Multiple sequence alignment - TraesCS2D01G235700

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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 TraesCS2D01G235700 chr2D 100.000 2815 0 0 1 2815 226333158 226335972 0.000000e+00 5199
1 TraesCS2D01G235700 chr2D 86.953 2261 236 43 3 2226 621361718 621363956 0.000000e+00 2486
2 TraesCS2D01G235700 chr2D 95.971 273 11 0 2543 2815 260845544 260845272 7.160000e-121 444
3 TraesCS2D01G235700 chr2D 95.238 273 12 1 2543 2815 226294486 226294757 5.570000e-117 431
4 TraesCS2D01G235700 chr2D 94.526 274 13 2 2543 2815 440577047 440576775 3.350000e-114 422
5 TraesCS2D01G235700 chr2D 91.362 301 24 2 2516 2815 430318804 430319103 7.260000e-111 411
6 TraesCS2D01G235700 chr6D 96.107 2543 87 5 3 2542 61814017 61811484 0.000000e+00 4137
7 TraesCS2D01G235700 chr6D 96.716 1340 44 0 217 1556 65307826 65309165 0.000000e+00 2231
8 TraesCS2D01G235700 chr6D 95.871 993 39 1 1552 2544 65317487 65318477 0.000000e+00 1605
9 TraesCS2D01G235700 chr5B 94.559 2573 112 20 3 2553 567869106 567866540 0.000000e+00 3951
10 TraesCS2D01G235700 chr5B 89.474 722 48 19 1845 2544 41904446 41903731 0.000000e+00 887
11 TraesCS2D01G235700 chr5B 87.466 367 17 12 2173 2539 542676793 542677130 2.030000e-106 396
12 TraesCS2D01G235700 chr3B 93.089 2561 121 30 3 2548 106957256 106954737 0.000000e+00 3698
13 TraesCS2D01G235700 chr3B 93.640 2280 104 24 3 2269 8785068 8787319 0.000000e+00 3369
14 TraesCS2D01G235700 chr3B 94.097 288 14 2 2262 2549 8788127 8788411 4.310000e-118 435
15 TraesCS2D01G235700 chr3D 95.477 2233 83 2 3 2235 535143557 535145771 0.000000e+00 3548
16 TraesCS2D01G235700 chr3D 94.872 273 14 0 2543 2815 292800961 292801233 7.210000e-116 427
17 TraesCS2D01G235700 chr3D 96.016 251 8 1 2296 2546 535145759 535146007 9.390000e-110 407
18 TraesCS2D01G235700 chr7A 87.913 2118 216 26 3 2093 683510164 683508060 0.000000e+00 2457
19 TraesCS2D01G235700 chr7A 88.557 2010 198 20 3 1988 683625670 683627671 0.000000e+00 2409
20 TraesCS2D01G235700 chr1B 89.831 1888 171 14 3 1875 7321294 7319413 0.000000e+00 2403
21 TraesCS2D01G235700 chr5D 96.493 1340 29 9 1203 2541 43163527 43162205 0.000000e+00 2198
22 TraesCS2D01G235700 chr5D 94.505 273 15 0 2543 2815 175887046 175886774 3.350000e-114 422
23 TraesCS2D01G235700 chr4A 87.005 1162 103 23 1 1123 649887672 649888824 0.000000e+00 1266
24 TraesCS2D01G235700 chr4B 91.465 703 51 7 4 699 38607826 38608526 0.000000e+00 957
25 TraesCS2D01G235700 chr1D 93.843 536 31 2 1 536 108680647 108680114 0.000000e+00 806
26 TraesCS2D01G235700 chr1D 85.859 495 32 21 2055 2544 108679299 108678838 2.520000e-135 492
27 TraesCS2D01G235700 chr4D 95.238 273 13 0 2543 2815 199796106 199795834 1.550000e-117 433
28 TraesCS2D01G235700 chr4D 95.238 273 13 0 2543 2815 232876445 232876717 1.550000e-117 433
29 TraesCS2D01G235700 chr7D 94.891 274 13 1 2543 2815 360441406 360441679 7.210000e-116 427


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 TraesCS2D01G235700 chr2D 226333158 226335972 2814 False 5199.0 5199 100.0000 1 2815 1 chr2D.!!$F2 2814
1 TraesCS2D01G235700 chr2D 621361718 621363956 2238 False 2486.0 2486 86.9530 3 2226 1 chr2D.!!$F4 2223
2 TraesCS2D01G235700 chr6D 61811484 61814017 2533 True 4137.0 4137 96.1070 3 2542 1 chr6D.!!$R1 2539
3 TraesCS2D01G235700 chr6D 65307826 65309165 1339 False 2231.0 2231 96.7160 217 1556 1 chr6D.!!$F1 1339
4 TraesCS2D01G235700 chr6D 65317487 65318477 990 False 1605.0 1605 95.8710 1552 2544 1 chr6D.!!$F2 992
5 TraesCS2D01G235700 chr5B 567866540 567869106 2566 True 3951.0 3951 94.5590 3 2553 1 chr5B.!!$R2 2550
6 TraesCS2D01G235700 chr5B 41903731 41904446 715 True 887.0 887 89.4740 1845 2544 1 chr5B.!!$R1 699
7 TraesCS2D01G235700 chr3B 106954737 106957256 2519 True 3698.0 3698 93.0890 3 2548 1 chr3B.!!$R1 2545
8 TraesCS2D01G235700 chr3B 8785068 8788411 3343 False 1902.0 3369 93.8685 3 2549 2 chr3B.!!$F1 2546
9 TraesCS2D01G235700 chr3D 535143557 535146007 2450 False 1977.5 3548 95.7465 3 2546 2 chr3D.!!$F2 2543
10 TraesCS2D01G235700 chr7A 683508060 683510164 2104 True 2457.0 2457 87.9130 3 2093 1 chr7A.!!$R1 2090
11 TraesCS2D01G235700 chr7A 683625670 683627671 2001 False 2409.0 2409 88.5570 3 1988 1 chr7A.!!$F1 1985
12 TraesCS2D01G235700 chr1B 7319413 7321294 1881 True 2403.0 2403 89.8310 3 1875 1 chr1B.!!$R1 1872
13 TraesCS2D01G235700 chr5D 43162205 43163527 1322 True 2198.0 2198 96.4930 1203 2541 1 chr5D.!!$R1 1338
14 TraesCS2D01G235700 chr4A 649887672 649888824 1152 False 1266.0 1266 87.0050 1 1123 1 chr4A.!!$F1 1122
15 TraesCS2D01G235700 chr4B 38607826 38608526 700 False 957.0 957 91.4650 4 699 1 chr4B.!!$F1 695
16 TraesCS2D01G235700 chr1D 108678838 108680647 1809 True 649.0 806 89.8510 1 2544 2 chr1D.!!$R1 2543

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
587 597 2.16503 CCAACCAATTGAGGCTGATGAC 59.835 50.0 7.12 0.0 38.15 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2062 2341 0.677731 ATACGGCAGCAGCACATGTT 60.678 50.0 2.65 0.0 44.61 2.71 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
63 64 4.406069 CAAGATGCATTTGTTGTACCTCG 58.594 43.478 0.00 0.00 0.00 4.63
181 182 3.002791 CTGATGCTGGTTACACGAATGT 58.997 45.455 0.00 0.00 43.30 2.71
184 185 3.671008 TGCTGGTTACACGAATGTACT 57.329 42.857 0.00 0.00 41.12 2.73
185 186 4.787260 TGCTGGTTACACGAATGTACTA 57.213 40.909 0.00 0.00 41.12 1.82
194 195 7.763071 GGTTACACGAATGTACTAGGATTTCTT 59.237 37.037 0.00 0.00 41.12 2.52
245 246 2.191128 AAGAGTGGGCATCAAGTCAC 57.809 50.000 0.00 0.00 0.00 3.67
569 579 6.672593 AGTGGATAATGAAATAGCTTCCCAA 58.327 36.000 0.00 0.00 32.53 4.12
587 597 2.165030 CCAACCAATTGAGGCTGATGAC 59.835 50.000 7.12 0.00 38.15 3.06
628 638 4.696877 TGTTCAAGTCACTAATGCATGGAG 59.303 41.667 0.00 3.37 0.00 3.86
642 652 2.507484 CATGGAGCAACTTCAGGAACA 58.493 47.619 0.00 0.00 0.00 3.18
666 676 9.793252 ACAAATTATCTAATGACATGTTTGCTC 57.207 29.630 0.00 0.00 0.00 4.26
673 683 7.420002 TCTAATGACATGTTTGCTCAATATGC 58.580 34.615 0.00 0.00 0.00 3.14
707 717 7.307493 TGCAAATTTACAGCAGTAGTATGAG 57.693 36.000 0.00 0.00 33.75 2.90
757 767 4.695455 TGCTTTTGTGGTAGCTAGATGTTC 59.305 41.667 0.00 0.00 38.22 3.18
819 865 4.090761 TGATGGATTAGCTGGATGTTCC 57.909 45.455 0.00 0.00 36.96 3.62
1042 1090 4.657055 TGTCTTTGTTGAACATCACAACG 58.343 39.130 0.00 0.00 46.96 4.10
1086 1134 4.516698 GGATGGAAGCCACATGTATACAAG 59.483 45.833 10.14 8.20 46.15 3.16
1225 1273 0.540830 CGGGTTTGGTTGGGATTGGA 60.541 55.000 0.00 0.00 0.00 3.53
1350 1405 7.202016 AGTGATTTACTTTGTATGTGTGTGG 57.798 36.000 0.00 0.00 35.67 4.17
1447 1502 1.210234 AGATCATGCAACCGGTGATGA 59.790 47.619 20.60 20.60 33.03 2.92
1458 1513 1.951602 CCGGTGATGATGCAATGACAT 59.048 47.619 0.00 0.00 0.00 3.06
1717 1778 6.110033 ACATGTTACGAGCATATGGTAAACA 58.890 36.000 22.03 22.03 34.37 2.83
1736 1797 6.445357 AAACACATCCTTAGTGAACGTTTT 57.555 33.333 0.46 0.00 40.16 2.43
1782 1843 3.269592 TGGAGTTTAGGAAGGAGTGGA 57.730 47.619 0.00 0.00 0.00 4.02
2004 2100 2.781945 AAGTGCTGCTGTTTGTAAGC 57.218 45.000 0.00 0.00 41.22 3.09
2062 2341 2.897436 CTGCTGTATAAGTGCTGCTGA 58.103 47.619 0.00 0.00 36.53 4.26
2077 2356 1.211969 CTGAACATGTGCTGCTGCC 59.788 57.895 13.47 5.20 38.71 4.85
2090 2381 0.249120 TGCTGCCGTATAAGTGCTGT 59.751 50.000 0.00 0.00 0.00 4.40
2155 2503 5.871524 GCTGCTGCTATATAATAAGTGCTGA 59.128 40.000 8.53 0.00 36.03 4.26
2553 3721 7.072177 TCCAAACAAAGCGTAAGAGATATTG 57.928 36.000 0.00 0.00 43.02 1.90
2554 3722 6.653320 TCCAAACAAAGCGTAAGAGATATTGT 59.347 34.615 0.00 0.00 43.02 2.71
2555 3723 6.742718 CCAAACAAAGCGTAAGAGATATTGTG 59.257 38.462 0.00 0.00 43.02 3.33
2556 3724 7.360861 CCAAACAAAGCGTAAGAGATATTGTGA 60.361 37.037 0.00 0.00 43.02 3.58
2557 3725 7.849804 AACAAAGCGTAAGAGATATTGTGAT 57.150 32.000 0.00 0.00 43.02 3.06
2558 3726 8.942338 AACAAAGCGTAAGAGATATTGTGATA 57.058 30.769 0.00 0.00 43.02 2.15
2559 3727 9.547753 AACAAAGCGTAAGAGATATTGTGATAT 57.452 29.630 0.00 0.00 43.02 1.63
2560 3728 9.197694 ACAAAGCGTAAGAGATATTGTGATATC 57.802 33.333 0.00 0.00 40.41 1.63
2561 3729 8.651588 CAAAGCGTAAGAGATATTGTGATATCC 58.348 37.037 0.00 0.00 40.70 2.59
2562 3730 6.868622 AGCGTAAGAGATATTGTGATATCCC 58.131 40.000 0.00 0.00 40.70 3.85
2563 3731 6.437477 AGCGTAAGAGATATTGTGATATCCCA 59.563 38.462 0.00 0.00 40.70 4.37
2564 3732 7.039011 AGCGTAAGAGATATTGTGATATCCCAA 60.039 37.037 2.97 2.97 40.70 4.12
2565 3733 7.276658 GCGTAAGAGATATTGTGATATCCCAAG 59.723 40.741 6.76 0.00 40.70 3.61
2566 3734 8.523658 CGTAAGAGATATTGTGATATCCCAAGA 58.476 37.037 6.76 2.39 43.40 3.02
2581 3749 6.975471 ATCCCAAGATATCCATAACATCCA 57.025 37.500 0.00 0.00 0.00 3.41
2582 3750 6.975471 TCCCAAGATATCCATAACATCCAT 57.025 37.500 0.00 0.00 0.00 3.41
2583 3751 6.724351 TCCCAAGATATCCATAACATCCATG 58.276 40.000 0.00 0.00 0.00 3.66
2584 3752 6.275381 TCCCAAGATATCCATAACATCCATGT 59.725 38.462 0.00 0.00 44.20 3.21
2585 3753 6.600822 CCCAAGATATCCATAACATCCATGTC 59.399 42.308 0.00 0.00 40.80 3.06
2586 3754 6.600822 CCAAGATATCCATAACATCCATGTCC 59.399 42.308 0.00 0.00 40.80 4.02
2587 3755 6.319048 AGATATCCATAACATCCATGTCCC 57.681 41.667 0.00 0.00 40.80 4.46
2588 3756 5.792188 AGATATCCATAACATCCATGTCCCA 59.208 40.000 0.00 0.00 40.80 4.37
2589 3757 4.812403 ATCCATAACATCCATGTCCCAA 57.188 40.909 0.00 0.00 40.80 4.12
2590 3758 3.897239 TCCATAACATCCATGTCCCAAC 58.103 45.455 0.00 0.00 40.80 3.77
2591 3759 3.268072 TCCATAACATCCATGTCCCAACA 59.732 43.478 0.00 0.00 40.80 3.33
2601 3769 2.435372 TGTCCCAACATGGAATAGCC 57.565 50.000 0.00 0.00 40.96 3.93
2602 3770 1.922447 TGTCCCAACATGGAATAGCCT 59.078 47.619 0.00 0.00 40.96 4.58
2603 3771 3.119319 TGTCCCAACATGGAATAGCCTA 58.881 45.455 0.00 0.00 40.96 3.93
2604 3772 3.118038 TGTCCCAACATGGAATAGCCTAC 60.118 47.826 0.00 0.00 40.96 3.18
2605 3773 3.118038 GTCCCAACATGGAATAGCCTACA 60.118 47.826 0.00 0.00 40.96 2.74
2606 3774 3.525609 TCCCAACATGGAATAGCCTACAA 59.474 43.478 0.00 0.00 40.96 2.41
2607 3775 3.632145 CCCAACATGGAATAGCCTACAAC 59.368 47.826 0.00 0.00 40.96 3.32
2608 3776 4.526970 CCAACATGGAATAGCCTACAACT 58.473 43.478 0.00 0.00 40.96 3.16
2609 3777 4.336433 CCAACATGGAATAGCCTACAACTG 59.664 45.833 0.00 0.00 40.96 3.16
2610 3778 3.545703 ACATGGAATAGCCTACAACTGC 58.454 45.455 0.00 0.00 37.63 4.40
2611 3779 3.054434 ACATGGAATAGCCTACAACTGCA 60.054 43.478 0.00 0.00 37.63 4.41
2612 3780 2.985896 TGGAATAGCCTACAACTGCAC 58.014 47.619 0.00 0.00 37.63 4.57
2613 3781 2.289565 GGAATAGCCTACAACTGCACC 58.710 52.381 0.00 0.00 0.00 5.01
2614 3782 2.092914 GGAATAGCCTACAACTGCACCT 60.093 50.000 0.00 0.00 0.00 4.00
2615 3783 2.698855 ATAGCCTACAACTGCACCTG 57.301 50.000 0.00 0.00 0.00 4.00
2616 3784 0.036388 TAGCCTACAACTGCACCTGC 60.036 55.000 0.00 0.00 42.50 4.85
2636 3804 4.700596 GCAACTAGCAACGCTATAAGAG 57.299 45.455 0.00 0.00 40.54 2.85
2637 3805 3.491267 GCAACTAGCAACGCTATAAGAGG 59.509 47.826 0.00 0.00 40.54 3.69
2638 3806 4.051922 CAACTAGCAACGCTATAAGAGGG 58.948 47.826 0.00 0.00 40.54 4.30
2639 3807 2.628657 ACTAGCAACGCTATAAGAGGGG 59.371 50.000 0.00 0.00 40.54 4.79
2640 3808 0.106894 AGCAACGCTATAAGAGGGGC 59.893 55.000 0.00 0.00 42.42 5.80
2641 3809 0.106894 GCAACGCTATAAGAGGGGCT 59.893 55.000 0.00 0.00 42.42 5.19
2642 3810 1.871080 CAACGCTATAAGAGGGGCTG 58.129 55.000 0.00 0.00 42.42 4.85
2643 3811 1.412710 CAACGCTATAAGAGGGGCTGA 59.587 52.381 0.00 0.00 42.42 4.26
2644 3812 1.333177 ACGCTATAAGAGGGGCTGAG 58.667 55.000 0.00 0.00 42.42 3.35
2645 3813 0.037790 CGCTATAAGAGGGGCTGAGC 60.038 60.000 0.00 0.00 34.46 4.26
2646 3814 1.051812 GCTATAAGAGGGGCTGAGCA 58.948 55.000 6.82 0.00 31.41 4.26
2647 3815 1.417890 GCTATAAGAGGGGCTGAGCAA 59.582 52.381 6.82 0.00 31.41 3.91
2648 3816 2.158755 GCTATAAGAGGGGCTGAGCAAA 60.159 50.000 6.82 0.00 31.41 3.68
2649 3817 2.725221 ATAAGAGGGGCTGAGCAAAG 57.275 50.000 6.82 0.00 0.00 2.77
2650 3818 0.035056 TAAGAGGGGCTGAGCAAAGC 60.035 55.000 6.82 2.17 42.75 3.51
2651 3819 3.130160 GAGGGGCTGAGCAAAGCG 61.130 66.667 6.82 0.00 44.52 4.68
2652 3820 4.729918 AGGGGCTGAGCAAAGCGG 62.730 66.667 6.82 0.00 44.52 5.52
2654 3822 2.046314 GGGCTGAGCAAAGCGGTA 60.046 61.111 6.82 0.00 44.52 4.02
2655 3823 1.674322 GGGCTGAGCAAAGCGGTAA 60.674 57.895 6.82 0.00 44.52 2.85
2656 3824 1.502190 GGCTGAGCAAAGCGGTAAC 59.498 57.895 6.82 0.00 44.52 2.50
2657 3825 1.234615 GGCTGAGCAAAGCGGTAACA 61.235 55.000 6.82 0.00 44.52 2.41
2658 3826 0.804989 GCTGAGCAAAGCGGTAACAT 59.195 50.000 0.00 0.00 32.56 2.71
2659 3827 2.006888 GCTGAGCAAAGCGGTAACATA 58.993 47.619 0.00 0.00 32.56 2.29
2660 3828 2.030946 GCTGAGCAAAGCGGTAACATAG 59.969 50.000 0.00 0.00 32.56 2.23
2661 3829 2.006888 TGAGCAAAGCGGTAACATAGC 58.993 47.619 0.00 0.00 0.00 2.97
2662 3830 1.330829 GAGCAAAGCGGTAACATAGCC 59.669 52.381 0.00 0.00 0.00 3.93
2663 3831 1.091537 GCAAAGCGGTAACATAGCCA 58.908 50.000 0.00 0.00 0.00 4.75
2664 3832 1.470890 GCAAAGCGGTAACATAGCCAA 59.529 47.619 0.00 0.00 0.00 4.52
2665 3833 2.094957 GCAAAGCGGTAACATAGCCAAA 60.095 45.455 0.00 0.00 0.00 3.28
2666 3834 3.498082 CAAAGCGGTAACATAGCCAAAC 58.502 45.455 0.00 0.00 0.00 2.93
2667 3835 2.483014 AGCGGTAACATAGCCAAACA 57.517 45.000 0.00 0.00 0.00 2.83
2668 3836 2.785562 AGCGGTAACATAGCCAAACAA 58.214 42.857 0.00 0.00 0.00 2.83
2669 3837 2.486592 AGCGGTAACATAGCCAAACAAC 59.513 45.455 0.00 0.00 0.00 3.32
2670 3838 2.726681 GCGGTAACATAGCCAAACAACG 60.727 50.000 0.00 0.00 0.00 4.10
2671 3839 2.159626 CGGTAACATAGCCAAACAACGG 60.160 50.000 0.00 0.00 0.00 4.44
2672 3840 2.815503 GGTAACATAGCCAAACAACGGT 59.184 45.455 0.00 0.00 0.00 4.83
2673 3841 3.253921 GGTAACATAGCCAAACAACGGTT 59.746 43.478 0.00 0.00 39.43 4.44
2681 3849 2.889200 AAACAACGGTTTGCTGGGA 58.111 47.368 0.00 0.00 45.22 4.37
2682 3850 1.187087 AAACAACGGTTTGCTGGGAA 58.813 45.000 0.00 0.00 45.22 3.97
2683 3851 0.744281 AACAACGGTTTGCTGGGAAG 59.256 50.000 0.00 0.00 36.00 3.46
2684 3852 1.106944 ACAACGGTTTGCTGGGAAGG 61.107 55.000 0.00 0.00 36.00 3.46
2685 3853 1.530655 AACGGTTTGCTGGGAAGGG 60.531 57.895 0.00 0.00 0.00 3.95
2686 3854 2.115266 CGGTTTGCTGGGAAGGGT 59.885 61.111 0.00 0.00 0.00 4.34
2687 3855 1.377229 CGGTTTGCTGGGAAGGGTA 59.623 57.895 0.00 0.00 0.00 3.69
2688 3856 0.250989 CGGTTTGCTGGGAAGGGTAA 60.251 55.000 0.00 0.00 0.00 2.85
2689 3857 1.820090 CGGTTTGCTGGGAAGGGTAAA 60.820 52.381 0.00 0.00 0.00 2.01
2690 3858 2.321719 GGTTTGCTGGGAAGGGTAAAA 58.678 47.619 0.00 0.00 0.00 1.52
2691 3859 2.701423 GGTTTGCTGGGAAGGGTAAAAA 59.299 45.455 0.00 0.00 0.00 1.94
2692 3860 3.244078 GGTTTGCTGGGAAGGGTAAAAAG 60.244 47.826 0.00 0.00 0.00 2.27
2693 3861 2.302587 TGCTGGGAAGGGTAAAAAGG 57.697 50.000 0.00 0.00 0.00 3.11
2694 3862 1.501604 TGCTGGGAAGGGTAAAAAGGT 59.498 47.619 0.00 0.00 0.00 3.50
2695 3863 2.090999 TGCTGGGAAGGGTAAAAAGGTT 60.091 45.455 0.00 0.00 0.00 3.50
2696 3864 3.140519 TGCTGGGAAGGGTAAAAAGGTTA 59.859 43.478 0.00 0.00 0.00 2.85
2697 3865 3.762288 GCTGGGAAGGGTAAAAAGGTTAG 59.238 47.826 0.00 0.00 0.00 2.34
2698 3866 4.341487 CTGGGAAGGGTAAAAAGGTTAGG 58.659 47.826 0.00 0.00 0.00 2.69
2699 3867 3.076333 TGGGAAGGGTAAAAAGGTTAGGG 59.924 47.826 0.00 0.00 0.00 3.53
2700 3868 3.565010 GGGAAGGGTAAAAAGGTTAGGGG 60.565 52.174 0.00 0.00 0.00 4.79
2701 3869 2.913603 AGGGTAAAAAGGTTAGGGGC 57.086 50.000 0.00 0.00 0.00 5.80
2702 3870 2.365183 AGGGTAAAAAGGTTAGGGGCT 58.635 47.619 0.00 0.00 0.00 5.19
2703 3871 3.544719 AGGGTAAAAAGGTTAGGGGCTA 58.455 45.455 0.00 0.00 0.00 3.93
2704 3872 4.124513 AGGGTAAAAAGGTTAGGGGCTAT 58.875 43.478 0.00 0.00 0.00 2.97
2705 3873 4.167502 AGGGTAAAAAGGTTAGGGGCTATC 59.832 45.833 0.00 0.00 0.00 2.08
2706 3874 4.079615 GGGTAAAAAGGTTAGGGGCTATCA 60.080 45.833 0.00 0.00 0.00 2.15
2707 3875 5.399842 GGGTAAAAAGGTTAGGGGCTATCAT 60.400 44.000 0.00 0.00 0.00 2.45
2708 3876 5.535030 GGTAAAAAGGTTAGGGGCTATCATG 59.465 44.000 0.00 0.00 0.00 3.07
2709 3877 3.884037 AAAGGTTAGGGGCTATCATGG 57.116 47.619 0.00 0.00 0.00 3.66
2710 3878 1.068121 AGGTTAGGGGCTATCATGGC 58.932 55.000 0.00 0.00 0.00 4.40
2711 3879 0.771127 GGTTAGGGGCTATCATGGCA 59.229 55.000 0.00 0.00 0.00 4.92
2712 3880 1.144913 GGTTAGGGGCTATCATGGCAA 59.855 52.381 0.00 0.00 0.00 4.52
2713 3881 2.225117 GGTTAGGGGCTATCATGGCAAT 60.225 50.000 0.00 0.00 0.00 3.56
2714 3882 3.500343 GTTAGGGGCTATCATGGCAATT 58.500 45.455 0.00 0.00 0.00 2.32
2715 3883 2.781403 AGGGGCTATCATGGCAATTT 57.219 45.000 0.00 0.00 0.00 1.82
2716 3884 2.322658 AGGGGCTATCATGGCAATTTG 58.677 47.619 0.00 0.00 0.00 2.32
2717 3885 1.345415 GGGGCTATCATGGCAATTTGG 59.655 52.381 0.00 0.00 0.00 3.28
2718 3886 1.345415 GGGCTATCATGGCAATTTGGG 59.655 52.381 0.00 0.00 0.00 4.12
2719 3887 2.318908 GGCTATCATGGCAATTTGGGA 58.681 47.619 0.00 0.00 0.00 4.37
2720 3888 2.298163 GGCTATCATGGCAATTTGGGAG 59.702 50.000 0.00 0.00 0.00 4.30
2721 3889 2.298163 GCTATCATGGCAATTTGGGAGG 59.702 50.000 0.00 0.00 0.00 4.30
2722 3890 1.125633 ATCATGGCAATTTGGGAGGC 58.874 50.000 0.00 0.00 0.00 4.70
2723 3891 0.041535 TCATGGCAATTTGGGAGGCT 59.958 50.000 0.00 0.00 0.00 4.58
2724 3892 0.906775 CATGGCAATTTGGGAGGCTT 59.093 50.000 0.00 0.00 0.00 4.35
2725 3893 0.906775 ATGGCAATTTGGGAGGCTTG 59.093 50.000 0.00 0.00 0.00 4.01
2726 3894 0.178938 TGGCAATTTGGGAGGCTTGA 60.179 50.000 0.00 0.00 0.00 3.02
2727 3895 1.197812 GGCAATTTGGGAGGCTTGAT 58.802 50.000 0.00 0.00 0.00 2.57
2728 3896 2.292126 TGGCAATTTGGGAGGCTTGATA 60.292 45.455 0.00 0.00 0.00 2.15
2729 3897 2.765699 GGCAATTTGGGAGGCTTGATAA 59.234 45.455 0.00 0.00 0.00 1.75
2730 3898 3.197549 GGCAATTTGGGAGGCTTGATAAA 59.802 43.478 0.00 0.00 0.00 1.40
2731 3899 4.183865 GCAATTTGGGAGGCTTGATAAAC 58.816 43.478 0.00 0.00 0.00 2.01
2732 3900 4.322650 GCAATTTGGGAGGCTTGATAAACA 60.323 41.667 0.00 0.00 0.00 2.83
2733 3901 5.792741 CAATTTGGGAGGCTTGATAAACAA 58.207 37.500 0.00 0.00 36.97 2.83
2746 3914 4.751060 TGATAAACAAGTGGTAGGTAGCG 58.249 43.478 0.00 0.00 0.00 4.26
2747 3915 1.804601 AAACAAGTGGTAGGTAGCGC 58.195 50.000 0.00 0.00 34.65 5.92
2748 3916 0.389426 AACAAGTGGTAGGTAGCGCG 60.389 55.000 0.00 0.00 39.04 6.86
2749 3917 1.246056 ACAAGTGGTAGGTAGCGCGA 61.246 55.000 12.10 0.00 39.04 5.87
2750 3918 0.801067 CAAGTGGTAGGTAGCGCGAC 60.801 60.000 12.10 12.67 39.04 5.19
2751 3919 2.262471 AAGTGGTAGGTAGCGCGACG 62.262 60.000 12.10 0.00 39.04 5.12
2752 3920 3.511595 TGGTAGGTAGCGCGACGG 61.512 66.667 12.10 0.00 0.00 4.79
2753 3921 3.204827 GGTAGGTAGCGCGACGGA 61.205 66.667 12.10 1.74 0.00 4.69
2754 3922 2.327244 GTAGGTAGCGCGACGGAG 59.673 66.667 12.10 0.00 0.00 4.63
2755 3923 3.580193 TAGGTAGCGCGACGGAGC 61.580 66.667 12.10 5.01 39.50 4.70
2777 3945 4.230314 GATAGCATCGAGACAACTAGCA 57.770 45.455 0.00 0.00 0.00 3.49
2778 3946 4.804108 GATAGCATCGAGACAACTAGCAT 58.196 43.478 0.00 0.00 0.00 3.79
2779 3947 5.944013 GATAGCATCGAGACAACTAGCATA 58.056 41.667 0.00 0.00 0.00 3.14
2780 3948 4.235939 AGCATCGAGACAACTAGCATAG 57.764 45.455 0.00 0.00 46.50 2.23
2781 3949 2.728839 GCATCGAGACAACTAGCATAGC 59.271 50.000 0.00 0.00 44.39 2.97
2782 3950 3.796844 GCATCGAGACAACTAGCATAGCA 60.797 47.826 0.00 0.00 44.39 3.49
2783 3951 4.363138 CATCGAGACAACTAGCATAGCAA 58.637 43.478 0.00 0.00 44.39 3.91
2784 3952 4.450082 TCGAGACAACTAGCATAGCAAA 57.550 40.909 0.00 0.00 44.39 3.68
2785 3953 4.424626 TCGAGACAACTAGCATAGCAAAG 58.575 43.478 0.00 0.00 44.39 2.77
2786 3954 4.157840 TCGAGACAACTAGCATAGCAAAGA 59.842 41.667 0.00 0.00 44.39 2.52
2787 3955 5.046529 CGAGACAACTAGCATAGCAAAGAT 58.953 41.667 0.00 0.00 44.39 2.40
2788 3956 6.039382 TCGAGACAACTAGCATAGCAAAGATA 59.961 38.462 0.00 0.00 44.39 1.98
2789 3957 6.362016 CGAGACAACTAGCATAGCAAAGATAG 59.638 42.308 0.00 0.00 44.39 2.08
2790 3958 7.118496 AGACAACTAGCATAGCAAAGATAGT 57.882 36.000 0.00 0.00 44.39 2.12
2791 3959 8.239038 AGACAACTAGCATAGCAAAGATAGTA 57.761 34.615 1.58 0.00 44.39 1.82
2792 3960 8.356657 AGACAACTAGCATAGCAAAGATAGTAG 58.643 37.037 1.58 0.00 44.39 2.57
2793 3961 8.012957 ACAACTAGCATAGCAAAGATAGTAGT 57.987 34.615 1.58 0.00 44.39 2.73
2794 3962 7.923344 ACAACTAGCATAGCAAAGATAGTAGTG 59.077 37.037 1.58 1.13 44.39 2.74
2795 3963 7.825331 ACTAGCATAGCAAAGATAGTAGTGA 57.175 36.000 0.00 0.00 44.39 3.41
2796 3964 7.881142 ACTAGCATAGCAAAGATAGTAGTGAG 58.119 38.462 0.00 0.00 44.39 3.51
2797 3965 6.968263 AGCATAGCAAAGATAGTAGTGAGA 57.032 37.500 0.00 0.00 0.00 3.27
2798 3966 7.537596 AGCATAGCAAAGATAGTAGTGAGAT 57.462 36.000 0.00 0.00 0.00 2.75
2799 3967 7.601856 AGCATAGCAAAGATAGTAGTGAGATC 58.398 38.462 0.00 0.00 0.00 2.75
2800 3968 7.451255 AGCATAGCAAAGATAGTAGTGAGATCT 59.549 37.037 0.00 0.00 0.00 2.75
2801 3969 8.735315 GCATAGCAAAGATAGTAGTGAGATCTA 58.265 37.037 0.00 0.00 29.71 1.98
2804 3972 8.177119 AGCAAAGATAGTAGTGAGATCTAAGG 57.823 38.462 0.00 0.00 29.71 2.69
2805 3973 7.782644 AGCAAAGATAGTAGTGAGATCTAAGGT 59.217 37.037 0.00 0.00 29.71 3.50
2806 3974 7.865385 GCAAAGATAGTAGTGAGATCTAAGGTG 59.135 40.741 0.00 0.00 29.71 4.00
2807 3975 9.126151 CAAAGATAGTAGTGAGATCTAAGGTGA 57.874 37.037 0.00 0.00 29.71 4.02
2808 3976 8.685838 AAGATAGTAGTGAGATCTAAGGTGAC 57.314 38.462 0.00 0.00 29.71 3.67
2809 3977 6.932400 AGATAGTAGTGAGATCTAAGGTGACG 59.068 42.308 0.00 0.00 0.00 4.35
2810 3978 4.200874 AGTAGTGAGATCTAAGGTGACGG 58.799 47.826 0.00 0.00 0.00 4.79
2811 3979 3.088789 AGTGAGATCTAAGGTGACGGT 57.911 47.619 0.00 0.00 0.00 4.83
2812 3980 3.018149 AGTGAGATCTAAGGTGACGGTC 58.982 50.000 0.00 0.00 0.00 4.79
2813 3981 2.753452 GTGAGATCTAAGGTGACGGTCA 59.247 50.000 6.76 6.76 0.00 4.02
2814 3982 3.381908 GTGAGATCTAAGGTGACGGTCAT 59.618 47.826 14.78 0.74 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 64 3.367395 GCCAAGAGAAAAAGCCATACCAC 60.367 47.826 0.00 0.00 0.00 4.16
181 182 6.384015 TCTGAATGGAGCAAGAAATCCTAGTA 59.616 38.462 0.00 0.00 36.50 1.82
184 185 5.698741 TCTGAATGGAGCAAGAAATCCTA 57.301 39.130 0.00 0.00 36.50 2.94
185 186 4.581309 TCTGAATGGAGCAAGAAATCCT 57.419 40.909 0.00 0.00 36.50 3.24
194 195 1.137675 CGAGTGGATCTGAATGGAGCA 59.862 52.381 0.00 0.00 0.00 4.26
245 246 0.471617 TGGCATTTTGGGGTTGTTGG 59.528 50.000 0.00 0.00 0.00 3.77
444 454 5.214417 TCGAATCTGCAACAATGTTCTTTG 58.786 37.500 0.00 0.00 0.00 2.77
569 579 1.742761 CGTCATCAGCCTCAATTGGT 58.257 50.000 5.42 0.00 0.00 3.67
587 597 6.706055 TGAACACTTCTTATTGAGTTAGCG 57.294 37.500 0.00 0.00 0.00 4.26
628 638 9.294030 CATTAGATAATTTGTTCCTGAAGTTGC 57.706 33.333 0.00 0.00 0.00 4.17
673 683 1.655099 GTAAATTTGCATGCGCCACAG 59.345 47.619 14.09 0.00 37.32 3.66
707 717 7.493743 AGACATCATCTTGCTAAATCACATC 57.506 36.000 0.00 0.00 31.62 3.06
757 767 7.544511 GCAAAATACATCATCTTGCTAATCG 57.455 36.000 0.00 0.00 39.39 3.34
819 865 3.466836 TCCGATAGCTATGCACAAAAGG 58.533 45.455 11.94 1.98 0.00 3.11
848 894 9.199645 TGGTGATGATGTACAAAATATCCAAAT 57.800 29.630 0.00 0.00 0.00 2.32
937 985 1.686052 TGTTTCTTCAACCATGGTGCC 59.314 47.619 20.60 1.01 33.97 5.01
976 1024 8.583296 CATCTCATCTCTCCATGTCAAGTAATA 58.417 37.037 0.00 0.00 0.00 0.98
992 1040 7.605691 CCAACAATACCTTATCCATCTCATCTC 59.394 40.741 0.00 0.00 0.00 2.75
1042 1090 0.039618 TTTTGGCCCTGATCACCTCC 59.960 55.000 0.00 0.00 0.00 4.30
1086 1134 4.761739 TCATGTATTGCCTTTATAGCAGCC 59.238 41.667 0.00 0.00 42.17 4.85
1225 1273 8.654997 ACTATCCATGAGTAGCTTGTTATTGAT 58.345 33.333 0.00 0.00 0.00 2.57
1350 1405 0.882484 GCTGCCTTCGGATTAGCCTC 60.882 60.000 0.00 0.00 0.00 4.70
1447 1502 3.257375 ACTTTCAGCACATGTCATTGCAT 59.743 39.130 16.92 5.23 41.48 3.96
1736 1797 2.489938 ACTCCATAAGCGCTTGGAAA 57.510 45.000 32.23 13.21 41.36 3.13
2004 2100 3.694734 ACAACACTTTTCATCAGCAACG 58.305 40.909 0.00 0.00 0.00 4.10
2062 2341 0.677731 ATACGGCAGCAGCACATGTT 60.678 50.000 2.65 0.00 44.61 2.71
2077 2356 3.186409 ACTTGCACAACAGCACTTATACG 59.814 43.478 0.00 0.00 45.61 3.06
2111 2405 4.025396 CAGCACATATACAGCAGCACTTAC 60.025 45.833 0.00 0.00 0.00 2.34
2556 3724 8.642964 TGGATGTTATGGATATCTTGGGATAT 57.357 34.615 2.05 0.00 44.93 1.63
2557 3725 8.496916 CATGGATGTTATGGATATCTTGGGATA 58.503 37.037 2.05 0.00 38.60 2.59
2558 3726 6.975471 TGGATGTTATGGATATCTTGGGAT 57.025 37.500 2.05 0.00 36.07 3.85
2559 3727 6.275381 ACATGGATGTTATGGATATCTTGGGA 59.725 38.462 2.05 0.00 37.90 4.37
2560 3728 6.487828 ACATGGATGTTATGGATATCTTGGG 58.512 40.000 2.05 0.00 37.90 4.12
2561 3729 6.600822 GGACATGGATGTTATGGATATCTTGG 59.399 42.308 2.05 0.00 41.95 3.61
2562 3730 6.600822 GGGACATGGATGTTATGGATATCTTG 59.399 42.308 2.05 0.00 41.95 3.02
2563 3731 6.275381 TGGGACATGGATGTTATGGATATCTT 59.725 38.462 2.05 0.00 41.95 2.40
2564 3732 5.792188 TGGGACATGGATGTTATGGATATCT 59.208 40.000 2.05 0.00 41.95 1.98
2565 3733 6.065976 TGGGACATGGATGTTATGGATATC 57.934 41.667 0.00 0.00 41.95 1.63
2566 3734 6.183361 TGTTGGGACATGGATGTTATGGATAT 60.183 38.462 0.00 0.00 41.95 1.63
2567 3735 5.133491 TGTTGGGACATGGATGTTATGGATA 59.867 40.000 0.00 0.00 41.95 2.59
2568 3736 4.079269 TGTTGGGACATGGATGTTATGGAT 60.079 41.667 0.00 0.00 41.95 3.41
2569 3737 3.268072 TGTTGGGACATGGATGTTATGGA 59.732 43.478 0.00 0.00 41.95 3.41
2570 3738 3.630168 TGTTGGGACATGGATGTTATGG 58.370 45.455 0.00 0.00 41.95 2.74
2582 3750 1.922447 AGGCTATTCCATGTTGGGACA 59.078 47.619 0.00 0.00 38.32 4.02
2583 3751 2.736670 AGGCTATTCCATGTTGGGAC 57.263 50.000 0.00 0.00 38.32 4.46
2584 3752 3.119319 TGTAGGCTATTCCATGTTGGGA 58.881 45.455 0.00 0.00 38.32 4.37
2585 3753 3.576078 TGTAGGCTATTCCATGTTGGG 57.424 47.619 0.00 0.00 38.32 4.12
2586 3754 4.336433 CAGTTGTAGGCTATTCCATGTTGG 59.664 45.833 0.00 0.00 39.43 3.77
2587 3755 4.201950 GCAGTTGTAGGCTATTCCATGTTG 60.202 45.833 0.00 0.00 37.29 3.33
2588 3756 3.947834 GCAGTTGTAGGCTATTCCATGTT 59.052 43.478 0.00 0.00 37.29 2.71
2589 3757 3.054434 TGCAGTTGTAGGCTATTCCATGT 60.054 43.478 0.00 0.00 37.29 3.21
2590 3758 3.313526 GTGCAGTTGTAGGCTATTCCATG 59.686 47.826 0.00 0.00 37.29 3.66
2591 3759 3.545703 GTGCAGTTGTAGGCTATTCCAT 58.454 45.455 0.00 0.00 37.29 3.41
2592 3760 2.355716 GGTGCAGTTGTAGGCTATTCCA 60.356 50.000 0.00 0.00 37.29 3.53
2593 3761 2.092914 AGGTGCAGTTGTAGGCTATTCC 60.093 50.000 0.00 0.00 0.00 3.01
2594 3762 2.939103 CAGGTGCAGTTGTAGGCTATTC 59.061 50.000 0.00 0.00 0.00 1.75
2595 3763 2.941415 GCAGGTGCAGTTGTAGGCTATT 60.941 50.000 0.00 0.00 41.59 1.73
2596 3764 1.407437 GCAGGTGCAGTTGTAGGCTAT 60.407 52.381 0.00 0.00 41.59 2.97
2597 3765 0.036388 GCAGGTGCAGTTGTAGGCTA 60.036 55.000 0.00 0.00 41.59 3.93
2598 3766 1.302832 GCAGGTGCAGTTGTAGGCT 60.303 57.895 0.00 0.00 41.59 4.58
2599 3767 3.267974 GCAGGTGCAGTTGTAGGC 58.732 61.111 0.00 0.00 41.59 3.93
2615 3783 3.491267 CCTCTTATAGCGTTGCTAGTTGC 59.509 47.826 4.70 0.00 44.66 4.17
2616 3784 4.051922 CCCTCTTATAGCGTTGCTAGTTG 58.948 47.826 4.70 0.00 44.66 3.16
2617 3785 3.069729 CCCCTCTTATAGCGTTGCTAGTT 59.930 47.826 4.70 0.00 44.66 2.24
2618 3786 2.628657 CCCCTCTTATAGCGTTGCTAGT 59.371 50.000 4.70 0.00 44.66 2.57
2619 3787 2.610727 GCCCCTCTTATAGCGTTGCTAG 60.611 54.545 4.70 0.00 44.66 3.42
2620 3788 1.343465 GCCCCTCTTATAGCGTTGCTA 59.657 52.381 0.38 0.38 45.55 3.49
2621 3789 0.106894 GCCCCTCTTATAGCGTTGCT 59.893 55.000 0.00 0.00 43.41 3.91
2622 3790 0.106894 AGCCCCTCTTATAGCGTTGC 59.893 55.000 0.00 0.00 0.00 4.17
2623 3791 1.412710 TCAGCCCCTCTTATAGCGTTG 59.587 52.381 0.00 0.00 0.00 4.10
2624 3792 1.689273 CTCAGCCCCTCTTATAGCGTT 59.311 52.381 0.00 0.00 0.00 4.84
2625 3793 1.333177 CTCAGCCCCTCTTATAGCGT 58.667 55.000 0.00 0.00 0.00 5.07
2626 3794 0.037790 GCTCAGCCCCTCTTATAGCG 60.038 60.000 0.00 0.00 0.00 4.26
2627 3795 1.051812 TGCTCAGCCCCTCTTATAGC 58.948 55.000 0.00 0.00 0.00 2.97
2628 3796 3.737850 CTTTGCTCAGCCCCTCTTATAG 58.262 50.000 0.00 0.00 0.00 1.31
2629 3797 2.158755 GCTTTGCTCAGCCCCTCTTATA 60.159 50.000 0.00 0.00 33.21 0.98
2630 3798 1.409381 GCTTTGCTCAGCCCCTCTTAT 60.409 52.381 0.00 0.00 33.21 1.73
2631 3799 0.035056 GCTTTGCTCAGCCCCTCTTA 60.035 55.000 0.00 0.00 33.21 2.10
2632 3800 1.303970 GCTTTGCTCAGCCCCTCTT 60.304 57.895 0.00 0.00 33.21 2.85
2633 3801 2.354343 GCTTTGCTCAGCCCCTCT 59.646 61.111 0.00 0.00 33.21 3.69
2634 3802 3.130160 CGCTTTGCTCAGCCCCTC 61.130 66.667 0.00 0.00 36.31 4.30
2635 3803 4.729918 CCGCTTTGCTCAGCCCCT 62.730 66.667 0.00 0.00 36.31 4.79
2636 3804 3.622060 TACCGCTTTGCTCAGCCCC 62.622 63.158 0.00 0.00 36.31 5.80
2637 3805 1.674322 TTACCGCTTTGCTCAGCCC 60.674 57.895 0.00 0.00 36.31 5.19
2638 3806 1.234615 TGTTACCGCTTTGCTCAGCC 61.235 55.000 0.00 0.00 36.31 4.85
2639 3807 0.804989 ATGTTACCGCTTTGCTCAGC 59.195 50.000 0.00 0.00 36.33 4.26
2640 3808 2.030946 GCTATGTTACCGCTTTGCTCAG 59.969 50.000 0.00 0.00 0.00 3.35
2641 3809 2.006888 GCTATGTTACCGCTTTGCTCA 58.993 47.619 0.00 0.00 0.00 4.26
2642 3810 1.330829 GGCTATGTTACCGCTTTGCTC 59.669 52.381 0.00 0.00 0.00 4.26
2643 3811 1.339631 TGGCTATGTTACCGCTTTGCT 60.340 47.619 0.00 0.00 0.00 3.91
2644 3812 1.091537 TGGCTATGTTACCGCTTTGC 58.908 50.000 0.00 0.00 0.00 3.68
2645 3813 3.057876 TGTTTGGCTATGTTACCGCTTTG 60.058 43.478 0.00 0.00 0.00 2.77
2646 3814 3.150767 TGTTTGGCTATGTTACCGCTTT 58.849 40.909 0.00 0.00 0.00 3.51
2647 3815 2.785562 TGTTTGGCTATGTTACCGCTT 58.214 42.857 0.00 0.00 0.00 4.68
2648 3816 2.483014 TGTTTGGCTATGTTACCGCT 57.517 45.000 0.00 0.00 0.00 5.52
2649 3817 2.726681 CGTTGTTTGGCTATGTTACCGC 60.727 50.000 0.00 0.00 0.00 5.68
2650 3818 2.159626 CCGTTGTTTGGCTATGTTACCG 60.160 50.000 0.00 0.00 0.00 4.02
2651 3819 2.815503 ACCGTTGTTTGGCTATGTTACC 59.184 45.455 0.00 0.00 0.00 2.85
2652 3820 4.492791 AACCGTTGTTTGGCTATGTTAC 57.507 40.909 0.00 0.00 0.00 2.50
2663 3831 1.136110 CTTCCCAGCAAACCGTTGTTT 59.864 47.619 0.00 0.00 45.46 2.83
2664 3832 0.744281 CTTCCCAGCAAACCGTTGTT 59.256 50.000 0.00 0.00 37.06 2.83
2665 3833 1.106944 CCTTCCCAGCAAACCGTTGT 61.107 55.000 0.00 0.00 37.06 3.32
2666 3834 1.659794 CCTTCCCAGCAAACCGTTG 59.340 57.895 0.00 0.00 37.83 4.10
2667 3835 1.530655 CCCTTCCCAGCAAACCGTT 60.531 57.895 0.00 0.00 0.00 4.44
2668 3836 1.420532 TACCCTTCCCAGCAAACCGT 61.421 55.000 0.00 0.00 0.00 4.83
2669 3837 0.250989 TTACCCTTCCCAGCAAACCG 60.251 55.000 0.00 0.00 0.00 4.44
2670 3838 2.003937 TTTACCCTTCCCAGCAAACC 57.996 50.000 0.00 0.00 0.00 3.27
2671 3839 3.244078 CCTTTTTACCCTTCCCAGCAAAC 60.244 47.826 0.00 0.00 0.00 2.93
2672 3840 2.969262 CCTTTTTACCCTTCCCAGCAAA 59.031 45.455 0.00 0.00 0.00 3.68
2673 3841 2.090999 ACCTTTTTACCCTTCCCAGCAA 60.091 45.455 0.00 0.00 0.00 3.91
2674 3842 1.501604 ACCTTTTTACCCTTCCCAGCA 59.498 47.619 0.00 0.00 0.00 4.41
2675 3843 2.304221 ACCTTTTTACCCTTCCCAGC 57.696 50.000 0.00 0.00 0.00 4.85
2676 3844 4.341487 CCTAACCTTTTTACCCTTCCCAG 58.659 47.826 0.00 0.00 0.00 4.45
2677 3845 3.076333 CCCTAACCTTTTTACCCTTCCCA 59.924 47.826 0.00 0.00 0.00 4.37
2678 3846 3.565010 CCCCTAACCTTTTTACCCTTCCC 60.565 52.174 0.00 0.00 0.00 3.97
2679 3847 3.705051 CCCCTAACCTTTTTACCCTTCC 58.295 50.000 0.00 0.00 0.00 3.46
2680 3848 3.094572 GCCCCTAACCTTTTTACCCTTC 58.905 50.000 0.00 0.00 0.00 3.46
2681 3849 2.725783 AGCCCCTAACCTTTTTACCCTT 59.274 45.455 0.00 0.00 0.00 3.95
2682 3850 2.365183 AGCCCCTAACCTTTTTACCCT 58.635 47.619 0.00 0.00 0.00 4.34
2683 3851 2.913603 AGCCCCTAACCTTTTTACCC 57.086 50.000 0.00 0.00 0.00 3.69
2684 3852 5.120054 TGATAGCCCCTAACCTTTTTACC 57.880 43.478 0.00 0.00 0.00 2.85
2685 3853 5.535030 CCATGATAGCCCCTAACCTTTTTAC 59.465 44.000 0.00 0.00 0.00 2.01
2686 3854 5.701224 CCATGATAGCCCCTAACCTTTTTA 58.299 41.667 0.00 0.00 0.00 1.52
2687 3855 4.546674 CCATGATAGCCCCTAACCTTTTT 58.453 43.478 0.00 0.00 0.00 1.94
2688 3856 3.691311 GCCATGATAGCCCCTAACCTTTT 60.691 47.826 0.00 0.00 0.00 2.27
2689 3857 2.158460 GCCATGATAGCCCCTAACCTTT 60.158 50.000 0.00 0.00 0.00 3.11
2690 3858 1.425448 GCCATGATAGCCCCTAACCTT 59.575 52.381 0.00 0.00 0.00 3.50
2691 3859 1.068121 GCCATGATAGCCCCTAACCT 58.932 55.000 0.00 0.00 0.00 3.50
2692 3860 0.771127 TGCCATGATAGCCCCTAACC 59.229 55.000 0.00 0.00 0.00 2.85
2693 3861 2.656947 TTGCCATGATAGCCCCTAAC 57.343 50.000 0.00 0.00 0.00 2.34
2694 3862 3.896888 CAAATTGCCATGATAGCCCCTAA 59.103 43.478 0.00 0.00 0.00 2.69
2695 3863 3.499338 CAAATTGCCATGATAGCCCCTA 58.501 45.455 0.00 0.00 0.00 3.53
2696 3864 2.322658 CAAATTGCCATGATAGCCCCT 58.677 47.619 0.00 0.00 0.00 4.79
2697 3865 1.345415 CCAAATTGCCATGATAGCCCC 59.655 52.381 0.00 0.00 0.00 5.80
2698 3866 1.345415 CCCAAATTGCCATGATAGCCC 59.655 52.381 0.00 0.00 0.00 5.19
2699 3867 2.298163 CTCCCAAATTGCCATGATAGCC 59.702 50.000 0.00 0.00 0.00 3.93
2700 3868 2.298163 CCTCCCAAATTGCCATGATAGC 59.702 50.000 0.00 0.00 0.00 2.97
2701 3869 2.298163 GCCTCCCAAATTGCCATGATAG 59.702 50.000 0.00 0.00 0.00 2.08
2702 3870 2.091166 AGCCTCCCAAATTGCCATGATA 60.091 45.455 0.00 0.00 0.00 2.15
2703 3871 1.125633 GCCTCCCAAATTGCCATGAT 58.874 50.000 0.00 0.00 0.00 2.45
2704 3872 0.041535 AGCCTCCCAAATTGCCATGA 59.958 50.000 0.00 0.00 0.00 3.07
2705 3873 0.906775 AAGCCTCCCAAATTGCCATG 59.093 50.000 0.00 0.00 0.00 3.66
2706 3874 0.906775 CAAGCCTCCCAAATTGCCAT 59.093 50.000 0.00 0.00 0.00 4.40
2707 3875 0.178938 TCAAGCCTCCCAAATTGCCA 60.179 50.000 0.00 0.00 0.00 4.92
2708 3876 1.197812 ATCAAGCCTCCCAAATTGCC 58.802 50.000 0.00 0.00 0.00 4.52
2709 3877 4.183865 GTTTATCAAGCCTCCCAAATTGC 58.816 43.478 0.00 0.00 0.00 3.56
2710 3878 5.404466 TGTTTATCAAGCCTCCCAAATTG 57.596 39.130 0.00 0.00 0.00 2.32
2711 3879 6.041423 CTTGTTTATCAAGCCTCCCAAATT 57.959 37.500 0.00 0.00 45.37 1.82
2712 3880 5.665916 CTTGTTTATCAAGCCTCCCAAAT 57.334 39.130 0.00 0.00 45.37 2.32
2723 3891 5.172934 CGCTACCTACCACTTGTTTATCAA 58.827 41.667 0.00 0.00 34.61 2.57
2724 3892 4.751060 CGCTACCTACCACTTGTTTATCA 58.249 43.478 0.00 0.00 0.00 2.15
2725 3893 3.554731 GCGCTACCTACCACTTGTTTATC 59.445 47.826 0.00 0.00 0.00 1.75
2726 3894 3.528532 GCGCTACCTACCACTTGTTTAT 58.471 45.455 0.00 0.00 0.00 1.40
2727 3895 2.671914 CGCGCTACCTACCACTTGTTTA 60.672 50.000 5.56 0.00 0.00 2.01
2728 3896 1.804601 GCGCTACCTACCACTTGTTT 58.195 50.000 0.00 0.00 0.00 2.83
2729 3897 0.389426 CGCGCTACCTACCACTTGTT 60.389 55.000 5.56 0.00 0.00 2.83
2730 3898 1.214589 CGCGCTACCTACCACTTGT 59.785 57.895 5.56 0.00 0.00 3.16
2731 3899 0.801067 GTCGCGCTACCTACCACTTG 60.801 60.000 5.56 0.00 0.00 3.16
2732 3900 1.509923 GTCGCGCTACCTACCACTT 59.490 57.895 5.56 0.00 0.00 3.16
2733 3901 2.758089 CGTCGCGCTACCTACCACT 61.758 63.158 5.56 0.00 0.00 4.00
2734 3902 2.277756 CGTCGCGCTACCTACCAC 60.278 66.667 5.56 0.00 0.00 4.16
2735 3903 3.511595 CCGTCGCGCTACCTACCA 61.512 66.667 5.56 0.00 0.00 3.25
2736 3904 3.178569 CTCCGTCGCGCTACCTACC 62.179 68.421 5.56 0.00 0.00 3.18
2737 3905 2.327244 CTCCGTCGCGCTACCTAC 59.673 66.667 5.56 0.00 0.00 3.18
2738 3906 3.580193 GCTCCGTCGCGCTACCTA 61.580 66.667 5.56 0.00 0.00 3.08
2746 3914 2.049985 ATGCTATCGCTCCGTCGC 60.050 61.111 0.00 0.00 36.97 5.19
2747 3915 1.794003 CGATGCTATCGCTCCGTCG 60.794 63.158 5.77 0.00 46.55 5.12
2748 3916 4.138722 CGATGCTATCGCTCCGTC 57.861 61.111 5.77 0.00 46.55 4.79
2756 3924 4.230314 TGCTAGTTGTCTCGATGCTATC 57.770 45.455 0.00 0.00 0.00 2.08
2757 3925 4.862902 ATGCTAGTTGTCTCGATGCTAT 57.137 40.909 0.00 0.00 0.00 2.97
2758 3926 4.320567 GCTATGCTAGTTGTCTCGATGCTA 60.321 45.833 0.00 0.00 0.00 3.49
2759 3927 3.551863 GCTATGCTAGTTGTCTCGATGCT 60.552 47.826 0.00 0.00 0.00 3.79
2760 3928 2.728839 GCTATGCTAGTTGTCTCGATGC 59.271 50.000 0.00 0.00 0.00 3.91
2761 3929 3.969899 TGCTATGCTAGTTGTCTCGATG 58.030 45.455 0.00 0.00 0.00 3.84
2762 3930 4.655762 TTGCTATGCTAGTTGTCTCGAT 57.344 40.909 0.00 0.00 0.00 3.59
2763 3931 4.157840 TCTTTGCTATGCTAGTTGTCTCGA 59.842 41.667 0.00 0.00 0.00 4.04
2764 3932 4.424626 TCTTTGCTATGCTAGTTGTCTCG 58.575 43.478 0.00 0.00 0.00 4.04
2765 3933 7.206687 ACTATCTTTGCTATGCTAGTTGTCTC 58.793 38.462 0.00 0.00 0.00 3.36
2766 3934 7.118496 ACTATCTTTGCTATGCTAGTTGTCT 57.882 36.000 0.00 0.00 0.00 3.41
2767 3935 8.138712 ACTACTATCTTTGCTATGCTAGTTGTC 58.861 37.037 3.67 0.00 0.00 3.18
2768 3936 7.923344 CACTACTATCTTTGCTATGCTAGTTGT 59.077 37.037 3.67 5.18 0.00 3.32
2769 3937 8.138074 TCACTACTATCTTTGCTATGCTAGTTG 58.862 37.037 3.67 4.69 0.00 3.16
2770 3938 8.239038 TCACTACTATCTTTGCTATGCTAGTT 57.761 34.615 3.67 0.00 0.00 2.24
2771 3939 7.721842 TCTCACTACTATCTTTGCTATGCTAGT 59.278 37.037 0.00 3.80 0.00 2.57
2772 3940 8.105097 TCTCACTACTATCTTTGCTATGCTAG 57.895 38.462 0.00 0.00 0.00 3.42
2773 3941 8.642935 ATCTCACTACTATCTTTGCTATGCTA 57.357 34.615 0.00 0.00 0.00 3.49
2774 3942 6.968263 TCTCACTACTATCTTTGCTATGCT 57.032 37.500 0.00 0.00 0.00 3.79
2775 3943 7.601856 AGATCTCACTACTATCTTTGCTATGC 58.398 38.462 0.00 0.00 0.00 3.14
2778 3946 9.290988 CCTTAGATCTCACTACTATCTTTGCTA 57.709 37.037 0.00 0.00 32.39 3.49
2779 3947 7.782644 ACCTTAGATCTCACTACTATCTTTGCT 59.217 37.037 0.00 0.00 32.39 3.91
2780 3948 7.865385 CACCTTAGATCTCACTACTATCTTTGC 59.135 40.741 0.00 0.00 32.39 3.68
2781 3949 9.126151 TCACCTTAGATCTCACTACTATCTTTG 57.874 37.037 0.00 0.00 32.39 2.77
2782 3950 9.127277 GTCACCTTAGATCTCACTACTATCTTT 57.873 37.037 0.00 0.00 32.39 2.52
2783 3951 7.442969 CGTCACCTTAGATCTCACTACTATCTT 59.557 40.741 0.00 0.00 32.39 2.40
2784 3952 6.932400 CGTCACCTTAGATCTCACTACTATCT 59.068 42.308 0.00 0.00 34.44 1.98
2785 3953 6.148150 CCGTCACCTTAGATCTCACTACTATC 59.852 46.154 0.00 0.00 0.00 2.08
2786 3954 5.998981 CCGTCACCTTAGATCTCACTACTAT 59.001 44.000 0.00 0.00 0.00 2.12
2787 3955 5.104610 ACCGTCACCTTAGATCTCACTACTA 60.105 44.000 0.00 0.00 0.00 1.82
2788 3956 4.200874 CCGTCACCTTAGATCTCACTACT 58.799 47.826 0.00 0.00 0.00 2.57
2789 3957 3.946558 ACCGTCACCTTAGATCTCACTAC 59.053 47.826 0.00 0.00 0.00 2.73
2790 3958 4.197750 GACCGTCACCTTAGATCTCACTA 58.802 47.826 0.00 0.00 0.00 2.74
2791 3959 3.018149 GACCGTCACCTTAGATCTCACT 58.982 50.000 0.00 0.00 0.00 3.41
2792 3960 2.753452 TGACCGTCACCTTAGATCTCAC 59.247 50.000 0.00 0.00 0.00 3.51
2793 3961 3.081710 TGACCGTCACCTTAGATCTCA 57.918 47.619 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.