Multiple sequence alignment - TraesCS5D01G337400

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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 TraesCS5D01G337400 chr5D 100.000 4583 0 0 1 4583 426171804 426167222 0.000000e+00 8464
1 TraesCS5D01G337400 chr5A 92.052 2680 130 23 477 3121 540372707 540370076 0.000000e+00 3692
2 TraesCS5D01G337400 chr5A 89.689 805 47 13 3209 3992 540369944 540369155 0.000000e+00 994
3 TraesCS5D01G337400 chr5A 87.432 366 16 8 4224 4583 540369103 540368762 1.200000e-105 394
4 TraesCS5D01G337400 chr5A 92.430 251 17 1 1873 2121 599410306 599410556 1.570000e-94 357
5 TraesCS5D01G337400 chr5A 91.837 147 7 1 1782 1923 504244644 504244498 2.800000e-47 200
6 TraesCS5D01G337400 chr5B 92.516 1991 89 20 1154 3121 516043691 516041738 0.000000e+00 2796
7 TraesCS5D01G337400 chr5B 89.294 906 47 14 3119 3992 516041701 516040814 0.000000e+00 1090
8 TraesCS5D01G337400 chr5B 90.385 520 17 18 604 1091 516044736 516044218 0.000000e+00 652
9 TraesCS5D01G337400 chr5B 93.199 397 20 3 5 394 516045430 516045034 1.110000e-160 577
10 TraesCS5D01G337400 chr5B 86.026 458 28 14 4137 4583 516040678 516040246 4.180000e-125 459
11 TraesCS5D01G337400 chr5B 92.829 251 16 1 1873 2121 658909590 658909840 3.370000e-96 363
12 TraesCS5D01G337400 chr5B 84.659 176 8 4 393 568 516044894 516044738 1.710000e-34 158
13 TraesCS5D01G337400 chr3D 92.678 478 28 2 1651 2121 30772615 30773092 0.000000e+00 682
14 TraesCS5D01G337400 chr4B 92.243 477 30 2 1651 2120 604275759 604276235 0.000000e+00 669
15 TraesCS5D01G337400 chr7B 90.062 483 34 7 1651 2121 452911414 452911894 8.430000e-172 614
16 TraesCS5D01G337400 chr7B 91.837 147 7 1 1782 1923 715130125 715129979 2.800000e-47 200
17 TraesCS5D01G337400 chr7B 91.837 147 7 1 1782 1923 715162774 715162628 2.800000e-47 200
18 TraesCS5D01G337400 chr6D 89.562 479 20 9 1651 2121 133888397 133887941 8.550000e-162 580
19 TraesCS5D01G337400 chr6B 92.430 251 17 1 1873 2121 636719863 636719613 1.570000e-94 357
20 TraesCS5D01G337400 chr6B 94.030 67 4 0 1652 1718 715035056 715035122 8.110000e-18 102
21 TraesCS5D01G337400 chr3B 91.571 261 18 3 1873 2129 795099107 795098847 1.570000e-94 357
22 TraesCS5D01G337400 chr2B 91.011 89 7 1 1649 1736 625470261 625470173 8.050000e-23 119
23 TraesCS5D01G337400 chr3A 92.647 68 5 0 1651 1718 90106873 90106806 1.050000e-16 99


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 TraesCS5D01G337400 chr5D 426167222 426171804 4582 True 8464.000000 8464 100.000000 1 4583 1 chr5D.!!$R1 4582
1 TraesCS5D01G337400 chr5A 540368762 540372707 3945 True 1693.333333 3692 89.724333 477 4583 3 chr5A.!!$R2 4106
2 TraesCS5D01G337400 chr5B 516040246 516045430 5184 True 955.333333 2796 89.346500 5 4583 6 chr5B.!!$R1 4578

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
469 616 0.040058 TCTTCCGTGGTAGCCTGGTA 59.960 55.0 0.00 0.00 0.00 3.25 F
1175 1828 0.174845 TTCGTCAGATTAGGTGCGGG 59.825 55.0 0.00 0.00 0.00 6.13 F
1639 2313 1.186267 TTGCTTCATGGTGGCATGCA 61.186 50.0 21.36 2.54 35.84 3.96 F
3160 3881 0.026285 GTTTGCTATACGGCGCAGTG 59.974 55.0 23.76 7.81 37.46 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1963 2640 1.207089 CAGGACCTGTTCGGCTATTCA 59.793 52.381 13.84 0.0 35.61 2.57 R
3146 3867 0.030235 TGTAGCACTGCGCCGTATAG 59.970 55.000 4.18 0.0 44.04 1.31 R
3264 4009 0.039527 GAACAACATGGTTCCCGCAC 60.040 55.000 0.00 0.0 40.97 5.34 R
4473 5253 0.545646 GGAGCCAGAAAGAGGAGCAT 59.454 55.000 0.00 0.0 0.00 3.79 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
23 24 5.860611 TCTCAAATCCGTTAACTCCAAGAA 58.139 37.500 3.71 0.00 0.00 2.52
24 25 6.292923 TCTCAAATCCGTTAACTCCAAGAAA 58.707 36.000 3.71 0.00 0.00 2.52
48 49 2.094338 GGGAGCAGAAAAATCAAGCCAG 60.094 50.000 0.00 0.00 0.00 4.85
51 52 4.262164 GGAGCAGAAAAATCAAGCCAGAAA 60.262 41.667 0.00 0.00 0.00 2.52
64 65 2.290641 AGCCAGAAAACAAACTAGTGCG 59.709 45.455 0.00 0.00 0.00 5.34
109 114 3.754850 GTGTGAACGGCCTACCTTAATTT 59.245 43.478 0.00 0.00 0.00 1.82
169 174 0.163146 GAAAAGGCGAACGAACGAGG 59.837 55.000 9.67 0.00 35.09 4.63
193 198 2.352651 CAGAACCATTCATAGTGTGGCG 59.647 50.000 0.00 0.00 36.47 5.69
212 217 3.936203 AACAGGCGCCGAAGTGGA 61.936 61.111 23.20 0.00 42.00 4.02
226 231 1.722034 AGTGGAGCTCTCTGGTTCAA 58.278 50.000 14.64 0.00 32.84 2.69
269 274 2.331265 GTGGCATCCCGCTTTATCC 58.669 57.895 0.00 0.00 41.91 2.59
317 325 4.494690 CGCGTATGAACATTTTGCTCATCT 60.495 41.667 0.00 0.00 35.16 2.90
318 326 5.335127 GCGTATGAACATTTTGCTCATCTT 58.665 37.500 0.00 0.00 35.16 2.40
378 386 0.986527 CCGTTTTGTACCCTACCCCT 59.013 55.000 0.00 0.00 0.00 4.79
388 396 1.329256 CCCTACCCCTGACTCGTATG 58.671 60.000 0.00 0.00 0.00 2.39
391 399 2.883386 CCTACCCCTGACTCGTATGTAC 59.117 54.545 0.00 0.00 0.00 2.90
394 402 1.687054 CCCCTGACTCGTATGTACCCA 60.687 57.143 0.00 0.00 0.00 4.51
401 548 4.992319 TGACTCGTATGTACCCACAAAAAG 59.008 41.667 0.00 0.00 38.42 2.27
402 549 4.320870 ACTCGTATGTACCCACAAAAAGG 58.679 43.478 0.00 0.00 38.42 3.11
403 550 4.040706 ACTCGTATGTACCCACAAAAAGGA 59.959 41.667 0.00 0.00 38.42 3.36
462 609 0.806102 CGTGCCATCTTCCGTGGTAG 60.806 60.000 0.00 0.00 39.01 3.18
463 610 1.090052 GTGCCATCTTCCGTGGTAGC 61.090 60.000 0.00 0.00 39.01 3.58
465 612 1.972660 GCCATCTTCCGTGGTAGCCT 61.973 60.000 0.00 0.00 39.01 4.58
466 613 0.179073 CCATCTTCCGTGGTAGCCTG 60.179 60.000 0.00 0.00 31.96 4.85
467 614 0.179073 CATCTTCCGTGGTAGCCTGG 60.179 60.000 0.00 0.00 0.00 4.45
468 615 0.617820 ATCTTCCGTGGTAGCCTGGT 60.618 55.000 0.00 0.00 0.00 4.00
469 616 0.040058 TCTTCCGTGGTAGCCTGGTA 59.960 55.000 0.00 0.00 0.00 3.25
470 617 0.175073 CTTCCGTGGTAGCCTGGTAC 59.825 60.000 0.00 0.00 0.00 3.34
471 618 0.251922 TTCCGTGGTAGCCTGGTACT 60.252 55.000 6.48 0.00 0.00 2.73
472 619 0.968901 TCCGTGGTAGCCTGGTACTG 60.969 60.000 6.48 0.00 0.00 2.74
501 648 0.390472 GTTCCTCGCTCTCCAACCTG 60.390 60.000 0.00 0.00 0.00 4.00
524 671 0.731417 CTACCTCACTCACCCGTACG 59.269 60.000 8.69 8.69 0.00 3.67
558 705 1.671054 AATCGGCTCAACCACACGG 60.671 57.895 0.00 0.00 39.03 4.94
574 726 2.674380 GGGAACACCAGCAGCCTG 60.674 66.667 0.00 0.00 39.85 4.85
587 739 3.284449 GCCTGGCCGTCAAACGTT 61.284 61.111 7.66 0.00 40.58 3.99
918 1095 4.031129 CCCTCCTGCTGCTGCTGT 62.031 66.667 17.00 0.00 40.48 4.40
919 1096 2.436292 CCTCCTGCTGCTGCTGTC 60.436 66.667 17.00 1.84 40.48 3.51
920 1097 2.663796 CTCCTGCTGCTGCTGTCT 59.336 61.111 17.00 0.00 40.48 3.41
1125 1324 0.247185 CCGGTAGGGTTTAAGCGACA 59.753 55.000 0.00 0.00 38.82 4.35
1126 1325 1.353076 CGGTAGGGTTTAAGCGACAC 58.647 55.000 0.00 0.00 38.82 3.67
1144 1343 0.328258 ACCGGGGTTTCAGAATCTGG 59.672 55.000 10.71 0.00 31.51 3.86
1145 1344 0.618458 CCGGGGTTTCAGAATCTGGA 59.382 55.000 10.71 0.00 31.51 3.86
1146 1345 1.407437 CCGGGGTTTCAGAATCTGGAG 60.407 57.143 10.71 0.00 31.51 3.86
1147 1346 1.555075 CGGGGTTTCAGAATCTGGAGA 59.445 52.381 10.71 0.00 31.51 3.71
1148 1347 2.678190 CGGGGTTTCAGAATCTGGAGAC 60.678 54.545 10.71 6.71 31.51 3.36
1149 1348 2.622436 GGGTTTCAGAATCTGGAGACG 58.378 52.381 10.71 0.00 31.51 4.18
1150 1349 2.003301 GGTTTCAGAATCTGGAGACGC 58.997 52.381 10.71 0.00 31.51 5.19
1151 1350 2.003301 GTTTCAGAATCTGGAGACGCC 58.997 52.381 10.71 0.00 31.51 5.68
1152 1351 1.266178 TTCAGAATCTGGAGACGCCA 58.734 50.000 10.71 0.00 46.96 5.69
1159 1358 2.338620 TGGAGACGCCAGTGTTCG 59.661 61.111 0.00 1.15 43.33 3.95
1160 1359 2.338984 GGAGACGCCAGTGTTCGT 59.661 61.111 7.29 7.29 42.09 3.85
1175 1828 0.174845 TTCGTCAGATTAGGTGCGGG 59.825 55.000 0.00 0.00 0.00 6.13
1258 1920 1.300080 GGTCGAAACGTCCGTGGAA 60.300 57.895 9.58 0.00 0.00 3.53
1328 1997 1.524482 GCTCCCTGTCCTAAGCCAG 59.476 63.158 0.00 0.00 0.00 4.85
1384 2057 3.202906 ACATATAACCGCATGTGACCAC 58.797 45.455 8.11 0.00 34.15 4.16
1502 2175 1.206849 TGCCATGATCGTGCTTACAGA 59.793 47.619 9.58 0.00 0.00 3.41
1503 2176 2.158914 TGCCATGATCGTGCTTACAGAT 60.159 45.455 9.58 0.00 0.00 2.90
1504 2177 2.478134 GCCATGATCGTGCTTACAGATC 59.522 50.000 9.58 0.00 40.68 2.75
1505 2178 3.801638 GCCATGATCGTGCTTACAGATCT 60.802 47.826 9.58 0.00 40.84 2.75
1507 2180 4.210746 CCATGATCGTGCTTACAGATCTTG 59.789 45.833 9.58 11.28 41.85 3.02
1508 2181 3.190079 TGATCGTGCTTACAGATCTTGC 58.810 45.455 0.00 0.00 40.84 4.01
1509 2182 3.118992 TGATCGTGCTTACAGATCTTGCT 60.119 43.478 0.00 0.00 40.84 3.91
1632 2306 2.756829 TGTTTGCATTGCTTCATGGTG 58.243 42.857 10.49 0.00 0.00 4.17
1639 2313 1.186267 TTGCTTCATGGTGGCATGCA 61.186 50.000 21.36 2.54 35.84 3.96
1674 2348 4.304110 CACTAAAGGCGTCTCACTTTACA 58.696 43.478 0.00 0.00 37.94 2.41
1680 2354 3.746492 AGGCGTCTCACTTTACATGAAAC 59.254 43.478 0.00 0.00 0.00 2.78
1832 2507 5.316987 ACATTCTATAGTAAAGCATGGGGC 58.683 41.667 0.00 0.00 45.30 5.80
1911 2588 8.918202 TGTGAACATTTCTTAGGAGTTATGTT 57.082 30.769 10.00 10.00 38.93 2.71
1912 2589 8.783093 TGTGAACATTTCTTAGGAGTTATGTTG 58.217 33.333 13.18 0.00 37.71 3.33
1963 2640 7.693969 TGTTGAAACCAAATGGAAAACAATT 57.306 28.000 6.42 0.00 38.94 2.32
2026 2703 6.034161 AGCATTACTTGGGGATATACGTAC 57.966 41.667 0.00 0.00 0.00 3.67
2048 2726 8.130469 CGTACCTGTTTTGGTTACTATTTTGTT 58.870 33.333 0.00 0.00 41.22 2.83
2068 2746 7.624360 TTGTTCTCTAGTTTCTGCTTTTCAA 57.376 32.000 0.00 0.00 0.00 2.69
2073 2751 7.576236 TCTCTAGTTTCTGCTTTTCAATTTCG 58.424 34.615 0.00 0.00 0.00 3.46
2096 2774 5.005012 CGGTGAAGCAGCATTGATAATTTTG 59.995 40.000 0.00 0.00 0.00 2.44
2191 2869 3.701542 TGTGGCATTGTTTTTCCACTGTA 59.298 39.130 10.99 0.00 46.74 2.74
2249 2927 6.811253 TGCCTTACTTACGAAATCATGTTT 57.189 33.333 0.00 0.00 0.00 2.83
2252 2930 6.349033 GCCTTACTTACGAAATCATGTTTGGT 60.349 38.462 11.10 11.10 0.00 3.67
2401 3079 5.405269 TCTGGTATTGCAATCGTATCAATCG 59.595 40.000 16.86 0.00 33.13 3.34
2458 3136 7.817418 TTGTTTCCCTACCTATTTGATATGC 57.183 36.000 0.00 0.00 0.00 3.14
2491 3169 7.514784 TCATATATGAAGGCAACATCCTTTG 57.485 36.000 13.12 0.00 45.92 2.77
2535 3213 6.406737 GCATGCTATCTGAGGCTATTCATCTA 60.407 42.308 11.37 0.00 0.00 1.98
2785 3463 9.650539 CCACATTGATTCAACCATAATTTAACA 57.349 29.630 0.15 0.00 0.00 2.41
2851 3529 6.721318 TGTTTCTGAAAGCCTACTATCCATT 58.279 36.000 2.48 0.00 0.00 3.16
3021 3699 1.745141 GCTGATCTTGGTGCCGATTCT 60.745 52.381 0.00 0.00 0.00 2.40
3058 3736 5.656859 AGTCAGCTGGATACTGTAATGTGTA 59.343 40.000 15.13 0.00 36.50 2.90
3146 3867 3.708563 TTGGCAGTAGTTTCTGTTTGC 57.291 42.857 0.00 0.00 37.70 3.68
3152 3873 5.220416 GGCAGTAGTTTCTGTTTGCTATACG 60.220 44.000 0.00 0.00 37.70 3.06
3155 3876 2.671396 AGTTTCTGTTTGCTATACGGCG 59.329 45.455 4.80 4.80 34.52 6.46
3156 3877 1.003851 TTCTGTTTGCTATACGGCGC 58.996 50.000 6.90 0.00 34.52 6.53
3157 3878 0.108567 TCTGTTTGCTATACGGCGCA 60.109 50.000 10.83 0.00 34.52 6.09
3158 3879 0.301687 CTGTTTGCTATACGGCGCAG 59.698 55.000 10.83 8.25 37.46 5.18
3159 3880 0.390603 TGTTTGCTATACGGCGCAGT 60.391 50.000 19.03 19.03 37.46 4.40
3160 3881 0.026285 GTTTGCTATACGGCGCAGTG 59.974 55.000 23.76 7.81 37.46 3.66
3161 3882 1.701545 TTTGCTATACGGCGCAGTGC 61.702 55.000 23.76 17.95 45.38 4.40
3162 3883 2.279517 GCTATACGGCGCAGTGCT 60.280 61.111 23.76 12.60 45.43 4.40
3180 3901 7.136119 GCAGTGCTACAACAACAAATAGTTTA 58.864 34.615 8.18 0.00 38.74 2.01
3258 4001 6.795399 TGTTCTCTTTTAGCAAAAGTTCCAG 58.205 36.000 16.01 9.56 46.18 3.86
3259 4002 6.377146 TGTTCTCTTTTAGCAAAAGTTCCAGT 59.623 34.615 16.01 0.00 46.18 4.00
3264 4009 4.630894 TTAGCAAAAGTTCCAGTGTGTG 57.369 40.909 0.00 0.00 0.00 3.82
3269 4014 1.095228 AAGTTCCAGTGTGTGTGCGG 61.095 55.000 0.00 0.00 0.00 5.69
3312 4057 5.078949 TCTTCATTTTGATCTTTGGGAGCA 58.921 37.500 0.00 0.00 38.70 4.26
3323 4068 1.422531 TTGGGAGCAGTTTTTGGCAT 58.577 45.000 0.00 0.00 0.00 4.40
3325 4070 1.260544 GGGAGCAGTTTTTGGCATCT 58.739 50.000 0.00 0.00 0.00 2.90
3341 4086 3.181520 GGCATCTGTACTTTGTTACTGCG 60.182 47.826 0.00 0.00 0.00 5.18
3358 4103 4.794169 ACTGCGGTTTATGCTAACTTTTG 58.206 39.130 0.00 0.00 0.00 2.44
3531 4277 4.435436 TCGAGCGCGCAGACCATT 62.435 61.111 35.10 10.81 37.46 3.16
3543 4289 0.606401 AGACCATTGCAACGGTGGAG 60.606 55.000 23.99 0.00 34.99 3.86
3754 4500 4.368315 AGCGGTTGTTGAAGGAATTTTTC 58.632 39.130 0.00 0.00 0.00 2.29
3804 4563 4.989279 ACATGATGTGCTGGAATTAACC 57.011 40.909 0.00 0.00 0.00 2.85
3873 4633 9.620660 AGCAAACGATCGTTTATAATTTTCTTT 57.379 25.926 37.53 15.20 45.32 2.52
3961 4730 6.208797 ACCGCTGCAAGTACTATTATATCTGA 59.791 38.462 0.00 0.00 35.30 3.27
3965 4734 7.010923 GCTGCAAGTACTATTATATCTGATGCC 59.989 40.741 0.00 0.00 35.30 4.40
3966 4735 8.138928 TGCAAGTACTATTATATCTGATGCCT 57.861 34.615 0.00 0.00 0.00 4.75
3968 4737 7.010923 GCAAGTACTATTATATCTGATGCCTGC 59.989 40.741 0.00 0.00 0.00 4.85
3969 4738 7.724490 AGTACTATTATATCTGATGCCTGCA 57.276 36.000 0.00 0.00 0.00 4.41
3992 4761 6.669741 GCACAAACTTTTCTGCTGTTTTGTAC 60.670 38.462 0.00 0.00 32.42 2.90
3994 4763 6.806739 ACAAACTTTTCTGCTGTTTTGTACTC 59.193 34.615 0.00 0.00 32.42 2.59
3996 4765 4.035208 ACTTTTCTGCTGTTTTGTACTCCG 59.965 41.667 0.00 0.00 0.00 4.63
3997 4766 2.902705 TCTGCTGTTTTGTACTCCGT 57.097 45.000 0.00 0.00 0.00 4.69
3998 4767 2.750948 TCTGCTGTTTTGTACTCCGTC 58.249 47.619 0.00 0.00 0.00 4.79
3999 4768 1.798813 CTGCTGTTTTGTACTCCGTCC 59.201 52.381 0.00 0.00 0.00 4.79
4000 4769 0.788391 GCTGTTTTGTACTCCGTCCG 59.212 55.000 0.00 0.00 0.00 4.79
4001 4770 1.870993 GCTGTTTTGTACTCCGTCCGT 60.871 52.381 0.00 0.00 0.00 4.69
4002 4771 2.056577 CTGTTTTGTACTCCGTCCGTC 58.943 52.381 0.00 0.00 0.00 4.79
4003 4772 1.269726 TGTTTTGTACTCCGTCCGTCC 60.270 52.381 0.00 0.00 0.00 4.79
4005 4774 0.827089 TTTGTACTCCGTCCGTCCCA 60.827 55.000 0.00 0.00 0.00 4.37
4007 4776 0.827089 TGTACTCCGTCCGTCCCAAA 60.827 55.000 0.00 0.00 0.00 3.28
4008 4777 0.318120 GTACTCCGTCCGTCCCAAAA 59.682 55.000 0.00 0.00 0.00 2.44
4011 4780 1.624813 ACTCCGTCCGTCCCAAAATAA 59.375 47.619 0.00 0.00 0.00 1.40
4012 4781 2.038820 ACTCCGTCCGTCCCAAAATAAA 59.961 45.455 0.00 0.00 0.00 1.40
4013 4782 2.676342 CTCCGTCCGTCCCAAAATAAAG 59.324 50.000 0.00 0.00 0.00 1.85
4014 4783 1.741145 CCGTCCGTCCCAAAATAAAGG 59.259 52.381 0.00 0.00 0.00 3.11
4015 4784 2.429478 CGTCCGTCCCAAAATAAAGGT 58.571 47.619 0.00 0.00 0.00 3.50
4016 4785 3.598299 CGTCCGTCCCAAAATAAAGGTA 58.402 45.455 0.00 0.00 0.00 3.08
4017 4786 3.619929 CGTCCGTCCCAAAATAAAGGTAG 59.380 47.826 0.00 0.00 0.00 3.18
4018 4787 4.582869 GTCCGTCCCAAAATAAAGGTAGT 58.417 43.478 0.00 0.00 0.00 2.73
4020 4789 5.582269 GTCCGTCCCAAAATAAAGGTAGTAC 59.418 44.000 0.00 0.00 0.00 2.73
4021 4790 5.248020 TCCGTCCCAAAATAAAGGTAGTACA 59.752 40.000 2.06 0.00 0.00 2.90
4022 4791 5.939296 CCGTCCCAAAATAAAGGTAGTACAA 59.061 40.000 2.06 0.00 0.00 2.41
4024 4793 7.361457 CCGTCCCAAAATAAAGGTAGTACAAAG 60.361 40.741 2.06 0.00 0.00 2.77
4025 4794 7.173735 CGTCCCAAAATAAAGGTAGTACAAAGT 59.826 37.037 2.06 0.00 0.00 2.66
4026 4795 8.853126 GTCCCAAAATAAAGGTAGTACAAAGTT 58.147 33.333 2.06 0.00 0.00 2.66
4043 4812 9.620660 GTACAAAGTTAAGTCACATATTTTGGG 57.379 33.333 0.00 0.00 0.00 4.12
4053 4822 5.439721 TCACATATTTTGGGACAGATGGAG 58.560 41.667 0.00 0.00 42.39 3.86
4055 4824 6.157820 TCACATATTTTGGGACAGATGGAGTA 59.842 38.462 0.00 0.00 42.39 2.59
4056 4825 7.000472 CACATATTTTGGGACAGATGGAGTAT 59.000 38.462 0.00 0.00 42.39 2.12
4058 4827 8.061304 ACATATTTTGGGACAGATGGAGTATTT 58.939 33.333 0.00 0.00 42.39 1.40
4072 4841 5.874895 GGAGTATTTTAAAACGCACTCCT 57.125 39.130 29.61 12.00 45.58 3.69
4073 4842 6.973229 GGAGTATTTTAAAACGCACTCCTA 57.027 37.500 29.61 9.11 45.58 2.94
4075 4844 6.592994 GGAGTATTTTAAAACGCACTCCTACT 59.407 38.462 29.61 19.97 45.58 2.57
4076 4845 7.118825 GGAGTATTTTAAAACGCACTCCTACTT 59.881 37.037 29.61 8.27 45.58 2.24
4077 4846 8.387190 AGTATTTTAAAACGCACTCCTACTTT 57.613 30.769 1.97 0.00 0.00 2.66
4078 4847 8.287503 AGTATTTTAAAACGCACTCCTACTTTG 58.712 33.333 1.97 0.00 0.00 2.77
4082 4851 5.668558 AAAACGCACTCCTACTTTGTTAG 57.331 39.130 0.00 0.00 0.00 2.34
4083 4852 4.332428 AACGCACTCCTACTTTGTTAGT 57.668 40.909 0.00 0.00 41.04 2.24
4085 4854 4.802999 ACGCACTCCTACTTTGTTAGTAC 58.197 43.478 0.00 0.00 38.33 2.73
4086 4855 4.522022 ACGCACTCCTACTTTGTTAGTACT 59.478 41.667 0.00 0.00 38.33 2.73
4087 4856 5.094134 CGCACTCCTACTTTGTTAGTACTC 58.906 45.833 0.00 0.00 38.33 2.59
4089 4858 5.638783 CACTCCTACTTTGTTAGTACTCCG 58.361 45.833 0.00 0.00 38.33 4.63
4090 4859 5.182760 CACTCCTACTTTGTTAGTACTCCGT 59.817 44.000 0.00 0.00 38.33 4.69
4094 4863 9.113838 CTCCTACTTTGTTAGTACTCCGTATAA 57.886 37.037 0.00 0.00 38.33 0.98
4095 4864 9.461312 TCCTACTTTGTTAGTACTCCGTATAAA 57.539 33.333 0.00 0.00 38.33 1.40
4096 4865 9.727627 CCTACTTTGTTAGTACTCCGTATAAAG 57.272 37.037 0.00 6.75 38.33 1.85
4099 4868 9.415544 ACTTTGTTAGTACTCCGTATAAAGTTG 57.584 33.333 0.00 0.00 33.52 3.16
4100 4869 9.415544 CTTTGTTAGTACTCCGTATAAAGTTGT 57.584 33.333 0.00 0.00 0.00 3.32
4102 4871 9.840427 TTGTTAGTACTCCGTATAAAGTTGTAC 57.160 33.333 0.00 0.00 0.00 2.90
4103 4872 9.231297 TGTTAGTACTCCGTATAAAGTTGTACT 57.769 33.333 0.00 0.00 41.02 2.73
4117 4886 9.788889 ATAAAGTTGTACTAAAACTAAGCCACT 57.211 29.630 0.00 0.00 36.87 4.00
4118 4887 8.515695 AAAGTTGTACTAAAACTAAGCCACTT 57.484 30.769 0.00 0.00 36.87 3.16
4119 4888 9.617523 AAAGTTGTACTAAAACTAAGCCACTTA 57.382 29.630 0.00 0.00 36.87 2.24
4120 4889 8.599055 AGTTGTACTAAAACTAAGCCACTTAC 57.401 34.615 0.00 0.00 36.11 2.34
4121 4890 8.427276 AGTTGTACTAAAACTAAGCCACTTACT 58.573 33.333 0.00 0.00 36.11 2.24
4122 4891 9.049523 GTTGTACTAAAACTAAGCCACTTACTT 57.950 33.333 0.00 0.00 0.00 2.24
4123 4892 9.617523 TTGTACTAAAACTAAGCCACTTACTTT 57.382 29.630 0.00 0.00 0.00 2.66
4124 4893 9.048446 TGTACTAAAACTAAGCCACTTACTTTG 57.952 33.333 0.00 0.00 0.00 2.77
4127 4896 4.717279 AACTAAGCCACTTACTTTGGGA 57.283 40.909 0.00 0.00 34.35 4.37
4128 4897 4.017177 ACTAAGCCACTTACTTTGGGAC 57.983 45.455 0.00 0.00 34.35 4.46
4129 4898 2.287977 AAGCCACTTACTTTGGGACC 57.712 50.000 0.00 0.00 34.35 4.46
4130 4899 1.446016 AGCCACTTACTTTGGGACCT 58.554 50.000 0.00 0.00 34.35 3.85
4131 4900 2.627933 AGCCACTTACTTTGGGACCTA 58.372 47.619 0.00 0.00 34.35 3.08
4132 4901 2.572104 AGCCACTTACTTTGGGACCTAG 59.428 50.000 0.00 0.00 34.35 3.02
4133 4902 2.355818 GCCACTTACTTTGGGACCTAGG 60.356 54.545 7.41 7.41 34.35 3.02
4134 4903 2.238898 CCACTTACTTTGGGACCTAGGG 59.761 54.545 14.81 0.00 0.00 3.53
4135 4904 3.178865 CACTTACTTTGGGACCTAGGGA 58.821 50.000 14.81 0.00 0.00 4.20
4147 4916 4.325109 GGGACCTAGGGAGTATTTGCTTTT 60.325 45.833 14.81 0.00 0.00 2.27
4148 4917 5.104235 GGGACCTAGGGAGTATTTGCTTTTA 60.104 44.000 14.81 0.00 0.00 1.52
4157 4926 7.509318 AGGGAGTATTTGCTTTTAGAAAGGTTT 59.491 33.333 2.95 0.00 0.00 3.27
4160 4929 9.744468 GAGTATTTGCTTTTAGAAAGGTTTTCA 57.256 29.630 4.56 0.00 0.00 2.69
4174 4943 2.546789 GGTTTTCACCTCGGTTACACTG 59.453 50.000 0.00 0.00 40.44 3.66
4181 4950 1.071071 CCTCGGTTACACTGGAACCAA 59.929 52.381 21.18 3.81 45.70 3.67
4197 4966 5.838521 TGGAACCAAGAGGCTAAGAAATTTT 59.161 36.000 0.00 0.00 39.06 1.82
4198 4967 6.326323 TGGAACCAAGAGGCTAAGAAATTTTT 59.674 34.615 0.00 0.00 39.06 1.94
4201 4970 9.929180 GAACCAAGAGGCTAAGAAATTTTTATT 57.071 29.630 0.00 0.00 39.06 1.40
4265 5035 2.890474 GGTGGACGCGCATTCGAT 60.890 61.111 5.73 0.00 38.10 3.59
4266 5036 2.461110 GGTGGACGCGCATTCGATT 61.461 57.895 5.73 0.00 38.10 3.34
4297 5067 6.097356 TCGTGGTTAAACTAGCAATGACTAG 58.903 40.000 9.18 9.18 44.38 2.57
4387 5157 2.699954 CAGCCTGGTTAGTGGTTACAG 58.300 52.381 0.00 0.00 0.00 2.74
4399 5172 1.829222 TGGTTACAGCCTAGTGGTAGC 59.171 52.381 0.00 0.00 35.27 3.58
4427 5203 9.601217 GTACAATCATCTGAGTGGTAGTTTTAT 57.399 33.333 11.78 0.00 43.65 1.40
4436 5216 8.946085 TCTGAGTGGTAGTTTTATATTTTGCTG 58.054 33.333 0.00 0.00 0.00 4.41
4449 5229 4.992740 TGCTGGTTTGGGCGGCAT 62.993 61.111 12.47 0.00 0.00 4.40
4450 5230 4.133796 GCTGGTTTGGGCGGCATC 62.134 66.667 12.47 0.00 0.00 3.91
4451 5231 3.814268 CTGGTTTGGGCGGCATCG 61.814 66.667 12.47 0.00 39.81 3.84
4452 5232 4.652131 TGGTTTGGGCGGCATCGT 62.652 61.111 12.47 0.00 38.89 3.73
4469 5249 4.512657 CATCGTTCGTTCTAGGTAGTACG 58.487 47.826 9.23 9.23 44.83 3.67
4471 5251 4.740268 TCGTTCGTTCTAGGTAGTACGTA 58.260 43.478 13.66 2.90 44.16 3.57
4473 5253 6.500910 TCGTTCGTTCTAGGTAGTACGTATA 58.499 40.000 13.66 0.00 44.16 1.47
4474 5254 7.145985 TCGTTCGTTCTAGGTAGTACGTATAT 58.854 38.462 13.66 0.00 44.16 0.86
4475 5255 7.114953 TCGTTCGTTCTAGGTAGTACGTATATG 59.885 40.741 13.66 8.03 44.16 1.78
4476 5256 6.712241 TCGTTCTAGGTAGTACGTATATGC 57.288 41.667 13.66 0.00 44.16 3.14
4477 5257 6.459066 TCGTTCTAGGTAGTACGTATATGCT 58.541 40.000 13.66 0.00 44.16 3.79
4478 5258 6.587990 TCGTTCTAGGTAGTACGTATATGCTC 59.412 42.308 13.66 0.00 44.16 4.26
4479 5259 6.183360 CGTTCTAGGTAGTACGTATATGCTCC 60.183 46.154 0.00 0.00 40.63 4.70
4480 5260 6.617782 TCTAGGTAGTACGTATATGCTCCT 57.382 41.667 0.00 4.52 0.00 3.69
4481 5261 6.638610 TCTAGGTAGTACGTATATGCTCCTC 58.361 44.000 0.00 0.00 0.00 3.71
4482 5262 5.502089 AGGTAGTACGTATATGCTCCTCT 57.498 43.478 0.00 0.00 0.00 3.69
4483 5263 5.878627 AGGTAGTACGTATATGCTCCTCTT 58.121 41.667 0.00 0.00 0.00 2.85
4484 5264 6.305411 AGGTAGTACGTATATGCTCCTCTTT 58.695 40.000 0.00 0.00 0.00 2.52
4485 5265 6.430616 AGGTAGTACGTATATGCTCCTCTTTC 59.569 42.308 0.00 0.00 0.00 2.62
4486 5266 6.430616 GGTAGTACGTATATGCTCCTCTTTCT 59.569 42.308 0.00 0.00 0.00 2.52
4487 5267 6.320494 AGTACGTATATGCTCCTCTTTCTG 57.680 41.667 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.477607 TCTTGGAGTTAACGGATTTGAGA 57.522 39.130 0.00 0.00 0.00 3.27
1 2 6.554334 TTTCTTGGAGTTAACGGATTTGAG 57.446 37.500 0.00 0.00 0.00 3.02
2 3 6.945938 TTTTCTTGGAGTTAACGGATTTGA 57.054 33.333 0.00 0.00 0.00 2.69
3 4 6.640907 CCTTTTTCTTGGAGTTAACGGATTTG 59.359 38.462 0.00 0.00 0.00 2.32
23 24 4.503817 GGCTTGATTTTTCTGCTCCCTTTT 60.504 41.667 0.00 0.00 0.00 2.27
24 25 3.007290 GGCTTGATTTTTCTGCTCCCTTT 59.993 43.478 0.00 0.00 0.00 3.11
48 49 3.958151 GTCGTTCGCACTAGTTTGTTTTC 59.042 43.478 0.00 0.00 0.00 2.29
51 52 1.862827 GGTCGTTCGCACTAGTTTGTT 59.137 47.619 0.00 0.00 0.00 2.83
116 121 2.103537 AGGCCATTTGCATTTTGCTC 57.896 45.000 5.01 0.00 45.31 4.26
169 174 2.684881 CACACTATGAATGGTTCTGGGC 59.315 50.000 0.00 0.00 0.00 5.36
193 198 4.389576 CACTTCGGCGCCTGTTGC 62.390 66.667 26.68 0.00 0.00 4.17
243 248 0.811616 GCGGGATGCCACTTAGTCAG 60.812 60.000 3.39 0.00 37.76 3.51
287 292 5.552472 GCAAAATGTTCATACGCGCTAAATG 60.552 40.000 5.73 5.46 0.00 2.32
293 298 1.840141 GAGCAAAATGTTCATACGCGC 59.160 47.619 5.73 0.00 0.00 6.86
294 299 3.116063 TGAGCAAAATGTTCATACGCG 57.884 42.857 3.53 3.53 32.63 6.01
295 300 4.913376 AGATGAGCAAAATGTTCATACGC 58.087 39.130 9.26 0.00 46.08 4.42
378 386 4.603989 TTTTGTGGGTACATACGAGTCA 57.396 40.909 0.00 0.00 36.53 3.41
417 564 6.153067 CCAGCTCTCAATAACTAAGGATACG 58.847 44.000 0.00 0.00 46.39 3.06
422 569 4.142138 ACGACCAGCTCTCAATAACTAAGG 60.142 45.833 0.00 0.00 0.00 2.69
462 609 2.836372 ACTTAACCTACCAGTACCAGGC 59.164 50.000 2.00 0.00 32.31 4.85
463 610 4.081254 GGAACTTAACCTACCAGTACCAGG 60.081 50.000 0.58 0.58 35.45 4.45
465 612 4.755437 AGGAACTTAACCTACCAGTACCA 58.245 43.478 0.00 0.00 35.84 3.25
466 613 4.142293 CGAGGAACTTAACCTACCAGTACC 60.142 50.000 0.00 0.00 41.55 3.34
467 614 4.676459 GCGAGGAACTTAACCTACCAGTAC 60.676 50.000 0.00 0.00 41.55 2.73
468 615 3.445096 GCGAGGAACTTAACCTACCAGTA 59.555 47.826 0.00 0.00 41.55 2.74
469 616 2.233186 GCGAGGAACTTAACCTACCAGT 59.767 50.000 0.00 0.00 41.55 4.00
470 617 2.496470 AGCGAGGAACTTAACCTACCAG 59.504 50.000 0.00 0.00 41.55 4.00
471 618 2.494870 GAGCGAGGAACTTAACCTACCA 59.505 50.000 0.00 0.00 41.55 3.25
472 619 2.759535 AGAGCGAGGAACTTAACCTACC 59.240 50.000 0.00 0.00 41.55 3.18
473 620 3.181488 GGAGAGCGAGGAACTTAACCTAC 60.181 52.174 0.00 0.00 41.55 3.18
474 621 3.022406 GGAGAGCGAGGAACTTAACCTA 58.978 50.000 0.00 0.00 41.55 3.08
475 622 1.826096 GGAGAGCGAGGAACTTAACCT 59.174 52.381 0.00 0.00 41.55 3.50
501 648 1.597461 GGGTGAGTGAGGTAGGTGC 59.403 63.158 0.00 0.00 0.00 5.01
558 705 2.674380 CCAGGCTGCTGGTGTTCC 60.674 66.667 9.56 0.00 39.56 3.62
643 795 0.947180 GAAAACGGTGGCGTGCTAGA 60.947 55.000 0.00 0.00 0.00 2.43
658 816 6.457257 CGTCGTTTGTTTTAGGAAGGAGAAAA 60.457 38.462 0.00 0.00 0.00 2.29
751 912 4.965858 CGATCTCGACGCCTCCGC 62.966 72.222 0.00 0.00 43.02 5.54
759 920 1.300233 GGCCCATGACGATCTCGAC 60.300 63.158 6.60 0.53 43.02 4.20
1017 1206 4.430765 GCGAAGGAGACGGCGGAA 62.431 66.667 13.24 0.00 33.39 4.30
1095 1294 4.647615 CTACCGGGCGCAGATCGG 62.648 72.222 22.52 22.52 46.58 4.18
1121 1320 0.321298 ATTCTGAAACCCCGGTGTCG 60.321 55.000 0.00 0.00 35.20 4.35
1123 1322 1.064825 AGATTCTGAAACCCCGGTGT 58.935 50.000 0.00 0.00 0.00 4.16
1125 1324 0.328258 CCAGATTCTGAAACCCCGGT 59.672 55.000 15.36 0.00 32.44 5.28
1126 1325 0.618458 TCCAGATTCTGAAACCCCGG 59.382 55.000 15.36 0.00 32.44 5.73
1147 1346 0.033504 AATCTGACGAACACTGGCGT 59.966 50.000 0.00 0.00 44.33 5.68
1148 1347 1.920574 CTAATCTGACGAACACTGGCG 59.079 52.381 0.00 0.00 0.00 5.69
1149 1348 2.271800 CCTAATCTGACGAACACTGGC 58.728 52.381 0.00 0.00 0.00 4.85
1150 1349 3.254060 CACCTAATCTGACGAACACTGG 58.746 50.000 0.00 0.00 0.00 4.00
1151 1350 2.668457 GCACCTAATCTGACGAACACTG 59.332 50.000 0.00 0.00 0.00 3.66
1152 1351 2.671351 CGCACCTAATCTGACGAACACT 60.671 50.000 0.00 0.00 0.00 3.55
1153 1352 1.654105 CGCACCTAATCTGACGAACAC 59.346 52.381 0.00 0.00 0.00 3.32
1154 1353 1.403647 CCGCACCTAATCTGACGAACA 60.404 52.381 0.00 0.00 0.00 3.18
1155 1354 1.278238 CCGCACCTAATCTGACGAAC 58.722 55.000 0.00 0.00 0.00 3.95
1156 1355 0.174845 CCCGCACCTAATCTGACGAA 59.825 55.000 0.00 0.00 0.00 3.85
1157 1356 0.968901 ACCCGCACCTAATCTGACGA 60.969 55.000 0.00 0.00 0.00 4.20
1158 1357 0.527817 GACCCGCACCTAATCTGACG 60.528 60.000 0.00 0.00 0.00 4.35
1159 1358 0.179081 GGACCCGCACCTAATCTGAC 60.179 60.000 0.00 0.00 0.00 3.51
1160 1359 1.672854 CGGACCCGCACCTAATCTGA 61.673 60.000 0.00 0.00 0.00 3.27
1161 1360 1.227263 CGGACCCGCACCTAATCTG 60.227 63.158 0.00 0.00 0.00 2.90
1328 1997 2.782222 TAGCACCGCCCAGATCGAC 61.782 63.158 0.00 0.00 0.00 4.20
1353 2022 6.539826 ACATGCGGTTATATGTATCATGATGG 59.460 38.462 18.72 0.00 35.86 3.51
1384 2057 1.588404 GATCCAACGAGTACGCACATG 59.412 52.381 0.00 0.00 43.96 3.21
1393 2066 2.346803 CAAACATCCGATCCAACGAGT 58.653 47.619 0.00 0.00 35.09 4.18
1610 2284 3.185594 CACCATGAAGCAATGCAAACAAG 59.814 43.478 8.35 1.57 0.00 3.16
1632 2306 2.159327 GGCAATCCTTAATGCATGCC 57.841 50.000 16.68 7.86 45.54 4.40
1674 2348 4.772100 CACCTAAACCTGGGAATGTTTCAT 59.228 41.667 0.00 0.00 36.23 2.57
1680 2354 4.599041 TCAATCACCTAAACCTGGGAATG 58.401 43.478 0.00 0.00 0.00 2.67
1832 2507 6.005583 ACACAGCATCAGTTTAATCAACAG 57.994 37.500 0.00 0.00 37.93 3.16
1893 2570 8.375506 TGTGTCTCAACATAACTCCTAAGAAAT 58.624 33.333 0.00 0.00 37.81 2.17
1911 2588 4.248058 CTGTGAAGCATGTATGTGTCTCA 58.752 43.478 0.00 0.00 0.00 3.27
1912 2589 3.063180 GCTGTGAAGCATGTATGTGTCTC 59.937 47.826 0.00 0.00 34.41 3.36
1963 2640 1.207089 CAGGACCTGTTCGGCTATTCA 59.793 52.381 13.84 0.00 35.61 2.57
2013 2690 4.141642 ACCAAAACAGGTACGTATATCCCC 60.142 45.833 0.00 0.00 40.98 4.81
2026 2703 8.630037 AGAGAACAAAATAGTAACCAAAACAGG 58.370 33.333 0.00 0.00 0.00 4.00
2048 2726 7.307989 CCGAAATTGAAAAGCAGAAACTAGAGA 60.308 37.037 0.00 0.00 0.00 3.10
2068 2746 2.161855 TCAATGCTGCTTCACCGAAAT 58.838 42.857 0.00 0.00 0.00 2.17
2073 2751 5.870978 ACAAAATTATCAATGCTGCTTCACC 59.129 36.000 0.00 0.00 0.00 4.02
2191 2869 6.079712 ACTAGGGAATAGCAAACCAGATTT 57.920 37.500 0.00 0.00 34.56 2.17
2249 2927 5.105797 GGCATTGATTGTCTGTAAATCACCA 60.106 40.000 7.09 0.00 42.28 4.17
2252 2930 6.209192 AGTTGGCATTGATTGTCTGTAAATCA 59.791 34.615 0.00 0.00 41.19 2.57
2262 2940 1.812571 GACCGAGTTGGCATTGATTGT 59.187 47.619 0.00 0.00 43.94 2.71
2458 3136 8.849168 TGTTGCCTTCATATATGAAACTAATGG 58.151 33.333 24.61 21.17 45.26 3.16
2491 3169 8.597662 AGCATGCATGATTAATTATTCCAAAC 57.402 30.769 30.64 5.91 0.00 2.93
2576 3254 6.992715 ACAGGGTTTTCTATATGATGCAGTAC 59.007 38.462 0.00 0.00 0.00 2.73
2667 3345 7.169813 CCAAAAAGAAACTAAGATTGCTGGAAC 59.830 37.037 0.00 0.00 0.00 3.62
2678 3356 6.664515 TGCACGATACCAAAAAGAAACTAAG 58.335 36.000 0.00 0.00 0.00 2.18
2679 3357 6.621316 TGCACGATACCAAAAAGAAACTAA 57.379 33.333 0.00 0.00 0.00 2.24
2785 3463 8.275040 ACCTGCCTATTAAATCAGAATTACAGT 58.725 33.333 0.00 0.00 0.00 3.55
2851 3529 6.841601 AGAATCATAGCAACAAAGCCCTATA 58.158 36.000 0.00 0.00 34.23 1.31
3021 3699 1.414919 AGCTGACTTACCGTGTCCAAA 59.585 47.619 0.00 0.00 33.83 3.28
3058 3736 4.847198 TGTTGCTAGGATGAACATGTGAT 58.153 39.130 0.00 0.00 0.00 3.06
3146 3867 0.030235 TGTAGCACTGCGCCGTATAG 59.970 55.000 4.18 0.00 44.04 1.31
3152 3873 1.082104 GTTGTTGTAGCACTGCGCC 60.082 57.895 4.18 0.00 44.04 6.53
3155 3876 5.108385 ACTATTTGTTGTTGTAGCACTGC 57.892 39.130 0.00 0.00 0.00 4.40
3156 3877 9.117145 CATAAACTATTTGTTGTTGTAGCACTG 57.883 33.333 0.00 0.00 39.13 3.66
3157 3878 8.846211 ACATAAACTATTTGTTGTTGTAGCACT 58.154 29.630 0.00 0.00 39.13 4.40
3158 3879 9.458374 AACATAAACTATTTGTTGTTGTAGCAC 57.542 29.630 0.00 0.00 39.13 4.40
3188 3909 7.215789 TGGGTTTCGTAGTCACAAAATACTTA 58.784 34.615 0.00 0.00 0.00 2.24
3258 4001 1.896660 ATGGTTCCCGCACACACAC 60.897 57.895 0.00 0.00 0.00 3.82
3259 4002 1.896183 CATGGTTCCCGCACACACA 60.896 57.895 0.00 0.00 0.00 3.72
3264 4009 0.039527 GAACAACATGGTTCCCGCAC 60.040 55.000 0.00 0.00 40.97 5.34
3269 4014 6.262273 TGAAGAAAGTAGAACAACATGGTTCC 59.738 38.462 10.21 0.00 46.52 3.62
3303 4048 1.198713 TGCCAAAAACTGCTCCCAAA 58.801 45.000 0.00 0.00 0.00 3.28
3306 4051 1.067354 CAGATGCCAAAAACTGCTCCC 60.067 52.381 0.00 0.00 0.00 4.30
3312 4057 5.852282 ACAAAGTACAGATGCCAAAAACT 57.148 34.783 0.00 0.00 0.00 2.66
3323 4068 3.738830 ACCGCAGTAACAAAGTACAGA 57.261 42.857 0.00 0.00 0.00 3.41
3325 4070 5.334260 GCATAAACCGCAGTAACAAAGTACA 60.334 40.000 0.00 0.00 0.00 2.90
3341 4086 7.200455 AGTGTTGACAAAAGTTAGCATAAACC 58.800 34.615 0.00 0.00 0.00 3.27
3358 4103 2.618241 TCATGCACAAAGGAGTGTTGAC 59.382 45.455 0.00 0.00 41.52 3.18
3454 4200 5.649395 CCATGACAATCTCAACCTACACAAT 59.351 40.000 0.00 0.00 30.60 2.71
3531 4277 4.980805 GCGTCCTCCACCGTTGCA 62.981 66.667 0.00 0.00 0.00 4.08
3543 4289 4.778143 ATGAGGTTGGCGGCGTCC 62.778 66.667 9.84 11.43 0.00 4.79
3754 4500 5.244626 ACCCTGAAATCATTCTTCAACAAGG 59.755 40.000 0.00 0.00 36.48 3.61
3772 4518 2.616256 GCACATCATGTTCAGACCCTGA 60.616 50.000 0.00 0.00 38.87 3.86
3773 4519 1.741706 GCACATCATGTTCAGACCCTG 59.258 52.381 0.00 0.00 0.00 4.45
3873 4633 7.883311 TGAAAATTACCAAAAACAACCCAAGAA 59.117 29.630 0.00 0.00 0.00 2.52
3874 4634 7.394816 TGAAAATTACCAAAAACAACCCAAGA 58.605 30.769 0.00 0.00 0.00 3.02
3875 4635 7.335673 ACTGAAAATTACCAAAAACAACCCAAG 59.664 33.333 0.00 0.00 0.00 3.61
3876 4636 7.168905 ACTGAAAATTACCAAAAACAACCCAA 58.831 30.769 0.00 0.00 0.00 4.12
3877 4637 6.712276 ACTGAAAATTACCAAAAACAACCCA 58.288 32.000 0.00 0.00 0.00 4.51
3878 4638 7.618502 AACTGAAAATTACCAAAAACAACCC 57.381 32.000 0.00 0.00 0.00 4.11
3961 4730 3.102052 CAGAAAAGTTTGTGCAGGCAT 57.898 42.857 0.00 0.00 0.00 4.40
3968 4737 5.844301 ACAAAACAGCAGAAAAGTTTGTG 57.156 34.783 0.00 0.00 35.79 3.33
3969 4738 6.687604 AGTACAAAACAGCAGAAAAGTTTGT 58.312 32.000 0.00 5.11 35.79 2.83
3992 4761 2.389962 TTATTTTGGGACGGACGGAG 57.610 50.000 0.00 0.00 0.00 4.63
3994 4763 1.741145 CCTTTATTTTGGGACGGACGG 59.259 52.381 0.00 0.00 0.00 4.79
3996 4765 4.582869 ACTACCTTTATTTTGGGACGGAC 58.417 43.478 0.00 0.00 0.00 4.79
3997 4766 4.914177 ACTACCTTTATTTTGGGACGGA 57.086 40.909 0.00 0.00 0.00 4.69
3998 4767 5.490159 TGTACTACCTTTATTTTGGGACGG 58.510 41.667 0.00 0.00 0.00 4.79
3999 4768 7.173735 ACTTTGTACTACCTTTATTTTGGGACG 59.826 37.037 0.00 0.00 0.00 4.79
4000 4769 8.400184 ACTTTGTACTACCTTTATTTTGGGAC 57.600 34.615 0.00 0.00 0.00 4.46
4001 4770 8.999905 AACTTTGTACTACCTTTATTTTGGGA 57.000 30.769 0.00 0.00 0.00 4.37
4017 4786 9.620660 CCCAAAATATGTGACTTAACTTTGTAC 57.379 33.333 11.74 0.00 0.00 2.90
4018 4787 9.575868 TCCCAAAATATGTGACTTAACTTTGTA 57.424 29.630 11.74 2.89 0.00 2.41
4020 4789 8.356657 TGTCCCAAAATATGTGACTTAACTTTG 58.643 33.333 8.32 8.32 37.33 2.77
4021 4790 8.472007 TGTCCCAAAATATGTGACTTAACTTT 57.528 30.769 0.00 0.00 37.33 2.66
4022 4791 7.942341 TCTGTCCCAAAATATGTGACTTAACTT 59.058 33.333 0.00 0.00 37.33 2.66
4024 4793 7.681939 TCTGTCCCAAAATATGTGACTTAAC 57.318 36.000 0.00 0.00 37.33 2.01
4025 4794 7.339212 CCATCTGTCCCAAAATATGTGACTTAA 59.661 37.037 0.00 0.00 37.33 1.85
4026 4795 6.828273 CCATCTGTCCCAAAATATGTGACTTA 59.172 38.462 0.00 0.00 37.33 2.24
4027 4796 5.653769 CCATCTGTCCCAAAATATGTGACTT 59.346 40.000 0.00 0.00 37.33 3.01
4028 4797 5.044919 TCCATCTGTCCCAAAATATGTGACT 60.045 40.000 0.00 0.00 37.33 3.41
4029 4798 5.192927 TCCATCTGTCCCAAAATATGTGAC 58.807 41.667 0.00 0.00 37.00 3.67
4030 4799 5.044919 ACTCCATCTGTCCCAAAATATGTGA 60.045 40.000 0.00 0.00 0.00 3.58
4031 4800 5.195940 ACTCCATCTGTCCCAAAATATGTG 58.804 41.667 0.00 0.00 0.00 3.21
4036 4805 8.893563 TTAAAATACTCCATCTGTCCCAAAAT 57.106 30.769 0.00 0.00 0.00 1.82
4037 4806 8.713708 TTTAAAATACTCCATCTGTCCCAAAA 57.286 30.769 0.00 0.00 0.00 2.44
4038 4807 8.581578 GTTTTAAAATACTCCATCTGTCCCAAA 58.418 33.333 3.52 0.00 0.00 3.28
4039 4808 7.094549 CGTTTTAAAATACTCCATCTGTCCCAA 60.095 37.037 3.52 0.00 0.00 4.12
4040 4809 6.373216 CGTTTTAAAATACTCCATCTGTCCCA 59.627 38.462 3.52 0.00 0.00 4.37
4041 4810 6.677187 GCGTTTTAAAATACTCCATCTGTCCC 60.677 42.308 3.52 0.00 0.00 4.46
4042 4811 6.128117 TGCGTTTTAAAATACTCCATCTGTCC 60.128 38.462 3.52 0.00 0.00 4.02
4043 4812 6.741358 GTGCGTTTTAAAATACTCCATCTGTC 59.259 38.462 3.52 0.00 0.00 3.51
4045 4814 6.842163 AGTGCGTTTTAAAATACTCCATCTG 58.158 36.000 3.52 0.00 0.00 2.90
4046 4815 7.073342 GAGTGCGTTTTAAAATACTCCATCT 57.927 36.000 20.73 8.05 30.93 2.90
4051 4820 7.592439 AGTAGGAGTGCGTTTTAAAATACTC 57.408 36.000 22.01 22.01 35.13 2.59
4053 4822 8.071967 ACAAAGTAGGAGTGCGTTTTAAAATAC 58.928 33.333 3.52 4.66 0.00 1.89
4055 4824 7.034685 ACAAAGTAGGAGTGCGTTTTAAAAT 57.965 32.000 3.52 0.00 0.00 1.82
4056 4825 6.439675 ACAAAGTAGGAGTGCGTTTTAAAA 57.560 33.333 0.00 0.00 0.00 1.52
4058 4827 6.762661 ACTAACAAAGTAGGAGTGCGTTTTAA 59.237 34.615 0.00 0.00 36.36 1.52
4094 4863 9.049523 GTAAGTGGCTTAGTTTTAGTACAACTT 57.950 33.333 7.00 0.00 35.95 2.66
4095 4864 8.427276 AGTAAGTGGCTTAGTTTTAGTACAACT 58.573 33.333 6.90 6.90 38.13 3.16
4096 4865 8.599055 AGTAAGTGGCTTAGTTTTAGTACAAC 57.401 34.615 0.00 0.00 0.00 3.32
4097 4866 9.617523 AAAGTAAGTGGCTTAGTTTTAGTACAA 57.382 29.630 13.07 0.00 43.04 2.41
4098 4867 9.048446 CAAAGTAAGTGGCTTAGTTTTAGTACA 57.952 33.333 15.16 0.00 43.04 2.90
4099 4868 8.501580 CCAAAGTAAGTGGCTTAGTTTTAGTAC 58.498 37.037 15.16 0.00 43.04 2.73
4100 4869 7.662669 CCCAAAGTAAGTGGCTTAGTTTTAGTA 59.337 37.037 15.16 0.00 43.04 1.82
4101 4870 6.489022 CCCAAAGTAAGTGGCTTAGTTTTAGT 59.511 38.462 15.16 0.00 43.04 2.24
4102 4871 6.713450 TCCCAAAGTAAGTGGCTTAGTTTTAG 59.287 38.462 15.16 11.19 43.04 1.85
4103 4872 6.487668 GTCCCAAAGTAAGTGGCTTAGTTTTA 59.512 38.462 15.16 5.74 43.04 1.52
4104 4873 5.301045 GTCCCAAAGTAAGTGGCTTAGTTTT 59.699 40.000 15.16 6.01 43.04 2.43
4105 4874 4.825634 GTCCCAAAGTAAGTGGCTTAGTTT 59.174 41.667 13.07 13.07 45.05 2.66
4106 4875 4.395625 GTCCCAAAGTAAGTGGCTTAGTT 58.604 43.478 3.83 3.83 40.13 2.24
4107 4876 3.244805 GGTCCCAAAGTAAGTGGCTTAGT 60.245 47.826 0.00 0.00 34.56 2.24
4108 4877 3.009143 AGGTCCCAAAGTAAGTGGCTTAG 59.991 47.826 0.00 0.00 34.56 2.18
4109 4878 2.983898 AGGTCCCAAAGTAAGTGGCTTA 59.016 45.455 0.00 0.00 34.56 3.09
4110 4879 1.780919 AGGTCCCAAAGTAAGTGGCTT 59.219 47.619 0.00 0.00 34.56 4.35
4111 4880 1.446016 AGGTCCCAAAGTAAGTGGCT 58.554 50.000 0.00 0.00 34.56 4.75
4112 4881 2.355818 CCTAGGTCCCAAAGTAAGTGGC 60.356 54.545 0.00 0.00 34.56 5.01
4113 4882 2.238898 CCCTAGGTCCCAAAGTAAGTGG 59.761 54.545 8.29 0.00 35.77 4.00
4114 4883 3.178865 TCCCTAGGTCCCAAAGTAAGTG 58.821 50.000 8.29 0.00 0.00 3.16
4115 4884 3.181398 ACTCCCTAGGTCCCAAAGTAAGT 60.181 47.826 8.29 0.00 0.00 2.24
4116 4885 3.451890 ACTCCCTAGGTCCCAAAGTAAG 58.548 50.000 8.29 0.00 0.00 2.34
4117 4886 3.572661 ACTCCCTAGGTCCCAAAGTAA 57.427 47.619 8.29 0.00 0.00 2.24
4118 4887 4.913154 ATACTCCCTAGGTCCCAAAGTA 57.087 45.455 8.29 6.03 0.00 2.24
4119 4888 3.797671 ATACTCCCTAGGTCCCAAAGT 57.202 47.619 8.29 4.05 0.00 2.66
4120 4889 4.781934 CAAATACTCCCTAGGTCCCAAAG 58.218 47.826 8.29 0.00 0.00 2.77
4121 4890 3.053917 GCAAATACTCCCTAGGTCCCAAA 60.054 47.826 8.29 0.00 0.00 3.28
4122 4891 2.508300 GCAAATACTCCCTAGGTCCCAA 59.492 50.000 8.29 0.00 0.00 4.12
4123 4892 2.124411 GCAAATACTCCCTAGGTCCCA 58.876 52.381 8.29 0.00 0.00 4.37
4124 4893 2.409570 AGCAAATACTCCCTAGGTCCC 58.590 52.381 8.29 0.00 0.00 4.46
4127 4896 6.886178 TCTAAAAGCAAATACTCCCTAGGT 57.114 37.500 8.29 0.00 0.00 3.08
4128 4897 7.283354 CCTTTCTAAAAGCAAATACTCCCTAGG 59.717 40.741 0.06 0.06 0.00 3.02
4129 4898 7.829706 ACCTTTCTAAAAGCAAATACTCCCTAG 59.170 37.037 0.00 0.00 0.00 3.02
4130 4899 7.696017 ACCTTTCTAAAAGCAAATACTCCCTA 58.304 34.615 0.00 0.00 0.00 3.53
4131 4900 6.552932 ACCTTTCTAAAAGCAAATACTCCCT 58.447 36.000 0.00 0.00 0.00 4.20
4132 4901 6.835819 ACCTTTCTAAAAGCAAATACTCCC 57.164 37.500 0.00 0.00 0.00 4.30
4133 4902 9.193133 GAAAACCTTTCTAAAAGCAAATACTCC 57.807 33.333 0.00 0.00 0.00 3.85
4134 4903 9.744468 TGAAAACCTTTCTAAAAGCAAATACTC 57.256 29.630 1.22 0.00 0.00 2.59
4135 4904 9.529325 GTGAAAACCTTTCTAAAAGCAAATACT 57.471 29.630 1.22 0.00 0.00 2.12
4147 4916 4.426736 AACCGAGGTGAAAACCTTTCTA 57.573 40.909 0.00 0.00 40.86 2.10
4148 4917 3.292492 AACCGAGGTGAAAACCTTTCT 57.708 42.857 0.00 0.00 40.86 2.52
4157 4926 1.707106 TCCAGTGTAACCGAGGTGAA 58.293 50.000 0.00 0.00 37.80 3.18
4160 4929 0.683412 GGTTCCAGTGTAACCGAGGT 59.317 55.000 1.38 0.00 37.26 3.85
4165 4934 2.779506 CCTCTTGGTTCCAGTGTAACC 58.220 52.381 10.57 10.57 45.53 2.85
4169 4938 1.729586 TAGCCTCTTGGTTCCAGTGT 58.270 50.000 0.00 0.00 35.27 3.55
4174 4943 5.984695 AAATTTCTTAGCCTCTTGGTTCC 57.015 39.130 0.00 0.00 35.27 3.62
4198 4967 8.236586 GCACTGAACATCATAACACAGAAAATA 58.763 33.333 0.00 0.00 0.00 1.40
4201 4970 5.530543 TGCACTGAACATCATAACACAGAAA 59.469 36.000 0.00 0.00 0.00 2.52
4249 5019 1.012234 GAATCGAATGCGCGTCCAC 60.012 57.895 8.43 0.00 37.46 4.02
4265 5035 6.927416 TGCTAGTTTAACCACGAGATTAGAA 58.073 36.000 0.00 0.00 0.00 2.10
4266 5036 6.519679 TGCTAGTTTAACCACGAGATTAGA 57.480 37.500 0.00 0.00 0.00 2.10
4387 5157 3.132289 TGATTGTACTGCTACCACTAGGC 59.868 47.826 0.00 0.00 39.06 3.93
4399 5172 6.214191 ACTACCACTCAGATGATTGTACTG 57.786 41.667 0.00 0.00 0.00 2.74
4427 5203 0.605589 CCGCCCAAACCAGCAAAATA 59.394 50.000 0.00 0.00 0.00 1.40
4436 5216 3.336715 GAACGATGCCGCCCAAACC 62.337 63.158 0.00 0.00 39.95 3.27
4449 5229 3.585862 ACGTACTACCTAGAACGAACGA 58.414 45.455 11.92 0.00 38.64 3.85
4450 5230 3.999229 ACGTACTACCTAGAACGAACG 57.001 47.619 0.23 0.00 38.64 3.95
4451 5231 7.012358 GCATATACGTACTACCTAGAACGAAC 58.988 42.308 0.00 0.00 38.64 3.95
4452 5232 6.931281 AGCATATACGTACTACCTAGAACGAA 59.069 38.462 0.00 0.00 38.64 3.85
4469 5249 4.562552 GGAGCCAGAAAGAGGAGCATATAC 60.563 50.000 0.00 0.00 0.00 1.47
4471 5251 2.371510 GGAGCCAGAAAGAGGAGCATAT 59.628 50.000 0.00 0.00 0.00 1.78
4473 5253 0.545646 GGAGCCAGAAAGAGGAGCAT 59.454 55.000 0.00 0.00 0.00 3.79
4474 5254 1.557269 GGGAGCCAGAAAGAGGAGCA 61.557 60.000 0.00 0.00 0.00 4.26
4475 5255 1.223211 GGGAGCCAGAAAGAGGAGC 59.777 63.158 0.00 0.00 0.00 4.70
4476 5256 1.911471 GGGGAGCCAGAAAGAGGAG 59.089 63.158 0.00 0.00 0.00 3.69
4477 5257 1.990060 CGGGGAGCCAGAAAGAGGA 60.990 63.158 0.00 0.00 0.00 3.71
4478 5258 1.990060 TCGGGGAGCCAGAAAGAGG 60.990 63.158 0.00 0.00 0.00 3.69
4479 5259 1.219393 GTCGGGGAGCCAGAAAGAG 59.781 63.158 0.00 0.00 28.12 2.85
4480 5260 2.291043 GGTCGGGGAGCCAGAAAGA 61.291 63.158 0.00 0.00 28.12 2.52
4481 5261 2.269241 GGTCGGGGAGCCAGAAAG 59.731 66.667 0.00 0.00 28.12 2.62


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

AutoCloner maintained by Alex Coulton.