Multiple sequence alignment - TraesCS2A01G472000

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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 TraesCS2A01G472000 chr2A 100.000 4087 0 0 1 4087 713915289 713919375 0.000000e+00 7548.0
1 TraesCS2A01G472000 chr2A 88.636 264 21 3 3183 3446 713930577 713930323 3.070000e-81 313.0
2 TraesCS2A01G472000 chr2B 97.639 1059 19 5 2125 3182 691778292 691779345 0.000000e+00 1812.0
3 TraesCS2A01G472000 chr2B 89.510 1306 79 24 835 2126 691776907 691778168 0.000000e+00 1600.0
4 TraesCS2A01G472000 chr2D 87.460 1244 90 24 833 2058 575760155 575761350 0.000000e+00 1373.0
5 TraesCS2A01G472000 chr2D 89.331 1106 84 14 2091 3182 575761347 575762432 0.000000e+00 1358.0
6 TraesCS2A01G472000 chr2D 89.776 401 37 4 833 1231 575690327 575690725 1.010000e-140 510.0
7 TraesCS2A01G472000 chr2D 90.705 312 28 1 102 413 575759485 575759795 8.170000e-112 414.0
8 TraesCS2A01G472000 chr2D 89.394 198 17 3 3665 3858 640721238 640721041 3.160000e-61 246.0
9 TraesCS2A01G472000 chr2D 89.404 151 13 2 3897 4045 640720971 640720822 1.940000e-43 187.0
10 TraesCS2A01G472000 chr2D 96.000 100 4 0 1 100 273019175 273019274 3.270000e-36 163.0
11 TraesCS2A01G472000 chr6A 96.635 624 9 2 3465 4087 608706331 608706943 0.000000e+00 1026.0
12 TraesCS2A01G472000 chr6A 88.258 264 22 3 3183 3446 608709212 608708958 1.430000e-79 307.0
13 TraesCS2A01G472000 chr6A 98.058 103 2 0 3269 3371 608706231 608706333 3.250000e-41 180.0
14 TraesCS2A01G472000 chr1B 86.471 680 55 12 3183 3858 395239146 395239792 0.000000e+00 712.0
15 TraesCS2A01G472000 chr1B 83.398 259 26 9 3178 3436 395242957 395242716 1.480000e-54 224.0
16 TraesCS2A01G472000 chr1B 89.610 154 12 3 3894 4045 395239912 395240063 4.170000e-45 193.0
17 TraesCS2A01G472000 chr1B 97.436 39 1 0 4049 4087 395240082 395240120 2.640000e-07 67.6
18 TraesCS2A01G472000 chr7B 86.303 679 58 9 3183 3858 501593223 501593869 0.000000e+00 706.0
19 TraesCS2A01G472000 chr7B 86.090 266 25 6 3183 3446 501597041 501596786 4.020000e-70 276.0
20 TraesCS2A01G472000 chr7B 88.961 154 13 3 3894 4045 501593989 501594140 1.940000e-43 187.0
21 TraesCS2A01G472000 chr4B 86.435 317 27 12 3257 3570 168712013 168712316 2.350000e-87 333.0
22 TraesCS2A01G472000 chr4B 88.298 282 23 4 3580 3858 168715130 168715404 3.050000e-86 329.0
23 TraesCS2A01G472000 chr4B 85.348 273 25 12 3178 3446 168718561 168718300 6.730000e-68 268.0
24 TraesCS2A01G472000 chr4B 89.610 154 12 3 3894 4045 168715524 168715675 4.170000e-45 193.0
25 TraesCS2A01G472000 chr4B 97.436 39 1 0 4049 4087 168715694 168715732 2.640000e-07 67.6
26 TraesCS2A01G472000 chrUn 88.837 215 15 3 3220 3434 479848653 479848858 5.240000e-64 255.0
27 TraesCS2A01G472000 chr5B 86.286 175 24 0 3185 3359 65106314 65106488 1.500000e-44 191.0
28 TraesCS2A01G472000 chr7D 97.030 101 3 0 1 101 232926209 232926309 1.950000e-38 171.0
29 TraesCS2A01G472000 chr7D 96.000 100 3 1 1 100 60331395 60331297 1.180000e-35 161.0
30 TraesCS2A01G472000 chr7D 95.000 100 5 0 1 100 149105715 149105616 1.520000e-34 158.0
31 TraesCS2A01G472000 chr7D 95.000 100 5 0 1 100 497911220 497911121 1.520000e-34 158.0
32 TraesCS2A01G472000 chr3D 95.050 101 5 0 1 101 87391298 87391398 4.230000e-35 159.0
33 TraesCS2A01G472000 chr1D 95.050 101 5 0 1 101 407810353 407810453 4.230000e-35 159.0
34 TraesCS2A01G472000 chr3B 95.918 98 2 2 1 97 418734455 418734359 1.520000e-34 158.0
35 TraesCS2A01G472000 chr3A 93.396 106 5 2 1 105 545291033 545290929 5.470000e-34 156.0
36 TraesCS2A01G472000 chr7A 97.059 34 1 0 268 301 127083459 127083492 1.590000e-04 58.4


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 TraesCS2A01G472000 chr2A 713915289 713919375 4086 False 7548.000000 7548 100.000000 1 4087 1 chr2A.!!$F1 4086
1 TraesCS2A01G472000 chr2B 691776907 691779345 2438 False 1706.000000 1812 93.574500 835 3182 2 chr2B.!!$F1 2347
2 TraesCS2A01G472000 chr2D 575759485 575762432 2947 False 1048.333333 1373 89.165333 102 3182 3 chr2D.!!$F3 3080
3 TraesCS2A01G472000 chr6A 608706231 608706943 712 False 603.000000 1026 97.346500 3269 4087 2 chr6A.!!$F1 818
4 TraesCS2A01G472000 chr1B 395239146 395240120 974 False 324.200000 712 91.172333 3183 4087 3 chr1B.!!$F1 904
5 TraesCS2A01G472000 chr7B 501593223 501594140 917 False 446.500000 706 87.632000 3183 4045 2 chr7B.!!$F1 862
6 TraesCS2A01G472000 chr4B 168712013 168715732 3719 False 230.650000 333 90.444750 3257 4087 4 chr4B.!!$F1 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
19 20 0.035056 CGGATTGGTTTGAGGAGCCT 60.035 55.0 0.0 0.0 0.00 4.58 F
506 507 0.037790 GTCTGAGTGCTTCTTCGGCT 60.038 55.0 0.0 0.0 0.00 5.52 F
512 513 0.110010 GTGCTTCTTCGGCTTTGAGC 60.110 55.0 0.0 0.0 41.46 4.26 F
513 514 0.250467 TGCTTCTTCGGCTTTGAGCT 60.250 50.0 0.0 0.0 41.99 4.09 F
966 1095 0.462375 CGACGATTCCATACCCACCA 59.538 55.0 0.0 0.0 0.00 4.17 F
1907 2056 0.593128 ATGGCGAGTTGTCTTTGCAC 59.407 50.0 0.0 0.0 0.00 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1293 1428 0.322187 AAAGGAATCGGGTGGGAACG 60.322 55.000 0.00 0.00 0.00 3.95 R
1736 1884 1.578583 ACACGGAAGTTCTGGTTTCG 58.421 50.000 16.08 6.08 46.40 3.46 R
1892 2040 2.609459 ACAAGAGTGCAAAGACAACTCG 59.391 45.455 0.00 0.00 33.12 4.18 R
1917 2066 3.073356 ACGGAATTGTTCTCCCACCTAAA 59.927 43.478 0.00 0.00 0.00 1.85 R
2400 2713 3.129813 TCACATTCTTGCATGAATCAGGC 59.870 43.478 21.43 13.41 41.79 4.85 R
3218 3546 0.038892 CAGGCACCAAACTGCACATC 60.039 55.000 0.00 0.00 39.08 3.06 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 2.482326 CGGATTGGTTTGAGGAGCC 58.518 57.895 0.00 0.00 0.00 4.70
19 20 0.035056 CGGATTGGTTTGAGGAGCCT 60.035 55.000 0.00 0.00 0.00 4.58
20 21 1.209504 CGGATTGGTTTGAGGAGCCTA 59.790 52.381 0.00 0.00 0.00 3.93
21 22 2.644676 GGATTGGTTTGAGGAGCCTAC 58.355 52.381 0.00 0.00 0.00 3.18
22 23 2.239907 GGATTGGTTTGAGGAGCCTACT 59.760 50.000 0.00 0.00 0.00 2.57
23 24 3.454812 GGATTGGTTTGAGGAGCCTACTA 59.545 47.826 0.00 0.00 0.00 1.82
24 25 4.443598 GGATTGGTTTGAGGAGCCTACTAG 60.444 50.000 0.00 0.00 0.00 2.57
25 26 3.185880 TGGTTTGAGGAGCCTACTAGT 57.814 47.619 0.00 0.00 0.00 2.57
26 27 2.832129 TGGTTTGAGGAGCCTACTAGTG 59.168 50.000 5.39 0.00 0.00 2.74
27 28 3.097614 GGTTTGAGGAGCCTACTAGTGA 58.902 50.000 5.39 0.00 0.00 3.41
28 29 3.514309 GGTTTGAGGAGCCTACTAGTGAA 59.486 47.826 5.39 0.00 0.00 3.18
29 30 4.020485 GGTTTGAGGAGCCTACTAGTGAAA 60.020 45.833 5.39 0.00 0.00 2.69
30 31 5.338463 GGTTTGAGGAGCCTACTAGTGAAAT 60.338 44.000 5.39 0.00 0.00 2.17
31 32 6.174049 GTTTGAGGAGCCTACTAGTGAAATT 58.826 40.000 5.39 0.00 0.00 1.82
32 33 5.344743 TGAGGAGCCTACTAGTGAAATTG 57.655 43.478 5.39 0.00 0.00 2.32
33 34 4.777896 TGAGGAGCCTACTAGTGAAATTGT 59.222 41.667 5.39 0.00 0.00 2.71
34 35 5.955959 TGAGGAGCCTACTAGTGAAATTGTA 59.044 40.000 5.39 0.00 0.00 2.41
35 36 6.439375 TGAGGAGCCTACTAGTGAAATTGTAA 59.561 38.462 5.39 0.00 0.00 2.41
36 37 6.641474 AGGAGCCTACTAGTGAAATTGTAAC 58.359 40.000 5.39 0.00 0.00 2.50
37 38 6.212791 AGGAGCCTACTAGTGAAATTGTAACA 59.787 38.462 5.39 0.00 0.00 2.41
38 39 7.048512 GGAGCCTACTAGTGAAATTGTAACAT 58.951 38.462 5.39 0.00 0.00 2.71
39 40 7.553044 GGAGCCTACTAGTGAAATTGTAACATT 59.447 37.037 5.39 0.00 0.00 2.71
40 41 8.863872 AGCCTACTAGTGAAATTGTAACATTT 57.136 30.769 5.39 0.00 0.00 2.32
41 42 8.947115 AGCCTACTAGTGAAATTGTAACATTTC 58.053 33.333 5.39 0.11 37.31 2.17
42 43 8.947115 GCCTACTAGTGAAATTGTAACATTTCT 58.053 33.333 5.39 0.00 37.59 2.52
46 47 9.337396 ACTAGTGAAATTGTAACATTTCTCACA 57.663 29.630 0.00 0.00 37.59 3.58
49 50 9.301153 AGTGAAATTGTAACATTTCTCACAAAC 57.699 29.630 14.28 7.38 37.59 2.93
50 51 8.259194 GTGAAATTGTAACATTTCTCACAAACG 58.741 33.333 7.48 0.00 37.59 3.60
51 52 8.184848 TGAAATTGTAACATTTCTCACAAACGA 58.815 29.630 7.48 0.00 37.59 3.85
52 53 9.180678 GAAATTGTAACATTTCTCACAAACGAT 57.819 29.630 0.00 0.00 34.79 3.73
53 54 8.506140 AATTGTAACATTTCTCACAAACGATG 57.494 30.769 0.00 0.00 34.79 3.84
54 55 6.612247 TGTAACATTTCTCACAAACGATGT 57.388 33.333 0.00 0.00 45.34 3.06
55 56 7.716768 TGTAACATTTCTCACAAACGATGTA 57.283 32.000 0.00 0.00 41.46 2.29
56 57 8.317891 TGTAACATTTCTCACAAACGATGTAT 57.682 30.769 0.00 0.00 41.46 2.29
57 58 8.779303 TGTAACATTTCTCACAAACGATGTATT 58.221 29.630 0.00 0.00 41.46 1.89
58 59 9.051027 GTAACATTTCTCACAAACGATGTATTG 57.949 33.333 0.00 0.00 41.46 1.90
59 60 6.611381 ACATTTCTCACAAACGATGTATTGG 58.389 36.000 0.00 0.00 41.46 3.16
60 61 6.206634 ACATTTCTCACAAACGATGTATTGGT 59.793 34.615 0.00 0.00 41.46 3.67
61 62 6.627395 TTTCTCACAAACGATGTATTGGTT 57.373 33.333 0.00 0.00 41.46 3.67
62 63 7.731882 TTTCTCACAAACGATGTATTGGTTA 57.268 32.000 0.00 0.00 41.46 2.85
63 64 7.915293 TTCTCACAAACGATGTATTGGTTAT 57.085 32.000 0.00 0.00 41.46 1.89
64 65 7.915293 TCTCACAAACGATGTATTGGTTATT 57.085 32.000 0.00 0.00 41.46 1.40
65 66 7.747888 TCTCACAAACGATGTATTGGTTATTG 58.252 34.615 0.00 0.00 41.46 1.90
66 67 6.318628 TCACAAACGATGTATTGGTTATTGC 58.681 36.000 0.00 0.00 41.46 3.56
67 68 6.150307 TCACAAACGATGTATTGGTTATTGCT 59.850 34.615 0.00 0.00 41.46 3.91
68 69 7.334671 TCACAAACGATGTATTGGTTATTGCTA 59.665 33.333 0.00 0.00 41.46 3.49
69 70 7.965655 CACAAACGATGTATTGGTTATTGCTAA 59.034 33.333 0.00 0.00 41.46 3.09
70 71 8.682710 ACAAACGATGTATTGGTTATTGCTAAT 58.317 29.630 0.00 0.00 41.63 1.73
71 72 8.957028 CAAACGATGTATTGGTTATTGCTAATG 58.043 33.333 0.00 0.00 0.00 1.90
72 73 8.445275 AACGATGTATTGGTTATTGCTAATGA 57.555 30.769 0.00 0.00 0.00 2.57
73 74 8.445275 ACGATGTATTGGTTATTGCTAATGAA 57.555 30.769 0.00 0.00 0.00 2.57
74 75 9.066892 ACGATGTATTGGTTATTGCTAATGAAT 57.933 29.630 0.00 0.00 0.00 2.57
131 132 9.343539 CTCCTTATAAAGTTCTTTATGGAAGGG 57.656 37.037 26.31 19.65 35.41 3.95
156 157 4.520492 TCCTCTGCAATTCTTTGAACTTCC 59.480 41.667 0.00 0.00 34.60 3.46
162 163 4.676924 GCAATTCTTTGAACTTCCACTTCG 59.323 41.667 0.00 0.00 34.60 3.79
169 170 4.139420 CTTCCACTTCGCGCGCTG 62.139 66.667 30.48 22.06 0.00 5.18
239 240 5.481105 TGCTAGGCAAATCAAGGAAATTTG 58.519 37.500 0.00 4.61 43.69 2.32
240 241 5.011943 TGCTAGGCAAATCAAGGAAATTTGT 59.988 36.000 0.00 0.00 43.09 2.83
254 255 4.039124 GGAAATTTGTCTTCAAGCCCAAGA 59.961 41.667 0.00 0.00 34.88 3.02
260 261 3.632145 TGTCTTCAAGCCCAAGAAAGAAC 59.368 43.478 0.00 0.00 31.60 3.01
262 263 1.604604 TCAAGCCCAAGAAAGAACGG 58.395 50.000 0.00 0.00 0.00 4.44
263 264 0.598065 CAAGCCCAAGAAAGAACGGG 59.402 55.000 0.00 0.00 42.03 5.28
303 304 7.946207 AGAAAAGGAAGGAAAGAGAATTTCAC 58.054 34.615 0.00 0.00 0.00 3.18
326 327 3.875727 CCAGAAGACATGCTTACATCAGG 59.124 47.826 0.00 0.00 36.83 3.86
351 352 4.201812 CGCAACCCTACAAACATGAGTATG 60.202 45.833 0.00 0.00 40.24 2.39
361 362 1.340017 ACATGAGTATGCACCACCACC 60.340 52.381 0.00 0.00 37.85 4.61
364 365 0.324943 GAGTATGCACCACCACCTGT 59.675 55.000 0.00 0.00 0.00 4.00
367 368 2.081462 GTATGCACCACCACCTGTAAC 58.919 52.381 0.00 0.00 0.00 2.50
381 382 6.102663 CCACCTGTAACTTCACTCTAGATTG 58.897 44.000 3.74 3.74 0.00 2.67
388 389 8.570488 TGTAACTTCACTCTAGATTGTACGAAA 58.430 33.333 9.66 0.00 0.00 3.46
390 391 7.216973 ACTTCACTCTAGATTGTACGAAACT 57.783 36.000 9.66 0.00 0.00 2.66
391 392 7.085116 ACTTCACTCTAGATTGTACGAAACTG 58.915 38.462 9.66 0.00 0.00 3.16
413 414 2.280524 TGTCCTTGAACGCGTGGG 60.281 61.111 14.98 13.38 0.00 4.61
416 417 3.283684 CCTTGAACGCGTGGGCAA 61.284 61.111 14.98 16.75 39.92 4.52
418 419 2.824489 TTGAACGCGTGGGCAACA 60.824 55.556 14.98 3.93 39.92 3.33
419 420 2.128853 CTTGAACGCGTGGGCAACAT 62.129 55.000 14.98 0.00 39.92 2.71
420 421 2.126888 GAACGCGTGGGCAACATG 60.127 61.111 14.98 0.00 39.92 3.21
421 422 3.609214 GAACGCGTGGGCAACATGG 62.609 63.158 14.98 0.00 39.92 3.66
424 425 3.762247 GCGTGGGCAACATGGCAT 61.762 61.111 6.25 0.00 45.76 4.40
425 426 2.972267 CGTGGGCAACATGGCATT 59.028 55.556 0.00 0.00 45.76 3.56
428 429 0.391528 GTGGGCAACATGGCATTTCC 60.392 55.000 0.00 0.00 45.76 3.13
431 432 2.041701 GGGCAACATGGCATTTCCTAT 58.958 47.619 0.00 0.00 45.76 2.57
432 433 2.036346 GGGCAACATGGCATTTCCTATC 59.964 50.000 0.00 0.00 45.76 2.08
434 435 4.144297 GGCAACATGGCATTTCCTATCTA 58.856 43.478 0.00 0.00 43.14 1.98
435 436 4.217118 GGCAACATGGCATTTCCTATCTAG 59.783 45.833 0.00 0.00 43.14 2.43
436 437 4.823989 GCAACATGGCATTTCCTATCTAGT 59.176 41.667 0.00 0.00 35.26 2.57
438 439 6.486657 GCAACATGGCATTTCCTATCTAGTAA 59.513 38.462 0.00 0.00 35.26 2.24
440 441 6.223852 ACATGGCATTTCCTATCTAGTAACG 58.776 40.000 0.00 0.00 35.26 3.18
441 442 4.628074 TGGCATTTCCTATCTAGTAACGC 58.372 43.478 0.00 0.00 35.26 4.84
443 444 4.448060 GGCATTTCCTATCTAGTAACGCAC 59.552 45.833 0.00 0.00 0.00 5.34
444 445 5.047847 GCATTTCCTATCTAGTAACGCACA 58.952 41.667 0.00 0.00 0.00 4.57
446 447 6.346919 GCATTTCCTATCTAGTAACGCACATG 60.347 42.308 0.00 0.00 0.00 3.21
448 449 5.690997 TCCTATCTAGTAACGCACATGAG 57.309 43.478 0.00 0.00 0.00 2.90
461 462 3.818961 CACATGAGTGCTAACTGTTGG 57.181 47.619 0.00 0.69 39.21 3.77
464 465 0.472044 TGAGTGCTAACTGTTGGGCA 59.528 50.000 15.38 15.38 36.52 5.36
480 481 1.228657 GGCAGTCCCAGTTCGACAAC 61.229 60.000 0.00 0.00 32.41 3.32
481 482 0.249911 GCAGTCCCAGTTCGACAACT 60.250 55.000 0.00 0.00 44.26 3.16
483 484 1.341531 CAGTCCCAGTTCGACAACTCT 59.658 52.381 0.00 0.00 41.24 3.24
484 485 1.341531 AGTCCCAGTTCGACAACTCTG 59.658 52.381 0.00 0.00 41.24 3.35
485 486 1.068741 GTCCCAGTTCGACAACTCTGT 59.931 52.381 0.00 0.00 41.24 3.41
487 488 1.867233 CCCAGTTCGACAACTCTGTTG 59.133 52.381 8.66 8.66 41.24 3.33
488 489 2.550978 CCAGTTCGACAACTCTGTTGT 58.449 47.619 14.80 14.80 41.24 3.32
489 490 2.540101 CCAGTTCGACAACTCTGTTGTC 59.460 50.000 25.02 25.02 41.24 3.18
490 491 3.448686 CAGTTCGACAACTCTGTTGTCT 58.551 45.455 28.91 15.51 44.79 3.41
491 492 3.243877 CAGTTCGACAACTCTGTTGTCTG 59.756 47.826 28.91 23.71 44.79 3.51
495 496 2.791560 CGACAACTCTGTTGTCTGAGTG 59.208 50.000 28.91 16.41 46.80 3.51
496 497 2.541762 GACAACTCTGTTGTCTGAGTGC 59.458 50.000 26.60 7.92 46.80 4.40
498 499 3.201290 CAACTCTGTTGTCTGAGTGCTT 58.799 45.455 8.13 0.00 46.80 3.91
499 500 3.104843 ACTCTGTTGTCTGAGTGCTTC 57.895 47.619 6.90 0.00 46.12 3.86
500 501 2.697751 ACTCTGTTGTCTGAGTGCTTCT 59.302 45.455 6.90 0.00 46.12 2.85
501 502 3.133721 ACTCTGTTGTCTGAGTGCTTCTT 59.866 43.478 6.90 0.00 46.12 2.52
502 503 3.722147 TCTGTTGTCTGAGTGCTTCTTC 58.278 45.455 0.00 0.00 0.00 2.87
503 504 2.473816 TGTTGTCTGAGTGCTTCTTCG 58.526 47.619 0.00 0.00 0.00 3.79
504 505 1.795286 GTTGTCTGAGTGCTTCTTCGG 59.205 52.381 0.00 0.00 0.00 4.30
506 507 0.037790 GTCTGAGTGCTTCTTCGGCT 60.038 55.000 0.00 0.00 0.00 5.52
507 508 0.681733 TCTGAGTGCTTCTTCGGCTT 59.318 50.000 0.00 0.00 0.00 4.35
508 509 1.070758 TCTGAGTGCTTCTTCGGCTTT 59.929 47.619 0.00 0.00 0.00 3.51
509 510 1.196354 CTGAGTGCTTCTTCGGCTTTG 59.804 52.381 0.00 0.00 0.00 2.77
511 512 1.462670 GAGTGCTTCTTCGGCTTTGAG 59.537 52.381 0.00 0.00 0.00 3.02
512 513 0.110010 GTGCTTCTTCGGCTTTGAGC 60.110 55.000 0.00 0.00 41.46 4.26
513 514 0.250467 TGCTTCTTCGGCTTTGAGCT 60.250 50.000 0.00 0.00 41.99 4.09
514 515 1.001974 TGCTTCTTCGGCTTTGAGCTA 59.998 47.619 0.00 0.00 41.99 3.32
515 516 2.284190 GCTTCTTCGGCTTTGAGCTAT 58.716 47.619 0.00 0.00 41.99 2.97
516 517 2.680339 GCTTCTTCGGCTTTGAGCTATT 59.320 45.455 0.00 0.00 41.99 1.73
517 518 3.127721 GCTTCTTCGGCTTTGAGCTATTT 59.872 43.478 0.00 0.00 41.99 1.40
518 519 4.379918 GCTTCTTCGGCTTTGAGCTATTTT 60.380 41.667 0.00 0.00 41.99 1.82
519 520 5.703876 CTTCTTCGGCTTTGAGCTATTTTT 58.296 37.500 0.00 0.00 41.99 1.94
520 521 6.622896 GCTTCTTCGGCTTTGAGCTATTTTTA 60.623 38.462 0.00 0.00 41.99 1.52
523 524 7.826690 TCTTCGGCTTTGAGCTATTTTTATTT 58.173 30.769 0.00 0.00 41.99 1.40
524 525 7.968405 TCTTCGGCTTTGAGCTATTTTTATTTC 59.032 33.333 0.00 0.00 41.99 2.17
525 526 7.391148 TCGGCTTTGAGCTATTTTTATTTCT 57.609 32.000 0.00 0.00 41.99 2.52
528 637 8.925700 CGGCTTTGAGCTATTTTTATTTCTTTT 58.074 29.630 0.00 0.00 41.99 2.27
669 798 9.567776 TGACAAACATTTTTAGATACCTTCTGA 57.432 29.630 0.00 0.00 35.79 3.27
767 896 8.568732 AAATACATGTTTTCGTGAAAATTCGT 57.431 26.923 2.30 9.99 41.64 3.85
768 897 9.666626 AAATACATGTTTTCGTGAAAATTCGTA 57.333 25.926 2.30 11.47 41.64 3.43
769 898 9.666626 AATACATGTTTTCGTGAAAATTCGTAA 57.333 25.926 2.30 0.00 41.64 3.18
770 899 9.834628 ATACATGTTTTCGTGAAAATTCGTAAT 57.165 25.926 2.30 0.34 41.64 1.89
771 900 8.568732 ACATGTTTTCGTGAAAATTCGTAATT 57.431 26.923 10.64 0.00 41.64 1.40
772 901 9.026074 ACATGTTTTCGTGAAAATTCGTAATTT 57.974 25.926 10.64 0.00 41.64 1.82
887 1016 2.436115 GTGACCGGCCCAGTTAGC 60.436 66.667 0.00 0.00 0.00 3.09
914 1043 4.643387 GCTCCCAGGCCACACGTT 62.643 66.667 5.01 0.00 0.00 3.99
960 1089 2.601562 GTGGGCGACGATTCCATAC 58.398 57.895 0.00 0.00 32.71 2.39
966 1095 0.462375 CGACGATTCCATACCCACCA 59.538 55.000 0.00 0.00 0.00 4.17
981 1110 1.384525 CACCAACGGTTTTCCACTCA 58.615 50.000 0.00 0.00 40.70 3.41
1239 1374 4.733371 TTCATCGCAGTCGCCGCA 62.733 61.111 0.00 0.00 35.26 5.69
1302 1437 4.452733 CGCCTCCTCGTTCCCACC 62.453 72.222 0.00 0.00 0.00 4.61
1373 1517 3.431346 GCTCATGTAGTCCTGATTGCAGA 60.431 47.826 0.00 0.00 45.17 4.26
1398 1542 6.560253 TGGAGCAATCTAGTTTGTTTTCTC 57.440 37.500 13.68 11.05 0.00 2.87
1409 1553 5.941788 AGTTTGTTTTCTCTACCTGGTCAT 58.058 37.500 0.63 0.00 0.00 3.06
1414 1558 5.306937 TGTTTTCTCTACCTGGTCATCAGAA 59.693 40.000 0.63 4.19 46.18 3.02
1415 1559 6.183361 TGTTTTCTCTACCTGGTCATCAGAAA 60.183 38.462 0.63 10.02 46.18 2.52
1417 1561 6.627087 TTCTCTACCTGGTCATCAGAAAAT 57.373 37.500 0.63 0.00 46.18 1.82
1500 1645 1.421268 TGTTCTGCTCACCTGAACCAT 59.579 47.619 9.53 0.00 46.11 3.55
1501 1646 1.808945 GTTCTGCTCACCTGAACCATG 59.191 52.381 0.00 0.00 42.96 3.66
1502 1647 1.059098 TCTGCTCACCTGAACCATGT 58.941 50.000 0.00 0.00 0.00 3.21
1594 1739 2.868583 CGATCTAGTGCTTCCAATGGTG 59.131 50.000 0.00 0.00 0.00 4.17
1597 1742 4.901197 TCTAGTGCTTCCAATGGTGTAA 57.099 40.909 0.00 0.00 0.00 2.41
1604 1750 5.757808 GTGCTTCCAATGGTGTAATTTTTGT 59.242 36.000 0.00 0.00 0.00 2.83
1608 1754 7.870445 GCTTCCAATGGTGTAATTTTTGTCTAA 59.130 33.333 0.00 0.00 0.00 2.10
1677 1823 2.024176 AGCCTTGCGGTTGTATACAG 57.976 50.000 5.56 0.00 0.00 2.74
1678 1824 1.278127 AGCCTTGCGGTTGTATACAGT 59.722 47.619 5.56 0.00 0.00 3.55
1679 1825 2.081462 GCCTTGCGGTTGTATACAGTT 58.919 47.619 5.56 0.00 0.00 3.16
1680 1826 3.055675 AGCCTTGCGGTTGTATACAGTTA 60.056 43.478 5.56 0.00 0.00 2.24
1681 1827 3.875134 GCCTTGCGGTTGTATACAGTTAT 59.125 43.478 5.56 0.00 0.00 1.89
1682 1828 5.051816 GCCTTGCGGTTGTATACAGTTATA 58.948 41.667 5.56 0.00 0.00 0.98
1683 1829 5.699458 GCCTTGCGGTTGTATACAGTTATAT 59.301 40.000 5.56 0.00 0.00 0.86
1684 1830 6.869913 GCCTTGCGGTTGTATACAGTTATATA 59.130 38.462 5.56 0.00 0.00 0.86
1708 1854 5.477984 ACATCAGTGTATTTGCATTTGGACT 59.522 36.000 0.00 0.00 36.63 3.85
1736 1884 2.029918 GCAAACTTGACTTGTCCATCCC 60.030 50.000 0.00 0.00 0.00 3.85
1751 1899 2.084546 CATCCCGAAACCAGAACTTCC 58.915 52.381 0.00 0.00 0.00 3.46
1777 1925 7.011576 CGTGTACTCTGTTGACTAGATCTACAT 59.988 40.741 0.00 0.00 41.38 2.29
1838 1986 1.544724 TTGCTGGGCATACAAGGTTC 58.455 50.000 0.00 0.00 38.76 3.62
1874 2022 2.297597 AGCCTTCTACTGATATGCCGTC 59.702 50.000 0.00 0.00 0.00 4.79
1892 2040 4.083802 GCCGTCTCTATGATTGTTAATGGC 60.084 45.833 0.00 0.00 0.00 4.40
1907 2056 0.593128 ATGGCGAGTTGTCTTTGCAC 59.407 50.000 0.00 0.00 0.00 4.57
1910 2059 1.221414 GCGAGTTGTCTTTGCACTCT 58.779 50.000 0.00 0.00 0.00 3.24
1916 2065 4.513442 AGTTGTCTTTGCACTCTTGTGTA 58.487 39.130 0.00 0.00 45.44 2.90
1917 2066 5.126067 AGTTGTCTTTGCACTCTTGTGTAT 58.874 37.500 0.00 0.00 45.44 2.29
1933 2082 5.570205 TGTGTATTTAGGTGGGAGAACAA 57.430 39.130 0.00 0.00 0.00 2.83
1978 2127 0.667993 CTTCAAGCACGGCTGGAAAA 59.332 50.000 14.23 0.00 46.32 2.29
1998 2147 6.016777 GGAAAACCAATATACTCTGCCATCAG 60.017 42.308 0.00 0.00 41.67 2.90
2005 2154 2.306341 ACTCTGCCATCAGTTCATCG 57.694 50.000 0.00 0.00 41.10 3.84
2026 2175 3.307691 CGGGCATAGATATGGTCATGGTT 60.308 47.826 2.22 0.00 34.32 3.67
2054 2203 7.172342 TGTAATAAGGTAGCCATTTGTCAAGT 58.828 34.615 0.00 0.00 0.00 3.16
2055 2204 8.322828 TGTAATAAGGTAGCCATTTGTCAAGTA 58.677 33.333 0.00 0.00 0.00 2.24
2056 2205 9.169592 GTAATAAGGTAGCCATTTGTCAAGTAA 57.830 33.333 0.00 0.00 0.00 2.24
2057 2206 8.823220 AATAAGGTAGCCATTTGTCAAGTAAT 57.177 30.769 0.00 0.00 0.00 1.89
2058 2207 6.515272 AAGGTAGCCATTTGTCAAGTAATG 57.485 37.500 0.00 0.00 0.00 1.90
2059 2208 4.399303 AGGTAGCCATTTGTCAAGTAATGC 59.601 41.667 0.00 0.00 31.85 3.56
2060 2209 3.874392 AGCCATTTGTCAAGTAATGCC 57.126 42.857 0.00 0.00 31.85 4.40
2061 2210 2.497273 AGCCATTTGTCAAGTAATGCCC 59.503 45.455 0.00 0.00 31.85 5.36
2062 2211 2.418609 GCCATTTGTCAAGTAATGCCCC 60.419 50.000 0.00 0.00 31.85 5.80
2063 2212 3.099141 CCATTTGTCAAGTAATGCCCCT 58.901 45.455 0.00 0.00 31.85 4.79
2064 2213 3.515104 CCATTTGTCAAGTAATGCCCCTT 59.485 43.478 0.00 0.00 31.85 3.95
2065 2214 4.381932 CCATTTGTCAAGTAATGCCCCTTC 60.382 45.833 0.00 0.00 31.85 3.46
2066 2215 3.517296 TTGTCAAGTAATGCCCCTTCA 57.483 42.857 0.00 0.00 0.00 3.02
2067 2216 3.737559 TGTCAAGTAATGCCCCTTCAT 57.262 42.857 0.00 0.00 0.00 2.57
2068 2217 4.046286 TGTCAAGTAATGCCCCTTCATT 57.954 40.909 0.00 0.00 39.70 2.57
2069 2218 4.415596 TGTCAAGTAATGCCCCTTCATTT 58.584 39.130 0.00 0.00 37.75 2.32
2070 2219 4.837860 TGTCAAGTAATGCCCCTTCATTTT 59.162 37.500 0.00 0.00 37.75 1.82
2071 2220 5.047377 TGTCAAGTAATGCCCCTTCATTTTC 60.047 40.000 0.00 0.00 37.75 2.29
2072 2221 5.047377 GTCAAGTAATGCCCCTTCATTTTCA 60.047 40.000 0.00 0.00 37.75 2.69
2073 2222 5.721000 TCAAGTAATGCCCCTTCATTTTCAT 59.279 36.000 0.00 0.00 37.75 2.57
2074 2223 5.603170 AGTAATGCCCCTTCATTTTCATG 57.397 39.130 0.00 0.00 37.75 3.07
2075 2224 5.271598 AGTAATGCCCCTTCATTTTCATGA 58.728 37.500 0.00 0.00 37.75 3.07
2076 2225 5.901276 AGTAATGCCCCTTCATTTTCATGAT 59.099 36.000 0.00 0.00 39.28 2.45
2077 2226 5.703730 AATGCCCCTTCATTTTCATGATT 57.296 34.783 0.00 0.00 39.28 2.57
2078 2227 5.703730 ATGCCCCTTCATTTTCATGATTT 57.296 34.783 0.00 0.00 39.28 2.17
2079 2228 5.502089 TGCCCCTTCATTTTCATGATTTT 57.498 34.783 0.00 0.00 39.28 1.82
2080 2229 5.878627 TGCCCCTTCATTTTCATGATTTTT 58.121 33.333 0.00 0.00 39.28 1.94
2400 2713 6.688637 TCAAATATGTTCCATCTGCTCTTG 57.311 37.500 0.00 0.00 0.00 3.02
2426 2743 4.461431 TGATTCATGCAAGAATGTGAAGCT 59.539 37.500 21.03 0.00 38.30 3.74
2428 2745 2.490509 TCATGCAAGAATGTGAAGCTGG 59.509 45.455 0.00 0.00 0.00 4.85
2641 2961 8.588290 AGTTGCTATTATAAACATTTGTGGGA 57.412 30.769 0.00 0.00 0.00 4.37
2785 3111 6.726258 TGTTCTGCTGTATGTTATGTTGAG 57.274 37.500 0.00 0.00 0.00 3.02
2851 3177 6.042781 ACTTGTGTGTCTTCTGGAGGTTATTA 59.957 38.462 0.00 0.00 0.00 0.98
3194 3522 6.604735 ACAATCTAATCGAGGTAAATGCAC 57.395 37.500 0.00 0.00 0.00 4.57
3218 3546 5.067273 TGGTGGTACATGAAGTTGTTTAGG 58.933 41.667 0.00 0.00 44.52 2.69
3235 3563 1.181098 AGGATGTGCAGTTTGGTGCC 61.181 55.000 0.00 0.00 43.28 5.01
3373 3701 3.382048 GGTACGAAGTGGAAGTGAAGT 57.618 47.619 0.00 0.00 45.73 3.01
3374 3702 3.057734 GGTACGAAGTGGAAGTGAAGTG 58.942 50.000 0.00 0.00 45.73 3.16
3379 3707 0.839946 AGTGGAAGTGAAGTGCTGGT 59.160 50.000 0.00 0.00 0.00 4.00
3381 3709 0.546122 TGGAAGTGAAGTGCTGGTGT 59.454 50.000 0.00 0.00 0.00 4.16
3388 3716 3.697439 AAGTGCTGGTGTGTGGCGT 62.697 57.895 0.00 0.00 0.00 5.68
3389 3717 3.209097 GTGCTGGTGTGTGGCGTT 61.209 61.111 0.00 0.00 0.00 4.84
3406 3734 1.136110 CGTTTTTGCAGAAACACCCCT 59.864 47.619 26.68 0.00 39.01 4.79
3407 3735 2.359531 CGTTTTTGCAGAAACACCCCTA 59.640 45.455 26.68 0.00 39.01 3.53
3416 3744 4.514401 CAGAAACACCCCTAACCTCATAC 58.486 47.826 0.00 0.00 0.00 2.39
3420 3748 2.326428 CACCCCTAACCTCATACCGAT 58.674 52.381 0.00 0.00 0.00 4.18
3423 3751 2.302157 CCCCTAACCTCATACCGATTCC 59.698 54.545 0.00 0.00 0.00 3.01
3450 3781 2.524569 AAAACCTGAACCGGCATTTG 57.475 45.000 0.00 0.00 0.00 2.32
3481 3812 1.935873 ACCTGAATCATGAATCGTGCG 59.064 47.619 0.00 0.00 0.00 5.34
3739 6874 0.907486 GGAGGTGTAGTACAACCCCC 59.093 60.000 14.83 12.39 36.16 5.40
3762 6898 3.976701 AAATCCCCGCTGGTGCTCG 62.977 63.158 0.00 0.00 36.97 5.03
3808 6947 3.448093 TGGTGCCCTGTAAATGAATGA 57.552 42.857 0.00 0.00 0.00 2.57
3902 7125 3.118298 GCTGGATAATTGCATTTTGGGGT 60.118 43.478 0.00 0.00 0.00 4.95
4058 7298 4.289245 ACCATGGGAATTTATTGGTGAGG 58.711 43.478 18.09 0.00 39.18 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.035056 AGGCTCCTCAAACCAATCCG 60.035 55.000 0.00 0.00 0.00 4.18
1 2 2.239907 AGTAGGCTCCTCAAACCAATCC 59.760 50.000 0.00 0.00 0.00 3.01
2 3 3.636153 AGTAGGCTCCTCAAACCAATC 57.364 47.619 0.00 0.00 0.00 2.67
3 4 4.080863 CACTAGTAGGCTCCTCAAACCAAT 60.081 45.833 1.45 0.00 0.00 3.16
4 5 3.260884 CACTAGTAGGCTCCTCAAACCAA 59.739 47.826 1.45 0.00 0.00 3.67
5 6 2.832129 CACTAGTAGGCTCCTCAAACCA 59.168 50.000 1.45 0.00 0.00 3.67
6 7 3.097614 TCACTAGTAGGCTCCTCAAACC 58.902 50.000 1.45 0.00 0.00 3.27
7 8 4.803098 TTCACTAGTAGGCTCCTCAAAC 57.197 45.455 1.45 0.00 0.00 2.93
8 9 6.173339 CAATTTCACTAGTAGGCTCCTCAAA 58.827 40.000 1.45 0.00 0.00 2.69
9 10 5.248477 ACAATTTCACTAGTAGGCTCCTCAA 59.752 40.000 1.45 0.00 0.00 3.02
10 11 4.777896 ACAATTTCACTAGTAGGCTCCTCA 59.222 41.667 1.45 0.00 0.00 3.86
11 12 5.346181 ACAATTTCACTAGTAGGCTCCTC 57.654 43.478 1.45 0.00 0.00 3.71
12 13 6.212791 TGTTACAATTTCACTAGTAGGCTCCT 59.787 38.462 1.45 0.00 0.00 3.69
13 14 6.403878 TGTTACAATTTCACTAGTAGGCTCC 58.596 40.000 1.45 0.00 0.00 4.70
14 15 8.494016 AATGTTACAATTTCACTAGTAGGCTC 57.506 34.615 1.45 0.00 0.00 4.70
15 16 8.863872 AAATGTTACAATTTCACTAGTAGGCT 57.136 30.769 1.45 0.00 0.00 4.58
16 17 8.947115 AGAAATGTTACAATTTCACTAGTAGGC 58.053 33.333 16.39 0.00 45.20 3.93
20 21 9.337396 TGTGAGAAATGTTACAATTTCACTAGT 57.663 29.630 18.49 0.00 45.20 2.57
23 24 9.301153 GTTTGTGAGAAATGTTACAATTTCACT 57.699 29.630 18.49 1.30 45.20 3.41
24 25 8.259194 CGTTTGTGAGAAATGTTACAATTTCAC 58.741 33.333 14.03 14.03 45.20 3.18
25 26 8.184848 TCGTTTGTGAGAAATGTTACAATTTCA 58.815 29.630 16.39 6.77 45.20 2.69
26 27 8.555166 TCGTTTGTGAGAAATGTTACAATTTC 57.445 30.769 10.21 10.21 43.79 2.17
27 28 8.967218 CATCGTTTGTGAGAAATGTTACAATTT 58.033 29.630 0.00 0.00 33.56 1.82
28 29 8.134895 ACATCGTTTGTGAGAAATGTTACAATT 58.865 29.630 0.00 0.00 37.11 2.32
29 30 7.648142 ACATCGTTTGTGAGAAATGTTACAAT 58.352 30.769 0.00 0.00 37.11 2.71
30 31 7.022055 ACATCGTTTGTGAGAAATGTTACAA 57.978 32.000 0.00 0.00 37.11 2.41
31 32 6.612247 ACATCGTTTGTGAGAAATGTTACA 57.388 33.333 0.00 0.00 37.11 2.41
32 33 9.051027 CAATACATCGTTTGTGAGAAATGTTAC 57.949 33.333 4.39 0.00 39.48 2.50
33 34 8.233868 CCAATACATCGTTTGTGAGAAATGTTA 58.766 33.333 4.39 0.00 39.48 2.41
34 35 7.083858 CCAATACATCGTTTGTGAGAAATGTT 58.916 34.615 4.39 0.00 39.48 2.71
35 36 6.206634 ACCAATACATCGTTTGTGAGAAATGT 59.793 34.615 4.39 0.00 39.48 2.71
36 37 6.611381 ACCAATACATCGTTTGTGAGAAATG 58.389 36.000 4.39 0.00 39.48 2.32
37 38 6.817765 ACCAATACATCGTTTGTGAGAAAT 57.182 33.333 4.39 0.00 39.48 2.17
38 39 6.627395 AACCAATACATCGTTTGTGAGAAA 57.373 33.333 4.39 0.00 39.48 2.52
39 40 7.915293 ATAACCAATACATCGTTTGTGAGAA 57.085 32.000 4.39 0.00 39.48 2.87
40 41 7.625395 GCAATAACCAATACATCGTTTGTGAGA 60.625 37.037 4.39 0.00 39.48 3.27
41 42 6.468956 GCAATAACCAATACATCGTTTGTGAG 59.531 38.462 4.39 0.00 39.48 3.51
42 43 6.150307 AGCAATAACCAATACATCGTTTGTGA 59.850 34.615 4.39 0.00 39.48 3.58
43 44 6.321717 AGCAATAACCAATACATCGTTTGTG 58.678 36.000 4.39 0.00 39.48 3.33
44 45 6.509418 AGCAATAACCAATACATCGTTTGT 57.491 33.333 0.00 0.00 42.62 2.83
45 46 8.957028 CATTAGCAATAACCAATACATCGTTTG 58.043 33.333 0.00 0.00 0.00 2.93
46 47 8.898761 TCATTAGCAATAACCAATACATCGTTT 58.101 29.630 0.00 0.00 0.00 3.60
47 48 8.445275 TCATTAGCAATAACCAATACATCGTT 57.555 30.769 0.00 0.00 0.00 3.85
48 49 8.445275 TTCATTAGCAATAACCAATACATCGT 57.555 30.769 0.00 0.00 0.00 3.73
125 126 2.174424 AGAATTGCAGAGGATCCCTTCC 59.826 50.000 8.55 0.00 45.85 3.46
131 132 5.893897 AGTTCAAAGAATTGCAGAGGATC 57.106 39.130 0.00 0.00 36.45 3.36
138 139 5.591099 GAAGTGGAAGTTCAAAGAATTGCA 58.409 37.500 5.01 0.00 45.59 4.08
139 140 4.676924 CGAAGTGGAAGTTCAAAGAATTGC 59.323 41.667 5.01 0.00 46.63 3.56
143 144 2.286833 CGCGAAGTGGAAGTTCAAAGAA 59.713 45.455 0.00 0.00 46.63 2.52
169 170 0.871722 TGTAGTTCACATGCGTTGCC 59.128 50.000 0.00 0.00 30.04 4.52
239 240 3.304057 CGTTCTTTCTTGGGCTTGAAGAC 60.304 47.826 0.00 0.00 0.00 3.01
240 241 2.878406 CGTTCTTTCTTGGGCTTGAAGA 59.122 45.455 0.00 0.00 0.00 2.87
254 255 4.546829 TTAGCATAGTGTCCCGTTCTTT 57.453 40.909 0.00 0.00 0.00 2.52
260 261 6.202954 CCTTTTCTTATTAGCATAGTGTCCCG 59.797 42.308 0.00 0.00 0.00 5.14
262 263 8.732746 TTCCTTTTCTTATTAGCATAGTGTCC 57.267 34.615 0.00 0.00 0.00 4.02
263 264 8.831550 CCTTCCTTTTCTTATTAGCATAGTGTC 58.168 37.037 0.00 0.00 0.00 3.67
303 304 3.875727 CTGATGTAAGCATGTCTTCTGGG 59.124 47.826 5.78 0.00 36.25 4.45
326 327 0.109319 CATGTTTGTAGGGTTGCGGC 60.109 55.000 0.00 0.00 0.00 6.53
351 352 1.235724 GAAGTTACAGGTGGTGGTGC 58.764 55.000 0.00 0.00 0.00 5.01
361 362 7.749808 TCGTACAATCTAGAGTGAAGTTACAG 58.250 38.462 25.87 13.07 0.00 2.74
364 365 8.790718 AGTTTCGTACAATCTAGAGTGAAGTTA 58.209 33.333 25.87 5.72 0.00 2.24
367 368 7.085116 ACAGTTTCGTACAATCTAGAGTGAAG 58.915 38.462 25.87 15.40 0.00 3.02
381 382 3.366440 AGGACACAGACAGTTTCGTAC 57.634 47.619 0.00 0.00 0.00 3.67
388 389 1.806623 GCGTTCAAGGACACAGACAGT 60.807 52.381 0.00 0.00 0.00 3.55
390 391 0.874175 CGCGTTCAAGGACACAGACA 60.874 55.000 0.00 0.00 0.00 3.41
391 392 0.874607 ACGCGTTCAAGGACACAGAC 60.875 55.000 5.58 0.00 0.00 3.51
413 414 4.823989 ACTAGATAGGAAATGCCATGTTGC 59.176 41.667 0.00 0.00 40.02 4.17
416 417 6.223852 CGTTACTAGATAGGAAATGCCATGT 58.776 40.000 0.00 0.00 40.02 3.21
418 419 5.221641 TGCGTTACTAGATAGGAAATGCCAT 60.222 40.000 0.00 0.00 40.02 4.40
419 420 4.100344 TGCGTTACTAGATAGGAAATGCCA 59.900 41.667 0.00 5.19 40.02 4.92
420 421 4.448060 GTGCGTTACTAGATAGGAAATGCC 59.552 45.833 0.00 0.00 35.88 4.40
421 422 5.047847 TGTGCGTTACTAGATAGGAAATGC 58.952 41.667 0.00 11.53 36.59 3.56
423 424 7.050970 TCATGTGCGTTACTAGATAGGAAAT 57.949 36.000 0.00 0.00 0.00 2.17
424 425 6.096423 ACTCATGTGCGTTACTAGATAGGAAA 59.904 38.462 0.00 0.00 0.00 3.13
425 426 5.593095 ACTCATGTGCGTTACTAGATAGGAA 59.407 40.000 0.00 0.00 0.00 3.36
441 442 2.485426 CCCAACAGTTAGCACTCATGTG 59.515 50.000 0.00 0.00 46.37 3.21
443 444 1.470098 GCCCAACAGTTAGCACTCATG 59.530 52.381 3.16 0.00 0.00 3.07
444 445 1.073763 TGCCCAACAGTTAGCACTCAT 59.926 47.619 6.15 0.00 0.00 2.90
446 447 1.160137 CTGCCCAACAGTTAGCACTC 58.840 55.000 6.15 0.00 41.86 3.51
461 462 1.070786 TTGTCGAACTGGGACTGCC 59.929 57.895 0.00 0.00 35.45 4.85
464 465 1.341531 CAGAGTTGTCGAACTGGGACT 59.658 52.381 0.00 0.00 42.80 3.85
465 466 1.068741 ACAGAGTTGTCGAACTGGGAC 59.931 52.381 0.00 0.00 42.80 4.46
467 468 1.867233 CAACAGAGTTGTCGAACTGGG 59.133 52.381 0.00 0.00 42.80 4.45
468 469 2.540101 GACAACAGAGTTGTCGAACTGG 59.460 50.000 22.41 0.00 42.80 4.00
469 470 3.843426 GACAACAGAGTTGTCGAACTG 57.157 47.619 22.41 0.00 42.80 3.16
475 476 2.541762 GCACTCAGACAACAGAGTTGTC 59.458 50.000 26.94 26.94 46.71 3.18
476 477 2.169352 AGCACTCAGACAACAGAGTTGT 59.831 45.455 14.68 14.68 40.09 3.32
477 478 2.831333 AGCACTCAGACAACAGAGTTG 58.169 47.619 8.24 8.24 40.09 3.16
480 481 3.383620 AGAAGCACTCAGACAACAGAG 57.616 47.619 0.00 0.00 36.06 3.35
481 482 3.722147 GAAGAAGCACTCAGACAACAGA 58.278 45.455 0.00 0.00 0.00 3.41
483 484 2.473816 CGAAGAAGCACTCAGACAACA 58.526 47.619 0.00 0.00 0.00 3.33
484 485 1.795286 CCGAAGAAGCACTCAGACAAC 59.205 52.381 0.00 0.00 0.00 3.32
485 486 1.873903 GCCGAAGAAGCACTCAGACAA 60.874 52.381 0.00 0.00 0.00 3.18
487 488 0.037790 AGCCGAAGAAGCACTCAGAC 60.038 55.000 0.00 0.00 0.00 3.51
488 489 0.681733 AAGCCGAAGAAGCACTCAGA 59.318 50.000 0.00 0.00 0.00 3.27
489 490 1.196354 CAAAGCCGAAGAAGCACTCAG 59.804 52.381 0.00 0.00 0.00 3.35
490 491 1.202639 TCAAAGCCGAAGAAGCACTCA 60.203 47.619 0.00 0.00 0.00 3.41
491 492 1.462670 CTCAAAGCCGAAGAAGCACTC 59.537 52.381 0.00 0.00 0.00 3.51
494 495 0.250467 AGCTCAAAGCCGAAGAAGCA 60.250 50.000 0.00 0.00 43.77 3.91
495 496 1.726853 TAGCTCAAAGCCGAAGAAGC 58.273 50.000 0.00 0.00 43.77 3.86
496 497 4.954092 AAATAGCTCAAAGCCGAAGAAG 57.046 40.909 0.00 0.00 43.77 2.85
498 499 7.391148 AATAAAAATAGCTCAAAGCCGAAGA 57.609 32.000 0.00 0.00 43.77 2.87
499 500 7.970614 AGAAATAAAAATAGCTCAAAGCCGAAG 59.029 33.333 0.00 0.00 43.77 3.79
500 501 7.826690 AGAAATAAAAATAGCTCAAAGCCGAA 58.173 30.769 0.00 0.00 43.77 4.30
501 502 7.391148 AGAAATAAAAATAGCTCAAAGCCGA 57.609 32.000 0.00 0.00 43.77 5.54
502 503 8.466086 AAAGAAATAAAAATAGCTCAAAGCCG 57.534 30.769 0.00 0.00 43.77 5.52
643 772 9.567776 TCAGAAGGTATCTAAAAATGTTTGTCA 57.432 29.630 0.00 0.00 36.32 3.58
741 870 9.666626 ACGAATTTTCACGAAAACATGTATTTA 57.333 25.926 7.09 0.00 42.32 1.40
742 871 8.568732 ACGAATTTTCACGAAAACATGTATTT 57.431 26.923 7.09 2.16 42.32 1.40
743 872 9.666626 TTACGAATTTTCACGAAAACATGTATT 57.333 25.926 7.09 0.00 42.32 1.89
744 873 9.834628 ATTACGAATTTTCACGAAAACATGTAT 57.165 25.926 7.09 0.00 42.32 2.29
745 874 9.666626 AATTACGAATTTTCACGAAAACATGTA 57.333 25.926 7.09 7.40 42.32 2.29
746 875 8.568732 AATTACGAATTTTCACGAAAACATGT 57.431 26.923 7.09 0.00 42.32 3.21
747 876 9.842444 AAAATTACGAATTTTCACGAAAACATG 57.158 25.926 7.09 0.00 45.32 3.21
845 974 0.181350 CGGCCCAAGGAGCTTAGATT 59.819 55.000 0.00 0.00 0.00 2.40
873 1002 2.928396 AGTGCTAACTGGGCCGGT 60.928 61.111 13.59 13.59 34.48 5.28
903 1032 2.955881 GCCCTAGAACGTGTGGCCT 61.956 63.158 3.32 0.00 36.07 5.19
960 1089 0.753848 AGTGGAAAACCGTTGGTGGG 60.754 55.000 0.00 0.00 35.34 4.61
966 1095 0.256464 TGGGTGAGTGGAAAACCGTT 59.744 50.000 0.00 0.00 34.62 4.44
1137 1269 4.176851 GACGACGCGGAGGAGGAC 62.177 72.222 12.47 0.00 0.00 3.85
1293 1428 0.322187 AAAGGAATCGGGTGGGAACG 60.322 55.000 0.00 0.00 0.00 3.95
1294 1429 1.816835 GAAAAGGAATCGGGTGGGAAC 59.183 52.381 0.00 0.00 0.00 3.62
1295 1430 1.272258 GGAAAAGGAATCGGGTGGGAA 60.272 52.381 0.00 0.00 0.00 3.97
1302 1437 1.009829 CTCGCTGGAAAAGGAATCGG 58.990 55.000 0.00 0.00 0.00 4.18
1373 1517 7.449704 AGAGAAAACAAACTAGATTGCTCCAAT 59.550 33.333 12.28 0.00 36.72 3.16
1385 1529 6.488769 TGACCAGGTAGAGAAAACAAACTA 57.511 37.500 0.00 0.00 0.00 2.24
1390 1534 4.838423 TCTGATGACCAGGTAGAGAAAACA 59.162 41.667 0.00 0.00 43.12 2.83
1409 1553 3.229293 TGGGTTGCACATCATTTTCTGA 58.771 40.909 0.00 0.00 38.53 3.27
1414 1558 4.620589 TTGATTGGGTTGCACATCATTT 57.379 36.364 0.00 0.00 0.00 2.32
1415 1559 4.620589 TTTGATTGGGTTGCACATCATT 57.379 36.364 0.00 0.00 0.00 2.57
1417 1561 3.865302 GCATTTGATTGGGTTGCACATCA 60.865 43.478 0.00 0.00 33.58 3.07
1422 1566 2.250031 AGAGCATTTGATTGGGTTGCA 58.750 42.857 0.00 0.00 35.79 4.08
1424 1568 5.840243 TGATAGAGCATTTGATTGGGTTG 57.160 39.130 0.00 0.00 0.00 3.77
1425 1569 6.189859 TCTTGATAGAGCATTTGATTGGGTT 58.810 36.000 0.00 0.00 0.00 4.11
1474 1619 6.058183 GGTTCAGGTGAGCAGAACATATTAT 58.942 40.000 19.01 0.00 42.50 1.28
1475 1620 5.045942 TGGTTCAGGTGAGCAGAACATATTA 60.046 40.000 19.01 0.75 42.50 0.98
1477 1622 3.264193 TGGTTCAGGTGAGCAGAACATAT 59.736 43.478 19.01 0.00 42.50 1.78
1478 1623 2.637382 TGGTTCAGGTGAGCAGAACATA 59.363 45.455 19.01 7.03 42.50 2.29
1580 1725 5.757808 ACAAAAATTACACCATTGGAAGCAC 59.242 36.000 10.37 0.00 0.00 4.40
1604 1750 4.201910 GGCGCAATGCTTGTAAATCTTAGA 60.202 41.667 10.83 0.00 45.43 2.10
1608 1754 2.094675 AGGCGCAATGCTTGTAAATCT 58.905 42.857 10.83 0.00 45.43 2.40
1683 1829 6.658816 AGTCCAAATGCAAATACACTGATGTA 59.341 34.615 0.00 0.00 45.37 2.29
1684 1830 5.477984 AGTCCAAATGCAAATACACTGATGT 59.522 36.000 0.00 0.00 43.30 3.06
1708 1854 5.054477 GGACAAGTCAAGTTTGCTAGTACA 58.946 41.667 2.29 0.00 0.00 2.90
1736 1884 1.578583 ACACGGAAGTTCTGGTTTCG 58.421 50.000 16.08 6.08 46.40 3.46
1751 1899 5.804692 AGATCTAGTCAACAGAGTACACG 57.195 43.478 0.00 0.00 0.00 4.49
1777 1925 5.942961 TCCTTGACCTATAACACAAAACCA 58.057 37.500 0.00 0.00 0.00 3.67
1838 1986 8.548721 CAGTAGAAGGCTTTATATAAAACCACG 58.451 37.037 23.38 8.24 34.64 4.94
1874 2022 6.258727 ACAACTCGCCATTAACAATCATAGAG 59.741 38.462 0.00 0.00 0.00 2.43
1892 2040 2.609459 ACAAGAGTGCAAAGACAACTCG 59.391 45.455 0.00 0.00 33.12 4.18
1907 2056 5.677319 TCTCCCACCTAAATACACAAGAG 57.323 43.478 0.00 0.00 0.00 2.85
1910 2059 5.570205 TGTTCTCCCACCTAAATACACAA 57.430 39.130 0.00 0.00 0.00 3.33
1916 2065 4.263771 ACGGAATTGTTCTCCCACCTAAAT 60.264 41.667 0.00 0.00 0.00 1.40
1917 2066 3.073356 ACGGAATTGTTCTCCCACCTAAA 59.927 43.478 0.00 0.00 0.00 1.85
1978 2127 5.130975 TGAACTGATGGCAGAGTATATTGGT 59.869 40.000 2.62 0.00 45.17 3.67
1998 2147 4.184629 GACCATATCTATGCCCGATGAAC 58.815 47.826 0.00 0.00 32.40 3.18
2005 2154 4.012374 CAACCATGACCATATCTATGCCC 58.988 47.826 0.00 0.00 32.40 5.36
2026 2175 6.943146 TGACAAATGGCTACCTTATTACAACA 59.057 34.615 0.00 0.00 0.00 3.33
2054 2203 6.811634 AATCATGAAAATGAAGGGGCATTA 57.188 33.333 0.00 0.00 37.50 1.90
2055 2204 5.703730 AATCATGAAAATGAAGGGGCATT 57.296 34.783 0.00 0.00 40.04 3.56
2056 2205 5.703730 AAATCATGAAAATGAAGGGGCAT 57.296 34.783 0.00 0.00 33.83 4.40
2057 2206 5.502089 AAAATCATGAAAATGAAGGGGCA 57.498 34.783 0.00 0.00 33.83 5.36
2400 2713 3.129813 TCACATTCTTGCATGAATCAGGC 59.870 43.478 21.43 13.41 41.79 4.85
2426 2743 6.878923 CCAAGTCAGAATTATACACACTTCCA 59.121 38.462 0.00 0.00 0.00 3.53
2428 2745 7.148407 CCACCAAGTCAGAATTATACACACTTC 60.148 40.741 0.00 0.00 0.00 3.01
2547 2864 5.958380 TCTGAGGTGTCTCCAGTACAATATT 59.042 40.000 0.00 0.00 39.23 1.28
2548 2865 5.361285 GTCTGAGGTGTCTCCAGTACAATAT 59.639 44.000 0.00 0.00 39.23 1.28
2757 3083 6.230472 ACATAACATACAGCAGAACAACTCA 58.770 36.000 0.00 0.00 0.00 3.41
2785 3111 8.782339 TTTACTGGTTACATTAGGCTCTAAAC 57.218 34.615 0.00 0.00 0.00 2.01
2870 3198 5.559148 AATTGTAGCCATTCACCCAAAAA 57.441 34.783 0.00 0.00 0.00 1.94
2871 3199 5.303971 CAAATTGTAGCCATTCACCCAAAA 58.696 37.500 0.00 0.00 0.00 2.44
2885 3213 5.886960 ACTTAGGCTTCAGCAAATTGTAG 57.113 39.130 0.30 0.00 44.36 2.74
2888 3216 6.261118 GTCATACTTAGGCTTCAGCAAATTG 58.739 40.000 0.30 0.00 44.36 2.32
2889 3217 5.358160 GGTCATACTTAGGCTTCAGCAAATT 59.642 40.000 0.30 0.00 44.36 1.82
3194 3522 5.181245 CCTAAACAACTTCATGTACCACCAG 59.819 44.000 0.00 0.00 32.02 4.00
3218 3546 0.038892 CAGGCACCAAACTGCACATC 60.039 55.000 0.00 0.00 39.08 3.06
3258 3586 3.705604 CAGAAACAAGTTTTCGCACCAT 58.294 40.909 0.00 0.00 33.86 3.55
3265 3593 3.065019 TGCTCGCAGAAACAAGTTTTC 57.935 42.857 0.00 0.00 34.09 2.29
3371 3699 3.697439 AACGCCACACACCAGCACT 62.697 57.895 0.00 0.00 0.00 4.40
3372 3700 2.278182 AAAACGCCACACACCAGCAC 62.278 55.000 0.00 0.00 0.00 4.40
3373 3701 1.599606 AAAAACGCCACACACCAGCA 61.600 50.000 0.00 0.00 0.00 4.41
3374 3702 1.140804 AAAAACGCCACACACCAGC 59.859 52.632 0.00 0.00 0.00 4.85
3379 3707 0.528017 TTCTGCAAAAACGCCACACA 59.472 45.000 0.00 0.00 0.00 3.72
3381 3709 1.067565 TGTTTCTGCAAAAACGCCACA 60.068 42.857 10.88 0.00 41.12 4.17
3388 3716 3.133183 GGTTAGGGGTGTTTCTGCAAAAA 59.867 43.478 0.00 0.00 0.00 1.94
3389 3717 2.696187 GGTTAGGGGTGTTTCTGCAAAA 59.304 45.455 0.00 0.00 0.00 2.44
3406 3734 3.918566 TCTGGGAATCGGTATGAGGTTA 58.081 45.455 0.00 0.00 0.00 2.85
3407 3735 2.759355 TCTGGGAATCGGTATGAGGTT 58.241 47.619 0.00 0.00 0.00 3.50
3433 3764 1.815817 GCCAAATGCCGGTTCAGGTT 61.816 55.000 1.90 0.00 0.00 3.50
3434 3765 2.275380 GCCAAATGCCGGTTCAGGT 61.275 57.895 1.90 0.00 0.00 4.00
3450 3781 2.790433 TGATTCAGGTAACAAGTGGCC 58.210 47.619 0.00 0.00 41.41 5.36
3481 3812 1.037579 GGGTTAGGGATTGCAGGTGC 61.038 60.000 0.00 0.00 42.50 5.01
3762 6898 5.666462 GAGAGTGAGAGAAATAAAGGGGTC 58.334 45.833 0.00 0.00 0.00 4.46
3902 7125 4.696877 CAGCAACAGACCTCATATTGACAA 59.303 41.667 0.00 0.00 0.00 3.18
4058 7298 3.631227 AGGATCAAATTCTTGCTAGCTGC 59.369 43.478 17.23 0.00 43.25 5.25


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

AutoCloner maintained by Alex Coulton.