Multiple sequence alignment - TraesCS7A01G217300

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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 TraesCS7A01G217300 chr7A 100.000 4776 0 0 1 4776 183859858 183855083 0.000000e+00 8820
1 TraesCS7A01G217300 chr7A 84.787 2682 325 46 998 3645 183951407 183948775 0.000000e+00 2615
2 TraesCS7A01G217300 chr7A 81.913 1244 176 30 2410 3633 183918191 183916977 0.000000e+00 1005
3 TraesCS7A01G217300 chr7A 77.405 1164 198 44 1286 2413 183920896 183919762 2.430000e-177 632
4 TraesCS7A01G217300 chr7A 83.205 518 81 4 4260 4773 512103943 512104458 2.010000e-128 470
5 TraesCS7A01G217300 chr7D 87.660 2658 245 33 998 3643 179537257 179534671 0.000000e+00 3014
6 TraesCS7A01G217300 chr7D 87.633 1787 178 28 2277 4049 179508958 179507201 0.000000e+00 2036
7 TraesCS7A01G217300 chr7D 80.400 2500 390 62 1190 3633 179523139 179520684 0.000000e+00 1810
8 TraesCS7A01G217300 chr7D 84.180 1024 103 29 3 990 179511277 179510277 0.000000e+00 939
9 TraesCS7A01G217300 chr7D 85.080 878 110 12 1182 2047 179510097 179509229 0.000000e+00 876
10 TraesCS7A01G217300 chr7D 93.561 528 33 1 4250 4776 500161376 500160849 0.000000e+00 785
11 TraesCS7A01G217300 chr7D 80.556 1044 111 40 7 990 179952891 179951880 0.000000e+00 719
12 TraesCS7A01G217300 chr7D 86.842 532 67 2 4247 4776 441356493 441357023 4.120000e-165 592
13 TraesCS7A01G217300 chr7D 79.050 821 153 14 2296 3108 94114612 94113803 3.250000e-151 545
14 TraesCS7A01G217300 chr7D 85.404 507 70 2 4264 4770 564081866 564082368 1.520000e-144 523
15 TraesCS7A01G217300 chr7B 89.585 2074 194 12 1610 3674 145740298 145738238 0.000000e+00 2614
16 TraesCS7A01G217300 chr7B 88.050 1749 167 26 2317 4049 145697359 145695637 0.000000e+00 2034
17 TraesCS7A01G217300 chr7B 80.751 2504 380 64 1190 3633 145711626 145709165 0.000000e+00 1860
18 TraesCS7A01G217300 chr7B 84.133 1021 98 31 3 990 145699890 145698901 0.000000e+00 929
19 TraesCS7A01G217300 chr7B 83.502 891 117 18 1182 2052 145698721 145697841 0.000000e+00 804
20 TraesCS7A01G217300 chr7B 83.019 848 100 26 795 1618 145741165 145740338 0.000000e+00 728
21 TraesCS7A01G217300 chr7B 78.762 824 156 14 2296 3111 48050320 48049508 7.040000e-148 534
22 TraesCS7A01G217300 chr7B 81.959 582 61 24 423 990 145790764 145790213 2.030000e-123 453
23 TraesCS7A01G217300 chr7B 94.000 150 9 0 4055 4204 145695561 145695412 1.340000e-55 228
24 TraesCS7A01G217300 chr5D 93.785 531 32 1 4247 4776 216048494 216047964 0.000000e+00 797
25 TraesCS7A01G217300 chr5D 76.446 242 50 6 2866 3104 549823129 549822892 1.800000e-24 124
26 TraesCS7A01G217300 chr6B 76.184 1394 256 47 2289 3620 672884465 672885844 0.000000e+00 665
27 TraesCS7A01G217300 chr6B 80.189 212 37 4 1666 1875 673616186 673615978 2.300000e-33 154
28 TraesCS7A01G217300 chr6D 79.051 864 159 18 2296 3145 445824608 445823753 1.490000e-159 573
29 TraesCS7A01G217300 chr6D 78.638 426 70 11 3215 3620 445894841 445895265 3.670000e-66 263
30 TraesCS7A01G217300 chr6D 75.255 392 73 15 1666 2035 445852816 445853205 1.060000e-36 165
31 TraesCS7A01G217300 chr4D 86.948 521 53 8 4257 4776 3983988 3984494 5.360000e-159 571
32 TraesCS7A01G217300 chr4D 86.381 514 66 3 4264 4776 504191132 504191642 4.170000e-155 558
33 TraesCS7A01G217300 chr3B 89.640 444 42 3 4336 4776 307611082 307611524 3.230000e-156 562
34 TraesCS7A01G217300 chr2D 83.144 528 89 0 4249 4776 72300836 72300309 2.580000e-132 483


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 TraesCS7A01G217300 chr7A 183855083 183859858 4775 True 8820.000000 8820 100.00000 1 4776 1 chr7A.!!$R1 4775
1 TraesCS7A01G217300 chr7A 183948775 183951407 2632 True 2615.000000 2615 84.78700 998 3645 1 chr7A.!!$R2 2647
2 TraesCS7A01G217300 chr7A 183916977 183920896 3919 True 818.500000 1005 79.65900 1286 3633 2 chr7A.!!$R3 2347
3 TraesCS7A01G217300 chr7A 512103943 512104458 515 False 470.000000 470 83.20500 4260 4773 1 chr7A.!!$F1 513
4 TraesCS7A01G217300 chr7D 179534671 179537257 2586 True 3014.000000 3014 87.66000 998 3643 1 chr7D.!!$R3 2645
5 TraesCS7A01G217300 chr7D 179520684 179523139 2455 True 1810.000000 1810 80.40000 1190 3633 1 chr7D.!!$R2 2443
6 TraesCS7A01G217300 chr7D 179507201 179511277 4076 True 1283.666667 2036 85.63100 3 4049 3 chr7D.!!$R6 4046
7 TraesCS7A01G217300 chr7D 500160849 500161376 527 True 785.000000 785 93.56100 4250 4776 1 chr7D.!!$R5 526
8 TraesCS7A01G217300 chr7D 179951880 179952891 1011 True 719.000000 719 80.55600 7 990 1 chr7D.!!$R4 983
9 TraesCS7A01G217300 chr7D 441356493 441357023 530 False 592.000000 592 86.84200 4247 4776 1 chr7D.!!$F1 529
10 TraesCS7A01G217300 chr7D 94113803 94114612 809 True 545.000000 545 79.05000 2296 3108 1 chr7D.!!$R1 812
11 TraesCS7A01G217300 chr7D 564081866 564082368 502 False 523.000000 523 85.40400 4264 4770 1 chr7D.!!$F2 506
12 TraesCS7A01G217300 chr7B 145709165 145711626 2461 True 1860.000000 1860 80.75100 1190 3633 1 chr7B.!!$R2 2443
13 TraesCS7A01G217300 chr7B 145738238 145741165 2927 True 1671.000000 2614 86.30200 795 3674 2 chr7B.!!$R5 2879
14 TraesCS7A01G217300 chr7B 145695412 145699890 4478 True 998.750000 2034 87.42125 3 4204 4 chr7B.!!$R4 4201
15 TraesCS7A01G217300 chr7B 48049508 48050320 812 True 534.000000 534 78.76200 2296 3111 1 chr7B.!!$R1 815
16 TraesCS7A01G217300 chr7B 145790213 145790764 551 True 453.000000 453 81.95900 423 990 1 chr7B.!!$R3 567
17 TraesCS7A01G217300 chr5D 216047964 216048494 530 True 797.000000 797 93.78500 4247 4776 1 chr5D.!!$R1 529
18 TraesCS7A01G217300 chr6B 672884465 672885844 1379 False 665.000000 665 76.18400 2289 3620 1 chr6B.!!$F1 1331
19 TraesCS7A01G217300 chr6D 445823753 445824608 855 True 573.000000 573 79.05100 2296 3145 1 chr6D.!!$R1 849
20 TraesCS7A01G217300 chr4D 3983988 3984494 506 False 571.000000 571 86.94800 4257 4776 1 chr4D.!!$F1 519
21 TraesCS7A01G217300 chr4D 504191132 504191642 510 False 558.000000 558 86.38100 4264 4776 1 chr4D.!!$F2 512
22 TraesCS7A01G217300 chr2D 72300309 72300836 527 True 483.000000 483 83.14400 4249 4776 1 chr2D.!!$R1 527

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
770 831 0.322008 GCTCCAGCTACCAGCAGTTT 60.322 55.0 5.97 0.0 45.56 2.66 F
1048 1157 0.530288 AGCAAAAACGCCACAACAGT 59.470 45.0 0.00 0.0 0.00 3.55 F
1136 1251 0.630673 AAACAGCCAGCCCCATGATA 59.369 50.0 0.00 0.0 0.00 2.15 F
2835 4927 0.394192 CCGGCTCCAAGATGATAGCA 59.606 55.0 0.00 0.0 36.68 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2695 4748 0.397816 TTCTTTGGTGGGGTTGGTGG 60.398 55.000 0.0 0.0 0.00 4.61 R
2697 4750 0.930726 TCTTCTTTGGTGGGGTTGGT 59.069 50.000 0.0 0.0 0.00 3.67 R
2972 5064 1.067060 AGTGCATAGCTTCGTATCGCA 59.933 47.619 0.0 0.0 0.00 5.10 R
4692 6913 0.036732 ATGCCTGAAAGAAGCGGACA 59.963 50.000 0.0 0.0 34.07 4.02 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
104 113 1.681166 GGCTGCATGTTCATGGAGACT 60.681 52.381 28.94 0.00 43.65 3.24
110 119 3.064545 GCATGTTCATGGAGACTAGTTGC 59.935 47.826 13.55 0.00 0.00 4.17
111 120 4.256110 CATGTTCATGGAGACTAGTTGCA 58.744 43.478 0.00 0.00 0.00 4.08
112 121 3.930336 TGTTCATGGAGACTAGTTGCAG 58.070 45.455 0.00 0.00 0.00 4.41
153 162 0.539986 TTGTCGTCTAATGGAGGCCC 59.460 55.000 0.00 0.00 0.00 5.80
200 212 1.301423 GGGTTTCGTACAGTGTGCAA 58.699 50.000 12.06 2.63 0.00 4.08
208 220 2.285083 GTACAGTGTGCAAGTGTCCAA 58.715 47.619 5.88 0.00 41.73 3.53
212 230 1.032014 GTGTGCAAGTGTCCAACCAT 58.968 50.000 0.00 0.00 0.00 3.55
219 237 3.056607 GCAAGTGTCCAACCATGCTATTT 60.057 43.478 0.00 0.00 38.48 1.40
220 238 4.487948 CAAGTGTCCAACCATGCTATTTG 58.512 43.478 0.00 0.00 0.00 2.32
236 254 3.675467 ATTTGACGATTTAGCTTCGGC 57.325 42.857 10.78 8.15 44.92 5.54
248 266 2.292267 AGCTTCGGCCTTTCACATATG 58.708 47.619 0.00 0.00 43.01 1.78
267 285 0.582960 GCATTGCACACCTTTGTTGC 59.417 50.000 3.15 0.00 31.66 4.17
268 286 1.937278 CATTGCACACCTTTGTTGCA 58.063 45.000 0.00 0.00 37.72 4.08
309 349 3.614092 TCAGGATTCAAACTGGAGATGC 58.386 45.455 0.00 0.00 35.47 3.91
317 357 3.152341 CAAACTGGAGATGCCTTGAACT 58.848 45.455 0.00 0.00 37.63 3.01
356 398 2.038557 CCATATTCCTGGGGGACTAACG 59.961 54.545 0.00 0.00 42.05 3.18
357 399 2.852714 TATTCCTGGGGGACTAACGA 57.147 50.000 0.00 0.00 42.05 3.85
362 404 1.280998 CCTGGGGGACTAACGATGTTT 59.719 52.381 0.00 0.00 33.58 2.83
378 420 6.534059 ACGATGTTTTGAGAAATATGACACG 58.466 36.000 0.00 0.00 28.21 4.49
411 453 3.611113 CCCGTACAGTTGTTCAAGATACG 59.389 47.826 12.26 12.26 35.04 3.06
442 488 8.507524 AGCATTCTAGTTTTATCCAGTAAACC 57.492 34.615 0.00 0.00 35.39 3.27
478 524 6.534793 CCACAAGAAAGTTACAGTGCAATTTT 59.465 34.615 0.00 0.00 0.00 1.82
481 527 7.009174 ACAAGAAAGTTACAGTGCAATTTTTCG 59.991 33.333 0.00 0.00 0.00 3.46
482 528 6.791303 AGAAAGTTACAGTGCAATTTTTCGA 58.209 32.000 0.00 0.00 0.00 3.71
483 529 7.254852 AGAAAGTTACAGTGCAATTTTTCGAA 58.745 30.769 0.00 0.00 0.00 3.71
484 530 7.920682 AGAAAGTTACAGTGCAATTTTTCGAAT 59.079 29.630 0.00 0.00 0.00 3.34
485 531 7.623268 AAGTTACAGTGCAATTTTTCGAATC 57.377 32.000 0.00 0.00 0.00 2.52
486 532 6.734137 AGTTACAGTGCAATTTTTCGAATCA 58.266 32.000 0.00 0.00 0.00 2.57
487 533 6.857964 AGTTACAGTGCAATTTTTCGAATCAG 59.142 34.615 0.00 0.00 0.00 2.90
518 564 7.653311 GGGTGTATTTTATTTGGATTCAGCATC 59.347 37.037 0.00 0.00 0.00 3.91
520 566 9.241317 GTGTATTTTATTTGGATTCAGCATCTG 57.759 33.333 0.00 0.00 31.67 2.90
548 603 3.244078 TGCACCAATAGTCTCTTTCGTGT 60.244 43.478 0.00 0.00 0.00 4.49
567 622 2.271800 GTTGTGTCGCTATCTTCCCTG 58.728 52.381 0.00 0.00 0.00 4.45
569 624 1.476891 TGTGTCGCTATCTTCCCTGTC 59.523 52.381 0.00 0.00 0.00 3.51
572 627 1.067821 GTCGCTATCTTCCCTGTCCTG 59.932 57.143 0.00 0.00 0.00 3.86
598 653 2.550699 ATTTTCGCCTCGCCCCATCA 62.551 55.000 0.00 0.00 0.00 3.07
605 662 1.595382 CTCGCCCCATCACGGATTC 60.595 63.158 0.00 0.00 36.56 2.52
672 732 5.133491 TGGGGACACATGATAATATCACCAA 59.867 40.000 4.93 0.00 37.53 3.67
673 733 6.183361 TGGGGACACATGATAATATCACCAAT 60.183 38.462 4.93 0.00 37.53 3.16
674 734 6.721208 GGGGACACATGATAATATCACCAATT 59.279 38.462 4.93 0.00 43.01 2.32
675 735 7.094205 GGGGACACATGATAATATCACCAATTC 60.094 40.741 4.93 0.00 43.01 2.17
676 736 7.448161 GGGACACATGATAATATCACCAATTCA 59.552 37.037 4.93 0.00 43.01 2.57
677 737 8.292448 GGACACATGATAATATCACCAATTCAC 58.708 37.037 4.93 0.00 43.01 3.18
678 738 8.169977 ACACATGATAATATCACCAATTCACC 57.830 34.615 4.93 0.00 43.01 4.02
679 739 7.779326 ACACATGATAATATCACCAATTCACCA 59.221 33.333 4.93 0.00 43.01 4.17
680 740 8.799367 CACATGATAATATCACCAATTCACCAT 58.201 33.333 4.93 0.00 43.01 3.55
681 741 8.799367 ACATGATAATATCACCAATTCACCATG 58.201 33.333 4.93 0.00 43.01 3.66
682 742 9.016438 CATGATAATATCACCAATTCACCATGA 57.984 33.333 4.93 0.00 43.01 3.07
683 743 8.625786 TGATAATATCACCAATTCACCATGAG 57.374 34.615 0.00 0.00 33.59 2.90
684 744 5.779529 AATATCACCAATTCACCATGAGC 57.220 39.130 0.00 0.00 0.00 4.26
714 774 1.191535 GGCCTCCCCATTTGTTAACC 58.808 55.000 2.48 0.00 0.00 2.85
770 831 0.322008 GCTCCAGCTACCAGCAGTTT 60.322 55.000 5.97 0.00 45.56 2.66
782 843 6.374613 GCTACCAGCAGTTTTCTACCTTAATT 59.625 38.462 0.00 0.00 41.89 1.40
783 844 7.551617 GCTACCAGCAGTTTTCTACCTTAATTA 59.448 37.037 0.00 0.00 41.89 1.40
836 897 4.512198 GTCTCCTCGAGAAGATGAACGATA 59.488 45.833 15.71 0.00 40.59 2.92
854 915 1.911057 TATCCGTCGGATGCTGATCT 58.089 50.000 32.49 10.73 43.06 2.75
857 918 1.609072 TCCGTCGGATGCTGATCTAAG 59.391 52.381 10.71 0.00 0.00 2.18
860 921 1.689273 GTCGGATGCTGATCTAAGGGT 59.311 52.381 0.00 0.00 0.00 4.34
892 965 9.651718 CTATAATTGCAATACCGTCTTTCTTTC 57.348 33.333 13.39 0.00 0.00 2.62
893 966 5.957842 ATTGCAATACCGTCTTTCTTTCA 57.042 34.783 11.02 0.00 0.00 2.69
895 968 3.185594 TGCAATACCGTCTTTCTTTCACG 59.814 43.478 0.00 0.00 0.00 4.35
908 981 5.356882 TTCTTTCACGTTGCTCCTTTATG 57.643 39.130 0.00 0.00 0.00 1.90
912 985 6.653320 TCTTTCACGTTGCTCCTTTATGTTAT 59.347 34.615 0.00 0.00 0.00 1.89
919 992 7.173218 ACGTTGCTCCTTTATGTTATGATATGG 59.827 37.037 0.00 0.00 0.00 2.74
978 1051 5.798132 CTTGCCTGGTGAGCTATATATTGA 58.202 41.667 0.00 0.00 0.00 2.57
993 1066 9.071221 GCTATATATTGAAGACAGATTCAGTCG 57.929 37.037 3.85 0.00 40.16 4.18
1007 1115 2.210013 AGTCGAGCTGAGGCACCAA 61.210 57.895 0.00 0.00 41.70 3.67
1035 1144 2.569354 AAATGGCGGCCGAGCAAAA 61.569 52.632 33.48 6.84 39.27 2.44
1048 1157 0.530288 AGCAAAAACGCCACAACAGT 59.470 45.000 0.00 0.00 0.00 3.55
1049 1158 1.067213 AGCAAAAACGCCACAACAGTT 60.067 42.857 0.00 0.00 0.00 3.16
1052 1161 2.271821 AAAACGCCACAACAGTTCAC 57.728 45.000 0.00 0.00 0.00 3.18
1057 1166 1.536766 CGCCACAACAGTTCACATGAT 59.463 47.619 0.00 0.00 0.00 2.45
1066 1175 7.331687 CACAACAGTTCACATGATATCACAGTA 59.668 37.037 7.78 0.00 0.00 2.74
1077 1186 4.814294 CACAGTAGACGGCCCCGC 62.814 72.222 6.63 0.00 44.19 6.13
1132 1247 2.037847 GGAAACAGCCAGCCCCAT 59.962 61.111 0.00 0.00 0.00 4.00
1136 1251 0.630673 AAACAGCCAGCCCCATGATA 59.369 50.000 0.00 0.00 0.00 2.15
1402 1529 2.031919 ACCGCATTTGCCTCGTCA 59.968 55.556 0.00 0.00 37.91 4.35
1415 1542 1.268794 CCTCGTCACTCGTGATCATCC 60.269 57.143 0.00 0.00 42.18 3.51
1439 1566 1.623557 CCATCCTCTTCCTCACCCTCA 60.624 57.143 0.00 0.00 0.00 3.86
1764 1962 0.890996 GGTGGCTTCTGGGACAACAG 60.891 60.000 0.00 0.00 38.70 3.16
1836 2034 1.157870 CGCCTGACGGTGTTCTTGTT 61.158 55.000 0.00 0.00 38.44 2.83
2054 2306 1.153823 GCATTGCTCCAAGCTGCAG 60.154 57.895 10.11 10.11 40.72 4.41
2057 2309 1.814394 CATTGCTCCAAGCTGCAGTTA 59.186 47.619 16.64 0.00 42.97 2.24
2064 2316 3.084039 TCCAAGCTGCAGTTATTCAAGG 58.916 45.455 16.64 6.65 0.00 3.61
2141 2408 1.407656 TTCGGTGTCAGGGAGCTTGT 61.408 55.000 0.00 0.00 0.00 3.16
2161 2428 4.388485 TGTCAAGAGCAATAACAAGAGCA 58.612 39.130 0.00 0.00 0.00 4.26
2249 2527 4.957954 TCCTCTGCAAATCATTGGCTTTAT 59.042 37.500 0.00 0.00 37.02 1.40
2315 2794 2.629137 TGCTCGTTCCCTTGTACTGTTA 59.371 45.455 0.00 0.00 0.00 2.41
2373 2852 4.414956 TGGATCCTCCCGGTGGCT 62.415 66.667 14.23 0.00 35.03 4.75
2388 2867 4.142780 GCTTCTGGCCGGGTAATC 57.857 61.111 12.87 0.00 34.27 1.75
2531 4584 2.113860 GCAAGGTTATGCTCCAGACA 57.886 50.000 0.00 0.00 43.06 3.41
2571 4624 3.500448 TGATACTGGACTTGTTTGGCA 57.500 42.857 0.00 0.00 0.00 4.92
2695 4748 3.058639 GTCTTCTTCACACTGAACCATGC 60.059 47.826 0.00 0.00 32.21 4.06
2696 4749 1.896220 TCTTCACACTGAACCATGCC 58.104 50.000 0.00 0.00 32.21 4.40
2697 4750 1.142667 TCTTCACACTGAACCATGCCA 59.857 47.619 0.00 0.00 32.21 4.92
2709 4765 3.516512 ATGCCACCAACCCCACCA 61.517 61.111 0.00 0.00 0.00 4.17
2786 4872 1.227556 GGCCGCGACCATCACTTAT 60.228 57.895 8.23 0.00 0.00 1.73
2835 4927 0.394192 CCGGCTCCAAGATGATAGCA 59.606 55.000 0.00 0.00 36.68 3.49
2879 4971 2.104281 CCTCCTATACAACTTTCCCCGG 59.896 54.545 0.00 0.00 0.00 5.73
2933 5025 1.371337 GCTTCATGCTGTCCATCGCA 61.371 55.000 0.00 0.00 40.87 5.10
2936 5028 0.741927 TCATGCTGTCCATCGCACTG 60.742 55.000 0.00 0.00 39.21 3.66
2972 5064 2.496679 ACCCACATCTATACAGGCCT 57.503 50.000 0.00 0.00 0.00 5.19
3152 5244 6.264518 TGGTATTCTTGTTGAAGGAAAGGAAC 59.735 38.462 0.00 0.00 38.18 3.62
3157 5249 5.656416 TCTTGTTGAAGGAAAGGAACAACAT 59.344 36.000 0.00 0.00 45.95 2.71
3189 5296 3.636231 CCGGTGAACTGGAGCCCA 61.636 66.667 1.76 0.00 45.36 5.36
3196 5303 0.329596 GAACTGGAGCCCATTGAGGT 59.670 55.000 0.00 0.00 34.66 3.85
3202 5309 1.673168 GAGCCCATTGAGGTAAGCAG 58.327 55.000 0.00 0.00 34.66 4.24
3203 5310 0.995024 AGCCCATTGAGGTAAGCAGT 59.005 50.000 0.00 0.00 34.66 4.40
3204 5311 1.355720 AGCCCATTGAGGTAAGCAGTT 59.644 47.619 0.00 0.00 34.66 3.16
3206 5313 2.795329 CCCATTGAGGTAAGCAGTTGT 58.205 47.619 0.00 0.00 34.66 3.32
3208 5315 3.689649 CCCATTGAGGTAAGCAGTTGTAC 59.310 47.826 0.00 0.00 34.66 2.90
3210 5317 4.154195 CCATTGAGGTAAGCAGTTGTACAC 59.846 45.833 0.00 0.00 0.00 2.90
3211 5318 3.396260 TGAGGTAAGCAGTTGTACACC 57.604 47.619 0.00 0.00 0.00 4.16
3302 5418 3.161450 GCCGGCCTAGATCCACCA 61.161 66.667 18.11 0.00 0.00 4.17
3332 5448 1.303561 GCAGCACAGTGGGAATGGA 60.304 57.895 0.00 0.00 0.00 3.41
3567 5707 0.613853 CAGGGGGTGGAAGACGTCTA 60.614 60.000 20.39 0.00 0.00 2.59
3589 5729 3.571571 TGTATGTCGTTGCACTAGTGAC 58.428 45.455 27.08 17.20 0.00 3.67
3687 5827 3.134623 CAGTGTGGATCCTGCATAGGTAA 59.865 47.826 14.23 0.00 44.88 2.85
3701 5841 2.663196 GTAACTCCAGCGGCACCT 59.337 61.111 1.45 0.00 0.00 4.00
3702 5842 1.741770 GTAACTCCAGCGGCACCTG 60.742 63.158 1.45 0.00 0.00 4.00
3726 5866 7.935520 TGTTTCTGTTTGATTATTAGTGTGCA 58.064 30.769 0.00 0.00 0.00 4.57
3733 5873 4.578871 TGATTATTAGTGTGCACTGCAGT 58.421 39.130 15.25 15.25 42.52 4.40
3744 5884 3.438087 GTGCACTGCAGTTCTGTTCATAT 59.562 43.478 18.94 0.00 40.08 1.78
3745 5885 3.437741 TGCACTGCAGTTCTGTTCATATG 59.562 43.478 18.94 2.09 33.32 1.78
3747 5887 4.154737 GCACTGCAGTTCTGTTCATATGAA 59.845 41.667 18.94 14.23 0.00 2.57
3753 5893 6.082338 GCAGTTCTGTTCATATGAAACAGTG 58.918 40.000 28.09 23.51 36.04 3.66
3779 5919 4.982916 AGTAAAGCCTGCGATTCTTATACG 59.017 41.667 0.00 0.00 0.00 3.06
3797 5937 7.441157 TCTTATACGCCTATCAAAATGTCAAGG 59.559 37.037 0.00 0.00 0.00 3.61
3807 5947 2.885135 AATGTCAAGGCAGGTGATCA 57.115 45.000 0.00 0.00 0.00 2.92
3817 5957 6.318648 TCAAGGCAGGTGATCATTTTGTATAC 59.681 38.462 0.00 0.00 0.00 1.47
3819 5959 4.278419 GGCAGGTGATCATTTTGTATACCC 59.722 45.833 0.00 0.00 0.00 3.69
3829 5969 7.227355 TCATTTTGTATACCCATTTCCCCTA 57.773 36.000 0.00 0.00 0.00 3.53
3836 5976 3.448277 ACCCATTTCCCCTAGTATCCA 57.552 47.619 0.00 0.00 0.00 3.41
3837 5977 3.053826 ACCCATTTCCCCTAGTATCCAC 58.946 50.000 0.00 0.00 0.00 4.02
3845 5991 5.562298 TCCCCTAGTATCCACTTTATTGC 57.438 43.478 0.00 0.00 36.14 3.56
3847 5993 6.387127 TCCCCTAGTATCCACTTTATTGCTA 58.613 40.000 0.00 0.00 36.14 3.49
3877 6023 9.802039 TGTAATACAAATAGAAAGTGGGAAACT 57.198 29.630 0.00 0.00 42.60 2.66
3904 6050 0.033601 TTTGTGGTGTGTGGCTCCTT 60.034 50.000 0.00 0.00 0.00 3.36
3967 6113 2.167281 GCTTGTCCAGTCTCTGCTATGA 59.833 50.000 0.00 0.00 0.00 2.15
3994 6140 3.815507 TCCTCCCCCTTTCTAGAATTGT 58.184 45.455 5.89 0.00 0.00 2.71
4023 6169 7.882791 TGTACTTGATGTTTGATGTAACTGGAT 59.117 33.333 0.00 0.00 0.00 3.41
4024 6170 7.765695 ACTTGATGTTTGATGTAACTGGATT 57.234 32.000 0.00 0.00 0.00 3.01
4052 6198 9.662947 TTTTAAATCCCTCAAACTAGCTAGTAC 57.337 33.333 26.29 0.00 34.99 2.73
4053 6199 8.605325 TTAAATCCCTCAAACTAGCTAGTACT 57.395 34.615 26.29 14.01 34.99 2.73
4113 6329 3.696051 GCTTCAGGCATATTTGGACTTGA 59.304 43.478 0.00 0.00 41.35 3.02
4139 6355 3.497942 GGGTGTAAACCTGAATCCAGTGT 60.498 47.826 1.05 0.00 38.74 3.55
4148 6364 3.346315 CTGAATCCAGTGTATGTGGCAA 58.654 45.455 0.00 0.00 35.70 4.52
4190 6406 9.712305 GAGCTATGTATGGTTCTACATTTACAT 57.288 33.333 2.40 0.00 41.42 2.29
4197 6413 6.918892 TGGTTCTACATTTACATGATTCGG 57.081 37.500 0.00 0.00 34.11 4.30
4201 6417 7.657761 GGTTCTACATTTACATGATTCGGAGAT 59.342 37.037 0.00 0.00 32.59 2.75
4207 6423 9.265901 ACATTTACATGATTCGGAGATTAAGAG 57.734 33.333 0.00 0.00 32.59 2.85
4208 6424 7.715265 TTTACATGATTCGGAGATTAAGAGC 57.285 36.000 0.00 0.00 35.04 4.09
4209 6425 5.282055 ACATGATTCGGAGATTAAGAGCA 57.718 39.130 0.00 0.00 35.04 4.26
4210 6426 5.295950 ACATGATTCGGAGATTAAGAGCAG 58.704 41.667 0.00 0.00 35.04 4.24
4211 6427 5.163364 ACATGATTCGGAGATTAAGAGCAGT 60.163 40.000 0.00 0.00 35.04 4.40
4212 6428 4.938080 TGATTCGGAGATTAAGAGCAGTC 58.062 43.478 0.00 0.00 35.04 3.51
4213 6429 4.646945 TGATTCGGAGATTAAGAGCAGTCT 59.353 41.667 0.00 0.00 35.04 3.24
4214 6430 5.127845 TGATTCGGAGATTAAGAGCAGTCTT 59.872 40.000 0.00 0.00 41.06 3.01
4215 6431 4.640789 TCGGAGATTAAGAGCAGTCTTC 57.359 45.455 0.00 0.00 42.40 2.87
4216 6432 4.017126 TCGGAGATTAAGAGCAGTCTTCA 58.983 43.478 0.00 0.00 42.40 3.02
4217 6433 4.646945 TCGGAGATTAAGAGCAGTCTTCAT 59.353 41.667 0.00 0.00 42.40 2.57
4218 6434 5.127845 TCGGAGATTAAGAGCAGTCTTCATT 59.872 40.000 0.00 0.00 42.40 2.57
4219 6435 6.321435 TCGGAGATTAAGAGCAGTCTTCATTA 59.679 38.462 0.00 0.00 42.40 1.90
4220 6436 7.014711 TCGGAGATTAAGAGCAGTCTTCATTAT 59.985 37.037 0.00 0.00 42.40 1.28
4221 6437 7.655328 CGGAGATTAAGAGCAGTCTTCATTATT 59.345 37.037 0.00 0.00 42.40 1.40
4222 6438 8.772705 GGAGATTAAGAGCAGTCTTCATTATTG 58.227 37.037 0.00 0.00 42.40 1.90
4223 6439 9.323985 GAGATTAAGAGCAGTCTTCATTATTGT 57.676 33.333 0.00 0.00 42.40 2.71
4224 6440 9.678260 AGATTAAGAGCAGTCTTCATTATTGTT 57.322 29.630 0.00 0.00 42.40 2.83
4228 6444 8.621532 AAGAGCAGTCTTCATTATTGTTAACA 57.378 30.769 3.59 3.59 38.84 2.41
4229 6445 8.034058 AGAGCAGTCTTCATTATTGTTAACAC 57.966 34.615 8.07 0.00 0.00 3.32
4230 6446 7.661437 AGAGCAGTCTTCATTATTGTTAACACA 59.339 33.333 8.07 0.30 0.00 3.72
4231 6447 7.584987 AGCAGTCTTCATTATTGTTAACACAC 58.415 34.615 8.07 0.00 30.32 3.82
4232 6448 7.228507 AGCAGTCTTCATTATTGTTAACACACA 59.771 33.333 8.07 0.00 30.32 3.72
4233 6449 7.860373 GCAGTCTTCATTATTGTTAACACACAA 59.140 33.333 8.07 3.08 40.92 3.33
4234 6450 9.729023 CAGTCTTCATTATTGTTAACACACAAA 57.271 29.630 8.07 0.91 40.07 2.83
4461 6677 1.680338 CTTTTATGGGAAGGAGGCCG 58.320 55.000 0.00 0.00 0.00 6.13
4508 6728 1.293924 GCTCATGTGGACGGATTCTG 58.706 55.000 0.00 0.00 0.00 3.02
4692 6913 3.083997 GGTCCCGATGGTCTGCCT 61.084 66.667 0.00 0.00 35.27 4.75
4704 6925 0.603975 GTCTGCCTGTCCGCTTCTTT 60.604 55.000 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.608130 ACAGGCTGTGCAAGTATCGA 59.392 50.000 21.37 0.00 0.00 3.59
1 2 0.723414 CACAGGCTGTGCAAGTATCG 59.277 55.000 32.39 8.04 41.89 2.92
22 23 2.185262 GCTTTGCGCAATTAACTAGGC 58.815 47.619 25.64 9.17 38.92 3.93
104 113 6.349300 ACAAAAGAAGAGAAGTCTGCAACTA 58.651 36.000 2.60 0.00 37.17 2.24
110 119 5.762218 ACCATGACAAAAGAAGAGAAGTCTG 59.238 40.000 0.00 0.00 31.37 3.51
111 120 5.934781 ACCATGACAAAAGAAGAGAAGTCT 58.065 37.500 0.00 0.00 32.81 3.24
112 121 6.038714 ACAACCATGACAAAAGAAGAGAAGTC 59.961 38.462 0.00 0.00 0.00 3.01
153 162 5.584649 TGGCTTCCACGTTTCTATATTCTTG 59.415 40.000 0.00 0.00 0.00 3.02
185 197 2.198406 GACACTTGCACACTGTACGAA 58.802 47.619 0.00 0.00 0.00 3.85
186 198 1.537348 GGACACTTGCACACTGTACGA 60.537 52.381 0.00 0.00 0.00 3.43
200 212 3.758554 GTCAAATAGCATGGTTGGACACT 59.241 43.478 1.12 0.00 0.00 3.55
208 220 5.126067 AGCTAAATCGTCAAATAGCATGGT 58.874 37.500 1.62 1.62 42.45 3.55
212 230 4.270084 CCGAAGCTAAATCGTCAAATAGCA 59.730 41.667 5.63 0.00 42.45 3.49
219 237 0.535335 AGGCCGAAGCTAAATCGTCA 59.465 50.000 0.00 0.00 38.60 4.35
220 238 1.653151 AAGGCCGAAGCTAAATCGTC 58.347 50.000 0.00 0.00 38.60 4.20
236 254 3.861113 GTGTGCAATGCATATGTGAAAGG 59.139 43.478 12.38 0.00 41.91 3.11
248 266 0.582960 GCAACAAAGGTGTGCAATGC 59.417 50.000 0.00 0.00 38.27 3.56
268 286 7.453393 TCCTGAACATATTTCAGTTCTCAACT 58.547 34.615 18.28 0.00 43.19 3.16
282 301 6.962182 TCTCCAGTTTGAATCCTGAACATAT 58.038 36.000 0.00 0.00 0.00 1.78
283 302 6.373005 TCTCCAGTTTGAATCCTGAACATA 57.627 37.500 0.00 0.00 0.00 2.29
284 303 5.246981 TCTCCAGTTTGAATCCTGAACAT 57.753 39.130 0.00 0.00 0.00 2.71
285 304 4.705110 TCTCCAGTTTGAATCCTGAACA 57.295 40.909 0.00 0.00 0.00 3.18
286 305 4.142513 GCATCTCCAGTTTGAATCCTGAAC 60.143 45.833 0.00 0.00 0.00 3.18
287 306 4.012374 GCATCTCCAGTTTGAATCCTGAA 58.988 43.478 0.00 0.00 0.00 3.02
288 307 3.614092 GCATCTCCAGTTTGAATCCTGA 58.386 45.455 0.00 0.00 0.00 3.86
291 310 3.010200 AGGCATCTCCAGTTTGAATCC 57.990 47.619 0.00 0.00 37.29 3.01
292 311 4.012374 TCAAGGCATCTCCAGTTTGAATC 58.988 43.478 0.00 0.00 37.29 2.52
309 349 3.023832 ACCTCAACACCAAAGTTCAAGG 58.976 45.455 0.00 0.00 37.43 3.61
317 357 1.327303 GGATGCACCTCAACACCAAA 58.673 50.000 0.00 0.00 35.41 3.28
356 398 9.638300 GATACGTGTCATATTTCTCAAAACATC 57.362 33.333 7.51 0.00 0.00 3.06
357 399 8.612619 GGATACGTGTCATATTTCTCAAAACAT 58.387 33.333 14.58 0.00 0.00 2.71
362 404 8.234136 ACTAGGATACGTGTCATATTTCTCAA 57.766 34.615 14.58 0.00 46.39 3.02
378 420 4.400567 ACAACTGTACGGGAACTAGGATAC 59.599 45.833 6.65 0.00 0.00 2.24
442 488 1.504359 TTCTTGTGGTTTCGTAGGCG 58.496 50.000 0.00 0.00 39.92 5.52
478 524 4.771114 ATACACCCATTCCTGATTCGAA 57.229 40.909 0.00 0.00 0.00 3.71
481 527 9.533253 CAAATAAAATACACCCATTCCTGATTC 57.467 33.333 0.00 0.00 0.00 2.52
482 528 8.485392 CCAAATAAAATACACCCATTCCTGATT 58.515 33.333 0.00 0.00 0.00 2.57
483 529 7.843760 TCCAAATAAAATACACCCATTCCTGAT 59.156 33.333 0.00 0.00 0.00 2.90
484 530 7.185565 TCCAAATAAAATACACCCATTCCTGA 58.814 34.615 0.00 0.00 0.00 3.86
485 531 7.416964 TCCAAATAAAATACACCCATTCCTG 57.583 36.000 0.00 0.00 0.00 3.86
486 532 8.622572 AATCCAAATAAAATACACCCATTCCT 57.377 30.769 0.00 0.00 0.00 3.36
487 533 8.482128 TGAATCCAAATAAAATACACCCATTCC 58.518 33.333 0.00 0.00 0.00 3.01
534 580 3.624900 CGACACAACACGAAAGAGACTA 58.375 45.455 0.00 0.00 0.00 2.59
548 603 1.899814 ACAGGGAAGATAGCGACACAA 59.100 47.619 0.00 0.00 0.00 3.33
567 622 1.472878 GGCGAAAATTCCTTCCAGGAC 59.527 52.381 0.00 0.00 45.78 3.85
569 624 1.745653 GAGGCGAAAATTCCTTCCAGG 59.254 52.381 0.00 0.00 36.46 4.45
572 627 0.098905 GCGAGGCGAAAATTCCTTCC 59.901 55.000 0.00 0.00 31.71 3.46
588 643 2.363172 TGAATCCGTGATGGGGCGA 61.363 57.895 0.00 0.00 38.76 5.54
598 653 0.387929 ATATGTCGCCGTGAATCCGT 59.612 50.000 0.00 0.00 0.00 4.69
601 658 2.096713 GCTTGATATGTCGCCGTGAATC 60.097 50.000 0.00 0.00 0.00 2.52
605 662 0.578683 CTGCTTGATATGTCGCCGTG 59.421 55.000 0.00 0.00 0.00 4.94
658 718 7.175467 GCTCATGGTGAATTGGTGATATTATCA 59.825 37.037 2.14 2.14 36.84 2.15
672 732 2.124151 GGGGCGCTCATGGTGAAT 60.124 61.111 10.74 0.00 0.00 2.57
673 733 4.424711 GGGGGCGCTCATGGTGAA 62.425 66.667 10.74 0.00 0.00 3.18
694 754 1.191535 GTTAACAAATGGGGAGGCCC 58.808 55.000 0.00 0.00 44.51 5.80
714 774 1.324435 CACATGCGTAACCTCATCGTG 59.676 52.381 0.00 0.00 0.00 4.35
726 786 3.294493 GGTTGCCACCACATGCGT 61.294 61.111 1.17 0.00 43.61 5.24
788 849 9.726438 ACCACTTCCTGCTGTATTTATATATTC 57.274 33.333 0.00 0.00 0.00 1.75
789 850 9.726438 GACCACTTCCTGCTGTATTTATATATT 57.274 33.333 0.00 0.00 0.00 1.28
790 851 9.105844 AGACCACTTCCTGCTGTATTTATATAT 57.894 33.333 0.00 0.00 0.00 0.86
791 852 8.492415 AGACCACTTCCTGCTGTATTTATATA 57.508 34.615 0.00 0.00 0.00 0.86
792 853 7.380423 AGACCACTTCCTGCTGTATTTATAT 57.620 36.000 0.00 0.00 0.00 0.86
793 854 6.183360 GGAGACCACTTCCTGCTGTATTTATA 60.183 42.308 0.00 0.00 0.00 0.98
806 867 1.474879 CTTCTCGAGGAGACCACTTCC 59.525 57.143 16.33 0.00 38.51 3.46
836 897 1.911057 TAGATCAGCATCCGACGGAT 58.089 50.000 23.78 23.78 44.21 4.18
854 915 9.667107 GTATTGCAATTATAGATAGCACCCTTA 57.333 33.333 18.75 0.00 34.56 2.69
857 918 6.037172 CGGTATTGCAATTATAGATAGCACCC 59.963 42.308 18.75 0.00 34.56 4.61
860 921 7.611770 AGACGGTATTGCAATTATAGATAGCA 58.388 34.615 18.75 0.00 0.00 3.49
892 965 5.794687 TCATAACATAAAGGAGCAACGTG 57.205 39.130 0.00 0.00 0.00 4.49
893 966 7.173218 CCATATCATAACATAAAGGAGCAACGT 59.827 37.037 0.00 0.00 0.00 3.99
895 968 8.292448 CACCATATCATAACATAAAGGAGCAAC 58.708 37.037 0.00 0.00 0.00 4.17
908 981 5.699001 TGGCATAACGTCACCATATCATAAC 59.301 40.000 0.00 0.00 0.00 1.89
912 985 3.494223 CCTGGCATAACGTCACCATATCA 60.494 47.826 0.00 0.00 0.00 2.15
919 992 1.463444 GACAACCTGGCATAACGTCAC 59.537 52.381 0.00 0.00 0.00 3.67
961 1034 7.839680 TCTGTCTTCAATATATAGCTCACCA 57.160 36.000 0.00 0.00 0.00 4.17
990 1063 0.674895 AATTGGTGCCTCAGCTCGAC 60.675 55.000 0.00 0.00 40.80 4.20
991 1064 0.674581 CAATTGGTGCCTCAGCTCGA 60.675 55.000 0.00 0.00 40.80 4.04
992 1065 1.798735 CAATTGGTGCCTCAGCTCG 59.201 57.895 0.00 0.00 40.80 5.03
1032 1141 2.029828 TGTGAACTGTTGTGGCGTTTTT 60.030 40.909 0.00 0.00 0.00 1.94
1035 1144 1.065401 CATGTGAACTGTTGTGGCGTT 59.935 47.619 0.00 0.00 0.00 4.84
1048 1157 5.736207 GCCGTCTACTGTGATATCATGTGAA 60.736 44.000 9.02 2.20 0.00 3.18
1049 1158 4.261614 GCCGTCTACTGTGATATCATGTGA 60.262 45.833 9.02 8.61 0.00 3.58
1052 1161 3.579709 GGCCGTCTACTGTGATATCATG 58.420 50.000 9.02 7.81 0.00 3.07
1057 1166 1.105167 CGGGGCCGTCTACTGTGATA 61.105 60.000 0.00 0.00 34.35 2.15
1089 1198 2.440980 GATTGGTGGCAGGAGGGC 60.441 66.667 0.00 0.00 43.73 5.19
1090 1199 2.153898 TTGGATTGGTGGCAGGAGGG 62.154 60.000 0.00 0.00 0.00 4.30
1132 1247 1.571955 TTGCAGGAGGCTGAGTATCA 58.428 50.000 0.00 0.00 46.23 2.15
1136 1251 0.323178 CCATTTGCAGGAGGCTGAGT 60.323 55.000 0.00 0.00 45.15 3.41
1201 1328 1.478510 AGGATGTACTTGCTCAGGTCG 59.521 52.381 0.00 0.00 0.00 4.79
1321 1448 0.469331 TCCGGATAATGGAGTCGCCT 60.469 55.000 0.00 0.00 37.63 5.52
1402 1529 1.037579 TGGCGAGGATGATCACGAGT 61.038 55.000 13.50 0.00 0.00 4.18
1415 1542 0.103937 GTGAGGAAGAGGATGGCGAG 59.896 60.000 0.00 0.00 0.00 5.03
1439 1566 4.216472 GCGGTTCTTCTTTTTCTCTTCCAT 59.784 41.667 0.00 0.00 0.00 3.41
1663 1844 1.342174 ACCTTTCGTAGCCGTTTCTCA 59.658 47.619 0.00 0.00 35.01 3.27
1836 2034 0.960364 GAACGCCAGGGCATTGAAGA 60.960 55.000 11.42 0.00 42.06 2.87
1864 2062 1.816835 AGCACCACAATGATGAGCAAG 59.183 47.619 0.00 0.00 0.00 4.01
2054 2306 6.972901 GCAGCTTTTATGGTACCTTGAATAAC 59.027 38.462 14.36 3.13 0.00 1.89
2057 2309 5.016173 TGCAGCTTTTATGGTACCTTGAAT 58.984 37.500 14.36 0.08 0.00 2.57
2064 2316 2.418628 TCGCTTGCAGCTTTTATGGTAC 59.581 45.455 0.00 0.00 39.60 3.34
2141 2408 3.753272 GGTGCTCTTGTTATTGCTCTTGA 59.247 43.478 0.00 0.00 0.00 3.02
2249 2527 0.693049 GGGGAGCAAAAGAGGTCAGA 59.307 55.000 0.00 0.00 37.74 3.27
2294 2593 1.045407 ACAGTACAAGGGAACGAGCA 58.955 50.000 0.00 0.00 0.00 4.26
2373 2852 2.904905 CCGATTACCCGGCCAGAA 59.095 61.111 2.24 0.00 43.25 3.02
2383 2862 1.145377 ATGTGGCCGTCCCGATTAC 59.855 57.895 0.00 0.00 35.87 1.89
2695 4748 0.397816 TTCTTTGGTGGGGTTGGTGG 60.398 55.000 0.00 0.00 0.00 4.61
2696 4749 1.039856 CTTCTTTGGTGGGGTTGGTG 58.960 55.000 0.00 0.00 0.00 4.17
2697 4750 0.930726 TCTTCTTTGGTGGGGTTGGT 59.069 50.000 0.00 0.00 0.00 3.67
2709 4765 6.531021 TCTCCACGGACTTAATTTCTTCTTT 58.469 36.000 0.00 0.00 0.00 2.52
2879 4971 1.797025 AGAAGAAGGCTGTGTAACGC 58.203 50.000 0.00 0.00 42.39 4.84
2972 5064 1.067060 AGTGCATAGCTTCGTATCGCA 59.933 47.619 0.00 0.00 0.00 5.10
3152 5244 1.732259 GCCGTGTCTTCAGGTATGTTG 59.268 52.381 0.00 0.00 0.00 3.33
3157 5249 2.642254 CCGGCCGTGTCTTCAGGTA 61.642 63.158 26.12 0.00 0.00 3.08
3188 5295 4.154195 GGTGTACAACTGCTTACCTCAATG 59.846 45.833 2.87 0.00 0.00 2.82
3189 5296 4.202419 TGGTGTACAACTGCTTACCTCAAT 60.202 41.667 13.07 0.00 0.00 2.57
3196 5303 4.385825 CTTTCCTGGTGTACAACTGCTTA 58.614 43.478 13.07 0.00 0.00 3.09
3202 5309 5.105675 TGTTTTTCCTTTCCTGGTGTACAAC 60.106 40.000 3.20 3.20 0.00 3.32
3203 5310 5.017490 TGTTTTTCCTTTCCTGGTGTACAA 58.983 37.500 0.00 0.00 0.00 2.41
3204 5311 4.601084 TGTTTTTCCTTTCCTGGTGTACA 58.399 39.130 0.00 0.00 0.00 2.90
3206 5313 5.205056 ACATGTTTTTCCTTTCCTGGTGTA 58.795 37.500 0.00 0.00 0.00 2.90
3208 5315 4.099266 TGACATGTTTTTCCTTTCCTGGTG 59.901 41.667 0.00 0.00 0.00 4.17
3210 5317 4.935352 TGACATGTTTTTCCTTTCCTGG 57.065 40.909 0.00 0.00 0.00 4.45
3211 5318 4.687483 GCATGACATGTTTTTCCTTTCCTG 59.313 41.667 16.62 0.00 0.00 3.86
3332 5448 4.825252 GGGTTGCCCGCGTCGTAT 62.825 66.667 4.92 0.00 32.13 3.06
3350 5466 3.021695 CCTCTGGTTGTCATGCATGATT 58.978 45.455 30.89 0.00 39.30 2.57
3417 5533 7.389803 AAATGATGATAACAACAATGGACGA 57.610 32.000 0.00 0.00 32.91 4.20
3567 5707 4.174009 GTCACTAGTGCAACGACATACAT 58.826 43.478 18.45 0.00 45.86 2.29
3589 5729 0.531974 AACATATACCAGCACGGCGG 60.532 55.000 13.24 0.66 39.03 6.13
3601 5741 7.553760 CCAGCACTATATGGATTGCAACATATA 59.446 37.037 20.29 20.29 39.99 0.86
3681 5821 1.610554 GGTGCCGCTGGAGTTACCTA 61.611 60.000 0.00 0.00 39.86 3.08
3687 5827 3.120086 AAACAGGTGCCGCTGGAGT 62.120 57.895 0.00 0.00 0.00 3.85
3701 5841 7.860373 GTGCACACTAATAATCAAACAGAAACA 59.140 33.333 13.17 0.00 0.00 2.83
3702 5842 8.076178 AGTGCACACTAATAATCAAACAGAAAC 58.924 33.333 21.04 0.00 40.43 2.78
3726 5866 5.764686 TGTTTCATATGAACAGAACTGCAGT 59.235 36.000 17.76 15.25 33.13 4.40
3733 5873 5.069318 TGCCACTGTTTCATATGAACAGAA 58.931 37.500 32.12 20.62 37.02 3.02
3768 5908 8.988934 TGACATTTTGATAGGCGTATAAGAATC 58.011 33.333 0.00 0.00 0.00 2.52
3779 5919 3.181483 CCTGCCTTGACATTTTGATAGGC 60.181 47.826 5.31 5.31 41.18 3.93
3797 5937 4.887071 TGGGTATACAAAATGATCACCTGC 59.113 41.667 5.01 0.00 0.00 4.85
3807 5947 7.233855 ACTAGGGGAAATGGGTATACAAAAT 57.766 36.000 5.01 0.00 0.00 1.82
3817 5957 3.327439 AGTGGATACTAGGGGAAATGGG 58.673 50.000 0.00 0.00 34.74 4.00
3819 5959 7.040409 GCAATAAAGTGGATACTAGGGGAAATG 60.040 40.741 0.00 0.00 35.69 2.32
3967 6113 2.993604 AGAAAGGGGGAGGAATAGGT 57.006 50.000 0.00 0.00 0.00 3.08
3994 6140 9.203421 CAGTTACATCAAACATCAAGTACACTA 57.797 33.333 0.00 0.00 0.00 2.74
4049 6195 8.615878 TGCCATTATGGTCAAATATACAGTAC 57.384 34.615 13.28 0.00 40.46 2.73
4051 6197 8.532186 TTTGCCATTATGGTCAAATATACAGT 57.468 30.769 21.13 0.00 40.46 3.55
4052 6198 9.814899 TTTTTGCCATTATGGTCAAATATACAG 57.185 29.630 23.64 0.00 40.47 2.74
4053 6199 9.593134 GTTTTTGCCATTATGGTCAAATATACA 57.407 29.630 23.64 12.77 40.47 2.29
4093 6309 4.922206 ACTCAAGTCCAAATATGCCTGAA 58.078 39.130 0.00 0.00 0.00 3.02
4113 6329 3.139397 TGGATTCAGGTTTACACCCAACT 59.861 43.478 0.00 0.00 45.63 3.16
4148 6364 1.912043 AGCTCCATAGTCCTGCAAACT 59.088 47.619 6.64 6.64 0.00 2.66
4158 6374 7.010771 TGTAGAACCATACATAGCTCCATAGT 58.989 38.462 0.00 0.00 30.76 2.12
4190 6406 4.646945 AGACTGCTCTTAATCTCCGAATCA 59.353 41.667 0.00 0.00 0.00 2.57
4197 6413 9.323985 ACAATAATGAAGACTGCTCTTAATCTC 57.676 33.333 0.00 0.00 36.82 2.75
4204 6420 7.661437 TGTGTTAACAATAATGAAGACTGCTCT 59.339 33.333 10.51 0.00 31.82 4.09
4205 6421 7.746475 GTGTGTTAACAATAATGAAGACTGCTC 59.254 37.037 10.51 0.00 38.27 4.26
4206 6422 7.228507 TGTGTGTTAACAATAATGAAGACTGCT 59.771 33.333 10.51 0.00 38.27 4.24
4207 6423 7.359595 TGTGTGTTAACAATAATGAAGACTGC 58.640 34.615 10.51 0.00 38.27 4.40
4208 6424 9.729023 TTTGTGTGTTAACAATAATGAAGACTG 57.271 29.630 10.51 0.00 39.68 3.51
4233 6449 2.293399 GTGTCCGCAAGTGATCCTTTTT 59.707 45.455 0.00 0.00 0.00 1.94
4234 6450 1.880027 GTGTCCGCAAGTGATCCTTTT 59.120 47.619 0.00 0.00 0.00 2.27
4235 6451 1.202758 TGTGTCCGCAAGTGATCCTTT 60.203 47.619 0.00 0.00 0.00 3.11
4236 6452 0.396435 TGTGTCCGCAAGTGATCCTT 59.604 50.000 0.00 0.00 0.00 3.36
4237 6453 0.615331 ATGTGTCCGCAAGTGATCCT 59.385 50.000 0.00 0.00 0.00 3.24
4238 6454 1.009829 GATGTGTCCGCAAGTGATCC 58.990 55.000 0.00 0.00 0.00 3.36
4239 6455 0.647410 CGATGTGTCCGCAAGTGATC 59.353 55.000 0.00 0.00 0.00 2.92
4240 6456 0.740868 CCGATGTGTCCGCAAGTGAT 60.741 55.000 0.00 0.00 0.00 3.06
4241 6457 1.374125 CCGATGTGTCCGCAAGTGA 60.374 57.895 0.00 0.00 0.00 3.41
4242 6458 2.390599 CCCGATGTGTCCGCAAGTG 61.391 63.158 0.00 0.00 0.00 3.16
4243 6459 2.047274 CCCGATGTGTCCGCAAGT 60.047 61.111 0.00 0.00 0.00 3.16
4244 6460 3.499737 GCCCGATGTGTCCGCAAG 61.500 66.667 0.00 0.00 0.00 4.01
4245 6461 3.620419 ATGCCCGATGTGTCCGCAA 62.620 57.895 0.00 0.00 32.01 4.85
4461 6677 0.183731 CTGGGGGTCCTGAAATAGCC 59.816 60.000 0.00 0.00 34.32 3.93
4531 6751 1.080538 GGGAGACACCACCCCTAGT 59.919 63.158 0.00 0.00 40.19 2.57
4692 6913 0.036732 ATGCCTGAAAGAAGCGGACA 59.963 50.000 0.00 0.00 34.07 4.02


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

AutoCloner maintained by Alex Coulton.