Multiple sequence alignment - TraesCS1A01G367300

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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 TraesCS1A01G367300 chr1A 100.000 5116 0 0 1 5116 545887238 545892353 0.000000e+00 9448
1 TraesCS1A01G367300 chr1A 84.536 194 24 6 4606 4796 117885721 117885531 2.430000e-43 187
2 TraesCS1A01G367300 chr1A 85.876 177 16 8 97 268 545867279 545867451 4.070000e-41 180
3 TraesCS1A01G367300 chr1D 92.263 3477 180 51 1 3442 451128056 451131478 0.000000e+00 4848
4 TraesCS1A01G367300 chr1D 88.774 1639 78 38 3446 5039 451131518 451133095 0.000000e+00 1910
5 TraesCS1A01G367300 chr1D 94.215 121 7 0 144 264 451075480 451075600 8.750000e-43 185
6 TraesCS1A01G367300 chr1D 83.598 189 24 6 4606 4789 111413387 111413201 2.450000e-38 171
7 TraesCS1A01G367300 chr1D 83.333 174 22 5 97 268 451068262 451068430 2.470000e-33 154
8 TraesCS1A01G367300 chr1D 96.970 66 2 0 114 179 451114939 451115004 1.510000e-20 111
9 TraesCS1A01G367300 chr1B 94.823 1719 63 10 983 2692 619416871 619418572 0.000000e+00 2658
10 TraesCS1A01G367300 chr1B 94.545 605 23 6 3446 4045 619419544 619420143 0.000000e+00 926
11 TraesCS1A01G367300 chr1B 96.897 419 12 1 2696 3114 619418702 619419119 0.000000e+00 701
12 TraesCS1A01G367300 chr1B 84.690 516 48 14 390 882 619416334 619416841 2.140000e-133 486
13 TraesCS1A01G367300 chr1B 94.754 305 13 2 3141 3443 619419202 619419505 6.000000e-129 472
14 TraesCS1A01G367300 chr1B 92.903 310 12 4 4043 4348 619420171 619420474 4.700000e-120 442
15 TraesCS1A01G367300 chr1B 93.676 253 11 2 4610 4858 619420794 619421045 1.740000e-99 374
16 TraesCS1A01G367300 chr1B 90.592 287 17 6 1 284 619416000 619416279 6.260000e-99 372
17 TraesCS1A01G367300 chr1B 93.820 178 10 1 4347 4524 619420578 619420754 3.040000e-67 267
18 TraesCS1A01G367300 chr1B 98.913 92 1 0 2730 2821 619419114 619419205 1.140000e-36 165
19 TraesCS1A01G367300 chr1B 85.430 151 22 0 114 264 619398682 619398832 1.910000e-34 158
20 TraesCS1A01G367300 chr7D 80.383 1565 206 63 2516 4040 44294055 44295558 0.000000e+00 1096
21 TraesCS1A01G367300 chr7D 85.398 226 27 3 1233 1452 44292650 44292875 3.980000e-56 230
22 TraesCS1A01G367300 chr7D 83.916 143 21 2 1062 1203 44292342 44292483 8.940000e-28 135
23 TraesCS1A01G367300 chr4A 84.549 932 113 21 2516 3434 655253177 655254090 0.000000e+00 894
24 TraesCS1A01G367300 chr4A 77.893 579 83 30 3473 4040 655254295 655254839 8.270000e-83 318
25 TraesCS1A01G367300 chr4A 86.638 232 24 4 1228 1452 655251737 655251968 3.060000e-62 250
26 TraesCS1A01G367300 chr4A 87.963 108 13 0 1087 1194 655251457 655251564 1.500000e-25 128
27 TraesCS1A01G367300 chr7A 81.368 1111 159 35 2263 3332 46711916 46713019 0.000000e+00 861
28 TraesCS1A01G367300 chr7A 76.788 685 88 49 3382 4040 46713029 46713668 8.270000e-83 318
29 TraesCS1A01G367300 chr7A 85.841 226 26 3 1233 1452 46710837 46711062 8.560000e-58 235
30 TraesCS1A01G367300 chr7A 83.916 143 21 2 1062 1203 46710529 46710670 8.940000e-28 135
31 TraesCS1A01G367300 chr5D 84.100 239 25 8 4629 4858 255564129 255564363 8.620000e-53 219
32 TraesCS1A01G367300 chr5D 81.116 233 31 12 4629 4855 255564437 255564662 1.890000e-39 174
33 TraesCS1A01G367300 chr5B 79.399 233 32 11 4629 4858 286701219 286701438 3.190000e-32 150
34 TraesCS1A01G367300 chr5B 79.565 230 32 11 4629 4855 286701503 286701720 3.190000e-32 150
35 TraesCS1A01G367300 chr5A 79.130 230 35 9 4629 4856 338846863 338847081 4.130000e-31 147
36 TraesCS1A01G367300 chr2D 93.827 81 4 1 110 190 582658384 582658463 2.500000e-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 TraesCS1A01G367300 chr1A 545887238 545892353 5115 False 9448.00 9448 100.000000 1 5116 1 chr1A.!!$F2 5115
1 TraesCS1A01G367300 chr1D 451128056 451133095 5039 False 3379.00 4848 90.518500 1 5039 2 chr1D.!!$F4 5038
2 TraesCS1A01G367300 chr1B 619416000 619421045 5045 False 686.30 2658 93.561300 1 4858 10 chr1B.!!$F2 4857
3 TraesCS1A01G367300 chr7D 44292342 44295558 3216 False 487.00 1096 83.232333 1062 4040 3 chr7D.!!$F1 2978
4 TraesCS1A01G367300 chr4A 655251457 655254839 3382 False 397.50 894 84.260750 1087 4040 4 chr4A.!!$F1 2953
5 TraesCS1A01G367300 chr7A 46710529 46713668 3139 False 387.25 861 81.978250 1062 4040 4 chr7A.!!$F1 2978

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
235 237 0.032130 ATATGCCGGTCTACGCTGTG 59.968 55.000 1.90 0.00 42.52 3.66 F
686 701 0.395686 CATCTGACCGGATCTGGCAT 59.604 55.000 21.17 1.25 0.00 4.40 F
687 702 0.395686 ATCTGACCGGATCTGGCATG 59.604 55.000 21.17 10.38 0.00 4.06 F
882 913 1.003118 GAGGGCCAATGCGGATGTATA 59.997 52.381 6.18 0.00 38.85 1.47 F
1491 1672 1.226746 GTAGTCGTGTTTGCTGGCTT 58.773 50.000 0.00 0.00 0.00 4.35 F
2728 3246 0.036875 AGCCCCTGAGTTGTTAGCAC 59.963 55.000 0.00 0.00 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1284 1458 0.181114 TCCACTGCTGTGCTTCTTGT 59.819 50.0 17.57 0.0 42.54 3.16 R
2381 2688 1.042229 AAAGCACAAATCCTGCAGCA 58.958 45.0 8.66 0.0 37.08 4.41 R
2552 2943 7.670009 CCAAGCAATGGTTTTCAATTTCATA 57.330 32.0 0.00 0.0 44.85 2.15 R
2694 3086 0.537188 GGGCTCCATCAAGTCGAAGA 59.463 55.0 0.00 0.0 0.00 2.87 R
3479 4262 1.394266 AACACAAGGGGTTGCAGCAG 61.394 55.0 2.05 0.0 0.00 4.24 R
4250 5083 0.036105 TGCTACACATGCCACAGGAG 60.036 55.0 0.00 0.0 0.00 3.69 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
36 38 4.980805 TCGTGCACAGGGAACGCC 62.981 66.667 18.64 0.00 37.24 5.68
47 49 0.763035 GGGAACGCCATGGTATAGGT 59.237 55.000 14.67 0.88 35.15 3.08
48 50 1.972795 GGGAACGCCATGGTATAGGTA 59.027 52.381 14.67 0.00 35.15 3.08
121 123 4.503734 CGTATAAATAAGCCCACGAAACGA 59.496 41.667 0.00 0.00 0.00 3.85
154 156 4.191015 CCCCCTTTAGCCCTCCGC 62.191 72.222 0.00 0.00 37.98 5.54
232 234 1.811359 GTCTATATGCCGGTCTACGCT 59.189 52.381 1.90 0.00 42.52 5.07
235 237 0.032130 ATATGCCGGTCTACGCTGTG 59.968 55.000 1.90 0.00 42.52 3.66
241 243 1.153745 GGTCTACGCTGTGCTCAGG 60.154 63.158 16.98 9.70 41.57 3.86
321 326 2.290916 GGCGAGCTTAATTAAAGGGAGC 59.709 50.000 0.00 0.00 35.58 4.70
353 358 2.396157 CCGCGTAAAGGAACCAGCC 61.396 63.158 4.92 0.00 0.00 4.85
354 359 2.736682 CGCGTAAAGGAACCAGCCG 61.737 63.158 0.00 0.00 0.00 5.52
480 485 3.771160 ATCCCGTGGTCTGTCGCC 61.771 66.667 0.00 0.00 0.00 5.54
488 493 4.451150 GTCTGTCGCCCCGCATCA 62.451 66.667 0.00 0.00 0.00 3.07
490 495 2.514592 CTGTCGCCCCGCATCATT 60.515 61.111 0.00 0.00 0.00 2.57
492 497 3.640000 GTCGCCCCGCATCATTCG 61.640 66.667 0.00 0.00 0.00 3.34
564 569 1.733041 CGCCAACTCGTCATCACGT 60.733 57.895 0.00 0.00 46.76 4.49
581 586 2.925706 TGCCGGCACCAGAGGTAA 60.926 61.111 29.03 0.00 32.11 2.85
582 587 2.125106 GCCGGCACCAGAGGTAAG 60.125 66.667 24.80 0.00 32.11 2.34
583 588 2.584608 CCGGCACCAGAGGTAAGG 59.415 66.667 0.00 0.00 32.11 2.69
584 589 2.125106 CGGCACCAGAGGTAAGGC 60.125 66.667 0.00 0.00 32.11 4.35
585 590 2.954684 CGGCACCAGAGGTAAGGCA 61.955 63.158 0.00 0.00 32.11 4.75
603 608 4.223953 AGGCAGGTCCTCTCGATTTTATA 58.776 43.478 0.00 0.00 43.20 0.98
605 610 6.017192 AGGCAGGTCCTCTCGATTTTATATA 58.983 40.000 0.00 0.00 43.20 0.86
606 611 6.670027 AGGCAGGTCCTCTCGATTTTATATAT 59.330 38.462 0.00 0.00 43.20 0.86
607 612 6.758886 GGCAGGTCCTCTCGATTTTATATATG 59.241 42.308 0.00 0.00 0.00 1.78
608 613 7.324178 GCAGGTCCTCTCGATTTTATATATGT 58.676 38.462 0.00 0.00 0.00 2.29
638 653 2.995574 AGAGGTTGGGGGACGACG 60.996 66.667 0.00 0.00 34.03 5.12
686 701 0.395686 CATCTGACCGGATCTGGCAT 59.604 55.000 21.17 1.25 0.00 4.40
687 702 0.395686 ATCTGACCGGATCTGGCATG 59.604 55.000 21.17 10.38 0.00 4.06
701 726 2.749044 CATGGCCGCTCTGCTGTT 60.749 61.111 0.00 0.00 0.00 3.16
706 731 2.435586 CCGCTCTGCTGTTGGGAG 60.436 66.667 0.00 0.00 34.52 4.30
709 734 2.045536 CTCTGCTGTTGGGAGGGC 60.046 66.667 0.00 0.00 33.98 5.19
748 773 3.453059 GGGGGAAGATAGATACGAGGA 57.547 52.381 0.00 0.00 0.00 3.71
761 786 3.844090 GAGGAGCTCTCGGTGGGC 61.844 72.222 14.64 0.00 32.18 5.36
767 792 3.764466 CTCTCGGTGGGCGAGCTT 61.764 66.667 0.00 0.00 33.88 3.74
823 849 3.352648 TGCTATTGAGTTAGGGTTTGGC 58.647 45.455 0.00 0.00 0.00 4.52
865 896 5.045578 TGTGAGAAAAATTAGAGAGGGGAGG 60.046 44.000 0.00 0.00 0.00 4.30
882 913 1.003118 GAGGGCCAATGCGGATGTATA 59.997 52.381 6.18 0.00 38.85 1.47
888 919 3.940852 GCCAATGCGGATGTATATGATGA 59.059 43.478 0.00 0.00 36.56 2.92
890 921 5.066893 GCCAATGCGGATGTATATGATGATT 59.933 40.000 0.00 0.00 36.56 2.57
891 922 6.492254 CCAATGCGGATGTATATGATGATTG 58.508 40.000 0.00 0.00 36.56 2.67
892 923 6.316890 CCAATGCGGATGTATATGATGATTGA 59.683 38.462 0.00 0.00 36.56 2.57
893 924 7.012989 CCAATGCGGATGTATATGATGATTGAT 59.987 37.037 0.00 0.00 36.56 2.57
894 925 6.913873 TGCGGATGTATATGATGATTGATG 57.086 37.500 0.00 0.00 0.00 3.07
895 926 5.295045 TGCGGATGTATATGATGATTGATGC 59.705 40.000 0.00 0.00 0.00 3.91
896 927 5.526479 GCGGATGTATATGATGATTGATGCT 59.474 40.000 0.00 0.00 0.00 3.79
897 928 6.292757 GCGGATGTATATGATGATTGATGCTC 60.293 42.308 0.00 0.00 0.00 4.26
900 931 8.427276 GGATGTATATGATGATTGATGCTCCTA 58.573 37.037 0.00 0.00 0.00 2.94
901 932 9.258826 GATGTATATGATGATTGATGCTCCTAC 57.741 37.037 0.00 0.00 0.00 3.18
902 933 8.371571 TGTATATGATGATTGATGCTCCTACT 57.628 34.615 0.00 0.00 0.00 2.57
903 934 8.255905 TGTATATGATGATTGATGCTCCTACTG 58.744 37.037 0.00 0.00 0.00 2.74
904 935 5.820404 ATGATGATTGATGCTCCTACTGA 57.180 39.130 0.00 0.00 0.00 3.41
905 936 5.820404 TGATGATTGATGCTCCTACTGAT 57.180 39.130 0.00 0.00 0.00 2.90
946 977 7.497249 GCTGCTATATGATATAAGGTTTCCTGG 59.503 40.741 0.00 0.00 32.13 4.45
949 980 8.207545 GCTATATGATATAAGGTTTCCTGGAGG 58.792 40.741 0.00 0.00 32.13 4.30
962 993 2.313041 TCCTGGAGGAGATCAAGAGTGA 59.687 50.000 0.00 0.00 39.78 3.41
968 999 4.098807 GGAGGAGATCAAGAGTGAAGGTAC 59.901 50.000 0.00 0.00 37.30 3.34
1283 1457 3.956199 CGAGGTGGTAGGGTTCTACAATA 59.044 47.826 5.99 0.00 45.76 1.90
1284 1458 4.403432 CGAGGTGGTAGGGTTCTACAATAA 59.597 45.833 5.99 0.00 45.76 1.40
1453 1634 7.724951 TGCTTTATCCCATGATTCATTATGTCA 59.275 33.333 0.00 0.00 32.18 3.58
1454 1635 8.579006 GCTTTATCCCATGATTCATTATGTCAA 58.421 33.333 0.00 0.00 32.18 3.18
1461 1642 9.146984 CCCATGATTCATTATGTCAATTTATGC 57.853 33.333 0.00 0.00 0.00 3.14
1491 1672 1.226746 GTAGTCGTGTTTGCTGGCTT 58.773 50.000 0.00 0.00 0.00 4.35
1492 1673 2.224090 TGTAGTCGTGTTTGCTGGCTTA 60.224 45.455 0.00 0.00 0.00 3.09
1493 1674 1.512926 AGTCGTGTTTGCTGGCTTAG 58.487 50.000 0.00 0.00 0.00 2.18
1499 1680 2.554032 GTGTTTGCTGGCTTAGTCATGT 59.446 45.455 0.00 0.00 0.00 3.21
1582 1763 8.514136 TTCGCAGGTTAATTTAGAACAATTTG 57.486 30.769 0.00 0.00 0.00 2.32
1733 1945 3.132289 TGTCTCAAGTTTCGAACACTCCT 59.868 43.478 0.00 0.00 0.00 3.69
1910 2129 5.818336 TCTGAACGTAAACAATTCCTTGTGA 59.182 36.000 0.00 0.00 44.83 3.58
2148 2377 6.218746 ACAAATTTTGGCACTTGATCTTCTC 58.781 36.000 13.42 0.00 34.12 2.87
2381 2688 7.623999 ATTGATATCACCATACTCCTGAGTT 57.376 36.000 4.48 0.00 42.54 3.01
2648 3040 8.887717 GGCATATTAGGCTATCTGTTTCTTATG 58.112 37.037 0.00 0.00 0.00 1.90
2728 3246 0.036875 AGCCCCTGAGTTGTTAGCAC 59.963 55.000 0.00 0.00 0.00 4.40
2773 3291 7.255730 GGCATATCAATAAGATGGAGTTGCTTT 60.256 37.037 0.00 0.00 37.57 3.51
2872 3390 0.464036 TGGATTTCTCGACCATCCGG 59.536 55.000 0.00 0.00 39.64 5.14
2973 3491 6.071221 ACCAATGCAATGAAGTACAATGATGT 60.071 34.615 2.50 0.00 43.74 3.06
3078 3596 4.303086 ACGAGGTGGATATTTGTAGTCG 57.697 45.455 0.00 0.00 0.00 4.18
3082 3600 4.380531 AGGTGGATATTTGTAGTCGCATG 58.619 43.478 0.00 0.00 0.00 4.06
3135 3653 2.979813 GCCATTTAGCGTTTGACAACAG 59.020 45.455 0.00 0.00 32.54 3.16
3170 3747 6.011628 TCCTATTCTTTCAGGAAAGGGAACAT 60.012 38.462 18.74 8.41 45.80 2.71
3173 3750 5.060427 TCTTTCAGGAAAGGGAACATGAA 57.940 39.130 18.74 0.00 45.80 2.57
3196 3773 2.607499 ACCAAATGATGCTCCAACCAA 58.393 42.857 0.00 0.00 0.00 3.67
3209 3786 4.442753 GCTCCAACCAAAAACATTTCTCCA 60.443 41.667 0.00 0.00 0.00 3.86
3254 3831 5.426833 AGCTGAAGATACTGGTAATGAGGTT 59.573 40.000 0.00 0.00 0.00 3.50
3324 3908 4.474394 AGCACTATATACTGACTGGCTCA 58.526 43.478 0.00 0.00 0.00 4.26
3329 3913 7.212976 CACTATATACTGACTGGCTCATGTTT 58.787 38.462 0.00 0.00 0.00 2.83
3343 3927 8.662781 TGGCTCATGTTTAGTATAGATTGTTC 57.337 34.615 0.00 0.00 0.00 3.18
3362 3946 6.139679 TGTTCAGAAAAATAGGTCCCAGAT 57.860 37.500 0.00 0.00 0.00 2.90
3479 4262 5.176223 GCATATTCACAAGCCAATTGCATAC 59.824 40.000 0.00 0.00 43.15 2.39
3500 4285 0.598065 GCTGCAACCCCTTGTGTTAG 59.402 55.000 0.00 0.00 0.00 2.34
3522 4317 6.442513 AGCTTGTTTGGTTAGATATTCAGC 57.557 37.500 0.00 0.00 0.00 4.26
3560 4355 5.122869 TGTCTTGCAGCTGAATGAGATTAAC 59.877 40.000 20.43 2.93 0.00 2.01
3653 4453 5.674569 GCACATCGATTTGACTGTTTGCTAT 60.675 40.000 15.60 0.00 0.00 2.97
3657 4457 7.280876 ACATCGATTTGACTGTTTGCTATGTAT 59.719 33.333 0.00 0.00 0.00 2.29
3735 4535 1.974265 TTGCAGGAAAATGACCACGA 58.026 45.000 0.00 0.00 0.00 4.35
3788 4588 3.876320 GCCAATTGTCTCCAGAAGATCTC 59.124 47.826 4.43 0.00 36.11 2.75
3880 4680 3.873952 GACATGGATGCTCAGGTAAAGTC 59.126 47.826 0.00 0.00 31.42 3.01
3882 4682 4.018960 ACATGGATGCTCAGGTAAAGTCTT 60.019 41.667 0.00 0.00 29.32 3.01
3884 4684 4.326826 TGGATGCTCAGGTAAAGTCTTTG 58.673 43.478 8.14 0.00 0.00 2.77
3886 4686 4.154918 GGATGCTCAGGTAAAGTCTTTGTG 59.845 45.833 8.14 3.43 0.00 3.33
3889 4689 5.676552 TGCTCAGGTAAAGTCTTTGTGTTA 58.323 37.500 8.14 0.00 0.00 2.41
3890 4690 6.116806 TGCTCAGGTAAAGTCTTTGTGTTAA 58.883 36.000 8.14 0.00 0.00 2.01
3907 4707 1.447099 TAAGTGCTAACCAACCCCCA 58.553 50.000 0.00 0.00 0.00 4.96
3931 4731 1.078918 TGCTCCTCCAAGCATCACG 60.079 57.895 0.00 0.00 47.00 4.35
3972 4775 0.463654 ACCGTGCTTCATGTGTGTGT 60.464 50.000 0.00 0.00 0.00 3.72
4060 4893 3.059188 GCGAATGAAAACACGAAGAGGAA 60.059 43.478 0.00 0.00 0.00 3.36
4061 4894 4.702392 CGAATGAAAACACGAAGAGGAAG 58.298 43.478 0.00 0.00 0.00 3.46
4062 4895 4.447724 CGAATGAAAACACGAAGAGGAAGA 59.552 41.667 0.00 0.00 0.00 2.87
4063 4896 5.050363 CGAATGAAAACACGAAGAGGAAGAA 60.050 40.000 0.00 0.00 0.00 2.52
4093 4926 1.134699 CAATGCTCTAGCCAAGACCGA 60.135 52.381 0.00 0.00 41.18 4.69
4204 5037 7.768582 CCCTTGTGTGAAGACATGTTGTATATA 59.231 37.037 0.00 0.00 33.63 0.86
4205 5038 9.330063 CCTTGTGTGAAGACATGTTGTATATAT 57.670 33.333 0.00 0.00 33.63 0.86
4247 5080 0.530650 AGATATGCTTGGTCGCACCG 60.531 55.000 0.00 0.00 42.58 4.94
4249 5082 2.252072 ATATGCTTGGTCGCACCGGT 62.252 55.000 0.00 0.00 42.58 5.28
4250 5083 2.845752 TATGCTTGGTCGCACCGGTC 62.846 60.000 2.59 0.00 42.58 4.79
4251 5084 4.681978 GCTTGGTCGCACCGGTCT 62.682 66.667 2.59 0.00 42.58 3.85
4252 5085 2.432628 CTTGGTCGCACCGGTCTC 60.433 66.667 2.59 0.00 42.58 3.36
4253 5086 3.934391 CTTGGTCGCACCGGTCTCC 62.934 68.421 2.59 5.47 42.58 3.71
4254 5087 4.988716 TGGTCGCACCGGTCTCCT 62.989 66.667 2.59 0.00 42.58 3.69
4255 5088 4.436998 GGTCGCACCGGTCTCCTG 62.437 72.222 2.59 0.00 0.00 3.86
4256 5089 3.681835 GTCGCACCGGTCTCCTGT 61.682 66.667 2.59 0.00 0.00 4.00
4257 5090 3.680786 TCGCACCGGTCTCCTGTG 61.681 66.667 2.59 0.00 40.82 3.66
4258 5091 4.742201 CGCACCGGTCTCCTGTGG 62.742 72.222 2.59 0.00 38.80 4.17
4287 5127 8.314021 TGTGTAGCATGCTATTTGTAGCTATAT 58.686 33.333 29.17 0.23 43.20 0.86
4288 5128 9.803315 GTGTAGCATGCTATTTGTAGCTATATA 57.197 33.333 29.17 0.81 43.20 0.86
4289 5129 9.803315 TGTAGCATGCTATTTGTAGCTATATAC 57.197 33.333 29.17 13.97 43.20 1.47
4290 5130 7.993821 AGCATGCTATTTGTAGCTATATACG 57.006 36.000 21.21 0.00 43.20 3.06
4362 5310 7.855409 TCGAAAAAGATAACATCAAATATGGCG 59.145 33.333 0.00 0.00 0.00 5.69
4368 5316 6.767902 AGATAACATCAAATATGGCGAACTGT 59.232 34.615 0.00 0.00 0.00 3.55
4408 5356 0.462375 AACGGTGTGTACTCTGCACA 59.538 50.000 0.00 0.00 43.60 4.57
4451 5399 7.248144 TGAAAATTCACCAGGAATCCTGACTC 61.248 42.308 29.60 13.32 45.46 3.36
4486 5434 2.308866 AGGTGATTGATTTCCCGGTCTT 59.691 45.455 0.00 0.00 0.00 3.01
4547 5495 5.618056 TTTCTAACTCATCAGCTTGCTTG 57.382 39.130 0.00 0.00 0.00 4.01
4554 5502 3.079578 TCATCAGCTTGCTTGAAGAAGG 58.920 45.455 0.00 0.00 32.82 3.46
4584 5532 2.799176 GGGGGCTGCACAAAGATAG 58.201 57.895 3.46 0.00 0.00 2.08
4588 5536 2.436417 GGGCTGCACAAAGATAGTCAA 58.564 47.619 0.50 0.00 0.00 3.18
4626 5594 5.902613 AAGAAATGAATCCATGCTTTCGA 57.097 34.783 0.00 0.00 32.36 3.71
4653 5630 1.202417 TGCCTCAGAGTATTACGCTGC 60.202 52.381 19.22 10.80 44.18 5.25
4683 5660 4.664677 AGCCGCACACTGGTCGTC 62.665 66.667 0.00 0.00 0.00 4.20
4766 5743 4.447724 TCGATCAAACCACGAAGAAAGAAG 59.552 41.667 0.00 0.00 33.20 2.85
4776 5753 5.926542 CCACGAAGAAAGAAGACATCAACTA 59.073 40.000 0.00 0.00 0.00 2.24
4791 5768 8.463607 AGACATCAACTAAACCGAAAAGAAAAA 58.536 29.630 0.00 0.00 0.00 1.94
4899 5877 4.386652 CAGAATCACAAATTTCAAAGCGGG 59.613 41.667 0.00 0.00 0.00 6.13
4908 5886 6.015434 ACAAATTTCAAAGCGGGATAAGAACT 60.015 34.615 0.00 0.00 0.00 3.01
4912 5890 0.464452 AAGCGGGATAAGAACTCGGG 59.536 55.000 0.00 0.00 0.00 5.14
4913 5891 1.594564 GCGGGATAAGAACTCGGGC 60.595 63.158 0.00 0.00 0.00 6.13
4914 5892 1.820581 CGGGATAAGAACTCGGGCA 59.179 57.895 0.00 0.00 0.00 5.36
4916 5894 0.106894 GGGATAAGAACTCGGGCAGG 59.893 60.000 0.00 0.00 0.00 4.85
4917 5895 0.533085 GGATAAGAACTCGGGCAGGC 60.533 60.000 0.00 0.00 0.00 4.85
4920 5898 0.398696 TAAGAACTCGGGCAGGCAAA 59.601 50.000 0.00 0.00 0.00 3.68
4921 5899 0.890996 AAGAACTCGGGCAGGCAAAG 60.891 55.000 0.00 0.00 0.00 2.77
4922 5900 2.982744 GAACTCGGGCAGGCAAAGC 61.983 63.158 0.00 0.00 0.00 3.51
4923 5901 3.497884 AACTCGGGCAGGCAAAGCT 62.498 57.895 0.00 0.00 0.00 3.74
4924 5902 3.437795 CTCGGGCAGGCAAAGCTG 61.438 66.667 0.00 0.00 0.00 4.24
4925 5903 4.269523 TCGGGCAGGCAAAGCTGT 62.270 61.111 0.00 0.00 0.00 4.40
4926 5904 4.047059 CGGGCAGGCAAAGCTGTG 62.047 66.667 0.00 0.00 0.00 3.66
4927 5905 2.914097 GGGCAGGCAAAGCTGTGT 60.914 61.111 5.61 0.00 0.00 3.72
4928 5906 2.647297 GGCAGGCAAAGCTGTGTC 59.353 61.111 0.00 0.00 0.00 3.67
4929 5907 2.195567 GGCAGGCAAAGCTGTGTCA 61.196 57.895 11.94 0.00 0.00 3.58
4930 5908 1.530013 GGCAGGCAAAGCTGTGTCAT 61.530 55.000 11.94 0.00 0.00 3.06
4931 5909 0.316204 GCAGGCAAAGCTGTGTCATT 59.684 50.000 11.94 0.00 0.00 2.57
4932 5910 1.541147 GCAGGCAAAGCTGTGTCATTA 59.459 47.619 11.94 0.00 0.00 1.90
4933 5911 2.669391 GCAGGCAAAGCTGTGTCATTAC 60.669 50.000 11.94 0.00 0.00 1.89
4934 5912 2.553602 CAGGCAAAGCTGTGTCATTACA 59.446 45.455 11.94 0.00 0.00 2.41
4959 5937 7.640630 CAGTAGTAGTTACGTAGAAATCAGCAG 59.359 40.741 0.00 0.00 37.35 4.24
4964 5942 0.654683 CGTAGAAATCAGCAGGCAGC 59.345 55.000 0.00 0.00 46.19 5.25
4991 5976 2.771943 TGCCAGACGGGAGATAGATTTT 59.228 45.455 0.00 0.00 40.01 1.82
5014 5999 0.951558 GCTTTTCTCCTTGGTGCGAA 59.048 50.000 0.00 0.00 0.00 4.70
5032 6017 2.097444 CGAAAGCGAAACAAATGGTTGC 60.097 45.455 0.00 0.00 40.35 4.17
5039 6024 1.112315 AACAAATGGTTGCAGCCGGA 61.112 50.000 15.43 0.00 38.60 5.14
5040 6025 0.899717 ACAAATGGTTGCAGCCGGAT 60.900 50.000 15.43 0.00 38.39 4.18
5041 6026 0.179129 CAAATGGTTGCAGCCGGATC 60.179 55.000 15.43 0.00 0.00 3.36
5042 6027 1.322538 AAATGGTTGCAGCCGGATCC 61.323 55.000 15.43 0.00 0.00 3.36
5043 6028 2.497792 AATGGTTGCAGCCGGATCCA 62.498 55.000 15.43 1.88 36.83 3.41
5044 6029 2.124151 GGTTGCAGCCGGATCCAT 60.124 61.111 13.41 0.00 0.00 3.41
5045 6030 2.189499 GGTTGCAGCCGGATCCATC 61.189 63.158 13.41 0.00 0.00 3.51
5046 6031 2.189499 GTTGCAGCCGGATCCATCC 61.189 63.158 13.41 0.00 43.65 3.51
5054 6039 4.963878 GGATCCATCCACGCAACT 57.036 55.556 6.95 0.00 46.38 3.16
5055 6040 2.695314 GGATCCATCCACGCAACTC 58.305 57.895 6.95 0.00 46.38 3.01
5056 6041 0.179000 GGATCCATCCACGCAACTCT 59.821 55.000 6.95 0.00 46.38 3.24
5057 6042 1.293924 GATCCATCCACGCAACTCTG 58.706 55.000 0.00 0.00 0.00 3.35
5058 6043 0.745845 ATCCATCCACGCAACTCTGC 60.746 55.000 0.00 0.00 45.75 4.26
5059 6044 2.401766 CCATCCACGCAACTCTGCC 61.402 63.158 0.00 0.00 46.56 4.85
5060 6045 2.045926 ATCCACGCAACTCTGCCC 60.046 61.111 0.00 0.00 46.56 5.36
5061 6046 2.894257 ATCCACGCAACTCTGCCCA 61.894 57.895 0.00 0.00 46.56 5.36
5062 6047 2.410322 ATCCACGCAACTCTGCCCAA 62.410 55.000 0.00 0.00 46.56 4.12
5063 6048 2.639286 CACGCAACTCTGCCCAAC 59.361 61.111 0.00 0.00 46.56 3.77
5064 6049 1.893808 CACGCAACTCTGCCCAACT 60.894 57.895 0.00 0.00 46.56 3.16
5065 6050 1.152963 ACGCAACTCTGCCCAACTT 60.153 52.632 0.00 0.00 46.56 2.66
5066 6051 1.283793 CGCAACTCTGCCCAACTTG 59.716 57.895 0.00 0.00 46.56 3.16
5067 6052 1.447317 CGCAACTCTGCCCAACTTGT 61.447 55.000 0.00 0.00 46.56 3.16
5068 6053 0.031178 GCAACTCTGCCCAACTTGTG 59.969 55.000 0.00 0.00 43.26 3.33
5069 6054 1.392589 CAACTCTGCCCAACTTGTGT 58.607 50.000 0.00 0.00 0.00 3.72
5070 6055 1.334869 CAACTCTGCCCAACTTGTGTC 59.665 52.381 0.00 0.00 0.00 3.67
5071 6056 0.179018 ACTCTGCCCAACTTGTGTCC 60.179 55.000 0.00 0.00 0.00 4.02
5072 6057 0.179020 CTCTGCCCAACTTGTGTCCA 60.179 55.000 0.00 0.00 0.00 4.02
5073 6058 0.465460 TCTGCCCAACTTGTGTCCAC 60.465 55.000 0.00 0.00 0.00 4.02
5074 6059 0.751277 CTGCCCAACTTGTGTCCACA 60.751 55.000 0.00 0.00 39.98 4.17
5075 6060 0.106268 TGCCCAACTTGTGTCCACAT 60.106 50.000 0.20 0.00 41.52 3.21
5076 6061 0.314935 GCCCAACTTGTGTCCACATG 59.685 55.000 10.69 10.69 41.52 3.21
5077 6062 0.961019 CCCAACTTGTGTCCACATGG 59.039 55.000 15.19 12.77 41.52 3.66
5078 6063 1.691196 CCAACTTGTGTCCACATGGT 58.309 50.000 15.19 7.88 41.52 3.55
5079 6064 2.031120 CCAACTTGTGTCCACATGGTT 58.969 47.619 15.19 13.02 41.52 3.67
5080 6065 2.430332 CCAACTTGTGTCCACATGGTTT 59.570 45.455 15.19 2.21 41.52 3.27
5081 6066 3.118811 CCAACTTGTGTCCACATGGTTTT 60.119 43.478 15.19 1.64 41.52 2.43
5082 6067 4.098654 CCAACTTGTGTCCACATGGTTTTA 59.901 41.667 15.19 0.00 41.52 1.52
5083 6068 5.394663 CCAACTTGTGTCCACATGGTTTTAA 60.395 40.000 15.19 0.00 41.52 1.52
5084 6069 6.279882 CAACTTGTGTCCACATGGTTTTAAT 58.720 36.000 15.19 0.00 41.52 1.40
5085 6070 6.084326 ACTTGTGTCCACATGGTTTTAATC 57.916 37.500 15.19 0.00 41.52 1.75
5086 6071 5.833131 ACTTGTGTCCACATGGTTTTAATCT 59.167 36.000 15.19 0.00 41.52 2.40
5087 6072 5.703978 TGTGTCCACATGGTTTTAATCTG 57.296 39.130 0.00 0.00 36.21 2.90
5088 6073 5.380900 TGTGTCCACATGGTTTTAATCTGA 58.619 37.500 0.00 0.00 36.21 3.27
5089 6074 5.240623 TGTGTCCACATGGTTTTAATCTGAC 59.759 40.000 0.00 0.00 36.21 3.51
5090 6075 4.454161 TGTCCACATGGTTTTAATCTGACG 59.546 41.667 0.00 0.00 36.34 4.35
5091 6076 4.454504 GTCCACATGGTTTTAATCTGACGT 59.545 41.667 0.00 0.00 36.34 4.34
5092 6077 5.048991 GTCCACATGGTTTTAATCTGACGTT 60.049 40.000 0.00 0.00 36.34 3.99
5093 6078 5.049060 TCCACATGGTTTTAATCTGACGTTG 60.049 40.000 0.00 0.00 36.34 4.10
5094 6079 4.616802 CACATGGTTTTAATCTGACGTTGC 59.383 41.667 0.00 0.00 0.00 4.17
5095 6080 4.518970 ACATGGTTTTAATCTGACGTTGCT 59.481 37.500 0.00 0.00 0.00 3.91
5096 6081 4.481930 TGGTTTTAATCTGACGTTGCTG 57.518 40.909 0.00 0.00 0.00 4.41
5097 6082 3.234386 GGTTTTAATCTGACGTTGCTGC 58.766 45.455 0.00 0.00 0.00 5.25
5098 6083 3.304391 GGTTTTAATCTGACGTTGCTGCA 60.304 43.478 0.00 0.00 0.00 4.41
5099 6084 3.811722 TTTAATCTGACGTTGCTGCAG 57.188 42.857 10.11 10.11 0.00 4.41
5100 6085 1.078709 TAATCTGACGTTGCTGCAGC 58.921 50.000 31.89 31.89 42.50 5.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 32 5.656213 ATACTACCTATACCATGGCGTTC 57.344 43.478 13.04 0.00 0.00 3.95
36 38 6.697455 CGCAAGCATATACTACCTATACCATG 59.303 42.308 0.00 0.00 0.00 3.66
47 49 2.696187 TGGACACCGCAAGCATATACTA 59.304 45.455 0.00 0.00 0.00 1.82
48 50 1.484653 TGGACACCGCAAGCATATACT 59.515 47.619 0.00 0.00 0.00 2.12
121 123 2.601367 GGCTTGTGGCATGGGTGT 60.601 61.111 0.00 0.00 44.01 4.16
154 156 3.114616 CGCTTGTCACTCCAGCCG 61.115 66.667 0.00 0.00 0.00 5.52
158 160 2.661537 CGCACGCTTGTCACTCCA 60.662 61.111 0.00 0.00 0.00 3.86
201 203 1.502231 CATATAGACGCACCACCTGC 58.498 55.000 0.00 0.00 43.21 4.85
202 204 1.502231 GCATATAGACGCACCACCTG 58.498 55.000 0.00 0.00 0.00 4.00
203 205 0.393077 GGCATATAGACGCACCACCT 59.607 55.000 0.00 0.00 0.00 4.00
232 234 1.151221 ACATTGGCACCTGAGCACA 59.849 52.632 3.43 0.00 35.83 4.57
235 237 0.322456 TACCACATTGGCACCTGAGC 60.322 55.000 3.43 0.00 42.67 4.26
241 243 8.899771 ACTAAATTAATAGTACCACATTGGCAC 58.100 33.333 0.00 0.00 42.67 5.01
284 289 3.430929 GCTCGCCCTGATCTTCTAAAAGA 60.431 47.826 0.00 0.00 45.36 2.52
285 290 2.869192 GCTCGCCCTGATCTTCTAAAAG 59.131 50.000 0.00 0.00 0.00 2.27
286 291 2.501723 AGCTCGCCCTGATCTTCTAAAA 59.498 45.455 0.00 0.00 0.00 1.52
289 294 1.781786 AAGCTCGCCCTGATCTTCTA 58.218 50.000 0.00 0.00 26.69 2.10
290 295 1.781786 TAAGCTCGCCCTGATCTTCT 58.218 50.000 0.00 0.00 34.91 2.85
291 296 2.604046 TTAAGCTCGCCCTGATCTTC 57.396 50.000 0.00 0.00 34.91 2.87
292 297 3.567478 AATTAAGCTCGCCCTGATCTT 57.433 42.857 0.00 0.00 36.94 2.40
293 298 4.689612 TTAATTAAGCTCGCCCTGATCT 57.310 40.909 0.00 0.00 0.00 2.75
294 299 4.214332 CCTTTAATTAAGCTCGCCCTGATC 59.786 45.833 0.00 0.00 32.19 2.92
295 300 4.137543 CCTTTAATTAAGCTCGCCCTGAT 58.862 43.478 0.00 0.00 32.19 2.90
296 301 3.541632 CCTTTAATTAAGCTCGCCCTGA 58.458 45.455 0.00 0.00 32.19 3.86
381 386 2.747855 GGCCTTTGAGTGGGCTCG 60.748 66.667 0.00 0.00 46.80 5.03
488 493 2.870372 GGCAGTTGCGCTTCGAAT 59.130 55.556 9.73 0.00 43.26 3.34
564 569 2.925706 TTACCTCTGGTGCCGGCA 60.926 61.111 29.03 29.03 36.19 5.69
582 587 2.981859 TAAAATCGAGAGGACCTGCC 57.018 50.000 0.00 0.00 0.00 4.85
583 588 7.324178 ACATATATAAAATCGAGAGGACCTGC 58.676 38.462 0.00 0.00 0.00 4.85
585 590 9.976776 TCTACATATATAAAATCGAGAGGACCT 57.023 33.333 0.00 0.00 0.00 3.85
603 608 5.170198 ACCTCTCTCTCTCCCTCTACATAT 58.830 45.833 0.00 0.00 0.00 1.78
605 610 3.403322 ACCTCTCTCTCTCCCTCTACAT 58.597 50.000 0.00 0.00 0.00 2.29
606 611 2.853430 ACCTCTCTCTCTCCCTCTACA 58.147 52.381 0.00 0.00 0.00 2.74
607 612 3.551846 CAACCTCTCTCTCTCCCTCTAC 58.448 54.545 0.00 0.00 0.00 2.59
608 613 2.512056 CCAACCTCTCTCTCTCCCTCTA 59.488 54.545 0.00 0.00 0.00 2.43
613 618 0.689412 CCCCCAACCTCTCTCTCTCC 60.689 65.000 0.00 0.00 0.00 3.71
709 734 3.155167 GCTCCTACCCCACCGAGG 61.155 72.222 0.00 0.00 37.03 4.63
761 786 2.538333 CCAATCGCAAATCAGAAGCTCG 60.538 50.000 0.00 0.00 0.00 5.03
763 788 1.747355 CCCAATCGCAAATCAGAAGCT 59.253 47.619 0.00 0.00 0.00 3.74
767 792 1.037030 GGCCCCAATCGCAAATCAGA 61.037 55.000 0.00 0.00 0.00 3.27
823 849 0.109272 CAATTCAGCAGCACCAGCAG 60.109 55.000 0.00 0.00 45.49 4.24
865 896 2.710377 TCATATACATCCGCATTGGCC 58.290 47.619 0.00 0.00 37.80 5.36
882 913 5.820404 TCAGTAGGAGCATCAATCATCAT 57.180 39.130 0.00 0.00 36.25 2.45
888 919 6.545298 GGAAGAAAATCAGTAGGAGCATCAAT 59.455 38.462 0.00 0.00 36.25 2.57
890 921 5.190528 AGGAAGAAAATCAGTAGGAGCATCA 59.809 40.000 0.00 0.00 36.25 3.07
891 922 5.679601 AGGAAGAAAATCAGTAGGAGCATC 58.320 41.667 0.00 0.00 0.00 3.91
892 923 5.707066 AGGAAGAAAATCAGTAGGAGCAT 57.293 39.130 0.00 0.00 0.00 3.79
893 924 5.505181 AAGGAAGAAAATCAGTAGGAGCA 57.495 39.130 0.00 0.00 0.00 4.26
894 925 5.392487 GCAAAGGAAGAAAATCAGTAGGAGC 60.392 44.000 0.00 0.00 0.00 4.70
895 926 5.942826 AGCAAAGGAAGAAAATCAGTAGGAG 59.057 40.000 0.00 0.00 0.00 3.69
896 927 5.707298 CAGCAAAGGAAGAAAATCAGTAGGA 59.293 40.000 0.00 0.00 0.00 2.94
897 928 5.620879 GCAGCAAAGGAAGAAAATCAGTAGG 60.621 44.000 0.00 0.00 0.00 3.18
900 931 3.893813 AGCAGCAAAGGAAGAAAATCAGT 59.106 39.130 0.00 0.00 0.00 3.41
901 932 4.235360 CAGCAGCAAAGGAAGAAAATCAG 58.765 43.478 0.00 0.00 0.00 2.90
902 933 3.553508 GCAGCAGCAAAGGAAGAAAATCA 60.554 43.478 0.00 0.00 41.58 2.57
903 934 2.991866 GCAGCAGCAAAGGAAGAAAATC 59.008 45.455 0.00 0.00 41.58 2.17
904 935 2.631545 AGCAGCAGCAAAGGAAGAAAAT 59.368 40.909 3.17 0.00 45.49 1.82
905 936 2.034124 AGCAGCAGCAAAGGAAGAAAA 58.966 42.857 3.17 0.00 45.49 2.29
946 977 4.707448 TGTACCTTCACTCTTGATCTCCTC 59.293 45.833 0.00 0.00 0.00 3.71
949 980 5.646606 GTCTGTACCTTCACTCTTGATCTC 58.353 45.833 0.00 0.00 0.00 2.75
962 993 1.605738 ACGGGAGCGTCTGTACCTT 60.606 57.895 0.00 0.00 0.00 3.50
990 1021 0.902531 CCACGGACATCTAGGGTTGT 59.097 55.000 0.00 0.00 0.00 3.32
1023 1054 4.083862 GACCACGCTCCCTCCACC 62.084 72.222 0.00 0.00 0.00 4.61
1122 1156 0.612174 CGGTCTTGGAGAGGAGGTCA 60.612 60.000 0.00 0.00 0.00 4.02
1283 1457 1.027357 CCACTGCTGTGCTTCTTGTT 58.973 50.000 17.57 0.00 42.54 2.83
1284 1458 0.181114 TCCACTGCTGTGCTTCTTGT 59.819 50.000 17.57 0.00 42.54 3.16
1363 1543 3.274586 CGCATGAGGTCGGGCATG 61.275 66.667 0.00 0.00 43.56 4.06
1453 1634 6.331369 ACTACACAAGCAACAGCATAAATT 57.669 33.333 0.00 0.00 0.00 1.82
1454 1635 5.390885 CGACTACACAAGCAACAGCATAAAT 60.391 40.000 0.00 0.00 0.00 1.40
1461 1642 2.201732 ACACGACTACACAAGCAACAG 58.798 47.619 0.00 0.00 0.00 3.16
1491 1672 7.879677 CCAGGATGCAAGAATATAACATGACTA 59.120 37.037 0.00 0.00 31.97 2.59
1492 1673 6.713903 CCAGGATGCAAGAATATAACATGACT 59.286 38.462 0.00 0.00 31.97 3.41
1493 1674 6.712095 TCCAGGATGCAAGAATATAACATGAC 59.288 38.462 0.00 0.00 31.97 3.06
1499 1680 5.308976 TGCTCCAGGATGCAAGAATATAA 57.691 39.130 10.25 0.00 36.15 0.98
1614 1798 6.054860 AGCATCTAGGTCGCCATATTTATT 57.945 37.500 0.00 0.00 0.00 1.40
1663 1874 3.995705 CTCTCTTGCTGGAAAGAACAGAG 59.004 47.826 0.00 0.00 38.20 3.35
1733 1945 6.040278 TGTTCATGGAAGCAAACACAGATTTA 59.960 34.615 0.00 0.00 0.00 1.40
2049 2278 7.606073 TGATTTTAACTGCAGTAGCTCAATACA 59.394 33.333 22.01 9.65 42.74 2.29
2124 2353 6.041296 AGAGAAGATCAAGTGCCAAAATTTGT 59.959 34.615 4.92 0.00 0.00 2.83
2381 2688 1.042229 AAAGCACAAATCCTGCAGCA 58.958 45.000 8.66 0.00 37.08 4.41
2552 2943 7.670009 CCAAGCAATGGTTTTCAATTTCATA 57.330 32.000 0.00 0.00 44.85 2.15
2692 3084 2.615493 GGGCTCCATCAAGTCGAAGAAA 60.615 50.000 0.00 0.00 39.69 2.52
2694 3086 0.537188 GGGCTCCATCAAGTCGAAGA 59.463 55.000 0.00 0.00 0.00 2.87
2773 3291 5.319043 AGATCCAGGTAAAGAAACCAACA 57.681 39.130 0.00 0.00 42.40 3.33
2872 3390 5.070446 ACTTTCCTTCCCTTCCATTTTGTTC 59.930 40.000 0.00 0.00 0.00 3.18
3078 3596 8.931385 ATCAGAACAAAAATGGTAATACATGC 57.069 30.769 0.00 0.00 0.00 4.06
3135 3653 5.880887 CCTGAAAGAATAGGACCCAACTTAC 59.119 44.000 0.00 0.00 36.11 2.34
3170 3747 3.765381 TGGAGCATCATTTGGTTCTTCA 58.235 40.909 0.00 0.00 35.82 3.02
3173 3750 2.827921 GGTTGGAGCATCATTTGGTTCT 59.172 45.455 0.00 0.00 35.82 3.01
3196 3773 3.006217 GGCAGCTTCTGGAGAAATGTTTT 59.994 43.478 0.00 0.00 33.07 2.43
3254 3831 1.656587 AACAGTACATGAGAGGGCCA 58.343 50.000 6.18 0.00 0.00 5.36
3389 3973 7.067615 TGGTACATCAACAGACAAAAGCTAAAA 59.932 33.333 0.00 0.00 0.00 1.52
3443 4028 4.956085 TGTGAATATGCAAGGCGTATACT 58.044 39.130 0.56 0.00 39.48 2.12
3479 4262 1.394266 AACACAAGGGGTTGCAGCAG 61.394 55.000 2.05 0.00 0.00 4.24
3500 4285 6.030228 GTGCTGAATATCTAACCAAACAAGC 58.970 40.000 0.00 0.00 0.00 4.01
3522 4317 5.403466 GCTGCAAGACAAGAAATAAAAGGTG 59.597 40.000 0.00 0.00 34.07 4.00
3536 4331 2.845363 TCTCATTCAGCTGCAAGACA 57.155 45.000 9.47 0.00 34.07 3.41
3672 4472 0.109723 ACCTTTTTAGGGTCAGCGCA 59.890 50.000 11.47 0.00 30.15 6.09
3693 4493 8.295288 GCAATATCAAGAGCTTAGCAAATGTAT 58.705 33.333 7.07 0.00 0.00 2.29
3735 4535 2.405172 GCCGAGTTTTCTCTTCTCGTT 58.595 47.619 11.69 0.00 46.10 3.85
3788 4588 0.798776 CCAACTCTAGCGCCTTGTTG 59.201 55.000 19.36 19.36 38.08 3.33
3880 4680 5.278604 GGTTGGTTAGCACTTAACACAAAG 58.721 41.667 0.00 0.00 42.85 2.77
3882 4682 3.633065 GGGTTGGTTAGCACTTAACACAA 59.367 43.478 0.00 0.00 42.85 3.33
3884 4684 2.555325 GGGGTTGGTTAGCACTTAACAC 59.445 50.000 0.00 0.00 42.85 3.32
3886 4686 2.165167 GGGGGTTGGTTAGCACTTAAC 58.835 52.381 0.00 0.00 40.79 2.01
3889 4689 0.558712 TTGGGGGTTGGTTAGCACTT 59.441 50.000 0.00 0.00 0.00 3.16
3890 4690 0.112412 CTTGGGGGTTGGTTAGCACT 59.888 55.000 0.00 0.00 0.00 4.40
3907 4707 1.303155 GCTTGGAGGAGCAGTGCTT 60.303 57.895 20.80 3.52 39.88 3.91
3956 4757 0.311790 CCCACACACACATGAAGCAC 59.688 55.000 0.00 0.00 0.00 4.40
3972 4775 4.056125 CGTCTCGCTCTGCACCCA 62.056 66.667 0.00 0.00 0.00 4.51
4060 4893 4.193826 AGAGCATTGTACATGTCGTTCT 57.806 40.909 0.00 0.00 0.00 3.01
4061 4894 4.026475 GCTAGAGCATTGTACATGTCGTTC 60.026 45.833 0.00 0.00 41.59 3.95
4062 4895 3.865745 GCTAGAGCATTGTACATGTCGTT 59.134 43.478 0.00 0.00 41.59 3.85
4063 4896 3.448686 GCTAGAGCATTGTACATGTCGT 58.551 45.455 0.00 0.00 41.59 4.34
4093 4926 6.574350 AGTTATCTCTTGATCCGTTTCGAAT 58.426 36.000 0.00 0.00 34.32 3.34
4106 4939 3.487574 CGAGCCGCTAAAGTTATCTCTTG 59.512 47.826 0.00 0.00 0.00 3.02
4204 5037 8.797438 TCTTAGTGCAGATTCATCTTCGTATAT 58.203 33.333 0.00 0.00 34.22 0.86
4205 5038 8.166422 TCTTAGTGCAGATTCATCTTCGTATA 57.834 34.615 0.00 0.00 34.22 1.47
4247 5080 0.613260 TACACATGCCACAGGAGACC 59.387 55.000 0.00 0.00 0.00 3.85
4249 5082 0.250234 GCTACACATGCCACAGGAGA 59.750 55.000 0.00 0.00 0.00 3.71
4250 5083 0.036105 TGCTACACATGCCACAGGAG 60.036 55.000 0.00 0.00 0.00 3.69
4251 5084 0.620030 ATGCTACACATGCCACAGGA 59.380 50.000 0.00 0.00 37.70 3.86
4252 5085 3.179925 ATGCTACACATGCCACAGG 57.820 52.632 0.00 0.00 37.70 4.00
4287 5127 9.601971 GTTCAACATTGCTCTTTATTTTACGTA 57.398 29.630 0.00 0.00 0.00 3.57
4288 5128 8.349983 AGTTCAACATTGCTCTTTATTTTACGT 58.650 29.630 0.00 0.00 0.00 3.57
4289 5129 8.728088 AGTTCAACATTGCTCTTTATTTTACG 57.272 30.769 0.00 0.00 0.00 3.18
4290 5130 9.899226 AGAGTTCAACATTGCTCTTTATTTTAC 57.101 29.630 0.00 0.00 35.02 2.01
4337 5180 7.855409 TCGCCATATTTGATGTTATCTTTTTCG 59.145 33.333 0.00 0.00 0.00 3.46
4357 5305 2.159114 AGCAAAACAAACAGTTCGCCAT 60.159 40.909 0.00 0.00 40.26 4.40
4362 5310 7.575332 TTTTCTGTAGCAAAACAAACAGTTC 57.425 32.000 0.00 0.00 40.26 3.01
4368 5316 7.760340 ACCGTTAATTTTCTGTAGCAAAACAAA 59.240 29.630 0.00 0.00 0.00 2.83
4408 5356 0.736636 CATGTCATTCGCACTGCCAT 59.263 50.000 0.00 0.00 0.00 4.40
4414 5362 4.324402 GGTGAATTTTCATGTCATTCGCAC 59.676 41.667 19.80 10.91 38.59 5.34
4421 5369 5.185635 GGATTCCTGGTGAATTTTCATGTCA 59.814 40.000 0.00 0.00 43.81 3.58
4451 5399 9.918630 AAATCAATCACCTCTGTTTTATTCTTG 57.081 29.630 0.00 0.00 0.00 3.02
4486 5434 1.273267 ACCAGTGGGCATCTAGACTCA 60.273 52.381 15.21 0.00 37.90 3.41
4547 5495 5.152623 CCCCCAAGAAAAATTCCTTCTTC 57.847 43.478 10.91 0.00 40.37 2.87
4626 5594 0.826715 ATACTCTGAGGCACGCATGT 59.173 50.000 9.85 0.00 37.62 3.21
4653 5630 1.373497 GCGGCTCTGGTGATATCCG 60.373 63.158 0.00 0.00 39.81 4.18
4766 5743 8.623310 TTTTTCTTTTCGGTTTAGTTGATGTC 57.377 30.769 0.00 0.00 0.00 3.06
4776 5753 5.276461 AGGCATCTTTTTCTTTTCGGTTT 57.724 34.783 0.00 0.00 0.00 3.27
4791 5768 1.543802 GATCTCCGATTCGAGGCATCT 59.456 52.381 7.83 0.00 0.00 2.90
4878 5855 4.555262 TCCCGCTTTGAAATTTGTGATTC 58.445 39.130 0.00 0.00 0.00 2.52
4899 5877 0.178068 TGCCTGCCCGAGTTCTTATC 59.822 55.000 0.00 0.00 0.00 1.75
4908 5886 4.269523 ACAGCTTTGCCTGCCCGA 62.270 61.111 0.00 0.00 36.29 5.14
4912 5890 0.316204 AATGACACAGCTTTGCCTGC 59.684 50.000 0.00 0.00 36.29 4.85
4913 5891 2.553602 TGTAATGACACAGCTTTGCCTG 59.446 45.455 0.00 0.00 38.78 4.85
4914 5892 2.816087 CTGTAATGACACAGCTTTGCCT 59.184 45.455 0.00 0.00 39.54 4.75
4923 5901 7.439157 ACGTAACTACTACTGTAATGACACA 57.561 36.000 0.00 0.00 0.00 3.72
4924 5902 8.873830 TCTACGTAACTACTACTGTAATGACAC 58.126 37.037 0.00 0.00 0.00 3.67
4925 5903 9.435688 TTCTACGTAACTACTACTGTAATGACA 57.564 33.333 0.00 0.00 0.00 3.58
4931 5909 8.607459 GCTGATTTCTACGTAACTACTACTGTA 58.393 37.037 0.00 0.00 0.00 2.74
4932 5910 7.120285 TGCTGATTTCTACGTAACTACTACTGT 59.880 37.037 0.00 0.00 0.00 3.55
4933 5911 7.470079 TGCTGATTTCTACGTAACTACTACTG 58.530 38.462 0.00 0.00 0.00 2.74
4934 5912 7.201714 CCTGCTGATTTCTACGTAACTACTACT 60.202 40.741 0.00 0.00 0.00 2.57
4938 5916 4.503370 GCCTGCTGATTTCTACGTAACTAC 59.497 45.833 0.00 0.00 0.00 2.73
4941 5919 3.259064 TGCCTGCTGATTTCTACGTAAC 58.741 45.455 0.00 0.00 0.00 2.50
4945 5923 0.654683 GCTGCCTGCTGATTTCTACG 59.345 55.000 0.00 0.00 38.95 3.51
4991 5976 1.819305 GCACCAAGGAGAAAAGCCTCA 60.819 52.381 0.00 0.00 33.76 3.86
5014 5999 2.472816 CTGCAACCATTTGTTTCGCTT 58.527 42.857 0.00 0.00 34.00 4.68
5022 6007 0.179129 GATCCGGCTGCAACCATTTG 60.179 55.000 6.99 0.00 35.62 2.32
5039 6024 0.745845 GCAGAGTTGCGTGGATGGAT 60.746 55.000 0.00 0.00 41.13 3.41
5040 6025 1.375908 GCAGAGTTGCGTGGATGGA 60.376 57.895 0.00 0.00 41.13 3.41
5041 6026 3.181367 GCAGAGTTGCGTGGATGG 58.819 61.111 0.00 0.00 41.13 3.51
5050 6035 1.334869 GACACAAGTTGGGCAGAGTTG 59.665 52.381 4.63 5.64 34.41 3.16
5051 6036 1.680338 GACACAAGTTGGGCAGAGTT 58.320 50.000 4.63 0.00 0.00 3.01
5052 6037 0.179018 GGACACAAGTTGGGCAGAGT 60.179 55.000 4.63 0.00 0.00 3.24
5053 6038 0.179020 TGGACACAAGTTGGGCAGAG 60.179 55.000 4.63 0.00 0.00 3.35
5054 6039 0.465460 GTGGACACAAGTTGGGCAGA 60.465 55.000 4.63 0.00 0.00 4.26
5055 6040 0.751277 TGTGGACACAAGTTGGGCAG 60.751 55.000 4.63 0.00 38.56 4.85
5056 6041 0.106268 ATGTGGACACAAGTTGGGCA 60.106 50.000 9.42 0.00 45.41 5.36
5057 6042 0.314935 CATGTGGACACAAGTTGGGC 59.685 55.000 9.42 0.00 45.41 5.36
5058 6043 0.961019 CCATGTGGACACAAGTTGGG 59.039 55.000 9.42 2.79 45.41 4.12
5059 6044 1.691196 ACCATGTGGACACAAGTTGG 58.309 50.000 17.55 17.55 45.41 3.77
5060 6045 3.799281 AAACCATGTGGACACAAGTTG 57.201 42.857 18.74 0.00 45.41 3.16
5061 6046 5.923733 TTAAAACCATGTGGACACAAGTT 57.076 34.783 9.42 12.62 45.41 2.66
5062 6047 5.833131 AGATTAAAACCATGTGGACACAAGT 59.167 36.000 9.42 7.37 45.41 3.16
5063 6048 6.016360 TCAGATTAAAACCATGTGGACACAAG 60.016 38.462 9.42 4.95 45.41 3.16
5064 6049 5.830457 TCAGATTAAAACCATGTGGACACAA 59.170 36.000 9.42 0.00 45.41 3.33
5065 6050 5.240623 GTCAGATTAAAACCATGTGGACACA 59.759 40.000 7.68 7.68 46.44 3.72
5066 6051 5.616866 CGTCAGATTAAAACCATGTGGACAC 60.617 44.000 5.96 0.00 38.94 3.67
5067 6052 4.454161 CGTCAGATTAAAACCATGTGGACA 59.546 41.667 5.96 0.00 38.94 4.02
5068 6053 4.454504 ACGTCAGATTAAAACCATGTGGAC 59.545 41.667 5.96 0.00 38.94 4.02
5069 6054 4.647611 ACGTCAGATTAAAACCATGTGGA 58.352 39.130 5.96 0.00 38.94 4.02
5070 6055 5.153513 CAACGTCAGATTAAAACCATGTGG 58.846 41.667 0.00 0.00 42.17 4.17
5071 6056 4.616802 GCAACGTCAGATTAAAACCATGTG 59.383 41.667 0.00 0.00 0.00 3.21
5072 6057 4.518970 AGCAACGTCAGATTAAAACCATGT 59.481 37.500 0.00 0.00 0.00 3.21
5073 6058 4.853196 CAGCAACGTCAGATTAAAACCATG 59.147 41.667 0.00 0.00 0.00 3.66
5074 6059 4.615912 GCAGCAACGTCAGATTAAAACCAT 60.616 41.667 0.00 0.00 0.00 3.55
5075 6060 3.304391 GCAGCAACGTCAGATTAAAACCA 60.304 43.478 0.00 0.00 0.00 3.67
5076 6061 3.234386 GCAGCAACGTCAGATTAAAACC 58.766 45.455 0.00 0.00 0.00 3.27
5077 6062 3.884169 TGCAGCAACGTCAGATTAAAAC 58.116 40.909 0.00 0.00 0.00 2.43
5078 6063 3.609175 GCTGCAGCAACGTCAGATTAAAA 60.609 43.478 33.36 0.00 41.59 1.52
5079 6064 2.095768 GCTGCAGCAACGTCAGATTAAA 60.096 45.455 33.36 0.00 41.59 1.52
5080 6065 1.464608 GCTGCAGCAACGTCAGATTAA 59.535 47.619 33.36 0.00 41.59 1.40
5081 6066 1.078709 GCTGCAGCAACGTCAGATTA 58.921 50.000 33.36 0.00 41.59 1.75
5082 6067 1.871772 GCTGCAGCAACGTCAGATT 59.128 52.632 33.36 0.00 41.59 2.40
5083 6068 3.571119 GCTGCAGCAACGTCAGAT 58.429 55.556 33.36 0.00 41.59 2.90
5087 6072 8.605793 GTTATAAAACTATGCTGCAGCAACGTC 61.606 40.741 42.25 22.66 42.46 4.34
5088 6073 6.892580 GTTATAAAACTATGCTGCAGCAACGT 60.893 38.462 42.25 34.97 42.46 3.99
5089 6074 5.452302 GTTATAAAACTATGCTGCAGCAACG 59.548 40.000 42.25 34.35 42.46 4.10
5090 6075 6.555315 AGTTATAAAACTATGCTGCAGCAAC 58.445 36.000 42.25 29.84 45.37 4.17
5091 6076 6.757897 AGTTATAAAACTATGCTGCAGCAA 57.242 33.333 42.25 28.69 45.37 3.91


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

AutoCloner maintained by Alex Coulton.