Multiple sequence alignment - TraesCS5B01G255700

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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 TraesCS5B01G255700 chr5B 100.000 5322 0 0 1 5322 438216328 438221649 0.000000e+00 9828.0
1 TraesCS5B01G255700 chr5B 100.000 567 0 0 5459 6025 438221786 438222352 0.000000e+00 1048.0
2 TraesCS5B01G255700 chr5B 84.424 443 51 11 1590 2017 24644898 24644459 2.600000e-113 420.0
3 TraesCS5B01G255700 chr5B 85.484 372 28 19 5490 5839 438482888 438483255 1.230000e-96 364.0
4 TraesCS5B01G255700 chr5B 90.299 134 9 2 4750 4883 438482225 438482354 8.030000e-39 172.0
5 TraesCS5B01G255700 chr5B 88.550 131 15 0 3529 3659 323708887 323708757 6.250000e-35 159.0
6 TraesCS5B01G255700 chr5A 92.623 3362 168 34 295 3603 471913354 471916688 0.000000e+00 4761.0
7 TraesCS5B01G255700 chr5A 92.994 1670 76 13 3655 5294 471916682 471918340 0.000000e+00 2398.0
8 TraesCS5B01G255700 chr5A 84.602 591 52 12 5462 6022 471918346 471918927 8.830000e-153 551.0
9 TraesCS5B01G255700 chr5A 81.439 431 44 22 5461 5875 471922414 471922824 2.710000e-83 320.0
10 TraesCS5B01G255700 chr5D 93.855 1611 76 12 3655 5258 369388646 369390240 0.000000e+00 2405.0
11 TraesCS5B01G255700 chr5D 89.844 1920 111 36 258 2132 369385440 369387320 0.000000e+00 2388.0
12 TraesCS5B01G255700 chr5D 93.683 839 40 2 2693 3527 369387816 369388645 0.000000e+00 1243.0
13 TraesCS5B01G255700 chr5D 87.331 592 47 8 5461 6025 369390264 369390854 0.000000e+00 652.0
14 TraesCS5B01G255700 chr5D 84.653 404 31 20 5461 5839 369416890 369417287 2.050000e-99 374.0
15 TraesCS5B01G255700 chr5D 85.906 149 18 3 3530 3678 412263324 412263469 8.090000e-34 156.0
16 TraesCS5B01G255700 chr5D 79.474 190 16 6 1 189 369385246 369385413 4.940000e-21 113.0
17 TraesCS5B01G255700 chr5D 100.000 28 0 0 5995 6022 369413833 369413860 1.100000e-02 52.8
18 TraesCS5B01G255700 chr4B 90.000 1180 68 24 987 2135 169927356 169926196 0.000000e+00 1480.0
19 TraesCS5B01G255700 chr4B 87.805 410 36 6 2258 2661 169926174 169925773 9.140000e-128 468.0
20 TraesCS5B01G255700 chr4B 91.167 317 18 2 2702 3017 169925762 169925455 7.220000e-114 422.0
21 TraesCS5B01G255700 chr7B 80.815 589 109 4 3721 4307 164976492 164977078 5.500000e-125 459.0
22 TraesCS5B01G255700 chr7A 80.306 589 112 4 3721 4307 211810467 211811053 5.540000e-120 442.0
23 TraesCS5B01G255700 chr7A 90.625 128 12 0 3530 3657 498590386 498590259 2.890000e-38 171.0
24 TraesCS5B01G255700 chr4A 90.840 131 11 1 3532 3662 477033207 477033336 2.230000e-39 174.0
25 TraesCS5B01G255700 chr4A 89.600 125 13 0 3535 3659 633353719 633353843 6.250000e-35 159.0
26 TraesCS5B01G255700 chr4D 91.270 126 9 2 3535 3659 208558679 208558555 2.890000e-38 171.0
27 TraesCS5B01G255700 chrUn 89.683 126 11 2 3535 3659 130475507 130475631 6.250000e-35 159.0
28 TraesCS5B01G255700 chr3A 88.550 131 15 0 3531 3661 332556166 332556296 6.250000e-35 159.0


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 TraesCS5B01G255700 chr5B 438216328 438222352 6024 False 5438.0 9828 100.000000 1 6025 2 chr5B.!!$F1 6024
1 TraesCS5B01G255700 chr5B 438482225 438483255 1030 False 268.0 364 87.891500 4750 5839 2 chr5B.!!$F2 1089
2 TraesCS5B01G255700 chr5A 471913354 471922824 9470 False 2007.5 4761 87.914500 295 6022 4 chr5A.!!$F1 5727
3 TraesCS5B01G255700 chr5D 369385246 369390854 5608 False 1360.2 2405 88.837400 1 6025 5 chr5D.!!$F2 6024
4 TraesCS5B01G255700 chr5D 369413833 369417287 3454 False 213.4 374 92.326500 5461 6022 2 chr5D.!!$F3 561
5 TraesCS5B01G255700 chr4B 169925455 169927356 1901 True 790.0 1480 89.657333 987 3017 3 chr4B.!!$R1 2030
6 TraesCS5B01G255700 chr7B 164976492 164977078 586 False 459.0 459 80.815000 3721 4307 1 chr7B.!!$F1 586
7 TraesCS5B01G255700 chr7A 211810467 211811053 586 False 442.0 442 80.306000 3721 4307 1 chr7A.!!$F1 586

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
263 264 0.041839 CACAAGCACAACGAGTCTGC 60.042 55.000 0.00 0.0 0.00 4.26 F
1350 1426 0.095935 CGAAGATCCGTGCTTGCTTG 59.904 55.000 0.00 0.0 0.00 4.01 F
2098 2189 2.664402 ACTGCTGGAAACCTGACATT 57.336 45.000 0.00 0.0 0.00 2.71 F
2986 3109 0.250038 ACCGATGATGGGATGCTTCG 60.250 55.000 0.00 0.0 0.00 3.79 F
4093 4221 1.061131 CTAAGTGCGCTTTGGTCGATG 59.939 52.381 19.18 0.0 36.22 3.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1362 1445 0.031178 GCCACTGCAAGAAACCACAG 59.969 55.0 0.0 0.0 37.43 3.66 R
2912 3035 0.882927 GTGCACGTAACTCCTTGGCA 60.883 55.0 0.0 0.0 0.00 4.92 R
3640 3768 0.031917 TAGTACGCCCTCCATCCCAA 60.032 55.0 0.0 0.0 0.00 4.12 R
4455 4586 0.179084 ATACCACTGACGAATGCGGG 60.179 55.0 0.0 0.0 43.17 6.13 R
5133 5270 0.405585 ACATAAGCCCAGCAACCACT 59.594 50.0 0.0 0.0 0.00 4.00 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
22 23 3.380142 CACGCAATGTAAGCAACCTTTT 58.620 40.909 0.00 0.00 32.47 2.27
47 48 4.704833 TGCTGGCCTGCGTCCTTC 62.705 66.667 27.08 2.39 35.36 3.46
62 63 1.014564 CCTTCGTTTCTCCTCACGCC 61.015 60.000 0.00 0.00 36.32 5.68
80 81 2.666190 GTCAGCAAGCTGCCACGA 60.666 61.111 16.89 0.00 46.52 4.35
81 82 2.357881 TCAGCAAGCTGCCACGAG 60.358 61.111 16.89 0.00 46.52 4.18
93 94 2.356313 CACGAGCGCCTCACAAGT 60.356 61.111 2.29 0.00 0.00 3.16
106 107 3.979495 CCTCACAAGTCACAACGTACTAC 59.021 47.826 0.00 0.00 0.00 2.73
153 154 2.022129 GCAACTGCTCGCACGTAGT 61.022 57.895 0.00 0.00 39.11 2.73
154 155 0.731514 GCAACTGCTCGCACGTAGTA 60.732 55.000 0.00 0.00 37.15 1.82
155 156 0.982673 CAACTGCTCGCACGTAGTAC 59.017 55.000 0.00 0.00 41.61 2.73
156 157 0.109412 AACTGCTCGCACGTAGTACC 60.109 55.000 0.00 0.00 41.61 3.34
158 159 2.277756 GCTCGCACGTAGTACCGG 60.278 66.667 0.00 0.00 41.61 5.28
161 162 4.118995 CGCACGTAGTACCGGCCA 62.119 66.667 0.00 0.00 41.61 5.36
162 163 2.507769 GCACGTAGTACCGGCCAC 60.508 66.667 0.00 0.00 41.61 5.01
163 164 2.182537 CACGTAGTACCGGCCACC 59.817 66.667 0.00 0.00 41.61 4.61
164 165 3.443045 ACGTAGTACCGGCCACCG 61.443 66.667 0.00 2.55 44.08 4.94
175 176 3.192922 GCCACCGGCGACATGTAC 61.193 66.667 9.30 0.00 39.62 2.90
236 237 4.256180 GGGGCCTGCTGATACGGG 62.256 72.222 0.84 0.00 39.28 5.28
241 242 4.529219 CTGCTGATACGGGCGGCA 62.529 66.667 12.47 7.53 44.77 5.69
242 243 4.529219 TGCTGATACGGGCGGCAG 62.529 66.667 12.47 10.04 42.32 4.85
256 257 2.353839 GCAGGCACAAGCACAACG 60.354 61.111 0.00 0.00 44.61 4.10
263 264 0.041839 CACAAGCACAACGAGTCTGC 60.042 55.000 0.00 0.00 0.00 4.26
284 285 0.721718 GAAGGTTCTGGCGATTCGTG 59.278 55.000 8.03 0.00 0.00 4.35
285 286 0.673644 AAGGTTCTGGCGATTCGTGG 60.674 55.000 8.03 0.00 0.00 4.94
286 287 1.079405 GGTTCTGGCGATTCGTGGA 60.079 57.895 8.03 1.29 0.00 4.02
290 291 2.434185 TGGCGATTCGTGGAGTGC 60.434 61.111 8.03 0.00 0.00 4.40
292 293 2.167861 GGCGATTCGTGGAGTGCTC 61.168 63.158 8.03 0.00 0.00 4.26
322 331 1.300156 GCGCACGAGCAGATGGATA 60.300 57.895 0.30 0.00 42.27 2.59
324 333 1.570813 CGCACGAGCAGATGGATAAA 58.429 50.000 5.50 0.00 42.27 1.40
349 358 2.755650 TCGAGAGAGAAAAGCACCAAC 58.244 47.619 0.00 0.00 34.84 3.77
400 409 1.226974 GCGCGCACTCAAGGATAGA 60.227 57.895 29.10 0.00 0.00 1.98
475 487 4.494515 GGTGTCACTTTCACCCCC 57.505 61.111 2.35 0.00 46.63 5.40
647 669 2.203294 ACACCACCGCTCCCAAAC 60.203 61.111 0.00 0.00 0.00 2.93
704 737 4.978083 AATCTGACCAAATGCTTAGCAG 57.022 40.909 13.74 0.98 43.65 4.24
715 748 2.110578 TGCTTAGCAGATGTAGGAGCA 58.889 47.619 1.39 0.00 36.43 4.26
920 958 3.771577 AGAAACCACTCGAGTCCAAAT 57.228 42.857 16.96 0.72 0.00 2.32
1088 1156 1.977009 CGGAAAGCAAACCCCCTCC 60.977 63.158 0.00 0.00 0.00 4.30
1092 1160 2.094170 AAAGCAAACCCCCTCCTCCC 62.094 60.000 0.00 0.00 0.00 4.30
1348 1424 2.103042 GCGAAGATCCGTGCTTGCT 61.103 57.895 0.00 0.00 0.00 3.91
1349 1425 1.639298 GCGAAGATCCGTGCTTGCTT 61.639 55.000 0.00 0.00 0.00 3.91
1350 1426 0.095935 CGAAGATCCGTGCTTGCTTG 59.904 55.000 0.00 0.00 0.00 4.01
1362 1445 3.068560 TGCTTGCTTGATTTGATTTGGC 58.931 40.909 0.00 0.00 0.00 4.52
1814 1905 6.218108 AGCCATCCATCAGAAAAGAAAATC 57.782 37.500 0.00 0.00 0.00 2.17
2098 2189 2.664402 ACTGCTGGAAACCTGACATT 57.336 45.000 0.00 0.00 0.00 2.71
2240 2336 3.034635 ACAGACCTGACATATCTGGGTC 58.965 50.000 16.46 10.05 45.90 4.46
2243 2339 3.645212 AGACCTGACATATCTGGGTCATG 59.355 47.826 15.40 0.00 45.90 3.07
2254 2350 9.166222 ACATATCTGGGTCATGTTACCTAAATA 57.834 33.333 3.76 0.00 39.65 1.40
2332 2439 6.365520 TCAGTACCTAAGCTCATACTCATCA 58.634 40.000 0.00 0.00 0.00 3.07
2345 2452 9.149225 GCTCATACTCATCATATGAAGGTAAAG 57.851 37.037 9.99 13.64 38.32 1.85
2435 2548 4.263462 TGACTACTCCCAAAGACATTGCAT 60.263 41.667 0.00 0.00 37.73 3.96
2565 2678 3.839293 ACACTGAGTGAAGAGCGATTAC 58.161 45.455 20.97 0.00 36.96 1.89
2650 2763 5.289595 TGTAGCTTGTTTAGTCAGTCACAG 58.710 41.667 0.00 0.00 0.00 3.66
2680 2793 4.968259 TGTTATGTGTTCTGCCAGTTACT 58.032 39.130 0.00 0.00 0.00 2.24
2686 2799 6.599356 TGTGTTCTGCCAGTTACTATCTTA 57.401 37.500 0.00 0.00 0.00 2.10
2753 2875 4.995487 GCTGCTGATACATCATCTGATCAA 59.005 41.667 0.00 0.00 36.02 2.57
2754 2876 5.469084 GCTGCTGATACATCATCTGATCAAA 59.531 40.000 0.00 0.00 36.02 2.69
2755 2877 6.566187 GCTGCTGATACATCATCTGATCAAAC 60.566 42.308 0.00 0.00 36.02 2.93
2756 2878 6.589135 TGCTGATACATCATCTGATCAAACT 58.411 36.000 0.00 0.00 36.02 2.66
2757 2879 7.729116 TGCTGATACATCATCTGATCAAACTA 58.271 34.615 0.00 0.00 36.02 2.24
2758 2880 7.654923 TGCTGATACATCATCTGATCAAACTAC 59.345 37.037 0.00 0.00 36.02 2.73
2759 2881 7.654923 GCTGATACATCATCTGATCAAACTACA 59.345 37.037 0.00 0.00 36.02 2.74
2760 2882 8.877808 TGATACATCATCTGATCAAACTACAC 57.122 34.615 0.00 0.00 34.46 2.90
2761 2883 8.477256 TGATACATCATCTGATCAAACTACACA 58.523 33.333 0.00 0.00 34.46 3.72
2912 3035 5.902431 AGCTTCTAGAGGAAATCATGGTACT 59.098 40.000 5.96 0.00 33.07 2.73
2986 3109 0.250038 ACCGATGATGGGATGCTTCG 60.250 55.000 0.00 0.00 0.00 3.79
3028 3151 8.547967 TTTCACTGTACTACTGAATTTCCATC 57.452 34.615 0.00 0.00 0.00 3.51
3036 3159 8.969267 GTACTACTGAATTTCCATCGTCATTAG 58.031 37.037 0.00 0.00 32.46 1.73
3064 3187 6.882678 GTGTCTTGTACTTTGTATTGGGGTAT 59.117 38.462 0.00 0.00 0.00 2.73
3297 3420 2.224867 ACCCAAAGGACTCCATTGTCTG 60.225 50.000 11.26 3.56 37.16 3.51
3363 3486 7.996385 ACAATAAGGATTTTCCAAATACGGAG 58.004 34.615 0.00 0.00 39.61 4.63
3379 3502 1.338200 CGGAGAAGTTGGAAGACCCTG 60.338 57.143 0.00 0.00 35.38 4.45
3435 3558 2.492773 GGCTGCTGCAGTGGTTGTT 61.493 57.895 28.50 0.00 41.91 2.83
3539 3667 5.350640 CCGACTTCTGTTTTGTATTACCTCC 59.649 44.000 0.00 0.00 0.00 4.30
3550 3678 8.945057 GTTTTGTATTACCTCCGTACCAAATTA 58.055 33.333 0.00 0.00 0.00 1.40
3552 3680 7.180322 TGTATTACCTCCGTACCAAATTACA 57.820 36.000 0.00 0.00 0.00 2.41
3553 3681 7.619050 TGTATTACCTCCGTACCAAATTACAA 58.381 34.615 0.00 0.00 0.00 2.41
3560 3688 4.998672 TCCGTACCAAATTACAAGTCTTGG 59.001 41.667 16.85 0.26 43.33 3.61
3576 3704 8.311836 ACAAGTCTTGGATTTTTCTAGATACGA 58.688 33.333 16.85 0.00 34.12 3.43
3611 3739 9.962783 AACACTAAAACGTATCTAGATACATCC 57.037 33.333 32.22 13.74 42.82 3.51
3612 3740 8.288208 ACACTAAAACGTATCTAGATACATCCG 58.712 37.037 32.22 23.79 42.82 4.18
3613 3741 8.288208 CACTAAAACGTATCTAGATACATCCGT 58.712 37.037 32.22 24.32 42.82 4.69
3614 3742 9.494271 ACTAAAACGTATCTAGATACATCCGTA 57.506 33.333 32.22 19.59 42.82 4.02
3631 3759 8.693120 ACATCCGTATCTAGACAAATCTAAGA 57.307 34.615 0.00 0.00 36.98 2.10
3632 3760 8.569641 ACATCCGTATCTAGACAAATCTAAGAC 58.430 37.037 0.00 0.00 36.98 3.01
3633 3761 8.568794 CATCCGTATCTAGACAAATCTAAGACA 58.431 37.037 0.00 0.00 36.98 3.41
3634 3762 8.515695 TCCGTATCTAGACAAATCTAAGACAA 57.484 34.615 0.00 0.00 36.98 3.18
3635 3763 8.622157 TCCGTATCTAGACAAATCTAAGACAAG 58.378 37.037 0.00 0.00 36.98 3.16
3636 3764 8.407064 CCGTATCTAGACAAATCTAAGACAAGT 58.593 37.037 0.00 0.00 36.98 3.16
3644 3772 9.014297 AGACAAATCTAAGACAAGTAATTTGGG 57.986 33.333 9.60 0.00 38.04 4.12
3645 3773 8.934023 ACAAATCTAAGACAAGTAATTTGGGA 57.066 30.769 9.60 0.00 41.25 4.37
3646 3774 9.533831 ACAAATCTAAGACAAGTAATTTGGGAT 57.466 29.630 9.60 0.00 41.25 3.85
3647 3775 9.793252 CAAATCTAAGACAAGTAATTTGGGATG 57.207 33.333 0.00 0.00 41.25 3.51
3648 3776 8.525290 AATCTAAGACAAGTAATTTGGGATGG 57.475 34.615 0.00 0.00 41.25 3.51
3649 3777 7.265599 TCTAAGACAAGTAATTTGGGATGGA 57.734 36.000 0.00 0.00 41.25 3.41
3650 3778 7.338710 TCTAAGACAAGTAATTTGGGATGGAG 58.661 38.462 0.00 0.00 41.25 3.86
3651 3779 4.860022 AGACAAGTAATTTGGGATGGAGG 58.140 43.478 0.00 0.00 41.25 4.30
3652 3780 3.954258 GACAAGTAATTTGGGATGGAGGG 59.046 47.826 0.00 0.00 41.25 4.30
3653 3781 2.695147 CAAGTAATTTGGGATGGAGGGC 59.305 50.000 0.00 0.00 32.95 5.19
4093 4221 1.061131 CTAAGTGCGCTTTGGTCGATG 59.939 52.381 19.18 0.00 36.22 3.84
4321 4449 7.106239 ACCTGGTGAGTTTATGAACTTATGAG 58.894 38.462 4.16 1.39 45.88 2.90
4370 4501 4.056740 CACCAATAGCTCAGCAGAGTATG 58.943 47.826 8.03 2.52 44.00 2.39
4383 4514 5.540337 CAGCAGAGTATGTCCCCTAATAAGA 59.460 44.000 0.00 0.00 0.00 2.10
4400 4531 7.663081 CCTAATAAGATTTCAGCTATTCTGCCA 59.337 37.037 0.00 0.00 42.56 4.92
4402 4533 5.769484 AAGATTTCAGCTATTCTGCCATG 57.231 39.130 0.00 0.00 42.56 3.66
4415 4546 7.255381 GCTATTCTGCCATGTTTTGATCTACAT 60.255 37.037 0.00 0.00 35.45 2.29
4416 4547 9.276590 CTATTCTGCCATGTTTTGATCTACATA 57.723 33.333 7.90 0.00 33.42 2.29
4417 4548 6.925610 TCTGCCATGTTTTGATCTACATAC 57.074 37.500 7.90 5.49 33.42 2.39
4421 4552 7.537715 TGCCATGTTTTGATCTACATACAAAG 58.462 34.615 7.90 0.00 35.48 2.77
4422 4553 7.392953 TGCCATGTTTTGATCTACATACAAAGA 59.607 33.333 7.90 0.00 35.48 2.52
4423 4554 8.243426 GCCATGTTTTGATCTACATACAAAGAA 58.757 33.333 7.90 0.00 35.48 2.52
4455 4586 5.491982 ACTTCTTCACCAACACTATGATCC 58.508 41.667 0.00 0.00 0.00 3.36
4458 4589 1.484653 TCACCAACACTATGATCCCCG 59.515 52.381 0.00 0.00 0.00 5.73
4568 4699 1.746220 CCTTGTGACGTTTTGGAACCA 59.254 47.619 0.00 0.00 31.93 3.67
4569 4700 2.360801 CCTTGTGACGTTTTGGAACCAT 59.639 45.455 0.00 0.00 31.93 3.55
4698 4829 3.610669 CCCTGGCTCGAGATCGGG 61.611 72.222 18.75 19.98 44.00 5.14
4931 5062 6.217294 GTTCCTCCTATGTATGACTAACTGC 58.783 44.000 0.00 0.00 0.00 4.40
5018 5149 5.234757 CCACGTAGGCTATATTGCGTTTTTA 59.765 40.000 9.51 0.00 33.43 1.52
5037 5168 8.879759 CGTTTTTATACTTACTGATGTGGATGT 58.120 33.333 0.00 0.00 0.00 3.06
5043 5174 8.948631 ATACTTACTGATGTGGATGTAACAAG 57.051 34.615 0.00 0.00 0.00 3.16
5071 5202 6.371825 GGTAGAAAAACTATGTCCAGTTCCTG 59.628 42.308 0.00 0.00 37.78 3.86
5073 5204 3.788227 AAACTATGTCCAGTTCCTGCA 57.212 42.857 0.00 0.00 37.78 4.41
5109 5246 5.462405 AGTGTAATCAGTTCGTTCTCTGTC 58.538 41.667 0.00 0.00 33.89 3.51
5114 5251 0.039074 AGTTCGTTCTCTGTCCTGCG 60.039 55.000 0.00 0.00 0.00 5.18
5133 5270 0.589223 GGCCACACACGAATTTCGAA 59.411 50.000 24.50 0.00 43.74 3.71
5140 5277 3.242608 ACACACGAATTTCGAAGTGGTTG 60.243 43.478 31.46 19.95 45.66 3.77
5144 5281 2.665519 CGAATTTCGAAGTGGTTGCTGG 60.666 50.000 13.45 0.00 43.74 4.85
5151 5288 1.474077 GAAGTGGTTGCTGGGCTTATG 59.526 52.381 0.00 0.00 0.00 1.90
5157 5294 2.484770 GGTTGCTGGGCTTATGTCGATA 60.485 50.000 0.00 0.00 0.00 2.92
5162 5299 4.100344 TGCTGGGCTTATGTCGATAAGTTA 59.900 41.667 7.45 0.00 42.21 2.24
5223 5361 0.457035 CAAACGATGGCTCCCAATGG 59.543 55.000 0.00 0.00 36.95 3.16
5232 5370 1.026718 GCTCCCAATGGACCGTTCAG 61.027 60.000 0.00 0.00 35.03 3.02
5237 5375 1.133025 CCAATGGACCGTTCAGAATGC 59.867 52.381 0.00 0.00 34.76 3.56
5246 5384 3.063997 ACCGTTCAGAATGCGATCAAATC 59.936 43.478 0.00 0.00 34.76 2.17
5247 5385 3.546815 CCGTTCAGAATGCGATCAAATCC 60.547 47.826 0.00 0.00 34.76 3.01
5258 5396 3.603770 GCGATCAAATCCAACTGAAAACG 59.396 43.478 0.00 0.00 0.00 3.60
5259 5397 4.612712 GCGATCAAATCCAACTGAAAACGA 60.613 41.667 0.00 0.00 0.00 3.85
5260 5398 5.082059 CGATCAAATCCAACTGAAAACGAG 58.918 41.667 0.00 0.00 0.00 4.18
5262 5400 4.204012 TCAAATCCAACTGAAAACGAGGT 58.796 39.130 0.00 0.00 0.00 3.85
5263 5401 5.369833 TCAAATCCAACTGAAAACGAGGTA 58.630 37.500 0.00 0.00 0.00 3.08
5264 5402 5.823570 TCAAATCCAACTGAAAACGAGGTAA 59.176 36.000 0.00 0.00 0.00 2.85
5265 5403 6.488683 TCAAATCCAACTGAAAACGAGGTAAT 59.511 34.615 0.00 0.00 0.00 1.89
5266 5404 6.496338 AATCCAACTGAAAACGAGGTAATC 57.504 37.500 0.00 0.00 0.00 1.75
5267 5405 4.320870 TCCAACTGAAAACGAGGTAATCC 58.679 43.478 0.00 0.00 0.00 3.01
5268 5406 4.069304 CCAACTGAAAACGAGGTAATCCA 58.931 43.478 0.00 0.00 35.89 3.41
5269 5407 4.517453 CCAACTGAAAACGAGGTAATCCAA 59.483 41.667 0.00 0.00 35.89 3.53
5270 5408 5.183140 CCAACTGAAAACGAGGTAATCCAAT 59.817 40.000 0.00 0.00 35.89 3.16
5271 5409 5.880054 ACTGAAAACGAGGTAATCCAATG 57.120 39.130 0.00 0.00 35.89 2.82
5272 5410 4.700213 ACTGAAAACGAGGTAATCCAATGG 59.300 41.667 0.00 0.00 35.89 3.16
5274 5412 5.505780 TGAAAACGAGGTAATCCAATGGAT 58.494 37.500 9.36 9.36 45.46 3.41
5275 5413 5.356751 TGAAAACGAGGTAATCCAATGGATG 59.643 40.000 16.52 4.51 42.27 3.51
5276 5414 2.851195 ACGAGGTAATCCAATGGATGC 58.149 47.619 16.52 11.57 42.27 3.91
5277 5415 2.154462 CGAGGTAATCCAATGGATGCC 58.846 52.381 16.52 19.49 42.27 4.40
5278 5416 2.224621 CGAGGTAATCCAATGGATGCCT 60.225 50.000 27.63 27.63 44.91 4.75
5304 5442 5.918608 TCTTAACAAGATAGTGCAGGATCC 58.081 41.667 2.48 2.48 31.20 3.36
5306 5444 2.769209 ACAAGATAGTGCAGGATCCCT 58.231 47.619 8.55 0.18 0.00 4.20
5308 5446 4.298626 ACAAGATAGTGCAGGATCCCTAA 58.701 43.478 8.55 0.00 29.64 2.69
5310 5448 5.191722 ACAAGATAGTGCAGGATCCCTAAAA 59.808 40.000 8.55 0.00 29.64 1.52
5517 5655 7.437748 ACAGAATTCCTTATCCAATCTCTACG 58.562 38.462 0.65 0.00 0.00 3.51
5536 10183 1.014352 GTAGCCGGCGATTTGTTGAT 58.986 50.000 23.20 0.95 0.00 2.57
5598 10249 6.552629 CCTATATATACGCTCTTTTCGCTGA 58.447 40.000 0.00 0.00 0.00 4.26
5603 10273 1.686566 CGCTCTTTTCGCTGATCGCA 61.687 55.000 9.58 0.00 39.08 5.10
5628 10298 2.247437 GCCCATCGTTCCGATCAGC 61.247 63.158 0.00 0.00 45.19 4.26
5654 10324 1.959899 CTGCTCACCGTTCACGATGC 61.960 60.000 0.00 0.55 43.02 3.91
5675 10345 3.071206 GAGCGCTCCTGGAGTCCA 61.071 66.667 27.22 12.40 31.39 4.02
5768 10453 2.427905 TCTCGTTCGCCGTGTTCG 60.428 61.111 0.00 0.00 37.94 3.95
5770 10455 2.983977 CTCGTTCGCCGTGTTCGTG 61.984 63.158 0.00 0.00 37.94 4.35
5962 10647 2.920912 ACGGCCCCAAAGACGAGA 60.921 61.111 0.00 0.00 0.00 4.04
5964 10649 2.033194 CGGCCCCAAAGACGAGAAC 61.033 63.158 0.00 0.00 0.00 3.01
5965 10650 2.033194 GGCCCCAAAGACGAGAACG 61.033 63.158 0.00 0.00 45.75 3.95
5968 10653 1.004918 CCCAAAGACGAGAACGCCT 60.005 57.895 0.00 0.00 43.96 5.52
5975 10660 2.430921 CGAGAACGCCTGCGAGTT 60.431 61.111 19.52 2.49 42.83 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 2.669569 GACGCAGGCCAGCAGAAA 60.670 61.111 21.12 0.00 0.00 2.52
29 30 4.711949 AAGGACGCAGGCCAGCAG 62.712 66.667 21.12 14.77 0.00 4.24
32 33 3.883744 AACGAAGGACGCAGGCCAG 62.884 63.158 5.01 0.00 46.94 4.85
47 48 2.049433 ACGGCGTGAGGAGAAACG 60.049 61.111 13.76 0.00 42.61 3.60
62 63 4.081030 CGTGGCAGCTTGCTGACG 62.081 66.667 24.67 20.78 44.28 4.35
80 81 1.146041 TTGTGACTTGTGAGGCGCT 59.854 52.632 7.64 0.00 42.16 5.92
81 82 1.279840 GTTGTGACTTGTGAGGCGC 59.720 57.895 0.00 0.00 41.99 6.53
84 85 3.093717 AGTACGTTGTGACTTGTGAGG 57.906 47.619 0.00 0.00 0.00 3.86
85 86 4.675565 CAGTAGTACGTTGTGACTTGTGAG 59.324 45.833 0.00 0.00 0.00 3.51
86 87 4.096833 ACAGTAGTACGTTGTGACTTGTGA 59.903 41.667 0.00 0.00 0.00 3.58
87 88 4.357142 ACAGTAGTACGTTGTGACTTGTG 58.643 43.478 0.00 0.00 0.00 3.33
88 89 4.644103 ACAGTAGTACGTTGTGACTTGT 57.356 40.909 0.00 0.00 0.00 3.16
106 107 4.745125 CCAAGATATGCTTACGTGGTACAG 59.255 45.833 0.00 0.00 34.52 2.74
146 147 2.182537 GGTGGCCGGTACTACGTG 59.817 66.667 1.90 0.00 0.00 4.49
158 159 3.192922 GTACATGTCGCCGGTGGC 61.193 66.667 14.01 14.01 46.75 5.01
166 167 2.689183 CGTGCTGCGTACATGTCG 59.311 61.111 0.00 7.49 35.54 4.35
241 242 1.153168 ACTCGTTGTGCTTGTGCCT 60.153 52.632 0.00 0.00 38.71 4.75
242 243 1.160329 AGACTCGTTGTGCTTGTGCC 61.160 55.000 0.00 0.00 38.71 5.01
243 244 0.041839 CAGACTCGTTGTGCTTGTGC 60.042 55.000 0.00 0.00 40.20 4.57
245 246 0.179073 AGCAGACTCGTTGTGCTTGT 60.179 50.000 5.76 0.00 45.31 3.16
246 247 0.234106 CAGCAGACTCGTTGTGCTTG 59.766 55.000 8.36 2.76 45.31 4.01
247 248 0.104855 TCAGCAGACTCGTTGTGCTT 59.895 50.000 8.36 0.00 45.31 3.91
249 250 0.510359 CTTCAGCAGACTCGTTGTGC 59.490 55.000 1.53 1.53 37.48 4.57
250 251 1.143305 CCTTCAGCAGACTCGTTGTG 58.857 55.000 0.00 0.00 0.00 3.33
251 252 0.753262 ACCTTCAGCAGACTCGTTGT 59.247 50.000 0.00 0.00 0.00 3.32
253 254 1.689273 AGAACCTTCAGCAGACTCGTT 59.311 47.619 0.00 0.00 0.00 3.85
256 257 1.943507 GCCAGAACCTTCAGCAGACTC 60.944 57.143 0.00 0.00 0.00 3.36
263 264 1.002366 CGAATCGCCAGAACCTTCAG 58.998 55.000 0.00 0.00 0.00 3.02
284 285 1.586564 CGTCGATTCGGAGCACTCC 60.587 63.158 6.62 6.62 46.18 3.85
285 286 2.224885 GCGTCGATTCGGAGCACTC 61.225 63.158 17.28 0.00 32.37 3.51
286 287 2.202623 GCGTCGATTCGGAGCACT 60.203 61.111 17.28 0.00 32.37 4.40
318 319 4.832590 TTCTCTCTCGATCGGTTTATCC 57.167 45.455 16.41 0.00 0.00 2.59
322 331 3.254892 GCTTTTCTCTCTCGATCGGTTT 58.745 45.455 16.41 0.00 0.00 3.27
324 333 1.819288 TGCTTTTCTCTCTCGATCGGT 59.181 47.619 16.41 0.00 0.00 4.69
349 358 2.094126 GATTCAGACGGCGCCATTCG 62.094 60.000 28.98 15.15 42.12 3.34
400 409 5.707495 AGACGGAGGAGAAGAAAGGTATAT 58.293 41.667 0.00 0.00 0.00 0.86
483 495 5.458041 AAATGGGTGAATGTTCTCAACAG 57.542 39.130 0.00 0.00 45.95 3.16
485 497 7.273381 CGAATTAAATGGGTGAATGTTCTCAAC 59.727 37.037 0.00 0.00 31.82 3.18
488 500 6.265577 CCGAATTAAATGGGTGAATGTTCTC 58.734 40.000 0.00 0.00 0.00 2.87
534 551 5.194432 CACAGGTACTACAGATAGACTGGT 58.806 45.833 0.00 0.00 44.60 4.00
631 653 2.983592 GGTTTGGGAGCGGTGGTG 60.984 66.667 0.00 0.00 0.00 4.17
679 712 3.323751 AAGCATTTGGTCAGATTTGGC 57.676 42.857 0.00 0.00 0.00 4.52
704 737 6.915349 AGATCGTATTTACTGCTCCTACATC 58.085 40.000 0.00 0.00 0.00 3.06
834 872 2.599142 GCGCGAATTTTCTATTCCCGTC 60.599 50.000 12.10 0.00 33.41 4.79
1047 1104 4.700365 GCGGGTGCTTGGTTTCGC 62.700 66.667 0.00 0.00 38.39 4.70
1342 1418 3.124636 CAGCCAAATCAAATCAAGCAAGC 59.875 43.478 0.00 0.00 0.00 4.01
1348 1424 4.686191 AACCACAGCCAAATCAAATCAA 57.314 36.364 0.00 0.00 0.00 2.57
1349 1425 4.344679 AGAAACCACAGCCAAATCAAATCA 59.655 37.500 0.00 0.00 0.00 2.57
1350 1426 4.886579 AGAAACCACAGCCAAATCAAATC 58.113 39.130 0.00 0.00 0.00 2.17
1362 1445 0.031178 GCCACTGCAAGAAACCACAG 59.969 55.000 0.00 0.00 37.43 3.66
2119 2210 6.598427 AAGGGAAAGGGCTTCTCTAATAAT 57.402 37.500 0.00 0.00 44.70 1.28
2232 2328 8.826765 CCTATATTTAGGTAACATGACCCAGAT 58.173 37.037 0.00 0.00 40.74 2.90
2240 2336 7.956420 TTGCGTCCTATATTTAGGTAACATG 57.044 36.000 8.84 0.00 44.75 3.21
2243 2339 8.429493 AGTTTTGCGTCCTATATTTAGGTAAC 57.571 34.615 8.84 1.07 44.75 2.50
2254 2350 6.047231 GTCATAGGTTAGTTTTGCGTCCTAT 58.953 40.000 0.00 0.00 38.35 2.57
2332 2439 8.677300 CAGTGCACAAATACTTTACCTTCATAT 58.323 33.333 21.04 0.00 0.00 1.78
2345 2452 5.048782 TCCAGTTCATTCAGTGCACAAATAC 60.049 40.000 21.04 13.21 0.00 1.89
2409 2522 5.880332 GCAATGTCTTTGGGAGTAGTCATAA 59.120 40.000 0.00 0.00 35.75 1.90
2452 2565 8.909708 TGAAAATAATAGGCATATATTTGCGC 57.090 30.769 11.35 0.00 43.71 6.09
2526 2639 5.063204 CAGTGTTCTGGTCCTAATGTTCAA 58.937 41.667 0.00 0.00 37.97 2.69
2540 2653 2.057316 CGCTCTTCACTCAGTGTTCTG 58.943 52.381 4.28 0.00 42.54 3.02
2620 2733 6.700520 ACTGACTAAACAAGCTACAGTGTAAC 59.299 38.462 4.21 0.00 36.63 2.50
2621 2734 6.812998 ACTGACTAAACAAGCTACAGTGTAA 58.187 36.000 4.21 0.00 36.63 2.41
2622 2735 6.040054 TGACTGACTAAACAAGCTACAGTGTA 59.960 38.462 2.36 2.36 37.45 2.90
2623 2736 5.163447 TGACTGACTAAACAAGCTACAGTGT 60.163 40.000 0.00 0.00 37.45 3.55
2650 2763 3.730061 GCAGAACACATAACATGCTCTGC 60.730 47.826 12.92 12.92 45.25 4.26
2680 2793 6.212791 AGCTGTTAGAACAACCCTGTAAGATA 59.787 38.462 0.00 0.00 38.66 1.98
2686 2799 4.699925 TTAGCTGTTAGAACAACCCTGT 57.300 40.909 0.00 0.00 38.66 4.00
2753 2875 4.876107 GCATTGGTACTAGCATGTGTAGTT 59.124 41.667 13.18 1.83 32.81 2.24
2754 2876 4.162320 AGCATTGGTACTAGCATGTGTAGT 59.838 41.667 12.70 12.70 34.96 2.73
2755 2877 4.509230 CAGCATTGGTACTAGCATGTGTAG 59.491 45.833 0.00 0.00 0.00 2.74
2756 2878 4.161377 TCAGCATTGGTACTAGCATGTGTA 59.839 41.667 0.00 0.00 0.00 2.90
2757 2879 3.055167 TCAGCATTGGTACTAGCATGTGT 60.055 43.478 0.00 0.00 0.00 3.72
2758 2880 3.534554 TCAGCATTGGTACTAGCATGTG 58.465 45.455 0.00 0.00 0.00 3.21
2759 2881 3.912496 TCAGCATTGGTACTAGCATGT 57.088 42.857 0.00 0.00 0.00 3.21
2760 2882 4.639334 AGATCAGCATTGGTACTAGCATG 58.361 43.478 0.00 0.00 0.00 4.06
2761 2883 4.560311 CGAGATCAGCATTGGTACTAGCAT 60.560 45.833 0.00 0.00 0.00 3.79
2805 2927 1.562008 TGGGGAAGTTGCGGAATGATA 59.438 47.619 0.00 0.00 0.00 2.15
2912 3035 0.882927 GTGCACGTAACTCCTTGGCA 60.883 55.000 0.00 0.00 0.00 4.92
2986 3109 6.981559 ACAGTGAAAGAGAAAGTACTTCTGAC 59.018 38.462 17.25 7.65 44.82 3.51
3028 3151 4.806330 AGTACAAGACACCACTAATGACG 58.194 43.478 0.00 0.00 0.00 4.35
3036 3159 5.048991 CCCAATACAAAGTACAAGACACCAC 60.049 44.000 0.00 0.00 0.00 4.16
3363 3486 3.403968 GAGTTCAGGGTCTTCCAACTTC 58.596 50.000 0.00 0.00 38.24 3.01
3435 3558 4.623932 AGCATGAACAAGAGTGGAGTTA 57.376 40.909 0.00 0.00 0.00 2.24
3539 3667 6.737254 ATCCAAGACTTGTAATTTGGTACG 57.263 37.500 14.03 0.00 40.68 3.67
3550 3678 8.311836 TCGTATCTAGAAAAATCCAAGACTTGT 58.688 33.333 14.03 0.00 0.00 3.16
3552 3680 9.892130 ATTCGTATCTAGAAAAATCCAAGACTT 57.108 29.630 0.00 0.00 0.00 3.01
3553 3681 9.319143 CATTCGTATCTAGAAAAATCCAAGACT 57.681 33.333 0.00 0.00 0.00 3.24
3605 3733 9.788889 TCTTAGATTTGTCTAGATACGGATGTA 57.211 33.333 0.00 0.00 34.45 2.29
3606 3734 8.569641 GTCTTAGATTTGTCTAGATACGGATGT 58.430 37.037 0.00 0.00 0.00 3.06
3607 3735 8.568794 TGTCTTAGATTTGTCTAGATACGGATG 58.431 37.037 0.00 0.00 0.00 3.51
3608 3736 8.693120 TGTCTTAGATTTGTCTAGATACGGAT 57.307 34.615 0.00 0.00 0.00 4.18
3609 3737 8.515695 TTGTCTTAGATTTGTCTAGATACGGA 57.484 34.615 0.00 0.00 0.00 4.69
3610 3738 8.407064 ACTTGTCTTAGATTTGTCTAGATACGG 58.593 37.037 0.00 0.00 0.00 4.02
3618 3746 9.014297 CCCAAATTACTTGTCTTAGATTTGTCT 57.986 33.333 0.00 0.00 34.40 3.41
3619 3747 9.010029 TCCCAAATTACTTGTCTTAGATTTGTC 57.990 33.333 0.00 0.00 34.40 3.18
3620 3748 8.934023 TCCCAAATTACTTGTCTTAGATTTGT 57.066 30.769 0.00 0.00 34.40 2.83
3621 3749 9.793252 CATCCCAAATTACTTGTCTTAGATTTG 57.207 33.333 0.00 0.00 35.40 2.32
3622 3750 8.971073 CCATCCCAAATTACTTGTCTTAGATTT 58.029 33.333 0.00 0.00 32.65 2.17
3623 3751 8.336235 TCCATCCCAAATTACTTGTCTTAGATT 58.664 33.333 0.00 0.00 32.65 2.40
3624 3752 7.872138 TCCATCCCAAATTACTTGTCTTAGAT 58.128 34.615 0.00 0.00 32.65 1.98
3625 3753 7.265599 TCCATCCCAAATTACTTGTCTTAGA 57.734 36.000 0.00 0.00 32.65 2.10
3626 3754 6.543831 CCTCCATCCCAAATTACTTGTCTTAG 59.456 42.308 0.00 0.00 32.65 2.18
3627 3755 6.423182 CCTCCATCCCAAATTACTTGTCTTA 58.577 40.000 0.00 0.00 32.65 2.10
3628 3756 5.264395 CCTCCATCCCAAATTACTTGTCTT 58.736 41.667 0.00 0.00 32.65 3.01
3629 3757 4.325344 CCCTCCATCCCAAATTACTTGTCT 60.325 45.833 0.00 0.00 32.65 3.41
3630 3758 3.954258 CCCTCCATCCCAAATTACTTGTC 59.046 47.826 0.00 0.00 32.65 3.18
3631 3759 3.881713 GCCCTCCATCCCAAATTACTTGT 60.882 47.826 0.00 0.00 32.65 3.16
3632 3760 2.695147 GCCCTCCATCCCAAATTACTTG 59.305 50.000 0.00 0.00 34.52 3.16
3633 3761 2.686715 CGCCCTCCATCCCAAATTACTT 60.687 50.000 0.00 0.00 0.00 2.24
3634 3762 1.133792 CGCCCTCCATCCCAAATTACT 60.134 52.381 0.00 0.00 0.00 2.24
3635 3763 1.318576 CGCCCTCCATCCCAAATTAC 58.681 55.000 0.00 0.00 0.00 1.89
3636 3764 0.923358 ACGCCCTCCATCCCAAATTA 59.077 50.000 0.00 0.00 0.00 1.40
3637 3765 0.923358 TACGCCCTCCATCCCAAATT 59.077 50.000 0.00 0.00 0.00 1.82
3638 3766 0.182775 GTACGCCCTCCATCCCAAAT 59.817 55.000 0.00 0.00 0.00 2.32
3639 3767 0.912487 AGTACGCCCTCCATCCCAAA 60.912 55.000 0.00 0.00 0.00 3.28
3640 3768 0.031917 TAGTACGCCCTCCATCCCAA 60.032 55.000 0.00 0.00 0.00 4.12
3641 3769 0.190069 ATAGTACGCCCTCCATCCCA 59.810 55.000 0.00 0.00 0.00 4.37
3642 3770 2.226962 TATAGTACGCCCTCCATCCC 57.773 55.000 0.00 0.00 0.00 3.85
3643 3771 4.466726 AGATTTATAGTACGCCCTCCATCC 59.533 45.833 0.00 0.00 0.00 3.51
3644 3772 5.185249 TGAGATTTATAGTACGCCCTCCATC 59.815 44.000 0.00 0.00 0.00 3.51
3645 3773 5.047235 GTGAGATTTATAGTACGCCCTCCAT 60.047 44.000 0.00 0.00 0.00 3.41
3646 3774 4.280174 GTGAGATTTATAGTACGCCCTCCA 59.720 45.833 0.00 0.00 0.00 3.86
3647 3775 4.523558 AGTGAGATTTATAGTACGCCCTCC 59.476 45.833 0.00 0.00 0.00 4.30
3648 3776 5.009811 ACAGTGAGATTTATAGTACGCCCTC 59.990 44.000 0.00 0.00 0.00 4.30
3649 3777 4.894114 ACAGTGAGATTTATAGTACGCCCT 59.106 41.667 0.00 0.00 0.00 5.19
3650 3778 5.197682 ACAGTGAGATTTATAGTACGCCC 57.802 43.478 0.00 0.00 0.00 6.13
3651 3779 8.813643 AAATACAGTGAGATTTATAGTACGCC 57.186 34.615 0.00 0.00 0.00 5.68
3685 3813 8.608844 ATTGAGTACATATTAGTGCTTTAGGC 57.391 34.615 0.00 0.00 34.49 3.93
4093 4221 2.489722 GTTGACCTTGCCTTTGAGATCC 59.510 50.000 0.00 0.00 0.00 3.36
4341 4472 3.054139 TGCTGAGCTATTGGTGAGGATTT 60.054 43.478 5.83 0.00 0.00 2.17
4343 4474 2.104451 CTGCTGAGCTATTGGTGAGGAT 59.896 50.000 5.83 0.00 0.00 3.24
4346 4477 2.168106 ACTCTGCTGAGCTATTGGTGAG 59.832 50.000 19.49 4.71 43.85 3.51
4354 4485 2.311463 GGGACATACTCTGCTGAGCTA 58.689 52.381 19.49 11.66 43.85 3.32
4359 4490 5.540337 TCTTATTAGGGGACATACTCTGCTG 59.460 44.000 0.00 0.00 0.00 4.41
4370 4501 8.379331 AGAATAGCTGAAATCTTATTAGGGGAC 58.621 37.037 0.00 0.00 0.00 4.46
4415 4546 9.477484 GTGAAGAAGTACAGAGATTTCTTTGTA 57.523 33.333 6.82 6.82 40.99 2.41
4416 4547 7.442666 GGTGAAGAAGTACAGAGATTTCTTTGT 59.557 37.037 8.58 8.58 42.84 2.83
4417 4548 7.442364 TGGTGAAGAAGTACAGAGATTTCTTTG 59.558 37.037 6.90 0.00 39.31 2.77
4421 4552 6.706270 TGTTGGTGAAGAAGTACAGAGATTTC 59.294 38.462 0.00 0.00 0.00 2.17
4422 4553 6.483640 GTGTTGGTGAAGAAGTACAGAGATTT 59.516 38.462 0.00 0.00 0.00 2.17
4423 4554 5.992217 GTGTTGGTGAAGAAGTACAGAGATT 59.008 40.000 0.00 0.00 0.00 2.40
4424 4555 5.305644 AGTGTTGGTGAAGAAGTACAGAGAT 59.694 40.000 0.00 0.00 0.00 2.75
4426 4557 4.950050 AGTGTTGGTGAAGAAGTACAGAG 58.050 43.478 0.00 0.00 0.00 3.35
4428 4559 6.455647 TCATAGTGTTGGTGAAGAAGTACAG 58.544 40.000 0.00 0.00 0.00 2.74
4429 4560 6.413783 TCATAGTGTTGGTGAAGAAGTACA 57.586 37.500 0.00 0.00 0.00 2.90
4430 4561 6.535508 GGATCATAGTGTTGGTGAAGAAGTAC 59.464 42.308 0.00 0.00 0.00 2.73
4431 4562 6.351881 GGGATCATAGTGTTGGTGAAGAAGTA 60.352 42.308 0.00 0.00 0.00 2.24
4432 4563 5.491982 GGATCATAGTGTTGGTGAAGAAGT 58.508 41.667 0.00 0.00 0.00 3.01
4433 4564 4.878397 GGGATCATAGTGTTGGTGAAGAAG 59.122 45.833 0.00 0.00 0.00 2.85
4434 4565 4.324254 GGGGATCATAGTGTTGGTGAAGAA 60.324 45.833 0.00 0.00 0.00 2.52
4435 4566 3.199946 GGGGATCATAGTGTTGGTGAAGA 59.800 47.826 0.00 0.00 0.00 2.87
4455 4586 0.179084 ATACCACTGACGAATGCGGG 60.179 55.000 0.00 0.00 43.17 6.13
4458 4589 4.003519 GTCAAATACCACTGACGAATGC 57.996 45.455 0.00 0.00 33.19 3.56
4568 4699 1.139058 AGCGATCAAGCGGGAAAGTAT 59.861 47.619 0.00 0.00 43.00 2.12
4569 4700 0.535335 AGCGATCAAGCGGGAAAGTA 59.465 50.000 0.00 0.00 43.00 2.24
4620 4751 2.701073 TCTCCTTCTCGTTGACGTTC 57.299 50.000 3.25 0.00 40.80 3.95
4698 4829 5.490213 CAGTATTTTCGGTATTTCGACAGC 58.510 41.667 0.00 0.00 39.01 4.40
4808 4939 9.860898 ACCAATAGCAAGCTTAAAAAGAATAAG 57.139 29.630 0.00 0.00 34.25 1.73
4820 4951 9.807649 CATAAAGAATTAACCAATAGCAAGCTT 57.192 29.630 0.00 0.00 0.00 3.74
4821 4952 7.922811 GCATAAAGAATTAACCAATAGCAAGCT 59.077 33.333 0.00 0.00 0.00 3.74
4831 4962 9.528489 AAAACCTAGAGCATAAAGAATTAACCA 57.472 29.630 0.00 0.00 0.00 3.67
4931 5062 1.956477 ACTAAACAGCTGGCACCTTTG 59.044 47.619 19.93 6.65 0.00 2.77
4997 5128 8.236084 AGTATAAAAACGCAATATAGCCTACG 57.764 34.615 0.00 0.00 0.00 3.51
5010 5141 7.298507 TCCACATCAGTAAGTATAAAAACGC 57.701 36.000 0.00 0.00 0.00 4.84
5018 5149 8.758829 TCTTGTTACATCCACATCAGTAAGTAT 58.241 33.333 0.00 0.00 0.00 2.12
5037 5168 9.444600 GGACATAGTTTTTCTACCATCTTGTTA 57.555 33.333 0.00 0.00 0.00 2.41
5040 5171 7.607991 ACTGGACATAGTTTTTCTACCATCTTG 59.392 37.037 0.00 0.00 0.00 3.02
5043 5174 7.065923 GGAACTGGACATAGTTTTTCTACCATC 59.934 40.741 0.00 0.00 40.78 3.51
5073 5204 5.649395 ACTGATTACACTTGCATTGCAGTAT 59.351 36.000 11.76 4.58 40.61 2.12
5082 5213 4.377021 AGAACGAACTGATTACACTTGCA 58.623 39.130 0.00 0.00 0.00 4.08
5083 5214 4.686554 AGAGAACGAACTGATTACACTTGC 59.313 41.667 0.00 0.00 0.00 4.01
5085 5216 5.844004 ACAGAGAACGAACTGATTACACTT 58.156 37.500 0.00 0.00 37.54 3.16
5087 5218 4.621886 GGACAGAGAACGAACTGATTACAC 59.378 45.833 0.00 0.00 37.54 2.90
5088 5219 4.523173 AGGACAGAGAACGAACTGATTACA 59.477 41.667 0.00 0.00 37.54 2.41
5089 5220 4.859798 CAGGACAGAGAACGAACTGATTAC 59.140 45.833 0.00 0.00 37.54 1.89
5091 5222 3.862642 GCAGGACAGAGAACGAACTGATT 60.863 47.826 0.00 0.00 37.54 2.57
5114 5251 0.589223 TTCGAAATTCGTGTGTGGCC 59.411 50.000 15.34 0.00 41.35 5.36
5133 5270 0.405585 ACATAAGCCCAGCAACCACT 59.594 50.000 0.00 0.00 0.00 4.00
5140 5277 3.113260 ACTTATCGACATAAGCCCAGC 57.887 47.619 5.83 0.00 43.89 4.85
5162 5299 8.609176 ACTTCGTGTGCATTATTACGATAATTT 58.391 29.630 11.73 0.00 43.89 1.82
5178 5315 2.097791 TGGGTTTGTAAACTTCGTGTGC 59.902 45.455 7.36 0.00 38.89 4.57
5223 5361 1.640428 TGATCGCATTCTGAACGGTC 58.360 50.000 6.70 6.70 37.45 4.79
5232 5370 4.621068 TCAGTTGGATTTGATCGCATTC 57.379 40.909 0.00 0.00 0.00 2.67
5237 5375 5.029650 TCGTTTTCAGTTGGATTTGATCG 57.970 39.130 0.00 0.00 0.00 3.69
5246 5384 4.069304 TGGATTACCTCGTTTTCAGTTGG 58.931 43.478 0.00 0.00 37.04 3.77
5247 5385 5.682943 TTGGATTACCTCGTTTTCAGTTG 57.317 39.130 0.00 0.00 37.04 3.16
5258 5396 3.515602 AGGCATCCATTGGATTACCTC 57.484 47.619 23.14 10.20 40.29 3.85
5259 5397 3.979501 AAGGCATCCATTGGATTACCT 57.020 42.857 23.14 23.14 43.86 3.08
5260 5398 5.574188 AGATAAGGCATCCATTGGATTACC 58.426 41.667 15.75 18.47 39.79 2.85
5262 5400 8.224025 TGTTAAGATAAGGCATCCATTGGATTA 58.776 33.333 15.75 7.15 39.79 1.75
5263 5401 7.068702 TGTTAAGATAAGGCATCCATTGGATT 58.931 34.615 15.75 5.05 39.79 3.01
5264 5402 6.613699 TGTTAAGATAAGGCATCCATTGGAT 58.386 36.000 12.62 12.62 44.21 3.41
5265 5403 6.012337 TGTTAAGATAAGGCATCCATTGGA 57.988 37.500 8.08 8.08 33.75 3.53
5266 5404 6.547141 TCTTGTTAAGATAAGGCATCCATTGG 59.453 38.462 0.00 0.00 33.75 3.16
5267 5405 7.572523 TCTTGTTAAGATAAGGCATCCATTG 57.427 36.000 0.00 0.00 33.75 2.82
5268 5406 9.512588 CTATCTTGTTAAGATAAGGCATCCATT 57.487 33.333 11.23 0.00 46.70 3.16
5269 5407 8.664079 ACTATCTTGTTAAGATAAGGCATCCAT 58.336 33.333 11.23 0.00 46.70 3.41
5270 5408 7.933577 CACTATCTTGTTAAGATAAGGCATCCA 59.066 37.037 11.23 0.00 46.70 3.41
5271 5409 7.095017 GCACTATCTTGTTAAGATAAGGCATCC 60.095 40.741 18.94 0.00 46.70 3.51
5272 5410 7.442364 TGCACTATCTTGTTAAGATAAGGCATC 59.558 37.037 20.83 8.16 46.70 3.91
5274 5412 6.649155 TGCACTATCTTGTTAAGATAAGGCA 58.351 36.000 20.83 20.83 46.70 4.75
5275 5413 6.203723 CCTGCACTATCTTGTTAAGATAAGGC 59.796 42.308 17.95 17.95 46.70 4.35
5276 5414 7.500992 TCCTGCACTATCTTGTTAAGATAAGG 58.499 38.462 14.94 14.94 46.70 2.69
5277 5415 9.202273 GATCCTGCACTATCTTGTTAAGATAAG 57.798 37.037 11.23 8.60 46.70 1.73
5278 5416 8.150945 GGATCCTGCACTATCTTGTTAAGATAA 58.849 37.037 3.84 0.00 46.70 1.75
5458 5596 3.347216 TCATCTTCTTGTTAAGGCCTGC 58.653 45.455 5.69 0.00 0.00 4.85
5459 5597 3.376546 GCTCATCTTCTTGTTAAGGCCTG 59.623 47.826 5.69 0.00 0.00 4.85
5464 5602 6.484977 GGATTAGGGCTCATCTTCTTGTTAAG 59.515 42.308 0.00 0.00 0.00 1.85
5517 5655 1.014352 ATCAACAAATCGCCGGCTAC 58.986 50.000 26.68 0.00 0.00 3.58
5536 10183 1.406180 TGCGGATCGGAGAAACGAATA 59.594 47.619 4.16 0.00 46.92 1.75
5598 10249 4.221422 ATGGGCGTACGCTGCGAT 62.221 61.111 36.24 21.53 41.60 4.58
5628 10298 2.731976 GTGAACGGTGAGCAGAGTTAAG 59.268 50.000 0.00 0.00 0.00 1.85
5654 10324 3.898509 CTCCAGGAGCGCTCTCGG 61.899 72.222 34.46 31.32 40.26 4.63
5731 10416 2.994995 ATCCAGACCGACGCCACA 60.995 61.111 0.00 0.00 0.00 4.17
5853 10538 2.805353 CGACACTCGCGAACCTGG 60.805 66.667 11.33 0.00 31.14 4.45
5903 10588 4.776322 CATGGAGGGCGTGGCGAA 62.776 66.667 0.00 0.00 0.00 4.70
5949 10634 2.033194 GGCGTTCTCGTCTTTGGGG 61.033 63.158 0.00 0.00 38.74 4.96
5957 10642 2.694829 AAACTCGCAGGCGTTCTCGT 62.695 55.000 13.83 2.17 40.74 4.18


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

AutoCloner maintained by Alex Coulton.