Multiple sequence alignment - TraesCS7B01G448200

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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 TraesCS7B01G448200 chr7B 100.000 4117 0 0 1 4117 711064196 711060080 0.000000e+00 7603.0
1 TraesCS7B01G448200 chr7B 78.135 933 135 31 1023 1919 711723025 711722126 2.820000e-146 529.0
2 TraesCS7B01G448200 chr7B 77.916 806 124 32 1023 1813 711638596 711639362 1.740000e-123 453.0
3 TraesCS7B01G448200 chr7B 88.679 53 5 1 1951 2003 711722128 711722077 3.440000e-06 63.9
4 TraesCS7B01G448200 chr7D 94.020 2040 78 15 45 2070 617020245 617018236 0.000000e+00 3051.0
5 TraesCS7B01G448200 chr7D 92.045 1320 65 19 2123 3410 617018232 617016921 0.000000e+00 1820.0
6 TraesCS7B01G448200 chr7D 94.521 365 16 4 3479 3841 617016923 617016561 9.990000e-156 560.0
7 TraesCS7B01G448200 chr7D 77.137 936 141 30 1023 1918 617645661 617644759 3.720000e-130 475.0
8 TraesCS7B01G448200 chr7D 91.450 269 21 2 3833 4101 215783328 215783594 6.500000e-98 368.0
9 TraesCS7B01G448200 chr7D 90.809 272 21 2 3837 4108 499792586 499792853 1.090000e-95 361.0
10 TraesCS7B01G448200 chr7D 78.209 592 95 18 1361 1937 617637360 617637932 8.470000e-92 348.0
11 TraesCS7B01G448200 chr7A 82.348 1099 137 30 952 2001 709734552 709733462 0.000000e+00 902.0
12 TraesCS7B01G448200 chr7A 77.679 896 129 40 1029 1904 711369230 711370074 8.000000e-132 481.0
13 TraesCS7B01G448200 chr7A 85.637 369 37 8 3479 3838 709731982 709731621 1.400000e-99 374.0
14 TraesCS7B01G448200 chr7A 88.435 294 24 4 45 337 709735324 709735040 3.050000e-91 346.0
15 TraesCS7B01G448200 chr7A 78.286 525 66 28 387 890 709735052 709734555 1.120000e-75 294.0
16 TraesCS7B01G448200 chr7A 87.603 121 13 2 3257 3375 709732151 709732031 5.550000e-29 139.0
17 TraesCS7B01G448200 chr7A 92.308 39 2 1 1 38 83302279 83302317 2.000000e-03 54.7
18 TraesCS7B01G448200 chr3B 92.509 267 17 1 3834 4100 480376939 480377202 3.000000e-101 379.0
19 TraesCS7B01G448200 chr3B 92.481 266 17 1 3835 4100 692738396 692738134 1.080000e-100 377.0
20 TraesCS7B01G448200 chr5B 90.141 284 24 2 3827 4110 281946544 281946823 2.340000e-97 366.0
21 TraesCS7B01G448200 chr5B 97.727 44 1 0 3439 3482 222593051 222593008 4.410000e-10 76.8
22 TraesCS7B01G448200 chr5B 93.333 45 3 0 1 45 652759343 652759299 2.660000e-07 67.6
23 TraesCS7B01G448200 chr4B 91.667 264 19 1 3837 4100 387492129 387491869 3.020000e-96 363.0
24 TraesCS7B01G448200 chr4B 87.500 72 7 2 2727 2797 119822942 119822872 9.490000e-12 82.4
25 TraesCS7B01G448200 chr4B 76.230 122 29 0 2725 2846 178072008 178072129 9.550000e-07 65.8
26 TraesCS7B01G448200 chr3D 91.386 267 20 1 3834 4100 369414160 369414423 3.020000e-96 363.0
27 TraesCS7B01G448200 chr3D 95.122 41 0 2 3427 3467 12162117 12162079 3.440000e-06 63.9
28 TraesCS7B01G448200 chr2D 90.580 276 22 3 3825 4100 398505259 398505530 3.020000e-96 363.0
29 TraesCS7B01G448200 chr2B 91.353 266 20 1 3836 4101 247919837 247919575 1.090000e-95 361.0
30 TraesCS7B01G448200 chr1B 85.417 144 21 0 1378 1521 18421191 18421048 2.560000e-32 150.0
31 TraesCS7B01G448200 chr1A 83.333 144 24 0 1378 1521 14506196 14506339 2.580000e-27 134.0
32 TraesCS7B01G448200 chr1A 86.111 72 10 0 2734 2805 117247554 117247625 1.230000e-10 78.7
33 TraesCS7B01G448200 chr1A 97.561 41 1 0 3440 3480 511001550 511001510 2.050000e-08 71.3
34 TraesCS7B01G448200 chr1A 90.698 43 2 2 1248 1290 229170535 229170495 5.750000e-04 56.5
35 TraesCS7B01G448200 chr6A 77.372 137 28 3 2725 2859 570382409 570382274 1.230000e-10 78.7
36 TraesCS7B01G448200 chr2A 97.778 45 1 0 3440 3484 636911499 636911543 1.230000e-10 78.7
37 TraesCS7B01G448200 chr2A 97.619 42 1 0 3439 3480 387641629 387641588 5.710000e-09 73.1
38 TraesCS7B01G448200 chr2A 97.619 42 1 0 3440 3481 690329380 690329421 5.710000e-09 73.1
39 TraesCS7B01G448200 chr4D 86.111 72 8 2 2727 2797 84545748 84545678 4.410000e-10 76.8
40 TraesCS7B01G448200 chr4D 77.869 122 27 0 2725 2846 116271077 116271198 4.410000e-10 76.8
41 TraesCS7B01G448200 chr4A 77.344 128 29 0 2725 2852 460239307 460239180 4.410000e-10 76.8
42 TraesCS7B01G448200 chr4A 86.111 72 8 2 2727 2797 497440580 497440510 4.410000e-10 76.8
43 TraesCS7B01G448200 chr3A 97.619 42 1 0 3439 3480 46723738 46723697 5.710000e-09 73.1
44 TraesCS7B01G448200 chr5D 100.000 38 0 0 3440 3477 231356321 231356358 2.050000e-08 71.3
45 TraesCS7B01G448200 chr5D 95.000 40 2 0 3446 3485 315412647 315412686 3.440000e-06 63.9
46 TraesCS7B01G448200 chr1D 94.595 37 1 1 1248 1284 171163722 171163687 5.750000e-04 56.5


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 TraesCS7B01G448200 chr7B 711060080 711064196 4116 True 7603.000000 7603 100.000000 1 4117 1 chr7B.!!$R1 4116
1 TraesCS7B01G448200 chr7B 711638596 711639362 766 False 453.000000 453 77.916000 1023 1813 1 chr7B.!!$F1 790
2 TraesCS7B01G448200 chr7B 711722077 711723025 948 True 296.450000 529 83.407000 1023 2003 2 chr7B.!!$R2 980
3 TraesCS7B01G448200 chr7D 617016561 617020245 3684 True 1810.333333 3051 93.528667 45 3841 3 chr7D.!!$R2 3796
4 TraesCS7B01G448200 chr7D 617644759 617645661 902 True 475.000000 475 77.137000 1023 1918 1 chr7D.!!$R1 895
5 TraesCS7B01G448200 chr7D 617637360 617637932 572 False 348.000000 348 78.209000 1361 1937 1 chr7D.!!$F3 576
6 TraesCS7B01G448200 chr7A 711369230 711370074 844 False 481.000000 481 77.679000 1029 1904 1 chr7A.!!$F2 875
7 TraesCS7B01G448200 chr7A 709731621 709735324 3703 True 411.000000 902 84.461800 45 3838 5 chr7A.!!$R1 3793

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
443 449 0.183492 AAGCTTCCAAGGCAGACACA 59.817 50.000 0.00 0.0 0.00 3.72 F
917 954 1.433534 GAGGCGAAAGGTCTCAACTG 58.566 55.000 0.00 0.0 46.90 3.16 F
1057 1095 1.439644 GGTGAGATCCTCCAGTCGC 59.560 63.158 0.00 0.0 0.00 5.19 F
1113 1160 1.601419 CGGCCACTAGGAACTTCCGA 61.601 60.000 2.24 0.0 42.75 4.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1405 1528 1.746615 CCAGATTGGGGTGCGACAG 60.747 63.158 0.0 0.0 32.67 3.51 R
2697 2997 1.771255 AGCAAAGGTTCAGACAGGACT 59.229 47.619 0.0 0.0 0.00 3.85 R
2987 3287 2.439156 GCCACCACCTGCTCCATC 60.439 66.667 0.0 0.0 0.00 3.51 R
3212 3546 0.402504 TGCCTAAAGAAGCGGGGAAA 59.597 50.000 0.0 0.0 0.00 3.13 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
38 39 3.793144 GCGGAGAGCTGCCAAACG 61.793 66.667 0.00 0.00 44.04 3.60
39 40 3.121030 CGGAGAGCTGCCAAACGG 61.121 66.667 0.00 0.00 0.00 4.44
40 41 2.747855 GGAGAGCTGCCAAACGGG 60.748 66.667 0.00 0.00 40.85 5.28
41 42 2.747855 GAGAGCTGCCAAACGGGG 60.748 66.667 0.00 0.00 37.04 5.73
68 69 6.143118 GCAAGATTATTCTCGTACTAGTGCTG 59.857 42.308 5.39 1.06 0.00 4.41
91 92 7.496529 TGTATAAGCCAATATGTTCTCTTGC 57.503 36.000 0.00 0.00 0.00 4.01
92 93 7.053498 TGTATAAGCCAATATGTTCTCTTGCA 58.947 34.615 0.00 0.00 0.00 4.08
93 94 7.555914 TGTATAAGCCAATATGTTCTCTTGCAA 59.444 33.333 0.00 0.00 0.00 4.08
94 95 5.726980 AAGCCAATATGTTCTCTTGCAAA 57.273 34.783 0.00 0.00 0.00 3.68
180 181 6.476380 TGCTGAAGTTCAACAACATGATTTTC 59.524 34.615 6.49 0.00 34.60 2.29
282 283 1.977594 GCGGCCTATGTTGAACACGG 61.978 60.000 0.00 5.62 0.00 4.94
299 300 1.437160 GGTGTTGGTGCCACTTGTG 59.563 57.895 0.00 0.00 33.31 3.33
347 348 0.606096 TACACTGGTGGTCACATCGG 59.394 55.000 5.70 0.00 40.07 4.18
350 355 1.480545 CACTGGTGGTCACATCGGATA 59.519 52.381 3.40 0.00 36.10 2.59
443 449 0.183492 AAGCTTCCAAGGCAGACACA 59.817 50.000 0.00 0.00 0.00 3.72
496 502 2.274542 TGGATGTACACATGGGTTCCT 58.725 47.619 16.46 0.66 36.57 3.36
549 555 2.558359 AGGTCATTGGTTGCTTAGTTGC 59.442 45.455 0.00 0.00 0.00 4.17
552 558 4.229876 GTCATTGGTTGCTTAGTTGCTTC 58.770 43.478 0.00 0.00 0.00 3.86
577 583 4.762289 AAGAGTTAGGTGGATCATGGAC 57.238 45.455 0.00 0.00 0.00 4.02
619 638 3.328931 ACAGTGGTGAAGAGTCCATGAAT 59.671 43.478 0.00 0.00 36.09 2.57
621 640 5.013079 ACAGTGGTGAAGAGTCCATGAATAA 59.987 40.000 0.00 0.00 36.09 1.40
624 643 4.883585 TGGTGAAGAGTCCATGAATAATGC 59.116 41.667 0.00 0.00 34.67 3.56
681 709 1.563924 AACATACTGGTCGGTGCCTA 58.436 50.000 0.00 0.00 0.00 3.93
688 716 1.448013 GGTCGGTGCCTACTGCTTC 60.448 63.158 0.00 0.00 42.00 3.86
736 765 3.253188 TCTTCTCCTTTTTGCGTCCATTG 59.747 43.478 0.00 0.00 0.00 2.82
818 847 2.449137 AATTAAGCTCAGCTGGGCAT 57.551 45.000 38.55 30.40 39.62 4.40
859 895 4.926238 GTCAGTAGTCAACCATCAGTCTTG 59.074 45.833 0.00 0.00 0.00 3.02
896 933 6.095300 TGGCTATATTAATTCAATCCGCCATG 59.905 38.462 0.00 0.00 37.91 3.66
917 954 1.433534 GAGGCGAAAGGTCTCAACTG 58.566 55.000 0.00 0.00 46.90 3.16
942 979 2.276732 TTCTCCCCTGCTTCAGTTTG 57.723 50.000 0.00 0.00 0.00 2.93
1057 1095 1.439644 GGTGAGATCCTCCAGTCGC 59.560 63.158 0.00 0.00 0.00 5.19
1064 1102 3.322466 CCTCCAGTCGCCCAACCT 61.322 66.667 0.00 0.00 0.00 3.50
1065 1103 2.266055 CTCCAGTCGCCCAACCTC 59.734 66.667 0.00 0.00 0.00 3.85
1066 1104 2.525629 TCCAGTCGCCCAACCTCA 60.526 61.111 0.00 0.00 0.00 3.86
1067 1105 2.046892 CCAGTCGCCCAACCTCAG 60.047 66.667 0.00 0.00 0.00 3.35
1068 1106 2.046892 CAGTCGCCCAACCTCAGG 60.047 66.667 0.00 0.00 0.00 3.86
1069 1107 2.203788 AGTCGCCCAACCTCAGGA 60.204 61.111 0.00 0.00 0.00 3.86
1070 1108 2.266055 GTCGCCCAACCTCAGGAG 59.734 66.667 0.00 0.00 0.00 3.69
1071 1109 3.706373 TCGCCCAACCTCAGGAGC 61.706 66.667 0.00 0.00 0.00 4.70
1072 1110 3.710722 CGCCCAACCTCAGGAGCT 61.711 66.667 0.00 0.00 0.00 4.09
1113 1160 1.601419 CGGCCACTAGGAACTTCCGA 61.601 60.000 2.24 0.00 42.75 4.55
1315 1389 4.885907 TCCCAATTCATTCATCTCTTCAGC 59.114 41.667 0.00 0.00 0.00 4.26
1405 1528 5.562890 GCTGAAGTGAATTACCTTGGACAAC 60.563 44.000 0.00 0.00 0.00 3.32
1567 1703 5.181245 CGTTCCATTGATCAGTTAACACCTT 59.819 40.000 8.61 0.00 0.00 3.50
1784 1941 7.787623 AGATGGGAAATGTTCTTCTTGATTT 57.212 32.000 0.00 0.00 0.00 2.17
1815 1972 7.920682 TGTTTCTGTTCTTTCCTTCTAATTTGC 59.079 33.333 0.00 0.00 0.00 3.68
1819 1976 7.667219 TCTGTTCTTTCCTTCTAATTTGCTGAT 59.333 33.333 0.00 0.00 0.00 2.90
1821 1978 8.641541 TGTTCTTTCCTTCTAATTTGCTGATTT 58.358 29.630 0.00 0.00 0.00 2.17
1822 1979 9.481340 GTTCTTTCCTTCTAATTTGCTGATTTT 57.519 29.630 0.00 0.00 0.00 1.82
1909 2079 1.962807 CTGTCTGATTTTGGGTTGGCA 59.037 47.619 0.00 0.00 0.00 4.92
2070 2241 5.125097 GTCTTCAAAGCCATGATCAGATGTT 59.875 40.000 0.09 0.00 0.00 2.71
2071 2242 5.713389 TCTTCAAAGCCATGATCAGATGTTT 59.287 36.000 0.09 0.00 0.00 2.83
2072 2243 5.988310 TCAAAGCCATGATCAGATGTTTT 57.012 34.783 0.09 0.08 0.00 2.43
2103 2274 8.623903 TGAATTTTAACCATGATCAGATGTAGC 58.376 33.333 0.09 0.00 0.00 3.58
2104 2275 8.523915 AATTTTAACCATGATCAGATGTAGCA 57.476 30.769 0.09 0.00 0.00 3.49
2105 2276 8.701908 ATTTTAACCATGATCAGATGTAGCAT 57.298 30.769 0.09 0.00 0.00 3.79
2106 2277 7.734924 TTTAACCATGATCAGATGTAGCATC 57.265 36.000 0.09 1.18 0.00 3.91
2107 2278 3.922910 ACCATGATCAGATGTAGCATCG 58.077 45.455 0.09 0.57 0.00 3.84
2108 2279 3.575687 ACCATGATCAGATGTAGCATCGA 59.424 43.478 0.09 0.00 0.00 3.59
2119 2290 9.741647 TCAGATGTAGCATCGATTATATTCATC 57.258 33.333 0.00 6.13 0.00 2.92
2120 2291 8.689069 CAGATGTAGCATCGATTATATTCATCG 58.311 37.037 0.00 9.63 44.09 3.84
2409 2629 9.276590 TGATTAATTAAGTATCACAGCCATCTG 57.723 33.333 3.94 0.00 45.71 2.90
2413 2633 3.123157 AGTATCACAGCCATCTGCATC 57.877 47.619 0.00 0.00 44.10 3.91
2501 2750 4.740822 ACAGGTCAATGGCGGCCC 62.741 66.667 17.97 0.00 0.00 5.80
2503 2752 2.690881 AGGTCAATGGCGGCCCTA 60.691 61.111 17.97 0.00 0.00 3.53
2529 2809 6.543831 ACTTGTTCTTTAGTTGATGAGCTGTT 59.456 34.615 0.00 0.00 0.00 3.16
2532 2812 8.445275 TGTTCTTTAGTTGATGAGCTGTTTAA 57.555 30.769 0.00 0.00 0.00 1.52
2541 2821 9.672673 AGTTGATGAGCTGTTTAATGTAATACT 57.327 29.630 0.00 0.00 0.00 2.12
2562 2842 9.875691 AATACTCATATAATCTTGCTAATGCGA 57.124 29.630 0.00 0.00 43.34 5.10
2585 2880 4.534500 AGTACACTAATCCATGGTGGTTCA 59.466 41.667 12.58 0.00 39.03 3.18
2601 2898 3.648067 TGGTTCATTGTCTTCTCCTCTGT 59.352 43.478 0.00 0.00 0.00 3.41
2658 2955 5.400066 TGATGTCTATCGAAACTGAACCA 57.600 39.130 0.00 0.00 36.04 3.67
2659 2956 5.168569 TGATGTCTATCGAAACTGAACCAC 58.831 41.667 0.00 0.00 36.04 4.16
2661 2958 5.970317 TGTCTATCGAAACTGAACCACTA 57.030 39.130 0.00 0.00 0.00 2.74
2691 2991 5.835819 AGCATCTAGTTGGACTGCTTATCTA 59.164 40.000 3.05 0.00 40.08 1.98
2695 2995 7.804843 TCTAGTTGGACTGCTTATCTACTAC 57.195 40.000 0.00 0.00 0.00 2.73
2696 2996 7.575505 TCTAGTTGGACTGCTTATCTACTACT 58.424 38.462 0.00 0.00 0.00 2.57
2697 2997 8.712103 TCTAGTTGGACTGCTTATCTACTACTA 58.288 37.037 0.00 0.00 0.00 1.82
2703 3003 6.428771 GGACTGCTTATCTACTACTAGTCCTG 59.571 46.154 0.00 0.00 45.83 3.86
2716 3016 2.262423 AGTCCTGTCTGAACCTTTGC 57.738 50.000 0.00 0.00 0.00 3.68
2967 3267 1.670967 CGCTCAAGTGCATCTCTGTCA 60.671 52.381 0.00 0.00 0.00 3.58
3005 3305 3.259314 ATGGAGCAGGTGGTGGCA 61.259 61.111 0.00 0.00 0.00 4.92
3152 3478 1.808945 GTGAGCACTGATGAAGGGTTG 59.191 52.381 0.00 0.00 0.00 3.77
3212 3546 2.638855 TGCAAATTCAGGGCTTCCATTT 59.361 40.909 0.00 0.00 0.00 2.32
3215 3549 4.154737 GCAAATTCAGGGCTTCCATTTTTC 59.845 41.667 0.00 0.00 0.00 2.29
3216 3550 4.558226 AATTCAGGGCTTCCATTTTTCC 57.442 40.909 0.00 0.00 0.00 3.13
3217 3551 1.937191 TCAGGGCTTCCATTTTTCCC 58.063 50.000 0.00 0.00 37.24 3.97
3218 3552 0.904649 CAGGGCTTCCATTTTTCCCC 59.095 55.000 0.00 0.00 37.70 4.81
3242 3576 3.845781 TCTTTAGGCAGGATGATGACC 57.154 47.619 0.00 0.00 39.69 4.02
3243 3577 3.114606 TCTTTAGGCAGGATGATGACCA 58.885 45.455 0.00 0.00 39.69 4.02
3246 3580 0.545171 AGGCAGGATGATGACCAGTG 59.455 55.000 0.00 0.00 39.69 3.66
3283 3646 7.392113 TCCCGTTAGAAATGAGCTGAAAAATAA 59.608 33.333 0.00 0.00 0.00 1.40
3310 3674 7.814264 TGCAAAAATGTTTTATTTCCATGGT 57.186 28.000 12.58 0.00 0.00 3.55
3313 3677 8.348507 GCAAAAATGTTTTATTTCCATGGTTGA 58.651 29.630 12.58 0.00 0.00 3.18
3338 3702 4.996758 TGGATCAATACTGCATGGTAATCG 59.003 41.667 0.00 0.00 0.00 3.34
3355 3720 2.325583 TCGGACCTGATGTTAATGGC 57.674 50.000 0.00 0.00 0.00 4.40
3410 3794 9.841295 TTTCTAACTGTTTGGTTATCTTGTACT 57.159 29.630 0.00 0.00 32.25 2.73
3411 3795 9.485206 TTCTAACTGTTTGGTTATCTTGTACTC 57.515 33.333 0.00 0.00 32.25 2.59
3412 3796 8.092687 TCTAACTGTTTGGTTATCTTGTACTCC 58.907 37.037 0.00 0.00 32.25 3.85
3413 3797 5.557866 ACTGTTTGGTTATCTTGTACTCCC 58.442 41.667 0.00 0.00 0.00 4.30
3414 3798 5.309806 ACTGTTTGGTTATCTTGTACTCCCT 59.690 40.000 0.00 0.00 0.00 4.20
3415 3799 5.801380 TGTTTGGTTATCTTGTACTCCCTC 58.199 41.667 0.00 0.00 0.00 4.30
3416 3800 5.546499 TGTTTGGTTATCTTGTACTCCCTCT 59.454 40.000 0.00 0.00 0.00 3.69
3417 3801 6.043938 TGTTTGGTTATCTTGTACTCCCTCTT 59.956 38.462 0.00 0.00 0.00 2.85
3418 3802 6.697641 TTGGTTATCTTGTACTCCCTCTTT 57.302 37.500 0.00 0.00 0.00 2.52
3419 3803 7.801893 TTGGTTATCTTGTACTCCCTCTTTA 57.198 36.000 0.00 0.00 0.00 1.85
3420 3804 7.801893 TGGTTATCTTGTACTCCCTCTTTAA 57.198 36.000 0.00 0.00 0.00 1.52
3421 3805 8.209802 TGGTTATCTTGTACTCCCTCTTTAAA 57.790 34.615 0.00 0.00 0.00 1.52
3422 3806 8.832735 TGGTTATCTTGTACTCCCTCTTTAAAT 58.167 33.333 0.00 0.00 0.00 1.40
3423 3807 9.682465 GGTTATCTTGTACTCCCTCTTTAAATT 57.318 33.333 0.00 0.00 0.00 1.82
3435 3819 9.937175 CTCCCTCTTTAAATTTTTATAAGAGCG 57.063 33.333 17.64 13.21 37.05 5.03
3436 3820 9.457436 TCCCTCTTTAAATTTTTATAAGAGCGT 57.543 29.630 17.64 0.00 37.05 5.07
3447 3831 8.997621 TTTTTATAAGAGCGTTGTAGTGATCT 57.002 30.769 0.00 0.00 0.00 2.75
3452 3836 6.893958 AAGAGCGTTGTAGTGATCTAAATG 57.106 37.500 0.00 0.00 0.00 2.32
3453 3837 4.806247 AGAGCGTTGTAGTGATCTAAATGC 59.194 41.667 0.00 0.00 34.02 3.56
3454 3838 4.759782 AGCGTTGTAGTGATCTAAATGCT 58.240 39.130 0.00 1.36 36.26 3.79
3455 3839 4.806247 AGCGTTGTAGTGATCTAAATGCTC 59.194 41.667 0.00 0.00 36.28 4.26
3456 3840 4.806247 GCGTTGTAGTGATCTAAATGCTCT 59.194 41.667 0.00 0.00 32.79 4.09
3457 3841 5.292101 GCGTTGTAGTGATCTAAATGCTCTT 59.708 40.000 0.00 0.00 32.79 2.85
3458 3842 6.475727 GCGTTGTAGTGATCTAAATGCTCTTA 59.524 38.462 0.00 0.00 32.79 2.10
3459 3843 7.169982 GCGTTGTAGTGATCTAAATGCTCTTAT 59.830 37.037 0.00 0.00 32.79 1.73
3460 3844 9.678941 CGTTGTAGTGATCTAAATGCTCTTATA 57.321 33.333 0.00 0.00 0.00 0.98
3475 3859 8.738645 ATGCTCTTATAAAAGTTTACAGAGGG 57.261 34.615 16.49 5.38 35.69 4.30
3476 3860 7.913789 TGCTCTTATAAAAGTTTACAGAGGGA 58.086 34.615 16.49 4.34 35.69 4.20
3477 3861 8.380099 TGCTCTTATAAAAGTTTACAGAGGGAA 58.620 33.333 16.49 0.00 35.69 3.97
3478 3862 9.397280 GCTCTTATAAAAGTTTACAGAGGGAAT 57.603 33.333 16.49 0.00 35.69 3.01
3516 3900 4.636206 AGAAATGCTGAAATTCTACGACCC 59.364 41.667 0.00 0.00 31.88 4.46
3522 3906 4.636206 GCTGAAATTCTACGACCCAGAAAT 59.364 41.667 0.00 0.00 35.73 2.17
3590 3978 4.144297 TCCCACAAGAAAGTCAAAGGATG 58.856 43.478 0.00 0.00 0.00 3.51
3626 4014 8.446489 TGCATAACAAATCTTAACATGTTTCG 57.554 30.769 17.78 8.35 37.25 3.46
3704 4092 2.098280 CACTATGGGTCTGACTCTGACG 59.902 54.545 9.42 0.00 33.99 4.35
3728 4116 6.747280 CGTAGTCCAACAATCATTTGAATTCC 59.253 38.462 2.27 0.00 36.64 3.01
3849 4240 7.842887 AGTTAGATTACTACTCCCTCCATTC 57.157 40.000 0.00 0.00 0.00 2.67
3850 4241 6.783482 AGTTAGATTACTACTCCCTCCATTCC 59.217 42.308 0.00 0.00 0.00 3.01
3851 4242 5.157770 AGATTACTACTCCCTCCATTCCA 57.842 43.478 0.00 0.00 0.00 3.53
3852 4243 5.151454 AGATTACTACTCCCTCCATTCCAG 58.849 45.833 0.00 0.00 0.00 3.86
3853 4244 4.620086 TTACTACTCCCTCCATTCCAGA 57.380 45.455 0.00 0.00 0.00 3.86
3854 4245 3.491766 ACTACTCCCTCCATTCCAGAA 57.508 47.619 0.00 0.00 0.00 3.02
3855 4246 4.014273 ACTACTCCCTCCATTCCAGAAT 57.986 45.455 0.00 0.00 0.00 2.40
3856 4247 5.157770 ACTACTCCCTCCATTCCAGAATA 57.842 43.478 0.00 0.00 0.00 1.75
3857 4248 5.731924 ACTACTCCCTCCATTCCAGAATAT 58.268 41.667 0.00 0.00 0.00 1.28
3858 4249 6.875469 ACTACTCCCTCCATTCCAGAATATA 58.125 40.000 0.00 0.00 0.00 0.86
3859 4250 7.313731 ACTACTCCCTCCATTCCAGAATATAA 58.686 38.462 0.00 0.00 0.00 0.98
3860 4251 6.694445 ACTCCCTCCATTCCAGAATATAAG 57.306 41.667 0.00 0.00 0.00 1.73
3861 4252 6.393897 ACTCCCTCCATTCCAGAATATAAGA 58.606 40.000 0.00 0.00 0.00 2.10
3862 4253 7.028131 ACTCCCTCCATTCCAGAATATAAGAT 58.972 38.462 0.00 0.00 0.00 2.40
3863 4254 7.037730 ACTCCCTCCATTCCAGAATATAAGATG 60.038 40.741 0.00 0.00 0.00 2.90
3864 4255 6.794493 TCCCTCCATTCCAGAATATAAGATGT 59.206 38.462 0.00 0.00 0.00 3.06
3865 4256 7.961431 TCCCTCCATTCCAGAATATAAGATGTA 59.039 37.037 0.00 0.00 0.00 2.29
3866 4257 8.776119 CCCTCCATTCCAGAATATAAGATGTAT 58.224 37.037 0.00 0.00 0.00 2.29
3869 4260 9.964354 TCCATTCCAGAATATAAGATGTATTGG 57.036 33.333 0.00 0.00 0.00 3.16
3870 4261 9.745018 CCATTCCAGAATATAAGATGTATTGGT 57.255 33.333 0.00 0.00 0.00 3.67
3874 4265 8.816894 TCCAGAATATAAGATGTATTGGTCTCC 58.183 37.037 0.00 0.00 0.00 3.71
3875 4266 7.761704 CCAGAATATAAGATGTATTGGTCTCCG 59.238 40.741 0.00 0.00 0.00 4.63
3876 4267 8.307483 CAGAATATAAGATGTATTGGTCTCCGT 58.693 37.037 0.00 0.00 0.00 4.69
3877 4268 8.307483 AGAATATAAGATGTATTGGTCTCCGTG 58.693 37.037 0.00 0.00 0.00 4.94
3878 4269 2.604046 AGATGTATTGGTCTCCGTGC 57.396 50.000 0.00 0.00 0.00 5.34
3879 4270 1.831106 AGATGTATTGGTCTCCGTGCA 59.169 47.619 0.00 0.00 0.00 4.57
3880 4271 2.236146 AGATGTATTGGTCTCCGTGCAA 59.764 45.455 0.00 0.00 0.00 4.08
3881 4272 2.093306 TGTATTGGTCTCCGTGCAAG 57.907 50.000 0.00 0.00 0.00 4.01
3882 4273 1.346395 TGTATTGGTCTCCGTGCAAGT 59.654 47.619 0.00 0.00 0.00 3.16
3883 4274 2.000447 GTATTGGTCTCCGTGCAAGTC 59.000 52.381 0.00 0.00 0.00 3.01
3884 4275 0.396435 ATTGGTCTCCGTGCAAGTCA 59.604 50.000 0.00 0.00 0.00 3.41
3885 4276 0.179234 TTGGTCTCCGTGCAAGTCAA 59.821 50.000 0.00 0.00 0.00 3.18
3886 4277 0.531974 TGGTCTCCGTGCAAGTCAAC 60.532 55.000 0.00 0.00 0.00 3.18
3887 4278 1.228657 GGTCTCCGTGCAAGTCAACC 61.229 60.000 0.00 0.00 0.00 3.77
3888 4279 0.531974 GTCTCCGTGCAAGTCAACCA 60.532 55.000 0.00 0.00 0.00 3.67
3889 4280 0.396435 TCTCCGTGCAAGTCAACCAT 59.604 50.000 0.00 0.00 0.00 3.55
3890 4281 1.202758 TCTCCGTGCAAGTCAACCATT 60.203 47.619 0.00 0.00 0.00 3.16
3891 4282 1.608590 CTCCGTGCAAGTCAACCATTT 59.391 47.619 0.00 0.00 0.00 2.32
3892 4283 1.606668 TCCGTGCAAGTCAACCATTTC 59.393 47.619 0.00 0.00 0.00 2.17
3893 4284 1.336440 CCGTGCAAGTCAACCATTTCA 59.664 47.619 0.00 0.00 0.00 2.69
3894 4285 2.223688 CCGTGCAAGTCAACCATTTCAA 60.224 45.455 0.00 0.00 0.00 2.69
3895 4286 3.552684 CCGTGCAAGTCAACCATTTCAAT 60.553 43.478 0.00 0.00 0.00 2.57
3896 4287 3.426191 CGTGCAAGTCAACCATTTCAATG 59.574 43.478 0.00 0.00 36.17 2.82
3897 4288 4.370917 GTGCAAGTCAACCATTTCAATGT 58.629 39.130 0.00 0.00 34.60 2.71
3898 4289 4.810491 GTGCAAGTCAACCATTTCAATGTT 59.190 37.500 0.00 0.00 34.60 2.71
3899 4290 5.294060 GTGCAAGTCAACCATTTCAATGTTT 59.706 36.000 0.00 0.00 34.60 2.83
3900 4291 5.293814 TGCAAGTCAACCATTTCAATGTTTG 59.706 36.000 3.96 3.96 39.34 2.93
3901 4292 5.523188 GCAAGTCAACCATTTCAATGTTTGA 59.477 36.000 8.08 8.08 42.89 2.69
3902 4293 6.203338 GCAAGTCAACCATTTCAATGTTTGAT 59.797 34.615 13.63 0.00 45.38 2.57
3903 4294 7.569957 GCAAGTCAACCATTTCAATGTTTGATC 60.570 37.037 13.63 8.91 45.38 2.92
3904 4295 7.053316 AGTCAACCATTTCAATGTTTGATCA 57.947 32.000 13.63 0.00 45.38 2.92
3905 4296 7.499292 AGTCAACCATTTCAATGTTTGATCAA 58.501 30.769 13.63 3.38 45.38 2.57
3906 4297 7.654520 AGTCAACCATTTCAATGTTTGATCAAG 59.345 33.333 13.63 0.00 45.38 3.02
3907 4298 7.652909 GTCAACCATTTCAATGTTTGATCAAGA 59.347 33.333 13.63 0.00 45.38 3.02
3908 4299 8.369424 TCAACCATTTCAATGTTTGATCAAGAT 58.631 29.630 8.41 2.40 41.11 2.40
3909 4300 8.995220 CAACCATTTCAATGTTTGATCAAGATT 58.005 29.630 8.41 8.36 40.09 2.40
3939 4330 9.463443 GGATAAAATAACAACATCTGCAATACC 57.537 33.333 0.00 0.00 0.00 2.73
3981 4372 8.641498 AAACTAGTTTTCATGATGGATCAAGT 57.359 30.769 15.22 0.00 40.69 3.16
3982 4373 8.641498 AACTAGTTTTCATGATGGATCAAGTT 57.359 30.769 1.12 0.00 40.69 2.66
3983 4374 9.739276 AACTAGTTTTCATGATGGATCAAGTTA 57.261 29.630 1.12 0.00 40.69 2.24
3984 4375 9.911788 ACTAGTTTTCATGATGGATCAAGTTAT 57.088 29.630 0.00 0.00 40.69 1.89
4042 4433 7.979115 TTTTCTAAAAACTCGGTCAAACATG 57.021 32.000 0.00 0.00 0.00 3.21
4043 4434 5.103290 TCTAAAAACTCGGTCAAACATGC 57.897 39.130 0.00 0.00 0.00 4.06
4044 4435 3.791973 AAAAACTCGGTCAAACATGCA 57.208 38.095 0.00 0.00 0.00 3.96
4045 4436 2.774439 AAACTCGGTCAAACATGCAC 57.226 45.000 0.00 0.00 0.00 4.57
4046 4437 1.967319 AACTCGGTCAAACATGCACT 58.033 45.000 0.00 0.00 0.00 4.40
4047 4438 1.512926 ACTCGGTCAAACATGCACTC 58.487 50.000 0.00 0.00 0.00 3.51
4048 4439 0.439985 CTCGGTCAAACATGCACTCG 59.560 55.000 0.00 0.00 0.00 4.18
4049 4440 0.249699 TCGGTCAAACATGCACTCGT 60.250 50.000 0.00 0.00 0.00 4.18
4050 4441 0.586319 CGGTCAAACATGCACTCGTT 59.414 50.000 0.00 0.00 0.00 3.85
4051 4442 1.002900 CGGTCAAACATGCACTCGTTT 60.003 47.619 5.20 5.20 35.76 3.60
4057 4448 4.370364 AAACATGCACTCGTTTGACTTT 57.630 36.364 9.29 0.00 34.16 2.66
4058 4449 4.370364 AACATGCACTCGTTTGACTTTT 57.630 36.364 0.00 0.00 0.00 2.27
4059 4450 3.694734 ACATGCACTCGTTTGACTTTTG 58.305 40.909 0.00 0.00 0.00 2.44
4060 4451 3.376859 ACATGCACTCGTTTGACTTTTGA 59.623 39.130 0.00 0.00 0.00 2.69
4061 4452 4.142491 ACATGCACTCGTTTGACTTTTGAA 60.142 37.500 0.00 0.00 0.00 2.69
4062 4453 4.427096 TGCACTCGTTTGACTTTTGAAA 57.573 36.364 0.00 0.00 0.00 2.69
4063 4454 4.799678 TGCACTCGTTTGACTTTTGAAAA 58.200 34.783 0.00 0.00 0.00 2.29
4064 4455 5.223382 TGCACTCGTTTGACTTTTGAAAAA 58.777 33.333 0.00 0.00 0.00 1.94
4095 4486 7.138054 ACACCTTATATAAAGGAACAGAGGG 57.862 40.000 10.67 4.11 39.81 4.30
4096 4487 6.906901 ACACCTTATATAAAGGAACAGAGGGA 59.093 38.462 10.67 0.00 39.81 4.20
4097 4488 7.071321 ACACCTTATATAAAGGAACAGAGGGAG 59.929 40.741 10.67 3.30 39.81 4.30
4098 4489 7.071321 CACCTTATATAAAGGAACAGAGGGAGT 59.929 40.741 10.67 0.00 39.81 3.85
4099 4490 8.294690 ACCTTATATAAAGGAACAGAGGGAGTA 58.705 37.037 10.67 0.00 39.81 2.59
4100 4491 9.327731 CCTTATATAAAGGAACAGAGGGAGTAT 57.672 37.037 0.00 0.00 39.81 2.12
4103 4494 6.987403 ATAAAGGAACAGAGGGAGTATCTC 57.013 41.667 0.00 0.00 33.92 2.75
4104 4495 2.938838 AGGAACAGAGGGAGTATCTCG 58.061 52.381 0.00 0.00 43.84 4.04
4105 4496 2.242708 AGGAACAGAGGGAGTATCTCGT 59.757 50.000 0.00 0.00 43.84 4.18
4106 4497 3.025262 GGAACAGAGGGAGTATCTCGTT 58.975 50.000 0.00 0.00 43.84 3.85
4107 4498 4.079901 AGGAACAGAGGGAGTATCTCGTTA 60.080 45.833 0.00 0.00 43.84 3.18
4108 4499 4.828387 GGAACAGAGGGAGTATCTCGTTAT 59.172 45.833 0.00 0.00 43.84 1.89
4109 4500 5.302313 GGAACAGAGGGAGTATCTCGTTATT 59.698 44.000 0.00 0.00 43.84 1.40
4110 4501 5.776173 ACAGAGGGAGTATCTCGTTATTG 57.224 43.478 0.00 0.00 43.84 1.90
4111 4502 5.202004 ACAGAGGGAGTATCTCGTTATTGT 58.798 41.667 0.00 0.00 43.84 2.71
4112 4503 5.657302 ACAGAGGGAGTATCTCGTTATTGTT 59.343 40.000 0.00 0.00 43.84 2.83
4113 4504 5.980116 CAGAGGGAGTATCTCGTTATTGTTG 59.020 44.000 0.00 0.00 43.84 3.33
4114 4505 5.892119 AGAGGGAGTATCTCGTTATTGTTGA 59.108 40.000 0.00 0.00 43.84 3.18
4115 4506 6.380274 AGAGGGAGTATCTCGTTATTGTTGAA 59.620 38.462 0.00 0.00 43.84 2.69
4116 4507 6.574350 AGGGAGTATCTCGTTATTGTTGAAG 58.426 40.000 0.00 0.00 43.84 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 4.567385 CTCTCCGCTCCGCAGCTC 62.567 72.222 0.00 0.00 44.40 4.09
21 22 3.793144 CGTTTGGCAGCTCTCCGC 61.793 66.667 0.00 0.00 39.57 5.54
22 23 3.121030 CCGTTTGGCAGCTCTCCG 61.121 66.667 0.00 0.00 0.00 4.63
23 24 2.747855 CCCGTTTGGCAGCTCTCC 60.748 66.667 0.00 0.00 0.00 3.71
24 25 2.747855 CCCCGTTTGGCAGCTCTC 60.748 66.667 0.00 0.00 0.00 3.20
32 33 1.309499 TAATCTTGCGCCCCGTTTGG 61.309 55.000 4.18 0.00 0.00 3.28
33 34 0.738389 ATAATCTTGCGCCCCGTTTG 59.262 50.000 4.18 0.00 0.00 2.93
34 35 1.404035 GAATAATCTTGCGCCCCGTTT 59.596 47.619 4.18 0.00 0.00 3.60
35 36 1.021968 GAATAATCTTGCGCCCCGTT 58.978 50.000 4.18 0.00 0.00 4.44
36 37 0.180406 AGAATAATCTTGCGCCCCGT 59.820 50.000 4.18 0.00 29.15 5.28
37 38 0.868406 GAGAATAATCTTGCGCCCCG 59.132 55.000 4.18 0.00 35.54 5.73
38 39 0.868406 CGAGAATAATCTTGCGCCCC 59.132 55.000 4.18 0.00 35.54 5.80
39 40 1.583054 ACGAGAATAATCTTGCGCCC 58.417 50.000 4.18 0.00 40.28 6.13
40 41 3.381949 AGTACGAGAATAATCTTGCGCC 58.618 45.455 4.18 0.00 40.28 6.53
41 42 5.115773 CACTAGTACGAGAATAATCTTGCGC 59.884 44.000 10.22 0.00 40.28 6.09
42 43 5.115773 GCACTAGTACGAGAATAATCTTGCG 59.884 44.000 10.22 0.00 40.28 4.85
43 44 6.143118 CAGCACTAGTACGAGAATAATCTTGC 59.857 42.308 10.22 6.44 40.28 4.01
68 69 7.496529 TGCAAGAGAACATATTGGCTTATAC 57.503 36.000 0.00 0.00 0.00 1.47
74 75 5.064441 AGTTTGCAAGAGAACATATTGGC 57.936 39.130 0.00 0.00 0.00 4.52
91 92 3.057946 GGAAAGGCTAGTCTGCAAGTTTG 60.058 47.826 0.00 0.00 33.76 2.93
92 93 3.149981 GGAAAGGCTAGTCTGCAAGTTT 58.850 45.455 0.00 0.00 33.76 2.66
93 94 2.106511 TGGAAAGGCTAGTCTGCAAGTT 59.893 45.455 0.00 0.00 33.76 2.66
94 95 1.699634 TGGAAAGGCTAGTCTGCAAGT 59.300 47.619 0.00 0.00 33.76 3.16
102 103 6.016555 ACCAAAACAATATGGAAAGGCTAGT 58.983 36.000 0.00 0.00 39.12 2.57
180 181 3.452627 AGAGTTAGGCTTCCACATACCAG 59.547 47.826 0.00 0.00 0.00 4.00
282 283 1.226945 GCACAAGTGGCACCAACAC 60.227 57.895 15.27 0.00 39.10 3.32
299 300 2.805671 TGGCGCATACATAGTACAATGC 59.194 45.455 10.83 1.72 41.00 3.56
378 383 2.484264 CACAAGTTGTAGCTACCTTGCC 59.516 50.000 28.48 12.45 38.24 4.52
383 388 1.076332 CGCCACAAGTTGTAGCTACC 58.924 55.000 21.43 6.72 32.83 3.18
386 391 1.442769 CATCGCCACAAGTTGTAGCT 58.557 50.000 21.43 3.88 32.83 3.32
443 449 3.426615 TGACCTTTGTTAATTCCGGCAT 58.573 40.909 0.00 0.00 0.00 4.40
508 514 1.904852 ATCTGCAGTTCTGCGTTGCG 61.905 55.000 14.67 6.08 40.62 4.85
514 520 2.680312 TGACCTATCTGCAGTTCTGC 57.320 50.000 14.67 16.65 0.00 4.26
549 555 5.551233 TGATCCACCTAACTCTTTGTGAAG 58.449 41.667 0.00 0.00 0.00 3.02
552 558 4.637534 CCATGATCCACCTAACTCTTTGTG 59.362 45.833 0.00 0.00 0.00 3.33
577 583 2.202570 CGTACGTGAAGGGCCTCG 60.203 66.667 6.46 9.38 0.00 4.63
621 640 6.127980 AGTGTAGTACTATATTGCGATCGCAT 60.128 38.462 40.15 29.86 44.01 4.73
624 643 5.508573 GCAGTGTAGTACTATATTGCGATCG 59.491 44.000 24.24 11.69 37.60 3.69
707 735 6.747739 GGACGCAAAAAGGAGAAGATTAATTC 59.252 38.462 0.00 0.00 0.00 2.17
818 847 4.281941 ACTGACTAGACATGCACAAAGAGA 59.718 41.667 0.00 0.00 0.00 3.10
859 895 2.417339 TATAGCCATCTGAACGCGTC 57.583 50.000 14.44 7.01 0.00 5.19
896 933 1.273886 AGTTGAGACCTTTCGCCTCTC 59.726 52.381 0.00 0.00 0.00 3.20
917 954 2.948315 CTGAAGCAGGGGAGAAATTAGC 59.052 50.000 0.00 0.00 0.00 3.09
949 986 0.538584 ACGAAGCAGCAGATGGATCA 59.461 50.000 0.00 0.00 0.00 2.92
1041 1079 1.758514 GGGCGACTGGAGGATCTCA 60.759 63.158 0.00 0.00 33.73 3.27
1071 1109 1.323271 TGAGCTCCCTGTAGGCGAAG 61.323 60.000 12.15 0.00 34.51 3.79
1072 1110 1.304962 TGAGCTCCCTGTAGGCGAA 60.305 57.895 12.15 0.00 34.51 4.70
1124 1171 2.804828 GAAGCCACCTTCACCGAGGG 62.805 65.000 0.00 0.00 45.44 4.30
1405 1528 1.746615 CCAGATTGGGGTGCGACAG 60.747 63.158 0.00 0.00 32.67 3.51
1567 1703 6.608405 TCATCCTCGGTAGTAACTAATTTGGA 59.392 38.462 0.00 0.00 0.00 3.53
1784 1941 6.601332 AGAAGGAAAGAACAGAAACATACCA 58.399 36.000 0.00 0.00 0.00 3.25
1909 2079 2.011044 ATCAGCTGGCCCATCCCTT 61.011 57.895 15.13 0.00 0.00 3.95
2045 2215 3.264947 TCTGATCATGGCTTTGAAGACG 58.735 45.455 0.00 0.00 36.62 4.18
2078 2249 8.623903 TGCTACATCTGATCATGGTTAAAATTC 58.376 33.333 0.00 0.00 0.00 2.17
2079 2250 8.523915 TGCTACATCTGATCATGGTTAAAATT 57.476 30.769 0.00 0.00 0.00 1.82
2080 2251 8.701908 ATGCTACATCTGATCATGGTTAAAAT 57.298 30.769 0.00 0.00 0.00 1.82
2081 2252 7.041848 CGATGCTACATCTGATCATGGTTAAAA 60.042 37.037 0.00 0.00 0.00 1.52
2082 2253 6.424812 CGATGCTACATCTGATCATGGTTAAA 59.575 38.462 0.00 0.00 0.00 1.52
2083 2254 5.928264 CGATGCTACATCTGATCATGGTTAA 59.072 40.000 0.00 0.00 0.00 2.01
2084 2255 5.243730 TCGATGCTACATCTGATCATGGTTA 59.756 40.000 0.00 0.00 0.00 2.85
2085 2256 4.039609 TCGATGCTACATCTGATCATGGTT 59.960 41.667 0.00 0.00 0.00 3.67
2086 2257 3.575687 TCGATGCTACATCTGATCATGGT 59.424 43.478 0.00 0.00 0.00 3.55
2087 2258 4.184079 TCGATGCTACATCTGATCATGG 57.816 45.455 0.00 0.00 0.00 3.66
2088 2259 9.694137 ATATAATCGATGCTACATCTGATCATG 57.306 33.333 0.00 0.00 0.00 3.07
2090 2261 9.741647 GAATATAATCGATGCTACATCTGATCA 57.258 33.333 0.00 0.00 0.00 2.92
2091 2262 9.741647 TGAATATAATCGATGCTACATCTGATC 57.258 33.333 0.00 0.00 0.00 2.92
2093 2264 9.741647 GATGAATATAATCGATGCTACATCTGA 57.258 33.333 0.00 5.56 0.00 3.27
2108 2279 9.249457 CGATACCAAGCATACGATGAATATAAT 57.751 33.333 0.00 0.00 0.00 1.28
2119 2290 2.134201 TCAGCGATACCAAGCATACG 57.866 50.000 0.00 0.00 35.48 3.06
2120 2291 3.302480 CGTTTCAGCGATACCAAGCATAC 60.302 47.826 0.00 0.00 35.48 2.39
2164 2375 3.599046 GCAAACTATCATGCTCGAAGG 57.401 47.619 0.00 0.00 39.46 3.46
2250 2469 9.515226 ACCAGCTCAAGAATTTTAATAGTGTTA 57.485 29.630 0.00 0.00 0.00 2.41
2272 2491 1.960040 TATGGCGTCCTCAGCACCAG 61.960 60.000 0.00 0.00 33.03 4.00
2413 2633 8.385898 TCCCTTAAATTAAAGTGCATATACCG 57.614 34.615 0.00 0.00 0.00 4.02
2501 2750 8.226448 CAGCTCATCAACTAAAGAACAAGTTAG 58.774 37.037 0.00 0.00 34.23 2.34
2503 2752 6.543831 ACAGCTCATCAACTAAAGAACAAGTT 59.456 34.615 0.00 0.00 36.38 2.66
2541 2821 8.303876 TGTACTCGCATTAGCAAGATTATATGA 58.696 33.333 0.00 0.00 42.27 2.15
2561 2841 4.755266 ACCACCATGGATTAGTGTACTC 57.245 45.455 21.47 0.00 40.96 2.59
2562 2842 4.534500 TGAACCACCATGGATTAGTGTACT 59.466 41.667 21.47 0.00 40.96 2.73
2585 2880 4.961730 AGATGCTACAGAGGAGAAGACAAT 59.038 41.667 0.00 0.00 0.00 2.71
2601 2898 5.592104 TCCTTGTTCGTATTCAGATGCTA 57.408 39.130 0.00 0.00 0.00 3.49
2669 2969 7.283625 AGTAGATAAGCAGTCCAACTAGATG 57.716 40.000 0.00 0.00 0.00 2.90
2691 2991 4.661247 AGGTTCAGACAGGACTAGTAGT 57.339 45.455 1.37 1.37 0.00 2.73
2695 2995 3.007398 AGCAAAGGTTCAGACAGGACTAG 59.993 47.826 0.00 0.00 0.00 2.57
2696 2996 2.972713 AGCAAAGGTTCAGACAGGACTA 59.027 45.455 0.00 0.00 0.00 2.59
2697 2997 1.771255 AGCAAAGGTTCAGACAGGACT 59.229 47.619 0.00 0.00 0.00 3.85
2703 3003 4.261614 CCCTGTTAAAGCAAAGGTTCAGAC 60.262 45.833 0.00 0.00 0.00 3.51
2716 3016 2.673368 GTCGTCAGATGCCCTGTTAAAG 59.327 50.000 3.57 0.00 43.38 1.85
2987 3287 2.439156 GCCACCACCTGCTCCATC 60.439 66.667 0.00 0.00 0.00 3.51
3212 3546 0.402504 TGCCTAAAGAAGCGGGGAAA 59.597 50.000 0.00 0.00 0.00 3.13
3215 3549 4.225497 CTGCCTAAAGAAGCGGGG 57.775 61.111 0.00 0.00 0.00 5.73
3217 3551 1.134401 TCATCCTGCCTAAAGAAGCGG 60.134 52.381 0.00 0.00 35.04 5.52
3218 3552 2.315925 TCATCCTGCCTAAAGAAGCG 57.684 50.000 0.00 0.00 0.00 4.68
3242 3576 2.021457 ACGGGAACAAAAACTCCACTG 58.979 47.619 0.00 0.00 32.95 3.66
3243 3577 2.430248 ACGGGAACAAAAACTCCACT 57.570 45.000 0.00 0.00 32.95 4.00
3246 3580 5.503662 TTTCTAACGGGAACAAAAACTCC 57.496 39.130 0.00 0.00 0.00 3.85
3313 3677 6.149973 CGATTACCATGCAGTATTGATCCATT 59.850 38.462 0.00 0.00 0.00 3.16
3316 3680 4.393062 CCGATTACCATGCAGTATTGATCC 59.607 45.833 0.00 0.00 0.00 3.36
3324 3688 1.134401 CAGGTCCGATTACCATGCAGT 60.134 52.381 0.00 0.00 42.40 4.40
3325 3689 1.138859 TCAGGTCCGATTACCATGCAG 59.861 52.381 0.00 0.00 42.40 4.41
3338 3702 3.953612 TGATTGCCATTAACATCAGGTCC 59.046 43.478 0.00 0.00 0.00 4.46
3410 3794 9.457436 ACGCTCTTATAAAAATTTAAAGAGGGA 57.543 29.630 30.38 12.76 42.81 4.20
3421 3805 9.601217 AGATCACTACAACGCTCTTATAAAAAT 57.399 29.630 0.00 0.00 0.00 1.82
3422 3806 8.997621 AGATCACTACAACGCTCTTATAAAAA 57.002 30.769 0.00 0.00 0.00 1.94
3426 3810 9.678941 CATTTAGATCACTACAACGCTCTTATA 57.321 33.333 0.00 0.00 0.00 0.98
3427 3811 7.169982 GCATTTAGATCACTACAACGCTCTTAT 59.830 37.037 0.00 0.00 0.00 1.73
3428 3812 6.475727 GCATTTAGATCACTACAACGCTCTTA 59.524 38.462 0.00 0.00 0.00 2.10
3429 3813 5.292101 GCATTTAGATCACTACAACGCTCTT 59.708 40.000 0.00 0.00 0.00 2.85
3430 3814 4.806247 GCATTTAGATCACTACAACGCTCT 59.194 41.667 0.00 0.00 0.00 4.09
3431 3815 4.806247 AGCATTTAGATCACTACAACGCTC 59.194 41.667 0.00 0.00 0.00 5.03
3432 3816 4.759782 AGCATTTAGATCACTACAACGCT 58.240 39.130 0.00 0.00 0.00 5.07
3433 3817 4.806247 AGAGCATTTAGATCACTACAACGC 59.194 41.667 0.00 0.00 34.30 4.84
3434 3818 6.893958 AAGAGCATTTAGATCACTACAACG 57.106 37.500 0.00 0.00 34.30 4.10
3449 3833 9.178758 CCCTCTGTAAACTTTTATAAGAGCATT 57.821 33.333 13.76 2.32 36.27 3.56
3450 3834 8.548877 TCCCTCTGTAAACTTTTATAAGAGCAT 58.451 33.333 13.76 0.00 36.27 3.79
3451 3835 7.913789 TCCCTCTGTAAACTTTTATAAGAGCA 58.086 34.615 13.76 0.00 36.27 4.26
3452 3836 8.788325 TTCCCTCTGTAAACTTTTATAAGAGC 57.212 34.615 13.76 0.00 36.27 4.09
3459 3843 9.856162 AACTTGTATTCCCTCTGTAAACTTTTA 57.144 29.630 0.00 0.00 0.00 1.52
3460 3844 8.762481 AACTTGTATTCCCTCTGTAAACTTTT 57.238 30.769 0.00 0.00 0.00 2.27
3461 3845 8.762481 AAACTTGTATTCCCTCTGTAAACTTT 57.238 30.769 0.00 0.00 0.00 2.66
3462 3846 7.447545 GGAAACTTGTATTCCCTCTGTAAACTT 59.552 37.037 0.00 0.00 40.41 2.66
3463 3847 6.940867 GGAAACTTGTATTCCCTCTGTAAACT 59.059 38.462 0.00 0.00 40.41 2.66
3464 3848 6.940867 AGGAAACTTGTATTCCCTCTGTAAAC 59.059 38.462 1.82 0.00 46.17 2.01
3465 3849 7.086685 AGGAAACTTGTATTCCCTCTGTAAA 57.913 36.000 1.82 0.00 46.17 2.01
3466 3850 6.296259 GGAGGAAACTTGTATTCCCTCTGTAA 60.296 42.308 0.00 0.00 46.17 2.41
3467 3851 5.189145 GGAGGAAACTTGTATTCCCTCTGTA 59.811 44.000 0.00 0.00 46.17 2.74
3468 3852 4.019231 GGAGGAAACTTGTATTCCCTCTGT 60.019 45.833 0.00 0.00 46.17 3.41
3469 3853 4.518249 GGAGGAAACTTGTATTCCCTCTG 58.482 47.826 0.00 0.00 46.17 3.35
3470 3854 3.523972 GGGAGGAAACTTGTATTCCCTCT 59.476 47.826 0.00 0.00 46.17 3.69
3471 3855 3.265995 TGGGAGGAAACTTGTATTCCCTC 59.734 47.826 8.67 0.00 46.17 4.30
3472 3856 3.265489 TGGGAGGAAACTTGTATTCCCT 58.735 45.455 8.67 0.00 46.17 4.20
3473 3857 3.265995 TCTGGGAGGAAACTTGTATTCCC 59.734 47.826 1.82 0.40 46.17 3.97
3474 3858 4.569719 TCTGGGAGGAAACTTGTATTCC 57.430 45.455 0.00 0.00 45.50 3.01
3475 3859 6.625960 GCATTTCTGGGAGGAAACTTGTATTC 60.626 42.308 0.00 0.00 44.43 1.75
3476 3860 5.185828 GCATTTCTGGGAGGAAACTTGTATT 59.814 40.000 0.00 0.00 44.43 1.89
3477 3861 4.706962 GCATTTCTGGGAGGAAACTTGTAT 59.293 41.667 0.00 0.00 44.43 2.29
3478 3862 4.079253 GCATTTCTGGGAGGAAACTTGTA 58.921 43.478 0.00 0.00 44.43 2.41
3479 3863 2.893489 GCATTTCTGGGAGGAAACTTGT 59.107 45.455 0.00 0.00 44.43 3.16
3480 3864 3.057033 CAGCATTTCTGGGAGGAAACTTG 60.057 47.826 0.00 0.00 39.13 3.16
3512 3896 9.838339 TTCTTATGAGAGAAATATTTCTGGGTC 57.162 33.333 30.65 22.93 46.84 4.46
3621 4009 4.056050 TGCTTCTGACTTACTTCCGAAAC 58.944 43.478 0.00 0.00 0.00 2.78
3626 4014 6.809630 AAATCTTGCTTCTGACTTACTTCC 57.190 37.500 0.00 0.00 0.00 3.46
3704 4092 7.830739 AGGAATTCAAATGATTGTTGGACTAC 58.169 34.615 7.93 0.00 37.79 2.73
3754 4142 6.665695 ACTCCACCACTTTAACCTCTTTTTA 58.334 36.000 0.00 0.00 0.00 1.52
3760 4148 5.472478 CCTTAAACTCCACCACTTTAACCTC 59.528 44.000 0.00 0.00 0.00 3.85
3797 4185 3.874392 ATGAAGTGCCAAAAGCCATAC 57.126 42.857 0.00 0.00 42.71 2.39
3835 4226 7.676043 TCTTATATTCTGGAATGGAGGGAGTAG 59.324 40.741 6.13 0.00 32.50 2.57
3838 4229 6.942163 TCTTATATTCTGGAATGGAGGGAG 57.058 41.667 6.13 0.00 32.50 4.30
3839 4230 6.794493 ACATCTTATATTCTGGAATGGAGGGA 59.206 38.462 6.13 0.24 32.50 4.20
3840 4231 7.025520 ACATCTTATATTCTGGAATGGAGGG 57.974 40.000 6.13 2.04 32.50 4.30
3843 4234 9.964354 CCAATACATCTTATATTCTGGAATGGA 57.036 33.333 6.13 1.09 32.50 3.41
3844 4235 9.745018 ACCAATACATCTTATATTCTGGAATGG 57.255 33.333 6.13 0.00 32.50 3.16
3848 4239 8.816894 GGAGACCAATACATCTTATATTCTGGA 58.183 37.037 0.00 0.00 0.00 3.86
3849 4240 7.761704 CGGAGACCAATACATCTTATATTCTGG 59.238 40.741 0.00 0.00 0.00 3.86
3850 4241 8.307483 ACGGAGACCAATACATCTTATATTCTG 58.693 37.037 0.00 0.00 0.00 3.02
3851 4242 8.307483 CACGGAGACCAATACATCTTATATTCT 58.693 37.037 0.00 0.00 0.00 2.40
3852 4243 7.063544 GCACGGAGACCAATACATCTTATATTC 59.936 40.741 0.00 0.00 0.00 1.75
3853 4244 6.874134 GCACGGAGACCAATACATCTTATATT 59.126 38.462 0.00 0.00 0.00 1.28
3854 4245 6.014584 TGCACGGAGACCAATACATCTTATAT 60.015 38.462 0.00 0.00 0.00 0.86
3855 4246 5.303333 TGCACGGAGACCAATACATCTTATA 59.697 40.000 0.00 0.00 0.00 0.98
3856 4247 4.100963 TGCACGGAGACCAATACATCTTAT 59.899 41.667 0.00 0.00 0.00 1.73
3857 4248 3.449377 TGCACGGAGACCAATACATCTTA 59.551 43.478 0.00 0.00 0.00 2.10
3858 4249 2.236146 TGCACGGAGACCAATACATCTT 59.764 45.455 0.00 0.00 0.00 2.40
3859 4250 1.831106 TGCACGGAGACCAATACATCT 59.169 47.619 0.00 0.00 0.00 2.90
3860 4251 2.309528 TGCACGGAGACCAATACATC 57.690 50.000 0.00 0.00 0.00 3.06
3861 4252 2.027192 ACTTGCACGGAGACCAATACAT 60.027 45.455 0.00 0.00 0.00 2.29
3862 4253 1.346395 ACTTGCACGGAGACCAATACA 59.654 47.619 0.00 0.00 0.00 2.29
3863 4254 2.000447 GACTTGCACGGAGACCAATAC 59.000 52.381 0.00 0.00 0.00 1.89
3864 4255 1.621317 TGACTTGCACGGAGACCAATA 59.379 47.619 0.00 0.00 0.00 1.90
3865 4256 0.396435 TGACTTGCACGGAGACCAAT 59.604 50.000 0.00 0.00 0.00 3.16
3866 4257 0.179234 TTGACTTGCACGGAGACCAA 59.821 50.000 0.00 0.00 0.00 3.67
3867 4258 0.531974 GTTGACTTGCACGGAGACCA 60.532 55.000 0.00 0.00 0.00 4.02
3868 4259 1.228657 GGTTGACTTGCACGGAGACC 61.229 60.000 0.00 0.00 0.00 3.85
3869 4260 0.531974 TGGTTGACTTGCACGGAGAC 60.532 55.000 0.00 0.00 0.00 3.36
3870 4261 0.396435 ATGGTTGACTTGCACGGAGA 59.604 50.000 0.00 0.00 0.00 3.71
3871 4262 1.238439 AATGGTTGACTTGCACGGAG 58.762 50.000 0.00 0.00 0.00 4.63
3872 4263 1.606668 GAAATGGTTGACTTGCACGGA 59.393 47.619 0.00 0.00 0.00 4.69
3873 4264 1.336440 TGAAATGGTTGACTTGCACGG 59.664 47.619 0.00 0.00 0.00 4.94
3874 4265 2.772568 TGAAATGGTTGACTTGCACG 57.227 45.000 0.00 0.00 0.00 5.34
3875 4266 4.370917 ACATTGAAATGGTTGACTTGCAC 58.629 39.130 7.87 0.00 40.70 4.57
3876 4267 4.669206 ACATTGAAATGGTTGACTTGCA 57.331 36.364 7.87 0.00 40.70 4.08
3877 4268 5.989551 AAACATTGAAATGGTTGACTTGC 57.010 34.783 5.53 0.00 44.21 4.01
3913 4304 9.463443 GGTATTGCAGATGTTGTTATTTTATCC 57.537 33.333 0.00 0.00 0.00 2.59
3955 4346 8.734386 ACTTGATCCATCATGAAAACTAGTTTC 58.266 33.333 20.78 14.21 38.29 2.78
3956 4347 8.641498 ACTTGATCCATCATGAAAACTAGTTT 57.359 30.769 15.22 15.22 36.56 2.66
3957 4348 8.641498 AACTTGATCCATCATGAAAACTAGTT 57.359 30.769 1.12 1.12 36.56 2.24
3958 4349 9.911788 ATAACTTGATCCATCATGAAAACTAGT 57.088 29.630 0.00 0.00 36.56 2.57
4016 4407 9.672086 CATGTTTGACCGAGTTTTTAGAAAATA 57.328 29.630 0.00 0.00 0.00 1.40
4017 4408 7.169140 GCATGTTTGACCGAGTTTTTAGAAAAT 59.831 33.333 0.00 0.00 0.00 1.82
4018 4409 6.474102 GCATGTTTGACCGAGTTTTTAGAAAA 59.526 34.615 0.00 0.00 0.00 2.29
4019 4410 5.974751 GCATGTTTGACCGAGTTTTTAGAAA 59.025 36.000 0.00 0.00 0.00 2.52
4020 4411 5.066634 TGCATGTTTGACCGAGTTTTTAGAA 59.933 36.000 0.00 0.00 0.00 2.10
4021 4412 4.576873 TGCATGTTTGACCGAGTTTTTAGA 59.423 37.500 0.00 0.00 0.00 2.10
4022 4413 4.675114 GTGCATGTTTGACCGAGTTTTTAG 59.325 41.667 0.00 0.00 0.00 1.85
4023 4414 4.336993 AGTGCATGTTTGACCGAGTTTTTA 59.663 37.500 0.00 0.00 0.00 1.52
4024 4415 3.130340 AGTGCATGTTTGACCGAGTTTTT 59.870 39.130 0.00 0.00 0.00 1.94
4025 4416 2.687935 AGTGCATGTTTGACCGAGTTTT 59.312 40.909 0.00 0.00 0.00 2.43
4026 4417 2.290641 GAGTGCATGTTTGACCGAGTTT 59.709 45.455 0.00 0.00 0.00 2.66
4027 4418 1.873591 GAGTGCATGTTTGACCGAGTT 59.126 47.619 0.00 0.00 0.00 3.01
4028 4419 1.512926 GAGTGCATGTTTGACCGAGT 58.487 50.000 0.00 0.00 0.00 4.18
4029 4420 0.439985 CGAGTGCATGTTTGACCGAG 59.560 55.000 0.00 0.00 0.00 4.63
4030 4421 0.249699 ACGAGTGCATGTTTGACCGA 60.250 50.000 0.00 0.00 0.00 4.69
4031 4422 0.586319 AACGAGTGCATGTTTGACCG 59.414 50.000 0.00 0.00 0.00 4.79
4032 4423 2.774439 AAACGAGTGCATGTTTGACC 57.226 45.000 12.15 0.00 36.96 4.02
4036 4427 4.370364 AAAGTCAAACGAGTGCATGTTT 57.630 36.364 8.36 8.36 38.76 2.83
4037 4428 4.104776 CAAAAGTCAAACGAGTGCATGTT 58.895 39.130 0.00 0.00 0.00 2.71
4038 4429 3.376859 TCAAAAGTCAAACGAGTGCATGT 59.623 39.130 0.00 0.00 0.00 3.21
4039 4430 3.951306 TCAAAAGTCAAACGAGTGCATG 58.049 40.909 0.00 0.00 0.00 4.06
4040 4431 4.630894 TTCAAAAGTCAAACGAGTGCAT 57.369 36.364 0.00 0.00 0.00 3.96
4041 4432 4.427096 TTTCAAAAGTCAAACGAGTGCA 57.573 36.364 0.00 0.00 0.00 4.57
4042 4433 5.755330 TTTTTCAAAAGTCAAACGAGTGC 57.245 34.783 0.00 0.00 0.00 4.40
4069 4460 8.881262 CCCTCTGTTCCTTTATATAAGGTGTAT 58.119 37.037 4.13 0.00 38.55 2.29
4070 4461 8.069356 TCCCTCTGTTCCTTTATATAAGGTGTA 58.931 37.037 4.13 0.00 38.55 2.90
4071 4462 6.906901 TCCCTCTGTTCCTTTATATAAGGTGT 59.093 38.462 4.13 0.00 38.55 4.16
4072 4463 7.071321 ACTCCCTCTGTTCCTTTATATAAGGTG 59.929 40.741 4.13 0.00 38.55 4.00
4073 4464 7.140304 ACTCCCTCTGTTCCTTTATATAAGGT 58.860 38.462 4.13 0.00 38.55 3.50
4074 4465 7.619512 ACTCCCTCTGTTCCTTTATATAAGG 57.380 40.000 0.00 0.00 38.78 2.69
4077 4468 9.756571 GAGATACTCCCTCTGTTCCTTTATATA 57.243 37.037 0.00 0.00 0.00 0.86
4078 4469 7.394923 CGAGATACTCCCTCTGTTCCTTTATAT 59.605 40.741 0.00 0.00 0.00 0.86
4079 4470 6.715718 CGAGATACTCCCTCTGTTCCTTTATA 59.284 42.308 0.00 0.00 0.00 0.98
4080 4471 5.536916 CGAGATACTCCCTCTGTTCCTTTAT 59.463 44.000 0.00 0.00 0.00 1.40
4081 4472 4.888239 CGAGATACTCCCTCTGTTCCTTTA 59.112 45.833 0.00 0.00 0.00 1.85
4082 4473 3.702045 CGAGATACTCCCTCTGTTCCTTT 59.298 47.826 0.00 0.00 0.00 3.11
4083 4474 3.292460 CGAGATACTCCCTCTGTTCCTT 58.708 50.000 0.00 0.00 0.00 3.36
4084 4475 2.242708 ACGAGATACTCCCTCTGTTCCT 59.757 50.000 0.00 0.00 0.00 3.36
4085 4476 2.657143 ACGAGATACTCCCTCTGTTCC 58.343 52.381 0.00 0.00 0.00 3.62
4086 4477 6.183360 ACAATAACGAGATACTCCCTCTGTTC 60.183 42.308 0.00 0.00 33.27 3.18
4087 4478 5.657302 ACAATAACGAGATACTCCCTCTGTT 59.343 40.000 0.00 0.00 34.47 3.16
4088 4479 5.202004 ACAATAACGAGATACTCCCTCTGT 58.798 41.667 0.00 0.00 0.00 3.41
4089 4480 5.776173 ACAATAACGAGATACTCCCTCTG 57.224 43.478 0.00 0.00 0.00 3.35
4090 4481 5.892119 TCAACAATAACGAGATACTCCCTCT 59.108 40.000 0.00 0.00 0.00 3.69
4091 4482 6.145338 TCAACAATAACGAGATACTCCCTC 57.855 41.667 0.00 0.00 0.00 4.30
4092 4483 6.540438 TTCAACAATAACGAGATACTCCCT 57.460 37.500 0.00 0.00 0.00 4.20
4093 4484 6.830114 CTTCAACAATAACGAGATACTCCC 57.170 41.667 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.