Multiple sequence alignment - TraesCS7B01G490500

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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 TraesCS7B01G490500 chr7B 100.000 5840 0 0 1 5840 743813951 743819790 0.000000e+00 10785.0
1 TraesCS7B01G490500 chr7B 86.849 4319 484 43 848 5151 744260949 744256700 0.000000e+00 4752.0
2 TraesCS7B01G490500 chr7B 84.938 3977 550 31 997 4961 743738189 743742128 0.000000e+00 3980.0
3 TraesCS7B01G490500 chr7B 87.086 3167 370 25 848 4008 744110747 744107614 0.000000e+00 3546.0
4 TraesCS7B01G490500 chr7B 82.724 2298 356 26 2018 4303 746738699 746740967 0.000000e+00 2006.0
5 TraesCS7B01G490500 chr7B 80.867 1960 322 39 3023 4969 746527120 746525201 0.000000e+00 1493.0
6 TraesCS7B01G490500 chr7B 86.556 900 113 6 904 1800 746531385 746530491 0.000000e+00 985.0
7 TraesCS7B01G490500 chr7B 85.828 882 124 1 1533 2414 744348053 744348933 0.000000e+00 935.0
8 TraesCS7B01G490500 chr7B 85.230 826 74 29 1 789 744261976 744261162 0.000000e+00 806.0
9 TraesCS7B01G490500 chr7B 95.473 486 6 4 5149 5624 744256577 744256098 0.000000e+00 761.0
10 TraesCS7B01G490500 chr7B 83.333 588 61 14 845 1431 744347502 744348053 5.220000e-140 508.0
11 TraesCS7B01G490500 chr7B 80.587 613 108 9 4362 4966 746740970 746741579 4.120000e-126 462.0
12 TraesCS7B01G490500 chr7B 93.871 310 4 3 5325 5624 744276867 744276563 2.480000e-123 453.0
13 TraesCS7B01G490500 chr7B 83.223 453 43 13 1 430 744111386 744110944 9.180000e-103 385.0
14 TraesCS7B01G490500 chr7B 94.000 200 8 2 5625 5821 744255938 744255740 3.420000e-77 300.0
15 TraesCS7B01G490500 chr7B 87.019 208 12 6 127 334 744347059 744347251 2.740000e-53 220.0
16 TraesCS7B01G490500 chr7B 96.923 65 2 0 787 851 744261101 744261037 6.190000e-20 110.0
17 TraesCS7B01G490500 chr7B 97.222 36 1 0 5726 5761 489830361 489830326 1.760000e-05 62.1
18 TraesCS7B01G490500 chr7A 83.538 2691 393 36 2292 4966 736341959 736344615 0.000000e+00 2470.0
19 TraesCS7B01G490500 chr7A 89.895 1336 126 6 937 2269 736340636 736341965 0.000000e+00 1711.0
20 TraesCS7B01G490500 chr7A 84.194 930 129 13 4046 4966 736292836 736293756 0.000000e+00 887.0
21 TraesCS7B01G490500 chr7A 84.969 326 49 0 3915 4240 736258812 736259137 1.210000e-86 331.0
22 TraesCS7B01G490500 chr7A 89.686 223 21 2 4744 4966 735814130 735814350 3.440000e-72 283.0
23 TraesCS7B01G490500 chr7A 80.000 310 33 16 1 296 736339969 736340263 9.920000e-48 202.0
24 TraesCS7B01G490500 chr7A 100.000 30 0 0 4939 4968 735836307 735836336 8.180000e-04 56.5
25 TraesCS7B01G490500 chr7A 100.000 30 0 0 4939 4968 736085868 736085897 8.180000e-04 56.5
26 TraesCS7B01G490500 chr7A 100.000 30 0 0 4939 4968 736321827 736321856 8.180000e-04 56.5
27 TraesCS7B01G490500 chr5B 84.819 1133 170 2 3070 4201 604164984 604166115 0.000000e+00 1138.0
28 TraesCS7B01G490500 chr1B 75.892 1933 420 33 1036 2954 631203716 631201816 0.000000e+00 946.0
29 TraesCS7B01G490500 chr3B 74.232 1824 427 38 3023 4823 559882967 559884770 0.000000e+00 725.0
30 TraesCS7B01G490500 chr7D 73.668 1914 431 51 1066 2943 5449053 5447177 0.000000e+00 675.0
31 TraesCS7B01G490500 chr7D 83.502 691 74 16 4046 4735 632042669 632042018 5.000000e-170 608.0
32 TraesCS7B01G490500 chr7D 72.532 1631 384 38 1347 2951 5486522 5484930 6.850000e-129 472.0
33 TraesCS7B01G490500 chr7D 97.222 36 1 0 5726 5761 465168094 465168059 1.760000e-05 62.1
34 TraesCS7B01G490500 chr4A 72.933 1947 450 50 1037 2951 736570774 736572675 6.470000e-169 604.0
35 TraesCS7B01G490500 chr4A 72.881 1947 452 50 1037 2951 734730697 734732599 8.370000e-168 601.0
36 TraesCS7B01G490500 chr4A 72.996 1859 427 50 1121 2943 736470575 736468756 3.030000e-162 582.0
37 TraesCS7B01G490500 chr4A 72.405 1917 441 57 1066 2943 736896837 736898704 4.010000e-146 529.0


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 TraesCS7B01G490500 chr7B 743813951 743819790 5839 False 10785.000000 10785 100.000000 1 5840 1 chr7B.!!$F2 5839
1 TraesCS7B01G490500 chr7B 743738189 743742128 3939 False 3980.000000 3980 84.938000 997 4961 1 chr7B.!!$F1 3964
2 TraesCS7B01G490500 chr7B 744107614 744111386 3772 True 1965.500000 3546 85.154500 1 4008 2 chr7B.!!$R3 4007
3 TraesCS7B01G490500 chr7B 744255740 744261976 6236 True 1345.800000 4752 91.695000 1 5821 5 chr7B.!!$R4 5820
4 TraesCS7B01G490500 chr7B 746525201 746531385 6184 True 1239.000000 1493 83.711500 904 4969 2 chr7B.!!$R5 4065
5 TraesCS7B01G490500 chr7B 746738699 746741579 2880 False 1234.000000 2006 81.655500 2018 4966 2 chr7B.!!$F4 2948
6 TraesCS7B01G490500 chr7B 744347059 744348933 1874 False 554.333333 935 85.393333 127 2414 3 chr7B.!!$F3 2287
7 TraesCS7B01G490500 chr7A 736339969 736344615 4646 False 1461.000000 2470 84.477667 1 4966 3 chr7A.!!$F7 4965
8 TraesCS7B01G490500 chr7A 736292836 736293756 920 False 887.000000 887 84.194000 4046 4966 1 chr7A.!!$F5 920
9 TraesCS7B01G490500 chr5B 604164984 604166115 1131 False 1138.000000 1138 84.819000 3070 4201 1 chr5B.!!$F1 1131
10 TraesCS7B01G490500 chr1B 631201816 631203716 1900 True 946.000000 946 75.892000 1036 2954 1 chr1B.!!$R1 1918
11 TraesCS7B01G490500 chr3B 559882967 559884770 1803 False 725.000000 725 74.232000 3023 4823 1 chr3B.!!$F1 1800
12 TraesCS7B01G490500 chr7D 5447177 5449053 1876 True 675.000000 675 73.668000 1066 2943 1 chr7D.!!$R1 1877
13 TraesCS7B01G490500 chr7D 632042018 632042669 651 True 608.000000 608 83.502000 4046 4735 1 chr7D.!!$R4 689
14 TraesCS7B01G490500 chr7D 5484930 5486522 1592 True 472.000000 472 72.532000 1347 2951 1 chr7D.!!$R2 1604
15 TraesCS7B01G490500 chr4A 736570774 736572675 1901 False 604.000000 604 72.933000 1037 2951 1 chr4A.!!$F2 1914
16 TraesCS7B01G490500 chr4A 734730697 734732599 1902 False 601.000000 601 72.881000 1037 2951 1 chr4A.!!$F1 1914
17 TraesCS7B01G490500 chr4A 736468756 736470575 1819 True 582.000000 582 72.996000 1121 2943 1 chr4A.!!$R1 1822
18 TraesCS7B01G490500 chr4A 736896837 736898704 1867 False 529.000000 529 72.405000 1066 2943 1 chr4A.!!$F3 1877

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
460 489 0.039618 TGATTTTCACTCCAGGGGCC 59.960 55.0 0.00 0.00 0.00 5.80 F
1390 1646 0.035630 GAGCAGGCTGTCCAATCTGT 60.036 55.0 17.16 0.00 33.74 3.41 F
2124 4524 1.243342 TTTCTGGTGCAGCAATCGGG 61.243 55.0 20.60 7.91 0.00 5.14 F
3606 6082 0.251341 AACAACATGGCCAGAGGGAC 60.251 55.0 13.05 0.00 45.44 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1511 1767 0.179048 TGGAATAGCAGATGCCGGTG 60.179 55.0 1.90 0.00 43.38 4.94 R
2267 4685 0.741221 GGGGTCGCTTAAGCTGTCAG 60.741 60.0 24.33 9.25 39.32 3.51 R
3899 6387 0.108585 AAGGTCAAGCCGAGAAAGCA 59.891 50.0 0.00 0.00 43.70 3.91 R
5058 7558 0.036952 ACACATGGGAGAGCTGAACG 60.037 55.0 0.00 0.00 0.00 3.95 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
63 64 4.084589 CCGGTTAATTTTTCAGCAAGTTGC 60.085 41.667 20.44 20.44 45.46 4.17
74 75 1.955762 GCAAGTTGCGCTAAAGACAG 58.044 50.000 12.95 0.00 31.71 3.51
75 76 1.264288 GCAAGTTGCGCTAAAGACAGT 59.736 47.619 12.95 0.00 31.71 3.55
76 77 2.908634 CAAGTTGCGCTAAAGACAGTG 58.091 47.619 9.73 0.00 0.00 3.66
77 78 2.526304 AGTTGCGCTAAAGACAGTGA 57.474 45.000 9.73 0.00 0.00 3.41
78 79 3.045601 AGTTGCGCTAAAGACAGTGAT 57.954 42.857 9.73 0.00 0.00 3.06
116 141 0.833949 GACCCCCATTGGAGAGTCTC 59.166 60.000 12.01 12.01 35.39 3.36
169 194 2.279784 GATTCGCCTCTCCCGCAG 60.280 66.667 0.00 0.00 0.00 5.18
228 256 1.202973 CGCTCGCTACCTTCGTCATG 61.203 60.000 0.00 0.00 0.00 3.07
257 285 1.929836 CTTCATCTGTGTAAGCTCGCC 59.070 52.381 0.00 0.00 0.00 5.54
264 292 3.195698 GTAAGCTCGCCGCCCTTG 61.196 66.667 0.00 0.00 40.39 3.61
274 302 0.963225 GCCGCCCTTGGTTTTCTTTA 59.037 50.000 0.00 0.00 0.00 1.85
306 334 8.713271 CCTGTTAGTCTTCTTCTTCAAATACAC 58.287 37.037 0.00 0.00 0.00 2.90
337 365 5.737063 GCACAAAGGCAAGAAGAAGAATCAA 60.737 40.000 0.00 0.00 0.00 2.57
343 371 3.850273 GCAAGAAGAAGAATCAATGTGCG 59.150 43.478 0.00 0.00 0.00 5.34
380 408 2.611292 GTGTGTTCTATGATGCAGCTCC 59.389 50.000 2.53 0.00 0.00 4.70
398 426 3.885901 GCTCCCTGATTTATTTCCCTGTC 59.114 47.826 0.00 0.00 0.00 3.51
430 458 4.619973 TGCAGGTTTTTCAACTATTGCTG 58.380 39.130 0.00 0.00 36.51 4.41
436 465 8.755018 CAGGTTTTTCAACTATTGCTGTAAAAG 58.245 33.333 0.00 0.00 32.90 2.27
455 484 4.861102 AAGCCTTTGATTTTCACTCCAG 57.139 40.909 0.00 0.00 0.00 3.86
456 485 3.160269 AGCCTTTGATTTTCACTCCAGG 58.840 45.455 0.00 0.00 0.00 4.45
457 486 2.232208 GCCTTTGATTTTCACTCCAGGG 59.768 50.000 0.00 0.00 0.00 4.45
458 487 2.827921 CCTTTGATTTTCACTCCAGGGG 59.172 50.000 0.00 0.00 0.00 4.79
459 488 1.923356 TTGATTTTCACTCCAGGGGC 58.077 50.000 0.00 0.00 0.00 5.80
460 489 0.039618 TGATTTTCACTCCAGGGGCC 59.960 55.000 0.00 0.00 0.00 5.80
461 490 0.039618 GATTTTCACTCCAGGGGCCA 59.960 55.000 4.39 0.00 0.00 5.36
462 491 0.712380 ATTTTCACTCCAGGGGCCAT 59.288 50.000 4.39 0.00 0.00 4.40
463 492 0.039618 TTTTCACTCCAGGGGCCATC 59.960 55.000 4.39 0.00 0.00 3.51
464 493 1.139498 TTTCACTCCAGGGGCCATCA 61.139 55.000 4.39 0.00 0.00 3.07
475 504 1.353694 GGGGCCATCATTAGAGCTCAT 59.646 52.381 17.77 3.63 0.00 2.90
476 505 2.434428 GGGCCATCATTAGAGCTCATG 58.566 52.381 17.77 11.99 0.00 3.07
477 506 1.811359 GGCCATCATTAGAGCTCATGC 59.189 52.381 17.77 5.94 40.05 4.06
490 519 1.679032 GCTCATGCTACCGTTTTCCCT 60.679 52.381 0.00 0.00 36.03 4.20
502 531 1.001706 GTTTTCCCTTCGGTCTTGTGC 60.002 52.381 0.00 0.00 0.00 4.57
511 540 1.673665 GGTCTTGTGCTGCCTCCAG 60.674 63.158 0.00 0.00 42.13 3.86
524 553 1.984570 CTCCAGTTCGCCTCTCCCA 60.985 63.158 0.00 0.00 0.00 4.37
531 598 1.254975 TTCGCCTCTCCCACAATCGA 61.255 55.000 0.00 0.00 0.00 3.59
538 605 3.766591 CCTCTCCCACAATCGATAGCTAT 59.233 47.826 5.76 5.76 0.00 2.97
547 614 7.040494 CCACAATCGATAGCTATCTTCATCAT 58.960 38.462 27.00 9.71 0.00 2.45
548 615 7.548427 CCACAATCGATAGCTATCTTCATCATT 59.452 37.037 27.00 13.94 0.00 2.57
552 619 9.941325 AATCGATAGCTATCTTCATCATTCTTT 57.059 29.630 27.00 5.66 0.00 2.52
564 631 7.772292 TCTTCATCATTCTTTACCCTTCATCAG 59.228 37.037 0.00 0.00 0.00 2.90
565 632 6.962182 TCATCATTCTTTACCCTTCATCAGT 58.038 36.000 0.00 0.00 0.00 3.41
566 633 6.825213 TCATCATTCTTTACCCTTCATCAGTG 59.175 38.462 0.00 0.00 0.00 3.66
567 634 6.126863 TCATTCTTTACCCTTCATCAGTGT 57.873 37.500 0.00 0.00 0.00 3.55
568 635 7.252612 TCATTCTTTACCCTTCATCAGTGTA 57.747 36.000 0.00 0.00 0.00 2.90
622 689 3.070159 TCACTGTTAGTCTTGCTCTTGCT 59.930 43.478 0.00 0.00 40.48 3.91
632 699 3.316308 TCTTGCTCTTGCTGTTTTCTTCC 59.684 43.478 0.00 0.00 40.48 3.46
671 741 4.826733 TGCACAAAAGCAGGAAGAAGAATA 59.173 37.500 0.00 0.00 40.11 1.75
722 793 6.881602 AGTTCACTGATTTATCTCCCTGTTTC 59.118 38.462 0.00 0.00 0.00 2.78
928 1176 4.855340 TCCCAATTTTCCTACCATGTCTC 58.145 43.478 0.00 0.00 0.00 3.36
930 1178 5.015178 TCCCAATTTTCCTACCATGTCTCTT 59.985 40.000 0.00 0.00 0.00 2.85
931 1179 6.216662 TCCCAATTTTCCTACCATGTCTCTTA 59.783 38.462 0.00 0.00 0.00 2.10
932 1180 6.318900 CCCAATTTTCCTACCATGTCTCTTAC 59.681 42.308 0.00 0.00 0.00 2.34
933 1181 7.112779 CCAATTTTCCTACCATGTCTCTTACT 58.887 38.462 0.00 0.00 0.00 2.24
934 1182 8.265055 CCAATTTTCCTACCATGTCTCTTACTA 58.735 37.037 0.00 0.00 0.00 1.82
936 1184 8.611051 ATTTTCCTACCATGTCTCTTACTACT 57.389 34.615 0.00 0.00 0.00 2.57
937 1185 8.431910 TTTTCCTACCATGTCTCTTACTACTT 57.568 34.615 0.00 0.00 0.00 2.24
938 1186 7.642082 TTCCTACCATGTCTCTTACTACTTC 57.358 40.000 0.00 0.00 0.00 3.01
939 1187 6.127793 TCCTACCATGTCTCTTACTACTTCC 58.872 44.000 0.00 0.00 0.00 3.46
940 1188 6.068971 TCCTACCATGTCTCTTACTACTTCCT 60.069 42.308 0.00 0.00 0.00 3.36
941 1189 7.128418 TCCTACCATGTCTCTTACTACTTCCTA 59.872 40.741 0.00 0.00 0.00 2.94
942 1190 7.446013 CCTACCATGTCTCTTACTACTTCCTAG 59.554 44.444 0.00 0.00 0.00 3.02
943 1191 6.971340 ACCATGTCTCTTACTACTTCCTAGA 58.029 40.000 0.00 0.00 0.00 2.43
977 1227 7.136203 AGAAAGAGATATATACATCCTCCCCC 58.864 42.308 0.00 0.00 0.00 5.40
1390 1646 0.035630 GAGCAGGCTGTCCAATCTGT 60.036 55.000 17.16 0.00 33.74 3.41
1507 1763 3.054655 TGGTAATAGTGTTGAGGCCTTCC 60.055 47.826 6.77 0.00 0.00 3.46
1511 1767 1.973812 GTGTTGAGGCCTTCCCAGC 60.974 63.158 6.77 2.81 35.39 4.85
1551 1807 4.158209 CCAGTTGATACATCATTTGCACCA 59.842 41.667 0.00 0.00 36.56 4.17
1582 1838 2.434185 GCCGTGACAAGGATCGCA 60.434 61.111 12.01 0.00 0.00 5.10
1616 1872 5.819991 AGATCTTCTTACCAAGCCAATTGA 58.180 37.500 7.12 0.00 41.83 2.57
1625 1890 3.006110 ACCAAGCCAATTGATGTTGAGTG 59.994 43.478 7.12 0.00 41.83 3.51
1686 1951 1.342374 GGAGGCATGGGAAAATCCACT 60.342 52.381 0.00 0.00 39.97 4.00
1694 1959 1.336795 GGGAAAATCCACTTTGGCACG 60.337 52.381 0.00 0.00 38.64 5.34
1703 1968 2.118683 CACTTTGGCACGACATGTTTG 58.881 47.619 0.00 1.57 0.00 2.93
1704 1969 1.748493 ACTTTGGCACGACATGTTTGT 59.252 42.857 0.00 0.00 39.32 2.83
1728 1993 6.635030 AATGACAAGAGGGTAAAAGAACAC 57.365 37.500 0.00 0.00 0.00 3.32
1875 4269 5.934625 GTGCATATTAAGGGACATACTGGAG 59.065 44.000 0.00 0.00 0.00 3.86
1877 4271 6.014242 TGCATATTAAGGGACATACTGGAGAG 60.014 42.308 0.00 0.00 0.00 3.20
1879 4273 7.178628 GCATATTAAGGGACATACTGGAGAGTA 59.821 40.741 0.00 0.00 39.07 2.59
1880 4274 9.090103 CATATTAAGGGACATACTGGAGAGTAA 57.910 37.037 0.00 0.00 38.21 2.24
1932 4329 3.130340 TCTGGTTTGAAGAAAGCACCAAC 59.870 43.478 0.00 0.00 43.07 3.77
1936 4333 1.593196 TGAAGAAAGCACCAACGAGG 58.407 50.000 0.00 0.00 45.67 4.63
1970 4370 9.535878 GGAAAAACTATTGTCTCCTCTAGTATG 57.464 37.037 0.00 0.00 0.00 2.39
2124 4524 1.243342 TTTCTGGTGCAGCAATCGGG 61.243 55.000 20.60 7.91 0.00 5.14
2267 4685 3.737850 CATGGGAAGATGCTCTAAGGAC 58.262 50.000 0.00 0.00 0.00 3.85
2273 4691 4.441356 GGAAGATGCTCTAAGGACTGACAG 60.441 50.000 0.00 0.00 0.00 3.51
2331 4750 7.344352 AGCTATGAGAAGTTAGATCCAAGTCTT 59.656 37.037 0.00 0.00 0.00 3.01
2375 4794 6.826741 TGTAGTTTATATCCAAAAGGCCACTC 59.173 38.462 5.01 0.00 0.00 3.51
2391 4810 5.075493 GGCCACTCCTATTTCATTGATGAT 58.925 41.667 0.00 0.00 36.56 2.45
2509 4928 4.821805 TCTCAGTTTCATTCCTTCAACCAC 59.178 41.667 0.00 0.00 0.00 4.16
2516 4935 6.385649 TTCATTCCTTCAACCACTTTACAC 57.614 37.500 0.00 0.00 0.00 2.90
2539 4958 0.465705 CACAGGTGGCATATCTCCGT 59.534 55.000 0.00 0.00 0.00 4.69
2540 4959 1.686587 CACAGGTGGCATATCTCCGTA 59.313 52.381 0.00 0.00 0.00 4.02
2541 4960 1.687123 ACAGGTGGCATATCTCCGTAC 59.313 52.381 0.00 0.00 0.00 3.67
2669 5088 8.560374 TGTTCGACATCTATCTATCTGTGTTAG 58.440 37.037 0.00 0.00 0.00 2.34
2833 5254 2.035066 AGCTTTTACAACAGCAGCAAGG 59.965 45.455 0.00 0.00 38.61 3.61
2859 5280 4.580167 CCTGAATCTGTTGGTGAACTGAAA 59.420 41.667 0.00 0.00 41.66 2.69
2928 5357 4.885907 CCTGGATCATTGTGTGCTCTTTAT 59.114 41.667 0.00 0.00 0.00 1.40
2932 5361 5.355071 GGATCATTGTGTGCTCTTTATCACA 59.645 40.000 0.00 0.00 40.50 3.58
2955 5384 8.177663 CACATGCAATTACTTAAGTTCAGTAGG 58.822 37.037 14.49 5.95 0.00 3.18
2966 5395 9.403583 ACTTAAGTTCAGTAGGAATGTCAAAAA 57.596 29.630 1.12 0.00 37.93 1.94
3058 5523 4.729868 AGGCAAGTTAACTTCACTCCAAT 58.270 39.130 18.00 0.88 33.11 3.16
3066 5531 6.483640 AGTTAACTTCACTCCAATGTCTCAAC 59.516 38.462 1.12 0.00 0.00 3.18
3094 5559 1.079612 GTGCAAAAGCAGATGGGCC 60.080 57.895 0.00 0.00 0.00 5.80
3124 5589 0.807496 GCAGCTGAAGGACATGAACC 59.193 55.000 20.43 2.33 0.00 3.62
3148 5613 4.200092 CCTTGGAGGCAGTTTAAGTATCC 58.800 47.826 0.00 0.00 0.00 2.59
3166 5631 6.284459 AGTATCCAAAATCTCGAGAATGTCC 58.716 40.000 20.91 6.44 0.00 4.02
3195 5660 2.299867 GGATCAAGCCTTGGAAGCAAAA 59.700 45.455 4.30 0.00 0.00 2.44
3204 5669 4.261994 GCCTTGGAAGCAAAACTACATCAA 60.262 41.667 0.00 0.00 0.00 2.57
3245 5710 3.411446 TGCACCTTGAATGGAGTTACAG 58.589 45.455 0.00 0.00 0.00 2.74
3248 5713 3.686726 CACCTTGAATGGAGTTACAGAGC 59.313 47.826 0.00 0.00 0.00 4.09
3257 5731 3.194329 TGGAGTTACAGAGCTGACATGAG 59.806 47.826 0.00 0.00 0.00 2.90
3424 5900 1.594194 CCTGGTTAATTGCAGCGCCA 61.594 55.000 2.29 0.00 0.00 5.69
3445 5921 5.649831 GCCATAGAAATCCTACCATCCAATC 59.350 44.000 0.00 0.00 0.00 2.67
3459 5935 1.203428 TCCAATCCCACTCTCCTTGGA 60.203 52.381 0.00 0.00 42.22 3.53
3475 5951 3.575687 CCTTGGAAATTGCTCCTCACTTT 59.424 43.478 0.00 0.00 36.35 2.66
3521 5997 6.837312 TGAAGACATTACCTTCTCTTCCAAA 58.163 36.000 0.00 0.00 40.37 3.28
3546 6022 5.048504 CAGCCTTGAAGAGTTAGCAATTGAA 60.049 40.000 10.34 0.00 0.00 2.69
3596 6072 5.121105 TGATGATGAGCTAGAACAACATGG 58.879 41.667 13.70 0.00 31.62 3.66
3606 6082 0.251341 AACAACATGGCCAGAGGGAC 60.251 55.000 13.05 0.00 45.44 4.46
3615 6091 0.251341 GCCAGAGGGACAACACCATT 60.251 55.000 0.00 0.00 35.59 3.16
3640 6116 3.728845 ACATACAACTTGAAGTCGCAGT 58.271 40.909 0.00 0.00 0.00 4.40
3665 6141 2.512910 TCCATGTGGGAGGTGGATAT 57.487 50.000 0.00 0.00 42.15 1.63
3678 6154 6.389869 GGGAGGTGGATATGGGATCAAATATA 59.610 42.308 0.00 0.00 0.00 0.86
3723 6199 5.879223 ACATTCATCTCTGAAGTGGTTGATC 59.121 40.000 0.00 0.00 44.32 2.92
3745 6221 7.496920 TGATCACTTCAATGGATGTTGATAGTC 59.503 37.037 0.00 0.00 37.88 2.59
3759 6235 7.009179 TGTTGATAGTCCTCATCTTCAAACT 57.991 36.000 0.00 0.00 0.00 2.66
3791 6267 5.428184 ACTCTAAAAAGAGAGGGTGATGG 57.572 43.478 9.31 0.00 46.22 3.51
3792 6268 4.846940 ACTCTAAAAAGAGAGGGTGATGGT 59.153 41.667 9.31 0.00 46.22 3.55
3800 6288 2.771943 GAGAGGGTGATGGTGTATTGGA 59.228 50.000 0.00 0.00 0.00 3.53
3802 6290 3.054361 AGAGGGTGATGGTGTATTGGAAC 60.054 47.826 0.00 0.00 0.00 3.62
3850 6338 2.435805 TGTTGCCATGAGGAGAGGATAC 59.564 50.000 0.00 0.00 36.89 2.24
3852 6340 0.605589 GCCATGAGGAGAGGATACGG 59.394 60.000 0.00 0.00 38.72 4.02
3890 6378 1.495579 ATCAGCCTGCCACTGGTTCT 61.496 55.000 0.00 0.00 35.78 3.01
3920 6408 1.068954 GCTTTCTCGGCTTGACCTTTG 60.069 52.381 0.00 0.00 35.61 2.77
3924 6412 0.875059 CTCGGCTTGACCTTTGTTCC 59.125 55.000 0.00 0.00 35.61 3.62
3972 6462 3.486383 TGTTTTCCTTGATGGTCTCACC 58.514 45.455 0.00 0.00 39.22 4.02
3987 6477 3.483421 TCTCACCTCACTGAGACGTTTA 58.517 45.455 7.69 0.00 41.49 2.01
4041 6531 1.135915 CCGTCAGAAGATGTCCTCCAG 59.864 57.143 0.00 0.00 0.00 3.86
4090 6580 2.281070 ACTCGTGCTGGTGCCTTG 60.281 61.111 0.00 0.00 38.71 3.61
4101 6591 1.922447 TGGTGCCTTGGATCATTAGGT 59.078 47.619 0.00 0.00 0.00 3.08
4178 6668 2.639347 TGGACTTCACATGTGGATCAGT 59.361 45.455 25.16 19.85 0.00 3.41
4260 6750 2.224281 CCTCAGTAGTGACTTGCCACAA 60.224 50.000 0.00 0.00 39.42 3.33
4268 6758 2.423538 GTGACTTGCCACAACTGAAACT 59.576 45.455 0.00 0.00 37.04 2.66
4281 6771 5.301551 ACAACTGAAACTTATTGACATGGCA 59.698 36.000 0.00 0.00 0.00 4.92
4319 6809 5.739752 TCATCATTGTCGATTGGTCATTC 57.260 39.130 0.00 0.00 0.00 2.67
4406 6896 2.126064 TGCAACTTGGCAGTGCAAT 58.874 47.368 18.61 0.00 39.25 3.56
4524 7014 4.655963 TGCTCTCTGCTGAAGGTTTTAAT 58.344 39.130 0.00 0.00 43.37 1.40
4539 7029 9.325198 GAAGGTTTTAATGTTCCAAGACATTTT 57.675 29.630 8.35 0.00 45.38 1.82
4604 7099 6.704937 TCAGCAGATTTATCATCTGTCATCAC 59.295 38.462 12.33 0.00 45.38 3.06
4686 7181 1.926510 CTGACGATGCTGCGAATTGTA 59.073 47.619 5.82 0.00 34.83 2.41
4693 7188 2.358957 TGCTGCGAATTGTAAGATGCT 58.641 42.857 0.00 0.00 0.00 3.79
4722 7217 9.986157 AATATATCATCATTACCTGATTTGCCT 57.014 29.630 0.00 0.00 42.07 4.75
4737 7232 0.909610 TGCCTTCTTCCCTCGACCAT 60.910 55.000 0.00 0.00 0.00 3.55
4809 7304 0.820226 GGGAAAGCTGGCCAAAGATC 59.180 55.000 7.01 3.12 0.00 2.75
5057 7557 2.613133 GTTTCTCAGGCTCTCATCATGC 59.387 50.000 0.00 0.00 0.00 4.06
5058 7558 0.757512 TCTCAGGCTCTCATCATGCC 59.242 55.000 0.00 0.00 46.42 4.40
5061 7561 4.547859 GGCTCTCATCATGCCGTT 57.452 55.556 0.00 0.00 37.11 4.44
5062 7562 2.315246 GGCTCTCATCATGCCGTTC 58.685 57.895 0.00 0.00 37.11 3.95
5063 7563 0.462581 GGCTCTCATCATGCCGTTCA 60.463 55.000 0.00 0.00 37.11 3.18
5064 7564 0.935898 GCTCTCATCATGCCGTTCAG 59.064 55.000 0.00 0.00 0.00 3.02
5065 7565 0.935898 CTCTCATCATGCCGTTCAGC 59.064 55.000 0.00 0.00 0.00 4.26
5066 7566 0.538584 TCTCATCATGCCGTTCAGCT 59.461 50.000 0.00 0.00 0.00 4.24
5067 7567 0.935898 CTCATCATGCCGTTCAGCTC 59.064 55.000 0.00 0.00 0.00 4.09
5068 7568 0.538584 TCATCATGCCGTTCAGCTCT 59.461 50.000 0.00 0.00 0.00 4.09
5069 7569 0.935898 CATCATGCCGTTCAGCTCTC 59.064 55.000 0.00 0.00 0.00 3.20
5070 7570 0.179062 ATCATGCCGTTCAGCTCTCC 60.179 55.000 0.00 0.00 0.00 3.71
5071 7571 1.817099 CATGCCGTTCAGCTCTCCC 60.817 63.158 0.00 0.00 0.00 4.30
5072 7572 2.293318 ATGCCGTTCAGCTCTCCCA 61.293 57.895 0.00 0.00 0.00 4.37
5073 7573 1.630126 ATGCCGTTCAGCTCTCCCAT 61.630 55.000 0.00 0.00 0.00 4.00
5074 7574 1.817099 GCCGTTCAGCTCTCCCATG 60.817 63.158 0.00 0.00 0.00 3.66
5078 7578 1.731720 GTTCAGCTCTCCCATGTGTC 58.268 55.000 0.00 0.00 0.00 3.67
5123 7623 2.378806 CATCGCCGATTTCTGCAATTC 58.621 47.619 0.00 0.00 0.00 2.17
5192 7817 5.068591 GGTTGTTTTGTTATCCTTGGAGTGT 59.931 40.000 0.00 0.00 0.00 3.55
5203 7828 3.392947 TCCTTGGAGTGTCACATTTGGTA 59.607 43.478 5.62 0.00 0.00 3.25
5272 7897 5.358725 TGAACTTGGGTAGTTTCTTTTGGAC 59.641 40.000 0.00 0.00 47.00 4.02
5304 7929 6.154534 GGAGGTTGCTTTATTTATCCTTTGGT 59.845 38.462 0.00 0.00 0.00 3.67
5357 7982 6.887376 TTCACTCAATCTGTTTATACGCTC 57.113 37.500 0.00 0.00 0.00 5.03
5358 7983 6.208988 TCACTCAATCTGTTTATACGCTCT 57.791 37.500 0.00 0.00 0.00 4.09
5537 8172 2.159000 CCATGTCTACATCAGAGCAGCA 60.159 50.000 0.00 0.00 33.61 4.41
5538 8173 2.955477 TGTCTACATCAGAGCAGCAG 57.045 50.000 0.00 0.00 32.51 4.24
5539 8174 1.134877 TGTCTACATCAGAGCAGCAGC 60.135 52.381 0.00 0.00 42.56 5.25
5582 8217 7.060864 GCAAATAAGTATAGTACGTAGCTGCTC 59.939 40.741 4.91 0.00 34.48 4.26
5635 8429 9.866655 ATAATCCAATAGGCTCAACTGATTTAA 57.133 29.630 0.00 0.00 33.74 1.52
5658 8452 2.427506 ACAATTTTCACGAGAGCTCCC 58.572 47.619 10.93 0.00 0.00 4.30
5666 8460 0.331954 ACGAGAGCTCCCCTCAACTA 59.668 55.000 10.93 0.00 43.31 2.24
5713 8507 5.916661 ATAGTGTCGTCTTCAGGTTGTAT 57.083 39.130 0.00 0.00 0.00 2.29
5724 8518 7.090808 GTCTTCAGGTTGTATTCCAAATTTCC 58.909 38.462 0.00 0.00 34.07 3.13
5765 8559 3.567797 GCAATCCGAGCGTCTGGC 61.568 66.667 0.00 0.00 44.05 4.85
5810 8607 0.883833 CCACTTGCCAACTGATGTCC 59.116 55.000 0.00 0.00 0.00 4.02
5811 8608 1.608055 CACTTGCCAACTGATGTCCA 58.392 50.000 0.00 0.00 0.00 4.02
5812 8609 1.267806 CACTTGCCAACTGATGTCCAC 59.732 52.381 0.00 0.00 0.00 4.02
5813 8610 1.143684 ACTTGCCAACTGATGTCCACT 59.856 47.619 0.00 0.00 0.00 4.00
5814 8611 1.538512 CTTGCCAACTGATGTCCACTG 59.461 52.381 0.00 0.00 0.00 3.66
5816 8613 1.133823 TGCCAACTGATGTCCACTGTT 60.134 47.619 0.00 0.00 0.00 3.16
5817 8614 1.267806 GCCAACTGATGTCCACTGTTG 59.732 52.381 0.00 0.00 42.49 3.33
5818 8615 2.849942 CCAACTGATGTCCACTGTTGA 58.150 47.619 15.36 0.00 44.16 3.18
5819 8616 2.549754 CCAACTGATGTCCACTGTTGAC 59.450 50.000 15.36 5.15 44.16 3.18
5820 8617 3.205338 CAACTGATGTCCACTGTTGACA 58.795 45.455 15.87 15.87 45.98 3.58
5821 8618 3.117491 ACTGATGTCCACTGTTGACAG 57.883 47.619 18.00 9.50 45.20 3.51
5822 8619 2.700371 ACTGATGTCCACTGTTGACAGA 59.300 45.455 18.00 8.14 45.20 3.41
5823 8620 3.244009 ACTGATGTCCACTGTTGACAGAG 60.244 47.826 18.00 16.97 45.20 3.35
5824 8621 2.700371 TGATGTCCACTGTTGACAGAGT 59.300 45.455 18.00 4.00 45.20 3.24
5825 8622 2.602257 TGTCCACTGTTGACAGAGTG 57.398 50.000 17.42 7.24 46.59 3.51
5826 8623 1.831106 TGTCCACTGTTGACAGAGTGT 59.169 47.619 17.42 0.00 46.59 3.55
5827 8624 2.236146 TGTCCACTGTTGACAGAGTGTT 59.764 45.455 17.42 0.00 46.59 3.32
5828 8625 3.270877 GTCCACTGTTGACAGAGTGTTT 58.729 45.455 17.42 0.00 46.59 2.83
5829 8626 3.063997 GTCCACTGTTGACAGAGTGTTTG 59.936 47.826 17.42 4.49 46.59 2.93
5830 8627 3.055458 TCCACTGTTGACAGAGTGTTTGA 60.055 43.478 17.42 0.25 46.59 2.69
5831 8628 3.063997 CCACTGTTGACAGAGTGTTTGAC 59.936 47.826 17.42 0.00 46.59 3.18
5832 8629 3.684305 CACTGTTGACAGAGTGTTTGACA 59.316 43.478 17.42 0.00 46.59 3.58
5833 8630 4.154015 CACTGTTGACAGAGTGTTTGACAA 59.846 41.667 17.42 0.00 46.59 3.18
5834 8631 4.759693 ACTGTTGACAGAGTGTTTGACAAA 59.240 37.500 17.42 0.00 46.59 2.83
5835 8632 5.240623 ACTGTTGACAGAGTGTTTGACAAAA 59.759 36.000 17.42 0.00 46.59 2.44
5836 8633 6.078202 TGTTGACAGAGTGTTTGACAAAAA 57.922 33.333 1.27 0.00 33.41 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 4.608222 GCGCAACTTGCTGAAAAATTAACC 60.608 41.667 11.93 0.00 42.25 2.85
47 48 2.514205 AGCGCAACTTGCTGAAAAAT 57.486 40.000 11.47 0.00 42.25 1.82
63 64 5.985530 TGAATGGATATCACTGTCTTTAGCG 59.014 40.000 4.83 0.00 0.00 4.26
67 68 7.571919 AGACATGAATGGATATCACTGTCTTT 58.428 34.615 4.83 0.00 39.65 2.52
69 70 6.744175 AGACATGAATGGATATCACTGTCT 57.256 37.500 4.83 9.40 38.87 3.41
70 71 6.765036 ACAAGACATGAATGGATATCACTGTC 59.235 38.462 4.83 7.52 36.58 3.51
71 72 6.656902 ACAAGACATGAATGGATATCACTGT 58.343 36.000 4.83 0.00 0.00 3.55
74 75 7.412853 GTCAACAAGACATGAATGGATATCAC 58.587 38.462 4.83 0.00 46.77 3.06
75 76 7.558161 GTCAACAAGACATGAATGGATATCA 57.442 36.000 4.83 0.00 46.77 2.15
116 141 3.978687 ACCATAAGAGAAATAGGACGCG 58.021 45.455 3.53 3.53 0.00 6.01
169 194 1.202698 CGATGAAGGGGAATGGGAGAC 60.203 57.143 0.00 0.00 0.00 3.36
217 242 1.672356 GGTGCAGCATGACGAAGGT 60.672 57.895 11.86 0.00 39.69 3.50
228 256 1.085091 CACAGATGAAGAGGTGCAGC 58.915 55.000 8.11 8.11 0.00 5.25
257 285 4.234574 GACAATAAAGAAAACCAAGGGCG 58.765 43.478 0.00 0.00 0.00 6.13
264 292 7.447545 AGACTAACAGGGACAATAAAGAAAACC 59.552 37.037 0.00 0.00 0.00 3.27
274 302 6.043243 TGAAGAAGAAGACTAACAGGGACAAT 59.957 38.462 0.00 0.00 0.00 2.71
306 334 1.821936 TTGCCTTTGTGCAAGTGGG 59.178 52.632 0.00 0.00 45.77 4.61
380 408 8.581253 AGTAAAAGACAGGGAAATAAATCAGG 57.419 34.615 0.00 0.00 0.00 3.86
398 426 5.514274 TGAAAAACCTGCAGGAGTAAAAG 57.486 39.130 39.19 10.39 38.94 2.27
430 458 6.512297 TGGAGTGAAAATCAAAGGCTTTTAC 58.488 36.000 10.36 0.00 28.43 2.01
436 465 2.232208 CCCTGGAGTGAAAATCAAAGGC 59.768 50.000 0.00 0.00 35.67 4.35
447 476 0.920763 AATGATGGCCCCTGGAGTGA 60.921 55.000 0.00 0.00 0.00 3.41
455 484 0.767375 TGAGCTCTAATGATGGCCCC 59.233 55.000 16.19 0.00 0.00 5.80
456 485 2.434428 CATGAGCTCTAATGATGGCCC 58.566 52.381 16.19 0.00 0.00 5.80
457 486 1.811359 GCATGAGCTCTAATGATGGCC 59.189 52.381 16.19 0.00 37.91 5.36
475 504 3.220447 CGAAGGGAAAACGGTAGCA 57.780 52.632 0.00 0.00 0.00 3.49
490 519 1.301716 GAGGCAGCACAAGACCGAA 60.302 57.895 0.00 0.00 0.00 4.30
502 531 2.125350 GAGGCGAACTGGAGGCAG 60.125 66.667 0.00 0.00 35.18 4.85
511 540 1.084370 CGATTGTGGGAGAGGCGAAC 61.084 60.000 0.00 0.00 0.00 3.95
524 553 8.530311 AGAATGATGAAGATAGCTATCGATTGT 58.470 33.333 24.53 13.02 37.76 2.71
531 598 9.110382 AGGGTAAAGAATGATGAAGATAGCTAT 57.890 33.333 5.76 5.76 0.00 2.97
538 605 7.632861 TGATGAAGGGTAAAGAATGATGAAGA 58.367 34.615 0.00 0.00 0.00 2.87
547 614 6.681729 ACTACACTGATGAAGGGTAAAGAA 57.318 37.500 0.00 0.00 44.34 2.52
548 615 7.578955 GCTTACTACACTGATGAAGGGTAAAGA 60.579 40.741 4.23 0.00 44.34 2.52
552 619 5.269991 AGCTTACTACACTGATGAAGGGTA 58.730 41.667 0.00 0.00 42.33 3.69
564 631 4.623002 GAAGGGCATAGAGCTTACTACAC 58.377 47.826 0.00 0.00 44.79 2.90
565 632 3.318275 CGAAGGGCATAGAGCTTACTACA 59.682 47.826 0.00 0.00 44.79 2.74
566 633 3.318557 ACGAAGGGCATAGAGCTTACTAC 59.681 47.826 0.00 0.00 44.79 2.73
567 634 3.563223 ACGAAGGGCATAGAGCTTACTA 58.437 45.455 0.00 0.00 44.79 1.82
568 635 2.389715 ACGAAGGGCATAGAGCTTACT 58.610 47.619 0.00 0.00 44.79 2.24
696 766 5.738909 ACAGGGAGATAAATCAGTGAACTG 58.261 41.667 3.98 3.98 45.08 3.16
722 793 3.190878 GGAAACCTGCATGAGCGG 58.809 61.111 0.00 0.00 46.23 5.52
918 1166 8.098963 TCTAGGAAGTAGTAAGAGACATGGTA 57.901 38.462 0.00 0.00 0.00 3.25
922 1170 9.310449 TGTTTTCTAGGAAGTAGTAAGAGACAT 57.690 33.333 0.00 0.00 0.00 3.06
934 1182 9.462606 TCTCTTTCTTTTTGTTTTCTAGGAAGT 57.537 29.630 0.00 0.00 0.00 3.01
953 1201 7.368198 GGGGGAGGATGTATATATCTCTTTC 57.632 44.000 9.09 3.47 0.00 2.62
977 1227 0.035439 AAGCACACCGTGGGATAAGG 60.035 55.000 4.51 0.00 33.64 2.69
978 1228 1.737793 GAAAGCACACCGTGGGATAAG 59.262 52.381 4.51 0.00 33.64 1.73
979 1229 1.612199 GGAAAGCACACCGTGGGATAA 60.612 52.381 4.51 0.00 33.64 1.75
1390 1646 1.136695 CAGCTGTTTGTTCTTTGGGCA 59.863 47.619 5.25 0.00 0.00 5.36
1511 1767 0.179048 TGGAATAGCAGATGCCGGTG 60.179 55.000 1.90 0.00 43.38 4.94
1523 1779 7.859377 GTGCAAATGATGTATCAACTGGAATAG 59.141 37.037 0.00 0.00 40.69 1.73
1551 1807 1.274167 TCACGGCCGATCACTTTTAGT 59.726 47.619 35.90 0.00 0.00 2.24
1616 1872 4.005650 CCTGCTTGTATCACACTCAACAT 58.994 43.478 0.00 0.00 0.00 2.71
1625 1890 4.572389 CACCAGAATACCTGCTTGTATCAC 59.428 45.833 0.19 0.00 41.57 3.06
1686 1951 4.036852 TCATTACAAACATGTCGTGCCAAA 59.963 37.500 0.00 0.00 0.00 3.28
1694 1959 5.473504 ACCCTCTTGTCATTACAAACATGTC 59.526 40.000 0.00 0.00 44.79 3.06
1703 1968 7.444487 AGTGTTCTTTTACCCTCTTGTCATTAC 59.556 37.037 0.00 0.00 0.00 1.89
1704 1969 7.514721 AGTGTTCTTTTACCCTCTTGTCATTA 58.485 34.615 0.00 0.00 0.00 1.90
1728 1993 1.352352 ACCCACATCCTGACCTCAAAG 59.648 52.381 0.00 0.00 0.00 2.77
1902 4296 4.336889 TTCTTCAAACCAGACATCGTCT 57.663 40.909 0.00 0.00 44.44 4.18
1932 4329 1.202770 AGTTTTTCCCACTCCACCTCG 60.203 52.381 0.00 0.00 0.00 4.63
1936 4333 5.070685 AGACAATAGTTTTTCCCACTCCAC 58.929 41.667 0.00 0.00 0.00 4.02
1970 4370 1.452145 TTTGCTTCCCGTCTGTTGGC 61.452 55.000 0.00 0.00 0.00 4.52
2083 4483 1.421268 TGCATGGTCCTTGAAGAGTGT 59.579 47.619 8.93 0.00 0.00 3.55
2124 4524 3.311110 TCACGCACCCTCTGGTCC 61.311 66.667 0.00 0.00 45.57 4.46
2142 4554 4.662468 TTCTGCAATAGTCTCTAGCTGG 57.338 45.455 0.00 0.00 0.00 4.85
2267 4685 0.741221 GGGGTCGCTTAAGCTGTCAG 60.741 60.000 24.33 9.25 39.32 3.51
2273 4691 0.822164 TCTACTGGGGTCGCTTAAGC 59.178 55.000 17.83 17.83 37.78 3.09
2283 4701 2.366916 CCATAGAAGTGCTCTACTGGGG 59.633 54.545 0.00 0.00 39.52 4.96
2375 4794 6.418819 GCGAACCAAATCATCAATGAAATAGG 59.581 38.462 0.00 0.71 40.69 2.57
2391 4810 1.529226 CTACCCACATGCGAACCAAA 58.471 50.000 0.00 0.00 0.00 3.28
2528 4947 4.832590 ACACAGTAGTACGGAGATATGC 57.167 45.455 7.48 0.00 0.00 3.14
2536 4955 4.678622 TCATGCATAACACAGTAGTACGG 58.321 43.478 0.00 0.00 0.00 4.02
2539 4958 6.098266 ACCAGATCATGCATAACACAGTAGTA 59.902 38.462 0.00 0.00 0.00 1.82
2540 4959 5.104776 ACCAGATCATGCATAACACAGTAGT 60.105 40.000 0.00 0.00 0.00 2.73
2541 4960 5.363101 ACCAGATCATGCATAACACAGTAG 58.637 41.667 0.00 0.00 0.00 2.57
2595 5014 6.605471 TCATCTTCTAACCTAAAGCAGACA 57.395 37.500 0.00 0.00 0.00 3.41
2669 5088 4.044426 GTGTTGATGTTGCTTCAAAGTCC 58.956 43.478 0.14 0.00 35.03 3.85
2833 5254 4.452455 CAGTTCACCAACAGATTCAGGTAC 59.548 45.833 0.00 0.00 34.60 3.34
2928 5357 7.744087 ACTGAACTTAAGTAATTGCATGTGA 57.256 32.000 8.92 0.00 0.00 3.58
2932 5361 9.686683 ATTCCTACTGAACTTAAGTAATTGCAT 57.313 29.630 8.92 0.00 35.31 3.96
2993 5422 9.775854 CACAATCCTCAAGATATCTCAACTTAT 57.224 33.333 5.51 0.00 33.66 1.73
3012 5447 1.571955 AAGGGATTTGGCCACAATCC 58.428 50.000 31.47 31.47 36.29 3.01
3014 5449 3.182887 TGTAAGGGATTTGGCCACAAT 57.817 42.857 3.88 9.02 36.29 2.71
3015 5450 2.685106 TGTAAGGGATTTGGCCACAA 57.315 45.000 3.88 3.52 34.07 3.33
3058 5523 2.797792 GCACGCAAAATTGGTTGAGACA 60.798 45.455 1.27 0.00 33.13 3.41
3094 5559 0.958876 TTCAGCTGCTGCACCTCATG 60.959 55.000 24.38 6.15 42.74 3.07
3124 5589 2.863809 ACTTAAACTGCCTCCAAGGTG 58.136 47.619 0.00 0.00 37.80 4.00
3148 5613 2.609459 CGGGGACATTCTCGAGATTTTG 59.391 50.000 17.44 16.05 0.00 2.44
3166 5631 1.926426 AAGGCTTGATCCTTCCCGGG 61.926 60.000 16.85 16.85 42.55 5.73
3245 5710 3.593096 TCATGTGAACTCATGTCAGCTC 58.407 45.455 13.81 0.00 43.70 4.09
3248 5713 7.606858 AAACTATCATGTGAACTCATGTCAG 57.393 36.000 13.81 13.46 43.70 3.51
3257 5731 9.906660 TTTCCAAATGTAAACTATCATGTGAAC 57.093 29.630 0.00 0.00 32.75 3.18
3403 5879 1.312371 GCGCTGCAATTAACCAGGGA 61.312 55.000 16.05 0.00 42.57 4.20
3408 5884 1.946768 TCTATGGCGCTGCAATTAACC 59.053 47.619 7.64 0.00 0.00 2.85
3424 5900 5.857283 TGGGATTGGATGGTAGGATTTCTAT 59.143 40.000 0.00 0.00 0.00 1.98
3445 5921 1.821136 GCAATTTCCAAGGAGAGTGGG 59.179 52.381 8.81 0.00 36.73 4.61
3459 5935 2.560105 GAGGCAAAGTGAGGAGCAATTT 59.440 45.455 0.00 0.00 44.79 1.82
3475 5951 3.269381 AGGTTTGGGATATTCTTGAGGCA 59.731 43.478 0.00 0.00 0.00 4.75
3521 5997 3.492102 TTGCTAACTCTTCAAGGCTGT 57.508 42.857 0.00 0.00 0.00 4.40
3574 6050 4.024218 GCCATGTTGTTCTAGCTCATCATC 60.024 45.833 0.00 0.00 0.00 2.92
3596 6072 0.251341 AATGGTGTTGTCCCTCTGGC 60.251 55.000 0.00 0.00 0.00 4.85
3606 6082 7.815641 TCAAGTTGTATGTCATAATGGTGTTG 58.184 34.615 2.11 0.00 0.00 3.33
3615 6091 5.474825 TGCGACTTCAAGTTGTATGTCATA 58.525 37.500 6.65 0.00 32.12 2.15
3640 6116 2.490718 CCACCTCCCACATGGAAGAAAA 60.491 50.000 0.00 0.00 44.57 2.29
3678 6154 6.105397 TGTTCCGACAATAGTACTTTCCTT 57.895 37.500 0.00 0.00 31.49 3.36
3723 6199 6.118170 AGGACTATCAACATCCATTGAAGTG 58.882 40.000 7.56 0.00 41.78 3.16
3791 6267 7.933577 TGATGATATCCTCTTGTTCCAATACAC 59.066 37.037 9.12 0.00 0.00 2.90
3792 6268 8.033178 TGATGATATCCTCTTGTTCCAATACA 57.967 34.615 9.12 0.00 0.00 2.29
3800 6288 5.378230 TGCCTTGATGATATCCTCTTGTT 57.622 39.130 9.12 0.00 0.00 2.83
3802 6290 4.700692 CCATGCCTTGATGATATCCTCTTG 59.299 45.833 9.12 2.84 0.00 3.02
3850 6338 2.811431 TGTTCCTTGTACAAATGAGCCG 59.189 45.455 10.03 0.00 0.00 5.52
3852 6340 5.627499 TGATGTTCCTTGTACAAATGAGC 57.373 39.130 10.03 11.30 0.00 4.26
3890 6378 1.405526 GCCGAGAAAGCACTGATGGTA 60.406 52.381 0.00 0.00 34.76 3.25
3899 6387 0.108585 AAGGTCAAGCCGAGAAAGCA 59.891 50.000 0.00 0.00 43.70 3.91
3920 6408 4.385825 TCCATCCGTAATAATGCAGGAAC 58.614 43.478 0.00 0.00 34.35 3.62
3924 6412 3.402110 TGCTCCATCCGTAATAATGCAG 58.598 45.455 0.00 0.00 0.00 4.41
3956 6444 1.902508 GTGAGGTGAGACCATCAAGGA 59.097 52.381 0.00 0.00 41.95 3.36
3972 6462 7.808381 TCTTTTAGTGATAAACGTCTCAGTGAG 59.192 37.037 14.36 14.36 0.00 3.51
4041 6531 3.065925 AGTTCTGAAGCTTTGTCAACTGC 59.934 43.478 0.00 2.46 0.00 4.40
4090 6580 3.802675 GCTCGTAACCCACCTAATGATCC 60.803 52.174 0.00 0.00 0.00 3.36
4101 6591 1.895238 GGTAGCAGCTCGTAACCCA 59.105 57.895 0.00 0.00 0.00 4.51
4260 6750 6.435277 AGAATGCCATGTCAATAAGTTTCAGT 59.565 34.615 0.00 0.00 0.00 3.41
4281 6771 4.217836 TGATGAAGAGCTTCTGCAGAAT 57.782 40.909 28.57 15.83 35.05 2.40
4319 6809 1.827969 ACAATCTTCTGAGGGAGGTCG 59.172 52.381 0.00 0.00 0.00 4.79
4406 6896 5.882040 TGAGGTTTGGGACATGTGTAAATA 58.118 37.500 1.15 0.00 39.30 1.40
4539 7029 4.298626 ACTCCTTGCATCCTATAAGACCA 58.701 43.478 0.00 0.00 0.00 4.02
4604 7099 8.694540 TGATTTCACAATCCATAAATAACAGGG 58.305 33.333 0.00 0.00 38.50 4.45
4686 7181 9.624373 GGTAATGATGATATATTGGAGCATCTT 57.376 33.333 10.85 4.40 37.01 2.40
4707 7202 4.017130 AGGGAAGAAGGCAAATCAGGTAAT 60.017 41.667 0.00 0.00 0.00 1.89
4722 7217 6.351033 GCACATATATATGGTCGAGGGAAGAA 60.351 42.308 23.44 0.00 38.00 2.52
4737 7232 6.437477 AGAGTTCAGAATCCCGCACATATATA 59.563 38.462 0.00 0.00 0.00 0.86
5057 7557 0.742281 CACATGGGAGAGCTGAACGG 60.742 60.000 0.00 0.00 0.00 4.44
5058 7558 0.036952 ACACATGGGAGAGCTGAACG 60.037 55.000 0.00 0.00 0.00 3.95
5059 7559 1.731720 GACACATGGGAGAGCTGAAC 58.268 55.000 0.00 0.00 0.00 3.18
5060 7560 0.247460 CGACACATGGGAGAGCTGAA 59.753 55.000 0.00 0.00 0.00 3.02
5061 7561 0.900182 ACGACACATGGGAGAGCTGA 60.900 55.000 0.00 0.00 0.00 4.26
5062 7562 0.817654 TACGACACATGGGAGAGCTG 59.182 55.000 0.00 0.00 0.00 4.24
5063 7563 1.107114 CTACGACACATGGGAGAGCT 58.893 55.000 0.00 0.00 0.00 4.09
5064 7564 0.103208 CCTACGACACATGGGAGAGC 59.897 60.000 0.00 0.00 0.00 4.09
5065 7565 1.405821 GACCTACGACACATGGGAGAG 59.594 57.143 0.00 0.00 0.00 3.20
5066 7566 1.471119 GACCTACGACACATGGGAGA 58.529 55.000 0.00 0.00 0.00 3.71
5067 7567 0.100682 CGACCTACGACACATGGGAG 59.899 60.000 0.00 0.00 45.77 4.30
5068 7568 0.322726 TCGACCTACGACACATGGGA 60.323 55.000 0.00 0.00 46.45 4.37
5069 7569 2.186155 TCGACCTACGACACATGGG 58.814 57.895 0.00 0.00 46.45 4.00
5078 7578 0.964358 AACTGAGGGGTCGACCTACG 60.964 60.000 32.52 18.57 42.10 3.51
5123 7623 5.545658 ATTTATGTACACGTCTTGGCAAG 57.454 39.130 21.17 21.17 0.00 4.01
5192 7817 4.103469 ACAACCAGTACCTACCAAATGTGA 59.897 41.667 0.00 0.00 0.00 3.58
5203 7828 1.645710 AGCAGCTACAACCAGTACCT 58.354 50.000 0.00 0.00 0.00 3.08
5272 7897 1.600023 TAAAGCAACCTCCACGTTGG 58.400 50.000 3.85 0.00 42.78 3.77
5337 7962 5.967088 ACAGAGCGTATAAACAGATTGAGT 58.033 37.500 0.00 0.00 0.00 3.41
5357 7982 8.535592 CGTCTAAAGTAAGCATCAATTCTACAG 58.464 37.037 0.00 0.00 0.00 2.74
5358 7983 7.010183 GCGTCTAAAGTAAGCATCAATTCTACA 59.990 37.037 0.00 0.00 0.00 2.74
5493 8128 8.110860 TGGAAAGTGAAAAATCCTGATACTTC 57.889 34.615 0.00 0.00 33.02 3.01
5537 8172 3.889815 TGCAGCAATTAAGATACCAGCT 58.110 40.909 0.00 0.00 0.00 4.24
5538 8173 4.637483 TTGCAGCAATTAAGATACCAGC 57.363 40.909 2.83 0.00 0.00 4.85
5539 8174 8.408601 ACTTATTTGCAGCAATTAAGATACCAG 58.591 33.333 35.29 20.31 38.49 4.00
5582 8217 8.242053 AGCAATATCATTTCAACTTGTTCAGAG 58.758 33.333 0.00 0.00 0.00 3.35
5635 8429 4.636206 GGGAGCTCTCGTGAAAATTGTAAT 59.364 41.667 14.64 0.00 0.00 1.89
5648 8442 0.741915 GTAGTTGAGGGGAGCTCTCG 59.258 60.000 14.64 0.00 34.19 4.04
5658 8452 2.457366 AAAGGAGCACGTAGTTGAGG 57.543 50.000 0.00 0.00 41.61 3.86
5666 8460 0.603975 GAGCCTCAAAAGGAGCACGT 60.604 55.000 0.00 0.00 46.67 4.49
5713 8507 1.892474 CCTTGGCTCGGAAATTTGGAA 59.108 47.619 0.00 0.00 0.00 3.53
5724 8518 2.656651 CGATCTCGCCTTGGCTCG 60.657 66.667 10.12 8.19 0.00 5.03
5765 8559 7.093354 ACAATGTATCATTCTAGATAGTGCCG 58.907 38.462 0.00 0.00 31.50 5.69
5772 8566 7.443575 GCAAGTGGACAATGTATCATTCTAGAT 59.556 37.037 0.00 0.00 0.00 1.98
5810 8607 3.684305 TGTCAAACACTCTGTCAACAGTG 59.316 43.478 9.82 9.88 44.83 3.66
5811 8608 3.937814 TGTCAAACACTCTGTCAACAGT 58.062 40.909 9.82 0.00 44.12 3.55
5812 8609 4.944962 TTGTCAAACACTCTGTCAACAG 57.055 40.909 3.69 3.69 45.08 3.16
5813 8610 5.697473 TTTTGTCAAACACTCTGTCAACA 57.303 34.783 0.00 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.