Multiple sequence alignment - TraesCS2B01G505100

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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 TraesCS2B01G505100 chr2B 100.000 3168 0 0 1 3168 699180314 699177147 0.000000e+00 5851.0
1 TraesCS2B01G505100 chr2B 87.037 216 20 3 4 218 68426263 68426471 1.470000e-58 237.0
2 TraesCS2B01G505100 chr2B 91.358 162 10 3 2617 2777 783655590 783655432 5.320000e-53 219.0
3 TraesCS2B01G505100 chr2B 96.610 59 1 1 3111 3168 441871505 441871563 2.600000e-16 97.1
4 TraesCS2B01G505100 chr2A 87.965 1130 74 31 1368 2478 718130112 718129026 0.000000e+00 1277.0
5 TraesCS2B01G505100 chr2A 87.435 581 44 16 747 1311 718130673 718130106 2.660000e-180 641.0
6 TraesCS2B01G505100 chr2A 82.435 575 47 31 2557 3113 718128987 718128449 1.340000e-123 453.0
7 TraesCS2B01G505100 chr2A 94.964 139 7 0 2651 2789 738175101 738174963 5.320000e-53 219.0
8 TraesCS2B01G505100 chr4A 92.472 704 50 2 1 701 667005409 667004706 0.000000e+00 1003.0
9 TraesCS2B01G505100 chr4A 91.447 152 10 3 2628 2778 236160648 236160499 4.140000e-49 206.0
10 TraesCS2B01G505100 chr4A 90.278 72 6 1 291 361 450765082 450765153 3.360000e-15 93.5
11 TraesCS2B01G505100 chr4A 93.548 62 2 2 3107 3168 606217001 606217060 1.210000e-14 91.6
12 TraesCS2B01G505100 chr3A 92.199 705 49 3 1 700 625330875 625330172 0.000000e+00 992.0
13 TraesCS2B01G505100 chr3A 87.097 124 12 3 388 511 391890585 391890704 1.530000e-28 137.0
14 TraesCS2B01G505100 chr1B 89.174 702 70 4 4 701 680318190 680318889 0.000000e+00 870.0
15 TraesCS2B01G505100 chr1B 90.095 525 43 6 187 704 666607048 666606526 0.000000e+00 673.0
16 TraesCS2B01G505100 chr1B 94.964 139 7 0 2639 2777 277456287 277456425 5.320000e-53 219.0
17 TraesCS2B01G505100 chr1B 93.706 143 7 2 2636 2778 626226866 626227006 2.480000e-51 213.0
18 TraesCS2B01G505100 chr7A 88.445 701 73 7 4 701 602227485 602226790 0.000000e+00 839.0
19 TraesCS2B01G505100 chr2D 91.923 520 22 5 1972 2486 580240542 580240038 0.000000e+00 710.0
20 TraesCS2B01G505100 chr2D 87.780 581 35 9 776 1353 580241722 580241175 0.000000e+00 647.0
21 TraesCS2B01G505100 chr2D 91.556 450 22 5 1371 1810 580240994 580240551 9.720000e-170 606.0
22 TraesCS2B01G505100 chr2D 83.526 346 38 15 2779 3113 580239794 580239457 3.970000e-79 305.0
23 TraesCS2B01G505100 chr2D 87.719 171 12 2 2483 2652 580239958 580239796 1.160000e-44 191.0
24 TraesCS2B01G505100 chr2D 92.857 70 4 1 2547 2616 72150591 72150523 2.010000e-17 100.0
25 TraesCS2B01G505100 chrUn 93.333 300 20 0 4 303 109010955 109010656 8.060000e-121 444.0
26 TraesCS2B01G505100 chrUn 92.727 55 1 1 2542 2596 87098453 87098402 3.390000e-10 76.8
27 TraesCS2B01G505100 chr1D 92.256 297 23 0 4 300 375969861 375970157 3.780000e-114 422.0
28 TraesCS2B01G505100 chr4B 90.236 297 26 2 4 300 664779332 664779625 4.960000e-103 385.0
29 TraesCS2B01G505100 chr4B 90.278 72 6 1 291 361 182260491 182260562 3.360000e-15 93.5
30 TraesCS2B01G505100 chr5A 90.941 287 21 4 3 288 704520629 704520911 6.410000e-102 381.0
31 TraesCS2B01G505100 chr5A 91.892 74 5 1 435 507 597758486 597758413 5.590000e-18 102.0
32 TraesCS2B01G505100 chr5A 96.429 56 2 0 3113 3168 188995551 188995606 3.360000e-15 93.5
33 TraesCS2B01G505100 chr5A 93.333 60 2 2 449 507 22235045 22234987 1.570000e-13 87.9
34 TraesCS2B01G505100 chr5A 92.727 55 1 1 2542 2596 422246763 422246712 3.390000e-10 76.8
35 TraesCS2B01G505100 chr7D 92.513 187 14 0 516 702 403146722 403146908 5.210000e-68 268.0
36 TraesCS2B01G505100 chr6D 91.579 190 15 1 516 705 29986139 29986327 8.720000e-66 261.0
37 TraesCS2B01G505100 chr1A 90.674 193 16 2 514 706 465955757 465955567 4.060000e-64 255.0
38 TraesCS2B01G505100 chr6A 89.529 191 16 3 516 706 429116637 429116451 4.080000e-59 239.0
39 TraesCS2B01G505100 chr6A 91.870 123 8 2 388 509 7127249 7127128 1.510000e-38 171.0
40 TraesCS2B01G505100 chr6A 86.364 110 10 3 2542 2649 584480015 584480121 7.180000e-22 115.0
41 TraesCS2B01G505100 chr6A 96.364 55 2 0 3114 3168 144258056 144258002 1.210000e-14 91.6
42 TraesCS2B01G505100 chr7B 96.947 131 4 0 2651 2781 182718803 182718933 1.480000e-53 220.0
43 TraesCS2B01G505100 chr7B 94.326 141 8 0 2641 2781 616550737 616550597 1.910000e-52 217.0
44 TraesCS2B01G505100 chr7B 100.000 55 0 0 3114 3168 110111894 110111840 5.590000e-18 102.0
45 TraesCS2B01G505100 chr7B 98.000 50 1 0 3119 3168 713593966 713593917 1.570000e-13 87.9
46 TraesCS2B01G505100 chr5B 95.652 138 4 2 2642 2778 538274848 538274712 1.480000e-53 220.0
47 TraesCS2B01G505100 chr5B 96.552 58 2 0 3111 3168 360417726 360417783 2.600000e-16 97.1
48 TraesCS2B01G505100 chr5B 98.148 54 1 0 3115 3168 44469654 44469601 9.350000e-16 95.3
49 TraesCS2B01G505100 chr5D 93.151 146 7 3 2642 2786 78807282 78807139 8.900000e-51 211.0
50 TraesCS2B01G505100 chr3B 98.182 55 1 0 3114 3168 819310306 819310252 2.600000e-16 97.1
51 TraesCS2B01G505100 chr3B 92.727 55 1 1 2542 2596 597106110 597106059 3.390000e-10 76.8
52 TraesCS2B01G505100 chr4D 90.278 72 6 1 291 361 119805788 119805859 3.360000e-15 93.5
53 TraesCS2B01G505100 chr3D 92.727 55 1 1 2542 2596 492105696 492105645 3.390000e-10 76.8
54 TraesCS2B01G505100 chr3D 92.727 55 1 1 2542 2596 560270470 560270521 3.390000e-10 76.8


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 TraesCS2B01G505100 chr2B 699177147 699180314 3167 True 5851.000000 5851 100.0000 1 3168 1 chr2B.!!$R1 3167
1 TraesCS2B01G505100 chr2A 718128449 718130673 2224 True 790.333333 1277 85.9450 747 3113 3 chr2A.!!$R2 2366
2 TraesCS2B01G505100 chr4A 667004706 667005409 703 True 1003.000000 1003 92.4720 1 701 1 chr4A.!!$R2 700
3 TraesCS2B01G505100 chr3A 625330172 625330875 703 True 992.000000 992 92.1990 1 700 1 chr3A.!!$R1 699
4 TraesCS2B01G505100 chr1B 680318190 680318889 699 False 870.000000 870 89.1740 4 701 1 chr1B.!!$F3 697
5 TraesCS2B01G505100 chr1B 666606526 666607048 522 True 673.000000 673 90.0950 187 704 1 chr1B.!!$R1 517
6 TraesCS2B01G505100 chr7A 602226790 602227485 695 True 839.000000 839 88.4450 4 701 1 chr7A.!!$R1 697
7 TraesCS2B01G505100 chr2D 580239457 580241722 2265 True 491.800000 710 88.5008 776 3113 5 chr2D.!!$R2 2337

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
718 727 0.729116 CGCTGCAACTAGGTCATTGG 59.271 55.0 0.0 0.0 0.0 3.16 F
1168 1192 0.254462 CTTCTTCTTCCCCCAGCTCC 59.746 60.0 0.0 0.0 0.0 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1932 2153 0.822164 GTCTCCGCTTAACTAGGCCA 59.178 55.0 5.01 0.0 0.0 5.36 R
2846 3184 0.329261 TCAGATGCACCTCCCCAAAG 59.671 55.0 0.00 0.0 0.0 2.77 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
36 37 1.381599 CTGGAGGAGGAGCTGAGCT 60.382 63.158 6.69 6.69 43.88 4.09
82 83 1.992277 AGGCAAGAGCGAGGGACAT 60.992 57.895 0.00 0.00 43.41 3.06
108 109 2.485038 GAGGAGAAGAAGAAGACGACGT 59.515 50.000 0.00 0.00 0.00 4.34
380 383 1.078848 GCATCACTGGAAGGTCGCT 60.079 57.895 0.00 0.00 39.30 4.93
402 405 3.129502 CACCGTCATGGCCAGCAG 61.130 66.667 13.05 3.61 43.94 4.24
563 572 9.445786 ACTTGTCATAAACGTGTTTAAATCTTG 57.554 29.630 9.06 3.64 38.38 3.02
701 710 6.798476 GTGGTAGTTTTTGGTTAAATACTCGC 59.202 38.462 0.00 0.00 38.47 5.03
702 711 6.711645 TGGTAGTTTTTGGTTAAATACTCGCT 59.288 34.615 0.00 0.00 38.47 4.93
703 712 7.019418 GGTAGTTTTTGGTTAAATACTCGCTG 58.981 38.462 0.00 0.00 38.47 5.18
704 713 5.458015 AGTTTTTGGTTAAATACTCGCTGC 58.542 37.500 0.00 0.00 34.37 5.25
705 714 5.009210 AGTTTTTGGTTAAATACTCGCTGCA 59.991 36.000 0.00 0.00 34.37 4.41
706 715 5.440234 TTTTGGTTAAATACTCGCTGCAA 57.560 34.783 0.00 0.00 0.00 4.08
707 716 4.413495 TTGGTTAAATACTCGCTGCAAC 57.587 40.909 0.00 0.00 0.00 4.17
708 717 3.670625 TGGTTAAATACTCGCTGCAACT 58.329 40.909 0.00 0.00 0.00 3.16
709 718 4.823157 TGGTTAAATACTCGCTGCAACTA 58.177 39.130 0.00 0.00 0.00 2.24
710 719 4.868171 TGGTTAAATACTCGCTGCAACTAG 59.132 41.667 0.00 0.00 0.00 2.57
711 720 4.270325 GGTTAAATACTCGCTGCAACTAGG 59.730 45.833 0.00 0.00 0.00 3.02
712 721 3.611766 AAATACTCGCTGCAACTAGGT 57.388 42.857 0.00 0.00 0.00 3.08
713 722 2.873133 ATACTCGCTGCAACTAGGTC 57.127 50.000 0.00 0.00 0.00 3.85
714 723 1.541379 TACTCGCTGCAACTAGGTCA 58.459 50.000 0.00 0.00 0.00 4.02
715 724 0.898320 ACTCGCTGCAACTAGGTCAT 59.102 50.000 0.00 0.00 0.00 3.06
716 725 1.276421 ACTCGCTGCAACTAGGTCATT 59.724 47.619 0.00 0.00 0.00 2.57
717 726 1.662629 CTCGCTGCAACTAGGTCATTG 59.337 52.381 0.00 0.00 0.00 2.82
718 727 0.729116 CGCTGCAACTAGGTCATTGG 59.271 55.000 0.00 0.00 0.00 3.16
719 728 1.826385 GCTGCAACTAGGTCATTGGT 58.174 50.000 0.00 0.00 0.00 3.67
720 729 1.740025 GCTGCAACTAGGTCATTGGTC 59.260 52.381 0.00 0.00 0.00 4.02
721 730 2.616510 GCTGCAACTAGGTCATTGGTCT 60.617 50.000 0.00 0.00 0.00 3.85
722 731 3.369471 GCTGCAACTAGGTCATTGGTCTA 60.369 47.826 0.00 0.00 0.00 2.59
723 732 4.437239 CTGCAACTAGGTCATTGGTCTAG 58.563 47.826 0.00 10.53 37.20 2.43
724 733 3.838317 TGCAACTAGGTCATTGGTCTAGT 59.162 43.478 11.45 11.45 43.66 2.57
725 734 5.020795 TGCAACTAGGTCATTGGTCTAGTA 58.979 41.667 15.22 3.78 41.74 1.82
726 735 5.661312 TGCAACTAGGTCATTGGTCTAGTAT 59.339 40.000 15.22 7.56 41.74 2.12
727 736 6.837048 TGCAACTAGGTCATTGGTCTAGTATA 59.163 38.462 15.22 6.92 41.74 1.47
728 737 7.014326 TGCAACTAGGTCATTGGTCTAGTATAG 59.986 40.741 15.22 11.40 41.74 1.31
729 738 7.014422 GCAACTAGGTCATTGGTCTAGTATAGT 59.986 40.741 15.22 0.00 41.74 2.12
730 739 9.570468 CAACTAGGTCATTGGTCTAGTATAGTA 57.430 37.037 15.22 0.00 41.74 1.82
731 740 9.796180 AACTAGGTCATTGGTCTAGTATAGTAG 57.204 37.037 15.22 8.14 41.74 2.57
732 741 8.947305 ACTAGGTCATTGGTCTAGTATAGTAGT 58.053 37.037 13.22 0.00 41.06 2.73
735 744 8.947305 AGGTCATTGGTCTAGTATAGTAGTAGT 58.053 37.037 13.22 0.00 40.38 2.73
856 870 2.141517 GCTTATCTGATGTGAGCGCAT 58.858 47.619 11.47 0.00 0.00 4.73
891 906 2.158325 TGGATTGCCACTTCCTTCCTTT 60.158 45.455 0.00 0.00 39.92 3.11
942 957 3.416156 ACAGGCTGTGATTTCCTTCTTC 58.584 45.455 21.37 0.00 0.00 2.87
951 966 6.795399 TGTGATTTCCTTCTTCTTGTTGTTC 58.205 36.000 0.00 0.00 0.00 3.18
1127 1151 1.862806 GCACTGTGCGTCCTCTTTC 59.137 57.895 17.93 0.00 31.71 2.62
1128 1152 0.601311 GCACTGTGCGTCCTCTTTCT 60.601 55.000 17.93 0.00 31.71 2.52
1129 1153 1.871080 CACTGTGCGTCCTCTTTCTT 58.129 50.000 0.00 0.00 0.00 2.52
1131 1155 2.221981 CACTGTGCGTCCTCTTTCTTTC 59.778 50.000 0.00 0.00 0.00 2.62
1164 1188 2.238395 CCTCTTCTTCTTCTTCCCCCAG 59.762 54.545 0.00 0.00 0.00 4.45
1168 1192 0.254462 CTTCTTCTTCCCCCAGCTCC 59.746 60.000 0.00 0.00 0.00 4.70
1169 1193 1.208165 TTCTTCTTCCCCCAGCTCCC 61.208 60.000 0.00 0.00 0.00 4.30
1170 1194 2.614013 TTCTTCCCCCAGCTCCCC 60.614 66.667 0.00 0.00 0.00 4.81
1181 1212 1.688884 AGCTCCCCTCTTCTCCTGC 60.689 63.158 0.00 0.00 0.00 4.85
1196 1227 1.336440 TCCTGCCACAATTTCGTGTTG 59.664 47.619 0.00 0.00 34.98 3.33
1197 1228 1.336440 CCTGCCACAATTTCGTGTTGA 59.664 47.619 4.67 0.00 34.98 3.18
1198 1229 2.030007 CCTGCCACAATTTCGTGTTGAT 60.030 45.455 4.67 0.00 34.98 2.57
1199 1230 3.552684 CCTGCCACAATTTCGTGTTGATT 60.553 43.478 4.67 0.00 34.98 2.57
1200 1231 3.637432 TGCCACAATTTCGTGTTGATTC 58.363 40.909 4.67 0.00 34.98 2.52
1201 1232 3.317711 TGCCACAATTTCGTGTTGATTCT 59.682 39.130 4.67 0.00 34.98 2.40
1202 1233 3.914364 GCCACAATTTCGTGTTGATTCTC 59.086 43.478 4.67 0.00 34.98 2.87
1203 1234 4.320494 GCCACAATTTCGTGTTGATTCTCT 60.320 41.667 4.67 0.00 34.98 3.10
1204 1235 5.149273 CCACAATTTCGTGTTGATTCTCTG 58.851 41.667 4.67 0.00 34.98 3.35
1205 1236 5.277974 CCACAATTTCGTGTTGATTCTCTGT 60.278 40.000 4.67 0.00 34.98 3.41
1206 1237 6.201517 CACAATTTCGTGTTGATTCTCTGTT 58.798 36.000 4.67 0.00 32.00 3.16
1207 1238 6.358030 CACAATTTCGTGTTGATTCTCTGTTC 59.642 38.462 4.67 0.00 32.00 3.18
1248 1291 2.573340 GCCTTTTCATGCCGTGGG 59.427 61.111 0.00 0.00 0.00 4.61
1254 1297 1.773856 TTTCATGCCGTGGGTCCTCA 61.774 55.000 0.00 0.00 0.00 3.86
1272 1315 6.833933 GGTCCTCAAAATCCCACATTTATAGT 59.166 38.462 0.00 0.00 0.00 2.12
1284 1327 6.463049 CCCACATTTATAGTCGGAGATCTTGT 60.463 42.308 0.00 0.00 40.67 3.16
1303 1346 1.063027 GTGCCGTAATTAACCGCCTTC 59.937 52.381 0.00 0.00 32.06 3.46
1339 1382 4.412528 CCCCCTTATTAAGCAACTAGGAGT 59.587 45.833 0.00 0.00 0.00 3.85
1353 1396 6.932960 GCAACTAGGAGTAACTTTTTCCTGTA 59.067 38.462 2.63 0.00 41.33 2.74
1354 1397 7.443272 GCAACTAGGAGTAACTTTTTCCTGTAA 59.557 37.037 2.63 0.00 41.33 2.41
1355 1398 9.333724 CAACTAGGAGTAACTTTTTCCTGTAAA 57.666 33.333 2.63 0.00 41.33 2.01
1356 1399 8.899427 ACTAGGAGTAACTTTTTCCTGTAAAC 57.101 34.615 2.63 0.00 41.33 2.01
1357 1400 6.856135 AGGAGTAACTTTTTCCTGTAAACG 57.144 37.500 0.00 0.00 39.80 3.60
1358 1401 5.237996 AGGAGTAACTTTTTCCTGTAAACGC 59.762 40.000 0.00 0.00 39.80 4.84
1359 1402 5.007921 GGAGTAACTTTTTCCTGTAAACGCA 59.992 40.000 0.00 0.00 0.00 5.24
1360 1403 6.439675 AGTAACTTTTTCCTGTAAACGCAA 57.560 33.333 0.00 0.00 0.00 4.85
1361 1404 7.034685 AGTAACTTTTTCCTGTAAACGCAAT 57.965 32.000 0.00 0.00 0.00 3.56
1362 1405 7.485810 AGTAACTTTTTCCTGTAAACGCAATT 58.514 30.769 0.00 0.00 0.00 2.32
1363 1406 6.822073 AACTTTTTCCTGTAAACGCAATTC 57.178 33.333 0.00 0.00 0.00 2.17
1364 1407 5.897050 ACTTTTTCCTGTAAACGCAATTCA 58.103 33.333 0.00 0.00 0.00 2.57
1365 1408 6.512297 ACTTTTTCCTGTAAACGCAATTCAT 58.488 32.000 0.00 0.00 0.00 2.57
1366 1409 6.420604 ACTTTTTCCTGTAAACGCAATTCATG 59.579 34.615 0.00 0.00 0.00 3.07
1367 1410 4.433186 TTCCTGTAAACGCAATTCATGG 57.567 40.909 0.00 0.00 0.00 3.66
1392 1598 4.081420 GTGTTCCATCCTCTTCTTCTGCTA 60.081 45.833 0.00 0.00 0.00 3.49
1412 1618 4.938226 GCTACCTGCTTGTCTTTTACAGAT 59.062 41.667 0.00 0.00 39.87 2.90
1415 1621 7.926555 GCTACCTGCTTGTCTTTTACAGATATA 59.073 37.037 0.00 0.00 39.87 0.86
1480 1686 5.100751 GCATGTGCCTGATGATTACTTAC 57.899 43.478 0.00 0.00 34.31 2.34
1496 1708 4.408182 ACTTACTGTGTTTCAGAGTGCT 57.592 40.909 9.29 0.00 46.27 4.40
1536 1748 4.798882 TCAAGGGTGACTTTGGTTACATT 58.201 39.130 1.78 0.00 46.58 2.71
1537 1749 4.582656 TCAAGGGTGACTTTGGTTACATTG 59.417 41.667 1.78 0.00 46.58 2.82
1538 1750 4.447138 AGGGTGACTTTGGTTACATTGA 57.553 40.909 0.00 0.00 34.21 2.57
1539 1751 4.998051 AGGGTGACTTTGGTTACATTGAT 58.002 39.130 0.00 0.00 34.21 2.57
1547 1759 8.553153 TGACTTTGGTTACATTGATTATCCCTA 58.447 33.333 0.00 0.00 0.00 3.53
1580 1792 2.598394 GCTGCTCACTTTGGGGCA 60.598 61.111 0.00 0.00 0.00 5.36
1698 1910 2.681344 GTCCCGGTAACCAATCATTCAC 59.319 50.000 0.00 0.00 0.00 3.18
1718 1934 3.071023 CACTCCCCTAATTATTCTCGCCA 59.929 47.826 0.00 0.00 0.00 5.69
1740 1956 7.985634 CCACATGGCTTGTTATTGTTTATAC 57.014 36.000 2.88 0.00 36.00 1.47
1749 1965 8.575454 GCTTGTTATTGTTTATACGCTTCAAAG 58.425 33.333 0.00 0.00 0.00 2.77
1800 2016 8.600449 ATTTAGACTCAACTTTCTTCAGACTG 57.400 34.615 0.00 0.00 0.00 3.51
1849 2069 6.989437 TCAAATGATAAATTGACTCGACGTC 58.011 36.000 5.18 5.18 43.14 4.34
1891 2112 1.825090 TGGCATGCTCGTTTCTCAAT 58.175 45.000 18.92 0.00 0.00 2.57
1905 2126 9.543018 CTCGTTTCTCAATAAACAAGAATTACC 57.457 33.333 0.00 0.00 38.93 2.85
1908 2129 9.974980 GTTTCTCAATAAACAAGAATTACCCAA 57.025 29.630 0.00 0.00 38.85 4.12
1920 2141 8.576442 ACAAGAATTACCCAAGTTTGTAATCTG 58.424 33.333 7.62 8.11 36.82 2.90
1925 2146 7.739498 TTACCCAAGTTTGTAATCTGTTCTC 57.261 36.000 0.00 0.00 0.00 2.87
1932 2153 7.807977 AGTTTGTAATCTGTTCTCAACATGT 57.192 32.000 0.00 0.00 41.26 3.21
1946 2167 2.024176 ACATGTGGCCTAGTTAAGCG 57.976 50.000 3.32 0.00 0.00 4.68
1947 2168 1.299541 CATGTGGCCTAGTTAAGCGG 58.700 55.000 3.32 0.00 0.00 5.52
1971 2192 8.415192 GGAGACGTAATGATATGTTTTGTACA 57.585 34.615 0.00 0.00 41.97 2.90
2000 2221 1.071471 CAGGGCGTGTCTTCCAAGT 59.929 57.895 0.00 0.00 0.00 3.16
2138 2359 3.978723 CTCGGCTCTGCTGTCACCG 62.979 68.421 12.76 12.76 45.15 4.94
2177 2399 5.060940 GTCATCGAAAAATAGCTGTTTTGCC 59.939 40.000 20.19 14.19 32.02 4.52
2191 2413 4.637276 TGTTTTGCCGTCTCTGAATCTTA 58.363 39.130 0.00 0.00 0.00 2.10
2217 2439 2.966309 GCTGTTCGCTTGGTTCCGG 61.966 63.158 0.00 0.00 35.14 5.14
2218 2440 1.597027 CTGTTCGCTTGGTTCCGGT 60.597 57.895 0.00 0.00 0.00 5.28
2219 2441 1.841663 CTGTTCGCTTGGTTCCGGTG 61.842 60.000 0.00 0.00 0.00 4.94
2220 2442 1.890510 GTTCGCTTGGTTCCGGTGT 60.891 57.895 0.00 0.00 0.00 4.16
2221 2443 1.890041 TTCGCTTGGTTCCGGTGTG 60.890 57.895 0.00 0.00 0.00 3.82
2222 2444 2.590575 CGCTTGGTTCCGGTGTGT 60.591 61.111 0.00 0.00 0.00 3.72
2253 2475 3.738282 GTGTGTGTGTGACTCTGAATCTC 59.262 47.826 0.00 0.00 0.00 2.75
2364 2590 7.588854 GTCGATTAGTATATGCGTGTGTTCTTA 59.411 37.037 0.00 0.00 0.00 2.10
2376 2602 4.627058 GTGTGTTCTTATTTTGGGGTTGG 58.373 43.478 0.00 0.00 0.00 3.77
2380 2606 6.070194 TGTGTTCTTATTTTGGGGTTGGAAAA 60.070 34.615 0.00 0.00 0.00 2.29
2396 2622 6.239176 GGTTGGAAAAATGATGGTTCAGTGTA 60.239 38.462 0.00 0.00 34.73 2.90
2413 2639 2.350498 GTGTAACTGTTCGCACACTTGT 59.650 45.455 14.65 0.00 38.56 3.16
2456 2684 3.995526 CTGTCTGACAGGTGCTTGA 57.004 52.632 26.36 0.00 42.35 3.02
2471 2699 2.040813 TGCTTGATCTTCTTTGCTCCCT 59.959 45.455 0.00 0.00 0.00 4.20
2472 2700 3.087781 GCTTGATCTTCTTTGCTCCCTT 58.912 45.455 0.00 0.00 0.00 3.95
2473 2701 3.119566 GCTTGATCTTCTTTGCTCCCTTG 60.120 47.826 0.00 0.00 0.00 3.61
2474 2702 3.795688 TGATCTTCTTTGCTCCCTTGT 57.204 42.857 0.00 0.00 0.00 3.16
2475 2703 4.104383 TGATCTTCTTTGCTCCCTTGTT 57.896 40.909 0.00 0.00 0.00 2.83
2476 2704 5.241403 TGATCTTCTTTGCTCCCTTGTTA 57.759 39.130 0.00 0.00 0.00 2.41
2477 2705 5.003804 TGATCTTCTTTGCTCCCTTGTTAC 58.996 41.667 0.00 0.00 0.00 2.50
2478 2706 4.431416 TCTTCTTTGCTCCCTTGTTACA 57.569 40.909 0.00 0.00 0.00 2.41
2479 2707 4.985538 TCTTCTTTGCTCCCTTGTTACAT 58.014 39.130 0.00 0.00 0.00 2.29
2483 2711 6.121776 TCTTTGCTCCCTTGTTACATCTTA 57.878 37.500 0.00 0.00 0.00 2.10
2484 2712 5.938125 TCTTTGCTCCCTTGTTACATCTTAC 59.062 40.000 0.00 0.00 0.00 2.34
2528 2849 5.497474 TCTCTGGGTTGAACTAATAAAGGC 58.503 41.667 0.00 0.00 0.00 4.35
2531 2852 2.686405 GGGTTGAACTAATAAAGGCGGG 59.314 50.000 0.00 0.00 0.00 6.13
2532 2853 2.686405 GGTTGAACTAATAAAGGCGGGG 59.314 50.000 0.00 0.00 0.00 5.73
2542 2864 1.241315 AAAGGCGGGGAAACGATGTG 61.241 55.000 0.00 0.00 35.47 3.21
2552 2874 3.265791 GGAAACGATGTGATCTCTGCTT 58.734 45.455 0.00 0.00 0.00 3.91
2662 2984 1.760192 TGTTAGCTACTCCCTCCGTC 58.240 55.000 0.00 0.00 0.00 4.79
2663 2985 1.031235 GTTAGCTACTCCCTCCGTCC 58.969 60.000 0.00 0.00 0.00 4.79
2664 2986 0.465097 TTAGCTACTCCCTCCGTCCG 60.465 60.000 0.00 0.00 0.00 4.79
2668 2990 0.682209 CTACTCCCTCCGTCCGGAAA 60.682 60.000 5.23 0.00 44.66 3.13
2675 2997 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
2678 3000 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
2679 3001 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
2680 3002 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
2681 3003 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
2682 3004 4.390603 CGTCCGGAAATACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
2685 3007 7.201574 CGTCCGGAAATACTTGTCATCAAAATA 60.202 37.037 5.23 0.00 32.87 1.40
2686 3008 8.455682 GTCCGGAAATACTTGTCATCAAAATAA 58.544 33.333 5.23 0.00 32.87 1.40
2687 3009 9.015367 TCCGGAAATACTTGTCATCAAAATAAA 57.985 29.630 0.00 0.00 32.87 1.40
2688 3010 9.801873 CCGGAAATACTTGTCATCAAAATAAAT 57.198 29.630 0.00 0.00 32.87 1.40
2764 3086 7.312154 TCCATTTTGATGACAACTATTTTCGG 58.688 34.615 0.00 0.00 35.63 4.30
2777 3099 0.890683 TTTTCGGACGGAGGGAGTAC 59.109 55.000 0.00 0.00 0.00 2.73
2781 3103 2.413142 GGACGGAGGGAGTACGTGG 61.413 68.421 0.00 0.00 41.40 4.94
2782 3104 2.362120 ACGGAGGGAGTACGTGGG 60.362 66.667 0.00 0.00 39.64 4.61
2783 3105 2.362120 CGGAGGGAGTACGTGGGT 60.362 66.667 0.00 0.00 0.00 4.51
2784 3106 2.707849 CGGAGGGAGTACGTGGGTG 61.708 68.421 0.00 0.00 0.00 4.61
2785 3107 2.356780 GGAGGGAGTACGTGGGTGG 61.357 68.421 0.00 0.00 0.00 4.61
2786 3108 1.304713 GAGGGAGTACGTGGGTGGA 60.305 63.158 0.00 0.00 0.00 4.02
2788 3110 0.632835 AGGGAGTACGTGGGTGGATA 59.367 55.000 0.00 0.00 0.00 2.59
2846 3184 6.971184 CAGGTGCATCTGAATCAGTATTTTTC 59.029 38.462 23.04 0.00 36.93 2.29
2849 3187 8.031277 GGTGCATCTGAATCAGTATTTTTCTTT 58.969 33.333 10.36 0.00 32.61 2.52
2852 3190 7.490402 GCATCTGAATCAGTATTTTTCTTTGGG 59.510 37.037 10.36 0.00 32.61 4.12
2853 3191 7.466746 TCTGAATCAGTATTTTTCTTTGGGG 57.533 36.000 10.36 0.00 32.61 4.96
2854 3192 7.237982 TCTGAATCAGTATTTTTCTTTGGGGA 58.762 34.615 10.36 0.00 32.61 4.81
2921 3263 4.270808 CCTTGGAATGAACAAAACTGCAAC 59.729 41.667 0.00 0.00 0.00 4.17
2925 3267 3.733443 ATGAACAAAACTGCAACCCTC 57.267 42.857 0.00 0.00 0.00 4.30
2969 3323 1.118838 CCAGATCTCCAGACCAGACC 58.881 60.000 0.00 0.00 0.00 3.85
3015 3369 3.833304 GCAGCCTGCAGATTACCC 58.167 61.111 17.39 0.00 44.26 3.69
3016 3370 1.225704 GCAGCCTGCAGATTACCCT 59.774 57.895 17.39 0.00 44.26 4.34
3017 3371 0.469917 GCAGCCTGCAGATTACCCTA 59.530 55.000 17.39 0.00 44.26 3.53
3018 3372 1.542108 GCAGCCTGCAGATTACCCTAG 60.542 57.143 17.39 0.00 44.26 3.02
3019 3373 1.765314 CAGCCTGCAGATTACCCTAGT 59.235 52.381 17.39 0.00 0.00 2.57
3020 3374 2.965831 CAGCCTGCAGATTACCCTAGTA 59.034 50.000 17.39 0.00 0.00 1.82
3021 3375 2.966516 AGCCTGCAGATTACCCTAGTAC 59.033 50.000 17.39 0.00 0.00 2.73
3039 3396 6.602009 CCTAGTACCATCCAAAGTAAAAAGGG 59.398 42.308 0.00 0.00 0.00 3.95
3040 3397 4.770531 AGTACCATCCAAAGTAAAAAGGGC 59.229 41.667 0.00 0.00 0.00 5.19
3041 3398 2.903784 ACCATCCAAAGTAAAAAGGGCC 59.096 45.455 0.00 0.00 0.00 5.80
3043 3400 3.326297 CCATCCAAAGTAAAAAGGGCCAA 59.674 43.478 6.18 0.00 0.00 4.52
3044 3401 4.314961 CATCCAAAGTAAAAAGGGCCAAC 58.685 43.478 6.18 0.00 0.00 3.77
3078 3438 7.446625 CCAAAAGAGGATACATTATTGGAGAGG 59.553 40.741 0.00 0.00 38.64 3.69
3079 3439 7.937700 AAAGAGGATACATTATTGGAGAGGA 57.062 36.000 0.00 0.00 41.41 3.71
3080 3440 6.926630 AGAGGATACATTATTGGAGAGGAC 57.073 41.667 0.00 0.00 41.41 3.85
3085 3445 7.995488 AGGATACATTATTGGAGAGGACTTTTG 59.005 37.037 0.00 0.00 41.41 2.44
3113 3473 1.865865 GGTACACACCACACAGTGAG 58.134 55.000 7.81 0.00 45.04 3.51
3114 3474 1.540363 GGTACACACCACACAGTGAGG 60.540 57.143 15.03 15.03 45.04 3.86
3115 3475 1.411246 GTACACACCACACAGTGAGGA 59.589 52.381 22.65 0.00 40.34 3.71
3116 3476 0.178068 ACACACCACACAGTGAGGAC 59.822 55.000 22.65 0.00 40.34 3.85
3117 3477 0.177836 CACACCACACAGTGAGGACA 59.822 55.000 22.65 0.00 40.34 4.02
3118 3478 0.908910 ACACCACACAGTGAGGACAA 59.091 50.000 22.65 0.00 40.34 3.18
3119 3479 1.280710 ACACCACACAGTGAGGACAAA 59.719 47.619 22.65 0.00 40.34 2.83
3120 3480 2.290641 ACACCACACAGTGAGGACAAAA 60.291 45.455 22.65 0.00 40.34 2.44
3121 3481 2.951642 CACCACACAGTGAGGACAAAAT 59.048 45.455 22.65 0.00 40.34 1.82
3122 3482 3.003689 CACCACACAGTGAGGACAAAATC 59.996 47.826 22.65 0.00 40.34 2.17
3123 3483 3.213506 CCACACAGTGAGGACAAAATCA 58.786 45.455 11.47 0.00 35.23 2.57
3124 3484 3.003689 CCACACAGTGAGGACAAAATCAC 59.996 47.826 11.47 0.00 44.97 3.06
3133 3493 7.066374 GTGAGGACAAAATCACTATTCTGAC 57.934 40.000 0.00 0.00 42.06 3.51
3134 3494 6.092807 GTGAGGACAAAATCACTATTCTGACC 59.907 42.308 0.00 0.00 42.06 4.02
3135 3495 5.501156 AGGACAAAATCACTATTCTGACCC 58.499 41.667 0.00 0.00 0.00 4.46
3136 3496 5.251700 AGGACAAAATCACTATTCTGACCCT 59.748 40.000 0.00 0.00 0.00 4.34
3137 3497 5.946377 GGACAAAATCACTATTCTGACCCTT 59.054 40.000 0.00 0.00 0.00 3.95
3138 3498 6.434340 GGACAAAATCACTATTCTGACCCTTT 59.566 38.462 0.00 0.00 0.00 3.11
3139 3499 7.362142 GGACAAAATCACTATTCTGACCCTTTC 60.362 40.741 0.00 0.00 0.00 2.62
3140 3500 7.004086 ACAAAATCACTATTCTGACCCTTTCA 58.996 34.615 0.00 0.00 0.00 2.69
3141 3501 7.505585 ACAAAATCACTATTCTGACCCTTTCAA 59.494 33.333 0.00 0.00 32.21 2.69
3142 3502 7.454260 AAATCACTATTCTGACCCTTTCAAC 57.546 36.000 0.00 0.00 32.21 3.18
3143 3503 4.566004 TCACTATTCTGACCCTTTCAACG 58.434 43.478 0.00 0.00 32.21 4.10
3144 3504 4.282449 TCACTATTCTGACCCTTTCAACGA 59.718 41.667 0.00 0.00 32.21 3.85
3145 3505 4.994852 CACTATTCTGACCCTTTCAACGAA 59.005 41.667 0.00 0.00 32.21 3.85
3146 3506 4.995487 ACTATTCTGACCCTTTCAACGAAC 59.005 41.667 0.00 0.00 32.21 3.95
3147 3507 3.553828 TTCTGACCCTTTCAACGAACT 57.446 42.857 0.00 0.00 32.21 3.01
3148 3508 3.553828 TCTGACCCTTTCAACGAACTT 57.446 42.857 0.00 0.00 32.21 2.66
3149 3509 3.881220 TCTGACCCTTTCAACGAACTTT 58.119 40.909 0.00 0.00 32.21 2.66
3150 3510 3.625764 TCTGACCCTTTCAACGAACTTTG 59.374 43.478 0.00 0.00 32.21 2.77
3151 3511 3.349022 TGACCCTTTCAACGAACTTTGT 58.651 40.909 0.00 0.00 0.00 2.83
3152 3512 3.375922 TGACCCTTTCAACGAACTTTGTC 59.624 43.478 0.00 0.00 0.00 3.18
3153 3513 3.349022 ACCCTTTCAACGAACTTTGTCA 58.651 40.909 0.00 0.00 0.00 3.58
3154 3514 3.128068 ACCCTTTCAACGAACTTTGTCAC 59.872 43.478 0.00 0.00 0.00 3.67
3155 3515 3.127895 CCCTTTCAACGAACTTTGTCACA 59.872 43.478 0.00 0.00 0.00 3.58
3156 3516 4.380023 CCCTTTCAACGAACTTTGTCACAA 60.380 41.667 0.00 0.00 0.00 3.33
3157 3517 5.157781 CCTTTCAACGAACTTTGTCACAAA 58.842 37.500 2.24 2.24 0.00 2.83
3158 3518 5.631512 CCTTTCAACGAACTTTGTCACAAAA 59.368 36.000 4.13 0.00 0.00 2.44
3159 3519 6.310224 CCTTTCAACGAACTTTGTCACAAAAT 59.690 34.615 4.13 0.00 0.00 1.82
3160 3520 6.624710 TTCAACGAACTTTGTCACAAAATG 57.375 33.333 4.13 0.00 0.00 2.32
3161 3521 5.944013 TCAACGAACTTTGTCACAAAATGA 58.056 33.333 4.13 0.39 33.79 2.57
3162 3522 6.382608 TCAACGAACTTTGTCACAAAATGAA 58.617 32.000 4.13 0.00 39.72 2.57
3163 3523 6.306837 TCAACGAACTTTGTCACAAAATGAAC 59.693 34.615 4.13 0.00 39.72 3.18
3164 3524 5.949735 ACGAACTTTGTCACAAAATGAACT 58.050 33.333 4.13 0.00 39.72 3.01
3165 3525 6.027749 ACGAACTTTGTCACAAAATGAACTC 58.972 36.000 4.13 0.00 39.72 3.01
3166 3526 5.169561 CGAACTTTGTCACAAAATGAACTCG 59.830 40.000 4.13 0.00 39.72 4.18
3167 3527 5.811399 ACTTTGTCACAAAATGAACTCGA 57.189 34.783 4.13 0.00 39.72 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 2.680352 GAGCTCGGAGGTCACCCA 60.680 66.667 27.34 0.00 42.03 4.51
82 83 3.437395 CGTCTTCTTCTTCTCCTCTTCGA 59.563 47.826 0.00 0.00 0.00 3.71
108 109 0.246635 GCCTTGTCTAGCTGTTCGGA 59.753 55.000 0.00 0.00 0.00 4.55
165 166 2.182030 GACTTCCTCCTGCGTCGG 59.818 66.667 0.00 0.00 0.00 4.79
364 367 0.824759 GGTAGCGACCTTCCAGTGAT 59.175 55.000 9.01 0.00 43.16 3.06
380 383 2.178876 CTGGCCATGACGGTGTGGTA 62.179 60.000 5.51 1.51 37.81 3.25
402 405 4.148825 ACATCGGCGAGGAGTGGC 62.149 66.667 29.32 0.00 0.00 5.01
525 532 2.863484 ACAAGTGGGGCCCATCCA 60.863 61.111 31.48 10.09 35.28 3.41
588 597 2.579410 AACCCGTGGCAAGAAACTAT 57.421 45.000 0.76 0.00 0.00 2.12
633 642 7.612633 TCCAGAAACTACCACTTTACAAGTTTT 59.387 33.333 0.00 0.00 40.46 2.43
637 646 6.018180 GTGTCCAGAAACTACCACTTTACAAG 60.018 42.308 0.00 0.00 0.00 3.16
701 710 3.340814 AGACCAATGACCTAGTTGCAG 57.659 47.619 0.00 0.00 0.00 4.41
702 711 3.838317 ACTAGACCAATGACCTAGTTGCA 59.162 43.478 0.00 0.00 39.84 4.08
703 712 4.473477 ACTAGACCAATGACCTAGTTGC 57.527 45.455 0.00 0.00 39.84 4.17
704 713 8.466617 ACTATACTAGACCAATGACCTAGTTG 57.533 38.462 15.59 10.85 42.04 3.16
705 714 9.796180 CTACTATACTAGACCAATGACCTAGTT 57.204 37.037 15.59 9.18 42.04 2.24
706 715 8.947305 ACTACTATACTAGACCAATGACCTAGT 58.053 37.037 15.03 15.03 43.67 2.57
709 718 8.947305 ACTACTACTATACTAGACCAATGACCT 58.053 37.037 0.00 0.00 0.00 3.85
740 749 9.773328 GGTTCCGGTATTTATTTGTTTTACTAC 57.227 33.333 0.00 0.00 0.00 2.73
741 750 8.663911 CGGTTCCGGTATTTATTTGTTTTACTA 58.336 33.333 0.00 0.00 0.00 1.82
742 751 7.361971 CCGGTTCCGGTATTTATTTGTTTTACT 60.362 37.037 20.65 0.00 43.86 2.24
743 752 6.746822 CCGGTTCCGGTATTTATTTGTTTTAC 59.253 38.462 20.65 0.00 43.86 2.01
744 753 6.850555 CCGGTTCCGGTATTTATTTGTTTTA 58.149 36.000 20.65 0.00 43.86 1.52
745 754 5.712004 CCGGTTCCGGTATTTATTTGTTTT 58.288 37.500 20.65 0.00 43.86 2.43
808 817 2.807967 GCGCACAGGATTATATTCTGCA 59.192 45.455 0.30 0.00 32.19 4.41
856 870 1.884075 AATCCACTACGCGCTGGTGA 61.884 55.000 22.14 9.02 33.10 4.02
858 872 1.447838 CAATCCACTACGCGCTGGT 60.448 57.895 5.73 3.27 0.00 4.00
860 874 2.703409 GCAATCCACTACGCGCTG 59.297 61.111 5.73 0.62 0.00 5.18
861 875 2.511600 GGCAATCCACTACGCGCT 60.512 61.111 5.73 0.00 0.00 5.92
862 876 2.817834 TGGCAATCCACTACGCGC 60.818 61.111 5.73 0.00 37.47 6.86
942 957 3.108144 CGGCAACAAGAAGAACAACAAG 58.892 45.455 0.00 0.00 0.00 3.16
951 966 0.674895 CCTCCTCCGGCAACAAGAAG 60.675 60.000 0.00 0.00 0.00 2.85
1164 1188 2.741055 GGCAGGAGAAGAGGGGAGC 61.741 68.421 0.00 0.00 0.00 4.70
1168 1192 0.622665 ATTGTGGCAGGAGAAGAGGG 59.377 55.000 0.00 0.00 0.00 4.30
1169 1193 2.503895 AATTGTGGCAGGAGAAGAGG 57.496 50.000 0.00 0.00 0.00 3.69
1170 1194 2.417933 CGAAATTGTGGCAGGAGAAGAG 59.582 50.000 0.00 0.00 0.00 2.85
1181 1212 5.149273 CAGAGAATCAACACGAAATTGTGG 58.851 41.667 5.80 0.00 40.37 4.17
1196 1227 4.808364 CCTTGGAGAATCGAACAGAGAATC 59.192 45.833 0.00 0.00 34.37 2.52
1197 1228 4.764172 CCTTGGAGAATCGAACAGAGAAT 58.236 43.478 0.00 0.00 34.37 2.40
1198 1229 3.617531 GCCTTGGAGAATCGAACAGAGAA 60.618 47.826 0.00 0.00 34.37 2.87
1199 1230 2.093973 GCCTTGGAGAATCGAACAGAGA 60.094 50.000 0.00 0.00 34.37 3.10
1200 1231 2.275318 GCCTTGGAGAATCGAACAGAG 58.725 52.381 0.00 0.00 34.37 3.35
1201 1232 1.066143 GGCCTTGGAGAATCGAACAGA 60.066 52.381 0.00 0.00 34.37 3.41
1202 1233 1.373570 GGCCTTGGAGAATCGAACAG 58.626 55.000 0.00 0.00 34.37 3.16
1203 1234 0.391130 CGGCCTTGGAGAATCGAACA 60.391 55.000 0.00 0.00 34.37 3.18
1204 1235 1.090052 CCGGCCTTGGAGAATCGAAC 61.090 60.000 0.00 0.00 34.37 3.95
1205 1236 1.220749 CCGGCCTTGGAGAATCGAA 59.779 57.895 0.00 0.00 34.37 3.71
1206 1237 1.048724 ATCCGGCCTTGGAGAATCGA 61.049 55.000 0.00 0.00 42.45 3.59
1207 1238 0.179045 AATCCGGCCTTGGAGAATCG 60.179 55.000 0.00 0.00 42.45 3.34
1233 1276 0.609131 AGGACCCACGGCATGAAAAG 60.609 55.000 0.00 0.00 0.00 2.27
1248 1291 7.254795 CGACTATAAATGTGGGATTTTGAGGAC 60.255 40.741 0.00 0.00 0.00 3.85
1254 1297 6.895782 TCTCCGACTATAAATGTGGGATTTT 58.104 36.000 0.00 0.00 40.55 1.82
1272 1315 1.179152 TTACGGCACAAGATCTCCGA 58.821 50.000 23.17 7.76 44.23 4.55
1339 1382 7.481642 TGAATTGCGTTTACAGGAAAAAGTTA 58.518 30.769 0.00 0.00 0.00 2.24
1357 1400 0.243365 TGGAACACGCCATGAATTGC 59.757 50.000 0.00 0.00 31.66 3.56
1358 1401 2.945447 ATGGAACACGCCATGAATTG 57.055 45.000 0.00 0.00 46.62 2.32
1392 1598 7.620880 TGTATATCTGTAAAAGACAAGCAGGT 58.379 34.615 0.00 0.00 37.88 4.00
1412 1618 8.671384 AACAGTGCTACTTTGTTTTCTGTATA 57.329 30.769 0.00 0.00 34.50 1.47
1415 1621 5.897377 AACAGTGCTACTTTGTTTTCTGT 57.103 34.783 0.00 0.00 36.64 3.41
1423 1629 8.032952 TCTCATCAATTAACAGTGCTACTTTG 57.967 34.615 0.00 0.00 0.00 2.77
1427 1633 9.282247 CATTTTCTCATCAATTAACAGTGCTAC 57.718 33.333 0.00 0.00 0.00 3.58
1431 1637 8.592155 CATGCATTTTCTCATCAATTAACAGTG 58.408 33.333 0.00 0.00 0.00 3.66
1463 1669 5.420725 ACACAGTAAGTAATCATCAGGCA 57.579 39.130 0.00 0.00 0.00 4.75
1480 1686 4.361451 AAAACAGCACTCTGAAACACAG 57.639 40.909 0.00 0.00 46.97 3.66
1536 1748 5.109500 TGCACAACATGTAGGGATAATCA 57.891 39.130 0.00 0.00 0.00 2.57
1537 1749 5.679734 CTGCACAACATGTAGGGATAATC 57.320 43.478 0.00 0.00 37.38 1.75
1547 1759 3.343972 GCGACCTGCACAACATGT 58.656 55.556 0.00 0.00 45.45 3.21
1698 1910 3.071023 TGTGGCGAGAATAATTAGGGGAG 59.929 47.826 0.00 0.00 0.00 4.30
1718 1934 6.094881 AGCGTATAAACAATAACAAGCCATGT 59.905 34.615 0.00 0.00 46.82 3.21
1749 1965 4.142838 TGTTGTCGAAGAATGATGTGATGC 60.143 41.667 0.00 0.00 39.69 3.91
1800 2016 2.033372 GTAGGTAGCCCCTCTCTGTTC 58.967 57.143 0.00 0.00 44.81 3.18
1849 2069 9.674824 GCCATAATCTTTGAGATATTTGACAAG 57.325 33.333 0.00 0.00 32.89 3.16
1857 2077 6.315642 CGAGCATGCCATAATCTTTGAGATAT 59.684 38.462 15.66 0.00 32.89 1.63
1905 2126 7.026631 TGTTGAGAACAGATTACAAACTTGG 57.973 36.000 0.00 0.00 36.25 3.61
1908 2129 7.255242 CCACATGTTGAGAACAGATTACAAACT 60.255 37.037 0.00 0.00 45.95 2.66
1909 2130 6.857964 CCACATGTTGAGAACAGATTACAAAC 59.142 38.462 0.00 0.00 45.95 2.93
1916 2137 2.040813 AGGCCACATGTTGAGAACAGAT 59.959 45.455 5.01 0.00 45.95 2.90
1920 2141 3.059352 ACTAGGCCACATGTTGAGAAC 57.941 47.619 5.01 0.00 0.00 3.01
1925 2146 2.095853 CGCTTAACTAGGCCACATGTTG 59.904 50.000 5.01 0.00 0.00 3.33
1932 2153 0.822164 GTCTCCGCTTAACTAGGCCA 59.178 55.000 5.01 0.00 0.00 5.36
1946 2167 8.415192 TGTACAAAACATATCATTACGTCTCC 57.585 34.615 0.00 0.00 31.43 3.71
1966 2187 5.641636 CACGCCCTGCAAATATATATGTACA 59.358 40.000 0.00 0.00 0.00 2.90
1967 2188 5.642063 ACACGCCCTGCAAATATATATGTAC 59.358 40.000 0.00 0.00 0.00 2.90
1968 2189 5.800296 ACACGCCCTGCAAATATATATGTA 58.200 37.500 0.00 0.00 0.00 2.29
1969 2190 4.651778 ACACGCCCTGCAAATATATATGT 58.348 39.130 0.00 0.00 0.00 2.29
1970 2191 4.937620 AGACACGCCCTGCAAATATATATG 59.062 41.667 0.00 0.00 0.00 1.78
1971 2192 5.165961 AGACACGCCCTGCAAATATATAT 57.834 39.130 0.00 0.00 0.00 0.86
1979 2200 2.281484 GGAAGACACGCCCTGCAA 60.281 61.111 0.00 0.00 0.00 4.08
2000 2221 2.444696 CATGGCCTTCACCCCCAA 59.555 61.111 3.32 0.00 31.43 4.12
2138 2359 2.030363 CGATGACTATGTCAGGGAGAGC 60.030 54.545 6.55 0.00 46.04 4.09
2177 2399 4.532276 CACTCGGATAAGATTCAGAGACG 58.468 47.826 8.29 0.00 39.43 4.18
2217 2439 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2218 2440 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2219 2441 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2220 2442 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2221 2443 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2222 2444 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2328 2551 9.727403 CGCATATACTAATCGACAACAATTAAG 57.273 33.333 0.00 0.00 0.00 1.85
2349 2575 4.156922 CCCCAAAATAAGAACACACGCATA 59.843 41.667 0.00 0.00 0.00 3.14
2364 2590 5.163001 ACCATCATTTTTCCAACCCCAAAAT 60.163 36.000 0.00 0.00 31.62 1.82
2369 2595 3.326297 TGAACCATCATTTTTCCAACCCC 59.674 43.478 0.00 0.00 0.00 4.95
2396 2622 1.014352 GGACAAGTGTGCGAACAGTT 58.986 50.000 11.04 11.04 33.91 3.16
2413 2639 4.508492 CACACACACAACTGTATTAACGGA 59.492 41.667 0.00 0.00 35.79 4.69
2456 2684 4.985538 TGTAACAAGGGAGCAAAGAAGAT 58.014 39.130 0.00 0.00 0.00 2.40
2471 2699 9.586435 CATCTCACATGTAGTAAGATGTAACAA 57.414 33.333 20.67 0.00 37.50 2.83
2472 2700 8.966868 TCATCTCACATGTAGTAAGATGTAACA 58.033 33.333 24.29 12.63 42.43 2.41
2473 2701 9.457110 CTCATCTCACATGTAGTAAGATGTAAC 57.543 37.037 24.29 0.00 42.43 2.50
2474 2702 9.408648 TCTCATCTCACATGTAGTAAGATGTAA 57.591 33.333 24.29 16.85 42.43 2.41
2475 2703 8.980481 TCTCATCTCACATGTAGTAAGATGTA 57.020 34.615 24.29 17.07 42.43 2.29
2476 2704 7.888250 TCTCATCTCACATGTAGTAAGATGT 57.112 36.000 24.29 0.31 42.43 3.06
2477 2705 9.761504 AATTCTCATCTCACATGTAGTAAGATG 57.238 33.333 21.85 21.85 42.93 2.90
2501 2822 9.025041 CCTTTATTAGTTCAACCCAGAGAAAAT 57.975 33.333 0.00 0.00 0.00 1.82
2504 2825 5.944007 GCCTTTATTAGTTCAACCCAGAGAA 59.056 40.000 0.00 0.00 0.00 2.87
2513 2834 4.304048 TTCCCCGCCTTTATTAGTTCAA 57.696 40.909 0.00 0.00 0.00 2.69
2528 2849 1.137086 AGAGATCACATCGTTTCCCCG 59.863 52.381 0.00 0.00 0.00 5.73
2531 2852 2.898705 AGCAGAGATCACATCGTTTCC 58.101 47.619 0.00 0.00 0.00 3.13
2532 2853 3.928992 TGAAGCAGAGATCACATCGTTTC 59.071 43.478 0.00 0.00 0.00 2.78
2542 2864 3.257469 TGTGGTGATGAAGCAGAGATC 57.743 47.619 0.00 0.00 36.83 2.75
2611 2933 3.474600 AGCAGCTACTTGCATAATCAGG 58.525 45.455 0.00 0.00 46.47 3.86
2662 2984 9.801873 ATTTATTTTGATGACAAGTATTTCCGG 57.198 29.630 0.00 0.00 37.32 5.14
2692 3014 9.845214 ACTAAAATACATCTAGATACATCCCCT 57.155 33.333 4.54 0.00 0.00 4.79
2738 3060 7.975616 CCGAAAATAGTTGTCATCAAAATGGAT 59.024 33.333 0.00 0.00 35.20 3.41
2739 3061 7.175816 TCCGAAAATAGTTGTCATCAAAATGGA 59.824 33.333 0.00 0.00 35.20 3.41
2740 3062 7.273381 GTCCGAAAATAGTTGTCATCAAAATGG 59.727 37.037 0.00 0.00 35.20 3.16
2741 3063 7.007367 CGTCCGAAAATAGTTGTCATCAAAATG 59.993 37.037 0.00 0.00 35.20 2.32
2742 3064 7.021196 CGTCCGAAAATAGTTGTCATCAAAAT 58.979 34.615 0.00 0.00 35.20 1.82
2743 3065 6.367421 CGTCCGAAAATAGTTGTCATCAAAA 58.633 36.000 0.00 0.00 35.20 2.44
2744 3066 5.106869 CCGTCCGAAAATAGTTGTCATCAAA 60.107 40.000 0.00 0.00 35.20 2.69
2745 3067 4.390603 CCGTCCGAAAATAGTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
2746 3068 3.930229 CCGTCCGAAAATAGTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
2747 3069 4.178540 TCCGTCCGAAAATAGTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
2748 3070 4.181578 CTCCGTCCGAAAATAGTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
2749 3071 3.581755 CTCCGTCCGAAAATAGTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
2750 3072 2.928116 CCTCCGTCCGAAAATAGTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
2751 3073 2.354403 CCCTCCGTCCGAAAATAGTTGT 60.354 50.000 0.00 0.00 0.00 3.32
2752 3074 2.093869 TCCCTCCGTCCGAAAATAGTTG 60.094 50.000 0.00 0.00 0.00 3.16
2753 3075 2.167900 CTCCCTCCGTCCGAAAATAGTT 59.832 50.000 0.00 0.00 0.00 2.24
2754 3076 1.755380 CTCCCTCCGTCCGAAAATAGT 59.245 52.381 0.00 0.00 0.00 2.12
2755 3077 1.755380 ACTCCCTCCGTCCGAAAATAG 59.245 52.381 0.00 0.00 0.00 1.73
2758 3080 0.890683 GTACTCCCTCCGTCCGAAAA 59.109 55.000 0.00 0.00 0.00 2.29
2762 3084 2.437359 ACGTACTCCCTCCGTCCG 60.437 66.667 0.00 0.00 0.00 4.79
2764 3086 2.413142 CCCACGTACTCCCTCCGTC 61.413 68.421 0.00 0.00 31.46 4.79
2777 3099 0.393077 GATCCACCTATCCACCCACG 59.607 60.000 0.00 0.00 0.00 4.94
2781 3103 6.323996 TCGATAATATGATCCACCTATCCACC 59.676 42.308 0.00 0.00 0.00 4.61
2782 3104 7.348080 TCGATAATATGATCCACCTATCCAC 57.652 40.000 0.00 0.00 0.00 4.02
2783 3105 8.007153 AGATCGATAATATGATCCACCTATCCA 58.993 37.037 0.00 0.00 41.52 3.41
2784 3106 8.415950 AGATCGATAATATGATCCACCTATCC 57.584 38.462 0.00 0.00 41.52 2.59
2785 3107 8.233868 CGAGATCGATAATATGATCCACCTATC 58.766 40.741 0.00 0.00 41.52 2.08
2786 3108 7.175816 CCGAGATCGATAATATGATCCACCTAT 59.824 40.741 0.00 0.00 41.52 2.57
2788 3110 5.300539 CCGAGATCGATAATATGATCCACCT 59.699 44.000 0.00 0.00 41.52 4.00
2846 3184 0.329261 TCAGATGCACCTCCCCAAAG 59.671 55.000 0.00 0.00 0.00 2.77
2849 3187 0.548031 GATTCAGATGCACCTCCCCA 59.452 55.000 0.00 0.00 0.00 4.96
2852 3190 2.706339 ACTGATTCAGATGCACCTCC 57.294 50.000 20.33 0.00 35.18 4.30
2853 3191 3.726607 CCTACTGATTCAGATGCACCTC 58.273 50.000 20.33 0.00 35.18 3.85
2854 3192 2.158842 GCCTACTGATTCAGATGCACCT 60.159 50.000 20.33 0.00 35.18 4.00
2921 3263 3.655211 ACTGGGCCAGCAAGAGGG 61.655 66.667 33.04 8.63 34.37 4.30
2925 3267 2.678934 ATGCACTGGGCCAGCAAG 60.679 61.111 33.04 22.92 43.89 4.01
3011 3365 7.811482 TTTTACTTTGGATGGTACTAGGGTA 57.189 36.000 0.00 0.00 0.00 3.69
3012 3366 6.707273 TTTTACTTTGGATGGTACTAGGGT 57.293 37.500 0.00 0.00 0.00 4.34
3013 3367 6.602009 CCTTTTTACTTTGGATGGTACTAGGG 59.398 42.308 0.00 0.00 0.00 3.53
3015 3369 6.095021 GCCCTTTTTACTTTGGATGGTACTAG 59.905 42.308 0.00 0.00 0.00 2.57
3016 3370 5.947566 GCCCTTTTTACTTTGGATGGTACTA 59.052 40.000 0.00 0.00 0.00 1.82
3017 3371 4.770531 GCCCTTTTTACTTTGGATGGTACT 59.229 41.667 0.00 0.00 0.00 2.73
3018 3372 4.081862 GGCCCTTTTTACTTTGGATGGTAC 60.082 45.833 0.00 0.00 0.00 3.34
3019 3373 4.090819 GGCCCTTTTTACTTTGGATGGTA 58.909 43.478 0.00 0.00 0.00 3.25
3020 3374 2.903784 GGCCCTTTTTACTTTGGATGGT 59.096 45.455 0.00 0.00 0.00 3.55
3021 3375 2.903135 TGGCCCTTTTTACTTTGGATGG 59.097 45.455 0.00 0.00 0.00 3.51
3039 3396 3.057245 CCTCTTTTGGCTTTCTAGTTGGC 60.057 47.826 0.00 0.00 0.00 4.52
3040 3397 4.398319 TCCTCTTTTGGCTTTCTAGTTGG 58.602 43.478 0.00 0.00 0.00 3.77
3041 3398 6.655003 TGTATCCTCTTTTGGCTTTCTAGTTG 59.345 38.462 0.00 0.00 0.00 3.16
3043 3400 6.374417 TGTATCCTCTTTTGGCTTTCTAGT 57.626 37.500 0.00 0.00 0.00 2.57
3044 3401 7.872113 AATGTATCCTCTTTTGGCTTTCTAG 57.128 36.000 0.00 0.00 0.00 2.43
3078 3438 4.393680 TGTGTACCACAACTGACAAAAGTC 59.606 41.667 0.00 0.00 41.69 3.01
3079 3439 4.155280 GTGTGTACCACAACTGACAAAAGT 59.845 41.667 8.95 0.00 46.28 2.66
3080 3440 4.658071 GTGTGTACCACAACTGACAAAAG 58.342 43.478 8.95 0.00 46.28 2.27
3113 3473 5.501156 AGGGTCAGAATAGTGATTTTGTCC 58.499 41.667 0.00 0.00 35.76 4.02
3114 3474 7.174946 TGAAAGGGTCAGAATAGTGATTTTGTC 59.825 37.037 0.00 0.00 30.84 3.18
3115 3475 7.004086 TGAAAGGGTCAGAATAGTGATTTTGT 58.996 34.615 0.00 0.00 30.84 2.83
3116 3476 7.452880 TGAAAGGGTCAGAATAGTGATTTTG 57.547 36.000 0.00 0.00 0.00 2.44
3117 3477 7.308589 CGTTGAAAGGGTCAGAATAGTGATTTT 60.309 37.037 0.00 0.00 37.61 1.82
3118 3478 6.149474 CGTTGAAAGGGTCAGAATAGTGATTT 59.851 38.462 0.00 0.00 37.61 2.17
3119 3479 5.643777 CGTTGAAAGGGTCAGAATAGTGATT 59.356 40.000 0.00 0.00 37.61 2.57
3120 3480 5.046591 TCGTTGAAAGGGTCAGAATAGTGAT 60.047 40.000 0.00 0.00 37.61 3.06
3121 3481 4.282449 TCGTTGAAAGGGTCAGAATAGTGA 59.718 41.667 0.00 0.00 37.61 3.41
3122 3482 4.566004 TCGTTGAAAGGGTCAGAATAGTG 58.434 43.478 0.00 0.00 37.61 2.74
3123 3483 4.884668 TCGTTGAAAGGGTCAGAATAGT 57.115 40.909 0.00 0.00 37.61 2.12
3124 3484 5.238583 AGTTCGTTGAAAGGGTCAGAATAG 58.761 41.667 0.00 0.00 37.61 1.73
3125 3485 5.223449 AGTTCGTTGAAAGGGTCAGAATA 57.777 39.130 0.00 0.00 37.61 1.75
3126 3486 4.086706 AGTTCGTTGAAAGGGTCAGAAT 57.913 40.909 0.00 0.00 37.61 2.40
3127 3487 3.553828 AGTTCGTTGAAAGGGTCAGAA 57.446 42.857 0.00 0.00 37.61 3.02
3128 3488 3.553828 AAGTTCGTTGAAAGGGTCAGA 57.446 42.857 0.00 0.00 37.61 3.27
3129 3489 3.377172 ACAAAGTTCGTTGAAAGGGTCAG 59.623 43.478 5.60 0.00 37.61 3.51
3130 3490 3.349022 ACAAAGTTCGTTGAAAGGGTCA 58.651 40.909 5.60 0.00 32.59 4.02
3131 3491 3.375922 TGACAAAGTTCGTTGAAAGGGTC 59.624 43.478 5.60 0.00 32.59 4.46
3132 3492 3.128068 GTGACAAAGTTCGTTGAAAGGGT 59.872 43.478 5.60 0.00 32.59 4.34
3133 3493 3.127895 TGTGACAAAGTTCGTTGAAAGGG 59.872 43.478 5.60 0.00 32.59 3.95
3134 3494 4.349663 TGTGACAAAGTTCGTTGAAAGG 57.650 40.909 5.60 0.00 32.59 3.11
3135 3495 6.683090 TTTTGTGACAAAGTTCGTTGAAAG 57.317 33.333 10.91 0.00 32.59 2.62
3136 3496 6.863645 TCATTTTGTGACAAAGTTCGTTGAAA 59.136 30.769 10.91 0.00 32.59 2.69
3137 3497 6.382608 TCATTTTGTGACAAAGTTCGTTGAA 58.617 32.000 10.91 0.00 32.59 2.69
3138 3498 5.944013 TCATTTTGTGACAAAGTTCGTTGA 58.056 33.333 10.91 6.38 32.59 3.18
3139 3499 6.307800 AGTTCATTTTGTGACAAAGTTCGTTG 59.692 34.615 10.91 4.41 36.32 4.10
3140 3500 6.386654 AGTTCATTTTGTGACAAAGTTCGTT 58.613 32.000 10.91 0.00 36.32 3.85
3141 3501 5.949735 AGTTCATTTTGTGACAAAGTTCGT 58.050 33.333 10.91 0.00 36.32 3.85
3142 3502 5.169561 CGAGTTCATTTTGTGACAAAGTTCG 59.830 40.000 10.91 10.21 36.32 3.95
3143 3503 6.255215 TCGAGTTCATTTTGTGACAAAGTTC 58.745 36.000 10.91 2.42 36.32 3.01
3144 3504 6.189677 TCGAGTTCATTTTGTGACAAAGTT 57.810 33.333 10.91 0.58 36.32 2.66
3145 3505 5.811399 TCGAGTTCATTTTGTGACAAAGT 57.189 34.783 10.91 5.51 36.32 2.66


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

AutoCloner maintained by Alex Coulton.