Multiple sequence alignment - TraesCS2D01G456900

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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 TraesCS2D01G456900 chr2D 100.000 3771 0 0 1 3771 564669525 564673295 0.000000e+00 6964.0
1 TraesCS2D01G456900 chr2A 90.040 3002 209 55 683 3622 705499173 705502146 0.000000e+00 3805.0
2 TraesCS2D01G456900 chr2A 84.706 340 26 13 218 535 705498838 705499173 2.190000e-82 316.0
3 TraesCS2D01G456900 chr2A 95.833 48 2 0 1 48 705493880 705493927 1.120000e-10 78.7
4 TraesCS2D01G456900 chr2B 90.094 2968 172 54 136 3025 676023109 676026032 0.000000e+00 3740.0
5 TraesCS2D01G456900 chr2B 84.731 334 25 4 2708 3022 676028043 676028369 1.020000e-80 311.0
6 TraesCS2D01G456900 chr2B 90.991 222 19 1 136 356 676020997 676021218 7.920000e-77 298.0
7 TraesCS2D01G456900 chr2B 97.917 48 1 0 1 48 676021784 676021831 2.410000e-12 84.2


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 TraesCS2D01G456900 chr2D 564669525 564673295 3770 False 6964.0 6964 100.00000 1 3771 1 chr2D.!!$F1 3770
1 TraesCS2D01G456900 chr2A 705498838 705502146 3308 False 2060.5 3805 87.37300 218 3622 2 chr2A.!!$F2 3404
2 TraesCS2D01G456900 chr2B 676020997 676028369 7372 False 1108.3 3740 90.93325 1 3025 4 chr2B.!!$F1 3024

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
854 2897 0.178992 CTCCTCTCATCTCCGCTCCT 60.179 60.0 0.00 0.0 0.00 3.69 F
855 2898 0.179004 TCCTCTCATCTCCGCTCCTC 60.179 60.0 0.00 0.0 0.00 3.71 F
2335 4461 0.179048 CACTCACCAGTGCACCAGAA 60.179 55.0 14.63 0.0 43.77 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2335 4461 0.251922 ATGGGCTCCATGTGTTTGCT 60.252 50.000 5.97 0.0 43.39 3.91 R
2601 4727 1.069296 CATGCACCATTTCGTTGTCGT 60.069 47.619 0.00 0.0 38.33 4.34 R
3598 6938 0.107456 CTGCTTCCTCACACCACACT 59.893 55.000 0.00 0.0 0.00 3.55 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
57 2068 8.392372 ACTTATCTTTAGTTTTGTCACCCTTC 57.608 34.615 0.00 0.00 0.00 3.46
62 2073 8.391075 TCTTTAGTTTTGTCACCCTTCTAATG 57.609 34.615 0.00 0.00 0.00 1.90
63 2074 6.569179 TTAGTTTTGTCACCCTTCTAATGC 57.431 37.500 0.00 0.00 0.00 3.56
64 2075 3.826729 AGTTTTGTCACCCTTCTAATGCC 59.173 43.478 0.00 0.00 0.00 4.40
65 2076 3.517296 TTTGTCACCCTTCTAATGCCA 57.483 42.857 0.00 0.00 0.00 4.92
72 2083 3.193479 CACCCTTCTAATGCCAAAAGTCC 59.807 47.826 0.00 0.00 0.00 3.85
80 2091 6.930731 TCTAATGCCAAAAGTCCCATTTAAC 58.069 36.000 0.00 0.00 0.00 2.01
85 2096 4.280929 GCCAAAAGTCCCATTTAACTGACT 59.719 41.667 0.00 0.00 39.66 3.41
86 2097 5.564848 GCCAAAAGTCCCATTTAACTGACTC 60.565 44.000 0.00 0.00 37.09 3.36
88 2099 3.611766 AGTCCCATTTAACTGACTCGG 57.388 47.619 0.00 0.00 32.85 4.63
89 2100 2.007608 GTCCCATTTAACTGACTCGGC 58.992 52.381 0.00 0.00 0.00 5.54
98 2109 0.468226 ACTGACTCGGCCAAACAGAA 59.532 50.000 18.50 0.00 33.53 3.02
101 2112 1.673920 TGACTCGGCCAAACAGAAAAC 59.326 47.619 2.24 0.00 0.00 2.43
107 2118 2.228822 CGGCCAAACAGAAAACTAGCAT 59.771 45.455 2.24 0.00 0.00 3.79
108 2119 3.438781 CGGCCAAACAGAAAACTAGCATA 59.561 43.478 2.24 0.00 0.00 3.14
109 2120 4.096382 CGGCCAAACAGAAAACTAGCATAT 59.904 41.667 2.24 0.00 0.00 1.78
110 2121 5.343249 GGCCAAACAGAAAACTAGCATATG 58.657 41.667 0.00 0.00 0.00 1.78
111 2122 5.125417 GGCCAAACAGAAAACTAGCATATGA 59.875 40.000 6.97 0.00 0.00 2.15
112 2123 6.183360 GGCCAAACAGAAAACTAGCATATGAT 60.183 38.462 6.97 1.82 0.00 2.45
113 2124 7.260603 GCCAAACAGAAAACTAGCATATGATT 58.739 34.615 6.97 0.00 0.00 2.57
114 2125 7.761249 GCCAAACAGAAAACTAGCATATGATTT 59.239 33.333 6.97 0.00 0.00 2.17
115 2126 9.643693 CCAAACAGAAAACTAGCATATGATTTT 57.356 29.630 6.97 6.97 0.00 1.82
134 2145 8.045176 TGATTTTATTTTTATTTTTGCGGGGG 57.955 30.769 0.00 0.00 0.00 5.40
135 2146 7.883311 TGATTTTATTTTTATTTTTGCGGGGGA 59.117 29.630 0.00 0.00 0.00 4.81
136 2147 7.674471 TTTTATTTTTATTTTTGCGGGGGAG 57.326 32.000 0.00 0.00 0.00 4.30
137 2148 2.753055 TTTTATTTTTGCGGGGGAGC 57.247 45.000 0.00 0.00 37.71 4.70
138 2149 1.633774 TTTATTTTTGCGGGGGAGCA 58.366 45.000 0.00 0.00 46.54 4.26
148 2159 1.271597 GCGGGGGAGCATATGATTCTT 60.272 52.381 6.97 0.00 37.05 2.52
157 2168 6.256757 GGGAGCATATGATTCTTATTAGACGC 59.743 42.308 6.97 0.00 0.00 5.19
198 2209 1.765314 AGCTTGGCCGACTATGATTCT 59.235 47.619 0.00 0.00 0.00 2.40
235 2246 5.869579 AGTAGCATGTCTCTTCCAAAAAGA 58.130 37.500 0.00 0.00 0.00 2.52
289 2301 5.037385 ACTTTTTCGCAGAAAAGAAAGCTC 58.963 37.500 21.59 0.00 45.90 4.09
290 2302 3.626028 TTTCGCAGAAAAGAAAGCTCC 57.374 42.857 0.00 0.00 45.90 4.70
306 2318 3.618351 AGCTCCATCAATCACCAAGAAG 58.382 45.455 0.00 0.00 0.00 2.85
335 2347 5.337554 TCGAAATTCGAGACGTGACAATAT 58.662 37.500 14.59 0.00 44.82 1.28
433 2445 3.503748 AGGTGAAATCTTGCGGAAAAGAG 59.496 43.478 0.00 0.00 39.47 2.85
434 2446 3.502211 GGTGAAATCTTGCGGAAAAGAGA 59.498 43.478 0.00 0.00 39.47 3.10
439 2451 6.475402 TGAAATCTTGCGGAAAAGAGAAAAAC 59.525 34.615 0.00 0.00 39.47 2.43
442 2454 5.715070 TCTTGCGGAAAAGAGAAAAACAAA 58.285 33.333 0.00 0.00 32.42 2.83
445 2457 3.245284 GCGGAAAAGAGAAAAACAAAGGC 59.755 43.478 0.00 0.00 0.00 4.35
446 2458 3.485743 CGGAAAAGAGAAAAACAAAGGCG 59.514 43.478 0.00 0.00 0.00 5.52
475 2500 1.542030 GCGATGGATAGACAGTCGGAT 59.458 52.381 0.00 0.00 33.26 4.18
544 2586 2.952978 GGATTAACCACACCACACACAA 59.047 45.455 0.00 0.00 38.79 3.33
561 2603 3.291101 AAGCGCCACGTACCGTCAT 62.291 57.895 2.29 0.00 38.32 3.06
580 2623 1.213013 CGAGACGTGACCTCCCTTG 59.787 63.158 0.00 0.00 0.00 3.61
595 2638 0.678048 CCTTGCCTTGCCAGTAGTCC 60.678 60.000 0.00 0.00 0.00 3.85
613 2656 1.422402 TCCTCCACTACCCAACAAACC 59.578 52.381 0.00 0.00 0.00 3.27
614 2657 1.144093 CCTCCACTACCCAACAAACCA 59.856 52.381 0.00 0.00 0.00 3.67
616 2659 2.819608 CTCCACTACCCAACAAACCATG 59.180 50.000 0.00 0.00 0.00 3.66
617 2660 1.892474 CCACTACCCAACAAACCATGG 59.108 52.381 11.19 11.19 36.42 3.66
633 2676 4.153330 GGGAGGGAGGGAGCGGTA 62.153 72.222 0.00 0.00 0.00 4.02
849 2892 3.386078 TCATTTTCCTCCTCTCATCTCCG 59.614 47.826 0.00 0.00 0.00 4.63
851 2894 0.260230 TTCCTCCTCTCATCTCCGCT 59.740 55.000 0.00 0.00 0.00 5.52
852 2895 0.179004 TCCTCCTCTCATCTCCGCTC 60.179 60.000 0.00 0.00 0.00 5.03
854 2897 0.178992 CTCCTCTCATCTCCGCTCCT 60.179 60.000 0.00 0.00 0.00 3.69
855 2898 0.179004 TCCTCTCATCTCCGCTCCTC 60.179 60.000 0.00 0.00 0.00 3.71
881 2928 0.612229 CCTGCTCTGCTCTCCTTTGA 59.388 55.000 0.00 0.00 0.00 2.69
884 2931 1.973515 TGCTCTGCTCTCCTTTGAAGA 59.026 47.619 0.00 0.00 0.00 2.87
938 3013 0.944311 TTGCCTCTGTTCTTCGTCGC 60.944 55.000 0.00 0.00 0.00 5.19
939 3014 2.095252 GCCTCTGTTCTTCGTCGCC 61.095 63.158 0.00 0.00 0.00 5.54
940 3015 1.446272 CCTCTGTTCTTCGTCGCCC 60.446 63.158 0.00 0.00 0.00 6.13
941 3016 1.801913 CTCTGTTCTTCGTCGCCCG 60.802 63.158 0.00 0.00 38.13 6.13
989 3064 2.356069 GTGCTCCGATTTTGAAGGATCC 59.644 50.000 2.48 2.48 33.04 3.36
991 3066 2.615912 GCTCCGATTTTGAAGGATCCAG 59.384 50.000 15.82 0.00 33.04 3.86
1072 3149 6.371809 TTTGTTGGAGTAGAACATGTTGAC 57.628 37.500 17.58 13.49 33.41 3.18
1107 3185 3.616821 GCCGCAGAACTGTTTTTCTTTTT 59.383 39.130 0.00 0.00 33.31 1.94
1199 3296 4.320608 TGTTGACCAAGCAGAAAATTCC 57.679 40.909 0.00 0.00 0.00 3.01
1215 3312 8.950210 CAGAAAATTCCTGCTGAAATTAGTAGA 58.050 33.333 0.00 0.00 36.33 2.59
1216 3313 9.520515 AGAAAATTCCTGCTGAAATTAGTAGAA 57.479 29.630 0.00 0.00 36.33 2.10
1217 3314 9.561270 GAAAATTCCTGCTGAAATTAGTAGAAC 57.439 33.333 0.00 0.00 36.33 3.01
1218 3315 6.910536 ATTCCTGCTGAAATTAGTAGAACG 57.089 37.500 0.00 0.00 36.33 3.95
1220 3317 5.790593 TCCTGCTGAAATTAGTAGAACGTT 58.209 37.500 0.00 0.00 32.88 3.99
1221 3318 5.637810 TCCTGCTGAAATTAGTAGAACGTTG 59.362 40.000 5.00 0.00 32.88 4.10
1222 3319 5.408604 CCTGCTGAAATTAGTAGAACGTTGT 59.591 40.000 5.00 3.64 32.88 3.32
1247 3347 6.308041 TGAATCGAGTCTAACAAAATCGTCTG 59.692 38.462 14.66 0.00 35.05 3.51
1466 3567 1.076438 ACCCTTTCCTCCCCAAGAAG 58.924 55.000 0.00 0.00 0.00 2.85
1467 3568 0.323816 CCCTTTCCTCCCCAAGAAGC 60.324 60.000 0.00 0.00 0.00 3.86
1470 3571 0.698818 TTTCCTCCCCAAGAAGCTCC 59.301 55.000 0.00 0.00 0.00 4.70
1472 3573 0.253347 TCCTCCCCAAGAAGCTCCAT 60.253 55.000 0.00 0.00 0.00 3.41
1473 3574 0.182299 CCTCCCCAAGAAGCTCCATC 59.818 60.000 0.00 0.00 0.00 3.51
1477 3578 1.681166 CCCCAAGAAGCTCCATCTGTG 60.681 57.143 0.00 0.00 0.00 3.66
1478 3579 1.280133 CCCAAGAAGCTCCATCTGTGA 59.720 52.381 0.00 0.00 0.00 3.58
1479 3580 2.092538 CCCAAGAAGCTCCATCTGTGAT 60.093 50.000 0.00 0.00 0.00 3.06
1480 3581 3.618351 CCAAGAAGCTCCATCTGTGATT 58.382 45.455 0.00 0.00 0.00 2.57
1481 3582 3.626670 CCAAGAAGCTCCATCTGTGATTC 59.373 47.826 0.00 0.00 34.06 2.52
1484 3585 2.328819 AGCTCCATCTGTGATTCTGC 57.671 50.000 0.00 0.00 0.00 4.26
1493 3594 6.100279 TCCATCTGTGATTCTGCTACCTTATT 59.900 38.462 0.00 0.00 0.00 1.40
1503 3607 6.328641 TCTGCTACCTTATTATCCGAGAAC 57.671 41.667 0.00 0.00 0.00 3.01
1508 3612 7.825270 TGCTACCTTATTATCCGAGAACAAAAA 59.175 33.333 0.00 0.00 0.00 1.94
1509 3613 8.837389 GCTACCTTATTATCCGAGAACAAAAAT 58.163 33.333 0.00 0.00 0.00 1.82
1520 3625 9.996554 ATCCGAGAACAAAAATTAAAAATCCTT 57.003 25.926 0.00 0.00 0.00 3.36
1521 3626 9.255304 TCCGAGAACAAAAATTAAAAATCCTTG 57.745 29.630 0.00 0.00 0.00 3.61
1543 3648 6.713762 TGTGATCTGACAAATGGTTTCTTT 57.286 33.333 0.00 0.00 0.00 2.52
2008 4122 5.690409 CCAGCAAAAGCATAATATCTTGCAG 59.310 40.000 11.21 0.00 41.20 4.41
2079 4193 9.099454 ACACACTAGCAGCTCTTTTATTATTAC 57.901 33.333 0.00 0.00 0.00 1.89
2157 4283 4.162320 TCAGAAATCCAAGGGCAGTAGTAG 59.838 45.833 0.00 0.00 0.00 2.57
2158 4284 4.080863 CAGAAATCCAAGGGCAGTAGTAGT 60.081 45.833 0.00 0.00 0.00 2.73
2159 4285 5.128827 CAGAAATCCAAGGGCAGTAGTAGTA 59.871 44.000 0.00 0.00 0.00 1.82
2186 4312 4.150627 CAGAAGAAGTGGTATGTGACAACG 59.849 45.833 0.00 0.00 37.04 4.10
2242 4368 5.348418 AGACAGTTGTTGTGAATGAATCG 57.652 39.130 0.00 0.00 41.05 3.34
2287 4413 3.286751 GACCTGCAAACTGCCGCA 61.287 61.111 0.00 0.00 44.23 5.69
2309 4435 5.509840 GCAGATATGGAACTGGATACTTCGT 60.510 44.000 0.00 0.00 35.05 3.85
2319 4445 2.015587 GGATACTTCGTCCGAGACACT 58.984 52.381 5.15 0.00 32.09 3.55
2335 4461 0.179048 CACTCACCAGTGCACCAGAA 60.179 55.000 14.63 0.00 43.77 3.02
2368 4494 1.607178 CCCATGGCTGGCAAACTCA 60.607 57.895 8.35 0.00 41.64 3.41
2389 4515 5.410924 TCACAGCAGTTCATGTACTATGTC 58.589 41.667 15.34 3.55 29.63 3.06
2441 4567 2.745037 GAAGTGTGCCGTACCCCA 59.255 61.111 0.00 0.00 0.00 4.96
2479 4605 0.520404 CAGATCAACAGCACCAGCAC 59.480 55.000 0.00 0.00 45.49 4.40
2698 4824 3.691342 TACAAGAGGTGCGCGGCT 61.691 61.111 8.83 0.00 0.00 5.52
2771 4897 1.336887 TGACGAGGCTCTGCTTGTAAC 60.337 52.381 13.50 0.00 0.00 2.50
2772 4898 0.969894 ACGAGGCTCTGCTTGTAACT 59.030 50.000 13.50 0.00 0.00 2.24
2777 4904 1.002544 GGCTCTGCTTGTAACTCTGGT 59.997 52.381 0.00 0.00 0.00 4.00
2782 4909 2.234908 CTGCTTGTAACTCTGGTAGGCT 59.765 50.000 0.00 0.00 0.00 4.58
2868 4996 7.223387 GTCGACGTTGACCTATATAATTTTGGT 59.777 37.037 23.14 0.00 32.61 3.67
2907 5035 5.547465 TCGATCGCCCTGATGTAAATTAAT 58.453 37.500 11.09 0.00 37.47 1.40
2975 5103 6.407202 AGGCCTTCTTAGTTGTACTATGTTG 58.593 40.000 0.00 0.00 29.64 3.33
2978 5106 7.148457 GGCCTTCTTAGTTGTACTATGTTGTTC 60.148 40.741 0.00 0.00 29.64 3.18
2979 5107 7.603024 GCCTTCTTAGTTGTACTATGTTGTTCT 59.397 37.037 0.00 0.00 29.64 3.01
2983 5111 9.472361 TCTTAGTTGTACTATGTTGTTCTTGAC 57.528 33.333 0.00 0.00 29.64 3.18
3057 5400 8.883731 CAAATGAACCGAAGACTTCATAACTAT 58.116 33.333 15.36 0.06 34.90 2.12
3126 5518 7.275920 GTGAATGTAATTAGATGAGGACTGGT 58.724 38.462 0.00 0.00 36.07 4.00
3150 5543 4.174762 GTTAAGCCTTCTTCTGTAGACGG 58.825 47.826 2.94 2.94 43.48 4.79
3158 5551 1.473278 CTTCTGTAGACGGTCCTCACC 59.527 57.143 4.14 0.00 39.69 4.02
3168 5561 0.685660 GGTCCTCACCGGAGAACTTT 59.314 55.000 9.46 0.00 44.20 2.66
3175 5568 3.664107 TCACCGGAGAACTTTCAGAATG 58.336 45.455 9.46 0.00 37.54 2.67
3196 5589 6.603237 ATGACGGATTATGTTGTATGTGTG 57.397 37.500 0.00 0.00 0.00 3.82
3200 5593 6.288294 ACGGATTATGTTGTATGTGTGCTAT 58.712 36.000 0.00 0.00 0.00 2.97
3226 5621 2.816087 CCACAGGTGAACTTGAATCAGG 59.184 50.000 0.00 0.00 0.00 3.86
3279 5702 4.412528 CCTACAAATAGGCCCCTCTTTAGT 59.587 45.833 0.00 0.00 41.80 2.24
3280 5703 4.505324 ACAAATAGGCCCCTCTTTAGTC 57.495 45.455 0.00 0.00 0.00 2.59
3282 5705 1.718280 ATAGGCCCCTCTTTAGTCCG 58.282 55.000 0.00 0.00 0.00 4.79
3329 5752 6.893020 ATCAGGGAGAAGTACCATAACTTT 57.107 37.500 0.00 0.00 39.78 2.66
3337 5760 9.841880 GGAGAAGTACCATAACTTTTGAAATTC 57.158 33.333 0.00 0.00 39.78 2.17
3391 5814 3.572255 GGTCACAAACTTGCATCCCTAAA 59.428 43.478 0.00 0.00 0.00 1.85
3404 5827 8.700439 TTGCATCCCTAAAACTACTACTTTTT 57.300 30.769 0.00 0.00 0.00 1.94
3406 5829 7.118680 TGCATCCCTAAAACTACTACTTTTTCG 59.881 37.037 0.00 0.00 0.00 3.46
3408 5831 5.934043 TCCCTAAAACTACTACTTTTTCGGC 59.066 40.000 0.00 0.00 30.01 5.54
3409 5832 5.936372 CCCTAAAACTACTACTTTTTCGGCT 59.064 40.000 0.00 0.00 30.01 5.52
3412 5835 8.654215 CCTAAAACTACTACTTTTTCGGCTAAG 58.346 37.037 0.00 0.00 0.00 2.18
3415 5838 8.667076 AAACTACTACTTTTTCGGCTAAGAAA 57.333 30.769 0.00 0.00 38.23 2.52
3436 5859 6.791466 AGAAAACCCTACTACCTTCTACCTTT 59.209 38.462 0.00 0.00 0.00 3.11
3448 6785 0.693049 CTACCTTTCAGTGCACCCCT 59.307 55.000 14.63 0.00 0.00 4.79
3452 6789 1.548582 CCTTTCAGTGCACCCCTTCAT 60.549 52.381 14.63 0.00 0.00 2.57
3456 6793 0.599558 CAGTGCACCCCTTCATTGTG 59.400 55.000 14.63 0.00 0.00 3.33
3462 6799 3.855689 CACCCCTTCATTGTGCTTTAG 57.144 47.619 0.00 0.00 0.00 1.85
3475 6812 1.277842 TGCTTTAGGATCCGTGCTGAA 59.722 47.619 5.98 0.00 0.00 3.02
3488 6825 4.631377 TCCGTGCTGAAGAACAATAAGATG 59.369 41.667 0.00 0.00 0.00 2.90
3490 6827 5.319139 CGTGCTGAAGAACAATAAGATGTG 58.681 41.667 0.00 0.00 32.81 3.21
3491 6828 5.091431 GTGCTGAAGAACAATAAGATGTGC 58.909 41.667 0.00 0.00 32.81 4.57
3492 6829 4.156556 TGCTGAAGAACAATAAGATGTGCC 59.843 41.667 0.00 0.00 32.81 5.01
3493 6830 4.397417 GCTGAAGAACAATAAGATGTGCCT 59.603 41.667 0.00 0.00 32.81 4.75
3507 6847 3.044305 GCCTGCAGTTCTTCGCGT 61.044 61.111 13.81 0.00 0.00 6.01
3520 6860 0.179084 TTCGCGTGGGAATCCAGATC 60.179 55.000 5.77 0.00 45.05 2.75
3523 6863 1.162800 GCGTGGGAATCCAGATCAGC 61.163 60.000 0.09 0.00 45.05 4.26
3525 6865 1.134280 CGTGGGAATCCAGATCAGCTT 60.134 52.381 0.09 0.00 45.05 3.74
3556 6896 0.736053 TCACAACGGTTGCAAGGAAC 59.264 50.000 20.20 0.00 0.00 3.62
3558 6898 1.135257 CACAACGGTTGCAAGGAACAA 60.135 47.619 20.20 0.00 0.00 2.83
3559 6899 1.135228 ACAACGGTTGCAAGGAACAAC 60.135 47.619 20.20 0.00 45.30 3.32
3573 6913 3.260884 AGGAACAACATCGAGAAGCCTAA 59.739 43.478 0.00 0.00 0.00 2.69
3598 6938 1.199327 GATGTATAGCCTAGCGACGCA 59.801 52.381 23.70 7.20 0.00 5.24
3599 6939 0.591659 TGTATAGCCTAGCGACGCAG 59.408 55.000 23.70 16.27 0.00 5.18
3623 6963 2.743928 GTGAGGAAGCAGGCGGTG 60.744 66.667 0.00 0.00 0.00 4.94
3624 6964 4.020617 TGAGGAAGCAGGCGGTGG 62.021 66.667 0.00 0.00 0.00 4.61
3625 6965 4.021925 GAGGAAGCAGGCGGTGGT 62.022 66.667 0.00 0.00 39.08 4.16
3626 6966 4.335647 AGGAAGCAGGCGGTGGTG 62.336 66.667 0.00 0.00 36.83 4.17
3651 6991 2.816958 GCGCTGCAGCTGCTAGAA 60.817 61.111 36.61 17.79 42.66 2.10
3652 6992 2.393768 GCGCTGCAGCTGCTAGAAA 61.394 57.895 36.61 17.40 42.66 2.52
3654 6994 0.738762 CGCTGCAGCTGCTAGAAAGA 60.739 55.000 36.61 15.90 42.66 2.52
3657 6997 2.223294 GCTGCAGCTGCTAGAAAGAATG 60.223 50.000 36.61 15.19 42.66 2.67
3658 6998 3.008330 CTGCAGCTGCTAGAAAGAATGT 58.992 45.455 36.61 0.00 42.66 2.71
3661 7001 3.603532 CAGCTGCTAGAAAGAATGTGGA 58.396 45.455 0.00 0.00 0.00 4.02
3662 7002 4.005650 CAGCTGCTAGAAAGAATGTGGAA 58.994 43.478 0.00 0.00 0.00 3.53
3663 7003 4.094590 CAGCTGCTAGAAAGAATGTGGAAG 59.905 45.833 0.00 0.00 0.00 3.46
3664 7004 3.376546 GCTGCTAGAAAGAATGTGGAAGG 59.623 47.826 0.00 0.00 0.00 3.46
3665 7005 3.944015 CTGCTAGAAAGAATGTGGAAGGG 59.056 47.826 0.00 0.00 0.00 3.95
3666 7006 3.330701 TGCTAGAAAGAATGTGGAAGGGT 59.669 43.478 0.00 0.00 0.00 4.34
3667 7007 4.534500 TGCTAGAAAGAATGTGGAAGGGTA 59.466 41.667 0.00 0.00 0.00 3.69
3668 7008 5.191722 TGCTAGAAAGAATGTGGAAGGGTAT 59.808 40.000 0.00 0.00 0.00 2.73
3670 7010 6.603599 GCTAGAAAGAATGTGGAAGGGTATTT 59.396 38.462 0.00 0.00 0.00 1.40
3672 7012 6.552008 AGAAAGAATGTGGAAGGGTATTTGA 58.448 36.000 0.00 0.00 0.00 2.69
3673 7013 6.660949 AGAAAGAATGTGGAAGGGTATTTGAG 59.339 38.462 0.00 0.00 0.00 3.02
3674 7014 5.779241 AGAATGTGGAAGGGTATTTGAGA 57.221 39.130 0.00 0.00 0.00 3.27
3676 7016 6.735556 AGAATGTGGAAGGGTATTTGAGATT 58.264 36.000 0.00 0.00 0.00 2.40
3677 7017 7.184862 AGAATGTGGAAGGGTATTTGAGATTT 58.815 34.615 0.00 0.00 0.00 2.17
3679 7019 6.588719 TGTGGAAGGGTATTTGAGATTTTG 57.411 37.500 0.00 0.00 0.00 2.44
3680 7020 5.047377 TGTGGAAGGGTATTTGAGATTTTGC 60.047 40.000 0.00 0.00 0.00 3.68
3683 7023 5.394553 GGAAGGGTATTTGAGATTTTGCCAG 60.395 44.000 0.00 0.00 0.00 4.85
3685 7025 4.706962 AGGGTATTTGAGATTTTGCCAGTC 59.293 41.667 0.00 0.00 0.00 3.51
3687 7027 4.462483 GGTATTTGAGATTTTGCCAGTCCA 59.538 41.667 0.00 0.00 0.00 4.02
3689 7029 5.750352 ATTTGAGATTTTGCCAGTCCAAT 57.250 34.783 0.00 0.00 0.00 3.16
3690 7030 5.549742 TTTGAGATTTTGCCAGTCCAATT 57.450 34.783 0.00 0.00 0.00 2.32
3691 7031 5.549742 TTGAGATTTTGCCAGTCCAATTT 57.450 34.783 0.00 0.00 0.00 1.82
3692 7032 4.885413 TGAGATTTTGCCAGTCCAATTTG 58.115 39.130 0.00 0.00 0.00 2.32
3693 7033 3.667360 AGATTTTGCCAGTCCAATTTGC 58.333 40.909 0.00 0.00 0.00 3.68
3695 7035 4.527816 AGATTTTGCCAGTCCAATTTGCTA 59.472 37.500 0.00 0.00 0.00 3.49
3696 7036 4.888326 TTTTGCCAGTCCAATTTGCTAT 57.112 36.364 0.00 0.00 0.00 2.97
3697 7037 4.888326 TTTGCCAGTCCAATTTGCTATT 57.112 36.364 0.00 0.00 0.00 1.73
3699 7039 3.164268 TGCCAGTCCAATTTGCTATTGT 58.836 40.909 10.03 0.00 0.00 2.71
3700 7040 3.056678 TGCCAGTCCAATTTGCTATTGTG 60.057 43.478 10.03 3.99 0.00 3.33
3703 7043 4.382254 CCAGTCCAATTTGCTATTGTGCAT 60.382 41.667 0.00 0.00 42.96 3.96
3704 7044 4.802039 CAGTCCAATTTGCTATTGTGCATC 59.198 41.667 0.00 0.00 42.96 3.91
3705 7045 3.792956 GTCCAATTTGCTATTGTGCATCG 59.207 43.478 0.00 0.00 42.96 3.84
3706 7046 3.117794 CCAATTTGCTATTGTGCATCGG 58.882 45.455 0.00 0.00 42.96 4.18
3707 7047 3.429272 CCAATTTGCTATTGTGCATCGGT 60.429 43.478 0.00 0.00 42.96 4.69
3708 7048 3.698029 ATTTGCTATTGTGCATCGGTC 57.302 42.857 0.00 0.00 42.96 4.79
3709 7049 2.106477 TTGCTATTGTGCATCGGTCA 57.894 45.000 0.00 0.00 42.96 4.02
3710 7050 1.655484 TGCTATTGTGCATCGGTCAG 58.345 50.000 0.00 0.00 38.12 3.51
3711 7051 0.305922 GCTATTGTGCATCGGTCAGC 59.694 55.000 0.00 0.00 0.00 4.26
3712 7052 1.945387 CTATTGTGCATCGGTCAGCT 58.055 50.000 0.00 0.00 0.00 4.24
3713 7053 2.803133 GCTATTGTGCATCGGTCAGCTA 60.803 50.000 0.00 0.00 0.00 3.32
3714 7054 1.945387 ATTGTGCATCGGTCAGCTAG 58.055 50.000 0.00 0.00 0.00 3.42
3715 7055 0.108186 TTGTGCATCGGTCAGCTAGG 60.108 55.000 0.00 0.00 0.00 3.02
3716 7056 1.257750 TGTGCATCGGTCAGCTAGGT 61.258 55.000 0.00 0.00 0.00 3.08
3717 7057 0.108138 GTGCATCGGTCAGCTAGGTT 60.108 55.000 0.00 0.00 0.00 3.50
3718 7058 0.613260 TGCATCGGTCAGCTAGGTTT 59.387 50.000 0.00 0.00 0.00 3.27
3719 7059 1.003118 TGCATCGGTCAGCTAGGTTTT 59.997 47.619 0.00 0.00 0.00 2.43
3723 7063 2.244695 TCGGTCAGCTAGGTTTTGAGA 58.755 47.619 0.00 0.00 0.00 3.27
3724 7064 2.832129 TCGGTCAGCTAGGTTTTGAGAT 59.168 45.455 0.00 0.00 0.00 2.75
3725 7065 3.260884 TCGGTCAGCTAGGTTTTGAGATT 59.739 43.478 0.00 0.00 0.00 2.40
3726 7066 4.464951 TCGGTCAGCTAGGTTTTGAGATTA 59.535 41.667 0.00 0.00 0.00 1.75
3727 7067 5.046878 TCGGTCAGCTAGGTTTTGAGATTAA 60.047 40.000 0.00 0.00 0.00 1.40
3728 7068 5.292101 CGGTCAGCTAGGTTTTGAGATTAAG 59.708 44.000 0.00 0.00 0.00 1.85
3730 7162 6.536941 GGTCAGCTAGGTTTTGAGATTAAGAG 59.463 42.308 0.00 0.00 0.00 2.85
3739 7171 9.799106 AGGTTTTGAGATTAAGAGATTCTTTGA 57.201 29.630 0.00 0.00 37.89 2.69
3752 7184 8.890124 AGAGATTCTTTGATACATCATGACTG 57.110 34.615 0.00 0.33 36.56 3.51
3753 7185 7.441760 AGAGATTCTTTGATACATCATGACTGC 59.558 37.037 0.00 0.00 36.56 4.40
3754 7186 6.485984 AGATTCTTTGATACATCATGACTGCC 59.514 38.462 0.00 0.00 36.56 4.85
3755 7187 5.101648 TCTTTGATACATCATGACTGCCA 57.898 39.130 0.00 0.00 36.56 4.92
3757 7189 3.198409 TGATACATCATGACTGCCACC 57.802 47.619 0.00 0.00 0.00 4.61
3759 7191 0.901827 TACATCATGACTGCCACCGT 59.098 50.000 0.00 0.00 0.00 4.83
3760 7192 0.674581 ACATCATGACTGCCACCGTG 60.675 55.000 0.00 0.00 0.00 4.94
3761 7193 0.391528 CATCATGACTGCCACCGTGA 60.392 55.000 0.00 0.00 33.43 4.35
3762 7194 0.543277 ATCATGACTGCCACCGTGAT 59.457 50.000 0.00 0.00 35.02 3.06
3764 7196 0.107993 CATGACTGCCACCGTGATCT 60.108 55.000 0.00 0.00 0.00 2.75
3766 7198 0.320683 TGACTGCCACCGTGATCTTG 60.321 55.000 0.00 0.00 0.00 3.02
3767 7199 1.639298 GACTGCCACCGTGATCTTGC 61.639 60.000 0.00 0.00 0.00 4.01
3768 7200 1.672030 CTGCCACCGTGATCTTGCA 60.672 57.895 0.00 0.00 0.00 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 2068 6.813152 CAGTTAAATGGGACTTTTGGCATTAG 59.187 38.462 0.00 0.00 0.00 1.73
60 2071 4.837860 TCAGTTAAATGGGACTTTTGGCAT 59.162 37.500 2.65 0.00 0.00 4.40
62 2073 4.280929 AGTCAGTTAAATGGGACTTTTGGC 59.719 41.667 2.65 0.00 37.31 4.52
63 2074 5.334879 CGAGTCAGTTAAATGGGACTTTTGG 60.335 44.000 2.65 0.00 40.48 3.28
64 2075 5.334879 CCGAGTCAGTTAAATGGGACTTTTG 60.335 44.000 2.65 0.00 40.48 2.44
65 2076 4.760204 CCGAGTCAGTTAAATGGGACTTTT 59.240 41.667 2.65 0.00 40.48 2.27
72 2083 2.107950 TGGCCGAGTCAGTTAAATGG 57.892 50.000 2.65 0.00 0.00 3.16
80 2091 1.593196 TTTCTGTTTGGCCGAGTCAG 58.407 50.000 16.58 16.58 0.00 3.51
85 2096 1.877443 GCTAGTTTTCTGTTTGGCCGA 59.123 47.619 0.00 0.00 0.00 5.54
86 2097 1.606668 TGCTAGTTTTCTGTTTGGCCG 59.393 47.619 0.00 0.00 0.00 6.13
88 2099 6.194796 TCATATGCTAGTTTTCTGTTTGGC 57.805 37.500 0.00 0.00 0.00 4.52
89 2100 9.643693 AAAATCATATGCTAGTTTTCTGTTTGG 57.356 29.630 0.00 0.00 0.00 3.28
108 2119 8.681806 CCCCCGCAAAAATAAAAATAAAATCAT 58.318 29.630 0.00 0.00 0.00 2.45
109 2120 7.883311 TCCCCCGCAAAAATAAAAATAAAATCA 59.117 29.630 0.00 0.00 0.00 2.57
110 2121 8.270080 TCCCCCGCAAAAATAAAAATAAAATC 57.730 30.769 0.00 0.00 0.00 2.17
111 2122 7.148154 GCTCCCCCGCAAAAATAAAAATAAAAT 60.148 33.333 0.00 0.00 0.00 1.82
112 2123 6.149640 GCTCCCCCGCAAAAATAAAAATAAAA 59.850 34.615 0.00 0.00 0.00 1.52
113 2124 5.644206 GCTCCCCCGCAAAAATAAAAATAAA 59.356 36.000 0.00 0.00 0.00 1.40
114 2125 5.179533 GCTCCCCCGCAAAAATAAAAATAA 58.820 37.500 0.00 0.00 0.00 1.40
115 2126 4.223032 TGCTCCCCCGCAAAAATAAAAATA 59.777 37.500 0.00 0.00 36.89 1.40
116 2127 3.008485 TGCTCCCCCGCAAAAATAAAAAT 59.992 39.130 0.00 0.00 36.89 1.82
117 2128 2.368875 TGCTCCCCCGCAAAAATAAAAA 59.631 40.909 0.00 0.00 36.89 1.94
118 2129 1.971357 TGCTCCCCCGCAAAAATAAAA 59.029 42.857 0.00 0.00 36.89 1.52
119 2130 1.633774 TGCTCCCCCGCAAAAATAAA 58.366 45.000 0.00 0.00 36.89 1.40
120 2131 1.859302 ATGCTCCCCCGCAAAAATAA 58.141 45.000 0.00 0.00 44.06 1.40
121 2132 2.738587 TATGCTCCCCCGCAAAAATA 57.261 45.000 0.00 0.00 44.06 1.40
122 2133 1.688197 CATATGCTCCCCCGCAAAAAT 59.312 47.619 0.00 0.00 44.06 1.82
123 2134 1.110442 CATATGCTCCCCCGCAAAAA 58.890 50.000 0.00 0.00 44.06 1.94
124 2135 0.257328 TCATATGCTCCCCCGCAAAA 59.743 50.000 0.00 0.00 44.06 2.44
125 2136 0.478072 ATCATATGCTCCCCCGCAAA 59.522 50.000 0.00 0.00 44.06 3.68
126 2137 0.478072 AATCATATGCTCCCCCGCAA 59.522 50.000 0.00 0.00 44.06 4.85
127 2138 0.036732 GAATCATATGCTCCCCCGCA 59.963 55.000 0.00 0.00 45.10 5.69
128 2139 0.326264 AGAATCATATGCTCCCCCGC 59.674 55.000 0.00 0.00 0.00 6.13
129 2140 2.867109 AAGAATCATATGCTCCCCCG 57.133 50.000 0.00 0.00 0.00 5.73
130 2141 7.051000 GTCTAATAAGAATCATATGCTCCCCC 58.949 42.308 0.00 0.00 32.16 5.40
131 2142 6.758886 CGTCTAATAAGAATCATATGCTCCCC 59.241 42.308 0.00 0.00 32.16 4.81
132 2143 6.256757 GCGTCTAATAAGAATCATATGCTCCC 59.743 42.308 0.00 0.00 32.16 4.30
133 2144 6.256757 GGCGTCTAATAAGAATCATATGCTCC 59.743 42.308 0.00 0.00 32.16 4.70
134 2145 7.038659 AGGCGTCTAATAAGAATCATATGCTC 58.961 38.462 0.00 0.00 32.16 4.26
135 2146 6.940739 AGGCGTCTAATAAGAATCATATGCT 58.059 36.000 0.00 0.00 32.16 3.79
136 2147 7.043986 CGTAGGCGTCTAATAAGAATCATATGC 60.044 40.741 0.00 0.00 32.16 3.14
137 2148 8.182227 TCGTAGGCGTCTAATAAGAATCATATG 58.818 37.037 0.00 0.00 39.49 1.78
138 2149 8.277490 TCGTAGGCGTCTAATAAGAATCATAT 57.723 34.615 0.00 0.00 39.49 1.78
139 2150 7.677454 TCGTAGGCGTCTAATAAGAATCATA 57.323 36.000 0.00 0.00 39.49 2.15
148 2159 6.016527 ACATCAAGAATCGTAGGCGTCTAATA 60.017 38.462 0.00 0.00 39.49 0.98
157 2168 6.682746 AGCTACATACATCAAGAATCGTAGG 58.317 40.000 0.00 0.00 0.00 3.18
162 2173 5.049129 GGCCAAGCTACATACATCAAGAATC 60.049 44.000 0.00 0.00 0.00 2.52
198 2209 2.375146 TGCTACTTCTCAGCCGTATGA 58.625 47.619 0.00 0.00 38.29 2.15
235 2246 1.040339 TTTGGGCGTGCTGGTTTTCT 61.040 50.000 0.00 0.00 0.00 2.52
289 2301 4.763793 ACTTGTCTTCTTGGTGATTGATGG 59.236 41.667 0.00 0.00 0.00 3.51
290 2302 5.390251 CGACTTGTCTTCTTGGTGATTGATG 60.390 44.000 0.00 0.00 0.00 3.07
306 2318 2.978489 ACGTCTCGAATTTCGACTTGTC 59.022 45.455 17.08 5.73 44.82 3.18
325 2337 4.108336 CAGTCAGTGAGGATATTGTCACG 58.892 47.826 10.95 7.72 46.43 4.35
329 2341 2.159043 CGCCAGTCAGTGAGGATATTGT 60.159 50.000 2.62 0.00 0.00 2.71
335 2347 0.976641 ATTTCGCCAGTCAGTGAGGA 59.023 50.000 2.62 0.00 0.00 3.71
410 2422 3.888930 TCTTTTCCGCAAGATTTCACCTT 59.111 39.130 0.00 0.00 43.02 3.50
433 2445 4.260212 GCCTCTTTTTCGCCTTTGTTTTTC 60.260 41.667 0.00 0.00 0.00 2.29
434 2446 3.621268 GCCTCTTTTTCGCCTTTGTTTTT 59.379 39.130 0.00 0.00 0.00 1.94
439 2451 0.591170 TCGCCTCTTTTTCGCCTTTG 59.409 50.000 0.00 0.00 0.00 2.77
442 2454 1.026718 CCATCGCCTCTTTTTCGCCT 61.027 55.000 0.00 0.00 0.00 5.52
445 2457 3.491267 GTCTATCCATCGCCTCTTTTTCG 59.509 47.826 0.00 0.00 0.00 3.46
446 2458 4.442706 TGTCTATCCATCGCCTCTTTTTC 58.557 43.478 0.00 0.00 0.00 2.29
475 2500 1.731709 CACGAAATGGATGCGTCTTCA 59.268 47.619 5.77 0.00 35.90 3.02
505 2530 1.748122 CATGTGCTGTGCTCCTCCC 60.748 63.158 0.00 0.00 0.00 4.30
506 2531 1.748122 CCATGTGCTGTGCTCCTCC 60.748 63.158 0.00 0.00 0.00 4.30
507 2532 0.107312 ATCCATGTGCTGTGCTCCTC 60.107 55.000 0.00 0.00 0.00 3.71
561 2603 1.074423 AAGGGAGGTCACGTCTCGA 59.926 57.895 0.00 0.00 32.34 4.04
580 2623 1.222113 GGAGGACTACTGGCAAGGC 59.778 63.158 0.00 0.00 0.00 4.35
595 2638 2.649531 TGGTTTGTTGGGTAGTGGAG 57.350 50.000 0.00 0.00 0.00 3.86
605 2648 1.549203 CTCCCTCCCATGGTTTGTTG 58.451 55.000 11.73 0.00 0.00 3.33
613 2656 3.554342 CGCTCCCTCCCTCCCATG 61.554 72.222 0.00 0.00 0.00 3.66
614 2657 4.888325 CCGCTCCCTCCCTCCCAT 62.888 72.222 0.00 0.00 0.00 4.00
616 2659 4.153330 TACCGCTCCCTCCCTCCC 62.153 72.222 0.00 0.00 0.00 4.30
617 2660 2.522193 CTACCGCTCCCTCCCTCC 60.522 72.222 0.00 0.00 0.00 4.30
618 2661 3.228017 GCTACCGCTCCCTCCCTC 61.228 72.222 0.00 0.00 0.00 4.30
619 2662 4.075793 TGCTACCGCTCCCTCCCT 62.076 66.667 0.00 0.00 36.97 4.20
633 2676 1.303155 GCTGCTTCCTTCACCTGCT 60.303 57.895 0.00 0.00 0.00 4.24
642 2685 2.999648 TGGCTCTCGCTGCTTCCT 61.000 61.111 0.00 0.00 36.09 3.36
643 2686 2.817396 GTGGCTCTCGCTGCTTCC 60.817 66.667 0.00 0.00 36.09 3.46
776 2819 2.761160 GGGGGAGAAAAAGGGCGA 59.239 61.111 0.00 0.00 0.00 5.54
804 2847 3.168604 CGTGTGCTGCGACGAGAG 61.169 66.667 16.32 0.00 37.81 3.20
849 2892 3.844090 GCAGGAGACGGGAGGAGC 61.844 72.222 0.00 0.00 0.00 4.70
851 2894 2.043852 GAGCAGGAGACGGGAGGA 60.044 66.667 0.00 0.00 0.00 3.71
852 2895 2.043450 AGAGCAGGAGACGGGAGG 60.043 66.667 0.00 0.00 0.00 4.30
854 2897 3.071206 GCAGAGCAGGAGACGGGA 61.071 66.667 0.00 0.00 0.00 5.14
855 2898 3.073735 AGCAGAGCAGGAGACGGG 61.074 66.667 0.00 0.00 0.00 5.28
881 2928 8.624776 CCTAATCTTTGTTGTTGTTTCTCTCTT 58.375 33.333 0.00 0.00 0.00 2.85
884 2931 7.255277 GCTCCTAATCTTTGTTGTTGTTTCTCT 60.255 37.037 0.00 0.00 0.00 3.10
939 3014 3.391665 AAATCGGGCTGAGAGGCGG 62.392 63.158 1.04 0.00 42.43 6.13
940 3015 2.176273 CAAATCGGGCTGAGAGGCG 61.176 63.158 1.04 0.00 42.43 5.52
941 3016 1.821332 CCAAATCGGGCTGAGAGGC 60.821 63.158 1.04 0.00 40.51 4.70
973 3048 4.125703 CTCTCTGGATCCTTCAAAATCGG 58.874 47.826 14.23 0.00 0.00 4.18
989 3064 4.582701 AAACGAGCCATATCTCTCTCTG 57.417 45.455 0.00 0.00 0.00 3.35
991 3066 4.938080 TGAAAACGAGCCATATCTCTCTC 58.062 43.478 0.00 0.00 0.00 3.20
1020 3095 5.064452 ACATCTGAACAAAGATCGAGCAATC 59.936 40.000 2.38 0.00 34.60 2.67
1051 3126 4.055360 CGTCAACATGTTCTACTCCAACA 58.945 43.478 8.48 0.00 38.12 3.33
1060 3135 4.452455 GTGGATCTTTCGTCAACATGTTCT 59.548 41.667 8.48 0.00 0.00 3.01
1072 3149 3.564027 GCGGCCGTGGATCTTTCG 61.564 66.667 28.70 0.00 0.00 3.46
1199 3296 6.145534 TCACAACGTTCTACTAATTTCAGCAG 59.854 38.462 0.00 0.00 0.00 4.24
1204 3301 7.946043 TCGATTCACAACGTTCTACTAATTTC 58.054 34.615 0.00 0.00 0.00 2.17
1207 3304 6.618811 ACTCGATTCACAACGTTCTACTAAT 58.381 36.000 0.00 0.00 0.00 1.73
1209 3306 5.410746 AGACTCGATTCACAACGTTCTACTA 59.589 40.000 0.00 0.00 0.00 1.82
1210 3307 4.215827 AGACTCGATTCACAACGTTCTACT 59.784 41.667 0.00 0.00 0.00 2.57
1211 3308 4.474113 AGACTCGATTCACAACGTTCTAC 58.526 43.478 0.00 0.00 0.00 2.59
1212 3309 4.761235 AGACTCGATTCACAACGTTCTA 57.239 40.909 0.00 0.00 0.00 2.10
1214 3311 4.678287 TGTTAGACTCGATTCACAACGTTC 59.322 41.667 0.00 0.00 0.00 3.95
1215 3312 4.613944 TGTTAGACTCGATTCACAACGTT 58.386 39.130 5.50 0.00 0.00 3.99
1216 3313 4.233123 TGTTAGACTCGATTCACAACGT 57.767 40.909 5.50 0.00 0.00 3.99
1217 3314 5.570262 TTTGTTAGACTCGATTCACAACG 57.430 39.130 5.50 0.00 0.00 4.10
1218 3315 6.732392 CGATTTTGTTAGACTCGATTCACAAC 59.268 38.462 5.50 8.91 0.00 3.32
1220 3317 5.924254 ACGATTTTGTTAGACTCGATTCACA 59.076 36.000 5.50 0.00 33.74 3.58
1221 3318 6.308282 AGACGATTTTGTTAGACTCGATTCAC 59.692 38.462 5.50 0.00 33.74 3.18
1222 3319 6.308041 CAGACGATTTTGTTAGACTCGATTCA 59.692 38.462 5.50 0.00 33.74 2.57
1466 3567 2.328819 AGCAGAATCACAGATGGAGC 57.671 50.000 0.00 0.00 0.00 4.70
1467 3568 3.387374 AGGTAGCAGAATCACAGATGGAG 59.613 47.826 0.00 0.00 0.00 3.86
1470 3571 9.149225 GATAATAAGGTAGCAGAATCACAGATG 57.851 37.037 0.00 0.00 0.00 2.90
1472 3573 7.523873 CGGATAATAAGGTAGCAGAATCACAGA 60.524 40.741 0.00 0.00 0.00 3.41
1473 3574 6.587990 CGGATAATAAGGTAGCAGAATCACAG 59.412 42.308 0.00 0.00 0.00 3.66
1477 3578 7.159322 TCTCGGATAATAAGGTAGCAGAATC 57.841 40.000 0.00 0.00 0.00 2.52
1478 3579 7.015292 TGTTCTCGGATAATAAGGTAGCAGAAT 59.985 37.037 0.00 0.00 0.00 2.40
1479 3580 6.322969 TGTTCTCGGATAATAAGGTAGCAGAA 59.677 38.462 0.00 0.00 0.00 3.02
1480 3581 5.831525 TGTTCTCGGATAATAAGGTAGCAGA 59.168 40.000 0.00 0.00 0.00 4.26
1481 3582 6.085555 TGTTCTCGGATAATAAGGTAGCAG 57.914 41.667 0.00 0.00 0.00 4.24
1509 3613 9.695526 CATTTGTCAGATCACAAGGATTTTTAA 57.304 29.630 0.00 0.00 37.57 1.52
1510 3615 8.306038 CCATTTGTCAGATCACAAGGATTTTTA 58.694 33.333 0.00 0.00 37.57 1.52
1520 3625 6.320926 TGAAAGAAACCATTTGTCAGATCACA 59.679 34.615 0.00 0.00 0.00 3.58
1521 3626 6.638468 GTGAAAGAAACCATTTGTCAGATCAC 59.362 38.462 0.00 0.00 0.00 3.06
1543 3648 0.457443 CTATGTGCTCTGCGGAGTGA 59.543 55.000 23.36 8.28 41.38 3.41
2015 4129 5.421056 TGTGGACTTGTTAAGATCGGATAGT 59.579 40.000 0.00 0.00 0.00 2.12
2091 4213 9.649167 ATTCATCAGAATTGGAAAAGATTGAAC 57.351 29.630 0.00 0.00 41.64 3.18
2309 4435 2.341452 CACTGGTGAGTGTCTCGGA 58.659 57.895 0.00 0.00 44.15 4.55
2319 4445 1.227943 GCTTCTGGTGCACTGGTGA 60.228 57.895 17.98 7.12 0.00 4.02
2335 4461 0.251922 ATGGGCTCCATGTGTTTGCT 60.252 50.000 5.97 0.00 43.39 3.91
2368 4494 4.383118 GGGACATAGTACATGAACTGCTGT 60.383 45.833 0.00 0.00 32.57 4.40
2441 4567 1.528824 CCTTGGGGCTCGATGACAT 59.471 57.895 0.00 0.00 0.00 3.06
2601 4727 1.069296 CATGCACCATTTCGTTGTCGT 60.069 47.619 0.00 0.00 38.33 4.34
2606 4732 3.798646 CAGCATGCACCATTTCGTT 57.201 47.368 21.98 0.00 0.00 3.85
2698 4824 1.078918 CTGCATCGCCTTGGTCTCA 60.079 57.895 0.00 0.00 0.00 3.27
2771 4897 2.428890 CTGTACCTCAAGCCTACCAGAG 59.571 54.545 0.00 0.00 0.00 3.35
2772 4898 2.042569 TCTGTACCTCAAGCCTACCAGA 59.957 50.000 0.00 0.00 0.00 3.86
2777 4904 3.170991 ACACTCTGTACCTCAAGCCTA 57.829 47.619 0.00 0.00 0.00 3.93
2782 4909 4.504864 CCCAATGAACACTCTGTACCTCAA 60.505 45.833 0.00 0.00 0.00 3.02
2868 4996 4.212847 GCGATCGATCCTACTACAACTACA 59.787 45.833 21.57 0.00 0.00 2.74
2907 5035 4.337274 CCATTGATGAGAGCTGTGCAATAA 59.663 41.667 0.00 0.00 0.00 1.40
2975 5103 4.712763 CGCTAAGTTCATTGGTCAAGAAC 58.287 43.478 13.20 13.20 41.37 3.01
2978 5106 2.159517 GGCGCTAAGTTCATTGGTCAAG 60.160 50.000 7.64 0.00 0.00 3.02
2979 5107 1.810151 GGCGCTAAGTTCATTGGTCAA 59.190 47.619 7.64 0.00 0.00 3.18
2981 5109 0.373716 CGGCGCTAAGTTCATTGGTC 59.626 55.000 7.64 0.00 0.00 4.02
2982 5110 0.036765 TCGGCGCTAAGTTCATTGGT 60.037 50.000 7.64 0.00 0.00 3.67
2983 5111 1.003545 CATCGGCGCTAAGTTCATTGG 60.004 52.381 7.64 0.00 0.00 3.16
3080 5425 2.941064 CCCAGCACAACACATCATCTAG 59.059 50.000 0.00 0.00 0.00 2.43
3081 5426 2.305635 ACCCAGCACAACACATCATCTA 59.694 45.455 0.00 0.00 0.00 1.98
3082 5427 1.074405 ACCCAGCACAACACATCATCT 59.926 47.619 0.00 0.00 0.00 2.90
3126 5518 5.227908 CGTCTACAGAAGAAGGCTTAACAA 58.772 41.667 0.00 0.00 35.47 2.83
3150 5543 1.343465 TGAAAGTTCTCCGGTGAGGAC 59.657 52.381 6.29 3.36 46.10 3.85
3158 5551 2.668457 CCGTCATTCTGAAAGTTCTCCG 59.332 50.000 0.00 0.00 33.76 4.63
3160 5553 7.278868 ACATAATCCGTCATTCTGAAAGTTCTC 59.721 37.037 0.00 0.00 33.76 2.87
3168 5561 7.224557 CACATACAACATAATCCGTCATTCTGA 59.775 37.037 0.00 0.00 0.00 3.27
3175 5568 4.570772 AGCACACATACAACATAATCCGTC 59.429 41.667 0.00 0.00 0.00 4.79
3226 5621 6.389830 TTCATCTGCTAGTCTCTGATTCTC 57.610 41.667 0.00 0.00 0.00 2.87
3277 5700 6.687081 TTTTGTTGATTTAGTTGTCGGACT 57.313 33.333 9.88 0.00 0.00 3.85
3308 5731 6.472887 TCAAAAGTTATGGTACTTCTCCCTG 58.527 40.000 0.00 0.00 37.37 4.45
3378 5801 7.923414 AAAGTAGTAGTTTTAGGGATGCAAG 57.077 36.000 0.00 0.00 0.00 4.01
3391 5814 8.554528 GTTTTCTTAGCCGAAAAAGTAGTAGTT 58.445 33.333 7.48 0.00 42.54 2.24
3404 5827 3.448660 GGTAGTAGGGTTTTCTTAGCCGA 59.551 47.826 0.00 0.00 40.61 5.54
3406 5829 5.189342 AGAAGGTAGTAGGGTTTTCTTAGCC 59.811 44.000 0.00 0.00 35.91 3.93
3408 5831 7.618907 AGGTAGAAGGTAGTAGGGTTTTCTTAG 59.381 40.741 0.00 0.00 0.00 2.18
3409 5832 7.482157 AGGTAGAAGGTAGTAGGGTTTTCTTA 58.518 38.462 0.00 0.00 0.00 2.10
3412 5835 6.617782 AAGGTAGAAGGTAGTAGGGTTTTC 57.382 41.667 0.00 0.00 0.00 2.29
3415 5838 5.658474 TGAAAGGTAGAAGGTAGTAGGGTT 58.342 41.667 0.00 0.00 0.00 4.11
3436 5859 0.478072 ACAATGAAGGGGTGCACTGA 59.522 50.000 17.98 0.00 0.00 3.41
3448 6785 3.689161 CACGGATCCTAAAGCACAATGAA 59.311 43.478 10.75 0.00 0.00 2.57
3452 6789 1.003118 AGCACGGATCCTAAAGCACAA 59.997 47.619 10.75 0.00 0.00 3.33
3456 6793 1.936547 CTTCAGCACGGATCCTAAAGC 59.063 52.381 10.75 8.23 0.00 3.51
3460 6797 2.176045 TGTTCTTCAGCACGGATCCTA 58.824 47.619 10.75 0.00 0.00 2.94
3462 6799 1.808411 TTGTTCTTCAGCACGGATCC 58.192 50.000 0.00 0.00 0.00 3.36
3475 6812 3.689347 TGCAGGCACATCTTATTGTTCT 58.311 40.909 0.00 0.00 0.00 3.01
3488 6825 2.558313 GCGAAGAACTGCAGGCAC 59.442 61.111 19.93 8.74 0.00 5.01
3490 6827 3.044305 ACGCGAAGAACTGCAGGC 61.044 61.111 19.93 9.51 0.00 4.85
3491 6828 2.671177 CCACGCGAAGAACTGCAGG 61.671 63.158 19.93 0.00 0.00 4.85
3492 6829 2.671177 CCCACGCGAAGAACTGCAG 61.671 63.158 15.93 13.48 0.00 4.41
3493 6830 2.652382 TTCCCACGCGAAGAACTGCA 62.652 55.000 15.93 0.00 0.00 4.41
3507 6847 2.848694 AGAAAGCTGATCTGGATTCCCA 59.151 45.455 0.00 0.00 40.95 4.37
3520 6860 3.849911 TGTGAGGATACGAAGAAAGCTG 58.150 45.455 0.00 0.00 46.39 4.24
3523 6863 3.612860 CCGTTGTGAGGATACGAAGAAAG 59.387 47.826 0.00 0.00 46.39 2.62
3525 6865 2.559668 ACCGTTGTGAGGATACGAAGAA 59.440 45.455 0.00 0.00 46.39 2.52
3556 6896 1.324736 GCGTTAGGCTTCTCGATGTTG 59.675 52.381 0.00 0.00 39.11 3.33
3558 6898 3.347411 GCGTTAGGCTTCTCGATGT 57.653 52.632 0.00 0.00 39.11 3.06
3573 6913 1.200252 CGCTAGGCTATACATCAGCGT 59.800 52.381 15.39 0.00 44.94 5.07
3598 6938 0.107456 CTGCTTCCTCACACCACACT 59.893 55.000 0.00 0.00 0.00 3.55
3599 6939 0.886490 CCTGCTTCCTCACACCACAC 60.886 60.000 0.00 0.00 0.00 3.82
3636 6976 1.446907 TTCTTTCTAGCAGCTGCAGC 58.553 50.000 38.24 31.53 45.16 5.25
3637 6977 3.008330 ACATTCTTTCTAGCAGCTGCAG 58.992 45.455 38.24 30.05 45.16 4.41
3641 6981 3.988976 TCCACATTCTTTCTAGCAGCT 57.011 42.857 0.00 0.00 0.00 4.24
3642 6982 3.376546 CCTTCCACATTCTTTCTAGCAGC 59.623 47.826 0.00 0.00 0.00 5.25
3643 6983 3.944015 CCCTTCCACATTCTTTCTAGCAG 59.056 47.826 0.00 0.00 0.00 4.24
3645 6985 3.956744 ACCCTTCCACATTCTTTCTAGC 58.043 45.455 0.00 0.00 0.00 3.42
3647 6987 7.695055 TCAAATACCCTTCCACATTCTTTCTA 58.305 34.615 0.00 0.00 0.00 2.10
3648 6988 6.552008 TCAAATACCCTTCCACATTCTTTCT 58.448 36.000 0.00 0.00 0.00 2.52
3651 6991 6.139679 TCTCAAATACCCTTCCACATTCTT 57.860 37.500 0.00 0.00 0.00 2.52
3652 6992 5.779241 TCTCAAATACCCTTCCACATTCT 57.221 39.130 0.00 0.00 0.00 2.40
3654 6994 7.614494 CAAAATCTCAAATACCCTTCCACATT 58.386 34.615 0.00 0.00 0.00 2.71
3657 6997 5.410924 GCAAAATCTCAAATACCCTTCCAC 58.589 41.667 0.00 0.00 0.00 4.02
3658 6998 4.466015 GGCAAAATCTCAAATACCCTTCCA 59.534 41.667 0.00 0.00 0.00 3.53
3661 7001 5.086621 ACTGGCAAAATCTCAAATACCCTT 58.913 37.500 0.00 0.00 0.00 3.95
3662 7002 4.677182 ACTGGCAAAATCTCAAATACCCT 58.323 39.130 0.00 0.00 0.00 4.34
3663 7003 4.142160 GGACTGGCAAAATCTCAAATACCC 60.142 45.833 0.00 0.00 0.00 3.69
3664 7004 4.462483 TGGACTGGCAAAATCTCAAATACC 59.538 41.667 0.00 0.00 0.00 2.73
3665 7005 5.643379 TGGACTGGCAAAATCTCAAATAC 57.357 39.130 0.00 0.00 0.00 1.89
3666 7006 6.855763 ATTGGACTGGCAAAATCTCAAATA 57.144 33.333 0.00 0.00 0.00 1.40
3667 7007 5.750352 ATTGGACTGGCAAAATCTCAAAT 57.250 34.783 0.00 0.00 0.00 2.32
3668 7008 5.549742 AATTGGACTGGCAAAATCTCAAA 57.450 34.783 0.00 0.00 0.00 2.69
3670 7010 4.800249 GCAAATTGGACTGGCAAAATCTCA 60.800 41.667 0.00 0.00 0.00 3.27
3672 7012 3.325716 AGCAAATTGGACTGGCAAAATCT 59.674 39.130 0.00 0.00 0.00 2.40
3673 7013 3.667360 AGCAAATTGGACTGGCAAAATC 58.333 40.909 0.00 0.00 0.00 2.17
3674 7014 3.775261 AGCAAATTGGACTGGCAAAAT 57.225 38.095 0.00 0.00 0.00 1.82
3676 7016 4.040217 ACAATAGCAAATTGGACTGGCAAA 59.960 37.500 14.18 0.00 33.56 3.68
3677 7017 3.577848 ACAATAGCAAATTGGACTGGCAA 59.422 39.130 14.18 0.00 33.56 4.52
3679 7019 3.514645 CACAATAGCAAATTGGACTGGC 58.485 45.455 14.18 0.00 33.56 4.85
3680 7020 3.056678 TGCACAATAGCAAATTGGACTGG 60.057 43.478 14.18 2.75 42.46 4.00
3692 7032 0.305922 GCTGACCGATGCACAATAGC 59.694 55.000 0.00 0.00 0.00 2.97
3693 7033 1.945387 AGCTGACCGATGCACAATAG 58.055 50.000 0.00 0.00 0.00 1.73
3695 7035 1.473965 CCTAGCTGACCGATGCACAAT 60.474 52.381 0.00 0.00 0.00 2.71
3696 7036 0.108186 CCTAGCTGACCGATGCACAA 60.108 55.000 0.00 0.00 0.00 3.33
3697 7037 1.257750 ACCTAGCTGACCGATGCACA 61.258 55.000 0.00 0.00 0.00 4.57
3699 7039 0.613260 AAACCTAGCTGACCGATGCA 59.387 50.000 0.00 0.00 0.00 3.96
3700 7040 1.398390 CAAAACCTAGCTGACCGATGC 59.602 52.381 0.00 0.00 0.00 3.91
3703 7043 2.244695 TCTCAAAACCTAGCTGACCGA 58.755 47.619 0.00 0.00 0.00 4.69
3704 7044 2.743636 TCTCAAAACCTAGCTGACCG 57.256 50.000 0.00 0.00 0.00 4.79
3705 7045 6.407202 TCTTAATCTCAAAACCTAGCTGACC 58.593 40.000 0.00 0.00 0.00 4.02
3706 7046 7.324178 TCTCTTAATCTCAAAACCTAGCTGAC 58.676 38.462 0.00 0.00 0.00 3.51
3707 7047 7.482169 TCTCTTAATCTCAAAACCTAGCTGA 57.518 36.000 0.00 0.00 0.00 4.26
3708 7048 8.729805 AATCTCTTAATCTCAAAACCTAGCTG 57.270 34.615 0.00 0.00 0.00 4.24
3709 7049 8.767436 AGAATCTCTTAATCTCAAAACCTAGCT 58.233 33.333 0.00 0.00 0.00 3.32
3710 7050 8.956533 AGAATCTCTTAATCTCAAAACCTAGC 57.043 34.615 0.00 0.00 0.00 3.42
3713 7053 9.799106 TCAAAGAATCTCTTAATCTCAAAACCT 57.201 29.630 0.00 0.00 35.27 3.50
3726 7066 9.327628 CAGTCATGATGTATCAAAGAATCTCTT 57.672 33.333 0.00 0.00 40.69 2.85
3727 7067 7.441760 GCAGTCATGATGTATCAAAGAATCTCT 59.558 37.037 0.00 0.00 40.69 3.10
3728 7068 7.307870 GGCAGTCATGATGTATCAAAGAATCTC 60.308 40.741 0.00 0.00 40.69 2.75
3730 7162 6.261603 TGGCAGTCATGATGTATCAAAGAATC 59.738 38.462 0.00 0.00 40.69 2.52
3737 7169 2.483538 CGGTGGCAGTCATGATGTATCA 60.484 50.000 0.00 0.00 41.70 2.15
3739 7171 1.486310 ACGGTGGCAGTCATGATGTAT 59.514 47.619 0.00 0.00 0.00 2.29
3740 7172 0.901827 ACGGTGGCAGTCATGATGTA 59.098 50.000 0.00 0.00 0.00 2.29
3744 7176 0.108186 GATCACGGTGGCAGTCATGA 60.108 55.000 8.50 0.00 0.00 3.07
3750 7182 1.672030 TGCAAGATCACGGTGGCAG 60.672 57.895 8.50 0.20 0.00 4.85
3752 7184 1.965930 TGTGCAAGATCACGGTGGC 60.966 57.895 8.50 3.86 39.73 5.01
3753 7185 4.377370 TGTGCAAGATCACGGTGG 57.623 55.556 8.50 0.00 39.73 4.61


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

AutoCloner maintained by Alex Coulton.