Multiple sequence alignment - TraesCS7B01G466400

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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 TraesCS7B01G466400 chr7B 100.000 4158 0 0 1 4158 723936796 723932639 0.000000e+00 7679.0
1 TraesCS7B01G466400 chr7B 80.000 860 97 44 685 1479 723957736 723956887 2.170000e-157 566.0
2 TraesCS7B01G466400 chr7B 81.705 481 69 14 997 1471 724002345 724001878 2.350000e-102 383.0
3 TraesCS7B01G466400 chr7B 80.992 484 77 11 3531 4001 707610828 707611309 1.830000e-98 370.0
4 TraesCS7B01G466400 chr7B 80.544 478 68 20 3531 3996 707611734 707612198 1.110000e-90 344.0
5 TraesCS7B01G466400 chr7B 94.595 185 8 2 376 559 640151576 640151759 6.800000e-73 285.0
6 TraesCS7B01G466400 chr7D 89.784 1204 114 9 2100 3297 625189237 625190437 0.000000e+00 1533.0
7 TraesCS7B01G466400 chr7D 84.785 953 97 18 1159 2105 625182200 625183110 0.000000e+00 913.0
8 TraesCS7B01G466400 chr7D 83.966 711 83 14 789 1483 625205873 625206568 0.000000e+00 652.0
9 TraesCS7B01G466400 chr7D 84.740 557 46 14 627 1167 625174468 625175001 4.760000e-144 521.0
10 TraesCS7B01G466400 chr7D 78.862 738 150 5 2428 3163 625145954 625146687 1.040000e-135 494.0
11 TraesCS7B01G466400 chr7D 81.405 484 65 21 992 1465 625143233 625143701 5.080000e-99 372.0
12 TraesCS7B01G466400 chr7D 83.535 413 52 15 1070 1470 625347610 625347202 5.080000e-99 372.0
13 TraesCS7B01G466400 chr7D 88.179 313 31 3 3177 3487 625208046 625208354 6.570000e-98 368.0
14 TraesCS7B01G466400 chr7A 85.177 1410 125 40 598 1945 720940716 720939329 0.000000e+00 1369.0
15 TraesCS7B01G466400 chr7A 86.996 1215 133 3 1974 3163 720934782 720933568 0.000000e+00 1345.0
16 TraesCS7B01G466400 chr7A 87.363 728 88 3 2444 3169 720913121 720912396 0.000000e+00 832.0
17 TraesCS7B01G466400 chr7A 83.792 944 72 30 598 1484 720914839 720913920 0.000000e+00 821.0
18 TraesCS7B01G466400 chr7A 88.693 566 56 6 3594 4156 720888874 720888314 0.000000e+00 684.0
19 TraesCS7B01G466400 chr7A 78.958 480 84 12 3526 3996 56737297 56736826 1.120000e-80 311.0
20 TraesCS7B01G466400 chr7A 79.130 460 80 11 3528 3974 707625198 707624742 1.880000e-78 303.0
21 TraesCS7B01G466400 chr7A 79.204 452 72 14 3528 3963 710755710 710756155 1.130000e-75 294.0
22 TraesCS7B01G466400 chr7A 93.229 192 13 0 376 567 635394827 635394636 2.450000e-72 283.0
23 TraesCS7B01G466400 chr7A 87.417 151 16 2 1 151 720940859 720940712 1.990000e-38 171.0
24 TraesCS7B01G466400 chr7A 86.047 86 10 2 602 687 720922700 720922617 1.590000e-14 91.6
25 TraesCS7B01G466400 chr7A 79.661 118 24 0 3301 3418 117240069 117240186 7.410000e-13 86.1
26 TraesCS7B01G466400 chr1B 94.313 211 10 2 167 375 112504969 112505179 5.190000e-84 322.0
27 TraesCS7B01G466400 chr1B 93.810 210 12 1 167 375 502969237 502969446 8.680000e-82 315.0
28 TraesCS7B01G466400 chr1B 94.022 184 11 0 376 559 232416214 232416031 3.170000e-71 279.0
29 TraesCS7B01G466400 chr1B 90.909 55 3 1 3292 3344 495142892 495142946 5.770000e-09 73.1
30 TraesCS7B01G466400 chr3B 94.203 207 11 1 170 375 496690918 496690712 8.680000e-82 315.0
31 TraesCS7B01G466400 chr2B 93.023 215 14 1 162 375 708704764 708704978 3.120000e-81 313.0
32 TraesCS7B01G466400 chr2B 77.941 476 75 24 3538 3998 38226217 38226677 1.910000e-68 270.0
33 TraesCS7B01G466400 chr2B 84.615 117 16 2 4036 4151 770489696 770489581 9.450000e-22 115.0
34 TraesCS7B01G466400 chr5D 83.881 335 42 9 3526 3854 527144691 527144363 4.040000e-80 309.0
35 TraesCS7B01G466400 chr4B 93.269 208 14 0 168 375 546681611 546681404 1.450000e-79 307.0
36 TraesCS7B01G466400 chr4B 92.857 210 15 0 166 375 591905704 591905913 5.220000e-79 305.0
37 TraesCS7B01G466400 chr4B 93.782 193 12 0 375 567 546681298 546681106 1.460000e-74 291.0
38 TraesCS7B01G466400 chr4B 77.987 159 35 0 2621 2779 632500242 632500400 2.640000e-17 100.0
39 TraesCS7B01G466400 chr4B 77.987 159 35 0 2621 2779 632661798 632661956 2.640000e-17 100.0
40 TraesCS7B01G466400 chr1D 93.301 209 13 1 168 375 45262936 45262728 1.450000e-79 307.0
41 TraesCS7B01G466400 chr1D 78.912 441 69 15 3526 3956 223365155 223365581 1.140000e-70 278.0
42 TraesCS7B01G466400 chrUn 92.857 210 15 0 166 375 220658420 220658629 5.220000e-79 305.0
43 TraesCS7B01G466400 chrUn 92.857 210 15 0 166 375 411819502 411819293 5.220000e-79 305.0
44 TraesCS7B01G466400 chr2D 95.652 184 7 1 376 559 29144013 29143831 1.130000e-75 294.0
45 TraesCS7B01G466400 chr2D 94.022 184 11 0 376 559 298459702 298459885 3.170000e-71 279.0
46 TraesCS7B01G466400 chr2D 84.483 116 14 4 4005 4118 650470667 650470780 1.220000e-20 111.0
47 TraesCS7B01G466400 chr4A 94.022 184 11 0 376 559 423431250 423431067 3.170000e-71 279.0
48 TraesCS7B01G466400 chr3A 94.022 184 11 0 376 559 34033191 34033008 3.170000e-71 279.0
49 TraesCS7B01G466400 chr3A 94.022 184 11 0 376 559 636156578 636156761 3.170000e-71 279.0
50 TraesCS7B01G466400 chr5A 78.161 261 34 15 3525 3780 610076958 610076716 1.200000e-30 145.0
51 TraesCS7B01G466400 chr5A 80.769 156 20 9 4005 4156 698766 698617 3.400000e-21 113.0
52 TraesCS7B01G466400 chr5A 84.536 97 15 0 2621 2717 673370577 673370673 3.420000e-16 97.1
53 TraesCS7B01G466400 chr5A 100.000 29 0 0 2689 2717 592620039 592620067 2.000000e-03 54.7
54 TraesCS7B01G466400 chr6B 92.857 84 6 0 3302 3385 437845769 437845852 5.640000e-24 122.0
55 TraesCS7B01G466400 chr3D 86.735 98 12 1 4059 4156 313081729 313081825 1.580000e-19 108.0
56 TraesCS7B01G466400 chr4D 79.085 153 28 4 4005 4156 323111603 323111752 7.350000e-18 102.0


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 TraesCS7B01G466400 chr7B 723932639 723936796 4157 True 7679.0 7679 100.0000 1 4158 1 chr7B.!!$R1 4157
1 TraesCS7B01G466400 chr7B 723956887 723957736 849 True 566.0 566 80.0000 685 1479 1 chr7B.!!$R2 794
2 TraesCS7B01G466400 chr7B 707610828 707612198 1370 False 357.0 370 80.7680 3531 4001 2 chr7B.!!$F2 470
3 TraesCS7B01G466400 chr7D 625189237 625190437 1200 False 1533.0 1533 89.7840 2100 3297 1 chr7D.!!$F3 1197
4 TraesCS7B01G466400 chr7D 625182200 625183110 910 False 913.0 913 84.7850 1159 2105 1 chr7D.!!$F2 946
5 TraesCS7B01G466400 chr7D 625174468 625175001 533 False 521.0 521 84.7400 627 1167 1 chr7D.!!$F1 540
6 TraesCS7B01G466400 chr7D 625205873 625208354 2481 False 510.0 652 86.0725 789 3487 2 chr7D.!!$F5 2698
7 TraesCS7B01G466400 chr7D 625143233 625146687 3454 False 433.0 494 80.1335 992 3163 2 chr7D.!!$F4 2171
8 TraesCS7B01G466400 chr7A 720933568 720934782 1214 True 1345.0 1345 86.9960 1974 3163 1 chr7A.!!$R6 1189
9 TraesCS7B01G466400 chr7A 720912396 720914839 2443 True 826.5 832 85.5775 598 3169 2 chr7A.!!$R7 2571
10 TraesCS7B01G466400 chr7A 720939329 720940859 1530 True 770.0 1369 86.2970 1 1945 2 chr7A.!!$R8 1944
11 TraesCS7B01G466400 chr7A 720888314 720888874 560 True 684.0 684 88.6930 3594 4156 1 chr7A.!!$R4 562
12 TraesCS7B01G466400 chr4B 546681106 546681611 505 True 299.0 307 93.5255 168 567 2 chr4B.!!$R1 399

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
943 1133 1.339055 ACTACGGACACGCCTGTACTA 60.339 52.381 0.0 0.0 46.04 1.82 F
1811 3832 0.040067 CTTTCCCAAACAGCACGCTC 60.040 55.000 0.0 0.0 0.00 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1853 3894 0.179176 CCACGTTCGAGAGCTCTCTG 60.179 60.0 34.69 27.83 40.61 3.35 R
3461 5603 0.246635 ACCATCCTTCGTCTTGTCCG 59.753 55.0 0.00 0.00 0.00 4.79 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
55 56 2.343101 TGATGGCGTGTAGTTAGTTGC 58.657 47.619 0.00 0.00 0.00 4.17
61 62 1.385743 CGTGTAGTTAGTTGCGCTGTC 59.614 52.381 9.73 0.00 0.00 3.51
62 63 1.385743 GTGTAGTTAGTTGCGCTGTCG 59.614 52.381 9.73 0.00 39.07 4.35
73 74 4.883026 GCTGTCGCGTCCTAAGAA 57.117 55.556 5.77 0.00 0.00 2.52
79 80 4.556104 GCTGTCGCGTCCTAAGAATGTATA 60.556 45.833 5.77 0.00 0.00 1.47
85 86 5.800941 CGCGTCCTAAGAATGTATAGAATCC 59.199 44.000 0.00 0.00 0.00 3.01
99 100 6.611236 TGTATAGAATCCACCTGTCATCTGAA 59.389 38.462 0.00 0.00 0.00 3.02
106 107 4.338118 TCCACCTGTCATCTGAAACAAAAC 59.662 41.667 0.00 0.00 0.00 2.43
107 108 4.097741 CCACCTGTCATCTGAAACAAAACA 59.902 41.667 0.00 0.00 0.00 2.83
108 109 5.036737 CACCTGTCATCTGAAACAAAACAC 58.963 41.667 0.00 0.00 0.00 3.32
109 110 4.704540 ACCTGTCATCTGAAACAAAACACA 59.295 37.500 0.00 0.00 0.00 3.72
112 113 6.589523 CCTGTCATCTGAAACAAAACACAAAA 59.410 34.615 0.00 0.00 0.00 2.44
146 147 3.489568 CGAGTGCTCGTCTCTAGAGAGTA 60.490 52.174 22.95 12.54 46.99 2.59
147 148 4.628074 GAGTGCTCGTCTCTAGAGAGTAT 58.372 47.826 22.95 5.12 42.60 2.12
148 149 5.563280 CGAGTGCTCGTCTCTAGAGAGTATA 60.563 48.000 22.95 7.74 46.99 1.47
149 150 5.779922 AGTGCTCGTCTCTAGAGAGTATAG 58.220 45.833 22.95 16.78 42.60 1.31
150 151 5.537295 AGTGCTCGTCTCTAGAGAGTATAGA 59.463 44.000 22.95 14.85 42.60 1.98
151 152 6.041182 AGTGCTCGTCTCTAGAGAGTATAGAA 59.959 42.308 22.95 9.50 42.60 2.10
152 153 6.702723 GTGCTCGTCTCTAGAGAGTATAGAAA 59.297 42.308 22.95 7.30 42.60 2.52
153 154 7.386848 GTGCTCGTCTCTAGAGAGTATAGAAAT 59.613 40.741 22.95 0.00 42.60 2.17
154 155 7.601130 TGCTCGTCTCTAGAGAGTATAGAAATC 59.399 40.741 22.95 6.19 42.60 2.17
155 156 7.201410 GCTCGTCTCTAGAGAGTATAGAAATCG 60.201 44.444 22.95 17.10 42.60 3.34
156 157 7.884257 TCGTCTCTAGAGAGTATAGAAATCGA 58.116 38.462 22.95 18.94 42.60 3.59
157 158 8.024865 TCGTCTCTAGAGAGTATAGAAATCGAG 58.975 40.741 22.95 0.00 42.60 4.04
158 159 7.811236 CGTCTCTAGAGAGTATAGAAATCGAGT 59.189 40.741 22.95 0.00 42.60 4.18
159 160 9.136952 GTCTCTAGAGAGTATAGAAATCGAGTC 57.863 40.741 22.95 1.24 42.60 3.36
160 161 8.024865 TCTCTAGAGAGTATAGAAATCGAGTCG 58.975 40.741 18.76 6.09 42.60 4.18
161 162 7.884257 TCTAGAGAGTATAGAAATCGAGTCGA 58.116 38.462 19.06 19.06 41.13 4.20
162 163 6.774354 AGAGAGTATAGAAATCGAGTCGAC 57.226 41.667 19.16 7.70 39.18 4.20
163 164 6.282167 AGAGAGTATAGAAATCGAGTCGACA 58.718 40.000 19.16 0.00 39.18 4.35
164 165 6.932400 AGAGAGTATAGAAATCGAGTCGACAT 59.068 38.462 19.16 9.65 39.18 3.06
165 166 7.117236 AGAGAGTATAGAAATCGAGTCGACATC 59.883 40.741 19.16 18.06 39.18 3.06
166 167 6.932400 AGAGTATAGAAATCGAGTCGACATCT 59.068 38.462 26.00 26.00 39.18 2.90
224 225 4.708726 CATCATGATGATGCATGCATCT 57.291 40.909 43.91 33.85 46.37 2.90
277 278 3.879932 AAAGTCTTACAGCTCGCAAAC 57.120 42.857 0.00 0.00 0.00 2.93
322 323 7.150783 AGGAAAATTACATGCTGAGAAAGAC 57.849 36.000 0.00 0.00 0.00 3.01
460 567 9.807649 GTTAAAAATCATATCATTCCTGCAGTT 57.192 29.630 13.81 0.00 0.00 3.16
489 596 4.335416 AGCCCATAATAGCGCACATATTT 58.665 39.130 11.47 0.00 0.00 1.40
495 602 7.148188 CCCATAATAGCGCACATATTTCAATCT 60.148 37.037 11.47 0.00 0.00 2.40
496 603 8.882736 CCATAATAGCGCACATATTTCAATCTA 58.117 33.333 11.47 0.00 0.00 1.98
505 612 8.746751 CGCACATATTTCAATCTATATACGAGG 58.253 37.037 0.00 0.00 0.00 4.63
532 639 3.806949 AATCTGTTCAACCCCAGCTAA 57.193 42.857 0.00 0.00 0.00 3.09
551 658 2.286365 ACCACGTCCCAAACAATGAT 57.714 45.000 0.00 0.00 0.00 2.45
559 666 4.741185 CGTCCCAAACAATGATGCAATATG 59.259 41.667 0.00 0.00 0.00 1.78
562 669 5.069383 TCCCAAACAATGATGCAATATGGAG 59.931 40.000 0.00 0.00 0.00 3.86
567 674 7.502120 AACAATGATGCAATATGGAGTAGAC 57.498 36.000 0.00 0.00 0.00 2.59
568 675 6.594744 ACAATGATGCAATATGGAGTAGACA 58.405 36.000 0.00 0.00 0.00 3.41
569 676 7.229308 ACAATGATGCAATATGGAGTAGACAT 58.771 34.615 0.00 0.00 0.00 3.06
570 677 7.174426 ACAATGATGCAATATGGAGTAGACATG 59.826 37.037 0.00 0.00 0.00 3.21
571 678 6.423776 TGATGCAATATGGAGTAGACATGA 57.576 37.500 0.00 0.00 0.00 3.07
572 679 6.461640 TGATGCAATATGGAGTAGACATGAG 58.538 40.000 0.00 0.00 0.00 2.90
573 680 5.876651 TGCAATATGGAGTAGACATGAGT 57.123 39.130 0.00 0.00 0.00 3.41
574 681 6.239217 TGCAATATGGAGTAGACATGAGTT 57.761 37.500 0.00 0.00 0.00 3.01
575 682 6.051074 TGCAATATGGAGTAGACATGAGTTG 58.949 40.000 0.00 0.00 0.00 3.16
576 683 6.127083 TGCAATATGGAGTAGACATGAGTTGA 60.127 38.462 0.00 0.00 0.00 3.18
577 684 6.201806 GCAATATGGAGTAGACATGAGTTGAC 59.798 42.308 0.00 0.00 0.00 3.18
578 685 3.850122 TGGAGTAGACATGAGTTGACG 57.150 47.619 0.00 0.00 0.00 4.35
579 686 3.418047 TGGAGTAGACATGAGTTGACGA 58.582 45.455 0.00 0.00 0.00 4.20
580 687 3.440522 TGGAGTAGACATGAGTTGACGAG 59.559 47.826 0.00 0.00 0.00 4.18
581 688 3.690139 GGAGTAGACATGAGTTGACGAGA 59.310 47.826 0.00 0.00 0.00 4.04
582 689 4.156190 GGAGTAGACATGAGTTGACGAGAA 59.844 45.833 0.00 0.00 0.00 2.87
583 690 5.303747 AGTAGACATGAGTTGACGAGAAG 57.696 43.478 0.00 0.00 0.00 2.85
584 691 4.762765 AGTAGACATGAGTTGACGAGAAGT 59.237 41.667 0.00 0.00 0.00 3.01
585 692 5.938710 AGTAGACATGAGTTGACGAGAAGTA 59.061 40.000 0.00 0.00 0.00 2.24
586 693 5.303747 AGACATGAGTTGACGAGAAGTAG 57.696 43.478 0.00 0.00 0.00 2.57
587 694 3.839293 ACATGAGTTGACGAGAAGTAGC 58.161 45.455 0.00 0.00 0.00 3.58
588 695 3.508012 ACATGAGTTGACGAGAAGTAGCT 59.492 43.478 0.00 0.00 0.00 3.32
589 696 3.833545 TGAGTTGACGAGAAGTAGCTC 57.166 47.619 0.00 0.00 0.00 4.09
607 714 2.841215 CTCGGGTTAGAGAGATCGAGT 58.159 52.381 0.00 0.00 40.57 4.18
622 729 3.741805 TCGAGTAGACATGAGTTGACG 57.258 47.619 0.00 0.00 0.00 4.35
647 754 2.548904 AGATCTCGACGAAAGATACGGG 59.451 50.000 0.00 0.00 33.64 5.28
813 991 3.610242 CACTTTCGTTGACTAGCTAGCTG 59.390 47.826 27.68 18.34 0.00 4.24
836 1014 7.220741 TGGTAGCTAGTTGATCTGATCATAC 57.779 40.000 20.16 18.60 39.39 2.39
837 1015 6.072452 TGGTAGCTAGTTGATCTGATCATACG 60.072 42.308 20.16 10.65 39.39 3.06
838 1016 6.072397 GGTAGCTAGTTGATCTGATCATACGT 60.072 42.308 20.16 8.53 39.39 3.57
839 1017 7.119407 GGTAGCTAGTTGATCTGATCATACGTA 59.881 40.741 20.16 0.00 39.39 3.57
840 1018 6.904498 AGCTAGTTGATCTGATCATACGTAC 58.096 40.000 20.16 14.60 39.39 3.67
844 1022 4.744136 TGATCTGATCATACGTACCGAC 57.256 45.455 16.06 0.00 33.59 4.79
883 1061 7.793222 ACTAATTGGGCTTATAAGTACCTACCT 59.207 37.037 21.33 12.02 0.00 3.08
901 1080 3.624777 ACCTCTTGCCATCACCTTAATG 58.375 45.455 0.00 0.00 0.00 1.90
929 1108 2.360165 AGTAGACGGCCAATTACTACGG 59.640 50.000 2.24 0.00 38.55 4.02
943 1133 1.339055 ACTACGGACACGCCTGTACTA 60.339 52.381 0.00 0.00 46.04 1.82
1017 1212 1.100510 CCATGAAGGGTCTCGTCGTA 58.899 55.000 0.00 0.00 0.00 3.43
1020 1215 1.446907 TGAAGGGTCTCGTCGTAGTC 58.553 55.000 0.00 0.00 0.00 2.59
1042 1237 1.191489 TCTGGGCCTTGTGATCGTCA 61.191 55.000 4.53 0.00 0.00 4.35
1394 1640 3.302092 GCTGAAATCACGCAACTATCTCG 60.302 47.826 0.00 0.00 0.00 4.04
1519 2505 4.402155 TGTGCTCATTTCTTTGTTCCAACT 59.598 37.500 0.00 0.00 0.00 3.16
1520 2506 5.105392 TGTGCTCATTTCTTTGTTCCAACTT 60.105 36.000 0.00 0.00 0.00 2.66
1521 2507 5.232838 GTGCTCATTTCTTTGTTCCAACTTG 59.767 40.000 0.00 0.00 0.00 3.16
1522 2508 4.209911 GCTCATTTCTTTGTTCCAACTTGC 59.790 41.667 0.00 0.00 0.00 4.01
1523 2509 5.336150 TCATTTCTTTGTTCCAACTTGCA 57.664 34.783 0.00 0.00 0.00 4.08
1524 2510 5.728471 TCATTTCTTTGTTCCAACTTGCAA 58.272 33.333 0.00 0.00 0.00 4.08
1525 2511 5.580297 TCATTTCTTTGTTCCAACTTGCAAC 59.420 36.000 0.00 0.00 0.00 4.17
1526 2512 3.143807 TCTTTGTTCCAACTTGCAACG 57.856 42.857 0.00 0.00 0.00 4.10
1527 2513 2.159310 TCTTTGTTCCAACTTGCAACGG 60.159 45.455 0.00 0.00 0.00 4.44
1529 2515 1.021202 TGTTCCAACTTGCAACGGAG 58.979 50.000 0.00 0.00 0.00 4.63
1545 2531 4.931661 ACGGAGTTCTTTTAGTGTGAGA 57.068 40.909 0.00 0.00 37.78 3.27
1557 2879 9.031537 TCTTTTAGTGTGAGATGGTATGTAGAA 57.968 33.333 0.00 0.00 0.00 2.10
1558 2880 9.653287 CTTTTAGTGTGAGATGGTATGTAGAAA 57.347 33.333 0.00 0.00 0.00 2.52
1589 2911 8.575565 AGCTTCATGTTACGTATATTACAGTG 57.424 34.615 0.00 0.00 0.00 3.66
1590 2912 7.652105 AGCTTCATGTTACGTATATTACAGTGG 59.348 37.037 0.00 0.00 0.00 4.00
1647 3130 5.778862 ACGGTGGACAAATAAAATTTCAGG 58.221 37.500 0.00 0.00 0.00 3.86
1649 3132 5.047660 CGGTGGACAAATAAAATTTCAGGGA 60.048 40.000 0.00 0.00 0.00 4.20
1684 3210 5.531659 CGTGTAGTATCTATATAGCAGGGGG 59.468 48.000 4.75 0.00 0.00 5.40
1778 3537 2.719046 CGAAAATGTGCTCAAAACGTCC 59.281 45.455 0.00 0.00 0.00 4.79
1811 3832 0.040067 CTTTCCCAAACAGCACGCTC 60.040 55.000 0.00 0.00 0.00 5.03
1826 3847 1.620819 ACGCTCTCAGTGGATTTGTCT 59.379 47.619 0.00 0.00 0.00 3.41
1853 3894 2.202892 GGAACCGATGTCCGAGGC 60.203 66.667 0.00 0.00 41.76 4.70
1864 3905 1.453015 TCCGAGGCAGAGAGCTCTC 60.453 63.158 32.45 32.45 44.79 3.20
1891 3932 0.179134 GGATCAGGAACCGAGACACG 60.179 60.000 0.00 0.00 42.18 4.49
1969 4041 8.563289 TGTTTTATGGTTAGTTTTACTTTGCG 57.437 30.769 0.00 0.00 0.00 4.85
1970 4042 7.648510 TGTTTTATGGTTAGTTTTACTTTGCGG 59.351 33.333 0.00 0.00 0.00 5.69
1971 4043 4.776795 ATGGTTAGTTTTACTTTGCGGG 57.223 40.909 0.00 0.00 0.00 6.13
1972 4044 3.818180 TGGTTAGTTTTACTTTGCGGGA 58.182 40.909 0.00 0.00 0.00 5.14
1987 4059 3.958018 TGCGGGATGTTTTATGGTTAGT 58.042 40.909 0.00 0.00 0.00 2.24
1994 4066 8.342634 CGGGATGTTTTATGGTTAGTTAATCAG 58.657 37.037 0.00 0.00 28.54 2.90
2027 4099 0.745486 TCACTTCATGCAGATGCCGG 60.745 55.000 0.00 0.00 41.18 6.13
2060 4132 7.443272 TCCCCTCTTTTCGAAAAAGTTAGTTAG 59.557 37.037 22.67 9.09 0.00 2.34
2061 4133 7.443272 CCCCTCTTTTCGAAAAAGTTAGTTAGA 59.557 37.037 22.67 12.57 0.00 2.10
2124 4196 7.120726 CCAAATTAAACCGAGTCCTAGTTTGAT 59.879 37.037 9.65 5.61 35.45 2.57
2137 4233 8.934697 AGTCCTAGTTTGATAACCATATGCTTA 58.065 33.333 0.00 0.00 34.71 3.09
2156 4252 6.639563 TGCTTATATGATGGCACGTATACAT 58.360 36.000 3.32 0.00 0.00 2.29
2208 4304 2.146724 TGGAGTGTCCCCTGTGGTG 61.147 63.158 0.00 0.00 35.03 4.17
2224 4320 7.067008 CCCCTGTGGTGTCTAATACAAATTTAG 59.933 40.741 0.00 0.00 40.63 1.85
2452 4586 2.875317 TGTATTTTGTGAGCAGAACGCA 59.125 40.909 0.00 0.00 46.13 5.24
2546 4680 1.337823 GCAGCCGTAAAGTCTCCAAGA 60.338 52.381 0.00 0.00 0.00 3.02
2556 4690 1.833630 AGTCTCCAAGATCATCGCCAA 59.166 47.619 0.00 0.00 0.00 4.52
2572 4706 1.352687 GCCAACTCCTTCTTCCTCCTT 59.647 52.381 0.00 0.00 0.00 3.36
2581 4715 2.852075 TTCCTCCTTGGCACCGGT 60.852 61.111 0.00 0.00 35.26 5.28
2629 4763 2.745884 TCCCAAGCCGATGTTGCG 60.746 61.111 0.00 0.00 0.00 4.85
2665 4799 0.671472 TCGTCTCGAACTACTCCGCA 60.671 55.000 0.00 0.00 31.06 5.69
2686 4820 1.486310 GCCATCACTGACCTGTATGGA 59.514 52.381 3.89 0.00 39.60 3.41
2719 4853 2.010145 AGTTCGGGATCATCAACACG 57.990 50.000 0.00 0.00 0.00 4.49
2728 4862 2.040544 CATCAACACGGGCCCAGTC 61.041 63.158 24.92 0.00 0.00 3.51
2797 4931 0.462047 ATGGAATGAACCGTCTCGCC 60.462 55.000 0.00 0.00 0.00 5.54
2800 4934 3.296709 AATGAACCGTCTCGCCGCT 62.297 57.895 0.00 0.00 0.00 5.52
2860 4994 4.640690 ACCACGACCAGGCTCCCT 62.641 66.667 0.00 0.00 0.00 4.20
2914 5048 2.203224 TCGCGGGCCAACTTCAAA 60.203 55.556 6.13 0.00 0.00 2.69
2920 5054 1.128200 GGGCCAACTTCAAAAACCCT 58.872 50.000 4.39 0.00 32.88 4.34
2970 5104 1.003839 CTTGCTGCGGGAGTGGTAA 60.004 57.895 0.00 0.00 0.00 2.85
3046 5180 5.106197 TGACGCATATGCTTTCTTTGACAAT 60.106 36.000 24.56 0.00 39.32 2.71
3055 5189 0.950836 TCTTTGACAATGTGCACCCG 59.049 50.000 15.69 4.98 0.00 5.28
3106 5240 1.896660 GCTCTTTGTTGACGGCCCA 60.897 57.895 0.00 0.00 0.00 5.36
3140 5274 1.004044 CACCCATCAGCTTCAAGGAGT 59.996 52.381 0.00 0.00 0.00 3.85
3163 5297 3.321039 AGCCCACCAGAGATGATTGATA 58.679 45.455 0.00 0.00 0.00 2.15
3166 5300 4.802248 GCCCACCAGAGATGATTGATAGAC 60.802 50.000 0.00 0.00 0.00 2.59
3171 5305 7.270779 CACCAGAGATGATTGATAGACTCAAA 58.729 38.462 0.00 0.00 46.62 2.69
3172 5306 7.767659 CACCAGAGATGATTGATAGACTCAAAA 59.232 37.037 0.00 0.00 46.62 2.44
3198 5332 8.591114 AAAACCAGAGATGATTGATTGATTCT 57.409 30.769 0.00 0.00 0.00 2.40
3201 5335 7.997482 ACCAGAGATGATTGATTGATTCTTTG 58.003 34.615 0.00 0.00 0.00 2.77
3203 5337 8.683615 CCAGAGATGATTGATTGATTCTTTGAA 58.316 33.333 0.00 0.00 0.00 2.69
3233 5369 8.489990 AGTACAAGACATGATTGATTCTCTTG 57.510 34.615 18.10 15.90 37.84 3.02
3247 5383 9.730705 ATTGATTCTCTTGAGTTTGAGTGATTA 57.269 29.630 0.00 0.00 0.00 1.75
3253 5389 9.591792 TCTCTTGAGTTTGAGTGATTATGTATG 57.408 33.333 0.00 0.00 0.00 2.39
3254 5390 9.376075 CTCTTGAGTTTGAGTGATTATGTATGT 57.624 33.333 0.00 0.00 0.00 2.29
3293 5433 7.716799 TTCAAAACTCCATATATTGCCAACT 57.283 32.000 0.00 0.00 0.00 3.16
3296 5436 9.249053 TCAAAACTCCATATATTGCCAACTAAA 57.751 29.630 0.00 0.00 0.00 1.85
3304 5444 9.013229 CCATATATTGCCAACTAAAAGCATCTA 57.987 33.333 0.00 0.00 36.20 1.98
3306 5446 4.701956 TTGCCAACTAAAAGCATCTAGC 57.298 40.909 0.00 0.00 46.19 3.42
3346 5488 3.922910 AGGAGTAAACGGCTGAGTAAAC 58.077 45.455 0.00 0.00 0.00 2.01
3349 5491 3.922910 AGTAAACGGCTGAGTAAACCTC 58.077 45.455 0.00 0.00 40.89 3.85
3363 5505 6.934645 TGAGTAAACCTCAGTGGAGTATTTTG 59.065 38.462 0.00 0.00 45.34 2.44
3370 5512 6.176183 CCTCAGTGGAGTATTTTGACTTCAT 58.824 40.000 0.00 0.00 37.29 2.57
3383 5525 7.979115 TTTTGACTTCATTAAGTTTTGGTCG 57.021 32.000 0.00 0.00 46.09 4.79
3385 5527 6.295039 TGACTTCATTAAGTTTTGGTCGTC 57.705 37.500 0.00 0.00 46.09 4.20
3392 5534 5.464030 TTAAGTTTTGGTCGTCTCTAGCT 57.536 39.130 0.00 0.00 0.00 3.32
3398 5540 2.566913 TGGTCGTCTCTAGCTGATCTC 58.433 52.381 0.00 0.00 0.00 2.75
3400 5542 1.529438 GTCGTCTCTAGCTGATCTCCG 59.471 57.143 0.00 0.00 0.00 4.63
3431 5573 4.143452 GCGGAGTAAAACTTACTCGAACAC 60.143 45.833 16.47 5.53 43.53 3.32
3443 5585 3.947841 GAACACTTGGCACGCGCA 61.948 61.111 5.73 0.00 41.24 6.09
3447 5589 4.609018 ACTTGGCACGCGCACTCT 62.609 61.111 5.73 0.00 41.24 3.24
3448 5590 2.432456 CTTGGCACGCGCACTCTA 60.432 61.111 5.73 0.00 41.24 2.43
3453 5595 2.126307 CACGCGCACTCTAGCACT 60.126 61.111 5.73 0.00 0.00 4.40
3461 5603 1.403514 GCACTCTAGCACTGACAGGAC 60.404 57.143 7.51 0.00 0.00 3.85
3480 5622 0.246635 CGGACAAGACGAAGGATGGT 59.753 55.000 0.00 0.00 0.00 3.55
3482 5624 1.275291 GGACAAGACGAAGGATGGTGA 59.725 52.381 0.00 0.00 0.00 4.02
3483 5625 2.093447 GGACAAGACGAAGGATGGTGAT 60.093 50.000 0.00 0.00 0.00 3.06
3486 5628 0.833287 AGACGAAGGATGGTGATGGG 59.167 55.000 0.00 0.00 0.00 4.00
3487 5629 0.830648 GACGAAGGATGGTGATGGGA 59.169 55.000 0.00 0.00 0.00 4.37
3488 5630 1.209504 GACGAAGGATGGTGATGGGAA 59.790 52.381 0.00 0.00 0.00 3.97
3489 5631 1.210478 ACGAAGGATGGTGATGGGAAG 59.790 52.381 0.00 0.00 0.00 3.46
3490 5632 1.475751 CGAAGGATGGTGATGGGAAGG 60.476 57.143 0.00 0.00 0.00 3.46
3491 5633 1.846439 GAAGGATGGTGATGGGAAGGA 59.154 52.381 0.00 0.00 0.00 3.36
3492 5634 1.985622 AGGATGGTGATGGGAAGGAA 58.014 50.000 0.00 0.00 0.00 3.36
3493 5635 1.566231 AGGATGGTGATGGGAAGGAAC 59.434 52.381 0.00 0.00 0.00 3.62
3494 5636 1.284785 GGATGGTGATGGGAAGGAACA 59.715 52.381 0.00 0.00 0.00 3.18
3495 5637 2.291540 GGATGGTGATGGGAAGGAACAA 60.292 50.000 0.00 0.00 0.00 2.83
3496 5638 3.628257 GGATGGTGATGGGAAGGAACAAT 60.628 47.826 0.00 0.00 0.00 2.71
3497 5639 4.386312 GGATGGTGATGGGAAGGAACAATA 60.386 45.833 0.00 0.00 0.00 1.90
3498 5640 4.666412 TGGTGATGGGAAGGAACAATAA 57.334 40.909 0.00 0.00 0.00 1.40
3499 5641 5.004361 TGGTGATGGGAAGGAACAATAAA 57.996 39.130 0.00 0.00 0.00 1.40
3500 5642 5.398236 TGGTGATGGGAAGGAACAATAAAA 58.602 37.500 0.00 0.00 0.00 1.52
3501 5643 5.841237 TGGTGATGGGAAGGAACAATAAAAA 59.159 36.000 0.00 0.00 0.00 1.94
3502 5644 6.500049 TGGTGATGGGAAGGAACAATAAAAAT 59.500 34.615 0.00 0.00 0.00 1.82
3503 5645 6.818142 GGTGATGGGAAGGAACAATAAAAATG 59.182 38.462 0.00 0.00 0.00 2.32
3504 5646 7.310361 GGTGATGGGAAGGAACAATAAAAATGA 60.310 37.037 0.00 0.00 0.00 2.57
3505 5647 8.260114 GTGATGGGAAGGAACAATAAAAATGAT 58.740 33.333 0.00 0.00 0.00 2.45
3506 5648 9.486123 TGATGGGAAGGAACAATAAAAATGATA 57.514 29.630 0.00 0.00 0.00 2.15
3507 5649 9.971922 GATGGGAAGGAACAATAAAAATGATAG 57.028 33.333 0.00 0.00 0.00 2.08
3508 5650 9.713684 ATGGGAAGGAACAATAAAAATGATAGA 57.286 29.630 0.00 0.00 0.00 1.98
3509 5651 9.713684 TGGGAAGGAACAATAAAAATGATAGAT 57.286 29.630 0.00 0.00 0.00 1.98
3529 5671 9.570488 GATAGATACATTAAAGACGTATCACCC 57.430 37.037 10.45 0.00 42.52 4.61
3536 5678 0.539986 AGACGTATCACCCGCCAAAT 59.460 50.000 0.00 0.00 0.00 2.32
3547 5690 4.339814 TCACCCGCCAAATTAAATATCCAC 59.660 41.667 0.00 0.00 0.00 4.02
3550 5693 4.500716 CCCGCCAAATTAAATATCCACCAC 60.501 45.833 0.00 0.00 0.00 4.16
3556 5699 7.580495 GCCAAATTAAATATCCACCACTTCCAA 60.580 37.037 0.00 0.00 0.00 3.53
3557 5700 7.981225 CCAAATTAAATATCCACCACTTCCAAG 59.019 37.037 0.00 0.00 0.00 3.61
3568 5711 3.138468 ACCACTTCCAAGATATAAGGGGC 59.862 47.826 3.73 0.00 45.94 5.80
3574 5717 6.332901 ACTTCCAAGATATAAGGGGCATTAGT 59.667 38.462 0.00 0.00 0.00 2.24
3577 5720 8.282801 TCCAAGATATAAGGGGCATTAGTTTA 57.717 34.615 0.00 0.00 0.00 2.01
3792 5946 9.167311 ACACCTCATATTTTGAAATAGAGTGAC 57.833 33.333 16.38 0.00 34.62 3.67
3794 5948 9.965902 ACCTCATATTTTGAAATAGAGTGACTT 57.034 29.630 14.59 0.00 34.62 3.01
3821 5977 3.885724 AAAGAAACCCAACAACACCAG 57.114 42.857 0.00 0.00 0.00 4.00
3825 5981 0.755327 AACCCAACAACACCAGAGGC 60.755 55.000 0.00 0.00 0.00 4.70
3826 5982 1.152777 CCCAACAACACCAGAGGCA 60.153 57.895 0.00 0.00 0.00 4.75
3858 6014 1.597461 CCACCCCTTCGAGTCTTCC 59.403 63.158 0.00 0.00 0.00 3.46
3897 6053 6.039382 CCCTAATTTGTAATGCCTTACAGTCC 59.961 42.308 13.28 0.00 45.90 3.85
3920 6076 7.976175 GTCCATTGAGGTCTCCAAATTAAATTC 59.024 37.037 0.00 0.00 39.02 2.17
3963 6119 6.073331 CGAGTCAAGAATTTCTCAAAGCTCTT 60.073 38.462 0.00 0.00 30.73 2.85
4033 6240 7.214381 TGACCGAGTCTAAAATTTCTCAAAGA 58.786 34.615 0.00 0.00 33.15 2.52
4035 6242 8.622948 ACCGAGTCTAAAATTTCTCAAAGATT 57.377 30.769 0.00 0.00 0.00 2.40
4037 6244 8.507249 CCGAGTCTAAAATTTCTCAAAGATTGT 58.493 33.333 0.00 0.00 0.00 2.71
4084 6939 6.856895 ACACTATGCTTCCTAATTTTCAAGC 58.143 36.000 7.61 7.61 41.43 4.01
4093 6948 6.560253 TCCTAATTTTCAAGCTCTCACAAC 57.440 37.500 0.00 0.00 0.00 3.32
4108 6963 6.672266 TCTCACAACTAATTGAGGTCTTCT 57.328 37.500 0.00 0.00 39.86 2.85
4141 6996 2.355716 GGTCATCCGATTTTGACTGGGA 60.356 50.000 3.39 0.00 41.55 4.37
4156 7011 4.952957 TGACTGGGACAACAATTTCTCAAA 59.047 37.500 0.00 0.00 38.70 2.69
4157 7012 5.067674 TGACTGGGACAACAATTTCTCAAAG 59.932 40.000 0.00 0.00 38.70 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 6.621613 ACACGCCATCATGTGTATATAGTAG 58.378 40.000 0.00 0.00 46.82 2.57
61 62 5.800941 GGATTCTATACATTCTTAGGACGCG 59.199 44.000 3.53 3.53 0.00 6.01
62 63 6.586844 GTGGATTCTATACATTCTTAGGACGC 59.413 42.308 0.00 0.00 0.00 5.19
73 74 6.784473 TCAGATGACAGGTGGATTCTATACAT 59.216 38.462 0.00 0.00 0.00 2.29
79 80 4.042062 TGTTTCAGATGACAGGTGGATTCT 59.958 41.667 0.00 0.00 0.00 2.40
85 86 5.036737 GTGTTTTGTTTCAGATGACAGGTG 58.963 41.667 0.00 0.00 0.00 4.00
112 113 4.647291 CGAGCACTCGTTCTTGTATTTT 57.353 40.909 11.82 0.00 46.99 1.82
126 127 4.682778 ATACTCTCTAGAGACGAGCACT 57.317 45.455 18.76 2.35 44.74 4.40
128 129 6.408107 TTCTATACTCTCTAGAGACGAGCA 57.592 41.667 18.76 0.61 44.74 4.26
130 131 8.024865 TCGATTTCTATACTCTCTAGAGACGAG 58.975 40.741 18.76 11.72 44.74 4.18
133 134 9.136952 GACTCGATTTCTATACTCTCTAGAGAC 57.863 40.741 18.76 4.17 44.74 3.36
142 143 7.124347 AGATGTCGACTCGATTTCTATACTC 57.876 40.000 17.92 0.00 38.42 2.59
246 247 7.096966 CGAGCTGTAAGACTTTTATGACGATAC 60.097 40.741 0.00 0.00 34.07 2.24
268 269 0.714439 GTTCTACTCCGTTTGCGAGC 59.286 55.000 0.00 0.00 41.33 5.03
300 301 7.327032 GGTTGTCTTTCTCAGCATGTAATTTTC 59.673 37.037 0.00 0.00 37.40 2.29
306 307 3.006430 TCGGTTGTCTTTCTCAGCATGTA 59.994 43.478 0.00 0.00 37.40 2.29
312 313 3.179830 CCGTATCGGTTGTCTTTCTCAG 58.820 50.000 0.00 0.00 42.73 3.35
406 513 7.375053 ACAACAAACTTTAACTTTCTTGCAGA 58.625 30.769 0.00 0.00 0.00 4.26
407 514 7.542130 AGACAACAAACTTTAACTTTCTTGCAG 59.458 33.333 0.00 0.00 0.00 4.41
460 567 3.709141 TGCGCTATTATGGGCTATATGGA 59.291 43.478 9.73 0.00 44.66 3.41
489 596 3.756963 ACTGCGCCTCGTATATAGATTGA 59.243 43.478 4.18 0.00 0.00 2.57
495 602 4.698780 ACAGATTACTGCGCCTCGTATATA 59.301 41.667 4.18 0.00 46.95 0.86
496 603 3.506455 ACAGATTACTGCGCCTCGTATAT 59.494 43.478 4.18 1.25 46.95 0.86
497 604 2.882761 ACAGATTACTGCGCCTCGTATA 59.117 45.455 4.18 0.00 46.95 1.47
505 612 1.130561 GGGTTGAACAGATTACTGCGC 59.869 52.381 0.00 0.00 46.95 6.09
532 639 1.885887 CATCATTGTTTGGGACGTGGT 59.114 47.619 0.00 0.00 0.00 4.16
551 658 5.876651 ACTCATGTCTACTCCATATTGCA 57.123 39.130 0.00 0.00 0.00 4.08
559 666 3.690139 TCTCGTCAACTCATGTCTACTCC 59.310 47.826 0.00 0.00 0.00 3.85
562 669 5.049398 ACTTCTCGTCAACTCATGTCTAC 57.951 43.478 0.00 0.00 0.00 2.59
567 674 4.101942 GAGCTACTTCTCGTCAACTCATG 58.898 47.826 0.00 0.00 0.00 3.07
568 675 4.364415 GAGCTACTTCTCGTCAACTCAT 57.636 45.455 0.00 0.00 0.00 2.90
569 676 3.833545 GAGCTACTTCTCGTCAACTCA 57.166 47.619 0.00 0.00 0.00 3.41
578 685 3.543665 TCTCTAACCCGAGCTACTTCTC 58.456 50.000 0.00 0.00 0.00 2.87
579 686 3.200385 TCTCTCTAACCCGAGCTACTTCT 59.800 47.826 0.00 0.00 0.00 2.85
580 687 3.543665 TCTCTCTAACCCGAGCTACTTC 58.456 50.000 0.00 0.00 0.00 3.01
581 688 3.648507 TCTCTCTAACCCGAGCTACTT 57.351 47.619 0.00 0.00 0.00 2.24
582 689 3.746940 GATCTCTCTAACCCGAGCTACT 58.253 50.000 0.00 0.00 0.00 2.57
583 690 2.481185 CGATCTCTCTAACCCGAGCTAC 59.519 54.545 0.00 0.00 0.00 3.58
584 691 2.367894 TCGATCTCTCTAACCCGAGCTA 59.632 50.000 0.00 0.00 0.00 3.32
585 692 1.141254 TCGATCTCTCTAACCCGAGCT 59.859 52.381 0.00 0.00 0.00 4.09
586 693 1.533731 CTCGATCTCTCTAACCCGAGC 59.466 57.143 0.00 0.00 37.35 5.03
587 694 2.841215 ACTCGATCTCTCTAACCCGAG 58.159 52.381 0.00 0.00 46.00 4.63
588 695 3.640498 TCTACTCGATCTCTCTAACCCGA 59.360 47.826 0.00 0.00 0.00 5.14
589 696 3.742369 GTCTACTCGATCTCTCTAACCCG 59.258 52.174 0.00 0.00 0.00 5.28
590 697 4.706035 TGTCTACTCGATCTCTCTAACCC 58.294 47.826 0.00 0.00 0.00 4.11
591 698 5.992829 TCATGTCTACTCGATCTCTCTAACC 59.007 44.000 0.00 0.00 0.00 2.85
592 699 6.704493 ACTCATGTCTACTCGATCTCTCTAAC 59.296 42.308 0.00 0.00 0.00 2.34
593 700 6.822442 ACTCATGTCTACTCGATCTCTCTAA 58.178 40.000 0.00 0.00 0.00 2.10
594 701 6.413783 ACTCATGTCTACTCGATCTCTCTA 57.586 41.667 0.00 0.00 0.00 2.43
595 702 5.290493 ACTCATGTCTACTCGATCTCTCT 57.710 43.478 0.00 0.00 0.00 3.10
596 703 5.525745 TCAACTCATGTCTACTCGATCTCTC 59.474 44.000 0.00 0.00 0.00 3.20
607 714 5.883115 AGATCTTCTCGTCAACTCATGTCTA 59.117 40.000 0.00 0.00 0.00 2.59
622 729 5.134640 CGTATCTTTCGTCGAGATCTTCTC 58.865 45.833 0.00 0.00 40.06 2.87
772 915 6.445451 AAGTGCCATGATCTTGGAGTATAT 57.555 37.500 27.35 8.13 39.25 0.86
813 991 6.072397 ACGTATGATCAGATCAACTAGCTACC 60.072 42.308 17.24 0.00 43.50 3.18
837 1015 0.109132 ACGGTTTGATCGGTCGGTAC 60.109 55.000 0.00 0.00 0.00 3.34
838 1016 1.132262 GTACGGTTTGATCGGTCGGTA 59.868 52.381 0.00 0.00 0.00 4.02
839 1017 0.109132 GTACGGTTTGATCGGTCGGT 60.109 55.000 0.00 0.00 0.00 4.69
840 1018 0.171903 AGTACGGTTTGATCGGTCGG 59.828 55.000 0.00 0.00 0.00 4.79
844 1022 3.558418 CCCAATTAGTACGGTTTGATCGG 59.442 47.826 6.36 0.00 0.00 4.18
883 1061 3.010027 TGGTCATTAAGGTGATGGCAAGA 59.990 43.478 0.00 0.00 30.84 3.02
901 1080 2.973694 TTGGCCGTCTACTAATGGTC 57.026 50.000 0.00 0.00 0.00 4.02
929 1108 4.574013 AGTACAGTATAGTACAGGCGTGTC 59.426 45.833 16.53 7.99 45.25 3.67
934 1113 8.613060 TGTGTATAGTACAGTATAGTACAGGC 57.387 38.462 6.97 0.00 45.25 4.85
943 1133 8.763984 AGCTAACCTTGTGTATAGTACAGTAT 57.236 34.615 0.00 0.00 39.77 2.12
981 1176 6.296087 CCTTCATGGCTGGCTATCTAAGAATA 60.296 42.308 2.00 0.00 0.00 1.75
986 1181 2.373169 CCCTTCATGGCTGGCTATCTAA 59.627 50.000 2.00 0.00 0.00 2.10
1020 1215 0.745845 CGATCACAAGGCCCAGAAGG 60.746 60.000 0.00 0.00 39.47 3.46
1042 1237 0.679002 CTGCTAGCACCAATGGCACT 60.679 55.000 14.93 0.00 0.00 4.40
1363 1609 2.632377 CGTGATTTCAGCACCAGGTAT 58.368 47.619 0.00 0.00 32.74 2.73
1394 1640 4.459089 GGTGAGAGCGCTGGGGAC 62.459 72.222 18.48 5.70 0.00 4.46
1519 2505 3.942748 ACACTAAAAGAACTCCGTTGCAA 59.057 39.130 0.00 0.00 0.00 4.08
1520 2506 3.311322 CACACTAAAAGAACTCCGTTGCA 59.689 43.478 0.00 0.00 0.00 4.08
1521 2507 3.558418 TCACACTAAAAGAACTCCGTTGC 59.442 43.478 0.00 0.00 0.00 4.17
1522 2508 5.047847 TCTCACACTAAAAGAACTCCGTTG 58.952 41.667 0.00 0.00 0.00 4.10
1523 2509 5.272283 TCTCACACTAAAAGAACTCCGTT 57.728 39.130 0.00 0.00 0.00 4.44
1524 2510 4.931661 TCTCACACTAAAAGAACTCCGT 57.068 40.909 0.00 0.00 0.00 4.69
1525 2511 4.627467 CCATCTCACACTAAAAGAACTCCG 59.373 45.833 0.00 0.00 0.00 4.63
1526 2512 5.552178 ACCATCTCACACTAAAAGAACTCC 58.448 41.667 0.00 0.00 0.00 3.85
1527 2513 7.819900 ACATACCATCTCACACTAAAAGAACTC 59.180 37.037 0.00 0.00 0.00 3.01
1529 2515 7.907214 ACATACCATCTCACACTAAAAGAAC 57.093 36.000 0.00 0.00 0.00 3.01
1530 2516 9.031537 TCTACATACCATCTCACACTAAAAGAA 57.968 33.333 0.00 0.00 0.00 2.52
1531 2517 8.589701 TCTACATACCATCTCACACTAAAAGA 57.410 34.615 0.00 0.00 0.00 2.52
1532 2518 9.653287 TTTCTACATACCATCTCACACTAAAAG 57.347 33.333 0.00 0.00 0.00 2.27
1608 3091 7.557724 TGTCCACCGTCTATATTGTTCATAAA 58.442 34.615 0.00 0.00 0.00 1.40
1623 3106 5.861787 CCTGAAATTTTATTTGTCCACCGTC 59.138 40.000 0.00 0.00 0.00 4.79
1644 3127 1.003355 ACGGCACAATCTGTCCCTG 60.003 57.895 0.00 0.00 0.00 4.45
1647 3130 1.337823 ACTACACGGCACAATCTGTCC 60.338 52.381 0.00 0.00 0.00 4.02
1649 3132 3.447586 AGATACTACACGGCACAATCTGT 59.552 43.478 0.00 0.00 0.00 3.41
1742 3501 8.850156 AGCACATTTTCGGCTAGAATATTAAAT 58.150 29.630 0.00 0.00 38.86 1.40
1748 3507 4.765273 TGAGCACATTTTCGGCTAGAATA 58.235 39.130 0.00 0.00 38.86 1.75
1759 3518 3.130340 AGTGGACGTTTTGAGCACATTTT 59.870 39.130 0.00 0.00 0.00 1.82
1764 3523 1.268539 CCAAGTGGACGTTTTGAGCAC 60.269 52.381 0.00 0.00 37.39 4.40
1811 3832 5.308825 AGTAAACCAGACAAATCCACTGAG 58.691 41.667 0.00 0.00 34.07 3.35
1826 3847 3.404899 GACATCGGTTCCAAGTAAACCA 58.595 45.455 5.92 0.00 45.35 3.67
1853 3894 0.179176 CCACGTTCGAGAGCTCTCTG 60.179 60.000 34.69 27.83 40.61 3.35
1864 3905 0.739813 GGTTCCTGATCCCACGTTCG 60.740 60.000 0.00 0.00 0.00 3.95
1891 3932 4.156915 GCGTACATGATCGACCTATACAC 58.843 47.826 15.56 0.00 0.00 2.90
1958 4030 6.159988 CCATAAAACATCCCGCAAAGTAAAA 58.840 36.000 0.00 0.00 0.00 1.52
1959 4031 5.244178 ACCATAAAACATCCCGCAAAGTAAA 59.756 36.000 0.00 0.00 0.00 2.01
1960 4032 4.767928 ACCATAAAACATCCCGCAAAGTAA 59.232 37.500 0.00 0.00 0.00 2.24
1961 4033 4.337145 ACCATAAAACATCCCGCAAAGTA 58.663 39.130 0.00 0.00 0.00 2.24
1962 4034 3.161866 ACCATAAAACATCCCGCAAAGT 58.838 40.909 0.00 0.00 0.00 2.66
1964 4036 4.767928 ACTAACCATAAAACATCCCGCAAA 59.232 37.500 0.00 0.00 0.00 3.68
1965 4037 4.337145 ACTAACCATAAAACATCCCGCAA 58.663 39.130 0.00 0.00 0.00 4.85
1966 4038 3.958018 ACTAACCATAAAACATCCCGCA 58.042 40.909 0.00 0.00 0.00 5.69
1967 4039 4.976224 AACTAACCATAAAACATCCCGC 57.024 40.909 0.00 0.00 0.00 6.13
1968 4040 8.215926 TGATTAACTAACCATAAAACATCCCG 57.784 34.615 0.00 0.00 0.00 5.14
1969 4041 9.403583 TCTGATTAACTAACCATAAAACATCCC 57.596 33.333 0.00 0.00 0.00 3.85
1987 4059 5.409520 GTGATTGCACACAGACTCTGATTAA 59.590 40.000 13.25 1.71 44.51 1.40
2060 4132 8.712363 TGCGCTTCTGATGATTAGTTAATTATC 58.288 33.333 9.73 8.79 38.46 1.75
2061 4133 8.499162 GTGCGCTTCTGATGATTAGTTAATTAT 58.501 33.333 9.73 0.00 0.00 1.28
2079 4151 3.907893 GTGCTTGTTGTGCGCTTC 58.092 55.556 9.73 2.14 37.87 3.86
2124 4196 6.538381 CGTGCCATCATATAAGCATATGGTTA 59.462 38.462 25.14 25.14 42.92 2.85
2163 4259 6.265577 ACAACACTTGCAGTTAATTGAGAAC 58.734 36.000 1.56 0.00 0.00 3.01
2441 4575 1.195674 GTTCTTTCCTGCGTTCTGCTC 59.804 52.381 0.00 0.00 46.63 4.26
2442 4576 1.230324 GTTCTTTCCTGCGTTCTGCT 58.770 50.000 0.00 0.00 46.63 4.24
2452 4586 5.587388 TCGATAACGGTATGTTCTTTCCT 57.413 39.130 0.00 0.00 42.09 3.36
2546 4680 2.420687 GGAAGAAGGAGTTGGCGATGAT 60.421 50.000 0.00 0.00 0.00 2.45
2556 4690 0.988063 GCCAAGGAGGAAGAAGGAGT 59.012 55.000 0.00 0.00 41.22 3.85
2572 4706 2.845752 GATCGTTGCTACCGGTGCCA 62.846 60.000 19.93 11.39 0.00 4.92
2665 4799 1.487976 CCATACAGGTCAGTGATGGCT 59.512 52.381 0.00 0.00 31.24 4.75
2686 4820 1.745489 GAACTTCCTCGCGCCCATT 60.745 57.895 0.00 0.00 0.00 3.16
2860 4994 4.753662 AGGGAGTACGCGAGGCCA 62.754 66.667 15.93 0.00 0.00 5.36
2912 5046 1.170290 CCGGTCGCTTGAGGGTTTTT 61.170 55.000 0.00 0.00 0.00 1.94
2914 5048 2.032071 CCGGTCGCTTGAGGGTTT 59.968 61.111 0.00 0.00 0.00 3.27
2953 5087 1.003839 CTTACCACTCCCGCAGCAA 60.004 57.895 0.00 0.00 0.00 3.91
3014 5148 1.762222 GCATATGCGTCACGGTCACC 61.762 60.000 12.82 0.00 0.00 4.02
3106 5240 0.753479 TGGGTGCGGTGATTTGTGTT 60.753 50.000 0.00 0.00 0.00 3.32
3140 5274 3.114606 TCAATCATCTCTGGTGGGCTAA 58.885 45.455 0.00 0.00 0.00 3.09
3172 5306 9.032624 AGAATCAATCAATCATCTCTGGTTTTT 57.967 29.630 0.00 0.00 0.00 1.94
3233 5369 9.546909 CAACAACATACATAATCACTCAAACTC 57.453 33.333 0.00 0.00 0.00 3.01
3253 5389 9.967245 GGAGTTTTGAAAAAGAAATACAACAAC 57.033 29.630 0.00 0.00 0.00 3.32
3254 5390 9.712305 TGGAGTTTTGAAAAAGAAATACAACAA 57.288 25.926 0.00 0.00 0.00 2.83
3271 5411 9.868277 TTTTAGTTGGCAATATATGGAGTTTTG 57.132 29.630 1.92 0.00 0.00 2.44
3293 5433 2.038557 GGGGATCGGCTAGATGCTTTTA 59.961 50.000 12.12 0.00 45.63 1.52
3296 5436 0.472734 AGGGGATCGGCTAGATGCTT 60.473 55.000 12.12 1.95 45.63 3.91
3346 5488 5.551233 TGAAGTCAAAATACTCCACTGAGG 58.449 41.667 0.00 0.00 43.29 3.86
3349 5491 9.003658 ACTTAATGAAGTCAAAATACTCCACTG 57.996 33.333 0.00 0.00 42.50 3.66
3359 5501 7.540299 ACGACCAAAACTTAATGAAGTCAAAA 58.460 30.769 0.00 0.00 45.50 2.44
3363 5505 6.424207 AGAGACGACCAAAACTTAATGAAGTC 59.576 38.462 0.00 0.00 45.50 3.01
3370 5512 5.010314 TCAGCTAGAGACGACCAAAACTTAA 59.990 40.000 0.00 0.00 0.00 1.85
3383 5525 3.630312 ACTTTCGGAGATCAGCTAGAGAC 59.370 47.826 0.00 0.00 35.04 3.36
3385 5527 4.647424 AACTTTCGGAGATCAGCTAGAG 57.353 45.455 0.00 0.00 35.04 2.43
3398 5540 3.992427 AGTTTTACTCCGCTAACTTTCGG 59.008 43.478 0.00 0.00 46.52 4.30
3400 5542 7.410193 CGAGTAAGTTTTACTCCGCTAACTTTC 60.410 40.741 18.35 3.41 40.30 2.62
3419 5561 1.455786 CGTGCCAAGTGTTCGAGTAAG 59.544 52.381 0.00 0.00 0.00 2.34
3431 5573 2.432456 TAGAGTGCGCGTGCCAAG 60.432 61.111 19.87 0.00 41.78 3.61
3442 5584 1.135546 CGTCCTGTCAGTGCTAGAGTG 60.136 57.143 0.00 0.00 0.00 3.51
3443 5585 1.169577 CGTCCTGTCAGTGCTAGAGT 58.830 55.000 0.00 0.00 0.00 3.24
3447 5589 0.538746 TGTCCGTCCTGTCAGTGCTA 60.539 55.000 0.00 0.00 0.00 3.49
3448 5590 1.399744 TTGTCCGTCCTGTCAGTGCT 61.400 55.000 0.00 0.00 0.00 4.40
3451 5593 0.674534 GTCTTGTCCGTCCTGTCAGT 59.325 55.000 0.00 0.00 0.00 3.41
3453 5595 0.820482 TCGTCTTGTCCGTCCTGTCA 60.820 55.000 0.00 0.00 0.00 3.58
3461 5603 0.246635 ACCATCCTTCGTCTTGTCCG 59.753 55.000 0.00 0.00 0.00 4.79
3480 5622 7.789202 TCATTTTTATTGTTCCTTCCCATCA 57.211 32.000 0.00 0.00 0.00 3.07
3482 5624 9.713684 TCTATCATTTTTATTGTTCCTTCCCAT 57.286 29.630 0.00 0.00 0.00 4.00
3483 5625 9.713684 ATCTATCATTTTTATTGTTCCTTCCCA 57.286 29.630 0.00 0.00 0.00 4.37
3508 5650 4.986659 GCGGGTGATACGTCTTTAATGTAT 59.013 41.667 0.00 0.00 41.77 2.29
3509 5651 4.362279 GCGGGTGATACGTCTTTAATGTA 58.638 43.478 0.00 0.00 33.91 2.29
3510 5652 3.192466 GCGGGTGATACGTCTTTAATGT 58.808 45.455 0.00 0.00 0.00 2.71
3511 5653 2.542595 GGCGGGTGATACGTCTTTAATG 59.457 50.000 0.00 0.00 32.37 1.90
3512 5654 2.168936 TGGCGGGTGATACGTCTTTAAT 59.831 45.455 0.00 0.00 36.79 1.40
3513 5655 1.549620 TGGCGGGTGATACGTCTTTAA 59.450 47.619 0.00 0.00 36.79 1.52
3514 5656 1.184431 TGGCGGGTGATACGTCTTTA 58.816 50.000 0.00 0.00 36.79 1.85
3515 5657 0.322322 TTGGCGGGTGATACGTCTTT 59.678 50.000 0.00 0.00 36.79 2.52
3516 5658 0.322322 TTTGGCGGGTGATACGTCTT 59.678 50.000 0.00 0.00 36.79 3.01
3517 5659 0.539986 ATTTGGCGGGTGATACGTCT 59.460 50.000 0.00 0.00 36.79 4.18
3518 5660 1.375551 AATTTGGCGGGTGATACGTC 58.624 50.000 0.00 0.00 36.31 4.34
3519 5661 2.695127 TAATTTGGCGGGTGATACGT 57.305 45.000 0.00 0.00 0.00 3.57
3520 5662 4.561735 ATTTAATTTGGCGGGTGATACG 57.438 40.909 0.00 0.00 0.00 3.06
3521 5663 6.207810 TGGATATTTAATTTGGCGGGTGATAC 59.792 38.462 0.00 0.00 0.00 2.24
3522 5664 6.207810 GTGGATATTTAATTTGGCGGGTGATA 59.792 38.462 0.00 0.00 0.00 2.15
3523 5665 5.010617 GTGGATATTTAATTTGGCGGGTGAT 59.989 40.000 0.00 0.00 0.00 3.06
3524 5666 4.339814 GTGGATATTTAATTTGGCGGGTGA 59.660 41.667 0.00 0.00 0.00 4.02
3525 5667 4.500716 GGTGGATATTTAATTTGGCGGGTG 60.501 45.833 0.00 0.00 0.00 4.61
3526 5668 3.639561 GGTGGATATTTAATTTGGCGGGT 59.360 43.478 0.00 0.00 0.00 5.28
3527 5669 3.639094 TGGTGGATATTTAATTTGGCGGG 59.361 43.478 0.00 0.00 0.00 6.13
3528 5670 4.340950 AGTGGTGGATATTTAATTTGGCGG 59.659 41.667 0.00 0.00 0.00 6.13
3529 5671 5.514274 AGTGGTGGATATTTAATTTGGCG 57.486 39.130 0.00 0.00 0.00 5.69
3547 5690 3.138283 TGCCCCTTATATCTTGGAAGTGG 59.862 47.826 0.00 0.00 0.00 4.00
3550 5693 6.784031 ACTAATGCCCCTTATATCTTGGAAG 58.216 40.000 0.00 0.00 0.00 3.46
3801 5957 3.436243 TCTGGTGTTGTTGGGTTTCTTT 58.564 40.909 0.00 0.00 0.00 2.52
3821 5977 4.389576 CGCGCTTTGGTGTGCCTC 62.390 66.667 5.56 0.00 40.01 4.70
3850 6006 5.293560 GGAGCATAGTGTTATGGAAGACTC 58.706 45.833 0.00 0.00 39.71 3.36
3858 6014 7.807977 ACAAATTAGGGAGCATAGTGTTATG 57.192 36.000 0.00 0.00 39.75 1.90
3897 6053 6.974622 CCGAATTTAATTTGGAGACCTCAATG 59.025 38.462 16.92 0.00 45.10 2.82
4003 6159 8.504005 TGAGAAATTTTAGACTCGGTCAAAATC 58.496 33.333 16.94 11.83 35.02 2.17
4084 6939 6.696411 AGAAGACCTCAATTAGTTGTGAGAG 58.304 40.000 2.28 0.00 43.32 3.20
4118 6973 3.118408 CCCAGTCAAAATCGGATGACCTA 60.118 47.826 6.61 0.00 45.55 3.08


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

AutoCloner maintained by Alex Coulton.