Multiple sequence alignment - TraesCS5B01G164900

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 TraesCS5B01G164900 chr5B 100.000 6572 0 0 1 6572 304817881 304824452 0.000000e+00 12137.0
1 TraesCS5B01G164900 chr5B 80.978 941 147 18 1 915 421722922 421721988 0.000000e+00 717.0
2 TraesCS5B01G164900 chr5B 87.055 309 23 9 4541 4840 304822117 304822417 3.800000e-87 333.0
3 TraesCS5B01G164900 chr5B 87.055 309 23 9 4237 4537 304822421 304822720 3.800000e-87 333.0
4 TraesCS5B01G164900 chr5D 94.946 5164 173 38 1000 6104 269237739 269242873 0.000000e+00 8010.0
5 TraesCS5B01G164900 chr5D 94.488 254 12 2 6294 6546 47520519 47520267 2.220000e-104 390.0
6 TraesCS5B01G164900 chr5D 91.039 279 22 3 6294 6572 269243045 269243320 2.240000e-99 374.0
7 TraesCS5B01G164900 chr5D 87.708 301 21 8 4549 4840 269241016 269241309 2.940000e-88 337.0
8 TraesCS5B01G164900 chr5D 98.333 60 1 0 6236 6295 560874508 560874449 9.010000e-19 106.0
9 TraesCS5B01G164900 chr5A 95.180 2531 100 11 1000 3513 357565086 357567611 0.000000e+00 3978.0
10 TraesCS5B01G164900 chr5A 95.799 976 33 3 4761 5734 357569370 357570339 0.000000e+00 1568.0
11 TraesCS5B01G164900 chr5A 94.532 695 35 3 3525 4218 357568027 357568719 0.000000e+00 1070.0
12 TraesCS5B01G164900 chr5A 82.460 878 128 15 1 866 458282318 458281455 0.000000e+00 745.0
13 TraesCS5B01G164900 chr5A 95.154 454 20 2 4278 4729 357568921 357569374 0.000000e+00 715.0
14 TraesCS5B01G164900 chr5A 89.195 435 19 10 5694 6104 357570355 357570785 9.770000e-143 518.0
15 TraesCS5B01G164900 chr5A 91.186 295 22 2 3016 3306 611029591 611029885 1.330000e-106 398.0
16 TraesCS5B01G164900 chr5A 90.909 297 23 2 3014 3306 660449496 660449792 4.780000e-106 396.0
17 TraesCS5B01G164900 chr5A 88.346 266 19 5 4583 4840 357568921 357569182 6.400000e-80 309.0
18 TraesCS5B01G164900 chr5A 87.938 257 29 2 6294 6548 577950108 577950364 1.070000e-77 302.0
19 TraesCS5B01G164900 chr5A 97.561 41 1 0 3310 3350 321924725 321924685 3.290000e-08 71.3
20 TraesCS5B01G164900 chrUn 80.101 990 153 27 1 969 359466747 359467713 0.000000e+00 697.0
21 TraesCS5B01G164900 chrUn 80.509 903 131 21 4 898 35565491 35566356 0.000000e+00 651.0
22 TraesCS5B01G164900 chrUn 80.000 680 103 19 307 969 350568222 350568885 7.710000e-129 472.0
23 TraesCS5B01G164900 chrUn 98.333 60 1 0 6236 6295 439559180 439559239 9.010000e-19 106.0
24 TraesCS5B01G164900 chr7A 80.101 990 153 27 1 969 31535636 31536602 0.000000e+00 697.0
25 TraesCS5B01G164900 chr7A 79.596 990 158 27 1 969 31554077 31555043 0.000000e+00 669.0
26 TraesCS5B01G164900 chr7A 80.000 680 103 19 307 969 31517498 31518161 7.710000e-129 472.0
27 TraesCS5B01G164900 chr7A 90.429 303 24 3 3009 3306 616470006 616469704 1.720000e-105 394.0
28 TraesCS5B01G164900 chr1A 81.914 857 119 21 135 974 495134457 495135294 0.000000e+00 691.0
29 TraesCS5B01G164900 chr1A 80.215 930 144 25 1 921 125990935 125990037 0.000000e+00 662.0
30 TraesCS5B01G164900 chr1A 91.525 295 20 3 3017 3306 2651306 2651600 1.030000e-107 401.0
31 TraesCS5B01G164900 chr1A 91.497 294 21 2 3017 3306 350489591 350489884 1.030000e-107 401.0
32 TraesCS5B01G164900 chr1A 92.520 254 15 4 6294 6546 500075713 500075963 1.740000e-95 361.0
33 TraesCS5B01G164900 chr3B 80.475 927 139 22 3 915 558191032 558190134 0.000000e+00 671.0
34 TraesCS5B01G164900 chr3B 82.361 703 99 17 227 915 167776962 167777653 7.340000e-164 588.0
35 TraesCS5B01G164900 chr3B 88.327 257 26 3 6294 6546 765087468 765087212 8.280000e-79 305.0
36 TraesCS5B01G164900 chr3B 98.333 60 1 0 6236 6295 201516719 201516660 9.010000e-19 106.0
37 TraesCS5B01G164900 chr3B 95.455 44 1 1 3310 3352 502811577 502811620 1.180000e-07 69.4
38 TraesCS5B01G164900 chr1B 80.903 864 128 20 52 898 606582116 606582959 0.000000e+00 647.0
39 TraesCS5B01G164900 chr1B 89.412 255 22 4 6293 6546 385174887 385175137 3.820000e-82 316.0
40 TraesCS5B01G164900 chr1B 87.938 257 30 1 6294 6549 69353471 69353215 1.070000e-77 302.0
41 TraesCS5B01G164900 chr6D 79.221 924 142 28 1 899 389918689 389919587 1.220000e-166 597.0
42 TraesCS5B01G164900 chr6D 84.127 378 58 1 48 425 446928809 446928434 1.350000e-96 364.0
43 TraesCS5B01G164900 chr6D 97.500 40 1 0 3311 3350 289507535 289507496 1.180000e-07 69.4
44 TraesCS5B01G164900 chr6D 97.500 40 1 0 3311 3350 423771142 423771103 1.180000e-07 69.4
45 TraesCS5B01G164900 chr1D 80.976 799 100 35 135 912 397637979 397638746 2.640000e-163 586.0
46 TraesCS5B01G164900 chr1D 81.603 549 77 12 48 576 433507245 433506701 3.640000e-117 433.0
47 TraesCS5B01G164900 chr1D 98.333 60 1 0 6236 6295 206075325 206075384 9.010000e-19 106.0
48 TraesCS5B01G164900 chr1D 96.667 60 2 0 6236 6295 254500038 254499979 4.190000e-17 100.0
49 TraesCS5B01G164900 chr1D 97.500 40 1 0 3311 3350 80020536 80020497 1.180000e-07 69.4
50 TraesCS5B01G164900 chr6A 83.553 456 64 7 468 913 551626998 551627452 3.670000e-112 416.0
51 TraesCS5B01G164900 chr4A 89.935 308 26 3 3003 3306 532067932 532067626 6.180000e-105 392.0
52 TraesCS5B01G164900 chr4A 87.988 333 28 10 2980 3306 478199709 478200035 3.720000e-102 383.0
53 TraesCS5B01G164900 chr4A 90.588 255 19 2 6294 6547 147557761 147557511 3.800000e-87 333.0
54 TraesCS5B01G164900 chr4A 98.333 60 1 0 6236 6295 538222020 538221961 9.010000e-19 106.0
55 TraesCS5B01G164900 chr3A 77.508 658 116 19 1 643 428567282 428567922 3.740000e-97 366.0
56 TraesCS5B01G164900 chr2A 90.625 256 22 2 6293 6546 744373968 744374223 8.160000e-89 339.0
57 TraesCS5B01G164900 chr2D 98.333 60 1 0 6236 6295 638826399 638826458 9.010000e-19 106.0
58 TraesCS5B01G164900 chr4D 90.123 81 6 2 6236 6316 66951166 66951244 3.240000e-18 104.0
59 TraesCS5B01G164900 chr4D 97.500 40 1 0 3311 3350 98888302 98888341 1.180000e-07 69.4
60 TraesCS5B01G164900 chr4D 97.500 40 1 0 3311 3350 298773239 298773278 1.180000e-07 69.4
61 TraesCS5B01G164900 chr7B 98.276 58 1 0 6237 6294 102631591 102631648 1.170000e-17 102.0


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 TraesCS5B01G164900 chr5B 304817881 304824452 6571 False 4267.666667 12137 91.370000 1 6572 3 chr5B.!!$F1 6571
1 TraesCS5B01G164900 chr5B 421721988 421722922 934 True 717.000000 717 80.978000 1 915 1 chr5B.!!$R1 914
2 TraesCS5B01G164900 chr5D 269237739 269243320 5581 False 2907.000000 8010 91.231000 1000 6572 3 chr5D.!!$F1 5572
3 TraesCS5B01G164900 chr5A 357565086 357570785 5699 False 1359.666667 3978 93.034333 1000 6104 6 chr5A.!!$F4 5104
4 TraesCS5B01G164900 chr5A 458281455 458282318 863 True 745.000000 745 82.460000 1 866 1 chr5A.!!$R2 865
5 TraesCS5B01G164900 chrUn 359466747 359467713 966 False 697.000000 697 80.101000 1 969 1 chrUn.!!$F3 968
6 TraesCS5B01G164900 chrUn 35565491 35566356 865 False 651.000000 651 80.509000 4 898 1 chrUn.!!$F1 894
7 TraesCS5B01G164900 chrUn 350568222 350568885 663 False 472.000000 472 80.000000 307 969 1 chrUn.!!$F2 662
8 TraesCS5B01G164900 chr7A 31535636 31536602 966 False 697.000000 697 80.101000 1 969 1 chr7A.!!$F2 968
9 TraesCS5B01G164900 chr7A 31554077 31555043 966 False 669.000000 669 79.596000 1 969 1 chr7A.!!$F3 968
10 TraesCS5B01G164900 chr7A 31517498 31518161 663 False 472.000000 472 80.000000 307 969 1 chr7A.!!$F1 662
11 TraesCS5B01G164900 chr1A 495134457 495135294 837 False 691.000000 691 81.914000 135 974 1 chr1A.!!$F3 839
12 TraesCS5B01G164900 chr1A 125990037 125990935 898 True 662.000000 662 80.215000 1 921 1 chr1A.!!$R1 920
13 TraesCS5B01G164900 chr3B 558190134 558191032 898 True 671.000000 671 80.475000 3 915 1 chr3B.!!$R2 912
14 TraesCS5B01G164900 chr3B 167776962 167777653 691 False 588.000000 588 82.361000 227 915 1 chr3B.!!$F1 688
15 TraesCS5B01G164900 chr1B 606582116 606582959 843 False 647.000000 647 80.903000 52 898 1 chr1B.!!$F2 846
16 TraesCS5B01G164900 chr6D 389918689 389919587 898 False 597.000000 597 79.221000 1 899 1 chr6D.!!$F1 898
17 TraesCS5B01G164900 chr1D 397637979 397638746 767 False 586.000000 586 80.976000 135 912 1 chr1D.!!$F2 777
18 TraesCS5B01G164900 chr1D 433506701 433507245 544 True 433.000000 433 81.603000 48 576 1 chr1D.!!$R3 528
19 TraesCS5B01G164900 chr3A 428567282 428567922 640 False 366.000000 366 77.508000 1 643 1 chr3A.!!$F1 642

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
992 1071 0.319555 TCGCCAGTTCACACTACTGC 60.320 55.000 0.00 0.0 41.28 4.40 F
1606 1688 0.305922 CCATTCCGCTGCTTCGATTC 59.694 55.000 0.00 0.0 0.00 2.52 F
2101 2188 0.326264 AGTGGCCGAAGCATTCTTCT 59.674 50.000 0.00 0.0 44.75 2.85 F
2686 2773 0.179015 TTTGCCGACTGCTTGGGTTA 60.179 50.000 0.00 0.0 42.00 2.85 F
2710 2797 1.002888 CAGAAGATGCCAGGTCAGTGT 59.997 52.381 0.00 0.0 0.00 3.55 F
3414 3544 1.350684 TCCATTGTTGTCTAGCCAGCA 59.649 47.619 0.00 0.0 0.00 4.41 F
3517 3647 2.744741 TGGTTGTGGTGTATATGTTGCG 59.255 45.455 0.00 0.0 0.00 4.85 F
3796 4331 3.133901 TCACTGAACAGTTTGAGCCAGTA 59.866 43.478 4.63 0.0 40.20 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1855 1942 1.150135 TCCTGGAACTCCTTCTCCTGT 59.850 52.381 0.0 0.0 36.82 4.00 R
2686 2773 1.911357 TGACCTGGCATCTTCTGTGAT 59.089 47.619 0.0 0.0 0.00 3.06 R
3970 4505 4.213482 GTGTCCACTTCAGTAATTGGTGAC 59.787 45.833 0.0 0.0 36.89 3.67 R
4123 4673 4.400120 AGCCCTTCCGTTACAAATTAACA 58.600 39.130 0.0 0.0 0.00 2.41 R
4246 4965 4.808364 GCTCTCCTTGACACTGAATCATAC 59.192 45.833 0.0 0.0 0.00 2.39 R
4728 5449 0.741221 CTCCGCAACCTACCTCAAGC 60.741 60.000 0.0 0.0 0.00 4.01 R
5005 5726 0.935898 GCTCCTCGATGCACTTGATG 59.064 55.000 0.0 0.0 0.00 3.07 R
5724 6447 0.032540 ACGTGGTTCGGTTACCTGAC 59.967 55.000 0.0 0.0 44.69 3.51 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
105 106 4.845580 CAATCTGCTCCGCCCGCT 62.846 66.667 0.00 0.00 0.00 5.52
248 249 1.746516 GCAGAGGGCAAGGAAGATGAG 60.747 57.143 0.00 0.00 43.97 2.90
324 336 3.441290 CCGACGAGGAGGAGCGTT 61.441 66.667 0.00 0.00 45.00 4.84
367 379 1.825474 CTCACTTACCACGGTGGAGAT 59.175 52.381 32.72 13.82 40.96 2.75
410 422 2.028043 AACGCCAAGCAGCTTTGC 59.972 55.556 19.17 19.17 0.00 3.68
414 426 2.567497 GCCAAGCAGCTTTGCCTCA 61.567 57.895 18.53 0.00 34.90 3.86
526 552 2.614057 GCGCTTACAAGGCTACATCATT 59.386 45.455 0.00 0.00 0.00 2.57
555 596 3.425713 CGGGTCCGACTTCGACGA 61.426 66.667 2.83 0.00 43.02 4.20
576 617 4.988716 TGACGTCGCCCCACCTCT 62.989 66.667 11.62 0.00 0.00 3.69
626 677 2.248835 CGAAAGGGCAAACGGTCGT 61.249 57.895 0.00 0.00 0.00 4.34
658 709 1.625818 TGAAGCTCACCCTCTCCTTTC 59.374 52.381 0.00 0.00 0.00 2.62
706 758 3.254060 AGAATGTGTCGGATCGTTGAAG 58.746 45.455 0.00 0.00 0.00 3.02
752 816 7.029563 GGTGATCTTTTGGTGATGTTTATGTC 58.970 38.462 0.00 0.00 0.00 3.06
790 855 7.663827 TGATATCGGTTTATATGTCCGTTTCT 58.336 34.615 12.34 3.21 43.94 2.52
793 859 4.330620 TCGGTTTATATGTCCGTTTCTTGC 59.669 41.667 12.34 0.00 43.94 4.01
879 957 5.934043 CGGATATGAGAATGCCAGTATGAAA 59.066 40.000 0.00 0.00 39.69 2.69
915 993 1.083806 TGTCTGATCAATGTCCGCGC 61.084 55.000 0.00 0.00 0.00 6.86
916 994 1.521457 TCTGATCAATGTCCGCGCC 60.521 57.895 0.00 0.00 0.00 6.53
934 1013 3.691342 CCGCGGTTGTCTGAGGGA 61.691 66.667 19.50 0.00 36.47 4.20
942 1021 2.698797 GGTTGTCTGAGGGATCGGATTA 59.301 50.000 0.00 0.00 0.00 1.75
944 1023 2.598565 TGTCTGAGGGATCGGATTAGG 58.401 52.381 0.00 0.00 0.00 2.69
945 1024 1.896465 GTCTGAGGGATCGGATTAGGG 59.104 57.143 0.00 0.00 0.00 3.53
956 1035 2.616634 GGATTAGGGAAGTCCGGTTC 57.383 55.000 0.00 0.00 41.52 3.62
974 1053 5.923684 CCGGTTCTAGATGCTCTTAATCTTC 59.076 44.000 0.00 0.00 35.92 2.87
975 1054 5.627367 CGGTTCTAGATGCTCTTAATCTTCG 59.373 44.000 0.00 0.00 35.92 3.79
976 1055 5.404066 GGTTCTAGATGCTCTTAATCTTCGC 59.596 44.000 0.00 0.00 35.92 4.70
977 1056 5.127693 TCTAGATGCTCTTAATCTTCGCC 57.872 43.478 0.00 0.00 35.92 5.54
978 1057 3.827008 AGATGCTCTTAATCTTCGCCA 57.173 42.857 0.00 0.00 29.94 5.69
979 1058 3.726607 AGATGCTCTTAATCTTCGCCAG 58.273 45.455 0.00 0.00 29.94 4.85
980 1059 3.133721 AGATGCTCTTAATCTTCGCCAGT 59.866 43.478 0.00 0.00 29.94 4.00
981 1060 3.334583 TGCTCTTAATCTTCGCCAGTT 57.665 42.857 0.00 0.00 0.00 3.16
982 1061 3.262420 TGCTCTTAATCTTCGCCAGTTC 58.738 45.455 0.00 0.00 0.00 3.01
983 1062 3.262420 GCTCTTAATCTTCGCCAGTTCA 58.738 45.455 0.00 0.00 0.00 3.18
984 1063 3.062774 GCTCTTAATCTTCGCCAGTTCAC 59.937 47.826 0.00 0.00 0.00 3.18
985 1064 4.245660 CTCTTAATCTTCGCCAGTTCACA 58.754 43.478 0.00 0.00 0.00 3.58
986 1065 3.994392 TCTTAATCTTCGCCAGTTCACAC 59.006 43.478 0.00 0.00 0.00 3.82
987 1066 2.550830 AATCTTCGCCAGTTCACACT 57.449 45.000 0.00 0.00 0.00 3.55
988 1067 3.678056 AATCTTCGCCAGTTCACACTA 57.322 42.857 0.00 0.00 0.00 2.74
989 1068 2.433868 TCTTCGCCAGTTCACACTAC 57.566 50.000 0.00 0.00 0.00 2.73
990 1069 1.961394 TCTTCGCCAGTTCACACTACT 59.039 47.619 0.00 0.00 0.00 2.57
991 1070 2.061773 CTTCGCCAGTTCACACTACTG 58.938 52.381 0.00 0.00 42.06 2.74
992 1071 0.319555 TCGCCAGTTCACACTACTGC 60.320 55.000 0.00 0.00 41.28 4.40
993 1072 0.599991 CGCCAGTTCACACTACTGCA 60.600 55.000 0.00 0.00 41.28 4.41
994 1073 1.151668 GCCAGTTCACACTACTGCAG 58.848 55.000 13.48 13.48 41.28 4.41
995 1074 1.541233 GCCAGTTCACACTACTGCAGT 60.541 52.381 25.12 25.12 41.28 4.40
996 1075 2.408050 CCAGTTCACACTACTGCAGTC 58.592 52.381 25.56 6.19 41.28 3.51
997 1076 2.224042 CCAGTTCACACTACTGCAGTCA 60.224 50.000 25.56 9.17 41.28 3.41
998 1077 3.555795 CCAGTTCACACTACTGCAGTCAT 60.556 47.826 25.56 10.08 41.28 3.06
1005 1084 1.821753 ACTACTGCAGTCATTCGCTCT 59.178 47.619 25.56 0.00 28.33 4.09
1008 1087 1.207390 CTGCAGTCATTCGCTCTAGC 58.793 55.000 5.25 0.00 37.78 3.42
1105 1184 0.470833 CTCGTCTCCATCCCCATCCT 60.471 60.000 0.00 0.00 0.00 3.24
1108 1187 1.152247 TCTCCATCCCCATCCTCCG 60.152 63.158 0.00 0.00 0.00 4.63
1189 1270 2.210144 CTTCCCCAATCCGCCTTCCA 62.210 60.000 0.00 0.00 0.00 3.53
1190 1271 2.440247 CCCCAATCCGCCTTCCAC 60.440 66.667 0.00 0.00 0.00 4.02
1295 1376 0.389948 CCTCGGCGAAAGTAAGTGCT 60.390 55.000 12.13 0.00 0.00 4.40
1396 1477 3.542648 GGTAGGTAGCCCTTGATTGTTC 58.457 50.000 0.00 0.00 42.66 3.18
1502 1584 3.498774 AGAAGCCGAATTGATGCCTAT 57.501 42.857 0.00 0.00 0.00 2.57
1508 1590 5.072741 AGCCGAATTGATGCCTATTTATGT 58.927 37.500 0.00 0.00 0.00 2.29
1516 1598 5.350633 TGATGCCTATTTATGTTTTGCTGC 58.649 37.500 0.00 0.00 0.00 5.25
1530 1612 1.407936 TGCTGCCCTTGCTAACAAAA 58.592 45.000 0.00 0.00 38.71 2.44
1534 1616 3.803368 GCTGCCCTTGCTAACAAAATTGT 60.803 43.478 0.00 0.00 40.02 2.71
1539 1621 5.737635 GCCCTTGCTAACAAAATTGTGTGTA 60.738 40.000 0.93 0.00 36.56 2.90
1587 1669 5.347012 ACATGTGCAATTTAAGCTTTTGC 57.653 34.783 21.95 21.95 44.59 3.68
1606 1688 0.305922 CCATTCCGCTGCTTCGATTC 59.694 55.000 0.00 0.00 0.00 2.52
1637 1724 7.698130 GCTGTTTGGATATGTTAACTGATTGTC 59.302 37.037 7.22 0.00 0.00 3.18
1644 1731 8.184192 GGATATGTTAACTGATTGTCTTGTTGG 58.816 37.037 7.22 0.00 0.00 3.77
1646 1733 4.037446 TGTTAACTGATTGTCTTGTTGGCC 59.963 41.667 7.22 0.00 0.00 5.36
1647 1734 1.620822 ACTGATTGTCTTGTTGGCCC 58.379 50.000 0.00 0.00 0.00 5.80
1648 1735 1.145738 ACTGATTGTCTTGTTGGCCCT 59.854 47.619 0.00 0.00 0.00 5.19
1664 1751 1.804372 GCCCTTATGCAGAGTCTGTCG 60.804 57.143 21.06 5.81 33.43 4.35
1825 1912 2.743928 CGTGGCCTTGAGCAGTCC 60.744 66.667 3.32 0.00 46.50 3.85
1978 2065 1.664659 CAGGAGAAAAGAGATGCTGCG 59.335 52.381 0.00 0.00 0.00 5.18
2011 2098 1.531259 TGGCAAGTCCAAGCTGTCA 59.469 52.632 0.00 0.00 43.21 3.58
2099 2186 1.168714 GAAGTGGCCGAAGCATTCTT 58.831 50.000 0.00 0.00 44.75 2.52
2101 2188 0.326264 AGTGGCCGAAGCATTCTTCT 59.674 50.000 0.00 0.00 44.75 2.85
2116 2203 3.401033 TCTTCTGAAGGAAATGCACGA 57.599 42.857 16.83 0.00 33.07 4.35
2163 2250 0.868406 CCTCGTTCTGAACTTGCCAC 59.132 55.000 17.60 0.00 0.00 5.01
2230 2317 5.487433 TCAGACAACAGAAAGAACTTGACA 58.513 37.500 0.00 0.00 0.00 3.58
2287 2374 1.949525 GCATCGCAACCATATGTCCTT 59.050 47.619 1.24 0.00 0.00 3.36
2323 2410 4.541705 TGGAGGACTTCTATTCTGGAGAG 58.458 47.826 0.00 0.00 0.00 3.20
2491 2578 1.132262 GATCGGGCGAAAAAGATTGCA 59.868 47.619 0.00 0.00 0.00 4.08
2686 2773 0.179015 TTTGCCGACTGCTTGGGTTA 60.179 50.000 0.00 0.00 42.00 2.85
2710 2797 1.002888 CAGAAGATGCCAGGTCAGTGT 59.997 52.381 0.00 0.00 0.00 3.55
2712 2799 2.499289 AGAAGATGCCAGGTCAGTGTAG 59.501 50.000 0.00 0.00 0.00 2.74
2727 2814 7.039011 AGGTCAGTGTAGTGATGAACTAATCAA 60.039 37.037 0.00 0.00 43.08 2.57
2869 2956 4.644685 GTGGGTAACATATTTGCTGGTCAT 59.355 41.667 0.00 0.00 39.74 3.06
2875 2962 5.824904 ACATATTTGCTGGTCATTGAGTC 57.175 39.130 0.00 0.00 0.00 3.36
2942 3029 3.579151 ACTACCACCTCCAGAAGTTCTTC 59.421 47.826 1.56 4.58 0.00 2.87
2945 3032 2.307098 CCACCTCCAGAAGTTCTTCCAT 59.693 50.000 1.56 0.00 0.00 3.41
3043 3157 6.296145 CCTCCTTTGGTTCATAGGATAGGATC 60.296 46.154 7.38 0.00 39.94 3.36
3071 3188 8.581253 AGGAATAGAAAACTTGTAGGAAATGG 57.419 34.615 0.00 0.00 0.00 3.16
3309 3434 3.855689 ATGAAATTCCGCCAAACTGAG 57.144 42.857 0.00 0.00 0.00 3.35
3414 3544 1.350684 TCCATTGTTGTCTAGCCAGCA 59.649 47.619 0.00 0.00 0.00 4.41
3419 3549 3.981071 TGTTGTCTAGCCAGCAGTTAT 57.019 42.857 0.00 0.00 0.00 1.89
3517 3647 2.744741 TGGTTGTGGTGTATATGTTGCG 59.255 45.455 0.00 0.00 0.00 4.85
3647 4182 7.934457 TCTTATGCTATTTGCCTTTTCTCATC 58.066 34.615 0.00 0.00 42.00 2.92
3658 4193 6.367161 TGCCTTTTCTCATCCATGATGATTA 58.633 36.000 7.19 0.00 46.16 1.75
3796 4331 3.133901 TCACTGAACAGTTTGAGCCAGTA 59.866 43.478 4.63 0.00 40.20 2.74
3958 4493 7.663905 TGCAAGAATACAATAAACTGTACCTGT 59.336 33.333 0.00 0.00 34.68 4.00
3970 4505 3.323979 ACTGTACCTGTACTTCCACCAAG 59.676 47.826 8.75 0.00 37.00 3.61
4007 4557 3.443681 AGTGGACACCAGTTGTTTCTTTG 59.556 43.478 0.00 0.00 39.17 2.77
4008 4558 3.192633 GTGGACACCAGTTGTTTCTTTGT 59.807 43.478 0.00 0.00 39.17 2.83
4009 4559 3.192422 TGGACACCAGTTGTTTCTTTGTG 59.808 43.478 0.00 0.00 39.17 3.33
4010 4560 3.192633 GGACACCAGTTGTTTCTTTGTGT 59.807 43.478 0.00 0.00 39.17 3.72
4011 4561 4.321675 GGACACCAGTTGTTTCTTTGTGTT 60.322 41.667 0.00 0.00 39.17 3.32
4012 4562 5.106078 GGACACCAGTTGTTTCTTTGTGTTA 60.106 40.000 0.00 0.00 39.17 2.41
4013 4563 5.705902 ACACCAGTTGTTTCTTTGTGTTAC 58.294 37.500 0.00 0.00 33.09 2.50
4014 4564 5.099575 CACCAGTTGTTTCTTTGTGTTACC 58.900 41.667 0.00 0.00 0.00 2.85
4015 4565 5.014202 ACCAGTTGTTTCTTTGTGTTACCT 58.986 37.500 0.00 0.00 0.00 3.08
4016 4566 5.479027 ACCAGTTGTTTCTTTGTGTTACCTT 59.521 36.000 0.00 0.00 0.00 3.50
4017 4567 6.033966 CCAGTTGTTTCTTTGTGTTACCTTC 58.966 40.000 0.00 0.00 0.00 3.46
4018 4568 6.033966 CAGTTGTTTCTTTGTGTTACCTTCC 58.966 40.000 0.00 0.00 0.00 3.46
4019 4569 5.949952 AGTTGTTTCTTTGTGTTACCTTCCT 59.050 36.000 0.00 0.00 0.00 3.36
4020 4570 6.436218 AGTTGTTTCTTTGTGTTACCTTCCTT 59.564 34.615 0.00 0.00 0.00 3.36
4021 4571 6.844097 TGTTTCTTTGTGTTACCTTCCTTT 57.156 33.333 0.00 0.00 0.00 3.11
4123 4673 3.253677 GCTATGCTACACAGATACCGTCT 59.746 47.826 0.00 0.00 37.80 4.18
4151 4701 3.488778 TGTAACGGAAGGGCTTTGTTA 57.511 42.857 0.00 0.00 0.00 2.41
4152 4702 3.818180 TGTAACGGAAGGGCTTTGTTAA 58.182 40.909 0.00 0.00 30.84 2.01
4153 4703 4.400120 TGTAACGGAAGGGCTTTGTTAAT 58.600 39.130 0.00 0.00 30.84 1.40
4246 4965 7.556844 ACTATTACCAGACATCTGTTACCTTG 58.443 38.462 8.06 0.00 42.27 3.61
4303 5022 6.040278 TGTTTGCATCCAGTGATTTCAAGTTA 59.960 34.615 0.00 0.00 0.00 2.24
4610 5331 9.076596 GTTTGCATCCTGTGATTTTAAGTTATC 57.923 33.333 0.00 0.00 0.00 1.75
4627 5348 4.591498 AGTTATCAGTGGTGTAGTGGTTCA 59.409 41.667 0.00 0.00 0.00 3.18
4639 5360 8.356657 TGGTGTAGTGGTTCAAAATTCAATTAG 58.643 33.333 0.00 0.00 0.00 1.73
5005 5726 1.530293 CTGTCTGCACTGAAAGCTGTC 59.470 52.381 0.00 0.00 37.60 3.51
5047 5768 3.217626 CAAACTGGAGGAGCAATATCCC 58.782 50.000 0.00 0.00 40.53 3.85
5094 5815 1.849823 AGCTGGAGAAGGCCAAGGT 60.850 57.895 5.01 0.00 37.52 3.50
5143 5864 3.059982 CCACAGTCGAAGAGGCCA 58.940 61.111 5.01 0.00 36.95 5.36
5178 5899 0.179100 CTCTATGCACCCCGTGTCAG 60.179 60.000 0.00 0.00 35.75 3.51
5260 5981 2.604174 GCAGTTTGTGTACGGCGCT 61.604 57.895 6.90 0.00 30.03 5.92
5314 6035 0.747255 CTCCCTACACCATCTCACCG 59.253 60.000 0.00 0.00 0.00 4.94
5703 6426 7.582435 TCATCTTTACTGTTCTTTCGTCATC 57.418 36.000 0.00 0.00 0.00 2.92
5724 6447 0.816825 CGGTGCTTCATCCATGGAGG 60.817 60.000 20.49 20.49 33.86 4.30
5746 6537 2.374995 GGTAACCGAACCACGTCGC 61.375 63.158 0.00 0.00 39.74 5.19
5778 6569 3.077359 CAGTTTTGGAGAGGCAGGTAAG 58.923 50.000 0.00 0.00 0.00 2.34
5821 6612 5.527951 TGCTGTCAATGAATTGCAATGTTTT 59.472 32.000 13.82 4.02 37.68 2.43
5888 6679 3.786635 ACGCCACATAAGAGAAGTGATC 58.213 45.455 0.00 0.00 35.33 2.92
5955 6746 6.884836 AGGGACATTACAAATAGTCTTCCAAC 59.115 38.462 0.00 0.00 0.00 3.77
6064 6855 1.942677 TATCGTGTGGTTTATGCGGG 58.057 50.000 0.00 0.00 0.00 6.13
6104 6906 2.814097 GCTTAAACCCTTGCTCACAGGA 60.814 50.000 0.00 0.00 0.00 3.86
6190 7034 8.076178 GTGAAATTTTTCTCGGGGATACATATG 58.924 37.037 0.00 0.00 38.02 1.78
6206 7050 4.973168 ACATATGCACATTCCGAATACCT 58.027 39.130 1.58 0.00 0.00 3.08
6209 7053 3.066291 TGCACATTCCGAATACCTGTT 57.934 42.857 0.00 0.00 0.00 3.16
6218 7062 6.790285 TTCCGAATACCTGTTGTAAGTTTC 57.210 37.500 0.00 0.00 31.94 2.78
6231 7075 6.364165 TGTTGTAAGTTTCGGTAGAAATCTCG 59.636 38.462 0.00 0.00 46.64 4.04
6233 7077 6.449698 TGTAAGTTTCGGTAGAAATCTCGTT 58.550 36.000 0.00 0.00 46.64 3.85
6234 7078 6.925165 TGTAAGTTTCGGTAGAAATCTCGTTT 59.075 34.615 0.00 0.00 46.64 3.60
6235 7079 6.463483 AAGTTTCGGTAGAAATCTCGTTTC 57.537 37.500 0.00 0.00 46.64 2.78
6236 7080 4.928020 AGTTTCGGTAGAAATCTCGTTTCC 59.072 41.667 0.00 0.00 46.64 3.13
6237 7081 4.796038 TTCGGTAGAAATCTCGTTTCCT 57.204 40.909 0.00 0.00 45.96 3.36
6238 7082 4.796038 TCGGTAGAAATCTCGTTTCCTT 57.204 40.909 0.00 0.00 45.96 3.36
6239 7083 5.902613 TCGGTAGAAATCTCGTTTCCTTA 57.097 39.130 0.00 0.00 45.96 2.69
6240 7084 5.888105 TCGGTAGAAATCTCGTTTCCTTAG 58.112 41.667 0.00 0.00 45.96 2.18
6241 7085 5.649395 TCGGTAGAAATCTCGTTTCCTTAGA 59.351 40.000 0.00 0.00 45.96 2.10
6242 7086 6.320672 TCGGTAGAAATCTCGTTTCCTTAGAT 59.679 38.462 0.00 0.00 45.96 1.98
6243 7087 6.979238 CGGTAGAAATCTCGTTTCCTTAGATT 59.021 38.462 0.00 0.00 45.96 2.40
6245 7089 9.813446 GGTAGAAATCTCGTTTCCTTAGATTTA 57.187 33.333 8.96 0.00 45.39 1.40
6254 7098 9.615295 CTCGTTTCCTTAGATTTATACTAGAGC 57.385 37.037 0.00 0.00 0.00 4.09
6255 7099 8.574737 TCGTTTCCTTAGATTTATACTAGAGCC 58.425 37.037 0.00 0.00 0.00 4.70
6256 7100 8.358148 CGTTTCCTTAGATTTATACTAGAGCCA 58.642 37.037 0.00 0.00 0.00 4.75
6257 7101 9.478768 GTTTCCTTAGATTTATACTAGAGCCAC 57.521 37.037 0.00 0.00 0.00 5.01
6258 7102 7.450124 TCCTTAGATTTATACTAGAGCCACG 57.550 40.000 0.00 0.00 0.00 4.94
6259 7103 7.229308 TCCTTAGATTTATACTAGAGCCACGA 58.771 38.462 0.00 0.00 0.00 4.35
6260 7104 7.889073 TCCTTAGATTTATACTAGAGCCACGAT 59.111 37.037 0.00 0.00 0.00 3.73
6261 7105 7.971168 CCTTAGATTTATACTAGAGCCACGATG 59.029 40.741 0.00 0.00 0.00 3.84
6262 7106 8.631480 TTAGATTTATACTAGAGCCACGATGA 57.369 34.615 0.00 0.00 0.00 2.92
6263 7107 7.710676 AGATTTATACTAGAGCCACGATGAT 57.289 36.000 0.00 0.00 0.00 2.45
6264 7108 8.128322 AGATTTATACTAGAGCCACGATGATT 57.872 34.615 0.00 0.00 0.00 2.57
6265 7109 8.589338 AGATTTATACTAGAGCCACGATGATTT 58.411 33.333 0.00 0.00 0.00 2.17
6266 7110 9.856488 GATTTATACTAGAGCCACGATGATTTA 57.144 33.333 0.00 0.00 0.00 1.40
6267 7111 9.862371 ATTTATACTAGAGCCACGATGATTTAG 57.138 33.333 0.00 0.00 0.00 1.85
6268 7112 6.902771 ATACTAGAGCCACGATGATTTAGT 57.097 37.500 0.00 0.00 0.00 2.24
6269 7113 5.189659 ACTAGAGCCACGATGATTTAGTC 57.810 43.478 0.00 0.00 0.00 2.59
6270 7114 4.890581 ACTAGAGCCACGATGATTTAGTCT 59.109 41.667 0.00 0.00 0.00 3.24
6271 7115 4.314740 AGAGCCACGATGATTTAGTCTC 57.685 45.455 0.00 0.00 0.00 3.36
6272 7116 3.701542 AGAGCCACGATGATTTAGTCTCA 59.298 43.478 0.00 0.00 0.00 3.27
6273 7117 4.160439 AGAGCCACGATGATTTAGTCTCAA 59.840 41.667 0.00 0.00 0.00 3.02
6274 7118 4.437239 AGCCACGATGATTTAGTCTCAAG 58.563 43.478 0.00 0.00 0.00 3.02
6275 7119 3.001736 GCCACGATGATTTAGTCTCAAGC 59.998 47.826 0.00 0.00 0.00 4.01
6276 7120 4.437239 CCACGATGATTTAGTCTCAAGCT 58.563 43.478 0.00 0.00 0.00 3.74
6277 7121 5.592054 CCACGATGATTTAGTCTCAAGCTA 58.408 41.667 0.00 0.00 0.00 3.32
6278 7122 6.042777 CCACGATGATTTAGTCTCAAGCTAA 58.957 40.000 0.00 0.00 0.00 3.09
6279 7123 6.535150 CCACGATGATTTAGTCTCAAGCTAAA 59.465 38.462 0.00 0.00 41.04 1.85
6280 7124 7.394872 CACGATGATTTAGTCTCAAGCTAAAC 58.605 38.462 0.00 0.00 40.04 2.01
6281 7125 7.063426 CACGATGATTTAGTCTCAAGCTAAACA 59.937 37.037 0.00 0.00 40.04 2.83
6282 7126 7.602644 ACGATGATTTAGTCTCAAGCTAAACAA 59.397 33.333 0.00 0.00 40.04 2.83
6283 7127 8.443160 CGATGATTTAGTCTCAAGCTAAACAAA 58.557 33.333 0.00 0.00 40.04 2.83
6286 7130 8.567948 TGATTTAGTCTCAAGCTAAACAAAAGG 58.432 33.333 0.00 0.00 40.04 3.11
6287 7131 4.837896 AGTCTCAAGCTAAACAAAAGGC 57.162 40.909 0.00 0.00 0.00 4.35
6288 7132 4.207165 AGTCTCAAGCTAAACAAAAGGCA 58.793 39.130 0.00 0.00 0.00 4.75
6289 7133 4.644685 AGTCTCAAGCTAAACAAAAGGCAA 59.355 37.500 0.00 0.00 0.00 4.52
6290 7134 4.978580 GTCTCAAGCTAAACAAAAGGCAAG 59.021 41.667 0.00 0.00 0.00 4.01
6291 7135 4.037923 TCTCAAGCTAAACAAAAGGCAAGG 59.962 41.667 0.00 0.00 0.00 3.61
6292 7136 3.069443 TCAAGCTAAACAAAAGGCAAGGG 59.931 43.478 0.00 0.00 0.00 3.95
6312 7156 5.399113 AGGGTTTGTTTTGGGCTATAGAAA 58.601 37.500 3.21 0.00 0.00 2.52
6429 7273 3.764237 TCCAGCTTTTTACCGAGTCTT 57.236 42.857 0.00 0.00 0.00 3.01
6436 7280 5.875359 AGCTTTTTACCGAGTCTTAGGAATG 59.125 40.000 2.71 0.00 0.00 2.67
6446 7290 5.744345 CGAGTCTTAGGAATGTGTGTATGTC 59.256 44.000 0.00 0.00 0.00 3.06
6500 7344 7.173047 AGCAACAGAAGTGTGTTTTTCAAAAAT 59.827 29.630 0.00 0.00 38.65 1.82
6504 7348 9.050601 ACAGAAGTGTGTTTTTCAAAAATTTCA 57.949 25.926 0.00 0.00 34.75 2.69
6534 7378 1.524621 CAATGGAGCCCGGTAGCTG 60.525 63.158 10.17 0.00 45.15 4.24
6535 7379 1.995626 AATGGAGCCCGGTAGCTGT 60.996 57.895 10.17 0.00 45.15 4.40
6546 7390 2.747446 CCGGTAGCTGTATGCACTTTTT 59.253 45.455 0.00 0.00 45.94 1.94
6549 7393 4.094887 CGGTAGCTGTATGCACTTTTTGAT 59.905 41.667 0.00 0.00 45.94 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
105 106 2.764128 GGTGGAGGAGGCCATCGA 60.764 66.667 5.01 0.00 40.68 3.59
157 158 2.047655 CGGCGAAGTGGGCACTAA 60.048 61.111 0.00 0.00 41.58 2.24
324 336 1.189524 CGGTACACCCACTGGAGGAA 61.190 60.000 0.00 0.00 34.81 3.36
367 379 2.029964 GAAGTCGTTGGGCGTCCA 59.970 61.111 3.51 3.51 42.25 4.02
376 388 2.927014 GCGTTGATCCTCTGAAGTCGTT 60.927 50.000 0.00 0.00 0.00 3.85
383 395 0.391661 GCTTGGCGTTGATCCTCTGA 60.392 55.000 0.00 0.00 0.00 3.27
414 426 1.303799 CGCTCAGGTTGCTCAATGCT 61.304 55.000 0.00 0.00 43.37 3.79
426 438 2.515523 CATTGCCTCCCGCTCAGG 60.516 66.667 0.00 0.00 38.78 3.86
441 453 4.457496 CCTCCACCGCTGTCGCAT 62.457 66.667 0.00 0.00 35.30 4.73
511 537 3.525199 AGGAGGAAATGATGTAGCCTTGT 59.475 43.478 0.00 0.00 0.00 3.16
526 552 1.305046 GGACCCGTCAGAGGAGGAA 60.305 63.158 0.00 0.00 0.00 3.36
555 596 3.681835 GTGGGGCGACGTCAGAGT 61.682 66.667 17.16 0.00 0.00 3.24
576 617 3.523087 TTGTAGGCGTCCGCAGCAA 62.523 57.895 14.19 11.41 44.11 3.91
620 671 2.178521 CCACTTCCTCGACGACCG 59.821 66.667 0.00 0.00 40.25 4.79
626 677 0.603569 GAGCTTCACCACTTCCTCGA 59.396 55.000 0.00 0.00 0.00 4.04
706 758 1.519408 AACGGGCATAGTTCACACAC 58.481 50.000 0.00 0.00 0.00 3.82
752 816 5.947228 ACCGATATCAAACAGGCATAATG 57.053 39.130 3.12 0.00 0.00 1.90
830 905 6.273825 CACCCTATATCCATACTATTCACGC 58.726 44.000 0.00 0.00 0.00 5.34
831 906 6.273825 GCACCCTATATCCATACTATTCACG 58.726 44.000 0.00 0.00 0.00 4.35
832 907 6.273825 CGCACCCTATATCCATACTATTCAC 58.726 44.000 0.00 0.00 0.00 3.18
834 909 5.597182 TCCGCACCCTATATCCATACTATTC 59.403 44.000 0.00 0.00 0.00 1.75
835 910 5.525484 TCCGCACCCTATATCCATACTATT 58.475 41.667 0.00 0.00 0.00 1.73
836 911 5.138758 TCCGCACCCTATATCCATACTAT 57.861 43.478 0.00 0.00 0.00 2.12
837 912 4.596354 TCCGCACCCTATATCCATACTA 57.404 45.455 0.00 0.00 0.00 1.82
838 913 3.468071 TCCGCACCCTATATCCATACT 57.532 47.619 0.00 0.00 0.00 2.12
879 957 0.249398 ACACTTCCTAAATCCGCGCT 59.751 50.000 5.56 0.00 0.00 5.92
915 993 4.760047 CCTCAGACAACCGCGGGG 62.760 72.222 31.76 23.38 40.11 5.73
916 994 4.760047 CCCTCAGACAACCGCGGG 62.760 72.222 31.76 15.62 0.00 6.13
919 997 1.519455 CGATCCCTCAGACAACCGC 60.519 63.158 0.00 0.00 0.00 5.68
920 998 1.141881 CCGATCCCTCAGACAACCG 59.858 63.158 0.00 0.00 0.00 4.44
921 999 1.123928 ATCCGATCCCTCAGACAACC 58.876 55.000 0.00 0.00 0.00 3.77
922 1000 2.990066 AATCCGATCCCTCAGACAAC 57.010 50.000 0.00 0.00 0.00 3.32
923 1001 2.965831 CCTAATCCGATCCCTCAGACAA 59.034 50.000 0.00 0.00 0.00 3.18
925 1003 1.896465 CCCTAATCCGATCCCTCAGAC 59.104 57.143 0.00 0.00 0.00 3.51
926 1004 1.787058 TCCCTAATCCGATCCCTCAGA 59.213 52.381 0.00 0.00 0.00 3.27
927 1005 2.310779 TCCCTAATCCGATCCCTCAG 57.689 55.000 0.00 0.00 0.00 3.35
929 1007 2.563620 GACTTCCCTAATCCGATCCCTC 59.436 54.545 0.00 0.00 0.00 4.30
930 1008 2.610873 GACTTCCCTAATCCGATCCCT 58.389 52.381 0.00 0.00 0.00 4.20
931 1009 1.624312 GGACTTCCCTAATCCGATCCC 59.376 57.143 0.00 0.00 0.00 3.85
942 1021 2.389715 CATCTAGAACCGGACTTCCCT 58.610 52.381 9.46 0.00 0.00 4.20
944 1023 1.757699 AGCATCTAGAACCGGACTTCC 59.242 52.381 9.46 0.00 0.00 3.46
945 1024 3.086818 GAGCATCTAGAACCGGACTTC 57.913 52.381 9.46 1.62 0.00 3.01
974 1053 0.599991 TGCAGTAGTGTGAACTGGCG 60.600 55.000 5.47 0.00 43.71 5.69
975 1054 1.151668 CTGCAGTAGTGTGAACTGGC 58.848 55.000 5.25 0.00 43.71 4.85
976 1055 2.224042 TGACTGCAGTAGTGTGAACTGG 60.224 50.000 21.73 0.00 43.71 4.00
977 1056 3.097877 TGACTGCAGTAGTGTGAACTG 57.902 47.619 21.73 0.00 45.80 3.16
978 1057 4.310769 GAATGACTGCAGTAGTGTGAACT 58.689 43.478 21.73 0.00 40.53 3.01
979 1058 3.121944 CGAATGACTGCAGTAGTGTGAAC 59.878 47.826 21.73 5.06 40.53 3.18
980 1059 3.317150 CGAATGACTGCAGTAGTGTGAA 58.683 45.455 21.73 0.00 40.53 3.18
981 1060 2.926586 GCGAATGACTGCAGTAGTGTGA 60.927 50.000 21.73 0.00 40.53 3.58
982 1061 1.391485 GCGAATGACTGCAGTAGTGTG 59.609 52.381 21.73 11.25 40.53 3.82
983 1062 1.273606 AGCGAATGACTGCAGTAGTGT 59.726 47.619 21.73 5.35 40.53 3.55
984 1063 1.923204 GAGCGAATGACTGCAGTAGTG 59.077 52.381 21.73 9.39 40.53 2.74
985 1064 1.821753 AGAGCGAATGACTGCAGTAGT 59.178 47.619 21.73 8.63 44.02 2.73
986 1065 2.575694 AGAGCGAATGACTGCAGTAG 57.424 50.000 21.73 10.10 0.00 2.57
987 1066 2.223595 GCTAGAGCGAATGACTGCAGTA 60.224 50.000 21.73 8.91 0.00 2.74
988 1067 1.470632 GCTAGAGCGAATGACTGCAGT 60.471 52.381 21.88 21.88 0.00 4.40
989 1068 1.207390 GCTAGAGCGAATGACTGCAG 58.793 55.000 13.48 13.48 0.00 4.41
990 1069 0.179100 GGCTAGAGCGAATGACTGCA 60.179 55.000 0.00 0.00 43.26 4.41
991 1070 0.179100 TGGCTAGAGCGAATGACTGC 60.179 55.000 0.00 0.00 43.26 4.40
992 1071 1.135915 AGTGGCTAGAGCGAATGACTG 59.864 52.381 0.00 0.00 43.26 3.51
993 1072 1.479709 AGTGGCTAGAGCGAATGACT 58.520 50.000 0.00 0.00 43.26 3.41
994 1073 2.544069 GGTAGTGGCTAGAGCGAATGAC 60.544 54.545 0.00 0.00 43.26 3.06
995 1074 1.681793 GGTAGTGGCTAGAGCGAATGA 59.318 52.381 0.00 0.00 43.26 2.57
996 1075 1.409064 TGGTAGTGGCTAGAGCGAATG 59.591 52.381 0.00 0.00 43.26 2.67
997 1076 1.683917 CTGGTAGTGGCTAGAGCGAAT 59.316 52.381 0.00 0.00 43.26 3.34
998 1077 1.103803 CTGGTAGTGGCTAGAGCGAA 58.896 55.000 0.00 0.00 43.26 4.70
1005 1084 0.759436 GGCCTAGCTGGTAGTGGCTA 60.759 60.000 14.37 0.00 42.84 3.93
1008 1087 2.444256 GGGGCCTAGCTGGTAGTGG 61.444 68.421 12.43 0.93 38.35 4.00
1105 1184 1.305201 GTGGAGTGTTGCTTTTCGGA 58.695 50.000 0.00 0.00 0.00 4.55
1108 1187 0.657368 CGCGTGGAGTGTTGCTTTTC 60.657 55.000 0.00 0.00 0.00 2.29
1189 1270 2.609920 GGAGGAGATCGAGGGGGT 59.390 66.667 0.00 0.00 0.00 4.95
1190 1271 2.203714 GGGAGGAGATCGAGGGGG 60.204 72.222 0.00 0.00 0.00 5.40
1295 1376 4.999310 TGAGACTAGGGAGAAGAAAGTGA 58.001 43.478 0.00 0.00 0.00 3.41
1502 1584 2.368221 AGCAAGGGCAGCAAAACATAAA 59.632 40.909 0.00 0.00 44.61 1.40
1508 1590 1.407936 TGTTAGCAAGGGCAGCAAAA 58.592 45.000 0.00 0.00 44.61 2.44
1516 1598 4.692228 ACACACAATTTTGTTAGCAAGGG 58.308 39.130 0.00 0.00 39.91 3.95
1572 1654 4.435917 GCGGAATGGCAAAAGCTTAAATTG 60.436 41.667 0.00 1.70 0.00 2.32
1587 1669 0.305922 GAATCGAAGCAGCGGAATGG 59.694 55.000 0.00 0.00 0.00 3.16
1606 1688 3.829886 AACATATCCAAACAGCACACG 57.170 42.857 0.00 0.00 0.00 4.49
1637 1724 1.747355 CTCTGCATAAGGGCCAACAAG 59.253 52.381 6.18 0.00 0.00 3.16
1644 1731 1.804372 CGACAGACTCTGCATAAGGGC 60.804 57.143 5.92 0.00 34.37 5.19
1646 1733 1.565305 GCGACAGACTCTGCATAAGG 58.435 55.000 5.92 0.00 34.37 2.69
1647 1734 1.134995 TGGCGACAGACTCTGCATAAG 60.135 52.381 5.92 0.00 34.37 1.73
1648 1735 0.894835 TGGCGACAGACTCTGCATAA 59.105 50.000 5.92 0.00 34.37 1.90
1825 1912 5.919141 CAGCTCATCAAACTTTTTCTTGAGG 59.081 40.000 0.00 0.00 35.14 3.86
1855 1942 1.150135 TCCTGGAACTCCTTCTCCTGT 59.850 52.381 0.00 0.00 36.82 4.00
1978 2065 5.008118 GGACTTGCCAAAGATCATAGCTAAC 59.992 44.000 0.00 0.00 36.84 2.34
2099 2186 2.162208 GCATTCGTGCATTTCCTTCAGA 59.838 45.455 0.00 0.00 34.41 3.27
2101 2188 1.885233 TGCATTCGTGCATTTCCTTCA 59.115 42.857 0.00 0.00 40.23 3.02
2116 2203 1.742411 GCAGCATTGCCATCTTGCATT 60.742 47.619 13.17 0.00 44.74 3.56
2287 2374 2.061848 TCCTCCAAGGAATCCAACACA 58.938 47.619 0.61 0.00 42.51 3.72
2323 2410 2.806945 TCCCATCCAACACCAGATTC 57.193 50.000 0.00 0.00 0.00 2.52
2422 2509 3.438087 CCTCAGACAACAAGCCAGTTATG 59.562 47.826 0.00 0.00 0.00 1.90
2549 2636 3.321396 TGAAGAAATGCATGTGCTTCCAA 59.679 39.130 22.94 10.80 42.66 3.53
2686 2773 1.911357 TGACCTGGCATCTTCTGTGAT 59.089 47.619 0.00 0.00 0.00 3.06
2710 2797 9.920133 GATAGATGCTTGATTAGTTCATCACTA 57.080 33.333 0.00 0.00 36.88 2.74
2712 2799 8.830201 AGATAGATGCTTGATTAGTTCATCAC 57.170 34.615 0.00 0.00 36.81 3.06
2727 2814 6.893583 ACAATGTTTACTGGAGATAGATGCT 58.106 36.000 0.00 0.00 0.00 3.79
2831 2918 2.863809 ACCCACAAGCTGGAAAACTAG 58.136 47.619 0.00 0.00 43.95 2.57
2849 2936 6.095440 ACTCAATGACCAGCAAATATGTTACC 59.905 38.462 0.00 0.00 0.00 2.85
2869 2956 3.595173 CACATATGTTCGGTGGACTCAA 58.405 45.455 5.37 0.00 0.00 3.02
2875 2962 2.487762 AGTTTGCACATATGTTCGGTGG 59.512 45.455 5.37 0.00 33.25 4.61
2942 3029 7.869429 GCAAAACTATCAATTCTGGGAATATGG 59.131 37.037 0.00 0.00 0.00 2.74
2945 3032 7.615365 ACAGCAAAACTATCAATTCTGGGAATA 59.385 33.333 0.00 0.00 0.00 1.75
3071 3188 8.316946 TCATAGGATTTGAGATACATGTCATCC 58.683 37.037 0.00 0.00 32.40 3.51
3476 3606 7.387948 ACAACCACACATCAGACTAAATAGAAC 59.612 37.037 0.00 0.00 0.00 3.01
3517 3647 5.520288 CAGATGCAACATAGTGTGGTACTAC 59.480 44.000 1.77 1.77 44.30 2.73
3690 4225 4.647564 ATGACACCTGTCCTCAAGAAAT 57.352 40.909 2.98 0.00 44.15 2.17
3958 4493 4.447138 AATTGGTGACTTGGTGGAAGTA 57.553 40.909 0.00 0.00 45.48 2.24
3970 4505 4.213482 GTGTCCACTTCAGTAATTGGTGAC 59.787 45.833 0.00 0.00 36.89 3.67
4015 4565 9.541143 GAATGGTTAATCAAACTTCAAAAGGAA 57.459 29.630 0.00 0.00 38.23 3.36
4016 4566 8.923270 AGAATGGTTAATCAAACTTCAAAAGGA 58.077 29.630 0.00 0.00 38.23 3.36
4017 4567 8.981647 CAGAATGGTTAATCAAACTTCAAAAGG 58.018 33.333 0.00 0.00 38.23 3.11
4018 4568 8.490355 GCAGAATGGTTAATCAAACTTCAAAAG 58.510 33.333 0.00 0.00 38.23 2.27
4019 4569 8.364129 GCAGAATGGTTAATCAAACTTCAAAA 57.636 30.769 0.00 0.00 38.23 2.44
4020 4570 7.945033 GCAGAATGGTTAATCAAACTTCAAA 57.055 32.000 0.00 0.00 38.23 2.69
4123 4673 4.400120 AGCCCTTCCGTTACAAATTAACA 58.600 39.130 0.00 0.00 0.00 2.41
4246 4965 4.808364 GCTCTCCTTGACACTGAATCATAC 59.192 45.833 0.00 0.00 0.00 2.39
4303 5022 8.691661 AGAATTTTGAACACTACACCACTAAT 57.308 30.769 0.00 0.00 0.00 1.73
4350 5071 9.160496 CAAATCCAATACTGATCTATCTAAGGC 57.840 37.037 0.00 0.00 0.00 4.35
4610 5331 5.067153 TGAATTTTGAACCACTACACCACTG 59.933 40.000 0.00 0.00 0.00 3.66
4728 5449 0.741221 CTCCGCAACCTACCTCAAGC 60.741 60.000 0.00 0.00 0.00 4.01
5005 5726 0.935898 GCTCCTCGATGCACTTGATG 59.064 55.000 0.00 0.00 0.00 3.07
5094 5815 1.853963 GACAGCCCTCCTCTTGTCTA 58.146 55.000 0.00 0.00 0.00 2.59
5143 5864 4.373116 AGCGATCCGTTGGCACGT 62.373 61.111 8.28 0.00 45.62 4.49
5610 6333 7.826690 TCGTATAGACAAAGCATATATCAGCA 58.173 34.615 2.61 0.00 0.00 4.41
5648 6371 0.248458 GTTGCAACCACGACCAACAG 60.248 55.000 19.15 0.00 37.93 3.16
5673 6396 4.116747 AGAACAGTAAAGATGAGCTCCG 57.883 45.455 12.15 0.00 0.00 4.63
5703 6426 2.711311 CATGGATGAAGCACCGCG 59.289 61.111 0.00 0.00 0.00 6.46
5724 6447 0.032540 ACGTGGTTCGGTTACCTGAC 59.967 55.000 0.00 0.00 44.69 3.51
5746 6537 4.503910 TCTCCAAAACTGATCACATACCG 58.496 43.478 0.00 0.00 0.00 4.02
5748 6539 4.333926 GCCTCTCCAAAACTGATCACATAC 59.666 45.833 0.00 0.00 0.00 2.39
5778 6569 3.732470 GCCCACCGCTATGCTTAC 58.268 61.111 0.00 0.00 0.00 2.34
5821 6612 0.320421 GCTTTCAGCTGGTACCGTGA 60.320 55.000 15.13 7.36 38.45 4.35
5888 6679 6.865205 CAGAAGGGCTCAAAATTTAAACAGAG 59.135 38.462 0.00 0.00 0.00 3.35
5902 6693 0.532573 CGAGTAAGCAGAAGGGCTCA 59.467 55.000 0.00 0.00 45.07 4.26
5955 6746 0.391661 AGCACTGCCGTATCCTTGTG 60.392 55.000 0.00 0.00 0.00 3.33
6001 6792 3.643978 CTATGGCTTCGCGCAGGC 61.644 66.667 24.52 24.52 41.67 4.85
6044 6835 2.281517 CCCGCATAAACCACACGATAA 58.718 47.619 0.00 0.00 0.00 1.75
6104 6906 0.913451 AGGTGCTGCAATCCCTCTCT 60.913 55.000 2.77 0.00 0.00 3.10
6169 7013 5.473504 GTGCATATGTATCCCCGAGAAAAAT 59.526 40.000 4.29 0.00 0.00 1.82
6176 7020 3.307410 GGAATGTGCATATGTATCCCCGA 60.307 47.826 4.29 0.00 0.00 5.14
6177 7021 3.009723 GGAATGTGCATATGTATCCCCG 58.990 50.000 4.29 0.00 0.00 5.73
6190 7034 2.747446 ACAACAGGTATTCGGAATGTGC 59.253 45.455 13.37 3.82 0.00 4.57
6206 7050 6.364165 CGAGATTTCTACCGAAACTTACAACA 59.636 38.462 0.00 0.00 41.58 3.33
6209 7053 6.017400 ACGAGATTTCTACCGAAACTTACA 57.983 37.500 0.00 0.00 41.58 2.41
6218 7062 5.888105 TCTAAGGAAACGAGATTTCTACCG 58.112 41.667 0.00 0.00 45.32 4.02
6231 7075 9.478768 GTGGCTCTAGTATAAATCTAAGGAAAC 57.521 37.037 0.00 0.00 0.00 2.78
6233 7077 7.722728 TCGTGGCTCTAGTATAAATCTAAGGAA 59.277 37.037 0.00 0.00 0.00 3.36
6234 7078 7.229308 TCGTGGCTCTAGTATAAATCTAAGGA 58.771 38.462 0.00 0.00 0.00 3.36
6235 7079 7.450124 TCGTGGCTCTAGTATAAATCTAAGG 57.550 40.000 0.00 0.00 0.00 2.69
6236 7080 8.731605 TCATCGTGGCTCTAGTATAAATCTAAG 58.268 37.037 0.00 0.00 0.00 2.18
6237 7081 8.631480 TCATCGTGGCTCTAGTATAAATCTAA 57.369 34.615 0.00 0.00 0.00 2.10
6238 7082 8.809468 ATCATCGTGGCTCTAGTATAAATCTA 57.191 34.615 0.00 0.00 0.00 1.98
6239 7083 7.710676 ATCATCGTGGCTCTAGTATAAATCT 57.289 36.000 0.00 0.00 0.00 2.40
6240 7084 8.764524 AAATCATCGTGGCTCTAGTATAAATC 57.235 34.615 0.00 0.00 0.00 2.17
6241 7085 9.862371 CTAAATCATCGTGGCTCTAGTATAAAT 57.138 33.333 0.00 0.00 0.00 1.40
6242 7086 8.857098 ACTAAATCATCGTGGCTCTAGTATAAA 58.143 33.333 0.00 0.00 0.00 1.40
6243 7087 8.405418 ACTAAATCATCGTGGCTCTAGTATAA 57.595 34.615 0.00 0.00 0.00 0.98
6244 7088 7.883833 AGACTAAATCATCGTGGCTCTAGTATA 59.116 37.037 0.00 0.00 0.00 1.47
6245 7089 6.717540 AGACTAAATCATCGTGGCTCTAGTAT 59.282 38.462 0.00 0.00 0.00 2.12
6246 7090 6.062749 AGACTAAATCATCGTGGCTCTAGTA 58.937 40.000 0.00 0.00 0.00 1.82
6247 7091 4.890581 AGACTAAATCATCGTGGCTCTAGT 59.109 41.667 0.00 0.00 0.00 2.57
6248 7092 5.009110 TGAGACTAAATCATCGTGGCTCTAG 59.991 44.000 0.00 0.00 0.00 2.43
6249 7093 4.887655 TGAGACTAAATCATCGTGGCTCTA 59.112 41.667 0.00 0.00 0.00 2.43
6250 7094 3.701542 TGAGACTAAATCATCGTGGCTCT 59.298 43.478 0.00 0.00 0.00 4.09
6251 7095 4.046938 TGAGACTAAATCATCGTGGCTC 57.953 45.455 0.00 0.00 0.00 4.70
6252 7096 4.437239 CTTGAGACTAAATCATCGTGGCT 58.563 43.478 0.00 0.00 0.00 4.75
6253 7097 3.001736 GCTTGAGACTAAATCATCGTGGC 59.998 47.826 0.00 0.00 0.00 5.01
6254 7098 4.437239 AGCTTGAGACTAAATCATCGTGG 58.563 43.478 0.00 0.00 0.00 4.94
6255 7099 7.063426 TGTTTAGCTTGAGACTAAATCATCGTG 59.937 37.037 0.00 0.00 40.62 4.35
6256 7100 7.097192 TGTTTAGCTTGAGACTAAATCATCGT 58.903 34.615 0.00 0.00 40.62 3.73
6257 7101 7.525688 TGTTTAGCTTGAGACTAAATCATCG 57.474 36.000 0.00 0.00 40.62 3.84
6260 7104 8.567948 CCTTTTGTTTAGCTTGAGACTAAATCA 58.432 33.333 0.00 0.00 40.62 2.57
6261 7105 7.539022 GCCTTTTGTTTAGCTTGAGACTAAATC 59.461 37.037 0.00 0.00 40.62 2.17
6262 7106 7.014230 TGCCTTTTGTTTAGCTTGAGACTAAAT 59.986 33.333 0.00 0.00 40.62 1.40
6263 7107 6.320164 TGCCTTTTGTTTAGCTTGAGACTAAA 59.680 34.615 0.00 0.00 37.28 1.85
6264 7108 5.825679 TGCCTTTTGTTTAGCTTGAGACTAA 59.174 36.000 0.00 0.00 0.00 2.24
6265 7109 5.373222 TGCCTTTTGTTTAGCTTGAGACTA 58.627 37.500 0.00 0.00 0.00 2.59
6266 7110 4.207165 TGCCTTTTGTTTAGCTTGAGACT 58.793 39.130 0.00 0.00 0.00 3.24
6267 7111 4.568152 TGCCTTTTGTTTAGCTTGAGAC 57.432 40.909 0.00 0.00 0.00 3.36
6268 7112 4.037923 CCTTGCCTTTTGTTTAGCTTGAGA 59.962 41.667 0.00 0.00 0.00 3.27
6269 7113 4.301628 CCTTGCCTTTTGTTTAGCTTGAG 58.698 43.478 0.00 0.00 0.00 3.02
6270 7114 3.069443 CCCTTGCCTTTTGTTTAGCTTGA 59.931 43.478 0.00 0.00 0.00 3.02
6271 7115 3.181466 ACCCTTGCCTTTTGTTTAGCTTG 60.181 43.478 0.00 0.00 0.00 4.01
6272 7116 3.038280 ACCCTTGCCTTTTGTTTAGCTT 58.962 40.909 0.00 0.00 0.00 3.74
6273 7117 2.677914 ACCCTTGCCTTTTGTTTAGCT 58.322 42.857 0.00 0.00 0.00 3.32
6274 7118 3.469008 AACCCTTGCCTTTTGTTTAGC 57.531 42.857 0.00 0.00 0.00 3.09
6275 7119 4.765273 ACAAACCCTTGCCTTTTGTTTAG 58.235 39.130 0.00 0.00 39.82 1.85
6276 7120 4.828072 ACAAACCCTTGCCTTTTGTTTA 57.172 36.364 0.00 0.00 39.82 2.01
6277 7121 3.712016 ACAAACCCTTGCCTTTTGTTT 57.288 38.095 0.00 0.00 39.82 2.83
6278 7122 3.712016 AACAAACCCTTGCCTTTTGTT 57.288 38.095 5.97 5.97 44.65 2.83
6279 7123 3.712016 AAACAAACCCTTGCCTTTTGT 57.288 38.095 0.00 0.00 43.61 2.83
6280 7124 3.128415 CCAAAACAAACCCTTGCCTTTTG 59.872 43.478 6.67 6.67 37.79 2.44
6281 7125 3.351740 CCAAAACAAACCCTTGCCTTTT 58.648 40.909 0.00 0.00 35.84 2.27
6282 7126 2.356638 CCCAAAACAAACCCTTGCCTTT 60.357 45.455 0.00 0.00 35.84 3.11
6283 7127 1.211703 CCCAAAACAAACCCTTGCCTT 59.788 47.619 0.00 0.00 35.84 4.35
6284 7128 0.836606 CCCAAAACAAACCCTTGCCT 59.163 50.000 0.00 0.00 35.84 4.75
6285 7129 0.817634 GCCCAAAACAAACCCTTGCC 60.818 55.000 0.00 0.00 35.84 4.52
6286 7130 0.180171 AGCCCAAAACAAACCCTTGC 59.820 50.000 0.00 0.00 35.84 4.01
6287 7131 4.770010 TCTATAGCCCAAAACAAACCCTTG 59.230 41.667 0.00 0.00 38.61 3.61
6288 7132 5.005628 TCTATAGCCCAAAACAAACCCTT 57.994 39.130 0.00 0.00 0.00 3.95
6289 7133 4.668138 TCTATAGCCCAAAACAAACCCT 57.332 40.909 0.00 0.00 0.00 4.34
6290 7134 5.731957 TTTCTATAGCCCAAAACAAACCC 57.268 39.130 0.00 0.00 0.00 4.11
6318 7162 9.542462 TTTCTCCTATATACCGTCAGAATTTTG 57.458 33.333 0.00 0.00 0.00 2.44
6322 7166 8.314751 CCATTTTCTCCTATATACCGTCAGAAT 58.685 37.037 0.00 0.00 0.00 2.40
6323 7167 7.507956 TCCATTTTCTCCTATATACCGTCAGAA 59.492 37.037 0.00 0.00 0.00 3.02
6330 7174 6.721318 TGGCATCCATTTTCTCCTATATACC 58.279 40.000 0.00 0.00 0.00 2.73
6405 7249 4.885325 AGACTCGGTAAAAAGCTGGAAAAA 59.115 37.500 0.00 0.00 0.00 1.94
6410 7254 3.933332 CCTAAGACTCGGTAAAAAGCTGG 59.067 47.826 0.00 0.00 0.00 4.85
6414 7258 6.649557 ACACATTCCTAAGACTCGGTAAAAAG 59.350 38.462 0.00 0.00 0.00 2.27
6424 7268 6.859112 AGACATACACACATTCCTAAGACT 57.141 37.500 0.00 0.00 0.00 3.24
6429 7273 5.047590 ACGTGAAGACATACACACATTCCTA 60.048 40.000 0.00 0.00 36.91 2.94
6436 7280 6.699895 TCAAATACGTGAAGACATACACAC 57.300 37.500 0.00 0.00 36.91 3.82
6500 7344 4.163427 TCCATTGCCCTTGGTATTTGAAA 58.837 39.130 0.00 0.00 35.64 2.69
6504 7348 2.110578 GCTCCATTGCCCTTGGTATTT 58.889 47.619 0.00 0.00 35.64 1.40
6527 7371 5.567138 ATCAAAAAGTGCATACAGCTACC 57.433 39.130 0.00 0.00 45.94 3.18
6534 7378 5.232838 GCTATGGCAATCAAAAAGTGCATAC 59.767 40.000 0.00 0.00 40.12 2.39
6535 7379 5.105432 TGCTATGGCAATCAAAAAGTGCATA 60.105 36.000 0.00 0.00 46.36 3.14


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

AutoCloner maintained by Alex Coulton.