Multiple sequence alignment - TraesCS4A01G386800

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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 TraesCS4A01G386800 chr4A 100.000 4650 0 0 1 4650 664447087 664442438 0.000000e+00 8588.0
1 TraesCS4A01G386800 chr4A 100.000 29 0 0 2827 2855 126584525 126584553 2.000000e-03 54.7
2 TraesCS4A01G386800 chr7A 94.812 3778 151 17 892 4650 52953098 52949347 0.000000e+00 5849.0
3 TraesCS4A01G386800 chr7A 83.249 591 43 16 184 728 52953842 52953262 4.180000e-135 492.0
4 TraesCS4A01G386800 chr7A 94.286 70 4 0 743 812 52953161 52953092 1.770000e-19 108.0
5 TraesCS4A01G386800 chr7D 94.765 3381 140 23 743 4109 49828925 49825568 0.000000e+00 5228.0
6 TraesCS4A01G386800 chr7D 83.024 701 53 27 83 728 49829716 49829027 4.040000e-160 575.0
7 TraesCS4A01G386800 chr7D 82.443 131 21 2 3181 3310 469032655 469032784 3.800000e-21 113.0
8 TraesCS4A01G386800 chr5A 77.726 1724 269 60 1335 3032 619957101 619958735 0.000000e+00 950.0
9 TraesCS4A01G386800 chr5A 93.023 86 6 0 811 896 524672275 524672190 4.880000e-25 126.0
10 TraesCS4A01G386800 chr5A 90.110 91 9 0 811 901 556090709 556090619 8.170000e-23 119.0
11 TraesCS4A01G386800 chr5A 80.992 121 17 6 999 1118 619957593 619957708 1.780000e-14 91.6
12 TraesCS4A01G386800 chr5D 78.062 1641 258 58 1404 3032 496134340 496135890 0.000000e+00 942.0
13 TraesCS4A01G386800 chr5D 80.374 321 56 5 3321 3635 496155471 496155790 2.160000e-58 237.0
14 TraesCS4A01G386800 chr5D 77.751 409 64 11 2296 2703 496153286 496153668 4.680000e-55 226.0
15 TraesCS4A01G386800 chr5D 92.045 88 7 0 811 898 539788456 539788369 1.760000e-24 124.0
16 TraesCS4A01G386800 chr5D 81.818 121 16 6 999 1118 496280722 496280837 3.830000e-16 97.1
17 TraesCS4A01G386800 chr5D 82.143 112 18 2 1008 1118 495906199 495906309 1.380000e-15 95.3
18 TraesCS4A01G386800 chr5D 82.569 109 17 2 1011 1118 496073032 496073139 1.380000e-15 95.3
19 TraesCS4A01G386800 chr5D 80.992 121 17 6 999 1118 496134760 496134875 1.780000e-14 91.6
20 TraesCS4A01G386800 chr4D 77.914 489 95 10 2827 3310 340990103 340989623 4.550000e-75 292.0
21 TraesCS4A01G386800 chr4D 92.222 90 7 0 806 895 113929781 113929692 1.360000e-25 128.0
22 TraesCS4A01G386800 chr4D 81.513 119 16 6 3195 3310 348732171 348732056 4.950000e-15 93.5
23 TraesCS4A01G386800 chr5B 78.164 403 60 12 2303 2703 613653712 613654088 1.010000e-56 231.0
24 TraesCS4A01G386800 chr5B 84.259 108 16 1 1011 1118 613280982 613281088 2.290000e-18 104.0
25 TraesCS4A01G386800 chr5B 83.486 109 16 2 1011 1118 613631110 613631217 2.960000e-17 100.0
26 TraesCS4A01G386800 chr4B 77.193 285 54 10 2827 3107 422374955 422374678 6.230000e-34 156.0
27 TraesCS4A01G386800 chr4B 83.019 106 15 3 3195 3298 532400839 532400943 4.950000e-15 93.5
28 TraesCS4A01G386800 chr2B 93.182 88 6 0 811 898 166044568 166044481 3.780000e-26 130.0
29 TraesCS4A01G386800 chr2D 93.103 87 6 0 811 897 529010329 529010243 1.360000e-25 128.0
30 TraesCS4A01G386800 chr2D 80.714 140 25 2 3184 3322 490911381 490911243 1.770000e-19 108.0
31 TraesCS4A01G386800 chr3B 92.045 88 7 0 810 897 10622598 10622511 1.760000e-24 124.0
32 TraesCS4A01G386800 chr1D 92.941 85 6 0 811 895 347215391 347215307 1.760000e-24 124.0
33 TraesCS4A01G386800 chr7B 85.185 108 12 4 3188 3293 413731726 413731831 1.770000e-19 108.0
34 TraesCS4A01G386800 chr6B 82.857 105 16 2 3195 3298 173080834 173080937 4.950000e-15 93.5
35 TraesCS4A01G386800 chr3D 83.019 106 15 3 3195 3298 541101204 541101308 4.950000e-15 93.5


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 TraesCS4A01G386800 chr4A 664442438 664447087 4649 True 8588.000000 8588 100.000000 1 4650 1 chr4A.!!$R1 4649
1 TraesCS4A01G386800 chr7A 52949347 52953842 4495 True 2149.666667 5849 90.782333 184 4650 3 chr7A.!!$R1 4466
2 TraesCS4A01G386800 chr7D 49825568 49829716 4148 True 2901.500000 5228 88.894500 83 4109 2 chr7D.!!$R1 4026
3 TraesCS4A01G386800 chr5A 619957101 619958735 1634 False 520.800000 950 79.359000 999 3032 2 chr5A.!!$F1 2033
4 TraesCS4A01G386800 chr5D 496134340 496135890 1550 False 516.800000 942 79.527000 999 3032 2 chr5D.!!$F4 2033
5 TraesCS4A01G386800 chr5D 496153286 496155790 2504 False 231.500000 237 79.062500 2296 3635 2 chr5D.!!$F5 1339

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
738 802 0.252479 TTTCCTTGCCGGCCGTATAA 59.748 50.000 26.77 14.58 0.0 0.98 F
739 803 0.252479 TTCCTTGCCGGCCGTATAAA 59.748 50.000 26.77 9.46 0.0 1.40 F
795 953 0.390735 ACGAGTACATGAAACCGGGC 60.391 55.000 6.32 0.00 0.0 6.13 F
1670 1935 0.449388 CGTGAAAAGGCCTCATCAGC 59.551 55.000 18.13 12.74 0.0 4.26 F
1738 2003 1.202065 CGCATGAAATCGGGTGAAGTG 60.202 52.381 0.00 0.00 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2413 2696 0.536460 GGGAACTCGCCCTTGAAACA 60.536 55.000 0.00 0.0 45.12 2.83 R
2696 2979 1.448013 GTACTGCAGGGACGCCTTC 60.448 63.158 19.93 0.0 0.00 3.46 R
2741 3024 0.107214 CCTTTGCATAGGCCGAGGAA 60.107 55.000 10.46 0.0 41.24 3.36 R
3546 5147 1.888512 CACCCATCTTCAGGTTGTTGG 59.111 52.381 0.00 0.0 32.72 3.77 R
3694 5298 4.035792 CCAACGATTCACTAACCAACAACA 59.964 41.667 0.00 0.0 0.00 3.33 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
18 19 3.729356 CTCGATCTGTGGACTGTGG 57.271 57.895 0.00 0.00 0.00 4.17
19 20 0.891373 CTCGATCTGTGGACTGTGGT 59.109 55.000 0.00 0.00 0.00 4.16
20 21 2.092323 CTCGATCTGTGGACTGTGGTA 58.908 52.381 0.00 0.00 0.00 3.25
21 22 1.816835 TCGATCTGTGGACTGTGGTAC 59.183 52.381 0.00 0.00 0.00 3.34
22 23 1.467543 CGATCTGTGGACTGTGGTACG 60.468 57.143 0.00 0.00 0.00 3.67
23 24 1.544691 GATCTGTGGACTGTGGTACGT 59.455 52.381 0.00 0.00 0.00 3.57
24 25 2.275134 TCTGTGGACTGTGGTACGTA 57.725 50.000 0.00 0.00 0.00 3.57
25 26 1.881973 TCTGTGGACTGTGGTACGTAC 59.118 52.381 17.56 17.56 0.00 3.67
26 27 1.610038 CTGTGGACTGTGGTACGTACA 59.390 52.381 26.02 8.74 0.00 2.90
27 28 2.030371 TGTGGACTGTGGTACGTACAA 58.970 47.619 26.02 13.80 0.00 2.41
28 29 2.223782 TGTGGACTGTGGTACGTACAAC 60.224 50.000 23.77 23.77 0.00 3.32
29 30 2.035066 GTGGACTGTGGTACGTACAACT 59.965 50.000 28.73 13.73 31.33 3.16
30 31 3.253188 GTGGACTGTGGTACGTACAACTA 59.747 47.826 28.73 16.66 31.33 2.24
31 32 3.253188 TGGACTGTGGTACGTACAACTAC 59.747 47.826 28.73 19.90 31.33 2.73
32 33 3.503748 GGACTGTGGTACGTACAACTACT 59.496 47.826 28.73 14.18 31.33 2.57
33 34 4.695455 GGACTGTGGTACGTACAACTACTA 59.305 45.833 28.73 11.79 31.33 1.82
34 35 5.390991 GGACTGTGGTACGTACAACTACTAC 60.391 48.000 28.73 13.01 31.33 2.73
35 36 5.063204 ACTGTGGTACGTACAACTACTACA 58.937 41.667 28.73 16.49 34.36 2.74
36 37 5.530915 ACTGTGGTACGTACAACTACTACAA 59.469 40.000 28.73 10.18 34.91 2.41
37 38 5.757886 TGTGGTACGTACAACTACTACAAC 58.242 41.667 28.73 7.27 33.04 3.32
38 39 5.154222 GTGGTACGTACAACTACTACAACC 58.846 45.833 26.02 8.13 0.00 3.77
39 40 4.083537 TGGTACGTACAACTACTACAACCG 60.084 45.833 26.02 0.00 0.00 4.44
40 41 4.083484 GGTACGTACAACTACTACAACCGT 60.083 45.833 26.02 0.00 0.00 4.83
41 42 4.147219 ACGTACAACTACTACAACCGTC 57.853 45.455 0.00 0.00 0.00 4.79
42 43 3.155998 CGTACAACTACTACAACCGTCG 58.844 50.000 0.00 0.00 0.00 5.12
43 44 3.120683 CGTACAACTACTACAACCGTCGA 60.121 47.826 0.00 0.00 0.00 4.20
44 45 3.549299 ACAACTACTACAACCGTCGAG 57.451 47.619 0.00 0.00 0.00 4.04
46 47 2.479566 ACTACTACAACCGTCGAGGA 57.520 50.000 6.70 0.00 45.00 3.71
47 48 2.079925 ACTACTACAACCGTCGAGGAC 58.920 52.381 6.70 0.00 45.00 3.85
48 49 1.399791 CTACTACAACCGTCGAGGACC 59.600 57.143 6.70 0.00 45.00 4.46
49 50 0.538057 ACTACAACCGTCGAGGACCA 60.538 55.000 6.70 0.00 45.00 4.02
50 51 0.599558 CTACAACCGTCGAGGACCAA 59.400 55.000 6.70 0.00 45.00 3.67
51 52 0.314935 TACAACCGTCGAGGACCAAC 59.685 55.000 6.70 0.00 45.00 3.77
52 53 1.366366 CAACCGTCGAGGACCAACT 59.634 57.895 6.70 0.00 45.00 3.16
53 54 0.944311 CAACCGTCGAGGACCAACTG 60.944 60.000 6.70 0.00 45.00 3.16
54 55 2.095978 AACCGTCGAGGACCAACTGG 62.096 60.000 6.70 0.00 45.00 4.00
113 114 8.450964 ACTAACTGTAATCATTTGTTCCATTCG 58.549 33.333 0.00 0.00 0.00 3.34
115 116 4.657055 TGTAATCATTTGTTCCATTCGCG 58.343 39.130 0.00 0.00 0.00 5.87
156 157 0.395686 ATGGCTGGACATGAGATCGG 59.604 55.000 0.00 0.00 0.00 4.18
163 164 1.115467 GACATGAGATCGGTGGGTCT 58.885 55.000 0.00 0.00 0.00 3.85
171 172 1.825474 GATCGGTGGGTCTCTTCTCAA 59.175 52.381 0.00 0.00 0.00 3.02
172 173 1.712056 TCGGTGGGTCTCTTCTCAAA 58.288 50.000 0.00 0.00 0.00 2.69
173 174 2.043992 TCGGTGGGTCTCTTCTCAAAA 58.956 47.619 0.00 0.00 0.00 2.44
174 175 2.037251 TCGGTGGGTCTCTTCTCAAAAG 59.963 50.000 0.00 0.00 0.00 2.27
175 176 2.784347 GGTGGGTCTCTTCTCAAAAGG 58.216 52.381 0.00 0.00 0.00 3.11
176 177 2.553247 GGTGGGTCTCTTCTCAAAAGGG 60.553 54.545 0.00 0.00 0.00 3.95
177 178 1.705186 TGGGTCTCTTCTCAAAAGGGG 59.295 52.381 0.00 0.00 0.00 4.79
179 180 2.578480 GGGTCTCTTCTCAAAAGGGGAT 59.422 50.000 0.00 0.00 0.00 3.85
180 181 3.615155 GGTCTCTTCTCAAAAGGGGATG 58.385 50.000 0.00 0.00 0.00 3.51
181 182 3.264450 GGTCTCTTCTCAAAAGGGGATGA 59.736 47.826 0.00 0.00 0.00 2.92
182 183 4.257731 GTCTCTTCTCAAAAGGGGATGAC 58.742 47.826 0.00 0.00 0.00 3.06
196 214 3.704231 ATGACATGGCTCACGGGGC 62.704 63.158 0.00 0.00 0.00 5.80
243 261 1.860078 GCACGTGGCAACTACTGAC 59.140 57.895 18.88 0.00 43.97 3.51
244 262 1.566018 GCACGTGGCAACTACTGACC 61.566 60.000 18.88 0.00 43.97 4.02
264 302 3.041940 GCAACAGACCCGGTCGTG 61.042 66.667 12.04 12.17 37.67 4.35
274 312 3.357504 CCGGTCGTGTAGGGATTTC 57.642 57.895 0.00 0.00 0.00 2.17
305 343 0.460311 AAAGTACCGATGGAGGAGCG 59.540 55.000 0.00 0.00 34.73 5.03
306 344 2.017559 AAGTACCGATGGAGGAGCGC 62.018 60.000 0.00 0.00 34.73 5.92
307 345 2.441348 TACCGATGGAGGAGCGCA 60.441 61.111 11.47 0.00 34.73 6.09
308 346 1.832608 TACCGATGGAGGAGCGCAT 60.833 57.895 11.47 0.00 34.73 4.73
334 377 2.262915 CTCAGCGTCCTCCACACC 59.737 66.667 0.00 0.00 0.00 4.16
360 403 0.402121 AGCCAACTGGAAGGAGAACC 59.598 55.000 0.00 0.00 39.30 3.62
404 447 1.135315 CACACCGCCCAGATGATTTTG 60.135 52.381 0.00 0.00 0.00 2.44
406 449 0.323725 ACCGCCCAGATGATTTTGCT 60.324 50.000 0.00 0.00 0.00 3.91
407 450 0.819582 CCGCCCAGATGATTTTGCTT 59.180 50.000 0.00 0.00 0.00 3.91
408 451 1.202336 CCGCCCAGATGATTTTGCTTC 60.202 52.381 0.00 0.00 0.00 3.86
409 452 1.747355 CGCCCAGATGATTTTGCTTCT 59.253 47.619 0.00 0.00 0.00 2.85
413 456 4.677250 GCCCAGATGATTTTGCTTCTCTTG 60.677 45.833 0.00 0.00 0.00 3.02
415 458 4.703575 CCAGATGATTTTGCTTCTCTTGGA 59.296 41.667 0.00 0.00 0.00 3.53
423 466 1.012841 GCTTCTCTTGGATCTTGGCG 58.987 55.000 0.00 0.00 0.00 5.69
441 484 3.058293 TGGCGTGATTCTTGATTCAACAC 60.058 43.478 7.47 7.47 0.00 3.32
443 486 3.736213 CGTGATTCTTGATTCAACACCG 58.264 45.455 10.53 4.79 0.00 4.94
444 487 3.492313 GTGATTCTTGATTCAACACCGC 58.508 45.455 6.60 0.00 0.00 5.68
446 490 3.758023 TGATTCTTGATTCAACACCGCAT 59.242 39.130 0.00 0.00 0.00 4.73
497 549 6.512903 GCAAGTAGTAGTACATCTATGCGTCA 60.513 42.308 10.33 0.00 0.00 4.35
511 563 1.425031 CGTCATTGTGGTGATGCCG 59.575 57.895 0.00 0.00 41.21 5.69
636 700 2.167398 CTGGTCACCACGTCGGGATT 62.167 60.000 0.00 0.00 40.22 3.01
643 707 0.796312 CCACGTCGGGATTTCAGTTG 59.204 55.000 0.00 0.00 0.00 3.16
644 708 1.606994 CCACGTCGGGATTTCAGTTGA 60.607 52.381 0.00 0.00 0.00 3.18
645 709 1.459592 CACGTCGGGATTTCAGTTGAC 59.540 52.381 0.00 0.00 0.00 3.18
646 710 1.069513 ACGTCGGGATTTCAGTTGACA 59.930 47.619 0.00 0.00 0.00 3.58
656 720 0.471780 TCAGTTGACAGGCAGAGGGA 60.472 55.000 0.00 0.00 0.00 4.20
661 725 2.530151 ACAGGCAGAGGGAAGGCA 60.530 61.111 0.00 0.00 0.00 4.75
663 727 3.013932 AGGCAGAGGGAAGGCAGG 61.014 66.667 0.00 0.00 0.00 4.85
672 736 2.352805 GAAGGCAGGGACCAGTGG 59.647 66.667 7.91 7.91 0.00 4.00
687 751 2.895680 TGGGCGAGACAGCTCATC 59.104 61.111 0.00 0.00 43.63 2.92
696 760 1.078848 ACAGCTCATCGGGACAAGC 60.079 57.895 0.00 0.00 0.00 4.01
728 792 2.699954 TCTCTCGTGATTTTCCTTGCC 58.300 47.619 0.00 0.00 0.00 4.52
729 793 1.394917 CTCTCGTGATTTTCCTTGCCG 59.605 52.381 0.00 0.00 0.00 5.69
730 794 0.447801 CTCGTGATTTTCCTTGCCGG 59.552 55.000 0.00 0.00 0.00 6.13
731 795 1.154035 CGTGATTTTCCTTGCCGGC 60.154 57.895 22.73 22.73 0.00 6.13
732 796 1.215382 GTGATTTTCCTTGCCGGCC 59.785 57.895 26.77 6.44 0.00 6.13
733 797 2.339556 TGATTTTCCTTGCCGGCCG 61.340 57.895 26.77 21.04 0.00 6.13
734 798 2.282887 ATTTTCCTTGCCGGCCGT 60.283 55.556 26.77 0.00 0.00 5.68
735 799 1.001887 ATTTTCCTTGCCGGCCGTA 60.002 52.632 26.77 10.17 0.00 4.02
738 802 0.252479 TTTCCTTGCCGGCCGTATAA 59.748 50.000 26.77 14.58 0.00 0.98
739 803 0.252479 TTCCTTGCCGGCCGTATAAA 59.748 50.000 26.77 9.46 0.00 1.40
740 804 0.470766 TCCTTGCCGGCCGTATAAAT 59.529 50.000 26.77 0.00 0.00 1.40
741 805 1.693062 TCCTTGCCGGCCGTATAAATA 59.307 47.619 26.77 0.00 0.00 1.40
777 935 1.278637 CGGCCGGATTCGCATTTAC 59.721 57.895 20.10 0.00 34.56 2.01
795 953 0.390735 ACGAGTACATGAAACCGGGC 60.391 55.000 6.32 0.00 0.00 6.13
806 964 4.774660 TGAAACCGGGCCAAGTATATAA 57.225 40.909 6.32 0.00 0.00 0.98
812 1053 6.535963 ACCGGGCCAAGTATATAATACTAC 57.464 41.667 6.32 0.00 0.00 2.73
813 1054 6.259123 ACCGGGCCAAGTATATAATACTACT 58.741 40.000 6.32 0.00 0.00 2.57
815 1056 6.606395 CCGGGCCAAGTATATAATACTACTCT 59.394 42.308 4.39 0.00 0.00 3.24
816 1057 7.201803 CCGGGCCAAGTATATAATACTACTCTC 60.202 44.444 4.39 0.00 0.00 3.20
817 1058 7.556996 CGGGCCAAGTATATAATACTACTCTCT 59.443 40.741 4.39 0.00 0.00 3.10
818 1059 8.905850 GGGCCAAGTATATAATACTACTCTCTC 58.094 40.741 4.39 0.00 0.00 3.20
819 1060 9.689501 GGCCAAGTATATAATACTACTCTCTCT 57.310 37.037 0.00 0.00 0.00 3.10
859 1100 9.688091 AGAGTGTCTAGATCACTACTTTAATGA 57.312 33.333 20.74 0.00 44.68 2.57
890 1131 8.433421 ACACTCTTATATTTGTTTACGGATGG 57.567 34.615 0.00 0.00 0.00 3.51
891 1132 8.262227 ACACTCTTATATTTGTTTACGGATGGA 58.738 33.333 0.00 0.00 0.00 3.41
892 1133 8.765219 CACTCTTATATTTGTTTACGGATGGAG 58.235 37.037 0.00 0.00 0.00 3.86
893 1134 8.483758 ACTCTTATATTTGTTTACGGATGGAGT 58.516 33.333 0.00 0.00 0.00 3.85
894 1135 9.976511 CTCTTATATTTGTTTACGGATGGAGTA 57.023 33.333 0.00 0.00 0.00 2.59
895 1136 9.754382 TCTTATATTTGTTTACGGATGGAGTAC 57.246 33.333 0.00 0.00 0.00 2.73
896 1137 9.760077 CTTATATTTGTTTACGGATGGAGTACT 57.240 33.333 0.00 0.00 0.00 2.73
901 1142 6.304356 TGTTTACGGATGGAGTACTATACG 57.696 41.667 8.44 8.44 44.89 3.06
902 1143 5.149977 GTTTACGGATGGAGTACTATACGC 58.850 45.833 9.71 0.00 43.53 4.42
903 1144 1.802960 ACGGATGGAGTACTATACGCG 59.197 52.381 3.53 3.53 43.53 6.01
904 1145 1.802960 CGGATGGAGTACTATACGCGT 59.197 52.381 19.17 19.17 34.82 6.01
905 1146 2.159734 CGGATGGAGTACTATACGCGTC 60.160 54.545 18.63 0.00 34.82 5.19
906 1147 3.072944 GGATGGAGTACTATACGCGTCT 58.927 50.000 18.63 9.26 0.00 4.18
909 1150 4.970662 TGGAGTACTATACGCGTCTTTT 57.029 40.909 18.63 1.06 0.00 2.27
938 1179 3.119280 TGCATTGCTTCATTCATGTCCTG 60.119 43.478 10.49 0.00 0.00 3.86
941 1182 1.005097 TGCTTCATTCATGTCCTGGCT 59.995 47.619 0.00 0.00 0.00 4.75
942 1183 2.239402 TGCTTCATTCATGTCCTGGCTA 59.761 45.455 0.00 0.00 0.00 3.93
943 1184 2.877168 GCTTCATTCATGTCCTGGCTAG 59.123 50.000 0.00 0.00 0.00 3.42
989 1230 3.220222 CACTCGATGCAGGGCCTA 58.780 61.111 5.28 0.00 0.00 3.93
1142 1390 9.520515 AACACTTGAATACAGTTCCATTCTTAT 57.479 29.630 0.00 0.00 33.26 1.73
1388 1648 7.165812 CGAATAAACAGTCTGACCAAACTTTTG 59.834 37.037 6.91 0.00 37.90 2.44
1390 1650 5.722021 AACAGTCTGACCAAACTTTTGTT 57.278 34.783 6.91 3.30 45.94 2.83
1391 1651 6.827586 AACAGTCTGACCAAACTTTTGTTA 57.172 33.333 6.91 0.00 42.67 2.41
1452 1717 1.107114 TGCAGCGTTTCAAAAGGGAA 58.893 45.000 0.00 0.00 0.00 3.97
1670 1935 0.449388 CGTGAAAAGGCCTCATCAGC 59.551 55.000 18.13 12.74 0.00 4.26
1738 2003 1.202065 CGCATGAAATCGGGTGAAGTG 60.202 52.381 0.00 0.00 0.00 3.16
2318 2599 5.619086 CGAACCGTCAAATAGGCTTTGATTT 60.619 40.000 5.02 0.00 40.12 2.17
2502 2785 1.984297 GTCGCCGAGAACAAACTAGAC 59.016 52.381 0.00 0.00 0.00 2.59
2628 2911 7.284489 GGCAACTCCCAATTTAGTGTCATAATA 59.716 37.037 0.00 0.00 0.00 0.98
2741 3024 9.753674 TGATATAGTGAAAAGTTCCCATTTTCT 57.246 29.630 11.23 0.00 43.74 2.52
2747 3030 5.009610 TGAAAAGTTCCCATTTTCTTCCTCG 59.990 40.000 11.23 0.00 43.74 4.63
2908 3191 4.098654 CCGAGTCATCTGGTCTCAGTTAAT 59.901 45.833 0.00 0.00 41.59 1.40
3072 4577 4.287067 ACATTGTCAAGAGGAAGGCTAAGA 59.713 41.667 0.00 0.00 0.00 2.10
3107 4612 2.435059 GAGCAGTTGAGGGACGGC 60.435 66.667 0.00 0.00 40.38 5.68
3275 4780 9.739276 AGTTCCATTTTTCTAATGTGTGATCTA 57.261 29.630 0.00 0.00 0.00 1.98
3315 4820 6.259167 GTGTCTGTGTGAAGTGTAAACCAATA 59.741 38.462 0.00 0.00 0.00 1.90
3317 4822 5.761234 TCTGTGTGAAGTGTAAACCAATACC 59.239 40.000 0.00 0.00 0.00 2.73
3354 4953 9.809096 AGTTGACATGTTATTCTACATAGACTG 57.191 33.333 0.00 0.00 36.64 3.51
3655 5259 4.374843 TGCCAATGTTGATTGATACTGC 57.625 40.909 0.00 0.00 41.49 4.40
3690 5294 6.488344 TGTGTTGGTGATAGTGCTTTCATTTA 59.512 34.615 0.00 0.00 0.00 1.40
3691 5295 7.013750 TGTGTTGGTGATAGTGCTTTCATTTAA 59.986 33.333 0.00 0.00 0.00 1.52
3692 5296 8.028938 GTGTTGGTGATAGTGCTTTCATTTAAT 58.971 33.333 0.00 0.00 0.00 1.40
3693 5297 8.584157 TGTTGGTGATAGTGCTTTCATTTAATT 58.416 29.630 0.00 0.00 0.00 1.40
3694 5298 9.423061 GTTGGTGATAGTGCTTTCATTTAATTT 57.577 29.630 0.00 0.00 0.00 1.82
3729 5333 1.204146 ATCGTTGGTGAGGGCAGTAT 58.796 50.000 0.00 0.00 0.00 2.12
3733 5337 2.790433 GTTGGTGAGGGCAGTATTGAA 58.210 47.619 0.00 0.00 0.00 2.69
3874 5478 9.552114 CTTTTGATGCAAGACTGAATAAGTAAG 57.448 33.333 0.00 0.00 40.07 2.34
3919 5523 5.665916 ATGTTCATTGGATTTTGGACTCC 57.334 39.130 0.00 0.00 0.00 3.85
3922 5526 4.402616 TCATTGGATTTTGGACTCCCTT 57.597 40.909 0.00 0.00 0.00 3.95
3940 5544 6.678857 ACTCCCTTCCTTCAAATTAGGTCTAT 59.321 38.462 0.00 0.00 34.29 1.98
3953 5557 5.750352 TTAGGTCTATCAGGTTCCGTTTT 57.250 39.130 0.00 0.00 0.00 2.43
3957 5561 2.907696 TCTATCAGGTTCCGTTTTCCCA 59.092 45.455 0.00 0.00 0.00 4.37
4065 5669 4.708909 TGTTGGTCATGCTTTATATTGCCA 59.291 37.500 0.00 0.00 0.00 4.92
4092 5696 2.479566 TTGCAGGTCAAGAGATCACC 57.520 50.000 0.00 0.00 0.00 4.02
4102 5706 4.338118 GTCAAGAGATCACCAGTAGAGGAG 59.662 50.000 0.00 0.00 0.00 3.69
4115 5719 5.949354 CCAGTAGAGGAGATATCTAGGGTTG 59.051 48.000 4.89 0.00 30.04 3.77
4125 5729 6.471146 AGATATCTAGGGTTGCAATCATGAC 58.529 40.000 12.67 0.00 0.00 3.06
4175 5779 4.055360 CCTATCACAAGTTCACAACACGA 58.945 43.478 0.00 0.00 0.00 4.35
4198 5802 4.681074 TCGTGTTAGCATGGGATCATAA 57.319 40.909 0.00 0.00 32.65 1.90
4283 5887 4.045636 GTGAAACAATGCTCTTGGTTGT 57.954 40.909 7.47 0.00 37.66 3.32
4288 5892 5.438761 AACAATGCTCTTGGTTGTTCTAC 57.561 39.130 4.90 0.00 40.87 2.59
4301 5905 0.249398 GTTCTACGCCCACCACTCAT 59.751 55.000 0.00 0.00 0.00 2.90
4302 5906 0.535335 TTCTACGCCCACCACTCATC 59.465 55.000 0.00 0.00 0.00 2.92
4335 5939 3.995705 GACCATCATCTAGCTGATCTTGC 59.004 47.826 6.10 0.00 33.59 4.01
4336 5940 3.390311 ACCATCATCTAGCTGATCTTGCA 59.610 43.478 6.10 0.00 33.59 4.08
4349 5953 5.239359 TGATCTTGCAAGAAATGAATCCG 57.761 39.130 31.55 0.09 38.77 4.18
4385 5989 3.952675 GCCAGTGTGCCACGTGTG 61.953 66.667 15.65 7.24 39.64 3.82
4388 5992 2.588877 AGTGTGCCACGTGTGCTC 60.589 61.111 23.38 20.71 39.64 4.26
4389 5993 2.588877 GTGTGCCACGTGTGCTCT 60.589 61.111 23.38 0.00 0.00 4.09
4403 6007 4.090642 CGTGTGCTCTGACAGAGTAAAATC 59.909 45.833 28.76 15.66 44.12 2.17
4451 6055 0.689745 AGCACTGGGGTAGCGGATAA 60.690 55.000 0.00 0.00 0.00 1.75
4474 6078 9.778741 ATAAATATGTCACCTCAACATAATCGT 57.221 29.630 0.57 0.00 41.54 3.73
4478 6082 3.623060 GTCACCTCAACATAATCGTGCAT 59.377 43.478 0.00 0.00 0.00 3.96
4484 6088 6.318648 ACCTCAACATAATCGTGCATAATTGT 59.681 34.615 0.00 0.00 0.00 2.71
4486 6090 7.166307 CCTCAACATAATCGTGCATAATTGTTG 59.834 37.037 17.07 17.07 42.34 3.33
4496 6100 3.193267 TGCATAATTGTTGGTGCTTCCTC 59.807 43.478 0.00 0.00 38.37 3.71
4525 6129 3.313526 CACACTGAGTTGTCCAAGAAAGG 59.686 47.826 0.00 0.00 0.00 3.11
4614 6218 2.613595 GAGACATTGTCTGTTGTGTGCA 59.386 45.455 23.57 0.00 43.53 4.57
4625 6229 1.391485 GTTGTGTGCATGAGCTCTACG 59.609 52.381 16.19 4.26 42.74 3.51
4637 6241 4.209452 GAGCTCTACGAGATCAACTCTG 57.791 50.000 6.43 0.00 43.57 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.891373 ACCACAGTCCACAGATCGAG 59.109 55.000 0.00 0.00 0.00 4.04
1 2 1.816835 GTACCACAGTCCACAGATCGA 59.183 52.381 0.00 0.00 0.00 3.59
2 3 1.467543 CGTACCACAGTCCACAGATCG 60.468 57.143 0.00 0.00 0.00 3.69
3 4 1.544691 ACGTACCACAGTCCACAGATC 59.455 52.381 0.00 0.00 0.00 2.75
5 6 1.881973 GTACGTACCACAGTCCACAGA 59.118 52.381 15.00 0.00 0.00 3.41
6 7 1.610038 TGTACGTACCACAGTCCACAG 59.390 52.381 22.43 0.00 0.00 3.66
7 8 1.689984 TGTACGTACCACAGTCCACA 58.310 50.000 22.43 0.00 0.00 4.17
8 9 2.035066 AGTTGTACGTACCACAGTCCAC 59.965 50.000 26.23 6.97 0.00 4.02
9 10 2.309613 AGTTGTACGTACCACAGTCCA 58.690 47.619 26.23 3.72 0.00 4.02
10 11 3.503748 AGTAGTTGTACGTACCACAGTCC 59.496 47.826 26.23 13.54 33.97 3.85
11 12 4.756084 AGTAGTTGTACGTACCACAGTC 57.244 45.455 26.23 17.04 33.97 3.51
12 13 5.063204 TGTAGTAGTTGTACGTACCACAGT 58.937 41.667 26.23 18.01 33.97 3.55
13 14 5.611796 TGTAGTAGTTGTACGTACCACAG 57.388 43.478 26.23 0.00 33.97 3.66
14 15 5.278266 GGTTGTAGTAGTTGTACGTACCACA 60.278 44.000 26.23 8.97 33.97 4.17
15 16 5.154222 GGTTGTAGTAGTTGTACGTACCAC 58.846 45.833 22.43 20.82 33.97 4.16
16 17 4.083537 CGGTTGTAGTAGTTGTACGTACCA 60.084 45.833 22.43 9.46 33.97 3.25
17 18 4.083484 ACGGTTGTAGTAGTTGTACGTACC 60.083 45.833 22.43 8.47 33.97 3.34
18 19 5.030874 ACGGTTGTAGTAGTTGTACGTAC 57.969 43.478 18.90 18.90 33.97 3.67
19 20 4.143200 CGACGGTTGTAGTAGTTGTACGTA 60.143 45.833 0.00 0.00 33.97 3.57
20 21 3.363970 CGACGGTTGTAGTAGTTGTACGT 60.364 47.826 0.00 0.00 33.97 3.57
21 22 3.120683 TCGACGGTTGTAGTAGTTGTACG 60.121 47.826 0.00 0.00 33.97 3.67
22 23 4.398247 CTCGACGGTTGTAGTAGTTGTAC 58.602 47.826 0.00 0.00 0.00 2.90
23 24 3.436704 CCTCGACGGTTGTAGTAGTTGTA 59.563 47.826 0.00 0.00 0.00 2.41
24 25 2.227388 CCTCGACGGTTGTAGTAGTTGT 59.773 50.000 0.00 0.00 0.00 3.32
25 26 2.485426 TCCTCGACGGTTGTAGTAGTTG 59.515 50.000 0.00 0.00 0.00 3.16
26 27 2.485814 GTCCTCGACGGTTGTAGTAGTT 59.514 50.000 0.00 0.00 0.00 2.24
27 28 2.079925 GTCCTCGACGGTTGTAGTAGT 58.920 52.381 0.00 0.00 0.00 2.73
28 29 1.399791 GGTCCTCGACGGTTGTAGTAG 59.600 57.143 0.00 0.00 32.65 2.57
29 30 1.271325 TGGTCCTCGACGGTTGTAGTA 60.271 52.381 0.00 0.00 32.65 1.82
30 31 0.538057 TGGTCCTCGACGGTTGTAGT 60.538 55.000 0.00 0.00 32.65 2.73
31 32 0.599558 TTGGTCCTCGACGGTTGTAG 59.400 55.000 0.00 0.00 32.65 2.74
32 33 0.314935 GTTGGTCCTCGACGGTTGTA 59.685 55.000 0.00 0.00 32.65 2.41
33 34 1.068585 GTTGGTCCTCGACGGTTGT 59.931 57.895 0.00 0.00 32.65 3.32
34 35 0.944311 CAGTTGGTCCTCGACGGTTG 60.944 60.000 0.00 0.00 34.93 3.77
35 36 1.366366 CAGTTGGTCCTCGACGGTT 59.634 57.895 0.00 0.00 34.93 4.44
36 37 2.571216 CCAGTTGGTCCTCGACGGT 61.571 63.158 0.00 0.00 34.93 4.83
37 38 2.261671 CCAGTTGGTCCTCGACGG 59.738 66.667 0.00 0.00 34.93 4.79
145 146 1.115467 GAGACCCACCGATCTCATGT 58.885 55.000 0.00 0.00 40.96 3.21
146 147 1.407936 AGAGACCCACCGATCTCATG 58.592 55.000 4.22 0.00 43.28 3.07
147 148 2.035632 GAAGAGACCCACCGATCTCAT 58.964 52.381 4.22 0.00 43.28 2.90
156 157 2.553247 CCCCTTTTGAGAAGAGACCCAC 60.553 54.545 0.00 0.00 0.00 4.61
163 164 4.568380 CCATGTCATCCCCTTTTGAGAAGA 60.568 45.833 0.00 0.00 0.00 2.87
171 172 1.002069 TGAGCCATGTCATCCCCTTT 58.998 50.000 0.00 0.00 0.00 3.11
172 173 0.257039 GTGAGCCATGTCATCCCCTT 59.743 55.000 0.00 0.00 0.00 3.95
173 174 1.918253 GTGAGCCATGTCATCCCCT 59.082 57.895 0.00 0.00 0.00 4.79
174 175 1.524621 CGTGAGCCATGTCATCCCC 60.525 63.158 0.00 0.00 0.00 4.81
175 176 1.524621 CCGTGAGCCATGTCATCCC 60.525 63.158 0.00 0.00 0.00 3.85
176 177 1.524621 CCCGTGAGCCATGTCATCC 60.525 63.158 0.00 0.00 0.00 3.51
177 178 1.524621 CCCCGTGAGCCATGTCATC 60.525 63.158 0.00 0.00 0.00 2.92
179 180 4.408821 GCCCCGTGAGCCATGTCA 62.409 66.667 0.00 0.00 0.00 3.58
199 217 0.459585 TAGTCACAAATCGCCTCCGC 60.460 55.000 0.00 0.00 0.00 5.54
210 228 1.411246 ACGTGCCTTCACTAGTCACAA 59.589 47.619 11.04 0.00 40.99 3.33
244 262 2.358737 GACCGGGTCTGTTGCCTG 60.359 66.667 19.92 0.00 0.00 4.85
269 307 2.202566 CTTTCGTAGCCGGGAGAAATC 58.797 52.381 2.18 0.00 32.97 2.17
274 312 0.101939 GGTACTTTCGTAGCCGGGAG 59.898 60.000 2.18 0.00 37.99 4.30
294 332 2.203112 TGCATGCGCTCCTCCATC 60.203 61.111 14.09 0.00 39.64 3.51
334 377 1.580845 CTTCCAGTTGGCTTCCGCTG 61.581 60.000 0.00 0.00 36.09 5.18
346 389 0.178929 ACCTCGGTTCTCCTTCCAGT 60.179 55.000 0.00 0.00 0.00 4.00
360 403 2.721603 CTGCGATTCGATTCTTACCTCG 59.278 50.000 10.88 0.00 36.25 4.63
404 447 1.012841 CGCCAAGATCCAAGAGAAGC 58.987 55.000 0.00 0.00 0.00 3.86
406 449 1.623311 TCACGCCAAGATCCAAGAGAA 59.377 47.619 0.00 0.00 0.00 2.87
407 450 1.266178 TCACGCCAAGATCCAAGAGA 58.734 50.000 0.00 0.00 0.00 3.10
408 451 2.322355 ATCACGCCAAGATCCAAGAG 57.678 50.000 0.00 0.00 0.00 2.85
409 452 2.237143 AGAATCACGCCAAGATCCAAGA 59.763 45.455 0.00 0.00 0.00 3.02
413 456 2.632377 TCAAGAATCACGCCAAGATCC 58.368 47.619 0.00 0.00 0.00 3.36
415 458 4.264253 TGAATCAAGAATCACGCCAAGAT 58.736 39.130 0.00 0.00 0.00 2.40
423 466 3.058293 TGCGGTGTTGAATCAAGAATCAC 60.058 43.478 0.00 0.87 0.00 3.06
441 484 4.543590 ACTCATAGAAAGGGATATGCGG 57.456 45.455 0.00 0.00 30.89 5.69
443 486 6.456501 ACGTTACTCATAGAAAGGGATATGC 58.543 40.000 0.00 0.00 30.89 3.14
444 487 7.658261 TGACGTTACTCATAGAAAGGGATATG 58.342 38.462 0.00 0.00 0.00 1.78
446 490 7.649533 TTGACGTTACTCATAGAAAGGGATA 57.350 36.000 0.00 0.00 0.00 2.59
497 549 1.678635 CCACCGGCATCACCACAAT 60.679 57.895 0.00 0.00 39.03 2.71
591 655 4.969196 CCCCGATGATCACCGGCG 62.969 72.222 24.07 11.46 44.07 6.46
636 700 0.397941 CCCTCTGCCTGTCAACTGAA 59.602 55.000 0.00 0.00 0.00 3.02
643 707 2.270527 GCCTTCCCTCTGCCTGTC 59.729 66.667 0.00 0.00 0.00 3.51
644 708 2.530151 TGCCTTCCCTCTGCCTGT 60.530 61.111 0.00 0.00 0.00 4.00
645 709 2.271497 CTGCCTTCCCTCTGCCTG 59.729 66.667 0.00 0.00 0.00 4.85
646 710 3.013932 CCTGCCTTCCCTCTGCCT 61.014 66.667 0.00 0.00 0.00 4.75
656 720 3.260100 CCCACTGGTCCCTGCCTT 61.260 66.667 0.00 0.00 0.00 4.35
661 725 4.316823 TCTCGCCCACTGGTCCCT 62.317 66.667 0.00 0.00 0.00 4.20
663 727 3.302347 CTGTCTCGCCCACTGGTCC 62.302 68.421 0.00 0.00 0.00 4.46
672 736 2.279120 CCGATGAGCTGTCTCGCC 60.279 66.667 0.00 0.00 42.26 5.54
696 760 0.457851 ACGAGAGATTTCTCCTGCCG 59.542 55.000 7.63 6.01 45.85 5.69
718 782 0.252479 TATACGGCCGGCAAGGAAAA 59.748 50.000 31.76 8.19 45.00 2.29
728 792 3.287312 TCGAACCTATTTATACGGCCG 57.713 47.619 26.86 26.86 0.00 6.13
729 793 3.370061 GCATCGAACCTATTTATACGGCC 59.630 47.826 0.00 0.00 0.00 6.13
730 794 3.991773 TGCATCGAACCTATTTATACGGC 59.008 43.478 0.00 0.00 0.00 5.68
731 795 6.533819 TTTGCATCGAACCTATTTATACGG 57.466 37.500 0.00 0.00 0.00 4.02
732 796 9.103048 GAATTTTGCATCGAACCTATTTATACG 57.897 33.333 0.00 0.00 0.00 3.06
733 797 9.394477 GGAATTTTGCATCGAACCTATTTATAC 57.606 33.333 0.00 0.00 0.00 1.47
734 798 8.286800 CGGAATTTTGCATCGAACCTATTTATA 58.713 33.333 0.00 0.00 0.00 0.98
735 799 7.138736 CGGAATTTTGCATCGAACCTATTTAT 58.861 34.615 0.00 0.00 0.00 1.40
738 802 4.202010 CCGGAATTTTGCATCGAACCTATT 60.202 41.667 0.00 0.00 0.00 1.73
739 803 3.315191 CCGGAATTTTGCATCGAACCTAT 59.685 43.478 0.00 0.00 0.00 2.57
740 804 2.680841 CCGGAATTTTGCATCGAACCTA 59.319 45.455 0.00 0.00 0.00 3.08
741 805 1.472480 CCGGAATTTTGCATCGAACCT 59.528 47.619 0.00 0.00 0.00 3.50
777 935 1.087771 GGCCCGGTTTCATGTACTCG 61.088 60.000 0.00 0.00 0.00 4.18
833 1074 9.688091 TCATTAAAGTAGTGATCTAGACACTCT 57.312 33.333 22.88 18.03 45.58 3.24
864 1105 8.889717 CCATCCGTAAACAAATATAAGAGTGTT 58.110 33.333 0.00 0.00 35.77 3.32
865 1106 8.262227 TCCATCCGTAAACAAATATAAGAGTGT 58.738 33.333 0.00 0.00 0.00 3.55
866 1107 8.657074 TCCATCCGTAAACAAATATAAGAGTG 57.343 34.615 0.00 0.00 0.00 3.51
867 1108 8.483758 ACTCCATCCGTAAACAAATATAAGAGT 58.516 33.333 0.00 0.00 0.00 3.24
868 1109 8.888579 ACTCCATCCGTAAACAAATATAAGAG 57.111 34.615 0.00 0.00 0.00 2.85
869 1110 9.754382 GTACTCCATCCGTAAACAAATATAAGA 57.246 33.333 0.00 0.00 0.00 2.10
870 1111 9.760077 AGTACTCCATCCGTAAACAAATATAAG 57.240 33.333 0.00 0.00 0.00 1.73
875 1116 7.864379 CGTATAGTACTCCATCCGTAAACAAAT 59.136 37.037 0.00 0.00 0.00 2.32
876 1117 7.195646 CGTATAGTACTCCATCCGTAAACAAA 58.804 38.462 0.00 0.00 0.00 2.83
877 1118 6.728200 CGTATAGTACTCCATCCGTAAACAA 58.272 40.000 0.00 0.00 0.00 2.83
878 1119 5.277974 GCGTATAGTACTCCATCCGTAAACA 60.278 44.000 0.00 0.00 0.00 2.83
879 1120 5.149977 GCGTATAGTACTCCATCCGTAAAC 58.850 45.833 0.00 0.00 0.00 2.01
880 1121 4.083855 CGCGTATAGTACTCCATCCGTAAA 60.084 45.833 0.00 0.00 0.00 2.01
881 1122 3.433274 CGCGTATAGTACTCCATCCGTAA 59.567 47.826 0.00 0.00 0.00 3.18
882 1123 2.995939 CGCGTATAGTACTCCATCCGTA 59.004 50.000 0.00 0.00 0.00 4.02
883 1124 1.802960 CGCGTATAGTACTCCATCCGT 59.197 52.381 0.00 0.00 0.00 4.69
884 1125 1.802960 ACGCGTATAGTACTCCATCCG 59.197 52.381 11.67 0.99 0.00 4.18
885 1126 3.072944 AGACGCGTATAGTACTCCATCC 58.927 50.000 13.97 0.00 0.00 3.51
886 1127 4.745837 AAGACGCGTATAGTACTCCATC 57.254 45.455 13.97 0.00 0.00 3.51
887 1128 5.511234 AAAAGACGCGTATAGTACTCCAT 57.489 39.130 13.97 0.00 0.00 3.41
888 1129 4.970662 AAAAGACGCGTATAGTACTCCA 57.029 40.909 13.97 0.00 0.00 3.86
909 1150 5.307926 TGAATGAAGCAATGCACGATAAA 57.692 34.783 8.35 0.00 0.00 1.40
921 1162 1.005097 AGCCAGGACATGAATGAAGCA 59.995 47.619 0.00 0.00 0.00 3.91
938 1179 7.441157 TGTTTGCAGTGATATATTGTACTAGCC 59.559 37.037 0.00 0.00 0.00 3.93
976 1217 1.040646 TTAGAGTAGGCCCTGCATCG 58.959 55.000 0.00 0.00 0.00 3.84
977 1218 1.269831 CGTTAGAGTAGGCCCTGCATC 60.270 57.143 0.00 0.00 0.00 3.91
978 1219 0.753262 CGTTAGAGTAGGCCCTGCAT 59.247 55.000 0.00 0.00 0.00 3.96
979 1220 1.327690 CCGTTAGAGTAGGCCCTGCA 61.328 60.000 0.00 0.00 0.00 4.41
989 1230 0.108804 CGTGCACATCCCGTTAGAGT 60.109 55.000 18.64 0.00 0.00 3.24
1247 1503 7.092533 TGGTACTCTATATAGAATAGTCCGCCT 60.093 40.741 13.41 0.00 0.00 5.52
1391 1651 9.802039 TTACCTACAGGAAGAAATAACAACAAT 57.198 29.630 1.29 0.00 38.94 2.71
1414 1679 4.072131 TGCACAAGTTCTTCTGGGATTAC 58.928 43.478 0.00 0.00 0.00 1.89
1452 1717 3.359110 AGCTTGATCTCCCCTAGGATT 57.641 47.619 11.48 0.00 42.93 3.01
1501 1766 0.605319 TGGATCTTGGCGACCACAAC 60.605 55.000 0.00 0.00 30.78 3.32
1670 1935 5.986135 CGAGGTATAAAAGGATCCAGAACAG 59.014 44.000 15.82 0.00 0.00 3.16
1738 2003 6.479001 TGAAGCCGTGAATAATAAAGACTAGC 59.521 38.462 0.00 0.00 0.00 3.42
1958 2223 1.692411 ACTGACAAAAGGGAGTTGGC 58.308 50.000 0.00 0.00 34.35 4.52
2413 2696 0.536460 GGGAACTCGCCCTTGAAACA 60.536 55.000 0.00 0.00 45.12 2.83
2502 2785 7.533426 AGACAAGCTTTTGATTATAGCAAGTG 58.467 34.615 0.00 0.00 37.37 3.16
2628 2911 2.545526 CTCGCAGCCATGTTTATCGAAT 59.454 45.455 0.00 0.00 0.00 3.34
2696 2979 1.448013 GTACTGCAGGGACGCCTTC 60.448 63.158 19.93 0.00 0.00 3.46
2710 2993 8.375493 TGGGAACTTTTCACTATATCAGTACT 57.625 34.615 0.00 0.00 34.98 2.73
2741 3024 0.107214 CCTTTGCATAGGCCGAGGAA 60.107 55.000 10.46 0.00 41.24 3.36
2791 3074 1.969064 CGGTTGGCGGTGATTCCAA 60.969 57.895 0.00 0.00 39.81 3.53
3072 4577 5.840149 ACTGCTCCTTCTGAGATGAAGATAT 59.160 40.000 5.90 0.00 44.42 1.63
3107 4612 2.671396 GGTCTTGTGTGCGGTAATGTAG 59.329 50.000 0.00 0.00 0.00 2.74
3275 4780 3.764434 ACAGACACCTACATGATCGAAGT 59.236 43.478 0.00 0.00 0.00 3.01
3315 4820 2.047061 TGTCAACTGCTTCCTACAGGT 58.953 47.619 0.00 0.00 39.55 4.00
3317 4822 3.668447 ACATGTCAACTGCTTCCTACAG 58.332 45.455 0.00 0.00 41.08 2.74
3354 4953 8.388484 AGAGTTACTTGATAATGGCATGAATC 57.612 34.615 0.00 8.38 0.00 2.52
3546 5147 1.888512 CACCCATCTTCAGGTTGTTGG 59.111 52.381 0.00 0.00 32.72 3.77
3655 5259 6.803320 CACTATCACCAACACAAAAGCATTAG 59.197 38.462 0.00 0.00 0.00 1.73
3690 5294 6.801575 ACGATTCACTAACCAACAACAAATT 58.198 32.000 0.00 0.00 0.00 1.82
3691 5295 6.385649 ACGATTCACTAACCAACAACAAAT 57.614 33.333 0.00 0.00 0.00 2.32
3692 5296 5.821516 ACGATTCACTAACCAACAACAAA 57.178 34.783 0.00 0.00 0.00 2.83
3693 5297 5.449314 CCAACGATTCACTAACCAACAACAA 60.449 40.000 0.00 0.00 0.00 2.83
3694 5298 4.035792 CCAACGATTCACTAACCAACAACA 59.964 41.667 0.00 0.00 0.00 3.33
3729 5333 8.952278 ACAATTCACTAACTAACACAACTTCAA 58.048 29.630 0.00 0.00 0.00 2.69
3733 5337 7.769044 ACAGACAATTCACTAACTAACACAACT 59.231 33.333 0.00 0.00 0.00 3.16
3874 5478 9.255304 ACATAAATTCAACACAACACAATTACC 57.745 29.630 0.00 0.00 0.00 2.85
3919 5523 6.995091 CCTGATAGACCTAATTTGAAGGAAGG 59.005 42.308 0.00 0.00 37.57 3.46
3922 5526 7.365652 GGAACCTGATAGACCTAATTTGAAGGA 60.366 40.741 0.00 0.00 37.57 3.36
3940 5544 2.668144 ATTGGGAAAACGGAACCTGA 57.332 45.000 0.00 0.00 0.00 3.86
3982 5586 6.652205 TCTAAACTTTCAGGGGGTAATGAT 57.348 37.500 0.00 0.00 0.00 2.45
4092 5696 5.417580 GCAACCCTAGATATCTCCTCTACTG 59.582 48.000 8.95 1.20 0.00 2.74
4102 5706 5.349817 CGTCATGATTGCAACCCTAGATATC 59.650 44.000 0.00 0.00 0.00 1.63
4115 5719 3.373748 TGTGTTGTATCCGTCATGATTGC 59.626 43.478 0.00 0.00 0.00 3.56
4175 5779 3.558931 TGATCCCATGCTAACACGATT 57.441 42.857 0.00 0.00 0.00 3.34
4283 5887 0.535335 GATGAGTGGTGGGCGTAGAA 59.465 55.000 0.00 0.00 0.00 2.10
4301 5905 4.667573 AGATGATGGTCTATCTAAGCCGA 58.332 43.478 0.00 0.00 36.71 5.54
4302 5906 5.449862 GCTAGATGATGGTCTATCTAAGCCG 60.450 48.000 0.00 0.00 35.96 5.52
4335 5939 6.035327 GCTTTGGAAATCGGATTCATTTCTTG 59.965 38.462 3.28 0.00 39.34 3.02
4336 5940 6.071165 AGCTTTGGAAATCGGATTCATTTCTT 60.071 34.615 3.28 0.00 39.34 2.52
4349 5953 3.242518 GGCACGTAAAGCTTTGGAAATC 58.757 45.455 22.02 6.33 0.00 2.17
4385 5989 3.935828 GGTGGATTTTACTCTGTCAGAGC 59.064 47.826 26.65 11.23 46.12 4.09
4388 5992 5.413309 AGAGGTGGATTTTACTCTGTCAG 57.587 43.478 0.00 0.00 38.76 3.51
4389 5993 6.440647 ACATAGAGGTGGATTTTACTCTGTCA 59.559 38.462 0.00 0.00 40.30 3.58
4403 6007 3.034635 AGGACTAAGCACATAGAGGTGG 58.965 50.000 0.00 0.00 39.19 4.61
4437 6041 3.904965 TGACATATTTATCCGCTACCCCA 59.095 43.478 0.00 0.00 0.00 4.96
4451 6055 6.017934 GCACGATTATGTTGAGGTGACATATT 60.018 38.462 0.00 0.00 39.12 1.28
4473 6077 3.056607 AGGAAGCACCAACAATTATGCAC 60.057 43.478 0.00 0.00 40.63 4.57
4474 6078 3.164268 AGGAAGCACCAACAATTATGCA 58.836 40.909 0.00 0.00 40.63 3.96
4478 6082 2.802719 GGGAGGAAGCACCAACAATTA 58.197 47.619 2.96 0.00 42.04 1.40
4484 6088 0.539986 GTATCGGGAGGAAGCACCAA 59.460 55.000 2.96 0.00 42.04 3.67
4486 6090 0.179081 GTGTATCGGGAGGAAGCACC 60.179 60.000 0.00 0.00 39.35 5.01
4496 6100 2.607187 GACAACTCAGTGTGTATCGGG 58.393 52.381 0.00 0.00 0.00 5.14
4560 6164 0.112218 AGCAAACTACATGGCACCCA 59.888 50.000 0.00 0.00 38.19 4.51
4561 6165 1.256812 AAGCAAACTACATGGCACCC 58.743 50.000 0.00 0.00 0.00 4.61
4563 6167 2.035832 ACCAAAGCAAACTACATGGCAC 59.964 45.455 0.00 0.00 30.93 5.01
4564 6168 2.315176 ACCAAAGCAAACTACATGGCA 58.685 42.857 0.00 0.00 30.93 4.92
4565 6169 3.506067 AGTACCAAAGCAAACTACATGGC 59.494 43.478 0.00 0.00 30.93 4.40
4567 6171 6.312399 TCAAGTACCAAAGCAAACTACATG 57.688 37.500 0.00 0.00 0.00 3.21
4568 6172 6.128282 CGATCAAGTACCAAAGCAAACTACAT 60.128 38.462 0.00 0.00 0.00 2.29
4569 6173 5.178623 CGATCAAGTACCAAAGCAAACTACA 59.821 40.000 0.00 0.00 0.00 2.74
4570 6174 5.407387 TCGATCAAGTACCAAAGCAAACTAC 59.593 40.000 0.00 0.00 0.00 2.73
4571 6175 5.543714 TCGATCAAGTACCAAAGCAAACTA 58.456 37.500 0.00 0.00 0.00 2.24
4572 6176 4.385825 TCGATCAAGTACCAAAGCAAACT 58.614 39.130 0.00 0.00 0.00 2.66
4573 6177 4.451096 TCTCGATCAAGTACCAAAGCAAAC 59.549 41.667 0.00 0.00 0.00 2.93
4625 6229 6.524101 AGTTCCTTAGTCAGAGTTGATCTC 57.476 41.667 0.00 0.00 43.05 2.75


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

AutoCloner maintained by Alex Coulton.