Multiple sequence alignment - TraesCS6A01G346100

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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 TraesCS6A01G346100 chr6A 100.000 4919 0 0 1 4919 579441032 579436114 0.000000e+00 9084.0
1 TraesCS6A01G346100 chr6B 91.974 4037 148 70 1 3927 654736610 654732640 0.000000e+00 5498.0
2 TraesCS6A01G346100 chr6B 93.600 625 39 1 4295 4919 654641965 654641342 0.000000e+00 931.0
3 TraesCS6A01G346100 chr6B 84.571 175 27 0 4103 4277 654673371 654673197 1.820000e-39 174.0
4 TraesCS6A01G346100 chr6D 90.593 3848 199 85 83 3843 433479649 433475878 0.000000e+00 4950.0
5 TraesCS6A01G346100 chr6D 90.016 631 37 8 1 607 433480349 433479721 0.000000e+00 793.0
6 TraesCS6A01G346100 chr6D 92.941 170 11 1 4750 4919 433444649 433444481 3.800000e-61 246.0
7 TraesCS6A01G346100 chr6D 89.655 116 12 0 4295 4410 433468347 433468232 1.100000e-31 148.0
8 TraesCS6A01G346100 chr6D 87.629 97 8 1 4026 4122 433474486 433474394 5.210000e-20 110.0
9 TraesCS6A01G346100 chr6D 91.139 79 3 3 3839 3917 433475733 433475659 2.420000e-18 104.0
10 TraesCS6A01G346100 chr6D 88.462 78 3 3 3932 4007 433475609 433475536 6.780000e-14 89.8
11 TraesCS6A01G346100 chr7B 85.164 1247 141 23 2161 3367 61910144 61908902 0.000000e+00 1238.0
12 TraesCS6A01G346100 chr7B 81.399 629 109 7 4295 4919 59638544 59637920 1.580000e-139 507.0
13 TraesCS6A01G346100 chr7B 83.469 490 69 8 1044 1527 61911105 61910622 3.490000e-121 446.0
14 TraesCS6A01G346100 chr7B 78.469 627 127 8 4297 4919 111319985 111319363 2.130000e-108 403.0
15 TraesCS6A01G346100 chr7A 85.164 1247 141 22 2161 3367 108237644 108236402 0.000000e+00 1238.0
16 TraesCS6A01G346100 chr7A 82.892 491 70 10 1044 1527 108238608 108238125 3.520000e-116 429.0
17 TraesCS6A01G346100 chr7A 78.797 632 120 14 4295 4919 1420103 1420727 3.540000e-111 412.0
18 TraesCS6A01G346100 chr7D 84.800 1250 143 24 2161 3367 104091829 104090584 0.000000e+00 1212.0
19 TraesCS6A01G346100 chr7D 82.892 491 70 10 1044 1527 104092790 104092307 3.520000e-116 429.0
20 TraesCS6A01G346100 chr7D 79.014 629 124 8 4295 4919 1015387 1014763 1.640000e-114 424.0
21 TraesCS6A01G346100 chr7D 77.287 634 107 26 4295 4917 1255796 1255189 6.100000e-89 339.0
22 TraesCS6A01G346100 chr7D 72.401 529 106 33 2681 3177 46839580 46839060 1.110000e-26 132.0
23 TraesCS6A01G346100 chr3D 78.768 1201 210 32 2169 3333 283316240 283317431 0.000000e+00 763.0
24 TraesCS6A01G346100 chr3B 78.518 1201 213 32 2169 3333 377424470 377425661 0.000000e+00 747.0
25 TraesCS6A01G346100 chr3B 81.399 629 109 8 4295 4919 747713267 747713891 1.580000e-139 507.0
26 TraesCS6A01G346100 chr3A 80.350 1028 161 29 2169 3162 370239450 370240470 0.000000e+00 741.0
27 TraesCS6A01G346100 chr4A 78.628 627 124 8 4296 4917 743645606 743644985 1.650000e-109 407.0
28 TraesCS6A01G346100 chr4A 100.000 29 0 0 2734 2762 115788505 115788533 2.000000e-03 54.7
29 TraesCS6A01G346100 chrUn 78.295 387 73 8 4538 4919 51466172 51465792 6.360000e-59 239.0
30 TraesCS6A01G346100 chrUn 78.295 387 73 8 4538 4919 245958850 245959230 6.360000e-59 239.0


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 TraesCS6A01G346100 chr6A 579436114 579441032 4918 True 9084.00 9084 100.0000 1 4919 1 chr6A.!!$R1 4918
1 TraesCS6A01G346100 chr6B 654732640 654736610 3970 True 5498.00 5498 91.9740 1 3927 1 chr6B.!!$R3 3926
2 TraesCS6A01G346100 chr6B 654641342 654641965 623 True 931.00 931 93.6000 4295 4919 1 chr6B.!!$R1 624
3 TraesCS6A01G346100 chr6D 433474394 433480349 5955 True 1209.36 4950 89.5678 1 4122 5 chr6D.!!$R3 4121
4 TraesCS6A01G346100 chr7B 61908902 61911105 2203 True 842.00 1238 84.3165 1044 3367 2 chr7B.!!$R3 2323
5 TraesCS6A01G346100 chr7B 59637920 59638544 624 True 507.00 507 81.3990 4295 4919 1 chr7B.!!$R1 624
6 TraesCS6A01G346100 chr7B 111319363 111319985 622 True 403.00 403 78.4690 4297 4919 1 chr7B.!!$R2 622
7 TraesCS6A01G346100 chr7A 108236402 108238608 2206 True 833.50 1238 84.0280 1044 3367 2 chr7A.!!$R1 2323
8 TraesCS6A01G346100 chr7A 1420103 1420727 624 False 412.00 412 78.7970 4295 4919 1 chr7A.!!$F1 624
9 TraesCS6A01G346100 chr7D 104090584 104092790 2206 True 820.50 1212 83.8460 1044 3367 2 chr7D.!!$R4 2323
10 TraesCS6A01G346100 chr7D 1014763 1015387 624 True 424.00 424 79.0140 4295 4919 1 chr7D.!!$R1 624
11 TraesCS6A01G346100 chr7D 1255189 1255796 607 True 339.00 339 77.2870 4295 4917 1 chr7D.!!$R2 622
12 TraesCS6A01G346100 chr3D 283316240 283317431 1191 False 763.00 763 78.7680 2169 3333 1 chr3D.!!$F1 1164
13 TraesCS6A01G346100 chr3B 377424470 377425661 1191 False 747.00 747 78.5180 2169 3333 1 chr3B.!!$F1 1164
14 TraesCS6A01G346100 chr3B 747713267 747713891 624 False 507.00 507 81.3990 4295 4919 1 chr3B.!!$F2 624
15 TraesCS6A01G346100 chr3A 370239450 370240470 1020 False 741.00 741 80.3500 2169 3162 1 chr3A.!!$F1 993
16 TraesCS6A01G346100 chr4A 743644985 743645606 621 True 407.00 407 78.6280 4296 4917 1 chr4A.!!$R1 621

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
920 1537 0.107945 GGAGAATTGCAGGAGAGCGT 60.108 55.0 0.00 0.0 37.31 5.07 F
1105 1752 0.666274 CCAGAACGCGCTCAAGTACA 60.666 55.0 12.67 0.0 0.00 2.90 F
2097 2835 0.032540 CCTCCATCATGCACGATCGA 59.967 55.0 24.34 0.0 0.00 3.59 F
2958 3773 0.733909 TGAGCAAGATCAGCGACGTG 60.734 55.0 0.00 0.0 37.01 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1870 2591 1.673033 GCCCCGATGAAGGATATGTCG 60.673 57.143 0.00 0.00 0.00 4.35 R
2150 2892 3.220110 TCCATGTCCTCCTACGTACATC 58.780 50.000 0.00 0.00 30.32 3.06 R
3478 4311 0.249447 TGGTGGATGATCGATCGTGC 60.249 55.000 26.87 26.87 35.08 5.34 R
4138 6219 0.098728 CGGTTGGGATGCGTCATTTC 59.901 55.000 8.47 0.00 0.00 2.17 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 7.260387 TGAACTAATTGGTACCTGTGGAATA 57.740 36.000 14.36 0.00 0.00 1.75
54 55 7.208064 ACTAATTGGTACCTGTGGAATATGT 57.792 36.000 14.36 4.13 0.00 2.29
211 218 0.698818 GGTCAGGACCCCAATGAACT 59.301 55.000 7.24 0.00 45.68 3.01
284 291 2.766263 CTGTGGCCAGTCTCACCTATTA 59.234 50.000 5.11 0.00 33.80 0.98
288 295 5.193679 GTGGCCAGTCTCACCTATTATTTT 58.806 41.667 5.11 0.00 0.00 1.82
339 346 6.379988 TCATCTTCTATATGGCGGCATAACTA 59.620 38.462 32.04 20.57 0.00 2.24
345 352 3.492102 ATGGCGGCATAACTACATTCT 57.508 42.857 24.59 0.00 0.00 2.40
351 358 6.164176 GGCGGCATAACTACATTCTAGTTAT 58.836 40.000 3.07 6.86 46.06 1.89
353 360 7.488471 GGCGGCATAACTACATTCTAGTTATAG 59.512 40.741 3.07 8.00 44.40 1.31
354 361 8.242053 GCGGCATAACTACATTCTAGTTATAGA 58.758 37.037 10.88 0.00 44.40 1.98
404 411 5.551233 ACATACATGTGGGAGCATACATAC 58.449 41.667 9.11 0.00 40.03 2.39
436 456 4.583871 ACCTCCTGAATTCATTGTCACTC 58.416 43.478 8.96 0.00 0.00 3.51
558 582 8.567948 GTTGTACATTGGAATCTGTATATTGGG 58.432 37.037 0.00 0.00 31.06 4.12
585 611 5.070770 TGCTTGGTGCTAAAATGTTATGG 57.929 39.130 0.00 0.00 43.37 2.74
624 669 3.340727 GCAATTGCAGAGCATGTCC 57.659 52.632 25.36 0.00 38.76 4.02
626 671 1.469251 GCAATTGCAGAGCATGTCCAG 60.469 52.381 25.36 0.00 38.76 3.86
676 1292 5.071955 GCTGATAACGTCTGCTTTGTATC 57.928 43.478 0.00 0.00 45.32 2.24
684 1300 2.678336 GTCTGCTTTGTATCCGGAAAGG 59.322 50.000 9.01 0.00 42.97 3.11
687 1303 2.289565 GCTTTGTATCCGGAAAGGGAG 58.710 52.381 9.01 5.66 40.02 4.30
688 1304 2.919228 CTTTGTATCCGGAAAGGGAGG 58.081 52.381 9.01 0.00 40.02 4.30
690 1306 1.789523 TGTATCCGGAAAGGGAGGAG 58.210 55.000 9.01 0.00 40.02 3.69
708 1324 2.211806 GAGATGAGCAGAATCTGTGGC 58.788 52.381 12.29 0.00 34.50 5.01
711 1327 0.622136 TGAGCAGAATCTGTGGCCAT 59.378 50.000 9.72 0.00 33.43 4.40
731 1347 0.883833 CCGCAAACTCAGCTGGAAAT 59.116 50.000 15.13 0.00 0.00 2.17
732 1348 1.401931 CCGCAAACTCAGCTGGAAATG 60.402 52.381 15.13 9.73 0.00 2.32
768 1385 0.391130 TAAGAGCCGACCACATGCAC 60.391 55.000 0.00 0.00 0.00 4.57
832 1449 3.615155 AGAGGAGCAGATTGCCTAAAAC 58.385 45.455 0.00 0.00 46.52 2.43
879 1496 1.467920 CTCCCTTGGCAATCTTCCAC 58.532 55.000 0.00 0.00 32.45 4.02
880 1497 0.322456 TCCCTTGGCAATCTTCCACG 60.322 55.000 0.00 0.00 32.45 4.94
891 1508 0.606096 TCTTCCACGGCTCGAATGAA 59.394 50.000 1.50 1.39 0.00 2.57
892 1509 1.002366 CTTCCACGGCTCGAATGAAG 58.998 55.000 1.50 6.42 0.00 3.02
893 1510 0.391130 TTCCACGGCTCGAATGAAGG 60.391 55.000 1.50 0.00 0.00 3.46
894 1511 1.218047 CCACGGCTCGAATGAAGGA 59.782 57.895 1.50 0.00 0.00 3.36
895 1512 0.391130 CCACGGCTCGAATGAAGGAA 60.391 55.000 1.50 0.00 0.00 3.36
916 1533 1.283029 CCTTGGGAGAATTGCAGGAGA 59.717 52.381 0.00 0.00 0.00 3.71
917 1534 2.641305 CTTGGGAGAATTGCAGGAGAG 58.359 52.381 0.00 0.00 0.00 3.20
918 1535 0.254178 TGGGAGAATTGCAGGAGAGC 59.746 55.000 0.00 0.00 0.00 4.09
919 1536 0.813210 GGGAGAATTGCAGGAGAGCG 60.813 60.000 0.00 0.00 37.31 5.03
920 1537 0.107945 GGAGAATTGCAGGAGAGCGT 60.108 55.000 0.00 0.00 37.31 5.07
921 1538 1.137086 GGAGAATTGCAGGAGAGCGTA 59.863 52.381 0.00 0.00 37.31 4.42
922 1539 2.468831 GAGAATTGCAGGAGAGCGTAG 58.531 52.381 0.00 0.00 37.31 3.51
925 1542 2.635229 ATTGCAGGAGAGCGTAGGCG 62.635 60.000 1.05 0.00 46.35 5.52
943 1564 1.000052 GCGTAGAGACATTAGGGAGGC 60.000 57.143 0.00 0.00 0.00 4.70
944 1565 1.267261 CGTAGAGACATTAGGGAGGCG 59.733 57.143 0.00 0.00 0.00 5.52
948 1587 1.611491 GAGACATTAGGGAGGCGAGAG 59.389 57.143 0.00 0.00 0.00 3.20
964 1603 2.033299 CGAGAGAGGAAGCTGATCTGAC 59.967 54.545 3.42 0.00 0.00 3.51
1105 1752 0.666274 CCAGAACGCGCTCAAGTACA 60.666 55.000 12.67 0.00 0.00 2.90
1293 1940 2.591429 TGCAAGGACGTGGTGCTG 60.591 61.111 13.87 0.00 39.09 4.41
1704 2369 6.128445 CGCAAGAGAACTTCATCATGTAAGTT 60.128 38.462 17.45 17.45 43.76 2.66
1746 2412 1.307355 CGCTGGTTCATGCATGGACA 61.307 55.000 33.72 23.56 38.05 4.02
2097 2835 0.032540 CCTCCATCATGCACGATCGA 59.967 55.000 24.34 0.00 0.00 3.59
2127 2869 3.867493 GCCTGCCATTAATCTTTCTTTGC 59.133 43.478 0.00 0.00 0.00 3.68
2150 2892 2.543848 GCAAATCTCAATGCATGCATGG 59.456 45.455 32.79 29.58 42.12 3.66
2583 3389 4.419921 GGCCCGGTGTACAAGGGG 62.420 72.222 28.80 25.81 45.18 4.79
2958 3773 0.733909 TGAGCAAGATCAGCGACGTG 60.734 55.000 0.00 0.00 37.01 4.49
3478 4311 0.963856 GGGGCCCGTAAGAAAACCAG 60.964 60.000 17.79 0.00 43.02 4.00
3518 4351 2.099141 TTCTCATCCTCCTTGTTGCG 57.901 50.000 0.00 0.00 0.00 4.85
3551 4395 2.034939 CGGGTAAATCATGTGCATGCAT 59.965 45.455 25.64 5.67 38.65 3.96
3552 4396 3.386486 GGGTAAATCATGTGCATGCATG 58.614 45.455 25.64 22.70 45.48 4.06
3632 4476 2.039084 AGAAGGCCCAACTACAACTGAG 59.961 50.000 0.00 0.00 0.00 3.35
3649 4493 1.344942 GAGCAAAGTCGCGTCGTGAT 61.345 55.000 12.27 3.00 36.85 3.06
3722 4576 4.382754 GTGTTTCGAAGGTTCATCATTTGC 59.617 41.667 0.00 0.00 0.00 3.68
3725 4579 4.424061 TCGAAGGTTCATCATTTGCAAG 57.576 40.909 0.00 0.00 0.00 4.01
3728 4582 3.587797 AGGTTCATCATTTGCAAGCAG 57.412 42.857 0.00 0.00 0.00 4.24
3754 4610 3.832615 AATTCTTCGCCCGTACCTAAT 57.167 42.857 0.00 0.00 0.00 1.73
3755 4611 4.942761 AATTCTTCGCCCGTACCTAATA 57.057 40.909 0.00 0.00 0.00 0.98
3756 4612 3.715628 TTCTTCGCCCGTACCTAATAC 57.284 47.619 0.00 0.00 0.00 1.89
3786 4642 2.981805 TCGTGGTTTCTTAATGTCGTCG 59.018 45.455 0.00 0.00 0.00 5.12
3799 4655 4.487412 CGTCGGTCGGTAGCCACC 62.487 72.222 0.00 0.00 41.93 4.61
3927 4944 5.172205 TGTTTTAAACCACTGTTTCTTGCC 58.828 37.500 5.32 0.00 43.50 4.52
3928 4945 4.394439 TTTAAACCACTGTTTCTTGCCC 57.606 40.909 0.00 0.00 43.50 5.36
3929 4946 2.159179 AAACCACTGTTTCTTGCCCT 57.841 45.000 0.00 0.00 40.68 5.19
3930 4947 1.402787 AACCACTGTTTCTTGCCCTG 58.597 50.000 0.00 0.00 0.00 4.45
3944 4986 0.741221 GCCCTGTGCTTCTCTTACCG 60.741 60.000 0.00 0.00 36.87 4.02
3948 4990 1.546476 CTGTGCTTCTCTTACCGGACT 59.454 52.381 9.46 0.00 0.00 3.85
3955 4997 0.736325 CTCTTACCGGACTTGTGGCG 60.736 60.000 9.46 0.00 0.00 5.69
4004 6085 4.516698 TGCATGACTCCTTCAGAAAAGAAC 59.483 41.667 0.00 0.00 37.77 3.01
4007 6088 5.359194 TGACTCCTTCAGAAAAGAACAGT 57.641 39.130 0.23 0.00 0.00 3.55
4024 6105 0.600557 AGTCGACTGCCACTCTGAAG 59.399 55.000 19.30 0.00 0.00 3.02
4026 6107 0.598562 TCGACTGCCACTCTGAAGTC 59.401 55.000 0.00 0.00 36.52 3.01
4028 6109 1.668337 CGACTGCCACTCTGAAGTCTG 60.668 57.143 5.26 0.00 37.49 3.51
4029 6110 1.615883 GACTGCCACTCTGAAGTCTGA 59.384 52.381 0.36 0.00 36.85 3.27
4030 6111 2.036475 GACTGCCACTCTGAAGTCTGAA 59.964 50.000 0.36 0.00 36.85 3.02
4031 6112 2.224161 ACTGCCACTCTGAAGTCTGAAC 60.224 50.000 0.00 0.00 31.71 3.18
4032 6113 2.036992 CTGCCACTCTGAAGTCTGAACT 59.963 50.000 0.00 0.00 37.32 3.01
4033 6114 3.230976 TGCCACTCTGAAGTCTGAACTA 58.769 45.455 0.00 0.00 33.48 2.24
4034 6115 3.834813 TGCCACTCTGAAGTCTGAACTAT 59.165 43.478 0.00 0.00 33.48 2.12
4035 6116 5.016831 TGCCACTCTGAAGTCTGAACTATA 58.983 41.667 0.00 0.00 33.48 1.31
4036 6117 5.105716 TGCCACTCTGAAGTCTGAACTATAC 60.106 44.000 0.00 0.00 33.48 1.47
4037 6118 5.126384 GCCACTCTGAAGTCTGAACTATACT 59.874 44.000 0.00 0.00 33.48 2.12
4038 6119 6.559810 CCACTCTGAAGTCTGAACTATACTG 58.440 44.000 0.00 0.00 33.48 2.74
4039 6120 6.033341 CACTCTGAAGTCTGAACTATACTGC 58.967 44.000 0.00 0.00 33.48 4.40
4040 6121 5.712446 ACTCTGAAGTCTGAACTATACTGCA 59.288 40.000 0.00 0.00 33.48 4.41
4041 6122 6.209589 ACTCTGAAGTCTGAACTATACTGCAA 59.790 38.462 0.00 0.00 33.48 4.08
4042 6123 7.093552 ACTCTGAAGTCTGAACTATACTGCAAT 60.094 37.037 0.00 0.00 33.48 3.56
4052 6133 7.785033 TGAACTATACTGCAATCAATCTCAGA 58.215 34.615 0.00 0.00 0.00 3.27
4098 6179 1.133606 TCTCCAACAGACCCCAAAACC 60.134 52.381 0.00 0.00 0.00 3.27
4101 6182 1.328279 CAACAGACCCCAAAACCCTC 58.672 55.000 0.00 0.00 0.00 4.30
4103 6184 0.996762 ACAGACCCCAAAACCCTCCA 60.997 55.000 0.00 0.00 0.00 3.86
4104 6185 0.539669 CAGACCCCAAAACCCTCCAC 60.540 60.000 0.00 0.00 0.00 4.02
4114 6195 3.009115 CCCTCCACATGTCCGGGT 61.009 66.667 0.00 0.00 0.00 5.28
4115 6196 2.268920 CCTCCACATGTCCGGGTG 59.731 66.667 0.00 0.79 34.82 4.61
4129 6210 2.529389 GGTGGACCCCTGGACACT 60.529 66.667 0.00 0.00 35.63 3.55
4130 6211 2.750350 GTGGACCCCTGGACACTG 59.250 66.667 0.00 0.00 33.78 3.66
4131 6212 2.147387 GTGGACCCCTGGACACTGT 61.147 63.158 0.00 0.00 33.78 3.55
4132 6213 1.385347 TGGACCCCTGGACACTGTT 60.385 57.895 0.00 0.00 0.00 3.16
4133 6214 1.375326 GGACCCCTGGACACTGTTC 59.625 63.158 0.00 0.00 0.00 3.18
4134 6215 1.004918 GACCCCTGGACACTGTTCG 60.005 63.158 0.00 0.00 0.00 3.95
4135 6216 2.347490 CCCCTGGACACTGTTCGG 59.653 66.667 0.00 0.00 0.00 4.30
4136 6217 2.214216 CCCCTGGACACTGTTCGGA 61.214 63.158 0.00 0.00 0.00 4.55
4137 6218 1.553690 CCCCTGGACACTGTTCGGAT 61.554 60.000 0.00 0.00 0.00 4.18
4138 6219 0.391661 CCCTGGACACTGTTCGGATG 60.392 60.000 0.00 0.00 0.00 3.51
4139 6220 0.608130 CCTGGACACTGTTCGGATGA 59.392 55.000 0.00 0.00 0.00 2.92
4140 6221 1.001974 CCTGGACACTGTTCGGATGAA 59.998 52.381 0.00 0.00 0.00 2.57
4141 6222 2.549992 CCTGGACACTGTTCGGATGAAA 60.550 50.000 0.00 0.00 35.46 2.69
4142 6223 3.338249 CTGGACACTGTTCGGATGAAAT 58.662 45.455 0.00 0.00 35.46 2.17
4143 6224 3.073678 TGGACACTGTTCGGATGAAATG 58.926 45.455 0.00 0.00 35.46 2.32
4144 6225 3.244387 TGGACACTGTTCGGATGAAATGA 60.244 43.478 0.00 0.00 35.46 2.57
4145 6226 3.125316 GGACACTGTTCGGATGAAATGAC 59.875 47.826 0.00 0.00 35.46 3.06
4146 6227 2.736721 ACACTGTTCGGATGAAATGACG 59.263 45.455 0.00 0.00 35.46 4.35
4147 6228 1.732259 ACTGTTCGGATGAAATGACGC 59.268 47.619 0.00 0.00 35.46 5.19
4148 6229 1.731709 CTGTTCGGATGAAATGACGCA 59.268 47.619 0.00 0.00 35.46 5.24
4149 6230 2.352651 CTGTTCGGATGAAATGACGCAT 59.647 45.455 0.00 0.00 35.46 4.73
4150 6231 2.351418 TGTTCGGATGAAATGACGCATC 59.649 45.455 0.00 0.00 40.05 3.91
4155 6236 3.070429 GATGAAATGACGCATCCCAAC 57.930 47.619 0.00 0.00 35.91 3.77
4156 6237 1.173043 TGAAATGACGCATCCCAACC 58.827 50.000 0.00 0.00 0.00 3.77
4157 6238 0.098728 GAAATGACGCATCCCAACCG 59.901 55.000 0.00 0.00 0.00 4.44
4158 6239 0.322098 AAATGACGCATCCCAACCGA 60.322 50.000 0.00 0.00 0.00 4.69
4159 6240 1.024579 AATGACGCATCCCAACCGAC 61.025 55.000 0.00 0.00 0.00 4.79
4160 6241 2.818274 GACGCATCCCAACCGACC 60.818 66.667 0.00 0.00 0.00 4.79
4161 6242 4.404098 ACGCATCCCAACCGACCC 62.404 66.667 0.00 0.00 0.00 4.46
4162 6243 4.096003 CGCATCCCAACCGACCCT 62.096 66.667 0.00 0.00 0.00 4.34
4163 6244 2.355115 GCATCCCAACCGACCCTT 59.645 61.111 0.00 0.00 0.00 3.95
4164 6245 1.605453 GCATCCCAACCGACCCTTA 59.395 57.895 0.00 0.00 0.00 2.69
4165 6246 0.182775 GCATCCCAACCGACCCTTAT 59.817 55.000 0.00 0.00 0.00 1.73
4166 6247 1.418637 GCATCCCAACCGACCCTTATA 59.581 52.381 0.00 0.00 0.00 0.98
4167 6248 2.809299 GCATCCCAACCGACCCTTATAC 60.809 54.545 0.00 0.00 0.00 1.47
4168 6249 2.250921 TCCCAACCGACCCTTATACA 57.749 50.000 0.00 0.00 0.00 2.29
4169 6250 1.832998 TCCCAACCGACCCTTATACAC 59.167 52.381 0.00 0.00 0.00 2.90
4170 6251 1.555992 CCCAACCGACCCTTATACACA 59.444 52.381 0.00 0.00 0.00 3.72
4171 6252 2.419574 CCCAACCGACCCTTATACACAG 60.420 54.545 0.00 0.00 0.00 3.66
4172 6253 2.277084 CAACCGACCCTTATACACAGC 58.723 52.381 0.00 0.00 0.00 4.40
4173 6254 0.828677 ACCGACCCTTATACACAGCC 59.171 55.000 0.00 0.00 0.00 4.85
4174 6255 0.106149 CCGACCCTTATACACAGCCC 59.894 60.000 0.00 0.00 0.00 5.19
4175 6256 0.828022 CGACCCTTATACACAGCCCA 59.172 55.000 0.00 0.00 0.00 5.36
4176 6257 1.416401 CGACCCTTATACACAGCCCAT 59.584 52.381 0.00 0.00 0.00 4.00
4177 6258 2.631062 CGACCCTTATACACAGCCCATA 59.369 50.000 0.00 0.00 0.00 2.74
4178 6259 3.260884 CGACCCTTATACACAGCCCATAT 59.739 47.826 0.00 0.00 0.00 1.78
4179 6260 4.579869 GACCCTTATACACAGCCCATATG 58.420 47.826 0.00 0.00 0.00 1.78
4180 6261 3.980698 ACCCTTATACACAGCCCATATGT 59.019 43.478 1.24 0.00 0.00 2.29
4181 6262 4.415512 ACCCTTATACACAGCCCATATGTT 59.584 41.667 1.24 0.00 0.00 2.71
4182 6263 5.103686 ACCCTTATACACAGCCCATATGTTT 60.104 40.000 1.24 0.00 0.00 2.83
4183 6264 5.473504 CCCTTATACACAGCCCATATGTTTC 59.526 44.000 1.24 0.00 0.00 2.78
4184 6265 5.179368 CCTTATACACAGCCCATATGTTTCG 59.821 44.000 1.24 0.00 0.00 3.46
4185 6266 1.750193 ACACAGCCCATATGTTTCGG 58.250 50.000 1.24 0.00 0.00 4.30
4186 6267 1.024271 CACAGCCCATATGTTTCGGG 58.976 55.000 1.24 0.00 43.42 5.14
4187 6268 0.623723 ACAGCCCATATGTTTCGGGT 59.376 50.000 1.24 0.00 42.44 5.28
4188 6269 1.005450 ACAGCCCATATGTTTCGGGTT 59.995 47.619 1.24 0.00 42.44 4.11
4189 6270 1.405105 CAGCCCATATGTTTCGGGTTG 59.595 52.381 1.24 0.00 43.58 3.77
4190 6271 1.005450 AGCCCATATGTTTCGGGTTGT 59.995 47.619 1.24 0.00 42.44 3.32
4191 6272 1.822371 GCCCATATGTTTCGGGTTGTT 59.178 47.619 1.24 0.00 42.44 2.83
4192 6273 2.159296 GCCCATATGTTTCGGGTTGTTC 60.159 50.000 1.24 0.00 42.44 3.18
4193 6274 2.096819 CCCATATGTTTCGGGTTGTTCG 59.903 50.000 1.24 0.00 35.03 3.95
4194 6275 2.096819 CCATATGTTTCGGGTTGTTCGG 59.903 50.000 1.24 0.00 0.00 4.30
4195 6276 1.158434 TATGTTTCGGGTTGTTCGGC 58.842 50.000 0.00 0.00 0.00 5.54
4196 6277 0.820074 ATGTTTCGGGTTGTTCGGCA 60.820 50.000 0.00 0.00 0.00 5.69
4197 6278 1.009335 GTTTCGGGTTGTTCGGCAC 60.009 57.895 0.00 0.00 0.00 5.01
4198 6279 2.188161 TTTCGGGTTGTTCGGCACC 61.188 57.895 0.00 0.00 0.00 5.01
4199 6280 4.629523 TCGGGTTGTTCGGCACCC 62.630 66.667 0.00 0.00 36.04 4.61
4201 6282 4.280019 GGGTTGTTCGGCACCCCT 62.280 66.667 6.33 0.00 45.51 4.79
4202 6283 2.203437 GGTTGTTCGGCACCCCTT 60.203 61.111 0.00 0.00 0.00 3.95
4203 6284 2.265904 GGTTGTTCGGCACCCCTTC 61.266 63.158 0.00 0.00 0.00 3.46
4204 6285 1.527380 GTTGTTCGGCACCCCTTCA 60.527 57.895 0.00 0.00 0.00 3.02
4205 6286 1.104577 GTTGTTCGGCACCCCTTCAA 61.105 55.000 0.00 0.00 0.00 2.69
4206 6287 0.395862 TTGTTCGGCACCCCTTCAAA 60.396 50.000 0.00 0.00 0.00 2.69
4207 6288 1.104577 TGTTCGGCACCCCTTCAAAC 61.105 55.000 0.00 0.00 0.00 2.93
4208 6289 1.529713 TTCGGCACCCCTTCAAACC 60.530 57.895 0.00 0.00 0.00 3.27
4209 6290 2.002018 TTCGGCACCCCTTCAAACCT 62.002 55.000 0.00 0.00 0.00 3.50
4210 6291 1.128809 TCGGCACCCCTTCAAACCTA 61.129 55.000 0.00 0.00 0.00 3.08
4211 6292 0.676782 CGGCACCCCTTCAAACCTAG 60.677 60.000 0.00 0.00 0.00 3.02
4212 6293 0.965866 GGCACCCCTTCAAACCTAGC 60.966 60.000 0.00 0.00 0.00 3.42
4213 6294 0.965866 GCACCCCTTCAAACCTAGCC 60.966 60.000 0.00 0.00 0.00 3.93
4214 6295 0.323451 CACCCCTTCAAACCTAGCCC 60.323 60.000 0.00 0.00 0.00 5.19
4215 6296 0.774491 ACCCCTTCAAACCTAGCCCA 60.774 55.000 0.00 0.00 0.00 5.36
4216 6297 0.631212 CCCCTTCAAACCTAGCCCAT 59.369 55.000 0.00 0.00 0.00 4.00
4217 6298 1.410224 CCCCTTCAAACCTAGCCCATC 60.410 57.143 0.00 0.00 0.00 3.51
4218 6299 1.410224 CCCTTCAAACCTAGCCCATCC 60.410 57.143 0.00 0.00 0.00 3.51
4219 6300 1.284785 CCTTCAAACCTAGCCCATCCA 59.715 52.381 0.00 0.00 0.00 3.41
4220 6301 2.091665 CCTTCAAACCTAGCCCATCCAT 60.092 50.000 0.00 0.00 0.00 3.41
4221 6302 3.138283 CCTTCAAACCTAGCCCATCCATA 59.862 47.826 0.00 0.00 0.00 2.74
4222 6303 4.202609 CCTTCAAACCTAGCCCATCCATAT 60.203 45.833 0.00 0.00 0.00 1.78
4223 6304 4.371624 TCAAACCTAGCCCATCCATATG 57.628 45.455 0.00 0.00 0.00 1.78
4234 6315 3.770046 CCATCCATATGGCAGATTTGGA 58.230 45.455 17.58 6.90 46.17 3.53
4235 6316 3.762288 CCATCCATATGGCAGATTTGGAG 59.238 47.826 17.58 3.44 46.17 3.86
4236 6317 2.867624 TCCATATGGCAGATTTGGAGC 58.132 47.619 17.58 0.00 32.80 4.70
4240 6321 3.521796 GGCAGATTTGGAGCCGCC 61.522 66.667 0.00 0.00 38.86 6.13
4241 6322 3.521796 GCAGATTTGGAGCCGCCC 61.522 66.667 0.00 0.00 34.97 6.13
4242 6323 2.045045 CAGATTTGGAGCCGCCCA 60.045 61.111 0.00 0.00 34.97 5.36
4243 6324 2.117156 CAGATTTGGAGCCGCCCAG 61.117 63.158 1.53 0.00 37.53 4.45
4244 6325 2.272146 GATTTGGAGCCGCCCAGA 59.728 61.111 1.53 0.00 37.53 3.86
4245 6326 1.152881 GATTTGGAGCCGCCCAGAT 60.153 57.895 4.28 4.28 37.53 2.90
4246 6327 1.450531 GATTTGGAGCCGCCCAGATG 61.451 60.000 8.15 0.00 37.53 2.90
4247 6328 4.802051 TTGGAGCCGCCCAGATGC 62.802 66.667 1.53 0.00 37.53 3.91
4274 6355 6.237887 TGACATATCAGATCCAACATGTCA 57.762 37.500 16.96 16.96 45.93 3.58
4275 6356 6.285990 TGACATATCAGATCCAACATGTCAG 58.714 40.000 16.96 0.00 44.28 3.51
4276 6357 6.098695 TGACATATCAGATCCAACATGTCAGA 59.901 38.462 16.96 0.00 44.28 3.27
4277 6358 6.286758 ACATATCAGATCCAACATGTCAGAC 58.713 40.000 0.00 0.00 0.00 3.51
4278 6359 6.099413 ACATATCAGATCCAACATGTCAGACT 59.901 38.462 0.00 0.00 0.00 3.24
4279 6360 4.897509 TCAGATCCAACATGTCAGACTT 57.102 40.909 0.00 0.00 0.00 3.01
4280 6361 6.550938 ATCAGATCCAACATGTCAGACTTA 57.449 37.500 0.00 0.00 0.00 2.24
4281 6362 5.724328 TCAGATCCAACATGTCAGACTTAC 58.276 41.667 0.00 0.00 0.00 2.34
4282 6363 4.872691 CAGATCCAACATGTCAGACTTACC 59.127 45.833 0.00 0.00 0.00 2.85
4283 6364 3.695830 TCCAACATGTCAGACTTACCC 57.304 47.619 0.00 0.00 0.00 3.69
4284 6365 3.248024 TCCAACATGTCAGACTTACCCT 58.752 45.455 0.00 0.00 0.00 4.34
4285 6366 4.422057 TCCAACATGTCAGACTTACCCTA 58.578 43.478 0.00 0.00 0.00 3.53
4286 6367 4.841813 TCCAACATGTCAGACTTACCCTAA 59.158 41.667 0.00 0.00 0.00 2.69
4287 6368 5.308497 TCCAACATGTCAGACTTACCCTAAA 59.692 40.000 0.00 0.00 0.00 1.85
4288 6369 6.012858 TCCAACATGTCAGACTTACCCTAAAT 60.013 38.462 0.00 0.00 0.00 1.40
4289 6370 6.316390 CCAACATGTCAGACTTACCCTAAATC 59.684 42.308 0.00 0.00 0.00 2.17
4290 6371 5.990668 ACATGTCAGACTTACCCTAAATCC 58.009 41.667 1.31 0.00 0.00 3.01
4291 6372 5.726793 ACATGTCAGACTTACCCTAAATCCT 59.273 40.000 1.31 0.00 0.00 3.24
4292 6373 6.215636 ACATGTCAGACTTACCCTAAATCCTT 59.784 38.462 1.31 0.00 0.00 3.36
4293 6374 6.295719 TGTCAGACTTACCCTAAATCCTTC 57.704 41.667 1.31 0.00 0.00 3.46
4326 6407 2.681848 CGCATTGAAGAGGAGCTGAAAT 59.318 45.455 0.00 0.00 0.00 2.17
4328 6409 4.514441 CGCATTGAAGAGGAGCTGAAATAT 59.486 41.667 0.00 0.00 0.00 1.28
4336 6417 9.601810 TGAAGAGGAGCTGAAATATATACCTTA 57.398 33.333 0.00 0.00 0.00 2.69
4369 6450 8.917414 ATCAAGGAGCTGGGTATAATAGATTA 57.083 34.615 0.00 0.00 0.00 1.75
4374 6455 6.405619 GGAGCTGGGTATAATAGATTACGACC 60.406 46.154 0.00 6.63 33.75 4.79
4401 6482 7.201741 GCCTTTTCTCATCTAAACTATCCCAAC 60.202 40.741 0.00 0.00 0.00 3.77
4486 6573 5.567037 AATATAGTACAATGGCCAGCAGA 57.433 39.130 13.05 0.00 0.00 4.26
4566 6653 1.081892 CGGCTCACTTCCATCAACAG 58.918 55.000 0.00 0.00 0.00 3.16
4615 6702 3.516615 CTCGACTCCAGGATCTTCAAAC 58.483 50.000 0.00 0.00 0.00 2.93
4660 6747 0.389426 GTTCCAAAGCTGCCTGCATG 60.389 55.000 0.00 0.00 45.94 4.06
4698 6785 2.585330 TCATTGCTTGTCCAAAGCTGA 58.415 42.857 11.05 5.06 43.38 4.26
4727 6814 3.282021 GCCAGCAAATCTTGGAGACATA 58.718 45.455 0.00 0.00 42.32 2.29
4766 6853 0.613260 AGGTATTTGAGTGCGAGGCA 59.387 50.000 0.00 0.00 35.60 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 9.533253 CCAATTAGTTCAAAAGACAACAATTCT 57.467 29.630 0.00 0.00 0.00 2.40
36 37 2.507886 CCCACATATTCCACAGGTACCA 59.492 50.000 15.94 0.00 0.00 3.25
51 52 3.365535 GCAAAAGGCGTCCCACAT 58.634 55.556 0.00 0.00 0.00 3.21
211 218 3.729108 AGATGACATCTTCTCCCTCCAA 58.271 45.455 12.37 0.00 35.76 3.53
351 358 7.449395 CCTGCCAGGAAATCAATTGATAATCTA 59.551 37.037 21.00 4.19 37.67 1.98
353 360 6.453092 CCTGCCAGGAAATCAATTGATAATC 58.547 40.000 21.00 19.78 37.67 1.75
354 361 5.221581 GCCTGCCAGGAAATCAATTGATAAT 60.222 40.000 21.00 13.11 37.67 1.28
404 411 0.325933 TTCAGGAGGTCACATGCTGG 59.674 55.000 11.32 0.00 36.81 4.85
436 456 4.192317 GCCCAACTCAAGTCTACAATAGG 58.808 47.826 0.00 0.00 0.00 2.57
558 582 4.559153 ACATTTTAGCACCAAGCATTGTC 58.441 39.130 0.00 0.00 46.99 3.18
585 611 5.914033 TGCATACCCAGTAACAGAAGATAC 58.086 41.667 0.00 0.00 0.00 2.24
618 663 2.234661 TGGTCTTCAGTAGCTGGACATG 59.765 50.000 0.00 0.00 28.84 3.21
619 664 2.540383 TGGTCTTCAGTAGCTGGACAT 58.460 47.619 0.00 0.00 28.84 3.06
624 669 3.006323 ACTCTGTTGGTCTTCAGTAGCTG 59.994 47.826 0.00 0.00 33.89 4.24
626 671 3.257127 AGACTCTGTTGGTCTTCAGTAGC 59.743 47.826 0.00 0.00 40.65 3.58
676 1292 0.755686 CTCATCTCCTCCCTTTCCGG 59.244 60.000 0.00 0.00 0.00 5.14
684 1300 2.699846 ACAGATTCTGCTCATCTCCTCC 59.300 50.000 13.64 0.00 34.37 4.30
687 1303 2.836262 CCACAGATTCTGCTCATCTCC 58.164 52.381 13.64 0.00 34.37 3.71
688 1304 2.211806 GCCACAGATTCTGCTCATCTC 58.788 52.381 13.64 0.00 34.37 2.75
690 1306 1.307097 GGCCACAGATTCTGCTCATC 58.693 55.000 13.64 0.00 34.37 2.92
708 1324 1.651240 CCAGCTGAGTTTGCGGATGG 61.651 60.000 17.39 0.00 43.49 3.51
711 1327 0.179032 TTTCCAGCTGAGTTTGCGGA 60.179 50.000 17.39 0.00 33.73 5.54
768 1385 5.581126 TTATTAAGCATGGCCTTGTTGAG 57.419 39.130 19.05 0.00 0.00 3.02
832 1449 2.063378 GTCAGGAGGGGAGGAGCTG 61.063 68.421 0.00 0.00 0.00 4.24
879 1496 0.108138 AGGTTCCTTCATTCGAGCCG 60.108 55.000 0.00 0.00 34.77 5.52
880 1497 1.740025 CAAGGTTCCTTCATTCGAGCC 59.260 52.381 0.60 0.00 0.00 4.70
891 1508 1.428912 TGCAATTCTCCCAAGGTTCCT 59.571 47.619 0.00 0.00 0.00 3.36
892 1509 1.821136 CTGCAATTCTCCCAAGGTTCC 59.179 52.381 0.00 0.00 0.00 3.62
893 1510 1.821136 CCTGCAATTCTCCCAAGGTTC 59.179 52.381 0.00 0.00 0.00 3.62
894 1511 1.428912 TCCTGCAATTCTCCCAAGGTT 59.571 47.619 0.00 0.00 0.00 3.50
895 1512 1.005215 CTCCTGCAATTCTCCCAAGGT 59.995 52.381 0.00 0.00 0.00 3.50
916 1533 1.390565 AATGTCTCTACGCCTACGCT 58.609 50.000 0.00 0.00 45.53 5.07
917 1534 2.350580 CCTAATGTCTCTACGCCTACGC 60.351 54.545 0.00 0.00 45.53 4.42
919 1536 3.484407 TCCCTAATGTCTCTACGCCTAC 58.516 50.000 0.00 0.00 0.00 3.18
920 1537 3.498121 CCTCCCTAATGTCTCTACGCCTA 60.498 52.174 0.00 0.00 0.00 3.93
921 1538 2.588620 CTCCCTAATGTCTCTACGCCT 58.411 52.381 0.00 0.00 0.00 5.52
922 1539 1.614413 CCTCCCTAATGTCTCTACGCC 59.386 57.143 0.00 0.00 0.00 5.68
925 1542 2.554893 CTCGCCTCCCTAATGTCTCTAC 59.445 54.545 0.00 0.00 0.00 2.59
943 1564 2.033299 GTCAGATCAGCTTCCTCTCTCG 59.967 54.545 0.00 0.00 0.00 4.04
944 1565 2.362077 GGTCAGATCAGCTTCCTCTCTC 59.638 54.545 0.00 0.00 0.00 3.20
948 1587 2.106566 TCAGGTCAGATCAGCTTCCTC 58.893 52.381 0.00 0.00 0.00 3.71
1105 1752 4.039357 CACCAGCGTCTCCGTCGT 62.039 66.667 0.00 0.00 36.15 4.34
1135 1782 3.249189 GTGGACCAGCACCAGGGA 61.249 66.667 0.00 0.00 38.14 4.20
1704 2369 1.067985 CGAGCAGAGCACAGAAAGAGA 60.068 52.381 0.00 0.00 0.00 3.10
1705 2370 1.348276 CGAGCAGAGCACAGAAAGAG 58.652 55.000 0.00 0.00 0.00 2.85
1707 2372 0.669932 AGCGAGCAGAGCACAGAAAG 60.670 55.000 0.00 0.00 37.01 2.62
1746 2412 3.054503 CTGTCCGTCCGTCCGTCT 61.055 66.667 0.00 0.00 0.00 4.18
1870 2591 1.673033 GCCCCGATGAAGGATATGTCG 60.673 57.143 0.00 0.00 0.00 4.35
2150 2892 3.220110 TCCATGTCCTCCTACGTACATC 58.780 50.000 0.00 0.00 30.32 3.06
3456 4289 1.303806 TTTTCTTACGGGCCCCTGC 60.304 57.895 18.66 0.00 0.00 4.85
3457 4290 0.963856 GGTTTTCTTACGGGCCCCTG 60.964 60.000 18.66 5.47 0.00 4.45
3458 4291 1.381463 GGTTTTCTTACGGGCCCCT 59.619 57.895 18.66 7.52 0.00 4.79
3478 4311 0.249447 TGGTGGATGATCGATCGTGC 60.249 55.000 26.87 26.87 35.08 5.34
3518 4351 0.533308 TTTACCCGTGTCAGTGTGGC 60.533 55.000 0.00 0.00 0.00 5.01
3553 4397 1.574925 GCTCATCGCATCCTGCATG 59.425 57.895 0.00 0.00 45.36 4.06
3554 4398 1.959738 CGCTCATCGCATCCTGCAT 60.960 57.895 0.00 0.00 45.36 3.96
3555 4399 2.373434 ATCGCTCATCGCATCCTGCA 62.373 55.000 0.00 0.00 45.36 4.41
3556 4400 1.624865 GATCGCTCATCGCATCCTGC 61.625 60.000 0.00 0.00 40.69 4.85
3557 4401 1.013005 GGATCGCTCATCGCATCCTG 61.013 60.000 0.00 0.00 39.54 3.86
3558 4402 1.291588 GGATCGCTCATCGCATCCT 59.708 57.895 0.00 0.00 39.54 3.24
3632 4476 0.785708 CAATCACGACGCGACTTTGC 60.786 55.000 15.93 0.00 0.00 3.68
3722 4576 3.181516 GGCGAAGAATTACAGTCTGCTTG 60.182 47.826 0.00 0.00 0.00 4.01
3725 4579 1.666189 GGGCGAAGAATTACAGTCTGC 59.334 52.381 0.00 0.00 0.00 4.26
3728 4582 2.005971 ACGGGCGAAGAATTACAGTC 57.994 50.000 0.00 0.00 0.00 3.51
3754 4610 2.622942 AGAAACCACGACCAAGTACGTA 59.377 45.455 0.00 0.00 40.76 3.57
3755 4611 1.410153 AGAAACCACGACCAAGTACGT 59.590 47.619 0.00 0.00 43.50 3.57
3756 4612 2.144482 AGAAACCACGACCAAGTACG 57.856 50.000 0.00 0.00 0.00 3.67
3757 4613 5.467735 ACATTAAGAAACCACGACCAAGTAC 59.532 40.000 0.00 0.00 0.00 2.73
3841 4847 6.199154 CGATTGCTTTCACCAGTATAGTACAG 59.801 42.308 0.00 0.00 0.00 2.74
3880 4886 3.539604 AGCTGGATCAAGAAATCTTCGG 58.460 45.455 0.00 0.00 33.11 4.30
3884 4893 5.176741 ACAAGAGCTGGATCAAGAAATCT 57.823 39.130 0.00 0.00 0.00 2.40
3927 4944 0.895530 TCCGGTAAGAGAAGCACAGG 59.104 55.000 0.00 0.00 0.00 4.00
3928 4945 1.546476 AGTCCGGTAAGAGAAGCACAG 59.454 52.381 0.00 0.00 0.00 3.66
3929 4946 1.629043 AGTCCGGTAAGAGAAGCACA 58.371 50.000 0.00 0.00 0.00 4.57
3930 4947 2.288886 ACAAGTCCGGTAAGAGAAGCAC 60.289 50.000 0.00 0.00 0.00 4.40
3944 4986 1.008538 CTGTTTGCGCCACAAGTCC 60.009 57.895 4.18 0.00 40.06 3.85
3955 4997 1.663161 GCTGTTAGGTTCGCTGTTTGC 60.663 52.381 0.00 0.00 38.57 3.68
4004 6085 0.315251 TTCAGAGTGGCAGTCGACTG 59.685 55.000 35.80 35.80 46.40 3.51
4007 6088 0.598562 GACTTCAGAGTGGCAGTCGA 59.401 55.000 16.24 13.38 35.88 4.20
4024 6105 7.708322 TGAGATTGATTGCAGTATAGTTCAGAC 59.292 37.037 0.00 0.00 0.00 3.51
4026 6107 7.924947 TCTGAGATTGATTGCAGTATAGTTCAG 59.075 37.037 8.55 8.55 0.00 3.02
4028 6109 8.140628 TCTCTGAGATTGATTGCAGTATAGTTC 58.859 37.037 2.58 0.00 0.00 3.01
4029 6110 8.016301 TCTCTGAGATTGATTGCAGTATAGTT 57.984 34.615 2.58 0.00 0.00 2.24
4030 6111 7.287466 ACTCTCTGAGATTGATTGCAGTATAGT 59.713 37.037 8.00 0.00 33.32 2.12
4031 6112 7.660112 ACTCTCTGAGATTGATTGCAGTATAG 58.340 38.462 8.00 0.00 33.32 1.31
4032 6113 7.594351 ACTCTCTGAGATTGATTGCAGTATA 57.406 36.000 8.00 0.00 33.32 1.47
4033 6114 6.482898 ACTCTCTGAGATTGATTGCAGTAT 57.517 37.500 8.00 0.00 33.32 2.12
4034 6115 5.929058 ACTCTCTGAGATTGATTGCAGTA 57.071 39.130 8.00 0.00 33.32 2.74
4035 6116 4.822685 ACTCTCTGAGATTGATTGCAGT 57.177 40.909 8.00 0.00 33.32 4.40
4036 6117 5.658468 TGTACTCTCTGAGATTGATTGCAG 58.342 41.667 8.00 0.00 33.32 4.41
4037 6118 5.420104 TCTGTACTCTCTGAGATTGATTGCA 59.580 40.000 8.00 0.52 33.32 4.08
4038 6119 5.900425 TCTGTACTCTCTGAGATTGATTGC 58.100 41.667 8.00 0.00 33.32 3.56
4039 6120 6.979817 CCTTCTGTACTCTCTGAGATTGATTG 59.020 42.308 8.00 0.00 33.32 2.67
4040 6121 6.894654 TCCTTCTGTACTCTCTGAGATTGATT 59.105 38.462 8.00 0.00 33.32 2.57
4041 6122 6.430864 TCCTTCTGTACTCTCTGAGATTGAT 58.569 40.000 8.00 0.00 33.32 2.57
4042 6123 5.821097 TCCTTCTGTACTCTCTGAGATTGA 58.179 41.667 8.00 0.28 33.32 2.57
4052 6133 6.609212 TGCTCTAATCAATCCTTCTGTACTCT 59.391 38.462 0.00 0.00 0.00 3.24
4082 6163 1.328279 GAGGGTTTTGGGGTCTGTTG 58.672 55.000 0.00 0.00 0.00 3.33
4098 6179 2.268920 CACCCGGACATGTGGAGG 59.731 66.667 1.15 2.74 0.00 4.30
4114 6195 1.385347 AACAGTGTCCAGGGGTCCA 60.385 57.895 0.00 0.00 0.00 4.02
4115 6196 1.375326 GAACAGTGTCCAGGGGTCC 59.625 63.158 0.00 0.00 0.00 4.46
4122 6203 2.920724 TTTCATCCGAACAGTGTCCA 57.079 45.000 0.00 0.00 0.00 4.02
4123 6204 3.125316 GTCATTTCATCCGAACAGTGTCC 59.875 47.826 0.00 0.00 0.00 4.02
4124 6205 3.181530 CGTCATTTCATCCGAACAGTGTC 60.182 47.826 0.00 0.00 0.00 3.67
4125 6206 2.736721 CGTCATTTCATCCGAACAGTGT 59.263 45.455 0.00 0.00 0.00 3.55
4126 6207 2.474526 GCGTCATTTCATCCGAACAGTG 60.475 50.000 0.00 0.00 0.00 3.66
4127 6208 1.732259 GCGTCATTTCATCCGAACAGT 59.268 47.619 0.00 0.00 0.00 3.55
4128 6209 1.731709 TGCGTCATTTCATCCGAACAG 59.268 47.619 0.00 0.00 0.00 3.16
4129 6210 1.802069 TGCGTCATTTCATCCGAACA 58.198 45.000 0.00 0.00 0.00 3.18
4130 6211 2.286418 GGATGCGTCATTTCATCCGAAC 60.286 50.000 8.47 0.00 46.23 3.95
4131 6212 1.939934 GGATGCGTCATTTCATCCGAA 59.060 47.619 8.47 0.00 46.23 4.30
4132 6213 1.581934 GGATGCGTCATTTCATCCGA 58.418 50.000 8.47 0.00 46.23 4.55
4135 6216 2.223572 GGTTGGGATGCGTCATTTCATC 60.224 50.000 8.47 0.00 38.60 2.92
4136 6217 1.750778 GGTTGGGATGCGTCATTTCAT 59.249 47.619 8.47 0.00 0.00 2.57
4137 6218 1.173043 GGTTGGGATGCGTCATTTCA 58.827 50.000 8.47 0.00 0.00 2.69
4138 6219 0.098728 CGGTTGGGATGCGTCATTTC 59.901 55.000 8.47 0.00 0.00 2.17
4139 6220 0.322098 TCGGTTGGGATGCGTCATTT 60.322 50.000 8.47 0.00 0.00 2.32
4140 6221 1.024579 GTCGGTTGGGATGCGTCATT 61.025 55.000 8.47 0.00 0.00 2.57
4141 6222 1.449601 GTCGGTTGGGATGCGTCAT 60.450 57.895 8.47 0.00 0.00 3.06
4142 6223 2.047655 GTCGGTTGGGATGCGTCA 60.048 61.111 8.47 0.00 0.00 4.35
4143 6224 2.818274 GGTCGGTTGGGATGCGTC 60.818 66.667 0.00 0.00 0.00 5.19
4144 6225 4.404098 GGGTCGGTTGGGATGCGT 62.404 66.667 0.00 0.00 0.00 5.24
4145 6226 2.246761 TAAGGGTCGGTTGGGATGCG 62.247 60.000 0.00 0.00 0.00 4.73
4146 6227 0.182775 ATAAGGGTCGGTTGGGATGC 59.817 55.000 0.00 0.00 0.00 3.91
4147 6228 2.436542 TGTATAAGGGTCGGTTGGGATG 59.563 50.000 0.00 0.00 0.00 3.51
4148 6229 2.436911 GTGTATAAGGGTCGGTTGGGAT 59.563 50.000 0.00 0.00 0.00 3.85
4149 6230 1.832998 GTGTATAAGGGTCGGTTGGGA 59.167 52.381 0.00 0.00 0.00 4.37
4150 6231 1.555992 TGTGTATAAGGGTCGGTTGGG 59.444 52.381 0.00 0.00 0.00 4.12
4151 6232 2.901249 CTGTGTATAAGGGTCGGTTGG 58.099 52.381 0.00 0.00 0.00 3.77
4152 6233 2.277084 GCTGTGTATAAGGGTCGGTTG 58.723 52.381 0.00 0.00 0.00 3.77
4153 6234 1.208776 GGCTGTGTATAAGGGTCGGTT 59.791 52.381 0.00 0.00 0.00 4.44
4154 6235 0.828677 GGCTGTGTATAAGGGTCGGT 59.171 55.000 0.00 0.00 0.00 4.69
4155 6236 0.106149 GGGCTGTGTATAAGGGTCGG 59.894 60.000 0.00 0.00 0.00 4.79
4156 6237 0.828022 TGGGCTGTGTATAAGGGTCG 59.172 55.000 0.00 0.00 0.00 4.79
4157 6238 4.041691 ACATATGGGCTGTGTATAAGGGTC 59.958 45.833 7.80 0.00 0.00 4.46
4158 6239 3.980698 ACATATGGGCTGTGTATAAGGGT 59.019 43.478 7.80 0.00 0.00 4.34
4159 6240 4.640771 ACATATGGGCTGTGTATAAGGG 57.359 45.455 7.80 0.00 0.00 3.95
4160 6241 5.179368 CGAAACATATGGGCTGTGTATAAGG 59.821 44.000 7.80 0.00 0.00 2.69
4161 6242 5.179368 CCGAAACATATGGGCTGTGTATAAG 59.821 44.000 7.80 0.00 0.00 1.73
4162 6243 5.060506 CCGAAACATATGGGCTGTGTATAA 58.939 41.667 7.80 0.00 0.00 0.98
4163 6244 4.504165 CCCGAAACATATGGGCTGTGTATA 60.504 45.833 7.80 0.00 35.82 1.47
4164 6245 3.476552 CCGAAACATATGGGCTGTGTAT 58.523 45.455 7.80 0.00 0.00 2.29
4165 6246 2.420827 CCCGAAACATATGGGCTGTGTA 60.421 50.000 7.80 0.00 35.82 2.90
4166 6247 1.681780 CCCGAAACATATGGGCTGTGT 60.682 52.381 7.80 0.00 35.82 3.72
4167 6248 1.024271 CCCGAAACATATGGGCTGTG 58.976 55.000 7.80 0.00 35.82 3.66
4168 6249 3.494850 CCCGAAACATATGGGCTGT 57.505 52.632 7.80 0.00 35.82 4.40
4173 6254 2.096819 CCGAACAACCCGAAACATATGG 59.903 50.000 7.80 0.00 0.00 2.74
4174 6255 2.477189 GCCGAACAACCCGAAACATATG 60.477 50.000 0.00 0.00 0.00 1.78
4175 6256 1.741145 GCCGAACAACCCGAAACATAT 59.259 47.619 0.00 0.00 0.00 1.78
4176 6257 1.158434 GCCGAACAACCCGAAACATA 58.842 50.000 0.00 0.00 0.00 2.29
4177 6258 0.820074 TGCCGAACAACCCGAAACAT 60.820 50.000 0.00 0.00 0.00 2.71
4178 6259 1.451567 TGCCGAACAACCCGAAACA 60.452 52.632 0.00 0.00 0.00 2.83
4179 6260 1.009335 GTGCCGAACAACCCGAAAC 60.009 57.895 0.00 0.00 0.00 2.78
4180 6261 2.188161 GGTGCCGAACAACCCGAAA 61.188 57.895 0.00 0.00 0.00 3.46
4181 6262 2.592287 GGTGCCGAACAACCCGAA 60.592 61.111 0.00 0.00 0.00 4.30
4186 6267 1.104577 TTGAAGGGGTGCCGAACAAC 61.105 55.000 0.00 0.00 34.06 3.32
4187 6268 0.395862 TTTGAAGGGGTGCCGAACAA 60.396 50.000 0.00 0.00 0.00 2.83
4188 6269 1.104577 GTTTGAAGGGGTGCCGAACA 61.105 55.000 0.00 0.00 0.00 3.18
4189 6270 1.658114 GTTTGAAGGGGTGCCGAAC 59.342 57.895 0.00 0.00 0.00 3.95
4190 6271 1.529713 GGTTTGAAGGGGTGCCGAA 60.530 57.895 0.00 0.00 0.00 4.30
4191 6272 1.128809 TAGGTTTGAAGGGGTGCCGA 61.129 55.000 0.00 0.00 0.00 5.54
4192 6273 0.676782 CTAGGTTTGAAGGGGTGCCG 60.677 60.000 0.00 0.00 0.00 5.69
4193 6274 0.965866 GCTAGGTTTGAAGGGGTGCC 60.966 60.000 0.00 0.00 0.00 5.01
4194 6275 0.965866 GGCTAGGTTTGAAGGGGTGC 60.966 60.000 0.00 0.00 0.00 5.01
4195 6276 0.323451 GGGCTAGGTTTGAAGGGGTG 60.323 60.000 0.00 0.00 0.00 4.61
4196 6277 0.774491 TGGGCTAGGTTTGAAGGGGT 60.774 55.000 0.00 0.00 0.00 4.95
4197 6278 0.631212 ATGGGCTAGGTTTGAAGGGG 59.369 55.000 0.00 0.00 0.00 4.79
4198 6279 1.410224 GGATGGGCTAGGTTTGAAGGG 60.410 57.143 0.00 0.00 0.00 3.95
4199 6280 1.284785 TGGATGGGCTAGGTTTGAAGG 59.715 52.381 0.00 0.00 0.00 3.46
4200 6281 2.806945 TGGATGGGCTAGGTTTGAAG 57.193 50.000 0.00 0.00 0.00 3.02
4201 6282 4.728772 CATATGGATGGGCTAGGTTTGAA 58.271 43.478 0.00 0.00 0.00 2.69
4202 6283 4.371624 CATATGGATGGGCTAGGTTTGA 57.628 45.455 0.00 0.00 0.00 2.69
4214 6295 3.192844 GCTCCAAATCTGCCATATGGATG 59.807 47.826 26.47 15.95 39.33 3.51
4215 6296 3.428532 GCTCCAAATCTGCCATATGGAT 58.571 45.455 26.47 7.29 39.33 3.41
4216 6297 2.489619 GGCTCCAAATCTGCCATATGGA 60.490 50.000 26.47 9.60 45.46 3.41
4217 6298 1.891150 GGCTCCAAATCTGCCATATGG 59.109 52.381 18.07 18.07 45.46 2.74
4218 6299 1.538512 CGGCTCCAAATCTGCCATATG 59.461 52.381 0.00 0.00 46.39 1.78
4219 6300 1.901591 CGGCTCCAAATCTGCCATAT 58.098 50.000 0.00 0.00 46.39 1.78
4220 6301 0.819259 GCGGCTCCAAATCTGCCATA 60.819 55.000 0.00 0.00 46.39 2.74
4221 6302 2.123428 GCGGCTCCAAATCTGCCAT 61.123 57.895 0.00 0.00 46.39 4.40
4222 6303 2.751436 GCGGCTCCAAATCTGCCA 60.751 61.111 0.00 0.00 46.39 4.92
4223 6304 3.521796 GGCGGCTCCAAATCTGCC 61.522 66.667 0.00 0.00 46.19 4.85
4224 6305 3.521796 GGGCGGCTCCAAATCTGC 61.522 66.667 9.56 0.00 36.21 4.26
4225 6306 2.045045 TGGGCGGCTCCAAATCTG 60.045 61.111 9.56 0.00 36.21 2.90
4226 6307 1.639635 ATCTGGGCGGCTCCAAATCT 61.640 55.000 9.56 0.00 36.21 2.40
4227 6308 1.152881 ATCTGGGCGGCTCCAAATC 60.153 57.895 9.56 0.00 36.21 2.17
4228 6309 1.454479 CATCTGGGCGGCTCCAAAT 60.454 57.895 9.56 1.86 36.21 2.32
4229 6310 2.045045 CATCTGGGCGGCTCCAAA 60.045 61.111 9.56 0.00 36.21 3.28
4230 6311 4.802051 GCATCTGGGCGGCTCCAA 62.802 66.667 9.56 4.14 36.21 3.53
4251 6332 6.098695 TCTGACATGTTGGATCTGATATGTCA 59.901 38.462 24.74 24.74 45.74 3.58
4252 6333 6.423302 GTCTGACATGTTGGATCTGATATGTC 59.577 42.308 20.77 20.77 41.75 3.06
4253 6334 6.099413 AGTCTGACATGTTGGATCTGATATGT 59.901 38.462 10.88 9.66 31.47 2.29
4254 6335 6.522946 AGTCTGACATGTTGGATCTGATATG 58.477 40.000 10.88 0.00 0.00 1.78
4255 6336 6.744175 AGTCTGACATGTTGGATCTGATAT 57.256 37.500 10.88 0.00 0.00 1.63
4256 6337 6.550938 AAGTCTGACATGTTGGATCTGATA 57.449 37.500 10.88 0.00 0.00 2.15
4257 6338 5.432680 AAGTCTGACATGTTGGATCTGAT 57.567 39.130 10.88 0.00 0.00 2.90
4258 6339 4.897509 AAGTCTGACATGTTGGATCTGA 57.102 40.909 10.88 0.00 0.00 3.27
4259 6340 4.872691 GGTAAGTCTGACATGTTGGATCTG 59.127 45.833 10.88 0.00 0.00 2.90
4260 6341 4.080863 GGGTAAGTCTGACATGTTGGATCT 60.081 45.833 10.88 0.07 0.00 2.75
4261 6342 4.080863 AGGGTAAGTCTGACATGTTGGATC 60.081 45.833 10.88 0.00 0.00 3.36
4262 6343 3.846588 AGGGTAAGTCTGACATGTTGGAT 59.153 43.478 10.88 0.00 0.00 3.41
4263 6344 3.248024 AGGGTAAGTCTGACATGTTGGA 58.752 45.455 10.88 0.00 0.00 3.53
4264 6345 3.703001 AGGGTAAGTCTGACATGTTGG 57.297 47.619 10.88 0.00 0.00 3.77
4265 6346 6.316390 GGATTTAGGGTAAGTCTGACATGTTG 59.684 42.308 10.88 0.00 0.00 3.33
4266 6347 6.215636 AGGATTTAGGGTAAGTCTGACATGTT 59.784 38.462 10.88 0.00 0.00 2.71
4267 6348 5.726793 AGGATTTAGGGTAAGTCTGACATGT 59.273 40.000 10.88 0.00 0.00 3.21
4268 6349 6.240549 AGGATTTAGGGTAAGTCTGACATG 57.759 41.667 10.88 0.00 0.00 3.21
4269 6350 6.443849 TGAAGGATTTAGGGTAAGTCTGACAT 59.556 38.462 10.88 0.00 0.00 3.06
4270 6351 5.783360 TGAAGGATTTAGGGTAAGTCTGACA 59.217 40.000 10.88 0.00 0.00 3.58
4271 6352 6.295719 TGAAGGATTTAGGGTAAGTCTGAC 57.704 41.667 0.00 0.00 0.00 3.51
4272 6353 6.945636 TTGAAGGATTTAGGGTAAGTCTGA 57.054 37.500 0.00 0.00 0.00 3.27
4273 6354 7.996098 TTTTGAAGGATTTAGGGTAAGTCTG 57.004 36.000 0.00 0.00 0.00 3.51
4274 6355 8.170730 ACATTTTGAAGGATTTAGGGTAAGTCT 58.829 33.333 0.00 0.00 0.00 3.24
4275 6356 8.349568 ACATTTTGAAGGATTTAGGGTAAGTC 57.650 34.615 0.00 0.00 0.00 3.01
4276 6357 9.462606 CTACATTTTGAAGGATTTAGGGTAAGT 57.537 33.333 0.00 0.00 0.00 2.24
4277 6358 9.681062 TCTACATTTTGAAGGATTTAGGGTAAG 57.319 33.333 0.00 0.00 0.00 2.34
4278 6359 9.681062 CTCTACATTTTGAAGGATTTAGGGTAA 57.319 33.333 0.00 0.00 0.00 2.85
4279 6360 7.773690 GCTCTACATTTTGAAGGATTTAGGGTA 59.226 37.037 0.00 0.00 0.00 3.69
4280 6361 6.603599 GCTCTACATTTTGAAGGATTTAGGGT 59.396 38.462 0.00 0.00 0.00 4.34
4281 6362 6.238484 CGCTCTACATTTTGAAGGATTTAGGG 60.238 42.308 0.00 0.00 0.00 3.53
4282 6363 6.719365 CGCTCTACATTTTGAAGGATTTAGG 58.281 40.000 0.00 0.00 0.00 2.69
4283 6364 6.183360 TGCGCTCTACATTTTGAAGGATTTAG 60.183 38.462 9.73 0.00 0.00 1.85
4284 6365 5.645929 TGCGCTCTACATTTTGAAGGATTTA 59.354 36.000 9.73 0.00 0.00 1.40
4285 6366 4.458989 TGCGCTCTACATTTTGAAGGATTT 59.541 37.500 9.73 0.00 0.00 2.17
4286 6367 4.009675 TGCGCTCTACATTTTGAAGGATT 58.990 39.130 9.73 0.00 0.00 3.01
4287 6368 3.609853 TGCGCTCTACATTTTGAAGGAT 58.390 40.909 9.73 0.00 0.00 3.24
4288 6369 3.052455 TGCGCTCTACATTTTGAAGGA 57.948 42.857 9.73 0.00 0.00 3.36
4289 6370 4.100529 CAATGCGCTCTACATTTTGAAGG 58.899 43.478 9.73 0.00 35.58 3.46
4290 6371 4.973396 TCAATGCGCTCTACATTTTGAAG 58.027 39.130 9.73 0.00 35.58 3.02
4291 6372 5.181056 TCTTCAATGCGCTCTACATTTTGAA 59.819 36.000 9.73 9.79 35.58 2.69
4292 6373 4.694982 TCTTCAATGCGCTCTACATTTTGA 59.305 37.500 9.73 2.60 35.58 2.69
4293 6374 4.973396 TCTTCAATGCGCTCTACATTTTG 58.027 39.130 9.73 0.21 35.58 2.44
4336 6417 7.821134 ATACCCAGCTCCTTGATAAATCTAT 57.179 36.000 0.00 0.00 0.00 1.98
4369 6450 0.608640 AGATGAGAAAAGGCGGTCGT 59.391 50.000 0.00 0.00 0.00 4.34
4374 6455 5.467063 GGGATAGTTTAGATGAGAAAAGGCG 59.533 44.000 0.00 0.00 0.00 5.52
4566 6653 8.723942 AGTAGGACATTTTTGTCATCAGATAC 57.276 34.615 8.25 0.00 40.38 2.24
4615 6702 6.980593 TCCACCAAATTTTCACATTCTACAG 58.019 36.000 0.00 0.00 0.00 2.74
4660 6747 5.061808 GCAATGATGTGCAATTTCTCAAGAC 59.938 40.000 0.00 0.00 44.29 3.01
4698 6785 2.154567 AGATTTGCTGGCATGGACAT 57.845 45.000 0.00 0.00 0.00 3.06
4766 6853 4.849813 TCCATCTGGAAATGTCATCAGT 57.150 40.909 0.00 0.00 42.18 3.41
4823 6910 0.179000 CTATCCTTGGGCAACGCTCT 59.821 55.000 0.00 0.00 37.60 4.09


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

AutoCloner maintained by Alex Coulton.