Multiple sequence alignment - TraesCS1A01G428600

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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 TraesCS1A01G428600 chr1A 100.000 3141 0 0 1 3141 582362710 582359570 0.000000e+00 5801.0
1 TraesCS1A01G428600 chr1A 78.231 1153 209 22 1153 2282 582415557 582414424 0.000000e+00 701.0
2 TraesCS1A01G428600 chr1A 77.055 523 42 31 691 1159 582416091 582415593 2.440000e-56 230.0
3 TraesCS1A01G428600 chr1A 91.150 113 10 0 1047 1159 582282153 582282041 1.510000e-33 154.0
4 TraesCS1A01G428600 chr1A 88.235 119 11 3 1043 1159 582295649 582295532 4.220000e-29 139.0
5 TraesCS1A01G428600 chr1D 95.255 1370 50 5 1153 2515 485093005 485091644 0.000000e+00 2156.0
6 TraesCS1A01G428600 chr1D 92.650 517 22 6 646 1159 485093544 485093041 0.000000e+00 730.0
7 TraesCS1A01G428600 chr1D 78.125 1152 212 22 1153 2282 485102875 485101742 0.000000e+00 695.0
8 TraesCS1A01G428600 chr1D 95.011 441 21 1 2702 3141 485091541 485091101 0.000000e+00 691.0
9 TraesCS1A01G428600 chr1D 78.444 617 40 40 603 1159 485103494 485102911 1.820000e-82 316.0
10 TraesCS1A01G428600 chr1D 89.888 178 7 5 480 654 485094674 485094505 5.270000e-53 219.0
11 TraesCS1A01G428600 chr1D 90.000 80 4 4 3 80 2472922 2472999 1.990000e-17 100.0
12 TraesCS1A01G428600 chr1B 91.139 1027 74 8 1231 2248 675545955 675544937 0.000000e+00 1376.0
13 TraesCS1A01G428600 chr1B 88.284 1084 54 24 79 1159 675550776 675549763 0.000000e+00 1230.0
14 TraesCS1A01G428600 chr1B 88.688 442 42 6 2702 3141 675544636 675544201 1.660000e-147 532.0
15 TraesCS1A01G428600 chr1B 92.116 241 13 4 2277 2516 675544938 675544703 5.020000e-88 335.0
16 TraesCS1A01G428600 chr1B 80.161 373 29 18 832 1159 675555708 675555336 1.460000e-58 237.0
17 TraesCS1A01G428600 chr1B 76.636 214 37 9 2115 2319 675388604 675388395 4.280000e-19 106.0
18 TraesCS1A01G428600 chr6B 100.000 181 0 0 2523 2703 475722870 475722690 5.020000e-88 335.0
19 TraesCS1A01G428600 chr6B 89.796 147 14 1 79 225 56963710 56963565 1.490000e-43 187.0
20 TraesCS1A01G428600 chr5D 98.429 191 2 1 2525 2714 338394651 338394461 5.020000e-88 335.0
21 TraesCS1A01G428600 chr5B 97.436 195 5 0 2521 2715 264932543 264932349 1.810000e-87 333.0
22 TraesCS1A01G428600 chr5B 97.423 194 1 2 2514 2703 433527152 433527345 8.400000e-86 327.0
23 TraesCS1A01G428600 chr4A 99.454 183 1 0 2521 2703 317089618 317089800 1.810000e-87 333.0
24 TraesCS1A01G428600 chr4A 100.000 179 0 0 2525 2703 710743712 710743534 6.490000e-87 331.0
25 TraesCS1A01G428600 chr2B 98.925 186 0 2 2518 2703 409336374 409336557 6.490000e-87 331.0
26 TraesCS1A01G428600 chr2B 87.654 81 10 0 1 81 594841355 594841275 9.270000e-16 95.3
27 TraesCS1A01G428600 chr3B 96.923 195 2 4 2508 2701 627921513 627921322 1.090000e-84 324.0
28 TraesCS1A01G428600 chr3B 89.796 147 14 1 79 225 372854230 372854375 1.490000e-43 187.0
29 TraesCS1A01G428600 chr2A 95.098 204 8 2 2500 2703 692453280 692453079 1.410000e-83 320.0
30 TraesCS1A01G428600 chr3D 91.837 147 11 1 79 225 277244808 277244663 1.480000e-48 204.0
31 TraesCS1A01G428600 chr2D 91.156 147 12 1 79 225 31977299 31977154 6.870000e-47 198.0
32 TraesCS1A01G428600 chr2D 91.156 147 12 1 79 225 630306093 630305948 6.870000e-47 198.0
33 TraesCS1A01G428600 chr2D 85.897 78 11 0 3 80 578883047 578882970 2.010000e-12 84.2
34 TraesCS1A01G428600 chr7D 90.476 147 14 0 79 225 412746674 412746820 8.890000e-46 195.0
35 TraesCS1A01G428600 chr7D 89.796 147 15 0 79 225 412753549 412753695 4.140000e-44 189.0
36 TraesCS1A01G428600 chr4D 90.476 147 13 1 79 225 37943346 37943201 3.200000e-45 193.0
37 TraesCS1A01G428600 chr4D 86.250 80 9 2 2 80 497616686 497616764 5.580000e-13 86.1
38 TraesCS1A01G428600 chr6D 89.116 147 15 1 79 225 30546553 30546408 6.920000e-42 182.0
39 TraesCS1A01G428600 chr6D 92.188 64 5 0 1088 1151 7567546 7567483 1.200000e-14 91.6
40 TraesCS1A01G428600 chr6A 98.750 80 1 0 1 80 74416430 74416351 3.270000e-30 143.0
41 TraesCS1A01G428600 chr6A 86.250 80 7 4 3 80 578610885 578610808 2.010000e-12 84.2
42 TraesCS1A01G428600 chr3A 95.000 80 4 0 1 80 110101448 110101369 3.290000e-25 126.0
43 TraesCS1A01G428600 chr4B 96.000 50 2 0 31 80 347367788 347367739 7.220000e-12 82.4
44 TraesCS1A01G428600 chr4B 94.000 50 3 0 31 80 235388308 235388259 3.360000e-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 TraesCS1A01G428600 chr1A 582359570 582362710 3140 True 5801.00 5801 100.00000 1 3141 1 chr1A.!!$R3 3140
1 TraesCS1A01G428600 chr1A 582414424 582416091 1667 True 465.50 701 77.64300 691 2282 2 chr1A.!!$R4 1591
2 TraesCS1A01G428600 chr1D 485091101 485094674 3573 True 949.00 2156 93.20100 480 3141 4 chr1D.!!$R1 2661
3 TraesCS1A01G428600 chr1D 485101742 485103494 1752 True 505.50 695 78.28450 603 2282 2 chr1D.!!$R2 1679
4 TraesCS1A01G428600 chr1B 675544201 675550776 6575 True 868.25 1376 90.05675 79 3141 4 chr1B.!!$R3 3062

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
34 35 0.315544 CGAACGTTTTCACCACCACG 60.316 55.0 0.46 0.0 38.62 4.94 F
1233 2318 0.246635 GCGTCAGCTTCCTCAACCTA 59.753 55.0 0.00 0.0 41.01 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1683 6475 0.252103 TCACTACCTCCCAGTCCACC 60.252 60.0 0.0 0.0 0.00 4.61 R
2555 7362 0.037303 ACCTCATGGTCACAAGGCAG 59.963 55.0 0.0 0.0 44.78 4.85 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
20 21 2.924903 TGTAGCTACAGTCAACGAACG 58.075 47.619 22.67 0.00 0.00 3.95
21 22 2.291465 TGTAGCTACAGTCAACGAACGT 59.709 45.455 22.67 0.00 0.00 3.99
22 23 2.503920 AGCTACAGTCAACGAACGTT 57.496 45.000 0.00 0.00 39.13 3.99
23 24 2.817901 AGCTACAGTCAACGAACGTTT 58.182 42.857 9.87 0.00 36.00 3.60
24 25 3.192466 AGCTACAGTCAACGAACGTTTT 58.808 40.909 9.87 0.00 36.00 2.43
25 26 3.244579 AGCTACAGTCAACGAACGTTTTC 59.755 43.478 9.87 6.53 36.00 2.29
26 27 3.000523 GCTACAGTCAACGAACGTTTTCA 59.999 43.478 9.87 0.00 36.00 2.69
27 28 3.378959 ACAGTCAACGAACGTTTTCAC 57.621 42.857 9.87 7.47 36.00 3.18
28 29 2.094734 ACAGTCAACGAACGTTTTCACC 59.905 45.455 9.87 0.00 36.00 4.02
29 30 2.094575 CAGTCAACGAACGTTTTCACCA 59.905 45.455 9.87 0.00 36.00 4.17
30 31 2.094734 AGTCAACGAACGTTTTCACCAC 59.905 45.455 9.87 0.00 36.00 4.16
31 32 1.397692 TCAACGAACGTTTTCACCACC 59.602 47.619 9.87 0.00 36.00 4.61
32 33 1.130749 CAACGAACGTTTTCACCACCA 59.869 47.619 9.87 0.00 36.00 4.17
33 34 0.728542 ACGAACGTTTTCACCACCAC 59.271 50.000 0.46 0.00 0.00 4.16
34 35 0.315544 CGAACGTTTTCACCACCACG 60.316 55.000 0.46 0.00 38.62 4.94
35 36 0.590481 GAACGTTTTCACCACCACGC 60.590 55.000 0.46 0.00 36.05 5.34
36 37 1.995646 AACGTTTTCACCACCACGCC 61.996 55.000 0.00 0.00 36.05 5.68
37 38 2.725641 GTTTTCACCACCACGCCC 59.274 61.111 0.00 0.00 0.00 6.13
38 39 2.519780 TTTTCACCACCACGCCCC 60.520 61.111 0.00 0.00 0.00 5.80
39 40 3.360423 TTTTCACCACCACGCCCCA 62.360 57.895 0.00 0.00 0.00 4.96
40 41 3.783362 TTTCACCACCACGCCCCAG 62.783 63.158 0.00 0.00 0.00 4.45
86 87 1.153549 GCTACGCCCCTGTCTTCAG 60.154 63.158 0.00 0.00 41.01 3.02
109 110 4.757149 GGTGATAAGTCAAAGAGCAAGTGT 59.243 41.667 0.00 0.00 35.80 3.55
110 111 5.334414 GGTGATAAGTCAAAGAGCAAGTGTG 60.334 44.000 0.00 0.00 35.80 3.82
129 130 3.491652 GCGCTTCTCGACAAGCCC 61.492 66.667 18.15 7.05 45.23 5.19
161 162 1.072331 GATGTTGGGTCAGTCACACCT 59.928 52.381 0.00 0.00 33.96 4.00
162 163 0.916086 TGTTGGGTCAGTCACACCTT 59.084 50.000 0.00 0.00 33.96 3.50
163 164 1.308998 GTTGGGTCAGTCACACCTTG 58.691 55.000 0.00 0.00 33.96 3.61
164 165 1.134220 GTTGGGTCAGTCACACCTTGA 60.134 52.381 0.00 0.00 33.96 3.02
183 184 3.194861 TGACATTTTATCGCCGAAGAGG 58.805 45.455 0.00 0.00 44.97 3.69
200 201 5.477291 CGAAGAGGCTAGATATTTCCCAGTA 59.523 44.000 0.00 0.00 0.00 2.74
207 208 6.352308 GGCTAGATATTTCCCAGTAGAATCCC 60.352 46.154 0.00 0.00 0.00 3.85
237 238 5.422331 ACTGTGCTGTAATTAAGAGCCTAGA 59.578 40.000 16.87 2.46 31.31 2.43
242 243 8.678199 GTGCTGTAATTAAGAGCCTAGAAAAAT 58.322 33.333 12.88 0.00 31.31 1.82
308 309 1.672898 CACAATTTGGGCCCACAGG 59.327 57.895 28.70 17.45 0.00 4.00
310 311 0.831711 ACAATTTGGGCCCACAGGTC 60.832 55.000 28.70 0.00 36.85 3.85
320 321 1.526575 CCCACAGGTCGCTGCAATTT 61.527 55.000 0.00 0.00 0.00 1.82
404 405 1.219393 CTGAGAGCGAAGTTCCCCC 59.781 63.158 0.00 0.00 39.04 5.40
407 408 1.962321 GAGAGCGAAGTTCCCCCTCC 61.962 65.000 0.00 0.00 39.04 4.30
408 409 1.990614 GAGCGAAGTTCCCCCTCCT 60.991 63.158 0.00 0.00 0.00 3.69
471 473 4.446413 GTCGTCGCCATCCCCGTT 62.446 66.667 0.00 0.00 0.00 4.44
679 1656 7.226325 GTGCTTAGAAAATCATGTGCTCTATCT 59.774 37.037 0.00 0.00 0.00 1.98
680 1657 8.424133 TGCTTAGAAAATCATGTGCTCTATCTA 58.576 33.333 0.00 0.00 0.00 1.98
742 1720 0.996583 TTTTATCCTTGGGCCGAGGT 59.003 50.000 34.21 24.47 36.45 3.85
794 1774 0.884514 TTCAGTGAGAGCAGAGTCCG 59.115 55.000 0.00 0.00 0.00 4.79
1068 2111 2.363147 AGCCTCTGGGACGACCTC 60.363 66.667 3.44 0.00 41.11 3.85
1074 2117 4.316823 TGGGACGACCTCCTGCCT 62.317 66.667 3.44 0.00 39.39 4.75
1131 2174 2.030412 TCGCTCTGCCGCTTCAAA 59.970 55.556 0.00 0.00 0.00 2.69
1233 2318 0.246635 GCGTCAGCTTCCTCAACCTA 59.753 55.000 0.00 0.00 41.01 3.08
1412 6197 2.203126 CAAGGAGATCTGGGCCGC 60.203 66.667 0.00 0.00 0.00 6.53
1431 6216 4.431131 CTGCCGGTGCCCCAGAAT 62.431 66.667 1.90 0.00 36.33 2.40
1476 6261 3.726517 CGCCTGTGCTTTGACCCG 61.727 66.667 0.00 0.00 34.43 5.28
1479 6264 2.281761 CTGTGCTTTGACCCGGCT 60.282 61.111 0.00 0.00 0.00 5.52
1480 6265 1.003839 CTGTGCTTTGACCCGGCTA 60.004 57.895 0.00 0.00 0.00 3.93
1481 6266 0.392998 CTGTGCTTTGACCCGGCTAT 60.393 55.000 0.00 0.00 0.00 2.97
1613 6402 2.208431 CTCCGAGAACCTCATGATTGC 58.792 52.381 0.00 0.00 0.00 3.56
1662 6454 1.134159 GGATCTCTGCATCTGGCTGTT 60.134 52.381 0.00 0.00 45.15 3.16
1683 6475 3.254629 CCATCCTGTGGTCAAGGTG 57.745 57.895 0.00 0.00 43.44 4.00
1684 6476 0.322816 CCATCCTGTGGTCAAGGTGG 60.323 60.000 0.00 0.00 43.44 4.61
1697 6489 2.529389 GGTGGTGGACTGGGAGGT 60.529 66.667 0.00 0.00 0.00 3.85
1812 6609 1.831286 AGGGACGCCTATACACCGG 60.831 63.158 0.00 0.00 0.00 5.28
1849 6646 0.811616 GTAGATGCCGGCTCTTGGTG 60.812 60.000 29.70 0.00 0.00 4.17
1955 6752 2.356135 CACCCAACGAATTCTACCAGG 58.644 52.381 3.52 0.79 0.00 4.45
1975 6772 1.154205 CGGTTGCGATCCATCCAGAC 61.154 60.000 10.21 0.00 33.66 3.51
2098 6898 1.215382 GGCGCAAAGATTTCACCCC 59.785 57.895 10.83 0.00 0.00 4.95
2166 6966 0.599558 GAGCAGCTTCACATTTGCCA 59.400 50.000 0.00 0.00 37.26 4.92
2170 6970 2.804212 GCAGCTTCACATTTGCCAAGTT 60.804 45.455 0.00 0.00 0.00 2.66
2256 7062 4.156455 TGATTGGATAGGTGCTCTTTCC 57.844 45.455 9.09 9.09 41.96 3.13
2270 7076 6.183360 GGTGCTCTTTCCATCCAGTTATTTAC 60.183 42.308 0.00 0.00 0.00 2.01
2287 7093 8.468399 AGTTATTTACTGCTAGTACCTTCACTC 58.532 37.037 0.00 0.00 35.19 3.51
2288 7094 8.468399 GTTATTTACTGCTAGTACCTTCACTCT 58.532 37.037 0.00 0.00 28.93 3.24
2289 7095 5.899120 TTACTGCTAGTACCTTCACTCTG 57.101 43.478 0.00 0.00 28.93 3.35
2315 7121 5.156355 GCAACTTGTTATGGATCACAGTTG 58.844 41.667 14.70 14.70 36.34 3.16
2399 7205 7.252612 TGAAATGGATGTCTCCTTTGTAGTA 57.747 36.000 0.00 0.00 42.59 1.82
2470 7276 4.934797 ACATTCTGGGAGATTCCTTCAA 57.065 40.909 0.00 0.00 36.57 2.69
2508 7315 6.571344 GCATTGTGTCAACCAATACCAATACA 60.571 38.462 0.00 0.00 31.52 2.29
2516 7323 6.542005 TCAACCAATACCAATACATGCTAGTG 59.458 38.462 0.00 0.00 0.00 2.74
2517 7324 6.247229 ACCAATACCAATACATGCTAGTGA 57.753 37.500 0.00 0.00 0.00 3.41
2518 7325 6.658849 ACCAATACCAATACATGCTAGTGAA 58.341 36.000 0.00 0.00 0.00 3.18
2519 7326 6.767902 ACCAATACCAATACATGCTAGTGAAG 59.232 38.462 0.00 0.00 0.00 3.02
2520 7327 6.992123 CCAATACCAATACATGCTAGTGAAGA 59.008 38.462 0.00 0.00 0.00 2.87
2521 7328 7.663081 CCAATACCAATACATGCTAGTGAAGAT 59.337 37.037 0.00 0.00 0.00 2.40
2522 7329 9.060347 CAATACCAATACATGCTAGTGAAGATT 57.940 33.333 0.00 0.00 0.00 2.40
2523 7330 6.932356 ACCAATACATGCTAGTGAAGATTG 57.068 37.500 0.00 0.00 0.00 2.67
2524 7331 5.824624 ACCAATACATGCTAGTGAAGATTGG 59.175 40.000 18.48 18.48 44.94 3.16
2525 7332 6.057533 CCAATACATGCTAGTGAAGATTGGA 58.942 40.000 16.56 0.00 43.05 3.53
2527 7334 7.255035 CCAATACATGCTAGTGAAGATTGGAAG 60.255 40.741 16.56 0.00 43.05 3.46
2528 7335 4.521146 ACATGCTAGTGAAGATTGGAAGG 58.479 43.478 0.00 0.00 0.00 3.46
2529 7336 3.634397 TGCTAGTGAAGATTGGAAGGG 57.366 47.619 0.00 0.00 0.00 3.95
2530 7337 2.239654 TGCTAGTGAAGATTGGAAGGGG 59.760 50.000 0.00 0.00 0.00 4.79
2531 7338 2.505819 GCTAGTGAAGATTGGAAGGGGA 59.494 50.000 0.00 0.00 0.00 4.81
2532 7339 3.432890 GCTAGTGAAGATTGGAAGGGGAG 60.433 52.174 0.00 0.00 0.00 4.30
2533 7340 1.283321 AGTGAAGATTGGAAGGGGAGC 59.717 52.381 0.00 0.00 0.00 4.70
2534 7341 0.625849 TGAAGATTGGAAGGGGAGCC 59.374 55.000 0.00 0.00 0.00 4.70
2537 7344 0.627986 AGATTGGAAGGGGAGCCTTG 59.372 55.000 0.00 0.00 0.00 3.61
2538 7345 0.396278 GATTGGAAGGGGAGCCTTGG 60.396 60.000 0.00 0.00 0.00 3.61
2539 7346 2.520657 ATTGGAAGGGGAGCCTTGGC 62.521 60.000 2.97 2.97 0.00 4.52
2540 7347 4.803908 GGAAGGGGAGCCTTGGCG 62.804 72.222 5.95 0.00 0.00 5.69
2549 7356 2.671619 GCCTTGGCGCAGTGGTAA 60.672 61.111 10.83 0.00 0.00 2.85
2552 7359 1.210155 CTTGGCGCAGTGGTAAAGC 59.790 57.895 10.83 0.00 0.00 3.51
2553 7360 1.228124 TTGGCGCAGTGGTAAAGCT 60.228 52.632 10.83 0.00 0.00 3.74
2554 7361 1.514678 TTGGCGCAGTGGTAAAGCTG 61.515 55.000 10.83 0.00 35.93 4.24
2559 7366 1.878775 CAGTGGTAAAGCTGCTGCC 59.121 57.895 12.44 7.07 40.80 4.85
2561 7368 0.111253 AGTGGTAAAGCTGCTGCCTT 59.889 50.000 12.44 8.34 40.80 4.35
2562 7369 0.242017 GTGGTAAAGCTGCTGCCTTG 59.758 55.000 12.44 0.00 40.80 3.61
2563 7370 0.178992 TGGTAAAGCTGCTGCCTTGT 60.179 50.000 12.44 0.00 40.80 3.16
2564 7371 0.242017 GGTAAAGCTGCTGCCTTGTG 59.758 55.000 12.44 0.00 40.80 3.33
2565 7372 1.238439 GTAAAGCTGCTGCCTTGTGA 58.762 50.000 12.44 0.00 40.80 3.58
2566 7373 1.068954 GTAAAGCTGCTGCCTTGTGAC 60.069 52.381 12.44 0.00 40.80 3.67
2567 7374 1.458639 AAAGCTGCTGCCTTGTGACC 61.459 55.000 12.44 0.00 40.80 4.02
2568 7375 2.595463 GCTGCTGCCTTGTGACCA 60.595 61.111 3.85 0.00 0.00 4.02
2569 7376 1.975407 GCTGCTGCCTTGTGACCAT 60.975 57.895 3.85 0.00 0.00 3.55
2570 7377 1.880894 CTGCTGCCTTGTGACCATG 59.119 57.895 0.00 0.00 0.00 3.66
2571 7378 0.607217 CTGCTGCCTTGTGACCATGA 60.607 55.000 0.00 0.00 0.00 3.07
2572 7379 0.607217 TGCTGCCTTGTGACCATGAG 60.607 55.000 0.00 0.00 0.00 2.90
2573 7380 1.310933 GCTGCCTTGTGACCATGAGG 61.311 60.000 0.00 0.00 42.21 3.86
2583 7390 4.617875 CCATGAGGTCACGGGTTC 57.382 61.111 0.00 0.00 0.00 3.62
2586 7393 1.442769 CATGAGGTCACGGGTTCAAG 58.557 55.000 0.00 0.00 0.00 3.02
2587 7394 1.056660 ATGAGGTCACGGGTTCAAGT 58.943 50.000 0.00 0.00 0.00 3.16
2588 7395 0.391597 TGAGGTCACGGGTTCAAGTC 59.608 55.000 0.00 0.00 0.00 3.01
2589 7396 0.320508 GAGGTCACGGGTTCAAGTCC 60.321 60.000 0.00 0.00 0.00 3.85
2590 7397 0.763223 AGGTCACGGGTTCAAGTCCT 60.763 55.000 0.00 0.00 0.00 3.85
2591 7398 0.602905 GGTCACGGGTTCAAGTCCTG 60.603 60.000 0.00 0.00 37.36 3.86
2592 7399 0.602905 GTCACGGGTTCAAGTCCTGG 60.603 60.000 0.00 0.00 35.79 4.45
2594 7401 0.107831 CACGGGTTCAAGTCCTGGAA 59.892 55.000 0.00 0.00 35.79 3.53
2596 7403 1.235724 CGGGTTCAAGTCCTGGAAAC 58.764 55.000 0.00 0.00 0.00 2.78
2597 7404 1.476110 CGGGTTCAAGTCCTGGAAACA 60.476 52.381 0.00 0.00 32.36 2.83
2608 7415 3.025924 TGGAAACAGCCTCTTGCAG 57.974 52.632 0.00 0.00 44.83 4.41
2609 7416 0.473755 TGGAAACAGCCTCTTGCAGA 59.526 50.000 0.00 0.00 44.83 4.26
2610 7417 1.133823 TGGAAACAGCCTCTTGCAGAA 60.134 47.619 0.00 0.00 44.83 3.02
2611 7418 1.956477 GGAAACAGCCTCTTGCAGAAA 59.044 47.619 0.00 0.00 44.83 2.52
2615 7422 3.423539 ACAGCCTCTTGCAGAAATGTA 57.576 42.857 0.00 0.00 44.83 2.29
2616 7423 3.341823 ACAGCCTCTTGCAGAAATGTAG 58.658 45.455 0.00 0.00 44.83 2.74
2617 7424 2.681848 CAGCCTCTTGCAGAAATGTAGG 59.318 50.000 0.00 0.00 44.83 3.18
2618 7425 2.019984 GCCTCTTGCAGAAATGTAGGG 58.980 52.381 0.00 0.00 40.77 3.53
2619 7426 2.356125 GCCTCTTGCAGAAATGTAGGGA 60.356 50.000 0.00 0.00 40.77 4.20
2620 7427 3.873801 GCCTCTTGCAGAAATGTAGGGAA 60.874 47.826 0.00 0.00 40.77 3.97
2621 7428 4.335416 CCTCTTGCAGAAATGTAGGGAAA 58.665 43.478 0.00 0.00 0.00 3.13
2622 7429 4.397417 CCTCTTGCAGAAATGTAGGGAAAG 59.603 45.833 0.00 0.00 0.00 2.62
2623 7430 4.335416 TCTTGCAGAAATGTAGGGAAAGG 58.665 43.478 0.00 0.00 0.00 3.11
2624 7431 2.446435 TGCAGAAATGTAGGGAAAGGC 58.554 47.619 0.00 0.00 0.00 4.35
2625 7432 2.041620 TGCAGAAATGTAGGGAAAGGCT 59.958 45.455 0.00 0.00 0.00 4.58
2626 7433 2.424956 GCAGAAATGTAGGGAAAGGCTG 59.575 50.000 0.00 0.00 0.00 4.85
2627 7434 2.424956 CAGAAATGTAGGGAAAGGCTGC 59.575 50.000 0.00 0.00 0.00 5.25
2628 7435 1.401905 GAAATGTAGGGAAAGGCTGCG 59.598 52.381 0.00 0.00 0.00 5.18
2629 7436 0.328258 AATGTAGGGAAAGGCTGCGT 59.672 50.000 0.00 0.00 0.00 5.24
2630 7437 1.200519 ATGTAGGGAAAGGCTGCGTA 58.799 50.000 0.00 0.00 0.00 4.42
2631 7438 0.248289 TGTAGGGAAAGGCTGCGTAC 59.752 55.000 0.00 0.00 37.28 3.67
2632 7439 0.248289 GTAGGGAAAGGCTGCGTACA 59.752 55.000 0.00 0.00 36.89 2.90
2633 7440 0.978151 TAGGGAAAGGCTGCGTACAA 59.022 50.000 0.00 0.00 0.00 2.41
2634 7441 0.328258 AGGGAAAGGCTGCGTACAAT 59.672 50.000 0.00 0.00 0.00 2.71
2635 7442 1.557832 AGGGAAAGGCTGCGTACAATA 59.442 47.619 0.00 0.00 0.00 1.90
2636 7443 1.940613 GGGAAAGGCTGCGTACAATAG 59.059 52.381 0.00 0.00 0.00 1.73
2637 7444 2.419574 GGGAAAGGCTGCGTACAATAGA 60.420 50.000 0.00 0.00 0.00 1.98
2638 7445 2.608090 GGAAAGGCTGCGTACAATAGAC 59.392 50.000 0.00 0.00 0.00 2.59
2639 7446 2.311124 AAGGCTGCGTACAATAGACC 57.689 50.000 0.00 0.00 0.00 3.85
2640 7447 0.464452 AGGCTGCGTACAATAGACCC 59.536 55.000 0.00 0.00 0.00 4.46
2641 7448 0.177141 GGCTGCGTACAATAGACCCA 59.823 55.000 0.00 0.00 0.00 4.51
2642 7449 1.406341 GGCTGCGTACAATAGACCCAA 60.406 52.381 0.00 0.00 0.00 4.12
2643 7450 2.352388 GCTGCGTACAATAGACCCAAA 58.648 47.619 0.00 0.00 0.00 3.28
2644 7451 2.351726 GCTGCGTACAATAGACCCAAAG 59.648 50.000 0.00 0.00 0.00 2.77
2645 7452 3.596214 CTGCGTACAATAGACCCAAAGT 58.404 45.455 0.00 0.00 0.00 2.66
2646 7453 3.331150 TGCGTACAATAGACCCAAAGTG 58.669 45.455 0.00 0.00 0.00 3.16
2647 7454 2.676342 GCGTACAATAGACCCAAAGTGG 59.324 50.000 0.00 0.00 37.25 4.00
2648 7455 3.867216 GCGTACAATAGACCCAAAGTGGT 60.867 47.826 0.00 0.00 42.79 4.16
2653 7460 4.373771 GACCCAAAGTGGTCGGAC 57.626 61.111 0.00 0.00 44.98 4.79
2654 7461 1.302271 GACCCAAAGTGGTCGGACC 60.302 63.158 20.36 20.36 44.98 4.46
2655 7462 2.033602 CCCAAAGTGGTCGGACCC 59.966 66.667 23.81 14.91 37.50 4.46
2656 7463 2.526046 CCCAAAGTGGTCGGACCCT 61.526 63.158 23.81 16.82 37.50 4.34
2657 7464 1.454539 CCAAAGTGGTCGGACCCTT 59.545 57.895 23.81 21.08 37.50 3.95
2658 7465 0.605589 CCAAAGTGGTCGGACCCTTC 60.606 60.000 23.81 13.97 37.50 3.46
2659 7466 0.605589 CAAAGTGGTCGGACCCTTCC 60.606 60.000 23.81 9.51 37.50 3.46
2660 7467 1.775934 AAAGTGGTCGGACCCTTCCC 61.776 60.000 23.81 7.17 38.99 3.97
2661 7468 3.714001 GTGGTCGGACCCTTCCCC 61.714 72.222 23.81 0.00 38.99 4.81
2662 7469 4.257810 TGGTCGGACCCTTCCCCA 62.258 66.667 23.81 0.69 38.99 4.96
2663 7470 3.400054 GGTCGGACCCTTCCCCAG 61.400 72.222 16.55 0.00 38.99 4.45
2664 7471 2.284405 GTCGGACCCTTCCCCAGA 60.284 66.667 0.00 0.00 38.99 3.86
2665 7472 2.284405 TCGGACCCTTCCCCAGAC 60.284 66.667 0.00 0.00 38.99 3.51
2666 7473 3.400054 CGGACCCTTCCCCAGACC 61.400 72.222 0.00 0.00 38.99 3.85
2667 7474 3.015753 GGACCCTTCCCCAGACCC 61.016 72.222 0.00 0.00 35.57 4.46
2668 7475 2.125225 GACCCTTCCCCAGACCCT 59.875 66.667 0.00 0.00 0.00 4.34
2669 7476 2.204151 ACCCTTCCCCAGACCCTG 60.204 66.667 0.00 0.00 0.00 4.45
2670 7477 3.732849 CCCTTCCCCAGACCCTGC 61.733 72.222 0.00 0.00 0.00 4.85
2671 7478 4.101448 CCTTCCCCAGACCCTGCG 62.101 72.222 0.00 0.00 0.00 5.18
2672 7479 4.785453 CTTCCCCAGACCCTGCGC 62.785 72.222 0.00 0.00 0.00 6.09
2693 7500 4.115279 CGGGAGCTACATGCACTG 57.885 61.111 0.00 0.00 45.94 3.66
2694 7501 1.522355 CGGGAGCTACATGCACTGG 60.522 63.158 0.00 0.00 45.94 4.00
2695 7502 1.153086 GGGAGCTACATGCACTGGG 60.153 63.158 0.00 0.00 45.94 4.45
2696 7503 1.153086 GGAGCTACATGCACTGGGG 60.153 63.158 0.00 0.00 45.94 4.96
2697 7504 1.821332 GAGCTACATGCACTGGGGC 60.821 63.158 0.00 0.00 45.94 5.80
2698 7505 2.262774 GAGCTACATGCACTGGGGCT 62.263 60.000 13.29 13.29 45.94 5.19
2699 7506 2.117156 GCTACATGCACTGGGGCTG 61.117 63.158 0.00 0.00 42.31 4.85
2700 7507 2.045045 TACATGCACTGGGGCTGC 60.045 61.111 0.00 0.00 35.03 5.25
2737 7545 3.149196 GGATATGTAATGCCACACAGGG 58.851 50.000 0.00 0.00 38.09 4.45
2742 7550 0.322456 TAATGCCACACAGGGTCAGC 60.322 55.000 0.00 0.00 38.09 4.26
2751 7559 0.615331 ACAGGGTCAGCGTTCATCAT 59.385 50.000 0.00 0.00 0.00 2.45
2752 7560 1.003580 ACAGGGTCAGCGTTCATCATT 59.996 47.619 0.00 0.00 0.00 2.57
2760 7568 4.210120 GTCAGCGTTCATCATTATCACTCC 59.790 45.833 0.00 0.00 0.00 3.85
2795 7604 5.990668 AGTGTCCTTGTTCTGAGTAAACTT 58.009 37.500 0.00 0.00 0.00 2.66
2817 7626 5.450818 TTCCAAGGCCATTATAGTTCTGT 57.549 39.130 5.01 0.00 0.00 3.41
2824 7633 6.662755 AGGCCATTATAGTTCTGTGATGAAA 58.337 36.000 5.01 0.00 0.00 2.69
2856 7665 6.582677 AGACTGCTATACCACTGTCATATC 57.417 41.667 0.00 0.00 37.25 1.63
2879 7688 8.823220 ATCCAGTGGCTTGTAAACTTTAATAT 57.177 30.769 3.51 0.00 0.00 1.28
2927 7736 4.801147 TGCTTGTCATTGAATAGCGATC 57.199 40.909 13.48 0.00 34.65 3.69
3015 7825 7.775729 ATAAATTTGAACGCGAACTTTAGTG 57.224 32.000 15.93 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.291465 ACGTTCGTTGACTGTAGCTACA 59.709 45.455 24.63 24.63 34.56 2.74
1 2 2.926165 ACGTTCGTTGACTGTAGCTAC 58.074 47.619 17.30 17.30 0.00 3.58
2 3 3.631145 AACGTTCGTTGACTGTAGCTA 57.369 42.857 9.77 0.00 0.00 3.32
3 4 2.503920 AACGTTCGTTGACTGTAGCT 57.496 45.000 9.77 0.00 0.00 3.32
4 5 3.000523 TGAAAACGTTCGTTGACTGTAGC 59.999 43.478 11.24 0.00 36.46 3.58
5 6 4.502558 GTGAAAACGTTCGTTGACTGTAG 58.497 43.478 11.24 0.00 36.46 2.74
6 7 3.306703 GGTGAAAACGTTCGTTGACTGTA 59.693 43.478 11.24 0.00 36.46 2.74
7 8 2.094734 GGTGAAAACGTTCGTTGACTGT 59.905 45.455 11.24 0.00 36.46 3.55
8 9 2.094575 TGGTGAAAACGTTCGTTGACTG 59.905 45.455 11.24 0.00 36.46 3.51
9 10 2.094734 GTGGTGAAAACGTTCGTTGACT 59.905 45.455 11.24 0.04 36.46 3.41
10 11 2.433808 GTGGTGAAAACGTTCGTTGAC 58.566 47.619 11.24 0.00 36.46 3.18
11 12 1.397692 GGTGGTGAAAACGTTCGTTGA 59.602 47.619 11.24 0.00 36.46 3.18
12 13 1.130749 TGGTGGTGAAAACGTTCGTTG 59.869 47.619 11.24 0.00 36.46 4.10
13 14 1.130938 GTGGTGGTGAAAACGTTCGTT 59.869 47.619 0.00 4.72 36.46 3.85
14 15 0.728542 GTGGTGGTGAAAACGTTCGT 59.271 50.000 0.00 0.00 36.46 3.85
15 16 0.315544 CGTGGTGGTGAAAACGTTCG 60.316 55.000 0.00 0.00 36.46 3.95
16 17 0.590481 GCGTGGTGGTGAAAACGTTC 60.590 55.000 0.00 0.00 38.28 3.95
17 18 1.430228 GCGTGGTGGTGAAAACGTT 59.570 52.632 0.00 0.00 38.28 3.99
18 19 2.474612 GGCGTGGTGGTGAAAACGT 61.475 57.895 0.00 0.00 38.28 3.99
19 20 2.330041 GGCGTGGTGGTGAAAACG 59.670 61.111 0.00 0.00 39.00 3.60
20 21 2.725641 GGGCGTGGTGGTGAAAAC 59.274 61.111 0.00 0.00 0.00 2.43
21 22 2.519780 GGGGCGTGGTGGTGAAAA 60.520 61.111 0.00 0.00 0.00 2.29
22 23 3.783362 CTGGGGCGTGGTGGTGAAA 62.783 63.158 0.00 0.00 0.00 2.69
23 24 4.263572 CTGGGGCGTGGTGGTGAA 62.264 66.667 0.00 0.00 0.00 3.18
68 69 1.153549 CTGAAGACAGGGGCGTAGC 60.154 63.158 0.00 0.00 46.69 3.58
77 78 6.459066 TCTTTGACTTATCACCTGAAGACAG 58.541 40.000 0.00 0.00 43.12 3.51
86 87 4.757149 ACACTTGCTCTTTGACTTATCACC 59.243 41.667 0.00 0.00 33.38 4.02
99 100 0.948141 GAAGCGCTCACACTTGCTCT 60.948 55.000 12.06 0.00 36.49 4.09
109 110 1.734477 GCTTGTCGAGAAGCGCTCA 60.734 57.895 28.59 0.00 44.15 4.26
110 111 3.076851 GCTTGTCGAGAAGCGCTC 58.923 61.111 28.59 6.71 39.10 5.03
129 130 1.479323 CCCAACATCATTGGAGGCTTG 59.521 52.381 7.27 0.00 42.06 4.01
161 162 3.621268 CCTCTTCGGCGATAAAATGTCAA 59.379 43.478 11.76 0.00 0.00 3.18
162 163 3.194861 CCTCTTCGGCGATAAAATGTCA 58.805 45.455 11.76 0.00 0.00 3.58
163 164 3.861569 CCTCTTCGGCGATAAAATGTC 57.138 47.619 11.76 0.00 0.00 3.06
183 184 6.442244 AGGGATTCTACTGGGAAATATCTAGC 59.558 42.308 0.00 0.00 0.00 3.42
253 254 5.701224 TCCCTTTTTCTAGGCTCTGAAAAA 58.299 37.500 25.50 25.50 44.62 1.94
265 266 7.687941 CTTTAGAGCACATTCCCTTTTTCTA 57.312 36.000 0.00 0.00 0.00 2.10
303 304 1.269206 ACAAAATTGCAGCGACCTGTG 60.269 47.619 0.00 0.00 41.26 3.66
305 306 1.411394 CACAAAATTGCAGCGACCTG 58.589 50.000 0.00 0.00 42.13 4.00
308 309 1.851658 AACCACAAAATTGCAGCGAC 58.148 45.000 0.00 0.00 0.00 5.19
310 311 1.261089 CCAAACCACAAAATTGCAGCG 59.739 47.619 0.00 0.00 0.00 5.18
320 321 1.045911 GCCCAAGGACCAAACCACAA 61.046 55.000 0.00 0.00 0.00 3.33
471 473 1.242989 TATTGTTGCCTCAAAGCGCA 58.757 45.000 11.47 0.00 34.65 6.09
587 595 2.681064 GCAGGCCCCATGCTTTCA 60.681 61.111 8.16 0.00 40.59 2.69
588 596 1.619807 AATGCAGGCCCCATGCTTTC 61.620 55.000 15.70 0.00 44.17 2.62
589 597 1.202769 AAATGCAGGCCCCATGCTTT 61.203 50.000 15.70 12.65 44.17 3.51
593 601 1.222387 CCAAAATGCAGGCCCCATG 59.778 57.895 0.00 0.00 0.00 3.66
652 1629 4.397417 AGAGCACATGATTTTCTAAGCACC 59.603 41.667 0.00 0.00 31.56 5.01
654 1631 7.278135 AGATAGAGCACATGATTTTCTAAGCA 58.722 34.615 0.00 0.00 33.62 3.91
679 1656 4.508405 GGCCCAAAATGTGCCCTAGATATA 60.508 45.833 0.00 0.00 39.30 0.86
680 1657 3.500343 GCCCAAAATGTGCCCTAGATAT 58.500 45.455 0.00 0.00 0.00 1.63
687 1665 2.994417 TCGGCCCAAAATGTGCCC 60.994 61.111 0.00 0.00 42.29 5.36
742 1720 2.997315 CTGCTCCGTGTCTCCCCA 60.997 66.667 0.00 0.00 0.00 4.96
773 1753 2.288457 CGGACTCTGCTCTCACTGAAAA 60.288 50.000 0.00 0.00 0.00 2.29
774 1754 1.270826 CGGACTCTGCTCTCACTGAAA 59.729 52.381 0.00 0.00 0.00 2.69
775 1755 0.884514 CGGACTCTGCTCTCACTGAA 59.115 55.000 0.00 0.00 0.00 3.02
776 1756 1.590610 GCGGACTCTGCTCTCACTGA 61.591 60.000 2.27 0.00 0.00 3.41
876 1867 1.301716 ACACCTCAAAGCGCGATGT 60.302 52.632 12.10 0.00 0.00 3.06
1049 2089 3.462678 GGTCGTCCCAGAGGCTCC 61.463 72.222 11.71 0.00 0.00 4.70
1061 2101 1.000993 ATCTCAGGCAGGAGGTCGT 59.999 57.895 6.39 0.00 35.58 4.34
1068 2111 2.503061 CGGTGGATCTCAGGCAGG 59.497 66.667 0.00 0.00 0.00 4.85
1074 2117 0.470080 GGATCTCCCGGTGGATCTCA 60.470 60.000 23.81 0.00 40.80 3.27
1159 2244 0.533032 GAGTAGCAGAAGAAGCCGGT 59.467 55.000 1.90 0.00 0.00 5.28
1326 6111 2.149973 TCCAGCAGTAGCAGATGAGA 57.850 50.000 0.00 0.00 45.49 3.27
1427 6212 1.495878 GCGCGTCATCATCTCATTCT 58.504 50.000 8.43 0.00 0.00 2.40
1431 6216 1.066422 GAGGCGCGTCATCATCTCA 59.934 57.895 24.22 0.00 0.00 3.27
1479 6264 1.153249 CTTGAAGCGGCGGGGAATA 60.153 57.895 9.78 0.00 0.00 1.75
1480 6265 2.438434 CTTGAAGCGGCGGGGAAT 60.438 61.111 9.78 0.00 0.00 3.01
1481 6266 4.715523 CCTTGAAGCGGCGGGGAA 62.716 66.667 9.78 0.00 0.00 3.97
1597 6386 2.208431 CTCGGCAATCATGAGGTTCTC 58.792 52.381 0.09 0.00 0.00 2.87
1682 6474 0.544357 CACTACCTCCCAGTCCACCA 60.544 60.000 0.00 0.00 0.00 4.17
1683 6475 0.252103 TCACTACCTCCCAGTCCACC 60.252 60.000 0.00 0.00 0.00 4.61
1684 6476 1.867363 ATCACTACCTCCCAGTCCAC 58.133 55.000 0.00 0.00 0.00 4.02
1697 6489 2.361119 GTGACCATGGAGCGTATCACTA 59.639 50.000 21.47 0.00 34.86 2.74
1812 6609 6.514048 GCATCTACCTTCATTTTCTACATGCC 60.514 42.308 0.00 0.00 0.00 4.40
1849 6646 1.808133 GCATGATCCTCGAGAACCCAC 60.808 57.143 15.71 0.00 0.00 4.61
1955 6752 2.513666 TGGATGGATCGCAACCGC 60.514 61.111 6.18 0.00 0.00 5.68
1975 6772 7.585867 CATCTTCAAGGAATATCAGATTGCAG 58.414 38.462 0.00 0.00 0.00 4.41
2098 6898 4.651778 TCTCCACAAAACAGGGAATGTAG 58.348 43.478 0.00 0.00 43.00 2.74
2270 7076 2.757868 AGCAGAGTGAAGGTACTAGCAG 59.242 50.000 0.00 0.00 38.49 4.24
2287 7093 3.441222 TGATCCATAACAAGTTGCAGCAG 59.559 43.478 2.55 0.00 0.00 4.24
2288 7094 3.191162 GTGATCCATAACAAGTTGCAGCA 59.809 43.478 2.55 0.00 0.00 4.41
2289 7095 3.191162 TGTGATCCATAACAAGTTGCAGC 59.809 43.478 1.81 0.00 0.00 5.25
2315 7121 8.818141 TCAGAACAGGACGATATCAATAATTC 57.182 34.615 3.12 0.00 0.00 2.17
2408 7214 4.948847 TGATCCAAGATTCGATGGTACTG 58.051 43.478 2.83 0.00 37.94 2.74
2409 7215 5.129485 AGTTGATCCAAGATTCGATGGTACT 59.871 40.000 2.83 1.30 37.94 2.73
2415 7221 6.047870 CAGAGAAGTTGATCCAAGATTCGAT 58.952 40.000 0.00 0.00 30.41 3.59
2417 7223 5.414360 TCAGAGAAGTTGATCCAAGATTCG 58.586 41.667 0.00 0.00 30.41 3.34
2470 7276 2.751259 ACACAATGCGAGCAGATTTCAT 59.249 40.909 3.58 0.00 0.00 2.57
2508 7315 3.117738 CCCCTTCCAATCTTCACTAGCAT 60.118 47.826 0.00 0.00 0.00 3.79
2516 7323 0.922626 AGGCTCCCCTTCCAATCTTC 59.077 55.000 0.00 0.00 38.74 2.87
2517 7324 3.127495 AGGCTCCCCTTCCAATCTT 57.873 52.632 0.00 0.00 38.74 2.40
2518 7325 4.952249 AGGCTCCCCTTCCAATCT 57.048 55.556 0.00 0.00 38.74 2.40
2530 7337 3.605749 TACCACTGCGCCAAGGCTC 62.606 63.158 4.18 1.20 39.32 4.70
2531 7338 2.690653 TTTACCACTGCGCCAAGGCT 62.691 55.000 4.18 0.00 39.32 4.58
2532 7339 2.200170 CTTTACCACTGCGCCAAGGC 62.200 60.000 4.18 0.00 37.85 4.35
2533 7340 1.875963 CTTTACCACTGCGCCAAGG 59.124 57.895 4.18 6.21 0.00 3.61
2534 7341 1.210155 GCTTTACCACTGCGCCAAG 59.790 57.895 4.18 0.00 0.00 3.61
2537 7344 2.870372 CAGCTTTACCACTGCGCC 59.130 61.111 4.18 0.00 0.00 6.53
2541 7348 0.607489 AGGCAGCAGCTTTACCACTG 60.607 55.000 0.00 0.00 41.70 3.66
2542 7349 0.111253 AAGGCAGCAGCTTTACCACT 59.889 50.000 0.00 0.00 38.40 4.00
2543 7350 0.242017 CAAGGCAGCAGCTTTACCAC 59.758 55.000 0.00 0.00 38.07 4.16
2545 7352 0.242017 CACAAGGCAGCAGCTTTACC 59.758 55.000 0.00 0.00 38.07 2.85
2549 7356 1.900498 GGTCACAAGGCAGCAGCTT 60.900 57.895 0.00 0.00 41.70 3.74
2552 7359 0.607217 TCATGGTCACAAGGCAGCAG 60.607 55.000 0.00 0.00 0.00 4.24
2553 7360 0.607217 CTCATGGTCACAAGGCAGCA 60.607 55.000 0.00 0.00 0.00 4.41
2554 7361 1.310933 CCTCATGGTCACAAGGCAGC 61.311 60.000 0.00 0.00 0.00 5.25
2555 7362 0.037303 ACCTCATGGTCACAAGGCAG 59.963 55.000 0.00 0.00 44.78 4.85
2556 7363 2.154139 ACCTCATGGTCACAAGGCA 58.846 52.632 0.00 0.00 44.78 4.75
2567 7374 1.270839 ACTTGAACCCGTGACCTCATG 60.271 52.381 0.00 0.00 0.00 3.07
2568 7375 1.002087 GACTTGAACCCGTGACCTCAT 59.998 52.381 0.00 0.00 0.00 2.90
2569 7376 0.391597 GACTTGAACCCGTGACCTCA 59.608 55.000 0.00 0.00 0.00 3.86
2570 7377 0.320508 GGACTTGAACCCGTGACCTC 60.321 60.000 0.00 0.00 0.00 3.85
2571 7378 0.763223 AGGACTTGAACCCGTGACCT 60.763 55.000 0.00 0.00 0.00 3.85
2572 7379 0.602905 CAGGACTTGAACCCGTGACC 60.603 60.000 0.00 0.00 0.00 4.02
2573 7380 0.602905 CCAGGACTTGAACCCGTGAC 60.603 60.000 0.00 0.00 0.00 3.67
2575 7382 0.107831 TTCCAGGACTTGAACCCGTG 59.892 55.000 0.00 0.00 0.00 4.94
2576 7383 0.841289 TTTCCAGGACTTGAACCCGT 59.159 50.000 0.00 0.00 0.00 5.28
2578 7385 2.230660 CTGTTTCCAGGACTTGAACCC 58.769 52.381 0.00 0.00 34.90 4.11
2579 7386 1.609072 GCTGTTTCCAGGACTTGAACC 59.391 52.381 0.00 0.00 39.22 3.62
2580 7387 1.609072 GGCTGTTTCCAGGACTTGAAC 59.391 52.381 0.00 0.00 39.22 3.18
2581 7388 1.494721 AGGCTGTTTCCAGGACTTGAA 59.505 47.619 0.00 0.00 39.22 2.69
2582 7389 1.072331 GAGGCTGTTTCCAGGACTTGA 59.928 52.381 0.00 0.00 39.22 3.02
2583 7390 1.072965 AGAGGCTGTTTCCAGGACTTG 59.927 52.381 0.00 0.00 39.22 3.16
2586 7393 1.528129 CAAGAGGCTGTTTCCAGGAC 58.472 55.000 0.00 0.00 39.22 3.85
2587 7394 0.250901 GCAAGAGGCTGTTTCCAGGA 60.251 55.000 0.00 0.00 39.22 3.86
2588 7395 0.538057 TGCAAGAGGCTGTTTCCAGG 60.538 55.000 0.00 0.00 45.15 4.45
2589 7396 0.879765 CTGCAAGAGGCTGTTTCCAG 59.120 55.000 0.00 0.00 45.15 3.86
2590 7397 0.473755 TCTGCAAGAGGCTGTTTCCA 59.526 50.000 0.00 0.00 38.67 3.53
2591 7398 3.329300 TCTGCAAGAGGCTGTTTCC 57.671 52.632 0.00 0.00 38.67 3.13
2601 7408 4.335416 CCTTTCCCTACATTTCTGCAAGA 58.665 43.478 0.00 0.00 44.68 3.02
2603 7410 2.825532 GCCTTTCCCTACATTTCTGCAA 59.174 45.455 0.00 0.00 0.00 4.08
2604 7411 2.041620 AGCCTTTCCCTACATTTCTGCA 59.958 45.455 0.00 0.00 0.00 4.41
2606 7413 2.424956 GCAGCCTTTCCCTACATTTCTG 59.575 50.000 0.00 0.00 0.00 3.02
2607 7414 2.728007 GCAGCCTTTCCCTACATTTCT 58.272 47.619 0.00 0.00 0.00 2.52
2608 7415 1.401905 CGCAGCCTTTCCCTACATTTC 59.598 52.381 0.00 0.00 0.00 2.17
2609 7416 1.271926 ACGCAGCCTTTCCCTACATTT 60.272 47.619 0.00 0.00 0.00 2.32
2610 7417 0.328258 ACGCAGCCTTTCCCTACATT 59.672 50.000 0.00 0.00 0.00 2.71
2611 7418 1.134491 GTACGCAGCCTTTCCCTACAT 60.134 52.381 0.00 0.00 0.00 2.29
2615 7422 0.328258 ATTGTACGCAGCCTTTCCCT 59.672 50.000 0.00 0.00 0.00 4.20
2616 7423 1.940613 CTATTGTACGCAGCCTTTCCC 59.059 52.381 0.00 0.00 0.00 3.97
2617 7424 2.608090 GTCTATTGTACGCAGCCTTTCC 59.392 50.000 0.00 0.00 0.00 3.13
2618 7425 2.608090 GGTCTATTGTACGCAGCCTTTC 59.392 50.000 0.00 0.00 0.00 2.62
2619 7426 2.629051 GGTCTATTGTACGCAGCCTTT 58.371 47.619 0.00 0.00 0.00 3.11
2620 7427 1.134491 GGGTCTATTGTACGCAGCCTT 60.134 52.381 0.00 0.00 0.00 4.35
2621 7428 0.464452 GGGTCTATTGTACGCAGCCT 59.536 55.000 0.00 0.00 0.00 4.58
2622 7429 0.177141 TGGGTCTATTGTACGCAGCC 59.823 55.000 0.00 0.00 35.18 4.85
2623 7430 2.018542 TTGGGTCTATTGTACGCAGC 57.981 50.000 0.00 0.00 40.36 5.25
2624 7431 3.370978 CACTTTGGGTCTATTGTACGCAG 59.629 47.826 0.00 0.00 40.36 5.18
2625 7432 3.331150 CACTTTGGGTCTATTGTACGCA 58.669 45.455 0.00 0.00 37.94 5.24
2626 7433 2.676342 CCACTTTGGGTCTATTGTACGC 59.324 50.000 0.00 0.00 32.67 4.42
2627 7434 3.934068 ACCACTTTGGGTCTATTGTACG 58.066 45.455 0.00 0.00 43.37 3.67
2637 7444 2.826003 GGGTCCGACCACTTTGGGT 61.826 63.158 19.43 0.00 43.37 4.51
2638 7445 2.033602 GGGTCCGACCACTTTGGG 59.966 66.667 19.43 0.00 43.37 4.12
2639 7446 0.605589 GAAGGGTCCGACCACTTTGG 60.606 60.000 19.43 0.00 41.02 3.28
2640 7447 0.605589 GGAAGGGTCCGACCACTTTG 60.606 60.000 19.43 0.00 41.02 2.77
2641 7448 1.759236 GGAAGGGTCCGACCACTTT 59.241 57.895 19.43 9.96 41.02 2.66
2642 7449 2.222013 GGGAAGGGTCCGACCACTT 61.222 63.158 19.43 17.88 46.04 3.16
2643 7450 2.606826 GGGAAGGGTCCGACCACT 60.607 66.667 19.43 10.80 46.04 4.00
2644 7451 3.714001 GGGGAAGGGTCCGACCAC 61.714 72.222 19.43 8.70 46.04 4.16
2645 7452 4.257810 TGGGGAAGGGTCCGACCA 62.258 66.667 19.43 0.00 46.04 4.02
2646 7453 3.400054 CTGGGGAAGGGTCCGACC 61.400 72.222 9.30 9.30 46.04 4.79
2647 7454 2.284405 TCTGGGGAAGGGTCCGAC 60.284 66.667 0.00 0.00 46.04 4.79
2648 7455 2.284405 GTCTGGGGAAGGGTCCGA 60.284 66.667 0.00 0.00 46.04 4.55
2649 7456 3.400054 GGTCTGGGGAAGGGTCCG 61.400 72.222 0.00 0.00 46.04 4.79
2650 7457 3.015753 GGGTCTGGGGAAGGGTCC 61.016 72.222 0.00 0.00 44.10 4.46
2651 7458 2.125225 AGGGTCTGGGGAAGGGTC 59.875 66.667 0.00 0.00 0.00 4.46
2652 7459 2.204151 CAGGGTCTGGGGAAGGGT 60.204 66.667 0.00 0.00 0.00 4.34
2653 7460 3.732849 GCAGGGTCTGGGGAAGGG 61.733 72.222 0.00 0.00 31.21 3.95
2654 7461 4.101448 CGCAGGGTCTGGGGAAGG 62.101 72.222 4.35 0.00 40.11 3.46
2655 7462 4.785453 GCGCAGGGTCTGGGGAAG 62.785 72.222 0.30 0.00 43.28 3.46
2667 7474 4.819761 TAGCTCCCGCTTGCGCAG 62.820 66.667 11.31 6.32 46.47 5.18
2670 7477 2.202932 ATGTAGCTCCCGCTTGCG 60.203 61.111 8.14 8.14 46.47 4.85
2671 7478 2.828128 GCATGTAGCTCCCGCTTGC 61.828 63.158 0.00 0.00 46.47 4.01
2672 7479 1.450134 TGCATGTAGCTCCCGCTTG 60.450 57.895 0.00 0.00 46.47 4.01
2673 7480 1.450312 GTGCATGTAGCTCCCGCTT 60.450 57.895 0.00 0.00 46.47 4.68
2675 7482 2.176273 CAGTGCATGTAGCTCCCGC 61.176 63.158 0.00 0.00 45.94 6.13
2676 7483 1.522355 CCAGTGCATGTAGCTCCCG 60.522 63.158 0.00 0.00 45.94 5.14
2677 7484 1.153086 CCCAGTGCATGTAGCTCCC 60.153 63.158 0.00 0.00 45.94 4.30
2678 7485 1.153086 CCCCAGTGCATGTAGCTCC 60.153 63.158 0.00 0.00 45.94 4.70
2679 7486 1.821332 GCCCCAGTGCATGTAGCTC 60.821 63.158 0.00 0.00 45.94 4.09
2680 7487 2.273449 GCCCCAGTGCATGTAGCT 59.727 61.111 0.00 0.00 45.94 3.32
2681 7488 2.117156 CAGCCCCAGTGCATGTAGC 61.117 63.158 0.00 0.00 45.96 3.58
2682 7489 2.117156 GCAGCCCCAGTGCATGTAG 61.117 63.158 0.00 0.00 40.86 2.74
2683 7490 2.045045 GCAGCCCCAGTGCATGTA 60.045 61.111 0.00 0.00 40.86 2.29
2694 7501 1.078143 CTTCACTAGTGGGCAGCCC 60.078 63.158 25.54 25.54 45.71 5.19
2695 7502 0.543749 ATCTTCACTAGTGGGCAGCC 59.456 55.000 22.48 1.26 0.00 4.85
2696 7503 2.012673 CAATCTTCACTAGTGGGCAGC 58.987 52.381 22.48 0.00 0.00 5.25
2697 7504 2.237143 TCCAATCTTCACTAGTGGGCAG 59.763 50.000 22.48 15.32 0.00 4.85
2698 7505 2.265367 TCCAATCTTCACTAGTGGGCA 58.735 47.619 22.48 7.00 0.00 5.36
2699 7506 3.567478 ATCCAATCTTCACTAGTGGGC 57.433 47.619 22.48 0.00 0.00 5.36
2700 7507 6.179906 ACATATCCAATCTTCACTAGTGGG 57.820 41.667 22.48 14.20 0.00 4.61
2737 7545 4.210120 GGAGTGATAATGATGAACGCTGAC 59.790 45.833 0.00 0.00 0.00 3.51
2742 7550 5.403766 GTGCTAGGAGTGATAATGATGAACG 59.596 44.000 0.00 0.00 0.00 3.95
2751 7559 2.561209 TGGGGTGCTAGGAGTGATAA 57.439 50.000 0.00 0.00 0.00 1.75
2752 7560 2.795291 ATGGGGTGCTAGGAGTGATA 57.205 50.000 0.00 0.00 0.00 2.15
2760 7568 1.794714 AGGACACTATGGGGTGCTAG 58.205 55.000 2.92 0.00 40.52 3.42
2795 7604 5.045213 TCACAGAACTATAATGGCCTTGGAA 60.045 40.000 3.32 0.00 0.00 3.53
2817 7626 6.244552 AGCAGTCTATTCAGGATTTCATCA 57.755 37.500 0.00 0.00 0.00 3.07
2824 7633 6.210385 CAGTGGTATAGCAGTCTATTCAGGAT 59.790 42.308 9.32 0.00 36.86 3.24
2831 7640 7.340743 GGATATGACAGTGGTATAGCAGTCTAT 59.659 40.741 19.20 14.96 38.89 1.98
2856 7665 8.129211 GCTATATTAAAGTTTACAAGCCACTGG 58.871 37.037 0.00 0.00 0.00 4.00
2879 7688 4.859304 TCACGAAAGTTTCCAGTAGCTA 57.141 40.909 10.01 0.00 46.40 3.32
2896 7705 3.684305 TCAATGACAAGCATACCTTCACG 59.316 43.478 0.00 0.00 35.78 4.35
2927 7736 4.642445 TTGCATTCCTATTCATGCTGTG 57.358 40.909 5.77 0.00 45.21 3.66
2996 7806 4.861389 TTCACTAAAGTTCGCGTTCAAA 57.139 36.364 5.77 0.00 0.00 2.69
3015 7825 8.817100 CAAAGGAAACCAAACATCTACTTTTTC 58.183 33.333 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.