Multiple sequence alignment - TraesCS5B01G428400

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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 TraesCS5B01G428400 chr5B 100.000 5048 0 0 1 5048 604063840 604068887 0.000000e+00 9323.0
1 TraesCS5B01G428400 chr5B 83.624 458 61 10 1492 1942 604164052 604163602 7.820000e-113 418.0
2 TraesCS5B01G428400 chr5A 92.257 3939 155 71 529 4386 611563650 611567519 0.000000e+00 5446.0
3 TraesCS5B01G428400 chr5A 91.769 571 33 5 4489 5048 611570370 611570937 0.000000e+00 782.0
4 TraesCS5B01G428400 chr5A 83.893 447 62 7 1492 1933 611652895 611652454 7.820000e-113 418.0
5 TraesCS5B01G428400 chr5A 79.605 456 83 10 1492 1942 191036391 191036841 8.160000e-83 318.0
6 TraesCS5B01G428400 chr5A 93.506 77 5 0 4378 4454 611570031 611570107 1.150000e-21 115.0
7 TraesCS5B01G428400 chr5A 98.148 54 1 0 427 480 611563595 611563648 1.500000e-15 95.3
8 TraesCS5B01G428400 chr5A 83.333 78 3 6 29 105 611563204 611563272 4.220000e-06 63.9
9 TraesCS5B01G428400 chr5D 92.418 3851 161 60 864 4668 489905292 489909057 0.000000e+00 5373.0
10 TraesCS5B01G428400 chr5D 83.624 458 61 10 1492 1942 490035215 490034765 7.820000e-113 418.0
11 TraesCS5B01G428400 chr5D 85.714 364 37 10 4694 5044 489909051 489909412 2.220000e-98 370.0
12 TraesCS5B01G428400 chr5D 88.936 235 13 3 529 756 489904983 489905211 1.380000e-70 278.0
13 TraesCS5B01G428400 chr5D 88.542 192 6 7 294 480 489904801 489904981 8.510000e-53 219.0
14 TraesCS5B01G428400 chr5D 82.500 80 4 7 29 107 489904572 489904642 1.520000e-05 62.1
15 TraesCS5B01G428400 chr2D 83.369 469 70 7 1481 1945 564095467 564095003 1.300000e-115 427.0
16 TraesCS5B01G428400 chr2B 82.729 469 73 7 1481 1945 675356153 675355689 1.310000e-110 411.0
17 TraesCS5B01G428400 chr2A 82.340 470 73 9 1481 1945 704776722 704776258 2.830000e-107 399.0
18 TraesCS5B01G428400 chr2A 91.228 57 4 1 4961 5017 486207543 486207598 5.420000e-10 76.8


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 TraesCS5B01G428400 chr5B 604063840 604068887 5047 False 9323.00 9323 100.0000 1 5048 1 chr5B.!!$F1 5047
1 TraesCS5B01G428400 chr5A 611563204 611570937 7733 False 1300.44 5446 91.8026 29 5048 5 chr5A.!!$F2 5019
2 TraesCS5B01G428400 chr5D 489904572 489909412 4840 False 1260.42 5373 87.6220 29 5044 5 chr5D.!!$F1 5015

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
980 1102 0.169672 TTCGTCTTGGTCCGATCGTC 59.830 55.000 15.09 6.68 32.44 4.20 F
2336 2497 1.001068 TGCCATTCAACTGCAACCATG 59.999 47.619 0.00 0.00 30.85 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2969 3149 0.033208 GAACCCATGGATGCCCTGAA 60.033 55.0 15.22 0.0 0.0 3.02 R
4217 4419 0.101399 CTGCCTGCCTCTACTACACG 59.899 60.0 0.00 0.0 0.0 4.49 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
17 18 4.840005 CGCCCCCTCTTCTTCGCC 62.840 72.222 0.00 0.00 0.00 5.54
18 19 4.491409 GCCCCCTCTTCTTCGCCC 62.491 72.222 0.00 0.00 0.00 6.13
19 20 4.162690 CCCCCTCTTCTTCGCCCG 62.163 72.222 0.00 0.00 0.00 6.13
20 21 4.840005 CCCCTCTTCTTCGCCCGC 62.840 72.222 0.00 0.00 0.00 6.13
21 22 4.840005 CCCTCTTCTTCGCCCGCC 62.840 72.222 0.00 0.00 0.00 6.13
22 23 4.840005 CCTCTTCTTCGCCCGCCC 62.840 72.222 0.00 0.00 0.00 6.13
62 63 2.288457 CCATGTCGAGGTCGCAGATAAT 60.288 50.000 0.00 0.00 40.67 1.28
63 64 3.057526 CCATGTCGAGGTCGCAGATAATA 60.058 47.826 0.00 0.00 40.67 0.98
64 65 4.546570 CATGTCGAGGTCGCAGATAATAA 58.453 43.478 0.00 0.00 40.67 1.40
65 66 4.224715 TGTCGAGGTCGCAGATAATAAG 57.775 45.455 0.00 0.00 40.67 1.73
66 67 3.630769 TGTCGAGGTCGCAGATAATAAGT 59.369 43.478 0.00 0.00 40.67 2.24
67 68 4.818005 TGTCGAGGTCGCAGATAATAAGTA 59.182 41.667 0.00 0.00 40.67 2.24
68 69 5.049612 TGTCGAGGTCGCAGATAATAAGTAG 60.050 44.000 0.00 0.00 40.67 2.57
69 70 4.083431 TCGAGGTCGCAGATAATAAGTAGC 60.083 45.833 0.00 0.00 40.67 3.58
70 71 4.320275 CGAGGTCGCAGATAATAAGTAGCA 60.320 45.833 0.00 0.00 40.67 3.49
76 77 6.797995 GTCGCAGATAATAAGTAGCAGTAGAC 59.202 42.308 0.00 0.00 40.67 2.59
79 80 5.790988 CAGATAATAAGTAGCAGTAGACGCG 59.209 44.000 3.53 3.53 0.00 6.01
101 102 3.873952 GGCTCGCTAATCATTGTCTCTTT 59.126 43.478 0.00 0.00 0.00 2.52
103 104 5.523916 GGCTCGCTAATCATTGTCTCTTTTA 59.476 40.000 0.00 0.00 0.00 1.52
105 106 7.122550 GCTCGCTAATCATTGTCTCTTTTAAG 58.877 38.462 0.00 0.00 0.00 1.85
106 107 7.201565 GCTCGCTAATCATTGTCTCTTTTAAGT 60.202 37.037 0.00 0.00 0.00 2.24
107 108 9.302345 CTCGCTAATCATTGTCTCTTTTAAGTA 57.698 33.333 0.00 0.00 0.00 2.24
134 135 8.083462 AGTCTTAATAACTAAGATAAGAGGCGC 58.917 37.037 0.00 0.00 46.09 6.53
140 141 0.462047 AAGATAAGAGGCGCCAACCG 60.462 55.000 31.54 0.00 40.75 4.44
152 158 4.596585 CAACCGCAACCCCCACCT 62.597 66.667 0.00 0.00 0.00 4.00
153 159 4.280019 AACCGCAACCCCCACCTC 62.280 66.667 0.00 0.00 0.00 3.85
156 162 4.410400 CGCAACCCCCACCTCCTC 62.410 72.222 0.00 0.00 0.00 3.71
157 163 4.048470 GCAACCCCCACCTCCTCC 62.048 72.222 0.00 0.00 0.00 4.30
158 164 2.204151 CAACCCCCACCTCCTCCT 60.204 66.667 0.00 0.00 0.00 3.69
187 193 4.507756 GTGGCTGGATTTCTTTTTGTTCAC 59.492 41.667 0.00 0.00 0.00 3.18
188 194 3.735746 GGCTGGATTTCTTTTTGTTCACG 59.264 43.478 0.00 0.00 0.00 4.35
189 195 4.499019 GGCTGGATTTCTTTTTGTTCACGA 60.499 41.667 0.00 0.00 0.00 4.35
190 196 5.040635 GCTGGATTTCTTTTTGTTCACGAA 58.959 37.500 0.00 0.00 0.00 3.85
208 249 1.651240 AAGTGCCGCTGCTGCTATTG 61.651 55.000 16.81 0.00 38.71 1.90
218 259 3.613432 GCTGCTGCTATTGCTTTTTGTCT 60.613 43.478 8.53 0.00 40.48 3.41
220 261 2.665052 GCTGCTATTGCTTTTTGTCTGC 59.335 45.455 0.00 0.00 40.48 4.26
222 263 2.029110 TGCTATTGCTTTTTGTCTGCCC 60.029 45.455 0.00 0.00 40.48 5.36
223 264 2.029110 GCTATTGCTTTTTGTCTGCCCA 60.029 45.455 0.00 0.00 36.03 5.36
237 278 2.768527 TCTGCCCATAGTCTTCTCCTTG 59.231 50.000 0.00 0.00 0.00 3.61
248 289 8.573035 CATAGTCTTCTCCTTGGTCTTAGATAC 58.427 40.741 0.00 0.00 0.00 2.24
249 290 6.737608 AGTCTTCTCCTTGGTCTTAGATACT 58.262 40.000 0.00 0.00 0.00 2.12
250 291 6.831868 AGTCTTCTCCTTGGTCTTAGATACTC 59.168 42.308 0.00 0.00 0.00 2.59
251 292 6.831868 GTCTTCTCCTTGGTCTTAGATACTCT 59.168 42.308 0.00 0.00 0.00 3.24
252 293 7.994334 GTCTTCTCCTTGGTCTTAGATACTCTA 59.006 40.741 0.00 0.00 0.00 2.43
257 298 7.005296 TCCTTGGTCTTAGATACTCTATCACC 58.995 42.308 0.00 5.61 37.65 4.02
259 300 5.938279 TGGTCTTAGATACTCTATCACCGT 58.062 41.667 0.00 0.00 35.40 4.83
321 362 1.132527 TCTTCCTTGTCCCCTTCCTCA 60.133 52.381 0.00 0.00 0.00 3.86
322 363 1.705186 CTTCCTTGTCCCCTTCCTCAA 59.295 52.381 0.00 0.00 0.00 3.02
324 365 1.916181 TCCTTGTCCCCTTCCTCAATC 59.084 52.381 0.00 0.00 0.00 2.67
325 366 1.635487 CCTTGTCCCCTTCCTCAATCA 59.365 52.381 0.00 0.00 0.00 2.57
326 367 2.619074 CCTTGTCCCCTTCCTCAATCAC 60.619 54.545 0.00 0.00 0.00 3.06
327 368 1.741028 TGTCCCCTTCCTCAATCACA 58.259 50.000 0.00 0.00 0.00 3.58
328 369 2.061848 TGTCCCCTTCCTCAATCACAA 58.938 47.619 0.00 0.00 0.00 3.33
331 372 2.092968 TCCCCTTCCTCAATCACAATCG 60.093 50.000 0.00 0.00 0.00 3.34
350 391 6.930722 ACAATCGCAACAGTATATCATCATCA 59.069 34.615 0.00 0.00 0.00 3.07
398 439 2.062519 GAGCTCTTCGTCCACAGTTTC 58.937 52.381 6.43 0.00 0.00 2.78
424 469 1.319079 GTTTTGTTTGTTGACGCCGTG 59.681 47.619 0.00 0.00 0.00 4.94
480 559 1.512926 TCGCCTTTGACTGCTTCTTC 58.487 50.000 0.00 0.00 0.00 2.87
481 560 1.070758 TCGCCTTTGACTGCTTCTTCT 59.929 47.619 0.00 0.00 0.00 2.85
482 561 1.462670 CGCCTTTGACTGCTTCTTCTC 59.537 52.381 0.00 0.00 0.00 2.87
483 562 2.777094 GCCTTTGACTGCTTCTTCTCT 58.223 47.619 0.00 0.00 0.00 3.10
484 563 3.145286 GCCTTTGACTGCTTCTTCTCTT 58.855 45.455 0.00 0.00 0.00 2.85
485 564 3.188254 GCCTTTGACTGCTTCTTCTCTTC 59.812 47.826 0.00 0.00 0.00 2.87
486 565 4.640364 CCTTTGACTGCTTCTTCTCTTCT 58.360 43.478 0.00 0.00 0.00 2.85
487 566 4.690280 CCTTTGACTGCTTCTTCTCTTCTC 59.310 45.833 0.00 0.00 0.00 2.87
488 567 5.511202 CCTTTGACTGCTTCTTCTCTTCTCT 60.511 44.000 0.00 0.00 0.00 3.10
489 568 5.543507 TTGACTGCTTCTTCTCTTCTCTT 57.456 39.130 0.00 0.00 0.00 2.85
490 569 5.132897 TGACTGCTTCTTCTCTTCTCTTC 57.867 43.478 0.00 0.00 0.00 2.87
491 570 4.021544 TGACTGCTTCTTCTCTTCTCTTCC 60.022 45.833 0.00 0.00 0.00 3.46
492 571 3.260632 ACTGCTTCTTCTCTTCTCTTCCC 59.739 47.826 0.00 0.00 0.00 3.97
493 572 3.515104 CTGCTTCTTCTCTTCTCTTCCCT 59.485 47.826 0.00 0.00 0.00 4.20
494 573 3.906846 TGCTTCTTCTCTTCTCTTCCCTT 59.093 43.478 0.00 0.00 0.00 3.95
495 574 4.349342 TGCTTCTTCTCTTCTCTTCCCTTT 59.651 41.667 0.00 0.00 0.00 3.11
496 575 4.935205 GCTTCTTCTCTTCTCTTCCCTTTC 59.065 45.833 0.00 0.00 0.00 2.62
497 576 5.487433 CTTCTTCTCTTCTCTTCCCTTTCC 58.513 45.833 0.00 0.00 0.00 3.13
498 577 4.757692 TCTTCTCTTCTCTTCCCTTTCCT 58.242 43.478 0.00 0.00 0.00 3.36
499 578 5.158889 TCTTCTCTTCTCTTCCCTTTCCTT 58.841 41.667 0.00 0.00 0.00 3.36
500 579 5.247337 TCTTCTCTTCTCTTCCCTTTCCTTC 59.753 44.000 0.00 0.00 0.00 3.46
501 580 4.757692 TCTCTTCTCTTCCCTTTCCTTCT 58.242 43.478 0.00 0.00 0.00 2.85
502 581 5.158889 TCTCTTCTCTTCCCTTTCCTTCTT 58.841 41.667 0.00 0.00 0.00 2.52
503 582 5.247337 TCTCTTCTCTTCCCTTTCCTTCTTC 59.753 44.000 0.00 0.00 0.00 2.87
504 583 5.158889 TCTTCTCTTCCCTTTCCTTCTTCT 58.841 41.667 0.00 0.00 0.00 2.85
505 584 5.608860 TCTTCTCTTCCCTTTCCTTCTTCTT 59.391 40.000 0.00 0.00 0.00 2.52
506 585 5.491323 TCTCTTCCCTTTCCTTCTTCTTC 57.509 43.478 0.00 0.00 0.00 2.87
507 586 5.158889 TCTCTTCCCTTTCCTTCTTCTTCT 58.841 41.667 0.00 0.00 0.00 2.85
508 587 5.247337 TCTCTTCCCTTTCCTTCTTCTTCTC 59.753 44.000 0.00 0.00 0.00 2.87
509 588 4.907875 TCTTCCCTTTCCTTCTTCTTCTCA 59.092 41.667 0.00 0.00 0.00 3.27
510 589 4.625607 TCCCTTTCCTTCTTCTTCTCAC 57.374 45.455 0.00 0.00 0.00 3.51
511 590 3.328050 TCCCTTTCCTTCTTCTTCTCACC 59.672 47.826 0.00 0.00 0.00 4.02
512 591 3.073062 CCCTTTCCTTCTTCTTCTCACCA 59.927 47.826 0.00 0.00 0.00 4.17
513 592 4.068599 CCTTTCCTTCTTCTTCTCACCAC 58.931 47.826 0.00 0.00 0.00 4.16
514 593 3.771577 TTCCTTCTTCTTCTCACCACC 57.228 47.619 0.00 0.00 0.00 4.61
515 594 2.977808 TCCTTCTTCTTCTCACCACCT 58.022 47.619 0.00 0.00 0.00 4.00
516 595 2.634940 TCCTTCTTCTTCTCACCACCTG 59.365 50.000 0.00 0.00 0.00 4.00
517 596 2.421619 CTTCTTCTTCTCACCACCTGC 58.578 52.381 0.00 0.00 0.00 4.85
518 597 0.687354 TCTTCTTCTCACCACCTGCC 59.313 55.000 0.00 0.00 0.00 4.85
519 598 0.671781 CTTCTTCTCACCACCTGCCG 60.672 60.000 0.00 0.00 0.00 5.69
520 599 2.046892 CTTCTCACCACCTGCCGG 60.047 66.667 0.00 0.00 0.00 6.13
521 600 4.329545 TTCTCACCACCTGCCGGC 62.330 66.667 22.73 22.73 0.00 6.13
588 678 3.632643 TTCTGCCTCTTGATGCATACA 57.367 42.857 0.00 0.00 36.79 2.29
590 680 3.473625 TCTGCCTCTTGATGCATACATG 58.526 45.455 0.00 2.68 36.35 3.21
601 691 3.175710 ATACATGGCCCCCGTCCC 61.176 66.667 0.00 0.00 0.00 4.46
728 818 1.064824 ATCCAGCCCATCTCTTCCCC 61.065 60.000 0.00 0.00 0.00 4.81
744 834 3.076079 TCCCCGTTGGAAGGTAAAATC 57.924 47.619 0.00 0.00 41.40 2.17
746 836 2.291346 CCCCGTTGGAAGGTAAAATCCT 60.291 50.000 0.00 0.00 39.84 3.24
754 844 6.911250 TGGAAGGTAAAATCCTTTCCTTTC 57.089 37.500 0.00 0.00 46.38 2.62
756 846 6.017192 GGAAGGTAAAATCCTTTCCTTTCCT 58.983 40.000 0.00 0.00 46.38 3.36
811 909 3.390017 CGCGCGTGATCTGATCGG 61.390 66.667 24.19 8.36 0.00 4.18
841 939 2.653702 GCAGAGCACCACGAGTCT 59.346 61.111 0.00 0.00 0.00 3.24
842 940 1.445238 GCAGAGCACCACGAGTCTC 60.445 63.158 0.00 0.00 0.00 3.36
843 941 1.214062 CAGAGCACCACGAGTCTCC 59.786 63.158 0.00 0.00 0.00 3.71
844 942 1.979693 AGAGCACCACGAGTCTCCC 60.980 63.158 0.00 0.00 0.00 4.30
845 943 3.343788 GAGCACCACGAGTCTCCCG 62.344 68.421 0.00 0.00 0.00 5.14
847 945 4.436998 CACCACGAGTCTCCCGCC 62.437 72.222 0.00 0.00 0.00 6.13
873 995 2.285368 TCCCGTGCTTGGATCCCT 60.285 61.111 9.90 0.00 0.00 4.20
975 1097 1.577922 CGTCTTCGTCTTGGTCCGA 59.422 57.895 0.00 0.00 0.00 4.55
976 1098 0.170561 CGTCTTCGTCTTGGTCCGAT 59.829 55.000 0.00 0.00 32.44 4.18
980 1102 0.169672 TTCGTCTTGGTCCGATCGTC 59.830 55.000 15.09 6.68 32.44 4.20
984 1106 1.153628 CTTGGTCCGATCGTCCCAC 60.154 63.158 19.20 8.42 0.00 4.61
990 1112 2.027605 CGATCGTCCCACCCATCG 59.972 66.667 7.03 0.00 32.83 3.84
991 1113 2.421739 GATCGTCCCACCCATCGG 59.578 66.667 0.00 0.00 0.00 4.18
992 1114 3.809374 GATCGTCCCACCCATCGGC 62.809 68.421 0.00 0.00 0.00 5.54
994 1116 4.838152 CGTCCCACCCATCGGCAG 62.838 72.222 0.00 0.00 0.00 4.85
1812 1954 2.400798 GTCATCGTCGGCGTCGTA 59.599 61.111 24.03 12.64 39.49 3.43
1990 2132 5.447279 GCAACCACCATTCTGTTACTAATCG 60.447 44.000 0.00 0.00 0.00 3.34
1996 2138 6.199154 CACCATTCTGTTACTAATCGTAGCTG 59.801 42.308 0.00 0.00 31.35 4.24
2034 2180 8.720562 CATTGTTTTCAGAAAAGGAAACACTTT 58.279 29.630 8.67 0.00 42.17 2.66
2036 2182 6.584563 TGTTTTCAGAAAAGGAAACACTTTCG 59.415 34.615 8.67 0.00 39.63 3.46
2044 2190 8.895737 AGAAAAGGAAACACTTTCGTATGTTTA 58.104 29.630 2.54 0.00 46.40 2.01
2168 2321 5.880901 ACCATGGTTCTGTATTTCTGTTCT 58.119 37.500 13.00 0.00 0.00 3.01
2235 2388 3.192001 ACTGATTGATGTGACCATGTTGC 59.808 43.478 0.00 0.00 0.00 4.17
2284 2437 4.386711 TGAATTTTGGCAATGCATTGTGA 58.613 34.783 33.67 20.99 39.88 3.58
2336 2497 1.001068 TGCCATTCAACTGCAACCATG 59.999 47.619 0.00 0.00 30.85 3.66
2356 2517 1.337703 GAACAGCTTGGTTGCACATCA 59.662 47.619 0.00 0.00 34.99 3.07
2364 2525 4.980434 GCTTGGTTGCACATCATTATCATC 59.020 41.667 0.00 0.00 0.00 2.92
2372 2533 4.277672 GCACATCATTATCATCCTGCAGTT 59.722 41.667 13.81 0.00 0.00 3.16
2421 2591 4.462508 TTCTCCACTGTAATCTCTGCTG 57.537 45.455 0.00 0.00 0.00 4.41
2425 2595 4.026052 TCCACTGTAATCTCTGCTGATGA 58.974 43.478 0.00 0.00 0.00 2.92
2460 2630 3.458118 TCCCAGGTCAAATATTCACCGAT 59.542 43.478 9.76 0.00 35.13 4.18
2490 2660 2.495409 CCCCTACTATGTCGCGCCA 61.495 63.158 0.00 0.00 0.00 5.69
2562 2732 6.273071 CGGTGTGATCATCTACATTCTGTTA 58.727 40.000 0.00 0.00 0.00 2.41
2609 2779 6.079763 CAGGTATGAATTGTGTTCACTTTCG 58.920 40.000 4.59 0.00 0.00 3.46
2651 2826 6.155827 ACACAATGCGCAATTACTTTACATT 58.844 32.000 17.11 0.00 0.00 2.71
2683 2862 7.093377 TGGCATTTTGATCTAATTACAGCCTTT 60.093 33.333 14.95 0.00 38.07 3.11
2699 2878 4.676924 CAGCCTTTGTTTCTTTTCATCGAC 59.323 41.667 0.00 0.00 0.00 4.20
2737 2916 5.511545 GGGCATATTCGAAGAGGTTCTACAT 60.512 44.000 6.30 0.00 38.43 2.29
2839 3018 1.276705 GACCCCAAGAAGAGACTGACC 59.723 57.143 0.00 0.00 0.00 4.02
2887 3066 9.371136 TCACTAAATTTCTCATCACATGACTAC 57.629 33.333 0.00 0.00 35.06 2.73
2965 3145 8.579682 AAGTCTGAAGATTGTTATTTTTGCAC 57.420 30.769 0.00 0.00 0.00 4.57
2969 3149 8.196771 TCTGAAGATTGTTATTTTTGCACTGTT 58.803 29.630 0.00 0.00 0.00 3.16
3071 3251 0.391661 TCTCGGCCATGAACAAGCTC 60.392 55.000 2.24 0.00 0.00 4.09
3122 3302 3.664107 TCACTTCCCGTCTTGAAATGAG 58.336 45.455 0.00 0.00 0.00 2.90
3175 3355 1.881973 GTCATCTTGCCTTTGTGCTCA 59.118 47.619 0.00 0.00 0.00 4.26
3176 3356 2.294233 GTCATCTTGCCTTTGTGCTCAA 59.706 45.455 0.00 0.00 0.00 3.02
3213 3393 3.200522 GCACTACCTGCCAATGCC 58.799 61.111 0.00 0.00 40.42 4.40
3214 3394 1.678635 GCACTACCTGCCAATGCCA 60.679 57.895 0.00 0.00 40.42 4.92
3258 3438 3.009363 TCATGGAAGAGACCAAGAATGCA 59.991 43.478 0.00 0.00 43.47 3.96
3294 3476 2.391879 GACTTGTCCTGACGTGTGTAC 58.608 52.381 0.00 0.00 0.00 2.90
3486 3668 1.009829 CTCATGCAGGCCGTAAGTTC 58.990 55.000 0.00 0.00 0.00 3.01
3487 3669 0.323302 TCATGCAGGCCGTAAGTTCA 59.677 50.000 0.00 0.00 0.00 3.18
3488 3670 1.164411 CATGCAGGCCGTAAGTTCAA 58.836 50.000 0.00 0.00 0.00 2.69
3489 3671 1.745087 CATGCAGGCCGTAAGTTCAAT 59.255 47.619 0.00 0.00 0.00 2.57
3491 3673 3.060736 TGCAGGCCGTAAGTTCAATAA 57.939 42.857 0.00 0.00 0.00 1.40
3492 3674 3.413327 TGCAGGCCGTAAGTTCAATAAA 58.587 40.909 0.00 0.00 0.00 1.40
3493 3675 3.438781 TGCAGGCCGTAAGTTCAATAAAG 59.561 43.478 0.00 0.00 0.00 1.85
3494 3676 3.730963 GCAGGCCGTAAGTTCAATAAAGC 60.731 47.826 0.00 0.00 0.00 3.51
3495 3677 3.689649 CAGGCCGTAAGTTCAATAAAGCT 59.310 43.478 0.00 0.00 0.00 3.74
3496 3678 4.156008 CAGGCCGTAAGTTCAATAAAGCTT 59.844 41.667 0.00 0.00 0.00 3.74
3497 3679 4.395231 AGGCCGTAAGTTCAATAAAGCTTC 59.605 41.667 0.00 0.00 0.00 3.86
3501 3683 6.183360 GCCGTAAGTTCAATAAAGCTTCTCAT 60.183 38.462 0.00 0.00 0.00 2.90
3502 3684 7.402640 CCGTAAGTTCAATAAAGCTTCTCATC 58.597 38.462 0.00 0.00 0.00 2.92
3503 3685 7.278868 CCGTAAGTTCAATAAAGCTTCTCATCT 59.721 37.037 0.00 0.00 0.00 2.90
3504 3686 8.324567 CGTAAGTTCAATAAAGCTTCTCATCTC 58.675 37.037 0.00 0.00 0.00 2.75
3507 3689 7.619050 AGTTCAATAAAGCTTCTCATCTCAGA 58.381 34.615 0.00 0.00 0.00 3.27
3508 3690 8.266473 AGTTCAATAAAGCTTCTCATCTCAGAT 58.734 33.333 0.00 0.00 0.00 2.90
3509 3691 8.336806 GTTCAATAAAGCTTCTCATCTCAGATG 58.663 37.037 8.54 8.54 0.00 2.90
3510 3692 7.789026 TCAATAAAGCTTCTCATCTCAGATGA 58.211 34.615 16.77 16.77 0.00 2.92
3511 3693 7.927092 TCAATAAAGCTTCTCATCTCAGATGAG 59.073 37.037 31.69 31.69 45.08 2.90
3512 3694 3.738830 AGCTTCTCATCTCAGATGAGC 57.261 47.619 32.40 24.21 43.79 4.26
3513 3695 2.034939 AGCTTCTCATCTCAGATGAGCG 59.965 50.000 32.40 26.03 43.79 5.03
3514 3696 2.034432 GCTTCTCATCTCAGATGAGCGA 59.966 50.000 32.40 23.33 43.79 4.93
3515 3697 3.854414 GCTTCTCATCTCAGATGAGCGAG 60.854 52.174 32.40 29.52 43.79 5.03
3516 3698 2.228925 TCTCATCTCAGATGAGCGAGG 58.771 52.381 32.40 15.38 43.79 4.63
3517 3699 2.158696 TCTCATCTCAGATGAGCGAGGA 60.159 50.000 32.40 17.24 43.79 3.71
3518 3700 2.821378 CTCATCTCAGATGAGCGAGGAT 59.179 50.000 28.02 0.00 41.80 3.24
3519 3701 2.557490 TCATCTCAGATGAGCGAGGATG 59.443 50.000 13.76 4.23 41.80 3.51
3520 3702 2.355010 TCTCAGATGAGCGAGGATGA 57.645 50.000 4.92 0.00 41.80 2.92
3521 3703 2.874014 TCTCAGATGAGCGAGGATGAT 58.126 47.619 4.92 0.00 41.80 2.45
3522 3704 3.229293 TCTCAGATGAGCGAGGATGATT 58.771 45.455 4.92 0.00 41.80 2.57
3525 3707 5.479724 TCTCAGATGAGCGAGGATGATTATT 59.520 40.000 4.92 0.00 41.80 1.40
3538 3720 9.056005 CGAGGATGATTATTAATCCAGTGAAAA 57.944 33.333 12.71 0.00 44.17 2.29
3557 3743 4.351131 AAAAACTTGGTCTTGACACGAC 57.649 40.909 3.53 3.53 0.00 4.34
3558 3744 2.684001 AACTTGGTCTTGACACGACA 57.316 45.000 13.47 0.00 33.11 4.35
3559 3745 2.910688 ACTTGGTCTTGACACGACAT 57.089 45.000 13.47 0.00 33.11 3.06
3560 3746 2.483876 ACTTGGTCTTGACACGACATG 58.516 47.619 13.47 5.76 33.11 3.21
3561 3747 2.102420 ACTTGGTCTTGACACGACATGA 59.898 45.455 13.47 0.00 33.11 3.07
3562 3748 3.244215 ACTTGGTCTTGACACGACATGAT 60.244 43.478 13.47 0.00 33.11 2.45
3563 3749 2.687370 TGGTCTTGACACGACATGATG 58.313 47.619 13.47 0.00 33.11 3.07
3833 4019 1.371558 GTCGGTCACAGCTTCCCTT 59.628 57.895 0.00 0.00 0.00 3.95
3838 4024 1.202940 GGTCACAGCTTCCCTTCCTTT 60.203 52.381 0.00 0.00 0.00 3.11
4014 4215 0.036022 GGTTGGAGAGCAGCTTCAGT 59.964 55.000 0.00 0.00 32.45 3.41
4044 4245 4.925861 GAGGCGCTGAGGATGGCC 62.926 72.222 7.64 0.00 45.91 5.36
4055 4256 0.693767 AGGATGGCCTGAAGGAGGAG 60.694 60.000 3.32 0.00 46.33 3.69
4056 4257 1.704007 GGATGGCCTGAAGGAGGAGG 61.704 65.000 3.32 0.00 46.33 4.30
4057 4258 0.692419 GATGGCCTGAAGGAGGAGGA 60.692 60.000 3.32 0.00 46.33 3.71
4078 4279 1.310904 GAGGAGCTAGGTGGTAGTCG 58.689 60.000 0.00 0.00 0.00 4.18
4082 4283 0.039326 AGCTAGGTGGTAGTCGTGGT 59.961 55.000 0.00 0.00 0.00 4.16
4140 4342 1.209019 GCAGAGACATGGTGAGGTGAT 59.791 52.381 0.00 0.00 0.00 3.06
4144 4346 3.012518 GAGACATGGTGAGGTGATTTGG 58.987 50.000 0.00 0.00 0.00 3.28
4158 4360 4.081697 GGTGATTTGGGTTTTCATAGGGTG 60.082 45.833 0.00 0.00 0.00 4.61
4160 4362 3.905493 TTTGGGTTTTCATAGGGTGGA 57.095 42.857 0.00 0.00 0.00 4.02
4217 4419 2.737376 GGACTCGGGACAACGTGC 60.737 66.667 0.00 0.00 34.94 5.34
4235 4437 1.945354 GCGTGTAGTAGAGGCAGGCA 61.945 60.000 7.08 0.00 41.73 4.75
4236 4438 0.101399 CGTGTAGTAGAGGCAGGCAG 59.899 60.000 0.00 0.00 0.00 4.85
4237 4439 0.461961 GTGTAGTAGAGGCAGGCAGG 59.538 60.000 0.00 0.00 0.00 4.85
4238 4440 1.330655 TGTAGTAGAGGCAGGCAGGC 61.331 60.000 0.00 0.00 44.61 4.85
4280 4482 2.028112 TGATTTTCTGCTCGCTACTGGT 60.028 45.455 0.00 0.00 0.00 4.00
4328 4532 9.827411 CTGAGTATAAACTACAAAAGGCTTTTC 57.173 33.333 21.77 7.30 35.56 2.29
4446 7170 2.978156 TGAAGAGCCCCAAACTCAAT 57.022 45.000 0.00 0.00 36.58 2.57
4514 7472 4.779733 GGCTCTCCCCCGTCCTCA 62.780 72.222 0.00 0.00 0.00 3.86
4516 7474 2.360980 CTCTCCCCCGTCCTCACT 59.639 66.667 0.00 0.00 0.00 3.41
4517 7475 2.037367 TCTCCCCCGTCCTCACTG 59.963 66.667 0.00 0.00 0.00 3.66
4536 7495 2.716017 GGCCACGAGTAGAGCAGCT 61.716 63.158 0.00 0.00 0.00 4.24
4551 7510 2.210013 AGCTGACCCAAGCAGACGA 61.210 57.895 0.00 0.00 46.08 4.20
4581 7540 4.818546 ACAAAGGAGAAACATCACACAGAG 59.181 41.667 0.00 0.00 0.00 3.35
4648 7608 1.234615 CCTTGCATTTCGGACCACGT 61.235 55.000 0.00 0.00 44.69 4.49
4674 7634 3.591023 GTGCCACTAGAAGAAGGAAGAC 58.409 50.000 0.00 0.00 0.00 3.01
4689 7649 4.815269 AGGAAGACGAGAAGAACTCATTG 58.185 43.478 0.00 0.00 45.14 2.82
4770 7730 3.000041 TCCTTCACATGCGTACAATCAC 59.000 45.455 0.00 0.00 0.00 3.06
4772 7732 1.355005 TCACATGCGTACAATCACGG 58.645 50.000 0.00 0.00 42.18 4.94
4805 7767 6.072893 TCCTTTATCAAACTACTTTTGCGGAC 60.073 38.462 0.00 0.00 43.90 4.79
4822 7784 2.355108 CGGACCATATATCCAAGCCCTG 60.355 54.545 6.12 0.00 35.83 4.45
4839 7801 2.374504 CCCTGGATAGCTCATGGACATT 59.625 50.000 0.00 0.00 0.00 2.71
4916 7888 3.113191 AGAAGATGAAGAGAGGCTCCA 57.887 47.619 11.71 1.86 0.00 3.86
4917 7889 3.656496 AGAAGATGAAGAGAGGCTCCAT 58.344 45.455 11.71 7.30 0.00 3.41
5007 7979 9.862149 CCCCTAAAATATAGCTTTTTAGAGGAA 57.138 33.333 22.35 0.00 42.57 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.840005 GGCGAAGAAGAGGGGGCG 62.840 72.222 0.00 0.00 0.00 6.13
1 2 4.491409 GGGCGAAGAAGAGGGGGC 62.491 72.222 0.00 0.00 0.00 5.80
2 3 4.162690 CGGGCGAAGAAGAGGGGG 62.163 72.222 0.00 0.00 0.00 5.40
3 4 4.840005 GCGGGCGAAGAAGAGGGG 62.840 72.222 0.00 0.00 0.00 4.79
4 5 4.840005 GGCGGGCGAAGAAGAGGG 62.840 72.222 0.00 0.00 0.00 4.30
5 6 4.840005 GGGCGGGCGAAGAAGAGG 62.840 72.222 0.00 0.00 0.00 3.69
62 63 0.379669 GCCGCGTCTACTGCTACTTA 59.620 55.000 4.92 0.00 0.00 2.24
63 64 1.139095 GCCGCGTCTACTGCTACTT 59.861 57.895 4.92 0.00 0.00 2.24
64 65 1.716826 GAGCCGCGTCTACTGCTACT 61.717 60.000 4.92 0.00 33.41 2.57
65 66 1.298488 GAGCCGCGTCTACTGCTAC 60.298 63.158 4.92 0.00 33.41 3.58
66 67 2.820619 CGAGCCGCGTCTACTGCTA 61.821 63.158 4.92 0.00 33.41 3.49
67 68 4.180946 CGAGCCGCGTCTACTGCT 62.181 66.667 4.92 4.94 36.62 4.24
79 80 3.104843 AGAGACAATGATTAGCGAGCC 57.895 47.619 0.00 0.00 0.00 4.70
111 112 7.152645 TGGCGCCTCTTATCTTAGTTATTAAG 58.847 38.462 29.70 0.00 40.16 1.85
112 113 7.058023 TGGCGCCTCTTATCTTAGTTATTAA 57.942 36.000 29.70 0.00 0.00 1.40
113 114 6.659745 TGGCGCCTCTTATCTTAGTTATTA 57.340 37.500 29.70 0.00 0.00 0.98
114 115 5.546621 TGGCGCCTCTTATCTTAGTTATT 57.453 39.130 29.70 0.00 0.00 1.40
115 116 5.298347 GTTGGCGCCTCTTATCTTAGTTAT 58.702 41.667 29.70 0.00 0.00 1.89
116 117 4.442472 GGTTGGCGCCTCTTATCTTAGTTA 60.442 45.833 29.70 0.00 0.00 2.24
117 118 3.532542 GTTGGCGCCTCTTATCTTAGTT 58.467 45.455 29.70 0.00 0.00 2.24
118 119 2.158943 GGTTGGCGCCTCTTATCTTAGT 60.159 50.000 29.70 0.00 0.00 2.24
121 122 0.462047 CGGTTGGCGCCTCTTATCTT 60.462 55.000 29.70 0.00 0.00 2.40
123 124 2.534903 GCGGTTGGCGCCTCTTATC 61.535 63.158 29.70 9.72 0.00 1.75
124 125 2.513897 GCGGTTGGCGCCTCTTAT 60.514 61.111 29.70 0.00 0.00 1.73
140 141 4.048470 GGAGGAGGTGGGGGTTGC 62.048 72.222 0.00 0.00 0.00 4.17
142 143 1.852626 CAAGGAGGAGGTGGGGGTT 60.853 63.158 0.00 0.00 0.00 4.11
143 144 2.204151 CAAGGAGGAGGTGGGGGT 60.204 66.667 0.00 0.00 0.00 4.95
146 152 3.732849 GGGCAAGGAGGAGGTGGG 61.733 72.222 0.00 0.00 0.00 4.61
147 153 4.101448 CGGGCAAGGAGGAGGTGG 62.101 72.222 0.00 0.00 0.00 4.61
148 154 3.322466 ACGGGCAAGGAGGAGGTG 61.322 66.667 0.00 0.00 0.00 4.00
149 155 3.322466 CACGGGCAAGGAGGAGGT 61.322 66.667 0.00 0.00 0.00 3.85
150 156 4.101448 CCACGGGCAAGGAGGAGG 62.101 72.222 0.00 0.00 0.00 4.30
204 245 5.016173 ACTATGGGCAGACAAAAAGCAATA 58.984 37.500 0.00 0.00 0.00 1.90
208 249 3.084786 AGACTATGGGCAGACAAAAAGC 58.915 45.455 0.00 0.00 0.00 3.51
218 259 1.839994 CCAAGGAGAAGACTATGGGCA 59.160 52.381 0.00 0.00 0.00 5.36
220 261 3.379452 AGACCAAGGAGAAGACTATGGG 58.621 50.000 0.00 0.00 32.36 4.00
222 263 7.595819 ATCTAAGACCAAGGAGAAGACTATG 57.404 40.000 0.00 0.00 0.00 2.23
223 264 8.507761 AGTATCTAAGACCAAGGAGAAGACTAT 58.492 37.037 0.00 0.00 0.00 2.12
248 289 1.831736 AGGAACCCAACGGTGATAGAG 59.168 52.381 0.00 0.00 43.71 2.43
249 290 1.829222 GAGGAACCCAACGGTGATAGA 59.171 52.381 0.00 0.00 43.71 1.98
250 291 1.831736 AGAGGAACCCAACGGTGATAG 59.168 52.381 0.00 0.00 43.71 2.08
251 292 1.829222 GAGAGGAACCCAACGGTGATA 59.171 52.381 0.00 0.00 43.71 2.15
252 293 0.613777 GAGAGGAACCCAACGGTGAT 59.386 55.000 0.00 0.00 43.71 3.06
257 298 1.215647 CGAGGAGAGGAACCCAACG 59.784 63.158 0.00 0.00 0.00 4.10
259 300 2.646175 CGCGAGGAGAGGAACCCAA 61.646 63.158 0.00 0.00 0.00 4.12
283 324 3.430497 CGAGGAGGGAGAGGGGGA 61.430 72.222 0.00 0.00 0.00 4.81
284 325 3.742248 GACGAGGAGGGAGAGGGGG 62.742 73.684 0.00 0.00 0.00 5.40
287 328 0.753848 GGAAGACGAGGAGGGAGAGG 60.754 65.000 0.00 0.00 0.00 3.69
289 330 0.705253 AAGGAAGACGAGGAGGGAGA 59.295 55.000 0.00 0.00 0.00 3.71
290 331 0.820871 CAAGGAAGACGAGGAGGGAG 59.179 60.000 0.00 0.00 0.00 4.30
291 332 0.114560 ACAAGGAAGACGAGGAGGGA 59.885 55.000 0.00 0.00 0.00 4.20
292 333 0.533032 GACAAGGAAGACGAGGAGGG 59.467 60.000 0.00 0.00 0.00 4.30
293 334 0.533032 GGACAAGGAAGACGAGGAGG 59.467 60.000 0.00 0.00 0.00 4.30
294 335 0.533032 GGGACAAGGAAGACGAGGAG 59.467 60.000 0.00 0.00 0.00 3.69
295 336 0.903454 GGGGACAAGGAAGACGAGGA 60.903 60.000 0.00 0.00 0.00 3.71
321 362 7.442062 TGATGATATACTGTTGCGATTGTGATT 59.558 33.333 0.00 0.00 0.00 2.57
322 363 6.930722 TGATGATATACTGTTGCGATTGTGAT 59.069 34.615 0.00 0.00 0.00 3.06
324 365 6.529463 TGATGATATACTGTTGCGATTGTG 57.471 37.500 0.00 0.00 0.00 3.33
325 366 6.930722 TGATGATGATATACTGTTGCGATTGT 59.069 34.615 0.00 0.00 0.00 2.71
326 367 7.355332 TGATGATGATATACTGTTGCGATTG 57.645 36.000 0.00 0.00 0.00 2.67
327 368 7.009907 CGATGATGATGATATACTGTTGCGATT 59.990 37.037 0.00 0.00 0.00 3.34
328 369 6.474751 CGATGATGATGATATACTGTTGCGAT 59.525 38.462 0.00 0.00 0.00 4.58
331 372 5.220548 GGCGATGATGATGATATACTGTTGC 60.221 44.000 0.00 0.00 0.00 4.17
369 410 4.516195 GAAGAGCTCGGGCGGGAC 62.516 72.222 8.37 0.00 44.37 4.46
398 439 3.830339 GCGTCAACAAACAAAACAAAACG 59.170 39.130 0.00 0.00 0.00 3.60
480 559 5.248248 AGAAGAAGGAAAGGGAAGAGAAGAG 59.752 44.000 0.00 0.00 0.00 2.85
481 560 5.158889 AGAAGAAGGAAAGGGAAGAGAAGA 58.841 41.667 0.00 0.00 0.00 2.87
482 561 5.497464 AGAAGAAGGAAAGGGAAGAGAAG 57.503 43.478 0.00 0.00 0.00 2.85
483 562 5.608860 AGAAGAAGAAGGAAAGGGAAGAGAA 59.391 40.000 0.00 0.00 0.00 2.87
484 563 5.158889 AGAAGAAGAAGGAAAGGGAAGAGA 58.841 41.667 0.00 0.00 0.00 3.10
485 564 5.012561 TGAGAAGAAGAAGGAAAGGGAAGAG 59.987 44.000 0.00 0.00 0.00 2.85
486 565 4.907875 TGAGAAGAAGAAGGAAAGGGAAGA 59.092 41.667 0.00 0.00 0.00 2.87
487 566 5.000591 GTGAGAAGAAGAAGGAAAGGGAAG 58.999 45.833 0.00 0.00 0.00 3.46
488 567 4.202472 GGTGAGAAGAAGAAGGAAAGGGAA 60.202 45.833 0.00 0.00 0.00 3.97
489 568 3.328050 GGTGAGAAGAAGAAGGAAAGGGA 59.672 47.826 0.00 0.00 0.00 4.20
490 569 3.073062 TGGTGAGAAGAAGAAGGAAAGGG 59.927 47.826 0.00 0.00 0.00 3.95
491 570 4.068599 GTGGTGAGAAGAAGAAGGAAAGG 58.931 47.826 0.00 0.00 0.00 3.11
492 571 4.068599 GGTGGTGAGAAGAAGAAGGAAAG 58.931 47.826 0.00 0.00 0.00 2.62
493 572 3.716872 AGGTGGTGAGAAGAAGAAGGAAA 59.283 43.478 0.00 0.00 0.00 3.13
494 573 3.071602 CAGGTGGTGAGAAGAAGAAGGAA 59.928 47.826 0.00 0.00 0.00 3.36
495 574 2.634940 CAGGTGGTGAGAAGAAGAAGGA 59.365 50.000 0.00 0.00 0.00 3.36
496 575 2.873649 GCAGGTGGTGAGAAGAAGAAGG 60.874 54.545 0.00 0.00 0.00 3.46
497 576 2.421619 GCAGGTGGTGAGAAGAAGAAG 58.578 52.381 0.00 0.00 0.00 2.85
498 577 1.072331 GGCAGGTGGTGAGAAGAAGAA 59.928 52.381 0.00 0.00 0.00 2.52
499 578 0.687354 GGCAGGTGGTGAGAAGAAGA 59.313 55.000 0.00 0.00 0.00 2.87
500 579 0.671781 CGGCAGGTGGTGAGAAGAAG 60.672 60.000 0.00 0.00 0.00 2.85
501 580 1.371183 CGGCAGGTGGTGAGAAGAA 59.629 57.895 0.00 0.00 0.00 2.52
502 581 2.583441 CCGGCAGGTGGTGAGAAGA 61.583 63.158 0.00 0.00 0.00 2.87
503 582 2.046892 CCGGCAGGTGGTGAGAAG 60.047 66.667 0.00 0.00 0.00 2.85
504 583 4.329545 GCCGGCAGGTGGTGAGAA 62.330 66.667 24.80 0.00 40.50 2.87
520 599 4.666253 TGGGCCTTGGTGCTCAGC 62.666 66.667 4.53 0.00 36.64 4.26
521 600 2.674380 GTGGGCCTTGGTGCTCAG 60.674 66.667 4.53 0.00 43.79 3.35
522 601 4.284550 GGTGGGCCTTGGTGCTCA 62.285 66.667 4.53 0.00 40.07 4.26
523 602 3.808218 TTGGTGGGCCTTGGTGCTC 62.808 63.158 4.53 0.00 35.27 4.26
524 603 3.831637 TTGGTGGGCCTTGGTGCT 61.832 61.111 4.53 0.00 35.27 4.40
525 604 3.615709 GTTGGTGGGCCTTGGTGC 61.616 66.667 4.53 0.00 35.27 5.01
526 605 2.917227 GGTTGGTGGGCCTTGGTG 60.917 66.667 4.53 0.00 35.27 4.17
527 606 2.730129 GATGGTTGGTGGGCCTTGGT 62.730 60.000 4.53 0.00 35.27 3.67
601 691 0.879400 GCCATGATCTGACGCCTCTG 60.879 60.000 0.00 0.00 0.00 3.35
676 766 0.823769 TAGCAGGATCGATGAGCCGT 60.824 55.000 0.54 0.00 43.66 5.68
677 767 0.109365 CTAGCAGGATCGATGAGCCG 60.109 60.000 0.54 0.00 43.66 5.52
743 833 4.170053 AGGAAAGGAAAGGAAAGGAAAGGA 59.830 41.667 0.00 0.00 0.00 3.36
744 834 4.483950 AGGAAAGGAAAGGAAAGGAAAGG 58.516 43.478 0.00 0.00 0.00 3.11
746 836 4.142038 CGAGGAAAGGAAAGGAAAGGAAA 58.858 43.478 0.00 0.00 0.00 3.13
754 844 0.322546 CCCACCGAGGAAAGGAAAGG 60.323 60.000 0.00 0.00 41.22 3.11
756 846 0.109723 CACCCACCGAGGAAAGGAAA 59.890 55.000 0.00 0.00 41.22 3.13
797 895 2.663188 GGGCCGATCAGATCACGC 60.663 66.667 11.12 10.48 0.00 5.34
798 896 2.029666 GGGGCCGATCAGATCACG 59.970 66.667 11.12 1.00 0.00 4.35
799 897 2.029666 CGGGGCCGATCAGATCAC 59.970 66.667 11.12 1.81 42.83 3.06
800 898 3.233980 CCGGGGCCGATCAGATCA 61.234 66.667 11.12 0.00 42.83 2.92
873 995 2.122413 ACCACCACTCCTGCTCCA 60.122 61.111 0.00 0.00 0.00 3.86
907 1029 4.048470 GGGGGACAGGACAAGGGC 62.048 72.222 0.00 0.00 0.00 5.19
935 1057 3.433615 GGAATCGCCGAATCTTTATGGAG 59.566 47.826 1.76 0.00 0.00 3.86
975 1097 3.861797 GCCGATGGGTGGGACGAT 61.862 66.667 0.00 0.00 34.97 3.73
996 1118 4.101790 CACGTGTTGCCCATCGCC 62.102 66.667 7.58 0.00 36.24 5.54
997 1119 4.759096 GCACGTGTTGCCCATCGC 62.759 66.667 18.38 0.00 46.63 4.58
1163 1302 2.401766 GCCTTGCTCACGATGTGGG 61.402 63.158 0.00 0.00 37.04 4.61
1896 2038 2.350522 CCAAAGTCGATGGTCTTGAGG 58.649 52.381 0.00 0.00 33.08 3.86
2083 2229 5.824624 AGTGCAATCCCTTGAATGTAGTATG 59.175 40.000 0.00 0.00 34.04 2.39
2084 2230 5.824624 CAGTGCAATCCCTTGAATGTAGTAT 59.175 40.000 0.00 0.00 34.04 2.12
2085 2231 5.185454 CAGTGCAATCCCTTGAATGTAGTA 58.815 41.667 0.00 0.00 34.04 1.82
2089 2235 1.547372 GCAGTGCAATCCCTTGAATGT 59.453 47.619 11.09 0.00 34.04 2.71
2099 2245 2.812591 CCCATCTAGATGCAGTGCAATC 59.187 50.000 23.90 18.73 43.62 2.67
2168 2321 7.479980 GTGACCGAATTATGGATCAAATCAAA 58.520 34.615 3.31 0.00 0.00 2.69
2270 2423 2.350498 GCTGAAATCACAATGCATTGCC 59.650 45.455 33.94 18.28 41.38 4.52
2336 2497 1.337703 TGATGTGCAACCAAGCTGTTC 59.662 47.619 0.00 0.00 34.36 3.18
2356 2517 7.893124 AAGATTCAAACTGCAGGATGATAAT 57.107 32.000 19.93 12.34 39.69 1.28
2364 2525 5.591472 TGATGGATAAGATTCAAACTGCAGG 59.409 40.000 19.93 0.00 0.00 4.85
2372 2533 9.334947 GTCTCAAATCTGATGGATAAGATTCAA 57.665 33.333 0.42 0.00 41.24 2.69
2421 2591 7.038017 TGACCTGGGATAATTAAGATCCTCATC 60.038 40.741 15.43 10.36 42.32 2.92
2425 2595 7.465900 TTTGACCTGGGATAATTAAGATCCT 57.534 36.000 15.43 0.60 42.32 3.24
2460 2630 0.834687 AGTAGGGGCTTCCGACAACA 60.835 55.000 10.98 0.00 42.68 3.33
2490 2660 5.356470 GCCATATTTCTTCTTCAGCACTTCT 59.644 40.000 0.00 0.00 0.00 2.85
2562 2732 1.470996 AAAATGGCGGCACACCACAT 61.471 50.000 16.34 0.00 46.46 3.21
2609 2779 6.823678 TTGTGTCGAAGAAGTAAAGAACTC 57.176 37.500 0.00 0.00 39.69 3.01
2683 2862 4.956085 TCTCTGGTCGATGAAAAGAAACA 58.044 39.130 0.00 0.00 0.00 2.83
2699 2878 2.125350 GCCCTGCTCGTTCTCTGG 60.125 66.667 0.00 0.00 0.00 3.86
2839 3018 0.999406 CACGTAGAACTTCATGGGCG 59.001 55.000 0.00 0.00 0.00 6.13
2887 3066 9.829507 AGACCATTGAGAGAACTAGAATTTATG 57.170 33.333 0.00 0.00 0.00 1.90
2965 3145 1.108776 CCATGGATGCCCTGAAACAG 58.891 55.000 5.56 0.00 0.00 3.16
2969 3149 0.033208 GAACCCATGGATGCCCTGAA 60.033 55.000 15.22 0.00 0.00 3.02
3071 3251 2.800250 ACCCTGAGAGCCATCTTTTTG 58.200 47.619 0.00 0.00 35.30 2.44
3111 3291 5.065859 TGCGAAAGAAACACTCATTTCAAGA 59.934 36.000 1.47 0.00 40.43 3.02
3122 3302 2.053627 CAAGGCATGCGAAAGAAACAC 58.946 47.619 12.44 0.00 0.00 3.32
3175 3355 4.275781 CCACTTGGCTTGGTGGTT 57.724 55.556 13.19 0.00 45.52 3.67
3209 3389 1.033746 CACCGAGCTCCAAATGGCAT 61.034 55.000 8.47 0.00 34.44 4.40
3210 3390 1.675310 CACCGAGCTCCAAATGGCA 60.675 57.895 8.47 0.00 34.44 4.92
3211 3391 2.409870 CCACCGAGCTCCAAATGGC 61.410 63.158 8.47 0.00 34.44 4.40
3212 3392 0.107017 ATCCACCGAGCTCCAAATGG 60.107 55.000 8.47 10.66 0.00 3.16
3213 3393 1.019673 CATCCACCGAGCTCCAAATG 58.980 55.000 8.47 1.19 0.00 2.32
3214 3394 0.620556 ACATCCACCGAGCTCCAAAT 59.379 50.000 8.47 0.00 0.00 2.32
3224 3404 4.060900 CTCTTCCATGATAACATCCACCG 58.939 47.826 0.00 0.00 34.15 4.94
3258 3438 5.508994 GGACAAGTCGATTTGGATGGTTTTT 60.509 40.000 22.59 0.44 32.32 1.94
3294 3476 0.875908 CACCTGGACAGACACACACG 60.876 60.000 0.00 0.00 0.00 4.49
3486 3668 7.307514 GCTCATCTGAGATGAGAAGCTTTATTG 60.308 40.741 41.54 20.95 46.25 1.90
3487 3669 6.707161 GCTCATCTGAGATGAGAAGCTTTATT 59.293 38.462 41.54 0.00 46.25 1.40
3488 3670 6.225318 GCTCATCTGAGATGAGAAGCTTTAT 58.775 40.000 41.54 0.00 46.25 1.40
3489 3671 5.599732 GCTCATCTGAGATGAGAAGCTTTA 58.400 41.667 41.54 13.94 46.25 1.85
3491 3673 3.491276 CGCTCATCTGAGATGAGAAGCTT 60.491 47.826 41.54 0.00 46.25 3.74
3492 3674 2.034939 CGCTCATCTGAGATGAGAAGCT 59.965 50.000 41.54 0.00 46.25 3.74
3493 3675 2.034432 TCGCTCATCTGAGATGAGAAGC 59.966 50.000 41.54 30.44 46.25 3.86
3494 3676 3.304861 CCTCGCTCATCTGAGATGAGAAG 60.305 52.174 41.54 34.76 46.25 2.85
3495 3677 2.622470 CCTCGCTCATCTGAGATGAGAA 59.378 50.000 41.54 30.20 46.25 2.87
3496 3678 2.158696 TCCTCGCTCATCTGAGATGAGA 60.159 50.000 41.54 27.18 46.25 3.27
3497 3679 2.228925 TCCTCGCTCATCTGAGATGAG 58.771 52.381 36.25 36.25 44.74 2.90
3501 3683 2.355010 TCATCCTCGCTCATCTGAGA 57.645 50.000 11.34 0.00 44.74 3.27
3502 3684 3.663995 AATCATCCTCGCTCATCTGAG 57.336 47.619 2.75 2.75 44.75 3.35
3503 3685 5.735285 AATAATCATCCTCGCTCATCTGA 57.265 39.130 0.00 0.00 0.00 3.27
3504 3686 7.224362 GGATTAATAATCATCCTCGCTCATCTG 59.776 40.741 14.19 0.00 39.71 2.90
3507 3689 6.950842 TGGATTAATAATCATCCTCGCTCAT 58.049 36.000 14.19 0.00 39.94 2.90
3508 3690 6.014242 ACTGGATTAATAATCATCCTCGCTCA 60.014 38.462 14.19 0.34 39.94 4.26
3509 3691 6.312426 CACTGGATTAATAATCATCCTCGCTC 59.688 42.308 14.19 0.00 39.94 5.03
3510 3692 6.014242 TCACTGGATTAATAATCATCCTCGCT 60.014 38.462 14.19 0.00 39.94 4.93
3511 3693 6.166279 TCACTGGATTAATAATCATCCTCGC 58.834 40.000 14.19 0.00 39.94 5.03
3512 3694 8.607441 TTTCACTGGATTAATAATCATCCTCG 57.393 34.615 14.19 0.00 39.94 4.63
3538 3720 2.980568 TGTCGTGTCAAGACCAAGTTT 58.019 42.857 15.13 0.00 37.80 2.66
3541 3723 2.754472 TCATGTCGTGTCAAGACCAAG 58.246 47.619 15.13 6.30 37.80 3.61
3546 3732 4.454728 TCATCATCATGTCGTGTCAAGA 57.545 40.909 0.00 0.00 0.00 3.02
3547 3733 5.535043 TTTCATCATCATGTCGTGTCAAG 57.465 39.130 0.00 0.00 0.00 3.02
3557 3743 4.498513 CGTTCACCCCATTTCATCATCATG 60.499 45.833 0.00 0.00 0.00 3.07
3558 3744 3.633525 CGTTCACCCCATTTCATCATCAT 59.366 43.478 0.00 0.00 0.00 2.45
3559 3745 3.016031 CGTTCACCCCATTTCATCATCA 58.984 45.455 0.00 0.00 0.00 3.07
3560 3746 2.223572 GCGTTCACCCCATTTCATCATC 60.224 50.000 0.00 0.00 0.00 2.92
3561 3747 1.750778 GCGTTCACCCCATTTCATCAT 59.249 47.619 0.00 0.00 0.00 2.45
3562 3748 1.173043 GCGTTCACCCCATTTCATCA 58.827 50.000 0.00 0.00 0.00 3.07
3563 3749 1.133025 CTGCGTTCACCCCATTTCATC 59.867 52.381 0.00 0.00 0.00 2.92
3818 4004 0.402121 AAGGAAGGGAAGCTGTGACC 59.598 55.000 0.00 0.00 0.00 4.02
3838 4024 2.944094 GCGCCCCCAAGAGAAGATAAAA 60.944 50.000 0.00 0.00 0.00 1.52
3842 4028 1.977293 GAGCGCCCCCAAGAGAAGAT 61.977 60.000 2.29 0.00 0.00 2.40
3852 4047 3.706373 TTCAGTCAGAGCGCCCCC 61.706 66.667 2.29 0.00 0.00 5.40
3997 4198 2.159184 CGATACTGAAGCTGCTCTCCAA 60.159 50.000 1.00 0.00 0.00 3.53
4014 4215 2.498941 CGCCTCCCTGAAGCCGATA 61.499 63.158 0.00 0.00 0.00 2.92
4044 4245 0.633921 TCCTCCTCCTCCTCCTTCAG 59.366 60.000 0.00 0.00 0.00 3.02
4055 4256 0.556747 TACCACCTAGCTCCTCCTCC 59.443 60.000 0.00 0.00 0.00 4.30
4056 4257 1.215924 ACTACCACCTAGCTCCTCCTC 59.784 57.143 0.00 0.00 0.00 3.71
4057 4258 1.215924 GACTACCACCTAGCTCCTCCT 59.784 57.143 0.00 0.00 0.00 3.69
4078 4279 2.735134 AGAACGAAATTAGCGTCACCAC 59.265 45.455 6.72 0.00 41.75 4.16
4082 4283 2.666508 GAGCAGAACGAAATTAGCGTCA 59.333 45.455 6.72 0.00 41.75 4.35
4121 4323 3.623906 AATCACCTCACCATGTCTCTG 57.376 47.619 0.00 0.00 0.00 3.35
4140 4342 3.905493 TCCACCCTATGAAAACCCAAA 57.095 42.857 0.00 0.00 0.00 3.28
4144 4346 3.509967 CCACTTTCCACCCTATGAAAACC 59.490 47.826 0.00 0.00 30.65 3.27
4158 4360 2.338785 GGAGCTGCTGCCACTTTCC 61.339 63.158 7.01 8.42 40.80 3.13
4160 4362 1.602888 CAGGAGCTGCTGCCACTTT 60.603 57.895 22.98 0.00 40.80 2.66
4217 4419 0.101399 CTGCCTGCCTCTACTACACG 59.899 60.000 0.00 0.00 0.00 4.49
4249 4451 1.678970 AGAAAATCACCGGGGCTGC 60.679 57.895 6.32 0.00 0.00 5.25
4324 4528 4.180723 ACTGTATACAAGGAGGGGGAAAA 58.819 43.478 7.06 0.00 0.00 2.29
4328 4532 2.626743 CGTACTGTATACAAGGAGGGGG 59.373 54.545 7.06 0.00 0.00 5.40
4364 4568 4.935352 AAAGCTAATCCAACTTGTGCAA 57.065 36.364 0.00 0.00 0.00 4.08
4446 7170 7.483881 AGAAAATCCCCTAAACTTATTCCCAA 58.516 34.615 0.00 0.00 0.00 4.12
4455 7179 6.409810 GGATGCTAGAGAAAATCCCCTAAACT 60.410 42.308 0.00 0.00 33.79 2.66
4508 7466 3.302347 CTCGTGGCCCAGTGAGGAC 62.302 68.421 0.00 0.00 41.22 3.85
4510 7468 1.949847 CTACTCGTGGCCCAGTGAGG 61.950 65.000 15.34 0.00 32.76 3.86
4511 7469 0.965866 TCTACTCGTGGCCCAGTGAG 60.966 60.000 10.60 10.60 34.65 3.51
4512 7470 0.965866 CTCTACTCGTGGCCCAGTGA 60.966 60.000 0.00 0.15 0.00 3.41
4514 7472 2.352032 GCTCTACTCGTGGCCCAGT 61.352 63.158 0.00 1.79 0.00 4.00
4516 7474 2.283604 TGCTCTACTCGTGGCCCA 60.284 61.111 0.00 0.00 0.00 5.36
4517 7475 2.496817 CTGCTCTACTCGTGGCCC 59.503 66.667 0.00 0.00 0.00 5.80
4536 7495 0.033504 GAGTTCGTCTGCTTGGGTCA 59.966 55.000 0.00 0.00 0.00 4.02
4593 7552 0.165944 GTTGGCGGACATGTTTCTCG 59.834 55.000 0.00 3.72 0.00 4.04
4604 7563 0.035915 TTGGAATCGATGTTGGCGGA 60.036 50.000 0.00 0.00 0.00 5.54
4648 7608 2.166459 CCTTCTTCTAGTGGCACGATGA 59.834 50.000 12.71 9.20 0.00 2.92
4663 7623 4.585162 TGAGTTCTTCTCGTCTTCCTTCTT 59.415 41.667 0.00 0.00 45.46 2.52
4674 7634 5.923114 TCTTCTTCACAATGAGTTCTTCTCG 59.077 40.000 0.00 0.00 45.46 4.04
4689 7649 5.455525 CACGGTTTCAACATTTCTTCTTCAC 59.544 40.000 0.00 0.00 0.00 3.18
4739 7699 3.123621 CGCATGTGAAGGAGTCTACAAAC 59.876 47.826 0.00 0.00 0.00 2.93
4770 7730 5.050490 AGTTTGATAAAGGATCATCGACCG 58.950 41.667 0.00 0.00 44.23 4.79
4772 7732 8.649973 AAGTAGTTTGATAAAGGATCATCGAC 57.350 34.615 0.00 0.00 44.23 4.20
4822 7784 4.348863 AGACAATGTCCATGAGCTATCC 57.651 45.455 10.12 0.00 32.18 2.59
4839 7801 1.905637 TGACTTCTCGCCACTAGACA 58.094 50.000 0.00 0.00 0.00 3.41
4916 7888 3.181446 CCAAACCAATTCAACCCCACAAT 60.181 43.478 0.00 0.00 0.00 2.71
4917 7889 2.171448 CCAAACCAATTCAACCCCACAA 59.829 45.455 0.00 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.