Multiple sequence alignment - TraesCS7D01G035900

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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 TraesCS7D01G035900 chr7D 100.000 4636 0 0 1 4636 18404884 18400249 0.000000e+00 8562.0
1 TraesCS7D01G035900 chr7D 78.349 1829 359 29 1344 3154 16361737 16363546 0.000000e+00 1149.0
2 TraesCS7D01G035900 chr7D 78.887 1653 325 20 1344 2981 16255321 16256964 0.000000e+00 1098.0
3 TraesCS7D01G035900 chr7D 100.000 229 0 0 550 778 381879667 381879895 1.540000e-114 424.0
4 TraesCS7D01G035900 chr7D 99.127 229 1 1 550 778 203527835 203528062 1.200000e-110 411.0
5 TraesCS7D01G035900 chr7D 96.943 229 7 0 550 778 307183049 307183277 7.280000e-103 385.0
6 TraesCS7D01G035900 chr7D 87.200 125 16 0 995 1119 18108370 18108246 4.840000e-30 143.0
7 TraesCS7D01G035900 chr7D 100.000 36 0 0 550 585 404384529 404384564 2.990000e-07 67.6
8 TraesCS7D01G035900 chr7A 92.861 3488 220 13 1104 4568 18844278 18840797 0.000000e+00 5035.0
9 TraesCS7D01G035900 chr7A 79.109 1886 357 28 1350 3214 17686427 17684558 0.000000e+00 1266.0
10 TraesCS7D01G035900 chr7A 78.567 1703 332 23 1342 3026 17595778 17594091 0.000000e+00 1092.0
11 TraesCS7D01G035900 chr7A 78.071 1742 331 40 1344 3057 17697358 17695640 0.000000e+00 1053.0
12 TraesCS7D01G035900 chr7A 76.986 1725 358 33 1351 3052 15099709 15101417 0.000000e+00 950.0
13 TraesCS7D01G035900 chr7A 95.166 331 13 2 777 1107 18853616 18853289 1.910000e-143 520.0
14 TraesCS7D01G035900 chr7A 77.875 574 116 10 2622 3191 17846737 17846171 3.430000e-91 346.0
15 TraesCS7D01G035900 chr7A 75.212 706 146 17 3392 4086 18052753 18052066 1.620000e-79 307.0
16 TraesCS7D01G035900 chr7A 93.296 179 11 1 283 460 18855348 18855170 3.560000e-66 263.0
17 TraesCS7D01G035900 chr7A 73.217 743 165 22 3358 4086 18202273 18202995 5.990000e-59 239.0
18 TraesCS7D01G035900 chr7A 72.813 743 171 20 3356 4086 18034828 18034105 1.680000e-54 224.0
19 TraesCS7D01G035900 chr7A 72.096 792 170 30 3317 4086 17423360 17422598 1.700000e-44 191.0
20 TraesCS7D01G035900 chr7A 98.113 106 2 0 444 549 18853721 18853616 7.920000e-43 185.0
21 TraesCS7D01G035900 chr7A 72.672 494 113 19 3605 4086 17772404 17771921 1.340000e-30 145.0
22 TraesCS7D01G035900 chr7A 72.233 497 122 13 3599 4086 17441665 17441176 6.250000e-29 139.0
23 TraesCS7D01G035900 chr7A 86.408 103 14 0 1017 1119 17913002 17912900 3.790000e-21 113.0
24 TraesCS7D01G035900 chr7A 82.474 97 17 0 3990 4086 17711799 17711703 8.260000e-13 86.1
25 TraesCS7D01G035900 chr7A 90.566 53 5 0 1110 1162 164786678 164786730 2.310000e-08 71.3
26 TraesCS7D01G035900 chr7A 97.059 34 1 0 4603 4636 18840743 18840710 1.800000e-04 58.4
27 TraesCS7D01G035900 chrUn 95.164 1675 75 3 2898 4571 303165502 303163833 0.000000e+00 2639.0
28 TraesCS7D01G035900 chrUn 95.164 1675 75 3 2898 4571 334438381 334436712 0.000000e+00 2639.0
29 TraesCS7D01G035900 chrUn 97.539 1219 30 0 1678 2896 424057295 424056077 0.000000e+00 2085.0
30 TraesCS7D01G035900 chrUn 76.374 1892 416 24 1341 3214 50594323 50592445 0.000000e+00 989.0
31 TraesCS7D01G035900 chrUn 89.785 558 32 11 5 549 50917570 50917025 0.000000e+00 691.0
32 TraesCS7D01G035900 chrUn 94.932 296 11 2 777 1068 50917025 50916730 1.180000e-125 460.0
33 TraesCS7D01G035900 chrUn 99.127 229 2 0 550 778 402971585 402971357 3.340000e-111 412.0
34 TraesCS7D01G035900 chrUn 94.472 199 7 4 1178 1373 393439582 393439779 2.100000e-78 303.0
35 TraesCS7D01G035900 chrUn 99.387 163 1 0 616 778 223717825 223717663 3.510000e-76 296.0
36 TraesCS7D01G035900 chrUn 76.724 464 90 14 3478 3937 89865884 89866333 4.630000e-60 243.0
37 TraesCS7D01G035900 chrUn 73.217 743 165 22 3358 4086 262124956 262124234 5.990000e-59 239.0
38 TraesCS7D01G035900 chrUn 86.822 129 16 1 991 1119 89863190 89863317 4.840000e-30 143.0
39 TraesCS7D01G035900 chr4A 78.449 1870 371 21 1341 3191 715006778 715008634 0.000000e+00 1192.0
40 TraesCS7D01G035900 chr4A 77.572 1886 378 35 1344 3208 718474015 718472154 0.000000e+00 1098.0
41 TraesCS7D01G035900 chr4A 78.629 1605 294 36 1344 2927 718563177 718561601 0.000000e+00 1018.0
42 TraesCS7D01G035900 chr4A 76.877 839 176 16 2378 3208 714946621 714947449 4.230000e-125 459.0
43 TraesCS7D01G035900 chr4A 73.046 742 167 21 3358 4086 715008810 715009531 1.000000e-56 231.0
44 TraesCS7D01G035900 chr4A 88.235 119 14 0 1001 1119 714418331 714418449 4.840000e-30 143.0
45 TraesCS7D01G035900 chr4D 99.127 229 2 0 550 778 123728856 123729084 3.340000e-111 412.0
46 TraesCS7D01G035900 chr4D 99.127 229 2 0 550 778 134971415 134971187 3.340000e-111 412.0
47 TraesCS7D01G035900 chr3D 98.253 229 4 0 550 778 501894366 501894138 7.230000e-108 401.0
48 TraesCS7D01G035900 chr2D 98.253 229 4 0 550 778 635021448 635021220 7.230000e-108 401.0
49 TraesCS7D01G035900 chr2A 93.478 46 3 0 1115 1160 25448132 25448087 8.320000e-08 69.4
50 TraesCS7D01G035900 chr2A 96.774 31 1 0 1112 1142 142713274 142713304 8.000000e-03 52.8
51 TraesCS7D01G035900 chr1D 94.872 39 2 0 1115 1153 394845814 394845776 1.390000e-05 62.1
52 TraesCS7D01G035900 chr1D 96.875 32 1 0 1115 1146 407673120 407673089 2.000000e-03 54.7
53 TraesCS7D01G035900 chr6D 96.875 32 1 0 1115 1146 22075329 22075298 2.000000e-03 54.7
54 TraesCS7D01G035900 chr5B 92.105 38 3 0 1115 1152 102629533 102629496 2.000000e-03 54.7
55 TraesCS7D01G035900 chr3A 100.000 28 0 0 1117 1144 642353787 642353760 8.000000e-03 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G035900 chr7D 18400249 18404884 4635 True 8562.000000 8562 100.0000 1 4636 1 chr7D.!!$R2 4635
1 TraesCS7D01G035900 chr7D 16361737 16363546 1809 False 1149.000000 1149 78.3490 1344 3154 1 chr7D.!!$F2 1810
2 TraesCS7D01G035900 chr7D 16255321 16256964 1643 False 1098.000000 1098 78.8870 1344 2981 1 chr7D.!!$F1 1637
3 TraesCS7D01G035900 chr7A 18840710 18844278 3568 True 2546.700000 5035 94.9600 1104 4636 2 chr7A.!!$R12 3532
4 TraesCS7D01G035900 chr7A 17684558 17686427 1869 True 1266.000000 1266 79.1090 1350 3214 1 chr7A.!!$R4 1864
5 TraesCS7D01G035900 chr7A 17594091 17595778 1687 True 1092.000000 1092 78.5670 1342 3026 1 chr7A.!!$R3 1684
6 TraesCS7D01G035900 chr7A 17695640 17697358 1718 True 1053.000000 1053 78.0710 1344 3057 1 chr7A.!!$R5 1713
7 TraesCS7D01G035900 chr7A 15099709 15101417 1708 False 950.000000 950 76.9860 1351 3052 1 chr7A.!!$F1 1701
8 TraesCS7D01G035900 chr7A 17846171 17846737 566 True 346.000000 346 77.8750 2622 3191 1 chr7A.!!$R8 569
9 TraesCS7D01G035900 chr7A 18853289 18855348 2059 True 322.666667 520 95.5250 283 1107 3 chr7A.!!$R13 824
10 TraesCS7D01G035900 chr7A 18052066 18052753 687 True 307.000000 307 75.2120 3392 4086 1 chr7A.!!$R11 694
11 TraesCS7D01G035900 chr7A 18202273 18202995 722 False 239.000000 239 73.2170 3358 4086 1 chr7A.!!$F2 728
12 TraesCS7D01G035900 chr7A 18034105 18034828 723 True 224.000000 224 72.8130 3356 4086 1 chr7A.!!$R10 730
13 TraesCS7D01G035900 chrUn 303163833 303165502 1669 True 2639.000000 2639 95.1640 2898 4571 1 chrUn.!!$R4 1673
14 TraesCS7D01G035900 chrUn 334436712 334438381 1669 True 2639.000000 2639 95.1640 2898 4571 1 chrUn.!!$R5 1673
15 TraesCS7D01G035900 chrUn 424056077 424057295 1218 True 2085.000000 2085 97.5390 1678 2896 1 chrUn.!!$R7 1218
16 TraesCS7D01G035900 chrUn 50592445 50594323 1878 True 989.000000 989 76.3740 1341 3214 1 chrUn.!!$R1 1873
17 TraesCS7D01G035900 chrUn 50916730 50917570 840 True 575.500000 691 92.3585 5 1068 2 chrUn.!!$R8 1063
18 TraesCS7D01G035900 chrUn 262124234 262124956 722 True 239.000000 239 73.2170 3358 4086 1 chrUn.!!$R3 728
19 TraesCS7D01G035900 chr4A 718472154 718474015 1861 True 1098.000000 1098 77.5720 1344 3208 1 chr4A.!!$R1 1864
20 TraesCS7D01G035900 chr4A 718561601 718563177 1576 True 1018.000000 1018 78.6290 1344 2927 1 chr4A.!!$R2 1583
21 TraesCS7D01G035900 chr4A 715006778 715009531 2753 False 711.500000 1192 75.7475 1341 4086 2 chr4A.!!$F3 2745
22 TraesCS7D01G035900 chr4A 714946621 714947449 828 False 459.000000 459 76.8770 2378 3208 1 chr4A.!!$F2 830

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
773 2252 0.036765 TTCCAACTCGTCCCGGAATG 60.037 55.000 0.73 0.00 32.61 2.67 F
1297 2780 0.655733 ACGTTGCTGCATAATACGGC 59.344 50.000 23.33 1.09 39.96 5.68 F
2802 4311 1.134907 ACTTGACCGCGGACGATAATT 60.135 47.619 35.90 6.14 43.93 1.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2450 3955 1.743958 CTCCTCATTGCTTCAAGGCTG 59.256 52.381 0.00 0.0 0.0 4.85 R
3223 4733 2.158885 GGCTGAAGACCAAGATAGGACC 60.159 54.545 0.00 0.0 0.0 4.46 R
4373 5899 0.178953 ACATTGGAGCCTTGGCTGTT 60.179 50.000 19.84 0.0 0.0 3.16 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 34 5.263599 TGACTGGTATTTCCTTGATGCAAT 58.736 37.500 0.00 0.00 37.07 3.56
59 60 6.633500 TTAGTGTGTAGCTTTCTTGCAATT 57.367 33.333 0.00 0.00 34.99 2.32
60 61 4.863491 AGTGTGTAGCTTTCTTGCAATTG 58.137 39.130 0.00 0.00 34.99 2.32
90 91 1.337118 TTTCATGGGACCCAACAAGC 58.663 50.000 19.58 0.00 36.95 4.01
91 92 0.541764 TTCATGGGACCCAACAAGCC 60.542 55.000 19.58 0.00 36.95 4.35
104 118 3.928375 CCAACAAGCCACAATAATTCAGC 59.072 43.478 0.00 0.00 0.00 4.26
105 119 4.558178 CAACAAGCCACAATAATTCAGCA 58.442 39.130 0.00 0.00 0.00 4.41
154 168 3.235944 CGTCGCTCGTGTGTCATAT 57.764 52.632 0.00 0.00 34.52 1.78
174 188 7.379529 GTCATATTCCAAAGGACAATTATTGCG 59.620 37.037 4.68 0.00 0.00 4.85
193 207 5.266733 TGCGTTAATTAGGATTAGGACGT 57.733 39.130 0.00 0.00 35.72 4.34
197 211 5.051240 CGTTAATTAGGATTAGGACGTGTGC 60.051 44.000 0.00 0.00 31.83 4.57
200 214 1.267121 AGGATTAGGACGTGTGCAGT 58.733 50.000 0.00 0.00 0.00 4.40
209 223 3.128938 AGGACGTGTGCAGTATAACTCTC 59.871 47.826 0.00 0.00 0.00 3.20
214 228 4.434520 GTGTGCAGTATAACTCTCTTCCC 58.565 47.826 0.00 0.00 0.00 3.97
218 232 5.069781 GTGCAGTATAACTCTCTTCCCTCAT 59.930 44.000 0.00 0.00 0.00 2.90
219 233 6.265649 GTGCAGTATAACTCTCTTCCCTCATA 59.734 42.308 0.00 0.00 0.00 2.15
220 234 6.265649 TGCAGTATAACTCTCTTCCCTCATAC 59.734 42.308 0.00 0.00 0.00 2.39
221 235 6.492087 GCAGTATAACTCTCTTCCCTCATACT 59.508 42.308 0.00 0.00 0.00 2.12
281 295 9.921637 TGAGTCAAAATTTCAAGTTTTGTTAGT 57.078 25.926 15.47 3.28 43.52 2.24
318 332 7.121168 ACATTGACACCTACAATACCAAATCAG 59.879 37.037 0.00 0.00 36.40 2.90
352 366 8.725148 AGATGATTATTCGGCTATGCTTTTTAG 58.275 33.333 0.00 0.00 0.00 1.85
361 375 5.455525 CGGCTATGCTTTTTAGTTAACATGC 59.544 40.000 8.61 1.81 0.00 4.06
519 1998 2.993449 TACATGTCGCTCGTGTGTTA 57.007 45.000 0.00 0.00 44.78 2.41
549 2028 6.096705 CCAAGGACCATTATTGCATTAACTCA 59.903 38.462 3.28 0.00 0.00 3.41
550 2029 6.699575 AGGACCATTATTGCATTAACTCAC 57.300 37.500 3.28 0.00 0.00 3.51
551 2030 5.594317 AGGACCATTATTGCATTAACTCACC 59.406 40.000 3.28 6.00 0.00 4.02
552 2031 5.359576 GGACCATTATTGCATTAACTCACCA 59.640 40.000 3.28 0.00 0.00 4.17
553 2032 6.127479 GGACCATTATTGCATTAACTCACCAA 60.127 38.462 3.28 0.00 0.00 3.67
554 2033 6.630071 ACCATTATTGCATTAACTCACCAAC 58.370 36.000 3.28 0.00 0.00 3.77
555 2034 6.210385 ACCATTATTGCATTAACTCACCAACA 59.790 34.615 3.28 0.00 0.00 3.33
556 2035 7.095910 CCATTATTGCATTAACTCACCAACAA 58.904 34.615 3.28 0.00 0.00 2.83
557 2036 7.276218 CCATTATTGCATTAACTCACCAACAAG 59.724 37.037 3.28 0.00 0.00 3.16
558 2037 5.789643 ATTGCATTAACTCACCAACAAGT 57.210 34.783 0.00 0.00 0.00 3.16
559 2038 4.829064 TGCATTAACTCACCAACAAGTC 57.171 40.909 0.00 0.00 0.00 3.01
560 2039 3.568007 TGCATTAACTCACCAACAAGTCC 59.432 43.478 0.00 0.00 0.00 3.85
561 2040 3.057526 GCATTAACTCACCAACAAGTCCC 60.058 47.826 0.00 0.00 0.00 4.46
562 2041 4.398319 CATTAACTCACCAACAAGTCCCT 58.602 43.478 0.00 0.00 0.00 4.20
563 2042 2.640316 AACTCACCAACAAGTCCCTC 57.360 50.000 0.00 0.00 0.00 4.30
564 2043 1.807814 ACTCACCAACAAGTCCCTCT 58.192 50.000 0.00 0.00 0.00 3.69
565 2044 1.694696 ACTCACCAACAAGTCCCTCTC 59.305 52.381 0.00 0.00 0.00 3.20
566 2045 1.694150 CTCACCAACAAGTCCCTCTCA 59.306 52.381 0.00 0.00 0.00 3.27
567 2046 2.304180 CTCACCAACAAGTCCCTCTCAT 59.696 50.000 0.00 0.00 0.00 2.90
568 2047 2.711009 TCACCAACAAGTCCCTCTCATT 59.289 45.455 0.00 0.00 0.00 2.57
569 2048 2.816087 CACCAACAAGTCCCTCTCATTG 59.184 50.000 0.00 0.00 0.00 2.82
570 2049 2.711009 ACCAACAAGTCCCTCTCATTGA 59.289 45.455 0.00 0.00 0.00 2.57
571 2050 3.244700 ACCAACAAGTCCCTCTCATTGAG 60.245 47.826 7.38 7.38 42.30 3.02
572 2051 3.008375 CCAACAAGTCCCTCTCATTGAGA 59.992 47.826 15.39 15.39 45.39 3.27
573 2052 4.324099 CCAACAAGTCCCTCTCATTGAGAT 60.324 45.833 16.48 0.00 45.39 2.75
574 2053 5.251764 CAACAAGTCCCTCTCATTGAGATT 58.748 41.667 16.48 5.35 45.39 2.40
575 2054 6.409704 CAACAAGTCCCTCTCATTGAGATTA 58.590 40.000 16.48 3.17 45.39 1.75
576 2055 6.627087 ACAAGTCCCTCTCATTGAGATTAA 57.373 37.500 16.48 2.86 45.39 1.40
577 2056 7.205515 ACAAGTCCCTCTCATTGAGATTAAT 57.794 36.000 16.48 2.59 45.39 1.40
578 2057 8.324191 ACAAGTCCCTCTCATTGAGATTAATA 57.676 34.615 16.48 0.00 45.39 0.98
579 2058 8.207545 ACAAGTCCCTCTCATTGAGATTAATAC 58.792 37.037 16.48 10.54 45.39 1.89
580 2059 7.309770 AGTCCCTCTCATTGAGATTAATACC 57.690 40.000 16.48 2.65 45.39 2.73
581 2060 6.846505 AGTCCCTCTCATTGAGATTAATACCA 59.153 38.462 16.48 0.00 45.39 3.25
582 2061 7.016072 AGTCCCTCTCATTGAGATTAATACCAG 59.984 40.741 16.48 2.33 45.39 4.00
583 2062 5.936956 CCCTCTCATTGAGATTAATACCAGC 59.063 44.000 16.48 0.00 45.39 4.85
584 2063 6.239829 CCCTCTCATTGAGATTAATACCAGCT 60.240 42.308 16.48 0.00 45.39 4.24
585 2064 7.222872 CCTCTCATTGAGATTAATACCAGCTT 58.777 38.462 16.48 0.00 45.39 3.74
586 2065 7.172875 CCTCTCATTGAGATTAATACCAGCTTG 59.827 40.741 16.48 0.59 45.39 4.01
587 2066 6.994496 TCTCATTGAGATTAATACCAGCTTGG 59.006 38.462 12.38 1.16 37.37 3.61
588 2067 7.365921 TCTCATTGAGATTAATACCAGCTTGGT 60.366 37.037 12.38 11.76 43.00 3.67
609 2088 5.890424 GTGAAACCGGAATTTCCTAATCA 57.110 39.130 9.46 9.24 37.72 2.57
610 2089 6.262193 GTGAAACCGGAATTTCCTAATCAA 57.738 37.500 9.46 0.00 37.72 2.57
611 2090 6.863275 GTGAAACCGGAATTTCCTAATCAAT 58.137 36.000 9.46 0.00 37.72 2.57
612 2091 6.972901 GTGAAACCGGAATTTCCTAATCAATC 59.027 38.462 9.46 3.89 37.72 2.67
613 2092 6.661377 TGAAACCGGAATTTCCTAATCAATCA 59.339 34.615 9.46 6.08 37.72 2.57
614 2093 7.177568 TGAAACCGGAATTTCCTAATCAATCAA 59.822 33.333 9.46 0.00 37.72 2.57
615 2094 7.475137 AACCGGAATTTCCTAATCAATCAAA 57.525 32.000 9.46 0.00 33.30 2.69
616 2095 7.660030 ACCGGAATTTCCTAATCAATCAAAT 57.340 32.000 9.46 0.00 33.30 2.32
617 2096 7.716612 ACCGGAATTTCCTAATCAATCAAATC 58.283 34.615 9.46 0.00 33.30 2.17
618 2097 7.561356 ACCGGAATTTCCTAATCAATCAAATCT 59.439 33.333 9.46 0.00 33.30 2.40
619 2098 8.416329 CCGGAATTTCCTAATCAATCAAATCTT 58.584 33.333 13.45 0.00 33.30 2.40
620 2099 9.455847 CGGAATTTCCTAATCAATCAAATCTTC 57.544 33.333 13.45 0.00 33.30 2.87
663 2142 8.460831 AAAATAACTCGTAAATTCATTGTGCC 57.539 30.769 0.00 0.00 0.00 5.01
664 2143 6.751514 ATAACTCGTAAATTCATTGTGCCA 57.248 33.333 0.00 0.00 0.00 4.92
665 2144 4.685169 ACTCGTAAATTCATTGTGCCAG 57.315 40.909 0.00 0.00 0.00 4.85
666 2145 4.323417 ACTCGTAAATTCATTGTGCCAGA 58.677 39.130 0.00 0.00 0.00 3.86
667 2146 4.759693 ACTCGTAAATTCATTGTGCCAGAA 59.240 37.500 0.00 0.00 0.00 3.02
668 2147 5.415701 ACTCGTAAATTCATTGTGCCAGAAT 59.584 36.000 0.00 0.00 33.68 2.40
669 2148 6.071952 ACTCGTAAATTCATTGTGCCAGAATT 60.072 34.615 0.00 0.00 42.10 2.17
670 2149 6.092092 TCGTAAATTCATTGTGCCAGAATTG 58.908 36.000 0.00 0.00 40.11 2.32
671 2150 6.072230 TCGTAAATTCATTGTGCCAGAATTGA 60.072 34.615 0.00 0.00 40.11 2.57
672 2151 6.753279 CGTAAATTCATTGTGCCAGAATTGAT 59.247 34.615 0.00 0.00 40.11 2.57
673 2152 7.043854 CGTAAATTCATTGTGCCAGAATTGATC 60.044 37.037 0.00 0.00 40.11 2.92
674 2153 5.925506 ATTCATTGTGCCAGAATTGATCA 57.074 34.783 0.00 0.00 0.00 2.92
675 2154 4.707030 TCATTGTGCCAGAATTGATCAC 57.293 40.909 0.00 0.00 0.00 3.06
676 2155 4.338012 TCATTGTGCCAGAATTGATCACT 58.662 39.130 0.00 0.00 32.50 3.41
677 2156 4.157105 TCATTGTGCCAGAATTGATCACTG 59.843 41.667 0.00 0.00 32.50 3.66
678 2157 3.421919 TGTGCCAGAATTGATCACTGA 57.578 42.857 12.20 0.00 34.07 3.41
679 2158 3.959293 TGTGCCAGAATTGATCACTGAT 58.041 40.909 12.20 0.00 34.07 2.90
680 2159 3.943381 TGTGCCAGAATTGATCACTGATC 59.057 43.478 11.59 11.59 39.31 2.92
681 2160 3.943381 GTGCCAGAATTGATCACTGATCA 59.057 43.478 16.44 16.44 45.78 2.92
699 2178 4.669206 ATCAGGTGTGATCAGTCTCATC 57.331 45.455 0.00 0.00 39.37 2.92
700 2179 2.762887 TCAGGTGTGATCAGTCTCATCC 59.237 50.000 0.00 0.00 30.97 3.51
701 2180 1.753649 AGGTGTGATCAGTCTCATCCG 59.246 52.381 0.00 0.00 30.97 4.18
702 2181 1.478510 GGTGTGATCAGTCTCATCCGT 59.521 52.381 0.00 0.00 31.27 4.69
703 2182 2.480416 GGTGTGATCAGTCTCATCCGTC 60.480 54.545 0.00 0.00 31.27 4.79
704 2183 2.425312 GTGTGATCAGTCTCATCCGTCT 59.575 50.000 0.00 0.00 31.27 4.18
705 2184 3.628032 GTGTGATCAGTCTCATCCGTCTA 59.372 47.826 0.00 0.00 31.27 2.59
706 2185 4.096532 GTGTGATCAGTCTCATCCGTCTAA 59.903 45.833 0.00 0.00 31.27 2.10
707 2186 4.336713 TGTGATCAGTCTCATCCGTCTAAG 59.663 45.833 0.00 0.00 0.00 2.18
708 2187 3.885901 TGATCAGTCTCATCCGTCTAAGG 59.114 47.826 0.00 0.00 0.00 2.69
709 2188 3.646736 TCAGTCTCATCCGTCTAAGGA 57.353 47.619 0.00 0.00 45.54 3.36
716 2195 2.803203 TCCGTCTAAGGATCCGGTG 58.197 57.895 5.98 0.13 41.17 4.94
717 2196 1.067582 CCGTCTAAGGATCCGGTGC 59.932 63.158 5.98 0.00 35.78 5.01
718 2197 1.299165 CGTCTAAGGATCCGGTGCG 60.299 63.158 5.98 5.30 0.00 5.34
719 2198 1.721664 CGTCTAAGGATCCGGTGCGA 61.722 60.000 5.98 0.00 0.00 5.10
720 2199 0.674534 GTCTAAGGATCCGGTGCGAT 59.325 55.000 5.98 0.00 0.00 4.58
721 2200 0.673985 TCTAAGGATCCGGTGCGATG 59.326 55.000 5.98 0.00 0.00 3.84
722 2201 0.673985 CTAAGGATCCGGTGCGATGA 59.326 55.000 5.98 0.00 0.00 2.92
723 2202 0.673985 TAAGGATCCGGTGCGATGAG 59.326 55.000 5.98 0.00 0.00 2.90
724 2203 1.330655 AAGGATCCGGTGCGATGAGT 61.331 55.000 5.98 0.00 0.00 3.41
725 2204 1.300233 GGATCCGGTGCGATGAGTC 60.300 63.158 0.00 0.00 0.00 3.36
726 2205 1.736586 GATCCGGTGCGATGAGTCT 59.263 57.895 0.00 0.00 0.00 3.24
727 2206 0.318275 GATCCGGTGCGATGAGTCTC 60.318 60.000 0.00 0.00 0.00 3.36
728 2207 1.037579 ATCCGGTGCGATGAGTCTCA 61.038 55.000 4.68 4.68 0.00 3.27
729 2208 1.037579 TCCGGTGCGATGAGTCTCAT 61.038 55.000 15.40 15.40 40.34 2.90
743 2222 8.594881 GATGAGTCTCATCCGTGTAATATTTT 57.405 34.615 26.40 0.00 45.66 1.82
744 2223 7.770801 TGAGTCTCATCCGTGTAATATTTTG 57.229 36.000 0.00 0.00 0.00 2.44
745 2224 6.761242 TGAGTCTCATCCGTGTAATATTTTGG 59.239 38.462 0.00 0.00 0.00 3.28
746 2225 6.884832 AGTCTCATCCGTGTAATATTTTGGA 58.115 36.000 0.00 0.00 0.00 3.53
747 2226 7.335627 AGTCTCATCCGTGTAATATTTTGGAA 58.664 34.615 0.00 0.00 0.00 3.53
748 2227 7.993183 AGTCTCATCCGTGTAATATTTTGGAAT 59.007 33.333 0.00 0.00 0.00 3.01
749 2228 8.621286 GTCTCATCCGTGTAATATTTTGGAATT 58.379 33.333 0.00 0.00 0.00 2.17
750 2229 8.836413 TCTCATCCGTGTAATATTTTGGAATTC 58.164 33.333 0.00 0.00 0.00 2.17
751 2230 7.936584 TCATCCGTGTAATATTTTGGAATTCC 58.063 34.615 18.17 18.17 0.00 3.01
752 2231 7.777910 TCATCCGTGTAATATTTTGGAATTCCT 59.222 33.333 24.73 7.60 36.82 3.36
753 2232 7.562454 TCCGTGTAATATTTTGGAATTCCTC 57.438 36.000 24.73 0.17 36.82 3.71
754 2233 7.343357 TCCGTGTAATATTTTGGAATTCCTCT 58.657 34.615 24.73 9.47 36.82 3.69
755 2234 7.832187 TCCGTGTAATATTTTGGAATTCCTCTT 59.168 33.333 24.73 9.95 36.82 2.85
756 2235 8.129211 CCGTGTAATATTTTGGAATTCCTCTTC 58.871 37.037 24.73 0.00 36.82 2.87
757 2236 8.129211 CGTGTAATATTTTGGAATTCCTCTTCC 58.871 37.037 24.73 0.00 44.23 3.46
764 2243 3.336138 GGAATTCCTCTTCCAACTCGT 57.664 47.619 17.73 0.00 43.56 4.18
765 2244 3.263261 GGAATTCCTCTTCCAACTCGTC 58.737 50.000 17.73 0.00 43.56 4.20
766 2245 3.263261 GAATTCCTCTTCCAACTCGTCC 58.737 50.000 0.00 0.00 0.00 4.79
767 2246 0.974383 TTCCTCTTCCAACTCGTCCC 59.026 55.000 0.00 0.00 0.00 4.46
768 2247 1.215647 CCTCTTCCAACTCGTCCCG 59.784 63.158 0.00 0.00 0.00 5.14
769 2248 1.215647 CTCTTCCAACTCGTCCCGG 59.784 63.158 0.00 0.00 0.00 5.73
770 2249 1.228644 TCTTCCAACTCGTCCCGGA 60.229 57.895 0.73 0.00 0.00 5.14
771 2250 0.828762 TCTTCCAACTCGTCCCGGAA 60.829 55.000 0.73 0.00 36.17 4.30
772 2251 0.249398 CTTCCAACTCGTCCCGGAAT 59.751 55.000 0.73 0.00 36.94 3.01
773 2252 0.036765 TTCCAACTCGTCCCGGAATG 60.037 55.000 0.73 0.00 32.61 2.67
774 2253 1.449601 CCAACTCGTCCCGGAATGG 60.450 63.158 0.73 0.00 37.55 3.16
875 2354 1.421268 TGAGACTTGGTTCACAGCCAT 59.579 47.619 0.00 0.00 35.71 4.40
993 2472 1.340248 TCGAGCAAAGAGAGAAACCGT 59.660 47.619 0.00 0.00 0.00 4.83
1120 2603 3.704566 TGTGCGAAAGGATATCTGGTACT 59.295 43.478 2.05 0.00 0.00 2.73
1122 2605 3.321111 TGCGAAAGGATATCTGGTACTCC 59.679 47.826 2.05 0.00 0.00 3.85
1126 2609 5.399113 GAAAGGATATCTGGTACTCCCTCT 58.601 45.833 2.05 0.00 0.00 3.69
1142 2625 5.012561 ACTCCCTCTGATCCATATTACTTGC 59.987 44.000 0.00 0.00 0.00 4.01
1148 2631 0.882927 TCCATATTACTTGCCGCGGC 60.883 55.000 42.35 42.35 42.35 6.53
1255 2738 5.353111 GGTCTAAAGTCTATTCACTGAGCC 58.647 45.833 0.00 0.00 0.00 4.70
1277 2760 3.191371 CACTGAGGTGCAAATTTCCCTAC 59.809 47.826 0.00 0.00 36.61 3.18
1284 2767 2.287909 TGCAAATTTCCCTACACGTTGC 60.288 45.455 0.00 0.00 40.15 4.17
1296 2779 1.663643 ACACGTTGCTGCATAATACGG 59.336 47.619 23.33 16.11 36.60 4.02
1297 2780 0.655733 ACGTTGCTGCATAATACGGC 59.344 50.000 23.33 1.09 39.96 5.68
1339 2823 7.087409 TGTTGTCCTACATTTCTTATGCATG 57.913 36.000 10.16 0.00 0.00 4.06
1886 3373 9.860898 AGTAAGGAAGATATTGTGCAAAAATTC 57.139 29.630 0.00 0.00 0.00 2.17
2061 3548 3.468770 CTCATGGAAGAGCTCAAGGATG 58.531 50.000 17.77 12.24 0.00 3.51
2158 3645 5.116084 AGCAATAATAGGAAAGGCAGTCA 57.884 39.130 0.00 0.00 0.00 3.41
2450 3955 2.180276 TCAGAGCTTGAGACTAACCCC 58.820 52.381 0.00 0.00 0.00 4.95
2802 4311 1.134907 ACTTGACCGCGGACGATAATT 60.135 47.619 35.90 6.14 43.93 1.40
2955 4465 1.165270 CCCTTTTTCACCTAGCACGG 58.835 55.000 0.00 0.00 0.00 4.94
3524 5043 2.219216 CACCGAGCAAAAATGCAAGTTG 59.781 45.455 0.00 0.00 37.25 3.16
3582 5101 2.499693 TCTCTTAATGTGGATGCGGACA 59.500 45.455 0.00 0.00 0.00 4.02
3623 5142 2.363683 CTGCATTCTGTTTCCTCTCCC 58.636 52.381 0.00 0.00 0.00 4.30
3694 5213 2.821969 CCAGACTGGATTGGAAGTTTGG 59.178 50.000 17.22 0.00 40.96 3.28
3728 5247 4.348863 AGATTTATCTAGGGCACAGCAG 57.651 45.455 0.00 0.00 34.85 4.24
3739 5261 0.036010 GCACAGCAGGCTAGAAGGAA 60.036 55.000 0.00 0.00 0.00 3.36
3896 5419 1.946768 GGATCGAGTGAGAGAGGTGAG 59.053 57.143 0.00 0.00 0.00 3.51
3946 5469 3.193267 GGCAAAGATACAAATCAGTGGCA 59.807 43.478 8.84 0.00 40.50 4.92
3948 5471 4.156556 GCAAAGATACAAATCAGTGGCAGA 59.843 41.667 0.00 0.00 34.28 4.26
4088 5614 1.141881 ATCCCGTGCTGCGACTAAG 59.858 57.895 2.97 0.00 44.77 2.18
4091 5617 2.509336 CGTGCTGCGACTAAGGGG 60.509 66.667 0.00 0.00 44.77 4.79
4149 5675 2.236146 TGAAGCGCTGGAGGAAGAATTA 59.764 45.455 12.58 0.00 0.00 1.40
4159 5685 7.415653 CGCTGGAGGAAGAATTAGCTAATTTTT 60.416 37.037 27.96 27.19 36.13 1.94
4296 5822 7.033530 AGCATATAGATAGCTATCAACCGAC 57.966 40.000 30.52 17.50 38.30 4.79
4297 5823 6.039941 AGCATATAGATAGCTATCAACCGACC 59.960 42.308 30.52 15.27 38.30 4.79
4310 5836 4.617959 TCAACCGACCGAGATGATAATTC 58.382 43.478 0.00 0.00 0.00 2.17
4466 5992 3.273434 TGCTGAAGATACAACTCATGGC 58.727 45.455 0.00 0.00 0.00 4.40
4531 6068 1.541588 GGCAACTGACAAGGATCCAAC 59.458 52.381 15.82 2.60 0.00 3.77
4537 6074 2.354729 CAAGGATCCAACGGGGCA 59.645 61.111 15.82 0.00 36.21 5.36
4571 6108 5.045140 CCTAACCCTTCCTTATTCAACCTGA 60.045 44.000 0.00 0.00 0.00 3.86
4572 6109 5.536497 AACCCTTCCTTATTCAACCTGAT 57.464 39.130 0.00 0.00 0.00 2.90
4577 6123 6.608808 CCCTTCCTTATTCAACCTGATGAAAT 59.391 38.462 0.00 0.00 42.22 2.17
4579 6125 9.189156 CCTTCCTTATTCAACCTGATGAAATTA 57.811 33.333 0.00 0.00 42.22 1.40
4590 6136 5.013079 ACCTGATGAAATTAGTGTGGACTGA 59.987 40.000 0.00 0.00 33.21 3.41
4596 6142 7.905604 TGAAATTAGTGTGGACTGAATACTG 57.094 36.000 0.00 0.00 33.21 2.74
4598 6144 4.819105 TTAGTGTGGACTGAATACTGGG 57.181 45.455 0.00 0.00 33.21 4.45
4632 6188 5.220815 GCTGATGAAATAAACTCCTCTGCTG 60.221 44.000 0.00 0.00 33.04 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 6.610075 AAATTGCATCAAGGAAATACCAGT 57.390 33.333 0.00 0.00 42.04 4.00
21 22 6.403866 ACACACTAAAAATTGCATCAAGGA 57.596 33.333 0.00 0.00 0.00 3.36
33 34 6.443934 TGCAAGAAAGCTACACACTAAAAA 57.556 33.333 0.00 0.00 34.99 1.94
74 75 1.228831 TGGCTTGTTGGGTCCCATG 60.229 57.895 12.68 3.96 31.53 3.66
75 76 1.228862 GTGGCTTGTTGGGTCCCAT 60.229 57.895 12.68 0.00 31.53 4.00
82 83 3.928375 GCTGAATTATTGTGGCTTGTTGG 59.072 43.478 0.00 0.00 0.00 3.77
90 91 9.079833 CAAAATACTTCTGCTGAATTATTGTGG 57.920 33.333 24.30 15.80 38.28 4.17
91 92 9.079833 CCAAAATACTTCTGCTGAATTATTGTG 57.920 33.333 24.69 24.69 39.81 3.33
104 118 9.757227 TTTATTGTTTGTCCCAAAATACTTCTG 57.243 29.630 0.00 0.00 0.00 3.02
152 166 6.767524 ACGCAATAATTGTCCTTTGGAATA 57.232 33.333 0.00 0.00 31.38 1.75
154 168 5.461032 AACGCAATAATTGTCCTTTGGAA 57.539 34.783 0.00 0.00 31.38 3.53
174 188 5.813672 TGCACACGTCCTAATCCTAATTAAC 59.186 40.000 0.00 0.00 0.00 2.01
193 207 4.353777 AGGGAAGAGAGTTATACTGCACA 58.646 43.478 0.00 0.00 0.00 4.57
197 211 9.575868 TTAGTATGAGGGAAGAGAGTTATACTG 57.424 37.037 0.00 0.00 33.57 2.74
289 303 6.811253 TGGTATTGTAGGTGTCAATGTTTC 57.189 37.500 0.00 0.00 36.92 2.78
318 332 4.982916 AGCCGAATAATCATCTAACGACAC 59.017 41.667 0.00 0.00 0.00 3.67
352 366 0.919710 AGGGGAGGGAGCATGTTAAC 59.080 55.000 0.00 0.00 0.00 2.01
361 375 0.253394 AGAAGGGAAAGGGGAGGGAG 60.253 60.000 0.00 0.00 0.00 4.30
419 433 0.736325 ACTCTTTTCTATGCGCGCGT 60.736 50.000 32.35 30.61 0.00 6.01
519 1998 3.299503 GCAATAATGGTCCTTGGATGGT 58.700 45.455 0.00 0.00 0.00 3.55
549 2028 2.711009 TCAATGAGAGGGACTTGTTGGT 59.289 45.455 0.00 0.00 41.55 3.67
550 2029 3.008375 TCTCAATGAGAGGGACTTGTTGG 59.992 47.826 9.18 0.00 44.81 3.77
551 2030 4.277515 TCTCAATGAGAGGGACTTGTTG 57.722 45.455 9.18 0.00 44.81 3.33
552 2031 5.511386 AATCTCAATGAGAGGGACTTGTT 57.489 39.130 18.49 2.61 42.26 2.83
553 2032 6.627087 TTAATCTCAATGAGAGGGACTTGT 57.373 37.500 18.49 0.00 42.26 3.16
554 2033 7.659390 GGTATTAATCTCAATGAGAGGGACTTG 59.341 40.741 18.49 0.00 42.26 3.16
555 2034 7.348274 TGGTATTAATCTCAATGAGAGGGACTT 59.652 37.037 18.49 9.77 42.26 3.01
556 2035 6.846505 TGGTATTAATCTCAATGAGAGGGACT 59.153 38.462 18.49 0.00 42.26 3.85
557 2036 7.067496 TGGTATTAATCTCAATGAGAGGGAC 57.933 40.000 18.49 10.94 42.26 4.46
558 2037 6.239714 GCTGGTATTAATCTCAATGAGAGGGA 60.240 42.308 18.49 6.87 42.26 4.20
559 2038 5.936956 GCTGGTATTAATCTCAATGAGAGGG 59.063 44.000 18.49 2.50 42.26 4.30
560 2039 6.767456 AGCTGGTATTAATCTCAATGAGAGG 58.233 40.000 18.49 2.04 42.26 3.69
561 2040 7.172875 CCAAGCTGGTATTAATCTCAATGAGAG 59.827 40.741 18.49 2.86 35.96 3.20
562 2041 6.994496 CCAAGCTGGTATTAATCTCAATGAGA 59.006 38.462 15.97 15.97 36.53 3.27
563 2042 7.199541 CCAAGCTGGTATTAATCTCAATGAG 57.800 40.000 3.38 3.38 31.35 2.90
579 2058 0.821711 TTCCGGTTTCACCAAGCTGG 60.822 55.000 0.00 0.00 45.02 4.85
580 2059 1.247567 ATTCCGGTTTCACCAAGCTG 58.752 50.000 0.00 0.00 38.47 4.24
581 2060 1.995376 AATTCCGGTTTCACCAAGCT 58.005 45.000 0.00 0.00 38.47 3.74
582 2061 2.609491 GGAAATTCCGGTTTCACCAAGC 60.609 50.000 16.74 0.00 38.47 4.01
583 2062 2.890945 AGGAAATTCCGGTTTCACCAAG 59.109 45.455 16.74 0.00 42.75 3.61
584 2063 2.952116 AGGAAATTCCGGTTTCACCAA 58.048 42.857 16.74 0.00 42.75 3.67
585 2064 2.668144 AGGAAATTCCGGTTTCACCA 57.332 45.000 16.74 0.00 42.75 4.17
586 2065 4.703093 TGATTAGGAAATTCCGGTTTCACC 59.297 41.667 16.74 9.86 42.75 4.02
587 2066 5.890424 TGATTAGGAAATTCCGGTTTCAC 57.110 39.130 16.74 8.27 42.75 3.18
588 2067 6.661377 TGATTGATTAGGAAATTCCGGTTTCA 59.339 34.615 16.74 6.20 42.75 2.69
589 2068 7.095695 TGATTGATTAGGAAATTCCGGTTTC 57.904 36.000 6.35 5.05 42.75 2.78
590 2069 7.475137 TTGATTGATTAGGAAATTCCGGTTT 57.525 32.000 6.35 0.00 42.75 3.27
591 2070 7.475137 TTTGATTGATTAGGAAATTCCGGTT 57.525 32.000 6.35 0.00 42.75 4.44
592 2071 7.561356 AGATTTGATTGATTAGGAAATTCCGGT 59.439 33.333 6.35 0.00 42.75 5.28
593 2072 7.945134 AGATTTGATTGATTAGGAAATTCCGG 58.055 34.615 6.35 0.00 42.75 5.14
594 2073 9.455847 GAAGATTTGATTGATTAGGAAATTCCG 57.544 33.333 6.35 0.00 42.75 4.30
637 2116 9.562583 GGCACAATGAATTTACGAGTTATTTTA 57.437 29.630 0.00 0.00 0.00 1.52
638 2117 8.085296 TGGCACAATGAATTTACGAGTTATTTT 58.915 29.630 0.00 0.00 31.92 1.82
639 2118 7.598278 TGGCACAATGAATTTACGAGTTATTT 58.402 30.769 0.00 0.00 31.92 1.40
640 2119 7.120579 TCTGGCACAATGAATTTACGAGTTATT 59.879 33.333 0.00 0.00 38.70 1.40
641 2120 6.597672 TCTGGCACAATGAATTTACGAGTTAT 59.402 34.615 0.00 0.00 38.70 1.89
642 2121 5.935206 TCTGGCACAATGAATTTACGAGTTA 59.065 36.000 0.00 0.00 38.70 2.24
643 2122 4.759693 TCTGGCACAATGAATTTACGAGTT 59.240 37.500 0.00 0.00 38.70 3.01
644 2123 4.323417 TCTGGCACAATGAATTTACGAGT 58.677 39.130 0.00 0.00 38.70 4.18
645 2124 4.944962 TCTGGCACAATGAATTTACGAG 57.055 40.909 0.00 0.00 38.70 4.18
646 2125 5.895636 ATTCTGGCACAATGAATTTACGA 57.104 34.783 0.00 0.00 38.70 3.43
647 2126 6.092092 TCAATTCTGGCACAATGAATTTACG 58.908 36.000 9.07 1.36 39.23 3.18
648 2127 7.760794 TGATCAATTCTGGCACAATGAATTTAC 59.239 33.333 9.07 5.71 39.23 2.01
649 2128 7.760794 GTGATCAATTCTGGCACAATGAATTTA 59.239 33.333 9.07 3.78 39.23 1.40
650 2129 6.592607 GTGATCAATTCTGGCACAATGAATTT 59.407 34.615 9.07 0.00 39.23 1.82
651 2130 6.070995 AGTGATCAATTCTGGCACAATGAATT 60.071 34.615 0.00 6.61 41.71 2.17
652 2131 5.421056 AGTGATCAATTCTGGCACAATGAAT 59.579 36.000 0.00 0.00 38.70 2.57
653 2132 4.768448 AGTGATCAATTCTGGCACAATGAA 59.232 37.500 0.00 0.00 38.70 2.57
654 2133 4.157105 CAGTGATCAATTCTGGCACAATGA 59.843 41.667 0.00 0.00 38.70 2.57
655 2134 4.157105 TCAGTGATCAATTCTGGCACAATG 59.843 41.667 10.87 0.00 38.70 2.82
656 2135 4.338012 TCAGTGATCAATTCTGGCACAAT 58.662 39.130 10.87 0.00 38.70 2.71
657 2136 3.753815 TCAGTGATCAATTCTGGCACAA 58.246 40.909 10.87 0.00 38.70 3.33
658 2137 3.421919 TCAGTGATCAATTCTGGCACA 57.578 42.857 10.87 0.00 33.41 4.57
659 2138 3.943381 TGATCAGTGATCAATTCTGGCAC 59.057 43.478 29.39 3.51 44.70 5.01
660 2139 4.196971 CTGATCAGTGATCAATTCTGGCA 58.803 43.478 30.50 10.42 46.51 4.92
661 2140 3.564644 CCTGATCAGTGATCAATTCTGGC 59.435 47.826 30.50 6.51 46.51 4.85
662 2141 4.575236 CACCTGATCAGTGATCAATTCTGG 59.425 45.833 30.50 27.87 46.51 3.86
663 2142 5.064834 CACACCTGATCAGTGATCAATTCTG 59.935 44.000 30.50 23.61 46.51 3.02
664 2143 5.046087 TCACACCTGATCAGTGATCAATTCT 60.046 40.000 30.50 14.72 46.51 2.40
665 2144 5.181009 TCACACCTGATCAGTGATCAATTC 58.819 41.667 30.50 10.11 46.51 2.17
666 2145 5.169992 TCACACCTGATCAGTGATCAATT 57.830 39.130 30.50 19.83 46.51 2.32
667 2146 4.831674 TCACACCTGATCAGTGATCAAT 57.168 40.909 30.50 21.06 46.51 2.57
668 2147 4.831674 ATCACACCTGATCAGTGATCAA 57.168 40.909 30.50 18.40 46.81 2.57
678 2157 3.387374 GGATGAGACTGATCACACCTGAT 59.613 47.826 4.23 0.00 40.07 2.90
679 2158 2.762887 GGATGAGACTGATCACACCTGA 59.237 50.000 4.23 0.00 30.46 3.86
680 2159 2.480932 CGGATGAGACTGATCACACCTG 60.481 54.545 4.23 0.00 31.10 4.00
681 2160 1.753649 CGGATGAGACTGATCACACCT 59.246 52.381 4.23 0.00 31.10 4.00
682 2161 1.478510 ACGGATGAGACTGATCACACC 59.521 52.381 4.23 0.00 30.46 4.16
683 2162 2.425312 AGACGGATGAGACTGATCACAC 59.575 50.000 4.23 0.00 30.46 3.82
684 2163 2.728007 AGACGGATGAGACTGATCACA 58.272 47.619 4.23 0.00 30.46 3.58
685 2164 4.261405 CCTTAGACGGATGAGACTGATCAC 60.261 50.000 4.23 0.00 30.46 3.06
686 2165 3.885901 CCTTAGACGGATGAGACTGATCA 59.114 47.826 4.23 0.00 0.00 2.92
687 2166 4.138290 TCCTTAGACGGATGAGACTGATC 58.862 47.826 0.00 0.00 0.00 2.92
688 2167 4.171878 TCCTTAGACGGATGAGACTGAT 57.828 45.455 0.00 0.00 0.00 2.90
689 2168 3.646736 TCCTTAGACGGATGAGACTGA 57.353 47.619 0.00 0.00 0.00 3.41
690 2169 3.254657 GGATCCTTAGACGGATGAGACTG 59.745 52.174 3.84 0.00 43.71 3.51
691 2170 3.492337 GGATCCTTAGACGGATGAGACT 58.508 50.000 3.84 0.00 43.71 3.24
692 2171 2.226912 CGGATCCTTAGACGGATGAGAC 59.773 54.545 10.75 0.00 43.71 3.36
693 2172 2.505405 CGGATCCTTAGACGGATGAGA 58.495 52.381 10.75 0.00 43.71 3.27
694 2173 2.999507 CGGATCCTTAGACGGATGAG 57.000 55.000 10.75 0.00 43.71 2.90
700 2179 1.299165 CGCACCGGATCCTTAGACG 60.299 63.158 9.46 3.47 0.00 4.18
701 2180 0.674534 ATCGCACCGGATCCTTAGAC 59.325 55.000 9.46 0.00 0.00 2.59
702 2181 0.673985 CATCGCACCGGATCCTTAGA 59.326 55.000 9.46 2.60 0.00 2.10
703 2182 0.673985 TCATCGCACCGGATCCTTAG 59.326 55.000 9.46 0.68 0.00 2.18
704 2183 0.673985 CTCATCGCACCGGATCCTTA 59.326 55.000 9.46 0.00 0.00 2.69
705 2184 1.330655 ACTCATCGCACCGGATCCTT 61.331 55.000 9.46 0.00 0.00 3.36
706 2185 1.739338 GACTCATCGCACCGGATCCT 61.739 60.000 9.46 0.00 0.00 3.24
707 2186 1.300233 GACTCATCGCACCGGATCC 60.300 63.158 9.46 0.00 0.00 3.36
708 2187 0.318275 GAGACTCATCGCACCGGATC 60.318 60.000 9.46 0.00 0.00 3.36
709 2188 1.037579 TGAGACTCATCGCACCGGAT 61.038 55.000 9.46 0.00 28.54 4.18
710 2189 1.037579 ATGAGACTCATCGCACCGGA 61.038 55.000 9.46 0.00 37.48 5.14
711 2190 0.596083 GATGAGACTCATCGCACCGG 60.596 60.000 25.68 0.00 43.11 5.28
712 2191 2.878743 GATGAGACTCATCGCACCG 58.121 57.895 25.68 0.00 43.11 4.94
719 2198 7.442364 CCAAAATATTACACGGATGAGACTCAT 59.558 37.037 17.98 17.98 40.34 2.90
720 2199 6.761242 CCAAAATATTACACGGATGAGACTCA 59.239 38.462 7.80 7.80 0.00 3.41
721 2200 6.984474 TCCAAAATATTACACGGATGAGACTC 59.016 38.462 0.00 0.00 0.00 3.36
722 2201 6.884832 TCCAAAATATTACACGGATGAGACT 58.115 36.000 0.00 0.00 0.00 3.24
723 2202 7.548196 TTCCAAAATATTACACGGATGAGAC 57.452 36.000 0.00 0.00 0.00 3.36
724 2203 8.746052 AATTCCAAAATATTACACGGATGAGA 57.254 30.769 0.00 0.00 0.00 3.27
725 2204 8.076178 GGAATTCCAAAATATTACACGGATGAG 58.924 37.037 20.04 0.00 35.64 2.90
726 2205 7.777910 AGGAATTCCAAAATATTACACGGATGA 59.222 33.333 26.22 0.00 38.89 2.92
727 2206 7.940850 AGGAATTCCAAAATATTACACGGATG 58.059 34.615 26.22 0.00 38.89 3.51
728 2207 7.998964 AGAGGAATTCCAAAATATTACACGGAT 59.001 33.333 26.22 0.00 38.89 4.18
729 2208 7.343357 AGAGGAATTCCAAAATATTACACGGA 58.657 34.615 26.22 0.00 38.89 4.69
730 2209 7.568199 AGAGGAATTCCAAAATATTACACGG 57.432 36.000 26.22 0.00 38.89 4.94
731 2210 8.129211 GGAAGAGGAATTCCAAAATATTACACG 58.871 37.037 26.22 0.00 46.77 4.49
745 2224 3.263261 GGACGAGTTGGAAGAGGAATTC 58.737 50.000 0.00 0.00 0.00 2.17
746 2225 2.027100 GGGACGAGTTGGAAGAGGAATT 60.027 50.000 0.00 0.00 0.00 2.17
747 2226 1.555533 GGGACGAGTTGGAAGAGGAAT 59.444 52.381 0.00 0.00 0.00 3.01
748 2227 0.974383 GGGACGAGTTGGAAGAGGAA 59.026 55.000 0.00 0.00 0.00 3.36
749 2228 2.667348 GGGACGAGTTGGAAGAGGA 58.333 57.895 0.00 0.00 0.00 3.71
766 2245 2.591715 GTCATCCGCCCATTCCGG 60.592 66.667 0.00 0.00 46.88 5.14
767 2246 2.715532 ATCGTCATCCGCCCATTCCG 62.716 60.000 0.00 0.00 36.19 4.30
768 2247 0.320374 TATCGTCATCCGCCCATTCC 59.680 55.000 0.00 0.00 36.19 3.01
769 2248 2.386661 ATATCGTCATCCGCCCATTC 57.613 50.000 0.00 0.00 36.19 2.67
770 2249 4.191544 CAATATATCGTCATCCGCCCATT 58.808 43.478 0.00 0.00 36.19 3.16
771 2250 3.197766 ACAATATATCGTCATCCGCCCAT 59.802 43.478 0.00 0.00 36.19 4.00
772 2251 2.565391 ACAATATATCGTCATCCGCCCA 59.435 45.455 0.00 0.00 36.19 5.36
773 2252 2.930040 CACAATATATCGTCATCCGCCC 59.070 50.000 0.00 0.00 36.19 6.13
774 2253 3.585862 ACACAATATATCGTCATCCGCC 58.414 45.455 0.00 0.00 36.19 6.13
775 2254 6.887376 AATACACAATATATCGTCATCCGC 57.113 37.500 0.00 0.00 36.19 5.54
776 2255 8.892905 CGATAATACACAATATATCGTCATCCG 58.107 37.037 6.01 0.00 34.10 4.18
875 2354 0.823769 ATAGCTGATCGACCGAGCCA 60.824 55.000 5.20 1.84 32.86 4.75
993 2472 3.399181 GTCCCTGCCATGTCCGGA 61.399 66.667 0.00 0.00 0.00 5.14
1120 2603 4.287067 GGCAAGTAATATGGATCAGAGGGA 59.713 45.833 0.00 0.00 0.00 4.20
1122 2605 4.248859 CGGCAAGTAATATGGATCAGAGG 58.751 47.826 0.00 0.00 0.00 3.69
1126 2609 2.412870 CGCGGCAAGTAATATGGATCA 58.587 47.619 0.00 0.00 0.00 2.92
1142 2625 1.435577 AAGTTGTACTAAAGCCGCGG 58.564 50.000 24.05 24.05 0.00 6.46
1228 2711 3.767673 AGTGAATAGACTTTAGACCCGCA 59.232 43.478 0.00 0.00 0.00 5.69
1229 2712 4.113354 CAGTGAATAGACTTTAGACCCGC 58.887 47.826 0.00 0.00 0.00 6.13
1277 2760 1.594518 GCCGTATTATGCAGCAACGTG 60.595 52.381 14.59 8.41 31.87 4.49
1284 2767 3.670895 CGTCCTAGAGCCGTATTATGCAG 60.671 52.174 0.00 0.00 0.00 4.41
1296 2779 1.332375 CAGCTAGTGTCGTCCTAGAGC 59.668 57.143 9.06 0.00 35.01 4.09
1297 2780 2.634600 ACAGCTAGTGTCGTCCTAGAG 58.365 52.381 9.06 4.57 31.90 2.43
1311 2795 6.538742 GCATAAGAAATGTAGGACAACAGCTA 59.461 38.462 0.00 0.00 31.70 3.32
1313 2797 5.123820 TGCATAAGAAATGTAGGACAACAGC 59.876 40.000 0.00 0.00 31.70 4.40
1339 2823 6.045955 TCTTTAATGAACCTGCCAAACAAAC 58.954 36.000 0.00 0.00 0.00 2.93
1400 2884 5.702622 TGTCTTTCATCTTAATCGCTTCG 57.297 39.130 0.00 0.00 0.00 3.79
1886 3373 2.880268 TGTGATCCAAGCAACACAAGAG 59.120 45.455 0.00 0.00 39.70 2.85
2158 3645 8.350722 CCATATCTCGTGTTGTTACTACTATGT 58.649 37.037 0.00 0.00 0.00 2.29
2402 3907 8.632906 GGAGATGATCATAAAATTGTCTCCAT 57.367 34.615 23.67 0.00 46.11 3.41
2450 3955 1.743958 CTCCTCATTGCTTCAAGGCTG 59.256 52.381 0.00 0.00 0.00 4.85
2669 4178 7.157347 TCACTCTTGATGGTATAATCATGCTC 58.843 38.462 0.00 0.00 36.48 4.26
2802 4311 7.540474 AATTCTCCTCTGTCACACTAGTTAA 57.460 36.000 0.00 0.00 0.00 2.01
2938 4448 2.178912 TCCCGTGCTAGGTGAAAAAG 57.821 50.000 0.00 0.00 0.00 2.27
2955 4465 3.645687 AGATCCAGGACTCTAAGCATTCC 59.354 47.826 0.00 0.00 0.00 3.01
3223 4733 2.158885 GGCTGAAGACCAAGATAGGACC 60.159 54.545 0.00 0.00 0.00 4.46
3524 5043 1.645034 TCTCGATAGCTGCACAAAGC 58.355 50.000 1.02 0.00 43.88 3.51
3623 5142 1.124477 GCTCCTCTCATGGGTAGGGG 61.124 65.000 10.17 8.44 35.76 4.79
3627 5146 0.636647 TGAGGCTCCTCTCATGGGTA 59.363 55.000 12.86 0.00 43.12 3.69
3628 5147 0.252881 TTGAGGCTCCTCTCATGGGT 60.253 55.000 12.86 0.00 42.57 4.51
3694 5213 8.778358 CCCTAGATAAATCTTCACTAAATGTGC 58.222 37.037 0.00 0.00 40.95 4.57
3728 5247 4.640647 CCATGGTTTTACTTCCTTCTAGCC 59.359 45.833 2.57 0.00 0.00 3.93
3739 5261 6.602009 GCACCTAATAGTTCCATGGTTTTACT 59.398 38.462 12.58 13.05 0.00 2.24
3946 5469 3.440173 CCAATAAATTCCACACAGCGTCT 59.560 43.478 0.00 0.00 0.00 4.18
3948 5471 2.094752 GCCAATAAATTCCACACAGCGT 60.095 45.455 0.00 0.00 0.00 5.07
4091 5617 1.312815 GTTATGCATGCTCCAGTCCC 58.687 55.000 20.33 0.00 0.00 4.46
4149 5675 2.528564 TGCTGCCTCCAAAAATTAGCT 58.471 42.857 0.00 0.00 0.00 3.32
4159 5685 2.271173 CTGCTGATGCTGCCTCCA 59.729 61.111 0.00 0.00 40.48 3.86
4229 5755 6.542370 GGAATGCAAGTTAATTAGCTGACCTA 59.458 38.462 2.26 0.00 0.00 3.08
4280 5806 2.812591 TCTCGGTCGGTTGATAGCTATC 59.187 50.000 24.27 24.27 0.00 2.08
4364 5890 0.754957 CCTTGGCTGTTGTGGACCAA 60.755 55.000 0.00 0.00 39.81 3.67
4366 5892 2.564721 GCCTTGGCTGTTGTGGACC 61.565 63.158 4.11 0.00 0.00 4.46
4367 5893 1.518903 GAGCCTTGGCTGTTGTGGAC 61.519 60.000 19.84 0.00 0.00 4.02
4373 5899 0.178953 ACATTGGAGCCTTGGCTGTT 60.179 50.000 19.84 0.00 0.00 3.16
4377 5903 2.019984 CTTCTACATTGGAGCCTTGGC 58.980 52.381 2.97 2.97 0.00 4.52
4466 5992 6.149308 TCTGAACCAATATATAAGGCAATGCG 59.851 38.462 0.00 0.00 0.00 4.73
4571 6108 7.554118 CCAGTATTCAGTCCACACTAATTTCAT 59.446 37.037 0.00 0.00 0.00 2.57
4572 6109 6.878923 CCAGTATTCAGTCCACACTAATTTCA 59.121 38.462 0.00 0.00 0.00 2.69
4577 6123 4.422057 TCCCAGTATTCAGTCCACACTAA 58.578 43.478 0.00 0.00 0.00 2.24
4579 6125 2.834549 CTCCCAGTATTCAGTCCACACT 59.165 50.000 0.00 0.00 0.00 3.55
4590 6136 0.740737 GCAAATGCGCTCCCAGTATT 59.259 50.000 9.73 0.00 0.00 1.89


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

AutoCloner maintained by Alex Coulton.