Multiple sequence alignment - TraesCS5B01G209400

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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 TraesCS5B01G209400 chr5B 100.000 6462 0 0 1 6462 379003275 378996814 0.000000e+00 11934
1 TraesCS5B01G209400 chr5D 95.697 3765 110 32 799 4538 326461416 326457679 0.000000e+00 6008
2 TraesCS5B01G209400 chr5D 91.245 1325 77 20 4537 5829 326457522 326456205 0.000000e+00 1768
3 TraesCS5B01G209400 chr5D 87.448 725 64 5 8 707 326462404 326461682 0.000000e+00 809
4 TraesCS5B01G209400 chr5D 83.932 473 70 2 5995 6462 326456161 326455690 1.280000e-121 448
5 TraesCS5B01G209400 chr5A 94.918 3778 119 36 799 4538 429980770 429984512 0.000000e+00 5845
6 TraesCS5B01G209400 chr5A 89.353 1794 101 39 4537 6264 429984669 429986438 0.000000e+00 2172
7 TraesCS5B01G209400 chr5A 83.824 680 78 9 91 744 429968148 429968821 9.210000e-173 617
8 TraesCS5B01G209400 chr6D 86.926 2157 183 55 2220 4331 411193395 411191293 0.000000e+00 2329
9 TraesCS5B01G209400 chr6D 79.620 790 97 37 1325 2101 411194286 411193548 5.780000e-140 508
10 TraesCS5B01G209400 chr6D 91.507 365 28 3 4581 4945 411191110 411190749 3.480000e-137 499
11 TraesCS5B01G209400 chr6D 84.783 276 35 7 5044 5315 411190459 411190187 2.970000e-68 270
12 TraesCS5B01G209400 chr6D 77.522 347 38 21 5316 5649 411190149 411189830 8.610000e-39 172
13 TraesCS5B01G209400 chr6A 87.773 1145 102 23 2263 3386 555934072 555932945 0.000000e+00 1304
14 TraesCS5B01G209400 chr6A 91.304 920 71 7 3391 4306 555932908 555931994 0.000000e+00 1247
15 TraesCS5B01G209400 chr6A 79.380 1033 143 41 1073 2086 555935083 555934102 0.000000e+00 664
16 TraesCS5B01G209400 chr6A 92.055 365 27 2 4581 4945 555931959 555931597 4.470000e-141 512
17 TraesCS5B01G209400 chr6A 77.385 650 75 37 5044 5649 555931300 555930679 2.910000e-83 320
18 TraesCS5B01G209400 chr6A 91.743 109 8 1 4302 4409 93798346 93798454 4.040000e-32 150
19 TraesCS5B01G209400 chr6B 86.960 1181 116 24 2218 3386 617982994 617981840 0.000000e+00 1293
20 TraesCS5B01G209400 chr6B 90.813 947 72 12 3368 4306 617981828 617980889 0.000000e+00 1253
21 TraesCS5B01G209400 chr6B 89.009 646 44 13 4406 5041 617980881 617980253 0.000000e+00 774
22 TraesCS5B01G209400 chr6B 79.757 1072 121 45 1073 2101 617984179 617983161 0.000000e+00 689
23 TraesCS5B01G209400 chr6B 78.909 678 67 41 5045 5649 617980035 617979361 2.180000e-104 390
24 TraesCS5B01G209400 chr7A 76.059 543 114 9 5754 6287 144135538 144135003 1.070000e-67 268
25 TraesCS5B01G209400 chr7B 90.909 121 9 2 4305 4423 162120908 162120788 1.860000e-35 161
26 TraesCS5B01G209400 chr4D 93.396 106 5 2 4305 4408 414999659 414999554 8.680000e-34 156
27 TraesCS5B01G209400 chr4B 93.333 105 6 1 4305 4408 511163805 511163701 3.120000e-33 154
28 TraesCS5B01G209400 chr3A 93.269 104 7 0 4305 4408 470095682 470095785 3.120000e-33 154
29 TraesCS5B01G209400 chr7D 94.000 100 6 0 4305 4404 580850179 580850080 1.120000e-32 152
30 TraesCS5B01G209400 chr3D 91.589 107 9 0 4302 4408 609983907 609983801 1.450000e-31 148


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 TraesCS5B01G209400 chr5B 378996814 379003275 6461 True 11934.00 11934 100.0000 1 6462 1 chr5B.!!$R1 6461
1 TraesCS5B01G209400 chr5D 326455690 326462404 6714 True 2258.25 6008 89.5805 8 6462 4 chr5D.!!$R1 6454
2 TraesCS5B01G209400 chr5A 429980770 429986438 5668 False 4008.50 5845 92.1355 799 6264 2 chr5A.!!$F2 5465
3 TraesCS5B01G209400 chr5A 429968148 429968821 673 False 617.00 617 83.8240 91 744 1 chr5A.!!$F1 653
4 TraesCS5B01G209400 chr6D 411189830 411194286 4456 True 755.60 2329 84.0716 1325 5649 5 chr6D.!!$R1 4324
5 TraesCS5B01G209400 chr6A 555930679 555935083 4404 True 809.40 1304 85.5794 1073 5649 5 chr6A.!!$R1 4576
6 TraesCS5B01G209400 chr6B 617979361 617984179 4818 True 879.80 1293 85.0896 1073 5649 5 chr6B.!!$R1 4576
7 TraesCS5B01G209400 chr7A 144135003 144135538 535 True 268.00 268 76.0590 5754 6287 1 chr7A.!!$R1 533

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
51 52 0.033405 TCCTTCGTCTTCCTCCCGAT 60.033 55.000 0.00 0.0 0.00 4.18 F
773 801 0.035458 TGTGTGTGTGTGTGTGTGGA 59.965 50.000 0.00 0.0 0.00 4.02 F
779 807 0.035534 TGTGTGTGTGTGGAGTGCTT 60.036 50.000 0.00 0.0 0.00 3.91 F
783 811 0.107897 TGTGTGTGGAGTGCTTCGTT 60.108 50.000 0.00 0.0 0.00 3.85 F
2179 2632 0.635688 TAGTACCCCTCCCCTCCCAT 60.636 60.000 0.00 0.0 0.00 4.00 F
3103 3570 3.681593 TTGCAGTGCAAGGCAATATTT 57.318 38.095 26.36 0.0 43.99 1.40 F
4330 4875 4.527038 TCCCTCCGATCCATAATAAGTGTC 59.473 45.833 0.00 0.0 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1298 1564 0.175989 GCTCGTTAGGTCTTGGGGAG 59.824 60.000 0.00 0.00 0.00 4.30 R
2179 2632 0.034198 TTGACGCTCAAACGGGATGA 59.966 50.000 0.00 0.00 32.71 2.92 R
2554 3015 6.094603 TCCTGCTCAATTTCTGAAATTAGCTC 59.905 38.462 30.34 20.82 38.97 4.09 R
2751 3212 8.364894 TGCACTAATAGGTACACACATAATAGG 58.635 37.037 0.00 0.00 31.59 2.57 R
3401 3935 1.144913 AGCTACCAAAGGAAGGCAACA 59.855 47.619 0.00 0.00 41.41 3.33 R
4371 4916 0.373716 GATCCAAAGTAAGTGCCGCG 59.626 55.000 0.00 0.00 0.00 6.46 R
6264 7638 0.179081 GGATTCTACTCGGCGGCTTT 60.179 55.000 7.21 0.00 0.00 3.51 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
29 30 6.072286 CCACACATGCATAATCTTATCTTCCC 60.072 42.308 0.00 0.00 0.00 3.97
48 49 0.466124 CCATCCTTCGTCTTCCTCCC 59.534 60.000 0.00 0.00 0.00 4.30
51 52 0.033405 TCCTTCGTCTTCCTCCCGAT 60.033 55.000 0.00 0.00 0.00 4.18
54 55 2.022195 CTTCGTCTTCCTCCCGATACA 58.978 52.381 0.00 0.00 0.00 2.29
83 84 8.542926 CCTTTTCCCTAATCAATTTTTCCTCAT 58.457 33.333 0.00 0.00 0.00 2.90
84 85 9.591792 CTTTTCCCTAATCAATTTTTCCTCATC 57.408 33.333 0.00 0.00 0.00 2.92
85 86 8.899887 TTTCCCTAATCAATTTTTCCTCATCT 57.100 30.769 0.00 0.00 0.00 2.90
113 117 1.073763 CCACCTGTCCAATTCCACTCA 59.926 52.381 0.00 0.00 0.00 3.41
162 166 1.302033 CGGTCTCCTGCTGCTTGTT 60.302 57.895 0.00 0.00 0.00 2.83
164 168 0.250467 GGTCTCCTGCTGCTTGTTCA 60.250 55.000 0.00 0.00 0.00 3.18
280 285 1.844771 GCACAATGACTGCTGCGACA 61.845 55.000 0.00 0.00 0.00 4.35
300 305 2.264166 GAGCTGCAAGACTCGCCT 59.736 61.111 1.02 0.00 34.07 5.52
301 306 1.375268 GAGCTGCAAGACTCGCCTT 60.375 57.895 1.02 0.00 34.07 4.35
346 351 3.634910 GGGTGTTGTAATGTCAACCAACT 59.365 43.478 9.68 0.00 44.66 3.16
361 366 1.098050 CAACTAATGCCCTCACTGCC 58.902 55.000 0.00 0.00 0.00 4.85
400 405 2.108157 AAACACTGCCGCGAGTCA 59.892 55.556 8.23 0.97 0.00 3.41
421 426 0.613853 ATGTGCTGCCATGGAGCTTT 60.614 50.000 26.29 14.40 37.35 3.51
432 437 2.598394 GAGCTTTGCCAGGCCACA 60.598 61.111 9.64 0.00 0.00 4.17
451 456 0.886563 ATTGCTGCAGTGGAGCTTTC 59.113 50.000 32.76 8.92 37.35 2.62
484 489 1.061711 GAGCTGCAATGAAGCACTACG 59.938 52.381 16.64 0.00 43.37 3.51
503 508 1.692411 GGGGTTGTTGAAGCTCAGTT 58.308 50.000 0.00 0.00 29.77 3.16
520 525 1.755959 AGTTGTGGTTGCAATGAAGCA 59.244 42.857 0.59 0.00 43.99 3.91
523 528 0.388659 GTGGTTGCAATGAAGCACCA 59.611 50.000 0.59 0.21 44.81 4.17
524 529 1.001181 GTGGTTGCAATGAAGCACCAT 59.999 47.619 0.59 0.00 44.81 3.55
527 533 0.109179 TTGCAATGAAGCACCATCGC 60.109 50.000 0.00 0.00 45.61 4.58
578 606 0.106708 TGAAGAGCCTCGTTGCACTT 59.893 50.000 10.19 10.19 43.42 3.16
646 674 1.000607 GTTGTAGCTCTGTCGGTGACA 60.001 52.381 0.00 0.00 40.50 3.58
681 709 1.815421 GGTGCTGGCTGGTACATCG 60.815 63.158 0.00 0.00 38.20 3.84
686 714 2.585247 GGCTGGTACATCGACGGC 60.585 66.667 0.00 0.00 38.20 5.68
707 735 2.434185 GCGACCGATTGGAGTGCA 60.434 61.111 5.81 0.00 39.21 4.57
716 744 0.245539 ATTGGAGTGCAACATGCTGC 59.754 50.000 14.21 14.21 45.31 5.25
722 750 3.368822 GCAACATGCTGCAAGGGA 58.631 55.556 16.08 0.00 42.17 4.20
724 752 1.888018 CAACATGCTGCAAGGGAGG 59.112 57.895 6.36 0.00 0.00 4.30
726 754 1.792757 AACATGCTGCAAGGGAGGGA 61.793 55.000 6.36 0.00 0.00 4.20
727 755 1.751927 CATGCTGCAAGGGAGGGAC 60.752 63.158 6.36 0.00 0.00 4.46
728 756 3.335356 ATGCTGCAAGGGAGGGACG 62.335 63.158 6.36 0.00 0.00 4.79
729 757 4.785453 GCTGCAAGGGAGGGACGG 62.785 72.222 0.00 0.00 0.00 4.79
730 758 4.101448 CTGCAAGGGAGGGACGGG 62.101 72.222 0.00 0.00 0.00 5.28
733 761 4.733725 CAAGGGAGGGACGGGGGA 62.734 72.222 0.00 0.00 0.00 4.81
734 762 4.735599 AAGGGAGGGACGGGGGAC 62.736 72.222 0.00 0.00 0.00 4.46
745 773 4.636435 GGGGGACGGGTGTGTGTG 62.636 72.222 0.00 0.00 0.00 3.82
746 774 3.868985 GGGGACGGGTGTGTGTGT 61.869 66.667 0.00 0.00 0.00 3.72
747 775 2.590575 GGGACGGGTGTGTGTGTG 60.591 66.667 0.00 0.00 0.00 3.82
748 776 2.188469 GGACGGGTGTGTGTGTGT 59.812 61.111 0.00 0.00 0.00 3.72
749 777 2.177580 GGACGGGTGTGTGTGTGTG 61.178 63.158 0.00 0.00 0.00 3.82
750 778 2.124901 ACGGGTGTGTGTGTGTGG 60.125 61.111 0.00 0.00 0.00 4.17
751 779 2.899838 CGGGTGTGTGTGTGTGGG 60.900 66.667 0.00 0.00 0.00 4.61
752 780 2.274104 GGGTGTGTGTGTGTGGGT 59.726 61.111 0.00 0.00 0.00 4.51
753 781 2.118404 GGGTGTGTGTGTGTGGGTG 61.118 63.158 0.00 0.00 0.00 4.61
754 782 1.377987 GGTGTGTGTGTGTGGGTGT 60.378 57.895 0.00 0.00 0.00 4.16
755 783 1.653094 GGTGTGTGTGTGTGGGTGTG 61.653 60.000 0.00 0.00 0.00 3.82
756 784 0.958382 GTGTGTGTGTGTGGGTGTGT 60.958 55.000 0.00 0.00 0.00 3.72
757 785 0.957888 TGTGTGTGTGTGGGTGTGTG 60.958 55.000 0.00 0.00 0.00 3.82
758 786 0.958382 GTGTGTGTGTGGGTGTGTGT 60.958 55.000 0.00 0.00 0.00 3.72
759 787 0.957888 TGTGTGTGTGGGTGTGTGTG 60.958 55.000 0.00 0.00 0.00 3.82
760 788 0.958382 GTGTGTGTGGGTGTGTGTGT 60.958 55.000 0.00 0.00 0.00 3.72
761 789 0.957888 TGTGTGTGGGTGTGTGTGTG 60.958 55.000 0.00 0.00 0.00 3.82
762 790 0.958382 GTGTGTGGGTGTGTGTGTGT 60.958 55.000 0.00 0.00 0.00 3.72
763 791 0.957888 TGTGTGGGTGTGTGTGTGTG 60.958 55.000 0.00 0.00 0.00 3.82
764 792 0.958382 GTGTGGGTGTGTGTGTGTGT 60.958 55.000 0.00 0.00 0.00 3.72
765 793 0.957888 TGTGGGTGTGTGTGTGTGTG 60.958 55.000 0.00 0.00 0.00 3.82
766 794 0.958382 GTGGGTGTGTGTGTGTGTGT 60.958 55.000 0.00 0.00 0.00 3.72
767 795 0.957888 TGGGTGTGTGTGTGTGTGTG 60.958 55.000 0.00 0.00 0.00 3.82
768 796 0.958382 GGGTGTGTGTGTGTGTGTGT 60.958 55.000 0.00 0.00 0.00 3.72
769 797 0.167908 GGTGTGTGTGTGTGTGTGTG 59.832 55.000 0.00 0.00 0.00 3.82
770 798 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
771 799 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
772 800 0.167908 GTGTGTGTGTGTGTGTGTGG 59.832 55.000 0.00 0.00 0.00 4.17
773 801 0.035458 TGTGTGTGTGTGTGTGTGGA 59.965 50.000 0.00 0.00 0.00 4.02
774 802 0.726827 GTGTGTGTGTGTGTGTGGAG 59.273 55.000 0.00 0.00 0.00 3.86
775 803 0.323302 TGTGTGTGTGTGTGTGGAGT 59.677 50.000 0.00 0.00 0.00 3.85
776 804 0.726827 GTGTGTGTGTGTGTGGAGTG 59.273 55.000 0.00 0.00 0.00 3.51
777 805 1.024046 TGTGTGTGTGTGTGGAGTGC 61.024 55.000 0.00 0.00 0.00 4.40
778 806 0.744414 GTGTGTGTGTGTGGAGTGCT 60.744 55.000 0.00 0.00 0.00 4.40
779 807 0.035534 TGTGTGTGTGTGGAGTGCTT 60.036 50.000 0.00 0.00 0.00 3.91
780 808 0.657840 GTGTGTGTGTGGAGTGCTTC 59.342 55.000 0.00 0.00 0.00 3.86
781 809 0.809636 TGTGTGTGTGGAGTGCTTCG 60.810 55.000 0.00 0.00 0.00 3.79
782 810 0.810031 GTGTGTGTGGAGTGCTTCGT 60.810 55.000 0.00 0.00 0.00 3.85
783 811 0.107897 TGTGTGTGGAGTGCTTCGTT 60.108 50.000 0.00 0.00 0.00 3.85
784 812 1.014352 GTGTGTGGAGTGCTTCGTTT 58.986 50.000 0.00 0.00 0.00 3.60
785 813 1.400494 GTGTGTGGAGTGCTTCGTTTT 59.600 47.619 0.00 0.00 0.00 2.43
786 814 2.088423 TGTGTGGAGTGCTTCGTTTTT 58.912 42.857 0.00 0.00 0.00 1.94
787 815 2.159448 TGTGTGGAGTGCTTCGTTTTTG 60.159 45.455 0.00 0.00 0.00 2.44
788 816 1.202245 TGTGGAGTGCTTCGTTTTTGC 60.202 47.619 0.00 0.00 0.00 3.68
789 817 1.098869 TGGAGTGCTTCGTTTTTGCA 58.901 45.000 0.00 0.00 0.00 4.08
790 818 1.474478 TGGAGTGCTTCGTTTTTGCAA 59.526 42.857 0.00 0.00 38.50 4.08
791 819 2.094494 TGGAGTGCTTCGTTTTTGCAAA 60.094 40.909 8.05 8.05 38.50 3.68
792 820 2.281498 GGAGTGCTTCGTTTTTGCAAAC 59.719 45.455 12.39 0.58 38.50 2.93
819 1021 1.521457 GATCGAAGGGTCATGCGCA 60.521 57.895 14.96 14.96 0.00 6.09
820 1022 1.766143 GATCGAAGGGTCATGCGCAC 61.766 60.000 14.90 0.00 0.00 5.34
841 1043 2.887568 GATCGGACGGCTGTGCAG 60.888 66.667 17.98 10.00 35.97 4.41
899 1101 2.095461 GGGGATCTTTTTGCAGAGACC 58.905 52.381 0.00 3.89 0.00 3.85
944 1147 1.001860 CCATCAAACGGCCCATGTTTT 59.998 47.619 4.67 0.00 37.44 2.43
984 1196 3.543665 AGCTCCGATTTACTCTAGTCGT 58.456 45.455 0.00 0.00 32.55 4.34
1002 1214 0.756070 GTTCCCGACCAACCCCAAAA 60.756 55.000 0.00 0.00 0.00 2.44
1004 1216 2.557372 CCCGACCAACCCCAAAACG 61.557 63.158 0.00 0.00 0.00 3.60
1005 1217 2.557372 CCGACCAACCCCAAAACGG 61.557 63.158 0.00 0.00 0.00 4.44
1157 1388 2.203451 GATCCCCGACTCCCGCTA 60.203 66.667 0.00 0.00 36.84 4.26
1200 1431 1.296715 GCACAAGGACGTGGAGGAT 59.703 57.895 0.00 0.00 37.37 3.24
1216 1447 2.699846 GAGGATGTCATCAAGAGGCTCT 59.300 50.000 12.24 12.24 0.00 4.09
1460 1740 1.021390 CGCGCTCAAGGTGATTTCCT 61.021 55.000 5.56 0.00 39.84 3.36
1485 1767 1.470098 CTCTGTGTGGCATTTAGGTGC 59.530 52.381 0.00 0.00 44.31 5.01
1590 1879 4.335315 GTGTTCGATATTGGAATGAAGGCA 59.665 41.667 0.00 0.00 0.00 4.75
1722 2014 6.096846 TCGGAGAGATGTATGATTCAGTTCAA 59.903 38.462 0.00 0.00 0.00 2.69
1740 2032 8.729756 TCAGTTCAATGTGTATTTGTATTGGAG 58.270 33.333 0.00 0.00 0.00 3.86
1796 2088 5.220080 CGATGTTCTCAATTTGCCAATTTCG 60.220 40.000 0.00 0.00 29.41 3.46
1798 2090 4.202202 TGTTCTCAATTTGCCAATTTCGGT 60.202 37.500 0.00 0.00 29.41 4.69
1868 2164 5.861222 TGTGCAATACTTACATCTGTGTG 57.139 39.130 0.00 0.00 39.39 3.82
1884 2180 3.031013 TGTGTGAACTGAAGGTCTCTCA 58.969 45.455 0.00 0.00 0.00 3.27
2052 2504 4.438744 GCTCGTTGTTCCTCCCATATTTTG 60.439 45.833 0.00 0.00 0.00 2.44
2067 2520 5.813672 CCATATTTTGGCATTTCCACTTGAG 59.186 40.000 0.00 0.00 46.55 3.02
2089 2542 5.220931 GAGCCATTTACTGGATTGTGTCATC 60.221 44.000 0.00 0.00 45.98 2.92
2090 2543 7.355301 GAGCCATTTACTGGATTGTGTCATCT 61.355 42.308 0.00 0.00 45.98 2.90
2091 2544 9.273096 GAGCCATTTACTGGATTGTGTCATCTG 62.273 44.444 0.00 0.00 45.98 2.90
2092 2545 6.748333 CATTTACTGGATTGTGTCATCTGT 57.252 37.500 0.00 0.00 0.00 3.41
2142 2595 7.157947 TGTACAATATCTAGTACTCCCTCCA 57.842 40.000 0.00 0.00 40.84 3.86
2165 2618 8.978472 TCCATCCCATATTACAATAGCTAGTAC 58.022 37.037 0.00 0.00 0.00 2.73
2169 2622 6.672657 CCCATATTACAATAGCTAGTACCCCT 59.327 42.308 0.00 0.00 0.00 4.79
2173 2626 2.258109 CAATAGCTAGTACCCCTCCCC 58.742 57.143 0.00 0.00 0.00 4.81
2174 2627 1.863386 ATAGCTAGTACCCCTCCCCT 58.137 55.000 0.00 0.00 0.00 4.79
2178 2631 1.231059 TAGTACCCCTCCCCTCCCA 60.231 63.158 0.00 0.00 0.00 4.37
2179 2632 0.635688 TAGTACCCCTCCCCTCCCAT 60.636 60.000 0.00 0.00 0.00 4.00
2553 3014 7.684529 AGAGGTAATTTGATGTCACTTCTCTT 58.315 34.615 0.00 0.00 0.00 2.85
2554 3015 7.605691 AGAGGTAATTTGATGTCACTTCTCTTG 59.394 37.037 0.00 0.00 0.00 3.02
2642 3103 5.769662 AGCAATTGAACACTACATGGAAGAA 59.230 36.000 10.34 0.00 0.00 2.52
2715 3176 7.819900 ACCTGTCAAAGACTATGCTAAACTTAG 59.180 37.037 0.00 0.00 33.15 2.18
2729 3190 7.972527 TGCTAAACTTAGTGTCACGTTAAAAA 58.027 30.769 0.00 0.00 33.32 1.94
2731 3192 9.099820 GCTAAACTTAGTGTCACGTTAAAAATC 57.900 33.333 0.00 0.00 33.32 2.17
2735 3196 7.412063 ACTTAGTGTCACGTTAAAAATCAACC 58.588 34.615 0.00 0.00 0.00 3.77
2738 3199 6.859017 AGTGTCACGTTAAAAATCAACCTTT 58.141 32.000 0.00 0.00 0.00 3.11
2739 3200 7.987649 AGTGTCACGTTAAAAATCAACCTTTA 58.012 30.769 0.00 0.00 0.00 1.85
2740 3201 8.460428 AGTGTCACGTTAAAAATCAACCTTTAA 58.540 29.630 0.00 0.00 0.00 1.52
2741 3202 9.074443 GTGTCACGTTAAAAATCAACCTTTAAA 57.926 29.630 0.00 0.00 30.85 1.52
2742 3203 9.635520 TGTCACGTTAAAAATCAACCTTTAAAA 57.364 25.926 0.00 0.00 30.85 1.52
2829 3295 9.967451 TTCCTTTAAAATGGTTTTTCTTTCCTT 57.033 25.926 0.00 0.00 36.47 3.36
2941 3407 9.524496 TTGTTAGAGGTACTTCTAATCTGTACA 57.476 33.333 25.02 17.03 41.55 2.90
3063 3529 7.859325 TTTTTCTCGAGATGGGGTAAATAAG 57.141 36.000 17.44 0.00 0.00 1.73
3072 3539 9.116067 CGAGATGGGGTAAATAAGAACATTTTA 57.884 33.333 0.00 0.00 30.84 1.52
3090 3557 9.577110 AACATTTTAGTCATGATATTTGCAGTG 57.423 29.630 0.00 0.00 0.00 3.66
3103 3570 3.681593 TTGCAGTGCAAGGCAATATTT 57.318 38.095 26.36 0.00 43.99 1.40
3197 3668 6.435428 AGCAGGTAAAACACAAAATAAGACG 58.565 36.000 0.00 0.00 0.00 4.18
3212 3683 9.503427 CAAAATAAGACGAGATATTGTTTTCCC 57.497 33.333 0.00 0.00 32.46 3.97
3372 3871 8.427902 TGAGCATATCACTGTTTCCTAGATAT 57.572 34.615 0.00 0.00 33.45 1.63
3432 3967 5.393866 TCCTTTGGTAGCTTCTGGAATTTT 58.606 37.500 0.00 0.00 0.00 1.82
3850 4385 9.443283 GCAACTAAGTGATGCTTATTTTATCTG 57.557 33.333 0.00 0.00 40.68 2.90
4313 4858 5.823045 CCATTGACTTTGTTATACTCCCTCC 59.177 44.000 0.00 0.00 0.00 4.30
4317 4862 5.068723 TGACTTTGTTATACTCCCTCCGATC 59.931 44.000 0.00 0.00 0.00 3.69
4330 4875 4.527038 TCCCTCCGATCCATAATAAGTGTC 59.473 45.833 0.00 0.00 0.00 3.67
4375 4920 1.799544 ACCTTAGTACAAAACCGCGG 58.200 50.000 26.86 26.86 0.00 6.46
4378 4923 0.867086 TTAGTACAAAACCGCGGCAC 59.133 50.000 28.58 13.44 0.00 5.01
4394 4939 2.280628 GGCACTTACTTTGGATCGGAG 58.719 52.381 0.00 0.00 0.00 4.63
4563 5281 7.109501 TCTGCTATCTCCAGTACATAGAGATC 58.890 42.308 19.56 11.12 44.30 2.75
4712 5430 9.571810 TGCTATTGTTTTCATGATTATTGTGAC 57.428 29.630 0.00 0.00 0.00 3.67
4865 5584 1.597663 GTTATCGCATGGGGTCTTTCG 59.402 52.381 10.21 0.00 0.00 3.46
4888 5607 5.393027 CGCTTGAAAGGTAAAACTGGCATAT 60.393 40.000 0.00 0.00 0.00 1.78
4893 5612 7.957002 TGAAAGGTAAAACTGGCATATTTTCA 58.043 30.769 11.57 8.00 30.80 2.69
5019 5973 2.365293 AGAAGCGCAAGGAAAACCAAAT 59.635 40.909 11.47 0.00 38.28 2.32
5285 6519 2.034879 CGCTTGGGGCTGTAGTGTG 61.035 63.158 0.00 0.00 39.13 3.82
5455 6746 6.806739 TCATGTTCGATACAAGTAGTGTCTTG 59.193 38.462 5.12 5.12 46.89 3.02
5488 6779 0.874175 TCTCCGTCTTGTGTTGCGTG 60.874 55.000 0.00 0.00 0.00 5.34
5619 6931 0.536460 TTTTGAAGCCCGTCCTGTCC 60.536 55.000 0.00 0.00 0.00 4.02
5649 6961 1.525995 CGGCCAACTGTGTGGACTT 60.526 57.895 2.24 0.00 45.54 3.01
5651 6963 1.235724 GGCCAACTGTGTGGACTTAC 58.764 55.000 0.00 0.00 44.17 2.34
5653 6965 2.294074 GCCAACTGTGTGGACTTACAA 58.706 47.619 11.54 0.00 41.65 2.41
5654 6966 2.032924 GCCAACTGTGTGGACTTACAAC 59.967 50.000 11.54 0.00 41.65 3.32
5655 6967 3.275143 CCAACTGTGTGGACTTACAACA 58.725 45.455 3.78 0.00 41.65 3.33
5656 6968 3.882888 CCAACTGTGTGGACTTACAACAT 59.117 43.478 3.78 0.00 41.65 2.71
5659 6995 3.069016 ACTGTGTGGACTTACAACATCGA 59.931 43.478 0.00 0.00 31.36 3.59
5697 7035 7.721402 TGCCTCATCTAACTAAGAGAGAAATC 58.279 38.462 0.00 0.00 37.74 2.17
5724 7062 4.320023 TGTGCTACAACACACCGATATTT 58.680 39.130 0.00 0.00 45.36 1.40
5743 7081 7.173907 CGATATTTCAAATGGGCATTACTCTCT 59.826 37.037 0.00 0.00 0.00 3.10
5765 7107 6.706295 TCTTTGATTGAACCCAACTTTTTGT 58.294 32.000 0.00 0.00 34.72 2.83
5772 7114 0.678950 CCCAACTTTTTGTCGCCCAT 59.321 50.000 0.00 0.00 0.00 4.00
5794 7136 1.540267 GTGACTCAGACTGTCGCCTTA 59.460 52.381 1.59 0.00 38.55 2.69
5817 7159 4.082125 GTTTTGATGTTGTGGAGGAGGAT 58.918 43.478 0.00 0.00 0.00 3.24
5851 7193 3.489785 CACTCTTTTAGCGAAAGACACGT 59.510 43.478 12.44 8.08 46.69 4.49
5860 7202 2.563976 CGAAAGACACGTGCATTTCTG 58.436 47.619 28.74 22.09 31.07 3.02
6005 7347 5.125367 TGAGGTGTCTAGATGCCTAAGTA 57.875 43.478 15.36 3.80 0.00 2.24
6051 7398 4.260784 CCAAAGCCTAATATCGACACTTGC 60.261 45.833 0.00 0.00 0.00 4.01
6066 7413 2.033801 CACTTGCAGAAAAGGTGGTCAG 59.966 50.000 0.00 0.00 0.00 3.51
6079 7426 3.054361 AGGTGGTCAGCGGATTCTTTATT 60.054 43.478 0.00 0.00 0.00 1.40
6099 7446 1.103398 GCGCTTGCATAGGGGACAAT 61.103 55.000 0.00 0.00 38.92 2.71
6100 7447 1.392589 CGCTTGCATAGGGGACAATT 58.607 50.000 0.00 0.00 33.37 2.32
6158 7531 4.462483 TCTGTGGTCCAAATCCTATTTTGC 59.538 41.667 0.00 0.00 35.67 3.68
6163 7536 4.443315 GGTCCAAATCCTATTTTGCATGGG 60.443 45.833 0.00 0.00 35.67 4.00
6185 7558 5.067283 GGGAAGCCAAGCGAAGAATTTAATA 59.933 40.000 0.00 0.00 0.00 0.98
6197 7570 6.073548 CGAAGAATTTAATATTGAGAGGCGCT 60.074 38.462 7.64 0.00 0.00 5.92
6214 7588 2.282180 TCAAGCCTCCCAAACCGC 60.282 61.111 0.00 0.00 0.00 5.68
6220 7594 2.978010 CTCCCAAACCGCGTGCTT 60.978 61.111 4.92 0.00 0.00 3.91
6224 7598 1.285641 CCAAACCGCGTGCTTCATT 59.714 52.632 4.92 0.00 0.00 2.57
6227 7601 1.169661 AAACCGCGTGCTTCATTGGA 61.170 50.000 4.92 0.00 0.00 3.53
6228 7602 1.169661 AACCGCGTGCTTCATTGGAA 61.170 50.000 4.92 0.00 0.00 3.53
6264 7638 2.569853 TGGAATTGGACTTTCTAGGCGA 59.430 45.455 0.00 0.00 0.00 5.54
6279 7653 2.488355 CGAAAGCCGCCGAGTAGA 59.512 61.111 0.00 0.00 0.00 2.59
6281 7655 0.527817 CGAAAGCCGCCGAGTAGAAT 60.528 55.000 0.00 0.00 0.00 2.40
6289 7663 1.230324 GCCGAGTAGAATCCATTGGC 58.770 55.000 0.00 0.00 0.00 4.52
6290 7664 1.502231 CCGAGTAGAATCCATTGGCG 58.498 55.000 0.00 0.00 0.00 5.69
6292 7666 1.202533 CGAGTAGAATCCATTGGCGGT 60.203 52.381 0.00 0.00 0.00 5.68
6319 7693 2.949714 CACACAATGTGGTCTTCGAC 57.050 50.000 18.37 0.00 44.27 4.20
6320 7694 2.209273 CACACAATGTGGTCTTCGACA 58.791 47.619 18.37 0.00 44.27 4.35
6358 7732 1.025812 CTACACAACGTGGCCCAAAA 58.974 50.000 0.00 0.00 37.94 2.44
6370 7744 4.373527 GTGGCCCAAAAAGTAACGAATTT 58.626 39.130 0.00 0.00 0.00 1.82
6374 7748 4.210328 GCCCAAAAAGTAACGAATTTGTGG 59.790 41.667 0.00 0.99 41.59 4.17
6375 7749 5.898630 CCAAAAAGTAACGAATTTGTGGG 57.101 39.130 0.00 0.00 39.27 4.61
6382 7756 0.893727 ACGAATTTGTGGGAGTGGGC 60.894 55.000 0.00 0.00 0.00 5.36
6383 7757 0.893270 CGAATTTGTGGGAGTGGGCA 60.893 55.000 0.00 0.00 0.00 5.36
6412 7786 8.119226 CGTGAAGTTTGAGGATATCTTGATTTC 58.881 37.037 2.05 0.56 0.00 2.17
6420 7794 7.382110 TGAGGATATCTTGATTTCGAAGATCC 58.618 38.462 2.05 7.06 40.09 3.36
6431 7805 4.412796 TTCGAAGATCCAAGCATCATCT 57.587 40.909 0.00 0.00 35.04 2.90
6435 7809 4.262121 CGAAGATCCAAGCATCATCTCTCT 60.262 45.833 0.00 0.00 0.00 3.10
6442 7816 4.130857 CAAGCATCATCTCTCTGAGCATT 58.869 43.478 0.00 0.00 0.00 3.56
6450 7824 8.622157 CATCATCTCTCTGAGCATTTTTAACAT 58.378 33.333 0.00 0.00 0.00 2.71
6452 7826 9.017509 TCATCTCTCTGAGCATTTTTAACATTT 57.982 29.630 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.877855 AGATAAGATTATGCATGTGTGGCTAG 59.122 38.462 10.16 0.00 0.00 3.42
1 2 6.772605 AGATAAGATTATGCATGTGTGGCTA 58.227 36.000 10.16 0.00 0.00 3.93
2 3 5.628130 AGATAAGATTATGCATGTGTGGCT 58.372 37.500 10.16 0.00 0.00 4.75
3 4 5.954296 AGATAAGATTATGCATGTGTGGC 57.046 39.130 10.16 0.00 0.00 5.01
4 5 6.072286 GGGAAGATAAGATTATGCATGTGTGG 60.072 42.308 10.16 0.00 0.00 4.17
5 6 6.072286 GGGGAAGATAAGATTATGCATGTGTG 60.072 42.308 10.16 0.00 0.00 3.82
6 7 6.006449 GGGGAAGATAAGATTATGCATGTGT 58.994 40.000 10.16 0.00 0.00 3.72
12 13 6.072199 AGGATGGGGAAGATAAGATTATGC 57.928 41.667 0.00 0.00 0.00 3.14
19 20 3.643792 AGACGAAGGATGGGGAAGATAAG 59.356 47.826 0.00 0.00 0.00 1.73
29 30 0.466124 GGGAGGAAGACGAAGGATGG 59.534 60.000 0.00 0.00 0.00 3.51
48 49 5.865085 TGATTAGGGAAAAGGGATGTATCG 58.135 41.667 0.00 0.00 0.00 2.92
51 52 8.909423 AAAATTGATTAGGGAAAAGGGATGTA 57.091 30.769 0.00 0.00 0.00 2.29
54 55 7.684186 AGGAAAAATTGATTAGGGAAAAGGGAT 59.316 33.333 0.00 0.00 0.00 3.85
83 84 1.754745 GACAGGTGGGAGCAACAGA 59.245 57.895 0.00 0.00 0.00 3.41
84 85 1.302832 GGACAGGTGGGAGCAACAG 60.303 63.158 0.00 0.00 0.00 3.16
85 86 1.640593 TTGGACAGGTGGGAGCAACA 61.641 55.000 0.00 0.00 0.00 3.33
113 117 1.439353 CTAGCATCATGCCGGCGTTT 61.439 55.000 21.21 6.74 46.52 3.60
162 166 3.372730 GGCCCGTTTGCAGCATGA 61.373 61.111 0.00 0.00 39.69 3.07
164 168 3.376078 CAGGCCCGTTTGCAGCAT 61.376 61.111 0.00 0.00 0.00 3.79
193 197 2.240162 GACCATGACCGGTGACTCCC 62.240 65.000 14.63 0.00 40.22 4.30
254 258 1.746615 CAGTCATTGTGCTCCGGGG 60.747 63.158 0.00 0.00 0.00 5.73
267 272 1.006922 CTCTGTGTCGCAGCAGTCA 60.007 57.895 8.61 0.00 44.66 3.41
268 273 2.378858 GCTCTGTGTCGCAGCAGTC 61.379 63.158 8.61 1.56 44.66 3.51
280 285 1.373999 GCGAGTCTTGCAGCTCTGT 60.374 57.895 7.24 0.00 0.00 3.41
290 295 0.531974 TTGTTGCGAAGGCGAGTCTT 60.532 50.000 0.00 0.00 44.10 3.01
346 351 2.124736 GCGGCAGTGAGGGCATTA 60.125 61.111 0.00 0.00 0.00 1.90
384 389 2.661866 GTGACTCGCGGCAGTGTT 60.662 61.111 6.13 0.00 0.00 3.32
400 405 2.050350 GCTCCATGGCAGCACATGT 61.050 57.895 23.33 0.00 45.21 3.21
421 426 2.992689 CAGCAATGTGGCCTGGCA 60.993 61.111 22.05 1.21 0.00 4.92
432 437 0.886563 GAAAGCTCCACTGCAGCAAT 59.113 50.000 15.27 0.00 39.56 3.56
484 489 1.338020 CAACTGAGCTTCAACAACCCC 59.662 52.381 0.00 0.00 0.00 4.95
503 508 0.388659 GGTGCTTCATTGCAACCACA 59.611 50.000 0.00 0.00 44.23 4.17
523 528 0.674895 GCTTCAAGGACCACTGCGAT 60.675 55.000 0.00 0.00 0.00 4.58
524 529 1.301716 GCTTCAAGGACCACTGCGA 60.302 57.895 0.00 0.00 0.00 5.10
527 533 0.397941 TGGAGCTTCAAGGACCACTG 59.602 55.000 0.00 0.00 0.00 3.66
578 606 2.154798 CTCTCCGCCGGTGAAGTTGA 62.155 60.000 18.79 3.40 0.00 3.18
630 658 3.086282 TGTATTGTCACCGACAGAGCTA 58.914 45.455 0.00 0.00 43.69 3.32
646 674 4.009675 AGCACCATCGTTGATGTTGTATT 58.990 39.130 6.27 0.00 38.28 1.89
694 722 0.179156 GCATGTTGCACTCCAATCGG 60.179 55.000 0.00 0.00 44.26 4.18
707 735 1.304713 CCCTCCCTTGCAGCATGTT 60.305 57.895 0.00 0.00 39.31 2.71
716 744 4.733725 TCCCCCGTCCCTCCCTTG 62.734 72.222 0.00 0.00 0.00 3.61
717 745 4.735599 GTCCCCCGTCCCTCCCTT 62.736 72.222 0.00 0.00 0.00 3.95
728 756 4.636435 CACACACACCCGTCCCCC 62.636 72.222 0.00 0.00 0.00 5.40
729 757 3.868985 ACACACACACCCGTCCCC 61.869 66.667 0.00 0.00 0.00 4.81
730 758 2.590575 CACACACACACCCGTCCC 60.591 66.667 0.00 0.00 0.00 4.46
731 759 2.177580 CACACACACACACCCGTCC 61.178 63.158 0.00 0.00 0.00 4.79
732 760 2.177580 CCACACACACACACCCGTC 61.178 63.158 0.00 0.00 0.00 4.79
733 761 2.124901 CCACACACACACACCCGT 60.125 61.111 0.00 0.00 0.00 5.28
734 762 2.899838 CCCACACACACACACCCG 60.900 66.667 0.00 0.00 0.00 5.28
735 763 2.118404 CACCCACACACACACACCC 61.118 63.158 0.00 0.00 0.00 4.61
736 764 1.377987 ACACCCACACACACACACC 60.378 57.895 0.00 0.00 0.00 4.16
737 765 0.958382 ACACACCCACACACACACAC 60.958 55.000 0.00 0.00 0.00 3.82
738 766 0.957888 CACACACCCACACACACACA 60.958 55.000 0.00 0.00 0.00 3.72
739 767 0.958382 ACACACACCCACACACACAC 60.958 55.000 0.00 0.00 0.00 3.82
740 768 0.957888 CACACACACCCACACACACA 60.958 55.000 0.00 0.00 0.00 3.72
741 769 0.958382 ACACACACACCCACACACAC 60.958 55.000 0.00 0.00 0.00 3.82
742 770 0.957888 CACACACACACCCACACACA 60.958 55.000 0.00 0.00 0.00 3.72
743 771 0.958382 ACACACACACACCCACACAC 60.958 55.000 0.00 0.00 0.00 3.82
744 772 0.957888 CACACACACACACCCACACA 60.958 55.000 0.00 0.00 0.00 3.72
745 773 0.958382 ACACACACACACACCCACAC 60.958 55.000 0.00 0.00 0.00 3.82
746 774 0.957888 CACACACACACACACCCACA 60.958 55.000 0.00 0.00 0.00 4.17
747 775 0.958382 ACACACACACACACACCCAC 60.958 55.000 0.00 0.00 0.00 4.61
748 776 0.957888 CACACACACACACACACCCA 60.958 55.000 0.00 0.00 0.00 4.51
749 777 0.958382 ACACACACACACACACACCC 60.958 55.000 0.00 0.00 0.00 4.61
750 778 0.167908 CACACACACACACACACACC 59.832 55.000 0.00 0.00 0.00 4.16
751 779 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
752 780 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
753 781 0.167908 CCACACACACACACACACAC 59.832 55.000 0.00 0.00 0.00 3.82
754 782 0.035458 TCCACACACACACACACACA 59.965 50.000 0.00 0.00 0.00 3.72
755 783 0.726827 CTCCACACACACACACACAC 59.273 55.000 0.00 0.00 0.00 3.82
756 784 0.323302 ACTCCACACACACACACACA 59.677 50.000 0.00 0.00 0.00 3.72
757 785 0.726827 CACTCCACACACACACACAC 59.273 55.000 0.00 0.00 0.00 3.82
758 786 1.024046 GCACTCCACACACACACACA 61.024 55.000 0.00 0.00 0.00 3.72
759 787 0.744414 AGCACTCCACACACACACAC 60.744 55.000 0.00 0.00 0.00 3.82
760 788 0.035534 AAGCACTCCACACACACACA 60.036 50.000 0.00 0.00 0.00 3.72
761 789 0.657840 GAAGCACTCCACACACACAC 59.342 55.000 0.00 0.00 0.00 3.82
762 790 0.809636 CGAAGCACTCCACACACACA 60.810 55.000 0.00 0.00 0.00 3.72
763 791 0.810031 ACGAAGCACTCCACACACAC 60.810 55.000 0.00 0.00 0.00 3.82
764 792 0.107897 AACGAAGCACTCCACACACA 60.108 50.000 0.00 0.00 0.00 3.72
765 793 1.014352 AAACGAAGCACTCCACACAC 58.986 50.000 0.00 0.00 0.00 3.82
766 794 1.745232 AAAACGAAGCACTCCACACA 58.255 45.000 0.00 0.00 0.00 3.72
767 795 2.450160 CAAAAACGAAGCACTCCACAC 58.550 47.619 0.00 0.00 0.00 3.82
768 796 1.202245 GCAAAAACGAAGCACTCCACA 60.202 47.619 0.00 0.00 0.00 4.17
769 797 1.202245 TGCAAAAACGAAGCACTCCAC 60.202 47.619 0.00 0.00 32.55 4.02
770 798 1.098869 TGCAAAAACGAAGCACTCCA 58.901 45.000 0.00 0.00 32.55 3.86
771 799 2.202295 TTGCAAAAACGAAGCACTCC 57.798 45.000 0.00 0.00 38.11 3.85
772 800 3.553053 GTTTGCAAAAACGAAGCACTC 57.447 42.857 14.67 0.00 38.11 3.51
787 815 1.019278 TCGATCCTCCTTGCGTTTGC 61.019 55.000 0.00 0.00 43.20 3.68
788 816 1.394917 CTTCGATCCTCCTTGCGTTTG 59.605 52.381 0.00 0.00 0.00 2.93
789 817 1.676014 CCTTCGATCCTCCTTGCGTTT 60.676 52.381 0.00 0.00 0.00 3.60
790 818 0.108138 CCTTCGATCCTCCTTGCGTT 60.108 55.000 0.00 0.00 0.00 4.84
791 819 1.517832 CCTTCGATCCTCCTTGCGT 59.482 57.895 0.00 0.00 0.00 5.24
792 820 1.227380 CCCTTCGATCCTCCTTGCG 60.227 63.158 0.00 0.00 0.00 4.85
793 821 0.179070 GACCCTTCGATCCTCCTTGC 60.179 60.000 0.00 0.00 0.00 4.01
794 822 1.195115 TGACCCTTCGATCCTCCTTG 58.805 55.000 0.00 0.00 0.00 3.61
795 823 1.765314 CATGACCCTTCGATCCTCCTT 59.235 52.381 0.00 0.00 0.00 3.36
796 824 1.418334 CATGACCCTTCGATCCTCCT 58.582 55.000 0.00 0.00 0.00 3.69
797 825 0.250081 GCATGACCCTTCGATCCTCC 60.250 60.000 0.00 0.00 0.00 4.30
819 1021 4.129737 CAGCCGTCCGATCCGTGT 62.130 66.667 0.00 0.00 0.00 4.49
820 1022 4.129737 ACAGCCGTCCGATCCGTG 62.130 66.667 0.00 0.00 0.00 4.94
959 1170 5.508200 ACTAGAGTAAATCGGAGCTTCAG 57.492 43.478 0.00 0.00 0.00 3.02
961 1172 4.035441 ACGACTAGAGTAAATCGGAGCTTC 59.965 45.833 0.00 0.00 38.88 3.86
984 1196 0.756070 GTTTTGGGGTTGGTCGGGAA 60.756 55.000 0.00 0.00 0.00 3.97
1004 1216 3.699134 GAGATGGGGAACACGGGCC 62.699 68.421 0.00 0.00 0.00 5.80
1005 1217 2.124695 GAGATGGGGAACACGGGC 60.125 66.667 0.00 0.00 0.00 6.13
1067 1292 2.819595 GCTTCGCCGCCATCTTCA 60.820 61.111 0.00 0.00 0.00 3.02
1069 1294 2.821366 CTGCTTCGCCGCCATCTT 60.821 61.111 0.00 0.00 0.00 2.40
1157 1388 2.756283 CGAGGGAGGAGGCGAAGT 60.756 66.667 0.00 0.00 0.00 3.01
1200 1431 0.820226 CGGAGAGCCTCTTGATGACA 59.180 55.000 0.00 0.00 0.00 3.58
1298 1564 0.175989 GCTCGTTAGGTCTTGGGGAG 59.824 60.000 0.00 0.00 0.00 4.30
1460 1740 3.196469 CCTAAATGCCACACAGAGAGAGA 59.804 47.826 0.00 0.00 0.00 3.10
1485 1767 2.662006 TTCACTCCAATCGAGCAGAG 57.338 50.000 6.78 6.78 43.01 3.35
1590 1879 0.183492 TCCACTTGTTCTTGGCTGCT 59.817 50.000 0.00 0.00 32.37 4.24
1722 2014 6.095440 GGCAAGTCTCCAATACAAATACACAT 59.905 38.462 0.00 0.00 0.00 3.21
1740 2032 1.432270 GCAGATACGGCAGGCAAGTC 61.432 60.000 0.00 0.00 0.00 3.01
1796 2088 6.255887 GCACTGTATTCTACATCTACAACACC 59.744 42.308 0.00 0.00 38.15 4.16
1798 2090 6.154534 AGGCACTGTATTCTACATCTACAACA 59.845 38.462 0.00 0.00 37.18 3.33
1818 2110 4.764172 AGAGTTGAACTATGATGAGGCAC 58.236 43.478 0.00 0.00 0.00 5.01
1820 2112 5.877012 TGAAAGAGTTGAACTATGATGAGGC 59.123 40.000 0.00 0.00 0.00 4.70
1868 2164 3.648009 CACACTGAGAGACCTTCAGTTC 58.352 50.000 5.23 0.00 42.12 3.01
1884 2180 4.489810 CTCGAGACAGATAAAAGCACACT 58.510 43.478 6.58 0.00 0.00 3.55
2052 2504 1.188863 ATGGCTCAAGTGGAAATGCC 58.811 50.000 0.00 0.00 40.62 4.40
2089 2542 1.794151 TTTGTGCCGTGCCATGACAG 61.794 55.000 0.00 0.00 0.00 3.51
2090 2543 1.177895 ATTTGTGCCGTGCCATGACA 61.178 50.000 0.00 0.00 0.00 3.58
2091 2544 0.808125 TATTTGTGCCGTGCCATGAC 59.192 50.000 0.00 0.00 0.00 3.06
2092 2545 1.093972 CTATTTGTGCCGTGCCATGA 58.906 50.000 0.00 0.00 0.00 3.07
2142 2595 7.347485 GGGGTACTAGCTATTGTAATATGGGAT 59.653 40.741 0.00 0.00 0.00 3.85
2165 2618 1.849823 GATGATGGGAGGGGAGGGG 60.850 68.421 0.00 0.00 0.00 4.79
2169 2622 2.122413 CGGGATGATGGGAGGGGA 60.122 66.667 0.00 0.00 0.00 4.81
2173 2626 1.959042 CTCAAACGGGATGATGGGAG 58.041 55.000 0.00 0.00 0.00 4.30
2174 2627 0.107214 GCTCAAACGGGATGATGGGA 60.107 55.000 0.00 0.00 0.00 4.37
2178 2631 0.249120 TGACGCTCAAACGGGATGAT 59.751 50.000 0.00 0.00 37.37 2.45
2179 2632 0.034198 TTGACGCTCAAACGGGATGA 59.966 50.000 0.00 0.00 32.71 2.92
2276 2736 7.909267 TCAAATCATCTATTACTTTGTCAGCG 58.091 34.615 0.00 0.00 0.00 5.18
2553 3014 6.127814 CCTGCTCAATTTCTGAAATTAGCTCA 60.128 38.462 30.34 22.70 38.97 4.26
2554 3015 6.094603 TCCTGCTCAATTTCTGAAATTAGCTC 59.905 38.462 30.34 20.82 38.97 4.09
2642 3103 9.652114 ATTTAGAATAGAAAAGGCATTGAGGAT 57.348 29.630 0.00 0.00 0.00 3.24
2715 3176 8.617761 TTAAAGGTTGATTTTTAACGTGACAC 57.382 30.769 0.00 0.00 0.00 3.67
2751 3212 8.364894 TGCACTAATAGGTACACACATAATAGG 58.635 37.037 0.00 0.00 31.59 2.57
2829 3295 1.480954 GATCCTTCCAGTCGCCACTTA 59.519 52.381 0.00 0.00 0.00 2.24
3063 3529 9.793252 ACTGCAAATATCATGACTAAAATGTTC 57.207 29.630 0.00 0.00 0.00 3.18
3090 3557 5.184711 TCCATTTTCCAAATATTGCCTTGC 58.815 37.500 0.00 0.00 0.00 4.01
3210 3681 6.901081 AACAGGTATGAGAAAAGAAAAGGG 57.099 37.500 0.00 0.00 0.00 3.95
3211 3682 7.716612 ACAAACAGGTATGAGAAAAGAAAAGG 58.283 34.615 0.00 0.00 0.00 3.11
3212 3683 9.884465 CTACAAACAGGTATGAGAAAAGAAAAG 57.116 33.333 0.00 0.00 0.00 2.27
3289 3762 3.709653 TGGCGACCTATCACTCCTAAATT 59.290 43.478 0.00 0.00 0.00 1.82
3401 3935 1.144913 AGCTACCAAAGGAAGGCAACA 59.855 47.619 0.00 0.00 41.41 3.33
3920 4455 4.693283 TGAATCGTTCAACAGAACAGAGT 58.307 39.130 8.82 6.16 41.30 3.24
4132 4674 6.094325 TGTGTGTGACATCTACGATATGTACA 59.906 38.462 0.00 0.00 37.69 2.90
4189 4734 7.939039 TCACAAATAAGACCTGAAATCAGAAGT 59.061 33.333 11.94 2.27 46.59 3.01
4313 4858 4.299155 ACTGCGACACTTATTATGGATCG 58.701 43.478 0.00 0.00 0.00 3.69
4317 4862 6.176975 TCAAAACTGCGACACTTATTATGG 57.823 37.500 0.00 0.00 0.00 2.74
4330 4875 4.545823 TCAACCTTAGTTCAAAACTGCG 57.454 40.909 2.65 0.00 42.84 5.18
4371 4916 0.373716 GATCCAAAGTAAGTGCCGCG 59.626 55.000 0.00 0.00 0.00 6.46
4375 4920 2.280628 CCTCCGATCCAAAGTAAGTGC 58.719 52.381 0.00 0.00 0.00 4.40
4378 4923 2.766828 ACTCCCTCCGATCCAAAGTAAG 59.233 50.000 0.00 0.00 0.00 2.34
4394 4939 7.010339 AGCAAGATCCATAAATACTACTCCC 57.990 40.000 0.00 0.00 0.00 4.30
4563 5281 4.020662 GGAGAGGAGAGGTGGCATTATTAG 60.021 50.000 0.00 0.00 0.00 1.73
4805 5524 3.976015 TCCCATGGGAAGTAACATTTCC 58.024 45.455 32.09 0.00 42.05 3.13
4865 5584 3.726291 TGCCAGTTTTACCTTTCAAGC 57.274 42.857 0.00 0.00 0.00 4.01
5003 5957 3.859386 GCTATCATTTGGTTTTCCTTGCG 59.141 43.478 0.00 0.00 41.38 4.85
5285 6519 6.481644 CCAGATAAAGTTCTATCAAGCTCACC 59.518 42.308 0.00 0.00 31.71 4.02
5619 6931 0.319469 GTTGGCCGTGGTTGGAAATG 60.319 55.000 0.00 0.00 0.00 2.32
5644 6956 2.695359 TGCCTTCGATGTTGTAAGTCC 58.305 47.619 0.00 0.00 0.00 3.85
5649 6961 5.957842 AATCTTTTGCCTTCGATGTTGTA 57.042 34.783 0.00 0.00 0.00 2.41
5651 6963 4.143263 GCAAATCTTTTGCCTTCGATGTTG 60.143 41.667 12.74 0.00 39.38 3.33
5653 6965 3.578688 GCAAATCTTTTGCCTTCGATGT 58.421 40.909 12.74 0.00 39.38 3.06
5724 7062 5.569355 TCAAAGAGAGTAATGCCCATTTGA 58.431 37.500 0.00 0.00 34.15 2.69
5743 7081 5.578727 CGACAAAAAGTTGGGTTCAATCAAA 59.421 36.000 0.00 0.00 39.22 2.69
5765 7107 1.609210 TCTGAGTCACCATGGGCGA 60.609 57.895 18.09 9.51 0.00 5.54
5772 7114 1.660355 GCGACAGTCTGAGTCACCA 59.340 57.895 6.91 0.00 35.77 4.17
5779 7121 3.069016 TCAAAACTAAGGCGACAGTCTGA 59.931 43.478 6.91 0.00 29.39 3.27
5794 7136 3.138283 TCCTCCTCCACAACATCAAAACT 59.862 43.478 0.00 0.00 0.00 2.66
5851 7193 5.456548 TTTGAAATGAGAGCAGAAATGCA 57.543 34.783 2.73 0.00 37.25 3.96
5860 7202 6.414109 CGTCATCAATCATTTGAAATGAGAGC 59.586 38.462 23.06 10.87 44.70 4.09
5864 7206 7.143514 TCACGTCATCAATCATTTGAAATGA 57.856 32.000 21.39 21.39 44.70 2.57
5865 7207 6.020916 GCTCACGTCATCAATCATTTGAAATG 60.021 38.462 11.54 11.54 44.70 2.32
5866 7208 6.032094 GCTCACGTCATCAATCATTTGAAAT 58.968 36.000 0.00 0.00 44.70 2.17
5910 7252 0.463620 CAACACCCCAAACCACAAGG 59.536 55.000 0.00 0.00 42.21 3.61
6005 7347 3.110705 ACATGATCAAGGAGTGGCTACT 58.889 45.455 0.69 0.69 40.66 2.57
6051 7398 0.250295 TCCGCTGACCACCTTTTCTG 60.250 55.000 0.00 0.00 0.00 3.02
6066 7413 2.111756 CAAGCGCAATAAAGAATCCGC 58.888 47.619 11.47 0.00 41.51 5.54
6099 7446 3.726607 GTGGATGGTCAAATTGTTGCAA 58.273 40.909 0.00 0.00 34.50 4.08
6100 7447 2.288091 CGTGGATGGTCAAATTGTTGCA 60.288 45.455 0.00 0.00 34.50 4.08
6158 7531 0.677731 TCTTCGCTTGGCTTCCCATG 60.678 55.000 0.00 0.00 41.78 3.66
6163 7536 7.915397 TCAATATTAAATTCTTCGCTTGGCTTC 59.085 33.333 0.00 0.00 0.00 3.86
6197 7570 2.282180 GCGGTTTGGGAGGCTTGA 60.282 61.111 0.00 0.00 0.00 3.02
6205 7579 2.141122 AATGAAGCACGCGGTTTGGG 62.141 55.000 12.47 0.00 31.57 4.12
6214 7588 2.679355 TCGTTTTCCAATGAAGCACG 57.321 45.000 0.00 0.00 38.97 5.34
6220 7594 2.029470 GGCACCATTCGTTTTCCAATGA 60.029 45.455 0.00 0.00 32.56 2.57
6224 7598 0.820074 ACGGCACCATTCGTTTTCCA 60.820 50.000 0.00 0.00 36.04 3.53
6227 7601 0.820074 TCCACGGCACCATTCGTTTT 60.820 50.000 0.00 0.00 37.53 2.43
6228 7602 0.820074 TTCCACGGCACCATTCGTTT 60.820 50.000 0.00 0.00 37.53 3.60
6264 7638 0.179081 GGATTCTACTCGGCGGCTTT 60.179 55.000 7.21 0.00 0.00 3.51
6272 7646 1.202533 ACCGCCAATGGATTCTACTCG 60.203 52.381 2.05 0.00 0.00 4.18
6279 7653 0.899717 AAGCACACCGCCAATGGATT 60.900 50.000 2.05 0.00 44.04 3.01
6281 7655 1.971167 GAAGCACACCGCCAATGGA 60.971 57.895 2.05 0.00 44.04 3.41
6316 7690 1.012086 CCAGCTCAATGTGGATGTCG 58.988 55.000 0.00 0.00 35.67 4.35
6318 7692 2.719739 CTTCCAGCTCAATGTGGATGT 58.280 47.619 0.00 0.00 42.55 3.06
6319 7693 1.404391 GCTTCCAGCTCAATGTGGATG 59.596 52.381 0.00 0.00 42.55 3.51
6320 7694 1.760192 GCTTCCAGCTCAATGTGGAT 58.240 50.000 0.00 0.00 42.55 3.41
6347 7721 0.945813 TCGTTACTTTTTGGGCCACG 59.054 50.000 5.23 3.73 0.00 4.94
6358 7732 3.818773 CCACTCCCACAAATTCGTTACTT 59.181 43.478 0.00 0.00 0.00 2.24
6370 7744 2.203280 CGTTTGCCCACTCCCACA 60.203 61.111 0.00 0.00 0.00 4.17
6374 7748 0.818040 ACTTCACGTTTGCCCACTCC 60.818 55.000 0.00 0.00 0.00 3.85
6375 7749 1.021968 AACTTCACGTTTGCCCACTC 58.978 50.000 0.00 0.00 29.63 3.51
6383 7757 6.934645 TCAAGATATCCTCAAACTTCACGTTT 59.065 34.615 0.00 0.00 46.41 3.60
6412 7786 3.989167 GAGAGATGATGCTTGGATCTTCG 59.011 47.826 10.58 0.00 33.68 3.79
6420 7794 3.180891 TGCTCAGAGAGATGATGCTTG 57.819 47.619 0.00 0.00 0.00 4.01
6431 7805 9.985730 AATTGAAATGTTAAAAATGCTCAGAGA 57.014 25.926 0.00 0.00 0.00 3.10


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

AutoCloner maintained by Alex Coulton.