Multiple sequence alignment - TraesCS2D01G015900

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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 TraesCS2D01G015900 chr2D 100.000 3236 0 0 1 3236 7694944 7698179 0.000000e+00 5976
1 TraesCS2D01G015900 chr2D 94.683 583 29 2 88 668 479171950 479171368 0.000000e+00 904
2 TraesCS2D01G015900 chr2D 85.035 568 83 2 91 657 339369740 339369174 7.780000e-161 577
3 TraesCS2D01G015900 chr2D 83.333 570 91 4 92 660 640278549 640279115 1.030000e-144 523
4 TraesCS2D01G015900 chr2D 96.907 97 2 1 1 96 391486265 391486169 9.290000e-36 161
5 TraesCS2D01G015900 chr2B 91.443 2571 169 27 666 3220 4131161 4133696 0.000000e+00 3482
6 TraesCS2D01G015900 chr2B 91.262 2575 170 31 666 3220 3838808 3841347 0.000000e+00 3458
7 TraesCS2D01G015900 chr2B 93.310 583 37 2 88 668 109303961 109304543 0.000000e+00 859
8 TraesCS2D01G015900 chrUn 95.325 1754 67 6 666 2407 359562769 359564519 0.000000e+00 2771
9 TraesCS2D01G015900 chrUn 78.462 585 105 15 1064 1630 220055072 220055653 2.370000e-96 363
10 TraesCS2D01G015900 chrUn 97.849 93 2 0 1 93 475285991 475286083 9.290000e-36 161
11 TraesCS2D01G015900 chr4B 91.409 582 46 3 88 668 18716164 18716742 0.000000e+00 795
12 TraesCS2D01G015900 chr4A 86.860 586 52 11 88 671 677976971 677977533 1.640000e-177 632
13 TraesCS2D01G015900 chr4A 76.718 786 145 27 1064 1815 707478196 707477415 1.400000e-108 403
14 TraesCS2D01G015900 chr4A 79.893 562 94 15 1064 1608 668852911 668853470 8.410000e-106 394
15 TraesCS2D01G015900 chr4A 78.938 584 104 16 1064 1630 705889506 705890087 2.360000e-101 379
16 TraesCS2D01G015900 chr4A 79.181 562 98 14 1064 1608 707177889 707178448 3.940000e-99 372
17 TraesCS2D01G015900 chr4A 79.181 562 98 14 1064 1608 707201414 707201973 3.940000e-99 372
18 TraesCS2D01G015900 chr4A 78.632 585 104 15 1064 1630 706095001 706095582 5.100000e-98 368
19 TraesCS2D01G015900 chr2A 85.026 581 85 2 91 669 451539911 451539331 1.000000e-164 590
20 TraesCS2D01G015900 chr2A 83.141 433 70 3 91 521 648528704 648528273 3.030000e-105 392
21 TraesCS2D01G015900 chr1B 92.593 324 12 5 347 668 410302906 410302593 3.810000e-124 455
22 TraesCS2D01G015900 chr7D 76.494 770 148 20 1076 1815 53793152 53792386 3.920000e-104 388
23 TraesCS2D01G015900 chr7D 79.074 583 105 13 1064 1630 24144935 24145516 5.060000e-103 385
24 TraesCS2D01G015900 chr7D 95.960 99 2 2 1 98 60442342 60442245 3.340000e-35 159
25 TraesCS2D01G015900 chr7D 95.918 98 3 1 2 99 589019718 589019814 1.200000e-34 158
26 TraesCS2D01G015900 chr1D 98.913 92 0 1 1 92 408190711 408190801 2.580000e-36 163
27 TraesCS2D01G015900 chr3A 96.875 96 3 0 1 96 11692848 11692753 9.290000e-36 161
28 TraesCS2D01G015900 chr3A 96.875 96 3 0 1 96 11718183 11718088 9.290000e-36 161
29 TraesCS2D01G015900 chr5D 96.000 100 1 3 1 100 27025580 27025676 3.340000e-35 159
30 TraesCS2D01G015900 chr5D 95.000 100 4 1 1 99 372477785 372477884 4.320000e-34 156


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 TraesCS2D01G015900 chr2D 7694944 7698179 3235 False 5976 5976 100.000 1 3236 1 chr2D.!!$F1 3235
1 TraesCS2D01G015900 chr2D 479171368 479171950 582 True 904 904 94.683 88 668 1 chr2D.!!$R3 580
2 TraesCS2D01G015900 chr2D 339369174 339369740 566 True 577 577 85.035 91 657 1 chr2D.!!$R1 566
3 TraesCS2D01G015900 chr2D 640278549 640279115 566 False 523 523 83.333 92 660 1 chr2D.!!$F2 568
4 TraesCS2D01G015900 chr2B 4131161 4133696 2535 False 3482 3482 91.443 666 3220 1 chr2B.!!$F2 2554
5 TraesCS2D01G015900 chr2B 3838808 3841347 2539 False 3458 3458 91.262 666 3220 1 chr2B.!!$F1 2554
6 TraesCS2D01G015900 chr2B 109303961 109304543 582 False 859 859 93.310 88 668 1 chr2B.!!$F3 580
7 TraesCS2D01G015900 chrUn 359562769 359564519 1750 False 2771 2771 95.325 666 2407 1 chrUn.!!$F2 1741
8 TraesCS2D01G015900 chrUn 220055072 220055653 581 False 363 363 78.462 1064 1630 1 chrUn.!!$F1 566
9 TraesCS2D01G015900 chr4B 18716164 18716742 578 False 795 795 91.409 88 668 1 chr4B.!!$F1 580
10 TraesCS2D01G015900 chr4A 677976971 677977533 562 False 632 632 86.860 88 671 1 chr4A.!!$F2 583
11 TraesCS2D01G015900 chr4A 707477415 707478196 781 True 403 403 76.718 1064 1815 1 chr4A.!!$R1 751
12 TraesCS2D01G015900 chr4A 668852911 668853470 559 False 394 394 79.893 1064 1608 1 chr4A.!!$F1 544
13 TraesCS2D01G015900 chr4A 705889506 705890087 581 False 379 379 78.938 1064 1630 1 chr4A.!!$F3 566
14 TraesCS2D01G015900 chr4A 707177889 707178448 559 False 372 372 79.181 1064 1608 1 chr4A.!!$F5 544
15 TraesCS2D01G015900 chr4A 707201414 707201973 559 False 372 372 79.181 1064 1608 1 chr4A.!!$F6 544
16 TraesCS2D01G015900 chr4A 706095001 706095582 581 False 368 368 78.632 1064 1630 1 chr4A.!!$F4 566
17 TraesCS2D01G015900 chr2A 451539331 451539911 580 True 590 590 85.026 91 669 1 chr2A.!!$R1 578
18 TraesCS2D01G015900 chr7D 53792386 53793152 766 True 388 388 76.494 1076 1815 1 chr7D.!!$R1 739
19 TraesCS2D01G015900 chr7D 24144935 24145516 581 False 385 385 79.074 1064 1630 1 chr7D.!!$F1 566

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
65 66 0.034863 GGCCTTATGAACCGGGACAA 60.035 55.0 6.32 0.00 0.00 3.18 F
231 233 0.174845 CAAATCTACGAGCGTGGGGA 59.825 55.0 5.69 2.19 0.00 4.81 F
1608 1662 0.396139 TGCATCCATTCTTCTGGGGC 60.396 55.0 0.00 0.00 36.89 5.80 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1906 1975 0.249489 GCACGTAGGGGAGCATACAG 60.249 60.000 0.0 0.0 0.00 2.74 R
2156 2225 2.143925 AGGTACGAGCTTGCTTCAAAC 58.856 47.619 0.0 0.0 0.00 2.93 R
2786 2859 0.036010 ACTCCACAAGAATGGCGAGG 60.036 55.000 0.0 0.0 39.85 4.63 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
23 24 5.354767 CATTAGTAACGACCCTTTAGTCCC 58.645 45.833 0.00 0.00 32.91 4.46
24 25 1.821136 AGTAACGACCCTTTAGTCCCG 59.179 52.381 0.00 0.00 32.91 5.14
25 26 1.134995 GTAACGACCCTTTAGTCCCGG 60.135 57.143 0.00 0.00 32.91 5.73
26 27 0.833409 AACGACCCTTTAGTCCCGGT 60.833 55.000 0.00 0.00 32.91 5.28
27 28 0.833409 ACGACCCTTTAGTCCCGGTT 60.833 55.000 0.00 0.00 32.91 4.44
28 29 0.108472 CGACCCTTTAGTCCCGGTTC 60.108 60.000 0.00 0.00 32.91 3.62
29 30 0.251354 GACCCTTTAGTCCCGGTTCC 59.749 60.000 0.00 0.00 0.00 3.62
30 31 1.203441 ACCCTTTAGTCCCGGTTCCC 61.203 60.000 0.00 0.00 0.00 3.97
31 32 1.605992 CCTTTAGTCCCGGTTCCCC 59.394 63.158 0.00 0.00 0.00 4.81
32 33 1.202769 CCTTTAGTCCCGGTTCCCCA 61.203 60.000 0.00 0.00 0.00 4.96
33 34 0.694196 CTTTAGTCCCGGTTCCCCAA 59.306 55.000 0.00 0.00 0.00 4.12
34 35 0.401356 TTTAGTCCCGGTTCCCCAAC 59.599 55.000 0.00 0.00 0.00 3.77
47 48 2.272146 CCAACCGGGACAGATGGG 59.728 66.667 6.32 0.00 40.01 4.00
48 49 2.438434 CAACCGGGACAGATGGGC 60.438 66.667 6.32 0.00 0.00 5.36
49 50 3.728373 AACCGGGACAGATGGGCC 61.728 66.667 6.32 0.00 0.00 5.80
50 51 4.741239 ACCGGGACAGATGGGCCT 62.741 66.667 6.32 0.00 0.00 5.19
51 52 3.411517 CCGGGACAGATGGGCCTT 61.412 66.667 4.53 0.00 0.00 4.35
52 53 2.070039 CCGGGACAGATGGGCCTTA 61.070 63.158 4.53 0.00 0.00 2.69
53 54 1.418908 CCGGGACAGATGGGCCTTAT 61.419 60.000 4.53 0.00 0.00 1.73
54 55 0.250467 CGGGACAGATGGGCCTTATG 60.250 60.000 12.06 12.06 0.00 1.90
55 56 1.140312 GGGACAGATGGGCCTTATGA 58.860 55.000 19.57 0.00 0.00 2.15
56 57 1.494721 GGGACAGATGGGCCTTATGAA 59.505 52.381 19.57 0.00 0.00 2.57
57 58 2.576615 GGACAGATGGGCCTTATGAAC 58.423 52.381 19.57 12.43 0.00 3.18
58 59 2.576615 GACAGATGGGCCTTATGAACC 58.423 52.381 19.57 5.77 0.00 3.62
59 60 1.134098 ACAGATGGGCCTTATGAACCG 60.134 52.381 19.57 0.00 0.00 4.44
60 61 0.474184 AGATGGGCCTTATGAACCGG 59.526 55.000 4.53 0.00 0.00 5.28
61 62 0.537371 GATGGGCCTTATGAACCGGG 60.537 60.000 6.32 0.00 0.00 5.73
62 63 0.991355 ATGGGCCTTATGAACCGGGA 60.991 55.000 6.32 0.00 0.00 5.14
63 64 1.153025 GGGCCTTATGAACCGGGAC 60.153 63.158 6.32 0.00 0.00 4.46
64 65 1.605453 GGCCTTATGAACCGGGACA 59.395 57.895 6.32 5.75 0.00 4.02
65 66 0.034863 GGCCTTATGAACCGGGACAA 60.035 55.000 6.32 0.00 0.00 3.18
66 67 1.614850 GGCCTTATGAACCGGGACAAA 60.615 52.381 6.32 2.62 0.00 2.83
67 68 2.375146 GCCTTATGAACCGGGACAAAT 58.625 47.619 6.32 0.00 0.00 2.32
68 69 2.099098 GCCTTATGAACCGGGACAAATG 59.901 50.000 6.32 0.20 0.00 2.32
69 70 2.687935 CCTTATGAACCGGGACAAATGG 59.312 50.000 6.32 5.49 0.00 3.16
70 71 1.757682 TATGAACCGGGACAAATGGC 58.242 50.000 6.32 0.00 0.00 4.40
71 72 0.970427 ATGAACCGGGACAAATGGCC 60.970 55.000 6.32 0.00 44.61 5.36
81 82 4.188247 GGACAAATGGCCCTTTTTCTAC 57.812 45.455 16.22 1.38 37.19 2.59
82 83 3.832490 GGACAAATGGCCCTTTTTCTACT 59.168 43.478 16.22 0.00 37.19 2.57
83 84 5.014202 GGACAAATGGCCCTTTTTCTACTA 58.986 41.667 16.22 0.00 37.19 1.82
84 85 5.125578 GGACAAATGGCCCTTTTTCTACTAG 59.874 44.000 16.22 1.81 37.19 2.57
85 86 5.641155 ACAAATGGCCCTTTTTCTACTAGT 58.359 37.500 2.87 0.00 0.00 2.57
86 87 5.476945 ACAAATGGCCCTTTTTCTACTAGTG 59.523 40.000 5.39 0.00 0.00 2.74
117 118 4.542662 CAAGTGGTGCAAGATATACAGC 57.457 45.455 0.00 0.00 0.00 4.40
148 150 2.118403 TTGGAGAGGGAGGTCAGTTT 57.882 50.000 0.00 0.00 0.00 2.66
153 155 0.615850 GAGGGAGGTCAGTTTCTGGG 59.384 60.000 0.00 0.00 31.51 4.45
219 221 6.672593 AGTTTTATGGAGGCCATCAAATCTA 58.327 36.000 5.01 0.00 40.74 1.98
231 233 0.174845 CAAATCTACGAGCGTGGGGA 59.825 55.000 5.69 2.19 0.00 4.81
242 244 1.988015 CGTGGGGATGGTGGTTAGT 59.012 57.895 0.00 0.00 0.00 2.24
361 386 8.771766 CATGTATATTGGAATCACTCTTGACAG 58.228 37.037 0.00 0.00 33.38 3.51
392 418 6.723298 TTTTGGAAACTGATTGCTCCTTTA 57.277 33.333 0.00 0.00 0.00 1.85
434 460 3.580458 AGAGTGTGTTGATAGGTCAAGCT 59.420 43.478 0.00 0.00 44.58 3.74
523 549 8.463055 AGATTAATAGGAGGGCAAATATGGTA 57.537 34.615 0.00 0.00 0.00 3.25
696 723 1.756538 ACTTTTGGGCTGGAACACTTG 59.243 47.619 0.00 0.00 0.00 3.16
704 738 1.134946 GCTGGAACACTTGCAACAACT 59.865 47.619 0.00 0.00 0.00 3.16
776 810 1.275573 AGACCAGCGTTTAAGTCCTCC 59.724 52.381 0.00 0.00 0.00 4.30
792 826 2.832129 TCCTCCAGCACGAAATAGAGTT 59.168 45.455 0.00 0.00 0.00 3.01
794 828 4.003648 CCTCCAGCACGAAATAGAGTTTT 58.996 43.478 0.00 0.00 0.00 2.43
799 833 6.206634 TCCAGCACGAAATAGAGTTTTCAATT 59.793 34.615 0.00 0.00 35.73 2.32
800 834 7.389330 TCCAGCACGAAATAGAGTTTTCAATTA 59.611 33.333 0.00 0.00 35.73 1.40
801 835 8.184192 CCAGCACGAAATAGAGTTTTCAATTAT 58.816 33.333 0.00 0.00 35.73 1.28
837 871 8.216453 GCAGTCTTTGTACATTAATTGCAAAAG 58.784 33.333 1.71 0.00 0.00 2.27
838 872 8.702438 CAGTCTTTGTACATTAATTGCAAAAGG 58.298 33.333 1.71 0.00 0.00 3.11
846 881 6.691508 ACATTAATTGCAAAAGGGAAGTCTC 58.308 36.000 1.71 0.00 0.00 3.36
908 943 9.048446 TCCAGTAAAACGCTATAAAATCCATAC 57.952 33.333 0.00 0.00 0.00 2.39
927 962 1.238439 CAAGAAAGCCTCTGCCGAAA 58.762 50.000 0.00 0.00 38.69 3.46
931 966 1.131315 GAAAGCCTCTGCCGAAACATC 59.869 52.381 0.00 0.00 38.69 3.06
938 973 1.204704 TCTGCCGAAACATCATCGAGT 59.795 47.619 0.00 0.00 42.76 4.18
946 981 2.568696 ACATCATCGAGTTCTGACGG 57.431 50.000 0.00 0.00 0.00 4.79
972 1007 8.654215 GCTTTTATTAGCTTGTACTCGTAGTTT 58.346 33.333 0.00 0.00 38.15 2.66
976 1011 9.793252 TTATTAGCTTGTACTCGTAGTTTAAGG 57.207 33.333 0.00 0.00 0.00 2.69
993 1028 6.706270 AGTTTAAGGGCATCAACATATCGTAG 59.294 38.462 0.00 0.00 0.00 3.51
996 1031 2.996621 GGGCATCAACATATCGTAGCTC 59.003 50.000 0.00 0.00 0.00 4.09
997 1032 3.554960 GGGCATCAACATATCGTAGCTCA 60.555 47.826 0.00 0.00 0.00 4.26
1032 1071 3.780850 ACAAGACTTACCCCTCCCATAAG 59.219 47.826 0.00 0.00 33.08 1.73
1056 1095 1.292223 CAACGGTGAGGTGGACGAT 59.708 57.895 0.00 0.00 32.78 3.73
1089 1128 4.821805 CCATTAATCCGCAAGTACAAGGAT 59.178 41.667 0.00 0.65 44.64 3.24
1220 1262 2.032681 GCGCCTGTTCCTTCCTGT 59.967 61.111 0.00 0.00 0.00 4.00
1281 1329 0.476771 ACGTCCATGGTGGTTCCTTT 59.523 50.000 12.58 0.00 39.03 3.11
1488 1536 4.082523 GCAGACCCTAGCCGCACA 62.083 66.667 0.00 0.00 0.00 4.57
1539 1587 2.650196 GTGTACCACACGGCCGTA 59.350 61.111 33.70 13.03 39.53 4.02
1608 1662 0.396139 TGCATCCATTCTTCTGGGGC 60.396 55.000 0.00 0.00 36.89 5.80
1686 1755 1.453928 GGTGGATAAGCTGTGGCCC 60.454 63.158 0.00 0.00 39.73 5.80
1760 1829 1.482278 GAGGAGATCGCGTTGCTAAG 58.518 55.000 5.77 0.00 0.00 2.18
1899 1968 1.616628 GGAGGGTGAGGACCATGGT 60.617 63.158 19.89 19.89 45.25 3.55
1905 1974 1.005924 GGTGAGGACCATGGTTTCCAT 59.994 52.381 20.85 3.45 46.37 3.41
1906 1975 2.369394 GTGAGGACCATGGTTTCCATC 58.631 52.381 20.85 14.01 43.15 3.51
1911 1980 3.788142 AGGACCATGGTTTCCATCTGTAT 59.212 43.478 20.85 0.00 43.15 2.29
1914 1983 3.053395 ACCATGGTTTCCATCTGTATGCT 60.053 43.478 13.00 0.00 43.15 3.79
2156 2225 0.379669 ACGACGAGCTATGGGTTACG 59.620 55.000 0.00 0.00 0.00 3.18
2172 2241 1.860676 TACGTTTGAAGCAAGCTCGT 58.139 45.000 9.98 9.98 34.17 4.18
2216 2285 2.093783 CACCAACTTCGGTAAGATTCGC 59.906 50.000 0.00 0.00 37.07 4.70
2237 2306 3.860536 GCGATGAGGAACTGTTTCTAGAC 59.139 47.826 0.25 0.00 41.55 2.59
2247 2316 2.637872 CTGTTTCTAGACCCAGTTCCCA 59.362 50.000 8.92 0.00 0.00 4.37
2309 2378 9.826574 ATGTATTCTTTTCATTATTGCTTGCAT 57.173 25.926 0.00 0.00 0.00 3.96
2322 2391 3.963665 TGCTTGCATGTTGAGTTTGTAC 58.036 40.909 1.14 0.00 0.00 2.90
2327 2396 3.242576 TGCATGTTGAGTTTGTACACGTG 60.243 43.478 15.48 15.48 0.00 4.49
2346 2415 6.071560 ACACGTGAAGGTTATGATCACTTCTA 60.072 38.462 25.01 7.92 40.95 2.10
2356 2425 5.906113 ATGATCACTTCTAGAGTCGTGTT 57.094 39.130 0.00 9.21 36.10 3.32
2421 2490 1.369209 CAAGTTCACGTTGCGGCTG 60.369 57.895 0.00 0.00 0.00 4.85
2425 2494 0.942410 GTTCACGTTGCGGCTGAGTA 60.942 55.000 0.00 0.00 0.00 2.59
2433 2502 0.250295 TGCGGCTGAGTAGTTGCTTT 60.250 50.000 0.00 0.00 0.00 3.51
2475 2544 4.760047 ATCCACCGCGTGCAGGAC 62.760 66.667 11.29 0.58 32.04 3.85
2515 2584 0.716108 CGATCACGGTGAGCTTTGTC 59.284 55.000 22.33 10.34 29.10 3.18
2529 2598 2.880890 GCTTTGTCTGTCTGGTTGTCAT 59.119 45.455 0.00 0.00 0.00 3.06
2543 2612 8.230486 GTCTGGTTGTCATGTGTTAGAATAAAG 58.770 37.037 0.00 0.00 0.00 1.85
2544 2613 7.390440 TCTGGTTGTCATGTGTTAGAATAAAGG 59.610 37.037 0.00 0.00 0.00 3.11
2545 2614 6.432783 TGGTTGTCATGTGTTAGAATAAAGGG 59.567 38.462 0.00 0.00 0.00 3.95
2547 2616 7.175990 GGTTGTCATGTGTTAGAATAAAGGGAA 59.824 37.037 0.00 0.00 0.00 3.97
2548 2617 7.681939 TGTCATGTGTTAGAATAAAGGGAAC 57.318 36.000 0.00 0.00 0.00 3.62
2549 2618 7.227873 TGTCATGTGTTAGAATAAAGGGAACA 58.772 34.615 0.00 0.00 0.00 3.18
2553 2622 9.410556 CATGTGTTAGAATAAAGGGAACAAAAG 57.589 33.333 0.00 0.00 32.20 2.27
2564 2633 5.854010 AGGGAACAAAAGGAAAGAAAGAC 57.146 39.130 0.00 0.00 0.00 3.01
2590 2659 0.027586 GATGCAATTACGGCGTCACC 59.972 55.000 19.21 0.00 44.67 4.02
2609 2678 6.754675 CGTCACCAAATTACCTCTTTTGTTTT 59.245 34.615 0.00 0.00 32.23 2.43
2613 2682 8.603181 CACCAAATTACCTCTTTTGTTTTTCTG 58.397 33.333 0.00 0.00 32.23 3.02
2617 2686 9.936759 AAATTACCTCTTTTGTTTTTCTGAACA 57.063 25.926 0.00 0.00 37.73 3.18
2618 2687 9.586435 AATTACCTCTTTTGTTTTTCTGAACAG 57.414 29.630 0.00 0.00 40.33 3.16
2619 2688 6.590234 ACCTCTTTTGTTTTTCTGAACAGT 57.410 33.333 1.73 0.00 40.33 3.55
2620 2689 6.993079 ACCTCTTTTGTTTTTCTGAACAGTT 58.007 32.000 1.73 0.00 40.33 3.16
2622 2691 7.931407 ACCTCTTTTGTTTTTCTGAACAGTTTT 59.069 29.630 1.73 0.00 40.33 2.43
2623 2692 8.223100 CCTCTTTTGTTTTTCTGAACAGTTTTG 58.777 33.333 1.73 0.00 40.33 2.44
2624 2693 7.571892 TCTTTTGTTTTTCTGAACAGTTTTGC 58.428 30.769 1.73 0.00 40.33 3.68
2625 2694 5.854431 TTGTTTTTCTGAACAGTTTTGCC 57.146 34.783 1.73 0.00 40.33 4.52
2626 2695 4.887748 TGTTTTTCTGAACAGTTTTGCCA 58.112 34.783 1.73 0.00 34.77 4.92
2627 2696 5.300752 TGTTTTTCTGAACAGTTTTGCCAA 58.699 33.333 1.73 0.00 34.77 4.52
2628 2697 5.760253 TGTTTTTCTGAACAGTTTTGCCAAA 59.240 32.000 1.73 0.00 34.77 3.28
2629 2698 6.073331 TGTTTTTCTGAACAGTTTTGCCAAAG 60.073 34.615 1.73 0.00 34.77 2.77
2630 2699 3.163630 TCTGAACAGTTTTGCCAAAGC 57.836 42.857 0.00 0.00 40.48 3.51
2643 2712 4.707030 TGCCAAAGCAGATTTAGATGTG 57.293 40.909 0.00 0.00 46.52 3.21
2644 2713 4.081406 TGCCAAAGCAGATTTAGATGTGT 58.919 39.130 0.00 0.00 46.52 3.72
2647 2716 4.096984 CCAAAGCAGATTTAGATGTGTCCC 59.903 45.833 0.00 0.00 0.00 4.46
2650 2719 5.121380 AGCAGATTTAGATGTGTCCCAAT 57.879 39.130 0.00 0.00 0.00 3.16
2658 2727 7.658525 TTTAGATGTGTCCCAATTATTGCAT 57.341 32.000 0.00 0.00 0.00 3.96
2663 2732 8.385491 AGATGTGTCCCAATTATTGCATATCTA 58.615 33.333 15.66 0.00 34.61 1.98
2668 2737 8.439971 TGTCCCAATTATTGCATATCTAAGTCT 58.560 33.333 0.00 0.00 0.00 3.24
2675 2744 9.964354 ATTATTGCATATCTAAGTCTTATGCCA 57.036 29.630 13.15 5.33 44.79 4.92
2694 2763 4.218200 TGCCAATTGATTTCACGTGAAGAT 59.782 37.500 28.21 23.06 35.21 2.40
2695 2764 5.163513 GCCAATTGATTTCACGTGAAGATT 58.836 37.500 28.21 21.97 35.21 2.40
2711 2780 4.681025 TGAAGATTCGTGCAAGCATTTTTC 59.319 37.500 0.00 0.00 0.00 2.29
2722 2795 6.479990 GTGCAAGCATTTTTCTAAAACTCCTT 59.520 34.615 0.00 0.00 0.00 3.36
2723 2796 6.701400 TGCAAGCATTTTTCTAAAACTCCTTC 59.299 34.615 0.00 0.00 0.00 3.46
2725 2798 7.436933 CAAGCATTTTTCTAAAACTCCTTCCT 58.563 34.615 0.00 0.00 0.00 3.36
2730 2803 5.924769 TTTCTAAAACTCCTTCCTTCCCT 57.075 39.130 0.00 0.00 0.00 4.20
2731 2804 4.910458 TCTAAAACTCCTTCCTTCCCTG 57.090 45.455 0.00 0.00 0.00 4.45
2746 2819 1.568597 TCCCTGGGGAATTACCATGTG 59.431 52.381 14.00 0.00 42.05 3.21
2747 2820 1.287739 CCCTGGGGAATTACCATGTGT 59.712 52.381 9.50 0.00 41.20 3.72
2748 2821 2.512056 CCCTGGGGAATTACCATGTGTA 59.488 50.000 9.50 0.00 41.20 2.90
2753 2826 4.202377 TGGGGAATTACCATGTGTATACCG 60.202 45.833 9.50 0.00 41.20 4.02
2758 2831 0.179094 ACCATGTGTATACCGCCGTG 60.179 55.000 0.00 0.60 0.00 4.94
2764 2837 1.153509 GTATACCGCCGTGTGCCTT 60.154 57.895 0.00 0.00 36.24 4.35
2767 2840 2.306255 ATACCGCCGTGTGCCTTAGG 62.306 60.000 0.00 0.00 36.24 2.69
2780 2853 1.960417 CCTTAGGGCAGCTAGCTTTC 58.040 55.000 16.46 9.90 44.79 2.62
2781 2854 1.475930 CCTTAGGGCAGCTAGCTTTCC 60.476 57.143 16.46 18.78 44.79 3.13
2782 2855 0.546598 TTAGGGCAGCTAGCTTTCCC 59.453 55.000 31.20 31.20 44.79 3.97
2783 2856 1.345715 TAGGGCAGCTAGCTTTCCCC 61.346 60.000 33.07 29.94 44.79 4.81
2784 2857 2.684499 GGGCAGCTAGCTTTCCCCT 61.684 63.158 29.44 2.83 44.79 4.79
2785 2858 1.153066 GGCAGCTAGCTTTCCCCTC 60.153 63.158 16.46 0.00 44.79 4.30
2786 2859 1.153066 GCAGCTAGCTTTCCCCTCC 60.153 63.158 16.46 0.00 41.15 4.30
2787 2860 1.529309 CAGCTAGCTTTCCCCTCCC 59.471 63.158 16.46 0.00 0.00 4.30
2788 2861 0.985490 CAGCTAGCTTTCCCCTCCCT 60.985 60.000 16.46 0.00 0.00 4.20
2789 2862 0.692756 AGCTAGCTTTCCCCTCCCTC 60.693 60.000 12.68 0.00 0.00 4.30
2790 2863 2.034048 GCTAGCTTTCCCCTCCCTCG 62.034 65.000 7.70 0.00 0.00 4.63
2791 2864 2.034048 CTAGCTTTCCCCTCCCTCGC 62.034 65.000 0.00 0.00 0.00 5.03
2792 2865 4.491409 GCTTTCCCCTCCCTCGCC 62.491 72.222 0.00 0.00 0.00 5.54
2793 2866 3.009115 CTTTCCCCTCCCTCGCCA 61.009 66.667 0.00 0.00 0.00 5.69
2794 2867 2.286121 TTTCCCCTCCCTCGCCAT 60.286 61.111 0.00 0.00 0.00 4.40
2795 2868 1.926426 CTTTCCCCTCCCTCGCCATT 61.926 60.000 0.00 0.00 0.00 3.16
2796 2869 1.921869 TTTCCCCTCCCTCGCCATTC 61.922 60.000 0.00 0.00 0.00 2.67
2797 2870 2.770048 CCCCTCCCTCGCCATTCT 60.770 66.667 0.00 0.00 0.00 2.40
2824 2897 1.332375 GTTTGACTTGTTGCAGCCGTA 59.668 47.619 0.00 0.00 0.00 4.02
2843 2916 3.364441 GTCTTGCCATGTGCGCCA 61.364 61.111 4.18 2.31 45.60 5.69
2851 2924 3.437795 ATGTGCGCCAGCTCTTGC 61.438 61.111 4.18 0.00 45.42 4.01
2857 2930 2.034687 GCCAGCTCTTGCCCAAGA 59.965 61.111 10.07 10.07 44.47 3.02
2858 2931 2.338785 GCCAGCTCTTGCCCAAGAC 61.339 63.158 6.62 4.98 42.06 3.01
2867 2940 0.322456 TTGCCCAAGACCGAGGATTG 60.322 55.000 0.00 0.76 0.00 2.67
2870 2943 0.462759 CCCAAGACCGAGGATTGCTC 60.463 60.000 0.00 0.00 0.00 4.26
2890 2963 1.685765 TGCACGTATCCTCTGGGCT 60.686 57.895 0.00 0.00 0.00 5.19
2897 2970 2.238319 TATCCTCTGGGCTGGTCGGT 62.238 60.000 0.00 0.00 0.00 4.69
2905 2978 0.826256 GGGCTGGTCGGTTCCTTTTT 60.826 55.000 0.00 0.00 0.00 1.94
2913 2986 1.116308 CGGTTCCTTTTTGGGTGGTT 58.884 50.000 0.00 0.00 36.20 3.67
2914 2987 1.483004 CGGTTCCTTTTTGGGTGGTTT 59.517 47.619 0.00 0.00 36.20 3.27
2920 2993 3.052793 TCCTTTTTGGGTGGTTTAGTGGA 60.053 43.478 0.00 0.00 36.20 4.02
2932 3005 3.371285 GGTTTAGTGGATCTTCGTTGCTC 59.629 47.826 0.00 0.00 0.00 4.26
2935 3008 2.898705 AGTGGATCTTCGTTGCTCATC 58.101 47.619 0.00 0.00 0.00 2.92
2938 3011 2.208431 GGATCTTCGTTGCTCATCCTG 58.792 52.381 0.00 0.00 31.78 3.86
2943 3016 3.447229 TCTTCGTTGCTCATCCTGATGTA 59.553 43.478 7.00 0.00 39.72 2.29
2945 3018 2.159099 TCGTTGCTCATCCTGATGTACC 60.159 50.000 7.00 0.00 39.72 3.34
2948 3021 0.104855 GCTCATCCTGATGTACCGCA 59.895 55.000 7.00 0.00 39.72 5.69
2957 3030 1.828595 TGATGTACCGCATGTGGTAGT 59.171 47.619 33.35 25.34 44.92 2.73
2965 3038 2.552315 CCGCATGTGGTAGTCTTTGTTT 59.448 45.455 17.59 0.00 0.00 2.83
2979 3052 1.388547 TTGTTTGCAGAGTGGTGGTC 58.611 50.000 0.00 0.00 0.00 4.02
2984 3057 0.837691 TGCAGAGTGGTGGTCCATCT 60.838 55.000 3.19 0.00 46.20 2.90
2989 3062 1.482593 GAGTGGTGGTCCATCTAGGTG 59.517 57.143 3.19 0.00 46.20 4.00
2994 3067 2.304761 GGTGGTCCATCTAGGTGTTTCA 59.695 50.000 1.52 0.00 39.02 2.69
3033 3106 3.689649 GTGGTGGTAGGTTCTTGCTATTG 59.310 47.826 0.00 0.00 0.00 1.90
3046 3119 4.218635 TCTTGCTATTGTCTCTTCGTGAGT 59.781 41.667 7.74 0.00 43.13 3.41
3049 3122 4.923871 TGCTATTGTCTCTTCGTGAGTTTC 59.076 41.667 7.74 2.84 43.13 2.78
3050 3123 4.923871 GCTATTGTCTCTTCGTGAGTTTCA 59.076 41.667 7.74 4.70 43.13 2.69
3051 3124 5.164041 GCTATTGTCTCTTCGTGAGTTTCAC 60.164 44.000 0.00 0.00 43.65 3.18
3068 3144 2.975266 TCACAAACGTGTAGTTGTGGT 58.025 42.857 23.55 0.00 43.37 4.16
3079 3155 0.751643 AGTTGTGGTTGTGGCACTCC 60.752 55.000 19.83 19.86 0.00 3.85
3080 3156 0.751643 GTTGTGGTTGTGGCACTCCT 60.752 55.000 24.27 0.00 0.00 3.69
3106 3182 2.617274 GCCCTGCACGACCTTTGTC 61.617 63.158 0.00 0.00 38.18 3.18
3121 3197 1.225855 TTGTCGGTGCTGATGACAAC 58.774 50.000 3.12 0.00 44.97 3.32
3150 3226 1.235724 GGACGTTGTTTTCCTCCTGG 58.764 55.000 0.00 0.00 0.00 4.45
3155 3231 0.930726 TTGTTTTCCTCCTGGGTGGT 59.069 50.000 7.49 0.00 37.07 4.16
3156 3232 0.184933 TGTTTTCCTCCTGGGTGGTG 59.815 55.000 7.49 0.00 37.07 4.17
3164 3240 1.301716 CCTGGGTGGTGTTGTCGAG 60.302 63.158 0.00 0.00 0.00 4.04
3165 3241 1.445942 CTGGGTGGTGTTGTCGAGT 59.554 57.895 0.00 0.00 0.00 4.18
3166 3242 0.179056 CTGGGTGGTGTTGTCGAGTT 60.179 55.000 0.00 0.00 0.00 3.01
3173 3249 1.429463 GTGTTGTCGAGTTGCCCTAG 58.571 55.000 0.00 0.00 0.00 3.02
3178 3254 0.108756 GTCGAGTTGCCCTAGTCCAC 60.109 60.000 0.00 0.00 0.00 4.02
3180 3256 1.602771 GAGTTGCCCTAGTCCACCC 59.397 63.158 0.00 0.00 0.00 4.61
3193 3269 2.735772 CCACCCTCATCCCTCGTGG 61.736 68.421 0.00 0.00 38.19 4.94
3195 3271 1.229529 ACCCTCATCCCTCGTGGTT 60.230 57.895 2.33 0.00 34.77 3.67
3203 3279 0.112606 TCCCTCGTGGTTCAGTCTCT 59.887 55.000 2.33 0.00 34.77 3.10
3204 3280 0.969894 CCCTCGTGGTTCAGTCTCTT 59.030 55.000 2.33 0.00 0.00 2.85
3207 3283 2.608261 CCTCGTGGTTCAGTCTCTTGTC 60.608 54.545 0.00 0.00 0.00 3.18
3215 3291 3.107642 TCAGTCTCTTGTCGAAAACCC 57.892 47.619 0.00 0.00 0.00 4.11
3220 3296 3.680458 GTCTCTTGTCGAAAACCCAGATC 59.320 47.826 0.00 0.00 0.00 2.75
3221 3297 3.003480 CTCTTGTCGAAAACCCAGATCC 58.997 50.000 0.00 0.00 0.00 3.36
3222 3298 1.732259 CTTGTCGAAAACCCAGATCCG 59.268 52.381 0.00 0.00 0.00 4.18
3223 3299 0.036765 TGTCGAAAACCCAGATCCGG 60.037 55.000 0.00 0.00 0.00 5.14
3224 3300 1.078708 TCGAAAACCCAGATCCGGC 60.079 57.895 0.00 0.00 0.00 6.13
3225 3301 1.376683 CGAAAACCCAGATCCGGCA 60.377 57.895 0.00 0.00 0.00 5.69
3226 3302 0.958382 CGAAAACCCAGATCCGGCAA 60.958 55.000 0.00 0.00 0.00 4.52
3227 3303 0.811281 GAAAACCCAGATCCGGCAAG 59.189 55.000 0.00 0.00 0.00 4.01
3228 3304 0.404040 AAAACCCAGATCCGGCAAGA 59.596 50.000 0.00 0.00 0.00 3.02
3229 3305 0.404040 AAACCCAGATCCGGCAAGAA 59.596 50.000 0.00 0.00 0.00 2.52
3230 3306 0.625849 AACCCAGATCCGGCAAGAAT 59.374 50.000 0.00 0.00 0.00 2.40
3231 3307 0.107017 ACCCAGATCCGGCAAGAATG 60.107 55.000 0.00 0.00 0.00 2.67
3232 3308 0.820891 CCCAGATCCGGCAAGAATGG 60.821 60.000 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.354767 GGGACTAAAGGGTCGTTACTAATG 58.645 45.833 0.00 0.00 37.12 1.90
1 2 4.098501 CGGGACTAAAGGGTCGTTACTAAT 59.901 45.833 0.00 0.00 37.12 1.73
2 3 3.443681 CGGGACTAAAGGGTCGTTACTAA 59.556 47.826 0.00 0.00 37.12 2.24
3 4 3.016736 CGGGACTAAAGGGTCGTTACTA 58.983 50.000 0.00 0.00 37.12 1.82
4 5 1.821136 CGGGACTAAAGGGTCGTTACT 59.179 52.381 0.00 0.00 37.12 2.24
5 6 1.134995 CCGGGACTAAAGGGTCGTTAC 60.135 57.143 0.00 0.00 37.12 2.50
6 7 1.185315 CCGGGACTAAAGGGTCGTTA 58.815 55.000 0.00 0.00 37.12 3.18
7 8 0.833409 ACCGGGACTAAAGGGTCGTT 60.833 55.000 6.32 0.00 37.12 3.85
8 9 0.833409 AACCGGGACTAAAGGGTCGT 60.833 55.000 6.32 0.00 37.12 4.34
9 10 0.108472 GAACCGGGACTAAAGGGTCG 60.108 60.000 6.32 0.00 37.12 4.79
10 11 0.251354 GGAACCGGGACTAAAGGGTC 59.749 60.000 6.32 0.00 40.88 4.46
11 12 1.203441 GGGAACCGGGACTAAAGGGT 61.203 60.000 6.32 0.00 40.86 4.34
12 13 1.605992 GGGAACCGGGACTAAAGGG 59.394 63.158 6.32 0.00 40.86 3.95
30 31 2.272146 CCCATCTGTCCCGGTTGG 59.728 66.667 0.00 0.00 31.38 3.77
31 32 2.438434 GCCCATCTGTCCCGGTTG 60.438 66.667 0.00 0.00 0.00 3.77
32 33 3.728373 GGCCCATCTGTCCCGGTT 61.728 66.667 0.00 0.00 0.00 4.44
33 34 2.833151 TAAGGCCCATCTGTCCCGGT 62.833 60.000 0.00 0.00 0.00 5.28
34 35 1.418908 ATAAGGCCCATCTGTCCCGG 61.419 60.000 0.00 0.00 0.00 5.73
35 36 0.250467 CATAAGGCCCATCTGTCCCG 60.250 60.000 0.00 0.00 0.00 5.14
36 37 1.140312 TCATAAGGCCCATCTGTCCC 58.860 55.000 0.00 0.00 0.00 4.46
37 38 2.576615 GTTCATAAGGCCCATCTGTCC 58.423 52.381 0.00 0.00 0.00 4.02
38 39 2.576615 GGTTCATAAGGCCCATCTGTC 58.423 52.381 0.00 0.00 0.00 3.51
39 40 1.134098 CGGTTCATAAGGCCCATCTGT 60.134 52.381 0.00 0.00 0.00 3.41
40 41 1.597742 CGGTTCATAAGGCCCATCTG 58.402 55.000 0.00 0.00 0.00 2.90
41 42 0.474184 CCGGTTCATAAGGCCCATCT 59.526 55.000 0.00 0.00 0.00 2.90
42 43 0.537371 CCCGGTTCATAAGGCCCATC 60.537 60.000 0.00 0.00 0.00 3.51
43 44 0.991355 TCCCGGTTCATAAGGCCCAT 60.991 55.000 0.00 0.00 0.00 4.00
44 45 1.616930 TCCCGGTTCATAAGGCCCA 60.617 57.895 0.00 0.00 0.00 5.36
45 46 1.153025 GTCCCGGTTCATAAGGCCC 60.153 63.158 0.00 0.00 0.00 5.80
46 47 0.034863 TTGTCCCGGTTCATAAGGCC 60.035 55.000 0.00 0.00 0.00 5.19
47 48 1.828979 TTTGTCCCGGTTCATAAGGC 58.171 50.000 0.00 0.00 0.00 4.35
48 49 2.687935 CCATTTGTCCCGGTTCATAAGG 59.312 50.000 0.00 0.00 0.00 2.69
49 50 2.099098 GCCATTTGTCCCGGTTCATAAG 59.901 50.000 0.00 0.00 0.00 1.73
50 51 2.096248 GCCATTTGTCCCGGTTCATAA 58.904 47.619 0.00 0.00 0.00 1.90
51 52 1.683629 GGCCATTTGTCCCGGTTCATA 60.684 52.381 0.00 0.00 0.00 2.15
52 53 0.970427 GGCCATTTGTCCCGGTTCAT 60.970 55.000 0.00 0.00 0.00 2.57
53 54 1.605165 GGCCATTTGTCCCGGTTCA 60.605 57.895 0.00 0.00 0.00 3.18
54 55 2.348104 GGGCCATTTGTCCCGGTTC 61.348 63.158 4.39 0.00 32.00 3.62
55 56 2.283604 GGGCCATTTGTCCCGGTT 60.284 61.111 4.39 0.00 32.00 4.44
59 60 1.977854 AGAAAAAGGGCCATTTGTCCC 59.022 47.619 25.73 11.52 42.94 4.46
60 61 3.832490 AGTAGAAAAAGGGCCATTTGTCC 59.168 43.478 25.73 13.84 28.13 4.02
61 62 5.710567 ACTAGTAGAAAAAGGGCCATTTGTC 59.289 40.000 22.82 22.82 0.00 3.18
62 63 5.476945 CACTAGTAGAAAAAGGGCCATTTGT 59.523 40.000 17.44 11.46 0.00 2.83
63 64 5.710099 TCACTAGTAGAAAAAGGGCCATTTG 59.290 40.000 17.44 3.54 0.00 2.32
64 65 5.887754 TCACTAGTAGAAAAAGGGCCATTT 58.112 37.500 10.16 10.16 0.00 2.32
65 66 5.514500 TCACTAGTAGAAAAAGGGCCATT 57.486 39.130 6.18 0.00 0.00 3.16
66 67 5.501156 CTTCACTAGTAGAAAAAGGGCCAT 58.499 41.667 6.18 0.00 0.00 4.40
67 68 4.263331 CCTTCACTAGTAGAAAAAGGGCCA 60.263 45.833 6.18 0.00 31.63 5.36
68 69 4.262617 CCTTCACTAGTAGAAAAAGGGCC 58.737 47.826 3.59 0.00 31.63 5.80
69 70 4.262617 CCCTTCACTAGTAGAAAAAGGGC 58.737 47.826 23.65 0.00 44.62 5.19
71 72 6.594547 GCTTACCCTTCACTAGTAGAAAAAGG 59.405 42.308 3.59 12.26 34.38 3.11
72 73 7.159372 TGCTTACCCTTCACTAGTAGAAAAAG 58.841 38.462 3.59 4.40 0.00 2.27
73 74 7.069877 TGCTTACCCTTCACTAGTAGAAAAA 57.930 36.000 3.59 0.00 0.00 1.94
74 75 6.675413 TGCTTACCCTTCACTAGTAGAAAA 57.325 37.500 3.59 0.00 0.00 2.29
75 76 6.269307 ACTTGCTTACCCTTCACTAGTAGAAA 59.731 38.462 3.59 0.00 0.00 2.52
76 77 5.778750 ACTTGCTTACCCTTCACTAGTAGAA 59.221 40.000 3.59 1.42 0.00 2.10
77 78 5.185249 CACTTGCTTACCCTTCACTAGTAGA 59.815 44.000 3.59 0.00 0.00 2.59
78 79 5.411781 CACTTGCTTACCCTTCACTAGTAG 58.588 45.833 0.00 0.00 0.00 2.57
79 80 4.222145 CCACTTGCTTACCCTTCACTAGTA 59.778 45.833 0.00 0.00 0.00 1.82
80 81 3.008049 CCACTTGCTTACCCTTCACTAGT 59.992 47.826 0.00 0.00 0.00 2.57
81 82 3.008049 ACCACTTGCTTACCCTTCACTAG 59.992 47.826 0.00 0.00 0.00 2.57
82 83 2.976882 ACCACTTGCTTACCCTTCACTA 59.023 45.455 0.00 0.00 0.00 2.74
83 84 1.774856 ACCACTTGCTTACCCTTCACT 59.225 47.619 0.00 0.00 0.00 3.41
84 85 1.880027 CACCACTTGCTTACCCTTCAC 59.120 52.381 0.00 0.00 0.00 3.18
85 86 2.270352 CACCACTTGCTTACCCTTCA 57.730 50.000 0.00 0.00 0.00 3.02
117 118 5.183904 CCTCCCTCTCCAAATTTGTGTTTAG 59.816 44.000 16.73 6.81 0.00 1.85
180 182 5.506832 CCATAAAACTTGCGTCGACATTAAC 59.493 40.000 17.16 0.00 0.00 2.01
201 203 3.244353 CTCGTAGATTTGATGGCCTCCAT 60.244 47.826 3.32 0.00 41.61 3.41
219 221 4.082523 CACCATCCCCACGCTCGT 62.083 66.667 0.00 0.00 0.00 4.18
242 244 3.329225 TGATAACCTGTCCATTGTGGTCA 59.671 43.478 0.00 0.00 39.03 4.02
326 328 5.894298 TTCCAATATACATGCCAGAGAGT 57.106 39.130 0.00 0.00 0.00 3.24
392 418 7.770897 ACACTCTTTTCCAAATATCGAAGCTAT 59.229 33.333 0.00 0.00 0.00 2.97
434 460 2.642807 CCTCCTTCTTTAGGTCCACCAA 59.357 50.000 0.00 0.00 45.03 3.67
523 549 0.905357 ACTTAGCAATCCCGTGAGCT 59.095 50.000 0.00 0.00 40.92 4.09
577 603 2.032054 CACGCAGGGCATAACAGTATTG 59.968 50.000 0.00 0.00 0.00 1.90
670 697 0.968405 TCCAGCCCAAAAGTTCATGC 59.032 50.000 0.00 0.00 0.00 4.06
680 707 0.685785 TTGCAAGTGTTCCAGCCCAA 60.686 50.000 0.00 0.00 0.00 4.12
682 709 1.363807 GTTGCAAGTGTTCCAGCCC 59.636 57.895 0.00 0.00 0.00 5.19
696 723 4.922471 TGGTTTAGGGTTTAGTTGTTGC 57.078 40.909 0.00 0.00 0.00 4.17
704 738 7.524367 CGTCTCTTCTAGTTGGTTTAGGGTTTA 60.524 40.741 0.00 0.00 0.00 2.01
737 771 1.973515 CTATATGCAGGCCTCAGGTCA 59.026 52.381 0.00 0.00 0.00 4.02
802 836 9.953565 TTAATGTACAAAGACTGCCTACTTATT 57.046 29.630 0.00 0.00 0.00 1.40
837 871 5.794894 TCTTTCAATACACAGAGACTTCCC 58.205 41.667 0.00 0.00 0.00 3.97
846 881 8.424274 TGCACTGTATATCTTTCAATACACAG 57.576 34.615 1.79 1.79 40.75 3.66
908 943 1.068954 GTTTCGGCAGAGGCTTTCTTG 60.069 52.381 0.00 0.00 40.87 3.02
911 946 1.131315 GATGTTTCGGCAGAGGCTTTC 59.869 52.381 0.00 0.00 40.87 2.62
927 962 1.469940 GCCGTCAGAACTCGATGATGT 60.470 52.381 5.49 0.00 31.75 3.06
931 966 1.714794 AAAGCCGTCAGAACTCGATG 58.285 50.000 0.00 0.00 0.00 3.84
938 973 5.001232 ACAAGCTAATAAAAGCCGTCAGAA 58.999 37.500 0.00 0.00 43.86 3.02
946 981 7.752557 ACTACGAGTACAAGCTAATAAAAGC 57.247 36.000 0.00 0.00 43.11 3.51
972 1007 4.283467 AGCTACGATATGTTGATGCCCTTA 59.717 41.667 0.00 0.00 0.00 2.69
976 1011 3.430218 GTGAGCTACGATATGTTGATGCC 59.570 47.826 0.00 0.00 0.00 4.40
993 1028 1.080298 GTTTGCAGGCATGGTGAGC 60.080 57.895 0.00 0.00 0.00 4.26
996 1031 0.675083 TCTTGTTTGCAGGCATGGTG 59.325 50.000 0.00 0.00 0.00 4.17
997 1032 0.675633 GTCTTGTTTGCAGGCATGGT 59.324 50.000 0.00 0.00 0.00 3.55
1032 1071 1.586154 CCACCTCACCGTTGGCATTC 61.586 60.000 0.00 0.00 0.00 2.67
1056 1095 5.042463 TGCGGATTAATGGGTAGAATTCA 57.958 39.130 8.44 0.00 0.00 2.57
1149 1191 2.725641 CTCGTCACCACACCACGA 59.274 61.111 0.00 0.00 40.14 4.35
1240 1282 2.529389 AACAAGGGGGAGCCTCGT 60.529 61.111 0.00 0.00 0.00 4.18
1398 1446 2.416836 CCATGTGTCATCGTAGGACGTT 60.417 50.000 0.00 0.00 43.14 3.99
1467 1515 2.412112 CGGCTAGGGTCTGCGTAC 59.588 66.667 0.00 0.00 0.00 3.67
1783 1852 1.004044 CAGGGTGTCCTTCTCTGCAAT 59.996 52.381 0.00 0.00 42.67 3.56
1840 1909 1.606313 CATCAACCCACCCACACCC 60.606 63.158 0.00 0.00 0.00 4.61
1899 1968 2.492025 AGGGGAGCATACAGATGGAAA 58.508 47.619 0.00 0.00 33.26 3.13
1905 1974 1.399714 CACGTAGGGGAGCATACAGA 58.600 55.000 0.00 0.00 0.00 3.41
1906 1975 0.249489 GCACGTAGGGGAGCATACAG 60.249 60.000 0.00 0.00 0.00 2.74
1911 1980 3.755628 GTCGCACGTAGGGGAGCA 61.756 66.667 0.00 0.00 0.00 4.26
1914 1983 3.066190 CTGGTCGCACGTAGGGGA 61.066 66.667 0.00 0.00 0.00 4.81
2156 2225 2.143925 AGGTACGAGCTTGCTTCAAAC 58.856 47.619 0.00 0.00 0.00 2.93
2216 2285 4.425520 GGTCTAGAAACAGTTCCTCATCG 58.574 47.826 0.00 0.00 33.92 3.84
2309 2378 3.619483 CCTTCACGTGTACAAACTCAACA 59.381 43.478 16.51 0.00 0.00 3.33
2322 2391 5.171476 AGAAGTGATCATAACCTTCACGTG 58.829 41.667 20.02 9.94 43.49 4.49
2327 2396 7.136119 CGACTCTAGAAGTGATCATAACCTTC 58.864 42.308 13.34 13.34 38.74 3.46
2346 2415 2.544267 GCAAAAGCACTAACACGACTCT 59.456 45.455 0.00 0.00 0.00 3.24
2375 2444 2.105984 GGCAGATACAATGCGCCAA 58.894 52.632 4.18 0.00 44.80 4.52
2421 2490 4.228912 ACAACATGCAAAGCAACTACTC 57.771 40.909 0.00 0.00 43.62 2.59
2425 2494 3.885297 AGACTACAACATGCAAAGCAACT 59.115 39.130 0.00 0.00 43.62 3.16
2433 2502 1.977188 CGACGAGACTACAACATGCA 58.023 50.000 0.00 0.00 0.00 3.96
2515 2584 4.631131 TCTAACACATGACAACCAGACAG 58.369 43.478 0.00 0.00 0.00 3.51
2529 2598 7.780745 TCCTTTTGTTCCCTTTATTCTAACACA 59.219 33.333 0.00 0.00 30.28 3.72
2543 2612 5.359860 TCTGTCTTTCTTTCCTTTTGTTCCC 59.640 40.000 0.00 0.00 0.00 3.97
2544 2613 6.451064 TCTGTCTTTCTTTCCTTTTGTTCC 57.549 37.500 0.00 0.00 0.00 3.62
2545 2614 8.757164 TTTTCTGTCTTTCTTTCCTTTTGTTC 57.243 30.769 0.00 0.00 0.00 3.18
2547 2616 8.122472 TCTTTTCTGTCTTTCTTTCCTTTTGT 57.878 30.769 0.00 0.00 0.00 2.83
2548 2617 9.028185 CATCTTTTCTGTCTTTCTTTCCTTTTG 57.972 33.333 0.00 0.00 0.00 2.44
2549 2618 7.708322 GCATCTTTTCTGTCTTTCTTTCCTTTT 59.292 33.333 0.00 0.00 0.00 2.27
2553 2622 6.076981 TGCATCTTTTCTGTCTTTCTTTCC 57.923 37.500 0.00 0.00 0.00 3.13
2564 2633 3.100817 CGCCGTAATTGCATCTTTTCTG 58.899 45.455 0.00 0.00 0.00 3.02
2609 2678 3.056250 TGCTTTGGCAAAACTGTTCAGAA 60.056 39.130 14.43 0.00 46.36 3.02
2623 2692 4.439289 GGACACATCTAAATCTGCTTTGGC 60.439 45.833 0.00 0.00 39.26 4.52
2624 2693 4.096984 GGGACACATCTAAATCTGCTTTGG 59.903 45.833 0.00 0.00 0.00 3.28
2625 2694 4.701651 TGGGACACATCTAAATCTGCTTTG 59.298 41.667 0.00 0.00 0.00 2.77
2626 2695 4.922206 TGGGACACATCTAAATCTGCTTT 58.078 39.130 0.00 0.00 0.00 3.51
2627 2696 4.574674 TGGGACACATCTAAATCTGCTT 57.425 40.909 0.00 0.00 0.00 3.91
2628 2697 4.574674 TTGGGACACATCTAAATCTGCT 57.425 40.909 0.00 0.00 39.29 4.24
2629 2698 5.841957 AATTGGGACACATCTAAATCTGC 57.158 39.130 0.00 0.00 39.29 4.26
2630 2699 7.864379 GCAATAATTGGGACACATCTAAATCTG 59.136 37.037 0.00 0.00 39.29 2.90
2631 2700 7.560991 TGCAATAATTGGGACACATCTAAATCT 59.439 33.333 0.00 0.00 39.29 2.40
2632 2701 7.715657 TGCAATAATTGGGACACATCTAAATC 58.284 34.615 0.00 0.00 39.29 2.17
2633 2702 7.658525 TGCAATAATTGGGACACATCTAAAT 57.341 32.000 0.00 0.00 39.29 1.40
2634 2703 7.658525 ATGCAATAATTGGGACACATCTAAA 57.341 32.000 0.00 0.00 39.29 1.85
2635 2704 8.938801 ATATGCAATAATTGGGACACATCTAA 57.061 30.769 0.00 0.00 30.33 2.10
2636 2705 8.385491 AGATATGCAATAATTGGGACACATCTA 58.615 33.333 0.00 0.00 30.33 1.98
2641 2710 8.396272 ACTTAGATATGCAATAATTGGGACAC 57.604 34.615 0.00 0.00 30.33 3.67
2643 2712 8.854614 AGACTTAGATATGCAATAATTGGGAC 57.145 34.615 0.00 0.00 29.06 4.46
2663 2732 6.071952 ACGTGAAATCAATTGGCATAAGACTT 60.072 34.615 5.42 0.00 0.00 3.01
2668 2737 5.635417 TCACGTGAAATCAATTGGCATAA 57.365 34.783 17.62 0.00 0.00 1.90
2674 2743 6.079763 ACGAATCTTCACGTGAAATCAATTG 58.920 36.000 29.32 16.95 41.17 2.32
2675 2744 6.241207 ACGAATCTTCACGTGAAATCAATT 57.759 33.333 29.32 23.48 41.17 2.32
2694 2763 6.039616 AGTTTTAGAAAAATGCTTGCACGAA 58.960 32.000 0.00 0.00 0.00 3.85
2695 2764 5.587289 AGTTTTAGAAAAATGCTTGCACGA 58.413 33.333 0.00 0.00 0.00 4.35
2711 2780 3.308473 CCCAGGGAAGGAAGGAGTTTTAG 60.308 52.174 0.00 0.00 0.00 1.85
2725 2798 6.598735 ATACACATGGTAATTCCCCAGGGAA 61.599 44.000 20.32 20.32 44.80 3.97
2730 2803 4.202377 CGGTATACACATGGTAATTCCCCA 60.202 45.833 5.01 0.00 35.14 4.96
2731 2804 4.320870 CGGTATACACATGGTAATTCCCC 58.679 47.826 5.01 0.00 35.14 4.81
2746 2819 0.102844 TAAGGCACACGGCGGTATAC 59.897 55.000 13.24 0.00 46.16 1.47
2747 2820 0.386476 CTAAGGCACACGGCGGTATA 59.614 55.000 13.24 0.00 46.16 1.47
2748 2821 1.143183 CTAAGGCACACGGCGGTAT 59.857 57.895 13.24 0.00 46.16 2.73
2764 2837 1.345715 GGGGAAAGCTAGCTGCCCTA 61.346 60.000 36.25 0.00 44.23 3.53
2767 2840 1.153066 GAGGGGAAAGCTAGCTGCC 60.153 63.158 20.16 21.66 44.23 4.85
2774 2847 3.403558 GCGAGGGAGGGGAAAGCT 61.404 66.667 0.00 0.00 0.00 3.74
2775 2848 4.491409 GGCGAGGGAGGGGAAAGC 62.491 72.222 0.00 0.00 0.00 3.51
2776 2849 1.926426 AATGGCGAGGGAGGGGAAAG 61.926 60.000 0.00 0.00 0.00 2.62
2777 2850 1.921869 GAATGGCGAGGGAGGGGAAA 61.922 60.000 0.00 0.00 0.00 3.13
2778 2851 2.286121 AATGGCGAGGGAGGGGAA 60.286 61.111 0.00 0.00 0.00 3.97
2779 2852 2.768344 GAATGGCGAGGGAGGGGA 60.768 66.667 0.00 0.00 0.00 4.81
2780 2853 2.378634 AAGAATGGCGAGGGAGGGG 61.379 63.158 0.00 0.00 0.00 4.79
2781 2854 1.153086 CAAGAATGGCGAGGGAGGG 60.153 63.158 0.00 0.00 0.00 4.30
2782 2855 0.745845 CACAAGAATGGCGAGGGAGG 60.746 60.000 0.00 0.00 0.00 4.30
2783 2856 0.745845 CCACAAGAATGGCGAGGGAG 60.746 60.000 0.00 0.00 31.52 4.30
2784 2857 1.198094 TCCACAAGAATGGCGAGGGA 61.198 55.000 0.00 0.00 39.85 4.20
2785 2858 0.745845 CTCCACAAGAATGGCGAGGG 60.746 60.000 0.00 0.00 39.85 4.30
2786 2859 0.036010 ACTCCACAAGAATGGCGAGG 60.036 55.000 0.00 0.00 39.85 4.63
2787 2860 1.813513 AACTCCACAAGAATGGCGAG 58.186 50.000 0.00 0.00 39.85 5.03
2788 2861 1.879380 CAAACTCCACAAGAATGGCGA 59.121 47.619 0.00 0.00 39.85 5.54
2789 2862 1.879380 TCAAACTCCACAAGAATGGCG 59.121 47.619 0.00 0.00 39.85 5.69
2790 2863 2.887152 AGTCAAACTCCACAAGAATGGC 59.113 45.455 0.00 0.00 39.85 4.40
2791 2864 4.339247 ACAAGTCAAACTCCACAAGAATGG 59.661 41.667 0.00 0.00 41.57 3.16
2792 2865 5.505173 ACAAGTCAAACTCCACAAGAATG 57.495 39.130 0.00 0.00 0.00 2.67
2793 2866 5.679638 GCAACAAGTCAAACTCCACAAGAAT 60.680 40.000 0.00 0.00 0.00 2.40
2794 2867 4.380444 GCAACAAGTCAAACTCCACAAGAA 60.380 41.667 0.00 0.00 0.00 2.52
2795 2868 3.128589 GCAACAAGTCAAACTCCACAAGA 59.871 43.478 0.00 0.00 0.00 3.02
2796 2869 3.119531 TGCAACAAGTCAAACTCCACAAG 60.120 43.478 0.00 0.00 0.00 3.16
2797 2870 2.822561 TGCAACAAGTCAAACTCCACAA 59.177 40.909 0.00 0.00 0.00 3.33
2824 2897 3.058160 GCGCACATGGCAAGACCT 61.058 61.111 0.30 0.00 45.17 3.85
2851 2924 0.462759 GAGCAATCCTCGGTCTTGGG 60.463 60.000 0.00 0.00 0.00 4.12
2852 2925 3.071580 GAGCAATCCTCGGTCTTGG 57.928 57.895 0.00 0.00 0.00 3.61
2867 2940 0.867753 CAGAGGATACGTGCACGAGC 60.868 60.000 42.94 27.75 43.02 5.03
2870 2943 1.226974 CCCAGAGGATACGTGCACG 60.227 63.158 35.99 35.99 46.39 5.34
2877 2950 1.742768 CGACCAGCCCAGAGGATAC 59.257 63.158 0.00 0.00 33.47 2.24
2890 2963 0.259356 ACCCAAAAAGGAACCGACCA 59.741 50.000 0.00 0.00 41.22 4.02
2897 2970 3.707102 CCACTAAACCACCCAAAAAGGAA 59.293 43.478 0.00 0.00 41.22 3.36
2905 2978 2.027561 CGAAGATCCACTAAACCACCCA 60.028 50.000 0.00 0.00 0.00 4.51
2913 2986 3.953712 TGAGCAACGAAGATCCACTAA 57.046 42.857 0.00 0.00 0.00 2.24
2914 2987 3.181475 GGATGAGCAACGAAGATCCACTA 60.181 47.826 0.00 0.00 33.96 2.74
2932 3005 1.869132 CACATGCGGTACATCAGGATG 59.131 52.381 7.70 7.70 43.11 3.51
2935 3008 0.107703 ACCACATGCGGTACATCAGG 60.108 55.000 2.82 0.00 37.57 3.86
2938 3011 2.100916 AGACTACCACATGCGGTACATC 59.899 50.000 8.58 9.36 40.67 3.06
2943 3016 1.071699 ACAAAGACTACCACATGCGGT 59.928 47.619 10.84 10.84 43.46 5.68
2945 3018 3.554524 CAAACAAAGACTACCACATGCG 58.445 45.455 0.00 0.00 0.00 4.73
2948 3021 4.460263 TCTGCAAACAAAGACTACCACAT 58.540 39.130 0.00 0.00 0.00 3.21
2957 3030 2.023673 CCACCACTCTGCAAACAAAGA 58.976 47.619 0.00 0.00 0.00 2.52
2979 3052 3.763360 TGCCAAATGAAACACCTAGATGG 59.237 43.478 0.00 0.00 42.93 3.51
2984 3057 1.883275 CCGTGCCAAATGAAACACCTA 59.117 47.619 0.00 0.00 0.00 3.08
2989 3062 1.857837 CACAACCGTGCCAAATGAAAC 59.142 47.619 0.00 0.00 36.06 2.78
2994 3067 1.456705 ACCCACAACCGTGCCAAAT 60.457 52.632 0.00 0.00 42.17 2.32
3050 3123 3.075884 ACAACCACAACTACACGTTTGT 58.924 40.909 0.00 0.00 40.02 2.83
3051 3124 3.421741 CACAACCACAACTACACGTTTG 58.578 45.455 0.00 0.00 32.27 2.93
3053 3126 2.011222 CCACAACCACAACTACACGTT 58.989 47.619 0.00 0.00 35.88 3.99
3055 3128 0.306533 GCCACAACCACAACTACACG 59.693 55.000 0.00 0.00 0.00 4.49
3056 3129 1.064952 GTGCCACAACCACAACTACAC 59.935 52.381 0.00 0.00 33.50 2.90
3057 3130 1.065053 AGTGCCACAACCACAACTACA 60.065 47.619 0.00 0.00 35.69 2.74
3058 3131 1.602377 GAGTGCCACAACCACAACTAC 59.398 52.381 0.00 0.00 35.69 2.73
3059 3132 1.476110 GGAGTGCCACAACCACAACTA 60.476 52.381 0.00 0.00 35.69 2.24
3084 3160 0.392998 AAAGGTCGTGCAGGGCTATG 60.393 55.000 11.25 0.00 0.00 2.23
3086 3162 1.003839 CAAAGGTCGTGCAGGGCTA 60.004 57.895 11.25 0.00 0.00 3.93
3097 3173 0.798776 CATCAGCACCGACAAAGGTC 59.201 55.000 0.00 0.00 43.89 3.85
3106 3182 0.943835 TGTCGTTGTCATCAGCACCG 60.944 55.000 0.00 0.00 0.00 4.94
3111 3187 2.245942 CGAGAGTGTCGTTGTCATCAG 58.754 52.381 0.67 0.00 44.20 2.90
3133 3209 0.549469 ACCCAGGAGGAAAACAACGT 59.451 50.000 0.00 0.00 39.89 3.99
3135 3211 1.328279 CCACCCAGGAGGAAAACAAC 58.672 55.000 0.00 0.00 41.22 3.32
3136 3212 0.930726 ACCACCCAGGAGGAAAACAA 59.069 50.000 7.20 0.00 41.22 2.83
3150 3226 1.647084 GCAACTCGACAACACCACC 59.353 57.895 0.00 0.00 0.00 4.61
3155 3231 1.000506 GACTAGGGCAACTCGACAACA 59.999 52.381 0.00 0.00 0.00 3.33
3156 3232 1.672145 GGACTAGGGCAACTCGACAAC 60.672 57.143 0.00 0.00 0.00 3.32
3164 3240 1.198759 TGAGGGTGGACTAGGGCAAC 61.199 60.000 0.00 0.00 0.00 4.17
3165 3241 0.253160 ATGAGGGTGGACTAGGGCAA 60.253 55.000 0.00 0.00 0.00 4.52
3166 3242 0.691078 GATGAGGGTGGACTAGGGCA 60.691 60.000 0.00 0.00 0.00 5.36
3173 3249 1.686110 ACGAGGGATGAGGGTGGAC 60.686 63.158 0.00 0.00 0.00 4.02
3178 3254 1.264749 TGAACCACGAGGGATGAGGG 61.265 60.000 3.29 0.00 41.15 4.30
3180 3256 0.898320 ACTGAACCACGAGGGATGAG 59.102 55.000 3.29 0.00 41.15 2.90
3193 3269 3.247886 GGGTTTTCGACAAGAGACTGAAC 59.752 47.826 0.00 0.00 0.00 3.18
3195 3271 2.432874 TGGGTTTTCGACAAGAGACTGA 59.567 45.455 0.00 0.00 0.00 3.41
3203 3279 1.609580 CCGGATCTGGGTTTTCGACAA 60.610 52.381 13.34 0.00 0.00 3.18
3204 3280 0.036765 CCGGATCTGGGTTTTCGACA 60.037 55.000 13.34 0.00 0.00 4.35
3207 3283 0.958382 TTGCCGGATCTGGGTTTTCG 60.958 55.000 22.38 0.00 0.00 3.46
3215 3291 0.749091 TGCCATTCTTGCCGGATCTG 60.749 55.000 5.05 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.