Multiple sequence alignment - TraesCS6D01G337200

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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 TraesCS6D01G337200 chr6D 100.000 5506 0 0 1 5506 437811443 437805938 0.000000e+00 10168.0
1 TraesCS6D01G337200 chr6D 88.770 187 19 2 241 426 462474957 462474772 1.540000e-55 228.0
2 TraesCS6D01G337200 chr6D 88.235 187 19 3 241 426 433034975 433035159 2.580000e-53 220.0
3 TraesCS6D01G337200 chr6B 89.413 4496 252 107 420 4825 662518060 662513699 0.000000e+00 5459.0
4 TraesCS6D01G337200 chr6B 96.465 396 13 1 5112 5506 662513646 662513251 0.000000e+00 652.0
5 TraesCS6D01G337200 chr6B 92.391 184 13 1 252 434 653017315 653017498 1.520000e-65 261.0
6 TraesCS6D01G337200 chr6A 93.033 1421 72 12 3438 4841 586102110 586100700 0.000000e+00 2050.0
7 TraesCS6D01G337200 chr6A 91.205 921 42 19 1999 2890 586103564 586102654 0.000000e+00 1216.0
8 TraesCS6D01G337200 chr6A 88.328 891 58 18 430 1303 586105551 586104690 0.000000e+00 1027.0
9 TraesCS6D01G337200 chr6A 92.785 596 15 7 4924 5506 586100602 586100022 0.000000e+00 837.0
10 TraesCS6D01G337200 chr6A 87.464 686 41 21 1313 1985 586104394 586103741 0.000000e+00 749.0
11 TraesCS6D01G337200 chr6A 88.417 518 38 6 2893 3394 586102620 586102109 6.100000e-169 604.0
12 TraesCS6D01G337200 chr6A 90.909 220 19 1 2 221 150962599 150962817 1.500000e-75 294.0
13 TraesCS6D01G337200 chr6A 100.000 31 0 0 4845 4875 586100662 586100632 2.140000e-04 58.4
14 TraesCS6D01G337200 chr1B 80.473 507 73 17 2096 2597 462783943 462783458 1.130000e-96 364.0
15 TraesCS6D01G337200 chr2B 91.855 221 16 2 2 221 401152176 401152395 1.930000e-79 307.0
16 TraesCS6D01G337200 chr2B 89.840 187 17 2 241 426 738336583 738336768 7.130000e-59 239.0
17 TraesCS6D01G337200 chr7A 91.324 219 18 1 2 220 467417334 467417551 1.160000e-76 298.0
18 TraesCS6D01G337200 chr7A 91.324 219 18 1 4 222 581131628 581131411 1.160000e-76 298.0
19 TraesCS6D01G337200 chr2D 90.991 222 18 1 2 221 566107697 566107476 1.160000e-76 298.0
20 TraesCS6D01G337200 chr2D 93.182 176 12 0 251 426 567683314 567683489 5.470000e-65 259.0
21 TraesCS6D01G337200 chr7D 90.179 224 18 1 2 221 227564573 227564350 6.980000e-74 289.0
22 TraesCS6D01G337200 chr7D 92.398 171 13 0 254 424 227563647 227563477 1.530000e-60 244.0
23 TraesCS6D01G337200 chr3D 90.455 220 20 1 2 221 104018964 104018746 6.980000e-74 289.0
24 TraesCS6D01G337200 chr3D 91.304 184 15 1 243 426 104018054 104017872 3.290000e-62 250.0
25 TraesCS6D01G337200 chr5D 90.000 220 21 1 2 221 77607293 77607511 3.250000e-72 283.0
26 TraesCS6D01G337200 chr2A 90.000 220 21 1 2 221 677047913 677048131 3.250000e-72 283.0
27 TraesCS6D01G337200 chr5A 89.189 185 18 2 241 424 27690239 27690422 4.290000e-56 230.0
28 TraesCS6D01G337200 chr7B 88.770 187 18 3 241 426 121050289 121050473 5.550000e-55 226.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G337200 chr6D 437805938 437811443 5505 True 10168.000000 10168 100.000000 1 5506 1 chr6D.!!$R1 5505
1 TraesCS6D01G337200 chr6B 662513251 662518060 4809 True 3055.500000 5459 92.939000 420 5506 2 chr6B.!!$R1 5086
2 TraesCS6D01G337200 chr6A 586100022 586105551 5529 True 934.485714 2050 91.604571 430 5506 7 chr6A.!!$R1 5076
3 TraesCS6D01G337200 chr7D 227563477 227564573 1096 True 266.500000 289 91.288500 2 424 2 chr7D.!!$R1 422
4 TraesCS6D01G337200 chr3D 104017872 104018964 1092 True 269.500000 289 90.879500 2 426 2 chr3D.!!$R1 424

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
952 1649 0.027979 CTGATGTGTATTTGCGGCCG 59.972 55.000 24.05 24.05 0.00 6.13 F
1222 1933 0.926293 TCCTTCACCCATTCCCCATC 59.074 55.000 0.00 0.00 0.00 3.51 F
2015 3209 0.575333 AGGCCCCCTCCTCTGAATAT 59.425 55.000 0.00 0.00 0.00 1.28 F
2935 4192 0.602562 CTTGGCGAGGCAATGGAAAA 59.397 50.000 12.42 0.00 0.00 2.29 F
2970 4227 1.602191 CAGTAACAACGCGGCAATTC 58.398 50.000 12.47 0.00 0.00 2.17 F
3165 4438 1.615392 ACTTTCTGAACCTGCCAATGC 59.385 47.619 0.00 0.00 38.26 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1902 2924 0.324091 CGACCACTACTGGGTAGGGT 60.324 60.0 13.58 13.58 42.74 4.34 R
3209 4482 0.240945 GGTCAACATTGGCAGGTTCG 59.759 55.0 3.94 1.98 33.59 3.95 R
3573 4846 0.863144 CCAGCAAAAATGCAGTGCAC 59.137 50.0 22.44 9.40 43.04 4.57 R
4275 5549 0.038166 ATTTCACGGTCCTGCCACAT 59.962 50.0 0.00 0.00 36.97 3.21 R
4276 5550 0.605319 GATTTCACGGTCCTGCCACA 60.605 55.0 0.00 0.00 36.97 4.17 R
5138 6467 0.181587 TTTCTCCGTTGGCCTGTGAA 59.818 50.0 3.32 0.09 0.00 3.18 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 80 1.459450 GGGCCGAAAAGTTGCAGATA 58.541 50.000 0.00 0.00 0.00 1.98
91 96 2.694829 GATATGCGGCCCTTCGTCGT 62.695 60.000 0.00 0.00 0.00 4.34
118 123 1.070471 CGAATTTGGCTTTTCCGGCG 61.070 55.000 0.00 0.00 37.80 6.46
189 194 2.361104 GGCAAAGTCCCATCGCCA 60.361 61.111 0.00 0.00 42.50 5.69
196 201 2.124612 TCCCATCGCCACATGCAG 60.125 61.111 0.00 0.00 41.33 4.41
221 226 3.142162 TTCGTCCTATCGCCGCCA 61.142 61.111 0.00 0.00 0.00 5.69
222 227 2.495409 TTCGTCCTATCGCCGCCAT 61.495 57.895 0.00 0.00 0.00 4.40
223 228 2.693250 TTCGTCCTATCGCCGCCATG 62.693 60.000 0.00 0.00 0.00 3.66
312 987 5.993441 CCGTGAATATCCTTTTATACGGGTT 59.007 40.000 0.00 0.00 44.26 4.11
370 1045 0.461961 CCCACAAAGCCGTTTTTCCA 59.538 50.000 0.00 0.00 0.00 3.53
426 1101 1.761784 CAGGGTCTGCTAGAGATGCTT 59.238 52.381 0.00 0.00 31.63 3.91
427 1102 2.170187 CAGGGTCTGCTAGAGATGCTTT 59.830 50.000 0.00 0.00 31.63 3.51
428 1103 2.170187 AGGGTCTGCTAGAGATGCTTTG 59.830 50.000 0.00 0.00 31.63 2.77
435 1110 3.386078 TGCTAGAGATGCTTTGAGTAGGG 59.614 47.826 0.00 0.00 0.00 3.53
447 1122 2.034066 GTAGGGCCTGCTTGCACA 59.966 61.111 18.53 0.00 37.02 4.57
464 1139 2.765807 AGCCCACAGAGGATCCGG 60.766 66.667 5.98 0.00 41.22 5.14
465 1140 3.866582 GCCCACAGAGGATCCGGG 61.867 72.222 15.53 15.53 41.29 5.73
466 1141 3.164269 CCCACAGAGGATCCGGGG 61.164 72.222 12.70 12.40 41.22 5.73
467 1142 2.041922 CCACAGAGGATCCGGGGA 60.042 66.667 5.98 0.00 41.22 4.81
468 1143 2.136878 CCACAGAGGATCCGGGGAG 61.137 68.421 5.98 0.00 41.22 4.30
612 1293 2.636830 GGACGACAGCTAGTACTGGTA 58.363 52.381 5.39 0.00 42.21 3.25
732 1417 3.143675 GCTAGTAGCAGCAGCAACA 57.856 52.632 17.47 0.00 45.49 3.33
733 1418 1.442769 GCTAGTAGCAGCAGCAACAA 58.557 50.000 17.47 0.00 45.49 2.83
800 1486 4.599434 GCGCACGCGACCAAACAA 62.599 61.111 15.93 0.00 42.83 2.83
801 1487 2.425124 CGCACGCGACCAAACAAG 60.425 61.111 15.93 0.00 42.83 3.16
802 1488 2.725815 GCACGCGACCAAACAAGC 60.726 61.111 15.93 0.00 0.00 4.01
803 1489 3.022287 CACGCGACCAAACAAGCT 58.978 55.556 15.93 0.00 0.00 3.74
804 1490 1.837538 GCACGCGACCAAACAAGCTA 61.838 55.000 15.93 0.00 0.00 3.32
813 1499 1.542547 CCAAACAAGCTACACCGAGGT 60.543 52.381 0.00 0.00 0.00 3.85
836 1526 0.031994 GAGAGCGAGAGATTGGGAGC 59.968 60.000 0.00 0.00 0.00 4.70
837 1527 0.396974 AGAGCGAGAGATTGGGAGCT 60.397 55.000 0.00 0.00 37.69 4.09
838 1528 0.031994 GAGCGAGAGATTGGGAGCTC 59.968 60.000 4.71 4.71 43.11 4.09
863 1560 0.324943 GGTAGCAGGAAGTTGAGCCA 59.675 55.000 0.00 0.00 0.00 4.75
928 1625 1.931841 GTTAGACGCGGGATTTCTTCC 59.068 52.381 12.47 0.00 44.62 3.46
940 1637 5.686159 GGATTTCTTCCATAGCTGATGTG 57.314 43.478 0.00 0.00 44.74 3.21
947 1644 5.528690 TCTTCCATAGCTGATGTGTATTTGC 59.471 40.000 0.00 0.00 33.19 3.68
948 1645 3.809279 TCCATAGCTGATGTGTATTTGCG 59.191 43.478 0.00 0.00 33.19 4.85
949 1646 3.058708 CCATAGCTGATGTGTATTTGCGG 60.059 47.826 0.00 0.00 33.19 5.69
950 1647 0.734889 AGCTGATGTGTATTTGCGGC 59.265 50.000 0.00 0.00 0.00 6.53
951 1648 0.248621 GCTGATGTGTATTTGCGGCC 60.249 55.000 0.00 0.00 0.00 6.13
952 1649 0.027979 CTGATGTGTATTTGCGGCCG 59.972 55.000 24.05 24.05 0.00 6.13
953 1650 1.355210 GATGTGTATTTGCGGCCGG 59.645 57.895 29.38 8.95 0.00 6.13
954 1651 2.662091 GATGTGTATTTGCGGCCGGC 62.662 60.000 29.38 21.18 43.96 6.13
955 1652 4.187810 GTGTATTTGCGGCCGGCC 62.188 66.667 36.69 36.69 42.61 6.13
973 1670 2.347490 GGCCGCTCTTGTCTTGGA 59.653 61.111 0.00 0.00 0.00 3.53
975 1672 2.035442 GCCGCTCTTGTCTTGGACC 61.035 63.158 0.00 0.00 0.00 4.46
1072 1769 2.753043 GGCCGTCGTCAGGTAGGA 60.753 66.667 0.00 0.00 0.00 2.94
1128 1836 5.390991 GCAAACCTCTTAACTCTTGAATCCG 60.391 44.000 0.00 0.00 0.00 4.18
1152 1860 2.487762 CTGATTTGAACTGCGCCCTTTA 59.512 45.455 4.18 0.00 0.00 1.85
1156 1864 3.363341 TTGAACTGCGCCCTTTAAAAG 57.637 42.857 4.18 0.00 0.00 2.27
1169 1880 7.201741 GCGCCCTTTAAAAGAAGAAGAAGATAT 60.202 37.037 0.00 0.00 0.00 1.63
1170 1881 8.678199 CGCCCTTTAAAAGAAGAAGAAGATATT 58.322 33.333 0.00 0.00 0.00 1.28
1171 1882 9.794685 GCCCTTTAAAAGAAGAAGAAGATATTG 57.205 33.333 0.00 0.00 0.00 1.90
1222 1933 0.926293 TCCTTCACCCATTCCCCATC 59.074 55.000 0.00 0.00 0.00 3.51
1223 1934 0.929244 CCTTCACCCATTCCCCATCT 59.071 55.000 0.00 0.00 0.00 2.90
1224 1935 2.135189 CCTTCACCCATTCCCCATCTA 58.865 52.381 0.00 0.00 0.00 1.98
1238 1950 2.224209 CCCATCTATCCCACAACCGTAC 60.224 54.545 0.00 0.00 0.00 3.67
1277 1989 1.623311 TCAGTCCAGATCTCGGCAAAA 59.377 47.619 0.00 0.00 0.00 2.44
1308 2020 1.077828 TGCTTTCTCTCTCTCCTGGGA 59.922 52.381 0.00 0.00 0.00 4.37
1321 2319 7.831193 TCTCTCTCCTGGGAATTAATTTTGAAG 59.169 37.037 1.43 0.00 0.00 3.02
1338 2339 2.036217 TGAAGTTTGCTCCTGCCATTTG 59.964 45.455 0.00 0.00 38.71 2.32
1380 2381 7.537306 CACGAAATCTTACACCAATTCGATTTT 59.463 33.333 12.01 0.00 41.39 1.82
1381 2382 8.079809 ACGAAATCTTACACCAATTCGATTTTT 58.920 29.630 12.01 0.00 41.39 1.94
1398 2399 4.657814 TTTTTACAGCCCAGAATCTCCT 57.342 40.909 0.00 0.00 0.00 3.69
1422 2423 3.508762 TGTTCCTCGATTCTTCGTTAGC 58.491 45.455 0.00 0.00 45.65 3.09
1423 2424 2.858941 GTTCCTCGATTCTTCGTTAGCC 59.141 50.000 0.00 0.00 45.65 3.93
1424 2425 1.065102 TCCTCGATTCTTCGTTAGCCG 59.935 52.381 0.00 0.00 45.65 5.52
1425 2426 1.065102 CCTCGATTCTTCGTTAGCCGA 59.935 52.381 0.00 0.00 45.65 5.54
1475 2476 3.129462 GCAGAAATTAGTGGCTTCTTCCC 59.871 47.826 0.00 0.00 0.00 3.97
1498 2499 5.333111 CCTTTTGTTCGTCGGTTCTTTCTAG 60.333 44.000 0.00 0.00 0.00 2.43
1565 2571 7.337938 TGAAACATTCCAGCAGTGAGATATTA 58.662 34.615 0.00 0.00 0.00 0.98
1582 2588 7.070198 TGAGATATTACGTGAGGAAATGGGTTA 59.930 37.037 0.00 0.00 37.56 2.85
1599 2605 2.147958 GTTAACGATTGCCACCTCACA 58.852 47.619 0.00 0.00 0.00 3.58
1600 2606 1.803334 TAACGATTGCCACCTCACAC 58.197 50.000 0.00 0.00 0.00 3.82
1601 2607 1.227999 AACGATTGCCACCTCACACG 61.228 55.000 0.00 0.00 0.00 4.49
1607 2613 2.970639 CCACCTCACACGGACGAT 59.029 61.111 0.00 0.00 0.00 3.73
1627 2639 7.430502 GGACGATATATACAACTACCAATACGC 59.569 40.741 0.00 0.00 0.00 4.42
1649 2661 3.783943 CGTAAGAAAATCGCAATTTCCCG 59.216 43.478 3.12 1.24 37.47 5.14
1652 2665 2.166254 AGAAAATCGCAATTTCCCGCAT 59.834 40.909 3.12 0.00 37.47 4.73
1659 2672 2.223066 CGCAATTTCCCGCATACGTTAA 60.223 45.455 0.00 0.00 37.70 2.01
1703 2716 9.638300 GCAACTGATTCTTCGTTGTATATTTAG 57.362 33.333 12.30 0.00 38.00 1.85
1789 2802 5.212745 AGTTTGGGGGTAATTTCTCACAAA 58.787 37.500 8.17 8.17 0.00 2.83
1818 2835 1.962822 GCTGTGCTGCTGTAGTGCA 60.963 57.895 0.00 0.00 41.05 4.57
1840 2857 1.246737 GCTTGCCTAGCCTTGCTTGT 61.247 55.000 0.00 0.00 44.48 3.16
1873 2895 2.575125 ATCTCTGCAGGCAGCTGTCG 62.575 60.000 16.64 10.60 45.94 4.35
1985 3015 4.211125 TCAGTAATTTGCTGTTGTTGGGA 58.789 39.130 13.23 0.00 35.60 4.37
2014 3208 2.036433 AGGCCCCCTCCTCTGAATA 58.964 57.895 0.00 0.00 0.00 1.75
2015 3209 0.575333 AGGCCCCCTCCTCTGAATAT 59.425 55.000 0.00 0.00 0.00 1.28
2016 3210 1.060244 AGGCCCCCTCCTCTGAATATT 60.060 52.381 0.00 0.00 0.00 1.28
2017 3211 2.184565 AGGCCCCCTCCTCTGAATATTA 59.815 50.000 0.00 0.00 0.00 0.98
2112 3306 4.342092 AGCAGCCAACAAGTCTGTAATTTT 59.658 37.500 0.00 0.00 33.45 1.82
2166 3360 9.339850 GGTAATACAACTACTAGATGACAGAGA 57.660 37.037 0.00 0.00 0.00 3.10
2174 3368 5.261209 ACTAGATGACAGAGAGTGAATGC 57.739 43.478 0.00 0.00 0.00 3.56
2211 3405 5.552870 TCTATGGCCTTAATTCTCTGACC 57.447 43.478 3.32 0.00 0.00 4.02
2213 3407 3.634397 TGGCCTTAATTCTCTGACCTG 57.366 47.619 3.32 0.00 0.00 4.00
2225 3419 4.809193 TCTCTGACCTGGTAGATAATGCT 58.191 43.478 0.00 0.00 0.00 3.79
2385 3587 2.086869 CCTGCCAATGTTGACCAGTAG 58.913 52.381 10.35 0.00 0.00 2.57
2386 3588 2.290260 CCTGCCAATGTTGACCAGTAGA 60.290 50.000 10.35 0.00 0.00 2.59
2387 3589 3.614092 CTGCCAATGTTGACCAGTAGAT 58.386 45.455 0.00 0.00 0.00 1.98
2388 3590 4.384098 CCTGCCAATGTTGACCAGTAGATA 60.384 45.833 10.35 0.00 0.00 1.98
2391 3593 5.589855 TGCCAATGTTGACCAGTAGATAATG 59.410 40.000 0.00 0.00 0.00 1.90
2392 3594 5.506317 GCCAATGTTGACCAGTAGATAATGC 60.506 44.000 0.00 0.00 0.00 3.56
2393 3595 5.009010 CCAATGTTGACCAGTAGATAATGCC 59.991 44.000 0.00 0.00 0.00 4.40
2394 3596 3.792401 TGTTGACCAGTAGATAATGCCG 58.208 45.455 0.00 0.00 0.00 5.69
2395 3597 3.131396 GTTGACCAGTAGATAATGCCGG 58.869 50.000 0.00 0.00 0.00 6.13
2396 3598 2.673258 TGACCAGTAGATAATGCCGGA 58.327 47.619 5.05 0.00 0.00 5.14
2416 3620 5.163854 CCGGAGTAAGTAAATCAGTTTGCTG 60.164 44.000 0.00 0.00 39.01 4.41
2424 3628 7.190920 AGTAAATCAGTTTGCTGTTAGTGTC 57.809 36.000 0.00 0.00 43.05 3.67
2432 3636 5.296035 AGTTTGCTGTTAGTGTCTAACCAAC 59.704 40.000 14.41 11.87 31.74 3.77
2666 3881 4.211125 TCACTCTCACCTATCATCACTCC 58.789 47.826 0.00 0.00 0.00 3.85
2839 4063 4.515361 TGGTCGTGTTTCCTTTTCAAGTA 58.485 39.130 0.00 0.00 0.00 2.24
2875 4099 4.677779 GCACACCCATGATTGAAACCATAC 60.678 45.833 0.00 0.00 0.00 2.39
2882 4106 4.412060 TGATTGAAACCATACCCCCTTT 57.588 40.909 0.00 0.00 0.00 3.11
2935 4192 0.602562 CTTGGCGAGGCAATGGAAAA 59.397 50.000 12.42 0.00 0.00 2.29
2970 4227 1.602191 CAGTAACAACGCGGCAATTC 58.398 50.000 12.47 0.00 0.00 2.17
2990 4248 6.704056 ATTCCTTAGGACAAAAGAAGAGGA 57.296 37.500 0.00 0.00 0.00 3.71
2992 4250 4.905456 TCCTTAGGACAAAAGAAGAGGACA 59.095 41.667 0.00 0.00 0.00 4.02
2993 4251 4.998033 CCTTAGGACAAAAGAAGAGGACAC 59.002 45.833 0.00 0.00 0.00 3.67
3001 4259 3.692257 AAGAAGAGGACACCTGTGATG 57.308 47.619 3.94 0.00 31.76 3.07
3061 4319 7.618502 AATACCGATTGTTTACAGCATAACA 57.381 32.000 0.00 0.00 32.76 2.41
3063 4321 5.879237 ACCGATTGTTTACAGCATAACATG 58.121 37.500 0.00 0.00 34.52 3.21
3086 4344 2.126307 CGAGACAGGCGTGACCAG 60.126 66.667 14.38 0.20 43.14 4.00
3089 4347 2.430921 GACAGGCGTGACCAGTCG 60.431 66.667 14.38 0.00 44.10 4.18
3165 4438 1.615392 ACTTTCTGAACCTGCCAATGC 59.385 47.619 0.00 0.00 38.26 3.56
3254 4527 6.973474 GTGTTAGTAAATCAGTCTGCTCGTAT 59.027 38.462 0.00 0.00 0.00 3.06
3430 4703 7.340122 TGTCAAGGAGAGTAGATACAGATTG 57.660 40.000 0.00 0.00 0.00 2.67
3498 4771 7.495934 CCTATTACTGAATTACTCCACCAGTTG 59.504 40.741 0.00 0.00 38.76 3.16
3533 4806 5.398603 ACTTCCGGCTGATCATATTCTAG 57.601 43.478 0.00 0.00 0.00 2.43
3554 4827 2.042686 TCTAGTGCCAATGGTCATGC 57.957 50.000 0.00 0.00 0.00 4.06
3564 4837 3.187842 CCAATGGTCATGCATATCAGTCG 59.812 47.826 0.00 0.00 0.00 4.18
3573 4846 7.596621 GGTCATGCATATCAGTCGGTATATATG 59.403 40.741 0.00 0.00 36.05 1.78
3611 4884 4.679662 CTGGGGTAAATGTACTGACTACG 58.320 47.826 0.00 0.00 0.00 3.51
3877 5150 2.351548 CGATCAATGGCAAGCGCG 60.352 61.111 0.00 0.00 39.92 6.86
3981 5254 2.422597 GTCAATGTCGATGTGGTGGAA 58.577 47.619 0.00 0.00 0.00 3.53
4057 5330 6.183360 TGCTAATTATTTACCACCACATGCTG 60.183 38.462 0.00 0.00 0.00 4.41
4094 5367 5.301805 GCTGGGTATATGCCATACTGTTTTT 59.698 40.000 12.29 0.00 0.00 1.94
4114 5387 2.928801 TCTGGTAACTGCACACATGT 57.071 45.000 0.00 0.00 35.12 3.21
4152 5425 7.801716 TCAAGCATGAAACACTAACTTTACT 57.198 32.000 0.00 0.00 30.99 2.24
4199 5472 4.817517 TGTTCTAGTGCAGCTAAGGTAAC 58.182 43.478 0.00 0.00 0.00 2.50
4445 5719 3.920144 GCTGATGAGCATGCTTGAC 57.080 52.632 23.61 15.65 45.46 3.18
4460 5734 2.540973 GCTTGACGAAAACGAAGCCTTT 60.541 45.455 0.00 0.00 35.76 3.11
4557 5831 0.682209 AGAAAAGGCATCCGCAGCAT 60.682 50.000 0.00 0.00 41.24 3.79
4572 5846 2.945440 GCAGCATGTCCATCTTTGGGTA 60.945 50.000 0.00 0.00 39.29 3.69
4754 6045 9.573166 AATGCAAGTGTGTGTATATGGTATTAT 57.427 29.630 0.00 0.00 0.00 1.28
4770 6061 7.838079 TGGTATTATGATTATTTTGCCAGCT 57.162 32.000 0.00 0.00 0.00 4.24
4771 6062 7.660112 TGGTATTATGATTATTTTGCCAGCTG 58.340 34.615 6.78 6.78 0.00 4.24
4777 6068 1.187974 TATTTTGCCAGCTGCTGCAT 58.812 45.000 23.86 12.47 42.74 3.96
4782 6075 0.967662 TGCCAGCTGCTGCATTTTTA 59.032 45.000 23.86 1.88 42.74 1.52
4827 6120 7.783090 ATGACATCTGATCTACAAATGTGAC 57.217 36.000 0.00 0.00 39.85 3.67
4875 6202 1.407618 TCTCCAACGGTCCATATCACG 59.592 52.381 0.00 0.00 0.00 4.35
4876 6203 0.462375 TCCAACGGTCCATATCACGG 59.538 55.000 0.00 0.00 0.00 4.94
4877 6204 1.157870 CCAACGGTCCATATCACGGC 61.158 60.000 0.00 0.00 0.00 5.68
4878 6205 0.461163 CAACGGTCCATATCACGGCA 60.461 55.000 0.00 0.00 0.00 5.69
4879 6206 0.179084 AACGGTCCATATCACGGCAG 60.179 55.000 0.00 0.00 0.00 4.85
4880 6207 1.956170 CGGTCCATATCACGGCAGC 60.956 63.158 0.00 0.00 0.00 5.25
4881 6208 1.146041 GGTCCATATCACGGCAGCA 59.854 57.895 0.00 0.00 0.00 4.41
4882 6209 0.463654 GGTCCATATCACGGCAGCAA 60.464 55.000 0.00 0.00 0.00 3.91
4885 6212 1.948834 TCCATATCACGGCAGCAAATG 59.051 47.619 0.00 0.00 0.00 2.32
4887 6214 2.358582 CCATATCACGGCAGCAAATGAA 59.641 45.455 0.00 0.00 0.00 2.57
4888 6215 3.005050 CCATATCACGGCAGCAAATGAAT 59.995 43.478 0.00 0.00 0.00 2.57
4889 6216 2.572191 ATCACGGCAGCAAATGAATG 57.428 45.000 0.00 0.00 0.00 2.67
4891 6218 1.079875 CACGGCAGCAAATGAATGGC 61.080 55.000 0.00 3.51 36.25 4.40
4893 6220 0.179094 CGGCAGCAAATGAATGGCAT 60.179 50.000 0.00 0.00 39.31 4.40
4894 6221 1.295792 GGCAGCAAATGAATGGCATG 58.704 50.000 0.00 0.00 37.28 4.06
4896 6223 1.931172 GCAGCAAATGAATGGCATGTC 59.069 47.619 0.00 1.70 37.28 3.06
4897 6224 2.675603 GCAGCAAATGAATGGCATGTCA 60.676 45.455 0.60 0.60 37.28 3.58
4898 6225 3.186909 CAGCAAATGAATGGCATGTCAG 58.813 45.455 6.04 0.00 37.28 3.51
4899 6226 2.167693 AGCAAATGAATGGCATGTCAGG 59.832 45.455 6.04 3.30 37.28 3.86
4903 6230 0.703488 TGAATGGCATGTCAGGGGAA 59.297 50.000 6.04 0.00 0.00 3.97
4904 6231 1.076841 TGAATGGCATGTCAGGGGAAA 59.923 47.619 6.04 0.00 0.00 3.13
4905 6232 2.178580 GAATGGCATGTCAGGGGAAAA 58.821 47.619 6.04 0.00 0.00 2.29
4906 6233 2.555732 ATGGCATGTCAGGGGAAAAT 57.444 45.000 6.04 0.00 0.00 1.82
4907 6234 3.686227 ATGGCATGTCAGGGGAAAATA 57.314 42.857 6.04 0.00 0.00 1.40
4908 6235 3.017048 TGGCATGTCAGGGGAAAATAG 57.983 47.619 0.00 0.00 0.00 1.73
4909 6236 2.580322 TGGCATGTCAGGGGAAAATAGA 59.420 45.455 0.00 0.00 0.00 1.98
4910 6237 3.217626 GGCATGTCAGGGGAAAATAGAG 58.782 50.000 0.00 0.00 0.00 2.43
4911 6238 3.372025 GGCATGTCAGGGGAAAATAGAGT 60.372 47.826 0.00 0.00 0.00 3.24
4912 6239 4.141482 GGCATGTCAGGGGAAAATAGAGTA 60.141 45.833 0.00 0.00 0.00 2.59
4913 6240 5.437060 GCATGTCAGGGGAAAATAGAGTAA 58.563 41.667 0.00 0.00 0.00 2.24
4914 6241 5.885912 GCATGTCAGGGGAAAATAGAGTAAA 59.114 40.000 0.00 0.00 0.00 2.01
4915 6242 6.038714 GCATGTCAGGGGAAAATAGAGTAAAG 59.961 42.308 0.00 0.00 0.00 1.85
4916 6243 6.945636 TGTCAGGGGAAAATAGAGTAAAGA 57.054 37.500 0.00 0.00 0.00 2.52
4917 6244 7.510675 TGTCAGGGGAAAATAGAGTAAAGAT 57.489 36.000 0.00 0.00 0.00 2.40
4918 6245 7.928873 TGTCAGGGGAAAATAGAGTAAAGATT 58.071 34.615 0.00 0.00 0.00 2.40
4919 6246 7.829211 TGTCAGGGGAAAATAGAGTAAAGATTG 59.171 37.037 0.00 0.00 0.00 2.67
4920 6247 7.829706 GTCAGGGGAAAATAGAGTAAAGATTGT 59.170 37.037 0.00 0.00 0.00 2.71
4921 6248 7.829211 TCAGGGGAAAATAGAGTAAAGATTGTG 59.171 37.037 0.00 0.00 0.00 3.33
4922 6249 7.829211 CAGGGGAAAATAGAGTAAAGATTGTGA 59.171 37.037 0.00 0.00 0.00 3.58
4991 6319 5.699097 AAGTAACAAGATGCGGCTAAAAA 57.301 34.783 0.00 0.00 0.00 1.94
5033 6362 2.027385 GAATGATCTTGGAGGGTTGGC 58.973 52.381 0.00 0.00 0.00 4.52
5049 6378 1.855295 TGGCATAACACTCTACCGGA 58.145 50.000 9.46 0.00 0.00 5.14
5138 6467 1.377725 CGGCTTGTTGGAGATGCCT 60.378 57.895 0.00 0.00 41.25 4.75
5162 6491 0.323957 AGGCCAACGGAGAAAGTACC 59.676 55.000 5.01 0.00 0.00 3.34
5176 6505 5.652518 AGAAAGTACCGAGAGAAATGTAGC 58.347 41.667 0.00 0.00 0.00 3.58
5247 6576 4.737578 AGTCAGGTAAGTTACAGACAGGA 58.262 43.478 26.36 10.19 37.57 3.86
5378 6716 2.048222 CGGTATGCGGCGATGGAT 60.048 61.111 12.98 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
101 106 1.291906 CCGCCGGAAAAGCCAAATT 59.708 52.632 5.05 0.00 35.94 1.82
131 136 0.744414 CGACCATTCCATCGCTTGGT 60.744 55.000 4.43 0.00 46.52 3.67
189 194 1.079405 CGAACCCGTACCTGCATGT 60.079 57.895 0.00 0.00 0.00 3.21
221 226 3.432046 CCGCAAATCCTAAATTTGGCCAT 60.432 43.478 6.09 0.00 38.91 4.40
222 227 2.093764 CCGCAAATCCTAAATTTGGCCA 60.094 45.455 0.00 0.00 38.91 5.36
223 228 2.549926 CCGCAAATCCTAAATTTGGCC 58.450 47.619 11.30 0.00 38.91 5.36
252 927 2.998480 TCGGCTTTGCGGGGTCTA 60.998 61.111 0.00 0.00 0.00 2.59
354 1029 1.096416 TCGTGGAAAAACGGCTTTGT 58.904 45.000 0.00 0.00 43.73 2.83
370 1045 0.179184 AAAACGCGTTTGCAGTTCGT 60.179 45.000 35.31 16.10 42.97 3.85
426 1101 1.002134 GCAAGCAGGCCCTACTCAA 60.002 57.895 0.00 0.00 0.00 3.02
427 1102 2.223443 TGCAAGCAGGCCCTACTCA 61.223 57.895 0.00 0.00 0.00 3.41
428 1103 1.746991 GTGCAAGCAGGCCCTACTC 60.747 63.158 0.00 0.00 0.00 2.59
447 1122 2.765807 CCGGATCCTCTGTGGGCT 60.766 66.667 10.75 0.00 36.20 5.19
465 1140 3.844090 GTGCGCTCCTCCTCCTCC 61.844 72.222 9.73 0.00 0.00 4.30
466 1141 3.071206 TGTGCGCTCCTCCTCCTC 61.071 66.667 9.73 0.00 0.00 3.71
467 1142 3.386237 GTGTGCGCTCCTCCTCCT 61.386 66.667 9.73 0.00 0.00 3.69
468 1143 4.803426 CGTGTGCGCTCCTCCTCC 62.803 72.222 9.73 0.00 0.00 4.30
481 1158 4.373116 CAGTAGCCGTGCCCGTGT 62.373 66.667 0.00 0.00 0.00 4.49
799 1485 2.291043 CCCCACCTCGGTGTAGCTT 61.291 63.158 14.51 0.00 44.02 3.74
800 1486 2.683933 CCCCACCTCGGTGTAGCT 60.684 66.667 14.51 0.00 44.02 3.32
801 1487 2.682494 TCCCCACCTCGGTGTAGC 60.682 66.667 14.51 0.00 44.02 3.58
802 1488 1.000019 TCTCCCCACCTCGGTGTAG 60.000 63.158 14.51 9.05 44.02 2.74
803 1489 1.000019 CTCTCCCCACCTCGGTGTA 60.000 63.158 14.51 0.03 44.02 2.90
804 1490 2.283966 CTCTCCCCACCTCGGTGT 60.284 66.667 14.51 0.00 44.02 4.16
813 1499 1.045350 CCAATCTCTCGCTCTCCCCA 61.045 60.000 0.00 0.00 0.00 4.96
814 1500 1.745264 CCAATCTCTCGCTCTCCCC 59.255 63.158 0.00 0.00 0.00 4.81
816 1502 0.673437 CTCCCAATCTCTCGCTCTCC 59.327 60.000 0.00 0.00 0.00 3.71
838 1528 2.185310 AACTTCCTGCTACCTGCCGG 62.185 60.000 0.00 0.00 45.85 6.13
846 1543 1.003580 CCTTGGCTCAACTTCCTGCTA 59.996 52.381 0.00 0.00 0.00 3.49
857 1554 4.020617 CGGTGGCTCCTTGGCTCA 62.021 66.667 3.83 0.00 42.34 4.26
888 1585 2.076863 CAAGGACGAAATGGTCAGGAC 58.923 52.381 0.00 0.00 38.70 3.85
928 1625 3.607775 GCCGCAAATACACATCAGCTATG 60.608 47.826 0.00 0.00 41.74 2.23
954 1651 3.121030 CAAGACAAGAGCGGCCGG 61.121 66.667 29.38 12.50 0.00 6.13
955 1652 3.121030 CCAAGACAAGAGCGGCCG 61.121 66.667 24.05 24.05 0.00 6.13
956 1653 2.035442 GTCCAAGACAAGAGCGGCC 61.035 63.158 0.00 0.00 32.09 6.13
957 1654 2.035442 GGTCCAAGACAAGAGCGGC 61.035 63.158 0.00 0.00 33.68 6.53
958 1655 4.285851 GGTCCAAGACAAGAGCGG 57.714 61.111 0.00 0.00 33.68 5.52
1072 1769 3.735029 GCAGCAAGAAGCAGCGCT 61.735 61.111 2.64 2.64 45.96 5.92
1091 1793 5.205759 AGAGGTTTGCTCAAAGGATTTTG 57.794 39.130 0.00 0.00 44.03 2.44
1092 1794 5.876651 AAGAGGTTTGCTCAAAGGATTTT 57.123 34.783 0.00 0.00 35.03 1.82
1128 1836 0.169009 GGCGCAGTTCAAATCAGGAC 59.831 55.000 10.83 0.00 0.00 3.85
1183 1894 3.244318 GGACGGACAGGTTCCTTTCTTTA 60.244 47.826 5.21 0.00 43.25 1.85
1222 1933 1.472728 GGCAGTACGGTTGTGGGATAG 60.473 57.143 0.00 0.00 0.00 2.08
1223 1934 0.538118 GGCAGTACGGTTGTGGGATA 59.462 55.000 0.00 0.00 0.00 2.59
1224 1935 1.298667 GGCAGTACGGTTGTGGGAT 59.701 57.895 0.00 0.00 0.00 3.85
1277 1989 0.545646 GAGAAAGCATGAGGGGAGCT 59.454 55.000 0.00 0.00 41.03 4.09
1308 2020 6.427853 GGCAGGAGCAAACTTCAAAATTAATT 59.572 34.615 0.00 0.00 44.61 1.40
1321 2319 2.531522 AACAAATGGCAGGAGCAAAC 57.468 45.000 0.00 0.00 44.61 2.93
1380 2381 3.454858 AGAAGGAGATTCTGGGCTGTAA 58.545 45.455 0.00 0.00 46.80 2.41
1381 2382 3.121929 AGAAGGAGATTCTGGGCTGTA 57.878 47.619 0.00 0.00 46.80 2.74
1426 2427 4.173924 GGCAGAGGCAGAGGAGGC 62.174 72.222 0.00 0.00 43.71 4.70
1456 2457 5.984695 AAAGGGAAGAAGCCACTAATTTC 57.015 39.130 0.00 0.00 0.00 2.17
1475 2476 4.531659 AGAAAGAACCGACGAACAAAAG 57.468 40.909 0.00 0.00 0.00 2.27
1527 2533 1.671379 GTTTCAGGCCGTCAGGTCC 60.671 63.158 0.00 0.00 45.21 4.46
1565 2571 2.037511 TCGTTAACCCATTTCCTCACGT 59.962 45.455 0.00 0.00 0.00 4.49
1582 2588 1.227999 CGTGTGAGGTGGCAATCGTT 61.228 55.000 0.00 0.00 0.00 3.85
1599 2605 6.882610 TTGGTAGTTGTATATATCGTCCGT 57.117 37.500 0.00 0.00 0.00 4.69
1600 2606 7.637519 CGTATTGGTAGTTGTATATATCGTCCG 59.362 40.741 0.00 0.00 0.00 4.79
1601 2607 7.430502 GCGTATTGGTAGTTGTATATATCGTCC 59.569 40.741 0.00 0.00 0.00 4.79
1607 2613 8.998377 TCTTACGCGTATTGGTAGTTGTATATA 58.002 33.333 21.30 0.00 0.00 0.86
1627 2639 3.783943 CGGGAAATTGCGATTTTCTTACG 59.216 43.478 15.96 8.59 35.65 3.18
1642 2654 4.806342 GTGATTAACGTATGCGGGAAAT 57.194 40.909 8.39 4.02 43.45 2.17
1703 2716 4.978580 GCGAGGCCTTTGATTAATTGATTC 59.021 41.667 6.77 0.00 0.00 2.52
1901 2923 1.064463 CGACCACTACTGGGTAGGGTA 60.064 57.143 13.64 0.00 42.74 3.69
1902 2924 0.324091 CGACCACTACTGGGTAGGGT 60.324 60.000 13.58 13.58 42.74 4.34
1904 2926 0.815734 CACGACCACTACTGGGTAGG 59.184 60.000 9.14 0.00 42.74 3.18
1985 3015 1.000866 GGGGGCCTCAAAAGCTCAT 59.999 57.895 4.16 0.00 29.87 2.90
2014 3208 7.304497 CCCAAGGCAGAATACTAGTAGTAAT 57.696 40.000 13.92 5.85 33.89 1.89
2015 3209 6.726490 CCCAAGGCAGAATACTAGTAGTAA 57.274 41.667 13.92 0.00 33.89 2.24
2060 3254 2.044551 CAAGCTTCCCCTGCTCCC 60.045 66.667 0.00 0.00 40.22 4.30
2112 3306 2.887152 GCAGCCCTCTTTTTCTCAGAAA 59.113 45.455 0.00 0.00 0.00 2.52
2166 3360 2.034878 TCTCAGCCTATCGCATTCACT 58.965 47.619 0.00 0.00 41.38 3.41
2174 3368 4.022416 GGCCATAGATATCTCAGCCTATCG 60.022 50.000 23.66 3.26 34.54 2.92
2225 3419 5.105752 GGTTGCGCCATAAATAAACAATCA 58.894 37.500 4.18 0.00 37.17 2.57
2237 3431 4.849310 GCCTCGGGTTGCGCCATA 62.849 66.667 4.18 0.00 39.65 2.74
2339 3535 5.697633 TCAGAAACGGTAATTTGGTCAGTAC 59.302 40.000 0.00 0.00 0.00 2.73
2385 3587 6.929606 ACTGATTTACTTACTCCGGCATTATC 59.070 38.462 0.00 0.00 0.00 1.75
2386 3588 6.827727 ACTGATTTACTTACTCCGGCATTAT 58.172 36.000 0.00 0.00 0.00 1.28
2387 3589 6.229936 ACTGATTTACTTACTCCGGCATTA 57.770 37.500 0.00 0.00 0.00 1.90
2388 3590 5.099042 ACTGATTTACTTACTCCGGCATT 57.901 39.130 0.00 0.00 0.00 3.56
2391 3593 4.436986 GCAAACTGATTTACTTACTCCGGC 60.437 45.833 0.00 0.00 0.00 6.13
2392 3594 4.935808 AGCAAACTGATTTACTTACTCCGG 59.064 41.667 0.00 0.00 0.00 5.14
2416 3620 5.284079 TCTGTTCGTTGGTTAGACACTAAC 58.716 41.667 11.68 11.68 42.17 2.34
2424 3628 5.704053 ACCCTTTTATCTGTTCGTTGGTTAG 59.296 40.000 0.00 0.00 0.00 2.34
2432 3636 9.471084 AAACAATTTAACCCTTTTATCTGTTCG 57.529 29.630 0.00 0.00 0.00 3.95
2688 3911 9.147732 TGGAACTAGAATATGATCAGCTAGAAA 57.852 33.333 21.61 8.83 34.24 2.52
2711 3934 6.438741 TCTTGTTTATTTACATGGCCATTGGA 59.561 34.615 17.92 5.67 0.00 3.53
2713 3936 8.721019 ATTCTTGTTTATTTACATGGCCATTG 57.279 30.769 17.92 14.28 0.00 2.82
2746 3969 6.424812 CCTATCTGCATTGATATCAACACGAA 59.575 38.462 20.19 6.14 38.86 3.85
2839 4063 2.898612 TGGGTGTGCATTGACATCAATT 59.101 40.909 4.32 0.00 43.48 2.32
2875 4099 2.772515 CAGAGGGAGTTACTAAAGGGGG 59.227 54.545 0.00 0.00 0.00 5.40
2882 4106 5.422331 CAGTGGAATTCAGAGGGAGTTACTA 59.578 44.000 7.93 0.00 27.87 1.82
2970 4227 4.998033 GTGTCCTCTTCTTTTGTCCTAAGG 59.002 45.833 0.00 0.00 0.00 2.69
2990 4248 2.015456 TCTCAGTCCATCACAGGTGT 57.985 50.000 0.00 0.00 0.00 4.16
2992 4250 4.813809 AGATATCTCAGTCCATCACAGGT 58.186 43.478 0.00 0.00 0.00 4.00
2993 4251 6.127394 CCATAGATATCTCAGTCCATCACAGG 60.127 46.154 8.95 0.00 0.00 4.00
3001 4259 5.080337 TGTGGACCATAGATATCTCAGTCC 58.920 45.833 26.90 26.90 38.75 3.85
3060 4318 1.227205 GCCTGTCTCGAGCCTCATG 60.227 63.158 7.81 5.45 0.00 3.07
3061 4319 2.780094 CGCCTGTCTCGAGCCTCAT 61.780 63.158 7.81 0.00 0.00 2.90
3063 4321 3.444805 ACGCCTGTCTCGAGCCTC 61.445 66.667 7.81 1.33 0.00 4.70
3086 4344 2.095919 AGCAACTCCAAATAAACGCGAC 60.096 45.455 15.93 0.00 0.00 5.19
3089 4347 3.234386 GACAGCAACTCCAAATAAACGC 58.766 45.455 0.00 0.00 0.00 4.84
3178 4451 4.456911 CGGCATGAATGGTGAAGCTATATT 59.543 41.667 0.00 0.00 0.00 1.28
3209 4482 0.240945 GGTCAACATTGGCAGGTTCG 59.759 55.000 3.94 1.98 33.59 3.95
3332 4605 5.163478 GCAATTCCCTGCAAGATCTGTTAAT 60.163 40.000 0.00 0.00 42.17 1.40
3337 4610 2.376109 AGCAATTCCCTGCAAGATCTG 58.624 47.619 0.00 0.00 45.18 2.90
3430 4703 5.622233 GCCATTTGGAACTTGGATGTACTTC 60.622 44.000 0.00 0.10 37.39 3.01
3533 4806 2.098117 GCATGACCATTGGCACTAGAAC 59.902 50.000 1.54 0.00 0.00 3.01
3554 4827 7.433425 CAGTGCACATATATACCGACTGATATG 59.567 40.741 21.04 0.00 37.97 1.78
3564 4837 6.144402 GCAAAAATGCAGTGCACATATATACC 59.856 38.462 22.44 0.00 43.04 2.73
3573 4846 0.863144 CCAGCAAAAATGCAGTGCAC 59.137 50.000 22.44 9.40 43.04 4.57
3611 4884 5.784177 TGTTAAGTCAGATTGAGTGAGTCC 58.216 41.667 0.00 0.00 28.97 3.85
3877 5150 3.392595 GAAGCAGCATGTCAGCGCC 62.393 63.158 2.29 0.00 39.31 6.53
3981 5254 1.709578 TCGCTATCCTCCTCATGCTT 58.290 50.000 0.00 0.00 0.00 3.91
4094 5367 3.207265 ACATGTGTGCAGTTACCAGAA 57.793 42.857 0.00 0.00 0.00 3.02
4108 5381 1.522668 TTTCAGGCCTCGAACATGTG 58.477 50.000 0.00 0.00 0.00 3.21
4114 5387 1.271325 TGCTTGATTTCAGGCCTCGAA 60.271 47.619 0.00 8.00 46.80 3.71
4152 5425 8.839343 CAATGCACAGGTCATCATAAGTTAATA 58.161 33.333 0.00 0.00 0.00 0.98
4275 5549 0.038166 ATTTCACGGTCCTGCCACAT 59.962 50.000 0.00 0.00 36.97 3.21
4276 5550 0.605319 GATTTCACGGTCCTGCCACA 60.605 55.000 0.00 0.00 36.97 4.17
4445 5719 1.259507 TCGTCAAAGGCTTCGTTTTCG 59.740 47.619 0.00 0.87 45.64 3.46
4460 5734 1.840737 CCTCTTCTCCTTCCTCGTCA 58.159 55.000 0.00 0.00 0.00 4.35
4572 5846 3.112263 TCCGGGATACTCTCAAATTGGT 58.888 45.455 0.00 0.00 0.00 3.67
4770 6061 8.923609 TCGAAATATGAAATAAAAATGCAGCA 57.076 26.923 0.00 0.00 29.06 4.41
4771 6062 9.839589 CTTCGAAATATGAAATAAAAATGCAGC 57.160 29.630 0.00 0.00 29.06 5.25
4800 6093 7.825761 TCACATTTGTAGATCAGATGTCATTGT 59.174 33.333 0.00 0.00 44.87 2.71
4802 6095 7.010830 CGTCACATTTGTAGATCAGATGTCATT 59.989 37.037 0.00 0.00 44.87 2.57
4827 6120 2.537639 TACGTCATGACACTAGTGCG 57.462 50.000 24.93 17.95 0.00 5.34
4841 6134 1.112113 TGGAGAAGCCCTGATACGTC 58.888 55.000 0.00 0.00 34.97 4.34
4843 6136 1.802880 CGTTGGAGAAGCCCTGATACG 60.803 57.143 0.00 0.00 34.97 3.06
4875 6202 1.295792 CATGCCATTCATTTGCTGCC 58.704 50.000 0.00 0.00 31.79 4.85
4876 6203 1.931172 GACATGCCATTCATTTGCTGC 59.069 47.619 0.00 0.00 31.79 5.25
4877 6204 3.186909 CTGACATGCCATTCATTTGCTG 58.813 45.455 0.00 0.00 31.79 4.41
4878 6205 2.167693 CCTGACATGCCATTCATTTGCT 59.832 45.455 0.00 0.00 31.79 3.91
4879 6206 2.546778 CCTGACATGCCATTCATTTGC 58.453 47.619 0.00 0.00 31.79 3.68
4880 6207 2.159014 CCCCTGACATGCCATTCATTTG 60.159 50.000 0.00 0.00 31.79 2.32
4881 6208 2.112998 CCCCTGACATGCCATTCATTT 58.887 47.619 0.00 0.00 31.79 2.32
4882 6209 1.288633 TCCCCTGACATGCCATTCATT 59.711 47.619 0.00 0.00 31.79 2.57
4885 6212 1.851304 TTTCCCCTGACATGCCATTC 58.149 50.000 0.00 0.00 0.00 2.67
4887 6214 2.555732 ATTTTCCCCTGACATGCCAT 57.444 45.000 0.00 0.00 0.00 4.40
4888 6215 2.580322 TCTATTTTCCCCTGACATGCCA 59.420 45.455 0.00 0.00 0.00 4.92
4889 6216 3.217626 CTCTATTTTCCCCTGACATGCC 58.782 50.000 0.00 0.00 0.00 4.40
4891 6218 7.338710 TCTTTACTCTATTTTCCCCTGACATG 58.661 38.462 0.00 0.00 0.00 3.21
4893 6220 6.945636 TCTTTACTCTATTTTCCCCTGACA 57.054 37.500 0.00 0.00 0.00 3.58
4894 6221 7.829706 ACAATCTTTACTCTATTTTCCCCTGAC 59.170 37.037 0.00 0.00 0.00 3.51
4896 6223 7.829211 TCACAATCTTTACTCTATTTTCCCCTG 59.171 37.037 0.00 0.00 0.00 4.45
4897 6224 7.928873 TCACAATCTTTACTCTATTTTCCCCT 58.071 34.615 0.00 0.00 0.00 4.79
4898 6225 8.575649 TTCACAATCTTTACTCTATTTTCCCC 57.424 34.615 0.00 0.00 0.00 4.81
4899 6226 9.841880 GTTTCACAATCTTTACTCTATTTTCCC 57.158 33.333 0.00 0.00 0.00 3.97
4905 6232 9.846248 GCAAATGTTTCACAATCTTTACTCTAT 57.154 29.630 0.00 0.00 0.00 1.98
4906 6233 9.066892 AGCAAATGTTTCACAATCTTTACTCTA 57.933 29.630 0.00 0.00 0.00 2.43
4907 6234 7.945134 AGCAAATGTTTCACAATCTTTACTCT 58.055 30.769 0.00 0.00 0.00 3.24
4908 6235 9.334693 CTAGCAAATGTTTCACAATCTTTACTC 57.665 33.333 0.00 0.00 0.00 2.59
4909 6236 7.809806 GCTAGCAAATGTTTCACAATCTTTACT 59.190 33.333 10.63 0.00 0.00 2.24
4910 6237 7.594758 TGCTAGCAAATGTTTCACAATCTTTAC 59.405 33.333 16.84 0.00 0.00 2.01
4911 6238 7.656412 TGCTAGCAAATGTTTCACAATCTTTA 58.344 30.769 16.84 0.00 0.00 1.85
4912 6239 6.514947 TGCTAGCAAATGTTTCACAATCTTT 58.485 32.000 16.84 0.00 0.00 2.52
4913 6240 6.088016 TGCTAGCAAATGTTTCACAATCTT 57.912 33.333 16.84 0.00 0.00 2.40
4914 6241 5.336213 CCTGCTAGCAAATGTTTCACAATCT 60.336 40.000 19.86 0.00 0.00 2.40
4915 6242 4.860907 CCTGCTAGCAAATGTTTCACAATC 59.139 41.667 19.86 0.00 0.00 2.67
4916 6243 4.523943 TCCTGCTAGCAAATGTTTCACAAT 59.476 37.500 19.86 0.00 0.00 2.71
4917 6244 3.888323 TCCTGCTAGCAAATGTTTCACAA 59.112 39.130 19.86 0.00 0.00 3.33
4918 6245 3.485394 TCCTGCTAGCAAATGTTTCACA 58.515 40.909 19.86 0.00 0.00 3.58
4919 6246 3.753272 TCTCCTGCTAGCAAATGTTTCAC 59.247 43.478 19.86 0.00 0.00 3.18
4920 6247 4.019792 TCTCCTGCTAGCAAATGTTTCA 57.980 40.909 19.86 0.00 0.00 2.69
4921 6248 4.216257 TGTTCTCCTGCTAGCAAATGTTTC 59.784 41.667 19.86 7.51 0.00 2.78
4922 6249 4.144297 TGTTCTCCTGCTAGCAAATGTTT 58.856 39.130 19.86 0.00 0.00 2.83
4933 6260 2.887152 GTGTTTGGATTGTTCTCCTGCT 59.113 45.455 0.00 0.00 36.20 4.24
4991 6319 3.963428 ACTACTGCATCTCGTTCCTTT 57.037 42.857 0.00 0.00 0.00 3.11
4994 6322 3.232213 TCAACTACTGCATCTCGTTCC 57.768 47.619 0.00 0.00 0.00 3.62
5033 6362 3.381908 AGCTTCTCCGGTAGAGTGTTATG 59.618 47.826 0.00 0.00 43.71 1.90
5049 6378 8.299570 CAAAGTATCCACAAATTAACAGCTTCT 58.700 33.333 0.00 0.00 0.00 2.85
5138 6467 0.181587 TTTCTCCGTTGGCCTGTGAA 59.818 50.000 3.32 0.09 0.00 3.18
5151 6480 5.074584 ACATTTCTCTCGGTACTTTCTCC 57.925 43.478 0.00 0.00 0.00 3.71
5162 6491 4.201666 GCTGTTCTTGCTACATTTCTCTCG 60.202 45.833 0.00 0.00 0.00 4.04
5176 6505 1.247567 ACCCCATTTCGCTGTTCTTG 58.752 50.000 0.00 0.00 0.00 3.02
5247 6576 4.822350 GCCTTCTTAGACTTGTTTTGGTCT 59.178 41.667 0.00 0.00 43.93 3.85
5378 6716 0.534203 GGCGGGTCTGTTTGAGAACA 60.534 55.000 0.00 0.00 40.67 3.18


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

AutoCloner maintained by Alex Coulton.