Multiple sequence alignment - TraesCS1D01G394700

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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 TraesCS1D01G394700 chr1D 100.000 3154 0 0 1 3154 463497846 463494693 0.000000e+00 5825.0
1 TraesCS1D01G394700 chr1A 88.420 1684 126 21 1 1656 555635206 555636848 0.000000e+00 1965.0
2 TraesCS1D01G394700 chr1A 92.571 848 57 4 1669 2512 555636913 555637758 0.000000e+00 1212.0
3 TraesCS1D01G394700 chr1A 87.288 118 13 2 2964 3081 555638315 555638430 1.970000e-27 134.0
4 TraesCS1D01G394700 chr1B 91.724 870 64 6 1669 2532 638931407 638932274 0.000000e+00 1201.0
5 TraesCS1D01G394700 chr1B 89.890 910 61 12 1 905 638929699 638930582 0.000000e+00 1142.0
6 TraesCS1D01G394700 chr1B 90.487 431 22 7 960 1374 638930586 638931013 4.600000e-153 551.0
7 TraesCS1D01G394700 chr1B 88.285 239 15 6 1419 1656 638931116 638931342 1.110000e-69 274.0
8 TraesCS1D01G394700 chr3B 93.684 95 6 0 1136 1230 486378039 486378133 3.280000e-30 143.0
9 TraesCS1D01G394700 chr3D 92.632 95 7 0 1136 1230 372314462 372314556 1.530000e-28 137.0
10 TraesCS1D01G394700 chr3D 97.500 40 1 0 3098 3137 444365621 444365660 5.640000e-08 69.4
11 TraesCS1D01G394700 chr3A 92.632 95 7 0 1136 1230 493712244 493712338 1.530000e-28 137.0
12 TraesCS1D01G394700 chr3A 88.462 52 6 0 3096 3147 572464814 572464763 2.630000e-06 63.9
13 TraesCS1D01G394700 chr7D 91.000 100 9 0 1136 1235 434912098 434911999 5.490000e-28 135.0
14 TraesCS1D01G394700 chr7D 93.617 47 3 0 3101 3147 494673681 494673635 1.570000e-08 71.3
15 TraesCS1D01G394700 chr7B 91.000 100 9 0 1136 1235 451656442 451656343 5.490000e-28 135.0
16 TraesCS1D01G394700 chr7B 95.652 46 2 0 1010 1055 451656560 451656515 1.210000e-09 75.0
17 TraesCS1D01G394700 chr7A 90.196 102 8 2 1136 1235 485200417 485200316 7.100000e-27 132.0
18 TraesCS1D01G394700 chr7A 97.826 46 1 0 1010 1055 485200535 485200490 2.610000e-11 80.5
19 TraesCS1D01G394700 chr7A 100.000 38 0 0 3099 3136 549104317 549104354 1.570000e-08 71.3
20 TraesCS1D01G394700 chr5B 93.750 48 3 0 3090 3137 341061962 341062009 4.360000e-09 73.1
21 TraesCS1D01G394700 chr2A 100.000 38 0 0 3098 3135 715702214 715702177 1.570000e-08 71.3
22 TraesCS1D01G394700 chr2A 88.462 52 4 2 3096 3147 480584724 480584773 9.450000e-06 62.1
23 TraesCS1D01G394700 chr6D 95.238 42 2 0 3095 3136 62245408 62245367 2.030000e-07 67.6
24 TraesCS1D01G394700 chr6D 87.500 56 5 2 3081 3135 53678817 53678871 2.630000e-06 63.9


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 TraesCS1D01G394700 chr1D 463494693 463497846 3153 True 5825.000000 5825 100.000000 1 3154 1 chr1D.!!$R1 3153
1 TraesCS1D01G394700 chr1A 555635206 555638430 3224 False 1103.666667 1965 89.426333 1 3081 3 chr1A.!!$F1 3080
2 TraesCS1D01G394700 chr1B 638929699 638932274 2575 False 792.000000 1201 90.096500 1 2532 4 chr1B.!!$F1 2531

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
429 432 0.322187 GCGGCCCTTTTCCTGTTCTA 60.322 55.0 0.0 0.0 0.0 2.1 F
1307 1332 0.034574 TGGTGGTTCAACTGTGCTGT 60.035 50.0 0.0 0.0 0.0 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1852 2000 1.135139 TCATGCGAGGAGACTAACAGC 59.865 52.381 0.00 0.0 44.43 4.40 R
2598 2904 0.675633 ACTTGTCCCAAGCAATGTGC 59.324 50.000 3.96 0.0 45.46 4.57 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
46 47 1.003116 ACGTATAAGACCTAGCACGCG 60.003 52.381 3.53 3.53 32.90 6.01
217 218 2.580815 CGTGCTCCTCTGGATGCA 59.419 61.111 0.00 0.00 35.00 3.96
239 240 1.148273 TTTCAGCCTTCGTGCCTGT 59.852 52.632 0.00 0.00 0.00 4.00
245 248 1.069765 CCTTCGTGCCTGTCTGTGT 59.930 57.895 0.00 0.00 0.00 3.72
248 251 2.658679 TTCGTGCCTGTCTGTGTGGG 62.659 60.000 0.00 0.00 0.00 4.61
251 254 2.281761 GCCTGTCTGTGTGGGGTG 60.282 66.667 0.00 0.00 0.00 4.61
252 255 2.281761 CCTGTCTGTGTGGGGTGC 60.282 66.667 0.00 0.00 0.00 5.01
275 278 4.629092 GGGAATCATCTAGGTTTACGGTC 58.371 47.826 0.00 0.00 0.00 4.79
289 292 1.287815 CGGTCGTGTGAGTGGCTTA 59.712 57.895 0.00 0.00 0.00 3.09
293 296 2.165845 GGTCGTGTGAGTGGCTTATACT 59.834 50.000 0.00 0.00 0.00 2.12
315 318 5.717654 ACTCGGGGATCTAGAAATAAGGATC 59.282 44.000 0.00 0.00 35.28 3.36
429 432 0.322187 GCGGCCCTTTTCCTGTTCTA 60.322 55.000 0.00 0.00 0.00 2.10
435 438 3.889538 GCCCTTTTCCTGTTCTAGTGTTT 59.110 43.478 0.00 0.00 0.00 2.83
443 446 5.850614 TCCTGTTCTAGTGTTTCTTGGTAC 58.149 41.667 0.00 0.00 0.00 3.34
450 453 6.518493 TCTAGTGTTTCTTGGTACGATTTGT 58.482 36.000 0.00 0.00 0.00 2.83
465 468 1.640428 TTTGTGGCTAGCTCGAATCG 58.360 50.000 15.72 0.00 0.00 3.34
485 488 8.422457 CGAATCGTACTGTATTATTATTGCGTT 58.578 33.333 0.00 0.00 0.00 4.84
551 554 6.037830 CACTTATGGGACCGGTTTTACTAATG 59.962 42.308 9.42 0.00 0.00 1.90
561 564 6.826741 ACCGGTTTTACTAATGTGATATGCTT 59.173 34.615 0.00 0.00 0.00 3.91
583 589 4.156455 AGTGGTGGAGTAATTGCCATAG 57.844 45.455 0.00 0.00 36.41 2.23
607 613 3.889815 TGGAAGTATGGAGCTTTGATGG 58.110 45.455 0.00 0.00 0.00 3.51
631 637 9.747898 TGGTATCCTTGATTTGTTACAGTTATT 57.252 29.630 0.00 0.00 0.00 1.40
677 683 6.431198 ACCGTTTGCTACAATATTTACCAG 57.569 37.500 0.00 0.00 0.00 4.00
686 692 9.555727 TGCTACAATATTTACCAGTAGAAATCC 57.444 33.333 11.96 0.00 35.38 3.01
709 715 2.564504 AGCTTCAGCCTTCATTTTTCCC 59.435 45.455 0.00 0.00 43.38 3.97
753 759 1.677217 CCTTGGGCAGCACTAGTTCTC 60.677 57.143 5.33 0.00 0.00 2.87
832 838 7.226128 ACATCATGCTTGTCATACAACTGATAG 59.774 37.037 0.00 0.00 33.96 2.08
883 891 2.488937 TCATACATTGCTGTTGCCTGTG 59.511 45.455 0.00 0.00 36.79 3.66
928 937 3.428532 ACATCTTTTCTGATGCTGCCTT 58.571 40.909 0.00 0.00 45.51 4.35
929 938 3.830755 ACATCTTTTCTGATGCTGCCTTT 59.169 39.130 0.00 0.00 45.51 3.11
939 948 3.879295 TGATGCTGCCTTTTGTAGATAGC 59.121 43.478 0.00 0.00 34.91 2.97
942 951 3.959573 CTGCCTTTTGTAGATAGCAGC 57.040 47.619 0.00 0.00 40.99 5.25
971 980 6.811253 TTGCTGTTTTACTATACTTGTGGG 57.189 37.500 0.00 0.00 0.00 4.61
1087 1096 2.429610 GCTGCCCAGATCATTGTTCAAT 59.570 45.455 0.00 0.00 0.00 2.57
1103 1112 9.665264 CATTGTTCAATGATCTCATGAATGTAG 57.335 33.333 17.41 0.00 36.56 2.74
1122 1132 3.380479 AGCTAACTTTGTGCTCACGTA 57.620 42.857 0.00 0.00 30.41 3.57
1220 1240 3.743396 CCAAGTACTTCTGTGAGTTCTGC 59.257 47.826 4.77 0.00 29.23 4.26
1243 1263 3.429410 GGCAAGGTAAATCTGTCAATGGC 60.429 47.826 0.00 0.00 0.00 4.40
1305 1330 1.103398 GCTGGTGGTTCAACTGTGCT 61.103 55.000 0.00 0.00 0.00 4.40
1306 1331 0.664761 CTGGTGGTTCAACTGTGCTG 59.335 55.000 0.00 0.00 0.00 4.41
1307 1332 0.034574 TGGTGGTTCAACTGTGCTGT 60.035 50.000 0.00 0.00 0.00 4.40
1308 1333 0.663153 GGTGGTTCAACTGTGCTGTC 59.337 55.000 0.00 0.00 0.00 3.51
1309 1334 1.668419 GTGGTTCAACTGTGCTGTCT 58.332 50.000 0.00 0.00 0.00 3.41
1401 1441 6.884280 ATGGTATAGGTTATTTGCTCTTGC 57.116 37.500 0.00 0.00 40.20 4.01
1405 1445 7.396055 TGGTATAGGTTATTTGCTCTTGCTTTT 59.604 33.333 0.00 0.00 40.48 2.27
1428 1520 8.908786 TTTCATGATGATGGTTTAGAGGATAC 57.091 34.615 0.00 0.00 0.00 2.24
1478 1570 5.106987 GCTGGTTGGCAAAACATAAAGAATG 60.107 40.000 0.00 0.00 41.74 2.67
1499 1591 5.811399 TGTATATTGTAGGCTGTTGCAAC 57.189 39.130 22.83 22.83 41.91 4.17
1500 1592 5.496556 TGTATATTGTAGGCTGTTGCAACT 58.503 37.500 28.61 12.34 41.91 3.16
1501 1593 5.943416 TGTATATTGTAGGCTGTTGCAACTT 59.057 36.000 28.61 14.61 41.91 2.66
1502 1594 3.648339 ATTGTAGGCTGTTGCAACTTG 57.352 42.857 28.61 21.34 41.91 3.16
1503 1595 0.667993 TGTAGGCTGTTGCAACTTGC 59.332 50.000 28.61 28.09 45.29 4.01
1533 1625 6.951062 TTGTATTGTCATGAGTTGTTTGGA 57.049 33.333 0.00 0.00 0.00 3.53
1542 1634 7.284261 TGTCATGAGTTGTTTGGATTTACTTCA 59.716 33.333 0.00 0.00 0.00 3.02
1620 1713 7.599998 AGCTTTGATTGTTTTGTATGATGAACC 59.400 33.333 0.00 0.00 0.00 3.62
1668 1761 9.005777 AGTTTAATATTACCGAACAGCTTTTGA 57.994 29.630 9.92 0.00 0.00 2.69
1669 1762 9.783256 GTTTAATATTACCGAACAGCTTTTGAT 57.217 29.630 0.00 0.00 0.00 2.57
1677 1823 4.539870 CGAACAGCTTTTGATTGACATGT 58.460 39.130 0.00 0.00 0.00 3.21
1690 1836 9.531942 TTTGATTGACATGTATATGGATTTTGC 57.468 29.630 0.00 0.00 38.66 3.68
1695 1841 6.606796 TGACATGTATATGGATTTTGCAACCT 59.393 34.615 0.00 0.00 38.66 3.50
1697 1843 6.040842 ACATGTATATGGATTTTGCAACCTCC 59.959 38.462 16.30 16.30 38.66 4.30
1701 1848 6.715347 ATATGGATTTTGCAACCTCCTAAC 57.285 37.500 21.29 2.65 0.00 2.34
1800 1947 5.865085 AGTCACTTTACACAATTCTAGCCA 58.135 37.500 0.00 0.00 0.00 4.75
1869 2017 1.257743 AAGCTGTTAGTCTCCTCGCA 58.742 50.000 0.00 0.00 0.00 5.10
1879 2027 3.726607 AGTCTCCTCGCATGATTCAATC 58.273 45.455 0.00 0.00 0.00 2.67
1882 2030 4.210955 GTCTCCTCGCATGATTCAATCTTC 59.789 45.833 0.00 0.00 0.00 2.87
1883 2031 4.100653 TCTCCTCGCATGATTCAATCTTCT 59.899 41.667 0.00 0.00 0.00 2.85
1890 2038 8.845942 TCGCATGATTCAATCTTCTTTTTATG 57.154 30.769 0.00 0.00 0.00 1.90
2012 2160 2.635714 TGAAGTATGTGCTGATGCCAG 58.364 47.619 0.00 0.00 43.22 4.85
2096 2245 0.537828 TCTGCATTTCCAGCACTGCA 60.538 50.000 3.30 0.00 41.98 4.41
2235 2384 4.094887 ACGCAATGTAGCCTAAATTGACAG 59.905 41.667 17.14 10.09 33.96 3.51
2271 2421 0.250295 TCGGCTTGTTGGGTTCTGAG 60.250 55.000 0.00 0.00 0.00 3.35
2308 2458 7.891782 ACGTTACAATGTGTATCTCGTTTATG 58.108 34.615 0.00 0.00 34.32 1.90
2309 2459 7.543172 ACGTTACAATGTGTATCTCGTTTATGT 59.457 33.333 0.00 0.00 34.32 2.29
2317 2467 7.317390 TGTGTATCTCGTTTATGTTGCTTAGA 58.683 34.615 0.00 0.00 0.00 2.10
2329 2479 4.424626 TGTTGCTTAGATGATCGTCTGAC 58.575 43.478 24.88 14.91 0.00 3.51
2330 2480 4.158579 TGTTGCTTAGATGATCGTCTGACT 59.841 41.667 24.88 3.85 0.00 3.41
2343 2493 2.726760 CGTCTGACTGTACTCTTTGTGC 59.273 50.000 6.21 0.00 0.00 4.57
2353 2503 0.927537 CTCTTTGTGCGTGTCGTTGA 59.072 50.000 0.00 0.00 0.00 3.18
2391 2541 8.613060 AATGCTATTGTCATCTGTTATTCGAT 57.387 30.769 0.00 0.00 0.00 3.59
2528 2680 2.102252 CCTCACATAGTTCCTGGCTCTC 59.898 54.545 0.00 0.00 0.00 3.20
2532 2684 1.339610 CATAGTTCCTGGCTCTCGAGG 59.660 57.143 13.56 4.50 0.00 4.63
2533 2685 0.395862 TAGTTCCTGGCTCTCGAGGG 60.396 60.000 13.56 11.08 0.00 4.30
2534 2686 3.077556 TTCCTGGCTCTCGAGGGC 61.078 66.667 29.60 29.60 0.00 5.19
2535 2687 3.608759 TTCCTGGCTCTCGAGGGCT 62.609 63.158 34.72 0.00 0.00 5.19
2536 2688 3.535962 CCTGGCTCTCGAGGGCTC 61.536 72.222 34.72 24.76 0.00 4.70
2556 2862 2.357952 TCGTAATCTCCCAGATGTCACG 59.642 50.000 8.30 8.30 34.65 4.35
2560 2866 1.627864 TCTCCCAGATGTCACGTTCA 58.372 50.000 0.00 0.00 0.00 3.18
2562 2868 1.273606 CTCCCAGATGTCACGTTCACT 59.726 52.381 0.00 0.00 0.00 3.41
2569 2875 2.823196 TGTCACGTTCACTTTGCTTG 57.177 45.000 0.00 0.00 0.00 4.01
2576 2882 1.748493 GTTCACTTTGCTTGTGGGACA 59.252 47.619 0.00 0.00 36.21 4.02
2577 2883 2.136298 TCACTTTGCTTGTGGGACAA 57.864 45.000 0.00 0.00 44.16 3.18
2592 2898 5.192927 GTGGGACAATTATGAAGGTCATCA 58.807 41.667 0.00 0.00 44.16 3.07
2594 2900 6.998074 GTGGGACAATTATGAAGGTCATCATA 59.002 38.462 0.00 0.00 44.16 2.15
2596 2902 7.072328 TGGGACAATTATGAAGGTCATCATAGA 59.928 37.037 0.00 0.00 38.32 1.98
2597 2903 7.389053 GGGACAATTATGAAGGTCATCATAGAC 59.611 40.741 0.00 0.00 41.83 2.59
2598 2904 7.116948 GGACAATTATGAAGGTCATCATAGACG 59.883 40.741 0.00 0.00 41.83 4.18
2600 2906 5.529581 TTATGAAGGTCATCATAGACGCA 57.470 39.130 0.00 0.00 41.83 5.24
2601 2907 3.165058 TGAAGGTCATCATAGACGCAC 57.835 47.619 0.00 0.00 39.42 5.34
2602 2908 2.495669 TGAAGGTCATCATAGACGCACA 59.504 45.455 0.00 0.00 39.42 4.57
2603 2909 3.132824 TGAAGGTCATCATAGACGCACAT 59.867 43.478 0.00 0.00 39.42 3.21
2604 2910 3.827008 AGGTCATCATAGACGCACATT 57.173 42.857 0.00 0.00 39.42 2.71
2605 2911 3.461061 AGGTCATCATAGACGCACATTG 58.539 45.455 0.00 0.00 39.42 2.82
2606 2912 2.032549 GGTCATCATAGACGCACATTGC 60.033 50.000 0.00 0.00 39.42 3.56
2607 2913 2.868583 GTCATCATAGACGCACATTGCT 59.131 45.455 0.00 0.00 42.25 3.91
2608 2914 3.310774 GTCATCATAGACGCACATTGCTT 59.689 43.478 0.00 0.00 42.25 3.91
2609 2915 3.310501 TCATCATAGACGCACATTGCTTG 59.689 43.478 0.00 0.00 42.25 4.01
2610 2916 2.009051 TCATAGACGCACATTGCTTGG 58.991 47.619 0.00 0.00 42.25 3.61
2611 2917 1.064505 CATAGACGCACATTGCTTGGG 59.935 52.381 0.00 0.00 42.25 4.12
2612 2918 0.323302 TAGACGCACATTGCTTGGGA 59.677 50.000 0.00 0.00 42.25 4.37
2613 2919 1.210155 GACGCACATTGCTTGGGAC 59.790 57.895 0.00 0.00 42.25 4.46
2614 2920 1.514678 GACGCACATTGCTTGGGACA 61.515 55.000 0.00 0.00 42.25 4.02
2615 2921 1.106351 ACGCACATTGCTTGGGACAA 61.106 50.000 0.00 0.00 42.25 3.18
2616 2922 0.387622 CGCACATTGCTTGGGACAAG 60.388 55.000 4.69 4.69 42.25 3.16
2617 2923 0.675633 GCACATTGCTTGGGACAAGT 59.324 50.000 10.34 0.00 40.96 3.16
2618 2924 1.885887 GCACATTGCTTGGGACAAGTA 59.114 47.619 10.34 3.46 40.96 2.24
2619 2925 2.493278 GCACATTGCTTGGGACAAGTAT 59.507 45.455 10.34 2.82 40.96 2.12
2620 2926 3.056607 GCACATTGCTTGGGACAAGTATT 60.057 43.478 10.34 0.68 40.96 1.89
2621 2927 4.157656 GCACATTGCTTGGGACAAGTATTA 59.842 41.667 10.34 0.00 40.96 0.98
2622 2928 5.336372 GCACATTGCTTGGGACAAGTATTAA 60.336 40.000 10.34 2.88 40.96 1.40
2623 2929 7.333352 GCACATTGCTTGGGACAAGTATTAAC 61.333 42.308 10.34 0.00 40.96 2.01
2646 2952 7.202016 ACCTTGTGATACAATTACACAGTTG 57.798 36.000 0.00 0.00 43.62 3.16
2668 2974 4.887071 TGGGACAATTGCTTATGTATCACC 59.113 41.667 5.05 0.00 31.92 4.02
2671 2977 6.460123 GGGACAATTGCTTATGTATCACCAAG 60.460 42.308 5.05 0.00 0.00 3.61
2677 2983 5.123227 TGCTTATGTATCACCAAGTTAGCC 58.877 41.667 0.00 0.00 0.00 3.93
2678 2984 4.211374 GCTTATGTATCACCAAGTTAGCCG 59.789 45.833 0.00 0.00 0.00 5.52
2679 2985 5.597806 CTTATGTATCACCAAGTTAGCCGA 58.402 41.667 0.00 0.00 0.00 5.54
2680 2986 4.689612 ATGTATCACCAAGTTAGCCGAT 57.310 40.909 0.00 0.00 0.00 4.18
2681 2987 4.054780 TGTATCACCAAGTTAGCCGATC 57.945 45.455 0.00 0.00 0.00 3.69
2682 2988 3.704566 TGTATCACCAAGTTAGCCGATCT 59.295 43.478 0.00 0.00 0.00 2.75
2683 2989 2.672961 TCACCAAGTTAGCCGATCTG 57.327 50.000 0.00 0.00 0.00 2.90
2684 2990 2.176045 TCACCAAGTTAGCCGATCTGA 58.824 47.619 0.00 0.00 0.00 3.27
2685 2991 2.565391 TCACCAAGTTAGCCGATCTGAA 59.435 45.455 0.00 0.00 0.00 3.02
2686 2992 3.197766 TCACCAAGTTAGCCGATCTGAAT 59.802 43.478 0.00 0.00 0.00 2.57
2687 2993 3.557595 CACCAAGTTAGCCGATCTGAATC 59.442 47.826 0.00 0.00 0.00 2.52
2688 2994 3.197766 ACCAAGTTAGCCGATCTGAATCA 59.802 43.478 0.00 0.00 31.76 2.57
2689 2995 4.141620 ACCAAGTTAGCCGATCTGAATCAT 60.142 41.667 0.00 0.00 31.76 2.45
2690 2996 4.450419 CCAAGTTAGCCGATCTGAATCATC 59.550 45.833 0.00 0.00 31.76 2.92
2694 3000 2.956913 AGCCGATCTGAATCATCGATG 58.043 47.619 19.61 19.61 44.95 3.84
2711 3017 5.582689 TCGATGAAGAGATACTTTGCTGA 57.417 39.130 0.00 0.00 39.13 4.26
2714 3020 5.752472 CGATGAAGAGATACTTTGCTGATGT 59.248 40.000 0.00 0.00 39.13 3.06
2720 3026 7.313740 AGAGATACTTTGCTGATGTGGATAT 57.686 36.000 0.00 0.00 0.00 1.63
2721 3027 8.427902 AGAGATACTTTGCTGATGTGGATATA 57.572 34.615 0.00 0.00 0.00 0.86
2722 3028 8.310382 AGAGATACTTTGCTGATGTGGATATAC 58.690 37.037 0.00 0.00 0.00 1.47
2725 3031 9.277783 GATACTTTGCTGATGTGGATATACTTT 57.722 33.333 0.00 0.00 0.00 2.66
2736 3042 8.915057 ATGTGGATATACTTTGGAGAAAGATG 57.085 34.615 0.00 0.00 41.12 2.90
2737 3043 8.089625 TGTGGATATACTTTGGAGAAAGATGA 57.910 34.615 0.00 0.00 41.12 2.92
2772 3092 1.064906 CAAGACCCATGATCTGCTGGT 60.065 52.381 0.00 0.00 0.00 4.00
2774 3094 1.077212 ACCCATGATCTGCTGGTGC 60.077 57.895 0.00 0.00 40.20 5.01
2819 3139 6.308908 GAGTATCATGGGCTACTAAAGCAGC 61.309 48.000 0.00 0.00 44.65 5.25
2837 3157 8.823220 AAAGCAGCTAAATTTAAGGAATAGGA 57.177 30.769 0.00 0.00 0.00 2.94
2838 3158 8.823220 AAGCAGCTAAATTTAAGGAATAGGAA 57.177 30.769 0.00 0.00 0.00 3.36
2840 3160 8.687242 AGCAGCTAAATTTAAGGAATAGGAAAC 58.313 33.333 0.00 0.00 0.00 2.78
2860 3180 8.057011 AGGAAACAAGTAAAGTTTTAGGAGGAA 58.943 33.333 0.00 0.00 39.15 3.36
2865 3185 9.503399 ACAAGTAAAGTTTTAGGAGGAATAGTG 57.497 33.333 0.00 0.00 0.00 2.74
2867 3187 7.110810 AGTAAAGTTTTAGGAGGAATAGTGGC 58.889 38.462 0.00 0.00 0.00 5.01
2868 3188 4.505324 AGTTTTAGGAGGAATAGTGGCC 57.495 45.455 0.00 0.00 0.00 5.36
2869 3189 3.850173 AGTTTTAGGAGGAATAGTGGCCA 59.150 43.478 0.00 0.00 0.00 5.36
2870 3190 4.478686 AGTTTTAGGAGGAATAGTGGCCAT 59.521 41.667 9.72 0.00 0.00 4.40
2871 3191 5.044105 AGTTTTAGGAGGAATAGTGGCCATT 60.044 40.000 9.72 7.59 0.00 3.16
2873 3193 2.492025 AGGAGGAATAGTGGCCATTCA 58.508 47.619 9.72 0.00 34.66 2.57
2874 3194 2.441001 AGGAGGAATAGTGGCCATTCAG 59.559 50.000 9.72 0.00 34.66 3.02
2877 3197 4.141482 GGAGGAATAGTGGCCATTCAGTAA 60.141 45.833 9.72 0.00 34.66 2.24
2879 3199 5.440610 AGGAATAGTGGCCATTCAGTAAAG 58.559 41.667 9.72 0.00 34.66 1.85
2880 3200 5.044846 AGGAATAGTGGCCATTCAGTAAAGT 60.045 40.000 9.72 0.00 34.66 2.66
2881 3201 5.066505 GGAATAGTGGCCATTCAGTAAAGTG 59.933 44.000 9.72 0.00 34.66 3.16
2882 3202 2.162681 AGTGGCCATTCAGTAAAGTGC 58.837 47.619 9.72 0.00 0.00 4.40
2883 3203 1.202348 GTGGCCATTCAGTAAAGTGCC 59.798 52.381 9.72 0.00 37.76 5.01
2884 3204 1.202989 TGGCCATTCAGTAAAGTGCCA 60.203 47.619 0.00 0.00 42.22 4.92
2885 3205 2.102578 GGCCATTCAGTAAAGTGCCAT 58.897 47.619 0.00 0.00 37.40 4.40
2886 3206 3.287222 GGCCATTCAGTAAAGTGCCATA 58.713 45.455 0.00 0.00 37.40 2.74
2887 3207 3.891366 GGCCATTCAGTAAAGTGCCATAT 59.109 43.478 0.00 0.00 37.40 1.78
2888 3208 5.070001 GGCCATTCAGTAAAGTGCCATATA 58.930 41.667 0.00 0.00 37.40 0.86
2889 3209 5.048713 GGCCATTCAGTAAAGTGCCATATAC 60.049 44.000 0.00 0.00 37.40 1.47
2901 3221 7.834068 AAGTGCCATATACTATATTCTTGCG 57.166 36.000 0.00 0.00 0.00 4.85
2936 3279 8.528044 TCCTGTTTGGAAATTAACTGTACTTT 57.472 30.769 0.00 0.00 42.94 2.66
2937 3280 8.973182 TCCTGTTTGGAAATTAACTGTACTTTT 58.027 29.630 0.00 0.00 42.94 2.27
2938 3281 9.594478 CCTGTTTGGAAATTAACTGTACTTTTT 57.406 29.630 0.00 0.00 38.35 1.94
2959 3302 3.810721 TTTCCCGAGGGTGGAAATTAA 57.189 42.857 8.20 0.00 44.76 1.40
2960 3303 2.793288 TCCCGAGGGTGGAAATTAAC 57.207 50.000 8.20 0.00 36.47 2.01
2961 3304 2.271777 TCCCGAGGGTGGAAATTAACT 58.728 47.619 8.20 0.00 36.47 2.24
2962 3305 2.026636 TCCCGAGGGTGGAAATTAACTG 60.027 50.000 8.20 0.00 36.47 3.16
3081 3424 1.539388 CGTAACCAATTCCTGCAGCAA 59.461 47.619 8.66 0.00 0.00 3.91
3082 3425 2.030363 CGTAACCAATTCCTGCAGCAAA 60.030 45.455 8.66 5.13 0.00 3.68
3083 3426 2.531522 AACCAATTCCTGCAGCAAAC 57.468 45.000 8.66 0.00 0.00 2.93
3084 3427 0.314935 ACCAATTCCTGCAGCAAACG 59.685 50.000 8.66 0.00 0.00 3.60
3085 3428 0.314935 CCAATTCCTGCAGCAAACGT 59.685 50.000 8.66 0.00 0.00 3.99
3086 3429 1.411394 CAATTCCTGCAGCAAACGTG 58.589 50.000 8.66 3.57 0.00 4.49
3087 3430 0.314935 AATTCCTGCAGCAAACGTGG 59.685 50.000 8.66 0.00 0.00 4.94
3088 3431 0.823356 ATTCCTGCAGCAAACGTGGT 60.823 50.000 8.66 0.00 35.28 4.16
3089 3432 1.444119 TTCCTGCAGCAAACGTGGTC 61.444 55.000 8.66 0.00 31.53 4.02
3090 3433 2.249309 CTGCAGCAAACGTGGTCG 59.751 61.111 0.00 0.00 43.34 4.79
3101 3444 3.733236 CGTGGTCGTGGTATCATGT 57.267 52.632 0.00 0.00 0.00 3.21
3102 3445 2.855660 CGTGGTCGTGGTATCATGTA 57.144 50.000 0.00 0.00 0.00 2.29
3103 3446 2.456989 CGTGGTCGTGGTATCATGTAC 58.543 52.381 0.00 0.00 0.00 2.90
3104 3447 2.098607 CGTGGTCGTGGTATCATGTACT 59.901 50.000 0.00 0.00 0.00 2.73
3105 3448 3.703420 GTGGTCGTGGTATCATGTACTC 58.297 50.000 0.00 0.00 0.00 2.59
3106 3449 2.691526 TGGTCGTGGTATCATGTACTCC 59.308 50.000 0.00 0.00 0.00 3.85
3107 3450 2.035576 GGTCGTGGTATCATGTACTCCC 59.964 54.545 0.00 0.00 0.00 4.30
3108 3451 2.957006 GTCGTGGTATCATGTACTCCCT 59.043 50.000 0.00 0.00 0.00 4.20
3109 3452 3.004524 GTCGTGGTATCATGTACTCCCTC 59.995 52.174 0.00 0.00 0.00 4.30
3110 3453 3.117625 TCGTGGTATCATGTACTCCCTCT 60.118 47.826 0.00 0.00 0.00 3.69
3111 3454 3.004839 CGTGGTATCATGTACTCCCTCTG 59.995 52.174 0.00 0.00 0.00 3.35
3112 3455 3.961408 GTGGTATCATGTACTCCCTCTGT 59.039 47.826 0.00 0.00 0.00 3.41
3113 3456 4.038162 GTGGTATCATGTACTCCCTCTGTC 59.962 50.000 0.00 0.00 0.00 3.51
3114 3457 3.574826 GGTATCATGTACTCCCTCTGTCC 59.425 52.174 0.00 0.00 0.00 4.02
3115 3458 2.160721 TCATGTACTCCCTCTGTCCC 57.839 55.000 0.00 0.00 0.00 4.46
3116 3459 1.361197 TCATGTACTCCCTCTGTCCCA 59.639 52.381 0.00 0.00 0.00 4.37
3117 3460 2.023015 TCATGTACTCCCTCTGTCCCAT 60.023 50.000 0.00 0.00 0.00 4.00
3118 3461 3.206639 TCATGTACTCCCTCTGTCCCATA 59.793 47.826 0.00 0.00 0.00 2.74
3119 3462 3.769189 TGTACTCCCTCTGTCCCATAA 57.231 47.619 0.00 0.00 0.00 1.90
3120 3463 4.280789 TGTACTCCCTCTGTCCCATAAT 57.719 45.455 0.00 0.00 0.00 1.28
3121 3464 5.412617 TGTACTCCCTCTGTCCCATAATA 57.587 43.478 0.00 0.00 0.00 0.98
3122 3465 5.977533 TGTACTCCCTCTGTCCCATAATAT 58.022 41.667 0.00 0.00 0.00 1.28
3123 3466 7.111136 TGTACTCCCTCTGTCCCATAATATA 57.889 40.000 0.00 0.00 0.00 0.86
3124 3467 7.541074 TGTACTCCCTCTGTCCCATAATATAA 58.459 38.462 0.00 0.00 0.00 0.98
3125 3468 7.674348 TGTACTCCCTCTGTCCCATAATATAAG 59.326 40.741 0.00 0.00 0.00 1.73
3126 3469 6.875469 ACTCCCTCTGTCCCATAATATAAGA 58.125 40.000 0.00 0.00 0.00 2.10
3127 3470 6.957020 ACTCCCTCTGTCCCATAATATAAGAG 59.043 42.308 0.00 0.00 0.00 2.85
3128 3471 5.721960 TCCCTCTGTCCCATAATATAAGAGC 59.278 44.000 0.00 0.00 0.00 4.09
3129 3472 5.485353 CCCTCTGTCCCATAATATAAGAGCA 59.515 44.000 0.00 0.00 0.00 4.26
3130 3473 6.157645 CCCTCTGTCCCATAATATAAGAGCAT 59.842 42.308 0.00 0.00 0.00 3.79
3131 3474 7.311549 CCCTCTGTCCCATAATATAAGAGCATT 60.312 40.741 0.00 0.00 0.00 3.56
3132 3475 8.105829 CCTCTGTCCCATAATATAAGAGCATTT 58.894 37.037 0.00 0.00 0.00 2.32
3133 3476 9.512588 CTCTGTCCCATAATATAAGAGCATTTT 57.487 33.333 0.00 0.00 0.00 1.82
3134 3477 9.866655 TCTGTCCCATAATATAAGAGCATTTTT 57.133 29.630 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
153 154 0.468400 GGGGAGAGCGTACCATCTCT 60.468 60.000 17.16 12.28 41.43 3.10
217 218 0.603975 GGCACGAAGGCTGAAACTCT 60.604 55.000 0.00 0.00 40.24 3.24
245 248 0.692756 TAGATGATTCCCGCACCCCA 60.693 55.000 0.00 0.00 0.00 4.96
248 251 0.759346 ACCTAGATGATTCCCGCACC 59.241 55.000 0.00 0.00 0.00 5.01
251 254 3.057734 CGTAAACCTAGATGATTCCCGC 58.942 50.000 0.00 0.00 0.00 6.13
252 255 3.069158 ACCGTAAACCTAGATGATTCCCG 59.931 47.826 0.00 0.00 0.00 5.14
275 278 2.451132 CGAGTATAAGCCACTCACACG 58.549 52.381 3.65 0.00 42.12 4.49
289 292 6.801953 TCCTTATTTCTAGATCCCCGAGTAT 58.198 40.000 0.00 0.00 0.00 2.12
293 296 5.024118 GGATCCTTATTTCTAGATCCCCGA 58.976 45.833 3.84 0.00 46.07 5.14
315 318 6.146673 ACCACGAGAAAAACTAGTAATTTCGG 59.853 38.462 20.04 17.90 37.95 4.30
429 432 4.274950 CCACAAATCGTACCAAGAAACACT 59.725 41.667 0.00 0.00 0.00 3.55
435 438 2.851263 AGCCACAAATCGTACCAAGA 57.149 45.000 0.00 0.00 0.00 3.02
443 446 1.640428 TTCGAGCTAGCCACAAATCG 58.360 50.000 12.13 13.14 0.00 3.34
450 453 1.333931 CAGTACGATTCGAGCTAGCCA 59.666 52.381 12.13 0.00 0.00 4.75
465 468 9.976255 TTTGACAACGCAATAATAATACAGTAC 57.024 29.630 0.00 0.00 0.00 2.73
485 488 6.072508 GCAACATCTTAACATCCTCTTTGACA 60.073 38.462 0.00 0.00 0.00 3.58
551 554 4.408182 ACTCCACCACTAAGCATATCAC 57.592 45.455 0.00 0.00 0.00 3.06
561 564 4.966168 TCTATGGCAATTACTCCACCACTA 59.034 41.667 0.00 0.00 34.81 2.74
583 589 5.009410 CCATCAAAGCTCCATACTTCCATTC 59.991 44.000 0.00 0.00 0.00 2.67
596 602 6.096001 ACAAATCAAGGATACCATCAAAGCTC 59.904 38.462 0.00 0.00 37.17 4.09
598 604 6.212888 ACAAATCAAGGATACCATCAAAGC 57.787 37.500 0.00 0.00 37.17 3.51
631 637 7.865889 CGGTAGAAGTTGCATACATACTGATAA 59.134 37.037 0.00 0.00 0.00 1.75
635 641 5.348986 ACGGTAGAAGTTGCATACATACTG 58.651 41.667 0.00 2.62 0.00 2.74
677 683 2.159028 AGGCTGAAGCTCGGATTTCTAC 60.159 50.000 1.74 0.00 41.70 2.59
686 692 3.496155 GAAAAATGAAGGCTGAAGCTCG 58.504 45.455 1.74 0.00 41.70 5.03
709 715 2.938451 TCATGCTAACCAATCGAGCTTG 59.062 45.455 0.00 0.00 40.74 4.01
832 838 8.685536 GTCGTACATAAAACGTCAGGATAATAC 58.314 37.037 0.00 0.00 41.08 1.89
844 850 6.252036 GTATGACCAGTCGTACATAAAACG 57.748 41.667 20.29 0.00 46.23 3.60
855 861 2.621338 ACAGCAATGTATGACCAGTCG 58.379 47.619 0.00 0.00 0.00 4.18
908 916 4.451629 AAAGGCAGCATCAGAAAAGATG 57.548 40.909 0.00 0.00 46.36 2.90
911 919 3.986277 ACAAAAGGCAGCATCAGAAAAG 58.014 40.909 0.00 0.00 0.00 2.27
928 937 5.649395 AGCAAAATGAGCTGCTATCTACAAA 59.351 36.000 0.15 0.00 46.92 2.83
929 938 5.188434 AGCAAAATGAGCTGCTATCTACAA 58.812 37.500 0.15 0.00 46.92 2.41
941 950 9.065871 CAAGTATAGTAAAACAGCAAAATGAGC 57.934 33.333 0.00 0.00 0.00 4.26
991 1000 5.082059 CGTCTGCAAATACATCAGAAACAC 58.918 41.667 0.00 0.00 38.42 3.32
1006 1015 3.345808 GGTGCGCTTCGTCTGCAA 61.346 61.111 9.73 0.00 40.83 4.08
1087 1096 8.043113 ACAAAGTTAGCTACATTCATGAGATCA 58.957 33.333 0.00 0.00 0.00 2.92
1103 1112 3.062234 GGATACGTGAGCACAAAGTTAGC 59.938 47.826 0.00 0.00 0.00 3.09
1122 1132 4.263331 CCTGGTACCTACACAACAAAGGAT 60.263 45.833 14.36 0.00 34.34 3.24
1220 1240 3.181497 CCATTGACAGATTTACCTTGCCG 60.181 47.826 0.00 0.00 0.00 5.69
1305 1330 8.445275 AAACACTTGTCATACAACATAAGACA 57.555 30.769 0.00 0.00 37.43 3.41
1306 1331 9.730420 AAAAACACTTGTCATACAACATAAGAC 57.270 29.630 0.00 0.00 33.96 3.01
1307 1332 9.729023 CAAAAACACTTGTCATACAACATAAGA 57.271 29.630 0.00 0.00 33.96 2.10
1308 1333 8.967218 CCAAAAACACTTGTCATACAACATAAG 58.033 33.333 0.00 0.00 33.96 1.73
1309 1334 7.436673 GCCAAAAACACTTGTCATACAACATAA 59.563 33.333 0.00 0.00 33.96 1.90
1401 1441 7.870509 TCCTCTAAACCATCATCATGAAAAG 57.129 36.000 0.00 0.00 30.57 2.27
1405 1445 6.789457 AGGTATCCTCTAAACCATCATCATGA 59.211 38.462 0.00 0.00 35.64 3.07
1428 1520 8.184192 CAGTTCAGCATATTAAAACCAAGTAGG 58.816 37.037 0.00 0.00 45.67 3.18
1452 1544 3.383620 TTATGTTTTGCCAACCAGCAG 57.616 42.857 0.00 0.00 45.13 4.24
1478 1570 6.258160 CAAGTTGCAACAGCCTACAATATAC 58.742 40.000 30.11 0.00 0.00 1.47
1499 1591 4.582701 TGACAATACAAAGGGTTGCAAG 57.417 40.909 0.00 0.00 38.39 4.01
1500 1592 4.586421 TCATGACAATACAAAGGGTTGCAA 59.414 37.500 0.00 0.00 38.39 4.08
1501 1593 4.148079 TCATGACAATACAAAGGGTTGCA 58.852 39.130 0.00 0.00 38.39 4.08
1502 1594 4.218417 ACTCATGACAATACAAAGGGTTGC 59.782 41.667 0.00 0.00 38.39 4.17
1503 1595 5.964958 ACTCATGACAATACAAAGGGTTG 57.035 39.130 0.00 0.00 40.84 3.77
1504 1596 5.833131 ACAACTCATGACAATACAAAGGGTT 59.167 36.000 0.00 0.00 0.00 4.11
1505 1597 5.385198 ACAACTCATGACAATACAAAGGGT 58.615 37.500 0.00 0.00 0.00 4.34
1533 1625 7.593644 GGTTAAAAGACGCAACATGAAGTAAAT 59.406 33.333 0.00 0.00 0.00 1.40
1542 1634 3.630312 ACAGTGGTTAAAAGACGCAACAT 59.370 39.130 0.00 0.00 0.00 2.71
1656 1749 9.229784 CATATACATGTCAATCAAAAGCTGTTC 57.770 33.333 0.00 0.00 0.00 3.18
1659 1752 7.933396 TCCATATACATGTCAATCAAAAGCTG 58.067 34.615 0.00 0.00 0.00 4.24
1660 1753 8.701908 ATCCATATACATGTCAATCAAAAGCT 57.298 30.769 0.00 0.00 0.00 3.74
1664 1757 9.531942 GCAAAATCCATATACATGTCAATCAAA 57.468 29.630 0.00 0.00 0.00 2.69
1665 1758 8.693625 TGCAAAATCCATATACATGTCAATCAA 58.306 29.630 0.00 0.00 0.00 2.57
1667 1760 8.971321 GTTGCAAAATCCATATACATGTCAATC 58.029 33.333 0.00 0.00 0.00 2.67
1668 1761 7.927629 GGTTGCAAAATCCATATACATGTCAAT 59.072 33.333 0.00 0.00 0.00 2.57
1669 1762 7.123997 AGGTTGCAAAATCCATATACATGTCAA 59.876 33.333 0.00 0.00 0.00 3.18
1670 1763 6.606796 AGGTTGCAAAATCCATATACATGTCA 59.393 34.615 0.00 0.00 0.00 3.58
1677 1823 7.582719 AGTTAGGAGGTTGCAAAATCCATATA 58.417 34.615 25.35 11.97 36.64 0.86
1690 1836 7.702348 GCAATAAGCATTAAAGTTAGGAGGTTG 59.298 37.037 0.00 0.00 44.79 3.77
1736 1883 3.494398 GGGCGCTGTTCCATATCTAGAAA 60.494 47.826 7.64 0.00 0.00 2.52
1759 1906 6.635755 AGTGACTAGAATAAAGAGAACTGGC 58.364 40.000 0.00 0.00 0.00 4.85
1795 1942 9.399797 GATGTTATCATCATTTCCATATGGCTA 57.600 33.333 17.58 7.46 46.78 3.93
1817 1964 8.427902 TTGACCTATCTATGAGCTATTGATGT 57.572 34.615 0.00 0.00 34.01 3.06
1822 1969 9.760926 TCACTATTGACCTATCTATGAGCTATT 57.239 33.333 0.00 0.00 0.00 1.73
1852 2000 1.135139 TCATGCGAGGAGACTAACAGC 59.865 52.381 0.00 0.00 44.43 4.40
1853 2001 3.724508 ATCATGCGAGGAGACTAACAG 57.275 47.619 0.00 0.00 44.43 3.16
1879 2027 9.710979 TCAAGAACGTGTTAACATAAAAAGAAG 57.289 29.630 12.26 0.00 0.00 2.85
1890 2038 6.044512 ACTGTGAATCAAGAACGTGTTAAC 57.955 37.500 0.00 0.00 0.00 2.01
1999 2147 1.202746 TGTGTAACTGGCATCAGCACA 60.203 47.619 9.81 9.81 44.59 4.57
2012 2160 9.931210 GCTATTTGGAAATATACAGTGTGTAAC 57.069 33.333 5.88 0.47 36.31 2.50
2235 2384 7.138736 ACAAGCCGATAAATAACATTGTATGC 58.861 34.615 0.00 0.00 0.00 3.14
2271 2421 5.459107 CACATTGTAACGTAGCCAGATACTC 59.541 44.000 0.00 0.00 0.00 2.59
2278 2428 5.333299 AGATACACATTGTAACGTAGCCA 57.667 39.130 0.00 0.00 36.31 4.75
2308 2458 4.502282 CAGTCAGACGATCATCTAAGCAAC 59.498 45.833 0.00 0.00 0.00 4.17
2309 2459 4.158579 ACAGTCAGACGATCATCTAAGCAA 59.841 41.667 0.00 0.00 0.00 3.91
2317 2467 5.184096 ACAAAGAGTACAGTCAGACGATCAT 59.816 40.000 0.00 0.00 0.00 2.45
2329 2479 1.452025 CGACACGCACAAAGAGTACAG 59.548 52.381 0.00 0.00 0.00 2.74
2330 2480 1.202325 ACGACACGCACAAAGAGTACA 60.202 47.619 0.00 0.00 0.00 2.90
2388 2538 1.156645 GCTGCCCTGCTAGTTCATCG 61.157 60.000 0.00 0.00 0.00 3.84
2391 2541 1.920325 AGGCTGCCCTGCTAGTTCA 60.920 57.895 16.57 0.00 40.94 3.18
2473 2625 6.956047 ACGGTCAAGTCAAGTAAATTTTCTC 58.044 36.000 0.00 0.00 0.00 2.87
2532 2684 1.689273 ACATCTGGGAGATTACGAGCC 59.311 52.381 0.00 0.00 31.32 4.70
2533 2685 2.362397 TGACATCTGGGAGATTACGAGC 59.638 50.000 0.00 0.00 31.32 5.03
2534 2686 3.549019 CGTGACATCTGGGAGATTACGAG 60.549 52.174 0.00 0.00 36.72 4.18
2535 2687 2.357952 CGTGACATCTGGGAGATTACGA 59.642 50.000 0.00 0.00 36.72 3.43
2536 2688 2.099263 ACGTGACATCTGGGAGATTACG 59.901 50.000 0.00 0.00 38.66 3.18
2537 2689 3.802948 ACGTGACATCTGGGAGATTAC 57.197 47.619 0.00 0.00 31.32 1.89
2541 2847 1.272490 GTGAACGTGACATCTGGGAGA 59.728 52.381 0.00 0.00 0.00 3.71
2556 2862 1.748493 TGTCCCACAAGCAAAGTGAAC 59.252 47.619 4.97 4.12 39.30 3.18
2560 2866 4.832266 TCATAATTGTCCCACAAGCAAAGT 59.168 37.500 0.00 0.00 41.94 2.66
2562 2868 5.279406 CCTTCATAATTGTCCCACAAGCAAA 60.279 40.000 0.00 0.00 41.94 3.68
2569 2875 5.192927 TGATGACCTTCATAATTGTCCCAC 58.807 41.667 0.00 0.00 37.20 4.61
2576 2882 6.425114 GTGCGTCTATGATGACCTTCATAATT 59.575 38.462 6.94 0.00 37.20 1.40
2577 2883 5.928839 GTGCGTCTATGATGACCTTCATAAT 59.071 40.000 6.94 0.00 37.20 1.28
2598 2904 0.675633 ACTTGTCCCAAGCAATGTGC 59.324 50.000 3.96 0.00 45.46 4.57
2600 2906 5.185056 GGTTAATACTTGTCCCAAGCAATGT 59.815 40.000 3.96 0.00 0.00 2.71
2601 2907 5.418840 AGGTTAATACTTGTCCCAAGCAATG 59.581 40.000 3.96 0.00 0.00 2.82
2602 2908 5.580022 AGGTTAATACTTGTCCCAAGCAAT 58.420 37.500 3.96 0.00 0.00 3.56
2603 2909 4.993028 AGGTTAATACTTGTCCCAAGCAA 58.007 39.130 3.96 0.00 0.00 3.91
2604 2910 4.650972 AGGTTAATACTTGTCCCAAGCA 57.349 40.909 3.96 0.00 0.00 3.91
2605 2911 5.310720 CAAGGTTAATACTTGTCCCAAGC 57.689 43.478 12.28 0.00 40.24 4.01
2618 2924 9.515226 ACTGTGTAATTGTATCACAAGGTTAAT 57.485 29.630 0.00 0.00 41.94 1.40
2619 2925 8.911918 ACTGTGTAATTGTATCACAAGGTTAA 57.088 30.769 0.00 0.00 41.94 2.01
2620 2926 8.779303 CAACTGTGTAATTGTATCACAAGGTTA 58.221 33.333 0.00 0.00 41.94 2.85
2621 2927 7.255451 CCAACTGTGTAATTGTATCACAAGGTT 60.255 37.037 0.00 0.00 41.94 3.50
2622 2928 6.206634 CCAACTGTGTAATTGTATCACAAGGT 59.793 38.462 0.00 0.00 41.94 3.50
2623 2929 6.349280 CCCAACTGTGTAATTGTATCACAAGG 60.349 42.308 0.00 0.00 41.94 3.61
2624 2930 6.429692 TCCCAACTGTGTAATTGTATCACAAG 59.570 38.462 0.00 0.00 41.94 3.16
2625 2931 6.205853 GTCCCAACTGTGTAATTGTATCACAA 59.794 38.462 0.00 0.00 42.95 3.33
2626 2932 5.703592 GTCCCAACTGTGTAATTGTATCACA 59.296 40.000 0.00 0.00 39.31 3.58
2627 2933 5.703592 TGTCCCAACTGTGTAATTGTATCAC 59.296 40.000 0.00 0.00 0.00 3.06
2632 2938 5.738783 GCAATTGTCCCAACTGTGTAATTGT 60.739 40.000 7.40 0.00 36.76 2.71
2638 2944 2.071778 AGCAATTGTCCCAACTGTGT 57.928 45.000 7.40 0.00 0.00 3.72
2640 2946 4.151883 ACATAAGCAATTGTCCCAACTGT 58.848 39.130 7.40 0.08 0.00 3.55
2646 2952 4.887071 TGGTGATACATAAGCAATTGTCCC 59.113 41.667 7.40 0.00 0.00 4.46
2659 2965 4.345257 AGATCGGCTAACTTGGTGATACAT 59.655 41.667 0.00 0.00 0.00 2.29
2668 2974 4.149571 CGATGATTCAGATCGGCTAACTTG 59.850 45.833 2.42 0.00 39.23 3.16
2671 2977 3.902150 TCGATGATTCAGATCGGCTAAC 58.098 45.455 9.19 0.00 42.43 2.34
2677 2983 5.697826 TCTCTTCATCGATGATTCAGATCG 58.302 41.667 27.75 15.98 43.32 3.69
2678 2984 8.461222 AGTATCTCTTCATCGATGATTCAGATC 58.539 37.037 29.48 23.54 36.56 2.75
2679 2985 8.352137 AGTATCTCTTCATCGATGATTCAGAT 57.648 34.615 29.00 29.00 36.56 2.90
2680 2986 7.757941 AGTATCTCTTCATCGATGATTCAGA 57.242 36.000 27.75 25.08 36.56 3.27
2681 2987 8.701540 CAAAGTATCTCTTCATCGATGATTCAG 58.298 37.037 27.75 21.40 36.56 3.02
2682 2988 7.170489 GCAAAGTATCTCTTCATCGATGATTCA 59.830 37.037 27.75 13.06 36.56 2.57
2683 2989 7.384660 AGCAAAGTATCTCTTCATCGATGATTC 59.615 37.037 27.75 11.10 36.56 2.52
2684 2990 7.171167 CAGCAAAGTATCTCTTCATCGATGATT 59.829 37.037 27.75 13.96 36.56 2.57
2685 2991 6.645827 CAGCAAAGTATCTCTTCATCGATGAT 59.354 38.462 27.75 15.41 36.56 2.45
2686 2992 5.981915 CAGCAAAGTATCTCTTCATCGATGA 59.018 40.000 23.99 23.99 35.02 2.92
2687 2993 5.981915 TCAGCAAAGTATCTCTTCATCGATG 59.018 40.000 19.61 19.61 35.02 3.84
2688 2994 6.154203 TCAGCAAAGTATCTCTTCATCGAT 57.846 37.500 0.00 0.00 35.02 3.59
2689 2995 5.582689 TCAGCAAAGTATCTCTTCATCGA 57.417 39.130 0.00 0.00 35.02 3.59
2690 2996 5.752472 ACATCAGCAAAGTATCTCTTCATCG 59.248 40.000 0.00 0.00 35.02 3.84
2694 3000 5.423015 TCCACATCAGCAAAGTATCTCTTC 58.577 41.667 0.00 0.00 35.02 2.87
2711 3017 8.717717 TCATCTTTCTCCAAAGTATATCCACAT 58.282 33.333 0.00 0.00 40.16 3.21
2714 3020 9.565090 CAATCATCTTTCTCCAAAGTATATCCA 57.435 33.333 0.00 0.00 40.16 3.41
2736 3042 9.573133 CATGGGTCTTGTACTTAAAAATCAATC 57.427 33.333 0.00 0.00 0.00 2.67
2737 3043 9.308000 TCATGGGTCTTGTACTTAAAAATCAAT 57.692 29.630 0.00 0.00 0.00 2.57
2749 3055 3.201290 CAGCAGATCATGGGTCTTGTAC 58.799 50.000 0.00 0.00 0.00 2.90
2752 3058 1.064906 ACCAGCAGATCATGGGTCTTG 60.065 52.381 14.09 0.00 41.13 3.02
2756 3062 1.077212 GCACCAGCAGATCATGGGT 60.077 57.895 14.09 4.92 41.13 4.51
2785 3105 5.440610 AGCCCATGATACTCCTTTACAAAG 58.559 41.667 0.00 0.00 35.79 2.77
2790 3110 7.472945 GCTTTAGTAGCCCATGATACTCCTTTA 60.473 40.741 8.05 0.00 42.49 1.85
2832 3152 9.516546 CCTCCTAAAACTTTACTTGTTTCCTAT 57.483 33.333 0.00 0.00 36.72 2.57
2833 3153 8.716779 TCCTCCTAAAACTTTACTTGTTTCCTA 58.283 33.333 0.00 0.00 36.72 2.94
2834 3154 7.580007 TCCTCCTAAAACTTTACTTGTTTCCT 58.420 34.615 0.00 0.00 36.72 3.36
2840 3160 8.947115 CCACTATTCCTCCTAAAACTTTACTTG 58.053 37.037 0.00 0.00 0.00 3.16
2842 3162 7.110810 GCCACTATTCCTCCTAAAACTTTACT 58.889 38.462 0.00 0.00 0.00 2.24
2843 3163 6.318144 GGCCACTATTCCTCCTAAAACTTTAC 59.682 42.308 0.00 0.00 0.00 2.01
2844 3164 6.012333 TGGCCACTATTCCTCCTAAAACTTTA 60.012 38.462 0.00 0.00 0.00 1.85
2845 3165 5.222254 TGGCCACTATTCCTCCTAAAACTTT 60.222 40.000 0.00 0.00 0.00 2.66
2846 3166 4.291249 TGGCCACTATTCCTCCTAAAACTT 59.709 41.667 0.00 0.00 0.00 2.66
2847 3167 3.850173 TGGCCACTATTCCTCCTAAAACT 59.150 43.478 0.00 0.00 0.00 2.66
2848 3168 4.230745 TGGCCACTATTCCTCCTAAAAC 57.769 45.455 0.00 0.00 0.00 2.43
2849 3169 5.044476 TGAATGGCCACTATTCCTCCTAAAA 60.044 40.000 8.16 0.00 34.43 1.52
2850 3170 4.476846 TGAATGGCCACTATTCCTCCTAAA 59.523 41.667 8.16 0.00 34.43 1.85
2860 3180 3.947834 GCACTTTACTGAATGGCCACTAT 59.052 43.478 8.16 0.00 0.00 2.12
2865 3185 1.544724 TGGCACTTTACTGAATGGCC 58.455 50.000 0.00 0.00 40.29 5.36
2877 3197 7.834068 CGCAAGAATATAGTATATGGCACTT 57.166 36.000 3.36 5.31 43.02 3.16
2912 3232 9.594478 AAAAAGTACAGTTAATTTCCAAACAGG 57.406 29.630 0.00 0.00 39.47 4.00
2940 3283 2.645797 AGTTAATTTCCACCCTCGGGAA 59.354 45.455 9.43 0.00 42.49 3.97
2941 3284 2.026636 CAGTTAATTTCCACCCTCGGGA 60.027 50.000 9.43 0.00 38.96 5.14
2942 3285 2.290705 ACAGTTAATTTCCACCCTCGGG 60.291 50.000 0.00 0.00 42.03 5.14
2943 3286 3.067684 ACAGTTAATTTCCACCCTCGG 57.932 47.619 0.00 0.00 0.00 4.63
2944 3287 4.828829 AGTACAGTTAATTTCCACCCTCG 58.171 43.478 0.00 0.00 0.00 4.63
2945 3288 6.235664 TCAAGTACAGTTAATTTCCACCCTC 58.764 40.000 0.00 0.00 0.00 4.30
2946 3289 6.195600 TCAAGTACAGTTAATTTCCACCCT 57.804 37.500 0.00 0.00 0.00 4.34
2947 3290 6.657541 TGATCAAGTACAGTTAATTTCCACCC 59.342 38.462 0.00 0.00 0.00 4.61
2948 3291 7.681939 TGATCAAGTACAGTTAATTTCCACC 57.318 36.000 0.00 0.00 0.00 4.61
2949 3292 8.730680 ACATGATCAAGTACAGTTAATTTCCAC 58.269 33.333 0.80 0.00 0.00 4.02
2950 3293 8.862325 ACATGATCAAGTACAGTTAATTTCCA 57.138 30.769 0.80 0.00 0.00 3.53
2958 3301 8.849168 TGAAATCAAACATGATCAAGTACAGTT 58.151 29.630 3.64 0.00 0.00 3.16
2959 3302 8.394971 TGAAATCAAACATGATCAAGTACAGT 57.605 30.769 3.64 0.00 0.00 3.55
3047 3390 8.626526 GGAATTGGTTACGGTATATTGATGTTT 58.373 33.333 0.00 0.00 0.00 2.83
3048 3391 7.996644 AGGAATTGGTTACGGTATATTGATGTT 59.003 33.333 0.00 0.00 0.00 2.71
3049 3392 7.444183 CAGGAATTGGTTACGGTATATTGATGT 59.556 37.037 0.00 0.00 0.00 3.06
3063 3406 2.030363 CGTTTGCTGCAGGAATTGGTTA 60.030 45.455 22.04 2.27 0.00 2.85
3067 3410 1.411394 CACGTTTGCTGCAGGAATTG 58.589 50.000 22.04 18.15 0.00 2.32
3072 3415 2.639286 GACCACGTTTGCTGCAGG 59.361 61.111 17.12 2.60 0.00 4.85
3083 3426 2.098607 AGTACATGATACCACGACCACG 59.901 50.000 0.00 0.00 45.75 4.94
3084 3427 3.490419 GGAGTACATGATACCACGACCAC 60.490 52.174 0.00 0.00 0.00 4.16
3085 3428 2.691526 GGAGTACATGATACCACGACCA 59.308 50.000 0.00 0.00 0.00 4.02
3086 3429 2.035576 GGGAGTACATGATACCACGACC 59.964 54.545 0.00 0.00 0.00 4.79
3087 3430 2.957006 AGGGAGTACATGATACCACGAC 59.043 50.000 0.00 0.00 0.00 4.34
3088 3431 3.117625 AGAGGGAGTACATGATACCACGA 60.118 47.826 0.00 0.00 0.00 4.35
3089 3432 3.004839 CAGAGGGAGTACATGATACCACG 59.995 52.174 0.00 0.00 0.00 4.94
3090 3433 3.961408 ACAGAGGGAGTACATGATACCAC 59.039 47.826 0.00 0.00 0.00 4.16
3091 3434 4.215908 GACAGAGGGAGTACATGATACCA 58.784 47.826 0.00 0.00 0.00 3.25
3092 3435 3.574826 GGACAGAGGGAGTACATGATACC 59.425 52.174 0.00 0.00 0.00 2.73
3093 3436 3.574826 GGGACAGAGGGAGTACATGATAC 59.425 52.174 0.00 0.00 0.00 2.24
3094 3437 3.206639 TGGGACAGAGGGAGTACATGATA 59.793 47.826 0.00 0.00 0.00 2.15
3095 3438 2.023015 TGGGACAGAGGGAGTACATGAT 60.023 50.000 0.00 0.00 0.00 2.45
3096 3439 1.361197 TGGGACAGAGGGAGTACATGA 59.639 52.381 0.00 0.00 0.00 3.07
3097 3440 1.866015 TGGGACAGAGGGAGTACATG 58.134 55.000 0.00 0.00 0.00 3.21


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

AutoCloner maintained by Alex Coulton.