Multiple sequence alignment - TraesCS6B01G341900

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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 TraesCS6B01G341900 chr6B 100.000 5214 0 0 1 5214 601872841 601878054 0.000000e+00 9629.0
1 TraesCS6B01G341900 chr6B 96.923 650 20 0 4565 5214 51220117 51219468 0.000000e+00 1090.0
2 TraesCS6B01G341900 chr6B 83.537 328 32 12 1240 1566 663291256 663291562 2.380000e-73 287.0
3 TraesCS6B01G341900 chr6B 84.615 273 18 7 946 1206 663290991 663291251 3.120000e-62 250.0
4 TraesCS6B01G341900 chr6B 92.188 64 4 1 791 854 663290929 663290991 7.190000e-14 89.8
5 TraesCS6B01G341900 chr6B 100.000 46 0 0 2610 2655 601875367 601875412 9.300000e-13 86.1
6 TraesCS6B01G341900 chr6B 100.000 46 0 0 2527 2572 601875450 601875495 9.300000e-13 86.1
7 TraesCS6B01G341900 chr6D 92.959 1690 81 18 888 2568 401300868 401302528 0.000000e+00 2427.0
8 TraesCS6B01G341900 chr6D 91.667 1152 55 12 2693 3841 401302530 401303643 0.000000e+00 1557.0
9 TraesCS6B01G341900 chr6D 94.109 696 31 7 3877 4566 401303649 401304340 0.000000e+00 1050.0
10 TraesCS6B01G341900 chr6D 87.126 435 10 14 426 831 401300061 401300478 7.960000e-123 451.0
11 TraesCS6B01G341900 chr6D 89.820 167 9 2 17 177 401299404 401299568 1.900000e-49 207.0
12 TraesCS6B01G341900 chr6D 82.353 204 12 7 162 355 401299582 401299771 6.990000e-34 156.0
13 TraesCS6B01G341900 chr6D 100.000 42 0 0 2610 2651 401302487 401302528 1.560000e-10 78.7
14 TraesCS6B01G341900 chr6A 91.901 1704 82 24 882 2568 547821901 547823565 0.000000e+00 2331.0
15 TraesCS6B01G341900 chr6A 97.120 764 21 1 2694 3457 547823568 547824330 0.000000e+00 1288.0
16 TraesCS6B01G341900 chr6A 94.494 563 26 5 4006 4566 547825019 547825578 0.000000e+00 863.0
17 TraesCS6B01G341900 chr6A 90.787 521 24 7 3470 3983 547824522 547825025 0.000000e+00 675.0
18 TraesCS6B01G341900 chr6A 92.308 169 10 3 493 660 547821284 547821450 2.430000e-58 237.0
19 TraesCS6B01G341900 chr3B 96.779 652 20 1 4563 5214 51910095 51910745 0.000000e+00 1086.0
20 TraesCS6B01G341900 chr2B 96.483 654 21 2 4562 5213 291598954 291599607 0.000000e+00 1079.0
21 TraesCS6B01G341900 chr2B 96.166 652 23 2 4563 5214 13033666 13033017 0.000000e+00 1064.0
22 TraesCS6B01G341900 chr1B 96.605 648 22 0 4567 5214 279187801 279187154 0.000000e+00 1075.0
23 TraesCS6B01G341900 chr1B 96.183 655 24 1 4560 5214 629798115 629797462 0.000000e+00 1070.0
24 TraesCS6B01G341900 chr1B 83.082 331 34 14 1237 1566 177477904 177477595 1.110000e-71 281.0
25 TraesCS6B01G341900 chr1B 95.652 46 2 0 791 836 177478661 177478616 2.010000e-09 75.0
26 TraesCS6B01G341900 chr1A 96.605 648 22 0 4567 5214 555305388 555304741 0.000000e+00 1075.0
27 TraesCS6B01G341900 chr2A 96.600 647 22 0 4568 5214 695285936 695285290 0.000000e+00 1074.0
28 TraesCS6B01G341900 chr2A 85.417 96 6 6 3166 3261 655292828 655292741 5.560000e-15 93.5
29 TraesCS6B01G341900 chr5B 96.055 659 25 1 4556 5214 482993937 482994594 0.000000e+00 1072.0
30 TraesCS6B01G341900 chr5B 83.735 332 30 15 1237 1566 28668621 28668930 5.110000e-75 292.0
31 TraesCS6B01G341900 chr5B 86.081 273 14 7 946 1206 28668359 28668619 6.650000e-69 272.0
32 TraesCS6B01G341900 chr5B 93.750 64 2 2 791 854 28668298 28668359 1.550000e-15 95.3
33 TraesCS6B01G341900 chr5B 100.000 28 0 0 2696 2723 159713548 159713575 9.000000e-03 52.8
34 TraesCS6B01G341900 chr7B 85.446 426 51 6 1989 2414 186745478 186745892 2.880000e-117 433.0
35 TraesCS6B01G341900 chr7B 83.891 329 29 16 1240 1566 579561257 579560951 5.110000e-75 292.0
36 TraesCS6B01G341900 chr7B 85.816 282 16 7 946 1215 579561522 579561253 1.430000e-70 278.0
37 TraesCS6B01G341900 chr7B 92.481 133 10 0 1290 1422 118976283 118976415 1.920000e-44 191.0
38 TraesCS6B01G341900 chr7B 93.220 59 3 1 1124 1181 118976137 118976195 9.300000e-13 86.1
39 TraesCS6B01G341900 chr5A 85.515 359 44 6 3076 3434 658994469 658994119 8.250000e-98 368.0
40 TraesCS6B01G341900 chr7A 92.593 135 10 0 1290 1424 211637940 211638074 1.480000e-45 195.0
41 TraesCS6B01G341900 chr7A 91.176 68 3 3 1117 1181 211637784 211637851 7.190000e-14 89.8
42 TraesCS6B01G341900 chr7D 91.852 135 11 0 1290 1424 156684568 156684702 6.890000e-44 189.0
43 TraesCS6B01G341900 chr7D 85.437 103 7 6 3166 3268 634366625 634366531 3.320000e-17 100.0
44 TraesCS6B01G341900 chr7D 91.176 68 3 3 1117 1181 156684413 156684480 7.190000e-14 89.8
45 TraesCS6B01G341900 chr4A 84.375 96 7 6 3166 3261 630045809 630045722 2.590000e-13 87.9


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 TraesCS6B01G341900 chr6B 601872841 601878054 5213 False 3267.066667 9629 100.000000 1 5214 3 chr6B.!!$F1 5213
1 TraesCS6B01G341900 chr6B 51219468 51220117 649 True 1090.000000 1090 96.923000 4565 5214 1 chr6B.!!$R1 649
2 TraesCS6B01G341900 chr6B 663290929 663291562 633 False 208.933333 287 86.780000 791 1566 3 chr6B.!!$F2 775
3 TraesCS6B01G341900 chr6D 401299404 401304340 4936 False 846.671429 2427 91.147714 17 4566 7 chr6D.!!$F1 4549
4 TraesCS6B01G341900 chr6A 547821284 547825578 4294 False 1078.800000 2331 93.322000 493 4566 5 chr6A.!!$F1 4073
5 TraesCS6B01G341900 chr3B 51910095 51910745 650 False 1086.000000 1086 96.779000 4563 5214 1 chr3B.!!$F1 651
6 TraesCS6B01G341900 chr2B 291598954 291599607 653 False 1079.000000 1079 96.483000 4562 5213 1 chr2B.!!$F1 651
7 TraesCS6B01G341900 chr2B 13033017 13033666 649 True 1064.000000 1064 96.166000 4563 5214 1 chr2B.!!$R1 651
8 TraesCS6B01G341900 chr1B 279187154 279187801 647 True 1075.000000 1075 96.605000 4567 5214 1 chr1B.!!$R1 647
9 TraesCS6B01G341900 chr1B 629797462 629798115 653 True 1070.000000 1070 96.183000 4560 5214 1 chr1B.!!$R2 654
10 TraesCS6B01G341900 chr1A 555304741 555305388 647 True 1075.000000 1075 96.605000 4567 5214 1 chr1A.!!$R1 647
11 TraesCS6B01G341900 chr2A 695285290 695285936 646 True 1074.000000 1074 96.600000 4568 5214 1 chr2A.!!$R2 646
12 TraesCS6B01G341900 chr5B 482993937 482994594 657 False 1072.000000 1072 96.055000 4556 5214 1 chr5B.!!$F2 658
13 TraesCS6B01G341900 chr5B 28668298 28668930 632 False 219.766667 292 87.855333 791 1566 3 chr5B.!!$F3 775
14 TraesCS6B01G341900 chr7B 579560951 579561522 571 True 285.000000 292 84.853500 946 1566 2 chr7B.!!$R1 620

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
398 662 0.031314 CAGTGAGGCTCGTATCGCAT 59.969 55.0 10.42 0.0 0.00 4.73 F
1219 1906 0.177141 TTTCCTTCGCCTCCGTATGG 59.823 55.0 0.00 0.0 35.54 2.74 F
2655 3342 0.594602 TGTCAGCTGCACTCAAATGC 59.405 50.0 9.47 0.0 46.32 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2068 2755 0.313672 GCCTGGCACGACAAAATGAA 59.686 50.0 15.17 0.00 0.00 2.57 R
3153 3840 0.034767 CAGCAAGGCTCTCCCAATCA 60.035 55.0 0.00 0.00 36.40 2.57 R
4435 5344 0.035056 AATGCAGAGGTAGGCACACC 60.035 55.0 0.00 0.25 43.75 4.16 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
23 24 2.412870 CTGGCTGATTGTGTGTTCGTA 58.587 47.619 0.00 0.00 0.00 3.43
31 32 1.566404 TGTGTGTTCGTAGCAGTGTG 58.434 50.000 0.00 0.00 0.00 3.82
57 58 2.480416 GCAGACTCCACGATTCTACCAG 60.480 54.545 0.00 0.00 0.00 4.00
59 60 0.824759 ACTCCACGATTCTACCAGCC 59.175 55.000 0.00 0.00 0.00 4.85
61 62 1.227263 CCACGATTCTACCAGCCGG 60.227 63.158 0.00 0.00 38.77 6.13
90 97 1.587088 GGCGCTCCAAAATGCATCG 60.587 57.895 7.64 0.00 0.00 3.84
94 101 1.274596 GCTCCAAAATGCATCGCAAG 58.725 50.000 0.00 0.00 43.62 4.01
194 230 6.685527 TGCATTTCACCGCTGTATATAAAA 57.314 33.333 0.00 0.00 0.00 1.52
212 255 2.972153 AATCCTCCAACCCCTCTACT 57.028 50.000 0.00 0.00 0.00 2.57
249 292 3.691342 CTTCCTCGGCCACGACCA 61.691 66.667 2.24 0.00 45.59 4.02
250 293 3.934391 CTTCCTCGGCCACGACCAC 62.934 68.421 2.24 0.00 45.59 4.16
252 295 4.742201 CCTCGGCCACGACCACAG 62.742 72.222 2.24 0.00 45.59 3.66
255 298 4.063967 CGGCCACGACCACAGCTA 62.064 66.667 2.24 0.00 44.60 3.32
256 299 2.434359 GGCCACGACCACAGCTAC 60.434 66.667 0.00 0.00 0.00 3.58
257 300 2.342279 GCCACGACCACAGCTACA 59.658 61.111 0.00 0.00 0.00 2.74
285 328 6.742718 CACGAACTGGATTTTGTTCATGTATC 59.257 38.462 0.00 0.00 41.67 2.24
286 329 6.655003 ACGAACTGGATTTTGTTCATGTATCT 59.345 34.615 0.00 0.00 41.67 1.98
287 330 7.148407 ACGAACTGGATTTTGTTCATGTATCTC 60.148 37.037 0.00 0.00 41.67 2.75
288 331 7.065085 CGAACTGGATTTTGTTCATGTATCTCT 59.935 37.037 0.00 0.00 41.67 3.10
289 332 7.621428 ACTGGATTTTGTTCATGTATCTCTG 57.379 36.000 0.00 0.00 0.00 3.35
290 333 7.170965 ACTGGATTTTGTTCATGTATCTCTGT 58.829 34.615 0.00 0.00 0.00 3.41
291 334 7.335422 ACTGGATTTTGTTCATGTATCTCTGTC 59.665 37.037 0.00 0.00 0.00 3.51
294 337 6.466308 TTTTGTTCATGTATCTCTGTCGTG 57.534 37.500 0.00 0.00 0.00 4.35
308 354 0.719465 GTCGTGTAATCTTGCACCGG 59.281 55.000 0.00 0.00 40.12 5.28
310 356 1.001068 TCGTGTAATCTTGCACCGGAA 59.999 47.619 9.46 0.00 40.12 4.30
315 361 3.689161 TGTAATCTTGCACCGGAAATCAG 59.311 43.478 9.46 0.00 0.00 2.90
317 363 1.808411 TCTTGCACCGGAAATCAGTC 58.192 50.000 9.46 0.00 0.00 3.51
324 370 1.202842 ACCGGAAATCAGTCGGGTTTT 60.203 47.619 9.46 0.00 46.02 2.43
326 372 2.095415 CCGGAAATCAGTCGGGTTTTTC 60.095 50.000 0.00 0.00 40.07 2.29
337 383 2.134346 CGGGTTTTTCGTTTAGTCGGA 58.866 47.619 0.00 0.00 0.00 4.55
340 386 4.530388 GGGTTTTTCGTTTAGTCGGAAAG 58.470 43.478 0.00 0.00 39.07 2.62
355 401 5.047306 AGTCGGAAAGTTCAGATCATGTGTA 60.047 40.000 0.00 0.00 34.10 2.90
357 403 6.313905 GTCGGAAAGTTCAGATCATGTGTAAT 59.686 38.462 0.00 0.00 34.10 1.89
359 405 6.536582 CGGAAAGTTCAGATCATGTGTAATCT 59.463 38.462 0.00 0.00 32.44 2.40
360 406 7.065085 CGGAAAGTTCAGATCATGTGTAATCTT 59.935 37.037 0.00 0.00 29.77 2.40
362 408 6.674694 AGTTCAGATCATGTGTAATCTTGC 57.325 37.500 0.00 0.00 29.77 4.01
363 409 6.175471 AGTTCAGATCATGTGTAATCTTGCA 58.825 36.000 0.00 0.00 29.77 4.08
365 411 4.877823 TCAGATCATGTGTAATCTTGCACC 59.122 41.667 8.38 0.00 42.16 5.01
368 414 1.468127 CATGTGTAATCTTGCACCGCA 59.532 47.619 8.38 0.00 42.16 5.69
369 415 1.598882 TGTGTAATCTTGCACCGCAA 58.401 45.000 8.38 0.92 46.80 4.85
379 643 2.180017 CACCGCAAATCAGCCAGC 59.820 61.111 0.00 0.00 0.00 4.85
383 647 1.154093 CGCAAATCAGCCAGCAGTG 60.154 57.895 0.00 0.00 0.00 3.66
392 656 3.288484 CCAGCAGTGAGGCTCGTA 58.712 61.111 10.42 0.00 43.68 3.43
393 657 1.819229 CCAGCAGTGAGGCTCGTAT 59.181 57.895 10.42 0.00 43.68 3.06
394 658 0.249238 CCAGCAGTGAGGCTCGTATC 60.249 60.000 10.42 0.57 43.68 2.24
395 659 0.593518 CAGCAGTGAGGCTCGTATCG 60.594 60.000 10.42 0.00 43.68 2.92
396 660 1.946650 GCAGTGAGGCTCGTATCGC 60.947 63.158 10.42 4.33 0.00 4.58
397 661 1.433471 CAGTGAGGCTCGTATCGCA 59.567 57.895 10.42 0.00 0.00 5.10
398 662 0.031314 CAGTGAGGCTCGTATCGCAT 59.969 55.000 10.42 0.00 0.00 4.73
399 663 0.031314 AGTGAGGCTCGTATCGCATG 59.969 55.000 10.42 0.00 0.00 4.06
400 664 0.941463 GTGAGGCTCGTATCGCATGG 60.941 60.000 10.42 0.00 0.00 3.66
401 665 1.373497 GAGGCTCGTATCGCATGGG 60.373 63.158 2.76 2.76 0.00 4.00
402 666 3.044305 GGCTCGTATCGCATGGGC 61.044 66.667 4.59 0.00 0.00 5.36
403 667 3.044305 GCTCGTATCGCATGGGCC 61.044 66.667 4.59 0.00 36.38 5.80
407 671 2.203153 GTATCGCATGGGCCCGTT 60.203 61.111 16.04 1.35 36.38 4.44
531 821 4.814294 ACGTGAGCCGCCGAATCC 62.814 66.667 0.00 0.00 41.42 3.01
533 823 4.467084 GTGAGCCGCCGAATCCCA 62.467 66.667 0.00 0.00 0.00 4.37
541 831 4.113815 CCGAATCCCAGCCAGCCA 62.114 66.667 0.00 0.00 0.00 4.75
603 894 3.839432 GGGCGAGGAGAGAACCCG 61.839 72.222 0.00 0.00 0.00 5.28
604 895 4.516195 GGCGAGGAGAGAACCCGC 62.516 72.222 0.00 0.00 43.41 6.13
745 1077 4.504916 CACAGCGAGCGAGGGGAG 62.505 72.222 0.00 0.00 0.00 4.30
751 1083 3.771160 GAGCGAGGGGAGCGGAAA 61.771 66.667 0.00 0.00 40.04 3.13
752 1084 3.724914 GAGCGAGGGGAGCGGAAAG 62.725 68.421 0.00 0.00 40.04 2.62
753 1085 3.771160 GCGAGGGGAGCGGAAAGA 61.771 66.667 0.00 0.00 0.00 2.52
756 1088 1.819905 GAGGGGAGCGGAAAGAGAG 59.180 63.158 0.00 0.00 0.00 3.20
762 1094 1.676006 GGAGCGGAAAGAGAGAGAGAG 59.324 57.143 0.00 0.00 0.00 3.20
885 1479 2.262915 CCGCCCGCAGATCTATCC 59.737 66.667 0.00 0.00 0.00 2.59
941 1613 4.157120 GATACCGCCCACCACGCT 62.157 66.667 0.00 0.00 0.00 5.07
1032 1707 1.599047 CTCTTGGACAGCCGTGGAT 59.401 57.895 0.00 0.00 36.79 3.41
1210 1897 1.032114 CCACCCATCTTTCCTTCGCC 61.032 60.000 0.00 0.00 0.00 5.54
1219 1906 0.177141 TTTCCTTCGCCTCCGTATGG 59.823 55.000 0.00 0.00 35.54 2.74
1227 1914 1.533469 GCCTCCGTATGGCCGTATCT 61.533 60.000 8.21 0.00 44.32 1.98
1228 1915 1.830279 CCTCCGTATGGCCGTATCTA 58.170 55.000 8.21 0.00 34.14 1.98
1229 1916 2.165167 CCTCCGTATGGCCGTATCTAA 58.835 52.381 8.21 0.00 34.14 2.10
1271 1958 1.475280 GCGTTTCCCTTACCCAATTCC 59.525 52.381 0.00 0.00 0.00 3.01
1272 1959 2.797786 CGTTTCCCTTACCCAATTCCA 58.202 47.619 0.00 0.00 0.00 3.53
1274 1961 4.528920 CGTTTCCCTTACCCAATTCCATA 58.471 43.478 0.00 0.00 0.00 2.74
1275 1962 5.137551 CGTTTCCCTTACCCAATTCCATAT 58.862 41.667 0.00 0.00 0.00 1.78
1456 2143 2.040947 CTCCCTCCTCTTCTTTTGCCTT 59.959 50.000 0.00 0.00 0.00 4.35
1476 2163 5.358090 CCTTTTACCGGATAGACTTCTTCC 58.642 45.833 9.46 0.00 0.00 3.46
1525 2212 2.487265 GGGTCCTGAGTTCTGCTTTGAA 60.487 50.000 0.00 0.00 0.00 2.69
1526 2213 3.416156 GGTCCTGAGTTCTGCTTTGAAT 58.584 45.455 0.00 0.00 0.00 2.57
1527 2214 3.438434 GGTCCTGAGTTCTGCTTTGAATC 59.562 47.826 0.00 0.00 0.00 2.52
1656 2343 3.088194 CATTTCCATGCCATCTTTCGG 57.912 47.619 0.00 0.00 0.00 4.30
1664 2351 1.982073 GCCATCTTTCGGCCGACAAG 61.982 60.000 31.19 29.72 44.22 3.16
1679 2366 2.061773 GACAAGTGTCAGTGTGATCCG 58.938 52.381 6.57 0.00 44.18 4.18
1702 2389 5.926542 CGTCTCAATTCTGGTCTTTTGTCTA 59.073 40.000 0.00 0.00 0.00 2.59
1706 2393 6.601332 TCAATTCTGGTCTTTTGTCTACCTT 58.399 36.000 0.00 0.00 34.23 3.50
1748 2435 2.093553 GCATTGAGAGAGAAGTCTGGCT 60.094 50.000 0.00 0.00 30.97 4.75
1758 2445 1.846712 AAGTCTGGCTTGGCTCCTCC 61.847 60.000 0.00 0.00 35.80 4.30
1759 2446 2.203983 TCTGGCTTGGCTCCTCCA 60.204 61.111 0.00 0.00 44.85 3.86
1795 2482 3.280197 TCTGCTGCCAATGTATGCTTA 57.720 42.857 0.00 0.00 0.00 3.09
1835 2522 5.371526 CTTTGCATCTATCCATGTGGTACT 58.628 41.667 0.00 0.00 36.34 2.73
1862 2549 5.874810 TGAACAATGTAGTTCCTGACTATGC 59.125 40.000 4.58 0.00 45.62 3.14
1884 2571 4.240096 CTGTTCCTTGTTCCATTTGATGC 58.760 43.478 0.00 0.00 0.00 3.91
1926 2613 2.111384 AGACGATGATAAGCTGGGTGT 58.889 47.619 0.00 0.00 0.00 4.16
2068 2755 4.148838 TGGCTTGCTGTATGGTTTTAGTT 58.851 39.130 0.00 0.00 0.00 2.24
2088 2775 1.080569 CATTTTGTCGTGCCAGGCC 60.081 57.895 9.64 0.00 0.00 5.19
2329 3016 2.108250 CAAAGTTCCTCCTTGGGGAAGA 59.892 50.000 0.00 0.00 42.63 2.87
2345 3032 2.355209 GGAAGACCATGAGGAGTCCAAC 60.355 54.545 12.86 5.68 38.69 3.77
2414 3101 7.539022 CAGCTGTATTAGTATGAGTACCAATCG 59.461 40.741 5.25 0.00 0.00 3.34
2568 3255 0.755079 AGTCTGTCAGCTGCACTCAA 59.245 50.000 9.47 0.00 0.00 3.02
2569 3256 1.139654 AGTCTGTCAGCTGCACTCAAA 59.860 47.619 9.47 0.00 0.00 2.69
2570 3257 2.149578 GTCTGTCAGCTGCACTCAAAT 58.850 47.619 9.47 0.00 0.00 2.32
2571 3258 2.095869 GTCTGTCAGCTGCACTCAAATG 60.096 50.000 9.47 0.00 0.00 2.32
2572 3259 2.148768 CTGTCAGCTGCACTCAAATGA 58.851 47.619 9.47 0.00 0.00 2.57
2573 3260 2.747989 CTGTCAGCTGCACTCAAATGAT 59.252 45.455 9.47 0.00 0.00 2.45
2574 3261 3.937079 CTGTCAGCTGCACTCAAATGATA 59.063 43.478 9.47 0.00 0.00 2.15
2575 3262 4.325972 TGTCAGCTGCACTCAAATGATAA 58.674 39.130 9.47 0.00 0.00 1.75
2576 3263 4.393990 TGTCAGCTGCACTCAAATGATAAG 59.606 41.667 9.47 0.00 0.00 1.73
2577 3264 3.376234 TCAGCTGCACTCAAATGATAAGC 59.624 43.478 9.47 0.00 0.00 3.09
2578 3265 2.353889 AGCTGCACTCAAATGATAAGCG 59.646 45.455 1.02 0.00 0.00 4.68
2579 3266 2.352651 GCTGCACTCAAATGATAAGCGA 59.647 45.455 0.00 0.00 0.00 4.93
2580 3267 3.786818 GCTGCACTCAAATGATAAGCGAC 60.787 47.826 0.00 0.00 0.00 5.19
2581 3268 2.348362 TGCACTCAAATGATAAGCGACG 59.652 45.455 0.00 0.00 0.00 5.12
2582 3269 2.348666 GCACTCAAATGATAAGCGACGT 59.651 45.455 0.00 0.00 0.00 4.34
2583 3270 3.181520 GCACTCAAATGATAAGCGACGTT 60.182 43.478 0.00 0.00 0.00 3.99
2584 3271 4.569029 CACTCAAATGATAAGCGACGTTC 58.431 43.478 0.00 0.00 0.00 3.95
2585 3272 3.617263 ACTCAAATGATAAGCGACGTTCC 59.383 43.478 0.00 0.00 0.00 3.62
2586 3273 3.857052 TCAAATGATAAGCGACGTTCCT 58.143 40.909 0.00 0.00 0.00 3.36
2587 3274 3.616821 TCAAATGATAAGCGACGTTCCTG 59.383 43.478 0.00 0.00 0.00 3.86
2588 3275 3.520290 AATGATAAGCGACGTTCCTGA 57.480 42.857 0.00 0.00 0.00 3.86
2589 3276 3.520290 ATGATAAGCGACGTTCCTGAA 57.480 42.857 0.00 0.00 0.00 3.02
2590 3277 3.520290 TGATAAGCGACGTTCCTGAAT 57.480 42.857 0.00 0.00 0.00 2.57
2591 3278 3.444916 TGATAAGCGACGTTCCTGAATC 58.555 45.455 0.00 0.00 0.00 2.52
2592 3279 3.130516 TGATAAGCGACGTTCCTGAATCT 59.869 43.478 0.00 0.00 0.00 2.40
2593 3280 1.714794 AAGCGACGTTCCTGAATCTG 58.285 50.000 0.00 0.00 0.00 2.90
2594 3281 0.603569 AGCGACGTTCCTGAATCTGT 59.396 50.000 0.00 0.00 0.00 3.41
2595 3282 1.000955 AGCGACGTTCCTGAATCTGTT 59.999 47.619 0.00 0.00 0.00 3.16
2596 3283 1.390463 GCGACGTTCCTGAATCTGTTC 59.610 52.381 0.00 0.00 34.85 3.18
2597 3284 1.993370 CGACGTTCCTGAATCTGTTCC 59.007 52.381 0.00 0.00 33.26 3.62
2598 3285 2.352814 CGACGTTCCTGAATCTGTTCCT 60.353 50.000 0.00 0.00 33.26 3.36
2599 3286 2.996621 GACGTTCCTGAATCTGTTCCTG 59.003 50.000 0.00 0.00 33.26 3.86
2600 3287 2.632996 ACGTTCCTGAATCTGTTCCTGA 59.367 45.455 0.00 0.00 33.26 3.86
2601 3288 3.071023 ACGTTCCTGAATCTGTTCCTGAA 59.929 43.478 0.00 0.00 33.26 3.02
2602 3289 4.256920 CGTTCCTGAATCTGTTCCTGAAT 58.743 43.478 0.00 0.00 33.26 2.57
2603 3290 5.046591 ACGTTCCTGAATCTGTTCCTGAATA 60.047 40.000 0.00 0.00 33.26 1.75
2604 3291 5.292101 CGTTCCTGAATCTGTTCCTGAATAC 59.708 44.000 0.00 0.00 33.26 1.89
2605 3292 6.173339 GTTCCTGAATCTGTTCCTGAATACA 58.827 40.000 0.00 0.00 33.26 2.29
2606 3293 6.566079 TCCTGAATCTGTTCCTGAATACAT 57.434 37.500 0.00 0.00 33.26 2.29
2607 3294 7.675161 TCCTGAATCTGTTCCTGAATACATA 57.325 36.000 0.00 0.00 33.26 2.29
2608 3295 8.089625 TCCTGAATCTGTTCCTGAATACATAA 57.910 34.615 0.00 0.00 33.26 1.90
2609 3296 8.717717 TCCTGAATCTGTTCCTGAATACATAAT 58.282 33.333 0.00 0.00 33.26 1.28
2610 3297 8.781196 CCTGAATCTGTTCCTGAATACATAATG 58.219 37.037 0.00 0.00 33.26 1.90
2611 3298 9.334947 CTGAATCTGTTCCTGAATACATAATGT 57.665 33.333 0.00 0.00 33.26 2.71
2612 3299 9.685276 TGAATCTGTTCCTGAATACATAATGTT 57.315 29.630 0.00 0.00 33.26 2.71
2616 3303 9.952030 TCTGTTCCTGAATACATAATGTTACAA 57.048 29.630 0.00 0.00 0.00 2.41
2646 3333 3.242549 CTGATAAGTCTGTCAGCTGCA 57.757 47.619 9.47 9.73 34.48 4.41
2647 3334 2.928757 CTGATAAGTCTGTCAGCTGCAC 59.071 50.000 9.47 9.02 34.48 4.57
2648 3335 2.564504 TGATAAGTCTGTCAGCTGCACT 59.435 45.455 9.47 5.25 0.00 4.40
2649 3336 2.732412 TAAGTCTGTCAGCTGCACTC 57.268 50.000 9.47 4.61 0.00 3.51
2650 3337 0.755079 AAGTCTGTCAGCTGCACTCA 59.245 50.000 9.47 4.81 0.00 3.41
2651 3338 0.755079 AGTCTGTCAGCTGCACTCAA 59.245 50.000 9.47 0.00 0.00 3.02
2652 3339 1.139654 AGTCTGTCAGCTGCACTCAAA 59.860 47.619 9.47 0.00 0.00 2.69
2653 3340 2.149578 GTCTGTCAGCTGCACTCAAAT 58.850 47.619 9.47 0.00 0.00 2.32
2654 3341 2.095869 GTCTGTCAGCTGCACTCAAATG 60.096 50.000 9.47 0.00 0.00 2.32
2655 3342 0.594602 TGTCAGCTGCACTCAAATGC 59.405 50.000 9.47 0.00 46.32 3.56
2656 3343 0.879765 GTCAGCTGCACTCAAATGCT 59.120 50.000 9.47 0.00 46.28 3.79
2657 3344 3.401577 CAGCTGCACTCAAATGCTG 57.598 52.632 0.00 7.37 46.28 4.41
2658 3345 0.596577 CAGCTGCACTCAAATGCTGT 59.403 50.000 12.34 0.00 46.28 4.40
2659 3346 1.000607 CAGCTGCACTCAAATGCTGTT 60.001 47.619 12.34 0.00 46.28 3.16
2660 3347 1.000607 AGCTGCACTCAAATGCTGTTG 60.001 47.619 1.02 0.00 46.28 3.33
2661 3348 1.415374 CTGCACTCAAATGCTGTTGC 58.585 50.000 0.00 0.00 46.28 4.17
2678 3365 7.816945 GCTGTTGCAAAATAGATAATGTGTT 57.183 32.000 0.00 0.00 39.41 3.32
2679 3366 8.909708 GCTGTTGCAAAATAGATAATGTGTTA 57.090 30.769 0.00 0.00 39.41 2.41
2680 3367 9.520204 GCTGTTGCAAAATAGATAATGTGTTAT 57.480 29.630 0.00 0.00 39.41 1.89
2756 3443 9.503427 GTTATTTGCACCTAAATGATAAGTGAC 57.497 33.333 0.00 0.00 32.79 3.67
3017 3704 3.198068 GCGGTGCTGATATCTTGAAGAA 58.802 45.455 0.00 0.00 0.00 2.52
3019 3706 3.557595 CGGTGCTGATATCTTGAAGAACC 59.442 47.826 0.00 7.59 35.29 3.62
3120 3807 3.795688 AGAAAACAGGAGCCTGATGAA 57.204 42.857 22.62 0.00 46.30 2.57
3128 3815 6.252599 ACAGGAGCCTGATGAATGTAATAA 57.747 37.500 22.62 0.00 46.30 1.40
3129 3816 6.845908 ACAGGAGCCTGATGAATGTAATAAT 58.154 36.000 22.62 0.00 46.30 1.28
3130 3817 6.713903 ACAGGAGCCTGATGAATGTAATAATG 59.286 38.462 22.62 0.00 46.30 1.90
3131 3818 6.713903 CAGGAGCCTGATGAATGTAATAATGT 59.286 38.462 11.08 0.00 46.30 2.71
3132 3819 7.230108 CAGGAGCCTGATGAATGTAATAATGTT 59.770 37.037 11.08 0.00 46.30 2.71
3133 3820 7.230108 AGGAGCCTGATGAATGTAATAATGTTG 59.770 37.037 0.00 0.00 0.00 3.33
3134 3821 7.281040 AGCCTGATGAATGTAATAATGTTGG 57.719 36.000 0.00 0.00 0.00 3.77
3135 3822 7.062322 AGCCTGATGAATGTAATAATGTTGGA 58.938 34.615 0.00 0.00 0.00 3.53
3136 3823 7.013655 AGCCTGATGAATGTAATAATGTTGGAC 59.986 37.037 0.00 0.00 0.00 4.02
3137 3824 7.201812 GCCTGATGAATGTAATAATGTTGGACA 60.202 37.037 0.00 0.00 0.00 4.02
3138 3825 8.685427 CCTGATGAATGTAATAATGTTGGACAA 58.315 33.333 0.00 0.00 0.00 3.18
3142 3829 9.874205 ATGAATGTAATAATGTTGGACAAAAGG 57.126 29.630 0.00 0.00 0.00 3.11
3143 3830 7.816995 TGAATGTAATAATGTTGGACAAAAGGC 59.183 33.333 0.00 0.00 0.00 4.35
3144 3831 5.704888 TGTAATAATGTTGGACAAAAGGCG 58.295 37.500 0.00 0.00 0.00 5.52
3145 3832 5.473846 TGTAATAATGTTGGACAAAAGGCGA 59.526 36.000 0.00 0.00 0.00 5.54
3146 3833 5.659440 AATAATGTTGGACAAAAGGCGAT 57.341 34.783 0.00 0.00 0.00 4.58
3147 3834 5.659440 ATAATGTTGGACAAAAGGCGATT 57.341 34.783 0.00 0.00 0.00 3.34
3148 3835 2.791383 TGTTGGACAAAAGGCGATTG 57.209 45.000 4.14 4.14 0.00 2.67
3149 3836 1.269517 TGTTGGACAAAAGGCGATTGC 60.270 47.619 0.00 0.00 41.71 3.56
3171 3885 0.924823 ATGATTGGGAGAGCCTTGCT 59.075 50.000 0.00 0.00 43.88 3.91
3186 3900 2.749076 CCTTGCTGATTCATTTCGACCA 59.251 45.455 0.00 0.00 0.00 4.02
3308 4022 5.308014 TCACTTTGTCACTGCAGATGTTAT 58.692 37.500 23.35 0.00 0.00 1.89
3333 4047 8.842358 TTTTCTGATAGGAAAATACTTGTCGT 57.158 30.769 0.00 0.00 39.37 4.34
3352 4066 5.182950 TGTCGTTTGATTGTGCTGGAAATAT 59.817 36.000 0.00 0.00 0.00 1.28
3458 4172 7.019774 TGCTTCTTATTTGTCATGCATACTC 57.980 36.000 0.00 0.00 0.00 2.59
3468 4362 1.339291 CATGCATACTCGAGGAGCAGA 59.661 52.381 25.31 10.31 38.75 4.26
3544 4438 9.665719 TGAAACTAATCATGCTGTATTTGTAGA 57.334 29.630 0.00 0.00 0.00 2.59
3545 4439 9.922305 GAAACTAATCATGCTGTATTTGTAGAC 57.078 33.333 0.00 0.00 0.00 2.59
3546 4440 9.672673 AAACTAATCATGCTGTATTTGTAGACT 57.327 29.630 0.00 0.00 0.00 3.24
3547 4441 9.672673 AACTAATCATGCTGTATTTGTAGACTT 57.327 29.630 0.00 0.00 0.00 3.01
3548 4442 9.102757 ACTAATCATGCTGTATTTGTAGACTTG 57.897 33.333 0.00 0.00 0.00 3.16
3549 4443 7.928307 AATCATGCTGTATTTGTAGACTTGT 57.072 32.000 0.00 0.00 0.00 3.16
3551 4445 8.654230 ATCATGCTGTATTTGTAGACTTGTAG 57.346 34.615 0.00 0.00 0.00 2.74
3618 4512 8.982723 AGTTGGTACACTCATACTAGATTTCAT 58.017 33.333 0.00 0.00 39.29 2.57
3632 4526 5.707242 AGATTTCATGGCTGCTCATAATG 57.293 39.130 0.00 0.00 0.00 1.90
3642 4536 3.188048 GCTGCTCATAATGTGGTATCTGC 59.812 47.826 0.00 0.00 0.00 4.26
3676 4570 3.441572 TGGTGTTAGTTAGTAGACTCGGC 59.558 47.826 0.00 0.00 0.00 5.54
3691 4585 1.070758 CTCGGCCTATGCAAGTGGTAT 59.929 52.381 0.00 0.00 40.13 2.73
3703 4597 7.798596 ATGCAAGTGGTATTTCTCTGAATAG 57.201 36.000 0.00 0.00 0.00 1.73
3715 4609 2.932614 CTCTGAATAGTTTCCAGTGCGG 59.067 50.000 0.00 0.00 0.00 5.69
3726 4620 1.699656 CCAGTGCGGAAGAAGATGCG 61.700 60.000 0.00 0.00 36.56 4.73
3788 4682 7.751732 TGATTTTGGAAATCATGTTAGACTCG 58.248 34.615 11.02 0.00 32.21 4.18
3930 4833 4.020307 TCCATCAATTACAGAGCACTGACA 60.020 41.667 18.54 3.91 46.03 3.58
4003 4906 3.130340 GGTTCTGTTGCTTGAACTTCCAA 59.870 43.478 0.00 0.00 41.42 3.53
4306 5214 6.676189 AGAAGAAGAGGGGAAACAGATAGATT 59.324 38.462 0.00 0.00 0.00 2.40
4350 5258 7.936496 TGTATTTACTCAATGCAGGAAATCA 57.064 32.000 6.28 3.92 37.91 2.57
4378 5286 5.531287 GGCTTTTCTAGTCCAAAAAGAGTGA 59.469 40.000 15.12 0.00 42.44 3.41
4435 5344 4.067896 ACTGTTCATTCTTGCACCTACAG 58.932 43.478 0.00 0.00 38.12 2.74
4470 5379 6.372659 CCTCTGCATTCTAAAGCTTCTGTTTA 59.627 38.462 0.00 0.00 0.00 2.01
4483 5392 4.330074 GCTTCTGTTTAGCGCATCTCTTTA 59.670 41.667 11.47 0.00 0.00 1.85
4534 5444 1.899814 TGTTCGCCAGAGTTGTATCCT 59.100 47.619 0.00 0.00 0.00 3.24
4626 5536 3.541632 CAACCAAGCCGTACAAGGATAT 58.458 45.455 0.00 0.00 0.00 1.63
4630 5540 3.531538 CAAGCCGTACAAGGATATGTGT 58.468 45.455 0.00 0.00 34.75 3.72
4669 5579 0.661020 ACACGCCCAAAAGAAACGAG 59.339 50.000 0.00 0.00 0.00 4.18
4677 5587 4.036380 GCCCAAAAGAAACGAGAGAGAAAA 59.964 41.667 0.00 0.00 0.00 2.29
5015 5925 1.228245 CCACCAGACCAACCACCAG 60.228 63.158 0.00 0.00 0.00 4.00
5067 5977 3.220658 TCTCACCACGACACCGCA 61.221 61.111 0.00 0.00 39.95 5.69
5081 5991 1.157870 ACCGCAAAGTGAGGACAACG 61.158 55.000 4.95 0.00 39.92 4.10
5098 6008 1.517257 CGCGGCGAAGAATCAGAGT 60.517 57.895 19.16 0.00 0.00 3.24
5159 6069 3.680786 CCTCCACCGTCAGCGACA 61.681 66.667 8.91 0.00 41.33 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.467844 AACACACAATCAGCCAGCCA 60.468 50.000 0.00 0.00 0.00 4.75
1 2 0.242017 GAACACACAATCAGCCAGCC 59.758 55.000 0.00 0.00 0.00 4.85
6 7 1.798223 TGCTACGAACACACAATCAGC 59.202 47.619 0.00 0.00 0.00 4.26
7 8 3.059884 ACTGCTACGAACACACAATCAG 58.940 45.455 0.00 0.00 0.00 2.90
8 9 2.799978 CACTGCTACGAACACACAATCA 59.200 45.455 0.00 0.00 0.00 2.57
9 10 2.800544 ACACTGCTACGAACACACAATC 59.199 45.455 0.00 0.00 0.00 2.67
10 11 2.543848 CACACTGCTACGAACACACAAT 59.456 45.455 0.00 0.00 0.00 2.71
11 12 1.930503 CACACTGCTACGAACACACAA 59.069 47.619 0.00 0.00 0.00 3.33
12 13 1.135333 TCACACTGCTACGAACACACA 59.865 47.619 0.00 0.00 0.00 3.72
13 14 1.787155 CTCACACTGCTACGAACACAC 59.213 52.381 0.00 0.00 0.00 3.82
14 15 1.269569 CCTCACACTGCTACGAACACA 60.270 52.381 0.00 0.00 0.00 3.72
15 16 1.000607 TCCTCACACTGCTACGAACAC 60.001 52.381 0.00 0.00 0.00 3.32
23 24 0.831288 AGTCTGCTCCTCACACTGCT 60.831 55.000 0.00 0.00 0.00 4.24
61 62 4.516195 GAGCGCCCCTCGAGGAAC 62.516 72.222 33.39 21.70 41.67 3.62
94 101 4.296690 GAATGCTTCAAGCCTATGAATGC 58.703 43.478 7.01 5.34 41.51 3.56
107 114 2.743664 CACATCCAAGACGAATGCTTCA 59.256 45.455 0.00 0.00 0.00 3.02
139 146 4.511527 TCATGCTTCAAGCCTAAGAAGAG 58.488 43.478 7.01 1.47 42.95 2.85
180 216 5.411669 GGTTGGAGGATTTTATATACAGCGG 59.588 44.000 0.00 0.00 0.00 5.52
194 230 1.366435 ACAGTAGAGGGGTTGGAGGAT 59.634 52.381 0.00 0.00 0.00 3.24
212 255 0.737367 CGCGAGGCTTCATCTTCACA 60.737 55.000 0.00 0.00 0.00 3.58
246 289 1.754380 TTCGTGGCTGTAGCTGTGGT 61.754 55.000 0.00 0.00 41.70 4.16
247 290 1.005037 TTCGTGGCTGTAGCTGTGG 60.005 57.895 0.00 0.00 41.70 4.17
248 291 0.319900 AGTTCGTGGCTGTAGCTGTG 60.320 55.000 0.00 0.00 41.70 3.66
249 292 0.319900 CAGTTCGTGGCTGTAGCTGT 60.320 55.000 0.00 0.00 41.70 4.40
250 293 1.016130 CCAGTTCGTGGCTGTAGCTG 61.016 60.000 0.00 0.00 40.39 4.24
251 294 1.293498 CCAGTTCGTGGCTGTAGCT 59.707 57.895 3.63 0.00 40.39 3.32
252 295 3.876300 CCAGTTCGTGGCTGTAGC 58.124 61.111 0.00 0.00 40.39 3.58
285 328 2.668457 GGTGCAAGATTACACGACAGAG 59.332 50.000 0.00 0.00 37.68 3.35
286 329 2.683968 GGTGCAAGATTACACGACAGA 58.316 47.619 0.00 0.00 37.68 3.41
287 330 1.390123 CGGTGCAAGATTACACGACAG 59.610 52.381 0.00 0.00 37.68 3.51
288 331 1.424403 CGGTGCAAGATTACACGACA 58.576 50.000 0.00 0.00 37.68 4.35
289 332 0.719465 CCGGTGCAAGATTACACGAC 59.281 55.000 0.00 0.00 37.68 4.34
290 333 0.604073 TCCGGTGCAAGATTACACGA 59.396 50.000 0.00 0.00 37.68 4.35
291 334 1.434555 TTCCGGTGCAAGATTACACG 58.565 50.000 0.00 0.00 37.68 4.49
294 337 3.689649 ACTGATTTCCGGTGCAAGATTAC 59.310 43.478 0.00 0.00 31.94 1.89
308 354 3.891056 ACGAAAAACCCGACTGATTTC 57.109 42.857 0.00 0.00 0.00 2.17
310 356 4.818005 ACTAAACGAAAAACCCGACTGATT 59.182 37.500 0.00 0.00 0.00 2.57
315 361 2.096762 CCGACTAAACGAAAAACCCGAC 60.097 50.000 0.00 0.00 35.09 4.79
317 363 2.134346 TCCGACTAAACGAAAAACCCG 58.866 47.619 0.00 0.00 35.09 5.28
320 366 6.250089 TGAACTTTCCGACTAAACGAAAAAC 58.750 36.000 0.00 0.00 35.09 2.43
324 370 4.935702 TCTGAACTTTCCGACTAAACGAA 58.064 39.130 0.00 0.00 35.09 3.85
326 372 4.921515 TGATCTGAACTTTCCGACTAAACG 59.078 41.667 0.00 0.00 0.00 3.60
337 383 7.175467 TGCAAGATTACACATGATCTGAACTTT 59.825 33.333 0.00 0.00 31.75 2.66
340 386 6.253746 GTGCAAGATTACACATGATCTGAAC 58.746 40.000 0.00 0.00 36.77 3.18
360 406 2.596923 TGGCTGATTTGCGGTGCA 60.597 55.556 0.00 0.00 36.47 4.57
362 408 2.180017 GCTGGCTGATTTGCGGTG 59.820 61.111 0.00 0.00 0.00 4.94
363 409 2.282391 TGCTGGCTGATTTGCGGT 60.282 55.556 0.00 0.00 0.00 5.68
365 411 1.154093 CACTGCTGGCTGATTTGCG 60.154 57.895 6.47 0.00 0.00 4.85
368 414 0.964358 GCCTCACTGCTGGCTGATTT 60.964 55.000 6.47 0.00 45.26 2.17
369 415 1.378250 GCCTCACTGCTGGCTGATT 60.378 57.895 6.47 0.00 45.26 2.57
370 416 2.271497 GCCTCACTGCTGGCTGAT 59.729 61.111 6.47 0.00 45.26 2.90
375 639 0.249238 GATACGAGCCTCACTGCTGG 60.249 60.000 0.00 0.00 42.95 4.85
379 643 0.031314 ATGCGATACGAGCCTCACTG 59.969 55.000 0.00 0.00 0.00 3.66
383 647 1.373497 CCCATGCGATACGAGCCTC 60.373 63.158 0.00 0.00 0.00 4.70
396 660 3.131478 GTTCCGAACGGGCCCATG 61.131 66.667 24.92 9.21 34.94 3.66
397 661 3.642503 TGTTCCGAACGGGCCCAT 61.643 61.111 24.92 10.28 34.94 4.00
398 662 4.629523 GTGTTCCGAACGGGCCCA 62.630 66.667 24.92 0.00 34.94 5.36
400 664 4.668118 TCGTGTTCCGAACGGGCC 62.668 66.667 13.29 0.00 44.03 5.80
429 693 1.438562 CGCGGAATCATGTGATGGCA 61.439 55.000 0.00 0.00 34.49 4.92
431 695 1.944035 CCGCGGAATCATGTGATGG 59.056 57.895 24.07 0.00 34.49 3.51
432 696 1.280746 GCCGCGGAATCATGTGATG 59.719 57.895 33.48 0.00 34.49 3.07
433 697 1.153188 TGCCGCGGAATCATGTGAT 60.153 52.632 33.48 0.00 36.07 3.06
434 698 2.106074 GTGCCGCGGAATCATGTGA 61.106 57.895 33.48 0.00 0.00 3.58
435 699 2.404789 GTGCCGCGGAATCATGTG 59.595 61.111 33.48 0.00 0.00 3.21
466 741 4.821589 CTGGACGCGCCTTCCCTC 62.822 72.222 17.84 1.88 37.63 4.30
513 803 3.554692 GATTCGGCGGCTCACGTG 61.555 66.667 9.94 9.94 46.52 4.49
531 821 4.729856 GCGCTTTTGGCTGGCTGG 62.730 66.667 0.00 0.00 39.13 4.85
533 823 3.982241 GTGCGCTTTTGGCTGGCT 61.982 61.111 9.73 0.00 39.13 4.75
559 849 1.758514 TCCGATCTGGGTCTCAGCC 60.759 63.158 0.00 0.00 43.06 4.85
560 850 1.439644 GTCCGATCTGGGTCTCAGC 59.560 63.158 0.00 0.00 43.06 4.26
561 851 1.729470 CCGTCCGATCTGGGTCTCAG 61.729 65.000 0.00 0.00 44.68 3.35
562 852 1.753078 CCGTCCGATCTGGGTCTCA 60.753 63.158 4.16 0.00 38.76 3.27
588 879 4.516195 GGCGGGTTCTCTCCTCGC 62.516 72.222 0.00 0.00 42.17 5.03
684 1011 4.465446 TAGAGAGGGCGGCTGGCT 62.465 66.667 19.72 4.84 42.94 4.75
685 1012 4.228567 GTAGAGAGGGCGGCTGGC 62.229 72.222 11.40 11.40 42.51 4.85
686 1013 3.541713 GGTAGAGAGGGCGGCTGG 61.542 72.222 9.56 0.00 0.00 4.85
687 1014 3.541713 GGGTAGAGAGGGCGGCTG 61.542 72.222 9.56 0.00 0.00 4.85
739 1071 0.686112 CTCTCTCTTTCCGCTCCCCT 60.686 60.000 0.00 0.00 0.00 4.79
740 1072 0.684805 TCTCTCTCTTTCCGCTCCCC 60.685 60.000 0.00 0.00 0.00 4.81
741 1073 0.744281 CTCTCTCTCTTTCCGCTCCC 59.256 60.000 0.00 0.00 0.00 4.30
742 1074 1.676006 CTCTCTCTCTCTTTCCGCTCC 59.324 57.143 0.00 0.00 0.00 4.70
744 1076 2.799126 TCTCTCTCTCTCTTTCCGCT 57.201 50.000 0.00 0.00 0.00 5.52
745 1077 4.385358 AATTCTCTCTCTCTCTTTCCGC 57.615 45.455 0.00 0.00 0.00 5.54
746 1078 5.960113 TGAAATTCTCTCTCTCTCTTTCCG 58.040 41.667 0.00 0.00 0.00 4.30
747 1079 8.614469 TTTTGAAATTCTCTCTCTCTCTTTCC 57.386 34.615 0.00 0.00 0.00 3.13
748 1080 8.229811 GCTTTTGAAATTCTCTCTCTCTCTTTC 58.770 37.037 0.00 0.00 0.00 2.62
749 1081 7.095271 CGCTTTTGAAATTCTCTCTCTCTCTTT 60.095 37.037 0.00 0.00 0.00 2.52
750 1082 6.368516 CGCTTTTGAAATTCTCTCTCTCTCTT 59.631 38.462 0.00 0.00 0.00 2.85
751 1083 5.868801 CGCTTTTGAAATTCTCTCTCTCTCT 59.131 40.000 0.00 0.00 0.00 3.10
752 1084 5.063312 CCGCTTTTGAAATTCTCTCTCTCTC 59.937 44.000 0.00 0.00 0.00 3.20
753 1085 4.934602 CCGCTTTTGAAATTCTCTCTCTCT 59.065 41.667 0.00 0.00 0.00 3.10
756 1088 3.127721 CCCCGCTTTTGAAATTCTCTCTC 59.872 47.826 0.00 0.00 0.00 3.20
866 1198 3.941657 GATAGATCTGCGGGCGGGC 62.942 68.421 5.18 0.00 0.00 6.13
867 1199 2.262915 GATAGATCTGCGGGCGGG 59.737 66.667 5.18 0.00 0.00 6.13
868 1200 2.262915 GGATAGATCTGCGGGCGG 59.737 66.667 5.18 0.00 0.00 6.13
869 1201 2.126307 CGGATAGATCTGCGGGCG 60.126 66.667 5.18 0.00 0.00 6.13
870 1202 1.080434 GACGGATAGATCTGCGGGC 60.080 63.158 5.18 0.17 36.64 6.13
871 1203 1.822506 TAGACGGATAGATCTGCGGG 58.177 55.000 5.18 0.00 36.64 6.13
872 1204 5.759506 ATTATAGACGGATAGATCTGCGG 57.240 43.478 5.18 4.58 36.64 5.69
873 1205 6.846786 CGTTATTATAGACGGATAGATCTGCG 59.153 42.308 5.18 0.00 36.64 5.18
874 1206 6.633634 GCGTTATTATAGACGGATAGATCTGC 59.366 42.308 5.18 0.00 39.52 4.26
875 1207 7.133513 GGCGTTATTATAGACGGATAGATCTG 58.866 42.308 5.18 0.00 39.52 2.90
876 1208 6.018098 CGGCGTTATTATAGACGGATAGATCT 60.018 42.308 0.00 0.00 39.52 2.75
877 1209 6.134730 CGGCGTTATTATAGACGGATAGATC 58.865 44.000 0.00 0.00 39.52 2.75
878 1210 5.505324 GCGGCGTTATTATAGACGGATAGAT 60.505 44.000 9.37 0.00 39.52 1.98
879 1211 4.201851 GCGGCGTTATTATAGACGGATAGA 60.202 45.833 9.37 0.00 39.52 1.98
880 1212 4.033684 GCGGCGTTATTATAGACGGATAG 58.966 47.826 9.37 0.00 39.52 2.08
885 1479 1.640915 GTCGCGGCGTTATTATAGACG 59.359 52.381 22.90 0.00 41.89 4.18
952 1624 1.818785 GCAGAGGCAGGATCTGTGC 60.819 63.158 11.00 11.00 44.92 4.57
1210 1897 3.181489 GGATTAGATACGGCCATACGGAG 60.181 52.174 2.24 0.00 38.39 4.63
1219 1906 1.014564 GCGCCAGGATTAGATACGGC 61.015 60.000 0.00 0.00 36.16 5.68
1227 1914 4.215742 CCGGACGCGCCAGGATTA 62.216 66.667 5.51 0.00 35.94 1.75
1271 1958 0.316442 CAGCAAAGGCACGCGATATG 60.316 55.000 15.93 0.69 44.61 1.78
1272 1959 2.016961 CAGCAAAGGCACGCGATAT 58.983 52.632 15.93 0.00 44.61 1.63
1274 1961 4.107051 GCAGCAAAGGCACGCGAT 62.107 61.111 15.93 0.00 44.61 4.58
1321 2008 2.284625 AGCCCGATGGACTCCACA 60.285 61.111 0.00 0.00 35.80 4.17
1456 2143 6.430007 ACTAGGAAGAAGTCTATCCGGTAAA 58.570 40.000 0.00 0.00 38.31 2.01
1525 2212 1.135094 ACTCGCAGGGGATTGATGAT 58.865 50.000 0.00 0.00 0.00 2.45
1526 2213 1.688735 CTACTCGCAGGGGATTGATGA 59.311 52.381 0.00 0.00 0.00 2.92
1527 2214 1.688735 TCTACTCGCAGGGGATTGATG 59.311 52.381 0.00 0.00 0.00 3.07
1647 2334 0.443869 CACTTGTCGGCCGAAAGATG 59.556 55.000 35.52 28.13 0.00 2.90
1651 2338 4.036977 GACACTTGTCGGCCGAAA 57.963 55.556 32.93 24.77 35.12 3.46
1664 2351 1.269723 TGAGACGGATCACACTGACAC 59.730 52.381 0.00 0.00 0.00 3.67
1679 2366 6.147985 GGTAGACAAAAGACCAGAATTGAGAC 59.852 42.308 0.00 0.00 33.16 3.36
1702 2389 5.435291 CTCTCCTGATGAGCAAATAAAGGT 58.565 41.667 0.00 0.00 41.18 3.50
1706 2393 3.434167 GCCCTCTCCTGATGAGCAAATAA 60.434 47.826 0.00 0.00 41.18 1.40
1758 2445 1.112315 AGATAGCTCCTCTGCCGGTG 61.112 60.000 1.90 0.00 0.00 4.94
1759 2446 1.112315 CAGATAGCTCCTCTGCCGGT 61.112 60.000 11.95 0.00 34.24 5.28
1795 2482 3.005155 GCAAAGGAAAGATGCAGACAACT 59.995 43.478 0.00 0.00 39.81 3.16
1835 2522 4.102524 AGTCAGGAACTACATTGTTCACCA 59.897 41.667 9.18 0.00 45.74 4.17
1884 2571 4.028852 TCGTCATCGGACATCTTTACAG 57.971 45.455 0.00 0.00 44.54 2.74
2068 2755 0.313672 GCCTGGCACGACAAAATGAA 59.686 50.000 15.17 0.00 0.00 2.57
2088 2775 8.870160 TGAAAATGTGACAACCAAAATTCTAG 57.130 30.769 0.00 0.00 0.00 2.43
2329 3016 2.238144 CTCATGTTGGACTCCTCATGGT 59.762 50.000 22.06 0.00 37.26 3.55
2405 3092 8.448615 ACTATTAGCTTTTGTTTCGATTGGTAC 58.551 33.333 0.00 0.00 0.00 3.34
2568 3255 3.520290 TCAGGAACGTCGCTTATCATT 57.480 42.857 0.00 0.00 0.00 2.57
2569 3256 3.520290 TTCAGGAACGTCGCTTATCAT 57.480 42.857 0.00 0.00 0.00 2.45
2570 3257 3.130516 AGATTCAGGAACGTCGCTTATCA 59.869 43.478 0.00 0.00 0.00 2.15
2571 3258 3.487574 CAGATTCAGGAACGTCGCTTATC 59.512 47.826 0.00 0.00 0.00 1.75
2572 3259 3.119101 ACAGATTCAGGAACGTCGCTTAT 60.119 43.478 0.00 0.00 0.00 1.73
2573 3260 2.230508 ACAGATTCAGGAACGTCGCTTA 59.769 45.455 0.00 0.00 0.00 3.09
2574 3261 1.000955 ACAGATTCAGGAACGTCGCTT 59.999 47.619 0.00 0.00 0.00 4.68
2575 3262 0.603569 ACAGATTCAGGAACGTCGCT 59.396 50.000 0.00 0.00 0.00 4.93
2576 3263 1.390463 GAACAGATTCAGGAACGTCGC 59.610 52.381 0.00 0.00 34.70 5.19
2577 3264 1.993370 GGAACAGATTCAGGAACGTCG 59.007 52.381 0.00 0.00 36.46 5.12
2578 3265 2.996621 CAGGAACAGATTCAGGAACGTC 59.003 50.000 0.00 0.00 36.46 4.34
2579 3266 2.632996 TCAGGAACAGATTCAGGAACGT 59.367 45.455 0.00 0.00 36.46 3.99
2580 3267 3.319137 TCAGGAACAGATTCAGGAACG 57.681 47.619 0.00 0.00 36.46 3.95
2581 3268 6.173339 TGTATTCAGGAACAGATTCAGGAAC 58.827 40.000 0.00 0.00 36.46 3.62
2582 3269 6.373005 TGTATTCAGGAACAGATTCAGGAA 57.627 37.500 0.00 0.00 36.46 3.36
2583 3270 6.566079 ATGTATTCAGGAACAGATTCAGGA 57.434 37.500 0.00 0.00 36.46 3.86
2584 3271 8.781196 CATTATGTATTCAGGAACAGATTCAGG 58.219 37.037 0.00 0.00 36.46 3.86
2585 3272 9.334947 ACATTATGTATTCAGGAACAGATTCAG 57.665 33.333 0.00 0.00 36.46 3.02
2586 3273 9.685276 AACATTATGTATTCAGGAACAGATTCA 57.315 29.630 0.00 0.00 36.46 2.57
2590 3277 9.952030 TTGTAACATTATGTATTCAGGAACAGA 57.048 29.630 0.00 0.00 0.00 3.41
2626 3313 2.928757 GTGCAGCTGACAGACTTATCAG 59.071 50.000 20.43 8.57 44.37 2.90
2627 3314 2.564504 AGTGCAGCTGACAGACTTATCA 59.435 45.455 20.43 0.00 0.00 2.15
2628 3315 3.186119 GAGTGCAGCTGACAGACTTATC 58.814 50.000 20.43 1.57 0.00 1.75
2629 3316 2.564504 TGAGTGCAGCTGACAGACTTAT 59.435 45.455 20.43 0.00 0.00 1.73
2630 3317 1.963515 TGAGTGCAGCTGACAGACTTA 59.036 47.619 20.43 6.93 0.00 2.24
2631 3318 0.755079 TGAGTGCAGCTGACAGACTT 59.245 50.000 20.43 1.48 0.00 3.01
2632 3319 0.755079 TTGAGTGCAGCTGACAGACT 59.245 50.000 20.43 12.65 0.00 3.24
2633 3320 1.586422 TTTGAGTGCAGCTGACAGAC 58.414 50.000 20.43 7.69 0.00 3.51
2634 3321 2.148768 CATTTGAGTGCAGCTGACAGA 58.851 47.619 20.43 7.08 0.00 3.41
2635 3322 1.401148 GCATTTGAGTGCAGCTGACAG 60.401 52.381 20.43 0.00 44.43 3.51
2636 3323 0.594602 GCATTTGAGTGCAGCTGACA 59.405 50.000 20.43 12.49 44.43 3.58
2637 3324 3.396491 GCATTTGAGTGCAGCTGAC 57.604 52.632 20.43 12.84 44.43 3.51
2644 3331 1.855513 TTGCAACAGCATTTGAGTGC 58.144 45.000 0.00 0.00 45.38 4.40
2645 3332 5.921976 TCTATTTTGCAACAGCATTTGAGTG 59.078 36.000 0.00 0.00 38.23 3.51
2646 3333 6.088016 TCTATTTTGCAACAGCATTTGAGT 57.912 33.333 0.00 0.00 38.23 3.41
2647 3334 8.692110 TTATCTATTTTGCAACAGCATTTGAG 57.308 30.769 0.00 0.00 38.23 3.02
2648 3335 9.089601 CATTATCTATTTTGCAACAGCATTTGA 57.910 29.630 0.00 0.00 38.23 2.69
2649 3336 8.875803 ACATTATCTATTTTGCAACAGCATTTG 58.124 29.630 0.00 0.00 38.23 2.32
2650 3337 8.875803 CACATTATCTATTTTGCAACAGCATTT 58.124 29.630 0.00 0.00 38.23 2.32
2651 3338 8.036575 ACACATTATCTATTTTGCAACAGCATT 58.963 29.630 0.00 0.00 38.23 3.56
2652 3339 7.549839 ACACATTATCTATTTTGCAACAGCAT 58.450 30.769 0.00 0.00 38.23 3.79
2653 3340 6.923012 ACACATTATCTATTTTGCAACAGCA 58.077 32.000 0.00 0.00 36.26 4.41
2654 3341 7.816945 AACACATTATCTATTTTGCAACAGC 57.183 32.000 0.00 0.00 0.00 4.40
2683 3370 9.987272 GAGCTGCATGTATATATATACCAATGA 57.013 33.333 24.20 12.13 38.17 2.57
2684 3371 9.993454 AGAGCTGCATGTATATATATACCAATG 57.007 33.333 23.94 21.51 38.17 2.82
2686 3373 8.642432 GGAGAGCTGCATGTATATATATACCAA 58.358 37.037 23.94 11.45 38.17 3.67
2687 3374 8.007153 AGGAGAGCTGCATGTATATATATACCA 58.993 37.037 23.94 16.01 38.17 3.25
2688 3375 8.303156 CAGGAGAGCTGCATGTATATATATACC 58.697 40.741 23.94 13.05 38.17 2.73
2689 3376 7.812191 GCAGGAGAGCTGCATGTATATATATAC 59.188 40.741 21.34 21.34 46.19 1.47
2690 3377 7.890515 GCAGGAGAGCTGCATGTATATATATA 58.109 38.462 1.02 0.00 46.19 0.86
2691 3378 6.757237 GCAGGAGAGCTGCATGTATATATAT 58.243 40.000 1.02 0.00 46.19 0.86
2692 3379 6.154203 GCAGGAGAGCTGCATGTATATATA 57.846 41.667 1.02 0.00 46.19 0.86
2756 3443 5.641209 AGATTCAAGAACAGATTCAGGAACG 59.359 40.000 0.00 0.00 37.29 3.95
2856 3543 3.715495 TGCAACAATTGTGACACCATTC 58.285 40.909 12.82 0.00 0.00 2.67
2889 3576 5.355596 ACTCTCTTGTTTGACAGAGTCTTG 58.644 41.667 0.00 0.00 28.75 3.02
2953 3640 2.380064 TGGATTGTTGGTTCCAGCTT 57.620 45.000 7.17 0.00 37.10 3.74
3120 3807 6.151985 TCGCCTTTTGTCCAACATTATTACAT 59.848 34.615 0.00 0.00 0.00 2.29
3128 3815 2.610232 GCAATCGCCTTTTGTCCAACAT 60.610 45.455 0.00 0.00 0.00 2.71
3129 3816 1.269517 GCAATCGCCTTTTGTCCAACA 60.270 47.619 0.00 0.00 0.00 3.33
3130 3817 1.418373 GCAATCGCCTTTTGTCCAAC 58.582 50.000 0.00 0.00 0.00 3.77
3131 3818 3.883997 GCAATCGCCTTTTGTCCAA 57.116 47.368 0.00 0.00 0.00 3.53
3150 3837 4.672681 AGCAAGGCTCTCCCAATCATGG 62.673 54.545 0.00 0.00 39.85 3.66
3151 3838 1.030457 GCAAGGCTCTCCCAATCATG 58.970 55.000 0.00 0.00 35.39 3.07
3152 3839 0.924823 AGCAAGGCTCTCCCAATCAT 59.075 50.000 0.00 0.00 30.62 2.45
3153 3840 0.034767 CAGCAAGGCTCTCCCAATCA 60.035 55.000 0.00 0.00 36.40 2.57
3154 3841 0.254178 TCAGCAAGGCTCTCCCAATC 59.746 55.000 0.00 0.00 36.40 2.67
3171 3885 4.250464 GGTACTGTGGTCGAAATGAATCA 58.750 43.478 0.00 0.00 0.00 2.57
3186 3900 1.420138 CAACCTGGGTTCTGGTACTGT 59.580 52.381 1.55 0.00 43.22 3.55
3308 4022 8.842358 ACGACAAGTATTTTCCTATCAGAAAA 57.158 30.769 2.27 2.27 46.63 2.29
3333 4047 9.585099 GTAATTCATATTTCCAGCACAATCAAA 57.415 29.630 0.00 0.00 0.00 2.69
3458 4172 2.564771 TGGCATATTTTCTGCTCCTCG 58.435 47.619 0.00 0.00 39.60 4.63
3544 4438 9.890629 TTCAAATAAGCATCTCATACTACAAGT 57.109 29.630 0.00 0.00 0.00 3.16
3587 4481 8.640063 TCTAGTATGAGTGTACCAACTGTAAA 57.360 34.615 0.00 0.00 0.00 2.01
3597 4491 7.383572 CAGCCATGAAATCTAGTATGAGTGTAC 59.616 40.741 0.00 0.00 0.00 2.90
3618 4512 3.392285 AGATACCACATTATGAGCAGCCA 59.608 43.478 0.00 0.00 0.00 4.75
3632 4526 7.915397 CACCAACTAAAATATTGCAGATACCAC 59.085 37.037 4.09 0.00 0.00 4.16
3676 4570 5.674525 TCAGAGAAATACCACTTGCATAGG 58.325 41.667 0.00 0.00 0.00 2.57
3691 4585 4.690748 CGCACTGGAAACTATTCAGAGAAA 59.309 41.667 0.00 0.00 37.29 2.52
3715 4609 1.797635 GGAGCTATGCGCATCTTCTTC 59.202 52.381 29.11 16.63 42.61 2.87
3788 4682 5.046910 GAGAGCTCACATGCTATCTCTAC 57.953 47.826 17.77 1.29 44.89 2.59
3964 4867 4.984161 CAGAACCACATGAAAATGTCAACC 59.016 41.667 0.00 0.00 40.50 3.77
4003 4906 2.760650 TGTCTCGTACTGATCCAATGCT 59.239 45.455 0.00 0.00 0.00 3.79
4018 4921 3.775202 ACGGAGAAGATTCAATGTCTCG 58.225 45.455 2.83 0.00 37.90 4.04
4216 5124 2.949644 ACTGTGCTTGGGTTTGTAGTTC 59.050 45.455 0.00 0.00 0.00 3.01
4306 5214 1.271840 ATGAACCCTAGGCCGAGCAA 61.272 55.000 7.47 0.00 0.00 3.91
4350 5258 7.945109 ACTCTTTTTGGACTAGAAAAGCCTAAT 59.055 33.333 0.00 0.00 40.77 1.73
4395 5303 6.481976 TGAACAGTAGACAAGTTACACATTGG 59.518 38.462 0.00 0.00 0.00 3.16
4435 5344 0.035056 AATGCAGAGGTAGGCACACC 60.035 55.000 0.00 0.25 43.75 4.16
4470 5379 0.528684 GTCGCCTAAAGAGATGCGCT 60.529 55.000 9.73 0.00 46.14 5.92
4483 5392 2.479566 ATGTCAGTTGATTGTCGCCT 57.520 45.000 0.00 0.00 0.00 5.52
4550 5460 6.127647 CCTTTTTCGGAAATGAGATCATCCAA 60.128 38.462 3.67 0.00 35.10 3.53
4626 5536 4.196778 TGCTTCCGCCCCAACACA 62.197 61.111 0.00 0.00 34.43 3.72
4650 5560 0.661020 CTCGTTTCTTTTGGGCGTGT 59.339 50.000 0.00 0.00 0.00 4.49
4669 5579 7.637519 GCATTTGTTTCTTTTGCTTTTTCTCTC 59.362 33.333 0.00 0.00 0.00 3.20
4677 5587 3.555547 GTCGGCATTTGTTTCTTTTGCTT 59.444 39.130 0.00 0.00 33.86 3.91
4758 5668 1.562942 TCGGAGTCTTGGAGCCTAGTA 59.437 52.381 0.00 0.00 0.00 1.82
5003 5913 2.985847 GCTGGCTGGTGGTTGGTC 60.986 66.667 0.00 0.00 0.00 4.02
5067 5977 2.251642 GCCGCGTTGTCCTCACTTT 61.252 57.895 4.92 0.00 0.00 2.66
5081 5991 1.475441 CGACTCTGATTCTTCGCCGC 61.475 60.000 0.00 0.00 0.00 6.53
5098 6008 2.759973 CTGCTGCCCTAGTCCCGA 60.760 66.667 0.00 0.00 0.00 5.14
5182 6092 3.625897 CGGGTCTGGTGTGCTCCA 61.626 66.667 0.00 0.00 36.00 3.86


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

AutoCloner maintained by Alex Coulton.