Multiple sequence alignment - TraesCS4A01G305600

Loading Multiple Alignment...

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 TraesCS4A01G305600 chr4A 100.000 3103 0 0 440 3542 600915515 600912413 0.000000e+00 5731
1 TraesCS4A01G305600 chr4A 84.943 1315 177 19 2235 3540 601016850 601015548 0.000000e+00 1312
2 TraesCS4A01G305600 chr4A 83.614 1306 194 19 2245 3540 600975487 600974192 0.000000e+00 1208
3 TraesCS4A01G305600 chr4A 80.562 1317 229 15 2235 3542 600930814 600929516 0.000000e+00 989
4 TraesCS4A01G305600 chr4A 83.723 1026 157 8 2235 3257 601008117 601007099 0.000000e+00 961
5 TraesCS4A01G305600 chr4A 81.162 1205 167 32 1062 2238 601018091 601016919 0.000000e+00 913
6 TraesCS4A01G305600 chr4A 81.304 1166 176 24 1086 2238 600976702 600975566 0.000000e+00 907
7 TraesCS4A01G305600 chr4A 81.201 766 125 17 1481 2238 601008940 601008186 1.820000e-167 599
8 TraesCS4A01G305600 chr4A 100.000 72 0 0 1 72 600915954 600915883 2.220000e-27 134
9 TraesCS4A01G305600 chr4B 93.107 3003 169 14 550 3540 4717586 4720562 0.000000e+00 4364
10 TraesCS4A01G305600 chr4B 82.903 2129 320 25 1444 3541 4998681 4996566 0.000000e+00 1875
11 TraesCS4A01G305600 chr4B 83.486 1314 201 14 2235 3540 5196817 5195512 0.000000e+00 1210
12 TraesCS4A01G305600 chr4B 80.347 1211 169 41 1062 2238 5016962 5015787 0.000000e+00 854
13 TraesCS4A01G305600 chr4B 83.053 655 106 3 2235 2888 5081116 5080466 1.100000e-164 590
14 TraesCS4A01G305600 chr4B 82.336 685 102 9 2862 3540 5245911 5245240 8.530000e-161 577
15 TraesCS4A01G305600 chr4B 83.305 593 89 8 2953 3540 5080432 5079845 4.020000e-149 538
16 TraesCS4A01G305600 chr4B 81.850 573 98 6 2245 2814 5178321 5177752 8.900000e-131 477
17 TraesCS4A01G305600 chr4B 80.031 636 105 16 1054 1680 5179607 5178985 5.390000e-123 451
18 TraesCS4A01G305600 chr4B 85.235 298 44 0 1094 1391 5197994 5197697 1.240000e-79 307
19 TraesCS4A01G305600 chr4B 85.333 225 29 2 1062 1282 5087689 5087465 2.750000e-56 230
20 TraesCS4A01G305600 chr4B 92.308 52 4 0 2778 2829 5245956 5245905 1.360000e-09 75
21 TraesCS4A01G305600 chr4D 92.385 1300 95 4 2245 3542 3840751 3839454 0.000000e+00 1849
22 TraesCS4A01G305600 chr4D 82.498 1337 190 29 2235 3540 3693111 3694434 0.000000e+00 1133
23 TraesCS4A01G305600 chr4D 80.706 1161 200 16 1088 2238 3691896 3693042 0.000000e+00 881
24 TraesCS4A01G305600 chr4D 81.220 410 48 20 710 1109 3843351 3842961 1.600000e-78 303
25 TraesCS4A01G305600 chr4D 91.667 72 6 0 1 72 3716482 3716553 2.250000e-17 100
26 TraesCS4A01G305600 chr5A 83.916 286 43 2 1106 1391 549187624 549187906 1.620000e-68 270
27 TraesCS4A01G305600 chr5B 83.234 167 25 2 1106 1272 528555978 528556141 2.200000e-32 150


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 TraesCS4A01G305600 chr4A 600912413 600915954 3541 True 2932.5 5731 100.0000 1 3542 2 chr4A.!!$R2 3541
1 TraesCS4A01G305600 chr4A 601015548 601018091 2543 True 1112.5 1312 83.0525 1062 3540 2 chr4A.!!$R5 2478
2 TraesCS4A01G305600 chr4A 600974192 600976702 2510 True 1057.5 1208 82.4590 1086 3540 2 chr4A.!!$R3 2454
3 TraesCS4A01G305600 chr4A 600929516 600930814 1298 True 989.0 989 80.5620 2235 3542 1 chr4A.!!$R1 1307
4 TraesCS4A01G305600 chr4A 601007099 601008940 1841 True 780.0 961 82.4620 1481 3257 2 chr4A.!!$R4 1776
5 TraesCS4A01G305600 chr4B 4717586 4720562 2976 False 4364.0 4364 93.1070 550 3540 1 chr4B.!!$F1 2990
6 TraesCS4A01G305600 chr4B 4996566 4998681 2115 True 1875.0 1875 82.9030 1444 3541 1 chr4B.!!$R1 2097
7 TraesCS4A01G305600 chr4B 5015787 5016962 1175 True 854.0 854 80.3470 1062 2238 1 chr4B.!!$R2 1176
8 TraesCS4A01G305600 chr4B 5195512 5197994 2482 True 758.5 1210 84.3605 1094 3540 2 chr4B.!!$R6 2446
9 TraesCS4A01G305600 chr4B 5079845 5081116 1271 True 564.0 590 83.1790 2235 3540 2 chr4B.!!$R4 1305
10 TraesCS4A01G305600 chr4B 5177752 5179607 1855 True 464.0 477 80.9405 1054 2814 2 chr4B.!!$R5 1760
11 TraesCS4A01G305600 chr4B 5245240 5245956 716 True 326.0 577 87.3220 2778 3540 2 chr4B.!!$R7 762
12 TraesCS4A01G305600 chr4D 3839454 3843351 3897 True 1076.0 1849 86.8025 710 3542 2 chr4D.!!$R1 2832
13 TraesCS4A01G305600 chr4D 3691896 3694434 2538 False 1007.0 1133 81.6020 1088 3540 2 chr4D.!!$F2 2452

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
538 539 0.027979 CTGGCGTGTGTTTGTGTGAG 59.972 55.0 0.00 0.0 0.0 3.51 F
541 542 0.934496 GCGTGTGTTTGTGTGAGCTA 59.066 50.0 0.00 0.0 0.0 3.32 F
1223 2245 1.048601 GCGAGGATATCAGGTGGGAA 58.951 55.0 4.83 0.0 0.0 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1982 3094 0.250901 AGGTCCATGCCACTCACAAC 60.251 55.000 0.00 0.0 0.0 3.32 R
2395 3582 5.176592 GTGCTTTAGTCTAAACGGAGGAAT 58.823 41.667 0.65 0.0 0.0 3.01 R
2541 3728 3.565307 TGAAGCTTGGGAAAATGTCACT 58.435 40.909 2.10 0.0 0.0 3.41 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
24 25 6.778834 AAGATCATGTTGATTATTGGCACA 57.221 33.333 0.00 0.00 37.20 4.57
25 26 6.140303 AGATCATGTTGATTATTGGCACAC 57.860 37.500 0.00 0.00 37.20 3.82
26 27 4.717233 TCATGTTGATTATTGGCACACC 57.283 40.909 0.00 0.00 39.29 4.16
27 28 3.128415 TCATGTTGATTATTGGCACACCG 59.872 43.478 0.00 0.00 39.29 4.94
28 29 1.815613 TGTTGATTATTGGCACACCGG 59.184 47.619 0.00 0.00 39.29 5.28
29 30 0.814457 TTGATTATTGGCACACCGGC 59.186 50.000 0.00 0.00 39.29 6.13
36 37 4.722700 GGCACACCGGCATGACCT 62.723 66.667 0.00 0.00 40.76 3.85
37 38 2.672996 GCACACCGGCATGACCTT 60.673 61.111 0.00 0.00 35.61 3.50
38 39 2.268076 GCACACCGGCATGACCTTT 61.268 57.895 0.00 0.00 35.61 3.11
39 40 1.875963 CACACCGGCATGACCTTTC 59.124 57.895 0.00 0.00 35.61 2.62
40 41 1.303317 ACACCGGCATGACCTTTCC 60.303 57.895 0.00 0.00 35.61 3.13
41 42 1.002134 CACCGGCATGACCTTTCCT 60.002 57.895 0.00 0.00 35.61 3.36
42 43 1.002134 ACCGGCATGACCTTTCCTG 60.002 57.895 0.00 0.00 35.61 3.86
43 44 1.002134 CCGGCATGACCTTTCCTGT 60.002 57.895 0.00 0.00 35.61 4.00
44 45 1.308069 CCGGCATGACCTTTCCTGTG 61.308 60.000 0.00 0.00 35.61 3.66
45 46 0.321564 CGGCATGACCTTTCCTGTGA 60.322 55.000 0.00 0.00 35.61 3.58
46 47 1.679944 CGGCATGACCTTTCCTGTGAT 60.680 52.381 0.00 0.00 35.61 3.06
47 48 1.747355 GGCATGACCTTTCCTGTGATG 59.253 52.381 0.00 0.00 34.51 3.07
48 49 2.440409 GCATGACCTTTCCTGTGATGT 58.560 47.619 0.00 0.00 31.10 3.06
49 50 3.609853 GCATGACCTTTCCTGTGATGTA 58.390 45.455 0.00 0.00 31.10 2.29
50 51 3.624861 GCATGACCTTTCCTGTGATGTAG 59.375 47.826 0.00 0.00 31.10 2.74
51 52 4.836825 CATGACCTTTCCTGTGATGTAGT 58.163 43.478 0.00 0.00 0.00 2.73
52 53 4.271696 TGACCTTTCCTGTGATGTAGTG 57.728 45.455 0.00 0.00 0.00 2.74
53 54 3.003480 GACCTTTCCTGTGATGTAGTGC 58.997 50.000 0.00 0.00 0.00 4.40
54 55 2.371841 ACCTTTCCTGTGATGTAGTGCA 59.628 45.455 0.00 0.00 0.00 4.57
55 56 3.009473 ACCTTTCCTGTGATGTAGTGCAT 59.991 43.478 0.00 0.00 41.24 3.96
56 57 3.376234 CCTTTCCTGTGATGTAGTGCATG 59.624 47.826 0.00 0.00 38.06 4.06
57 58 3.701205 TTCCTGTGATGTAGTGCATGT 57.299 42.857 0.00 0.00 38.06 3.21
58 59 2.976589 TCCTGTGATGTAGTGCATGTG 58.023 47.619 0.00 0.00 38.06 3.21
59 60 2.011947 CCTGTGATGTAGTGCATGTGG 58.988 52.381 0.00 0.00 38.06 4.17
60 61 1.399440 CTGTGATGTAGTGCATGTGGC 59.601 52.381 0.00 0.00 45.13 5.01
61 62 1.003464 TGTGATGTAGTGCATGTGGCT 59.997 47.619 0.00 0.00 45.15 4.75
62 63 2.235898 TGTGATGTAGTGCATGTGGCTA 59.764 45.455 0.00 0.00 45.15 3.93
63 64 3.118298 TGTGATGTAGTGCATGTGGCTAT 60.118 43.478 0.00 0.00 45.15 2.97
64 65 3.249320 GTGATGTAGTGCATGTGGCTATG 59.751 47.826 0.00 0.00 45.15 2.23
65 66 2.330440 TGTAGTGCATGTGGCTATGG 57.670 50.000 0.00 0.00 45.15 2.74
66 67 1.836802 TGTAGTGCATGTGGCTATGGA 59.163 47.619 0.00 0.00 45.15 3.41
67 68 2.439135 TGTAGTGCATGTGGCTATGGAT 59.561 45.455 0.00 0.00 45.15 3.41
68 69 3.645687 TGTAGTGCATGTGGCTATGGATA 59.354 43.478 0.00 0.00 45.15 2.59
69 70 3.862877 AGTGCATGTGGCTATGGATAA 57.137 42.857 0.00 0.00 45.15 1.75
70 71 4.377762 AGTGCATGTGGCTATGGATAAT 57.622 40.909 0.00 0.00 45.15 1.28
71 72 4.733165 AGTGCATGTGGCTATGGATAATT 58.267 39.130 0.00 0.00 45.15 1.40
463 464 7.502120 CATCAATTCTACCCTATTTCCTGTG 57.498 40.000 0.00 0.00 0.00 3.66
464 465 6.001449 TCAATTCTACCCTATTTCCTGTGG 57.999 41.667 0.00 0.00 0.00 4.17
465 466 5.491078 TCAATTCTACCCTATTTCCTGTGGT 59.509 40.000 0.00 0.00 0.00 4.16
466 467 4.837093 TTCTACCCTATTTCCTGTGGTG 57.163 45.455 0.00 0.00 0.00 4.17
467 468 3.798515 TCTACCCTATTTCCTGTGGTGT 58.201 45.455 0.00 0.00 0.00 4.16
468 469 2.879103 ACCCTATTTCCTGTGGTGTG 57.121 50.000 0.00 0.00 0.00 3.82
469 470 2.344592 ACCCTATTTCCTGTGGTGTGA 58.655 47.619 0.00 0.00 0.00 3.58
470 471 2.919602 ACCCTATTTCCTGTGGTGTGAT 59.080 45.455 0.00 0.00 0.00 3.06
471 472 3.333680 ACCCTATTTCCTGTGGTGTGATT 59.666 43.478 0.00 0.00 0.00 2.57
472 473 4.202673 ACCCTATTTCCTGTGGTGTGATTT 60.203 41.667 0.00 0.00 0.00 2.17
473 474 4.399303 CCCTATTTCCTGTGGTGTGATTTC 59.601 45.833 0.00 0.00 0.00 2.17
474 475 5.256474 CCTATTTCCTGTGGTGTGATTTCT 58.744 41.667 0.00 0.00 0.00 2.52
475 476 5.711976 CCTATTTCCTGTGGTGTGATTTCTT 59.288 40.000 0.00 0.00 0.00 2.52
476 477 6.209391 CCTATTTCCTGTGGTGTGATTTCTTT 59.791 38.462 0.00 0.00 0.00 2.52
477 478 5.930837 TTTCCTGTGGTGTGATTTCTTTT 57.069 34.783 0.00 0.00 0.00 2.27
478 479 5.930837 TTCCTGTGGTGTGATTTCTTTTT 57.069 34.783 0.00 0.00 0.00 1.94
479 480 5.514274 TCCTGTGGTGTGATTTCTTTTTC 57.486 39.130 0.00 0.00 0.00 2.29
480 481 5.200483 TCCTGTGGTGTGATTTCTTTTTCT 58.800 37.500 0.00 0.00 0.00 2.52
481 482 5.656416 TCCTGTGGTGTGATTTCTTTTTCTT 59.344 36.000 0.00 0.00 0.00 2.52
482 483 5.979517 CCTGTGGTGTGATTTCTTTTTCTTC 59.020 40.000 0.00 0.00 0.00 2.87
483 484 6.183360 CCTGTGGTGTGATTTCTTTTTCTTCT 60.183 38.462 0.00 0.00 0.00 2.85
484 485 6.563422 TGTGGTGTGATTTCTTTTTCTTCTG 58.437 36.000 0.00 0.00 0.00 3.02
485 486 6.152661 TGTGGTGTGATTTCTTTTTCTTCTGT 59.847 34.615 0.00 0.00 0.00 3.41
486 487 7.035612 GTGGTGTGATTTCTTTTTCTTCTGTT 58.964 34.615 0.00 0.00 0.00 3.16
487 488 7.220875 GTGGTGTGATTTCTTTTTCTTCTGTTC 59.779 37.037 0.00 0.00 0.00 3.18
488 489 6.414987 GGTGTGATTTCTTTTTCTTCTGTTCG 59.585 38.462 0.00 0.00 0.00 3.95
489 490 6.967199 GTGTGATTTCTTTTTCTTCTGTTCGT 59.033 34.615 0.00 0.00 0.00 3.85
490 491 6.966632 TGTGATTTCTTTTTCTTCTGTTCGTG 59.033 34.615 0.00 0.00 0.00 4.35
491 492 6.414987 GTGATTTCTTTTTCTTCTGTTCGTGG 59.585 38.462 0.00 0.00 0.00 4.94
492 493 5.890424 TTTCTTTTTCTTCTGTTCGTGGT 57.110 34.783 0.00 0.00 0.00 4.16
493 494 4.875544 TCTTTTTCTTCTGTTCGTGGTG 57.124 40.909 0.00 0.00 0.00 4.17
494 495 4.509616 TCTTTTTCTTCTGTTCGTGGTGA 58.490 39.130 0.00 0.00 0.00 4.02
495 496 5.123227 TCTTTTTCTTCTGTTCGTGGTGAT 58.877 37.500 0.00 0.00 0.00 3.06
496 497 6.285224 TCTTTTTCTTCTGTTCGTGGTGATA 58.715 36.000 0.00 0.00 0.00 2.15
497 498 5.917541 TTTTCTTCTGTTCGTGGTGATAC 57.082 39.130 0.00 0.00 0.00 2.24
498 499 4.866508 TTCTTCTGTTCGTGGTGATACT 57.133 40.909 0.00 0.00 0.00 2.12
499 500 4.436242 TCTTCTGTTCGTGGTGATACTC 57.564 45.455 0.00 0.00 0.00 2.59
500 501 2.913777 TCTGTTCGTGGTGATACTCG 57.086 50.000 0.00 0.00 0.00 4.18
501 502 1.471287 TCTGTTCGTGGTGATACTCGG 59.529 52.381 0.00 0.00 0.00 4.63
502 503 0.528924 TGTTCGTGGTGATACTCGGG 59.471 55.000 0.00 0.00 0.00 5.14
503 504 0.529378 GTTCGTGGTGATACTCGGGT 59.471 55.000 0.00 0.00 0.00 5.28
504 505 1.067354 GTTCGTGGTGATACTCGGGTT 60.067 52.381 0.00 0.00 0.00 4.11
505 506 0.813184 TCGTGGTGATACTCGGGTTC 59.187 55.000 0.00 0.00 0.00 3.62
506 507 0.528924 CGTGGTGATACTCGGGTTCA 59.471 55.000 0.00 0.00 0.00 3.18
507 508 1.469251 CGTGGTGATACTCGGGTTCAG 60.469 57.143 0.00 0.00 0.00 3.02
508 509 1.822990 GTGGTGATACTCGGGTTCAGA 59.177 52.381 0.00 0.00 0.00 3.27
509 510 2.431057 GTGGTGATACTCGGGTTCAGAT 59.569 50.000 0.00 0.00 0.00 2.90
510 511 3.104512 TGGTGATACTCGGGTTCAGATT 58.895 45.455 0.00 0.00 0.00 2.40
511 512 3.132289 TGGTGATACTCGGGTTCAGATTC 59.868 47.826 0.00 0.00 0.00 2.52
512 513 3.492829 GGTGATACTCGGGTTCAGATTCC 60.493 52.174 0.00 0.00 0.00 3.01
513 514 2.361119 TGATACTCGGGTTCAGATTCCG 59.639 50.000 0.00 5.79 44.59 4.30
518 519 2.380084 CGGGTTCAGATTCCGAAGAA 57.620 50.000 6.17 0.00 45.96 2.52
519 520 2.000447 CGGGTTCAGATTCCGAAGAAC 59.000 52.381 6.17 0.00 45.96 3.01
520 521 2.353803 CGGGTTCAGATTCCGAAGAACT 60.354 50.000 6.17 0.00 45.96 3.01
521 522 3.003480 GGGTTCAGATTCCGAAGAACTG 58.997 50.000 10.09 8.28 33.97 3.16
522 523 3.003480 GGTTCAGATTCCGAAGAACTGG 58.997 50.000 10.09 0.00 33.97 4.00
523 524 2.386661 TCAGATTCCGAAGAACTGGC 57.613 50.000 10.66 0.00 33.97 4.85
524 525 1.002366 CAGATTCCGAAGAACTGGCG 58.998 55.000 0.00 0.00 33.97 5.69
525 526 0.608640 AGATTCCGAAGAACTGGCGT 59.391 50.000 0.00 0.00 33.97 5.68
526 527 0.721718 GATTCCGAAGAACTGGCGTG 59.278 55.000 0.00 0.00 33.97 5.34
527 528 0.034896 ATTCCGAAGAACTGGCGTGT 59.965 50.000 0.00 0.00 33.97 4.49
528 529 0.878523 TTCCGAAGAACTGGCGTGTG 60.879 55.000 0.00 0.00 0.00 3.82
529 530 1.594293 CCGAAGAACTGGCGTGTGT 60.594 57.895 0.00 0.00 0.00 3.72
530 531 1.157870 CCGAAGAACTGGCGTGTGTT 61.158 55.000 0.00 0.00 0.00 3.32
531 532 0.655733 CGAAGAACTGGCGTGTGTTT 59.344 50.000 0.00 0.00 0.00 2.83
532 533 1.594518 CGAAGAACTGGCGTGTGTTTG 60.595 52.381 0.00 0.00 0.00 2.93
533 534 1.400494 GAAGAACTGGCGTGTGTTTGT 59.600 47.619 0.00 0.00 0.00 2.83
534 535 0.732571 AGAACTGGCGTGTGTTTGTG 59.267 50.000 0.00 0.00 0.00 3.33
535 536 0.450184 GAACTGGCGTGTGTTTGTGT 59.550 50.000 0.00 0.00 0.00 3.72
536 537 0.170116 AACTGGCGTGTGTTTGTGTG 59.830 50.000 0.00 0.00 0.00 3.82
537 538 0.675208 ACTGGCGTGTGTTTGTGTGA 60.675 50.000 0.00 0.00 0.00 3.58
538 539 0.027979 CTGGCGTGTGTTTGTGTGAG 59.972 55.000 0.00 0.00 0.00 3.51
539 540 1.298339 GGCGTGTGTTTGTGTGAGC 60.298 57.895 0.00 0.00 0.00 4.26
540 541 1.714899 GGCGTGTGTTTGTGTGAGCT 61.715 55.000 0.00 0.00 0.00 4.09
541 542 0.934496 GCGTGTGTTTGTGTGAGCTA 59.066 50.000 0.00 0.00 0.00 3.32
542 543 1.531149 GCGTGTGTTTGTGTGAGCTAT 59.469 47.619 0.00 0.00 0.00 2.97
543 544 2.032030 GCGTGTGTTTGTGTGAGCTATT 60.032 45.455 0.00 0.00 0.00 1.73
544 545 3.544651 CGTGTGTTTGTGTGAGCTATTG 58.455 45.455 0.00 0.00 0.00 1.90
545 546 3.247411 CGTGTGTTTGTGTGAGCTATTGA 59.753 43.478 0.00 0.00 0.00 2.57
546 547 4.527564 GTGTGTTTGTGTGAGCTATTGAC 58.472 43.478 0.00 0.00 0.00 3.18
547 548 4.035091 GTGTGTTTGTGTGAGCTATTGACA 59.965 41.667 0.00 0.00 0.00 3.58
548 549 4.035091 TGTGTTTGTGTGAGCTATTGACAC 59.965 41.667 9.69 9.69 40.38 3.67
574 575 5.932303 GCCAAATCGAATTAGGATGCTACTA 59.068 40.000 0.00 0.00 0.00 1.82
581 582 5.508153 CGAATTAGGATGCTACTACTGCTGT 60.508 44.000 0.66 0.66 0.00 4.40
585 586 2.093973 GGATGCTACTACTGCTGTGTGT 60.094 50.000 6.48 7.80 0.00 3.72
600 601 1.135915 GTGTGTTGCCATGTTTGACCA 59.864 47.619 0.00 0.00 0.00 4.02
602 603 2.035704 TGTGTTGCCATGTTTGACCATC 59.964 45.455 0.00 0.00 0.00 3.51
609 610 4.178540 GCCATGTTTGACCATCTTGATTG 58.821 43.478 0.00 0.00 0.00 2.67
610 611 4.751060 CCATGTTTGACCATCTTGATTGG 58.249 43.478 0.00 0.00 40.26 3.16
611 612 4.382254 CCATGTTTGACCATCTTGATTGGG 60.382 45.833 0.00 0.00 38.64 4.12
617 618 1.995542 ACCATCTTGATTGGGACCTGT 59.004 47.619 0.00 0.00 38.64 4.00
628 629 2.736347 TGGGACCTGTTAGCTAGAGAC 58.264 52.381 0.00 0.00 0.00 3.36
633 634 2.832733 ACCTGTTAGCTAGAGACAACCC 59.167 50.000 0.00 0.00 0.00 4.11
641 642 3.008485 AGCTAGAGACAACCCTTTTCAGG 59.992 47.826 0.00 0.00 40.45 3.86
672 673 2.820845 AACCCAGGACTTTGGTTGC 58.179 52.632 0.00 0.00 40.75 4.17
677 678 2.104622 CCCAGGACTTTGGTTGCAAATT 59.895 45.455 0.00 0.00 36.45 1.82
684 685 5.759763 GGACTTTGGTTGCAAATTCTGAATT 59.240 36.000 9.76 9.76 0.00 2.17
685 686 6.928492 GGACTTTGGTTGCAAATTCTGAATTA 59.072 34.615 15.45 0.00 0.00 1.40
686 687 7.095649 GGACTTTGGTTGCAAATTCTGAATTAC 60.096 37.037 15.45 11.44 0.00 1.89
727 728 3.206150 TGTGTGGTTCTTTCTCTCTTGC 58.794 45.455 0.00 0.00 0.00 4.01
738 739 3.497297 TCTCTCTTGCGCGTAACATAA 57.503 42.857 5.23 0.00 0.00 1.90
815 821 4.884164 GTCTGGAAATTACTCCATTCCTGG 59.116 45.833 0.00 0.00 44.59 4.45
841 847 6.154363 TCTCAGGAACACAAAAGGAAACAATT 59.846 34.615 0.00 0.00 0.00 2.32
842 848 7.340743 TCTCAGGAACACAAAAGGAAACAATTA 59.659 33.333 0.00 0.00 0.00 1.40
844 850 8.482128 TCAGGAACACAAAAGGAAACAATTAAT 58.518 29.630 0.00 0.00 0.00 1.40
888 894 7.342581 TGTCCATTGTGTTAGCCTTTGATATA 58.657 34.615 0.00 0.00 0.00 0.86
933 939 3.509575 TGTTAATCATTGGTTGGTGCCTC 59.490 43.478 0.00 0.00 0.00 4.70
1018 1024 1.068055 GCATGCCAAGACCAAGACTTG 60.068 52.381 6.36 8.31 42.72 3.16
1083 1109 3.773418 TTCCATTGTCGTTCCCTTACA 57.227 42.857 0.00 0.00 0.00 2.41
1152 2174 2.315781 TAGCCCAAGGAGCTGCATCG 62.316 60.000 8.35 0.00 41.71 3.84
1153 2175 2.515523 CCCAAGGAGCTGCATCGG 60.516 66.667 8.35 4.21 0.00 4.18
1223 2245 1.048601 GCGAGGATATCAGGTGGGAA 58.951 55.000 4.83 0.00 0.00 3.97
1405 2427 3.362831 CCGCAACAACTACGTAGTAAGTG 59.637 47.826 27.59 23.03 45.13 3.16
1426 2472 2.938838 CCTTCCAAGGTTTGTACACCA 58.061 47.619 0.00 0.00 41.41 4.17
1427 2473 3.496331 CCTTCCAAGGTTTGTACACCAT 58.504 45.455 0.00 0.00 41.41 3.55
1428 2474 3.255642 CCTTCCAAGGTTTGTACACCATG 59.744 47.826 0.00 0.00 41.41 3.66
1429 2475 2.235016 TCCAAGGTTTGTACACCATGC 58.765 47.619 0.00 0.00 39.62 4.06
1432 2478 2.622942 CAAGGTTTGTACACCATGCACT 59.377 45.455 0.00 0.00 39.62 4.40
1433 2479 3.780804 AGGTTTGTACACCATGCACTA 57.219 42.857 0.00 0.00 39.62 2.74
1521 2573 4.569966 CAGTTGAGGTATCTTGACATGAGC 59.430 45.833 0.00 0.00 0.00 4.26
1541 2593 4.655963 AGCTACAATGACTTCAACCACAT 58.344 39.130 0.00 0.00 0.00 3.21
1648 2700 4.811557 CCCAACTCGGTAATCTCTCAAATC 59.188 45.833 0.00 0.00 0.00 2.17
1696 2796 7.279313 GGGATTATTACAATGTTCTGTACACGT 59.721 37.037 0.00 0.00 40.19 4.49
1701 2801 3.558418 ACAATGTTCTGTACACGTTGGAC 59.442 43.478 16.76 3.76 42.95 4.02
1704 2804 2.223876 TGTTCTGTACACGTTGGACCTC 60.224 50.000 0.00 0.00 27.33 3.85
1705 2805 1.991121 TCTGTACACGTTGGACCTCT 58.009 50.000 0.00 0.00 27.33 3.69
1748 2848 5.119898 CACTGTTGAGCTATCTTGACTTGAC 59.880 44.000 0.00 0.00 0.00 3.18
1795 2895 2.030628 GGTTGGGTTCACATGGTTAACG 60.031 50.000 0.00 0.00 0.00 3.18
1796 2896 1.898902 TGGGTTCACATGGTTAACGG 58.101 50.000 0.00 0.00 0.00 4.44
1982 3094 2.896443 GGAGCTTCACCTCTCCCG 59.104 66.667 0.00 0.00 42.30 5.14
2395 3582 8.600668 TGAAAATGGATATTGAACCAAATTGGA 58.399 29.630 20.25 0.00 40.96 3.53
2541 3728 7.773489 TGATGTTATTCCTGATTGGTTTTGA 57.227 32.000 0.00 0.00 37.07 2.69
2647 3834 2.435805 GCCATCAGTATTGGTCTGGAGA 59.564 50.000 6.59 0.00 36.57 3.71
2648 3835 3.494048 GCCATCAGTATTGGTCTGGAGAG 60.494 52.174 6.59 0.00 36.57 3.20
3140 4335 3.748048 AGATCAAACATGTTCAGTGGTCG 59.252 43.478 12.39 0.00 0.00 4.79
3331 4562 3.938963 AGGCCAAACACGTGATTATACTG 59.061 43.478 25.01 4.94 0.00 2.74
3358 4589 3.607775 CGTCTTCAGCCAAGTTGTGAATG 60.608 47.826 8.80 5.06 33.27 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.694411 GTGTGCCAATAATCAACATGATCTTC 59.306 38.462 0.00 0.00 35.76 2.87
1 2 6.406177 GGTGTGCCAATAATCAACATGATCTT 60.406 38.462 0.00 0.00 33.30 2.40
2 3 5.068198 GGTGTGCCAATAATCAACATGATCT 59.932 40.000 0.00 0.00 33.30 2.75
3 4 5.284079 GGTGTGCCAATAATCAACATGATC 58.716 41.667 0.00 0.00 33.30 2.92
4 5 4.202040 CGGTGTGCCAATAATCAACATGAT 60.202 41.667 0.00 0.00 34.91 2.45
5 6 3.128415 CGGTGTGCCAATAATCAACATGA 59.872 43.478 0.00 0.00 34.09 3.07
6 7 3.437428 CGGTGTGCCAATAATCAACATG 58.563 45.455 0.00 0.00 34.09 3.21
7 8 2.426738 CCGGTGTGCCAATAATCAACAT 59.573 45.455 0.00 0.00 34.09 2.71
8 9 1.815613 CCGGTGTGCCAATAATCAACA 59.184 47.619 0.00 0.00 34.09 3.33
9 10 1.469079 GCCGGTGTGCCAATAATCAAC 60.469 52.381 1.90 0.00 34.09 3.18
10 11 0.814457 GCCGGTGTGCCAATAATCAA 59.186 50.000 1.90 0.00 34.09 2.57
11 12 0.322906 TGCCGGTGTGCCAATAATCA 60.323 50.000 1.90 0.00 34.09 2.57
12 13 1.032014 ATGCCGGTGTGCCAATAATC 58.968 50.000 1.90 0.00 34.09 1.75
13 14 0.746063 CATGCCGGTGTGCCAATAAT 59.254 50.000 1.90 0.00 34.09 1.28
14 15 0.322906 TCATGCCGGTGTGCCAATAA 60.323 50.000 1.90 0.00 34.09 1.40
15 16 1.029408 GTCATGCCGGTGTGCCAATA 61.029 55.000 1.90 0.00 34.09 1.90
16 17 2.035469 TCATGCCGGTGTGCCAAT 59.965 55.556 1.90 0.00 34.09 3.16
17 18 2.983030 GTCATGCCGGTGTGCCAA 60.983 61.111 1.90 0.00 34.09 4.52
19 20 4.722700 AGGTCATGCCGGTGTGCC 62.723 66.667 1.90 8.23 43.70 5.01
20 21 2.200170 GAAAGGTCATGCCGGTGTGC 62.200 60.000 1.90 0.00 43.70 4.57
21 22 1.586154 GGAAAGGTCATGCCGGTGTG 61.586 60.000 1.90 2.10 43.70 3.82
22 23 1.303317 GGAAAGGTCATGCCGGTGT 60.303 57.895 1.90 0.00 43.70 4.16
23 24 1.002134 AGGAAAGGTCATGCCGGTG 60.002 57.895 1.90 0.00 43.70 4.94
24 25 1.002134 CAGGAAAGGTCATGCCGGT 60.002 57.895 1.90 0.00 43.70 5.28
25 26 1.002134 ACAGGAAAGGTCATGCCGG 60.002 57.895 0.00 0.00 39.19 6.13
26 27 0.321564 TCACAGGAAAGGTCATGCCG 60.322 55.000 0.00 0.00 39.19 5.69
27 28 1.747355 CATCACAGGAAAGGTCATGCC 59.253 52.381 0.00 0.00 39.19 4.40
28 29 2.440409 ACATCACAGGAAAGGTCATGC 58.560 47.619 0.00 0.00 39.19 4.06
29 30 4.633126 CACTACATCACAGGAAAGGTCATG 59.367 45.833 0.00 0.00 41.40 3.07
30 31 4.836825 CACTACATCACAGGAAAGGTCAT 58.163 43.478 0.00 0.00 0.00 3.06
31 32 3.557054 GCACTACATCACAGGAAAGGTCA 60.557 47.826 0.00 0.00 0.00 4.02
32 33 3.003480 GCACTACATCACAGGAAAGGTC 58.997 50.000 0.00 0.00 0.00 3.85
33 34 2.371841 TGCACTACATCACAGGAAAGGT 59.628 45.455 0.00 0.00 0.00 3.50
34 35 3.057969 TGCACTACATCACAGGAAAGG 57.942 47.619 0.00 0.00 0.00 3.11
35 36 4.005650 ACATGCACTACATCACAGGAAAG 58.994 43.478 0.00 0.00 36.64 2.62
36 37 3.752747 CACATGCACTACATCACAGGAAA 59.247 43.478 0.00 0.00 36.64 3.13
37 38 3.337358 CACATGCACTACATCACAGGAA 58.663 45.455 0.00 0.00 36.64 3.36
38 39 2.355007 CCACATGCACTACATCACAGGA 60.355 50.000 0.00 0.00 36.64 3.86
39 40 2.011947 CCACATGCACTACATCACAGG 58.988 52.381 0.00 0.00 36.64 4.00
40 41 1.399440 GCCACATGCACTACATCACAG 59.601 52.381 0.00 0.00 36.64 3.66
41 42 1.003464 AGCCACATGCACTACATCACA 59.997 47.619 0.00 0.00 44.83 3.58
42 43 1.742761 AGCCACATGCACTACATCAC 58.257 50.000 0.00 0.00 44.83 3.06
43 44 3.469739 CATAGCCACATGCACTACATCA 58.530 45.455 0.00 0.00 44.83 3.07
44 45 2.810274 CCATAGCCACATGCACTACATC 59.190 50.000 0.00 0.00 44.83 3.06
45 46 2.439135 TCCATAGCCACATGCACTACAT 59.561 45.455 0.00 0.00 44.83 2.29
46 47 1.836802 TCCATAGCCACATGCACTACA 59.163 47.619 0.00 0.00 44.83 2.74
47 48 2.620251 TCCATAGCCACATGCACTAC 57.380 50.000 0.00 0.00 44.83 2.73
48 49 4.972751 TTATCCATAGCCACATGCACTA 57.027 40.909 0.00 0.00 44.83 2.74
49 50 3.862877 TTATCCATAGCCACATGCACT 57.137 42.857 0.00 0.00 44.83 4.40
439 440 6.488006 CCACAGGAAATAGGGTAGAATTGATG 59.512 42.308 0.00 0.00 0.00 3.07
440 441 6.160459 ACCACAGGAAATAGGGTAGAATTGAT 59.840 38.462 0.00 0.00 0.00 2.57
441 442 5.491078 ACCACAGGAAATAGGGTAGAATTGA 59.509 40.000 0.00 0.00 0.00 2.57
442 443 5.590259 CACCACAGGAAATAGGGTAGAATTG 59.410 44.000 0.00 0.00 0.00 2.32
443 444 5.253096 ACACCACAGGAAATAGGGTAGAATT 59.747 40.000 0.00 0.00 0.00 2.17
444 445 4.788617 ACACCACAGGAAATAGGGTAGAAT 59.211 41.667 0.00 0.00 0.00 2.40
445 446 4.019681 CACACCACAGGAAATAGGGTAGAA 60.020 45.833 0.00 0.00 0.00 2.10
446 447 3.517901 CACACCACAGGAAATAGGGTAGA 59.482 47.826 0.00 0.00 0.00 2.59
447 448 3.517901 TCACACCACAGGAAATAGGGTAG 59.482 47.826 0.00 0.00 0.00 3.18
448 449 3.522759 TCACACCACAGGAAATAGGGTA 58.477 45.455 0.00 0.00 0.00 3.69
449 450 2.344592 TCACACCACAGGAAATAGGGT 58.655 47.619 0.00 0.00 0.00 4.34
450 451 3.652057 ATCACACCACAGGAAATAGGG 57.348 47.619 0.00 0.00 0.00 3.53
451 452 5.256474 AGAAATCACACCACAGGAAATAGG 58.744 41.667 0.00 0.00 0.00 2.57
452 453 6.824305 AAGAAATCACACCACAGGAAATAG 57.176 37.500 0.00 0.00 0.00 1.73
453 454 7.595819 AAAAGAAATCACACCACAGGAAATA 57.404 32.000 0.00 0.00 0.00 1.40
454 455 6.484364 AAAAGAAATCACACCACAGGAAAT 57.516 33.333 0.00 0.00 0.00 2.17
455 456 5.930837 AAAAGAAATCACACCACAGGAAA 57.069 34.783 0.00 0.00 0.00 3.13
456 457 5.656416 AGAAAAAGAAATCACACCACAGGAA 59.344 36.000 0.00 0.00 0.00 3.36
457 458 5.200483 AGAAAAAGAAATCACACCACAGGA 58.800 37.500 0.00 0.00 0.00 3.86
458 459 5.520376 AGAAAAAGAAATCACACCACAGG 57.480 39.130 0.00 0.00 0.00 4.00
459 460 6.694411 CAGAAGAAAAAGAAATCACACCACAG 59.306 38.462 0.00 0.00 0.00 3.66
460 461 6.152661 ACAGAAGAAAAAGAAATCACACCACA 59.847 34.615 0.00 0.00 0.00 4.17
461 462 6.564328 ACAGAAGAAAAAGAAATCACACCAC 58.436 36.000 0.00 0.00 0.00 4.16
462 463 6.773976 ACAGAAGAAAAAGAAATCACACCA 57.226 33.333 0.00 0.00 0.00 4.17
463 464 6.414987 CGAACAGAAGAAAAAGAAATCACACC 59.585 38.462 0.00 0.00 0.00 4.16
464 465 6.967199 ACGAACAGAAGAAAAAGAAATCACAC 59.033 34.615 0.00 0.00 0.00 3.82
465 466 6.966632 CACGAACAGAAGAAAAAGAAATCACA 59.033 34.615 0.00 0.00 0.00 3.58
466 467 6.414987 CCACGAACAGAAGAAAAAGAAATCAC 59.585 38.462 0.00 0.00 0.00 3.06
467 468 6.094881 ACCACGAACAGAAGAAAAAGAAATCA 59.905 34.615 0.00 0.00 0.00 2.57
468 469 6.414987 CACCACGAACAGAAGAAAAAGAAATC 59.585 38.462 0.00 0.00 0.00 2.17
469 470 6.094881 TCACCACGAACAGAAGAAAAAGAAAT 59.905 34.615 0.00 0.00 0.00 2.17
470 471 5.413213 TCACCACGAACAGAAGAAAAAGAAA 59.587 36.000 0.00 0.00 0.00 2.52
471 472 4.938832 TCACCACGAACAGAAGAAAAAGAA 59.061 37.500 0.00 0.00 0.00 2.52
472 473 4.509616 TCACCACGAACAGAAGAAAAAGA 58.490 39.130 0.00 0.00 0.00 2.52
473 474 4.875544 TCACCACGAACAGAAGAAAAAG 57.124 40.909 0.00 0.00 0.00 2.27
474 475 6.053005 AGTATCACCACGAACAGAAGAAAAA 58.947 36.000 0.00 0.00 0.00 1.94
475 476 5.607477 AGTATCACCACGAACAGAAGAAAA 58.393 37.500 0.00 0.00 0.00 2.29
476 477 5.209818 AGTATCACCACGAACAGAAGAAA 57.790 39.130 0.00 0.00 0.00 2.52
477 478 4.615223 CGAGTATCACCACGAACAGAAGAA 60.615 45.833 0.00 0.00 33.17 2.52
478 479 3.119955 CGAGTATCACCACGAACAGAAGA 60.120 47.826 0.00 0.00 33.17 2.87
479 480 3.172050 CGAGTATCACCACGAACAGAAG 58.828 50.000 0.00 0.00 33.17 2.85
480 481 2.094906 CCGAGTATCACCACGAACAGAA 60.095 50.000 0.00 0.00 33.17 3.02
481 482 1.471287 CCGAGTATCACCACGAACAGA 59.529 52.381 0.00 0.00 33.17 3.41
482 483 1.469251 CCCGAGTATCACCACGAACAG 60.469 57.143 0.00 0.00 33.17 3.16
483 484 0.528924 CCCGAGTATCACCACGAACA 59.471 55.000 0.00 0.00 33.17 3.18
484 485 0.529378 ACCCGAGTATCACCACGAAC 59.471 55.000 0.00 0.00 33.17 3.95
485 486 1.203052 GAACCCGAGTATCACCACGAA 59.797 52.381 0.00 0.00 33.17 3.85
486 487 0.813184 GAACCCGAGTATCACCACGA 59.187 55.000 0.00 0.00 33.17 4.35
487 488 0.528924 TGAACCCGAGTATCACCACG 59.471 55.000 0.00 0.00 33.17 4.94
488 489 1.822990 TCTGAACCCGAGTATCACCAC 59.177 52.381 0.00 0.00 33.17 4.16
489 490 2.225382 TCTGAACCCGAGTATCACCA 57.775 50.000 0.00 0.00 33.17 4.17
490 491 3.492829 GGAATCTGAACCCGAGTATCACC 60.493 52.174 0.00 0.00 33.17 4.02
491 492 3.718815 GGAATCTGAACCCGAGTATCAC 58.281 50.000 0.00 0.00 33.17 3.06
492 493 2.361119 CGGAATCTGAACCCGAGTATCA 59.639 50.000 13.59 0.00 45.58 2.15
493 494 2.621998 TCGGAATCTGAACCCGAGTATC 59.378 50.000 16.37 0.00 46.17 2.24
494 495 2.662866 TCGGAATCTGAACCCGAGTAT 58.337 47.619 16.37 0.00 46.17 2.12
495 496 2.133281 TCGGAATCTGAACCCGAGTA 57.867 50.000 16.37 0.00 46.17 2.59
496 497 2.971676 TCGGAATCTGAACCCGAGT 58.028 52.632 16.37 0.00 46.17 4.18
499 500 2.000447 GTTCTTCGGAATCTGAACCCG 59.000 52.381 12.89 12.89 44.22 5.28
500 501 3.003480 CAGTTCTTCGGAATCTGAACCC 58.997 50.000 14.23 0.00 39.45 4.11
501 502 3.003480 CCAGTTCTTCGGAATCTGAACC 58.997 50.000 14.23 0.00 39.45 3.62
502 503 2.416893 GCCAGTTCTTCGGAATCTGAAC 59.583 50.000 11.35 11.35 39.06 3.18
503 504 2.699954 GCCAGTTCTTCGGAATCTGAA 58.300 47.619 4.27 4.27 36.32 3.02
504 505 1.404181 CGCCAGTTCTTCGGAATCTGA 60.404 52.381 14.68 0.00 36.32 3.27
505 506 1.002366 CGCCAGTTCTTCGGAATCTG 58.998 55.000 0.00 1.42 36.27 2.90
506 507 0.608640 ACGCCAGTTCTTCGGAATCT 59.391 50.000 0.00 0.00 36.27 2.40
507 508 0.721718 CACGCCAGTTCTTCGGAATC 59.278 55.000 0.00 0.00 36.27 2.52
508 509 0.034896 ACACGCCAGTTCTTCGGAAT 59.965 50.000 0.00 0.00 36.27 3.01
509 510 0.878523 CACACGCCAGTTCTTCGGAA 60.879 55.000 0.00 0.00 0.00 4.30
510 511 1.300620 CACACGCCAGTTCTTCGGA 60.301 57.895 0.00 0.00 0.00 4.55
511 512 1.157870 AACACACGCCAGTTCTTCGG 61.158 55.000 0.00 0.00 0.00 4.30
512 513 0.655733 AAACACACGCCAGTTCTTCG 59.344 50.000 0.00 0.00 0.00 3.79
513 514 1.400494 ACAAACACACGCCAGTTCTTC 59.600 47.619 0.00 0.00 0.00 2.87
514 515 1.132262 CACAAACACACGCCAGTTCTT 59.868 47.619 0.00 0.00 0.00 2.52
515 516 0.732571 CACAAACACACGCCAGTTCT 59.267 50.000 0.00 0.00 0.00 3.01
516 517 0.450184 ACACAAACACACGCCAGTTC 59.550 50.000 0.00 0.00 0.00 3.01
517 518 0.170116 CACACAAACACACGCCAGTT 59.830 50.000 0.00 0.00 0.00 3.16
518 519 0.675208 TCACACAAACACACGCCAGT 60.675 50.000 0.00 0.00 0.00 4.00
519 520 0.027979 CTCACACAAACACACGCCAG 59.972 55.000 0.00 0.00 0.00 4.85
520 521 1.987704 GCTCACACAAACACACGCCA 61.988 55.000 0.00 0.00 0.00 5.69
521 522 1.298339 GCTCACACAAACACACGCC 60.298 57.895 0.00 0.00 0.00 5.68
522 523 0.934496 TAGCTCACACAAACACACGC 59.066 50.000 0.00 0.00 0.00 5.34
523 524 3.247411 TCAATAGCTCACACAAACACACG 59.753 43.478 0.00 0.00 0.00 4.49
524 525 4.035091 TGTCAATAGCTCACACAAACACAC 59.965 41.667 0.00 0.00 0.00 3.82
525 526 4.035091 GTGTCAATAGCTCACACAAACACA 59.965 41.667 11.38 0.00 40.22 3.72
526 527 4.035091 TGTGTCAATAGCTCACACAAACAC 59.965 41.667 14.97 10.74 45.72 3.32
527 528 4.195416 TGTGTCAATAGCTCACACAAACA 58.805 39.130 14.97 1.36 45.72 2.83
528 529 4.811555 TGTGTCAATAGCTCACACAAAC 57.188 40.909 14.97 0.00 45.72 2.93
531 532 2.416747 GCTGTGTCAATAGCTCACACA 58.583 47.619 15.93 15.93 46.35 3.72
532 533 1.734465 GGCTGTGTCAATAGCTCACAC 59.266 52.381 1.29 6.23 40.23 3.82
533 534 1.347378 TGGCTGTGTCAATAGCTCACA 59.653 47.619 5.22 5.22 40.23 3.58
534 535 2.099141 TGGCTGTGTCAATAGCTCAC 57.901 50.000 9.47 0.00 40.23 3.51
535 536 2.857186 TTGGCTGTGTCAATAGCTCA 57.143 45.000 9.47 4.64 40.23 4.26
536 537 3.242543 CGATTTGGCTGTGTCAATAGCTC 60.243 47.826 9.47 2.62 40.23 4.09
537 538 2.679837 CGATTTGGCTGTGTCAATAGCT 59.320 45.455 9.47 0.00 40.23 3.32
538 539 2.677836 TCGATTTGGCTGTGTCAATAGC 59.322 45.455 2.48 2.48 39.68 2.97
539 540 4.944962 TTCGATTTGGCTGTGTCAATAG 57.055 40.909 0.00 0.00 0.00 1.73
540 541 5.895636 AATTCGATTTGGCTGTGTCAATA 57.104 34.783 0.00 0.00 0.00 1.90
541 542 4.789012 AATTCGATTTGGCTGTGTCAAT 57.211 36.364 0.00 0.00 0.00 2.57
542 543 4.155826 CCTAATTCGATTTGGCTGTGTCAA 59.844 41.667 2.86 0.00 0.00 3.18
543 544 3.689161 CCTAATTCGATTTGGCTGTGTCA 59.311 43.478 2.86 0.00 0.00 3.58
544 545 3.938963 TCCTAATTCGATTTGGCTGTGTC 59.061 43.478 2.86 0.00 35.51 3.67
545 546 3.950397 TCCTAATTCGATTTGGCTGTGT 58.050 40.909 2.86 0.00 35.51 3.72
546 547 4.790766 GCATCCTAATTCGATTTGGCTGTG 60.791 45.833 2.86 1.24 34.98 3.66
547 548 3.316308 GCATCCTAATTCGATTTGGCTGT 59.684 43.478 2.86 0.00 34.98 4.40
548 549 3.567164 AGCATCCTAATTCGATTTGGCTG 59.433 43.478 2.86 5.52 35.41 4.85
585 586 3.229293 TCAAGATGGTCAAACATGGCAA 58.771 40.909 0.00 0.00 0.00 4.52
600 601 3.525199 AGCTAACAGGTCCCAATCAAGAT 59.475 43.478 0.00 0.00 0.00 2.40
602 603 3.356529 AGCTAACAGGTCCCAATCAAG 57.643 47.619 0.00 0.00 0.00 3.02
609 610 2.736347 TGTCTCTAGCTAACAGGTCCC 58.264 52.381 0.00 0.00 0.00 4.46
610 611 3.119065 GGTTGTCTCTAGCTAACAGGTCC 60.119 52.174 0.00 0.00 0.00 4.46
611 612 3.119065 GGGTTGTCTCTAGCTAACAGGTC 60.119 52.174 0.00 0.00 0.00 3.85
617 618 5.280011 CCTGAAAAGGGTTGTCTCTAGCTAA 60.280 44.000 0.00 0.00 0.00 3.09
633 634 4.021102 TGCCTCTAAGTTCCCTGAAAAG 57.979 45.455 0.00 0.00 0.00 2.27
641 642 1.340114 CCTGGGTTGCCTCTAAGTTCC 60.340 57.143 0.00 0.00 0.00 3.62
645 646 1.280457 AGTCCTGGGTTGCCTCTAAG 58.720 55.000 0.00 0.00 0.00 2.18
677 678 8.958119 AAAGCGTAATATTCCAGTAATTCAGA 57.042 30.769 0.00 0.00 0.00 3.27
716 717 2.143008 TGTTACGCGCAAGAGAGAAA 57.857 45.000 5.73 0.00 40.82 2.52
754 756 1.393603 TAGTGAGCCATCTGACGAGG 58.606 55.000 0.00 0.00 31.40 4.63
815 821 4.398044 TGTTTCCTTTTGTGTTCCTGAGAC 59.602 41.667 0.00 0.00 0.00 3.36
841 847 4.100653 CAGATCAGACTTGAGCCTCCATTA 59.899 45.833 0.00 0.00 40.59 1.90
842 848 3.113824 AGATCAGACTTGAGCCTCCATT 58.886 45.455 0.00 0.00 40.59 3.16
844 850 1.829849 CAGATCAGACTTGAGCCTCCA 59.170 52.381 0.00 0.00 40.59 3.86
888 894 1.560505 GACCAGGGCATCACCATTTT 58.439 50.000 0.00 0.00 42.05 1.82
933 939 7.588512 AGTTTCTTGCTATTAGCTCAAAAGTG 58.411 34.615 16.29 0.00 42.97 3.16
950 956 2.358898 CAGTGGTTGGTGGAGTTTCTTG 59.641 50.000 0.00 0.00 0.00 3.02
1018 1024 4.574674 TGGTCCATGATATGCTATTCCC 57.425 45.455 0.00 0.00 0.00 3.97
1083 1109 2.225394 TGGAAGAGGGAGAACAGCTACT 60.225 50.000 0.00 0.00 0.00 2.57
1152 2174 5.453567 AGAAAATCAACAGGCAAAGTACC 57.546 39.130 0.00 0.00 0.00 3.34
1153 2175 6.756542 ACAAAGAAAATCAACAGGCAAAGTAC 59.243 34.615 0.00 0.00 0.00 2.73
1421 2467 3.306780 GGACTTGTAGTAGTGCATGGTGT 60.307 47.826 0.00 0.00 36.59 4.16
1422 2468 3.262420 GGACTTGTAGTAGTGCATGGTG 58.738 50.000 0.00 0.00 36.59 4.17
1425 2471 4.314961 TGTTGGACTTGTAGTAGTGCATG 58.685 43.478 0.00 0.78 44.38 4.06
1426 2472 4.569943 CTGTTGGACTTGTAGTAGTGCAT 58.430 43.478 0.00 0.00 44.38 3.96
1427 2473 3.802329 GCTGTTGGACTTGTAGTAGTGCA 60.802 47.826 0.00 0.00 43.51 4.57
1428 2474 2.737252 GCTGTTGGACTTGTAGTAGTGC 59.263 50.000 0.00 0.00 37.05 4.40
1429 2475 3.006967 AGGCTGTTGGACTTGTAGTAGTG 59.993 47.826 0.00 0.00 0.00 2.74
1432 2478 3.236047 TCAGGCTGTTGGACTTGTAGTA 58.764 45.455 15.27 0.00 0.00 1.82
1433 2479 2.037772 CTCAGGCTGTTGGACTTGTAGT 59.962 50.000 15.27 0.00 0.00 2.73
1521 2573 6.149308 TGCTTATGTGGTTGAAGTCATTGTAG 59.851 38.462 0.00 0.00 0.00 2.74
1541 2593 2.016318 CCATGAACGCAGGAATGCTTA 58.984 47.619 0.00 0.00 0.00 3.09
1648 2700 7.397221 TCCCCACTAATATCAAGATATTGCAG 58.603 38.462 20.23 14.57 42.26 4.41
1685 2761 2.295349 GAGAGGTCCAACGTGTACAGAA 59.705 50.000 0.00 0.00 0.00 3.02
1696 2796 2.054021 TGACAACCATGAGAGGTCCAA 58.946 47.619 0.00 0.00 42.25 3.53
1701 2801 3.623906 AGATGTGACAACCATGAGAGG 57.376 47.619 0.00 0.00 0.00 3.69
1704 2804 5.522824 CAGTGATAGATGTGACAACCATGAG 59.477 44.000 0.00 0.00 0.00 2.90
1705 2805 5.046376 ACAGTGATAGATGTGACAACCATGA 60.046 40.000 0.00 0.00 0.00 3.07
1795 2895 4.075682 AGCACTTTTAGAGAAGAAAGCCC 58.924 43.478 0.00 0.00 36.56 5.19
1796 2896 5.615764 CGAAGCACTTTTAGAGAAGAAAGCC 60.616 44.000 0.00 0.00 36.56 4.35
1847 2953 8.621532 ATTTGATTTTGAAGTAGCAGACACTA 57.378 30.769 0.00 0.00 0.00 2.74
1982 3094 0.250901 AGGTCCATGCCACTCACAAC 60.251 55.000 0.00 0.00 0.00 3.32
2395 3582 5.176592 GTGCTTTAGTCTAAACGGAGGAAT 58.823 41.667 0.65 0.00 0.00 3.01
2541 3728 3.565307 TGAAGCTTGGGAAAATGTCACT 58.435 40.909 2.10 0.00 0.00 3.41
2647 3834 9.268282 TGGAACTAGACCTGTAAGATTATTTCT 57.732 33.333 0.00 0.00 34.07 2.52
2648 3835 9.315525 GTGGAACTAGACCTGTAAGATTATTTC 57.684 37.037 0.00 0.00 34.07 2.17
2943 4138 5.120519 GTCTAGACTATACATCCGAGAACCG 59.879 48.000 15.91 0.00 38.18 4.44
3048 4243 8.830915 TTGGCAATATTCCAAAGAACCTATTA 57.169 30.769 13.64 0.00 40.35 0.98
3108 4303 4.326826 ACATGTTTGATCTCACCGTCAAT 58.673 39.130 0.00 0.00 34.60 2.57
3140 4335 4.398358 GGCAAGTAAGGTTCTTGGGAATAC 59.602 45.833 7.58 0.00 41.50 1.89


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

AutoCloner maintained by Alex Coulton.