Multiple sequence alignment - TraesCS7D01G555300

Loading Multiple Alignment...

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 TraesCS7D01G555300 chr7D 100.000 4221 0 0 1 4221 638670281 638666061 0.000000e+00 7795.0
1 TraesCS7D01G555300 chr7D 80.108 3162 537 57 2 3122 631393981 631397091 0.000000e+00 2270.0
2 TraesCS7D01G555300 chr7D 75.781 2560 538 60 116 2621 631425103 631427634 0.000000e+00 1218.0
3 TraesCS7D01G555300 chr7D 100.000 52 0 0 3558 3609 638666649 638666598 3.470000e-16 97.1
4 TraesCS7D01G555300 chr7D 100.000 52 0 0 3633 3684 638666724 638666673 3.470000e-16 97.1
5 TraesCS7D01G555300 chr7B 83.715 3623 450 65 1 3559 733798252 733801798 0.000000e+00 3293.0
6 TraesCS7D01G555300 chr7B 89.261 1285 136 2 1 1284 733759823 733761106 0.000000e+00 1607.0
7 TraesCS7D01G555300 chr7B 79.799 1693 303 27 1458 3122 733761331 733763012 0.000000e+00 1195.0
8 TraesCS7D01G555300 chr7B 75.615 2563 540 62 116 2621 733811893 733814427 0.000000e+00 1192.0
9 TraesCS7D01G555300 chr7B 88.006 617 55 14 3607 4221 733801809 733802408 0.000000e+00 712.0
10 TraesCS7D01G555300 chr7B 71.378 1974 438 83 38 1938 1036878 1034959 8.500000e-107 398.0
11 TraesCS7D01G555300 chr7B 72.669 1394 296 62 32 1360 1348667 1350040 6.620000e-103 385.0
12 TraesCS7D01G555300 chr7B 77.947 263 56 2 2152 2413 746862479 746862218 3.380000e-36 163.0
13 TraesCS7D01G555300 chr7A 80.852 3264 551 54 1 3210 726685592 726682349 0.000000e+00 2497.0
14 TraesCS7D01G555300 chr7A 84.052 2157 299 28 54 2186 726814230 726812095 0.000000e+00 2036.0
15 TraesCS7D01G555300 chr7A 80.102 1176 189 26 591 1754 731929371 731930513 0.000000e+00 833.0
16 TraesCS7D01G555300 chr7A 74.914 1746 407 27 2 1726 727229349 727231084 0.000000e+00 769.0
17 TraesCS7D01G555300 chr7A 84.800 125 14 5 3430 3551 727209655 727209777 2.060000e-23 121.0
18 TraesCS7D01G555300 chr7A 87.912 91 9 2 3422 3511 726750643 726750732 5.770000e-19 106.0
19 TraesCS7D01G555300 chr1B 74.000 2300 505 69 19 2259 626244643 626246908 0.000000e+00 848.0
20 TraesCS7D01G555300 chr6D 72.885 2305 517 78 38 2273 468255366 468253101 0.000000e+00 695.0
21 TraesCS7D01G555300 chrUn 80.203 788 144 10 2431 3209 283734741 283735525 7.870000e-162 580.0
22 TraesCS7D01G555300 chrUn 80.255 785 143 10 2434 3209 422907549 422906768 7.870000e-162 580.0
23 TraesCS7D01G555300 chrUn 79.771 786 151 6 2431 3209 277754940 277755724 7.920000e-157 564.0
24 TraesCS7D01G555300 chrUn 79.771 786 151 6 2431 3209 304658883 304659667 7.920000e-157 564.0
25 TraesCS7D01G555300 chrUn 80.685 730 129 10 2489 3209 442902055 442901329 1.330000e-154 556.0
26 TraesCS7D01G555300 chrUn 79.185 466 88 9 2750 3209 277751229 277751691 8.810000e-82 315.0
27 TraesCS7D01G555300 chr4D 71.231 2023 455 91 38 1975 509854431 509852451 1.100000e-105 394.0
28 TraesCS7D01G555300 chr4B 72.664 1295 282 49 123 1360 656879672 656880951 8.620000e-97 364.0
29 TraesCS7D01G555300 chr5D 73.569 734 149 25 32 735 551879130 551879848 5.450000e-59 239.0


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 TraesCS7D01G555300 chr7D 638666061 638670281 4220 True 2663.066667 7795 100.0000 1 4221 3 chr7D.!!$R1 4220
1 TraesCS7D01G555300 chr7D 631393981 631397091 3110 False 2270.000000 2270 80.1080 2 3122 1 chr7D.!!$F1 3120
2 TraesCS7D01G555300 chr7D 631425103 631427634 2531 False 1218.000000 1218 75.7810 116 2621 1 chr7D.!!$F2 2505
3 TraesCS7D01G555300 chr7B 733798252 733802408 4156 False 2002.500000 3293 85.8605 1 4221 2 chr7B.!!$F4 4220
4 TraesCS7D01G555300 chr7B 733759823 733763012 3189 False 1401.000000 1607 84.5300 1 3122 2 chr7B.!!$F3 3121
5 TraesCS7D01G555300 chr7B 733811893 733814427 2534 False 1192.000000 1192 75.6150 116 2621 1 chr7B.!!$F2 2505
6 TraesCS7D01G555300 chr7B 1034959 1036878 1919 True 398.000000 398 71.3780 38 1938 1 chr7B.!!$R1 1900
7 TraesCS7D01G555300 chr7B 1348667 1350040 1373 False 385.000000 385 72.6690 32 1360 1 chr7B.!!$F1 1328
8 TraesCS7D01G555300 chr7A 726682349 726685592 3243 True 2497.000000 2497 80.8520 1 3210 1 chr7A.!!$R1 3209
9 TraesCS7D01G555300 chr7A 726812095 726814230 2135 True 2036.000000 2036 84.0520 54 2186 1 chr7A.!!$R2 2132
10 TraesCS7D01G555300 chr7A 731929371 731930513 1142 False 833.000000 833 80.1020 591 1754 1 chr7A.!!$F4 1163
11 TraesCS7D01G555300 chr7A 727229349 727231084 1735 False 769.000000 769 74.9140 2 1726 1 chr7A.!!$F3 1724
12 TraesCS7D01G555300 chr1B 626244643 626246908 2265 False 848.000000 848 74.0000 19 2259 1 chr1B.!!$F1 2240
13 TraesCS7D01G555300 chr6D 468253101 468255366 2265 True 695.000000 695 72.8850 38 2273 1 chr6D.!!$R1 2235
14 TraesCS7D01G555300 chrUn 283734741 283735525 784 False 580.000000 580 80.2030 2431 3209 1 chrUn.!!$F1 778
15 TraesCS7D01G555300 chrUn 422906768 422907549 781 True 580.000000 580 80.2550 2434 3209 1 chrUn.!!$R1 775
16 TraesCS7D01G555300 chrUn 304658883 304659667 784 False 564.000000 564 79.7710 2431 3209 1 chrUn.!!$F2 778
17 TraesCS7D01G555300 chrUn 442901329 442902055 726 True 556.000000 556 80.6850 2489 3209 1 chrUn.!!$R2 720
18 TraesCS7D01G555300 chrUn 277751229 277755724 4495 False 439.500000 564 79.4780 2431 3209 2 chrUn.!!$F3 778
19 TraesCS7D01G555300 chr4D 509852451 509854431 1980 True 394.000000 394 71.2310 38 1975 1 chr4D.!!$R1 1937
20 TraesCS7D01G555300 chr4B 656879672 656880951 1279 False 364.000000 364 72.6640 123 1360 1 chr4B.!!$F1 1237
21 TraesCS7D01G555300 chr5D 551879130 551879848 718 False 239.000000 239 73.5690 32 735 1 chr5D.!!$F1 703

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
161 165 0.257905 GGTCCAGGGGGTATTGGAAC 59.742 60.000 0.00 0.0 44.61 3.62 F
268 272 0.448197 TGACGAGCTTAGACTCAGCG 59.552 55.000 3.03 0.0 42.55 5.18 F
1894 2048 1.080498 TGTTGGGGTCTCTCCACCTAT 59.920 52.381 0.00 0.0 39.29 2.57 F
2571 3856 0.322906 CCTTTCCCTGCTTCCCTCAC 60.323 60.000 0.00 0.0 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1830 1984 0.391597 ACCAACTAGGACCACGTGTG 59.608 55.000 15.65 8.62 41.22 3.82 R
2102 2256 1.065102 CGGATGCATTCAAGCCTTGAG 59.935 52.381 7.29 0.00 41.38 3.02 R
3218 4527 0.034574 TACGTACCTTGGTCGGGCTA 60.035 55.000 13.17 0.00 0.00 3.93 R
3594 4903 0.035881 TTGGCACTGGAGCTCTCAAG 59.964 55.000 14.64 11.40 36.70 3.02 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
161 165 0.257905 GGTCCAGGGGGTATTGGAAC 59.742 60.000 0.00 0.00 44.61 3.62
252 256 7.120579 TGGGTATGTGTATCAACTGATTTTGAC 59.879 37.037 0.00 0.00 38.31 3.18
268 272 0.448197 TGACGAGCTTAGACTCAGCG 59.552 55.000 3.03 0.00 42.55 5.18
404 438 5.533528 TCTTTGATGATATGTGGGAATGCAG 59.466 40.000 0.00 0.00 0.00 4.41
477 514 2.344025 GGTAACATGGTTCTCGTCACC 58.656 52.381 0.00 0.00 34.52 4.02
496 533 6.349280 CGTCACCACTCAATTTCCAACAATAT 60.349 38.462 0.00 0.00 0.00 1.28
678 728 1.581447 GCCGCTAGCAGCAAAAACT 59.419 52.632 18.08 0.00 42.58 2.66
681 731 1.400242 CCGCTAGCAGCAAAAACTGTC 60.400 52.381 16.45 0.00 42.58 3.51
799 852 6.625532 TGCCATCATTGAGGATTAGCTATA 57.374 37.500 0.00 0.00 0.00 1.31
802 855 7.772292 TGCCATCATTGAGGATTAGCTATAATC 59.228 37.037 0.00 0.00 44.47 1.75
819 872 9.723601 AGCTATAATCATCTTCCTTTTCATCTC 57.276 33.333 0.00 0.00 0.00 2.75
985 1057 6.865726 CGTGAAGGAAGTAGATGATGATAAGG 59.134 42.308 0.00 0.00 0.00 2.69
987 1062 7.870445 GTGAAGGAAGTAGATGATGATAAGGAC 59.130 40.741 0.00 0.00 0.00 3.85
998 1073 6.299805 TGATGATAAGGACCCATACTATGC 57.700 41.667 0.00 0.00 0.00 3.14
1061 1136 4.910195 TCACAAGAGTGCCTCAACATATT 58.090 39.130 5.21 0.00 45.49 1.28
1121 1199 4.688879 TGTTCGACACTTATCCATCACAAC 59.311 41.667 0.00 0.00 0.00 3.32
1292 1373 4.277921 GGGTCTCCGTGTCCTACTTATAAG 59.722 50.000 11.05 11.05 0.00 1.73
1301 1382 6.095160 CGTGTCCTACTTATAAGAGTGAGGTT 59.905 42.308 19.38 0.00 0.00 3.50
1354 1456 2.965671 TATCCACCTCCGGTACCTAG 57.034 55.000 10.90 7.23 32.11 3.02
1365 1467 2.681344 CCGGTACCTAGAAATTTGGCAC 59.319 50.000 10.90 0.00 0.00 5.01
1366 1468 2.681344 CGGTACCTAGAAATTTGGCACC 59.319 50.000 10.90 0.20 35.45 5.01
1369 1472 2.807676 ACCTAGAAATTTGGCACCCAG 58.192 47.619 0.00 0.00 33.81 4.45
1390 1522 7.735321 ACCCAGATCTATACTGTAGGCTAATTT 59.265 37.037 0.00 0.00 34.04 1.82
1454 1586 5.047377 ACCTTGTTGATTTGTGTCACAGTTT 60.047 36.000 5.67 0.00 0.00 2.66
1501 1636 6.196353 CCGCCTTATCAATTTACGTCATTTTG 59.804 38.462 0.00 0.00 0.00 2.44
1525 1660 4.197498 GCGATGCACACCATGGCC 62.197 66.667 13.04 0.00 46.30 5.36
1534 1669 2.040544 CACCATGGCCGTGTTCCTC 61.041 63.158 23.39 0.00 0.00 3.71
1571 1706 6.738114 TGAAATGTTTACAGGAGCTCAAAAG 58.262 36.000 17.19 4.24 0.00 2.27
1585 1720 6.348868 GGAGCTCAAAAGATTCAGTGTTAAGG 60.349 42.308 17.19 0.00 0.00 2.69
1691 1826 2.446435 GGCAACAATGGAAGAGGCTAA 58.554 47.619 0.00 0.00 0.00 3.09
1817 1971 7.201679 CCCTAATCTTGAAGCACTTGTCATTAG 60.202 40.741 0.00 0.00 0.00 1.73
1830 1984 5.126061 ACTTGTCATTAGAAATCATGGTGGC 59.874 40.000 0.00 0.00 0.00 5.01
1864 2018 2.426738 AGTTGGTTGTGTGGTGACATTG 59.573 45.455 0.00 0.00 46.14 2.82
1894 2048 1.080498 TGTTGGGGTCTCTCCACCTAT 59.920 52.381 0.00 0.00 39.29 2.57
2051 2205 8.020244 GTGAATTTGAAGAGGATTGTTCTTCTC 58.980 37.037 14.05 6.02 46.78 2.87
2054 2208 5.157940 TGAAGAGGATTGTTCTTCTCAGG 57.842 43.478 14.05 0.00 46.78 3.86
2121 2275 2.372264 TCTCAAGGCTTGAATGCATCC 58.628 47.619 28.27 0.00 39.58 3.51
2181 2341 3.068024 CCTGGAGTGCTCTGTCTCTTATC 59.932 52.174 0.00 0.00 0.00 1.75
2304 2470 5.587443 TCCACAAAGCTGTCTTATGATGATG 59.413 40.000 0.00 0.00 31.64 3.07
2452 3734 2.188062 TCAGCAGATGCAACATCACA 57.812 45.000 7.68 0.00 45.16 3.58
2460 3742 1.546961 TGCAACATCACATGGCATGA 58.453 45.000 32.74 14.07 33.60 3.07
2479 3761 0.839946 AACTGCAGGACTTCAGGTGT 59.160 50.000 19.93 0.00 34.76 4.16
2482 3764 0.394192 TGCAGGACTTCAGGTGTCTG 59.606 55.000 0.00 0.00 42.21 3.51
2487 3769 0.389166 GACTTCAGGTGTCTGCGAGG 60.389 60.000 0.00 0.00 40.69 4.63
2492 3774 0.668706 CAGGTGTCTGCGAGGACTTG 60.669 60.000 9.06 3.14 37.16 3.16
2499 3781 3.210857 TGCGAGGACTTGCAGTAAC 57.789 52.632 10.11 0.00 44.49 2.50
2571 3856 0.322906 CCTTTCCCTGCTTCCCTCAC 60.323 60.000 0.00 0.00 0.00 3.51
2580 3865 1.899814 TGCTTCCCTCACGTATCTTGT 59.100 47.619 0.00 0.00 0.00 3.16
2589 3874 5.351458 CCTCACGTATCTTGTGATTGATGA 58.649 41.667 0.00 0.00 44.70 2.92
2590 3875 5.461407 CCTCACGTATCTTGTGATTGATGAG 59.539 44.000 0.00 0.00 44.70 2.90
2714 3999 3.576982 TCTTATCACGGTCAACCTCAACT 59.423 43.478 0.00 0.00 0.00 3.16
2715 4000 4.768448 TCTTATCACGGTCAACCTCAACTA 59.232 41.667 0.00 0.00 0.00 2.24
2720 4005 3.813166 CACGGTCAACCTCAACTATTTGT 59.187 43.478 0.00 0.00 34.02 2.83
2721 4006 3.813166 ACGGTCAACCTCAACTATTTGTG 59.187 43.478 0.00 0.00 34.02 3.33
2812 4097 0.538287 GGACCAGCCTATCATTGCCC 60.538 60.000 0.00 0.00 0.00 5.36
2860 4163 0.917533 AGGTGGATTGCATCTCAGCT 59.082 50.000 8.82 8.82 35.20 4.24
2866 4169 2.558378 GATTGCATCTCAGCTGTGCTA 58.442 47.619 23.43 18.27 36.40 3.49
2885 4188 1.279496 AGTTGCTCCCATCTGTAGCA 58.721 50.000 0.00 0.00 44.15 3.49
2912 4215 2.547430 GCTGCTACCCTCCGGTATTTAC 60.547 54.545 0.00 0.00 43.89 2.01
2913 4216 1.682854 TGCTACCCTCCGGTATTTACG 59.317 52.381 0.00 0.00 43.89 3.18
2920 4223 3.057734 CCTCCGGTATTTACGATTCAGC 58.942 50.000 0.00 0.00 0.00 4.26
2922 4225 4.369182 CTCCGGTATTTACGATTCAGCTT 58.631 43.478 0.00 0.00 0.00 3.74
2987 4290 1.001503 CAGCTCCTCACCTCCCTCT 59.998 63.158 0.00 0.00 0.00 3.69
3063 4366 0.908198 AGCCTTCCTTCTCTTCGCAT 59.092 50.000 0.00 0.00 0.00 4.73
3129 4432 1.449778 GCTTCCCCACTCCGCTAAC 60.450 63.158 0.00 0.00 0.00 2.34
3130 4433 1.900545 GCTTCCCCACTCCGCTAACT 61.901 60.000 0.00 0.00 0.00 2.24
3140 4449 2.819608 ACTCCGCTAACTGTAACCGTAA 59.180 45.455 0.00 0.00 0.00 3.18
3141 4450 3.174375 CTCCGCTAACTGTAACCGTAAC 58.826 50.000 0.00 0.00 0.00 2.50
3161 4470 2.161486 GGTTGCAGTCGCGAGCTAG 61.161 63.158 19.39 7.20 45.06 3.42
3182 4491 7.532682 CTAGAAGAGCAACTCTGGAAATTAC 57.467 40.000 0.00 0.00 40.28 1.89
3200 4509 1.331214 ACAGGCAACAAACCCAGATG 58.669 50.000 0.00 0.00 41.41 2.90
3216 4525 3.924073 CCAGATGTTGATGTGTGCATTTG 59.076 43.478 0.00 0.00 35.07 2.32
3217 4526 3.366724 CAGATGTTGATGTGTGCATTTGC 59.633 43.478 0.00 0.00 42.50 3.68
3218 4527 3.257375 AGATGTTGATGTGTGCATTTGCT 59.743 39.130 3.94 0.00 42.66 3.91
3219 4528 4.460034 AGATGTTGATGTGTGCATTTGCTA 59.540 37.500 3.94 0.00 42.66 3.49
3220 4529 4.163458 TGTTGATGTGTGCATTTGCTAG 57.837 40.909 3.94 0.00 42.66 3.42
3221 4530 2.919229 GTTGATGTGTGCATTTGCTAGC 59.081 45.455 8.10 8.10 42.66 3.42
3222 4531 1.473677 TGATGTGTGCATTTGCTAGCC 59.526 47.619 13.29 0.00 42.66 3.93
3223 4532 0.819582 ATGTGTGCATTTGCTAGCCC 59.180 50.000 13.29 0.00 42.66 5.19
3224 4533 1.137404 GTGTGCATTTGCTAGCCCG 59.863 57.895 13.29 0.00 42.66 6.13
3225 4534 1.002746 TGTGCATTTGCTAGCCCGA 60.003 52.632 13.29 0.00 42.66 5.14
3226 4535 1.305219 TGTGCATTTGCTAGCCCGAC 61.305 55.000 13.29 1.08 42.66 4.79
3227 4536 1.748879 TGCATTTGCTAGCCCGACC 60.749 57.895 13.29 0.00 42.66 4.79
3228 4537 1.748879 GCATTTGCTAGCCCGACCA 60.749 57.895 13.29 0.00 38.21 4.02
3229 4538 1.312371 GCATTTGCTAGCCCGACCAA 61.312 55.000 13.29 0.00 38.21 3.67
3230 4539 0.734889 CATTTGCTAGCCCGACCAAG 59.265 55.000 13.29 0.00 0.00 3.61
3231 4540 0.394352 ATTTGCTAGCCCGACCAAGG 60.394 55.000 13.29 0.00 0.00 3.61
3232 4541 1.774894 TTTGCTAGCCCGACCAAGGT 61.775 55.000 13.29 0.00 0.00 3.50
3246 4555 4.558496 CGACCAAGGTACGTAACTGGTAAA 60.558 45.833 25.15 0.00 0.00 2.01
3256 4565 2.200373 AACTGGTAAAATGCGAGCCT 57.800 45.000 0.00 0.00 0.00 4.58
3279 4588 7.439356 GCCTTTCTTCTGTTTTCTGCTAATTTT 59.561 33.333 0.00 0.00 0.00 1.82
3280 4589 9.317936 CCTTTCTTCTGTTTTCTGCTAATTTTT 57.682 29.630 0.00 0.00 0.00 1.94
3345 4654 5.394562 TTCAGGTCTCAGATCCTAGATCA 57.605 43.478 7.30 0.00 32.26 2.92
3375 4684 2.129607 GTGTGCATTGCTTGTTTGGAG 58.870 47.619 10.49 0.00 0.00 3.86
3379 4688 4.039004 TGTGCATTGCTTGTTTGGAGTATT 59.961 37.500 10.49 0.00 0.00 1.89
3380 4689 4.386652 GTGCATTGCTTGTTTGGAGTATTG 59.613 41.667 10.49 0.00 0.00 1.90
3381 4690 3.928375 GCATTGCTTGTTTGGAGTATTGG 59.072 43.478 0.16 0.00 0.00 3.16
3382 4691 4.497300 CATTGCTTGTTTGGAGTATTGGG 58.503 43.478 0.00 0.00 0.00 4.12
3383 4692 2.524306 TGCTTGTTTGGAGTATTGGGG 58.476 47.619 0.00 0.00 0.00 4.96
3384 4693 2.109128 TGCTTGTTTGGAGTATTGGGGA 59.891 45.455 0.00 0.00 0.00 4.81
3385 4694 3.161866 GCTTGTTTGGAGTATTGGGGAA 58.838 45.455 0.00 0.00 0.00 3.97
3386 4695 3.576550 GCTTGTTTGGAGTATTGGGGAAA 59.423 43.478 0.00 0.00 0.00 3.13
3387 4696 4.222810 GCTTGTTTGGAGTATTGGGGAAAT 59.777 41.667 0.00 0.00 0.00 2.17
3388 4697 5.420739 GCTTGTTTGGAGTATTGGGGAAATA 59.579 40.000 0.00 0.00 0.00 1.40
3389 4698 6.098266 GCTTGTTTGGAGTATTGGGGAAATAT 59.902 38.462 0.00 0.00 33.32 1.28
3390 4699 7.286775 GCTTGTTTGGAGTATTGGGGAAATATA 59.713 37.037 0.00 0.00 33.32 0.86
3391 4700 9.367160 CTTGTTTGGAGTATTGGGGAAATATAT 57.633 33.333 0.00 0.00 33.32 0.86
3397 4706 8.924303 TGGAGTATTGGGGAAATATATATCTCG 58.076 37.037 0.00 0.00 33.32 4.04
3483 4792 3.619242 CCATTGTTTGGTGGCATAATGCA 60.619 43.478 0.00 0.00 42.34 3.96
3559 4868 3.585748 TTTCAAGCTCTTCGTTTCGTG 57.414 42.857 0.00 0.00 0.00 4.35
3560 4869 2.502213 TCAAGCTCTTCGTTTCGTGA 57.498 45.000 0.00 0.00 0.00 4.35
3561 4870 2.816689 TCAAGCTCTTCGTTTCGTGAA 58.183 42.857 0.00 0.00 0.00 3.18
3562 4871 2.794910 TCAAGCTCTTCGTTTCGTGAAG 59.205 45.455 0.00 0.00 43.31 3.02
3563 4872 2.510768 AGCTCTTCGTTTCGTGAAGT 57.489 45.000 3.00 0.00 42.68 3.01
3564 4873 2.822764 AGCTCTTCGTTTCGTGAAGTT 58.177 42.857 3.00 0.00 42.68 2.66
3565 4874 3.195661 AGCTCTTCGTTTCGTGAAGTTT 58.804 40.909 3.00 0.00 42.68 2.66
3566 4875 3.001330 AGCTCTTCGTTTCGTGAAGTTTG 59.999 43.478 3.00 0.00 42.68 2.93
3569 4878 3.311322 TCTTCGTTTCGTGAAGTTTGCAT 59.689 39.130 0.00 0.00 42.68 3.96
3570 4879 4.508492 TCTTCGTTTCGTGAAGTTTGCATA 59.492 37.500 0.00 0.00 42.68 3.14
3571 4880 5.178623 TCTTCGTTTCGTGAAGTTTGCATAT 59.821 36.000 0.00 0.00 42.68 1.78
3572 4881 6.366604 TCTTCGTTTCGTGAAGTTTGCATATA 59.633 34.615 0.00 0.00 42.68 0.86
3573 4882 6.656314 TCGTTTCGTGAAGTTTGCATATAT 57.344 33.333 0.00 0.00 0.00 0.86
3574 4883 6.474364 TCGTTTCGTGAAGTTTGCATATATG 58.526 36.000 8.45 8.45 0.00 1.78
3575 4884 5.676744 CGTTTCGTGAAGTTTGCATATATGG 59.323 40.000 14.51 0.00 0.00 2.74
3576 4885 6.551736 GTTTCGTGAAGTTTGCATATATGGT 58.448 36.000 14.51 0.00 0.00 3.55
3577 4886 5.733226 TCGTGAAGTTTGCATATATGGTG 57.267 39.130 14.51 0.00 0.00 4.17
3578 4887 5.423886 TCGTGAAGTTTGCATATATGGTGA 58.576 37.500 14.51 0.00 0.00 4.02
3579 4888 5.877564 TCGTGAAGTTTGCATATATGGTGAA 59.122 36.000 14.51 0.00 0.00 3.18
3580 4889 6.037062 TCGTGAAGTTTGCATATATGGTGAAG 59.963 38.462 14.51 0.00 0.00 3.02
3581 4890 6.183360 CGTGAAGTTTGCATATATGGTGAAGT 60.183 38.462 14.51 0.00 0.00 3.01
3582 4891 7.538575 GTGAAGTTTGCATATATGGTGAAGTT 58.461 34.615 14.51 4.50 0.00 2.66
3583 4892 8.028938 GTGAAGTTTGCATATATGGTGAAGTTT 58.971 33.333 14.51 0.00 0.00 2.66
3584 4893 8.028354 TGAAGTTTGCATATATGGTGAAGTTTG 58.972 33.333 14.51 0.00 0.00 2.93
3585 4894 7.701539 AGTTTGCATATATGGTGAAGTTTGA 57.298 32.000 14.51 0.00 0.00 2.69
3586 4895 7.538575 AGTTTGCATATATGGTGAAGTTTGAC 58.461 34.615 14.51 0.00 0.00 3.18
3587 4896 7.394359 AGTTTGCATATATGGTGAAGTTTGACT 59.606 33.333 14.51 0.00 0.00 3.41
3588 4897 7.701539 TTGCATATATGGTGAAGTTTGACTT 57.298 32.000 14.51 0.00 41.95 3.01
3589 4898 7.087409 TGCATATATGGTGAAGTTTGACTTG 57.913 36.000 14.51 0.00 38.80 3.16
3590 4899 5.973565 GCATATATGGTGAAGTTTGACTTGC 59.026 40.000 14.51 0.00 38.80 4.01
3591 4900 6.404623 GCATATATGGTGAAGTTTGACTTGCA 60.405 38.462 14.51 0.00 38.80 4.08
3592 4901 7.682741 GCATATATGGTGAAGTTTGACTTGCAT 60.683 37.037 14.51 0.00 38.80 3.96
3593 4902 3.988379 TGGTGAAGTTTGACTTGCATC 57.012 42.857 0.00 0.00 38.80 3.91
3594 4903 2.622942 TGGTGAAGTTTGACTTGCATCC 59.377 45.455 0.00 3.05 38.80 3.51
3595 4904 2.887152 GGTGAAGTTTGACTTGCATCCT 59.113 45.455 0.00 0.00 38.80 3.24
3596 4905 3.319122 GGTGAAGTTTGACTTGCATCCTT 59.681 43.478 0.00 0.00 38.80 3.36
3597 4906 4.293415 GTGAAGTTTGACTTGCATCCTTG 58.707 43.478 0.00 0.00 38.80 3.61
3598 4907 4.036734 GTGAAGTTTGACTTGCATCCTTGA 59.963 41.667 0.00 0.00 38.80 3.02
3599 4908 4.276678 TGAAGTTTGACTTGCATCCTTGAG 59.723 41.667 0.00 0.00 38.80 3.02
3600 4909 4.090761 AGTTTGACTTGCATCCTTGAGA 57.909 40.909 0.00 0.00 0.00 3.27
3601 4910 4.070716 AGTTTGACTTGCATCCTTGAGAG 58.929 43.478 0.00 0.00 0.00 3.20
3602 4911 2.105006 TGACTTGCATCCTTGAGAGC 57.895 50.000 0.00 0.00 0.00 4.09
3603 4912 1.627329 TGACTTGCATCCTTGAGAGCT 59.373 47.619 0.00 0.00 0.00 4.09
3604 4913 2.278854 GACTTGCATCCTTGAGAGCTC 58.721 52.381 5.27 5.27 0.00 4.09
3605 4914 1.065564 ACTTGCATCCTTGAGAGCTCC 60.066 52.381 10.93 2.40 0.00 4.70
3628 4937 1.588082 CCAACTGCATCTTGGGCAC 59.412 57.895 13.37 0.00 36.11 5.01
3635 4944 0.890542 GCATCTTGGGCACACTGTGA 60.891 55.000 15.86 0.00 35.23 3.58
3646 4955 3.057315 GGCACACTGTGAAGTTTGCATAT 60.057 43.478 15.86 0.00 44.55 1.78
3672 4981 4.293415 GTGAAGTTTGACTTGCATCCTTG 58.707 43.478 0.00 0.00 38.80 3.61
3706 5015 9.191995 CAGTCAAAATTTGGTAGGTTCAATTAC 57.808 33.333 5.83 0.00 0.00 1.89
3708 5017 8.077386 GTCAAAATTTGGTAGGTTCAATTACGA 58.923 33.333 5.83 0.00 0.00 3.43
3710 5019 6.505044 AATTTGGTAGGTTCAATTACGACC 57.495 37.500 0.00 0.00 0.00 4.79
3712 5021 4.196626 TGGTAGGTTCAATTACGACCAG 57.803 45.455 0.00 0.00 35.89 4.00
3713 5022 2.934553 GGTAGGTTCAATTACGACCAGC 59.065 50.000 0.00 0.00 35.89 4.85
3714 5023 3.369157 GGTAGGTTCAATTACGACCAGCT 60.369 47.826 0.00 0.00 35.89 4.24
3715 5024 2.973945 AGGTTCAATTACGACCAGCTC 58.026 47.619 0.00 0.00 35.89 4.09
3777 5087 7.756722 CCTTACCTTGCTAATTTTCTCACATTG 59.243 37.037 0.00 0.00 0.00 2.82
3798 5108 9.793252 ACATTGTATTCATTACTTTCATTCTGC 57.207 29.630 0.00 0.00 0.00 4.26
3799 5109 9.791820 CATTGTATTCATTACTTTCATTCTGCA 57.208 29.630 0.00 0.00 0.00 4.41
3801 5111 8.791327 TGTATTCATTACTTTCATTCTGCAGA 57.209 30.769 13.74 13.74 0.00 4.26
3802 5112 9.230122 TGTATTCATTACTTTCATTCTGCAGAA 57.770 29.630 30.23 30.23 38.56 3.02
3803 5113 9.495754 GTATTCATTACTTTCATTCTGCAGAAC 57.504 33.333 30.66 9.25 36.80 3.01
3863 5175 4.941263 AGACAAAAGAAGCATATGCCGTAA 59.059 37.500 23.96 0.00 43.38 3.18
3864 5176 5.590259 AGACAAAAGAAGCATATGCCGTAAT 59.410 36.000 23.96 1.96 43.38 1.89
3865 5177 5.581605 ACAAAAGAAGCATATGCCGTAATG 58.418 37.500 23.96 17.23 43.38 1.90
3868 5180 3.403038 AGAAGCATATGCCGTAATGTCC 58.597 45.455 23.96 3.41 43.38 4.02
3869 5181 3.071602 AGAAGCATATGCCGTAATGTCCT 59.928 43.478 23.96 5.50 43.38 3.85
3870 5182 2.771089 AGCATATGCCGTAATGTCCTG 58.229 47.619 23.96 0.00 43.38 3.86
3871 5183 1.806542 GCATATGCCGTAATGTCCTGG 59.193 52.381 17.26 0.00 34.31 4.45
3873 5185 2.902705 TATGCCGTAATGTCCTGGAC 57.097 50.000 19.96 19.96 0.00 4.02
3874 5186 1.204146 ATGCCGTAATGTCCTGGACT 58.796 50.000 26.03 10.82 33.15 3.85
3875 5187 0.249120 TGCCGTAATGTCCTGGACTG 59.751 55.000 26.03 11.36 33.15 3.51
3876 5188 0.462047 GCCGTAATGTCCTGGACTGG 60.462 60.000 26.03 19.14 33.15 4.00
3877 5189 1.191535 CCGTAATGTCCTGGACTGGA 58.808 55.000 26.03 8.07 33.15 3.86
3878 5190 1.137086 CCGTAATGTCCTGGACTGGAG 59.863 57.143 26.03 13.77 36.69 3.86
3879 5191 1.137086 CGTAATGTCCTGGACTGGAGG 59.863 57.143 26.03 12.92 36.69 4.30
3880 5192 2.467880 GTAATGTCCTGGACTGGAGGA 58.532 52.381 26.03 6.57 37.27 3.71
3881 5193 1.577736 AATGTCCTGGACTGGAGGAG 58.422 55.000 26.03 0.00 40.42 3.69
3882 5194 0.980231 ATGTCCTGGACTGGAGGAGC 60.980 60.000 26.03 0.00 40.42 4.70
3883 5195 1.305718 GTCCTGGACTGGAGGAGCT 60.306 63.158 19.53 0.00 40.42 4.09
3884 5196 1.305633 TCCTGGACTGGAGGAGCTG 60.306 63.158 0.00 0.00 34.49 4.24
3885 5197 2.583520 CTGGACTGGAGGAGCTGC 59.416 66.667 0.00 0.00 0.00 5.25
3886 5198 3.005539 TGGACTGGAGGAGCTGCC 61.006 66.667 0.00 0.00 0.00 4.85
3903 5215 1.296392 CCCAGTTCTGCATCGACCA 59.704 57.895 0.00 0.00 0.00 4.02
3909 5230 0.249120 TTCTGCATCGACCATCCGTT 59.751 50.000 0.00 0.00 0.00 4.44
3920 5241 1.427819 CATCCGTTAGTTTGGCCGC 59.572 57.895 0.00 0.00 0.00 6.53
3946 5267 7.294584 TCATTCACTTCTTTTAGAAAGGGGAA 58.705 34.615 1.04 0.00 33.19 3.97
3947 5268 7.448469 TCATTCACTTCTTTTAGAAAGGGGAAG 59.552 37.037 0.00 0.00 33.19 3.46
3957 5278 6.658555 TTAGAAAGGGGAAGAAAGATCCAT 57.341 37.500 0.00 0.00 38.80 3.41
3961 5282 6.909158 AGAAAGGGGAAGAAAGATCCATACTA 59.091 38.462 0.00 0.00 38.80 1.82
3970 5291 5.128827 AGAAAGATCCATACTAAAGCACCGA 59.871 40.000 0.00 0.00 0.00 4.69
4094 5415 4.966123 TTGGCTGTTGACCAACGA 57.034 50.000 8.18 0.00 42.23 3.85
4098 5419 0.317854 GGCTGTTGACCAACGAAAGC 60.318 55.000 12.48 12.48 43.94 3.51
4105 5426 2.571212 TGACCAACGAAAGCAATGACT 58.429 42.857 0.00 0.00 0.00 3.41
4108 5429 2.549754 ACCAACGAAAGCAATGACTGAG 59.450 45.455 0.00 0.00 0.00 3.35
4109 5430 2.807967 CCAACGAAAGCAATGACTGAGA 59.192 45.455 0.00 0.00 0.00 3.27
4142 5463 7.361438 TCCATGAATCCCATTACCTTGTTTAT 58.639 34.615 0.00 0.00 31.94 1.40
4143 5464 7.843760 TCCATGAATCCCATTACCTTGTTTATT 59.156 33.333 0.00 0.00 31.94 1.40
4144 5465 7.927629 CCATGAATCCCATTACCTTGTTTATTG 59.072 37.037 0.00 0.00 31.94 1.90
4176 5497 3.220110 AGTCTGACACTCGTTACTTGGA 58.780 45.455 10.88 0.00 0.00 3.53
4179 5500 4.386049 GTCTGACACTCGTTACTTGGATTG 59.614 45.833 2.24 0.00 0.00 2.67
4186 5507 3.935203 CTCGTTACTTGGATTGTGCAGAT 59.065 43.478 0.00 0.00 0.00 2.90
4192 5513 5.733620 ACTTGGATTGTGCAGATCAATTT 57.266 34.783 11.05 0.00 35.94 1.82
4195 5516 5.725325 TGGATTGTGCAGATCAATTTCAA 57.275 34.783 11.05 0.00 35.94 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
161 165 1.064952 GGTGTTGGGTGAAAGTTGTCG 59.935 52.381 0.00 0.00 0.00 4.35
252 256 1.135660 TGTTCGCTGAGTCTAAGCTCG 60.136 52.381 7.64 0.00 38.57 5.03
268 272 2.674796 ATGCTACGAAGGACCTGTTC 57.325 50.000 0.00 0.00 0.00 3.18
393 427 0.962356 CCTCACCACTGCATTCCCAC 60.962 60.000 0.00 0.00 0.00 4.61
404 438 4.040339 ACAAATTTTTCCATCCCTCACCAC 59.960 41.667 0.00 0.00 0.00 4.16
477 514 9.865321 ATTTCAGATATTGTTGGAAATTGAGTG 57.135 29.630 0.00 0.00 35.32 3.51
496 533 3.228188 AGCTGTTTCCACCATTTCAGA 57.772 42.857 0.00 0.00 0.00 3.27
520 563 5.818678 TCCAGACCTTGTAGTGTTATTGT 57.181 39.130 0.00 0.00 0.00 2.71
654 704 4.821589 GCTGCTAGCGGCGAACCT 62.822 66.667 31.50 0.00 45.43 3.50
672 722 4.761975 TCAGTAACAGACCGACAGTTTTT 58.238 39.130 0.00 0.00 31.09 1.94
678 728 2.281539 TCCTCAGTAACAGACCGACA 57.718 50.000 0.00 0.00 0.00 4.35
681 731 2.168496 TCCTTCCTCAGTAACAGACCG 58.832 52.381 0.00 0.00 0.00 4.79
933 999 9.354673 AGAAAACCATTCTCTACAAATTCTTCA 57.645 29.630 0.00 0.00 0.00 3.02
998 1073 9.524106 ACAGTTCATGTAATAAATCATGCATTG 57.476 29.630 0.00 0.00 41.60 2.82
1061 1136 7.825270 TGTCACCAACTCTAAAACTTGAACTAA 59.175 33.333 0.00 0.00 0.00 2.24
1121 1199 7.573968 AAATTCCCTTCAAATCTATCTTCCG 57.426 36.000 0.00 0.00 0.00 4.30
1170 1248 6.664515 CAAATTGCAAATGTCAATCTTGCTT 58.335 32.000 1.71 4.01 44.57 3.91
1179 1257 1.793258 CCCGCAAATTGCAAATGTCA 58.207 45.000 18.65 0.00 45.36 3.58
1256 1337 4.015764 ACGGAGACCCTCTACTTCTTTAC 58.984 47.826 0.00 0.00 0.00 2.01
1292 1373 5.463392 GGCAAAAATTCTTTGAACCTCACTC 59.537 40.000 13.72 0.00 0.00 3.51
1301 1382 7.862512 AAATTGAGTGGCAAAAATTCTTTGA 57.137 28.000 13.72 0.00 40.48 2.69
1354 1456 6.016777 CAGTATAGATCTGGGTGCCAAATTTC 60.017 42.308 5.18 0.00 30.80 2.17
1365 1467 7.726033 AATTAGCCTACAGTATAGATCTGGG 57.274 40.000 5.18 0.00 37.25 4.45
1366 1468 9.030452 AGAAATTAGCCTACAGTATAGATCTGG 57.970 37.037 5.18 0.00 37.25 3.86
1429 1561 5.189928 ACTGTGACACAAATCAACAAGGTA 58.810 37.500 10.02 0.00 0.00 3.08
1442 1574 9.661563 CCTTAGGTAATTATAAACTGTGACACA 57.338 33.333 8.26 8.26 0.00 3.72
1467 1602 8.173130 CGTAAATTGATAAGGCGGTTAATATCC 58.827 37.037 0.00 0.00 0.00 2.59
1501 1636 2.255252 GTGTGCATCGCCAACACC 59.745 61.111 0.00 0.00 33.30 4.16
1525 1660 2.424705 TTTCCGACCCGAGGAACACG 62.425 60.000 0.00 0.00 46.36 4.49
1534 1669 2.356135 ACATTTCATCTTTCCGACCCG 58.644 47.619 0.00 0.00 0.00 5.28
1571 1706 6.459923 ACACTCTCTTCCTTAACACTGAATC 58.540 40.000 0.00 0.00 0.00 2.52
1585 1720 5.760253 TCAGTTCAAATCCAACACTCTCTTC 59.240 40.000 0.00 0.00 0.00 2.87
1691 1826 1.767759 ACACACAAGCTTGGCTTCTT 58.232 45.000 29.18 5.25 46.77 2.52
1728 1863 5.957798 TCTGTACCACAATCTAACGTAAGG 58.042 41.667 0.00 0.00 46.39 2.69
1817 1971 0.881118 ACGTGTGCCACCATGATTTC 59.119 50.000 0.00 0.00 0.00 2.17
1830 1984 0.391597 ACCAACTAGGACCACGTGTG 59.608 55.000 15.65 8.62 41.22 3.82
1864 2018 1.901833 AGACCCCAACATTTTGATGCC 59.098 47.619 0.00 0.00 34.24 4.40
1894 2048 1.204146 GCCCCAAGACACATCCTCTA 58.796 55.000 0.00 0.00 0.00 2.43
2054 2208 3.435671 CCCACTCGACAAATTCAGGTAAC 59.564 47.826 0.00 0.00 0.00 2.50
2102 2256 1.065102 CGGATGCATTCAAGCCTTGAG 59.935 52.381 7.29 0.00 41.38 3.02
2121 2275 2.256391 TGGGACAATCTTTGCAGCG 58.744 52.632 0.00 0.00 31.92 5.18
2181 2341 6.538021 TCAACAACAAAATTTGACAGATTGGG 59.462 34.615 13.19 3.83 0.00 4.12
2304 2470 2.310538 CCCATCAATAACCAAGCCCTC 58.689 52.381 0.00 0.00 0.00 4.30
2403 2581 1.004560 TCAGTTTGCTGAGCTCCGG 60.005 57.895 12.15 5.31 45.94 5.14
2428 2616 5.183522 TGTGATGTTGCATCTGCTGAAATAA 59.816 36.000 10.02 0.00 42.66 1.40
2460 3742 0.839946 ACACCTGAAGTCCTGCAGTT 59.160 50.000 13.81 0.00 0.00 3.16
2475 3757 2.029844 GCAAGTCCTCGCAGACACC 61.030 63.158 7.30 0.00 39.34 4.16
2499 3781 2.032549 CGAAAGAAGTTGCCACAGTCTG 60.033 50.000 0.00 0.00 0.00 3.51
2571 3856 5.595885 ACTCCTCATCAATCACAAGATACG 58.404 41.667 0.00 0.00 33.08 3.06
2580 3865 3.986996 TGCTTGACTCCTCATCAATCA 57.013 42.857 0.00 0.00 35.57 2.57
2589 3874 0.689055 TGACTGCATGCTTGACTCCT 59.311 50.000 20.33 0.00 0.00 3.69
2590 3875 1.527034 TTGACTGCATGCTTGACTCC 58.473 50.000 20.33 1.89 0.00 3.85
2632 3917 4.704540 ACCAGTCTTAGATCAGTGAGACAG 59.295 45.833 15.48 10.01 40.66 3.51
2695 3980 5.670792 AATAGTTGAGGTTGACCGTGATA 57.329 39.130 0.00 0.00 42.08 2.15
2770 4055 2.280628 GCTACCACCAATTCCGAGAAG 58.719 52.381 0.00 0.00 0.00 2.85
2799 4084 3.357079 CCGCGGGCAATGATAGGC 61.357 66.667 20.10 0.00 0.00 3.93
2812 4097 4.394712 AGTTGGAAGGAGCCCGCG 62.395 66.667 0.00 0.00 0.00 6.46
2866 4169 1.279496 TGCTACAGATGGGAGCAACT 58.721 50.000 0.00 0.00 43.03 3.16
2885 4188 1.834822 GGAGGGTAGCAGCGAGGAT 60.835 63.158 0.00 0.00 0.00 3.24
2912 4215 1.004185 CCGCTGATCAAAGCTGAATCG 60.004 52.381 0.00 0.00 41.24 3.34
2913 4216 1.332997 CCCGCTGATCAAAGCTGAATC 59.667 52.381 0.00 0.00 41.24 2.52
2920 4223 1.131883 CTTTCTGCCCGCTGATCAAAG 59.868 52.381 0.00 0.00 0.00 2.77
2922 4225 1.308069 GCTTTCTGCCCGCTGATCAA 61.308 55.000 0.00 0.00 35.15 2.57
2987 4290 7.469870 CGGGCAATCCTCAAATTTGATGTAATA 60.470 37.037 20.76 3.53 36.46 0.98
3063 4366 4.458397 AGGACAACGTTCGATATCTAGGA 58.542 43.478 0.00 0.00 0.00 2.94
3122 4425 1.913403 CGTTACGGTTACAGTTAGCGG 59.087 52.381 14.95 0.00 40.52 5.52
3129 4432 0.792031 GCAACCCGTTACGGTTACAG 59.208 55.000 22.78 9.18 44.54 2.74
3130 4433 0.105593 TGCAACCCGTTACGGTTACA 59.894 50.000 22.78 13.94 44.54 2.41
3161 4470 5.123027 CCTGTAATTTCCAGAGTTGCTCTTC 59.877 44.000 6.43 0.00 38.99 2.87
3173 4482 3.070302 GGGTTTGTTGCCTGTAATTTCCA 59.930 43.478 0.00 0.00 0.00 3.53
3174 4483 3.070302 TGGGTTTGTTGCCTGTAATTTCC 59.930 43.478 0.00 0.00 0.00 3.13
3182 4491 1.331214 ACATCTGGGTTTGTTGCCTG 58.669 50.000 0.00 0.00 0.00 4.85
3200 4509 2.919229 GCTAGCAAATGCACACATCAAC 59.081 45.455 10.63 0.00 45.16 3.18
3216 4525 1.143401 GTACCTTGGTCGGGCTAGC 59.857 63.158 6.04 6.04 0.00 3.42
3217 4526 1.318158 ACGTACCTTGGTCGGGCTAG 61.318 60.000 13.17 0.00 0.00 3.42
3218 4527 0.034574 TACGTACCTTGGTCGGGCTA 60.035 55.000 13.17 0.00 0.00 3.93
3219 4528 0.899717 TTACGTACCTTGGTCGGGCT 60.900 55.000 0.00 0.45 0.00 5.19
3220 4529 0.737367 GTTACGTACCTTGGTCGGGC 60.737 60.000 0.00 0.00 0.00 6.13
3221 4530 0.890683 AGTTACGTACCTTGGTCGGG 59.109 55.000 0.00 0.00 0.00 5.14
3222 4531 1.403249 CCAGTTACGTACCTTGGTCGG 60.403 57.143 0.00 0.00 0.00 4.79
3223 4532 1.270550 ACCAGTTACGTACCTTGGTCG 59.729 52.381 15.48 3.11 37.60 4.79
3224 4533 4.519540 TTACCAGTTACGTACCTTGGTC 57.480 45.455 21.53 0.00 41.05 4.02
3225 4534 4.953940 TTTACCAGTTACGTACCTTGGT 57.046 40.909 21.58 21.58 44.00 3.67
3226 4535 5.391203 GCATTTTACCAGTTACGTACCTTGG 60.391 44.000 14.46 14.46 35.07 3.61
3227 4536 5.624292 GCATTTTACCAGTTACGTACCTTG 58.376 41.667 0.00 0.00 0.00 3.61
3228 4537 4.389687 CGCATTTTACCAGTTACGTACCTT 59.610 41.667 0.00 0.00 0.00 3.50
3229 4538 3.928375 CGCATTTTACCAGTTACGTACCT 59.072 43.478 0.00 0.00 0.00 3.08
3230 4539 3.925913 TCGCATTTTACCAGTTACGTACC 59.074 43.478 0.00 0.00 0.00 3.34
3231 4540 4.491441 GCTCGCATTTTACCAGTTACGTAC 60.491 45.833 0.00 0.00 0.00 3.67
3232 4541 3.613737 GCTCGCATTTTACCAGTTACGTA 59.386 43.478 0.00 0.00 0.00 3.57
3246 4555 2.191128 ACAGAAGAAAGGCTCGCATT 57.809 45.000 0.00 0.00 0.00 3.56
3313 4622 8.501070 AGGATCTGAGACCTGAAATATTTCAAT 58.499 33.333 26.57 19.28 45.61 2.57
3315 4624 7.443302 AGGATCTGAGACCTGAAATATTTCA 57.557 36.000 25.44 25.44 44.31 2.69
3345 4654 1.334960 GCAATGCACACAACGTAGCTT 60.335 47.619 0.00 0.00 0.00 3.74
3375 4684 9.765795 CTTCCGAGATATATATTTCCCCAATAC 57.234 37.037 7.49 0.00 29.65 1.89
3379 4688 7.808279 AACTTCCGAGATATATATTTCCCCA 57.192 36.000 7.49 0.00 0.00 4.96
3395 4704 9.967346 CACTCTTATATCATCTAAAACTTCCGA 57.033 33.333 0.00 0.00 0.00 4.55
3396 4705 8.704234 GCACTCTTATATCATCTAAAACTTCCG 58.296 37.037 0.00 0.00 0.00 4.30
3397 4706 9.771534 AGCACTCTTATATCATCTAAAACTTCC 57.228 33.333 0.00 0.00 0.00 3.46
3426 4735 5.008613 GTGTGGTGCTTACCCATATACATTG 59.991 44.000 0.00 0.00 33.76 2.82
3483 4792 5.238650 CAGAAAACGGTGAGGAAACATAGTT 59.761 40.000 0.00 0.00 0.00 2.24
3559 4868 8.243426 TCAAACTTCACCATATATGCAAACTTC 58.757 33.333 7.24 0.00 0.00 3.01
3560 4869 8.028938 GTCAAACTTCACCATATATGCAAACTT 58.971 33.333 7.24 0.00 0.00 2.66
3561 4870 7.394359 AGTCAAACTTCACCATATATGCAAACT 59.606 33.333 7.24 0.00 0.00 2.66
3562 4871 7.538575 AGTCAAACTTCACCATATATGCAAAC 58.461 34.615 7.24 0.00 0.00 2.93
3563 4872 7.701539 AGTCAAACTTCACCATATATGCAAA 57.298 32.000 7.24 0.68 0.00 3.68
3564 4873 7.537715 CAAGTCAAACTTCACCATATATGCAA 58.462 34.615 7.24 0.00 36.03 4.08
3565 4874 6.404623 GCAAGTCAAACTTCACCATATATGCA 60.405 38.462 7.24 0.00 36.03 3.96
3566 4875 5.973565 GCAAGTCAAACTTCACCATATATGC 59.026 40.000 7.24 0.00 36.03 3.14
3569 4878 6.318648 GGATGCAAGTCAAACTTCACCATATA 59.681 38.462 0.00 0.00 36.03 0.86
3570 4879 5.126061 GGATGCAAGTCAAACTTCACCATAT 59.874 40.000 0.00 0.00 36.03 1.78
3571 4880 4.458989 GGATGCAAGTCAAACTTCACCATA 59.541 41.667 0.00 0.00 36.03 2.74
3572 4881 3.256631 GGATGCAAGTCAAACTTCACCAT 59.743 43.478 0.00 0.00 36.03 3.55
3573 4882 2.622942 GGATGCAAGTCAAACTTCACCA 59.377 45.455 0.00 0.00 36.03 4.17
3574 4883 2.887152 AGGATGCAAGTCAAACTTCACC 59.113 45.455 0.00 0.00 36.03 4.02
3575 4884 4.036734 TCAAGGATGCAAGTCAAACTTCAC 59.963 41.667 0.00 0.00 36.03 3.18
3576 4885 4.206375 TCAAGGATGCAAGTCAAACTTCA 58.794 39.130 0.00 0.00 36.03 3.02
3577 4886 4.516698 TCTCAAGGATGCAAGTCAAACTTC 59.483 41.667 0.00 0.00 36.03 3.01
3578 4887 4.464008 TCTCAAGGATGCAAGTCAAACTT 58.536 39.130 0.00 0.00 39.39 2.66
3579 4888 4.070716 CTCTCAAGGATGCAAGTCAAACT 58.929 43.478 0.00 0.00 0.00 2.66
3580 4889 3.365767 GCTCTCAAGGATGCAAGTCAAAC 60.366 47.826 0.00 0.00 0.00 2.93
3581 4890 2.816087 GCTCTCAAGGATGCAAGTCAAA 59.184 45.455 0.00 0.00 0.00 2.69
3582 4891 2.039480 AGCTCTCAAGGATGCAAGTCAA 59.961 45.455 0.00 0.00 0.00 3.18
3583 4892 1.627329 AGCTCTCAAGGATGCAAGTCA 59.373 47.619 0.00 0.00 0.00 3.41
3584 4893 2.278854 GAGCTCTCAAGGATGCAAGTC 58.721 52.381 6.43 0.00 0.00 3.01
3585 4894 1.065564 GGAGCTCTCAAGGATGCAAGT 60.066 52.381 14.64 0.00 0.00 3.16
3586 4895 1.065636 TGGAGCTCTCAAGGATGCAAG 60.066 52.381 14.64 0.00 0.00 4.01
3587 4896 0.986527 TGGAGCTCTCAAGGATGCAA 59.013 50.000 14.64 0.00 0.00 4.08
3588 4897 0.540454 CTGGAGCTCTCAAGGATGCA 59.460 55.000 14.64 0.00 0.00 3.96
3589 4898 0.540923 ACTGGAGCTCTCAAGGATGC 59.459 55.000 14.64 0.00 34.92 3.91
3590 4899 1.743091 GCACTGGAGCTCTCAAGGATG 60.743 57.143 14.64 5.91 34.92 3.51
3591 4900 0.540923 GCACTGGAGCTCTCAAGGAT 59.459 55.000 14.64 0.00 34.92 3.24
3592 4901 1.548357 GGCACTGGAGCTCTCAAGGA 61.548 60.000 14.64 0.00 34.92 3.36
3593 4902 1.078567 GGCACTGGAGCTCTCAAGG 60.079 63.158 14.64 6.13 34.92 3.61
3594 4903 0.035881 TTGGCACTGGAGCTCTCAAG 59.964 55.000 14.64 11.40 36.70 3.02
3595 4904 0.250467 GTTGGCACTGGAGCTCTCAA 60.250 55.000 14.64 6.40 34.17 3.02
3596 4905 1.123861 AGTTGGCACTGGAGCTCTCA 61.124 55.000 14.64 9.11 34.17 3.27
3597 4906 0.673022 CAGTTGGCACTGGAGCTCTC 60.673 60.000 14.64 4.40 46.10 3.20
3598 4907 1.374190 CAGTTGGCACTGGAGCTCT 59.626 57.895 14.64 0.00 46.10 4.09
3599 4908 3.978272 CAGTTGGCACTGGAGCTC 58.022 61.111 4.71 4.71 46.10 4.09
3628 4937 6.093909 TCACCATATATGCAAACTTCACAGTG 59.906 38.462 7.24 5.76 31.60 3.66
3635 4944 8.028938 GTCAAACTTCACCATATATGCAAACTT 58.971 33.333 7.24 0.00 0.00 2.66
3646 4955 4.458989 GGATGCAAGTCAAACTTCACCATA 59.541 41.667 0.00 0.00 36.03 2.74
3672 4981 3.823304 ACCAAATTTTGACTGGAGCTCTC 59.177 43.478 14.64 3.94 34.16 3.20
3706 5015 3.589988 AGACATTACTTTGAGCTGGTCG 58.410 45.455 0.00 0.00 0.00 4.79
3708 5017 4.938226 GCTTAGACATTACTTTGAGCTGGT 59.062 41.667 0.00 0.00 0.00 4.00
3710 5019 6.538021 AGATGCTTAGACATTACTTTGAGCTG 59.462 38.462 0.00 0.00 0.00 4.24
3712 5021 6.917217 AGATGCTTAGACATTACTTTGAGC 57.083 37.500 0.00 0.00 0.00 4.26
3777 5087 9.495754 GTTCTGCAGAATGAAAGTAATGAATAC 57.504 33.333 30.65 9.72 39.69 1.89
3791 5101 4.696877 TGACTGTAATGGTTCTGCAGAATG 59.303 41.667 30.65 15.28 36.33 2.67
3792 5102 4.910195 TGACTGTAATGGTTCTGCAGAAT 58.090 39.130 30.65 17.78 36.33 2.40
3793 5103 4.350368 TGACTGTAATGGTTCTGCAGAA 57.650 40.909 25.16 25.16 0.00 3.02
3794 5104 4.065088 GTTGACTGTAATGGTTCTGCAGA 58.935 43.478 13.74 13.74 0.00 4.26
3795 5105 4.067896 AGTTGACTGTAATGGTTCTGCAG 58.932 43.478 7.63 7.63 0.00 4.41
3796 5106 3.814842 CAGTTGACTGTAATGGTTCTGCA 59.185 43.478 2.98 0.00 39.09 4.41
3797 5107 4.410492 CAGTTGACTGTAATGGTTCTGC 57.590 45.455 2.98 0.00 39.09 4.26
3863 5175 0.980231 GCTCCTCCAGTCCAGGACAT 60.980 60.000 22.31 4.07 34.91 3.06
3864 5176 1.610673 GCTCCTCCAGTCCAGGACA 60.611 63.158 22.31 0.00 34.91 4.02
3865 5177 1.305718 AGCTCCTCCAGTCCAGGAC 60.306 63.158 12.25 12.25 34.91 3.85
3868 5180 2.583520 GCAGCTCCTCCAGTCCAG 59.416 66.667 0.00 0.00 0.00 3.86
3869 5181 3.005539 GGCAGCTCCTCCAGTCCA 61.006 66.667 0.00 0.00 0.00 4.02
3870 5182 3.791586 GGGCAGCTCCTCCAGTCC 61.792 72.222 0.00 0.00 34.39 3.85
3871 5183 3.005539 TGGGCAGCTCCTCCAGTC 61.006 66.667 0.00 0.00 34.39 3.51
3874 5186 2.530151 AACTGGGCAGCTCCTCCA 60.530 61.111 0.00 0.00 34.39 3.86
3875 5187 2.270527 GAACTGGGCAGCTCCTCC 59.729 66.667 0.00 0.00 34.39 4.30
3876 5188 1.078567 CAGAACTGGGCAGCTCCTC 60.079 63.158 0.00 0.00 34.39 3.71
3877 5189 3.076092 CAGAACTGGGCAGCTCCT 58.924 61.111 0.00 0.00 34.39 3.69
3878 5190 2.749441 GCAGAACTGGGCAGCTCC 60.749 66.667 3.99 0.00 0.00 4.70
3879 5191 1.375098 GATGCAGAACTGGGCAGCTC 61.375 60.000 3.99 0.00 44.24 4.09
3880 5192 1.378250 GATGCAGAACTGGGCAGCT 60.378 57.895 3.99 0.00 44.24 4.24
3881 5193 2.758089 CGATGCAGAACTGGGCAGC 61.758 63.158 3.99 0.00 44.24 5.25
3882 5194 1.078918 TCGATGCAGAACTGGGCAG 60.079 57.895 3.99 0.00 44.24 4.85
3883 5195 1.375908 GTCGATGCAGAACTGGGCA 60.376 57.895 3.99 0.00 45.23 5.36
3884 5196 2.109126 GGTCGATGCAGAACTGGGC 61.109 63.158 3.99 0.00 0.00 5.36
3885 5197 0.107508 ATGGTCGATGCAGAACTGGG 60.108 55.000 3.99 0.00 0.00 4.45
3886 5198 1.293924 GATGGTCGATGCAGAACTGG 58.706 55.000 3.99 0.00 0.00 4.00
3903 5215 0.743345 GAGCGGCCAAACTAACGGAT 60.743 55.000 2.24 0.00 0.00 4.18
3909 5230 1.003118 AGTGAATGAGCGGCCAAACTA 59.997 47.619 2.24 0.00 0.00 2.24
3920 5241 6.942576 TCCCCTTTCTAAAAGAAGTGAATGAG 59.057 38.462 1.06 0.00 35.37 2.90
3946 5267 5.128827 TCGGTGCTTTAGTATGGATCTTTCT 59.871 40.000 0.00 0.00 0.00 2.52
3947 5268 5.357257 TCGGTGCTTTAGTATGGATCTTTC 58.643 41.667 0.00 0.00 0.00 2.62
3987 5308 0.250901 AACCTGGTCACTGATGCCAC 60.251 55.000 0.00 0.00 31.36 5.01
4094 5415 9.412460 TGGATATAATTTCTCAGTCATTGCTTT 57.588 29.630 0.00 0.00 0.00 3.51
4160 5481 3.120649 GCACAATCCAAGTAACGAGTGTC 60.121 47.826 0.00 0.00 35.29 3.67
4176 5497 5.471556 TGGTTGAAATTGATCTGCACAAT 57.528 34.783 0.00 0.00 39.25 2.71
4179 5500 4.619973 TGTTGGTTGAAATTGATCTGCAC 58.380 39.130 0.00 0.00 0.00 4.57
4186 5507 5.867903 AATCCACTGTTGGTTGAAATTGA 57.132 34.783 0.00 0.00 44.35 2.57
4192 5513 4.062293 CGTCTAAATCCACTGTTGGTTGA 58.938 43.478 0.00 0.00 44.35 3.18
4195 5516 3.764237 ACGTCTAAATCCACTGTTGGT 57.236 42.857 0.00 0.00 44.35 3.67


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

AutoCloner maintained by Alex Coulton.