Multiple sequence alignment - TraesCS3B01G373800

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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 TraesCS3B01G373800 chr3B 100.000 4876 0 0 1 4876 586694125 586699000 0.000000e+00 9005.0
1 TraesCS3B01G373800 chr3B 87.196 1601 143 28 2108 3676 83472932 83471362 0.000000e+00 1764.0
2 TraesCS3B01G373800 chr3B 86.658 802 88 11 2886 3676 83468447 83467654 0.000000e+00 870.0
3 TraesCS3B01G373800 chr3B 87.472 447 39 7 1660 2094 83473415 83472974 2.620000e-137 499.0
4 TraesCS3B01G373800 chr3B 83.964 449 38 20 1076 1505 83473851 83473418 2.730000e-107 399.0
5 TraesCS3B01G373800 chr3B 81.623 419 49 18 3763 4173 83467658 83467260 6.090000e-84 322.0
6 TraesCS3B01G373800 chr3B 79.878 328 35 21 3763 4075 83471366 83471055 1.380000e-50 211.0
7 TraesCS3B01G373800 chr3B 84.507 142 11 5 2650 2780 83468591 83468450 3.960000e-26 130.0
8 TraesCS3B01G373800 chr3B 98.214 56 1 0 3714 3769 586697782 586697837 1.120000e-16 99.0
9 TraesCS3B01G373800 chr3B 98.214 56 1 0 3658 3713 586697838 586697893 1.120000e-16 99.0
10 TraesCS3B01G373800 chr3B 88.312 77 7 1 4336 4412 586731992 586732066 1.870000e-14 91.6
11 TraesCS3B01G373800 chr3B 87.692 65 4 4 641 702 586694722 586694785 6.770000e-09 73.1
12 TraesCS3B01G373800 chr3B 87.692 65 4 4 598 661 586694765 586694826 6.770000e-09 73.1
13 TraesCS3B01G373800 chr3D 94.268 2111 95 18 2108 4204 447561398 447563496 0.000000e+00 3205.0
14 TraesCS3B01G373800 chr3D 89.126 1030 50 34 636 1620 447559892 447560904 0.000000e+00 1225.0
15 TraesCS3B01G373800 chr3D 87.640 712 72 11 2969 3676 52812426 52811727 0.000000e+00 813.0
16 TraesCS3B01G373800 chr3D 95.127 513 22 2 4338 4848 447563589 447564100 0.000000e+00 806.0
17 TraesCS3B01G373800 chr3D 87.368 475 37 17 1636 2091 447560853 447561323 1.560000e-144 523.0
18 TraesCS3B01G373800 chr3D 84.116 447 24 16 95 524 447559471 447559887 5.920000e-104 388.0
19 TraesCS3B01G373800 chr3D 83.178 428 56 3 4422 4848 447578666 447579078 1.280000e-100 377.0
20 TraesCS3B01G373800 chr3D 96.875 128 4 0 1075 1202 52816697 52816570 1.060000e-51 215.0
21 TraesCS3B01G373800 chr3D 96.429 56 1 1 1 55 447554346 447554401 1.870000e-14 91.6
22 TraesCS3B01G373800 chr3D 100.000 45 0 0 598 642 447559897 447559941 3.130000e-12 84.2
23 TraesCS3B01G373800 chr3A 87.356 1653 101 65 1 1614 588932924 588934507 0.000000e+00 1796.0
24 TraesCS3B01G373800 chr3A 88.224 1036 95 13 2644 3657 64325709 64324679 0.000000e+00 1212.0
25 TraesCS3B01G373800 chr3A 89.512 963 66 26 2121 3064 588934993 588935939 0.000000e+00 1186.0
26 TraesCS3B01G373800 chr3A 94.516 620 31 2 3068 3685 588935973 588936591 0.000000e+00 953.0
27 TraesCS3B01G373800 chr3A 90.855 503 37 2 4349 4848 588937155 588937651 0.000000e+00 665.0
28 TraesCS3B01G373800 chr3A 93.864 440 18 6 3742 4180 588936564 588936995 0.000000e+00 654.0
29 TraesCS3B01G373800 chr3A 89.813 481 31 12 1625 2091 588934450 588934926 6.980000e-168 601.0
30 TraesCS3B01G373800 chr3A 90.676 429 40 0 4421 4849 589188265 589188693 5.480000e-159 571.0
31 TraesCS3B01G373800 chr3A 82.009 428 61 3 4422 4848 589243282 589243694 2.790000e-92 350.0
32 TraesCS3B01G373800 chr3A 81.166 446 49 21 1075 1505 64326468 64326043 4.710000e-85 326.0
33 TraesCS3B01G373800 chr3A 81.633 294 35 11 3782 4074 64320007 64319732 4.910000e-55 226.0
34 TraesCS3B01G373800 chr3A 100.000 28 0 0 3686 3713 588936564 588936591 9.000000e-03 52.8
35 TraesCS3B01G373800 chr3A 100.000 28 0 0 3714 3741 588936564 588936591 9.000000e-03 52.8
36 TraesCS3B01G373800 chrUn 87.640 712 72 11 2969 3676 304503119 304503818 0.000000e+00 813.0
37 TraesCS3B01G373800 chr1D 87.692 130 15 1 1057 1186 6217943 6218071 3.040000e-32 150.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G373800 chr3B 586694125 586699000 4875 False 9005.000000 9005 100.000000 1 4876 1 chr3B.!!$F1 4875
1 TraesCS3B01G373800 chr3B 83467260 83473851 6591 True 599.285714 1764 84.471143 1076 4173 7 chr3B.!!$R1 3097
2 TraesCS3B01G373800 chr3D 447559471 447564100 4629 False 1038.533333 3205 91.667500 95 4848 6 chr3D.!!$F3 4753
3 TraesCS3B01G373800 chr3D 52811727 52812426 699 True 813.000000 813 87.640000 2969 3676 1 chr3D.!!$R1 707
4 TraesCS3B01G373800 chr3A 64324679 64326468 1789 True 769.000000 1212 84.695000 1075 3657 2 chr3A.!!$R2 2582
5 TraesCS3B01G373800 chr3A 588932924 588937651 4727 False 745.075000 1796 93.239500 1 4848 8 chr3A.!!$F3 4847
6 TraesCS3B01G373800 chrUn 304503119 304503818 699 False 813.000000 813 87.640000 2969 3676 1 chrUn.!!$F1 707

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
71 72 0.038618 TCGAGATCAACACCCACACG 60.039 55.0 0.00 0.0 0.00 4.49 F
528 545 0.110328 CGCACTTCTTCTTGCAGCAG 60.110 55.0 0.00 0.0 38.76 4.24 F
1570 1686 0.179048 TAACTGGCGATGGGCTGATG 60.179 55.0 14.42 0.0 42.94 3.07 F
3161 3429 0.759346 ATCCTCTAATGGTCCACGGC 59.241 55.0 0.00 0.0 0.00 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1616 1732 0.466124 TGTGTCATCACCGACCACAA 59.534 50.0 0.00 0.0 43.26 3.33 R
1921 2054 0.545071 AAGGGGGTGCTTTCAATGGG 60.545 55.0 0.00 0.0 0.00 4.00 R
3164 3432 1.975363 GCCTCGCTGTGATCTTGTGC 61.975 60.0 0.00 0.0 0.00 4.57 R
4534 8645 0.179073 CCACCGGAGAGCATTTCGAT 60.179 55.0 9.46 0.0 0.00 3.59 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
36 37 0.935194 TCCCTTCTACTCCTCCTCCC 59.065 60.000 0.00 0.00 0.00 4.30
37 38 0.938192 CCCTTCTACTCCTCCTCCCT 59.062 60.000 0.00 0.00 0.00 4.20
41 42 0.048117 TCTACTCCTCCTCCCTCCCT 59.952 60.000 0.00 0.00 0.00 4.20
42 43 0.187361 CTACTCCTCCTCCCTCCCTG 59.813 65.000 0.00 0.00 0.00 4.45
43 44 1.950748 TACTCCTCCTCCCTCCCTGC 61.951 65.000 0.00 0.00 0.00 4.85
44 45 4.095400 TCCTCCTCCCTCCCTGCC 62.095 72.222 0.00 0.00 0.00 4.85
46 47 4.101077 CTCCTCCCTCCCTGCCCT 62.101 72.222 0.00 0.00 0.00 5.19
47 48 2.623763 TCCTCCCTCCCTGCCCTA 60.624 66.667 0.00 0.00 0.00 3.53
48 49 2.027059 TCCTCCCTCCCTGCCCTAT 61.027 63.158 0.00 0.00 0.00 2.57
49 50 1.537643 CCTCCCTCCCTGCCCTATC 60.538 68.421 0.00 0.00 0.00 2.08
50 51 1.537643 CTCCCTCCCTGCCCTATCC 60.538 68.421 0.00 0.00 0.00 2.59
51 52 2.290393 CCCTCCCTGCCCTATCCA 59.710 66.667 0.00 0.00 0.00 3.41
52 53 1.151721 CCCTCCCTGCCCTATCCAT 60.152 63.158 0.00 0.00 0.00 3.41
53 54 1.204113 CCCTCCCTGCCCTATCCATC 61.204 65.000 0.00 0.00 0.00 3.51
54 55 1.548357 CCTCCCTGCCCTATCCATCG 61.548 65.000 0.00 0.00 0.00 3.84
55 56 0.542938 CTCCCTGCCCTATCCATCGA 60.543 60.000 0.00 0.00 0.00 3.59
56 57 0.542938 TCCCTGCCCTATCCATCGAG 60.543 60.000 0.00 0.00 0.00 4.04
57 58 0.542938 CCCTGCCCTATCCATCGAGA 60.543 60.000 0.00 0.00 0.00 4.04
58 59 1.566211 CCTGCCCTATCCATCGAGAT 58.434 55.000 0.00 0.00 0.00 2.75
59 60 1.480137 CCTGCCCTATCCATCGAGATC 59.520 57.143 0.00 0.00 0.00 2.75
60 61 2.174360 CTGCCCTATCCATCGAGATCA 58.826 52.381 0.00 0.00 0.00 2.92
61 62 2.564504 CTGCCCTATCCATCGAGATCAA 59.435 50.000 0.00 0.00 0.00 2.57
62 63 2.300152 TGCCCTATCCATCGAGATCAAC 59.700 50.000 0.00 0.00 0.00 3.18
63 64 2.300152 GCCCTATCCATCGAGATCAACA 59.700 50.000 0.00 0.00 0.00 3.33
64 65 3.862642 GCCCTATCCATCGAGATCAACAC 60.863 52.174 0.00 0.00 0.00 3.32
65 66 3.306364 CCCTATCCATCGAGATCAACACC 60.306 52.174 0.00 0.00 0.00 4.16
66 67 2.918712 ATCCATCGAGATCAACACCC 57.081 50.000 0.00 0.00 0.00 4.61
67 68 1.567357 TCCATCGAGATCAACACCCA 58.433 50.000 0.00 0.00 0.00 4.51
71 72 0.038618 TCGAGATCAACACCCACACG 60.039 55.000 0.00 0.00 0.00 4.49
73 74 1.298859 GAGATCAACACCCACACGGC 61.299 60.000 0.00 0.00 33.26 5.68
83 84 2.821810 CACACGGCCACACACACA 60.822 61.111 2.24 0.00 0.00 3.72
84 85 2.822255 ACACGGCCACACACACAC 60.822 61.111 2.24 0.00 0.00 3.82
86 87 4.868116 ACGGCCACACACACACCC 62.868 66.667 2.24 0.00 0.00 4.61
87 88 4.866224 CGGCCACACACACACCCA 62.866 66.667 2.24 0.00 0.00 4.51
148 157 0.895559 CCTTGACCAGGCAAGAACCC 60.896 60.000 14.96 0.00 46.31 4.11
245 254 4.007457 GCATCCTTCAAGCCAGCA 57.993 55.556 0.00 0.00 0.00 4.41
246 255 1.509923 GCATCCTTCAAGCCAGCAC 59.490 57.895 0.00 0.00 0.00 4.40
263 272 4.463879 CCAGCACTGCGAGGAGGG 62.464 72.222 9.29 0.00 32.04 4.30
270 279 1.984570 CTGCGAGGAGGGGAGTGAA 60.985 63.158 0.00 0.00 0.00 3.18
273 282 1.617947 GCGAGGAGGGGAGTGAATGT 61.618 60.000 0.00 0.00 0.00 2.71
347 364 5.830991 AGAGAGAGAGAGAGAGAGAGAGTAC 59.169 48.000 0.00 0.00 0.00 2.73
381 398 0.111253 AGTTCCCTGCCTGGTTTCTG 59.889 55.000 0.00 0.00 0.00 3.02
462 479 2.414825 CTGCCGCTTCTTCTTCTTCTTC 59.585 50.000 0.00 0.00 0.00 2.87
463 480 2.037772 TGCCGCTTCTTCTTCTTCTTCT 59.962 45.455 0.00 0.00 0.00 2.85
464 481 2.670905 GCCGCTTCTTCTTCTTCTTCTC 59.329 50.000 0.00 0.00 0.00 2.87
502 519 3.257127 AGACACCTCTTCTTCTTTCTCCG 59.743 47.826 0.00 0.00 0.00 4.63
526 543 0.165511 CTCGCACTTCTTCTTGCAGC 59.834 55.000 0.00 0.00 38.76 5.25
527 544 0.532640 TCGCACTTCTTCTTGCAGCA 60.533 50.000 0.00 0.00 38.76 4.41
528 545 0.110328 CGCACTTCTTCTTGCAGCAG 60.110 55.000 0.00 0.00 38.76 4.24
529 546 0.386985 GCACTTCTTCTTGCAGCAGC 60.387 55.000 0.00 0.00 38.68 5.25
731 782 4.680237 TCCGGCAGCACACTTCGG 62.680 66.667 0.00 0.00 39.95 4.30
740 791 1.507141 GCACACTTCGGTCCCAACAG 61.507 60.000 0.00 0.00 0.00 3.16
743 794 0.944311 CACTTCGGTCCCAACAGTCG 60.944 60.000 0.00 0.00 0.00 4.18
761 812 1.064458 GCGGTTCGAGCTCTCTACC 59.936 63.158 12.85 14.25 0.00 3.18
769 820 2.692557 TCGAGCTCTCTACCTACGTACT 59.307 50.000 12.85 0.00 0.00 2.73
966 1035 0.610232 CTTTTCTCCCCACAGCCTGG 60.610 60.000 0.00 0.00 40.26 4.45
1284 1380 5.293569 CGAGTAAAAGTCTCTCTCTCTCTCC 59.706 48.000 0.00 0.00 0.00 3.71
1285 1381 6.388619 AGTAAAAGTCTCTCTCTCTCTCCT 57.611 41.667 0.00 0.00 0.00 3.69
1446 1560 4.640364 TCCATTTCACCAATTTTCTTGGC 58.360 39.130 3.94 0.00 43.23 4.52
1480 1596 5.108254 GCTTTTAGTTTTGTCACTTCATGCG 60.108 40.000 0.00 0.00 0.00 4.73
1497 1613 1.973281 CGTGAGCAAGCCCCAACAT 60.973 57.895 0.00 0.00 0.00 2.71
1506 1622 2.362077 CAAGCCCCAACATATTGCTACC 59.638 50.000 0.00 0.00 34.17 3.18
1526 1642 2.029728 CCGCTCTTCTTGTTAATGCTCG 59.970 50.000 0.00 0.00 0.00 5.03
1543 1659 4.565022 TGCTCGTATCATTGTTCAGTCAA 58.435 39.130 0.00 0.00 0.00 3.18
1558 1674 6.533367 TGTTCAGTCAATTGTTTTTAACTGGC 59.467 34.615 17.71 13.07 35.86 4.85
1564 1680 3.651803 TTGTTTTTAACTGGCGATGGG 57.348 42.857 0.00 0.00 0.00 4.00
1565 1681 1.271102 TGTTTTTAACTGGCGATGGGC 59.729 47.619 0.00 0.00 42.51 5.36
1566 1682 1.544246 GTTTTTAACTGGCGATGGGCT 59.456 47.619 2.36 0.00 42.94 5.19
1567 1683 1.173043 TTTTAACTGGCGATGGGCTG 58.827 50.000 6.62 6.62 42.94 4.85
1568 1684 0.326595 TTTAACTGGCGATGGGCTGA 59.673 50.000 14.42 0.00 42.94 4.26
1569 1685 0.546122 TTAACTGGCGATGGGCTGAT 59.454 50.000 14.42 5.75 42.94 2.90
1570 1686 0.179048 TAACTGGCGATGGGCTGATG 60.179 55.000 14.42 0.00 42.94 3.07
1571 1687 2.593725 CTGGCGATGGGCTGATGG 60.594 66.667 2.36 0.00 42.94 3.51
1600 1716 4.157289 CCATTTCACTTTGCTCATGCTAGT 59.843 41.667 0.00 0.00 40.48 2.57
1603 1719 4.128925 TCACTTTGCTCATGCTAGTAGG 57.871 45.455 0.00 0.00 40.48 3.18
1615 1731 5.817296 TCATGCTAGTAGGTGCTTATTTGTG 59.183 40.000 0.00 0.00 0.00 3.33
1616 1732 5.160607 TGCTAGTAGGTGCTTATTTGTGT 57.839 39.130 0.00 0.00 0.00 3.72
1617 1733 5.556915 TGCTAGTAGGTGCTTATTTGTGTT 58.443 37.500 0.00 0.00 0.00 3.32
1618 1734 5.411361 TGCTAGTAGGTGCTTATTTGTGTTG 59.589 40.000 0.00 0.00 0.00 3.33
1619 1735 5.411669 GCTAGTAGGTGCTTATTTGTGTTGT 59.588 40.000 0.00 0.00 0.00 3.32
1620 1736 5.689383 AGTAGGTGCTTATTTGTGTTGTG 57.311 39.130 0.00 0.00 0.00 3.33
1621 1737 4.518970 AGTAGGTGCTTATTTGTGTTGTGG 59.481 41.667 0.00 0.00 0.00 4.17
1622 1738 3.295973 AGGTGCTTATTTGTGTTGTGGT 58.704 40.909 0.00 0.00 0.00 4.16
1623 1739 3.317993 AGGTGCTTATTTGTGTTGTGGTC 59.682 43.478 0.00 0.00 0.00 4.02
1628 1744 2.045561 ATTTGTGTTGTGGTCGGTGA 57.954 45.000 0.00 0.00 0.00 4.02
1665 1782 3.006110 ACCATTTCACTTTGTCCATGCTG 59.994 43.478 0.00 0.00 0.00 4.41
1685 1802 1.450025 GTAGGTGCTTAGTTGTGGCC 58.550 55.000 0.00 0.00 0.00 5.36
1718 1839 6.173339 TCCTTTGAGATTATCTGGTGTTGTC 58.827 40.000 0.00 0.00 0.00 3.18
1811 1944 9.362539 CATTTTCTATCATTAATTATGCAGGGC 57.637 33.333 0.00 0.00 34.06 5.19
1894 2027 8.543774 ACATCCTCTTGATTAGTGTAACAAGAT 58.456 33.333 0.00 0.00 44.52 2.40
1897 2030 8.188799 TCCTCTTGATTAGTGTAACAAGATACG 58.811 37.037 0.00 0.00 44.52 3.06
1898 2031 7.974501 CCTCTTGATTAGTGTAACAAGATACGT 59.025 37.037 0.00 0.00 44.52 3.57
1921 2054 8.818057 ACGTATTTGAGAGATTGTGTTATTAGC 58.182 33.333 0.00 0.00 0.00 3.09
1935 2068 4.159506 TGTTATTAGCCCATTGAAAGCACC 59.840 41.667 0.00 0.00 0.00 5.01
1992 2129 2.360350 ATTGGTGGCGCAGACCAG 60.360 61.111 24.56 0.00 44.36 4.00
2003 2140 0.886563 GCAGACCAGCAAGAGCAAAT 59.113 50.000 0.00 0.00 45.49 2.32
2019 2160 3.197265 GCAAATGCTCAACCACAAAACT 58.803 40.909 0.00 0.00 38.21 2.66
2020 2161 3.001533 GCAAATGCTCAACCACAAAACTG 59.998 43.478 0.00 0.00 38.21 3.16
2029 2170 6.636850 GCTCAACCACAAAACTGTACAATAAG 59.363 38.462 0.00 0.00 0.00 1.73
2056 2198 7.643579 ACATAACTGCAAGAAAGAAGAAGAAC 58.356 34.615 0.00 0.00 37.43 3.01
2094 2236 5.677319 ACTGCCAAATAAGACTAGCTGTA 57.323 39.130 0.00 0.00 31.78 2.74
2095 2237 6.240549 ACTGCCAAATAAGACTAGCTGTAT 57.759 37.500 0.00 0.00 31.78 2.29
2096 2238 6.653989 ACTGCCAAATAAGACTAGCTGTATT 58.346 36.000 0.00 0.00 34.21 1.89
2097 2239 7.112779 ACTGCCAAATAAGACTAGCTGTATTT 58.887 34.615 0.00 0.00 31.90 1.40
2099 2241 8.348285 TGCCAAATAAGACTAGCTGTATTTTT 57.652 30.769 0.00 0.00 31.90 1.94
2255 2455 2.673775 TTCCATGCTCCCTGTGAAAA 57.326 45.000 0.00 0.00 0.00 2.29
2271 2471 8.562892 CCCTGTGAAAATAAGCTGAATACTATG 58.437 37.037 0.00 0.00 0.00 2.23
2349 2555 3.177884 AGGCTGGGCTCACACCAA 61.178 61.111 3.75 0.00 37.59 3.67
2350 2556 2.036256 GGCTGGGCTCACACCAAT 59.964 61.111 0.00 0.00 37.59 3.16
2373 2579 8.455682 CAATGCATTGGAAGAATTTATTTGCTT 58.544 29.630 28.34 0.00 34.22 3.91
2540 2755 7.096551 ACCTTAAACGCTGCAAAATAAATGAT 58.903 30.769 0.00 0.00 0.00 2.45
2745 2966 9.520204 CCATTCCAATAATTTTATCACTCACAC 57.480 33.333 0.00 0.00 0.00 3.82
2761 2988 1.265095 CACACTGCACACTTGTCCATC 59.735 52.381 0.00 0.00 0.00 3.51
2776 3003 4.744570 TGTCCATCTCGTAGTGAAACATC 58.255 43.478 0.00 0.00 41.43 3.06
2792 3019 9.561069 AGTGAAACATCAGTTGATACTTTACTT 57.439 29.630 0.00 0.00 41.43 2.24
2793 3020 9.813080 GTGAAACATCAGTTGATACTTTACTTC 57.187 33.333 0.00 0.00 38.17 3.01
2794 3021 8.999431 TGAAACATCAGTTGATACTTTACTTCC 58.001 33.333 0.00 0.00 38.17 3.46
2795 3022 8.918202 AAACATCAGTTGATACTTTACTTCCA 57.082 30.769 0.00 0.00 38.17 3.53
3075 3338 7.067129 TGGTCTATTCTACTGTAGCAGTTAGTG 59.933 40.741 9.98 0.00 42.59 2.74
3083 3346 9.419297 TCTACTGTAGCAGTTAGTGTATTTTTG 57.581 33.333 9.98 0.00 42.59 2.44
3088 3351 8.679100 TGTAGCAGTTAGTGTATTTTTGTTGTT 58.321 29.630 0.00 0.00 0.00 2.83
3107 3375 8.183830 TGTTGTTTCAAGTGACATTTCAATTC 57.816 30.769 0.00 0.00 37.96 2.17
3155 3423 5.594725 TCTGTACTGTGATCCTCTAATGGTC 59.405 44.000 0.00 0.00 0.00 4.02
3161 3429 0.759346 ATCCTCTAATGGTCCACGGC 59.241 55.000 0.00 0.00 0.00 5.68
3164 3432 2.203015 CTAATGGTCCACGGCGGG 60.203 66.667 13.24 7.16 34.36 6.13
3281 3549 7.559170 AGCAAGCAAAAGATAAAGGATATCACT 59.441 33.333 4.83 0.00 0.00 3.41
3570 3841 1.366366 GGTCCGATGTATGGGTCCG 59.634 63.158 0.00 0.00 0.00 4.79
3685 7752 8.812972 ACACCATTTCTTCAGTAGACAGTATAA 58.187 33.333 0.00 0.00 30.90 0.98
3686 7753 9.653287 CACCATTTCTTCAGTAGACAGTATAAA 57.347 33.333 0.00 0.00 30.90 1.40
3691 7758 9.485206 TTTCTTCAGTAGACAGTATAAAACACC 57.515 33.333 0.00 0.00 30.90 4.16
3692 7759 8.185506 TCTTCAGTAGACAGTATAAAACACCA 57.814 34.615 0.00 0.00 0.00 4.17
3693 7760 8.812972 TCTTCAGTAGACAGTATAAAACACCAT 58.187 33.333 0.00 0.00 0.00 3.55
3694 7761 9.436957 CTTCAGTAGACAGTATAAAACACCATT 57.563 33.333 0.00 0.00 0.00 3.16
3695 7762 9.787435 TTCAGTAGACAGTATAAAACACCATTT 57.213 29.630 0.00 0.00 0.00 2.32
3696 7763 9.431887 TCAGTAGACAGTATAAAACACCATTTC 57.568 33.333 0.00 0.00 0.00 2.17
3697 7764 9.436957 CAGTAGACAGTATAAAACACCATTTCT 57.563 33.333 0.00 0.00 0.00 2.52
3700 7767 8.918202 AGACAGTATAAAACACCATTTCTTCA 57.082 30.769 0.00 0.00 0.00 3.02
3701 7768 9.003658 AGACAGTATAAAACACCATTTCTTCAG 57.996 33.333 0.00 0.00 0.00 3.02
3702 7769 8.691661 ACAGTATAAAACACCATTTCTTCAGT 57.308 30.769 0.00 0.00 0.00 3.41
3703 7770 9.787435 ACAGTATAAAACACCATTTCTTCAGTA 57.213 29.630 0.00 0.00 0.00 2.74
3707 7774 8.918202 ATAAAACACCATTTCTTCAGTAGACA 57.082 30.769 0.00 0.00 30.90 3.41
3708 7775 6.867662 AAACACCATTTCTTCAGTAGACAG 57.132 37.500 0.00 0.00 30.90 3.51
3709 7776 5.552870 ACACCATTTCTTCAGTAGACAGT 57.447 39.130 0.00 0.00 30.90 3.55
3710 7777 6.665992 ACACCATTTCTTCAGTAGACAGTA 57.334 37.500 0.00 0.00 30.90 2.74
3711 7778 7.246171 ACACCATTTCTTCAGTAGACAGTAT 57.754 36.000 0.00 0.00 30.90 2.12
3712 7779 8.362464 ACACCATTTCTTCAGTAGACAGTATA 57.638 34.615 0.00 0.00 30.90 1.47
3713 7780 8.812972 ACACCATTTCTTCAGTAGACAGTATAA 58.187 33.333 0.00 0.00 30.90 0.98
3714 7781 9.653287 CACCATTTCTTCAGTAGACAGTATAAA 57.347 33.333 0.00 0.00 30.90 1.40
3719 7786 9.485206 TTTCTTCAGTAGACAGTATAAAACACC 57.515 33.333 0.00 0.00 30.90 4.16
3720 7787 8.185506 TCTTCAGTAGACAGTATAAAACACCA 57.814 34.615 0.00 0.00 0.00 4.17
3721 7788 8.812972 TCTTCAGTAGACAGTATAAAACACCAT 58.187 33.333 0.00 0.00 0.00 3.55
3722 7789 9.436957 CTTCAGTAGACAGTATAAAACACCATT 57.563 33.333 0.00 0.00 0.00 3.16
3723 7790 9.787435 TTCAGTAGACAGTATAAAACACCATTT 57.213 29.630 0.00 0.00 0.00 2.32
3724 7791 9.431887 TCAGTAGACAGTATAAAACACCATTTC 57.568 33.333 0.00 0.00 0.00 2.17
3725 7792 9.436957 CAGTAGACAGTATAAAACACCATTTCT 57.563 33.333 0.00 0.00 0.00 2.52
3728 7795 8.918202 AGACAGTATAAAACACCATTTCTTCA 57.082 30.769 0.00 0.00 0.00 3.02
3729 7796 9.003658 AGACAGTATAAAACACCATTTCTTCAG 57.996 33.333 0.00 0.00 0.00 3.02
3730 7797 8.691661 ACAGTATAAAACACCATTTCTTCAGT 57.308 30.769 0.00 0.00 0.00 3.41
3731 7798 9.787435 ACAGTATAAAACACCATTTCTTCAGTA 57.213 29.630 0.00 0.00 0.00 2.74
3735 7802 8.918202 ATAAAACACCATTTCTTCAGTAGACA 57.082 30.769 0.00 0.00 30.90 3.41
3736 7803 6.867662 AAACACCATTTCTTCAGTAGACAG 57.132 37.500 0.00 0.00 30.90 3.51
3737 7804 5.552870 ACACCATTTCTTCAGTAGACAGT 57.447 39.130 0.00 0.00 30.90 3.55
3738 7805 6.665992 ACACCATTTCTTCAGTAGACAGTA 57.334 37.500 0.00 0.00 30.90 2.74
3739 7806 7.246171 ACACCATTTCTTCAGTAGACAGTAT 57.754 36.000 0.00 0.00 30.90 2.12
3740 7807 8.362464 ACACCATTTCTTCAGTAGACAGTATA 57.638 34.615 0.00 0.00 30.90 1.47
3741 7808 8.812972 ACACCATTTCTTCAGTAGACAGTATAA 58.187 33.333 0.00 0.00 30.90 0.98
3742 7809 9.653287 CACCATTTCTTCAGTAGACAGTATAAA 57.347 33.333 0.00 0.00 30.90 1.40
3747 7814 9.485206 TTTCTTCAGTAGACAGTATAAAACACC 57.515 33.333 0.00 0.00 30.90 4.16
3748 7815 8.185506 TCTTCAGTAGACAGTATAAAACACCA 57.814 34.615 0.00 0.00 0.00 4.17
3749 7816 8.812972 TCTTCAGTAGACAGTATAAAACACCAT 58.187 33.333 0.00 0.00 0.00 3.55
3750 7817 9.436957 CTTCAGTAGACAGTATAAAACACCATT 57.563 33.333 0.00 0.00 0.00 3.16
3751 7818 9.787435 TTCAGTAGACAGTATAAAACACCATTT 57.213 29.630 0.00 0.00 0.00 2.32
3752 7819 9.431887 TCAGTAGACAGTATAAAACACCATTTC 57.568 33.333 0.00 0.00 0.00 2.17
3753 7820 9.436957 CAGTAGACAGTATAAAACACCATTTCT 57.563 33.333 0.00 0.00 0.00 2.52
3756 7823 8.918202 AGACAGTATAAAACACCATTTCTTCA 57.082 30.769 0.00 0.00 0.00 3.02
3757 7824 9.003658 AGACAGTATAAAACACCATTTCTTCAG 57.996 33.333 0.00 0.00 0.00 3.02
3758 7825 7.593825 ACAGTATAAAACACCATTTCTTCAGC 58.406 34.615 0.00 0.00 0.00 4.26
3759 7826 7.230510 ACAGTATAAAACACCATTTCTTCAGCA 59.769 33.333 0.00 0.00 0.00 4.41
3760 7827 7.752239 CAGTATAAAACACCATTTCTTCAGCAG 59.248 37.037 0.00 0.00 0.00 4.24
3761 7828 6.899393 ATAAAACACCATTTCTTCAGCAGA 57.101 33.333 0.00 0.00 0.00 4.26
3762 7829 4.574599 AAACACCATTTCTTCAGCAGAC 57.425 40.909 0.00 0.00 0.00 3.51
3763 7830 3.213206 ACACCATTTCTTCAGCAGACA 57.787 42.857 0.00 0.00 0.00 3.41
3764 7831 3.144506 ACACCATTTCTTCAGCAGACAG 58.855 45.455 0.00 0.00 0.00 3.51
3765 7832 3.144506 CACCATTTCTTCAGCAGACAGT 58.855 45.455 0.00 0.00 0.00 3.55
3766 7833 4.202357 ACACCATTTCTTCAGCAGACAGTA 60.202 41.667 0.00 0.00 0.00 2.74
3767 7834 4.940046 CACCATTTCTTCAGCAGACAGTAT 59.060 41.667 0.00 0.00 0.00 2.12
3768 7835 6.108687 CACCATTTCTTCAGCAGACAGTATA 58.891 40.000 0.00 0.00 0.00 1.47
3776 7843 7.454225 TCTTCAGCAGACAGTATAGCTCTATA 58.546 38.462 0.00 0.00 34.61 1.31
3809 7879 6.544931 ACTGAATCTGATATGATGTTGGTTGG 59.455 38.462 0.00 0.00 0.00 3.77
3810 7880 6.425735 TGAATCTGATATGATGTTGGTTGGT 58.574 36.000 0.00 0.00 0.00 3.67
3883 7953 4.968197 GTCTGGGTGACACGAGAC 57.032 61.111 16.39 16.39 44.73 3.36
3896 7966 0.665369 ACGAGACGTTGTTTAGCCGG 60.665 55.000 0.00 0.00 36.35 6.13
3941 8011 3.218453 TGCCTTAGTGTAAAAAGCAGCA 58.782 40.909 0.00 0.00 0.00 4.41
4010 8080 1.880027 GCTCGAGTGGAATTGGTTTGT 59.120 47.619 15.13 0.00 0.00 2.83
4022 8092 3.512033 TTGGTTTGTTTTTCTCGTGGG 57.488 42.857 0.00 0.00 0.00 4.61
4040 8111 4.579869 GTGGGAATAGTTTGAGAAGCTGA 58.420 43.478 0.00 0.00 0.00 4.26
4041 8112 5.189180 GTGGGAATAGTTTGAGAAGCTGAT 58.811 41.667 0.00 0.00 0.00 2.90
4099 8173 0.865769 CAAGTGTTGGTACGCAGACC 59.134 55.000 0.00 0.00 40.21 3.85
4145 8219 4.058721 AGCTGTTTTGGGTGTTCATTTC 57.941 40.909 0.00 0.00 0.00 2.17
4149 8223 4.753233 TGTTTTGGGTGTTCATTTCTGTG 58.247 39.130 0.00 0.00 0.00 3.66
4160 8234 4.944619 TCATTTCTGTGAGACTCAGTGT 57.055 40.909 5.10 0.00 34.86 3.55
4161 8235 5.282055 TCATTTCTGTGAGACTCAGTGTT 57.718 39.130 5.10 0.00 34.86 3.32
4189 8263 8.773404 ACAGTGTAAATGTAACTATCAGAACC 57.227 34.615 0.00 0.00 47.00 3.62
4191 8265 8.656849 CAGTGTAAATGTAACTATCAGAACCAC 58.343 37.037 0.00 0.00 0.00 4.16
4194 8268 5.670792 AATGTAACTATCAGAACCACCGA 57.329 39.130 0.00 0.00 0.00 4.69
4201 8275 5.844004 ACTATCAGAACCACCGATTATGTC 58.156 41.667 0.00 0.00 0.00 3.06
4213 8287 4.170125 CGATTATGTCGCTCACAAACTC 57.830 45.455 0.00 0.00 44.33 3.01
4214 8288 3.859961 CGATTATGTCGCTCACAAACTCT 59.140 43.478 0.00 0.00 44.33 3.24
4215 8289 4.027295 CGATTATGTCGCTCACAAACTCTC 60.027 45.833 0.00 0.00 44.33 3.20
4216 8290 2.086054 ATGTCGCTCACAAACTCTCC 57.914 50.000 0.00 0.00 38.97 3.71
4217 8291 1.040646 TGTCGCTCACAAACTCTCCT 58.959 50.000 0.00 0.00 29.30 3.69
4218 8292 1.412710 TGTCGCTCACAAACTCTCCTT 59.587 47.619 0.00 0.00 29.30 3.36
4219 8293 1.795286 GTCGCTCACAAACTCTCCTTG 59.205 52.381 0.00 0.00 0.00 3.61
4220 8294 1.151668 CGCTCACAAACTCTCCTTGG 58.848 55.000 0.00 0.00 0.00 3.61
4221 8295 1.270305 CGCTCACAAACTCTCCTTGGA 60.270 52.381 0.00 0.00 0.00 3.53
4222 8296 2.421619 GCTCACAAACTCTCCTTGGAG 58.578 52.381 10.28 10.28 39.09 3.86
4223 8297 2.037772 GCTCACAAACTCTCCTTGGAGA 59.962 50.000 17.37 17.37 37.13 3.71
4257 8331 3.321682 CCAGGCCTCTGAAAAATCAACAA 59.678 43.478 0.00 0.00 43.49 2.83
4277 8351 7.232534 TCAACAAAGTTTCCAGCCAATATAACT 59.767 33.333 0.00 0.00 0.00 2.24
4278 8352 6.924111 ACAAAGTTTCCAGCCAATATAACTG 58.076 36.000 0.00 0.00 0.00 3.16
4280 8354 6.515272 AAGTTTCCAGCCAATATAACTGTG 57.485 37.500 0.00 0.00 0.00 3.66
4295 8369 8.691661 ATATAACTGTGGCGGAAAAGAATTAT 57.308 30.769 0.00 0.00 0.00 1.28
4305 8382 7.041372 TGGCGGAAAAGAATTATAGTTAGCATC 60.041 37.037 0.00 0.00 0.00 3.91
4334 8412 1.673033 GCACTCGCCAACAGTGTCTAT 60.673 52.381 0.00 0.00 42.89 1.98
4335 8413 2.416836 GCACTCGCCAACAGTGTCTATA 60.417 50.000 0.00 0.00 42.89 1.31
4336 8414 3.179830 CACTCGCCAACAGTGTCTATAC 58.820 50.000 0.00 0.00 37.15 1.47
4401 8512 6.872020 CCATTTCATGTGCAGAAGAAGAAATT 59.128 34.615 1.66 0.00 33.42 1.82
4728 8839 1.597854 CGTCCTGGCAGCACTTCAA 60.598 57.895 9.56 0.00 0.00 2.69
4833 8944 3.328343 TGGTAAGCTGCCTTTACCTACAA 59.672 43.478 23.28 7.90 31.55 2.41
4848 8959 5.161943 ACCTACAACAAGGATCAGGTTAC 57.838 43.478 0.00 0.00 39.15 2.50
4849 8960 4.019591 ACCTACAACAAGGATCAGGTTACC 60.020 45.833 0.00 0.00 39.15 2.85
4850 8961 4.019681 CCTACAACAAGGATCAGGTTACCA 60.020 45.833 3.51 0.00 39.15 3.25
4851 8962 4.447138 ACAACAAGGATCAGGTTACCAA 57.553 40.909 3.51 0.00 0.00 3.67
4852 8963 4.798882 ACAACAAGGATCAGGTTACCAAA 58.201 39.130 3.51 0.00 0.00 3.28
4853 8964 5.393866 ACAACAAGGATCAGGTTACCAAAT 58.606 37.500 3.51 0.00 0.00 2.32
4854 8965 5.838521 ACAACAAGGATCAGGTTACCAAATT 59.161 36.000 3.51 0.00 0.00 1.82
4855 8966 7.007723 ACAACAAGGATCAGGTTACCAAATTA 58.992 34.615 3.51 0.00 0.00 1.40
4856 8967 7.673926 ACAACAAGGATCAGGTTACCAAATTAT 59.326 33.333 3.51 0.00 0.00 1.28
4857 8968 8.531146 CAACAAGGATCAGGTTACCAAATTATT 58.469 33.333 3.51 0.00 0.00 1.40
4858 8969 9.762381 AACAAGGATCAGGTTACCAAATTATTA 57.238 29.630 3.51 0.00 0.00 0.98
4859 8970 9.185680 ACAAGGATCAGGTTACCAAATTATTAC 57.814 33.333 3.51 0.00 0.00 1.89
4860 8971 8.630037 CAAGGATCAGGTTACCAAATTATTACC 58.370 37.037 3.51 0.00 0.00 2.85
4861 8972 7.878495 AGGATCAGGTTACCAAATTATTACCA 58.122 34.615 3.51 0.00 0.00 3.25
4862 8973 8.340757 AGGATCAGGTTACCAAATTATTACCAA 58.659 33.333 3.51 0.00 0.00 3.67
4863 8974 8.410912 GGATCAGGTTACCAAATTATTACCAAC 58.589 37.037 3.51 0.00 0.00 3.77
4864 8975 8.887264 ATCAGGTTACCAAATTATTACCAACA 57.113 30.769 3.51 0.00 0.00 3.33
4865 8976 8.113173 TCAGGTTACCAAATTATTACCAACAC 57.887 34.615 3.51 0.00 0.00 3.32
4866 8977 7.945664 TCAGGTTACCAAATTATTACCAACACT 59.054 33.333 3.51 0.00 0.00 3.55
4867 8978 8.241367 CAGGTTACCAAATTATTACCAACACTC 58.759 37.037 3.51 0.00 0.00 3.51
4868 8979 8.168058 AGGTTACCAAATTATTACCAACACTCT 58.832 33.333 3.51 0.00 0.00 3.24
4869 8980 8.799367 GGTTACCAAATTATTACCAACACTCTT 58.201 33.333 0.00 0.00 0.00 2.85
4873 8984 9.010029 ACCAAATTATTACCAACACTCTTACTG 57.990 33.333 0.00 0.00 0.00 2.74
4874 8985 9.226606 CCAAATTATTACCAACACTCTTACTGA 57.773 33.333 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 0.542938 TCGATGGATAGGGCAGGGAG 60.543 60.000 0.00 0.00 0.00 4.30
37 38 0.542938 CTCGATGGATAGGGCAGGGA 60.543 60.000 0.00 0.00 0.00 4.20
41 42 2.300152 GTTGATCTCGATGGATAGGGCA 59.700 50.000 0.00 0.00 0.00 5.36
42 43 2.300152 TGTTGATCTCGATGGATAGGGC 59.700 50.000 0.00 0.00 0.00 5.19
43 44 3.306364 GGTGTTGATCTCGATGGATAGGG 60.306 52.174 0.00 0.00 0.00 3.53
44 45 3.306364 GGGTGTTGATCTCGATGGATAGG 60.306 52.174 0.00 0.00 0.00 2.57
46 47 3.069586 GTGGGTGTTGATCTCGATGGATA 59.930 47.826 0.00 0.00 0.00 2.59
47 48 2.118679 TGGGTGTTGATCTCGATGGAT 58.881 47.619 0.00 0.00 0.00 3.41
48 49 1.207089 GTGGGTGTTGATCTCGATGGA 59.793 52.381 0.00 0.00 0.00 3.41
49 50 1.066215 TGTGGGTGTTGATCTCGATGG 60.066 52.381 0.00 0.00 0.00 3.51
50 51 2.002586 GTGTGGGTGTTGATCTCGATG 58.997 52.381 0.00 0.00 0.00 3.84
51 52 1.404181 CGTGTGGGTGTTGATCTCGAT 60.404 52.381 0.00 0.00 0.00 3.59
52 53 0.038618 CGTGTGGGTGTTGATCTCGA 60.039 55.000 0.00 0.00 0.00 4.04
53 54 1.014044 CCGTGTGGGTGTTGATCTCG 61.014 60.000 0.00 0.00 0.00 4.04
54 55 1.298859 GCCGTGTGGGTGTTGATCTC 61.299 60.000 0.00 0.00 38.44 2.75
55 56 1.302511 GCCGTGTGGGTGTTGATCT 60.303 57.895 0.00 0.00 38.44 2.75
56 57 2.332654 GGCCGTGTGGGTGTTGATC 61.333 63.158 0.00 0.00 38.44 2.92
57 58 2.282180 GGCCGTGTGGGTGTTGAT 60.282 61.111 0.00 0.00 38.44 2.57
58 59 3.798511 TGGCCGTGTGGGTGTTGA 61.799 61.111 0.00 0.00 38.44 3.18
59 60 3.591835 GTGGCCGTGTGGGTGTTG 61.592 66.667 0.00 0.00 38.44 3.33
60 61 4.116585 TGTGGCCGTGTGGGTGTT 62.117 61.111 0.00 0.00 38.44 3.32
61 62 4.868116 GTGTGGCCGTGTGGGTGT 62.868 66.667 0.00 0.00 38.44 4.16
62 63 4.866224 TGTGTGGCCGTGTGGGTG 62.866 66.667 0.00 0.00 38.44 4.61
63 64 4.868116 GTGTGTGGCCGTGTGGGT 62.868 66.667 0.00 0.00 38.44 4.51
64 65 4.866224 TGTGTGTGGCCGTGTGGG 62.866 66.667 0.00 0.00 39.58 4.61
65 66 3.582120 GTGTGTGTGGCCGTGTGG 61.582 66.667 0.00 0.00 38.77 4.17
66 67 2.821810 TGTGTGTGTGGCCGTGTG 60.822 61.111 0.00 0.00 0.00 3.82
67 68 2.822255 GTGTGTGTGTGGCCGTGT 60.822 61.111 0.00 0.00 0.00 4.49
71 72 1.832167 AATGGGTGTGTGTGTGGCC 60.832 57.895 0.00 0.00 0.00 5.36
73 74 1.397672 TTCAATGGGTGTGTGTGTGG 58.602 50.000 0.00 0.00 0.00 4.17
83 84 4.918588 AGACGGTTTCTATTTCAATGGGT 58.081 39.130 0.00 0.00 30.17 4.51
84 85 5.897377 AAGACGGTTTCTATTTCAATGGG 57.103 39.130 0.00 0.00 32.51 4.00
86 87 8.507249 AGAGAAAAGACGGTTTCTATTTCAATG 58.493 33.333 9.99 0.00 45.67 2.82
87 88 8.622948 AGAGAAAAGACGGTTTCTATTTCAAT 57.377 30.769 9.99 0.00 45.67 2.57
148 157 3.125829 TCTTCAGCTTAATTTGCTCTGCG 59.874 43.478 3.12 0.00 38.92 5.18
245 254 3.699894 CCTCCTCGCAGTGCTGGT 61.700 66.667 14.33 0.00 0.00 4.00
246 255 4.463879 CCCTCCTCGCAGTGCTGG 62.464 72.222 14.33 14.91 0.00 4.85
263 272 2.354259 CTCAGGCTCAACATTCACTCC 58.646 52.381 0.00 0.00 0.00 3.85
270 279 0.322277 CACTGGCTCAGGCTCAACAT 60.322 55.000 0.00 0.00 35.51 2.71
273 282 2.033141 GCACTGGCTCAGGCTCAA 59.967 61.111 0.00 0.00 35.51 3.02
347 364 8.110908 AGGCAGGGAACTATACTCTAGTAATAG 58.889 40.741 0.00 0.00 40.21 1.73
381 398 1.546029 GGATTGGGAAAAGCTGGACAC 59.454 52.381 0.00 0.00 0.00 3.67
462 479 2.282147 CTGCGACAGAGGAGCCAGAG 62.282 65.000 1.18 0.00 32.44 3.35
463 480 2.283173 TGCGACAGAGGAGCCAGA 60.283 61.111 0.00 0.00 0.00 3.86
464 481 2.183811 CTGCGACAGAGGAGCCAG 59.816 66.667 1.18 0.00 32.44 4.85
502 519 1.801178 CAAGAAGAAGTGCGAGGGAAC 59.199 52.381 0.00 0.00 0.00 3.62
526 543 1.246737 GGAAGGAAACAGGCCTGCTG 61.247 60.000 33.06 11.22 35.50 4.41
527 544 1.075659 GGAAGGAAACAGGCCTGCT 59.924 57.895 33.06 19.23 35.50 4.24
528 545 2.335712 CGGAAGGAAACAGGCCTGC 61.336 63.158 33.06 16.45 35.50 4.85
529 546 3.987404 CGGAAGGAAACAGGCCTG 58.013 61.111 31.60 31.60 35.50 4.85
694 715 2.451493 TGAACTTGGGGCAGGGGA 60.451 61.111 0.00 0.00 0.00 4.81
696 717 2.283173 GGTGAACTTGGGGCAGGG 60.283 66.667 0.00 0.00 0.00 4.45
697 718 1.303643 GAGGTGAACTTGGGGCAGG 60.304 63.158 0.00 0.00 0.00 4.85
699 720 2.843545 GGAGGTGAACTTGGGGCA 59.156 61.111 0.00 0.00 0.00 5.36
700 721 2.359975 CGGAGGTGAACTTGGGGC 60.360 66.667 0.00 0.00 0.00 5.80
731 782 2.280592 AACCGCGACTGTTGGGAC 60.281 61.111 8.23 0.00 0.00 4.46
740 791 1.703438 TAGAGAGCTCGAACCGCGAC 61.703 60.000 8.23 0.00 45.59 5.19
743 794 1.064458 GGTAGAGAGCTCGAACCGC 59.936 63.158 16.18 4.11 33.23 5.68
754 805 5.070580 GGGGTAGTAAGTACGTAGGTAGAGA 59.929 48.000 0.00 0.00 31.59 3.10
761 812 3.557595 CGTCTGGGGTAGTAAGTACGTAG 59.442 52.174 0.00 0.00 31.59 3.51
1284 1380 6.019559 CGGCCTTGAAAGAAGAAAAGAAAAAG 60.020 38.462 0.00 0.00 0.00 2.27
1285 1381 5.810074 CGGCCTTGAAAGAAGAAAAGAAAAA 59.190 36.000 0.00 0.00 0.00 1.94
1382 1490 3.784511 ACTCATTCCATCAGCCCATAG 57.215 47.619 0.00 0.00 0.00 2.23
1446 1560 7.530861 GTGACAAAACTAAAAGCAGTATTCTCG 59.469 37.037 0.00 0.00 0.00 4.04
1480 1596 1.767759 ATATGTTGGGGCTTGCTCAC 58.232 50.000 0.00 0.00 0.00 3.51
1506 1622 2.668457 ACGAGCATTAACAAGAAGAGCG 59.332 45.455 0.00 0.00 0.00 5.03
1543 1659 3.616317 GCCCATCGCCAGTTAAAAACAAT 60.616 43.478 0.00 0.00 0.00 2.71
1558 1674 0.882042 GTACTGCCATCAGCCCATCG 60.882 60.000 0.00 0.00 44.10 3.84
1570 1686 2.558359 AGCAAAGTGAAATGGTACTGCC 59.442 45.455 0.00 0.00 37.90 4.85
1571 1687 3.253188 TGAGCAAAGTGAAATGGTACTGC 59.747 43.478 0.00 0.00 0.00 4.40
1600 1716 4.465886 ACCACAACACAAATAAGCACCTA 58.534 39.130 0.00 0.00 0.00 3.08
1603 1719 3.296628 CGACCACAACACAAATAAGCAC 58.703 45.455 0.00 0.00 0.00 4.40
1615 1731 0.865769 GTGTCATCACCGACCACAAC 59.134 55.000 0.00 0.00 38.51 3.32
1616 1732 0.466124 TGTGTCATCACCGACCACAA 59.534 50.000 0.00 0.00 43.26 3.33
1617 1733 0.684535 ATGTGTCATCACCGACCACA 59.315 50.000 0.00 0.00 43.26 4.17
1618 1734 1.078709 CATGTGTCATCACCGACCAC 58.921 55.000 0.00 0.00 43.26 4.16
1619 1735 0.972883 TCATGTGTCATCACCGACCA 59.027 50.000 0.00 0.00 43.26 4.02
1620 1736 1.337728 TGTCATGTGTCATCACCGACC 60.338 52.381 12.18 0.00 43.26 4.79
1621 1737 1.995484 CTGTCATGTGTCATCACCGAC 59.005 52.381 0.00 9.50 43.26 4.79
1622 1738 1.618343 ACTGTCATGTGTCATCACCGA 59.382 47.619 0.00 0.00 43.26 4.69
1623 1739 2.084610 ACTGTCATGTGTCATCACCG 57.915 50.000 0.00 0.00 43.26 4.94
1628 1744 5.412594 GTGAAATGGTACTGTCATGTGTCAT 59.587 40.000 0.00 0.00 0.00 3.06
1665 1782 1.450025 GCCACAACTAAGCACCTACC 58.550 55.000 0.00 0.00 0.00 3.18
1685 1802 7.362142 CCAGATAATCTCAAAGGATGATGCATG 60.362 40.741 2.46 0.00 37.44 4.06
1718 1839 5.006068 CGTCACAGTCATCAACCAATCTATG 59.994 44.000 0.00 0.00 0.00 2.23
1762 1895 4.724399 ACACACCATGAACCACATCTTAA 58.276 39.130 0.00 0.00 37.07 1.85
1811 1944 9.438291 CTAAACAAAGAAGACACATTAACAGTG 57.562 33.333 8.02 8.02 42.56 3.66
1895 2028 8.818057 GCTAATAACACAATCTCTCAAATACGT 58.182 33.333 0.00 0.00 0.00 3.57
1896 2029 8.276325 GGCTAATAACACAATCTCTCAAATACG 58.724 37.037 0.00 0.00 0.00 3.06
1897 2030 8.560374 GGGCTAATAACACAATCTCTCAAATAC 58.440 37.037 0.00 0.00 0.00 1.89
1898 2031 8.271458 TGGGCTAATAACACAATCTCTCAAATA 58.729 33.333 0.00 0.00 0.00 1.40
1921 2054 0.545071 AAGGGGGTGCTTTCAATGGG 60.545 55.000 0.00 0.00 0.00 4.00
1935 2068 8.953313 CAAGTTACAATTTAGGTAAGTAAGGGG 58.047 37.037 0.00 0.00 34.23 4.79
2003 2140 3.348119 TGTACAGTTTTGTGGTTGAGCA 58.652 40.909 0.00 0.00 38.23 4.26
2029 2170 8.311650 TCTTCTTCTTTCTTGCAGTTATGTAC 57.688 34.615 0.00 0.00 0.00 2.90
2056 2198 1.536709 GCAGTTGTGTTCTTTGCCCTG 60.537 52.381 0.00 0.00 0.00 4.45
2128 2328 6.153680 CCAGTTAGTAAGACCTCAGAAGACAT 59.846 42.308 0.00 0.00 0.00 3.06
2132 2332 4.464597 AGCCAGTTAGTAAGACCTCAGAAG 59.535 45.833 0.00 0.00 0.00 2.85
2271 2471 6.430000 TCTGGCACTTTCTTGTACTATTTTCC 59.570 38.462 0.00 0.00 0.00 3.13
2313 2519 6.373779 CAGCCTGTTGTTAACTTCATAACAG 58.626 40.000 20.69 20.69 44.21 3.16
2349 2555 8.570068 AAAGCAAATAAATTCTTCCAATGCAT 57.430 26.923 0.00 0.00 33.89 3.96
2350 2556 7.982761 AAAGCAAATAAATTCTTCCAATGCA 57.017 28.000 0.00 0.00 33.89 3.96
2540 2755 6.348498 CACATGACAATCTTGTGTCCCTATA 58.652 40.000 13.81 0.00 46.13 1.31
2761 2988 7.030165 AGTATCAACTGATGTTTCACTACGAG 58.970 38.462 2.36 0.00 36.05 4.18
2776 3003 7.441157 TGACTTGTGGAAGTAAAGTATCAACTG 59.559 37.037 0.00 0.00 42.80 3.16
2792 3019 5.071788 AGGAATCAGTTAGTTGACTTGTGGA 59.928 40.000 0.00 0.00 0.00 4.02
2793 3020 5.308825 AGGAATCAGTTAGTTGACTTGTGG 58.691 41.667 0.00 0.00 0.00 4.17
2794 3021 6.483307 TGAAGGAATCAGTTAGTTGACTTGTG 59.517 38.462 0.00 0.00 33.04 3.33
2795 3022 6.591935 TGAAGGAATCAGTTAGTTGACTTGT 58.408 36.000 0.00 0.00 33.04 3.16
2846 3078 5.755375 TCAAGAAGTTCACAGAAGTTGCTAG 59.245 40.000 5.50 0.00 0.00 3.42
2936 3168 8.630054 AGTGTACCATAAAAGCACAATCTTTA 57.370 30.769 0.00 0.00 35.41 1.85
3007 3243 3.688272 CAGAAACTGAGCAAACTGTGTG 58.312 45.455 0.00 0.00 32.44 3.82
3083 3346 8.411318 AGAATTGAAATGTCACTTGAAACAAC 57.589 30.769 0.00 0.00 31.90 3.32
3088 3351 9.304731 CTGAAAAGAATTGAAATGTCACTTGAA 57.695 29.630 0.00 0.00 31.90 2.69
3107 3375 3.690460 ACCAAGCCTCATACCTGAAAAG 58.310 45.455 0.00 0.00 0.00 2.27
3161 3429 2.743752 CGCTGTGATCTTGTGCCCG 61.744 63.158 0.00 0.00 0.00 6.13
3164 3432 1.975363 GCCTCGCTGTGATCTTGTGC 61.975 60.000 0.00 0.00 0.00 4.57
3548 3816 2.725641 CCATACATCGGACCGCGA 59.274 61.111 8.23 0.00 0.00 5.87
3685 7752 6.357367 ACTGTCTACTGAAGAAATGGTGTTT 58.643 36.000 0.00 0.00 35.47 2.83
3686 7753 5.930135 ACTGTCTACTGAAGAAATGGTGTT 58.070 37.500 0.00 0.00 35.47 3.32
3687 7754 5.552870 ACTGTCTACTGAAGAAATGGTGT 57.447 39.130 0.00 0.00 35.47 4.16
3688 7755 9.653287 TTTATACTGTCTACTGAAGAAATGGTG 57.347 33.333 0.00 0.00 35.47 4.17
3693 7760 9.485206 GGTGTTTTATACTGTCTACTGAAGAAA 57.515 33.333 0.00 0.00 35.47 2.52
3694 7761 8.644216 TGGTGTTTTATACTGTCTACTGAAGAA 58.356 33.333 0.00 0.00 35.47 2.52
3695 7762 8.185506 TGGTGTTTTATACTGTCTACTGAAGA 57.814 34.615 0.00 0.00 0.00 2.87
3696 7763 9.436957 AATGGTGTTTTATACTGTCTACTGAAG 57.563 33.333 0.00 0.00 0.00 3.02
3697 7764 9.787435 AAATGGTGTTTTATACTGTCTACTGAA 57.213 29.630 0.00 0.00 0.00 3.02
3698 7765 9.431887 GAAATGGTGTTTTATACTGTCTACTGA 57.568 33.333 0.00 0.00 0.00 3.41
3699 7766 9.436957 AGAAATGGTGTTTTATACTGTCTACTG 57.563 33.333 0.00 0.00 0.00 2.74
3703 7770 8.918202 TGAAGAAATGGTGTTTTATACTGTCT 57.082 30.769 0.00 0.00 0.00 3.41
3704 7771 8.784043 ACTGAAGAAATGGTGTTTTATACTGTC 58.216 33.333 0.00 0.00 0.00 3.51
3705 7772 8.691661 ACTGAAGAAATGGTGTTTTATACTGT 57.308 30.769 0.00 0.00 0.00 3.55
3710 7777 8.918202 TGTCTACTGAAGAAATGGTGTTTTAT 57.082 30.769 0.00 0.00 35.47 1.40
3711 7778 7.990886 ACTGTCTACTGAAGAAATGGTGTTTTA 59.009 33.333 0.00 0.00 35.47 1.52
3712 7779 6.828785 ACTGTCTACTGAAGAAATGGTGTTTT 59.171 34.615 0.00 0.00 35.47 2.43
3713 7780 6.357367 ACTGTCTACTGAAGAAATGGTGTTT 58.643 36.000 0.00 0.00 35.47 2.83
3714 7781 5.930135 ACTGTCTACTGAAGAAATGGTGTT 58.070 37.500 0.00 0.00 35.47 3.32
3715 7782 5.552870 ACTGTCTACTGAAGAAATGGTGT 57.447 39.130 0.00 0.00 35.47 4.16
3716 7783 9.653287 TTTATACTGTCTACTGAAGAAATGGTG 57.347 33.333 0.00 0.00 35.47 4.17
3721 7788 9.485206 GGTGTTTTATACTGTCTACTGAAGAAA 57.515 33.333 0.00 0.00 35.47 2.52
3722 7789 8.644216 TGGTGTTTTATACTGTCTACTGAAGAA 58.356 33.333 0.00 0.00 35.47 2.52
3723 7790 8.185506 TGGTGTTTTATACTGTCTACTGAAGA 57.814 34.615 0.00 0.00 0.00 2.87
3724 7791 9.436957 AATGGTGTTTTATACTGTCTACTGAAG 57.563 33.333 0.00 0.00 0.00 3.02
3725 7792 9.787435 AAATGGTGTTTTATACTGTCTACTGAA 57.213 29.630 0.00 0.00 0.00 3.02
3726 7793 9.431887 GAAATGGTGTTTTATACTGTCTACTGA 57.568 33.333 0.00 0.00 0.00 3.41
3727 7794 9.436957 AGAAATGGTGTTTTATACTGTCTACTG 57.563 33.333 0.00 0.00 0.00 2.74
3731 7798 8.918202 TGAAGAAATGGTGTTTTATACTGTCT 57.082 30.769 0.00 0.00 0.00 3.41
3732 7799 7.750903 GCTGAAGAAATGGTGTTTTATACTGTC 59.249 37.037 0.00 0.00 0.00 3.51
3733 7800 7.230510 TGCTGAAGAAATGGTGTTTTATACTGT 59.769 33.333 0.00 0.00 0.00 3.55
3734 7801 7.592938 TGCTGAAGAAATGGTGTTTTATACTG 58.407 34.615 0.00 0.00 0.00 2.74
3735 7802 7.665559 TCTGCTGAAGAAATGGTGTTTTATACT 59.334 33.333 0.00 0.00 29.54 2.12
3736 7803 7.750903 GTCTGCTGAAGAAATGGTGTTTTATAC 59.249 37.037 0.00 0.00 36.40 1.47
3737 7804 7.446931 TGTCTGCTGAAGAAATGGTGTTTTATA 59.553 33.333 0.00 0.00 36.40 0.98
3738 7805 6.265196 TGTCTGCTGAAGAAATGGTGTTTTAT 59.735 34.615 0.00 0.00 36.40 1.40
3739 7806 5.592282 TGTCTGCTGAAGAAATGGTGTTTTA 59.408 36.000 0.00 0.00 36.40 1.52
3740 7807 4.402155 TGTCTGCTGAAGAAATGGTGTTTT 59.598 37.500 0.00 0.00 36.40 2.43
3741 7808 3.953612 TGTCTGCTGAAGAAATGGTGTTT 59.046 39.130 0.00 0.00 36.40 2.83
3742 7809 3.554934 TGTCTGCTGAAGAAATGGTGTT 58.445 40.909 0.00 0.00 36.40 3.32
3743 7810 3.144506 CTGTCTGCTGAAGAAATGGTGT 58.855 45.455 0.00 0.00 36.40 4.16
3744 7811 3.144506 ACTGTCTGCTGAAGAAATGGTG 58.855 45.455 0.00 0.00 36.40 4.17
3745 7812 3.498774 ACTGTCTGCTGAAGAAATGGT 57.501 42.857 0.00 0.00 36.40 3.55
3746 7813 5.236047 GCTATACTGTCTGCTGAAGAAATGG 59.764 44.000 0.00 0.50 36.40 3.16
3747 7814 6.047870 AGCTATACTGTCTGCTGAAGAAATG 58.952 40.000 0.00 0.00 36.40 2.32
3748 7815 6.098124 AGAGCTATACTGTCTGCTGAAGAAAT 59.902 38.462 6.80 0.00 36.40 2.17
3749 7816 5.420421 AGAGCTATACTGTCTGCTGAAGAAA 59.580 40.000 6.80 0.00 36.40 2.52
3750 7817 4.952957 AGAGCTATACTGTCTGCTGAAGAA 59.047 41.667 6.80 0.00 36.40 2.52
3751 7818 4.531854 AGAGCTATACTGTCTGCTGAAGA 58.468 43.478 6.80 0.00 35.76 2.87
3752 7819 4.916983 AGAGCTATACTGTCTGCTGAAG 57.083 45.455 6.80 0.00 35.76 3.02
3753 7820 7.454225 TCTATAGAGCTATACTGTCTGCTGAA 58.546 38.462 0.00 0.00 35.76 3.02
3754 7821 7.010339 TCTATAGAGCTATACTGTCTGCTGA 57.990 40.000 0.00 0.00 35.76 4.26
3755 7822 7.626240 GCTTCTATAGAGCTATACTGTCTGCTG 60.626 44.444 13.67 0.00 35.76 4.41
3756 7823 6.374333 GCTTCTATAGAGCTATACTGTCTGCT 59.626 42.308 13.67 2.55 38.59 4.24
3757 7824 6.404293 GGCTTCTATAGAGCTATACTGTCTGC 60.404 46.154 17.89 0.00 0.00 4.26
3758 7825 6.884295 AGGCTTCTATAGAGCTATACTGTCTG 59.116 42.308 17.89 0.00 0.00 3.51
3759 7826 7.027874 AGGCTTCTATAGAGCTATACTGTCT 57.972 40.000 17.89 6.75 0.00 3.41
3760 7827 8.044908 AGTAGGCTTCTATAGAGCTATACTGTC 58.955 40.741 22.75 10.19 33.39 3.51
3761 7828 7.827236 CAGTAGGCTTCTATAGAGCTATACTGT 59.173 40.741 28.58 16.53 40.10 3.55
3762 7829 8.044309 TCAGTAGGCTTCTATAGAGCTATACTG 58.956 40.741 29.47 29.47 42.69 2.74
3763 7830 8.153221 TCAGTAGGCTTCTATAGAGCTATACT 57.847 38.462 20.64 20.64 34.20 2.12
3764 7831 8.795842 TTCAGTAGGCTTCTATAGAGCTATAC 57.204 38.462 17.89 18.32 0.00 1.47
3765 7832 9.621629 GATTCAGTAGGCTTCTATAGAGCTATA 57.378 37.037 17.89 0.00 0.00 1.31
3766 7833 8.336235 AGATTCAGTAGGCTTCTATAGAGCTAT 58.664 37.037 17.89 12.23 0.00 2.97
3767 7834 7.609918 CAGATTCAGTAGGCTTCTATAGAGCTA 59.390 40.741 17.89 9.69 0.00 3.32
3768 7835 6.434028 CAGATTCAGTAGGCTTCTATAGAGCT 59.566 42.308 17.89 0.00 0.00 4.09
3776 7843 7.235193 ACATCATATCAGATTCAGTAGGCTTCT 59.765 37.037 0.00 0.00 0.00 2.85
3883 7953 1.635663 CTCCTGCCGGCTAAACAACG 61.636 60.000 29.70 5.68 0.00 4.10
3896 7966 1.194781 TCTCAGACCCCAACTCCTGC 61.195 60.000 0.00 0.00 0.00 4.85
3975 8045 4.632251 CACTCGAGCTAAACTACTCTCAGA 59.368 45.833 13.61 0.00 0.00 3.27
4010 8080 6.292923 TCTCAAACTATTCCCACGAGAAAAA 58.707 36.000 0.00 0.00 0.00 1.94
4041 8112 9.502035 AGGCTAAGGGCAAATACTGTATATATA 57.498 33.333 0.00 0.00 44.01 0.86
4092 8166 3.365265 GCAAACCCTGGGTCTGCG 61.365 66.667 27.11 12.99 39.95 5.18
4099 8173 3.492482 CCTTGTAAAACTGCAAACCCTGG 60.492 47.826 0.00 0.00 0.00 4.45
4145 8219 5.233050 CACTGTAAAACACTGAGTCTCACAG 59.767 44.000 0.00 5.01 40.68 3.66
4149 8223 7.766219 TTTACACTGTAAAACACTGAGTCTC 57.234 36.000 11.27 0.00 33.28 3.36
4194 8268 4.081420 AGGAGAGTTTGTGAGCGACATAAT 60.081 41.667 0.00 0.00 33.40 1.28
4201 8275 1.151668 CCAAGGAGAGTTTGTGAGCG 58.848 55.000 0.00 0.00 0.00 5.03
4202 8276 2.037772 TCTCCAAGGAGAGTTTGTGAGC 59.962 50.000 14.66 0.00 45.26 4.26
4210 8284 9.270534 GGCTAACCATATTTCTCCAAGGAGAGT 62.271 44.444 17.58 13.28 43.10 3.24
4211 8285 6.966095 GGCTAACCATATTTCTCCAAGGAGAG 60.966 46.154 17.58 8.69 43.10 3.20
4212 8286 5.163195 GGCTAACCATATTTCTCCAAGGAGA 60.163 44.000 14.66 14.66 41.77 3.71
4213 8287 5.066593 GGCTAACCATATTTCTCCAAGGAG 58.933 45.833 9.90 9.90 38.61 3.69
4214 8288 4.476846 TGGCTAACCATATTTCTCCAAGGA 59.523 41.667 0.00 0.00 42.67 3.36
4215 8289 4.792068 TGGCTAACCATATTTCTCCAAGG 58.208 43.478 0.00 0.00 42.67 3.61
4244 8318 5.584251 GGCTGGAAACTTTGTTGATTTTTCA 59.416 36.000 0.00 0.00 0.00 2.69
4257 8331 5.418840 CCACAGTTATATTGGCTGGAAACTT 59.581 40.000 0.00 0.00 34.79 2.66
4277 8351 6.037830 GCTAACTATAATTCTTTTCCGCCACA 59.962 38.462 0.00 0.00 0.00 4.17
4278 8352 6.037830 TGCTAACTATAATTCTTTTCCGCCAC 59.962 38.462 0.00 0.00 0.00 5.01
4280 8354 6.613755 TGCTAACTATAATTCTTTTCCGCC 57.386 37.500 0.00 0.00 0.00 6.13
4295 8369 5.439721 AGTGCAAATGATGGATGCTAACTA 58.560 37.500 0.00 0.00 40.66 2.24
4305 8382 0.527113 TTGGCGAGTGCAAATGATGG 59.473 50.000 0.00 0.00 45.35 3.51
4334 8412 2.369203 TGTGTTTGAAGATCACGGGGTA 59.631 45.455 0.00 0.00 35.20 3.69
4335 8413 1.142060 TGTGTTTGAAGATCACGGGGT 59.858 47.619 0.00 0.00 35.20 4.95
4336 8414 1.535462 GTGTGTTTGAAGATCACGGGG 59.465 52.381 0.00 0.00 35.20 5.73
4387 8498 1.135286 CCGGGCAATTTCTTCTTCTGC 60.135 52.381 0.00 0.00 0.00 4.26
4401 8512 4.329545 GACAGTTCCTGCCGGGCA 62.330 66.667 22.39 22.39 34.37 5.36
4534 8645 0.179073 CCACCGGAGAGCATTTCGAT 60.179 55.000 9.46 0.00 0.00 3.59
4699 8810 4.337060 CAGGACGACACCGACGCA 62.337 66.667 0.00 0.00 39.50 5.24
4728 8839 0.907230 GAGGTTCCTCTCACTGGCCT 60.907 60.000 3.32 0.00 34.13 5.19
4833 8944 9.185680 GTAATAATTTGGTAACCTGATCCTTGT 57.814 33.333 0.00 0.00 0.00 3.16
4848 8959 9.226606 TCAGTAAGAGTGTTGGTAATAATTTGG 57.773 33.333 0.00 0.00 0.00 3.28


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

AutoCloner maintained by Alex Coulton.