Multiple sequence alignment - TraesCS4D01G029100

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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 TraesCS4D01G029100 chr4D 100.000 2536 0 0 492 3027 12719629 12717094 0.000000e+00 4684.0
1 TraesCS4D01G029100 chr4D 87.394 1769 108 53 753 2451 12696518 12698241 0.000000e+00 1925.0
2 TraesCS4D01G029100 chr4D 86.422 464 31 13 1334 1790 12738454 12738016 2.110000e-131 479.0
3 TraesCS4D01G029100 chr4D 100.000 223 0 0 1 223 12720120 12719898 2.170000e-111 412.0
4 TraesCS4D01G029100 chr4A 91.850 1546 67 25 947 2457 589600215 589601736 0.000000e+00 2102.0
5 TraesCS4D01G029100 chr4A 92.441 807 32 9 1664 2457 589683439 589682649 0.000000e+00 1125.0
6 TraesCS4D01G029100 chr4A 85.033 755 51 21 1040 1790 589595673 589596369 0.000000e+00 712.0
7 TraesCS4D01G029100 chr4A 89.884 346 14 7 947 1279 589684421 589684084 2.790000e-115 425.0
8 TraesCS4D01G029100 chr4A 89.474 190 10 6 2819 3002 589671723 589671538 6.530000e-57 231.0
9 TraesCS4D01G029100 chr4B 88.851 1462 92 30 695 2116 23418628 23417198 0.000000e+00 1731.0
10 TraesCS4D01G029100 chr4B 87.427 1543 102 46 959 2457 23401359 23402853 0.000000e+00 1690.0
11 TraesCS4D01G029100 chr4B 87.478 575 29 12 2455 3012 23416714 23416166 9.220000e-175 623.0
12 TraesCS4D01G029100 chr4B 94.135 341 16 2 2118 2457 23417101 23416764 1.610000e-142 516.0
13 TraesCS4D01G029100 chrUn 92.251 813 34 9 1658 2457 371047381 371048177 0.000000e+00 1125.0
14 TraesCS4D01G029100 chrUn 94.413 358 13 3 2456 2813 371048307 371048657 7.380000e-151 544.0
15 TraesCS4D01G029100 chr1D 90.411 73 7 0 1356 1428 363108578 363108650 2.480000e-16 97.1
16 TraesCS4D01G029100 chr1B 91.935 62 5 0 1367 1428 486346048 486346109 1.490000e-13 87.9


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G029100 chr4D 12717094 12720120 3026 True 2548.000000 4684 100.000000 1 3027 2 chr4D.!!$R2 3026
1 TraesCS4D01G029100 chr4D 12696518 12698241 1723 False 1925.000000 1925 87.394000 753 2451 1 chr4D.!!$F1 1698
2 TraesCS4D01G029100 chr4A 589595673 589601736 6063 False 1407.000000 2102 88.441500 947 2457 2 chr4A.!!$F1 1510
3 TraesCS4D01G029100 chr4A 589682649 589684421 1772 True 775.000000 1125 91.162500 947 2457 2 chr4A.!!$R2 1510
4 TraesCS4D01G029100 chr4B 23401359 23402853 1494 False 1690.000000 1690 87.427000 959 2457 1 chr4B.!!$F1 1498
5 TraesCS4D01G029100 chr4B 23416166 23418628 2462 True 956.666667 1731 90.154667 695 3012 3 chr4B.!!$R1 2317
6 TraesCS4D01G029100 chrUn 371047381 371048657 1276 False 834.500000 1125 93.332000 1658 2813 2 chrUn.!!$F1 1155

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
511 512 0.032403 CACGTTCCCGGACAACACTA 59.968 55.0 0.73 0.0 38.78 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2491 6558 2.20675 TGGAGTTTGTCGTGCTTGTAC 58.793 47.619 0.0 0.0 0.0 2.9 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 4.141965 TGATCCGCCACGCACGAT 62.142 61.111 0.00 0.00 0.00 3.73
25 26 3.630148 GATCCGCCACGCACGATG 61.630 66.667 0.00 0.00 0.00 3.84
27 28 4.794439 TCCGCCACGCACGATGAG 62.794 66.667 0.00 0.00 0.00 2.90
30 31 4.152625 GCCACGCACGATGAGCAC 62.153 66.667 0.00 0.00 0.00 4.40
31 32 2.738139 CCACGCACGATGAGCACA 60.738 61.111 0.00 0.00 0.00 4.57
32 33 2.471607 CACGCACGATGAGCACAC 59.528 61.111 0.00 0.00 0.00 3.82
34 35 3.842126 CGCACGATGAGCACACCG 61.842 66.667 0.00 0.00 0.00 4.94
35 36 2.738521 GCACGATGAGCACACCGT 60.739 61.111 0.00 0.00 35.46 4.83
36 37 3.159070 CACGATGAGCACACCGTG 58.841 61.111 16.67 16.67 44.66 4.94
37 38 2.048222 ACGATGAGCACACCGTGG 60.048 61.111 1.60 0.00 33.64 4.94
38 39 3.490759 CGATGAGCACACCGTGGC 61.491 66.667 3.03 3.80 33.64 5.01
40 41 3.899981 GATGAGCACACCGTGGCCA 62.900 63.158 0.00 0.00 33.64 5.36
41 42 3.272364 ATGAGCACACCGTGGCCAT 62.272 57.895 9.72 0.00 33.64 4.40
42 43 3.434319 GAGCACACCGTGGCCATG 61.434 66.667 18.73 18.73 33.64 3.66
45 46 3.055719 CACACCGTGGCCATGTCC 61.056 66.667 23.39 2.26 0.00 4.02
47 48 4.343323 CACCGTGGCCATGTCCCA 62.343 66.667 23.39 0.00 0.00 4.37
50 51 4.720902 CGTGGCCATGTCCCAGCA 62.721 66.667 17.42 0.00 31.89 4.41
51 52 3.064324 GTGGCCATGTCCCAGCAC 61.064 66.667 9.72 0.00 31.89 4.40
52 53 3.578286 TGGCCATGTCCCAGCACA 61.578 61.111 0.00 0.00 0.00 4.57
54 55 2.352422 GCCATGTCCCAGCACAGA 59.648 61.111 0.00 0.00 0.00 3.41
55 56 1.077212 GCCATGTCCCAGCACAGAT 60.077 57.895 0.00 0.00 0.00 2.90
56 57 1.099879 GCCATGTCCCAGCACAGATC 61.100 60.000 0.00 0.00 0.00 2.75
57 58 0.465097 CCATGTCCCAGCACAGATCC 60.465 60.000 0.00 0.00 0.00 3.36
58 59 0.812811 CATGTCCCAGCACAGATCCG 60.813 60.000 0.00 0.00 0.00 4.18
60 61 4.147449 TCCCAGCACAGATCCGCG 62.147 66.667 0.00 0.00 0.00 6.46
63 64 2.125952 CAGCACAGATCCGCGACA 60.126 61.111 8.23 0.00 0.00 4.35
64 65 1.737735 CAGCACAGATCCGCGACAA 60.738 57.895 8.23 0.00 0.00 3.18
65 66 1.738099 AGCACAGATCCGCGACAAC 60.738 57.895 8.23 0.00 0.00 3.32
66 67 3.071459 GCACAGATCCGCGACAACG 62.071 63.158 8.23 0.00 42.93 4.10
71 72 4.446413 ATCCGCGACAACGGGTCC 62.446 66.667 8.23 0.00 45.53 4.46
75 76 4.754667 GCGACAACGGGTCCCTCC 62.755 72.222 6.29 0.00 43.95 4.30
98 99 4.235762 GCCGCGGCCTCTTCCATA 62.236 66.667 39.89 0.00 34.56 2.74
99 100 2.029666 CCGCGGCCTCTTCCATAG 59.970 66.667 14.67 0.00 0.00 2.23
100 101 2.663188 CGCGGCCTCTTCCATAGC 60.663 66.667 0.00 0.00 0.00 2.97
101 102 2.825264 GCGGCCTCTTCCATAGCT 59.175 61.111 0.00 0.00 0.00 3.32
103 104 1.826024 CGGCCTCTTCCATAGCTGT 59.174 57.895 0.00 0.00 0.00 4.40
104 105 0.179000 CGGCCTCTTCCATAGCTGTT 59.821 55.000 0.00 0.00 0.00 3.16
106 107 1.065126 GGCCTCTTCCATAGCTGTTGT 60.065 52.381 0.00 0.00 0.00 3.32
108 109 2.544685 CCTCTTCCATAGCTGTTGTCG 58.455 52.381 0.00 0.00 0.00 4.35
109 110 1.929836 CTCTTCCATAGCTGTTGTCGC 59.070 52.381 0.00 0.00 0.00 5.19
110 111 1.009829 CTTCCATAGCTGTTGTCGCC 58.990 55.000 0.00 0.00 0.00 5.54
111 112 0.392461 TTCCATAGCTGTTGTCGCCC 60.392 55.000 0.00 0.00 0.00 6.13
112 113 1.078497 CCATAGCTGTTGTCGCCCA 60.078 57.895 0.00 0.00 0.00 5.36
114 115 0.729116 CATAGCTGTTGTCGCCCAAG 59.271 55.000 0.00 0.00 32.51 3.61
117 118 2.328099 GCTGTTGTCGCCCAAGGAG 61.328 63.158 0.00 0.00 32.51 3.69
118 119 1.371183 CTGTTGTCGCCCAAGGAGA 59.629 57.895 0.00 0.00 32.51 3.71
122 123 2.182030 GTCGCCCAAGGAGACGAG 59.818 66.667 1.66 0.00 42.04 4.18
123 124 3.760035 TCGCCCAAGGAGACGAGC 61.760 66.667 0.00 0.00 0.00 5.03
126 127 4.069232 CCCAAGGAGACGAGCGCA 62.069 66.667 11.47 0.00 0.00 6.09
127 128 2.048222 CCAAGGAGACGAGCGCAA 60.048 61.111 11.47 0.00 0.00 4.85
128 129 1.448540 CCAAGGAGACGAGCGCAAT 60.449 57.895 11.47 0.00 0.00 3.56
129 130 1.699656 CCAAGGAGACGAGCGCAATG 61.700 60.000 11.47 0.02 0.00 2.82
130 131 1.448540 AAGGAGACGAGCGCAATGG 60.449 57.895 11.47 0.00 0.00 3.16
131 132 2.125512 GGAGACGAGCGCAATGGT 60.126 61.111 11.47 0.34 0.00 3.55
132 133 2.456119 GGAGACGAGCGCAATGGTG 61.456 63.158 11.47 0.00 0.00 4.17
134 135 2.742372 GACGAGCGCAATGGTGGT 60.742 61.111 11.47 0.00 39.89 4.16
135 136 2.740714 GACGAGCGCAATGGTGGTC 61.741 63.158 11.47 2.59 44.57 4.02
137 138 2.742372 GAGCGCAATGGTGGTCGT 60.742 61.111 11.47 0.00 41.55 4.34
141 142 3.799755 GCAATGGTGGTCGTCCGC 61.800 66.667 3.45 3.45 42.95 5.54
146 147 4.955774 GGTGGTCGTCCGCACGTT 62.956 66.667 14.14 0.00 46.76 3.99
148 149 4.210093 TGGTCGTCCGCACGTTGT 62.210 61.111 0.00 0.00 46.76 3.32
149 150 3.400590 GGTCGTCCGCACGTTGTC 61.401 66.667 0.00 0.00 46.76 3.18
151 152 3.951464 TCGTCCGCACGTTGTCGA 61.951 61.111 0.00 0.02 46.76 4.20
152 153 3.458579 CGTCCGCACGTTGTCGAG 61.459 66.667 0.00 0.00 41.42 4.04
153 154 3.103911 GTCCGCACGTTGTCGAGG 61.104 66.667 3.54 0.00 40.62 4.63
154 155 3.598715 TCCGCACGTTGTCGAGGT 61.599 61.111 3.54 0.00 40.62 3.85
158 159 3.403057 CACGTTGTCGAGGTGCGG 61.403 66.667 0.05 0.00 41.33 5.69
159 160 3.908081 ACGTTGTCGAGGTGCGGT 61.908 61.111 0.00 0.00 41.33 5.68
161 162 2.028484 GTTGTCGAGGTGCGGTCA 59.972 61.111 0.00 0.00 41.33 4.02
167 168 2.680352 GAGGTGCGGTCAGGAGGA 60.680 66.667 0.00 0.00 0.00 3.71
169 170 4.459089 GGTGCGGTCAGGAGGAGC 62.459 72.222 0.00 0.00 40.65 4.70
170 171 4.459089 GTGCGGTCAGGAGGAGCC 62.459 72.222 0.00 0.00 40.99 4.70
197 198 4.832608 GGGCGCGGAATTCGAGGT 62.833 66.667 8.83 0.00 42.43 3.85
201 202 2.165301 CGCGGAATTCGAGGTGTCC 61.165 63.158 0.00 0.00 42.43 4.02
204 205 1.895238 GGAATTCGAGGTGTCCCGA 59.105 57.895 0.00 0.00 35.12 5.14
205 206 0.459759 GGAATTCGAGGTGTCCCGAC 60.460 60.000 0.00 0.00 34.26 4.79
206 207 0.245539 GAATTCGAGGTGTCCCGACA 59.754 55.000 0.00 0.00 39.32 4.35
207 208 0.246635 AATTCGAGGTGTCCCGACAG 59.753 55.000 0.00 0.00 42.74 3.51
508 509 2.901813 ACACGTTCCCGGACAACA 59.098 55.556 0.73 0.00 38.78 3.33
509 510 1.522130 ACACGTTCCCGGACAACAC 60.522 57.895 0.73 0.00 38.78 3.32
510 511 1.227438 CACGTTCCCGGACAACACT 60.227 57.895 0.73 0.00 38.78 3.55
511 512 0.032403 CACGTTCCCGGACAACACTA 59.968 55.000 0.73 0.00 38.78 2.74
512 513 0.032540 ACGTTCCCGGACAACACTAC 59.967 55.000 0.73 0.00 38.78 2.73
514 515 1.505425 GTTCCCGGACAACACTACAC 58.495 55.000 0.73 0.00 0.00 2.90
516 517 1.108727 TCCCGGACAACACTACACGT 61.109 55.000 0.73 0.00 0.00 4.49
517 518 0.597568 CCCGGACAACACTACACGTA 59.402 55.000 0.73 0.00 0.00 3.57
518 519 1.666888 CCCGGACAACACTACACGTAC 60.667 57.143 0.73 0.00 0.00 3.67
519 520 1.321016 CGGACAACACTACACGTACG 58.679 55.000 15.01 15.01 0.00 3.67
520 521 1.334059 CGGACAACACTACACGTACGT 60.334 52.381 16.72 16.72 31.04 3.57
521 522 2.096466 CGGACAACACTACACGTACGTA 60.096 50.000 22.34 5.54 31.04 3.57
522 523 3.605922 CGGACAACACTACACGTACGTAA 60.606 47.826 22.34 11.42 31.04 3.18
524 525 4.917415 GGACAACACTACACGTACGTAATT 59.083 41.667 22.34 10.91 0.00 1.40
525 526 5.402270 GGACAACACTACACGTACGTAATTT 59.598 40.000 22.34 8.33 0.00 1.82
526 527 6.074356 GGACAACACTACACGTACGTAATTTT 60.074 38.462 22.34 6.94 0.00 1.82
527 528 7.232945 ACAACACTACACGTACGTAATTTTT 57.767 32.000 22.34 7.49 0.00 1.94
558 559 5.302357 CTTACAAAGGAGCTTAGCTTTGG 57.698 43.478 17.84 6.75 39.88 3.28
559 560 3.508845 ACAAAGGAGCTTAGCTTTGGA 57.491 42.857 17.84 0.00 39.88 3.53
560 561 3.416156 ACAAAGGAGCTTAGCTTTGGAG 58.584 45.455 17.84 8.23 39.88 3.86
561 562 3.073062 ACAAAGGAGCTTAGCTTTGGAGA 59.927 43.478 17.84 0.00 39.88 3.71
562 563 4.074970 CAAAGGAGCTTAGCTTTGGAGAA 58.925 43.478 8.58 0.00 39.88 2.87
563 564 3.625649 AGGAGCTTAGCTTTGGAGAAG 57.374 47.619 8.58 0.00 39.88 2.85
564 565 3.177228 AGGAGCTTAGCTTTGGAGAAGA 58.823 45.455 8.58 0.00 39.88 2.87
566 567 4.042187 AGGAGCTTAGCTTTGGAGAAGAAA 59.958 41.667 8.58 0.00 39.88 2.52
567 568 4.762251 GGAGCTTAGCTTTGGAGAAGAAAA 59.238 41.667 8.58 0.00 39.88 2.29
568 569 5.106357 GGAGCTTAGCTTTGGAGAAGAAAAG 60.106 44.000 8.58 0.00 39.88 2.27
569 570 5.380900 AGCTTAGCTTTGGAGAAGAAAAGT 58.619 37.500 0.00 0.00 33.89 2.66
572 573 6.567511 GCTTAGCTTTGGAGAAGAAAAGTGAG 60.568 42.308 0.00 0.00 36.09 3.51
573 574 4.140536 AGCTTTGGAGAAGAAAAGTGAGG 58.859 43.478 0.00 0.00 36.09 3.86
574 575 3.304996 GCTTTGGAGAAGAAAAGTGAGGC 60.305 47.826 0.00 0.00 36.09 4.70
575 576 2.568623 TGGAGAAGAAAAGTGAGGCC 57.431 50.000 0.00 0.00 0.00 5.19
576 577 1.270839 TGGAGAAGAAAAGTGAGGCCG 60.271 52.381 0.00 0.00 0.00 6.13
577 578 1.443802 GAGAAGAAAAGTGAGGCCGG 58.556 55.000 0.00 0.00 0.00 6.13
578 579 0.036875 AGAAGAAAAGTGAGGCCGGG 59.963 55.000 2.18 0.00 0.00 5.73
579 580 1.587043 GAAGAAAAGTGAGGCCGGGC 61.587 60.000 22.67 22.67 0.00 6.13
595 596 3.392066 GGCCCCACCCTGTAAAATT 57.608 52.632 0.00 0.00 0.00 1.82
597 598 1.551329 GGCCCCACCCTGTAAAATTGA 60.551 52.381 0.00 0.00 0.00 2.57
598 599 1.824852 GCCCCACCCTGTAAAATTGAG 59.175 52.381 0.00 0.00 0.00 3.02
599 600 2.456577 CCCCACCCTGTAAAATTGAGG 58.543 52.381 0.00 0.00 0.00 3.86
600 601 2.225267 CCCCACCCTGTAAAATTGAGGT 60.225 50.000 0.00 0.00 0.00 3.85
601 602 3.010808 CCCCACCCTGTAAAATTGAGGTA 59.989 47.826 0.00 0.00 0.00 3.08
603 604 4.270008 CCACCCTGTAAAATTGAGGTAGG 58.730 47.826 0.00 0.00 0.00 3.18
604 605 4.270008 CACCCTGTAAAATTGAGGTAGGG 58.730 47.826 0.00 0.00 46.91 3.53
606 607 3.372675 CCCTGTAAAATTGAGGTAGGGGG 60.373 52.174 0.00 0.00 39.73 5.40
607 608 3.268595 CCTGTAAAATTGAGGTAGGGGGT 59.731 47.826 0.00 0.00 0.00 4.95
609 610 3.658705 TGTAAAATTGAGGTAGGGGGTGT 59.341 43.478 0.00 0.00 0.00 4.16
610 611 2.899303 AAATTGAGGTAGGGGGTGTG 57.101 50.000 0.00 0.00 0.00 3.82
612 613 0.919289 ATTGAGGTAGGGGGTGTGGG 60.919 60.000 0.00 0.00 0.00 4.61
615 616 2.185533 GAGGTAGGGGGTGTGGGGTA 62.186 65.000 0.00 0.00 0.00 3.69
616 617 1.005156 GGTAGGGGGTGTGGGGTAT 59.995 63.158 0.00 0.00 0.00 2.73
617 618 0.625387 GGTAGGGGGTGTGGGGTATT 60.625 60.000 0.00 0.00 0.00 1.89
618 619 1.345319 GGTAGGGGGTGTGGGGTATTA 60.345 57.143 0.00 0.00 0.00 0.98
619 620 2.052468 GTAGGGGGTGTGGGGTATTAG 58.948 57.143 0.00 0.00 0.00 1.73
620 621 0.424368 AGGGGGTGTGGGGTATTAGT 59.576 55.000 0.00 0.00 0.00 2.24
621 622 1.203648 AGGGGGTGTGGGGTATTAGTT 60.204 52.381 0.00 0.00 0.00 2.24
622 623 2.047580 AGGGGGTGTGGGGTATTAGTTA 59.952 50.000 0.00 0.00 0.00 2.24
623 624 2.440627 GGGGGTGTGGGGTATTAGTTAG 59.559 54.545 0.00 0.00 0.00 2.34
625 626 3.118149 GGGGTGTGGGGTATTAGTTAGTG 60.118 52.174 0.00 0.00 0.00 2.74
626 627 3.776417 GGGTGTGGGGTATTAGTTAGTGA 59.224 47.826 0.00 0.00 0.00 3.41
627 628 4.411212 GGGTGTGGGGTATTAGTTAGTGAT 59.589 45.833 0.00 0.00 0.00 3.06
628 629 5.365619 GGTGTGGGGTATTAGTTAGTGATG 58.634 45.833 0.00 0.00 0.00 3.07
629 630 5.365619 GTGTGGGGTATTAGTTAGTGATGG 58.634 45.833 0.00 0.00 0.00 3.51
631 632 5.727279 TGTGGGGTATTAGTTAGTGATGGAA 59.273 40.000 0.00 0.00 0.00 3.53
633 634 5.368523 TGGGGTATTAGTTAGTGATGGAAGG 59.631 44.000 0.00 0.00 0.00 3.46
634 635 5.368816 GGGGTATTAGTTAGTGATGGAAGGT 59.631 44.000 0.00 0.00 0.00 3.50
635 636 6.126565 GGGGTATTAGTTAGTGATGGAAGGTT 60.127 42.308 0.00 0.00 0.00 3.50
636 637 7.344134 GGGTATTAGTTAGTGATGGAAGGTTT 58.656 38.462 0.00 0.00 0.00 3.27
673 674 9.434420 TTTAGTAAAAATTAGCGTAGGTTAGCA 57.566 29.630 0.00 0.00 40.68 3.49
674 675 7.910441 AGTAAAAATTAGCGTAGGTTAGCAA 57.090 32.000 0.00 0.00 40.68 3.91
675 676 8.502105 AGTAAAAATTAGCGTAGGTTAGCAAT 57.498 30.769 0.00 0.00 40.68 3.56
677 678 9.563898 GTAAAAATTAGCGTAGGTTAGCAATTT 57.436 29.630 0.00 0.00 40.68 1.82
679 680 8.460831 AAAATTAGCGTAGGTTAGCAATTTTG 57.539 30.769 15.29 0.00 39.49 2.44
680 681 6.995511 ATTAGCGTAGGTTAGCAATTTTGA 57.004 33.333 0.00 0.00 40.68 2.69
681 682 6.995511 TTAGCGTAGGTTAGCAATTTTGAT 57.004 33.333 0.00 0.00 40.68 2.57
682 683 5.235305 AGCGTAGGTTAGCAATTTTGATG 57.765 39.130 0.00 0.00 35.48 3.07
684 685 7.646351 AGCGTAGGTTAGCAATTTTGATGCG 62.646 44.000 0.00 0.00 42.29 4.73
697 698 2.706555 TGATGCGTTCTCTATAGGCG 57.293 50.000 0.00 1.78 0.00 5.52
705 706 0.178998 TCTCTATAGGCGCGTTCCCT 60.179 55.000 8.36 8.66 36.47 4.20
706 707 1.072806 TCTCTATAGGCGCGTTCCCTA 59.927 52.381 8.36 10.90 39.17 3.53
709 710 1.338973 CTATAGGCGCGTTCCCTACAA 59.661 52.381 8.36 4.58 37.75 2.41
710 711 0.538118 ATAGGCGCGTTCCCTACAAA 59.462 50.000 8.36 0.00 37.75 2.83
751 752 0.804989 GGTCAATCGGACTGCTTTGG 59.195 55.000 0.00 0.00 46.16 3.28
779 780 4.520874 TGTGTTTTCGATCCAATGGCTAAA 59.479 37.500 0.00 0.00 0.00 1.85
813 814 3.266772 TGGAGATGCCCAAATAACTGACT 59.733 43.478 0.00 0.00 34.97 3.41
836 837 6.148480 ACTGCAGTCAGATAAGATTTCACAAC 59.852 38.462 15.25 0.00 42.95 3.32
852 853 9.086336 GATTTCACAACAATTTCAGAGTCAAAA 57.914 29.630 0.00 0.00 0.00 2.44
859 860 5.244626 ACAATTTCAGAGTCAAAATCCCTGG 59.755 40.000 4.54 0.00 0.00 4.45
916 919 2.181521 AGTCCGAGCTCGATCCGTC 61.182 63.158 36.59 17.10 43.02 4.79
930 933 2.433868 TCCGTCGACTCTCAAAAAGG 57.566 50.000 14.70 3.97 0.00 3.11
931 934 1.000506 TCCGTCGACTCTCAAAAAGGG 59.999 52.381 14.70 3.20 0.00 3.95
932 935 0.790814 CGTCGACTCTCAAAAAGGGC 59.209 55.000 14.70 0.00 0.00 5.19
933 936 0.790814 GTCGACTCTCAAAAAGGGCG 59.209 55.000 8.70 0.00 0.00 6.13
934 937 0.320421 TCGACTCTCAAAAAGGGCGG 60.320 55.000 0.00 0.00 0.00 6.13
936 939 0.036306 GACTCTCAAAAAGGGCGGGA 59.964 55.000 0.00 0.00 0.00 5.14
937 940 0.476771 ACTCTCAAAAAGGGCGGGAA 59.523 50.000 0.00 0.00 0.00 3.97
938 941 1.168714 CTCTCAAAAAGGGCGGGAAG 58.831 55.000 0.00 0.00 0.00 3.46
939 942 0.251165 TCTCAAAAAGGGCGGGAAGG 60.251 55.000 0.00 0.00 0.00 3.46
940 943 0.251165 CTCAAAAAGGGCGGGAAGGA 60.251 55.000 0.00 0.00 0.00 3.36
941 944 0.251165 TCAAAAAGGGCGGGAAGGAG 60.251 55.000 0.00 0.00 0.00 3.69
942 945 1.076727 AAAAAGGGCGGGAAGGAGG 59.923 57.895 0.00 0.00 0.00 4.30
998 4595 0.797249 CTCACGCGCCGCCTATATAC 60.797 60.000 5.73 0.00 0.00 1.47
1000 4597 0.457853 CACGCGCCGCCTATATACAT 60.458 55.000 5.73 0.00 0.00 2.29
1064 4671 0.248702 GCCGATCGAACTCCTCTCAC 60.249 60.000 18.66 0.00 0.00 3.51
1315 4935 2.851071 GCGAGTCTCGGGGAGATGG 61.851 68.421 23.09 0.00 40.98 3.51
1316 4936 2.851071 CGAGTCTCGGGGAGATGGC 61.851 68.421 14.68 0.00 40.98 4.40
1333 4962 2.434884 CTGGCGGCAAGATCGTGT 60.435 61.111 14.48 0.00 0.00 4.49
1631 5272 2.658593 CGGATACAGCCGCTTCCG 60.659 66.667 15.66 15.66 45.38 4.30
1855 5739 4.260253 GCGAAATTAGGGTTTAGCTCTTCG 60.260 45.833 0.00 0.00 36.95 3.79
1878 5762 2.088423 AGAGAACACTAGAGCTGTCCG 58.912 52.381 0.00 0.00 0.00 4.79
1913 5825 6.354130 TGTACTCAGAAAAGTTGTAAAGCCT 58.646 36.000 0.00 0.00 0.00 4.58
1930 5842 4.851639 AGCCTTGTACAGATGATTTCCT 57.148 40.909 0.00 0.00 0.00 3.36
1986 5898 4.102838 AGGATCAACTCTGATGATTCCTGG 59.897 45.833 0.00 0.00 42.60 4.45
1991 5903 5.045651 TCAACTCTGATGATTCCTGGCTTAA 60.046 40.000 0.00 0.00 0.00 1.85
1992 5904 5.643421 ACTCTGATGATTCCTGGCTTAAT 57.357 39.130 0.00 0.00 0.00 1.40
1993 5905 6.011122 ACTCTGATGATTCCTGGCTTAATT 57.989 37.500 0.00 0.00 0.00 1.40
1994 5906 7.141758 ACTCTGATGATTCCTGGCTTAATTA 57.858 36.000 0.00 0.00 0.00 1.40
2037 5949 8.854614 AGATTATGCTAGGAACATATTTGTCC 57.145 34.615 0.00 0.00 34.06 4.02
2038 5950 8.439971 AGATTATGCTAGGAACATATTTGTCCA 58.560 33.333 0.00 0.00 34.06 4.02
2039 5951 8.627208 ATTATGCTAGGAACATATTTGTCCAG 57.373 34.615 0.00 4.86 34.06 3.86
2040 5952 4.780815 TGCTAGGAACATATTTGTCCAGG 58.219 43.478 0.00 0.00 34.06 4.45
2041 5953 4.473196 TGCTAGGAACATATTTGTCCAGGA 59.527 41.667 0.00 0.00 34.06 3.86
2116 6030 2.060326 TCGCTGGAGTACAAAGTTCG 57.940 50.000 0.00 0.00 0.00 3.95
2326 6338 8.397148 GTTGAGAGAAAATTGAAATTTTGGCAA 58.603 29.630 16.36 11.81 45.70 4.52
2342 6354 6.365970 TTTGGCAATTGTTTACCACCATAT 57.634 33.333 7.40 0.00 27.47 1.78
2468 6535 6.280643 TCCATCGACGACTGAATTATCAAAT 58.719 36.000 0.00 0.00 34.49 2.32
2643 6788 2.459060 TGTGGCCAAATTCTTGCATG 57.541 45.000 7.24 0.00 0.00 4.06
2654 6799 8.066000 GCCAAATTCTTGCATGCTATTTTTATC 58.934 33.333 20.33 4.55 0.00 1.75
2669 6814 8.021396 GCTATTTTTATCGTAAATGGATCACCC 58.979 37.037 0.00 0.00 34.81 4.61
2678 6823 3.761896 TGGATCACCCAATGCAACA 57.238 47.368 0.00 0.00 43.29 3.33
2734 6879 6.430000 GGAAAATACTAGAGCTGTGACCAAAA 59.570 38.462 0.00 0.00 0.00 2.44
2791 6941 6.861065 AGTACAGTTTACACCAGTGAAATG 57.139 37.500 4.48 1.78 42.66 2.32
2874 7024 4.279169 ACACTAGTAAGAACAACCAGCGTA 59.721 41.667 0.00 0.00 0.00 4.42
2900 7060 3.697542 TCCACATGAATGGAGCTTTGATG 59.302 43.478 0.00 0.00 44.14 3.07
2901 7061 3.697542 CCACATGAATGGAGCTTTGATGA 59.302 43.478 0.00 0.00 43.02 2.92
2902 7062 4.439700 CCACATGAATGGAGCTTTGATGAC 60.440 45.833 0.00 0.00 43.02 3.06
2903 7063 3.376234 ACATGAATGGAGCTTTGATGACG 59.624 43.478 0.00 0.00 0.00 4.35
2904 7064 1.739466 TGAATGGAGCTTTGATGACGC 59.261 47.619 0.00 0.00 0.00 5.19
2905 7065 1.739466 GAATGGAGCTTTGATGACGCA 59.261 47.619 0.00 0.00 0.00 5.24
2906 7066 1.825090 ATGGAGCTTTGATGACGCAA 58.175 45.000 0.00 0.00 0.00 4.85
2934 7094 5.365403 TGTTAGCGAAAAATGTCGGAATT 57.635 34.783 0.00 0.00 41.40 2.17
2956 7116 4.148838 TCAAAGGGAATCCACACGAAAAT 58.851 39.130 0.09 0.00 34.83 1.82
2995 7155 8.894768 TTAGAAAGAGAGAAGAAGGAAAACTG 57.105 34.615 0.00 0.00 0.00 3.16
2999 7159 8.759481 AAAGAGAGAAGAAGGAAAACTGATTT 57.241 30.769 0.00 0.00 0.00 2.17
3002 7162 5.049129 AGAGAAGAAGGAAAACTGATTTGCG 60.049 40.000 0.00 0.00 43.48 4.85
3008 7168 3.609214 AAACTGATTTGCGCGGCCG 62.609 57.895 24.05 24.05 37.57 6.13
3012 7172 4.520846 GATTTGCGCGGCCGACTG 62.521 66.667 33.48 19.04 36.29 3.51
3017 7177 4.789075 GCGCGGCCGACTGAAGTA 62.789 66.667 33.48 0.00 36.29 2.24
3018 7178 2.126228 CGCGGCCGACTGAAGTAA 60.126 61.111 33.48 0.00 36.29 2.24
3019 7179 1.518572 CGCGGCCGACTGAAGTAAT 60.519 57.895 33.48 0.00 36.29 1.89
3020 7180 1.082117 CGCGGCCGACTGAAGTAATT 61.082 55.000 33.48 0.00 36.29 1.40
3021 7181 0.373716 GCGGCCGACTGAAGTAATTG 59.626 55.000 33.48 0.00 0.00 2.32
3022 7182 1.722011 CGGCCGACTGAAGTAATTGT 58.278 50.000 24.07 0.00 0.00 2.71
3023 7183 2.073816 CGGCCGACTGAAGTAATTGTT 58.926 47.619 24.07 0.00 0.00 2.83
3024 7184 2.159707 CGGCCGACTGAAGTAATTGTTG 60.160 50.000 24.07 0.00 0.00 3.33
3025 7185 3.071479 GGCCGACTGAAGTAATTGTTGA 58.929 45.455 0.00 0.00 0.00 3.18
3026 7186 3.125316 GGCCGACTGAAGTAATTGTTGAG 59.875 47.826 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.106332 GTGGCGGATCACGTAGGG 59.894 66.667 0.00 0.00 46.52 3.53
7 8 4.141965 ATCGTGCGTGGCGGATCA 62.142 61.111 0.00 0.00 0.00 2.92
8 9 3.630148 CATCGTGCGTGGCGGATC 61.630 66.667 0.00 0.00 0.00 3.36
9 10 4.141965 TCATCGTGCGTGGCGGAT 62.142 61.111 0.00 0.00 0.00 4.18
10 11 4.794439 CTCATCGTGCGTGGCGGA 62.794 66.667 0.00 0.00 0.00 5.54
13 14 4.152625 GTGCTCATCGTGCGTGGC 62.153 66.667 0.00 0.00 0.00 5.01
16 17 2.738521 GGTGTGCTCATCGTGCGT 60.739 61.111 0.00 0.00 0.00 5.24
22 23 3.127533 GGCCACGGTGTGCTCATC 61.128 66.667 17.14 0.00 31.34 2.92
23 24 3.272364 ATGGCCACGGTGTGCTCAT 62.272 57.895 8.16 15.33 31.34 2.90
24 25 3.952508 ATGGCCACGGTGTGCTCA 61.953 61.111 8.16 14.20 31.34 4.26
25 26 3.434319 CATGGCCACGGTGTGCTC 61.434 66.667 8.16 10.41 31.34 4.26
27 28 3.737172 GACATGGCCACGGTGTGC 61.737 66.667 15.13 9.87 31.34 4.57
28 29 3.055719 GGACATGGCCACGGTGTG 61.056 66.667 14.59 8.48 0.00 3.82
30 31 4.343323 TGGGACATGGCCACGGTG 62.343 66.667 22.13 5.14 0.00 4.94
31 32 4.033776 CTGGGACATGGCCACGGT 62.034 66.667 22.13 10.22 38.20 4.83
34 35 3.064324 GTGCTGGGACATGGCCAC 61.064 66.667 22.13 9.70 38.20 5.01
35 36 3.572447 CTGTGCTGGGACATGGCCA 62.572 63.158 22.13 8.56 38.20 5.36
36 37 2.563013 ATCTGTGCTGGGACATGGCC 62.563 60.000 10.00 10.00 38.20 5.36
37 38 1.077212 ATCTGTGCTGGGACATGGC 60.077 57.895 0.00 0.00 38.20 4.40
38 39 0.465097 GGATCTGTGCTGGGACATGG 60.465 60.000 0.00 0.00 38.20 3.66
40 41 1.524002 CGGATCTGTGCTGGGACAT 59.476 57.895 0.00 0.00 38.20 3.06
41 42 2.981302 CGGATCTGTGCTGGGACA 59.019 61.111 0.00 0.00 0.00 4.02
42 43 2.512515 GCGGATCTGTGCTGGGAC 60.513 66.667 2.89 0.00 0.00 4.46
45 46 2.887568 GTCGCGGATCTGTGCTGG 60.888 66.667 6.13 0.00 0.00 4.85
47 48 1.738099 GTTGTCGCGGATCTGTGCT 60.738 57.895 6.13 0.00 0.00 4.40
49 50 3.072598 CGTTGTCGCGGATCTGTG 58.927 61.111 6.13 8.91 0.00 3.66
81 82 4.235762 TATGGAAGAGGCCGCGGC 62.236 66.667 41.63 41.63 41.06 6.53
82 83 2.029666 CTATGGAAGAGGCCGCGG 59.970 66.667 24.05 24.05 0.00 6.46
83 84 2.663188 GCTATGGAAGAGGCCGCG 60.663 66.667 0.00 0.00 0.00 6.46
84 85 1.596477 CAGCTATGGAAGAGGCCGC 60.596 63.158 0.00 0.00 0.00 6.53
89 90 1.929836 GCGACAACAGCTATGGAAGAG 59.070 52.381 3.96 0.00 0.00 2.85
90 91 1.405526 GGCGACAACAGCTATGGAAGA 60.406 52.381 3.96 0.00 34.52 2.87
91 92 1.009829 GGCGACAACAGCTATGGAAG 58.990 55.000 3.96 0.00 34.52 3.46
92 93 0.392461 GGGCGACAACAGCTATGGAA 60.392 55.000 0.00 0.00 34.52 3.53
93 94 1.220749 GGGCGACAACAGCTATGGA 59.779 57.895 0.00 0.00 34.52 3.41
94 95 0.676466 TTGGGCGACAACAGCTATGG 60.676 55.000 0.00 0.00 33.18 2.74
95 96 0.729116 CTTGGGCGACAACAGCTATG 59.271 55.000 0.00 0.00 34.76 2.23
96 97 0.392998 CCTTGGGCGACAACAGCTAT 60.393 55.000 0.00 0.00 34.76 2.97
97 98 1.003839 CCTTGGGCGACAACAGCTA 60.004 57.895 0.00 0.00 34.76 3.32
98 99 2.281761 CCTTGGGCGACAACAGCT 60.282 61.111 0.00 0.00 34.76 4.24
99 100 2.281484 TCCTTGGGCGACAACAGC 60.281 61.111 0.00 0.00 34.76 4.40
100 101 0.951040 GTCTCCTTGGGCGACAACAG 60.951 60.000 0.00 0.00 34.76 3.16
101 102 1.070786 GTCTCCTTGGGCGACAACA 59.929 57.895 0.00 0.00 34.76 3.33
103 104 2.154798 CTCGTCTCCTTGGGCGACAA 62.155 60.000 7.35 0.00 37.55 3.18
104 105 2.599281 TCGTCTCCTTGGGCGACA 60.599 61.111 7.35 0.00 0.00 4.35
106 107 3.760035 GCTCGTCTCCTTGGGCGA 61.760 66.667 0.00 0.00 0.00 5.54
109 110 2.859273 ATTGCGCTCGTCTCCTTGGG 62.859 60.000 9.73 0.00 0.00 4.12
110 111 1.448540 ATTGCGCTCGTCTCCTTGG 60.449 57.895 9.73 0.00 0.00 3.61
111 112 1.699656 CCATTGCGCTCGTCTCCTTG 61.700 60.000 9.73 0.00 0.00 3.61
112 113 1.448540 CCATTGCGCTCGTCTCCTT 60.449 57.895 9.73 0.00 0.00 3.36
114 115 2.125512 ACCATTGCGCTCGTCTCC 60.126 61.111 9.73 0.00 0.00 3.71
117 118 2.740714 GACCACCATTGCGCTCGTC 61.741 63.158 9.73 0.00 0.00 4.20
118 119 2.742372 GACCACCATTGCGCTCGT 60.742 61.111 9.73 0.00 0.00 4.18
119 120 3.853330 CGACCACCATTGCGCTCG 61.853 66.667 9.73 2.46 0.00 5.03
121 122 2.742372 GACGACCACCATTGCGCT 60.742 61.111 9.73 0.00 0.00 5.92
122 123 3.799755 GGACGACCACCATTGCGC 61.800 66.667 0.00 0.00 35.97 6.09
123 124 3.487202 CGGACGACCACCATTGCG 61.487 66.667 4.48 0.00 35.59 4.85
124 125 3.799755 GCGGACGACCACCATTGC 61.800 66.667 4.48 0.00 35.59 3.56
126 127 2.358247 GTGCGGACGACCACCATT 60.358 61.111 4.48 0.00 35.59 3.16
137 138 3.598715 ACCTCGACAACGTGCGGA 61.599 61.111 0.00 0.00 40.69 5.54
141 142 3.403057 CCGCACCTCGACAACGTG 61.403 66.667 0.00 0.00 41.67 4.49
145 146 2.338620 CTGACCGCACCTCGACAA 59.661 61.111 0.00 0.00 41.67 3.18
146 147 3.680786 CCTGACCGCACCTCGACA 61.681 66.667 0.00 0.00 41.67 4.35
148 149 3.062466 CTCCTGACCGCACCTCGA 61.062 66.667 0.00 0.00 41.67 4.04
149 150 4.135153 CCTCCTGACCGCACCTCG 62.135 72.222 0.00 0.00 38.08 4.63
151 152 2.681778 CTCCTCCTGACCGCACCT 60.682 66.667 0.00 0.00 0.00 4.00
152 153 4.459089 GCTCCTCCTGACCGCACC 62.459 72.222 0.00 0.00 0.00 5.01
153 154 4.459089 GGCTCCTCCTGACCGCAC 62.459 72.222 0.00 0.00 0.00 5.34
175 176 2.203015 GAATTCCGCGCCCTGCTA 60.203 61.111 0.00 0.00 43.27 3.49
178 179 3.264897 CTCGAATTCCGCGCCCTG 61.265 66.667 0.00 0.00 38.37 4.45
179 180 4.530857 CCTCGAATTCCGCGCCCT 62.531 66.667 0.00 0.00 38.37 5.19
180 181 4.832608 ACCTCGAATTCCGCGCCC 62.833 66.667 0.00 0.00 38.37 6.13
181 182 3.564027 CACCTCGAATTCCGCGCC 61.564 66.667 0.00 0.00 38.37 6.53
182 183 2.799540 GACACCTCGAATTCCGCGC 61.800 63.158 0.00 0.00 38.37 6.86
183 184 2.165301 GGACACCTCGAATTCCGCG 61.165 63.158 0.00 0.00 38.37 6.46
184 185 1.814169 GGGACACCTCGAATTCCGC 60.814 63.158 0.00 0.00 38.37 5.54
187 188 0.245539 TGTCGGGACACCTCGAATTC 59.754 55.000 0.00 0.00 37.14 2.17
188 189 0.246635 CTGTCGGGACACCTCGAATT 59.753 55.000 0.00 0.00 37.14 2.17
189 190 1.890894 CTGTCGGGACACCTCGAAT 59.109 57.895 0.00 0.00 37.14 3.34
190 191 2.927580 GCTGTCGGGACACCTCGAA 61.928 63.158 0.00 0.00 37.14 3.71
191 192 3.371063 GCTGTCGGGACACCTCGA 61.371 66.667 0.00 0.00 36.21 4.04
194 195 3.374402 CTCGCTGTCGGGACACCT 61.374 66.667 0.00 0.00 38.83 4.00
197 198 4.988716 ACCCTCGCTGTCGGGACA 62.989 66.667 0.58 1.05 43.44 4.02
495 496 1.505425 GTGTAGTGTTGTCCGGGAAC 58.495 55.000 0.00 5.93 0.00 3.62
496 497 0.032403 CGTGTAGTGTTGTCCGGGAA 59.968 55.000 0.00 0.00 0.00 3.97
497 498 1.108727 ACGTGTAGTGTTGTCCGGGA 61.109 55.000 0.00 0.00 0.00 5.14
498 499 0.597568 TACGTGTAGTGTTGTCCGGG 59.402 55.000 0.00 0.00 0.00 5.73
500 501 1.321016 CGTACGTGTAGTGTTGTCCG 58.679 55.000 7.22 0.00 0.00 4.79
501 502 2.405892 ACGTACGTGTAGTGTTGTCC 57.594 50.000 22.14 0.00 0.00 4.02
502 503 6.438327 AAATTACGTACGTGTAGTGTTGTC 57.562 37.500 30.25 0.00 0.00 3.18
503 504 6.826893 AAAATTACGTACGTGTAGTGTTGT 57.173 33.333 30.25 8.32 0.00 3.32
536 537 5.003804 TCCAAAGCTAAGCTCCTTTGTAAG 58.996 41.667 22.34 13.46 43.86 2.34
537 538 4.980573 TCCAAAGCTAAGCTCCTTTGTAA 58.019 39.130 22.34 13.44 43.86 2.41
538 539 4.286032 TCTCCAAAGCTAAGCTCCTTTGTA 59.714 41.667 22.34 12.95 43.86 2.41
539 540 3.073062 TCTCCAAAGCTAAGCTCCTTTGT 59.927 43.478 22.34 0.00 43.86 2.83
541 542 4.042187 TCTTCTCCAAAGCTAAGCTCCTTT 59.958 41.667 0.00 0.00 38.25 3.11
542 543 3.584848 TCTTCTCCAAAGCTAAGCTCCTT 59.415 43.478 0.00 0.00 38.25 3.36
543 544 3.177228 TCTTCTCCAAAGCTAAGCTCCT 58.823 45.455 0.00 0.00 38.25 3.69
544 545 3.618690 TCTTCTCCAAAGCTAAGCTCC 57.381 47.619 0.00 0.00 38.25 4.70
545 546 5.471797 ACTTTTCTTCTCCAAAGCTAAGCTC 59.528 40.000 0.00 0.00 38.25 4.09
546 547 5.240403 CACTTTTCTTCTCCAAAGCTAAGCT 59.760 40.000 0.00 0.00 42.56 3.74
551 552 4.140536 CCTCACTTTTCTTCTCCAAAGCT 58.859 43.478 0.00 0.00 33.92 3.74
552 553 3.304996 GCCTCACTTTTCTTCTCCAAAGC 60.305 47.826 0.00 0.00 33.92 3.51
553 554 3.254411 GGCCTCACTTTTCTTCTCCAAAG 59.746 47.826 0.00 0.00 36.28 2.77
554 555 3.222603 GGCCTCACTTTTCTTCTCCAAA 58.777 45.455 0.00 0.00 0.00 3.28
555 556 2.810400 CGGCCTCACTTTTCTTCTCCAA 60.810 50.000 0.00 0.00 0.00 3.53
556 557 1.270839 CGGCCTCACTTTTCTTCTCCA 60.271 52.381 0.00 0.00 0.00 3.86
558 559 1.443802 CCGGCCTCACTTTTCTTCTC 58.556 55.000 0.00 0.00 0.00 2.87
559 560 0.036875 CCCGGCCTCACTTTTCTTCT 59.963 55.000 0.00 0.00 0.00 2.85
560 561 1.587043 GCCCGGCCTCACTTTTCTTC 61.587 60.000 0.00 0.00 0.00 2.87
561 562 1.603739 GCCCGGCCTCACTTTTCTT 60.604 57.895 0.00 0.00 0.00 2.52
562 563 2.034221 GCCCGGCCTCACTTTTCT 59.966 61.111 0.00 0.00 0.00 2.52
563 564 3.062466 GGCCCGGCCTCACTTTTC 61.062 66.667 22.31 0.00 46.69 2.29
577 578 0.901827 CAATTTTACAGGGTGGGGCC 59.098 55.000 0.00 0.00 0.00 5.80
578 579 1.824852 CTCAATTTTACAGGGTGGGGC 59.175 52.381 0.00 0.00 0.00 5.80
579 580 2.225267 ACCTCAATTTTACAGGGTGGGG 60.225 50.000 0.00 0.00 35.83 4.96
580 581 3.169512 ACCTCAATTTTACAGGGTGGG 57.830 47.619 0.00 0.00 0.00 4.61
583 584 3.268595 CCCCTACCTCAATTTTACAGGGT 59.731 47.826 0.00 0.00 39.76 4.34
584 585 3.372675 CCCCCTACCTCAATTTTACAGGG 60.373 52.174 0.00 0.00 40.86 4.45
586 587 4.263771 ACACCCCCTACCTCAATTTTACAG 60.264 45.833 0.00 0.00 0.00 2.74
587 588 3.658705 ACACCCCCTACCTCAATTTTACA 59.341 43.478 0.00 0.00 0.00 2.41
588 589 4.014406 CACACCCCCTACCTCAATTTTAC 58.986 47.826 0.00 0.00 0.00 2.01
589 590 3.010808 CCACACCCCCTACCTCAATTTTA 59.989 47.826 0.00 0.00 0.00 1.52
590 591 2.225267 CCACACCCCCTACCTCAATTTT 60.225 50.000 0.00 0.00 0.00 1.82
591 592 1.357761 CCACACCCCCTACCTCAATTT 59.642 52.381 0.00 0.00 0.00 1.82
593 594 0.919289 CCCACACCCCCTACCTCAAT 60.919 60.000 0.00 0.00 0.00 2.57
594 595 1.540367 CCCACACCCCCTACCTCAA 60.540 63.158 0.00 0.00 0.00 3.02
595 596 2.124085 CCCACACCCCCTACCTCA 59.876 66.667 0.00 0.00 0.00 3.86
597 598 1.543020 ATACCCCACACCCCCTACCT 61.543 60.000 0.00 0.00 0.00 3.08
598 599 0.625387 AATACCCCACACCCCCTACC 60.625 60.000 0.00 0.00 0.00 3.18
599 600 2.052468 CTAATACCCCACACCCCCTAC 58.948 57.143 0.00 0.00 0.00 3.18
600 601 1.658248 ACTAATACCCCACACCCCCTA 59.342 52.381 0.00 0.00 0.00 3.53
601 602 0.424368 ACTAATACCCCACACCCCCT 59.576 55.000 0.00 0.00 0.00 4.79
603 604 3.117745 ACTAACTAATACCCCACACCCC 58.882 50.000 0.00 0.00 0.00 4.95
604 605 3.776417 TCACTAACTAATACCCCACACCC 59.224 47.826 0.00 0.00 0.00 4.61
606 607 5.129815 TCCATCACTAACTAATACCCCACAC 59.870 44.000 0.00 0.00 0.00 3.82
607 608 5.282129 TCCATCACTAACTAATACCCCACA 58.718 41.667 0.00 0.00 0.00 4.17
609 610 5.368523 CCTTCCATCACTAACTAATACCCCA 59.631 44.000 0.00 0.00 0.00 4.96
610 611 5.368816 ACCTTCCATCACTAACTAATACCCC 59.631 44.000 0.00 0.00 0.00 4.95
612 613 9.543783 CTAAACCTTCCATCACTAACTAATACC 57.456 37.037 0.00 0.00 0.00 2.73
616 617 8.534496 GGTACTAAACCTTCCATCACTAACTAA 58.466 37.037 0.00 0.00 45.75 2.24
617 618 8.071177 GGTACTAAACCTTCCATCACTAACTA 57.929 38.462 0.00 0.00 45.75 2.24
618 619 6.944096 GGTACTAAACCTTCCATCACTAACT 58.056 40.000 0.00 0.00 45.75 2.24
647 648 9.434420 TGCTAACCTACGCTAATTTTTACTAAA 57.566 29.630 0.00 0.00 0.00 1.85
648 649 9.434420 TTGCTAACCTACGCTAATTTTTACTAA 57.566 29.630 0.00 0.00 0.00 2.24
649 650 9.603921 ATTGCTAACCTACGCTAATTTTTACTA 57.396 29.630 0.00 0.00 0.00 1.82
650 651 7.910441 TTGCTAACCTACGCTAATTTTTACT 57.090 32.000 0.00 0.00 0.00 2.24
653 654 8.921670 CAAAATTGCTAACCTACGCTAATTTTT 58.078 29.630 0.00 0.00 36.24 1.94
655 656 7.822658 TCAAAATTGCTAACCTACGCTAATTT 58.177 30.769 0.00 0.00 33.05 1.82
656 657 7.385778 TCAAAATTGCTAACCTACGCTAATT 57.614 32.000 0.00 0.00 0.00 1.40
657 658 6.995511 TCAAAATTGCTAACCTACGCTAAT 57.004 33.333 0.00 0.00 0.00 1.73
658 659 6.676943 GCATCAAAATTGCTAACCTACGCTAA 60.677 38.462 0.00 0.00 37.14 3.09
659 660 5.220777 GCATCAAAATTGCTAACCTACGCTA 60.221 40.000 0.00 0.00 37.14 4.26
660 661 4.438744 GCATCAAAATTGCTAACCTACGCT 60.439 41.667 0.00 0.00 37.14 5.07
661 662 3.791353 GCATCAAAATTGCTAACCTACGC 59.209 43.478 0.00 0.00 37.14 4.42
662 663 4.028383 CGCATCAAAATTGCTAACCTACG 58.972 43.478 0.00 0.00 37.96 3.51
664 665 5.414454 AGAACGCATCAAAATTGCTAACCTA 59.586 36.000 0.00 0.00 37.96 3.08
665 666 4.218417 AGAACGCATCAAAATTGCTAACCT 59.782 37.500 0.00 0.00 37.96 3.50
667 668 5.393962 AGAGAACGCATCAAAATTGCTAAC 58.606 37.500 0.00 0.00 37.96 2.34
668 669 5.627499 AGAGAACGCATCAAAATTGCTAA 57.373 34.783 0.00 0.00 37.96 3.09
669 670 6.925610 ATAGAGAACGCATCAAAATTGCTA 57.074 33.333 0.00 0.00 37.96 3.49
673 674 5.050091 CGCCTATAGAGAACGCATCAAAATT 60.050 40.000 0.00 0.00 0.00 1.82
674 675 4.449068 CGCCTATAGAGAACGCATCAAAAT 59.551 41.667 0.00 0.00 0.00 1.82
675 676 3.802139 CGCCTATAGAGAACGCATCAAAA 59.198 43.478 0.00 0.00 0.00 2.44
677 678 2.862530 GCGCCTATAGAGAACGCATCAA 60.863 50.000 16.50 0.00 43.46 2.57
679 680 1.341606 GCGCCTATAGAGAACGCATC 58.658 55.000 16.50 0.34 43.46 3.91
680 681 0.387367 CGCGCCTATAGAGAACGCAT 60.387 55.000 19.76 0.00 43.89 4.73
681 682 1.008881 CGCGCCTATAGAGAACGCA 60.009 57.895 19.76 0.00 43.89 5.24
682 683 0.594284 AACGCGCCTATAGAGAACGC 60.594 55.000 5.73 12.81 41.73 4.84
684 685 1.602416 GGGAACGCGCCTATAGAGAAC 60.602 57.143 5.73 0.00 0.00 3.01
685 686 0.672342 GGGAACGCGCCTATAGAGAA 59.328 55.000 5.73 0.00 0.00 2.87
686 687 0.178998 AGGGAACGCGCCTATAGAGA 60.179 55.000 5.73 0.00 0.00 3.10
687 688 1.199558 GTAGGGAACGCGCCTATAGAG 59.800 57.143 5.73 0.00 0.00 2.43
688 689 1.242076 GTAGGGAACGCGCCTATAGA 58.758 55.000 5.73 0.00 0.00 1.98
689 690 0.956633 TGTAGGGAACGCGCCTATAG 59.043 55.000 5.73 0.00 0.00 1.31
690 691 1.401761 TTGTAGGGAACGCGCCTATA 58.598 50.000 5.73 4.68 0.00 1.31
691 692 0.538118 TTTGTAGGGAACGCGCCTAT 59.462 50.000 5.73 0.00 0.00 2.57
692 693 0.390209 GTTTGTAGGGAACGCGCCTA 60.390 55.000 5.73 6.43 0.00 3.93
693 694 1.670083 GTTTGTAGGGAACGCGCCT 60.670 57.895 5.73 7.64 0.00 5.52
726 727 2.126228 GTCCGATTGACCGCGTCA 60.126 61.111 4.92 6.31 41.09 4.35
727 728 2.158959 CAGTCCGATTGACCGCGTC 61.159 63.158 4.92 3.35 45.68 5.19
728 729 2.126071 CAGTCCGATTGACCGCGT 60.126 61.111 4.92 0.00 45.68 6.01
729 730 3.554692 GCAGTCCGATTGACCGCG 61.555 66.667 0.00 0.00 45.68 6.46
734 735 0.690192 TCCCAAAGCAGTCCGATTGA 59.310 50.000 0.00 0.00 0.00 2.57
779 780 0.757188 CATCTCCAGCGACCTACCCT 60.757 60.000 0.00 0.00 0.00 4.34
813 814 5.997129 TGTTGTGAAATCTTATCTGACTGCA 59.003 36.000 0.00 0.00 0.00 4.41
836 837 5.477984 TCCAGGGATTTTGACTCTGAAATTG 59.522 40.000 0.00 0.00 38.01 2.32
866 869 5.407407 AGAAAACTTCGGCTCTCTAATGA 57.593 39.130 0.00 0.00 34.02 2.57
899 902 2.328639 GACGGATCGAGCTCGGAC 59.671 66.667 33.98 25.78 40.29 4.79
916 919 1.298859 CCCGCCCTTTTTGAGAGTCG 61.299 60.000 0.00 0.00 0.00 4.18
920 923 0.251165 CCTTCCCGCCCTTTTTGAGA 60.251 55.000 0.00 0.00 0.00 3.27
921 924 0.251165 TCCTTCCCGCCCTTTTTGAG 60.251 55.000 0.00 0.00 0.00 3.02
922 925 0.251165 CTCCTTCCCGCCCTTTTTGA 60.251 55.000 0.00 0.00 0.00 2.69
923 926 1.250840 CCTCCTTCCCGCCCTTTTTG 61.251 60.000 0.00 0.00 0.00 2.44
924 927 1.076727 CCTCCTTCCCGCCCTTTTT 59.923 57.895 0.00 0.00 0.00 1.94
925 928 2.763902 CCTCCTTCCCGCCCTTTT 59.236 61.111 0.00 0.00 0.00 2.27
929 932 4.048470 AAAGCCTCCTTCCCGCCC 62.048 66.667 0.00 0.00 0.00 6.13
930 933 2.751837 CAAAGCCTCCTTCCCGCC 60.752 66.667 0.00 0.00 0.00 6.13
931 934 3.443925 GCAAAGCCTCCTTCCCGC 61.444 66.667 0.00 0.00 0.00 6.13
932 935 1.379044 ATGCAAAGCCTCCTTCCCG 60.379 57.895 0.00 0.00 0.00 5.14
933 936 1.325476 CCATGCAAAGCCTCCTTCCC 61.325 60.000 0.00 0.00 0.00 3.97
934 937 0.613012 ACCATGCAAAGCCTCCTTCC 60.613 55.000 0.00 0.00 0.00 3.46
936 939 0.112995 TGACCATGCAAAGCCTCCTT 59.887 50.000 0.00 0.00 0.00 3.36
937 940 0.610232 GTGACCATGCAAAGCCTCCT 60.610 55.000 0.00 0.00 0.00 3.69
938 941 0.610232 AGTGACCATGCAAAGCCTCC 60.610 55.000 0.00 0.00 0.00 4.30
939 942 1.200948 GAAGTGACCATGCAAAGCCTC 59.799 52.381 0.00 0.00 0.00 4.70
940 943 1.251251 GAAGTGACCATGCAAAGCCT 58.749 50.000 0.00 0.00 0.00 4.58
941 944 0.244721 GGAAGTGACCATGCAAAGCC 59.755 55.000 0.00 0.00 0.00 4.35
942 945 0.109597 CGGAAGTGACCATGCAAAGC 60.110 55.000 0.00 0.00 0.00 3.51
944 947 1.202758 ACTCGGAAGTGACCATGCAAA 60.203 47.619 0.00 0.00 33.32 3.68
972 4569 0.179145 GGCGGCGCGTGAGTATATAT 60.179 55.000 26.95 0.00 0.00 0.86
973 4570 1.210931 GGCGGCGCGTGAGTATATA 59.789 57.895 26.95 0.00 0.00 0.86
974 4571 1.239296 TAGGCGGCGCGTGAGTATAT 61.239 55.000 34.05 10.28 0.00 0.86
975 4572 1.239296 ATAGGCGGCGCGTGAGTATA 61.239 55.000 34.05 15.73 0.00 1.47
976 4573 1.239296 TATAGGCGGCGCGTGAGTAT 61.239 55.000 34.05 22.23 0.00 2.12
1064 4671 0.459585 CGTGTGGGTAATCGTGGAGG 60.460 60.000 0.00 0.00 0.00 4.30
1296 4916 1.826054 CATCTCCCCGAGACTCGCT 60.826 63.158 19.55 0.00 41.76 4.93
1302 4922 2.444706 CCAGCCATCTCCCCGAGA 60.445 66.667 0.00 0.00 43.20 4.04
1315 4935 3.869272 CACGATCTTGCCGCCAGC 61.869 66.667 0.00 0.00 44.14 4.85
1316 4936 2.434884 ACACGATCTTGCCGCCAG 60.435 61.111 0.00 0.00 0.00 4.85
1321 4950 3.084579 CGCTGACACGATCTTGCC 58.915 61.111 0.00 0.00 34.06 4.52
1368 4997 3.097728 GTGACGGACACGAGCACG 61.098 66.667 0.76 0.76 44.60 5.34
1640 5281 2.730672 GGCTTGTCGTAGCAGCACG 61.731 63.158 10.13 10.13 43.02 5.34
1855 5739 3.066203 GGACAGCTCTAGTGTTCTCTAGC 59.934 52.174 0.00 0.00 37.78 3.42
1878 5762 4.720649 TTCTGAGTACATAGCAGTGACC 57.279 45.455 0.00 0.00 0.00 4.02
1930 5842 6.550938 ACTGAGGACATGAGACATTTCATA 57.449 37.500 0.00 0.00 36.08 2.15
1986 5898 7.751047 TGTTACAGTCGACAGATAATTAAGC 57.249 36.000 19.50 2.06 0.00 3.09
1993 5905 9.516314 CATAATCTTTGTTACAGTCGACAGATA 57.484 33.333 19.50 3.79 0.00 1.98
1994 5906 7.010552 GCATAATCTTTGTTACAGTCGACAGAT 59.989 37.037 19.50 11.30 0.00 2.90
2036 5948 2.821969 CAAAAGTTGATCCTGGTCCTGG 59.178 50.000 8.53 8.53 0.00 4.45
2037 5949 3.490348 ACAAAAGTTGATCCTGGTCCTG 58.510 45.455 0.00 0.00 0.00 3.86
2038 5950 3.884037 ACAAAAGTTGATCCTGGTCCT 57.116 42.857 0.00 0.00 0.00 3.85
2039 5951 3.552890 GCAACAAAAGTTGATCCTGGTCC 60.553 47.826 12.12 0.00 36.50 4.46
2040 5952 3.319122 AGCAACAAAAGTTGATCCTGGTC 59.681 43.478 12.12 0.00 36.50 4.02
2041 5953 3.299503 AGCAACAAAAGTTGATCCTGGT 58.700 40.909 12.12 0.00 36.50 4.00
2061 5973 9.330063 TGCTCTTCCTGTAATACAATTATGAAG 57.670 33.333 0.00 3.09 0.00 3.02
2253 6263 7.063898 TCTCTCGAGTGCAAAATTTATCTTCTG 59.936 37.037 13.13 0.00 0.00 3.02
2291 6301 7.730364 TCAATTTTCTCTCAACAGAAGTACC 57.270 36.000 0.00 0.00 33.85 3.34
2468 6535 6.932901 CGTATTTCGTAAACTGTCCTTGTA 57.067 37.500 0.00 0.00 34.52 2.41
2491 6558 2.206750 TGGAGTTTGTCGTGCTTGTAC 58.793 47.619 0.00 0.00 0.00 2.90
2598 6743 1.741770 CCTCGCTTTCAGGTTCCGG 60.742 63.158 0.00 0.00 0.00 5.14
2643 6788 8.021396 GGGTGATCCATTTACGATAAAAATAGC 58.979 37.037 0.00 0.00 35.00 2.97
2654 6799 2.687425 TGCATTGGGTGATCCATTTACG 59.313 45.455 0.00 0.00 46.52 3.18
2669 6814 4.454847 TGGGCATAAAATTGTGTTGCATTG 59.545 37.500 7.45 0.00 35.04 2.82
2678 6823 3.778265 AGGTGTCTGGGCATAAAATTGT 58.222 40.909 0.00 0.00 0.00 2.71
2734 6879 1.212935 ACTTGTCACAGCAGAAACCCT 59.787 47.619 0.00 0.00 0.00 4.34
2791 6941 6.448006 AGTGAGTACAATTCAGTACAGTGAC 58.552 40.000 0.00 0.00 45.25 3.67
2900 7060 3.984018 TCGCTAACATTTACTTGCGTC 57.016 42.857 0.00 0.00 43.23 5.19
2901 7061 4.735662 TTTCGCTAACATTTACTTGCGT 57.264 36.364 0.00 0.00 43.23 5.24
2902 7062 6.087555 ACATTTTTCGCTAACATTTACTTGCG 59.912 34.615 0.00 0.00 43.95 4.85
2903 7063 7.333288 ACATTTTTCGCTAACATTTACTTGC 57.667 32.000 0.00 0.00 0.00 4.01
2904 7064 7.201232 CCGACATTTTTCGCTAACATTTACTTG 60.201 37.037 0.00 0.00 37.70 3.16
2905 7065 6.799925 CCGACATTTTTCGCTAACATTTACTT 59.200 34.615 0.00 0.00 37.70 2.24
2906 7066 6.148150 TCCGACATTTTTCGCTAACATTTACT 59.852 34.615 0.00 0.00 37.70 2.24
2907 7067 6.308675 TCCGACATTTTTCGCTAACATTTAC 58.691 36.000 0.00 0.00 37.70 2.01
2908 7068 6.483385 TCCGACATTTTTCGCTAACATTTA 57.517 33.333 0.00 0.00 37.70 1.40
2934 7094 2.940994 TTCGTGTGGATTCCCTTTGA 57.059 45.000 0.00 0.00 0.00 2.69
2956 7116 9.144298 TCTCTCTTTCTAAAGTCTGGTTTAAGA 57.856 33.333 2.58 0.00 37.31 2.10
2995 7155 4.520846 CAGTCGGCCGCGCAAATC 62.521 66.667 23.51 4.39 0.00 2.17
3002 7162 0.373716 CAATTACTTCAGTCGGCCGC 59.626 55.000 23.51 16.31 0.00 6.53


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

AutoCloner maintained by Alex Coulton.