Multiple sequence alignment - TraesCS3D01G037000

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 TraesCS3D01G037000 chr3D 100.000 3235 0 0 1 3235 13308500 13305266 0.000000e+00 5975.0
1 TraesCS3D01G037000 chr3D 80.118 1016 120 42 2266 3235 13296146 13295167 0.000000e+00 682.0
2 TraesCS3D01G037000 chr3B 83.404 2350 198 108 991 3235 19262824 19260562 0.000000e+00 2002.0
3 TraesCS3D01G037000 chr3B 91.195 477 14 9 2 459 19263885 19263418 9.860000e-175 623.0
4 TraesCS3D01G037000 chr3B 85.266 414 43 11 2603 3010 397259425 397259826 8.350000e-111 411.0
5 TraesCS3D01G037000 chr3B 86.402 353 33 10 2603 2947 19251085 19250740 3.940000e-99 372.0
6 TraesCS3D01G037000 chr3B 87.189 281 17 6 631 909 19263159 19262896 5.250000e-78 302.0
7 TraesCS3D01G037000 chr3B 89.109 101 8 1 770 870 385854118 385854215 4.380000e-24 122.0
8 TraesCS3D01G037000 chr3A 83.996 931 67 41 873 1774 23830055 23830932 0.000000e+00 819.0
9 TraesCS3D01G037000 chr3A 89.062 640 55 8 2598 3235 23831704 23832330 0.000000e+00 780.0
10 TraesCS3D01G037000 chr3A 86.981 699 60 14 1844 2530 23830970 23831649 0.000000e+00 758.0
11 TraesCS3D01G037000 chr3A 81.231 991 115 41 2290 3235 23839099 23840063 0.000000e+00 734.0
12 TraesCS3D01G037000 chr3A 93.510 339 10 7 1 329 23828900 23829236 8.060000e-136 494.0
13 TraesCS3D01G037000 chr3A 81.143 350 53 10 2260 2604 23838254 23838595 5.320000e-68 268.0
14 TraesCS3D01G037000 chr3A 80.827 266 29 13 1080 1332 118413499 118413755 4.260000e-44 189.0
15 TraesCS3D01G037000 chr3A 81.481 243 28 13 646 883 23829543 23829773 1.980000e-42 183.0
16 TraesCS3D01G037000 chr3A 91.262 103 4 3 357 459 23829229 23829326 5.630000e-28 135.0
17 TraesCS3D01G037000 chr3A 91.304 69 3 1 983 1051 357504550 357504485 1.240000e-14 91.6
18 TraesCS3D01G037000 chr3A 74.030 335 34 28 721 1051 118413214 118413499 1.600000e-13 87.9
19 TraesCS3D01G037000 chr3A 97.500 40 1 0 721 760 328661172 328661133 5.790000e-08 69.4
20 TraesCS3D01G037000 chr3A 90.000 50 5 0 650 699 357504812 357504763 7.490000e-07 65.8
21 TraesCS3D01G037000 chr4B 80.660 1091 154 29 1953 3010 205684924 205683858 0.000000e+00 793.0
22 TraesCS3D01G037000 chr4B 86.719 128 13 3 2886 3010 357624021 357624147 4.350000e-29 139.0
23 TraesCS3D01G037000 chr4B 86.822 129 11 3 2886 3010 476631931 476632057 4.350000e-29 139.0
24 TraesCS3D01G037000 chr4B 87.013 77 7 2 772 848 230638780 230638707 2.070000e-12 84.2
25 TraesCS3D01G037000 chr4B 100.000 33 0 0 721 753 587712211 587712243 9.690000e-06 62.1
26 TraesCS3D01G037000 chr6B 80.512 1093 151 34 1953 3010 610405028 610406093 0.000000e+00 782.0
27 TraesCS3D01G037000 chr6B 80.808 198 25 8 1147 1332 233934405 233934601 3.360000e-30 143.0
28 TraesCS3D01G037000 chr6D 85.185 216 18 8 1127 1332 10408050 10408261 3.270000e-50 209.0
29 TraesCS3D01G037000 chr6D 88.596 114 10 1 770 883 201578617 201578507 5.630000e-28 135.0
30 TraesCS3D01G037000 chr6A 83.871 217 18 12 1127 1332 11906000 11906210 1.180000e-44 191.0
31 TraesCS3D01G037000 chr6A 80.000 265 31 14 1080 1331 341650511 341650766 3.320000e-40 176.0
32 TraesCS3D01G037000 chr6A 88.679 53 6 0 647 699 341650179 341650231 7.490000e-07 65.8
33 TraesCS3D01G037000 chr2A 80.524 267 28 15 1080 1332 157140990 157141246 1.980000e-42 183.0
34 TraesCS3D01G037000 chr2A 87.826 115 10 2 770 884 377020453 377020343 7.280000e-27 132.0
35 TraesCS3D01G037000 chr2A 88.235 68 8 0 817 884 379386163 379386096 7.440000e-12 82.4
36 TraesCS3D01G037000 chr2A 92.000 50 4 0 650 699 283479231 283479182 1.610000e-08 71.3
37 TraesCS3D01G037000 chr2A 90.000 50 5 0 650 699 211194033 211193984 7.490000e-07 65.8
38 TraesCS3D01G037000 chr5A 81.429 210 26 11 1127 1332 81081209 81081409 3.340000e-35 159.0
39 TraesCS3D01G037000 chr5A 78.659 164 11 6 721 884 460849673 460849534 1.600000e-13 87.9
40 TraesCS3D01G037000 chr5A 90.566 53 5 0 647 699 202427517 202427569 1.610000e-08 71.3
41 TraesCS3D01G037000 chr5A 90.000 50 5 0 650 699 460849718 460849669 7.490000e-07 65.8
42 TraesCS3D01G037000 chr7B 86.822 129 11 3 2886 3010 243750777 243750651 4.350000e-29 139.0
43 TraesCS3D01G037000 chr7B 80.864 162 20 4 1182 1332 575752222 575752061 2.040000e-22 117.0
44 TraesCS3D01G037000 chr7B 87.129 101 10 2 770 870 576358554 576358651 9.490000e-21 111.0
45 TraesCS3D01G037000 chr2B 85.271 129 13 3 2886 3010 453888061 453888187 9.420000e-26 128.0
46 TraesCS3D01G037000 chr1B 89.109 101 8 1 770 870 303874431 303874334 4.380000e-24 122.0
47 TraesCS3D01G037000 chr1B 91.071 56 5 0 642 697 80098539 80098484 3.460000e-10 76.8
48 TraesCS3D01G037000 chr7A 91.304 69 3 1 983 1051 145758870 145758935 1.240000e-14 91.6
49 TraesCS3D01G037000 chr7A 88.679 53 6 0 647 699 145758602 145758654 7.490000e-07 65.8
50 TraesCS3D01G037000 chr1A 92.188 64 2 2 988 1051 422685286 422685346 1.600000e-13 87.9
51 TraesCS3D01G037000 chr4A 97.500 40 1 0 721 760 472339111 472339072 5.790000e-08 69.4
52 TraesCS3D01G037000 chr2D 95.349 43 2 0 657 699 220707872 220707830 5.790000e-08 69.4


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 TraesCS3D01G037000 chr3D 13305266 13308500 3234 True 5975.000000 5975 100.000000 1 3235 1 chr3D.!!$R2 3234
1 TraesCS3D01G037000 chr3D 13295167 13296146 979 True 682.000000 682 80.118000 2266 3235 1 chr3D.!!$R1 969
2 TraesCS3D01G037000 chr3B 19260562 19263885 3323 True 975.666667 2002 87.262667 2 3235 3 chr3B.!!$R2 3233
3 TraesCS3D01G037000 chr3A 23828900 23832330 3430 False 528.166667 819 87.715333 1 3235 6 chr3A.!!$F1 3234
4 TraesCS3D01G037000 chr3A 23838254 23840063 1809 False 501.000000 734 81.187000 2260 3235 2 chr3A.!!$F2 975
5 TraesCS3D01G037000 chr4B 205683858 205684924 1066 True 793.000000 793 80.660000 1953 3010 1 chr4B.!!$R1 1057
6 TraesCS3D01G037000 chr6B 610405028 610406093 1065 False 782.000000 782 80.512000 1953 3010 1 chr6B.!!$F2 1057

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
586 718 0.532573 TCTGTTGGAGATGACGGCTC 59.467 55.0 0.0 0.0 0.00 4.70 F
1393 1888 0.250513 CAGTTCCACTCTGGTAGCCC 59.749 60.0 0.0 0.0 39.03 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1595 2095 0.249238 CATGAGTCTACTCTGGCCGC 60.249 60.0 11.22 0.0 43.25 6.53 R
2690 4104 0.666274 TGACACGCCAGTTCGATCAC 60.666 55.0 0.00 0.0 0.00 3.06 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
119 120 1.217689 CTGAGAGTGGAGAGGGGAGAT 59.782 57.143 0.00 0.00 0.00 2.75
304 322 2.348472 TGAGGATGAGAAGGTTTGGGT 58.652 47.619 0.00 0.00 0.00 4.51
340 359 5.964477 ACCTGTGGACTGATTAGAAATCCTA 59.036 40.000 0.00 0.00 0.00 2.94
347 366 6.098409 GGACTGATTAGAAATCCTACCTGTCA 59.902 42.308 0.00 0.00 0.00 3.58
348 367 7.202047 GGACTGATTAGAAATCCTACCTGTCAT 60.202 40.741 0.00 0.00 0.00 3.06
349 368 7.504403 ACTGATTAGAAATCCTACCTGTCATG 58.496 38.462 0.00 0.00 0.00 3.07
350 369 6.291377 TGATTAGAAATCCTACCTGTCATGC 58.709 40.000 0.00 0.00 0.00 4.06
351 370 3.567478 AGAAATCCTACCTGTCATGCC 57.433 47.619 0.00 0.00 0.00 4.40
352 371 2.846206 AGAAATCCTACCTGTCATGCCA 59.154 45.455 0.00 0.00 0.00 4.92
416 436 8.784043 GTTGTTGAAACTTATTACCATGTCTCT 58.216 33.333 0.00 0.00 0.00 3.10
417 437 8.322906 TGTTGAAACTTATTACCATGTCTCTG 57.677 34.615 0.00 0.00 0.00 3.35
418 438 7.936847 TGTTGAAACTTATTACCATGTCTCTGT 59.063 33.333 0.00 0.00 0.00 3.41
452 472 7.032580 TGTGTTTTATCCACTTTCACTTTGTG 58.967 34.615 0.00 0.00 33.92 3.33
453 473 7.094162 TGTGTTTTATCCACTTTCACTTTGTGA 60.094 33.333 0.00 0.00 35.95 3.58
454 474 7.920682 GTGTTTTATCCACTTTCACTTTGTGAT 59.079 33.333 1.05 0.00 42.40 3.06
455 475 7.920151 TGTTTTATCCACTTTCACTTTGTGATG 59.080 33.333 1.05 1.44 42.40 3.07
456 476 3.988379 TCCACTTTCACTTTGTGATGC 57.012 42.857 1.05 0.00 42.40 3.91
457 477 3.554934 TCCACTTTCACTTTGTGATGCT 58.445 40.909 1.05 0.00 42.40 3.79
458 478 3.316029 TCCACTTTCACTTTGTGATGCTG 59.684 43.478 1.05 0.00 42.40 4.41
459 479 3.047796 CACTTTCACTTTGTGATGCTGC 58.952 45.455 1.05 0.00 42.40 5.25
460 480 2.689471 ACTTTCACTTTGTGATGCTGCA 59.311 40.909 4.13 4.13 42.40 4.41
463 556 1.068125 TCACTTTGTGATGCTGCATGC 60.068 47.619 21.53 11.82 37.67 4.06
476 569 2.159544 GCTGCATGCTGTTCTTCTCTTC 60.160 50.000 23.42 1.72 38.95 2.87
507 636 2.292103 TTTTTGCAGGCAGTGTGTTC 57.708 45.000 0.00 0.00 0.00 3.18
514 643 0.753262 AGGCAGTGTGTTCGTCTCTT 59.247 50.000 0.00 0.00 0.00 2.85
515 644 1.140816 GGCAGTGTGTTCGTCTCTTC 58.859 55.000 0.00 0.00 0.00 2.87
516 645 1.269831 GGCAGTGTGTTCGTCTCTTCT 60.270 52.381 0.00 0.00 0.00 2.85
517 646 2.055100 GCAGTGTGTTCGTCTCTTCTC 58.945 52.381 0.00 0.00 0.00 2.87
518 647 2.287909 GCAGTGTGTTCGTCTCTTCTCT 60.288 50.000 0.00 0.00 0.00 3.10
519 648 3.560503 CAGTGTGTTCGTCTCTTCTCTC 58.439 50.000 0.00 0.00 0.00 3.20
520 649 3.252215 CAGTGTGTTCGTCTCTTCTCTCT 59.748 47.826 0.00 0.00 0.00 3.10
521 650 3.886505 AGTGTGTTCGTCTCTTCTCTCTT 59.113 43.478 0.00 0.00 0.00 2.85
522 651 3.978217 GTGTGTTCGTCTCTTCTCTCTTG 59.022 47.826 0.00 0.00 0.00 3.02
523 652 2.983803 GTGTTCGTCTCTTCTCTCTTGC 59.016 50.000 0.00 0.00 0.00 4.01
524 653 2.029828 TGTTCGTCTCTTCTCTCTTGCC 60.030 50.000 0.00 0.00 0.00 4.52
525 654 2.208132 TCGTCTCTTCTCTCTTGCCT 57.792 50.000 0.00 0.00 0.00 4.75
557 689 2.224305 ACTAACTGTGGGTTGCAGAGTC 60.224 50.000 0.00 0.00 38.75 3.36
571 703 0.680280 AGAGTCGTGCGGGTATCTGT 60.680 55.000 0.00 0.00 0.00 3.41
574 706 1.082117 GTCGTGCGGGTATCTGTTGG 61.082 60.000 0.00 0.00 0.00 3.77
575 707 1.216977 CGTGCGGGTATCTGTTGGA 59.783 57.895 0.00 0.00 0.00 3.53
586 718 0.532573 TCTGTTGGAGATGACGGCTC 59.467 55.000 0.00 0.00 0.00 4.70
587 719 0.803768 CTGTTGGAGATGACGGCTCG 60.804 60.000 0.00 0.00 33.19 5.03
588 720 1.519455 GTTGGAGATGACGGCTCGG 60.519 63.158 0.00 0.00 33.19 4.63
589 721 1.680989 TTGGAGATGACGGCTCGGA 60.681 57.895 0.00 0.00 33.19 4.55
591 723 2.026879 GAGATGACGGCTCGGAGC 59.973 66.667 21.57 21.57 41.46 4.70
632 775 4.144727 GGCGGAGAGAGGAGGGGA 62.145 72.222 0.00 0.00 0.00 4.81
633 776 2.520741 GCGGAGAGAGGAGGGGAG 60.521 72.222 0.00 0.00 0.00 4.30
634 777 2.197324 CGGAGAGAGGAGGGGAGG 59.803 72.222 0.00 0.00 0.00 4.30
635 778 2.612251 GGAGAGAGGAGGGGAGGG 59.388 72.222 0.00 0.00 0.00 4.30
636 779 2.612251 GAGAGAGGAGGGGAGGGG 59.388 72.222 0.00 0.00 0.00 4.79
637 780 3.039526 AGAGAGGAGGGGAGGGGG 61.040 72.222 0.00 0.00 0.00 5.40
691 834 2.391389 GCTACAGTTGCCAGCGACC 61.391 63.158 6.39 0.00 0.00 4.79
702 845 1.444553 CAGCGACCGAGGTGAGAAC 60.445 63.158 0.00 0.00 41.72 3.01
716 861 7.041508 CCGAGGTGAGAACGTACTACTATAATT 60.042 40.741 0.00 0.00 0.00 1.40
744 901 4.373116 CTGGACGGACGGTGGTGG 62.373 72.222 0.00 0.00 0.00 4.61
768 925 3.706373 CCACCGTCCAGGGTCCAG 61.706 72.222 0.00 0.00 46.96 3.86
886 1336 1.138266 CCTTCCTACCATACCACACCG 59.862 57.143 0.00 0.00 0.00 4.94
927 1377 1.888436 CTGCTTCGCCACTCCCACTA 61.888 60.000 0.00 0.00 0.00 2.74
928 1378 1.153549 GCTTCGCCACTCCCACTAG 60.154 63.158 0.00 0.00 0.00 2.57
929 1379 1.517832 CTTCGCCACTCCCACTAGG 59.482 63.158 0.00 0.00 0.00 3.02
930 1380 0.970937 CTTCGCCACTCCCACTAGGA 60.971 60.000 0.00 0.00 44.91 2.94
1056 1528 3.385749 CTCCACGCGGGTAAGCCAT 62.386 63.158 12.47 0.00 38.11 4.40
1057 1529 2.895372 CCACGCGGGTAAGCCATC 60.895 66.667 12.47 0.00 36.17 3.51
1063 1535 1.227674 CGGGTAAGCCATCTCAGCC 60.228 63.158 0.00 0.00 36.17 4.85
1078 1550 2.196925 AGCCTCGCTACCATCCTCG 61.197 63.158 0.00 0.00 36.99 4.63
1079 1551 2.194212 GCCTCGCTACCATCCTCGA 61.194 63.158 0.00 0.00 0.00 4.04
1080 1552 1.528292 GCCTCGCTACCATCCTCGAT 61.528 60.000 0.00 0.00 0.00 3.59
1081 1553 0.962489 CCTCGCTACCATCCTCGATT 59.038 55.000 0.00 0.00 0.00 3.34
1083 1555 0.959553 TCGCTACCATCCTCGATTCC 59.040 55.000 0.00 0.00 0.00 3.01
1085 1557 1.068194 CGCTACCATCCTCGATTCCTC 60.068 57.143 0.00 0.00 0.00 3.71
1112 1584 4.535116 CTTTGCTTGACTTCTTTCTGCTC 58.465 43.478 0.00 0.00 0.00 4.26
1113 1585 2.138320 TGCTTGACTTCTTTCTGCTCG 58.862 47.619 0.00 0.00 0.00 5.03
1114 1586 2.139118 GCTTGACTTCTTTCTGCTCGT 58.861 47.619 0.00 0.00 0.00 4.18
1133 1605 1.848932 TTTCTCGCTTGCTGCTGCTG 61.849 55.000 17.00 10.41 40.48 4.41
1136 1608 4.760840 CGCTTGCTGCTGCTGCTG 62.761 66.667 27.67 21.23 40.48 4.41
1157 1629 3.072476 CTGCAGGTGGTAGCTGGT 58.928 61.111 5.57 0.00 43.49 4.00
1158 1630 1.078848 CTGCAGGTGGTAGCTGGTC 60.079 63.158 5.57 0.00 43.49 4.02
1164 1636 2.682494 TGGTAGCTGGTCCGTCCC 60.682 66.667 0.00 0.00 34.77 4.46
1180 1652 1.900016 CCCTGCTGCTTGCTGTGAA 60.900 57.895 0.00 0.00 43.37 3.18
1358 1853 2.288518 ACTCTCGCCACACTCTTTTCTC 60.289 50.000 0.00 0.00 0.00 2.87
1365 1860 2.802816 CCACACTCTTTTCTCTTCACCG 59.197 50.000 0.00 0.00 0.00 4.94
1386 1881 1.071385 AGAGTTGGCAGTTCCACTCTG 59.929 52.381 15.94 0.00 46.55 3.35
1390 1885 0.976641 TGGCAGTTCCACTCTGGTAG 59.023 55.000 0.00 0.00 40.72 3.18
1393 1888 0.250513 CAGTTCCACTCTGGTAGCCC 59.749 60.000 0.00 0.00 39.03 5.19
1397 1892 2.722201 CCACTCTGGTAGCCCGTCC 61.722 68.421 0.00 0.00 31.35 4.79
1431 1926 1.545428 GCCATGGGTTGACTGACTGAA 60.545 52.381 15.13 0.00 0.00 3.02
1438 1933 5.875224 TGGGTTGACTGACTGAATGAATTA 58.125 37.500 0.00 0.00 0.00 1.40
1439 1934 6.484288 TGGGTTGACTGACTGAATGAATTAT 58.516 36.000 0.00 0.00 0.00 1.28
1450 1945 7.613022 TGACTGAATGAATTATTTCTTGCTCCT 59.387 33.333 0.00 0.00 32.78 3.69
1462 1957 0.541063 TTGCTCCTCACGTACAGGGA 60.541 55.000 11.85 5.58 0.00 4.20
1467 1962 0.460311 CCTCACGTACAGGGATGTCC 59.540 60.000 5.00 0.00 0.00 4.02
1497 1992 4.704833 GCCAGCTCCGCCTTCACA 62.705 66.667 0.00 0.00 0.00 3.58
1575 2075 2.285818 ATCGTAAGCCCACCCCCA 60.286 61.111 0.00 0.00 37.18 4.96
1586 2086 1.685820 CACCCCCACCTTCCTCTTC 59.314 63.158 0.00 0.00 0.00 2.87
1590 2090 0.621082 CCCCACCTTCCTCTTCTTCC 59.379 60.000 0.00 0.00 0.00 3.46
1591 2091 0.621082 CCCACCTTCCTCTTCTTCCC 59.379 60.000 0.00 0.00 0.00 3.97
1595 2095 0.250513 CCTTCCTCTTCTTCCCCACG 59.749 60.000 0.00 0.00 0.00 4.94
1599 2099 4.388499 TCTTCTTCCCCACGCGGC 62.388 66.667 12.47 0.00 0.00 6.53
1763 2287 1.078143 CAGCAAGTACTGGCTCCCC 60.078 63.158 22.42 0.00 38.56 4.81
1774 2298 3.462678 GCTCCCCGAGGTCAGTCC 61.463 72.222 0.00 0.00 0.00 3.85
1795 2328 4.999311 TCCTCACACTCTGAATGTTCAATG 59.001 41.667 0.00 0.00 36.64 2.82
1796 2329 4.379186 CCTCACACTCTGAATGTTCAATGC 60.379 45.833 0.00 0.00 36.64 3.56
1797 2330 3.503363 TCACACTCTGAATGTTCAATGCC 59.497 43.478 0.00 0.00 36.64 4.40
1798 2331 3.253921 CACACTCTGAATGTTCAATGCCA 59.746 43.478 0.00 0.00 36.64 4.92
1799 2332 4.082408 CACACTCTGAATGTTCAATGCCAT 60.082 41.667 0.00 0.00 36.64 4.40
1800 2333 4.525487 ACACTCTGAATGTTCAATGCCATT 59.475 37.500 0.00 0.00 36.64 3.16
1801 2334 5.711506 ACACTCTGAATGTTCAATGCCATTA 59.288 36.000 0.00 0.00 36.64 1.90
1802 2335 6.032094 CACTCTGAATGTTCAATGCCATTAC 58.968 40.000 0.00 0.00 36.64 1.89
1803 2336 5.948162 ACTCTGAATGTTCAATGCCATTACT 59.052 36.000 0.00 0.00 36.64 2.24
1804 2337 6.127814 ACTCTGAATGTTCAATGCCATTACTG 60.128 38.462 0.00 0.00 36.64 2.74
1805 2338 5.125900 TCTGAATGTTCAATGCCATTACTGG 59.874 40.000 0.00 0.00 40.17 4.00
1814 2347 3.869623 CCATTACTGGCTCTGCACT 57.130 52.632 0.00 0.00 35.23 4.40
1817 2350 2.548875 CATTACTGGCTCTGCACTCTC 58.451 52.381 0.00 0.00 0.00 3.20
1818 2351 1.632589 TTACTGGCTCTGCACTCTCA 58.367 50.000 0.00 0.00 0.00 3.27
1825 2358 1.875009 CTCTGCACTCTCACAGCAAA 58.125 50.000 0.00 0.00 37.89 3.68
1828 2361 1.945394 CTGCACTCTCACAGCAAAACT 59.055 47.619 0.00 0.00 37.89 2.66
1831 2364 3.944650 TGCACTCTCACAGCAAAACTAAA 59.055 39.130 0.00 0.00 34.97 1.85
1842 2378 6.086765 CACAGCAAAACTAAAATTCAGTAGCG 59.913 38.462 0.00 0.00 0.00 4.26
1859 2395 1.398595 GCGTTGTGCATTGTCTGAAC 58.601 50.000 0.00 0.00 45.45 3.18
1872 2408 1.527311 GTCTGAACGTTCTTGTGCCTC 59.473 52.381 27.32 0.26 0.00 4.70
1873 2409 0.508641 CTGAACGTTCTTGTGCCTCG 59.491 55.000 27.32 3.07 0.00 4.63
1889 2425 3.338249 GCCTCGGCATATCACATATGTT 58.662 45.455 5.37 0.00 43.52 2.71
1898 2441 6.040842 GGCATATCACATATGTTTGGTTCCTT 59.959 38.462 5.37 0.00 43.52 3.36
1993 2536 1.004918 CCTTGCCGTCGACCTCTTT 60.005 57.895 10.58 0.00 0.00 2.52
1996 2539 2.048127 GCCGTCGACCTCTTTGCT 60.048 61.111 10.58 0.00 0.00 3.91
2009 2552 1.134128 TCTTTGCTGCAAGGTCAGTCA 60.134 47.619 21.58 2.02 36.49 3.41
2013 2556 1.673665 CTGCAAGGTCAGTCAGCCC 60.674 63.158 0.00 0.00 0.00 5.19
2016 2559 2.938354 CAAGGTCAGTCAGCCCTTG 58.062 57.895 3.50 3.50 46.57 3.61
2020 2563 1.202818 AGGTCAGTCAGCCCTTGTTTC 60.203 52.381 0.00 0.00 0.00 2.78
2048 2591 5.238432 ACTTTCAAGTGTATGCGATTGTGAA 59.762 36.000 0.00 0.00 37.98 3.18
2049 2592 4.661993 TCAAGTGTATGCGATTGTGAAC 57.338 40.909 0.00 0.00 0.00 3.18
2050 2593 3.435327 TCAAGTGTATGCGATTGTGAACC 59.565 43.478 0.00 0.00 0.00 3.62
2069 2622 5.596836 AACCAGATGTTCATGTTTGTGTT 57.403 34.783 0.00 0.00 28.45 3.32
2070 2623 5.596836 ACCAGATGTTCATGTTTGTGTTT 57.403 34.783 0.00 0.00 0.00 2.83
2071 2624 5.591099 ACCAGATGTTCATGTTTGTGTTTC 58.409 37.500 0.00 0.00 0.00 2.78
2072 2625 4.984161 CCAGATGTTCATGTTTGTGTTTCC 59.016 41.667 0.00 0.00 0.00 3.13
2114 2668 3.619733 GCAGACAAGTGTACCATGATGGA 60.620 47.826 20.11 0.00 40.96 3.41
2207 2761 1.805945 CGCGCTGACCAAGGTACTC 60.806 63.158 5.56 0.00 38.49 2.59
2246 2804 1.374252 ACACTGACGACCGATTGCC 60.374 57.895 0.00 0.00 0.00 4.52
2274 2832 2.025887 CAGGCTCCCCTTGTTTAGATGT 60.026 50.000 0.00 0.00 40.33 3.06
2331 2892 3.387374 TGATTTGGTGCACCATTTGTTCT 59.613 39.130 37.97 17.38 46.97 3.01
2434 2995 5.141182 TCATAGAAGGGCTAGTAGAACAGG 58.859 45.833 0.00 0.00 31.33 4.00
2445 3008 6.760298 GGCTAGTAGAACAGGTTATTTGTACC 59.240 42.308 0.00 0.00 35.85 3.34
2457 3021 6.046593 GGTTATTTGTACCATCGAGTCATGA 58.953 40.000 0.00 0.00 35.67 3.07
2513 3077 5.924825 GTCTCAGATTTAACGGTAACACACT 59.075 40.000 0.00 0.00 0.00 3.55
2585 3970 5.772521 ACTGCACTTGTGGATTTGTTTATC 58.227 37.500 2.81 0.00 0.00 1.75
2690 4104 4.260091 GCGTAAACCTATTGAAGCGGTAAG 60.260 45.833 0.00 0.00 0.00 2.34
2696 4112 3.736252 CCTATTGAAGCGGTAAGTGATCG 59.264 47.826 0.00 0.00 33.53 3.69
2746 4173 3.181420 ACCTTCCAGCCCGTATATCTACT 60.181 47.826 0.00 0.00 0.00 2.57
2749 4176 5.498393 CTTCCAGCCCGTATATCTACTCTA 58.502 45.833 0.00 0.00 0.00 2.43
2753 4180 7.813331 TCCAGCCCGTATATCTACTCTATATT 58.187 38.462 0.00 0.00 0.00 1.28
2755 4182 8.353684 CCAGCCCGTATATCTACTCTATATTTG 58.646 40.741 0.00 0.00 0.00 2.32
2804 4231 3.325870 TGTATAACGGCATAGCATCTGC 58.674 45.455 0.00 0.00 42.49 4.26
2964 4404 3.274288 GCACTCTAGCTAGGCAAAATGT 58.726 45.455 20.58 6.00 0.00 2.71
2975 4415 4.970662 AGGCAAAATGTATACACTGCTG 57.029 40.909 24.52 14.82 32.83 4.41
2982 4426 7.481798 GCAAAATGTATACACTGCTGTAGTTTC 59.518 37.037 20.98 0.14 37.60 2.78
3051 4503 1.202867 TGCACCACATCTTTGTAGGCA 60.203 47.619 0.00 0.00 34.77 4.75
3060 4512 5.066893 CACATCTTTGTAGGCATAGTTGCAT 59.933 40.000 0.00 0.00 46.23 3.96
3062 4514 8.337104 ACATCTTTGTAGGCATAGTTGCATGC 62.337 42.308 11.82 11.82 43.86 4.06
3102 4556 1.369091 CGTAGCTGCAAGGCGGATTT 61.369 55.000 1.02 0.00 37.02 2.17
3136 4595 7.008440 TCATGTCAAATCTTGTGATCGAATC 57.992 36.000 0.00 0.00 31.51 2.52
3178 4641 1.650825 AAAAAGCGCAAGTGTTTGGG 58.349 45.000 11.47 0.57 46.67 4.12
3182 4645 0.881118 AGCGCAAGTGTTTGGGTATG 59.119 50.000 11.47 0.00 45.93 2.39
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
119 120 4.040755 CTCCCCTCTTTATTTCTCTCCCA 58.959 47.826 0.00 0.00 0.00 4.37
165 166 7.549147 AACCAACTCAGACCAACTAAGTATA 57.451 36.000 0.00 0.00 0.00 1.47
176 181 2.538512 AACGGTAACCAACTCAGACC 57.461 50.000 0.00 0.00 0.00 3.85
304 322 1.303236 CACAGGTCGGGCCATTTGA 60.303 57.895 4.39 0.00 40.61 2.69
340 359 0.112995 ACCAACATGGCATGACAGGT 59.887 50.000 32.74 28.59 42.67 4.00
347 366 1.352017 TGTCTCAGACCAACATGGCAT 59.648 47.619 1.24 0.00 42.67 4.40
348 367 0.764271 TGTCTCAGACCAACATGGCA 59.236 50.000 1.24 0.00 42.67 4.92
349 368 1.271054 ACTGTCTCAGACCAACATGGC 60.271 52.381 1.24 0.00 36.53 4.40
350 369 2.847327 ACTGTCTCAGACCAACATGG 57.153 50.000 1.24 0.00 38.04 3.66
351 370 4.261322 CCAAAACTGTCTCAGACCAACATG 60.261 45.833 1.24 0.00 35.18 3.21
352 371 3.885297 CCAAAACTGTCTCAGACCAACAT 59.115 43.478 1.24 0.00 35.18 2.71
416 436 5.869888 GTGGATAAAACACAAACCAACAACA 59.130 36.000 0.00 0.00 38.67 3.33
417 437 6.103330 AGTGGATAAAACACAAACCAACAAC 58.897 36.000 0.00 0.00 41.21 3.32
418 438 6.287589 AGTGGATAAAACACAAACCAACAA 57.712 33.333 0.00 0.00 41.21 2.83
455 475 1.451067 AGAGAAGAACAGCATGCAGC 58.549 50.000 21.98 5.73 42.53 5.25
456 476 2.419324 GGAAGAGAAGAACAGCATGCAG 59.581 50.000 21.98 15.38 42.53 4.41
457 477 2.039480 AGGAAGAGAAGAACAGCATGCA 59.961 45.455 21.98 0.00 42.53 3.96
458 478 2.709213 AGGAAGAGAAGAACAGCATGC 58.291 47.619 10.51 10.51 42.53 4.06
459 479 5.702349 AAAAGGAAGAGAAGAACAGCATG 57.298 39.130 0.00 0.00 46.00 4.06
507 636 2.605030 CAAGGCAAGAGAGAAGAGACG 58.395 52.381 0.00 0.00 0.00 4.18
514 643 1.593787 CTCGGCAAGGCAAGAGAGA 59.406 57.895 7.00 0.00 37.14 3.10
515 644 1.449246 CCTCGGCAAGGCAAGAGAG 60.449 63.158 12.40 5.35 38.67 3.20
516 645 2.665000 CCTCGGCAAGGCAAGAGA 59.335 61.111 12.40 0.00 38.67 3.10
534 663 2.549754 CTCTGCAACCCACAGTTAGTTG 59.450 50.000 7.76 7.76 42.95 3.16
557 689 0.806102 CTCCAACAGATACCCGCACG 60.806 60.000 0.00 0.00 0.00 5.34
571 703 1.667154 CTCCGAGCCGTCATCTCCAA 61.667 60.000 0.00 0.00 0.00 3.53
574 706 2.026879 GCTCCGAGCCGTCATCTC 59.973 66.667 9.42 0.00 34.48 2.75
575 707 2.755876 TGCTCCGAGCCGTCATCT 60.756 61.111 17.81 0.00 41.51 2.90
616 759 2.520741 CTCCCCTCCTCTCTCCGC 60.521 72.222 0.00 0.00 0.00 5.54
618 761 2.612251 CCCTCCCCTCCTCTCTCC 59.388 72.222 0.00 0.00 0.00 3.71
619 762 2.612251 CCCCTCCCCTCCTCTCTC 59.388 72.222 0.00 0.00 0.00 3.20
620 763 3.039526 CCCCCTCCCCTCCTCTCT 61.040 72.222 0.00 0.00 0.00 3.10
636 779 2.034221 GCCTTCACTGGGACACCC 59.966 66.667 0.00 0.00 45.71 4.61
637 780 1.003233 GAGCCTTCACTGGGACACC 60.003 63.158 0.00 0.00 37.24 4.16
638 781 1.374758 CGAGCCTTCACTGGGACAC 60.375 63.158 0.00 0.00 0.00 3.67
639 782 2.583441 CCGAGCCTTCACTGGGACA 61.583 63.158 0.00 0.00 37.73 4.02
648 791 2.825836 CCCATGTGCCGAGCCTTC 60.826 66.667 0.00 0.00 0.00 3.46
685 828 2.963371 GTTCTCACCTCGGTCGCT 59.037 61.111 0.00 0.00 0.00 4.93
691 834 6.834959 TTATAGTAGTACGTTCTCACCTCG 57.165 41.667 0.00 0.00 0.00 4.63
702 845 6.698766 GGTTCACCACCAATTATAGTAGTACG 59.301 42.308 0.00 0.00 46.42 3.67
800 957 2.665603 GGCAGGTCAGGTCAGGTC 59.334 66.667 0.00 0.00 0.00 3.85
801 958 2.930562 GGGCAGGTCAGGTCAGGT 60.931 66.667 0.00 0.00 0.00 4.00
804 961 2.224159 GGAAGGGCAGGTCAGGTCA 61.224 63.158 0.00 0.00 0.00 4.02
927 1377 3.309994 CCCCTTTGTACTAGTCCTCTCCT 60.310 52.174 0.00 0.00 0.00 3.69
928 1378 3.032459 CCCCTTTGTACTAGTCCTCTCC 58.968 54.545 0.00 0.00 0.00 3.71
929 1379 3.978610 TCCCCTTTGTACTAGTCCTCTC 58.021 50.000 0.00 0.00 0.00 3.20
930 1380 4.354662 CTTCCCCTTTGTACTAGTCCTCT 58.645 47.826 0.00 0.00 0.00 3.69
931 1381 3.451540 CCTTCCCCTTTGTACTAGTCCTC 59.548 52.174 0.00 0.00 0.00 3.71
932 1382 3.078612 TCCTTCCCCTTTGTACTAGTCCT 59.921 47.826 0.00 0.00 0.00 3.85
933 1383 3.447950 TCCTTCCCCTTTGTACTAGTCC 58.552 50.000 0.00 0.00 0.00 3.85
934 1384 3.451540 CCTCCTTCCCCTTTGTACTAGTC 59.548 52.174 0.00 0.00 0.00 2.59
1039 1511 3.379865 GATGGCTTACCCGCGTGGA 62.380 63.158 18.79 0.00 37.49 4.02
1056 1528 1.109920 GGATGGTAGCGAGGCTGAGA 61.110 60.000 0.00 0.00 40.10 3.27
1057 1529 1.112315 AGGATGGTAGCGAGGCTGAG 61.112 60.000 0.00 0.00 40.10 3.35
1063 1535 1.068194 GGAATCGAGGATGGTAGCGAG 60.068 57.143 0.00 0.00 36.12 5.03
1078 1550 1.135575 CAAGCAAAGGCACGAGGAATC 60.136 52.381 0.00 0.00 44.61 2.52
1079 1551 0.883833 CAAGCAAAGGCACGAGGAAT 59.116 50.000 0.00 0.00 44.61 3.01
1080 1552 0.179032 TCAAGCAAAGGCACGAGGAA 60.179 50.000 0.00 0.00 44.61 3.36
1081 1553 0.884704 GTCAAGCAAAGGCACGAGGA 60.885 55.000 0.00 0.00 44.61 3.71
1083 1555 0.947244 AAGTCAAGCAAAGGCACGAG 59.053 50.000 0.00 0.00 44.61 4.18
1085 1557 0.947244 AGAAGTCAAGCAAAGGCACG 59.053 50.000 0.00 0.00 44.61 5.34
1136 1608 3.130160 GCTACCACCTGCAGCAGC 61.130 66.667 17.81 7.41 42.57 5.25
1137 1609 1.744368 CAGCTACCACCTGCAGCAG 60.744 63.158 16.23 16.23 37.78 4.24
1138 1610 2.348620 CAGCTACCACCTGCAGCA 59.651 61.111 8.66 0.00 37.78 4.41
1139 1611 2.437359 CCAGCTACCACCTGCAGC 60.437 66.667 8.66 0.00 35.49 5.25
1140 1612 1.078848 GACCAGCTACCACCTGCAG 60.079 63.158 6.78 6.78 0.00 4.41
1141 1613 2.592993 GGACCAGCTACCACCTGCA 61.593 63.158 0.00 0.00 0.00 4.41
1142 1614 2.269241 GGACCAGCTACCACCTGC 59.731 66.667 0.00 0.00 0.00 4.85
1143 1615 2.227089 GACGGACCAGCTACCACCTG 62.227 65.000 0.00 0.00 0.00 4.00
1144 1616 1.982938 GACGGACCAGCTACCACCT 60.983 63.158 0.00 0.00 0.00 4.00
1145 1617 2.577593 GACGGACCAGCTACCACC 59.422 66.667 0.00 0.00 0.00 4.61
1146 1618 2.577593 GGACGGACCAGCTACCAC 59.422 66.667 0.00 0.00 38.79 4.16
1147 1619 2.682494 GGGACGGACCAGCTACCA 60.682 66.667 0.00 0.00 41.20 3.25
1157 1629 4.704833 GCAAGCAGCAGGGACGGA 62.705 66.667 0.00 0.00 44.79 4.69
1164 1636 1.081376 GCTTCACAGCAAGCAGCAG 60.081 57.895 0.00 0.00 46.93 4.24
1358 1853 0.034059 ACTGCCAACTCTCGGTGAAG 59.966 55.000 0.00 0.00 0.00 3.02
1386 1881 4.139234 GGTCGTGGACGGGCTACC 62.139 72.222 0.00 0.00 40.29 3.18
1393 1888 2.805353 CTTGCGAGGTCGTGGACG 60.805 66.667 0.69 0.00 42.22 4.79
1431 1926 5.882557 ACGTGAGGAGCAAGAAATAATTCAT 59.117 36.000 0.00 0.00 38.06 2.57
1438 1933 3.589988 CTGTACGTGAGGAGCAAGAAAT 58.410 45.455 0.00 0.00 0.00 2.17
1439 1934 2.288825 CCTGTACGTGAGGAGCAAGAAA 60.289 50.000 9.35 0.00 31.48 2.52
1450 1945 0.892755 GTGGACATCCCTGTACGTGA 59.107 55.000 0.00 0.00 39.27 4.35
1462 1957 0.392998 GCAATCTGGGACGTGGACAT 60.393 55.000 0.00 0.00 0.00 3.06
1467 1962 2.401766 GCTGGCAATCTGGGACGTG 61.402 63.158 0.00 0.00 0.00 4.49
1556 2051 2.516225 GGGGTGGGCTTACGATGC 60.516 66.667 0.00 0.00 0.00 3.91
1575 2075 1.363246 GTGGGGAAGAAGAGGAAGGT 58.637 55.000 0.00 0.00 0.00 3.50
1590 2090 4.514577 CTACTCTGGCCGCGTGGG 62.515 72.222 18.41 3.39 39.58 4.61
1591 2091 3.449227 TCTACTCTGGCCGCGTGG 61.449 66.667 11.67 11.67 38.77 4.94
1595 2095 0.249238 CATGAGTCTACTCTGGCCGC 60.249 60.000 11.22 0.00 43.25 6.53
1774 2298 4.379186 GGCATTGAACATTCAGAGTGTGAG 60.379 45.833 0.00 0.00 38.61 3.51
1775 2299 3.503363 GGCATTGAACATTCAGAGTGTGA 59.497 43.478 0.00 0.00 38.61 3.58
1779 2312 5.948162 AGTAATGGCATTGAACATTCAGAGT 59.052 36.000 22.57 0.00 38.61 3.24
1796 2329 1.209019 AGAGTGCAGAGCCAGTAATGG 59.791 52.381 4.42 4.42 0.00 3.16
1797 2330 2.093816 TGAGAGTGCAGAGCCAGTAATG 60.094 50.000 0.00 0.00 0.00 1.90
1798 2331 2.093764 GTGAGAGTGCAGAGCCAGTAAT 60.094 50.000 0.00 0.00 0.00 1.89
1799 2332 1.273606 GTGAGAGTGCAGAGCCAGTAA 59.726 52.381 0.00 0.00 0.00 2.24
1800 2333 0.891373 GTGAGAGTGCAGAGCCAGTA 59.109 55.000 0.00 0.00 0.00 2.74
1801 2334 1.117749 TGTGAGAGTGCAGAGCCAGT 61.118 55.000 0.00 0.00 0.00 4.00
1802 2335 0.390078 CTGTGAGAGTGCAGAGCCAG 60.390 60.000 0.00 0.00 34.87 4.85
1803 2336 1.670015 CTGTGAGAGTGCAGAGCCA 59.330 57.895 0.00 0.00 34.87 4.75
1804 2337 1.741032 GCTGTGAGAGTGCAGAGCC 60.741 63.158 0.00 0.00 46.14 4.70
1805 2338 3.873449 GCTGTGAGAGTGCAGAGC 58.127 61.111 0.00 0.00 45.89 4.09
1806 2339 1.875009 TTTGCTGTGAGAGTGCAGAG 58.125 50.000 0.00 0.00 38.01 3.35
1807 2340 1.942657 GTTTTGCTGTGAGAGTGCAGA 59.057 47.619 0.00 0.00 38.01 4.26
1808 2341 1.945394 AGTTTTGCTGTGAGAGTGCAG 59.055 47.619 0.00 0.00 38.01 4.41
1809 2342 2.042686 AGTTTTGCTGTGAGAGTGCA 57.957 45.000 0.00 0.00 34.69 4.57
1810 2343 4.552166 TTTAGTTTTGCTGTGAGAGTGC 57.448 40.909 0.00 0.00 0.00 4.40
1811 2344 7.195646 TGAATTTTAGTTTTGCTGTGAGAGTG 58.804 34.615 0.00 0.00 0.00 3.51
1812 2345 7.067494 ACTGAATTTTAGTTTTGCTGTGAGAGT 59.933 33.333 0.00 0.00 0.00 3.24
1813 2346 7.420800 ACTGAATTTTAGTTTTGCTGTGAGAG 58.579 34.615 0.00 0.00 0.00 3.20
1814 2347 7.333528 ACTGAATTTTAGTTTTGCTGTGAGA 57.666 32.000 0.00 0.00 0.00 3.27
1817 2350 6.086765 CGCTACTGAATTTTAGTTTTGCTGTG 59.913 38.462 0.00 0.00 0.00 3.66
1818 2351 6.142817 CGCTACTGAATTTTAGTTTTGCTGT 58.857 36.000 0.00 0.00 0.00 4.40
1825 2358 5.008217 TGCACAACGCTACTGAATTTTAGTT 59.992 36.000 0.00 0.00 43.06 2.24
1828 2361 5.621197 ATGCACAACGCTACTGAATTTTA 57.379 34.783 0.00 0.00 43.06 1.52
1831 2364 3.253188 ACAATGCACAACGCTACTGAATT 59.747 39.130 0.00 0.00 43.06 2.17
1842 2378 2.755836 ACGTTCAGACAATGCACAAC 57.244 45.000 0.00 0.00 0.00 3.32
1872 2408 5.437289 AACCAAACATATGTGATATGCCG 57.563 39.130 9.63 0.00 45.05 5.69
1873 2409 5.536161 AGGAACCAAACATATGTGATATGCC 59.464 40.000 9.63 7.87 45.05 4.40
1877 2413 8.274322 AGATCAAGGAACCAAACATATGTGATA 58.726 33.333 9.63 0.00 0.00 2.15
1879 2415 6.484288 AGATCAAGGAACCAAACATATGTGA 58.516 36.000 9.63 0.00 0.00 3.58
1880 2416 6.764308 AGATCAAGGAACCAAACATATGTG 57.236 37.500 9.63 0.00 0.00 3.21
1881 2417 6.350445 GCAAGATCAAGGAACCAAACATATGT 60.350 38.462 1.41 1.41 0.00 2.29
1882 2418 6.038356 GCAAGATCAAGGAACCAAACATATG 58.962 40.000 0.00 0.00 0.00 1.78
1886 2422 2.293122 CGCAAGATCAAGGAACCAAACA 59.707 45.455 0.00 0.00 43.02 2.83
1887 2423 2.293399 ACGCAAGATCAAGGAACCAAAC 59.707 45.455 0.00 0.00 43.62 2.93
1889 2425 1.879380 CACGCAAGATCAAGGAACCAA 59.121 47.619 0.00 0.00 43.62 3.67
1898 2441 1.438651 GGCAACTACACGCAAGATCA 58.561 50.000 0.00 0.00 43.62 2.92
1993 2536 4.785767 CTGACTGACCTTGCAGCA 57.214 55.556 0.00 0.00 39.51 4.41
1996 2539 2.431683 GGGCTGACTGACCTTGCA 59.568 61.111 0.00 0.00 41.93 4.08
2009 2552 3.631250 TGAAAGTGAAGAAACAAGGGCT 58.369 40.909 0.00 0.00 0.00 5.19
2048 2591 5.451798 GGAAACACAAACATGAACATCTGGT 60.452 40.000 0.00 0.00 0.00 4.00
2049 2592 4.984161 GGAAACACAAACATGAACATCTGG 59.016 41.667 0.00 0.00 0.00 3.86
2050 2593 5.835257 AGGAAACACAAACATGAACATCTG 58.165 37.500 0.00 0.00 0.00 2.90
2114 2668 4.641396 TGGTCTCGATGTTGTTCTTGATT 58.359 39.130 0.00 0.00 0.00 2.57
2195 2749 2.163601 AACCCGCGAGTACCTTGGTC 62.164 60.000 8.23 0.00 0.00 4.02
2198 2752 1.447314 GGAACCCGCGAGTACCTTG 60.447 63.158 8.23 0.00 0.00 3.61
2246 2804 1.997874 AAGGGGAGCCTGCCTACAG 60.998 63.158 1.05 0.00 44.05 2.74
2352 2913 3.662759 TCCAATAGAATGGGTGGGAAC 57.337 47.619 0.00 0.00 41.05 3.62
2445 3008 3.236632 TCTTGGTGTCATGACTCGATG 57.763 47.619 25.55 19.60 0.00 3.84
2541 3922 8.243426 TGCAGTTGAAAGCGATATTTTATCTTT 58.757 29.630 0.00 0.00 0.00 2.52
2544 3925 7.189512 AGTGCAGTTGAAAGCGATATTTTATC 58.810 34.615 0.00 0.00 0.00 1.75
2551 3934 3.058983 CACAAGTGCAGTTGAAAGCGATA 60.059 43.478 35.07 0.00 0.00 2.92
2560 3943 3.441496 ACAAATCCACAAGTGCAGTTG 57.559 42.857 28.65 28.65 0.00 3.16
2585 3970 6.467723 AGTTGTAGTCTATTTGCTTGAACG 57.532 37.500 0.00 0.00 0.00 3.95
2690 4104 0.666274 TGACACGCCAGTTCGATCAC 60.666 55.000 0.00 0.00 0.00 3.06
2696 4112 3.414700 CCGCTGACACGCCAGTTC 61.415 66.667 0.00 0.00 36.57 3.01
2773 4200 7.597369 TGCTATGCCGTTATACATACAGTAAAG 59.403 37.037 0.00 0.00 36.05 1.85
2804 4231 7.488471 ACCGTATATTCGACAAGAAGAAAGAAG 59.512 37.037 3.00 0.00 42.92 2.85
2805 4232 7.318141 ACCGTATATTCGACAAGAAGAAAGAA 58.682 34.615 3.00 0.00 42.92 2.52
2806 4233 6.860080 ACCGTATATTCGACAAGAAGAAAGA 58.140 36.000 3.00 0.00 42.92 2.52
2868 4295 1.296715 CCCGGTTGTGGAGAAGAGG 59.703 63.158 0.00 0.00 0.00 3.69
2964 4404 8.118976 ACTTGTAGAAACTACAGCAGTGTATA 57.881 34.615 12.46 0.00 38.51 1.47
2975 4415 6.444633 TCACAGCAGTACTTGTAGAAACTAC 58.555 40.000 0.00 0.00 0.00 2.73
2982 4426 6.528423 GTCTATGTTCACAGCAGTACTTGTAG 59.472 42.308 0.00 0.00 0.00 2.74
3051 4503 6.264744 AGAGCATAAATCTTGCATGCAACTAT 59.735 34.615 28.80 20.82 45.95 2.12
3060 4512 3.737774 CGATCGAGAGCATAAATCTTGCA 59.262 43.478 10.26 0.00 42.62 4.08
3062 4514 3.181546 CGCGATCGAGAGCATAAATCTTG 60.182 47.826 21.57 0.00 38.10 3.02
3063 4515 2.983136 CGCGATCGAGAGCATAAATCTT 59.017 45.455 21.57 0.00 38.10 2.40
3102 4556 9.059260 CACAAGATTTGACATGATATGGTATCA 57.941 33.333 0.00 2.46 33.60 2.15
3136 4595 3.313249 TCAGTTCATGTCTTGTGCAACTG 59.687 43.478 11.46 11.46 41.31 3.16
3165 4628 1.529226 TCCATACCCAAACACTTGCG 58.471 50.000 0.00 0.00 0.00 4.85
3178 4641 4.608445 GCGCAAACGAGTATGATTCCATAC 60.608 45.833 0.30 7.32 45.59 2.39
3182 4645 1.663643 TGCGCAAACGAGTATGATTCC 59.336 47.619 8.16 0.00 43.93 3.01
3211 4674 1.338020 GGGAGAACTGTGCCAACAAAG 59.662 52.381 0.00 0.00 37.15 2.77


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

AutoCloner maintained by Alex Coulton.