Multiple sequence alignment - TraesCS5A01G488600

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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 TraesCS5A01G488600 chr5A 100.000 3557 0 0 1 3557 658596509 658600065 0.000000e+00 6569.0
1 TraesCS5A01G488600 chr5A 88.889 135 12 2 3225 3356 658507849 658507715 2.840000e-36 163.0
2 TraesCS5A01G488600 chr5B 90.380 2474 158 33 578 2991 669481300 669483753 0.000000e+00 3177.0
3 TraesCS5A01G488600 chr5B 88.663 591 53 11 1 581 669480672 669481258 0.000000e+00 708.0
4 TraesCS5A01G488600 chr5B 92.268 194 15 0 3228 3421 669484171 669484364 3.500000e-70 276.0
5 TraesCS5A01G488600 chr5B 85.772 246 31 3 3172 3415 669439110 669438867 1.270000e-64 257.0
6 TraesCS5A01G488600 chr5B 84.454 238 34 2 3181 3416 669434904 669434668 7.680000e-57 231.0
7 TraesCS5A01G488600 chr5B 97.521 121 3 0 3435 3555 669485109 669485229 1.290000e-49 207.0
8 TraesCS5A01G488600 chr5B 86.740 181 24 0 3235 3415 669443242 669443062 6.020000e-48 202.0
9 TraesCS5A01G488600 chr5D 91.549 2118 130 25 901 2992 530404717 530406811 0.000000e+00 2874.0
10 TraesCS5A01G488600 chr5D 87.500 592 42 19 1 581 530403887 530404457 0.000000e+00 654.0
11 TraesCS5A01G488600 chr5D 93.519 216 12 1 579 792 530404500 530404715 1.590000e-83 320.0
12 TraesCS5A01G488600 chr5D 93.264 193 13 0 3228 3420 530407115 530407307 5.810000e-73 285.0
13 TraesCS5A01G488600 chr5D 85.425 247 33 2 3172 3416 530221087 530220842 1.640000e-63 254.0
14 TraesCS5A01G488600 chr5D 85.366 246 33 2 3172 3415 530302881 530302637 5.890000e-63 252.0
15 TraesCS5A01G488600 chr5D 95.041 121 6 0 3435 3555 530407688 530407808 1.300000e-44 191.0
16 TraesCS5A01G488600 chr5D 89.256 121 13 0 3435 3555 530169682 530169562 6.150000e-33 152.0
17 TraesCS5A01G488600 chr5D 87.603 121 15 0 3435 3555 530301859 530301739 1.330000e-29 141.0
18 TraesCS5A01G488600 chr5D 85.366 123 11 3 3435 3554 530346670 530346552 1.730000e-23 121.0
19 TraesCS5A01G488600 chr2D 87.805 123 12 2 3436 3555 627843201 627843079 1.330000e-29 141.0
20 TraesCS5A01G488600 chr2B 87.097 124 13 2 3435 3555 770100612 770100489 1.720000e-28 137.0
21 TraesCS5A01G488600 chr2B 86.179 123 14 2 3436 3555 770671176 770671298 2.880000e-26 130.0
22 TraesCS5A01G488600 chr6D 88.764 89 10 0 3469 3557 14360653 14360741 3.750000e-20 110.0
23 TraesCS5A01G488600 chr6D 96.970 33 0 1 3014 3046 187432674 187432705 2.000000e-03 54.7


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 TraesCS5A01G488600 chr5A 658596509 658600065 3556 False 6569.0 6569 100.000000 1 3557 1 chr5A.!!$F1 3556
1 TraesCS5A01G488600 chr5B 669480672 669485229 4557 False 1092.0 3177 92.208000 1 3555 4 chr5B.!!$F1 3554
2 TraesCS5A01G488600 chr5B 669434668 669443242 8574 True 230.0 257 85.655333 3172 3416 3 chr5B.!!$R1 244
3 TraesCS5A01G488600 chr5D 530403887 530407808 3921 False 864.8 2874 92.174600 1 3555 5 chr5D.!!$F1 3554

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
167 182 0.107017 AAATATGCCACCTCGCTGCT 60.107 50.0 0.0 0.0 0.00 4.24 F
1526 1676 0.472044 TGCAGACACCAAGGCAAGTA 59.528 50.0 0.0 0.0 32.54 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1606 1756 0.179023 TGCAGAACTGGCACATGACA 60.179 50.0 0.0 0.0 38.2 3.58 R
3099 3285 0.032952 TTCTAAACAGGTGCGTCGCT 59.967 50.0 19.5 0.0 0.0 4.93 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
49 50 2.813042 GCTGAGCAGGCGAGTGAC 60.813 66.667 0.00 0.00 0.00 3.67
64 65 1.842920 TGACCTGCAGGAGGAAGCA 60.843 57.895 39.19 21.13 46.33 3.91
80 81 3.865383 CATCGGCTGGCCCTGCTA 61.865 66.667 12.66 1.78 0.00 3.49
81 82 3.866582 ATCGGCTGGCCCTGCTAC 61.867 66.667 12.66 0.00 0.00 3.58
115 130 3.462678 GGAGGAGCTCGACCCCAC 61.463 72.222 7.83 0.00 0.00 4.61
167 182 0.107017 AAATATGCCACCTCGCTGCT 60.107 50.000 0.00 0.00 0.00 4.24
239 255 3.560453 GGTTAGCTTCCATGGTTGGTGTA 60.560 47.826 12.58 2.28 44.06 2.90
240 256 2.969821 AGCTTCCATGGTTGGTGTAA 57.030 45.000 12.58 0.00 44.06 2.41
291 311 2.613977 CCGATGTCATTAGAGGGGATGC 60.614 54.545 0.00 0.00 0.00 3.91
302 325 3.425659 AGAGGGGATGCAAGTCTTTTTC 58.574 45.455 0.00 0.00 0.00 2.29
342 368 8.116651 TCTAGACTGGATGATAACTGCTAATC 57.883 38.462 0.00 0.00 0.00 1.75
366 392 6.323996 TCAGACAACCTGGTAATATCACCTAG 59.676 42.308 0.00 0.00 43.12 3.02
456 485 9.776158 GTAATATCACCTAGACAATCTGATACG 57.224 37.037 0.00 0.00 0.00 3.06
475 504 8.089115 TGATACGTATCTTCTACAGTCTGATG 57.911 38.462 30.20 0.00 33.88 3.07
483 512 7.482169 TCTTCTACAGTCTGATGGTTACAAT 57.518 36.000 6.91 0.00 0.00 2.71
522 551 4.124851 CAGACTACCTGGTAATGTCACC 57.875 50.000 21.45 3.34 39.23 4.02
534 563 2.338577 ATGTCACCCAGCTAATCTGC 57.661 50.000 0.00 0.00 41.50 4.26
540 569 3.519510 TCACCCAGCTAATCTGCTAGTTT 59.480 43.478 0.00 0.00 41.98 2.66
639 759 9.862149 AGGATAACCATAATTCCGTATTTTTCT 57.138 29.630 0.00 0.00 38.94 2.52
677 797 2.618816 GCTGAAGGTGGAATGGATCACA 60.619 50.000 0.00 0.00 35.74 3.58
691 811 9.793259 GGAATGGATCACAAATAACCTTCTATA 57.207 33.333 0.00 0.00 0.00 1.31
843 965 8.342634 TGGTCGAAACAAAAGAGAGAATTTTAG 58.657 33.333 0.00 0.00 0.00 1.85
864 986 5.929058 AGATGAAGTGAAGATAGTGAGCA 57.071 39.130 0.00 0.00 0.00 4.26
866 988 6.887013 AGATGAAGTGAAGATAGTGAGCAAT 58.113 36.000 0.00 0.00 0.00 3.56
867 989 8.016301 AGATGAAGTGAAGATAGTGAGCAATA 57.984 34.615 0.00 0.00 0.00 1.90
876 1021 6.849085 AGATAGTGAGCAATACCTAGATGG 57.151 41.667 0.00 0.00 42.93 3.51
893 1038 1.072266 TGGAAGGGTGTAGGTGCATT 58.928 50.000 0.00 0.00 0.00 3.56
894 1039 2.270858 TGGAAGGGTGTAGGTGCATTA 58.729 47.619 0.00 0.00 0.00 1.90
933 1078 6.040955 TCCATCTCTAAACAATATCTCAGCGT 59.959 38.462 0.00 0.00 0.00 5.07
934 1079 6.703607 CCATCTCTAAACAATATCTCAGCGTT 59.296 38.462 0.00 0.00 0.00 4.84
1029 1178 1.066587 GGCAGATCGAAGACCTCCG 59.933 63.158 0.00 0.00 42.51 4.63
1178 1327 6.647067 ACTCGAAGTTTGAAGATCAAGTAAGG 59.353 38.462 0.00 0.00 37.70 2.69
1183 1332 8.519799 AAGTTTGAAGATCAAGTAAGGTTTCA 57.480 30.769 0.00 0.00 37.70 2.69
1205 1355 4.640201 CAGTTTTCGGTCCCATCATTATGT 59.360 41.667 0.00 0.00 0.00 2.29
1221 1371 6.899089 TCATTATGTACACCATCCAGACAAT 58.101 36.000 0.00 0.00 34.86 2.71
1222 1372 7.345691 TCATTATGTACACCATCCAGACAATT 58.654 34.615 0.00 0.00 34.86 2.32
1223 1373 7.282901 TCATTATGTACACCATCCAGACAATTG 59.717 37.037 3.24 3.24 34.86 2.32
1224 1374 4.365514 TGTACACCATCCAGACAATTGT 57.634 40.909 11.78 11.78 0.00 2.71
1225 1375 4.724399 TGTACACCATCCAGACAATTGTT 58.276 39.130 13.36 0.00 0.00 2.83
1226 1376 5.870706 TGTACACCATCCAGACAATTGTTA 58.129 37.500 13.36 0.00 0.00 2.41
1227 1377 6.299922 TGTACACCATCCAGACAATTGTTAA 58.700 36.000 13.36 0.00 0.00 2.01
1228 1378 6.945435 TGTACACCATCCAGACAATTGTTAAT 59.055 34.615 13.36 0.00 0.00 1.40
1380 1530 7.293745 GTCAAGTAATCACACAATTCAGACAG 58.706 38.462 0.00 0.00 0.00 3.51
1385 1535 6.889301 AATCACACAATTCAGACAGTCAAT 57.111 33.333 2.66 0.00 0.00 2.57
1389 1539 9.671279 ATCACACAATTCAGACAGTCAATATAA 57.329 29.630 2.66 0.00 0.00 0.98
1481 1631 3.386768 ACTGTTGCTAATGTCGTCACT 57.613 42.857 0.00 0.00 0.00 3.41
1526 1676 0.472044 TGCAGACACCAAGGCAAGTA 59.528 50.000 0.00 0.00 32.54 2.24
1606 1756 6.588719 TGCATAGCCATTTTTCAACTAACT 57.411 33.333 0.00 0.00 0.00 2.24
1756 1906 1.933853 GACTACACAATGATCGCCACC 59.066 52.381 0.00 0.00 0.00 4.61
1776 1926 4.510340 CACCACAACACTGGTAAGTAAGAC 59.490 45.833 0.00 0.00 43.15 3.01
1803 1956 6.168389 GTTTATAGGGTAATGGGTACATCGG 58.832 44.000 0.00 0.00 35.94 4.18
1823 1976 8.593679 ACATCGGAATATATGTTACCTTCATCA 58.406 33.333 0.00 0.00 32.43 3.07
1844 1997 8.905850 TCATCAATGCATATTAAGCAAGAAGAA 58.094 29.630 0.00 0.00 46.27 2.52
1846 1999 8.284945 TCAATGCATATTAAGCAAGAAGAACT 57.715 30.769 0.00 0.00 46.27 3.01
1849 2002 6.845302 TGCATATTAAGCAAGAAGAACTGTG 58.155 36.000 0.00 0.00 39.39 3.66
1850 2003 6.654582 TGCATATTAAGCAAGAAGAACTGTGA 59.345 34.615 0.00 0.00 39.39 3.58
1995 2148 6.472016 TGCATGTGATAACCTTCTTTCTGTA 58.528 36.000 0.00 0.00 0.00 2.74
2027 2180 4.185467 CTACATCAGCACTTCTGTCAGT 57.815 45.455 0.00 0.00 43.32 3.41
2039 2192 7.123397 AGCACTTCTGTCAGTCTGATTTATAGA 59.877 37.037 5.68 3.26 0.00 1.98
2051 2204 8.159447 AGTCTGATTTATAGATTATGCCTTGCA 58.841 33.333 0.00 0.00 44.86 4.08
2178 2334 1.503542 GGCATCAACGTTGCTCCTG 59.496 57.895 23.47 16.92 40.03 3.86
2208 2364 0.038744 CCTTGATGGTCACAGCCCTT 59.961 55.000 0.00 0.00 30.24 3.95
2263 2419 1.577736 AGCTCTCCTGCCATGTTACT 58.422 50.000 0.00 0.00 0.00 2.24
2361 2530 2.435805 ACACAAGAGTTCTCTTCTGCCA 59.564 45.455 14.50 0.00 0.00 4.92
2421 2590 2.271800 CTCAAGACGGCACATAACCTC 58.728 52.381 0.00 0.00 0.00 3.85
2499 2668 1.071471 GACCCCCTACATCCATGCG 59.929 63.158 0.00 0.00 0.00 4.73
2560 2729 1.880027 ACAAACTCCTTGAATGACGGC 59.120 47.619 0.00 0.00 38.50 5.68
2564 2733 3.627395 ACTCCTTGAATGACGGCATAA 57.373 42.857 2.90 0.00 33.44 1.90
2566 2735 3.879295 ACTCCTTGAATGACGGCATAATG 59.121 43.478 2.90 0.00 33.44 1.90
2569 2738 3.304257 CCTTGAATGACGGCATAATGAGC 60.304 47.826 2.90 0.00 33.44 4.26
2570 2739 3.198409 TGAATGACGGCATAATGAGCT 57.802 42.857 2.90 0.00 33.44 4.09
2572 2741 4.702831 TGAATGACGGCATAATGAGCTTA 58.297 39.130 2.90 0.00 33.44 3.09
2573 2742 5.308014 TGAATGACGGCATAATGAGCTTAT 58.692 37.500 2.90 0.00 33.44 1.73
2574 2743 6.463360 TGAATGACGGCATAATGAGCTTATA 58.537 36.000 2.90 0.00 33.44 0.98
2575 2744 7.105588 TGAATGACGGCATAATGAGCTTATAT 58.894 34.615 2.90 0.00 33.44 0.86
2576 2745 6.915544 ATGACGGCATAATGAGCTTATATG 57.084 37.500 0.00 8.99 31.57 1.78
2577 2746 5.793817 TGACGGCATAATGAGCTTATATGT 58.206 37.500 12.88 0.00 31.25 2.29
2579 2748 6.368791 TGACGGCATAATGAGCTTATATGTTC 59.631 38.462 12.88 9.19 31.25 3.18
2580 2749 6.467677 ACGGCATAATGAGCTTATATGTTCT 58.532 36.000 12.88 0.00 31.25 3.01
2582 2751 7.095060 ACGGCATAATGAGCTTATATGTTCTTG 60.095 37.037 12.88 5.08 31.25 3.02
2584 2753 7.308770 GGCATAATGAGCTTATATGTTCTTGCA 60.309 37.037 12.88 0.00 31.25 4.08
2585 2754 8.242053 GCATAATGAGCTTATATGTTCTTGCAT 58.758 33.333 12.88 0.00 31.25 3.96
2591 2760 4.797275 GCTTATATGTTCTTGCATTGCCCC 60.797 45.833 6.12 0.00 0.00 5.80
2592 2761 2.530460 TATGTTCTTGCATTGCCCCT 57.470 45.000 6.12 0.00 0.00 4.79
2593 2762 1.188863 ATGTTCTTGCATTGCCCCTC 58.811 50.000 6.12 0.00 0.00 4.30
2597 2769 2.681064 TTGCATTGCCCCTCCAGC 60.681 61.111 6.12 0.00 0.00 4.85
2599 2771 3.145551 GCATTGCCCCTCCAGCTG 61.146 66.667 6.78 6.78 0.00 4.24
2627 2799 7.218228 ACAAACTGTTGATAGCAATTCATCA 57.782 32.000 0.00 0.00 38.20 3.07
2635 2807 4.571984 TGATAGCAATTCATCAACCTGTCG 59.428 41.667 0.00 0.00 0.00 4.35
2636 2808 3.057969 AGCAATTCATCAACCTGTCGA 57.942 42.857 0.00 0.00 0.00 4.20
2637 2809 2.744202 AGCAATTCATCAACCTGTCGAC 59.256 45.455 9.11 9.11 0.00 4.20
2638 2810 2.483877 GCAATTCATCAACCTGTCGACA 59.516 45.455 18.88 18.88 0.00 4.35
2639 2811 3.127548 GCAATTCATCAACCTGTCGACAT 59.872 43.478 20.40 1.42 0.00 3.06
2642 2814 5.964958 ATTCATCAACCTGTCGACATTTT 57.035 34.783 20.40 12.15 0.00 1.82
2643 2815 5.356882 TTCATCAACCTGTCGACATTTTC 57.643 39.130 20.40 0.00 0.00 2.29
2644 2816 4.384940 TCATCAACCTGTCGACATTTTCA 58.615 39.130 20.40 1.67 0.00 2.69
2683 2858 2.343101 TCGGTTTACATTGAGCCGAAG 58.657 47.619 1.27 0.00 46.81 3.79
2685 2860 2.739913 CGGTTTACATTGAGCCGAAGAA 59.260 45.455 0.00 0.00 44.57 2.52
2694 2869 1.623311 TGAGCCGAAGAACATTGGAGA 59.377 47.619 0.00 0.00 0.00 3.71
2699 2874 4.636206 AGCCGAAGAACATTGGAGAATTAC 59.364 41.667 0.00 0.00 0.00 1.89
2703 2882 7.265673 CCGAAGAACATTGGAGAATTACTAGA 58.734 38.462 0.00 0.00 0.00 2.43
2719 2898 9.982291 GAATTACTAGAGTATATTGCTCTCTCG 57.018 37.037 11.32 5.39 41.85 4.04
2721 2900 5.250200 ACTAGAGTATATTGCTCTCTCGGG 58.750 45.833 11.32 0.00 41.85 5.14
2722 2901 3.426615 AGAGTATATTGCTCTCTCGGGG 58.573 50.000 4.29 0.00 38.86 5.73
2724 2903 3.574826 GAGTATATTGCTCTCTCGGGGTT 59.425 47.826 0.00 0.00 0.00 4.11
2730 2909 1.726533 GCTCTCTCGGGGTTAGACGG 61.727 65.000 0.00 0.00 0.00 4.79
2731 2910 1.726533 CTCTCTCGGGGTTAGACGGC 61.727 65.000 0.00 0.00 0.00 5.68
2735 2914 1.000233 TCGGGGTTAGACGGCCTAA 60.000 57.895 0.00 0.00 35.11 2.69
2737 2916 1.828081 GGGGTTAGACGGCCTAAGG 59.172 63.158 0.00 0.00 37.98 2.69
2738 2917 0.979709 GGGGTTAGACGGCCTAAGGT 60.980 60.000 0.00 0.00 37.98 3.50
2739 2918 1.689258 GGGGTTAGACGGCCTAAGGTA 60.689 57.143 0.00 0.00 37.98 3.08
2740 2919 2.323599 GGGTTAGACGGCCTAAGGTAT 58.676 52.381 0.00 0.00 37.98 2.73
2741 2920 3.500343 GGGTTAGACGGCCTAAGGTATA 58.500 50.000 0.00 0.00 37.98 1.47
2742 2921 3.897505 GGGTTAGACGGCCTAAGGTATAA 59.102 47.826 0.00 0.00 37.98 0.98
2749 2928 5.658190 AGACGGCCTAAGGTATAAGTTTGTA 59.342 40.000 0.00 0.00 0.00 2.41
2750 2929 6.155049 AGACGGCCTAAGGTATAAGTTTGTAA 59.845 38.462 0.00 0.00 0.00 2.41
2902 3088 4.442753 GGTTGTTGGCATTTTCCTTTCTGA 60.443 41.667 0.00 0.00 0.00 3.27
2939 3125 8.641498 AGTTGATATTTTTCCTCTGTTGACAT 57.359 30.769 0.00 0.00 0.00 3.06
2940 3126 9.082313 AGTTGATATTTTTCCTCTGTTGACATT 57.918 29.630 0.00 0.00 0.00 2.71
2941 3127 9.696917 GTTGATATTTTTCCTCTGTTGACATTT 57.303 29.630 0.00 0.00 0.00 2.32
2942 3128 9.912634 TTGATATTTTTCCTCTGTTGACATTTC 57.087 29.630 0.00 0.00 0.00 2.17
2943 3129 8.236586 TGATATTTTTCCTCTGTTGACATTTCG 58.763 33.333 0.00 0.00 0.00 3.46
2996 3182 8.463930 AAAACTTATCTTTGAAGACCATGTCA 57.536 30.769 0.00 0.00 37.98 3.58
2997 3183 8.463930 AAACTTATCTTTGAAGACCATGTCAA 57.536 30.769 0.00 0.00 37.98 3.18
2998 3184 7.678947 ACTTATCTTTGAAGACCATGTCAAG 57.321 36.000 0.00 0.00 37.98 3.02
2999 3185 7.453393 ACTTATCTTTGAAGACCATGTCAAGA 58.547 34.615 0.00 0.00 37.98 3.02
3000 3186 7.389053 ACTTATCTTTGAAGACCATGTCAAGAC 59.611 37.037 0.00 0.00 37.98 3.01
3002 3188 5.684704 TCTTTGAAGACCATGTCAAGACTT 58.315 37.500 1.53 0.00 35.29 3.01
3003 3189 5.528690 TCTTTGAAGACCATGTCAAGACTTG 59.471 40.000 9.03 9.03 35.29 3.16
3005 3191 4.129380 TGAAGACCATGTCAAGACTTGTG 58.871 43.478 14.75 6.24 35.46 3.33
3007 3193 4.156455 AGACCATGTCAAGACTTGTGTT 57.844 40.909 14.75 0.00 35.46 3.32
3008 3194 4.130118 AGACCATGTCAAGACTTGTGTTC 58.870 43.478 14.75 4.67 35.46 3.18
3009 3195 3.876914 GACCATGTCAAGACTTGTGTTCA 59.123 43.478 14.75 10.27 35.46 3.18
3011 3197 5.504665 GACCATGTCAAGACTTGTGTTCAAG 60.505 44.000 14.75 6.44 42.77 3.02
3012 3198 7.841735 GACCATGTCAAGACTTGTGTTCAAGT 61.842 42.308 14.75 12.43 46.89 3.16
3020 3206 3.199880 CTTGTGTTCAAGTCCCTCAGT 57.800 47.619 0.00 0.00 44.09 3.41
3022 3208 1.416401 TGTGTTCAAGTCCCTCAGTCC 59.584 52.381 0.00 0.00 0.00 3.85
3024 3210 1.056660 GTTCAAGTCCCTCAGTCCCA 58.943 55.000 0.00 0.00 0.00 4.37
3025 3211 1.630878 GTTCAAGTCCCTCAGTCCCAT 59.369 52.381 0.00 0.00 0.00 4.00
3028 3214 3.736094 TCAAGTCCCTCAGTCCCATAAT 58.264 45.455 0.00 0.00 0.00 1.28
3030 3216 5.476983 TCAAGTCCCTCAGTCCCATAATAT 58.523 41.667 0.00 0.00 0.00 1.28
3031 3217 6.630131 TCAAGTCCCTCAGTCCCATAATATA 58.370 40.000 0.00 0.00 0.00 0.86
3036 3222 7.016661 AGTCCCTCAGTCCCATAATATAAAGTG 59.983 40.741 0.00 0.00 0.00 3.16
3037 3223 6.849697 TCCCTCAGTCCCATAATATAAAGTGT 59.150 38.462 0.00 0.00 0.00 3.55
3038 3224 7.349859 TCCCTCAGTCCCATAATATAAAGTGTT 59.650 37.037 0.00 0.00 0.00 3.32
3039 3225 7.998964 CCCTCAGTCCCATAATATAAAGTGTTT 59.001 37.037 0.00 0.00 0.00 2.83
3040 3226 9.408648 CCTCAGTCCCATAATATAAAGTGTTTT 57.591 33.333 0.00 0.00 0.00 2.43
3062 3248 9.199982 GTTTTGTACACTAGTGCTATGTAAGAA 57.800 33.333 22.90 4.02 30.90 2.52
3063 3249 9.767228 TTTTGTACACTAGTGCTATGTAAGAAA 57.233 29.630 22.90 8.64 30.90 2.52
3064 3250 9.938280 TTTGTACACTAGTGCTATGTAAGAAAT 57.062 29.630 22.90 0.96 30.90 2.17
3069 3255 9.284968 ACACTAGTGCTATGTAAGAAATTTTGT 57.715 29.630 22.90 0.00 0.00 2.83
3072 3258 7.759489 AGTGCTATGTAAGAAATTTTGTGGA 57.241 32.000 0.00 0.00 0.00 4.02
3073 3259 7.820648 AGTGCTATGTAAGAAATTTTGTGGAG 58.179 34.615 0.00 0.00 0.00 3.86
3077 3263 9.937175 GCTATGTAAGAAATTTTGTGGAGTATC 57.063 33.333 0.00 0.00 0.00 2.24
3082 3268 6.683974 AGAAATTTTGTGGAGTATCATCCG 57.316 37.500 0.00 0.00 42.77 4.18
3083 3269 6.414732 AGAAATTTTGTGGAGTATCATCCGA 58.585 36.000 0.00 0.00 42.77 4.55
3084 3270 6.316390 AGAAATTTTGTGGAGTATCATCCGAC 59.684 38.462 0.00 0.00 42.77 4.79
3086 3272 3.801114 TTGTGGAGTATCATCCGACTG 57.199 47.619 0.00 0.00 42.77 3.51
3092 3278 4.039245 TGGAGTATCATCCGACTGAATTCC 59.961 45.833 2.27 0.00 42.77 3.01
3094 3280 3.967326 AGTATCATCCGACTGAATTCCCA 59.033 43.478 2.27 0.00 0.00 4.37
3096 3282 3.266510 TCATCCGACTGAATTCCCAAG 57.733 47.619 2.27 0.00 0.00 3.61
3098 3284 2.762535 TCCGACTGAATTCCCAAGTC 57.237 50.000 12.30 12.30 0.00 3.01
3099 3285 1.974957 TCCGACTGAATTCCCAAGTCA 59.025 47.619 19.03 3.81 33.99 3.41
3103 3289 2.099141 CTGAATTCCCAAGTCAGCGA 57.901 50.000 2.27 0.00 45.12 4.93
3104 3290 1.734465 CTGAATTCCCAAGTCAGCGAC 59.266 52.381 2.27 1.15 45.12 5.19
3106 3292 1.298859 AATTCCCAAGTCAGCGACGC 61.299 55.000 13.03 13.03 37.67 5.19
3109 3295 3.414700 CCAAGTCAGCGACGCACC 61.415 66.667 23.70 8.94 37.67 5.01
3110 3296 2.356313 CAAGTCAGCGACGCACCT 60.356 61.111 23.70 11.23 37.67 4.00
3111 3297 2.356313 AAGTCAGCGACGCACCTG 60.356 61.111 23.70 12.00 37.67 4.00
3115 3301 0.942410 GTCAGCGACGCACCTGTTTA 60.942 55.000 23.70 0.00 0.00 2.01
3117 3303 0.666274 CAGCGACGCACCTGTTTAGA 60.666 55.000 23.70 0.00 0.00 2.10
3118 3304 0.032952 AGCGACGCACCTGTTTAGAA 59.967 50.000 23.70 0.00 0.00 2.10
3120 3306 1.068474 CGACGCACCTGTTTAGAAGG 58.932 55.000 0.00 0.00 40.93 3.46
3122 3308 2.762745 GACGCACCTGTTTAGAAGGAA 58.237 47.619 0.00 0.00 38.27 3.36
3123 3309 3.335579 GACGCACCTGTTTAGAAGGAAT 58.664 45.455 0.00 0.00 38.27 3.01
3124 3310 4.501071 GACGCACCTGTTTAGAAGGAATA 58.499 43.478 0.00 0.00 38.27 1.75
3126 3312 4.250464 CGCACCTGTTTAGAAGGAATACA 58.750 43.478 0.00 0.00 38.27 2.29
3128 3314 5.180492 CGCACCTGTTTAGAAGGAATACAAA 59.820 40.000 0.00 0.00 38.27 2.83
3130 3316 7.029563 GCACCTGTTTAGAAGGAATACAAATG 58.970 38.462 0.00 0.00 38.27 2.32
3131 3317 7.538575 CACCTGTTTAGAAGGAATACAAATGG 58.461 38.462 0.00 0.00 38.27 3.16
3132 3318 7.393234 CACCTGTTTAGAAGGAATACAAATGGA 59.607 37.037 0.00 0.00 38.27 3.41
3133 3319 7.611855 ACCTGTTTAGAAGGAATACAAATGGAG 59.388 37.037 0.00 0.00 38.27 3.86
3134 3320 7.391148 TGTTTAGAAGGAATACAAATGGAGC 57.609 36.000 0.00 0.00 0.00 4.70
3135 3321 7.175104 TGTTTAGAAGGAATACAAATGGAGCT 58.825 34.615 0.00 0.00 0.00 4.09
3136 3322 7.336931 TGTTTAGAAGGAATACAAATGGAGCTC 59.663 37.037 4.71 4.71 0.00 4.09
3137 3323 5.707066 AGAAGGAATACAAATGGAGCTCT 57.293 39.130 14.64 0.00 0.00 4.09
3138 3324 5.435291 AGAAGGAATACAAATGGAGCTCTG 58.565 41.667 14.64 6.40 0.00 3.35
3139 3325 4.851639 AGGAATACAAATGGAGCTCTGT 57.148 40.909 14.64 12.39 0.00 3.41
3140 3326 4.521146 AGGAATACAAATGGAGCTCTGTG 58.479 43.478 14.64 9.04 0.00 3.66
3141 3327 3.065925 GGAATACAAATGGAGCTCTGTGC 59.934 47.826 14.64 4.53 43.29 4.57
3142 3328 2.113860 TACAAATGGAGCTCTGTGCC 57.886 50.000 14.64 0.00 44.23 5.01
3143 3329 0.111061 ACAAATGGAGCTCTGTGCCA 59.889 50.000 14.64 3.21 44.23 4.92
3144 3330 1.272313 ACAAATGGAGCTCTGTGCCAT 60.272 47.619 14.64 5.82 43.95 4.40
3146 3332 1.035932 AATGGAGCTCTGTGCCATGC 61.036 55.000 14.64 0.00 41.36 4.06
3148 3334 1.453379 GGAGCTCTGTGCCATGCAT 60.453 57.895 14.64 0.00 41.91 3.96
3149 3335 1.725557 GGAGCTCTGTGCCATGCATG 61.726 60.000 20.19 20.19 41.91 4.06
3150 3336 1.001269 AGCTCTGTGCCATGCATGT 60.001 52.632 24.58 0.18 41.91 3.21
3151 3337 1.138883 GCTCTGTGCCATGCATGTG 59.861 57.895 24.58 16.68 41.91 3.21
3152 3338 1.310216 GCTCTGTGCCATGCATGTGA 61.310 55.000 24.58 8.31 41.91 3.58
3153 3339 1.389555 CTCTGTGCCATGCATGTGAT 58.610 50.000 24.58 0.00 41.91 3.06
3154 3340 1.333931 CTCTGTGCCATGCATGTGATC 59.666 52.381 24.58 12.43 41.91 2.92
3155 3341 0.028902 CTGTGCCATGCATGTGATCG 59.971 55.000 24.58 10.45 41.91 3.69
3157 3343 0.306840 GTGCCATGCATGTGATCGAG 59.693 55.000 24.58 9.02 41.91 4.04
3158 3344 0.107557 TGCCATGCATGTGATCGAGT 60.108 50.000 24.58 0.00 31.71 4.18
3160 3346 1.003116 GCCATGCATGTGATCGAGTTC 60.003 52.381 24.58 0.00 0.00 3.01
3170 3356 4.889427 TCGAGTTCGACCATGCTG 57.111 55.556 0.00 0.00 44.22 4.41
3172 3358 2.456119 CGAGTTCGACCATGCTGCC 61.456 63.158 0.00 0.00 43.02 4.85
3173 3359 2.045926 AGTTCGACCATGCTGCCC 60.046 61.111 0.00 0.00 0.00 5.36
3174 3360 2.045926 GTTCGACCATGCTGCCCT 60.046 61.111 0.00 0.00 0.00 5.19
3176 3362 4.783621 TCGACCATGCTGCCCTGC 62.784 66.667 0.00 0.00 0.00 4.85
3191 7290 3.596066 CTGCCCCGAGAGTGGTGTG 62.596 68.421 0.00 0.00 0.00 3.82
3210 7309 1.897133 TGGATGCTTTGCTTGCAGATT 59.103 42.857 0.00 0.00 44.04 2.40
3215 7314 2.624364 TGCTTTGCTTGCAGATTTGAGA 59.376 40.909 0.00 0.00 35.31 3.27
3216 7315 2.985139 GCTTTGCTTGCAGATTTGAGAC 59.015 45.455 0.00 0.00 0.00 3.36
3218 7317 3.909776 TTGCTTGCAGATTTGAGACAG 57.090 42.857 0.00 0.00 0.00 3.51
3362 7525 1.112315 AGAGCAGGCTGGGTCGATAG 61.112 60.000 17.64 0.00 40.14 2.08
3421 7584 1.605058 GGCAGCTGGAGTCGAAGGTA 61.605 60.000 17.12 0.00 0.00 3.08
3422 7585 0.458716 GCAGCTGGAGTCGAAGGTAC 60.459 60.000 17.12 0.00 0.00 3.34
3424 7587 0.971447 AGCTGGAGTCGAAGGTACCC 60.971 60.000 8.74 0.00 0.00 3.69
3425 7588 1.255667 GCTGGAGTCGAAGGTACCCA 61.256 60.000 8.74 0.00 0.00 4.51
3426 7589 1.263356 CTGGAGTCGAAGGTACCCAA 58.737 55.000 8.74 0.00 0.00 4.12
3427 7590 1.621814 CTGGAGTCGAAGGTACCCAAA 59.378 52.381 8.74 0.00 0.00 3.28
3429 7592 2.224354 TGGAGTCGAAGGTACCCAAAAC 60.224 50.000 8.74 2.54 0.00 2.43
3431 7594 1.150827 GTCGAAGGTACCCAAAACCG 58.849 55.000 8.74 3.70 42.15 4.44
3432 7595 0.758123 TCGAAGGTACCCAAAACCGT 59.242 50.000 8.74 0.00 42.15 4.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 1.835927 GCTTCCTCCTGCAGGTCACT 61.836 60.000 31.58 0.00 43.95 3.41
49 50 1.523258 CGATGCTTCCTCCTGCAGG 60.523 63.158 27.87 27.87 45.15 4.85
64 65 3.866582 GTAGCAGGGCCAGCCGAT 61.867 66.667 18.16 1.44 36.85 4.18
90 91 4.154347 GAGCTCCTCCCAGTGGCG 62.154 72.222 2.61 0.00 0.00 5.69
91 92 4.154347 CGAGCTCCTCCCAGTGGC 62.154 72.222 8.47 0.00 0.00 5.01
94 109 2.363147 GGTCGAGCTCCTCCCAGT 60.363 66.667 8.47 0.00 0.00 4.00
291 311 6.317789 TCTAAGCACATGGAAAAAGACTTG 57.682 37.500 0.00 0.00 0.00 3.16
302 325 6.435591 TCCAGTCTAGATATCTAAGCACATGG 59.564 42.308 13.41 13.91 0.00 3.66
342 368 5.359194 AGGTGATATTACCAGGTTGTCTG 57.641 43.478 18.19 0.00 43.37 3.51
366 392 5.334724 GCAACTAGCAGATTGCCAGATTATC 60.335 44.000 3.58 0.00 46.52 1.75
448 474 7.498443 TCAGACTGTAGAAGATACGTATCAGA 58.502 38.462 31.52 14.39 35.17 3.27
455 484 5.759506 ACCATCAGACTGTAGAAGATACG 57.240 43.478 1.59 0.00 0.00 3.06
456 485 7.997482 TGTAACCATCAGACTGTAGAAGATAC 58.003 38.462 1.59 0.69 0.00 2.24
483 512 9.359653 GGTAGTCTGTTAGGACTTACCATATTA 57.640 37.037 2.47 0.00 43.14 0.98
494 523 5.421374 ACATTACCAGGTAGTCTGTTAGGAC 59.579 44.000 0.00 0.00 41.83 3.85
522 551 5.363101 TCATGAAACTAGCAGATTAGCTGG 58.637 41.667 0.00 0.00 46.11 4.85
534 563 6.238566 CCACCATATGTTGCTCATGAAACTAG 60.239 42.308 10.75 0.00 37.91 2.57
540 569 3.054508 TGACCACCATATGTTGCTCATGA 60.055 43.478 1.24 0.00 37.91 3.07
639 759 1.976474 GCATGACCCCTTTCGGCAA 60.976 57.895 0.00 0.00 0.00 4.52
657 777 3.354948 TGTGATCCATTCCACCTTCAG 57.645 47.619 0.00 0.00 32.61 3.02
691 811 7.828223 AGAGCTGATCTGAAACTATCATTTTGT 59.172 33.333 3.42 0.00 37.44 2.83
692 812 8.211116 AGAGCTGATCTGAAACTATCATTTTG 57.789 34.615 3.42 0.00 37.44 2.44
843 965 7.170658 GGTATTGCTCACTATCTTCACTTCATC 59.829 40.741 0.00 0.00 0.00 2.92
864 986 5.155905 CCTACACCCTTCCATCTAGGTATT 58.844 45.833 0.00 0.00 39.02 1.89
866 988 3.534747 ACCTACACCCTTCCATCTAGGTA 59.465 47.826 0.00 0.00 39.02 3.08
867 989 2.318207 ACCTACACCCTTCCATCTAGGT 59.682 50.000 0.00 0.00 39.02 3.08
876 1021 2.238898 ACCTAATGCACCTACACCCTTC 59.761 50.000 0.00 0.00 0.00 3.46
894 1039 8.797438 GTTTAGAGATGGAATTTTCTGAAACCT 58.203 33.333 1.58 0.00 0.00 3.50
1080 1229 8.791327 TTGTTTTGATAGCTTCATCATCACTA 57.209 30.769 0.00 0.00 34.95 2.74
1178 1327 2.882137 TGATGGGACCGAAAACTGAAAC 59.118 45.455 0.00 0.00 0.00 2.78
1183 1332 4.855340 ACATAATGATGGGACCGAAAACT 58.145 39.130 0.00 0.00 37.39 2.66
1205 1355 8.303156 CAAATTAACAATTGTCTGGATGGTGTA 58.697 33.333 12.39 0.00 0.00 2.90
1222 1372 9.787435 ACTAGACACCATTCTAACAAATTAACA 57.213 29.630 0.00 0.00 0.00 2.41
1429 1579 7.595819 ACATTTTTATCACCTGGTTCAAAGA 57.404 32.000 0.00 0.00 0.00 2.52
1430 1580 7.542130 GCTACATTTTTATCACCTGGTTCAAAG 59.458 37.037 0.00 0.00 0.00 2.77
1481 1631 6.263168 GTCCAAGAAAGATGAAAGGAAGTGAA 59.737 38.462 0.00 0.00 0.00 3.18
1526 1676 5.967088 AGCAATCTAGTTGTTCGTAGATGT 58.033 37.500 6.83 0.00 40.07 3.06
1606 1756 0.179023 TGCAGAACTGGCACATGACA 60.179 50.000 0.00 0.00 38.20 3.58
1756 1906 5.758296 ACATGTCTTACTTACCAGTGTTGTG 59.242 40.000 0.00 0.00 34.06 3.33
1776 1926 7.333423 CGATGTACCCATTACCCTATAAACATG 59.667 40.741 0.00 0.00 0.00 3.21
1822 1975 7.972277 ACAGTTCTTCTTGCTTAATATGCATTG 59.028 33.333 3.54 0.00 40.34 2.82
1823 1976 7.972277 CACAGTTCTTCTTGCTTAATATGCATT 59.028 33.333 3.54 0.00 40.34 3.56
1844 1997 7.346751 AGTTTGGTTACATTGAATTCACAGT 57.653 32.000 7.89 11.95 0.00 3.55
1846 1999 7.776107 TCAAGTTTGGTTACATTGAATTCACA 58.224 30.769 7.89 0.00 0.00 3.58
1849 2002 8.702438 CACATCAAGTTTGGTTACATTGAATTC 58.298 33.333 0.00 0.00 33.91 2.17
1850 2003 8.203485 ACACATCAAGTTTGGTTACATTGAATT 58.797 29.630 0.00 0.00 33.91 2.17
1963 2116 3.062763 GGTTATCACATGCAGATCTCGG 58.937 50.000 4.66 0.00 0.00 4.63
2020 2173 9.149225 GGCATAATCTATAAATCAGACTGACAG 57.851 37.037 7.47 0.00 0.00 3.51
2023 2176 9.716531 CAAGGCATAATCTATAAATCAGACTGA 57.283 33.333 7.80 7.80 0.00 3.41
2086 2242 8.853077 TGTGTGAAGAAGATCAAATACTTCAT 57.147 30.769 16.52 0.00 45.04 2.57
2096 2252 2.369860 AGGCACTGTGTGAAGAAGATCA 59.630 45.455 9.86 0.00 37.18 2.92
2178 2334 1.397390 CCATCAAGGGCTGGAATGGC 61.397 60.000 0.00 0.00 34.24 4.40
2208 2364 1.206878 CCTCCATCATCCCAGTGTGA 58.793 55.000 0.00 0.00 0.00 3.58
2242 2398 2.012673 GTAACATGGCAGGAGAGCTTG 58.987 52.381 5.99 0.00 34.17 4.01
2263 2419 8.660435 CCCTAGGATGGTCTATTATTCTGAAAA 58.340 37.037 11.48 0.00 0.00 2.29
2312 2479 4.875466 TTTCAAGGGAAAGGCCATAGATGG 60.875 45.833 5.01 4.02 43.08 3.51
2321 2488 2.627699 TGTGTCATTTCAAGGGAAAGGC 59.372 45.455 0.00 0.00 45.58 4.35
2322 2489 3.636300 TGTGTGTCATTTCAAGGGAAAGG 59.364 43.478 0.00 0.00 45.58 3.11
2331 2499 5.674525 AGAGAACTCTTGTGTGTCATTTCA 58.325 37.500 0.00 0.00 36.31 2.69
2388 2557 2.682836 GTCTTGAGCTCTGGTTCTGTC 58.317 52.381 16.19 0.00 0.00 3.51
2394 2563 2.210013 TGCCGTCTTGAGCTCTGGT 61.210 57.895 16.19 0.00 0.00 4.00
2421 2590 0.459237 GCAGAGACGACATCCTGTGG 60.459 60.000 0.00 0.00 31.64 4.17
2544 2713 3.627395 TTATGCCGTCATTCAAGGAGT 57.373 42.857 0.00 0.00 34.22 3.85
2547 2716 3.304257 GCTCATTATGCCGTCATTCAAGG 60.304 47.826 0.00 0.00 34.22 3.61
2564 2733 6.444633 GCAATGCAAGAACATATAAGCTCAT 58.555 36.000 0.00 0.00 0.00 2.90
2566 2735 5.218139 GGCAATGCAAGAACATATAAGCTC 58.782 41.667 7.79 0.00 0.00 4.09
2569 2738 4.586001 AGGGGCAATGCAAGAACATATAAG 59.414 41.667 7.79 0.00 0.00 1.73
2570 2739 4.545678 AGGGGCAATGCAAGAACATATAA 58.454 39.130 7.79 0.00 0.00 0.98
2572 2741 2.961062 GAGGGGCAATGCAAGAACATAT 59.039 45.455 7.79 0.00 0.00 1.78
2573 2742 2.378038 GAGGGGCAATGCAAGAACATA 58.622 47.619 7.79 0.00 0.00 2.29
2574 2743 1.188863 GAGGGGCAATGCAAGAACAT 58.811 50.000 7.79 0.00 0.00 2.71
2575 2744 0.899717 GGAGGGGCAATGCAAGAACA 60.900 55.000 7.79 0.00 0.00 3.18
2576 2745 0.899717 TGGAGGGGCAATGCAAGAAC 60.900 55.000 7.79 0.00 0.00 3.01
2577 2746 0.612732 CTGGAGGGGCAATGCAAGAA 60.613 55.000 7.79 0.00 0.00 2.52
2579 2748 2.718073 GCTGGAGGGGCAATGCAAG 61.718 63.158 7.79 0.00 0.00 4.01
2580 2749 2.681064 GCTGGAGGGGCAATGCAA 60.681 61.111 7.79 0.00 0.00 4.08
2582 2751 3.145551 CAGCTGGAGGGGCAATGC 61.146 66.667 5.57 0.00 0.00 3.56
2584 2753 1.792757 TTGACAGCTGGAGGGGCAAT 61.793 55.000 19.93 0.00 0.00 3.56
2585 2754 2.459969 TTGACAGCTGGAGGGGCAA 61.460 57.895 19.93 1.19 0.00 4.52
2587 2756 2.360475 GTTGACAGCTGGAGGGGC 60.360 66.667 19.93 0.00 0.00 5.80
2591 2760 2.292267 ACAGTTTGTTGACAGCTGGAG 58.708 47.619 19.93 0.00 36.05 3.86
2592 2761 2.418368 ACAGTTTGTTGACAGCTGGA 57.582 45.000 19.93 0.29 36.05 3.86
2619 2791 5.964958 AAATGTCGACAGGTTGATGAATT 57.035 34.783 24.41 6.15 0.00 2.17
2627 2799 3.243068 GCAGTTGAAAATGTCGACAGGTT 60.243 43.478 24.41 18.93 42.51 3.50
2635 2807 4.379374 GCAATGTGCAGTTGAAAATGTC 57.621 40.909 14.24 0.00 44.26 3.06
2694 2869 8.952278 CCGAGAGAGCAATATACTCTAGTAATT 58.048 37.037 7.91 0.00 44.50 1.40
2699 2874 4.638421 CCCCGAGAGAGCAATATACTCTAG 59.362 50.000 7.91 0.00 44.50 2.43
2703 2882 3.246416 ACCCCGAGAGAGCAATATACT 57.754 47.619 0.00 0.00 0.00 2.12
2719 2898 0.979709 ACCTTAGGCCGTCTAACCCC 60.980 60.000 0.00 0.00 34.51 4.95
2721 2900 4.586421 ACTTATACCTTAGGCCGTCTAACC 59.414 45.833 0.00 0.00 34.51 2.85
2722 2901 5.781210 ACTTATACCTTAGGCCGTCTAAC 57.219 43.478 0.00 0.00 34.51 2.34
2724 2903 5.658190 ACAAACTTATACCTTAGGCCGTCTA 59.342 40.000 0.00 0.00 0.00 2.59
2730 2909 9.828039 ATACAGTTACAAACTTATACCTTAGGC 57.172 33.333 0.00 0.00 40.46 3.93
2779 2959 7.325097 CAGTATTTGTGGGAAAACAATTACGAC 59.675 37.037 12.66 0.00 44.21 4.34
2781 2961 7.142680 ACAGTATTTGTGGGAAAACAATTACG 58.857 34.615 12.66 10.99 44.21 3.18
2843 3027 9.502091 TCATTCTACTAAACTACAACAGCAAAT 57.498 29.630 0.00 0.00 0.00 2.32
2846 3030 8.364894 TCTTCATTCTACTAAACTACAACAGCA 58.635 33.333 0.00 0.00 0.00 4.41
2847 3031 8.648968 GTCTTCATTCTACTAAACTACAACAGC 58.351 37.037 0.00 0.00 0.00 4.40
2848 3032 9.692749 TGTCTTCATTCTACTAAACTACAACAG 57.307 33.333 0.00 0.00 0.00 3.16
2883 3069 5.138125 TGATCAGAAAGGAAAATGCCAAC 57.862 39.130 0.00 0.00 0.00 3.77
2887 3073 7.105241 AGGTAATGATCAGAAAGGAAAATGC 57.895 36.000 0.09 0.00 0.00 3.56
2925 3111 4.956085 TCTTCGAAATGTCAACAGAGGAA 58.044 39.130 0.00 0.00 0.00 3.36
2928 3114 6.948353 TCTTTTCTTCGAAATGTCAACAGAG 58.052 36.000 0.00 0.00 0.00 3.35
2976 3162 7.453393 AGTCTTGACATGGTCTTCAAAGATAA 58.547 34.615 0.00 0.00 37.39 1.75
2978 3164 5.874093 AGTCTTGACATGGTCTTCAAAGAT 58.126 37.500 0.00 0.00 37.39 2.40
2981 3167 5.066375 CACAAGTCTTGACATGGTCTTCAAA 59.934 40.000 19.53 0.00 31.41 2.69
3000 3186 3.134458 GACTGAGGGACTTGAACACAAG 58.866 50.000 8.18 8.18 41.55 3.16
3002 3188 1.416401 GGACTGAGGGACTTGAACACA 59.584 52.381 0.00 0.00 41.55 3.72
3003 3189 1.270893 GGGACTGAGGGACTTGAACAC 60.271 57.143 0.00 0.00 41.55 3.32
3005 3191 1.056660 TGGGACTGAGGGACTTGAAC 58.943 55.000 0.00 0.00 41.55 3.18
3007 3193 2.940514 TATGGGACTGAGGGACTTGA 57.059 50.000 0.00 0.00 41.55 3.02
3008 3194 5.832539 ATATTATGGGACTGAGGGACTTG 57.167 43.478 0.00 0.00 41.55 3.16
3009 3195 7.572861 ACTTTATATTATGGGACTGAGGGACTT 59.427 37.037 0.00 0.00 41.55 3.01
3011 3197 7.162082 CACTTTATATTATGGGACTGAGGGAC 58.838 42.308 0.00 0.00 0.00 4.46
3012 3198 6.849697 ACACTTTATATTATGGGACTGAGGGA 59.150 38.462 0.00 0.00 0.00 4.20
3014 3200 8.980481 AAACACTTTATATTATGGGACTGAGG 57.020 34.615 0.00 0.00 0.00 3.86
3036 3222 8.752766 TCTTACATAGCACTAGTGTACAAAAC 57.247 34.615 23.44 5.58 0.00 2.43
3037 3223 9.767228 TTTCTTACATAGCACTAGTGTACAAAA 57.233 29.630 23.44 10.61 0.00 2.44
3038 3224 9.938280 ATTTCTTACATAGCACTAGTGTACAAA 57.062 29.630 23.44 10.13 0.00 2.83
3039 3225 9.938280 AATTTCTTACATAGCACTAGTGTACAA 57.062 29.630 23.44 7.75 0.00 2.41
3040 3226 9.938280 AAATTTCTTACATAGCACTAGTGTACA 57.062 29.630 23.44 9.81 0.00 2.90
3045 3231 8.730680 CCACAAAATTTCTTACATAGCACTAGT 58.269 33.333 0.00 0.00 0.00 2.57
3046 3232 8.946085 TCCACAAAATTTCTTACATAGCACTAG 58.054 33.333 0.00 0.00 0.00 2.57
3048 3234 7.448469 ACTCCACAAAATTTCTTACATAGCACT 59.552 33.333 0.00 0.00 0.00 4.40
3051 3237 9.937175 GATACTCCACAAAATTTCTTACATAGC 57.063 33.333 0.00 0.00 0.00 2.97
3058 3244 6.884295 TCGGATGATACTCCACAAAATTTCTT 59.116 34.615 0.00 0.00 34.78 2.52
3062 3248 5.586243 CAGTCGGATGATACTCCACAAAATT 59.414 40.000 0.00 0.00 34.78 1.82
3063 3249 5.104941 TCAGTCGGATGATACTCCACAAAAT 60.105 40.000 0.00 0.00 34.78 1.82
3064 3250 4.221924 TCAGTCGGATGATACTCCACAAAA 59.778 41.667 0.00 0.00 34.78 2.44
3067 3253 3.012934 TCAGTCGGATGATACTCCACA 57.987 47.619 0.00 0.00 34.78 4.17
3068 3254 4.592485 ATTCAGTCGGATGATACTCCAC 57.408 45.455 0.00 0.00 34.78 4.02
3069 3255 4.039245 GGAATTCAGTCGGATGATACTCCA 59.961 45.833 7.93 0.00 34.78 3.86
3072 3258 3.967326 TGGGAATTCAGTCGGATGATACT 59.033 43.478 7.93 0.00 0.00 2.12
3073 3259 4.336889 TGGGAATTCAGTCGGATGATAC 57.663 45.455 7.93 0.00 0.00 2.24
3077 3263 2.939103 GACTTGGGAATTCAGTCGGATG 59.061 50.000 7.93 0.00 0.00 3.51
3079 3265 1.974957 TGACTTGGGAATTCAGTCGGA 59.025 47.619 15.71 1.80 32.68 4.55
3082 3268 1.734465 CGCTGACTTGGGAATTCAGTC 59.266 52.381 14.50 14.50 39.56 3.51
3083 3269 1.347707 TCGCTGACTTGGGAATTCAGT 59.652 47.619 7.93 1.99 39.56 3.41
3084 3270 1.734465 GTCGCTGACTTGGGAATTCAG 59.266 52.381 7.93 0.00 40.14 3.02
3086 3272 0.721718 CGTCGCTGACTTGGGAATTC 59.278 55.000 0.00 0.00 0.00 2.17
3092 3278 3.414700 GGTGCGTCGCTGACTTGG 61.415 66.667 19.50 0.00 0.00 3.61
3094 3280 2.356313 CAGGTGCGTCGCTGACTT 60.356 61.111 19.50 2.37 0.00 3.01
3096 3282 0.942410 TAAACAGGTGCGTCGCTGAC 60.942 55.000 19.50 9.01 0.00 3.51
3098 3284 0.666274 TCTAAACAGGTGCGTCGCTG 60.666 55.000 19.50 11.05 0.00 5.18
3099 3285 0.032952 TTCTAAACAGGTGCGTCGCT 59.967 50.000 19.50 0.00 0.00 4.93
3100 3286 0.438830 CTTCTAAACAGGTGCGTCGC 59.561 55.000 11.10 11.10 0.00 5.19
3101 3287 1.068474 CCTTCTAAACAGGTGCGTCG 58.932 55.000 0.00 0.00 0.00 5.12
3103 3289 2.922740 TTCCTTCTAAACAGGTGCGT 57.077 45.000 0.00 0.00 32.59 5.24
3104 3290 4.250464 TGTATTCCTTCTAAACAGGTGCG 58.750 43.478 0.00 0.00 32.59 5.34
3106 3292 7.393234 TCCATTTGTATTCCTTCTAAACAGGTG 59.607 37.037 0.00 0.00 32.59 4.00
3109 3295 7.337942 AGCTCCATTTGTATTCCTTCTAAACAG 59.662 37.037 0.00 0.00 0.00 3.16
3110 3296 7.175104 AGCTCCATTTGTATTCCTTCTAAACA 58.825 34.615 0.00 0.00 0.00 2.83
3111 3297 7.554476 AGAGCTCCATTTGTATTCCTTCTAAAC 59.446 37.037 10.93 0.00 0.00 2.01
3115 3301 5.045286 ACAGAGCTCCATTTGTATTCCTTCT 60.045 40.000 10.93 0.00 0.00 2.85
3117 3303 4.946157 CACAGAGCTCCATTTGTATTCCTT 59.054 41.667 10.93 0.00 0.00 3.36
3118 3304 4.521146 CACAGAGCTCCATTTGTATTCCT 58.479 43.478 10.93 0.00 0.00 3.36
3120 3306 3.065925 GGCACAGAGCTCCATTTGTATTC 59.934 47.826 10.93 1.44 44.79 1.75
3122 3308 2.025981 TGGCACAGAGCTCCATTTGTAT 60.026 45.455 10.93 0.00 44.79 2.29
3123 3309 1.350684 TGGCACAGAGCTCCATTTGTA 59.649 47.619 10.93 0.00 44.79 2.41
3124 3310 0.111061 TGGCACAGAGCTCCATTTGT 59.889 50.000 10.93 5.19 44.79 2.83
3137 3323 0.392729 TCGATCACATGCATGGCACA 60.393 50.000 29.41 11.14 43.04 4.57
3138 3324 0.306840 CTCGATCACATGCATGGCAC 59.693 55.000 29.41 16.19 43.04 5.01
3139 3325 0.107557 ACTCGATCACATGCATGGCA 60.108 50.000 29.41 16.14 44.86 4.92
3140 3326 1.003116 GAACTCGATCACATGCATGGC 60.003 52.381 29.41 14.77 0.00 4.40
3141 3327 1.259770 CGAACTCGATCACATGCATGG 59.740 52.381 29.41 18.30 43.02 3.66
3142 3328 2.195922 TCGAACTCGATCACATGCATG 58.804 47.619 25.09 25.09 44.22 4.06
3143 3329 2.584492 TCGAACTCGATCACATGCAT 57.416 45.000 0.00 0.00 44.22 3.96
3152 3338 0.807667 GCAGCATGGTCGAACTCGAT 60.808 55.000 0.33 0.00 43.86 3.59
3153 3339 1.446099 GCAGCATGGTCGAACTCGA 60.446 57.895 0.33 0.00 41.13 4.04
3154 3340 2.456119 GGCAGCATGGTCGAACTCG 61.456 63.158 0.33 0.00 37.35 4.18
3155 3341 2.109126 GGGCAGCATGGTCGAACTC 61.109 63.158 0.33 0.00 35.86 3.01
3157 3343 2.045926 AGGGCAGCATGGTCGAAC 60.046 61.111 0.00 0.00 35.86 3.95
3158 3344 2.046023 CAGGGCAGCATGGTCGAA 60.046 61.111 0.00 0.00 35.86 3.71
3172 3358 4.087892 CACCACTCTCGGGGCAGG 62.088 72.222 0.00 0.00 0.00 4.85
3173 3359 3.314331 ACACCACTCTCGGGGCAG 61.314 66.667 0.00 0.00 29.74 4.85
3174 3360 3.625897 CACACCACTCTCGGGGCA 61.626 66.667 0.00 0.00 29.74 5.36
3176 3362 1.990060 ATCCACACCACTCTCGGGG 60.990 63.158 0.00 0.00 34.65 5.73
3177 3363 1.219124 CATCCACACCACTCTCGGG 59.781 63.158 0.00 0.00 0.00 5.14
3179 3365 0.036952 AAGCATCCACACCACTCTCG 60.037 55.000 0.00 0.00 0.00 4.04
3191 7290 2.667473 AATCTGCAAGCAAAGCATCC 57.333 45.000 0.00 0.00 41.82 3.51
3272 7435 1.673477 ACGAGAGTTCCAGCATGCA 59.327 52.632 21.98 0.00 46.40 3.96
3356 7519 0.470456 ACATTACCGGGGGCTATCGA 60.470 55.000 6.32 0.00 0.00 3.59
3362 7525 1.751544 GTGGAACATTACCGGGGGC 60.752 63.158 6.32 0.00 44.52 5.80
3421 7584 2.227194 GTTCATCTCACGGTTTTGGGT 58.773 47.619 0.00 0.00 0.00 4.51
3422 7585 1.196808 CGTTCATCTCACGGTTTTGGG 59.803 52.381 0.00 0.00 33.86 4.12
3424 7587 1.399727 GGCGTTCATCTCACGGTTTTG 60.400 52.381 0.00 0.00 38.13 2.44
3425 7588 0.872388 GGCGTTCATCTCACGGTTTT 59.128 50.000 0.00 0.00 38.13 2.43
3426 7589 1.289109 CGGCGTTCATCTCACGGTTT 61.289 55.000 0.00 0.00 38.13 3.27
3427 7590 1.736645 CGGCGTTCATCTCACGGTT 60.737 57.895 0.00 0.00 38.13 4.44
3429 7592 2.885644 CCGGCGTTCATCTCACGG 60.886 66.667 6.01 0.00 38.13 4.94
3431 7594 3.554692 CGCCGGCGTTCATCTCAC 61.555 66.667 39.71 0.00 34.35 3.51
3457 8611 3.764466 CTGCTTCGCCCTCGACCT 61.764 66.667 0.00 0.00 45.43 3.85
3458 8612 3.708220 CTCTGCTTCGCCCTCGACC 62.708 68.421 0.00 0.00 45.43 4.79


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

AutoCloner maintained by Alex Coulton.