Multiple sequence alignment - TraesCS2B01G190800

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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 TraesCS2B01G190800 chr2B 100.000 2111 0 0 1 2111 166407887 166405777 0.000000e+00 3899.0
1 TraesCS2B01G190800 chr2B 89.086 394 38 5 801 1191 166466669 166466278 3.150000e-133 484.0
2 TraesCS2B01G190800 chr2B 94.845 97 4 1 706 802 361570483 361570388 1.300000e-32 150.0
3 TraesCS2B01G190800 chr2B 82.927 164 15 7 1268 1421 166466284 166466124 3.650000e-28 135.0
4 TraesCS2B01G190800 chr2B 96.296 54 1 1 657 710 184777080 184777028 1.040000e-13 87.9
5 TraesCS2B01G190800 chr2B 93.333 60 2 2 651 709 361570491 361570433 1.040000e-13 87.9
6 TraesCS2B01G190800 chr2B 94.545 55 2 1 1203 1256 772391230 772391176 1.340000e-12 84.2
7 TraesCS2B01G190800 chr2D 93.760 641 28 7 1264 1892 115929132 115928492 0.000000e+00 952.0
8 TraesCS2B01G190800 chr2D 88.598 649 41 15 3 645 115930156 115929535 0.000000e+00 758.0
9 TraesCS2B01G190800 chr2D 87.071 379 43 4 815 1191 115942665 115942291 6.960000e-115 424.0
10 TraesCS2B01G190800 chr2D 95.217 230 10 1 962 1191 115929350 115929122 1.540000e-96 363.0
11 TraesCS2B01G190800 chr2D 92.045 176 13 1 810 984 115929537 115929362 1.620000e-61 246.0
12 TraesCS2B01G190800 chr2D 91.919 99 7 1 706 804 206685555 206685652 1.020000e-28 137.0
13 TraesCS2B01G190800 chr2A 92.985 613 27 9 1435 2032 117355956 117355345 0.000000e+00 880.0
14 TraesCS2B01G190800 chr2A 90.661 514 31 8 1 508 117364075 117363573 0.000000e+00 667.0
15 TraesCS2B01G190800 chr2A 87.848 395 40 8 801 1191 117388261 117387871 6.870000e-125 457.0
16 TraesCS2B01G190800 chr2A 89.944 358 18 6 835 1191 117363386 117363046 1.490000e-121 446.0
17 TraesCS2B01G190800 chr2A 85.311 177 15 6 488 660 117363559 117363390 2.780000e-39 172.0
18 TraesCS2B01G190800 chr2A 92.000 100 7 1 706 805 603084643 603084741 2.820000e-29 139.0
19 TraesCS2B01G190800 chr7D 93.000 100 6 1 706 805 83082492 83082394 6.070000e-31 145.0
20 TraesCS2B01G190800 chr7D 89.394 66 5 2 643 707 566017151 566017215 4.830000e-12 82.4
21 TraesCS2B01G190800 chr7A 93.814 97 5 1 706 802 109080872 109080777 6.070000e-31 145.0
22 TraesCS2B01G190800 chr7B 92.857 98 6 1 706 803 743401007 743401103 7.850000e-30 141.0
23 TraesCS2B01G190800 chr4B 92.784 97 6 1 706 802 501586075 501585980 2.820000e-29 139.0
24 TraesCS2B01G190800 chr4B 95.349 43 1 1 1216 1257 578046182 578046140 1.350000e-07 67.6
25 TraesCS2B01G190800 chr3D 92.784 97 6 1 706 802 527004749 527004844 2.820000e-29 139.0
26 TraesCS2B01G190800 chr3D 83.333 174 5 14 650 802 545069343 545069513 2.820000e-29 139.0
27 TraesCS2B01G190800 chr4A 91.000 100 6 2 706 804 532353507 532353604 4.730000e-27 132.0
28 TraesCS2B01G190800 chr5B 96.429 56 1 1 655 710 550149003 550149057 8.020000e-15 91.6
29 TraesCS2B01G190800 chr5B 94.545 55 2 1 1203 1256 369608433 369608487 1.340000e-12 84.2
30 TraesCS2B01G190800 chr5A 96.429 56 1 1 655 710 611541469 611541523 8.020000e-15 91.6
31 TraesCS2B01G190800 chr1B 98.000 50 0 1 648 697 8935532 8935580 3.730000e-13 86.1
32 TraesCS2B01G190800 chr5D 90.625 64 5 1 647 709 207244281 207244344 1.340000e-12 84.2
33 TraesCS2B01G190800 chr6B 87.500 72 6 2 654 723 140616209 140616279 1.740000e-11 80.5
34 TraesCS2B01G190800 chr6B 92.727 55 3 1 1203 1256 599805671 599805617 6.240000e-11 78.7
35 TraesCS2B01G190800 chr3B 94.000 50 3 0 1202 1251 187800007 187800056 2.250000e-10 76.8
36 TraesCS2B01G190800 chr6D 92.000 50 4 0 1202 1251 88783937 88783888 1.040000e-08 71.3
37 TraesCS2B01G190800 chr6D 87.931 58 5 2 1200 1256 47809880 47809824 1.350000e-07 67.6


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 TraesCS2B01G190800 chr2B 166405777 166407887 2110 True 3899.000000 3899 100.000000 1 2111 1 chr2B.!!$R1 2110
1 TraesCS2B01G190800 chr2B 166466124 166466669 545 True 309.500000 484 86.006500 801 1421 2 chr2B.!!$R4 620
2 TraesCS2B01G190800 chr2D 115928492 115930156 1664 True 579.750000 952 92.405000 3 1892 4 chr2D.!!$R2 1889
3 TraesCS2B01G190800 chr2A 117355345 117355956 611 True 880.000000 880 92.985000 1435 2032 1 chr2A.!!$R1 597
4 TraesCS2B01G190800 chr2A 117363046 117364075 1029 True 428.333333 667 88.638667 1 1191 3 chr2A.!!$R3 1190

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
655 713 0.615331 ACAACCTGTCGCCATGATCT 59.385 50.0 0.0 0.0 0.0 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2088 2218 0.25361 TTTGTGTGTGTCCGGGTTCT 59.746 50.0 0.0 0.0 0.0 3.01 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
422 446 4.101119 TCAAAACCGGAAGAGAGAGTCTTT 59.899 41.667 9.46 0.00 46.21 2.52
435 459 3.908213 AGAGTCTTTCGAAGTCTGCTTC 58.092 45.455 0.00 0.00 45.68 3.86
506 564 1.066430 TGACAAACCTCGACCTATGCC 60.066 52.381 0.00 0.00 0.00 4.40
566 624 7.713507 CGTTGAATAGGATTTCCAGGTATACAA 59.286 37.037 5.01 0.00 38.89 2.41
572 630 9.936329 ATAGGATTTCCAGGTATACAACATTTT 57.064 29.630 5.01 0.00 38.89 1.82
596 654 1.801178 CCTTGAACTTGAAGCGAGGTC 59.199 52.381 0.00 0.00 32.49 3.85
625 683 4.368391 CGAGGTTGACTTGCTGCT 57.632 55.556 0.00 0.00 0.00 4.24
645 703 5.587289 TGCTTTTTGTATTGACAACCTGTC 58.413 37.500 0.00 0.00 45.29 3.51
655 713 0.615331 ACAACCTGTCGCCATGATCT 59.385 50.000 0.00 0.00 0.00 2.75
660 718 4.258702 ACCTGTCGCCATGATCTTATAC 57.741 45.455 0.00 0.00 0.00 1.47
662 720 4.021894 ACCTGTCGCCATGATCTTATACTC 60.022 45.833 0.00 0.00 0.00 2.59
663 721 4.489810 CTGTCGCCATGATCTTATACTCC 58.510 47.826 0.00 0.00 0.00 3.85
664 722 3.258372 TGTCGCCATGATCTTATACTCCC 59.742 47.826 0.00 0.00 0.00 4.30
665 723 3.511934 GTCGCCATGATCTTATACTCCCT 59.488 47.826 0.00 0.00 0.00 4.20
666 724 3.764434 TCGCCATGATCTTATACTCCCTC 59.236 47.826 0.00 0.00 0.00 4.30
667 725 3.118956 CGCCATGATCTTATACTCCCTCC 60.119 52.174 0.00 0.00 0.00 4.30
668 726 3.118956 GCCATGATCTTATACTCCCTCCG 60.119 52.174 0.00 0.00 0.00 4.63
669 727 4.090090 CCATGATCTTATACTCCCTCCGT 58.910 47.826 0.00 0.00 0.00 4.69
670 728 4.528596 CCATGATCTTATACTCCCTCCGTT 59.471 45.833 0.00 0.00 0.00 4.44
671 729 5.012148 CCATGATCTTATACTCCCTCCGTTT 59.988 44.000 0.00 0.00 0.00 3.60
672 730 5.786264 TGATCTTATACTCCCTCCGTTTC 57.214 43.478 0.00 0.00 0.00 2.78
673 731 5.205821 TGATCTTATACTCCCTCCGTTTCA 58.794 41.667 0.00 0.00 0.00 2.69
674 732 5.659525 TGATCTTATACTCCCTCCGTTTCAA 59.340 40.000 0.00 0.00 0.00 2.69
675 733 6.155565 TGATCTTATACTCCCTCCGTTTCAAA 59.844 38.462 0.00 0.00 0.00 2.69
676 734 6.363167 TCTTATACTCCCTCCGTTTCAAAA 57.637 37.500 0.00 0.00 0.00 2.44
677 735 6.954232 TCTTATACTCCCTCCGTTTCAAAAT 58.046 36.000 0.00 0.00 0.00 1.82
678 736 8.081517 TCTTATACTCCCTCCGTTTCAAAATA 57.918 34.615 0.00 0.00 0.00 1.40
679 737 8.202137 TCTTATACTCCCTCCGTTTCAAAATAG 58.798 37.037 0.00 0.00 0.00 1.73
680 738 4.903045 ACTCCCTCCGTTTCAAAATAGA 57.097 40.909 0.00 0.00 0.00 1.98
681 739 5.437191 ACTCCCTCCGTTTCAAAATAGAT 57.563 39.130 0.00 0.00 0.00 1.98
682 740 5.186198 ACTCCCTCCGTTTCAAAATAGATG 58.814 41.667 0.00 0.00 0.00 2.90
683 741 5.045869 ACTCCCTCCGTTTCAAAATAGATGA 60.046 40.000 0.00 0.00 0.00 2.92
684 742 5.183228 TCCCTCCGTTTCAAAATAGATGAC 58.817 41.667 0.00 0.00 0.00 3.06
685 743 5.045869 TCCCTCCGTTTCAAAATAGATGACT 60.046 40.000 0.00 0.00 0.00 3.41
686 744 5.294552 CCCTCCGTTTCAAAATAGATGACTC 59.705 44.000 0.00 0.00 0.00 3.36
687 745 5.874810 CCTCCGTTTCAAAATAGATGACTCA 59.125 40.000 0.00 0.00 0.00 3.41
688 746 6.371548 CCTCCGTTTCAAAATAGATGACTCAA 59.628 38.462 0.00 0.00 0.00 3.02
689 747 7.066284 CCTCCGTTTCAAAATAGATGACTCAAT 59.934 37.037 0.00 0.00 0.00 2.57
690 748 8.335532 TCCGTTTCAAAATAGATGACTCAATT 57.664 30.769 0.00 0.00 0.00 2.32
691 749 8.792633 TCCGTTTCAAAATAGATGACTCAATTT 58.207 29.630 0.00 0.00 0.00 1.82
692 750 9.410556 CCGTTTCAAAATAGATGACTCAATTTT 57.589 29.630 0.00 0.00 33.07 1.82
719 777 7.054491 ACTAACTTTAACTACCTCCGTTTCA 57.946 36.000 0.00 0.00 0.00 2.69
720 778 7.500141 ACTAACTTTAACTACCTCCGTTTCAA 58.500 34.615 0.00 0.00 0.00 2.69
721 779 7.986889 ACTAACTTTAACTACCTCCGTTTCAAA 59.013 33.333 0.00 0.00 0.00 2.69
722 780 7.628769 AACTTTAACTACCTCCGTTTCAAAA 57.371 32.000 0.00 0.00 0.00 2.44
723 781 7.812690 ACTTTAACTACCTCCGTTTCAAAAT 57.187 32.000 0.00 0.00 0.00 1.82
724 782 8.907222 ACTTTAACTACCTCCGTTTCAAAATA 57.093 30.769 0.00 0.00 0.00 1.40
725 783 9.341078 ACTTTAACTACCTCCGTTTCAAAATAA 57.659 29.630 0.00 0.00 0.00 1.40
729 787 7.989416 ACTACCTCCGTTTCAAAATAAATGA 57.011 32.000 0.00 0.00 0.00 2.57
730 788 7.813645 ACTACCTCCGTTTCAAAATAAATGAC 58.186 34.615 0.00 0.00 0.00 3.06
731 789 6.894339 ACCTCCGTTTCAAAATAAATGACT 57.106 33.333 0.00 0.00 0.00 3.41
732 790 6.909909 ACCTCCGTTTCAAAATAAATGACTC 58.090 36.000 0.00 0.00 0.00 3.36
733 791 6.488683 ACCTCCGTTTCAAAATAAATGACTCA 59.511 34.615 0.00 0.00 0.00 3.41
734 792 7.013846 ACCTCCGTTTCAAAATAAATGACTCAA 59.986 33.333 0.00 0.00 0.00 3.02
735 793 7.326063 CCTCCGTTTCAAAATAAATGACTCAAC 59.674 37.037 0.00 0.00 0.00 3.18
736 794 7.936584 TCCGTTTCAAAATAAATGACTCAACT 58.063 30.769 0.00 0.00 0.00 3.16
737 795 8.410141 TCCGTTTCAAAATAAATGACTCAACTT 58.590 29.630 0.00 0.00 0.00 2.66
738 796 9.030301 CCGTTTCAAAATAAATGACTCAACTTT 57.970 29.630 0.00 0.00 0.00 2.66
793 851 9.893305 AAAGTTGAGTCATCTATTTTAAAACGG 57.107 29.630 1.97 0.00 0.00 4.44
794 852 8.842358 AGTTGAGTCATCTATTTTAAAACGGA 57.158 30.769 1.97 5.09 0.00 4.69
795 853 8.936864 AGTTGAGTCATCTATTTTAAAACGGAG 58.063 33.333 1.97 1.74 0.00 4.63
796 854 7.843490 TGAGTCATCTATTTTAAAACGGAGG 57.157 36.000 1.97 6.55 0.00 4.30
797 855 6.821665 TGAGTCATCTATTTTAAAACGGAGGG 59.178 38.462 1.97 2.46 0.00 4.30
798 856 6.954232 AGTCATCTATTTTAAAACGGAGGGA 58.046 36.000 1.97 4.48 0.00 4.20
799 857 7.048512 AGTCATCTATTTTAAAACGGAGGGAG 58.951 38.462 1.97 0.00 0.00 4.30
800 858 6.822170 GTCATCTATTTTAAAACGGAGGGAGT 59.178 38.462 1.97 0.00 0.00 3.85
801 859 7.983484 GTCATCTATTTTAAAACGGAGGGAGTA 59.017 37.037 1.97 0.00 0.00 2.59
802 860 8.202137 TCATCTATTTTAAAACGGAGGGAGTAG 58.798 37.037 1.97 0.00 0.00 2.57
803 861 7.486407 TCTATTTTAAAACGGAGGGAGTAGT 57.514 36.000 1.97 0.00 0.00 2.73
804 862 8.593945 TCTATTTTAAAACGGAGGGAGTAGTA 57.406 34.615 1.97 0.00 0.00 1.82
805 863 9.034800 TCTATTTTAAAACGGAGGGAGTAGTAA 57.965 33.333 1.97 0.00 0.00 2.24
806 864 9.310716 CTATTTTAAAACGGAGGGAGTAGTAAG 57.689 37.037 1.97 0.00 0.00 2.34
807 865 3.606595 AAAACGGAGGGAGTAGTAAGC 57.393 47.619 0.00 0.00 0.00 3.09
808 866 2.528673 AACGGAGGGAGTAGTAAGCT 57.471 50.000 0.00 0.00 0.00 3.74
809 867 2.528673 ACGGAGGGAGTAGTAAGCTT 57.471 50.000 3.48 3.48 0.00 3.74
810 868 2.100989 ACGGAGGGAGTAGTAAGCTTG 58.899 52.381 9.86 0.00 0.00 4.01
811 869 2.100989 CGGAGGGAGTAGTAAGCTTGT 58.899 52.381 9.86 0.00 0.00 3.16
830 888 0.905357 TAGTGCTTCTTGCCCTCCTC 59.095 55.000 0.00 0.00 42.00 3.71
833 891 1.153469 GCTTCTTGCCCTCCTCTCG 60.153 63.158 0.00 0.00 35.15 4.04
849 907 2.184322 CGGACACTAGGCGCACAT 59.816 61.111 10.83 0.00 0.00 3.21
888 947 4.229876 GTTTGATGTTGTGCTTTAGCCTC 58.770 43.478 0.00 0.00 41.18 4.70
952 1011 9.002600 GTACATTTGATCATGTATCATGGCTAA 57.997 33.333 11.36 6.44 44.13 3.09
1037 1131 2.958355 ACTTGGGTTTCATCACCAACTG 59.042 45.455 0.00 0.00 39.22 3.16
1066 1169 4.022935 GCATCTTCATCTTTGTGTTGGTCA 60.023 41.667 0.00 0.00 0.00 4.02
1067 1170 5.336213 GCATCTTCATCTTTGTGTTGGTCAT 60.336 40.000 0.00 0.00 0.00 3.06
1068 1171 5.947228 TCTTCATCTTTGTGTTGGTCATC 57.053 39.130 0.00 0.00 0.00 2.92
1069 1172 4.452114 TCTTCATCTTTGTGTTGGTCATCG 59.548 41.667 0.00 0.00 0.00 3.84
1070 1173 2.483877 TCATCTTTGTGTTGGTCATCGC 59.516 45.455 0.00 0.00 0.00 4.58
1071 1174 0.865111 TCTTTGTGTTGGTCATCGCG 59.135 50.000 0.00 0.00 0.00 5.87
1072 1175 0.586319 CTTTGTGTTGGTCATCGCGT 59.414 50.000 5.77 0.00 0.00 6.01
1073 1176 1.795872 CTTTGTGTTGGTCATCGCGTA 59.204 47.619 5.77 0.00 0.00 4.42
1074 1177 1.141645 TTGTGTTGGTCATCGCGTAC 58.858 50.000 5.77 3.02 0.00 3.67
1125 1228 8.553459 ACGAGAACTGATCATCTTTTGTTTAT 57.447 30.769 0.00 0.00 0.00 1.40
1137 1240 5.938322 TCTTTTGTTTATCAATGAGACCGC 58.062 37.500 0.00 0.00 35.84 5.68
1158 1261 4.670621 CGCATTATACTCGGAACAAATTGC 59.329 41.667 0.00 0.00 0.00 3.56
1191 1294 1.906105 TAATGGGGACGGAGCGCTTT 61.906 55.000 13.26 0.00 0.00 3.51
1192 1295 3.976701 ATGGGGACGGAGCGCTTTG 62.977 63.158 13.26 10.16 0.00 2.77
1193 1296 4.699522 GGGGACGGAGCGCTTTGT 62.700 66.667 13.26 13.93 0.00 2.83
1194 1297 3.423154 GGGACGGAGCGCTTTGTG 61.423 66.667 13.26 4.31 0.00 3.33
1195 1298 4.090057 GGACGGAGCGCTTTGTGC 62.090 66.667 13.26 15.15 39.59 4.57
1204 1307 2.050477 GCGCTTTGTGCTATTGTTGT 57.950 45.000 0.00 0.00 40.11 3.32
1205 1308 2.393764 GCGCTTTGTGCTATTGTTGTT 58.606 42.857 0.00 0.00 40.11 2.83
1206 1309 2.405025 GCGCTTTGTGCTATTGTTGTTC 59.595 45.455 0.00 0.00 40.11 3.18
1207 1310 3.853307 GCGCTTTGTGCTATTGTTGTTCT 60.853 43.478 0.00 0.00 40.11 3.01
1208 1311 3.908382 CGCTTTGTGCTATTGTTGTTCTC 59.092 43.478 0.00 0.00 40.11 2.87
1209 1312 4.319766 CGCTTTGTGCTATTGTTGTTCTCT 60.320 41.667 0.00 0.00 40.11 3.10
1210 1313 5.149977 GCTTTGTGCTATTGTTGTTCTCTC 58.850 41.667 0.00 0.00 38.95 3.20
1211 1314 5.689383 TTTGTGCTATTGTTGTTCTCTCC 57.311 39.130 0.00 0.00 0.00 3.71
1212 1315 4.623932 TGTGCTATTGTTGTTCTCTCCT 57.376 40.909 0.00 0.00 0.00 3.69
1213 1316 5.738619 TGTGCTATTGTTGTTCTCTCCTA 57.261 39.130 0.00 0.00 0.00 2.94
1214 1317 5.479306 TGTGCTATTGTTGTTCTCTCCTAC 58.521 41.667 0.00 0.00 0.00 3.18
1215 1318 4.870991 GTGCTATTGTTGTTCTCTCCTACC 59.129 45.833 0.00 0.00 0.00 3.18
1216 1319 4.777896 TGCTATTGTTGTTCTCTCCTACCT 59.222 41.667 0.00 0.00 0.00 3.08
1217 1320 5.955959 TGCTATTGTTGTTCTCTCCTACCTA 59.044 40.000 0.00 0.00 0.00 3.08
1218 1321 6.611642 TGCTATTGTTGTTCTCTCCTACCTAT 59.388 38.462 0.00 0.00 0.00 2.57
1219 1322 7.149307 GCTATTGTTGTTCTCTCCTACCTATC 58.851 42.308 0.00 0.00 0.00 2.08
1220 1323 7.201920 GCTATTGTTGTTCTCTCCTACCTATCA 60.202 40.741 0.00 0.00 0.00 2.15
1221 1324 6.928348 TTGTTGTTCTCTCCTACCTATCAA 57.072 37.500 0.00 0.00 0.00 2.57
1222 1325 7.496346 TTGTTGTTCTCTCCTACCTATCAAT 57.504 36.000 0.00 0.00 0.00 2.57
1223 1326 6.878317 TGTTGTTCTCTCCTACCTATCAATG 58.122 40.000 0.00 0.00 0.00 2.82
1224 1327 6.667848 TGTTGTTCTCTCCTACCTATCAATGA 59.332 38.462 0.00 0.00 0.00 2.57
1225 1328 7.180229 TGTTGTTCTCTCCTACCTATCAATGAA 59.820 37.037 0.00 0.00 0.00 2.57
1226 1329 7.733773 TGTTCTCTCCTACCTATCAATGAAA 57.266 36.000 0.00 0.00 0.00 2.69
1227 1330 8.146053 TGTTCTCTCCTACCTATCAATGAAAA 57.854 34.615 0.00 0.00 0.00 2.29
1228 1331 8.260818 TGTTCTCTCCTACCTATCAATGAAAAG 58.739 37.037 0.00 0.00 0.00 2.27
1229 1332 8.478877 GTTCTCTCCTACCTATCAATGAAAAGA 58.521 37.037 0.00 0.00 0.00 2.52
1230 1333 8.789767 TCTCTCCTACCTATCAATGAAAAGAT 57.210 34.615 0.00 0.00 0.00 2.40
1231 1334 9.883293 TCTCTCCTACCTATCAATGAAAAGATA 57.117 33.333 0.00 0.00 0.00 1.98
1232 1335 9.921637 CTCTCCTACCTATCAATGAAAAGATAC 57.078 37.037 0.00 0.00 0.00 2.24
1233 1336 8.577296 TCTCCTACCTATCAATGAAAAGATACG 58.423 37.037 0.00 0.00 0.00 3.06
1234 1337 7.152645 TCCTACCTATCAATGAAAAGATACGC 58.847 38.462 0.00 0.00 0.00 4.42
1235 1338 6.929049 CCTACCTATCAATGAAAAGATACGCA 59.071 38.462 0.00 0.00 0.00 5.24
1236 1339 7.441157 CCTACCTATCAATGAAAAGATACGCAA 59.559 37.037 0.00 0.00 0.00 4.85
1238 1341 6.138761 CCTATCAATGAAAAGATACGCAAGC 58.861 40.000 0.00 0.00 45.62 4.01
1239 1342 5.824904 ATCAATGAAAAGATACGCAAGCT 57.175 34.783 0.00 0.00 45.62 3.74
1240 1343 5.627499 TCAATGAAAAGATACGCAAGCTT 57.373 34.783 0.00 0.00 45.62 3.74
1241 1344 5.631026 TCAATGAAAAGATACGCAAGCTTC 58.369 37.500 0.00 0.00 45.62 3.86
1242 1345 3.722555 TGAAAAGATACGCAAGCTTCG 57.277 42.857 14.15 14.15 45.62 3.79
1243 1346 2.159707 TGAAAAGATACGCAAGCTTCGC 60.160 45.455 15.23 12.63 45.62 4.70
1250 1353 4.552797 GCAAGCTTCGCGTATTCG 57.447 55.556 5.77 0.00 40.37 3.34
1264 1367 4.254745 CGTATTCGCAAAAGGAAGGTAC 57.745 45.455 0.00 0.00 0.00 3.34
1265 1368 3.241868 CGTATTCGCAAAAGGAAGGTACG 60.242 47.826 0.00 0.00 30.75 3.67
1266 1369 2.529780 TTCGCAAAAGGAAGGTACGA 57.470 45.000 0.00 0.00 0.00 3.43
1267 1370 2.529780 TCGCAAAAGGAAGGTACGAA 57.470 45.000 0.00 0.00 0.00 3.85
1268 1371 2.409975 TCGCAAAAGGAAGGTACGAAG 58.590 47.619 0.00 0.00 0.00 3.79
1269 1372 1.136057 CGCAAAAGGAAGGTACGAAGC 60.136 52.381 0.00 0.00 0.00 3.86
1270 1373 1.136057 GCAAAAGGAAGGTACGAAGCG 60.136 52.381 0.00 0.00 0.00 4.68
1271 1374 1.136057 CAAAAGGAAGGTACGAAGCGC 60.136 52.381 0.00 0.00 0.00 5.92
1272 1375 0.320697 AAAGGAAGGTACGAAGCGCT 59.679 50.000 2.64 2.64 0.00 5.92
1273 1376 0.320697 AAGGAAGGTACGAAGCGCTT 59.679 50.000 25.35 25.35 0.00 4.68
1407 1521 3.132646 TCCTGCTTGTTGCTTGTTTGATT 59.867 39.130 0.00 0.00 43.37 2.57
1431 1545 5.813513 TGTGATCTGTATGTATGCCAGAT 57.186 39.130 1.27 1.27 45.95 2.90
1459 1574 5.122554 TGAACTTCTGAAAACACAAGCGTTA 59.877 36.000 0.00 0.00 0.00 3.18
1600 1720 2.511600 GACAGATGGAACGGCCGG 60.512 66.667 31.76 11.44 40.66 6.13
1727 1847 1.939934 CCCGCATCGAGCATTTTTCTA 59.060 47.619 7.47 0.00 46.13 2.10
1823 1948 0.114168 TGCCTTTGTTGGGTGCCTAT 59.886 50.000 0.00 0.00 0.00 2.57
1842 1970 1.930567 TCCTAGTTAAATCGTGCGCC 58.069 50.000 4.18 0.00 0.00 6.53
1856 1984 4.673403 CGCCTGTGTGCACTTCTA 57.327 55.556 19.41 0.00 0.00 2.10
1860 1988 2.417379 CGCCTGTGTGCACTTCTATAGT 60.417 50.000 19.41 0.00 37.68 2.12
1897 2025 1.568612 AACAATCCGACGTGCTGCTG 61.569 55.000 0.00 0.00 0.00 4.41
1916 2046 0.596082 GGTTGGGTTGGATTGACGTG 59.404 55.000 0.00 0.00 0.00 4.49
1998 2128 2.911819 TTTTCGCTTTGGCTTATCCG 57.088 45.000 0.00 0.00 37.80 4.18
2011 2141 2.288395 GCTTATCCGGAAATGGCAATGG 60.288 50.000 9.01 0.00 0.00 3.16
2016 2146 2.634940 TCCGGAAATGGCAATGGAAAAA 59.365 40.909 0.00 0.00 0.00 1.94
2037 2167 7.757941 AAAAATATGTTTTGGTTTCCCATGG 57.242 32.000 4.14 4.14 41.49 3.66
2038 2168 6.694445 AAATATGTTTTGGTTTCCCATGGA 57.306 33.333 15.22 0.00 41.49 3.41
2039 2169 6.694445 AATATGTTTTGGTTTCCCATGGAA 57.306 33.333 15.22 2.63 41.49 3.53
2040 2170 3.828875 TGTTTTGGTTTCCCATGGAAC 57.171 42.857 15.22 10.69 41.87 3.62
2041 2171 3.379452 TGTTTTGGTTTCCCATGGAACT 58.621 40.909 15.22 0.00 41.87 3.01
2042 2172 3.133721 TGTTTTGGTTTCCCATGGAACTG 59.866 43.478 15.22 0.00 41.87 3.16
2043 2173 3.320610 TTTGGTTTCCCATGGAACTGA 57.679 42.857 15.22 0.00 41.87 3.41
2044 2174 2.584835 TGGTTTCCCATGGAACTGAG 57.415 50.000 15.22 0.00 41.87 3.35
2045 2175 2.061848 TGGTTTCCCATGGAACTGAGA 58.938 47.619 15.22 0.00 41.87 3.27
2046 2176 2.040278 TGGTTTCCCATGGAACTGAGAG 59.960 50.000 15.22 0.00 41.87 3.20
2047 2177 2.305927 GGTTTCCCATGGAACTGAGAGA 59.694 50.000 15.22 0.00 41.87 3.10
2048 2178 3.339141 GTTTCCCATGGAACTGAGAGAC 58.661 50.000 15.22 2.22 41.87 3.36
2049 2179 1.573108 TCCCATGGAACTGAGAGACC 58.427 55.000 15.22 0.00 0.00 3.85
2050 2180 1.079490 TCCCATGGAACTGAGAGACCT 59.921 52.381 15.22 0.00 0.00 3.85
2051 2181 1.912043 CCCATGGAACTGAGAGACCTT 59.088 52.381 15.22 0.00 0.00 3.50
2052 2182 3.107601 CCCATGGAACTGAGAGACCTTA 58.892 50.000 15.22 0.00 0.00 2.69
2053 2183 3.118592 CCCATGGAACTGAGAGACCTTAC 60.119 52.174 15.22 0.00 0.00 2.34
2054 2184 3.772025 CCATGGAACTGAGAGACCTTACT 59.228 47.826 5.56 0.00 0.00 2.24
2055 2185 4.223923 CCATGGAACTGAGAGACCTTACTT 59.776 45.833 5.56 0.00 0.00 2.24
2056 2186 5.415221 CATGGAACTGAGAGACCTTACTTC 58.585 45.833 0.00 0.00 0.00 3.01
2057 2187 3.833070 TGGAACTGAGAGACCTTACTTCC 59.167 47.826 0.00 0.00 0.00 3.46
2058 2188 4.090819 GGAACTGAGAGACCTTACTTCCT 58.909 47.826 0.00 0.00 0.00 3.36
2059 2189 4.158949 GGAACTGAGAGACCTTACTTCCTC 59.841 50.000 0.00 0.00 0.00 3.71
2060 2190 4.390129 ACTGAGAGACCTTACTTCCTCA 57.610 45.455 0.00 0.00 0.00 3.86
2061 2191 4.083565 ACTGAGAGACCTTACTTCCTCAC 58.916 47.826 0.00 0.00 0.00 3.51
2062 2192 4.202631 ACTGAGAGACCTTACTTCCTCACT 60.203 45.833 0.00 0.00 0.00 3.41
2063 2193 4.082845 TGAGAGACCTTACTTCCTCACTG 58.917 47.826 0.00 0.00 0.00 3.66
2064 2194 4.202577 TGAGAGACCTTACTTCCTCACTGA 60.203 45.833 0.00 0.00 0.00 3.41
2065 2195 4.742012 AGAGACCTTACTTCCTCACTGAA 58.258 43.478 0.00 0.00 0.00 3.02
2066 2196 4.525100 AGAGACCTTACTTCCTCACTGAAC 59.475 45.833 0.00 0.00 0.00 3.18
2067 2197 4.223953 AGACCTTACTTCCTCACTGAACA 58.776 43.478 0.00 0.00 0.00 3.18
2068 2198 4.841246 AGACCTTACTTCCTCACTGAACAT 59.159 41.667 0.00 0.00 0.00 2.71
2069 2199 5.308237 AGACCTTACTTCCTCACTGAACATT 59.692 40.000 0.00 0.00 0.00 2.71
2070 2200 5.552178 ACCTTACTTCCTCACTGAACATTC 58.448 41.667 0.00 0.00 0.00 2.67
2071 2201 4.627467 CCTTACTTCCTCACTGAACATTCG 59.373 45.833 0.00 0.00 0.00 3.34
2072 2202 3.045601 ACTTCCTCACTGAACATTCGG 57.954 47.619 0.00 0.00 39.48 4.30
2073 2203 2.632996 ACTTCCTCACTGAACATTCGGA 59.367 45.455 7.45 0.00 37.03 4.55
2074 2204 3.261897 ACTTCCTCACTGAACATTCGGAT 59.738 43.478 7.45 0.00 37.03 4.18
2075 2205 3.251479 TCCTCACTGAACATTCGGATG 57.749 47.619 0.88 0.88 37.03 3.51
2076 2206 2.093500 TCCTCACTGAACATTCGGATGG 60.093 50.000 8.93 6.23 37.60 3.51
2077 2207 2.093500 CCTCACTGAACATTCGGATGGA 60.093 50.000 8.93 0.00 37.60 3.41
2078 2208 2.932614 CTCACTGAACATTCGGATGGAC 59.067 50.000 8.93 2.07 37.60 4.02
2079 2209 2.301583 TCACTGAACATTCGGATGGACA 59.698 45.455 8.93 6.76 37.60 4.02
2080 2210 2.674852 CACTGAACATTCGGATGGACAG 59.325 50.000 22.22 22.22 41.62 3.51
2081 2211 2.283298 CTGAACATTCGGATGGACAGG 58.717 52.381 18.52 6.18 37.14 4.00
2082 2212 1.017387 GAACATTCGGATGGACAGGC 58.983 55.000 8.93 0.00 37.60 4.85
2083 2213 0.394352 AACATTCGGATGGACAGGCC 60.394 55.000 8.93 0.00 37.60 5.19
2084 2214 1.889105 CATTCGGATGGACAGGCCG 60.889 63.158 0.00 9.32 46.08 6.13
2085 2215 3.106986 ATTCGGATGGACAGGCCGG 62.107 63.158 0.00 0.00 44.87 6.13
2086 2216 4.770362 TCGGATGGACAGGCCGGA 62.770 66.667 10.86 0.00 44.87 5.14
2087 2217 4.530857 CGGATGGACAGGCCGGAC 62.531 72.222 10.86 0.00 41.29 4.79
2088 2218 3.399181 GGATGGACAGGCCGGACA 61.399 66.667 11.69 8.74 40.66 4.02
2089 2219 2.187946 GATGGACAGGCCGGACAG 59.812 66.667 11.69 2.94 40.66 3.51
2090 2220 2.284625 ATGGACAGGCCGGACAGA 60.285 61.111 11.69 0.00 40.66 3.41
2091 2221 1.899437 GATGGACAGGCCGGACAGAA 61.899 60.000 11.69 0.00 40.66 3.02
2092 2222 2.047179 GGACAGGCCGGACAGAAC 60.047 66.667 11.69 1.00 0.00 3.01
2093 2223 2.047179 GACAGGCCGGACAGAACC 60.047 66.667 11.69 0.00 0.00 3.62
2094 2224 3.607370 GACAGGCCGGACAGAACCC 62.607 68.421 11.69 0.00 0.00 4.11
2095 2225 4.760047 CAGGCCGGACAGAACCCG 62.760 72.222 11.69 0.00 46.10 5.28
2100 2230 2.048503 CGGACAGAACCCGGACAC 60.049 66.667 0.73 0.00 43.05 3.67
2101 2231 2.863346 CGGACAGAACCCGGACACA 61.863 63.158 0.73 0.00 43.05 3.72
2102 2232 1.301479 GGACAGAACCCGGACACAC 60.301 63.158 0.73 0.00 0.00 3.82
2103 2233 1.444250 GACAGAACCCGGACACACA 59.556 57.895 0.73 0.00 0.00 3.72
2104 2234 0.878961 GACAGAACCCGGACACACAC 60.879 60.000 0.73 0.00 0.00 3.82
2105 2235 1.145156 CAGAACCCGGACACACACA 59.855 57.895 0.73 0.00 0.00 3.72
2106 2236 0.462937 CAGAACCCGGACACACACAA 60.463 55.000 0.73 0.00 0.00 3.33
2107 2237 0.253610 AGAACCCGGACACACACAAA 59.746 50.000 0.73 0.00 0.00 2.83
2108 2238 1.096416 GAACCCGGACACACACAAAA 58.904 50.000 0.73 0.00 0.00 2.44
2109 2239 0.812549 AACCCGGACACACACAAAAC 59.187 50.000 0.73 0.00 0.00 2.43
2110 2240 0.322636 ACCCGGACACACACAAAACA 60.323 50.000 0.73 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
265 273 9.715121 ACAGCAACATTTCTTAAATTCATGAAT 57.285 25.926 15.36 15.36 0.00 2.57
506 564 6.477053 TTCTCTGAGGTGATCCTATTCAAG 57.523 41.667 4.59 0.00 45.24 3.02
527 585 6.899114 TCCTATTCAACGCTTCTTCTTTTTC 58.101 36.000 0.00 0.00 0.00 2.29
566 624 5.682212 GCTTCAAGTTCAAGGACCAAAATGT 60.682 40.000 0.00 0.00 0.00 2.71
572 630 1.140052 TCGCTTCAAGTTCAAGGACCA 59.860 47.619 0.00 0.00 0.00 4.02
596 654 0.647410 CAACCTCGCGTAATCTGCTG 59.353 55.000 5.77 0.00 0.00 4.41
645 703 3.118956 GGAGGGAGTATAAGATCATGGCG 60.119 52.174 0.00 0.00 0.00 5.69
655 713 8.081517 TCTATTTTGAAACGGAGGGAGTATAA 57.918 34.615 0.00 0.00 0.00 0.98
660 718 5.294552 GTCATCTATTTTGAAACGGAGGGAG 59.705 44.000 0.00 0.00 0.00 4.30
662 720 5.186198 AGTCATCTATTTTGAAACGGAGGG 58.814 41.667 0.00 0.00 0.00 4.30
663 721 5.874810 TGAGTCATCTATTTTGAAACGGAGG 59.125 40.000 0.00 0.00 0.00 4.30
664 722 6.968131 TGAGTCATCTATTTTGAAACGGAG 57.032 37.500 0.00 0.00 0.00 4.63
665 723 7.921786 ATTGAGTCATCTATTTTGAAACGGA 57.078 32.000 0.00 0.00 0.00 4.69
666 724 8.970691 AAATTGAGTCATCTATTTTGAAACGG 57.029 30.769 0.00 0.00 37.52 4.44
693 751 8.806146 TGAAACGGAGGTAGTTAAAGTTAGTAT 58.194 33.333 0.00 0.00 0.00 2.12
694 752 8.177119 TGAAACGGAGGTAGTTAAAGTTAGTA 57.823 34.615 0.00 0.00 0.00 1.82
695 753 7.054491 TGAAACGGAGGTAGTTAAAGTTAGT 57.946 36.000 0.00 0.00 0.00 2.24
696 754 7.951530 TTGAAACGGAGGTAGTTAAAGTTAG 57.048 36.000 0.00 0.00 0.00 2.34
697 755 8.729805 TTTTGAAACGGAGGTAGTTAAAGTTA 57.270 30.769 0.00 0.00 0.00 2.24
698 756 7.628769 TTTTGAAACGGAGGTAGTTAAAGTT 57.371 32.000 0.00 0.00 0.00 2.66
699 757 7.812690 ATTTTGAAACGGAGGTAGTTAAAGT 57.187 32.000 0.00 0.00 0.00 2.66
703 761 9.504708 TCATTTATTTTGAAACGGAGGTAGTTA 57.495 29.630 0.00 0.00 0.00 2.24
704 762 8.294577 GTCATTTATTTTGAAACGGAGGTAGTT 58.705 33.333 0.00 0.00 0.00 2.24
705 763 7.664318 AGTCATTTATTTTGAAACGGAGGTAGT 59.336 33.333 0.00 0.00 0.00 2.73
706 764 8.040716 AGTCATTTATTTTGAAACGGAGGTAG 57.959 34.615 0.00 0.00 0.00 3.18
707 765 7.662258 TGAGTCATTTATTTTGAAACGGAGGTA 59.338 33.333 0.00 0.00 0.00 3.08
708 766 6.488683 TGAGTCATTTATTTTGAAACGGAGGT 59.511 34.615 0.00 0.00 0.00 3.85
709 767 6.908825 TGAGTCATTTATTTTGAAACGGAGG 58.091 36.000 0.00 0.00 0.00 4.30
710 768 8.076178 AGTTGAGTCATTTATTTTGAAACGGAG 58.924 33.333 0.00 0.00 0.00 4.63
711 769 7.936584 AGTTGAGTCATTTATTTTGAAACGGA 58.063 30.769 0.00 0.00 0.00 4.69
712 770 8.574196 AAGTTGAGTCATTTATTTTGAAACGG 57.426 30.769 0.00 0.00 0.00 4.44
767 825 9.893305 CCGTTTTAAAATAGATGACTCAACTTT 57.107 29.630 3.52 0.00 0.00 2.66
768 826 9.280174 TCCGTTTTAAAATAGATGACTCAACTT 57.720 29.630 3.52 0.00 0.00 2.66
769 827 8.842358 TCCGTTTTAAAATAGATGACTCAACT 57.158 30.769 3.52 0.00 0.00 3.16
770 828 8.175716 CCTCCGTTTTAAAATAGATGACTCAAC 58.824 37.037 3.52 0.00 0.00 3.18
771 829 7.335924 CCCTCCGTTTTAAAATAGATGACTCAA 59.664 37.037 3.52 0.00 0.00 3.02
772 830 6.821665 CCCTCCGTTTTAAAATAGATGACTCA 59.178 38.462 3.52 0.00 0.00 3.41
773 831 7.046033 TCCCTCCGTTTTAAAATAGATGACTC 58.954 38.462 3.52 0.00 0.00 3.36
774 832 6.954232 TCCCTCCGTTTTAAAATAGATGACT 58.046 36.000 3.52 0.00 0.00 3.41
775 833 6.822170 ACTCCCTCCGTTTTAAAATAGATGAC 59.178 38.462 3.52 0.00 0.00 3.06
776 834 6.954232 ACTCCCTCCGTTTTAAAATAGATGA 58.046 36.000 3.52 3.96 0.00 2.92
777 835 7.985752 ACTACTCCCTCCGTTTTAAAATAGATG 59.014 37.037 3.52 2.01 0.00 2.90
778 836 8.087303 ACTACTCCCTCCGTTTTAAAATAGAT 57.913 34.615 3.52 0.00 0.00 1.98
779 837 7.486407 ACTACTCCCTCCGTTTTAAAATAGA 57.514 36.000 3.52 3.61 0.00 1.98
780 838 9.310716 CTTACTACTCCCTCCGTTTTAAAATAG 57.689 37.037 3.52 1.99 0.00 1.73
781 839 7.765819 GCTTACTACTCCCTCCGTTTTAAAATA 59.234 37.037 3.52 0.00 0.00 1.40
782 840 6.596888 GCTTACTACTCCCTCCGTTTTAAAAT 59.403 38.462 3.52 0.00 0.00 1.82
783 841 5.934043 GCTTACTACTCCCTCCGTTTTAAAA 59.066 40.000 0.00 0.00 0.00 1.52
784 842 5.246883 AGCTTACTACTCCCTCCGTTTTAAA 59.753 40.000 0.00 0.00 0.00 1.52
785 843 4.774200 AGCTTACTACTCCCTCCGTTTTAA 59.226 41.667 0.00 0.00 0.00 1.52
786 844 4.347607 AGCTTACTACTCCCTCCGTTTTA 58.652 43.478 0.00 0.00 0.00 1.52
787 845 3.171528 AGCTTACTACTCCCTCCGTTTT 58.828 45.455 0.00 0.00 0.00 2.43
788 846 2.817665 AGCTTACTACTCCCTCCGTTT 58.182 47.619 0.00 0.00 0.00 3.60
789 847 2.496470 CAAGCTTACTACTCCCTCCGTT 59.504 50.000 0.00 0.00 0.00 4.44
790 848 2.100989 CAAGCTTACTACTCCCTCCGT 58.899 52.381 0.00 0.00 0.00 4.69
791 849 2.100989 ACAAGCTTACTACTCCCTCCG 58.899 52.381 0.00 0.00 0.00 4.63
792 850 4.098196 CACTACAAGCTTACTACTCCCTCC 59.902 50.000 0.00 0.00 0.00 4.30
793 851 4.440387 GCACTACAAGCTTACTACTCCCTC 60.440 50.000 0.00 0.00 0.00 4.30
794 852 3.447944 GCACTACAAGCTTACTACTCCCT 59.552 47.826 0.00 0.00 0.00 4.20
795 853 3.447944 AGCACTACAAGCTTACTACTCCC 59.552 47.826 0.00 0.00 39.87 4.30
796 854 4.722361 AGCACTACAAGCTTACTACTCC 57.278 45.455 0.00 0.00 39.87 3.85
805 863 1.884067 GGGCAAGAAGCACTACAAGCT 60.884 52.381 0.00 0.00 45.63 3.74
806 864 0.523519 GGGCAAGAAGCACTACAAGC 59.476 55.000 0.00 0.00 45.63 4.01
830 888 2.202623 GTGCGCCTAGTGTCCGAG 60.203 66.667 4.18 0.00 0.00 4.63
833 891 0.528684 GAGATGTGCGCCTAGTGTCC 60.529 60.000 4.18 0.00 0.00 4.02
849 907 5.462530 TCAAACAGAGGTTATGAACGAGA 57.537 39.130 0.00 0.00 35.82 4.04
888 947 6.423302 GTCAGAAGTATATGACATGGAAGCAG 59.577 42.308 0.00 0.00 44.21 4.24
952 1011 7.746703 AGGATAGTTAAGGTCTGAAAACAAGT 58.253 34.615 0.00 0.00 0.00 3.16
1027 1121 2.036256 GCCCAGGCAGTTGGTGAT 59.964 61.111 3.12 0.00 41.49 3.06
1037 1131 1.407979 CAAAGATGAAGATGCCCAGGC 59.592 52.381 0.38 0.38 42.35 4.85
1069 1172 0.168128 GCCATCACAAAGTGGTACGC 59.832 55.000 0.00 0.00 37.81 4.42
1070 1173 0.442310 CGCCATCACAAAGTGGTACG 59.558 55.000 0.00 0.00 37.81 3.67
1071 1174 0.802494 CCGCCATCACAAAGTGGTAC 59.198 55.000 0.00 0.00 37.81 3.34
1072 1175 0.687920 TCCGCCATCACAAAGTGGTA 59.312 50.000 0.00 0.00 37.81 3.25
1073 1176 0.889186 GTCCGCCATCACAAAGTGGT 60.889 55.000 0.00 0.00 37.81 4.16
1074 1177 1.586154 GGTCCGCCATCACAAAGTGG 61.586 60.000 0.00 0.00 38.55 4.00
1125 1228 4.546570 CGAGTATAATGCGGTCTCATTGA 58.453 43.478 0.00 0.00 37.27 2.57
1137 1240 6.043327 TCGCAATTTGTTCCGAGTATAATG 57.957 37.500 0.00 0.00 0.00 1.90
1158 1261 4.212636 GTCCCCATTAACCGACATATTTCG 59.787 45.833 4.25 4.25 38.80 3.46
1191 1294 4.623932 AGGAGAGAACAACAATAGCACA 57.376 40.909 0.00 0.00 0.00 4.57
1192 1295 4.870991 GGTAGGAGAGAACAACAATAGCAC 59.129 45.833 0.00 0.00 0.00 4.40
1193 1296 4.777896 AGGTAGGAGAGAACAACAATAGCA 59.222 41.667 0.00 0.00 0.00 3.49
1194 1297 5.346181 AGGTAGGAGAGAACAACAATAGC 57.654 43.478 0.00 0.00 0.00 2.97
1195 1298 8.239038 TGATAGGTAGGAGAGAACAACAATAG 57.761 38.462 0.00 0.00 0.00 1.73
1196 1299 8.603898 TTGATAGGTAGGAGAGAACAACAATA 57.396 34.615 0.00 0.00 0.00 1.90
1197 1300 7.496346 TTGATAGGTAGGAGAGAACAACAAT 57.504 36.000 0.00 0.00 0.00 2.71
1198 1301 6.928348 TTGATAGGTAGGAGAGAACAACAA 57.072 37.500 0.00 0.00 0.00 2.83
1199 1302 6.667848 TCATTGATAGGTAGGAGAGAACAACA 59.332 38.462 0.00 0.00 0.00 3.33
1200 1303 7.113658 TCATTGATAGGTAGGAGAGAACAAC 57.886 40.000 0.00 0.00 0.00 3.32
1201 1304 7.733773 TTCATTGATAGGTAGGAGAGAACAA 57.266 36.000 0.00 0.00 0.00 2.83
1202 1305 7.733773 TTTCATTGATAGGTAGGAGAGAACA 57.266 36.000 0.00 0.00 0.00 3.18
1203 1306 8.478877 TCTTTTCATTGATAGGTAGGAGAGAAC 58.521 37.037 0.00 0.00 0.00 3.01
1204 1307 8.609617 TCTTTTCATTGATAGGTAGGAGAGAA 57.390 34.615 0.00 0.00 0.00 2.87
1205 1308 8.789767 ATCTTTTCATTGATAGGTAGGAGAGA 57.210 34.615 0.00 0.00 0.00 3.10
1206 1309 9.921637 GTATCTTTTCATTGATAGGTAGGAGAG 57.078 37.037 0.00 0.00 0.00 3.20
1207 1310 8.577296 CGTATCTTTTCATTGATAGGTAGGAGA 58.423 37.037 0.00 0.00 0.00 3.71
1208 1311 7.329717 GCGTATCTTTTCATTGATAGGTAGGAG 59.670 40.741 10.84 1.25 35.05 3.69
1209 1312 7.152645 GCGTATCTTTTCATTGATAGGTAGGA 58.847 38.462 10.84 0.00 35.05 2.94
1210 1313 6.929049 TGCGTATCTTTTCATTGATAGGTAGG 59.071 38.462 0.00 0.00 35.05 3.18
1211 1314 7.946655 TGCGTATCTTTTCATTGATAGGTAG 57.053 36.000 0.00 0.00 35.05 3.18
1212 1315 7.042051 GCTTGCGTATCTTTTCATTGATAGGTA 60.042 37.037 0.00 0.00 35.05 3.08
1213 1316 6.238484 GCTTGCGTATCTTTTCATTGATAGGT 60.238 38.462 0.00 0.00 35.05 3.08
1214 1317 6.017605 AGCTTGCGTATCTTTTCATTGATAGG 60.018 38.462 0.00 0.00 35.44 2.57
1215 1318 6.952743 AGCTTGCGTATCTTTTCATTGATAG 58.047 36.000 0.00 0.00 0.00 2.08
1216 1319 6.925610 AGCTTGCGTATCTTTTCATTGATA 57.074 33.333 0.00 0.00 0.00 2.15
1217 1320 5.824904 AGCTTGCGTATCTTTTCATTGAT 57.175 34.783 0.00 0.00 0.00 2.57
1218 1321 5.627499 AAGCTTGCGTATCTTTTCATTGA 57.373 34.783 0.00 0.00 0.00 2.57
1219 1322 4.493350 CGAAGCTTGCGTATCTTTTCATTG 59.507 41.667 2.10 0.00 0.00 2.82
1220 1323 4.651994 CGAAGCTTGCGTATCTTTTCATT 58.348 39.130 2.10 0.00 0.00 2.57
1221 1324 4.264543 CGAAGCTTGCGTATCTTTTCAT 57.735 40.909 2.10 0.00 0.00 2.57
1222 1325 3.722555 CGAAGCTTGCGTATCTTTTCA 57.277 42.857 2.10 0.00 0.00 2.69
1243 1346 3.241868 CGTACCTTCCTTTTGCGAATACG 60.242 47.826 0.00 0.74 42.93 3.06
1244 1347 3.928375 TCGTACCTTCCTTTTGCGAATAC 59.072 43.478 0.00 0.00 0.00 1.89
1245 1348 4.191033 TCGTACCTTCCTTTTGCGAATA 57.809 40.909 0.00 0.00 0.00 1.75
1246 1349 3.048337 TCGTACCTTCCTTTTGCGAAT 57.952 42.857 0.00 0.00 0.00 3.34
1247 1350 2.529780 TCGTACCTTCCTTTTGCGAA 57.470 45.000 0.00 0.00 0.00 4.70
1248 1351 2.409975 CTTCGTACCTTCCTTTTGCGA 58.590 47.619 0.00 0.00 0.00 5.10
1249 1352 1.136057 GCTTCGTACCTTCCTTTTGCG 60.136 52.381 0.00 0.00 0.00 4.85
1250 1353 1.136057 CGCTTCGTACCTTCCTTTTGC 60.136 52.381 0.00 0.00 0.00 3.68
1251 1354 1.136057 GCGCTTCGTACCTTCCTTTTG 60.136 52.381 0.00 0.00 0.00 2.44
1252 1355 1.154197 GCGCTTCGTACCTTCCTTTT 58.846 50.000 0.00 0.00 0.00 2.27
1253 1356 0.320697 AGCGCTTCGTACCTTCCTTT 59.679 50.000 2.64 0.00 0.00 3.11
1254 1357 0.320697 AAGCGCTTCGTACCTTCCTT 59.679 50.000 18.98 0.00 0.00 3.36
1255 1358 0.389948 CAAGCGCTTCGTACCTTCCT 60.390 55.000 22.21 0.00 0.00 3.36
1256 1359 0.389426 TCAAGCGCTTCGTACCTTCC 60.389 55.000 22.21 0.00 0.00 3.46
1257 1360 0.714439 GTCAAGCGCTTCGTACCTTC 59.286 55.000 22.21 0.95 0.00 3.46
1258 1361 1.007336 CGTCAAGCGCTTCGTACCTT 61.007 55.000 22.21 0.00 0.00 3.50
1259 1362 1.443872 CGTCAAGCGCTTCGTACCT 60.444 57.895 22.21 0.00 0.00 3.08
1260 1363 0.801067 ATCGTCAAGCGCTTCGTACC 60.801 55.000 22.21 5.36 41.07 3.34
1261 1364 0.989890 AATCGTCAAGCGCTTCGTAC 59.010 50.000 22.21 17.14 41.07 3.67
1262 1365 1.135489 AGAATCGTCAAGCGCTTCGTA 60.135 47.619 22.21 11.97 46.54 3.43
1263 1366 0.388649 AGAATCGTCAAGCGCTTCGT 60.389 50.000 22.21 6.88 46.54 3.85
1264 1367 0.716108 AAGAATCGTCAAGCGCTTCG 59.284 50.000 22.21 21.71 46.54 3.79
1265 1368 1.996191 AGAAGAATCGTCAAGCGCTTC 59.004 47.619 22.21 9.44 43.58 3.86
1266 1369 2.086054 AGAAGAATCGTCAAGCGCTT 57.914 45.000 18.98 18.98 41.07 4.68
1267 1370 2.086054 AAGAAGAATCGTCAAGCGCT 57.914 45.000 2.64 2.64 41.07 5.92
1268 1371 3.368236 ACTTAAGAAGAATCGTCAAGCGC 59.632 43.478 10.09 0.00 41.07 5.92
1269 1372 4.722346 GCACTTAAGAAGAATCGTCAAGCG 60.722 45.833 10.09 0.00 43.01 4.68
1270 1373 4.152402 TGCACTTAAGAAGAATCGTCAAGC 59.848 41.667 10.09 0.00 0.00 4.01
1271 1374 5.845985 TGCACTTAAGAAGAATCGTCAAG 57.154 39.130 10.09 0.00 0.00 3.02
1272 1375 6.612247 TTTGCACTTAAGAAGAATCGTCAA 57.388 33.333 10.09 0.00 0.00 3.18
1273 1376 6.801539 ATTTGCACTTAAGAAGAATCGTCA 57.198 33.333 10.09 0.00 0.00 4.35
1278 1381 8.193438 GCCAGATAATTTGCACTTAAGAAGAAT 58.807 33.333 10.09 1.41 0.00 2.40
1335 1442 7.729124 ATCTTTTGAAATCTCCATGGTTCAT 57.271 32.000 12.58 0.00 30.51 2.57
1371 1478 1.964552 GCAGGAGCTAACATGAGCAT 58.035 50.000 8.91 0.00 45.43 3.79
1407 1521 6.916360 TCTGGCATACATACAGATCACATA 57.084 37.500 0.00 0.00 36.41 2.29
1459 1574 4.879545 GGTAACCATCAACACGGACATAAT 59.120 41.667 0.00 0.00 0.00 1.28
1621 1741 2.004808 GCTGCGGGAATGGCTTTACC 62.005 60.000 4.28 4.28 34.56 2.85
1727 1847 1.700042 CGCCAAAGCCCCCTCTATCT 61.700 60.000 0.00 0.00 34.57 1.98
1764 1886 4.612943 GAAGCTACCTCGTAGATCTTTGG 58.387 47.826 0.00 0.97 38.29 3.28
1823 1948 1.479323 AGGCGCACGATTTAACTAGGA 59.521 47.619 10.83 0.00 0.00 2.94
1842 1970 4.098654 AGGCTACTATAGAAGTGCACACAG 59.901 45.833 21.04 8.51 39.39 3.66
1856 1984 8.630054 TGTTGTTATTGTGAAAAGGCTACTAT 57.370 30.769 0.00 0.00 0.00 2.12
1860 1988 7.375053 GGATTGTTGTTATTGTGAAAAGGCTA 58.625 34.615 0.00 0.00 0.00 3.93
1897 2025 0.596082 CACGTCAATCCAACCCAACC 59.404 55.000 0.00 0.00 0.00 3.77
1916 2046 0.729140 CGAAGGTTTTGGCATCGCAC 60.729 55.000 0.00 0.00 0.00 5.34
2032 2162 3.772025 AGTAAGGTCTCTCAGTTCCATGG 59.228 47.826 4.97 4.97 0.00 3.66
2033 2163 5.413309 AAGTAAGGTCTCTCAGTTCCATG 57.587 43.478 0.00 0.00 0.00 3.66
2034 2164 4.468153 GGAAGTAAGGTCTCTCAGTTCCAT 59.532 45.833 0.00 0.00 33.75 3.41
2035 2165 3.833070 GGAAGTAAGGTCTCTCAGTTCCA 59.167 47.826 0.00 0.00 33.75 3.53
2036 2166 4.090819 AGGAAGTAAGGTCTCTCAGTTCC 58.909 47.826 0.00 0.00 33.74 3.62
2037 2167 4.767928 TGAGGAAGTAAGGTCTCTCAGTTC 59.232 45.833 0.00 0.00 0.00 3.01
2038 2168 4.525100 GTGAGGAAGTAAGGTCTCTCAGTT 59.475 45.833 0.00 0.00 32.79 3.16
2039 2169 4.083565 GTGAGGAAGTAAGGTCTCTCAGT 58.916 47.826 0.00 0.00 32.79 3.41
2040 2170 4.157656 CAGTGAGGAAGTAAGGTCTCTCAG 59.842 50.000 0.00 0.00 32.79 3.35
2041 2171 4.082845 CAGTGAGGAAGTAAGGTCTCTCA 58.917 47.826 0.00 0.00 0.00 3.27
2042 2172 4.337145 TCAGTGAGGAAGTAAGGTCTCTC 58.663 47.826 0.00 0.00 0.00 3.20
2043 2173 4.390129 TCAGTGAGGAAGTAAGGTCTCT 57.610 45.455 0.00 0.00 0.00 3.10
2044 2174 4.281182 TGTTCAGTGAGGAAGTAAGGTCTC 59.719 45.833 0.00 0.00 0.00 3.36
2045 2175 4.223953 TGTTCAGTGAGGAAGTAAGGTCT 58.776 43.478 0.00 0.00 0.00 3.85
2046 2176 4.602340 TGTTCAGTGAGGAAGTAAGGTC 57.398 45.455 0.00 0.00 0.00 3.85
2047 2177 5.552178 GAATGTTCAGTGAGGAAGTAAGGT 58.448 41.667 0.00 0.00 0.00 3.50
2048 2178 4.627467 CGAATGTTCAGTGAGGAAGTAAGG 59.373 45.833 0.00 0.00 0.00 2.69
2049 2179 4.627467 CCGAATGTTCAGTGAGGAAGTAAG 59.373 45.833 0.00 0.00 0.00 2.34
2050 2180 4.282449 TCCGAATGTTCAGTGAGGAAGTAA 59.718 41.667 0.00 0.00 0.00 2.24
2051 2181 3.830178 TCCGAATGTTCAGTGAGGAAGTA 59.170 43.478 0.00 0.00 0.00 2.24
2052 2182 2.632996 TCCGAATGTTCAGTGAGGAAGT 59.367 45.455 0.00 0.00 0.00 3.01
2053 2183 3.319137 TCCGAATGTTCAGTGAGGAAG 57.681 47.619 0.00 0.00 0.00 3.46
2054 2184 3.599343 CATCCGAATGTTCAGTGAGGAA 58.401 45.455 1.07 0.00 0.00 3.36
2055 2185 2.093500 CCATCCGAATGTTCAGTGAGGA 60.093 50.000 0.00 0.00 0.00 3.71
2056 2186 2.093500 TCCATCCGAATGTTCAGTGAGG 60.093 50.000 0.00 0.00 0.00 3.86
2057 2187 2.932614 GTCCATCCGAATGTTCAGTGAG 59.067 50.000 0.00 0.00 0.00 3.51
2058 2188 2.301583 TGTCCATCCGAATGTTCAGTGA 59.698 45.455 0.00 0.00 0.00 3.41
2059 2189 2.674852 CTGTCCATCCGAATGTTCAGTG 59.325 50.000 0.00 0.00 32.20 3.66
2060 2190 2.355108 CCTGTCCATCCGAATGTTCAGT 60.355 50.000 3.57 0.00 33.59 3.41
2061 2191 2.283298 CCTGTCCATCCGAATGTTCAG 58.717 52.381 0.00 0.00 34.41 3.02
2062 2192 1.678728 GCCTGTCCATCCGAATGTTCA 60.679 52.381 0.00 0.00 0.00 3.18
2063 2193 1.017387 GCCTGTCCATCCGAATGTTC 58.983 55.000 0.00 0.00 0.00 3.18
2064 2194 0.394352 GGCCTGTCCATCCGAATGTT 60.394 55.000 0.00 0.00 34.01 2.71
2065 2195 1.224592 GGCCTGTCCATCCGAATGT 59.775 57.895 0.00 0.00 34.01 2.71
2066 2196 1.889105 CGGCCTGTCCATCCGAATG 60.889 63.158 0.00 0.00 45.53 2.67
2067 2197 2.505982 CGGCCTGTCCATCCGAAT 59.494 61.111 0.00 0.00 45.53 3.34
2068 2198 3.781307 CCGGCCTGTCCATCCGAA 61.781 66.667 0.00 0.00 45.53 4.30
2069 2199 4.770362 TCCGGCCTGTCCATCCGA 62.770 66.667 0.00 0.00 45.53 4.55
2070 2200 4.530857 GTCCGGCCTGTCCATCCG 62.531 72.222 0.00 0.00 42.58 4.18
2071 2201 3.391665 CTGTCCGGCCTGTCCATCC 62.392 68.421 0.00 0.00 34.01 3.51
2072 2202 1.899437 TTCTGTCCGGCCTGTCCATC 61.899 60.000 0.00 0.00 34.01 3.51
2073 2203 1.918293 TTCTGTCCGGCCTGTCCAT 60.918 57.895 0.00 0.00 34.01 3.41
2074 2204 2.525629 TTCTGTCCGGCCTGTCCA 60.526 61.111 0.00 0.00 34.01 4.02
2075 2205 2.047179 GTTCTGTCCGGCCTGTCC 60.047 66.667 0.00 0.00 0.00 4.02
2076 2206 2.047179 GGTTCTGTCCGGCCTGTC 60.047 66.667 0.00 0.00 0.00 3.51
2077 2207 3.637273 GGGTTCTGTCCGGCCTGT 61.637 66.667 0.00 0.00 0.00 4.00
2078 2208 4.760047 CGGGTTCTGTCCGGCCTG 62.760 72.222 0.00 0.00 43.45 4.85
2083 2213 2.048503 GTGTCCGGGTTCTGTCCG 60.049 66.667 0.00 0.00 46.43 4.79
2084 2214 1.301479 GTGTGTCCGGGTTCTGTCC 60.301 63.158 0.00 0.00 0.00 4.02
2085 2215 0.878961 GTGTGTGTCCGGGTTCTGTC 60.879 60.000 0.00 0.00 0.00 3.51
2086 2216 1.145377 GTGTGTGTCCGGGTTCTGT 59.855 57.895 0.00 0.00 0.00 3.41
2087 2217 0.462937 TTGTGTGTGTCCGGGTTCTG 60.463 55.000 0.00 0.00 0.00 3.02
2088 2218 0.253610 TTTGTGTGTGTCCGGGTTCT 59.746 50.000 0.00 0.00 0.00 3.01
2089 2219 1.096416 TTTTGTGTGTGTCCGGGTTC 58.904 50.000 0.00 0.00 0.00 3.62
2090 2220 0.812549 GTTTTGTGTGTGTCCGGGTT 59.187 50.000 0.00 0.00 0.00 4.11
2091 2221 0.322636 TGTTTTGTGTGTGTCCGGGT 60.323 50.000 0.00 0.00 0.00 5.28
2092 2222 2.483441 TGTTTTGTGTGTGTCCGGG 58.517 52.632 0.00 0.00 0.00 5.73


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

AutoCloner maintained by Alex Coulton.