Multiple sequence alignment - TraesCS5B01G087300

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 TraesCS5B01G087300 chr5B 100.000 5483 0 0 1 5483 111910296 111904814 0.000000e+00 10126.0
1 TraesCS5B01G087300 chr5B 94.382 89 2 3 4954 5041 103322344 103322430 3.450000e-27 134.0
2 TraesCS5B01G087300 chr5B 100.000 31 0 0 648 678 437569044 437569014 2.130000e-04 58.4
3 TraesCS5B01G087300 chr5B 90.909 44 3 1 651 694 513984009 513983967 2.130000e-04 58.4
4 TraesCS5B01G087300 chr5A 95.674 4693 154 23 816 5481 97225783 97230453 0.000000e+00 7496.0
5 TraesCS5B01G087300 chr5A 94.309 246 10 2 1 242 97224636 97224881 1.860000e-99 374.0
6 TraesCS5B01G087300 chr5A 91.195 159 12 2 262 418 97225365 97225523 1.200000e-51 215.0
7 TraesCS5B01G087300 chr5A 85.965 114 10 3 703 814 97225578 97225687 3.470000e-22 117.0
8 TraesCS5B01G087300 chr5D 97.254 3788 80 9 1263 5030 102286759 102282976 0.000000e+00 6397.0
9 TraesCS5B01G087300 chr5D 95.025 402 11 5 816 1215 102287151 102286757 1.680000e-174 623.0
10 TraesCS5B01G087300 chr5D 88.632 475 20 21 3 443 102287899 102287425 1.040000e-151 547.0
11 TraesCS5B01G087300 chr5D 92.857 364 20 4 5122 5481 102282131 102281770 1.750000e-144 523.0
12 TraesCS5B01G087300 chr5D 85.121 289 17 9 4992 5275 102282406 102282139 7.000000e-69 272.0
13 TraesCS5B01G087300 chr5D 94.545 165 9 0 442 606 46311054 46310890 7.050000e-64 255.0
14 TraesCS5B01G087300 chr5D 93.064 173 8 3 442 610 517855171 517854999 3.280000e-62 250.0
15 TraesCS5B01G087300 chr5D 91.753 97 6 2 4954 5049 305712696 305712791 3.450000e-27 134.0
16 TraesCS5B01G087300 chr5D 85.714 119 8 8 703 814 102287363 102287247 3.470000e-22 117.0
17 TraesCS5B01G087300 chr5D 95.745 47 2 0 602 648 102287426 102287380 5.890000e-10 76.8
18 TraesCS5B01G087300 chr4B 95.679 162 7 0 439 600 63753838 63753999 1.510000e-65 261.0
19 TraesCS5B01G087300 chr4B 100.000 32 0 0 649 680 96930779 96930810 5.930000e-05 60.2
20 TraesCS5B01G087300 chr3D 96.226 159 6 0 442 600 238999414 238999572 1.510000e-65 261.0
21 TraesCS5B01G087300 chr3D 94.012 167 10 0 442 608 540255705 540255539 2.530000e-63 254.0
22 TraesCS5B01G087300 chr3D 100.000 31 0 0 651 681 63353112 63353142 2.130000e-04 58.4
23 TraesCS5B01G087300 chr2D 94.578 166 9 0 441 606 445733833 445733668 1.960000e-64 257.0
24 TraesCS5B01G087300 chr2D 94.512 164 9 0 441 604 305514868 305515031 2.530000e-63 254.0
25 TraesCS5B01G087300 chr2D 93.529 170 10 1 442 611 81574924 81575092 9.120000e-63 252.0
26 TraesCS5B01G087300 chr4D 93.529 170 8 3 442 610 58643917 58643750 3.280000e-62 250.0
27 TraesCS5B01G087300 chr4D 100.000 32 0 0 649 680 66303743 66303774 5.930000e-05 60.2
28 TraesCS5B01G087300 chr1B 93.684 95 2 3 4949 5043 422514245 422514155 7.410000e-29 139.0
29 TraesCS5B01G087300 chr1A 93.478 92 4 2 4954 5045 47806856 47806945 9.580000e-28 135.0
30 TraesCS5B01G087300 chr1A 92.473 93 6 1 4954 5046 537973603 537973694 1.240000e-26 132.0
31 TraesCS5B01G087300 chr1A 92.308 91 5 2 4954 5044 121132421 121132333 1.600000e-25 128.0
32 TraesCS5B01G087300 chr1D 90.099 101 8 2 4954 5052 439868662 439868562 4.460000e-26 130.0
33 TraesCS5B01G087300 chr1D 100.000 31 0 0 651 681 303340612 303340642 2.130000e-04 58.4
34 TraesCS5B01G087300 chr7B 100.000 32 0 0 649 680 638921270 638921301 5.930000e-05 60.2
35 TraesCS5B01G087300 chr4A 100.000 32 0 0 649 680 514922171 514922202 5.930000e-05 60.2
36 TraesCS5B01G087300 chr2A 100.000 30 0 0 651 680 385979266 385979295 7.670000e-04 56.5
37 TraesCS5B01G087300 chr2B 94.286 35 2 0 651 685 118066819 118066785 3.000000e-03 54.7


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 TraesCS5B01G087300 chr5B 111904814 111910296 5482 True 10126.000000 10126 100.000000 1 5483 1 chr5B.!!$R1 5482
1 TraesCS5B01G087300 chr5A 97224636 97230453 5817 False 2050.500000 7496 91.785750 1 5481 4 chr5A.!!$F1 5480
2 TraesCS5B01G087300 chr5D 102281770 102287899 6129 True 1222.257143 6397 91.478286 3 5481 7 chr5D.!!$R3 5478

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
116 121 0.034896 GGGGAAACAACAGAGAGCGA 59.965 55.000 0.00 0.00 0.00 4.93 F
1654 2256 0.394938 TTAAGTTCCCGAGTGCAGCA 59.605 50.000 0.00 0.00 0.00 4.41 F
2830 3432 0.806868 AGAAGTCGCCAATGCACATG 59.193 50.000 0.00 0.00 37.32 3.21 F
3152 3754 3.633986 CAGAAGGTGCTTTCCTTTGTTCT 59.366 43.478 9.11 1.36 46.38 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1739 2341 1.165270 GTAAACATGCTGGCCTTCGT 58.835 50.0 3.32 0.00 0.00 3.85 R
3101 3703 2.220133 CACCGGAAACAACAGTAAGTCG 59.780 50.0 9.46 0.00 0.00 4.18 R
4047 4664 0.546267 AGATCACTGGGCTGAGTGGT 60.546 55.0 14.51 9.37 43.16 4.16 R
4949 5566 0.033405 ACTGAGCTAGACGGGCCTAA 60.033 55.0 0.84 0.00 0.00 2.69 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
116 121 0.034896 GGGGAAACAACAGAGAGCGA 59.965 55.000 0.00 0.00 0.00 4.93
117 122 1.433534 GGGAAACAACAGAGAGCGAG 58.566 55.000 0.00 0.00 0.00 5.03
272 741 7.659799 TCATGTTATTAGGATGGTGTTAATCCG 59.340 37.037 0.00 0.00 46.97 4.18
420 919 7.429633 TCTTTAATTTGGTCGCAGATTTTCAA 58.570 30.769 0.00 0.00 40.67 2.69
441 940 4.675063 ACATCCCCCAGAATTAACTGTT 57.325 40.909 0.00 0.00 36.30 3.16
442 941 5.789574 ACATCCCCCAGAATTAACTGTTA 57.210 39.130 0.00 0.00 36.30 2.41
443 942 5.506708 ACATCCCCCAGAATTAACTGTTAC 58.493 41.667 0.00 0.00 36.30 2.50
444 943 5.253096 ACATCCCCCAGAATTAACTGTTACT 59.747 40.000 0.00 0.00 36.30 2.24
445 944 5.431179 TCCCCCAGAATTAACTGTTACTC 57.569 43.478 0.00 0.72 36.30 2.59
446 945 4.226620 TCCCCCAGAATTAACTGTTACTCC 59.773 45.833 0.00 0.00 36.30 3.85
447 946 4.524053 CCCCAGAATTAACTGTTACTCCC 58.476 47.826 0.00 0.00 36.30 4.30
448 947 4.227527 CCCCAGAATTAACTGTTACTCCCT 59.772 45.833 0.00 0.00 36.30 4.20
449 948 5.429130 CCCAGAATTAACTGTTACTCCCTC 58.571 45.833 0.00 0.00 36.30 4.30
450 949 5.429130 CCAGAATTAACTGTTACTCCCTCC 58.571 45.833 0.00 0.00 36.30 4.30
451 950 5.109903 CAGAATTAACTGTTACTCCCTCCG 58.890 45.833 0.00 0.00 33.73 4.63
452 951 4.776308 AGAATTAACTGTTACTCCCTCCGT 59.224 41.667 0.00 0.00 0.00 4.69
453 952 5.247792 AGAATTAACTGTTACTCCCTCCGTT 59.752 40.000 0.00 0.00 0.00 4.44
454 953 4.525912 TTAACTGTTACTCCCTCCGTTC 57.474 45.455 0.00 0.00 0.00 3.95
455 954 1.264295 ACTGTTACTCCCTCCGTTCC 58.736 55.000 0.00 0.00 0.00 3.62
456 955 1.203149 ACTGTTACTCCCTCCGTTCCT 60.203 52.381 0.00 0.00 0.00 3.36
457 956 2.042162 ACTGTTACTCCCTCCGTTCCTA 59.958 50.000 0.00 0.00 0.00 2.94
458 957 3.094572 CTGTTACTCCCTCCGTTCCTAA 58.905 50.000 0.00 0.00 0.00 2.69
459 958 3.509442 TGTTACTCCCTCCGTTCCTAAA 58.491 45.455 0.00 0.00 0.00 1.85
460 959 4.098894 TGTTACTCCCTCCGTTCCTAAAT 58.901 43.478 0.00 0.00 0.00 1.40
461 960 5.271598 TGTTACTCCCTCCGTTCCTAAATA 58.728 41.667 0.00 0.00 0.00 1.40
462 961 5.901276 TGTTACTCCCTCCGTTCCTAAATAT 59.099 40.000 0.00 0.00 0.00 1.28
463 962 7.068702 TGTTACTCCCTCCGTTCCTAAATATA 58.931 38.462 0.00 0.00 0.00 0.86
464 963 7.564660 TGTTACTCCCTCCGTTCCTAAATATAA 59.435 37.037 0.00 0.00 0.00 0.98
465 964 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
466 965 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
467 966 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
468 967 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
469 968 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
470 969 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
471 970 7.441458 CCCTCCGTTCCTAAATATAAGTCTTTG 59.559 40.741 0.00 0.00 0.00 2.77
472 971 7.985752 CCTCCGTTCCTAAATATAAGTCTTTGT 59.014 37.037 0.00 0.00 0.00 2.83
490 989 9.646427 AGTCTTTGTAGAGATTTCACTATGAAC 57.354 33.333 0.00 0.00 35.89 3.18
491 990 8.874816 GTCTTTGTAGAGATTTCACTATGAACC 58.125 37.037 0.00 0.00 35.89 3.62
492 991 8.593679 TCTTTGTAGAGATTTCACTATGAACCA 58.406 33.333 0.00 0.00 35.89 3.67
493 992 8.547967 TTTGTAGAGATTTCACTATGAACCAC 57.452 34.615 0.00 0.00 35.89 4.16
494 993 7.239763 TGTAGAGATTTCACTATGAACCACA 57.760 36.000 0.00 0.00 35.89 4.17
495 994 7.851228 TGTAGAGATTTCACTATGAACCACAT 58.149 34.615 0.00 0.00 35.89 3.21
496 995 8.977412 TGTAGAGATTTCACTATGAACCACATA 58.023 33.333 0.00 0.00 35.89 2.29
497 996 9.250624 GTAGAGATTTCACTATGAACCACATAC 57.749 37.037 0.00 0.00 35.89 2.39
498 997 6.980978 AGAGATTTCACTATGAACCACATACG 59.019 38.462 0.00 0.00 35.89 3.06
499 998 6.049149 AGATTTCACTATGAACCACATACGG 58.951 40.000 0.00 0.00 35.89 4.02
500 999 5.408880 TTTCACTATGAACCACATACGGA 57.591 39.130 0.00 0.00 35.89 4.69
501 1000 5.607939 TTCACTATGAACCACATACGGAT 57.392 39.130 0.00 0.00 40.07 4.18
502 1001 4.944048 TCACTATGAACCACATACGGATG 58.056 43.478 5.94 5.94 40.07 3.51
503 1002 5.105106 TTCACTATGAACCACATACGGATGT 60.105 40.000 7.68 7.68 37.89 3.06
504 1003 5.595133 TCACTATGAACCACATACGGATGTA 59.405 40.000 14.23 0.00 44.82 2.29
505 1004 6.266786 TCACTATGAACCACATACGGATGTAT 59.733 38.462 14.23 5.54 44.82 2.29
523 1022 9.077674 CGGATGTATGTAGATGTATTTTAGAGC 57.922 37.037 0.00 0.00 0.00 4.09
524 1023 9.077674 GGATGTATGTAGATGTATTTTAGAGCG 57.922 37.037 0.00 0.00 0.00 5.03
525 1024 8.988064 ATGTATGTAGATGTATTTTAGAGCGG 57.012 34.615 0.00 0.00 0.00 5.52
526 1025 7.948357 TGTATGTAGATGTATTTTAGAGCGGT 58.052 34.615 0.00 0.00 0.00 5.68
527 1026 7.865889 TGTATGTAGATGTATTTTAGAGCGGTG 59.134 37.037 0.00 0.00 0.00 4.94
528 1027 6.459670 TGTAGATGTATTTTAGAGCGGTGA 57.540 37.500 0.00 0.00 0.00 4.02
529 1028 7.050970 TGTAGATGTATTTTAGAGCGGTGAT 57.949 36.000 0.00 0.00 0.00 3.06
530 1029 7.497595 TGTAGATGTATTTTAGAGCGGTGATT 58.502 34.615 0.00 0.00 0.00 2.57
531 1030 7.652105 TGTAGATGTATTTTAGAGCGGTGATTC 59.348 37.037 0.00 0.00 0.00 2.52
532 1031 6.582636 AGATGTATTTTAGAGCGGTGATTCA 58.417 36.000 0.00 0.00 0.00 2.57
533 1032 6.480320 AGATGTATTTTAGAGCGGTGATTCAC 59.520 38.462 8.34 8.34 0.00 3.18
534 1033 5.730550 TGTATTTTAGAGCGGTGATTCACT 58.269 37.500 16.02 0.00 34.40 3.41
535 1034 5.810587 TGTATTTTAGAGCGGTGATTCACTC 59.189 40.000 16.02 6.59 34.40 3.51
536 1035 3.953712 TTTAGAGCGGTGATTCACTCA 57.046 42.857 16.02 0.00 34.40 3.41
537 1036 4.471904 TTTAGAGCGGTGATTCACTCAT 57.528 40.909 16.02 2.76 35.97 2.90
538 1037 4.471904 TTAGAGCGGTGATTCACTCATT 57.528 40.909 16.02 0.82 35.97 2.57
539 1038 3.340814 AGAGCGGTGATTCACTCATTT 57.659 42.857 16.02 0.00 35.97 2.32
540 1039 3.679389 AGAGCGGTGATTCACTCATTTT 58.321 40.909 16.02 0.00 35.97 1.82
541 1040 3.438087 AGAGCGGTGATTCACTCATTTTG 59.562 43.478 16.02 0.58 35.97 2.44
542 1041 2.095059 AGCGGTGATTCACTCATTTTGC 60.095 45.455 16.02 8.98 35.97 3.68
543 1042 2.095059 GCGGTGATTCACTCATTTTGCT 60.095 45.455 16.02 0.00 35.97 3.91
544 1043 3.751621 CGGTGATTCACTCATTTTGCTC 58.248 45.455 16.02 0.00 35.97 4.26
545 1044 3.426695 CGGTGATTCACTCATTTTGCTCC 60.427 47.826 16.02 0.00 35.97 4.70
546 1045 3.426695 GGTGATTCACTCATTTTGCTCCG 60.427 47.826 16.02 0.00 35.97 4.63
547 1046 3.189287 GTGATTCACTCATTTTGCTCCGT 59.811 43.478 9.59 0.00 35.97 4.69
548 1047 4.391830 GTGATTCACTCATTTTGCTCCGTA 59.608 41.667 9.59 0.00 35.97 4.02
549 1048 5.065218 GTGATTCACTCATTTTGCTCCGTAT 59.935 40.000 9.59 0.00 35.97 3.06
550 1049 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
551 1050 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
552 1051 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
553 1052 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
554 1053 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
555 1054 5.351465 CACTCATTTTGCTCCGTATGTAGTT 59.649 40.000 0.00 0.00 0.00 2.24
556 1055 5.581085 ACTCATTTTGCTCCGTATGTAGTTC 59.419 40.000 0.00 0.00 0.00 3.01
557 1056 5.483811 TCATTTTGCTCCGTATGTAGTTCA 58.516 37.500 0.00 0.00 0.00 3.18
558 1057 6.112734 TCATTTTGCTCCGTATGTAGTTCAT 58.887 36.000 0.00 0.00 40.25 2.57
559 1058 7.269316 TCATTTTGCTCCGTATGTAGTTCATA 58.731 34.615 0.00 0.00 37.91 2.15
560 1059 7.438160 TCATTTTGCTCCGTATGTAGTTCATAG 59.562 37.037 0.00 0.00 39.36 2.23
561 1060 5.847111 TTGCTCCGTATGTAGTTCATAGT 57.153 39.130 0.00 0.00 39.36 2.12
562 1061 5.183014 TGCTCCGTATGTAGTTCATAGTG 57.817 43.478 0.00 0.00 39.36 2.74
563 1062 4.037565 TGCTCCGTATGTAGTTCATAGTGG 59.962 45.833 2.99 2.99 39.36 4.00
564 1063 4.277672 GCTCCGTATGTAGTTCATAGTGGA 59.722 45.833 9.16 9.16 39.94 4.02
565 1064 5.221185 GCTCCGTATGTAGTTCATAGTGGAA 60.221 44.000 10.20 0.00 40.80 3.53
566 1065 6.516860 GCTCCGTATGTAGTTCATAGTGGAAT 60.517 42.308 10.20 0.00 40.80 3.01
567 1066 6.978338 TCCGTATGTAGTTCATAGTGGAATC 58.022 40.000 7.73 0.00 39.60 2.52
568 1067 6.776116 TCCGTATGTAGTTCATAGTGGAATCT 59.224 38.462 7.73 0.00 39.60 2.40
569 1068 7.040617 TCCGTATGTAGTTCATAGTGGAATCTC 60.041 40.741 7.73 0.00 39.60 2.75
570 1069 7.040340 CCGTATGTAGTTCATAGTGGAATCTCT 60.040 40.741 3.20 0.00 39.36 3.10
571 1070 9.000486 CGTATGTAGTTCATAGTGGAATCTCTA 58.000 37.037 0.00 0.00 39.36 2.43
573 1072 8.768501 ATGTAGTTCATAGTGGAATCTCTACA 57.231 34.615 0.00 0.00 37.82 2.74
574 1073 8.589701 TGTAGTTCATAGTGGAATCTCTACAA 57.410 34.615 0.00 0.00 34.07 2.41
575 1074 9.031537 TGTAGTTCATAGTGGAATCTCTACAAA 57.968 33.333 0.00 0.00 34.07 2.83
576 1075 9.522804 GTAGTTCATAGTGGAATCTCTACAAAG 57.477 37.037 0.00 0.00 30.38 2.77
577 1076 8.367660 AGTTCATAGTGGAATCTCTACAAAGA 57.632 34.615 0.00 0.00 29.47 2.52
578 1077 8.254508 AGTTCATAGTGGAATCTCTACAAAGAC 58.745 37.037 0.00 0.00 29.47 3.01
579 1078 7.962995 TCATAGTGGAATCTCTACAAAGACT 57.037 36.000 0.00 0.00 29.47 3.24
580 1079 8.367660 TCATAGTGGAATCTCTACAAAGACTT 57.632 34.615 0.00 0.00 29.47 3.01
581 1080 9.475620 TCATAGTGGAATCTCTACAAAGACTTA 57.524 33.333 0.00 0.00 29.47 2.24
596 1095 8.943909 ACAAAGACTTATATTTAGGAACGGAG 57.056 34.615 0.00 0.00 0.00 4.63
597 1096 7.985752 ACAAAGACTTATATTTAGGAACGGAGG 59.014 37.037 0.00 0.00 0.00 4.30
598 1097 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
599 1098 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
600 1099 6.842807 AGACTTATATTTAGGAACGGAGGGAA 59.157 38.462 0.00 0.00 0.00 3.97
648 1147 4.423625 AAGGTCACAGCTGTTAGTCTTT 57.576 40.909 18.94 4.84 0.00 2.52
649 1148 5.546621 AAGGTCACAGCTGTTAGTCTTTA 57.453 39.130 18.94 0.00 0.00 1.85
650 1149 4.884247 AGGTCACAGCTGTTAGTCTTTAC 58.116 43.478 18.94 5.35 0.00 2.01
651 1150 3.995048 GGTCACAGCTGTTAGTCTTTACC 59.005 47.826 18.94 10.54 0.00 2.85
652 1151 4.262506 GGTCACAGCTGTTAGTCTTTACCT 60.263 45.833 18.94 0.00 0.00 3.08
654 1153 4.021368 TCACAGCTGTTAGTCTTTACCTCC 60.021 45.833 18.94 0.00 0.00 4.30
655 1154 3.056749 ACAGCTGTTAGTCTTTACCTCCG 60.057 47.826 15.25 0.00 0.00 4.63
656 1155 3.056749 CAGCTGTTAGTCTTTACCTCCGT 60.057 47.826 5.25 0.00 0.00 4.69
659 1158 5.067544 AGCTGTTAGTCTTTACCTCCGTATC 59.932 44.000 0.00 0.00 0.00 2.24
660 1159 5.163581 GCTGTTAGTCTTTACCTCCGTATCA 60.164 44.000 0.00 0.00 0.00 2.15
661 1160 6.626623 GCTGTTAGTCTTTACCTCCGTATCAA 60.627 42.308 0.00 0.00 0.00 2.57
662 1161 7.230849 TGTTAGTCTTTACCTCCGTATCAAA 57.769 36.000 0.00 0.00 0.00 2.69
663 1162 7.669427 TGTTAGTCTTTACCTCCGTATCAAAA 58.331 34.615 0.00 0.00 0.00 2.44
665 1164 9.807649 GTTAGTCTTTACCTCCGTATCAAAATA 57.192 33.333 0.00 0.00 0.00 1.40
672 1171 9.467258 TTTACCTCCGTATCAAAATATAAGACG 57.533 33.333 0.00 0.00 0.00 4.18
673 1172 7.047460 ACCTCCGTATCAAAATATAAGACGT 57.953 36.000 0.00 0.00 0.00 4.34
674 1173 7.495055 ACCTCCGTATCAAAATATAAGACGTT 58.505 34.615 0.00 0.00 0.00 3.99
675 1174 7.983484 ACCTCCGTATCAAAATATAAGACGTTT 59.017 33.333 0.00 0.00 0.00 3.60
676 1175 8.823818 CCTCCGTATCAAAATATAAGACGTTTT 58.176 33.333 0.00 0.00 0.00 2.43
697 1196 5.662674 TTTTGGAATATTTTGGTACGGGG 57.337 39.130 0.00 0.00 0.00 5.73
698 1197 3.300239 TGGAATATTTTGGTACGGGGG 57.700 47.619 0.00 0.00 0.00 5.40
699 1198 2.581709 TGGAATATTTTGGTACGGGGGT 59.418 45.455 0.00 0.00 0.00 4.95
700 1199 3.784763 TGGAATATTTTGGTACGGGGGTA 59.215 43.478 0.00 0.00 0.00 3.69
701 1200 4.141436 TGGAATATTTTGGTACGGGGGTAG 60.141 45.833 0.00 0.00 0.00 3.18
702 1201 4.141413 GGAATATTTTGGTACGGGGGTAGT 60.141 45.833 0.00 0.00 0.00 2.73
703 1202 5.439721 GAATATTTTGGTACGGGGGTAGTT 58.560 41.667 0.00 0.00 0.00 2.24
704 1203 2.857186 TTTTGGTACGGGGGTAGTTC 57.143 50.000 0.00 0.00 0.00 3.01
705 1204 2.028561 TTTGGTACGGGGGTAGTTCT 57.971 50.000 0.00 0.00 0.00 3.01
716 1215 4.325119 GGGGGTAGTTCTCTTCAAGAAAC 58.675 47.826 0.00 0.00 45.50 2.78
722 1228 5.523438 AGTTCTCTTCAAGAAACTCGAGT 57.477 39.130 13.58 13.58 45.50 4.18
724 1230 4.148563 TCTCTTCAAGAAACTCGAGTCG 57.851 45.455 20.33 6.09 0.00 4.18
725 1231 3.813724 TCTCTTCAAGAAACTCGAGTCGA 59.186 43.478 20.33 15.64 0.00 4.20
728 1234 8.910094 TTCTCTTCAAGAAACTCGAGTCGAGAT 61.910 40.741 41.08 30.58 46.89 2.75
738 1244 4.603989 TCGAGTCGAGATGGACTATACT 57.396 45.455 12.09 0.00 46.85 2.12
739 1245 5.718724 TCGAGTCGAGATGGACTATACTA 57.281 43.478 12.09 0.00 46.85 1.82
740 1246 5.712004 TCGAGTCGAGATGGACTATACTAG 58.288 45.833 12.09 0.00 46.85 2.57
779 1285 8.175925 TGGAATACATGATTTTCTCAACAACA 57.824 30.769 0.00 0.00 37.44 3.33
806 1312 6.408858 AACACGTCATGATGAGTTCAATAC 57.591 37.500 21.75 0.00 38.03 1.89
814 1320 9.926751 GTCATGATGAGTTCAATACAAGTTATG 57.073 33.333 0.00 0.00 38.03 1.90
815 1321 9.112725 TCATGATGAGTTCAATACAAGTTATGG 57.887 33.333 0.00 0.00 38.03 2.74
816 1322 7.320443 TGATGAGTTCAATACAAGTTATGGC 57.680 36.000 0.00 0.00 0.00 4.40
817 1323 6.883756 TGATGAGTTCAATACAAGTTATGGCA 59.116 34.615 0.00 0.00 0.00 4.92
864 1466 4.985413 AGAAAAACATATGATGGCACGTG 58.015 39.130 12.28 12.28 33.60 4.49
865 1467 4.699735 AGAAAAACATATGATGGCACGTGA 59.300 37.500 22.23 0.00 33.60 4.35
867 1469 5.384063 AAAACATATGATGGCACGTGAAA 57.616 34.783 22.23 6.38 33.60 2.69
868 1470 5.581126 AAACATATGATGGCACGTGAAAT 57.419 34.783 22.23 11.65 33.60 2.17
869 1471 6.691754 AAACATATGATGGCACGTGAAATA 57.308 33.333 22.23 8.91 33.60 1.40
870 1472 6.882610 AACATATGATGGCACGTGAAATAT 57.117 33.333 22.23 10.75 33.60 1.28
871 1473 6.245115 ACATATGATGGCACGTGAAATATG 57.755 37.500 22.23 21.84 34.31 1.78
872 1474 5.181811 ACATATGATGGCACGTGAAATATGG 59.818 40.000 22.23 10.43 33.05 2.74
873 1475 2.296792 TGATGGCACGTGAAATATGGG 58.703 47.619 22.23 0.00 0.00 4.00
877 1479 4.365514 TGGCACGTGAAATATGGGATAT 57.634 40.909 22.23 0.00 0.00 1.63
882 1484 6.205853 GGCACGTGAAATATGGGATATTACAA 59.794 38.462 22.23 0.00 34.50 2.41
991 1593 4.087510 TCTGCATTGATTTCAGCTTTCG 57.912 40.909 0.00 0.00 0.00 3.46
994 1596 2.179589 CATTGATTTCAGCTTTCGCCG 58.820 47.619 0.00 0.00 36.60 6.46
1213 1815 7.624344 GCCTTACTGTCTTTACATGATTGTGTC 60.624 40.741 0.00 0.00 36.53 3.67
1228 1830 7.050970 TGATTGTGTCTGTTACTAGTCAAGT 57.949 36.000 0.00 0.00 42.62 3.16
1231 1833 5.839621 TGTGTCTGTTACTAGTCAAGTTCC 58.160 41.667 0.00 0.00 39.80 3.62
1255 1857 6.350110 CCTCACTTTGTTTTTCCTTGTCTTGA 60.350 38.462 0.00 0.00 0.00 3.02
1323 1925 1.877443 GGTTGCAAAAAGGCTCGACTA 59.123 47.619 0.00 0.00 34.04 2.59
1466 2068 5.069318 TCAGGTATGTGCTCAAATTCAACA 58.931 37.500 0.00 0.00 0.00 3.33
1592 2194 5.365619 TGTTCTGAGTCCCAAGAAAACTAC 58.634 41.667 0.00 0.00 0.00 2.73
1654 2256 0.394938 TTAAGTTCCCGAGTGCAGCA 59.605 50.000 0.00 0.00 0.00 4.41
1677 2279 6.017852 GCATGTGGCTAAAATTACTCTAGACC 60.018 42.308 0.00 0.00 40.25 3.85
1703 2305 6.018994 CCGTATTAATCGCTAACTGCTTTCTT 60.019 38.462 0.00 0.00 40.11 2.52
1711 2313 6.627243 TCGCTAACTGCTTTCTTATACTCAA 58.373 36.000 0.00 0.00 40.11 3.02
1959 2561 1.927895 ATGAACGAATCGAGCTCCAC 58.072 50.000 10.55 0.00 0.00 4.02
2152 2754 3.438434 CCTCTAAGCAGAAAAGCCTTGAC 59.562 47.826 0.00 0.00 34.23 3.18
2445 3047 2.568623 AAATCTGACCTTGAAGGCGT 57.431 45.000 11.96 0.00 39.63 5.68
2830 3432 0.806868 AGAAGTCGCCAATGCACATG 59.193 50.000 0.00 0.00 37.32 3.21
3007 3609 7.393515 ACAGAAGGAAATTTGTACCCTGATTAC 59.606 37.037 0.00 0.00 0.00 1.89
3152 3754 3.633986 CAGAAGGTGCTTTCCTTTGTTCT 59.366 43.478 9.11 1.36 46.38 3.01
3406 4009 9.688592 TTTAAACACAGAGTAGCTAACTTCTAC 57.311 33.333 0.00 0.00 39.07 2.59
3564 4167 5.583061 ACTTGCATGCATTTTACCATGATTG 59.417 36.000 23.37 0.00 40.92 2.67
3565 4168 3.872182 TGCATGCATTTTACCATGATTGC 59.128 39.130 18.46 0.00 40.92 3.56
3654 4271 5.163723 ACCGACATTTGAAGATATGCAACTG 60.164 40.000 0.00 0.00 32.82 3.16
3718 4335 5.068198 GGAGAATATGCTGCCAATTTCAAGA 59.932 40.000 0.00 0.00 0.00 3.02
3958 4575 4.794762 CCTTGCACATTTATGTCAATGACG 59.205 41.667 9.00 0.00 39.39 4.35
4194 4811 1.950909 CACATCTACGACTCCTCCCTC 59.049 57.143 0.00 0.00 0.00 4.30
4277 4894 0.836400 GTCCTTGAGGAGGTGTGGGA 60.836 60.000 0.00 0.00 46.49 4.37
4319 4936 0.954452 CTTCAGTGGAAGCCCAACAC 59.046 55.000 0.00 0.00 45.59 3.32
4389 5006 2.430244 AACCTGCTGTACGACGCG 60.430 61.111 3.53 3.53 0.00 6.01
4491 5108 3.868757 ATCGACGAATGACTTCTGGAA 57.131 42.857 0.00 0.00 0.00 3.53
4528 5145 1.535028 CTGAACACTTGGCAATGCGTA 59.465 47.619 0.00 0.00 0.00 4.42
4529 5146 1.535028 TGAACACTTGGCAATGCGTAG 59.465 47.619 0.00 1.20 0.00 3.51
4530 5147 1.804151 GAACACTTGGCAATGCGTAGA 59.196 47.619 11.30 0.00 0.00 2.59
4717 5334 3.323243 GTTGGTATACGCACAGTGTCTT 58.677 45.455 1.61 0.00 0.00 3.01
4726 5343 2.483876 GCACAGTGTCTTGAGCAGTTA 58.516 47.619 1.61 0.00 35.19 2.24
4798 5415 6.754209 TGAACATGTAAAATGCTCGTTTTTGT 59.246 30.769 0.00 2.34 33.62 2.83
4802 5419 7.918562 ACATGTAAAATGCTCGTTTTTGTAAGT 59.081 29.630 0.00 0.00 33.62 2.24
4818 5435 8.496707 TTTTGTAAGTAGGAAAACGTTCTTCT 57.503 30.769 0.00 0.00 33.92 2.85
4841 5458 4.095610 GTGAACGAATAGGAATTTTGGCG 58.904 43.478 0.00 0.00 0.00 5.69
4847 5464 7.972832 ACGAATAGGAATTTTGGCGATATTA 57.027 32.000 0.00 0.00 0.00 0.98
4868 5485 4.669206 ATCTGATGATCACTGTGGTCTC 57.331 45.455 20.73 15.35 0.00 3.36
4869 5486 2.762887 TCTGATGATCACTGTGGTCTCC 59.237 50.000 20.73 12.88 0.00 3.71
4880 5497 3.655481 GGTCTCCAACCGTTGCTG 58.345 61.111 5.68 1.10 38.58 4.41
4889 5506 0.818040 AACCGTTGCTGTGGTCCTTC 60.818 55.000 0.00 0.00 37.54 3.46
4907 5524 5.237344 GTCCTTCGAATTTGCAGCTATACAT 59.763 40.000 0.00 0.00 0.00 2.29
4914 5531 9.705290 TCGAATTTGCAGCTATACATTATCTTA 57.295 29.630 0.00 0.00 0.00 2.10
4915 5532 9.964253 CGAATTTGCAGCTATACATTATCTTAG 57.036 33.333 0.00 0.00 0.00 2.18
4977 5600 3.011119 CGTCTAGCTCAGTTGGTAGAGT 58.989 50.000 0.00 0.00 44.42 3.24
5032 6263 1.375396 CCACAGTGGGCGATTTCGA 60.375 57.895 12.40 0.00 41.87 3.71
5033 6264 0.953471 CCACAGTGGGCGATTTCGAA 60.953 55.000 12.40 0.00 41.87 3.71
5035 6266 1.468520 CACAGTGGGCGATTTCGAATT 59.531 47.619 0.00 0.00 43.02 2.17
5036 6267 1.737793 ACAGTGGGCGATTTCGAATTC 59.262 47.619 9.50 9.50 43.02 2.17
5037 6268 2.009774 CAGTGGGCGATTTCGAATTCT 58.990 47.619 15.79 0.00 43.02 2.40
5065 6297 6.961359 TTACATTGTAGATGGTTCAGTTCG 57.039 37.500 0.00 0.00 0.00 3.95
5085 6318 4.871513 TCGATGTATACTTGGCAGATGAC 58.128 43.478 4.17 0.00 0.00 3.06
5101 6334 7.025963 GGCAGATGACTCAATTCTAACTTTTG 58.974 38.462 0.00 0.00 0.00 2.44
5129 6362 4.083003 TGTTGTTTGTGTCACACCTTCTTC 60.083 41.667 4.80 0.00 32.73 2.87
5130 6363 3.013921 TGTTTGTGTCACACCTTCTTCC 58.986 45.455 4.80 0.00 32.73 3.46
5232 6475 4.794762 CACAGCAATACAACAATCCAATCG 59.205 41.667 0.00 0.00 0.00 3.34
5233 6476 4.699735 ACAGCAATACAACAATCCAATCGA 59.300 37.500 0.00 0.00 0.00 3.59
5234 6477 5.182950 ACAGCAATACAACAATCCAATCGAA 59.817 36.000 0.00 0.00 0.00 3.71
5235 6478 6.127647 ACAGCAATACAACAATCCAATCGAAT 60.128 34.615 0.00 0.00 0.00 3.34
5236 6479 6.415867 CAGCAATACAACAATCCAATCGAATC 59.584 38.462 0.00 0.00 0.00 2.52
5263 6669 6.710744 AGGACGTTTGAATAGAAAGTGACAAT 59.289 34.615 0.00 0.00 0.00 2.71
5298 6704 6.511767 GATTATTAATCCGGTGAACAGCACAG 60.512 42.308 0.00 0.00 39.37 3.66
5313 6719 4.878397 ACAGCACAGCATAGGATTACTTTC 59.122 41.667 0.00 0.00 0.00 2.62
5314 6720 4.274459 CAGCACAGCATAGGATTACTTTCC 59.726 45.833 0.00 0.00 35.90 3.13
5336 6742 7.867305 TCCAATATTAAAACGCATGTTCCTA 57.133 32.000 0.00 0.00 37.31 2.94
5446 6852 5.337089 CCTTGCTTCTCTATGTGTTCTCTGA 60.337 44.000 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
116 121 5.300752 CATTGACGGACTAATGCCTATTCT 58.699 41.667 0.00 0.00 0.00 2.40
117 122 4.452455 CCATTGACGGACTAATGCCTATTC 59.548 45.833 0.00 0.00 33.92 1.75
400 899 4.942852 TGTTGAAAATCTGCGACCAAATT 58.057 34.783 0.00 0.00 0.00 1.82
401 900 4.582701 TGTTGAAAATCTGCGACCAAAT 57.417 36.364 0.00 0.00 0.00 2.32
420 919 4.675063 AACAGTTAATTCTGGGGGATGT 57.325 40.909 0.00 0.00 39.48 3.06
441 940 7.300658 ACTTATATTTAGGAACGGAGGGAGTA 58.699 38.462 0.00 0.00 0.00 2.59
442 941 6.141790 ACTTATATTTAGGAACGGAGGGAGT 58.858 40.000 0.00 0.00 0.00 3.85
443 942 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
444 943 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
445 944 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
446 945 7.985752 ACAAAGACTTATATTTAGGAACGGAGG 59.014 37.037 0.00 0.00 0.00 4.30
447 946 8.943909 ACAAAGACTTATATTTAGGAACGGAG 57.056 34.615 0.00 0.00 0.00 4.63
464 963 9.646427 GTTCATAGTGAAATCTCTACAAAGACT 57.354 33.333 0.00 0.00 38.22 3.24
465 964 8.874816 GGTTCATAGTGAAATCTCTACAAAGAC 58.125 37.037 0.00 0.00 38.22 3.01
466 965 8.593679 TGGTTCATAGTGAAATCTCTACAAAGA 58.406 33.333 0.00 0.00 38.22 2.52
467 966 8.660373 GTGGTTCATAGTGAAATCTCTACAAAG 58.340 37.037 0.00 0.00 38.22 2.77
468 967 8.154203 TGTGGTTCATAGTGAAATCTCTACAAA 58.846 33.333 0.00 0.00 38.22 2.83
469 968 7.676004 TGTGGTTCATAGTGAAATCTCTACAA 58.324 34.615 0.00 0.00 38.22 2.41
470 969 7.239763 TGTGGTTCATAGTGAAATCTCTACA 57.760 36.000 0.00 0.00 38.22 2.74
471 970 9.250624 GTATGTGGTTCATAGTGAAATCTCTAC 57.749 37.037 0.00 0.00 38.22 2.59
472 971 8.135529 CGTATGTGGTTCATAGTGAAATCTCTA 58.864 37.037 0.00 0.00 38.22 2.43
473 972 6.980978 CGTATGTGGTTCATAGTGAAATCTCT 59.019 38.462 0.00 0.00 38.22 3.10
474 973 6.201044 CCGTATGTGGTTCATAGTGAAATCTC 59.799 42.308 0.00 0.00 38.22 2.75
475 974 6.049149 CCGTATGTGGTTCATAGTGAAATCT 58.951 40.000 0.00 0.00 38.22 2.40
476 975 6.046593 TCCGTATGTGGTTCATAGTGAAATC 58.953 40.000 0.00 0.00 38.22 2.17
477 976 5.984725 TCCGTATGTGGTTCATAGTGAAAT 58.015 37.500 0.00 0.00 38.22 2.17
478 977 5.408880 TCCGTATGTGGTTCATAGTGAAA 57.591 39.130 0.00 0.00 38.22 2.69
479 978 5.105106 ACATCCGTATGTGGTTCATAGTGAA 60.105 40.000 0.00 0.00 44.79 3.18
480 979 4.404394 ACATCCGTATGTGGTTCATAGTGA 59.596 41.667 0.00 0.00 44.79 3.41
481 980 4.693283 ACATCCGTATGTGGTTCATAGTG 58.307 43.478 0.00 0.00 44.79 2.74
482 981 6.455647 CATACATCCGTATGTGGTTCATAGT 58.544 40.000 3.56 0.00 46.70 2.12
483 982 6.951256 CATACATCCGTATGTGGTTCATAG 57.049 41.667 3.56 0.00 46.70 2.23
497 996 9.077674 GCTCTAAAATACATCTACATACATCCG 57.922 37.037 0.00 0.00 0.00 4.18
498 997 9.077674 CGCTCTAAAATACATCTACATACATCC 57.922 37.037 0.00 0.00 0.00 3.51
499 998 9.077674 CCGCTCTAAAATACATCTACATACATC 57.922 37.037 0.00 0.00 0.00 3.06
500 999 8.585881 ACCGCTCTAAAATACATCTACATACAT 58.414 33.333 0.00 0.00 0.00 2.29
501 1000 7.865889 CACCGCTCTAAAATACATCTACATACA 59.134 37.037 0.00 0.00 0.00 2.29
502 1001 8.080417 TCACCGCTCTAAAATACATCTACATAC 58.920 37.037 0.00 0.00 0.00 2.39
503 1002 8.173542 TCACCGCTCTAAAATACATCTACATA 57.826 34.615 0.00 0.00 0.00 2.29
504 1003 7.050970 TCACCGCTCTAAAATACATCTACAT 57.949 36.000 0.00 0.00 0.00 2.29
505 1004 6.459670 TCACCGCTCTAAAATACATCTACA 57.540 37.500 0.00 0.00 0.00 2.74
506 1005 7.652105 TGAATCACCGCTCTAAAATACATCTAC 59.348 37.037 0.00 0.00 0.00 2.59
507 1006 7.652105 GTGAATCACCGCTCTAAAATACATCTA 59.348 37.037 1.10 0.00 0.00 1.98
508 1007 6.480320 GTGAATCACCGCTCTAAAATACATCT 59.520 38.462 1.10 0.00 0.00 2.90
509 1008 6.480320 AGTGAATCACCGCTCTAAAATACATC 59.520 38.462 10.12 0.00 34.49 3.06
510 1009 6.349300 AGTGAATCACCGCTCTAAAATACAT 58.651 36.000 10.12 0.00 34.49 2.29
511 1010 5.730550 AGTGAATCACCGCTCTAAAATACA 58.269 37.500 10.12 0.00 34.49 2.29
512 1011 5.810587 TGAGTGAATCACCGCTCTAAAATAC 59.189 40.000 10.12 0.00 42.49 1.89
513 1012 5.972935 TGAGTGAATCACCGCTCTAAAATA 58.027 37.500 10.12 0.00 42.49 1.40
514 1013 4.832248 TGAGTGAATCACCGCTCTAAAAT 58.168 39.130 10.12 0.00 42.49 1.82
515 1014 4.265904 TGAGTGAATCACCGCTCTAAAA 57.734 40.909 10.12 0.00 42.49 1.52
516 1015 3.953712 TGAGTGAATCACCGCTCTAAA 57.046 42.857 10.12 0.00 42.49 1.85
517 1016 4.471904 AATGAGTGAATCACCGCTCTAA 57.528 40.909 10.12 0.00 41.91 2.10
518 1017 4.471904 AAATGAGTGAATCACCGCTCTA 57.528 40.909 10.12 0.00 41.91 2.43
519 1018 3.340814 AAATGAGTGAATCACCGCTCT 57.659 42.857 10.12 0.00 41.91 4.09
520 1019 3.751621 CAAAATGAGTGAATCACCGCTC 58.248 45.455 10.12 1.96 41.91 5.03
521 1020 2.095059 GCAAAATGAGTGAATCACCGCT 60.095 45.455 10.12 0.00 41.91 5.52
522 1021 2.095059 AGCAAAATGAGTGAATCACCGC 60.095 45.455 10.12 3.36 41.91 5.68
523 1022 3.426695 GGAGCAAAATGAGTGAATCACCG 60.427 47.826 10.12 0.00 41.91 4.94
524 1023 3.426695 CGGAGCAAAATGAGTGAATCACC 60.427 47.826 10.12 2.45 41.91 4.02
525 1024 3.189287 ACGGAGCAAAATGAGTGAATCAC 59.811 43.478 5.02 5.02 41.91 3.06
526 1025 3.411446 ACGGAGCAAAATGAGTGAATCA 58.589 40.909 0.00 0.00 43.70 2.57
527 1026 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
528 1027 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
529 1028 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
530 1029 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
531 1030 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
532 1031 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
533 1032 5.580691 TGAACTACATACGGAGCAAAATGAG 59.419 40.000 0.00 0.00 0.00 2.90
534 1033 5.483811 TGAACTACATACGGAGCAAAATGA 58.516 37.500 0.00 0.00 0.00 2.57
535 1034 5.794687 TGAACTACATACGGAGCAAAATG 57.205 39.130 0.00 0.00 0.00 2.32
536 1035 7.224753 CACTATGAACTACATACGGAGCAAAAT 59.775 37.037 0.00 0.00 40.07 1.82
537 1036 6.533723 CACTATGAACTACATACGGAGCAAAA 59.466 38.462 0.00 0.00 40.07 2.44
538 1037 6.040247 CACTATGAACTACATACGGAGCAAA 58.960 40.000 0.00 0.00 40.07 3.68
539 1038 5.451381 CCACTATGAACTACATACGGAGCAA 60.451 44.000 0.00 0.00 40.07 3.91
540 1039 4.037565 CCACTATGAACTACATACGGAGCA 59.962 45.833 0.00 0.00 40.07 4.26
541 1040 4.277672 TCCACTATGAACTACATACGGAGC 59.722 45.833 0.00 0.00 40.07 4.70
542 1041 6.387041 TTCCACTATGAACTACATACGGAG 57.613 41.667 0.00 0.00 38.29 4.63
543 1042 6.776116 AGATTCCACTATGAACTACATACGGA 59.224 38.462 0.00 0.00 40.07 4.69
544 1043 6.982852 AGATTCCACTATGAACTACATACGG 58.017 40.000 0.00 0.00 40.07 4.02
545 1044 7.877003 AGAGATTCCACTATGAACTACATACG 58.123 38.462 0.00 0.00 40.07 3.06
547 1046 9.862149 TGTAGAGATTCCACTATGAACTACATA 57.138 33.333 0.00 0.00 40.07 2.29
548 1047 8.768501 TGTAGAGATTCCACTATGAACTACAT 57.231 34.615 0.00 0.00 42.39 2.29
549 1048 8.589701 TTGTAGAGATTCCACTATGAACTACA 57.410 34.615 0.00 0.00 33.29 2.74
550 1049 9.522804 CTTTGTAGAGATTCCACTATGAACTAC 57.477 37.037 0.00 0.00 0.00 2.73
551 1050 9.475620 TCTTTGTAGAGATTCCACTATGAACTA 57.524 33.333 0.00 0.00 0.00 2.24
552 1051 8.254508 GTCTTTGTAGAGATTCCACTATGAACT 58.745 37.037 0.00 0.00 0.00 3.01
553 1052 8.254508 AGTCTTTGTAGAGATTCCACTATGAAC 58.745 37.037 0.00 0.00 0.00 3.18
554 1053 8.367660 AGTCTTTGTAGAGATTCCACTATGAA 57.632 34.615 0.00 0.00 0.00 2.57
555 1054 7.962995 AGTCTTTGTAGAGATTCCACTATGA 57.037 36.000 0.00 0.00 0.00 2.15
571 1070 7.985752 CCTCCGTTCCTAAATATAAGTCTTTGT 59.014 37.037 0.00 0.00 0.00 2.83
572 1071 7.441458 CCCTCCGTTCCTAAATATAAGTCTTTG 59.559 40.741 0.00 0.00 0.00 2.77
573 1072 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
574 1073 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
575 1074 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
576 1075 6.661304 TCCCTCCGTTCCTAAATATAAGTC 57.339 41.667 0.00 0.00 0.00 3.01
577 1076 7.628501 ATTCCCTCCGTTCCTAAATATAAGT 57.371 36.000 0.00 0.00 0.00 2.24
578 1077 9.032624 TCTATTCCCTCCGTTCCTAAATATAAG 57.967 37.037 0.00 0.00 0.00 1.73
579 1078 8.961293 TCTATTCCCTCCGTTCCTAAATATAA 57.039 34.615 0.00 0.00 0.00 0.98
581 1080 9.731001 ATATCTATTCCCTCCGTTCCTAAATAT 57.269 33.333 0.00 0.00 0.00 1.28
582 1081 9.556772 AATATCTATTCCCTCCGTTCCTAAATA 57.443 33.333 0.00 0.00 0.00 1.40
583 1082 8.450780 AATATCTATTCCCTCCGTTCCTAAAT 57.549 34.615 0.00 0.00 0.00 1.40
584 1083 7.867160 AATATCTATTCCCTCCGTTCCTAAA 57.133 36.000 0.00 0.00 0.00 1.85
585 1084 7.867160 AAATATCTATTCCCTCCGTTCCTAA 57.133 36.000 0.00 0.00 0.00 2.69
586 1085 7.618512 CCTAAATATCTATTCCCTCCGTTCCTA 59.381 40.741 0.00 0.00 0.00 2.94
587 1086 6.440965 CCTAAATATCTATTCCCTCCGTTCCT 59.559 42.308 0.00 0.00 0.00 3.36
588 1087 6.439692 TCCTAAATATCTATTCCCTCCGTTCC 59.560 42.308 0.00 0.00 0.00 3.62
589 1088 7.477945 TCCTAAATATCTATTCCCTCCGTTC 57.522 40.000 0.00 0.00 0.00 3.95
590 1089 9.556772 TTATCCTAAATATCTATTCCCTCCGTT 57.443 33.333 0.00 0.00 0.00 4.44
591 1090 9.203163 CTTATCCTAAATATCTATTCCCTCCGT 57.797 37.037 0.00 0.00 0.00 4.69
592 1091 8.145122 GCTTATCCTAAATATCTATTCCCTCCG 58.855 40.741 0.00 0.00 0.00 4.63
593 1092 8.433599 GGCTTATCCTAAATATCTATTCCCTCC 58.566 40.741 0.00 0.00 0.00 4.30
594 1093 8.433599 GGGCTTATCCTAAATATCTATTCCCTC 58.566 40.741 0.00 0.00 34.39 4.30
595 1094 7.351187 GGGGCTTATCCTAAATATCTATTCCCT 59.649 40.741 0.00 0.00 34.39 4.20
596 1095 7.421499 GGGGGCTTATCCTAAATATCTATTCCC 60.421 44.444 0.00 0.00 34.39 3.97
597 1096 7.128883 TGGGGGCTTATCCTAAATATCTATTCC 59.871 40.741 0.00 0.00 34.39 3.01
598 1097 8.102484 TGGGGGCTTATCCTAAATATCTATTC 57.898 38.462 0.00 0.00 34.39 1.75
599 1098 8.476829 TTGGGGGCTTATCCTAAATATCTATT 57.523 34.615 0.00 0.00 34.39 1.73
600 1099 8.476829 TTTGGGGGCTTATCCTAAATATCTAT 57.523 34.615 0.00 0.00 31.28 1.98
633 1132 3.056749 CGGAGGTAAAGACTAACAGCTGT 60.057 47.826 15.25 15.25 0.00 4.40
648 1147 8.169977 ACGTCTTATATTTTGATACGGAGGTA 57.830 34.615 0.00 0.00 33.44 3.08
649 1148 7.047460 ACGTCTTATATTTTGATACGGAGGT 57.953 36.000 0.00 0.00 33.44 3.85
650 1149 7.941795 AACGTCTTATATTTTGATACGGAGG 57.058 36.000 0.00 0.00 33.44 4.30
674 1173 5.046520 CCCCCGTACCAAAATATTCCAAAAA 60.047 40.000 0.00 0.00 0.00 1.94
675 1174 4.466726 CCCCCGTACCAAAATATTCCAAAA 59.533 41.667 0.00 0.00 0.00 2.44
676 1175 4.024670 CCCCCGTACCAAAATATTCCAAA 58.975 43.478 0.00 0.00 0.00 3.28
677 1176 3.011482 ACCCCCGTACCAAAATATTCCAA 59.989 43.478 0.00 0.00 0.00 3.53
678 1177 2.581709 ACCCCCGTACCAAAATATTCCA 59.418 45.455 0.00 0.00 0.00 3.53
679 1178 3.301794 ACCCCCGTACCAAAATATTCC 57.698 47.619 0.00 0.00 0.00 3.01
680 1179 5.039920 ACTACCCCCGTACCAAAATATTC 57.960 43.478 0.00 0.00 0.00 1.75
681 1180 5.192321 AGAACTACCCCCGTACCAAAATATT 59.808 40.000 0.00 0.00 0.00 1.28
682 1181 4.723285 AGAACTACCCCCGTACCAAAATAT 59.277 41.667 0.00 0.00 0.00 1.28
683 1182 4.103342 AGAACTACCCCCGTACCAAAATA 58.897 43.478 0.00 0.00 0.00 1.40
684 1183 2.914941 AGAACTACCCCCGTACCAAAAT 59.085 45.455 0.00 0.00 0.00 1.82
685 1184 2.302733 GAGAACTACCCCCGTACCAAAA 59.697 50.000 0.00 0.00 0.00 2.44
686 1185 1.901833 GAGAACTACCCCCGTACCAAA 59.098 52.381 0.00 0.00 0.00 3.28
687 1186 1.077663 AGAGAACTACCCCCGTACCAA 59.922 52.381 0.00 0.00 0.00 3.67
688 1187 0.706433 AGAGAACTACCCCCGTACCA 59.294 55.000 0.00 0.00 0.00 3.25
689 1188 1.753649 GAAGAGAACTACCCCCGTACC 59.246 57.143 0.00 0.00 0.00 3.34
690 1189 2.450476 TGAAGAGAACTACCCCCGTAC 58.550 52.381 0.00 0.00 0.00 3.67
691 1190 2.905415 TGAAGAGAACTACCCCCGTA 57.095 50.000 0.00 0.00 0.00 4.02
692 1191 1.900486 CTTGAAGAGAACTACCCCCGT 59.100 52.381 0.00 0.00 0.00 5.28
693 1192 2.176889 TCTTGAAGAGAACTACCCCCG 58.823 52.381 0.00 0.00 0.00 5.73
694 1193 4.041815 AGTTTCTTGAAGAGAACTACCCCC 59.958 45.833 15.91 0.00 43.90 5.40
695 1194 5.230323 AGTTTCTTGAAGAGAACTACCCC 57.770 43.478 15.91 0.00 43.90 4.95
696 1195 4.924462 CGAGTTTCTTGAAGAGAACTACCC 59.076 45.833 16.84 8.70 43.90 3.69
697 1196 5.770417 TCGAGTTTCTTGAAGAGAACTACC 58.230 41.667 16.84 9.16 43.90 3.18
698 1197 6.440436 ACTCGAGTTTCTTGAAGAGAACTAC 58.560 40.000 13.58 11.97 43.90 2.73
699 1198 6.566187 CGACTCGAGTTTCTTGAAGAGAACTA 60.566 42.308 21.08 7.26 43.90 2.24
700 1199 5.523438 ACTCGAGTTTCTTGAAGAGAACT 57.477 39.130 13.58 16.83 43.90 3.01
701 1200 4.380382 CGACTCGAGTTTCTTGAAGAGAAC 59.620 45.833 21.08 10.30 43.90 3.01
702 1201 4.275196 TCGACTCGAGTTTCTTGAAGAGAA 59.725 41.667 21.08 0.00 42.56 2.87
703 1202 3.813724 TCGACTCGAGTTTCTTGAAGAGA 59.186 43.478 21.08 4.22 0.00 3.10
704 1203 4.148563 TCGACTCGAGTTTCTTGAAGAG 57.851 45.455 21.08 2.02 0.00 2.85
716 1215 5.803461 CTAGTATAGTCCATCTCGACTCGAG 59.197 48.000 20.49 20.49 43.51 4.04
772 1278 3.003171 TCATGACGTGTTCCATGTTGTTG 59.997 43.478 12.93 0.00 40.59 3.33
779 1285 3.616956 ACTCATCATGACGTGTTCCAT 57.383 42.857 0.00 0.00 0.00 3.41
797 1303 8.353423 AGAAATGCCATAACTTGTATTGAACT 57.647 30.769 0.00 0.00 0.00 3.01
814 1320 8.584157 TCTGAGAGAGAATTAGATAGAAATGCC 58.416 37.037 0.00 0.00 0.00 4.40
815 1321 9.979578 TTCTGAGAGAGAATTAGATAGAAATGC 57.020 33.333 0.00 0.00 35.64 3.56
877 1479 7.911343 TCGCGCAGAAATAAAGATATTTGTAA 58.089 30.769 8.75 0.00 40.87 2.41
882 1484 5.700832 TCCATCGCGCAGAAATAAAGATATT 59.299 36.000 8.75 0.00 33.06 1.28
895 1497 0.516877 TTTCACTTTCCATCGCGCAG 59.483 50.000 8.75 0.00 0.00 5.18
898 1500 3.303990 CCCATATTTCACTTTCCATCGCG 60.304 47.826 0.00 0.00 0.00 5.87
991 1593 3.508840 CTCCGCCATTGTTCCGGC 61.509 66.667 0.00 0.00 45.28 6.13
994 1596 3.140814 GCCCTCCGCCATTGTTCC 61.141 66.667 0.00 0.00 0.00 3.62
1188 1790 7.604164 AGACACAATCATGTAAAGACAGTAAGG 59.396 37.037 0.00 0.00 39.50 2.69
1193 1795 6.791887 ACAGACACAATCATGTAAAGACAG 57.208 37.500 0.00 0.00 39.50 3.51
1213 1815 6.334102 AGTGAGGAACTTGACTAGTAACAG 57.666 41.667 0.00 0.00 41.55 3.16
1228 1830 5.714806 AGACAAGGAAAAACAAAGTGAGGAA 59.285 36.000 0.00 0.00 0.00 3.36
1231 1833 6.620678 TCAAGACAAGGAAAAACAAAGTGAG 58.379 36.000 0.00 0.00 0.00 3.51
1323 1925 3.689649 GCCAAGAAAGATGTGGTTATCGT 59.310 43.478 0.00 0.00 34.71 3.73
1466 2068 6.093909 GCCTTTACCATTAAAGCAAATGCAAT 59.906 34.615 8.28 0.00 42.05 3.56
1565 2167 4.916041 TTCTTGGGACTCAGAACATGAT 57.084 40.909 0.00 0.00 37.28 2.45
1592 2194 3.334691 TGAAAATTGACAGGTAGGCTCG 58.665 45.455 0.00 0.00 0.00 5.03
1654 2256 6.409349 GGGGTCTAGAGTAATTTTAGCCACAT 60.409 42.308 0.00 0.00 0.00 3.21
1667 2269 4.697352 GCGATTAATACGGGGTCTAGAGTA 59.303 45.833 0.00 0.00 0.00 2.59
1674 2276 3.985925 CAGTTAGCGATTAATACGGGGTC 59.014 47.826 8.63 0.00 0.00 4.46
1703 2305 5.393135 CGCTGTCAGTCTCCTTTTGAGTATA 60.393 44.000 0.93 0.00 42.12 1.47
1711 2313 2.103263 AGAAACGCTGTCAGTCTCCTTT 59.897 45.455 0.93 0.00 0.00 3.11
1739 2341 1.165270 GTAAACATGCTGGCCTTCGT 58.835 50.000 3.32 0.00 0.00 3.85
1871 2473 5.128827 AGCATTTTGAATGATGGATTGAGCT 59.871 36.000 4.92 0.00 0.00 4.09
1959 2561 2.023673 CCTGACTAGAGCCTGTCTCAG 58.976 57.143 0.00 0.00 44.35 3.35
2152 2754 1.268265 TCGAGTGATGCGTTGAATCG 58.732 50.000 3.20 3.20 0.00 3.34
2445 3047 7.168219 AGGCATTCTTGTACTGATGACTTTTA 58.832 34.615 0.00 0.00 0.00 1.52
2821 3423 8.800332 AGAGAAGTTATTCTTTTCATGTGCATT 58.200 29.630 0.00 0.00 45.98 3.56
3007 3609 6.922247 ATATCTGCTGTTCTTTCTGTGATG 57.078 37.500 0.00 0.00 0.00 3.07
3101 3703 2.220133 CACCGGAAACAACAGTAAGTCG 59.780 50.000 9.46 0.00 0.00 4.18
3152 3754 8.904834 AGAATGCTACGTAAATCTTCTTCTAGA 58.095 33.333 0.00 0.00 0.00 2.43
3406 4009 6.470235 GCTTCATATTTTCATGACTGTTTCGG 59.530 38.462 0.00 0.00 34.69 4.30
3564 4167 7.871853 TCCTTAAAAATAGAATAATGCCTCGC 58.128 34.615 0.00 0.00 0.00 5.03
3565 4168 9.884465 CTTCCTTAAAAATAGAATAATGCCTCG 57.116 33.333 0.00 0.00 0.00 4.63
3654 4271 1.561542 ACCAACCACTCATCATCCTCC 59.438 52.381 0.00 0.00 0.00 4.30
3718 4335 3.555966 GCCTAATTAGCCACTGGTCATT 58.444 45.455 6.99 0.00 0.00 2.57
4047 4664 0.546267 AGATCACTGGGCTGAGTGGT 60.546 55.000 14.51 9.37 43.16 4.16
4194 4811 4.953868 TGCCACGGACCGTTGACG 62.954 66.667 21.42 8.63 38.32 4.35
4277 4894 3.326747 CTCAGGTAGCAGCTAACGTTTT 58.673 45.455 12.00 0.00 0.00 2.43
4319 4936 1.372499 ACAATGTCGTCCACCGTCG 60.372 57.895 0.00 0.00 37.94 5.12
4389 5006 4.357947 TCCAGCGCGACACACTCC 62.358 66.667 12.10 0.00 0.00 3.85
4491 5108 8.854614 AGTGTTCAGAGACAATTAGCTTTTAT 57.145 30.769 0.00 0.00 0.00 1.40
4528 5145 5.858381 TGCTTTCTGTGTCTAGAAACATCT 58.142 37.500 16.22 0.00 40.66 2.90
4529 5146 5.928839 TCTGCTTTCTGTGTCTAGAAACATC 59.071 40.000 16.22 4.74 40.66 3.06
4530 5147 5.858381 TCTGCTTTCTGTGTCTAGAAACAT 58.142 37.500 16.22 0.00 40.66 2.71
4592 5209 6.534634 AGCACATAACTAAGACCTGTCTTTT 58.465 36.000 16.96 9.43 46.95 2.27
4717 5334 2.289072 GGACAGTCAGCTTAACTGCTCA 60.289 50.000 20.80 0.00 46.48 4.26
4726 5343 5.658634 TGATATCACTTAGGACAGTCAGCTT 59.341 40.000 0.00 0.00 0.00 3.74
4798 5415 6.808829 TCACAGAAGAACGTTTTCCTACTTA 58.191 36.000 0.46 0.00 31.28 2.24
4802 5419 5.978934 GTTCACAGAAGAACGTTTTCCTA 57.021 39.130 0.46 0.00 38.58 2.94
4818 5435 4.378978 CGCCAAAATTCCTATTCGTTCACA 60.379 41.667 0.00 0.00 0.00 3.58
4841 5458 8.530311 AGACCACAGTGATCATCAGATAATATC 58.470 37.037 0.62 0.00 33.72 1.63
4847 5464 3.387374 GGAGACCACAGTGATCATCAGAT 59.613 47.826 0.62 0.00 37.13 2.90
4868 5485 2.551912 GGACCACAGCAACGGTTGG 61.552 63.158 21.37 8.52 34.99 3.77
4869 5486 1.101049 AAGGACCACAGCAACGGTTG 61.101 55.000 16.35 16.35 34.99 3.77
4875 5492 2.270352 AATTCGAAGGACCACAGCAA 57.730 45.000 3.35 0.00 0.00 3.91
4880 5497 1.401539 GCTGCAAATTCGAAGGACCAC 60.402 52.381 3.35 0.00 0.00 4.16
4889 5506 9.964253 CTAAGATAATGTATAGCTGCAAATTCG 57.036 33.333 1.02 0.00 0.00 3.34
4934 5551 6.597562 ACGGGCCTAATATCTGAAAAACATA 58.402 36.000 0.84 0.00 0.00 2.29
4937 5554 5.123936 AGACGGGCCTAATATCTGAAAAAC 58.876 41.667 0.84 0.00 0.00 2.43
4938 5555 5.367945 AGACGGGCCTAATATCTGAAAAA 57.632 39.130 0.84 0.00 0.00 1.94
4940 5557 4.021368 GCTAGACGGGCCTAATATCTGAAA 60.021 45.833 0.84 0.00 0.00 2.69
4943 5560 3.093057 AGCTAGACGGGCCTAATATCTG 58.907 50.000 0.84 0.00 0.00 2.90
4944 5561 3.245300 TGAGCTAGACGGGCCTAATATCT 60.245 47.826 0.84 1.27 0.00 1.98
4945 5562 3.090037 TGAGCTAGACGGGCCTAATATC 58.910 50.000 0.84 0.00 0.00 1.63
4946 5563 3.093057 CTGAGCTAGACGGGCCTAATAT 58.907 50.000 0.84 0.00 0.00 1.28
4949 5566 0.033405 ACTGAGCTAGACGGGCCTAA 60.033 55.000 0.84 0.00 0.00 2.69
4950 5567 0.033405 AACTGAGCTAGACGGGCCTA 60.033 55.000 0.84 0.00 0.00 3.93
5018 6249 2.403252 AGAATTCGAAATCGCCCACT 57.597 45.000 0.00 0.00 39.60 4.00
5065 6297 5.847304 TGAGTCATCTGCCAAGTATACATC 58.153 41.667 5.50 0.00 0.00 3.06
5085 6318 8.819974 ACAACAATTGCAAAAGTTAGAATTGAG 58.180 29.630 16.44 8.54 37.42 3.02
5101 6334 3.061965 GGTGTGACACAAACAACAATTGC 59.938 43.478 18.40 0.00 35.25 3.56
5175 6410 6.174720 TCTGTCAAAGTTAGGTGTGATTCT 57.825 37.500 0.00 0.00 0.00 2.40
5187 6422 6.998074 TGTGATGGATAGTTTCTGTCAAAGTT 59.002 34.615 0.00 0.00 0.00 2.66
5232 6475 7.746475 CACTTTCTATTCAAACGTCCTTGATTC 59.254 37.037 3.63 0.00 35.31 2.52
5233 6476 7.444183 TCACTTTCTATTCAAACGTCCTTGATT 59.556 33.333 3.63 3.63 35.31 2.57
5234 6477 6.934645 TCACTTTCTATTCAAACGTCCTTGAT 59.065 34.615 3.63 0.00 35.31 2.57
5235 6478 6.202188 GTCACTTTCTATTCAAACGTCCTTGA 59.798 38.462 0.00 0.00 33.48 3.02
5236 6479 6.018262 TGTCACTTTCTATTCAAACGTCCTTG 60.018 38.462 0.00 0.00 0.00 3.61
5283 6689 0.673333 TATGCTGTGCTGTTCACCGG 60.673 55.000 0.00 0.00 45.03 5.28
5291 6697 4.274459 GGAAAGTAATCCTATGCTGTGCTG 59.726 45.833 0.00 0.00 36.50 4.41
5313 6719 7.703328 ACTAGGAACATGCGTTTTAATATTGG 58.297 34.615 0.00 0.00 34.75 3.16
5314 6720 8.394877 TGACTAGGAACATGCGTTTTAATATTG 58.605 33.333 0.00 0.00 34.75 1.90
5326 6732 7.928706 AGACTAATATTGTGACTAGGAACATGC 59.071 37.037 0.00 0.00 0.00 4.06


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

AutoCloner maintained by Alex Coulton.