Multiple sequence alignment - TraesCS4B01G356100

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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 TraesCS4B01G356100 chr4B 100.000 3895 0 0 1 3895 646861872 646865766 0.000000e+00 7193.0
1 TraesCS4B01G356100 chr4B 100.000 28 0 0 564 591 646862462 646862435 7.000000e-03 52.8
2 TraesCS4B01G356100 chr4D 93.259 1884 88 16 585 2453 502488244 502490103 0.000000e+00 2739.0
3 TraesCS4B01G356100 chr4D 82.054 1081 154 22 2842 3895 502517881 502518948 0.000000e+00 885.0
4 TraesCS4B01G356100 chr4D 88.255 596 38 13 1 594 502485663 502486228 0.000000e+00 684.0
5 TraesCS4B01G356100 chr4D 92.398 171 12 1 2450 2620 502490365 502490534 3.890000e-60 243.0
6 TraesCS4B01G356100 chr5A 93.176 1275 73 4 1180 2454 685793306 685794566 0.000000e+00 1860.0
7 TraesCS4B01G356100 chr5A 83.829 1144 111 32 2790 3895 685757700 685758807 0.000000e+00 1020.0
8 TraesCS4B01G356100 chr5A 91.974 461 19 5 689 1146 685756296 685756741 7.100000e-177 630.0
9 TraesCS4B01G356100 chr5A 82.913 515 72 6 1199 1702 685873940 685874449 2.130000e-122 449.0
10 TraesCS4B01G356100 chr5A 88.496 226 20 3 1 226 685742578 685742797 6.410000e-68 268.0
11 TraesCS4B01G356100 chr5A 79.370 349 54 13 3553 3894 129593246 129592909 3.030000e-56 230.0
12 TraesCS4B01G356100 chr5A 77.874 348 59 13 3553 3894 433938876 433939211 2.370000e-47 200.0
13 TraesCS4B01G356100 chr5A 90.833 120 11 0 2334 2453 685756765 685756884 1.120000e-35 161.0
14 TraesCS4B01G356100 chr5A 94.118 102 4 2 2465 2566 685794620 685794719 1.870000e-33 154.0
15 TraesCS4B01G356100 chr5A 91.667 72 5 1 2667 2738 685795058 685795128 8.910000e-17 99.0
16 TraesCS4B01G356100 chr5A 91.935 62 2 1 640 698 685749320 685749381 2.490000e-12 84.2
17 TraesCS4B01G356100 chr5A 88.525 61 5 2 3836 3895 685863966 685864025 5.400000e-09 73.1
18 TraesCS4B01G356100 chr6A 85.252 278 41 0 1207 1484 8192314 8192037 1.770000e-73 287.0
19 TraesCS4B01G356100 chr6A 77.372 137 22 4 3759 3895 477139663 477139790 5.400000e-09 73.1
20 TraesCS4B01G356100 chr3A 80.692 347 54 8 3553 3895 422307753 422307416 1.390000e-64 257.0
21 TraesCS4B01G356100 chr3A 93.478 46 3 0 3850 3895 331286313 331286358 6.980000e-08 69.4
22 TraesCS4B01G356100 chr1D 79.310 348 56 11 3553 3894 62221413 62221076 3.030000e-56 230.0
23 TraesCS4B01G356100 chr1D 76.724 348 65 12 3552 3894 101989366 101989702 3.090000e-41 180.0
24 TraesCS4B01G356100 chr1B 79.143 350 55 13 3553 3895 98974394 98974056 3.920000e-55 226.0
25 TraesCS4B01G356100 chr6B 78.632 351 54 16 3553 3893 276495588 276495249 3.050000e-51 213.0
26 TraesCS4B01G356100 chr6B 78.386 347 59 10 3553 3894 198372507 198372172 1.100000e-50 211.0
27 TraesCS4B01G356100 chr7A 78.261 345 59 10 3554 3895 158486060 158486391 1.420000e-49 207.0
28 TraesCS4B01G356100 chr7A 80.460 87 15 1 193 277 725722459 725722373 9.030000e-07 65.8
29 TraesCS4B01G356100 chr7D 77.681 345 63 10 3553 3894 376933575 376933242 8.540000e-47 198.0
30 TraesCS4B01G356100 chr4A 81.959 194 30 5 3553 3741 17305093 17305286 4.030000e-35 159.0
31 TraesCS4B01G356100 chr5B 86.538 104 11 2 1856 1956 658547577 658547680 1.140000e-20 111.0
32 TraesCS4B01G356100 chr2A 74.653 288 53 10 3610 3895 659690534 659690803 4.110000e-20 110.0
33 TraesCS4B01G356100 chr2D 88.525 61 7 0 3835 3895 566305713 566305773 1.500000e-09 75.0


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 TraesCS4B01G356100 chr4B 646861872 646865766 3894 False 7193.000000 7193 100.000000 1 3895 1 chr4B.!!$F1 3894
1 TraesCS4B01G356100 chr4D 502485663 502490534 4871 False 1222.000000 2739 91.304000 1 2620 3 chr4D.!!$F2 2619
2 TraesCS4B01G356100 chr4D 502517881 502518948 1067 False 885.000000 885 82.054000 2842 3895 1 chr4D.!!$F1 1053
3 TraesCS4B01G356100 chr5A 685793306 685795128 1822 False 704.333333 1860 92.987000 1180 2738 3 chr5A.!!$F7 1558
4 TraesCS4B01G356100 chr5A 685756296 685758807 2511 False 603.666667 1020 88.878667 689 3895 3 chr5A.!!$F6 3206
5 TraesCS4B01G356100 chr5A 685873940 685874449 509 False 449.000000 449 82.913000 1199 1702 1 chr5A.!!$F5 503

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
159 160 0.178973 TGACCCTCTTGGAGACGTCA 60.179 55.000 19.50 10.9 36.85 4.35 F
460 463 0.317479 GTGTGGCGTCTCCTGTACTT 59.683 55.000 0.00 0.0 35.26 2.24 F
1139 3179 1.005037 CTGGCGCACAGGTCAGTTA 60.005 57.895 10.83 0.0 43.70 2.24 F
2348 4400 0.034896 GACTTGCCGGAGAGGTTCAA 59.965 55.000 5.05 0.0 43.70 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1163 3203 0.033504 GTCACTTCAGCGACCCAAGA 59.966 55.0 0.00 0.0 0.00 3.02 R
1787 3839 0.035056 GAGGACTGTTGGGGACATGG 60.035 60.0 0.00 0.0 42.32 3.66 R
2840 5675 0.035630 ATCTCAGTTGTGCAGAGGCC 60.036 55.0 0.00 0.0 40.13 5.19 R
3434 6303 0.250727 CCTTGGCCTTCACCGAAAGA 60.251 55.0 3.32 0.0 0.00 2.52 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
19 20 2.842394 CTACACTCCACCGCTGGCAG 62.842 65.000 10.94 10.94 37.49 4.85
36 37 2.562912 GCGACATGCTTGTGGGTG 59.437 61.111 10.37 0.00 41.73 4.61
38 39 1.868997 CGACATGCTTGTGGGTGTC 59.131 57.895 10.37 0.00 35.79 3.67
51 52 1.671742 GGTGTCGCTTCCCTCTTGA 59.328 57.895 0.00 0.00 0.00 3.02
63 64 0.600255 CCTCTTGAAGGCGTCGTTGT 60.600 55.000 0.00 0.00 38.67 3.32
75 76 0.397564 GTCGTTGTGGGTCCCCTAAA 59.602 55.000 5.13 0.00 36.94 1.85
87 88 0.395724 CCCCTAAAGGTGCCATGTCC 60.396 60.000 0.00 0.00 0.00 4.02
119 120 4.528987 ACCCTAGTCCTTCTTTTCAGACTC 59.471 45.833 0.00 0.00 40.07 3.36
122 123 4.245845 AGTCCTTCTTTTCAGACTCGAC 57.754 45.455 0.00 0.00 34.53 4.20
149 150 1.296715 GTGGCGTCATGACCCTCTT 59.703 57.895 24.81 0.00 0.00 2.85
159 160 0.178973 TGACCCTCTTGGAGACGTCA 60.179 55.000 19.50 10.90 36.85 4.35
160 161 1.187087 GACCCTCTTGGAGACGTCAT 58.813 55.000 19.50 2.45 38.00 3.06
173 174 1.300465 CGTCATCATGGAGCTCCGG 60.300 63.158 27.43 21.41 39.43 5.14
228 229 3.216800 GCATGCCTTGATCCTTACATGA 58.783 45.455 6.36 0.00 37.65 3.07
236 237 2.037641 TGATCCTTACATGAGGCATCCG 59.962 50.000 0.00 0.00 36.71 4.18
285 288 6.183361 TGGTCTCCTATCCTATACATGTTCCT 60.183 42.308 2.30 0.00 0.00 3.36
286 289 6.378848 GGTCTCCTATCCTATACATGTTCCTC 59.621 46.154 2.30 0.00 0.00 3.71
291 294 5.888982 ATCCTATACATGTTCCTCCGTTT 57.111 39.130 2.30 0.00 0.00 3.60
302 305 1.226030 CCTCCGTTTTCACCGTGGTC 61.226 60.000 0.00 0.00 0.00 4.02
311 314 3.760035 ACCGTGGTCCTAGCAGCG 61.760 66.667 0.00 0.00 0.00 5.18
352 355 3.080121 AGGCGGCCCTCTCAAGAG 61.080 66.667 17.02 0.00 36.46 2.85
353 356 3.077556 GGCGGCCCTCTCAAGAGA 61.078 66.667 8.12 1.68 44.74 3.10
354 357 2.439104 GGCGGCCCTCTCAAGAGAT 61.439 63.158 8.12 0.00 44.74 2.75
372 375 2.236146 AGATGGCTTGGTGTGTTCGATA 59.764 45.455 0.00 0.00 0.00 2.92
397 400 2.266055 GTCCGGTGGCCTCTCAAG 59.734 66.667 3.32 0.00 0.00 3.02
425 428 2.719739 TGGTTCCGTCCTAGTAGTCTG 58.280 52.381 0.00 0.00 0.00 3.51
458 461 1.080025 GGTGTGGCGTCTCCTGTAC 60.080 63.158 0.00 0.00 35.26 2.90
460 463 0.317479 GTGTGGCGTCTCCTGTACTT 59.683 55.000 0.00 0.00 35.26 2.24
478 481 2.226437 ACTTGTGCTCGGCATTAAGTTG 59.774 45.455 17.35 4.98 41.97 3.16
480 483 2.710377 TGTGCTCGGCATTAAGTTGAT 58.290 42.857 1.90 0.00 41.91 2.57
481 484 3.867857 TGTGCTCGGCATTAAGTTGATA 58.132 40.909 1.90 0.00 41.91 2.15
482 485 3.621268 TGTGCTCGGCATTAAGTTGATAC 59.379 43.478 1.90 0.00 41.91 2.24
491 494 7.982919 TCGGCATTAAGTTGATACTAGCTTTTA 59.017 33.333 0.00 0.00 33.17 1.52
526 529 4.037923 TGGATGCTGTTTTTCTTTGACCTC 59.962 41.667 0.00 0.00 0.00 3.85
533 536 5.949735 TGTTTTTCTTTGACCTCAAGTGTC 58.050 37.500 0.00 0.00 37.15 3.67
557 560 2.457598 AGGATTTCCTCACTACTCGCA 58.542 47.619 0.00 0.00 44.77 5.10
558 561 3.034635 AGGATTTCCTCACTACTCGCAT 58.965 45.455 0.00 0.00 44.77 4.73
575 578 1.730121 GCATGGCGATGTCACTTTGTG 60.730 52.381 10.59 0.00 34.45 3.33
577 580 2.183478 TGGCGATGTCACTTTGTGAT 57.817 45.000 3.65 0.00 44.63 3.06
578 581 2.076100 TGGCGATGTCACTTTGTGATC 58.924 47.619 3.65 0.00 44.63 2.92
580 583 2.159653 GGCGATGTCACTTTGTGATCAC 60.160 50.000 19.27 19.27 44.63 3.06
581 584 2.480037 GCGATGTCACTTTGTGATCACA 59.520 45.455 24.56 24.56 44.63 3.58
607 2631 6.354938 AGTGACATGAGTTGCAGATATCATT 58.645 36.000 5.32 0.00 30.09 2.57
630 2659 3.493524 GGCAAGTAGCTGATCCTTACCTC 60.494 52.174 0.00 0.00 44.79 3.85
706 2738 4.507756 TGCAATCGCTGTACATATGAGTTC 59.492 41.667 10.38 0.00 39.64 3.01
771 2804 2.899838 AGGCACGCACGAAAGCAA 60.900 55.556 0.00 0.00 0.00 3.91
780 2817 3.437395 ACGCACGAAAGCAACCATAATAA 59.563 39.130 0.00 0.00 0.00 1.40
781 2818 4.083217 ACGCACGAAAGCAACCATAATAAA 60.083 37.500 0.00 0.00 0.00 1.40
843 2880 4.943705 AGAAAGGTCAATCACGTGCATTAT 59.056 37.500 11.67 0.00 0.00 1.28
855 2892 3.447586 ACGTGCATTATCACTAGTCCACT 59.552 43.478 0.00 0.00 34.92 4.00
856 2893 4.081642 ACGTGCATTATCACTAGTCCACTT 60.082 41.667 0.00 0.00 34.92 3.16
857 2894 5.126545 ACGTGCATTATCACTAGTCCACTTA 59.873 40.000 0.00 0.00 34.92 2.24
858 2895 6.040247 CGTGCATTATCACTAGTCCACTTAA 58.960 40.000 0.00 0.00 34.92 1.85
932 2969 3.307906 CCGGGACTGGACGTGGAA 61.308 66.667 0.00 0.00 0.00 3.53
963 3000 1.791103 CTCCGTCTCCTCTCATCGGC 61.791 65.000 0.00 0.00 40.81 5.54
994 3031 4.778415 GAGCAACCGCGAGCTCGA 62.778 66.667 38.74 0.00 46.53 4.04
995 3032 4.135153 AGCAACCGCGAGCTCGAT 62.135 61.111 38.74 20.31 45.49 3.59
996 3033 3.621394 GCAACCGCGAGCTCGATC 61.621 66.667 38.74 21.04 43.02 3.69
997 3034 3.315521 CAACCGCGAGCTCGATCG 61.316 66.667 38.74 30.31 45.48 3.69
1015 3052 2.786777 TCGCCACTACTCTTACTGACA 58.213 47.619 0.00 0.00 0.00 3.58
1019 3056 4.575236 CGCCACTACTCTTACTGACATAGA 59.425 45.833 0.00 0.00 0.00 1.98
1055 3092 2.627699 GGTGCTGAAAAATCCACTTCCA 59.372 45.455 0.00 0.00 0.00 3.53
1114 3154 1.139058 ACTCCATACAAGATGGGCGAC 59.861 52.381 3.81 0.00 39.60 5.19
1139 3179 1.005037 CTGGCGCACAGGTCAGTTA 60.005 57.895 10.83 0.00 43.70 2.24
1146 3186 3.062234 GCGCACAGGTCAGTTAATTACTC 59.938 47.826 0.30 0.00 33.85 2.59
1147 3187 3.303495 CGCACAGGTCAGTTAATTACTCG 59.697 47.826 0.00 0.00 33.85 4.18
1149 3189 5.109903 GCACAGGTCAGTTAATTACTCGAT 58.890 41.667 0.00 0.00 33.85 3.59
1151 3191 5.455849 CACAGGTCAGTTAATTACTCGATCG 59.544 44.000 9.36 9.36 33.85 3.69
1152 3192 5.125097 ACAGGTCAGTTAATTACTCGATCGT 59.875 40.000 15.94 0.00 33.85 3.73
1153 3193 6.034591 CAGGTCAGTTAATTACTCGATCGTT 58.965 40.000 15.94 6.12 33.85 3.85
1154 3194 6.530534 CAGGTCAGTTAATTACTCGATCGTTT 59.469 38.462 15.94 5.74 33.85 3.60
1155 3195 6.750963 AGGTCAGTTAATTACTCGATCGTTTC 59.249 38.462 15.94 0.00 33.85 2.78
1157 3197 6.750963 GTCAGTTAATTACTCGATCGTTTCCT 59.249 38.462 15.94 0.00 33.85 3.36
1160 3200 8.744011 CAGTTAATTACTCGATCGTTTCCTTAG 58.256 37.037 15.94 5.58 33.85 2.18
1161 3201 8.680903 AGTTAATTACTCGATCGTTTCCTTAGA 58.319 33.333 15.94 0.00 28.23 2.10
1162 3202 9.294030 GTTAATTACTCGATCGTTTCCTTAGAA 57.706 33.333 15.94 0.97 0.00 2.10
1164 3204 8.576936 AATTACTCGATCGTTTCCTTAGAATC 57.423 34.615 15.94 0.00 0.00 2.52
1167 3207 6.037098 ACTCGATCGTTTCCTTAGAATCTTG 58.963 40.000 15.94 0.00 0.00 3.02
1168 3208 5.348986 TCGATCGTTTCCTTAGAATCTTGG 58.651 41.667 15.94 0.00 0.00 3.61
1169 3209 4.508124 CGATCGTTTCCTTAGAATCTTGGG 59.492 45.833 7.03 0.00 0.00 4.12
1171 3211 4.828829 TCGTTTCCTTAGAATCTTGGGTC 58.171 43.478 0.00 0.00 0.00 4.46
1172 3212 3.617263 CGTTTCCTTAGAATCTTGGGTCG 59.383 47.826 0.00 0.00 0.00 4.79
1173 3213 2.981859 TCCTTAGAATCTTGGGTCGC 57.018 50.000 0.00 0.00 0.00 5.19
1174 3214 2.467880 TCCTTAGAATCTTGGGTCGCT 58.532 47.619 0.00 0.00 0.00 4.93
1175 3215 2.168521 TCCTTAGAATCTTGGGTCGCTG 59.831 50.000 0.00 0.00 0.00 5.18
1176 3216 2.168521 CCTTAGAATCTTGGGTCGCTGA 59.831 50.000 0.00 0.00 0.00 4.26
1517 3560 7.576861 TCCTCGTACCTTTTTCTTTTCAAAT 57.423 32.000 0.00 0.00 0.00 2.32
1589 3639 4.023792 TGTCAAGTCTCAATCATGTTGCAC 60.024 41.667 0.00 0.00 0.00 4.57
1761 3813 3.272334 CCGCTAGGAACGCCATGC 61.272 66.667 0.00 0.00 41.02 4.06
1787 3839 5.473504 AGCCGGTAATTAATGATCAACCATC 59.526 40.000 1.90 3.54 0.00 3.51
1797 3849 1.215173 GATCAACCATCCATGTCCCCA 59.785 52.381 0.00 0.00 0.00 4.96
1813 3865 2.716424 TCCCCAACAGTCCTCATCTTTT 59.284 45.455 0.00 0.00 0.00 2.27
1822 3874 5.029014 CAGTCCTCATCTTTTCTACGTACG 58.971 45.833 15.01 15.01 0.00 3.67
1823 3875 4.699257 AGTCCTCATCTTTTCTACGTACGT 59.301 41.667 25.98 25.98 0.00 3.57
1824 3876 5.877012 AGTCCTCATCTTTTCTACGTACGTA 59.123 40.000 25.41 25.41 0.00 3.57
1825 3877 5.962423 GTCCTCATCTTTTCTACGTACGTAC 59.038 44.000 23.60 15.90 0.00 3.67
1848 3900 1.129251 AGTTTGCAACGCTGATCATCG 59.871 47.619 16.88 16.88 36.23 3.84
2243 4295 2.046285 CCTTCATGGTGAACGGGGC 61.046 63.158 0.00 0.00 32.21 5.80
2332 4384 4.974438 TCCTGGCCAACCCCGACT 62.974 66.667 7.01 0.00 33.59 4.18
2348 4400 0.034896 GACTTGCCGGAGAGGTTCAA 59.965 55.000 5.05 0.00 43.70 2.69
2349 4401 0.472471 ACTTGCCGGAGAGGTTCAAA 59.528 50.000 5.05 0.00 43.70 2.69
2397 4449 1.204941 AGGAGCACGTTCTACACATCC 59.795 52.381 0.00 0.00 0.00 3.51
2400 4452 0.989890 GCACGTTCTACACATCCGAC 59.010 55.000 0.00 0.00 0.00 4.79
2438 4490 4.941263 CACCGATTACCCTTTTCTTGATCA 59.059 41.667 0.00 0.00 0.00 2.92
2466 5061 1.878953 AGCTAACTGGTTGGTTCACG 58.121 50.000 0.00 0.00 0.00 4.35
2469 5064 2.140717 CTAACTGGTTGGTTCACGGTC 58.859 52.381 0.00 0.00 0.00 4.79
2524 5119 8.543774 CATCATCGTTGATTAAGAAGTAACTCC 58.456 37.037 6.24 0.00 40.70 3.85
2566 5161 3.766151 CATAGCACACAAAATCAGGCTG 58.234 45.455 8.58 8.58 33.10 4.85
2610 5211 5.997746 TGTTAGCTCCAGATTGTATTATGGC 59.002 40.000 0.00 0.00 32.63 4.40
2630 5234 0.924823 AAGGCATCTGCAGATCCCTT 59.075 50.000 36.49 36.49 45.44 3.95
2675 5508 5.534207 AAAATGATGTTGAGCCAACTTGA 57.466 34.783 15.91 7.33 43.85 3.02
2683 5516 3.350219 TGAGCCAACTTGAAGATACCC 57.650 47.619 0.00 0.00 0.00 3.69
2745 5579 3.510531 ACCCCAAAAACTTCCTCTCTC 57.489 47.619 0.00 0.00 0.00 3.20
2747 5581 3.073209 ACCCCAAAAACTTCCTCTCTCTC 59.927 47.826 0.00 0.00 0.00 3.20
2753 5587 6.389906 CAAAAACTTCCTCTCTCTCTCTCTC 58.610 44.000 0.00 0.00 0.00 3.20
2754 5588 5.520748 AAACTTCCTCTCTCTCTCTCTCT 57.479 43.478 0.00 0.00 0.00 3.10
2755 5589 4.762289 ACTTCCTCTCTCTCTCTCTCTC 57.238 50.000 0.00 0.00 0.00 3.20
2756 5590 4.366267 ACTTCCTCTCTCTCTCTCTCTCT 58.634 47.826 0.00 0.00 0.00 3.10
2757 5591 4.407296 ACTTCCTCTCTCTCTCTCTCTCTC 59.593 50.000 0.00 0.00 0.00 3.20
2758 5592 4.271807 TCCTCTCTCTCTCTCTCTCTCT 57.728 50.000 0.00 0.00 0.00 3.10
2759 5593 4.219115 TCCTCTCTCTCTCTCTCTCTCTC 58.781 52.174 0.00 0.00 0.00 3.20
2760 5594 4.078922 TCCTCTCTCTCTCTCTCTCTCTCT 60.079 50.000 0.00 0.00 0.00 3.10
2761 5595 4.280677 CCTCTCTCTCTCTCTCTCTCTCTC 59.719 54.167 0.00 0.00 0.00 3.20
2762 5596 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
2763 5597 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2764 5598 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2765 5599 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2766 5600 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2767 5601 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2768 5602 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2769 5603 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2770 5604 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2771 5605 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2772 5606 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2773 5607 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2774 5608 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2775 5609 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2776 5610 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2777 5611 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2778 5612 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2779 5613 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2780 5614 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2781 5615 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2782 5616 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2783 5617 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2784 5618 4.871822 TCTCTCTCTCTCTCTCTCTCTCA 58.128 47.826 0.00 0.00 0.00 3.27
2785 5619 5.462240 TCTCTCTCTCTCTCTCTCTCTCAT 58.538 45.833 0.00 0.00 0.00 2.90
2786 5620 6.614657 TCTCTCTCTCTCTCTCTCTCTCATA 58.385 44.000 0.00 0.00 0.00 2.15
2787 5621 6.718912 TCTCTCTCTCTCTCTCTCTCTCATAG 59.281 46.154 0.00 0.00 0.00 2.23
2788 5622 5.777223 TCTCTCTCTCTCTCTCTCTCATAGG 59.223 48.000 0.00 0.00 0.00 2.57
2826 5660 7.373778 AGGACGCTTTATTACTTAAAAGGTG 57.626 36.000 0.00 0.00 34.07 4.00
2830 5665 8.387190 ACGCTTTATTACTTAAAAGGTGAAGT 57.613 30.769 0.00 0.00 39.25 3.01
2847 5682 1.120530 AGTATTACACCCGGCCTCTG 58.879 55.000 0.00 0.00 0.00 3.35
2850 5685 2.536997 ATTACACCCGGCCTCTGCAC 62.537 60.000 0.00 0.00 40.13 4.57
2855 5690 3.052082 CCGGCCTCTGCACAACTG 61.052 66.667 0.00 0.00 40.13 3.16
2886 5722 2.168313 CAGCCAAACCAAGTCCAAGTTT 59.832 45.455 0.00 0.00 34.13 2.66
2946 5789 2.373502 GCCTAAGATGTAAGAGGGCCAT 59.626 50.000 6.18 0.00 32.86 4.40
2974 5817 2.146920 TCATGCTGCCATCCATTTCA 57.853 45.000 0.00 0.00 0.00 2.69
2981 5824 3.181483 GCTGCCATCCATTTCAGGTTAAG 60.181 47.826 0.00 0.00 0.00 1.85
3016 5859 0.673644 GCCTCCAAGCGTGTACACAT 60.674 55.000 24.98 10.65 0.00 3.21
3020 5863 1.893137 TCCAAGCGTGTACACATCTCT 59.107 47.619 24.98 12.82 0.00 3.10
3028 5871 4.625742 GCGTGTACACATCTCTGTAAACAT 59.374 41.667 24.98 0.00 35.36 2.71
3093 5936 9.709495 GGAGTATACCGGTACATCTATAGATAG 57.291 40.741 18.55 11.62 32.63 2.08
3125 5968 9.927668 AGAAGAGAAGAACTTTTATCTCTCTTG 57.072 33.333 14.94 0.00 45.90 3.02
3163 6006 1.336517 TGCGAGTGAGTAAAACTCCCG 60.337 52.381 4.69 6.85 44.44 5.14
3167 6011 0.035739 GTGAGTAAAACTCCCGCCCA 59.964 55.000 4.69 0.00 44.44 5.36
3182 6050 2.530661 CCACCCCACCACCTACCA 60.531 66.667 0.00 0.00 0.00 3.25
3185 6053 3.712907 CCCCACCACCTACCACCG 61.713 72.222 0.00 0.00 0.00 4.94
3191 6059 3.454573 CACCTACCACCGCCGCTA 61.455 66.667 0.00 0.00 0.00 4.26
3273 6142 2.324014 CTGCACCCCTAGCGCCAATA 62.324 60.000 2.29 0.00 33.85 1.90
3275 6144 1.830145 CACCCCTAGCGCCAATACT 59.170 57.895 2.29 0.00 0.00 2.12
3303 6172 2.692557 CCACCATCGGCCATGAATTTTA 59.307 45.455 14.52 0.00 33.80 1.52
3358 6227 1.548357 AACCTCATCGGCAGCAGAGT 61.548 55.000 0.65 0.00 35.61 3.24
3402 6271 5.071788 AGTTCCTTCAGAGTGACCACAATAA 59.928 40.000 2.78 0.00 0.00 1.40
3410 6279 6.042781 TCAGAGTGACCACAATAACTACCTTT 59.957 38.462 2.78 0.00 0.00 3.11
3412 6281 5.937111 AGTGACCACAATAACTACCTTTGT 58.063 37.500 2.78 0.00 34.03 2.83
3414 6283 4.992319 TGACCACAATAACTACCTTTGTCG 59.008 41.667 0.00 0.00 31.48 4.35
3419 6288 5.351465 CACAATAACTACCTTTGTCGAGCAT 59.649 40.000 0.00 0.00 31.48 3.79
3433 6302 1.379843 AGCATACCGGCAAAAGGGG 60.380 57.895 0.00 0.00 35.83 4.79
3434 6303 1.680989 GCATACCGGCAAAAGGGGT 60.681 57.895 0.00 0.00 37.84 4.95
3436 6305 0.034477 CATACCGGCAAAAGGGGTCT 60.034 55.000 0.00 0.00 35.28 3.85
3438 6307 0.479378 TACCGGCAAAAGGGGTCTTT 59.521 50.000 0.00 0.00 44.40 2.52
3439 6308 0.826256 ACCGGCAAAAGGGGTCTTTC 60.826 55.000 0.00 0.00 41.92 2.62
3441 6310 1.862602 CGGCAAAAGGGGTCTTTCGG 61.863 60.000 0.00 0.00 41.92 4.30
3454 6323 1.866853 CTTTCGGTGAAGGCCAAGGC 61.867 60.000 5.01 1.52 41.06 4.35
3455 6324 2.632602 TTTCGGTGAAGGCCAAGGCA 62.633 55.000 13.87 0.00 44.11 4.75
3478 6347 2.475466 CCAACATGGCAGCGCTAGG 61.475 63.158 10.99 0.00 0.00 3.02
3483 6352 2.066393 ATGGCAGCGCTAGGGAAGA 61.066 57.895 10.99 0.00 0.00 2.87
3499 6368 8.961634 GCTAGGGAAGAAAAAGAAGATTATTGT 58.038 33.333 0.00 0.00 0.00 2.71
3503 6372 6.528072 GGAAGAAAAAGAAGATTATTGTGGCG 59.472 38.462 0.00 0.00 0.00 5.69
3607 6478 0.396811 AGGATTATCGCCTTTCCCCG 59.603 55.000 0.00 0.00 29.44 5.73
3608 6479 1.235281 GGATTATCGCCTTTCCCCGC 61.235 60.000 0.00 0.00 0.00 6.13
3627 6498 2.159142 CGCGAGGTAACCCTGAGTTATT 60.159 50.000 0.00 0.00 42.86 1.40
3635 6506 4.675063 AACCCTGAGTTATTGAACCCAT 57.325 40.909 0.00 0.00 36.74 4.00
3637 6508 3.591527 ACCCTGAGTTATTGAACCCATGA 59.408 43.478 0.00 0.00 36.08 3.07
3647 6519 1.168714 GAACCCATGAAGGACTGTGC 58.831 55.000 0.00 0.00 41.22 4.57
3669 6541 4.918588 CCCTTTAAGCTAGGGTCTCAAAA 58.081 43.478 11.49 0.00 46.16 2.44
3711 6583 7.519032 TTAATTTCAACTTTTGACCGGATCT 57.481 32.000 9.46 0.00 39.87 2.75
3730 6602 6.750501 CGGATCTTAAATCGAACTTGACACTA 59.249 38.462 0.00 0.00 0.00 2.74
3775 6648 6.380846 ACATGCATGGTATGTGGTCTTAATTT 59.619 34.615 29.41 0.00 37.38 1.82
3784 6657 7.751793 GGTATGTGGTCTTAATTTTTACAACCG 59.248 37.037 0.00 0.00 0.00 4.44
3825 6698 4.846779 AACATGACCTTAATTTGTGCGT 57.153 36.364 0.00 0.00 0.00 5.24
3826 6699 5.950758 AACATGACCTTAATTTGTGCGTA 57.049 34.783 0.00 0.00 0.00 4.42
3827 6700 5.950758 ACATGACCTTAATTTGTGCGTAA 57.049 34.783 0.00 0.00 0.00 3.18
3828 6701 6.320494 ACATGACCTTAATTTGTGCGTAAA 57.680 33.333 0.00 0.00 0.00 2.01
3829 6702 6.740110 ACATGACCTTAATTTGTGCGTAAAA 58.260 32.000 0.00 0.00 0.00 1.52
3830 6703 7.203910 ACATGACCTTAATTTGTGCGTAAAAA 58.796 30.769 0.00 0.00 0.00 1.94
3831 6704 7.381139 ACATGACCTTAATTTGTGCGTAAAAAG 59.619 33.333 0.00 0.00 0.00 2.27
3832 6705 6.797454 TGACCTTAATTTGTGCGTAAAAAGT 58.203 32.000 0.00 0.00 0.00 2.66
3847 6720 6.293790 GCGTAAAAAGTTGGAAGTCACCTATT 60.294 38.462 0.00 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 2.187599 GACACCCACAAGCATGTCGC 62.188 60.000 0.00 0.00 37.82 5.19
20 21 1.868997 GACACCCACAAGCATGTCG 59.131 57.895 0.00 0.00 37.82 4.35
22 23 2.260869 GCGACACCCACAAGCATGT 61.261 57.895 0.00 0.00 41.61 3.21
23 24 1.518056 AAGCGACACCCACAAGCATG 61.518 55.000 0.00 0.00 0.00 4.06
24 25 1.228245 AAGCGACACCCACAAGCAT 60.228 52.632 0.00 0.00 0.00 3.79
36 37 1.021920 GCCTTCAAGAGGGAAGCGAC 61.022 60.000 1.97 0.00 46.40 5.19
38 39 2.103042 CGCCTTCAAGAGGGAAGCG 61.103 63.158 1.97 0.00 46.40 4.68
51 52 2.280592 GACCCACAACGACGCCTT 60.281 61.111 0.00 0.00 0.00 4.35
75 76 1.480212 TTCACTCGGACATGGCACCT 61.480 55.000 0.00 0.00 0.00 4.00
87 88 3.258622 AGAAGGACTAGGGTTTTCACTCG 59.741 47.826 0.00 0.00 34.26 4.18
139 140 1.187087 GACGTCTCCAAGAGGGTCAT 58.813 55.000 8.70 0.00 35.36 3.06
149 150 0.461548 GCTCCATGATGACGTCTCCA 59.538 55.000 17.92 14.32 0.00 3.86
159 160 2.143419 GGGACCGGAGCTCCATGAT 61.143 63.158 31.67 13.84 35.14 2.45
160 161 2.764128 GGGACCGGAGCTCCATGA 60.764 66.667 31.67 0.00 35.14 3.07
173 174 1.886542 CCTAGTGCAACCAAAAGGGAC 59.113 52.381 0.00 0.00 41.15 4.46
228 229 2.673200 ATGCCAGTCACGGATGCCT 61.673 57.895 0.00 0.00 0.00 4.75
236 237 2.361610 CCACCCCATGCCAGTCAC 60.362 66.667 0.00 0.00 0.00 3.67
285 288 1.227615 GGACCACGGTGAAAACGGA 60.228 57.895 10.28 0.00 35.23 4.69
286 289 0.033781 TAGGACCACGGTGAAAACGG 59.966 55.000 10.28 0.00 35.23 4.44
291 294 1.972198 CTGCTAGGACCACGGTGAA 59.028 57.895 10.28 0.00 0.00 3.18
302 305 2.280660 CCATGGAGCGCTGCTAGG 60.281 66.667 29.46 24.89 39.88 3.02
335 338 2.887738 ATCTCTTGAGAGGGCCGCCT 62.888 60.000 9.86 1.79 42.30 5.52
336 339 2.439104 ATCTCTTGAGAGGGCCGCC 61.439 63.158 2.73 0.00 42.30 6.13
337 340 1.227497 CATCTCTTGAGAGGGCCGC 60.227 63.158 0.00 0.00 42.30 6.53
338 341 1.445095 CCATCTCTTGAGAGGGCCG 59.555 63.158 16.74 0.00 42.30 6.13
341 344 1.134159 CCAAGCCATCTCTTGAGAGGG 60.134 57.143 22.50 22.50 44.61 4.30
342 345 1.558756 ACCAAGCCATCTCTTGAGAGG 59.441 52.381 8.09 5.95 44.61 3.69
343 346 2.027377 ACACCAAGCCATCTCTTGAGAG 60.027 50.000 6.49 1.51 44.61 3.20
344 347 1.980765 ACACCAAGCCATCTCTTGAGA 59.019 47.619 2.59 2.59 44.61 3.27
345 348 2.082231 CACACCAAGCCATCTCTTGAG 58.918 52.381 5.19 0.00 44.61 3.02
346 349 1.421268 ACACACCAAGCCATCTCTTGA 59.579 47.619 5.19 0.00 44.61 3.02
347 350 1.901591 ACACACCAAGCCATCTCTTG 58.098 50.000 0.00 0.00 42.23 3.02
348 351 2.508526 GAACACACCAAGCCATCTCTT 58.491 47.619 0.00 0.00 0.00 2.85
349 352 1.609061 CGAACACACCAAGCCATCTCT 60.609 52.381 0.00 0.00 0.00 3.10
350 353 0.798776 CGAACACACCAAGCCATCTC 59.201 55.000 0.00 0.00 0.00 2.75
351 354 0.396435 TCGAACACACCAAGCCATCT 59.604 50.000 0.00 0.00 0.00 2.90
352 355 1.453155 ATCGAACACACCAAGCCATC 58.547 50.000 0.00 0.00 0.00 3.51
353 356 2.290008 TGTATCGAACACACCAAGCCAT 60.290 45.455 0.00 0.00 31.43 4.40
354 357 1.070914 TGTATCGAACACACCAAGCCA 59.929 47.619 0.00 0.00 31.43 4.75
372 375 4.922026 GCCACCGGACACCGTTGT 62.922 66.667 9.46 0.00 46.80 3.32
384 387 3.732849 CCCCCTTGAGAGGCCACC 61.733 72.222 5.01 0.00 42.09 4.61
425 428 2.227194 CACACCTAACAGAACCAACCC 58.773 52.381 0.00 0.00 0.00 4.11
458 461 2.483877 TCAACTTAATGCCGAGCACAAG 59.516 45.455 14.81 14.81 43.04 3.16
460 463 2.177394 TCAACTTAATGCCGAGCACA 57.823 45.000 0.50 0.00 43.04 4.57
555 558 0.523072 ACAAAGTGACATCGCCATGC 59.477 50.000 0.00 0.00 32.57 4.06
557 560 2.183478 TCACAAAGTGACATCGCCAT 57.817 45.000 0.00 0.00 37.67 4.40
558 561 2.076100 GATCACAAAGTGACATCGCCA 58.924 47.619 1.43 0.00 45.65 5.69
575 578 4.023792 TGCAACTCATGTCACTTTGTGATC 60.024 41.667 3.65 0.00 44.63 2.92
577 580 3.277715 TGCAACTCATGTCACTTTGTGA 58.722 40.909 0.00 0.00 40.50 3.58
578 581 3.313249 TCTGCAACTCATGTCACTTTGTG 59.687 43.478 0.00 0.00 34.45 3.33
580 583 4.761235 ATCTGCAACTCATGTCACTTTG 57.239 40.909 0.00 0.00 0.00 2.77
581 584 6.175471 TGATATCTGCAACTCATGTCACTTT 58.825 36.000 3.98 0.00 0.00 2.66
582 585 5.737860 TGATATCTGCAACTCATGTCACTT 58.262 37.500 3.98 0.00 0.00 3.16
607 2631 2.170607 GGTAAGGATCAGCTACTTGCCA 59.829 50.000 16.35 0.00 43.64 4.92
657 2689 6.309737 CCAAAAGAAAAGCATCTATCAACAGC 59.690 38.462 0.00 0.00 0.00 4.40
706 2738 1.421382 CAATCAAAGCAAGGCAACGG 58.579 50.000 0.00 0.00 46.39 4.44
745 2778 3.934962 TGCGTGCCTGTGCCTGTA 61.935 61.111 0.00 0.00 36.33 2.74
750 2783 3.862063 CTTTCGTGCGTGCCTGTGC 62.862 63.158 0.00 0.00 38.26 4.57
780 2817 9.543783 TGTAGGTTTGTTTTAACTTTGTTGTTT 57.456 25.926 0.00 0.00 0.00 2.83
781 2818 8.980610 GTGTAGGTTTGTTTTAACTTTGTTGTT 58.019 29.630 0.00 0.00 0.00 2.83
805 2842 3.569701 ACCTTTCTGGCTGTGTAATTGTG 59.430 43.478 0.00 0.00 40.22 3.33
858 2895 9.503427 GCTTCTATTGCGTCAAATTAAGTTAAT 57.497 29.630 2.10 2.10 0.00 1.40
963 3000 4.663166 CGGTTGCTCGATGGACTATATAG 58.337 47.826 8.27 8.27 0.00 1.31
994 3031 3.353557 TGTCAGTAAGAGTAGTGGCGAT 58.646 45.455 0.00 0.00 37.99 4.58
995 3032 2.786777 TGTCAGTAAGAGTAGTGGCGA 58.213 47.619 0.00 0.00 37.99 5.54
996 3033 3.784701 ATGTCAGTAAGAGTAGTGGCG 57.215 47.619 0.00 0.00 37.99 5.69
997 3034 6.642707 ATCTATGTCAGTAAGAGTAGTGGC 57.357 41.667 0.00 0.00 36.05 5.01
1015 3052 3.322254 CACCACGGCCTTCTTCTATCTAT 59.678 47.826 0.00 0.00 0.00 1.98
1019 3056 0.107654 GCACCACGGCCTTCTTCTAT 60.108 55.000 0.00 0.00 0.00 1.98
1055 3092 2.237143 TCGTCTCCATGCTTCCTTCAAT 59.763 45.455 0.00 0.00 0.00 2.57
1114 3154 2.949106 CTGTGCGCCAGGTTGAAG 59.051 61.111 15.59 0.00 37.54 3.02
1139 3179 8.414778 AGATTCTAAGGAAACGATCGAGTAATT 58.585 33.333 24.34 12.71 34.90 1.40
1146 3186 4.508124 CCCAAGATTCTAAGGAAACGATCG 59.492 45.833 14.88 14.88 34.90 3.69
1147 3187 5.429130 ACCCAAGATTCTAAGGAAACGATC 58.571 41.667 8.51 0.00 34.90 3.69
1149 3189 4.619863 CGACCCAAGATTCTAAGGAAACGA 60.620 45.833 8.51 0.00 34.90 3.85
1151 3191 3.374367 GCGACCCAAGATTCTAAGGAAAC 59.626 47.826 8.51 0.00 34.90 2.78
1152 3192 3.263425 AGCGACCCAAGATTCTAAGGAAA 59.737 43.478 8.51 0.00 34.90 3.13
1153 3193 2.838202 AGCGACCCAAGATTCTAAGGAA 59.162 45.455 8.51 0.00 35.78 3.36
1154 3194 2.168521 CAGCGACCCAAGATTCTAAGGA 59.831 50.000 8.51 0.00 0.00 3.36
1155 3195 2.168521 TCAGCGACCCAAGATTCTAAGG 59.831 50.000 0.00 1.29 0.00 2.69
1157 3197 3.260884 ACTTCAGCGACCCAAGATTCTAA 59.739 43.478 0.00 0.00 0.00 2.10
1160 3200 1.734465 CACTTCAGCGACCCAAGATTC 59.266 52.381 0.00 0.00 0.00 2.52
1161 3201 1.347707 TCACTTCAGCGACCCAAGATT 59.652 47.619 0.00 0.00 0.00 2.40
1162 3202 0.976641 TCACTTCAGCGACCCAAGAT 59.023 50.000 0.00 0.00 0.00 2.40
1163 3203 0.033504 GTCACTTCAGCGACCCAAGA 59.966 55.000 0.00 0.00 0.00 3.02
1164 3204 1.284982 CGTCACTTCAGCGACCCAAG 61.285 60.000 0.00 0.00 0.00 3.61
1167 3207 3.112709 GCGTCACTTCAGCGACCC 61.113 66.667 0.00 0.00 0.00 4.46
1173 3213 2.434884 ATGGCCGCGTCACTTCAG 60.435 61.111 4.92 0.00 0.00 3.02
1174 3214 2.741985 CATGGCCGCGTCACTTCA 60.742 61.111 4.92 0.00 0.00 3.02
1175 3215 3.499737 CCATGGCCGCGTCACTTC 61.500 66.667 4.92 0.00 0.00 3.01
1176 3216 4.329545 ACCATGGCCGCGTCACTT 62.330 61.111 13.04 0.00 0.00 3.16
1196 3236 4.264638 AACCCTGCGTTGCGTTGC 62.265 61.111 0.00 0.00 31.79 4.17
1471 3511 1.546589 ATGTTCTACCGGTGGGCGAA 61.547 55.000 19.93 11.56 36.48 4.70
1517 3560 5.311265 ACACGATAGGTACGAGGATAATCA 58.689 41.667 0.00 0.00 43.77 2.57
1556 3606 5.657470 TTGAGACTTGACACTTTGATTCG 57.343 39.130 0.00 0.00 0.00 3.34
1589 3639 2.636830 CCATTAGGCTGGAACTCTGTG 58.363 52.381 0.00 0.00 38.69 3.66
1702 3754 1.152819 TGGGGTATCTCCTCCGTCG 60.153 63.158 0.00 0.00 35.35 5.12
1761 3813 4.084013 GGTTGATCATTAATTACCGGCTCG 60.084 45.833 0.00 0.00 0.00 5.03
1787 3839 0.035056 GAGGACTGTTGGGGACATGG 60.035 60.000 0.00 0.00 42.32 3.66
1797 3849 5.470047 ACGTAGAAAAGATGAGGACTGTT 57.530 39.130 0.00 0.00 0.00 3.16
1822 3874 1.788308 TCAGCGTTGCAAACTACGTAC 59.212 47.619 0.00 0.00 46.99 3.67
1823 3875 2.137129 TCAGCGTTGCAAACTACGTA 57.863 45.000 0.00 0.00 46.99 3.57
1824 3876 1.459592 GATCAGCGTTGCAAACTACGT 59.540 47.619 0.00 0.00 46.99 3.57
1825 3877 1.459209 TGATCAGCGTTGCAAACTACG 59.541 47.619 0.00 1.67 46.99 3.51
2243 4295 2.768492 CCTTCCTCCCGGTCGTACG 61.768 68.421 9.53 9.53 0.00 3.67
2289 4341 1.876714 CCCGTACGCCACAAGATCG 60.877 63.158 10.49 0.00 0.00 3.69
2332 4384 1.604604 CTTTTGAACCTCTCCGGCAA 58.395 50.000 0.00 0.00 35.61 4.52
2348 4400 0.321653 ATTCAGAGCGGCGTTCCTTT 60.322 50.000 20.21 0.00 0.00 3.11
2349 4401 0.535335 TATTCAGAGCGGCGTTCCTT 59.465 50.000 20.21 0.00 0.00 3.36
2358 4410 5.188327 TCCTGTCATACTTATTCAGAGCG 57.812 43.478 0.00 0.00 0.00 5.03
2397 4449 0.250124 TGTAGCCAACAACAGGGTCG 60.250 55.000 0.00 0.00 38.04 4.79
2400 4452 1.234615 CGGTGTAGCCAACAACAGGG 61.235 60.000 5.75 0.00 46.97 4.45
2438 4490 3.456277 CCAACCAGTTAGCTAATCCTCCT 59.544 47.826 9.88 0.00 0.00 3.69
2466 5061 2.710724 AAGTCCCAAGCACGACGACC 62.711 60.000 0.00 0.00 34.10 4.79
2469 5064 2.317609 CCAAGTCCCAAGCACGACG 61.318 63.158 0.00 0.00 34.10 5.12
2566 5161 3.580895 ACACCACATAAAAACATTCCCCC 59.419 43.478 0.00 0.00 0.00 5.40
2656 5260 4.401022 TCTTCAAGTTGGCTCAACATCAT 58.599 39.130 16.93 2.09 45.66 2.45
2658 5262 5.163713 GGTATCTTCAAGTTGGCTCAACATC 60.164 44.000 16.93 0.00 45.66 3.06
2659 5263 4.702131 GGTATCTTCAAGTTGGCTCAACAT 59.298 41.667 16.93 5.65 45.66 2.71
2661 5265 3.440522 GGGTATCTTCAAGTTGGCTCAAC 59.559 47.826 2.34 9.31 43.83 3.18
2662 5266 3.330701 AGGGTATCTTCAAGTTGGCTCAA 59.669 43.478 2.34 0.00 0.00 3.02
2675 5508 4.105858 GGCCTTTTGGGTATAGGGTATCTT 59.894 45.833 0.00 0.00 40.82 2.40
2683 5516 5.738619 AAGTTTTGGCCTTTTGGGTATAG 57.261 39.130 3.32 0.00 40.82 1.31
2724 5557 4.240323 AGAGAGAGGAAGTTTTTGGGGTA 58.760 43.478 0.00 0.00 0.00 3.69
2738 5572 4.222336 AGAGAGAGAGAGAGAGAGAGAGG 58.778 52.174 0.00 0.00 0.00 3.69
2740 5574 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2742 5576 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2745 5579 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2747 5581 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2753 5587 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2754 5588 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2755 5589 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2756 5590 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2757 5591 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2758 5592 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2759 5593 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2760 5594 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
2761 5595 4.892345 TGAGAGAGAGAGAGAGAGAGAGAG 59.108 50.000 0.00 0.00 0.00 3.20
2762 5596 4.871822 TGAGAGAGAGAGAGAGAGAGAGA 58.128 47.826 0.00 0.00 0.00 3.10
2763 5597 5.804944 ATGAGAGAGAGAGAGAGAGAGAG 57.195 47.826 0.00 0.00 0.00 3.20
2764 5598 5.777223 CCTATGAGAGAGAGAGAGAGAGAGA 59.223 48.000 0.00 0.00 0.00 3.10
2765 5599 5.541868 ACCTATGAGAGAGAGAGAGAGAGAG 59.458 48.000 0.00 0.00 0.00 3.20
2766 5600 5.467738 ACCTATGAGAGAGAGAGAGAGAGA 58.532 45.833 0.00 0.00 0.00 3.10
2767 5601 5.815233 ACCTATGAGAGAGAGAGAGAGAG 57.185 47.826 0.00 0.00 0.00 3.20
2768 5602 6.575244 AAACCTATGAGAGAGAGAGAGAGA 57.425 41.667 0.00 0.00 0.00 3.10
2769 5603 7.645058 AAAAACCTATGAGAGAGAGAGAGAG 57.355 40.000 0.00 0.00 0.00 3.20
2802 5636 7.163441 TCACCTTTTAAGTAATAAAGCGTCCT 58.837 34.615 0.00 0.00 35.03 3.85
2803 5637 7.368480 TCACCTTTTAAGTAATAAAGCGTCC 57.632 36.000 0.00 0.00 35.03 4.79
2805 5639 8.387190 ACTTCACCTTTTAAGTAATAAAGCGT 57.613 30.769 0.00 0.00 35.03 5.07
2826 5660 1.761198 AGAGGCCGGGTGTAATACTTC 59.239 52.381 2.18 0.00 0.00 3.01
2830 5665 0.978667 TGCAGAGGCCGGGTGTAATA 60.979 55.000 2.18 0.00 40.13 0.98
2840 5675 0.035630 ATCTCAGTTGTGCAGAGGCC 60.036 55.000 0.00 0.00 40.13 5.19
2847 5682 0.946528 TGTGTGCATCTCAGTTGTGC 59.053 50.000 0.00 0.00 39.26 4.57
2850 5685 0.520404 GGCTGTGTGCATCTCAGTTG 59.480 55.000 15.08 0.00 45.15 3.16
2855 5690 0.242017 GGTTTGGCTGTGTGCATCTC 59.758 55.000 0.00 0.00 45.15 2.75
2924 5767 1.270358 GGCCCTCTTACATCTTAGGCG 60.270 57.143 0.00 0.00 39.87 5.52
2937 5780 0.761802 GATCTTCGGAATGGCCCTCT 59.238 55.000 0.00 0.00 0.00 3.69
2946 5789 0.252761 TGGCAGCATGATCTTCGGAA 59.747 50.000 0.00 0.00 39.69 4.30
3016 5859 6.404844 GGAGAATCGAGACATGTTTACAGAGA 60.405 42.308 0.00 0.00 34.37 3.10
3020 5863 5.168569 GTGGAGAATCGAGACATGTTTACA 58.831 41.667 0.00 0.00 34.37 2.41
3028 5871 3.006859 ACAACATGTGGAGAATCGAGACA 59.993 43.478 7.39 0.00 34.37 3.41
3093 5936 8.038351 AGATAAAAGTTCTTCTCTTCTGTAGGC 58.962 37.037 0.00 0.00 0.00 3.93
3125 5968 0.248458 CATGGCCGCGAACCAAATAC 60.248 55.000 22.05 0.00 41.49 1.89
3163 6006 4.043100 GTAGGTGGTGGGGTGGGC 62.043 72.222 0.00 0.00 0.00 5.36
3167 6011 2.530916 GGTGGTAGGTGGTGGGGT 60.531 66.667 0.00 0.00 0.00 4.95
3203 6071 4.995058 AGGGAAGGGTTGGCCGGA 62.995 66.667 5.05 0.00 34.97 5.14
3204 6072 4.740822 CAGGGAAGGGTTGGCCGG 62.741 72.222 0.00 0.00 34.97 6.13
3273 6142 1.990060 CCGATGGTGGGTCTCCAGT 60.990 63.158 0.00 0.00 45.05 4.00
3275 6144 3.399181 GCCGATGGTGGGTCTCCA 61.399 66.667 0.00 0.00 41.58 3.86
3402 6271 2.159282 CGGTATGCTCGACAAAGGTAGT 60.159 50.000 0.00 0.00 0.00 2.73
3410 6279 0.320858 TTTTGCCGGTATGCTCGACA 60.321 50.000 1.90 0.00 0.00 4.35
3412 6281 0.742990 CCTTTTGCCGGTATGCTCGA 60.743 55.000 1.90 0.00 0.00 4.04
3414 6283 1.384222 CCCCTTTTGCCGGTATGCTC 61.384 60.000 1.90 0.00 0.00 4.26
3419 6288 0.479378 AAAGACCCCTTTTGCCGGTA 59.521 50.000 1.90 0.00 39.45 4.02
3433 6302 0.875059 CTTGGCCTTCACCGAAAGAC 59.125 55.000 3.32 0.00 0.00 3.01
3434 6303 0.250727 CCTTGGCCTTCACCGAAAGA 60.251 55.000 3.32 0.00 0.00 2.52
3436 6305 1.901464 GCCTTGGCCTTCACCGAAA 60.901 57.895 3.32 0.00 0.00 3.46
3438 6307 3.551496 CTGCCTTGGCCTTCACCGA 62.551 63.158 3.32 0.00 0.00 4.69
3439 6308 3.058160 CTGCCTTGGCCTTCACCG 61.058 66.667 3.32 0.00 0.00 4.94
3441 6310 3.741476 CGCTGCCTTGGCCTTCAC 61.741 66.667 3.32 0.00 0.00 3.18
3476 6345 7.310052 GCCACAATAATCTTCTTTTTCTTCCCT 60.310 37.037 0.00 0.00 0.00 4.20
3478 6347 6.528072 CGCCACAATAATCTTCTTTTTCTTCC 59.472 38.462 0.00 0.00 0.00 3.46
3483 6352 5.856455 CGTTCGCCACAATAATCTTCTTTTT 59.144 36.000 0.00 0.00 0.00 1.94
3539 6408 4.098196 GGAAGTAATCAAGTAGACCTCGCT 59.902 45.833 0.00 0.00 0.00 4.93
3546 6415 7.311092 TCACCAAAGGAAGTAATCAAGTAGA 57.689 36.000 0.00 0.00 0.00 2.59
3603 6473 4.157120 CAGGGTTACCTCGCGGGG 62.157 72.222 27.07 27.07 46.95 5.73
3607 6478 3.118884 TCAATAACTCAGGGTTACCTCGC 60.119 47.826 0.00 0.00 46.95 5.03
3608 6479 4.730949 TCAATAACTCAGGGTTACCTCG 57.269 45.455 0.00 0.00 46.95 4.63
3627 6498 1.545428 GCACAGTCCTTCATGGGTTCA 60.545 52.381 0.00 0.00 36.20 3.18
3635 6506 2.814097 GCTTAAAGGGCACAGTCCTTCA 60.814 50.000 3.02 0.00 45.35 3.02
3696 6568 5.484715 TCGATTTAAGATCCGGTCAAAAGT 58.515 37.500 0.00 0.00 0.00 2.66
3711 6583 9.493206 GTGTTTTTAGTGTCAAGTTCGATTTAA 57.507 29.630 0.00 0.00 0.00 1.52
3797 6670 7.377398 CACAAATTAAGGTCATGTTTGATCCA 58.623 34.615 9.03 0.00 33.08 3.41
3806 6679 7.381139 ACTTTTTACGCACAAATTAAGGTCATG 59.619 33.333 0.00 0.00 0.00 3.07
3811 6684 6.697892 TCCAACTTTTTACGCACAAATTAAGG 59.302 34.615 0.00 0.00 0.00 2.69
3826 6699 8.990163 TCTTAATAGGTGACTTCCAACTTTTT 57.010 30.769 0.00 0.00 40.69 1.94
3827 6700 9.014297 CATCTTAATAGGTGACTTCCAACTTTT 57.986 33.333 0.00 0.00 40.69 2.27
3828 6701 8.164070 ACATCTTAATAGGTGACTTCCAACTTT 58.836 33.333 0.00 0.00 40.69 2.66
3829 6702 7.607991 CACATCTTAATAGGTGACTTCCAACTT 59.392 37.037 0.00 0.00 40.69 2.66
3830 6703 7.106239 CACATCTTAATAGGTGACTTCCAACT 58.894 38.462 0.00 0.00 46.42 3.16
3831 6704 6.183360 GCACATCTTAATAGGTGACTTCCAAC 60.183 42.308 9.52 0.00 43.67 3.77
3832 6705 5.880332 GCACATCTTAATAGGTGACTTCCAA 59.120 40.000 9.52 0.00 43.67 3.53
3847 6720 7.549134 ACTTCGATTCATAACAAGCACATCTTA 59.451 33.333 0.00 0.00 32.74 2.10


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

AutoCloner maintained by Alex Coulton.