Multiple sequence alignment - TraesCS2B01G117300

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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 TraesCS2B01G117300 chr2B 100.000 5532 0 0 1 5532 80259380 80253849 0.000000e+00 10216.0
1 TraesCS2B01G117300 chr2B 89.480 865 85 4 4671 5531 721747244 721746382 0.000000e+00 1088.0
2 TraesCS2B01G117300 chr2B 97.600 250 6 0 1283 1532 80256486 80256237 3.960000e-116 429.0
3 TraesCS2B01G117300 chr2B 74.155 1006 239 16 3153 4142 20144069 20145069 1.120000e-106 398.0
4 TraesCS2B01G117300 chr2B 75.922 461 104 6 4784 5239 494737777 494737319 4.310000e-56 230.0
5 TraesCS2B01G117300 chr2A 92.012 1640 99 16 1534 3149 739661312 739659681 0.000000e+00 2274.0
6 TraesCS2B01G117300 chr2A 91.038 1272 70 15 3141 4396 52766172 52764929 0.000000e+00 1677.0
7 TraesCS2B01G117300 chr2A 88.638 1329 93 24 1 1283 52767481 52766165 0.000000e+00 1565.0
8 TraesCS2B01G117300 chr2A 92.885 253 16 2 4412 4662 52763926 52763674 3.150000e-97 366.0
9 TraesCS2B01G117300 chr2A 90.566 265 18 3 1283 1544 739664671 739664411 1.480000e-90 344.0
10 TraesCS2B01G117300 chr2A 97.674 43 1 0 4371 4413 52764930 52764888 2.140000e-09 75.0
11 TraesCS2B01G117300 chr6D 91.718 1618 119 12 1534 3144 468032129 468030520 0.000000e+00 2231.0
12 TraesCS2B01G117300 chr5D 89.640 1612 145 18 1534 3135 549779668 549781267 0.000000e+00 2032.0
13 TraesCS2B01G117300 chr5D 87.254 1624 185 19 1534 3146 425070229 425071841 0.000000e+00 1832.0
14 TraesCS2B01G117300 chr5D 72.727 1001 238 21 3155 4132 438046126 438047114 2.500000e-78 303.0
15 TraesCS2B01G117300 chr5D 87.295 244 21 9 1306 1544 425066778 425067016 2.540000e-68 270.0
16 TraesCS2B01G117300 chr5D 86.463 229 22 8 1306 1530 425071614 425071837 5.540000e-60 243.0
17 TraesCS2B01G117300 chr5D 74.555 562 125 12 3585 4141 438522973 438522425 4.310000e-56 230.0
18 TraesCS2B01G117300 chr5D 96.970 33 1 0 531 563 483235527 483235559 7.740000e-04 56.5
19 TraesCS2B01G117300 chr5D 100.000 28 0 0 536 563 552779873 552779846 1.000000e-02 52.8
20 TraesCS2B01G117300 chr7D 88.999 1618 162 14 1534 3144 575061835 575060227 0.000000e+00 1988.0
21 TraesCS2B01G117300 chr7D 87.300 1622 186 16 1534 3145 53622439 53624050 0.000000e+00 1836.0
22 TraesCS2B01G117300 chr7D 87.705 244 20 9 1306 1544 20341801 20341563 5.460000e-70 276.0
23 TraesCS2B01G117300 chr7D 86.831 243 24 7 1306 1544 53613563 53613801 1.180000e-66 265.0
24 TraesCS2B01G117300 chr7D 87.446 231 20 8 1306 1532 20336972 20336747 1.980000e-64 257.0
25 TraesCS2B01G117300 chr7D 87.013 231 21 7 1306 1532 53623824 53624049 9.200000e-63 252.0
26 TraesCS2B01G117300 chr5A 89.316 1535 151 9 1534 3062 552624098 552622571 0.000000e+00 1914.0
27 TraesCS2B01G117300 chr5A 100.000 29 0 0 535 563 589580886 589580914 3.000000e-03 54.7
28 TraesCS2B01G117300 chr7B 86.766 1617 192 17 1543 3150 561309786 561308183 0.000000e+00 1781.0
29 TraesCS2B01G117300 chr7B 83.212 274 35 9 1276 1544 561313093 561312826 1.990000e-59 241.0
30 TraesCS2B01G117300 chr1B 85.547 1619 207 24 1536 3144 637551125 637549524 0.000000e+00 1668.0
31 TraesCS2B01G117300 chr1B 80.808 792 141 9 4734 5519 666294421 666295207 1.320000e-170 610.0
32 TraesCS2B01G117300 chr1D 84.584 733 106 5 4790 5517 141524491 141525221 0.000000e+00 721.0
33 TraesCS2B01G117300 chr1D 100.000 29 0 0 535 563 260318862 260318834 3.000000e-03 54.7
34 TraesCS2B01G117300 chr1D 100.000 29 0 0 535 563 418301243 418301215 3.000000e-03 54.7
35 TraesCS2B01G117300 chr3A 81.513 833 137 14 4699 5519 66816428 66815601 0.000000e+00 669.0
36 TraesCS2B01G117300 chr3A 76.765 779 161 16 4740 5506 71592276 71593046 8.570000e-113 418.0
37 TraesCS2B01G117300 chr3A 81.452 496 78 13 4753 5240 126118869 126118380 1.440000e-105 394.0
38 TraesCS2B01G117300 chr1A 79.460 852 160 11 4679 5519 68382333 68383180 1.720000e-164 590.0
39 TraesCS2B01G117300 chr5B 75.390 1089 227 25 3153 4216 533381286 533380214 6.440000e-134 488.0
40 TraesCS2B01G117300 chr5B 74.977 1067 210 42 3164 4199 533511188 533510148 6.580000e-119 438.0
41 TraesCS2B01G117300 chr5B 72.848 1057 243 23 3155 4184 532548322 532549361 6.910000e-84 322.0
42 TraesCS2B01G117300 chr5B 72.566 1068 237 42 3153 4188 533391659 533390616 1.170000e-76 298.0
43 TraesCS2B01G117300 chr3B 79.447 506 96 5 4740 5239 101518218 101518721 8.820000e-93 351.0
44 TraesCS2B01G117300 chr2D 71.402 1091 265 35 3146 4198 37278127 37279208 5.540000e-60 243.0
45 TraesCS2B01G117300 chr2D 78.571 140 27 1 4376 4512 37279430 37279569 7.630000e-14 89.8
46 TraesCS2B01G117300 chr3D 82.447 188 32 1 1073 1259 7501515 7501328 4.430000e-36 163.0
47 TraesCS2B01G117300 chr4D 100.000 29 0 0 535 563 17076260 17076288 3.000000e-03 54.7


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 TraesCS2B01G117300 chr2B 80253849 80259380 5531 True 5322.500000 10216 98.80000 1 5532 2 chr2B.!!$R3 5531
1 TraesCS2B01G117300 chr2B 721746382 721747244 862 True 1088.000000 1088 89.48000 4671 5531 1 chr2B.!!$R2 860
2 TraesCS2B01G117300 chr2B 20144069 20145069 1000 False 398.000000 398 74.15500 3153 4142 1 chr2B.!!$F1 989
3 TraesCS2B01G117300 chr2A 739659681 739664671 4990 True 1309.000000 2274 91.28900 1283 3149 2 chr2A.!!$R2 1866
4 TraesCS2B01G117300 chr2A 52763674 52767481 3807 True 920.750000 1677 92.55875 1 4662 4 chr2A.!!$R1 4661
5 TraesCS2B01G117300 chr6D 468030520 468032129 1609 True 2231.000000 2231 91.71800 1534 3144 1 chr6D.!!$R1 1610
6 TraesCS2B01G117300 chr5D 549779668 549781267 1599 False 2032.000000 2032 89.64000 1534 3135 1 chr5D.!!$F3 1601
7 TraesCS2B01G117300 chr5D 425066778 425071841 5063 False 781.666667 1832 87.00400 1306 3146 3 chr5D.!!$F4 1840
8 TraesCS2B01G117300 chr5D 438046126 438047114 988 False 303.000000 303 72.72700 3155 4132 1 chr5D.!!$F1 977
9 TraesCS2B01G117300 chr5D 438522425 438522973 548 True 230.000000 230 74.55500 3585 4141 1 chr5D.!!$R1 556
10 TraesCS2B01G117300 chr7D 575060227 575061835 1608 True 1988.000000 1988 88.99900 1534 3144 1 chr7D.!!$R3 1610
11 TraesCS2B01G117300 chr7D 53622439 53624050 1611 False 1044.000000 1836 87.15650 1306 3145 2 chr7D.!!$F2 1839
12 TraesCS2B01G117300 chr5A 552622571 552624098 1527 True 1914.000000 1914 89.31600 1534 3062 1 chr5A.!!$R1 1528
13 TraesCS2B01G117300 chr7B 561308183 561313093 4910 True 1011.000000 1781 84.98900 1276 3150 2 chr7B.!!$R1 1874
14 TraesCS2B01G117300 chr1B 637549524 637551125 1601 True 1668.000000 1668 85.54700 1536 3144 1 chr1B.!!$R1 1608
15 TraesCS2B01G117300 chr1B 666294421 666295207 786 False 610.000000 610 80.80800 4734 5519 1 chr1B.!!$F1 785
16 TraesCS2B01G117300 chr1D 141524491 141525221 730 False 721.000000 721 84.58400 4790 5517 1 chr1D.!!$F1 727
17 TraesCS2B01G117300 chr3A 66815601 66816428 827 True 669.000000 669 81.51300 4699 5519 1 chr3A.!!$R1 820
18 TraesCS2B01G117300 chr3A 71592276 71593046 770 False 418.000000 418 76.76500 4740 5506 1 chr3A.!!$F1 766
19 TraesCS2B01G117300 chr1A 68382333 68383180 847 False 590.000000 590 79.46000 4679 5519 1 chr1A.!!$F1 840
20 TraesCS2B01G117300 chr5B 533380214 533381286 1072 True 488.000000 488 75.39000 3153 4216 1 chr5B.!!$R1 1063
21 TraesCS2B01G117300 chr5B 533510148 533511188 1040 True 438.000000 438 74.97700 3164 4199 1 chr5B.!!$R3 1035
22 TraesCS2B01G117300 chr5B 532548322 532549361 1039 False 322.000000 322 72.84800 3155 4184 1 chr5B.!!$F1 1029
23 TraesCS2B01G117300 chr5B 533390616 533391659 1043 True 298.000000 298 72.56600 3153 4188 1 chr5B.!!$R2 1035
24 TraesCS2B01G117300 chr3B 101518218 101518721 503 False 351.000000 351 79.44700 4740 5239 1 chr3B.!!$F1 499

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
34 35 0.248054 CACCATGTATCGTTTGCCGC 60.248 55.0 0.0 0.0 36.19 6.53 F
1214 1261 0.178068 CTGGGGATCTGGTACAACGG 59.822 60.0 0.0 0.0 38.70 4.44 F
3070 6469 0.322322 CCAACCTAACTACCGCACCA 59.678 55.0 0.0 0.0 0.00 4.17 F
3989 7424 0.108186 CAGGTTCACTCGCATAGGCA 60.108 55.0 0.0 0.0 41.24 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1222 1269 0.606604 ACCCACACGATCGTAAGCTT 59.393 50.0 22.26 3.48 37.18 3.74 R
3151 6553 0.038159 GTGAAGGAGAGTGTCGGTGG 60.038 60.0 0.00 0.00 0.00 4.61 R
4132 7567 0.454600 CTGCGCTAGACTTTCCGGTA 59.545 55.0 9.73 0.00 0.00 4.02 R
5470 9907 0.407528 TATGGCCCCACTTCTTGCAA 59.592 50.0 0.00 0.00 0.00 4.08 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 2.569853 TCCTCACCACCATGTATCGTTT 59.430 45.455 0.00 0.00 0.00 3.60
33 34 0.376852 CCACCATGTATCGTTTGCCG 59.623 55.000 0.00 0.00 38.13 5.69
34 35 0.248054 CACCATGTATCGTTTGCCGC 60.248 55.000 0.00 0.00 36.19 6.53
50 51 1.463444 GCCGCGTACTTGTGATCTTTT 59.537 47.619 4.92 0.00 0.00 2.27
56 57 6.347079 CCGCGTACTTGTGATCTTTTCTTTAA 60.347 38.462 4.92 0.00 0.00 1.52
68 69 8.889717 TGATCTTTTCTTTAACTATAAAGCGGG 58.110 33.333 0.00 0.00 45.03 6.13
96 97 3.454082 AGCCTATTTCTGAGAGGGAACAG 59.546 47.826 0.00 0.00 35.72 3.16
103 104 3.576861 TCTGAGAGGGAACAGAAACTCA 58.423 45.455 0.00 0.00 39.68 3.41
111 112 3.486383 GGAACAGAAACTCATTGACCCA 58.514 45.455 0.00 0.00 0.00 4.51
160 161 7.583860 AAGATAAGCTTTAAACTCAGTCGTC 57.416 36.000 3.20 0.00 31.11 4.20
206 207 2.871096 TGGAATCAAGGGTGGTGTAC 57.129 50.000 0.00 0.00 0.00 2.90
232 233 3.056628 CGAAGCAAGGCTCTAGTGG 57.943 57.895 0.00 0.00 38.25 4.00
247 248 2.287977 AGTGGTTTTACAAGAGGGCC 57.712 50.000 0.00 0.00 0.00 5.80
272 273 3.866651 AGATGCAAGTGCTTAGGTAGTG 58.133 45.455 4.69 0.00 42.66 2.74
281 282 2.265683 GCTTAGGTAGTGGCGTGTTAC 58.734 52.381 0.00 0.00 0.00 2.50
301 302 2.287788 ACTTTCTGCCGTTCTTGCAATG 60.288 45.455 0.00 0.00 38.46 2.82
318 319 3.699038 GCAATGGGTTTATGCTTACTCCA 59.301 43.478 0.00 0.00 37.12 3.86
330 331 5.212532 TGCTTACTCCAACATGCAAAAAT 57.787 34.783 0.00 0.00 0.00 1.82
332 333 6.934056 TGCTTACTCCAACATGCAAAAATAT 58.066 32.000 0.00 0.00 0.00 1.28
333 334 8.060931 TGCTTACTCCAACATGCAAAAATATA 57.939 30.769 0.00 0.00 0.00 0.86
369 373 6.043243 ACCAACAGACATATATTAGGGTGAGG 59.957 42.308 0.00 0.00 0.00 3.86
389 393 3.855689 GCAGACATATGCCAAACAAGT 57.144 42.857 1.58 0.00 40.43 3.16
390 394 4.963276 GCAGACATATGCCAAACAAGTA 57.037 40.909 1.58 0.00 40.43 2.24
399 403 5.981088 ATGCCAAACAAGTATGTGATGAA 57.019 34.783 0.00 0.00 40.46 2.57
400 404 5.375417 TGCCAAACAAGTATGTGATGAAG 57.625 39.130 0.00 0.00 40.46 3.02
411 415 0.593128 GTGATGAAGTGCAGGCGTTT 59.407 50.000 0.00 0.00 0.00 3.60
426 430 6.183360 TGCAGGCGTTTATATGCAGATTTTTA 60.183 34.615 0.00 0.00 43.34 1.52
474 478 4.722193 CATGCCGTGGATATCCCC 57.278 61.111 19.34 6.74 34.29 4.81
522 528 4.634443 AGGTGATTTAGTGCGGTTTCATAC 59.366 41.667 0.00 0.00 0.00 2.39
524 530 3.942748 TGATTTAGTGCGGTTTCATACCC 59.057 43.478 0.00 0.00 44.70 3.69
529 535 1.467342 GTGCGGTTTCATACCCTGAAC 59.533 52.381 0.00 0.00 43.54 3.18
531 537 1.365699 CGGTTTCATACCCTGAACGG 58.634 55.000 0.00 0.00 43.54 4.44
533 539 2.081462 GGTTTCATACCCTGAACGGTG 58.919 52.381 0.00 0.00 43.54 4.94
539 545 4.410400 CCCTGAACGGTGCTCCCC 62.410 72.222 0.00 0.00 0.00 4.81
564 571 6.530534 CCGTCCCATAATATAAGAGCGTTTAG 59.469 42.308 0.00 0.00 0.00 1.85
566 573 7.811236 CGTCCCATAATATAAGAGCGTTTAGAA 59.189 37.037 0.00 0.00 0.00 2.10
641 655 5.333645 CGCACTTCCTGATTTAGTCATATGC 60.334 44.000 0.00 0.00 35.97 3.14
647 661 8.985315 TTCCTGATTTAGTCATATGCTTTCAT 57.015 30.769 0.00 0.00 35.97 2.57
666 680 9.980780 GCTTTCATTTTCTAACAAGATCTAGTC 57.019 33.333 0.00 0.00 0.00 2.59
674 688 7.731882 TCTAACAAGATCTAGTCGAATCGAT 57.268 36.000 9.10 0.00 38.42 3.59
685 699 1.476488 TCGAATCGATGTTGGAGCAGA 59.524 47.619 0.00 0.00 0.00 4.26
700 714 1.453762 GCAGACGGACCGGTATAGCT 61.454 60.000 20.00 0.00 0.00 3.32
777 799 3.341823 GACATGGACAGCTGAGATGTTT 58.658 45.455 23.35 4.20 0.00 2.83
807 829 1.625315 AGCATACTGTCAACTGCTCCA 59.375 47.619 0.00 0.00 40.85 3.86
809 831 2.160417 GCATACTGTCAACTGCTCCAAC 59.840 50.000 0.00 0.00 0.00 3.77
817 839 4.081752 TGTCAACTGCTCCAACACAAAAAT 60.082 37.500 0.00 0.00 0.00 1.82
829 851 7.271511 TCCAACACAAAAATCTTTGCATTACT 58.728 30.769 0.00 0.00 44.96 2.24
831 853 7.224362 CCAACACAAAAATCTTTGCATTACTGA 59.776 33.333 0.00 0.00 44.96 3.41
835 857 4.361451 AAATCTTTGCATTACTGAGCCG 57.639 40.909 0.00 0.00 0.00 5.52
837 859 2.778299 TCTTTGCATTACTGAGCCGTT 58.222 42.857 0.00 0.00 0.00 4.44
860 882 2.598589 CTTCCGCAATCAAACATGTGG 58.401 47.619 0.00 0.00 46.28 4.17
864 886 1.604947 CGCAATCAAACATGTGGCCAA 60.605 47.619 7.24 0.00 0.00 4.52
881 903 3.700754 CCAAGGCTGGAACGAGTCCTC 62.701 61.905 10.53 3.79 46.92 3.71
890 912 2.484947 GGAACGAGTCCTCCTTGTTTGT 60.485 50.000 0.00 0.00 45.95 2.83
892 914 1.269621 ACGAGTCCTCCTTGTTTGTCG 60.270 52.381 0.00 0.00 33.76 4.35
918 940 4.422840 CATTTTGTGCTTGTGAGTTGTGA 58.577 39.130 0.00 0.00 0.00 3.58
919 941 3.485947 TTTGTGCTTGTGAGTTGTGAC 57.514 42.857 0.00 0.00 0.00 3.67
920 942 1.378531 TGTGCTTGTGAGTTGTGACC 58.621 50.000 0.00 0.00 0.00 4.02
921 943 1.339535 TGTGCTTGTGAGTTGTGACCA 60.340 47.619 0.00 0.00 0.00 4.02
922 944 1.742831 GTGCTTGTGAGTTGTGACCAA 59.257 47.619 0.00 0.00 0.00 3.67
923 945 2.016318 TGCTTGTGAGTTGTGACCAAG 58.984 47.619 0.00 0.00 36.47 3.61
924 946 1.334869 GCTTGTGAGTTGTGACCAAGG 59.665 52.381 0.00 0.00 34.51 3.61
925 947 1.334869 CTTGTGAGTTGTGACCAAGGC 59.665 52.381 0.00 0.00 31.19 4.35
926 948 0.546122 TGTGAGTTGTGACCAAGGCT 59.454 50.000 0.00 0.00 0.00 4.58
927 949 1.765904 TGTGAGTTGTGACCAAGGCTA 59.234 47.619 0.00 0.00 0.00 3.93
928 950 2.371841 TGTGAGTTGTGACCAAGGCTAT 59.628 45.455 0.00 0.00 0.00 2.97
970 992 3.004002 GCAGCATCAATAGCACATTAGCA 59.996 43.478 0.00 0.00 36.85 3.49
971 993 4.321008 GCAGCATCAATAGCACATTAGCAT 60.321 41.667 0.00 0.00 36.85 3.79
972 994 5.154222 CAGCATCAATAGCACATTAGCATG 58.846 41.667 0.00 0.00 36.85 4.06
973 995 4.217767 AGCATCAATAGCACATTAGCATGG 59.782 41.667 0.00 0.00 34.27 3.66
974 996 4.617530 GCATCAATAGCACATTAGCATGGG 60.618 45.833 0.00 0.00 36.80 4.00
997 1025 5.291905 AGTATGCTTTAGGCCTTAACGAT 57.708 39.130 12.58 3.07 40.92 3.73
1004 1032 1.410004 AGGCCTTAACGATCGATGGA 58.590 50.000 24.34 2.55 0.00 3.41
1005 1033 1.341531 AGGCCTTAACGATCGATGGAG 59.658 52.381 24.34 12.27 0.00 3.86
1014 1042 2.037620 GATCGATGGAGTGGCAGGCT 62.038 60.000 0.54 0.00 0.00 4.58
1015 1043 2.037620 ATCGATGGAGTGGCAGGCTC 62.038 60.000 0.00 0.00 0.00 4.70
1017 1045 1.145819 GATGGAGTGGCAGGCTCTC 59.854 63.158 15.92 15.92 33.73 3.20
1018 1046 2.322638 GATGGAGTGGCAGGCTCTCC 62.323 65.000 29.65 29.65 45.46 3.71
1027 1073 1.605992 CAGGCTCTCCCATGCTTCA 59.394 57.895 0.00 0.00 35.39 3.02
1033 1079 2.609299 TCCCATGCTTCACCGGGA 60.609 61.111 6.32 0.00 45.66 5.14
1047 1093 2.818274 GGGACCGCCGTGTTGATC 60.818 66.667 0.00 0.00 33.83 2.92
1060 1106 5.290386 CCGTGTTGATCCTTCTTATAGTCC 58.710 45.833 0.00 0.00 0.00 3.85
1081 1128 1.372004 CCGTTTAGTGCGTCCGACA 60.372 57.895 0.00 0.00 0.00 4.35
1121 1168 2.771762 GCTCTCCCCTGGCTCCAT 60.772 66.667 0.00 0.00 0.00 3.41
1173 1220 1.378762 CTTCTTCGCCCCCTCCAAA 59.621 57.895 0.00 0.00 0.00 3.28
1189 1236 1.203050 CCAAATCCACTCCCACCAAGT 60.203 52.381 0.00 0.00 0.00 3.16
1200 1247 0.251165 CCACCAAGTTGTACCTGGGG 60.251 60.000 1.45 0.00 28.77 4.96
1212 1259 1.286248 ACCTGGGGATCTGGTACAAC 58.714 55.000 0.00 0.00 44.49 3.32
1214 1261 0.178068 CTGGGGATCTGGTACAACGG 59.822 60.000 0.00 0.00 38.70 4.44
1221 1268 1.451387 CTGGTACAACGGCATCCCC 60.451 63.158 0.00 0.00 38.70 4.81
1222 1269 2.191786 CTGGTACAACGGCATCCCCA 62.192 60.000 0.00 0.00 38.70 4.96
1227 1274 1.978617 CAACGGCATCCCCAAGCTT 60.979 57.895 0.00 0.00 0.00 3.74
1230 1277 2.180204 CGGCATCCCCAAGCTTACG 61.180 63.158 0.00 0.00 0.00 3.18
1231 1278 1.223487 GGCATCCCCAAGCTTACGA 59.777 57.895 0.00 0.00 0.00 3.43
1379 1426 3.127030 TGCGTGTGTGTTTGTTGTAATCA 59.873 39.130 0.00 0.00 0.00 2.57
1391 1439 7.442969 TGTTTGTTGTAATCAGGTAGTTAGGTG 59.557 37.037 0.00 0.00 0.00 4.00
1456 1506 3.008157 TCAATCCAACCTAACTACCGCAA 59.992 43.478 0.00 0.00 0.00 4.85
1458 1508 1.693062 TCCAACCTAACTACCGCAACA 59.307 47.619 0.00 0.00 0.00 3.33
1470 1520 6.406692 ACTACCGCAACATGTATCTTATCT 57.593 37.500 0.00 0.00 0.00 1.98
1471 1521 6.448006 ACTACCGCAACATGTATCTTATCTC 58.552 40.000 0.00 0.00 0.00 2.75
1473 1523 6.650427 ACCGCAACATGTATCTTATCTCTA 57.350 37.500 0.00 0.00 0.00 2.43
1515 1565 1.705337 CCTGTCCAAAGGCATACGCG 61.705 60.000 3.53 3.53 39.92 6.01
1538 1588 3.438781 TCCACGCAAACTTTCATGGTATC 59.561 43.478 0.00 0.00 0.00 2.24
1539 1589 3.190327 CCACGCAAACTTTCATGGTATCA 59.810 43.478 0.00 0.00 0.00 2.15
1540 1590 4.406069 CACGCAAACTTTCATGGTATCAG 58.594 43.478 0.00 0.00 0.00 2.90
1541 1591 4.154015 CACGCAAACTTTCATGGTATCAGA 59.846 41.667 0.00 0.00 0.00 3.27
1855 5213 8.343168 TCCAAGTTAAGTGAAAAACTTCAGAA 57.657 30.769 0.00 0.00 46.60 3.02
1891 5254 9.061435 CAAATTATCCAAAGGAGATACTTCCTC 57.939 37.037 0.00 0.00 46.90 3.71
1911 5274 6.875076 TCCTCGTTCTTTTATAGGAAAGGAG 58.125 40.000 0.00 0.00 37.27 3.69
2072 5438 7.940850 TGGGAATTGAAGTCAGAAAAGTAAAG 58.059 34.615 0.00 0.00 0.00 1.85
2099 5465 6.003950 TGGAATACTTCTCACCCAAGAAAAG 58.996 40.000 0.00 0.00 34.95 2.27
2200 5567 6.545504 TTGTCAAAAGAAGAAGGAGAATCG 57.454 37.500 0.00 0.00 34.37 3.34
2251 5619 3.343617 GAGTATGGTAGGTGCTTTGCAA 58.656 45.455 0.00 0.00 41.47 4.08
2275 5643 8.950210 CAATATTTAACACTGACAAGACCTGAT 58.050 33.333 0.00 0.00 0.00 2.90
2342 5711 5.242615 CCTACTTCTCAGCATATGACAGCTA 59.757 44.000 6.97 0.00 39.50 3.32
2410 5780 8.349983 GGTCTAAAATTTACAAAGTCAAGCTCA 58.650 33.333 0.00 0.00 0.00 4.26
2494 5864 4.082245 ACAGGAGGTTTCTGTGTGTTTTTG 60.082 41.667 0.00 0.00 43.07 2.44
2495 5865 4.082245 CAGGAGGTTTCTGTGTGTTTTTGT 60.082 41.667 0.00 0.00 0.00 2.83
2508 5879 8.282455 TGTGTGTTTTTGTTCCTAACTTGATA 57.718 30.769 0.00 0.00 0.00 2.15
2529 5900 0.792640 CTTGGAGTGCACGTAAGCAG 59.207 55.000 12.01 0.33 46.69 4.24
2535 5906 0.669318 GTGCACGTAAGCAGGCTACA 60.669 55.000 0.00 0.00 46.69 2.74
2540 5911 1.893801 ACGTAAGCAGGCTACAGTCTT 59.106 47.619 0.00 0.00 45.62 3.01
2550 5921 2.100087 GGCTACAGTCTTCAGGTCTAGC 59.900 54.545 0.00 0.00 0.00 3.42
2611 5982 5.123227 CCGAGATTATTTGGGTTCAAGCTA 58.877 41.667 0.00 0.00 33.98 3.32
2622 5993 2.860735 GGTTCAAGCTATGCTACGTGAG 59.139 50.000 0.00 0.00 38.25 3.51
2679 6050 3.063452 GGTGTGATAACATTGGTGCTACG 59.937 47.826 0.00 0.00 0.00 3.51
2691 6062 4.665833 TGGTGCTACGTATTTATCTGCT 57.334 40.909 0.00 0.00 0.00 4.24
2721 6092 6.869913 CAGTATTTCATGCAAGGACAAAACAT 59.130 34.615 0.00 0.00 0.00 2.71
2790 6161 4.331968 TGCTGGTCATTCGTTTTATTCCT 58.668 39.130 0.00 0.00 0.00 3.36
2802 6173 5.057149 CGTTTTATTCCTACAGGGGATCAG 58.943 45.833 0.00 0.00 34.50 2.90
2951 6322 1.574134 ATAAACCGTATTCACCCGCG 58.426 50.000 0.00 0.00 0.00 6.46
3070 6469 0.322322 CCAACCTAACTACCGCACCA 59.678 55.000 0.00 0.00 0.00 4.17
3082 6482 4.833380 ACTACCGCACCATGTATCTTATCT 59.167 41.667 0.00 0.00 0.00 1.98
3150 6552 1.063912 CACGCAAACTTTCAGTCTGCA 59.936 47.619 3.27 0.00 0.00 4.41
3151 6553 1.064060 ACGCAAACTTTCAGTCTGCAC 59.936 47.619 3.27 0.00 0.00 4.57
3237 6639 2.503356 TGTTCTTTGGGCAACAACCAAT 59.497 40.909 0.00 0.00 46.55 3.16
3304 6709 0.179100 CACCGGCAATCTCGTCATCT 60.179 55.000 0.00 0.00 0.00 2.90
3309 6714 1.216122 GCAATCTCGTCATCTGCTCC 58.784 55.000 0.00 0.00 0.00 4.70
3320 6725 3.058160 CTGCTCCCCAAACGGCAG 61.058 66.667 0.00 0.00 44.45 4.85
3613 7042 1.153329 ACCGCCTTCGTTGACAACA 60.153 52.632 18.09 3.08 0.00 3.33
3873 7308 1.813513 CCAGCAAACATCGAGGAGTT 58.186 50.000 3.06 0.00 0.00 3.01
3966 7401 2.511600 GCCGGGGATGAAGTCACG 60.512 66.667 2.18 0.00 0.00 4.35
3989 7424 0.108186 CAGGTTCACTCGCATAGGCA 60.108 55.000 0.00 0.00 41.24 4.75
3990 7425 0.833287 AGGTTCACTCGCATAGGCAT 59.167 50.000 0.00 0.00 41.24 4.40
4021 7456 0.957395 CATTTGAGGAGTGTGCGGCT 60.957 55.000 0.00 0.00 0.00 5.52
4132 7567 1.384191 GGCTGGGGAGTTGGTTGAT 59.616 57.895 0.00 0.00 0.00 2.57
4240 7675 5.063880 GGTTTCTTGCTCTTTCTCCAACTA 58.936 41.667 0.00 0.00 0.00 2.24
4241 7676 5.180304 GGTTTCTTGCTCTTTCTCCAACTAG 59.820 44.000 0.00 0.00 0.00 2.57
4246 7681 6.260936 TCTTGCTCTTTCTCCAACTAGTTTTG 59.739 38.462 5.07 0.18 0.00 2.44
4247 7682 4.275936 TGCTCTTTCTCCAACTAGTTTTGC 59.724 41.667 5.07 1.32 0.00 3.68
4248 7683 4.320567 GCTCTTTCTCCAACTAGTTTTGCC 60.321 45.833 5.07 0.00 0.00 4.52
4249 7684 4.787551 TCTTTCTCCAACTAGTTTTGCCA 58.212 39.130 5.07 0.00 0.00 4.92
4250 7685 5.197451 TCTTTCTCCAACTAGTTTTGCCAA 58.803 37.500 5.07 0.00 0.00 4.52
4251 7686 5.833131 TCTTTCTCCAACTAGTTTTGCCAAT 59.167 36.000 5.07 0.00 0.00 3.16
4252 7687 6.323739 TCTTTCTCCAACTAGTTTTGCCAATT 59.676 34.615 5.07 0.00 0.00 2.32
4253 7688 5.705609 TCTCCAACTAGTTTTGCCAATTC 57.294 39.130 5.07 0.00 0.00 2.17
4256 7691 5.136828 TCCAACTAGTTTTGCCAATTCTCA 58.863 37.500 5.07 0.00 0.00 3.27
4260 7695 1.680735 AGTTTTGCCAATTCTCACGCA 59.319 42.857 0.00 0.00 0.00 5.24
4275 7711 4.097741 TCTCACGCATTTTATCCAATTGGG 59.902 41.667 24.29 7.43 35.71 4.12
4277 7713 4.221703 TCACGCATTTTATCCAATTGGGTT 59.778 37.500 24.29 14.37 38.93 4.11
4278 7714 4.934602 CACGCATTTTATCCAATTGGGTTT 59.065 37.500 24.29 11.96 38.93 3.27
4279 7715 4.934602 ACGCATTTTATCCAATTGGGTTTG 59.065 37.500 24.29 13.50 38.21 2.93
4280 7716 4.934602 CGCATTTTATCCAATTGGGTTTGT 59.065 37.500 24.29 8.28 38.11 2.83
4281 7717 5.063312 CGCATTTTATCCAATTGGGTTTGTC 59.937 40.000 24.29 4.75 38.11 3.18
4282 7718 5.936956 GCATTTTATCCAATTGGGTTTGTCA 59.063 36.000 24.29 3.29 38.11 3.58
4283 7719 6.598850 GCATTTTATCCAATTGGGTTTGTCAT 59.401 34.615 24.29 10.83 38.11 3.06
4284 7720 7.121020 GCATTTTATCCAATTGGGTTTGTCATT 59.879 33.333 24.29 0.00 38.11 2.57
4285 7721 9.012161 CATTTTATCCAATTGGGTTTGTCATTT 57.988 29.630 24.29 0.00 38.11 2.32
4286 7722 8.614469 TTTTATCCAATTGGGTTTGTCATTTC 57.386 30.769 24.29 0.00 38.11 2.17
4287 7723 7.552050 TTATCCAATTGGGTTTGTCATTTCT 57.448 32.000 24.29 0.00 38.11 2.52
4288 7724 5.467035 TCCAATTGGGTTTGTCATTTCTC 57.533 39.130 24.29 0.00 38.11 2.87
4289 7725 4.283212 TCCAATTGGGTTTGTCATTTCTCC 59.717 41.667 24.29 0.00 38.11 3.71
4290 7726 4.563374 CCAATTGGGTTTGTCATTTCTCCC 60.563 45.833 17.36 0.00 35.85 4.30
4291 7727 3.611025 TTGGGTTTGTCATTTCTCCCT 57.389 42.857 0.00 0.00 36.23 4.20
4292 7728 3.611025 TGGGTTTGTCATTTCTCCCTT 57.389 42.857 0.00 0.00 36.23 3.95
4293 7729 3.496331 TGGGTTTGTCATTTCTCCCTTC 58.504 45.455 0.00 0.00 36.23 3.46
4294 7730 2.826128 GGGTTTGTCATTTCTCCCTTCC 59.174 50.000 0.00 0.00 32.89 3.46
4318 7754 5.417894 CCCCCTACTGGTTTTGTTATTTCTC 59.582 44.000 0.00 0.00 0.00 2.87
4327 7763 7.722363 TGGTTTTGTTATTTCTCCCTCTTTTC 58.278 34.615 0.00 0.00 0.00 2.29
4329 7765 5.622770 TTGTTATTTCTCCCTCTTTTCGC 57.377 39.130 0.00 0.00 0.00 4.70
4332 7768 1.523758 TTTCTCCCTCTTTTCGCTGC 58.476 50.000 0.00 0.00 0.00 5.25
4356 7792 4.215399 TGGTTTTTGTCTTCGCTTCCATAG 59.785 41.667 0.00 0.00 0.00 2.23
4363 7799 4.220821 TGTCTTCGCTTCCATAGTTCTCTT 59.779 41.667 0.00 0.00 0.00 2.85
4429 8853 4.021981 GGTAAAAGGACAAAGAGCAATGCT 60.022 41.667 7.79 7.79 43.88 3.79
4448 8872 2.875672 GCTGTGAGGATTGTGCTACCAA 60.876 50.000 0.00 0.00 0.00 3.67
4480 8904 3.515630 CAGTGTTCTCGTGCTCATATGT 58.484 45.455 1.90 0.00 0.00 2.29
4489 8913 4.918588 TCGTGCTCATATGTATCTCCCTA 58.081 43.478 1.90 0.00 0.00 3.53
4537 8962 8.450434 ACCTTTGGTTACTATCCTTAGGAAAAA 58.550 33.333 4.56 0.00 29.87 1.94
4578 9004 2.923121 AGTCGACGCCTACTACCATAA 58.077 47.619 10.46 0.00 0.00 1.90
4585 9011 3.835978 ACGCCTACTACCATAATATGCCA 59.164 43.478 0.00 0.00 0.00 4.92
4602 9028 8.721019 AATATGCCATCACAATTTGGTTAAAG 57.279 30.769 0.78 0.00 35.34 1.85
4605 9031 6.586344 TGCCATCACAATTTGGTTAAAGAAA 58.414 32.000 0.78 0.00 35.34 2.52
4612 9038 8.744652 TCACAATTTGGTTAAAGAAACTTCTCA 58.255 29.630 0.78 0.00 38.23 3.27
4626 9052 8.697507 AGAAACTTCTCAACCACTTGAATAAT 57.302 30.769 0.00 0.00 35.92 1.28
4657 9083 9.720667 AGTAAAACAAATAACGTTTAGGTGTTC 57.279 29.630 5.91 1.84 35.57 3.18
4663 9089 9.720667 ACAAATAACGTTTAGGTGTTCTTTTAC 57.279 29.630 5.91 0.00 0.00 2.01
4664 9090 8.885108 CAAATAACGTTTAGGTGTTCTTTTACG 58.115 33.333 5.91 0.00 0.00 3.18
4665 9091 4.457433 ACGTTTAGGTGTTCTTTTACGC 57.543 40.909 0.00 0.00 0.00 4.42
4666 9092 4.122046 ACGTTTAGGTGTTCTTTTACGCT 58.878 39.130 0.00 0.00 0.00 5.07
4667 9093 5.288804 ACGTTTAGGTGTTCTTTTACGCTA 58.711 37.500 0.00 0.00 0.00 4.26
4668 9094 5.175673 ACGTTTAGGTGTTCTTTTACGCTAC 59.824 40.000 0.00 0.00 0.00 3.58
4669 9095 5.602516 GTTTAGGTGTTCTTTTACGCTACG 58.397 41.667 0.00 0.00 0.00 3.51
4674 9100 2.029649 TGTTCTTTTACGCTACGAGCCT 60.030 45.455 0.00 0.00 38.18 4.58
4681 9107 3.213402 GCTACGAGCCTCTCCGCT 61.213 66.667 0.00 0.00 43.42 5.52
4693 9119 4.772231 TCCGCTTAGCCCCTCCGT 62.772 66.667 0.00 0.00 0.00 4.69
4780 9208 1.740296 ACGGCGAACACCATACTGC 60.740 57.895 16.62 0.00 0.00 4.40
4781 9209 1.447838 CGGCGAACACCATACTGCT 60.448 57.895 0.00 0.00 0.00 4.24
4798 9232 1.377725 CTCCACGATGGCTTTGGCT 60.378 57.895 0.00 0.00 37.47 4.75
4803 9237 0.035152 ACGATGGCTTTGGCTGATCA 60.035 50.000 0.00 0.00 38.73 2.92
4846 9280 0.036388 TTGCGCTAGAGGTTTGGAGG 60.036 55.000 9.73 0.00 0.00 4.30
4939 9373 0.532573 GCTCCAAGATCCGTCTCACA 59.467 55.000 0.00 0.00 32.15 3.58
4981 9415 0.392336 TCTTGGCATGTTTTGGTGGC 59.608 50.000 0.00 0.00 40.89 5.01
5121 9558 3.935172 TCAATTTCCTTCTTTGGGGGTT 58.065 40.909 0.00 0.00 0.00 4.11
5245 9682 2.110011 AGCTCTTAGATCTCCCTCCTCC 59.890 54.545 0.00 0.00 0.00 4.30
5255 9692 2.592512 TCTCCCTCCTCCTACCAGAATT 59.407 50.000 0.00 0.00 0.00 2.17
5263 9700 3.553922 CCTCCTACCAGAATTCTGATCGC 60.554 52.174 32.49 0.00 46.59 4.58
5268 9705 2.026822 ACCAGAATTCTGATCGCAACCT 60.027 45.455 32.49 1.45 46.59 3.50
5454 9891 1.964223 TCGGCCCAGTTGCAAAAATAA 59.036 42.857 0.00 0.00 0.00 1.40
5455 9892 2.365617 TCGGCCCAGTTGCAAAAATAAA 59.634 40.909 0.00 0.00 0.00 1.40
5470 9907 7.042187 TGCAAAAATAAAATCAAATGTCGTGCT 60.042 29.630 0.00 0.00 0.00 4.40
5485 9922 2.202395 TGCTTGCAAGAAGTGGGGC 61.202 57.895 30.39 13.14 0.00 5.80
5488 9925 0.901580 CTTGCAAGAAGTGGGGCCAT 60.902 55.000 22.31 0.00 0.00 4.40
5497 9934 1.148273 GTGGGGCCATATTGCTCGA 59.852 57.895 4.39 0.00 30.27 4.04
5506 9943 3.370366 GCCATATTGCTCGAGATTGCTAG 59.630 47.826 18.75 0.02 0.00 3.42
5511 9948 2.369394 TGCTCGAGATTGCTAGTCTGA 58.631 47.619 18.75 0.00 0.00 3.27
5520 9957 1.365633 GCTAGTCTGATGGGCCTCG 59.634 63.158 4.53 0.00 0.00 4.63
5524 9961 4.147449 TCTGATGGGCCTCGTGCG 62.147 66.667 4.53 0.00 42.61 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 2.095853 GCAAACGATACATGGTGGTGAG 59.904 50.000 0.00 0.00 0.00 3.51
29 30 0.037697 AAGATCACAAGTACGCGGCA 60.038 50.000 12.47 0.00 0.00 5.69
33 34 7.573627 AGTTAAAGAAAAGATCACAAGTACGC 58.426 34.615 0.00 0.00 0.00 4.42
50 51 3.132646 TCGCCCCGCTTTATAGTTAAAGA 59.867 43.478 9.14 0.00 44.75 2.52
56 57 1.949465 CTTTCGCCCCGCTTTATAGT 58.051 50.000 0.00 0.00 0.00 2.12
96 97 5.649782 ATTGTCATGGGTCAATGAGTTTC 57.350 39.130 9.58 0.00 37.24 2.78
103 104 3.269381 AGGTGGTATTGTCATGGGTCAAT 59.731 43.478 13.14 13.14 36.82 2.57
111 112 3.440173 CGCTGAAAAGGTGGTATTGTCAT 59.560 43.478 0.00 0.00 0.00 3.06
147 148 8.085909 TCTGATACAAATTGACGACTGAGTTTA 58.914 33.333 0.00 0.00 0.00 2.01
206 207 0.674895 AGCCTTGCTTCGCTAACCTG 60.675 55.000 0.00 0.00 33.89 4.00
228 229 1.544759 CGGCCCTCTTGTAAAACCACT 60.545 52.381 0.00 0.00 0.00 4.00
232 233 3.667360 TCTAACGGCCCTCTTGTAAAAC 58.333 45.455 0.00 0.00 0.00 2.43
247 248 3.262420 ACCTAAGCACTTGCATCTAACG 58.738 45.455 3.62 0.00 45.16 3.18
272 273 1.226030 ACGGCAGAAAGTAACACGCC 61.226 55.000 0.00 0.00 36.16 5.68
281 282 2.322161 CATTGCAAGAACGGCAGAAAG 58.678 47.619 4.94 0.00 43.05 2.62
301 302 4.440112 GCATGTTGGAGTAAGCATAAACCC 60.440 45.833 0.00 0.00 0.00 4.11
318 319 9.941325 TCCTGACAATTTATATTTTTGCATGTT 57.059 25.926 0.00 0.00 0.00 2.71
330 331 6.774673 TGTCTGTTGGTCCTGACAATTTATA 58.225 36.000 0.00 0.00 39.42 0.98
332 333 5.042463 TGTCTGTTGGTCCTGACAATTTA 57.958 39.130 0.00 0.00 39.42 1.40
333 334 3.897239 TGTCTGTTGGTCCTGACAATTT 58.103 40.909 0.00 0.00 39.42 1.82
336 337 4.908601 ATATGTCTGTTGGTCCTGACAA 57.091 40.909 10.09 0.00 43.53 3.18
369 373 3.855689 ACTTGTTTGGCATATGTCTGC 57.144 42.857 9.09 0.00 41.53 4.26
387 391 2.636830 GCCTGCACTTCATCACATACT 58.363 47.619 0.00 0.00 0.00 2.12
388 392 1.328680 CGCCTGCACTTCATCACATAC 59.671 52.381 0.00 0.00 0.00 2.39
389 393 1.066215 ACGCCTGCACTTCATCACATA 60.066 47.619 0.00 0.00 0.00 2.29
390 394 0.321919 ACGCCTGCACTTCATCACAT 60.322 50.000 0.00 0.00 0.00 3.21
399 403 1.942657 CTGCATATAAACGCCTGCACT 59.057 47.619 0.00 0.00 39.54 4.40
400 404 1.939934 TCTGCATATAAACGCCTGCAC 59.060 47.619 0.00 0.00 39.54 4.57
426 430 2.557056 TGACACGCAGCTAACTTAGACT 59.443 45.455 0.00 0.00 0.00 3.24
522 528 4.410400 GGGGAGCACCGTTCAGGG 62.410 72.222 0.00 0.00 46.96 4.45
524 530 4.760047 CGGGGGAGCACCGTTCAG 62.760 72.222 0.00 0.00 46.03 3.02
531 537 1.705997 ATTATGGGACGGGGGAGCAC 61.706 60.000 0.00 0.00 0.00 4.40
533 539 1.286248 ATATTATGGGACGGGGGAGC 58.714 55.000 0.00 0.00 0.00 4.70
539 545 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
647 661 8.456471 TCGATTCGACTAGATCTTGTTAGAAAA 58.544 33.333 22.19 13.71 33.20 2.29
658 672 5.109662 TCCAACATCGATTCGACTAGATC 57.890 43.478 11.56 0.00 39.18 2.75
662 676 2.425668 TGCTCCAACATCGATTCGACTA 59.574 45.455 11.56 0.00 39.18 2.59
666 680 1.590238 GTCTGCTCCAACATCGATTCG 59.410 52.381 0.00 0.00 0.00 3.34
674 688 2.741092 GGTCCGTCTGCTCCAACA 59.259 61.111 0.00 0.00 0.00 3.33
685 699 5.990120 AATATTAAGCTATACCGGTCCGT 57.010 39.130 12.40 0.32 0.00 4.69
717 731 2.294791 GTCACTGCTGACTAGTCACACT 59.705 50.000 21.74 10.55 43.26 3.55
777 799 5.187772 AGTTGACAGTATGCTGGATTGAGTA 59.812 40.000 15.65 0.00 46.62 2.59
807 829 7.042523 GCTCAGTAATGCAAAGATTTTTGTGTT 60.043 33.333 10.14 7.86 44.41 3.32
809 831 6.128742 GGCTCAGTAATGCAAAGATTTTTGTG 60.129 38.462 10.14 0.56 44.41 3.33
817 839 2.472695 ACGGCTCAGTAATGCAAAGA 57.527 45.000 0.00 0.00 0.00 2.52
856 878 2.203480 GTTCCAGCCTTGGCCACA 60.203 61.111 3.88 0.00 44.63 4.17
860 882 2.032681 ACTCGTTCCAGCCTTGGC 59.967 61.111 2.97 2.97 44.63 4.52
881 903 4.050553 ACAAAATGCATCGACAAACAAGG 58.949 39.130 0.00 0.00 0.00 3.61
925 947 6.095021 TGCTAAGTGGTGTCGGCTATATATAG 59.905 42.308 14.45 14.45 0.00 1.31
926 948 5.947566 TGCTAAGTGGTGTCGGCTATATATA 59.052 40.000 0.00 0.00 0.00 0.86
927 949 4.770531 TGCTAAGTGGTGTCGGCTATATAT 59.229 41.667 0.00 0.00 0.00 0.86
928 950 4.146564 TGCTAAGTGGTGTCGGCTATATA 58.853 43.478 0.00 0.00 0.00 0.86
943 965 3.877559 TGTGCTATTGATGCTGCTAAGT 58.122 40.909 0.00 0.00 0.00 2.24
947 969 3.252701 GCTAATGTGCTATTGATGCTGCT 59.747 43.478 0.00 0.00 0.00 4.24
970 992 2.422746 AGGCCTAAAGCATACTCCCAT 58.577 47.619 1.29 0.00 46.50 4.00
971 993 1.893315 AGGCCTAAAGCATACTCCCA 58.107 50.000 1.29 0.00 46.50 4.37
972 994 4.135306 GTTAAGGCCTAAAGCATACTCCC 58.865 47.826 5.16 0.00 46.50 4.30
973 995 3.808174 CGTTAAGGCCTAAAGCATACTCC 59.192 47.826 5.16 0.00 46.50 3.85
974 996 4.690122 TCGTTAAGGCCTAAAGCATACTC 58.310 43.478 5.16 0.00 46.50 2.59
981 1009 3.741344 CCATCGATCGTTAAGGCCTAAAG 59.259 47.826 15.94 3.62 0.00 1.85
997 1025 2.685017 AGCCTGCCACTCCATCGA 60.685 61.111 0.00 0.00 0.00 3.59
1014 1042 2.669133 CCCGGTGAAGCATGGGAGA 61.669 63.158 0.00 0.00 44.88 3.71
1015 1043 2.124570 CCCGGTGAAGCATGGGAG 60.125 66.667 0.00 0.00 44.88 4.30
1017 1045 2.438434 GTCCCGGTGAAGCATGGG 60.438 66.667 0.00 0.00 43.36 4.00
1018 1046 2.438434 GGTCCCGGTGAAGCATGG 60.438 66.667 0.00 0.00 0.00 3.66
1033 1079 1.375523 GAAGGATCAACACGGCGGT 60.376 57.895 13.24 3.10 0.00 5.68
1047 1093 3.821421 AACGGCAGGACTATAAGAAGG 57.179 47.619 0.00 0.00 0.00 3.46
1060 1106 2.726691 CGGACGCACTAAACGGCAG 61.727 63.158 0.00 0.00 41.50 4.85
1098 1145 3.721706 CCAGGGGAGAGCGGCTTT 61.722 66.667 2.97 0.00 0.00 3.51
1173 1220 1.149101 ACAACTTGGTGGGAGTGGAT 58.851 50.000 0.00 0.00 0.00 3.41
1189 1236 2.953093 TACCAGATCCCCAGGTACAA 57.047 50.000 0.00 0.00 36.87 2.41
1200 1247 1.583054 GGATGCCGTTGTACCAGATC 58.417 55.000 0.00 0.00 0.00 2.75
1212 1259 2.180204 CGTAAGCTTGGGGATGCCG 61.180 63.158 9.86 0.00 0.00 5.69
1214 1261 1.230324 GATCGTAAGCTTGGGGATGC 58.770 55.000 9.86 0.81 37.18 3.91
1221 1268 0.999406 CCCACACGATCGTAAGCTTG 59.001 55.000 22.26 10.08 37.18 4.01
1222 1269 0.606604 ACCCACACGATCGTAAGCTT 59.393 50.000 22.26 3.48 37.18 3.74
1227 1274 2.486504 GCGACCCACACGATCGTA 59.513 61.111 22.26 0.00 38.13 3.43
1230 1277 2.047655 TTGGCGACCCACACGATC 60.048 61.111 0.00 0.00 41.97 3.69
1231 1278 2.358247 GTTGGCGACCCACACGAT 60.358 61.111 0.00 0.00 41.97 3.73
1275 1322 8.021973 AGTACAATACTTTCTAACACAGACGAG 58.978 37.037 0.00 0.00 34.86 4.18
1347 1394 1.067846 ACACACACGCACACGATCTAT 60.068 47.619 0.00 0.00 43.93 1.98
1379 1426 3.860647 ACCCTAACCACCTAACTACCT 57.139 47.619 0.00 0.00 0.00 3.08
1391 1439 6.126739 ACAAGATCTGAGGATAAACCCTAACC 60.127 42.308 0.00 0.00 40.05 2.85
1490 1540 2.429930 CCTTTGGACAGGGACGCA 59.570 61.111 0.00 0.00 0.00 5.24
1500 1550 1.448893 GGACGCGTATGCCTTTGGA 60.449 57.895 13.97 0.00 38.08 3.53
1515 1565 1.336755 ACCATGAAAGTTTGCGTGGAC 59.663 47.619 22.53 0.00 42.50 4.02
1538 1588 2.680312 TTGCTACTAGCCTTGCTCTG 57.320 50.000 5.58 0.00 41.51 3.35
1539 1589 2.093235 CCTTTGCTACTAGCCTTGCTCT 60.093 50.000 5.58 0.00 41.51 4.09
1540 1590 2.284190 CCTTTGCTACTAGCCTTGCTC 58.716 52.381 5.58 0.00 41.51 4.26
1541 1591 1.065126 CCCTTTGCTACTAGCCTTGCT 60.065 52.381 5.58 0.00 41.51 3.91
1676 5034 0.865769 ACGCGTTCTGAACATCCAAC 59.134 50.000 19.56 1.95 0.00 3.77
1802 5160 3.154710 AGCCCTAGGTGCTTGTTTTAAC 58.845 45.455 16.47 0.00 34.87 2.01
1855 5213 8.028652 TCCTTTGGATAATTTGAAACCAAGTT 57.971 30.769 0.00 0.00 40.80 2.66
1870 5233 5.455872 ACGAGGAAGTATCTCCTTTGGATA 58.544 41.667 0.00 0.00 46.33 2.59
1891 5254 9.982651 TGATATCTCCTTTCCTATAAAAGAACG 57.017 33.333 3.98 0.00 38.30 3.95
1952 5315 2.416747 TCTTGTGATGAGCTGGAAACG 58.583 47.619 0.00 0.00 0.00 3.60
1992 5355 9.129532 CAAGGCAAAATCCTTCTTAAGATCTAT 57.870 33.333 5.89 0.00 44.24 1.98
2126 5492 5.649557 TGAAATCTGCAATTTACCATTCCG 58.350 37.500 6.78 0.00 0.00 4.30
2184 5551 3.307762 CCCCAACGATTCTCCTTCTTCTT 60.308 47.826 0.00 0.00 0.00 2.52
2198 5565 2.530958 GATTCTTCGGCCCCCAACGA 62.531 60.000 0.00 0.00 37.33 3.85
2200 5567 0.610785 TTGATTCTTCGGCCCCCAAC 60.611 55.000 0.00 0.00 0.00 3.77
2275 5643 6.783708 ACCTTGTTGACAGGAAAACAAATA 57.216 33.333 2.96 0.00 43.59 1.40
2406 5776 7.695618 CAGAGAAAGCACTAACAATATTTGAGC 59.304 37.037 0.00 0.00 0.00 4.26
2410 5780 8.186821 GCATCAGAGAAAGCACTAACAATATTT 58.813 33.333 0.00 0.00 0.00 1.40
2494 5864 6.258947 GCACTCCAAGATATCAAGTTAGGAAC 59.741 42.308 5.32 0.00 0.00 3.62
2495 5865 6.070251 TGCACTCCAAGATATCAAGTTAGGAA 60.070 38.462 5.32 0.00 0.00 3.36
2508 5879 1.001974 TGCTTACGTGCACTCCAAGAT 59.998 47.619 16.19 0.00 38.12 2.40
2529 5900 2.100087 GCTAGACCTGAAGACTGTAGCC 59.900 54.545 0.00 0.00 0.00 3.93
2535 5906 3.088532 CTCTGTGCTAGACCTGAAGACT 58.911 50.000 0.00 0.00 0.00 3.24
2540 5911 0.040351 AGCCTCTGTGCTAGACCTGA 59.960 55.000 0.00 0.00 40.56 3.86
2550 5921 4.199432 AGATTTGTACTCAGCCTCTGTG 57.801 45.455 0.00 0.00 32.61 3.66
2589 5960 6.662616 CATAGCTTGAACCCAAATAATCTCG 58.337 40.000 0.00 0.00 0.00 4.04
2622 5993 2.754552 TGGTGAATGCATAACTCCAAGC 59.245 45.455 18.64 3.44 0.00 4.01
2691 6062 6.422333 TGTCCTTGCATGAAATACTGGATTA 58.578 36.000 0.00 0.00 0.00 1.75
2774 6145 5.190132 TCCCCTGTAGGAATAAAACGAATGA 59.810 40.000 0.00 0.00 38.24 2.57
2790 6161 0.911769 CTGCAACCTGATCCCCTGTA 59.088 55.000 0.00 0.00 0.00 2.74
2951 6322 3.439476 ACGCACACGATCTATCCCTATAC 59.561 47.826 0.00 0.00 43.93 1.47
3082 6482 4.539870 GCGTACGTGTTTATATAGCCAGA 58.460 43.478 17.90 0.00 0.00 3.86
3150 6552 0.469331 TGAAGGAGAGTGTCGGTGGT 60.469 55.000 0.00 0.00 0.00 4.16
3151 6553 0.038159 GTGAAGGAGAGTGTCGGTGG 60.038 60.000 0.00 0.00 0.00 4.61
3210 6612 1.104577 TTGCCCAAAGAACACGTCCC 61.105 55.000 0.00 0.00 0.00 4.46
3309 6714 1.373246 CAACATGCTGCCGTTTGGG 60.373 57.895 0.00 0.00 39.58 4.12
3320 6725 1.262151 CAAAGCTTTGCCACAACATGC 59.738 47.619 25.26 0.00 0.00 4.06
3561 6969 2.032799 GGAGTTGTTGTTCATGCGTTGA 59.967 45.455 0.00 0.00 0.00 3.18
3613 7042 8.958506 GGTATACGTGACATATATCTCTTCCTT 58.041 37.037 0.00 0.00 0.00 3.36
3657 7088 0.882927 CACGTACCTTGTGTGGGTGG 60.883 60.000 0.00 0.00 37.65 4.61
3658 7089 2.612200 CACGTACCTTGTGTGGGTG 58.388 57.895 0.00 0.00 37.65 4.61
3803 7238 1.594293 CTGGCAACACCGTCTCGTT 60.594 57.895 0.00 0.00 46.17 3.85
3873 7308 0.472925 TGAGAACCTACCACTGGCCA 60.473 55.000 4.71 4.71 0.00 5.36
3966 7401 2.480416 CCTATGCGAGTGAACCTGTCTC 60.480 54.545 0.00 0.00 0.00 3.36
3989 7424 3.016736 CCTCAAATGTACTTCCGCCAAT 58.983 45.455 0.00 0.00 0.00 3.16
3990 7425 2.039216 TCCTCAAATGTACTTCCGCCAA 59.961 45.455 0.00 0.00 0.00 4.52
4132 7567 0.454600 CTGCGCTAGACTTTCCGGTA 59.545 55.000 9.73 0.00 0.00 4.02
4208 7643 2.033424 AGAGCAAGAAACCGAGTTTTGC 59.967 45.455 13.66 13.66 38.65 3.68
4240 7675 1.680735 TGCGTGAGAATTGGCAAAACT 59.319 42.857 3.01 6.63 31.50 2.66
4241 7676 2.132740 TGCGTGAGAATTGGCAAAAC 57.867 45.000 3.01 1.11 31.50 2.43
4246 7681 4.044426 GGATAAAATGCGTGAGAATTGGC 58.956 43.478 0.00 0.00 38.81 4.52
4247 7682 5.247507 TGGATAAAATGCGTGAGAATTGG 57.752 39.130 0.00 0.00 38.81 3.16
4248 7683 7.254185 CCAATTGGATAAAATGCGTGAGAATTG 60.254 37.037 20.50 0.00 37.02 2.32
4249 7684 6.757947 CCAATTGGATAAAATGCGTGAGAATT 59.242 34.615 20.50 0.00 38.12 2.17
4250 7685 6.275335 CCAATTGGATAAAATGCGTGAGAAT 58.725 36.000 20.50 0.00 37.39 2.40
4251 7686 5.394005 CCCAATTGGATAAAATGCGTGAGAA 60.394 40.000 26.60 0.00 37.39 2.87
4252 7687 4.097741 CCCAATTGGATAAAATGCGTGAGA 59.902 41.667 26.60 0.00 37.39 3.27
4253 7688 4.142182 ACCCAATTGGATAAAATGCGTGAG 60.142 41.667 26.60 6.08 37.39 3.51
4256 7691 4.817318 AACCCAATTGGATAAAATGCGT 57.183 36.364 26.60 8.67 37.39 5.24
4260 7695 9.230122 GAAATGACAAACCCAATTGGATAAAAT 57.770 29.630 26.60 6.44 37.39 1.82
4275 7711 2.826128 GGGGAAGGGAGAAATGACAAAC 59.174 50.000 0.00 0.00 0.00 2.93
4277 7713 1.357761 GGGGGAAGGGAGAAATGACAA 59.642 52.381 0.00 0.00 0.00 3.18
4278 7714 0.999712 GGGGGAAGGGAGAAATGACA 59.000 55.000 0.00 0.00 0.00 3.58
4279 7715 3.905331 GGGGGAAGGGAGAAATGAC 57.095 57.895 0.00 0.00 0.00 3.06
4294 7730 5.330233 AGAAATAACAAAACCAGTAGGGGG 58.670 41.667 0.00 0.00 42.91 5.40
4311 7747 3.055094 AGCAGCGAAAAGAGGGAGAAATA 60.055 43.478 0.00 0.00 0.00 1.40
4318 7754 0.890996 AACCAGCAGCGAAAAGAGGG 60.891 55.000 0.00 0.00 0.00 4.30
4327 7763 1.758783 GAAGACAAAAACCAGCAGCG 58.241 50.000 0.00 0.00 0.00 5.18
4329 7765 1.334869 AGCGAAGACAAAAACCAGCAG 59.665 47.619 0.00 0.00 0.00 4.24
4332 7768 2.357637 TGGAAGCGAAGACAAAAACCAG 59.642 45.455 0.00 0.00 0.00 4.00
4356 7792 7.484140 AGAGAAAAACATTGTGGAAAGAGAAC 58.516 34.615 0.00 0.00 0.00 3.01
4363 7799 7.595819 ACCATAAGAGAAAAACATTGTGGAA 57.404 32.000 6.57 0.00 37.36 3.53
4399 7860 5.183140 GCTCTTTGTCCTTTTACCTATGCAA 59.817 40.000 0.00 0.00 0.00 4.08
4429 8853 3.719268 ATTGGTAGCACAATCCTCACA 57.281 42.857 0.00 0.00 36.36 3.58
4448 8872 2.287788 CGAGAACACTGCTGCCAAAAAT 60.288 45.455 0.00 0.00 0.00 1.82
4480 8904 5.912149 ATTTGAACCATGCTAGGGAGATA 57.088 39.130 0.00 0.00 0.00 1.98
4489 8913 4.961438 ACCTTTGAATTTGAACCATGCT 57.039 36.364 0.00 0.00 0.00 3.79
4537 8962 7.881232 TCGACTTCCAAGTTGGTCTAATAAAAT 59.119 33.333 21.35 0.00 39.88 1.82
4540 8965 6.161381 GTCGACTTCCAAGTTGGTCTAATAA 58.839 40.000 21.35 6.54 39.88 1.40
4578 9004 8.076910 TCTTTAACCAAATTGTGATGGCATAT 57.923 30.769 0.00 0.00 40.51 1.78
4585 9011 9.750125 GAGAAGTTTCTTTAACCAAATTGTGAT 57.250 29.630 0.00 0.00 37.73 3.06
4635 9061 9.642327 AAAAGAACACCTAAACGTTATTTGTTT 57.358 25.926 0.00 0.00 36.83 2.83
4653 9079 2.029649 AGGCTCGTAGCGTAAAAGAACA 60.030 45.455 1.14 0.00 43.62 3.18
4657 9083 2.452105 GAGAGGCTCGTAGCGTAAAAG 58.548 52.381 9.22 0.00 43.62 2.27
4662 9088 3.203412 CGGAGAGGCTCGTAGCGT 61.203 66.667 9.22 2.45 43.62 5.07
4663 9089 4.615834 GCGGAGAGGCTCGTAGCG 62.616 72.222 9.22 0.00 43.62 4.26
4664 9090 1.445716 TAAGCGGAGAGGCTCGTAGC 61.446 60.000 18.53 18.53 43.93 3.58
4665 9091 0.589223 CTAAGCGGAGAGGCTCGTAG 59.411 60.000 9.22 5.36 43.93 3.51
4666 9092 1.445716 GCTAAGCGGAGAGGCTCGTA 61.446 60.000 9.22 0.00 43.93 3.43
4667 9093 2.776913 GCTAAGCGGAGAGGCTCGT 61.777 63.158 9.22 0.00 43.93 4.18
4668 9094 2.026879 GCTAAGCGGAGAGGCTCG 59.973 66.667 9.22 0.00 43.93 5.03
4669 9095 2.419620 GGCTAAGCGGAGAGGCTC 59.580 66.667 6.34 6.34 43.93 4.70
4674 9100 2.444140 GGAGGGGCTAAGCGGAGA 60.444 66.667 0.00 0.00 0.00 3.71
4681 9107 3.145551 GCTCGACGGAGGGGCTAA 61.146 66.667 0.00 0.00 40.80 3.09
4780 9208 1.377725 AGCCAAAGCCATCGTGGAG 60.378 57.895 8.04 0.00 40.96 3.86
4781 9209 1.675310 CAGCCAAAGCCATCGTGGA 60.675 57.895 8.04 0.00 40.96 4.02
4798 9232 5.304778 TGACCTTTGTCGAAATTCTGATCA 58.695 37.500 0.00 0.00 44.86 2.92
4803 9237 5.368989 AGTCTTGACCTTTGTCGAAATTCT 58.631 37.500 0.00 0.00 44.86 2.40
4846 9280 1.204146 TGATAGGCACTCCCCACTTC 58.796 55.000 0.00 0.00 41.75 3.01
4939 9373 4.406003 AGAATAGTAGCAACCGAATCCACT 59.594 41.667 0.00 0.00 0.00 4.00
4981 9415 1.081892 CCTTGAACAGAGATGCACGG 58.918 55.000 0.00 0.00 0.00 4.94
5030 9464 3.831911 ACTTCTTTGGAGGAGACAGAGAG 59.168 47.826 0.00 0.00 31.76 3.20
5121 9558 3.564133 CCAAGATGAATTTGGTCCTCCCA 60.564 47.826 0.00 0.00 43.27 4.37
5245 9682 3.557595 GGTTGCGATCAGAATTCTGGTAG 59.442 47.826 30.33 25.53 43.91 3.18
5255 9692 0.901827 TTGCCTAGGTTGCGATCAGA 59.098 50.000 11.31 0.00 0.00 3.27
5263 9700 2.359900 GATCTGGTGTTGCCTAGGTTG 58.640 52.381 11.31 0.00 38.35 3.77
5268 9705 1.412710 GATCCGATCTGGTGTTGCCTA 59.587 52.381 0.75 0.00 39.52 3.93
5454 9891 3.367992 TGCAAGCACGACATTTGATTT 57.632 38.095 0.00 0.00 0.00 2.17
5455 9892 3.004629 TCTTGCAAGCACGACATTTGATT 59.995 39.130 21.99 0.00 0.00 2.57
5470 9907 0.407528 TATGGCCCCACTTCTTGCAA 59.592 50.000 0.00 0.00 0.00 4.08
5485 9922 4.564041 ACTAGCAATCTCGAGCAATATGG 58.436 43.478 7.81 0.00 0.00 2.74
5488 9925 4.580580 TCAGACTAGCAATCTCGAGCAATA 59.419 41.667 7.81 0.00 0.00 1.90
5497 9934 1.419387 GGCCCATCAGACTAGCAATCT 59.581 52.381 0.00 0.00 0.00 2.40
5506 9943 2.512515 GCACGAGGCCCATCAGAC 60.513 66.667 0.00 0.00 36.11 3.51


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

AutoCloner maintained by Alex Coulton.