Multiple sequence alignment - TraesCS2A01G276300

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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 TraesCS2A01G276300 chr2A 100.000 6011 0 0 1 6011 456500798 456494788 0.000000e+00 11101.0
1 TraesCS2A01G276300 chr2B 95.772 3169 113 11 924 4077 410185674 410182512 0.000000e+00 5090.0
2 TraesCS2A01G276300 chr2B 94.310 1195 42 7 4159 5339 410182514 410181332 0.000000e+00 1807.0
3 TraesCS2A01G276300 chr2B 89.049 904 72 11 1 890 410195550 410194660 0.000000e+00 1096.0
4 TraesCS2A01G276300 chr2B 78.808 151 27 3 5666 5815 560273648 560273794 4.960000e-16 97.1
5 TraesCS2A01G276300 chr2B 100.000 33 0 0 5575 5607 410181063 410181031 1.810000e-05 62.1
6 TraesCS2A01G276300 chr2D 91.184 1985 90 38 1 1957 344974230 344972303 0.000000e+00 2617.0
7 TraesCS2A01G276300 chr2D 90.347 1875 107 24 4161 6011 344970208 344968384 0.000000e+00 2392.0
8 TraesCS2A01G276300 chr2D 91.403 663 46 8 2524 3185 344971869 344971217 0.000000e+00 898.0
9 TraesCS2A01G276300 chr2D 90.933 375 18 2 2158 2527 344972295 344971932 1.950000e-134 490.0
10 TraesCS2A01G276300 chr2D 89.770 391 25 6 3691 4075 344970591 344970210 2.520000e-133 486.0
11 TraesCS2A01G276300 chr2D 85.751 386 39 9 3231 3606 344971130 344970751 1.570000e-105 394.0
12 TraesCS2A01G276300 chr2D 96.739 92 1 2 4076 4166 619321009 619321099 1.040000e-32 152.0
13 TraesCS2A01G276300 chr2D 91.743 109 6 3 4061 4167 331544247 331544140 1.350000e-31 148.0
14 TraesCS2A01G276300 chr5D 88.618 369 32 7 21 380 324981956 324981589 1.990000e-119 440.0
15 TraesCS2A01G276300 chr5D 78.646 384 58 15 5644 6006 3520159 3519779 3.620000e-57 233.0
16 TraesCS2A01G276300 chr3D 86.856 388 29 11 1 375 537039813 537039435 1.210000e-111 414.0
17 TraesCS2A01G276300 chr3D 81.039 385 54 15 5643 6010 412093702 412093320 7.620000e-74 289.0
18 TraesCS2A01G276300 chr3D 82.745 255 38 3 5763 6011 351601645 351601899 7.840000e-54 222.0
19 TraesCS2A01G276300 chr3D 93.396 106 4 3 4065 4169 411724334 411724437 2.900000e-33 154.0
20 TraesCS2A01G276300 chr3D 93.878 98 4 2 4072 4169 294583565 294583660 4.850000e-31 147.0
21 TraesCS2A01G276300 chrUn 85.302 381 44 8 1 371 21283804 21284182 3.400000e-102 383.0
22 TraesCS2A01G276300 chr5B 84.675 385 49 7 5 380 377481096 377480713 5.690000e-100 375.0
23 TraesCS2A01G276300 chr5B 78.571 378 70 9 5644 6011 210171110 210171486 7.790000e-59 239.0
24 TraesCS2A01G276300 chr5B 97.674 43 1 0 4799 4841 403781321 403781363 2.320000e-09 75.0
25 TraesCS2A01G276300 chr5A 84.474 380 50 7 1 371 681407370 681406991 3.420000e-97 366.0
26 TraesCS2A01G276300 chr5A 90.000 50 5 0 4792 4841 707705968 707706017 1.400000e-06 65.8
27 TraesCS2A01G276300 chr4B 84.399 391 39 10 5 380 519036124 519035741 1.230000e-96 364.0
28 TraesCS2A01G276300 chr6A 84.456 386 37 11 1 371 447122222 447122599 5.730000e-95 359.0
29 TraesCS2A01G276300 chr6A 90.526 95 9 0 1 95 268589173 268589267 6.320000e-25 126.0
30 TraesCS2A01G276300 chr6A 85.833 120 14 3 376 494 522825636 522825753 2.270000e-24 124.0
31 TraesCS2A01G276300 chr4D 83.990 381 41 8 5 371 372343271 372343645 1.240000e-91 348.0
32 TraesCS2A01G276300 chr4D 84.436 257 27 8 5767 6011 32224827 32225082 2.160000e-59 241.0
33 TraesCS2A01G276300 chr4D 94.898 98 3 2 4072 4169 7759971 7759876 1.040000e-32 152.0
34 TraesCS2A01G276300 chr4D 90.000 110 6 4 4076 4185 218516199 218516303 2.920000e-28 137.0
35 TraesCS2A01G276300 chr6D 82.940 381 39 12 1 371 193574770 193575134 2.700000e-83 320.0
36 TraesCS2A01G276300 chr6D 83.803 142 20 3 353 494 381544639 381544777 1.360000e-26 132.0
37 TraesCS2A01G276300 chr1B 81.794 379 51 12 5645 6011 323293861 323293489 9.790000e-78 302.0
38 TraesCS2A01G276300 chr1D 81.627 381 52 11 5643 6011 223743102 223742728 3.520000e-77 300.0
39 TraesCS2A01G276300 chr1D 96.739 92 3 0 4071 4162 239335391 239335482 2.900000e-33 154.0
40 TraesCS2A01G276300 chr1D 91.304 46 4 0 4790 4835 370350952 370350907 5.030000e-06 63.9
41 TraesCS2A01G276300 chr7D 82.558 258 35 8 5763 6011 420293717 420293461 1.010000e-52 219.0
42 TraesCS2A01G276300 chr7D 93.069 101 4 3 4069 4169 64381204 64381301 1.750000e-30 145.0
43 TraesCS2A01G276300 chr1A 78.827 307 52 10 5709 6007 252796933 252797234 1.710000e-45 195.0
44 TraesCS2A01G276300 chr1A 91.667 48 2 2 4795 4841 256813832 256813786 1.400000e-06 65.8
45 TraesCS2A01G276300 chr1A 89.796 49 5 0 4793 4841 348694164 348694212 5.030000e-06 63.9
46 TraesCS2A01G276300 chr4A 93.939 99 3 3 4065 4162 440964812 440964908 4.850000e-31 147.0
47 TraesCS2A01G276300 chr4A 91.837 49 3 1 4792 4840 546610342 546610295 3.890000e-07 67.6
48 TraesCS2A01G276300 chr4A 91.837 49 3 1 4792 4840 546636409 546636362 3.890000e-07 67.6


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 TraesCS2A01G276300 chr2A 456494788 456500798 6010 True 11101.000000 11101 100.000 1 6011 1 chr2A.!!$R1 6010
1 TraesCS2A01G276300 chr2B 410181031 410185674 4643 True 2319.700000 5090 96.694 924 5607 3 chr2B.!!$R2 4683
2 TraesCS2A01G276300 chr2B 410194660 410195550 890 True 1096.000000 1096 89.049 1 890 1 chr2B.!!$R1 889
3 TraesCS2A01G276300 chr2D 344968384 344974230 5846 True 1212.833333 2617 89.898 1 6011 6 chr2D.!!$R2 6010

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
877 906 0.250338 GGAGCACCCGATATTCACCC 60.250 60.0 0.0 0.0 0.00 4.61 F
1203 1235 0.110486 AGCAGGACCAAACCAACGAT 59.890 50.0 0.0 0.0 0.00 3.73 F
1651 1684 0.255890 TCCTGGTTATCAGCTTGGGC 59.744 55.0 0.0 0.0 42.05 5.36 F
2485 2523 0.391597 GGAGACACGACCTGTTTGGA 59.608 55.0 0.0 0.0 39.71 3.53 F
2582 2686 0.678395 ATAGTCATCCTGCCTGAGCG 59.322 55.0 0.0 0.0 44.31 5.03 F
2717 2821 0.793617 AACCCCCTTCTCCTCTCTCA 59.206 55.0 0.0 0.0 0.00 3.27 F
4091 4331 0.264955 ATGTACTCCCTCCGTCCCAT 59.735 55.0 0.0 0.0 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2717 2821 0.821517 TGACGGTCTCACACAACACT 59.178 50.000 9.88 0.00 0.00 3.55 R
3197 3324 2.034842 GCAAATCGACAAGGACGTATCG 60.035 50.000 0.00 0.00 35.91 2.92 R
3377 3525 0.513820 AAATCAAACGTGCCGTACCG 59.486 50.000 0.00 0.00 39.99 4.02 R
3463 3612 1.032014 AAATCTTGCCACGCTTGTGT 58.968 45.000 0.00 0.00 42.24 3.72 R
3853 4083 1.079127 GACCAAGCAGAAGCCGCTA 60.079 57.895 0.00 0.00 43.56 4.26 R
4711 4951 1.079503 CAGCAGGCGTTAGGACTTTC 58.920 55.000 0.00 0.00 0.00 2.62 R
5732 6045 0.454600 TACGAGAGATGCCGGTCAAC 59.545 55.000 1.90 0.19 0.00 3.18 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
45 46 9.918630 CAGAAAATGTTCCATTCTTTGAATAGT 57.081 29.630 0.00 0.00 33.92 2.12
85 86 4.314522 ACATGTCATGTTGGGGTAATGA 57.685 40.909 12.87 0.00 41.63 2.57
95 96 4.252878 GTTGGGGTAATGAAATTGCAAGG 58.747 43.478 4.94 0.00 41.00 3.61
101 102 4.953579 GGTAATGAAATTGCAAGGACCCTA 59.046 41.667 4.94 0.00 41.00 3.53
264 275 7.609056 AGCATCTTCCCAAATATCAATATTGC 58.391 34.615 10.76 0.00 33.51 3.56
281 292 0.816018 TGCGACCATTTCCAACACGT 60.816 50.000 0.00 0.00 0.00 4.49
426 441 9.877178 ACTAAGAATCTGTTCGAGAATACAAAT 57.123 29.630 0.00 0.00 39.38 2.32
434 449 6.406370 TGTTCGAGAATACAAATGATGTCCT 58.594 36.000 0.00 0.00 42.70 3.85
617 633 0.322098 TTCGATCGGTTTGGCCACAT 60.322 50.000 16.41 0.00 36.97 3.21
625 641 2.230660 GGTTTGGCCACATCTATAGCC 58.769 52.381 3.88 0.00 45.96 3.93
632 648 0.321671 CACATCTATAGCCACGGGGG 59.678 60.000 5.47 0.00 40.85 5.40
641 657 1.304134 GCCACGGGGGAAGTTTCAT 60.304 57.895 5.47 0.00 40.01 2.57
668 684 1.345415 CCGCCCCTTATATGTTACCGT 59.655 52.381 0.00 0.00 0.00 4.83
669 685 2.409975 CGCCCCTTATATGTTACCGTG 58.590 52.381 0.00 0.00 0.00 4.94
699 715 1.379710 TGGGCCGTTGGATTGGATG 60.380 57.895 0.00 0.00 0.00 3.51
700 716 1.077068 GGGCCGTTGGATTGGATGA 60.077 57.895 0.00 0.00 0.00 2.92
701 717 0.682855 GGGCCGTTGGATTGGATGAA 60.683 55.000 0.00 0.00 0.00 2.57
702 718 1.402787 GGCCGTTGGATTGGATGAAT 58.597 50.000 0.00 0.00 0.00 2.57
703 719 1.756538 GGCCGTTGGATTGGATGAATT 59.243 47.619 0.00 0.00 0.00 2.17
708 724 5.045215 CCGTTGGATTGGATGAATTTCATG 58.955 41.667 16.41 0.00 37.20 3.07
711 727 6.405065 CGTTGGATTGGATGAATTTCATGTCT 60.405 38.462 16.41 0.00 37.20 3.41
712 728 6.459670 TGGATTGGATGAATTTCATGTCTG 57.540 37.500 16.41 0.00 37.20 3.51
719 735 5.237127 GGATGAATTTCATGTCTGACGCATA 59.763 40.000 16.41 0.00 37.20 3.14
741 757 0.687354 AGAAGTTGATGGACCTGCGT 59.313 50.000 0.00 0.00 0.00 5.24
830 859 4.246712 AGATCCAACGGTTCCTAGTAGA 57.753 45.455 0.00 0.00 0.00 2.59
845 874 6.787170 TCCTAGTAGACCGTATCATGGTATT 58.213 40.000 0.00 0.00 37.69 1.89
877 906 0.250338 GGAGCACCCGATATTCACCC 60.250 60.000 0.00 0.00 0.00 4.61
878 907 0.468226 GAGCACCCGATATTCACCCA 59.532 55.000 0.00 0.00 0.00 4.51
879 908 1.072331 GAGCACCCGATATTCACCCAT 59.928 52.381 0.00 0.00 0.00 4.00
891 920 1.878211 TCACCCATAGCTGTGATCCA 58.122 50.000 12.67 0.00 36.62 3.41
892 921 2.195727 TCACCCATAGCTGTGATCCAA 58.804 47.619 12.67 0.00 36.62 3.53
917 946 6.394345 AAAGGAATTTACTCCCTCATCAGT 57.606 37.500 0.00 0.00 35.95 3.41
918 947 7.510675 AAAGGAATTTACTCCCTCATCAGTA 57.489 36.000 0.00 0.00 35.95 2.74
919 948 7.510675 AAGGAATTTACTCCCTCATCAGTAA 57.489 36.000 0.00 0.00 35.95 2.24
920 949 6.890293 AGGAATTTACTCCCTCATCAGTAAC 58.110 40.000 0.00 0.00 35.32 2.50
921 950 6.443849 AGGAATTTACTCCCTCATCAGTAACA 59.556 38.462 0.00 0.00 35.32 2.41
922 951 7.037586 AGGAATTTACTCCCTCATCAGTAACAA 60.038 37.037 0.00 0.00 35.32 2.83
926 955 8.934023 TTTACTCCCTCATCAGTAACAAAAAT 57.066 30.769 0.00 0.00 35.32 1.82
1038 1070 0.555769 TCAGGTTCCAAGCCCAAACT 59.444 50.000 0.00 0.00 0.00 2.66
1143 1175 2.420058 AATCAACCAATCCCGTCTCC 57.580 50.000 0.00 0.00 0.00 3.71
1203 1235 0.110486 AGCAGGACCAAACCAACGAT 59.890 50.000 0.00 0.00 0.00 3.73
1396 1429 3.948719 TGCCGGGTCCTGTCCAAC 61.949 66.667 2.18 0.00 0.00 3.77
1421 1454 1.756430 TCAGCGTGTCTCTATGCTCT 58.244 50.000 0.00 0.00 40.80 4.09
1425 1458 2.757868 AGCGTGTCTCTATGCTCTTCTT 59.242 45.455 0.00 0.00 38.50 2.52
1531 1564 1.587043 CGAGCCAGGACGTTGAGAGA 61.587 60.000 0.00 0.00 0.00 3.10
1651 1684 0.255890 TCCTGGTTATCAGCTTGGGC 59.744 55.000 0.00 0.00 42.05 5.36
1685 1718 1.190643 GGAGCTTCTGAGGTAGCTGT 58.809 55.000 13.33 0.00 44.29 4.40
1987 2020 9.146984 CACATTGAAAATTTTCTGTAGCATCAT 57.853 29.630 26.73 6.82 38.02 2.45
2031 2064 2.876892 GCTGTACACCCGTACCCAAAAT 60.877 50.000 0.00 0.00 46.33 1.82
2105 2138 3.426292 GCTACCAAGATTTTTGAGTCGCC 60.426 47.826 0.00 0.00 0.00 5.54
2142 2175 1.968704 TATGACTCCGACTCAGCGAT 58.031 50.000 0.00 0.00 0.00 4.58
2259 2292 4.517453 TGTTGTATCCTGTTTGCCTGTAAC 59.483 41.667 0.00 0.00 0.00 2.50
2473 2511 7.809806 CCATTGTTCTAATTCTTTTGGAGACAC 59.190 37.037 0.00 0.00 42.67 3.67
2485 2523 0.391597 GGAGACACGACCTGTTTGGA 59.608 55.000 0.00 0.00 39.71 3.53
2566 2670 4.082081 TGTCAGCAAAATGGCAGGAAATAG 60.082 41.667 0.00 0.00 35.83 1.73
2582 2686 0.678395 ATAGTCATCCTGCCTGAGCG 59.322 55.000 0.00 0.00 44.31 5.03
2600 2704 1.535462 GCGCAACCATAGTTTCACAGT 59.465 47.619 0.30 0.00 32.45 3.55
2610 2714 8.834004 ACCATAGTTTCACAGTATTCTAGGTA 57.166 34.615 0.00 0.00 0.00 3.08
2627 2731 1.614317 GGTAGCAGGGTGAGCAACATT 60.614 52.381 0.00 0.00 0.00 2.71
2717 2821 0.793617 AACCCCCTTCTCCTCTCTCA 59.206 55.000 0.00 0.00 0.00 3.27
2771 2875 1.144913 TGGAGGGGGTGAGAAAACTTG 59.855 52.381 0.00 0.00 0.00 3.16
2801 2905 2.233922 AGTCACATAGGACGGGTCAAAG 59.766 50.000 0.75 0.00 42.62 2.77
2809 2913 1.308998 GACGGGTCAAAGCATATGGG 58.691 55.000 4.56 0.00 0.00 4.00
2898 3002 5.043248 CACGGGCATTCTGATTTATTTTCC 58.957 41.667 0.00 0.00 0.00 3.13
2911 3015 7.811282 TGATTTATTTTCCTGGCCTCATACTA 58.189 34.615 3.32 0.00 0.00 1.82
3029 3133 3.186001 GGTATGCGATCTTGAATGCTCAG 59.814 47.826 0.00 0.00 31.69 3.35
3110 3214 2.094026 GTGGATTCAAGACCAATTGGGC 60.094 50.000 27.89 26.05 46.16 5.36
3296 3443 7.026631 TGTTGCAGCATATATTGTTTACTCC 57.973 36.000 0.00 0.00 0.00 3.85
3377 3525 6.417930 GGAACAGTGTCTAACTTGCAAATTTC 59.582 38.462 0.00 0.00 36.83 2.17
3405 3553 4.351192 GGCACGTTTGATTTATAGCTTGG 58.649 43.478 0.00 0.00 0.00 3.61
3463 3612 4.513406 AGTGTGGGTAAGAAAAACTGGA 57.487 40.909 0.00 0.00 0.00 3.86
3509 3663 5.751243 AAAGTTAAGTGTGACACATGACC 57.249 39.130 18.95 0.00 36.74 4.02
3589 3744 7.992497 AAACTATGGTTCGCCTAAGGTTAGGT 61.992 42.308 15.70 0.00 42.30 3.08
3633 3819 1.946747 GCATGTGCCCTTGGTTACGTA 60.947 52.381 0.00 0.00 34.31 3.57
3652 3838 4.142902 ACGTAATTTTGTGGATCTTGAGCG 60.143 41.667 0.00 0.00 0.00 5.03
3672 3858 2.666508 CGTATGCTGGTATTATGACGCC 59.333 50.000 0.00 0.00 0.00 5.68
3673 3859 3.614150 CGTATGCTGGTATTATGACGCCT 60.614 47.826 0.00 0.00 0.00 5.52
3706 3936 7.595130 TCATATTAGCACTAGTTATTGTCTGCG 59.405 37.037 0.00 0.00 0.00 5.18
3818 4048 5.019785 AGGGGAATTACTGCTTTACTACG 57.980 43.478 0.00 0.00 0.00 3.51
3853 4083 6.302269 AGAAACAAAGTCATGGAGAACTGAT 58.698 36.000 0.00 0.00 0.00 2.90
3928 4158 2.672181 GGCATTGGGCTTGGGCATT 61.672 57.895 0.00 0.00 44.01 3.56
4075 4315 7.396540 AGAACACTTGTTTTTCTTCTCATGT 57.603 32.000 0.00 0.00 38.56 3.21
4076 4316 8.506168 AGAACACTTGTTTTTCTTCTCATGTA 57.494 30.769 0.00 0.00 38.56 2.29
4077 4317 8.398665 AGAACACTTGTTTTTCTTCTCATGTAC 58.601 33.333 0.00 0.00 38.56 2.90
4078 4318 7.865706 ACACTTGTTTTTCTTCTCATGTACT 57.134 32.000 0.00 0.00 0.00 2.73
4079 4319 7.920738 ACACTTGTTTTTCTTCTCATGTACTC 58.079 34.615 0.00 0.00 0.00 2.59
4080 4320 7.012421 ACACTTGTTTTTCTTCTCATGTACTCC 59.988 37.037 0.00 0.00 0.00 3.85
4081 4321 6.486993 ACTTGTTTTTCTTCTCATGTACTCCC 59.513 38.462 0.00 0.00 0.00 4.30
4082 4322 6.187727 TGTTTTTCTTCTCATGTACTCCCT 57.812 37.500 0.00 0.00 0.00 4.20
4083 4323 6.231211 TGTTTTTCTTCTCATGTACTCCCTC 58.769 40.000 0.00 0.00 0.00 4.30
4084 4324 5.422214 TTTTCTTCTCATGTACTCCCTCC 57.578 43.478 0.00 0.00 0.00 4.30
4085 4325 2.656002 TCTTCTCATGTACTCCCTCCG 58.344 52.381 0.00 0.00 0.00 4.63
4086 4326 2.025226 TCTTCTCATGTACTCCCTCCGT 60.025 50.000 0.00 0.00 0.00 4.69
4087 4327 2.054232 TCTCATGTACTCCCTCCGTC 57.946 55.000 0.00 0.00 0.00 4.79
4088 4328 1.033574 CTCATGTACTCCCTCCGTCC 58.966 60.000 0.00 0.00 0.00 4.79
4089 4329 0.396695 TCATGTACTCCCTCCGTCCC 60.397 60.000 0.00 0.00 0.00 4.46
4090 4330 0.686441 CATGTACTCCCTCCGTCCCA 60.686 60.000 0.00 0.00 0.00 4.37
4091 4331 0.264955 ATGTACTCCCTCCGTCCCAT 59.735 55.000 0.00 0.00 0.00 4.00
4092 4332 0.928505 TGTACTCCCTCCGTCCCATA 59.071 55.000 0.00 0.00 0.00 2.74
4093 4333 1.288633 TGTACTCCCTCCGTCCCATAA 59.711 52.381 0.00 0.00 0.00 1.90
4094 4334 2.090943 TGTACTCCCTCCGTCCCATAAT 60.091 50.000 0.00 0.00 0.00 1.28
4095 4335 3.140707 TGTACTCCCTCCGTCCCATAATA 59.859 47.826 0.00 0.00 0.00 0.98
4096 4336 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
4097 4337 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
4098 4338 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
4099 4339 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
4100 4340 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
4101 4341 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
4102 4342 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
4103 4343 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
4104 4344 4.084287 TCCGTCCCATAATATAAGAGCGT 58.916 43.478 0.00 0.00 0.00 5.07
4105 4345 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
4106 4346 5.011329 TCCGTCCCATAATATAAGAGCGTTT 59.989 40.000 0.00 0.00 0.00 3.60
4107 4347 5.699458 CCGTCCCATAATATAAGAGCGTTTT 59.301 40.000 0.00 0.00 0.00 2.43
4108 4348 6.204108 CCGTCCCATAATATAAGAGCGTTTTT 59.796 38.462 0.00 0.00 0.00 1.94
4134 4374 7.781763 GACACTACACTAATGTCAAAAATGC 57.218 36.000 0.00 0.00 41.94 3.56
4135 4375 7.510549 ACACTACACTAATGTCAAAAATGCT 57.489 32.000 0.00 0.00 40.48 3.79
4136 4376 7.584987 ACACTACACTAATGTCAAAAATGCTC 58.415 34.615 0.00 0.00 40.48 4.26
4137 4377 7.445402 ACACTACACTAATGTCAAAAATGCTCT 59.555 33.333 0.00 0.00 40.48 4.09
4138 4378 8.292448 CACTACACTAATGTCAAAAATGCTCTT 58.708 33.333 0.00 0.00 40.48 2.85
4139 4379 9.502091 ACTACACTAATGTCAAAAATGCTCTTA 57.498 29.630 0.00 0.00 40.48 2.10
4149 4389 9.639563 TGTCAAAAATGCTCTTATATTATGGGA 57.360 29.630 0.00 0.00 0.00 4.37
4150 4390 9.899226 GTCAAAAATGCTCTTATATTATGGGAC 57.101 33.333 0.00 0.00 0.00 4.46
4151 4391 8.783093 TCAAAAATGCTCTTATATTATGGGACG 58.217 33.333 0.00 0.00 0.00 4.79
4152 4392 7.687941 AAAATGCTCTTATATTATGGGACGG 57.312 36.000 0.00 0.00 0.00 4.79
4153 4393 6.620877 AATGCTCTTATATTATGGGACGGA 57.379 37.500 0.00 0.00 0.00 4.69
4154 4394 5.661056 TGCTCTTATATTATGGGACGGAG 57.339 43.478 0.00 0.00 0.00 4.63
4155 4395 4.466370 TGCTCTTATATTATGGGACGGAGG 59.534 45.833 0.00 0.00 0.00 4.30
4156 4396 4.141914 GCTCTTATATTATGGGACGGAGGG 60.142 50.000 0.00 0.00 0.00 4.30
4157 4397 5.269991 CTCTTATATTATGGGACGGAGGGA 58.730 45.833 0.00 0.00 0.00 4.20
4158 4398 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
4191 4431 9.136952 GTTACTAAGCATGTTATAGGATTACGG 57.863 37.037 0.00 0.00 0.00 4.02
4261 4501 3.619038 GTCTAGTGGAGGAAAAGATTGCG 59.381 47.826 0.00 0.00 31.21 4.85
4271 4511 3.371168 GAAAAGATTGCGTGCTGTTCAA 58.629 40.909 0.00 0.00 30.42 2.69
4520 4760 1.369692 CCGCAAGTCAGGTACCACA 59.630 57.895 15.94 0.00 0.00 4.17
4528 4768 2.753452 AGTCAGGTACCACATACGTCAG 59.247 50.000 15.94 0.00 34.22 3.51
4583 4823 4.403432 ACCAGTGCCATTTCCATCTTATTG 59.597 41.667 0.00 0.00 0.00 1.90
4711 4951 4.615452 GCTGTTTCTGAGAAAGATGCCAAG 60.615 45.833 8.06 0.00 33.93 3.61
4785 5025 6.647895 CCAAGTACACTTACCAATCGTAGTTT 59.352 38.462 0.00 0.00 34.28 2.66
4788 5028 4.382291 ACACTTACCAATCGTAGTTTGCA 58.618 39.130 0.00 0.00 0.00 4.08
4824 5064 3.627577 CCCTCCGATCCAAAATAAGTGTG 59.372 47.826 0.00 0.00 0.00 3.82
4926 5166 1.339438 GCCACTCCTTGCTGAATGAGA 60.339 52.381 0.00 0.00 30.56 3.27
5109 5360 4.970662 TGACGCCTTTTACTACTCGTAT 57.029 40.909 0.00 0.00 0.00 3.06
5145 5399 0.613260 CCGAGGGAAGGTCATTGTGA 59.387 55.000 0.00 0.00 0.00 3.58
5161 5415 7.872483 GGTCATTGTGACTGGTTTTATTGATTT 59.128 33.333 9.66 0.00 46.19 2.17
5172 5426 7.869800 TGGTTTTATTGATTTGAAAACATGGC 58.130 30.769 10.57 0.00 42.30 4.40
5229 5484 3.512329 TCCAGTTACAAGGTATGCGAGAA 59.488 43.478 0.00 0.00 0.00 2.87
5354 5609 3.694566 GGATTCCGCCTGAACAAAACTAT 59.305 43.478 0.00 0.00 35.31 2.12
5355 5610 4.879545 GGATTCCGCCTGAACAAAACTATA 59.120 41.667 0.00 0.00 35.31 1.31
5356 5611 5.007724 GGATTCCGCCTGAACAAAACTATAG 59.992 44.000 0.00 0.00 35.31 1.31
5357 5612 3.267483 TCCGCCTGAACAAAACTATAGC 58.733 45.455 0.00 0.00 0.00 2.97
5358 5613 3.006940 CCGCCTGAACAAAACTATAGCA 58.993 45.455 0.00 0.00 0.00 3.49
5359 5614 3.063997 CCGCCTGAACAAAACTATAGCAG 59.936 47.826 0.00 0.00 0.00 4.24
5375 5630 8.930846 ACTATAGCAGATCAAATTAGCCAAAT 57.069 30.769 0.00 0.00 0.00 2.32
5493 5748 2.360600 TGGTATGTGTTGGCCCGC 60.361 61.111 0.00 0.00 0.00 6.13
5507 5762 2.707039 CCGCGTGCTTTATTCGGG 59.293 61.111 4.92 0.00 36.73 5.14
5527 5782 1.456892 ACATGGAGCCGACCCGATA 60.457 57.895 0.00 0.00 0.00 2.92
5528 5783 1.290324 CATGGAGCCGACCCGATAG 59.710 63.158 0.00 0.00 0.00 2.08
5529 5784 1.153061 ATGGAGCCGACCCGATAGA 59.847 57.895 0.00 0.00 39.76 1.98
5530 5785 1.179814 ATGGAGCCGACCCGATAGAC 61.180 60.000 0.00 0.00 39.76 2.59
5532 5787 2.905807 GAGCCGACCCGATAGACCG 61.906 68.421 0.00 0.00 39.76 4.79
5539 5794 3.292936 CCGATAGACCGGGACCCG 61.293 72.222 26.87 26.87 45.43 5.28
5540 5795 2.203252 CGATAGACCGGGACCCGA 60.203 66.667 34.84 15.02 45.94 5.14
5541 5796 1.602888 CGATAGACCGGGACCCGAT 60.603 63.158 34.84 19.99 45.94 4.18
5542 5797 0.321919 CGATAGACCGGGACCCGATA 60.322 60.000 34.84 22.25 45.94 2.92
5561 5816 4.988716 ACCGGGTGACTCGCCTCA 62.989 66.667 6.32 0.00 33.98 3.86
5569 5824 1.323271 TGACTCGCCTCATGTCCCTC 61.323 60.000 0.00 0.00 0.00 4.30
5633 5936 6.820656 CACAAAATAGAGAGTGGTAAGAGCAT 59.179 38.462 0.00 0.00 0.00 3.79
5643 5946 3.619038 GTGGTAAGAGCATAGTCAAGTGC 59.381 47.826 0.00 0.00 41.57 4.40
5645 5948 3.118592 GGTAAGAGCATAGTCAAGTGCCT 60.119 47.826 0.00 0.00 42.20 4.75
5650 5953 3.944015 GAGCATAGTCAAGTGCCTCAAAT 59.056 43.478 0.00 0.00 42.20 2.32
5651 5954 3.693085 AGCATAGTCAAGTGCCTCAAATG 59.307 43.478 0.00 0.00 42.20 2.32
5653 5956 1.251251 AGTCAAGTGCCTCAAATGCC 58.749 50.000 0.00 0.00 0.00 4.40
5655 5958 1.213537 CAAGTGCCTCAAATGCCCG 59.786 57.895 0.00 0.00 0.00 6.13
5656 5959 1.978617 AAGTGCCTCAAATGCCCGG 60.979 57.895 0.00 0.00 0.00 5.73
5657 5960 2.361104 GTGCCTCAAATGCCCGGA 60.361 61.111 0.73 0.00 0.00 5.14
5658 5961 2.361104 TGCCTCAAATGCCCGGAC 60.361 61.111 0.73 0.00 0.00 4.79
5659 5962 3.508840 GCCTCAAATGCCCGGACG 61.509 66.667 0.73 0.00 0.00 4.79
5660 5963 2.824041 CCTCAAATGCCCGGACGG 60.824 66.667 0.73 3.25 0.00 4.79
5661 5964 2.267642 CTCAAATGCCCGGACGGA 59.732 61.111 13.13 0.00 37.50 4.69
5662 5965 1.153168 CTCAAATGCCCGGACGGAT 60.153 57.895 13.13 0.00 37.50 4.18
5663 5966 1.439353 CTCAAATGCCCGGACGGATG 61.439 60.000 13.13 0.00 37.50 3.51
5664 5967 2.124320 AAATGCCCGGACGGATGG 60.124 61.111 13.13 0.00 37.50 3.51
5678 5991 0.753111 GGATGGCCCAGTCATTGACC 60.753 60.000 13.14 0.00 32.18 4.02
5689 6002 3.066064 CAGTCATTGACCGGTCACAAAAA 59.934 43.478 36.40 22.16 39.66 1.94
5692 6005 4.023193 GTCATTGACCGGTCACAAAAATCT 60.023 41.667 36.40 10.94 39.66 2.40
5704 6017 6.706270 GGTCACAAAAATCTAACTCAGACTGA 59.294 38.462 4.78 4.78 35.62 3.41
5707 6020 7.987458 TCACAAAAATCTAACTCAGACTGACTT 59.013 33.333 0.00 1.83 35.62 3.01
5708 6021 8.279103 CACAAAAATCTAACTCAGACTGACTTC 58.721 37.037 0.00 0.00 35.62 3.01
5718 6031 2.737252 CAGACTGACTTCTTAAACGGGC 59.263 50.000 0.00 0.00 0.00 6.13
5726 6039 2.642154 TCTTAAACGGGCCTCAAACA 57.358 45.000 0.84 0.00 0.00 2.83
5728 6041 3.492337 TCTTAAACGGGCCTCAAACATT 58.508 40.909 0.84 0.00 0.00 2.71
5732 6045 2.406616 CGGGCCTCAAACATTCGGG 61.407 63.158 0.84 0.00 0.00 5.14
5733 6046 1.304134 GGGCCTCAAACATTCGGGT 60.304 57.895 0.84 0.00 0.00 5.28
5749 6062 1.519455 GGTTGACCGGCATCTCTCG 60.519 63.158 0.00 0.00 0.00 4.04
5758 6071 0.037790 GGCATCTCTCGTATCCAGCC 60.038 60.000 0.00 0.00 0.00 4.85
5759 6072 0.965439 GCATCTCTCGTATCCAGCCT 59.035 55.000 0.00 0.00 0.00 4.58
5770 6083 2.907458 ATCCAGCCTAAATATGGGGC 57.093 50.000 5.92 5.92 45.57 5.80
5812 6136 2.285442 ACCTGACAGCCCTACCCC 60.285 66.667 0.00 0.00 0.00 4.95
5813 6137 2.285368 CCTGACAGCCCTACCCCA 60.285 66.667 0.00 0.00 0.00 4.96
5815 6139 2.609610 TGACAGCCCTACCCCACC 60.610 66.667 0.00 0.00 0.00 4.61
5816 6140 2.609610 GACAGCCCTACCCCACCA 60.610 66.667 0.00 0.00 0.00 4.17
5817 6141 2.933834 ACAGCCCTACCCCACCAC 60.934 66.667 0.00 0.00 0.00 4.16
5819 6143 2.610859 AGCCCTACCCCACCACAG 60.611 66.667 0.00 0.00 0.00 3.66
5822 6146 2.076597 GCCCTACCCCACCACAGTTT 62.077 60.000 0.00 0.00 0.00 2.66
5823 6147 0.251165 CCCTACCCCACCACAGTTTG 60.251 60.000 0.00 0.00 0.00 2.93
5825 6149 0.179004 CTACCCCACCACAGTTTGCA 60.179 55.000 0.00 0.00 0.00 4.08
5826 6150 0.480690 TACCCCACCACAGTTTGCAT 59.519 50.000 0.00 0.00 0.00 3.96
5827 6151 0.827507 ACCCCACCACAGTTTGCATC 60.828 55.000 0.00 0.00 0.00 3.91
5830 6154 1.619827 CCCACCACAGTTTGCATCAAT 59.380 47.619 0.00 0.00 0.00 2.57
5831 6155 2.037511 CCCACCACAGTTTGCATCAATT 59.962 45.455 0.00 0.00 0.00 2.32
5832 6156 3.319755 CCACCACAGTTTGCATCAATTC 58.680 45.455 0.00 0.00 0.00 2.17
5833 6157 3.319755 CACCACAGTTTGCATCAATTCC 58.680 45.455 0.00 0.00 0.00 3.01
5834 6158 2.964464 ACCACAGTTTGCATCAATTCCA 59.036 40.909 0.00 0.00 0.00 3.53
5835 6159 3.579586 ACCACAGTTTGCATCAATTCCAT 59.420 39.130 0.00 0.00 0.00 3.41
5836 6160 4.178540 CCACAGTTTGCATCAATTCCATC 58.821 43.478 0.00 0.00 0.00 3.51
5837 6161 4.322123 CCACAGTTTGCATCAATTCCATCA 60.322 41.667 0.00 0.00 0.00 3.07
5838 6162 5.231702 CACAGTTTGCATCAATTCCATCAA 58.768 37.500 0.00 0.00 0.00 2.57
5839 6163 5.697178 CACAGTTTGCATCAATTCCATCAAA 59.303 36.000 0.00 0.00 0.00 2.69
5872 6196 2.743179 CCGCCCTCCTACCTTTCCC 61.743 68.421 0.00 0.00 0.00 3.97
5884 6208 4.966787 TTTCCCGCGCCCAAGCTT 62.967 61.111 0.00 0.00 36.60 3.74
5885 6209 4.966787 TTCCCGCGCCCAAGCTTT 62.967 61.111 0.00 0.00 36.60 3.51
5914 6238 1.693640 CACCCTTGCTCCCATCCTT 59.306 57.895 0.00 0.00 0.00 3.36
5917 6241 0.183731 CCCTTGCTCCCATCCTTACC 59.816 60.000 0.00 0.00 0.00 2.85
5952 6276 1.360551 CGCCCTAGATGTCGTCCAG 59.639 63.158 0.00 0.00 0.00 3.86
5992 6316 2.179517 GAGACTGCGTCCACCTCG 59.820 66.667 5.29 0.00 32.18 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 1.673920 GTTGGACTTTGTCGCTTGGAA 59.326 47.619 0.00 0.00 32.65 3.53
80 81 6.096705 CACATAGGGTCCTTGCAATTTCATTA 59.903 38.462 0.00 0.00 0.00 1.90
85 86 2.497273 GCACATAGGGTCCTTGCAATTT 59.503 45.455 0.00 0.00 33.24 1.82
200 208 8.893727 GTGCAAATTAAGTAATCACACCTAGAT 58.106 33.333 0.00 0.00 0.00 1.98
218 226 4.497300 CTTGATCCCGAATTGTGCAAATT 58.503 39.130 0.00 0.00 0.00 1.82
264 275 1.222300 TGACGTGTTGGAAATGGTCG 58.778 50.000 0.00 0.00 0.00 4.79
426 441 4.518970 GGCTTCAAGTTTTACAGGACATCA 59.481 41.667 0.00 0.00 0.00 3.07
434 449 6.348132 CGTCATGTATGGCTTCAAGTTTTACA 60.348 38.462 0.00 0.00 0.00 2.41
480 495 4.275936 GTGTCTTTAAGCTCTCAAAGGCAA 59.724 41.667 18.66 6.32 45.15 4.52
530 545 3.792047 CACGCCGTGTGCCATCTG 61.792 66.667 9.53 0.00 42.70 2.90
566 581 1.065418 CGGCAGAGGACTAAATGGGTT 60.065 52.381 0.00 0.00 0.00 4.11
617 633 0.263765 ACTTCCCCCGTGGCTATAGA 59.736 55.000 3.21 0.00 0.00 1.98
625 641 0.881118 CACATGAAACTTCCCCCGTG 59.119 55.000 0.00 0.00 0.00 4.94
632 648 2.354821 GGGCGGTATCACATGAAACTTC 59.645 50.000 0.00 0.00 0.00 3.01
641 657 3.244582 ACATATAAGGGGCGGTATCACA 58.755 45.455 0.00 0.00 0.00 3.58
676 692 3.645268 AATCCAACGGCCCAGGAGC 62.645 63.158 10.78 0.00 34.40 4.70
699 715 6.201615 TCTCATATGCGTCAGACATGAAATTC 59.798 38.462 0.00 0.00 37.14 2.17
700 716 6.051074 TCTCATATGCGTCAGACATGAAATT 58.949 36.000 0.00 0.00 37.14 1.82
701 717 5.604565 TCTCATATGCGTCAGACATGAAAT 58.395 37.500 0.00 0.00 37.14 2.17
702 718 5.009854 TCTCATATGCGTCAGACATGAAA 57.990 39.130 0.00 0.00 37.14 2.69
703 719 4.654091 TCTCATATGCGTCAGACATGAA 57.346 40.909 0.00 0.00 37.14 2.57
708 724 4.424626 TCAACTTCTCATATGCGTCAGAC 58.575 43.478 0.00 0.00 0.00 3.51
711 727 4.122046 CCATCAACTTCTCATATGCGTCA 58.878 43.478 0.00 0.00 0.00 4.35
712 728 4.210120 GTCCATCAACTTCTCATATGCGTC 59.790 45.833 0.00 0.00 0.00 5.19
719 735 2.679059 CGCAGGTCCATCAACTTCTCAT 60.679 50.000 0.00 0.00 0.00 2.90
741 757 6.991531 AGCCATTCAAGAGTTTTAAAATTGCA 59.008 30.769 3.52 0.00 0.00 4.08
802 819 4.290942 AGGAACCGTTGGATCTTAGATCT 58.709 43.478 20.01 0.00 0.00 2.75
808 825 4.401837 GTCTACTAGGAACCGTTGGATCTT 59.598 45.833 0.00 0.00 0.00 2.40
830 859 4.558095 GCTCACGTAATACCATGATACGGT 60.558 45.833 17.96 2.07 44.87 4.83
845 874 3.138798 GCTCCCGAGGCTCACGTA 61.139 66.667 15.95 0.00 0.00 3.57
892 921 7.241628 ACTGATGAGGGAGTAAATTCCTTTTT 58.758 34.615 0.00 0.00 37.40 1.94
897 926 6.650120 TGTTACTGATGAGGGAGTAAATTCC 58.350 40.000 0.00 0.00 36.63 3.01
898 927 8.561738 TTTGTTACTGATGAGGGAGTAAATTC 57.438 34.615 0.00 0.00 36.63 2.17
899 928 8.934023 TTTTGTTACTGATGAGGGAGTAAATT 57.066 30.769 0.00 0.00 36.63 1.82
901 930 8.934023 ATTTTTGTTACTGATGAGGGAGTAAA 57.066 30.769 0.00 0.00 36.63 2.01
910 939 9.825109 TCCGTCATATATTTTTGTTACTGATGA 57.175 29.630 0.00 0.00 0.00 2.92
912 941 9.832445 ACTCCGTCATATATTTTTGTTACTGAT 57.168 29.630 0.00 0.00 0.00 2.90
917 946 9.256477 CAGCTACTCCGTCATATATTTTTGTTA 57.744 33.333 0.00 0.00 0.00 2.41
918 947 7.769044 ACAGCTACTCCGTCATATATTTTTGTT 59.231 33.333 0.00 0.00 0.00 2.83
919 948 7.224753 CACAGCTACTCCGTCATATATTTTTGT 59.775 37.037 0.00 0.00 0.00 2.83
920 949 7.438160 TCACAGCTACTCCGTCATATATTTTTG 59.562 37.037 0.00 0.00 0.00 2.44
921 950 7.438459 GTCACAGCTACTCCGTCATATATTTTT 59.562 37.037 0.00 0.00 0.00 1.94
922 951 6.924060 GTCACAGCTACTCCGTCATATATTTT 59.076 38.462 0.00 0.00 0.00 1.82
926 955 3.819337 GGTCACAGCTACTCCGTCATATA 59.181 47.826 0.00 0.00 0.00 0.86
930 959 0.251209 AGGTCACAGCTACTCCGTCA 60.251 55.000 0.00 0.00 0.00 4.35
1038 1070 1.377463 CGCCATTTTGGGGGTACGA 60.377 57.895 2.82 0.00 45.66 3.43
1087 1119 1.576421 CGGGTTTGTGCTGCTTCTC 59.424 57.895 0.00 0.00 0.00 2.87
1143 1175 1.220529 TCTGCTTGTGCGTCTTCTTG 58.779 50.000 0.00 0.00 43.34 3.02
1396 1429 3.295785 CATAGAGACACGCTGAATCGAG 58.704 50.000 0.00 0.00 0.00 4.04
1421 1454 3.820467 CCATCCAACACTTACAGCAAGAA 59.180 43.478 0.00 0.00 37.71 2.52
1425 1458 3.719268 ATCCATCCAACACTTACAGCA 57.281 42.857 0.00 0.00 0.00 4.41
1531 1564 1.340017 CCCTTCACATGGTCACCGAAT 60.340 52.381 0.00 0.00 0.00 3.34
1651 1684 0.805322 GCTCCAGTGATCTCAGTGCG 60.805 60.000 9.13 4.47 43.97 5.34
1987 2020 7.892551 CAGCATGACTAGAAAATTGCAATAGCA 60.893 37.037 13.39 8.65 45.70 3.49
1997 2030 5.186198 GGGTGTACAGCATGACTAGAAAAT 58.814 41.667 25.23 0.00 39.69 1.82
2004 2037 1.552578 TACGGGTGTACAGCATGACT 58.447 50.000 25.23 6.22 39.69 3.41
2031 2064 2.779430 ACTGAAGATGGATGCACCCATA 59.221 45.455 14.31 0.00 46.34 2.74
2068 2101 2.767394 TGGTAGCAACCCTAGCGATTAA 59.233 45.455 0.00 0.00 46.16 1.40
2069 2102 2.390696 TGGTAGCAACCCTAGCGATTA 58.609 47.619 0.00 0.00 46.16 1.75
2259 2292 4.153986 CAGAGCTGCTTTATTTGTGAACG 58.846 43.478 2.53 0.00 0.00 3.95
2359 2397 8.970020 AGGTTGCAGATATCACAAAAATAATGA 58.030 29.630 11.47 0.00 0.00 2.57
2582 2686 6.743575 AGAATACTGTGAAACTATGGTTGC 57.256 37.500 0.00 0.00 38.04 4.17
2600 2704 3.231818 GCTCACCCTGCTACCTAGAATA 58.768 50.000 0.00 0.00 0.00 1.75
2610 2714 0.957395 CGAATGTTGCTCACCCTGCT 60.957 55.000 0.00 0.00 0.00 4.24
2627 2731 4.672251 GGCTACCACCCTAGACGA 57.328 61.111 0.00 0.00 0.00 4.20
2717 2821 0.821517 TGACGGTCTCACACAACACT 59.178 50.000 9.88 0.00 0.00 3.55
2771 2875 4.541779 CGTCCTATGTGACTAAGAGCATC 58.458 47.826 0.00 0.00 32.97 3.91
2898 3002 7.770897 ACTGAATAAAAACTAGTATGAGGCCAG 59.229 37.037 5.01 2.74 0.00 4.85
3029 3133 3.084786 AGACATAAGCCAGACAAAAGCC 58.915 45.455 0.00 0.00 0.00 4.35
3197 3324 2.034842 GCAAATCGACAAGGACGTATCG 60.035 50.000 0.00 0.00 35.91 2.92
3301 3448 5.592104 ATTAGTTTCGCAAAAATAGGGGG 57.408 39.130 0.00 0.00 0.00 5.40
3377 3525 0.513820 AAATCAAACGTGCCGTACCG 59.486 50.000 0.00 0.00 39.99 4.02
3405 3553 4.229876 CACTTGCCTTAGCTTAGTTTTGC 58.770 43.478 0.00 0.00 40.80 3.68
3463 3612 1.032014 AAATCTTGCCACGCTTGTGT 58.968 45.000 0.00 0.00 42.24 3.72
3509 3663 7.827156 CATTGCTGCACTTTAATATTCTACG 57.173 36.000 0.00 0.00 0.00 3.51
3589 3744 1.912731 TCCCAGCCACAGTTTGCTATA 59.087 47.619 0.00 0.00 35.69 1.31
3633 3819 5.677091 GCATACGCTCAAGATCCACAAAATT 60.677 40.000 0.00 0.00 34.30 1.82
3652 3838 3.926616 AGGCGTCATAATACCAGCATAC 58.073 45.455 0.00 0.00 0.00 2.39
3706 3936 7.011016 CCAACTTTTTATTGTTTCTGTTGGGAC 59.989 37.037 12.17 0.00 45.30 4.46
3818 4048 7.754027 CCATGACTTTGTTTCTTCAATGAGATC 59.246 37.037 0.00 0.00 0.00 2.75
3853 4083 1.079127 GACCAAGCAGAAGCCGCTA 60.079 57.895 0.00 0.00 43.56 4.26
3928 4158 9.778741 ATCAAGAAGTTTAATCTCAACACTGTA 57.221 29.630 0.00 0.00 0.00 2.74
4075 4315 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
4076 4316 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
4077 4317 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
4078 4318 5.269991 CTCTTATATTATGGGACGGAGGGA 58.730 45.833 0.00 0.00 0.00 4.20
4079 4319 4.141914 GCTCTTATATTATGGGACGGAGGG 60.142 50.000 0.00 0.00 0.00 4.30
4080 4320 4.440250 CGCTCTTATATTATGGGACGGAGG 60.440 50.000 0.00 0.00 0.00 4.30
4081 4321 4.158025 ACGCTCTTATATTATGGGACGGAG 59.842 45.833 0.00 0.00 0.00 4.63
4082 4322 4.084287 ACGCTCTTATATTATGGGACGGA 58.916 43.478 0.00 0.00 0.00 4.69
4083 4323 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
4084 4324 6.780706 AAAACGCTCTTATATTATGGGACG 57.219 37.500 0.00 0.00 0.00 4.79
4110 4350 7.584987 AGCATTTTTGACATTAGTGTAGTGTC 58.415 34.615 0.00 3.35 43.31 3.67
4111 4351 7.445402 AGAGCATTTTTGACATTAGTGTAGTGT 59.555 33.333 0.00 0.00 39.09 3.55
4112 4352 7.810658 AGAGCATTTTTGACATTAGTGTAGTG 58.189 34.615 0.00 0.00 39.09 2.74
4113 4353 7.986085 AGAGCATTTTTGACATTAGTGTAGT 57.014 32.000 0.00 0.00 39.09 2.73
4123 4363 9.639563 TCCCATAATATAAGAGCATTTTTGACA 57.360 29.630 0.00 0.00 0.00 3.58
4124 4364 9.899226 GTCCCATAATATAAGAGCATTTTTGAC 57.101 33.333 0.00 0.00 0.00 3.18
4125 4365 8.783093 CGTCCCATAATATAAGAGCATTTTTGA 58.217 33.333 0.00 0.00 0.00 2.69
4126 4366 8.023128 CCGTCCCATAATATAAGAGCATTTTTG 58.977 37.037 0.00 0.00 0.00 2.44
4127 4367 7.942341 TCCGTCCCATAATATAAGAGCATTTTT 59.058 33.333 0.00 0.00 0.00 1.94
4128 4368 7.458397 TCCGTCCCATAATATAAGAGCATTTT 58.542 34.615 0.00 0.00 0.00 1.82
4129 4369 7.016153 TCCGTCCCATAATATAAGAGCATTT 57.984 36.000 0.00 0.00 0.00 2.32
4130 4370 6.352222 CCTCCGTCCCATAATATAAGAGCATT 60.352 42.308 0.00 0.00 0.00 3.56
4131 4371 5.129485 CCTCCGTCCCATAATATAAGAGCAT 59.871 44.000 0.00 0.00 0.00 3.79
4132 4372 4.466370 CCTCCGTCCCATAATATAAGAGCA 59.534 45.833 0.00 0.00 0.00 4.26
4133 4373 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
4134 4374 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
4135 4375 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
4136 4376 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
4137 4377 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
4138 4378 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
4139 4379 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
4140 4380 4.687262 ATACTCCCTCCGTCCCATAATA 57.313 45.455 0.00 0.00 0.00 0.98
4141 4381 3.562108 ATACTCCCTCCGTCCCATAAT 57.438 47.619 0.00 0.00 0.00 1.28
4142 4382 3.339713 AATACTCCCTCCGTCCCATAA 57.660 47.619 0.00 0.00 0.00 1.90
4143 4383 4.202749 ACATAATACTCCCTCCGTCCCATA 60.203 45.833 0.00 0.00 0.00 2.74
4144 4384 3.173965 CATAATACTCCCTCCGTCCCAT 58.826 50.000 0.00 0.00 0.00 4.00
4145 4385 2.090943 ACATAATACTCCCTCCGTCCCA 60.091 50.000 0.00 0.00 0.00 4.37
4146 4386 2.606378 ACATAATACTCCCTCCGTCCC 58.394 52.381 0.00 0.00 0.00 4.46
4147 4387 4.831710 AGTAACATAATACTCCCTCCGTCC 59.168 45.833 0.00 0.00 30.26 4.79
4148 4388 7.516198 TTAGTAACATAATACTCCCTCCGTC 57.484 40.000 0.00 0.00 37.34 4.79
4149 4389 6.015603 GCTTAGTAACATAATACTCCCTCCGT 60.016 42.308 0.00 0.00 37.34 4.69
4150 4390 6.015688 TGCTTAGTAACATAATACTCCCTCCG 60.016 42.308 0.00 0.00 37.34 4.63
4151 4391 7.299246 TGCTTAGTAACATAATACTCCCTCC 57.701 40.000 0.00 0.00 37.34 4.30
4152 4392 8.368668 ACATGCTTAGTAACATAATACTCCCTC 58.631 37.037 0.00 0.00 37.34 4.30
4153 4393 8.263854 ACATGCTTAGTAACATAATACTCCCT 57.736 34.615 0.00 0.00 37.34 4.20
4154 4394 8.904099 AACATGCTTAGTAACATAATACTCCC 57.096 34.615 0.00 0.00 37.34 4.30
4191 4431 7.421530 TCAGTCAACTTCTAACATTAACAGC 57.578 36.000 0.00 0.00 0.00 4.40
4271 4511 9.890629 AGAATGACAATGTACATGTATTACTGT 57.109 29.630 9.63 7.95 0.00 3.55
4324 4564 4.095483 GCAAAACTGCTCTATACAGCACAT 59.905 41.667 0.00 0.00 44.73 3.21
4483 4723 5.654044 GCGGTAGCGTAAACAAATTAAAC 57.346 39.130 16.63 0.00 0.00 2.01
4520 4760 1.271379 TGTCCGAAGTTGCTGACGTAT 59.729 47.619 0.00 0.00 0.00 3.06
4528 4768 3.896648 TTTCTGAATGTCCGAAGTTGC 57.103 42.857 0.00 0.00 0.00 4.17
4595 4835 3.138304 ACTCGTTGCTGCATCAAAAGTA 58.862 40.909 14.54 0.00 0.00 2.24
4711 4951 1.079503 CAGCAGGCGTTAGGACTTTC 58.920 55.000 0.00 0.00 0.00 2.62
4785 5025 3.071602 GGAGGGAGTAATATCTTGCTGCA 59.928 47.826 0.00 0.00 37.20 4.41
4788 5028 3.845860 TCGGAGGGAGTAATATCTTGCT 58.154 45.455 0.00 0.00 0.00 3.91
4824 5064 3.699538 ACTCCCTTTGAACTGAAACAACC 59.300 43.478 0.00 0.00 0.00 3.77
4926 5166 6.639632 AACATTGTATGTCTTGCAGACTTT 57.360 33.333 14.60 7.35 45.27 2.66
5028 5279 2.953453 TGTACACCACTACACAGGAGT 58.047 47.619 0.00 0.00 33.28 3.85
5109 5360 9.169592 CTTCCCTCGGAAAACAAAACTATATTA 57.830 33.333 0.00 0.00 41.54 0.98
5126 5380 0.613260 TCACAATGACCTTCCCTCGG 59.387 55.000 0.00 0.00 0.00 4.63
5145 5399 9.054922 CCATGTTTTCAAATCAATAAAACCAGT 57.945 29.630 0.00 0.00 40.64 4.00
5161 5415 3.825585 TGAATGCTGTAGCCATGTTTTCA 59.174 39.130 0.80 0.00 41.18 2.69
5172 5426 6.726258 TGAGTGTAATTGTGAATGCTGTAG 57.274 37.500 0.00 0.00 0.00 2.74
5229 5484 1.401931 GCGAATGCAGCAACACATTCT 60.402 47.619 0.00 0.00 46.43 2.40
5354 5609 7.643569 TTGATTTGGCTAATTTGATCTGCTA 57.356 32.000 0.00 0.00 0.00 3.49
5355 5610 6.534475 TTGATTTGGCTAATTTGATCTGCT 57.466 33.333 0.00 0.00 0.00 4.24
5356 5611 5.233689 GCTTGATTTGGCTAATTTGATCTGC 59.766 40.000 0.00 0.00 0.00 4.26
5357 5612 5.751990 GGCTTGATTTGGCTAATTTGATCTG 59.248 40.000 0.00 0.00 0.00 2.90
5358 5613 5.163374 GGGCTTGATTTGGCTAATTTGATCT 60.163 40.000 0.00 0.00 0.00 2.75
5359 5614 5.052481 GGGCTTGATTTGGCTAATTTGATC 58.948 41.667 0.00 0.00 0.00 2.92
5375 5630 3.744940 ATGAAGGAAGAATGGGCTTGA 57.255 42.857 0.00 0.00 0.00 3.02
5468 5723 1.543802 CCAACACATACCACGCCAATT 59.456 47.619 0.00 0.00 0.00 2.32
5470 5725 1.519751 GCCAACACATACCACGCCAA 61.520 55.000 0.00 0.00 0.00 4.52
5493 5748 1.330521 CATGTCCCCGAATAAAGCACG 59.669 52.381 0.00 0.00 0.00 5.34
5507 5762 4.530857 CGGGTCGGCTCCATGTCC 62.531 72.222 0.00 0.00 0.00 4.02
5539 5794 1.359475 GCGAGTCACCCGGTCTATC 59.641 63.158 0.00 0.00 0.00 2.08
5540 5795 2.125961 GGCGAGTCACCCGGTCTAT 61.126 63.158 0.00 0.00 0.00 1.98
5541 5796 2.753043 GGCGAGTCACCCGGTCTA 60.753 66.667 0.00 0.00 0.00 2.59
5542 5797 4.680537 AGGCGAGTCACCCGGTCT 62.681 66.667 0.00 0.00 0.00 3.85
5569 5824 4.338118 AGTGTGTCAAAACATGTTACCCAG 59.662 41.667 12.39 0.70 37.81 4.45
5622 5925 3.369471 GGCACTTGACTATGCTCTTACCA 60.369 47.826 0.00 0.00 41.74 3.25
5633 5936 2.436417 GGCATTTGAGGCACTTGACTA 58.564 47.619 0.00 0.00 41.55 2.59
5643 5946 2.608970 ATCCGTCCGGGCATTTGAGG 62.609 60.000 6.96 0.00 34.94 3.86
5645 5948 1.451207 CATCCGTCCGGGCATTTGA 60.451 57.895 6.96 0.00 34.94 2.69
5655 5958 2.270874 AATGACTGGGCCATCCGTCC 62.271 60.000 18.52 4.94 37.87 4.79
5656 5959 1.097547 CAATGACTGGGCCATCCGTC 61.098 60.000 6.72 12.34 38.57 4.79
5657 5960 1.077501 CAATGACTGGGCCATCCGT 60.078 57.895 6.72 0.21 38.76 4.69
5658 5961 1.097547 GTCAATGACTGGGCCATCCG 61.098 60.000 6.72 0.00 38.76 4.18
5659 5962 0.753111 GGTCAATGACTGGGCCATCC 60.753 60.000 6.72 1.96 32.47 3.51
5660 5963 1.097547 CGGTCAATGACTGGGCCATC 61.098 60.000 14.16 7.87 35.49 3.51
5661 5964 1.077501 CGGTCAATGACTGGGCCAT 60.078 57.895 14.16 0.00 35.49 4.40
5662 5965 2.350895 CGGTCAATGACTGGGCCA 59.649 61.111 14.16 5.85 35.49 5.36
5667 5970 1.877637 TTGTGACCGGTCAATGACTG 58.122 50.000 37.75 14.96 41.85 3.51
5668 5971 2.631160 TTTGTGACCGGTCAATGACT 57.369 45.000 37.75 0.00 41.85 3.41
5678 5991 5.696724 AGTCTGAGTTAGATTTTTGTGACCG 59.303 40.000 0.00 0.00 37.83 4.79
5689 6002 8.024285 CGTTTAAGAAGTCAGTCTGAGTTAGAT 58.976 37.037 20.56 12.92 39.91 1.98
5692 6005 6.444633 CCGTTTAAGAAGTCAGTCTGAGTTA 58.555 40.000 20.56 5.27 39.91 2.24
5704 6017 2.882761 GTTTGAGGCCCGTTTAAGAAGT 59.117 45.455 0.00 0.00 0.00 3.01
5707 6020 2.642154 TGTTTGAGGCCCGTTTAAGA 57.358 45.000 0.00 0.00 0.00 2.10
5708 6021 3.669557 CGAATGTTTGAGGCCCGTTTAAG 60.670 47.826 0.00 0.00 0.00 1.85
5718 6031 1.539827 GGTCAACCCGAATGTTTGAGG 59.460 52.381 0.00 0.00 0.00 3.86
5732 6045 0.454600 TACGAGAGATGCCGGTCAAC 59.545 55.000 1.90 0.19 0.00 3.18
5733 6046 1.337071 GATACGAGAGATGCCGGTCAA 59.663 52.381 1.90 0.00 0.00 3.18
5740 6053 0.965439 AGGCTGGATACGAGAGATGC 59.035 55.000 0.00 0.00 42.51 3.91
5741 6054 4.855715 TTTAGGCTGGATACGAGAGATG 57.144 45.455 0.00 0.00 42.51 2.90
5742 6055 6.097554 CCATATTTAGGCTGGATACGAGAGAT 59.902 42.308 0.00 0.00 42.51 2.75
5745 6058 4.466370 CCCATATTTAGGCTGGATACGAGA 59.534 45.833 0.00 0.00 42.51 4.04
5749 6062 3.621558 GCCCCATATTTAGGCTGGATAC 58.378 50.000 0.00 0.00 43.62 2.24
5758 6071 1.519408 CCCGAACGCCCCATATTTAG 58.481 55.000 0.00 0.00 0.00 1.85
5759 6072 0.535553 GCCCGAACGCCCCATATTTA 60.536 55.000 0.00 0.00 0.00 1.40
5786 6110 2.916052 GCTGTCAGGTCCGACGTGA 61.916 63.158 17.81 17.81 40.25 4.35
5797 6121 2.670148 GGTGGGGTAGGGCTGTCAG 61.670 68.421 0.00 0.00 0.00 3.51
5812 6136 3.243805 TGGAATTGATGCAAACTGTGGTG 60.244 43.478 0.00 0.00 0.00 4.17
5813 6137 2.964464 TGGAATTGATGCAAACTGTGGT 59.036 40.909 0.00 0.00 0.00 4.16
5815 6139 4.811908 TGATGGAATTGATGCAAACTGTG 58.188 39.130 0.00 0.00 30.96 3.66
5816 6140 5.471556 TTGATGGAATTGATGCAAACTGT 57.528 34.783 0.00 0.00 30.96 3.55
5817 6141 5.121142 GGTTTGATGGAATTGATGCAAACTG 59.879 40.000 1.28 0.00 42.60 3.16
5819 6143 5.240121 AGGTTTGATGGAATTGATGCAAAC 58.760 37.500 0.00 0.00 42.40 2.93
5822 6146 4.081531 GGAAGGTTTGATGGAATTGATGCA 60.082 41.667 0.00 0.00 0.00 3.96
5823 6147 4.161001 AGGAAGGTTTGATGGAATTGATGC 59.839 41.667 0.00 0.00 0.00 3.91
5825 6149 4.958581 GGAGGAAGGTTTGATGGAATTGAT 59.041 41.667 0.00 0.00 0.00 2.57
5826 6150 4.044571 AGGAGGAAGGTTTGATGGAATTGA 59.955 41.667 0.00 0.00 0.00 2.57
5827 6151 4.347607 AGGAGGAAGGTTTGATGGAATTG 58.652 43.478 0.00 0.00 0.00 2.32
5830 6154 2.308866 GGAGGAGGAAGGTTTGATGGAA 59.691 50.000 0.00 0.00 0.00 3.53
5831 6155 1.916181 GGAGGAGGAAGGTTTGATGGA 59.084 52.381 0.00 0.00 0.00 3.41
5832 6156 1.064389 GGGAGGAGGAAGGTTTGATGG 60.064 57.143 0.00 0.00 0.00 3.51
5833 6157 1.407437 CGGGAGGAGGAAGGTTTGATG 60.407 57.143 0.00 0.00 0.00 3.07
5834 6158 0.912486 CGGGAGGAGGAAGGTTTGAT 59.088 55.000 0.00 0.00 0.00 2.57
5835 6159 1.838073 GCGGGAGGAGGAAGGTTTGA 61.838 60.000 0.00 0.00 0.00 2.69
5836 6160 1.377333 GCGGGAGGAGGAAGGTTTG 60.377 63.158 0.00 0.00 0.00 2.93
5837 6161 2.603652 GGCGGGAGGAGGAAGGTTT 61.604 63.158 0.00 0.00 0.00 3.27
5838 6162 3.009714 GGCGGGAGGAGGAAGGTT 61.010 66.667 0.00 0.00 0.00 3.50
5889 6213 4.329545 GAGCAAGGGTGGCGGACA 62.330 66.667 0.00 0.00 36.08 4.02
5914 6238 2.442643 GGATCGGGACCGGTGGTA 60.443 66.667 14.63 0.00 35.25 3.25
5932 6256 2.027751 GACGACATCTAGGGCGGC 59.972 66.667 0.00 0.00 0.00 6.53
5933 6257 2.076622 CTGGACGACATCTAGGGCGG 62.077 65.000 0.00 0.00 32.30 6.13


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

AutoCloner maintained by Alex Coulton.