Multiple sequence alignment - TraesCS1B01G186900

Loading Multiple Alignment...

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 TraesCS1B01G186900 chr1B 100.000 5421 0 0 1 5421 334246064 334240644 0.000000e+00 10011
1 TraesCS1B01G186900 chr1D 94.757 2651 94 17 837 3464 239809758 239807130 0.000000e+00 4084
2 TraesCS1B01G186900 chr1D 95.680 1111 46 2 3460 4569 239807097 239805988 0.000000e+00 1784
3 TraesCS1B01G186900 chr1D 94.245 556 25 2 101 649 239810437 239809882 0.000000e+00 843
4 TraesCS1B01G186900 chr1D 94.091 220 8 2 4696 4911 239805660 239805442 4.050000e-86 329
5 TraesCS1B01G186900 chr1D 91.549 213 6 2 5178 5378 239804968 239804756 3.200000e-72 283
6 TraesCS1B01G186900 chr1D 93.662 142 9 0 633 774 178459653 178459512 4.250000e-51 213
7 TraesCS1B01G186900 chr1D 93.443 122 6 2 4921 5042 239805331 239805212 4.310000e-41 180
8 TraesCS1B01G186900 chr1D 100.000 54 0 0 1 54 239810490 239810437 3.460000e-17 100
9 TraesCS1B01G186900 chr1A 94.355 2657 97 20 830 3464 303857350 303854725 0.000000e+00 4026
10 TraesCS1B01G186900 chr1A 95.918 1225 47 2 3460 4683 303854692 303853470 0.000000e+00 1982
11 TraesCS1B01G186900 chr1A 92.609 663 34 7 1 649 303858102 303857441 0.000000e+00 939
12 TraesCS1B01G186900 chr1A 91.403 221 13 4 4696 4911 303853039 303852820 1.140000e-76 298
13 TraesCS1B01G186900 chr1A 96.111 180 4 1 5202 5378 303852252 303852073 1.910000e-74 291
14 TraesCS1B01G186900 chr2B 82.904 1591 164 47 1579 3120 476397305 476398836 0.000000e+00 1332
15 TraesCS1B01G186900 chr2B 86.273 998 98 12 3457 4424 476399885 476400873 0.000000e+00 1048
16 TraesCS1B01G186900 chr2B 93.571 140 9 0 646 785 620596806 620596667 5.500000e-50 209
17 TraesCS1B01G186900 chr2D 85.657 1004 99 14 3457 4424 402307688 402306694 0.000000e+00 1014
18 TraesCS1B01G186900 chr2D 87.549 763 73 6 2381 3125 402308869 402308111 0.000000e+00 863
19 TraesCS1B01G186900 chr2D 81.232 698 79 22 1604 2300 402309636 402308990 2.890000e-142 516
20 TraesCS1B01G186900 chr2D 77.577 553 77 28 7 527 402311867 402311330 1.910000e-74 291
21 TraesCS1B01G186900 chr2D 88.785 214 18 5 3219 3428 402307901 402307690 1.940000e-64 257
22 TraesCS1B01G186900 chr2D 84.825 257 30 6 1180 1431 402311241 402310989 3.240000e-62 250
23 TraesCS1B01G186900 chr2A 85.329 1002 104 14 3457 4424 539394457 539393465 0.000000e+00 996
24 TraesCS1B01G186900 chr2A 87.148 817 76 12 2328 3126 539395558 539394753 0.000000e+00 900
25 TraesCS1B01G186900 chr2A 80.855 585 76 23 1810 2383 539396242 539395683 1.400000e-115 427
26 TraesCS1B01G186900 chr2A 77.541 423 61 16 112 518 539398371 539397967 1.960000e-54 224
27 TraesCS1B01G186900 chr2A 93.525 139 9 0 640 778 749872867 749872729 1.980000e-49 207
28 TraesCS1B01G186900 chr2A 91.837 147 9 3 644 789 746976978 746977122 9.210000e-48 202
29 TraesCS1B01G186900 chr2A 87.324 142 17 1 3287 3428 539394599 539394459 1.560000e-35 161
30 TraesCS1B01G186900 chr4B 87.671 219 21 3 4696 4909 68119318 68119101 3.240000e-62 250
31 TraesCS1B01G186900 chr4B 93.243 148 8 2 628 774 82019268 82019122 3.290000e-52 217
32 TraesCS1B01G186900 chr4D 87.383 214 21 3 4701 4909 46622094 46621882 1.950000e-59 241
33 TraesCS1B01G186900 chr4A 86.574 216 23 3 4701 4911 533461541 533461327 3.260000e-57 233
34 TraesCS1B01G186900 chr4A 85.714 217 25 3 4698 4909 552256431 552256646 1.960000e-54 224
35 TraesCS1B01G186900 chr5D 94.776 134 7 0 641 774 122278006 122278139 5.500000e-50 209
36 TraesCS1B01G186900 chr3A 93.571 140 9 0 639 778 187060585 187060724 5.500000e-50 209
37 TraesCS1B01G186900 chr6A 92.958 142 8 2 644 785 457399352 457399491 7.120000e-49 206
38 TraesCS1B01G186900 chrUn 92.361 144 8 3 633 774 52994422 52994564 9.210000e-48 202


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 TraesCS1B01G186900 chr1B 334240644 334246064 5420 True 10011.000000 10011 100.000000 1 5421 1 chr1B.!!$R1 5420
1 TraesCS1B01G186900 chr1D 239804756 239810490 5734 True 1086.142857 4084 94.823571 1 5378 7 chr1D.!!$R2 5377
2 TraesCS1B01G186900 chr1A 303852073 303858102 6029 True 1507.200000 4026 94.079200 1 5378 5 chr1A.!!$R1 5377
3 TraesCS1B01G186900 chr2B 476397305 476400873 3568 False 1190.000000 1332 84.588500 1579 4424 2 chr2B.!!$F1 2845
4 TraesCS1B01G186900 chr2D 402306694 402311867 5173 True 531.833333 1014 84.270833 7 4424 6 chr2D.!!$R1 4417
5 TraesCS1B01G186900 chr2A 539393465 539398371 4906 True 541.600000 996 83.639400 112 4424 5 chr2A.!!$R2 4312

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
770 818 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.0 13.64 4.95 46.06 4.20 F
1106 1215 0.037447 AGCAGGCCAAAGGAGAAGTC 59.963 55.0 5.01 0.00 0.00 3.01 F
1170 1286 0.179084 CGTGGATACCCTCATTGCGT 60.179 55.0 0.00 0.00 0.00 5.24 F
1172 1288 0.180171 TGGATACCCTCATTGCGTGG 59.820 55.0 0.00 0.00 0.00 4.94 F
1177 1293 0.180406 ACCCTCATTGCGTGGATACC 59.820 55.0 0.00 0.00 0.00 2.73 F
1178 1294 0.880278 CCCTCATTGCGTGGATACCG 60.880 60.0 0.00 0.00 0.00 4.02 F
1224 1343 1.473258 TTCCATTGCTCCATTTCCCG 58.527 50.0 0.00 0.00 0.00 5.14 F
3452 6060 0.819582 CTGCATTAGGGGTGCTTTGG 59.180 55.0 0.00 0.00 42.92 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1865 3263 0.038166 TGGTGGTTTGATCTGGCTCC 59.962 55.000 0.0 0.0 0.00 4.70 R
2417 4025 2.479566 ATCTTCTTCGCTCTGCCAAA 57.520 45.000 0.0 0.0 0.00 3.28 R
3123 4818 1.201647 CTCGTTTTAGCAGGACTCGGA 59.798 52.381 0.0 0.0 0.00 4.55 R
3296 5320 4.460382 CAGCCCCATCACATATTAATCACC 59.540 45.833 0.0 0.0 0.00 4.02 R
3444 6052 6.759497 AATCTATCCTGTAAACCAAAGCAC 57.241 37.500 0.0 0.0 0.00 4.40 R
3452 6060 8.499403 AGCAAGAAGAAATCTATCCTGTAAAC 57.501 34.615 0.0 0.0 37.42 2.01 R
3559 6223 5.536161 ACATCTTTGCTGGACAAATGTAACT 59.464 36.000 0.0 0.0 46.90 2.24 R
5398 8869 0.526662 TGCCGGTTGTTTCGTTTGTT 59.473 45.000 1.9 0.0 0.00 2.83 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
95 96 8.645814 TCAGTAAGACAACAATCTACTAGGAA 57.354 34.615 0.00 0.00 0.00 3.36
97 98 9.877178 CAGTAAGACAACAATCTACTAGGAAAT 57.123 33.333 0.00 0.00 0.00 2.17
137 144 3.199880 AGAATAAGAATGCCAGGTCCG 57.800 47.619 0.00 0.00 0.00 4.79
139 146 0.179018 ATAAGAATGCCAGGTCCGCC 60.179 55.000 0.00 0.00 0.00 6.13
193 200 4.787551 TCATGGATTGGTAATGTGGGTAC 58.212 43.478 0.00 0.00 0.00 3.34
228 235 0.038251 GGGCCAAAAAGTAGCTGCAC 60.038 55.000 4.39 0.00 0.00 4.57
246 253 5.514204 GCTGCACAATCATCACTGTAATTTC 59.486 40.000 0.00 0.00 0.00 2.17
386 417 0.940126 GCGGTATCAACATGGAGCAG 59.060 55.000 0.00 0.00 0.00 4.24
389 420 3.792401 CGGTATCAACATGGAGCAGTAA 58.208 45.455 0.00 0.00 0.00 2.24
416 451 2.076628 GCGTTGACATTGCAGCACG 61.077 57.895 0.00 0.00 0.00 5.34
425 460 2.096496 ACATTGCAGCACGCTATCTTTC 59.904 45.455 0.00 0.00 43.06 2.62
432 467 1.640428 CACGCTATCTTTCCGCTTCA 58.360 50.000 0.00 0.00 0.00 3.02
444 479 2.778679 GCTTCAACCACTAGCGCG 59.221 61.111 0.00 0.00 0.00 6.86
446 481 2.047655 TTCAACCACTAGCGCGGG 60.048 61.111 8.83 1.71 0.00 6.13
656 704 9.841295 TCAACATAATAAAATAGTACACCCTCC 57.159 33.333 0.00 0.00 0.00 4.30
657 705 8.770828 CAACATAATAAAATAGTACACCCTCCG 58.229 37.037 0.00 0.00 0.00 4.63
658 706 8.026396 ACATAATAAAATAGTACACCCTCCGT 57.974 34.615 0.00 0.00 0.00 4.69
659 707 8.146412 ACATAATAAAATAGTACACCCTCCGTC 58.854 37.037 0.00 0.00 0.00 4.79
660 708 3.900966 AAAATAGTACACCCTCCGTCC 57.099 47.619 0.00 0.00 0.00 4.79
661 709 2.537633 AATAGTACACCCTCCGTCCA 57.462 50.000 0.00 0.00 0.00 4.02
662 710 2.068834 ATAGTACACCCTCCGTCCAG 57.931 55.000 0.00 0.00 0.00 3.86
663 711 0.994247 TAGTACACCCTCCGTCCAGA 59.006 55.000 0.00 0.00 0.00 3.86
664 712 0.113776 AGTACACCCTCCGTCCAGAA 59.886 55.000 0.00 0.00 0.00 3.02
665 713 0.971386 GTACACCCTCCGTCCAGAAA 59.029 55.000 0.00 0.00 0.00 2.52
666 714 1.553704 GTACACCCTCCGTCCAGAAAT 59.446 52.381 0.00 0.00 0.00 2.17
667 715 1.946984 ACACCCTCCGTCCAGAAATA 58.053 50.000 0.00 0.00 0.00 1.40
668 716 2.262637 ACACCCTCCGTCCAGAAATAA 58.737 47.619 0.00 0.00 0.00 1.40
669 717 2.844348 ACACCCTCCGTCCAGAAATAAT 59.156 45.455 0.00 0.00 0.00 1.28
670 718 3.265995 ACACCCTCCGTCCAGAAATAATT 59.734 43.478 0.00 0.00 0.00 1.40
671 719 3.627577 CACCCTCCGTCCAGAAATAATTG 59.372 47.826 0.00 0.00 0.00 2.32
672 720 3.265995 ACCCTCCGTCCAGAAATAATTGT 59.734 43.478 0.00 0.00 0.00 2.71
673 721 3.877508 CCCTCCGTCCAGAAATAATTGTC 59.122 47.826 0.00 0.00 0.00 3.18
674 722 4.513442 CCTCCGTCCAGAAATAATTGTCA 58.487 43.478 0.00 0.00 0.00 3.58
675 723 5.126067 CCTCCGTCCAGAAATAATTGTCAT 58.874 41.667 0.00 0.00 0.00 3.06
676 724 5.237344 CCTCCGTCCAGAAATAATTGTCATC 59.763 44.000 0.00 0.00 0.00 2.92
677 725 5.739959 TCCGTCCAGAAATAATTGTCATCA 58.260 37.500 0.00 0.00 0.00 3.07
678 726 6.176896 TCCGTCCAGAAATAATTGTCATCAA 58.823 36.000 0.00 0.00 37.98 2.57
679 727 6.657117 TCCGTCCAGAAATAATTGTCATCAAA 59.343 34.615 0.00 0.00 37.11 2.69
680 728 7.175816 TCCGTCCAGAAATAATTGTCATCAAAA 59.824 33.333 0.00 0.00 37.11 2.44
681 729 7.975616 CCGTCCAGAAATAATTGTCATCAAAAT 59.024 33.333 0.00 0.00 37.11 1.82
682 730 8.800972 CGTCCAGAAATAATTGTCATCAAAATG 58.199 33.333 0.00 0.00 37.11 2.32
683 731 9.090692 GTCCAGAAATAATTGTCATCAAAATGG 57.909 33.333 0.00 0.00 37.11 3.16
684 732 9.033711 TCCAGAAATAATTGTCATCAAAATGGA 57.966 29.630 0.00 0.00 37.11 3.41
685 733 9.090692 CCAGAAATAATTGTCATCAAAATGGAC 57.909 33.333 0.00 0.00 37.11 4.02
686 734 9.642327 CAGAAATAATTGTCATCAAAATGGACA 57.358 29.630 0.00 0.00 37.11 4.02
692 740 8.961294 AATTGTCATCAAAATGGACAAAAAGA 57.039 26.923 10.06 0.00 36.93 2.52
693 741 8.597662 ATTGTCATCAAAATGGACAAAAAGAG 57.402 30.769 10.06 0.00 36.93 2.85
694 742 7.345422 TGTCATCAAAATGGACAAAAAGAGA 57.655 32.000 0.00 0.00 33.42 3.10
695 743 7.954835 TGTCATCAAAATGGACAAAAAGAGAT 58.045 30.769 0.00 0.00 33.42 2.75
696 744 7.868922 TGTCATCAAAATGGACAAAAAGAGATG 59.131 33.333 0.00 0.00 33.42 2.90
697 745 7.869429 GTCATCAAAATGGACAAAAAGAGATGT 59.131 33.333 0.00 0.00 33.42 3.06
698 746 9.076781 TCATCAAAATGGACAAAAAGAGATGTA 57.923 29.630 0.00 0.00 33.42 2.29
699 747 9.865321 CATCAAAATGGACAAAAAGAGATGTAT 57.135 29.630 0.00 0.00 0.00 2.29
701 749 9.300681 TCAAAATGGACAAAAAGAGATGTATCT 57.699 29.630 0.00 0.00 40.50 1.98
706 754 9.606631 ATGGACAAAAAGAGATGTATCTAGAAC 57.393 33.333 0.00 0.00 37.25 3.01
707 755 8.816894 TGGACAAAAAGAGATGTATCTAGAACT 58.183 33.333 0.00 0.00 37.25 3.01
731 779 9.845214 ACTAAAATACATCTAGATACATCCCCT 57.155 33.333 4.54 0.00 0.00 4.79
749 797 9.082313 ACATCCCCTTATATTCATTTTGATGAC 57.918 33.333 0.00 0.00 32.39 3.06
750 798 9.081204 CATCCCCTTATATTCATTTTGATGACA 57.919 33.333 0.00 0.00 0.00 3.58
751 799 9.659135 ATCCCCTTATATTCATTTTGATGACAA 57.341 29.630 0.00 0.00 0.00 3.18
752 800 9.135189 TCCCCTTATATTCATTTTGATGACAAG 57.865 33.333 0.00 0.00 37.32 3.16
753 801 8.917088 CCCCTTATATTCATTTTGATGACAAGT 58.083 33.333 0.00 0.00 37.32 3.16
760 808 8.915871 ATTCATTTTGATGACAAGTATTTCCG 57.084 30.769 0.00 0.00 37.32 4.30
761 809 6.851609 TCATTTTGATGACAAGTATTTCCGG 58.148 36.000 0.00 0.00 37.32 5.14
762 810 6.657117 TCATTTTGATGACAAGTATTTCCGGA 59.343 34.615 0.00 0.00 37.32 5.14
763 811 5.873179 TTTGATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
764 812 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
765 813 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
766 814 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
767 815 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
768 816 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
769 817 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
770 818 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
771 819 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
804 897 4.039366 AGAACTCGAGACCAAAGCTAAAGT 59.961 41.667 21.68 0.00 0.00 2.66
824 919 9.494271 CTAAAGTGATATATTAGCAGGCAAAGA 57.506 33.333 0.00 0.00 0.00 2.52
835 944 3.815352 GCAAAGAGCGCAACGTTC 58.185 55.556 11.47 0.00 37.36 3.95
905 1014 0.687757 TGAGACCAAGGGCTATCGCT 60.688 55.000 0.00 0.00 37.04 4.93
953 1062 6.009115 CCTTCAACAAGGTAACAATGTACC 57.991 41.667 0.00 0.00 44.11 3.34
968 1077 0.247145 GTACCGTGTACGTACGTCGG 60.247 60.000 36.86 36.86 45.07 4.79
1090 1199 2.759191 CTTGCTCACACAGAACTAGCA 58.241 47.619 0.00 0.00 41.19 3.49
1106 1215 0.037447 AGCAGGCCAAAGGAGAAGTC 59.963 55.000 5.01 0.00 0.00 3.01
1107 1216 0.250901 GCAGGCCAAAGGAGAAGTCA 60.251 55.000 5.01 0.00 0.00 3.41
1108 1217 1.528129 CAGGCCAAAGGAGAAGTCAC 58.472 55.000 5.01 0.00 0.00 3.67
1168 1284 0.463654 TGCGTGGATACCCTCATTGC 60.464 55.000 0.00 0.00 0.00 3.56
1169 1285 1.498865 GCGTGGATACCCTCATTGCG 61.499 60.000 0.00 0.00 0.00 4.85
1170 1286 0.179084 CGTGGATACCCTCATTGCGT 60.179 55.000 0.00 0.00 0.00 5.24
1171 1287 1.299541 GTGGATACCCTCATTGCGTG 58.700 55.000 0.00 0.00 0.00 5.34
1172 1288 0.180171 TGGATACCCTCATTGCGTGG 59.820 55.000 0.00 0.00 0.00 4.94
1175 1291 2.301870 GGATACCCTCATTGCGTGGATA 59.698 50.000 0.00 0.00 0.00 2.59
1176 1292 2.902705 TACCCTCATTGCGTGGATAC 57.097 50.000 0.00 0.00 0.00 2.24
1177 1293 0.180406 ACCCTCATTGCGTGGATACC 59.820 55.000 0.00 0.00 0.00 2.73
1178 1294 0.880278 CCCTCATTGCGTGGATACCG 60.880 60.000 0.00 0.00 0.00 4.02
1224 1343 1.473258 TTCCATTGCTCCATTTCCCG 58.527 50.000 0.00 0.00 0.00 5.14
1320 1439 7.588143 AGTTGTGATCTTAGTTCGATCTTTG 57.412 36.000 0.48 0.00 38.43 2.77
1388 1512 9.354673 CATAATTGGTTAGTGTCAAGGGATTAT 57.645 33.333 0.00 0.00 0.00 1.28
1459 1590 9.073368 CATTGAATGAGAAATTAAACTGCTGAG 57.927 33.333 0.00 0.00 0.00 3.35
1486 2725 2.368439 TGTTGATTAGCCAGCACATCC 58.632 47.619 0.00 0.00 0.00 3.51
1639 2976 9.477484 AATTAGTCAACTCACCGCTAATATTAG 57.523 33.333 16.79 16.79 33.56 1.73
1673 3010 2.437281 CTGAAGACCCACCTAGCATGAT 59.563 50.000 0.00 0.00 0.00 2.45
1713 3050 6.969828 AGTTACAACTACTTCAGCTATTGC 57.030 37.500 0.00 0.00 37.52 3.56
1714 3051 5.875359 AGTTACAACTACTTCAGCTATTGCC 59.125 40.000 0.00 0.00 37.42 4.52
1715 3052 4.559862 ACAACTACTTCAGCTATTGCCT 57.440 40.909 0.00 0.00 40.80 4.75
1745 3083 5.470098 GGTGAAAGAGTTAGAACAGATTGCA 59.530 40.000 0.00 0.00 0.00 4.08
1759 3097 8.188799 AGAACAGATTGCATGATCATTTGTTAG 58.811 33.333 5.16 0.00 0.00 2.34
1935 3333 3.603532 TGGAGATCTCAAACTGTCATGC 58.396 45.455 23.85 2.93 0.00 4.06
1937 3335 3.622163 GGAGATCTCAAACTGTCATGCTG 59.378 47.826 23.85 0.00 0.00 4.41
1981 3379 3.321111 TGAAGGAGTAGAAGCTTGTCGTT 59.679 43.478 2.10 3.10 0.00 3.85
2010 3408 6.441924 TCCTCCTCTATCTTCAGTTCAAATGT 59.558 38.462 0.00 0.00 0.00 2.71
2028 3426 2.907634 TGTGAAACAGCGTGAGGTTTA 58.092 42.857 0.00 0.00 45.67 2.01
2192 3592 4.827692 CTGTAACCAGGCACTACACAATA 58.172 43.478 0.00 0.00 36.02 1.90
2245 3645 8.923270 TGAAATGAAAGGAAGATTACCAAAAGT 58.077 29.630 0.00 0.00 0.00 2.66
2324 3734 2.607635 CACATACCGGCATGAGTGTAAC 59.392 50.000 21.75 0.00 0.00 2.50
2366 3792 3.246880 ACCGTGGTGGGGGAACTC 61.247 66.667 0.00 0.00 44.64 3.01
2708 4330 2.627221 TGTTAGCCAGCATTTTCAGCAA 59.373 40.909 0.00 0.00 0.00 3.91
3002 4624 2.511218 TGATCCAAGAAGAATCCCTGGG 59.489 50.000 6.33 6.33 32.38 4.45
3123 4818 8.085296 CGAGGCTTCATTAATCAGAACTAGTAT 58.915 37.037 0.00 0.00 0.00 2.12
3192 5134 4.834534 ACCTTTGTGTGTTGTGTACAGTA 58.165 39.130 0.00 0.00 37.45 2.74
3266 5276 9.294030 CATGATTTTCTATTTACTTGCAGGAAC 57.706 33.333 1.40 0.00 0.00 3.62
3296 5320 5.342806 TGAGTTGTAAGATTTGTTCTGCG 57.657 39.130 0.00 0.00 33.93 5.18
3444 6052 3.355378 TGAAATGTGACTGCATTAGGGG 58.645 45.455 0.00 0.00 38.03 4.79
3452 6060 0.819582 CTGCATTAGGGGTGCTTTGG 59.180 55.000 0.00 0.00 42.92 3.28
3495 6141 3.914312 TGCTCTAACTGAAGTGTGTAGC 58.086 45.455 0.00 0.00 0.00 3.58
3559 6223 6.068853 ACATTGATATCCTCCTCTTTTCCCAA 60.069 38.462 0.00 0.00 0.00 4.12
3701 6365 3.626996 CTCATTGCCCTGGACCGCA 62.627 63.158 0.00 0.00 0.00 5.69
3874 6562 0.751643 GCCTATTCGCCATTGGGTGT 60.752 55.000 4.53 0.00 45.25 4.16
4057 6745 0.104304 ACGCCGTCACACTCTTCTTT 59.896 50.000 0.00 0.00 0.00 2.52
4099 6787 2.031157 GTGTGCTACTTCGGCAAACAAT 60.031 45.455 4.39 0.00 44.63 2.71
4231 6919 6.956435 TGGTCACTGAGAAGATATATGGCTAT 59.044 38.462 0.00 0.00 0.00 2.97
4282 6970 2.749839 GCACAAGGGGCGTATGCA 60.750 61.111 9.59 0.00 45.35 3.96
4500 7188 5.830912 TGTTTTGGTTGTAAATCAGAGCAG 58.169 37.500 0.00 0.00 38.76 4.24
4566 7254 7.466746 ACAAAGTGCCAACATTACAAGATAT 57.533 32.000 0.00 0.00 0.00 1.63
4567 7255 8.574251 ACAAAGTGCCAACATTACAAGATATA 57.426 30.769 0.00 0.00 0.00 0.86
4568 7256 9.019656 ACAAAGTGCCAACATTACAAGATATAA 57.980 29.630 0.00 0.00 0.00 0.98
4571 7259 8.396272 AGTGCCAACATTACAAGATATAATCC 57.604 34.615 0.00 0.00 0.00 3.01
4572 7260 7.998383 AGTGCCAACATTACAAGATATAATCCA 59.002 33.333 0.00 0.00 0.00 3.41
4583 7271 8.297470 ACAAGATATAATCCAAGCACATTGTT 57.703 30.769 0.00 0.00 37.17 2.83
4594 7282 6.264292 TCCAAGCACATTGTTTACTTGTACAT 59.736 34.615 16.69 0.00 36.78 2.29
4597 7285 6.668323 AGCACATTGTTTACTTGTACATGAC 58.332 36.000 15.13 4.30 0.00 3.06
4616 7304 7.810658 ACATGACAACTTAAACTGCTATCTTG 58.189 34.615 0.00 0.00 0.00 3.02
4629 7317 7.102847 ACTGCTATCTTGTAGAACTTAGACC 57.897 40.000 0.00 0.00 0.00 3.85
4648 7336 5.428253 AGACCACTGCATTTCGTGTATAAT 58.572 37.500 3.47 0.00 0.00 1.28
4676 7364 0.678950 AAATGCACAAAGTTCCCCGG 59.321 50.000 0.00 0.00 0.00 5.73
4680 7368 1.583495 GCACAAAGTTCCCCGGCTAC 61.583 60.000 0.00 0.00 0.00 3.58
4683 7371 1.094785 CAAAGTTCCCCGGCTACATG 58.905 55.000 0.00 0.00 0.00 3.21
4684 7372 0.679960 AAAGTTCCCCGGCTACATGC 60.680 55.000 0.00 0.00 41.94 4.06
4685 7373 1.562672 AAGTTCCCCGGCTACATGCT 61.563 55.000 0.00 0.00 42.39 3.79
4686 7374 0.689745 AGTTCCCCGGCTACATGCTA 60.690 55.000 0.00 0.00 42.39 3.49
4687 7375 0.532196 GTTCCCCGGCTACATGCTAC 60.532 60.000 0.00 0.00 42.39 3.58
4688 7376 0.978667 TTCCCCGGCTACATGCTACA 60.979 55.000 0.00 0.00 42.39 2.74
4691 7379 1.151777 CCCGGCTACATGCTACAACG 61.152 60.000 0.00 0.00 42.39 4.10
4692 7380 0.459585 CCGGCTACATGCTACAACGT 60.460 55.000 0.00 0.00 42.39 3.99
4694 7382 1.850441 CGGCTACATGCTACAACGTAC 59.150 52.381 0.00 0.00 42.39 3.67
4758 7867 4.021456 TCCTGTAGTACATGTCAACAGTGG 60.021 45.833 23.11 15.28 36.63 4.00
4840 7953 8.721478 GTTAATGCAGAAGAGAATCAAAGTGTA 58.279 33.333 0.00 0.00 37.82 2.90
4889 8002 1.725641 TGTCTGTATTTGCAGGCTCG 58.274 50.000 2.07 0.00 41.33 5.03
4902 8015 0.543174 AGGCTCGGTGTCTTCTCCTT 60.543 55.000 0.00 0.00 0.00 3.36
4913 8145 7.341256 TCGGTGTCTTCTCCTTTACATAGTAAT 59.659 37.037 0.00 0.00 0.00 1.89
4952 8184 2.055100 GACGTCAGTGCAGAAGAGAAC 58.945 52.381 11.55 0.00 0.00 3.01
5057 8341 1.138859 CATTAGCATCGACCCACCTCA 59.861 52.381 0.00 0.00 0.00 3.86
5078 8362 2.350738 AAAAATCACAGGGCCACCG 58.649 52.632 6.18 0.00 43.47 4.94
5080 8364 0.609131 AAAATCACAGGGCCACCGAG 60.609 55.000 6.18 0.00 43.47 4.63
5113 8398 9.981114 ATTCAAAGAAAACTTACCTTATGGTTG 57.019 29.630 5.49 2.72 46.05 3.77
5114 8399 7.430441 TCAAAGAAAACTTACCTTATGGTTGC 58.570 34.615 5.49 0.00 46.05 4.17
5115 8400 6.969993 AAGAAAACTTACCTTATGGTTGCA 57.030 33.333 5.49 0.00 46.05 4.08
5116 8401 7.539034 AAGAAAACTTACCTTATGGTTGCAT 57.461 32.000 5.49 0.00 46.05 3.96
5117 8402 7.539034 AGAAAACTTACCTTATGGTTGCATT 57.461 32.000 5.49 0.00 46.05 3.56
5118 8403 7.962441 AGAAAACTTACCTTATGGTTGCATTT 58.038 30.769 5.49 3.85 46.05 2.32
5119 8404 7.872483 AGAAAACTTACCTTATGGTTGCATTTG 59.128 33.333 5.49 0.00 46.05 2.32
5120 8405 6.664428 AACTTACCTTATGGTTGCATTTGT 57.336 33.333 5.49 0.00 46.05 2.83
5121 8406 7.768807 AACTTACCTTATGGTTGCATTTGTA 57.231 32.000 5.49 0.00 46.05 2.41
5122 8407 7.391148 ACTTACCTTATGGTTGCATTTGTAG 57.609 36.000 5.49 0.00 46.05 2.74
5123 8408 7.172342 ACTTACCTTATGGTTGCATTTGTAGA 58.828 34.615 5.49 0.00 46.05 2.59
5124 8409 7.668052 ACTTACCTTATGGTTGCATTTGTAGAA 59.332 33.333 5.49 0.00 46.05 2.10
5125 8410 6.909550 ACCTTATGGTTGCATTTGTAGAAA 57.090 33.333 0.00 0.00 46.05 2.52
5126 8411 7.480760 ACCTTATGGTTGCATTTGTAGAAAT 57.519 32.000 0.00 0.00 46.05 2.17
5127 8412 7.906327 ACCTTATGGTTGCATTTGTAGAAATT 58.094 30.769 0.00 0.00 46.05 1.82
5128 8413 8.034804 ACCTTATGGTTGCATTTGTAGAAATTC 58.965 33.333 0.00 0.00 46.05 2.17
5129 8414 7.492344 CCTTATGGTTGCATTTGTAGAAATTCC 59.508 37.037 0.00 0.00 28.65 3.01
5130 8415 4.804108 TGGTTGCATTTGTAGAAATTCCG 58.196 39.130 0.00 0.00 28.65 4.30
5131 8416 4.520874 TGGTTGCATTTGTAGAAATTCCGA 59.479 37.500 0.00 0.00 28.65 4.55
5132 8417 5.184864 TGGTTGCATTTGTAGAAATTCCGAT 59.815 36.000 0.00 0.00 28.65 4.18
5133 8418 5.516339 GGTTGCATTTGTAGAAATTCCGATG 59.484 40.000 0.00 0.00 28.65 3.84
5134 8419 4.671377 TGCATTTGTAGAAATTCCGATGC 58.329 39.130 0.00 0.00 39.15 3.91
5135 8420 4.157472 TGCATTTGTAGAAATTCCGATGCA 59.843 37.500 12.09 12.09 44.23 3.96
5136 8421 4.500477 GCATTTGTAGAAATTCCGATGCAC 59.500 41.667 0.00 0.00 38.69 4.57
5137 8422 4.335082 TTTGTAGAAATTCCGATGCACG 57.665 40.909 0.00 0.00 42.18 5.34
5138 8423 2.967362 TGTAGAAATTCCGATGCACGT 58.033 42.857 0.00 0.00 40.78 4.49
5139 8424 3.331150 TGTAGAAATTCCGATGCACGTT 58.669 40.909 0.00 0.00 40.78 3.99
5140 8425 2.900122 AGAAATTCCGATGCACGTTG 57.100 45.000 0.00 0.00 40.78 4.10
5141 8426 1.135689 AGAAATTCCGATGCACGTTGC 60.136 47.619 0.00 3.44 45.29 4.17
5142 8427 0.109319 AAATTCCGATGCACGTTGCC 60.109 50.000 7.38 0.00 44.23 4.52
5143 8428 1.240641 AATTCCGATGCACGTTGCCA 61.241 50.000 7.38 0.00 44.23 4.92
5144 8429 1.031571 ATTCCGATGCACGTTGCCAT 61.032 50.000 7.38 0.84 44.23 4.40
5145 8430 1.240641 TTCCGATGCACGTTGCCATT 61.241 50.000 7.38 0.00 44.23 3.16
5146 8431 1.212490 CCGATGCACGTTGCCATTT 59.788 52.632 7.38 0.00 44.23 2.32
5147 8432 0.798009 CCGATGCACGTTGCCATTTC 60.798 55.000 7.38 0.65 44.23 2.17
5152 8437 1.135915 TGCACGTTGCCATTTCTTGTT 59.864 42.857 7.38 0.00 44.23 2.83
5153 8438 1.786579 GCACGTTGCCATTTCTTGTTC 59.213 47.619 0.00 0.00 37.42 3.18
5155 8440 1.339929 ACGTTGCCATTTCTTGTTCCC 59.660 47.619 0.00 0.00 0.00 3.97
5159 8444 4.388485 GTTGCCATTTCTTGTTCCCATTT 58.612 39.130 0.00 0.00 0.00 2.32
5175 8460 3.252215 CCCATTTTGAACTGCTTCACGTA 59.748 43.478 0.00 0.00 36.06 3.57
5288 8759 2.197283 AAAAGAGGCAGAGCAAGGAG 57.803 50.000 0.00 0.00 0.00 3.69
5378 8849 1.795768 TCGATCACAGTCAAAGGCAC 58.204 50.000 0.00 0.00 0.00 5.01
5379 8850 1.069978 TCGATCACAGTCAAAGGCACA 59.930 47.619 0.00 0.00 0.00 4.57
5380 8851 1.195448 CGATCACAGTCAAAGGCACAC 59.805 52.381 0.00 0.00 0.00 3.82
5381 8852 2.221169 GATCACAGTCAAAGGCACACA 58.779 47.619 0.00 0.00 0.00 3.72
5382 8853 1.378531 TCACAGTCAAAGGCACACAC 58.621 50.000 0.00 0.00 0.00 3.82
5383 8854 1.093972 CACAGTCAAAGGCACACACA 58.906 50.000 0.00 0.00 0.00 3.72
5384 8855 1.677576 CACAGTCAAAGGCACACACAT 59.322 47.619 0.00 0.00 0.00 3.21
5385 8856 2.099592 CACAGTCAAAGGCACACACATT 59.900 45.455 0.00 0.00 0.00 2.71
5386 8857 3.314913 CACAGTCAAAGGCACACACATTA 59.685 43.478 0.00 0.00 0.00 1.90
5387 8858 4.022935 CACAGTCAAAGGCACACACATTAT 60.023 41.667 0.00 0.00 0.00 1.28
5388 8859 5.181056 CACAGTCAAAGGCACACACATTATA 59.819 40.000 0.00 0.00 0.00 0.98
5389 8860 5.767665 ACAGTCAAAGGCACACACATTATAA 59.232 36.000 0.00 0.00 0.00 0.98
5390 8861 6.086222 CAGTCAAAGGCACACACATTATAAC 58.914 40.000 0.00 0.00 0.00 1.89
5391 8862 5.767665 AGTCAAAGGCACACACATTATAACA 59.232 36.000 0.00 0.00 0.00 2.41
5392 8863 5.856455 GTCAAAGGCACACACATTATAACAC 59.144 40.000 0.00 0.00 0.00 3.32
5393 8864 5.048364 TCAAAGGCACACACATTATAACACC 60.048 40.000 0.00 0.00 0.00 4.16
5394 8865 4.027674 AGGCACACACATTATAACACCA 57.972 40.909 0.00 0.00 0.00 4.17
5395 8866 4.402829 AGGCACACACATTATAACACCAA 58.597 39.130 0.00 0.00 0.00 3.67
5396 8867 4.830046 AGGCACACACATTATAACACCAAA 59.170 37.500 0.00 0.00 0.00 3.28
5397 8868 4.920927 GGCACACACATTATAACACCAAAC 59.079 41.667 0.00 0.00 0.00 2.93
5398 8869 5.508153 GGCACACACATTATAACACCAAACA 60.508 40.000 0.00 0.00 0.00 2.83
5399 8870 5.980116 GCACACACATTATAACACCAAACAA 59.020 36.000 0.00 0.00 0.00 2.83
5400 8871 6.074569 GCACACACATTATAACACCAAACAAC 60.075 38.462 0.00 0.00 0.00 3.32
5401 8872 6.975197 CACACACATTATAACACCAAACAACA 59.025 34.615 0.00 0.00 0.00 3.33
5402 8873 7.489435 CACACACATTATAACACCAAACAACAA 59.511 33.333 0.00 0.00 0.00 2.83
5403 8874 8.035394 ACACACATTATAACACCAAACAACAAA 58.965 29.630 0.00 0.00 0.00 2.83
5404 8875 8.324567 CACACATTATAACACCAAACAACAAAC 58.675 33.333 0.00 0.00 0.00 2.93
5405 8876 7.221067 ACACATTATAACACCAAACAACAAACG 59.779 33.333 0.00 0.00 0.00 3.60
5406 8877 7.432545 CACATTATAACACCAAACAACAAACGA 59.567 33.333 0.00 0.00 0.00 3.85
5407 8878 7.974501 ACATTATAACACCAAACAACAAACGAA 59.025 29.630 0.00 0.00 0.00 3.85
5408 8879 8.808529 CATTATAACACCAAACAACAAACGAAA 58.191 29.630 0.00 0.00 0.00 3.46
5409 8880 4.975921 AACACCAAACAACAAACGAAAC 57.024 36.364 0.00 0.00 0.00 2.78
5410 8881 3.978687 ACACCAAACAACAAACGAAACA 58.021 36.364 0.00 0.00 0.00 2.83
5411 8882 4.369182 ACACCAAACAACAAACGAAACAA 58.631 34.783 0.00 0.00 0.00 2.83
5412 8883 4.209495 ACACCAAACAACAAACGAAACAAC 59.791 37.500 0.00 0.00 0.00 3.32
5413 8884 3.741856 ACCAAACAACAAACGAAACAACC 59.258 39.130 0.00 0.00 0.00 3.77
5414 8885 3.181539 CCAAACAACAAACGAAACAACCG 60.182 43.478 0.00 0.00 0.00 4.44
5415 8886 2.265647 ACAACAAACGAAACAACCGG 57.734 45.000 0.00 0.00 0.00 5.28
5416 8887 0.917939 CAACAAACGAAACAACCGGC 59.082 50.000 0.00 0.00 0.00 6.13
5417 8888 0.526662 AACAAACGAAACAACCGGCA 59.473 45.000 0.00 0.00 0.00 5.69
5418 8889 0.526662 ACAAACGAAACAACCGGCAA 59.473 45.000 0.00 0.00 0.00 4.52
5419 8890 1.135333 ACAAACGAAACAACCGGCAAT 59.865 42.857 0.00 0.00 0.00 3.56
5420 8891 1.520590 CAAACGAAACAACCGGCAATG 59.479 47.619 0.00 0.09 0.00 2.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
139 146 2.637025 CAACACGCCCACCTTTCG 59.363 61.111 0.00 0.00 0.00 3.46
193 200 0.379669 GCCCAAGATCGACATTGCAG 59.620 55.000 6.02 2.01 0.00 4.41
228 235 7.294676 TGTCTCGAAATTACAGTGATGATTG 57.705 36.000 0.00 0.00 0.00 2.67
258 277 2.599973 CTGACTTGTGCACTGTTTTTGC 59.400 45.455 19.41 5.51 40.63 3.68
262 281 0.740737 GGCTGACTTGTGCACTGTTT 59.259 50.000 19.41 0.00 0.00 2.83
311 336 0.107459 GGAGATCCCCTTGTGCTGTC 60.107 60.000 0.00 0.00 0.00 3.51
386 417 1.265635 TGTCAACGCCAAGTGCATTAC 59.734 47.619 0.00 0.00 41.33 1.89
389 420 0.961019 AATGTCAACGCCAAGTGCAT 59.039 45.000 0.00 0.00 41.33 3.96
416 451 2.096013 GTGGTTGAAGCGGAAAGATAGC 59.904 50.000 0.00 0.00 0.00 2.97
432 467 1.964373 CAAACCCGCGCTAGTGGTT 60.964 57.895 10.44 10.44 46.35 3.67
444 479 5.722021 ACACATTGTTTCTATCCAAACCC 57.278 39.130 0.00 0.00 35.69 4.11
446 481 9.906660 TCATTAACACATTGTTTCTATCCAAAC 57.093 29.630 0.00 0.00 41.45 2.93
545 585 6.346096 CCGATGGTTTATCCTACTTTTCAGA 58.654 40.000 0.00 0.00 37.07 3.27
647 695 1.946984 ATTTCTGGACGGAGGGTGTA 58.053 50.000 0.00 0.00 0.00 2.90
648 696 1.946984 TATTTCTGGACGGAGGGTGT 58.053 50.000 0.00 0.00 0.00 4.16
649 697 3.560636 ATTATTTCTGGACGGAGGGTG 57.439 47.619 0.00 0.00 0.00 4.61
650 698 3.265995 ACAATTATTTCTGGACGGAGGGT 59.734 43.478 0.00 0.00 0.00 4.34
651 699 3.877508 GACAATTATTTCTGGACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
652 700 4.513442 TGACAATTATTTCTGGACGGAGG 58.487 43.478 0.00 0.00 0.00 4.30
653 701 5.817296 TGATGACAATTATTTCTGGACGGAG 59.183 40.000 0.00 0.00 0.00 4.63
654 702 5.739959 TGATGACAATTATTTCTGGACGGA 58.260 37.500 0.00 0.00 0.00 4.69
655 703 6.435430 TTGATGACAATTATTTCTGGACGG 57.565 37.500 0.00 0.00 0.00 4.79
656 704 8.800972 CATTTTGATGACAATTATTTCTGGACG 58.199 33.333 0.00 0.00 35.85 4.79
657 705 9.090692 CCATTTTGATGACAATTATTTCTGGAC 57.909 33.333 0.00 0.00 35.85 4.02
658 706 9.033711 TCCATTTTGATGACAATTATTTCTGGA 57.966 29.630 0.00 0.00 35.85 3.86
659 707 9.090692 GTCCATTTTGATGACAATTATTTCTGG 57.909 33.333 0.00 0.00 35.85 3.86
660 708 9.642327 TGTCCATTTTGATGACAATTATTTCTG 57.358 29.630 0.00 0.00 35.85 3.02
667 715 8.961294 TCTTTTTGTCCATTTTGATGACAATT 57.039 26.923 5.27 0.00 35.96 2.32
668 716 8.423349 TCTCTTTTTGTCCATTTTGATGACAAT 58.577 29.630 5.27 0.00 35.96 2.71
669 717 7.780064 TCTCTTTTTGTCCATTTTGATGACAA 58.220 30.769 0.00 0.00 34.47 3.18
670 718 7.345422 TCTCTTTTTGTCCATTTTGATGACA 57.655 32.000 0.00 0.00 0.00 3.58
671 719 7.869429 ACATCTCTTTTTGTCCATTTTGATGAC 59.131 33.333 0.00 0.00 33.85 3.06
672 720 7.954835 ACATCTCTTTTTGTCCATTTTGATGA 58.045 30.769 0.00 0.00 33.85 2.92
673 721 9.865321 ATACATCTCTTTTTGTCCATTTTGATG 57.135 29.630 0.00 0.00 35.23 3.07
675 723 9.300681 AGATACATCTCTTTTTGTCCATTTTGA 57.699 29.630 0.00 0.00 29.30 2.69
680 728 9.606631 GTTCTAGATACATCTCTTTTTGTCCAT 57.393 33.333 0.00 0.00 38.32 3.41
681 729 8.816894 AGTTCTAGATACATCTCTTTTTGTCCA 58.183 33.333 0.00 0.00 38.32 4.02
705 753 9.845214 AGGGGATGTATCTAGATGTATTTTAGT 57.155 33.333 15.79 0.00 0.00 2.24
723 771 9.082313 GTCATCAAAATGAATATAAGGGGATGT 57.918 33.333 0.00 0.00 43.42 3.06
724 772 9.081204 TGTCATCAAAATGAATATAAGGGGATG 57.919 33.333 0.00 0.00 43.42 3.51
725 773 9.659135 TTGTCATCAAAATGAATATAAGGGGAT 57.341 29.630 0.00 0.00 43.42 3.85
726 774 9.135189 CTTGTCATCAAAATGAATATAAGGGGA 57.865 33.333 0.00 0.00 43.42 4.81
727 775 8.917088 ACTTGTCATCAAAATGAATATAAGGGG 58.083 33.333 0.00 0.00 43.42 4.79
735 783 7.975616 CCGGAAATACTTGTCATCAAAATGAAT 59.024 33.333 0.00 0.00 43.42 2.57
736 784 7.175816 TCCGGAAATACTTGTCATCAAAATGAA 59.824 33.333 0.00 0.00 43.42 2.57
737 785 6.657117 TCCGGAAATACTTGTCATCAAAATGA 59.343 34.615 0.00 0.00 39.63 2.57
738 786 6.747280 GTCCGGAAATACTTGTCATCAAAATG 59.253 38.462 5.23 0.00 32.87 2.32
739 787 6.403200 CGTCCGGAAATACTTGTCATCAAAAT 60.403 38.462 5.23 0.00 32.87 1.82
740 788 5.106869 CGTCCGGAAATACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
741 789 4.390603 CGTCCGGAAATACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
742 790 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
743 791 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
744 792 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
745 793 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
746 794 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
747 795 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
748 796 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
749 797 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
750 798 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
751 799 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
752 800 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
753 801 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
754 802 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
755 803 0.251742 TTACTCCCTCCGTCCGGAAA 60.252 55.000 5.23 0.00 44.66 3.13
756 804 0.251742 TTTACTCCCTCCGTCCGGAA 60.252 55.000 5.23 0.00 44.66 4.30
757 805 0.251742 TTTTACTCCCTCCGTCCGGA 60.252 55.000 0.00 0.00 42.90 5.14
758 806 0.609662 TTTTTACTCCCTCCGTCCGG 59.390 55.000 0.00 0.00 0.00 5.14
759 807 1.547372 TCTTTTTACTCCCTCCGTCCG 59.453 52.381 0.00 0.00 0.00 4.79
760 808 3.690475 TTCTTTTTACTCCCTCCGTCC 57.310 47.619 0.00 0.00 0.00 4.79
761 809 4.891260 TCTTTCTTTTTACTCCCTCCGTC 58.109 43.478 0.00 0.00 0.00 4.79
762 810 4.968971 TCTTTCTTTTTACTCCCTCCGT 57.031 40.909 0.00 0.00 0.00 4.69
763 811 5.306394 AGTTCTTTCTTTTTACTCCCTCCG 58.694 41.667 0.00 0.00 0.00 4.63
764 812 5.408909 CGAGTTCTTTCTTTTTACTCCCTCC 59.591 44.000 0.00 0.00 33.39 4.30
765 813 6.221659 TCGAGTTCTTTCTTTTTACTCCCTC 58.778 40.000 0.00 0.00 33.39 4.30
766 814 6.041751 TCTCGAGTTCTTTCTTTTTACTCCCT 59.958 38.462 13.13 0.00 33.39 4.20
767 815 6.145858 GTCTCGAGTTCTTTCTTTTTACTCCC 59.854 42.308 13.13 0.00 33.39 4.30
768 816 6.145858 GGTCTCGAGTTCTTTCTTTTTACTCC 59.854 42.308 13.13 0.00 33.39 3.85
769 817 6.700520 TGGTCTCGAGTTCTTTCTTTTTACTC 59.299 38.462 13.13 0.00 33.58 2.59
770 818 6.579865 TGGTCTCGAGTTCTTTCTTTTTACT 58.420 36.000 13.13 0.00 0.00 2.24
771 819 6.839820 TGGTCTCGAGTTCTTTCTTTTTAC 57.160 37.500 13.13 0.00 0.00 2.01
804 897 4.931601 CGCTCTTTGCCTGCTAATATATCA 59.068 41.667 0.00 0.00 38.78 2.15
815 908 2.127118 CGTTGCGCTCTTTGCCTG 60.127 61.111 9.73 0.00 38.78 4.85
824 919 1.507141 CCTTCTTGGAACGTTGCGCT 61.507 55.000 15.33 0.00 38.35 5.92
835 944 3.431725 GCGGCGGTTCCTTCTTGG 61.432 66.667 9.78 0.00 37.10 3.61
905 1014 3.401033 TGTTCAAAGATCTGCTTCGGA 57.599 42.857 0.00 0.00 35.24 4.55
946 1055 2.473868 CGACGTACGTACACGGTACATT 60.474 50.000 22.87 0.00 46.12 2.71
948 1057 0.436913 CGACGTACGTACACGGTACA 59.563 55.000 22.87 0.00 46.12 2.90
949 1058 0.247145 CCGACGTACGTACACGGTAC 60.247 60.000 33.44 17.73 46.12 3.34
950 1059 1.962092 GCCGACGTACGTACACGGTA 61.962 60.000 37.13 5.65 46.12 4.02
951 1060 2.860293 CCGACGTACGTACACGGT 59.140 61.111 33.44 22.19 46.12 4.83
952 1061 2.574212 GCCGACGTACGTACACGG 60.574 66.667 35.50 35.50 46.12 4.94
954 1063 3.233345 GCGCCGACGTACGTACAC 61.233 66.667 22.87 16.14 42.83 2.90
968 1077 2.025727 GGCTTGATCATGCAGCGC 59.974 61.111 28.58 12.35 33.64 5.92
994 1103 3.075882 TCCAAGTGGAAACCCATGATCTT 59.924 43.478 0.00 0.00 42.18 2.40
1090 1199 0.402121 GGTGACTTCTCCTTTGGCCT 59.598 55.000 3.32 0.00 0.00 5.19
1106 1215 1.080025 GACGTCTTCCCTTCCGGTG 60.080 63.158 8.70 0.00 0.00 4.94
1107 1216 2.633509 CGACGTCTTCCCTTCCGGT 61.634 63.158 14.70 0.00 0.00 5.28
1108 1217 2.181021 CGACGTCTTCCCTTCCGG 59.819 66.667 14.70 0.00 0.00 5.14
1168 1284 0.939577 CGCATCTTCCGGTATCCACG 60.940 60.000 0.00 0.00 0.00 4.94
1169 1285 0.387929 TCGCATCTTCCGGTATCCAC 59.612 55.000 0.00 0.00 0.00 4.02
1170 1286 1.116308 TTCGCATCTTCCGGTATCCA 58.884 50.000 0.00 0.00 0.00 3.41
1171 1287 1.202486 TGTTCGCATCTTCCGGTATCC 60.202 52.381 0.00 0.00 0.00 2.59
1172 1288 2.128035 CTGTTCGCATCTTCCGGTATC 58.872 52.381 0.00 0.00 0.00 2.24
1175 1291 0.892755 TACTGTTCGCATCTTCCGGT 59.107 50.000 0.00 0.00 0.00 5.28
1176 1292 1.135083 ACTACTGTTCGCATCTTCCGG 60.135 52.381 0.00 0.00 0.00 5.14
1177 1293 2.159366 AGACTACTGTTCGCATCTTCCG 60.159 50.000 0.00 0.00 0.00 4.30
1178 1294 3.512033 AGACTACTGTTCGCATCTTCC 57.488 47.619 0.00 0.00 0.00 3.46
1388 1512 4.842531 TCTCCCATGTGAGCTAAAATGA 57.157 40.909 2.30 0.00 32.22 2.57
1423 1554 6.409524 TTTCTCATTCAATGATAATGGGGC 57.590 37.500 0.00 0.00 38.85 5.80
1459 1590 2.925563 GCTGGCTAATCAACATGTTTGC 59.074 45.455 8.77 8.31 0.00 3.68
1639 2976 2.418976 GGTCTTCAGTCCGTTAATTGGC 59.581 50.000 0.00 0.00 0.00 4.52
1710 3047 7.001674 TCTAACTCTTTCACCAAAATAGGCAA 58.998 34.615 0.00 0.00 0.00 4.52
1711 3048 6.539173 TCTAACTCTTTCACCAAAATAGGCA 58.461 36.000 0.00 0.00 0.00 4.75
1712 3049 7.040686 TGTTCTAACTCTTTCACCAAAATAGGC 60.041 37.037 0.00 0.00 0.00 3.93
1713 3050 8.391075 TGTTCTAACTCTTTCACCAAAATAGG 57.609 34.615 0.00 0.00 0.00 2.57
1714 3051 9.273016 TCTGTTCTAACTCTTTCACCAAAATAG 57.727 33.333 0.00 0.00 0.00 1.73
1715 3052 9.793259 ATCTGTTCTAACTCTTTCACCAAAATA 57.207 29.630 0.00 0.00 0.00 1.40
1865 3263 0.038166 TGGTGGTTTGATCTGGCTCC 59.962 55.000 0.00 0.00 0.00 4.70
1935 3333 3.256631 AGAAAGGCAAAACATAGGCACAG 59.743 43.478 0.00 0.00 0.00 3.66
1937 3335 3.005791 ACAGAAAGGCAAAACATAGGCAC 59.994 43.478 0.00 0.00 0.00 5.01
1966 3364 2.987821 GGAGTCAACGACAAGCTTCTAC 59.012 50.000 0.00 0.00 34.60 2.59
1981 3379 4.871871 ACTGAAGATAGAGGAGGAGTCA 57.128 45.455 0.00 0.00 0.00 3.41
2010 3408 3.188159 ACTAAACCTCACGCTGTTTCA 57.812 42.857 0.00 0.00 36.23 2.69
2028 3426 8.478066 TCATTTAGATCAACTGTACTGCATACT 58.522 33.333 0.00 0.00 34.56 2.12
2256 3658 5.802064 TCAGTTGTTGAACACGATTGTAAC 58.198 37.500 0.00 0.00 33.55 2.50
2324 3734 7.792508 GTCCAGTAAATTACGCGAAATATTCTG 59.207 37.037 15.93 13.09 0.00 3.02
2417 4025 2.479566 ATCTTCTTCGCTCTGCCAAA 57.520 45.000 0.00 0.00 0.00 3.28
2708 4330 5.620738 TTATAGCTCTCCAGAATGCAACT 57.379 39.130 0.00 0.00 31.97 3.16
3123 4818 1.201647 CTCGTTTTAGCAGGACTCGGA 59.798 52.381 0.00 0.00 0.00 4.55
3296 5320 4.460382 CAGCCCCATCACATATTAATCACC 59.540 45.833 0.00 0.00 0.00 4.02
3444 6052 6.759497 AATCTATCCTGTAAACCAAAGCAC 57.241 37.500 0.00 0.00 0.00 4.40
3452 6060 8.499403 AGCAAGAAGAAATCTATCCTGTAAAC 57.501 34.615 0.00 0.00 37.42 2.01
3559 6223 5.536161 ACATCTTTGCTGGACAAATGTAACT 59.464 36.000 0.00 0.00 46.90 2.24
4057 6745 2.639347 CCAGCTGATGGTGATACCCATA 59.361 50.000 17.39 0.00 45.31 2.74
4099 6787 1.672854 CTACCTCCGCGAACATGGGA 61.673 60.000 8.23 0.00 0.00 4.37
4130 6818 0.031585 GCGTAGATCATGGTGCGGTA 59.968 55.000 0.00 0.00 0.00 4.02
4231 6919 2.605837 TGTTTACAGTCTTGGCGTCA 57.394 45.000 0.00 0.00 0.00 4.35
4282 6970 2.367486 GTTAGTAGCCCTCTCGACAGT 58.633 52.381 0.00 0.00 0.00 3.55
4500 7188 9.678260 ATTTCCCTGATAGCATATATTGTCTTC 57.322 33.333 0.00 0.00 0.00 2.87
4566 7254 7.283625 ACAAGTAAACAATGTGCTTGGATTA 57.716 32.000 20.86 0.60 40.35 1.75
4567 7255 6.160576 ACAAGTAAACAATGTGCTTGGATT 57.839 33.333 20.86 6.19 40.35 3.01
4568 7256 5.789643 ACAAGTAAACAATGTGCTTGGAT 57.210 34.783 20.86 6.69 40.35 3.41
4570 7258 5.826586 TGTACAAGTAAACAATGTGCTTGG 58.173 37.500 20.86 9.82 40.35 3.61
4571 7259 7.113404 GTCATGTACAAGTAAACAATGTGCTTG 59.887 37.037 17.62 17.62 41.40 4.01
4572 7260 7.138736 GTCATGTACAAGTAAACAATGTGCTT 58.861 34.615 0.00 0.00 31.94 3.91
4594 7282 8.364894 TCTACAAGATAGCAGTTTAAGTTGTCA 58.635 33.333 0.00 0.00 0.00 3.58
4597 7285 9.209175 AGTTCTACAAGATAGCAGTTTAAGTTG 57.791 33.333 0.00 0.00 0.00 3.16
4616 7304 5.062308 CGAAATGCAGTGGTCTAAGTTCTAC 59.938 44.000 0.00 0.00 0.00 2.59
4625 7313 2.831685 TACACGAAATGCAGTGGTCT 57.168 45.000 8.49 0.00 42.25 3.85
4626 7314 5.734855 ATTATACACGAAATGCAGTGGTC 57.265 39.130 8.49 0.00 42.25 4.02
4629 7317 9.554724 AAAGTTAATTATACACGAAATGCAGTG 57.445 29.630 2.49 2.49 43.46 3.66
4676 7364 4.171005 TCTTGTACGTTGTAGCATGTAGC 58.829 43.478 0.00 0.00 46.19 3.58
4680 7368 6.090763 TGAATCTTCTTGTACGTTGTAGCATG 59.909 38.462 0.00 0.00 0.00 4.06
4683 7371 6.648725 ATGAATCTTCTTGTACGTTGTAGC 57.351 37.500 0.00 0.00 0.00 3.58
4684 7372 9.530129 GAAAATGAATCTTCTTGTACGTTGTAG 57.470 33.333 0.00 0.00 0.00 2.74
4685 7373 9.047371 TGAAAATGAATCTTCTTGTACGTTGTA 57.953 29.630 0.00 0.00 0.00 2.41
4686 7374 7.925993 TGAAAATGAATCTTCTTGTACGTTGT 58.074 30.769 0.00 0.00 0.00 3.32
4687 7375 8.955061 ATGAAAATGAATCTTCTTGTACGTTG 57.045 30.769 0.00 0.00 0.00 4.10
4840 7953 3.713764 CTCCACATCTAGGGATTCAGGTT 59.286 47.826 0.00 0.00 31.57 3.50
4928 8160 1.957177 TCTTCTGCACTGACGTCTCTT 59.043 47.619 17.92 0.00 0.00 2.85
4936 8168 3.558931 TTTGGTTCTCTTCTGCACTGA 57.441 42.857 0.00 0.00 0.00 3.41
4952 8184 3.258872 TGAGGATTCAGGTTGCATTTTGG 59.741 43.478 0.00 0.00 0.00 3.28
5078 8362 9.181805 GGTAAGTTTTCTTTGAATTTAGTGCTC 57.818 33.333 0.00 0.00 40.91 4.26
5080 8364 9.529325 AAGGTAAGTTTTCTTTGAATTTAGTGC 57.471 29.630 0.00 0.00 40.91 4.40
5113 8398 4.500477 GTGCATCGGAATTTCTACAAATGC 59.500 41.667 0.00 0.00 38.90 3.56
5114 8399 4.730042 CGTGCATCGGAATTTCTACAAATG 59.270 41.667 0.00 0.00 32.49 2.32
5115 8400 4.394920 ACGTGCATCGGAATTTCTACAAAT 59.605 37.500 12.18 0.00 44.69 2.32
5116 8401 3.749088 ACGTGCATCGGAATTTCTACAAA 59.251 39.130 12.18 0.00 44.69 2.83
5117 8402 3.331150 ACGTGCATCGGAATTTCTACAA 58.669 40.909 12.18 0.00 44.69 2.41
5118 8403 2.967362 ACGTGCATCGGAATTTCTACA 58.033 42.857 12.18 0.00 44.69 2.74
5119 8404 3.670203 CAACGTGCATCGGAATTTCTAC 58.330 45.455 12.18 0.00 44.69 2.59
5120 8405 2.095213 GCAACGTGCATCGGAATTTCTA 59.905 45.455 12.18 0.00 44.26 2.10
5121 8406 1.135689 GCAACGTGCATCGGAATTTCT 60.136 47.619 12.18 0.00 44.26 2.52
5122 8407 1.259316 GCAACGTGCATCGGAATTTC 58.741 50.000 12.18 0.00 44.26 2.17
5123 8408 3.399879 GCAACGTGCATCGGAATTT 57.600 47.368 12.18 0.00 44.26 1.82
5133 8418 1.786579 GAACAAGAAATGGCAACGTGC 59.213 47.619 0.00 0.00 44.08 5.34
5134 8419 2.393764 GGAACAAGAAATGGCAACGTG 58.606 47.619 0.00 0.00 42.51 4.49
5135 8420 1.339929 GGGAACAAGAAATGGCAACGT 59.660 47.619 0.00 0.00 42.51 3.99
5136 8421 1.339610 TGGGAACAAGAAATGGCAACG 59.660 47.619 0.00 0.00 37.44 4.10
5144 8429 8.323562 GAAGCAGTTCAAAATGGGAACAAGAAA 61.324 37.037 7.87 0.00 45.45 2.52
5145 8430 6.904261 GAAGCAGTTCAAAATGGGAACAAGAA 60.904 38.462 7.87 0.00 45.45 2.52
5146 8431 5.451798 GAAGCAGTTCAAAATGGGAACAAGA 60.452 40.000 7.87 0.00 45.45 3.02
5147 8432 4.746611 GAAGCAGTTCAAAATGGGAACAAG 59.253 41.667 7.87 1.82 45.45 3.16
5152 8437 2.293122 CGTGAAGCAGTTCAAAATGGGA 59.707 45.455 0.00 0.00 44.44 4.37
5153 8438 2.034558 ACGTGAAGCAGTTCAAAATGGG 59.965 45.455 0.00 0.00 44.44 4.00
5155 8440 6.092122 TCCTATACGTGAAGCAGTTCAAAATG 59.908 38.462 0.00 0.00 44.44 2.32
5159 8444 4.794278 TCCTATACGTGAAGCAGTTCAA 57.206 40.909 0.00 0.00 44.44 2.69
5175 8460 1.072159 GCTGGCGCCTGAATCCTAT 59.928 57.895 34.52 0.00 0.00 2.57
5241 8712 1.730612 GACGGTCTGTTTTCGATTCCC 59.269 52.381 0.00 0.00 0.00 3.97
5288 8759 4.631813 CCTCTTTTATGTAGTCACTGGTGC 59.368 45.833 0.00 0.00 0.00 5.01
5378 8849 7.993821 TTGTTGTTTGGTGTTATAATGTGTG 57.006 32.000 0.00 0.00 0.00 3.82
5379 8850 7.221067 CGTTTGTTGTTTGGTGTTATAATGTGT 59.779 33.333 0.00 0.00 0.00 3.72
5380 8851 7.432545 TCGTTTGTTGTTTGGTGTTATAATGTG 59.567 33.333 0.00 0.00 0.00 3.21
5381 8852 7.481642 TCGTTTGTTGTTTGGTGTTATAATGT 58.518 30.769 0.00 0.00 0.00 2.71
5382 8853 7.916128 TCGTTTGTTGTTTGGTGTTATAATG 57.084 32.000 0.00 0.00 0.00 1.90
5383 8854 8.809478 GTTTCGTTTGTTGTTTGGTGTTATAAT 58.191 29.630 0.00 0.00 0.00 1.28
5384 8855 7.811236 TGTTTCGTTTGTTGTTTGGTGTTATAA 59.189 29.630 0.00 0.00 0.00 0.98
5385 8856 7.310664 TGTTTCGTTTGTTGTTTGGTGTTATA 58.689 30.769 0.00 0.00 0.00 0.98
5386 8857 6.157211 TGTTTCGTTTGTTGTTTGGTGTTAT 58.843 32.000 0.00 0.00 0.00 1.89
5387 8858 5.526115 TGTTTCGTTTGTTGTTTGGTGTTA 58.474 33.333 0.00 0.00 0.00 2.41
5388 8859 4.369182 TGTTTCGTTTGTTGTTTGGTGTT 58.631 34.783 0.00 0.00 0.00 3.32
5389 8860 3.978687 TGTTTCGTTTGTTGTTTGGTGT 58.021 36.364 0.00 0.00 0.00 4.16
5390 8861 4.376514 GGTTGTTTCGTTTGTTGTTTGGTG 60.377 41.667 0.00 0.00 0.00 4.17
5391 8862 3.741856 GGTTGTTTCGTTTGTTGTTTGGT 59.258 39.130 0.00 0.00 0.00 3.67
5392 8863 3.181539 CGGTTGTTTCGTTTGTTGTTTGG 60.182 43.478 0.00 0.00 0.00 3.28
5393 8864 3.181539 CCGGTTGTTTCGTTTGTTGTTTG 60.182 43.478 0.00 0.00 0.00 2.93
5394 8865 2.987821 CCGGTTGTTTCGTTTGTTGTTT 59.012 40.909 0.00 0.00 0.00 2.83
5395 8866 2.597520 CCGGTTGTTTCGTTTGTTGTT 58.402 42.857 0.00 0.00 0.00 2.83
5396 8867 1.733061 GCCGGTTGTTTCGTTTGTTGT 60.733 47.619 1.90 0.00 0.00 3.32
5397 8868 0.917939 GCCGGTTGTTTCGTTTGTTG 59.082 50.000 1.90 0.00 0.00 3.33
5398 8869 0.526662 TGCCGGTTGTTTCGTTTGTT 59.473 45.000 1.90 0.00 0.00 2.83
5399 8870 0.526662 TTGCCGGTTGTTTCGTTTGT 59.473 45.000 1.90 0.00 0.00 2.83
5400 8871 1.520590 CATTGCCGGTTGTTTCGTTTG 59.479 47.619 1.90 0.00 0.00 2.93
5401 8872 1.846541 CATTGCCGGTTGTTTCGTTT 58.153 45.000 1.90 0.00 0.00 3.60
5402 8873 3.560826 CATTGCCGGTTGTTTCGTT 57.439 47.368 1.90 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.