Multiple sequence alignment - TraesCS3D01G150000

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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 TraesCS3D01G150000 chr3D 100.000 4483 0 0 874 5356 114677568 114682050 0.000000e+00 8279.0
1 TraesCS3D01G150000 chr3D 100.000 459 0 0 1 459 114676695 114677153 0.000000e+00 848.0
2 TraesCS3D01G150000 chr3D 81.493 643 71 22 2822 3455 15294439 15295042 8.070000e-133 484.0
3 TraesCS3D01G150000 chr3D 84.424 443 55 11 2822 3254 54334103 54334541 1.780000e-114 424.0
4 TraesCS3D01G150000 chr3D 87.838 148 17 1 3309 3455 54334559 54334706 7.130000e-39 172.0
5 TraesCS3D01G150000 chr3D 90.196 51 3 2 2592 2640 52627542 52627592 1.250000e-06 65.8
6 TraesCS3D01G150000 chr3B 90.000 1780 74 32 874 2590 166152478 166150740 0.000000e+00 2206.0
7 TraesCS3D01G150000 chr3B 93.062 1254 71 8 2639 3883 166150756 166149510 0.000000e+00 1820.0
8 TraesCS3D01G150000 chr3B 93.029 832 50 5 3924 4749 166149011 166148182 0.000000e+00 1208.0
9 TraesCS3D01G150000 chr3B 90.224 624 26 14 4755 5350 166148115 166147499 0.000000e+00 782.0
10 TraesCS3D01G150000 chr3B 88.075 478 27 13 2 451 166153005 166152530 1.700000e-149 540.0
11 TraesCS3D01G150000 chr3B 83.981 412 58 6 2822 3228 51864475 51864883 6.510000e-104 388.0
12 TraesCS3D01G150000 chr3B 93.878 49 1 1 2590 2636 289583566 289583518 7.440000e-09 73.1
13 TraesCS3D01G150000 chr3B 97.297 37 1 0 3890 3926 166149129 166149093 4.480000e-06 63.9
14 TraesCS3D01G150000 chr3A 91.287 1251 87 18 2640 3877 110790585 110791826 0.000000e+00 1687.0
15 TraesCS3D01G150000 chr3A 91.864 885 54 7 3876 4749 110791997 110792874 0.000000e+00 1219.0
16 TraesCS3D01G150000 chr3A 89.282 877 75 13 1724 2583 110789719 110790593 0.000000e+00 1081.0
17 TraesCS3D01G150000 chr3A 85.466 633 42 24 898 1502 110788456 110789066 9.860000e-172 614.0
18 TraesCS3D01G150000 chr3A 81.741 471 40 17 2 441 110787913 110788368 8.530000e-93 351.0
19 TraesCS3D01G150000 chr3A 92.857 56 2 1 2592 2645 162356504 162356449 4.450000e-11 80.5
20 TraesCS3D01G150000 chr1B 83.070 632 92 12 2822 3446 211635798 211635175 1.300000e-155 560.0
21 TraesCS3D01G150000 chr1B 94.340 53 1 2 2590 2640 251940083 251940031 4.450000e-11 80.5
22 TraesCS3D01G150000 chr1B 92.727 55 2 1 2590 2642 344597141 344597195 1.600000e-10 78.7
23 TraesCS3D01G150000 chr6A 84.966 439 57 7 2822 3254 585063648 585064083 2.290000e-118 436.0
24 TraesCS3D01G150000 chr6A 87.162 148 18 1 3309 3455 585064101 585064248 3.320000e-37 167.0
25 TraesCS3D01G150000 chrUn 83.777 413 58 7 2822 3228 117282266 117282675 3.030000e-102 383.0
26 TraesCS3D01G150000 chr5B 83.212 411 56 7 2823 3228 702384878 702385280 1.100000e-96 364.0
27 TraesCS3D01G150000 chr5B 83.871 310 44 6 2922 3228 420932247 420932553 1.890000e-74 291.0
28 TraesCS3D01G150000 chr5B 87.162 148 18 1 3309 3455 581760746 581760893 3.320000e-37 167.0
29 TraesCS3D01G150000 chr5B 86.577 149 19 1 3308 3455 702385317 702385465 4.290000e-36 163.0
30 TraesCS3D01G150000 chr5B 86.486 148 19 1 3309 3455 420932591 420932738 1.540000e-35 161.0
31 TraesCS3D01G150000 chr7D 96.226 53 0 1 2590 2640 406517452 406517400 9.560000e-13 86.1
32 TraesCS3D01G150000 chr7D 90.566 53 3 1 2590 2640 77686348 77686296 9.630000e-08 69.4
33 TraesCS3D01G150000 chr6B 96.226 53 0 1 2592 2642 38733070 38733122 9.560000e-13 86.1
34 TraesCS3D01G150000 chr2B 94.444 54 1 1 2590 2641 44082028 44081975 1.240000e-11 82.4


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 TraesCS3D01G150000 chr3D 114676695 114682050 5355 False 4563.500000 8279 100.000000 1 5356 2 chr3D.!!$F4 5355
1 TraesCS3D01G150000 chr3D 15294439 15295042 603 False 484.000000 484 81.493000 2822 3455 1 chr3D.!!$F1 633
2 TraesCS3D01G150000 chr3D 54334103 54334706 603 False 298.000000 424 86.131000 2822 3455 2 chr3D.!!$F3 633
3 TraesCS3D01G150000 chr3B 166147499 166153005 5506 True 1103.316667 2206 91.947833 2 5350 6 chr3B.!!$R2 5348
4 TraesCS3D01G150000 chr3A 110787913 110792874 4961 False 990.400000 1687 87.928000 2 4749 5 chr3A.!!$F1 4747
5 TraesCS3D01G150000 chr1B 211635175 211635798 623 True 560.000000 560 83.070000 2822 3446 1 chr1B.!!$R1 624
6 TraesCS3D01G150000 chr6A 585063648 585064248 600 False 301.500000 436 86.064000 2822 3455 2 chr6A.!!$F1 633
7 TraesCS3D01G150000 chr5B 702384878 702385465 587 False 263.500000 364 84.894500 2823 3455 2 chr5B.!!$F3 632

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
931 983 0.266152 AATCCCACCAACCAACCCAA 59.734 50.0 0.0 0.0 0.00 4.12 F
1382 1469 1.844544 GAGCGGGTGGTTTTCCCCTA 61.845 60.0 0.0 0.0 41.78 3.53 F
2626 3177 0.324943 GGGCTTTGCTCCACAGTAGA 59.675 55.0 0.0 0.0 0.00 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2607 3158 0.324943 TCTACTGTGGAGCAAAGCCC 59.675 55.0 0.00 0.00 0.00 5.19 R
3032 3593 0.596082 CCAAACAACTTACCGCTGGG 59.404 55.0 0.00 0.00 40.11 4.45 R
4525 5571 0.248843 GCTGACTCTCAAGGGTCTGG 59.751 60.0 15.94 8.48 33.85 3.86 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
135 138 6.748658 CCGTATCAATCGTTGTACAAACTCTA 59.251 38.462 10.51 0.00 0.00 2.43
136 139 7.274033 CCGTATCAATCGTTGTACAAACTCTAA 59.726 37.037 10.51 0.00 0.00 2.10
167 170 3.626028 AACTCGCTTTGGTGAATGTTC 57.374 42.857 0.00 0.00 0.00 3.18
201 208 9.878599 GCATAGTTTGTGAAATACATATACACC 57.121 33.333 0.00 0.00 39.48 4.16
451 489 3.911698 ACGAGCGTGGCACAGTGA 61.912 61.111 19.09 0.00 41.80 3.41
926 978 2.983192 TCTGTAGAATCCCACCAACCAA 59.017 45.455 0.00 0.00 0.00 3.67
927 979 3.081804 CTGTAGAATCCCACCAACCAAC 58.918 50.000 0.00 0.00 0.00 3.77
931 983 0.266152 AATCCCACCAACCAACCCAA 59.734 50.000 0.00 0.00 0.00 4.12
985 1050 4.953868 CGGCGTCCGGTGTGTCAA 62.954 66.667 0.00 0.00 44.15 3.18
1210 1287 2.187073 CCGGTGTTCTACTACGGCT 58.813 57.895 0.00 0.00 37.93 5.52
1314 1396 2.667473 TCTGCGGCCTCTTTTAGTAC 57.333 50.000 0.00 0.00 0.00 2.73
1315 1397 2.176889 TCTGCGGCCTCTTTTAGTACT 58.823 47.619 0.00 0.00 0.00 2.73
1316 1398 3.359033 TCTGCGGCCTCTTTTAGTACTA 58.641 45.455 0.00 0.00 0.00 1.82
1335 1417 8.489676 AGTACTATCATCAATCATTCAGAGGT 57.510 34.615 0.00 0.00 0.00 3.85
1382 1469 1.844544 GAGCGGGTGGTTTTCCCCTA 61.845 60.000 0.00 0.00 41.78 3.53
1441 1535 7.011950 TGCATTAGTTGATACGTTAAGAATGGG 59.988 37.037 0.00 0.00 0.00 4.00
1442 1536 6.913873 TTAGTTGATACGTTAAGAATGGGC 57.086 37.500 0.00 0.00 0.00 5.36
1443 1537 4.839121 AGTTGATACGTTAAGAATGGGCA 58.161 39.130 0.00 0.00 0.00 5.36
1539 1637 2.514803 TCTTTAGTGAAAGCCTTGCCC 58.485 47.619 0.00 0.00 41.68 5.36
1569 1667 2.845363 TTCGAGGTTCCCTTGGTTAC 57.155 50.000 0.00 0.00 35.77 2.50
1646 2087 6.569780 TGTTTTCTATGCTGCTTAGATCGTA 58.430 36.000 21.40 7.96 0.00 3.43
1703 2158 7.668052 TCCTATTGAATTGGGTAAAATATCCCG 59.332 37.037 5.84 0.00 46.13 5.14
1720 2175 2.496070 TCCCGGTTCATGTGAGTTCTAG 59.504 50.000 0.00 0.00 0.00 2.43
1758 2289 9.424319 TCACTTAAGAATTCAGACAGATGTAAC 57.576 33.333 10.09 0.00 0.00 2.50
1876 2412 9.039165 AGAGAAAACATAAATTGGAATGTGGAT 57.961 29.630 2.99 0.00 36.47 3.41
1902 2438 6.688813 GCCTTTTCACTTTGATATTTAGAGCG 59.311 38.462 0.00 0.00 0.00 5.03
1907 2443 8.716646 TTCACTTTGATATTTAGAGCGATTCA 57.283 30.769 0.00 0.00 0.00 2.57
1915 2451 9.546428 TGATATTTAGAGCGATTCATTTTCAGA 57.454 29.630 0.00 0.00 0.00 3.27
1943 2482 8.746052 TTGAAATTTGAGACTAGACTTTTCCA 57.254 30.769 11.81 2.53 0.00 3.53
1949 2488 5.794894 TGAGACTAGACTTTTCCATGGTTC 58.205 41.667 12.58 2.05 0.00 3.62
2056 2603 2.771943 TGGGAAGGTACTAGCAGGAATG 59.228 50.000 0.00 0.00 38.49 2.67
2142 2693 7.884877 GGAATGTATACATCAATCATGGAAGGA 59.115 37.037 18.52 0.00 36.72 3.36
2143 2694 8.859236 AATGTATACATCAATCATGGAAGGAG 57.141 34.615 18.52 0.00 36.72 3.69
2144 2695 6.772605 TGTATACATCAATCATGGAAGGAGG 58.227 40.000 0.08 0.00 36.72 4.30
2384 2935 6.504398 ACTTTAACTTGAAGGCTTTAGTTGC 58.496 36.000 26.03 6.67 33.28 4.17
2482 3033 5.977489 ATTCTACTTGGTTGGGTTTTAGC 57.023 39.130 0.00 0.00 0.00 3.09
2485 3036 3.812156 ACTTGGTTGGGTTTTAGCAAC 57.188 42.857 0.00 0.00 0.00 4.17
2498 3049 6.201997 GGGTTTTAGCAACTGTTGGTTATTTG 59.798 38.462 27.53 0.00 42.20 2.32
2503 3054 5.531634 AGCAACTGTTGGTTATTTGACATG 58.468 37.500 18.65 0.00 38.40 3.21
2506 3057 6.920758 GCAACTGTTGGTTATTTGACATGTTA 59.079 34.615 21.01 0.00 36.23 2.41
2535 3086 3.586100 TTCCGTCGACATGATTTCTCA 57.414 42.857 17.16 0.00 35.41 3.27
2560 3111 9.674824 CAATTTCCTGTTCTATAGATTTCATGC 57.325 33.333 2.58 0.00 0.00 4.06
2583 3134 8.442632 TGCATGTTTGGTTATCAAAAATCAAA 57.557 26.923 0.00 0.00 45.74 2.69
2584 3135 8.341173 TGCATGTTTGGTTATCAAAAATCAAAC 58.659 29.630 15.21 15.21 45.74 2.93
2587 3138 8.430801 TGTTTGGTTATCAAAAATCAAACAGG 57.569 30.769 19.01 0.00 45.74 4.00
2588 3139 7.497249 TGTTTGGTTATCAAAAATCAAACAGGG 59.503 33.333 19.01 0.00 45.74 4.45
2589 3140 6.107901 TGGTTATCAAAAATCAAACAGGGG 57.892 37.500 0.00 0.00 0.00 4.79
2590 3141 5.604650 TGGTTATCAAAAATCAAACAGGGGT 59.395 36.000 0.00 0.00 0.00 4.95
2591 3142 6.100424 TGGTTATCAAAAATCAAACAGGGGTT 59.900 34.615 0.00 0.00 39.43 4.11
2604 3155 5.801531 AACAGGGGTTTGGAATAAAAGAC 57.198 39.130 0.00 0.00 31.83 3.01
2605 3156 5.074746 ACAGGGGTTTGGAATAAAAGACT 57.925 39.130 0.00 0.00 0.00 3.24
2606 3157 4.832823 ACAGGGGTTTGGAATAAAAGACTG 59.167 41.667 0.00 0.00 0.00 3.51
2607 3158 4.220602 CAGGGGTTTGGAATAAAAGACTGG 59.779 45.833 0.00 0.00 0.00 4.00
2608 3159 3.513912 GGGGTTTGGAATAAAAGACTGGG 59.486 47.826 0.00 0.00 0.00 4.45
2609 3160 3.513912 GGGTTTGGAATAAAAGACTGGGG 59.486 47.826 0.00 0.00 0.00 4.96
2610 3161 3.056107 GGTTTGGAATAAAAGACTGGGGC 60.056 47.826 0.00 0.00 0.00 5.80
2611 3162 3.825908 TTGGAATAAAAGACTGGGGCT 57.174 42.857 0.00 0.00 0.00 5.19
2612 3163 3.825908 TGGAATAAAAGACTGGGGCTT 57.174 42.857 0.00 0.00 0.00 4.35
2613 3164 4.126520 TGGAATAAAAGACTGGGGCTTT 57.873 40.909 0.00 0.00 37.18 3.51
2614 3165 3.831911 TGGAATAAAAGACTGGGGCTTTG 59.168 43.478 0.00 0.00 35.86 2.77
2615 3166 3.368427 GGAATAAAAGACTGGGGCTTTGC 60.368 47.826 0.00 0.00 35.86 3.68
2616 3167 2.675658 TAAAAGACTGGGGCTTTGCT 57.324 45.000 0.00 0.00 35.86 3.91
2617 3168 1.332195 AAAAGACTGGGGCTTTGCTC 58.668 50.000 0.00 0.00 35.86 4.26
2625 3176 2.859992 GGGCTTTGCTCCACAGTAG 58.140 57.895 0.00 0.00 0.00 2.57
2626 3177 0.324943 GGGCTTTGCTCCACAGTAGA 59.675 55.000 0.00 0.00 0.00 2.59
2627 3178 1.065126 GGGCTTTGCTCCACAGTAGAT 60.065 52.381 0.00 0.00 0.00 1.98
2628 3179 2.170607 GGGCTTTGCTCCACAGTAGATA 59.829 50.000 0.00 0.00 0.00 1.98
2629 3180 3.462021 GGCTTTGCTCCACAGTAGATAG 58.538 50.000 0.00 0.00 0.00 2.08
2630 3181 3.118592 GGCTTTGCTCCACAGTAGATAGT 60.119 47.826 0.00 0.00 0.00 2.12
2631 3182 4.508662 GCTTTGCTCCACAGTAGATAGTT 58.491 43.478 0.00 0.00 0.00 2.24
2632 3183 4.938226 GCTTTGCTCCACAGTAGATAGTTT 59.062 41.667 0.00 0.00 0.00 2.66
2633 3184 5.064071 GCTTTGCTCCACAGTAGATAGTTTC 59.936 44.000 0.00 0.00 0.00 2.78
2634 3185 5.738619 TTGCTCCACAGTAGATAGTTTCA 57.261 39.130 0.00 0.00 0.00 2.69
2635 3186 5.738619 TGCTCCACAGTAGATAGTTTCAA 57.261 39.130 0.00 0.00 0.00 2.69
2636 3187 6.109156 TGCTCCACAGTAGATAGTTTCAAA 57.891 37.500 0.00 0.00 0.00 2.69
2637 3188 6.530120 TGCTCCACAGTAGATAGTTTCAAAA 58.470 36.000 0.00 0.00 0.00 2.44
2638 3189 6.995686 TGCTCCACAGTAGATAGTTTCAAAAA 59.004 34.615 0.00 0.00 0.00 1.94
2686 3238 7.378728 GTGTTAAAGAAAAATTACTTGCGAGCT 59.621 33.333 0.00 0.00 0.00 4.09
2735 3288 9.495754 GAGCATTTTGTAATGTAATTCTCTGTC 57.504 33.333 0.00 0.00 42.56 3.51
3002 3563 2.760374 AGAGTCTTGCCTTCAAAGACG 58.240 47.619 9.87 0.00 36.43 4.18
3032 3593 8.110860 TCTTACCTGTGAATCCAAAATTTCTC 57.889 34.615 0.00 0.00 0.00 2.87
3058 3620 4.098807 AGCGGTAAGTTGTTTGGTTTTCAT 59.901 37.500 0.00 0.00 0.00 2.57
3075 3637 6.128172 GGTTTTCATCTTCTGTGACACCTATG 60.128 42.308 2.45 0.49 31.10 2.23
3077 3639 3.118629 TCATCTTCTGTGACACCTATGCC 60.119 47.826 2.45 0.00 0.00 4.40
3101 3665 7.962918 GCCGCTAATCCACAATTACTAATAATG 59.037 37.037 0.00 0.00 31.07 1.90
3230 3794 8.562892 ACTTTGTCATCTTATTGTCTTTCACTG 58.437 33.333 0.00 0.00 0.00 3.66
3250 3814 5.821470 CACTGGCTCATTTTCTCATCATACT 59.179 40.000 0.00 0.00 0.00 2.12
3297 3861 2.149578 AGCTGTGAGATGCTCAACAAC 58.850 47.619 0.00 0.00 42.46 3.32
3301 3865 3.807553 TGTGAGATGCTCAACAACTGAA 58.192 40.909 0.00 0.00 42.46 3.02
3312 3876 5.679638 GCTCAACAACTGAAACAGGACAATT 60.680 40.000 0.00 0.00 35.51 2.32
3358 3923 1.886542 CCTGTTTTCCTGCAGGTTACC 59.113 52.381 31.58 18.25 45.28 2.85
3418 3983 3.062234 GTGAGGTGAGCTATTGCGTAAAC 59.938 47.826 0.00 0.00 45.42 2.01
3448 4014 5.437289 TCCTGTCACACAGCTTTTAAATG 57.563 39.130 0.00 0.00 44.63 2.32
3478 4044 2.989166 GGCTGCTTAATGTTTCTGTTGC 59.011 45.455 0.00 0.00 0.00 4.17
3567 4133 7.384439 TGTTGAGTTTGTCAATGTAAGAACA 57.616 32.000 0.00 0.00 46.99 3.18
3570 4136 9.301153 GTTGAGTTTGTCAATGTAAGAACAAAT 57.699 29.630 3.21 0.00 46.99 2.32
3575 4143 6.509418 TGTCAATGTAAGAACAAATAGCCC 57.491 37.500 0.00 0.00 39.58 5.19
3576 4144 6.007076 TGTCAATGTAAGAACAAATAGCCCA 58.993 36.000 0.00 0.00 39.58 5.36
3591 4159 1.774856 AGCCCATTTATCCGTAGCCTT 59.225 47.619 0.00 0.00 0.00 4.35
3610 4180 7.978099 AGCCTTACTCCCAATTTAATTGAAT 57.022 32.000 18.13 4.25 42.83 2.57
3627 4197 5.475273 TTGAATGATTTTCTGCTAGCTCG 57.525 39.130 17.23 7.27 0.00 5.03
3698 4276 2.143925 GGTCAGTGCCTGTAGTTTGTC 58.856 52.381 2.68 0.00 32.61 3.18
3702 4280 3.580895 TCAGTGCCTGTAGTTTGTCCATA 59.419 43.478 2.68 0.00 32.61 2.74
3720 4298 5.009911 GTCCATAATTTGCATGGTCAGCATA 59.990 40.000 3.30 0.00 43.03 3.14
3742 4320 2.851824 GCTCCTGTTTGTTGTTTTCACG 59.148 45.455 0.00 0.00 0.00 4.35
3743 4321 3.426963 GCTCCTGTTTGTTGTTTTCACGA 60.427 43.478 0.00 0.00 0.00 4.35
3744 4322 4.342772 CTCCTGTTTGTTGTTTTCACGAG 58.657 43.478 0.00 0.00 0.00 4.18
3745 4323 3.754323 TCCTGTTTGTTGTTTTCACGAGT 59.246 39.130 0.00 0.00 0.00 4.18
3746 4324 4.936411 TCCTGTTTGTTGTTTTCACGAGTA 59.064 37.500 0.00 0.00 0.00 2.59
3747 4325 5.025826 CCTGTTTGTTGTTTTCACGAGTAC 58.974 41.667 0.00 0.00 0.00 2.73
3748 4326 4.639959 TGTTTGTTGTTTTCACGAGTACG 58.360 39.130 0.00 0.00 45.75 3.67
3785 4365 6.515272 AATAACATTAGCCACTGTTCCAAG 57.485 37.500 0.00 0.00 36.92 3.61
3786 4366 2.162681 ACATTAGCCACTGTTCCAAGC 58.837 47.619 0.00 0.00 0.00 4.01
3810 4390 1.180029 ACCATTCACATTCTGCTGCC 58.820 50.000 0.00 0.00 0.00 4.85
3818 4398 2.483877 CACATTCTGCTGCCTCGTTTTA 59.516 45.455 0.00 0.00 0.00 1.52
3825 4406 2.143925 GCTGCCTCGTTTTAAGTGTCT 58.856 47.619 0.00 0.00 0.00 3.41
3838 4419 3.340814 AAGTGTCTACCAAGATGCCAG 57.659 47.619 0.00 0.00 33.30 4.85
3845 4426 5.221843 TGTCTACCAAGATGCCAGTTTAGTT 60.222 40.000 0.00 0.00 33.30 2.24
3865 4446 3.517296 TCTGCCCTGAACACCATTTTA 57.483 42.857 0.00 0.00 0.00 1.52
3877 4458 7.506114 TGAACACCATTTTACTTAGACTGACT 58.494 34.615 0.00 0.00 0.00 3.41
3878 4459 7.990886 TGAACACCATTTTACTTAGACTGACTT 59.009 33.333 0.00 0.00 0.00 3.01
3883 4464 9.057089 ACCATTTTACTTAGACTGACTTCAAAG 57.943 33.333 0.00 0.00 0.00 2.77
3884 4465 9.057089 CCATTTTACTTAGACTGACTTCAAAGT 57.943 33.333 0.00 0.00 43.16 2.66
3886 4467 7.478520 TTTACTTAGACTGACTTCAAAGTGC 57.521 36.000 0.00 0.00 39.88 4.40
3892 4847 2.173569 ACTGACTTCAAAGTGCCTTCCT 59.826 45.455 0.00 0.00 39.88 3.36
3966 5006 6.049149 GCACTCTGGTGAATAAGTATGCTAA 58.951 40.000 0.00 0.00 45.61 3.09
4004 5044 7.771927 ATGTCTGATTTTCATTCTTTCACCT 57.228 32.000 0.00 0.00 0.00 4.00
4063 5107 9.516546 TCGAGTGGTACATTCTCTACATTATAT 57.483 33.333 0.00 0.00 43.22 0.86
4103 5149 4.164796 TCAGAGAGCCCATTTCATATGTGT 59.835 41.667 1.90 0.00 0.00 3.72
4259 5305 5.016173 TGTTCCCTACCCAAAATTCAGATG 58.984 41.667 0.00 0.00 0.00 2.90
4265 5311 6.414732 CCTACCCAAAATTCAGATGTCTGTA 58.585 40.000 9.65 1.04 44.12 2.74
4266 5312 7.056635 CCTACCCAAAATTCAGATGTCTGTAT 58.943 38.462 9.65 3.41 44.12 2.29
4338 5384 2.358015 CGGTGAAGCCCCGTTTAAATA 58.642 47.619 0.00 0.00 40.59 1.40
4525 5571 0.110486 TGGAAAGGGACTGGCTGAAC 59.890 55.000 0.00 0.00 40.86 3.18
4617 5673 4.701651 CCATTCAGAGTAATTTCTGTGGCA 59.298 41.667 8.97 0.00 43.96 4.92
4723 5780 7.399523 GTTGTCGCTGTTATTCCTATAGTTTG 58.600 38.462 0.00 0.00 0.00 2.93
4749 5806 5.440234 TGCTATTCTGCCGTTTTAAAACA 57.560 34.783 26.24 9.82 38.81 2.83
4750 5807 5.457140 TGCTATTCTGCCGTTTTAAAACAG 58.543 37.500 26.24 18.37 38.81 3.16
4752 5809 4.929819 ATTCTGCCGTTTTAAAACAGGT 57.070 36.364 26.24 11.86 38.81 4.00
4753 5810 4.722361 TTCTGCCGTTTTAAAACAGGTT 57.278 36.364 26.24 0.00 38.81 3.50
4771 5889 2.418746 GGTTGACTGCGATCCTGTACAT 60.419 50.000 0.00 0.00 0.00 2.29
4808 5928 3.007614 AGGTAATGCTGTAAAGGTCACGT 59.992 43.478 0.00 0.00 0.00 4.49
4923 6043 3.932710 TGTCAGCATATTCGAGTGGAAAC 59.067 43.478 0.00 0.00 38.36 2.78
4953 6073 5.007039 CGTCTGTCTGTTGATTAATGGATGG 59.993 44.000 0.00 0.00 0.00 3.51
4954 6074 5.297776 GTCTGTCTGTTGATTAATGGATGGG 59.702 44.000 0.00 0.00 0.00 4.00
4956 6076 4.017591 TGTCTGTTGATTAATGGATGGGGT 60.018 41.667 0.00 0.00 0.00 4.95
4998 6119 1.501169 TGATCTATGGATGCAACGCG 58.499 50.000 3.53 3.53 31.46 6.01
5039 6160 1.359833 TTTTTCTGGCAGCAGCGTG 59.640 52.632 10.34 0.00 43.41 5.34
5049 6170 2.061773 GCAGCAGCGTGTATATCGATT 58.938 47.619 1.71 0.00 0.00 3.34
5104 6231 4.102649 TCGTTCTACGATGCAATACACAG 58.897 43.478 0.00 0.00 46.73 3.66
5120 6247 2.866762 ACACAGACGAGTTTTCAGCTTC 59.133 45.455 0.00 0.00 0.00 3.86
5156 6283 1.443828 GGGCCTGCTACTGCTACTC 59.556 63.158 0.84 0.00 40.48 2.59
5184 6311 4.673298 TCGAGCGCCCGCAAGAAA 62.673 61.111 6.39 0.00 44.88 2.52
5185 6312 3.499737 CGAGCGCCCGCAAGAAAT 61.500 61.111 15.50 0.00 44.88 2.17
5186 6313 2.100991 GAGCGCCCGCAAGAAATG 59.899 61.111 15.50 0.00 44.88 2.32
5188 6315 4.496927 GCGCCCGCAAGAAATGGG 62.497 66.667 7.91 0.00 46.22 4.00
5353 6497 2.805353 CCGGCTGTGTCGTCGAAG 60.805 66.667 0.00 0.00 32.97 3.79
5354 6498 2.254350 CGGCTGTGTCGTCGAAGA 59.746 61.111 0.00 0.00 32.97 2.87
5355 6499 1.371267 CGGCTGTGTCGTCGAAGAA 60.371 57.895 1.62 0.00 39.69 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 7.502120 AAAACATGCTATATGATGGAGTGTC 57.498 36.000 0.00 0.00 0.00 3.67
119 122 9.531942 TCTTTGTTATTAGAGTTTGTACAACGA 57.468 29.630 8.07 0.00 0.00 3.85
135 138 7.174253 TCACCAAAGCGAGTTATCTTTGTTATT 59.826 33.333 12.03 0.00 44.51 1.40
136 139 6.653320 TCACCAAAGCGAGTTATCTTTGTTAT 59.347 34.615 12.03 0.00 44.51 1.89
202 209 1.582680 CAAAGCGCGCGGAATTACC 60.583 57.895 33.06 12.91 0.00 2.85
240 258 3.417101 TGTTGGTCGATGGTTTAATGCT 58.583 40.909 0.00 0.00 0.00 3.79
241 259 3.840890 TGTTGGTCGATGGTTTAATGC 57.159 42.857 0.00 0.00 0.00 3.56
441 479 4.720127 ATGCGATTCACTGTGCCA 57.280 50.000 2.12 0.00 0.00 4.92
970 1035 2.604174 CCTTTGACACACCGGACGC 61.604 63.158 9.46 0.00 0.00 5.19
973 1038 2.280524 CGCCTTTGACACACCGGA 60.281 61.111 9.46 0.00 0.00 5.14
975 1040 2.604174 GGTCGCCTTTGACACACCG 61.604 63.158 0.00 0.00 40.72 4.94
976 1041 2.604174 CGGTCGCCTTTGACACACC 61.604 63.158 0.00 0.00 40.72 4.16
977 1042 2.935955 CGGTCGCCTTTGACACAC 59.064 61.111 0.00 0.00 40.72 3.82
1254 1334 2.266372 CCAATGTACCCGGCGTCA 59.734 61.111 6.01 0.00 0.00 4.35
1291 1371 4.216411 ACTAAAAGAGGCCGCAGAATTA 57.784 40.909 9.88 1.50 0.00 1.40
1314 1396 6.430308 CCCAACCTCTGAATGATTGATGATAG 59.570 42.308 0.00 0.00 0.00 2.08
1315 1397 6.101588 TCCCAACCTCTGAATGATTGATGATA 59.898 38.462 0.00 0.00 0.00 2.15
1316 1398 5.103813 TCCCAACCTCTGAATGATTGATGAT 60.104 40.000 0.00 0.00 0.00 2.45
1335 1417 0.469144 GCCTTCCAACCAAGTCCCAA 60.469 55.000 0.00 0.00 0.00 4.12
1382 1469 1.227383 GTCAAATCCCCCTCCGCAT 59.773 57.895 0.00 0.00 0.00 4.73
1441 1535 4.965119 ATGAGGGAAAAAGATAACGTGC 57.035 40.909 0.00 0.00 0.00 5.34
1442 1536 5.572896 GCAAATGAGGGAAAAAGATAACGTG 59.427 40.000 0.00 0.00 0.00 4.49
1443 1537 5.619086 CGCAAATGAGGGAAAAAGATAACGT 60.619 40.000 0.00 0.00 0.00 3.99
1539 1637 4.733972 GGAACCTCGAAAAGAAGAACAG 57.266 45.455 0.00 0.00 0.00 3.16
1569 1667 2.064762 CTCTGAAGCGAAACCTCACTG 58.935 52.381 0.00 0.00 0.00 3.66
1630 2071 2.695666 ACACCTACGATCTAAGCAGCAT 59.304 45.455 0.00 0.00 0.00 3.79
1646 2087 8.650143 AACCAGAATATTAATCAAACACACCT 57.350 30.769 0.00 0.00 0.00 4.00
1664 2105 9.189156 CCAATTCAATAGGATCTAAAACCAGAA 57.811 33.333 0.00 0.00 0.00 3.02
1666 2107 7.561356 ACCCAATTCAATAGGATCTAAAACCAG 59.439 37.037 0.00 0.00 0.00 4.00
1686 2131 5.132043 TGAACCGGGATATTTTACCCAAT 57.868 39.130 6.32 0.00 45.83 3.16
1703 2158 7.981789 TGATATGTTCTAGAACTCACATGAACC 59.018 37.037 30.47 12.58 41.67 3.62
1777 2308 9.970553 ACGAGTAGATCAGGGTTACATATATTA 57.029 33.333 0.00 0.00 0.00 0.98
1778 2309 8.880991 ACGAGTAGATCAGGGTTACATATATT 57.119 34.615 0.00 0.00 0.00 1.28
1781 2312 7.174599 GTGTACGAGTAGATCAGGGTTACATAT 59.825 40.741 0.00 0.00 0.00 1.78
1782 2313 6.484643 GTGTACGAGTAGATCAGGGTTACATA 59.515 42.308 0.00 0.00 0.00 2.29
1783 2314 5.298777 GTGTACGAGTAGATCAGGGTTACAT 59.701 44.000 0.00 0.00 0.00 2.29
1876 2412 7.538575 GCTCTAAATATCAAAGTGAAAAGGCA 58.461 34.615 0.00 0.00 0.00 4.75
1917 2453 9.354673 TGGAAAAGTCTAGTCTCAAATTTCAAT 57.645 29.630 11.44 0.00 0.00 2.57
1919 2455 8.786898 CATGGAAAAGTCTAGTCTCAAATTTCA 58.213 33.333 11.44 3.00 0.00 2.69
1920 2456 8.239998 CCATGGAAAAGTCTAGTCTCAAATTTC 58.760 37.037 5.56 4.33 0.00 2.17
1943 2482 5.432680 ACAGACATCTGAATCAGAACCAT 57.567 39.130 17.59 2.98 46.59 3.55
2056 2603 9.411801 GGAAAGGAAAAACACTTATCATTTCTC 57.588 33.333 10.34 0.52 40.49 2.87
2142 2693 1.545706 GCCCTCTCGTTTGTCCTCCT 61.546 60.000 0.00 0.00 0.00 3.69
2143 2694 1.079057 GCCCTCTCGTTTGTCCTCC 60.079 63.158 0.00 0.00 0.00 4.30
2144 2695 1.446272 CGCCCTCTCGTTTGTCCTC 60.446 63.158 0.00 0.00 0.00 3.71
2249 2800 6.203530 GCACTCAAGAATATAGCTATGCACAA 59.796 38.462 16.77 0.00 0.00 3.33
2482 3033 8.864069 TTAACATGTCAAATAACCAACAGTTG 57.136 30.769 6.28 6.28 39.67 3.16
2485 3036 9.528018 AGTTTTAACATGTCAAATAACCAACAG 57.472 29.630 0.00 0.00 0.00 3.16
2498 3049 7.476492 GTCGACGGAATAAAGTTTTAACATGTC 59.524 37.037 0.00 0.00 0.00 3.06
2503 3054 7.512297 TCATGTCGACGGAATAAAGTTTTAAC 58.488 34.615 11.62 0.00 0.00 2.01
2506 3057 6.737254 ATCATGTCGACGGAATAAAGTTTT 57.263 33.333 11.62 0.00 0.00 2.43
2535 3086 9.412460 TGCATGAAATCTATAGAACAGGAAATT 57.588 29.630 6.52 0.00 0.00 1.82
2560 3111 9.866936 CTGTTTGATTTTTGATAACCAAACATG 57.133 29.630 15.70 0.00 46.49 3.21
2583 3134 4.832823 CAGTCTTTTATTCCAAACCCCTGT 59.167 41.667 0.00 0.00 0.00 4.00
2584 3135 4.220602 CCAGTCTTTTATTCCAAACCCCTG 59.779 45.833 0.00 0.00 0.00 4.45
2585 3136 4.416516 CCAGTCTTTTATTCCAAACCCCT 58.583 43.478 0.00 0.00 0.00 4.79
2586 3137 3.513912 CCCAGTCTTTTATTCCAAACCCC 59.486 47.826 0.00 0.00 0.00 4.95
2587 3138 3.513912 CCCCAGTCTTTTATTCCAAACCC 59.486 47.826 0.00 0.00 0.00 4.11
2588 3139 3.056107 GCCCCAGTCTTTTATTCCAAACC 60.056 47.826 0.00 0.00 0.00 3.27
2589 3140 3.832490 AGCCCCAGTCTTTTATTCCAAAC 59.168 43.478 0.00 0.00 0.00 2.93
2590 3141 4.126520 AGCCCCAGTCTTTTATTCCAAA 57.873 40.909 0.00 0.00 0.00 3.28
2591 3142 3.825908 AGCCCCAGTCTTTTATTCCAA 57.174 42.857 0.00 0.00 0.00 3.53
2592 3143 3.825908 AAGCCCCAGTCTTTTATTCCA 57.174 42.857 0.00 0.00 0.00 3.53
2593 3144 3.368427 GCAAAGCCCCAGTCTTTTATTCC 60.368 47.826 0.00 0.00 31.94 3.01
2594 3145 3.511540 AGCAAAGCCCCAGTCTTTTATTC 59.488 43.478 0.00 0.00 31.94 1.75
2595 3146 3.510459 AGCAAAGCCCCAGTCTTTTATT 58.490 40.909 0.00 0.00 31.94 1.40
2596 3147 3.092301 GAGCAAAGCCCCAGTCTTTTAT 58.908 45.455 0.00 0.00 31.94 1.40
2597 3148 2.514803 GAGCAAAGCCCCAGTCTTTTA 58.485 47.619 0.00 0.00 31.94 1.52
2598 3149 1.332195 GAGCAAAGCCCCAGTCTTTT 58.668 50.000 0.00 0.00 31.94 2.27
2599 3150 0.540597 GGAGCAAAGCCCCAGTCTTT 60.541 55.000 0.00 0.00 34.37 2.52
2600 3151 1.075659 GGAGCAAAGCCCCAGTCTT 59.924 57.895 0.00 0.00 0.00 3.01
2601 3152 2.156098 TGGAGCAAAGCCCCAGTCT 61.156 57.895 0.00 0.00 0.00 3.24
2602 3153 1.973812 GTGGAGCAAAGCCCCAGTC 60.974 63.158 0.00 0.00 0.00 3.51
2603 3154 2.116125 GTGGAGCAAAGCCCCAGT 59.884 61.111 0.00 0.00 0.00 4.00
2604 3155 1.975407 CTGTGGAGCAAAGCCCCAG 60.975 63.158 0.00 0.00 0.00 4.45
2605 3156 1.422977 TACTGTGGAGCAAAGCCCCA 61.423 55.000 0.00 0.00 0.00 4.96
2606 3157 0.678048 CTACTGTGGAGCAAAGCCCC 60.678 60.000 0.00 0.00 0.00 5.80
2607 3158 0.324943 TCTACTGTGGAGCAAAGCCC 59.675 55.000 0.00 0.00 0.00 5.19
2608 3159 2.409948 ATCTACTGTGGAGCAAAGCC 57.590 50.000 0.00 0.00 0.00 4.35
2609 3160 4.130286 ACTATCTACTGTGGAGCAAAGC 57.870 45.455 0.00 0.00 0.00 3.51
2610 3161 6.166279 TGAAACTATCTACTGTGGAGCAAAG 58.834 40.000 0.00 0.00 0.00 2.77
2611 3162 6.109156 TGAAACTATCTACTGTGGAGCAAA 57.891 37.500 0.00 0.00 0.00 3.68
2612 3163 5.738619 TGAAACTATCTACTGTGGAGCAA 57.261 39.130 0.00 0.00 0.00 3.91
2613 3164 5.738619 TTGAAACTATCTACTGTGGAGCA 57.261 39.130 0.00 0.00 0.00 4.26
2614 3165 7.435068 TTTTTGAAACTATCTACTGTGGAGC 57.565 36.000 0.00 0.00 0.00 4.70
2639 3190 5.045213 ACACCTTTTCCCCTGTTTGATTTTT 60.045 36.000 0.00 0.00 0.00 1.94
2640 3191 4.473196 ACACCTTTTCCCCTGTTTGATTTT 59.527 37.500 0.00 0.00 0.00 1.82
2641 3192 4.037222 ACACCTTTTCCCCTGTTTGATTT 58.963 39.130 0.00 0.00 0.00 2.17
2642 3193 3.653164 ACACCTTTTCCCCTGTTTGATT 58.347 40.909 0.00 0.00 0.00 2.57
2643 3194 3.328535 ACACCTTTTCCCCTGTTTGAT 57.671 42.857 0.00 0.00 0.00 2.57
2644 3195 2.838637 ACACCTTTTCCCCTGTTTGA 57.161 45.000 0.00 0.00 0.00 2.69
2645 3196 5.128008 TCTTTAACACCTTTTCCCCTGTTTG 59.872 40.000 0.00 0.00 0.00 2.93
2646 3197 5.274015 TCTTTAACACCTTTTCCCCTGTTT 58.726 37.500 0.00 0.00 0.00 2.83
2647 3198 4.874199 TCTTTAACACCTTTTCCCCTGTT 58.126 39.130 0.00 0.00 0.00 3.16
2648 3199 4.529716 TCTTTAACACCTTTTCCCCTGT 57.470 40.909 0.00 0.00 0.00 4.00
2649 3200 5.862678 TTTCTTTAACACCTTTTCCCCTG 57.137 39.130 0.00 0.00 0.00 4.45
2659 3210 7.358105 GCTCGCAAGTAATTTTTCTTTAACACC 60.358 37.037 0.00 0.00 39.48 4.16
3002 3563 4.689612 TGGATTCACAGGTAAGATAGCC 57.310 45.455 0.00 0.00 0.00 3.93
3032 3593 0.596082 CCAAACAACTTACCGCTGGG 59.404 55.000 0.00 0.00 40.11 4.45
3058 3620 1.204704 CGGCATAGGTGTCACAGAAGA 59.795 52.381 5.12 0.00 0.00 2.87
3075 3637 5.941948 ATTAGTAATTGTGGATTAGCGGC 57.058 39.130 0.00 0.00 31.01 6.53
3077 3639 8.999431 ACCATTATTAGTAATTGTGGATTAGCG 58.001 33.333 22.96 5.29 31.01 4.26
3101 3665 1.003696 GGCCAGGCAGAATAGGATACC 59.996 57.143 15.19 0.00 37.17 2.73
3230 3794 7.765307 TGAAAAGTATGATGAGAAAATGAGCC 58.235 34.615 0.00 0.00 0.00 4.70
3297 3861 9.480053 ACATTTCATTTAATTGTCCTGTTTCAG 57.520 29.630 0.00 0.00 27.88 3.02
3418 3983 2.362736 CTGTGTGACAGGATGATTGGG 58.637 52.381 0.00 0.00 42.35 4.12
3478 4044 3.238108 ACGAGAGACCTGCAATTACAG 57.762 47.619 0.00 0.00 37.42 2.74
3567 4133 4.042934 AGGCTACGGATAAATGGGCTATTT 59.957 41.667 13.51 13.51 41.68 1.40
3570 4136 2.616524 AGGCTACGGATAAATGGGCTA 58.383 47.619 0.00 0.00 0.00 3.93
3575 4143 4.039973 TGGGAGTAAGGCTACGGATAAATG 59.960 45.833 0.00 0.00 32.87 2.32
3576 4144 4.228824 TGGGAGTAAGGCTACGGATAAAT 58.771 43.478 0.00 0.00 32.87 1.40
3610 4180 3.738281 GCTACCGAGCTAGCAGAAAATCA 60.738 47.826 18.83 0.00 45.98 2.57
3698 4276 8.186365 AGCTATGCTGACCATGCAAATTATGG 62.186 42.308 1.63 1.63 43.30 2.74
3702 4280 3.028850 AGCTATGCTGACCATGCAAATT 58.971 40.909 0.00 0.00 44.01 1.82
3720 4298 3.427503 CGTGAAAACAACAAACAGGAGCT 60.428 43.478 0.00 0.00 0.00 4.09
3761 4341 6.572314 GCTTGGAACAGTGGCTAATGTTATTT 60.572 38.462 16.03 0.00 44.28 1.40
3785 4365 2.416431 GCAGAATGTGAATGGTTGGAGC 60.416 50.000 0.00 0.00 39.31 4.70
3786 4366 3.087031 AGCAGAATGTGAATGGTTGGAG 58.913 45.455 0.00 0.00 39.31 3.86
3810 4390 6.401153 GCATCTTGGTAGACACTTAAAACGAG 60.401 42.308 0.00 0.00 31.99 4.18
3818 4398 2.639839 ACTGGCATCTTGGTAGACACTT 59.360 45.455 0.00 0.00 31.99 3.16
3825 4406 5.245531 CAGAACTAAACTGGCATCTTGGTA 58.754 41.667 0.00 0.00 0.00 3.25
3838 4419 2.552743 GGTGTTCAGGGCAGAACTAAAC 59.447 50.000 18.63 11.04 46.19 2.01
3845 4426 2.380064 AAAATGGTGTTCAGGGCAGA 57.620 45.000 0.00 0.00 0.00 4.26
3865 4446 4.101741 AGGCACTTTGAAGTCAGTCTAAGT 59.898 41.667 0.00 0.00 42.04 2.24
3883 4464 2.024414 AGTGTTTTGTGAGGAAGGCAC 58.976 47.619 0.00 0.00 36.81 5.01
3884 4465 2.426738 CAAGTGTTTTGTGAGGAAGGCA 59.573 45.455 0.00 0.00 0.00 4.75
3886 4467 2.426738 TGCAAGTGTTTTGTGAGGAAGG 59.573 45.455 0.00 0.00 0.00 3.46
3892 4847 3.573598 CTGTTGTGCAAGTGTTTTGTGA 58.426 40.909 0.00 0.00 0.00 3.58
3979 5019 8.186709 AGGTGAAAGAATGAAAATCAGACATT 57.813 30.769 0.00 0.00 37.03 2.71
3991 5031 2.716424 ACAAGGGGAGGTGAAAGAATGA 59.284 45.455 0.00 0.00 0.00 2.57
4004 5044 7.580007 AGTAAGAGTAAAGAAAAACAAGGGGA 58.420 34.615 0.00 0.00 0.00 4.81
4041 5081 9.982651 ACACATATAATGTAGAGAATGTACCAC 57.017 33.333 0.00 0.00 42.70 4.16
4063 5107 4.286808 TCTCTGATGGGAAGAAATGACACA 59.713 41.667 0.00 0.00 0.00 3.72
4109 5155 5.350365 GCGTTTAACATGAGAGGTGATTGTA 59.650 40.000 0.00 0.00 0.00 2.41
4118 5164 1.992667 TGCGAGCGTTTAACATGAGAG 59.007 47.619 0.00 0.00 0.00 3.20
4259 5305 6.038271 CCACCAAGGTTAGCAAATATACAGAC 59.962 42.308 0.00 0.00 0.00 3.51
4265 5311 3.707316 TGCCACCAAGGTTAGCAAATAT 58.293 40.909 10.43 0.00 40.61 1.28
4266 5312 3.162147 TGCCACCAAGGTTAGCAAATA 57.838 42.857 10.43 0.00 40.61 1.40
4338 5384 3.800826 GTCAGTTTGACACCACCCT 57.199 52.632 4.42 0.00 46.22 4.34
4525 5571 0.248843 GCTGACTCTCAAGGGTCTGG 59.751 60.000 15.94 8.48 33.85 3.86
4723 5780 0.168128 AAACGGCAGAATAGCAACGC 59.832 50.000 0.00 0.00 35.83 4.84
4749 5806 1.204941 GTACAGGATCGCAGTCAACCT 59.795 52.381 0.00 0.00 0.00 3.50
4750 5807 1.067142 TGTACAGGATCGCAGTCAACC 60.067 52.381 0.00 0.00 0.00 3.77
4752 5809 3.261580 CAATGTACAGGATCGCAGTCAA 58.738 45.455 0.33 0.00 0.00 3.18
4753 5810 2.233676 ACAATGTACAGGATCGCAGTCA 59.766 45.455 0.33 0.00 0.00 3.41
4759 5877 1.324435 CACGCACAATGTACAGGATCG 59.676 52.381 0.33 7.79 0.00 3.69
4771 5889 2.046009 TACCTGCCTTCCACGCACAA 62.046 55.000 0.00 0.00 31.61 3.33
4805 5925 1.202440 TCGTTTGTGCACTTCCTACGT 60.202 47.619 19.41 0.00 0.00 3.57
4808 5928 2.869801 CACTTCGTTTGTGCACTTCCTA 59.130 45.455 19.41 0.00 0.00 2.94
4828 5948 1.153842 CCACGCATACGCTCACTCA 60.154 57.895 0.00 0.00 45.53 3.41
4844 5964 3.577415 TGTCAATTCAAATGATGCACCCA 59.423 39.130 0.00 0.00 0.00 4.51
4923 6043 0.869880 TCAACAGACAGACGCGTGTG 60.870 55.000 31.96 31.96 36.30 3.82
4953 6073 1.207329 ACTAGGCAGTTCGATGAACCC 59.793 52.381 6.09 2.12 42.85 4.11
4954 6074 2.094182 TCACTAGGCAGTTCGATGAACC 60.094 50.000 6.09 0.00 42.85 3.62
4956 6076 3.089284 TCTCACTAGGCAGTTCGATGAA 58.911 45.455 0.00 0.00 30.46 2.57
4967 6087 5.991933 TCCATAGATCATTCTCACTAGGC 57.008 43.478 0.00 0.00 33.17 3.93
4998 6119 7.464830 AAATACATCTAATCTGTGTACGTGC 57.535 36.000 0.00 0.00 31.79 5.34
5028 6149 0.318699 TCGATATACACGCTGCTGCC 60.319 55.000 10.24 0.00 35.36 4.85
5029 6150 1.702886 ATCGATATACACGCTGCTGC 58.297 50.000 5.34 5.34 0.00 5.25
5068 6194 4.971830 CGTAGAACGAACACTCTTTACACA 59.028 41.667 0.00 0.00 46.05 3.72
5104 6231 4.467735 GGATTTGAAGCTGAAAACTCGTC 58.532 43.478 0.00 0.00 0.00 4.20
5120 6247 0.239879 CCGGACGTTGTTGGGATTTG 59.760 55.000 0.00 0.00 0.00 2.32
5156 6283 2.161486 GCGCTCGACAGCCAACTAG 61.161 63.158 0.00 0.00 43.56 2.57
5181 6308 1.814169 GAGGTCGTCGCCCCATTTC 60.814 63.158 0.00 0.00 0.00 2.17
5182 6309 2.240162 GAGAGGTCGTCGCCCCATTT 62.240 60.000 0.00 0.00 0.00 2.32
5183 6310 2.683933 AGAGGTCGTCGCCCCATT 60.684 61.111 0.00 0.00 0.00 3.16
5184 6311 3.148279 GAGAGGTCGTCGCCCCAT 61.148 66.667 0.00 0.00 0.00 4.00
5185 6312 4.671590 TGAGAGGTCGTCGCCCCA 62.672 66.667 0.00 0.00 0.00 4.96
5186 6313 3.827898 CTGAGAGGTCGTCGCCCC 61.828 72.222 0.00 0.00 0.00 5.80
5188 6315 2.486042 GACTGAGAGGTCGTCGCC 59.514 66.667 0.00 0.00 0.00 5.54
5226 6356 0.740737 ATGAAGGCGCCATACAAAGC 59.259 50.000 31.54 3.70 0.00 3.51
5227 6357 1.003545 CGATGAAGGCGCCATACAAAG 60.004 52.381 31.54 17.52 0.00 2.77
5239 6369 3.257561 CCTGCGCGTCGATGAAGG 61.258 66.667 9.31 7.87 0.00 3.46


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

AutoCloner maintained by Alex Coulton.