Multiple sequence alignment - TraesCS5A01G097600

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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 TraesCS5A01G097600 chr5A 100.000 3767 0 0 1 3767 138431585 138427819 0.000000e+00 6957.0
1 TraesCS5A01G097600 chr5A 85.981 1769 241 5 984 2752 538349036 538350797 0.000000e+00 1886.0
2 TraesCS5A01G097600 chr5A 94.068 118 7 0 657 774 536275210 536275327 2.990000e-41 180.0
3 TraesCS5A01G097600 chr5A 93.860 114 7 0 3116 3229 318592039 318592152 5.000000e-39 172.0
4 TraesCS5A01G097600 chr5A 96.341 82 3 0 1 82 598081263 598081182 6.560000e-28 135.0
5 TraesCS5A01G097600 chr5A 93.333 90 6 0 1 90 533481382 533481293 2.360000e-27 134.0
6 TraesCS5A01G097600 chr5A 95.122 82 4 0 1 82 599553168 599553087 3.050000e-26 130.0
7 TraesCS5A01G097600 chr5B 93.689 2361 120 11 776 3117 137112968 137110618 0.000000e+00 3507.0
8 TraesCS5A01G097600 chr5B 85.908 1774 240 9 1000 2770 513711453 513713219 0.000000e+00 1882.0
9 TraesCS5A01G097600 chr5B 92.970 1010 62 5 2113 3117 137109974 137108969 0.000000e+00 1463.0
10 TraesCS5A01G097600 chr5B 89.711 554 45 10 3221 3767 137110619 137110071 0.000000e+00 697.0
11 TraesCS5A01G097600 chr5B 87.140 591 46 11 87 650 137113556 137112969 0.000000e+00 643.0
12 TraesCS5A01G097600 chr5B 91.949 236 15 3 3221 3455 137108970 137108738 1.010000e-85 327.0
13 TraesCS5A01G097600 chr5B 93.043 115 7 1 3116 3229 515669459 515669573 2.330000e-37 167.0
14 TraesCS5A01G097600 chr5D 93.897 1491 84 6 1634 3117 124391946 124390456 0.000000e+00 2242.0
15 TraesCS5A01G097600 chr5D 97.341 865 22 1 776 1640 124398151 124397288 0.000000e+00 1469.0
16 TraesCS5A01G097600 chr5D 91.501 553 36 8 3221 3767 124390457 124389910 0.000000e+00 750.0
17 TraesCS5A01G097600 chr5D 94.485 272 11 4 382 653 124398417 124398150 2.090000e-112 416.0
18 TraesCS5A01G097600 chr5D 93.151 146 9 1 249 394 124398579 124398435 2.950000e-51 213.0
19 TraesCS5A01G097600 chr5D 91.736 121 7 3 3116 3235 491692748 491692866 8.370000e-37 165.0
20 TraesCS5A01G097600 chr7B 82.827 1712 271 13 1061 2767 572507606 572505913 0.000000e+00 1511.0
21 TraesCS5A01G097600 chr7B 80.327 1713 318 17 1024 2725 157687794 157689498 0.000000e+00 1279.0
22 TraesCS5A01G097600 chr7D 82.089 1714 282 14 1061 2767 531977407 531975712 0.000000e+00 1441.0
23 TraesCS5A01G097600 chr7D 80.740 1729 316 15 1007 2725 193935005 193936726 0.000000e+00 1332.0
24 TraesCS5A01G097600 chr7D 92.562 121 9 0 657 777 599881391 599881271 1.390000e-39 174.0
25 TraesCS5A01G097600 chr7A 80.703 1679 313 9 1065 2736 203525571 203527245 0.000000e+00 1295.0
26 TraesCS5A01G097600 chr7A 96.341 82 3 0 1 82 54686556 54686475 6.560000e-28 135.0
27 TraesCS5A01G097600 chr7A 96.341 82 3 0 1 82 64484794 64484875 6.560000e-28 135.0
28 TraesCS5A01G097600 chr2A 80.302 1721 314 14 1061 2773 74253727 74252024 0.000000e+00 1277.0
29 TraesCS5A01G097600 chr2A 94.215 121 7 0 657 777 7724640 7724520 6.430000e-43 185.0
30 TraesCS5A01G097600 chr6D 95.082 122 6 0 657 778 62116141 62116262 3.840000e-45 193.0
31 TraesCS5A01G097600 chr6D 96.296 81 3 0 1 81 102243447 102243367 2.360000e-27 134.0
32 TraesCS5A01G097600 chr6D 88.235 102 9 2 3558 3659 216891499 216891401 6.610000e-23 119.0
33 TraesCS5A01G097600 chr4D 94.262 122 7 0 657 778 506203526 506203647 1.790000e-43 187.0
34 TraesCS5A01G097600 chr2D 94.215 121 7 0 657 777 376857742 376857622 6.430000e-43 185.0
35 TraesCS5A01G097600 chr2D 92.632 95 6 1 1 95 640283448 640283355 6.560000e-28 135.0
36 TraesCS5A01G097600 chr1D 94.783 115 6 0 657 771 482898410 482898524 2.990000e-41 180.0
37 TraesCS5A01G097600 chr1D 93.220 118 8 0 657 774 324396710 324396827 1.390000e-39 174.0
38 TraesCS5A01G097600 chr6A 91.935 124 10 0 657 780 617825337 617825214 1.390000e-39 174.0
39 TraesCS5A01G097600 chr6A 93.860 114 7 0 3116 3229 190662834 190662947 5.000000e-39 172.0
40 TraesCS5A01G097600 chr6A 93.860 114 7 0 3116 3229 190690072 190690185 5.000000e-39 172.0
41 TraesCS5A01G097600 chr6A 93.860 114 7 0 3116 3229 190741169 190741282 5.000000e-39 172.0
42 TraesCS5A01G097600 chr6A 94.253 87 4 1 1 86 580333354 580333268 8.490000e-27 132.0
43 TraesCS5A01G097600 chr6A 95.122 82 4 0 1 82 4921619 4921538 3.050000e-26 130.0
44 TraesCS5A01G097600 chr1A 94.393 107 6 0 3116 3222 547323767 547323661 8.370000e-37 165.0
45 TraesCS5A01G097600 chr1A 88.119 101 8 2 3558 3658 488207018 488206922 2.380000e-22 117.0
46 TraesCS5A01G097600 chr4A 90.756 119 9 2 3113 3230 582827136 582827019 1.400000e-34 158.0
47 TraesCS5A01G097600 chr3A 87.218 133 15 2 3115 3246 557089149 557089018 2.340000e-32 150.0
48 TraesCS5A01G097600 chr3A 89.412 85 9 0 3559 3643 13537683 13537599 1.430000e-19 108.0
49 TraesCS5A01G097600 chr2B 92.308 91 7 0 3558 3648 417250686 417250776 3.050000e-26 130.0
50 TraesCS5A01G097600 chr3D 91.209 91 8 0 3558 3648 6675410 6675500 1.420000e-24 124.0
51 TraesCS5A01G097600 chr3D 89.041 73 7 1 3558 3630 431225827 431225756 5.180000e-14 89.8
52 TraesCS5A01G097600 chr1B 85.417 96 11 3 3541 3635 522764813 522764906 3.100000e-16 97.1


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 TraesCS5A01G097600 chr5A 138427819 138431585 3766 True 6957.000000 6957 100.000000 1 3767 1 chr5A.!!$R1 3766
1 TraesCS5A01G097600 chr5A 538349036 538350797 1761 False 1886.000000 1886 85.981000 984 2752 1 chr5A.!!$F3 1768
2 TraesCS5A01G097600 chr5B 513711453 513713219 1766 False 1882.000000 1882 85.908000 1000 2770 1 chr5B.!!$F1 1770
3 TraesCS5A01G097600 chr5B 137108738 137113556 4818 True 1327.400000 3507 91.091800 87 3767 5 chr5B.!!$R1 3680
4 TraesCS5A01G097600 chr5D 124389910 124391946 2036 True 1496.000000 2242 92.699000 1634 3767 2 chr5D.!!$R1 2133
5 TraesCS5A01G097600 chr5D 124397288 124398579 1291 True 699.333333 1469 94.992333 249 1640 3 chr5D.!!$R2 1391
6 TraesCS5A01G097600 chr7B 572505913 572507606 1693 True 1511.000000 1511 82.827000 1061 2767 1 chr7B.!!$R1 1706
7 TraesCS5A01G097600 chr7B 157687794 157689498 1704 False 1279.000000 1279 80.327000 1024 2725 1 chr7B.!!$F1 1701
8 TraesCS5A01G097600 chr7D 531975712 531977407 1695 True 1441.000000 1441 82.089000 1061 2767 1 chr7D.!!$R1 1706
9 TraesCS5A01G097600 chr7D 193935005 193936726 1721 False 1332.000000 1332 80.740000 1007 2725 1 chr7D.!!$F1 1718
10 TraesCS5A01G097600 chr7A 203525571 203527245 1674 False 1295.000000 1295 80.703000 1065 2736 1 chr7A.!!$F2 1671
11 TraesCS5A01G097600 chr2A 74252024 74253727 1703 True 1277.000000 1277 80.302000 1061 2773 1 chr2A.!!$R2 1712

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
83 84 0.031917 TCCCCACTATAACCAGCCGA 60.032 55.0 0.00 0.00 0.00 5.54 F
84 85 0.393077 CCCCACTATAACCAGCCGAG 59.607 60.0 0.00 0.00 0.00 4.63 F
647 705 0.659957 GCATGCACTTGCTAGCTACC 59.340 55.0 17.23 0.62 42.66 3.18 F
1944 2022 0.457443 TCATCGATGCAAGAGTCGCT 59.543 50.0 20.81 0.00 37.74 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1383 1459 1.142748 GCTCTCCACCGTCATGAGG 59.857 63.158 8.47 8.47 0.00 3.86 R
1944 2022 1.685077 CTCCTGCAGCCTCTCCTCA 60.685 63.158 8.66 0.00 0.00 3.86 R
2162 2248 2.122768 AGTAGAAGGAGCCTTGGATGG 58.877 52.381 6.49 0.00 36.26 3.51 R
3008 3097 0.472471 TCGCTTTTGGGTCAACTCCT 59.528 50.000 0.00 0.00 0.00 3.69 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
67 68 9.021807 TGCATGATACTAGTATAAGTTACTCCC 57.978 37.037 15.42 0.27 0.00 4.30
68 69 8.468399 GCATGATACTAGTATAAGTTACTCCCC 58.532 40.741 15.42 0.00 0.00 4.81
69 70 9.529823 CATGATACTAGTATAAGTTACTCCCCA 57.470 37.037 15.42 5.35 0.00 4.96
70 71 8.930846 TGATACTAGTATAAGTTACTCCCCAC 57.069 38.462 15.42 0.00 0.00 4.61
71 72 8.730948 TGATACTAGTATAAGTTACTCCCCACT 58.269 37.037 15.42 0.00 0.00 4.00
77 78 8.718158 AGTATAAGTTACTCCCCACTATAACC 57.282 38.462 0.00 0.00 0.00 2.85
78 79 8.291745 AGTATAAGTTACTCCCCACTATAACCA 58.708 37.037 0.00 0.00 0.00 3.67
79 80 5.952347 AAGTTACTCCCCACTATAACCAG 57.048 43.478 0.00 0.00 0.00 4.00
80 81 3.710165 AGTTACTCCCCACTATAACCAGC 59.290 47.826 0.00 0.00 0.00 4.85
81 82 1.508256 ACTCCCCACTATAACCAGCC 58.492 55.000 0.00 0.00 0.00 4.85
82 83 0.393077 CTCCCCACTATAACCAGCCG 59.607 60.000 0.00 0.00 0.00 5.52
83 84 0.031917 TCCCCACTATAACCAGCCGA 60.032 55.000 0.00 0.00 0.00 5.54
84 85 0.393077 CCCCACTATAACCAGCCGAG 59.607 60.000 0.00 0.00 0.00 4.63
85 86 0.393077 CCCACTATAACCAGCCGAGG 59.607 60.000 0.00 0.00 0.00 4.63
90 91 2.158943 ACTATAACCAGCCGAGGAAAGC 60.159 50.000 0.00 0.00 0.00 3.51
96 97 1.754745 AGCCGAGGAAAGCTGAACA 59.245 52.632 0.00 0.00 38.11 3.18
100 101 1.273606 CCGAGGAAAGCTGAACAGAGA 59.726 52.381 5.97 0.00 0.00 3.10
101 102 2.289072 CCGAGGAAAGCTGAACAGAGAA 60.289 50.000 5.97 0.00 0.00 2.87
137 138 3.000041 CGATCCTTGTCAATCACCGAAA 59.000 45.455 0.00 0.00 0.00 3.46
140 141 2.105821 TCCTTGTCAATCACCGAAACCT 59.894 45.455 0.00 0.00 0.00 3.50
141 142 2.226437 CCTTGTCAATCACCGAAACCTG 59.774 50.000 0.00 0.00 0.00 4.00
143 144 3.417069 TGTCAATCACCGAAACCTGAT 57.583 42.857 0.00 0.00 0.00 2.90
227 228 1.278238 GCATGTTAGTCGTCCGGAAG 58.722 55.000 5.23 8.93 0.00 3.46
239 240 1.933853 GTCCGGAAGACATGCATGTAC 59.066 52.381 31.45 22.87 45.55 2.90
241 242 1.665679 CCGGAAGACATGCATGTACAC 59.334 52.381 31.45 22.44 41.95 2.90
242 243 2.345876 CGGAAGACATGCATGTACACA 58.654 47.619 31.45 0.00 41.95 3.72
245 246 4.320129 CGGAAGACATGCATGTACACAAAA 60.320 41.667 31.45 0.00 41.95 2.44
267 290 2.370189 ACTGGCAGAAGTAGCTTTCAGT 59.630 45.455 23.66 0.00 0.00 3.41
296 319 1.676529 TGGAAAACCGCAAAATCACGA 59.323 42.857 0.00 0.00 0.00 4.35
345 368 4.133820 TCGTCTCTTTGATTTGAAAGCCA 58.866 39.130 0.00 0.00 33.63 4.75
358 381 2.034939 TGAAAGCCATGACTTGCAACAG 59.965 45.455 0.00 0.00 32.01 3.16
422 474 6.758254 ACAAAGTTTTTAGCCATACAAGCAT 58.242 32.000 0.00 0.00 0.00 3.79
451 503 0.839946 AGGCAAATCCCGCTGACTAT 59.160 50.000 0.00 0.00 34.51 2.12
478 530 1.801771 TGACGTACAGGCAAATTTCGG 59.198 47.619 0.00 0.00 32.75 4.30
506 563 7.766278 CAGGCATTGTGATAAAACTACTAGACT 59.234 37.037 0.00 0.00 0.00 3.24
546 603 7.201384 GCTATTTTGCTTGATAGAAACTGTTGC 60.201 37.037 0.00 0.00 0.00 4.17
647 705 0.659957 GCATGCACTTGCTAGCTACC 59.340 55.000 17.23 0.62 42.66 3.18
650 708 2.386661 TGCACTTGCTAGCTACCTTC 57.613 50.000 17.23 1.65 42.66 3.46
651 709 1.902508 TGCACTTGCTAGCTACCTTCT 59.097 47.619 17.23 0.00 42.66 2.85
652 710 3.096852 TGCACTTGCTAGCTACCTTCTA 58.903 45.455 17.23 0.00 42.66 2.10
653 711 3.706594 TGCACTTGCTAGCTACCTTCTAT 59.293 43.478 17.23 0.00 42.66 1.98
654 712 4.162320 TGCACTTGCTAGCTACCTTCTATT 59.838 41.667 17.23 0.00 42.66 1.73
655 713 5.362717 TGCACTTGCTAGCTACCTTCTATTA 59.637 40.000 17.23 0.00 42.66 0.98
656 714 5.692654 GCACTTGCTAGCTACCTTCTATTAC 59.307 44.000 17.23 0.00 38.21 1.89
657 715 6.461788 GCACTTGCTAGCTACCTTCTATTACT 60.462 42.308 17.23 0.00 38.21 2.24
658 716 7.142680 CACTTGCTAGCTACCTTCTATTACTC 58.857 42.308 17.23 0.00 0.00 2.59
659 717 6.265876 ACTTGCTAGCTACCTTCTATTACTCC 59.734 42.308 17.23 0.00 0.00 3.85
660 718 4.760715 TGCTAGCTACCTTCTATTACTCCG 59.239 45.833 17.23 0.00 0.00 4.63
661 719 4.761227 GCTAGCTACCTTCTATTACTCCGT 59.239 45.833 7.70 0.00 0.00 4.69
662 720 5.241285 GCTAGCTACCTTCTATTACTCCGTT 59.759 44.000 7.70 0.00 0.00 4.44
663 721 6.238981 GCTAGCTACCTTCTATTACTCCGTTT 60.239 42.308 7.70 0.00 0.00 3.60
664 722 6.146601 AGCTACCTTCTATTACTCCGTTTC 57.853 41.667 0.00 0.00 0.00 2.78
665 723 5.655532 AGCTACCTTCTATTACTCCGTTTCA 59.344 40.000 0.00 0.00 0.00 2.69
666 724 6.154021 AGCTACCTTCTATTACTCCGTTTCAA 59.846 38.462 0.00 0.00 0.00 2.69
667 725 6.815142 GCTACCTTCTATTACTCCGTTTCAAA 59.185 38.462 0.00 0.00 0.00 2.69
668 726 7.494952 GCTACCTTCTATTACTCCGTTTCAAAT 59.505 37.037 0.00 0.00 0.00 2.32
669 727 9.379791 CTACCTTCTATTACTCCGTTTCAAATT 57.620 33.333 0.00 0.00 0.00 1.82
671 729 9.379791 ACCTTCTATTACTCCGTTTCAAATTAG 57.620 33.333 0.00 0.00 0.00 1.73
672 730 9.379791 CCTTCTATTACTCCGTTTCAAATTAGT 57.620 33.333 0.00 0.00 0.00 2.24
675 733 9.932207 TCTATTACTCCGTTTCAAATTAGTTGA 57.068 29.630 0.00 0.00 44.74 3.18
676 734 9.968743 CTATTACTCCGTTTCAAATTAGTTGAC 57.031 33.333 0.00 0.00 46.09 3.18
677 735 8.617290 ATTACTCCGTTTCAAATTAGTTGACT 57.383 30.769 0.00 0.00 46.09 3.41
678 736 6.937436 ACTCCGTTTCAAATTAGTTGACTT 57.063 33.333 0.00 0.00 46.09 3.01
679 737 6.725246 ACTCCGTTTCAAATTAGTTGACTTG 58.275 36.000 0.00 0.00 46.09 3.16
680 738 6.540914 ACTCCGTTTCAAATTAGTTGACTTGA 59.459 34.615 0.00 0.00 46.09 3.02
681 739 7.066525 ACTCCGTTTCAAATTAGTTGACTTGAA 59.933 33.333 0.00 0.00 46.09 2.69
682 740 7.936584 TCCGTTTCAAATTAGTTGACTTGAAT 58.063 30.769 0.00 0.00 46.09 2.57
683 741 8.410141 TCCGTTTCAAATTAGTTGACTTGAATT 58.590 29.630 0.00 0.00 46.09 2.17
684 742 9.030301 CCGTTTCAAATTAGTTGACTTGAATTT 57.970 29.630 0.00 0.00 46.09 1.82
768 826 8.446599 AATATAGGTCAAGTAATTTGGAACGG 57.553 34.615 0.00 0.00 37.39 4.44
769 827 4.360951 AGGTCAAGTAATTTGGAACGGA 57.639 40.909 0.00 0.00 37.39 4.69
770 828 4.324267 AGGTCAAGTAATTTGGAACGGAG 58.676 43.478 0.00 0.00 37.39 4.63
771 829 3.439129 GGTCAAGTAATTTGGAACGGAGG 59.561 47.826 0.00 0.00 37.39 4.30
772 830 3.439129 GTCAAGTAATTTGGAACGGAGGG 59.561 47.826 0.00 0.00 37.39 4.30
773 831 3.328343 TCAAGTAATTTGGAACGGAGGGA 59.672 43.478 0.00 0.00 37.39 4.20
774 832 4.076394 CAAGTAATTTGGAACGGAGGGAA 58.924 43.478 0.00 0.00 32.95 3.97
817 875 1.591158 GAACTCACTCACGCGAAAACA 59.409 47.619 15.93 0.00 0.00 2.83
819 877 2.210116 ACTCACTCACGCGAAAACATT 58.790 42.857 15.93 0.00 0.00 2.71
820 878 2.032894 ACTCACTCACGCGAAAACATTG 60.033 45.455 15.93 0.00 0.00 2.82
821 879 1.044725 CACTCACGCGAAAACATTGC 58.955 50.000 15.93 0.00 34.84 3.56
824 882 1.710249 CTCACGCGAAAACATTGCAAG 59.290 47.619 15.93 0.00 38.46 4.01
825 883 0.777631 CACGCGAAAACATTGCAAGG 59.222 50.000 15.93 10.01 38.46 3.61
846 904 6.365970 AGGTTTATATGACAGATAGGCAGG 57.634 41.667 0.00 0.00 39.86 4.85
866 928 4.336713 CAGGTCAGATACTCGATGAAGTCA 59.663 45.833 0.00 0.00 0.00 3.41
867 929 4.578516 AGGTCAGATACTCGATGAAGTCAG 59.421 45.833 0.00 0.00 0.00 3.51
868 930 4.576873 GGTCAGATACTCGATGAAGTCAGA 59.423 45.833 0.00 0.00 0.00 3.27
869 931 5.504994 GGTCAGATACTCGATGAAGTCAGAC 60.505 48.000 0.00 0.00 0.00 3.51
886 948 1.915614 GACTCCAACGTGCATGCCTG 61.916 60.000 16.68 10.11 0.00 4.85
904 966 1.401552 CTGCACAAATATGACCGGGTG 59.598 52.381 3.30 2.19 0.00 4.61
913 978 1.129058 ATGACCGGGTGGAATAGGAC 58.871 55.000 3.30 0.00 39.21 3.85
1152 1227 1.271108 TGCACCATCACCAACACGTAT 60.271 47.619 0.00 0.00 0.00 3.06
1307 1383 1.748879 GCATTCCCAAGCTGGCGTA 60.749 57.895 0.00 0.00 35.79 4.42
1502 1578 2.044053 CATCGGGGGCATGTTGGT 60.044 61.111 0.00 0.00 0.00 3.67
1584 1660 1.112113 GGCTGAGGATCGTAACTCCA 58.888 55.000 0.00 0.00 38.61 3.86
1944 2022 0.457443 TCATCGATGCAAGAGTCGCT 59.543 50.000 20.81 0.00 37.74 4.93
1951 2029 0.895559 TGCAAGAGTCGCTGAGGAGA 60.896 55.000 0.00 0.00 0.00 3.71
1974 2058 2.579201 CAGGAGAACGGCACCGAT 59.421 61.111 17.40 3.14 42.83 4.18
2040 2124 2.773487 CAACGGTCCTATGGTTTCACA 58.227 47.619 0.00 0.00 0.00 3.58
2070 2154 3.616560 GCGTCTCTTTCACAAGATACCCA 60.617 47.826 0.00 0.00 38.42 4.51
2148 2234 2.284995 GGCCTCCTCACCTCCTGT 60.285 66.667 0.00 0.00 0.00 4.00
2606 2692 2.281539 TGGACTGACCAAGTACTCGA 57.718 50.000 0.00 0.00 46.75 4.04
2757 2843 2.354109 GAGTCTGCTCGTTCATCACA 57.646 50.000 0.00 0.00 31.39 3.58
2794 2880 1.281656 GCGCTTTGCCACGTTAAGT 59.718 52.632 0.00 0.00 37.76 2.24
2829 2915 4.157289 AGCCTGTCAGTTGCTTCATTATTG 59.843 41.667 0.00 0.00 29.17 1.90
2851 2940 4.080807 TGTTGTTTCACCTGAGTTGGACTA 60.081 41.667 0.00 0.00 0.00 2.59
2933 3022 5.111989 CAGTATGTTATGTGTGAGGTGGAG 58.888 45.833 0.00 0.00 0.00 3.86
3008 3097 5.252547 ACATATGTGTGCCATGTTCACTTA 58.747 37.500 7.78 11.19 37.14 2.24
3023 3112 4.781775 TCACTTAGGAGTTGACCCAAAA 57.218 40.909 0.00 0.00 32.54 2.44
3028 3117 1.073923 AGGAGTTGACCCAAAAGCGAT 59.926 47.619 0.00 0.00 0.00 4.58
3050 3144 4.118168 ACACAAATTCACTCCCTTCCAT 57.882 40.909 0.00 0.00 0.00 3.41
3077 3172 2.032965 TACTAGTGACCCCAAAGCCA 57.967 50.000 5.39 0.00 0.00 4.75
3117 3212 7.339466 TCATTCCTAGGGAGCTTTGAATTTTAC 59.661 37.037 9.46 0.00 31.21 2.01
3118 3213 6.388619 TCCTAGGGAGCTTTGAATTTTACT 57.611 37.500 9.46 0.00 0.00 2.24
3119 3214 6.790319 TCCTAGGGAGCTTTGAATTTTACTT 58.210 36.000 9.46 0.00 0.00 2.24
3120 3215 6.884836 TCCTAGGGAGCTTTGAATTTTACTTC 59.115 38.462 9.46 0.00 0.00 3.01
3121 3216 5.984695 AGGGAGCTTTGAATTTTACTTCC 57.015 39.130 0.00 0.00 0.00 3.46
3122 3217 5.645201 AGGGAGCTTTGAATTTTACTTCCT 58.355 37.500 0.00 0.00 0.00 3.36
3123 3218 5.712446 AGGGAGCTTTGAATTTTACTTCCTC 59.288 40.000 0.00 0.00 25.79 3.71
3124 3219 5.105716 GGGAGCTTTGAATTTTACTTCCTCC 60.106 44.000 0.00 0.00 33.01 4.30
3125 3220 5.392057 GGAGCTTTGAATTTTACTTCCTCCG 60.392 44.000 0.00 0.00 0.00 4.63
3126 3221 5.070685 AGCTTTGAATTTTACTTCCTCCGT 58.929 37.500 0.00 0.00 0.00 4.69
3127 3222 5.535030 AGCTTTGAATTTTACTTCCTCCGTT 59.465 36.000 0.00 0.00 0.00 4.44
3128 3223 5.856986 GCTTTGAATTTTACTTCCTCCGTTC 59.143 40.000 0.00 0.00 0.00 3.95
3129 3224 5.952526 TTGAATTTTACTTCCTCCGTTCC 57.047 39.130 0.00 0.00 0.00 3.62
3130 3225 3.998341 TGAATTTTACTTCCTCCGTTCCG 59.002 43.478 0.00 0.00 0.00 4.30
3131 3226 3.967332 ATTTTACTTCCTCCGTTCCGA 57.033 42.857 0.00 0.00 0.00 4.55
3132 3227 3.749665 TTTTACTTCCTCCGTTCCGAA 57.250 42.857 0.00 0.00 0.00 4.30
3133 3228 3.967332 TTTACTTCCTCCGTTCCGAAT 57.033 42.857 0.00 0.00 0.00 3.34
3134 3229 3.967332 TTACTTCCTCCGTTCCGAATT 57.033 42.857 0.00 0.00 0.00 2.17
3135 3230 5.404466 TTTACTTCCTCCGTTCCGAATTA 57.596 39.130 0.00 0.00 0.00 1.40
3136 3231 3.242549 ACTTCCTCCGTTCCGAATTAC 57.757 47.619 0.00 0.00 0.00 1.89
3137 3232 2.830321 ACTTCCTCCGTTCCGAATTACT 59.170 45.455 0.00 0.00 0.00 2.24
3138 3233 3.260128 ACTTCCTCCGTTCCGAATTACTT 59.740 43.478 0.00 0.00 0.00 2.24
3139 3234 3.241067 TCCTCCGTTCCGAATTACTTG 57.759 47.619 0.00 0.00 0.00 3.16
3140 3235 2.564062 TCCTCCGTTCCGAATTACTTGT 59.436 45.455 0.00 0.00 0.00 3.16
3141 3236 3.007182 TCCTCCGTTCCGAATTACTTGTT 59.993 43.478 0.00 0.00 0.00 2.83
3142 3237 3.124636 CCTCCGTTCCGAATTACTTGTTG 59.875 47.826 0.00 0.00 0.00 3.33
3143 3238 2.481185 TCCGTTCCGAATTACTTGTTGC 59.519 45.455 0.00 0.00 0.00 4.17
3144 3239 2.224549 CCGTTCCGAATTACTTGTTGCA 59.775 45.455 0.00 0.00 0.00 4.08
3145 3240 3.119990 CCGTTCCGAATTACTTGTTGCAT 60.120 43.478 0.00 0.00 0.00 3.96
3146 3241 3.845775 CGTTCCGAATTACTTGTTGCATG 59.154 43.478 0.00 0.00 0.00 4.06
3147 3242 4.612712 CGTTCCGAATTACTTGTTGCATGT 60.613 41.667 0.00 0.00 0.00 3.21
3148 3243 5.390040 CGTTCCGAATTACTTGTTGCATGTA 60.390 40.000 0.00 0.00 0.00 2.29
3149 3244 6.551736 GTTCCGAATTACTTGTTGCATGTAT 58.448 36.000 0.00 0.00 0.00 2.29
3150 3245 6.117911 TCCGAATTACTTGTTGCATGTATG 57.882 37.500 0.00 0.00 0.00 2.39
3151 3246 5.065859 TCCGAATTACTTGTTGCATGTATGG 59.934 40.000 0.00 0.00 0.00 2.74
3152 3247 5.065859 CCGAATTACTTGTTGCATGTATGGA 59.934 40.000 0.00 0.00 0.00 3.41
3153 3248 6.238731 CCGAATTACTTGTTGCATGTATGGAT 60.239 38.462 0.00 0.00 0.00 3.41
3154 3249 6.634035 CGAATTACTTGTTGCATGTATGGATG 59.366 38.462 0.00 0.00 0.00 3.51
3155 3250 7.408756 AATTACTTGTTGCATGTATGGATGT 57.591 32.000 0.00 0.00 0.00 3.06
3156 3251 8.518430 AATTACTTGTTGCATGTATGGATGTA 57.482 30.769 0.00 0.00 0.00 2.29
3157 3252 8.696043 ATTACTTGTTGCATGTATGGATGTAT 57.304 30.769 0.00 0.00 0.00 2.29
3158 3253 6.624352 ACTTGTTGCATGTATGGATGTATC 57.376 37.500 0.00 0.00 0.00 2.24
3159 3254 6.359804 ACTTGTTGCATGTATGGATGTATCT 58.640 36.000 0.00 0.00 0.00 1.98
3160 3255 7.508687 ACTTGTTGCATGTATGGATGTATCTA 58.491 34.615 0.00 0.00 0.00 1.98
3161 3256 7.658982 ACTTGTTGCATGTATGGATGTATCTAG 59.341 37.037 0.00 0.00 0.00 2.43
3162 3257 7.301868 TGTTGCATGTATGGATGTATCTAGA 57.698 36.000 0.00 0.00 0.00 2.43
3163 3258 7.910584 TGTTGCATGTATGGATGTATCTAGAT 58.089 34.615 10.73 10.73 0.00 1.98
3164 3259 7.820872 TGTTGCATGTATGGATGTATCTAGATG 59.179 37.037 15.79 0.00 0.00 2.90
3165 3260 7.486407 TGCATGTATGGATGTATCTAGATGT 57.514 36.000 15.79 1.25 0.00 3.06
3166 3261 8.593945 TGCATGTATGGATGTATCTAGATGTA 57.406 34.615 15.79 4.44 0.00 2.29
3167 3262 9.205513 TGCATGTATGGATGTATCTAGATGTAT 57.794 33.333 15.79 9.11 0.00 2.29
3198 3293 9.775854 ATTCTAGATACATCCATTTCTGTGAAG 57.224 33.333 0.00 0.00 0.00 3.02
3199 3294 8.539117 TCTAGATACATCCATTTCTGTGAAGA 57.461 34.615 0.00 0.00 0.00 2.87
3200 3295 8.637099 TCTAGATACATCCATTTCTGTGAAGAG 58.363 37.037 0.00 0.00 0.00 2.85
3201 3296 7.192852 AGATACATCCATTTCTGTGAAGAGT 57.807 36.000 0.00 0.00 0.00 3.24
3202 3297 8.311395 AGATACATCCATTTCTGTGAAGAGTA 57.689 34.615 0.00 0.00 0.00 2.59
3203 3298 8.762645 AGATACATCCATTTCTGTGAAGAGTAA 58.237 33.333 0.00 0.00 0.00 2.24
3204 3299 9.553064 GATACATCCATTTCTGTGAAGAGTAAT 57.447 33.333 0.00 0.00 0.00 1.89
3205 3300 9.911788 ATACATCCATTTCTGTGAAGAGTAATT 57.088 29.630 0.00 0.00 0.00 1.40
3206 3301 8.641498 ACATCCATTTCTGTGAAGAGTAATTT 57.359 30.769 0.00 0.00 0.00 1.82
3207 3302 8.517878 ACATCCATTTCTGTGAAGAGTAATTTG 58.482 33.333 0.00 0.00 0.00 2.32
3208 3303 7.452880 TCCATTTCTGTGAAGAGTAATTTGG 57.547 36.000 0.00 0.00 0.00 3.28
3209 3304 7.230747 TCCATTTCTGTGAAGAGTAATTTGGA 58.769 34.615 0.00 0.00 0.00 3.53
3210 3305 7.723616 TCCATTTCTGTGAAGAGTAATTTGGAA 59.276 33.333 0.00 0.00 0.00 3.53
3211 3306 7.809806 CCATTTCTGTGAAGAGTAATTTGGAAC 59.190 37.037 0.00 0.00 0.00 3.62
3212 3307 6.539649 TTCTGTGAAGAGTAATTTGGAACG 57.460 37.500 0.00 0.00 0.00 3.95
3213 3308 4.994852 TCTGTGAAGAGTAATTTGGAACGG 59.005 41.667 0.00 0.00 0.00 4.44
3214 3309 4.963373 TGTGAAGAGTAATTTGGAACGGA 58.037 39.130 0.00 0.00 0.00 4.69
3215 3310 4.994852 TGTGAAGAGTAATTTGGAACGGAG 59.005 41.667 0.00 0.00 0.00 4.63
3216 3311 4.392138 GTGAAGAGTAATTTGGAACGGAGG 59.608 45.833 0.00 0.00 0.00 4.30
3217 3312 4.285003 TGAAGAGTAATTTGGAACGGAGGA 59.715 41.667 0.00 0.00 0.00 3.71
3218 3313 4.903045 AGAGTAATTTGGAACGGAGGAA 57.097 40.909 0.00 0.00 0.00 3.36
3219 3314 4.833390 AGAGTAATTTGGAACGGAGGAAG 58.167 43.478 0.00 0.00 0.00 3.46
3220 3315 4.286291 AGAGTAATTTGGAACGGAGGAAGT 59.714 41.667 0.00 0.00 0.00 3.01
3221 3316 5.482878 AGAGTAATTTGGAACGGAGGAAGTA 59.517 40.000 0.00 0.00 0.00 2.24
3231 3326 5.126707 GGAACGGAGGAAGTAGAAGATACAA 59.873 44.000 0.00 0.00 0.00 2.41
3276 3371 7.172868 ACTCCATTTGCATTTGATATTCACA 57.827 32.000 0.00 0.00 0.00 3.58
3279 3374 6.919115 TCCATTTGCATTTGATATTCACATCG 59.081 34.615 0.00 0.00 0.00 3.84
3282 3377 6.682423 TTGCATTTGATATTCACATCGACT 57.318 33.333 0.00 0.00 0.00 4.18
3402 3498 6.135290 TGCTATAGATGAAATTGTGGCAAC 57.865 37.500 3.21 0.00 0.00 4.17
3455 3551 2.886523 CAACAAGAAAGTGAGATGCCCA 59.113 45.455 0.00 0.00 0.00 5.36
3457 3553 4.574674 ACAAGAAAGTGAGATGCCCATA 57.425 40.909 0.00 0.00 0.00 2.74
3458 3554 5.121380 ACAAGAAAGTGAGATGCCCATAT 57.879 39.130 0.00 0.00 0.00 1.78
3459 3555 5.128919 ACAAGAAAGTGAGATGCCCATATC 58.871 41.667 0.00 0.00 0.00 1.63
3460 3556 4.000331 AGAAAGTGAGATGCCCATATCG 58.000 45.455 0.00 0.00 32.02 2.92
3461 3557 3.389329 AGAAAGTGAGATGCCCATATCGT 59.611 43.478 0.00 0.00 32.02 3.73
3462 3558 3.845781 AAGTGAGATGCCCATATCGTT 57.154 42.857 0.00 0.00 32.02 3.85
3463 3559 3.845781 AGTGAGATGCCCATATCGTTT 57.154 42.857 0.00 0.00 32.02 3.60
3464 3560 4.955811 AGTGAGATGCCCATATCGTTTA 57.044 40.909 0.00 0.00 32.02 2.01
3465 3561 5.489792 AGTGAGATGCCCATATCGTTTAT 57.510 39.130 0.00 0.00 32.02 1.40
3466 3562 6.605471 AGTGAGATGCCCATATCGTTTATA 57.395 37.500 0.00 0.00 32.02 0.98
3468 3564 7.624549 AGTGAGATGCCCATATCGTTTATAAT 58.375 34.615 0.00 0.00 32.02 1.28
3469 3565 8.103305 AGTGAGATGCCCATATCGTTTATAATT 58.897 33.333 0.00 0.00 32.02 1.40
3472 3568 8.635765 AGATGCCCATATCGTTTATAATTTGT 57.364 30.769 0.00 0.00 32.33 2.83
3474 3570 9.769093 GATGCCCATATCGTTTATAATTTGTAC 57.231 33.333 0.00 0.00 0.00 2.90
3475 3571 8.678593 TGCCCATATCGTTTATAATTTGTACA 57.321 30.769 0.00 0.00 0.00 2.90
3476 3572 9.290988 TGCCCATATCGTTTATAATTTGTACAT 57.709 29.630 0.00 0.00 0.00 2.29
3477 3573 9.554724 GCCCATATCGTTTATAATTTGTACATG 57.445 33.333 0.00 0.00 0.00 3.21
3478 3574 9.554724 CCCATATCGTTTATAATTTGTACATGC 57.445 33.333 0.00 0.00 0.00 4.06
3479 3575 9.261318 CCATATCGTTTATAATTTGTACATGCG 57.739 33.333 0.00 0.00 0.00 4.73
3519 3619 6.048732 AGGCCCGTTGATTTGAAATTTATT 57.951 33.333 0.00 0.00 0.00 1.40
3599 3699 3.213506 TCCTCAAACAATGGCCATATCG 58.786 45.455 21.15 13.31 0.00 2.92
3627 3727 7.624360 ACAATTTGAGGCAAAATATAGTCGA 57.376 32.000 2.79 0.00 36.90 4.20
3737 3837 5.633182 CACAATTTCCAAAATACGAAGGGTG 59.367 40.000 0.00 0.00 0.00 4.61
3744 3844 4.517453 CCAAAATACGAAGGGTGTGAGAAA 59.483 41.667 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 9.914131 GTATCATGCATATGACACTAGTCTAAA 57.086 33.333 6.97 0.00 45.54 1.85
25 26 9.301897 AGTATCATGCATATGACACTAGTCTAA 57.698 33.333 6.97 0.00 46.40 2.10
26 27 8.870075 AGTATCATGCATATGACACTAGTCTA 57.130 34.615 6.97 0.00 46.40 2.59
27 28 7.773489 AGTATCATGCATATGACACTAGTCT 57.227 36.000 6.97 0.00 46.40 3.24
41 42 9.021807 GGGAGTAACTTATACTAGTATCATGCA 57.978 37.037 18.68 0.00 0.00 3.96
42 43 8.468399 GGGGAGTAACTTATACTAGTATCATGC 58.532 40.741 18.68 7.64 0.00 4.06
43 44 9.529823 TGGGGAGTAACTTATACTAGTATCATG 57.470 37.037 18.68 12.10 0.00 3.07
44 45 9.531158 GTGGGGAGTAACTTATACTAGTATCAT 57.469 37.037 18.68 6.75 0.00 2.45
45 46 8.730948 AGTGGGGAGTAACTTATACTAGTATCA 58.269 37.037 18.68 7.60 0.00 2.15
51 52 9.813826 GGTTATAGTGGGGAGTAACTTATACTA 57.186 37.037 0.00 0.00 0.00 1.82
52 53 8.291745 TGGTTATAGTGGGGAGTAACTTATACT 58.708 37.037 0.00 0.00 0.00 2.12
53 54 8.482852 TGGTTATAGTGGGGAGTAACTTATAC 57.517 38.462 0.00 0.00 0.00 1.47
54 55 7.234166 GCTGGTTATAGTGGGGAGTAACTTATA 59.766 40.741 0.00 0.00 0.00 0.98
55 56 6.042897 GCTGGTTATAGTGGGGAGTAACTTAT 59.957 42.308 0.00 0.00 0.00 1.73
56 57 5.364735 GCTGGTTATAGTGGGGAGTAACTTA 59.635 44.000 0.00 0.00 0.00 2.24
57 58 4.163649 GCTGGTTATAGTGGGGAGTAACTT 59.836 45.833 0.00 0.00 0.00 2.66
58 59 3.710165 GCTGGTTATAGTGGGGAGTAACT 59.290 47.826 0.00 0.00 0.00 2.24
59 60 3.181457 GGCTGGTTATAGTGGGGAGTAAC 60.181 52.174 0.00 0.00 0.00 2.50
60 61 3.043418 GGCTGGTTATAGTGGGGAGTAA 58.957 50.000 0.00 0.00 0.00 2.24
61 62 2.686119 GGCTGGTTATAGTGGGGAGTA 58.314 52.381 0.00 0.00 0.00 2.59
62 63 1.508256 GGCTGGTTATAGTGGGGAGT 58.492 55.000 0.00 0.00 0.00 3.85
63 64 0.393077 CGGCTGGTTATAGTGGGGAG 59.607 60.000 0.00 0.00 0.00 4.30
64 65 0.031917 TCGGCTGGTTATAGTGGGGA 60.032 55.000 0.00 0.00 0.00 4.81
65 66 0.393077 CTCGGCTGGTTATAGTGGGG 59.607 60.000 0.00 0.00 0.00 4.96
66 67 0.393077 CCTCGGCTGGTTATAGTGGG 59.607 60.000 0.00 0.00 0.00 4.61
67 68 1.410004 TCCTCGGCTGGTTATAGTGG 58.590 55.000 0.00 0.00 0.00 4.00
68 69 3.458189 CTTTCCTCGGCTGGTTATAGTG 58.542 50.000 0.00 0.00 0.00 2.74
69 70 2.158943 GCTTTCCTCGGCTGGTTATAGT 60.159 50.000 0.00 0.00 0.00 2.12
70 71 2.103263 AGCTTTCCTCGGCTGGTTATAG 59.897 50.000 0.00 0.00 37.41 1.31
71 72 2.116238 AGCTTTCCTCGGCTGGTTATA 58.884 47.619 0.00 0.00 37.41 0.98
72 73 0.912486 AGCTTTCCTCGGCTGGTTAT 59.088 50.000 0.00 0.00 37.41 1.89
73 74 2.372852 AGCTTTCCTCGGCTGGTTA 58.627 52.632 0.00 0.00 37.41 2.85
74 75 3.161557 AGCTTTCCTCGGCTGGTT 58.838 55.556 0.00 0.00 37.41 3.67
78 79 0.321122 CTGTTCAGCTTTCCTCGGCT 60.321 55.000 0.00 0.00 39.60 5.52
79 80 0.320771 TCTGTTCAGCTTTCCTCGGC 60.321 55.000 0.00 0.00 0.00 5.54
80 81 1.273606 TCTCTGTTCAGCTTTCCTCGG 59.726 52.381 0.00 0.00 0.00 4.63
81 82 2.732412 TCTCTGTTCAGCTTTCCTCG 57.268 50.000 0.00 0.00 0.00 4.63
82 83 4.999950 TGATTTCTCTGTTCAGCTTTCCTC 59.000 41.667 0.00 0.00 0.00 3.71
83 84 4.978099 TGATTTCTCTGTTCAGCTTTCCT 58.022 39.130 0.00 0.00 0.00 3.36
84 85 5.695851 TTGATTTCTCTGTTCAGCTTTCC 57.304 39.130 0.00 0.00 0.00 3.13
85 86 5.917447 GGTTTGATTTCTCTGTTCAGCTTTC 59.083 40.000 0.00 0.00 0.00 2.62
90 91 5.532406 TCTTGGGTTTGATTTCTCTGTTCAG 59.468 40.000 0.00 0.00 0.00 3.02
96 97 3.077359 CGCTCTTGGGTTTGATTTCTCT 58.923 45.455 0.00 0.00 0.00 3.10
100 101 2.755103 GGATCGCTCTTGGGTTTGATTT 59.245 45.455 0.00 0.00 0.00 2.17
101 102 2.025887 AGGATCGCTCTTGGGTTTGATT 60.026 45.455 0.00 0.00 0.00 2.57
227 228 4.681025 CCAGTTTTTGTGTACATGCATGTC 59.319 41.667 34.54 24.41 41.97 3.06
239 240 3.316308 AGCTACTTCTGCCAGTTTTTGTG 59.684 43.478 0.00 0.00 0.00 3.33
241 242 4.574599 AAGCTACTTCTGCCAGTTTTTG 57.425 40.909 0.00 0.00 0.00 2.44
242 243 4.644685 TGAAAGCTACTTCTGCCAGTTTTT 59.355 37.500 0.00 0.00 0.00 1.94
245 246 3.181450 ACTGAAAGCTACTTCTGCCAGTT 60.181 43.478 5.27 0.00 37.60 3.16
267 290 3.358111 TGCGGTTTTCCATCCATCTTA 57.642 42.857 0.00 0.00 40.70 2.10
345 368 1.985473 TCTTGGCTGTTGCAAGTCAT 58.015 45.000 0.00 0.00 41.91 3.06
358 381 2.029020 GGTTGGATGTCCTTTTCTTGGC 60.029 50.000 0.09 0.00 36.82 4.52
422 474 3.287222 CGGGATTTGCCTAATGGAGAAA 58.713 45.455 0.00 0.00 36.66 2.52
478 530 6.743575 AGTAGTTTTATCACAATGCCTGTC 57.256 37.500 0.00 0.00 35.47 3.51
506 563 6.112058 AGCAAAATAGCAAAAGGAAAACACA 58.888 32.000 0.00 0.00 36.85 3.72
514 571 8.650714 GTTTCTATCAAGCAAAATAGCAAAAGG 58.349 33.333 0.00 0.00 36.85 3.11
546 603 1.672356 CTTGAGGGAACAGCGTGGG 60.672 63.158 0.00 0.00 0.00 4.61
615 672 1.328680 GTGCATGCGTGGACTAATGAG 59.671 52.381 21.96 0.00 42.72 2.90
650 708 9.968743 GTCAACTAATTTGAAACGGAGTAATAG 57.031 33.333 0.00 0.00 46.09 1.73
651 709 9.715121 AGTCAACTAATTTGAAACGGAGTAATA 57.285 29.630 0.00 0.00 46.09 0.98
652 710 8.617290 AGTCAACTAATTTGAAACGGAGTAAT 57.383 30.769 0.00 0.00 46.09 1.89
653 711 8.339714 CAAGTCAACTAATTTGAAACGGAGTAA 58.660 33.333 0.00 0.00 46.09 2.24
654 712 7.711772 TCAAGTCAACTAATTTGAAACGGAGTA 59.288 33.333 0.00 0.00 46.09 2.59
655 713 6.540914 TCAAGTCAACTAATTTGAAACGGAGT 59.459 34.615 0.00 0.00 46.09 3.85
656 714 6.954944 TCAAGTCAACTAATTTGAAACGGAG 58.045 36.000 0.00 0.00 46.09 4.63
657 715 6.928979 TCAAGTCAACTAATTTGAAACGGA 57.071 33.333 0.00 0.00 46.09 4.69
658 716 8.574196 AATTCAAGTCAACTAATTTGAAACGG 57.426 30.769 3.05 0.00 46.09 4.44
742 800 8.899771 CCGTTCCAAATTACTTGACCTATATTT 58.100 33.333 0.00 0.00 37.17 1.40
743 801 8.269317 TCCGTTCCAAATTACTTGACCTATATT 58.731 33.333 0.00 0.00 37.17 1.28
744 802 7.798071 TCCGTTCCAAATTACTTGACCTATAT 58.202 34.615 0.00 0.00 37.17 0.86
745 803 7.185318 TCCGTTCCAAATTACTTGACCTATA 57.815 36.000 0.00 0.00 37.17 1.31
746 804 6.057321 TCCGTTCCAAATTACTTGACCTAT 57.943 37.500 0.00 0.00 37.17 2.57
747 805 5.484715 CTCCGTTCCAAATTACTTGACCTA 58.515 41.667 0.00 0.00 37.17 3.08
748 806 4.324267 CTCCGTTCCAAATTACTTGACCT 58.676 43.478 0.00 0.00 37.17 3.85
749 807 3.439129 CCTCCGTTCCAAATTACTTGACC 59.561 47.826 0.00 0.00 37.17 4.02
750 808 3.439129 CCCTCCGTTCCAAATTACTTGAC 59.561 47.826 0.00 0.00 37.17 3.18
751 809 3.328343 TCCCTCCGTTCCAAATTACTTGA 59.672 43.478 0.00 0.00 37.17 3.02
752 810 3.681593 TCCCTCCGTTCCAAATTACTTG 58.318 45.455 0.00 0.00 34.52 3.16
753 811 4.376225 TTCCCTCCGTTCCAAATTACTT 57.624 40.909 0.00 0.00 0.00 2.24
754 812 4.586306 ATTCCCTCCGTTCCAAATTACT 57.414 40.909 0.00 0.00 0.00 2.24
755 813 5.677567 TCTATTCCCTCCGTTCCAAATTAC 58.322 41.667 0.00 0.00 0.00 1.89
756 814 5.961398 TCTATTCCCTCCGTTCCAAATTA 57.039 39.130 0.00 0.00 0.00 1.40
757 815 4.855298 TCTATTCCCTCCGTTCCAAATT 57.145 40.909 0.00 0.00 0.00 1.82
758 816 4.660771 AGATCTATTCCCTCCGTTCCAAAT 59.339 41.667 0.00 0.00 0.00 2.32
759 817 4.037927 AGATCTATTCCCTCCGTTCCAAA 58.962 43.478 0.00 0.00 0.00 3.28
760 818 3.388024 CAGATCTATTCCCTCCGTTCCAA 59.612 47.826 0.00 0.00 0.00 3.53
761 819 2.965831 CAGATCTATTCCCTCCGTTCCA 59.034 50.000 0.00 0.00 0.00 3.53
762 820 2.966516 ACAGATCTATTCCCTCCGTTCC 59.033 50.000 0.00 0.00 0.00 3.62
763 821 3.304794 CGACAGATCTATTCCCTCCGTTC 60.305 52.174 0.00 0.00 0.00 3.95
764 822 2.623889 CGACAGATCTATTCCCTCCGTT 59.376 50.000 0.00 0.00 0.00 4.44
765 823 2.231529 CGACAGATCTATTCCCTCCGT 58.768 52.381 0.00 0.00 0.00 4.69
766 824 1.542030 CCGACAGATCTATTCCCTCCG 59.458 57.143 0.00 0.00 0.00 4.63
767 825 2.599677 ACCGACAGATCTATTCCCTCC 58.400 52.381 0.00 0.00 0.00 4.30
768 826 5.302313 AGTTAACCGACAGATCTATTCCCTC 59.698 44.000 0.88 0.00 0.00 4.30
769 827 5.209659 AGTTAACCGACAGATCTATTCCCT 58.790 41.667 0.88 0.00 0.00 4.20
770 828 5.532664 AGTTAACCGACAGATCTATTCCC 57.467 43.478 0.88 0.00 0.00 3.97
771 829 6.338937 ACAAGTTAACCGACAGATCTATTCC 58.661 40.000 0.88 0.00 0.00 3.01
772 830 7.544566 TCAACAAGTTAACCGACAGATCTATTC 59.455 37.037 0.88 0.00 0.00 1.75
773 831 7.383687 TCAACAAGTTAACCGACAGATCTATT 58.616 34.615 0.88 0.00 0.00 1.73
774 832 6.931838 TCAACAAGTTAACCGACAGATCTAT 58.068 36.000 0.88 0.00 0.00 1.98
817 875 7.175641 GCCTATCTGTCATATAAACCTTGCAAT 59.824 37.037 0.00 0.00 0.00 3.56
819 877 5.997746 GCCTATCTGTCATATAAACCTTGCA 59.002 40.000 0.00 0.00 0.00 4.08
820 878 5.997746 TGCCTATCTGTCATATAAACCTTGC 59.002 40.000 0.00 0.00 0.00 4.01
821 879 6.652481 CCTGCCTATCTGTCATATAAACCTTG 59.348 42.308 0.00 0.00 0.00 3.61
824 882 6.115448 ACCTGCCTATCTGTCATATAAACC 57.885 41.667 0.00 0.00 0.00 3.27
825 883 6.759272 TGACCTGCCTATCTGTCATATAAAC 58.241 40.000 0.00 0.00 33.09 2.01
846 904 5.295787 AGTCTGACTTCATCGAGTATCTGAC 59.704 44.000 4.06 12.76 0.00 3.51
866 928 1.672356 GGCATGCACGTTGGAGTCT 60.672 57.895 21.36 0.00 0.00 3.24
867 929 1.672356 AGGCATGCACGTTGGAGTC 60.672 57.895 21.36 0.00 0.00 3.36
868 930 1.968017 CAGGCATGCACGTTGGAGT 60.968 57.895 21.36 0.00 0.00 3.85
869 931 2.872557 CAGGCATGCACGTTGGAG 59.127 61.111 21.36 0.00 0.00 3.86
886 948 0.738389 CCACCCGGTCATATTTGTGC 59.262 55.000 0.00 0.00 0.00 4.57
904 966 3.632333 CTTGGGGGAAAAGTCCTATTCC 58.368 50.000 0.00 0.00 44.28 3.01
913 978 1.667722 GCACAGCTTGGGGGAAAAG 59.332 57.895 0.00 0.00 0.00 2.27
1383 1459 1.142748 GCTCTCCACCGTCATGAGG 59.857 63.158 8.47 8.47 0.00 3.86
1944 2022 1.685077 CTCCTGCAGCCTCTCCTCA 60.685 63.158 8.66 0.00 0.00 3.86
1951 2029 4.400961 GCCGTTCTCCTGCAGCCT 62.401 66.667 8.66 0.00 0.00 4.58
2162 2248 2.122768 AGTAGAAGGAGCCTTGGATGG 58.877 52.381 6.49 0.00 36.26 3.51
2606 2692 4.080582 TGACGTTGGGAGTTCCATTGATAT 60.081 41.667 0.00 0.00 46.52 1.63
2757 2843 3.304794 GCGCGAGTCACCTCTAATAATCT 60.305 47.826 12.10 0.00 35.43 2.40
2774 2860 2.165362 CTTAACGTGGCAAAGCGCGA 62.165 55.000 12.10 0.00 43.84 5.87
2808 2894 5.633830 ACAATAATGAAGCAACTGACAGG 57.366 39.130 7.51 0.00 0.00 4.00
2829 2915 3.279434 AGTCCAACTCAGGTGAAACAAC 58.721 45.455 0.00 0.00 39.98 3.32
2882 2971 8.812513 TCCACATTCATCAGATAAAAGTGAAT 57.187 30.769 3.56 0.00 39.39 2.57
2902 2991 4.694982 CACACATAACATACTGCTTCCACA 59.305 41.667 0.00 0.00 0.00 4.17
2933 3022 7.119262 AGCACAACCACACATATAAGAACTTAC 59.881 37.037 0.00 0.00 0.00 2.34
3008 3097 0.472471 TCGCTTTTGGGTCAACTCCT 59.528 50.000 0.00 0.00 0.00 3.69
3023 3112 3.055094 AGGGAGTGAATTTGTGTATCGCT 60.055 43.478 0.00 0.00 36.68 4.93
3028 3117 4.715534 TGGAAGGGAGTGAATTTGTGTA 57.284 40.909 0.00 0.00 0.00 2.90
3050 3144 2.090437 TGGGGTCACTAGTATGCCCATA 60.090 50.000 22.39 12.61 37.55 2.74
3070 3165 1.503542 GCACTCCATCGTGGCTTTG 59.496 57.895 0.00 0.00 37.47 2.77
3125 3220 4.794169 ACATGCAACAAGTAATTCGGAAC 58.206 39.130 0.00 0.00 0.00 3.62
3126 3221 6.404184 CCATACATGCAACAAGTAATTCGGAA 60.404 38.462 0.00 0.00 0.00 4.30
3127 3222 5.065859 CCATACATGCAACAAGTAATTCGGA 59.934 40.000 0.00 0.00 0.00 4.55
3128 3223 5.065859 TCCATACATGCAACAAGTAATTCGG 59.934 40.000 0.00 0.00 0.00 4.30
3129 3224 6.117911 TCCATACATGCAACAAGTAATTCG 57.882 37.500 0.00 0.00 0.00 3.34
3130 3225 7.483307 ACATCCATACATGCAACAAGTAATTC 58.517 34.615 0.00 0.00 0.00 2.17
3131 3226 7.408756 ACATCCATACATGCAACAAGTAATT 57.591 32.000 0.00 0.00 0.00 1.40
3132 3227 8.696043 ATACATCCATACATGCAACAAGTAAT 57.304 30.769 0.00 0.00 0.00 1.89
3133 3228 7.992608 AGATACATCCATACATGCAACAAGTAA 59.007 33.333 0.00 0.00 0.00 2.24
3134 3229 7.508687 AGATACATCCATACATGCAACAAGTA 58.491 34.615 0.00 0.00 0.00 2.24
3135 3230 6.359804 AGATACATCCATACATGCAACAAGT 58.640 36.000 0.00 0.00 0.00 3.16
3136 3231 6.872628 AGATACATCCATACATGCAACAAG 57.127 37.500 0.00 0.00 0.00 3.16
3137 3232 7.734942 TCTAGATACATCCATACATGCAACAA 58.265 34.615 0.00 0.00 0.00 2.83
3138 3233 7.301868 TCTAGATACATCCATACATGCAACA 57.698 36.000 0.00 0.00 0.00 3.33
3139 3234 7.821359 ACATCTAGATACATCCATACATGCAAC 59.179 37.037 4.54 0.00 0.00 4.17
3140 3235 7.910584 ACATCTAGATACATCCATACATGCAA 58.089 34.615 4.54 0.00 0.00 4.08
3141 3236 7.486407 ACATCTAGATACATCCATACATGCA 57.514 36.000 4.54 0.00 0.00 3.96
3172 3267 9.775854 CTTCACAGAAATGGATGTATCTAGAAT 57.224 33.333 0.00 0.00 0.00 2.40
3173 3268 8.981659 TCTTCACAGAAATGGATGTATCTAGAA 58.018 33.333 0.00 0.00 0.00 2.10
3174 3269 8.539117 TCTTCACAGAAATGGATGTATCTAGA 57.461 34.615 0.00 0.00 0.00 2.43
3175 3270 8.420222 ACTCTTCACAGAAATGGATGTATCTAG 58.580 37.037 0.00 0.00 0.00 2.43
3176 3271 8.311395 ACTCTTCACAGAAATGGATGTATCTA 57.689 34.615 0.00 0.00 0.00 1.98
3177 3272 7.192852 ACTCTTCACAGAAATGGATGTATCT 57.807 36.000 0.00 0.00 0.00 1.98
3178 3273 8.948631 TTACTCTTCACAGAAATGGATGTATC 57.051 34.615 0.00 0.00 0.00 2.24
3179 3274 9.911788 AATTACTCTTCACAGAAATGGATGTAT 57.088 29.630 0.00 0.00 0.00 2.29
3180 3275 9.739276 AAATTACTCTTCACAGAAATGGATGTA 57.261 29.630 0.00 0.00 0.00 2.29
3181 3276 8.517878 CAAATTACTCTTCACAGAAATGGATGT 58.482 33.333 0.00 0.00 0.00 3.06
3182 3277 7.972277 CCAAATTACTCTTCACAGAAATGGATG 59.028 37.037 0.00 0.00 0.00 3.51
3183 3278 7.890127 TCCAAATTACTCTTCACAGAAATGGAT 59.110 33.333 0.00 0.00 0.00 3.41
3184 3279 7.230747 TCCAAATTACTCTTCACAGAAATGGA 58.769 34.615 0.00 0.00 0.00 3.41
3185 3280 7.452880 TCCAAATTACTCTTCACAGAAATGG 57.547 36.000 0.00 0.00 0.00 3.16
3186 3281 7.535258 CGTTCCAAATTACTCTTCACAGAAATG 59.465 37.037 0.00 0.00 0.00 2.32
3187 3282 7.308589 CCGTTCCAAATTACTCTTCACAGAAAT 60.309 37.037 0.00 0.00 0.00 2.17
3188 3283 6.017440 CCGTTCCAAATTACTCTTCACAGAAA 60.017 38.462 0.00 0.00 0.00 2.52
3189 3284 5.468746 CCGTTCCAAATTACTCTTCACAGAA 59.531 40.000 0.00 0.00 0.00 3.02
3190 3285 4.994852 CCGTTCCAAATTACTCTTCACAGA 59.005 41.667 0.00 0.00 0.00 3.41
3191 3286 4.994852 TCCGTTCCAAATTACTCTTCACAG 59.005 41.667 0.00 0.00 0.00 3.66
3192 3287 4.963373 TCCGTTCCAAATTACTCTTCACA 58.037 39.130 0.00 0.00 0.00 3.58
3193 3288 4.392138 CCTCCGTTCCAAATTACTCTTCAC 59.608 45.833 0.00 0.00 0.00 3.18
3194 3289 4.285003 TCCTCCGTTCCAAATTACTCTTCA 59.715 41.667 0.00 0.00 0.00 3.02
3195 3290 4.828829 TCCTCCGTTCCAAATTACTCTTC 58.171 43.478 0.00 0.00 0.00 2.87
3196 3291 4.903045 TCCTCCGTTCCAAATTACTCTT 57.097 40.909 0.00 0.00 0.00 2.85
3197 3292 4.286291 ACTTCCTCCGTTCCAAATTACTCT 59.714 41.667 0.00 0.00 0.00 3.24
3198 3293 4.576879 ACTTCCTCCGTTCCAAATTACTC 58.423 43.478 0.00 0.00 0.00 2.59
3199 3294 4.635699 ACTTCCTCCGTTCCAAATTACT 57.364 40.909 0.00 0.00 0.00 2.24
3200 3295 5.727434 TCTACTTCCTCCGTTCCAAATTAC 58.273 41.667 0.00 0.00 0.00 1.89
3201 3296 6.211986 TCTTCTACTTCCTCCGTTCCAAATTA 59.788 38.462 0.00 0.00 0.00 1.40
3202 3297 4.903045 TCTACTTCCTCCGTTCCAAATT 57.097 40.909 0.00 0.00 0.00 1.82
3203 3298 4.530946 TCTTCTACTTCCTCCGTTCCAAAT 59.469 41.667 0.00 0.00 0.00 2.32
3204 3299 3.899360 TCTTCTACTTCCTCCGTTCCAAA 59.101 43.478 0.00 0.00 0.00 3.28
3205 3300 3.503365 TCTTCTACTTCCTCCGTTCCAA 58.497 45.455 0.00 0.00 0.00 3.53
3206 3301 3.165087 TCTTCTACTTCCTCCGTTCCA 57.835 47.619 0.00 0.00 0.00 3.53
3207 3302 4.643784 TGTATCTTCTACTTCCTCCGTTCC 59.356 45.833 0.00 0.00 0.00 3.62
3208 3303 5.831702 TGTATCTTCTACTTCCTCCGTTC 57.168 43.478 0.00 0.00 0.00 3.95
3209 3304 6.600882 TTTGTATCTTCTACTTCCTCCGTT 57.399 37.500 0.00 0.00 0.00 4.44
3210 3305 6.600882 TTTTGTATCTTCTACTTCCTCCGT 57.399 37.500 0.00 0.00 0.00 4.69
3211 3306 6.872020 TGTTTTTGTATCTTCTACTTCCTCCG 59.128 38.462 0.00 0.00 0.00 4.63
3212 3307 7.660208 TGTGTTTTTGTATCTTCTACTTCCTCC 59.340 37.037 0.00 0.00 0.00 4.30
3213 3308 8.496751 GTGTGTTTTTGTATCTTCTACTTCCTC 58.503 37.037 0.00 0.00 0.00 3.71
3214 3309 7.990886 TGTGTGTTTTTGTATCTTCTACTTCCT 59.009 33.333 0.00 0.00 0.00 3.36
3215 3310 8.149973 TGTGTGTTTTTGTATCTTCTACTTCC 57.850 34.615 0.00 0.00 0.00 3.46
3231 3326 7.069331 TGGAGTCCAGAAATTTATGTGTGTTTT 59.931 33.333 8.12 0.00 0.00 2.43
3276 3371 9.667107 TTTTAGACCATCAATTTTAGAGTCGAT 57.333 29.630 0.00 0.00 0.00 3.59
3402 3498 6.539649 TTTGTGAGTCAAATTCCTTACTCG 57.460 37.500 0.00 0.00 40.99 4.18
3457 3553 9.433317 CTTTCGCATGTACAAATTATAAACGAT 57.567 29.630 0.00 0.00 0.00 3.73
3458 3554 8.444715 ACTTTCGCATGTACAAATTATAAACGA 58.555 29.630 0.00 0.00 0.00 3.85
3459 3555 8.595781 ACTTTCGCATGTACAAATTATAAACG 57.404 30.769 0.00 0.00 0.00 3.60
3464 3560 9.378551 TCTCTTACTTTCGCATGTACAAATTAT 57.621 29.630 0.00 0.00 0.00 1.28
3465 3561 8.766000 TCTCTTACTTTCGCATGTACAAATTA 57.234 30.769 0.00 0.00 0.00 1.40
3466 3562 7.667043 TCTCTTACTTTCGCATGTACAAATT 57.333 32.000 0.00 0.00 0.00 1.82
3468 3564 6.649141 ACATCTCTTACTTTCGCATGTACAAA 59.351 34.615 0.00 0.00 0.00 2.83
3469 3565 6.163476 ACATCTCTTACTTTCGCATGTACAA 58.837 36.000 0.00 0.00 0.00 2.41
3472 3568 5.961272 TGACATCTCTTACTTTCGCATGTA 58.039 37.500 0.00 0.00 0.00 2.29
3474 3570 5.220548 CCTTGACATCTCTTACTTTCGCATG 60.221 44.000 0.00 0.00 0.00 4.06
3475 3571 4.872691 CCTTGACATCTCTTACTTTCGCAT 59.127 41.667 0.00 0.00 0.00 4.73
3476 3572 4.245660 CCTTGACATCTCTTACTTTCGCA 58.754 43.478 0.00 0.00 0.00 5.10
3477 3573 3.062774 GCCTTGACATCTCTTACTTTCGC 59.937 47.826 0.00 0.00 0.00 4.70
3478 3574 3.619038 GGCCTTGACATCTCTTACTTTCG 59.381 47.826 0.00 0.00 0.00 3.46
3479 3575 3.942115 GGGCCTTGACATCTCTTACTTTC 59.058 47.826 0.84 0.00 0.00 2.62
3480 3576 3.619979 CGGGCCTTGACATCTCTTACTTT 60.620 47.826 0.84 0.00 0.00 2.66
3519 3619 6.356556 TGACTGTCCAATTCTCTTCTTTTCA 58.643 36.000 5.17 0.00 0.00 2.69
3621 3721 1.404391 GAACTCGAATGGCCTCGACTA 59.596 52.381 12.70 0.00 42.69 2.59
3627 3727 0.984230 TCTTGGAACTCGAATGGCCT 59.016 50.000 3.32 0.00 0.00 5.19
3682 3782 3.730715 GTGATTCTTTGTTTTGCTGGACG 59.269 43.478 0.00 0.00 0.00 4.79
3737 3837 4.689345 ACTACGGTTGTATGCTTTTCTCAC 59.311 41.667 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.