Multiple sequence alignment - TraesCS4B01G182600

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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 TraesCS4B01G182600 chr4B 100.000 4551 0 0 1 4551 400398491 400403041 0.000000e+00 8405
1 TraesCS4B01G182600 chr4B 92.109 659 43 6 3774 4428 480286919 480287572 0.000000e+00 920
2 TraesCS4B01G182600 chr4B 96.850 127 3 1 4426 4551 584428264 584428138 1.280000e-50 211
3 TraesCS4B01G182600 chr4D 96.238 1781 32 8 986 2748 320210672 320208909 0.000000e+00 2885
4 TraesCS4B01G182600 chr4D 94.863 876 29 6 2899 3774 320208903 320208044 0.000000e+00 1354
5 TraesCS4B01G182600 chr4D 89.062 640 28 24 1 615 320211702 320211080 0.000000e+00 756
6 TraesCS4B01G182600 chr4D 93.855 179 10 1 625 802 320211035 320210857 7.500000e-68 268
7 TraesCS4B01G182600 chr4D 94.521 73 4 0 818 890 320210772 320210700 3.720000e-21 113
8 TraesCS4B01G182600 chr4A 96.949 1442 40 3 961 2398 152738564 152740005 0.000000e+00 2416
9 TraesCS4B01G182600 chr4A 94.169 1372 60 11 2403 3774 152740057 152741408 0.000000e+00 2073
10 TraesCS4B01G182600 chr4A 87.017 724 37 26 1 689 152651299 152652000 0.000000e+00 763
11 TraesCS4B01G182600 chr4A 92.754 138 8 2 4416 4551 30867444 30867307 9.990000e-47 198
12 TraesCS4B01G182600 chr1B 92.470 664 39 7 3774 4428 137966218 137965557 0.000000e+00 939
13 TraesCS4B01G182600 chr1B 91.867 664 42 6 3774 4428 603491081 603491741 0.000000e+00 917
14 TraesCS4B01G182600 chr1B 93.814 485 17 8 1 476 638035752 638036232 0.000000e+00 717
15 TraesCS4B01G182600 chr1B 87.912 91 7 3 522 612 638043157 638043243 2.240000e-18 104
16 TraesCS4B01G182600 chr6B 92.204 667 40 6 3774 4431 213251524 213250861 0.000000e+00 933
17 TraesCS4B01G182600 chr6B 92.066 668 40 6 3774 4431 366674870 366674206 0.000000e+00 928
18 TraesCS4B01G182600 chr6B 91.754 667 44 5 3774 4431 347842577 347841913 0.000000e+00 917
19 TraesCS4B01G182600 chr5B 91.843 662 43 4 3779 4431 49589842 49589183 0.000000e+00 913
20 TraesCS4B01G182600 chr5B 91.604 667 44 5 3774 4431 335876879 335876216 0.000000e+00 911
21 TraesCS4B01G182600 chr3B 91.679 661 44 5 3780 4431 594383811 594383153 0.000000e+00 905
22 TraesCS4B01G182600 chr3B 92.958 142 7 3 4411 4551 513598575 513598714 2.150000e-48 204
23 TraesCS4B01G182600 chr2D 98.361 122 2 0 4430 4551 628155119 628155240 9.920000e-52 215
24 TraesCS4B01G182600 chr2D 90.210 143 13 1 2751 2893 27519790 27519649 7.770000e-43 185
25 TraesCS4B01G182600 chr7B 97.581 124 3 0 4428 4551 655112188 655112311 3.570000e-51 213
26 TraesCS4B01G182600 chr6A 96.124 129 4 1 4424 4551 575366452 575366324 4.610000e-50 209
27 TraesCS4B01G182600 chr2B 97.541 122 3 0 4430 4551 124153 124032 4.610000e-50 209
28 TraesCS4B01G182600 chr3A 93.478 138 7 2 4416 4551 227179442 227179305 2.150000e-48 204
29 TraesCS4B01G182600 chr2A 92.361 144 9 2 4410 4551 389959056 389959199 2.150000e-48 204


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 TraesCS4B01G182600 chr4B 400398491 400403041 4550 False 8405.0 8405 100.0000 1 4551 1 chr4B.!!$F1 4550
1 TraesCS4B01G182600 chr4B 480286919 480287572 653 False 920.0 920 92.1090 3774 4428 1 chr4B.!!$F2 654
2 TraesCS4B01G182600 chr4D 320208044 320211702 3658 True 1075.2 2885 93.7078 1 3774 5 chr4D.!!$R1 3773
3 TraesCS4B01G182600 chr4A 152738564 152741408 2844 False 2244.5 2416 95.5590 961 3774 2 chr4A.!!$F2 2813
4 TraesCS4B01G182600 chr4A 152651299 152652000 701 False 763.0 763 87.0170 1 689 1 chr4A.!!$F1 688
5 TraesCS4B01G182600 chr1B 137965557 137966218 661 True 939.0 939 92.4700 3774 4428 1 chr1B.!!$R1 654
6 TraesCS4B01G182600 chr1B 603491081 603491741 660 False 917.0 917 91.8670 3774 4428 1 chr1B.!!$F1 654
7 TraesCS4B01G182600 chr6B 213250861 213251524 663 True 933.0 933 92.2040 3774 4431 1 chr6B.!!$R1 657
8 TraesCS4B01G182600 chr6B 366674206 366674870 664 True 928.0 928 92.0660 3774 4431 1 chr6B.!!$R3 657
9 TraesCS4B01G182600 chr6B 347841913 347842577 664 True 917.0 917 91.7540 3774 4431 1 chr6B.!!$R2 657
10 TraesCS4B01G182600 chr5B 49589183 49589842 659 True 913.0 913 91.8430 3779 4431 1 chr5B.!!$R1 652
11 TraesCS4B01G182600 chr5B 335876216 335876879 663 True 911.0 911 91.6040 3774 4431 1 chr5B.!!$R2 657
12 TraesCS4B01G182600 chr3B 594383153 594383811 658 True 905.0 905 91.6790 3780 4431 1 chr3B.!!$R1 651

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
860 1009 0.165944 GGCACGTAACTGACACATGC 59.834 55.0 0.00 0.0 32.71 4.06 F
865 1014 0.165944 GTAACTGACACATGCCACGC 59.834 55.0 0.00 0.0 0.00 5.34 F
2761 2977 0.179009 TCAATAGCAGGGATGCAGGC 60.179 55.0 2.73 0.0 37.25 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2848 3064 0.870393 CGCTCCGCCTCGTAGTATAA 59.130 55.000 0.0 0.0 0.00 0.98 R
2859 3075 4.899239 CACCTGATCCGCTCCGCC 62.899 72.222 0.0 0.0 0.00 6.13 R
4489 4718 0.100503 GAATTTAATGCACCGCGCCT 59.899 50.000 0.0 0.0 41.33 5.52 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
140 141 4.580167 ACTATAAGTCGCACGGTACCATAA 59.420 41.667 13.54 0.00 0.00 1.90
141 142 2.973694 AAGTCGCACGGTACCATAAT 57.026 45.000 13.54 0.00 0.00 1.28
142 143 5.710513 ATAAGTCGCACGGTACCATAATA 57.289 39.130 13.54 0.00 0.00 0.98
143 144 4.595762 AAGTCGCACGGTACCATAATAT 57.404 40.909 13.54 0.00 0.00 1.28
145 146 5.306532 AGTCGCACGGTACCATAATATAG 57.693 43.478 13.54 0.00 0.00 1.31
146 147 3.855950 GTCGCACGGTACCATAATATAGC 59.144 47.826 13.54 2.59 0.00 2.97
147 148 3.119388 TCGCACGGTACCATAATATAGCC 60.119 47.826 13.54 0.00 0.00 3.93
148 149 3.528532 GCACGGTACCATAATATAGCCC 58.471 50.000 13.54 0.00 0.00 5.19
152 153 6.463897 GCACGGTACCATAATATAGCCCATAT 60.464 42.308 13.54 0.00 0.00 1.78
190 198 7.170277 TCAAGAATGATCAGATGGAGAAACAA 58.830 34.615 0.09 0.00 0.00 2.83
192 200 6.120905 AGAATGATCAGATGGAGAAACAAGG 58.879 40.000 0.09 0.00 0.00 3.61
195 203 3.423539 TCAGATGGAGAAACAAGGGTG 57.576 47.619 0.00 0.00 0.00 4.61
196 204 2.711009 TCAGATGGAGAAACAAGGGTGT 59.289 45.455 0.00 0.00 40.75 4.16
219 228 2.502213 TATATGTGACTCGGCGTTGG 57.498 50.000 6.85 1.00 0.00 3.77
429 443 3.458163 GACCCGGCGGACATCTCA 61.458 66.667 30.79 0.00 0.00 3.27
487 501 5.177696 GCTTAGCTTGGAACCAATCGTATAG 59.822 44.000 6.74 2.58 35.20 1.31
507 534 4.647424 AGTGCTTACTGTATCTCAGAGC 57.353 45.455 1.79 1.05 46.27 4.09
508 535 4.277476 AGTGCTTACTGTATCTCAGAGCT 58.723 43.478 8.03 0.00 46.27 4.09
509 536 5.441500 AGTGCTTACTGTATCTCAGAGCTA 58.558 41.667 8.03 0.00 46.27 3.32
511 538 4.824537 TGCTTACTGTATCTCAGAGCTAGG 59.175 45.833 8.03 0.00 46.27 3.02
513 540 5.998981 GCTTACTGTATCTCAGAGCTAGGTA 59.001 44.000 0.00 0.00 46.27 3.08
514 541 6.148811 GCTTACTGTATCTCAGAGCTAGGTAG 59.851 46.154 0.00 0.00 46.27 3.18
515 542 5.897851 ACTGTATCTCAGAGCTAGGTAGA 57.102 43.478 0.00 0.00 46.27 2.59
516 543 6.255294 ACTGTATCTCAGAGCTAGGTAGAA 57.745 41.667 0.00 0.00 46.27 2.10
517 544 6.296026 ACTGTATCTCAGAGCTAGGTAGAAG 58.704 44.000 0.00 0.00 46.27 2.85
518 545 6.100569 ACTGTATCTCAGAGCTAGGTAGAAGA 59.899 42.308 0.00 0.00 46.27 2.87
519 546 7.085476 TGTATCTCAGAGCTAGGTAGAAGAT 57.915 40.000 13.67 13.67 0.00 2.40
520 547 8.208575 TGTATCTCAGAGCTAGGTAGAAGATA 57.791 38.462 12.25 12.25 0.00 1.98
521 548 8.318412 TGTATCTCAGAGCTAGGTAGAAGATAG 58.682 40.741 14.90 1.01 0.00 2.08
522 549 5.556915 TCTCAGAGCTAGGTAGAAGATAGC 58.443 45.833 0.00 0.00 41.79 2.97
523 550 5.072464 TCTCAGAGCTAGGTAGAAGATAGCA 59.928 44.000 0.00 0.00 43.49 3.49
524 551 5.312895 TCAGAGCTAGGTAGAAGATAGCAG 58.687 45.833 0.00 0.00 43.49 4.24
525 552 4.079253 AGAGCTAGGTAGAAGATAGCAGC 58.921 47.826 0.00 0.00 43.49 5.25
526 553 3.161866 AGCTAGGTAGAAGATAGCAGCC 58.838 50.000 6.25 0.00 43.49 4.85
527 554 3.161866 GCTAGGTAGAAGATAGCAGCCT 58.838 50.000 0.00 0.00 41.25 4.58
528 555 3.056891 GCTAGGTAGAAGATAGCAGCCTG 60.057 52.174 0.00 0.00 41.25 4.85
529 556 3.320610 AGGTAGAAGATAGCAGCCTGA 57.679 47.619 0.00 0.00 0.00 3.86
535 576 4.899239 ATAGCAGCCTGACCGCGC 62.899 66.667 0.00 0.00 0.00 6.86
549 591 3.793144 GCGCGCTGTCTTGGAAGG 61.793 66.667 26.67 0.00 0.00 3.46
553 595 1.016653 GCGCTGTCTTGGAAGGTCTC 61.017 60.000 0.00 0.00 0.00 3.36
615 657 0.244721 TCATCTGCGAGGTGTGTCTG 59.755 55.000 0.00 0.00 0.00 3.51
617 659 0.244994 ATCTGCGAGGTGTGTCTGTC 59.755 55.000 0.00 0.00 0.00 3.51
618 660 0.823769 TCTGCGAGGTGTGTCTGTCT 60.824 55.000 0.00 0.00 0.00 3.41
620 662 0.596577 TGCGAGGTGTGTCTGTCTAC 59.403 55.000 0.00 0.00 0.00 2.59
623 700 2.668834 GCGAGGTGTGTCTGTCTACTTC 60.669 54.545 0.00 0.00 0.00 3.01
685 765 5.496387 GTTGATGATTGCAGTATTGTCGAG 58.504 41.667 0.00 0.00 0.00 4.04
691 771 3.251479 TGCAGTATTGTCGAGCTCAAT 57.749 42.857 15.40 9.33 38.72 2.57
704 784 3.545475 CGAGCTCAATGGATAATCGATCG 59.455 47.826 15.40 9.36 35.12 3.69
724 804 1.882198 CGTGCGACAAATTGTGATCC 58.118 50.000 2.20 0.00 0.00 3.36
727 807 2.095853 GTGCGACAAATTGTGATCCGAT 59.904 45.455 2.20 0.00 0.00 4.18
743 823 1.342555 CGATGAAGACGTGCGGTTTA 58.657 50.000 0.00 0.00 0.00 2.01
773 853 1.299544 CGGCGTTTCCAACCAAACC 60.300 57.895 0.00 0.00 33.37 3.27
778 858 2.800273 GCGTTTCCAACCAAACCGAAAT 60.800 45.455 0.00 0.00 33.37 2.17
814 904 8.628630 TTTGTTTTGTTTTGAGGGAAAGAAAT 57.371 26.923 0.00 0.00 33.54 2.17
815 905 7.841915 TGTTTTGTTTTGAGGGAAAGAAATC 57.158 32.000 0.00 0.00 33.54 2.17
816 906 7.390027 TGTTTTGTTTTGAGGGAAAGAAATCA 58.610 30.769 0.00 0.00 33.54 2.57
823 972 6.935240 TTGAGGGAAAGAAATCAGAGTAGA 57.065 37.500 0.00 0.00 0.00 2.59
860 1009 0.165944 GGCACGTAACTGACACATGC 59.834 55.000 0.00 0.00 32.71 4.06
865 1014 0.165944 GTAACTGACACATGCCACGC 59.834 55.000 0.00 0.00 0.00 5.34
884 1033 1.282157 GCCACCAACCTTATCAGTCCT 59.718 52.381 0.00 0.00 0.00 3.85
885 1034 2.290960 GCCACCAACCTTATCAGTCCTT 60.291 50.000 0.00 0.00 0.00 3.36
886 1035 3.814316 GCCACCAACCTTATCAGTCCTTT 60.814 47.826 0.00 0.00 0.00 3.11
887 1036 4.407365 CCACCAACCTTATCAGTCCTTTT 58.593 43.478 0.00 0.00 0.00 2.27
888 1037 4.832823 CCACCAACCTTATCAGTCCTTTTT 59.167 41.667 0.00 0.00 0.00 1.94
950 1099 4.577834 TCCGGAGAAAACAAAAACATCC 57.422 40.909 0.00 0.00 0.00 3.51
956 1105 6.636850 CGGAGAAAACAAAAACATCCAAGTAG 59.363 38.462 0.00 0.00 0.00 2.57
957 1106 6.420903 GGAGAAAACAAAAACATCCAAGTAGC 59.579 38.462 0.00 0.00 0.00 3.58
958 1107 6.872920 AGAAAACAAAAACATCCAAGTAGCA 58.127 32.000 0.00 0.00 0.00 3.49
959 1108 6.756542 AGAAAACAAAAACATCCAAGTAGCAC 59.243 34.615 0.00 0.00 0.00 4.40
984 1133 2.691409 TTTATCAGAACCGCCCTGAG 57.309 50.000 0.00 0.00 43.07 3.35
1019 1168 2.778659 CAGCACTTCGCAATTTAGAGC 58.221 47.619 0.00 0.00 46.13 4.09
1069 1226 1.764571 AAGCACACGGTCCCAAGCTA 61.765 55.000 0.00 0.00 0.00 3.32
1108 1265 0.179108 AGACGCTAGCCCGATTTCAC 60.179 55.000 9.66 0.00 0.00 3.18
1612 1770 1.632589 AAATCCAACTTGGCTGGTCC 58.367 50.000 2.52 0.00 37.47 4.46
1697 1859 9.482627 GGAAAATCTCACTCGAACTCAATATAT 57.517 33.333 0.00 0.00 0.00 0.86
1704 1866 6.015095 TCACTCGAACTCAATATATCCATGCT 60.015 38.462 0.00 0.00 0.00 3.79
1907 2076 1.621107 CATTGCCGTTTCATCTGTGC 58.379 50.000 0.00 0.00 0.00 4.57
2024 2193 2.617274 GGGCCAAACAGAGCACGAC 61.617 63.158 4.39 0.00 0.00 4.34
2145 2314 4.778143 GGTCGCCGAGGCCATTGT 62.778 66.667 5.01 0.00 46.14 2.71
2148 2317 2.745884 CGCCGAGGCCATTGTGAA 60.746 61.111 5.01 0.00 37.98 3.18
2314 2483 8.437742 CAGCCAATATTTGTTGTTTTGATTCTC 58.562 33.333 0.00 0.00 0.00 2.87
2505 2721 7.446931 TGCATTCTAGTTAATTTGTGTTCCTGA 59.553 33.333 0.00 0.00 0.00 3.86
2600 2816 1.255882 CTATTGCACCCTTGTTGCCA 58.744 50.000 0.00 0.00 0.00 4.92
2688 2904 8.843885 ACAGATAACAGACTTTAAGGTTAACC 57.156 34.615 17.41 17.41 30.41 2.85
2749 2965 5.038033 CACTAGAAGTCTTCGGTCAATAGC 58.962 45.833 6.94 0.00 34.02 2.97
2759 2975 1.602311 GGTCAATAGCAGGGATGCAG 58.398 55.000 2.73 0.00 37.25 4.41
2761 2977 0.179009 TCAATAGCAGGGATGCAGGC 60.179 55.000 2.73 0.00 37.25 4.85
2800 3016 4.213482 CCCGCATAAGTAGGAAAATAGTGC 59.787 45.833 0.00 0.00 0.00 4.40
2803 3019 6.422223 CGCATAAGTAGGAAAATAGTGCAAG 58.578 40.000 0.00 0.00 0.00 4.01
2809 3025 4.972514 AGGAAAATAGTGCAAGCTAAGC 57.027 40.909 4.23 4.23 0.00 3.09
2816 3032 6.625873 AATAGTGCAAGCTAAGCTAAATCC 57.374 37.500 11.76 0.00 38.25 3.01
2864 3080 3.544684 TCTGTTTATACTACGAGGCGGA 58.455 45.455 0.00 0.00 0.00 5.54
2865 3081 3.562973 TCTGTTTATACTACGAGGCGGAG 59.437 47.826 0.00 0.00 44.37 4.63
2887 3103 3.677284 ATCAGGTGCCGCTCTGCAG 62.677 63.158 7.63 7.63 43.02 4.41
2897 3113 1.143620 GCTCTGCAGCCCTAGTCAG 59.856 63.158 9.47 0.00 40.14 3.51
2951 3167 5.536497 AGAAAAATCATCAAGGGTAGGGT 57.464 39.130 0.00 0.00 0.00 4.34
2968 3185 2.158415 AGGGTGATATGCATTCTTGGGG 60.158 50.000 3.54 0.00 0.00 4.96
2973 3190 4.646492 GTGATATGCATTCTTGGGGAAGTT 59.354 41.667 3.54 0.00 37.36 2.66
3015 3232 8.608317 GTCATCTTAGATAAGTTTGAGGAAAGC 58.392 37.037 0.00 0.00 34.93 3.51
3062 3279 6.084925 CAGAAATGCTCTCTTCATTTGTCAC 58.915 40.000 5.78 0.00 42.30 3.67
3085 3302 5.126061 ACATGGGCACTAAGATGAATTTGTC 59.874 40.000 0.00 0.00 0.00 3.18
3219 3436 5.121925 GCAGATCATATGTTAGCATCCACAG 59.878 44.000 1.90 0.00 36.58 3.66
3220 3437 6.228995 CAGATCATATGTTAGCATCCACAGT 58.771 40.000 1.90 0.00 36.58 3.55
3221 3438 7.381323 CAGATCATATGTTAGCATCCACAGTA 58.619 38.462 1.90 0.00 36.58 2.74
3222 3439 8.039538 CAGATCATATGTTAGCATCCACAGTAT 58.960 37.037 1.90 0.00 36.58 2.12
3327 3544 8.965986 AAAGAAACGGAAATTGCTCTTATTAC 57.034 30.769 0.00 0.00 0.00 1.89
3359 3576 7.173907 CCAACTTTCAATACTCAGTGAAGACAT 59.826 37.037 0.00 0.00 39.68 3.06
3438 3655 2.633967 TGGCATGACAAAGGAGCAATTT 59.366 40.909 0.00 0.00 0.00 1.82
3476 3693 5.188359 AGTTTATACAAGGCCGGAGTTCTAA 59.812 40.000 5.05 0.00 0.00 2.10
3572 3789 4.060205 AGCTTGTGGAAATGTCAAATTGC 58.940 39.130 0.00 0.00 0.00 3.56
3621 3838 8.724229 ACGTTGTTTTACTTTGAAGTTTCTACT 58.276 29.630 1.20 0.00 40.37 2.57
3661 3878 6.238759 CCCTTTTAGCTGCAGTAATGTTATCC 60.239 42.308 16.64 0.00 0.00 2.59
3662 3879 5.984233 TTTAGCTGCAGTAATGTTATCCG 57.016 39.130 16.64 0.00 0.00 4.18
3663 3880 3.819564 AGCTGCAGTAATGTTATCCGA 57.180 42.857 16.64 0.00 0.00 4.55
3664 3881 3.458189 AGCTGCAGTAATGTTATCCGAC 58.542 45.455 16.64 0.00 0.00 4.79
3665 3882 3.118775 AGCTGCAGTAATGTTATCCGACA 60.119 43.478 16.64 0.00 0.00 4.35
3666 3883 3.809832 GCTGCAGTAATGTTATCCGACAT 59.190 43.478 16.64 0.00 41.83 3.06
3667 3884 4.084328 GCTGCAGTAATGTTATCCGACATC 60.084 45.833 16.64 0.00 39.25 3.06
3672 3889 6.273071 CAGTAATGTTATCCGACATCTGACA 58.727 40.000 0.00 0.00 39.25 3.58
3690 3907 0.320374 CAAACGTCAGCTGGGAGGTA 59.680 55.000 15.13 0.00 35.04 3.08
3695 3912 1.781786 GTCAGCTGGGAGGTAGATGA 58.218 55.000 15.13 0.00 38.16 2.92
3710 3927 4.691216 GGTAGATGACAGGTGAACACTTTC 59.309 45.833 4.96 0.79 0.00 2.62
3727 3944 4.023707 CACTTTCTTCTGGCAGTTTCGAAT 60.024 41.667 15.27 0.00 0.00 3.34
3745 3962 5.162794 TCGAATGATGGCAATTTTGAACAG 58.837 37.500 0.00 0.00 0.00 3.16
3749 3966 7.307278 CGAATGATGGCAATTTTGAACAGAAAA 60.307 33.333 0.00 0.00 0.00 2.29
3770 3987 8.856490 GAAAATGTGTTTTTCTGAAGAAGCTA 57.144 30.769 0.00 0.00 46.42 3.32
3776 3993 6.038271 GTGTTTTTCTGAAGAAGCTACCAGAA 59.962 38.462 12.85 12.85 42.00 3.02
3883 4100 2.038820 ACGTCGGTATTTCCCCAAAGAA 59.961 45.455 0.00 0.00 0.00 2.52
3895 4112 4.379875 TCCCCAAAGAAGAAGGGATGATA 58.620 43.478 0.00 0.00 43.81 2.15
3929 4146 4.585162 ACGATAGGTATTTCCCTCAGTGAG 59.415 45.833 13.56 13.56 43.77 3.51
3930 4147 4.827835 CGATAGGTATTTCCCTCAGTGAGA 59.172 45.833 22.09 1.33 35.97 3.27
3934 4151 5.284582 AGGTATTTCCCTCAGTGAGAAGAT 58.715 41.667 22.09 11.67 36.75 2.40
3949 4166 7.759886 CAGTGAGAAGATTAAGGTTATCGAACA 59.240 37.037 0.00 0.00 37.29 3.18
3963 4180 6.872547 GGTTATCGAACAAGTAGAAGAACCTT 59.127 38.462 0.00 0.00 37.29 3.50
4085 4304 7.608761 AGATAGGCAAATAACGTGAGGTAAAAA 59.391 33.333 0.00 0.00 36.50 1.94
4191 4417 5.402398 ACAAAGGAAAATAGATCGCAAAGC 58.598 37.500 0.00 0.00 0.00 3.51
4214 4440 5.360714 GCCAAATATGATGAAAAGAGACCCA 59.639 40.000 0.00 0.00 0.00 4.51
4230 4457 1.153628 CCAGGGCTCGTAGGTTTCG 60.154 63.158 0.00 0.00 0.00 3.46
4267 4494 3.187637 CGAGAAAAATAGCAAACGGTGGA 59.812 43.478 0.00 0.00 0.00 4.02
4299 4528 9.533831 AATTACTGTTGGGATTGATAGAACTTT 57.466 29.630 0.00 0.00 0.00 2.66
4300 4529 6.824305 ACTGTTGGGATTGATAGAACTTTG 57.176 37.500 0.00 0.00 0.00 2.77
4330 4559 4.356405 TGACGATATCCAGGCAATGATT 57.644 40.909 0.00 0.00 0.00 2.57
4374 4603 1.376543 TTAGTAGACCGACTCCTGCG 58.623 55.000 0.00 0.00 0.00 5.18
4397 4626 6.349445 GCGTGCATCTACTACTATTACTCCAT 60.349 42.308 0.00 0.00 0.00 3.41
4432 4661 7.345422 CTATCCAGCATGCATCTAGTATACT 57.655 40.000 21.98 10.87 31.97 2.12
4433 4662 5.651387 TCCAGCATGCATCTAGTATACTC 57.349 43.478 21.98 0.00 31.97 2.59
4434 4663 4.464244 TCCAGCATGCATCTAGTATACTCC 59.536 45.833 21.98 0.00 31.97 3.85
4435 4664 4.382470 CCAGCATGCATCTAGTATACTCCC 60.382 50.000 21.98 0.00 31.97 4.30
4436 4665 4.465660 CAGCATGCATCTAGTATACTCCCT 59.534 45.833 21.98 0.00 0.00 4.20
4437 4666 4.709397 AGCATGCATCTAGTATACTCCCTC 59.291 45.833 21.98 0.00 0.00 4.30
4438 4667 4.142049 GCATGCATCTAGTATACTCCCTCC 60.142 50.000 14.21 0.00 0.00 4.30
4439 4668 3.687125 TGCATCTAGTATACTCCCTCCG 58.313 50.000 9.12 0.00 0.00 4.63
4440 4669 3.074094 TGCATCTAGTATACTCCCTCCGT 59.926 47.826 9.12 0.00 0.00 4.69
4441 4670 3.690628 GCATCTAGTATACTCCCTCCGTC 59.309 52.174 9.12 0.00 0.00 4.79
4442 4671 4.566070 GCATCTAGTATACTCCCTCCGTCT 60.566 50.000 9.12 0.00 0.00 4.18
4443 4672 5.338219 GCATCTAGTATACTCCCTCCGTCTA 60.338 48.000 9.12 0.00 0.00 2.59
4444 4673 5.999205 TCTAGTATACTCCCTCCGTCTAG 57.001 47.826 9.12 0.00 0.00 2.43
4445 4674 4.776837 TCTAGTATACTCCCTCCGTCTAGG 59.223 50.000 9.12 0.00 42.97 3.02
4446 4675 3.325605 AGTATACTCCCTCCGTCTAGGT 58.674 50.000 0.00 0.00 41.99 3.08
4447 4676 2.660670 ATACTCCCTCCGTCTAGGTG 57.339 55.000 0.00 0.00 41.99 4.00
4448 4677 1.293062 TACTCCCTCCGTCTAGGTGT 58.707 55.000 0.00 0.00 41.99 4.16
4449 4678 0.323542 ACTCCCTCCGTCTAGGTGTG 60.324 60.000 0.00 0.00 41.99 3.82
4450 4679 0.323542 CTCCCTCCGTCTAGGTGTGT 60.324 60.000 0.00 0.00 41.99 3.72
4451 4680 0.994247 TCCCTCCGTCTAGGTGTGTA 59.006 55.000 0.00 0.00 41.99 2.90
4452 4681 1.355381 TCCCTCCGTCTAGGTGTGTAA 59.645 52.381 0.00 0.00 41.99 2.41
4453 4682 2.173519 CCCTCCGTCTAGGTGTGTAAA 58.826 52.381 0.00 0.00 41.99 2.01
4454 4683 2.764572 CCCTCCGTCTAGGTGTGTAAAT 59.235 50.000 0.00 0.00 41.99 1.40
4455 4684 3.181478 CCCTCCGTCTAGGTGTGTAAATC 60.181 52.174 0.00 0.00 41.99 2.17
4456 4685 3.446161 CCTCCGTCTAGGTGTGTAAATCA 59.554 47.826 0.00 0.00 41.99 2.57
4457 4686 4.099573 CCTCCGTCTAGGTGTGTAAATCAT 59.900 45.833 0.00 0.00 41.99 2.45
4458 4687 5.258456 TCCGTCTAGGTGTGTAAATCATC 57.742 43.478 0.00 0.00 41.99 2.92
4459 4688 4.954202 TCCGTCTAGGTGTGTAAATCATCT 59.046 41.667 0.00 0.00 41.99 2.90
4460 4689 5.421056 TCCGTCTAGGTGTGTAAATCATCTT 59.579 40.000 0.00 0.00 41.99 2.40
4461 4690 6.604396 TCCGTCTAGGTGTGTAAATCATCTTA 59.396 38.462 0.00 0.00 41.99 2.10
4462 4691 6.696148 CCGTCTAGGTGTGTAAATCATCTTAC 59.304 42.308 0.00 0.00 34.51 2.34
4463 4692 6.414109 CGTCTAGGTGTGTAAATCATCTTACG 59.586 42.308 0.00 0.00 35.00 3.18
4464 4693 7.478322 GTCTAGGTGTGTAAATCATCTTACGA 58.522 38.462 0.00 0.00 35.00 3.43
4465 4694 7.972277 GTCTAGGTGTGTAAATCATCTTACGAA 59.028 37.037 0.00 0.00 35.00 3.85
4466 4695 8.525316 TCTAGGTGTGTAAATCATCTTACGAAA 58.475 33.333 0.00 0.00 35.00 3.46
4467 4696 7.972832 AGGTGTGTAAATCATCTTACGAAAA 57.027 32.000 0.00 0.00 35.00 2.29
4468 4697 8.561738 AGGTGTGTAAATCATCTTACGAAAAT 57.438 30.769 0.00 0.00 35.00 1.82
4469 4698 8.665685 AGGTGTGTAAATCATCTTACGAAAATC 58.334 33.333 0.00 0.00 35.00 2.17
4470 4699 8.447833 GGTGTGTAAATCATCTTACGAAAATCA 58.552 33.333 0.00 0.00 35.00 2.57
4471 4700 9.820229 GTGTGTAAATCATCTTACGAAAATCAA 57.180 29.630 0.00 0.00 35.00 2.57
4480 4709 9.402320 TCATCTTACGAAAATCAAATATTCCCA 57.598 29.630 0.00 0.00 0.00 4.37
4485 4714 9.982651 TTACGAAAATCAAATATTCCCAAAACA 57.017 25.926 0.00 0.00 0.00 2.83
4486 4715 8.305441 ACGAAAATCAAATATTCCCAAAACAC 57.695 30.769 0.00 0.00 0.00 3.32
4487 4716 8.147704 ACGAAAATCAAATATTCCCAAAACACT 58.852 29.630 0.00 0.00 0.00 3.55
4488 4717 8.987890 CGAAAATCAAATATTCCCAAAACACTT 58.012 29.630 0.00 0.00 0.00 3.16
4491 4720 9.942850 AAATCAAATATTCCCAAAACACTTAGG 57.057 29.630 0.00 0.00 0.00 2.69
4492 4721 6.930731 TCAAATATTCCCAAAACACTTAGGC 58.069 36.000 0.00 0.00 0.00 3.93
4493 4722 5.576447 AATATTCCCAAAACACTTAGGCG 57.424 39.130 0.00 0.00 0.00 5.52
4494 4723 0.955905 TTCCCAAAACACTTAGGCGC 59.044 50.000 0.00 0.00 0.00 6.53
4495 4724 1.209127 CCCAAAACACTTAGGCGCG 59.791 57.895 0.00 0.00 0.00 6.86
4496 4725 1.209127 CCAAAACACTTAGGCGCGG 59.791 57.895 8.83 0.00 0.00 6.46
4497 4726 1.512156 CCAAAACACTTAGGCGCGGT 61.512 55.000 8.83 0.00 0.00 5.68
4498 4727 0.385473 CAAAACACTTAGGCGCGGTG 60.385 55.000 8.83 9.75 37.05 4.94
4499 4728 2.125202 AAAACACTTAGGCGCGGTGC 62.125 55.000 8.83 4.64 45.38 5.01
4509 4738 3.622459 GCGCGGTGCATTAAATTCT 57.378 47.368 8.83 0.00 45.45 2.40
4510 4739 2.748461 GCGCGGTGCATTAAATTCTA 57.252 45.000 8.83 0.00 45.45 2.10
4511 4740 2.372350 GCGCGGTGCATTAAATTCTAC 58.628 47.619 8.83 0.00 45.45 2.59
4512 4741 2.853281 GCGCGGTGCATTAAATTCTACC 60.853 50.000 8.83 0.00 45.45 3.18
4513 4742 2.612212 CGCGGTGCATTAAATTCTACCT 59.388 45.455 0.00 0.00 0.00 3.08
4514 4743 3.303132 CGCGGTGCATTAAATTCTACCTC 60.303 47.826 0.00 0.00 0.00 3.85
4515 4744 3.303132 GCGGTGCATTAAATTCTACCTCG 60.303 47.826 0.00 0.00 0.00 4.63
4516 4745 3.869246 CGGTGCATTAAATTCTACCTCGT 59.131 43.478 0.00 0.00 0.00 4.18
4517 4746 4.331717 CGGTGCATTAAATTCTACCTCGTT 59.668 41.667 0.00 0.00 0.00 3.85
4518 4747 5.163794 CGGTGCATTAAATTCTACCTCGTTT 60.164 40.000 0.00 0.00 0.00 3.60
4519 4748 6.255950 GGTGCATTAAATTCTACCTCGTTTC 58.744 40.000 0.00 0.00 0.00 2.78
4520 4749 6.093633 GGTGCATTAAATTCTACCTCGTTTCT 59.906 38.462 0.00 0.00 0.00 2.52
4521 4750 7.361799 GGTGCATTAAATTCTACCTCGTTTCTT 60.362 37.037 0.00 0.00 0.00 2.52
4522 4751 7.481798 GTGCATTAAATTCTACCTCGTTTCTTG 59.518 37.037 0.00 0.00 0.00 3.02
4523 4752 7.174253 TGCATTAAATTCTACCTCGTTTCTTGT 59.826 33.333 0.00 0.00 0.00 3.16
4524 4753 8.021396 GCATTAAATTCTACCTCGTTTCTTGTT 58.979 33.333 0.00 0.00 0.00 2.83
4525 4754 9.893305 CATTAAATTCTACCTCGTTTCTTGTTT 57.107 29.630 0.00 0.00 0.00 2.83
4527 4756 7.803279 AAATTCTACCTCGTTTCTTGTTTCT 57.197 32.000 0.00 0.00 0.00 2.52
4528 4757 7.803279 AATTCTACCTCGTTTCTTGTTTCTT 57.197 32.000 0.00 0.00 0.00 2.52
4529 4758 6.598753 TTCTACCTCGTTTCTTGTTTCTTG 57.401 37.500 0.00 0.00 0.00 3.02
4530 4759 5.909477 TCTACCTCGTTTCTTGTTTCTTGA 58.091 37.500 0.00 0.00 0.00 3.02
4531 4760 4.877323 ACCTCGTTTCTTGTTTCTTGAC 57.123 40.909 0.00 0.00 0.00 3.18
4532 4761 4.258543 ACCTCGTTTCTTGTTTCTTGACA 58.741 39.130 0.00 0.00 0.00 3.58
4533 4762 4.881850 ACCTCGTTTCTTGTTTCTTGACAT 59.118 37.500 0.00 0.00 0.00 3.06
4534 4763 6.053005 ACCTCGTTTCTTGTTTCTTGACATA 58.947 36.000 0.00 0.00 0.00 2.29
4535 4764 6.710744 ACCTCGTTTCTTGTTTCTTGACATAT 59.289 34.615 0.00 0.00 0.00 1.78
4536 4765 7.095187 ACCTCGTTTCTTGTTTCTTGACATATC 60.095 37.037 0.00 0.00 0.00 1.63
4537 4766 7.095229 CCTCGTTTCTTGTTTCTTGACATATCA 60.095 37.037 0.00 0.00 0.00 2.15
4538 4767 8.148807 TCGTTTCTTGTTTCTTGACATATCAA 57.851 30.769 0.00 0.00 42.73 2.57
4539 4768 8.067784 TCGTTTCTTGTTTCTTGACATATCAAC 58.932 33.333 0.00 0.00 40.01 3.18
4540 4769 7.323656 CGTTTCTTGTTTCTTGACATATCAACC 59.676 37.037 0.00 0.00 40.01 3.77
4541 4770 7.815840 TTCTTGTTTCTTGACATATCAACCA 57.184 32.000 0.00 0.00 40.01 3.67
4542 4771 7.815840 TCTTGTTTCTTGACATATCAACCAA 57.184 32.000 0.00 0.00 40.01 3.67
4543 4772 8.408043 TCTTGTTTCTTGACATATCAACCAAT 57.592 30.769 0.00 0.00 40.01 3.16
4544 4773 9.513906 TCTTGTTTCTTGACATATCAACCAATA 57.486 29.630 0.00 0.00 40.01 1.90
4547 4776 9.513906 TGTTTCTTGACATATCAACCAATAAGA 57.486 29.630 0.00 0.00 40.01 2.10
4548 4777 9.994432 GTTTCTTGACATATCAACCAATAAGAG 57.006 33.333 0.00 0.00 40.01 2.85
4549 4778 9.958180 TTTCTTGACATATCAACCAATAAGAGA 57.042 29.630 0.00 0.00 40.01 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
107 108 3.243737 TGCGACTTATAGTTGGCGATGAT 60.244 43.478 0.00 0.00 32.74 2.45
121 122 5.710513 ATATTATGGTACCGTGCGACTTA 57.289 39.130 17.34 0.00 0.00 2.24
170 171 5.198965 CCCTTGTTTCTCCATCTGATCATT 58.801 41.667 0.00 0.00 0.00 2.57
190 198 5.510861 GCCGAGTCACATATATAAACACCCT 60.511 44.000 0.00 0.00 0.00 4.34
192 200 4.384846 CGCCGAGTCACATATATAAACACC 59.615 45.833 0.00 0.00 0.00 4.16
195 203 5.107607 CCAACGCCGAGTCACATATATAAAC 60.108 44.000 0.00 0.00 0.00 2.01
196 204 4.986034 CCAACGCCGAGTCACATATATAAA 59.014 41.667 0.00 0.00 0.00 1.40
197 205 4.552355 CCAACGCCGAGTCACATATATAA 58.448 43.478 0.00 0.00 0.00 0.98
198 206 3.057104 CCCAACGCCGAGTCACATATATA 60.057 47.826 0.00 0.00 0.00 0.86
199 207 2.288825 CCCAACGCCGAGTCACATATAT 60.289 50.000 0.00 0.00 0.00 0.86
219 228 3.074412 CCCTACACACAGACAATCAACC 58.926 50.000 0.00 0.00 0.00 3.77
306 320 2.991076 GCAGTAGCTCGACGTGGGT 61.991 63.158 0.00 0.00 37.91 4.51
423 437 0.792640 GCACGTTGACAGGTGAGATG 59.207 55.000 11.60 0.00 40.64 2.90
429 443 4.539083 TGGCGCACGTTGACAGGT 62.539 61.111 10.83 0.00 0.00 4.00
487 501 4.647424 AGCTCTGAGATACAGTAAGCAC 57.353 45.455 9.28 0.00 44.04 4.40
507 534 4.217550 GTCAGGCTGCTATCTTCTACCTAG 59.782 50.000 10.34 0.00 0.00 3.02
508 535 4.145807 GTCAGGCTGCTATCTTCTACCTA 58.854 47.826 10.34 0.00 0.00 3.08
509 536 2.962421 GTCAGGCTGCTATCTTCTACCT 59.038 50.000 10.34 0.00 0.00 3.08
511 538 2.287909 CGGTCAGGCTGCTATCTTCTAC 60.288 54.545 10.34 0.00 0.00 2.59
513 540 0.749649 CGGTCAGGCTGCTATCTTCT 59.250 55.000 10.34 0.00 0.00 2.85
514 541 0.878086 GCGGTCAGGCTGCTATCTTC 60.878 60.000 10.34 0.00 45.76 2.87
515 542 1.144936 GCGGTCAGGCTGCTATCTT 59.855 57.895 10.34 0.00 45.76 2.40
516 543 2.818132 GCGGTCAGGCTGCTATCT 59.182 61.111 10.34 0.00 45.76 1.98
535 576 0.734253 CGAGACCTTCCAAGACAGCG 60.734 60.000 0.00 0.00 0.00 5.18
541 583 1.848652 TAGGACCGAGACCTTCCAAG 58.151 55.000 0.00 0.00 38.76 3.61
549 591 4.189639 ACTGAACAAATAGGACCGAGAC 57.810 45.455 0.00 0.00 0.00 3.36
553 595 3.365969 GGCAAACTGAACAAATAGGACCG 60.366 47.826 0.00 0.00 0.00 4.79
685 765 2.028523 CGCGATCGATTATCCATTGAGC 59.971 50.000 21.57 0.00 38.10 4.26
691 771 1.001745 CGCACGCGATCGATTATCCA 61.002 55.000 21.57 0.00 42.83 3.41
704 784 1.250476 GATCACAATTTGTCGCACGC 58.750 50.000 0.00 0.00 0.00 5.34
714 794 3.618594 CACGTCTTCATCGGATCACAATT 59.381 43.478 0.00 0.00 0.00 2.32
724 804 1.320555 CTAAACCGCACGTCTTCATCG 59.679 52.381 0.00 0.00 0.00 3.84
727 807 0.947180 GCCTAAACCGCACGTCTTCA 60.947 55.000 0.00 0.00 0.00 3.02
773 853 7.014702 ACAAAACAAAAAGAACTGCAATTTCG 58.985 30.769 0.00 0.00 0.00 3.46
778 858 7.697691 TCAAAACAAAACAAAAAGAACTGCAA 58.302 26.923 0.00 0.00 0.00 4.08
814 904 4.438336 CGTATGGTTTCGCTTCTACTCTGA 60.438 45.833 0.00 0.00 0.00 3.27
815 905 3.791887 CGTATGGTTTCGCTTCTACTCTG 59.208 47.826 0.00 0.00 0.00 3.35
816 906 4.030134 CGTATGGTTTCGCTTCTACTCT 57.970 45.455 0.00 0.00 0.00 3.24
860 1009 0.322098 TGATAAGGTTGGTGGCGTGG 60.322 55.000 0.00 0.00 0.00 4.94
865 1014 3.721087 AAGGACTGATAAGGTTGGTGG 57.279 47.619 0.00 0.00 0.00 4.61
950 1099 9.250624 GGTTCTGATAAATACTAGTGCTACTTG 57.749 37.037 5.39 0.00 0.00 3.16
956 1105 4.448060 GGCGGTTCTGATAAATACTAGTGC 59.552 45.833 5.39 0.00 0.00 4.40
957 1106 4.989168 GGGCGGTTCTGATAAATACTAGTG 59.011 45.833 5.39 0.00 0.00 2.74
958 1107 4.900054 AGGGCGGTTCTGATAAATACTAGT 59.100 41.667 0.00 0.00 0.00 2.57
959 1108 5.010719 TCAGGGCGGTTCTGATAAATACTAG 59.989 44.000 0.00 0.00 36.46 2.57
984 1133 0.880278 TGCTGCACCGAACTGAAGAC 60.880 55.000 0.00 0.00 0.00 3.01
1019 1168 5.266242 CGACCTTTTGACTTTTGAGAACTG 58.734 41.667 0.00 0.00 0.00 3.16
1069 1226 0.999406 CGATTTGGTTGAGCGATCGT 59.001 50.000 17.81 3.24 35.98 3.73
1551 1708 0.605589 AAGAAGCGTGTGAGGAGAGG 59.394 55.000 0.00 0.00 0.00 3.69
1612 1770 7.328249 GTCTACTGAGAAACTGAACAGATTGAG 59.672 40.741 8.87 2.34 31.96 3.02
1697 1859 5.181811 CACACAAGAATTTCACTAGCATGGA 59.818 40.000 0.00 0.00 0.00 3.41
1704 1866 3.820467 CTGCCCACACAAGAATTTCACTA 59.180 43.478 0.00 0.00 0.00 2.74
1800 1969 3.505449 GTGTTGAACACTAGCAACTCG 57.495 47.619 20.39 0.00 45.27 4.18
1907 2076 2.763249 AGAAGACAACAAGCAAAGCG 57.237 45.000 0.00 0.00 0.00 4.68
2035 2204 1.228337 AGTGACAGGCATGCAAGCA 60.228 52.632 21.36 8.80 35.83 3.91
2145 2314 3.252215 CACCAAGTTGCGGTTATTCTTCA 59.748 43.478 0.00 0.00 33.25 3.02
2148 2317 2.159382 CCACCAAGTTGCGGTTATTCT 58.841 47.619 0.00 0.00 33.25 2.40
2314 2483 8.127327 CAGAGTTTCATAATTTGAGCACCATAG 58.873 37.037 0.00 0.00 35.27 2.23
2773 2989 8.041323 CACTATTTTCCTACTTATGCGGGATAT 58.959 37.037 0.00 0.00 0.00 1.63
2800 3016 2.614057 CACCCGGATTTAGCTTAGCTTG 59.386 50.000 13.44 0.00 40.44 4.01
2803 3019 2.484889 CTCACCCGGATTTAGCTTAGC 58.515 52.381 0.73 0.00 0.00 3.09
2809 3025 7.450903 ACTATAATTTCCTCACCCGGATTTAG 58.549 38.462 0.73 0.00 32.02 1.85
2816 3032 7.767198 TCAACTTAACTATAATTTCCTCACCCG 59.233 37.037 0.00 0.00 0.00 5.28
2848 3064 0.870393 CGCTCCGCCTCGTAGTATAA 59.130 55.000 0.00 0.00 0.00 0.98
2859 3075 4.899239 CACCTGATCCGCTCCGCC 62.899 72.222 0.00 0.00 0.00 6.13
2887 3103 2.224161 CCTTGATGCTACTGACTAGGGC 60.224 54.545 0.00 0.00 0.00 5.19
2897 3113 2.822764 CGGAAGTACCCTTGATGCTAC 58.177 52.381 0.00 0.00 34.64 3.58
2929 3145 5.015178 TCACCCTACCCTTGATGATTTTTCT 59.985 40.000 0.00 0.00 0.00 2.52
2951 3167 4.524802 ACTTCCCCAAGAATGCATATCA 57.475 40.909 0.00 0.00 32.82 2.15
2973 3190 0.854218 TGACCCCTACCAGGCAAAAA 59.146 50.000 0.00 0.00 32.73 1.94
3015 3232 1.825191 CCGAATGACCCATGGCCTG 60.825 63.158 6.09 0.00 0.00 4.85
3044 3261 3.754850 CCATGTGACAAATGAAGAGAGCA 59.245 43.478 7.22 0.00 0.00 4.26
3062 3279 5.585390 GACAAATTCATCTTAGTGCCCATG 58.415 41.667 0.00 0.00 0.00 3.66
3085 3302 5.293324 TCGAACTGGATTGGTATGAATTTCG 59.707 40.000 0.00 0.00 34.81 3.46
3092 3309 2.868583 CAGCTCGAACTGGATTGGTATG 59.131 50.000 7.98 0.00 33.85 2.39
3476 3693 3.678056 TCTACAACTTCGATGGTGCTT 57.322 42.857 15.70 0.81 0.00 3.91
3565 3782 7.987458 TCTTCCAGTAATAGGAGTAGCAATTTG 59.013 37.037 0.00 0.00 36.33 2.32
3572 3789 5.455872 TGGGTCTTCCAGTAATAGGAGTAG 58.544 45.833 0.00 0.00 41.46 2.57
3638 3855 6.257849 TCGGATAACATTACTGCAGCTAAAAG 59.742 38.462 15.27 5.71 0.00 2.27
3672 3889 0.608640 CTACCTCCCAGCTGACGTTT 59.391 55.000 17.39 0.00 0.00 3.60
3690 3907 4.696479 AGAAAGTGTTCACCTGTCATCT 57.304 40.909 0.00 0.00 36.09 2.90
3695 3912 3.545703 CCAGAAGAAAGTGTTCACCTGT 58.454 45.455 0.00 0.00 35.44 4.00
3710 3927 3.181503 CCATCATTCGAAACTGCCAGAAG 60.182 47.826 0.00 0.00 0.00 2.85
3727 3944 6.766944 ACATTTTCTGTTCAAAATTGCCATCA 59.233 30.769 0.00 0.00 34.37 3.07
3749 3966 5.827797 TGGTAGCTTCTTCAGAAAAACACAT 59.172 36.000 0.00 0.00 33.07 3.21
3767 3984 6.481644 CCTAATCACAAATCTCTTCTGGTAGC 59.518 42.308 0.00 0.00 0.00 3.58
3770 3987 6.627087 TCCTAATCACAAATCTCTTCTGGT 57.373 37.500 0.00 0.00 0.00 4.00
3776 3993 5.251700 ACCAGGTTCCTAATCACAAATCTCT 59.748 40.000 0.00 0.00 0.00 3.10
3883 4100 5.416326 GTCGCTATACTGTATCATCCCTTCT 59.584 44.000 3.09 0.00 0.00 2.85
3895 4112 6.128063 GGAAATACCTATCGTCGCTATACTGT 60.128 42.308 0.00 0.00 35.41 3.55
3929 4146 9.798994 TCTACTTGTTCGATAACCTTAATCTTC 57.201 33.333 0.00 0.00 34.49 2.87
3934 4151 9.415544 GTTCTTCTACTTGTTCGATAACCTTAA 57.584 33.333 0.00 0.00 34.49 1.85
3949 4166 4.654262 TGGTGTGAGAAGGTTCTTCTACTT 59.346 41.667 9.80 0.00 37.73 2.24
3963 4180 1.137282 TGCTGTTTACGTGGTGTGAGA 59.863 47.619 0.00 0.00 0.00 3.27
4055 4273 5.584649 CCTCACGTTATTTGCCTATCTTGAA 59.415 40.000 0.00 0.00 0.00 2.69
4086 4305 8.353684 CGCGATCTATTTATCCTATCTACCATT 58.646 37.037 0.00 0.00 0.00 3.16
4168 4394 5.402398 GCTTTGCGATCTATTTTCCTTTGT 58.598 37.500 0.00 0.00 0.00 2.83
4191 4417 6.040166 CCTGGGTCTCTTTTCATCATATTTGG 59.960 42.308 0.00 0.00 0.00 3.28
4214 4440 0.682209 TAGCGAAACCTACGAGCCCT 60.682 55.000 0.00 0.00 0.00 5.19
4230 4457 3.851976 TTCTCGAGAGAAACCACTAGC 57.148 47.619 15.94 0.00 43.79 3.42
4299 4528 6.108687 GCCTGGATATCGTCATGATTATTCA 58.891 40.000 0.00 1.79 38.57 2.57
4300 4529 6.108687 TGCCTGGATATCGTCATGATTATTC 58.891 40.000 0.00 0.00 38.57 1.75
4349 4578 4.882427 CAGGAGTCGGTCTACTAATCTTGA 59.118 45.833 0.00 0.00 34.61 3.02
4374 4603 9.011095 TGTATGGAGTAATAGTAGTAGATGCAC 57.989 37.037 0.00 0.00 0.00 4.57
4397 4626 0.596577 GCTGGATAGCGGTCGATGTA 59.403 55.000 0.00 0.00 40.67 2.29
4428 4657 1.851653 ACACCTAGACGGAGGGAGTAT 59.148 52.381 5.42 0.00 41.36 2.12
4431 4660 0.323542 ACACACCTAGACGGAGGGAG 60.324 60.000 5.42 0.78 41.36 4.30
4432 4661 0.994247 TACACACCTAGACGGAGGGA 59.006 55.000 5.42 0.00 41.36 4.20
4433 4662 1.843368 TTACACACCTAGACGGAGGG 58.157 55.000 5.42 0.00 41.36 4.30
4434 4663 3.446161 TGATTTACACACCTAGACGGAGG 59.554 47.826 0.00 0.00 42.89 4.30
4435 4664 4.713824 TGATTTACACACCTAGACGGAG 57.286 45.455 0.00 0.00 36.31 4.63
4436 4665 4.954202 AGATGATTTACACACCTAGACGGA 59.046 41.667 0.00 0.00 36.31 4.69
4437 4666 5.263968 AGATGATTTACACACCTAGACGG 57.736 43.478 0.00 0.00 39.35 4.79
4438 4667 6.414109 CGTAAGATGATTTACACACCTAGACG 59.586 42.308 0.00 0.00 43.02 4.18
4439 4668 7.478322 TCGTAAGATGATTTACACACCTAGAC 58.522 38.462 0.00 0.00 45.01 2.59
4440 4669 7.634671 TCGTAAGATGATTTACACACCTAGA 57.365 36.000 0.00 0.00 45.01 2.43
4459 4688 9.982651 TGTTTTGGGAATATTTGATTTTCGTAA 57.017 25.926 0.00 0.00 0.00 3.18
4460 4689 9.413048 GTGTTTTGGGAATATTTGATTTTCGTA 57.587 29.630 0.00 0.00 0.00 3.43
4461 4690 8.147704 AGTGTTTTGGGAATATTTGATTTTCGT 58.852 29.630 0.00 0.00 0.00 3.85
4462 4691 8.532977 AGTGTTTTGGGAATATTTGATTTTCG 57.467 30.769 0.00 0.00 0.00 3.46
4465 4694 9.942850 CCTAAGTGTTTTGGGAATATTTGATTT 57.057 29.630 0.00 0.00 0.00 2.17
4466 4695 8.040727 GCCTAAGTGTTTTGGGAATATTTGATT 58.959 33.333 0.00 0.00 30.91 2.57
4467 4696 7.555965 GCCTAAGTGTTTTGGGAATATTTGAT 58.444 34.615 0.00 0.00 30.91 2.57
4468 4697 6.349777 CGCCTAAGTGTTTTGGGAATATTTGA 60.350 38.462 0.00 0.00 30.91 2.69
4469 4698 5.804979 CGCCTAAGTGTTTTGGGAATATTTG 59.195 40.000 0.00 0.00 30.91 2.32
4470 4699 5.623596 GCGCCTAAGTGTTTTGGGAATATTT 60.624 40.000 0.00 0.00 30.91 1.40
4471 4700 4.142249 GCGCCTAAGTGTTTTGGGAATATT 60.142 41.667 0.00 0.00 30.91 1.28
4472 4701 3.380320 GCGCCTAAGTGTTTTGGGAATAT 59.620 43.478 0.00 0.00 30.91 1.28
4473 4702 2.750712 GCGCCTAAGTGTTTTGGGAATA 59.249 45.455 0.00 0.00 30.91 1.75
4474 4703 1.544246 GCGCCTAAGTGTTTTGGGAAT 59.456 47.619 0.00 0.00 30.91 3.01
4475 4704 0.955905 GCGCCTAAGTGTTTTGGGAA 59.044 50.000 0.00 0.00 30.91 3.97
4476 4705 1.231958 CGCGCCTAAGTGTTTTGGGA 61.232 55.000 0.00 0.00 30.91 4.37
4477 4706 1.209127 CGCGCCTAAGTGTTTTGGG 59.791 57.895 0.00 0.00 30.91 4.12
4478 4707 1.209127 CCGCGCCTAAGTGTTTTGG 59.791 57.895 0.00 0.00 33.04 3.28
4479 4708 0.385473 CACCGCGCCTAAGTGTTTTG 60.385 55.000 0.00 0.00 0.00 2.44
4480 4709 1.946267 CACCGCGCCTAAGTGTTTT 59.054 52.632 0.00 0.00 0.00 2.43
4481 4710 2.613506 GCACCGCGCCTAAGTGTTT 61.614 57.895 12.83 0.00 33.96 2.83
4482 4711 3.047877 GCACCGCGCCTAAGTGTT 61.048 61.111 12.83 0.00 33.96 3.32
4483 4712 3.605749 ATGCACCGCGCCTAAGTGT 62.606 57.895 12.83 0.00 41.33 3.55
4484 4713 1.087202 TAATGCACCGCGCCTAAGTG 61.087 55.000 0.00 4.02 41.33 3.16
4485 4714 0.391927 TTAATGCACCGCGCCTAAGT 60.392 50.000 0.00 0.00 41.33 2.24
4486 4715 0.730265 TTTAATGCACCGCGCCTAAG 59.270 50.000 0.00 0.00 41.33 2.18
4487 4716 1.384525 ATTTAATGCACCGCGCCTAA 58.615 45.000 0.00 0.00 41.33 2.69
4488 4717 1.332375 GAATTTAATGCACCGCGCCTA 59.668 47.619 0.00 0.00 41.33 3.93
4489 4718 0.100503 GAATTTAATGCACCGCGCCT 59.899 50.000 0.00 0.00 41.33 5.52
4490 4719 0.100503 AGAATTTAATGCACCGCGCC 59.899 50.000 0.00 0.00 41.33 6.53
4491 4720 2.372350 GTAGAATTTAATGCACCGCGC 58.628 47.619 0.00 0.00 42.89 6.86
4492 4721 2.612212 AGGTAGAATTTAATGCACCGCG 59.388 45.455 0.00 0.00 0.00 6.46
4493 4722 3.303132 CGAGGTAGAATTTAATGCACCGC 60.303 47.826 0.00 0.00 0.00 5.68
4494 4723 3.869246 ACGAGGTAGAATTTAATGCACCG 59.131 43.478 0.00 0.00 0.00 4.94
4495 4724 5.813080 AACGAGGTAGAATTTAATGCACC 57.187 39.130 0.00 0.00 0.00 5.01
4496 4725 7.073342 AGAAACGAGGTAGAATTTAATGCAC 57.927 36.000 0.00 0.00 0.00 4.57
4497 4726 7.174253 ACAAGAAACGAGGTAGAATTTAATGCA 59.826 33.333 0.00 0.00 0.00 3.96
4498 4727 7.527457 ACAAGAAACGAGGTAGAATTTAATGC 58.473 34.615 0.00 0.00 0.00 3.56
4499 4728 9.893305 AAACAAGAAACGAGGTAGAATTTAATG 57.107 29.630 0.00 0.00 0.00 1.90
4501 4730 9.333724 AGAAACAAGAAACGAGGTAGAATTTAA 57.666 29.630 0.00 0.00 0.00 1.52
4502 4731 8.897872 AGAAACAAGAAACGAGGTAGAATTTA 57.102 30.769 0.00 0.00 0.00 1.40
4503 4732 7.803279 AGAAACAAGAAACGAGGTAGAATTT 57.197 32.000 0.00 0.00 0.00 1.82
4504 4733 7.497909 TCAAGAAACAAGAAACGAGGTAGAATT 59.502 33.333 0.00 0.00 0.00 2.17
4505 4734 6.990349 TCAAGAAACAAGAAACGAGGTAGAAT 59.010 34.615 0.00 0.00 0.00 2.40
4506 4735 6.257193 GTCAAGAAACAAGAAACGAGGTAGAA 59.743 38.462 0.00 0.00 0.00 2.10
4507 4736 5.751990 GTCAAGAAACAAGAAACGAGGTAGA 59.248 40.000 0.00 0.00 0.00 2.59
4508 4737 5.522460 TGTCAAGAAACAAGAAACGAGGTAG 59.478 40.000 0.00 0.00 0.00 3.18
4509 4738 5.421277 TGTCAAGAAACAAGAAACGAGGTA 58.579 37.500 0.00 0.00 0.00 3.08
4510 4739 4.258543 TGTCAAGAAACAAGAAACGAGGT 58.741 39.130 0.00 0.00 0.00 3.85
4511 4740 4.875544 TGTCAAGAAACAAGAAACGAGG 57.124 40.909 0.00 0.00 0.00 4.63
4512 4741 7.796838 TGATATGTCAAGAAACAAGAAACGAG 58.203 34.615 0.00 0.00 31.81 4.18
4513 4742 7.722795 TGATATGTCAAGAAACAAGAAACGA 57.277 32.000 0.00 0.00 31.81 3.85
4514 4743 7.323656 GGTTGATATGTCAAGAAACAAGAAACG 59.676 37.037 4.98 0.00 44.58 3.60
4515 4744 8.134895 TGGTTGATATGTCAAGAAACAAGAAAC 58.865 33.333 4.98 0.00 44.58 2.78
4516 4745 8.231692 TGGTTGATATGTCAAGAAACAAGAAA 57.768 30.769 4.98 0.00 44.58 2.52
4517 4746 7.815840 TGGTTGATATGTCAAGAAACAAGAA 57.184 32.000 4.98 0.00 44.58 2.52
4518 4747 7.815840 TTGGTTGATATGTCAAGAAACAAGA 57.184 32.000 4.98 0.00 44.58 3.02
4521 4750 9.513906 TCTTATTGGTTGATATGTCAAGAAACA 57.486 29.630 4.98 0.63 44.58 2.83
4522 4751 9.994432 CTCTTATTGGTTGATATGTCAAGAAAC 57.006 33.333 4.98 0.00 44.58 2.78
4523 4752 9.958180 TCTCTTATTGGTTGATATGTCAAGAAA 57.042 29.630 4.98 3.84 44.58 2.52


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

AutoCloner maintained by Alex Coulton.