Multiple sequence alignment - TraesCS3A01G208300

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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 TraesCS3A01G208300 chr3A 100.000 4647 0 0 1 4647 368410113 368414759 0.000000e+00 8582.0
1 TraesCS3A01G208300 chr3A 93.640 283 14 4 4366 4647 741646408 741646129 2.000000e-113 420.0
2 TraesCS3A01G208300 chr3A 80.396 505 63 21 1298 1783 30344859 30345346 7.400000e-93 351.0
3 TraesCS3A01G208300 chr3A 77.099 393 76 11 3296 3684 30346610 30346992 1.010000e-51 215.0
4 TraesCS3A01G208300 chr3B 94.968 2007 57 14 2164 4141 368540670 368538679 0.000000e+00 3107.0
5 TraesCS3A01G208300 chr3B 90.702 1710 105 22 1 1676 368548107 368546418 0.000000e+00 2228.0
6 TraesCS3A01G208300 chr3B 94.747 495 14 3 1671 2161 368541202 368540716 0.000000e+00 760.0
7 TraesCS3A01G208300 chr3B 94.366 284 13 1 4364 4647 52750726 52750446 2.570000e-117 433.0
8 TraesCS3A01G208300 chr3B 93.662 284 15 1 4364 4647 807123739 807124019 5.560000e-114 422.0
9 TraesCS3A01G208300 chr3B 75.944 715 123 34 2520 3222 35875405 35874728 5.800000e-84 322.0
10 TraesCS3A01G208300 chr3B 79.297 512 60 25 1298 1784 35876649 35876159 2.700000e-82 316.0
11 TraesCS3A01G208300 chr3B 93.194 191 6 1 4174 4364 368538682 368538499 1.650000e-69 274.0
12 TraesCS3A01G208300 chr3B 89.552 134 11 3 4364 4496 650919662 650919531 2.880000e-37 167.0
13 TraesCS3A01G208300 chr3D 93.834 1946 55 27 2343 4266 282332467 282330565 0.000000e+00 2868.0
14 TraesCS3A01G208300 chr3D 94.403 1197 51 6 1156 2347 282336587 282335402 0.000000e+00 1825.0
15 TraesCS3A01G208300 chr3D 90.300 1134 87 13 1 1125 282337705 282336586 0.000000e+00 1463.0
16 TraesCS3A01G208300 chr3D 87.234 47 6 0 4263 4309 70718777 70718731 2.000000e-03 54.7
17 TraesCS3A01G208300 chr4A 95.470 287 12 1 4362 4647 610091114 610091400 1.520000e-124 457.0
18 TraesCS3A01G208300 chr4A 92.933 283 16 2 4365 4647 740162431 740162709 4.330000e-110 409.0
19 TraesCS3A01G208300 chr4A 90.909 44 3 1 4258 4301 668698346 668698304 1.810000e-04 58.4
20 TraesCS3A01G208300 chr1B 92.958 284 15 3 4364 4647 267809102 267809380 4.330000e-110 409.0
21 TraesCS3A01G208300 chr1B 79.798 99 16 4 4263 4358 624606757 624606854 8.340000e-08 69.4
22 TraesCS3A01G208300 chr1B 91.111 45 4 0 4314 4358 269041507 269041551 1.400000e-05 62.1
23 TraesCS3A01G208300 chr1A 91.065 291 15 5 4360 4647 4226510 4226228 2.620000e-102 383.0
24 TraesCS3A01G208300 chr1A 90.654 214 10 3 4364 4574 321886014 321885808 4.580000e-70 276.0
25 TraesCS3A01G208300 chr1A 94.444 36 2 0 4256 4291 513711778 513711743 6.500000e-04 56.5
26 TraesCS3A01G208300 chr6A 90.210 286 22 4 4365 4647 36257957 36258239 7.350000e-98 368.0
27 TraesCS3A01G208300 chr6A 95.455 44 2 0 1962 2005 613688465 613688422 2.320000e-08 71.3
28 TraesCS3A01G208300 chr6A 94.444 36 2 0 4256 4291 96781476 96781511 6.500000e-04 56.5
29 TraesCS3A01G208300 chr6A 94.444 36 2 0 4256 4291 540792408 540792373 6.500000e-04 56.5
30 TraesCS3A01G208300 chr6D 86.538 312 26 10 4340 4647 71537635 71537934 3.470000e-86 329.0
31 TraesCS3A01G208300 chr6D 100.000 28 0 0 4263 4290 472581347 472581320 8.000000e-03 52.8
32 TraesCS3A01G208300 chr5A 86.525 282 14 9 4366 4647 701297479 701297222 5.880000e-74 289.0
33 TraesCS3A01G208300 chr5A 94.444 36 2 0 4256 4291 476640522 476640487 6.500000e-04 56.5
34 TraesCS3A01G208300 chr2A 84.806 283 17 10 4365 4647 707986194 707985938 1.280000e-65 261.0
35 TraesCS3A01G208300 chr2B 79.000 100 19 2 4261 4358 546768525 546768426 3.000000e-07 67.6
36 TraesCS3A01G208300 chr5B 94.444 36 2 0 4256 4291 307173620 307173655 6.500000e-04 56.5
37 TraesCS3A01G208300 chr5B 94.595 37 1 1 4254 4290 542829868 542829833 6.500000e-04 56.5
38 TraesCS3A01G208300 chr6B 96.774 31 1 0 4260 4290 699139303 699139333 8.000000e-03 52.8


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 TraesCS3A01G208300 chr3A 368410113 368414759 4646 False 8582.000000 8582 100.000000 1 4647 1 chr3A.!!$F1 4646
1 TraesCS3A01G208300 chr3A 30344859 30346992 2133 False 283.000000 351 78.747500 1298 3684 2 chr3A.!!$F2 2386
2 TraesCS3A01G208300 chr3B 368546418 368548107 1689 True 2228.000000 2228 90.702000 1 1676 1 chr3B.!!$R2 1675
3 TraesCS3A01G208300 chr3B 368538499 368541202 2703 True 1380.333333 3107 94.303000 1671 4364 3 chr3B.!!$R5 2693
4 TraesCS3A01G208300 chr3B 35874728 35876649 1921 True 319.000000 322 77.620500 1298 3222 2 chr3B.!!$R4 1924
5 TraesCS3A01G208300 chr3D 282330565 282337705 7140 True 2052.000000 2868 92.845667 1 4266 3 chr3D.!!$R2 4265

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
623 636 0.252103 TCCGGACTCCTGTAAAGCCT 60.252 55.0 0.0 0.0 0.0 4.58 F
1922 1997 0.174845 TCAAGCCGTGTTCTATCCCG 59.825 55.0 0.0 0.0 0.0 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1924 1999 0.321034 GAACCCAGTTACCCACGACC 60.321 60.0 0.0 0.0 0.00 4.79 R
3826 7186 1.342082 CTAAGTTGCCGTCGTGGTCG 61.342 60.0 0.0 0.0 41.21 4.79 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
32 33 2.095919 GCTTTTCTGCCAATACGACGTT 60.096 45.455 5.50 0.00 0.00 3.99
44 45 2.300066 CGACGTTGAAGTGCGCTCA 61.300 57.895 9.73 0.13 0.00 4.26
45 46 1.617755 CGACGTTGAAGTGCGCTCAT 61.618 55.000 9.73 0.00 0.00 2.90
128 131 1.668101 GCCTCGTCCATCCTCTCGTT 61.668 60.000 0.00 0.00 0.00 3.85
210 223 1.601171 CTGCTAGTTGGCCAGCTCT 59.399 57.895 26.87 17.53 38.63 4.09
223 236 4.233408 GCTCTTGCTTTTGTGCGG 57.767 55.556 0.00 0.00 36.03 5.69
226 239 0.662619 CTCTTGCTTTTGTGCGGTGA 59.337 50.000 0.00 0.00 35.36 4.02
266 279 0.904865 TTGGAGCTCGAGGTCATGGT 60.905 55.000 37.21 9.20 43.82 3.55
275 288 1.471119 GAGGTCATGGTAGACGTGGA 58.529 55.000 0.00 0.00 39.42 4.02
290 303 1.751351 CGTGGAGCAACTAGGAGATCA 59.249 52.381 0.00 0.00 0.00 2.92
303 316 1.743321 GAGATCAGGAGCGGAGGTGG 61.743 65.000 0.00 0.00 39.88 4.61
410 423 1.376037 CGCCAGAGTGGGTTTCTCC 60.376 63.158 0.00 0.00 38.19 3.71
470 483 1.202405 GGCAACCTATTTGAATGCGGG 60.202 52.381 0.00 0.00 37.39 6.13
507 520 1.086696 GCCGCTCTAGCATTGAACAA 58.913 50.000 2.44 0.00 42.21 2.83
513 526 2.076100 TCTAGCATTGAACAAGTGCGG 58.924 47.619 12.37 10.62 43.37 5.69
548 561 1.139734 GAGCAGCATTCTCGGTCGA 59.860 57.895 0.00 0.00 0.00 4.20
551 564 2.202623 AGCATTCTCGGTCGACGC 60.203 61.111 9.92 5.32 43.86 5.19
566 579 3.479269 CGCGTGCGAGAGGGTTTC 61.479 66.667 8.89 0.00 42.83 2.78
568 581 2.049433 CGTGCGAGAGGGTTTCGT 60.049 61.111 0.00 0.00 40.08 3.85
611 624 4.309950 GTGCCAACGGTCCGGACT 62.310 66.667 32.52 12.83 0.00 3.85
614 627 2.995574 CCAACGGTCCGGACTCCT 60.996 66.667 32.52 14.97 0.00 3.69
623 636 0.252103 TCCGGACTCCTGTAAAGCCT 60.252 55.000 0.00 0.00 0.00 4.58
632 645 1.496429 CCTGTAAAGCCTCATCCCCAT 59.504 52.381 0.00 0.00 0.00 4.00
633 646 2.711009 CCTGTAAAGCCTCATCCCCATA 59.289 50.000 0.00 0.00 0.00 2.74
643 656 3.181425 CCTCATCCCCATAGATTTGCCTT 60.181 47.826 0.00 0.00 0.00 4.35
667 680 5.978934 GGTTTACGAGAAAACAGAGTTGA 57.021 39.130 12.38 0.00 40.42 3.18
673 686 3.550233 CGAGAAAACAGAGTTGAGACCGA 60.550 47.826 0.00 0.00 0.00 4.69
680 693 2.489722 CAGAGTTGAGACCGATCTGTGA 59.510 50.000 0.00 0.00 34.34 3.58
682 695 3.192422 AGAGTTGAGACCGATCTGTGAAG 59.808 47.826 0.00 0.00 34.34 3.02
700 713 3.004629 TGAAGCAATGACAAAATGCGTCT 59.995 39.130 19.63 6.20 45.02 4.18
732 745 2.125961 AGGACGGATACAGGCGGTC 61.126 63.158 0.00 0.00 35.58 4.79
748 761 0.603569 GGTCTGAGAGTCCGCTTTGA 59.396 55.000 0.00 0.00 0.00 2.69
797 817 1.537202 AGAAAGCTGCTTTACTTGCGG 59.463 47.619 26.08 0.00 33.49 5.69
838 858 0.958822 GTCATGTTTTTGGCCGTCCT 59.041 50.000 0.00 0.00 0.00 3.85
922 942 9.444534 GAAGAGAAGAAAAGAAACTGCTAAAAG 57.555 33.333 0.00 0.00 0.00 2.27
1064 1090 2.035961 GTCACACTGCCACTGAACTCTA 59.964 50.000 0.00 0.00 0.00 2.43
1066 1092 1.344763 ACACTGCCACTGAACTCTACC 59.655 52.381 0.00 0.00 0.00 3.18
1067 1093 1.620819 CACTGCCACTGAACTCTACCT 59.379 52.381 0.00 0.00 0.00 3.08
1068 1094 2.826128 CACTGCCACTGAACTCTACCTA 59.174 50.000 0.00 0.00 0.00 3.08
1069 1095 3.093057 ACTGCCACTGAACTCTACCTAG 58.907 50.000 0.00 0.00 0.00 3.02
1070 1096 3.093057 CTGCCACTGAACTCTACCTAGT 58.907 50.000 0.00 0.00 0.00 2.57
1071 1097 4.263816 ACTGCCACTGAACTCTACCTAGTA 60.264 45.833 0.00 0.00 0.00 1.82
1072 1098 4.015084 TGCCACTGAACTCTACCTAGTAC 58.985 47.826 0.00 0.00 0.00 2.73
1073 1099 4.263816 TGCCACTGAACTCTACCTAGTACT 60.264 45.833 0.00 0.00 0.00 2.73
1091 1117 1.098050 CTCCTACAAGCACAATGCCC 58.902 55.000 0.00 0.00 46.52 5.36
1145 1171 0.442699 GAGCCGTTAAACGAGCAAGG 59.557 55.000 0.00 0.00 46.05 3.61
1151 1177 0.326927 TTAAACGAGCAAGGGGAGGG 59.673 55.000 0.00 0.00 0.00 4.30
1240 1276 1.276421 CTTCCCGCCTTCTTCTTCTGA 59.724 52.381 0.00 0.00 0.00 3.27
1241 1277 1.573108 TCCCGCCTTCTTCTTCTGAT 58.427 50.000 0.00 0.00 0.00 2.90
1381 1417 4.736896 GTCGCCGAGGCCGTCTTT 62.737 66.667 8.72 0.00 37.98 2.52
1391 1427 1.623973 GGCCGTCTTTTTCGTCCTCG 61.624 60.000 0.00 0.00 38.55 4.63
1420 1462 2.514824 GCCGACATCTGCCCTTCC 60.515 66.667 0.00 0.00 0.00 3.46
1492 1540 0.393537 CGGCCAAGAAGAAGAGCCAT 60.394 55.000 2.24 0.00 44.06 4.40
1873 1948 3.120718 GCTTCTCGCTCTTCTTTTCAGTG 60.121 47.826 0.00 0.00 35.14 3.66
1921 1996 1.473434 CCTCAAGCCGTGTTCTATCCC 60.473 57.143 0.00 0.00 0.00 3.85
1922 1997 0.174845 TCAAGCCGTGTTCTATCCCG 59.825 55.000 0.00 0.00 0.00 5.14
1923 1998 0.108329 CAAGCCGTGTTCTATCCCGT 60.108 55.000 0.00 0.00 0.00 5.28
1924 1999 0.108329 AAGCCGTGTTCTATCCCGTG 60.108 55.000 0.00 0.00 0.00 4.94
1925 2000 1.520787 GCCGTGTTCTATCCCGTGG 60.521 63.158 0.00 0.00 0.00 4.94
1926 2001 1.895238 CCGTGTTCTATCCCGTGGT 59.105 57.895 0.00 0.00 0.00 4.16
1991 2066 0.251165 AGGTTTTACTGGCCGCATGT 60.251 50.000 0.00 0.00 0.00 3.21
2047 2122 7.172190 CGTTTAGGAGTATCTGGTTATACGAGA 59.828 40.741 0.00 0.00 37.36 4.04
2332 2468 8.469200 CAACATAATGGTGATTGGTCAAGTATT 58.531 33.333 0.00 0.00 37.20 1.89
2491 5820 7.731882 TGTCCTATCTTCTCGAATACTAGTG 57.268 40.000 5.39 0.00 0.00 2.74
2621 5960 3.576078 ATTGACAGGGTGAGTGTTTGA 57.424 42.857 0.00 0.00 0.00 2.69
3109 6456 0.896923 TCCATTGGCATGCCTGTTTC 59.103 50.000 35.53 10.37 36.94 2.78
3263 6611 2.964464 TCTTGTGTGGATGCATGGTTTT 59.036 40.909 2.46 0.00 0.00 2.43
3264 6612 3.005684 TCTTGTGTGGATGCATGGTTTTC 59.994 43.478 2.46 0.00 0.00 2.29
3265 6613 2.314246 TGTGTGGATGCATGGTTTTCA 58.686 42.857 2.46 0.00 0.00 2.69
3266 6614 2.296752 TGTGTGGATGCATGGTTTTCAG 59.703 45.455 2.46 0.00 0.00 3.02
3338 6687 3.057456 AGACGTTTGAAGACGCTGATACT 60.057 43.478 0.00 0.00 46.47 2.12
3428 6777 4.897051 AGAACATGACCCTACCCTATCTT 58.103 43.478 0.00 0.00 0.00 2.40
3451 6800 7.554835 TCTTAGGTTTGAGTTTGAAAGCTACAA 59.445 33.333 0.00 0.00 41.01 2.41
3735 7085 5.811190 TGAATATCGGGTTTCCTGAGAAAA 58.189 37.500 3.69 0.00 42.74 2.29
3740 7090 3.881089 TCGGGTTTCCTGAGAAAAAGAAC 59.119 43.478 0.00 0.00 43.48 3.01
3768 7118 9.667107 CTCATAACCACCTACTGAAGAAAATTA 57.333 33.333 0.00 0.00 0.00 1.40
3885 7245 6.489700 TCATGAGCTCAAACTGGTATTTTCAA 59.510 34.615 22.50 0.00 0.00 2.69
3908 7268 6.791867 AAGCTGTACATACATCACTCCTTA 57.208 37.500 0.00 0.00 35.36 2.69
3917 7277 6.155221 ACATACATCACTCCTTAAGCTCTGAA 59.845 38.462 0.00 0.00 0.00 3.02
3966 7326 3.190874 CTCGAGCTTGTACAAGGGAATC 58.809 50.000 31.42 17.35 38.80 2.52
4119 7479 4.118410 TGCATTAGCTTTGGTTGTTGTTG 58.882 39.130 0.00 0.00 42.74 3.33
4124 7484 7.525759 CATTAGCTTTGGTTGTTGTTGTTTTT 58.474 30.769 0.00 0.00 0.00 1.94
4211 7571 6.992063 AAATACTGCTGAACAATCTACCTG 57.008 37.500 0.00 0.00 0.00 4.00
4272 7632 8.059565 AGGGACATATATATAGTACTCCCTCC 57.940 42.308 16.66 5.53 42.43 4.30
4277 7637 7.350389 ACATATATATAGTACTCCCTCCGTCCT 59.650 40.741 0.00 0.00 0.00 3.85
4302 7662 9.902196 CTAAAATAAATGTCGTGGGTTTAGTTT 57.098 29.630 7.40 7.40 38.41 2.66
4331 7691 8.804688 TTTGGATAAATTTGAACTAAACCACG 57.195 30.769 0.00 0.00 0.00 4.94
4332 7692 7.747155 TGGATAAATTTGAACTAAACCACGA 57.253 32.000 0.00 0.00 0.00 4.35
4333 7693 7.586747 TGGATAAATTTGAACTAAACCACGAC 58.413 34.615 0.00 0.00 0.00 4.34
4334 7694 7.228906 TGGATAAATTTGAACTAAACCACGACA 59.771 33.333 0.00 0.00 0.00 4.35
4335 7695 8.241367 GGATAAATTTGAACTAAACCACGACAT 58.759 33.333 0.00 0.00 0.00 3.06
4359 7719 2.180159 TTTGGGACGGAGGCAGTAGC 62.180 60.000 0.00 0.00 41.10 3.58
4364 7724 0.037232 GACGGAGGCAGTAGCAAGTT 60.037 55.000 0.00 0.00 44.61 2.66
4365 7725 0.396811 ACGGAGGCAGTAGCAAGTTT 59.603 50.000 0.00 0.00 44.61 2.66
4366 7726 1.202770 ACGGAGGCAGTAGCAAGTTTT 60.203 47.619 0.00 0.00 44.61 2.43
4367 7727 1.880027 CGGAGGCAGTAGCAAGTTTTT 59.120 47.619 0.00 0.00 44.61 1.94
4391 7751 5.333566 TTTGGAAATGGAGGTATATCCCC 57.666 43.478 0.00 0.00 38.72 4.81
4392 7752 2.910319 TGGAAATGGAGGTATATCCCCG 59.090 50.000 0.00 0.00 38.72 5.73
4393 7753 2.238898 GGAAATGGAGGTATATCCCCGG 59.761 54.545 0.00 0.00 38.72 5.73
4394 7754 1.286248 AATGGAGGTATATCCCCGGC 58.714 55.000 0.00 0.00 38.72 6.13
4395 7755 0.620700 ATGGAGGTATATCCCCGGCC 60.621 60.000 0.00 0.00 38.72 6.13
4396 7756 1.080538 GGAGGTATATCCCCGGCCT 59.919 63.158 0.00 0.00 36.75 5.19
4397 7757 0.976590 GGAGGTATATCCCCGGCCTC 60.977 65.000 12.24 12.24 43.56 4.70
4398 7758 0.041386 GAGGTATATCCCCGGCCTCT 59.959 60.000 13.12 0.00 41.68 3.69
4399 7759 0.252284 AGGTATATCCCCGGCCTCTG 60.252 60.000 0.00 0.00 36.75 3.35
4400 7760 1.597461 GTATATCCCCGGCCTCTGC 59.403 63.158 0.00 0.00 0.00 4.26
4401 7761 1.157513 TATATCCCCGGCCTCTGCA 59.842 57.895 0.00 0.00 40.13 4.41
4402 7762 0.252696 TATATCCCCGGCCTCTGCAT 60.253 55.000 0.00 0.00 40.13 3.96
4403 7763 1.557269 ATATCCCCGGCCTCTGCATC 61.557 60.000 0.00 0.00 40.13 3.91
4404 7764 2.963391 TATCCCCGGCCTCTGCATCA 62.963 60.000 0.00 0.00 40.13 3.07
4405 7765 3.882326 CCCCGGCCTCTGCATCAT 61.882 66.667 0.00 0.00 40.13 2.45
4406 7766 2.593725 CCCGGCCTCTGCATCATG 60.594 66.667 0.00 0.00 40.13 3.07
4407 7767 2.507452 CCGGCCTCTGCATCATGA 59.493 61.111 0.00 0.00 40.13 3.07
4408 7768 1.072678 CCGGCCTCTGCATCATGAT 59.927 57.895 1.18 1.18 40.13 2.45
4409 7769 1.235281 CCGGCCTCTGCATCATGATG 61.235 60.000 28.04 28.04 41.60 3.07
4410 7770 0.250166 CGGCCTCTGCATCATGATGA 60.250 55.000 34.65 19.93 41.20 2.92
4411 7771 1.610886 CGGCCTCTGCATCATGATGAT 60.611 52.381 34.65 1.25 41.20 2.45
4420 7780 2.599659 CATCATGATGATGCATGCAGC 58.400 47.619 28.44 28.44 46.37 5.25
4421 7781 0.958822 TCATGATGATGCATGCAGCC 59.041 50.000 31.30 22.02 44.08 4.85
4422 7782 0.038251 CATGATGATGCATGCAGCCC 60.038 55.000 31.30 22.76 44.83 5.19
4423 7783 0.178961 ATGATGATGCATGCAGCCCT 60.179 50.000 31.30 19.53 44.83 5.19
4424 7784 0.396556 TGATGATGCATGCAGCCCTT 60.397 50.000 31.30 17.14 44.83 3.95
4425 7785 0.750850 GATGATGCATGCAGCCCTTT 59.249 50.000 31.30 14.63 44.83 3.11
4426 7786 1.138266 GATGATGCATGCAGCCCTTTT 59.862 47.619 31.30 10.63 44.83 2.27
4427 7787 1.849977 TGATGCATGCAGCCCTTTTA 58.150 45.000 31.30 10.43 44.83 1.52
4428 7788 2.390696 TGATGCATGCAGCCCTTTTAT 58.609 42.857 31.30 9.02 44.83 1.40
4429 7789 2.767394 TGATGCATGCAGCCCTTTTATT 59.233 40.909 31.30 8.21 44.83 1.40
4430 7790 3.959449 TGATGCATGCAGCCCTTTTATTA 59.041 39.130 31.30 8.11 44.83 0.98
4431 7791 4.405036 TGATGCATGCAGCCCTTTTATTAA 59.595 37.500 31.30 7.33 44.83 1.40
4432 7792 4.815533 TGCATGCAGCCCTTTTATTAAA 57.184 36.364 18.46 0.00 44.83 1.52
4433 7793 5.157940 TGCATGCAGCCCTTTTATTAAAA 57.842 34.783 18.46 1.85 44.83 1.52
4434 7794 5.555017 TGCATGCAGCCCTTTTATTAAAAA 58.445 33.333 18.46 0.00 44.83 1.94
4435 7795 6.179040 TGCATGCAGCCCTTTTATTAAAAAT 58.821 32.000 18.46 0.00 44.83 1.82
4436 7796 6.658391 TGCATGCAGCCCTTTTATTAAAAATT 59.342 30.769 18.46 0.00 44.83 1.82
4437 7797 7.148272 TGCATGCAGCCCTTTTATTAAAAATTC 60.148 33.333 18.46 0.00 44.83 2.17
4438 7798 7.148272 GCATGCAGCCCTTTTATTAAAAATTCA 60.148 33.333 14.21 0.00 33.89 2.57
4439 7799 7.903995 TGCAGCCCTTTTATTAAAAATTCAG 57.096 32.000 3.37 0.00 34.18 3.02
4440 7800 7.675062 TGCAGCCCTTTTATTAAAAATTCAGA 58.325 30.769 3.37 0.00 34.18 3.27
4441 7801 8.153550 TGCAGCCCTTTTATTAAAAATTCAGAA 58.846 29.630 3.37 0.00 34.18 3.02
4442 7802 8.998377 GCAGCCCTTTTATTAAAAATTCAGAAA 58.002 29.630 3.37 0.00 34.18 2.52
4467 7827 9.686683 AAGTATCATCATAAAGGTTTTACAGCT 57.313 29.630 0.00 0.00 33.27 4.24
4468 7828 9.331282 AGTATCATCATAAAGGTTTTACAGCTC 57.669 33.333 0.00 0.00 30.69 4.09
4469 7829 6.662414 TCATCATAAAGGTTTTACAGCTCG 57.338 37.500 0.00 0.00 30.69 5.03
4470 7830 4.939509 TCATAAAGGTTTTACAGCTCGC 57.060 40.909 0.00 0.00 30.69 5.03
4471 7831 4.320023 TCATAAAGGTTTTACAGCTCGCA 58.680 39.130 0.00 0.00 30.69 5.10
4472 7832 4.757657 TCATAAAGGTTTTACAGCTCGCAA 59.242 37.500 0.00 0.00 30.69 4.85
4473 7833 5.239744 TCATAAAGGTTTTACAGCTCGCAAA 59.760 36.000 0.00 0.00 30.69 3.68
4474 7834 3.349488 AAGGTTTTACAGCTCGCAAAC 57.651 42.857 0.00 0.00 30.69 2.93
4475 7835 1.263217 AGGTTTTACAGCTCGCAAACG 59.737 47.619 0.00 0.00 42.01 3.60
4476 7836 1.662026 GGTTTTACAGCTCGCAAACGG 60.662 52.381 0.00 0.00 40.63 4.44
4477 7837 1.262151 GTTTTACAGCTCGCAAACGGA 59.738 47.619 0.00 0.00 40.63 4.69
4478 7838 1.144969 TTTACAGCTCGCAAACGGAG 58.855 50.000 0.00 0.00 40.63 4.63
4479 7839 1.289109 TTACAGCTCGCAAACGGAGC 61.289 55.000 5.69 5.69 40.47 4.70
4480 7840 2.428960 TACAGCTCGCAAACGGAGCA 62.429 55.000 15.27 0.00 41.70 4.26
4481 7841 2.280797 AGCTCGCAAACGGAGCAA 60.281 55.556 15.27 0.00 41.70 3.91
4482 7842 1.891919 AGCTCGCAAACGGAGCAAA 60.892 52.632 15.27 0.00 41.70 3.68
4483 7843 1.441016 GCTCGCAAACGGAGCAAAG 60.441 57.895 8.77 0.00 40.14 2.77
4484 7844 1.941812 CTCGCAAACGGAGCAAAGT 59.058 52.632 0.00 0.00 40.63 2.66
4485 7845 0.110644 CTCGCAAACGGAGCAAAGTC 60.111 55.000 0.00 0.00 40.63 3.01
4486 7846 0.812014 TCGCAAACGGAGCAAAGTCA 60.812 50.000 0.00 0.00 40.63 3.41
4487 7847 0.238289 CGCAAACGGAGCAAAGTCAT 59.762 50.000 0.00 0.00 34.97 3.06
4488 7848 1.463056 CGCAAACGGAGCAAAGTCATA 59.537 47.619 0.00 0.00 34.97 2.15
4489 7849 2.474526 CGCAAACGGAGCAAAGTCATAG 60.475 50.000 0.00 0.00 34.97 2.23
4490 7850 2.729156 GCAAACGGAGCAAAGTCATAGC 60.729 50.000 0.00 0.00 0.00 2.97
4491 7851 2.472695 AACGGAGCAAAGTCATAGCA 57.527 45.000 0.00 0.00 0.00 3.49
4492 7852 2.698855 ACGGAGCAAAGTCATAGCAT 57.301 45.000 0.00 0.00 0.00 3.79
4493 7853 3.819564 ACGGAGCAAAGTCATAGCATA 57.180 42.857 0.00 0.00 0.00 3.14
4494 7854 4.137116 ACGGAGCAAAGTCATAGCATAA 57.863 40.909 0.00 0.00 0.00 1.90
4495 7855 4.513442 ACGGAGCAAAGTCATAGCATAAA 58.487 39.130 0.00 0.00 0.00 1.40
4496 7856 4.572389 ACGGAGCAAAGTCATAGCATAAAG 59.428 41.667 0.00 0.00 0.00 1.85
4497 7857 4.811024 CGGAGCAAAGTCATAGCATAAAGA 59.189 41.667 0.00 0.00 0.00 2.52
4498 7858 5.468072 CGGAGCAAAGTCATAGCATAAAGAT 59.532 40.000 0.00 0.00 0.00 2.40
4499 7859 6.347240 CGGAGCAAAGTCATAGCATAAAGATC 60.347 42.308 0.00 0.00 0.00 2.75
4500 7860 6.709846 GGAGCAAAGTCATAGCATAAAGATCT 59.290 38.462 0.00 0.00 0.00 2.75
4501 7861 7.307870 GGAGCAAAGTCATAGCATAAAGATCTG 60.308 40.741 0.00 0.00 0.00 2.90
4502 7862 7.278135 AGCAAAGTCATAGCATAAAGATCTGA 58.722 34.615 0.00 0.00 0.00 3.27
4503 7863 7.772292 AGCAAAGTCATAGCATAAAGATCTGAA 59.228 33.333 0.00 0.00 0.00 3.02
4504 7864 8.400947 GCAAAGTCATAGCATAAAGATCTGAAA 58.599 33.333 0.00 0.00 0.00 2.69
4554 7914 4.367386 CCGATACGGTGATAATAGGGAC 57.633 50.000 1.80 0.00 42.73 4.46
4555 7915 3.760151 CCGATACGGTGATAATAGGGACA 59.240 47.826 1.80 0.00 42.73 4.02
4556 7916 4.219070 CCGATACGGTGATAATAGGGACAA 59.781 45.833 1.80 0.00 42.73 3.18
4557 7917 5.399858 CGATACGGTGATAATAGGGACAAG 58.600 45.833 0.00 0.00 0.00 3.16
4558 7918 3.470645 ACGGTGATAATAGGGACAAGC 57.529 47.619 0.00 0.00 0.00 4.01
4559 7919 3.039011 ACGGTGATAATAGGGACAAGCT 58.961 45.455 0.00 0.00 0.00 3.74
4560 7920 3.069729 ACGGTGATAATAGGGACAAGCTC 59.930 47.826 0.00 0.00 0.00 4.09
4561 7921 3.322254 CGGTGATAATAGGGACAAGCTCT 59.678 47.826 0.00 0.00 0.00 4.09
4562 7922 4.559704 CGGTGATAATAGGGACAAGCTCTC 60.560 50.000 0.00 0.00 0.00 3.20
4563 7923 4.591072 GGTGATAATAGGGACAAGCTCTCT 59.409 45.833 0.00 0.00 32.71 3.10
4564 7924 5.775701 GGTGATAATAGGGACAAGCTCTCTA 59.224 44.000 0.00 0.00 36.32 2.43
4565 7925 6.071616 GGTGATAATAGGGACAAGCTCTCTAG 60.072 46.154 0.00 0.00 35.25 2.43
4576 7936 2.899303 GCTCTCTAGCCCTCTATCCT 57.101 55.000 0.00 0.00 43.40 3.24
4577 7937 2.446435 GCTCTCTAGCCCTCTATCCTG 58.554 57.143 0.00 0.00 43.40 3.86
4578 7938 2.225017 GCTCTCTAGCCCTCTATCCTGT 60.225 54.545 0.00 0.00 43.40 4.00
4579 7939 3.753846 GCTCTCTAGCCCTCTATCCTGTT 60.754 52.174 0.00 0.00 43.40 3.16
4580 7940 4.507691 GCTCTCTAGCCCTCTATCCTGTTA 60.508 50.000 0.00 0.00 43.40 2.41
4581 7941 5.809702 GCTCTCTAGCCCTCTATCCTGTTAT 60.810 48.000 0.00 0.00 43.40 1.89
4582 7942 5.575157 TCTCTAGCCCTCTATCCTGTTATG 58.425 45.833 0.00 0.00 0.00 1.90
4583 7943 4.090090 TCTAGCCCTCTATCCTGTTATGC 58.910 47.826 0.00 0.00 0.00 3.14
4584 7944 1.620819 AGCCCTCTATCCTGTTATGCG 59.379 52.381 0.00 0.00 0.00 4.73
4585 7945 1.618837 GCCCTCTATCCTGTTATGCGA 59.381 52.381 0.00 0.00 0.00 5.10
4586 7946 2.610727 GCCCTCTATCCTGTTATGCGAC 60.611 54.545 0.00 0.00 0.00 5.19
4587 7947 2.028930 CCCTCTATCCTGTTATGCGACC 60.029 54.545 0.00 0.00 0.00 4.79
4588 7948 2.351835 CCTCTATCCTGTTATGCGACCG 60.352 54.545 0.00 0.00 0.00 4.79
4589 7949 1.000607 TCTATCCTGTTATGCGACCGC 60.001 52.381 7.53 7.53 42.35 5.68
4590 7950 0.032952 TATCCTGTTATGCGACCGCC 59.967 55.000 12.08 0.00 41.09 6.13
4591 7951 1.966901 ATCCTGTTATGCGACCGCCA 61.967 55.000 12.08 1.69 41.09 5.69
4592 7952 1.523711 CCTGTTATGCGACCGCCAT 60.524 57.895 12.08 8.00 41.09 4.40
4593 7953 1.498865 CCTGTTATGCGACCGCCATC 61.499 60.000 12.08 1.22 41.09 3.51
4594 7954 1.498865 CTGTTATGCGACCGCCATCC 61.499 60.000 12.08 0.00 41.09 3.51
4595 7955 2.279851 TTATGCGACCGCCATCCG 60.280 61.111 12.08 0.00 41.09 4.18
4596 7956 2.787567 TTATGCGACCGCCATCCGA 61.788 57.895 12.08 0.00 41.09 4.55
4597 7957 2.299503 TTATGCGACCGCCATCCGAA 62.300 55.000 12.08 0.00 41.09 4.30
4598 7958 2.964438 TATGCGACCGCCATCCGAAC 62.964 60.000 12.08 0.00 41.09 3.95
4605 7965 2.046700 GCCATCCGAACCGGTTGA 60.047 61.111 27.87 17.58 46.01 3.18
4606 7966 1.673009 GCCATCCGAACCGGTTGAA 60.673 57.895 27.87 10.11 46.01 2.69
4607 7967 1.029947 GCCATCCGAACCGGTTGAAT 61.030 55.000 27.87 12.13 46.01 2.57
4608 7968 1.744456 GCCATCCGAACCGGTTGAATA 60.744 52.381 27.87 7.68 46.01 1.75
4609 7969 2.846193 CCATCCGAACCGGTTGAATAT 58.154 47.619 27.87 9.83 46.01 1.28
4610 7970 3.804411 GCCATCCGAACCGGTTGAATATA 60.804 47.826 27.87 4.15 46.01 0.86
4611 7971 3.994392 CCATCCGAACCGGTTGAATATAG 59.006 47.826 27.87 8.12 46.01 1.31
4612 7972 3.432252 CATCCGAACCGGTTGAATATAGC 59.568 47.826 27.87 6.43 46.01 2.97
4613 7973 2.140717 CCGAACCGGTTGAATATAGCC 58.859 52.381 27.87 5.62 42.73 3.93
4614 7974 2.140717 CGAACCGGTTGAATATAGCCC 58.859 52.381 27.87 4.79 0.00 5.19
4615 7975 2.140717 GAACCGGTTGAATATAGCCCG 58.859 52.381 27.87 0.00 38.39 6.13
4616 7976 1.416243 ACCGGTTGAATATAGCCCGA 58.584 50.000 0.00 0.00 41.08 5.14
4617 7977 1.343465 ACCGGTTGAATATAGCCCGAG 59.657 52.381 0.00 0.00 41.08 4.63
4618 7978 1.343465 CCGGTTGAATATAGCCCGAGT 59.657 52.381 0.00 0.00 41.08 4.18
4619 7979 2.224209 CCGGTTGAATATAGCCCGAGTT 60.224 50.000 0.00 0.00 41.08 3.01
4620 7980 3.006110 CCGGTTGAATATAGCCCGAGTTA 59.994 47.826 0.00 0.00 41.08 2.24
4621 7981 3.985925 CGGTTGAATATAGCCCGAGTTAC 59.014 47.826 0.00 0.00 41.08 2.50
4622 7982 4.313282 GGTTGAATATAGCCCGAGTTACC 58.687 47.826 0.00 0.00 0.00 2.85
4623 7983 4.202284 GGTTGAATATAGCCCGAGTTACCA 60.202 45.833 0.00 0.00 0.00 3.25
4624 7984 5.512576 GGTTGAATATAGCCCGAGTTACCAT 60.513 44.000 0.00 0.00 0.00 3.55
4625 7985 5.401531 TGAATATAGCCCGAGTTACCATC 57.598 43.478 0.00 0.00 0.00 3.51
4626 7986 5.084519 TGAATATAGCCCGAGTTACCATCT 58.915 41.667 0.00 0.00 0.00 2.90
4627 7987 5.185249 TGAATATAGCCCGAGTTACCATCTC 59.815 44.000 0.00 0.00 0.00 2.75
4628 7988 1.700955 TAGCCCGAGTTACCATCTCC 58.299 55.000 0.00 0.00 0.00 3.71
4629 7989 0.032017 AGCCCGAGTTACCATCTCCT 60.032 55.000 0.00 0.00 0.00 3.69
4630 7990 1.217183 AGCCCGAGTTACCATCTCCTA 59.783 52.381 0.00 0.00 0.00 2.94
4631 7991 2.158295 AGCCCGAGTTACCATCTCCTAT 60.158 50.000 0.00 0.00 0.00 2.57
4632 7992 2.633481 GCCCGAGTTACCATCTCCTATT 59.367 50.000 0.00 0.00 0.00 1.73
4633 7993 3.555168 GCCCGAGTTACCATCTCCTATTG 60.555 52.174 0.00 0.00 0.00 1.90
4634 7994 3.006967 CCCGAGTTACCATCTCCTATTGG 59.993 52.174 0.00 0.00 39.02 3.16
4636 7996 4.101119 CCGAGTTACCATCTCCTATTGGTT 59.899 45.833 0.00 0.00 43.73 3.67
4637 7997 5.050490 CGAGTTACCATCTCCTATTGGTTG 58.950 45.833 0.00 0.00 43.73 3.77
4638 7998 4.781934 AGTTACCATCTCCTATTGGTTGC 58.218 43.478 0.00 0.00 43.73 4.17
4639 7999 4.227300 AGTTACCATCTCCTATTGGTTGCA 59.773 41.667 0.00 0.00 43.73 4.08
4640 8000 3.004752 ACCATCTCCTATTGGTTGCAC 57.995 47.619 0.00 0.00 43.73 4.57
4641 8001 2.301346 CCATCTCCTATTGGTTGCACC 58.699 52.381 0.00 0.00 39.22 5.01
4642 8002 2.301346 CATCTCCTATTGGTTGCACCC 58.699 52.381 0.00 0.00 37.50 4.61
4643 8003 1.367346 TCTCCTATTGGTTGCACCCA 58.633 50.000 0.00 0.00 37.50 4.51
4644 8004 1.281867 TCTCCTATTGGTTGCACCCAG 59.718 52.381 2.20 0.00 37.50 4.45
4645 8005 1.004745 CTCCTATTGGTTGCACCCAGT 59.995 52.381 2.20 2.77 37.50 4.00
4646 8006 2.238646 CTCCTATTGGTTGCACCCAGTA 59.761 50.000 2.20 4.01 37.50 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 2.756829 TCAACGTCGTATTGGCAGAAA 58.243 42.857 0.00 0.00 0.00 2.52
44 45 1.538512 GCATATCATTGGAGCACGCAT 59.461 47.619 0.00 0.00 0.00 4.73
45 46 0.946528 GCATATCATTGGAGCACGCA 59.053 50.000 0.00 0.00 0.00 5.24
92 94 1.515519 GCATACGACGACAAGCCGA 60.516 57.895 0.00 0.00 0.00 5.54
210 223 1.065401 CTCTTCACCGCACAAAAGCAA 59.935 47.619 0.00 0.00 0.00 3.91
216 229 1.597854 CAGCCTCTTCACCGCACAA 60.598 57.895 0.00 0.00 0.00 3.33
220 233 2.435059 GGACAGCCTCTTCACCGC 60.435 66.667 0.00 0.00 0.00 5.68
266 279 2.026542 TCTCCTAGTTGCTCCACGTCTA 60.027 50.000 0.00 0.00 0.00 2.59
275 288 2.038659 GCTCCTGATCTCCTAGTTGCT 58.961 52.381 0.00 0.00 0.00 3.91
369 382 2.804527 CCGCATTCACACATCCTATCAG 59.195 50.000 0.00 0.00 0.00 2.90
373 386 1.470805 CGTCCGCATTCACACATCCTA 60.471 52.381 0.00 0.00 0.00 2.94
445 458 2.871096 TTCAAATAGGTTGCCCGTCT 57.129 45.000 0.00 0.00 37.13 4.18
470 483 4.131088 GTGACCGGACGGCTCTCC 62.131 72.222 9.46 0.00 39.32 3.71
496 509 0.877071 CTCCGCACTTGTTCAATGCT 59.123 50.000 13.43 0.00 37.20 3.79
534 547 2.202623 GCGTCGACCGAGAATGCT 60.203 61.111 10.58 0.00 39.56 3.79
548 561 4.295119 AAACCCTCTCGCACGCGT 62.295 61.111 5.58 5.58 40.74 6.01
551 564 1.219522 AAACGAAACCCTCTCGCACG 61.220 55.000 0.00 0.00 39.97 5.34
566 579 1.227734 AACACCTCGGTCCCAAACG 60.228 57.895 0.00 0.00 0.00 3.60
568 581 0.179040 GTCAACACCTCGGTCCCAAA 60.179 55.000 0.00 0.00 0.00 3.28
611 624 1.213296 GGGGATGAGGCTTTACAGGA 58.787 55.000 0.00 0.00 0.00 3.86
614 627 3.664320 TCTATGGGGATGAGGCTTTACA 58.336 45.455 0.00 0.00 0.00 2.41
623 636 3.496692 CGAAGGCAAATCTATGGGGATGA 60.497 47.826 0.00 0.00 0.00 2.92
643 656 4.311816 ACTCTGTTTTCTCGTAAACCGA 57.688 40.909 0.00 0.00 45.00 4.69
665 678 1.256812 TGCTTCACAGATCGGTCTCA 58.743 50.000 0.00 0.00 30.42 3.27
667 680 2.234661 TCATTGCTTCACAGATCGGTCT 59.765 45.455 0.00 0.00 34.14 3.85
673 686 4.927425 GCATTTTGTCATTGCTTCACAGAT 59.073 37.500 0.00 0.00 33.61 2.90
680 693 3.311106 CAGACGCATTTTGTCATTGCTT 58.689 40.909 0.00 0.00 38.83 3.91
682 695 1.987770 CCAGACGCATTTTGTCATTGC 59.012 47.619 0.00 0.00 38.83 3.56
700 713 1.596934 GTCCTGATCAAGCGGTCCA 59.403 57.895 0.00 0.00 0.00 4.02
732 745 2.732412 TCTTCAAAGCGGACTCTCAG 57.268 50.000 0.00 0.00 0.00 3.35
768 781 9.468532 CAAGTAAAGCAGCTTTCTTAATCTTTT 57.531 29.630 23.94 0.00 35.21 2.27
773 793 5.393962 CGCAAGTAAAGCAGCTTTCTTAAT 58.606 37.500 23.94 3.37 35.21 1.40
864 884 5.287035 GCTTTATCTGCTTTTGTCGATTTGG 59.713 40.000 0.00 0.00 0.00 3.28
922 942 7.809546 TTTCTTTCTTCTTTTCTCTCTTCCC 57.190 36.000 0.00 0.00 0.00 3.97
1064 1090 4.043608 TGTGCTTGTAGGAGTACTAGGT 57.956 45.455 0.00 0.00 33.88 3.08
1066 1092 4.806247 GCATTGTGCTTGTAGGAGTACTAG 59.194 45.833 0.00 0.00 40.96 2.57
1067 1093 4.382685 GGCATTGTGCTTGTAGGAGTACTA 60.383 45.833 0.00 0.00 44.28 1.82
1068 1094 3.600388 GCATTGTGCTTGTAGGAGTACT 58.400 45.455 0.00 0.00 40.96 2.73
1069 1095 2.678336 GGCATTGTGCTTGTAGGAGTAC 59.322 50.000 1.64 0.00 44.28 2.73
1070 1096 2.355716 GGGCATTGTGCTTGTAGGAGTA 60.356 50.000 1.64 0.00 44.28 2.59
1071 1097 1.614317 GGGCATTGTGCTTGTAGGAGT 60.614 52.381 1.64 0.00 44.28 3.85
1072 1098 1.098050 GGGCATTGTGCTTGTAGGAG 58.902 55.000 1.64 0.00 44.28 3.69
1073 1099 0.676466 CGGGCATTGTGCTTGTAGGA 60.676 55.000 1.64 0.00 44.28 2.94
1091 1117 1.860078 GTGTCGTTTTGAGGGCTCG 59.140 57.895 0.00 0.00 0.00 5.03
1098 1124 2.968156 CCGGCCGTGTCGTTTTGA 60.968 61.111 26.12 0.00 0.00 2.69
1151 1177 4.446413 CGTACCCCACCACCGCTC 62.446 72.222 0.00 0.00 0.00 5.03
1163 1198 4.157120 AGTCCATGGCGGCGTACC 62.157 66.667 6.96 2.01 33.14 3.34
1420 1462 3.578272 CGCGAGGAGGAGGACGAG 61.578 72.222 0.00 0.00 0.00 4.18
1873 1948 5.582689 AAAACATATAAACTGCTCCCTGC 57.417 39.130 0.00 0.00 43.25 4.85
1921 1996 1.373748 CCAGTTACCCACGACCACG 60.374 63.158 0.00 0.00 45.75 4.94
1922 1997 1.004200 CCCAGTTACCCACGACCAC 60.004 63.158 0.00 0.00 0.00 4.16
1923 1998 1.055551 AACCCAGTTACCCACGACCA 61.056 55.000 0.00 0.00 0.00 4.02
1924 1999 0.321034 GAACCCAGTTACCCACGACC 60.321 60.000 0.00 0.00 0.00 4.79
1925 2000 0.683412 AGAACCCAGTTACCCACGAC 59.317 55.000 0.00 0.00 0.00 4.34
1926 2001 0.682852 CAGAACCCAGTTACCCACGA 59.317 55.000 0.00 0.00 0.00 4.35
1956 2031 2.426842 ACCTATTCCTTTCAGGCTGC 57.573 50.000 10.34 0.00 34.61 5.25
1980 2055 1.202521 TGTCACTATACATGCGGCCAG 60.203 52.381 2.24 0.00 0.00 4.85
3109 6456 8.130307 GCAATAACCATTTGCATAACCTAAAG 57.870 34.615 3.68 0.00 46.78 1.85
3263 6611 9.357652 CTGAAATTTTTCTGAAACTGAAACTGA 57.642 29.630 1.58 0.00 38.07 3.41
3264 6612 9.143631 ACTGAAATTTTTCTGAAACTGAAACTG 57.856 29.630 14.45 1.40 38.84 3.16
3338 6687 3.181429 GGCTGATTTTCCCATCCCTATCA 60.181 47.826 0.00 0.00 0.00 2.15
3428 6777 6.038936 GGTTGTAGCTTTCAAACTCAAACCTA 59.961 38.462 10.72 0.00 32.60 3.08
3451 6800 7.120432 ACAAAACAACAATTGCAGTTAATTGGT 59.880 29.630 20.47 11.12 46.02 3.67
3735 7085 5.542635 TCAGTAGGTGGTTATGAGTGTTCTT 59.457 40.000 0.00 0.00 0.00 2.52
3740 7090 5.661056 TCTTCAGTAGGTGGTTATGAGTG 57.339 43.478 0.00 0.00 0.00 3.51
3768 7118 2.224523 ACAATCAACAGTCACCGATGGT 60.225 45.455 0.00 0.00 35.62 3.55
3826 7186 1.342082 CTAAGTTGCCGTCGTGGTCG 61.342 60.000 0.00 0.00 41.21 4.79
3885 7245 5.683876 AAGGAGTGATGTATGTACAGCTT 57.316 39.130 9.50 0.00 42.66 3.74
3966 7326 1.078848 CTTCCGGAGCCTTGTCTGG 60.079 63.158 3.34 0.00 43.63 3.86
4124 7484 7.320399 GTTTCTGACCCAAAAAGAAGAAGAAA 58.680 34.615 0.00 0.00 31.89 2.52
4211 7571 5.389859 TGATTGGTCCATGAAACAACATC 57.610 39.130 0.00 0.00 0.00 3.06
4272 7632 4.632688 ACCCACGACATTTATTTTAGGACG 59.367 41.667 0.00 0.00 0.00 4.79
4329 7689 3.677190 TCCGTCCCAAAATAAATGTCGT 58.323 40.909 0.00 0.00 0.00 4.34
4330 7690 3.064820 CCTCCGTCCCAAAATAAATGTCG 59.935 47.826 0.00 0.00 0.00 4.35
4331 7691 3.181490 GCCTCCGTCCCAAAATAAATGTC 60.181 47.826 0.00 0.00 0.00 3.06
4332 7692 2.758423 GCCTCCGTCCCAAAATAAATGT 59.242 45.455 0.00 0.00 0.00 2.71
4333 7693 2.757868 TGCCTCCGTCCCAAAATAAATG 59.242 45.455 0.00 0.00 0.00 2.32
4334 7694 3.023832 CTGCCTCCGTCCCAAAATAAAT 58.976 45.455 0.00 0.00 0.00 1.40
4335 7695 2.224917 ACTGCCTCCGTCCCAAAATAAA 60.225 45.455 0.00 0.00 0.00 1.40
4367 7727 6.140377 GGGGATATACCTCCATTTCCAAAAA 58.860 40.000 3.33 0.00 37.01 1.94
4368 7728 5.691704 CGGGGATATACCTCCATTTCCAAAA 60.692 44.000 3.33 0.00 37.01 2.44
4369 7729 4.202524 CGGGGATATACCTCCATTTCCAAA 60.203 45.833 3.33 0.00 37.01 3.28
4370 7730 3.329520 CGGGGATATACCTCCATTTCCAA 59.670 47.826 3.33 0.00 37.01 3.53
4371 7731 2.910319 CGGGGATATACCTCCATTTCCA 59.090 50.000 3.33 0.00 37.01 3.53
4372 7732 2.238898 CCGGGGATATACCTCCATTTCC 59.761 54.545 3.33 0.00 37.01 3.13
4373 7733 2.355818 GCCGGGGATATACCTCCATTTC 60.356 54.545 2.18 0.00 37.01 2.17
4374 7734 1.633945 GCCGGGGATATACCTCCATTT 59.366 52.381 2.18 0.00 37.01 2.32
4375 7735 1.286248 GCCGGGGATATACCTCCATT 58.714 55.000 2.18 0.00 37.01 3.16
4376 7736 0.620700 GGCCGGGGATATACCTCCAT 60.621 60.000 2.18 0.00 37.01 3.41
4377 7737 1.229400 GGCCGGGGATATACCTCCA 60.229 63.158 2.18 0.00 37.01 3.86
4378 7738 0.976590 GAGGCCGGGGATATACCTCC 60.977 65.000 2.18 3.25 40.91 4.30
4379 7739 0.041386 AGAGGCCGGGGATATACCTC 59.959 60.000 12.64 12.64 45.99 3.85
4380 7740 0.252284 CAGAGGCCGGGGATATACCT 60.252 60.000 2.18 0.00 38.98 3.08
4381 7741 1.900545 GCAGAGGCCGGGGATATACC 61.901 65.000 2.18 0.00 38.08 2.73
4382 7742 1.192146 TGCAGAGGCCGGGGATATAC 61.192 60.000 2.18 0.00 40.13 1.47
4383 7743 0.252696 ATGCAGAGGCCGGGGATATA 60.253 55.000 2.18 0.00 40.13 0.86
4384 7744 1.539869 ATGCAGAGGCCGGGGATAT 60.540 57.895 2.18 0.00 40.13 1.63
4385 7745 2.122413 ATGCAGAGGCCGGGGATA 60.122 61.111 2.18 0.00 40.13 2.59
4386 7746 3.564218 GATGCAGAGGCCGGGGAT 61.564 66.667 2.18 0.00 40.13 3.85
4388 7748 3.882326 ATGATGCAGAGGCCGGGG 61.882 66.667 2.18 0.00 40.13 5.73
4389 7749 2.407440 ATCATGATGCAGAGGCCGGG 62.407 60.000 7.59 0.00 40.13 5.73
4390 7750 1.072678 ATCATGATGCAGAGGCCGG 59.927 57.895 7.59 0.00 40.13 6.13
4391 7751 0.250166 TCATCATGATGCAGAGGCCG 60.250 55.000 27.68 4.34 40.13 6.13
4392 7752 1.813178 CATCATCATGATGCAGAGGCC 59.187 52.381 27.68 0.00 46.37 5.19
4401 7761 1.546029 GGCTGCATGCATCATCATGAT 59.454 47.619 22.97 1.18 44.94 2.45
4402 7762 0.958822 GGCTGCATGCATCATCATGA 59.041 50.000 22.97 0.00 44.94 3.07
4403 7763 0.038251 GGGCTGCATGCATCATCATG 60.038 55.000 22.97 8.76 44.93 3.07
4404 7764 0.178961 AGGGCTGCATGCATCATCAT 60.179 50.000 22.97 5.97 45.15 2.45
4405 7765 0.396556 AAGGGCTGCATGCATCATCA 60.397 50.000 22.97 0.00 45.15 3.07
4406 7766 0.750850 AAAGGGCTGCATGCATCATC 59.249 50.000 22.97 12.92 45.15 2.92
4407 7767 1.200519 AAAAGGGCTGCATGCATCAT 58.799 45.000 22.97 11.63 45.15 2.45
4408 7768 1.849977 TAAAAGGGCTGCATGCATCA 58.150 45.000 22.97 0.00 45.15 3.07
4409 7769 3.464111 AATAAAAGGGCTGCATGCATC 57.536 42.857 22.97 17.75 45.15 3.91
4410 7770 5.356291 TTTAATAAAAGGGCTGCATGCAT 57.644 34.783 22.97 6.91 45.15 3.96
4411 7771 4.815533 TTTAATAAAAGGGCTGCATGCA 57.184 36.364 21.29 21.29 45.15 3.96
4412 7772 6.682423 ATTTTTAATAAAAGGGCTGCATGC 57.318 33.333 11.82 11.82 36.73 4.06
4413 7773 8.266392 TGAATTTTTAATAAAAGGGCTGCATG 57.734 30.769 0.50 0.00 36.73 4.06
4414 7774 8.320617 TCTGAATTTTTAATAAAAGGGCTGCAT 58.679 29.630 0.50 0.00 36.73 3.96
4415 7775 7.675062 TCTGAATTTTTAATAAAAGGGCTGCA 58.325 30.769 0.50 0.00 36.73 4.41
4416 7776 8.546597 TTCTGAATTTTTAATAAAAGGGCTGC 57.453 30.769 0.00 0.00 36.73 5.25
4441 7801 9.686683 AGCTGTAAAACCTTTATGATGATACTT 57.313 29.630 0.00 0.00 0.00 2.24
4442 7802 9.331282 GAGCTGTAAAACCTTTATGATGATACT 57.669 33.333 0.00 0.00 0.00 2.12
4443 7803 8.276325 CGAGCTGTAAAACCTTTATGATGATAC 58.724 37.037 0.00 0.00 0.00 2.24
4444 7804 7.042051 GCGAGCTGTAAAACCTTTATGATGATA 60.042 37.037 0.00 0.00 0.00 2.15
4445 7805 6.238484 GCGAGCTGTAAAACCTTTATGATGAT 60.238 38.462 0.00 0.00 0.00 2.45
4446 7806 5.064707 GCGAGCTGTAAAACCTTTATGATGA 59.935 40.000 0.00 0.00 0.00 2.92
4447 7807 5.163764 TGCGAGCTGTAAAACCTTTATGATG 60.164 40.000 0.00 0.00 0.00 3.07
4448 7808 4.941263 TGCGAGCTGTAAAACCTTTATGAT 59.059 37.500 0.00 0.00 0.00 2.45
4449 7809 4.320023 TGCGAGCTGTAAAACCTTTATGA 58.680 39.130 0.00 0.00 0.00 2.15
4450 7810 4.678509 TGCGAGCTGTAAAACCTTTATG 57.321 40.909 0.00 0.00 0.00 1.90
4451 7811 5.458015 GTTTGCGAGCTGTAAAACCTTTAT 58.542 37.500 0.00 0.00 33.80 1.40
4452 7812 4.553156 CGTTTGCGAGCTGTAAAACCTTTA 60.553 41.667 0.00 0.00 41.33 1.85
4453 7813 3.702330 GTTTGCGAGCTGTAAAACCTTT 58.298 40.909 0.00 0.00 33.80 3.11
4454 7814 2.286772 CGTTTGCGAGCTGTAAAACCTT 60.287 45.455 0.00 0.00 41.33 3.50
4455 7815 1.263217 CGTTTGCGAGCTGTAAAACCT 59.737 47.619 0.00 0.00 41.33 3.50
4456 7816 1.662026 CCGTTTGCGAGCTGTAAAACC 60.662 52.381 0.00 0.00 41.33 3.27
4457 7817 1.262151 TCCGTTTGCGAGCTGTAAAAC 59.738 47.619 0.00 0.00 41.33 2.43
4458 7818 1.529438 CTCCGTTTGCGAGCTGTAAAA 59.471 47.619 0.00 0.00 41.33 1.52
4459 7819 1.144969 CTCCGTTTGCGAGCTGTAAA 58.855 50.000 0.00 0.00 41.33 2.01
4460 7820 1.289109 GCTCCGTTTGCGAGCTGTAA 61.289 55.000 0.00 0.00 41.33 2.41
4461 7821 1.736645 GCTCCGTTTGCGAGCTGTA 60.737 57.895 0.00 0.00 41.33 2.74
4462 7822 3.044305 GCTCCGTTTGCGAGCTGT 61.044 61.111 0.00 0.00 41.33 4.40
4463 7823 2.116736 TTTGCTCCGTTTGCGAGCTG 62.117 55.000 10.82 0.00 39.85 4.24
4464 7824 1.845809 CTTTGCTCCGTTTGCGAGCT 61.846 55.000 10.82 0.00 39.85 4.09
4465 7825 1.441016 CTTTGCTCCGTTTGCGAGC 60.441 57.895 2.88 2.88 41.33 5.03
4466 7826 0.110644 GACTTTGCTCCGTTTGCGAG 60.111 55.000 0.00 0.00 41.33 5.03
4467 7827 0.812014 TGACTTTGCTCCGTTTGCGA 60.812 50.000 0.00 0.00 41.33 5.10
4468 7828 0.238289 ATGACTTTGCTCCGTTTGCG 59.762 50.000 0.00 0.00 37.95 4.85
4469 7829 2.729156 GCTATGACTTTGCTCCGTTTGC 60.729 50.000 0.00 0.00 0.00 3.68
4470 7830 2.483877 TGCTATGACTTTGCTCCGTTTG 59.516 45.455 0.00 0.00 0.00 2.93
4471 7831 2.778299 TGCTATGACTTTGCTCCGTTT 58.222 42.857 0.00 0.00 0.00 3.60
4472 7832 2.472695 TGCTATGACTTTGCTCCGTT 57.527 45.000 0.00 0.00 0.00 4.44
4473 7833 2.698855 ATGCTATGACTTTGCTCCGT 57.301 45.000 0.00 0.00 0.00 4.69
4474 7834 4.811024 TCTTTATGCTATGACTTTGCTCCG 59.189 41.667 0.00 0.00 0.00 4.63
4475 7835 6.709846 AGATCTTTATGCTATGACTTTGCTCC 59.290 38.462 0.00 0.00 0.00 4.70
4476 7836 7.440556 TCAGATCTTTATGCTATGACTTTGCTC 59.559 37.037 0.00 0.00 0.00 4.26
4477 7837 7.278135 TCAGATCTTTATGCTATGACTTTGCT 58.722 34.615 0.00 0.00 0.00 3.91
4478 7838 7.488187 TCAGATCTTTATGCTATGACTTTGC 57.512 36.000 0.00 0.00 0.00 3.68
4534 7894 5.381174 TTGTCCCTATTATCACCGTATCG 57.619 43.478 0.00 0.00 0.00 2.92
4535 7895 5.047235 AGCTTGTCCCTATTATCACCGTATC 60.047 44.000 0.00 0.00 0.00 2.24
4536 7896 4.838986 AGCTTGTCCCTATTATCACCGTAT 59.161 41.667 0.00 0.00 0.00 3.06
4537 7897 4.220724 AGCTTGTCCCTATTATCACCGTA 58.779 43.478 0.00 0.00 0.00 4.02
4538 7898 3.039011 AGCTTGTCCCTATTATCACCGT 58.961 45.455 0.00 0.00 0.00 4.83
4539 7899 3.322254 AGAGCTTGTCCCTATTATCACCG 59.678 47.826 0.00 0.00 0.00 4.94
4540 7900 4.591072 AGAGAGCTTGTCCCTATTATCACC 59.409 45.833 0.00 0.00 0.00 4.02
4541 7901 5.799827 AGAGAGCTTGTCCCTATTATCAC 57.200 43.478 0.00 0.00 0.00 3.06
4542 7902 5.478679 GCTAGAGAGCTTGTCCCTATTATCA 59.521 44.000 0.00 0.00 45.98 2.15
4543 7903 5.961272 GCTAGAGAGCTTGTCCCTATTATC 58.039 45.833 0.00 0.00 45.98 1.75
4544 7904 5.993748 GCTAGAGAGCTTGTCCCTATTAT 57.006 43.478 0.00 0.00 45.98 1.28
4558 7918 3.806949 ACAGGATAGAGGGCTAGAGAG 57.193 52.381 0.00 0.00 0.00 3.20
4559 7919 5.575157 CATAACAGGATAGAGGGCTAGAGA 58.425 45.833 0.00 0.00 0.00 3.10
4560 7920 4.159506 GCATAACAGGATAGAGGGCTAGAG 59.840 50.000 0.00 0.00 0.00 2.43
4561 7921 4.090090 GCATAACAGGATAGAGGGCTAGA 58.910 47.826 0.00 0.00 0.00 2.43
4562 7922 3.119316 CGCATAACAGGATAGAGGGCTAG 60.119 52.174 0.00 0.00 0.00 3.42
4563 7923 2.826128 CGCATAACAGGATAGAGGGCTA 59.174 50.000 0.00 0.00 0.00 3.93
4564 7924 1.620819 CGCATAACAGGATAGAGGGCT 59.379 52.381 0.00 0.00 0.00 5.19
4565 7925 1.618837 TCGCATAACAGGATAGAGGGC 59.381 52.381 0.00 0.00 0.00 5.19
4566 7926 2.028930 GGTCGCATAACAGGATAGAGGG 60.029 54.545 0.00 0.00 0.00 4.30
4567 7927 2.351835 CGGTCGCATAACAGGATAGAGG 60.352 54.545 0.00 0.00 0.00 3.69
4568 7928 2.922758 GCGGTCGCATAACAGGATAGAG 60.923 54.545 10.67 0.00 41.49 2.43
4569 7929 1.000607 GCGGTCGCATAACAGGATAGA 60.001 52.381 10.67 0.00 41.49 1.98
4570 7930 1.419374 GCGGTCGCATAACAGGATAG 58.581 55.000 10.67 0.00 41.49 2.08
4571 7931 0.032952 GGCGGTCGCATAACAGGATA 59.967 55.000 17.21 0.00 44.11 2.59
4572 7932 1.227556 GGCGGTCGCATAACAGGAT 60.228 57.895 17.21 0.00 44.11 3.24
4573 7933 1.966901 ATGGCGGTCGCATAACAGGA 61.967 55.000 17.21 0.00 44.11 3.86
4574 7934 1.498865 GATGGCGGTCGCATAACAGG 61.499 60.000 17.21 0.00 44.11 4.00
4575 7935 1.498865 GGATGGCGGTCGCATAACAG 61.499 60.000 17.21 0.00 44.11 3.16
4576 7936 1.522806 GGATGGCGGTCGCATAACA 60.523 57.895 17.21 6.12 44.11 2.41
4577 7937 2.594962 CGGATGGCGGTCGCATAAC 61.595 63.158 17.21 4.44 44.11 1.89
4578 7938 2.279851 CGGATGGCGGTCGCATAA 60.280 61.111 17.21 2.61 44.11 1.90
4579 7939 2.787567 TTCGGATGGCGGTCGCATA 61.788 57.895 17.21 5.89 44.11 3.14
4580 7940 4.155733 TTCGGATGGCGGTCGCAT 62.156 61.111 17.21 8.55 44.11 4.73
4594 7954 2.140717 GGGCTATATTCAACCGGTTCG 58.859 52.381 19.24 13.41 0.00 3.95
4595 7955 2.140717 CGGGCTATATTCAACCGGTTC 58.859 52.381 19.24 3.02 40.79 3.62
4596 7956 1.764134 TCGGGCTATATTCAACCGGTT 59.236 47.619 15.86 15.86 44.36 4.44
4597 7957 1.343465 CTCGGGCTATATTCAACCGGT 59.657 52.381 0.00 0.00 44.36 5.28
4598 7958 1.343465 ACTCGGGCTATATTCAACCGG 59.657 52.381 0.00 0.00 44.36 5.28
4599 7959 2.814280 ACTCGGGCTATATTCAACCG 57.186 50.000 0.00 0.00 45.52 4.44
4600 7960 4.202284 TGGTAACTCGGGCTATATTCAACC 60.202 45.833 0.00 0.00 37.61 3.77
4601 7961 4.952460 TGGTAACTCGGGCTATATTCAAC 58.048 43.478 0.00 0.00 37.61 3.18
4602 7962 5.542635 AGATGGTAACTCGGGCTATATTCAA 59.457 40.000 0.00 0.00 37.61 2.69
4603 7963 5.084519 AGATGGTAACTCGGGCTATATTCA 58.915 41.667 0.00 0.00 37.61 2.57
4604 7964 5.394333 GGAGATGGTAACTCGGGCTATATTC 60.394 48.000 0.00 0.00 35.49 1.75
4605 7965 4.466726 GGAGATGGTAACTCGGGCTATATT 59.533 45.833 0.00 0.00 35.49 1.28
4606 7966 4.024670 GGAGATGGTAACTCGGGCTATAT 58.975 47.826 0.00 0.00 35.49 0.86
4607 7967 3.075582 AGGAGATGGTAACTCGGGCTATA 59.924 47.826 0.00 0.00 35.49 1.31
4608 7968 2.158295 AGGAGATGGTAACTCGGGCTAT 60.158 50.000 0.00 0.00 35.49 2.97
4609 7969 1.217183 AGGAGATGGTAACTCGGGCTA 59.783 52.381 0.00 0.00 35.49 3.93
4610 7970 0.032017 AGGAGATGGTAACTCGGGCT 60.032 55.000 0.00 0.00 35.49 5.19
4611 7971 1.700955 TAGGAGATGGTAACTCGGGC 58.299 55.000 0.00 0.00 35.49 6.13
4612 7972 3.006967 CCAATAGGAGATGGTAACTCGGG 59.993 52.174 0.00 0.00 36.89 5.14
4613 7973 4.258702 CCAATAGGAGATGGTAACTCGG 57.741 50.000 0.00 0.00 36.89 4.63


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

AutoCloner maintained by Alex Coulton.