Multiple sequence alignment - TraesCS6D01G046800

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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 TraesCS6D01G046800 chr6D 100.000 3572 0 0 1 3572 21049295 21052866 0.000000e+00 6597.0
1 TraesCS6D01G046800 chr6D 85.973 827 106 8 1786 2609 21376266 21377085 0.000000e+00 876.0
2 TraesCS6D01G046800 chr6D 81.341 552 76 18 1039 1565 21700411 21700960 1.190000e-114 424.0
3 TraesCS6D01G046800 chr6D 80.254 552 96 10 1029 1572 21904189 21904735 1.540000e-108 403.0
4 TraesCS6D01G046800 chr6D 88.095 336 33 3 1109 1437 21914759 21914424 3.340000e-105 392.0
5 TraesCS6D01G046800 chr6D 95.556 45 2 0 1521 1565 21889428 21889472 4.950000e-09 73.1
6 TraesCS6D01G046800 chr6A 93.326 2682 144 14 2 2678 21305284 21307935 0.000000e+00 3928.0
7 TraesCS6D01G046800 chr6A 87.158 475 38 14 3114 3572 21309544 21310011 5.290000e-143 518.0
8 TraesCS6D01G046800 chr6A 92.308 286 22 0 2836 3121 21307934 21308219 1.190000e-109 407.0
9 TraesCS6D01G046800 chr6A 84.906 318 42 2 1094 1405 21505146 21505463 2.070000e-82 316.0
10 TraesCS6D01G046800 chr6A 85.321 109 12 3 2176 2282 19885717 19885611 3.770000e-20 110.0
11 TraesCS6D01G046800 chr6B 83.001 1153 127 34 455 1565 36038451 36039576 0.000000e+00 979.0
12 TraesCS6D01G046800 chr6B 86.557 424 50 4 1021 1437 36176049 36176472 9.040000e-126 460.0
13 TraesCS6D01G046800 chr6B 80.832 553 91 11 1029 1572 36137588 36138134 1.530000e-113 420.0
14 TraesCS6D01G046800 chr6B 82.398 392 53 11 1188 1565 36131651 36132040 9.560000e-86 327.0
15 TraesCS6D01G046800 chr2A 80.851 376 58 10 1144 1509 758526635 758526264 2.100000e-72 283.0
16 TraesCS6D01G046800 chr5B 98.148 162 2 1 2677 2837 490757573 490757412 7.550000e-72 281.0
17 TraesCS6D01G046800 chr7B 96.471 170 4 2 2675 2843 11441306 11441138 2.720000e-71 279.0
18 TraesCS6D01G046800 chr7B 94.350 177 8 2 2672 2847 618334343 618334168 1.630000e-68 270.0
19 TraesCS6D01G046800 chr7B 95.322 171 6 2 2672 2841 618761020 618761189 1.630000e-68 270.0
20 TraesCS6D01G046800 chr4B 96.988 166 5 0 2672 2837 100321406 100321241 2.720000e-71 279.0
21 TraesCS6D01G046800 chr2D 97.561 164 2 2 2675 2837 624881948 624881786 2.720000e-71 279.0
22 TraesCS6D01G046800 chr2B 95.906 171 5 2 2675 2843 66994807 66994637 3.510000e-70 276.0
23 TraesCS6D01G046800 chr4D 95.376 173 6 2 2671 2842 471702478 471702649 1.260000e-69 274.0
24 TraesCS6D01G046800 chr7D 95.322 171 3 4 2673 2841 488692762 488692595 2.110000e-67 267.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G046800 chr6D 21049295 21052866 3571 False 6597.000000 6597 100.000000 1 3572 1 chr6D.!!$F1 3571
1 TraesCS6D01G046800 chr6D 21376266 21377085 819 False 876.000000 876 85.973000 1786 2609 1 chr6D.!!$F2 823
2 TraesCS6D01G046800 chr6D 21700411 21700960 549 False 424.000000 424 81.341000 1039 1565 1 chr6D.!!$F3 526
3 TraesCS6D01G046800 chr6D 21904189 21904735 546 False 403.000000 403 80.254000 1029 1572 1 chr6D.!!$F5 543
4 TraesCS6D01G046800 chr6A 21305284 21310011 4727 False 1617.666667 3928 90.930667 2 3572 3 chr6A.!!$F2 3570
5 TraesCS6D01G046800 chr6B 36038451 36039576 1125 False 979.000000 979 83.001000 455 1565 1 chr6B.!!$F1 1110
6 TraesCS6D01G046800 chr6B 36137588 36138134 546 False 420.000000 420 80.832000 1029 1572 1 chr6B.!!$F3 543

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
647 660 0.032813 ATTGGGTTGGGATCAGGCTG 60.033 55.0 8.58 8.58 0.00 4.85 F
701 714 0.179001 CCAAAACCCTGTCCGGTCTT 60.179 55.0 0.00 0.00 33.98 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1924 1985 0.038166 TCAGGTGGGGATTCAGCAAC 59.962 55.0 0.00 0.0 37.59 4.17 R
2637 2700 0.824109 CCCGCTGACCAGAATGACTA 59.176 55.0 0.47 0.0 39.69 2.59 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
28 29 3.286751 ACACATGCCCACACACGC 61.287 61.111 0.00 0.00 0.00 5.34
29 30 3.285982 CACATGCCCACACACGCA 61.286 61.111 0.00 0.00 39.79 5.24
30 31 3.286751 ACATGCCCACACACGCAC 61.287 61.111 0.00 0.00 37.93 5.34
31 32 4.388080 CATGCCCACACACGCACG 62.388 66.667 0.00 0.00 37.93 5.34
86 87 0.890542 GATGTTGGTGAGCAGTGGCA 60.891 55.000 0.00 0.00 44.61 4.92
94 95 2.959357 GAGCAGTGGCACAACGAGC 61.959 63.158 21.41 14.56 44.16 5.03
115 116 1.386533 GGAAGATGCTGGTGACATGG 58.613 55.000 0.00 0.00 41.51 3.66
123 124 0.911525 CTGGTGACATGGAGGAGGGT 60.912 60.000 0.00 0.00 41.51 4.34
126 127 1.616327 TGACATGGAGGAGGGTGGG 60.616 63.158 0.00 0.00 0.00 4.61
189 190 0.951040 GAGGTAGGGCGCATGCATAC 60.951 60.000 19.57 13.58 45.35 2.39
212 213 4.103103 CGACGAGGCGAGTGAGCA 62.103 66.667 0.00 0.00 39.27 4.26
214 215 4.427661 ACGAGGCGAGTGAGCAGC 62.428 66.667 0.00 0.00 39.27 5.25
218 219 2.358003 GGCGAGTGAGCAGCTGTT 60.358 61.111 16.64 9.79 39.27 3.16
239 240 4.626081 GTGGCGTGGTGGAGCTGT 62.626 66.667 0.00 0.00 0.00 4.40
242 243 2.740055 GCGTGGTGGAGCTGTGAG 60.740 66.667 0.00 0.00 0.00 3.51
310 311 2.636830 CAAGACATGTGGAGATGGGAC 58.363 52.381 1.15 0.00 0.00 4.46
318 319 2.119495 GTGGAGATGGGACTGTGGTAT 58.881 52.381 0.00 0.00 0.00 2.73
319 320 2.118679 TGGAGATGGGACTGTGGTATG 58.881 52.381 0.00 0.00 0.00 2.39
320 321 1.417890 GGAGATGGGACTGTGGTATGG 59.582 57.143 0.00 0.00 0.00 2.74
361 362 3.208592 AGAGGTGGGGGAGGGACA 61.209 66.667 0.00 0.00 0.00 4.02
369 370 3.493303 GGGAGGGACATGGGCCTC 61.493 72.222 4.53 0.00 0.00 4.70
382 383 1.452833 GGCCTCCATTCCTCACAGC 60.453 63.158 0.00 0.00 0.00 4.40
446 447 2.350895 CGTGGGCATGGGTGAGAA 59.649 61.111 0.00 0.00 0.00 2.87
450 451 1.139498 TGGGCATGGGTGAGAAGGAA 61.139 55.000 0.00 0.00 0.00 3.36
477 478 5.345202 GTCGCTCGAGAAAATCTTTTACTGA 59.655 40.000 18.75 0.00 0.00 3.41
489 490 9.546428 AAAATCTTTTACTGAGATTGGGTTTTG 57.454 29.630 0.58 0.00 41.66 2.44
647 660 0.032813 ATTGGGTTGGGATCAGGCTG 60.033 55.000 8.58 8.58 0.00 4.85
698 711 2.518933 CCCAAAACCCTGTCCGGT 59.481 61.111 0.00 0.00 37.93 5.28
701 714 0.179001 CCAAAACCCTGTCCGGTCTT 60.179 55.000 0.00 0.00 33.98 3.01
706 719 2.663196 CCTGTCCGGTCTTGTCCC 59.337 66.667 0.00 0.00 0.00 4.46
744 757 6.942532 TTTCTTGAGCTTAGTGTGAACAAT 57.057 33.333 0.00 0.00 0.00 2.71
745 758 6.942532 TTCTTGAGCTTAGTGTGAACAATT 57.057 33.333 0.00 0.00 0.00 2.32
891 917 3.066900 CGTATTCTCTGATCCCGAACTGT 59.933 47.826 0.00 0.00 0.00 3.55
1227 1279 3.970410 CTCCTGCTGCCCCCAACA 61.970 66.667 0.00 0.00 0.00 3.33
1343 1395 1.076995 TCCTCGGCTTCCTCGATGA 60.077 57.895 0.00 0.00 36.01 2.92
1377 1432 1.688269 CCGTAACCCCGCCTTATCCA 61.688 60.000 0.00 0.00 0.00 3.41
1425 1480 2.047179 GCCGCCGACTTCTCCTTT 60.047 61.111 0.00 0.00 0.00 3.11
1578 1639 4.078516 CCCCTGTTCCCCGACGAC 62.079 72.222 0.00 0.00 0.00 4.34
1580 1641 2.995574 CCTGTTCCCCGACGACCT 60.996 66.667 0.00 0.00 0.00 3.85
1598 1659 0.533755 CTAGCCGCTTCATTGGAGGG 60.534 60.000 0.00 2.00 0.00 4.30
1606 1667 2.203394 CATTGGAGGGCCCATCCG 60.203 66.667 27.56 11.34 46.10 4.18
1618 1679 0.240945 CCCATCCGCGATAAAATGGC 59.759 55.000 8.23 0.00 37.85 4.40
1632 1693 2.044123 AATGGCGTGAATCCTTCCTC 57.956 50.000 0.00 0.00 0.00 3.71
1635 1696 0.806492 GGCGTGAATCCTTCCTCGTC 60.806 60.000 0.00 0.00 0.00 4.20
1734 1795 3.809905 ACTGTTCACCTTTGTCTTCTCC 58.190 45.455 0.00 0.00 0.00 3.71
1738 1799 4.202264 TGTTCACCTTTGTCTTCTCCTCTC 60.202 45.833 0.00 0.00 0.00 3.20
1757 1818 2.048603 GCACTGGACAATGGGGAGC 61.049 63.158 0.00 0.00 0.00 4.70
1933 1994 1.347707 TGGAGTTCTCCGTTGCTGAAT 59.652 47.619 13.27 0.00 0.00 2.57
2002 2063 2.981560 GCTGGGGTGTTCGTGCATG 61.982 63.158 0.00 0.00 0.00 4.06
2009 2070 0.518636 GTGTTCGTGCATGCTCATGT 59.481 50.000 20.33 0.00 40.80 3.21
2083 2144 2.551459 CAGTGGCAGGAGAAGAAAACAG 59.449 50.000 0.00 0.00 0.00 3.16
2100 2161 7.410174 AGAAAACAGTATCATTGGGTTATGGA 58.590 34.615 0.00 0.00 0.00 3.41
2112 2173 8.102676 TCATTGGGTTATGGATACTACATCATG 58.897 37.037 0.00 0.00 37.61 3.07
2267 2329 1.953686 CTTCCCACCATCGTTGTTGTT 59.046 47.619 0.00 0.00 0.00 2.83
2282 2344 3.127589 TGTTGTTGTCACCGACAGTATG 58.872 45.455 0.00 0.00 43.69 2.39
2285 2347 4.061357 TGTTGTCACCGACAGTATGAAA 57.939 40.909 0.00 0.00 43.69 2.69
2303 2365 8.483758 AGTATGAAACGGTAAACTTCCTATCAT 58.516 33.333 0.00 0.00 0.00 2.45
2369 2431 5.353956 TGACAGTTCATTATTGGGATTGACG 59.646 40.000 0.00 0.00 0.00 4.35
2429 2491 1.909700 TTTGGCAAGGTTAGCTCAGG 58.090 50.000 0.00 0.00 0.00 3.86
2523 2585 6.937392 AGAAAGGAAGGATCTTACACACTAC 58.063 40.000 0.00 0.00 0.00 2.73
2635 2698 4.262164 CCTTTGGATTGTTTCACCTTGGAG 60.262 45.833 0.00 0.00 0.00 3.86
2637 2700 4.387026 TGGATTGTTTCACCTTGGAGAT 57.613 40.909 0.00 0.00 0.00 2.75
2653 2716 3.386078 TGGAGATAGTCATTCTGGTCAGC 59.614 47.826 0.00 0.00 0.00 4.26
2660 2723 0.036010 CATTCTGGTCAGCGGGACTT 60.036 55.000 10.68 0.00 46.16 3.01
2664 2727 2.743928 GGTCAGCGGGACTTGCAG 60.744 66.667 10.68 0.00 46.16 4.41
2665 2728 3.426568 GTCAGCGGGACTTGCAGC 61.427 66.667 4.55 0.00 43.46 5.25
2667 2730 2.265739 CAGCGGGACTTGCAGCTA 59.734 61.111 0.00 0.00 37.94 3.32
2678 2741 6.495706 GGGACTTGCAGCTACAAATTTATAC 58.504 40.000 0.11 0.00 0.00 1.47
2679 2742 6.318900 GGGACTTGCAGCTACAAATTTATACT 59.681 38.462 0.11 0.00 0.00 2.12
2680 2743 7.410485 GGACTTGCAGCTACAAATTTATACTC 58.590 38.462 0.11 0.00 0.00 2.59
2681 2744 7.321745 ACTTGCAGCTACAAATTTATACTCC 57.678 36.000 0.11 0.00 0.00 3.85
2682 2745 6.318900 ACTTGCAGCTACAAATTTATACTCCC 59.681 38.462 0.11 0.00 0.00 4.30
2683 2746 6.001449 TGCAGCTACAAATTTATACTCCCT 57.999 37.500 0.00 0.00 0.00 4.20
2684 2747 6.055588 TGCAGCTACAAATTTATACTCCCTC 58.944 40.000 0.00 0.00 0.00 4.30
2685 2748 5.470437 GCAGCTACAAATTTATACTCCCTCC 59.530 44.000 0.00 0.00 0.00 4.30
2686 2749 5.696724 CAGCTACAAATTTATACTCCCTCCG 59.303 44.000 0.00 0.00 0.00 4.63
2687 2750 5.365895 AGCTACAAATTTATACTCCCTCCGT 59.634 40.000 0.00 0.00 0.00 4.69
2688 2751 6.053650 GCTACAAATTTATACTCCCTCCGTT 58.946 40.000 0.00 0.00 0.00 4.44
2689 2752 6.202379 GCTACAAATTTATACTCCCTCCGTTC 59.798 42.308 0.00 0.00 0.00 3.95
2690 2753 5.434408 ACAAATTTATACTCCCTCCGTTCC 58.566 41.667 0.00 0.00 0.00 3.62
2691 2754 5.191124 ACAAATTTATACTCCCTCCGTTCCT 59.809 40.000 0.00 0.00 0.00 3.36
2692 2755 6.384886 ACAAATTTATACTCCCTCCGTTCCTA 59.615 38.462 0.00 0.00 0.00 2.94
2693 2756 7.092757 ACAAATTTATACTCCCTCCGTTCCTAA 60.093 37.037 0.00 0.00 0.00 2.69
2694 2757 7.441903 AATTTATACTCCCTCCGTTCCTAAA 57.558 36.000 0.00 0.00 0.00 1.85
2695 2758 7.628501 ATTTATACTCCCTCCGTTCCTAAAT 57.371 36.000 0.00 0.00 0.00 1.40
2696 2759 8.731591 ATTTATACTCCCTCCGTTCCTAAATA 57.268 34.615 0.00 0.00 0.00 1.40
2697 2760 8.731591 TTTATACTCCCTCCGTTCCTAAATAT 57.268 34.615 0.00 0.00 0.00 1.28
2698 2761 9.827198 TTTATACTCCCTCCGTTCCTAAATATA 57.173 33.333 0.00 0.00 0.00 0.86
2699 2762 9.827198 TTATACTCCCTCCGTTCCTAAATATAA 57.173 33.333 0.00 0.00 0.00 0.98
2700 2763 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
2701 2764 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
2702 2765 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
2703 2766 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
2704 2767 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
2705 2768 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
2706 2769 7.991460 CCCTCCGTTCCTAAATATAAGTCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
2707 2770 9.392259 CCTCCGTTCCTAAATATAAGTCTTTTT 57.608 33.333 0.00 0.00 0.00 1.94
2724 2787 8.380742 AGTCTTTTTAGAGATTCCACTATGGA 57.619 34.615 0.00 0.00 46.61 3.41
2735 2798 4.442401 TCCACTATGGACTACATACGGA 57.558 45.455 0.00 0.00 42.67 4.69
2736 2799 4.395625 TCCACTATGGACTACATACGGAG 58.604 47.826 0.00 0.00 42.67 4.63
2737 2800 3.057456 CCACTATGGACTACATACGGAGC 60.057 52.174 0.00 0.00 40.96 4.70
2738 2801 3.568430 CACTATGGACTACATACGGAGCA 59.432 47.826 0.00 0.00 41.03 4.26
2739 2802 4.037565 CACTATGGACTACATACGGAGCAA 59.962 45.833 0.00 0.00 41.03 3.91
2740 2803 4.647853 ACTATGGACTACATACGGAGCAAA 59.352 41.667 0.00 0.00 41.03 3.68
2741 2804 3.965379 TGGACTACATACGGAGCAAAA 57.035 42.857 0.00 0.00 0.00 2.44
2742 2805 4.481368 TGGACTACATACGGAGCAAAAT 57.519 40.909 0.00 0.00 0.00 1.82
2743 2806 4.188462 TGGACTACATACGGAGCAAAATG 58.812 43.478 0.00 0.00 0.00 2.32
2744 2807 4.081365 TGGACTACATACGGAGCAAAATGA 60.081 41.667 0.00 0.00 0.00 2.57
2745 2808 4.508124 GGACTACATACGGAGCAAAATGAG 59.492 45.833 0.00 0.00 0.00 2.90
2746 2809 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
2747 2810 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
2748 2811 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
2749 2812 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
2750 2813 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
2751 2814 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
2752 2815 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
2753 2816 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
2754 2817 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
2755 2818 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
2756 2819 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
2790 2853 8.865420 ATGTCTATATACATCCGTCTGTAGTT 57.135 34.615 0.00 0.00 35.08 2.24
2791 2854 8.687292 TGTCTATATACATCCGTCTGTAGTTT 57.313 34.615 1.56 0.00 35.21 2.66
2792 2855 8.565416 TGTCTATATACATCCGTCTGTAGTTTG 58.435 37.037 1.56 0.00 35.21 2.93
2793 2856 8.566260 GTCTATATACATCCGTCTGTAGTTTGT 58.434 37.037 1.56 0.00 35.21 2.83
2794 2857 9.783081 TCTATATACATCCGTCTGTAGTTTGTA 57.217 33.333 1.56 0.00 35.21 2.41
2796 2859 6.770746 ATACATCCGTCTGTAGTTTGTAGT 57.229 37.500 1.56 0.00 35.21 2.73
2797 2860 4.806330 ACATCCGTCTGTAGTTTGTAGTG 58.194 43.478 0.00 0.00 0.00 2.74
2798 2861 3.928727 TCCGTCTGTAGTTTGTAGTGG 57.071 47.619 0.00 0.00 0.00 4.00
2799 2862 3.489355 TCCGTCTGTAGTTTGTAGTGGA 58.511 45.455 0.00 0.00 0.00 4.02
2800 2863 3.890756 TCCGTCTGTAGTTTGTAGTGGAA 59.109 43.478 0.00 0.00 0.00 3.53
2801 2864 4.525487 TCCGTCTGTAGTTTGTAGTGGAAT 59.475 41.667 0.00 0.00 0.00 3.01
2802 2865 4.863131 CCGTCTGTAGTTTGTAGTGGAATC 59.137 45.833 0.00 0.00 0.00 2.52
2803 2866 5.336531 CCGTCTGTAGTTTGTAGTGGAATCT 60.337 44.000 0.00 0.00 0.00 2.40
2804 2867 5.800941 CGTCTGTAGTTTGTAGTGGAATCTC 59.199 44.000 0.00 0.00 0.00 2.75
2805 2868 6.349445 CGTCTGTAGTTTGTAGTGGAATCTCT 60.349 42.308 0.00 0.00 0.00 3.10
2806 2869 7.148289 CGTCTGTAGTTTGTAGTGGAATCTCTA 60.148 40.741 0.00 0.00 0.00 2.43
2807 2870 8.521176 GTCTGTAGTTTGTAGTGGAATCTCTAA 58.479 37.037 0.00 0.00 0.00 2.10
2808 2871 9.085645 TCTGTAGTTTGTAGTGGAATCTCTAAA 57.914 33.333 0.00 0.00 0.00 1.85
2809 2872 9.706691 CTGTAGTTTGTAGTGGAATCTCTAAAA 57.293 33.333 0.00 0.00 0.00 1.52
2810 2873 9.706691 TGTAGTTTGTAGTGGAATCTCTAAAAG 57.293 33.333 0.00 0.00 0.00 2.27
2811 2874 9.924650 GTAGTTTGTAGTGGAATCTCTAAAAGA 57.075 33.333 0.00 0.00 38.72 2.52
2812 2875 8.834749 AGTTTGTAGTGGAATCTCTAAAAGAC 57.165 34.615 0.00 0.00 36.65 3.01
2813 2876 8.652290 AGTTTGTAGTGGAATCTCTAAAAGACT 58.348 33.333 0.00 0.00 36.65 3.24
2814 2877 9.274206 GTTTGTAGTGGAATCTCTAAAAGACTT 57.726 33.333 0.00 0.00 36.65 3.01
2816 2879 9.924650 TTGTAGTGGAATCTCTAAAAGACTTAC 57.075 33.333 0.00 0.00 36.65 2.34
2817 2880 9.085645 TGTAGTGGAATCTCTAAAAGACTTACA 57.914 33.333 0.00 0.00 36.65 2.41
2827 2890 9.635520 TCTCTAAAAGACTTACATTTAGGAACG 57.364 33.333 0.00 0.00 39.07 3.95
2828 2891 8.767478 TCTAAAAGACTTACATTTAGGAACGG 57.233 34.615 0.00 0.00 39.07 4.44
2829 2892 8.587608 TCTAAAAGACTTACATTTAGGAACGGA 58.412 33.333 0.00 0.00 39.07 4.69
2830 2893 7.668525 AAAAGACTTACATTTAGGAACGGAG 57.331 36.000 0.00 0.00 0.00 4.63
2831 2894 5.340439 AGACTTACATTTAGGAACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
2832 2895 4.161754 AGACTTACATTTAGGAACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
2833 2896 4.098894 ACTTACATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
2834 2897 4.161754 ACTTACATTTAGGAACGGAGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
2835 2898 2.547990 ACATTTAGGAACGGAGGGAGT 58.452 47.619 0.00 0.00 0.00 3.85
2836 2899 3.716431 ACATTTAGGAACGGAGGGAGTA 58.284 45.455 0.00 0.00 0.00 2.59
2853 2916 3.119495 GGAGTATCATGTGTTGGTTTGGC 60.119 47.826 0.00 0.00 36.25 4.52
2871 2934 7.123397 TGGTTTGGCATAAATCTGCATAACTAA 59.877 33.333 0.00 0.00 44.12 2.24
2885 2948 8.469200 TCTGCATAACTAATATTTTTGCAGCTT 58.531 29.630 21.63 2.74 44.54 3.74
2888 2951 9.185192 GCATAACTAATATTTTTGCAGCTTAGG 57.815 33.333 0.00 0.00 0.00 2.69
2902 2965 0.322975 CTTAGGTGCTGAGCCACACT 59.677 55.000 0.23 0.00 37.46 3.55
2904 2967 1.121407 TAGGTGCTGAGCCACACTGT 61.121 55.000 0.23 0.00 37.46 3.55
2913 2976 2.369860 TGAGCCACACTGTTTGATCTCT 59.630 45.455 13.32 0.42 0.00 3.10
2921 2984 7.710907 GCCACACTGTTTGATCTCTTGTATATA 59.289 37.037 0.00 0.00 0.00 0.86
2964 3027 6.888632 ACTGGAATGATGCTGATTAGTTTCTT 59.111 34.615 0.00 0.00 0.00 2.52
2971 3034 8.268850 TGATGCTGATTAGTTTCTTAAGGAAC 57.731 34.615 17.61 17.61 33.13 3.62
2997 3060 7.172875 CCATTCCAAATTTGTTTGCTCAATACA 59.827 33.333 16.73 0.00 0.00 2.29
3000 3063 7.215789 TCCAAATTTGTTTGCTCAATACACAT 58.784 30.769 16.73 0.00 0.00 3.21
3040 3103 2.086869 GAGCTTGCCATCTTGTGCTTA 58.913 47.619 0.00 0.00 0.00 3.09
3048 3111 3.753272 GCCATCTTGTGCTTAGAAAGTGA 59.247 43.478 0.00 0.00 0.00 3.41
3065 3128 3.467803 AGTGAACCAGCTTGTTGTCTAC 58.532 45.455 8.09 2.51 0.00 2.59
3082 3145 5.428253 TGTCTACATAAATTGGAGGCAGTC 58.572 41.667 0.00 0.00 46.21 3.51
3182 4577 2.034066 TTGCCGGCAAGGAGGAAG 59.966 61.111 37.30 0.00 45.00 3.46
3183 4578 3.567579 TTGCCGGCAAGGAGGAAGG 62.568 63.158 37.30 0.00 45.00 3.46
3211 4612 1.299850 TTGTCCACAGAGTCGCACG 60.300 57.895 0.00 0.00 0.00 5.34
3236 4637 4.184079 GCAGAGAGCCAACAATCATTTT 57.816 40.909 0.00 0.00 37.23 1.82
3245 4646 4.611130 GCCAACAATCATTTTTGGAAAGCG 60.611 41.667 18.01 0.00 42.17 4.68
3258 4659 4.142609 TGGAAAGCGCTCTTAATCATCT 57.857 40.909 12.06 0.00 31.02 2.90
3265 4666 4.115516 GCGCTCTTAATCATCTTCTGACA 58.884 43.478 0.00 0.00 36.48 3.58
3308 4716 6.266168 TCATGTTCACAGTTTTTGTCAGTT 57.734 33.333 0.00 0.00 38.16 3.16
3309 4717 6.321717 TCATGTTCACAGTTTTTGTCAGTTC 58.678 36.000 0.00 0.00 38.16 3.01
3331 4741 7.278868 AGTTCAACTGTTCTTCTGTAAAGACTG 59.721 37.037 0.00 0.00 0.00 3.51
3332 4742 6.640518 TCAACTGTTCTTCTGTAAAGACTGT 58.359 36.000 0.00 0.00 0.00 3.55
3334 4744 8.255206 TCAACTGTTCTTCTGTAAAGACTGTAA 58.745 33.333 0.00 0.00 0.00 2.41
3335 4745 8.328864 CAACTGTTCTTCTGTAAAGACTGTAAC 58.671 37.037 0.00 0.00 0.00 2.50
3336 4746 7.783042 ACTGTTCTTCTGTAAAGACTGTAACT 58.217 34.615 0.00 0.00 0.00 2.24
3338 4748 7.778083 TGTTCTTCTGTAAAGACTGTAACTCA 58.222 34.615 0.00 0.00 0.00 3.41
3340 4750 7.818997 TCTTCTGTAAAGACTGTAACTCAGA 57.181 36.000 1.79 0.00 46.27 3.27
3341 4751 8.234136 TCTTCTGTAAAGACTGTAACTCAGAA 57.766 34.615 0.00 0.00 46.27 3.02
3354 4764 7.661847 ACTGTAACTCAGAAAGAAATAACCAGG 59.338 37.037 1.79 0.00 46.27 4.45
3363 4773 8.001292 CAGAAAGAAATAACCAGGGAGGATATT 58.999 37.037 0.00 0.00 44.56 1.28
3365 4775 9.286170 GAAAGAAATAACCAGGGAGGATATTAC 57.714 37.037 0.00 0.00 42.59 1.89
3458 4869 5.634859 GGATTGTTGTTTTGAGCGATCAAAT 59.365 36.000 27.48 12.32 39.07 2.32
3459 4870 5.886715 TTGTTGTTTTGAGCGATCAAATG 57.113 34.783 27.48 0.00 39.07 2.32
3465 4876 5.215160 GTTTTGAGCGATCAAATGAACAGT 58.785 37.500 27.48 0.00 39.07 3.55
3526 4937 9.717892 GAATTACTTTTTCAGATATTTCCGGAC 57.282 33.333 1.83 0.00 0.00 4.79
3529 4940 5.648092 ACTTTTTCAGATATTTCCGGACCTG 59.352 40.000 1.83 7.14 0.00 4.00
3539 4950 0.817634 TCCGGACCTGTTGCTTGTTG 60.818 55.000 0.00 0.00 0.00 3.33
3540 4951 1.008538 CGGACCTGTTGCTTGTTGC 60.009 57.895 0.00 0.00 43.25 4.17
3547 4958 3.233231 TTGCTTGTTGCCCTGCCC 61.233 61.111 0.00 0.00 42.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.466856 GGCATGTGTGTGGTGATCAT 58.533 50.000 0.00 0.00 0.00 2.45
28 29 0.456312 GCGTCTACCTCAAGACCGTG 60.456 60.000 0.00 0.00 42.46 4.94
29 30 1.593296 GGCGTCTACCTCAAGACCGT 61.593 60.000 0.00 0.00 42.46 4.83
30 31 1.139095 GGCGTCTACCTCAAGACCG 59.861 63.158 0.00 0.00 42.46 4.79
31 32 1.139095 CGGCGTCTACCTCAAGACC 59.861 63.158 0.00 0.00 42.46 3.85
86 87 1.741770 GCATCTTCCCGCTCGTTGT 60.742 57.895 0.00 0.00 0.00 3.32
94 95 0.107508 ATGTCACCAGCATCTTCCCG 60.108 55.000 0.00 0.00 0.00 5.14
129 130 2.516589 CGTGTCCCATGTGATCGCG 61.517 63.158 0.00 0.00 0.00 5.87
161 162 2.952245 CCCTACCTCGGCGATACG 59.048 66.667 11.27 3.39 0.00 3.06
227 228 1.302033 CCACTCACAGCTCCACCAC 60.302 63.158 0.00 0.00 0.00 4.16
301 302 1.417890 CCCATACCACAGTCCCATCTC 59.582 57.143 0.00 0.00 0.00 2.75
310 311 0.391130 CACGTGTCCCCATACCACAG 60.391 60.000 7.58 0.00 0.00 3.66
318 319 1.049855 ACCTGTTACACGTGTCCCCA 61.050 55.000 27.16 18.16 0.00 4.96
319 320 0.107268 AACCTGTTACACGTGTCCCC 59.893 55.000 27.16 14.40 0.00 4.81
320 321 1.223187 CAACCTGTTACACGTGTCCC 58.777 55.000 27.16 17.03 0.00 4.46
325 326 0.831966 TCCACCAACCTGTTACACGT 59.168 50.000 0.00 0.00 0.00 4.49
369 370 2.124570 CCCCGCTGTGAGGAATGG 60.125 66.667 0.00 0.00 0.00 3.16
441 442 0.805614 CGAGCGACTCTTCCTTCTCA 59.194 55.000 5.53 0.00 0.00 3.27
446 447 1.535833 TTTCTCGAGCGACTCTTCCT 58.464 50.000 7.81 0.00 0.00 3.36
450 451 3.859411 AAGATTTTCTCGAGCGACTCT 57.141 42.857 7.81 4.86 0.00 3.24
477 478 3.806949 TGAGTAGCCAAAACCCAATCT 57.193 42.857 0.00 0.00 0.00 2.40
544 545 9.663904 CGAATAATATGACAAATTGTACTTGGG 57.336 33.333 0.00 0.00 0.00 4.12
601 614 7.095857 CGAGCAATATGAAGAGTGACTATTTCC 60.096 40.741 0.00 0.00 0.00 3.13
698 711 1.191489 TCATGGACAGCGGGACAAGA 61.191 55.000 0.00 0.00 0.00 3.02
701 714 1.480212 AACTCATGGACAGCGGGACA 61.480 55.000 0.00 0.00 0.00 4.02
706 719 3.250762 TCAAGAAAAACTCATGGACAGCG 59.749 43.478 0.00 0.00 0.00 5.18
907 934 7.564793 TCAGAGTATATGCATTTTACTGTGGT 58.435 34.615 27.79 10.24 37.65 4.16
1214 1263 2.233566 AGATCTGTTGGGGGCAGCA 61.234 57.895 0.00 0.00 34.21 4.41
1227 1279 3.532155 GAGGCGCGGACCAGATCT 61.532 66.667 8.83 0.00 0.00 2.75
1343 1395 2.430704 TACGGGGTGGAAGACTCGGT 62.431 60.000 0.00 0.00 41.33 4.69
1425 1480 2.689771 GGGCCGGGTAGGAAGGAA 60.690 66.667 2.18 0.00 45.00 3.36
1449 1504 1.229209 GTCCAGGACCTCCCAGTCA 60.229 63.158 8.65 0.00 38.59 3.41
1578 1639 0.533755 CCTCCAATGAAGCGGCTAGG 60.534 60.000 1.35 0.00 0.00 3.02
1580 1641 1.526887 CCCTCCAATGAAGCGGCTA 59.473 57.895 1.35 0.00 0.00 3.93
1598 1659 0.240945 CCATTTTATCGCGGATGGGC 59.759 55.000 6.13 0.00 36.29 5.36
1606 1667 2.290641 AGGATTCACGCCATTTTATCGC 59.709 45.455 0.00 0.00 0.00 4.58
1624 1685 2.683933 GGCTGGGACGAGGAAGGA 60.684 66.667 0.00 0.00 0.00 3.36
1664 1725 2.162608 ACTCTGAATGACGTCTCTTCCG 59.837 50.000 17.92 14.82 0.00 4.30
1734 1795 0.742281 CCCATTGTCCAGTGCGAGAG 60.742 60.000 0.00 0.00 0.00 3.20
1738 1799 1.746615 CTCCCCATTGTCCAGTGCG 60.747 63.158 0.00 0.00 0.00 5.34
1757 1818 2.788956 TCCAACTCGGGGATGGAACAG 61.789 57.143 4.12 0.00 40.19 3.16
1924 1985 0.038166 TCAGGTGGGGATTCAGCAAC 59.962 55.000 0.00 0.00 37.59 4.17
1984 2045 2.672996 ATGCACGAACACCCCAGC 60.673 61.111 0.00 0.00 0.00 4.85
2002 2063 2.019984 GAACTTGGATCCCACATGAGC 58.980 52.381 9.90 0.00 30.78 4.26
2009 2070 4.473196 TGCTATAACTGAACTTGGATCCCA 59.527 41.667 9.90 0.00 0.00 4.37
2074 2135 7.893302 TCCATAACCCAATGATACTGTTTTCTT 59.107 33.333 0.00 0.00 0.00 2.52
2083 2144 9.601217 GATGTAGTATCCATAACCCAATGATAC 57.399 37.037 0.00 0.00 0.00 2.24
2100 2161 4.407621 TCCGTTGAACCCATGATGTAGTAT 59.592 41.667 0.00 0.00 0.00 2.12
2112 2173 1.264295 AGTACCTCTCCGTTGAACCC 58.736 55.000 0.00 0.00 0.00 4.11
2267 2329 2.608506 CCGTTTCATACTGTCGGTGACA 60.609 50.000 0.00 0.00 40.50 3.58
2282 2344 7.929785 TGGATATGATAGGAAGTTTACCGTTTC 59.070 37.037 0.00 0.00 0.00 2.78
2285 2347 6.014499 CCTGGATATGATAGGAAGTTTACCGT 60.014 42.308 0.00 0.00 33.33 4.83
2327 2389 3.066621 TGTCAGGAATCAAACAAGTGTGC 59.933 43.478 0.00 0.00 0.00 4.57
2369 2431 8.834749 AGTACCAAGTCATTTAAAGAAGAGTC 57.165 34.615 0.00 0.00 0.00 3.36
2398 2460 5.159273 ACCTTGCCAAAAGAACAGAAAAA 57.841 34.783 0.00 0.00 0.00 1.94
2429 2491 8.550376 ACAAACAAACAAATCACAATTATGCTC 58.450 29.630 0.00 0.00 0.00 4.26
2523 2585 1.417890 ACCCCTCAGGAATGCTTATCG 59.582 52.381 0.00 0.00 39.89 2.92
2603 2666 7.254761 GGTGAAACAATCCAAAGGTGAAAATTC 60.255 37.037 0.00 0.00 39.98 2.17
2635 2698 2.546795 CCCGCTGACCAGAATGACTATC 60.547 54.545 0.47 0.00 39.69 2.08
2637 2700 0.824109 CCCGCTGACCAGAATGACTA 59.176 55.000 0.47 0.00 39.69 2.59
2653 2716 1.453155 ATTTGTAGCTGCAAGTCCCG 58.547 50.000 16.93 0.00 35.30 5.14
2660 2723 6.001449 AGGGAGTATAAATTTGTAGCTGCA 57.999 37.500 0.00 0.00 0.00 4.41
2664 2727 5.608449 ACGGAGGGAGTATAAATTTGTAGC 58.392 41.667 0.00 0.00 0.00 3.58
2665 2728 6.704937 GGAACGGAGGGAGTATAAATTTGTAG 59.295 42.308 0.00 0.00 0.00 2.74
2667 2730 5.191124 AGGAACGGAGGGAGTATAAATTTGT 59.809 40.000 0.00 0.00 0.00 2.83
2678 2741 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
2679 2742 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
2680 2743 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
2681 2744 8.959705 AAAAGACTTATATTTAGGAACGGAGG 57.040 34.615 0.00 0.00 0.00 4.30
2698 2761 8.826765 TCCATAGTGGAATCTCTAAAAAGACTT 58.173 33.333 0.00 0.00 45.00 3.01
2699 2762 8.380742 TCCATAGTGGAATCTCTAAAAAGACT 57.619 34.615 0.00 0.00 45.00 3.24
2714 2777 4.395625 CTCCGTATGTAGTCCATAGTGGA 58.604 47.826 0.00 0.00 45.98 4.02
2715 2778 3.057456 GCTCCGTATGTAGTCCATAGTGG 60.057 52.174 0.00 0.00 36.71 4.00
2716 2779 3.568430 TGCTCCGTATGTAGTCCATAGTG 59.432 47.826 0.00 0.00 36.71 2.74
2717 2780 3.828921 TGCTCCGTATGTAGTCCATAGT 58.171 45.455 0.00 0.00 36.71 2.12
2718 2781 4.848562 TTGCTCCGTATGTAGTCCATAG 57.151 45.455 0.00 0.00 36.71 2.23
2719 2782 5.601583 TTTTGCTCCGTATGTAGTCCATA 57.398 39.130 0.00 0.00 34.86 2.74
2720 2783 4.481368 TTTTGCTCCGTATGTAGTCCAT 57.519 40.909 0.00 0.00 37.58 3.41
2721 2784 3.965379 TTTTGCTCCGTATGTAGTCCA 57.035 42.857 0.00 0.00 0.00 4.02
2722 2785 4.439057 TCATTTTGCTCCGTATGTAGTCC 58.561 43.478 0.00 0.00 0.00 3.85
2723 2786 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
2724 2787 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
2725 2788 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
2726 2789 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
2727 2790 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
2728 2791 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
2729 2792 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
2730 2793 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
2731 2794 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
2732 2795 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
2733 2796 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
2734 2797 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
2764 2827 9.955102 AACTACAGACGGATGTATATAGACATA 57.045 33.333 12.82 0.00 40.18 2.29
2765 2828 8.865420 AACTACAGACGGATGTATATAGACAT 57.135 34.615 12.70 12.70 42.82 3.06
2766 2829 8.565416 CAAACTACAGACGGATGTATATAGACA 58.435 37.037 2.07 2.07 35.21 3.41
2767 2830 8.566260 ACAAACTACAGACGGATGTATATAGAC 58.434 37.037 2.89 0.00 35.21 2.59
2768 2831 8.687292 ACAAACTACAGACGGATGTATATAGA 57.313 34.615 2.89 0.00 35.21 1.98
2770 2833 9.565090 ACTACAAACTACAGACGGATGTATATA 57.435 33.333 2.89 0.00 35.21 0.86
2771 2834 8.350722 CACTACAAACTACAGACGGATGTATAT 58.649 37.037 2.89 0.00 35.21 0.86
2772 2835 7.201758 CCACTACAAACTACAGACGGATGTATA 60.202 40.741 2.89 0.00 35.21 1.47
2773 2836 6.405508 CCACTACAAACTACAGACGGATGTAT 60.406 42.308 2.89 0.00 35.21 2.29
2774 2837 5.106038 CCACTACAAACTACAGACGGATGTA 60.106 44.000 2.54 2.54 34.56 2.29
2775 2838 4.321750 CCACTACAAACTACAGACGGATGT 60.322 45.833 0.32 0.32 37.19 3.06
2776 2839 4.082408 TCCACTACAAACTACAGACGGATG 60.082 45.833 0.00 0.00 0.00 3.51
2777 2840 4.084287 TCCACTACAAACTACAGACGGAT 58.916 43.478 0.00 0.00 0.00 4.18
2778 2841 3.489355 TCCACTACAAACTACAGACGGA 58.511 45.455 0.00 0.00 0.00 4.69
2779 2842 3.928727 TCCACTACAAACTACAGACGG 57.071 47.619 0.00 0.00 0.00 4.79
2780 2843 5.710984 AGATTCCACTACAAACTACAGACG 58.289 41.667 0.00 0.00 0.00 4.18
2781 2844 6.926313 AGAGATTCCACTACAAACTACAGAC 58.074 40.000 0.00 0.00 0.00 3.51
2782 2845 8.645814 TTAGAGATTCCACTACAAACTACAGA 57.354 34.615 0.00 0.00 0.00 3.41
2783 2846 9.706691 TTTTAGAGATTCCACTACAAACTACAG 57.293 33.333 0.00 0.00 0.00 2.74
2784 2847 9.706691 CTTTTAGAGATTCCACTACAAACTACA 57.293 33.333 0.00 0.00 0.00 2.74
2785 2848 9.924650 TCTTTTAGAGATTCCACTACAAACTAC 57.075 33.333 0.00 0.00 0.00 2.73
2786 2849 9.924650 GTCTTTTAGAGATTCCACTACAAACTA 57.075 33.333 0.00 0.00 36.61 2.24
2787 2850 8.652290 AGTCTTTTAGAGATTCCACTACAAACT 58.348 33.333 0.00 0.00 36.61 2.66
2788 2851 8.834749 AGTCTTTTAGAGATTCCACTACAAAC 57.165 34.615 0.00 0.00 36.61 2.93
2790 2853 9.924650 GTAAGTCTTTTAGAGATTCCACTACAA 57.075 33.333 0.00 0.00 36.61 2.41
2791 2854 9.085645 TGTAAGTCTTTTAGAGATTCCACTACA 57.914 33.333 0.00 0.00 36.61 2.74
2801 2864 9.635520 CGTTCCTAAATGTAAGTCTTTTAGAGA 57.364 33.333 11.88 7.17 41.88 3.10
2802 2865 8.870879 CCGTTCCTAAATGTAAGTCTTTTAGAG 58.129 37.037 11.88 5.70 41.88 2.43
2803 2866 8.587608 TCCGTTCCTAAATGTAAGTCTTTTAGA 58.412 33.333 11.88 0.00 41.88 2.10
2804 2867 8.767478 TCCGTTCCTAAATGTAAGTCTTTTAG 57.233 34.615 0.00 0.00 40.44 1.85
2805 2868 7.820872 CCTCCGTTCCTAAATGTAAGTCTTTTA 59.179 37.037 0.00 0.00 0.00 1.52
2806 2869 6.653740 CCTCCGTTCCTAAATGTAAGTCTTTT 59.346 38.462 0.00 0.00 0.00 2.27
2807 2870 6.171213 CCTCCGTTCCTAAATGTAAGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
2808 2871 5.338137 CCCTCCGTTCCTAAATGTAAGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
2809 2872 4.161754 CCCTCCGTTCCTAAATGTAAGTCT 59.838 45.833 0.00 0.00 0.00 3.24
2810 2873 4.161001 TCCCTCCGTTCCTAAATGTAAGTC 59.839 45.833 0.00 0.00 0.00 3.01
2811 2874 4.098894 TCCCTCCGTTCCTAAATGTAAGT 58.901 43.478 0.00 0.00 0.00 2.24
2812 2875 4.161754 ACTCCCTCCGTTCCTAAATGTAAG 59.838 45.833 0.00 0.00 0.00 2.34
2813 2876 4.098894 ACTCCCTCCGTTCCTAAATGTAA 58.901 43.478 0.00 0.00 0.00 2.41
2814 2877 3.716431 ACTCCCTCCGTTCCTAAATGTA 58.284 45.455 0.00 0.00 0.00 2.29
2815 2878 2.547990 ACTCCCTCCGTTCCTAAATGT 58.452 47.619 0.00 0.00 0.00 2.71
2816 2879 4.344102 TGATACTCCCTCCGTTCCTAAATG 59.656 45.833 0.00 0.00 0.00 2.32
2817 2880 4.553678 TGATACTCCCTCCGTTCCTAAAT 58.446 43.478 0.00 0.00 0.00 1.40
2818 2881 3.985127 TGATACTCCCTCCGTTCCTAAA 58.015 45.455 0.00 0.00 0.00 1.85
2819 2882 3.675348 TGATACTCCCTCCGTTCCTAA 57.325 47.619 0.00 0.00 0.00 2.69
2820 2883 3.117246 ACATGATACTCCCTCCGTTCCTA 60.117 47.826 0.00 0.00 0.00 2.94
2821 2884 2.320781 CATGATACTCCCTCCGTTCCT 58.679 52.381 0.00 0.00 0.00 3.36
2822 2885 2.040178 ACATGATACTCCCTCCGTTCC 58.960 52.381 0.00 0.00 0.00 3.62
2823 2886 2.431057 ACACATGATACTCCCTCCGTTC 59.569 50.000 0.00 0.00 0.00 3.95
2824 2887 2.467880 ACACATGATACTCCCTCCGTT 58.532 47.619 0.00 0.00 0.00 4.44
2825 2888 2.160721 ACACATGATACTCCCTCCGT 57.839 50.000 0.00 0.00 0.00 4.69
2826 2889 2.483714 CCAACACATGATACTCCCTCCG 60.484 54.545 0.00 0.00 0.00 4.63
2827 2890 2.505819 ACCAACACATGATACTCCCTCC 59.494 50.000 0.00 0.00 0.00 4.30
2828 2891 3.914426 ACCAACACATGATACTCCCTC 57.086 47.619 0.00 0.00 0.00 4.30
2829 2892 4.335416 CAAACCAACACATGATACTCCCT 58.665 43.478 0.00 0.00 0.00 4.20
2830 2893 3.443681 CCAAACCAACACATGATACTCCC 59.556 47.826 0.00 0.00 0.00 4.30
2831 2894 3.119495 GCCAAACCAACACATGATACTCC 60.119 47.826 0.00 0.00 0.00 3.85
2832 2895 3.505680 TGCCAAACCAACACATGATACTC 59.494 43.478 0.00 0.00 0.00 2.59
2833 2896 3.495331 TGCCAAACCAACACATGATACT 58.505 40.909 0.00 0.00 0.00 2.12
2834 2897 3.932545 TGCCAAACCAACACATGATAC 57.067 42.857 0.00 0.00 0.00 2.24
2835 2898 6.596309 TTTATGCCAAACCAACACATGATA 57.404 33.333 0.00 0.00 0.00 2.15
2836 2899 5.480642 TTTATGCCAAACCAACACATGAT 57.519 34.783 0.00 0.00 0.00 2.45
2885 2948 1.121407 ACAGTGTGGCTCAGCACCTA 61.121 55.000 0.00 0.00 36.35 3.08
2888 2951 0.029834 CAAACAGTGTGGCTCAGCAC 59.970 55.000 0.00 0.00 35.98 4.40
2921 2984 5.192927 TCCAGTTTTCCTCGCATCATTATT 58.807 37.500 0.00 0.00 0.00 1.40
2971 3034 6.563222 ATTGAGCAAACAAATTTGGAATGG 57.437 33.333 21.74 6.97 44.64 3.16
2977 3040 7.853524 ACATGTGTATTGAGCAAACAAATTTG 58.146 30.769 16.67 16.67 46.81 2.32
2997 3060 9.217278 GCTCTTCTTGATATATGAATGACATGT 57.783 33.333 0.00 0.00 39.77 3.21
3021 3084 2.089980 CTAAGCACAAGATGGCAAGCT 58.910 47.619 0.00 0.00 0.00 3.74
3040 3103 3.356290 ACAACAAGCTGGTTCACTTTCT 58.644 40.909 2.59 0.00 0.00 2.52
3048 3111 7.370383 CAATTTATGTAGACAACAAGCTGGTT 58.630 34.615 0.00 0.00 42.70 3.67
3096 3159 5.529800 GGCTGGTGAAAGTTTTAACTGTCTA 59.470 40.000 12.67 0.00 42.56 2.59
3101 3164 2.621526 CGGGCTGGTGAAAGTTTTAACT 59.378 45.455 0.00 0.00 42.04 2.24
3105 3168 1.739667 GCGGGCTGGTGAAAGTTTT 59.260 52.632 0.00 0.00 0.00 2.43
3144 4539 2.665603 GGCTCCGGCTCATATCCC 59.334 66.667 0.00 0.00 38.73 3.85
3187 4582 0.946221 GACTCTGTGGACAACTGCGG 60.946 60.000 0.00 0.00 0.00 5.69
3194 4595 2.335011 CGTGCGACTCTGTGGACA 59.665 61.111 0.00 0.00 0.00 4.02
3211 4612 0.034670 ATTGTTGGCTCTCTGCTCCC 60.035 55.000 0.00 0.00 42.39 4.30
3229 4630 4.525912 AAGAGCGCTTTCCAAAAATGAT 57.474 36.364 13.26 0.00 0.00 2.45
3236 4637 4.517285 AGATGATTAAGAGCGCTTTCCAA 58.483 39.130 13.26 4.22 35.56 3.53
3245 4646 5.752955 GTCCTGTCAGAAGATGATTAAGAGC 59.247 44.000 0.00 0.00 40.92 4.09
3258 4659 4.516698 GCTGAAAATGAAGTCCTGTCAGAA 59.483 41.667 0.00 0.00 34.30 3.02
3265 4666 4.978099 TGAAGAGCTGAAAATGAAGTCCT 58.022 39.130 0.00 0.00 0.00 3.85
3308 4716 6.640518 ACAGTCTTTACAGAAGAACAGTTGA 58.359 36.000 0.00 0.00 0.00 3.18
3309 4717 6.910536 ACAGTCTTTACAGAAGAACAGTTG 57.089 37.500 0.00 0.00 0.00 3.16
3331 4741 7.166167 TCCCTGGTTATTTCTTTCTGAGTTAC 58.834 38.462 0.00 0.00 0.00 2.50
3332 4742 7.324388 TCCCTGGTTATTTCTTTCTGAGTTA 57.676 36.000 0.00 0.00 0.00 2.24
3334 4744 5.280727 CCTCCCTGGTTATTTCTTTCTGAGT 60.281 44.000 0.00 0.00 0.00 3.41
3335 4745 5.045578 TCCTCCCTGGTTATTTCTTTCTGAG 60.046 44.000 0.00 0.00 37.07 3.35
3336 4746 4.849810 TCCTCCCTGGTTATTTCTTTCTGA 59.150 41.667 0.00 0.00 37.07 3.27
3338 4748 7.713704 ATATCCTCCCTGGTTATTTCTTTCT 57.286 36.000 0.00 0.00 37.07 2.52
3339 4749 9.286170 GTAATATCCTCCCTGGTTATTTCTTTC 57.714 37.037 0.00 0.00 39.84 2.62
3340 4750 9.015146 AGTAATATCCTCCCTGGTTATTTCTTT 57.985 33.333 0.00 0.00 39.84 2.52
3341 4751 8.582891 AGTAATATCCTCCCTGGTTATTTCTT 57.417 34.615 0.00 0.00 39.84 2.52
3430 4841 4.130857 TCGCTCAAAACAACAATCCAGTA 58.869 39.130 0.00 0.00 0.00 2.74
3431 4842 2.948979 TCGCTCAAAACAACAATCCAGT 59.051 40.909 0.00 0.00 0.00 4.00
3458 4869 9.841295 AACTACTGGAAATAGTTTAACTGTTCA 57.159 29.630 18.44 9.43 39.34 3.18
3504 4915 6.821665 CAGGTCCGGAAATATCTGAAAAAGTA 59.178 38.462 5.23 0.00 33.44 2.24
3505 4916 5.648092 CAGGTCCGGAAATATCTGAAAAAGT 59.352 40.000 5.23 0.00 33.44 2.66
3506 4917 5.648092 ACAGGTCCGGAAATATCTGAAAAAG 59.352 40.000 5.23 0.00 33.44 2.27
3509 4920 4.837093 ACAGGTCCGGAAATATCTGAAA 57.163 40.909 5.23 0.00 33.44 2.69
3518 4929 0.106918 ACAAGCAACAGGTCCGGAAA 60.107 50.000 5.23 0.00 0.00 3.13
3522 4933 1.008538 GCAACAAGCAACAGGTCCG 60.009 57.895 0.00 0.00 44.79 4.79
3547 4958 3.433615 AGACGCTAGCTAACTTTTGCAAG 59.566 43.478 13.93 0.00 35.92 4.01


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

AutoCloner maintained by Alex Coulton.