Multiple sequence alignment - TraesCS4A01G135900

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 TraesCS4A01G135900 chr4A 100.000 3886 0 0 1 3886 188636346 188632461 0.000000e+00 7177.0
1 TraesCS4A01G135900 chr4A 78.558 527 75 20 254 758 631374553 631375063 2.920000e-81 313.0
2 TraesCS4A01G135900 chr4A 75.444 338 56 19 356 673 511857557 511857227 5.240000e-29 139.0
3 TraesCS4A01G135900 chr4A 94.382 89 5 0 1 89 51655175 51655087 1.880000e-28 137.0
4 TraesCS4A01G135900 chr4A 97.222 36 1 0 3801 3836 330103222 330103257 1.170000e-05 62.1
5 TraesCS4A01G135900 chr4D 93.008 3032 144 33 245 3238 298107493 298110494 0.000000e+00 4362.0
6 TraesCS4A01G135900 chr4D 88.214 560 45 9 3240 3785 298110836 298111388 0.000000e+00 649.0
7 TraesCS4A01G135900 chr4D 84.375 160 17 6 86 244 298107258 298107410 2.420000e-32 150.0
8 TraesCS4A01G135900 chr4B 95.512 2451 62 11 825 3238 369484964 369487403 0.000000e+00 3873.0
9 TraesCS4A01G135900 chr4B 87.900 562 52 6 3238 3785 369487757 369488316 0.000000e+00 647.0
10 TraesCS4A01G135900 chr1A 84.456 579 66 11 3229 3785 574682472 574683048 2.040000e-152 549.0
11 TraesCS4A01G135900 chr1A 77.887 407 68 12 361 749 514596194 514596596 2.330000e-57 233.0
12 TraesCS4A01G135900 chr1A 94.382 89 5 0 1 89 181327285 181327373 1.880000e-28 137.0
13 TraesCS4A01G135900 chr1A 92.500 40 3 0 3801 3840 520817736 520817775 1.510000e-04 58.4
14 TraesCS4A01G135900 chr5D 84.452 566 67 10 3238 3785 536544288 536543726 4.420000e-149 538.0
15 TraesCS4A01G135900 chr3B 84.127 567 69 10 3238 3785 504082468 504083032 2.660000e-146 529.0
16 TraesCS4A01G135900 chr3B 77.966 531 85 15 251 756 40920820 40921343 1.750000e-78 303.0
17 TraesCS4A01G135900 chr3B 94.595 37 1 1 3810 3846 439865073 439865038 5.420000e-04 56.5
18 TraesCS4A01G135900 chr2B 82.447 564 79 9 3238 3783 791125506 791124945 3.510000e-130 475.0
19 TraesCS4A01G135900 chr2B 84.483 116 16 2 1522 1637 653841581 653841468 3.170000e-21 113.0
20 TraesCS4A01G135900 chr6B 81.273 550 83 13 3256 3785 140364915 140364366 9.980000e-116 427.0
21 TraesCS4A01G135900 chr6B 85.000 60 5 2 3782 3837 227828402 227828461 1.510000e-04 58.4
22 TraesCS4A01G135900 chr1D 81.283 561 74 10 3256 3785 436819709 436819149 3.590000e-115 425.0
23 TraesCS4A01G135900 chr1D 76.087 368 67 6 361 712 32221590 32221952 5.160000e-39 172.0
24 TraesCS4A01G135900 chr1D 76.636 214 34 14 362 567 457174766 457174561 1.910000e-18 104.0
25 TraesCS4A01G135900 chr1D 96.875 32 1 0 3810 3841 83688891 83688860 2.000000e-03 54.7
26 TraesCS4A01G135900 chr7D 82.831 431 58 7 3370 3785 420777000 420776571 4.740000e-99 372.0
27 TraesCS4A01G135900 chr7D 78.378 148 26 6 3268 3410 606958554 606958700 1.490000e-14 91.6
28 TraesCS4A01G135900 chrUn 77.451 408 69 13 361 749 932952 933355 5.050000e-54 222.0
29 TraesCS4A01G135900 chrUn 77.295 414 71 13 361 755 946755 946346 5.050000e-54 222.0
30 TraesCS4A01G135900 chrUn 97.222 36 1 0 3801 3836 186734162 186734127 1.170000e-05 62.1
31 TraesCS4A01G135900 chr6A 95.506 89 4 0 1 89 551730643 551730555 4.050000e-30 143.0
32 TraesCS4A01G135900 chr6A 93.617 94 6 0 1 94 370996665 370996572 1.460000e-29 141.0
33 TraesCS4A01G135900 chr6A 94.382 89 5 0 1 89 581587369 581587457 1.880000e-28 137.0
34 TraesCS4A01G135900 chr6A 91.667 96 8 0 1 96 117169148 117169053 2.440000e-27 134.0
35 TraesCS4A01G135900 chr2A 95.506 89 4 0 1 89 313102122 313102210 4.050000e-30 143.0
36 TraesCS4A01G135900 chr2A 94.737 38 2 0 3801 3838 302053461 302053498 4.190000e-05 60.2
37 TraesCS4A01G135900 chr5A 94.505 91 5 0 1 91 549531514 549531424 1.460000e-29 141.0
38 TraesCS4A01G135900 chr5A 94.737 38 2 0 3801 3838 679871204 679871241 4.190000e-05 60.2
39 TraesCS4A01G135900 chr3D 94.382 89 5 0 1 89 36327342 36327430 1.880000e-28 137.0
40 TraesCS4A01G135900 chr1B 93.617 47 2 1 3801 3846 166597563 166597517 6.970000e-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 TraesCS4A01G135900 chr4A 188632461 188636346 3885 True 7177.000000 7177 100.000000 1 3886 1 chr4A.!!$R2 3885
1 TraesCS4A01G135900 chr4A 631374553 631375063 510 False 313.000000 313 78.558000 254 758 1 chr4A.!!$F2 504
2 TraesCS4A01G135900 chr4D 298107258 298111388 4130 False 1720.333333 4362 88.532333 86 3785 3 chr4D.!!$F1 3699
3 TraesCS4A01G135900 chr4B 369484964 369488316 3352 False 2260.000000 3873 91.706000 825 3785 2 chr4B.!!$F1 2960
4 TraesCS4A01G135900 chr1A 574682472 574683048 576 False 549.000000 549 84.456000 3229 3785 1 chr1A.!!$F4 556
5 TraesCS4A01G135900 chr5D 536543726 536544288 562 True 538.000000 538 84.452000 3238 3785 1 chr5D.!!$R1 547
6 TraesCS4A01G135900 chr3B 504082468 504083032 564 False 529.000000 529 84.127000 3238 3785 1 chr3B.!!$F2 547
7 TraesCS4A01G135900 chr3B 40920820 40921343 523 False 303.000000 303 77.966000 251 756 1 chr3B.!!$F1 505
8 TraesCS4A01G135900 chr2B 791124945 791125506 561 True 475.000000 475 82.447000 3238 3783 1 chr2B.!!$R2 545
9 TraesCS4A01G135900 chr6B 140364366 140364915 549 True 427.000000 427 81.273000 3256 3785 1 chr6B.!!$R1 529
10 TraesCS4A01G135900 chr1D 436819149 436819709 560 True 425.000000 425 81.283000 3256 3785 1 chr1D.!!$R2 529

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
641 746 0.251354 GGCCAGAGTCATCAGAAGCA 59.749 55.0 0.00 0.00 0.00 3.91 F
725 830 0.299300 TCGCGTTCAAACTGTTCGTG 59.701 50.0 5.77 6.58 0.00 4.35 F
799 913 0.699399 TTTATGGACCCGCCTTGGAA 59.301 50.0 0.00 0.00 42.00 3.53 F
829 943 0.958822 AAAACCATCGGACAACTGGC 59.041 50.0 0.00 0.00 33.12 4.85 F
1160 1278 1.027815 ACCCCCAGTTATCTCCTCCT 58.972 55.0 0.00 0.00 0.00 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1897 2057 0.847373 TCAACCCCTTACCAGTGCAA 59.153 50.000 0.00 0.00 0.0 4.08 R
2639 2803 1.141858 TGATTATGCATGCCCGGTACA 59.858 47.619 16.68 5.88 0.0 2.90 R
2765 2929 0.532573 CATACCTGTCCACGTGCTCT 59.467 55.000 10.91 0.00 0.0 4.09 R
2877 3041 4.148128 ACTTCGAGGCAGATCAATCATT 57.852 40.909 0.00 0.00 0.0 2.57 R
2945 3109 4.419522 ACGATGCAGAAATACAACAACC 57.580 40.909 0.00 0.00 0.0 3.77 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
22 23 4.888917 TGTGTTGTGATATCTTTCCGTGA 58.111 39.130 3.98 0.00 0.00 4.35
23 24 4.929211 TGTGTTGTGATATCTTTCCGTGAG 59.071 41.667 3.98 0.00 0.00 3.51
24 25 4.929808 GTGTTGTGATATCTTTCCGTGAGT 59.070 41.667 3.98 0.00 0.00 3.41
25 26 5.062308 GTGTTGTGATATCTTTCCGTGAGTC 59.938 44.000 3.98 0.00 0.00 3.36
26 27 5.168569 GTTGTGATATCTTTCCGTGAGTCA 58.831 41.667 3.98 0.00 0.00 3.41
27 28 5.598416 TGTGATATCTTTCCGTGAGTCAT 57.402 39.130 3.98 0.00 0.00 3.06
28 29 5.977635 TGTGATATCTTTCCGTGAGTCATT 58.022 37.500 3.98 0.00 0.00 2.57
29 30 5.812127 TGTGATATCTTTCCGTGAGTCATTG 59.188 40.000 3.98 0.00 0.00 2.82
30 31 6.042777 GTGATATCTTTCCGTGAGTCATTGA 58.957 40.000 3.98 0.00 0.00 2.57
31 32 6.703607 GTGATATCTTTCCGTGAGTCATTGAT 59.296 38.462 3.98 0.00 0.00 2.57
32 33 6.925718 TGATATCTTTCCGTGAGTCATTGATC 59.074 38.462 3.98 0.00 0.00 2.92
33 34 4.808414 TCTTTCCGTGAGTCATTGATCT 57.192 40.909 0.00 0.00 0.00 2.75
34 35 5.152623 TCTTTCCGTGAGTCATTGATCTT 57.847 39.130 0.00 0.00 0.00 2.40
35 36 4.931601 TCTTTCCGTGAGTCATTGATCTTG 59.068 41.667 0.00 0.00 0.00 3.02
36 37 4.535526 TTCCGTGAGTCATTGATCTTGA 57.464 40.909 0.00 0.00 0.00 3.02
37 38 4.743057 TCCGTGAGTCATTGATCTTGAT 57.257 40.909 0.00 0.00 0.00 2.57
38 39 5.089970 TCCGTGAGTCATTGATCTTGATT 57.910 39.130 0.00 0.00 0.00 2.57
39 40 6.220726 TCCGTGAGTCATTGATCTTGATTA 57.779 37.500 0.00 0.00 0.00 1.75
40 41 6.820335 TCCGTGAGTCATTGATCTTGATTAT 58.180 36.000 0.00 0.00 0.00 1.28
41 42 7.951591 TCCGTGAGTCATTGATCTTGATTATA 58.048 34.615 0.00 0.00 0.00 0.98
42 43 7.867909 TCCGTGAGTCATTGATCTTGATTATAC 59.132 37.037 0.00 0.00 0.00 1.47
43 44 7.653311 CCGTGAGTCATTGATCTTGATTATACA 59.347 37.037 0.00 0.00 0.00 2.29
44 45 9.201127 CGTGAGTCATTGATCTTGATTATACAT 57.799 33.333 0.00 0.00 0.00 2.29
54 55 9.271828 TGATCTTGATTATACATATTTGCGTGT 57.728 29.630 0.00 0.00 0.00 4.49
65 66 7.786178 ACATATTTGCGTGTATGATTAGTGT 57.214 32.000 8.47 0.00 33.56 3.55
66 67 8.880878 ACATATTTGCGTGTATGATTAGTGTA 57.119 30.769 8.47 0.00 33.56 2.90
67 68 9.489084 ACATATTTGCGTGTATGATTAGTGTAT 57.511 29.630 8.47 0.00 33.56 2.29
68 69 9.745323 CATATTTGCGTGTATGATTAGTGTATG 57.255 33.333 0.00 0.00 31.48 2.39
69 70 6.597262 TTTGCGTGTATGATTAGTGTATGG 57.403 37.500 0.00 0.00 0.00 2.74
70 71 5.270893 TGCGTGTATGATTAGTGTATGGT 57.729 39.130 0.00 0.00 0.00 3.55
71 72 5.286438 TGCGTGTATGATTAGTGTATGGTC 58.714 41.667 0.00 0.00 0.00 4.02
72 73 5.163499 TGCGTGTATGATTAGTGTATGGTCA 60.163 40.000 0.00 0.00 0.00 4.02
73 74 5.751509 GCGTGTATGATTAGTGTATGGTCAA 59.248 40.000 0.00 0.00 0.00 3.18
74 75 6.256975 GCGTGTATGATTAGTGTATGGTCAAA 59.743 38.462 0.00 0.00 0.00 2.69
75 76 7.042051 GCGTGTATGATTAGTGTATGGTCAAAT 60.042 37.037 0.00 0.00 0.00 2.32
76 77 8.487970 CGTGTATGATTAGTGTATGGTCAAATC 58.512 37.037 0.00 0.00 0.00 2.17
77 78 8.487970 GTGTATGATTAGTGTATGGTCAAATCG 58.512 37.037 0.00 0.00 0.00 3.34
78 79 8.417884 TGTATGATTAGTGTATGGTCAAATCGA 58.582 33.333 0.00 0.00 0.00 3.59
79 80 7.953158 ATGATTAGTGTATGGTCAAATCGAG 57.047 36.000 0.00 0.00 0.00 4.04
80 81 6.280643 TGATTAGTGTATGGTCAAATCGAGG 58.719 40.000 0.00 0.00 0.00 4.63
81 82 3.543680 AGTGTATGGTCAAATCGAGGG 57.456 47.619 0.00 0.00 0.00 4.30
82 83 1.940613 GTGTATGGTCAAATCGAGGGC 59.059 52.381 0.00 0.00 0.00 5.19
83 84 1.217882 GTATGGTCAAATCGAGGGCG 58.782 55.000 0.00 0.00 39.35 6.13
84 85 0.828022 TATGGTCAAATCGAGGGCGT 59.172 50.000 0.00 0.00 38.98 5.68
85 86 0.462047 ATGGTCAAATCGAGGGCGTC 60.462 55.000 0.00 0.00 38.98 5.19
86 87 1.079405 GGTCAAATCGAGGGCGTCA 60.079 57.895 8.06 0.00 38.98 4.35
87 88 1.359459 GGTCAAATCGAGGGCGTCAC 61.359 60.000 8.06 0.00 38.98 3.67
88 89 0.669318 GTCAAATCGAGGGCGTCACA 60.669 55.000 8.06 0.00 38.98 3.58
89 90 0.669318 TCAAATCGAGGGCGTCACAC 60.669 55.000 8.06 0.00 38.98 3.82
90 91 1.375523 AAATCGAGGGCGTCACACC 60.376 57.895 8.06 0.00 38.98 4.16
120 121 4.715523 CGGGCCGTTGGTGTGGAT 62.716 66.667 19.97 0.00 0.00 3.41
122 123 3.061848 GGCCGTTGGTGTGGATGG 61.062 66.667 0.00 0.00 0.00 3.51
123 124 2.282180 GCCGTTGGTGTGGATGGT 60.282 61.111 0.00 0.00 0.00 3.55
155 156 1.825474 TCCATCTGTTCCTCGAACTCC 59.175 52.381 6.13 0.00 42.39 3.85
156 157 1.550524 CCATCTGTTCCTCGAACTCCA 59.449 52.381 6.13 0.00 42.39 3.86
165 166 3.103911 CGAACTCCACGTCCGTGC 61.104 66.667 14.06 0.00 44.16 5.34
166 167 2.338984 GAACTCCACGTCCGTGCT 59.661 61.111 14.06 0.00 44.16 4.40
189 190 1.845664 TAGACCTTGCCTGGCACCA 60.846 57.895 23.30 6.91 38.71 4.17
193 194 3.136123 CTTGCCTGGCACCATCGG 61.136 66.667 23.30 3.85 38.71 4.18
229 230 0.971447 GGCTACTGGTCCTCCTCGTT 60.971 60.000 0.00 0.00 34.23 3.85
232 233 1.255667 TACTGGTCCTCCTCGTTGCC 61.256 60.000 0.00 0.00 34.23 4.52
320 402 1.005289 ATGTGGAGGGAGATGGGCT 59.995 57.895 0.00 0.00 0.00 5.19
344 434 1.051556 GGGGAGGAGGAGGATGTGAC 61.052 65.000 0.00 0.00 0.00 3.67
441 531 0.886043 GTAACGGCCGGAGTTGGTTT 60.886 55.000 31.76 14.40 33.42 3.27
446 536 1.005394 GCCGGAGTTGGTTTCTCGA 60.005 57.895 5.05 0.00 33.26 4.04
447 537 0.601841 GCCGGAGTTGGTTTCTCGAA 60.602 55.000 5.05 0.00 33.26 3.71
459 549 2.940410 GTTTCTCGAAAACCTGTGTCCA 59.060 45.455 10.32 0.00 31.33 4.02
467 557 4.439426 CGAAAACCTGTGTCCACATTGAAA 60.439 41.667 0.00 0.00 41.01 2.69
469 559 3.011566 ACCTGTGTCCACATTGAAACA 57.988 42.857 0.00 0.00 41.01 2.83
526 616 1.251527 CCCTCCCTCCGGTCATATCG 61.252 65.000 0.00 0.00 0.00 2.92
564 668 4.783621 TGCTCTGGACCGGCATGC 62.784 66.667 9.90 9.90 0.00 4.06
568 672 2.438975 CTGGACCGGCATGCATGT 60.439 61.111 26.79 15.58 0.00 3.21
595 699 1.966493 GCATCGAAAGGAAAGCGCGA 61.966 55.000 12.10 0.00 35.32 5.87
628 733 1.458588 GGGTTTTTGGTGGGCCAGA 60.459 57.895 6.40 0.00 46.91 3.86
632 737 0.260230 TTTTTGGTGGGCCAGAGTCA 59.740 50.000 6.40 0.00 46.91 3.41
641 746 0.251354 GGCCAGAGTCATCAGAAGCA 59.749 55.000 0.00 0.00 0.00 3.91
643 748 1.654317 CCAGAGTCATCAGAAGCAGC 58.346 55.000 0.00 0.00 0.00 5.25
652 757 1.130054 TCAGAAGCAGCCTTGGGAGT 61.130 55.000 0.00 0.00 0.00 3.85
677 782 1.239347 GGACTTCCGCAAAGCTTTCT 58.761 50.000 9.23 0.00 38.67 2.52
685 790 3.880490 TCCGCAAAGCTTTCTCACTTTTA 59.120 39.130 9.23 0.00 33.92 1.52
687 792 5.009610 TCCGCAAAGCTTTCTCACTTTTATT 59.990 36.000 9.23 0.00 33.92 1.40
691 796 7.043458 CGCAAAGCTTTCTCACTTTTATTTTCA 60.043 33.333 9.23 0.00 33.92 2.69
723 828 2.294479 AATCGCGTTCAAACTGTTCG 57.706 45.000 5.77 0.00 0.00 3.95
724 829 1.214367 ATCGCGTTCAAACTGTTCGT 58.786 45.000 5.77 0.00 0.00 3.85
725 830 0.299300 TCGCGTTCAAACTGTTCGTG 59.701 50.000 5.77 6.58 0.00 4.35
726 831 0.299300 CGCGTTCAAACTGTTCGTGA 59.701 50.000 0.00 0.00 34.64 4.35
727 832 1.267136 CGCGTTCAAACTGTTCGTGAA 60.267 47.619 0.00 5.53 34.64 3.18
728 833 2.098870 GCGTTCAAACTGTTCGTGAAC 58.901 47.619 20.40 20.40 44.93 3.18
736 842 5.525745 TCAAACTGTTCGTGAACACATACAT 59.474 36.000 11.21 0.00 45.42 2.29
758 864 1.066502 TCGATGTTGGATGGCTTTCGA 60.067 47.619 0.00 0.00 0.00 3.71
763 869 2.237143 TGTTGGATGGCTTTCGAGATCT 59.763 45.455 0.00 0.00 0.00 2.75
769 883 1.139654 TGGCTTTCGAGATCTGGATGG 59.860 52.381 8.37 5.81 0.00 3.51
771 885 2.478831 GCTTTCGAGATCTGGATGGTC 58.521 52.381 8.37 0.00 0.00 4.02
774 888 1.025041 TCGAGATCTGGATGGTCACG 58.975 55.000 0.00 0.00 0.00 4.35
776 890 1.403814 GAGATCTGGATGGTCACGGA 58.596 55.000 0.00 0.00 0.00 4.69
778 892 1.759445 AGATCTGGATGGTCACGGAAG 59.241 52.381 0.00 0.00 0.00 3.46
779 893 1.757118 GATCTGGATGGTCACGGAAGA 59.243 52.381 0.00 0.00 0.00 2.87
784 898 4.408921 TCTGGATGGTCACGGAAGATTTAT 59.591 41.667 0.00 0.00 0.00 1.40
785 899 4.450976 TGGATGGTCACGGAAGATTTATG 58.549 43.478 0.00 0.00 0.00 1.90
787 901 4.444306 GGATGGTCACGGAAGATTTATGGA 60.444 45.833 0.00 0.00 0.00 3.41
799 913 0.699399 TTTATGGACCCGCCTTGGAA 59.301 50.000 0.00 0.00 42.00 3.53
804 918 1.678970 GACCCGCCTTGGAAATGCT 60.679 57.895 0.00 0.00 42.00 3.79
816 930 5.243730 CCTTGGAAATGCTAAGAGAAAACCA 59.756 40.000 0.00 0.00 37.27 3.67
820 934 5.449177 GGAAATGCTAAGAGAAAACCATCGG 60.449 44.000 0.00 0.00 0.00 4.18
829 943 0.958822 AAAACCATCGGACAACTGGC 59.041 50.000 0.00 0.00 33.12 4.85
1160 1278 1.027815 ACCCCCAGTTATCTCCTCCT 58.972 55.000 0.00 0.00 0.00 3.69
1165 1283 3.118223 CCCCAGTTATCTCCTCCTGTTTC 60.118 52.174 0.00 0.00 0.00 2.78
1216 1334 2.810274 ACTACAGCTGTGTGATTGCAAG 59.190 45.455 29.57 16.80 37.52 4.01
1362 1484 4.485163 CTTTTGGCTTTCATTTCGTAGGG 58.515 43.478 0.00 0.00 0.00 3.53
1519 1641 5.578336 GCCATTAAGTTTTGCTCTGAATTCC 59.422 40.000 2.27 0.00 0.00 3.01
1566 1688 8.120140 TCACCATTGAAATACATGTGATTCAA 57.880 30.769 28.16 28.16 43.53 2.69
1611 1733 2.236146 TGGCCACCTGTACATACTGAAG 59.764 50.000 0.00 0.00 0.00 3.02
1612 1734 2.236395 GGCCACCTGTACATACTGAAGT 59.764 50.000 0.00 0.00 0.00 3.01
1613 1735 3.307480 GGCCACCTGTACATACTGAAGTT 60.307 47.826 0.00 0.00 0.00 2.66
1616 1738 5.523916 GCCACCTGTACATACTGAAGTTATG 59.476 44.000 0.00 0.00 0.00 1.90
1704 1841 8.420222 AGTATCAATACTCAAATGAGAGACCAG 58.580 37.037 16.93 2.62 44.74 4.00
1739 1876 2.566833 ACCTGTCATACTGCAAAGCA 57.433 45.000 0.00 0.00 36.92 3.91
1856 2016 7.907389 TGAATCTCTGGTACACTTAATTGACT 58.093 34.615 0.00 0.00 0.00 3.41
2221 2385 9.853177 AAATAAGTAAGGAACCTTATCCATGAG 57.147 33.333 15.08 0.00 42.27 2.90
2637 2801 1.952296 GCAGAGAAATGTAGGGGCATG 59.048 52.381 0.00 0.00 0.00 4.06
2639 2803 3.624777 CAGAGAAATGTAGGGGCATGTT 58.375 45.455 0.00 0.00 0.00 2.71
2765 2929 5.544948 ACCTGTACTTTACCATAGACACCAA 59.455 40.000 0.00 0.00 0.00 3.67
2877 3041 8.083828 ACCTAGAAGCTTCATCAGAGATAAAA 57.916 34.615 27.57 0.00 0.00 1.52
2936 3100 9.109533 CATTTTTACGCTCGTTAAATAGTTTGT 57.890 29.630 7.29 0.00 0.00 2.83
2945 3109 8.047859 GCTCGTTAAATAGTTTGTGTTTGTTTG 58.952 33.333 0.00 0.00 0.00 2.93
3023 3187 3.262405 ACCGAAGCTTGATTTAGGTACCA 59.738 43.478 15.94 0.00 0.00 3.25
3088 3252 0.108472 CAGAAGATCGCAGCACCTCA 60.108 55.000 0.00 0.00 0.00 3.86
3138 3302 3.438183 AGTGATCTACGTGTTACCCCTT 58.562 45.455 0.00 0.00 0.00 3.95
3309 3949 3.129988 CCAGTGATGCATCTTCCCTTTTC 59.870 47.826 26.32 0.00 0.00 2.29
3327 3967 0.187851 TCCTATCGGAACCTCCCCTC 59.812 60.000 0.00 0.00 36.03 4.30
3330 3970 2.651841 TATCGGAACCTCCCCTCCCG 62.652 65.000 0.00 0.00 41.36 5.14
3334 3974 3.330720 AACCTCCCCTCCCGCTTG 61.331 66.667 0.00 0.00 0.00 4.01
3348 3990 0.742990 CGCTTGGTTTCCGCCATAGA 60.743 55.000 0.00 0.00 38.48 1.98
3403 4057 6.862469 AAATCAAATGATGTCCACCTCATT 57.138 33.333 4.82 4.82 41.02 2.57
3468 4133 9.809096 GTAGAGTGGGTTAAACTAAGTTATACC 57.191 37.037 0.00 0.00 32.17 2.73
3548 4213 0.944386 AATGCACACTGACGTTGGAC 59.056 50.000 0.00 0.00 0.00 4.02
3566 4231 0.955428 ACGCGAGTGGCAATGTGAAT 60.955 50.000 15.93 0.00 46.97 2.57
3679 4344 4.772624 TCTTCTACTCTTAGCCTCTTTGCA 59.227 41.667 0.00 0.00 0.00 4.08
3728 4393 5.354792 ACACCACGTTAACATTAGTGTGTTT 59.645 36.000 15.70 4.13 42.08 2.83
3735 4400 7.011576 ACGTTAACATTAGTGTGTTTGTCATCA 59.988 33.333 6.39 0.00 42.08 3.07
3755 4423 6.312180 TCATCAACACATCATCTTCTTTCTCG 59.688 38.462 0.00 0.00 0.00 4.04
3761 4429 5.641209 CACATCATCTTCTTTCTCGTTCCTT 59.359 40.000 0.00 0.00 0.00 3.36
3785 4455 4.674885 GCCAACTAGTTCTCGTTCCTACTC 60.675 50.000 4.77 0.00 0.00 2.59
3786 4456 4.142425 CCAACTAGTTCTCGTTCCTACTCC 60.142 50.000 4.77 0.00 0.00 3.85
3787 4457 3.619419 ACTAGTTCTCGTTCCTACTCCC 58.381 50.000 0.00 0.00 0.00 4.30
3788 4458 2.903375 AGTTCTCGTTCCTACTCCCT 57.097 50.000 0.00 0.00 0.00 4.20
3789 4459 2.725637 AGTTCTCGTTCCTACTCCCTC 58.274 52.381 0.00 0.00 0.00 4.30
3790 4460 1.750206 GTTCTCGTTCCTACTCCCTCC 59.250 57.143 0.00 0.00 0.00 4.30
3791 4461 0.997363 TCTCGTTCCTACTCCCTCCA 59.003 55.000 0.00 0.00 0.00 3.86
3792 4462 1.569548 TCTCGTTCCTACTCCCTCCAT 59.430 52.381 0.00 0.00 0.00 3.41
3793 4463 2.024273 TCTCGTTCCTACTCCCTCCATT 60.024 50.000 0.00 0.00 0.00 3.16
3794 4464 2.362717 CTCGTTCCTACTCCCTCCATTC 59.637 54.545 0.00 0.00 0.00 2.67
3795 4465 1.413077 CGTTCCTACTCCCTCCATTCC 59.587 57.143 0.00 0.00 0.00 3.01
3796 4466 2.478292 GTTCCTACTCCCTCCATTCCA 58.522 52.381 0.00 0.00 0.00 3.53
3797 4467 2.844348 GTTCCTACTCCCTCCATTCCAA 59.156 50.000 0.00 0.00 0.00 3.53
3798 4468 3.214694 TCCTACTCCCTCCATTCCAAA 57.785 47.619 0.00 0.00 0.00 3.28
3799 4469 3.537337 TCCTACTCCCTCCATTCCAAAA 58.463 45.455 0.00 0.00 0.00 2.44
3800 4470 4.119155 TCCTACTCCCTCCATTCCAAAAT 58.881 43.478 0.00 0.00 0.00 1.82
3801 4471 5.293643 TCCTACTCCCTCCATTCCAAAATA 58.706 41.667 0.00 0.00 0.00 1.40
3802 4472 5.734140 TCCTACTCCCTCCATTCCAAAATAA 59.266 40.000 0.00 0.00 0.00 1.40
3803 4473 6.064717 CCTACTCCCTCCATTCCAAAATAAG 58.935 44.000 0.00 0.00 0.00 1.73
3804 4474 4.871822 ACTCCCTCCATTCCAAAATAAGG 58.128 43.478 0.00 0.00 31.34 2.69
3805 4475 3.638627 CTCCCTCCATTCCAAAATAAGGC 59.361 47.826 0.00 0.00 30.67 4.35
3806 4476 3.272020 TCCCTCCATTCCAAAATAAGGCT 59.728 43.478 0.00 0.00 30.67 4.58
3807 4477 3.385755 CCCTCCATTCCAAAATAAGGCTG 59.614 47.826 0.00 0.00 30.67 4.85
3808 4478 3.385755 CCTCCATTCCAAAATAAGGCTGG 59.614 47.826 0.00 0.00 32.86 4.85
3809 4479 3.373830 TCCATTCCAAAATAAGGCTGGG 58.626 45.455 0.00 0.00 32.61 4.45
3810 4480 3.012274 TCCATTCCAAAATAAGGCTGGGA 59.988 43.478 0.00 0.00 32.61 4.37
3811 4481 3.132824 CCATTCCAAAATAAGGCTGGGAC 59.867 47.826 0.00 0.00 0.00 4.46
3812 4482 3.534357 TTCCAAAATAAGGCTGGGACA 57.466 42.857 0.00 0.00 0.00 4.02
3813 4483 2.802719 TCCAAAATAAGGCTGGGACAC 58.197 47.619 0.00 0.00 0.00 3.67
3814 4484 2.378547 TCCAAAATAAGGCTGGGACACT 59.621 45.455 0.00 0.00 0.00 3.55
3815 4485 3.165071 CCAAAATAAGGCTGGGACACTT 58.835 45.455 0.00 0.00 0.00 3.16
3816 4486 4.043561 TCCAAAATAAGGCTGGGACACTTA 59.956 41.667 0.00 0.00 32.72 2.24
3817 4487 4.956075 CCAAAATAAGGCTGGGACACTTAT 59.044 41.667 0.00 0.00 38.65 1.73
3818 4488 5.422012 CCAAAATAAGGCTGGGACACTTATT 59.578 40.000 0.00 0.00 44.22 1.40
3820 4490 7.553504 AAAATAAGGCTGGGACACTTATTTT 57.446 32.000 20.15 20.15 46.89 1.82
3821 4491 6.530019 AATAAGGCTGGGACACTTATTTTG 57.470 37.500 0.00 0.00 41.62 2.44
3822 4492 2.807676 AGGCTGGGACACTTATTTTGG 58.192 47.619 0.00 0.00 0.00 3.28
3823 4493 1.824852 GGCTGGGACACTTATTTTGGG 59.175 52.381 0.00 0.00 0.00 4.12
3824 4494 2.556559 GGCTGGGACACTTATTTTGGGA 60.557 50.000 0.00 0.00 0.00 4.37
3825 4495 3.365472 GCTGGGACACTTATTTTGGGAT 58.635 45.455 0.00 0.00 0.00 3.85
3826 4496 3.131046 GCTGGGACACTTATTTTGGGATG 59.869 47.826 0.00 0.00 0.00 3.51
3827 4497 3.701040 CTGGGACACTTATTTTGGGATGG 59.299 47.826 0.00 0.00 0.00 3.51
3828 4498 3.335183 TGGGACACTTATTTTGGGATGGA 59.665 43.478 0.00 0.00 0.00 3.41
3829 4499 3.954258 GGGACACTTATTTTGGGATGGAG 59.046 47.826 0.00 0.00 0.00 3.86
3830 4500 3.954258 GGACACTTATTTTGGGATGGAGG 59.046 47.826 0.00 0.00 0.00 4.30
3831 4501 3.954258 GACACTTATTTTGGGATGGAGGG 59.046 47.826 0.00 0.00 0.00 4.30
3832 4502 3.596046 ACACTTATTTTGGGATGGAGGGA 59.404 43.478 0.00 0.00 0.00 4.20
3833 4503 4.210331 CACTTATTTTGGGATGGAGGGAG 58.790 47.826 0.00 0.00 0.00 4.30
3834 4504 3.858638 ACTTATTTTGGGATGGAGGGAGT 59.141 43.478 0.00 0.00 0.00 3.85
3835 4505 5.043762 ACTTATTTTGGGATGGAGGGAGTA 58.956 41.667 0.00 0.00 0.00 2.59
3836 4506 5.494706 ACTTATTTTGGGATGGAGGGAGTAA 59.505 40.000 0.00 0.00 0.00 2.24
3837 4507 6.162241 ACTTATTTTGGGATGGAGGGAGTAAT 59.838 38.462 0.00 0.00 0.00 1.89
3838 4508 4.965283 TTTTGGGATGGAGGGAGTAATT 57.035 40.909 0.00 0.00 0.00 1.40
3839 4509 4.965283 TTTGGGATGGAGGGAGTAATTT 57.035 40.909 0.00 0.00 0.00 1.82
3840 4510 4.965283 TTGGGATGGAGGGAGTAATTTT 57.035 40.909 0.00 0.00 0.00 1.82
3841 4511 4.965283 TGGGATGGAGGGAGTAATTTTT 57.035 40.909 0.00 0.00 0.00 1.94
3842 4512 6.410222 TTGGGATGGAGGGAGTAATTTTTA 57.590 37.500 0.00 0.00 0.00 1.52
3843 4513 6.013554 TGGGATGGAGGGAGTAATTTTTAG 57.986 41.667 0.00 0.00 0.00 1.85
3844 4514 5.734140 TGGGATGGAGGGAGTAATTTTTAGA 59.266 40.000 0.00 0.00 0.00 2.10
3845 4515 6.218730 TGGGATGGAGGGAGTAATTTTTAGAA 59.781 38.462 0.00 0.00 0.00 2.10
3846 4516 7.091537 TGGGATGGAGGGAGTAATTTTTAGAAT 60.092 37.037 0.00 0.00 0.00 2.40
3847 4517 8.445588 GGGATGGAGGGAGTAATTTTTAGAATA 58.554 37.037 0.00 0.00 0.00 1.75
3848 4518 9.286170 GGATGGAGGGAGTAATTTTTAGAATAC 57.714 37.037 0.00 0.00 0.00 1.89
3849 4519 9.286170 GATGGAGGGAGTAATTTTTAGAATACC 57.714 37.037 0.00 0.00 0.00 2.73
3850 4520 7.580007 TGGAGGGAGTAATTTTTAGAATACCC 58.420 38.462 0.00 0.00 0.00 3.69
3851 4521 7.407918 TGGAGGGAGTAATTTTTAGAATACCCT 59.592 37.037 0.00 0.00 45.28 4.34
3852 4522 8.280084 GGAGGGAGTAATTTTTAGAATACCCTT 58.720 37.037 0.00 0.00 43.09 3.95
3853 4523 9.696572 GAGGGAGTAATTTTTAGAATACCCTTT 57.303 33.333 0.00 0.00 43.09 3.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.929808 ACTCACGGAAAGATATCACAACAC 59.070 41.667 5.32 0.00 0.00 3.32
2 3 5.147330 ACTCACGGAAAGATATCACAACA 57.853 39.130 5.32 0.00 0.00 3.33
3 4 5.168569 TGACTCACGGAAAGATATCACAAC 58.831 41.667 5.32 0.00 0.00 3.32
4 5 5.400066 TGACTCACGGAAAGATATCACAA 57.600 39.130 5.32 0.00 0.00 3.33
5 6 5.598416 ATGACTCACGGAAAGATATCACA 57.402 39.130 5.32 0.00 0.00 3.58
6 7 6.042777 TCAATGACTCACGGAAAGATATCAC 58.957 40.000 5.32 0.00 0.00 3.06
7 8 6.220726 TCAATGACTCACGGAAAGATATCA 57.779 37.500 5.32 0.00 0.00 2.15
9 10 7.060383 AGATCAATGACTCACGGAAAGATAT 57.940 36.000 0.00 0.00 0.00 1.63
10 11 6.471233 AGATCAATGACTCACGGAAAGATA 57.529 37.500 0.00 0.00 0.00 1.98
11 12 5.350504 AGATCAATGACTCACGGAAAGAT 57.649 39.130 0.00 0.00 0.00 2.40
12 13 4.808414 AGATCAATGACTCACGGAAAGA 57.192 40.909 0.00 0.00 0.00 2.52
13 14 4.931601 TCAAGATCAATGACTCACGGAAAG 59.068 41.667 0.00 0.00 0.00 2.62
14 15 4.893608 TCAAGATCAATGACTCACGGAAA 58.106 39.130 0.00 0.00 0.00 3.13
15 16 4.535526 TCAAGATCAATGACTCACGGAA 57.464 40.909 0.00 0.00 0.00 4.30
16 17 4.743057 ATCAAGATCAATGACTCACGGA 57.257 40.909 3.62 0.00 0.00 4.69
17 18 7.653311 TGTATAATCAAGATCAATGACTCACGG 59.347 37.037 3.62 0.00 0.00 4.94
18 19 8.579682 TGTATAATCAAGATCAATGACTCACG 57.420 34.615 3.62 0.00 0.00 4.35
28 29 9.271828 ACACGCAAATATGTATAATCAAGATCA 57.728 29.630 0.00 0.00 0.00 2.92
39 40 9.489084 ACACTAATCATACACGCAAATATGTAT 57.511 29.630 0.00 0.00 41.63 2.29
40 41 8.880878 ACACTAATCATACACGCAAATATGTA 57.119 30.769 0.00 0.00 35.82 2.29
41 42 7.786178 ACACTAATCATACACGCAAATATGT 57.214 32.000 0.00 0.00 31.82 2.29
42 43 9.745323 CATACACTAATCATACACGCAAATATG 57.255 33.333 0.00 0.00 0.00 1.78
43 44 8.935844 CCATACACTAATCATACACGCAAATAT 58.064 33.333 0.00 0.00 0.00 1.28
44 45 7.929245 ACCATACACTAATCATACACGCAAATA 59.071 33.333 0.00 0.00 0.00 1.40
45 46 6.765989 ACCATACACTAATCATACACGCAAAT 59.234 34.615 0.00 0.00 0.00 2.32
46 47 6.110033 ACCATACACTAATCATACACGCAAA 58.890 36.000 0.00 0.00 0.00 3.68
47 48 5.666462 ACCATACACTAATCATACACGCAA 58.334 37.500 0.00 0.00 0.00 4.85
48 49 5.163499 TGACCATACACTAATCATACACGCA 60.163 40.000 0.00 0.00 0.00 5.24
49 50 5.286438 TGACCATACACTAATCATACACGC 58.714 41.667 0.00 0.00 0.00 5.34
50 51 7.764695 TTTGACCATACACTAATCATACACG 57.235 36.000 0.00 0.00 0.00 4.49
51 52 8.487970 CGATTTGACCATACACTAATCATACAC 58.512 37.037 0.00 0.00 32.03 2.90
52 53 8.417884 TCGATTTGACCATACACTAATCATACA 58.582 33.333 0.00 0.00 32.03 2.29
53 54 8.812147 TCGATTTGACCATACACTAATCATAC 57.188 34.615 0.00 0.00 32.03 2.39
54 55 8.088365 CCTCGATTTGACCATACACTAATCATA 58.912 37.037 0.00 0.00 32.03 2.15
55 56 6.931281 CCTCGATTTGACCATACACTAATCAT 59.069 38.462 0.00 0.00 32.03 2.45
56 57 6.280643 CCTCGATTTGACCATACACTAATCA 58.719 40.000 0.00 0.00 32.03 2.57
57 58 5.696724 CCCTCGATTTGACCATACACTAATC 59.303 44.000 0.00 0.00 0.00 1.75
58 59 5.611374 CCCTCGATTTGACCATACACTAAT 58.389 41.667 0.00 0.00 0.00 1.73
59 60 4.682320 GCCCTCGATTTGACCATACACTAA 60.682 45.833 0.00 0.00 0.00 2.24
60 61 3.181469 GCCCTCGATTTGACCATACACTA 60.181 47.826 0.00 0.00 0.00 2.74
61 62 2.420129 GCCCTCGATTTGACCATACACT 60.420 50.000 0.00 0.00 0.00 3.55
62 63 1.940613 GCCCTCGATTTGACCATACAC 59.059 52.381 0.00 0.00 0.00 2.90
63 64 1.472552 CGCCCTCGATTTGACCATACA 60.473 52.381 0.00 0.00 38.10 2.29
64 65 1.217882 CGCCCTCGATTTGACCATAC 58.782 55.000 0.00 0.00 38.10 2.39
65 66 0.828022 ACGCCCTCGATTTGACCATA 59.172 50.000 0.00 0.00 39.41 2.74
66 67 0.462047 GACGCCCTCGATTTGACCAT 60.462 55.000 0.00 0.00 39.41 3.55
67 68 1.079405 GACGCCCTCGATTTGACCA 60.079 57.895 0.00 0.00 39.41 4.02
68 69 1.079405 TGACGCCCTCGATTTGACC 60.079 57.895 0.00 0.00 39.41 4.02
69 70 0.669318 TGTGACGCCCTCGATTTGAC 60.669 55.000 0.00 0.00 39.41 3.18
70 71 0.669318 GTGTGACGCCCTCGATTTGA 60.669 55.000 0.00 0.00 39.41 2.69
71 72 1.635663 GGTGTGACGCCCTCGATTTG 61.636 60.000 3.20 0.00 39.41 2.32
72 73 1.375523 GGTGTGACGCCCTCGATTT 60.376 57.895 3.20 0.00 39.41 2.17
73 74 2.264794 GGTGTGACGCCCTCGATT 59.735 61.111 3.20 0.00 39.41 3.34
82 83 3.925362 TTCGCCATCGGGTGTGACG 62.925 63.158 0.00 0.00 45.25 4.35
83 84 2.047655 TTCGCCATCGGGTGTGAC 60.048 61.111 0.00 0.00 45.25 3.67
84 85 2.264480 CTTCGCCATCGGGTGTGA 59.736 61.111 0.00 0.00 45.25 3.58
85 86 3.499737 GCTTCGCCATCGGGTGTG 61.500 66.667 0.00 0.00 45.25 3.82
155 156 4.710695 TACGCCAGCACGGACGTG 62.711 66.667 19.53 19.53 44.00 4.49
156 157 4.415332 CTACGCCAGCACGGACGT 62.415 66.667 15.10 15.10 45.43 4.34
169 170 1.741770 GTGCCAGGCAAGGTCTACG 60.742 63.158 18.28 0.00 41.47 3.51
208 209 1.380112 GAGGAGGACCAGTAGCCGT 60.380 63.158 0.00 0.00 38.94 5.68
210 211 0.971447 AACGAGGAGGACCAGTAGCC 60.971 60.000 0.00 0.00 38.94 3.93
211 212 0.173708 CAACGAGGAGGACCAGTAGC 59.826 60.000 0.00 0.00 38.94 3.58
212 213 0.173708 GCAACGAGGAGGACCAGTAG 59.826 60.000 0.00 0.00 38.94 2.57
213 214 1.255667 GGCAACGAGGAGGACCAGTA 61.256 60.000 0.00 0.00 38.94 2.74
214 215 2.584391 GGCAACGAGGAGGACCAGT 61.584 63.158 0.00 0.00 38.94 4.00
215 216 2.266055 GGCAACGAGGAGGACCAG 59.734 66.667 0.00 0.00 38.94 4.00
229 230 1.902508 GGATCTTCATATCCTCCGGCA 59.097 52.381 0.00 0.00 41.99 5.69
232 233 1.478510 CGGGGATCTTCATATCCTCCG 59.521 57.143 14.24 14.24 42.75 4.63
244 245 4.798682 AGGCGGTTCCGGGGATCT 62.799 66.667 13.16 0.00 40.77 2.75
320 402 3.368501 CCTCCTCCTCCCCTCCCA 61.369 72.222 0.00 0.00 0.00 4.37
354 444 2.467566 ATTTTAAGTCGTGCTCCGGT 57.532 45.000 0.00 0.00 37.11 5.28
365 455 0.393267 TGGCCGCGGCTATTTTAAGT 60.393 50.000 45.23 0.00 41.60 2.24
366 456 0.307760 CTGGCCGCGGCTATTTTAAG 59.692 55.000 45.23 25.40 41.60 1.85
369 459 2.828549 CCTGGCCGCGGCTATTTT 60.829 61.111 45.23 0.00 41.60 1.82
391 481 4.285851 GGTTGACCGGCTCTTCAG 57.714 61.111 0.00 0.00 0.00 3.02
423 513 0.603439 GAAACCAACTCCGGCCGTTA 60.603 55.000 26.12 11.10 0.00 3.18
441 531 1.483004 TGTGGACACAGGTTTTCGAGA 59.517 47.619 0.13 0.00 36.21 4.04
446 536 4.221703 TGTTTCAATGTGGACACAGGTTTT 59.778 37.500 11.13 0.00 45.48 2.43
447 537 3.766591 TGTTTCAATGTGGACACAGGTTT 59.233 39.130 11.13 0.00 45.48 3.27
454 544 0.950836 CCGCTGTTTCAATGTGGACA 59.049 50.000 0.00 0.00 33.56 4.02
459 549 1.286880 GCAGCCGCTGTTTCAATGT 59.713 52.632 21.29 0.00 33.43 2.71
564 668 1.910216 TTCGATGCACACGCCACATG 61.910 55.000 9.76 0.00 37.32 3.21
568 672 2.324330 CCTTTCGATGCACACGCCA 61.324 57.895 9.76 0.00 37.32 5.69
573 677 0.516877 CGCTTTCCTTTCGATGCACA 59.483 50.000 0.00 0.00 0.00 4.57
595 699 2.303660 AACCCATTACCCATCCCTCT 57.696 50.000 0.00 0.00 0.00 3.69
601 705 2.909662 CCACCAAAAACCCATTACCCAT 59.090 45.455 0.00 0.00 0.00 4.00
607 711 0.695803 TGGCCCACCAAAAACCCATT 60.696 50.000 0.00 0.00 45.37 3.16
609 713 2.368594 TGGCCCACCAAAAACCCA 59.631 55.556 0.00 0.00 45.37 4.51
628 733 1.339824 CCAAGGCTGCTTCTGATGACT 60.340 52.381 0.00 0.00 0.00 3.41
632 737 0.255318 CTCCCAAGGCTGCTTCTGAT 59.745 55.000 0.00 0.00 0.00 2.90
641 746 3.322466 CGGACCACTCCCAAGGCT 61.322 66.667 0.00 0.00 31.93 4.58
643 748 2.606519 TCCGGACCACTCCCAAGG 60.607 66.667 0.00 0.00 31.93 3.61
674 779 8.625651 TCCGTCAATTGAAAATAAAAGTGAGAA 58.374 29.630 10.35 0.00 31.71 2.87
675 780 8.160521 TCCGTCAATTGAAAATAAAAGTGAGA 57.839 30.769 10.35 0.00 31.71 3.27
677 782 8.625651 TCTTCCGTCAATTGAAAATAAAAGTGA 58.374 29.630 10.35 0.00 0.00 3.41
685 790 5.572896 GCGATTTCTTCCGTCAATTGAAAAT 59.427 36.000 10.35 11.05 31.71 1.82
687 792 4.472286 GCGATTTCTTCCGTCAATTGAAA 58.528 39.130 10.35 0.00 0.00 2.69
691 796 2.073816 ACGCGATTTCTTCCGTCAATT 58.926 42.857 15.93 0.00 29.02 2.32
695 800 1.065358 TGAACGCGATTTCTTCCGTC 58.935 50.000 15.93 0.00 32.43 4.79
696 801 1.504359 TTGAACGCGATTTCTTCCGT 58.496 45.000 15.93 0.00 34.20 4.69
723 828 5.315982 CAACATCGACATGTATGTGTTCAC 58.684 41.667 13.67 0.00 42.89 3.18
724 829 4.391523 CCAACATCGACATGTATGTGTTCA 59.608 41.667 13.67 0.00 42.89 3.18
725 830 4.629634 TCCAACATCGACATGTATGTGTTC 59.370 41.667 13.67 0.00 42.89 3.18
726 831 4.574892 TCCAACATCGACATGTATGTGTT 58.425 39.130 13.67 13.54 42.89 3.32
727 832 4.200838 TCCAACATCGACATGTATGTGT 57.799 40.909 13.67 8.85 42.89 3.72
728 833 4.024641 CCATCCAACATCGACATGTATGTG 60.025 45.833 13.67 8.28 42.89 3.21
729 834 4.129380 CCATCCAACATCGACATGTATGT 58.871 43.478 8.20 8.20 42.89 2.29
736 842 2.083774 GAAAGCCATCCAACATCGACA 58.916 47.619 0.00 0.00 0.00 4.35
758 864 1.759445 CTTCCGTGACCATCCAGATCT 59.241 52.381 0.00 0.00 0.00 2.75
763 869 4.450976 CATAAATCTTCCGTGACCATCCA 58.549 43.478 0.00 0.00 0.00 3.41
769 883 3.203716 GGGTCCATAAATCTTCCGTGAC 58.796 50.000 0.00 0.00 0.00 3.67
771 885 2.210116 CGGGTCCATAAATCTTCCGTG 58.790 52.381 0.00 0.00 0.00 4.94
774 888 1.143073 AGGCGGGTCCATAAATCTTCC 59.857 52.381 0.00 0.00 37.29 3.46
776 890 2.654863 CAAGGCGGGTCCATAAATCTT 58.345 47.619 0.00 0.00 37.29 2.40
778 892 1.133915 TCCAAGGCGGGTCCATAAATC 60.134 52.381 0.00 0.00 37.29 2.17
779 893 0.923358 TCCAAGGCGGGTCCATAAAT 59.077 50.000 0.00 0.00 37.29 1.40
784 898 1.304052 CATTTCCAAGGCGGGTCCA 60.304 57.895 0.00 0.00 37.29 4.02
785 899 2.710902 GCATTTCCAAGGCGGGTCC 61.711 63.158 0.00 0.00 34.36 4.46
787 901 0.039035 TTAGCATTTCCAAGGCGGGT 59.961 50.000 0.00 0.00 44.12 5.28
799 913 4.636206 GTCCGATGGTTTTCTCTTAGCATT 59.364 41.667 0.00 0.00 33.03 3.56
804 918 4.994852 CAGTTGTCCGATGGTTTTCTCTTA 59.005 41.667 0.00 0.00 0.00 2.10
816 930 1.153628 GTAGCGCCAGTTGTCCGAT 60.154 57.895 2.29 0.00 0.00 4.18
820 934 3.488090 GCGGTAGCGCCAGTTGTC 61.488 66.667 28.01 0.00 36.97 3.18
1083 1201 0.528017 GGTGCACTGAGAGTCGATGA 59.472 55.000 17.98 0.00 0.00 2.92
1160 1278 0.250295 CCCGAACTCAGCAGGAAACA 60.250 55.000 0.00 0.00 0.00 2.83
1165 1283 0.323629 TTTACCCCGAACTCAGCAGG 59.676 55.000 0.00 0.00 0.00 4.85
1216 1334 0.167908 TCACAACATCCAATTCGCGC 59.832 50.000 0.00 0.00 0.00 6.86
1253 1375 0.534203 TCGGAAAGCCCAGTGACAAC 60.534 55.000 0.00 0.00 34.14 3.32
1362 1484 2.341760 CACGCACGCTTCTTCTACTTAC 59.658 50.000 0.00 0.00 0.00 2.34
1478 1600 9.277783 ACTTAATGGCATGATCTCAATTACTAC 57.722 33.333 0.00 0.00 0.00 2.73
1479 1601 9.851686 AACTTAATGGCATGATCTCAATTACTA 57.148 29.630 0.00 0.00 0.00 1.82
1480 1602 8.757982 AACTTAATGGCATGATCTCAATTACT 57.242 30.769 0.00 0.00 0.00 2.24
1566 1688 3.540314 TGCCATGTTTGCTTTGAGTTT 57.460 38.095 0.00 0.00 0.00 2.66
1704 1841 6.770746 TGACAGGTTAGTACTCCTAATGAC 57.229 41.667 0.00 0.00 37.93 3.06
1836 1973 6.868622 AGCTAGTCAATTAAGTGTACCAGAG 58.131 40.000 2.43 0.86 0.00 3.35
1856 2016 6.720288 AGGACAGTACTCTTGAAGTTAAGCTA 59.280 38.462 0.00 0.00 39.55 3.32
1897 2057 0.847373 TCAACCCCTTACCAGTGCAA 59.153 50.000 0.00 0.00 0.00 4.08
2221 2385 9.944663 TCTGTTGAAATATGTAAGAACACAAAC 57.055 29.630 0.00 0.00 38.78 2.93
2483 2647 5.922544 CCTGTGAAGAATTTTCATTGGTCAC 59.077 40.000 6.41 0.00 35.30 3.67
2637 2801 1.384525 TTATGCATGCCCGGTACAAC 58.615 50.000 16.68 0.00 0.00 3.32
2639 2803 1.141858 TGATTATGCATGCCCGGTACA 59.858 47.619 16.68 5.88 0.00 2.90
2765 2929 0.532573 CATACCTGTCCACGTGCTCT 59.467 55.000 10.91 0.00 0.00 4.09
2877 3041 4.148128 ACTTCGAGGCAGATCAATCATT 57.852 40.909 0.00 0.00 0.00 2.57
2936 3100 6.091441 GCAGAAATACAACAACCAAACAAACA 59.909 34.615 0.00 0.00 0.00 2.83
2945 3109 4.419522 ACGATGCAGAAATACAACAACC 57.580 40.909 0.00 0.00 0.00 3.77
3023 3187 9.725019 TCTTATTGATCAACAGTACACTGAAAT 57.275 29.630 11.07 6.09 46.59 2.17
3088 3252 6.235664 ACAGAGGTGTTAAACGATATTGGTT 58.764 36.000 0.00 0.00 30.30 3.67
3330 3970 1.017387 CTCTATGGCGGAAACCAAGC 58.983 55.000 0.00 0.00 44.65 4.01
3331 3971 1.668419 CCTCTATGGCGGAAACCAAG 58.332 55.000 0.00 0.00 44.65 3.61
3332 3972 0.254747 CCCTCTATGGCGGAAACCAA 59.745 55.000 0.00 0.00 44.65 3.67
3334 3974 0.179054 GTCCCTCTATGGCGGAAACC 60.179 60.000 0.00 0.00 0.00 3.27
3348 3990 1.707427 ACTCCAGCAAGAAATGTCCCT 59.293 47.619 0.00 0.00 0.00 4.20
3378 4032 6.028146 TGAGGTGGACATCATTTGATTTTG 57.972 37.500 0.00 0.00 31.11 2.44
3403 4057 1.139256 TCCCTATAATGCACGGCGAAA 59.861 47.619 16.62 0.00 0.00 3.46
3514 4179 4.022416 GTGTGCATTTACCAGGTTGAATGA 60.022 41.667 23.17 11.49 32.61 2.57
3548 4213 0.521867 CATTCACATTGCCACTCGCG 60.522 55.000 0.00 0.00 42.08 5.87
3560 4225 6.367374 TTGGTGACTAGGAATACATTCACA 57.633 37.500 4.45 0.00 38.53 3.58
3566 4231 6.183360 GGAGCTTATTGGTGACTAGGAATACA 60.183 42.308 0.00 0.00 0.00 2.29
3679 4344 1.617850 TGGCGCCAATGAAACATCTTT 59.382 42.857 30.74 0.00 0.00 2.52
3728 4393 6.938596 AGAAAGAAGATGATGTGTTGATGACA 59.061 34.615 0.00 0.00 35.42 3.58
3735 4400 5.409826 GGAACGAGAAAGAAGATGATGTGTT 59.590 40.000 0.00 0.00 0.00 3.32
3755 4423 2.737252 CGAGAACTAGTTGGCAAGGAAC 59.263 50.000 14.14 0.00 0.00 3.62
3761 4429 1.968493 AGGAACGAGAACTAGTTGGCA 59.032 47.619 14.14 0.00 0.00 4.92
3785 4455 3.385755 CAGCCTTATTTTGGAATGGAGGG 59.614 47.826 0.00 0.00 33.72 4.30
3786 4456 3.385755 CCAGCCTTATTTTGGAATGGAGG 59.614 47.826 0.00 0.00 35.98 4.30
3787 4457 3.385755 CCCAGCCTTATTTTGGAATGGAG 59.614 47.826 0.00 0.00 35.98 3.86
3788 4458 3.012274 TCCCAGCCTTATTTTGGAATGGA 59.988 43.478 0.00 0.00 35.98 3.41
3789 4459 3.132824 GTCCCAGCCTTATTTTGGAATGG 59.867 47.826 0.00 0.00 33.76 3.16
3790 4460 3.768757 TGTCCCAGCCTTATTTTGGAATG 59.231 43.478 0.00 0.00 33.76 2.67
3791 4461 3.769300 GTGTCCCAGCCTTATTTTGGAAT 59.231 43.478 0.00 0.00 33.76 3.01
3792 4462 3.161866 GTGTCCCAGCCTTATTTTGGAA 58.838 45.455 0.00 0.00 33.76 3.53
3793 4463 2.378547 AGTGTCCCAGCCTTATTTTGGA 59.621 45.455 0.00 0.00 33.76 3.53
3794 4464 2.807676 AGTGTCCCAGCCTTATTTTGG 58.192 47.619 0.00 0.00 0.00 3.28
3795 4465 6.530019 AATAAGTGTCCCAGCCTTATTTTG 57.470 37.500 0.00 0.00 37.87 2.44
3796 4466 7.553504 AAAATAAGTGTCCCAGCCTTATTTT 57.446 32.000 17.25 17.25 46.35 1.82
3797 4467 6.070824 CCAAAATAAGTGTCCCAGCCTTATTT 60.071 38.462 9.60 9.60 45.94 1.40
3798 4468 5.422012 CCAAAATAAGTGTCCCAGCCTTATT 59.578 40.000 0.00 0.00 41.02 1.40
3799 4469 4.956075 CCAAAATAAGTGTCCCAGCCTTAT 59.044 41.667 0.00 0.00 33.86 1.73
3800 4470 4.340617 CCAAAATAAGTGTCCCAGCCTTA 58.659 43.478 0.00 0.00 0.00 2.69
3801 4471 3.165071 CCAAAATAAGTGTCCCAGCCTT 58.835 45.455 0.00 0.00 0.00 4.35
3802 4472 2.557452 CCCAAAATAAGTGTCCCAGCCT 60.557 50.000 0.00 0.00 0.00 4.58
3803 4473 1.824852 CCCAAAATAAGTGTCCCAGCC 59.175 52.381 0.00 0.00 0.00 4.85
3804 4474 2.802719 TCCCAAAATAAGTGTCCCAGC 58.197 47.619 0.00 0.00 0.00 4.85
3805 4475 3.701040 CCATCCCAAAATAAGTGTCCCAG 59.299 47.826 0.00 0.00 0.00 4.45
3806 4476 3.335183 TCCATCCCAAAATAAGTGTCCCA 59.665 43.478 0.00 0.00 0.00 4.37
3807 4477 3.954258 CTCCATCCCAAAATAAGTGTCCC 59.046 47.826 0.00 0.00 0.00 4.46
3808 4478 3.954258 CCTCCATCCCAAAATAAGTGTCC 59.046 47.826 0.00 0.00 0.00 4.02
3809 4479 3.954258 CCCTCCATCCCAAAATAAGTGTC 59.046 47.826 0.00 0.00 0.00 3.67
3810 4480 3.596046 TCCCTCCATCCCAAAATAAGTGT 59.404 43.478 0.00 0.00 0.00 3.55
3811 4481 4.210331 CTCCCTCCATCCCAAAATAAGTG 58.790 47.826 0.00 0.00 0.00 3.16
3812 4482 3.858638 ACTCCCTCCATCCCAAAATAAGT 59.141 43.478 0.00 0.00 0.00 2.24
3813 4483 4.526438 ACTCCCTCCATCCCAAAATAAG 57.474 45.455 0.00 0.00 0.00 1.73
3814 4484 6.606241 ATTACTCCCTCCATCCCAAAATAA 57.394 37.500 0.00 0.00 0.00 1.40
3815 4485 6.606241 AATTACTCCCTCCATCCCAAAATA 57.394 37.500 0.00 0.00 0.00 1.40
3816 4486 5.487861 AATTACTCCCTCCATCCCAAAAT 57.512 39.130 0.00 0.00 0.00 1.82
3817 4487 4.965283 AATTACTCCCTCCATCCCAAAA 57.035 40.909 0.00 0.00 0.00 2.44
3818 4488 4.965283 AAATTACTCCCTCCATCCCAAA 57.035 40.909 0.00 0.00 0.00 3.28
3819 4489 4.965283 AAAATTACTCCCTCCATCCCAA 57.035 40.909 0.00 0.00 0.00 4.12
3820 4490 4.965283 AAAAATTACTCCCTCCATCCCA 57.035 40.909 0.00 0.00 0.00 4.37
3821 4491 6.262056 TCTAAAAATTACTCCCTCCATCCC 57.738 41.667 0.00 0.00 0.00 3.85
3822 4492 9.286170 GTATTCTAAAAATTACTCCCTCCATCC 57.714 37.037 0.00 0.00 0.00 3.51
3823 4493 9.286170 GGTATTCTAAAAATTACTCCCTCCATC 57.714 37.037 0.00 0.00 0.00 3.51
3824 4494 8.225416 GGGTATTCTAAAAATTACTCCCTCCAT 58.775 37.037 0.00 0.00 0.00 3.41
3825 4495 7.407918 AGGGTATTCTAAAAATTACTCCCTCCA 59.592 37.037 0.00 0.00 37.15 3.86
3826 4496 7.813331 AGGGTATTCTAAAAATTACTCCCTCC 58.187 38.462 0.00 0.00 37.15 4.30
3827 4497 9.696572 AAAGGGTATTCTAAAAATTACTCCCTC 57.303 33.333 0.00 0.00 40.31 4.30


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

AutoCloner maintained by Alex Coulton.