Multiple sequence alignment - TraesCS5B01G182800

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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 TraesCS5B01G182800 chr5B 100.000 7072 0 0 1 7072 332639002 332631931 0.000000e+00 13060.0
1 TraesCS5B01G182800 chr5B 80.233 86 15 2 263 347 576089011 576088927 5.920000e-06 63.9
2 TraesCS5B01G182800 chr5D 98.334 4742 69 8 1658 6390 291928073 291923333 0.000000e+00 8311.0
3 TraesCS5B01G182800 chr5D 97.639 720 9 3 761 1479 291928781 291928069 0.000000e+00 1229.0
4 TraesCS5B01G182800 chr5D 92.716 659 40 4 3 654 291929439 291928782 0.000000e+00 944.0
5 TraesCS5B01G182800 chr5D 93.586 343 16 3 6425 6761 291923341 291922999 2.280000e-139 507.0
6 TraesCS5B01G182800 chr5D 86.982 338 27 5 6744 7070 291921101 291920770 1.450000e-96 364.0
7 TraesCS5B01G182800 chr5A 95.612 1618 63 5 1904 3516 384353078 384351464 0.000000e+00 2588.0
8 TraesCS5B01G182800 chr5A 92.764 1755 92 17 5152 6877 384347236 384345488 0.000000e+00 2505.0
9 TraesCS5B01G182800 chr5A 93.818 1666 79 9 3514 5169 384349185 384347534 0.000000e+00 2484.0
10 TraesCS5B01G182800 chr5A 94.509 692 21 8 793 1479 384354214 384353535 0.000000e+00 1051.0
11 TraesCS5B01G182800 chr5A 88.296 581 58 4 1 572 384355367 384354788 0.000000e+00 688.0
12 TraesCS5B01G182800 chr5A 88.785 107 6 3 1658 1763 384353539 384353438 7.450000e-25 126.0
13 TraesCS5B01G182800 chrUn 100.000 391 0 0 2795 3185 479906590 479906980 0.000000e+00 723.0
14 TraesCS5B01G182800 chr2A 96.277 188 7 0 1476 1663 72943072 72943259 6.890000e-80 309.0
15 TraesCS5B01G182800 chr2A 90.598 117 9 2 652 766 12616497 12616613 3.420000e-33 154.0
16 TraesCS5B01G182800 chr7A 94.059 202 11 1 1471 1671 645312697 645312898 8.910000e-79 305.0
17 TraesCS5B01G182800 chr6B 94.845 194 9 1 1471 1663 213152567 213152374 1.150000e-77 302.0
18 TraesCS5B01G182800 chr6B 90.244 123 9 3 648 767 631968712 631968834 2.640000e-34 158.0
19 TraesCS5B01G182800 chr6B 88.000 125 11 4 649 769 281236261 281236385 2.060000e-30 145.0
20 TraesCS5B01G182800 chr3B 94.845 194 8 2 1475 1666 608423011 608423204 1.150000e-77 302.0
21 TraesCS5B01G182800 chr3B 94.792 192 7 2 1472 1663 702842064 702842252 5.360000e-76 296.0
22 TraesCS5B01G182800 chr3B 92.233 206 13 3 1474 1676 795486285 795486490 8.980000e-74 289.0
23 TraesCS5B01G182800 chr3B 89.167 120 11 2 649 766 34000162 34000281 1.590000e-31 148.0
24 TraesCS5B01G182800 chr4A 95.263 190 7 1 1474 1663 662620988 662621175 4.150000e-77 300.0
25 TraesCS5B01G182800 chr4B 94.792 192 9 1 1476 1666 531689864 531690055 1.490000e-76 298.0
26 TraesCS5B01G182800 chr2B 94.764 191 9 1 1477 1666 649145068 649145258 5.360000e-76 296.0
27 TraesCS5B01G182800 chr7D 92.308 117 7 2 652 766 433882953 433883069 1.580000e-36 165.0
28 TraesCS5B01G182800 chr7D 88.189 127 12 3 642 766 630954633 630954758 1.590000e-31 148.0
29 TraesCS5B01G182800 chr1D 91.667 120 8 2 652 769 401658583 401658464 1.580000e-36 165.0
30 TraesCS5B01G182800 chr2D 90.984 122 8 3 648 766 61804243 61804364 2.040000e-35 161.0
31 TraesCS5B01G182800 chr7B 89.831 118 10 2 651 766 668027968 668028085 4.420000e-32 150.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G182800 chr5B 332631931 332639002 7071 True 13060.000000 13060 100.000000 1 7072 1 chr5B.!!$R1 7071
1 TraesCS5B01G182800 chr5D 291920770 291929439 8669 True 2271.000000 8311 93.851400 3 7070 5 chr5D.!!$R1 7067
2 TraesCS5B01G182800 chr5A 384345488 384355367 9879 True 1573.666667 2588 92.297333 1 6877 6 chr5A.!!$R1 6876

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
758 1252 0.108041 GGCAAGTATTTCCGGACGGA 60.108 55.000 1.83 9.76 43.52 4.69 F
1569 2069 0.394938 ATACAACCCACGTCAGCACA 59.605 50.000 0.00 0.00 0.00 4.57 F
1570 2070 0.531090 TACAACCCACGTCAGCACAC 60.531 55.000 0.00 0.00 0.00 3.82 F
2242 2966 1.178276 ACTCACTCCGTGATCTCACC 58.822 55.000 4.81 0.00 41.94 4.02 F
2626 3350 1.371635 CGGGAAAACAAGCCTTGCG 60.372 57.895 3.88 0.00 0.00 4.85 F
3597 6604 3.030291 TGATTTGGCATGAACCCCATAC 58.970 45.455 0.00 0.00 33.31 2.39 F
4605 7613 1.074405 AGTTCCAAATGCTGCCTGAGA 59.926 47.619 0.00 0.00 0.00 3.27 F
5889 9241 1.515020 CAAGAGCCTCAGGACCTCG 59.485 63.158 0.00 0.00 0.00 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1981 2700 0.397941 TCTTGTCCCACTCCAGCTTG 59.602 55.000 0.00 0.0 0.00 4.01 R
2626 3350 3.119388 TGGCATCATTGAAAACTAGCTGC 60.119 43.478 0.00 0.0 0.00 5.25 R
3453 4177 4.670221 GCTCCAAAGAACTTACTTGATGCG 60.670 45.833 0.00 0.0 0.00 4.73 R
4202 7210 2.229784 GGACAAAGTGGAAGCATCAAGG 59.770 50.000 0.00 0.0 0.00 3.61 R
4605 7613 6.373774 TGAAGTGAACAAATGTTGCCAAAAAT 59.626 30.769 3.05 0.0 38.56 1.82 R
5479 8828 3.244911 CCCTGGAATAAGTGGTGTGTCTT 60.245 47.826 0.00 0.0 0.00 3.01 R
5977 9329 1.434555 TTTGATTACGTGGCCGTCAG 58.565 50.000 0.00 0.0 46.28 3.51 R
7015 12297 0.236449 CTGGTTTGCGTCCGGTTTAC 59.764 55.000 0.00 0.0 0.00 2.01 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
52 54 3.586100 AGGCAAAACGTTGAACACTTT 57.414 38.095 0.00 0.00 36.83 2.66
82 84 2.077821 GAGGTCTACCAGCTAGCCGC 62.078 65.000 12.13 0.00 38.89 6.53
105 107 2.017049 GCGTTGATCCCAAACTAGCAT 58.983 47.619 0.00 0.00 33.49 3.79
125 128 2.347490 GCTGGACGTGTGGATGGT 59.653 61.111 0.00 0.00 0.00 3.55
137 140 1.002773 GTGGATGGTCGGTTAAGGTGT 59.997 52.381 0.00 0.00 0.00 4.16
147 150 0.887387 GTTAAGGTGTGCAAGCCCGA 60.887 55.000 4.36 0.00 0.00 5.14
215 218 4.201679 AATCGGTCGATGCGGCGA 62.202 61.111 12.98 0.00 38.07 5.54
350 356 4.794439 CGATGGCAGGTGCGTCGA 62.794 66.667 18.14 0.00 45.88 4.20
405 411 1.060308 CGCAATGTTTACTCGGCCG 59.940 57.895 22.12 22.12 0.00 6.13
463 469 6.347483 GGCAGAGGAGTAAAACTTTTACTTCG 60.347 42.308 22.29 12.38 36.00 3.79
472 478 4.934075 AACTTTTACTTCGGTATTCGGC 57.066 40.909 0.00 0.00 39.77 5.54
485 496 1.614241 ATTCGGCTTCGGCTAGGTGT 61.614 55.000 0.00 0.00 41.44 4.16
517 528 6.004574 AGGAGTGAACTAAAAAGCCCTTAAG 58.995 40.000 0.00 0.00 0.00 1.85
650 1144 7.218228 TGCACAATGTGTAGATTTCTTCATT 57.782 32.000 15.36 0.00 35.75 2.57
656 1150 9.994432 CAATGTGTAGATTTCTTCATTTACTCC 57.006 33.333 0.00 0.00 0.00 3.85
657 1151 8.738645 ATGTGTAGATTTCTTCATTTACTCCC 57.261 34.615 0.00 0.00 0.00 4.30
658 1152 7.110155 TGTGTAGATTTCTTCATTTACTCCCC 58.890 38.462 0.00 0.00 0.00 4.81
659 1153 6.542735 GTGTAGATTTCTTCATTTACTCCCCC 59.457 42.308 0.00 0.00 0.00 5.40
660 1154 6.447084 TGTAGATTTCTTCATTTACTCCCCCT 59.553 38.462 0.00 0.00 0.00 4.79
661 1155 6.007485 AGATTTCTTCATTTACTCCCCCTC 57.993 41.667 0.00 0.00 0.00 4.30
662 1156 4.586306 TTTCTTCATTTACTCCCCCTCC 57.414 45.455 0.00 0.00 0.00 4.30
663 1157 2.488836 TCTTCATTTACTCCCCCTCCC 58.511 52.381 0.00 0.00 0.00 4.30
664 1158 1.141053 CTTCATTTACTCCCCCTCCCG 59.859 57.143 0.00 0.00 0.00 5.14
665 1159 0.340558 TCATTTACTCCCCCTCCCGA 59.659 55.000 0.00 0.00 0.00 5.14
666 1160 1.209621 CATTTACTCCCCCTCCCGAA 58.790 55.000 0.00 0.00 0.00 4.30
667 1161 1.562475 CATTTACTCCCCCTCCCGAAA 59.438 52.381 0.00 0.00 0.00 3.46
668 1162 1.975471 TTTACTCCCCCTCCCGAAAT 58.025 50.000 0.00 0.00 0.00 2.17
669 1163 2.873053 TTACTCCCCCTCCCGAAATA 57.127 50.000 0.00 0.00 0.00 1.40
670 1164 2.092598 TACTCCCCCTCCCGAAATAC 57.907 55.000 0.00 0.00 0.00 1.89
671 1165 0.342313 ACTCCCCCTCCCGAAATACT 59.658 55.000 0.00 0.00 0.00 2.12
672 1166 1.274242 ACTCCCCCTCCCGAAATACTT 60.274 52.381 0.00 0.00 0.00 2.24
673 1167 1.141053 CTCCCCCTCCCGAAATACTTG 59.859 57.143 0.00 0.00 0.00 3.16
674 1168 0.916809 CCCCCTCCCGAAATACTTGT 59.083 55.000 0.00 0.00 0.00 3.16
675 1169 1.134189 CCCCCTCCCGAAATACTTGTC 60.134 57.143 0.00 0.00 0.00 3.18
676 1170 1.472728 CCCCTCCCGAAATACTTGTCG 60.473 57.143 0.00 0.00 37.01 4.35
677 1171 1.287425 CCTCCCGAAATACTTGTCGC 58.713 55.000 0.00 0.00 35.93 5.19
678 1172 1.404986 CCTCCCGAAATACTTGTCGCA 60.405 52.381 0.00 0.00 35.93 5.10
679 1173 2.343101 CTCCCGAAATACTTGTCGCAA 58.657 47.619 0.00 0.00 35.93 4.85
680 1174 2.739913 CTCCCGAAATACTTGTCGCAAA 59.260 45.455 0.00 0.00 35.93 3.68
681 1175 3.139850 TCCCGAAATACTTGTCGCAAAA 58.860 40.909 0.00 0.00 35.93 2.44
682 1176 3.564644 TCCCGAAATACTTGTCGCAAAAA 59.435 39.130 0.00 0.00 35.93 1.94
683 1177 4.216687 TCCCGAAATACTTGTCGCAAAAAT 59.783 37.500 0.00 0.00 35.93 1.82
684 1178 4.323336 CCCGAAATACTTGTCGCAAAAATG 59.677 41.667 0.00 0.00 35.93 2.32
685 1179 4.323336 CCGAAATACTTGTCGCAAAAATGG 59.677 41.667 0.00 0.00 35.93 3.16
686 1180 5.150683 CGAAATACTTGTCGCAAAAATGGA 58.849 37.500 0.00 0.00 0.00 3.41
687 1181 5.799936 CGAAATACTTGTCGCAAAAATGGAT 59.200 36.000 0.00 0.00 0.00 3.41
688 1182 6.964370 CGAAATACTTGTCGCAAAAATGGATA 59.036 34.615 0.00 0.00 0.00 2.59
689 1183 7.483375 CGAAATACTTGTCGCAAAAATGGATAA 59.517 33.333 0.00 0.00 0.00 1.75
690 1184 9.134734 GAAATACTTGTCGCAAAAATGGATAAA 57.865 29.630 0.00 0.00 0.00 1.40
691 1185 9.482627 AAATACTTGTCGCAAAAATGGATAAAA 57.517 25.926 0.00 0.00 0.00 1.52
692 1186 9.482627 AATACTTGTCGCAAAAATGGATAAAAA 57.517 25.926 0.00 0.00 0.00 1.94
693 1187 7.961325 ACTTGTCGCAAAAATGGATAAAAAT 57.039 28.000 0.00 0.00 0.00 1.82
694 1188 7.795859 ACTTGTCGCAAAAATGGATAAAAATG 58.204 30.769 0.00 0.00 0.00 2.32
695 1189 7.655328 ACTTGTCGCAAAAATGGATAAAAATGA 59.345 29.630 0.00 0.00 0.00 2.57
696 1190 7.953158 TGTCGCAAAAATGGATAAAAATGAA 57.047 28.000 0.00 0.00 0.00 2.57
697 1191 8.545229 TGTCGCAAAAATGGATAAAAATGAAT 57.455 26.923 0.00 0.00 0.00 2.57
698 1192 8.441608 TGTCGCAAAAATGGATAAAAATGAATG 58.558 29.630 0.00 0.00 0.00 2.67
699 1193 7.426169 GTCGCAAAAATGGATAAAAATGAATGC 59.574 33.333 0.00 0.00 0.00 3.56
700 1194 7.118825 TCGCAAAAATGGATAAAAATGAATGCA 59.881 29.630 0.00 0.00 0.00 3.96
701 1195 7.911205 CGCAAAAATGGATAAAAATGAATGCAT 59.089 29.630 0.00 0.00 35.91 3.96
702 1196 9.228636 GCAAAAATGGATAAAAATGAATGCATC 57.771 29.630 0.00 0.00 33.60 3.91
719 1213 9.982291 TGAATGCATCTAAAACTAAAATACGAC 57.018 29.630 0.00 0.00 0.00 4.34
738 1232 8.967664 ATACGACTAGATACATCTATTCCTCC 57.032 38.462 0.00 0.00 38.60 4.30
739 1233 5.875910 ACGACTAGATACATCTATTCCTCCG 59.124 44.000 0.00 3.77 38.60 4.63
740 1234 5.294799 CGACTAGATACATCTATTCCTCCGG 59.705 48.000 0.00 0.00 38.60 5.14
741 1235 4.951094 ACTAGATACATCTATTCCTCCGGC 59.049 45.833 0.00 0.00 38.60 6.13
742 1236 3.779444 AGATACATCTATTCCTCCGGCA 58.221 45.455 0.00 0.00 34.85 5.69
743 1237 4.160329 AGATACATCTATTCCTCCGGCAA 58.840 43.478 0.00 0.00 34.85 4.52
744 1238 2.918712 ACATCTATTCCTCCGGCAAG 57.081 50.000 0.00 0.00 0.00 4.01
745 1239 2.119495 ACATCTATTCCTCCGGCAAGT 58.881 47.619 0.00 0.00 0.00 3.16
746 1240 3.305720 ACATCTATTCCTCCGGCAAGTA 58.694 45.455 0.00 0.00 0.00 2.24
747 1241 3.904339 ACATCTATTCCTCCGGCAAGTAT 59.096 43.478 0.00 0.00 0.00 2.12
748 1242 4.348168 ACATCTATTCCTCCGGCAAGTATT 59.652 41.667 0.00 0.00 0.00 1.89
749 1243 5.163195 ACATCTATTCCTCCGGCAAGTATTT 60.163 40.000 0.00 0.00 0.00 1.40
750 1244 4.957296 TCTATTCCTCCGGCAAGTATTTC 58.043 43.478 0.00 0.00 0.00 2.17
751 1245 2.413310 TTCCTCCGGCAAGTATTTCC 57.587 50.000 0.00 0.00 0.00 3.13
752 1246 0.177141 TCCTCCGGCAAGTATTTCCG 59.823 55.000 0.00 0.00 42.58 4.30
756 1250 2.003672 CGGCAAGTATTTCCGGACG 58.996 57.895 1.83 0.00 39.52 4.79
757 1251 1.426041 CGGCAAGTATTTCCGGACGG 61.426 60.000 1.83 3.96 39.52 4.79
758 1252 0.108041 GGCAAGTATTTCCGGACGGA 60.108 55.000 1.83 9.76 43.52 4.69
988 1487 1.725169 TTGGTCCACCCCCTTCCTTG 61.725 60.000 0.00 0.00 34.29 3.61
989 1488 2.160853 GGTCCACCCCCTTCCTTGT 61.161 63.158 0.00 0.00 0.00 3.16
990 1489 1.379146 GTCCACCCCCTTCCTTGTC 59.621 63.158 0.00 0.00 0.00 3.18
991 1490 1.850755 TCCACCCCCTTCCTTGTCC 60.851 63.158 0.00 0.00 0.00 4.02
992 1491 1.852626 CCACCCCCTTCCTTGTCCT 60.853 63.158 0.00 0.00 0.00 3.85
993 1492 1.435346 CCACCCCCTTCCTTGTCCTT 61.435 60.000 0.00 0.00 0.00 3.36
998 1497 1.068121 CCCTTCCTTGTCCTTCCAGT 58.932 55.000 0.00 0.00 0.00 4.00
1200 1699 2.994995 TTCGGAAGCGAGAGGGCA 60.995 61.111 0.00 0.00 34.64 5.36
1349 1848 7.981102 AGTTTGGTCTGAGTAAATAGTTTCC 57.019 36.000 0.00 0.00 0.00 3.13
1409 1909 4.714802 TCTTCCCAGGAGTTATGATTTCGA 59.285 41.667 0.00 0.00 0.00 3.71
1458 1958 8.950210 CAACTCACTAACATCTTGTTATCCATT 58.050 33.333 0.92 0.00 41.45 3.16
1541 2041 8.424274 AATTTGGTCTCATTCACTTTGAAAAC 57.576 30.769 0.00 0.00 40.12 2.43
1542 2042 6.522625 TTGGTCTCATTCACTTTGAAAACA 57.477 33.333 0.00 0.00 40.12 2.83
1543 2043 6.522625 TGGTCTCATTCACTTTGAAAACAA 57.477 33.333 0.00 0.00 40.12 2.83
1544 2044 6.563422 TGGTCTCATTCACTTTGAAAACAAG 58.437 36.000 0.00 0.00 40.12 3.16
1545 2045 6.376864 TGGTCTCATTCACTTTGAAAACAAGA 59.623 34.615 0.00 0.00 40.12 3.02
1546 2046 6.914757 GGTCTCATTCACTTTGAAAACAAGAG 59.085 38.462 0.00 0.00 40.12 2.85
1547 2047 6.416161 GTCTCATTCACTTTGAAAACAAGAGC 59.584 38.462 0.00 0.00 40.12 4.09
1548 2048 6.095300 TCTCATTCACTTTGAAAACAAGAGCA 59.905 34.615 0.00 0.00 40.12 4.26
1549 2049 6.808829 TCATTCACTTTGAAAACAAGAGCAT 58.191 32.000 0.00 0.00 40.12 3.79
1550 2050 7.939782 TCATTCACTTTGAAAACAAGAGCATA 58.060 30.769 0.00 0.00 40.12 3.14
1551 2051 8.579006 TCATTCACTTTGAAAACAAGAGCATAT 58.421 29.630 0.00 0.00 40.12 1.78
1552 2052 9.844790 CATTCACTTTGAAAACAAGAGCATATA 57.155 29.630 0.00 0.00 40.12 0.86
1553 2053 9.846248 ATTCACTTTGAAAACAAGAGCATATAC 57.154 29.630 0.00 0.00 40.12 1.47
1554 2054 8.389779 TCACTTTGAAAACAAGAGCATATACA 57.610 30.769 0.00 0.00 0.00 2.29
1555 2055 8.845227 TCACTTTGAAAACAAGAGCATATACAA 58.155 29.630 0.00 0.00 0.00 2.41
1556 2056 8.905702 CACTTTGAAAACAAGAGCATATACAAC 58.094 33.333 0.00 0.00 0.00 3.32
1557 2057 8.082242 ACTTTGAAAACAAGAGCATATACAACC 58.918 33.333 0.00 0.00 0.00 3.77
1558 2058 6.509418 TGAAAACAAGAGCATATACAACCC 57.491 37.500 0.00 0.00 0.00 4.11
1559 2059 6.007076 TGAAAACAAGAGCATATACAACCCA 58.993 36.000 0.00 0.00 0.00 4.51
1560 2060 5.897377 AAACAAGAGCATATACAACCCAC 57.103 39.130 0.00 0.00 0.00 4.61
1561 2061 3.531538 ACAAGAGCATATACAACCCACG 58.468 45.455 0.00 0.00 0.00 4.94
1562 2062 3.055385 ACAAGAGCATATACAACCCACGT 60.055 43.478 0.00 0.00 0.00 4.49
1563 2063 3.454371 AGAGCATATACAACCCACGTC 57.546 47.619 0.00 0.00 0.00 4.34
1564 2064 2.764010 AGAGCATATACAACCCACGTCA 59.236 45.455 0.00 0.00 0.00 4.35
1565 2065 3.123804 GAGCATATACAACCCACGTCAG 58.876 50.000 0.00 0.00 0.00 3.51
1566 2066 1.597663 GCATATACAACCCACGTCAGC 59.402 52.381 0.00 0.00 0.00 4.26
1567 2067 2.899976 CATATACAACCCACGTCAGCA 58.100 47.619 0.00 0.00 0.00 4.41
1568 2068 2.373540 TATACAACCCACGTCAGCAC 57.626 50.000 0.00 0.00 0.00 4.40
1569 2069 0.394938 ATACAACCCACGTCAGCACA 59.605 50.000 0.00 0.00 0.00 4.57
1570 2070 0.531090 TACAACCCACGTCAGCACAC 60.531 55.000 0.00 0.00 0.00 3.82
1571 2071 1.817520 CAACCCACGTCAGCACACA 60.818 57.895 0.00 0.00 0.00 3.72
1572 2072 1.817941 AACCCACGTCAGCACACAC 60.818 57.895 0.00 0.00 0.00 3.82
1573 2073 3.337889 CCCACGTCAGCACACACG 61.338 66.667 0.00 0.00 41.90 4.49
1574 2074 4.000557 CCACGTCAGCACACACGC 62.001 66.667 0.00 0.00 39.73 5.34
1575 2075 3.261216 CACGTCAGCACACACGCA 61.261 61.111 0.00 0.00 39.73 5.24
1576 2076 2.280119 ACGTCAGCACACACGCAT 60.280 55.556 0.00 0.00 39.73 4.73
1577 2077 2.310233 ACGTCAGCACACACGCATC 61.310 57.895 0.00 0.00 39.73 3.91
1578 2078 2.023771 CGTCAGCACACACGCATCT 61.024 57.895 0.00 0.00 0.00 2.90
1579 2079 1.560004 CGTCAGCACACACGCATCTT 61.560 55.000 0.00 0.00 0.00 2.40
1580 2080 1.428448 GTCAGCACACACGCATCTTA 58.572 50.000 0.00 0.00 0.00 2.10
1581 2081 2.002586 GTCAGCACACACGCATCTTAT 58.997 47.619 0.00 0.00 0.00 1.73
1582 2082 3.186909 GTCAGCACACACGCATCTTATA 58.813 45.455 0.00 0.00 0.00 0.98
1583 2083 3.243877 GTCAGCACACACGCATCTTATAG 59.756 47.826 0.00 0.00 0.00 1.31
1584 2084 2.033407 CAGCACACACGCATCTTATAGC 60.033 50.000 0.00 0.00 0.00 2.97
1585 2085 1.933181 GCACACACGCATCTTATAGCA 59.067 47.619 0.00 0.00 0.00 3.49
1586 2086 2.545526 GCACACACGCATCTTATAGCAT 59.454 45.455 0.00 0.00 0.00 3.79
1587 2087 3.363378 GCACACACGCATCTTATAGCATC 60.363 47.826 0.00 0.00 0.00 3.91
1588 2088 3.803778 CACACACGCATCTTATAGCATCA 59.196 43.478 0.00 0.00 0.00 3.07
1589 2089 4.450080 CACACACGCATCTTATAGCATCAT 59.550 41.667 0.00 0.00 0.00 2.45
1590 2090 5.634859 CACACACGCATCTTATAGCATCATA 59.365 40.000 0.00 0.00 0.00 2.15
1591 2091 6.312180 CACACACGCATCTTATAGCATCATAT 59.688 38.462 0.00 0.00 0.00 1.78
1592 2092 6.533012 ACACACGCATCTTATAGCATCATATC 59.467 38.462 0.00 0.00 0.00 1.63
1593 2093 6.019237 CACACGCATCTTATAGCATCATATCC 60.019 42.308 0.00 0.00 0.00 2.59
1594 2094 6.044682 CACGCATCTTATAGCATCATATCCA 58.955 40.000 0.00 0.00 0.00 3.41
1595 2095 6.536224 CACGCATCTTATAGCATCATATCCAA 59.464 38.462 0.00 0.00 0.00 3.53
1596 2096 7.226128 CACGCATCTTATAGCATCATATCCAAT 59.774 37.037 0.00 0.00 0.00 3.16
1597 2097 7.226128 ACGCATCTTATAGCATCATATCCAATG 59.774 37.037 0.00 0.00 0.00 2.82
1598 2098 7.307811 CGCATCTTATAGCATCATATCCAATGG 60.308 40.741 0.00 0.00 0.00 3.16
1599 2099 7.521748 GCATCTTATAGCATCATATCCAATGGC 60.522 40.741 0.00 0.00 0.00 4.40
1600 2100 7.204243 TCTTATAGCATCATATCCAATGGCT 57.796 36.000 0.00 0.00 0.00 4.75
1601 2101 8.322905 TCTTATAGCATCATATCCAATGGCTA 57.677 34.615 0.00 0.00 0.00 3.93
1602 2102 8.942033 TCTTATAGCATCATATCCAATGGCTAT 58.058 33.333 0.00 0.00 32.32 2.97
1606 2106 9.925545 ATAGCATCATATCCAATGGCTATAAAA 57.074 29.630 0.00 0.00 0.00 1.52
1607 2107 8.289939 AGCATCATATCCAATGGCTATAAAAG 57.710 34.615 0.00 0.00 0.00 2.27
1608 2108 7.341256 AGCATCATATCCAATGGCTATAAAAGG 59.659 37.037 0.00 0.00 0.00 3.11
1609 2109 7.123247 GCATCATATCCAATGGCTATAAAAGGT 59.877 37.037 0.00 0.00 0.00 3.50
1610 2110 8.464404 CATCATATCCAATGGCTATAAAAGGTG 58.536 37.037 0.00 0.00 0.00 4.00
1611 2111 7.754624 TCATATCCAATGGCTATAAAAGGTGA 58.245 34.615 0.00 0.00 0.00 4.02
1612 2112 8.224025 TCATATCCAATGGCTATAAAAGGTGAA 58.776 33.333 0.00 0.00 0.00 3.18
1613 2113 9.028284 CATATCCAATGGCTATAAAAGGTGAAT 57.972 33.333 0.00 0.00 0.00 2.57
1614 2114 6.713762 TCCAATGGCTATAAAAGGTGAATG 57.286 37.500 0.00 0.00 0.00 2.67
1615 2115 6.430864 TCCAATGGCTATAAAAGGTGAATGA 58.569 36.000 0.00 0.00 0.00 2.57
1616 2116 6.547141 TCCAATGGCTATAAAAGGTGAATGAG 59.453 38.462 0.00 0.00 0.00 2.90
1617 2117 6.547141 CCAATGGCTATAAAAGGTGAATGAGA 59.453 38.462 0.00 0.00 0.00 3.27
1618 2118 7.420800 CAATGGCTATAAAAGGTGAATGAGAC 58.579 38.462 0.00 0.00 0.00 3.36
1619 2119 5.437060 TGGCTATAAAAGGTGAATGAGACC 58.563 41.667 0.00 0.00 0.00 3.85
1620 2120 5.045213 TGGCTATAAAAGGTGAATGAGACCA 60.045 40.000 0.00 0.00 35.76 4.02
1621 2121 5.885912 GGCTATAAAAGGTGAATGAGACCAA 59.114 40.000 0.00 0.00 35.76 3.67
1622 2122 6.377146 GGCTATAAAAGGTGAATGAGACCAAA 59.623 38.462 0.00 0.00 35.76 3.28
1623 2123 7.068716 GGCTATAAAAGGTGAATGAGACCAAAT 59.931 37.037 0.00 0.00 35.76 2.32
1624 2124 8.470002 GCTATAAAAGGTGAATGAGACCAAATT 58.530 33.333 0.00 0.00 35.76 1.82
1630 2130 9.927081 AAAGGTGAATGAGACCAAATTATATCT 57.073 29.630 0.00 0.00 35.76 1.98
1631 2131 9.566432 AAGGTGAATGAGACCAAATTATATCTC 57.434 33.333 0.00 6.03 38.46 2.75
1958 2677 9.138062 GTGAATGTATAGAGCTCTCAACATATG 57.862 37.037 29.84 0.00 32.90 1.78
1981 2700 2.028748 ACCACCAAAATCTTGAGCATGC 60.029 45.455 10.51 10.51 34.14 4.06
2242 2966 1.178276 ACTCACTCCGTGATCTCACC 58.822 55.000 4.81 0.00 41.94 4.02
2567 3291 6.127925 GGACATGATAATGCAGAAAAGTGTCA 60.128 38.462 17.85 4.77 35.27 3.58
2626 3350 1.371635 CGGGAAAACAAGCCTTGCG 60.372 57.895 3.88 0.00 0.00 4.85
3185 3909 5.654497 CCAAGGATAAAGAAATGTGGAAGC 58.346 41.667 0.00 0.00 0.00 3.86
3388 4112 3.866651 CAGACATGGAACCTTACCTCTG 58.133 50.000 0.00 0.00 0.00 3.35
3597 6604 3.030291 TGATTTGGCATGAACCCCATAC 58.970 45.455 0.00 0.00 33.31 2.39
3734 6742 9.567848 CTAAAATCAACTAAAATGTAACCGCAT 57.432 29.630 0.00 0.00 0.00 4.73
4605 7613 1.074405 AGTTCCAAATGCTGCCTGAGA 59.926 47.619 0.00 0.00 0.00 3.27
4844 7852 6.875726 GCCTTAAAAAGCTCCAAAATCTTGAT 59.124 34.615 0.00 0.00 34.14 2.57
5012 8020 9.454859 GGAGATCTGAAAGGAAAGAAGAAATTA 57.545 33.333 0.00 0.00 0.00 1.40
5207 8536 4.752661 ATGCAAATTTGAACCATGTTGC 57.247 36.364 22.31 3.42 41.28 4.17
5277 8626 7.784037 TGTTAGTTGTACTCAAACTGGAACTA 58.216 34.615 7.21 1.14 35.20 2.24
5417 8766 5.441500 TGGGGCAGTCAATTATTTTCGATA 58.558 37.500 0.00 0.00 0.00 2.92
5467 8816 7.094205 CCAATGTCCTTATTTCTTGTTGTAGCT 60.094 37.037 0.00 0.00 0.00 3.32
5479 8828 8.445275 TTCTTGTTGTAGCTAAATGAAACTGA 57.555 30.769 0.00 0.00 0.00 3.41
5841 9193 4.790878 TGTATGTGTCTACGTGTGAGTTC 58.209 43.478 0.00 0.00 0.00 3.01
5843 9195 3.620929 TGTGTCTACGTGTGAGTTCTC 57.379 47.619 0.00 0.00 0.00 2.87
5889 9241 1.515020 CAAGAGCCTCAGGACCTCG 59.485 63.158 0.00 0.00 0.00 4.63
5899 9251 3.190874 CTCAGGACCTCGTAAAAGATGC 58.809 50.000 0.00 0.00 0.00 3.91
5900 9252 2.832129 TCAGGACCTCGTAAAAGATGCT 59.168 45.455 0.00 0.00 0.00 3.79
5977 9329 2.879462 CACCGTAGAAGGCGACGC 60.879 66.667 12.43 12.43 41.03 5.19
6203 9555 4.162320 TGGTTAGGAGAGATTGTTGCCTAG 59.838 45.833 0.00 0.00 33.17 3.02
6213 9565 4.341235 AGATTGTTGCCTAGCTACGTCATA 59.659 41.667 0.00 0.00 37.12 2.15
6399 9751 8.870075 ACCTCTATTTTGATTTTTAGCAGACT 57.130 30.769 0.00 0.00 0.00 3.24
6466 9818 6.238869 GCTGAGTTCTCCTTCAAAACTTGATT 60.239 38.462 0.00 0.00 39.84 2.57
6504 9856 5.482878 ACTTGGCATTGATCTCTTTCCAAAT 59.517 36.000 0.00 0.00 32.50 2.32
6505 9857 5.333299 TGGCATTGATCTCTTTCCAAATG 57.667 39.130 0.00 0.00 0.00 2.32
6615 9967 9.498176 CTTGTAAGTACTACCTTTGTACCAAAT 57.502 33.333 0.00 0.00 40.61 2.32
6654 10006 8.426569 TGTAGGCTATATTTTAATACGGAGGT 57.573 34.615 0.00 0.00 0.00 3.85
6846 12118 4.979197 CGGAACATCTAGCTAAGCTAAGTG 59.021 45.833 0.00 0.00 40.82 3.16
6877 12149 2.227194 ACCGATTTCACAGACCCAAAC 58.773 47.619 0.00 0.00 0.00 2.93
6878 12150 2.226330 CCGATTTCACAGACCCAAACA 58.774 47.619 0.00 0.00 0.00 2.83
6880 12152 2.616376 CGATTTCACAGACCCAAACACA 59.384 45.455 0.00 0.00 0.00 3.72
6882 12154 4.610945 GATTTCACAGACCCAAACACAAG 58.389 43.478 0.00 0.00 0.00 3.16
6883 12155 2.799126 TCACAGACCCAAACACAAGT 57.201 45.000 0.00 0.00 0.00 3.16
6884 12156 2.364632 TCACAGACCCAAACACAAGTG 58.635 47.619 0.00 0.00 0.00 3.16
6885 12157 1.102978 ACAGACCCAAACACAAGTGC 58.897 50.000 0.00 0.00 0.00 4.40
6886 12158 0.385390 CAGACCCAAACACAAGTGCC 59.615 55.000 0.00 0.00 0.00 5.01
6896 12178 0.609131 CACAAGTGCCCCCTAAGGTG 60.609 60.000 0.00 0.00 0.00 4.00
6899 12181 4.796495 GTGCCCCCTAAGGTGGCG 62.796 72.222 11.05 0.00 46.86 5.69
6929 12211 4.005650 GCATCTCCAACACAGATTCTCAA 58.994 43.478 0.00 0.00 0.00 3.02
6934 12216 4.531854 TCCAACACAGATTCTCAAAACCA 58.468 39.130 0.00 0.00 0.00 3.67
6942 12224 4.458295 CAGATTCTCAAAACCAGATGCAGT 59.542 41.667 0.00 0.00 0.00 4.40
6953 12235 3.054139 ACCAGATGCAGTTGTATGGACAT 60.054 43.478 5.72 0.00 34.86 3.06
6960 12242 4.155826 TGCAGTTGTATGGACATAGTTTGC 59.844 41.667 0.00 2.65 34.86 3.68
7005 12287 4.331356 CGAACGAGTCCGGTTGTT 57.669 55.556 0.00 0.00 40.78 2.83
7009 12291 0.102844 AACGAGTCCGGTTGTTCGAA 59.897 50.000 20.22 0.00 40.78 3.71
7014 12296 1.346722 AGTCCGGTTGTTCGAATTCCT 59.653 47.619 0.00 0.00 0.00 3.36
7015 12297 1.463444 GTCCGGTTGTTCGAATTCCTG 59.537 52.381 0.00 1.55 0.00 3.86
7022 12304 4.460505 GTTGTTCGAATTCCTGTAAACCG 58.539 43.478 0.00 0.00 0.00 4.44
7034 12316 0.236449 GTAAACCGGACGCAAACCAG 59.764 55.000 9.46 0.00 0.00 4.00
7038 12320 4.323477 CGGACGCAAACCAGGGGA 62.323 66.667 0.00 0.00 0.00 4.81
7045 12327 1.398958 GCAAACCAGGGGACTTTGCA 61.399 55.000 16.71 0.00 46.23 4.08
7048 12330 0.178990 AACCAGGGGACTTTGCAGAC 60.179 55.000 0.00 0.00 40.21 3.51
7053 12335 0.951040 GGGGACTTTGCAGACGTCTG 60.951 60.000 35.80 35.80 46.40 3.51
7054 12336 0.033504 GGGACTTTGCAGACGTCTGA 59.966 55.000 42.03 26.44 46.59 3.27
7070 12352 0.095245 CTGAACTGCCGCAACATACG 59.905 55.000 0.00 0.00 0.00 3.06
7071 12353 0.601576 TGAACTGCCGCAACATACGT 60.602 50.000 0.00 0.00 0.00 3.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 54 1.273098 GGTAGACCTCCACCTCCTTGA 60.273 57.143 0.00 0.00 0.00 3.02
58 60 1.008403 TAGCTGGTAGACCTCCACCT 58.992 55.000 0.00 0.00 35.73 4.00
82 84 0.391927 TAGTTTGGGATCAACGCCGG 60.392 55.000 0.00 0.00 31.78 6.13
92 94 3.903783 GCGCATGCTAGTTTGGGA 58.096 55.556 17.13 0.00 38.39 4.37
105 107 4.002506 ATCCACACGTCCAGCGCA 62.003 61.111 11.47 0.00 46.11 6.09
110 113 2.654289 CGACCATCCACACGTCCA 59.346 61.111 0.00 0.00 0.00 4.02
113 116 0.680618 TTAACCGACCATCCACACGT 59.319 50.000 0.00 0.00 0.00 4.49
125 128 0.887387 GGCTTGCACACCTTAACCGA 60.887 55.000 0.00 0.00 0.00 4.69
137 140 1.820906 GCATCTCATCGGGCTTGCA 60.821 57.895 0.00 0.00 0.00 4.08
215 218 2.481449 GGATGAGCTGAAATACCGTCGT 60.481 50.000 0.00 0.00 0.00 4.34
350 356 1.681327 ACCCCTACTGCATCGACGT 60.681 57.895 0.00 0.00 0.00 4.34
405 411 1.692411 AAAACACTTGACCTCCAGGC 58.308 50.000 0.00 0.00 39.32 4.85
463 469 0.319641 CCTAGCCGAAGCCGAATACC 60.320 60.000 0.00 0.00 41.25 2.73
472 478 2.617308 TCTAATCGACACCTAGCCGAAG 59.383 50.000 0.00 0.00 35.87 3.79
485 496 6.812160 GCTTTTTAGTTCACTCCTCTAATCGA 59.188 38.462 0.00 0.00 0.00 3.59
517 528 3.956744 ACTCAAGTCTAAATTGGGGCTC 58.043 45.455 0.00 0.00 32.14 4.70
624 1118 7.218228 TGAAGAAATCTACACATTGTGCAAT 57.782 32.000 16.62 5.19 36.98 3.56
650 1144 2.022722 AGTATTTCGGGAGGGGGAGTAA 60.023 50.000 0.00 0.00 0.00 2.24
654 1148 1.209621 CAAGTATTTCGGGAGGGGGA 58.790 55.000 0.00 0.00 0.00 4.81
655 1149 0.916809 ACAAGTATTTCGGGAGGGGG 59.083 55.000 0.00 0.00 0.00 5.40
656 1150 1.472728 CGACAAGTATTTCGGGAGGGG 60.473 57.143 0.00 0.00 0.00 4.79
657 1151 1.935933 CGACAAGTATTTCGGGAGGG 58.064 55.000 0.00 0.00 0.00 4.30
658 1152 1.287425 GCGACAAGTATTTCGGGAGG 58.713 55.000 0.00 0.00 35.73 4.30
659 1153 2.004583 TGCGACAAGTATTTCGGGAG 57.995 50.000 0.00 0.00 35.73 4.30
660 1154 2.459060 TTGCGACAAGTATTTCGGGA 57.541 45.000 0.00 0.00 35.73 5.14
661 1155 3.546002 TTTTGCGACAAGTATTTCGGG 57.454 42.857 0.00 0.00 35.73 5.14
662 1156 4.323336 CCATTTTTGCGACAAGTATTTCGG 59.677 41.667 0.00 0.00 35.73 4.30
663 1157 5.150683 TCCATTTTTGCGACAAGTATTTCG 58.849 37.500 0.00 0.00 38.31 3.46
664 1158 8.682128 TTATCCATTTTTGCGACAAGTATTTC 57.318 30.769 0.00 0.00 0.00 2.17
665 1159 9.482627 TTTTATCCATTTTTGCGACAAGTATTT 57.517 25.926 0.00 0.00 0.00 1.40
666 1160 9.482627 TTTTTATCCATTTTTGCGACAAGTATT 57.517 25.926 0.00 0.00 0.00 1.89
667 1161 9.651913 ATTTTTATCCATTTTTGCGACAAGTAT 57.348 25.926 0.00 0.00 0.00 2.12
668 1162 8.920665 CATTTTTATCCATTTTTGCGACAAGTA 58.079 29.630 0.00 0.00 0.00 2.24
669 1163 7.655328 TCATTTTTATCCATTTTTGCGACAAGT 59.345 29.630 0.00 0.00 0.00 3.16
670 1164 8.016497 TCATTTTTATCCATTTTTGCGACAAG 57.984 30.769 0.00 0.00 0.00 3.16
671 1165 7.953158 TCATTTTTATCCATTTTTGCGACAA 57.047 28.000 0.00 0.00 0.00 3.18
672 1166 7.953158 TTCATTTTTATCCATTTTTGCGACA 57.047 28.000 0.00 0.00 0.00 4.35
673 1167 7.426169 GCATTCATTTTTATCCATTTTTGCGAC 59.574 33.333 0.00 0.00 0.00 5.19
674 1168 7.118825 TGCATTCATTTTTATCCATTTTTGCGA 59.881 29.630 0.00 0.00 0.00 5.10
675 1169 7.242079 TGCATTCATTTTTATCCATTTTTGCG 58.758 30.769 0.00 0.00 0.00 4.85
676 1170 9.228636 GATGCATTCATTTTTATCCATTTTTGC 57.771 29.630 0.00 0.00 31.96 3.68
693 1187 9.982291 GTCGTATTTTAGTTTTAGATGCATTCA 57.018 29.630 0.00 0.00 0.00 2.57
738 1232 1.426041 CCGTCCGGAAATACTTGCCG 61.426 60.000 5.23 1.25 44.42 5.69
739 1233 0.108041 TCCGTCCGGAAATACTTGCC 60.108 55.000 5.23 0.00 42.05 4.52
740 1234 3.446507 TCCGTCCGGAAATACTTGC 57.553 52.632 5.23 0.00 42.05 4.01
749 1243 2.374504 AGATATACTCCTTCCGTCCGGA 59.625 50.000 0.00 0.00 43.52 5.14
750 1244 2.488545 CAGATATACTCCTTCCGTCCGG 59.511 54.545 0.00 0.00 0.00 5.14
751 1245 2.095161 GCAGATATACTCCTTCCGTCCG 60.095 54.545 0.00 0.00 0.00 4.79
752 1246 2.095161 CGCAGATATACTCCTTCCGTCC 60.095 54.545 0.00 0.00 0.00 4.79
753 1247 2.553172 ACGCAGATATACTCCTTCCGTC 59.447 50.000 0.00 0.00 0.00 4.79
754 1248 2.584236 ACGCAGATATACTCCTTCCGT 58.416 47.619 0.00 0.00 0.00 4.69
755 1249 3.644884 AACGCAGATATACTCCTTCCG 57.355 47.619 0.00 0.00 0.00 4.30
756 1250 4.694339 ACAAACGCAGATATACTCCTTCC 58.306 43.478 0.00 0.00 0.00 3.46
757 1251 5.398711 CGTACAAACGCAGATATACTCCTTC 59.601 44.000 0.00 0.00 43.12 3.46
758 1252 5.279384 CGTACAAACGCAGATATACTCCTT 58.721 41.667 0.00 0.00 43.12 3.36
759 1253 4.856664 CGTACAAACGCAGATATACTCCT 58.143 43.478 0.00 0.00 43.12 3.69
791 1285 5.205056 TGTAGAACCAACCCTTCAAATGTT 58.795 37.500 0.00 0.00 0.00 2.71
988 1487 1.073923 ACCAACCATGACTGGAAGGAC 59.926 52.381 17.19 0.00 46.37 3.85
989 1488 1.444933 ACCAACCATGACTGGAAGGA 58.555 50.000 17.19 0.00 46.37 3.36
990 1489 2.711542 GTACCAACCATGACTGGAAGG 58.288 52.381 17.19 2.56 46.37 3.46
991 1490 2.346803 CGTACCAACCATGACTGGAAG 58.653 52.381 17.19 6.46 46.37 3.46
992 1491 1.002659 CCGTACCAACCATGACTGGAA 59.997 52.381 17.19 0.00 46.37 3.53
993 1492 0.611200 CCGTACCAACCATGACTGGA 59.389 55.000 17.19 1.96 46.37 3.86
998 1497 1.134521 GCATCTCCGTACCAACCATGA 60.135 52.381 0.00 0.00 0.00 3.07
1200 1699 2.034687 AGCCAGTGCCGCAGATTT 59.965 55.556 0.00 0.00 38.69 2.17
1349 1848 4.115516 CAGATCTGGTCCAAATCGTACAG 58.884 47.826 15.38 0.00 0.00 2.74
1409 1909 6.219473 TGAAATTATTGCACAAATTCGTGGT 58.781 32.000 0.00 0.00 37.37 4.16
1420 1920 8.970691 ATGTTAGTGAGTTGAAATTATTGCAC 57.029 30.769 0.00 0.00 0.00 4.57
1479 1979 7.420029 AGATGAGTTCTAGGTACTCCCTTAAA 58.580 38.462 17.72 4.58 42.73 1.52
1480 1980 6.982899 AGATGAGTTCTAGGTACTCCCTTAA 58.017 40.000 17.72 5.09 42.73 1.85
1481 1981 6.593759 AGATGAGTTCTAGGTACTCCCTTA 57.406 41.667 17.72 5.36 42.73 2.69
1482 1982 5.475398 AGATGAGTTCTAGGTACTCCCTT 57.525 43.478 17.72 7.62 42.73 3.95
1483 1983 7.475654 CATCTAGATGAGTTCTAGGTACTCCCT 60.476 44.444 25.78 16.34 44.99 4.20
1484 1984 6.657541 CATCTAGATGAGTTCTAGGTACTCCC 59.342 46.154 25.78 12.05 44.99 4.30
1485 1985 7.455058 TCATCTAGATGAGTTCTAGGTACTCC 58.545 42.308 27.93 8.04 44.99 3.85
1515 2015 9.528018 GTTTTCAAAGTGAATGAGACCAAATTA 57.472 29.630 0.00 0.00 36.11 1.40
1516 2016 8.040132 TGTTTTCAAAGTGAATGAGACCAAATT 58.960 29.630 0.00 0.00 36.11 1.82
1517 2017 7.555087 TGTTTTCAAAGTGAATGAGACCAAAT 58.445 30.769 0.00 0.00 36.11 2.32
1518 2018 6.929625 TGTTTTCAAAGTGAATGAGACCAAA 58.070 32.000 0.00 0.00 36.11 3.28
1519 2019 6.522625 TGTTTTCAAAGTGAATGAGACCAA 57.477 33.333 0.00 0.00 36.11 3.67
1520 2020 6.376864 TCTTGTTTTCAAAGTGAATGAGACCA 59.623 34.615 0.00 0.00 39.47 4.02
1521 2021 6.795399 TCTTGTTTTCAAAGTGAATGAGACC 58.205 36.000 0.00 0.00 39.47 3.85
1522 2022 6.416161 GCTCTTGTTTTCAAAGTGAATGAGAC 59.584 38.462 0.00 0.00 39.47 3.36
1523 2023 6.095300 TGCTCTTGTTTTCAAAGTGAATGAGA 59.905 34.615 0.00 0.00 39.47 3.27
1524 2024 6.267817 TGCTCTTGTTTTCAAAGTGAATGAG 58.732 36.000 0.00 0.00 39.47 2.90
1525 2025 6.206395 TGCTCTTGTTTTCAAAGTGAATGA 57.794 33.333 0.00 0.00 39.47 2.57
1526 2026 8.752766 ATATGCTCTTGTTTTCAAAGTGAATG 57.247 30.769 0.00 0.00 39.47 2.67
1527 2027 9.846248 GTATATGCTCTTGTTTTCAAAGTGAAT 57.154 29.630 0.00 0.00 39.47 2.57
1528 2028 8.845227 TGTATATGCTCTTGTTTTCAAAGTGAA 58.155 29.630 0.00 0.00 39.47 3.18
1529 2029 8.389779 TGTATATGCTCTTGTTTTCAAAGTGA 57.610 30.769 0.00 0.00 39.47 3.41
1530 2030 8.905702 GTTGTATATGCTCTTGTTTTCAAAGTG 58.094 33.333 0.00 0.00 39.47 3.16
1531 2031 8.082242 GGTTGTATATGCTCTTGTTTTCAAAGT 58.918 33.333 0.00 0.00 39.47 2.66
1532 2032 7.542130 GGGTTGTATATGCTCTTGTTTTCAAAG 59.458 37.037 0.00 0.00 39.47 2.77
1533 2033 7.014711 TGGGTTGTATATGCTCTTGTTTTCAAA 59.985 33.333 0.00 0.00 39.47 2.69
1534 2034 6.491745 TGGGTTGTATATGCTCTTGTTTTCAA 59.508 34.615 0.00 0.00 38.21 2.69
1535 2035 6.007076 TGGGTTGTATATGCTCTTGTTTTCA 58.993 36.000 0.00 0.00 0.00 2.69
1536 2036 6.322491 GTGGGTTGTATATGCTCTTGTTTTC 58.678 40.000 0.00 0.00 0.00 2.29
1537 2037 5.106317 CGTGGGTTGTATATGCTCTTGTTTT 60.106 40.000 0.00 0.00 0.00 2.43
1538 2038 4.394920 CGTGGGTTGTATATGCTCTTGTTT 59.605 41.667 0.00 0.00 0.00 2.83
1539 2039 3.938963 CGTGGGTTGTATATGCTCTTGTT 59.061 43.478 0.00 0.00 0.00 2.83
1540 2040 3.055385 ACGTGGGTTGTATATGCTCTTGT 60.055 43.478 0.00 0.00 0.00 3.16
1541 2041 3.531538 ACGTGGGTTGTATATGCTCTTG 58.468 45.455 0.00 0.00 0.00 3.02
1542 2042 3.196901 TGACGTGGGTTGTATATGCTCTT 59.803 43.478 0.00 0.00 0.00 2.85
1543 2043 2.764010 TGACGTGGGTTGTATATGCTCT 59.236 45.455 0.00 0.00 0.00 4.09
1544 2044 3.123804 CTGACGTGGGTTGTATATGCTC 58.876 50.000 0.00 0.00 0.00 4.26
1545 2045 2.741878 GCTGACGTGGGTTGTATATGCT 60.742 50.000 0.00 0.00 0.00 3.79
1546 2046 1.597663 GCTGACGTGGGTTGTATATGC 59.402 52.381 0.00 0.00 0.00 3.14
1547 2047 2.607635 GTGCTGACGTGGGTTGTATATG 59.392 50.000 0.00 0.00 0.00 1.78
1548 2048 2.235155 TGTGCTGACGTGGGTTGTATAT 59.765 45.455 0.00 0.00 0.00 0.86
1549 2049 1.619332 TGTGCTGACGTGGGTTGTATA 59.381 47.619 0.00 0.00 0.00 1.47
1550 2050 0.394938 TGTGCTGACGTGGGTTGTAT 59.605 50.000 0.00 0.00 0.00 2.29
1551 2051 0.531090 GTGTGCTGACGTGGGTTGTA 60.531 55.000 0.00 0.00 0.00 2.41
1552 2052 1.817941 GTGTGCTGACGTGGGTTGT 60.818 57.895 0.00 0.00 0.00 3.32
1553 2053 1.817520 TGTGTGCTGACGTGGGTTG 60.818 57.895 0.00 0.00 0.00 3.77
1554 2054 1.817941 GTGTGTGCTGACGTGGGTT 60.818 57.895 0.00 0.00 0.00 4.11
1555 2055 2.203015 GTGTGTGCTGACGTGGGT 60.203 61.111 0.00 0.00 0.00 4.51
1556 2056 3.337889 CGTGTGTGCTGACGTGGG 61.338 66.667 0.00 0.00 0.00 4.61
1557 2057 4.000557 GCGTGTGTGCTGACGTGG 62.001 66.667 0.00 0.00 37.89 4.94
1558 2058 2.484631 GATGCGTGTGTGCTGACGTG 62.485 60.000 0.00 0.00 37.89 4.49
1559 2059 2.280119 ATGCGTGTGTGCTGACGT 60.280 55.556 0.00 0.00 37.89 4.34
1560 2060 1.560004 AAGATGCGTGTGTGCTGACG 61.560 55.000 0.00 0.00 38.63 4.35
1561 2061 1.428448 TAAGATGCGTGTGTGCTGAC 58.572 50.000 0.00 0.00 35.36 3.51
1562 2062 2.385013 ATAAGATGCGTGTGTGCTGA 57.615 45.000 0.00 0.00 35.36 4.26
1563 2063 2.033407 GCTATAAGATGCGTGTGTGCTG 60.033 50.000 0.00 0.00 35.36 4.41
1564 2064 2.205074 GCTATAAGATGCGTGTGTGCT 58.795 47.619 0.00 0.00 35.36 4.40
1565 2065 1.933181 TGCTATAAGATGCGTGTGTGC 59.067 47.619 0.00 0.00 0.00 4.57
1566 2066 3.803778 TGATGCTATAAGATGCGTGTGTG 59.196 43.478 0.00 0.00 0.00 3.82
1567 2067 4.058721 TGATGCTATAAGATGCGTGTGT 57.941 40.909 0.00 0.00 0.00 3.72
1568 2068 6.019237 GGATATGATGCTATAAGATGCGTGTG 60.019 42.308 0.00 0.00 0.00 3.82
1569 2069 6.045318 GGATATGATGCTATAAGATGCGTGT 58.955 40.000 0.00 0.00 0.00 4.49
1570 2070 6.044682 TGGATATGATGCTATAAGATGCGTG 58.955 40.000 0.00 0.00 0.00 5.34
1571 2071 6.225981 TGGATATGATGCTATAAGATGCGT 57.774 37.500 0.00 0.00 0.00 5.24
1572 2072 7.307811 CCATTGGATATGATGCTATAAGATGCG 60.308 40.741 0.00 0.00 0.00 4.73
1573 2073 7.521748 GCCATTGGATATGATGCTATAAGATGC 60.522 40.741 6.95 0.00 0.00 3.91
1574 2074 7.720074 AGCCATTGGATATGATGCTATAAGATG 59.280 37.037 6.95 0.00 0.00 2.90
1575 2075 7.813331 AGCCATTGGATATGATGCTATAAGAT 58.187 34.615 6.95 0.00 0.00 2.40
1576 2076 7.204243 AGCCATTGGATATGATGCTATAAGA 57.796 36.000 6.95 0.00 0.00 2.10
1580 2080 9.925545 TTTTATAGCCATTGGATATGATGCTAT 57.074 29.630 21.07 12.50 34.94 2.97
1581 2081 9.399797 CTTTTATAGCCATTGGATATGATGCTA 57.600 33.333 21.07 6.59 34.94 3.49
1582 2082 7.341256 CCTTTTATAGCCATTGGATATGATGCT 59.659 37.037 21.07 4.64 34.94 3.79
1583 2083 7.123247 ACCTTTTATAGCCATTGGATATGATGC 59.877 37.037 21.07 0.00 34.94 3.91
1584 2084 8.464404 CACCTTTTATAGCCATTGGATATGATG 58.536 37.037 21.07 12.10 34.94 3.07
1585 2085 8.393259 TCACCTTTTATAGCCATTGGATATGAT 58.607 33.333 21.07 2.11 34.94 2.45
1586 2086 7.754624 TCACCTTTTATAGCCATTGGATATGA 58.245 34.615 21.07 11.91 34.94 2.15
1587 2087 8.408043 TTCACCTTTTATAGCCATTGGATATG 57.592 34.615 21.07 8.35 34.94 1.78
1588 2088 9.028284 CATTCACCTTTTATAGCCATTGGATAT 57.972 33.333 17.09 17.09 37.99 1.63
1589 2089 8.224025 TCATTCACCTTTTATAGCCATTGGATA 58.776 33.333 6.95 4.68 0.00 2.59
1590 2090 7.068702 TCATTCACCTTTTATAGCCATTGGAT 58.931 34.615 6.95 1.78 0.00 3.41
1591 2091 6.430864 TCATTCACCTTTTATAGCCATTGGA 58.569 36.000 6.95 0.00 0.00 3.53
1592 2092 6.547141 TCTCATTCACCTTTTATAGCCATTGG 59.453 38.462 0.00 0.00 0.00 3.16
1593 2093 7.420800 GTCTCATTCACCTTTTATAGCCATTG 58.579 38.462 0.00 0.00 0.00 2.82
1594 2094 6.547510 GGTCTCATTCACCTTTTATAGCCATT 59.452 38.462 0.00 0.00 0.00 3.16
1595 2095 6.064717 GGTCTCATTCACCTTTTATAGCCAT 58.935 40.000 0.00 0.00 0.00 4.40
1596 2096 5.045213 TGGTCTCATTCACCTTTTATAGCCA 60.045 40.000 0.00 0.00 34.66 4.75
1597 2097 5.437060 TGGTCTCATTCACCTTTTATAGCC 58.563 41.667 0.00 0.00 34.66 3.93
1598 2098 7.391148 TTTGGTCTCATTCACCTTTTATAGC 57.609 36.000 0.00 0.00 34.66 2.97
1604 2104 9.927081 AGATATAATTTGGTCTCATTCACCTTT 57.073 29.630 0.00 0.00 34.66 3.11
1605 2105 9.566432 GAGATATAATTTGGTCTCATTCACCTT 57.434 33.333 8.11 0.00 37.60 3.50
1606 2106 8.717717 TGAGATATAATTTGGTCTCATTCACCT 58.282 33.333 10.50 0.00 41.40 4.00
1607 2107 8.908786 TGAGATATAATTTGGTCTCATTCACC 57.091 34.615 10.50 0.00 41.40 4.02
1718 2218 1.243342 TGCTGGCATGCACTGGTAAC 61.243 55.000 21.36 0.00 38.12 2.50
1753 2253 7.524065 CATGAACGCATATAATCATCATGTGT 58.476 34.615 0.00 0.00 43.32 3.72
1906 2408 8.039603 TGCATATTATGGTAAAAAGATAGCCG 57.960 34.615 5.84 0.00 0.00 5.52
1958 2677 2.238521 TGCTCAAGATTTTGGTGGTCC 58.761 47.619 0.00 0.00 34.97 4.46
1981 2700 0.397941 TCTTGTCCCACTCCAGCTTG 59.602 55.000 0.00 0.00 0.00 4.01
2626 3350 3.119388 TGGCATCATTGAAAACTAGCTGC 60.119 43.478 0.00 0.00 0.00 5.25
3185 3909 7.831691 TGTCTTCAGGATAATCTTCCTCTAG 57.168 40.000 0.00 0.00 44.54 2.43
3388 4112 8.144478 TCAATATACTTCTCAGCAGTTACATCC 58.856 37.037 0.00 0.00 0.00 3.51
3453 4177 4.670221 GCTCCAAAGAACTTACTTGATGCG 60.670 45.833 0.00 0.00 0.00 4.73
3660 6667 6.521162 TCACACTTGCTTGTAAGAGTTCATA 58.479 36.000 5.52 0.00 30.67 2.15
4202 7210 2.229784 GGACAAAGTGGAAGCATCAAGG 59.770 50.000 0.00 0.00 0.00 3.61
4605 7613 6.373774 TGAAGTGAACAAATGTTGCCAAAAAT 59.626 30.769 3.05 0.00 38.56 1.82
5141 8154 9.553064 CAGGAACTCAATCTATAGCAAAACTAT 57.447 33.333 0.00 0.00 40.51 2.12
5277 8626 8.499162 CAGTGAGATTACTTCAACGAAGAAATT 58.501 33.333 10.58 0.00 41.71 1.82
5467 8816 6.119536 AGTGGTGTGTCTTCAGTTTCATTTA 58.880 36.000 0.00 0.00 0.00 1.40
5479 8828 3.244911 CCCTGGAATAAGTGGTGTGTCTT 60.245 47.826 0.00 0.00 0.00 3.01
5744 9093 5.515106 ACTATGGTAAGCAAGCCCAAATAA 58.485 37.500 0.00 0.00 0.00 1.40
5810 9162 5.971792 CACGTAGACACATACATGAGGTTAG 59.028 44.000 0.00 0.00 0.00 2.34
5841 9193 5.515797 TCGTTGGATTGAGTACCTATGAG 57.484 43.478 0.00 0.00 0.00 2.90
5843 9195 6.978343 TTTTCGTTGGATTGAGTACCTATG 57.022 37.500 0.00 0.00 0.00 2.23
5899 9251 9.107177 AGCATATGTTTTCTTCAGTAATCAGAG 57.893 33.333 4.29 0.00 0.00 3.35
5900 9252 9.102757 GAGCATATGTTTTCTTCAGTAATCAGA 57.897 33.333 4.29 0.00 0.00 3.27
5977 9329 1.434555 TTTGATTACGTGGCCGTCAG 58.565 50.000 0.00 0.00 46.28 3.51
6203 9555 1.482278 GCAGAGCAGTATGACGTAGC 58.518 55.000 0.00 0.00 39.69 3.58
6213 9565 2.283145 ATCAAAACAGGCAGAGCAGT 57.717 45.000 0.00 0.00 0.00 4.40
6273 9625 5.838521 ACCCAAACTTGAAATAACACCTCAT 59.161 36.000 0.00 0.00 0.00 2.90
6423 9775 2.620115 CAGCCTTCTTCTCAAGCACAAA 59.380 45.455 0.00 0.00 0.00 2.83
6466 9818 3.429492 TGCCAAGTTGCCAAATCTATGA 58.571 40.909 0.00 0.00 0.00 2.15
6768 12040 3.691498 CCGTGTGTTCAAGGTTCTTTTC 58.309 45.455 0.00 0.00 38.18 2.29
6846 12118 3.181495 TGTGAAATCGGTTTGTGTTCCAC 60.181 43.478 0.00 0.00 34.56 4.02
6877 12149 0.609131 CACCTTAGGGGGCACTTGTG 60.609 60.000 2.32 0.00 40.03 3.33
6878 12150 1.767692 CACCTTAGGGGGCACTTGT 59.232 57.895 2.32 0.00 40.03 3.16
6880 12152 2.919096 GCCACCTTAGGGGGCACTT 61.919 63.158 37.35 0.00 43.69 3.16
6882 12154 4.796495 CGCCACCTTAGGGGGCAC 62.796 72.222 39.55 15.83 44.12 5.01
6884 12156 4.796495 CACGCCACCTTAGGGGGC 62.796 72.222 33.49 33.49 45.21 5.80
6885 12157 3.327404 ACACGCCACCTTAGGGGG 61.327 66.667 16.80 16.80 45.21 5.40
6886 12158 2.046314 CACACGCCACCTTAGGGG 60.046 66.667 2.32 0.00 46.27 4.79
6896 12178 1.520342 GGAGATGCTCTCACACGCC 60.520 63.158 13.06 0.00 45.12 5.68
6899 12181 2.072298 GTGTTGGAGATGCTCTCACAC 58.928 52.381 14.79 14.79 45.12 3.82
6918 12200 4.401022 TGCATCTGGTTTTGAGAATCTGT 58.599 39.130 0.00 0.00 34.92 3.41
6919 12201 4.458295 ACTGCATCTGGTTTTGAGAATCTG 59.542 41.667 0.00 0.00 34.92 2.90
6920 12202 4.660168 ACTGCATCTGGTTTTGAGAATCT 58.340 39.130 0.00 0.00 34.92 2.40
6924 12206 3.554934 ACAACTGCATCTGGTTTTGAGA 58.445 40.909 0.00 0.00 0.00 3.27
6929 12211 3.758554 GTCCATACAACTGCATCTGGTTT 59.241 43.478 0.00 0.00 0.00 3.27
6934 12216 5.620738 ACTATGTCCATACAACTGCATCT 57.379 39.130 0.00 0.00 39.58 2.90
6942 12224 4.887071 GGATGGCAAACTATGTCCATACAA 59.113 41.667 0.00 0.00 41.99 2.41
6953 12235 3.168035 ACCACATTGGATGGCAAACTA 57.832 42.857 0.00 0.00 40.96 2.24
7005 12287 2.671914 CGTCCGGTTTACAGGAATTCGA 60.672 50.000 0.00 0.00 41.73 3.71
7009 12291 0.322322 TGCGTCCGGTTTACAGGAAT 59.678 50.000 0.00 0.00 41.73 3.01
7014 12296 0.463295 TGGTTTGCGTCCGGTTTACA 60.463 50.000 0.00 0.00 0.00 2.41
7015 12297 0.236449 CTGGTTTGCGTCCGGTTTAC 59.764 55.000 0.00 0.00 0.00 2.01
7022 12304 2.671963 GTCCCCTGGTTTGCGTCC 60.672 66.667 0.00 0.00 0.00 4.79
7034 12316 0.951040 CAGACGTCTGCAAAGTCCCC 60.951 60.000 31.00 0.00 37.10 4.81
7038 12320 2.205074 CAGTTCAGACGTCTGCAAAGT 58.795 47.619 35.48 25.63 43.46 2.66
7045 12327 2.049063 GCGGCAGTTCAGACGTCT 60.049 61.111 13.58 13.58 43.41 4.18
7048 12330 1.568612 ATGTTGCGGCAGTTCAGACG 61.569 55.000 1.67 0.00 44.61 4.18
7053 12335 2.159181 ACGTATGTTGCGGCAGTTC 58.841 52.632 1.67 0.00 0.00 3.01
7054 12336 4.371975 ACGTATGTTGCGGCAGTT 57.628 50.000 1.67 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.