Multiple sequence alignment - TraesCS2D01G368600

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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 TraesCS2D01G368600 chr2D 100.000 5416 0 0 1 5416 473156713 473162128 0.000000e+00 10002.0
1 TraesCS2D01G368600 chr2D 97.674 86 1 1 4948 5032 473161575 473161660 4.370000e-31 147.0
2 TraesCS2D01G368600 chr2D 97.674 86 1 1 4863 4948 473161660 473161744 4.370000e-31 147.0
3 TraesCS2D01G368600 chr2D 86.486 74 10 0 6 79 67569835 67569762 1.250000e-11 82.4
4 TraesCS2D01G368600 chr2D 90.385 52 4 1 4609 4659 591576377 591576326 3.500000e-07 67.6
5 TraesCS2D01G368600 chr2A 92.330 4407 234 51 242 4585 615258686 615263051 0.000000e+00 6170.0
6 TraesCS2D01G368600 chr2A 88.861 395 39 5 5026 5416 615265995 615266388 1.060000e-131 481.0
7 TraesCS2D01G368600 chr2A 94.521 219 11 1 4397 4615 615263048 615263265 2.420000e-88 337.0
8 TraesCS2D01G368600 chr2A 95.082 183 8 1 4433 4615 615263283 615263464 2.470000e-73 287.0
9 TraesCS2D01G368600 chr2A 96.104 77 3 0 4949 5025 615265861 615265937 5.690000e-25 126.0
10 TraesCS2D01G368600 chr2A 80.851 94 16 2 2 94 19268976 19269068 7.520000e-09 73.1
11 TraesCS2D01G368600 chr2A 85.246 61 5 4 4608 4666 564622008 564622066 5.860000e-05 60.2
12 TraesCS2D01G368600 chr2B 92.625 2183 124 19 2705 4863 553166896 553169065 0.000000e+00 3105.0
13 TraesCS2D01G368600 chr2B 93.894 1785 81 11 1 1764 553164289 553166066 0.000000e+00 2667.0
14 TraesCS2D01G368600 chr2B 90.647 834 59 12 1834 2655 553166071 553166897 0.000000e+00 1090.0
15 TraesCS2D01G368600 chr2B 85.944 249 26 3 5175 5416 553554908 553555154 1.940000e-64 257.0
16 TraesCS2D01G368600 chr2B 85.944 249 26 3 5175 5416 553560543 553560297 1.940000e-64 257.0
17 TraesCS2D01G368600 chr2B 85.542 249 27 3 5175 5416 553567642 553567888 9.010000e-63 252.0
18 TraesCS2D01G368600 chr2B 92.763 152 10 1 5025 5175 553169292 553169443 9.130000e-53 219.0
19 TraesCS2D01G368600 chr2B 96.552 87 2 1 4861 4947 553169155 553169240 5.650000e-30 143.0
20 TraesCS2D01G368600 chr2B 97.590 83 2 0 4949 5031 553169158 553169240 5.650000e-30 143.0
21 TraesCS2D01G368600 chr2B 100.000 31 0 0 4949 4979 553169094 553169124 2.110000e-04 58.4
22 TraesCS2D01G368600 chr1D 92.208 77 5 1 4949 5025 97528306 97528381 2.060000e-19 108.0
23 TraesCS2D01G368600 chr1D 81.928 83 13 2 2 83 12417646 12417727 9.730000e-08 69.4
24 TraesCS2D01G368600 chr4B 83.333 84 12 2 2 84 631184706 631184788 5.820000e-10 76.8
25 TraesCS2D01G368600 chr4B 81.928 83 13 2 2 83 2409135 2409216 9.730000e-08 69.4
26 TraesCS2D01G368600 chr5B 83.750 80 11 2 5 83 480245918 480245840 2.090000e-09 75.0
27 TraesCS2D01G368600 chr5B 85.075 67 6 4 4609 4673 608656009 608656073 1.260000e-06 65.8
28 TraesCS2D01G368600 chr5B 86.441 59 5 3 4609 4665 541304515 541304572 1.630000e-05 62.1
29 TraesCS2D01G368600 chr3B 86.765 68 7 2 4607 4672 676955705 676955638 2.090000e-09 75.0
30 TraesCS2D01G368600 chr6B 81.319 91 15 2 5 94 396545442 396545353 7.520000e-09 73.1
31 TraesCS2D01G368600 chr1B 82.500 80 12 2 5 83 563758617 563758539 9.730000e-08 69.4
32 TraesCS2D01G368600 chr1B 87.931 58 6 1 4608 4664 90405563 90405620 3.500000e-07 67.6
33 TraesCS2D01G368600 chrUn 87.931 58 6 1 4608 4664 430287748 430287805 3.500000e-07 67.6
34 TraesCS2D01G368600 chr5D 90.196 51 3 2 4609 4658 354536559 354536510 1.260000e-06 65.8


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 TraesCS2D01G368600 chr2D 473156713 473162128 5415 False 3432.000000 10002 98.449333 1 5416 3 chr2D.!!$F1 5415
1 TraesCS2D01G368600 chr2A 615258686 615266388 7702 False 1480.200000 6170 93.379600 242 5416 5 chr2A.!!$F3 5174
2 TraesCS2D01G368600 chr2B 553164289 553169443 5154 False 1060.771429 3105 94.867286 1 5175 7 chr2B.!!$F3 5174

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
28 29 0.033920 CAAGGGCAAAGCTTGGGTTC 59.966 55.0 0.00 0.0 0.00 3.62 F
42 43 0.322546 GGGTTCTCATCCGGCAAACT 60.323 55.0 0.00 0.0 0.00 2.66 F
187 188 0.400213 ACATGGTTTTCGGAGCCTCA 59.600 50.0 0.00 0.0 0.00 3.86 F
1691 1719 0.036010 ACCTTCAATGCCGAGGTGAG 60.036 55.0 2.78 0.0 42.04 3.51 F
2947 3005 0.320858 TTCGGCATACAAAGTCGGCA 60.321 50.0 0.00 0.0 34.34 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1668 1696 1.338769 ACCTCGGCATTGAAGGTGTAC 60.339 52.381 5.36 0.0 0.00 2.90 R
1691 1719 2.017049 ACATTCATAGGAGCAAACGCC 58.983 47.619 0.00 0.0 35.66 5.68 R
2185 2226 1.303074 AGGCTCGTACGTGTCCTCA 60.303 57.895 17.43 0.0 0.00 3.86 R
3199 3257 1.153958 GTTTGCTGCCGCTCCAATC 60.154 57.895 0.70 0.0 36.97 2.67 R
4904 7511 0.107945 AAGATCGAGCAAGGAGGTGC 60.108 55.000 2.38 0.0 45.28 5.01 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 0.033920 CAAGGGCAAAGCTTGGGTTC 59.966 55.000 0.00 0.00 0.00 3.62
42 43 0.322546 GGGTTCTCATCCGGCAAACT 60.323 55.000 0.00 0.00 0.00 2.66
83 84 2.525629 TGAAGGGGCTCCACGACA 60.526 61.111 4.79 0.00 34.83 4.35
98 99 2.425668 CACGACAAAACCTCCAAAACCT 59.574 45.455 0.00 0.00 0.00 3.50
102 103 4.682787 GACAAAACCTCCAAAACCTCAAG 58.317 43.478 0.00 0.00 0.00 3.02
140 141 1.375523 GACAACACCGCCACCTAGG 60.376 63.158 7.41 7.41 41.84 3.02
155 156 2.755655 ACCTAGGTGACAAGAGATGACG 59.244 50.000 15.42 0.00 0.00 4.35
158 159 2.239400 AGGTGACAAGAGATGACGACA 58.761 47.619 0.00 0.00 0.00 4.35
159 160 2.029828 AGGTGACAAGAGATGACGACAC 60.030 50.000 0.00 0.00 0.00 3.67
164 165 2.300152 ACAAGAGATGACGACACACCAT 59.700 45.455 0.00 0.00 0.00 3.55
187 188 0.400213 ACATGGTTTTCGGAGCCTCA 59.600 50.000 0.00 0.00 0.00 3.86
206 207 1.080093 GCTCCGACATCCACAACGA 60.080 57.895 0.00 0.00 0.00 3.85
281 283 2.288458 GCAAATTCAAAGCAGCAAAGCA 59.712 40.909 0.00 0.00 36.85 3.91
289 291 0.754472 AGCAGCAAAGCACCAAATGT 59.246 45.000 0.00 0.00 36.85 2.71
303 305 2.475864 CCAAATGTCACACAAAATGCGG 59.524 45.455 0.00 0.00 0.00 5.69
314 316 5.065859 CACACAAAATGCGGGAGATATAACA 59.934 40.000 0.00 0.00 0.00 2.41
395 398 5.943416 TCAAGCTCCGATTTTCTTAATGGAA 59.057 36.000 0.00 0.00 0.00 3.53
408 416 5.902681 TCTTAATGGAATGTCAGTACTCCG 58.097 41.667 0.00 0.00 0.00 4.63
448 456 2.093235 AGAGCTCTCACATTACTTGGCC 60.093 50.000 11.45 0.00 0.00 5.36
523 534 6.649973 TGATAACACAATCAGCCAAAATTTGG 59.350 34.615 19.81 19.81 41.09 3.28
547 559 8.423906 GGACCTATCCATAATAAACTGAGAGA 57.576 38.462 0.00 0.00 45.47 3.10
603 620 3.850122 AAGAAGGAAAATTACGCTGCC 57.150 42.857 0.00 0.00 0.00 4.85
681 705 9.613428 CTCACCTATCTATCTTCTATCCACTAG 57.387 40.741 0.00 0.00 0.00 2.57
760 784 1.597663 CGAAATTCCTCGCCATGTACC 59.402 52.381 0.00 0.00 31.04 3.34
763 787 2.040009 ATTCCTCGCCATGTACCCCG 62.040 60.000 0.00 0.00 0.00 5.73
765 789 3.849951 CTCGCCATGTACCCCGCT 61.850 66.667 0.00 0.00 0.00 5.52
766 790 4.155733 TCGCCATGTACCCCGCTG 62.156 66.667 0.00 0.00 0.00 5.18
810 835 6.825721 TGCTCTATCCTCTCATTTTCTTTTCC 59.174 38.462 0.00 0.00 0.00 3.13
824 849 7.625828 TTTTCTTTTCCTTTTTCGAGAGAGT 57.374 32.000 0.00 0.00 43.69 3.24
926 951 4.838486 CTCCGTGCCGTCGCTCTC 62.838 72.222 0.00 0.00 35.36 3.20
1691 1719 0.036010 ACCTTCAATGCCGAGGTGAG 60.036 55.000 2.78 0.00 42.04 3.51
1692 1720 0.745845 CCTTCAATGCCGAGGTGAGG 60.746 60.000 0.00 0.00 0.00 3.86
1714 1742 4.098416 GCGTTTGCTCCTATGAATGTTTC 58.902 43.478 0.00 0.00 38.39 2.78
1727 1755 5.168526 TGAATGTTTCCGACTGTCTTTTG 57.831 39.130 6.21 0.00 0.00 2.44
1755 1786 6.827586 ACCAAAGCTCATTTTCGGTTATTA 57.172 33.333 0.00 0.00 0.00 0.98
1760 1791 7.448748 AAGCTCATTTTCGGTTATTACACTT 57.551 32.000 0.00 0.00 0.00 3.16
1785 1817 9.627123 TTTATCTAGCTTATTAAACATGCTGGT 57.373 29.630 0.00 0.00 34.58 4.00
1800 1832 5.301551 ACATGCTGGTTGTTCACTTCATTAA 59.698 36.000 0.00 0.00 0.00 1.40
1801 1833 5.437289 TGCTGGTTGTTCACTTCATTAAG 57.563 39.130 0.00 0.00 38.77 1.85
1829 1861 4.641396 TGTCATACCATAACAGCCTATGC 58.359 43.478 0.00 0.00 37.95 3.14
1881 1913 5.105716 ACATCACACTAGCACACTACCTTAG 60.106 44.000 0.00 0.00 0.00 2.18
1908 1940 5.591643 TCAGTCTATGAACAGAAAAACGC 57.408 39.130 0.00 0.00 34.02 4.84
1948 1981 6.844696 TTATTTTGAGGATCGCATACAGAC 57.155 37.500 0.00 0.00 38.61 3.51
2002 2041 4.692625 GGTGTATCATGTATCAGTGATGCC 59.307 45.833 16.15 6.76 36.86 4.40
2185 2226 4.461081 TGGTAGGTAAATGCGCAAGATTTT 59.539 37.500 17.11 13.40 43.02 1.82
2347 2388 4.462834 GGATTTAAAGGGTACTGCTTGCTT 59.537 41.667 0.00 0.00 0.00 3.91
2358 2399 0.956633 TGCTTGCTTGCTCTCCTTTG 59.043 50.000 3.47 0.00 0.00 2.77
2360 2401 1.610522 GCTTGCTTGCTCTCCTTTGAA 59.389 47.619 0.00 0.00 0.00 2.69
2364 2409 3.079578 TGCTTGCTCTCCTTTGAATCTG 58.920 45.455 0.00 0.00 0.00 2.90
2367 2412 4.332268 GCTTGCTCTCCTTTGAATCTGTAG 59.668 45.833 0.00 0.00 0.00 2.74
2371 2416 4.622695 GCTCTCCTTTGAATCTGTAGTGCT 60.623 45.833 0.00 0.00 0.00 4.40
2373 2418 5.482908 TCTCCTTTGAATCTGTAGTGCTTC 58.517 41.667 0.00 0.00 0.00 3.86
2374 2419 5.012046 TCTCCTTTGAATCTGTAGTGCTTCA 59.988 40.000 0.00 0.00 0.00 3.02
2381 2426 1.694150 TCTGTAGTGCTTCAGCCTTGT 59.306 47.619 0.00 0.00 41.18 3.16
2392 2437 6.201806 GTGCTTCAGCCTTGTACTATTAGATG 59.798 42.308 0.00 0.00 41.18 2.90
2424 2474 5.178797 ACACTAATGTCACTATTGGTGCTC 58.821 41.667 12.80 0.00 46.93 4.26
2430 2480 5.375417 TGTCACTATTGGTGCTCATTTTG 57.625 39.130 0.00 0.00 44.98 2.44
2435 2485 5.048504 CACTATTGGTGCTCATTTTGTGTCT 60.049 40.000 0.00 0.00 39.22 3.41
2436 2486 3.713858 TTGGTGCTCATTTTGTGTCTG 57.286 42.857 0.00 0.00 0.00 3.51
2461 2511 6.656632 AGGTACATCGTATCTGATTGTGAT 57.343 37.500 0.00 0.00 0.00 3.06
2506 2556 3.764434 ACCAGACATACACGAGTTCAGAT 59.236 43.478 0.00 0.00 0.00 2.90
2530 2580 5.807520 TGAAGATTCAGTAGCGATTGTTCTC 59.192 40.000 0.00 0.00 32.50 2.87
2536 2586 1.666189 GTAGCGATTGTTCTCAAGGCC 59.334 52.381 0.00 0.00 37.53 5.19
2545 2595 1.804748 GTTCTCAAGGCCGGTTAGTTG 59.195 52.381 1.90 1.98 0.00 3.16
2581 2631 0.930310 TTTCGCTGAGCATCGCATAC 59.070 50.000 4.88 0.00 38.61 2.39
2587 2642 3.181536 CGCTGAGCATCGCATACTTTATC 60.182 47.826 4.88 0.00 38.61 1.75
2590 2645 4.309933 TGAGCATCGCATACTTTATCAGG 58.690 43.478 0.00 0.00 38.61 3.86
2593 2648 6.071391 TGAGCATCGCATACTTTATCAGGATA 60.071 38.462 0.00 0.00 38.61 2.59
2599 2654 7.836842 TCGCATACTTTATCAGGATATTGCTA 58.163 34.615 0.00 0.00 0.00 3.49
2619 2674 8.596781 TTGCTATCTTTCTAGACTAGGACTTT 57.403 34.615 9.64 0.00 31.99 2.66
2620 2675 8.596781 TGCTATCTTTCTAGACTAGGACTTTT 57.403 34.615 9.64 0.00 31.99 2.27
2630 2685 8.384718 TCTAGACTAGGACTTTTACTTCTCAGT 58.615 37.037 9.64 0.00 36.99 3.41
2638 2693 9.847224 AGGACTTTTACTTCTCAGTTCAATAAA 57.153 29.630 0.00 0.00 34.06 1.40
2639 2694 9.880064 GGACTTTTACTTCTCAGTTCAATAAAC 57.120 33.333 0.00 0.00 38.21 2.01
2651 2706 8.850454 TCAGTTCAATAAACACTACAAAAAGC 57.150 30.769 0.00 0.00 40.56 3.51
2655 2710 9.900264 GTTCAATAAACACTACAAAAAGCAAAG 57.100 29.630 0.00 0.00 37.82 2.77
2656 2711 9.862371 TTCAATAAACACTACAAAAAGCAAAGA 57.138 25.926 0.00 0.00 0.00 2.52
2663 2718 9.463443 AACACTACAAAAAGCAAAGATTATGAC 57.537 29.630 0.00 0.00 0.00 3.06
2664 2719 8.850156 ACACTACAAAAAGCAAAGATTATGACT 58.150 29.630 0.00 0.00 0.00 3.41
2689 2744 9.640952 CTTTGGGAGATTAGGGACATAAAATTA 57.359 33.333 0.00 0.00 0.00 1.40
2703 2761 9.008965 GGACATAAAATTAATTTTTGGCCAACT 57.991 29.630 30.91 16.40 41.00 3.16
2720 2778 5.279456 GGCCAACTAATGTGAACTCCATTTT 60.279 40.000 0.00 0.00 34.51 1.82
2725 2783 4.525912 AATGTGAACTCCATTTTGAGGC 57.474 40.909 0.00 0.00 36.66 4.70
2741 2799 3.668447 TGAGGCTTCTACTTTCTGCTTG 58.332 45.455 0.00 0.00 0.00 4.01
2745 2803 2.810852 GCTTCTACTTTCTGCTTGCAGT 59.189 45.455 20.20 6.50 0.00 4.40
2751 2809 1.672363 CTTTCTGCTTGCAGTGTGACA 59.328 47.619 20.20 0.00 0.00 3.58
2753 2811 0.465287 TCTGCTTGCAGTGTGACAGA 59.535 50.000 20.20 0.00 0.00 3.41
2754 2812 1.071228 TCTGCTTGCAGTGTGACAGAT 59.929 47.619 20.20 0.00 0.00 2.90
2755 2813 1.878088 CTGCTTGCAGTGTGACAGATT 59.122 47.619 13.89 0.00 0.00 2.40
2783 2841 5.637006 ATATGAACTTTTACGCTTTGCCA 57.363 34.783 0.00 0.00 0.00 4.92
2791 2849 3.757745 TTACGCTTTGCCAGAATTAGC 57.242 42.857 0.00 0.00 0.00 3.09
2796 2854 3.442100 GCTTTGCCAGAATTAGCATGAC 58.558 45.455 0.00 0.00 39.11 3.06
2797 2855 3.688272 CTTTGCCAGAATTAGCATGACG 58.312 45.455 0.00 0.00 39.11 4.35
2802 2860 2.289002 CCAGAATTAGCATGACGAAGGC 59.711 50.000 0.00 0.00 0.00 4.35
2804 2862 3.247173 CAGAATTAGCATGACGAAGGCTC 59.753 47.826 5.37 0.00 39.01 4.70
2835 2893 7.549488 TCTTCTCGAAATAGATTTCTTTGACCC 59.451 37.037 12.03 0.00 42.96 4.46
2843 2901 4.401925 AGATTTCTTTGACCCACCTTCTG 58.598 43.478 0.00 0.00 0.00 3.02
2864 2922 6.653020 TCTGTATATCATTCAACCAAGCAGT 58.347 36.000 0.00 0.00 0.00 4.40
2947 3005 0.320858 TTCGGCATACAAAGTCGGCA 60.321 50.000 0.00 0.00 34.34 5.69
2977 3035 8.840833 AGAAAGGAAAGATACAAGAAGAAGAC 57.159 34.615 0.00 0.00 0.00 3.01
3016 3074 8.911918 TTTATAACCTGTTTTCTGTTCAGCTA 57.088 30.769 0.00 0.00 0.00 3.32
3038 3096 3.066760 ACGCCTTGGACTTTTTGAGAAAG 59.933 43.478 0.00 0.00 0.00 2.62
3082 3140 0.749454 GACTAGGCCCCAGCAATGTG 60.749 60.000 0.00 0.00 42.56 3.21
3133 3191 1.003696 GAAGCTGTAAGGCAGGGAACT 59.996 52.381 0.00 0.00 45.14 3.01
3152 3210 3.393800 ACTGTCCTGTTGAAGAACGATG 58.606 45.455 0.00 0.00 34.49 3.84
3199 3257 9.539825 AGAAGTGAAGTTAGTCATATTGCTATG 57.460 33.333 0.00 0.00 36.79 2.23
3330 3388 0.312102 GCCTCACTTTGTTCAGGTGC 59.688 55.000 0.00 0.00 0.00 5.01
3439 3497 1.401905 GACTCAACGGATGGATTTGGC 59.598 52.381 0.00 0.00 0.00 4.52
3523 3581 2.755655 TCAGGAGACCGAAGATCTTGAC 59.244 50.000 14.00 0.00 0.00 3.18
3598 3656 4.095036 GCCAGTGTAACAAAGAAGCCTATC 59.905 45.833 0.00 0.00 41.43 2.08
3607 3665 2.386661 AGAAGCCTATCGTGTTGGTG 57.613 50.000 0.00 0.00 0.00 4.17
3616 3674 4.792087 GTGTTGGTGATCACGGGT 57.208 55.556 19.33 0.00 0.00 5.28
3628 3686 2.770904 ACGGGTGGTGGTCCTGTT 60.771 61.111 0.00 0.00 41.20 3.16
3703 3761 1.915078 ATCCAGGAGAAGTTGGCGGG 61.915 60.000 0.00 0.00 34.38 6.13
3756 3814 8.258708 AGAGTACAATCCAGGTGAGTAAATAAC 58.741 37.037 0.00 0.00 0.00 1.89
3757 3815 7.913789 AGTACAATCCAGGTGAGTAAATAACA 58.086 34.615 0.00 0.00 0.00 2.41
3761 3819 4.188462 TCCAGGTGAGTAAATAACATGCG 58.812 43.478 0.00 0.00 0.00 4.73
3764 3822 4.034048 CAGGTGAGTAAATAACATGCGGTC 59.966 45.833 0.00 0.00 0.00 4.79
3765 3823 3.936453 GGTGAGTAAATAACATGCGGTCA 59.064 43.478 0.00 0.00 0.00 4.02
3769 3827 7.201661 GGTGAGTAAATAACATGCGGTCAAATA 60.202 37.037 0.00 0.00 0.00 1.40
3770 3828 7.850982 GTGAGTAAATAACATGCGGTCAAATAG 59.149 37.037 0.00 0.00 0.00 1.73
3775 3850 8.460831 AAATAACATGCGGTCAAATAGAAAAC 57.539 30.769 0.00 0.00 0.00 2.43
3782 3857 5.708230 TGCGGTCAAATAGAAAACCTTGTAT 59.292 36.000 0.00 0.00 0.00 2.29
3807 3882 7.028926 TGTTAGCTAATCTAGTACACTCTGC 57.971 40.000 9.88 0.00 0.00 4.26
3811 3886 6.068010 AGCTAATCTAGTACACTCTGCTGAT 58.932 40.000 0.00 0.00 0.00 2.90
3812 3887 6.016360 AGCTAATCTAGTACACTCTGCTGATG 60.016 42.308 0.00 0.00 0.00 3.07
3813 3888 6.016693 GCTAATCTAGTACACTCTGCTGATGA 60.017 42.308 0.00 0.00 0.00 2.92
3828 3903 3.428589 GCTGATGACAGGAGGAAAATTGC 60.429 47.826 0.00 0.00 43.62 3.56
3830 3905 1.923356 TGACAGGAGGAAAATTGCCC 58.077 50.000 0.00 0.00 0.00 5.36
3833 3908 2.428530 GACAGGAGGAAAATTGCCCATC 59.571 50.000 0.00 0.00 0.00 3.51
3845 3920 0.844661 TGCCCATCACTTGGTACCCT 60.845 55.000 10.07 0.00 44.83 4.34
3898 3973 0.693049 AACATGAGAGCCGACCCTTT 59.307 50.000 0.00 0.00 0.00 3.11
3943 4018 3.364277 GGTTCTACACCGGAGATGC 57.636 57.895 9.46 0.00 35.12 3.91
3986 4061 4.916249 GGTCTGAGTTACACAAAGTACTCG 59.084 45.833 0.00 0.00 35.46 4.18
4094 4169 1.520787 GGACGGGCTGGATTACGTG 60.521 63.158 0.00 0.00 39.95 4.49
4152 4227 0.099613 CTCTGTCCACATCTCGGTCG 59.900 60.000 0.00 0.00 0.00 4.79
4190 4265 3.766691 GGGAGCCACGCCGTTCTA 61.767 66.667 0.00 0.00 0.00 2.10
4197 4272 1.342082 CCACGCCGTTCTACTGTTCG 61.342 60.000 0.00 0.00 0.00 3.95
4287 4362 1.971167 GCCGGCAGATCAACCAACA 60.971 57.895 24.80 0.00 0.00 3.33
4316 4391 1.076485 GGTGGATCCCTGCAAGCAT 60.076 57.895 9.90 0.00 0.00 3.79
4371 4446 1.422781 TGCTTCTGGGATCCCATCATC 59.577 52.381 33.89 21.84 46.15 2.92
4423 4498 7.841915 TTGTCATCGAAGCATAACAATCTAA 57.158 32.000 0.00 0.00 0.00 2.10
4549 5008 5.174943 GGTTGAACCGATTTTGCAGTAAAAG 59.825 40.000 0.00 0.00 41.26 2.27
4550 5009 5.759506 TGAACCGATTTTGCAGTAAAAGA 57.240 34.783 2.71 0.00 41.26 2.52
4553 5012 6.695278 TGAACCGATTTTGCAGTAAAAGAAAG 59.305 34.615 2.71 0.00 41.26 2.62
4556 5015 5.461737 CCGATTTTGCAGTAAAAGAAAGCAA 59.538 36.000 2.71 0.00 41.26 3.91
4562 5021 5.174395 TGCAGTAAAAGAAAGCAAAAGCAA 58.826 33.333 0.00 0.00 31.42 3.91
4598 5057 8.922676 CGCTGTTCTAGTTCTATTTTTGTTAGA 58.077 33.333 0.00 0.00 0.00 2.10
4673 7249 6.976934 AGGCAGAAAGAAATTAACAGGAAA 57.023 33.333 0.00 0.00 0.00 3.13
4679 7255 7.061094 CAGAAAGAAATTAACAGGAAATGTCGC 59.939 37.037 0.00 0.00 43.00 5.19
4695 7271 0.394938 TCGCAAGCCCAACAAGTAGA 59.605 50.000 0.00 0.00 37.18 2.59
4713 7289 4.663444 GCTACCAGCTAGCATCCG 57.337 61.111 18.83 3.12 46.56 4.18
4716 7292 0.319728 CTACCAGCTAGCATCCGCAT 59.680 55.000 18.83 0.00 42.27 4.73
4725 7301 2.113139 CATCCGCATACCCACCCC 59.887 66.667 0.00 0.00 0.00 4.95
4741 7317 3.627237 CCACCCCCAAATACATGCTACTT 60.627 47.826 0.00 0.00 0.00 2.24
4742 7318 3.381272 CACCCCCAAATACATGCTACTTG 59.619 47.826 0.00 0.00 0.00 3.16
4762 7340 7.393551 ACTTGCATAAAGATTTGAAAACACG 57.606 32.000 0.00 0.00 39.38 4.49
4779 7357 1.284408 CGTAGCTCTGGCCGATCTC 59.716 63.158 0.00 0.00 39.73 2.75
4797 7375 6.462207 CCGATCTCCAAGTTTGTATCTCATCT 60.462 42.308 0.00 0.00 0.00 2.90
4828 7407 5.255443 AGGTTAACAAATTGGGGGATAGTCT 59.745 40.000 8.10 0.00 0.00 3.24
4833 7412 4.202673 ACAAATTGGGGGATAGTCTGTTGT 60.203 41.667 0.00 0.00 0.00 3.32
4836 7415 1.004277 TGGGGGATAGTCTGTTGTTGC 59.996 52.381 0.00 0.00 0.00 4.17
4841 7420 2.009774 GATAGTCTGTTGTTGCGCCAT 58.990 47.619 4.18 0.00 0.00 4.40
4845 7424 2.819608 AGTCTGTTGTTGCGCCATATTT 59.180 40.909 4.18 0.00 0.00 1.40
4849 7428 2.816672 TGTTGTTGCGCCATATTTCTGA 59.183 40.909 4.18 0.00 0.00 3.27
4858 7437 1.330521 CCATATTTCTGAACACCCGCG 59.669 52.381 0.00 0.00 0.00 6.46
4883 7490 7.409697 GCATTAGAATGACTAGCGAATCAAAA 58.590 34.615 6.43 0.00 38.70 2.44
4895 7502 3.365767 GCGAATCAAAAGCTCTTTCTGCT 60.366 43.478 0.00 0.00 43.32 4.24
4903 7510 2.411904 AGCTCTTTCTGCTTGTCTTCG 58.588 47.619 0.00 0.00 37.52 3.79
4904 7511 1.462670 GCTCTTTCTGCTTGTCTTCGG 59.537 52.381 0.00 0.00 0.00 4.30
4905 7512 1.462670 CTCTTTCTGCTTGTCTTCGGC 59.537 52.381 0.00 0.00 0.00 5.54
4906 7513 1.202639 TCTTTCTGCTTGTCTTCGGCA 60.203 47.619 0.00 0.00 34.66 5.69
4907 7514 0.944386 TTTCTGCTTGTCTTCGGCAC 59.056 50.000 0.00 0.00 32.33 5.01
4908 7515 0.884704 TTCTGCTTGTCTTCGGCACC 60.885 55.000 0.00 0.00 32.33 5.01
4909 7516 1.302033 CTGCTTGTCTTCGGCACCT 60.302 57.895 0.00 0.00 32.33 4.00
4911 7518 2.035442 GCTTGTCTTCGGCACCTCC 61.035 63.158 0.00 0.00 0.00 4.30
4912 7519 1.674057 CTTGTCTTCGGCACCTCCT 59.326 57.895 0.00 0.00 0.00 3.69
4913 7520 0.035458 CTTGTCTTCGGCACCTCCTT 59.965 55.000 0.00 0.00 0.00 3.36
4914 7521 0.250295 TTGTCTTCGGCACCTCCTTG 60.250 55.000 0.00 0.00 0.00 3.61
4915 7522 2.035442 GTCTTCGGCACCTCCTTGC 61.035 63.158 0.00 0.00 42.18 4.01
4916 7523 2.217038 TCTTCGGCACCTCCTTGCT 61.217 57.895 0.00 0.00 42.56 3.91
4917 7524 1.743252 CTTCGGCACCTCCTTGCTC 60.743 63.158 0.00 0.00 42.56 4.26
4918 7525 3.589654 TTCGGCACCTCCTTGCTCG 62.590 63.158 0.00 0.00 42.56 5.03
4919 7526 4.069232 CGGCACCTCCTTGCTCGA 62.069 66.667 0.00 0.00 42.56 4.04
4920 7527 2.586792 GGCACCTCCTTGCTCGAT 59.413 61.111 0.00 0.00 42.56 3.59
4921 7528 1.522580 GGCACCTCCTTGCTCGATC 60.523 63.158 0.00 0.00 42.56 3.69
4922 7529 1.519719 GCACCTCCTTGCTCGATCT 59.480 57.895 0.00 0.00 39.59 2.75
4923 7530 0.107945 GCACCTCCTTGCTCGATCTT 60.108 55.000 0.00 0.00 39.59 2.40
4925 7532 2.801342 GCACCTCCTTGCTCGATCTTAG 60.801 54.545 0.00 0.00 39.59 2.18
4926 7533 1.410882 ACCTCCTTGCTCGATCTTAGC 59.589 52.381 9.38 9.38 40.50 3.09
4927 7534 1.270041 CCTCCTTGCTCGATCTTAGCC 60.270 57.143 12.75 0.00 39.30 3.93
4928 7535 1.410517 CTCCTTGCTCGATCTTAGCCA 59.589 52.381 12.75 3.28 39.30 4.75
4929 7536 1.137086 TCCTTGCTCGATCTTAGCCAC 59.863 52.381 12.75 0.00 39.30 5.01
4930 7537 1.576356 CTTGCTCGATCTTAGCCACC 58.424 55.000 12.75 0.00 39.30 4.61
4931 7538 0.901827 TTGCTCGATCTTAGCCACCA 59.098 50.000 12.75 0.00 39.30 4.17
4932 7539 0.175760 TGCTCGATCTTAGCCACCAC 59.824 55.000 12.75 0.00 39.30 4.16
4933 7540 0.461961 GCTCGATCTTAGCCACCACT 59.538 55.000 5.79 0.00 33.73 4.00
4934 7541 1.537135 GCTCGATCTTAGCCACCACTC 60.537 57.143 5.79 0.00 33.73 3.51
4935 7542 1.067821 CTCGATCTTAGCCACCACTCC 59.932 57.143 0.00 0.00 0.00 3.85
4936 7543 1.115467 CGATCTTAGCCACCACTCCT 58.885 55.000 0.00 0.00 0.00 3.69
4937 7544 1.067821 CGATCTTAGCCACCACTCCTC 59.932 57.143 0.00 0.00 0.00 3.71
4938 7545 1.414550 GATCTTAGCCACCACTCCTCC 59.585 57.143 0.00 0.00 0.00 4.30
4939 7546 0.116342 TCTTAGCCACCACTCCTCCA 59.884 55.000 0.00 0.00 0.00 3.86
4940 7547 0.539051 CTTAGCCACCACTCCTCCAG 59.461 60.000 0.00 0.00 0.00 3.86
4941 7548 0.909610 TTAGCCACCACTCCTCCAGG 60.910 60.000 0.00 0.00 0.00 4.45
4942 7549 1.811025 TAGCCACCACTCCTCCAGGA 61.811 60.000 0.00 0.00 43.08 3.86
4943 7550 1.997874 GCCACCACTCCTCCAGGAT 60.998 63.158 0.00 0.00 44.46 3.24
4944 7551 1.910722 CCACCACTCCTCCAGGATG 59.089 63.158 0.00 0.00 44.46 3.51
4945 7552 0.911525 CCACCACTCCTCCAGGATGT 60.912 60.000 0.00 0.00 44.46 3.06
4946 7553 0.539051 CACCACTCCTCCAGGATGTC 59.461 60.000 0.00 0.00 44.46 3.06
4947 7554 0.415429 ACCACTCCTCCAGGATGTCT 59.585 55.000 0.00 0.00 44.46 3.41
5029 7694 1.681666 CACCACTCCTCCAGCATGT 59.318 57.895 0.00 0.00 0.00 3.21
5128 7794 2.536365 GCGTCTTGTAATCCATGTCGA 58.464 47.619 0.00 0.00 33.69 4.20
5130 7796 3.000322 GCGTCTTGTAATCCATGTCGAAG 60.000 47.826 0.00 0.00 33.69 3.79
5131 7797 3.000322 CGTCTTGTAATCCATGTCGAAGC 60.000 47.826 0.00 0.00 33.69 3.86
5158 7824 3.081710 TCAGAGGTCCAGACACGATAA 57.918 47.619 0.00 0.00 0.00 1.75
5165 7831 3.132289 GGTCCAGACACGATAATGGAGAA 59.868 47.826 0.00 0.00 42.35 2.87
5193 7859 9.616156 AAGCCATATGAATATTTTGCATTTGAA 57.384 25.926 3.65 0.00 0.00 2.69
5194 7860 9.048446 AGCCATATGAATATTTTGCATTTGAAC 57.952 29.630 3.65 2.06 0.00 3.18
5197 7863 9.033481 CATATGAATATTTTGCATTTGAACGGT 57.967 29.630 0.00 0.00 0.00 4.83
5206 7872 1.068434 CATTTGAACGGTGCCCAACTT 59.932 47.619 0.00 0.00 0.00 2.66
5209 7875 1.187087 TGAACGGTGCCCAACTTTTT 58.813 45.000 0.00 0.00 0.00 1.94
5232 7898 2.877691 GCAATGAGCGGGTGAACC 59.122 61.111 0.00 0.00 0.00 3.62
5233 7899 1.971167 GCAATGAGCGGGTGAACCA 60.971 57.895 1.16 0.00 40.22 3.67
5234 7900 1.315257 GCAATGAGCGGGTGAACCAT 61.315 55.000 1.16 0.00 40.22 3.55
5236 7902 1.315257 AATGAGCGGGTGAACCATGC 61.315 55.000 1.16 4.90 40.22 4.06
5237 7903 3.134127 GAGCGGGTGAACCATGCC 61.134 66.667 11.12 2.03 39.02 4.40
5238 7904 3.918253 GAGCGGGTGAACCATGCCA 62.918 63.158 11.12 0.00 39.02 4.92
5239 7905 2.755469 GCGGGTGAACCATGCCAT 60.755 61.111 1.16 0.00 40.22 4.40
5240 7906 3.067480 GCGGGTGAACCATGCCATG 62.067 63.158 0.00 0.00 40.22 3.66
5265 7934 5.874810 GCACAACATCTTGTAGGTAGATTGA 59.125 40.000 0.00 0.00 38.66 2.57
5266 7935 6.036517 GCACAACATCTTGTAGGTAGATTGAG 59.963 42.308 0.00 0.00 38.66 3.02
5278 7947 3.003897 GGTAGATTGAGCCGAGTACTGAG 59.996 52.174 0.00 0.00 0.00 3.35
5301 7970 1.222936 GGCACTCCATCTCCAGGTG 59.777 63.158 0.00 0.00 0.00 4.00
5339 8008 8.040132 GGTGCTAATATTAAGAGAGATGATGCT 58.960 37.037 0.00 0.00 0.00 3.79
5340 8009 8.871862 GTGCTAATATTAAGAGAGATGATGCTG 58.128 37.037 0.00 0.00 0.00 4.41
5343 8012 9.288124 CTAATATTAAGAGAGATGATGCTGACG 57.712 37.037 0.00 0.00 0.00 4.35
5346 8015 1.680735 AGAGAGATGATGCTGACGACC 59.319 52.381 0.00 0.00 0.00 4.79
5393 8062 0.531200 GCTAGACCTGCACCTTACGT 59.469 55.000 0.00 0.00 0.00 3.57
5402 8071 1.893137 TGCACCTTACGTCTGTGATCT 59.107 47.619 14.11 0.00 31.66 2.75
5408 8077 5.066117 CACCTTACGTCTGTGATCTAGCTTA 59.934 44.000 0.00 0.00 31.66 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 1.203287 GGATGAGAACCCAAGCTTTGC 59.797 52.381 0.00 0.00 0.00 3.68
28 29 0.173481 TCTCGAGTTTGCCGGATGAG 59.827 55.000 13.13 0.36 0.00 2.90
42 43 0.810426 CCTCGTCATCTCGGTCTCGA 60.810 60.000 0.00 0.00 43.86 4.04
58 59 2.285743 AGCCCCTTCACCTCCCTC 60.286 66.667 0.00 0.00 0.00 4.30
120 121 3.229156 TAGGTGGCGGTGTTGTCGG 62.229 63.158 0.00 0.00 0.00 4.79
125 126 2.747686 CACCTAGGTGGCGGTGTT 59.252 61.111 31.15 0.00 44.38 3.32
140 141 2.726760 GTGTGTCGTCATCTCTTGTCAC 59.273 50.000 0.00 0.00 0.00 3.67
164 165 1.243902 GCTCCGAAAACCATGTTGGA 58.756 50.000 0.00 0.00 40.96 3.53
187 188 1.079819 CGTTGTGGATGTCGGAGCT 60.080 57.895 0.00 0.00 0.00 4.09
231 232 1.745489 GGGTGTTGGAGCCATCGAC 60.745 63.158 0.00 0.00 42.41 4.20
239 240 2.594303 TGCGCAAGGGTGTTGGAG 60.594 61.111 8.16 0.00 38.28 3.86
281 283 3.122297 CGCATTTTGTGTGACATTTGGT 58.878 40.909 0.00 0.00 40.86 3.67
289 291 2.198827 ATCTCCCGCATTTTGTGTGA 57.801 45.000 0.00 0.00 40.86 3.58
350 352 2.303022 AGTGATTCCCTGTGTCGTGATT 59.697 45.455 0.00 0.00 0.00 2.57
351 353 1.902508 AGTGATTCCCTGTGTCGTGAT 59.097 47.619 0.00 0.00 0.00 3.06
395 398 1.664321 GCGGACCGGAGTACTGACAT 61.664 60.000 17.22 0.00 0.00 3.06
408 416 2.865308 GCTTGTTTACGGCGGACC 59.135 61.111 13.24 0.00 0.00 4.46
433 441 4.009675 TGCTAAAGGCCAAGTAATGTGAG 58.990 43.478 5.01 0.00 40.92 3.51
436 444 5.076873 TCTTTGCTAAAGGCCAAGTAATGT 58.923 37.500 5.01 0.00 42.25 2.71
448 456 3.494626 TGTCTGCGTCTTCTTTGCTAAAG 59.505 43.478 0.00 0.00 39.88 1.85
523 534 8.024285 CGTCTCTCAGTTTATTATGGATAGGTC 58.976 40.741 0.00 0.00 0.00 3.85
547 559 1.645034 CCAATTGAGTGCGAGATCGT 58.355 50.000 7.12 0.00 42.22 3.73
559 571 3.117701 TCTTGAAGACCACACCCAATTGA 60.118 43.478 7.12 0.00 0.00 2.57
681 705 2.656560 AGACAGTCGTCATTGTAGCC 57.343 50.000 0.00 0.00 45.23 3.93
810 835 3.944055 TCTCCCACTCTCTCGAAAAAG 57.056 47.619 0.00 0.00 0.00 2.27
837 862 3.731089 GGCTGAGAAGATGAGAGGATTG 58.269 50.000 0.00 0.00 0.00 2.67
924 949 5.297029 TCATATAGGTTCAGTCGTCAGTGAG 59.703 44.000 0.00 0.00 33.29 3.51
926 951 5.500645 TCATATAGGTTCAGTCGTCAGTG 57.499 43.478 0.00 0.00 0.00 3.66
1668 1696 1.338769 ACCTCGGCATTGAAGGTGTAC 60.339 52.381 5.36 0.00 0.00 2.90
1691 1719 2.017049 ACATTCATAGGAGCAAACGCC 58.983 47.619 0.00 0.00 35.66 5.68
1692 1720 3.764885 AACATTCATAGGAGCAAACGC 57.235 42.857 0.00 0.00 0.00 4.84
1714 1742 6.548441 TTTGGTAATACAAAAGACAGTCGG 57.452 37.500 0.00 0.00 37.40 4.79
1727 1755 6.190954 ACCGAAAATGAGCTTTGGTAATAC 57.809 37.500 0.00 0.00 0.00 1.89
1760 1791 9.627123 AACCAGCATGTTTAATAAGCTAGATAA 57.373 29.630 0.00 0.00 33.59 1.75
1780 1812 5.438761 ACTTAATGAAGTGAACAACCAGC 57.561 39.130 0.00 0.00 44.50 4.85
1785 1817 9.990360 TGACATACTACTTAATGAAGTGAACAA 57.010 29.630 5.64 0.00 45.74 2.83
1800 1832 6.782988 AGGCTGTTATGGTATGACATACTACT 59.217 38.462 21.88 11.29 36.04 2.57
1801 1833 6.994221 AGGCTGTTATGGTATGACATACTAC 58.006 40.000 21.88 15.46 36.04 2.73
1802 1834 8.749354 CATAGGCTGTTATGGTATGACATACTA 58.251 37.037 21.88 17.84 36.04 1.82
1927 1960 5.028549 AGTCTGTATGCGATCCTCAAAAT 57.971 39.130 0.00 0.00 0.00 1.82
1930 1963 3.291584 AGAGTCTGTATGCGATCCTCAA 58.708 45.455 0.00 0.00 0.00 3.02
1931 1964 2.937519 AGAGTCTGTATGCGATCCTCA 58.062 47.619 0.00 0.00 0.00 3.86
2002 2041 5.739752 TGGCACAGATATTTTGATTCTCG 57.260 39.130 0.00 0.00 0.00 4.04
2037 2076 4.199432 AGAAGCGACTCTGTGATTTCAT 57.801 40.909 0.00 0.00 0.00 2.57
2185 2226 1.303074 AGGCTCGTACGTGTCCTCA 60.303 57.895 17.43 0.00 0.00 3.86
2347 2388 4.825422 CACTACAGATTCAAAGGAGAGCA 58.175 43.478 0.00 0.00 0.00 4.26
2358 2399 3.258971 AGGCTGAAGCACTACAGATTC 57.741 47.619 4.43 0.00 44.36 2.52
2360 2401 2.304180 ACAAGGCTGAAGCACTACAGAT 59.696 45.455 4.43 0.00 44.36 2.90
2364 2409 3.320673 AGTACAAGGCTGAAGCACTAC 57.679 47.619 4.43 0.00 44.36 2.73
2367 2412 5.661458 TCTAATAGTACAAGGCTGAAGCAC 58.339 41.667 4.43 0.00 44.36 4.40
2371 2416 7.047891 CCAACATCTAATAGTACAAGGCTGAA 58.952 38.462 0.00 0.00 0.00 3.02
2373 2418 6.582636 TCCAACATCTAATAGTACAAGGCTG 58.417 40.000 0.00 0.00 0.00 4.85
2374 2419 6.808321 TCCAACATCTAATAGTACAAGGCT 57.192 37.500 0.00 0.00 0.00 4.58
2413 2461 5.181811 TCAGACACAAAATGAGCACCAATAG 59.818 40.000 0.00 0.00 0.00 1.73
2424 2474 5.179368 ACGATGTACCTTCAGACACAAAATG 59.821 40.000 0.00 0.00 0.00 2.32
2430 2480 5.066117 TCAGATACGATGTACCTTCAGACAC 59.934 44.000 0.00 0.00 0.00 3.67
2435 2485 6.096282 TCACAATCAGATACGATGTACCTTCA 59.904 38.462 0.00 0.00 0.00 3.02
2436 2486 6.504398 TCACAATCAGATACGATGTACCTTC 58.496 40.000 0.00 0.00 0.00 3.46
2476 2526 3.054166 CGTGTATGTCTGGTTTTCGTGA 58.946 45.455 0.00 0.00 0.00 4.35
2506 2556 5.724328 AGAACAATCGCTACTGAATCTTCA 58.276 37.500 0.00 0.00 35.57 3.02
2530 2580 3.274067 GGCAACTAACCGGCCTTG 58.726 61.111 0.00 0.00 44.32 3.61
2545 2595 2.705730 GAAAGAGAGAGGGTTTCAGGC 58.294 52.381 0.00 0.00 31.68 4.85
2593 2648 8.776061 AAGTCCTAGTCTAGAAAGATAGCAAT 57.224 34.615 8.56 0.00 33.30 3.56
2630 2685 9.862371 TCTTTGCTTTTTGTAGTGTTTATTGAA 57.138 25.926 0.00 0.00 0.00 2.69
2638 2693 8.850156 AGTCATAATCTTTGCTTTTTGTAGTGT 58.150 29.630 0.00 0.00 0.00 3.55
2639 2694 9.683069 AAGTCATAATCTTTGCTTTTTGTAGTG 57.317 29.630 0.00 0.00 0.00 2.74
2642 2697 9.474920 CCAAAGTCATAATCTTTGCTTTTTGTA 57.525 29.630 11.40 0.00 45.73 2.41
2643 2698 7.442062 CCCAAAGTCATAATCTTTGCTTTTTGT 59.558 33.333 11.40 0.00 45.73 2.83
2644 2699 7.656948 TCCCAAAGTCATAATCTTTGCTTTTTG 59.343 33.333 11.40 0.00 45.73 2.44
2649 2704 5.819991 TCTCCCAAAGTCATAATCTTTGCT 58.180 37.500 11.40 0.00 45.73 3.91
2650 2705 6.705863 ATCTCCCAAAGTCATAATCTTTGC 57.294 37.500 11.40 0.00 45.73 3.68
2651 2706 8.844244 CCTAATCTCCCAAAGTCATAATCTTTG 58.156 37.037 10.29 10.29 46.27 2.77
2655 2710 6.937465 GTCCCTAATCTCCCAAAGTCATAATC 59.063 42.308 0.00 0.00 0.00 1.75
2656 2711 6.389869 TGTCCCTAATCTCCCAAAGTCATAAT 59.610 38.462 0.00 0.00 0.00 1.28
2657 2712 5.729229 TGTCCCTAATCTCCCAAAGTCATAA 59.271 40.000 0.00 0.00 0.00 1.90
2658 2713 5.285401 TGTCCCTAATCTCCCAAAGTCATA 58.715 41.667 0.00 0.00 0.00 2.15
2659 2714 4.111577 TGTCCCTAATCTCCCAAAGTCAT 58.888 43.478 0.00 0.00 0.00 3.06
2660 2715 3.526899 TGTCCCTAATCTCCCAAAGTCA 58.473 45.455 0.00 0.00 0.00 3.41
2661 2716 4.779993 ATGTCCCTAATCTCCCAAAGTC 57.220 45.455 0.00 0.00 0.00 3.01
2662 2717 6.652205 TTTATGTCCCTAATCTCCCAAAGT 57.348 37.500 0.00 0.00 0.00 2.66
2663 2718 8.539117 AATTTTATGTCCCTAATCTCCCAAAG 57.461 34.615 0.00 0.00 0.00 2.77
2664 2719 9.998752 TTAATTTTATGTCCCTAATCTCCCAAA 57.001 29.630 0.00 0.00 0.00 3.28
2689 2744 6.591001 AGTTCACATTAGTTGGCCAAAAATT 58.409 32.000 22.47 8.97 0.00 1.82
2691 2746 5.452636 GGAGTTCACATTAGTTGGCCAAAAA 60.453 40.000 22.47 17.97 0.00 1.94
2703 2761 5.324409 AGCCTCAAAATGGAGTTCACATTA 58.676 37.500 0.00 0.00 37.55 1.90
2720 2778 3.668447 CAAGCAGAAAGTAGAAGCCTCA 58.332 45.455 0.00 0.00 0.00 3.86
2725 2783 3.812053 ACACTGCAAGCAGAAAGTAGAAG 59.188 43.478 27.17 8.33 46.30 2.85
2741 2799 9.624697 TTCATATTTTAAAATCTGTCACACTGC 57.375 29.630 16.56 0.00 0.00 4.40
2771 2829 3.078097 TGCTAATTCTGGCAAAGCGTAA 58.922 40.909 0.00 0.00 35.89 3.18
2775 2833 3.442100 GTCATGCTAATTCTGGCAAAGC 58.558 45.455 5.09 0.00 42.95 3.51
2777 2835 3.342719 TCGTCATGCTAATTCTGGCAAA 58.657 40.909 5.09 0.00 42.95 3.68
2783 2841 3.118629 TGAGCCTTCGTCATGCTAATTCT 60.119 43.478 0.00 0.00 34.99 2.40
2791 2849 2.625737 AGATGTTGAGCCTTCGTCATG 58.374 47.619 0.00 0.00 0.00 3.07
2796 2854 1.923204 CGAGAAGATGTTGAGCCTTCG 59.077 52.381 0.00 0.00 40.71 3.79
2797 2855 3.238108 TCGAGAAGATGTTGAGCCTTC 57.762 47.619 0.00 0.00 37.23 3.46
2835 2893 7.467811 GCTTGGTTGAATGATATACAGAAGGTG 60.468 40.741 0.00 0.00 0.00 4.00
2843 2901 9.884465 GAAATACTGCTTGGTTGAATGATATAC 57.116 33.333 0.00 0.00 0.00 1.47
2864 2922 8.985315 ACAGGAATCATATTCAGCAAGAAATA 57.015 30.769 2.36 0.00 40.22 1.40
2947 3005 8.314751 TCTTCTTGTATCTTTCCTTTCTCGATT 58.685 33.333 0.00 0.00 0.00 3.34
2977 3035 6.319658 ACAGGTTATAAAGAGCATGGTTGATG 59.680 38.462 0.00 0.00 34.84 3.07
3016 3074 2.341846 TCTCAAAAAGTCCAAGGCGT 57.658 45.000 0.00 0.00 0.00 5.68
3061 3119 1.995626 ATTGCTGGGGCCTAGTCGT 60.996 57.895 18.90 1.59 37.74 4.34
3133 3191 3.181470 TGTCATCGTTCTTCAACAGGACA 60.181 43.478 0.00 0.00 34.71 4.02
3137 3195 5.409643 AAACTGTCATCGTTCTTCAACAG 57.590 39.130 0.00 0.00 39.90 3.16
3199 3257 1.153958 GTTTGCTGCCGCTCCAATC 60.154 57.895 0.70 0.00 36.97 2.67
3397 3455 5.925397 GTCACATGATACATTTTTGCAACCA 59.075 36.000 0.00 0.00 0.00 3.67
3439 3497 1.372582 TAGCTGCTTCAATGGCTTCG 58.627 50.000 7.79 0.00 36.40 3.79
3469 3527 3.061322 CCCAGCAATCACAACAACAATG 58.939 45.455 0.00 0.00 0.00 2.82
3523 3581 1.552792 GGAAGGAGAAGGGTCACTCTG 59.447 57.143 0.00 0.00 34.11 3.35
3559 3617 4.816385 ACACTGGCAATGATATTTACGAGG 59.184 41.667 1.60 0.00 0.00 4.63
3607 3665 2.267961 GGACCACCACCCGTGATC 59.732 66.667 0.00 0.00 46.20 2.92
3616 3674 2.174639 AGAAACATCAACAGGACCACCA 59.825 45.455 0.00 0.00 38.94 4.17
3628 3686 1.870402 TGCTTCGCGAAAGAAACATCA 59.130 42.857 23.54 7.63 37.12 3.07
3653 3711 3.067180 CACAGGACACTTGCAATTCTTGT 59.933 43.478 0.00 7.16 0.00 3.16
3691 3749 1.152756 AACTTGCCCGCCAACTTCT 60.153 52.632 0.00 0.00 0.00 2.85
3703 3761 5.459536 AAAGAATTTCTGGGAGAACTTGC 57.540 39.130 0.00 0.00 33.26 4.01
3756 3814 4.701956 AGGTTTTCTATTTGACCGCATG 57.298 40.909 0.00 0.00 37.26 4.06
3757 3815 4.522789 ACAAGGTTTTCTATTTGACCGCAT 59.477 37.500 0.00 0.00 37.26 4.73
3769 3827 9.740710 AGATTAGCTAACAATACAAGGTTTTCT 57.259 29.630 8.70 0.00 0.00 2.52
3782 3857 7.339721 AGCAGAGTGTACTAGATTAGCTAACAA 59.660 37.037 8.70 0.00 0.00 2.83
3796 3871 2.495270 CCTGTCATCAGCAGAGTGTACT 59.505 50.000 0.00 0.00 40.09 2.73
3807 3882 3.129988 GGCAATTTTCCTCCTGTCATCAG 59.870 47.826 0.00 0.00 41.01 2.90
3811 3886 1.146774 TGGGCAATTTTCCTCCTGTCA 59.853 47.619 0.00 0.00 0.00 3.58
3812 3887 1.923356 TGGGCAATTTTCCTCCTGTC 58.077 50.000 0.00 0.00 0.00 3.51
3813 3888 2.225343 TGATGGGCAATTTTCCTCCTGT 60.225 45.455 0.00 0.00 0.00 4.00
3943 4018 2.108700 CGTAACCGAAACCGTATACCG 58.891 52.381 0.00 0.00 35.63 4.02
3986 4061 3.211045 TGGACCTTGCAAGAAGTTGTAC 58.789 45.455 28.05 16.83 35.92 2.90
4088 4163 2.605837 TGTCTTCAACCTGCACGTAA 57.394 45.000 0.00 0.00 0.00 3.18
4094 4169 1.291877 ACGCGATGTCTTCAACCTGC 61.292 55.000 15.93 0.00 0.00 4.85
4152 4227 4.101790 CATGGCACCGTCGTTGGC 62.102 66.667 9.49 9.49 0.00 4.52
4160 4235 4.838152 CTCCCGTCCATGGCACCG 62.838 72.222 6.96 9.05 0.00 4.94
4187 4262 1.648504 TCGATCTCGCGAACAGTAGA 58.351 50.000 11.33 2.56 37.35 2.59
4190 4265 0.522180 ACTTCGATCTCGCGAACAGT 59.478 50.000 11.33 3.01 44.43 3.55
4287 4362 2.061061 GGGATCCACCTTGATCTCCAT 58.939 52.381 15.23 0.00 40.80 3.41
4316 4391 2.817834 GTGTTGGCCGCGCTCATA 60.818 61.111 5.56 0.00 0.00 2.15
4371 4446 2.480416 GCACTTCGTCTCCTACCATGAG 60.480 54.545 0.00 0.00 0.00 2.90
4423 4498 5.344066 CAGCTATAGAAGTGACACACGATT 58.656 41.667 8.59 0.00 39.64 3.34
4511 4969 2.022764 TCAACCGTACATGCATCCAG 57.977 50.000 0.00 0.00 0.00 3.86
4556 5015 6.215845 AGAACAGCGTCAAATTTATTGCTTT 58.784 32.000 7.31 6.31 0.00 3.51
4562 5021 7.907214 AGAACTAGAACAGCGTCAAATTTAT 57.093 32.000 0.00 0.00 0.00 1.40
4615 5074 9.935682 AATATGATACGCAATTTGTTACTCTTG 57.064 29.630 0.00 0.00 0.00 3.02
4648 7224 6.575162 TCCTGTTAATTTCTTTCTGCCTTC 57.425 37.500 0.00 0.00 0.00 3.46
4657 7233 6.325919 TGCGACATTTCCTGTTAATTTCTT 57.674 33.333 0.00 0.00 38.54 2.52
4665 7241 0.598065 GGCTTGCGACATTTCCTGTT 59.402 50.000 0.00 0.00 38.54 3.16
4673 7249 0.823356 ACTTGTTGGGCTTGCGACAT 60.823 50.000 0.00 0.00 0.00 3.06
4679 7255 2.191128 AGCTCTACTTGTTGGGCTTG 57.809 50.000 3.88 0.00 0.00 4.01
4708 7284 2.113139 GGGGTGGGTATGCGGATG 59.887 66.667 0.00 0.00 0.00 3.51
4713 7289 1.063567 TGTATTTGGGGGTGGGTATGC 60.064 52.381 0.00 0.00 0.00 3.14
4716 7292 1.063567 GCATGTATTTGGGGGTGGGTA 60.064 52.381 0.00 0.00 0.00 3.69
4741 7317 6.580791 GCTACGTGTTTTCAAATCTTTATGCA 59.419 34.615 0.00 0.00 0.00 3.96
4742 7318 6.801862 AGCTACGTGTTTTCAAATCTTTATGC 59.198 34.615 0.00 0.00 0.00 3.14
4779 7357 9.258826 CTCATTCTAGATGAGATACAAACTTGG 57.741 37.037 19.39 0.00 46.25 3.61
4797 7375 5.955355 CCCCCAATTTGTTAACCTCATTCTA 59.045 40.000 2.48 0.00 0.00 2.10
4828 7407 2.816672 TCAGAAATATGGCGCAACAACA 59.183 40.909 10.83 0.00 0.00 3.33
4833 7412 2.163412 GGTGTTCAGAAATATGGCGCAA 59.837 45.455 10.83 0.00 0.00 4.85
4836 7415 1.330521 CGGGTGTTCAGAAATATGGCG 59.669 52.381 0.00 0.00 0.00 5.69
4841 7420 0.320858 TGCGCGGGTGTTCAGAAATA 60.321 50.000 8.83 0.00 0.00 1.40
4845 7424 0.739462 CTAATGCGCGGGTGTTCAGA 60.739 55.000 8.83 0.00 0.00 3.27
4849 7428 0.732571 CATTCTAATGCGCGGGTGTT 59.267 50.000 8.83 0.00 0.00 3.32
4858 7437 6.530913 TTGATTCGCTAGTCATTCTAATGC 57.469 37.500 0.00 0.00 36.36 3.56
4883 7490 2.411904 CGAAGACAAGCAGAAAGAGCT 58.588 47.619 0.00 0.00 45.97 4.09
4895 7502 0.250295 CAAGGAGGTGCCGAAGACAA 60.250 55.000 0.00 0.00 43.43 3.18
4896 7503 1.371183 CAAGGAGGTGCCGAAGACA 59.629 57.895 0.00 0.00 43.43 3.41
4897 7504 2.035442 GCAAGGAGGTGCCGAAGAC 61.035 63.158 0.00 0.00 43.43 3.01
4899 7506 1.743252 GAGCAAGGAGGTGCCGAAG 60.743 63.158 0.00 0.00 46.14 3.79
4901 7508 4.069232 CGAGCAAGGAGGTGCCGA 62.069 66.667 0.00 0.00 46.14 5.54
4902 7509 3.376935 ATCGAGCAAGGAGGTGCCG 62.377 63.158 0.00 0.00 46.14 5.69
4903 7510 1.522580 GATCGAGCAAGGAGGTGCC 60.523 63.158 0.00 0.00 46.14 5.01
4904 7511 0.107945 AAGATCGAGCAAGGAGGTGC 60.108 55.000 2.38 0.00 45.28 5.01
4905 7512 2.801342 GCTAAGATCGAGCAAGGAGGTG 60.801 54.545 15.42 0.00 39.84 4.00
4906 7513 1.410882 GCTAAGATCGAGCAAGGAGGT 59.589 52.381 15.42 0.00 39.84 3.85
4907 7514 1.270041 GGCTAAGATCGAGCAAGGAGG 60.270 57.143 20.12 0.00 41.98 4.30
4908 7515 1.410517 TGGCTAAGATCGAGCAAGGAG 59.589 52.381 20.12 0.00 41.98 3.69
4909 7516 1.137086 GTGGCTAAGATCGAGCAAGGA 59.863 52.381 20.12 3.09 41.98 3.36
4911 7518 1.134699 TGGTGGCTAAGATCGAGCAAG 60.135 52.381 20.12 0.51 41.98 4.01
4912 7519 0.901827 TGGTGGCTAAGATCGAGCAA 59.098 50.000 20.12 9.71 41.98 3.91
4913 7520 0.175760 GTGGTGGCTAAGATCGAGCA 59.824 55.000 20.12 7.51 41.98 4.26
4914 7521 0.461961 AGTGGTGGCTAAGATCGAGC 59.538 55.000 12.76 12.76 39.33 5.03
4915 7522 1.067821 GGAGTGGTGGCTAAGATCGAG 59.932 57.143 0.00 0.00 0.00 4.04
4916 7523 1.112113 GGAGTGGTGGCTAAGATCGA 58.888 55.000 0.00 0.00 0.00 3.59
4917 7524 1.067821 GAGGAGTGGTGGCTAAGATCG 59.932 57.143 0.00 0.00 0.00 3.69
4918 7525 1.414550 GGAGGAGTGGTGGCTAAGATC 59.585 57.143 0.00 0.00 0.00 2.75
4919 7526 1.273838 TGGAGGAGTGGTGGCTAAGAT 60.274 52.381 0.00 0.00 0.00 2.40
4920 7527 0.116342 TGGAGGAGTGGTGGCTAAGA 59.884 55.000 0.00 0.00 0.00 2.10
4921 7528 0.539051 CTGGAGGAGTGGTGGCTAAG 59.461 60.000 0.00 0.00 0.00 2.18
4922 7529 0.909610 CCTGGAGGAGTGGTGGCTAA 60.910 60.000 0.00 0.00 37.39 3.09
4923 7530 1.306141 CCTGGAGGAGTGGTGGCTA 60.306 63.158 0.00 0.00 37.39 3.93
4925 7532 2.607750 TCCTGGAGGAGTGGTGGC 60.608 66.667 0.00 0.00 39.78 5.01
4931 7538 8.298493 AGTCATTCTAGACATCCTGGAGGAGT 62.298 46.154 16.28 7.15 40.85 3.85
4932 7539 5.927515 AGTCATTCTAGACATCCTGGAGGAG 60.928 48.000 16.28 2.15 40.85 3.69
4933 7540 4.078922 AGTCATTCTAGACATCCTGGAGGA 60.079 45.833 16.28 0.00 41.35 3.71
4934 7541 4.222336 AGTCATTCTAGACATCCTGGAGG 58.778 47.826 6.84 6.84 40.98 4.30
4935 7542 5.048083 GCTAGTCATTCTAGACATCCTGGAG 60.048 48.000 1.52 0.00 46.53 3.86
4936 7543 4.830046 GCTAGTCATTCTAGACATCCTGGA 59.170 45.833 0.00 0.00 46.53 3.86
4937 7544 4.320861 CGCTAGTCATTCTAGACATCCTGG 60.321 50.000 0.00 0.00 46.53 4.45
4938 7545 4.517075 TCGCTAGTCATTCTAGACATCCTG 59.483 45.833 0.00 0.00 46.53 3.86
4939 7546 4.720046 TCGCTAGTCATTCTAGACATCCT 58.280 43.478 0.00 0.00 46.53 3.24
4940 7547 5.440234 TTCGCTAGTCATTCTAGACATCC 57.560 43.478 0.00 0.00 46.53 3.51
4941 7548 6.673106 TGATTCGCTAGTCATTCTAGACATC 58.327 40.000 0.00 4.59 46.53 3.06
4942 7549 6.641169 TGATTCGCTAGTCATTCTAGACAT 57.359 37.500 0.00 0.00 46.53 3.06
4943 7550 6.451064 TTGATTCGCTAGTCATTCTAGACA 57.549 37.500 0.00 0.00 46.53 3.41
4944 7551 6.074569 GCTTTGATTCGCTAGTCATTCTAGAC 60.075 42.308 0.00 0.00 46.53 2.59
4945 7552 5.980116 GCTTTGATTCGCTAGTCATTCTAGA 59.020 40.000 6.13 0.00 46.53 2.43
4946 7553 5.982516 AGCTTTGATTCGCTAGTCATTCTAG 59.017 40.000 0.00 0.00 46.39 2.43
4947 7554 5.907207 AGCTTTGATTCGCTAGTCATTCTA 58.093 37.500 0.00 0.00 34.11 2.10
5029 7694 3.855895 GCAGTGTGTTTACGCTAGACAGA 60.856 47.826 0.00 0.00 45.46 3.41
5128 7794 1.342076 TGGACCTCTGATAGACGGCTT 60.342 52.381 0.00 0.00 0.00 4.35
5130 7796 0.671251 CTGGACCTCTGATAGACGGC 59.329 60.000 0.00 0.00 0.00 5.68
5131 7797 1.950909 GTCTGGACCTCTGATAGACGG 59.049 57.143 0.00 0.00 0.00 4.79
5158 7824 8.716674 AAATATTCATATGGCTTGTTCTCCAT 57.283 30.769 2.13 0.00 44.62 3.41
5165 7831 8.832521 CAAATGCAAAATATTCATATGGCTTGT 58.167 29.630 2.13 0.00 0.00 3.16
5197 7863 4.613925 TTGCATATGAAAAAGTTGGGCA 57.386 36.364 6.97 0.00 0.00 5.36
5206 7872 3.023119 ACCCGCTCATTGCATATGAAAA 58.977 40.909 6.97 0.00 43.06 2.29
5209 7875 1.140652 TCACCCGCTCATTGCATATGA 59.859 47.619 6.97 10.01 43.06 2.15
5234 7900 2.097464 ACAAGATGTTGTGCCATGGCA 61.097 47.619 35.59 35.59 45.58 4.92
5236 7902 2.424601 CCTACAAGATGTTGTGCCATGG 59.575 50.000 17.92 7.63 46.75 3.66
5237 7903 3.084039 ACCTACAAGATGTTGTGCCATG 58.916 45.455 17.92 4.75 46.75 3.66
5238 7904 3.439857 ACCTACAAGATGTTGTGCCAT 57.560 42.857 17.92 0.00 46.75 4.40
5239 7905 2.949177 ACCTACAAGATGTTGTGCCA 57.051 45.000 17.92 0.00 46.75 4.92
5240 7906 4.202245 TCTACCTACAAGATGTTGTGCC 57.798 45.455 17.92 0.00 46.75 5.01
5241 7907 5.874810 TCAATCTACCTACAAGATGTTGTGC 59.125 40.000 17.92 0.00 46.75 4.57
5242 7908 6.036517 GCTCAATCTACCTACAAGATGTTGTG 59.963 42.308 17.92 5.10 46.75 3.33
5244 7910 5.525378 GGCTCAATCTACCTACAAGATGTTG 59.475 44.000 0.13 0.13 39.82 3.33
5265 7934 2.045242 TCCGCTCAGTACTCGGCT 60.045 61.111 14.91 0.00 42.65 5.52
5266 7935 2.409651 CTCCGCTCAGTACTCGGC 59.590 66.667 14.91 10.67 42.65 5.54
5281 7950 0.980231 ACCTGGAGATGGAGTGCCTC 60.980 60.000 0.00 0.00 34.31 4.70
5301 7970 1.828979 TTAGCACCCCCGACATTTTC 58.171 50.000 0.00 0.00 0.00 2.29
5339 8008 1.067425 CAAACCTATGGTCGGTCGTCA 60.067 52.381 0.00 0.00 33.12 4.35
5340 8009 1.203052 TCAAACCTATGGTCGGTCGTC 59.797 52.381 0.00 0.00 33.12 4.20
5343 8012 3.259902 GTTCTCAAACCTATGGTCGGTC 58.740 50.000 0.00 0.00 33.12 4.79
5375 8044 2.093106 AGACGTAAGGTGCAGGTCTAG 58.907 52.381 0.00 0.00 38.87 2.43
5376 8045 1.816835 CAGACGTAAGGTGCAGGTCTA 59.183 52.381 0.00 0.00 38.67 2.59
5388 8057 5.191426 ACCTAAGCTAGATCACAGACGTAA 58.809 41.667 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.