Multiple sequence alignment - TraesCS1B01G346300

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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 TraesCS1B01G346300 chr1B 100.000 4594 0 0 1 4594 575438926 575443519 0.000000e+00 8484.0
1 TraesCS1B01G346300 chr1D 92.669 3683 155 48 875 4498 425298223 425301849 0.000000e+00 5199.0
2 TraesCS1B01G346300 chr1D 93.548 62 3 1 724 784 425297487 425297548 1.760000e-14 91.6
3 TraesCS1B01G346300 chr1A 90.253 3960 220 77 724 4594 520937853 520941735 0.000000e+00 5022.0
4 TraesCS1B01G346300 chr2A 95.267 486 21 2 2442 2927 746931081 746930598 0.000000e+00 769.0
5 TraesCS1B01G346300 chr2A 96.029 277 9 1 2949 3225 746927718 746927444 2.520000e-122 449.0
6 TraesCS1B01G346300 chr2A 85.144 451 45 15 4162 4594 746927418 746926972 4.220000e-120 442.0
7 TraesCS1B01G346300 chr2A 87.719 57 6 1 4532 4587 38597696 38597752 1.070000e-06 65.8
8 TraesCS1B01G346300 chr3D 84.866 522 64 9 203 721 26158239 26157730 3.170000e-141 512.0
9 TraesCS1B01G346300 chr3D 86.577 298 37 2 2355 2649 413677201 413676904 4.430000e-85 326.0
10 TraesCS1B01G346300 chr2B 80.258 542 57 27 155 682 686097029 686097534 3.380000e-96 363.0
11 TraesCS1B01G346300 chr2B 81.481 351 40 13 384 726 784769450 784769783 9.800000e-67 265.0
12 TraesCS1B01G346300 chr2B 85.246 183 24 2 553 734 796178951 796178771 7.850000e-43 185.0
13 TraesCS1B01G346300 chr2B 85.000 180 20 4 550 726 792465884 792466059 4.720000e-40 176.0
14 TraesCS1B01G346300 chr2B 89.394 66 6 1 4529 4594 58672719 58672783 1.060000e-11 82.4
15 TraesCS1B01G346300 chr3B 86.577 298 37 2 2355 2649 539943428 539943131 4.430000e-85 326.0
16 TraesCS1B01G346300 chr3B 95.652 46 2 0 4532 4577 107962831 107962786 1.770000e-09 75.0
17 TraesCS1B01G346300 chr3A 86.441 295 37 2 2355 2646 536896501 536896795 2.060000e-83 320.0
18 TraesCS1B01G346300 chr6B 87.615 218 24 3 378 593 667077754 667077538 2.740000e-62 250.0
19 TraesCS1B01G346300 chr5B 86.188 181 22 2 550 729 278248121 278247943 4.690000e-45 193.0
20 TraesCS1B01G346300 chr5B 83.799 179 23 5 553 728 378089526 378089701 1.020000e-36 165.0
21 TraesCS1B01G346300 chr6A 85.475 179 21 4 553 729 115034620 115034795 1.020000e-41 182.0
22 TraesCS1B01G346300 chr2D 85.795 176 20 4 553 726 159308891 159308719 1.020000e-41 182.0
23 TraesCS1B01G346300 chr2D 96.040 101 3 1 2290 2390 532435019 532435118 3.680000e-36 163.0
24 TraesCS1B01G346300 chr2D 88.136 59 7 0 4529 4587 35508079 35508137 2.290000e-08 71.3
25 TraesCS1B01G346300 chr2D 84.375 64 9 1 4524 4587 23837471 23837409 1.380000e-05 62.1
26 TraesCS1B01G346300 chr4B 87.421 159 15 4 570 726 174087033 174086878 1.310000e-40 178.0
27 TraesCS1B01G346300 chr7D 84.416 77 11 1 4515 4591 167522367 167522292 1.770000e-09 75.0
28 TraesCS1B01G346300 chr6D 91.304 46 4 0 4532 4577 53592238 53592283 3.840000e-06 63.9


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G346300 chr1B 575438926 575443519 4593 False 8484.000000 8484 100.000000 1 4594 1 chr1B.!!$F1 4593
1 TraesCS1B01G346300 chr1D 425297487 425301849 4362 False 2645.300000 5199 93.108500 724 4498 2 chr1D.!!$F1 3774
2 TraesCS1B01G346300 chr1A 520937853 520941735 3882 False 5022.000000 5022 90.253000 724 4594 1 chr1A.!!$F1 3870
3 TraesCS1B01G346300 chr2A 746926972 746931081 4109 True 553.333333 769 92.146667 2442 4594 3 chr2A.!!$R1 2152
4 TraesCS1B01G346300 chr3D 26157730 26158239 509 True 512.000000 512 84.866000 203 721 1 chr3D.!!$R1 518
5 TraesCS1B01G346300 chr2B 686097029 686097534 505 False 363.000000 363 80.258000 155 682 1 chr2B.!!$F2 527

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
97 98 0.038166 TCGCCCTCTGCCTGAAAAAT 59.962 50.0 0.00 0.00 36.24 1.82 F
99 100 0.108472 GCCCTCTGCCTGAAAAATGC 60.108 55.0 0.00 0.00 0.00 3.56 F
347 350 0.179067 TACCGCCGCCTAATTTGAGG 60.179 55.0 0.00 0.00 39.88 3.86 F
2122 2778 0.394565 AGTGTTCCTCAGTGGCTCAC 59.605 55.0 0.00 7.41 38.44 3.51 F
2123 2779 0.394565 GTGTTCCTCAGTGGCTCACT 59.605 55.0 2.38 2.38 46.51 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1433 2067 0.508641 CGCAAATCGCCTCGGATTAG 59.491 55.000 0.0 0.0 35.65 1.73 R
1803 2454 1.735376 TTACATCCTCGCTCCTCGCC 61.735 60.000 0.0 0.0 38.27 5.54 R
2170 2826 2.167219 CGTATGTGCTCGCCCTGTG 61.167 63.158 0.0 0.0 0.00 3.66 R
3195 6835 1.867233 GGTGATTCATCGATCAACCCG 59.133 52.381 0.0 0.0 37.70 5.28 R
3648 7292 5.711976 AGTCATACAAATTGAAACTCCCCAG 59.288 40.000 0.0 0.0 0.00 4.45 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
51 52 4.416738 GCCAGCCTGACCCACCTC 62.417 72.222 0.00 0.00 0.00 3.85
52 53 2.930019 CCAGCCTGACCCACCTCA 60.930 66.667 0.00 0.00 0.00 3.86
53 54 2.348998 CAGCCTGACCCACCTCAC 59.651 66.667 0.00 0.00 0.00 3.51
54 55 2.930562 AGCCTGACCCACCTCACC 60.931 66.667 0.00 0.00 0.00 4.02
55 56 4.394712 GCCTGACCCACCTCACCG 62.395 72.222 0.00 0.00 0.00 4.94
56 57 4.394712 CCTGACCCACCTCACCGC 62.395 72.222 0.00 0.00 0.00 5.68
57 58 4.394712 CTGACCCACCTCACCGCC 62.395 72.222 0.00 0.00 0.00 6.13
76 77 4.785453 CTGGTTCCAGCGCCCCTC 62.785 72.222 2.29 0.00 0.00 4.30
79 80 4.475135 GTTCCAGCGCCCCTCCTC 62.475 72.222 2.29 0.00 0.00 3.71
91 92 3.847602 CTCCTCGCCCTCTGCCTG 61.848 72.222 0.00 0.00 36.24 4.85
92 93 4.382541 TCCTCGCCCTCTGCCTGA 62.383 66.667 0.00 0.00 36.24 3.86
93 94 3.393970 CCTCGCCCTCTGCCTGAA 61.394 66.667 0.00 0.00 36.24 3.02
94 95 2.665000 CTCGCCCTCTGCCTGAAA 59.335 61.111 0.00 0.00 36.24 2.69
95 96 1.003355 CTCGCCCTCTGCCTGAAAA 60.003 57.895 0.00 0.00 36.24 2.29
96 97 0.606401 CTCGCCCTCTGCCTGAAAAA 60.606 55.000 0.00 0.00 36.24 1.94
97 98 0.038166 TCGCCCTCTGCCTGAAAAAT 59.962 50.000 0.00 0.00 36.24 1.82
98 99 0.171903 CGCCCTCTGCCTGAAAAATG 59.828 55.000 0.00 0.00 36.24 2.32
99 100 0.108472 GCCCTCTGCCTGAAAAATGC 60.108 55.000 0.00 0.00 0.00 3.56
100 101 0.533951 CCCTCTGCCTGAAAAATGCC 59.466 55.000 0.00 0.00 0.00 4.40
101 102 1.553706 CCTCTGCCTGAAAAATGCCT 58.446 50.000 0.00 0.00 0.00 4.75
102 103 1.203994 CCTCTGCCTGAAAAATGCCTG 59.796 52.381 0.00 0.00 0.00 4.85
103 104 0.604578 TCTGCCTGAAAAATGCCTGC 59.395 50.000 0.00 0.00 0.00 4.85
104 105 0.319083 CTGCCTGAAAAATGCCTGCA 59.681 50.000 0.00 0.00 0.00 4.41
105 106 0.978151 TGCCTGAAAAATGCCTGCAT 59.022 45.000 0.00 0.00 38.46 3.96
106 107 1.066716 TGCCTGAAAAATGCCTGCATC 60.067 47.619 4.89 0.00 35.31 3.91
107 108 1.066716 GCCTGAAAAATGCCTGCATCA 60.067 47.619 4.89 0.00 35.31 3.07
108 109 2.613474 GCCTGAAAAATGCCTGCATCAA 60.613 45.455 4.89 0.00 35.31 2.57
109 110 2.997986 CCTGAAAAATGCCTGCATCAAC 59.002 45.455 4.89 0.00 35.31 3.18
110 111 2.997986 CTGAAAAATGCCTGCATCAACC 59.002 45.455 4.89 0.00 35.31 3.77
111 112 2.633967 TGAAAAATGCCTGCATCAACCT 59.366 40.909 4.89 0.00 35.31 3.50
112 113 3.071312 TGAAAAATGCCTGCATCAACCTT 59.929 39.130 4.89 0.00 35.31 3.50
113 114 3.775261 AAAATGCCTGCATCAACCTTT 57.225 38.095 4.89 0.00 35.31 3.11
114 115 3.323751 AAATGCCTGCATCAACCTTTC 57.676 42.857 4.89 0.00 35.31 2.62
115 116 0.813184 ATGCCTGCATCAACCTTTCG 59.187 50.000 0.00 0.00 29.42 3.46
116 117 1.153958 GCCTGCATCAACCTTTCGC 60.154 57.895 0.00 0.00 0.00 4.70
117 118 1.135315 CCTGCATCAACCTTTCGCG 59.865 57.895 0.00 0.00 0.00 5.87
118 119 1.135315 CTGCATCAACCTTTCGCGG 59.865 57.895 6.13 0.00 0.00 6.46
119 120 2.202479 GCATCAACCTTTCGCGGC 60.202 61.111 6.13 0.00 0.00 6.53
120 121 2.098298 CATCAACCTTTCGCGGCG 59.902 61.111 17.70 17.70 0.00 6.46
121 122 2.047655 ATCAACCTTTCGCGGCGA 60.048 55.556 22.69 22.69 0.00 5.54
122 123 2.388232 ATCAACCTTTCGCGGCGAC 61.388 57.895 26.40 0.11 34.89 5.19
141 142 4.143333 CCGCCACCCGATTCGACT 62.143 66.667 7.83 0.00 40.02 4.18
142 143 2.125673 CGCCACCCGATTCGACTT 60.126 61.111 7.83 0.00 40.02 3.01
143 144 2.165301 CGCCACCCGATTCGACTTC 61.165 63.158 7.83 0.00 40.02 3.01
144 145 1.814169 GCCACCCGATTCGACTTCC 60.814 63.158 7.83 0.00 0.00 3.46
145 146 1.153429 CCACCCGATTCGACTTCCC 60.153 63.158 7.83 0.00 0.00 3.97
146 147 1.153429 CACCCGATTCGACTTCCCC 60.153 63.158 7.83 0.00 0.00 4.81
147 148 2.364780 ACCCGATTCGACTTCCCCC 61.365 63.158 7.83 0.00 0.00 5.40
180 181 4.424711 TGCCAGATTCCCCCGCAC 62.425 66.667 0.00 0.00 0.00 5.34
272 273 1.480219 CGCCGCCTGATTCGAGTTAC 61.480 60.000 0.00 0.00 0.00 2.50
276 277 0.459585 GCCTGATTCGAGTTACCGCA 60.460 55.000 0.00 0.00 0.00 5.69
278 279 0.924090 CTGATTCGAGTTACCGCAGC 59.076 55.000 0.00 0.00 0.00 5.25
281 282 1.940883 ATTCGAGTTACCGCAGCCGA 61.941 55.000 0.00 0.00 36.29 5.54
329 331 2.202570 GCTTCTCGCGCCGTTCTA 60.203 61.111 0.00 0.00 0.00 2.10
332 335 3.672255 TTCTCGCGCCGTTCTACCG 62.672 63.158 0.00 0.00 0.00 4.02
345 348 0.825410 TCTACCGCCGCCTAATTTGA 59.175 50.000 0.00 0.00 0.00 2.69
347 350 0.179067 TACCGCCGCCTAATTTGAGG 60.179 55.000 0.00 0.00 39.88 3.86
350 353 0.935196 CGCCGCCTAATTTGAGGTAC 59.065 55.000 0.00 0.00 39.02 3.34
355 358 2.285977 GCCTAATTTGAGGTACCACCG 58.714 52.381 15.94 0.00 44.90 4.94
356 359 2.914059 CCTAATTTGAGGTACCACCGG 58.086 52.381 15.94 0.00 44.90 5.28
358 361 0.675522 AATTTGAGGTACCACCGGCG 60.676 55.000 15.94 0.00 44.90 6.46
374 377 1.347221 GCGGCCATTCGAGTTAACG 59.653 57.895 2.24 0.00 0.00 3.18
378 381 1.343506 GCCATTCGAGTTAACGTCGT 58.656 50.000 19.69 0.00 38.60 4.34
380 383 2.587956 CCATTCGAGTTAACGTCGTCA 58.412 47.619 19.69 12.34 38.60 4.35
391 394 0.809385 ACGTCGTCACCTGATTCGAT 59.191 50.000 0.00 0.00 34.93 3.59
403 406 3.165160 ATTCGATTCCCCTCCGCGG 62.165 63.158 22.12 22.12 0.00 6.46
430 433 1.712018 GCCCGATTTGAGTTACCGCC 61.712 60.000 0.00 0.00 0.00 6.13
431 434 1.426041 CCCGATTTGAGTTACCGCCG 61.426 60.000 0.00 0.00 0.00 6.46
432 435 0.738412 CCGATTTGAGTTACCGCCGT 60.738 55.000 0.00 0.00 0.00 5.68
449 452 3.849951 TCGGCCATTCGAGCTCCC 61.850 66.667 8.47 0.86 34.82 4.30
488 491 4.862092 CGCTGCGCAGATCCTCGT 62.862 66.667 40.21 0.00 0.00 4.18
489 492 2.959071 GCTGCGCAGATCCTCGTC 60.959 66.667 40.21 16.41 0.00 4.20
490 493 2.653448 CTGCGCAGATCCTCGTCG 60.653 66.667 33.66 0.65 0.00 5.12
491 494 4.854784 TGCGCAGATCCTCGTCGC 62.855 66.667 5.66 6.83 40.43 5.19
492 495 4.560856 GCGCAGATCCTCGTCGCT 62.561 66.667 0.30 0.00 38.34 4.93
493 496 2.352915 CGCAGATCCTCGTCGCTC 60.353 66.667 0.00 0.00 0.00 5.03
494 497 2.352915 GCAGATCCTCGTCGCTCG 60.353 66.667 0.00 0.00 41.41 5.03
495 498 2.329690 CAGATCCTCGTCGCTCGG 59.670 66.667 0.00 0.00 40.32 4.63
496 499 3.587933 AGATCCTCGTCGCTCGGC 61.588 66.667 0.00 0.00 40.32 5.54
497 500 4.632458 GATCCTCGTCGCTCGGCC 62.632 72.222 0.00 0.00 40.32 6.13
513 516 4.180946 CCGTCGGCACTCCTCTCG 62.181 72.222 0.00 0.00 0.00 4.04
514 517 3.125573 CGTCGGCACTCCTCTCGA 61.126 66.667 0.00 0.00 0.00 4.04
515 518 2.687805 CGTCGGCACTCCTCTCGAA 61.688 63.158 0.00 0.00 33.33 3.71
516 519 1.137825 GTCGGCACTCCTCTCGAAG 59.862 63.158 0.00 0.00 33.33 3.79
517 520 2.202676 CGGCACTCCTCTCGAAGC 60.203 66.667 0.00 0.00 0.00 3.86
518 521 2.705821 CGGCACTCCTCTCGAAGCT 61.706 63.158 0.00 0.00 0.00 3.74
519 522 1.140804 GGCACTCCTCTCGAAGCTC 59.859 63.158 0.00 0.00 0.00 4.09
520 523 1.226547 GCACTCCTCTCGAAGCTCG 60.227 63.158 0.00 0.00 42.10 5.03
521 524 1.431440 CACTCCTCTCGAAGCTCGG 59.569 63.158 5.87 0.00 40.88 4.63
522 525 2.411290 CTCCTCTCGAAGCTCGGC 59.589 66.667 5.87 0.00 40.88 5.54
523 526 3.132481 CTCCTCTCGAAGCTCGGCC 62.132 68.421 0.00 0.00 40.88 6.13
524 527 4.560856 CCTCTCGAAGCTCGGCCG 62.561 72.222 22.12 22.12 40.88 6.13
540 543 4.845580 CGCTGCCGCTTGATCCCT 62.846 66.667 0.00 0.00 0.00 4.20
541 544 2.439156 GCTGCCGCTTGATCCCTT 60.439 61.111 0.00 0.00 0.00 3.95
542 545 2.768492 GCTGCCGCTTGATCCCTTG 61.768 63.158 0.00 0.00 0.00 3.61
543 546 2.045045 TGCCGCTTGATCCCTTGG 60.045 61.111 0.00 0.00 0.00 3.61
544 547 2.272146 GCCGCTTGATCCCTTGGA 59.728 61.111 0.00 0.00 35.55 3.53
545 548 1.821332 GCCGCTTGATCCCTTGGAG 60.821 63.158 0.00 0.00 34.05 3.86
546 549 1.604378 CCGCTTGATCCCTTGGAGT 59.396 57.895 0.00 0.00 34.05 3.85
547 550 0.830648 CCGCTTGATCCCTTGGAGTA 59.169 55.000 0.00 0.00 34.05 2.59
548 551 1.202580 CCGCTTGATCCCTTGGAGTAG 60.203 57.143 0.00 0.00 34.05 2.57
549 552 1.482593 CGCTTGATCCCTTGGAGTAGT 59.517 52.381 0.00 0.00 34.05 2.73
550 553 2.693591 CGCTTGATCCCTTGGAGTAGTA 59.306 50.000 0.00 0.00 34.05 1.82
551 554 3.243569 CGCTTGATCCCTTGGAGTAGTAG 60.244 52.174 0.00 0.00 34.05 2.57
552 555 3.707102 GCTTGATCCCTTGGAGTAGTAGT 59.293 47.826 0.00 0.00 34.05 2.73
553 556 4.162509 GCTTGATCCCTTGGAGTAGTAGTT 59.837 45.833 0.00 0.00 34.05 2.24
554 557 5.338463 GCTTGATCCCTTGGAGTAGTAGTTT 60.338 44.000 0.00 0.00 34.05 2.66
555 558 6.697641 TTGATCCCTTGGAGTAGTAGTTTT 57.302 37.500 0.00 0.00 34.05 2.43
556 559 7.580882 GCTTGATCCCTTGGAGTAGTAGTTTTA 60.581 40.741 0.00 0.00 34.05 1.52
557 560 7.179076 TGATCCCTTGGAGTAGTAGTTTTAC 57.821 40.000 0.00 0.00 34.05 2.01
558 561 6.727231 TGATCCCTTGGAGTAGTAGTTTTACA 59.273 38.462 0.00 0.00 34.05 2.41
559 562 7.402071 TGATCCCTTGGAGTAGTAGTTTTACAT 59.598 37.037 0.00 0.00 34.05 2.29
560 563 7.179076 TCCCTTGGAGTAGTAGTTTTACATC 57.821 40.000 0.00 0.00 31.96 3.06
561 564 6.958192 TCCCTTGGAGTAGTAGTTTTACATCT 59.042 38.462 0.00 0.00 31.96 2.90
562 565 7.456902 TCCCTTGGAGTAGTAGTTTTACATCTT 59.543 37.037 0.00 0.00 31.96 2.40
563 566 7.549488 CCCTTGGAGTAGTAGTTTTACATCTTG 59.451 40.741 0.00 0.00 31.96 3.02
564 567 8.311836 CCTTGGAGTAGTAGTTTTACATCTTGA 58.688 37.037 0.00 0.00 31.96 3.02
565 568 9.706691 CTTGGAGTAGTAGTTTTACATCTTGAA 57.293 33.333 0.00 0.00 31.96 2.69
581 584 8.991243 ACATCTTGAAATACATCATTTGTTGG 57.009 30.769 0.00 0.00 39.87 3.77
582 585 8.805175 ACATCTTGAAATACATCATTTGTTGGA 58.195 29.630 0.00 0.00 39.87 3.53
583 586 9.811995 CATCTTGAAATACATCATTTGTTGGAT 57.188 29.630 0.00 0.00 39.87 3.41
585 588 9.642327 TCTTGAAATACATCATTTGTTGGATTG 57.358 29.630 0.90 0.00 39.87 2.67
586 589 7.830940 TGAAATACATCATTTGTTGGATTGC 57.169 32.000 0.90 0.16 39.87 3.56
587 590 7.613585 TGAAATACATCATTTGTTGGATTGCT 58.386 30.769 6.25 0.00 39.87 3.91
588 591 7.760794 TGAAATACATCATTTGTTGGATTGCTC 59.239 33.333 6.25 1.09 39.87 4.26
589 592 7.414222 AATACATCATTTGTTGGATTGCTCT 57.586 32.000 0.00 0.00 39.87 4.09
590 593 5.733620 ACATCATTTGTTGGATTGCTCTT 57.266 34.783 0.00 0.00 33.74 2.85
591 594 6.105397 ACATCATTTGTTGGATTGCTCTTT 57.895 33.333 0.00 0.00 33.74 2.52
592 595 6.527423 ACATCATTTGTTGGATTGCTCTTTT 58.473 32.000 0.00 0.00 33.74 2.27
593 596 7.669427 ACATCATTTGTTGGATTGCTCTTTTA 58.331 30.769 0.00 0.00 33.74 1.52
594 597 7.599998 ACATCATTTGTTGGATTGCTCTTTTAC 59.400 33.333 0.00 0.00 33.74 2.01
595 598 7.048629 TCATTTGTTGGATTGCTCTTTTACA 57.951 32.000 0.00 0.00 0.00 2.41
596 599 7.669427 TCATTTGTTGGATTGCTCTTTTACAT 58.331 30.769 0.00 0.00 0.00 2.29
597 600 7.814107 TCATTTGTTGGATTGCTCTTTTACATC 59.186 33.333 0.00 0.00 0.00 3.06
598 601 6.899393 TTGTTGGATTGCTCTTTTACATCT 57.101 33.333 0.00 0.00 0.00 2.90
599 602 6.500684 TGTTGGATTGCTCTTTTACATCTC 57.499 37.500 0.00 0.00 0.00 2.75
600 603 5.415701 TGTTGGATTGCTCTTTTACATCTCC 59.584 40.000 0.00 0.00 0.00 3.71
601 604 5.178096 TGGATTGCTCTTTTACATCTCCA 57.822 39.130 0.00 0.00 0.00 3.86
602 605 5.569355 TGGATTGCTCTTTTACATCTCCAA 58.431 37.500 0.00 0.00 29.77 3.53
603 606 6.189859 TGGATTGCTCTTTTACATCTCCAAT 58.810 36.000 0.00 0.00 29.77 3.16
604 607 7.345691 TGGATTGCTCTTTTACATCTCCAATA 58.654 34.615 0.00 0.00 29.77 1.90
605 608 8.000709 TGGATTGCTCTTTTACATCTCCAATAT 58.999 33.333 0.00 0.00 29.77 1.28
606 609 9.507329 GGATTGCTCTTTTACATCTCCAATATA 57.493 33.333 0.00 0.00 0.00 0.86
608 611 9.851686 ATTGCTCTTTTACATCTCCAATATACA 57.148 29.630 0.00 0.00 0.00 2.29
609 612 9.851686 TTGCTCTTTTACATCTCCAATATACAT 57.148 29.630 0.00 0.00 0.00 2.29
610 613 9.494271 TGCTCTTTTACATCTCCAATATACATC 57.506 33.333 0.00 0.00 0.00 3.06
611 614 9.494271 GCTCTTTTACATCTCCAATATACATCA 57.506 33.333 0.00 0.00 0.00 3.07
618 621 8.433249 ACATCTCCAATATACATCATCTCTGT 57.567 34.615 0.00 0.00 0.00 3.41
619 622 8.878211 ACATCTCCAATATACATCATCTCTGTT 58.122 33.333 0.00 0.00 0.00 3.16
620 623 9.152595 CATCTCCAATATACATCATCTCTGTTG 57.847 37.037 0.00 0.00 0.00 3.33
621 624 7.674120 TCTCCAATATACATCATCTCTGTTGG 58.326 38.462 0.00 0.00 0.00 3.77
622 625 7.510343 TCTCCAATATACATCATCTCTGTTGGA 59.490 37.037 0.00 0.00 31.98 3.53
623 626 7.674120 TCCAATATACATCATCTCTGTTGGAG 58.326 38.462 0.00 0.00 43.12 3.86
624 627 7.290948 TCCAATATACATCATCTCTGTTGGAGT 59.709 37.037 0.00 0.00 42.40 3.85
625 628 7.935755 CCAATATACATCATCTCTGTTGGAGTT 59.064 37.037 0.00 0.00 42.40 3.01
626 629 8.771766 CAATATACATCATCTCTGTTGGAGTTG 58.228 37.037 0.00 0.00 42.40 3.16
627 630 3.341823 ACATCATCTCTGTTGGAGTTGC 58.658 45.455 0.00 0.00 42.40 4.17
628 631 2.479566 TCATCTCTGTTGGAGTTGCC 57.520 50.000 0.00 0.00 42.40 4.52
629 632 1.980765 TCATCTCTGTTGGAGTTGCCT 59.019 47.619 0.00 0.00 42.40 4.75
630 633 2.027745 TCATCTCTGTTGGAGTTGCCTC 60.028 50.000 0.00 0.00 42.40 4.70
631 634 1.722034 TCTCTGTTGGAGTTGCCTCT 58.278 50.000 0.00 0.00 42.40 3.69
632 635 2.050144 TCTCTGTTGGAGTTGCCTCTT 58.950 47.619 0.00 0.00 42.40 2.85
633 636 2.439507 TCTCTGTTGGAGTTGCCTCTTT 59.560 45.455 0.00 0.00 42.40 2.52
634 637 3.117888 TCTCTGTTGGAGTTGCCTCTTTT 60.118 43.478 0.00 0.00 42.40 2.27
635 638 3.631250 TCTGTTGGAGTTGCCTCTTTTT 58.369 40.909 0.00 0.00 37.86 1.94
657 660 8.729805 TTTTTGGAGATGTAAAATGCAGTTTT 57.270 26.923 18.18 13.41 42.47 2.43
658 661 8.729805 TTTTGGAGATGTAAAATGCAGTTTTT 57.270 26.923 18.18 10.21 40.40 1.94
659 662 9.823647 TTTTGGAGATGTAAAATGCAGTTTTTA 57.176 25.926 18.18 9.17 40.40 1.52
660 663 9.823647 TTTGGAGATGTAAAATGCAGTTTTTAA 57.176 25.926 18.18 4.36 40.40 1.52
661 664 9.823647 TTGGAGATGTAAAATGCAGTTTTTAAA 57.176 25.926 18.18 7.60 40.40 1.52
662 665 9.474920 TGGAGATGTAAAATGCAGTTTTTAAAG 57.525 29.630 18.18 0.00 40.40 1.85
663 666 9.691362 GGAGATGTAAAATGCAGTTTTTAAAGA 57.309 29.630 18.18 0.00 40.40 2.52
711 714 9.959749 TTTTACGTCTCTAAATTTGCATTTTCT 57.040 25.926 0.00 0.00 34.29 2.52
715 718 9.559958 ACGTCTCTAAATTTGCATTTTCTATTG 57.440 29.630 0.00 0.00 34.29 1.90
716 719 9.773328 CGTCTCTAAATTTGCATTTTCTATTGA 57.227 29.630 0.00 0.00 34.29 2.57
765 769 6.177310 TGTTGTGTTAACCCTAGCTTTAGA 57.823 37.500 2.48 0.00 0.00 2.10
802 1045 6.803807 GCAATTAATATTTAGCACTGCTAGCC 59.196 38.462 13.29 0.00 42.34 3.93
824 1067 4.456911 CCAGTACGGAGTAGTTGTCAACTA 59.543 45.833 19.42 19.42 45.54 2.24
826 1069 6.084925 CAGTACGGAGTAGTTGTCAACTAAG 58.915 44.000 23.80 17.50 45.54 2.18
855 1098 2.605366 GTGGCGCTTTAAGTTTTGCAAA 59.395 40.909 8.05 8.05 0.00 3.68
866 1366 8.890124 TTTAAGTTTTGCAAAGTATTAACCCC 57.110 30.769 12.41 0.00 0.00 4.95
890 1390 4.762765 TCTCAGTCTCTGTCTGTTCCTTAC 59.237 45.833 0.00 0.00 34.86 2.34
934 1519 6.534436 GCGACTTCTCATACGTATCTATAGGA 59.466 42.308 4.74 0.00 0.00 2.94
935 1520 7.254185 GCGACTTCTCATACGTATCTATAGGAG 60.254 44.444 4.74 8.39 31.90 3.69
976 1569 3.567397 ACTCCGGTCTAGCATTGACTAT 58.433 45.455 0.00 0.00 35.04 2.12
978 1571 4.202161 ACTCCGGTCTAGCATTGACTATTG 60.202 45.833 0.00 0.00 35.04 1.90
985 1578 8.727910 CGGTCTAGCATTGACTATTGTACTATA 58.272 37.037 0.00 0.00 35.04 1.31
991 1584 8.524487 AGCATTGACTATTGTACTATAGCTACC 58.476 37.037 20.05 10.28 32.45 3.18
993 1586 7.444629 TTGACTATTGTACTATAGCTACCGG 57.555 40.000 20.05 0.00 32.45 5.28
994 1587 5.413833 TGACTATTGTACTATAGCTACCGGC 59.586 44.000 20.05 2.07 42.19 6.13
1088 1694 3.445857 GGCTGGAGTATACTTGACGAAC 58.554 50.000 6.88 0.00 0.00 3.95
1227 1833 1.215647 GCGACCTCCCAGTGTAGTG 59.784 63.158 0.00 0.00 0.00 2.74
1438 2072 1.289380 CCGCCTCGCCCTACTAATC 59.711 63.158 0.00 0.00 0.00 1.75
1448 2082 1.893801 CCCTACTAATCCGAGGCGATT 59.106 52.381 0.00 0.00 36.45 3.34
1552 2193 2.309755 TGCCCAGATTCTGTGATTTCCT 59.690 45.455 12.54 0.00 0.00 3.36
1553 2194 2.948315 GCCCAGATTCTGTGATTTCCTC 59.052 50.000 12.54 0.00 0.00 3.71
1670 2311 5.114780 CAGATGGTCTCGATCTGATTTTGT 58.885 41.667 13.70 0.00 46.73 2.83
1691 2332 0.591659 GCTCCCGTGGTTTTCAACTC 59.408 55.000 0.00 0.00 0.00 3.01
1701 2342 7.921745 CCCGTGGTTTTCAACTCTTTTTATTTA 59.078 33.333 0.00 0.00 0.00 1.40
1737 2385 1.270826 TCTCGCTTCCTGTCACTCTTG 59.729 52.381 0.00 0.00 0.00 3.02
1852 2503 4.861102 AATCCTTTCAGCAGGTTTTCAG 57.139 40.909 0.00 0.00 35.15 3.02
1945 2601 3.889538 TGATAGCAGCGTATGTAGGTTCT 59.110 43.478 0.00 0.00 0.00 3.01
1984 2640 5.506151 CGTGTACAGTGGACAGTAGTTGTAA 60.506 44.000 8.93 0.00 41.05 2.41
2122 2778 0.394565 AGTGTTCCTCAGTGGCTCAC 59.605 55.000 0.00 7.41 38.44 3.51
2123 2779 0.394565 GTGTTCCTCAGTGGCTCACT 59.605 55.000 2.38 2.38 46.51 3.41
2154 2810 6.018098 AGTGATGCTGAAATCAAGAATCGATC 60.018 38.462 0.00 0.00 38.28 3.69
2209 2868 2.731217 CACTGTGATCGATGCGTATGA 58.269 47.619 0.54 0.00 0.00 2.15
2219 2878 1.224315 TGCGTATGAAGCAGCCCAT 59.776 52.632 3.67 3.67 40.01 4.00
2229 2888 4.077108 TGAAGCAGCCCATTATCATCATC 58.923 43.478 0.00 0.00 0.00 2.92
2234 2893 4.008330 CAGCCCATTATCATCATCACCTC 58.992 47.826 0.00 0.00 0.00 3.85
2251 2910 3.813724 CACCTCATGCTTGATCAATCGAT 59.186 43.478 8.96 0.00 33.31 3.59
2261 2920 1.002033 GATCAATCGATTGCAGGTGCC 60.002 52.381 29.32 11.33 37.68 5.01
2358 3050 3.688159 GCAACAAGGCCCTGCAGG 61.688 66.667 26.87 26.87 36.09 4.85
2396 3088 4.293648 CACTGGTCGGCGTCCACA 62.294 66.667 21.59 8.38 0.00 4.17
2611 3303 1.515088 ACGAGATCGACAAGCTGCG 60.515 57.895 9.58 0.00 43.02 5.18
2654 3346 1.747367 CGACGACCTCCTGCTCTCT 60.747 63.158 0.00 0.00 0.00 3.10
2813 3505 4.208686 GACGGAGGCGGCGATCTT 62.209 66.667 12.98 0.00 0.00 2.40
3195 6835 2.431454 CTTTCTTCACTCAGGAAGCCC 58.569 52.381 0.00 0.00 43.14 5.19
3242 6882 0.250424 TGGGCATATGCATGGTCTCG 60.250 55.000 28.07 0.00 44.36 4.04
3255 6895 1.809209 GTCTCGAGCTGCTCCAAGC 60.809 63.158 22.97 12.67 43.88 4.01
3407 7051 1.194218 AAGGTTTTGCAGCCACTGTT 58.806 45.000 6.77 0.00 33.43 3.16
3545 7189 6.632834 CGGTTTTCTCTTGTGAGTTTTGTATG 59.367 38.462 0.00 0.00 40.98 2.39
3552 7196 8.154203 TCTCTTGTGAGTTTTGTATGTCCATTA 58.846 33.333 0.00 0.00 40.98 1.90
3580 7224 8.621532 TCTATCTTTGTAATATGATTGGTGCC 57.378 34.615 0.00 0.00 0.00 5.01
3581 7225 6.655078 ATCTTTGTAATATGATTGGTGCCC 57.345 37.500 0.00 0.00 0.00 5.36
3635 7279 1.686587 CTCCCTTTTGTTGTTGGGGTC 59.313 52.381 0.00 0.00 40.05 4.46
3648 7292 6.151985 TGTTGTTGGGGTCATACATGATTAAC 59.848 38.462 0.00 1.03 39.30 2.01
3742 7388 4.395231 ACTTATTTTGCGCCTACTCTTTCC 59.605 41.667 4.18 0.00 0.00 3.13
3751 7397 2.355818 GCCTACTCTTTCCGGAAACCAT 60.356 50.000 25.67 15.07 0.00 3.55
3801 7470 5.007724 GGTCATATCCGAGTTTCCATTTCAC 59.992 44.000 0.00 0.00 0.00 3.18
3905 7577 1.116536 TGGTTCACTCCTACGCCACA 61.117 55.000 0.00 0.00 0.00 4.17
3937 7609 4.253685 CGGGACTAGTGTGATTTGTCATT 58.746 43.478 0.00 0.00 0.00 2.57
3938 7610 4.695455 CGGGACTAGTGTGATTTGTCATTT 59.305 41.667 0.00 0.00 0.00 2.32
3939 7611 5.872617 CGGGACTAGTGTGATTTGTCATTTA 59.127 40.000 0.00 0.00 0.00 1.40
3940 7612 6.036083 CGGGACTAGTGTGATTTGTCATTTAG 59.964 42.308 0.00 0.00 0.00 1.85
4018 7690 1.234821 TCGGTTGCAATCCTGAACAC 58.765 50.000 0.59 0.00 0.00 3.32
4022 7694 3.578688 GGTTGCAATCCTGAACACATTC 58.421 45.455 0.59 0.00 35.18 2.67
4065 7737 8.518430 TGCAGTTGAATAAAGCCTATAATTCA 57.482 30.769 0.00 0.00 36.75 2.57
4183 7885 5.330455 TGCCTACACAATGTTTGTTTGAA 57.670 34.783 0.00 0.00 43.23 2.69
4375 8094 9.657419 AAATTATATCAAAGACTTTGCAAAGGG 57.343 29.630 35.65 21.63 40.31 3.95
4398 8118 6.820152 GGGAAAGCATCATTTATTTTGAAGCT 59.180 34.615 0.00 0.00 46.69 3.74
4403 8123 8.611654 AGCATCATTTATTTTGAAGCTTTGTT 57.388 26.923 0.00 0.00 43.43 2.83
4421 8141 6.660887 TTTGTTGAAAGAAAATGGCTTGAC 57.339 33.333 0.00 0.00 0.00 3.18
4430 8150 6.817765 AGAAAATGGCTTGACTTTAATCGA 57.182 33.333 0.00 0.00 0.00 3.59
4454 8174 7.148918 CGATGCTTTAACAATTTGTTGAGAAGG 60.149 37.037 22.04 11.55 41.30 3.46
4455 8175 7.106439 TGCTTTAACAATTTGTTGAGAAGGA 57.894 32.000 22.04 19.01 41.30 3.36
4506 8226 3.811497 GGTGCCCCATATTTTACGTACTC 59.189 47.826 0.00 0.00 0.00 2.59
4517 8237 8.604035 CATATTTTACGTACTCAGTGCTCATTT 58.396 33.333 0.00 0.00 0.00 2.32
4519 8239 3.386768 ACGTACTCAGTGCTCATTTGT 57.613 42.857 0.00 0.00 0.00 2.83
4526 8246 2.106338 TCAGTGCTCATTTGTCCAAGGA 59.894 45.455 0.00 0.00 0.00 3.36
4530 8250 4.702131 AGTGCTCATTTGTCCAAGGATAAC 59.298 41.667 0.00 0.00 0.00 1.89
4536 8256 7.970614 GCTCATTTGTCCAAGGATAACTTTAAG 59.029 37.037 0.00 0.00 37.29 1.85
4566 8287 6.044404 TCCCTCTTACCTTCTCTTTTCACATT 59.956 38.462 0.00 0.00 0.00 2.71
4571 8292 9.090103 TCTTACCTTCTCTTTTCACATTAGAGA 57.910 33.333 0.00 0.00 41.85 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 4.416738 GAGGTGGGTCAGGCTGGC 62.417 72.222 15.73 13.70 0.00 4.85
35 36 2.930019 TGAGGTGGGTCAGGCTGG 60.930 66.667 15.73 0.00 0.00 4.85
36 37 2.348998 GTGAGGTGGGTCAGGCTG 59.651 66.667 8.58 8.58 0.00 4.85
37 38 2.930562 GGTGAGGTGGGTCAGGCT 60.931 66.667 0.00 0.00 0.00 4.58
38 39 4.394712 CGGTGAGGTGGGTCAGGC 62.395 72.222 0.00 0.00 0.00 4.85
39 40 4.394712 GCGGTGAGGTGGGTCAGG 62.395 72.222 0.00 0.00 0.00 3.86
40 41 4.394712 GGCGGTGAGGTGGGTCAG 62.395 72.222 0.00 0.00 0.00 3.51
59 60 4.785453 GAGGGGCGCTGGAACCAG 62.785 72.222 9.52 15.64 46.15 4.00
62 63 4.475135 GAGGAGGGGCGCTGGAAC 62.475 72.222 9.52 0.00 0.00 3.62
74 75 3.847602 CAGGCAGAGGGCGAGGAG 61.848 72.222 0.00 0.00 46.16 3.69
75 76 3.905153 TTCAGGCAGAGGGCGAGGA 62.905 63.158 0.00 0.00 46.16 3.71
76 77 2.469465 TTTTCAGGCAGAGGGCGAGG 62.469 60.000 0.00 0.00 46.16 4.63
77 78 0.606401 TTTTTCAGGCAGAGGGCGAG 60.606 55.000 0.00 0.00 46.16 5.03
78 79 0.038166 ATTTTTCAGGCAGAGGGCGA 59.962 50.000 0.00 0.00 46.16 5.54
79 80 0.171903 CATTTTTCAGGCAGAGGGCG 59.828 55.000 0.00 0.00 46.16 6.13
80 81 0.108472 GCATTTTTCAGGCAGAGGGC 60.108 55.000 0.00 0.00 43.74 5.19
81 82 0.533951 GGCATTTTTCAGGCAGAGGG 59.466 55.000 0.00 0.00 0.00 4.30
82 83 1.203994 CAGGCATTTTTCAGGCAGAGG 59.796 52.381 0.00 0.00 0.00 3.69
83 84 1.403780 GCAGGCATTTTTCAGGCAGAG 60.404 52.381 0.00 0.00 0.00 3.35
84 85 0.604578 GCAGGCATTTTTCAGGCAGA 59.395 50.000 0.00 0.00 0.00 4.26
85 86 0.319083 TGCAGGCATTTTTCAGGCAG 59.681 50.000 0.00 0.00 0.00 4.85
86 87 0.978151 ATGCAGGCATTTTTCAGGCA 59.022 45.000 0.00 0.00 31.82 4.75
87 88 1.066716 TGATGCAGGCATTTTTCAGGC 60.067 47.619 8.34 0.00 36.70 4.85
88 89 2.997986 GTTGATGCAGGCATTTTTCAGG 59.002 45.455 8.34 0.00 36.70 3.86
89 90 2.997986 GGTTGATGCAGGCATTTTTCAG 59.002 45.455 8.34 0.00 36.70 3.02
90 91 2.633967 AGGTTGATGCAGGCATTTTTCA 59.366 40.909 8.34 0.00 36.70 2.69
91 92 3.323751 AGGTTGATGCAGGCATTTTTC 57.676 42.857 8.34 0.00 36.70 2.29
92 93 3.775261 AAGGTTGATGCAGGCATTTTT 57.225 38.095 8.34 0.00 36.70 1.94
93 94 3.667360 GAAAGGTTGATGCAGGCATTTT 58.333 40.909 8.34 4.54 36.70 1.82
94 95 2.353011 CGAAAGGTTGATGCAGGCATTT 60.353 45.455 8.34 0.00 36.70 2.32
95 96 1.203052 CGAAAGGTTGATGCAGGCATT 59.797 47.619 8.34 0.00 36.70 3.56
96 97 0.813184 CGAAAGGTTGATGCAGGCAT 59.187 50.000 6.44 6.44 39.69 4.40
97 98 1.865788 GCGAAAGGTTGATGCAGGCA 61.866 55.000 0.00 0.00 0.00 4.75
98 99 1.153958 GCGAAAGGTTGATGCAGGC 60.154 57.895 0.00 0.00 0.00 4.85
99 100 1.135315 CGCGAAAGGTTGATGCAGG 59.865 57.895 0.00 0.00 0.00 4.85
100 101 1.135315 CCGCGAAAGGTTGATGCAG 59.865 57.895 8.23 0.00 0.00 4.41
101 102 2.976840 GCCGCGAAAGGTTGATGCA 61.977 57.895 8.23 0.00 0.00 3.96
102 103 2.202479 GCCGCGAAAGGTTGATGC 60.202 61.111 8.23 0.00 0.00 3.91
103 104 2.098298 CGCCGCGAAAGGTTGATG 59.902 61.111 8.23 0.00 0.00 3.07
104 105 2.047655 TCGCCGCGAAAGGTTGAT 60.048 55.556 14.27 0.00 31.06 2.57
105 106 3.039588 GTCGCCGCGAAAGGTTGA 61.040 61.111 18.71 0.00 37.72 3.18
106 107 4.424430 CGTCGCCGCGAAAGGTTG 62.424 66.667 18.71 0.00 37.72 3.77
124 125 3.659089 AAGTCGAATCGGGTGGCGG 62.659 63.158 1.76 0.00 0.00 6.13
125 126 2.125673 AAGTCGAATCGGGTGGCG 60.126 61.111 1.76 0.00 0.00 5.69
126 127 1.814169 GGAAGTCGAATCGGGTGGC 60.814 63.158 1.76 0.00 0.00 5.01
127 128 1.153429 GGGAAGTCGAATCGGGTGG 60.153 63.158 1.76 0.00 0.00 4.61
128 129 1.153429 GGGGAAGTCGAATCGGGTG 60.153 63.158 1.76 0.00 0.00 4.61
129 130 2.364780 GGGGGAAGTCGAATCGGGT 61.365 63.158 1.76 0.00 0.00 5.28
130 131 2.504519 GGGGGAAGTCGAATCGGG 59.495 66.667 1.76 0.00 0.00 5.14
166 167 2.438434 GGTGTGCGGGGGAATCTG 60.438 66.667 0.00 0.00 0.00 2.90
211 212 1.227380 CCAGAAGCTCGAATCGGGG 60.227 63.158 4.15 0.00 0.00 5.73
260 261 0.459585 GGCTGCGGTAACTCGAATCA 60.460 55.000 0.00 0.00 0.00 2.57
299 301 2.553079 GAGAAGCTCGAATCAGACGT 57.447 50.000 0.00 0.00 0.00 4.34
329 331 1.451387 CCTCAAATTAGGCGGCGGT 60.451 57.895 9.78 0.00 0.00 5.68
332 335 1.306148 GGTACCTCAAATTAGGCGGC 58.694 55.000 4.06 0.00 40.62 6.53
336 339 2.914059 CCGGTGGTACCTCAAATTAGG 58.086 52.381 14.36 3.85 42.82 2.69
347 350 4.789123 AATGGCCGCCGGTGGTAC 62.789 66.667 33.67 26.14 0.00 3.34
355 358 1.719709 GTTAACTCGAATGGCCGCC 59.280 57.895 1.04 1.04 0.00 6.13
356 359 1.347221 CGTTAACTCGAATGGCCGC 59.653 57.895 3.71 0.00 0.00 6.53
358 361 0.643820 CGACGTTAACTCGAATGGCC 59.356 55.000 17.21 0.00 32.65 5.36
374 377 2.194271 GGAATCGAATCAGGTGACGAC 58.806 52.381 2.36 0.00 37.58 4.34
378 381 1.762957 GAGGGGAATCGAATCAGGTGA 59.237 52.381 2.36 0.00 0.00 4.02
380 383 1.132500 GGAGGGGAATCGAATCAGGT 58.868 55.000 2.36 0.00 0.00 4.00
408 411 1.805120 CGGTAACTCAAATCGGGCGAT 60.805 52.381 0.00 0.00 36.23 4.58
409 412 0.458889 CGGTAACTCAAATCGGGCGA 60.459 55.000 0.00 0.00 0.00 5.54
430 433 2.956964 GAGCTCGAATGGCCGACG 60.957 66.667 0.00 3.75 34.56 5.12
431 434 2.586357 GGAGCTCGAATGGCCGAC 60.586 66.667 7.83 0.00 34.56 4.79
432 435 3.849951 GGGAGCTCGAATGGCCGA 61.850 66.667 7.83 0.00 37.03 5.54
473 476 2.653448 CGACGAGGATCTGCGCAG 60.653 66.667 31.53 31.53 0.00 5.18
474 477 4.854784 GCGACGAGGATCTGCGCA 62.855 66.667 10.98 10.98 46.19 6.09
476 479 2.352915 GAGCGACGAGGATCTGCG 60.353 66.667 0.00 6.28 0.00 5.18
477 480 2.352915 CGAGCGACGAGGATCTGC 60.353 66.667 0.00 0.00 45.77 4.26
478 481 2.329690 CCGAGCGACGAGGATCTG 59.670 66.667 0.00 0.00 45.77 2.90
479 482 3.587933 GCCGAGCGACGAGGATCT 61.588 66.667 0.00 0.00 45.77 2.75
480 483 4.632458 GGCCGAGCGACGAGGATC 62.632 72.222 0.00 0.00 45.77 3.36
496 499 4.180946 CGAGAGGAGTGCCGACGG 62.181 72.222 10.29 10.29 39.96 4.79
497 500 2.585170 CTTCGAGAGGAGTGCCGACG 62.585 65.000 0.00 0.00 39.96 5.12
498 501 1.137825 CTTCGAGAGGAGTGCCGAC 59.862 63.158 0.00 0.00 39.96 4.79
499 502 2.701780 GCTTCGAGAGGAGTGCCGA 61.702 63.158 0.00 0.00 39.60 5.54
500 503 2.202676 GCTTCGAGAGGAGTGCCG 60.203 66.667 0.00 0.00 39.60 5.69
501 504 1.140804 GAGCTTCGAGAGGAGTGCC 59.859 63.158 0.00 0.00 39.60 5.01
502 505 1.226547 CGAGCTTCGAGAGGAGTGC 60.227 63.158 0.00 0.00 43.74 4.40
503 506 1.431440 CCGAGCTTCGAGAGGAGTG 59.569 63.158 7.07 0.00 43.74 3.51
504 507 2.411504 GCCGAGCTTCGAGAGGAGT 61.412 63.158 7.07 0.00 43.74 3.85
505 508 2.411290 GCCGAGCTTCGAGAGGAG 59.589 66.667 7.07 0.00 43.74 3.69
506 509 3.141488 GGCCGAGCTTCGAGAGGA 61.141 66.667 7.07 0.00 43.74 3.71
507 510 4.560856 CGGCCGAGCTTCGAGAGG 62.561 72.222 24.07 0.00 43.74 3.69
524 527 2.439156 AAGGGATCAAGCGGCAGC 60.439 61.111 0.00 0.00 45.58 5.25
525 528 2.117156 CCAAGGGATCAAGCGGCAG 61.117 63.158 1.45 0.00 0.00 4.85
526 529 2.045045 CCAAGGGATCAAGCGGCA 60.045 61.111 1.45 0.00 0.00 5.69
527 530 1.821332 CTCCAAGGGATCAAGCGGC 60.821 63.158 0.00 0.00 0.00 6.53
528 531 0.830648 TACTCCAAGGGATCAAGCGG 59.169 55.000 0.00 0.00 0.00 5.52
529 532 1.482593 ACTACTCCAAGGGATCAAGCG 59.517 52.381 0.00 0.00 0.00 4.68
530 533 3.707102 ACTACTACTCCAAGGGATCAAGC 59.293 47.826 0.00 0.00 0.00 4.01
531 534 5.941555 AACTACTACTCCAAGGGATCAAG 57.058 43.478 0.00 0.00 0.00 3.02
532 535 6.697641 AAAACTACTACTCCAAGGGATCAA 57.302 37.500 0.00 0.00 0.00 2.57
533 536 6.727231 TGTAAAACTACTACTCCAAGGGATCA 59.273 38.462 0.00 0.00 0.00 2.92
534 537 7.179076 TGTAAAACTACTACTCCAAGGGATC 57.821 40.000 0.00 0.00 0.00 3.36
535 538 7.624077 AGATGTAAAACTACTACTCCAAGGGAT 59.376 37.037 0.00 0.00 0.00 3.85
536 539 6.958192 AGATGTAAAACTACTACTCCAAGGGA 59.042 38.462 0.00 0.00 0.00 4.20
537 540 7.184067 AGATGTAAAACTACTACTCCAAGGG 57.816 40.000 0.00 0.00 0.00 3.95
538 541 8.311836 TCAAGATGTAAAACTACTACTCCAAGG 58.688 37.037 0.00 0.00 0.00 3.61
539 542 9.706691 TTCAAGATGTAAAACTACTACTCCAAG 57.293 33.333 0.00 0.00 0.00 3.61
556 559 8.805175 TCCAACAAATGATGTATTTCAAGATGT 58.195 29.630 0.00 0.00 42.99 3.06
557 560 9.811995 ATCCAACAAATGATGTATTTCAAGATG 57.188 29.630 0.00 0.00 42.99 2.90
559 562 9.642327 CAATCCAACAAATGATGTATTTCAAGA 57.358 29.630 0.00 0.00 42.99 3.02
560 563 8.385111 GCAATCCAACAAATGATGTATTTCAAG 58.615 33.333 0.00 0.00 42.99 3.02
561 564 8.095792 AGCAATCCAACAAATGATGTATTTCAA 58.904 29.630 0.00 0.00 42.99 2.69
562 565 7.613585 AGCAATCCAACAAATGATGTATTTCA 58.386 30.769 0.00 0.00 42.99 2.69
563 566 7.977853 AGAGCAATCCAACAAATGATGTATTTC 59.022 33.333 0.00 0.00 42.99 2.17
564 567 7.844009 AGAGCAATCCAACAAATGATGTATTT 58.156 30.769 0.00 0.00 42.99 1.40
565 568 7.414222 AGAGCAATCCAACAAATGATGTATT 57.586 32.000 0.00 0.00 42.99 1.89
566 569 7.414222 AAGAGCAATCCAACAAATGATGTAT 57.586 32.000 0.00 0.00 42.99 2.29
567 570 6.839124 AAGAGCAATCCAACAAATGATGTA 57.161 33.333 0.00 0.00 42.99 2.29
568 571 5.733620 AAGAGCAATCCAACAAATGATGT 57.266 34.783 0.00 0.00 46.82 3.06
569 572 7.599621 TGTAAAAGAGCAATCCAACAAATGATG 59.400 33.333 0.00 0.00 0.00 3.07
570 573 7.669427 TGTAAAAGAGCAATCCAACAAATGAT 58.331 30.769 0.00 0.00 0.00 2.45
571 574 7.048629 TGTAAAAGAGCAATCCAACAAATGA 57.951 32.000 0.00 0.00 0.00 2.57
572 575 7.816031 AGATGTAAAAGAGCAATCCAACAAATG 59.184 33.333 0.00 0.00 0.00 2.32
573 576 7.899973 AGATGTAAAAGAGCAATCCAACAAAT 58.100 30.769 0.00 0.00 0.00 2.32
574 577 7.288810 AGATGTAAAAGAGCAATCCAACAAA 57.711 32.000 0.00 0.00 0.00 2.83
575 578 6.071952 GGAGATGTAAAAGAGCAATCCAACAA 60.072 38.462 0.00 0.00 0.00 2.83
576 579 5.415701 GGAGATGTAAAAGAGCAATCCAACA 59.584 40.000 0.00 0.00 0.00 3.33
577 580 5.415701 TGGAGATGTAAAAGAGCAATCCAAC 59.584 40.000 0.00 0.00 34.07 3.77
578 581 5.569355 TGGAGATGTAAAAGAGCAATCCAA 58.431 37.500 0.00 0.00 34.07 3.53
579 582 5.178096 TGGAGATGTAAAAGAGCAATCCA 57.822 39.130 0.00 0.00 34.38 3.41
580 583 6.705863 ATTGGAGATGTAAAAGAGCAATCC 57.294 37.500 0.00 0.00 0.00 3.01
582 585 9.851686 TGTATATTGGAGATGTAAAAGAGCAAT 57.148 29.630 0.00 0.00 0.00 3.56
583 586 9.851686 ATGTATATTGGAGATGTAAAAGAGCAA 57.148 29.630 0.00 0.00 0.00 3.91
584 587 9.494271 GATGTATATTGGAGATGTAAAAGAGCA 57.506 33.333 0.00 0.00 0.00 4.26
585 588 9.494271 TGATGTATATTGGAGATGTAAAAGAGC 57.506 33.333 0.00 0.00 0.00 4.09
592 595 9.539194 ACAGAGATGATGTATATTGGAGATGTA 57.461 33.333 0.00 0.00 0.00 2.29
593 596 8.433249 ACAGAGATGATGTATATTGGAGATGT 57.567 34.615 0.00 0.00 0.00 3.06
594 597 9.152595 CAACAGAGATGATGTATATTGGAGATG 57.847 37.037 0.00 0.00 0.00 2.90
595 598 8.319881 CCAACAGAGATGATGTATATTGGAGAT 58.680 37.037 0.00 0.00 29.88 2.75
596 599 7.510343 TCCAACAGAGATGATGTATATTGGAGA 59.490 37.037 0.00 0.00 31.87 3.71
597 600 7.674120 TCCAACAGAGATGATGTATATTGGAG 58.326 38.462 0.00 0.00 31.87 3.86
598 601 7.290948 ACTCCAACAGAGATGATGTATATTGGA 59.709 37.037 0.00 0.00 46.50 3.53
599 602 7.448420 ACTCCAACAGAGATGATGTATATTGG 58.552 38.462 0.00 0.00 46.50 3.16
600 603 8.771766 CAACTCCAACAGAGATGATGTATATTG 58.228 37.037 0.00 0.00 45.77 1.90
601 604 7.443575 GCAACTCCAACAGAGATGATGTATATT 59.556 37.037 4.37 0.00 45.77 1.28
602 605 6.933521 GCAACTCCAACAGAGATGATGTATAT 59.066 38.462 4.37 0.00 45.77 0.86
603 606 6.283694 GCAACTCCAACAGAGATGATGTATA 58.716 40.000 4.37 0.00 45.77 1.47
604 607 5.121811 GCAACTCCAACAGAGATGATGTAT 58.878 41.667 4.37 0.00 45.77 2.29
605 608 4.507710 GCAACTCCAACAGAGATGATGTA 58.492 43.478 4.37 0.00 45.77 2.29
606 609 3.341823 GCAACTCCAACAGAGATGATGT 58.658 45.455 4.37 0.00 45.77 3.06
607 610 2.681848 GGCAACTCCAACAGAGATGATG 59.318 50.000 4.37 0.00 45.77 3.07
608 611 2.996631 GGCAACTCCAACAGAGATGAT 58.003 47.619 4.37 0.00 45.77 2.45
609 612 2.479566 GGCAACTCCAACAGAGATGA 57.520 50.000 4.37 0.00 45.77 2.92
632 635 8.729805 AAAACTGCATTTTACATCTCCAAAAA 57.270 26.923 2.11 0.00 38.79 1.94
633 636 8.729805 AAAAACTGCATTTTACATCTCCAAAA 57.270 26.923 2.11 0.00 39.70 2.44
634 637 9.823647 TTAAAAACTGCATTTTACATCTCCAAA 57.176 25.926 2.11 0.00 39.70 3.28
635 638 9.823647 TTTAAAAACTGCATTTTACATCTCCAA 57.176 25.926 2.11 0.00 39.70 3.53
636 639 9.474920 CTTTAAAAACTGCATTTTACATCTCCA 57.525 29.630 2.11 0.00 39.70 3.86
637 640 9.691362 TCTTTAAAAACTGCATTTTACATCTCC 57.309 29.630 2.11 0.00 39.70 3.71
685 688 9.959749 AGAAAATGCAAATTTAGAGACGTAAAA 57.040 25.926 0.00 0.00 0.00 1.52
689 692 9.559958 CAATAGAAAATGCAAATTTAGAGACGT 57.440 29.630 0.00 0.00 0.00 4.34
690 693 9.773328 TCAATAGAAAATGCAAATTTAGAGACG 57.227 29.630 0.00 0.00 0.00 4.18
722 725 8.173775 CACAACAGTGAATTAGCTCAATAAGAG 58.826 37.037 0.00 0.00 40.29 2.85
802 1045 4.500603 AGTTGACAACTACTCCGTACTG 57.499 45.455 19.28 0.00 40.69 2.74
824 1067 2.750350 AGCGCCACCAGCTTACTT 59.250 55.556 2.29 0.00 43.24 2.24
855 1098 5.205056 CAGAGACTGAGAGGGGTTAATACT 58.795 45.833 0.00 0.00 32.44 2.12
866 1366 3.420893 AGGAACAGACAGAGACTGAGAG 58.579 50.000 5.76 0.00 38.55 3.20
890 1390 6.705782 AGTCGCGTCACATCAAATTAATTAG 58.294 36.000 5.77 0.00 0.00 1.73
934 1519 7.092935 CGGAGTATAGATAGAGGTAGGGTTACT 60.093 44.444 0.00 0.00 0.00 2.24
935 1520 7.047271 CGGAGTATAGATAGAGGTAGGGTTAC 58.953 46.154 0.00 0.00 0.00 2.50
938 1523 4.474287 CCGGAGTATAGATAGAGGTAGGGT 59.526 50.000 0.00 0.00 0.00 4.34
939 1524 4.474287 ACCGGAGTATAGATAGAGGTAGGG 59.526 50.000 9.46 0.00 0.00 3.53
1088 1694 1.194098 CGATACCTACGTGCTACTCCG 59.806 57.143 0.00 0.00 0.00 4.63
1367 1998 1.398578 GCTTTTGAGGAAGAACGCGAC 60.399 52.381 15.93 6.52 0.00 5.19
1433 2067 0.508641 CGCAAATCGCCTCGGATTAG 59.491 55.000 0.00 0.00 35.65 1.73
1448 2082 4.722700 GCCAGCTTCTCCCCGCAA 62.723 66.667 0.00 0.00 0.00 4.85
1568 2209 3.378742 TGAGGATCTACGACTCAAGAAGC 59.621 47.826 0.00 0.00 38.22 3.86
1617 2258 2.207988 TGTGGATCCAGGATTCCATGT 58.792 47.619 16.81 0.00 34.50 3.21
1619 2260 2.109480 CCATGTGGATCCAGGATTCCAT 59.891 50.000 16.81 11.10 37.39 3.41
1670 2311 1.886886 GTTGAAAACCACGGGAGCTA 58.113 50.000 0.00 0.00 42.21 3.32
1737 2385 2.808543 CCTATGCCGGAAATAGCAAGTC 59.191 50.000 5.05 0.00 43.36 3.01
1774 2425 6.038271 ACTCATTTAGTAACCATCAAATCCGC 59.962 38.462 0.00 0.00 36.36 5.54
1803 2454 1.735376 TTACATCCTCGCTCCTCGCC 61.735 60.000 0.00 0.00 38.27 5.54
1945 2601 6.315144 CACTGTACACGGATTTATGGATGAAA 59.685 38.462 0.00 0.00 0.00 2.69
1984 2640 3.245518 TGTATGCATCGTGCTACAGTT 57.754 42.857 0.19 0.00 45.31 3.16
2154 2810 3.367806 CCCTGTGGCAGTAGATCATATCG 60.368 52.174 0.00 0.00 0.00 2.92
2170 2826 2.167219 CGTATGTGCTCGCCCTGTG 61.167 63.158 0.00 0.00 0.00 3.66
2204 2863 5.005740 TGATGATAATGGGCTGCTTCATAC 58.994 41.667 0.00 1.74 0.00 2.39
2209 2868 3.825014 GTGATGATGATAATGGGCTGCTT 59.175 43.478 0.00 0.00 0.00 3.91
2215 2874 4.398358 GCATGAGGTGATGATGATAATGGG 59.602 45.833 0.00 0.00 0.00 4.00
2219 2878 5.932455 TCAAGCATGAGGTGATGATGATAA 58.068 37.500 0.00 0.00 0.00 1.75
2229 2888 3.200483 TCGATTGATCAAGCATGAGGTG 58.800 45.455 22.50 5.46 39.39 4.00
2234 2893 3.959943 TGCAATCGATTGATCAAGCATG 58.040 40.909 36.10 17.55 40.14 4.06
2341 3033 3.688159 CCTGCAGGGCCTTGTTGC 61.688 66.667 26.14 14.68 38.30 4.17
2504 3196 1.522569 GTAGAGCTGGATGGCCGTT 59.477 57.895 0.00 0.00 36.79 4.44
2746 3438 4.889856 CCATCATGGACGCCGCGA 62.890 66.667 21.79 0.00 40.96 5.87
2813 3505 1.839994 CTCAGGCTCATGAACCCCTTA 59.160 52.381 11.63 1.68 0.00 2.69
3092 6732 2.582498 CCATCGGAAGCGACGTCC 60.582 66.667 10.58 2.76 0.00 4.79
3195 6835 1.867233 GGTGATTCATCGATCAACCCG 59.133 52.381 0.00 0.00 37.70 5.28
3635 7279 6.828273 TGAAACTCCCCAGTTAATCATGTATG 59.172 38.462 0.00 0.00 42.45 2.39
3648 7292 5.711976 AGTCATACAAATTGAAACTCCCCAG 59.288 40.000 0.00 0.00 0.00 4.45
3714 7360 7.052142 AGAGTAGGCGCAAAATAAGTATACT 57.948 36.000 10.83 0.00 0.00 2.12
3905 7577 6.534475 TCACACTAGTCCCGTTTATATTGT 57.466 37.500 0.00 0.00 0.00 2.71
4183 7885 8.109705 TGTGCACTTTGTATCATCTATTTTGT 57.890 30.769 19.41 0.00 0.00 2.83
4195 7897 9.520204 GCTAATAATTGATTGTGCACTTTGTAT 57.480 29.630 19.41 3.57 32.17 2.29
4373 8092 7.008440 GCTTCAAAATAAATGATGCTTTCCC 57.992 36.000 7.03 0.00 41.89 3.97
4379 8098 8.497554 TCAACAAAGCTTCAAAATAAATGATGC 58.502 29.630 0.00 6.35 44.10 3.91
4398 8118 6.405538 AGTCAAGCCATTTTCTTTCAACAAA 58.594 32.000 0.00 0.00 0.00 2.83
4402 8122 9.260002 GATTAAAGTCAAGCCATTTTCTTTCAA 57.740 29.630 0.00 0.00 0.00 2.69
4403 8123 7.594758 CGATTAAAGTCAAGCCATTTTCTTTCA 59.405 33.333 0.00 0.00 0.00 2.69
4430 8150 7.725251 TCCTTCTCAACAAATTGTTAAAGCAT 58.275 30.769 11.33 0.00 38.77 3.79
4462 8182 9.946418 GCACCAATTAAAAACGAAATATTACAC 57.054 29.630 0.00 0.00 0.00 2.90
4506 8226 2.507484 TCCTTGGACAAATGAGCACTG 58.493 47.619 0.00 0.00 0.00 3.66
4517 8237 7.027874 ACCATCTTAAAGTTATCCTTGGACA 57.972 36.000 0.00 0.00 32.32 4.02
4519 8239 6.353602 GGGACCATCTTAAAGTTATCCTTGGA 60.354 42.308 0.00 0.00 32.32 3.53
4526 8246 7.628101 AGGTAAGAGGGACCATCTTAAAGTTAT 59.372 37.037 25.96 9.22 40.11 1.89
4530 8250 5.959583 AGGTAAGAGGGACCATCTTAAAG 57.040 43.478 25.96 0.00 40.11 1.85
4536 8256 3.648739 AGAGAAGGTAAGAGGGACCATC 58.351 50.000 0.00 0.00 39.65 3.51
4566 8287 9.922477 TGAGTAACTCTTCCATTCTTATCTCTA 57.078 33.333 0.00 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.