2719 4067 5.116180 TGTCATCCCACATTATTTCGTCTC 58.884 41.667 0.00 0.00 0.00 3.36
2720 4068 5.116180 GTCATCCCACATTATTTCGTCTCA 58.884 41.667 0.00 0.00 0.00 3.27
2721 4069 5.760253 GTCATCCCACATTATTTCGTCTCAT 59.240 40.000 0.00 0.00 0.00 2.90
2722 4070 6.260936 GTCATCCCACATTATTTCGTCTCATT 59.739 38.462 0.00 0.00 0.00 2.57
2723 4071 6.828273 TCATCCCACATTATTTCGTCTCATTT 59.172 34.615 0.00 0.00 0.00 2.32
2724 4072 7.339212 TCATCCCACATTATTTCGTCTCATTTT 59.661 33.333 0.00 0.00 0.00 1.82
2725 4073 7.461182 TCCCACATTATTTCGTCTCATTTTT 57.539 32.000 0.00 0.00 0.00 1.94
2754 4102 9.736023 AAAAAGCTATAACTTTTGAACTGAGTG 57.264 29.630 13.25 0.00 46.49 3.51
2755 4103 8.451908 AAAGCTATAACTTTTGAACTGAGTGT 57.548 30.769 0.00 0.00 36.47 3.55
2756 4104 7.659652 AGCTATAACTTTTGAACTGAGTGTC 57.340 36.000 0.00 0.00 0.00 3.67
2757 4105 7.217200 AGCTATAACTTTTGAACTGAGTGTCA 58.783 34.615 0.00 0.00 0.00 3.58
2758 4106 7.715249 AGCTATAACTTTTGAACTGAGTGTCAA 59.285 33.333 6.24 6.24 0.00 3.18
2759 4107 8.342634 GCTATAACTTTTGAACTGAGTGTCAAA 58.657 33.333 14.49 14.49 0.00 2.69
2762 4110 7.816945 AACTTTTGAACTGAGTGTCAAAATG 57.183 32.000 23.02 19.92 40.03 2.32
2763 4111 7.156876 ACTTTTGAACTGAGTGTCAAAATGA 57.843 32.000 23.02 11.23 40.03 2.57
2764 4112 7.601856 ACTTTTGAACTGAGTGTCAAAATGAA 58.398 30.769 23.02 11.00 40.03 2.57
2765 4113 8.087750 ACTTTTGAACTGAGTGTCAAAATGAAA 58.912 29.630 23.02 10.77 40.03 2.69
2766 4114 8.824159 TTTTGAACTGAGTGTCAAAATGAAAA 57.176 26.923 20.91 2.89 37.21 2.29
2767 4115 9.434420 TTTTGAACTGAGTGTCAAAATGAAAAT 57.566 25.926 20.91 0.00 37.21 1.82
2768 4116 8.633075 TTGAACTGAGTGTCAAAATGAAAATC 57.367 30.769 7.44 0.00 29.91 2.17
2769 4117 7.202526 TGAACTGAGTGTCAAAATGAAAATCC 58.797 34.615 0.00 0.00 28.16 3.01
2770 4118 5.762045 ACTGAGTGTCAAAATGAAAATCCG 58.238 37.500 0.00 0.00 28.16 4.18
2771 4119 5.299279 ACTGAGTGTCAAAATGAAAATCCGT 59.701 36.000 0.00 0.00 28.16 4.69
2772 4120 6.142818 TGAGTGTCAAAATGAAAATCCGTT 57.857 33.333 0.00 0.00 28.16 4.44
2773 4121 6.568869 TGAGTGTCAAAATGAAAATCCGTTT 58.431 32.000 0.00 0.00 28.16 3.60
2774 4122 7.038659 TGAGTGTCAAAATGAAAATCCGTTTT 58.961 30.769 0.00 0.00 40.13 2.43
2786 4134 6.413783 AAAATCCGTTTTCACCATTAGGTT 57.586 33.333 0.00 0.00 37.70 3.50
2787 4135 6.822442 AAAATCCGTTTTCACCATTAGGTTT 58.178 32.000 0.00 0.00 37.70 3.27
2788 4136 7.276658 AAAATCCGTTTTCACCATTAGGTTTT 58.723 30.769 0.00 0.00 37.70 2.43
2789 4137 7.771361 AAAATCCGTTTTCACCATTAGGTTTTT 59.229 29.630 0.00 0.00 37.70 1.94
2798 4146 4.322101 CCATTAGGTTTTTCGTGACGAG 57.678 45.455 8.02 0.00 37.14 4.18
2799 4147 3.991773 CCATTAGGTTTTTCGTGACGAGA 59.008 43.478 8.02 0.00 37.14 4.04
2800 4148 4.630069 CCATTAGGTTTTTCGTGACGAGAT 59.370 41.667 8.02 0.00 37.14 2.75
2801 4149 5.121768 CCATTAGGTTTTTCGTGACGAGATT 59.878 40.000 8.02 0.00 37.14 2.40
2802 4150 6.348213 CCATTAGGTTTTTCGTGACGAGATTT 60.348 38.462 8.02 0.00 37.14 2.17
2803 4151 6.607735 TTAGGTTTTTCGTGACGAGATTTT 57.392 33.333 8.02 0.00 37.14 1.82
2804 4152 5.091910 AGGTTTTTCGTGACGAGATTTTC 57.908 39.130 8.02 0.00 37.14 2.29
2805 4153 4.573201 AGGTTTTTCGTGACGAGATTTTCA 59.427 37.500 8.02 0.00 37.14 2.69
2806 4154 5.065474 AGGTTTTTCGTGACGAGATTTTCAA 59.935 36.000 8.02 0.00 37.14 2.69
2807 4155 5.740099 GGTTTTTCGTGACGAGATTTTCAAA 59.260 36.000 8.02 1.01 37.14 2.69
2808 4156 6.251801 GGTTTTTCGTGACGAGATTTTCAAAA 59.748 34.615 8.02 7.53 37.14 2.44
2809 4157 6.784068 TTTTCGTGACGAGATTTTCAAAAC 57.216 33.333 8.02 0.00 37.14 2.43
2810 4158 5.728351 TTCGTGACGAGATTTTCAAAACT 57.272 34.783 8.02 0.00 37.14 2.66
2811 4159 6.831727 TTCGTGACGAGATTTTCAAAACTA 57.168 33.333 8.02 0.00 37.14 2.24
2812 4160 6.448053 TCGTGACGAGATTTTCAAAACTAG 57.552 37.500 2.39 0.00 0.00 2.57
2813 4161 6.210796 TCGTGACGAGATTTTCAAAACTAGA 58.789 36.000 2.39 0.00 0.00 2.43
2814 4162 6.866770 TCGTGACGAGATTTTCAAAACTAGAT 59.133 34.615 2.39 0.00 0.00 1.98
2815 4163 7.061905 TCGTGACGAGATTTTCAAAACTAGATC 59.938 37.037 2.39 0.00 0.00 2.75
2816 4164 7.457060 GTGACGAGATTTTCAAAACTAGATCC 58.543 38.462 0.00 0.00 0.00 3.36
2817 4165 6.594159 TGACGAGATTTTCAAAACTAGATCCC 59.406 38.462 0.00 0.00 0.00 3.85
2818 4166 6.472887 ACGAGATTTTCAAAACTAGATCCCA 58.527 36.000 0.00 0.00 0.00 4.37
2819 4167 7.112779 ACGAGATTTTCAAAACTAGATCCCAT 58.887 34.615 0.00 0.00 0.00 4.00
2820 4168 8.265055 ACGAGATTTTCAAAACTAGATCCCATA 58.735 33.333 0.00 0.00 0.00 2.74
2821 4169 9.277783 CGAGATTTTCAAAACTAGATCCCATAT 57.722 33.333 0.00 0.00 0.00 1.78
2823 4171 9.927081 AGATTTTCAAAACTAGATCCCATATGT 57.073 29.630 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 4.179298 GACCGTAAAACAGACACCCTATC 58.821 47.826 0.00 0.00 0.00 2.08
7 8 1.142474 CGACCGTAAAACAGACACCC 58.858 55.000 0.00 0.00 0.00 4.61
67 68 0.372334 CACCGCTATAAACGCACACC 59.628 55.000 0.00 0.00 0.00 4.16
102 103 1.086696 ACATACGCAAGCGCTCAAAT 58.913 45.000 12.06 0.00 44.19 2.32
137 138 3.388308 TCAAATTTTTGATGCACCCGTG 58.612 40.909 1.66 0.00 41.88 4.94
138 139 3.742433 TCAAATTTTTGATGCACCCGT 57.258 38.095 1.66 0.00 41.88 5.28
240 246 1.204941 GGTACGAACAGAGGATGCAGT 59.795 52.381 0.00 0.00 0.00 4.40
432 457 1.039785 CACGAGGATGAGGGAGCAGA 61.040 60.000 0.00 0.00 0.00 4.26
446 471 2.202362 CAGGTCGACGAGCACGAG 60.202 66.667 27.01 11.26 42.66 4.18
477 502 1.137675 CACTGATGGCGAGGAAGATGA 59.862 52.381 0.00 0.00 0.00 2.92
500 525 3.103911 GTTGACGCCGAGGACGTG 61.104 66.667 14.24 0.00 45.24 4.49
584 617 1.372128 CGATCGATCAGGCGCATCA 60.372 57.895 24.40 0.00 0.00 3.07
601 634 1.374252 CCCTGTCTTTGGTCCGTCG 60.374 63.158 0.00 0.00 0.00 5.12
608 641 2.239400 GTTCTTTCCCCCTGTCTTTGG 58.761 52.381 0.00 0.00 0.00 3.28
620 653 1.866925 CCTGTTCGCCGTTCTTTCC 59.133 57.895 0.00 0.00 0.00 3.13
886 932 0.867753 GCTCGATCGTGTGGTGCTAG 60.868 60.000 15.94 2.57 0.00 3.42
985 1034 1.458064 GTGCGTCTTTTGCTAGCGTTA 59.542 47.619 10.77 0.00 0.00 3.18
1007 1056 0.179018 GGCCTCAGGTTGTGTCTGTT 60.179 55.000 0.00 0.00 34.15 3.16
1026 1075 1.129437 GCGAAAAGCAGTAAGGCTCTG 59.871 52.381 0.00 0.00 45.07 3.35
1032 1081 7.800983 CTTTTCCTCGGCGAAAAGCAGTAAG 62.801 48.000 16.70 8.43 46.93 2.34
1043 1092 1.401931 CGACTAACTTTTCCTCGGCGA 60.402 52.381 10.14 10.14 0.00 5.54
1045 1094 1.991264 GACGACTAACTTTTCCTCGGC 59.009 52.381 0.00 0.00 0.00 5.54
1046 1095 3.243336 CTGACGACTAACTTTTCCTCGG 58.757 50.000 0.00 0.00 0.00 4.63
1055 1104 4.883083 TCTTGATTTGCTGACGACTAACT 58.117 39.130 0.00 0.00 0.00 2.24
1056 1105 5.405571 TCTTCTTGATTTGCTGACGACTAAC 59.594 40.000 0.00 0.00 0.00 2.34
1057 1106 5.538118 TCTTCTTGATTTGCTGACGACTAA 58.462 37.500 0.00 0.00 0.00 2.24
1058 1107 5.048013 TCTCTTCTTGATTTGCTGACGACTA 60.048 40.000 0.00 0.00 0.00 2.59
1070 1119 1.406614 CGGCTGGCTCTCTTCTTGATT 60.407 52.381 0.00 0.00 0.00 2.57
1110 1159 9.814899 CACTTCACTTGATCAGTTTATCTATCT 57.185 33.333 0.00 0.00 30.92 1.98
1206 1255 1.335182 CTGCGTCTCGATGTAGGTGAT 59.665 52.381 0.00 0.00 0.00 3.06
1353 1405 4.724602 TCCAGTGACAGCGCTCGC 62.725 66.667 7.13 4.10 42.33 5.03
1373 1425 0.892755 TGGACGTGAAATAGCTCGGT 59.107 50.000 0.00 0.00 0.00 4.69
1402 1454 0.679505 AGCTGCACTAACAACCGAGA 59.320 50.000 1.02 0.00 0.00 4.04
1459 1511 4.217159 GCTCCGGGTAATCGCCGT 62.217 66.667 0.00 0.00 0.00 5.68
1470 1522 2.294078 AAAGTCCCTCCAGCTCCGG 61.294 63.158 0.00 0.00 0.00 5.14
1792 1853 1.246649 TGTATGCAGGTGGTTTGCTG 58.753 50.000 0.00 0.00 42.02 4.41
1794 1855 1.818060 TCATGTATGCAGGTGGTTTGC 59.182 47.619 0.00 0.00 41.86 3.68
1800 1861 4.694982 TGTACTTTGTCATGTATGCAGGTG 59.305 41.667 0.00 0.00 0.00 4.00
1801 1862 4.905429 TGTACTTTGTCATGTATGCAGGT 58.095 39.130 0.00 0.00 0.00 4.00
1803 1864 6.667370 TGTTTGTACTTTGTCATGTATGCAG 58.333 36.000 0.00 0.00 0.00 4.41
1804 1865 6.625873 TGTTTGTACTTTGTCATGTATGCA 57.374 33.333 0.00 0.00 0.00 3.96
1805 1866 7.922505 TTTGTTTGTACTTTGTCATGTATGC 57.077 32.000 0.00 0.00 0.00 3.14
1806 1867 9.515020 ACTTTTGTTTGTACTTTGTCATGTATG 57.485 29.630 0.00 0.00 0.00 2.39
1807 1868 9.515020 CACTTTTGTTTGTACTTTGTCATGTAT 57.485 29.630 0.00 0.00 0.00 2.29
1808 1869 8.516234 ACACTTTTGTTTGTACTTTGTCATGTA 58.484 29.630 0.00 0.00 28.43 2.29
1911 3259 6.154445 TGCCTTATATAAAGCTGTAGTACGC 58.846 40.000 15.37 8.48 0.00 4.42
1913 3261 9.930693 AATCTGCCTTATATAAAGCTGTAGTAC 57.069 33.333 15.37 0.00 0.00 2.73
1967 3315 1.154814 TGCTACGCTTGTTGTTCGCA 61.155 50.000 0.00 0.00 0.00 5.10
1977 3325 2.006772 GCGCTGTTATGCTACGCTT 58.993 52.632 0.00 0.00 45.71 4.68
1981 3329 0.652592 CAGGTGCGCTGTTATGCTAC 59.347 55.000 9.73 0.00 0.00 3.58
1987 3335 1.666553 CGAACCAGGTGCGCTGTTA 60.667 57.895 7.16 0.00 0.00 2.41
1992 3340 2.357034 TCTTCGAACCAGGTGCGC 60.357 61.111 16.17 0.00 34.09 6.09
1993 3341 1.284982 CTGTCTTCGAACCAGGTGCG 61.285 60.000 14.73 14.73 35.64 5.34
1994 3342 1.569479 GCTGTCTTCGAACCAGGTGC 61.569 60.000 17.38 0.00 0.00 5.01
2076 3424 4.351938 CCGGCGTTGGTCGAGACA 62.352 66.667 6.01 0.00 46.20 3.41
2112 3460 0.241481 AGCGAAGAACTGTCGGAGTC 59.759 55.000 0.00 0.00 38.93 3.36
2159 3507 1.004044 CAACTTGCCACCTCCTCTCAT 59.996 52.381 0.00 0.00 0.00 2.90
2194 3542 3.378112 GTGCTGTTTGCCTGCTTATCATA 59.622 43.478 0.00 0.00 42.00 2.15
2195 3543 2.165030 GTGCTGTTTGCCTGCTTATCAT 59.835 45.455 0.00 0.00 42.00 2.45
2237 3585 8.470002 GGGCAAAACTTGTAATATCAGATTCTT 58.530 33.333 0.00 0.00 0.00 2.52
2243 3591 7.156876 TCTTGGGCAAAACTTGTAATATCAG 57.843 36.000 0.00 0.00 0.00 2.90
2263 3611 5.649557 TGTCACATTTCTTGGTTGTTCTTG 58.350 37.500 0.00 0.00 0.00 3.02
2318 3666 6.728632 AGAAAAATTTCTAATGCCAAGGGGTA 59.271 34.615 6.62 0.00 45.17 3.69
2361 3709 6.491403 ACCATCCCAAGAATAATATGCAAGAC 59.509 38.462 0.00 0.00 0.00 3.01
2363 3711 6.684686 CACCATCCCAAGAATAATATGCAAG 58.315 40.000 0.00 0.00 0.00 4.01
2388 3736 1.284982 CCGGAGAGCAGTTCACAACG 61.285 60.000 0.00 0.00 36.23 4.10
2446 3794 9.988815 AATTTATACCAGCTCTGTATAACTCTG 57.011 33.333 18.45 0.00 0.00 3.35
2505 3853 9.224058 GCGCGTTTAAGTATTTGGAAAATATAA 57.776 29.630 8.43 0.00 0.00 0.98
2508 3856 6.609533 TGCGCGTTTAAGTATTTGGAAAATA 58.390 32.000 8.43 0.00 0.00 1.40
2513 3861 3.499157 AGTTGCGCGTTTAAGTATTTGGA 59.501 39.130 8.43 0.00 0.00 3.53
2514 3862 3.602062 CAGTTGCGCGTTTAAGTATTTGG 59.398 43.478 8.43 0.00 0.00 3.28
2515 3863 3.057609 GCAGTTGCGCGTTTAAGTATTTG 59.942 43.478 8.43 0.00 0.00 2.32
2516 3864 3.231160 GCAGTTGCGCGTTTAAGTATTT 58.769 40.909 8.43 0.00 0.00 1.40
2517 3865 2.846693 GCAGTTGCGCGTTTAAGTATT 58.153 42.857 8.43 0.00 0.00 1.89
2518 3866 2.520686 GCAGTTGCGCGTTTAAGTAT 57.479 45.000 8.43 0.00 0.00 2.12
2520 3868 4.914291 GCAGTTGCGCGTTTAAGT 57.086 50.000 8.43 0.96 0.00 2.24
2530 3878 2.711924 GCCAGATAGCGCAGTTGC 59.288 61.111 11.47 0.00 37.78 4.17
2558 3906 1.154205 ATCGGATAGCTTGCGTGTGC 61.154 55.000 0.00 0.00 40.49 4.57
2559 3907 0.578683 CATCGGATAGCTTGCGTGTG 59.421 55.000 0.00 0.00 40.49 3.82
2560 3908 1.154205 GCATCGGATAGCTTGCGTGT 61.154 55.000 0.00 0.00 40.49 4.49
2561 3909 0.877649 AGCATCGGATAGCTTGCGTG 60.878 55.000 0.00 0.48 38.01 5.34
2562 3910 1.443407 AGCATCGGATAGCTTGCGT 59.557 52.632 0.00 0.00 38.01 5.24
2563 3911 4.350620 AGCATCGGATAGCTTGCG 57.649 55.556 0.00 0.00 38.01 4.85
2567 3915 3.603144 GCTCAAGCATCGGATAGCT 57.397 52.632 8.49 8.49 44.31 3.32
2584 3932 0.319555 TCTTGTCGTGTAGCAGGTGC 60.320 55.000 0.00 0.00 42.49 5.01
2585 3933 1.000163 AGTCTTGTCGTGTAGCAGGTG 60.000 52.381 0.00 0.00 0.00 4.00
2586 3934 1.000163 CAGTCTTGTCGTGTAGCAGGT 60.000 52.381 0.00 0.00 0.00 4.00
2587 3935 1.702886 CAGTCTTGTCGTGTAGCAGG 58.297 55.000 0.00 0.00 0.00 4.85
2588 3936 1.063806 GCAGTCTTGTCGTGTAGCAG 58.936 55.000 0.00 0.00 0.00 4.24
2589 3937 0.673985 AGCAGTCTTGTCGTGTAGCA 59.326 50.000 0.00 0.00 0.00 3.49
2590 3938 2.631418 TAGCAGTCTTGTCGTGTAGC 57.369 50.000 0.00 0.00 0.00 3.58
2591 3939 4.421033 TCTTAGCAGTCTTGTCGTGTAG 57.579 45.455 0.00 0.00 0.00 2.74
2592 3940 4.841443 TTCTTAGCAGTCTTGTCGTGTA 57.159 40.909 0.00 0.00 0.00 2.90
2593 3941 3.728076 TTCTTAGCAGTCTTGTCGTGT 57.272 42.857 0.00 0.00 0.00 4.49
2594 3942 4.270084 TGTTTTCTTAGCAGTCTTGTCGTG 59.730 41.667 0.00 0.00 0.00 4.35
2595 3943 4.439057 TGTTTTCTTAGCAGTCTTGTCGT 58.561 39.130 0.00 0.00 0.00 4.34
2596 3944 5.006746 AGTTGTTTTCTTAGCAGTCTTGTCG 59.993 40.000 0.00 0.00 0.00 4.35
2597 3945 6.364945 AGTTGTTTTCTTAGCAGTCTTGTC 57.635 37.500 0.00 0.00 0.00 3.18
2598 3946 6.759497 AAGTTGTTTTCTTAGCAGTCTTGT 57.241 33.333 0.00 0.00 0.00 3.16
2599 3947 7.670894 GAAAGTTGTTTTCTTAGCAGTCTTG 57.329 36.000 0.00 0.00 41.61 3.02
2611 3959 4.024809 CACGAGGAGGAGAAAGTTGTTTTC 60.025 45.833 0.00 0.00 44.52 2.29
2612 3960 3.877508 CACGAGGAGGAGAAAGTTGTTTT 59.122 43.478 0.00 0.00 0.00 2.43
2613 3961 3.134081 TCACGAGGAGGAGAAAGTTGTTT 59.866 43.478 0.00 0.00 0.00 2.83
2614 3962 2.698797 TCACGAGGAGGAGAAAGTTGTT 59.301 45.455 0.00 0.00 0.00 2.83
2615 3963 2.317040 TCACGAGGAGGAGAAAGTTGT 58.683 47.619 0.00 0.00 0.00 3.32
2616 3964 3.257393 CATCACGAGGAGGAGAAAGTTG 58.743 50.000 0.00 0.00 0.00 3.16
2617 3965 2.900546 ACATCACGAGGAGGAGAAAGTT 59.099 45.455 0.00 0.00 0.00 2.66
2618 3966 2.530701 ACATCACGAGGAGGAGAAAGT 58.469 47.619 0.00 0.00 0.00 2.66
2619 3967 3.181485 GGTACATCACGAGGAGGAGAAAG 60.181 52.174 0.00 0.00 0.00 2.62
2620 3968 2.758979 GGTACATCACGAGGAGGAGAAA 59.241 50.000 0.00 0.00 0.00 2.52
2621 3969 2.025226 AGGTACATCACGAGGAGGAGAA 60.025 50.000 0.00 0.00 0.00 2.87
2622 3970 1.564818 AGGTACATCACGAGGAGGAGA 59.435 52.381 0.00 0.00 0.00 3.71
2623 3971 1.678627 CAGGTACATCACGAGGAGGAG 59.321 57.143 0.00 0.00 0.00 3.69
2624 3972 1.283905 TCAGGTACATCACGAGGAGGA 59.716 52.381 0.00 0.00 0.00 3.71
2625 3973 1.405821 GTCAGGTACATCACGAGGAGG 59.594 57.143 0.00 0.00 0.00 4.30
2626 3974 1.064208 CGTCAGGTACATCACGAGGAG 59.936 57.143 0.00 0.00 34.06 3.69
2627 3975 1.092348 CGTCAGGTACATCACGAGGA 58.908 55.000 0.00 0.00 34.06 3.71
2628 3976 0.809385 ACGTCAGGTACATCACGAGG 59.191 55.000 11.73 0.00 36.14 4.63
2629 3977 2.251040 CAACGTCAGGTACATCACGAG 58.749 52.381 11.73 0.00 36.14 4.18
2630 3978 1.610038 ACAACGTCAGGTACATCACGA 59.390 47.619 11.73 0.00 36.14 4.35
2631 3979 2.060326 ACAACGTCAGGTACATCACG 57.940 50.000 1.44 1.44 38.24 4.35
2632 3980 3.924686 CCTAACAACGTCAGGTACATCAC 59.075 47.826 0.00 0.00 0.00 3.06
2633 3981 3.575256 ACCTAACAACGTCAGGTACATCA 59.425 43.478 8.79 0.00 40.93 3.07
2634 3982 3.924686 CACCTAACAACGTCAGGTACATC 59.075 47.826 9.86 0.00 40.77 3.06
2635 3983 3.306502 CCACCTAACAACGTCAGGTACAT 60.307 47.826 9.86 0.00 40.77 2.29
2636 3984 2.036217 CCACCTAACAACGTCAGGTACA 59.964 50.000 9.86 0.00 40.77 2.90
2637 3985 2.036346 ACCACCTAACAACGTCAGGTAC 59.964 50.000 9.86 0.00 40.77 3.34
2638 3986 2.036217 CACCACCTAACAACGTCAGGTA 59.964 50.000 9.86 0.00 40.77 3.08
2639 3987 1.125633 ACCACCTAACAACGTCAGGT 58.874 50.000 5.54 5.54 43.56 4.00
2640 3988 1.508632 CACCACCTAACAACGTCAGG 58.491 55.000 0.00 0.00 35.45 3.86
2641 3989 1.069513 TCCACCACCTAACAACGTCAG 59.930 52.381 0.00 0.00 0.00 3.51
2642 3990 1.121378 TCCACCACCTAACAACGTCA 58.879 50.000 0.00 0.00 0.00 4.35
2643 3991 2.073816 CATCCACCACCTAACAACGTC 58.926 52.381 0.00 0.00 0.00 4.34
2644 3992 1.271163 CCATCCACCACCTAACAACGT 60.271 52.381 0.00 0.00 0.00 3.99
2645 3993 1.271163 ACCATCCACCACCTAACAACG 60.271 52.381 0.00 0.00 0.00 4.10
2646 3994 2.224670 TGACCATCCACCACCTAACAAC 60.225 50.000 0.00 0.00 0.00 3.32
2647 3995 2.058705 TGACCATCCACCACCTAACAA 58.941 47.619 0.00 0.00 0.00 2.83
2648 3996 1.349688 GTGACCATCCACCACCTAACA 59.650 52.381 0.00 0.00 0.00 2.41
2649 3997 1.628846 AGTGACCATCCACCACCTAAC 59.371 52.381 0.00 0.00 37.76 2.34
2650 3998 2.038863 AGTGACCATCCACCACCTAA 57.961 50.000 0.00 0.00 37.76 2.69
2651 3999 2.932184 TAGTGACCATCCACCACCTA 57.068 50.000 0.00 0.00 37.76 3.08
2652 4000 1.909302 CTTAGTGACCATCCACCACCT 59.091 52.381 0.00 0.00 37.76 4.00
2653 4001 1.065418 CCTTAGTGACCATCCACCACC 60.065 57.143 0.00 0.00 37.76 4.61
2654 4002 1.906574 TCCTTAGTGACCATCCACCAC 59.093 52.381 0.00 0.00 37.76 4.16
2655 4003 2.335681 TCCTTAGTGACCATCCACCA 57.664 50.000 0.00 0.00 37.76 4.17
2656 4004 3.933861 AATCCTTAGTGACCATCCACC 57.066 47.619 0.00 0.00 37.76 4.61
2657 4005 4.409247 AGGTAATCCTTAGTGACCATCCAC 59.591 45.833 0.00 0.00 42.12 4.02
2658 4006 4.408921 CAGGTAATCCTTAGTGACCATCCA 59.591 45.833 0.00 0.00 43.07 3.41
2659 4007 4.743955 GCAGGTAATCCTTAGTGACCATCC 60.744 50.000 0.00 0.00 43.07 3.51
2660 4008 4.141711 TGCAGGTAATCCTTAGTGACCATC 60.142 45.833 0.00 0.00 43.07 3.51
2661 4009 3.780294 TGCAGGTAATCCTTAGTGACCAT 59.220 43.478 0.00 0.00 43.07 3.55
2662 4010 3.178046 TGCAGGTAATCCTTAGTGACCA 58.822 45.455 0.00 0.00 43.07 4.02
2663 4011 3.906720 TGCAGGTAATCCTTAGTGACC 57.093 47.619 0.00 0.00 43.07 4.02
2664 4012 3.561725 GCATGCAGGTAATCCTTAGTGAC 59.438 47.826 14.21 0.00 43.07 3.67
2665 4013 3.199727 TGCATGCAGGTAATCCTTAGTGA 59.800 43.478 18.46 0.00 43.07 3.41
2666 4014 3.544684 TGCATGCAGGTAATCCTTAGTG 58.455 45.455 18.46 0.00 43.07 2.74
2667 4015 3.931907 TGCATGCAGGTAATCCTTAGT 57.068 42.857 18.46 0.00 43.07 2.24
2668 4016 5.942236 ACATATGCATGCAGGTAATCCTTAG 59.058 40.000 26.69 7.37 36.82 2.18
2669 4017 5.879763 ACATATGCATGCAGGTAATCCTTA 58.120 37.500 26.69 10.32 36.82 2.69
2670 4018 4.733165 ACATATGCATGCAGGTAATCCTT 58.267 39.130 26.69 8.22 36.82 3.36
2671 4019 4.377762 ACATATGCATGCAGGTAATCCT 57.622 40.909 26.69 9.00 38.95 3.24
2672 4020 4.520111 TCAACATATGCATGCAGGTAATCC 59.480 41.667 26.69 0.00 35.39 3.01
2673 4021 5.694231 TCAACATATGCATGCAGGTAATC 57.306 39.130 26.69 0.00 35.39 1.75
2674 4022 5.537295 ACATCAACATATGCATGCAGGTAAT 59.463 36.000 26.69 16.13 35.39 1.89
2675 4023 4.888823 ACATCAACATATGCATGCAGGTAA 59.111 37.500 26.69 14.78 35.39 2.85
2676 4024 4.463070 ACATCAACATATGCATGCAGGTA 58.537 39.130 26.69 14.89 35.39 3.08
2677 4025 3.293337 ACATCAACATATGCATGCAGGT 58.707 40.909 26.69 19.88 35.39 4.00
2678 4026 3.316868 TGACATCAACATATGCATGCAGG 59.683 43.478 26.69 19.23 35.39 4.85
2679 4027 4.561735 TGACATCAACATATGCATGCAG 57.438 40.909 26.69 15.02 35.39 4.41
2680 4028 4.022676 GGATGACATCAACATATGCATGCA 60.023 41.667 25.04 25.04 34.76 3.96
2681 4029 4.482386 GGATGACATCAACATATGCATGC 58.518 43.478 17.08 11.82 35.39 4.06
2682 4030 4.521256 TGGGATGACATCAACATATGCATG 59.479 41.667 17.08 5.57 38.21 4.06
2683 4031 4.521639 GTGGGATGACATCAACATATGCAT 59.478 41.667 17.08 3.79 0.00 3.96
2684 4032 3.884693 GTGGGATGACATCAACATATGCA 59.115 43.478 17.08 0.00 0.00 3.96
2685 4033 3.884693 TGTGGGATGACATCAACATATGC 59.115 43.478 17.08 4.75 0.00 3.14
2686 4034 6.644248 AATGTGGGATGACATCAACATATG 57.356 37.500 24.88 0.00 37.22 1.78
2687 4035 8.945195 AATAATGTGGGATGACATCAACATAT 57.055 30.769 24.88 18.97 37.22 1.78
2688 4036 8.765488 AAATAATGTGGGATGACATCAACATA 57.235 30.769 24.88 17.95 37.22 2.29
2689 4037 7.469043 CGAAATAATGTGGGATGACATCAACAT 60.469 37.037 21.53 21.53 38.78 2.71
2690 4038 6.183360 CGAAATAATGTGGGATGACATCAACA 60.183 38.462 19.61 19.61 35.43 3.33
2691 4039 6.183360 ACGAAATAATGTGGGATGACATCAAC 60.183 38.462 17.08 14.02 35.43 3.18
2692 4040 5.885352 ACGAAATAATGTGGGATGACATCAA 59.115 36.000 17.08 2.03 35.43 2.57
2693 4041 5.436175 ACGAAATAATGTGGGATGACATCA 58.564 37.500 17.08 0.00 35.43 3.07
2694 4042 5.760253 AGACGAAATAATGTGGGATGACATC 59.240 40.000 6.91 6.91 35.43 3.06
2695 4043 5.684704 AGACGAAATAATGTGGGATGACAT 58.315 37.500 0.00 0.00 38.23 3.06
2696 4044 5.097742 AGACGAAATAATGTGGGATGACA 57.902 39.130 0.00 0.00 0.00 3.58
2697 4045 5.116180 TGAGACGAAATAATGTGGGATGAC 58.884 41.667 0.00 0.00 0.00 3.06
2698 4046 5.351948 TGAGACGAAATAATGTGGGATGA 57.648 39.130 0.00 0.00 0.00 2.92
2699 4047 6.624352 AATGAGACGAAATAATGTGGGATG 57.376 37.500 0.00 0.00 0.00 3.51
2700 4048 7.645058 AAAATGAGACGAAATAATGTGGGAT 57.355 32.000 0.00 0.00 0.00 3.85
2701 4049 7.461182 AAAAATGAGACGAAATAATGTGGGA 57.539 32.000 0.00 0.00 0.00 4.37
2728 4076 9.736023 CACTCAGTTCAAAAGTTATAGCTTTTT 57.264 29.630 20.74 7.51 43.66 1.94
2729 4077 8.903820 ACACTCAGTTCAAAAGTTATAGCTTTT 58.096 29.630 18.40 18.40 46.08 2.27
2730 4078 8.451908 ACACTCAGTTCAAAAGTTATAGCTTT 57.548 30.769 8.61 8.61 40.07 3.51
2731 4079 7.715249 TGACACTCAGTTCAAAAGTTATAGCTT 59.285 33.333 0.00 0.00 0.00 3.74
2732 4080 7.217200 TGACACTCAGTTCAAAAGTTATAGCT 58.783 34.615 0.00 0.00 0.00 3.32
2733 4081 7.421530 TGACACTCAGTTCAAAAGTTATAGC 57.578 36.000 0.00 0.00 0.00 2.97
2736 4084 9.520204 CATTTTGACACTCAGTTCAAAAGTTAT 57.480 29.630 21.74 10.70 38.90 1.89
2737 4085 8.735315 TCATTTTGACACTCAGTTCAAAAGTTA 58.265 29.630 21.74 13.04 38.90 2.24
2738 4086 7.601856 TCATTTTGACACTCAGTTCAAAAGTT 58.398 30.769 21.74 11.38 38.90 2.66
2739 4087 7.156876 TCATTTTGACACTCAGTTCAAAAGT 57.843 32.000 21.74 13.33 38.90 2.66
2740 4088 8.464770 TTTCATTTTGACACTCAGTTCAAAAG 57.535 30.769 21.74 16.66 38.90 2.27
2741 4089 8.824159 TTTTCATTTTGACACTCAGTTCAAAA 57.176 26.923 20.56 20.56 39.35 2.44
2742 4090 9.086336 GATTTTCATTTTGACACTCAGTTCAAA 57.914 29.630 9.69 9.69 0.00 2.69
2743 4091 7.706179 GGATTTTCATTTTGACACTCAGTTCAA 59.294 33.333 0.00 0.00 0.00 2.69
2744 4092 7.202526 GGATTTTCATTTTGACACTCAGTTCA 58.797 34.615 0.00 0.00 0.00 3.18
2745 4093 6.360681 CGGATTTTCATTTTGACACTCAGTTC 59.639 38.462 0.00 0.00 0.00 3.01
2746 4094 6.183360 ACGGATTTTCATTTTGACACTCAGTT 60.183 34.615 0.00 0.00 0.00 3.16
2747 4095 5.299279 ACGGATTTTCATTTTGACACTCAGT 59.701 36.000 0.00 0.00 0.00 3.41
2748 4096 5.762045 ACGGATTTTCATTTTGACACTCAG 58.238 37.500 0.00 0.00 0.00 3.35
2749 4097 5.766150 ACGGATTTTCATTTTGACACTCA 57.234 34.783 0.00 0.00 0.00 3.41
2750 4098 7.463469 AAAACGGATTTTCATTTTGACACTC 57.537 32.000 0.00 0.00 32.29 3.51
2762 4110 6.020971 ACCTAATGGTGAAAACGGATTTTC 57.979 37.500 5.71 5.71 46.51 2.29
2771 4119 9.011307 TCGTCACGAAAAACCTAATGGTGAAAA 62.011 37.037 0.00 0.00 38.79 2.29
2772 4120 7.619665 TCGTCACGAAAAACCTAATGGTGAAA 61.620 38.462 0.00 0.00 38.79 2.69
2773 4121 6.197173 TCGTCACGAAAAACCTAATGGTGAA 61.197 40.000 0.00 0.00 38.79 3.18
2774 4122 4.740034 TCGTCACGAAAAACCTAATGGTGA 60.740 41.667 0.00 0.00 38.79 4.02
2775 4123 3.495377 TCGTCACGAAAAACCTAATGGTG 59.505 43.478 0.00 0.00 38.79 4.17
2776 4124 3.731089 TCGTCACGAAAAACCTAATGGT 58.269 40.909 0.00 0.00 39.92 3.55
2777 4125 3.991773 TCTCGTCACGAAAAACCTAATGG 59.008 43.478 0.00 0.00 34.74 3.16
2778 4126 5.779806 ATCTCGTCACGAAAAACCTAATG 57.220 39.130 0.00 0.00 34.74 1.90
2779 4127 6.796705 AAATCTCGTCACGAAAAACCTAAT 57.203 33.333 0.00 0.00 34.74 1.73
2780 4128 6.258287 TGAAAATCTCGTCACGAAAAACCTAA 59.742 34.615 0.00 0.00 34.74 2.69
2781 4129 5.754406 TGAAAATCTCGTCACGAAAAACCTA 59.246 36.000 0.00 0.00 34.74 3.08
2782 4130 4.573201 TGAAAATCTCGTCACGAAAAACCT 59.427 37.500 0.00 0.00 34.74 3.50
2783 4131 4.839796 TGAAAATCTCGTCACGAAAAACC 58.160 39.130 0.00 0.00 34.74 3.27
2784 4132 6.784068 TTTGAAAATCTCGTCACGAAAAAC 57.216 33.333 0.00 0.00 34.74 2.43
2785 4133 7.024768 AGTTTTGAAAATCTCGTCACGAAAAA 58.975 30.769 0.00 0.18 34.74 1.94
2786 4134 6.548171 AGTTTTGAAAATCTCGTCACGAAAA 58.452 32.000 0.00 0.00 34.74 2.29
2787 4135 6.114221 AGTTTTGAAAATCTCGTCACGAAA 57.886 33.333 0.00 0.00 34.74 3.46
2788 4136 5.728351 AGTTTTGAAAATCTCGTCACGAA 57.272 34.783 0.00 0.00 34.74 3.85
2789 4137 6.210796 TCTAGTTTTGAAAATCTCGTCACGA 58.789 36.000 0.00 0.00 0.00 4.35
2790 4138 6.448053 TCTAGTTTTGAAAATCTCGTCACG 57.552 37.500 0.00 0.00 0.00 4.35
2791 4139 7.413109 GGGATCTAGTTTTGAAAATCTCGTCAC 60.413 40.741 0.00 0.00 0.00 3.67
2792 4140 6.594159 GGGATCTAGTTTTGAAAATCTCGTCA 59.406 38.462 0.00 0.00 0.00 4.35
2793 4141 6.594159 TGGGATCTAGTTTTGAAAATCTCGTC 59.406 38.462 0.00 0.00 0.00 4.20
2794 4142 6.472887 TGGGATCTAGTTTTGAAAATCTCGT 58.527 36.000 0.00 0.00 0.00 4.18
2795 4143 6.985188 TGGGATCTAGTTTTGAAAATCTCG 57.015 37.500 0.00 0.00 0.00 4.04
2797 4145 9.927081 ACATATGGGATCTAGTTTTGAAAATCT 57.073 29.630 7.80 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.