Multiple sequence alignment - TraesCS3A01G400700

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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 TraesCS3A01G400700 chr3A 100.000 2804 0 0 1 2804 647237690 647234887 0.000000e+00 5179.0
1 TraesCS3A01G400700 chr3A 86.808 849 95 10 1025 1869 647379031 647378196 0.000000e+00 931.0
2 TraesCS3A01G400700 chr3A 82.831 996 144 10 1001 1986 647267485 647266507 0.000000e+00 867.0
3 TraesCS3A01G400700 chr3A 91.468 504 29 8 2098 2591 647272955 647272456 0.000000e+00 680.0
4 TraesCS3A01G400700 chr3A 84.419 706 88 10 1355 2055 647274084 647273396 0.000000e+00 675.0
5 TraesCS3A01G400700 chr3A 76.409 1047 197 30 840 1862 647359045 647358025 1.150000e-143 520.0
6 TraesCS3A01G400700 chr3A 82.000 150 21 2 998 1141 647276923 647276774 3.790000e-24 122.0
7 TraesCS3A01G400700 chr3A 91.429 70 6 0 1974 2043 647266438 647266369 2.300000e-16 97.1
8 TraesCS3A01G400700 chr3D 88.085 2031 173 37 140 2161 511275616 511273646 0.000000e+00 2346.0
9 TraesCS3A01G400700 chr3D 87.561 1640 153 14 1012 2625 511289429 511287815 0.000000e+00 1851.0
10 TraesCS3A01G400700 chr3D 88.073 1417 114 28 589 1986 511071514 511070134 0.000000e+00 1629.0
11 TraesCS3A01G400700 chr3D 80.412 1312 186 43 581 1869 511259173 511257910 0.000000e+00 933.0
12 TraesCS3A01G400700 chr3D 90.226 665 38 12 1974 2625 511070060 511069410 0.000000e+00 843.0
13 TraesCS3A01G400700 chr3D 84.870 575 48 18 1 550 511077797 511077237 6.830000e-151 544.0
14 TraesCS3A01G400700 chr3D 78.467 274 39 14 840 1099 510857909 510857642 8.040000e-36 161.0
15 TraesCS3A01G400700 chr3B 81.494 1513 200 45 581 2067 672633996 672632538 0.000000e+00 1170.0
16 TraesCS3A01G400700 chr3B 89.174 545 33 13 2089 2625 672632479 672631953 0.000000e+00 656.0
17 TraesCS3A01G400700 chr3B 80.180 111 18 3 1387 1495 672542405 672542297 2.320000e-11 80.5
18 TraesCS3A01G400700 chr2D 87.978 183 22 0 2622 2804 627584780 627584962 1.690000e-52 217.0
19 TraesCS3A01G400700 chr5B 87.912 182 22 0 2623 2804 549565863 549566044 6.080000e-52 215.0
20 TraesCS3A01G400700 chr5B 86.813 182 22 2 2623 2804 22031292 22031113 4.740000e-48 202.0
21 TraesCS3A01G400700 chr5B 83.803 142 14 6 5 140 120574257 120574119 2.930000e-25 126.0
22 TraesCS3A01G400700 chr5B 82.517 143 19 5 7 144 664031470 664031611 1.360000e-23 121.0
23 TraesCS3A01G400700 chr5B 81.818 143 20 5 7 144 664032356 664032497 6.350000e-22 115.0
24 TraesCS3A01G400700 chr6A 87.778 180 22 0 2625 2804 70915746 70915567 7.870000e-51 211.0
25 TraesCS3A01G400700 chr7B 87.778 180 21 1 2625 2804 320259080 320259258 2.830000e-50 209.0
26 TraesCS3A01G400700 chr7B 86.559 186 25 0 2619 2804 55741735 55741920 3.660000e-49 206.0
27 TraesCS3A01G400700 chr7B 85.616 146 9 10 1 139 683437080 683437220 2.910000e-30 143.0
28 TraesCS3A01G400700 chr2A 87.363 182 23 0 2623 2804 406159512 406159331 2.830000e-50 209.0
29 TraesCS3A01G400700 chr5D 88.000 175 20 1 2625 2799 262832929 262833102 3.660000e-49 206.0
30 TraesCS3A01G400700 chr4D 86.667 180 24 0 2625 2804 6802915 6802736 1.700000e-47 200.0
31 TraesCS3A01G400700 chr4D 81.250 144 18 8 1 139 183390279 183390418 1.060000e-19 108.0
32 TraesCS3A01G400700 chr7D 83.846 130 15 5 14 139 423324314 423324441 4.910000e-23 119.0
33 TraesCS3A01G400700 chr2B 82.069 145 16 9 1 139 776035927 776035787 6.350000e-22 115.0
34 TraesCS3A01G400700 chr2B 80.263 152 20 8 1 146 24257122 24257269 3.820000e-19 106.0


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 TraesCS3A01G400700 chr3A 647234887 647237690 2803 True 5179.000000 5179 100.000000 1 2804 1 chr3A.!!$R1 2803
1 TraesCS3A01G400700 chr3A 647378196 647379031 835 True 931.000000 931 86.808000 1025 1869 1 chr3A.!!$R3 844
2 TraesCS3A01G400700 chr3A 647358025 647359045 1020 True 520.000000 520 76.409000 840 1862 1 chr3A.!!$R2 1022
3 TraesCS3A01G400700 chr3A 647272456 647276923 4467 True 492.333333 680 85.962333 998 2591 3 chr3A.!!$R5 1593
4 TraesCS3A01G400700 chr3A 647266369 647267485 1116 True 482.050000 867 87.130000 1001 2043 2 chr3A.!!$R4 1042
5 TraesCS3A01G400700 chr3D 511273646 511275616 1970 True 2346.000000 2346 88.085000 140 2161 1 chr3D.!!$R4 2021
6 TraesCS3A01G400700 chr3D 511287815 511289429 1614 True 1851.000000 1851 87.561000 1012 2625 1 chr3D.!!$R5 1613
7 TraesCS3A01G400700 chr3D 511069410 511071514 2104 True 1236.000000 1629 89.149500 589 2625 2 chr3D.!!$R6 2036
8 TraesCS3A01G400700 chr3D 511257910 511259173 1263 True 933.000000 933 80.412000 581 1869 1 chr3D.!!$R3 1288
9 TraesCS3A01G400700 chr3D 511077237 511077797 560 True 544.000000 544 84.870000 1 550 1 chr3D.!!$R2 549
10 TraesCS3A01G400700 chr3B 672631953 672633996 2043 True 913.000000 1170 85.334000 581 2625 2 chr3B.!!$R2 2044

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
554 581 0.036388 ACGTAACCTGCTGACCATGG 60.036 55.0 11.19 11.19 0.00 3.66 F
786 832 0.237498 CGGGTGAGTTTTTCCGAAGC 59.763 55.0 0.00 0.00 44.69 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1643 4216 0.462047 CCTCCATTTTCGACTCCGGG 60.462 60.0 0.0 0.0 36.24 5.73 R
2687 5827 0.033366 GGTGCGTTGGGCTGATTTTT 59.967 50.0 0.0 0.0 44.05 1.94 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
98 100 4.362932 TGAAACTTTCAAACATGTCGCA 57.637 36.364 0.00 0.00 36.59 5.10
110 116 5.949233 AACATGTCGCAAAGTTTTCTTTC 57.051 34.783 0.00 0.00 46.89 2.62
113 119 6.042143 ACATGTCGCAAAGTTTTCTTTCAAT 58.958 32.000 0.00 0.00 46.89 2.57
226 236 5.391256 ACCAGCATGTGATTGGATGATTAT 58.609 37.500 12.53 0.00 35.89 1.28
247 257 2.666812 GTTACCCCTGACCCACCG 59.333 66.667 0.00 0.00 0.00 4.94
262 272 1.816224 CCACCGGGAATAAAACCACAG 59.184 52.381 6.32 0.00 35.59 3.66
276 286 6.983474 AAAACCACAGATTTGAAAACCTTG 57.017 33.333 0.00 0.00 0.00 3.61
309 319 8.490355 CATTAAGACAGAAAATTTGTTTCAGCC 58.510 33.333 0.00 0.00 0.00 4.85
316 326 5.360714 AGAAAATTTGTTTCAGCCAGAGTCA 59.639 36.000 0.00 0.00 0.00 3.41
322 332 2.325583 TTCAGCCAGAGTCAACGTTT 57.674 45.000 0.00 0.00 0.00 3.60
370 392 7.414984 GGGTGACTTTTCATGATTCTGATCTTC 60.415 40.741 0.00 0.00 33.11 2.87
377 399 6.416631 TCATGATTCTGATCTTCAGTAGGG 57.583 41.667 4.56 0.00 44.58 3.53
414 436 3.257375 TGCGTCTACATTGTACTCCTTGT 59.743 43.478 0.00 0.00 0.00 3.16
415 437 4.243270 GCGTCTACATTGTACTCCTTGTT 58.757 43.478 0.00 0.00 0.00 2.83
473 496 8.698973 TTTTGAGAAATCACCTTACACCATAA 57.301 30.769 0.00 0.00 0.00 1.90
474 497 8.877864 TTTGAGAAATCACCTTACACCATAAT 57.122 30.769 0.00 0.00 0.00 1.28
475 498 8.506168 TTGAGAAATCACCTTACACCATAATC 57.494 34.615 0.00 0.00 0.00 1.75
476 499 7.629157 TGAGAAATCACCTTACACCATAATCA 58.371 34.615 0.00 0.00 0.00 2.57
477 500 8.274322 TGAGAAATCACCTTACACCATAATCAT 58.726 33.333 0.00 0.00 0.00 2.45
478 501 9.778741 GAGAAATCACCTTACACCATAATCATA 57.221 33.333 0.00 0.00 0.00 2.15
491 514 6.536582 CACCATAATCATATGATCGAACTCCC 59.463 42.308 18.44 0.00 41.25 4.30
508 535 6.517864 CGAACTCCCTAAACCTGACTTTCTTA 60.518 42.308 0.00 0.00 0.00 2.10
521 548 7.345914 ACCTGACTTTCTTAGGCAATAGAGTAT 59.654 37.037 0.00 0.00 42.80 2.12
533 560 8.171164 AGGCAATAGAGTATTATTTTCCTTGC 57.829 34.615 0.00 0.00 35.68 4.01
554 581 0.036388 ACGTAACCTGCTGACCATGG 60.036 55.000 11.19 11.19 0.00 3.66
557 584 1.496444 TAACCTGCTGACCATGGCCA 61.496 55.000 13.04 8.56 0.00 5.36
652 684 8.761497 CGTCTACAAGACTTCAGAAATTAACAA 58.239 33.333 5.59 0.00 42.92 2.83
740 772 0.538287 AGGTGGTGGCTTCTGCTTTC 60.538 55.000 0.00 0.00 39.59 2.62
785 831 0.872388 CCGGGTGAGTTTTTCCGAAG 59.128 55.000 0.00 0.00 44.69 3.79
786 832 0.237498 CGGGTGAGTTTTTCCGAAGC 59.763 55.000 0.00 0.00 44.69 3.86
787 833 0.596577 GGGTGAGTTTTTCCGAAGCC 59.403 55.000 0.00 0.00 0.00 4.35
788 834 0.237498 GGTGAGTTTTTCCGAAGCCG 59.763 55.000 0.00 0.00 0.00 5.52
789 835 1.223187 GTGAGTTTTTCCGAAGCCGA 58.777 50.000 0.00 0.00 38.22 5.54
790 836 1.600485 GTGAGTTTTTCCGAAGCCGAA 59.400 47.619 0.00 0.00 38.22 4.30
802 848 2.003301 GAAGCCGAAACACCTCATCTC 58.997 52.381 0.00 0.00 0.00 2.75
868 933 2.930950 TGAAGCCTGCTTTGTAGTGTT 58.069 42.857 5.76 0.00 36.26 3.32
929 998 1.949525 AGCGTTCTTGCACATGTCTTT 59.050 42.857 0.00 0.00 37.31 2.52
946 1021 3.935828 GTCTTTATCAGGTGAAGCTGGAC 59.064 47.826 9.48 5.19 0.00 4.02
955 1030 2.485479 GGTGAAGCTGGACTTGACAAGA 60.485 50.000 21.95 0.00 43.58 3.02
956 1031 2.545946 GTGAAGCTGGACTTGACAAGAC 59.454 50.000 21.95 15.15 41.64 3.01
957 1032 2.170397 TGAAGCTGGACTTGACAAGACA 59.830 45.455 21.95 17.10 39.29 3.41
958 1033 2.540265 AGCTGGACTTGACAAGACAG 57.460 50.000 26.11 26.11 38.82 3.51
970 1045 2.687935 GACAAGACAGAAGTTTTGGCCA 59.312 45.455 0.00 0.00 40.91 5.36
1003 1079 3.885901 TGTTTCATTCCCGTTTGTGATGA 59.114 39.130 0.00 0.00 0.00 2.92
1010 1086 1.739466 CCCGTTTGTGATGACTGATGG 59.261 52.381 0.00 0.00 0.00 3.51
1021 1097 4.285775 TGATGACTGATGGTACCAAGTTCA 59.714 41.667 20.76 17.03 0.00 3.18
1062 1147 2.991190 CAGCTCATCATTGTGTTTTGGC 59.009 45.455 0.00 0.00 0.00 4.52
1068 1153 4.768448 TCATCATTGTGTTTTGGCTCTGAT 59.232 37.500 0.00 0.00 0.00 2.90
1093 1178 2.254152 TATCCAGTGCCTGAGGTCTT 57.746 50.000 0.00 0.00 32.44 3.01
1149 1234 5.478332 ACTCAATTCCTCTTGGGATTTTGAC 59.522 40.000 0.00 0.00 44.66 3.18
1152 1237 5.728637 ATTCCTCTTGGGATTTTGACAAC 57.271 39.130 0.00 0.00 44.66 3.32
1154 1239 4.803452 TCCTCTTGGGATTTTGACAACTT 58.197 39.130 0.00 0.00 39.58 2.66
1155 1240 4.584325 TCCTCTTGGGATTTTGACAACTTG 59.416 41.667 0.00 0.00 39.58 3.16
1156 1241 4.262164 CCTCTTGGGATTTTGACAACTTGG 60.262 45.833 0.00 0.00 37.23 3.61
1157 1242 4.541705 TCTTGGGATTTTGACAACTTGGA 58.458 39.130 0.00 0.00 0.00 3.53
1159 1244 2.962421 TGGGATTTTGACAACTTGGACC 59.038 45.455 0.00 0.00 0.00 4.46
1162 1247 3.304458 GGATTTTGACAACTTGGACCGAC 60.304 47.826 0.00 0.00 0.00 4.79
1178 1263 1.516423 GACCTAGCTCCGTTGGGTC 59.484 63.158 0.00 0.00 39.41 4.46
1193 1278 4.079253 GTTGGGTCCATATGCCGATTTAT 58.921 43.478 0.00 0.00 0.00 1.40
1233 1318 1.279271 CCCGATGAGAACAGGGTTCTT 59.721 52.381 12.42 0.00 39.05 2.52
1325 2397 1.742768 GCCTGGACCTGTCGGATAG 59.257 63.158 0.00 0.00 0.00 2.08
1408 3981 7.851228 TCTGGATCTCTCAAACAATAGCTTTA 58.149 34.615 0.00 0.00 0.00 1.85
1422 3995 5.717119 ATAGCTTTACAGGTGAAATCCCT 57.283 39.130 0.00 0.00 31.45 4.20
1505 4078 2.552315 GTCAAATTCCAGAGCGGTTCAA 59.448 45.455 0.00 0.00 35.57 2.69
1600 4173 7.491372 CACATGTCTTCTCGCCTTTATACTTTA 59.509 37.037 0.00 0.00 0.00 1.85
1643 4216 2.040544 CACCATTGGACGAGTGCCC 61.041 63.158 10.37 0.00 0.00 5.36
1655 4232 4.011517 GTGCCCCCGGAGTCGAAA 62.012 66.667 0.73 0.00 39.00 3.46
1683 4275 0.541392 TGATACCAATCAGGCTGCGT 59.459 50.000 10.34 5.66 43.14 5.24
1770 4362 2.262423 ACTTCCACTTGTTCTGCTCC 57.738 50.000 0.00 0.00 0.00 4.70
1771 4363 1.490490 ACTTCCACTTGTTCTGCTCCA 59.510 47.619 0.00 0.00 0.00 3.86
1794 4386 1.777272 AGGCTCCTTCCTTGTGTCTTT 59.223 47.619 0.00 0.00 30.82 2.52
2044 4738 2.284417 CGATTTACTAGCCGTTTCTGCC 59.716 50.000 0.00 0.00 0.00 4.85
2058 5142 4.318121 CGTTTCTGCCATTCGATAAGCTAC 60.318 45.833 0.00 0.00 0.00 3.58
2086 5208 6.282930 GGTTACATTCAATATTGCAGGCAAT 58.717 36.000 21.66 21.66 46.85 3.56
2087 5209 6.762661 GGTTACATTCAATATTGCAGGCAATT 59.237 34.615 22.92 5.96 43.32 2.32
2097 5219 1.894466 TGCAGGCAATTGTGTTAGCAT 59.106 42.857 7.40 0.00 0.00 3.79
2152 5278 4.998672 CCTATGAACTTTGTTGGTAACCGA 59.001 41.667 0.00 0.00 0.00 4.69
2211 5337 5.742453 ACACGATCAACGATCATTACAGTAC 59.258 40.000 4.95 0.00 45.77 2.73
2248 5374 1.603236 CGTCTGCTCCAAGAGGCTCT 61.603 60.000 12.24 12.24 33.74 4.09
2314 5443 7.576236 TCTTTCGAAAAGATGATTCACTTGTC 58.424 34.615 12.41 8.16 0.00 3.18
2334 5463 4.202223 TGTCCTGAACAGTAACCTCAGTTC 60.202 45.833 0.00 0.00 40.45 3.01
2418 5547 1.681264 GCTTTGGTTTGCCTGTAGTGT 59.319 47.619 0.00 0.00 35.27 3.55
2469 5604 5.285651 CGATCATCTTTCTACTGAGAACCC 58.714 45.833 0.00 0.00 41.52 4.11
2545 5683 3.706594 TCTAGCAAGTACTAGCAGGCAAT 59.293 43.478 0.00 0.00 39.64 3.56
2556 5694 9.057089 AGTACTAGCAGGCAATAATTTATGTTC 57.943 33.333 0.00 0.00 0.00 3.18
2591 5731 5.015391 AGACTTCCTCCTCTACCAAACTCTA 59.985 44.000 0.00 0.00 0.00 2.43
2592 5732 5.844601 ACTTCCTCCTCTACCAAACTCTAT 58.155 41.667 0.00 0.00 0.00 1.98
2593 5733 6.982899 ACTTCCTCCTCTACCAAACTCTATA 58.017 40.000 0.00 0.00 0.00 1.31
2602 5742 9.163899 CCTCTACCAAACTCTATAAAGGTTTTC 57.836 37.037 0.00 0.00 31.87 2.29
2607 5747 6.127730 CCAAACTCTATAAAGGTTTTCGCCAT 60.128 38.462 0.00 0.00 31.87 4.40
2625 5765 5.584649 TCGCCATTTAGTTCAGTCCAATTAG 59.415 40.000 0.00 0.00 0.00 1.73
2626 5766 5.584649 CGCCATTTAGTTCAGTCCAATTAGA 59.415 40.000 0.00 0.00 0.00 2.10
2627 5767 6.238211 CGCCATTTAGTTCAGTCCAATTAGAG 60.238 42.308 0.00 0.00 0.00 2.43
2628 5768 6.458888 GCCATTTAGTTCAGTCCAATTAGAGC 60.459 42.308 0.00 0.00 0.00 4.09
2629 5769 6.599244 CCATTTAGTTCAGTCCAATTAGAGCA 59.401 38.462 0.00 0.00 0.00 4.26
2630 5770 7.121168 CCATTTAGTTCAGTCCAATTAGAGCAA 59.879 37.037 0.00 0.00 0.00 3.91
2631 5771 7.435068 TTTAGTTCAGTCCAATTAGAGCAAC 57.565 36.000 0.00 0.00 0.00 4.17
2632 5772 5.234466 AGTTCAGTCCAATTAGAGCAACT 57.766 39.130 0.00 0.00 0.00 3.16
2633 5773 5.625150 AGTTCAGTCCAATTAGAGCAACTT 58.375 37.500 0.00 0.00 0.00 2.66
2634 5774 5.703130 AGTTCAGTCCAATTAGAGCAACTTC 59.297 40.000 0.00 0.00 0.00 3.01
2635 5775 5.227569 TCAGTCCAATTAGAGCAACTTCA 57.772 39.130 0.00 0.00 0.00 3.02
2636 5776 5.620206 TCAGTCCAATTAGAGCAACTTCAA 58.380 37.500 0.00 0.00 0.00 2.69
2637 5777 6.240894 TCAGTCCAATTAGAGCAACTTCAAT 58.759 36.000 0.00 0.00 0.00 2.57
2638 5778 6.149973 TCAGTCCAATTAGAGCAACTTCAATG 59.850 38.462 0.00 0.00 0.00 2.82
2639 5779 6.149973 CAGTCCAATTAGAGCAACTTCAATGA 59.850 38.462 0.00 0.00 0.00 2.57
2640 5780 6.373774 AGTCCAATTAGAGCAACTTCAATGAG 59.626 38.462 0.00 0.00 0.00 2.90
2641 5781 5.649395 TCCAATTAGAGCAACTTCAATGAGG 59.351 40.000 0.00 0.00 0.00 3.86
2642 5782 5.338365 CAATTAGAGCAACTTCAATGAGGC 58.662 41.667 0.00 0.00 0.00 4.70
2643 5783 1.446907 AGAGCAACTTCAATGAGGCG 58.553 50.000 0.00 0.00 0.00 5.52
2644 5784 1.002430 AGAGCAACTTCAATGAGGCGA 59.998 47.619 0.00 0.00 0.00 5.54
2645 5785 1.129437 GAGCAACTTCAATGAGGCGAC 59.871 52.381 0.00 0.00 0.00 5.19
2658 5798 0.517316 AGGCGACTCATTTTGTTCGC 59.483 50.000 6.28 6.28 44.51 4.70
2659 5799 3.001576 GCGACTCATTTTGTTCGCC 57.998 52.632 3.50 0.00 40.19 5.54
2660 5800 0.789383 GCGACTCATTTTGTTCGCCG 60.789 55.000 3.50 0.00 40.19 6.46
2661 5801 0.789383 CGACTCATTTTGTTCGCCGC 60.789 55.000 0.00 0.00 0.00 6.53
2662 5802 0.454452 GACTCATTTTGTTCGCCGCC 60.454 55.000 0.00 0.00 0.00 6.13
2663 5803 1.511887 CTCATTTTGTTCGCCGCCG 60.512 57.895 0.00 0.00 0.00 6.46
2664 5804 2.182614 CTCATTTTGTTCGCCGCCGT 62.183 55.000 0.00 0.00 35.54 5.68
2665 5805 1.795962 CATTTTGTTCGCCGCCGTC 60.796 57.895 0.00 0.00 35.54 4.79
2666 5806 1.964373 ATTTTGTTCGCCGCCGTCT 60.964 52.632 0.00 0.00 35.54 4.18
2667 5807 0.671163 ATTTTGTTCGCCGCCGTCTA 60.671 50.000 0.00 0.00 35.54 2.59
2668 5808 0.671163 TTTTGTTCGCCGCCGTCTAT 60.671 50.000 0.00 0.00 35.54 1.98
2669 5809 0.671163 TTTGTTCGCCGCCGTCTATT 60.671 50.000 0.00 0.00 35.54 1.73
2670 5810 0.671163 TTGTTCGCCGCCGTCTATTT 60.671 50.000 0.00 0.00 35.54 1.40
2671 5811 1.347221 GTTCGCCGCCGTCTATTTG 59.653 57.895 0.00 0.00 35.54 2.32
2672 5812 1.812093 TTCGCCGCCGTCTATTTGG 60.812 57.895 0.00 0.00 35.54 3.28
2673 5813 3.269347 CGCCGCCGTCTATTTGGG 61.269 66.667 0.00 0.00 0.00 4.12
2674 5814 2.124860 GCCGCCGTCTATTTGGGT 60.125 61.111 0.00 0.00 0.00 4.51
2675 5815 2.178235 GCCGCCGTCTATTTGGGTC 61.178 63.158 0.00 0.00 0.00 4.46
2676 5816 1.881252 CCGCCGTCTATTTGGGTCG 60.881 63.158 0.00 0.00 0.00 4.79
2677 5817 1.881252 CGCCGTCTATTTGGGTCGG 60.881 63.158 0.00 0.00 43.37 4.79
2678 5818 4.120085 CCGTCTATTTGGGTCGGC 57.880 61.111 0.00 0.00 35.01 5.54
2679 5819 1.219664 CCGTCTATTTGGGTCGGCA 59.780 57.895 0.00 0.00 35.01 5.69
2680 5820 1.087771 CCGTCTATTTGGGTCGGCAC 61.088 60.000 0.00 0.00 35.01 5.01
2695 5835 2.619013 GGCACGGACAGAAAAATCAG 57.381 50.000 0.00 0.00 0.00 2.90
2696 5836 1.401539 GGCACGGACAGAAAAATCAGC 60.402 52.381 0.00 0.00 0.00 4.26
2697 5837 1.401539 GCACGGACAGAAAAATCAGCC 60.402 52.381 0.00 0.00 0.00 4.85
2698 5838 1.200020 CACGGACAGAAAAATCAGCCC 59.800 52.381 0.00 0.00 0.00 5.19
2699 5839 1.202879 ACGGACAGAAAAATCAGCCCA 60.203 47.619 0.00 0.00 0.00 5.36
2700 5840 1.885887 CGGACAGAAAAATCAGCCCAA 59.114 47.619 0.00 0.00 0.00 4.12
2701 5841 2.351738 CGGACAGAAAAATCAGCCCAAC 60.352 50.000 0.00 0.00 0.00 3.77
2702 5842 2.351738 GGACAGAAAAATCAGCCCAACG 60.352 50.000 0.00 0.00 0.00 4.10
2703 5843 1.000274 ACAGAAAAATCAGCCCAACGC 60.000 47.619 0.00 0.00 37.98 4.84
2704 5844 1.000385 CAGAAAAATCAGCCCAACGCA 60.000 47.619 0.00 0.00 41.38 5.24
2705 5845 1.000274 AGAAAAATCAGCCCAACGCAC 60.000 47.619 0.00 0.00 41.38 5.34
2706 5846 0.033366 AAAAATCAGCCCAACGCACC 59.967 50.000 0.00 0.00 41.38 5.01
2707 5847 2.141122 AAAATCAGCCCAACGCACCG 62.141 55.000 0.00 0.00 41.38 4.94
2708 5848 3.545124 AATCAGCCCAACGCACCGA 62.545 57.895 0.00 0.00 41.38 4.69
2709 5849 4.980805 TCAGCCCAACGCACCGAC 62.981 66.667 0.00 0.00 41.38 4.79
2712 5852 4.382320 GCCCAACGCACCGACCTA 62.382 66.667 0.00 0.00 37.47 3.08
2713 5853 2.344500 CCCAACGCACCGACCTAA 59.656 61.111 0.00 0.00 0.00 2.69
2714 5854 1.301874 CCCAACGCACCGACCTAAA 60.302 57.895 0.00 0.00 0.00 1.85
2715 5855 1.571215 CCCAACGCACCGACCTAAAC 61.571 60.000 0.00 0.00 0.00 2.01
2716 5856 1.489824 CAACGCACCGACCTAAACG 59.510 57.895 0.00 0.00 0.00 3.60
2723 5863 3.455685 CGACCTAAACGGACGTGC 58.544 61.111 0.00 0.00 44.21 5.34
2724 5864 2.430942 CGACCTAAACGGACGTGCG 61.431 63.158 28.33 28.33 44.21 5.34
2725 5865 1.372128 GACCTAAACGGACGTGCGT 60.372 57.895 29.92 29.92 36.31 5.24
2726 5866 1.339946 GACCTAAACGGACGTGCGTC 61.340 60.000 34.66 17.68 43.87 5.19
2734 5874 4.117372 GACGTGCGTCCGCTTTCG 62.117 66.667 13.31 15.59 42.51 3.46
2735 5875 4.936823 ACGTGCGTCCGCTTTCGT 62.937 61.111 13.31 16.15 42.51 3.85
2736 5876 4.117372 CGTGCGTCCGCTTTCGTC 62.117 66.667 13.31 0.00 42.51 4.20
2737 5877 3.774702 GTGCGTCCGCTTTCGTCC 61.775 66.667 13.31 0.00 42.51 4.79
2738 5878 3.986006 TGCGTCCGCTTTCGTCCT 61.986 61.111 13.31 0.00 42.51 3.85
2739 5879 3.179939 GCGTCCGCTTTCGTCCTC 61.180 66.667 4.10 0.00 38.26 3.71
2740 5880 2.506438 CGTCCGCTTTCGTCCTCC 60.506 66.667 0.00 0.00 0.00 4.30
2741 5881 2.971452 GTCCGCTTTCGTCCTCCT 59.029 61.111 0.00 0.00 0.00 3.69
2742 5882 1.446272 GTCCGCTTTCGTCCTCCTG 60.446 63.158 0.00 0.00 0.00 3.86
2743 5883 2.815647 CCGCTTTCGTCCTCCTGC 60.816 66.667 0.00 0.00 0.00 4.85
2744 5884 2.815647 CGCTTTCGTCCTCCTGCC 60.816 66.667 0.00 0.00 0.00 4.85
2745 5885 2.815647 GCTTTCGTCCTCCTGCCG 60.816 66.667 0.00 0.00 0.00 5.69
2746 5886 2.970639 CTTTCGTCCTCCTGCCGA 59.029 61.111 0.00 0.00 0.00 5.54
2747 5887 1.446272 CTTTCGTCCTCCTGCCGAC 60.446 63.158 0.00 0.00 0.00 4.79
2748 5888 2.837371 CTTTCGTCCTCCTGCCGACC 62.837 65.000 0.00 0.00 0.00 4.79
2749 5889 4.671590 TCGTCCTCCTGCCGACCA 62.672 66.667 0.00 0.00 0.00 4.02
2750 5890 3.691342 CGTCCTCCTGCCGACCAA 61.691 66.667 0.00 0.00 0.00 3.67
2751 5891 2.990479 GTCCTCCTGCCGACCAAT 59.010 61.111 0.00 0.00 0.00 3.16
2752 5892 1.299976 GTCCTCCTGCCGACCAATT 59.700 57.895 0.00 0.00 0.00 2.32
2753 5893 0.744771 GTCCTCCTGCCGACCAATTC 60.745 60.000 0.00 0.00 0.00 2.17
2754 5894 0.909610 TCCTCCTGCCGACCAATTCT 60.910 55.000 0.00 0.00 0.00 2.40
2755 5895 0.462759 CCTCCTGCCGACCAATTCTC 60.463 60.000 0.00 0.00 0.00 2.87
2756 5896 0.807667 CTCCTGCCGACCAATTCTCG 60.808 60.000 0.00 0.00 0.00 4.04
2757 5897 1.218047 CCTGCCGACCAATTCTCGA 59.782 57.895 4.00 0.00 32.65 4.04
2758 5898 1.084370 CCTGCCGACCAATTCTCGAC 61.084 60.000 4.00 0.00 32.65 4.20
2759 5899 1.079405 TGCCGACCAATTCTCGACC 60.079 57.895 4.00 0.00 32.65 4.79
2760 5900 1.814169 GCCGACCAATTCTCGACCC 60.814 63.158 4.00 0.00 32.65 4.46
2761 5901 1.594833 CCGACCAATTCTCGACCCA 59.405 57.895 4.00 0.00 32.65 4.51
2762 5902 0.178068 CCGACCAATTCTCGACCCAT 59.822 55.000 4.00 0.00 32.65 4.00
2763 5903 1.406887 CCGACCAATTCTCGACCCATT 60.407 52.381 4.00 0.00 32.65 3.16
2764 5904 2.356135 CGACCAATTCTCGACCCATTT 58.644 47.619 0.00 0.00 32.65 2.32
2765 5905 2.747446 CGACCAATTCTCGACCCATTTT 59.253 45.455 0.00 0.00 32.65 1.82
2766 5906 3.190535 CGACCAATTCTCGACCCATTTTT 59.809 43.478 0.00 0.00 32.65 1.94
2767 5907 4.485163 GACCAATTCTCGACCCATTTTTG 58.515 43.478 0.00 0.00 0.00 2.44
2768 5908 4.148838 ACCAATTCTCGACCCATTTTTGA 58.851 39.130 0.00 0.00 0.00 2.69
2769 5909 4.218417 ACCAATTCTCGACCCATTTTTGAG 59.782 41.667 0.00 0.00 0.00 3.02
2770 5910 4.168760 CAATTCTCGACCCATTTTTGAGC 58.831 43.478 0.00 0.00 0.00 4.26
2771 5911 1.821216 TCTCGACCCATTTTTGAGCC 58.179 50.000 0.00 0.00 0.00 4.70
2772 5912 0.447801 CTCGACCCATTTTTGAGCCG 59.552 55.000 0.00 0.00 0.00 5.52
2773 5913 0.958382 TCGACCCATTTTTGAGCCGG 60.958 55.000 0.00 0.00 0.00 6.13
2774 5914 0.958382 CGACCCATTTTTGAGCCGGA 60.958 55.000 5.05 0.00 0.00 5.14
2775 5915 1.474330 GACCCATTTTTGAGCCGGAT 58.526 50.000 5.05 0.00 0.00 4.18
2776 5916 1.824852 GACCCATTTTTGAGCCGGATT 59.175 47.619 5.05 0.00 0.00 3.01
2777 5917 2.233676 GACCCATTTTTGAGCCGGATTT 59.766 45.455 5.05 0.00 0.00 2.17
2778 5918 2.028203 ACCCATTTTTGAGCCGGATTTG 60.028 45.455 5.05 0.00 0.00 2.32
2779 5919 2.001872 CCATTTTTGAGCCGGATTTGC 58.998 47.619 5.05 0.00 0.00 3.68
2780 5920 1.655099 CATTTTTGAGCCGGATTTGCG 59.345 47.619 5.05 0.00 0.00 4.85
2781 5921 0.671251 TTTTTGAGCCGGATTTGCGT 59.329 45.000 5.05 0.00 0.00 5.24
2782 5922 0.239879 TTTTGAGCCGGATTTGCGTC 59.760 50.000 5.05 0.00 0.00 5.19
2783 5923 1.906994 TTTGAGCCGGATTTGCGTCG 61.907 55.000 5.05 0.00 0.00 5.12
2784 5924 3.564027 GAGCCGGATTTGCGTCGG 61.564 66.667 5.05 0.00 45.84 4.79
2796 5936 3.299585 CGTCGGCGCAGATACAAG 58.700 61.111 14.65 0.00 0.00 3.16
2797 5937 1.226575 CGTCGGCGCAGATACAAGA 60.227 57.895 14.65 0.00 0.00 3.02
2798 5938 1.472276 CGTCGGCGCAGATACAAGAC 61.472 60.000 14.65 6.05 0.00 3.01
2799 5939 0.457853 GTCGGCGCAGATACAAGACA 60.458 55.000 14.65 0.00 0.00 3.41
2800 5940 0.179137 TCGGCGCAGATACAAGACAG 60.179 55.000 10.83 0.00 0.00 3.51
2801 5941 0.179137 CGGCGCAGATACAAGACAGA 60.179 55.000 10.83 0.00 0.00 3.41
2802 5942 1.281899 GGCGCAGATACAAGACAGAC 58.718 55.000 10.83 0.00 0.00 3.51
2803 5943 0.917259 GCGCAGATACAAGACAGACG 59.083 55.000 0.30 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
94 96 5.290643 CCAACATTGAAAGAAAACTTTGCGA 59.709 36.000 0.00 0.00 0.00 5.10
95 97 5.063312 ACCAACATTGAAAGAAAACTTTGCG 59.937 36.000 0.00 0.00 0.00 4.85
96 98 6.421377 ACCAACATTGAAAGAAAACTTTGC 57.579 33.333 0.00 0.00 0.00 3.68
97 99 9.328721 GAAAACCAACATTGAAAGAAAACTTTG 57.671 29.630 0.00 0.00 0.00 2.77
98 100 8.227119 CGAAAACCAACATTGAAAGAAAACTTT 58.773 29.630 0.00 0.00 0.00 2.66
113 119 8.269317 AGGGAGAATATTATACGAAAACCAACA 58.731 33.333 0.00 0.00 0.00 3.33
128 134 9.726438 CCTACGAAATGAATTAGGGAGAATATT 57.274 33.333 0.00 0.00 0.00 1.28
204 214 5.475564 TCATAATCATCCAATCACATGCTGG 59.524 40.000 0.00 0.00 0.00 4.85
238 248 1.272037 GGTTTTATTCCCGGTGGGTCA 60.272 52.381 0.00 0.00 44.74 4.02
247 257 7.172532 GGTTTTCAAATCTGTGGTTTTATTCCC 59.827 37.037 0.00 0.00 0.00 3.97
259 269 6.547141 TGAGACATCAAGGTTTTCAAATCTGT 59.453 34.615 0.00 0.00 30.61 3.41
262 272 9.912634 TTAATGAGACATCAAGGTTTTCAAATC 57.087 29.630 0.00 0.00 39.39 2.17
298 308 2.354510 CGTTGACTCTGGCTGAAACAAA 59.645 45.455 11.92 0.00 0.00 2.83
339 349 3.805066 TCATGAAAAGTCACCCCATGA 57.195 42.857 0.00 0.00 40.61 3.07
344 354 5.884792 AGATCAGAATCATGAAAAGTCACCC 59.115 40.000 0.00 0.00 36.31 4.61
370 392 1.003580 ACACTCATGCAACCCCTACTG 59.996 52.381 0.00 0.00 0.00 2.74
377 399 1.081906 CGCACACACTCATGCAACC 60.082 57.895 0.00 0.00 42.17 3.77
447 470 7.781324 ATGGTGTAAGGTGATTTCTCAAAAT 57.219 32.000 0.00 0.00 37.80 1.82
452 475 8.682936 ATGATTATGGTGTAAGGTGATTTCTC 57.317 34.615 0.00 0.00 0.00 2.87
473 496 6.498651 AGGTTTAGGGAGTTCGATCATATGAT 59.501 38.462 18.21 18.21 37.51 2.45
474 497 5.839063 AGGTTTAGGGAGTTCGATCATATGA 59.161 40.000 8.10 8.10 0.00 2.15
475 498 5.928839 CAGGTTTAGGGAGTTCGATCATATG 59.071 44.000 0.00 0.00 0.00 1.78
476 499 5.839063 TCAGGTTTAGGGAGTTCGATCATAT 59.161 40.000 0.00 0.00 0.00 1.78
477 500 5.068723 GTCAGGTTTAGGGAGTTCGATCATA 59.931 44.000 0.00 0.00 0.00 2.15
478 501 4.030913 TCAGGTTTAGGGAGTTCGATCAT 58.969 43.478 0.00 0.00 0.00 2.45
491 514 8.041323 TCTATTGCCTAAGAAAGTCAGGTTTAG 58.959 37.037 0.00 0.00 0.00 1.85
508 535 8.001292 AGCAAGGAAAATAATACTCTATTGCCT 58.999 33.333 0.00 0.00 39.98 4.75
521 548 5.122711 GCAGGTTACGTAGCAAGGAAAATAA 59.877 40.000 11.70 0.00 0.00 1.40
533 560 2.540515 CATGGTCAGCAGGTTACGTAG 58.459 52.381 0.00 0.00 0.00 3.51
652 684 6.660521 TCCAATAGAGCACATCACATTTTTCT 59.339 34.615 0.00 0.00 0.00 2.52
708 740 2.489329 CCACCACCTGCAACTATTCAAG 59.511 50.000 0.00 0.00 0.00 3.02
745 777 1.795170 GCTCGGCCAAAACTTGCAGA 61.795 55.000 2.24 0.00 0.00 4.26
785 831 0.389948 ACGAGATGAGGTGTTTCGGC 60.390 55.000 0.00 0.00 35.72 5.54
786 832 1.630148 GACGAGATGAGGTGTTTCGG 58.370 55.000 0.00 0.00 35.72 4.30
787 833 1.067846 TGGACGAGATGAGGTGTTTCG 60.068 52.381 0.00 0.00 37.31 3.46
788 834 2.743636 TGGACGAGATGAGGTGTTTC 57.256 50.000 0.00 0.00 0.00 2.78
789 835 2.567169 TCATGGACGAGATGAGGTGTTT 59.433 45.455 0.00 0.00 0.00 2.83
790 836 2.179427 TCATGGACGAGATGAGGTGTT 58.821 47.619 0.00 0.00 0.00 3.32
802 848 2.270923 TCTTCGCTGATTTCATGGACG 58.729 47.619 0.00 0.00 0.00 4.79
886 952 7.305474 GCTTAAGAACTCCGATTCAATCAAAA 58.695 34.615 6.67 0.00 0.00 2.44
905 971 3.187227 AGACATGTGCAAGAACGCTTAAG 59.813 43.478 1.15 0.00 31.81 1.85
929 998 3.055819 GTCAAGTCCAGCTTCACCTGATA 60.056 47.826 0.00 0.00 34.69 2.15
946 1021 4.354587 GCCAAAACTTCTGTCTTGTCAAG 58.645 43.478 6.21 6.21 0.00 3.02
955 1030 1.410153 CTGCTTGGCCAAAACTTCTGT 59.590 47.619 20.91 0.00 0.00 3.41
956 1031 1.870993 GCTGCTTGGCCAAAACTTCTG 60.871 52.381 20.91 6.96 0.00 3.02
957 1032 0.390492 GCTGCTTGGCCAAAACTTCT 59.610 50.000 20.91 0.00 0.00 2.85
958 1033 0.390492 AGCTGCTTGGCCAAAACTTC 59.610 50.000 20.91 7.88 0.00 3.01
970 1045 3.493176 GGGAATGAAACAAACAGCTGCTT 60.493 43.478 15.27 4.71 0.00 3.91
1003 1079 5.505181 AAGATGAACTTGGTACCATCAGT 57.495 39.130 17.17 14.58 38.22 3.41
1062 1147 4.283978 AGGCACTGGATATCAAGATCAGAG 59.716 45.833 14.38 6.56 37.18 3.35
1149 1234 0.608640 AGCTAGGTCGGTCCAAGTTG 59.391 55.000 0.00 0.00 39.02 3.16
1155 1240 2.050934 AACGGAGCTAGGTCGGTCC 61.051 63.158 28.43 11.02 45.71 4.46
1156 1241 1.139095 CAACGGAGCTAGGTCGGTC 59.861 63.158 28.43 10.38 0.00 4.79
1157 1242 2.348888 CCAACGGAGCTAGGTCGGT 61.349 63.158 24.50 24.50 0.00 4.69
1159 1244 2.280823 GACCCAACGGAGCTAGGTCG 62.281 65.000 15.43 12.79 37.83 4.79
1162 1247 1.338136 ATGGACCCAACGGAGCTAGG 61.338 60.000 0.00 0.00 0.00 3.02
1178 1263 4.321156 CCACACCAATAAATCGGCATATGG 60.321 45.833 4.56 0.00 0.00 2.74
1193 1278 2.203337 GCCAGCAGTCCACACCAA 60.203 61.111 0.00 0.00 0.00 3.67
1233 1318 0.458543 GATTGCCGAGTCGCAGAGAA 60.459 55.000 7.12 0.00 40.53 2.87
1321 2393 5.757850 ATCGGTCCTGAAAATTTGCTATC 57.242 39.130 0.00 0.00 0.00 2.08
1325 2397 3.511699 GGAATCGGTCCTGAAAATTTGC 58.488 45.455 0.00 0.00 43.98 3.68
1408 3981 3.884037 ACTTTGAGGGATTTCACCTGT 57.116 42.857 0.00 0.00 38.79 4.00
1422 3995 7.178274 AGGTATGCCAAATTTGTGATACTTTGA 59.822 33.333 23.15 1.24 37.19 2.69
1505 4078 1.346395 TGGTTAACCGACTGAGCATGT 59.654 47.619 19.65 0.00 39.43 3.21
1538 4111 2.433239 GGCCCCGACAAGAAGTTATCTA 59.567 50.000 0.00 0.00 37.42 1.98
1600 4173 2.158130 AAAGGCCCCGGTTACCAGT 61.158 57.895 0.00 0.00 0.00 4.00
1643 4216 0.462047 CCTCCATTTTCGACTCCGGG 60.462 60.000 0.00 0.00 36.24 5.73
1683 4275 3.698289 ACTGGACTCTTCGTTGATCCTA 58.302 45.455 0.00 0.00 0.00 2.94
1770 4362 1.072965 ACACAAGGAAGGAGCCTCTTG 59.927 52.381 13.48 13.48 41.46 3.02
1771 4363 1.349357 GACACAAGGAAGGAGCCTCTT 59.651 52.381 0.00 0.00 37.26 2.85
1794 4386 0.673333 AACAAGTGGATCATGCGCGA 60.673 50.000 12.10 0.00 0.00 5.87
2002 4696 5.362263 TCGTTCTATAAGTTGGTTATGCCC 58.638 41.667 0.00 0.00 33.16 5.36
2058 5142 6.144854 CCTGCAATATTGAATGTAACCGATG 58.855 40.000 19.73 0.00 0.00 3.84
2152 5278 1.149627 TGTACCGCAACAAAGCCCT 59.850 52.632 0.00 0.00 0.00 5.19
2211 5337 1.134280 ACGAAGGAATGCAGGATCCAG 60.134 52.381 15.82 7.25 38.23 3.86
2248 5374 3.320256 TCATATGCAACAACAAAGGCACA 59.680 39.130 0.00 0.00 39.34 4.57
2314 5443 4.336889 TGAACTGAGGTTACTGTTCAGG 57.663 45.455 13.87 0.00 45.97 3.86
2334 5463 7.975616 ACTTCAATATGTTCCGGAATTGAAATG 59.024 33.333 29.64 24.14 43.78 2.32
2556 5694 6.655930 AGAGGAGGAAGTCTACAGTTACTAG 58.344 44.000 0.00 0.00 0.00 2.57
2591 5731 7.039993 ACTGAACTAAATGGCGAAAACCTTTAT 60.040 33.333 0.00 0.00 0.00 1.40
2592 5732 6.263617 ACTGAACTAAATGGCGAAAACCTTTA 59.736 34.615 0.00 0.00 0.00 1.85
2593 5733 5.068591 ACTGAACTAAATGGCGAAAACCTTT 59.931 36.000 0.00 0.00 0.00 3.11
2602 5742 4.701956 AATTGGACTGAACTAAATGGCG 57.298 40.909 0.00 0.00 0.00 5.69
2607 5747 7.224297 AGTTGCTCTAATTGGACTGAACTAAA 58.776 34.615 4.46 0.00 0.00 1.85
2625 5765 1.129437 GTCGCCTCATTGAAGTTGCTC 59.871 52.381 0.00 0.00 0.00 4.26
2626 5766 1.160137 GTCGCCTCATTGAAGTTGCT 58.840 50.000 0.00 0.00 0.00 3.91
2627 5767 1.129437 GAGTCGCCTCATTGAAGTTGC 59.871 52.381 0.00 0.00 37.67 4.17
2628 5768 2.416747 TGAGTCGCCTCATTGAAGTTG 58.583 47.619 0.00 0.00 42.80 3.16
2629 5769 2.839486 TGAGTCGCCTCATTGAAGTT 57.161 45.000 0.00 0.00 42.80 2.66
2638 5778 1.464189 GCGAACAAAATGAGTCGCCTC 60.464 52.381 16.56 0.00 43.30 4.70
2639 5779 0.517316 GCGAACAAAATGAGTCGCCT 59.483 50.000 16.56 0.00 43.30 5.52
2640 5780 3.001576 GCGAACAAAATGAGTCGCC 57.998 52.632 16.56 5.19 43.30 5.54
2641 5781 0.789383 CGGCGAACAAAATGAGTCGC 60.789 55.000 18.11 18.11 45.94 5.19
2642 5782 0.789383 GCGGCGAACAAAATGAGTCG 60.789 55.000 12.98 0.00 33.77 4.18
2643 5783 0.454452 GGCGGCGAACAAAATGAGTC 60.454 55.000 12.98 0.00 0.00 3.36
2644 5784 1.579429 GGCGGCGAACAAAATGAGT 59.421 52.632 12.98 0.00 0.00 3.41
2645 5785 1.511887 CGGCGGCGAACAAAATGAG 60.512 57.895 29.19 0.00 0.00 2.90
2646 5786 2.177654 GACGGCGGCGAACAAAATGA 62.178 55.000 38.93 0.00 0.00 2.57
2647 5787 1.795962 GACGGCGGCGAACAAAATG 60.796 57.895 38.93 5.69 0.00 2.32
2648 5788 0.671163 TAGACGGCGGCGAACAAAAT 60.671 50.000 38.93 14.02 0.00 1.82
2649 5789 0.671163 ATAGACGGCGGCGAACAAAA 60.671 50.000 38.93 18.68 0.00 2.44
2650 5790 0.671163 AATAGACGGCGGCGAACAAA 60.671 50.000 38.93 20.89 0.00 2.83
2651 5791 0.671163 AAATAGACGGCGGCGAACAA 60.671 50.000 38.93 19.51 0.00 2.83
2652 5792 1.079681 AAATAGACGGCGGCGAACA 60.080 52.632 38.93 21.04 0.00 3.18
2653 5793 1.347221 CAAATAGACGGCGGCGAAC 59.653 57.895 38.93 28.00 0.00 3.95
2654 5794 1.812093 CCAAATAGACGGCGGCGAA 60.812 57.895 38.93 22.11 0.00 4.70
2655 5795 2.202824 CCAAATAGACGGCGGCGA 60.203 61.111 38.93 16.95 0.00 5.54
2656 5796 3.269347 CCCAAATAGACGGCGGCG 61.269 66.667 31.06 31.06 0.00 6.46
2657 5797 2.124860 ACCCAAATAGACGGCGGC 60.125 61.111 13.24 8.92 0.00 6.53
2658 5798 1.881252 CGACCCAAATAGACGGCGG 60.881 63.158 13.24 0.00 0.00 6.13
2659 5799 1.881252 CCGACCCAAATAGACGGCG 60.881 63.158 4.80 4.80 37.32 6.46
2660 5800 4.120085 CCGACCCAAATAGACGGC 57.880 61.111 0.00 0.00 37.32 5.68
2661 5801 1.087771 GTGCCGACCCAAATAGACGG 61.088 60.000 0.00 0.00 45.26 4.79
2662 5802 1.418342 CGTGCCGACCCAAATAGACG 61.418 60.000 0.00 0.00 0.00 4.18
2663 5803 1.087771 CCGTGCCGACCCAAATAGAC 61.088 60.000 0.00 0.00 0.00 2.59
2664 5804 1.219664 CCGTGCCGACCCAAATAGA 59.780 57.895 0.00 0.00 0.00 1.98
2665 5805 1.087771 GTCCGTGCCGACCCAAATAG 61.088 60.000 0.00 0.00 0.00 1.73
2666 5806 1.078988 GTCCGTGCCGACCCAAATA 60.079 57.895 0.00 0.00 0.00 1.40
2667 5807 2.359478 GTCCGTGCCGACCCAAAT 60.359 61.111 0.00 0.00 0.00 2.32
2668 5808 3.818121 CTGTCCGTGCCGACCCAAA 62.818 63.158 0.00 0.00 31.35 3.28
2669 5809 4.308458 CTGTCCGTGCCGACCCAA 62.308 66.667 0.00 0.00 31.35 4.12
2671 5811 2.999739 TTTTCTGTCCGTGCCGACCC 63.000 60.000 0.00 0.00 31.35 4.46
2672 5812 1.161563 TTTTTCTGTCCGTGCCGACC 61.162 55.000 0.00 0.00 31.35 4.79
2673 5813 0.872388 ATTTTTCTGTCCGTGCCGAC 59.128 50.000 0.00 0.00 0.00 4.79
2674 5814 1.153353 GATTTTTCTGTCCGTGCCGA 58.847 50.000 0.00 0.00 0.00 5.54
2675 5815 0.871722 TGATTTTTCTGTCCGTGCCG 59.128 50.000 0.00 0.00 0.00 5.69
2676 5816 1.401539 GCTGATTTTTCTGTCCGTGCC 60.402 52.381 0.00 0.00 0.00 5.01
2677 5817 1.401539 GGCTGATTTTTCTGTCCGTGC 60.402 52.381 0.00 0.00 0.00 5.34
2678 5818 1.200020 GGGCTGATTTTTCTGTCCGTG 59.800 52.381 0.00 0.00 0.00 4.94
2679 5819 1.202879 TGGGCTGATTTTTCTGTCCGT 60.203 47.619 0.11 0.00 36.32 4.69
2680 5820 1.533625 TGGGCTGATTTTTCTGTCCG 58.466 50.000 0.11 0.00 36.32 4.79
2681 5821 2.351738 CGTTGGGCTGATTTTTCTGTCC 60.352 50.000 0.00 0.00 34.48 4.02
2682 5822 2.922335 GCGTTGGGCTGATTTTTCTGTC 60.922 50.000 0.00 0.00 39.11 3.51
2683 5823 1.000274 GCGTTGGGCTGATTTTTCTGT 60.000 47.619 0.00 0.00 39.11 3.41
2684 5824 1.000385 TGCGTTGGGCTGATTTTTCTG 60.000 47.619 0.00 0.00 44.05 3.02
2685 5825 1.000274 GTGCGTTGGGCTGATTTTTCT 60.000 47.619 0.00 0.00 44.05 2.52
2686 5826 1.418373 GTGCGTTGGGCTGATTTTTC 58.582 50.000 0.00 0.00 44.05 2.29
2687 5827 0.033366 GGTGCGTTGGGCTGATTTTT 59.967 50.000 0.00 0.00 44.05 1.94
2688 5828 1.665442 GGTGCGTTGGGCTGATTTT 59.335 52.632 0.00 0.00 44.05 1.82
2689 5829 2.625823 CGGTGCGTTGGGCTGATTT 61.626 57.895 0.00 0.00 44.05 2.17
2690 5830 3.055719 CGGTGCGTTGGGCTGATT 61.056 61.111 0.00 0.00 44.05 2.57
2691 5831 4.015406 TCGGTGCGTTGGGCTGAT 62.015 61.111 0.00 0.00 44.05 2.90
2692 5832 4.980805 GTCGGTGCGTTGGGCTGA 62.981 66.667 0.00 0.00 44.05 4.26
2695 5835 3.887335 TTAGGTCGGTGCGTTGGGC 62.887 63.158 0.00 0.00 43.96 5.36
2696 5836 1.301874 TTTAGGTCGGTGCGTTGGG 60.302 57.895 0.00 0.00 0.00 4.12
2697 5837 1.864176 GTTTAGGTCGGTGCGTTGG 59.136 57.895 0.00 0.00 0.00 3.77
2698 5838 1.489824 CGTTTAGGTCGGTGCGTTG 59.510 57.895 0.00 0.00 0.00 4.10
2699 5839 1.665599 CCGTTTAGGTCGGTGCGTT 60.666 57.895 0.00 0.00 42.62 4.84
2700 5840 2.048877 CCGTTTAGGTCGGTGCGT 60.049 61.111 0.00 0.00 42.62 5.24
2701 5841 2.090524 GTCCGTTTAGGTCGGTGCG 61.091 63.158 4.36 0.00 46.86 5.34
2702 5842 2.090524 CGTCCGTTTAGGTCGGTGC 61.091 63.158 4.36 0.00 45.53 5.01
2703 5843 4.157817 CGTCCGTTTAGGTCGGTG 57.842 61.111 4.36 0.00 45.53 4.94
2707 5847 1.339946 GACGCACGTCCGTTTAGGTC 61.340 60.000 5.75 0.00 42.24 3.85
2708 5848 1.372128 GACGCACGTCCGTTTAGGT 60.372 57.895 5.75 0.00 42.24 3.08
2709 5849 3.455685 GACGCACGTCCGTTTAGG 58.544 61.111 5.75 0.00 42.24 2.69
2717 5857 4.117372 CGAAAGCGGACGCACGTC 62.117 66.667 19.48 14.58 44.88 4.34
2718 5858 4.936823 ACGAAAGCGGACGCACGT 62.937 61.111 19.48 21.14 44.88 4.49
2719 5859 4.117372 GACGAAAGCGGACGCACG 62.117 66.667 19.48 20.56 44.88 5.34
2720 5860 3.774702 GGACGAAAGCGGACGCAC 61.775 66.667 19.48 8.69 44.88 5.34
2721 5861 3.909258 GAGGACGAAAGCGGACGCA 62.909 63.158 19.48 0.00 44.88 5.24
2722 5862 3.179939 GAGGACGAAAGCGGACGC 61.180 66.667 8.91 8.91 43.17 5.19
2723 5863 2.506438 GGAGGACGAAAGCGGACG 60.506 66.667 0.00 0.00 43.17 4.79
2724 5864 1.446272 CAGGAGGACGAAAGCGGAC 60.446 63.158 0.00 0.00 43.17 4.79
2725 5865 2.970639 CAGGAGGACGAAAGCGGA 59.029 61.111 0.00 0.00 43.17 5.54
2726 5866 2.815647 GCAGGAGGACGAAAGCGG 60.816 66.667 0.00 0.00 43.17 5.52
2727 5867 2.815647 GGCAGGAGGACGAAAGCG 60.816 66.667 0.00 0.00 44.79 4.68
2734 5874 0.744771 GAATTGGTCGGCAGGAGGAC 60.745 60.000 0.00 0.00 0.00 3.85
2735 5875 0.909610 AGAATTGGTCGGCAGGAGGA 60.910 55.000 0.00 0.00 0.00 3.71
2736 5876 0.462759 GAGAATTGGTCGGCAGGAGG 60.463 60.000 0.00 0.00 0.00 4.30
2737 5877 0.807667 CGAGAATTGGTCGGCAGGAG 60.808 60.000 0.00 0.00 33.66 3.69
2738 5878 1.218047 CGAGAATTGGTCGGCAGGA 59.782 57.895 0.00 0.00 33.66 3.86
2739 5879 1.084370 GTCGAGAATTGGTCGGCAGG 61.084 60.000 6.54 0.00 41.70 4.85
2740 5880 1.084370 GGTCGAGAATTGGTCGGCAG 61.084 60.000 12.15 0.00 43.90 4.85
2741 5881 1.079405 GGTCGAGAATTGGTCGGCA 60.079 57.895 12.15 0.00 43.90 5.69
2742 5882 1.814169 GGGTCGAGAATTGGTCGGC 60.814 63.158 6.90 5.17 41.36 5.54
2743 5883 0.178068 ATGGGTCGAGAATTGGTCGG 59.822 55.000 6.90 0.00 38.02 4.79
2744 5884 2.024176 AATGGGTCGAGAATTGGTCG 57.976 50.000 0.00 1.15 38.84 4.79
2745 5885 4.217550 TCAAAAATGGGTCGAGAATTGGTC 59.782 41.667 0.00 0.00 0.00 4.02
2746 5886 4.148838 TCAAAAATGGGTCGAGAATTGGT 58.851 39.130 0.00 0.00 0.00 3.67
2747 5887 4.737054 CTCAAAAATGGGTCGAGAATTGG 58.263 43.478 0.00 0.00 0.00 3.16
2748 5888 4.168760 GCTCAAAAATGGGTCGAGAATTG 58.831 43.478 0.00 0.00 0.00 2.32
2749 5889 3.193479 GGCTCAAAAATGGGTCGAGAATT 59.807 43.478 0.00 0.00 0.00 2.17
2750 5890 2.755103 GGCTCAAAAATGGGTCGAGAAT 59.245 45.455 0.00 0.00 0.00 2.40
2751 5891 2.159382 GGCTCAAAAATGGGTCGAGAA 58.841 47.619 0.00 0.00 0.00 2.87
2752 5892 1.821216 GGCTCAAAAATGGGTCGAGA 58.179 50.000 0.00 0.00 0.00 4.04
2753 5893 0.447801 CGGCTCAAAAATGGGTCGAG 59.552 55.000 0.00 0.00 0.00 4.04
2754 5894 0.958382 CCGGCTCAAAAATGGGTCGA 60.958 55.000 3.99 0.00 0.00 4.20
2755 5895 0.958382 TCCGGCTCAAAAATGGGTCG 60.958 55.000 0.00 0.00 0.00 4.79
2756 5896 1.474330 ATCCGGCTCAAAAATGGGTC 58.526 50.000 0.00 0.00 0.00 4.46
2757 5897 1.937191 AATCCGGCTCAAAAATGGGT 58.063 45.000 0.00 0.00 0.00 4.51
2758 5898 2.620242 CAAATCCGGCTCAAAAATGGG 58.380 47.619 0.00 0.00 0.00 4.00
2759 5899 2.001872 GCAAATCCGGCTCAAAAATGG 58.998 47.619 0.00 0.00 0.00 3.16
2760 5900 1.655099 CGCAAATCCGGCTCAAAAATG 59.345 47.619 0.00 0.00 0.00 2.32
2761 5901 1.272212 ACGCAAATCCGGCTCAAAAAT 59.728 42.857 0.00 0.00 0.00 1.82
2762 5902 0.671251 ACGCAAATCCGGCTCAAAAA 59.329 45.000 0.00 0.00 0.00 1.94
2763 5903 0.239879 GACGCAAATCCGGCTCAAAA 59.760 50.000 0.00 0.00 32.31 2.44
2764 5904 1.873165 GACGCAAATCCGGCTCAAA 59.127 52.632 0.00 0.00 32.31 2.69
2765 5905 2.387445 CGACGCAAATCCGGCTCAA 61.387 57.895 0.00 0.00 33.03 3.02
2766 5906 2.813474 CGACGCAAATCCGGCTCA 60.813 61.111 0.00 0.00 33.03 4.26
2767 5907 3.564027 CCGACGCAAATCCGGCTC 61.564 66.667 0.00 0.00 36.62 4.70
2779 5919 1.226575 TCTTGTATCTGCGCCGACG 60.227 57.895 4.18 0.00 44.07 5.12
2780 5920 0.457853 TGTCTTGTATCTGCGCCGAC 60.458 55.000 4.18 0.00 0.00 4.79
2781 5921 0.179137 CTGTCTTGTATCTGCGCCGA 60.179 55.000 4.18 3.73 0.00 5.54
2782 5922 0.179137 TCTGTCTTGTATCTGCGCCG 60.179 55.000 4.18 0.00 0.00 6.46
2783 5923 1.281899 GTCTGTCTTGTATCTGCGCC 58.718 55.000 4.18 0.00 0.00 6.53
2784 5924 0.917259 CGTCTGTCTTGTATCTGCGC 59.083 55.000 0.00 0.00 0.00 6.09


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

AutoCloner maintained by Alex Coulton.