Multiple sequence alignment - TraesCS4D01G341000

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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 TraesCS4D01G341000 chr4D 100.000 6435 0 0 1 6435 497950340 497943906 0.000000e+00 11884.0
1 TraesCS4D01G341000 chr4B 89.173 3870 202 77 2343 6051 639850635 639846822 0.000000e+00 4625.0
2 TraesCS4D01G341000 chr4B 89.970 2323 122 43 1 2287 639853047 639850800 0.000000e+00 2896.0
3 TraesCS4D01G341000 chr4B 94.169 343 20 0 6093 6435 639846820 639846478 2.060000e-144 523.0
4 TraesCS4D01G341000 chr4B 89.328 253 20 2 975 1220 154978918 154978666 1.740000e-80 311.0
5 TraesCS4D01G341000 chr5A 91.889 2059 130 20 2343 4389 678272163 678270130 0.000000e+00 2843.0
6 TraesCS4D01G341000 chr5A 93.550 1752 68 26 608 2332 678274024 678272291 0.000000e+00 2567.0
7 TraesCS4D01G341000 chr5A 90.904 1836 94 30 4633 6435 678269816 678268021 0.000000e+00 2398.0
8 TraesCS4D01G341000 chr5A 90.365 602 42 6 1 593 678274933 678274339 0.000000e+00 776.0
9 TraesCS4D01G341000 chr5A 86.154 520 45 14 1000 1496 649696130 649695615 2.640000e-148 536.0
10 TraesCS4D01G341000 chr7A 87.814 517 49 10 988 1496 652373172 652373682 1.540000e-165 593.0
11 TraesCS4D01G341000 chr7A 85.768 534 45 16 988 1496 107669170 107668643 2.640000e-148 536.0
12 TraesCS4D01G341000 chr6B 85.038 528 60 12 988 1503 608273866 608274386 2.660000e-143 520.0
13 TraesCS4D01G341000 chr6D 86.405 331 32 5 995 1322 17253501 17253821 3.690000e-92 350.0
14 TraesCS4D01G341000 chrUn 83.529 340 36 13 1007 1330 205346675 205346340 3.770000e-77 300.0
15 TraesCS4D01G341000 chrUn 89.831 236 21 1 988 1220 471169951 471170186 3.770000e-77 300.0
16 TraesCS4D01G341000 chrUn 83.235 340 37 14 1007 1330 349933071 349933406 1.750000e-75 294.0
17 TraesCS4D01G341000 chr3B 83.529 340 37 11 1007 1330 35682657 35682993 3.770000e-77 300.0
18 TraesCS4D01G341000 chr5B 92.754 69 2 2 1429 1496 531180140 531180074 5.310000e-16 97.1


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 TraesCS4D01G341000 chr4D 497943906 497950340 6434 True 11884.000000 11884 100.000 1 6435 1 chr4D.!!$R1 6434
1 TraesCS4D01G341000 chr4B 639846478 639853047 6569 True 2681.333333 4625 91.104 1 6435 3 chr4B.!!$R2 6434
2 TraesCS4D01G341000 chr5A 678268021 678274933 6912 True 2146.000000 2843 91.677 1 6435 4 chr5A.!!$R2 6434
3 TraesCS4D01G341000 chr5A 649695615 649696130 515 True 536.000000 536 86.154 1000 1496 1 chr5A.!!$R1 496
4 TraesCS4D01G341000 chr7A 652373172 652373682 510 False 593.000000 593 87.814 988 1496 1 chr7A.!!$F1 508
5 TraesCS4D01G341000 chr7A 107668643 107669170 527 True 536.000000 536 85.768 988 1496 1 chr7A.!!$R1 508
6 TraesCS4D01G341000 chr6B 608273866 608274386 520 False 520.000000 520 85.038 988 1503 1 chr6B.!!$F1 515

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
358 361 1.001293 TGATCCATGCTGACCGATAGC 59.999 52.381 0.0 0.0 41.49 2.97 F
2327 2745 0.327000 ACCCAGCCTCTTATGCCTCT 60.327 55.000 0.0 0.0 0.00 3.69 F
2367 2907 1.215647 CGTCCCACTTCTTCCTCCG 59.784 63.158 0.0 0.0 0.00 4.63 F
3814 4410 0.167470 CACAGCGACCATCTGCAAAG 59.833 55.000 0.0 0.0 35.04 2.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2335 2753 0.396811 GGGACGGGGGATCACATAAG 59.603 60.000 0.0 0.0 0.00 1.73 R
3276 3847 1.666189 GATGCTCAAGTAAGAACCCGC 59.334 52.381 0.0 0.0 0.00 6.13 R
4119 4719 1.765074 CCCCGTTCCTTCCTCCAAA 59.235 57.895 0.0 0.0 0.00 3.28 R
5750 6569 0.864797 GGTCATTCGAGACGCCGTAC 60.865 60.000 0.0 0.0 39.42 3.67 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
90 93 8.045176 ACTATTTAAAGCCATCTCAAAGTCAC 57.955 34.615 0.00 0.00 0.00 3.67
124 127 5.551760 AAAAGCGGATTACACTCTTGATG 57.448 39.130 0.00 0.00 0.00 3.07
167 170 8.030106 AGTAATCTTTTACCTCAGAGAAGTTCG 58.970 37.037 0.00 0.00 38.81 3.95
170 173 6.812998 TCTTTTACCTCAGAGAAGTTCGAAA 58.187 36.000 0.00 0.00 0.00 3.46
172 175 7.767198 TCTTTTACCTCAGAGAAGTTCGAAAAA 59.233 33.333 0.00 0.00 0.00 1.94
204 207 6.140110 GCATGCTTTCTAGAACGTTGTTTAA 58.860 36.000 11.37 0.00 0.00 1.52
358 361 1.001293 TGATCCATGCTGACCGATAGC 59.999 52.381 0.00 0.00 41.49 2.97
360 363 1.995376 TCCATGCTGACCGATAGCTA 58.005 50.000 0.00 0.00 41.66 3.32
365 368 3.371102 TGCTGACCGATAGCTACAATC 57.629 47.619 0.00 0.00 41.66 2.67
499 506 1.689273 CTCCTTCCCCACCTTCTATCG 59.311 57.143 0.00 0.00 0.00 2.92
500 507 1.289830 TCCTTCCCCACCTTCTATCGA 59.710 52.381 0.00 0.00 0.00 3.59
501 508 2.090719 TCCTTCCCCACCTTCTATCGAT 60.091 50.000 2.16 2.16 0.00 3.59
502 509 2.300437 CCTTCCCCACCTTCTATCGATC 59.700 54.545 0.00 0.00 0.00 3.69
528 535 6.397272 CATCTCTCTTACCAGCCTTATCATC 58.603 44.000 0.00 0.00 0.00 2.92
540 547 4.103311 AGCCTTATCATCACCCTACCTTTC 59.897 45.833 0.00 0.00 0.00 2.62
604 625 2.170397 TCTCTCTCTCTCTCATCGTGCT 59.830 50.000 0.00 0.00 0.00 4.40
794 1109 5.957771 TGCTAACCAACTCTCCTCATTAT 57.042 39.130 0.00 0.00 0.00 1.28
806 1121 4.016105 TCTCCTCATTATATCCCCCTCTCC 60.016 50.000 0.00 0.00 0.00 3.71
807 1122 3.939182 TCCTCATTATATCCCCCTCTCCT 59.061 47.826 0.00 0.00 0.00 3.69
826 1142 2.091055 CCTCTCCCTCCTCTCCATGTAA 60.091 54.545 0.00 0.00 0.00 2.41
1005 1325 3.008240 GATCGATCGGCGCATGCAG 62.008 63.158 19.57 11.69 45.35 4.41
1285 1609 1.311747 GGCCTCCTCCACTCCTACT 59.688 63.158 0.00 0.00 0.00 2.57
1372 1701 3.446516 CGCTACCTACCTACCACTTCTTT 59.553 47.826 0.00 0.00 0.00 2.52
1373 1702 4.439837 CGCTACCTACCTACCACTTCTTTC 60.440 50.000 0.00 0.00 0.00 2.62
1380 1709 2.169769 CCTACCACTTCTTTCCGCCATA 59.830 50.000 0.00 0.00 0.00 2.74
1390 1726 1.730451 TTCCGCCATAGATCGCGTCA 61.730 55.000 5.77 0.00 46.83 4.35
1667 2055 9.434275 TGTCTGTATTATATTCCTCTCTTTCCA 57.566 33.333 0.00 0.00 0.00 3.53
1698 2086 9.198837 TGTTTCACTTTTGGACTAAAAAGAAAC 57.801 29.630 26.69 26.69 46.96 2.78
1714 2102 4.052159 AGAAACTGCTATCATCAGGTCG 57.948 45.455 0.00 0.00 35.94 4.79
1802 2192 8.912988 TGTCATGTCTCAAAGTAAAAGGAAAAT 58.087 29.630 0.00 0.00 0.00 1.82
1807 2197 9.364989 TGTCTCAAAGTAAAAGGAAAATTGTTG 57.635 29.630 0.00 0.00 0.00 3.33
1808 2198 9.366216 GTCTCAAAGTAAAAGGAAAATTGTTGT 57.634 29.630 0.00 0.00 0.00 3.32
1809 2199 9.936759 TCTCAAAGTAAAAGGAAAATTGTTGTT 57.063 25.926 0.00 0.00 0.00 2.83
1810 2200 9.971744 CTCAAAGTAAAAGGAAAATTGTTGTTG 57.028 29.630 0.00 0.00 0.00 3.33
1811 2201 9.495572 TCAAAGTAAAAGGAAAATTGTTGTTGT 57.504 25.926 0.00 0.00 0.00 3.32
1827 2217 5.160641 GTTGTTGTTGTTGTTGTCATGTCT 58.839 37.500 0.00 0.00 0.00 3.41
1978 2394 6.953101 TCACTATGAAATAAGGTTGCAGGTA 58.047 36.000 0.00 0.00 0.00 3.08
2000 2416 1.409661 GGGAGAATACATTTGGGCCGT 60.410 52.381 0.00 0.00 0.00 5.68
2007 2423 1.931635 ACATTTGGGCCGTGGTTTAT 58.068 45.000 0.00 0.00 0.00 1.40
2035 2451 2.005971 GGTTTGCACCCTAGTACGAG 57.994 55.000 0.00 0.00 37.03 4.18
2103 2519 7.292356 ACCCTAACAAATTCCAAATTCCTCTTT 59.708 33.333 0.00 0.00 0.00 2.52
2191 2607 6.575162 AAAGTTAACAAGATGGACATCACC 57.425 37.500 14.16 0.00 40.22 4.02
2206 2622 2.470983 TCACCGAAGCATGATGTTCA 57.529 45.000 0.00 0.00 0.00 3.18
2327 2745 0.327000 ACCCAGCCTCTTATGCCTCT 60.327 55.000 0.00 0.00 0.00 3.69
2332 2750 3.072944 CAGCCTCTTATGCCTCTTATGC 58.927 50.000 0.00 0.00 0.00 3.14
2334 2752 2.039613 GCCTCTTATGCCTCTTATGCCT 59.960 50.000 0.00 0.00 0.00 4.75
2335 2753 3.867984 GCCTCTTATGCCTCTTATGCCTC 60.868 52.174 0.00 0.00 0.00 4.70
2339 2757 6.070309 CCTCTTATGCCTCTTATGCCTCTTAT 60.070 42.308 0.00 0.00 0.00 1.73
2340 2758 6.705302 TCTTATGCCTCTTATGCCTCTTATG 58.295 40.000 0.00 0.00 0.00 1.90
2367 2907 1.215647 CGTCCCACTTCTTCCTCCG 59.784 63.158 0.00 0.00 0.00 4.63
2398 2938 1.553417 CCTCTCTGGAGAACCCCTTCA 60.553 57.143 1.86 0.00 41.86 3.02
2407 2947 2.578480 GAGAACCCCTTCATCCTCCTTT 59.422 50.000 0.00 0.00 0.00 3.11
2411 2951 1.407437 CCCCTTCATCCTCCTTTCACG 60.407 57.143 0.00 0.00 0.00 4.35
2591 3136 7.338196 TGGAAGACTTCAGTAACAATGTGAAAA 59.662 33.333 16.85 0.00 30.00 2.29
2622 3168 1.379176 CCCTCTCTCACGCTCCTCA 60.379 63.158 0.00 0.00 0.00 3.86
2647 3193 4.793201 AGGTAAGAAGGGGCAATATTGTC 58.207 43.478 16.61 14.31 0.00 3.18
2659 3205 5.284079 GGCAATATTGTCCATGCTGTTTAG 58.716 41.667 16.61 0.00 38.79 1.85
2714 3268 5.416271 TTTTGCTAGAGACCGGAATAACT 57.584 39.130 9.46 2.43 0.00 2.24
2715 3269 4.650754 TTGCTAGAGACCGGAATAACTC 57.349 45.455 9.46 8.73 0.00 3.01
2724 3278 3.481112 CCGGAATAACTCGGTTTTTGG 57.519 47.619 0.00 0.00 41.23 3.28
2729 3283 6.127952 CCGGAATAACTCGGTTTTTGGAATAA 60.128 38.462 0.00 0.00 41.23 1.40
2778 3332 5.046231 GGTTATTTCCACCCCAAAAGCATTA 60.046 40.000 0.00 0.00 0.00 1.90
2838 3392 3.807553 AGGAAAGTTTGCCAAAACCATG 58.192 40.909 3.17 0.00 45.75 3.66
2875 3433 4.447138 TTTTTCTTTCTGCTCCCTACCA 57.553 40.909 0.00 0.00 0.00 3.25
2889 3447 3.165071 CCCTACCAGAAAGGCATGTTTT 58.835 45.455 0.00 0.00 43.14 2.43
2949 3508 1.272648 CCCTCCATTTTGCTCCTTCCA 60.273 52.381 0.00 0.00 0.00 3.53
3034 3593 7.119846 GGAGAAACTGTGTATTCAGCTTACAAT 59.880 37.037 0.00 0.00 38.84 2.71
3051 3610 6.821665 GCTTACAATGTAGAAATAGACACCCA 59.178 38.462 0.00 0.00 0.00 4.51
3052 3611 7.335924 GCTTACAATGTAGAAATAGACACCCAA 59.664 37.037 0.00 0.00 0.00 4.12
3053 3612 9.226606 CTTACAATGTAGAAATAGACACCCAAA 57.773 33.333 0.00 0.00 0.00 3.28
3054 3613 9.747898 TTACAATGTAGAAATAGACACCCAAAT 57.252 29.630 0.00 0.00 0.00 2.32
3055 3614 8.650143 ACAATGTAGAAATAGACACCCAAATT 57.350 30.769 0.00 0.00 0.00 1.82
3056 3615 8.522830 ACAATGTAGAAATAGACACCCAAATTG 58.477 33.333 0.00 0.00 0.00 2.32
3057 3616 7.645058 ATGTAGAAATAGACACCCAAATTGG 57.355 36.000 4.74 4.74 37.25 3.16
3058 3617 5.417580 TGTAGAAATAGACACCCAAATTGGC 59.582 40.000 6.48 0.00 35.79 4.52
3082 3641 7.387673 GGCAAATTTAAGCAAGGTGAACTTAAT 59.612 33.333 3.25 0.00 37.29 1.40
3096 3655 6.541278 GGTGAACTTAATAACTATGGGTGGTC 59.459 42.308 0.00 0.00 0.00 4.02
3116 3675 4.224433 GTCGAAATGTACGTTCACTCTCA 58.776 43.478 0.00 0.00 0.00 3.27
3147 3714 5.023533 TGAGCTCAACCATATACTCCAAC 57.976 43.478 15.67 0.00 0.00 3.77
3220 3791 6.972328 TGAGCAAACACAAAAGTGAAGTAATC 59.028 34.615 2.22 0.00 0.00 1.75
3221 3792 5.971202 AGCAAACACAAAAGTGAAGTAATCG 59.029 36.000 2.22 0.00 0.00 3.34
3248 3819 3.686726 GCTCAAAAGACTGTCGATGGAAT 59.313 43.478 1.52 0.00 0.00 3.01
3253 3824 4.657436 AAGACTGTCGATGGAATAGGTC 57.343 45.455 1.52 0.00 0.00 3.85
3276 3847 3.194542 ACTCTTGTCTAACTAGCTGCCTG 59.805 47.826 0.00 0.00 0.00 4.85
3277 3848 2.093973 TCTTGTCTAACTAGCTGCCTGC 60.094 50.000 0.00 0.00 43.29 4.85
3293 3864 1.079503 CTGCGGGTTCTTACTTGAGC 58.920 55.000 0.00 0.00 0.00 4.26
3318 3889 3.693085 CACATGATCCTGGAGACAAAAGG 59.307 47.826 0.00 0.81 42.06 3.11
3319 3890 3.331889 ACATGATCCTGGAGACAAAAGGT 59.668 43.478 0.00 1.35 42.06 3.50
3378 3949 3.745975 TCGCGCCCTTATTATGAGAAATG 59.254 43.478 0.00 0.00 0.00 2.32
3432 4003 0.661483 GCTCTTTTGACAAGTGCGGC 60.661 55.000 0.00 0.00 0.00 6.53
3495 4069 0.447801 CGCTGAAATGGCTGTACACC 59.552 55.000 0.00 0.00 0.00 4.16
3557 4131 8.392612 GTTTGACAAAGTTTTGCTAGTACTACA 58.607 33.333 0.00 0.00 41.79 2.74
3571 4149 9.211485 TGCTAGTACTACATTTTGTTTCTAACC 57.789 33.333 0.00 0.00 0.00 2.85
3586 4164 1.272490 CTAACCCAAGTCACGCTCAGA 59.728 52.381 0.00 0.00 0.00 3.27
3667 4247 2.531522 AAAACCTGAAGTTGCATGGC 57.468 45.000 0.00 0.00 39.19 4.40
3678 4258 1.186267 TTGCATGGCAAGCATCCACA 61.186 50.000 18.90 0.00 43.99 4.17
3679 4259 0.973496 TGCATGGCAAGCATCCACAT 60.973 50.000 14.12 0.00 37.02 3.21
3680 4260 0.529773 GCATGGCAAGCATCCACATG 60.530 55.000 10.23 0.00 41.26 3.21
3707 4295 1.550524 TGCATGTGTCTCTACTCCACC 59.449 52.381 0.00 0.00 0.00 4.61
3713 4301 3.511540 TGTGTCTCTACTCCACCTGATTG 59.488 47.826 0.00 0.00 0.00 2.67
3743 4335 1.476891 TGAGTAGTTTCCTGGCTAGCG 59.523 52.381 9.00 0.00 0.00 4.26
3744 4336 1.477295 GAGTAGTTTCCTGGCTAGCGT 59.523 52.381 9.00 0.00 0.00 5.07
3814 4410 0.167470 CACAGCGACCATCTGCAAAG 59.833 55.000 0.00 0.00 35.04 2.77
3848 4444 6.563939 GCGTATAAGATCATGCGTCAAATCAA 60.564 38.462 0.00 0.00 36.54 2.57
4089 4689 8.454106 CCTATCTGAGTTTCATTGTTAACCTTG 58.546 37.037 2.48 0.89 0.00 3.61
4119 4719 1.485124 TGTATGGATCAGGTGCGTCT 58.515 50.000 0.00 0.00 0.00 4.18
4131 4731 0.034896 GTGCGTCTTTGGAGGAAGGA 59.965 55.000 0.00 0.00 0.00 3.36
4218 4818 3.243873 TGGATATGAGCTCGAATGGACAC 60.244 47.826 9.64 0.00 0.00 3.67
4257 4857 1.152504 TCTGGTACCCACGGACACA 60.153 57.895 10.07 0.00 0.00 3.72
4287 4887 0.547471 TCATGGAGAGGGTCAGGCAA 60.547 55.000 0.00 0.00 0.00 4.52
4290 4890 0.473694 TGGAGAGGGTCAGGCAAGAA 60.474 55.000 0.00 0.00 0.00 2.52
4318 4918 7.437862 TCAAAATTGAACTCAAACAGGTATTGC 59.562 33.333 0.00 0.00 39.55 3.56
4326 4926 6.785191 ACTCAAACAGGTATTGCGAATTATG 58.215 36.000 0.00 0.00 0.00 1.90
4327 4927 6.374333 ACTCAAACAGGTATTGCGAATTATGT 59.626 34.615 0.00 0.00 0.00 2.29
4329 4929 7.247728 TCAAACAGGTATTGCGAATTATGTTC 58.752 34.615 0.00 0.00 0.00 3.18
4331 4931 7.391148 AACAGGTATTGCGAATTATGTTCTT 57.609 32.000 0.00 0.00 0.00 2.52
4332 4932 6.785191 ACAGGTATTGCGAATTATGTTCTTG 58.215 36.000 0.00 0.00 0.00 3.02
4333 4933 6.597672 ACAGGTATTGCGAATTATGTTCTTGA 59.402 34.615 0.00 0.00 0.00 3.02
4334 4934 7.120579 ACAGGTATTGCGAATTATGTTCTTGAA 59.879 33.333 0.00 0.00 0.00 2.69
4335 4935 7.641411 CAGGTATTGCGAATTATGTTCTTGAAG 59.359 37.037 0.00 0.00 0.00 3.02
4337 4937 7.640240 GGTATTGCGAATTATGTTCTTGAAGAC 59.360 37.037 0.00 0.00 0.00 3.01
4338 4938 6.801539 TTGCGAATTATGTTCTTGAAGACT 57.198 33.333 0.00 0.00 0.00 3.24
4339 4939 6.169419 TGCGAATTATGTTCTTGAAGACTG 57.831 37.500 0.00 0.00 0.00 3.51
4341 4941 6.426633 TGCGAATTATGTTCTTGAAGACTGAA 59.573 34.615 0.00 0.00 0.00 3.02
4357 4995 9.033481 TGAAGACTGAATTTGCTACAAAATTTG 57.967 29.630 3.89 3.89 39.31 2.32
4358 4996 9.248291 GAAGACTGAATTTGCTACAAAATTTGA 57.752 29.630 13.19 0.00 39.31 2.69
4370 5008 9.347934 TGCTACAAAATTTGAATGTTATTACCG 57.652 29.630 13.19 0.00 0.00 4.02
4392 5120 5.220931 CCGCCTTCCAAAAATAGATCTCTTG 60.221 44.000 0.00 0.00 0.00 3.02
4453 5185 9.730705 TTTGGATATGTGCAAAATTATTTGGAA 57.269 25.926 6.67 0.00 46.51 3.53
4496 5250 9.158233 CTGGCATCAAATTTGTCTTGAAAATAT 57.842 29.630 17.47 0.00 36.43 1.28
4533 5287 8.185505 TGACCATTTAAAACAGTACTCAAACAC 58.814 33.333 0.00 0.00 0.00 3.32
4550 5304 9.449719 ACTCAAACACTCATATAAAAGTAAGGG 57.550 33.333 0.00 0.00 0.00 3.95
4551 5305 8.276252 TCAAACACTCATATAAAAGTAAGGGC 57.724 34.615 0.00 0.00 0.00 5.19
4552 5306 7.338449 TCAAACACTCATATAAAAGTAAGGGCC 59.662 37.037 0.00 0.00 0.00 5.80
4571 5328 4.097892 GGGCCAAAATTATGTACTGGACAG 59.902 45.833 4.39 0.00 42.79 3.51
4576 5333 6.267817 CAAAATTATGTACTGGACAGCATGG 58.732 40.000 0.00 0.00 42.79 3.66
4592 5349 4.569162 CAGCATGGCAAAACCTAAATCATG 59.431 41.667 0.00 0.00 40.22 3.07
4593 5350 3.872771 GCATGGCAAAACCTAAATCATGG 59.127 43.478 0.00 0.00 40.22 3.66
4597 5354 4.021544 TGGCAAAACCTAAATCATGGTGAC 60.022 41.667 0.00 0.00 40.22 3.67
4598 5355 4.220602 GGCAAAACCTAAATCATGGTGACT 59.779 41.667 0.00 0.00 36.57 3.41
4599 5356 5.163513 GCAAAACCTAAATCATGGTGACTG 58.836 41.667 0.00 0.00 36.57 3.51
4600 5357 5.278957 GCAAAACCTAAATCATGGTGACTGT 60.279 40.000 0.00 0.00 36.57 3.55
4601 5358 6.381801 CAAAACCTAAATCATGGTGACTGTC 58.618 40.000 0.00 0.00 36.57 3.51
4602 5359 5.505181 AACCTAAATCATGGTGACTGTCT 57.495 39.130 9.51 0.00 36.57 3.41
4603 5360 5.505181 ACCTAAATCATGGTGACTGTCTT 57.495 39.130 9.51 0.00 34.90 3.01
4631 5388 1.404391 GAGTGCCATGGAAGCTTGATG 59.596 52.381 18.40 5.86 0.00 3.07
4632 5389 1.005097 AGTGCCATGGAAGCTTGATGA 59.995 47.619 18.40 0.00 0.00 2.92
4638 5395 4.521639 GCCATGGAAGCTTGATGATATCAA 59.478 41.667 18.40 4.39 46.30 2.57
4941 5717 3.315191 ACCAAAACTTGTTCCATCAGACG 59.685 43.478 0.00 0.00 0.00 4.18
4944 5720 0.321653 ACTTGTTCCATCAGACGGCC 60.322 55.000 0.00 0.00 0.00 6.13
4995 5771 1.351017 TCCCATTCCTTGTCTGGTGTC 59.649 52.381 0.00 0.00 0.00 3.67
5046 5822 8.523523 TCTCAATTGCATGATGTTTACTTTTG 57.476 30.769 0.00 0.00 0.00 2.44
5050 5826 9.719279 CAATTGCATGATGTTTACTTTTGTTTT 57.281 25.926 0.00 0.00 0.00 2.43
5051 5827 9.719279 AATTGCATGATGTTTACTTTTGTTTTG 57.281 25.926 0.00 0.00 0.00 2.44
5368 6145 2.223900 TGATCCATCAGTTAGAGCGCAG 60.224 50.000 11.47 0.00 32.11 5.18
5369 6146 5.897027 TGATCCATCAGTTAGAGCGCAGC 62.897 52.174 11.47 0.00 43.05 5.25
5641 6447 3.311106 CGTTGCAATTGTTGAGCTGATT 58.689 40.909 0.59 0.00 0.00 2.57
5695 6509 5.831702 TTTTTGTTGTGGGTACATACGTT 57.168 34.783 0.00 0.00 36.53 3.99
5697 6511 5.421212 TTTGTTGTGGGTACATACGTTTC 57.579 39.130 0.00 0.00 36.53 2.78
5699 6513 3.181457 TGTTGTGGGTACATACGTTTCCA 60.181 43.478 0.00 0.00 36.53 3.53
5701 6515 5.177326 GTTGTGGGTACATACGTTTCCATA 58.823 41.667 0.00 0.00 36.53 2.74
5750 6569 1.243342 TTGAGCGTTCCATGGCCTTG 61.243 55.000 6.96 11.68 0.00 3.61
5774 6593 0.095417 GCGTCTCGAATGACCAAAGC 59.905 55.000 0.00 0.00 33.70 3.51
5785 6604 5.563475 CGAATGACCAAAGCAAAAGAGATGT 60.563 40.000 0.00 0.00 0.00 3.06
5838 6657 0.173481 GTGCTGTCGTCCATAGCTGA 59.827 55.000 0.00 0.00 39.94 4.26
5894 6715 3.131240 GGTGATAACATTCAACGGTGC 57.869 47.619 0.00 0.00 0.00 5.01
5914 6735 1.340465 CGTACGCGTCTTGATGCAC 59.660 57.895 18.63 4.42 0.00 4.57
5991 6812 1.726791 CTTGAATTGGACGACGACTGG 59.273 52.381 0.00 0.00 0.00 4.00
6053 6910 0.035458 AGTCCCAGACTTTTCCAGCG 59.965 55.000 0.00 0.00 40.28 5.18
6054 6911 0.034896 GTCCCAGACTTTTCCAGCGA 59.965 55.000 0.00 0.00 0.00 4.93
6055 6912 0.762418 TCCCAGACTTTTCCAGCGAA 59.238 50.000 0.00 0.00 0.00 4.70
6056 6913 1.351017 TCCCAGACTTTTCCAGCGAAT 59.649 47.619 0.00 0.00 0.00 3.34
6057 6914 2.569853 TCCCAGACTTTTCCAGCGAATA 59.430 45.455 0.00 0.00 0.00 1.75
6058 6915 3.008594 TCCCAGACTTTTCCAGCGAATAA 59.991 43.478 0.00 0.00 0.00 1.40
6059 6916 3.127030 CCCAGACTTTTCCAGCGAATAAC 59.873 47.826 0.00 0.00 0.00 1.89
6060 6917 3.181520 CCAGACTTTTCCAGCGAATAACG 60.182 47.826 0.00 0.00 45.66 3.18
6061 6918 3.678072 CAGACTTTTCCAGCGAATAACGA 59.322 43.478 0.00 0.00 45.77 3.85
6062 6919 4.151689 CAGACTTTTCCAGCGAATAACGAA 59.848 41.667 0.00 0.00 45.77 3.85
6063 6920 4.389077 AGACTTTTCCAGCGAATAACGAAG 59.611 41.667 0.00 0.00 45.77 3.79
6064 6921 3.120304 ACTTTTCCAGCGAATAACGAAGC 60.120 43.478 0.00 0.00 45.77 3.86
6065 6922 1.365699 TTCCAGCGAATAACGAAGCC 58.634 50.000 0.00 0.00 45.77 4.35
6066 6923 0.535335 TCCAGCGAATAACGAAGCCT 59.465 50.000 0.00 0.00 45.77 4.58
6067 6924 1.066430 TCCAGCGAATAACGAAGCCTT 60.066 47.619 0.00 0.00 45.77 4.35
6068 6925 1.327764 CCAGCGAATAACGAAGCCTTC 59.672 52.381 0.00 0.00 45.77 3.46
6069 6926 2.271800 CAGCGAATAACGAAGCCTTCT 58.728 47.619 2.49 0.00 45.77 2.85
6070 6927 2.673368 CAGCGAATAACGAAGCCTTCTT 59.327 45.455 2.49 0.00 45.77 2.52
6071 6928 3.125316 CAGCGAATAACGAAGCCTTCTTT 59.875 43.478 2.49 2.02 45.77 2.52
6072 6929 3.371285 AGCGAATAACGAAGCCTTCTTTC 59.629 43.478 2.49 0.61 45.77 2.62
6073 6930 3.371285 GCGAATAACGAAGCCTTCTTTCT 59.629 43.478 2.49 0.00 45.77 2.52
6074 6931 4.565564 GCGAATAACGAAGCCTTCTTTCTA 59.434 41.667 2.49 0.00 45.77 2.10
6075 6932 5.234543 GCGAATAACGAAGCCTTCTTTCTAT 59.765 40.000 2.49 0.00 45.77 1.98
6076 6933 6.420008 GCGAATAACGAAGCCTTCTTTCTATA 59.580 38.462 2.49 0.00 45.77 1.31
6077 6934 7.042925 GCGAATAACGAAGCCTTCTTTCTATAA 60.043 37.037 2.49 0.00 45.77 0.98
6078 6935 8.480853 CGAATAACGAAGCCTTCTTTCTATAAG 58.519 37.037 2.49 0.00 45.77 1.73
6079 6936 8.664211 AATAACGAAGCCTTCTTTCTATAAGG 57.336 34.615 2.49 0.00 44.32 2.69
6080 6937 5.678955 ACGAAGCCTTCTTTCTATAAGGT 57.321 39.130 2.49 0.00 43.55 3.50
6081 6938 5.662456 ACGAAGCCTTCTTTCTATAAGGTC 58.338 41.667 2.49 0.00 43.55 3.85
6082 6939 5.422650 ACGAAGCCTTCTTTCTATAAGGTCT 59.577 40.000 2.49 0.00 43.55 3.85
6083 6940 5.980715 CGAAGCCTTCTTTCTATAAGGTCTC 59.019 44.000 2.49 0.00 43.55 3.36
6084 6941 6.405953 CGAAGCCTTCTTTCTATAAGGTCTCA 60.406 42.308 2.49 0.00 43.55 3.27
6085 6942 6.875972 AGCCTTCTTTCTATAAGGTCTCAA 57.124 37.500 0.00 0.00 43.55 3.02
6086 6943 6.645306 AGCCTTCTTTCTATAAGGTCTCAAC 58.355 40.000 0.00 0.00 43.55 3.18
6087 6944 5.818336 GCCTTCTTTCTATAAGGTCTCAACC 59.182 44.000 0.00 0.00 43.55 3.77
6112 6969 7.011189 CACATACACATATATGTTGTGCATCG 58.989 38.462 25.23 12.66 46.65 3.84
6126 6983 1.336240 TGCATCGTCATCATCTAGGCG 60.336 52.381 0.00 0.00 0.00 5.52
6140 6997 1.748329 TAGGCGGCTATGGTGCAGAG 61.748 60.000 15.70 0.00 34.04 3.35
6176 7033 1.271163 TGTAGGCCTTACTGGTGCAAC 60.271 52.381 12.58 0.00 38.35 4.17
6196 7053 1.597854 GCCAAAAGCCAAAGCCCAC 60.598 57.895 0.00 0.00 41.25 4.61
6200 7057 2.026945 AAAAGCCAAAGCCCACGGTG 62.027 55.000 0.00 0.00 41.25 4.94
6214 7071 3.072476 CCCACGGTGAAATATCAGGGTAT 59.928 47.826 10.28 0.00 35.88 2.73
6222 7079 6.127026 GGTGAAATATCAGGGTATAGCCTAGG 60.127 46.154 22.80 12.10 35.88 3.02
6224 7081 7.618512 GTGAAATATCAGGGTATAGCCTAGGTA 59.381 40.741 22.80 16.77 35.88 3.08
6298 7155 3.557577 TCTGCACCAACAAATTCATCG 57.442 42.857 0.00 0.00 0.00 3.84
6310 7167 7.693951 CCAACAAATTCATCGTCAGATTTAGAC 59.306 37.037 0.00 0.00 34.23 2.59
6351 7208 1.459592 GCACAGCTTAGTAACACACCG 59.540 52.381 0.00 0.00 0.00 4.94
6429 7286 2.249139 ACACCCAGAGGAACTACAGAC 58.751 52.381 0.00 0.00 41.55 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 5.949354 ACCAAGAAAATATCGACCCATTTGA 59.051 36.000 0.00 0.00 0.00 2.69
107 110 3.525537 ACAGCATCAAGAGTGTAATCCG 58.474 45.455 0.00 0.00 0.00 4.18
124 127 9.476202 AAAGATTACTAAATTTGGTGAAACAGC 57.524 29.630 16.66 0.00 39.98 4.40
170 173 7.538678 CGTTCTAGAAAGCATGCAGTAAATTTT 59.461 33.333 21.98 9.54 0.00 1.82
172 175 6.149474 ACGTTCTAGAAAGCATGCAGTAAATT 59.851 34.615 21.98 0.36 0.00 1.82
173 176 5.643777 ACGTTCTAGAAAGCATGCAGTAAAT 59.356 36.000 21.98 2.90 0.00 1.40
332 335 1.674441 GGTCAGCATGGATCATGTGTG 59.326 52.381 9.28 7.58 43.10 3.82
499 506 2.301583 GGCTGGTAAGAGAGATGGGATC 59.698 54.545 0.00 0.00 0.00 3.36
500 507 2.090267 AGGCTGGTAAGAGAGATGGGAT 60.090 50.000 0.00 0.00 0.00 3.85
501 508 1.292242 AGGCTGGTAAGAGAGATGGGA 59.708 52.381 0.00 0.00 0.00 4.37
502 509 1.799933 AGGCTGGTAAGAGAGATGGG 58.200 55.000 0.00 0.00 0.00 4.00
528 535 1.210538 GTAGGGGGAAAGGTAGGGTG 58.789 60.000 0.00 0.00 0.00 4.61
540 547 1.002242 AGAGAGAGGAGGGTAGGGGG 61.002 65.000 0.00 0.00 0.00 5.40
622 933 1.180029 AGCATGCAAGGACACCAATC 58.820 50.000 21.98 0.00 0.00 2.67
675 990 1.520787 CGCCCGTATCACCTCAACC 60.521 63.158 0.00 0.00 0.00 3.77
794 1109 0.026415 AGGGAGAGGAGAGGGGGATA 60.026 60.000 0.00 0.00 0.00 2.59
806 1121 3.320610 TTACATGGAGAGGAGGGAGAG 57.679 52.381 0.00 0.00 0.00 3.20
807 1122 3.647636 CTTTACATGGAGAGGAGGGAGA 58.352 50.000 0.00 0.00 0.00 3.71
889 1205 1.068055 GTGGCGTCGGGTATGTATAGG 60.068 57.143 0.00 0.00 0.00 2.57
1380 1709 2.879002 AGATGAACATGACGCGATCT 57.121 45.000 15.93 4.77 0.00 2.75
1390 1726 2.159476 GCACGCACATGAAGATGAACAT 60.159 45.455 0.00 0.00 33.36 2.71
1580 1965 6.056090 AGAAGAGGATCCTTTTTACCAGTC 57.944 41.667 17.42 2.70 33.66 3.51
1596 1982 3.955524 TCCAGGTAGGTAGAGAAGAGG 57.044 52.381 0.00 0.00 39.02 3.69
1667 2055 7.654022 TTTAGTCCAAAAGTGAAACAGGAAT 57.346 32.000 0.00 0.00 41.43 3.01
1670 2058 7.543756 TCTTTTTAGTCCAAAAGTGAAACAGG 58.456 34.615 5.96 0.00 42.26 4.00
1698 2086 1.068281 AGCACGACCTGATGATAGCAG 59.932 52.381 0.00 0.00 0.00 4.24
1714 2102 6.151975 GTGTATAAAATTGCACCAAAGCAC 57.848 37.500 0.00 0.00 45.61 4.40
1768 2157 6.604735 ACTTTGAGACATGACAACAACTAC 57.395 37.500 0.00 0.00 0.00 2.73
1802 2192 5.292765 ACATGACAACAACAACAACAACAA 58.707 33.333 0.00 0.00 0.00 2.83
1806 2196 5.182950 AGAAGACATGACAACAACAACAACA 59.817 36.000 0.00 0.00 0.00 3.33
1807 2197 5.640732 AGAAGACATGACAACAACAACAAC 58.359 37.500 0.00 0.00 0.00 3.32
1808 2198 5.895636 AGAAGACATGACAACAACAACAA 57.104 34.783 0.00 0.00 0.00 2.83
1809 2199 5.414144 TGAAGAAGACATGACAACAACAACA 59.586 36.000 0.00 0.00 0.00 3.33
1810 2200 5.739161 GTGAAGAAGACATGACAACAACAAC 59.261 40.000 0.00 0.00 0.00 3.32
1811 2201 5.447144 CGTGAAGAAGACATGACAACAACAA 60.447 40.000 0.00 0.00 0.00 2.83
1812 2202 4.033932 CGTGAAGAAGACATGACAACAACA 59.966 41.667 0.00 0.00 0.00 3.33
1827 2217 5.558273 GCTTTGAGATTTTCGACGTGAAGAA 60.558 40.000 0.00 0.00 37.99 2.52
1978 2394 2.686715 CGGCCCAAATGTATTCTCCCTT 60.687 50.000 0.00 0.00 0.00 3.95
2000 2416 3.761897 CAAACCCAGTCCTGATAAACCA 58.238 45.455 0.00 0.00 0.00 3.67
2007 2423 1.150536 GGTGCAAACCCAGTCCTGA 59.849 57.895 0.00 0.00 0.00 3.86
2061 2477 4.105733 GTTTTAACCGGCCGGGCG 62.106 66.667 44.99 40.52 40.62 6.13
2153 2569 6.895782 TGTTAACTTTACCTAGCATGCCTAT 58.104 36.000 15.66 0.00 0.00 2.57
2191 2607 1.202222 GGGCTTGAACATCATGCTTCG 60.202 52.381 15.11 0.00 44.17 3.79
2206 2622 2.198334 AGCTATTGGGAGTAGGGCTT 57.802 50.000 0.00 0.00 0.00 4.35
2257 2673 0.597898 GCGGCGAGGAAGATTAGGTC 60.598 60.000 12.98 0.00 0.00 3.85
2258 2674 1.327690 TGCGGCGAGGAAGATTAGGT 61.328 55.000 12.98 0.00 0.00 3.08
2285 2701 0.672711 GGTAGACGGGGTGCAGAAAC 60.673 60.000 0.00 0.00 0.00 2.78
2289 2705 1.144057 GATGGTAGACGGGGTGCAG 59.856 63.158 0.00 0.00 0.00 4.41
2327 2745 3.330701 GGGGGATCACATAAGAGGCATAA 59.669 47.826 0.00 0.00 0.00 1.90
2332 2750 1.344763 GACGGGGGATCACATAAGAGG 59.655 57.143 0.00 0.00 0.00 3.69
2334 2752 1.420430 GGACGGGGGATCACATAAGA 58.580 55.000 0.00 0.00 0.00 2.10
2335 2753 0.396811 GGGACGGGGGATCACATAAG 59.603 60.000 0.00 0.00 0.00 1.73
2339 2757 3.006728 GTGGGACGGGGGATCACA 61.007 66.667 0.00 0.00 0.00 3.58
2340 2758 2.253403 GAAGTGGGACGGGGGATCAC 62.253 65.000 0.00 0.00 0.00 3.06
2367 2907 3.902881 TCCAGAGAGGAGAAAGAATGC 57.097 47.619 0.00 0.00 43.07 3.56
2391 2931 1.407437 CGTGAAAGGAGGATGAAGGGG 60.407 57.143 0.00 0.00 0.00 4.79
2398 2938 1.079127 CGTGGCGTGAAAGGAGGAT 60.079 57.895 0.00 0.00 0.00 3.24
2411 2951 0.872021 CATAGAGAACTCGCCGTGGC 60.872 60.000 0.00 0.00 37.85 5.01
2591 3136 2.238395 GAGAGAGGGTGCCAAGAGAAAT 59.762 50.000 0.00 0.00 0.00 2.17
2622 3168 5.432060 ACAATATTGCCCCTTCTTACCTACT 59.568 40.000 15.48 0.00 0.00 2.57
2647 3193 5.132502 TGGGATTATGTCTAAACAGCATGG 58.867 41.667 0.00 0.00 43.62 3.66
2652 3198 5.116180 TCGCTTGGGATTATGTCTAAACAG 58.884 41.667 0.00 0.00 39.20 3.16
2659 3205 2.622064 ACCTCGCTTGGGATTATGTC 57.378 50.000 0.00 0.00 0.00 3.06
2752 3306 2.679429 TTTGGGGTGGAAATAACCGT 57.321 45.000 0.00 0.00 38.70 4.83
2762 3316 4.615588 TTTTCTAATGCTTTTGGGGTGG 57.384 40.909 0.00 0.00 0.00 4.61
2838 3392 8.090831 AGAAAGAAAAATACCAGCCAGAATTTC 58.909 33.333 0.00 0.00 0.00 2.17
2875 3433 6.156519 GGAAAATACGAAAACATGCCTTTCT 58.843 36.000 15.25 7.94 31.80 2.52
2908 3466 2.827921 GCCTTGTGATCAGGGTTTTCAT 59.172 45.455 0.00 0.00 41.98 2.57
2911 3469 1.632589 GGCCTTGTGATCAGGGTTTT 58.367 50.000 0.00 0.00 41.98 2.43
2970 3529 9.413048 GTAAAAGCTAGTGATATGGAGTATGTC 57.587 37.037 0.00 0.00 0.00 3.06
3034 3593 5.417580 GCCAATTTGGGTGTCTATTTCTACA 59.582 40.000 17.03 0.00 38.19 2.74
3051 3610 6.060788 TCACCTTGCTTAAATTTGCCAATTT 58.939 32.000 12.58 12.58 43.67 1.82
3052 3611 5.619220 TCACCTTGCTTAAATTTGCCAATT 58.381 33.333 0.00 0.00 33.72 2.32
3053 3612 5.226194 TCACCTTGCTTAAATTTGCCAAT 57.774 34.783 0.00 0.00 0.00 3.16
3054 3613 4.679373 TCACCTTGCTTAAATTTGCCAA 57.321 36.364 0.00 0.93 0.00 4.52
3055 3614 4.100808 AGTTCACCTTGCTTAAATTTGCCA 59.899 37.500 0.00 0.00 0.00 4.92
3056 3615 4.631131 AGTTCACCTTGCTTAAATTTGCC 58.369 39.130 0.00 0.00 0.00 4.52
3057 3616 7.707774 TTAAGTTCACCTTGCTTAAATTTGC 57.292 32.000 0.00 0.00 33.43 3.68
3082 3641 4.829872 ACATTTCGACCACCCATAGTTA 57.170 40.909 0.00 0.00 0.00 2.24
3096 3655 3.978855 TGTGAGAGTGAACGTACATTTCG 59.021 43.478 0.00 0.00 0.00 3.46
3116 3675 1.133513 TGGTTGAGCTCAATTGGGTGT 60.134 47.619 30.65 0.00 38.24 4.16
3147 3714 2.146342 AGATTGAGACACGGTGCAAAG 58.854 47.619 8.30 0.00 0.00 2.77
3220 3791 3.029074 CGACAGTCTTTTGAGCAAAACG 58.971 45.455 4.39 2.82 35.57 3.60
3221 3792 4.273005 TCGACAGTCTTTTGAGCAAAAC 57.727 40.909 4.39 0.00 35.57 2.43
3248 3819 5.648526 CAGCTAGTTAGACAAGAGTGACCTA 59.351 44.000 0.00 0.00 0.00 3.08
3253 3824 3.194542 AGGCAGCTAGTTAGACAAGAGTG 59.805 47.826 0.00 0.00 0.00 3.51
3276 3847 1.666189 GATGCTCAAGTAAGAACCCGC 59.334 52.381 0.00 0.00 0.00 6.13
3277 3848 2.673368 GTGATGCTCAAGTAAGAACCCG 59.327 50.000 0.00 0.00 0.00 5.28
3293 3864 3.832615 TGTCTCCAGGATCATGTGATG 57.167 47.619 6.62 0.00 34.37 3.07
3378 3949 6.655078 ATATAATTGAAGGGCAATCCACAC 57.345 37.500 0.00 0.00 46.25 3.82
3557 4131 5.735070 GCGTGACTTGGGTTAGAAACAAAAT 60.735 40.000 0.00 0.00 0.00 1.82
3571 4149 2.666619 GCAAAATCTGAGCGTGACTTGG 60.667 50.000 0.00 0.00 0.00 3.61
3586 4164 6.294675 CCGACATGAATATATGGTGGCAAAAT 60.295 38.462 0.00 0.00 32.32 1.82
3707 4295 8.489990 AAACTACTCATCAACAGATCAATCAG 57.510 34.615 0.00 0.00 0.00 2.90
3713 4301 5.814705 CCAGGAAACTACTCATCAACAGATC 59.185 44.000 0.00 0.00 40.21 2.75
3814 4410 5.432157 CATGATCTTATACGCGTTTGGAAC 58.568 41.667 20.78 11.69 0.00 3.62
4047 4647 8.934697 ACTCAGATAGGGCAAACTATATACAAA 58.065 33.333 0.00 0.00 33.95 2.83
4089 4689 2.224843 TGATCCATACATCCACATGGCC 60.225 50.000 0.00 0.00 41.33 5.36
4119 4719 1.765074 CCCCGTTCCTTCCTCCAAA 59.235 57.895 0.00 0.00 0.00 3.28
4131 4731 2.359478 GACATTGTCGCCCCCGTT 60.359 61.111 0.13 0.00 35.54 4.44
4218 4818 2.537560 GCCGAAGCCCATCATGTCG 61.538 63.158 0.00 0.00 0.00 4.35
4257 4857 4.461119 TCCATGAGGGAACGCTCT 57.539 55.556 17.16 3.64 44.80 4.09
4287 4887 7.093771 ACCTGTTTGAGTTCAATTTTGAGTTCT 60.094 33.333 0.00 0.00 38.61 3.01
4290 4890 6.530019 ACCTGTTTGAGTTCAATTTTGAGT 57.470 33.333 0.00 0.00 38.61 3.41
4318 4918 9.831737 AAATTCAGTCTTCAAGAACATAATTCG 57.168 29.630 0.00 0.00 0.00 3.34
4326 4926 6.959361 TGTAGCAAATTCAGTCTTCAAGAAC 58.041 36.000 0.00 0.00 0.00 3.01
4327 4927 7.566760 TTGTAGCAAATTCAGTCTTCAAGAA 57.433 32.000 0.00 0.00 0.00 2.52
4329 4929 8.807667 ATTTTGTAGCAAATTCAGTCTTCAAG 57.192 30.769 0.00 0.00 0.00 3.02
4331 4931 9.033481 CAAATTTTGTAGCAAATTCAGTCTTCA 57.967 29.630 0.78 0.00 0.00 3.02
4332 4932 9.248291 TCAAATTTTGTAGCAAATTCAGTCTTC 57.752 29.630 8.89 0.00 0.00 2.87
4333 4933 9.598517 TTCAAATTTTGTAGCAAATTCAGTCTT 57.401 25.926 8.89 0.00 0.00 3.01
4334 4934 9.768662 ATTCAAATTTTGTAGCAAATTCAGTCT 57.231 25.926 8.89 0.00 0.00 3.24
4335 4935 9.801714 CATTCAAATTTTGTAGCAAATTCAGTC 57.198 29.630 8.89 0.00 0.00 3.51
4357 4995 5.570234 TTTGGAAGGCGGTAATAACATTC 57.430 39.130 0.00 0.00 0.00 2.67
4358 4996 5.986501 TTTTGGAAGGCGGTAATAACATT 57.013 34.783 0.00 0.00 0.00 2.71
4370 5008 5.654209 ACCAAGAGATCTATTTTTGGAAGGC 59.346 40.000 23.78 0.00 40.52 4.35
4392 5120 7.945134 AGGAAAATGATTGCATGTATTCTACC 58.055 34.615 7.13 0.00 34.26 3.18
4453 5185 3.782523 TGCCAGTATCTTCCCTTGAGAAT 59.217 43.478 0.00 0.00 0.00 2.40
4508 5262 8.403236 AGTGTTTGAGTACTGTTTTAAATGGTC 58.597 33.333 0.00 0.00 0.00 4.02
4529 5283 6.727394 TGGCCCTTACTTTTATATGAGTGTT 58.273 36.000 0.00 0.00 0.00 3.32
4550 5304 4.157656 TGCTGTCCAGTACATAATTTTGGC 59.842 41.667 0.00 0.00 37.50 4.52
4551 5305 5.895636 TGCTGTCCAGTACATAATTTTGG 57.104 39.130 0.00 0.00 37.50 3.28
4552 5306 6.267817 CCATGCTGTCCAGTACATAATTTTG 58.732 40.000 0.00 0.00 37.50 2.44
4571 5328 3.872771 CCATGATTTAGGTTTTGCCATGC 59.127 43.478 0.00 0.00 40.61 4.06
4576 5333 5.163513 CAGTCACCATGATTTAGGTTTTGC 58.836 41.667 0.00 0.00 35.52 3.68
4592 5349 3.008049 ACTCCCAATGTAAGACAGTCACC 59.992 47.826 2.66 0.00 0.00 4.02
4593 5350 3.997021 CACTCCCAATGTAAGACAGTCAC 59.003 47.826 2.66 0.00 0.00 3.67
4597 5354 2.290260 TGGCACTCCCAATGTAAGACAG 60.290 50.000 0.00 0.00 41.82 3.51
4598 5355 1.702401 TGGCACTCCCAATGTAAGACA 59.298 47.619 0.00 0.00 41.82 3.41
4599 5356 2.489938 TGGCACTCCCAATGTAAGAC 57.510 50.000 0.00 0.00 41.82 3.01
4638 5395 6.112927 ACCCTGCAACAATGAATTTAACAT 57.887 33.333 0.00 0.00 0.00 2.71
4649 5406 3.030291 TGACTTGAAACCCTGCAACAAT 58.970 40.909 0.00 0.00 0.00 2.71
4679 5437 1.847737 AGTATCTCCTCCCTCACGTCT 59.152 52.381 0.00 0.00 0.00 4.18
4941 5717 2.185867 CACCATGCAATGCAGGCC 59.814 61.111 14.98 0.00 44.97 5.19
5059 5835 8.306038 ACTCATGCACATATGTACAACATTTTT 58.694 29.630 12.70 0.00 39.88 1.94
5060 5836 7.829725 ACTCATGCACATATGTACAACATTTT 58.170 30.769 12.70 0.00 39.88 1.82
5070 5846 8.962884 TTATTGACTTACTCATGCACATATGT 57.037 30.769 1.41 1.41 0.00 2.29
5305 6081 4.730081 TCGATCCGAAGCGAATGG 57.270 55.556 0.00 0.00 40.95 3.16
5750 6569 0.864797 GGTCATTCGAGACGCCGTAC 60.865 60.000 0.00 0.00 39.42 3.67
5774 6593 2.095364 GCAGAGGTGCACATCTCTTTTG 60.095 50.000 29.85 20.03 46.19 2.44
5838 6657 7.049754 AGCATCCTTTGAAAGTTGAAACAAAT 58.950 30.769 4.02 0.00 33.01 2.32
5914 6735 1.405821 AGCACTAGAGATTCCGTTCCG 59.594 52.381 0.00 0.00 0.00 4.30
6016 6837 1.795170 CTTTGTCTTGTGGCGGTGGG 61.795 60.000 0.00 0.00 0.00 4.61
6051 6908 3.371285 AGAAAGAAGGCTTCGTTATTCGC 59.629 43.478 24.81 13.96 39.67 4.70
6052 6909 6.830114 ATAGAAAGAAGGCTTCGTTATTCG 57.170 37.500 24.81 0.00 41.41 3.34
6053 6910 8.766151 CCTTATAGAAAGAAGGCTTCGTTATTC 58.234 37.037 24.81 22.24 37.28 1.75
6054 6911 8.265764 ACCTTATAGAAAGAAGGCTTCGTTATT 58.734 33.333 24.81 18.60 46.27 1.40
6055 6912 7.793036 ACCTTATAGAAAGAAGGCTTCGTTAT 58.207 34.615 24.81 23.70 46.27 1.89
6056 6913 7.123847 AGACCTTATAGAAAGAAGGCTTCGTTA 59.876 37.037 24.81 13.32 46.27 3.18
6057 6914 6.051179 ACCTTATAGAAAGAAGGCTTCGTT 57.949 37.500 24.99 24.99 46.27 3.85
6058 6915 5.422650 AGACCTTATAGAAAGAAGGCTTCGT 59.577 40.000 20.78 15.63 46.27 3.85
6059 6916 5.908341 AGACCTTATAGAAAGAAGGCTTCG 58.092 41.667 20.78 5.83 46.27 3.79
6060 6917 6.879400 TGAGACCTTATAGAAAGAAGGCTTC 58.121 40.000 19.53 19.53 46.27 3.86
6061 6918 6.875972 TGAGACCTTATAGAAAGAAGGCTT 57.124 37.500 0.00 0.00 46.27 4.35
6062 6919 6.352308 GGTTGAGACCTTATAGAAAGAAGGCT 60.352 42.308 0.54 0.00 46.27 4.58
6063 6920 5.818336 GGTTGAGACCTTATAGAAAGAAGGC 59.182 44.000 0.54 0.00 46.27 4.35
6065 6922 7.386851 TGTGGTTGAGACCTTATAGAAAGAAG 58.613 38.462 0.00 0.00 46.66 2.85
6066 6923 7.311092 TGTGGTTGAGACCTTATAGAAAGAA 57.689 36.000 0.00 0.00 46.66 2.52
6067 6924 6.928348 TGTGGTTGAGACCTTATAGAAAGA 57.072 37.500 0.00 0.00 46.66 2.52
6068 6925 8.258007 TGTATGTGGTTGAGACCTTATAGAAAG 58.742 37.037 0.00 0.00 46.66 2.62
6069 6926 8.038944 GTGTATGTGGTTGAGACCTTATAGAAA 58.961 37.037 0.00 0.00 46.66 2.52
6070 6927 7.179516 TGTGTATGTGGTTGAGACCTTATAGAA 59.820 37.037 0.00 0.00 46.66 2.10
6071 6928 6.666113 TGTGTATGTGGTTGAGACCTTATAGA 59.334 38.462 0.00 0.00 46.66 1.98
6072 6929 6.873997 TGTGTATGTGGTTGAGACCTTATAG 58.126 40.000 0.00 0.00 46.66 1.31
6073 6930 6.860790 TGTGTATGTGGTTGAGACCTTATA 57.139 37.500 0.00 0.00 46.66 0.98
6074 6931 5.755409 TGTGTATGTGGTTGAGACCTTAT 57.245 39.130 0.00 0.00 46.66 1.73
6075 6932 5.755409 ATGTGTATGTGGTTGAGACCTTA 57.245 39.130 0.00 0.00 46.66 2.69
6076 6933 4.640771 ATGTGTATGTGGTTGAGACCTT 57.359 40.909 0.00 0.00 46.66 3.50
6077 6934 5.957771 ATATGTGTATGTGGTTGAGACCT 57.042 39.130 0.00 0.00 46.66 3.85
6078 6935 7.217200 ACATATATGTGTATGTGGTTGAGACC 58.783 38.462 17.60 0.00 42.20 3.85
6079 6936 8.551205 CAACATATATGTGTATGTGGTTGAGAC 58.449 37.037 18.94 0.00 42.79 3.36
6080 6937 8.264347 ACAACATATATGTGTATGTGGTTGAGA 58.736 33.333 18.94 0.00 43.43 3.27
6081 6938 8.337532 CACAACATATATGTGTATGTGGTTGAG 58.662 37.037 27.18 13.03 43.43 3.02
6082 6939 7.201688 GCACAACATATATGTGTATGTGGTTGA 60.202 37.037 31.39 0.00 43.43 3.18
6083 6940 6.912051 GCACAACATATATGTGTATGTGGTTG 59.088 38.462 31.39 20.77 43.43 3.77
6084 6941 6.601217 TGCACAACATATATGTGTATGTGGTT 59.399 34.615 31.39 11.36 43.43 3.67
6085 6942 6.118852 TGCACAACATATATGTGTATGTGGT 58.881 36.000 31.39 15.33 45.63 4.16
6112 6969 2.417924 CCATAGCCGCCTAGATGATGAC 60.418 54.545 0.00 0.00 0.00 3.06
6126 6983 4.608948 AACTATACTCTGCACCATAGCC 57.391 45.455 0.00 0.00 0.00 3.93
6140 6997 6.289064 AGGCCTACAGTTTGCATAACTATAC 58.711 40.000 1.29 3.88 0.00 1.47
6176 7033 1.301953 GGGCTTTGGCTTTTGGCTG 60.302 57.895 0.00 0.00 46.20 4.85
6196 7053 4.223032 AGGCTATACCCTGATATTTCACCG 59.777 45.833 0.00 0.00 40.58 4.94
6200 7057 8.476447 GTTACCTAGGCTATACCCTGATATTTC 58.524 40.741 9.30 0.00 40.58 2.17
6214 7071 2.531771 TGCTGTGTGTTACCTAGGCTA 58.468 47.619 9.30 0.00 0.00 3.93
6222 7079 2.154462 AGCCTGAATGCTGTGTGTTAC 58.846 47.619 0.00 0.00 40.90 2.50
6224 7081 1.242076 GAGCCTGAATGCTGTGTGTT 58.758 50.000 0.00 0.00 42.95 3.32
6298 7155 5.235516 TGGAAGGTTTCGTCTAAATCTGAC 58.764 41.667 0.00 0.00 37.56 3.51
6310 7167 1.021202 TGCAGTGTTGGAAGGTTTCG 58.979 50.000 0.00 0.00 0.00 3.46
6351 7208 3.585862 TCTCCGAATAAATATGAGCGGC 58.414 45.455 0.00 0.00 38.68 6.53


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

AutoCloner maintained by Alex Coulton.