Multiple sequence alignment - TraesCS2A01G130800

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Download Multiple Sequence Alignment: (Fasta) (Clustal)



BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2A01G130800 chr2A 100.000 5968 0 0 1 5968 78559529 78565496 0.000000e+00 11021.0
1 TraesCS2A01G130800 chr2B 92.676 5161 228 77 693 5811 119634203 119629151 0.000000e+00 7299.0
2 TraesCS2A01G130800 chr2B 87.440 1242 110 24 1122 2342 456699990 456698774 0.000000e+00 1387.0
3 TraesCS2A01G130800 chr2B 87.279 1242 112 24 1122 2342 693044171 693042955 0.000000e+00 1376.0
4 TraesCS2A01G130800 chr2B 87.925 1176 109 20 1189 2342 123135794 123136958 0.000000e+00 1354.0
5 TraesCS2A01G130800 chr2B 86.591 440 34 14 7 446 119634917 119634503 4.210000e-126 462.0
6 TraesCS2A01G130800 chr2B 84.559 136 3 10 311 446 120533454 120533337 1.050000e-22 119.0
7 TraesCS2A01G130800 chr2B 95.918 49 2 0 405 453 120182630 120182582 4.960000e-11 80.5
8 TraesCS2A01G130800 chr2D 91.671 4130 180 71 2 4056 77384399 77380359 0.000000e+00 5570.0
9 TraesCS2A01G130800 chr2D 87.722 1686 126 39 4320 5968 77380203 77378562 0.000000e+00 1892.0
10 TraesCS2A01G130800 chr2D 83.742 326 30 16 825 1132 78009152 78008832 2.720000e-73 287.0
11 TraesCS2A01G130800 chr2D 82.353 255 16 14 106 360 77458188 77457963 1.700000e-45 195.0
12 TraesCS2A01G130800 chr2D 88.889 117 9 2 936 1051 77449967 77449854 2.240000e-29 141.0
13 TraesCS2A01G130800 chr2D 85.714 119 9 5 186 304 78010967 78010857 1.050000e-22 119.0
14 TraesCS2A01G130800 chr2D 94.521 73 4 0 409 481 78010437 78010365 4.890000e-21 113.0
15 TraesCS2A01G130800 chr2D 93.651 63 3 1 400 461 77457956 77457894 6.370000e-15 93.5
16 TraesCS2A01G130800 chr2D 94.340 53 3 0 1082 1134 77449852 77449800 1.380000e-11 82.4
17 TraesCS2A01G130800 chr2D 96.000 50 2 0 331 380 78010540 78010491 1.380000e-11 82.4
18 TraesCS2A01G130800 chr4D 90.550 1164 96 12 1189 2342 456261485 456260326 0.000000e+00 1528.0
19 TraesCS2A01G130800 chr4D 76.754 684 109 31 2597 3277 242939517 242940153 2.660000e-88 337.0
20 TraesCS2A01G130800 chr7B 87.279 1242 112 24 1122 2342 25067212 25068428 0.000000e+00 1376.0
21 TraesCS2A01G130800 chr7B 87.329 584 51 13 1770 2342 197406455 197405884 0.000000e+00 647.0
22 TraesCS2A01G130800 chr1B 86.876 1242 116 26 1122 2342 345335044 345336259 0.000000e+00 1347.0
23 TraesCS2A01G130800 chr1D 85.425 494 41 13 1124 1613 163479377 163479843 8.990000e-133 484.0
24 TraesCS2A01G130800 chr4A 76.496 685 101 34 2600 3277 237096600 237095969 9.650000e-83 318.0
25 TraesCS2A01G130800 chr4B 78.017 464 81 14 2597 3057 300802219 300802664 7.620000e-69 272.0
26 TraesCS2A01G130800 chr4B 76.966 178 38 3 3383 3559 172775223 172775398 1.370000e-16 99.0
27 TraesCS2A01G130800 chr3A 80.242 248 43 5 3651 3897 746084869 746084627 1.320000e-41 182.0
28 TraesCS2A01G130800 chr3D 79.435 248 40 8 3651 3897 611160757 611160520 1.330000e-36 165.0


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 TraesCS2A01G130800 chr2A 78559529 78565496 5967 False 11021.0 11021 100.0000 1 5968 1 chr2A.!!$F1 5967
1 TraesCS2A01G130800 chr2B 119629151 119634917 5766 True 3880.5 7299 89.6335 7 5811 2 chr2B.!!$R5 5804
2 TraesCS2A01G130800 chr2B 456698774 456699990 1216 True 1387.0 1387 87.4400 1122 2342 1 chr2B.!!$R3 1220
3 TraesCS2A01G130800 chr2B 693042955 693044171 1216 True 1376.0 1376 87.2790 1122 2342 1 chr2B.!!$R4 1220
4 TraesCS2A01G130800 chr2B 123135794 123136958 1164 False 1354.0 1354 87.9250 1189 2342 1 chr2B.!!$F1 1153
5 TraesCS2A01G130800 chr2D 77378562 77384399 5837 True 3731.0 5570 89.6965 2 5968 2 chr2D.!!$R1 5966
6 TraesCS2A01G130800 chr4D 456260326 456261485 1159 True 1528.0 1528 90.5500 1189 2342 1 chr4D.!!$R1 1153
7 TraesCS2A01G130800 chr4D 242939517 242940153 636 False 337.0 337 76.7540 2597 3277 1 chr4D.!!$F1 680
8 TraesCS2A01G130800 chr7B 25067212 25068428 1216 False 1376.0 1376 87.2790 1122 2342 1 chr7B.!!$F1 1220
9 TraesCS2A01G130800 chr7B 197405884 197406455 571 True 647.0 647 87.3290 1770 2342 1 chr7B.!!$R1 572
10 TraesCS2A01G130800 chr1B 345335044 345336259 1215 False 1347.0 1347 86.8760 1122 2342 1 chr1B.!!$F1 1220
11 TraesCS2A01G130800 chr4A 237095969 237096600 631 True 318.0 318 76.4960 2600 3277 1 chr4A.!!$R1 677


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
229 231 0.034059 AAGACAGACAGGCTTGGACG 59.966 55.0 0.0 0.0 46.33 4.79 F
675 755 0.104934 AAGACAGACAGACACCCCCT 60.105 55.0 0.0 0.0 0.00 4.79 F
2239 2342 0.326264 GATCAGGTGGGTTGCTCTGT 59.674 55.0 0.0 0.0 0.00 3.41 F
2712 2832 0.468226 AAGGCTCGAAACACACTCCA 59.532 50.0 0.0 0.0 0.00 3.86 F
2981 3108 0.747283 TCTCGTCTCCGGGTAAGAGC 60.747 60.0 0.0 0.0 35.53 4.09 F
3202 3334 0.796312 ACAATCATGTCCGTGCGTTC 59.204 50.0 0.0 0.0 33.41 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1181 1267 0.107800 CTCGACGTACTCCTCCTGGA 60.108 60.000 0.00 0.00 40.69 3.86 R
2373 2486 0.036952 CACTGACAGGGTAGCACTGG 60.037 60.000 7.51 1.49 40.23 4.00 R
3067 3194 1.138069 GAAAGCCTAGAGACAGAGGGC 59.862 57.143 0.00 0.00 42.74 5.19 R
4278 4423 2.760634 TTGCTCACCACATACACGAT 57.239 45.000 0.00 0.00 0.00 3.73 R
4286 4431 3.698539 TCAAGTTTTGATTGCTCACCACA 59.301 39.130 0.00 0.00 34.08 4.17 R
5116 5291 0.110104 AGAAGGCTTGCACTGAAGCT 59.890 50.000 3.46 0.00 46.43 3.74 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
33 35 1.676967 GGAGGCTGCAAGAGGTTGG 60.677 63.158 0.00 0.00 34.07 3.77
43 45 2.352127 GCAAGAGGTTGGATTGTCAAGC 60.352 50.000 0.00 0.00 43.20 4.01
47 49 3.960102 AGAGGTTGGATTGTCAAGCAAAA 59.040 39.130 2.81 0.00 44.70 2.44
62 64 5.415701 TCAAGCAAAATGACATTCCCTCTAC 59.584 40.000 0.05 0.00 0.00 2.59
103 105 9.439500 AAATTTGATTAATCCACATCAAACTGG 57.561 29.630 12.90 0.00 46.88 4.00
108 110 1.234821 TCCACATCAAACTGGTTCGC 58.765 50.000 0.00 0.00 0.00 4.70
139 141 4.241999 GCGGGCACGTCATCATGC 62.242 66.667 11.45 0.00 43.45 4.06
144 146 0.316442 GGCACGTCATCATGCGAATG 60.316 55.000 0.00 0.00 43.02 2.67
157 159 1.154488 CGAATGCGTCGTGGGTTTG 60.154 57.895 1.64 0.00 45.09 2.93
167 169 3.608662 TGGGTTTGCTGCTGCTGC 61.609 61.111 22.51 22.51 40.48 5.25
168 170 3.300765 GGGTTTGCTGCTGCTGCT 61.301 61.111 27.67 0.00 40.48 4.24
169 171 2.049433 GGTTTGCTGCTGCTGCTG 60.049 61.111 27.67 16.73 40.48 4.41
183 185 1.540267 GCTGCTGATGGATATGGCTTG 59.460 52.381 0.00 0.00 0.00 4.01
214 216 4.570930 CAGTGGAAACCTAGGAGAAAGAC 58.429 47.826 17.98 4.71 0.00 3.01
218 220 4.283722 TGGAAACCTAGGAGAAAGACAGAC 59.716 45.833 17.98 0.00 0.00 3.51
221 223 3.436243 ACCTAGGAGAAAGACAGACAGG 58.564 50.000 17.98 0.00 0.00 4.00
223 225 2.022718 AGGAGAAAGACAGACAGGCT 57.977 50.000 0.00 0.00 36.92 4.58
229 231 0.034059 AAGACAGACAGGCTTGGACG 59.966 55.000 0.00 0.00 46.33 4.79
290 292 5.527582 ACGGATTGATTGATTAGTTGGCTAC 59.472 40.000 0.00 0.00 0.00 3.58
291 293 5.760253 CGGATTGATTGATTAGTTGGCTACT 59.240 40.000 6.84 6.84 41.04 2.57
292 294 6.293081 CGGATTGATTGATTAGTTGGCTACTG 60.293 42.308 11.92 0.00 37.73 2.74
296 298 6.582636 TGATTGATTAGTTGGCTACTGGTAG 58.417 40.000 11.92 3.62 37.73 3.18
299 301 6.461110 TGATTAGTTGGCTACTGGTAGTAC 57.539 41.667 11.92 0.00 37.73 2.73
381 384 2.102588 ACCCACGCATTAACCTAGCTAG 59.897 50.000 14.20 14.20 0.00 3.42
383 386 3.006967 CCCACGCATTAACCTAGCTAGAT 59.993 47.826 22.70 12.66 0.00 1.98
385 388 5.162075 CCACGCATTAACCTAGCTAGATAC 58.838 45.833 22.70 1.57 0.00 2.24
386 389 5.047943 CCACGCATTAACCTAGCTAGATACT 60.048 44.000 22.70 6.47 0.00 2.12
387 390 6.150641 CCACGCATTAACCTAGCTAGATACTA 59.849 42.308 22.70 4.85 0.00 1.82
388 391 7.244898 CACGCATTAACCTAGCTAGATACTAG 58.755 42.308 22.70 6.61 37.46 2.57
389 392 6.941436 ACGCATTAACCTAGCTAGATACTAGT 59.059 38.462 22.70 7.27 36.23 2.57
390 393 8.099537 ACGCATTAACCTAGCTAGATACTAGTA 58.900 37.037 22.70 4.77 36.23 1.82
391 394 8.605746 CGCATTAACCTAGCTAGATACTAGTAG 58.394 40.741 22.70 4.40 36.23 2.57
392 395 8.895737 GCATTAACCTAGCTAGATACTAGTAGG 58.104 40.741 22.70 19.90 36.23 3.18
393 396 8.895737 CATTAACCTAGCTAGATACTAGTAGGC 58.104 40.741 22.70 9.63 36.23 3.93
394 397 6.707273 AACCTAGCTAGATACTAGTAGGCT 57.293 41.667 22.70 19.08 36.23 4.58
395 398 7.811482 AACCTAGCTAGATACTAGTAGGCTA 57.189 40.000 22.70 19.20 36.23 3.93
397 400 7.191210 ACCTAGCTAGATACTAGTAGGCTAGA 58.809 42.308 31.48 19.54 45.86 2.43
445 458 1.989706 ACCACCACAATAACCACCAC 58.010 50.000 0.00 0.00 0.00 4.16
459 472 1.764854 ACCACCAAGACGACCCTGT 60.765 57.895 0.00 0.00 0.00 4.00
460 473 1.004918 CCACCAAGACGACCCTGTC 60.005 63.158 0.00 0.00 39.21 3.51
473 486 0.517316 CCCTGTCAGTAAACGCAAGC 59.483 55.000 0.00 0.00 45.62 4.01
478 491 2.875317 TGTCAGTAAACGCAAGCATCAA 59.125 40.909 0.00 0.00 45.62 2.57
480 493 2.225491 TCAGTAAACGCAAGCATCAACC 59.775 45.455 0.00 0.00 45.62 3.77
486 520 0.785979 CGCAAGCATCAACCTTTTGC 59.214 50.000 0.00 0.00 40.40 3.68
495 529 4.260743 GCATCAACCTTTTGCCTTTGTTTC 60.261 41.667 0.00 0.00 32.17 2.78
512 546 4.312443 TGTTTCTAAGTCCGGTTGCTAAG 58.688 43.478 0.00 0.00 0.00 2.18
526 562 6.422223 CGGTTGCTAAGCTTATTCTGTAATG 58.578 40.000 6.64 0.00 0.00 1.90
544 588 9.814899 TCTGTAATGTGTTGAATTTTGACAAAT 57.185 25.926 0.50 0.00 33.72 2.32
557 601 8.611654 AATTTTGACAAATTCCTCCAAATCTG 57.388 30.769 0.50 0.00 38.02 2.90
558 602 5.726980 TTGACAAATTCCTCCAAATCTGG 57.273 39.130 0.00 0.00 45.08 3.86
559 603 3.511146 TGACAAATTCCTCCAAATCTGGC 59.489 43.478 0.00 0.00 43.17 4.85
560 604 3.766051 GACAAATTCCTCCAAATCTGGCT 59.234 43.478 0.00 0.00 43.17 4.75
562 606 4.594491 ACAAATTCCTCCAAATCTGGCTTT 59.406 37.500 0.00 0.00 43.17 3.51
611 680 4.470304 GGATGGGAGTAGTACCAAGTTTCT 59.530 45.833 5.35 0.00 40.73 2.52
613 682 5.223449 TGGGAGTAGTACCAAGTTTCTTG 57.777 43.478 0.00 2.90 32.89 3.02
616 696 5.875359 GGGAGTAGTACCAAGTTTCTTGATG 59.125 44.000 10.54 0.00 0.00 3.07
622 702 9.665264 GTAGTACCAAGTTTCTTGATGAAAAAG 57.335 33.333 10.54 0.00 45.10 2.27
634 714 7.378181 TCTTGATGAAAAAGGGCAGATAAAAC 58.622 34.615 0.00 0.00 0.00 2.43
635 715 6.662865 TGATGAAAAAGGGCAGATAAAACA 57.337 33.333 0.00 0.00 0.00 2.83
636 716 6.690530 TGATGAAAAAGGGCAGATAAAACAG 58.309 36.000 0.00 0.00 0.00 3.16
666 746 2.213499 ACAAAGCGGAAAGACAGACAG 58.787 47.619 0.00 0.00 0.00 3.51
667 747 2.158957 ACAAAGCGGAAAGACAGACAGA 60.159 45.455 0.00 0.00 0.00 3.41
669 749 1.040646 AGCGGAAAGACAGACAGACA 58.959 50.000 0.00 0.00 0.00 3.41
671 751 1.784525 CGGAAAGACAGACAGACACC 58.215 55.000 0.00 0.00 0.00 4.16
672 752 1.605712 CGGAAAGACAGACAGACACCC 60.606 57.143 0.00 0.00 0.00 4.61
673 753 1.270893 GGAAAGACAGACAGACACCCC 60.271 57.143 0.00 0.00 0.00 4.95
674 754 0.765510 AAAGACAGACAGACACCCCC 59.234 55.000 0.00 0.00 0.00 5.40
675 755 0.104934 AAGACAGACAGACACCCCCT 60.105 55.000 0.00 0.00 0.00 4.79
676 756 0.543174 AGACAGACAGACACCCCCTC 60.543 60.000 0.00 0.00 0.00 4.30
677 757 1.536662 ACAGACAGACACCCCCTCC 60.537 63.158 0.00 0.00 0.00 4.30
678 758 1.536418 CAGACAGACACCCCCTCCA 60.536 63.158 0.00 0.00 0.00 3.86
679 759 1.229336 AGACAGACACCCCCTCCAG 60.229 63.158 0.00 0.00 0.00 3.86
680 760 2.203998 ACAGACACCCCCTCCAGG 60.204 66.667 0.00 0.00 0.00 4.45
681 761 3.721706 CAGACACCCCCTCCAGGC 61.722 72.222 0.00 0.00 0.00 4.85
732 812 4.452733 CCAACCCCGTCTCCTCGC 62.453 72.222 0.00 0.00 0.00 5.03
786 866 3.591835 CCCCTCTCGCTCTCGCTC 61.592 72.222 0.00 0.00 35.26 5.03
787 867 2.515991 CCCTCTCGCTCTCGCTCT 60.516 66.667 0.00 0.00 35.26 4.09
789 869 2.625906 CTCTCGCTCTCGCTCTCG 59.374 66.667 0.00 0.00 35.26 4.04
790 870 3.506312 CTCTCGCTCTCGCTCTCGC 62.506 68.421 0.00 0.00 35.26 5.03
791 871 3.572539 CTCGCTCTCGCTCTCGCT 61.573 66.667 0.00 0.00 35.26 4.93
792 872 3.107104 CTCGCTCTCGCTCTCGCTT 62.107 63.158 0.00 0.00 35.26 4.68
793 873 2.948648 CGCTCTCGCTCTCGCTTG 60.949 66.667 0.00 0.00 35.26 4.01
794 874 3.253930 GCTCTCGCTCTCGCTTGC 61.254 66.667 0.00 0.00 35.26 4.01
799 879 4.126390 CGCTCTCGCTTGCGTGTG 62.126 66.667 14.70 13.51 46.09 3.82
800 880 3.038417 GCTCTCGCTTGCGTGTGT 61.038 61.111 14.70 0.00 0.00 3.72
801 881 2.849007 CTCTCGCTTGCGTGTGTG 59.151 61.111 14.70 4.52 0.00 3.82
802 882 1.951130 CTCTCGCTTGCGTGTGTGT 60.951 57.895 14.70 0.00 0.00 3.72
803 883 2.150809 CTCTCGCTTGCGTGTGTGTG 62.151 60.000 14.70 0.33 0.00 3.82
804 884 2.510464 TCGCTTGCGTGTGTGTGT 60.510 55.556 14.70 0.00 0.00 3.72
822 905 3.244422 TGTGTGTGTCTCCATTAACTCCC 60.244 47.826 0.00 0.00 0.00 4.30
899 982 1.812922 CCGCTGAAGGTGCTAGCTG 60.813 63.158 17.23 0.00 35.36 4.24
1172 1258 4.889856 CGATGCCGACCGCCATCA 62.890 66.667 12.68 0.00 38.22 3.07
1203 1289 2.708255 GAGGAGTACGTCGAGCGG 59.292 66.667 0.00 0.00 46.52 5.52
1287 1373 3.376078 TACCTGTGGACGGACGGC 61.376 66.667 0.00 0.00 0.00 5.68
1374 1460 4.509737 GCCACCTACGAGGGCGAC 62.510 72.222 0.00 0.00 40.58 5.19
1440 1526 2.666098 CGGGGACACCTACAAGGGG 61.666 68.421 0.00 0.00 46.86 4.79
1468 1554 1.675641 ATGAACCTCAAGCACGGCC 60.676 57.895 0.00 0.00 0.00 6.13
1573 1659 2.505557 GCAACGGGACCGAGTACG 60.506 66.667 18.80 1.67 42.83 3.67
2239 2342 0.326264 GATCAGGTGGGTTGCTCTGT 59.674 55.000 0.00 0.00 0.00 3.41
2267 2370 2.366916 CCCTCCATTAGCGACTCTGAAT 59.633 50.000 0.00 0.00 0.00 2.57
2285 2398 5.068198 TCTGAATTATGCAGATTTTGGAGCC 59.932 40.000 0.00 0.00 37.46 4.70
2292 2405 1.475682 CAGATTTTGGAGCCTTGGCTC 59.524 52.381 28.17 28.17 36.20 4.70
2319 2432 6.542370 GGAATTTGATCAACCGGAGAGATTTA 59.458 38.462 9.46 0.00 0.00 1.40
2354 2467 4.739195 GCACCTTTGCCGATTTATTTACA 58.261 39.130 0.00 0.00 43.66 2.41
2402 2515 2.979678 ACCCTGTCAGTGGTGAATTAGT 59.020 45.455 11.06 0.00 33.27 2.24
2403 2516 4.164981 ACCCTGTCAGTGGTGAATTAGTA 58.835 43.478 11.06 0.00 33.27 1.82
2404 2517 4.020485 ACCCTGTCAGTGGTGAATTAGTAC 60.020 45.833 11.06 0.00 33.27 2.73
2486 2602 2.163818 TCCGATTTCGATACATGGCC 57.836 50.000 0.00 0.00 43.02 5.36
2492 2608 0.546122 TTCGATACATGGCCAAGGCT 59.454 50.000 10.96 0.00 41.60 4.58
2493 2609 0.546122 TCGATACATGGCCAAGGCTT 59.454 50.000 10.96 0.00 41.60 4.35
2501 2617 0.608035 TGGCCAAGGCTTTTCTACCG 60.608 55.000 0.61 0.00 41.60 4.02
2513 2629 2.933495 TTCTACCGTGTGGATTCTCG 57.067 50.000 0.00 0.00 39.21 4.04
2622 2742 1.538687 ATGCAGTTGGGAAGCAAGGC 61.539 55.000 0.00 0.00 42.15 4.35
2640 2760 1.810030 CCCGGTTACGCTTGAGCTC 60.810 63.158 6.82 6.82 39.22 4.09
2712 2832 0.468226 AAGGCTCGAAACACACTCCA 59.532 50.000 0.00 0.00 0.00 3.86
2724 2844 0.889186 ACACTCCACGGCACAATTCC 60.889 55.000 0.00 0.00 0.00 3.01
2785 2905 1.523758 GTTGGTCATCACTCACCACC 58.476 55.000 0.00 0.00 42.61 4.61
2809 2929 7.161773 CCCCCATTTCAAAGCTACATATATG 57.838 40.000 11.29 11.29 0.00 1.78
2810 2930 6.947733 CCCCCATTTCAAAGCTACATATATGA 59.052 38.462 19.63 2.59 0.00 2.15
2811 2931 7.616935 CCCCCATTTCAAAGCTACATATATGAT 59.383 37.037 19.63 6.41 0.00 2.45
2812 2932 8.464404 CCCCATTTCAAAGCTACATATATGATG 58.536 37.037 19.63 11.57 0.00 3.07
2813 2933 9.234827 CCCATTTCAAAGCTACATATATGATGA 57.765 33.333 19.63 9.88 0.00 2.92
2839 2959 1.555075 TGATGTACCTGCCTTCTGGTC 59.445 52.381 0.00 0.00 42.61 4.02
2981 3108 0.747283 TCTCGTCTCCGGGTAAGAGC 60.747 60.000 0.00 0.00 35.53 4.09
3067 3194 4.082245 AGTGAAGGTTTGTTCTTTGTGGTG 60.082 41.667 0.00 0.00 0.00 4.17
3202 3334 0.796312 ACAATCATGTCCGTGCGTTC 59.204 50.000 0.00 0.00 33.41 3.95
3232 3364 4.215613 ACTCTAGTGACCAAATTTTTCGGC 59.784 41.667 0.00 0.00 0.00 5.54
3244 3376 4.864704 ATTTTTCGGCCTACATTGTGTT 57.135 36.364 0.00 0.00 0.00 3.32
3450 3594 9.585099 CTATTCTGCTCTCATAATTCTATCCAC 57.415 37.037 0.00 0.00 0.00 4.02
3489 3633 4.717629 TCGTCTCTTGGCCGCACG 62.718 66.667 0.00 1.55 0.00 5.34
3898 4042 6.264292 ACCTTACAATGTGCACTGTTTGATTA 59.736 34.615 24.59 11.60 0.00 1.75
3905 4049 5.587289 TGTGCACTGTTTGATTAAAGGTTC 58.413 37.500 19.41 0.00 0.00 3.62
3960 4104 2.565391 TCGGCTTTCAAGAGGATACACA 59.435 45.455 0.00 0.00 41.41 3.72
4011 4155 7.236225 GGGTAAGCTAGATATTTTACCACCCTA 59.764 40.741 12.68 0.00 44.30 3.53
4103 4247 4.380531 TCTCTGTGTTTGATCCTTGTGTC 58.619 43.478 0.00 0.00 0.00 3.67
4176 4320 1.473258 TCGAGCCATTTTTCATGGGG 58.527 50.000 3.07 0.00 39.53 4.96
4248 4393 9.284968 CAAGGAAATTTGGTACTTCTCTTTCTA 57.715 33.333 0.00 0.00 0.00 2.10
4278 4423 9.844790 CAGCATTTTAATTCTAATGAGAACACA 57.155 29.630 13.69 0.00 44.50 3.72
4286 4431 8.948631 AATTCTAATGAGAACACATCGTGTAT 57.051 30.769 0.00 0.00 46.79 2.29
4428 4573 9.130661 TCTTCTGTGACCTATTCAATTTCAAAA 57.869 29.630 0.00 0.00 35.39 2.44
4567 4738 6.018994 GCTGAACAGTAGGTTGTAAATATCCG 60.019 42.308 3.77 0.00 40.63 4.18
4575 4746 8.042515 AGTAGGTTGTAAATATCCGCAAAACTA 58.957 33.333 0.00 0.00 0.00 2.24
4661 4835 8.719648 GGCATTTACTTGAGATATTCATCTGAG 58.280 37.037 0.00 0.00 41.78 3.35
4680 4854 7.377766 TCTGAGTATTTGTGAATAAACAGGC 57.622 36.000 0.00 0.00 35.82 4.85
4975 5149 3.244033 AGAGGACAGCTGAAAAGATCG 57.756 47.619 23.35 0.00 0.00 3.69
4976 5150 2.564947 AGAGGACAGCTGAAAAGATCGT 59.435 45.455 23.35 7.74 0.00 3.73
4978 5152 2.300152 AGGACAGCTGAAAAGATCGTGA 59.700 45.455 23.35 0.00 0.00 4.35
4988 5162 4.212004 TGAAAAGATCGTGAAGCTTGACAG 59.788 41.667 16.45 8.89 0.00 3.51
5015 5190 4.469883 CCCCCGATGCAGATGAAG 57.530 61.111 0.00 0.00 0.00 3.02
5016 5191 1.528824 CCCCCGATGCAGATGAAGT 59.471 57.895 0.00 0.00 0.00 3.01
5034 5209 6.564709 TGAAGTTTGAGATGTCAATGGAAG 57.435 37.500 6.07 0.00 42.41 3.46
5035 5210 6.298361 TGAAGTTTGAGATGTCAATGGAAGA 58.702 36.000 6.07 0.00 42.41 2.87
5036 5211 6.772233 TGAAGTTTGAGATGTCAATGGAAGAA 59.228 34.615 6.07 0.00 42.41 2.52
5079 5254 1.073548 GGGGTGCCCGAACTTGTAA 59.926 57.895 0.54 0.00 36.85 2.41
5115 5290 0.618458 TACAAGGATGGGGTGAGTGC 59.382 55.000 0.00 0.00 0.00 4.40
5116 5291 1.379916 CAAGGATGGGGTGAGTGCA 59.620 57.895 0.00 0.00 0.00 4.57
5124 5299 1.072159 GGGTGAGTGCAGCTTCAGT 59.928 57.895 0.00 0.00 42.08 3.41
5135 5310 2.638744 GCTTCAGTGCAAGCCTTCT 58.361 52.632 13.28 0.00 42.68 2.85
5138 5313 0.473755 TTCAGTGCAAGCCTTCTGGA 59.526 50.000 0.00 0.00 34.57 3.86
5139 5314 0.694771 TCAGTGCAAGCCTTCTGGAT 59.305 50.000 0.00 0.00 34.57 3.41
5144 5319 0.957362 GCAAGCCTTCTGGATATGGC 59.043 55.000 0.00 0.00 45.21 4.40
5164 5339 1.471684 CAGAGTTGCTCCAGAAATGGC 59.528 52.381 0.00 0.00 0.00 4.40
5275 5453 5.488341 TGGAGTTGGAGATGTTAACTTAGC 58.512 41.667 7.22 0.00 34.99 3.09
5299 5479 6.422400 GCGATTCAAGTTAAAGATAGGAGAGG 59.578 42.308 0.00 0.00 0.00 3.69
5340 5520 1.541379 GCCCGGGAGTTGTAAATGTT 58.459 50.000 29.31 0.00 0.00 2.71
5345 5525 4.082949 CCCGGGAGTTGTAAATGTTTCTTC 60.083 45.833 18.48 0.00 0.00 2.87
5348 5528 6.238925 CCGGGAGTTGTAAATGTTTCTTCTTT 60.239 38.462 0.00 0.00 0.00 2.52
5369 5549 4.387026 TTTTTCACCTGATGATGAGGGT 57.613 40.909 2.34 0.00 37.11 4.34
5370 5550 5.512942 TTTTTCACCTGATGATGAGGGTA 57.487 39.130 2.34 0.00 37.11 3.69
5414 5595 7.793927 TTGTGGGGTAAAAATTTGTTGATTC 57.206 32.000 0.00 0.00 0.00 2.52
5417 5598 7.443575 TGTGGGGTAAAAATTTGTTGATTCATG 59.556 33.333 0.00 0.00 0.00 3.07
5418 5599 7.659390 GTGGGGTAAAAATTTGTTGATTCATGA 59.341 33.333 0.00 0.00 0.00 3.07
5419 5600 7.659390 TGGGGTAAAAATTTGTTGATTCATGAC 59.341 33.333 0.00 0.00 0.00 3.06
5429 5612 4.152223 TGTTGATTCATGACTACGCTTGTG 59.848 41.667 0.00 0.00 0.00 3.33
5451 5634 0.773014 CATACATGCCCATGGGAGGA 59.227 55.000 36.00 19.92 42.91 3.71
5475 5658 4.458295 ACATGCTTGGATTTCTTCTGTCTG 59.542 41.667 4.44 0.00 0.00 3.51
5476 5659 2.816087 TGCTTGGATTTCTTCTGTCTGC 59.184 45.455 0.00 0.00 0.00 4.26
5498 5681 4.381566 GCACATTGTACATTGTTTTCCGTC 59.618 41.667 18.34 3.50 0.00 4.79
5515 5698 3.136123 CTGGGACCTGGCATTGCG 61.136 66.667 1.91 0.00 0.00 4.85
5516 5699 4.738998 TGGGACCTGGCATTGCGG 62.739 66.667 1.91 1.67 0.00 5.69
5520 5703 4.764771 ACCTGGCATTGCGGGCAT 62.765 61.111 15.98 0.00 42.89 4.40
5521 5704 2.519063 CCTGGCATTGCGGGCATA 60.519 61.111 1.91 0.00 42.89 3.14
5522 5705 2.558286 CCTGGCATTGCGGGCATAG 61.558 63.158 1.91 0.00 42.89 2.23
5523 5706 1.526686 CTGGCATTGCGGGCATAGA 60.527 57.895 1.91 0.00 42.89 1.98
5524 5707 1.512996 CTGGCATTGCGGGCATAGAG 61.513 60.000 1.91 0.00 42.89 2.43
5530 5713 1.329913 TTGCGGGCATAGAGAGAGCA 61.330 55.000 0.00 0.00 0.00 4.26
5554 5737 2.887152 AGTGATGCCTCAGTTTTGTTCC 59.113 45.455 0.00 0.00 30.58 3.62
5556 5739 1.200020 GATGCCTCAGTTTTGTTCCCG 59.800 52.381 0.00 0.00 0.00 5.14
5557 5740 0.821711 TGCCTCAGTTTTGTTCCCGG 60.822 55.000 0.00 0.00 0.00 5.73
5558 5741 1.524008 GCCTCAGTTTTGTTCCCGGG 61.524 60.000 16.85 16.85 0.00 5.73
5559 5742 1.524008 CCTCAGTTTTGTTCCCGGGC 61.524 60.000 18.49 2.59 0.00 6.13
5561 5744 0.821711 TCAGTTTTGTTCCCGGGCTG 60.822 55.000 18.49 15.73 0.00 4.85
5562 5745 0.821711 CAGTTTTGTTCCCGGGCTGA 60.822 55.000 18.49 0.19 0.00 4.26
5642 5832 1.456287 AGGCCAACTGAACCTCACC 59.544 57.895 5.01 0.00 0.00 4.02
5643 5833 1.062488 AGGCCAACTGAACCTCACCT 61.062 55.000 5.01 0.00 0.00 4.00
5644 5834 0.606673 GGCCAACTGAACCTCACCTC 60.607 60.000 0.00 0.00 0.00 3.85
5645 5835 0.108585 GCCAACTGAACCTCACCTCA 59.891 55.000 0.00 0.00 0.00 3.86
5646 5836 1.884235 CCAACTGAACCTCACCTCAC 58.116 55.000 0.00 0.00 0.00 3.51
5647 5837 1.543429 CCAACTGAACCTCACCTCACC 60.543 57.143 0.00 0.00 0.00 4.02
5648 5838 1.417890 CAACTGAACCTCACCTCACCT 59.582 52.381 0.00 0.00 0.00 4.00
5649 5839 1.343069 ACTGAACCTCACCTCACCTC 58.657 55.000 0.00 0.00 0.00 3.85
5650 5840 1.342074 CTGAACCTCACCTCACCTCA 58.658 55.000 0.00 0.00 0.00 3.86
5651 5841 1.274728 CTGAACCTCACCTCACCTCAG 59.725 57.143 0.00 0.00 0.00 3.35
5652 5842 1.343069 GAACCTCACCTCACCTCAGT 58.657 55.000 0.00 0.00 0.00 3.41
5726 5916 2.089201 TGATGGCTTGTCTGCAATCAG 58.911 47.619 2.77 0.00 45.39 2.90
5737 5927 2.342956 GCAATCAGCAAAAGTCGCG 58.657 52.632 0.00 0.00 44.79 5.87
5799 5989 2.450320 CCTCCCCTGCCATGAGAGG 61.450 68.421 0.00 0.00 38.32 3.69
5820 6010 1.542108 GGCAGATTCATCGGCTAGCTT 60.542 52.381 15.72 0.00 45.40 3.74
5821 6011 2.289072 GGCAGATTCATCGGCTAGCTTA 60.289 50.000 15.72 3.13 45.40 3.09
5822 6012 2.992543 GCAGATTCATCGGCTAGCTTAG 59.007 50.000 15.72 6.86 43.27 2.18
5823 6013 3.583806 CAGATTCATCGGCTAGCTTAGG 58.416 50.000 15.72 4.93 0.00 2.69
5824 6014 3.006323 CAGATTCATCGGCTAGCTTAGGT 59.994 47.826 15.72 0.00 0.00 3.08
5825 6015 3.643792 AGATTCATCGGCTAGCTTAGGTT 59.356 43.478 15.72 0.00 0.00 3.50
5829 6019 0.535335 TCGGCTAGCTTAGGTTGGTG 59.465 55.000 15.72 0.00 0.00 4.17
5831 6021 0.253327 GGCTAGCTTAGGTTGGTGCT 59.747 55.000 15.72 0.00 39.30 4.40
5836 6026 2.230660 AGCTTAGGTTGGTGCTTGTTC 58.769 47.619 0.00 0.00 30.96 3.18
5848 6038 3.303791 GGTGCTTGTTCGAGTTTAACCTG 60.304 47.826 0.00 0.00 0.00 4.00
5849 6039 3.558418 GTGCTTGTTCGAGTTTAACCTGA 59.442 43.478 0.00 0.00 0.00 3.86
5850 6040 3.558418 TGCTTGTTCGAGTTTAACCTGAC 59.442 43.478 0.00 0.00 0.00 3.51
5851 6041 3.808174 GCTTGTTCGAGTTTAACCTGACT 59.192 43.478 0.00 0.00 0.00 3.41
5852 6042 4.318831 GCTTGTTCGAGTTTAACCTGACTG 60.319 45.833 0.00 0.00 0.00 3.51
5877 6067 8.573885 TGAATCAGATCAATCTAAATTGGATGC 58.426 33.333 0.00 0.00 42.19 3.91
5878 6068 8.473358 AATCAGATCAATCTAAATTGGATGCA 57.527 30.769 0.00 0.00 42.19 3.96
5903 6093 5.546621 AACTAGAAGGAACTGCAACAGTA 57.453 39.130 0.00 0.00 44.62 2.74
5905 6095 5.482908 ACTAGAAGGAACTGCAACAGTATG 58.517 41.667 0.00 0.00 44.62 2.39
5927 6117 9.313118 GTATGTCTGATAACAACATCACATGTA 57.687 33.333 0.00 0.00 44.07 2.29
5950 6140 8.883302 TGTATCCATCAATCTAAATCAGATCCA 58.117 33.333 0.00 0.00 43.56 3.41
5953 6143 6.559921 TCCATCAATCTAAATCAGATCCAGGA 59.440 38.462 0.00 0.00 43.56 3.86
5954 6144 7.239143 TCCATCAATCTAAATCAGATCCAGGAT 59.761 37.037 0.00 0.00 43.56 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.885388 CTCCGTTTGTGGTGCGTGA 60.885 57.895 0.00 0.00 0.00 4.35
4 5 2.594592 AGCCTCCGTTTGTGGTGC 60.595 61.111 0.00 0.00 0.00 5.01
43 45 6.840780 AAAGGTAGAGGGAATGTCATTTTG 57.159 37.500 0.00 0.00 0.00 2.44
71 73 9.656040 TGATGTGGATTAATCAAATTTTCCAAG 57.344 29.630 17.07 0.00 36.05 3.61
81 83 7.537596 AACCAGTTTGATGTGGATTAATCAA 57.462 32.000 17.07 2.74 40.21 2.57
82 84 6.128035 CGAACCAGTTTGATGTGGATTAATCA 60.128 38.462 17.07 0.00 37.27 2.57
83 85 6.258160 CGAACCAGTTTGATGTGGATTAATC 58.742 40.000 6.93 6.93 37.27 1.75
84 86 5.393027 GCGAACCAGTTTGATGTGGATTAAT 60.393 40.000 1.81 0.00 37.27 1.40
86 88 3.438781 GCGAACCAGTTTGATGTGGATTA 59.561 43.478 1.81 0.00 37.27 1.75
88 90 1.812571 GCGAACCAGTTTGATGTGGAT 59.187 47.619 1.81 0.00 37.27 3.41
91 93 0.586319 ACGCGAACCAGTTTGATGTG 59.414 50.000 15.93 0.00 0.00 3.21
92 94 1.002900 CAACGCGAACCAGTTTGATGT 60.003 47.619 15.93 0.00 0.00 3.06
93 95 1.673760 CAACGCGAACCAGTTTGATG 58.326 50.000 15.93 0.00 0.00 3.07
103 105 1.061887 ACAACAGTGCAACGCGAAC 59.938 52.632 15.93 5.43 45.86 3.95
144 146 4.683334 GCAGCAAACCCACGACGC 62.683 66.667 0.00 0.00 0.00 5.19
151 153 3.300765 AGCAGCAGCAGCAAACCC 61.301 61.111 12.92 0.00 45.49 4.11
157 159 0.534427 TATCCATCAGCAGCAGCAGC 60.534 55.000 3.17 0.46 45.49 5.25
167 169 4.001652 CAGTAGCAAGCCATATCCATCAG 58.998 47.826 0.00 0.00 0.00 2.90
168 170 3.392285 ACAGTAGCAAGCCATATCCATCA 59.608 43.478 0.00 0.00 0.00 3.07
169 171 3.750130 CACAGTAGCAAGCCATATCCATC 59.250 47.826 0.00 0.00 0.00 3.51
183 185 0.875059 GGTTTCCACTGCACAGTAGC 59.125 55.000 2.38 0.00 40.20 3.58
214 216 2.046892 CCCGTCCAAGCCTGTCTG 60.047 66.667 0.00 0.00 0.00 3.51
218 220 4.785453 GCCTCCCGTCCAAGCCTG 62.785 72.222 0.00 0.00 0.00 4.85
221 223 3.036429 ATGAGCCTCCCGTCCAAGC 62.036 63.158 0.00 0.00 0.00 4.01
223 225 2.669133 CCATGAGCCTCCCGTCCAA 61.669 63.158 0.00 0.00 0.00 3.53
224 226 3.083349 CCATGAGCCTCCCGTCCA 61.083 66.667 0.00 0.00 0.00 4.02
229 231 3.092511 TCTGCCCATGAGCCTCCC 61.093 66.667 0.00 0.00 0.00 4.30
296 298 4.142293 GCACAAGGGTGGTAGTAGTAGTAC 60.142 50.000 6.61 6.61 45.38 2.73
299 301 3.521947 GCACAAGGGTGGTAGTAGTAG 57.478 52.381 0.00 0.00 45.38 2.57
381 384 6.363167 TCCTCTGTCTAGCCTACTAGTATC 57.637 45.833 2.33 0.00 45.32 2.24
383 386 5.427806 TGTTCCTCTGTCTAGCCTACTAGTA 59.572 44.000 1.89 1.89 45.32 1.82
385 388 4.783055 TGTTCCTCTGTCTAGCCTACTAG 58.217 47.826 0.00 0.00 46.30 2.57
386 389 4.857130 TGTTCCTCTGTCTAGCCTACTA 57.143 45.455 0.00 0.00 0.00 1.82
387 390 3.741245 TGTTCCTCTGTCTAGCCTACT 57.259 47.619 0.00 0.00 0.00 2.57
388 391 4.017808 TCTTGTTCCTCTGTCTAGCCTAC 58.982 47.826 0.00 0.00 0.00 3.18
389 392 4.017808 GTCTTGTTCCTCTGTCTAGCCTA 58.982 47.826 0.00 0.00 0.00 3.93
390 393 2.829120 GTCTTGTTCCTCTGTCTAGCCT 59.171 50.000 0.00 0.00 0.00 4.58
391 394 2.563179 TGTCTTGTTCCTCTGTCTAGCC 59.437 50.000 0.00 0.00 0.00 3.93
392 395 3.944055 TGTCTTGTTCCTCTGTCTAGC 57.056 47.619 0.00 0.00 0.00 3.42
393 396 4.241681 GCTTGTCTTGTTCCTCTGTCTAG 58.758 47.826 0.00 0.00 0.00 2.43
394 397 3.641436 TGCTTGTCTTGTTCCTCTGTCTA 59.359 43.478 0.00 0.00 0.00 2.59
395 398 2.435805 TGCTTGTCTTGTTCCTCTGTCT 59.564 45.455 0.00 0.00 0.00 3.41
396 399 2.545946 GTGCTTGTCTTGTTCCTCTGTC 59.454 50.000 0.00 0.00 0.00 3.51
397 400 2.565841 GTGCTTGTCTTGTTCCTCTGT 58.434 47.619 0.00 0.00 0.00 3.41
445 458 1.254026 TACTGACAGGGTCGTCTTGG 58.746 55.000 7.51 0.00 36.82 3.61
459 472 2.225491 GGTTGATGCTTGCGTTTACTGA 59.775 45.455 0.00 0.00 0.00 3.41
460 473 2.226437 AGGTTGATGCTTGCGTTTACTG 59.774 45.455 0.00 0.00 0.00 2.74
473 486 5.118286 AGAAACAAAGGCAAAAGGTTGATG 58.882 37.500 0.00 0.00 36.83 3.07
478 491 5.163447 GGACTTAGAAACAAAGGCAAAAGGT 60.163 40.000 0.00 0.00 33.32 3.50
480 493 4.976116 CGGACTTAGAAACAAAGGCAAAAG 59.024 41.667 0.00 0.00 33.32 2.27
486 520 3.304458 GCAACCGGACTTAGAAACAAAGG 60.304 47.826 9.46 0.00 0.00 3.11
495 529 2.674796 AGCTTAGCAACCGGACTTAG 57.325 50.000 9.46 7.00 0.00 2.18
555 599 4.201792 CGTGATTCTCATTCTGAAAGCCAG 60.202 45.833 0.00 0.00 44.27 4.85
556 600 3.686241 CGTGATTCTCATTCTGAAAGCCA 59.314 43.478 0.00 0.00 0.00 4.75
557 601 3.064545 CCGTGATTCTCATTCTGAAAGCC 59.935 47.826 0.00 0.00 0.00 4.35
558 602 3.064545 CCCGTGATTCTCATTCTGAAAGC 59.935 47.826 0.00 0.00 0.00 3.51
559 603 3.624861 CCCCGTGATTCTCATTCTGAAAG 59.375 47.826 0.00 0.00 0.00 2.62
560 604 3.609853 CCCCGTGATTCTCATTCTGAAA 58.390 45.455 0.00 0.00 0.00 2.69
562 606 1.486310 CCCCCGTGATTCTCATTCTGA 59.514 52.381 0.00 0.00 0.00 3.27
568 612 2.000701 ATGGCCCCCGTGATTCTCA 61.001 57.895 0.00 0.00 0.00 3.27
569 613 1.526917 CATGGCCCCCGTGATTCTC 60.527 63.158 0.00 0.00 42.73 2.87
572 616 4.141876 CCCATGGCCCCCGTGATT 62.142 66.667 6.09 0.00 42.73 2.57
591 656 4.903049 TCAAGAAACTTGGTACTACTCCCA 59.097 41.667 10.84 0.00 0.00 4.37
594 659 8.603242 TTTCATCAAGAAACTTGGTACTACTC 57.397 34.615 10.84 0.00 41.17 2.59
595 660 8.974060 TTTTCATCAAGAAACTTGGTACTACT 57.026 30.769 10.84 0.00 45.48 2.57
597 662 8.846211 CCTTTTTCATCAAGAAACTTGGTACTA 58.154 33.333 10.84 0.00 45.48 1.82
611 680 7.060383 TGTTTTATCTGCCCTTTTTCATCAA 57.940 32.000 0.00 0.00 0.00 2.57
613 682 5.578336 GCTGTTTTATCTGCCCTTTTTCATC 59.422 40.000 0.00 0.00 0.00 2.92
616 696 4.881920 TGCTGTTTTATCTGCCCTTTTTC 58.118 39.130 0.00 0.00 0.00 2.29
622 702 2.019984 CCTCTGCTGTTTTATCTGCCC 58.980 52.381 0.00 0.00 0.00 5.36
634 714 1.335324 CCGCTTTGTTTTCCTCTGCTG 60.335 52.381 0.00 0.00 0.00 4.41
635 715 0.954452 CCGCTTTGTTTTCCTCTGCT 59.046 50.000 0.00 0.00 0.00 4.24
636 716 0.951558 TCCGCTTTGTTTTCCTCTGC 59.048 50.000 0.00 0.00 0.00 4.26
672 752 4.748798 AGGTGGAGGCCTGGAGGG 62.749 72.222 12.00 0.00 37.50 4.30
673 753 3.086600 GAGGTGGAGGCCTGGAGG 61.087 72.222 12.00 0.00 39.34 4.30
674 754 3.086600 GGAGGTGGAGGCCTGGAG 61.087 72.222 12.00 0.00 39.34 3.86
675 755 4.741239 GGGAGGTGGAGGCCTGGA 62.741 72.222 12.00 0.00 39.34 3.86
677 757 4.748798 AGGGGAGGTGGAGGCCTG 62.749 72.222 12.00 0.00 39.34 4.85
678 758 4.423209 GAGGGGAGGTGGAGGCCT 62.423 72.222 3.86 3.86 42.53 5.19
681 761 4.825679 GGGGAGGGGAGGTGGAGG 62.826 77.778 0.00 0.00 0.00 4.30
682 762 3.700350 AGGGGAGGGGAGGTGGAG 61.700 72.222 0.00 0.00 0.00 3.86
738 818 1.909700 AAGAAATGCGCTTTGGGAGA 58.090 45.000 9.73 0.00 0.00 3.71
786 866 2.246397 CACACACACGCAAGCGAG 59.754 61.111 22.30 15.97 42.83 5.03
787 867 2.510464 ACACACACACGCAAGCGA 60.510 55.556 22.30 0.00 42.83 4.93
789 869 1.583451 CACACACACACACGCAAGC 60.583 57.895 0.00 0.00 45.62 4.01
791 871 0.672091 AGACACACACACACACGCAA 60.672 50.000 0.00 0.00 0.00 4.85
792 872 1.079474 AGACACACACACACACGCA 60.079 52.632 0.00 0.00 0.00 5.24
793 873 1.636340 GAGACACACACACACACGC 59.364 57.895 0.00 0.00 0.00 5.34
794 874 0.459411 TGGAGACACACACACACACG 60.459 55.000 0.00 0.00 33.40 4.49
795 875 3.451793 TGGAGACACACACACACAC 57.548 52.632 0.00 0.00 33.40 3.82
822 905 4.169696 TGAGGCGGGTAATGGCGG 62.170 66.667 0.00 0.00 36.92 6.13
883 966 0.179936 ATCCAGCTAGCACCTTCAGC 59.820 55.000 18.83 0.00 35.49 4.26
884 967 1.202627 GGATCCAGCTAGCACCTTCAG 60.203 57.143 18.83 0.00 0.00 3.02
885 968 0.833287 GGATCCAGCTAGCACCTTCA 59.167 55.000 18.83 0.00 0.00 3.02
886 969 0.833287 TGGATCCAGCTAGCACCTTC 59.167 55.000 18.83 8.25 0.00 3.46
887 970 0.543749 GTGGATCCAGCTAGCACCTT 59.456 55.000 16.81 0.00 0.00 3.50
888 971 1.341156 GGTGGATCCAGCTAGCACCT 61.341 60.000 32.11 0.00 40.83 4.00
952 1038 2.368011 CGTCTCCCCTTCTTCCCCC 61.368 68.421 0.00 0.00 0.00 5.40
953 1039 2.368011 CCGTCTCCCCTTCTTCCCC 61.368 68.421 0.00 0.00 0.00 4.81
955 1041 1.612739 ACCCGTCTCCCCTTCTTCC 60.613 63.158 0.00 0.00 0.00 3.46
956 1042 1.192803 ACACCCGTCTCCCCTTCTTC 61.193 60.000 0.00 0.00 0.00 2.87
957 1043 1.152096 ACACCCGTCTCCCCTTCTT 60.152 57.895 0.00 0.00 0.00 2.52
958 1044 1.913762 CACACCCGTCTCCCCTTCT 60.914 63.158 0.00 0.00 0.00 2.85
959 1045 2.663196 CACACCCGTCTCCCCTTC 59.337 66.667 0.00 0.00 0.00 3.46
960 1046 2.928396 CCACACCCGTCTCCCCTT 60.928 66.667 0.00 0.00 0.00 3.95
1172 1258 3.461773 CCTCCTGGATGTCGCGGT 61.462 66.667 6.13 0.00 34.57 5.68
1177 1263 1.677052 GACGTACTCCTCCTGGATGTC 59.323 57.143 0.00 0.00 42.29 3.06
1178 1264 1.765230 GACGTACTCCTCCTGGATGT 58.235 55.000 0.00 0.00 42.29 3.06
1181 1267 0.107800 CTCGACGTACTCCTCCTGGA 60.108 60.000 0.00 0.00 40.69 3.86
1266 1352 0.388134 CGTCCGTCCACAGGTACTTG 60.388 60.000 2.98 2.98 34.60 3.16
1287 1373 1.330655 ACTCCCCCTCGTACATGCAG 61.331 60.000 0.00 0.00 0.00 4.41
1374 1460 1.089920 CCATGAAGCCGTCCTTGAAG 58.910 55.000 0.00 0.00 32.78 3.02
1440 1526 1.077429 GAGGTTCATGGACCAGGCC 60.077 63.158 25.54 7.46 42.35 5.19
1468 1554 1.517257 CGTAGCTCTTCCTGCCGTG 60.517 63.158 0.00 0.00 0.00 4.94
1824 1916 4.351054 AAGCCCGGCAACTCCCTG 62.351 66.667 13.15 0.00 0.00 4.45
2151 2252 2.045536 GTCTCCCCCTGCTGCTTG 60.046 66.667 0.00 0.00 0.00 4.01
2209 2312 2.108566 CCTGATCCCGAGCTGCAG 59.891 66.667 10.11 10.11 0.00 4.41
2239 2342 1.133167 TCGCTAATGGAGGGAGATGGA 60.133 52.381 0.00 0.00 41.94 3.41
2267 2370 3.448301 CCAAGGCTCCAAAATCTGCATAA 59.552 43.478 0.00 0.00 0.00 1.90
2285 2398 4.381292 GGTTGATCAAATTCCAGAGCCAAG 60.381 45.833 10.35 0.00 0.00 3.61
2292 2405 3.609853 TCTCCGGTTGATCAAATTCCAG 58.390 45.455 10.35 0.00 0.00 3.86
2354 2467 5.131142 CACTGGTATCCCCTAATTCAGACTT 59.869 44.000 0.00 0.00 0.00 3.01
2373 2486 0.036952 CACTGACAGGGTAGCACTGG 60.037 60.000 7.51 1.49 40.23 4.00
2378 2491 0.685097 TTCACCACTGACAGGGTAGC 59.315 55.000 13.35 0.00 35.09 3.58
2379 2492 3.703001 AATTCACCACTGACAGGGTAG 57.297 47.619 13.35 9.39 35.09 3.18
2402 2515 5.553123 TGATTCGAAGCAAACCCTTTAGTA 58.447 37.500 14.73 0.00 0.00 1.82
2403 2516 4.394729 TGATTCGAAGCAAACCCTTTAGT 58.605 39.130 14.73 0.00 0.00 2.24
2404 2517 5.335127 CATGATTCGAAGCAAACCCTTTAG 58.665 41.667 21.22 0.00 0.00 1.85
2486 2602 1.535462 CCACACGGTAGAAAAGCCTTG 59.465 52.381 0.00 0.00 0.00 3.61
2492 2608 3.256383 TCGAGAATCCACACGGTAGAAAA 59.744 43.478 0.00 0.00 0.00 2.29
2493 2609 2.821378 TCGAGAATCCACACGGTAGAAA 59.179 45.455 0.00 0.00 0.00 2.52
2501 2617 4.033358 GTCATGTTGATCGAGAATCCACAC 59.967 45.833 0.00 0.00 41.38 3.82
2513 2629 4.877823 TGACTAATGGCTGTCATGTTGATC 59.122 41.667 0.00 0.00 38.15 2.92
2712 2832 2.031919 TCGCAGGAATTGTGCCGT 59.968 55.556 4.22 0.00 37.67 5.68
2785 2905 6.947733 TCATATATGTAGCTTTGAAATGGGGG 59.052 38.462 12.42 0.00 0.00 5.40
2808 2928 4.823442 GGCAGGTACATCATCAATTCATCA 59.177 41.667 0.00 0.00 0.00 3.07
2809 2929 5.068636 AGGCAGGTACATCATCAATTCATC 58.931 41.667 0.00 0.00 0.00 2.92
2810 2930 5.057843 AGGCAGGTACATCATCAATTCAT 57.942 39.130 0.00 0.00 0.00 2.57
2811 2931 4.508551 AGGCAGGTACATCATCAATTCA 57.491 40.909 0.00 0.00 0.00 2.57
2812 2932 5.008415 CAGAAGGCAGGTACATCATCAATTC 59.992 44.000 0.00 0.00 0.00 2.17
2813 2933 4.885907 CAGAAGGCAGGTACATCATCAATT 59.114 41.667 0.00 0.00 0.00 2.32
2814 2934 4.458397 CAGAAGGCAGGTACATCATCAAT 58.542 43.478 0.00 0.00 0.00 2.57
2815 2935 3.370846 CCAGAAGGCAGGTACATCATCAA 60.371 47.826 0.00 0.00 0.00 2.57
2816 2936 2.171237 CCAGAAGGCAGGTACATCATCA 59.829 50.000 0.00 0.00 0.00 3.07
2817 2937 2.171448 ACCAGAAGGCAGGTACATCATC 59.829 50.000 0.00 0.00 39.06 2.92
2826 2946 3.474600 CATAATGAGACCAGAAGGCAGG 58.525 50.000 0.00 0.00 39.06 4.85
2829 2949 2.877168 CAGCATAATGAGACCAGAAGGC 59.123 50.000 0.00 0.00 39.06 4.35
2839 2959 7.683437 ATGGTATGTTGATCAGCATAATGAG 57.317 36.000 27.52 0.00 36.50 2.90
2981 3108 2.231478 TGTCAGGTAGAAGAAGCTTCCG 59.769 50.000 22.81 4.34 31.34 4.30
3067 3194 1.138069 GAAAGCCTAGAGACAGAGGGC 59.862 57.143 0.00 0.00 42.74 5.19
3202 3334 5.776173 ATTTGGTCACTAGAGTATCCTCG 57.224 43.478 0.00 0.00 42.86 4.63
3229 3361 4.201783 GCTAACTTAACACAATGTAGGCCG 60.202 45.833 0.00 0.00 0.00 6.13
3232 3364 5.163754 GCCAGCTAACTTAACACAATGTAGG 60.164 44.000 0.00 0.00 0.00 3.18
3450 3594 2.669391 GCCTTTCAGATCAAAACGCCTG 60.669 50.000 0.00 0.00 0.00 4.85
3489 3633 2.288666 TCAGTTTGTGGCTTGTCAGTC 58.711 47.619 0.00 0.00 0.00 3.51
3647 3791 8.706492 CATTATGGACTAAATGCACAAATTGT 57.294 30.769 0.00 0.00 0.00 2.71
3824 3968 8.531622 TTGATAAGTTTGCAAATGTGTTATGG 57.468 30.769 16.21 0.00 0.00 2.74
3826 3970 9.762933 ACTTTGATAAGTTTGCAAATGTGTTAT 57.237 25.926 16.21 14.85 41.85 1.89
3852 3996 8.927675 AAGGTATAAACAACCAACTGATTGTA 57.072 30.769 0.00 0.00 38.08 2.41
3898 4042 4.956075 GGTATCATTGTCCATGGAACCTTT 59.044 41.667 18.20 2.80 36.15 3.11
3905 4049 4.015764 TGTGTTGGTATCATTGTCCATGG 58.984 43.478 4.97 4.97 33.07 3.66
3960 4104 6.845758 TTTGGATCAGCAAGAAATTGATCT 57.154 33.333 11.96 0.00 36.55 2.75
4069 4213 9.593134 GATCAAACACAGAGATATACAGAAGTT 57.407 33.333 0.00 0.00 0.00 2.66
4086 4230 5.607119 ATTACGACACAAGGATCAAACAC 57.393 39.130 0.00 0.00 0.00 3.32
4103 4247 6.518493 TGAAGCCTACCTAATACCAATTACG 58.482 40.000 0.00 0.00 0.00 3.18
4176 4320 3.689649 CCGGCATATATAAGCAAAGGGAC 59.310 47.826 11.74 0.00 0.00 4.46
4278 4423 2.760634 TTGCTCACCACATACACGAT 57.239 45.000 0.00 0.00 0.00 3.73
4286 4431 3.698539 TCAAGTTTTGATTGCTCACCACA 59.301 39.130 0.00 0.00 34.08 4.17
4522 4680 5.762711 TCAGCTAGTTGACAGCACATAAAAA 59.237 36.000 5.01 0.00 41.66 1.94
4567 4738 6.292865 GCCCTGTCTTGAAATTTTAGTTTTGC 60.293 38.462 0.00 0.00 0.00 3.68
4575 4746 5.385198 TCTGTAGCCCTGTCTTGAAATTTT 58.615 37.500 0.00 0.00 0.00 1.82
4661 4835 7.145932 AGACAGCCTGTTTATTCACAAATAC 57.854 36.000 0.00 0.00 0.00 1.89
4680 4854 4.994852 TGTCCCGAGTTTGATTTTAGACAG 59.005 41.667 0.00 0.00 0.00 3.51
5015 5190 5.860716 GCTTTCTTCCATTGACATCTCAAAC 59.139 40.000 0.00 0.00 39.90 2.93
5016 5191 5.771666 AGCTTTCTTCCATTGACATCTCAAA 59.228 36.000 0.00 0.00 39.90 2.69
5034 5209 0.604780 TGTGCAGAGGCTGAGCTTTC 60.605 55.000 3.72 2.74 41.91 2.62
5035 5210 0.605860 CTGTGCAGAGGCTGAGCTTT 60.606 55.000 3.72 0.00 41.91 3.51
5036 5211 1.003597 CTGTGCAGAGGCTGAGCTT 60.004 57.895 3.72 0.00 41.91 3.74
5107 5282 1.849976 GCACTGAAGCTGCACTCACC 61.850 60.000 1.02 0.00 34.56 4.02
5115 5290 0.240411 GAAGGCTTGCACTGAAGCTG 59.760 55.000 3.46 0.00 46.43 4.24
5116 5291 0.110104 AGAAGGCTTGCACTGAAGCT 59.890 50.000 3.46 0.00 46.43 3.74
5124 5299 1.751733 GCCATATCCAGAAGGCTTGCA 60.752 52.381 3.46 0.00 43.70 4.08
5132 5307 2.923121 GCAACTCTGCCATATCCAGAA 58.077 47.619 4.63 0.00 43.26 3.02
5144 5319 1.471684 GCCATTTCTGGAGCAACTCTG 59.528 52.381 0.00 0.00 46.37 3.35
5206 5381 6.055588 GTGAGCCCTATGTGTTGTATGTATT 58.944 40.000 0.00 0.00 0.00 1.89
5217 5395 5.371526 ACAAATATCAGTGAGCCCTATGTG 58.628 41.667 0.00 0.00 0.00 3.21
5275 5453 7.436673 CACCTCTCCTATCTTTAACTTGAATCG 59.563 40.741 0.00 0.00 0.00 3.34
5299 5479 1.440353 CTTGCGCGCTTGGTTACAC 60.440 57.895 33.29 0.00 0.00 2.90
5322 5502 3.418047 AGAAACATTTACAACTCCCGGG 58.582 45.455 16.85 16.85 0.00 5.73
5348 5528 4.387026 ACCCTCATCATCAGGTGAAAAA 57.613 40.909 0.00 0.00 40.97 1.94
5363 5543 0.692476 AACACATGCTGCTACCCTCA 59.308 50.000 0.00 0.00 0.00 3.86
5365 5545 1.210478 CCTAACACATGCTGCTACCCT 59.790 52.381 0.00 0.00 0.00 4.34
5366 5546 1.065418 ACCTAACACATGCTGCTACCC 60.065 52.381 0.00 0.00 0.00 3.69
5367 5547 2.403252 ACCTAACACATGCTGCTACC 57.597 50.000 0.00 0.00 0.00 3.18
5414 5595 2.078849 TGTCCACAAGCGTAGTCATG 57.921 50.000 0.00 0.00 0.00 3.07
5417 5598 3.226346 TGTATGTCCACAAGCGTAGTC 57.774 47.619 0.00 0.00 0.00 2.59
5418 5599 3.521560 CATGTATGTCCACAAGCGTAGT 58.478 45.455 0.00 0.00 30.84 2.73
5419 5600 2.285220 GCATGTATGTCCACAAGCGTAG 59.715 50.000 0.00 0.00 33.96 3.51
5451 5634 5.048224 CAGACAGAAGAAATCCAAGCATGTT 60.048 40.000 0.00 0.00 0.00 2.71
5475 5658 4.295051 ACGGAAAACAATGTACAATGTGC 58.705 39.130 17.07 9.67 0.00 4.57
5476 5659 5.624900 CAGACGGAAAACAATGTACAATGTG 59.375 40.000 17.07 9.77 0.00 3.21
5498 5681 3.136123 CGCAATGCCAGGTCCCAG 61.136 66.667 0.00 0.00 0.00 4.45
5515 5698 2.295909 CACTACTGCTCTCTCTATGCCC 59.704 54.545 0.00 0.00 0.00 5.36
5516 5699 3.218453 TCACTACTGCTCTCTCTATGCC 58.782 50.000 0.00 0.00 0.00 4.40
5518 5701 4.321156 GGCATCACTACTGCTCTCTCTATG 60.321 50.000 0.00 0.00 39.60 2.23
5519 5702 3.826157 GGCATCACTACTGCTCTCTCTAT 59.174 47.826 0.00 0.00 39.60 1.98
5520 5703 3.117701 AGGCATCACTACTGCTCTCTCTA 60.118 47.826 0.00 0.00 39.60 2.43
5521 5704 2.031120 GGCATCACTACTGCTCTCTCT 58.969 52.381 0.00 0.00 39.60 3.10
5522 5705 2.031120 AGGCATCACTACTGCTCTCTC 58.969 52.381 0.00 0.00 39.60 3.20
5523 5706 2.031120 GAGGCATCACTACTGCTCTCT 58.969 52.381 0.00 0.00 39.60 3.10
5524 5707 1.753649 TGAGGCATCACTACTGCTCTC 59.246 52.381 0.00 0.00 39.60 3.20
5530 5713 4.357918 ACAAAACTGAGGCATCACTACT 57.642 40.909 0.00 0.00 0.00 2.57
5554 5737 0.744414 ACACGATCATTTCAGCCCGG 60.744 55.000 0.00 0.00 0.00 5.73
5556 5739 2.029838 AGACACGATCATTTCAGCCC 57.970 50.000 0.00 0.00 0.00 5.19
5557 5740 2.096496 CCAAGACACGATCATTTCAGCC 59.904 50.000 0.00 0.00 0.00 4.85
5558 5741 2.096496 CCCAAGACACGATCATTTCAGC 59.904 50.000 0.00 0.00 0.00 4.26
5559 5742 2.096496 GCCCAAGACACGATCATTTCAG 59.904 50.000 0.00 0.00 0.00 3.02
5561 5744 2.083774 TGCCCAAGACACGATCATTTC 58.916 47.619 0.00 0.00 0.00 2.17
5562 5745 2.198827 TGCCCAAGACACGATCATTT 57.801 45.000 0.00 0.00 0.00 2.32
5637 5827 1.821753 CCACTACTGAGGTGAGGTGAG 59.178 57.143 0.00 0.00 36.89 3.51
5639 5829 0.247736 GCCACTACTGAGGTGAGGTG 59.752 60.000 0.00 0.00 36.89 4.00
5640 5830 0.178932 TGCCACTACTGAGGTGAGGT 60.179 55.000 0.00 0.00 36.89 3.85
5641 5831 0.534412 CTGCCACTACTGAGGTGAGG 59.466 60.000 0.00 0.00 36.89 3.86
5642 5832 0.108424 GCTGCCACTACTGAGGTGAG 60.108 60.000 0.00 0.00 36.89 3.51
5643 5833 0.542938 AGCTGCCACTACTGAGGTGA 60.543 55.000 0.00 0.00 36.89 4.02
5644 5834 0.390866 CAGCTGCCACTACTGAGGTG 60.391 60.000 0.00 0.00 33.10 4.00
5645 5835 0.542938 TCAGCTGCCACTACTGAGGT 60.543 55.000 9.47 0.00 35.58 3.85
5646 5836 2.280835 TCAGCTGCCACTACTGAGG 58.719 57.895 9.47 0.00 35.58 3.86
5648 5838 1.892819 GCCTCAGCTGCCACTACTGA 61.893 60.000 9.47 0.00 38.09 3.41
5649 5839 1.449246 GCCTCAGCTGCCACTACTG 60.449 63.158 9.47 0.00 35.50 2.74
5650 5840 1.270414 ATGCCTCAGCTGCCACTACT 61.270 55.000 9.47 0.00 40.80 2.57
5651 5841 0.813210 GATGCCTCAGCTGCCACTAC 60.813 60.000 9.47 0.00 40.80 2.73
5652 5842 1.266867 TGATGCCTCAGCTGCCACTA 61.267 55.000 9.47 0.00 40.80 2.74
5726 5916 1.059942 CAATTTCCCGCGACTTTTGC 58.940 50.000 8.23 0.00 0.00 3.68
5737 5927 4.000325 GCAAACATTACACCCAATTTCCC 59.000 43.478 0.00 0.00 0.00 3.97
5799 5989 0.952984 GCTAGCCGATGAATCTGCCC 60.953 60.000 2.29 0.00 37.70 5.36
5801 5991 1.876322 AAGCTAGCCGATGAATCTGC 58.124 50.000 12.13 0.00 37.30 4.26
5820 6010 1.414919 ACTCGAACAAGCACCAACCTA 59.585 47.619 0.00 0.00 0.00 3.08
5821 6011 0.180406 ACTCGAACAAGCACCAACCT 59.820 50.000 0.00 0.00 0.00 3.50
5822 6012 1.021968 AACTCGAACAAGCACCAACC 58.978 50.000 0.00 0.00 0.00 3.77
5823 6013 2.844122 AAACTCGAACAAGCACCAAC 57.156 45.000 0.00 0.00 0.00 3.77
5824 6014 3.065648 GGTTAAACTCGAACAAGCACCAA 59.934 43.478 0.00 0.00 0.00 3.67
5825 6015 2.614983 GGTTAAACTCGAACAAGCACCA 59.385 45.455 0.00 0.00 0.00 4.17
5829 6019 3.808174 AGTCAGGTTAAACTCGAACAAGC 59.192 43.478 0.00 0.00 0.00 4.01
5831 6021 5.013568 TCAGTCAGGTTAAACTCGAACAA 57.986 39.130 0.00 0.00 0.00 2.83
5836 6026 6.102663 ATCTGATTCAGTCAGGTTAAACTCG 58.897 40.000 13.23 0.00 46.20 4.18
5848 6038 9.334947 TCCAATTTAGATTGATCTGATTCAGTC 57.665 33.333 13.23 10.45 44.37 3.51
5849 6039 9.863650 ATCCAATTTAGATTGATCTGATTCAGT 57.136 29.630 13.23 1.42 44.37 3.41
5851 6041 8.573885 GCATCCAATTTAGATTGATCTGATTCA 58.426 33.333 7.53 0.00 44.37 2.57
5852 6042 8.573885 TGCATCCAATTTAGATTGATCTGATTC 58.426 33.333 7.53 0.00 44.37 2.52
5867 6057 6.721318 TCCTTCTAGTTAGTGCATCCAATTT 58.279 36.000 0.00 0.00 0.00 1.82
5877 6067 5.297547 TGTTGCAGTTCCTTCTAGTTAGTG 58.702 41.667 0.00 0.00 0.00 2.74
5878 6068 5.070580 ACTGTTGCAGTTCCTTCTAGTTAGT 59.929 40.000 0.00 0.00 42.59 2.24
5903 6093 8.969260 ATACATGTGATGTTGTTATCAGACAT 57.031 30.769 9.11 0.00 41.63 3.06
5905 6095 7.495606 TGGATACATGTGATGTTGTTATCAGAC 59.504 37.037 9.11 0.00 46.17 3.51
5927 6117 7.239143 TCCTGGATCTGATTTAGATTGATGGAT 59.761 37.037 0.00 0.00 46.12 3.41



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

AutoCloner maintained by Alex Coulton.