Multiple sequence alignment - TraesCS2A01G104500

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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 TraesCS2A01G104500 chr2A 100.000 3953 0 0 1 3953 57833074 57829122 0.000000e+00 7300.0
1 TraesCS2A01G104500 chr2A 100.000 49 0 0 3143 3191 57829511 57829463 1.510000e-14 91.6
2 TraesCS2A01G104500 chr2A 100.000 49 0 0 3564 3612 57829932 57829884 1.510000e-14 91.6
3 TraesCS2A01G104500 chr2B 94.760 3130 119 22 1 3109 88933623 88930518 0.000000e+00 4830.0
4 TraesCS2A01G104500 chr2B 95.374 281 10 2 3674 3953 88930486 88930208 1.010000e-120 444.0
5 TraesCS2A01G104500 chr2B 95.333 150 6 1 2625 2773 88919415 88919266 1.840000e-58 237.0
6 TraesCS2A01G104500 chr2B 100.000 85 0 0 2865 2949 88919242 88919158 1.470000e-34 158.0
7 TraesCS2A01G104500 chr2B 92.500 80 6 0 2425 2504 88919512 88919433 8.980000e-22 115.0
8 TraesCS2A01G104500 chr2D 94.728 3130 113 20 2 3109 56203777 56200678 0.000000e+00 4819.0
9 TraesCS2A01G104500 chr2D 91.718 326 12 4 2625 2949 56191454 56191143 4.690000e-119 438.0
10 TraesCS2A01G104500 chr2D 94.942 257 6 4 3200 3452 56199933 56199680 2.860000e-106 396.0
11 TraesCS2A01G104500 chr2D 94.624 186 7 1 3622 3804 56197167 56196982 6.470000e-73 285.0
12 TraesCS2A01G104500 chr2D 87.500 152 5 1 3802 3953 56196745 56196608 3.160000e-36 163.0
13 TraesCS2A01G104500 chr2D 91.429 105 9 0 2400 2504 56191576 56191472 1.140000e-30 145.0
14 TraesCS2A01G104500 chr4D 78.397 574 114 9 1097 1665 300783435 300784003 8.070000e-97 364.0
15 TraesCS2A01G104500 chr4D 88.889 72 6 1 3132 3201 207367304 207367375 1.960000e-13 87.9
16 TraesCS2A01G104500 chr4B 78.049 574 116 9 1097 1665 373981844 373982412 1.750000e-93 353.0
17 TraesCS2A01G104500 chr6B 89.862 217 19 2 3200 3416 35377243 35377030 3.890000e-70 276.0
18 TraesCS2A01G104500 chr6B 95.745 47 2 0 3419 3465 91201199 91201245 4.240000e-10 76.8
19 TraesCS2A01G104500 chr6A 88.479 217 22 2 3200 3416 19830319 19830532 3.920000e-65 259.0
20 TraesCS2A01G104500 chr6A 90.625 64 6 0 3419 3482 19830578 19830641 7.040000e-13 86.1
21 TraesCS2A01G104500 chr6A 92.453 53 4 0 3425 3477 51478680 51478628 4.240000e-10 76.8
22 TraesCS2A01G104500 chr5A 94.286 70 2 1 3132 3199 164646106 164646175 5.400000e-19 106.0
23 TraesCS2A01G104500 chr5A 95.918 49 2 0 3561 3609 164646114 164646162 3.270000e-11 80.5
24 TraesCS2A01G104500 chr7D 92.857 70 2 2 3132 3199 398875479 398875411 9.040000e-17 99.0
25 TraesCS2A01G104500 chr7D 94.000 50 1 1 3565 3612 398875468 398875419 1.520000e-09 75.0
26 TraesCS2A01G104500 chr6D 91.525 59 5 0 3419 3477 39489961 39490019 9.100000e-12 82.4
27 TraesCS2A01G104500 chr6D 91.071 56 5 0 3425 3480 39672035 39671980 4.240000e-10 76.8


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 TraesCS2A01G104500 chr2A 57829122 57833074 3952 True 2494.40 7300 100.0000 1 3953 3 chr2A.!!$R1 3952
1 TraesCS2A01G104500 chr2B 88930208 88933623 3415 True 2637.00 4830 95.0670 1 3953 2 chr2B.!!$R2 3952
2 TraesCS2A01G104500 chr2D 56196608 56203777 7169 True 1415.75 4819 92.9485 2 3953 4 chr2D.!!$R2 3951
3 TraesCS2A01G104500 chr4D 300783435 300784003 568 False 364.00 364 78.3970 1097 1665 1 chr4D.!!$F2 568
4 TraesCS2A01G104500 chr4B 373981844 373982412 568 False 353.00 353 78.0490 1097 1665 1 chr4B.!!$F1 568

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
28 34 0.389166 GGCTGAGTCGAGGTGTTGAG 60.389 60.000 0.00 0.0 0.00 3.02 F
393 405 0.471617 GGCCAGTGATAGGTGCTGAT 59.528 55.000 0.00 0.0 32.39 2.90 F
406 418 1.450134 GCTGATGGTCGGTGATGCA 60.450 57.895 0.00 0.0 0.00 3.96 F
2129 2143 2.409948 AGGCCATGCTAACTGACTTC 57.590 50.000 5.01 0.0 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1691 1705 2.358898 ACCAAGATATGAATGCCAACGC 59.641 45.455 0.00 0.0 0.00 4.84 R
2129 2143 0.179163 GGAATTCTTTCGCAAGGCCG 60.179 55.000 5.23 0.0 38.47 6.13 R
2390 2404 3.808728 CTGAACTTTGTCTCTGTTCCCA 58.191 45.455 0.00 0.0 39.24 4.37 R
3125 3152 0.038890 AAAGGAGCAGAGAAAGGGCC 59.961 55.000 0.00 0.0 0.00 5.80 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
28 34 0.389166 GGCTGAGTCGAGGTGTTGAG 60.389 60.000 0.00 0.00 0.00 3.02
39 45 0.673644 GGTGTTGAGCATAGCGTGGT 60.674 55.000 0.00 0.00 42.28 4.16
47 53 1.070758 AGCATAGCGTGGTTAGGATGG 59.929 52.381 0.00 0.00 34.12 3.51
51 57 1.120530 AGCGTGGTTAGGATGGTAGG 58.879 55.000 0.00 0.00 0.00 3.18
54 60 2.104281 GCGTGGTTAGGATGGTAGGATT 59.896 50.000 0.00 0.00 0.00 3.01
55 61 3.728845 CGTGGTTAGGATGGTAGGATTG 58.271 50.000 0.00 0.00 0.00 2.67
56 62 3.134081 CGTGGTTAGGATGGTAGGATTGT 59.866 47.826 0.00 0.00 0.00 2.71
57 63 4.451900 GTGGTTAGGATGGTAGGATTGTG 58.548 47.826 0.00 0.00 0.00 3.33
58 64 3.458118 TGGTTAGGATGGTAGGATTGTGG 59.542 47.826 0.00 0.00 0.00 4.17
59 65 3.714798 GGTTAGGATGGTAGGATTGTGGA 59.285 47.826 0.00 0.00 0.00 4.02
60 66 4.165372 GGTTAGGATGGTAGGATTGTGGAA 59.835 45.833 0.00 0.00 0.00 3.53
61 67 5.368989 GTTAGGATGGTAGGATTGTGGAAG 58.631 45.833 0.00 0.00 0.00 3.46
80 86 5.894393 TGGAAGTTGGAAGTACAATTTTGGA 59.106 36.000 0.00 0.00 31.57 3.53
91 97 4.237349 ACAATTTTGGACTAAAGGCACG 57.763 40.909 0.00 0.00 0.00 5.34
92 98 3.634910 ACAATTTTGGACTAAAGGCACGT 59.365 39.130 0.00 0.00 0.00 4.49
162 174 7.931948 TCTGGAAGTAACTTTCGAGAAATCTTT 59.068 33.333 0.00 0.00 38.46 2.52
167 179 8.312896 AGTAACTTTCGAGAAATCTTTTCTCC 57.687 34.615 19.17 7.20 41.31 3.71
171 183 6.992715 ACTTTCGAGAAATCTTTTCTCCTTGA 59.007 34.615 19.17 11.16 41.31 3.02
186 198 5.121811 TCTCCTTGATAGATTGCAAAGCTC 58.878 41.667 1.71 0.00 38.98 4.09
187 199 4.202441 TCCTTGATAGATTGCAAAGCTCC 58.798 43.478 1.71 1.18 38.98 4.70
190 202 2.947652 TGATAGATTGCAAAGCTCCAGC 59.052 45.455 1.71 0.00 38.98 4.85
206 218 1.846261 AGCTTCCTTGTGCTGGGAA 59.154 52.632 0.00 0.00 38.21 3.97
228 240 6.594159 GGAATTTAGTACACTATGCACACTGT 59.406 38.462 0.00 0.00 0.00 3.55
229 241 7.119262 GGAATTTAGTACACTATGCACACTGTT 59.881 37.037 0.00 0.00 0.00 3.16
230 242 7.596749 ATTTAGTACACTATGCACACTGTTC 57.403 36.000 0.00 0.00 0.00 3.18
231 243 4.600692 AGTACACTATGCACACTGTTCA 57.399 40.909 0.00 0.00 0.00 3.18
232 244 4.307432 AGTACACTATGCACACTGTTCAC 58.693 43.478 0.00 0.00 0.00 3.18
233 245 3.475566 ACACTATGCACACTGTTCACT 57.524 42.857 0.00 0.00 0.00 3.41
234 246 3.133691 ACACTATGCACACTGTTCACTG 58.866 45.455 0.00 0.00 0.00 3.66
253 265 1.144708 TGTTCAGGATGTTTGAGGGCA 59.855 47.619 0.00 0.00 37.40 5.36
255 267 2.827921 GTTCAGGATGTTTGAGGGCATT 59.172 45.455 0.00 0.00 37.40 3.56
299 311 3.625649 TGCAGTGATGCACCTTACATA 57.374 42.857 0.00 0.00 40.23 2.29
329 341 1.086634 GTGAAGCCGCAGAGTCATCC 61.087 60.000 0.00 0.00 0.00 3.51
383 395 2.097825 GCTTCAAATGAGGCCAGTGAT 58.902 47.619 5.01 0.00 40.74 3.06
393 405 0.471617 GGCCAGTGATAGGTGCTGAT 59.528 55.000 0.00 0.00 32.39 2.90
394 406 1.590932 GCCAGTGATAGGTGCTGATG 58.409 55.000 0.00 0.00 32.39 3.07
406 418 1.450134 GCTGATGGTCGGTGATGCA 60.450 57.895 0.00 0.00 0.00 3.96
452 464 6.605594 TCAACTGATTGTCCCTTAGTTTTGTT 59.394 34.615 0.00 0.00 37.11 2.83
684 698 7.119387 TCTTCCAATACTAGATGAGACTGACA 58.881 38.462 0.00 0.00 0.00 3.58
950 964 6.311690 GCAGGAGTCATTAGTTTCAGTAAGTC 59.688 42.308 0.00 0.00 0.00 3.01
1188 1202 4.949856 ACAGAACTTTGTGTTGTTGATCCT 59.050 37.500 0.00 0.00 39.30 3.24
1356 1370 5.664908 AGATGGATCATCAGAACTTGTAGGT 59.335 40.000 10.08 0.00 42.72 3.08
1669 1683 4.141914 GGTACTCCTTTCAGGTAGGTCATG 60.142 50.000 0.00 0.00 36.53 3.07
1691 1705 9.918630 TCATGTGTATACATATTGTCATCTCTG 57.081 33.333 12.01 0.24 45.53 3.35
1857 1871 9.646427 TTTCACTTGTTAGTAATTTTGTTTGCT 57.354 25.926 0.00 0.00 31.96 3.91
2046 2060 5.695816 GCCATGTAAGAATTCTTTGTTGCAA 59.304 36.000 25.02 3.28 35.08 4.08
2067 2081 3.028130 ACCAACAATCCCGTTTTGTCTT 58.972 40.909 0.00 0.00 36.32 3.01
2073 2087 4.887655 ACAATCCCGTTTTGTCTTCTCTTT 59.112 37.500 0.00 0.00 31.87 2.52
2075 2089 4.145365 TCCCGTTTTGTCTTCTCTTTGA 57.855 40.909 0.00 0.00 0.00 2.69
2129 2143 2.409948 AGGCCATGCTAACTGACTTC 57.590 50.000 5.01 0.00 0.00 3.01
2390 2404 2.026945 CTTTGCAGCCCCCGTTTGTT 62.027 55.000 0.00 0.00 0.00 2.83
2459 2473 3.071167 AGCTTCCTCCGTTTTTGACTAGT 59.929 43.478 0.00 0.00 0.00 2.57
2465 2479 4.058817 CTCCGTTTTTGACTAGTGAAGCT 58.941 43.478 0.00 0.00 0.00 3.74
2496 2510 3.562557 GCTGAAAGGAGTACGTTTTCCAA 59.437 43.478 17.23 3.06 35.88 3.53
2540 2554 7.555965 ACATCATGTAGTAACTCATAGCACAA 58.444 34.615 0.00 0.00 0.00 3.33
2551 2565 9.976511 GTAACTCATAGCACAAATAGTACCATA 57.023 33.333 0.00 0.00 0.00 2.74
2591 2609 4.326504 AAAAACAGCATGAGGGAAACTG 57.673 40.909 0.00 0.00 39.69 3.16
2593 2611 0.610232 ACAGCATGAGGGAAACTGGC 60.610 55.000 0.00 0.00 39.69 4.85
2613 2632 8.051901 ACTGGCCAGTTAACTGTTTTATTATC 57.948 34.615 33.20 11.23 42.27 1.75
2614 2633 7.888546 ACTGGCCAGTTAACTGTTTTATTATCT 59.111 33.333 33.20 2.63 42.27 1.98
2649 2668 3.425577 TTTCAGTTGCTGCACAAAGAG 57.574 42.857 0.00 0.00 40.82 2.85
2699 2718 1.797713 CGGCAGCGACGAGATAAAGAA 60.798 52.381 0.00 0.00 35.20 2.52
2743 2762 3.706373 GGAGGAAGCTGGACGCCA 61.706 66.667 0.00 0.00 40.39 5.69
2965 2988 1.208052 CTAGCTAGGCTGCAAGGTTCA 59.792 52.381 13.32 0.00 40.10 3.18
2975 2998 1.071605 GCAAGGTTCACTCTAGTGCG 58.928 55.000 5.21 0.00 45.25 5.34
3058 3083 7.389232 TGGCCTGTATGATGTATAGATTCTTG 58.611 38.462 3.32 0.00 0.00 3.02
3110 3137 4.955811 TTGGAAACAGAGAGCAACTAGA 57.044 40.909 0.00 0.00 44.54 2.43
3111 3138 4.527509 TGGAAACAGAGAGCAACTAGAG 57.472 45.455 0.00 0.00 35.01 2.43
3113 3140 4.588951 TGGAAACAGAGAGCAACTAGAGAA 59.411 41.667 0.00 0.00 35.01 2.87
3114 3141 5.167845 GGAAACAGAGAGCAACTAGAGAAG 58.832 45.833 0.00 0.00 0.00 2.85
3116 3143 9.044290 TGGAAACAGAGAGCAACTAGAGAAGTT 62.044 40.741 0.00 0.00 42.06 2.66
3127 3154 2.734276 AGAGAAGTTGAGAAGTCGGC 57.266 50.000 0.00 0.00 0.00 5.54
3128 3155 1.273886 AGAGAAGTTGAGAAGTCGGCC 59.726 52.381 0.00 0.00 0.00 6.13
3129 3156 0.321996 AGAAGTTGAGAAGTCGGCCC 59.678 55.000 0.00 0.00 0.00 5.80
3131 3158 0.765510 AAGTTGAGAAGTCGGCCCTT 59.234 50.000 0.00 0.00 0.00 3.95
3132 3159 0.765510 AGTTGAGAAGTCGGCCCTTT 59.234 50.000 0.00 0.00 0.00 3.11
3135 3162 0.608640 TGAGAAGTCGGCCCTTTCTC 59.391 55.000 22.43 22.43 44.39 2.87
3136 3163 0.899019 GAGAAGTCGGCCCTTTCTCT 59.101 55.000 22.14 9.22 42.12 3.10
3138 3165 1.003233 AAGTCGGCCCTTTCTCTGC 60.003 57.895 0.00 0.00 0.00 4.26
3139 3166 1.484444 AAGTCGGCCCTTTCTCTGCT 61.484 55.000 0.00 0.00 0.00 4.24
3140 3167 1.448717 GTCGGCCCTTTCTCTGCTC 60.449 63.158 0.00 0.00 0.00 4.26
3141 3168 2.124942 CGGCCCTTTCTCTGCTCC 60.125 66.667 0.00 0.00 0.00 4.70
3142 3169 2.664081 CGGCCCTTTCTCTGCTCCT 61.664 63.158 0.00 0.00 0.00 3.69
3144 3171 0.038890 GGCCCTTTCTCTGCTCCTTT 59.961 55.000 0.00 0.00 0.00 3.11
3145 3172 1.548809 GGCCCTTTCTCTGCTCCTTTT 60.549 52.381 0.00 0.00 0.00 2.27
3146 3173 2.242926 GCCCTTTCTCTGCTCCTTTTT 58.757 47.619 0.00 0.00 0.00 1.94
3147 3174 2.230025 GCCCTTTCTCTGCTCCTTTTTC 59.770 50.000 0.00 0.00 0.00 2.29
3148 3175 3.490348 CCCTTTCTCTGCTCCTTTTTCA 58.510 45.455 0.00 0.00 0.00 2.69
3150 3177 4.140536 CCTTTCTCTGCTCCTTTTTCACT 58.859 43.478 0.00 0.00 0.00 3.41
3151 3178 4.215185 CCTTTCTCTGCTCCTTTTTCACTC 59.785 45.833 0.00 0.00 0.00 3.51
3152 3179 4.422073 TTCTCTGCTCCTTTTTCACTCA 57.578 40.909 0.00 0.00 0.00 3.41
3153 3180 4.422073 TCTCTGCTCCTTTTTCACTCAA 57.578 40.909 0.00 0.00 0.00 3.02
3154 3181 4.978099 TCTCTGCTCCTTTTTCACTCAAT 58.022 39.130 0.00 0.00 0.00 2.57
3157 3184 5.319453 TCTGCTCCTTTTTCACTCAATGAT 58.681 37.500 0.00 0.00 37.11 2.45
3159 3186 6.017400 TGCTCCTTTTTCACTCAATGATTC 57.983 37.500 0.00 0.00 37.11 2.52
3160 3187 5.047802 TGCTCCTTTTTCACTCAATGATTCC 60.048 40.000 0.00 0.00 37.11 3.01
3161 3188 5.184671 GCTCCTTTTTCACTCAATGATTCCT 59.815 40.000 0.00 0.00 37.11 3.36
3165 3192 7.287466 TCCTTTTTCACTCAATGATTCCTTTGA 59.713 33.333 0.00 0.00 37.11 2.69
3166 3193 7.927629 CCTTTTTCACTCAATGATTCCTTTGAA 59.072 33.333 0.00 0.00 37.11 2.69
3167 3194 9.485206 CTTTTTCACTCAATGATTCCTTTGAAT 57.515 29.630 0.00 0.00 43.91 2.57
3168 3195 9.835389 TTTTTCACTCAATGATTCCTTTGAATT 57.165 25.926 0.00 0.00 41.30 2.17
3169 3196 9.835389 TTTTCACTCAATGATTCCTTTGAATTT 57.165 25.926 0.00 0.00 41.30 1.82
3171 3198 6.869913 TCACTCAATGATTCCTTTGAATTTGC 59.130 34.615 0.00 0.00 41.30 3.68
3172 3199 6.091713 CACTCAATGATTCCTTTGAATTTGCC 59.908 38.462 0.00 0.00 41.30 4.52
3173 3200 5.170021 TCAATGATTCCTTTGAATTTGCCG 58.830 37.500 0.00 0.00 41.30 5.69
3174 3201 5.047448 TCAATGATTCCTTTGAATTTGCCGA 60.047 36.000 0.00 0.00 41.30 5.54
3175 3202 4.173036 TGATTCCTTTGAATTTGCCGAC 57.827 40.909 0.00 0.00 41.30 4.79
3176 3203 3.056891 TGATTCCTTTGAATTTGCCGACC 60.057 43.478 0.00 0.00 41.30 4.79
3178 3205 2.311463 TCCTTTGAATTTGCCGACCAA 58.689 42.857 0.00 0.00 0.00 3.67
3179 3206 2.695666 TCCTTTGAATTTGCCGACCAAA 59.304 40.909 4.15 4.15 46.64 3.28
3180 3207 3.133003 TCCTTTGAATTTGCCGACCAAAA 59.867 39.130 5.52 0.00 45.80 2.44
3183 3210 5.008514 CCTTTGAATTTGCCGACCAAAAATT 59.991 36.000 5.52 0.00 45.80 1.82
3184 3211 5.665381 TTGAATTTGCCGACCAAAAATTC 57.335 34.783 11.35 11.35 45.80 2.17
3185 3212 4.954875 TGAATTTGCCGACCAAAAATTCT 58.045 34.783 16.60 0.00 45.80 2.40
3186 3213 6.090483 TGAATTTGCCGACCAAAAATTCTA 57.910 33.333 16.60 5.47 45.80 2.10
3188 3215 6.589523 TGAATTTGCCGACCAAAAATTCTATG 59.410 34.615 16.60 0.00 45.80 2.23
3189 3216 5.461032 TTTGCCGACCAAAAATTCTATGT 57.539 34.783 0.00 0.00 40.32 2.29
3190 3217 4.695217 TGCCGACCAAAAATTCTATGTC 57.305 40.909 0.00 0.00 0.00 3.06
3193 3220 6.119536 TGCCGACCAAAAATTCTATGTCTAT 58.880 36.000 0.00 0.00 0.00 1.98
3194 3221 6.601613 TGCCGACCAAAAATTCTATGTCTATT 59.398 34.615 0.00 0.00 0.00 1.73
3195 3222 7.132863 GCCGACCAAAAATTCTATGTCTATTC 58.867 38.462 0.00 0.00 0.00 1.75
3196 3223 7.012421 GCCGACCAAAAATTCTATGTCTATTCT 59.988 37.037 0.00 0.00 0.00 2.40
3197 3224 9.542462 CCGACCAAAAATTCTATGTCTATTCTA 57.458 33.333 0.00 0.00 0.00 2.10
3210 3892 5.842907 TGTCTATTCTATGTCCGACAATGG 58.157 41.667 5.07 0.00 0.00 3.16
3216 3898 2.047655 GTCCGACAATGGCACCGA 60.048 61.111 0.00 0.00 0.00 4.69
3223 3905 2.794981 CGACAATGGCACCGACTACTAG 60.795 54.545 0.00 0.00 0.00 2.57
3245 3927 1.966451 GACCACGGTGAAGCCAAGG 60.966 63.158 10.28 0.00 36.97 3.61
3360 4046 2.207229 GGGGGACAAACCAGGTTGC 61.207 63.158 5.30 0.00 41.20 4.17
3450 4136 2.205022 TGGCTTCCAAGAGAATGTGG 57.795 50.000 0.00 0.00 32.82 4.17
3451 4137 1.272092 TGGCTTCCAAGAGAATGTGGG 60.272 52.381 0.00 0.00 35.46 4.61
3452 4138 0.813821 GCTTCCAAGAGAATGTGGGC 59.186 55.000 0.00 0.00 35.46 5.36
3453 4139 1.467920 CTTCCAAGAGAATGTGGGCC 58.532 55.000 0.00 0.00 35.46 5.80
3454 4140 0.776810 TTCCAAGAGAATGTGGGCCA 59.223 50.000 0.00 0.00 35.46 5.36
3455 4141 0.329261 TCCAAGAGAATGTGGGCCAG 59.671 55.000 6.40 0.00 35.46 4.85
3456 4142 0.038744 CCAAGAGAATGTGGGCCAGT 59.961 55.000 6.40 0.00 0.00 4.00
3457 4143 1.281867 CCAAGAGAATGTGGGCCAGTA 59.718 52.381 6.40 0.00 0.00 2.74
3458 4144 2.290896 CCAAGAGAATGTGGGCCAGTAA 60.291 50.000 6.40 0.00 0.00 2.24
3464 4150 0.912486 ATGTGGGCCAGTAAGGTCTC 59.088 55.000 6.40 0.00 43.45 3.36
3480 4166 3.118000 AGGTCTCGGACAAACCTTCTTTT 60.118 43.478 6.41 0.00 40.53 2.27
3482 4168 2.616842 TCTCGGACAAACCTTCTTTTGC 59.383 45.455 0.00 0.00 39.67 3.68
3483 4169 2.618709 CTCGGACAAACCTTCTTTTGCT 59.381 45.455 0.00 0.00 39.67 3.91
3485 4171 2.357637 CGGACAAACCTTCTTTTGCTGA 59.642 45.455 0.00 0.00 39.67 4.26
3486 4172 3.181491 CGGACAAACCTTCTTTTGCTGAA 60.181 43.478 0.00 0.00 39.67 3.02
3487 4173 4.112634 GGACAAACCTTCTTTTGCTGAAC 58.887 43.478 0.00 0.00 39.67 3.18
3488 4174 4.142160 GGACAAACCTTCTTTTGCTGAACT 60.142 41.667 0.00 0.00 39.67 3.01
3489 4175 4.747810 ACAAACCTTCTTTTGCTGAACTG 58.252 39.130 0.00 0.00 39.67 3.16
3490 4176 3.443099 AACCTTCTTTTGCTGAACTGC 57.557 42.857 0.00 0.00 0.00 4.40
3491 4177 2.378038 ACCTTCTTTTGCTGAACTGCA 58.622 42.857 2.46 2.46 41.65 4.41
3509 4195 2.815647 GCCGTCGGCTTCCAAGAG 60.816 66.667 28.98 0.00 46.69 2.85
3510 4196 2.970639 CCGTCGGCTTCCAAGAGA 59.029 61.111 0.00 0.00 0.00 3.10
3511 4197 1.292223 CCGTCGGCTTCCAAGAGAA 59.708 57.895 0.00 0.00 0.00 2.87
3512 4198 0.108138 CCGTCGGCTTCCAAGAGAAT 60.108 55.000 0.00 0.00 32.82 2.40
3514 4200 1.673033 CGTCGGCTTCCAAGAGAATGT 60.673 52.381 0.00 0.00 32.82 2.71
3516 4202 0.449388 CGGCTTCCAAGAGAATGTGC 59.551 55.000 0.00 0.00 32.82 4.57
3517 4203 0.449388 GGCTTCCAAGAGAATGTGCG 59.551 55.000 0.00 0.00 32.82 5.34
3518 4204 0.179179 GCTTCCAAGAGAATGTGCGC 60.179 55.000 0.00 0.00 32.82 6.09
3522 4208 0.169672 CCAAGAGAATGTGCGCCAAG 59.830 55.000 4.18 0.00 0.00 3.61
3524 4210 1.135859 CAAGAGAATGTGCGCCAAGAC 60.136 52.381 4.18 0.00 0.00 3.01
3531 6638 0.814457 TGTGCGCCAAGACAAACTTT 59.186 45.000 4.18 0.00 36.61 2.66
3533 6640 1.098869 TGCGCCAAGACAAACTTTCA 58.901 45.000 4.18 0.00 36.61 2.69
3581 6688 9.044150 TGTTTTCATTTTTCACTCAATGATTCC 57.956 29.630 0.00 0.00 38.81 3.01
3582 6689 9.264719 GTTTTCATTTTTCACTCAATGATTCCT 57.735 29.630 0.00 0.00 38.81 3.36
3583 6690 9.835389 TTTTCATTTTTCACTCAATGATTCCTT 57.165 25.926 0.00 0.00 38.81 3.36
3584 6691 9.835389 TTTCATTTTTCACTCAATGATTCCTTT 57.165 25.926 0.00 0.00 38.81 3.11
3585 6692 8.821147 TCATTTTTCACTCAATGATTCCTTTG 57.179 30.769 0.00 0.00 37.11 2.77
3586 6693 8.640651 TCATTTTTCACTCAATGATTCCTTTGA 58.359 29.630 0.00 0.00 37.11 2.69
3587 6694 9.263538 CATTTTTCACTCAATGATTCCTTTGAA 57.736 29.630 0.00 0.00 37.11 2.69
3589 6696 9.835389 TTTTTCACTCAATGATTCCTTTGAATT 57.165 25.926 0.00 0.00 41.30 2.17
3590 6697 9.835389 TTTTCACTCAATGATTCCTTTGAATTT 57.165 25.926 0.00 0.00 41.30 1.82
3591 6698 8.821147 TTCACTCAATGATTCCTTTGAATTTG 57.179 30.769 0.00 0.00 41.30 2.32
3592 6699 6.869913 TCACTCAATGATTCCTTTGAATTTGC 59.130 34.615 0.00 0.00 41.30 3.68
3593 6700 6.091713 CACTCAATGATTCCTTTGAATTTGCC 59.908 38.462 0.00 0.00 41.30 4.52
3594 6701 5.170021 TCAATGATTCCTTTGAATTTGCCG 58.830 37.500 0.00 0.00 41.30 5.69
3595 6702 5.047448 TCAATGATTCCTTTGAATTTGCCGA 60.047 36.000 0.00 0.00 41.30 5.54
3596 6703 4.173036 TGATTCCTTTGAATTTGCCGAC 57.827 40.909 0.00 0.00 41.30 4.79
3597 6704 3.056891 TGATTCCTTTGAATTTGCCGACC 60.057 43.478 0.00 0.00 41.30 4.79
3598 6705 1.988293 TCCTTTGAATTTGCCGACCA 58.012 45.000 0.00 0.00 0.00 4.02
3599 6706 2.311463 TCCTTTGAATTTGCCGACCAA 58.689 42.857 0.00 0.00 0.00 3.67
3600 6707 2.695666 TCCTTTGAATTTGCCGACCAAA 59.304 40.909 4.15 4.15 46.64 3.28
3601 6708 3.133003 TCCTTTGAATTTGCCGACCAAAA 59.867 39.130 5.52 0.00 45.80 2.44
3602 6709 3.873952 CCTTTGAATTTGCCGACCAAAAA 59.126 39.130 5.52 0.00 45.80 1.94
3603 6710 4.514816 CCTTTGAATTTGCCGACCAAAAAT 59.485 37.500 5.52 0.00 45.80 1.82
3604 6711 5.008514 CCTTTGAATTTGCCGACCAAAAATT 59.991 36.000 5.52 0.00 45.80 1.82
3605 6712 5.665381 TTGAATTTGCCGACCAAAAATTC 57.335 34.783 11.35 11.35 45.80 2.17
3606 6713 4.954875 TGAATTTGCCGACCAAAAATTCT 58.045 34.783 16.60 0.00 45.80 2.40
3607 6714 6.090483 TGAATTTGCCGACCAAAAATTCTA 57.910 33.333 16.60 5.47 45.80 2.10
3608 6715 6.696411 TGAATTTGCCGACCAAAAATTCTAT 58.304 32.000 16.60 0.00 45.80 1.98
3609 6716 6.589523 TGAATTTGCCGACCAAAAATTCTATG 59.410 34.615 16.60 0.00 45.80 2.23
3610 6717 5.461032 TTTGCCGACCAAAAATTCTATGT 57.539 34.783 0.00 0.00 40.32 2.29
3611 6718 4.695217 TGCCGACCAAAAATTCTATGTC 57.305 40.909 0.00 0.00 0.00 3.06
3612 6719 3.442273 TGCCGACCAAAAATTCTATGTCC 59.558 43.478 0.00 0.00 0.00 4.02
3613 6720 3.486875 GCCGACCAAAAATTCTATGTCCG 60.487 47.826 0.00 0.00 0.00 4.79
3614 6721 3.486875 CCGACCAAAAATTCTATGTCCGC 60.487 47.826 0.00 0.00 0.00 5.54
3615 6722 3.374058 CGACCAAAAATTCTATGTCCGCT 59.626 43.478 0.00 0.00 0.00 5.52
3616 6723 4.662145 GACCAAAAATTCTATGTCCGCTG 58.338 43.478 0.00 0.00 0.00 5.18
3617 6724 4.331968 ACCAAAAATTCTATGTCCGCTGA 58.668 39.130 0.00 0.00 0.00 4.26
3618 6725 4.156008 ACCAAAAATTCTATGTCCGCTGAC 59.844 41.667 0.64 0.64 42.12 3.51
3696 6806 7.010160 TCCTAACCAAATCCAGTCAGATTTTT 58.990 34.615 0.00 0.00 42.46 1.94
3785 6895 9.216117 CAGATCAGTCATATATGCATTCTTCAA 57.784 33.333 3.54 0.00 0.00 2.69
3878 7227 3.340814 AACGTCCAGAAGCATGAATCT 57.659 42.857 0.00 0.00 0.00 2.40
3879 7228 2.898705 ACGTCCAGAAGCATGAATCTC 58.101 47.619 0.00 0.00 0.00 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 1.134965 GCTATGCTCAACACCTCGACT 60.135 52.381 0.00 0.00 0.00 4.18
15 18 1.281899 GCTATGCTCAACACCTCGAC 58.718 55.000 0.00 0.00 0.00 4.20
28 34 1.202651 ACCATCCTAACCACGCTATGC 60.203 52.381 0.00 0.00 0.00 3.14
39 45 5.036916 ACTTCCACAATCCTACCATCCTAA 58.963 41.667 0.00 0.00 0.00 2.69
47 53 4.652822 ACTTCCAACTTCCACAATCCTAC 58.347 43.478 0.00 0.00 0.00 3.18
51 57 6.575162 ATTGTACTTCCAACTTCCACAATC 57.425 37.500 0.00 0.00 31.37 2.67
54 60 6.406400 CCAAAATTGTACTTCCAACTTCCACA 60.406 38.462 0.00 0.00 0.00 4.17
55 61 5.983118 CCAAAATTGTACTTCCAACTTCCAC 59.017 40.000 0.00 0.00 0.00 4.02
56 62 5.894393 TCCAAAATTGTACTTCCAACTTCCA 59.106 36.000 0.00 0.00 0.00 3.53
57 63 6.040504 AGTCCAAAATTGTACTTCCAACTTCC 59.959 38.462 0.00 0.00 0.00 3.46
58 64 7.039313 AGTCCAAAATTGTACTTCCAACTTC 57.961 36.000 0.00 0.00 0.00 3.01
59 65 8.528044 TTAGTCCAAAATTGTACTTCCAACTT 57.472 30.769 0.00 0.00 29.74 2.66
60 66 8.528044 TTTAGTCCAAAATTGTACTTCCAACT 57.472 30.769 0.00 0.00 29.74 3.16
61 67 7.865889 CCTTTAGTCCAAAATTGTACTTCCAAC 59.134 37.037 0.00 0.00 29.74 3.77
80 86 1.878953 CAGGACAACGTGCCTTTAGT 58.121 50.000 2.41 0.00 30.41 2.24
113 119 7.119699 CAGATTCTTAGAACACAAAGGCATACA 59.880 37.037 0.00 0.00 0.00 2.29
127 136 8.582437 TCGAAAGTTACTTCCAGATTCTTAGAA 58.418 33.333 0.00 0.00 0.00 2.10
162 174 5.503927 AGCTTTGCAATCTATCAAGGAGAA 58.496 37.500 0.00 0.00 0.00 2.87
167 179 4.497674 GCTGGAGCTTTGCAATCTATCAAG 60.498 45.833 0.00 0.87 38.21 3.02
190 202 4.082125 ACTAAATTCCCAGCACAAGGAAG 58.918 43.478 0.00 0.00 45.09 3.46
195 207 4.980573 AGTGTACTAAATTCCCAGCACAA 58.019 39.130 0.00 0.00 0.00 3.33
202 214 6.037172 CAGTGTGCATAGTGTACTAAATTCCC 59.963 42.308 9.96 0.00 33.97 3.97
206 218 7.117812 GTGAACAGTGTGCATAGTGTACTAAAT 59.882 37.037 22.36 7.47 33.97 1.40
228 240 4.136796 CCTCAAACATCCTGAACAGTGAA 58.863 43.478 0.00 0.00 0.00 3.18
229 241 3.496692 CCCTCAAACATCCTGAACAGTGA 60.497 47.826 0.00 0.00 0.00 3.41
230 242 2.816087 CCCTCAAACATCCTGAACAGTG 59.184 50.000 1.18 0.00 0.00 3.66
231 243 2.815589 GCCCTCAAACATCCTGAACAGT 60.816 50.000 1.18 0.00 0.00 3.55
232 244 1.815003 GCCCTCAAACATCCTGAACAG 59.185 52.381 0.00 0.00 0.00 3.16
233 245 1.144708 TGCCCTCAAACATCCTGAACA 59.855 47.619 0.00 0.00 0.00 3.18
234 246 1.909700 TGCCCTCAAACATCCTGAAC 58.090 50.000 0.00 0.00 0.00 3.18
253 265 2.676839 CAGCAGTTCGAGCATCTTGAAT 59.323 45.455 1.01 0.00 36.43 2.57
255 267 1.273327 TCAGCAGTTCGAGCATCTTGA 59.727 47.619 1.01 0.00 0.00 3.02
296 308 3.804325 CGGCTTCACCACTTACAGATATG 59.196 47.826 0.00 0.00 39.03 1.78
299 311 1.676014 GCGGCTTCACCACTTACAGAT 60.676 52.381 0.00 0.00 39.03 2.90
307 319 2.029844 GACTCTGCGGCTTCACCAC 61.030 63.158 0.00 0.00 39.03 4.16
310 322 1.086634 GGATGACTCTGCGGCTTCAC 61.087 60.000 0.00 0.00 0.00 3.18
329 341 3.804193 GCAAGGAAGAAGCCGGCG 61.804 66.667 23.20 4.01 0.00 6.46
332 344 1.131883 CAATCAGCAAGGAAGAAGCCG 59.868 52.381 0.00 0.00 0.00 5.52
383 395 0.613572 TCACCGACCATCAGCACCTA 60.614 55.000 0.00 0.00 0.00 3.08
393 405 0.107643 TCAGTTTGCATCACCGACCA 59.892 50.000 0.00 0.00 0.00 4.02
394 406 0.798776 CTCAGTTTGCATCACCGACC 59.201 55.000 0.00 0.00 0.00 4.79
406 418 3.177228 ACTACTGGCAGGATCTCAGTTT 58.823 45.455 20.34 0.00 41.37 2.66
441 453 6.642950 ACTCTCTCGACATCAACAAAACTAAG 59.357 38.462 0.00 0.00 0.00 2.18
452 464 3.615110 GCAGGAAAACTCTCTCGACATCA 60.615 47.826 0.00 0.00 0.00 3.07
684 698 6.877611 AAACGGACACAGAACAGATAAATT 57.122 33.333 0.00 0.00 0.00 1.82
816 830 7.219484 AGTTGAAGTTTCCACTATGAATTGG 57.781 36.000 0.00 0.00 32.11 3.16
950 964 2.581354 CTCCAGGGCAAGTCTCCG 59.419 66.667 0.00 0.00 0.00 4.63
1095 1109 3.070018 AGCATTTTCAGAGGAGACAACG 58.930 45.455 0.00 0.00 0.00 4.10
1188 1202 4.025858 GGAGCTGCAGGGCTGTCA 62.026 66.667 17.12 0.00 43.20 3.58
1356 1370 6.235231 AGTTCCTTTTCTTCTGTAGTGTGA 57.765 37.500 0.00 0.00 0.00 3.58
1669 1683 6.863645 ACGCAGAGATGACAATATGTATACAC 59.136 38.462 7.96 0.00 0.00 2.90
1691 1705 2.358898 ACCAAGATATGAATGCCAACGC 59.641 45.455 0.00 0.00 0.00 4.84
1857 1871 3.889815 AGGCATGTGCAGCTATCTTTTA 58.110 40.909 7.36 0.00 44.36 1.52
2046 2060 2.661718 AGACAAAACGGGATTGTTGGT 58.338 42.857 4.58 0.00 40.90 3.67
2073 2087 8.833493 CACAAGCAAATAGATGTCAGATAATCA 58.167 33.333 0.00 0.00 0.00 2.57
2075 2089 7.255381 GGCACAAGCAAATAGATGTCAGATAAT 60.255 37.037 0.00 0.00 44.61 1.28
2129 2143 0.179163 GGAATTCTTTCGCAAGGCCG 60.179 55.000 5.23 0.00 38.47 6.13
2390 2404 3.808728 CTGAACTTTGTCTCTGTTCCCA 58.191 45.455 0.00 0.00 39.24 4.37
2459 2473 1.043022 TCAGCAGTGAGTGAGCTTCA 58.957 50.000 0.00 0.00 36.26 3.02
2465 2479 2.042464 ACTCCTTTCAGCAGTGAGTGA 58.958 47.619 0.00 0.00 35.12 3.41
2471 2485 3.470645 AAACGTACTCCTTTCAGCAGT 57.529 42.857 0.00 0.00 0.00 4.40
2515 2529 7.112452 TGTGCTATGAGTTACTACATGATGT 57.888 36.000 2.65 2.65 0.00 3.06
2519 2533 9.534565 ACTATTTGTGCTATGAGTTACTACATG 57.465 33.333 0.00 0.00 0.00 3.21
2523 2537 9.192642 TGGTACTATTTGTGCTATGAGTTACTA 57.807 33.333 0.00 0.00 0.00 1.82
2699 2718 1.447317 CGGCTTGAACCACTTGTGCT 61.447 55.000 0.00 0.00 0.00 4.40
2743 2762 2.841988 GCTCGGCTGGATCTCCCT 60.842 66.667 0.00 0.00 35.38 4.20
2965 2988 1.080025 GTTTCGGGCGCACTAGAGT 60.080 57.895 8.62 0.00 0.00 3.24
2989 3012 5.565592 ATGAACTAGATCAAAATTGCGCA 57.434 34.783 5.66 5.66 32.06 6.09
3021 3044 0.391661 ACAGGCCATAGAACACAGCG 60.392 55.000 5.01 0.00 0.00 5.18
3058 3083 1.466360 CCGCAAGTAAAGCAGATGCAC 60.466 52.381 7.68 0.00 45.16 4.57
3109 3136 1.673329 GGGCCGACTTCTCAACTTCTC 60.673 57.143 0.00 0.00 0.00 2.87
3110 3137 0.321996 GGGCCGACTTCTCAACTTCT 59.678 55.000 0.00 0.00 0.00 2.85
3111 3138 0.321996 AGGGCCGACTTCTCAACTTC 59.678 55.000 0.00 0.00 0.00 3.01
3113 3140 0.765510 AAAGGGCCGACTTCTCAACT 59.234 50.000 0.00 0.00 0.00 3.16
3114 3141 1.157585 GAAAGGGCCGACTTCTCAAC 58.842 55.000 0.00 0.00 0.00 3.18
3116 3143 0.608640 GAGAAAGGGCCGACTTCTCA 59.391 55.000 27.21 0.00 31.18 3.27
3117 3144 0.899019 AGAGAAAGGGCCGACTTCTC 59.101 55.000 25.92 25.92 0.00 2.87
3118 3145 0.610687 CAGAGAAAGGGCCGACTTCT 59.389 55.000 15.59 15.59 0.00 2.85
3119 3146 1.021920 GCAGAGAAAGGGCCGACTTC 61.022 60.000 0.00 2.74 0.00 3.01
3124 3151 2.124942 GGAGCAGAGAAAGGGCCG 60.125 66.667 0.00 0.00 0.00 6.13
3125 3152 0.038890 AAAGGAGCAGAGAAAGGGCC 59.961 55.000 0.00 0.00 0.00 5.80
3127 3154 3.254411 GTGAAAAAGGAGCAGAGAAAGGG 59.746 47.826 0.00 0.00 0.00 3.95
3128 3155 4.140536 AGTGAAAAAGGAGCAGAGAAAGG 58.859 43.478 0.00 0.00 0.00 3.11
3129 3156 4.818546 TGAGTGAAAAAGGAGCAGAGAAAG 59.181 41.667 0.00 0.00 0.00 2.62
3131 3158 4.422073 TGAGTGAAAAAGGAGCAGAGAA 57.578 40.909 0.00 0.00 0.00 2.87
3132 3159 4.422073 TTGAGTGAAAAAGGAGCAGAGA 57.578 40.909 0.00 0.00 0.00 3.10
3135 3162 5.640189 ATCATTGAGTGAAAAAGGAGCAG 57.360 39.130 0.00 0.00 40.97 4.24
3136 3163 5.047802 GGAATCATTGAGTGAAAAAGGAGCA 60.048 40.000 0.00 0.00 40.97 4.26
3138 3165 6.830873 AGGAATCATTGAGTGAAAAAGGAG 57.169 37.500 0.00 0.00 40.97 3.69
3139 3166 7.287466 TCAAAGGAATCATTGAGTGAAAAAGGA 59.713 33.333 0.00 0.00 40.97 3.36
3140 3167 7.436118 TCAAAGGAATCATTGAGTGAAAAAGG 58.564 34.615 0.00 0.00 40.97 3.11
3141 3168 8.876275 TTCAAAGGAATCATTGAGTGAAAAAG 57.124 30.769 0.00 0.00 40.97 2.27
3142 3169 9.835389 AATTCAAAGGAATCATTGAGTGAAAAA 57.165 25.926 0.00 0.00 42.87 1.94
3144 3171 9.263538 CAAATTCAAAGGAATCATTGAGTGAAA 57.736 29.630 0.00 0.00 42.87 2.69
3145 3172 7.385752 GCAAATTCAAAGGAATCATTGAGTGAA 59.614 33.333 0.00 0.00 42.87 3.18
3146 3173 6.869913 GCAAATTCAAAGGAATCATTGAGTGA 59.130 34.615 0.00 0.00 42.87 3.41
3147 3174 6.091713 GGCAAATTCAAAGGAATCATTGAGTG 59.908 38.462 0.00 3.82 42.87 3.51
3148 3175 6.168389 GGCAAATTCAAAGGAATCATTGAGT 58.832 36.000 6.20 0.00 42.87 3.41
3150 3177 5.047448 TCGGCAAATTCAAAGGAATCATTGA 60.047 36.000 6.20 0.00 42.87 2.57
3151 3178 5.062558 GTCGGCAAATTCAAAGGAATCATTG 59.937 40.000 0.00 0.00 42.87 2.82
3152 3179 5.170748 GTCGGCAAATTCAAAGGAATCATT 58.829 37.500 0.00 0.00 42.87 2.57
3153 3180 4.381932 GGTCGGCAAATTCAAAGGAATCAT 60.382 41.667 0.00 0.00 42.87 2.45
3154 3181 3.056891 GGTCGGCAAATTCAAAGGAATCA 60.057 43.478 0.00 0.00 42.87 2.57
3157 3184 2.311463 TGGTCGGCAAATTCAAAGGAA 58.689 42.857 0.00 0.00 37.45 3.36
3159 3186 2.810439 TTGGTCGGCAAATTCAAAGG 57.190 45.000 0.00 0.00 0.00 3.11
3160 3187 5.671742 ATTTTTGGTCGGCAAATTCAAAG 57.328 34.783 0.00 0.00 0.00 2.77
3161 3188 5.819901 AGAATTTTTGGTCGGCAAATTCAAA 59.180 32.000 19.84 5.75 44.28 2.69
3165 3192 6.463360 ACATAGAATTTTTGGTCGGCAAATT 58.537 32.000 0.00 0.00 33.70 1.82
3166 3193 6.036577 ACATAGAATTTTTGGTCGGCAAAT 57.963 33.333 0.00 0.00 0.00 2.32
3167 3194 5.242838 AGACATAGAATTTTTGGTCGGCAAA 59.757 36.000 0.00 0.00 0.00 3.68
3168 3195 4.764823 AGACATAGAATTTTTGGTCGGCAA 59.235 37.500 0.00 0.00 0.00 4.52
3169 3196 4.331968 AGACATAGAATTTTTGGTCGGCA 58.668 39.130 0.00 0.00 0.00 5.69
3171 3198 8.438676 AGAATAGACATAGAATTTTTGGTCGG 57.561 34.615 0.00 0.00 0.00 4.79
3179 3206 9.915629 GTCGGACATAGAATAGACATAGAATTT 57.084 33.333 2.62 0.00 0.00 1.82
3180 3207 9.078990 TGTCGGACATAGAATAGACATAGAATT 57.921 33.333 6.76 0.00 34.24 2.17
3183 3210 8.515414 CATTGTCGGACATAGAATAGACATAGA 58.485 37.037 12.26 0.00 38.24 1.98
3184 3211 7.757173 CCATTGTCGGACATAGAATAGACATAG 59.243 40.741 12.26 0.00 38.24 2.23
3185 3212 7.602753 CCATTGTCGGACATAGAATAGACATA 58.397 38.462 12.26 0.00 38.24 2.29
3186 3213 6.459066 CCATTGTCGGACATAGAATAGACAT 58.541 40.000 12.26 0.00 38.24 3.06
3188 3215 4.686554 GCCATTGTCGGACATAGAATAGAC 59.313 45.833 12.26 0.00 0.00 2.59
3189 3216 4.343814 TGCCATTGTCGGACATAGAATAGA 59.656 41.667 12.26 0.00 0.00 1.98
3190 3217 4.449068 GTGCCATTGTCGGACATAGAATAG 59.551 45.833 12.26 0.00 0.00 1.73
3193 3220 2.627945 GTGCCATTGTCGGACATAGAA 58.372 47.619 12.26 0.00 0.00 2.10
3194 3221 1.134521 GGTGCCATTGTCGGACATAGA 60.135 52.381 12.26 0.00 0.00 1.98
3195 3222 1.299541 GGTGCCATTGTCGGACATAG 58.700 55.000 12.26 7.45 0.00 2.23
3196 3223 0.461163 CGGTGCCATTGTCGGACATA 60.461 55.000 12.26 3.71 0.00 2.29
3197 3224 1.745115 CGGTGCCATTGTCGGACAT 60.745 57.895 12.26 0.00 0.00 3.06
3198 3225 2.358125 CGGTGCCATTGTCGGACA 60.358 61.111 6.76 6.76 0.00 4.02
3210 3892 1.337387 GGTCATCCTAGTAGTCGGTGC 59.663 57.143 0.00 0.00 0.00 5.01
3216 3898 2.025605 TCACCGTGGTCATCCTAGTAGT 60.026 50.000 0.00 0.00 34.23 2.73
3223 3905 1.745489 GGCTTCACCGTGGTCATCC 60.745 63.158 0.00 0.00 0.00 3.51
3245 3927 0.807496 GAGTTGAGCTTGTCCATGGC 59.193 55.000 6.96 2.72 0.00 4.40
3360 4046 2.747855 GGGCCAGCTTCAGGAACG 60.748 66.667 4.39 0.00 0.00 3.95
3450 4136 1.255667 TGTCCGAGACCTTACTGGCC 61.256 60.000 0.00 0.00 40.22 5.36
3451 4137 0.606604 TTGTCCGAGACCTTACTGGC 59.393 55.000 2.23 0.00 40.22 4.85
3452 4138 2.612221 GGTTTGTCCGAGACCTTACTGG 60.612 54.545 2.23 0.00 42.93 4.00
3453 4139 2.299297 AGGTTTGTCCGAGACCTTACTG 59.701 50.000 2.23 0.00 40.83 2.74
3454 4140 2.606378 AGGTTTGTCCGAGACCTTACT 58.394 47.619 2.23 0.00 40.83 2.24
3458 4144 1.718280 AGAAGGTTTGTCCGAGACCT 58.282 50.000 2.23 0.00 45.42 3.85
3464 4150 2.357637 TCAGCAAAAGAAGGTTTGTCCG 59.642 45.455 0.00 0.00 40.06 4.79
3482 4168 3.114616 CCGACGGCTGCAGTTCAG 61.115 66.667 16.64 6.93 45.62 3.02
3493 4179 0.108138 ATTCTCTTGGAAGCCGACGG 60.108 55.000 10.29 10.29 37.36 4.79
3494 4180 1.002366 CATTCTCTTGGAAGCCGACG 58.998 55.000 0.00 0.00 37.36 5.12
3495 4181 1.734465 CACATTCTCTTGGAAGCCGAC 59.266 52.381 0.00 0.00 37.36 4.79
3496 4182 1.945819 GCACATTCTCTTGGAAGCCGA 60.946 52.381 0.00 0.00 37.36 5.54
3498 4184 0.449388 CGCACATTCTCTTGGAAGCC 59.551 55.000 0.00 0.00 37.36 4.35
3501 4187 0.250684 TGGCGCACATTCTCTTGGAA 60.251 50.000 10.83 0.00 38.41 3.53
3502 4188 0.250684 TTGGCGCACATTCTCTTGGA 60.251 50.000 10.83 0.00 0.00 3.53
3503 4189 0.169672 CTTGGCGCACATTCTCTTGG 59.830 55.000 10.83 0.00 0.00 3.61
3504 4190 1.135859 GTCTTGGCGCACATTCTCTTG 60.136 52.381 10.83 0.00 0.00 3.02
3505 4191 1.160137 GTCTTGGCGCACATTCTCTT 58.840 50.000 10.83 0.00 0.00 2.85
3507 4193 0.874390 TTGTCTTGGCGCACATTCTC 59.126 50.000 10.83 0.00 0.00 2.87
3509 4195 1.001378 AGTTTGTCTTGGCGCACATTC 60.001 47.619 10.83 1.34 0.00 2.67
3510 4196 1.032014 AGTTTGTCTTGGCGCACATT 58.968 45.000 10.83 0.00 0.00 2.71
3511 4197 1.032014 AAGTTTGTCTTGGCGCACAT 58.968 45.000 10.83 0.00 34.77 3.21
3512 4198 0.814457 AAAGTTTGTCTTGGCGCACA 59.186 45.000 10.83 0.86 36.40 4.57
3514 4200 1.098869 TGAAAGTTTGTCTTGGCGCA 58.901 45.000 10.83 0.00 36.40 6.09
3516 4202 2.354510 TCTGTGAAAGTTTGTCTTGGCG 59.645 45.455 0.00 0.00 36.40 5.69
3517 4203 4.574599 ATCTGTGAAAGTTTGTCTTGGC 57.425 40.909 0.00 0.00 36.40 4.52
3518 4204 7.012327 TCACTAATCTGTGAAAGTTTGTCTTGG 59.988 37.037 0.00 0.00 43.08 3.61
3555 6662 9.044150 GGAATCATTGAGTGAAAAATGAAAACA 57.956 29.630 2.52 0.00 43.86 2.83
3556 6663 9.264719 AGGAATCATTGAGTGAAAAATGAAAAC 57.735 29.630 2.52 0.00 43.86 2.43
3557 6664 9.835389 AAGGAATCATTGAGTGAAAAATGAAAA 57.165 25.926 2.52 0.00 43.86 2.29
3558 6665 9.835389 AAAGGAATCATTGAGTGAAAAATGAAA 57.165 25.926 2.52 0.00 43.86 2.69
3559 6666 9.263538 CAAAGGAATCATTGAGTGAAAAATGAA 57.736 29.630 2.52 0.00 43.86 2.57
3560 6667 8.640651 TCAAAGGAATCATTGAGTGAAAAATGA 58.359 29.630 0.00 0.97 44.54 2.57
3561 6668 8.821147 TCAAAGGAATCATTGAGTGAAAAATG 57.179 30.769 0.00 0.00 40.97 2.32
3563 6670 9.835389 AATTCAAAGGAATCATTGAGTGAAAAA 57.165 25.926 0.00 0.00 42.87 1.94
3564 6671 9.835389 AAATTCAAAGGAATCATTGAGTGAAAA 57.165 25.926 0.00 0.00 42.87 2.29
3565 6672 9.263538 CAAATTCAAAGGAATCATTGAGTGAAA 57.736 29.630 0.00 0.00 42.87 2.69
3566 6673 7.385752 GCAAATTCAAAGGAATCATTGAGTGAA 59.614 33.333 0.00 0.00 42.87 3.18
3567 6674 6.869913 GCAAATTCAAAGGAATCATTGAGTGA 59.130 34.615 0.00 0.00 42.87 3.41
3568 6675 6.091713 GGCAAATTCAAAGGAATCATTGAGTG 59.908 38.462 0.00 3.82 42.87 3.51
3569 6676 6.168389 GGCAAATTCAAAGGAATCATTGAGT 58.832 36.000 6.20 0.00 42.87 3.41
3570 6677 5.290158 CGGCAAATTCAAAGGAATCATTGAG 59.710 40.000 6.20 0.00 42.87 3.02
3571 6678 5.047448 TCGGCAAATTCAAAGGAATCATTGA 60.047 36.000 6.20 0.00 42.87 2.57
3572 6679 5.062558 GTCGGCAAATTCAAAGGAATCATTG 59.937 40.000 0.00 0.00 42.87 2.82
3573 6680 5.170748 GTCGGCAAATTCAAAGGAATCATT 58.829 37.500 0.00 0.00 42.87 2.57
3574 6681 4.381932 GGTCGGCAAATTCAAAGGAATCAT 60.382 41.667 0.00 0.00 42.87 2.45
3575 6682 3.056891 GGTCGGCAAATTCAAAGGAATCA 60.057 43.478 0.00 0.00 42.87 2.57
3576 6683 3.056891 TGGTCGGCAAATTCAAAGGAATC 60.057 43.478 0.00 0.00 42.87 2.52
3577 6684 2.896685 TGGTCGGCAAATTCAAAGGAAT 59.103 40.909 0.00 0.00 45.57 3.01
3578 6685 2.311463 TGGTCGGCAAATTCAAAGGAA 58.689 42.857 0.00 0.00 37.45 3.36
3579 6686 1.988293 TGGTCGGCAAATTCAAAGGA 58.012 45.000 0.00 0.00 0.00 3.36
3580 6687 2.810439 TTGGTCGGCAAATTCAAAGG 57.190 45.000 0.00 0.00 0.00 3.11
3581 6688 5.671742 ATTTTTGGTCGGCAAATTCAAAG 57.328 34.783 0.00 0.00 0.00 2.77
3582 6689 5.819901 AGAATTTTTGGTCGGCAAATTCAAA 59.180 32.000 19.84 5.75 44.28 2.69
3583 6690 5.363939 AGAATTTTTGGTCGGCAAATTCAA 58.636 33.333 19.84 0.07 44.28 2.69
3584 6691 4.954875 AGAATTTTTGGTCGGCAAATTCA 58.045 34.783 19.84 0.00 44.28 2.57
3585 6692 6.589907 ACATAGAATTTTTGGTCGGCAAATTC 59.410 34.615 13.33 13.33 43.07 2.17
3586 6693 6.463360 ACATAGAATTTTTGGTCGGCAAATT 58.537 32.000 0.00 0.00 33.70 1.82
3587 6694 6.036577 ACATAGAATTTTTGGTCGGCAAAT 57.963 33.333 0.00 0.00 0.00 2.32
3588 6695 5.461032 ACATAGAATTTTTGGTCGGCAAA 57.539 34.783 0.00 0.00 0.00 3.68
3589 6696 4.082463 GGACATAGAATTTTTGGTCGGCAA 60.082 41.667 0.00 0.00 0.00 4.52
3590 6697 3.442273 GGACATAGAATTTTTGGTCGGCA 59.558 43.478 0.00 0.00 0.00 5.69
3591 6698 3.486875 CGGACATAGAATTTTTGGTCGGC 60.487 47.826 0.00 0.00 0.00 5.54
3592 6699 3.486875 GCGGACATAGAATTTTTGGTCGG 60.487 47.826 0.00 0.00 0.00 4.79
3593 6700 3.374058 AGCGGACATAGAATTTTTGGTCG 59.626 43.478 0.00 0.00 0.00 4.79
3594 6701 4.394920 TCAGCGGACATAGAATTTTTGGTC 59.605 41.667 0.00 0.00 0.00 4.02
3595 6702 4.156008 GTCAGCGGACATAGAATTTTTGGT 59.844 41.667 12.41 0.00 43.73 3.67
3596 6703 4.662145 GTCAGCGGACATAGAATTTTTGG 58.338 43.478 12.41 0.00 43.73 3.28
3609 6716 3.896648 TTCAAGAATTTGTCAGCGGAC 57.103 42.857 10.32 10.32 44.57 4.79
3610 6717 5.452078 AAATTCAAGAATTTGTCAGCGGA 57.548 34.783 17.34 0.00 45.99 5.54
3660 6770 7.291566 TGGATTTGGTTAGGAAGTTCAAAGTA 58.708 34.615 5.01 0.00 32.03 2.24
3696 6806 5.308014 TCATGCTTCTCAACTTTCAGCTTA 58.692 37.500 0.00 0.00 0.00 3.09


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

AutoCloner maintained by Alex Coulton.