Multiple sequence alignment - TraesCS5D01G309500

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 TraesCS5D01G309500 chr5D 100.000 2549 0 0 1 2549 406463558 406461010 0.000000e+00 4708
1 TraesCS5D01G309500 chr5D 97.337 676 18 0 1874 2549 386600584 386601259 0.000000e+00 1149
2 TraesCS5D01G309500 chr5D 90.560 678 62 2 1873 2549 108515248 108514572 0.000000e+00 896
3 TraesCS5D01G309500 chr5D 84.287 961 69 35 9 960 406423766 406422879 0.000000e+00 863
4 TraesCS5D01G309500 chr5D 93.271 431 13 2 1177 1607 406422671 406422257 2.790000e-174 621
5 TraesCS5D01G309500 chr5D 92.260 323 23 2 1269 1590 406475758 406475437 8.310000e-125 457
6 TraesCS5D01G309500 chr5D 92.857 308 19 2 973 1277 406477220 406476913 6.470000e-121 444
7 TraesCS5D01G309500 chr5D 82.008 528 56 12 1 514 406478130 406477628 1.820000e-111 412
8 TraesCS5D01G309500 chr5D 94.194 155 9 0 973 1127 406422824 406422670 1.180000e-58 237
9 TraesCS5D01G309500 chr5D 86.364 198 18 7 571 764 406477532 406477340 9.240000e-50 207
10 TraesCS5D01G309500 chr5D 92.500 80 0 3 779 858 406477350 406477277 2.680000e-20 110
11 TraesCS5D01G309500 chr1D 97.633 676 16 0 1874 2549 448381316 448381991 0.000000e+00 1160
12 TraesCS5D01G309500 chr1D 81.707 164 27 3 1606 1766 385091376 385091213 1.590000e-27 134
13 TraesCS5D01G309500 chr5A 85.059 1024 46 23 600 1596 512068048 512067105 0.000000e+00 944
14 TraesCS5D01G309500 chr5A 86.093 302 30 3 104 393 512085361 512085060 5.290000e-82 315
15 TraesCS5D01G309500 chr5A 93.939 99 6 0 1 99 512119259 512119161 1.580000e-32 150
16 TraesCS5D01G309500 chr5B 92.097 658 42 5 958 1607 487471722 487471067 0.000000e+00 918
17 TraesCS5D01G309500 chr5B 84.399 782 75 23 571 1346 487488114 487487374 0.000000e+00 725
18 TraesCS5D01G309500 chr5B 81.694 661 93 17 1895 2547 462751032 462750392 2.250000e-145 525
19 TraesCS5D01G309500 chr5B 83.774 530 47 15 1 516 487488730 487488226 1.380000e-127 466
20 TraesCS5D01G309500 chr5B 86.472 377 32 5 1 366 487478888 487478520 1.840000e-106 396
21 TraesCS5D01G309500 chr5B 92.143 280 13 4 1336 1607 487487327 487487049 1.110000e-103 387
22 TraesCS5D01G309500 chr5B 92.793 111 1 4 776 885 487471847 487471743 1.220000e-33 154
23 TraesCS5D01G309500 chr4D 89.956 677 57 5 1874 2549 100355609 100354943 0.000000e+00 863
24 TraesCS5D01G309500 chr4D 83.962 424 55 10 2128 2547 421969995 421969581 6.610000e-106 394
25 TraesCS5D01G309500 chr4D 85.882 255 34 2 1870 2123 421970450 421970197 1.160000e-68 270
26 TraesCS5D01G309500 chr4A 83.554 681 86 16 1873 2547 435440885 435440225 4.660000e-172 614
27 TraesCS5D01G309500 chr4A 87.903 124 11 2 1605 1724 624300163 624300040 2.640000e-30 143
28 TraesCS5D01G309500 chr2B 82.405 682 88 19 1874 2547 325831148 325831805 1.320000e-157 566
29 TraesCS5D01G309500 chr2B 84.071 565 78 11 990 1551 170852377 170851822 3.730000e-148 534
30 TraesCS5D01G309500 chr7D 82.786 639 90 16 1870 2502 15133980 15133356 1.030000e-153 553
31 TraesCS5D01G309500 chr2A 83.186 565 77 15 990 1551 120671854 120671305 3.790000e-138 501
32 TraesCS5D01G309500 chr1A 80.046 436 76 8 1099 1527 9476242 9476673 1.900000e-81 313
33 TraesCS5D01G309500 chr1A 80.000 170 31 2 1600 1766 358920545 358920714 3.440000e-24 122
34 TraesCS5D01G309500 chr3D 81.683 202 31 4 1603 1799 459486963 459487163 2.030000e-36 163
35 TraesCS5D01G309500 chr3D 90.909 121 9 2 1606 1724 68438761 68438881 7.300000e-36 161
36 TraesCS5D01G309500 chr1B 80.808 198 32 4 1605 1797 42311199 42311003 1.580000e-32 150
37 TraesCS5D01G309500 chr6A 86.765 136 14 3 1593 1724 613638674 613638809 5.680000e-32 148
38 TraesCS5D01G309500 chrUn 79.882 169 31 3 1600 1766 33278231 33278398 1.240000e-23 121
39 TraesCS5D01G309500 chrUn 79.882 169 31 3 1600 1766 400230303 400230136 1.240000e-23 121


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 TraesCS5D01G309500 chr5D 406461010 406463558 2548 True 4708.000000 4708 100.0000 1 2549 1 chr5D.!!$R2 2548
1 TraesCS5D01G309500 chr5D 386600584 386601259 675 False 1149.000000 1149 97.3370 1874 2549 1 chr5D.!!$F1 675
2 TraesCS5D01G309500 chr5D 108514572 108515248 676 True 896.000000 896 90.5600 1873 2549 1 chr5D.!!$R1 676
3 TraesCS5D01G309500 chr5D 406422257 406423766 1509 True 573.666667 863 90.5840 9 1607 3 chr5D.!!$R3 1598
4 TraesCS5D01G309500 chr5D 406475437 406478130 2693 True 326.000000 457 89.1978 1 1590 5 chr5D.!!$R4 1589
5 TraesCS5D01G309500 chr1D 448381316 448381991 675 False 1160.000000 1160 97.6330 1874 2549 1 chr1D.!!$F1 675
6 TraesCS5D01G309500 chr5A 512067105 512068048 943 True 944.000000 944 85.0590 600 1596 1 chr5A.!!$R1 996
7 TraesCS5D01G309500 chr5B 487471067 487471847 780 True 536.000000 918 92.4450 776 1607 2 chr5B.!!$R3 831
8 TraesCS5D01G309500 chr5B 487487049 487488730 1681 True 526.000000 725 86.7720 1 1607 3 chr5B.!!$R4 1606
9 TraesCS5D01G309500 chr5B 462750392 462751032 640 True 525.000000 525 81.6940 1895 2547 1 chr5B.!!$R1 652
10 TraesCS5D01G309500 chr4D 100354943 100355609 666 True 863.000000 863 89.9560 1874 2549 1 chr4D.!!$R1 675
11 TraesCS5D01G309500 chr4D 421969581 421970450 869 True 332.000000 394 84.9220 1870 2547 2 chr4D.!!$R2 677
12 TraesCS5D01G309500 chr4A 435440225 435440885 660 True 614.000000 614 83.5540 1873 2547 1 chr4A.!!$R1 674
13 TraesCS5D01G309500 chr2B 325831148 325831805 657 False 566.000000 566 82.4050 1874 2547 1 chr2B.!!$F1 673
14 TraesCS5D01G309500 chr2B 170851822 170852377 555 True 534.000000 534 84.0710 990 1551 1 chr2B.!!$R1 561
15 TraesCS5D01G309500 chr7D 15133356 15133980 624 True 553.000000 553 82.7860 1870 2502 1 chr7D.!!$R1 632
16 TraesCS5D01G309500 chr2A 120671305 120671854 549 True 501.000000 501 83.1860 990 1551 1 chr2A.!!$R1 561

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
506 527 0.109723 GGCCACACCCTGTTAACTGA 59.89 55.0 13.56 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1828 3265 0.034616 CTCGATCTCTTCATGCCCCC 59.965 60.0 0.0 0.0 0.0 5.4 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
77 78 3.635836 CAGACTGCTGTCATGGAGAGATA 59.364 47.826 23.61 0.00 45.20 1.98
98 99 6.770286 ATATGAAATATCTGTCCACCCAGT 57.230 37.500 0.00 0.00 33.21 4.00
99 100 4.487714 TGAAATATCTGTCCACCCAGTC 57.512 45.455 0.00 0.00 34.02 3.51
121 122 1.875514 GTGCATTCTCACAGCTCAACA 59.124 47.619 0.00 0.00 36.97 3.33
140 141 3.759581 ACAAGCAACATCCACTTCTCAT 58.240 40.909 0.00 0.00 0.00 2.90
144 145 2.936993 GCAACATCCACTTCTCATCGGT 60.937 50.000 0.00 0.00 0.00 4.69
198 199 0.892814 GCTTGGCAGAAGCACTTCCT 60.893 55.000 13.35 0.00 44.61 3.36
202 203 1.552337 TGGCAGAAGCACTTCCTAGAG 59.448 52.381 6.77 0.00 44.61 2.43
205 206 1.552337 CAGAAGCACTTCCTAGAGGCA 59.448 52.381 6.77 0.00 40.33 4.75
334 346 1.023513 GCTGGGCTTCAGTGTGCTAG 61.024 60.000 9.82 9.53 45.08 3.42
352 364 0.249489 AGCGCGAACAAGAAGTGTCT 60.249 50.000 12.10 0.00 40.60 3.41
354 366 0.111089 CGCGAACAAGAAGTGTCTGC 60.111 55.000 0.00 0.00 40.60 4.26
361 373 2.996168 AAGAAGTGTCTGCGCGGCTT 62.996 55.000 12.58 9.47 33.05 4.35
506 527 0.109723 GGCCACACCCTGTTAACTGA 59.890 55.000 13.56 0.00 0.00 3.41
534 555 6.759497 AAAATACTCCCTCCGATTCAAAAG 57.241 37.500 0.00 0.00 0.00 2.27
535 556 5.437191 AATACTCCCTCCGATTCAAAAGT 57.563 39.130 0.00 0.00 0.00 2.66
584 669 9.284968 GTTAGGGTGTAATATATTCTGTGCATT 57.715 33.333 0.00 0.00 0.00 3.56
646 735 7.012989 ACCCACAGATCTAAACAAAACACTAAC 59.987 37.037 0.00 0.00 0.00 2.34
647 736 7.228706 CCCACAGATCTAAACAAAACACTAACT 59.771 37.037 0.00 0.00 0.00 2.24
648 737 8.621286 CCACAGATCTAAACAAAACACTAACTT 58.379 33.333 0.00 0.00 0.00 2.66
650 739 9.391006 ACAGATCTAAACAAAACACTAACTTCA 57.609 29.630 0.00 0.00 0.00 3.02
700 789 6.725369 ACCAGATGATCAGAGCAGTAGATAAT 59.275 38.462 0.09 0.00 0.00 1.28
708 797 9.226606 GATCAGAGCAGTAGATAATACTAGTGT 57.773 37.037 5.39 0.00 42.44 3.55
819 921 7.832769 TGTTAGTTGTGACAGCTACATATACA 58.167 34.615 8.72 7.59 27.52 2.29
823 925 3.704061 TGTGACAGCTACATATACAGGCA 59.296 43.478 0.00 0.00 0.00 4.75
824 926 4.344968 TGTGACAGCTACATATACAGGCAT 59.655 41.667 0.00 0.00 0.00 4.40
825 927 4.687948 GTGACAGCTACATATACAGGCATG 59.312 45.833 0.00 0.00 0.00 4.06
826 928 3.668447 ACAGCTACATATACAGGCATGC 58.332 45.455 9.90 9.90 0.00 4.06
827 929 3.071457 ACAGCTACATATACAGGCATGCA 59.929 43.478 21.36 0.00 0.00 3.96
828 930 3.683340 CAGCTACATATACAGGCATGCAG 59.317 47.826 21.36 13.91 0.00 4.41
900 1016 1.591863 GCCGATGAAGCCTACGGAC 60.592 63.158 0.00 0.00 46.94 4.79
935 1051 1.776034 GAATCCATCGGCAGGAACGC 61.776 60.000 0.00 0.00 38.93 4.84
936 1052 2.257409 AATCCATCGGCAGGAACGCT 62.257 55.000 0.00 0.00 38.93 5.07
937 1053 2.930385 ATCCATCGGCAGGAACGCTG 62.930 60.000 0.00 0.00 38.93 5.18
938 1054 3.869272 CATCGGCAGGAACGCTGC 61.869 66.667 5.07 5.07 46.20 5.25
943 1059 2.558313 GCAGGAACGCTGCACTTC 59.442 61.111 8.42 0.00 46.19 3.01
1288 2619 2.732619 CGGTACCAGGGCCTCTTCC 61.733 68.421 13.54 3.12 0.00 3.46
1292 2623 0.118346 TACCAGGGCCTCTTCCTCAA 59.882 55.000 0.95 0.00 31.06 3.02
1579 3013 1.588667 CCTGTTGGTTTGTGTGCGC 60.589 57.895 0.00 0.00 0.00 6.09
1607 3044 5.062558 GTGCTATCGTGTACGTTGGTAAATT 59.937 40.000 0.00 0.00 40.80 1.82
1608 3045 5.289193 TGCTATCGTGTACGTTGGTAAATTC 59.711 40.000 0.00 0.00 40.80 2.17
1609 3046 5.517770 GCTATCGTGTACGTTGGTAAATTCT 59.482 40.000 0.00 0.00 40.80 2.40
1610 3047 6.692681 GCTATCGTGTACGTTGGTAAATTCTA 59.307 38.462 0.00 0.00 40.80 2.10
1611 3048 7.220683 GCTATCGTGTACGTTGGTAAATTCTAA 59.779 37.037 0.00 0.00 40.80 2.10
1612 3049 7.887996 ATCGTGTACGTTGGTAAATTCTAAA 57.112 32.000 0.00 0.00 40.80 1.85
1613 3050 7.887996 TCGTGTACGTTGGTAAATTCTAAAT 57.112 32.000 0.00 0.00 40.80 1.40
1614 3051 8.978564 TCGTGTACGTTGGTAAATTCTAAATA 57.021 30.769 0.00 0.00 40.80 1.40
1615 3052 9.585099 TCGTGTACGTTGGTAAATTCTAAATAT 57.415 29.630 0.00 0.00 40.80 1.28
1629 3066 9.930158 AAATTCTAAATATACTAAACCTGGCCA 57.070 29.630 4.71 4.71 0.00 5.36
1630 3067 9.574516 AATTCTAAATATACTAAACCTGGCCAG 57.425 33.333 26.87 26.87 0.00 4.85
1646 3083 7.781324 CCTGGCCAGGTTTAATTTATCATAT 57.219 36.000 39.52 0.00 43.61 1.78
1647 3084 8.193953 CCTGGCCAGGTTTAATTTATCATATT 57.806 34.615 39.52 0.00 43.61 1.28
1648 3085 8.650490 CCTGGCCAGGTTTAATTTATCATATTT 58.350 33.333 39.52 0.00 43.61 1.40
1677 3114 8.289618 TGACTTTTTCTTATCAGTCAAAATCGG 58.710 33.333 0.00 0.00 42.09 4.18
1678 3115 8.391075 ACTTTTTCTTATCAGTCAAAATCGGA 57.609 30.769 0.00 0.00 0.00 4.55
1679 3116 8.290325 ACTTTTTCTTATCAGTCAAAATCGGAC 58.710 33.333 0.00 0.00 35.50 4.79
1680 3117 6.737254 TTTCTTATCAGTCAAAATCGGACC 57.263 37.500 0.00 0.00 35.89 4.46
1681 3118 5.414789 TCTTATCAGTCAAAATCGGACCA 57.585 39.130 0.00 0.00 35.89 4.02
1682 3119 5.800296 TCTTATCAGTCAAAATCGGACCAA 58.200 37.500 0.00 0.00 35.89 3.67
1683 3120 6.414732 TCTTATCAGTCAAAATCGGACCAAT 58.585 36.000 0.00 0.00 35.89 3.16
1684 3121 4.970662 ATCAGTCAAAATCGGACCAATG 57.029 40.909 0.00 0.00 35.89 2.82
1685 3122 3.081061 TCAGTCAAAATCGGACCAATGG 58.919 45.455 0.00 0.00 35.89 3.16
1686 3123 2.164219 CAGTCAAAATCGGACCAATGGG 59.836 50.000 3.55 0.00 35.89 4.00
1696 3133 3.443045 CCAATGGGTGAGCGGCAC 61.443 66.667 1.45 0.00 46.98 5.01
1710 3147 1.510844 GGCACGTGCTTTAATGGGG 59.489 57.895 36.84 0.00 41.70 4.96
1711 3148 0.963355 GGCACGTGCTTTAATGGGGA 60.963 55.000 36.84 0.00 41.70 4.81
1712 3149 1.102978 GCACGTGCTTTAATGGGGAT 58.897 50.000 32.55 0.00 38.21 3.85
1713 3150 2.294074 GCACGTGCTTTAATGGGGATA 58.706 47.619 32.55 0.00 38.21 2.59
1714 3151 2.032924 GCACGTGCTTTAATGGGGATAC 59.967 50.000 32.55 0.00 38.21 2.24
1715 3152 3.275143 CACGTGCTTTAATGGGGATACA 58.725 45.455 0.82 0.00 39.74 2.29
1716 3153 3.312421 CACGTGCTTTAATGGGGATACAG 59.688 47.826 0.82 0.00 39.74 2.74
1717 3154 2.290641 CGTGCTTTAATGGGGATACAGC 59.709 50.000 0.00 0.00 39.74 4.40
1718 3155 2.623416 GTGCTTTAATGGGGATACAGCC 59.377 50.000 0.00 0.00 39.74 4.85
1719 3156 2.243478 TGCTTTAATGGGGATACAGCCA 59.757 45.455 0.00 0.00 39.74 4.75
1720 3157 2.887152 GCTTTAATGGGGATACAGCCAG 59.113 50.000 0.00 0.00 39.74 4.85
1721 3158 3.490348 CTTTAATGGGGATACAGCCAGG 58.510 50.000 0.00 0.00 39.74 4.45
1722 3159 2.206322 TAATGGGGATACAGCCAGGT 57.794 50.000 0.00 0.00 39.74 4.00
1723 3160 2.206322 AATGGGGATACAGCCAGGTA 57.794 50.000 0.00 0.00 39.74 3.08
1724 3161 2.440494 ATGGGGATACAGCCAGGTAT 57.560 50.000 0.00 0.00 36.70 2.73
1725 3162 1.434188 TGGGGATACAGCCAGGTATG 58.566 55.000 0.00 0.00 34.22 2.39
1726 3163 0.036875 GGGGATACAGCCAGGTATGC 59.963 60.000 4.40 4.40 40.23 3.14
1727 3164 0.764890 GGGATACAGCCAGGTATGCA 59.235 55.000 12.18 0.00 42.02 3.96
1728 3165 1.271054 GGGATACAGCCAGGTATGCAG 60.271 57.143 12.18 0.00 42.02 4.41
1729 3166 1.517242 GATACAGCCAGGTATGCAGC 58.483 55.000 0.00 0.00 34.22 5.25
1730 3167 1.071385 GATACAGCCAGGTATGCAGCT 59.929 52.381 0.00 0.00 34.22 4.24
1732 3169 1.077930 CAGCCAGGTATGCAGCTGT 60.078 57.895 16.64 0.00 46.72 4.40
1733 3170 1.077930 AGCCAGGTATGCAGCTGTG 60.078 57.895 16.64 4.06 46.72 3.66
1734 3171 1.377725 GCCAGGTATGCAGCTGTGT 60.378 57.895 16.64 6.90 46.72 3.72
1735 3172 1.651240 GCCAGGTATGCAGCTGTGTG 61.651 60.000 16.64 4.09 46.72 3.82
1736 3173 1.651240 CCAGGTATGCAGCTGTGTGC 61.651 60.000 16.64 7.75 46.72 4.57
1760 3197 4.458164 CGAATGCCGCTGGAAAAC 57.542 55.556 0.00 0.00 0.00 2.43
1761 3198 1.578926 CGAATGCCGCTGGAAAACA 59.421 52.632 0.00 0.00 0.00 2.83
1762 3199 0.171007 CGAATGCCGCTGGAAAACAT 59.829 50.000 0.00 0.00 0.00 2.71
1763 3200 1.400142 CGAATGCCGCTGGAAAACATA 59.600 47.619 0.00 0.00 0.00 2.29
1764 3201 2.159448 CGAATGCCGCTGGAAAACATAA 60.159 45.455 0.00 0.00 0.00 1.90
1765 3202 3.671971 CGAATGCCGCTGGAAAACATAAA 60.672 43.478 0.00 0.00 0.00 1.40
1766 3203 4.432712 GAATGCCGCTGGAAAACATAAAT 58.567 39.130 0.00 0.00 0.00 1.40
1767 3204 3.951775 TGCCGCTGGAAAACATAAATT 57.048 38.095 0.00 0.00 0.00 1.82
1768 3205 5.590530 ATGCCGCTGGAAAACATAAATTA 57.409 34.783 0.00 0.00 0.00 1.40
1769 3206 5.392767 TGCCGCTGGAAAACATAAATTAA 57.607 34.783 0.00 0.00 0.00 1.40
1770 3207 5.406649 TGCCGCTGGAAAACATAAATTAAG 58.593 37.500 0.00 0.00 0.00 1.85
1771 3208 4.803613 GCCGCTGGAAAACATAAATTAAGG 59.196 41.667 0.00 0.00 0.00 2.69
1772 3209 5.393678 GCCGCTGGAAAACATAAATTAAGGA 60.394 40.000 0.00 0.00 0.00 3.36
1773 3210 6.682861 GCCGCTGGAAAACATAAATTAAGGAT 60.683 38.462 0.00 0.00 0.00 3.24
1774 3211 7.264947 CCGCTGGAAAACATAAATTAAGGATT 58.735 34.615 0.00 0.00 0.00 3.01
1775 3212 7.763985 CCGCTGGAAAACATAAATTAAGGATTT 59.236 33.333 0.00 0.00 40.88 2.17
1776 3213 9.796120 CGCTGGAAAACATAAATTAAGGATTTA 57.204 29.630 0.00 0.00 42.68 1.40
1792 3229 7.631717 AAGGATTTAGTTCTCTATTGGTTGC 57.368 36.000 0.00 0.00 0.00 4.17
1793 3230 6.721318 AGGATTTAGTTCTCTATTGGTTGCA 58.279 36.000 0.00 0.00 0.00 4.08
1794 3231 7.349598 AGGATTTAGTTCTCTATTGGTTGCAT 58.650 34.615 0.00 0.00 0.00 3.96
1795 3232 7.284034 AGGATTTAGTTCTCTATTGGTTGCATG 59.716 37.037 0.00 0.00 0.00 4.06
1796 3233 7.067494 GGATTTAGTTCTCTATTGGTTGCATGT 59.933 37.037 0.00 0.00 0.00 3.21
1797 3234 6.985188 TTAGTTCTCTATTGGTTGCATGTC 57.015 37.500 0.00 0.00 0.00 3.06
1798 3235 4.265073 AGTTCTCTATTGGTTGCATGTCC 58.735 43.478 0.00 0.00 0.00 4.02
1799 3236 3.998913 TCTCTATTGGTTGCATGTCCA 57.001 42.857 0.00 0.00 0.00 4.02
1800 3237 4.508551 TCTCTATTGGTTGCATGTCCAT 57.491 40.909 6.62 1.87 33.50 3.41
1801 3238 4.201657 TCTCTATTGGTTGCATGTCCATG 58.798 43.478 2.86 2.86 41.60 3.66
1817 3254 4.025040 TCCATGCAGGACCATATGATTC 57.975 45.455 3.65 0.00 43.07 2.52
1818 3255 3.654321 TCCATGCAGGACCATATGATTCT 59.346 43.478 3.65 0.00 43.07 2.40
1819 3256 4.845796 TCCATGCAGGACCATATGATTCTA 59.154 41.667 3.65 0.00 43.07 2.10
1820 3257 5.310331 TCCATGCAGGACCATATGATTCTAA 59.690 40.000 3.65 0.00 43.07 2.10
1821 3258 6.012245 TCCATGCAGGACCATATGATTCTAAT 60.012 38.462 3.65 0.00 43.07 1.73
1822 3259 6.662234 CCATGCAGGACCATATGATTCTAATT 59.338 38.462 3.65 0.00 41.22 1.40
1823 3260 7.362660 CCATGCAGGACCATATGATTCTAATTG 60.363 40.741 3.65 0.00 41.22 2.32
1824 3261 6.005823 TGCAGGACCATATGATTCTAATTGG 58.994 40.000 3.65 0.00 0.00 3.16
1825 3262 5.105997 GCAGGACCATATGATTCTAATTGGC 60.106 44.000 3.65 0.00 0.00 4.52
1826 3263 5.122869 CAGGACCATATGATTCTAATTGGCG 59.877 44.000 3.65 0.00 0.00 5.69
1827 3264 4.142600 GGACCATATGATTCTAATTGGCGC 60.143 45.833 3.65 0.00 0.00 6.53
1828 3265 3.436704 ACCATATGATTCTAATTGGCGCG 59.563 43.478 0.00 0.00 0.00 6.86
1829 3266 3.181507 CCATATGATTCTAATTGGCGCGG 60.182 47.826 8.83 0.00 0.00 6.46
1830 3267 1.238439 ATGATTCTAATTGGCGCGGG 58.762 50.000 8.83 0.00 0.00 6.13
1831 3268 0.817634 TGATTCTAATTGGCGCGGGG 60.818 55.000 8.83 0.00 0.00 5.73
1832 3269 1.515521 GATTCTAATTGGCGCGGGGG 61.516 60.000 8.83 0.00 0.00 5.40
1833 3270 4.868116 TCTAATTGGCGCGGGGGC 62.868 66.667 8.83 11.83 42.69 5.80
1842 3279 4.161295 CGCGGGGGCATGAAGAGA 62.161 66.667 0.00 0.00 0.00 3.10
1843 3280 2.512896 GCGGGGGCATGAAGAGAT 59.487 61.111 0.00 0.00 0.00 2.75
1844 3281 1.599240 GCGGGGGCATGAAGAGATC 60.599 63.158 0.00 0.00 0.00 2.75
1845 3282 1.301244 CGGGGGCATGAAGAGATCG 60.301 63.158 0.00 0.00 0.00 3.69
1846 3283 1.748329 CGGGGGCATGAAGAGATCGA 61.748 60.000 0.00 0.00 0.00 3.59
1847 3284 0.034616 GGGGGCATGAAGAGATCGAG 59.965 60.000 0.00 0.00 0.00 4.04
1848 3285 0.755686 GGGGCATGAAGAGATCGAGT 59.244 55.000 0.00 0.00 0.00 4.18
1849 3286 1.139853 GGGGCATGAAGAGATCGAGTT 59.860 52.381 0.00 0.00 0.00 3.01
1850 3287 2.420687 GGGGCATGAAGAGATCGAGTTT 60.421 50.000 0.00 0.00 0.00 2.66
1851 3288 2.611292 GGGCATGAAGAGATCGAGTTTG 59.389 50.000 0.00 0.00 0.00 2.93
1852 3289 2.031437 GGCATGAAGAGATCGAGTTTGC 59.969 50.000 0.00 0.00 0.00 3.68
1853 3290 2.285486 GCATGAAGAGATCGAGTTTGCG 60.285 50.000 0.00 0.00 0.00 4.85
1854 3291 3.182182 CATGAAGAGATCGAGTTTGCGA 58.818 45.455 0.00 0.00 45.22 5.10
1855 3292 2.596452 TGAAGAGATCGAGTTTGCGAC 58.404 47.619 0.00 0.00 43.79 5.19
1856 3293 1.921230 GAAGAGATCGAGTTTGCGACC 59.079 52.381 0.00 0.00 43.79 4.79
1857 3294 0.888619 AGAGATCGAGTTTGCGACCA 59.111 50.000 0.00 0.00 43.79 4.02
1858 3295 0.992802 GAGATCGAGTTTGCGACCAC 59.007 55.000 0.00 0.00 43.79 4.16
1859 3296 0.603569 AGATCGAGTTTGCGACCACT 59.396 50.000 0.00 0.00 43.79 4.00
1860 3297 1.000955 AGATCGAGTTTGCGACCACTT 59.999 47.619 0.00 0.00 43.79 3.16
1861 3298 1.390463 GATCGAGTTTGCGACCACTTC 59.610 52.381 0.00 0.00 43.79 3.01
1862 3299 0.599204 TCGAGTTTGCGACCACTTCC 60.599 55.000 0.00 0.00 35.01 3.46
1863 3300 0.878523 CGAGTTTGCGACCACTTCCA 60.879 55.000 0.00 0.00 0.00 3.53
1864 3301 1.523758 GAGTTTGCGACCACTTCCAT 58.476 50.000 0.00 0.00 0.00 3.41
1865 3302 1.880027 GAGTTTGCGACCACTTCCATT 59.120 47.619 0.00 0.00 0.00 3.16
1866 3303 1.880027 AGTTTGCGACCACTTCCATTC 59.120 47.619 0.00 0.00 0.00 2.67
1867 3304 1.068541 GTTTGCGACCACTTCCATTCC 60.069 52.381 0.00 0.00 0.00 3.01
1868 3305 0.953471 TTGCGACCACTTCCATTCCG 60.953 55.000 0.00 0.00 0.00 4.30
1869 3306 1.375523 GCGACCACTTCCATTCCGT 60.376 57.895 0.00 0.00 0.00 4.69
1870 3307 1.359459 GCGACCACTTCCATTCCGTC 61.359 60.000 0.00 0.00 0.00 4.79
1871 3308 0.739813 CGACCACTTCCATTCCGTCC 60.740 60.000 0.00 0.00 0.00 4.79
1905 3342 4.077184 CGCCTTGGCGTGAGGGTA 62.077 66.667 24.03 0.00 34.75 3.69
1943 3380 6.577103 TGTGTCCAAACAAATATTGCTCAAA 58.423 32.000 0.00 0.00 37.08 2.69
1947 3384 9.770097 TGTCCAAACAAATATTGCTCAAATTAA 57.230 25.926 0.00 0.00 30.70 1.40
2175 3812 3.307762 GGAAGTACCAAGAGCAGGAACAT 60.308 47.826 0.00 0.00 38.79 2.71
2260 3898 1.285578 GCTGCCTTCTCGATCAACTC 58.714 55.000 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 78 4.474651 TGACTGGGTGGACAGATATTTCAT 59.525 41.667 0.00 0.00 40.97 2.57
96 97 1.347050 AGCTGTGAGAATGCACTGACT 59.653 47.619 0.00 0.00 39.27 3.41
97 98 1.731160 GAGCTGTGAGAATGCACTGAC 59.269 52.381 0.00 0.00 39.27 3.51
98 99 1.345415 TGAGCTGTGAGAATGCACTGA 59.655 47.619 0.00 0.00 39.27 3.41
99 100 1.804601 TGAGCTGTGAGAATGCACTG 58.195 50.000 0.00 0.00 39.49 3.66
121 122 3.005554 CGATGAGAAGTGGATGTTGCTT 58.994 45.455 0.00 0.00 0.00 3.91
125 126 3.244561 ACAACCGATGAGAAGTGGATGTT 60.245 43.478 0.00 0.00 34.29 2.71
140 141 2.047655 CGCTTGGGCTACAACCGA 60.048 61.111 4.19 0.00 39.84 4.69
144 145 1.557832 AGGTATTCGCTTGGGCTACAA 59.442 47.619 0.00 0.00 37.55 2.41
198 199 5.453339 CCCGATTAATTGAGAAGTGCCTCTA 60.453 44.000 4.10 0.00 34.38 2.43
202 203 2.033424 GCCCGATTAATTGAGAAGTGCC 59.967 50.000 4.10 0.00 0.00 5.01
205 206 3.261981 ACGCCCGATTAATTGAGAAGT 57.738 42.857 4.10 0.00 0.00 3.01
334 346 0.111089 CAGACACTTCTTGTTCGCGC 60.111 55.000 0.00 0.00 39.17 6.86
361 373 0.546122 AGTTGTGTTCCAGTGAGCCA 59.454 50.000 0.00 0.00 0.00 4.75
517 538 4.184629 CACTACTTTTGAATCGGAGGGAG 58.815 47.826 0.00 0.00 0.00 4.30
518 539 3.581332 ACACTACTTTTGAATCGGAGGGA 59.419 43.478 0.00 0.00 0.00 4.20
520 541 4.378459 GCAACACTACTTTTGAATCGGAGG 60.378 45.833 0.00 0.00 0.00 4.30
523 544 4.024048 ACTGCAACACTACTTTTGAATCGG 60.024 41.667 0.00 0.00 0.00 4.18
525 546 7.275560 ACAAAACTGCAACACTACTTTTGAATC 59.724 33.333 7.48 0.00 34.29 2.52
526 547 7.096551 ACAAAACTGCAACACTACTTTTGAAT 58.903 30.769 7.48 0.00 34.29 2.57
529 550 7.985634 ATACAAAACTGCAACACTACTTTTG 57.014 32.000 0.00 0.00 35.61 2.44
530 551 8.247562 TCAATACAAAACTGCAACACTACTTTT 58.752 29.630 0.00 0.00 0.00 2.27
531 552 7.767261 TCAATACAAAACTGCAACACTACTTT 58.233 30.769 0.00 0.00 0.00 2.66
532 553 7.328277 TCAATACAAAACTGCAACACTACTT 57.672 32.000 0.00 0.00 0.00 2.24
533 554 6.017109 CCTCAATACAAAACTGCAACACTACT 60.017 38.462 0.00 0.00 0.00 2.57
534 555 6.142817 CCTCAATACAAAACTGCAACACTAC 58.857 40.000 0.00 0.00 0.00 2.73
535 556 5.825679 ACCTCAATACAAAACTGCAACACTA 59.174 36.000 0.00 0.00 0.00 2.74
624 713 9.391006 TGAAGTTAGTGTTTTGTTTAGATCTGT 57.609 29.630 5.18 0.00 0.00 3.41
646 735 5.290885 CACATTTGCAACCATCATCATGAAG 59.709 40.000 0.00 0.00 30.57 3.02
647 736 5.172205 CACATTTGCAACCATCATCATGAA 58.828 37.500 0.00 0.00 30.57 2.57
648 737 4.382147 CCACATTTGCAACCATCATCATGA 60.382 41.667 0.00 0.00 30.57 3.07
650 739 3.516300 ACCACATTTGCAACCATCATCAT 59.484 39.130 0.00 0.00 0.00 2.45
683 772 9.581289 AACACTAGTATTATCTACTGCTCTGAT 57.419 33.333 0.00 0.00 0.00 2.90
705 794 9.952188 ACAAGAATTCTTTAGCTTTCTAAACAC 57.048 29.630 18.16 0.00 39.23 3.32
825 927 3.249559 GCTAACAATAGACCTGCATCTGC 59.750 47.826 0.00 0.00 42.50 4.26
826 928 3.812053 GGCTAACAATAGACCTGCATCTG 59.188 47.826 0.00 0.00 30.16 2.90
827 929 3.713764 AGGCTAACAATAGACCTGCATCT 59.286 43.478 0.00 0.00 37.97 2.90
828 930 3.812053 CAGGCTAACAATAGACCTGCATC 59.188 47.826 10.96 0.00 41.82 3.91
900 1016 2.289002 GGATTCAGCTTGCTCATAACGG 59.711 50.000 0.00 0.00 0.00 4.44
935 1051 1.233285 GCTGAGGTGTGGAAGTGCAG 61.233 60.000 0.00 0.00 0.00 4.41
936 1052 1.227943 GCTGAGGTGTGGAAGTGCA 60.228 57.895 0.00 0.00 0.00 4.57
937 1053 1.072159 AGCTGAGGTGTGGAAGTGC 59.928 57.895 0.00 0.00 0.00 4.40
938 1054 0.394192 TCAGCTGAGGTGTGGAAGTG 59.606 55.000 13.74 0.00 32.43 3.16
939 1055 1.131638 TTCAGCTGAGGTGTGGAAGT 58.868 50.000 17.43 0.00 32.43 3.01
940 1056 1.876156 GTTTCAGCTGAGGTGTGGAAG 59.124 52.381 17.43 0.00 32.43 3.46
943 1059 1.202687 TCAGTTTCAGCTGAGGTGTGG 60.203 52.381 17.43 6.21 40.23 4.17
1101 1269 0.179032 ACAGGTGGATGTGCGTGAAA 60.179 50.000 0.00 0.00 30.46 2.69
1102 1270 0.682292 TACAGGTGGATGTGCGTGAA 59.318 50.000 0.00 0.00 34.56 3.18
1607 3044 7.074653 CCTGGCCAGGTTTAGTATATTTAGA 57.925 40.000 39.52 0.00 43.61 2.10
1651 3088 8.289618 CCGATTTTGACTGATAAGAAAAAGTCA 58.710 33.333 0.40 0.40 45.43 3.41
1652 3089 8.504005 TCCGATTTTGACTGATAAGAAAAAGTC 58.496 33.333 0.00 0.00 39.59 3.01
1653 3090 8.290325 GTCCGATTTTGACTGATAAGAAAAAGT 58.710 33.333 0.00 0.00 0.00 2.66
1654 3091 7.750903 GGTCCGATTTTGACTGATAAGAAAAAG 59.249 37.037 0.00 0.00 33.22 2.27
1655 3092 7.229707 TGGTCCGATTTTGACTGATAAGAAAAA 59.770 33.333 0.00 0.00 33.22 1.94
1656 3093 6.712998 TGGTCCGATTTTGACTGATAAGAAAA 59.287 34.615 0.00 0.00 33.22 2.29
1657 3094 6.234920 TGGTCCGATTTTGACTGATAAGAAA 58.765 36.000 0.00 0.00 33.22 2.52
1658 3095 5.800296 TGGTCCGATTTTGACTGATAAGAA 58.200 37.500 0.00 0.00 33.22 2.52
1659 3096 5.414789 TGGTCCGATTTTGACTGATAAGA 57.585 39.130 0.00 0.00 33.22 2.10
1660 3097 6.458751 CCATTGGTCCGATTTTGACTGATAAG 60.459 42.308 0.00 0.00 33.22 1.73
1661 3098 5.356751 CCATTGGTCCGATTTTGACTGATAA 59.643 40.000 0.00 0.00 33.22 1.75
1662 3099 4.881273 CCATTGGTCCGATTTTGACTGATA 59.119 41.667 0.00 0.00 33.22 2.15
1663 3100 3.696051 CCATTGGTCCGATTTTGACTGAT 59.304 43.478 0.00 0.00 33.22 2.90
1664 3101 3.081061 CCATTGGTCCGATTTTGACTGA 58.919 45.455 0.00 0.00 33.22 3.41
1665 3102 2.164219 CCCATTGGTCCGATTTTGACTG 59.836 50.000 1.20 0.00 33.22 3.51
1666 3103 2.225017 ACCCATTGGTCCGATTTTGACT 60.225 45.455 1.20 0.00 43.06 3.41
1667 3104 2.094752 CACCCATTGGTCCGATTTTGAC 60.095 50.000 1.20 0.00 45.57 3.18
1668 3105 2.166829 CACCCATTGGTCCGATTTTGA 58.833 47.619 1.20 0.00 45.57 2.69
1669 3106 2.164219 CTCACCCATTGGTCCGATTTTG 59.836 50.000 1.20 0.00 45.57 2.44
1670 3107 2.446435 CTCACCCATTGGTCCGATTTT 58.554 47.619 1.20 0.00 45.57 1.82
1671 3108 1.955208 GCTCACCCATTGGTCCGATTT 60.955 52.381 1.20 0.00 45.57 2.17
1672 3109 0.394352 GCTCACCCATTGGTCCGATT 60.394 55.000 1.20 0.00 45.57 3.34
1673 3110 1.224592 GCTCACCCATTGGTCCGAT 59.775 57.895 1.20 0.00 45.57 4.18
1674 3111 2.668632 GCTCACCCATTGGTCCGA 59.331 61.111 1.20 0.00 45.57 4.55
1675 3112 2.819595 CGCTCACCCATTGGTCCG 60.820 66.667 1.20 0.00 45.57 4.79
1676 3113 2.438434 CCGCTCACCCATTGGTCC 60.438 66.667 1.20 0.00 45.57 4.46
1677 3114 3.134127 GCCGCTCACCCATTGGTC 61.134 66.667 1.20 0.00 45.57 4.02
1679 3116 3.443045 GTGCCGCTCACCCATTGG 61.443 66.667 0.00 0.00 39.79 3.16
1680 3117 3.803082 CGTGCCGCTCACCCATTG 61.803 66.667 0.00 0.00 42.69 2.82
1681 3118 4.329545 ACGTGCCGCTCACCCATT 62.330 61.111 0.00 0.00 42.69 3.16
1686 3123 1.837538 TTAAAGCACGTGCCGCTCAC 61.838 55.000 35.51 7.99 43.38 3.51
1687 3124 0.953471 ATTAAAGCACGTGCCGCTCA 60.953 50.000 35.51 17.32 43.38 4.26
1688 3125 0.521242 CATTAAAGCACGTGCCGCTC 60.521 55.000 35.51 9.58 43.38 5.03
1689 3126 1.501741 CATTAAAGCACGTGCCGCT 59.498 52.632 35.51 22.28 43.38 5.52
1690 3127 1.514014 CCATTAAAGCACGTGCCGC 60.514 57.895 35.51 13.00 43.38 6.53
1691 3128 1.136565 CCCATTAAAGCACGTGCCG 59.863 57.895 35.51 17.08 43.38 5.69
1692 3129 0.963355 TCCCCATTAAAGCACGTGCC 60.963 55.000 35.51 18.54 43.38 5.01
1693 3130 1.102978 ATCCCCATTAAAGCACGTGC 58.897 50.000 32.79 32.79 42.49 5.34
1694 3131 3.275143 TGTATCCCCATTAAAGCACGTG 58.725 45.455 12.28 12.28 0.00 4.49
1695 3132 3.541632 CTGTATCCCCATTAAAGCACGT 58.458 45.455 0.00 0.00 0.00 4.49
1696 3133 2.290641 GCTGTATCCCCATTAAAGCACG 59.709 50.000 0.00 0.00 0.00 5.34
1697 3134 2.623416 GGCTGTATCCCCATTAAAGCAC 59.377 50.000 0.00 0.00 0.00 4.40
1698 3135 2.243478 TGGCTGTATCCCCATTAAAGCA 59.757 45.455 0.00 0.00 0.00 3.91
1699 3136 2.887152 CTGGCTGTATCCCCATTAAAGC 59.113 50.000 0.00 0.00 0.00 3.51
1700 3137 3.117512 ACCTGGCTGTATCCCCATTAAAG 60.118 47.826 0.00 0.00 0.00 1.85
1701 3138 2.856231 ACCTGGCTGTATCCCCATTAAA 59.144 45.455 0.00 0.00 0.00 1.52
1702 3139 2.498441 ACCTGGCTGTATCCCCATTAA 58.502 47.619 0.00 0.00 0.00 1.40
1703 3140 2.206322 ACCTGGCTGTATCCCCATTA 57.794 50.000 0.00 0.00 0.00 1.90
1704 3141 2.206322 TACCTGGCTGTATCCCCATT 57.794 50.000 0.00 0.00 0.00 3.16
1705 3142 1.988107 CATACCTGGCTGTATCCCCAT 59.012 52.381 0.00 0.00 28.98 4.00
1706 3143 1.434188 CATACCTGGCTGTATCCCCA 58.566 55.000 0.00 0.00 28.98 4.96
1707 3144 0.036875 GCATACCTGGCTGTATCCCC 59.963 60.000 0.00 0.00 28.98 4.81
1708 3145 0.764890 TGCATACCTGGCTGTATCCC 59.235 55.000 0.00 0.00 28.98 3.85
1709 3146 1.879796 GCTGCATACCTGGCTGTATCC 60.880 57.143 0.00 0.00 33.36 2.59
1710 3147 1.071385 AGCTGCATACCTGGCTGTATC 59.929 52.381 1.02 0.00 33.50 2.24
1711 3148 1.135094 AGCTGCATACCTGGCTGTAT 58.865 50.000 1.02 0.00 33.50 2.29
1712 3149 0.178767 CAGCTGCATACCTGGCTGTA 59.821 55.000 13.60 0.00 44.69 2.74
1713 3150 1.077930 CAGCTGCATACCTGGCTGT 60.078 57.895 13.60 0.00 44.69 4.40
1714 3151 3.823402 CAGCTGCATACCTGGCTG 58.177 61.111 0.00 8.73 44.45 4.85
1715 3152 1.077930 CACAGCTGCATACCTGGCT 60.078 57.895 15.27 2.55 33.43 4.75
1716 3153 1.377725 ACACAGCTGCATACCTGGC 60.378 57.895 15.27 0.28 33.43 4.85
1717 3154 1.651240 GCACACAGCTGCATACCTGG 61.651 60.000 15.27 0.00 41.15 4.45
1718 3155 1.798735 GCACACAGCTGCATACCTG 59.201 57.895 15.27 5.86 41.15 4.00
1719 3156 1.742880 CGCACACAGCTGCATACCT 60.743 57.895 15.27 0.00 42.61 3.08
1720 3157 2.034879 ACGCACACAGCTGCATACC 61.035 57.895 15.27 0.00 42.61 2.73
1721 3158 1.133253 CACGCACACAGCTGCATAC 59.867 57.895 15.27 0.00 42.61 2.39
1722 3159 0.037790 TACACGCACACAGCTGCATA 60.038 50.000 15.27 0.00 42.61 3.14
1723 3160 1.293963 CTACACGCACACAGCTGCAT 61.294 55.000 15.27 0.00 42.61 3.96
1724 3161 1.955663 CTACACGCACACAGCTGCA 60.956 57.895 15.27 0.00 42.61 4.41
1725 3162 2.856032 CTACACGCACACAGCTGC 59.144 61.111 15.27 0.00 42.61 5.25
1726 3163 2.856032 GCTACACGCACACAGCTG 59.144 61.111 13.48 13.48 42.61 4.24
1727 3164 2.693250 TTCGCTACACGCACACAGCT 62.693 55.000 0.00 0.00 43.23 4.24
1728 3165 1.626654 ATTCGCTACACGCACACAGC 61.627 55.000 0.00 0.00 43.23 4.40
1729 3166 0.093535 CATTCGCTACACGCACACAG 59.906 55.000 0.00 0.00 43.23 3.66
1730 3167 1.896339 GCATTCGCTACACGCACACA 61.896 55.000 0.00 0.00 43.23 3.72
1731 3168 1.225745 GCATTCGCTACACGCACAC 60.226 57.895 0.00 0.00 43.23 3.82
1732 3169 2.387445 GGCATTCGCTACACGCACA 61.387 57.895 0.00 0.00 43.23 4.57
1733 3170 2.399611 GGCATTCGCTACACGCAC 59.600 61.111 0.00 0.00 43.23 5.34
1734 3171 3.185365 CGGCATTCGCTACACGCA 61.185 61.111 0.00 0.00 43.23 5.24
1743 3180 0.171007 ATGTTTTCCAGCGGCATTCG 59.829 50.000 1.45 0.00 42.76 3.34
1744 3181 3.502191 TTATGTTTTCCAGCGGCATTC 57.498 42.857 1.45 0.00 0.00 2.67
1745 3182 3.951775 TTTATGTTTTCCAGCGGCATT 57.048 38.095 1.45 0.00 0.00 3.56
1746 3183 4.470334 AATTTATGTTTTCCAGCGGCAT 57.530 36.364 1.45 0.00 0.00 4.40
1747 3184 3.951775 AATTTATGTTTTCCAGCGGCA 57.048 38.095 1.45 0.00 0.00 5.69
1748 3185 4.803613 CCTTAATTTATGTTTTCCAGCGGC 59.196 41.667 0.00 0.00 0.00 6.53
1749 3186 6.202516 TCCTTAATTTATGTTTTCCAGCGG 57.797 37.500 0.00 0.00 0.00 5.52
1750 3187 8.702163 AAATCCTTAATTTATGTTTTCCAGCG 57.298 30.769 0.00 0.00 35.77 5.18
1766 3203 9.174166 GCAACCAATAGAGAACTAAATCCTTAA 57.826 33.333 0.00 0.00 32.04 1.85
1767 3204 8.325787 TGCAACCAATAGAGAACTAAATCCTTA 58.674 33.333 0.00 0.00 32.04 2.69
1768 3205 7.175104 TGCAACCAATAGAGAACTAAATCCTT 58.825 34.615 0.00 0.00 32.04 3.36
1769 3206 6.721318 TGCAACCAATAGAGAACTAAATCCT 58.279 36.000 0.00 0.00 32.04 3.24
1770 3207 7.067494 ACATGCAACCAATAGAGAACTAAATCC 59.933 37.037 0.00 0.00 32.04 3.01
1771 3208 7.989826 ACATGCAACCAATAGAGAACTAAATC 58.010 34.615 0.00 0.00 32.04 2.17
1772 3209 7.067494 GGACATGCAACCAATAGAGAACTAAAT 59.933 37.037 0.00 0.00 32.04 1.40
1773 3210 6.374333 GGACATGCAACCAATAGAGAACTAAA 59.626 38.462 0.00 0.00 32.04 1.85
1774 3211 5.880332 GGACATGCAACCAATAGAGAACTAA 59.120 40.000 0.00 0.00 32.04 2.24
1775 3212 5.045942 TGGACATGCAACCAATAGAGAACTA 60.046 40.000 7.93 0.00 32.93 2.24
1776 3213 4.263462 TGGACATGCAACCAATAGAGAACT 60.263 41.667 7.93 0.00 32.93 3.01
1777 3214 4.009675 TGGACATGCAACCAATAGAGAAC 58.990 43.478 7.93 0.00 32.93 3.01
1778 3215 4.299586 TGGACATGCAACCAATAGAGAA 57.700 40.909 7.93 0.00 32.93 2.87
1779 3216 3.998913 TGGACATGCAACCAATAGAGA 57.001 42.857 7.93 0.00 32.93 3.10
1780 3217 4.563337 CATGGACATGCAACCAATAGAG 57.437 45.455 13.13 1.17 39.69 2.43
1796 3233 3.654321 AGAATCATATGGTCCTGCATGGA 59.346 43.478 2.13 1.25 43.86 3.41
1797 3234 4.030314 AGAATCATATGGTCCTGCATGG 57.970 45.455 2.13 0.00 37.10 3.66
1798 3235 7.362660 CCAATTAGAATCATATGGTCCTGCATG 60.363 40.741 2.13 0.00 0.00 4.06
1799 3236 6.662234 CCAATTAGAATCATATGGTCCTGCAT 59.338 38.462 2.13 0.00 0.00 3.96
1800 3237 6.005823 CCAATTAGAATCATATGGTCCTGCA 58.994 40.000 2.13 0.00 0.00 4.41
1801 3238 5.105997 GCCAATTAGAATCATATGGTCCTGC 60.106 44.000 2.13 0.00 0.00 4.85
1802 3239 5.122869 CGCCAATTAGAATCATATGGTCCTG 59.877 44.000 2.13 0.00 0.00 3.86
1803 3240 5.248640 CGCCAATTAGAATCATATGGTCCT 58.751 41.667 2.13 0.00 0.00 3.85
1804 3241 4.142600 GCGCCAATTAGAATCATATGGTCC 60.143 45.833 2.13 0.00 0.00 4.46
1805 3242 4.436050 CGCGCCAATTAGAATCATATGGTC 60.436 45.833 0.00 1.13 0.00 4.02
1806 3243 3.436704 CGCGCCAATTAGAATCATATGGT 59.563 43.478 0.00 0.00 0.00 3.55
1807 3244 3.181507 CCGCGCCAATTAGAATCATATGG 60.182 47.826 0.00 0.00 0.00 2.74
1808 3245 3.181507 CCCGCGCCAATTAGAATCATATG 60.182 47.826 0.00 0.00 0.00 1.78
1809 3246 3.009723 CCCGCGCCAATTAGAATCATAT 58.990 45.455 0.00 0.00 0.00 1.78
1810 3247 2.422597 CCCGCGCCAATTAGAATCATA 58.577 47.619 0.00 0.00 0.00 2.15
1811 3248 1.238439 CCCGCGCCAATTAGAATCAT 58.762 50.000 0.00 0.00 0.00 2.45
1812 3249 0.817634 CCCCGCGCCAATTAGAATCA 60.818 55.000 0.00 0.00 0.00 2.57
1813 3250 1.515521 CCCCCGCGCCAATTAGAATC 61.516 60.000 0.00 0.00 0.00 2.52
1814 3251 1.528309 CCCCCGCGCCAATTAGAAT 60.528 57.895 0.00 0.00 0.00 2.40
1815 3252 2.124487 CCCCCGCGCCAATTAGAA 60.124 61.111 0.00 0.00 0.00 2.10
1816 3253 4.868116 GCCCCCGCGCCAATTAGA 62.868 66.667 0.00 0.00 0.00 2.10
1818 3255 4.514585 ATGCCCCCGCGCCAATTA 62.515 61.111 0.00 0.00 38.08 1.40
1825 3262 3.466791 ATCTCTTCATGCCCCCGCG 62.467 63.158 0.00 0.00 38.08 6.46
1826 3263 1.599240 GATCTCTTCATGCCCCCGC 60.599 63.158 0.00 0.00 0.00 6.13
1827 3264 1.301244 CGATCTCTTCATGCCCCCG 60.301 63.158 0.00 0.00 0.00 5.73
1828 3265 0.034616 CTCGATCTCTTCATGCCCCC 59.965 60.000 0.00 0.00 0.00 5.40
1829 3266 0.755686 ACTCGATCTCTTCATGCCCC 59.244 55.000 0.00 0.00 0.00 5.80
1830 3267 2.611225 AACTCGATCTCTTCATGCCC 57.389 50.000 0.00 0.00 0.00 5.36
1831 3268 2.031437 GCAAACTCGATCTCTTCATGCC 59.969 50.000 0.00 0.00 0.00 4.40
1832 3269 2.285486 CGCAAACTCGATCTCTTCATGC 60.285 50.000 0.00 0.00 0.00 4.06
1833 3270 3.000277 GTCGCAAACTCGATCTCTTCATG 60.000 47.826 0.00 0.00 40.84 3.07
1834 3271 3.182967 GTCGCAAACTCGATCTCTTCAT 58.817 45.455 0.00 0.00 40.84 2.57
1835 3272 2.596452 GTCGCAAACTCGATCTCTTCA 58.404 47.619 0.00 0.00 40.84 3.02
1836 3273 1.921230 GGTCGCAAACTCGATCTCTTC 59.079 52.381 0.00 0.00 40.84 2.87
1837 3274 1.272490 TGGTCGCAAACTCGATCTCTT 59.728 47.619 0.00 0.00 40.07 2.85
1838 3275 0.888619 TGGTCGCAAACTCGATCTCT 59.111 50.000 0.00 0.00 40.07 3.10
1839 3276 0.992802 GTGGTCGCAAACTCGATCTC 59.007 55.000 0.00 0.00 40.07 2.75
1840 3277 0.603569 AGTGGTCGCAAACTCGATCT 59.396 50.000 0.00 0.00 40.07 2.75
1841 3278 1.390463 GAAGTGGTCGCAAACTCGATC 59.610 52.381 0.00 0.00 40.84 3.69
1842 3279 1.429463 GAAGTGGTCGCAAACTCGAT 58.571 50.000 0.00 0.00 40.84 3.59
1843 3280 0.599204 GGAAGTGGTCGCAAACTCGA 60.599 55.000 0.00 0.00 35.95 4.04
1844 3281 0.878523 TGGAAGTGGTCGCAAACTCG 60.879 55.000 0.00 0.00 0.00 4.18
1845 3282 1.523758 ATGGAAGTGGTCGCAAACTC 58.476 50.000 0.00 0.00 0.00 3.01
1846 3283 1.880027 GAATGGAAGTGGTCGCAAACT 59.120 47.619 0.00 0.00 0.00 2.66
1847 3284 1.068541 GGAATGGAAGTGGTCGCAAAC 60.069 52.381 0.00 0.00 0.00 2.93
1848 3285 1.243902 GGAATGGAAGTGGTCGCAAA 58.756 50.000 0.00 0.00 0.00 3.68
1849 3286 0.953471 CGGAATGGAAGTGGTCGCAA 60.953 55.000 0.00 0.00 0.00 4.85
1850 3287 1.375396 CGGAATGGAAGTGGTCGCA 60.375 57.895 0.00 0.00 0.00 5.10
1851 3288 1.359459 GACGGAATGGAAGTGGTCGC 61.359 60.000 0.00 0.00 0.00 5.19
1852 3289 0.739813 GGACGGAATGGAAGTGGTCG 60.740 60.000 0.00 0.00 0.00 4.79
1853 3290 0.613777 AGGACGGAATGGAAGTGGTC 59.386 55.000 0.00 0.00 0.00 4.02
1854 3291 1.553704 GTAGGACGGAATGGAAGTGGT 59.446 52.381 0.00 0.00 0.00 4.16
1855 3292 1.831736 AGTAGGACGGAATGGAAGTGG 59.168 52.381 0.00 0.00 0.00 4.00
1856 3293 3.952323 TCTAGTAGGACGGAATGGAAGTG 59.048 47.826 0.00 0.00 0.00 3.16
1857 3294 4.246712 TCTAGTAGGACGGAATGGAAGT 57.753 45.455 0.00 0.00 0.00 3.01
1858 3295 4.083217 CGATCTAGTAGGACGGAATGGAAG 60.083 50.000 0.00 0.00 0.00 3.46
1859 3296 3.819337 CGATCTAGTAGGACGGAATGGAA 59.181 47.826 0.00 0.00 0.00 3.53
1860 3297 3.409570 CGATCTAGTAGGACGGAATGGA 58.590 50.000 0.00 0.00 0.00 3.41
1861 3298 2.488545 CCGATCTAGTAGGACGGAATGG 59.511 54.545 22.24 1.23 45.31 3.16
1862 3299 3.833545 CCGATCTAGTAGGACGGAATG 57.166 52.381 22.24 4.32 45.31 2.67
1866 3303 2.032204 CGTTTCCGATCTAGTAGGACGG 60.032 54.545 21.33 21.33 44.09 4.79
1867 3304 2.601741 GCGTTTCCGATCTAGTAGGACG 60.602 54.545 0.00 3.93 35.63 4.79
1868 3305 2.601741 CGCGTTTCCGATCTAGTAGGAC 60.602 54.545 0.00 0.00 35.63 3.85
1869 3306 1.600957 CGCGTTTCCGATCTAGTAGGA 59.399 52.381 0.00 0.00 35.63 2.94
1870 3307 1.925068 GCGCGTTTCCGATCTAGTAGG 60.925 57.143 8.43 0.00 35.63 3.18
1871 3308 1.396644 GCGCGTTTCCGATCTAGTAG 58.603 55.000 8.43 0.00 35.63 2.57
1898 3335 0.759812 TGTTGTGACCGGTACCCTCA 60.760 55.000 7.34 4.50 0.00 3.86
1943 3380 5.069516 TCGCTAAACCCGACTTCCTATTAAT 59.930 40.000 0.00 0.00 0.00 1.40
1947 3384 2.381911 TCGCTAAACCCGACTTCCTAT 58.618 47.619 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.