Multiple sequence alignment - TraesCS4A01G106400

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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 TraesCS4A01G106400 chr4A 100.000 4454 0 0 1 4454 120608334 120603881 0.000000e+00 8226.0
1 TraesCS4A01G106400 chr4D 93.789 2753 96 31 238 2962 344944082 344941377 0.000000e+00 4067.0
2 TraesCS4A01G106400 chr4D 96.461 763 21 2 3697 4454 211356414 211355653 0.000000e+00 1254.0
3 TraesCS4A01G106400 chr4D 95.979 771 23 3 3691 4454 16229568 16230337 0.000000e+00 1245.0
4 TraesCS4A01G106400 chr4D 94.251 487 21 3 3208 3694 344940920 344940441 0.000000e+00 737.0
5 TraesCS4A01G106400 chr4D 97.917 48 1 0 1 48 166531137 166531184 2.850000e-12 84.2
6 TraesCS4A01G106400 chr4B 90.511 1802 91 35 61 1819 426766220 426767984 0.000000e+00 2307.0
7 TraesCS4A01G106400 chr4B 94.321 1127 37 9 1816 2934 426768020 426769127 0.000000e+00 1701.0
8 TraesCS4A01G106400 chr4B 93.056 504 31 2 3195 3694 426769245 426769748 0.000000e+00 734.0
9 TraesCS4A01G106400 chr4B 85.827 127 18 0 2297 2423 404079416 404079542 7.770000e-28 135.0
10 TraesCS4A01G106400 chr2D 95.850 771 25 2 3691 4454 11225881 11225111 0.000000e+00 1240.0
11 TraesCS4A01G106400 chr2D 95.331 771 28 3 3691 4454 631046642 631045873 0.000000e+00 1218.0
12 TraesCS4A01G106400 chr2D 97.917 48 1 0 1 48 28834393 28834346 2.850000e-12 84.2
13 TraesCS4A01G106400 chr2D 93.878 49 2 1 131 178 638323170 638323122 6.180000e-09 73.1
14 TraesCS4A01G106400 chr6D 95.460 771 28 2 3691 4454 334322958 334323728 0.000000e+00 1223.0
15 TraesCS4A01G106400 chr6D 94.825 773 30 5 3691 4454 20094381 20093610 0.000000e+00 1197.0
16 TraesCS4A01G106400 chr5D 95.460 771 28 2 3691 4454 285846897 285846127 0.000000e+00 1223.0
17 TraesCS4A01G106400 chr5D 97.917 48 1 0 1 48 76233171 76233124 2.850000e-12 84.2
18 TraesCS4A01G106400 chr5D 97.917 48 1 0 1 48 496154343 496154390 2.850000e-12 84.2
19 TraesCS4A01G106400 chr7D 95.331 771 28 3 3691 4454 255930177 255929408 0.000000e+00 1218.0
20 TraesCS4A01G106400 chr7D 86.957 138 18 0 1437 1574 64277169 64277032 5.970000e-34 156.0
21 TraesCS4A01G106400 chr7D 100.000 45 0 0 1 45 609898626 609898670 2.850000e-12 84.2
22 TraesCS4A01G106400 chrUn 95.201 771 29 3 3691 4454 104623908 104624677 0.000000e+00 1212.0
23 TraesCS4A01G106400 chrUn 93.878 49 2 1 125 172 135090813 135090765 6.180000e-09 73.1
24 TraesCS4A01G106400 chrUn 93.878 49 2 1 125 172 152687669 152687621 6.180000e-09 73.1
25 TraesCS4A01G106400 chr7A 83.708 178 23 6 2252 2426 10190205 10190031 3.560000e-36 163.0
26 TraesCS4A01G106400 chr7A 86.765 136 18 0 1439 1574 68093819 68093684 7.720000e-33 152.0
27 TraesCS4A01G106400 chr7A 97.619 42 0 1 132 172 129877027 129876986 2.220000e-08 71.3
28 TraesCS4A01G106400 chr7B 86.232 138 19 0 1439 1576 5520613 5520476 2.780000e-32 150.0
29 TraesCS4A01G106400 chr7B 97.917 48 1 0 1 48 510398422 510398375 2.850000e-12 84.2
30 TraesCS4A01G106400 chr2B 78.448 232 44 6 1978 2208 131106694 131106468 3.590000e-31 147.0
31 TraesCS4A01G106400 chr2B 79.592 98 14 4 132 227 182153938 182154031 1.030000e-06 65.8
32 TraesCS4A01G106400 chr3D 97.917 48 1 0 1 48 614376040 614376087 2.850000e-12 84.2
33 TraesCS4A01G106400 chr1A 97.917 48 1 0 1 48 580597274 580597321 2.850000e-12 84.2
34 TraesCS4A01G106400 chr5A 89.231 65 4 2 1 62 600474835 600474899 1.330000e-10 78.7
35 TraesCS4A01G106400 chr1B 92.727 55 3 1 125 178 24513567 24513513 1.330000e-10 78.7
36 TraesCS4A01G106400 chr5B 89.474 57 2 4 127 180 712408263 712408318 7.990000e-08 69.4
37 TraesCS4A01G106400 chr2A 78.899 109 18 5 135 240 601704608 601704714 7.990000e-08 69.4


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 TraesCS4A01G106400 chr4A 120603881 120608334 4453 True 8226.000000 8226 100.000000 1 4454 1 chr4A.!!$R1 4453
1 TraesCS4A01G106400 chr4D 344940441 344944082 3641 True 2402.000000 4067 94.020000 238 3694 2 chr4D.!!$R2 3456
2 TraesCS4A01G106400 chr4D 211355653 211356414 761 True 1254.000000 1254 96.461000 3697 4454 1 chr4D.!!$R1 757
3 TraesCS4A01G106400 chr4D 16229568 16230337 769 False 1245.000000 1245 95.979000 3691 4454 1 chr4D.!!$F1 763
4 TraesCS4A01G106400 chr4B 426766220 426769748 3528 False 1580.666667 2307 92.629333 61 3694 3 chr4B.!!$F2 3633
5 TraesCS4A01G106400 chr2D 11225111 11225881 770 True 1240.000000 1240 95.850000 3691 4454 1 chr2D.!!$R1 763
6 TraesCS4A01G106400 chr2D 631045873 631046642 769 True 1218.000000 1218 95.331000 3691 4454 1 chr2D.!!$R3 763
7 TraesCS4A01G106400 chr6D 334322958 334323728 770 False 1223.000000 1223 95.460000 3691 4454 1 chr6D.!!$F1 763
8 TraesCS4A01G106400 chr6D 20093610 20094381 771 True 1197.000000 1197 94.825000 3691 4454 1 chr6D.!!$R1 763
9 TraesCS4A01G106400 chr5D 285846127 285846897 770 True 1223.000000 1223 95.460000 3691 4454 1 chr5D.!!$R2 763
10 TraesCS4A01G106400 chr7D 255929408 255930177 769 True 1218.000000 1218 95.331000 3691 4454 1 chr7D.!!$R2 763
11 TraesCS4A01G106400 chrUn 104623908 104624677 769 False 1212.000000 1212 95.201000 3691 4454 1 chrUn.!!$F1 763

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
49 50 0.033699 AAGCCTTTGGAGGATCTGCC 60.034 55.0 0.00 0.0 46.74 4.85 F
1220 1267 0.032540 CTTGCCAGGTTTGGTCAAGC 59.967 55.0 13.66 0.0 46.80 4.01 F
1286 1333 0.259647 TCTGGCCATGGGGAAAGATG 59.740 55.0 15.13 0.0 35.59 2.90 F
2974 3089 0.037975 TAGGAAGCAAACCGTCCGTC 60.038 55.0 0.00 0.0 45.52 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1876 1986 0.178964 CCACCCAAGAACACCATGGT 60.179 55.0 13.00 13.0 32.13 3.55 R
2268 2378 0.102481 CGTCCTCGTTCCGGATGAAT 59.898 55.0 4.15 0.0 39.43 2.57 R
3034 3149 0.323178 TCCCTCCGTCCTGTAGTGTC 60.323 60.0 0.00 0.0 0.00 3.67 R
4115 4533 1.270907 GTCTCACTGTCACCTGGGAT 58.729 55.0 0.00 0.0 0.00 3.85 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
18 19 2.785868 CTGCCAAGTATCACCAGCC 58.214 57.895 0.00 0.00 0.00 4.85
19 20 1.078497 TGCCAAGTATCACCAGCCG 60.078 57.895 0.00 0.00 0.00 5.52
20 21 1.220749 GCCAAGTATCACCAGCCGA 59.779 57.895 0.00 0.00 0.00 5.54
21 22 1.090052 GCCAAGTATCACCAGCCGAC 61.090 60.000 0.00 0.00 0.00 4.79
22 23 0.249120 CCAAGTATCACCAGCCGACA 59.751 55.000 0.00 0.00 0.00 4.35
23 24 1.359848 CAAGTATCACCAGCCGACAC 58.640 55.000 0.00 0.00 0.00 3.67
24 25 0.973632 AAGTATCACCAGCCGACACA 59.026 50.000 0.00 0.00 0.00 3.72
25 26 0.532573 AGTATCACCAGCCGACACAG 59.467 55.000 0.00 0.00 0.00 3.66
26 27 1.084370 GTATCACCAGCCGACACAGC 61.084 60.000 0.00 0.00 0.00 4.40
27 28 1.257750 TATCACCAGCCGACACAGCT 61.258 55.000 0.00 0.00 42.70 4.24
28 29 2.116983 ATCACCAGCCGACACAGCTT 62.117 55.000 0.00 0.00 38.95 3.74
29 30 2.281070 ACCAGCCGACACAGCTTG 60.281 61.111 0.00 0.00 38.95 4.01
30 31 2.031012 CCAGCCGACACAGCTTGA 59.969 61.111 3.37 0.00 38.95 3.02
31 32 1.597854 CCAGCCGACACAGCTTGAA 60.598 57.895 3.37 0.00 38.95 2.69
32 33 1.572085 CCAGCCGACACAGCTTGAAG 61.572 60.000 3.37 0.00 38.95 3.02
33 34 1.963338 AGCCGACACAGCTTGAAGC 60.963 57.895 9.59 9.59 42.84 3.86
34 35 2.970974 GCCGACACAGCTTGAAGCC 61.971 63.158 14.45 0.00 43.77 4.35
35 36 1.302033 CCGACACAGCTTGAAGCCT 60.302 57.895 14.45 0.00 43.77 4.58
36 37 0.886490 CCGACACAGCTTGAAGCCTT 60.886 55.000 14.45 0.00 43.77 4.35
37 38 0.947244 CGACACAGCTTGAAGCCTTT 59.053 50.000 14.45 0.00 43.77 3.11
38 39 1.334419 CGACACAGCTTGAAGCCTTTG 60.334 52.381 14.45 10.81 43.77 2.77
39 40 1.000938 GACACAGCTTGAAGCCTTTGG 60.001 52.381 14.45 2.10 43.77 3.28
40 41 1.321474 CACAGCTTGAAGCCTTTGGA 58.679 50.000 14.45 0.00 43.77 3.53
41 42 1.268899 CACAGCTTGAAGCCTTTGGAG 59.731 52.381 14.45 0.00 43.77 3.86
42 43 0.886563 CAGCTTGAAGCCTTTGGAGG 59.113 55.000 14.45 0.00 43.77 4.30
43 44 0.773644 AGCTTGAAGCCTTTGGAGGA 59.226 50.000 14.45 0.00 46.74 3.71
44 45 1.357079 AGCTTGAAGCCTTTGGAGGAT 59.643 47.619 14.45 0.00 46.74 3.24
45 46 1.747924 GCTTGAAGCCTTTGGAGGATC 59.252 52.381 5.74 0.00 46.74 3.36
46 47 2.620108 GCTTGAAGCCTTTGGAGGATCT 60.620 50.000 5.74 0.00 46.74 2.75
47 48 2.795231 TGAAGCCTTTGGAGGATCTG 57.205 50.000 0.00 0.00 46.74 2.90
48 49 1.340405 TGAAGCCTTTGGAGGATCTGC 60.340 52.381 0.00 0.00 46.74 4.26
49 50 0.033699 AAGCCTTTGGAGGATCTGCC 60.034 55.000 0.00 0.00 46.74 4.85
50 51 1.454663 GCCTTTGGAGGATCTGCCC 60.455 63.158 0.00 0.00 46.74 5.36
51 52 2.001803 CCTTTGGAGGATCTGCCCA 58.998 57.895 0.00 0.00 46.74 5.36
52 53 0.106819 CCTTTGGAGGATCTGCCCAG 60.107 60.000 0.00 0.00 46.74 4.45
53 54 0.750911 CTTTGGAGGATCTGCCCAGC 60.751 60.000 0.00 0.00 37.37 4.85
54 55 1.210204 TTTGGAGGATCTGCCCAGCT 61.210 55.000 0.00 0.00 37.37 4.24
55 56 1.630126 TTGGAGGATCTGCCCAGCTC 61.630 60.000 0.00 0.00 37.37 4.09
56 57 2.068821 GGAGGATCTGCCCAGCTCA 61.069 63.158 2.09 0.00 37.37 4.26
57 58 1.145819 GAGGATCTGCCCAGCTCAC 59.854 63.158 2.09 0.00 37.37 3.51
58 59 2.191641 GGATCTGCCCAGCTCACC 59.808 66.667 2.09 0.00 0.00 4.02
59 60 2.373707 GGATCTGCCCAGCTCACCT 61.374 63.158 2.09 0.00 0.00 4.00
72 73 0.543277 CTCACCTGCTTGCATCCCTA 59.457 55.000 0.00 0.00 0.00 3.53
77 78 1.747355 CCTGCTTGCATCCCTACTTTG 59.253 52.381 0.00 0.00 0.00 2.77
81 82 5.052693 TGCTTGCATCCCTACTTTGATAT 57.947 39.130 0.00 0.00 0.00 1.63
82 83 6.186420 TGCTTGCATCCCTACTTTGATATA 57.814 37.500 0.00 0.00 0.00 0.86
83 84 6.233434 TGCTTGCATCCCTACTTTGATATAG 58.767 40.000 0.00 0.00 0.00 1.31
84 85 5.123027 GCTTGCATCCCTACTTTGATATAGC 59.877 44.000 0.00 0.00 0.00 2.97
85 86 5.823861 TGCATCCCTACTTTGATATAGCA 57.176 39.130 0.00 0.00 0.00 3.49
122 123 1.103803 ATCACTCATGGTACGCGTCT 58.896 50.000 18.63 0.00 0.00 4.18
132 134 2.034939 TGGTACGCGTCTCAAGAGAAAA 59.965 45.455 18.63 0.00 39.48 2.29
139 141 4.088781 CGCGTCTCAAGAGAAAAACTACTC 59.911 45.833 0.00 0.00 39.48 2.59
144 146 5.246429 TCTCAAGAGAAAAACTACTCCCTCC 59.754 44.000 0.00 0.00 33.91 4.30
145 147 4.021368 TCAAGAGAAAAACTACTCCCTCCG 60.021 45.833 0.00 0.00 34.13 4.63
228 233 5.520748 AAAACTTCTCATGTATGGGACCT 57.479 39.130 0.00 0.00 36.93 3.85
233 238 3.576861 TCTCATGTATGGGACCTAGTGG 58.423 50.000 0.00 0.00 30.96 4.00
254 259 3.118738 GGGTATGTGATTCCACGACTCTT 60.119 47.826 0.00 0.00 46.06 2.85
313 319 2.159226 AGATTTGGAGCGTAGACTTCCG 60.159 50.000 0.00 0.00 0.00 4.30
392 399 1.665442 GTCAAATGGCACCACACCC 59.335 57.895 0.00 0.00 0.00 4.61
479 486 2.440247 CCCCTGGATTTCCACGCC 60.440 66.667 0.00 0.00 42.01 5.68
480 487 2.440247 CCCTGGATTTCCACGCCC 60.440 66.667 0.00 0.00 42.01 6.13
481 488 2.677228 CCTGGATTTCCACGCCCT 59.323 61.111 0.00 0.00 42.01 5.19
482 489 1.452108 CCTGGATTTCCACGCCCTC 60.452 63.158 0.00 0.00 42.01 4.30
483 490 1.299648 CTGGATTTCCACGCCCTCA 59.700 57.895 0.00 0.00 42.01 3.86
484 491 0.322456 CTGGATTTCCACGCCCTCAA 60.322 55.000 0.00 0.00 42.01 3.02
489 496 2.725203 TTTCCACGCCCTCAACCTCG 62.725 60.000 0.00 0.00 0.00 4.63
614 632 2.548875 GTCCATACAAGAGAGCAGCAG 58.451 52.381 0.00 0.00 0.00 4.24
615 633 1.134580 TCCATACAAGAGAGCAGCAGC 60.135 52.381 0.00 0.00 42.56 5.25
643 661 1.070105 TTGACCGTTGAACCCTCCG 59.930 57.895 0.00 0.00 0.00 4.63
736 766 1.324736 CGATACGCACAGAAAAGAGCC 59.675 52.381 0.00 0.00 0.00 4.70
764 794 4.021631 CGCACCAGCACAGCACAG 62.022 66.667 0.00 0.00 42.27 3.66
765 795 4.338539 GCACCAGCACAGCACAGC 62.339 66.667 0.00 0.00 41.58 4.40
907 952 3.499918 CCGGGATAAAGTCAATCATCAGC 59.500 47.826 0.00 0.00 0.00 4.26
908 953 4.384056 CGGGATAAAGTCAATCATCAGCT 58.616 43.478 0.00 0.00 0.00 4.24
909 954 4.450419 CGGGATAAAGTCAATCATCAGCTC 59.550 45.833 0.00 0.00 0.00 4.09
910 955 5.371526 GGGATAAAGTCAATCATCAGCTCA 58.628 41.667 0.00 0.00 0.00 4.26
911 956 5.469421 GGGATAAAGTCAATCATCAGCTCAG 59.531 44.000 0.00 0.00 0.00 3.35
912 957 5.049543 GGATAAAGTCAATCATCAGCTCAGC 60.050 44.000 0.00 0.00 0.00 4.26
993 1040 1.597742 TGAGAGTTTCTTGGCTGTGC 58.402 50.000 0.00 0.00 0.00 4.57
1208 1255 2.358957 TCACCATCGATTTCTTGCCAG 58.641 47.619 0.00 0.00 0.00 4.85
1210 1257 1.004745 ACCATCGATTTCTTGCCAGGT 59.995 47.619 0.00 0.00 0.00 4.00
1220 1267 0.032540 CTTGCCAGGTTTGGTCAAGC 59.967 55.000 13.66 0.00 46.80 4.01
1265 1312 4.529731 GGGGGATTGGCTCTGGGC 62.530 72.222 0.00 0.00 40.90 5.36
1286 1333 0.259647 TCTGGCCATGGGGAAAGATG 59.740 55.000 15.13 0.00 35.59 2.90
1341 1391 7.769220 ACAACACTAGTTTAGTCGCACTATAT 58.231 34.615 0.00 0.00 36.76 0.86
1386 1436 6.100004 TGTTAGTAATCTGTTAGTGCTCTGC 58.900 40.000 0.00 0.00 0.00 4.26
1398 1448 3.357079 CTCTGCGGTTGGTGGTGC 61.357 66.667 0.00 0.00 0.00 5.01
1606 1656 1.895798 TCTCTTCCGCTTCAGATGTGT 59.104 47.619 0.00 0.00 0.00 3.72
1607 1657 1.998315 CTCTTCCGCTTCAGATGTGTG 59.002 52.381 0.00 0.00 0.00 3.82
1608 1658 1.344438 TCTTCCGCTTCAGATGTGTGT 59.656 47.619 0.00 0.00 0.00 3.72
1609 1659 2.560981 TCTTCCGCTTCAGATGTGTGTA 59.439 45.455 0.00 0.00 0.00 2.90
1735 1796 1.303799 ACGACGTCTACATCGCCACT 61.304 55.000 14.70 0.00 42.12 4.00
1812 1873 4.504340 GGAAGAACACTGCCAGGTAGTAAA 60.504 45.833 10.30 0.00 29.93 2.01
1876 1986 7.228308 TGACAATTTGATCCGTATATTCATGCA 59.772 33.333 2.79 0.00 0.00 3.96
1879 1989 4.615588 TGATCCGTATATTCATGCACCA 57.384 40.909 0.00 0.00 0.00 4.17
1899 2009 0.467290 TGGTGTTCTTGGGTGGCTTC 60.467 55.000 0.00 0.00 0.00 3.86
2004 2114 2.546494 GCTGCTGAACGCCAACTGT 61.546 57.895 0.00 0.00 38.05 3.55
2268 2378 4.648626 ACCGACGACGACCTGGGA 62.649 66.667 9.28 0.00 42.66 4.37
2397 2507 1.561643 TCGAGAGGATGCTCACCTTT 58.438 50.000 17.24 0.00 37.93 3.11
2430 2540 2.280797 ATCACAGGTGCGTTGCGT 60.281 55.556 0.00 0.00 0.00 5.24
2431 2541 2.227968 GATCACAGGTGCGTTGCGTC 62.228 60.000 0.00 0.00 0.00 5.19
2541 2651 1.202290 CGTGCTTTGTTGACTGGCTTT 60.202 47.619 0.00 0.00 0.00 3.51
2593 2703 3.989817 GCTAAAAACATCTTTGTGCTGGG 59.010 43.478 0.00 0.00 35.83 4.45
2605 2715 5.128827 TCTTTGTGCTGGGTATAAGTAGGAG 59.871 44.000 0.00 0.00 0.00 3.69
2750 2862 6.434652 TGCCTATCTTTGGAGCTAGTAGTATC 59.565 42.308 0.00 0.00 0.00 2.24
2768 2880 0.888619 TCTGCTGTAGACGACAAGGG 59.111 55.000 0.00 0.00 37.70 3.95
2928 3043 3.637998 AGTAGCTTTTTGAGACGTCGA 57.362 42.857 10.46 0.00 0.00 4.20
2934 3049 2.129823 TTTTGAGACGTCGACCAGAC 57.870 50.000 10.58 0.00 46.16 3.51
2947 3062 5.462530 TCGACCAGACAATTCTAGTGAAA 57.537 39.130 0.00 0.00 35.63 2.69
2948 3063 5.849510 TCGACCAGACAATTCTAGTGAAAA 58.150 37.500 0.00 0.00 35.63 2.29
2962 3077 8.065073 ATTCTAGTGAAAAGAAGGCTAGGAAGC 61.065 40.741 0.00 0.00 40.06 3.86
2972 3087 2.750815 CTAGGAAGCAAACCGTCCG 58.249 57.895 0.00 0.00 45.52 4.79
2974 3089 0.037975 TAGGAAGCAAACCGTCCGTC 60.038 55.000 0.00 0.00 45.52 4.79
2975 3090 1.301479 GGAAGCAAACCGTCCGTCT 60.301 57.895 0.00 0.00 32.40 4.18
2976 3091 1.289800 GGAAGCAAACCGTCCGTCTC 61.290 60.000 0.00 0.00 32.40 3.36
2977 3092 0.599204 GAAGCAAACCGTCCGTCTCA 60.599 55.000 0.00 0.00 0.00 3.27
2979 3094 0.892755 AGCAAACCGTCCGTCTCATA 59.107 50.000 0.00 0.00 0.00 2.15
2982 3097 3.131577 AGCAAACCGTCCGTCTCATAATA 59.868 43.478 0.00 0.00 0.00 0.98
2983 3098 4.056050 GCAAACCGTCCGTCTCATAATAT 58.944 43.478 0.00 0.00 0.00 1.28
2989 3104 6.002704 ACCGTCCGTCTCATAATATAGAAGT 58.997 40.000 0.00 0.00 0.00 3.01
2994 3109 9.530633 GTCCGTCTCATAATATAGAAGTGTTTT 57.469 33.333 0.00 0.00 0.00 2.43
3012 3127 8.747538 AGTGTTTTTGTCATTATATAGTCCCC 57.252 34.615 0.00 0.00 0.00 4.81
3013 3128 7.778382 AGTGTTTTTGTCATTATATAGTCCCCC 59.222 37.037 0.00 0.00 0.00 5.40
3014 3129 7.558444 GTGTTTTTGTCATTATATAGTCCCCCA 59.442 37.037 0.00 0.00 0.00 4.96
3015 3130 7.777910 TGTTTTTGTCATTATATAGTCCCCCAG 59.222 37.037 0.00 0.00 0.00 4.45
3016 3131 7.460214 TTTTGTCATTATATAGTCCCCCAGT 57.540 36.000 0.00 0.00 0.00 4.00
3017 3132 6.681729 TTGTCATTATATAGTCCCCCAGTC 57.318 41.667 0.00 0.00 0.00 3.51
3018 3133 5.977533 TGTCATTATATAGTCCCCCAGTCT 58.022 41.667 0.00 0.00 0.00 3.24
3019 3134 6.017192 TGTCATTATATAGTCCCCCAGTCTC 58.983 44.000 0.00 0.00 0.00 3.36
3020 3135 6.017192 GTCATTATATAGTCCCCCAGTCTCA 58.983 44.000 0.00 0.00 0.00 3.27
3021 3136 6.670027 GTCATTATATAGTCCCCCAGTCTCAT 59.330 42.308 0.00 0.00 0.00 2.90
3022 3137 7.839705 GTCATTATATAGTCCCCCAGTCTCATA 59.160 40.741 0.00 0.00 0.00 2.15
3023 3138 8.406643 TCATTATATAGTCCCCCAGTCTCATAA 58.593 37.037 0.00 0.00 0.00 1.90
3024 3139 9.218525 CATTATATAGTCCCCCAGTCTCATAAT 57.781 37.037 0.00 0.00 0.00 1.28
3026 3141 9.937876 TTATATAGTCCCCCAGTCTCATAATAG 57.062 37.037 0.00 0.00 0.00 1.73
3027 3142 4.561254 AGTCCCCCAGTCTCATAATAGT 57.439 45.455 0.00 0.00 0.00 2.12
3028 3143 4.227197 AGTCCCCCAGTCTCATAATAGTG 58.773 47.826 0.00 0.00 0.00 2.74
3029 3144 3.967987 GTCCCCCAGTCTCATAATAGTGT 59.032 47.826 0.00 0.00 0.00 3.55
3030 3145 4.409247 GTCCCCCAGTCTCATAATAGTGTT 59.591 45.833 0.00 0.00 0.00 3.32
3031 3146 5.036916 TCCCCCAGTCTCATAATAGTGTTT 58.963 41.667 0.00 0.00 0.00 2.83
3032 3147 5.491078 TCCCCCAGTCTCATAATAGTGTTTT 59.509 40.000 0.00 0.00 0.00 2.43
3033 3148 6.011981 TCCCCCAGTCTCATAATAGTGTTTTT 60.012 38.462 0.00 0.00 0.00 1.94
3034 3149 6.095440 CCCCCAGTCTCATAATAGTGTTTTTG 59.905 42.308 0.00 0.00 0.00 2.44
3035 3150 6.884295 CCCCAGTCTCATAATAGTGTTTTTGA 59.116 38.462 0.00 0.00 0.00 2.69
3036 3151 7.148239 CCCCAGTCTCATAATAGTGTTTTTGAC 60.148 40.741 0.00 0.00 0.00 3.18
3037 3152 7.390440 CCCAGTCTCATAATAGTGTTTTTGACA 59.610 37.037 0.00 0.00 35.42 3.58
3048 3163 3.199677 TGTTTTTGACACTACAGGACGG 58.800 45.455 0.00 0.00 32.00 4.79
3049 3164 3.118702 TGTTTTTGACACTACAGGACGGA 60.119 43.478 0.00 0.00 32.00 4.69
3050 3165 3.380479 TTTTGACACTACAGGACGGAG 57.620 47.619 0.00 0.00 0.00 4.63
3051 3166 1.254026 TTGACACTACAGGACGGAGG 58.746 55.000 0.00 0.00 0.00 4.30
3052 3167 0.611062 TGACACTACAGGACGGAGGG 60.611 60.000 0.00 0.00 0.00 4.30
3053 3168 0.323178 GACACTACAGGACGGAGGGA 60.323 60.000 0.00 0.00 0.00 4.20
3054 3169 0.323542 ACACTACAGGACGGAGGGAG 60.324 60.000 0.00 0.00 0.00 4.30
3055 3170 0.323542 CACTACAGGACGGAGGGAGT 60.324 60.000 0.00 0.00 0.00 3.85
3056 3171 1.064906 CACTACAGGACGGAGGGAGTA 60.065 57.143 0.00 0.00 0.00 2.59
3057 3172 1.064832 ACTACAGGACGGAGGGAGTAC 60.065 57.143 0.00 0.00 0.00 2.73
3058 3173 0.994247 TACAGGACGGAGGGAGTACA 59.006 55.000 0.00 0.00 0.00 2.90
3059 3174 0.335361 ACAGGACGGAGGGAGTACAT 59.665 55.000 0.00 0.00 0.00 2.29
3063 3178 3.449737 CAGGACGGAGGGAGTACATTTTA 59.550 47.826 0.00 0.00 0.00 1.52
3065 3180 4.720273 AGGACGGAGGGAGTACATTTTATT 59.280 41.667 0.00 0.00 0.00 1.40
3073 3188 8.182227 GGAGGGAGTACATTTTATTTTTCTTCG 58.818 37.037 0.00 0.00 0.00 3.79
3090 3205 8.842358 TTTTCTTCGGTTATACTTGATGTCTT 57.158 30.769 0.00 0.00 0.00 3.01
3094 3209 9.399797 TCTTCGGTTATACTTGATGTCTTAGTA 57.600 33.333 0.00 0.00 0.00 1.82
3104 3222 6.699204 ACTTGATGTCTTAGTATGCATTCTCG 59.301 38.462 9.33 3.00 0.00 4.04
3127 3245 4.667668 GCTGAAATTGCTCTTGTCACGTAG 60.668 45.833 0.00 0.00 0.00 3.51
3128 3246 4.627058 TGAAATTGCTCTTGTCACGTAGA 58.373 39.130 0.00 0.00 0.00 2.59
3129 3247 5.053811 TGAAATTGCTCTTGTCACGTAGAA 58.946 37.500 0.00 0.00 0.00 2.10
3130 3248 5.525745 TGAAATTGCTCTTGTCACGTAGAAA 59.474 36.000 0.00 0.00 0.00 2.52
3131 3249 5.597813 AATTGCTCTTGTCACGTAGAAAG 57.402 39.130 0.00 0.00 0.00 2.62
3132 3250 3.728076 TGCTCTTGTCACGTAGAAAGT 57.272 42.857 0.00 0.00 0.00 2.66
3133 3251 4.054780 TGCTCTTGTCACGTAGAAAGTT 57.945 40.909 0.00 0.00 0.00 2.66
3134 3252 4.439057 TGCTCTTGTCACGTAGAAAGTTT 58.561 39.130 0.00 0.00 0.00 2.66
3135 3253 4.873827 TGCTCTTGTCACGTAGAAAGTTTT 59.126 37.500 0.00 0.00 0.00 2.43
3136 3254 5.353123 TGCTCTTGTCACGTAGAAAGTTTTT 59.647 36.000 0.00 0.00 0.00 1.94
3185 3303 8.915057 TTTTTGCCATTTTCATTGAATAAGGA 57.085 26.923 13.19 0.00 0.00 3.36
3186 3304 8.550710 TTTTGCCATTTTCATTGAATAAGGAG 57.449 30.769 13.19 4.10 0.00 3.69
3187 3305 6.855763 TGCCATTTTCATTGAATAAGGAGT 57.144 33.333 13.19 0.00 0.00 3.85
3188 3306 7.953005 TGCCATTTTCATTGAATAAGGAGTA 57.047 32.000 13.19 0.00 0.00 2.59
3189 3307 8.537728 TGCCATTTTCATTGAATAAGGAGTAT 57.462 30.769 13.19 0.00 0.00 2.12
3190 3308 8.632679 TGCCATTTTCATTGAATAAGGAGTATC 58.367 33.333 13.19 0.00 0.00 2.24
3191 3309 8.632679 GCCATTTTCATTGAATAAGGAGTATCA 58.367 33.333 13.19 0.00 36.25 2.15
3195 3313 8.668510 TTTCATTGAATAAGGAGTATCAGAGC 57.331 34.615 0.00 0.00 36.25 4.09
3196 3314 7.609097 TCATTGAATAAGGAGTATCAGAGCT 57.391 36.000 0.00 0.00 36.25 4.09
3197 3315 7.665690 TCATTGAATAAGGAGTATCAGAGCTC 58.334 38.462 5.27 5.27 36.25 4.09
3198 3316 7.508636 TCATTGAATAAGGAGTATCAGAGCTCT 59.491 37.037 11.45 11.45 36.25 4.09
3199 3317 7.667575 TTGAATAAGGAGTATCAGAGCTCTT 57.332 36.000 15.27 2.80 36.25 2.85
3200 3318 7.048629 TGAATAAGGAGTATCAGAGCTCTTG 57.951 40.000 15.27 10.10 36.25 3.02
3201 3319 6.609212 TGAATAAGGAGTATCAGAGCTCTTGT 59.391 38.462 15.27 8.22 36.25 3.16
3202 3320 6.648879 ATAAGGAGTATCAGAGCTCTTGTC 57.351 41.667 15.27 6.27 36.25 3.18
3203 3321 3.974719 AGGAGTATCAGAGCTCTTGTCA 58.025 45.455 15.27 0.00 36.25 3.58
3204 3322 3.953612 AGGAGTATCAGAGCTCTTGTCAG 59.046 47.826 15.27 2.07 36.25 3.51
3209 3327 2.451490 TCAGAGCTCTTGTCAGGTAGG 58.549 52.381 15.27 0.00 0.00 3.18
3219 3631 6.282199 TCTTGTCAGGTAGGAAGTTATGTC 57.718 41.667 0.00 0.00 0.00 3.06
3245 3657 9.307121 CTCATCAGTTAATTAGTGTCTTACTGG 57.693 37.037 10.01 0.00 40.65 4.00
3269 3681 6.374333 GGTGTGGATTCTTACTGAATTTGCTA 59.626 38.462 0.00 0.00 44.70 3.49
3363 3775 2.067197 CACGGACCCCTTCTCCTTT 58.933 57.895 0.00 0.00 0.00 3.11
3405 3817 1.347707 ACGGAAGACCAGATGAAGCAA 59.652 47.619 0.00 0.00 35.59 3.91
3455 3867 3.924922 ACCCCAACTTCCGATACTAGAT 58.075 45.455 0.00 0.00 0.00 1.98
3484 3896 1.005097 CCTAGTTACCCAACCCCCAAC 59.995 57.143 0.00 0.00 35.05 3.77
3499 3911 3.118186 CCCCCAACAGTATGATTTCGGTA 60.118 47.826 0.00 0.00 39.69 4.02
3567 3979 2.537625 GCGCACTGCATTTGTTTGTTTA 59.462 40.909 0.30 0.00 45.45 2.01
3596 4008 4.397730 TGTAAGTTGTTGCTGCTTCTTCAA 59.602 37.500 0.00 0.00 0.00 2.69
3610 4022 3.943671 TCTTCAAACCTTTGTCCCTCA 57.056 42.857 0.00 0.00 39.18 3.86
3646 4058 4.796038 AAGTTTGGAGCATGATTTGAGG 57.204 40.909 0.00 0.00 0.00 3.86
3887 4300 4.661709 TCCTAGTTGGTGTTAGGAAAAGGT 59.338 41.667 0.00 0.00 41.81 3.50
3967 4380 6.005823 CAGACTTGCCAAATGGGATATCATA 58.994 40.000 4.83 0.00 40.01 2.15
3983 4396 6.295349 GGATATCATATGTCGACCAAAGGACT 60.295 42.308 14.12 0.00 34.31 3.85
3987 4400 2.297698 TGTCGACCAAAGGACTAGGA 57.702 50.000 14.12 0.00 34.31 2.94
3991 4404 1.895866 CGACCAAAGGACTAGGAGGGT 60.896 57.143 0.00 0.00 0.00 4.34
4045 4463 7.796054 ACAGATGTCTTTAAGTGGCTGTATAT 58.204 34.615 0.00 0.00 33.99 0.86
4115 4533 6.360370 AAGTATCTGCAGTCCAAGACTTTA 57.640 37.500 14.67 0.00 41.37 1.85
4178 4596 3.118956 AGGGACTTATGAGAGTCAAAGCG 60.119 47.826 7.27 0.00 46.21 4.68
4184 4602 0.603707 TGAGAGTCAAAGCGGCCTTG 60.604 55.000 4.95 4.95 0.00 3.61
4192 4610 4.521256 AGTCAAAGCGGCCTTGTTTAATAA 59.479 37.500 10.84 0.00 0.00 1.40
4235 4653 1.069765 CACCACCACTCGCTTCTGT 59.930 57.895 0.00 0.00 0.00 3.41
4260 4678 2.335316 TACTTGGCTTGGTGAAACGT 57.665 45.000 0.00 0.00 38.12 3.99
4300 4718 4.276678 TCCGTCCCTGTATAGTATTGTTCG 59.723 45.833 0.00 0.00 0.00 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.091771 CGGCTGGTGATACTTGGCAG 61.092 60.000 0.00 0.00 0.00 4.85
1 2 1.078497 CGGCTGGTGATACTTGGCA 60.078 57.895 0.00 0.00 0.00 4.92
3 4 0.249120 TGTCGGCTGGTGATACTTGG 59.751 55.000 0.00 0.00 0.00 3.61
4 5 1.337728 TGTGTCGGCTGGTGATACTTG 60.338 52.381 0.00 0.00 0.00 3.16
5 6 0.973632 TGTGTCGGCTGGTGATACTT 59.026 50.000 0.00 0.00 0.00 2.24
7 8 1.084370 GCTGTGTCGGCTGGTGATAC 61.084 60.000 0.00 0.00 32.24 2.24
8 9 1.218047 GCTGTGTCGGCTGGTGATA 59.782 57.895 0.00 0.00 32.24 2.15
9 10 2.046892 GCTGTGTCGGCTGGTGAT 60.047 61.111 0.00 0.00 32.24 3.06
10 11 2.807107 AAGCTGTGTCGGCTGGTGA 61.807 57.895 3.78 0.00 46.32 4.02
11 12 2.281070 AAGCTGTGTCGGCTGGTG 60.281 61.111 3.78 0.00 46.32 4.17
12 13 2.281070 CAAGCTGTGTCGGCTGGT 60.281 61.111 3.78 0.00 46.32 4.00
13 14 1.572085 CTTCAAGCTGTGTCGGCTGG 61.572 60.000 3.78 1.29 46.32 4.85
14 15 1.864862 CTTCAAGCTGTGTCGGCTG 59.135 57.895 3.78 0.00 46.32 4.85
16 17 2.558313 GCTTCAAGCTGTGTCGGC 59.442 61.111 0.71 0.00 38.45 5.54
17 18 0.886490 AAGGCTTCAAGCTGTGTCGG 60.886 55.000 9.83 0.00 41.99 4.79
18 19 0.947244 AAAGGCTTCAAGCTGTGTCG 59.053 50.000 9.83 0.00 41.99 4.35
19 20 1.000938 CCAAAGGCTTCAAGCTGTGTC 60.001 52.381 9.83 0.00 41.99 3.67
20 21 1.035139 CCAAAGGCTTCAAGCTGTGT 58.965 50.000 9.83 0.00 41.99 3.72
21 22 1.268899 CTCCAAAGGCTTCAAGCTGTG 59.731 52.381 9.83 5.02 41.99 3.66
22 23 1.613836 CTCCAAAGGCTTCAAGCTGT 58.386 50.000 9.83 0.00 41.99 4.40
23 24 0.886563 CCTCCAAAGGCTTCAAGCTG 59.113 55.000 9.83 0.00 41.99 4.24
24 25 0.773644 TCCTCCAAAGGCTTCAAGCT 59.226 50.000 9.83 0.00 43.02 3.74
25 26 1.747924 GATCCTCCAAAGGCTTCAAGC 59.252 52.381 0.00 0.00 43.02 4.01
26 27 3.015327 CAGATCCTCCAAAGGCTTCAAG 58.985 50.000 0.00 0.00 43.02 3.02
27 28 2.881403 GCAGATCCTCCAAAGGCTTCAA 60.881 50.000 0.00 0.00 43.02 2.69
28 29 1.340405 GCAGATCCTCCAAAGGCTTCA 60.340 52.381 0.00 0.00 43.02 3.02
29 30 1.387539 GCAGATCCTCCAAAGGCTTC 58.612 55.000 0.00 0.00 43.02 3.86
30 31 0.033699 GGCAGATCCTCCAAAGGCTT 60.034 55.000 0.00 0.00 43.02 4.35
31 32 1.611965 GGCAGATCCTCCAAAGGCT 59.388 57.895 0.00 0.00 43.02 4.58
32 33 1.454663 GGGCAGATCCTCCAAAGGC 60.455 63.158 3.59 0.00 43.02 4.35
33 34 0.106819 CTGGGCAGATCCTCCAAAGG 60.107 60.000 3.59 0.00 44.89 3.11
34 35 0.750911 GCTGGGCAGATCCTCCAAAG 60.751 60.000 3.59 2.09 34.39 2.77
35 36 1.210204 AGCTGGGCAGATCCTCCAAA 61.210 55.000 3.59 0.00 34.39 3.28
36 37 1.617536 AGCTGGGCAGATCCTCCAA 60.618 57.895 3.59 0.00 34.39 3.53
37 38 2.041762 AGCTGGGCAGATCCTCCA 59.958 61.111 3.59 1.91 34.39 3.86
38 39 2.068821 TGAGCTGGGCAGATCCTCC 61.069 63.158 0.00 0.00 42.79 4.30
39 40 1.145819 GTGAGCTGGGCAGATCCTC 59.854 63.158 0.00 0.00 42.79 3.71
40 41 2.373707 GGTGAGCTGGGCAGATCCT 61.374 63.158 0.00 0.00 42.79 3.24
41 42 2.191641 GGTGAGCTGGGCAGATCC 59.808 66.667 0.00 0.00 42.79 3.36
42 43 1.153208 CAGGTGAGCTGGGCAGATC 60.153 63.158 3.23 0.00 43.66 2.75
43 44 2.996395 CAGGTGAGCTGGGCAGAT 59.004 61.111 3.23 0.00 0.00 2.90
44 45 4.025858 GCAGGTGAGCTGGGCAGA 62.026 66.667 14.04 0.00 0.00 4.26
45 46 3.564345 AAGCAGGTGAGCTGGGCAG 62.564 63.158 14.04 0.00 45.89 4.85
46 47 3.573229 AAGCAGGTGAGCTGGGCA 61.573 61.111 14.04 0.00 45.89 5.36
47 48 3.060615 CAAGCAGGTGAGCTGGGC 61.061 66.667 14.04 0.00 45.89 5.36
48 49 3.060615 GCAAGCAGGTGAGCTGGG 61.061 66.667 14.04 0.00 45.89 4.45
49 50 1.654954 GATGCAAGCAGGTGAGCTGG 61.655 60.000 14.04 0.00 45.89 4.85
50 51 1.654954 GGATGCAAGCAGGTGAGCTG 61.655 60.000 7.39 7.39 45.89 4.24
52 53 2.413142 GGGATGCAAGCAGGTGAGC 61.413 63.158 0.00 0.00 0.00 4.26
53 54 0.543277 TAGGGATGCAAGCAGGTGAG 59.457 55.000 0.00 0.00 0.00 3.51
54 55 0.253044 GTAGGGATGCAAGCAGGTGA 59.747 55.000 0.00 0.00 0.00 4.02
55 56 0.254178 AGTAGGGATGCAAGCAGGTG 59.746 55.000 0.00 0.00 0.00 4.00
56 57 0.995024 AAGTAGGGATGCAAGCAGGT 59.005 50.000 0.00 0.00 0.00 4.00
57 58 1.747355 CAAAGTAGGGATGCAAGCAGG 59.253 52.381 0.00 0.00 0.00 4.85
58 59 2.715046 TCAAAGTAGGGATGCAAGCAG 58.285 47.619 0.00 0.00 0.00 4.24
59 60 2.877097 TCAAAGTAGGGATGCAAGCA 57.123 45.000 0.00 0.00 0.00 3.91
96 97 4.049186 GCGTACCATGAGTGATTCGTTAT 58.951 43.478 0.00 0.00 0.00 1.89
102 103 1.476891 AGACGCGTACCATGAGTGATT 59.523 47.619 13.97 0.00 0.00 2.57
107 108 1.132453 TCTTGAGACGCGTACCATGAG 59.868 52.381 13.97 8.61 0.00 2.90
111 112 1.241165 TTCTCTTGAGACGCGTACCA 58.759 50.000 13.97 10.73 0.00 3.25
122 123 4.021368 CGGAGGGAGTAGTTTTTCTCTTGA 60.021 45.833 0.00 0.00 0.00 3.02
132 134 0.338814 ATGGGACGGAGGGAGTAGTT 59.661 55.000 0.00 0.00 0.00 2.24
139 141 2.969950 TCTTACATTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
168 173 6.801377 TGCAATGTCGAAAATTGTCTTATGTC 59.199 34.615 18.35 5.21 37.35 3.06
175 180 5.927030 TCTACTGCAATGTCGAAAATTGTC 58.073 37.500 18.35 13.03 37.35 3.18
178 183 7.667043 TTACTCTACTGCAATGTCGAAAATT 57.333 32.000 0.00 0.00 0.00 1.82
226 231 3.492656 CGTGGAATCACATACCCACTAGG 60.493 52.174 0.00 0.00 45.04 3.02
227 232 3.383505 TCGTGGAATCACATACCCACTAG 59.616 47.826 0.00 0.00 45.04 2.57
228 233 3.131577 GTCGTGGAATCACATACCCACTA 59.868 47.826 0.00 0.00 45.04 2.74
233 238 3.802948 AGAGTCGTGGAATCACATACC 57.197 47.619 0.00 0.00 43.79 2.73
396 403 0.383949 TTGTTTTGCTTGGCGAGTCC 59.616 50.000 3.19 0.00 0.00 3.85
479 486 1.293498 CAGGGTGTCGAGGTTGAGG 59.707 63.158 0.00 0.00 0.00 3.86
480 487 1.374758 GCAGGGTGTCGAGGTTGAG 60.375 63.158 0.00 0.00 0.00 3.02
481 488 2.741092 GCAGGGTGTCGAGGTTGA 59.259 61.111 0.00 0.00 0.00 3.18
482 489 2.738521 CGCAGGGTGTCGAGGTTG 60.739 66.667 0.00 0.00 0.00 3.77
483 490 2.915659 TCGCAGGGTGTCGAGGTT 60.916 61.111 0.00 0.00 0.00 3.50
484 491 3.681835 GTCGCAGGGTGTCGAGGT 61.682 66.667 0.00 0.00 35.21 3.85
697 716 4.875713 CCGGGAATTGAGGGGCCG 62.876 72.222 0.00 0.00 0.00 6.13
698 717 4.522975 CCCGGGAATTGAGGGGCC 62.523 72.222 18.48 0.00 41.43 5.80
727 756 1.355066 CGCGGTCTCTGGCTCTTTTC 61.355 60.000 0.00 0.00 0.00 2.29
761 791 2.903855 GCACACCACAGCTGCTGT 60.904 61.111 28.49 28.49 46.51 4.40
762 792 2.593725 AGCACACCACAGCTGCTG 60.594 61.111 27.02 27.02 39.82 4.41
763 793 2.281345 GAGCACACCACAGCTGCT 60.281 61.111 15.27 3.35 44.04 4.24
764 794 3.360340 GGAGCACACCACAGCTGC 61.360 66.667 15.27 0.00 42.04 5.25
765 795 2.670934 GGGAGCACACCACAGCTG 60.671 66.667 13.48 13.48 42.04 4.24
865 910 1.539280 GCTCTCGATTCTTGTAGGGGC 60.539 57.143 0.00 0.00 0.00 5.80
907 952 1.446791 GGATGAGGCTGAGGCTGAG 59.553 63.158 15.18 0.00 38.98 3.35
908 953 2.068821 GGGATGAGGCTGAGGCTGA 61.069 63.158 15.18 5.08 38.98 4.26
909 954 2.509916 GGGATGAGGCTGAGGCTG 59.490 66.667 15.18 0.00 38.98 4.85
910 955 3.160047 CGGGATGAGGCTGAGGCT 61.160 66.667 8.79 8.79 42.48 4.58
911 956 3.036429 AACGGGATGAGGCTGAGGC 62.036 63.158 0.00 0.00 37.82 4.70
912 957 1.153289 CAACGGGATGAGGCTGAGG 60.153 63.158 0.00 0.00 0.00 3.86
956 1001 2.229784 CTCAAAACCCAATCACAGGAGC 59.770 50.000 0.00 0.00 0.00 4.70
993 1040 1.424493 GAGCGCCGTCCATTCTCAAG 61.424 60.000 2.29 0.00 0.00 3.02
1208 1255 1.299850 GCAACGGCTTGACCAAACC 60.300 57.895 1.62 0.00 39.03 3.27
1210 1257 2.718731 CGCAACGGCTTGACCAAA 59.281 55.556 1.62 0.00 39.03 3.28
1265 1312 1.076485 CTTTCCCCATGGCCAGAGG 60.076 63.158 13.05 16.04 0.00 3.69
1266 1313 0.554792 ATCTTTCCCCATGGCCAGAG 59.445 55.000 13.05 6.25 0.00 3.35
1267 1314 0.259647 CATCTTTCCCCATGGCCAGA 59.740 55.000 13.05 0.00 0.00 3.86
1268 1315 0.757935 CCATCTTTCCCCATGGCCAG 60.758 60.000 13.05 3.10 33.37 4.85
1269 1316 1.310715 CCATCTTTCCCCATGGCCA 59.689 57.895 8.56 8.56 33.37 5.36
1286 1333 2.175715 AGGAGTGAATTGGCCTAATCCC 59.824 50.000 3.32 0.00 0.00 3.85
1332 1382 7.630026 TGCTCAACTGATAAAAATATAGTGCG 58.370 34.615 0.00 0.00 0.00 5.34
1376 1426 1.005037 CACCAACCGCAGAGCACTA 60.005 57.895 0.00 0.00 0.00 2.74
1386 1436 1.821216 AGATTAAGCACCACCAACCG 58.179 50.000 0.00 0.00 0.00 4.44
1398 1448 7.693969 AGTGGAATTTCAGGACAAGATTAAG 57.306 36.000 0.00 0.00 0.00 1.85
1493 1543 0.375454 TGTTGTTGTCGAAGGCGTTG 59.625 50.000 0.00 0.00 38.98 4.10
1579 1629 3.005261 TCTGAAGCGGAAGAGATAGATGC 59.995 47.826 0.00 0.00 0.00 3.91
1606 1656 5.163457 TGCCGAATTCAGTCAGATACATACA 60.163 40.000 6.22 0.00 0.00 2.29
1607 1657 5.289595 TGCCGAATTCAGTCAGATACATAC 58.710 41.667 6.22 0.00 0.00 2.39
1608 1658 5.529581 TGCCGAATTCAGTCAGATACATA 57.470 39.130 6.22 0.00 0.00 2.29
1609 1659 4.406648 TGCCGAATTCAGTCAGATACAT 57.593 40.909 6.22 0.00 0.00 2.29
1735 1796 1.591703 GTCCGTGTCCATGAGCTCA 59.408 57.895 20.79 20.79 0.00 4.26
1812 1873 5.860941 TCGATGGCTTATTTCTCTTCTCT 57.139 39.130 0.00 0.00 0.00 3.10
1876 1986 0.178964 CCACCCAAGAACACCATGGT 60.179 55.000 13.00 13.00 32.13 3.55
1879 1989 0.188342 AAGCCACCCAAGAACACCAT 59.812 50.000 0.00 0.00 0.00 3.55
2004 2114 1.550327 AGTCGCAGATCTTGAGGTCA 58.450 50.000 0.00 0.00 40.67 4.02
2268 2378 0.102481 CGTCCTCGTTCCGGATGAAT 59.898 55.000 4.15 0.00 39.43 2.57
2340 2450 1.604593 CTGCACCTTGGGGAACTGG 60.605 63.158 0.00 0.00 36.25 4.00
2397 2507 0.975556 TGATCCTCTGCAGCGGGTTA 60.976 55.000 22.30 9.82 0.00 2.85
2593 2703 7.757624 GCAGATTGCATCTACTCCTACTTATAC 59.242 40.741 0.00 0.00 44.26 1.47
2634 2744 9.931210 GTCCACATGCAGTAAACTTAAATATAC 57.069 33.333 0.00 0.00 0.00 1.47
2638 2748 6.892658 TGTCCACATGCAGTAAACTTAAAT 57.107 33.333 0.00 0.00 0.00 1.40
2750 2862 0.737715 GCCCTTGTCGTCTACAGCAG 60.738 60.000 0.00 0.00 39.87 4.24
2768 2880 1.221466 TTCTGCACTACACGCACAGC 61.221 55.000 0.00 0.00 35.08 4.40
2801 2913 6.483974 TGCCAAAAACAGATACGTTTCTTCTA 59.516 34.615 5.73 0.00 38.13 2.10
2802 2914 5.298276 TGCCAAAAACAGATACGTTTCTTCT 59.702 36.000 5.73 0.00 38.13 2.85
2803 2915 5.516090 TGCCAAAAACAGATACGTTTCTTC 58.484 37.500 5.73 0.00 38.13 2.87
2805 2917 5.163602 TGTTGCCAAAAACAGATACGTTTCT 60.164 36.000 2.36 2.36 38.13 2.52
2806 2918 5.038033 TGTTGCCAAAAACAGATACGTTTC 58.962 37.500 0.00 0.00 38.13 2.78
2807 2919 5.000012 TGTTGCCAAAAACAGATACGTTT 58.000 34.783 0.00 0.00 40.79 3.60
2836 2951 2.485903 CTGCAGCAGATCTCTTCCATC 58.514 52.381 18.42 0.00 32.44 3.51
2928 3043 6.712547 CCTTCTTTTCACTAGAATTGTCTGGT 59.287 38.462 0.00 0.00 45.78 4.00
2934 3049 7.106239 TCCTAGCCTTCTTTTCACTAGAATTG 58.894 38.462 0.00 0.00 33.66 2.32
2938 3053 5.337652 GCTTCCTAGCCTTCTTTTCACTAGA 60.338 44.000 0.00 0.00 41.74 2.43
2939 3054 4.873259 GCTTCCTAGCCTTCTTTTCACTAG 59.127 45.833 0.00 0.00 41.74 2.57
2962 3077 6.675026 TCTATATTATGAGACGGACGGTTTG 58.325 40.000 0.00 0.00 0.00 2.93
2966 3081 6.072618 ACACTTCTATATTATGAGACGGACGG 60.073 42.308 0.00 0.00 0.00 4.79
2968 3083 9.530633 AAAACACTTCTATATTATGAGACGGAC 57.469 33.333 0.00 0.00 0.00 4.79
2989 3104 7.644062 TGGGGGACTATATAATGACAAAAACA 58.356 34.615 0.00 0.00 0.00 2.83
2994 3109 6.390504 AGACTGGGGGACTATATAATGACAA 58.609 40.000 0.00 0.00 0.00 3.18
2995 3110 5.977533 AGACTGGGGGACTATATAATGACA 58.022 41.667 0.00 0.00 0.00 3.58
2996 3111 6.017192 TGAGACTGGGGGACTATATAATGAC 58.983 44.000 0.00 0.00 0.00 3.06
2997 3112 6.227624 TGAGACTGGGGGACTATATAATGA 57.772 41.667 0.00 0.00 0.00 2.57
2998 3113 8.609617 TTATGAGACTGGGGGACTATATAATG 57.390 38.462 0.00 0.00 0.00 1.90
3000 3115 9.937876 CTATTATGAGACTGGGGGACTATATAA 57.062 37.037 0.00 0.00 0.00 0.98
3001 3116 9.081508 ACTATTATGAGACTGGGGGACTATATA 57.918 37.037 0.00 0.00 0.00 0.86
3002 3117 7.841729 CACTATTATGAGACTGGGGGACTATAT 59.158 40.741 0.00 0.00 0.00 0.86
3003 3118 7.182760 CACTATTATGAGACTGGGGGACTATA 58.817 42.308 0.00 0.00 0.00 1.31
3004 3119 6.019748 CACTATTATGAGACTGGGGGACTAT 58.980 44.000 0.00 0.00 0.00 2.12
3005 3120 5.103215 ACACTATTATGAGACTGGGGGACTA 60.103 44.000 0.00 0.00 0.00 2.59
3006 3121 4.227197 CACTATTATGAGACTGGGGGACT 58.773 47.826 0.00 0.00 0.00 3.85
3007 3122 3.967987 ACACTATTATGAGACTGGGGGAC 59.032 47.826 0.00 0.00 0.00 4.46
3008 3123 4.280789 ACACTATTATGAGACTGGGGGA 57.719 45.455 0.00 0.00 0.00 4.81
3009 3124 5.373812 AAACACTATTATGAGACTGGGGG 57.626 43.478 0.00 0.00 0.00 5.40
3010 3125 6.884295 TCAAAAACACTATTATGAGACTGGGG 59.116 38.462 0.00 0.00 0.00 4.96
3011 3126 7.390440 TGTCAAAAACACTATTATGAGACTGGG 59.610 37.037 0.00 0.00 31.20 4.45
3012 3127 8.322906 TGTCAAAAACACTATTATGAGACTGG 57.677 34.615 0.00 0.00 31.20 4.00
3027 3142 3.118702 TCCGTCCTGTAGTGTCAAAAACA 60.119 43.478 0.00 0.00 34.78 2.83
3028 3143 3.460103 TCCGTCCTGTAGTGTCAAAAAC 58.540 45.455 0.00 0.00 0.00 2.43
3029 3144 3.493699 CCTCCGTCCTGTAGTGTCAAAAA 60.494 47.826 0.00 0.00 0.00 1.94
3030 3145 2.036733 CCTCCGTCCTGTAGTGTCAAAA 59.963 50.000 0.00 0.00 0.00 2.44
3031 3146 1.616865 CCTCCGTCCTGTAGTGTCAAA 59.383 52.381 0.00 0.00 0.00 2.69
3032 3147 1.254026 CCTCCGTCCTGTAGTGTCAA 58.746 55.000 0.00 0.00 0.00 3.18
3033 3148 0.611062 CCCTCCGTCCTGTAGTGTCA 60.611 60.000 0.00 0.00 0.00 3.58
3034 3149 0.323178 TCCCTCCGTCCTGTAGTGTC 60.323 60.000 0.00 0.00 0.00 3.67
3035 3150 0.323542 CTCCCTCCGTCCTGTAGTGT 60.324 60.000 0.00 0.00 0.00 3.55
3036 3151 0.323542 ACTCCCTCCGTCCTGTAGTG 60.324 60.000 0.00 0.00 0.00 2.74
3037 3152 1.064832 GTACTCCCTCCGTCCTGTAGT 60.065 57.143 0.00 0.00 0.00 2.73
3038 3153 1.064906 TGTACTCCCTCCGTCCTGTAG 60.065 57.143 0.00 0.00 0.00 2.74
3039 3154 0.994247 TGTACTCCCTCCGTCCTGTA 59.006 55.000 0.00 0.00 0.00 2.74
3040 3155 0.335361 ATGTACTCCCTCCGTCCTGT 59.665 55.000 0.00 0.00 0.00 4.00
3041 3156 1.486211 AATGTACTCCCTCCGTCCTG 58.514 55.000 0.00 0.00 0.00 3.86
3042 3157 2.249309 AAATGTACTCCCTCCGTCCT 57.751 50.000 0.00 0.00 0.00 3.85
3043 3158 4.684484 ATAAAATGTACTCCCTCCGTCC 57.316 45.455 0.00 0.00 0.00 4.79
3044 3159 6.997239 AAAATAAAATGTACTCCCTCCGTC 57.003 37.500 0.00 0.00 0.00 4.79
3045 3160 7.173032 AGAAAAATAAAATGTACTCCCTCCGT 58.827 34.615 0.00 0.00 0.00 4.69
3046 3161 7.625828 AGAAAAATAAAATGTACTCCCTCCG 57.374 36.000 0.00 0.00 0.00 4.63
3047 3162 8.182227 CGAAGAAAAATAAAATGTACTCCCTCC 58.818 37.037 0.00 0.00 0.00 4.30
3048 3163 8.182227 CCGAAGAAAAATAAAATGTACTCCCTC 58.818 37.037 0.00 0.00 0.00 4.30
3049 3164 7.668469 ACCGAAGAAAAATAAAATGTACTCCCT 59.332 33.333 0.00 0.00 0.00 4.20
3050 3165 7.823665 ACCGAAGAAAAATAAAATGTACTCCC 58.176 34.615 0.00 0.00 0.00 4.30
3063 3178 9.449719 AGACATCAAGTATAACCGAAGAAAAAT 57.550 29.630 0.00 0.00 0.00 1.82
3065 3180 8.842358 AAGACATCAAGTATAACCGAAGAAAA 57.158 30.769 0.00 0.00 0.00 2.29
3073 3188 9.712305 ATGCATACTAAGACATCAAGTATAACC 57.288 33.333 0.00 2.11 35.26 2.85
3090 3205 5.277490 GCAATTTCAGCGAGAATGCATACTA 60.277 40.000 0.00 0.00 40.38 1.82
3094 3209 2.426024 AGCAATTTCAGCGAGAATGCAT 59.574 40.909 17.06 0.00 42.16 3.96
3104 3222 2.031682 ACGTGACAAGAGCAATTTCAGC 60.032 45.455 0.00 0.00 0.00 4.26
3160 3278 8.915057 TCCTTATTCAATGAAAATGGCAAAAA 57.085 26.923 0.00 0.00 0.00 1.94
3161 3279 8.156165 ACTCCTTATTCAATGAAAATGGCAAAA 58.844 29.630 0.00 0.00 0.00 2.44
3162 3280 7.678837 ACTCCTTATTCAATGAAAATGGCAAA 58.321 30.769 0.00 0.00 0.00 3.68
3163 3281 7.243604 ACTCCTTATTCAATGAAAATGGCAA 57.756 32.000 0.00 0.00 0.00 4.52
3164 3282 6.855763 ACTCCTTATTCAATGAAAATGGCA 57.144 33.333 0.00 0.00 0.00 4.92
3165 3283 8.632679 TGATACTCCTTATTCAATGAAAATGGC 58.367 33.333 0.00 0.00 0.00 4.40
3169 3287 9.113838 GCTCTGATACTCCTTATTCAATGAAAA 57.886 33.333 0.00 0.00 0.00 2.29
3170 3288 8.489489 AGCTCTGATACTCCTTATTCAATGAAA 58.511 33.333 0.00 0.00 0.00 2.69
3171 3289 8.027524 AGCTCTGATACTCCTTATTCAATGAA 57.972 34.615 0.00 0.00 0.00 2.57
3172 3290 7.508636 AGAGCTCTGATACTCCTTATTCAATGA 59.491 37.037 17.42 0.00 33.18 2.57
3173 3291 7.669427 AGAGCTCTGATACTCCTTATTCAATG 58.331 38.462 17.42 0.00 33.18 2.82
3174 3292 7.854166 AGAGCTCTGATACTCCTTATTCAAT 57.146 36.000 17.42 0.00 33.18 2.57
3175 3293 7.124901 ACAAGAGCTCTGATACTCCTTATTCAA 59.875 37.037 19.06 0.00 33.18 2.69
3176 3294 6.609212 ACAAGAGCTCTGATACTCCTTATTCA 59.391 38.462 19.06 0.00 33.18 2.57
3177 3295 7.049799 ACAAGAGCTCTGATACTCCTTATTC 57.950 40.000 19.06 0.00 33.18 1.75
3178 3296 6.609212 TGACAAGAGCTCTGATACTCCTTATT 59.391 38.462 19.06 0.00 33.18 1.40
3179 3297 6.132658 TGACAAGAGCTCTGATACTCCTTAT 58.867 40.000 19.06 0.00 33.18 1.73
3180 3298 5.510430 TGACAAGAGCTCTGATACTCCTTA 58.490 41.667 19.06 0.00 33.18 2.69
3181 3299 4.348486 TGACAAGAGCTCTGATACTCCTT 58.652 43.478 19.06 0.00 33.18 3.36
3182 3300 3.953612 CTGACAAGAGCTCTGATACTCCT 59.046 47.826 19.06 0.00 33.18 3.69
3183 3301 3.068024 CCTGACAAGAGCTCTGATACTCC 59.932 52.174 19.06 3.50 33.18 3.85
3184 3302 3.699038 ACCTGACAAGAGCTCTGATACTC 59.301 47.826 19.06 8.07 0.00 2.59
3185 3303 3.707316 ACCTGACAAGAGCTCTGATACT 58.293 45.455 19.06 0.00 0.00 2.12
3186 3304 4.037446 CCTACCTGACAAGAGCTCTGATAC 59.963 50.000 19.06 9.97 0.00 2.24
3187 3305 4.079730 TCCTACCTGACAAGAGCTCTGATA 60.080 45.833 19.06 3.54 0.00 2.15
3188 3306 3.030291 CCTACCTGACAAGAGCTCTGAT 58.970 50.000 19.06 8.52 0.00 2.90
3189 3307 2.041755 TCCTACCTGACAAGAGCTCTGA 59.958 50.000 19.06 2.76 0.00 3.27
3190 3308 2.451490 TCCTACCTGACAAGAGCTCTG 58.549 52.381 19.06 13.84 0.00 3.35
3191 3309 2.909504 TCCTACCTGACAAGAGCTCT 57.090 50.000 11.45 11.45 0.00 4.09
3192 3310 2.829120 ACTTCCTACCTGACAAGAGCTC 59.171 50.000 5.27 5.27 0.00 4.09
3193 3311 2.896039 ACTTCCTACCTGACAAGAGCT 58.104 47.619 0.00 0.00 0.00 4.09
3194 3312 3.686916 AACTTCCTACCTGACAAGAGC 57.313 47.619 0.00 0.00 0.00 4.09
3195 3313 6.153680 AGACATAACTTCCTACCTGACAAGAG 59.846 42.308 0.00 0.00 0.00 2.85
3196 3314 6.017192 AGACATAACTTCCTACCTGACAAGA 58.983 40.000 0.00 0.00 0.00 3.02
3197 3315 6.071334 TGAGACATAACTTCCTACCTGACAAG 60.071 42.308 0.00 0.00 0.00 3.16
3198 3316 5.778241 TGAGACATAACTTCCTACCTGACAA 59.222 40.000 0.00 0.00 0.00 3.18
3199 3317 5.330233 TGAGACATAACTTCCTACCTGACA 58.670 41.667 0.00 0.00 0.00 3.58
3200 3318 5.916661 TGAGACATAACTTCCTACCTGAC 57.083 43.478 0.00 0.00 0.00 3.51
3201 3319 6.194967 TGATGAGACATAACTTCCTACCTGA 58.805 40.000 0.00 0.00 0.00 3.86
3202 3320 6.097554 ACTGATGAGACATAACTTCCTACCTG 59.902 42.308 0.00 0.00 0.00 4.00
3203 3321 6.198639 ACTGATGAGACATAACTTCCTACCT 58.801 40.000 0.00 0.00 0.00 3.08
3204 3322 6.472686 ACTGATGAGACATAACTTCCTACC 57.527 41.667 0.00 0.00 0.00 3.18
3219 3631 9.307121 CCAGTAAGACACTAATTAACTGATGAG 57.693 37.037 11.17 0.00 34.98 2.90
3240 3652 6.620877 ATTCAGTAAGAATCCACACCAGTA 57.379 37.500 0.00 0.00 43.42 2.74
3245 3657 6.259550 AGCAAATTCAGTAAGAATCCACAC 57.740 37.500 0.00 0.00 46.09 3.82
3269 3681 2.490903 GCCTCTTCAACTGCATCACAAT 59.509 45.455 0.00 0.00 0.00 2.71
3363 3775 2.159819 GAGGGTGCTGCTCGAAGTCA 62.160 60.000 0.00 0.00 0.00 3.41
3405 3817 3.535561 CAGGGCTTCGTTGAATATGAGT 58.464 45.455 0.00 0.00 0.00 3.41
3455 3867 5.339695 GGGTTGGGTAACTAGGAATGAATCA 60.340 44.000 0.00 0.00 36.99 2.57
3471 3883 0.407918 CATACTGTTGGGGGTTGGGT 59.592 55.000 0.00 0.00 0.00 4.51
3484 3896 9.314321 AGACAGTTTTATACCGAAATCATACTG 57.686 33.333 0.00 0.00 33.00 2.74
3567 3979 3.885297 AGCAGCAACAACTTACACAGAAT 59.115 39.130 0.00 0.00 0.00 2.40
3596 4008 0.846693 ACAGCTGAGGGACAAAGGTT 59.153 50.000 23.35 0.00 0.00 3.50
3610 4022 4.037446 TCCAAACTTTTTATTCGCACAGCT 59.963 37.500 0.00 0.00 0.00 4.24
3646 4058 9.113838 TCTTCATAAACTAGAGAATGATTTGCC 57.886 33.333 0.00 0.00 0.00 4.52
3694 4106 3.134623 TCAGCTTACGATGGTGAATGGAT 59.865 43.478 0.00 0.00 38.71 3.41
3695 4107 2.499693 TCAGCTTACGATGGTGAATGGA 59.500 45.455 0.00 0.00 38.71 3.41
3967 4380 2.761208 CTCCTAGTCCTTTGGTCGACAT 59.239 50.000 18.91 0.00 0.00 3.06
3983 4396 4.620086 TCTCAATACCAAGACCCTCCTA 57.380 45.455 0.00 0.00 0.00 2.94
3987 4400 5.488919 TCAAGATTCTCAATACCAAGACCCT 59.511 40.000 0.00 0.00 0.00 4.34
3991 4404 7.679783 TGACTTCAAGATTCTCAATACCAAGA 58.320 34.615 0.00 0.00 0.00 3.02
4115 4533 1.270907 GTCTCACTGTCACCTGGGAT 58.729 55.000 0.00 0.00 0.00 3.85
4178 4596 9.923143 ATAAACTTTGTCTTATTAAACAAGGCC 57.077 29.630 0.00 0.00 36.31 5.19
4192 4610 6.537660 GCCATTACCGACTATAAACTTTGTCT 59.462 38.462 0.00 0.00 0.00 3.41
4235 4653 2.265367 TCACCAAGCCAAGTATCCTCA 58.735 47.619 0.00 0.00 0.00 3.86
4300 4718 2.298300 CAACAAAAGCATCACGTCGTC 58.702 47.619 0.00 0.00 0.00 4.20
4336 4754 7.724061 TCCTAAACTGAATATTAAGGGGAATGC 59.276 37.037 4.78 0.00 0.00 3.56


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

AutoCloner maintained by Alex Coulton.