Multiple sequence alignment - TraesCS7D01G258100

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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 TraesCS7D01G258100 chr7D 100.000 4790 0 0 1 4790 234070309 234075098 0.000000e+00 8846.0
1 TraesCS7D01G258100 chr7D 94.253 87 5 0 3362 3448 234073756 234073670 3.010000e-27 134.0
2 TraesCS7D01G258100 chr7A 95.664 2145 51 7 2681 4790 246710146 246712283 0.000000e+00 3408.0
3 TraesCS7D01G258100 chr7A 89.854 2050 103 25 516 2513 246708161 246710157 0.000000e+00 2536.0
4 TraesCS7D01G258100 chr7B 94.658 2003 89 9 516 2513 205388551 205390540 0.000000e+00 3090.0
5 TraesCS7D01G258100 chr7B 94.355 1311 51 13 3490 4790 205391295 205392592 0.000000e+00 1989.0
6 TraesCS7D01G258100 chr7B 87.943 705 55 13 2681 3367 205390529 205391221 0.000000e+00 804.0
7 TraesCS7D01G258100 chr7B 87.500 456 21 18 1 447 205387662 205388090 1.200000e-135 494.0
8 TraesCS7D01G258100 chr1A 97.006 167 3 2 2511 2677 566690931 566691095 3.650000e-71 279.0
9 TraesCS7D01G258100 chr1A 93.182 176 4 5 2511 2680 62951569 62951396 7.960000e-63 252.0
10 TraesCS7D01G258100 chr4A 95.706 163 6 1 2511 2672 522127145 522126983 1.320000e-65 261.0
11 TraesCS7D01G258100 chr3D 94.643 168 7 2 2511 2676 157363170 157363337 4.760000e-65 259.0
12 TraesCS7D01G258100 chr3D 75.796 157 26 8 117 269 171330210 171330062 8.600000e-08 69.4
13 TraesCS7D01G258100 chr1D 93.491 169 8 3 2511 2676 433947570 433947402 1.030000e-61 248.0
14 TraesCS7D01G258100 chr1B 92.529 174 7 3 2511 2679 93178154 93177982 1.330000e-60 244.0
15 TraesCS7D01G258100 chr1B 91.124 169 11 3 2511 2676 101235173 101235006 4.820000e-55 226.0
16 TraesCS7D01G258100 chr1B 94.175 103 6 0 345 447 53316020 53316122 1.780000e-34 158.0
17 TraesCS7D01G258100 chr6D 91.813 171 11 3 2511 2681 352909048 352909215 8.010000e-58 235.0
18 TraesCS7D01G258100 chr3B 89.888 178 12 2 2512 2683 41214153 41213976 1.730000e-54 224.0
19 TraesCS7D01G258100 chr3B 85.714 77 8 3 4584 4659 754802599 754802525 1.430000e-10 78.7
20 TraesCS7D01G258100 chr3B 84.211 57 8 1 216 271 250272153 250272097 2.000000e-03 54.7
21 TraesCS7D01G258100 chr6B 96.471 85 2 1 3365 3448 135505596 135505680 6.460000e-29 139.0
22 TraesCS7D01G258100 chr6B 94.118 85 4 1 3361 3444 135505681 135505597 1.400000e-25 128.0
23 TraesCS7D01G258100 chr2B 96.471 85 2 1 3364 3448 794694550 794694467 6.460000e-29 139.0
24 TraesCS7D01G258100 chr2B 96.471 85 2 1 3364 3448 794803451 794803368 6.460000e-29 139.0
25 TraesCS7D01G258100 chr6A 96.386 83 2 1 3363 3444 62810768 62810686 8.360000e-28 135.0
26 TraesCS7D01G258100 chr6A 94.253 87 4 1 3366 3451 62810686 62810772 1.080000e-26 132.0
27 TraesCS7D01G258100 chr2D 93.407 91 2 2 3365 3451 294473952 294474042 1.080000e-26 132.0


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 TraesCS7D01G258100 chr7D 234070309 234075098 4789 False 8846.00 8846 100.000 1 4790 1 chr7D.!!$F1 4789
1 TraesCS7D01G258100 chr7A 246708161 246712283 4122 False 2972.00 3408 92.759 516 4790 2 chr7A.!!$F1 4274
2 TraesCS7D01G258100 chr7B 205387662 205392592 4930 False 1594.25 3090 91.114 1 4790 4 chr7B.!!$F1 4789

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
474 567 0.169009 GCATTCGAGAAAGGCACACC 59.831 55.0 7.62 0.0 44.01 4.16 F
1575 2011 0.179121 CGCACCAGCATTGCATGATT 60.179 50.0 11.91 0.0 40.20 2.57 F
2524 2987 0.322187 ATACCACTTTGGGTCACCGC 60.322 55.0 0.00 0.0 43.37 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2459 2922 0.472471 TCCAGACAGACAAACACCCC 59.528 55.0 0.0 0.0 0.0 4.95 R
2541 3004 0.035439 TCTCCCGGCATCAAAAGACC 60.035 55.0 0.0 0.0 0.0 3.85 R
4097 4620 0.625683 ACCCAGATCCTCCAAGCCAT 60.626 55.0 0.0 0.0 0.0 4.40 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
42 43 3.490759 CAGCCGCCGTCACATGTC 61.491 66.667 0.00 0.00 0.00 3.06
132 140 5.472320 TTTTTAGCTTTTCGGTTTTTGCC 57.528 34.783 0.00 0.00 0.00 4.52
205 213 7.256286 GCACATCTATGCTTCTTGAAGAAAAT 58.744 34.615 13.87 8.25 42.62 1.82
240 249 5.534207 TGTTTCTCATGGAAGCACAAATT 57.466 34.783 8.61 0.00 39.58 1.82
241 250 5.916318 TGTTTCTCATGGAAGCACAAATTT 58.084 33.333 8.61 0.00 39.58 1.82
242 251 5.754406 TGTTTCTCATGGAAGCACAAATTTG 59.246 36.000 16.67 16.67 39.58 2.32
243 252 3.916761 TCTCATGGAAGCACAAATTTGC 58.083 40.909 18.12 6.03 43.34 3.68
244 253 3.321396 TCTCATGGAAGCACAAATTTGCA 59.679 39.130 18.12 7.19 45.62 4.08
245 254 4.020928 TCTCATGGAAGCACAAATTTGCAT 60.021 37.500 18.12 9.15 45.62 3.96
246 255 4.247258 TCATGGAAGCACAAATTTGCATC 58.753 39.130 18.12 8.32 45.62 3.91
247 256 4.020928 TCATGGAAGCACAAATTTGCATCT 60.021 37.500 18.12 9.46 45.62 2.90
248 257 3.916761 TGGAAGCACAAATTTGCATCTC 58.083 40.909 18.12 9.68 45.62 2.75
249 258 3.321396 TGGAAGCACAAATTTGCATCTCA 59.679 39.130 18.12 7.25 45.62 3.27
250 259 4.202233 TGGAAGCACAAATTTGCATCTCAA 60.202 37.500 18.12 1.46 45.62 3.02
251 260 4.387862 GGAAGCACAAATTTGCATCTCAAG 59.612 41.667 18.12 0.13 45.62 3.02
252 261 4.859304 AGCACAAATTTGCATCTCAAGA 57.141 36.364 18.12 0.00 45.62 3.02
253 262 5.204409 AGCACAAATTTGCATCTCAAGAA 57.796 34.783 18.12 0.00 45.62 2.52
254 263 5.227908 AGCACAAATTTGCATCTCAAGAAG 58.772 37.500 18.12 0.00 45.62 2.85
255 264 4.143179 GCACAAATTTGCATCTCAAGAAGC 60.143 41.667 18.12 0.42 42.49 3.86
256 265 4.986034 CACAAATTTGCATCTCAAGAAGCA 59.014 37.500 18.12 5.86 45.49 3.91
257 266 4.986659 ACAAATTTGCATCTCAAGAAGCAC 59.013 37.500 18.12 0.00 46.58 4.40
258 267 4.859304 AATTTGCATCTCAAGAAGCACA 57.141 36.364 9.27 4.18 46.58 4.57
308 317 1.347378 TGCTTCAGTCATAGGCACACA 59.653 47.619 0.00 0.00 0.00 3.72
364 374 8.883954 TTCACTTTATTGAAATCATGTTGCAA 57.116 26.923 0.00 0.00 32.42 4.08
380 390 2.198406 TGCAATCGCATAGTTACGGTC 58.802 47.619 0.00 0.00 45.36 4.79
393 403 4.457466 AGTTACGGTCAATTGGTTTGTCT 58.543 39.130 5.42 0.00 36.65 3.41
394 404 5.613329 AGTTACGGTCAATTGGTTTGTCTA 58.387 37.500 5.42 0.00 36.65 2.59
461 554 3.177605 AGTTTCGGTTTTACGCATTCG 57.822 42.857 0.00 0.00 42.43 3.34
468 561 3.723835 CGGTTTTACGCATTCGAGAAAGG 60.724 47.826 0.00 0.00 39.41 3.11
469 562 3.161306 GTTTTACGCATTCGAGAAAGGC 58.839 45.455 0.00 3.69 41.21 4.35
470 563 2.087501 TTACGCATTCGAGAAAGGCA 57.912 45.000 11.47 0.00 44.82 4.75
471 564 1.355971 TACGCATTCGAGAAAGGCAC 58.644 50.000 11.47 0.00 44.82 5.01
472 565 0.602638 ACGCATTCGAGAAAGGCACA 60.603 50.000 11.47 0.00 44.82 4.57
474 567 0.169009 GCATTCGAGAAAGGCACACC 59.831 55.000 7.62 0.00 44.01 4.16
475 568 0.443869 CATTCGAGAAAGGCACACCG 59.556 55.000 0.00 0.00 42.76 4.94
497 590 5.405571 CCGGTTGGATTAGAATTCTATCACG 59.594 44.000 15.82 13.39 37.49 4.35
502 595 2.046283 TAGAATTCTATCACGCGCGG 57.954 50.000 35.22 22.52 0.00 6.46
509 602 2.990674 CTATCACGCGCGGAGTCAGG 62.991 65.000 35.22 13.41 0.00 3.86
545 948 5.723672 TGAGATCTAGTTTCGAACACCTT 57.276 39.130 0.00 0.00 0.00 3.50
573 976 5.181245 GGGAGAAATCTGACAATGAAAACGA 59.819 40.000 0.00 0.00 0.00 3.85
579 982 3.120338 TCTGACAATGAAAACGATTCGGC 60.120 43.478 11.29 0.00 0.00 5.54
603 1012 6.381801 CATTTGGACACATGGTTTAAGAGAC 58.618 40.000 0.00 0.00 0.00 3.36
609 1018 6.863126 GGACACATGGTTTAAGAGACAAAATG 59.137 38.462 0.00 0.00 0.00 2.32
622 1031 6.808829 AGAGACAAAATGCTTTGAATGAACA 58.191 32.000 5.51 0.00 44.03 3.18
731 1167 4.382754 GCACGATTGAAAACAAAGGTCATC 59.617 41.667 0.00 0.00 0.00 2.92
754 1190 3.144506 CGAATCTTGCTCATATTGGGCT 58.855 45.455 0.52 0.00 46.08 5.19
841 1277 1.515521 AAGCGGCCTTTTGTCCTTCG 61.516 55.000 0.00 0.00 0.00 3.79
846 1282 0.250770 GCCTTTTGTCCTTCGGAGGT 60.251 55.000 10.32 0.00 43.97 3.85
1128 1564 3.251043 CGCTCGCTCGAAGGCTTC 61.251 66.667 17.33 17.33 0.00 3.86
1178 1614 2.126734 GCTTGATGTTGCGCGCTT 60.127 55.556 33.29 14.38 0.00 4.68
1188 1624 4.120331 GCGCGCTTGCAATCCCTT 62.120 61.111 26.67 0.00 39.07 3.95
1203 1639 1.279846 TCCCTTGTTTGGATCGGGTAC 59.720 52.381 0.00 0.00 36.30 3.34
1248 1684 0.998928 TGCTTAGGGCCCTGAAATCA 59.001 50.000 35.81 20.07 40.92 2.57
1340 1776 6.017275 CGATCTGGTTAGGGGTATCGTATATC 60.017 46.154 0.00 0.00 33.42 1.63
1575 2011 0.179121 CGCACCAGCATTGCATGATT 60.179 50.000 11.91 0.00 40.20 2.57
1708 2164 6.255020 CACCTGATCTCTTAAATGCAAATTGC 59.745 38.462 11.58 11.58 45.29 3.56
1998 2454 1.073763 AGGCAAAGCACTGTGGATGTA 59.926 47.619 10.21 0.00 0.00 2.29
2094 2550 2.859165 TCCCAAAACCTGTAGCTGAG 57.141 50.000 0.00 0.00 0.00 3.35
2098 2554 3.691609 CCCAAAACCTGTAGCTGAGATTC 59.308 47.826 0.00 0.00 0.00 2.52
2103 2559 5.606348 AACCTGTAGCTGAGATTCCTAAG 57.394 43.478 0.00 0.00 0.00 2.18
2146 2602 4.031129 AGACCCCTGCTGCTGCTG 62.031 66.667 17.00 15.58 40.48 4.41
2151 2607 2.984155 CCTGCTGCTGCTGCTGTT 60.984 61.111 27.67 0.00 39.81 3.16
2214 2676 2.182537 GCGCCAAAGCAATCCCAG 59.817 61.111 0.00 0.00 39.83 4.45
2493 2956 5.067674 TCTGTCTGGATCCAAAAGTTTTGTG 59.932 40.000 23.29 15.91 0.00 3.33
2509 2972 5.240844 AGTTTTGTGTGCCTAGTTTCATACC 59.759 40.000 0.00 0.00 0.00 2.73
2510 2973 4.359434 TTGTGTGCCTAGTTTCATACCA 57.641 40.909 0.00 0.00 0.00 3.25
2511 2974 3.670625 TGTGTGCCTAGTTTCATACCAC 58.329 45.455 0.00 0.00 0.00 4.16
2512 2975 3.326588 TGTGTGCCTAGTTTCATACCACT 59.673 43.478 0.00 0.00 0.00 4.00
2513 2976 4.202419 TGTGTGCCTAGTTTCATACCACTT 60.202 41.667 0.00 0.00 0.00 3.16
2514 2977 4.760204 GTGTGCCTAGTTTCATACCACTTT 59.240 41.667 0.00 0.00 0.00 2.66
2515 2978 4.759693 TGTGCCTAGTTTCATACCACTTTG 59.240 41.667 0.00 0.00 0.00 2.77
2516 2979 4.156008 GTGCCTAGTTTCATACCACTTTGG 59.844 45.833 0.00 0.00 45.02 3.28
2517 2980 3.694566 GCCTAGTTTCATACCACTTTGGG 59.305 47.826 0.00 0.00 43.37 4.12
2518 2981 4.809691 GCCTAGTTTCATACCACTTTGGGT 60.810 45.833 0.00 0.00 43.37 4.51
2519 2982 4.941873 CCTAGTTTCATACCACTTTGGGTC 59.058 45.833 0.00 0.00 43.37 4.46
2520 2983 4.447138 AGTTTCATACCACTTTGGGTCA 57.553 40.909 0.00 0.00 43.37 4.02
2521 2984 4.142038 AGTTTCATACCACTTTGGGTCAC 58.858 43.478 0.00 0.00 43.37 3.67
2522 2985 2.871096 TCATACCACTTTGGGTCACC 57.129 50.000 0.00 0.00 43.37 4.02
2523 2986 1.002659 TCATACCACTTTGGGTCACCG 59.997 52.381 0.00 0.00 43.37 4.94
2524 2987 0.322187 ATACCACTTTGGGTCACCGC 60.322 55.000 0.00 0.00 43.37 5.68
2525 2988 2.400269 TACCACTTTGGGTCACCGCC 62.400 60.000 0.00 0.00 43.37 6.13
2526 2989 3.353836 CACTTTGGGTCACCGCCG 61.354 66.667 0.00 0.00 40.75 6.46
2527 2990 4.636435 ACTTTGGGTCACCGCCGG 62.636 66.667 0.00 0.00 40.75 6.13
2535 2998 4.896829 TCACCGCCGGGGCAAAAA 62.897 61.111 14.15 0.00 42.06 1.94
2554 3017 3.683365 AAATGTGGGTCTTTTGATGCC 57.317 42.857 0.00 0.00 0.00 4.40
2555 3018 1.176527 ATGTGGGTCTTTTGATGCCG 58.823 50.000 0.00 0.00 0.00 5.69
2556 3019 0.893270 TGTGGGTCTTTTGATGCCGG 60.893 55.000 0.00 0.00 0.00 6.13
2557 3020 1.304052 TGGGTCTTTTGATGCCGGG 60.304 57.895 2.18 0.00 0.00 5.73
2558 3021 1.001393 GGGTCTTTTGATGCCGGGA 60.001 57.895 2.18 0.00 0.00 5.14
2559 3022 1.032114 GGGTCTTTTGATGCCGGGAG 61.032 60.000 2.18 0.00 0.00 4.30
2560 3023 0.035439 GGTCTTTTGATGCCGGGAGA 60.035 55.000 2.18 0.00 0.00 3.71
2561 3024 1.373570 GTCTTTTGATGCCGGGAGAG 58.626 55.000 2.18 0.00 0.00 3.20
2562 3025 0.984230 TCTTTTGATGCCGGGAGAGT 59.016 50.000 2.18 0.00 0.00 3.24
2563 3026 2.093658 GTCTTTTGATGCCGGGAGAGTA 60.094 50.000 2.18 0.00 0.00 2.59
2564 3027 2.569853 TCTTTTGATGCCGGGAGAGTAA 59.430 45.455 2.18 0.00 0.00 2.24
2565 3028 3.199946 TCTTTTGATGCCGGGAGAGTAAT 59.800 43.478 2.18 0.00 0.00 1.89
2566 3029 2.620251 TTGATGCCGGGAGAGTAATG 57.380 50.000 2.18 0.00 0.00 1.90
2567 3030 1.788229 TGATGCCGGGAGAGTAATGA 58.212 50.000 2.18 0.00 0.00 2.57
2568 3031 1.412710 TGATGCCGGGAGAGTAATGAC 59.587 52.381 2.18 0.00 0.00 3.06
2569 3032 0.759346 ATGCCGGGAGAGTAATGACC 59.241 55.000 2.18 0.00 0.00 4.02
2570 3033 0.616395 TGCCGGGAGAGTAATGACCA 60.616 55.000 2.18 0.00 0.00 4.02
2571 3034 0.759346 GCCGGGAGAGTAATGACCAT 59.241 55.000 2.18 0.00 0.00 3.55
2572 3035 1.541233 GCCGGGAGAGTAATGACCATG 60.541 57.143 2.18 0.00 0.00 3.66
2573 3036 2.039418 CCGGGAGAGTAATGACCATGA 58.961 52.381 0.00 0.00 0.00 3.07
2574 3037 2.634940 CCGGGAGAGTAATGACCATGAT 59.365 50.000 0.00 0.00 0.00 2.45
2575 3038 3.555795 CCGGGAGAGTAATGACCATGATG 60.556 52.174 0.00 0.00 0.00 3.07
2576 3039 3.070159 CGGGAGAGTAATGACCATGATGT 59.930 47.826 0.00 0.00 0.00 3.06
2577 3040 4.280929 CGGGAGAGTAATGACCATGATGTA 59.719 45.833 0.00 0.00 0.00 2.29
2578 3041 5.221441 CGGGAGAGTAATGACCATGATGTAA 60.221 44.000 0.00 0.00 0.00 2.41
2579 3042 6.519043 CGGGAGAGTAATGACCATGATGTAAT 60.519 42.308 0.00 0.00 0.00 1.89
2580 3043 7.309805 CGGGAGAGTAATGACCATGATGTAATA 60.310 40.741 0.00 0.00 0.00 0.98
2581 3044 8.543774 GGGAGAGTAATGACCATGATGTAATAT 58.456 37.037 0.00 0.00 0.00 1.28
2582 3045 9.950496 GGAGAGTAATGACCATGATGTAATATT 57.050 33.333 0.00 0.00 0.00 1.28
2607 3070 7.692908 TTTTAGTTTCTTTACAATGTGCTGC 57.307 32.000 0.00 0.00 0.00 5.25
2608 3071 4.916983 AGTTTCTTTACAATGTGCTGCA 57.083 36.364 0.00 0.00 0.00 4.41
2609 3072 5.261209 AGTTTCTTTACAATGTGCTGCAA 57.739 34.783 2.77 0.00 0.00 4.08
2610 3073 5.659463 AGTTTCTTTACAATGTGCTGCAAA 58.341 33.333 2.77 0.00 0.00 3.68
2611 3074 5.519927 AGTTTCTTTACAATGTGCTGCAAAC 59.480 36.000 2.77 0.33 0.00 2.93
2612 3075 4.916983 TCTTTACAATGTGCTGCAAACT 57.083 36.364 2.77 0.00 0.00 2.66
2613 3076 4.858935 TCTTTACAATGTGCTGCAAACTC 58.141 39.130 2.77 0.00 0.00 3.01
2614 3077 4.580167 TCTTTACAATGTGCTGCAAACTCT 59.420 37.500 2.77 0.00 0.00 3.24
2615 3078 4.916983 TTACAATGTGCTGCAAACTCTT 57.083 36.364 2.77 0.00 0.00 2.85
2616 3079 3.088194 ACAATGTGCTGCAAACTCTTG 57.912 42.857 2.77 3.34 35.49 3.02
2617 3080 2.428171 ACAATGTGCTGCAAACTCTTGT 59.572 40.909 2.77 4.04 34.79 3.16
2618 3081 3.047796 CAATGTGCTGCAAACTCTTGTC 58.952 45.455 2.77 0.00 34.79 3.18
2619 3082 1.024271 TGTGCTGCAAACTCTTGTCC 58.976 50.000 2.77 0.00 34.79 4.02
2620 3083 0.040958 GTGCTGCAAACTCTTGTCCG 60.041 55.000 2.77 0.00 34.79 4.79
2621 3084 0.463654 TGCTGCAAACTCTTGTCCGT 60.464 50.000 0.00 0.00 34.79 4.69
2622 3085 0.663153 GCTGCAAACTCTTGTCCGTT 59.337 50.000 0.00 0.00 34.79 4.44
2623 3086 1.065551 GCTGCAAACTCTTGTCCGTTT 59.934 47.619 0.00 0.00 34.79 3.60
2624 3087 2.854805 GCTGCAAACTCTTGTCCGTTTC 60.855 50.000 0.00 0.00 34.79 2.78
2625 3088 1.673920 TGCAAACTCTTGTCCGTTTCC 59.326 47.619 0.00 0.00 34.79 3.13
2626 3089 1.947456 GCAAACTCTTGTCCGTTTCCT 59.053 47.619 0.00 0.00 34.79 3.36
2627 3090 2.357952 GCAAACTCTTGTCCGTTTCCTT 59.642 45.455 0.00 0.00 34.79 3.36
2628 3091 3.548214 GCAAACTCTTGTCCGTTTCCTTC 60.548 47.826 0.00 0.00 34.79 3.46
2629 3092 3.840124 AACTCTTGTCCGTTTCCTTCT 57.160 42.857 0.00 0.00 0.00 2.85
2630 3093 3.840124 ACTCTTGTCCGTTTCCTTCTT 57.160 42.857 0.00 0.00 0.00 2.52
2631 3094 4.950205 ACTCTTGTCCGTTTCCTTCTTA 57.050 40.909 0.00 0.00 0.00 2.10
2632 3095 5.286267 ACTCTTGTCCGTTTCCTTCTTAA 57.714 39.130 0.00 0.00 0.00 1.85
2633 3096 5.866207 ACTCTTGTCCGTTTCCTTCTTAAT 58.134 37.500 0.00 0.00 0.00 1.40
2634 3097 6.296803 ACTCTTGTCCGTTTCCTTCTTAATT 58.703 36.000 0.00 0.00 0.00 1.40
2635 3098 7.447594 ACTCTTGTCCGTTTCCTTCTTAATTA 58.552 34.615 0.00 0.00 0.00 1.40
2636 3099 7.935210 ACTCTTGTCCGTTTCCTTCTTAATTAA 59.065 33.333 0.00 0.00 0.00 1.40
2637 3100 8.857694 TCTTGTCCGTTTCCTTCTTAATTAAT 57.142 30.769 0.00 0.00 0.00 1.40
2638 3101 8.726988 TCTTGTCCGTTTCCTTCTTAATTAATG 58.273 33.333 0.00 0.00 0.00 1.90
2639 3102 7.385778 TGTCCGTTTCCTTCTTAATTAATGG 57.614 36.000 0.00 2.56 0.00 3.16
2640 3103 7.169591 TGTCCGTTTCCTTCTTAATTAATGGA 58.830 34.615 0.00 4.78 0.00 3.41
2641 3104 7.832187 TGTCCGTTTCCTTCTTAATTAATGGAT 59.168 33.333 12.50 0.00 34.32 3.41
2642 3105 8.129211 GTCCGTTTCCTTCTTAATTAATGGATG 58.871 37.037 12.50 5.14 34.32 3.51
2643 3106 8.050325 TCCGTTTCCTTCTTAATTAATGGATGA 58.950 33.333 12.50 0.00 0.00 2.92
2644 3107 8.345565 CCGTTTCCTTCTTAATTAATGGATGAG 58.654 37.037 12.50 8.49 0.00 2.90
2645 3108 8.345565 CGTTTCCTTCTTAATTAATGGATGAGG 58.654 37.037 12.50 7.01 0.00 3.86
2646 3109 7.823745 TTCCTTCTTAATTAATGGATGAGGC 57.176 36.000 12.50 0.00 0.00 4.70
2647 3110 6.910191 TCCTTCTTAATTAATGGATGAGGCA 58.090 36.000 0.00 0.00 0.00 4.75
2648 3111 7.353525 TCCTTCTTAATTAATGGATGAGGCAA 58.646 34.615 0.00 0.00 0.00 4.52
2649 3112 7.838696 TCCTTCTTAATTAATGGATGAGGCAAA 59.161 33.333 0.00 0.00 0.00 3.68
2650 3113 8.139989 CCTTCTTAATTAATGGATGAGGCAAAG 58.860 37.037 0.00 0.00 0.00 2.77
2651 3114 7.042797 TCTTAATTAATGGATGAGGCAAAGC 57.957 36.000 0.00 0.00 0.00 3.51
2652 3115 6.835488 TCTTAATTAATGGATGAGGCAAAGCT 59.165 34.615 0.00 0.00 0.00 3.74
2653 3116 5.945144 AATTAATGGATGAGGCAAAGCTT 57.055 34.783 0.00 0.00 0.00 3.74
2654 3117 5.945144 ATTAATGGATGAGGCAAAGCTTT 57.055 34.783 5.69 5.69 0.00 3.51
2655 3118 5.743636 TTAATGGATGAGGCAAAGCTTTT 57.256 34.783 9.53 0.00 0.00 2.27
2656 3119 3.604875 ATGGATGAGGCAAAGCTTTTG 57.395 42.857 9.53 6.62 0.00 2.44
2668 3131 3.957383 GCTTTTGCCTCCGTTTCAA 57.043 47.368 0.00 0.00 40.15 2.69
2669 3132 2.217429 GCTTTTGCCTCCGTTTCAAA 57.783 45.000 0.00 0.00 40.15 2.69
2670 3133 2.545731 GCTTTTGCCTCCGTTTCAAAA 58.454 42.857 0.00 0.00 40.15 2.44
2671 3134 2.933260 GCTTTTGCCTCCGTTTCAAAAA 59.067 40.909 0.00 0.00 38.65 1.94
2672 3135 3.559655 GCTTTTGCCTCCGTTTCAAAAAT 59.440 39.130 0.00 0.00 38.65 1.82
2673 3136 4.747605 GCTTTTGCCTCCGTTTCAAAAATA 59.252 37.500 0.00 0.00 38.65 1.40
2674 3137 5.235401 GCTTTTGCCTCCGTTTCAAAAATAA 59.765 36.000 0.00 0.00 38.65 1.40
2675 3138 6.238239 GCTTTTGCCTCCGTTTCAAAAATAAA 60.238 34.615 0.00 0.00 38.65 1.40
2676 3139 7.519809 GCTTTTGCCTCCGTTTCAAAAATAAAT 60.520 33.333 0.00 0.00 38.65 1.40
2677 3140 8.888579 TTTTGCCTCCGTTTCAAAAATAAATA 57.111 26.923 0.00 0.00 36.93 1.40
2678 3141 8.888579 TTTGCCTCCGTTTCAAAAATAAATAA 57.111 26.923 0.00 0.00 0.00 1.40
2679 3142 8.888579 TTGCCTCCGTTTCAAAAATAAATAAA 57.111 26.923 0.00 0.00 0.00 1.40
2680 3143 9.495572 TTGCCTCCGTTTCAAAAATAAATAAAT 57.504 25.926 0.00 0.00 0.00 1.40
2681 3144 9.495572 TGCCTCCGTTTCAAAAATAAATAAATT 57.504 25.926 0.00 0.00 0.00 1.82
2973 3436 4.326826 TGGTTCACATGAATGAGGAAGAC 58.673 43.478 0.00 0.00 36.33 3.01
3024 3487 7.197071 ACTACACGAACTTAATTTGATGCAA 57.803 32.000 0.00 0.00 0.00 4.08
3135 3598 4.695455 TGAGCAATGTAAGACTAAACTGGC 59.305 41.667 0.00 0.00 0.00 4.85
3215 3678 9.013229 TGAAATTGTAGCAGTTGAGTGATTTAT 57.987 29.630 0.00 0.00 0.00 1.40
3216 3679 9.846248 GAAATTGTAGCAGTTGAGTGATTTATT 57.154 29.630 0.00 0.00 0.00 1.40
3248 3729 1.202200 GCTTGGCGTTTGTGTGTTGTA 60.202 47.619 0.00 0.00 0.00 2.41
3398 3879 9.241317 TCCGTAAAGAAATATAAGAGCGTTTAG 57.759 33.333 0.00 0.00 0.00 1.85
3537 4055 7.712639 AGAGCAATACCATGTAACACATCTAAG 59.287 37.037 0.00 0.00 36.53 2.18
3637 4156 2.568623 AACCTCTGCCTTTACCAGTG 57.431 50.000 0.00 0.00 0.00 3.66
3730 4253 1.132689 AGGGCCCTCGGAAGAAGATAT 60.133 52.381 22.28 0.00 41.32 1.63
3959 4482 3.365976 GAGAGCTGCTCCATCTGTG 57.634 57.895 25.09 0.00 37.69 3.66
4062 4585 6.518208 ACTATTAGTCTTGACAGTGGAGTC 57.482 41.667 3.49 0.00 38.99 3.36
4126 4649 3.435601 GGAGGATCTGGGTGTTGCATATT 60.436 47.826 0.00 0.00 33.73 1.28
4190 4713 1.666700 GTTGCGTGTACTGTGGTGAAA 59.333 47.619 0.00 0.00 0.00 2.69
4311 4834 1.339055 TGCTAAATGGTCAGCTCGCTT 60.339 47.619 0.00 0.00 38.63 4.68
4423 4947 3.006967 GGTGTGATGAGTGAACAGGTAGT 59.993 47.826 0.00 0.00 0.00 2.73
4439 4963 6.650120 ACAGGTAGTTATAAGGACATGTTGG 58.350 40.000 0.00 0.00 33.37 3.77
4570 5094 7.208777 TGATTTTGTTGCTGATTGTACAATGT 58.791 30.769 25.42 3.29 31.30 2.71
4615 5139 8.035394 ACTAGATAATTCTCATCGTGTTGTTGT 58.965 33.333 0.00 0.00 33.17 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
205 213 8.634335 TCCATGAGAAACACAATCAGATTTTA 57.366 30.769 0.00 0.00 0.00 1.52
210 219 4.456911 GCTTCCATGAGAAACACAATCAGA 59.543 41.667 0.00 0.00 32.88 3.27
226 235 4.020928 TGAGATGCAAATTTGTGCTTCCAT 60.021 37.500 19.03 12.21 45.27 3.41
242 251 3.439476 ACAGATTGTGCTTCTTGAGATGC 59.561 43.478 10.87 10.87 43.15 3.91
243 252 4.971008 CACAGATTGTGCTTCTTGAGATG 58.029 43.478 0.00 0.00 41.89 2.90
256 265 3.111853 TCTGACGAAAGCACAGATTGT 57.888 42.857 0.00 0.00 40.80 2.71
257 266 3.666374 GCTTCTGACGAAAGCACAGATTG 60.666 47.826 3.12 0.00 43.45 2.67
258 267 2.481952 GCTTCTGACGAAAGCACAGATT 59.518 45.455 3.12 0.00 43.45 2.40
315 324 2.540931 CACACATTTGCTTCTTGCCAAC 59.459 45.455 0.00 0.00 42.00 3.77
364 374 3.807622 CCAATTGACCGTAACTATGCGAT 59.192 43.478 7.12 0.00 36.72 4.58
369 379 6.235664 AGACAAACCAATTGACCGTAACTAT 58.764 36.000 7.12 0.00 41.85 2.12
394 404 9.347240 CCCATTCAAGATACATGAAACTATTCT 57.653 33.333 0.00 0.00 39.98 2.40
417 427 0.548197 ACCAATTACCCGAGTCCCCA 60.548 55.000 0.00 0.00 0.00 4.96
461 554 1.515521 CCAACCGGTGTGCCTTTCTC 61.516 60.000 8.52 0.00 0.00 2.87
468 561 1.816074 TTCTAATCCAACCGGTGTGC 58.184 50.000 8.52 0.00 0.00 4.57
469 562 4.261801 AGAATTCTAATCCAACCGGTGTG 58.738 43.478 8.52 8.91 0.00 3.82
470 563 4.569719 AGAATTCTAATCCAACCGGTGT 57.430 40.909 8.52 0.00 0.00 4.16
471 564 6.202954 GTGATAGAATTCTAATCCAACCGGTG 59.797 42.308 18.79 1.82 31.39 4.94
472 565 6.289064 GTGATAGAATTCTAATCCAACCGGT 58.711 40.000 18.79 0.00 31.39 5.28
474 567 5.107453 GCGTGATAGAATTCTAATCCAACCG 60.107 44.000 18.79 15.98 31.39 4.44
475 568 5.107453 CGCGTGATAGAATTCTAATCCAACC 60.107 44.000 18.79 10.07 31.39 3.77
502 595 8.268850 TCTCATTTTAATAAACTGCCTGACTC 57.731 34.615 0.00 0.00 0.00 3.36
545 948 5.440207 TCATTGTCAGATTTCTCCCATCA 57.560 39.130 0.00 0.00 0.00 3.07
573 976 1.477700 CCATGTGTCCAAATGCCGAAT 59.522 47.619 0.00 0.00 0.00 3.34
579 982 6.016360 TGTCTCTTAAACCATGTGTCCAAATG 60.016 38.462 0.00 0.00 0.00 2.32
609 1018 8.246180 TCTTCCATAGATTTGTTCATTCAAAGC 58.754 33.333 0.00 0.00 41.91 3.51
731 1167 2.096069 CCCAATATGAGCAAGATTCGCG 60.096 50.000 0.00 0.00 0.00 5.87
754 1190 2.674754 GGGCTGGGACCGAAATCA 59.325 61.111 0.00 0.00 0.00 2.57
841 1277 2.636403 AGGCACCGGTATAATTACCTCC 59.364 50.000 6.87 0.00 45.01 4.30
846 1282 2.051692 AGGCAGGCACCGGTATAATTA 58.948 47.619 6.87 0.00 33.69 1.40
855 1291 0.962356 ATTTTCTCAGGCAGGCACCG 60.962 55.000 0.00 0.00 33.69 4.94
1178 1614 1.818060 CGATCCAAACAAGGGATTGCA 59.182 47.619 0.00 0.00 45.05 4.08
1188 1624 1.475280 CTCGAGTACCCGATCCAAACA 59.525 52.381 3.62 0.00 37.96 2.83
1216 1652 2.083774 CCTAAGCAACATTTCCGAGCA 58.916 47.619 0.00 0.00 0.00 4.26
1248 1684 2.743718 CAGTGCCACGAACTCCCT 59.256 61.111 0.00 0.00 0.00 4.20
1400 1836 2.670905 GACACAGCCAACAAAAACAACC 59.329 45.455 0.00 0.00 0.00 3.77
1575 2011 4.037803 CCATCAGTGACAACATTGTTCCAA 59.962 41.667 0.00 0.00 42.43 3.53
1641 2081 5.702349 AGAGTTTCTTGAAGCTGAAATGG 57.298 39.130 4.52 0.00 35.13 3.16
1708 2164 6.909357 GCAAATAAACAGACTAATAGCAGCAG 59.091 38.462 0.00 0.00 0.00 4.24
1998 2454 7.065563 CGAAGATCTGGAACTGATGATTTCTTT 59.934 37.037 0.00 0.00 46.89 2.52
2094 2550 5.735766 ACAGGTTTAGCACTCTTAGGAATC 58.264 41.667 0.00 0.00 0.00 2.52
2098 2554 4.894784 TGAACAGGTTTAGCACTCTTAGG 58.105 43.478 0.00 0.00 0.00 2.69
2103 2559 5.751243 TCTTTTGAACAGGTTTAGCACTC 57.249 39.130 0.00 0.00 0.00 3.51
2146 2602 2.355481 GGCAGCAACAGCAACAGC 60.355 61.111 0.00 0.00 0.00 4.40
2147 2603 2.337532 GGGCAGCAACAGCAACAG 59.662 61.111 0.00 0.00 0.00 3.16
2148 2604 3.594775 CGGGCAGCAACAGCAACA 61.595 61.111 0.00 0.00 0.00 3.33
2149 2605 3.542629 GACGGGCAGCAACAGCAAC 62.543 63.158 0.00 0.00 0.00 4.17
2150 2606 3.286751 GACGGGCAGCAACAGCAA 61.287 61.111 0.00 0.00 0.00 3.91
2214 2676 5.104900 TGCATAGAACTCTCCTACCTTTTCC 60.105 44.000 0.00 0.00 0.00 3.13
2277 2739 6.985059 ACCACTAGACTAGAACAAGAAACAAC 59.015 38.462 16.55 0.00 0.00 3.32
2459 2922 0.472471 TCCAGACAGACAAACACCCC 59.528 55.000 0.00 0.00 0.00 4.95
2493 2956 4.156008 CCAAAGTGGTATGAAACTAGGCAC 59.844 45.833 0.00 0.00 31.35 5.01
2509 2972 3.353836 CGGCGGTGACCCAAAGTG 61.354 66.667 0.00 0.00 0.00 3.16
2510 2973 4.636435 CCGGCGGTGACCCAAAGT 62.636 66.667 19.97 0.00 0.00 2.66
2518 2981 4.896829 TTTTTGCCCCGGCGGTGA 62.897 61.111 26.32 4.77 45.51 4.02
2532 2995 4.388485 GGCATCAAAAGACCCACATTTTT 58.612 39.130 0.00 0.00 0.00 1.94
2533 2996 3.554752 CGGCATCAAAAGACCCACATTTT 60.555 43.478 0.00 0.00 0.00 1.82
2534 2997 2.029110 CGGCATCAAAAGACCCACATTT 60.029 45.455 0.00 0.00 0.00 2.32
2535 2998 1.545582 CGGCATCAAAAGACCCACATT 59.454 47.619 0.00 0.00 0.00 2.71
2536 2999 1.176527 CGGCATCAAAAGACCCACAT 58.823 50.000 0.00 0.00 0.00 3.21
2537 3000 0.893270 CCGGCATCAAAAGACCCACA 60.893 55.000 0.00 0.00 0.00 4.17
2538 3001 1.595093 CCCGGCATCAAAAGACCCAC 61.595 60.000 0.00 0.00 0.00 4.61
2539 3002 1.304052 CCCGGCATCAAAAGACCCA 60.304 57.895 0.00 0.00 0.00 4.51
2540 3003 1.001393 TCCCGGCATCAAAAGACCC 60.001 57.895 0.00 0.00 0.00 4.46
2541 3004 0.035439 TCTCCCGGCATCAAAAGACC 60.035 55.000 0.00 0.00 0.00 3.85
2542 3005 1.339151 ACTCTCCCGGCATCAAAAGAC 60.339 52.381 0.00 0.00 0.00 3.01
2543 3006 0.984230 ACTCTCCCGGCATCAAAAGA 59.016 50.000 0.00 0.00 0.00 2.52
2544 3007 2.691409 TACTCTCCCGGCATCAAAAG 57.309 50.000 0.00 0.00 0.00 2.27
2545 3008 3.054728 TCATTACTCTCCCGGCATCAAAA 60.055 43.478 0.00 0.00 0.00 2.44
2546 3009 2.503765 TCATTACTCTCCCGGCATCAAA 59.496 45.455 0.00 0.00 0.00 2.69
2547 3010 2.115427 TCATTACTCTCCCGGCATCAA 58.885 47.619 0.00 0.00 0.00 2.57
2548 3011 1.412710 GTCATTACTCTCCCGGCATCA 59.587 52.381 0.00 0.00 0.00 3.07
2549 3012 1.270358 GGTCATTACTCTCCCGGCATC 60.270 57.143 0.00 0.00 0.00 3.91
2550 3013 0.759346 GGTCATTACTCTCCCGGCAT 59.241 55.000 0.00 0.00 0.00 4.40
2551 3014 0.616395 TGGTCATTACTCTCCCGGCA 60.616 55.000 0.00 0.00 0.00 5.69
2552 3015 0.759346 ATGGTCATTACTCTCCCGGC 59.241 55.000 0.00 0.00 0.00 6.13
2553 3016 2.039418 TCATGGTCATTACTCTCCCGG 58.961 52.381 0.00 0.00 0.00 5.73
2554 3017 3.070159 ACATCATGGTCATTACTCTCCCG 59.930 47.826 0.00 0.00 0.00 5.14
2555 3018 4.696479 ACATCATGGTCATTACTCTCCC 57.304 45.455 0.00 0.00 0.00 4.30
2556 3019 9.950496 AATATTACATCATGGTCATTACTCTCC 57.050 33.333 0.00 0.00 0.00 3.71
2582 3045 7.761704 TGCAGCACATTGTAAAGAAACTAAAAA 59.238 29.630 0.00 0.00 0.00 1.94
2583 3046 7.261325 TGCAGCACATTGTAAAGAAACTAAAA 58.739 30.769 0.00 0.00 0.00 1.52
2584 3047 6.800543 TGCAGCACATTGTAAAGAAACTAAA 58.199 32.000 0.00 0.00 0.00 1.85
2585 3048 6.384258 TGCAGCACATTGTAAAGAAACTAA 57.616 33.333 0.00 0.00 0.00 2.24
2586 3049 6.384258 TTGCAGCACATTGTAAAGAAACTA 57.616 33.333 0.00 0.00 0.00 2.24
2587 3050 4.916983 TGCAGCACATTGTAAAGAAACT 57.083 36.364 0.00 0.00 0.00 2.66
2588 3051 5.519927 AGTTTGCAGCACATTGTAAAGAAAC 59.480 36.000 0.00 0.00 34.15 2.78
2589 3052 5.659463 AGTTTGCAGCACATTGTAAAGAAA 58.341 33.333 0.00 0.00 34.15 2.52
2590 3053 5.067674 AGAGTTTGCAGCACATTGTAAAGAA 59.932 36.000 0.00 0.00 34.15 2.52
2591 3054 4.580167 AGAGTTTGCAGCACATTGTAAAGA 59.420 37.500 0.00 0.00 34.15 2.52
2592 3055 4.863491 AGAGTTTGCAGCACATTGTAAAG 58.137 39.130 0.00 0.00 34.15 1.85
2593 3056 4.916983 AGAGTTTGCAGCACATTGTAAA 57.083 36.364 0.00 0.00 31.59 2.01
2594 3057 4.097741 ACAAGAGTTTGCAGCACATTGTAA 59.902 37.500 14.74 0.00 37.85 2.41
2595 3058 3.631686 ACAAGAGTTTGCAGCACATTGTA 59.368 39.130 14.74 0.00 37.85 2.41
2596 3059 2.428171 ACAAGAGTTTGCAGCACATTGT 59.572 40.909 0.00 12.30 37.85 2.71
2597 3060 3.047796 GACAAGAGTTTGCAGCACATTG 58.952 45.455 0.00 11.44 37.85 2.82
2598 3061 2.035066 GGACAAGAGTTTGCAGCACATT 59.965 45.455 0.00 0.00 37.85 2.71
2599 3062 1.610522 GGACAAGAGTTTGCAGCACAT 59.389 47.619 0.00 0.00 37.85 3.21
2600 3063 1.024271 GGACAAGAGTTTGCAGCACA 58.976 50.000 0.00 0.00 37.85 4.57
2601 3064 0.040958 CGGACAAGAGTTTGCAGCAC 60.041 55.000 0.00 0.00 37.85 4.40
2602 3065 0.463654 ACGGACAAGAGTTTGCAGCA 60.464 50.000 0.00 0.00 37.85 4.41
2603 3066 0.663153 AACGGACAAGAGTTTGCAGC 59.337 50.000 0.00 0.00 37.85 5.25
2604 3067 2.287009 GGAAACGGACAAGAGTTTGCAG 60.287 50.000 7.50 0.00 44.44 4.41
2605 3068 1.673920 GGAAACGGACAAGAGTTTGCA 59.326 47.619 7.50 0.00 44.44 4.08
2606 3069 1.947456 AGGAAACGGACAAGAGTTTGC 59.053 47.619 4.77 4.77 45.07 3.68
2607 3070 3.877508 AGAAGGAAACGGACAAGAGTTTG 59.122 43.478 0.00 0.00 40.24 2.93
2608 3071 4.152284 AGAAGGAAACGGACAAGAGTTT 57.848 40.909 0.00 0.00 42.50 2.66
2609 3072 3.840124 AGAAGGAAACGGACAAGAGTT 57.160 42.857 0.00 0.00 0.00 3.01
2610 3073 3.840124 AAGAAGGAAACGGACAAGAGT 57.160 42.857 0.00 0.00 0.00 3.24
2611 3074 6.803154 AATTAAGAAGGAAACGGACAAGAG 57.197 37.500 0.00 0.00 0.00 2.85
2612 3075 8.726988 CATTAATTAAGAAGGAAACGGACAAGA 58.273 33.333 3.94 0.00 0.00 3.02
2613 3076 7.968405 CCATTAATTAAGAAGGAAACGGACAAG 59.032 37.037 3.94 0.00 0.00 3.16
2614 3077 7.666388 TCCATTAATTAAGAAGGAAACGGACAA 59.334 33.333 12.07 0.00 0.00 3.18
2615 3078 7.169591 TCCATTAATTAAGAAGGAAACGGACA 58.830 34.615 12.07 0.00 0.00 4.02
2616 3079 7.619964 TCCATTAATTAAGAAGGAAACGGAC 57.380 36.000 12.07 0.00 0.00 4.79
2617 3080 8.050325 TCATCCATTAATTAAGAAGGAAACGGA 58.950 33.333 16.25 10.98 0.00 4.69
2618 3081 8.220755 TCATCCATTAATTAAGAAGGAAACGG 57.779 34.615 16.25 9.56 0.00 4.44
2619 3082 8.345565 CCTCATCCATTAATTAAGAAGGAAACG 58.654 37.037 16.25 10.55 0.00 3.60
2620 3083 8.138074 GCCTCATCCATTAATTAAGAAGGAAAC 58.862 37.037 16.25 5.73 0.00 2.78
2621 3084 7.838696 TGCCTCATCCATTAATTAAGAAGGAAA 59.161 33.333 16.25 9.73 0.00 3.13
2622 3085 7.353525 TGCCTCATCCATTAATTAAGAAGGAA 58.646 34.615 16.25 2.80 0.00 3.36
2623 3086 6.910191 TGCCTCATCCATTAATTAAGAAGGA 58.090 36.000 15.20 15.20 0.00 3.36
2624 3087 7.587037 TTGCCTCATCCATTAATTAAGAAGG 57.413 36.000 3.94 6.02 0.00 3.46
2625 3088 7.650903 GCTTTGCCTCATCCATTAATTAAGAAG 59.349 37.037 3.94 0.00 0.00 2.85
2626 3089 7.342799 AGCTTTGCCTCATCCATTAATTAAGAA 59.657 33.333 3.94 0.00 0.00 2.52
2627 3090 6.835488 AGCTTTGCCTCATCCATTAATTAAGA 59.165 34.615 3.94 0.00 0.00 2.10
2628 3091 7.047460 AGCTTTGCCTCATCCATTAATTAAG 57.953 36.000 3.94 0.00 0.00 1.85
2629 3092 7.422465 AAGCTTTGCCTCATCCATTAATTAA 57.578 32.000 0.00 0.00 0.00 1.40
2630 3093 7.422465 AAAGCTTTGCCTCATCCATTAATTA 57.578 32.000 11.80 0.00 0.00 1.40
2631 3094 5.945144 AAGCTTTGCCTCATCCATTAATT 57.055 34.783 0.00 0.00 0.00 1.40
2632 3095 5.945144 AAAGCTTTGCCTCATCCATTAAT 57.055 34.783 11.80 0.00 0.00 1.40
2633 3096 5.481105 CAAAAGCTTTGCCTCATCCATTAA 58.519 37.500 13.54 0.00 0.00 1.40
2634 3097 4.621274 GCAAAAGCTTTGCCTCATCCATTA 60.621 41.667 13.54 0.00 39.38 1.90
2635 3098 3.867216 GCAAAAGCTTTGCCTCATCCATT 60.867 43.478 13.54 0.00 39.38 3.16
2636 3099 2.354403 GCAAAAGCTTTGCCTCATCCAT 60.354 45.455 13.54 0.00 39.38 3.41
2637 3100 1.001181 GCAAAAGCTTTGCCTCATCCA 59.999 47.619 13.54 0.00 39.38 3.41
2638 3101 1.718396 GCAAAAGCTTTGCCTCATCC 58.282 50.000 13.54 0.00 39.38 3.51
2645 3108 0.249447 AACGGAGGCAAAAGCTTTGC 60.249 50.000 13.54 17.13 44.22 3.68
2646 3109 2.127251 GAAACGGAGGCAAAAGCTTTG 58.873 47.619 13.54 8.26 0.00 2.77
2647 3110 1.754226 TGAAACGGAGGCAAAAGCTTT 59.246 42.857 5.69 5.69 0.00 3.51
2648 3111 1.398692 TGAAACGGAGGCAAAAGCTT 58.601 45.000 0.00 0.00 0.00 3.74
2649 3112 1.398692 TTGAAACGGAGGCAAAAGCT 58.601 45.000 0.00 0.00 0.00 3.74
2650 3113 2.217429 TTTGAAACGGAGGCAAAAGC 57.783 45.000 0.00 0.00 0.00 3.51
2651 3114 6.836577 TTATTTTTGAAACGGAGGCAAAAG 57.163 33.333 0.00 0.00 41.02 2.27
2652 3115 7.793927 ATTTATTTTTGAAACGGAGGCAAAA 57.206 28.000 0.00 0.00 39.08 2.44
2653 3116 8.888579 TTATTTATTTTTGAAACGGAGGCAAA 57.111 26.923 0.00 0.00 0.00 3.68
2654 3117 8.888579 TTTATTTATTTTTGAAACGGAGGCAA 57.111 26.923 0.00 0.00 0.00 4.52
2655 3118 9.495572 AATTTATTTATTTTTGAAACGGAGGCA 57.504 25.926 0.00 0.00 0.00 4.75
2682 3145 9.865321 GACAAGAATAACTGTACAGTGGTATTA 57.135 33.333 28.55 16.79 41.58 0.98
2683 3146 8.594550 AGACAAGAATAACTGTACAGTGGTATT 58.405 33.333 28.55 25.66 41.58 1.89
2684 3147 8.135382 AGACAAGAATAACTGTACAGTGGTAT 57.865 34.615 28.55 19.57 41.58 2.73
2685 3148 7.534723 AGACAAGAATAACTGTACAGTGGTA 57.465 36.000 28.55 18.21 41.58 3.25
2686 3149 6.420913 AGACAAGAATAACTGTACAGTGGT 57.579 37.500 28.55 16.59 41.58 4.16
2687 3150 7.827701 TCTAGACAAGAATAACTGTACAGTGG 58.172 38.462 28.55 14.00 41.58 4.00
2851 3314 2.574006 TCAAACATGCCTCTTCAGCT 57.426 45.000 0.00 0.00 0.00 4.24
2973 3436 6.039047 CCATTGGAATTCCTAGTGACTTCATG 59.961 42.308 24.73 9.25 35.05 3.07
3248 3729 8.163408 AGATAGAGAGACAGACAGCATAGTAAT 58.837 37.037 0.00 0.00 0.00 1.89
3412 3899 9.099454 CCTCTGTAAAGAAATATAAGAGCGTTT 57.901 33.333 0.00 0.00 0.00 3.60
3508 4023 4.935205 TGTGTTACATGGTATTGCTCTGAC 59.065 41.667 0.00 0.00 0.00 3.51
3537 4055 2.774439 AATGGACGTTGTTGCAGTTC 57.226 45.000 0.00 0.00 0.00 3.01
3832 4355 1.481363 GGCTCGCCTTAAGTTACTCCT 59.519 52.381 0.97 0.00 0.00 3.69
3959 4482 8.910351 AAACTAGCATCCAAATATTCTAGGTC 57.090 34.615 9.96 0.56 0.00 3.85
4097 4620 0.625683 ACCCAGATCCTCCAAGCCAT 60.626 55.000 0.00 0.00 0.00 4.40
4190 4713 2.040813 ACCTTCACAACATCAGGCAGAT 59.959 45.455 0.00 0.00 37.48 2.90
4423 4947 3.699038 GCTTGCCCAACATGTCCTTATAA 59.301 43.478 0.00 0.00 0.00 0.98
4439 4963 1.294857 TTTTTGGCTTTTCGCTTGCC 58.705 45.000 0.00 0.00 46.26 4.52
4497 5021 9.678941 TGCTAAGACGATTATATGTGTTAGAAG 57.321 33.333 14.04 0.00 41.77 2.85
4514 5038 7.148407 GGAATGGTGGATAATAATGCTAAGACG 60.148 40.741 0.00 0.00 0.00 4.18
4694 5218 0.180642 TCCTTAACAACACACGGGCA 59.819 50.000 0.00 0.00 0.00 5.36
4761 5285 7.816031 TGTTACTAGTCTGTTGGTTGTTATAGC 59.184 37.037 0.00 0.00 0.00 2.97


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

AutoCloner maintained by Alex Coulton.