Multiple sequence alignment - TraesCS4A01G091300

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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 TraesCS4A01G091300 chr4A 100.000 3633 0 0 1 3633 97876989 97873357 0.000000e+00 6709.0
1 TraesCS4A01G091300 chr4B 90.334 2245 115 35 1 2193 451901481 451903675 0.000000e+00 2850.0
2 TraesCS4A01G091300 chr4B 93.373 498 27 1 2194 2691 451903712 451904203 0.000000e+00 732.0
3 TraesCS4A01G091300 chr4B 94.633 354 15 2 3283 3633 451907519 451907871 2.470000e-151 545.0
4 TraesCS4A01G091300 chr4B 85.538 325 19 7 3126 3422 451907141 451907465 7.570000e-82 315.0
5 TraesCS4A01G091300 chr4B 84.942 259 32 5 1581 1836 30595269 30595015 4.660000e-64 255.0
6 TraesCS4A01G091300 chr4B 90.991 111 6 1 2761 2871 451907032 451907138 2.920000e-31 147.0
7 TraesCS4A01G091300 chr4D 93.849 1447 66 8 751 2193 367042012 367043439 0.000000e+00 2158.0
8 TraesCS4A01G091300 chr4D 94.611 668 29 2 2194 2861 367043476 367044136 0.000000e+00 1027.0
9 TraesCS4A01G091300 chr4D 90.994 533 20 7 3122 3633 367044534 367045059 0.000000e+00 693.0
10 TraesCS4A01G091300 chr4D 81.491 805 63 36 1 747 367041191 367041967 1.880000e-162 582.0
11 TraesCS4A01G091300 chr4D 86.053 380 45 8 1550 1925 154924617 154924992 5.650000e-108 401.0
12 TraesCS4A01G091300 chr2D 86.065 775 83 11 1156 1925 325249143 325248389 0.000000e+00 809.0
13 TraesCS4A01G091300 chr2D 92.208 77 5 1 3120 3195 50102252 50102328 1.380000e-19 108.0
14 TraesCS4A01G091300 chr7D 85.733 778 87 10 1153 1925 31931016 31931774 0.000000e+00 800.0
15 TraesCS4A01G091300 chr7D 89.744 78 7 1 3120 3196 263827877 263827954 8.300000e-17 99.0
16 TraesCS4A01G091300 chrUn 82.817 774 90 18 1156 1925 390962484 390961750 0.000000e+00 652.0
17 TraesCS4A01G091300 chr5D 91.060 302 24 2 1581 1880 389494869 389494569 4.370000e-109 405.0
18 TraesCS4A01G091300 chr5B 88.621 290 32 1 1154 1443 620779783 620779495 5.770000e-93 351.0
19 TraesCS4A01G091300 chr6B 84.083 289 38 7 1551 1836 259709512 259709795 4.620000e-69 272.0
20 TraesCS4A01G091300 chr6B 85.714 77 10 1 3120 3195 607313131 607313207 3.010000e-11 80.5
21 TraesCS4A01G091300 chr2B 85.659 258 31 5 1581 1836 311671658 311671911 2.150000e-67 267.0
22 TraesCS4A01G091300 chr3A 94.595 74 3 1 3123 3195 620571918 620571845 2.960000e-21 113.0
23 TraesCS4A01G091300 chr3D 93.243 74 4 1 3123 3195 476984033 476983960 1.380000e-19 108.0
24 TraesCS4A01G091300 chr3D 95.000 60 3 0 3136 3195 337315147 337315088 1.070000e-15 95.3
25 TraesCS4A01G091300 chr3B 93.243 74 4 1 3123 3195 636108972 636108899 1.380000e-19 108.0
26 TraesCS4A01G091300 chr3B 91.429 70 5 1 3123 3191 784665294 784665225 1.070000e-15 95.3


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 TraesCS4A01G091300 chr4A 97873357 97876989 3632 True 6709.0 6709 100.00000 1 3633 1 chr4A.!!$R1 3632
1 TraesCS4A01G091300 chr4B 451901481 451907871 6390 False 917.8 2850 90.97380 1 3633 5 chr4B.!!$F1 3632
2 TraesCS4A01G091300 chr4D 367041191 367045059 3868 False 1115.0 2158 90.23625 1 3633 4 chr4D.!!$F2 3632
3 TraesCS4A01G091300 chr2D 325248389 325249143 754 True 809.0 809 86.06500 1156 1925 1 chr2D.!!$R1 769
4 TraesCS4A01G091300 chr7D 31931016 31931774 758 False 800.0 800 85.73300 1153 1925 1 chr7D.!!$F1 772
5 TraesCS4A01G091300 chrUn 390961750 390962484 734 True 652.0 652 82.81700 1156 1925 1 chrUn.!!$R1 769

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
311 322 0.170116 TTCGGATGTGAAAATGGCGC 59.830 50.0 0.00 0.0 0.0 6.53 F
313 324 0.523968 CGGATGTGAAAATGGCGCTG 60.524 55.0 7.64 0.0 0.0 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2299 2456 1.079127 AGATCTTGAACGGTGGCGG 60.079 57.895 0.0 0.0 0.0 6.13 R
2670 2827 8.810652 TGCAAAGTAACTAAAATTCCAACATC 57.189 30.769 0.0 0.0 0.0 3.06 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
54 55 1.514443 GAGAAAGTCTCGCGTCCGG 60.514 63.158 5.77 0.00 33.35 5.14
56 57 3.628280 GAAAGTCTCGCGTCCGGCT 62.628 63.158 5.77 0.00 40.44 5.52
150 155 2.661537 TGTCGCAGGTCGCAACTG 60.662 61.111 0.00 0.00 42.60 3.16
151 156 2.355837 GTCGCAGGTCGCAACTGA 60.356 61.111 5.52 0.00 42.60 3.41
152 157 1.738099 GTCGCAGGTCGCAACTGAT 60.738 57.895 5.52 0.00 42.60 2.90
153 158 0.457853 GTCGCAGGTCGCAACTGATA 60.458 55.000 5.52 0.00 42.60 2.15
243 249 1.062148 GGCGACGAAGCAAAGGTATTC 59.938 52.381 0.00 0.00 39.27 1.75
244 250 2.000447 GCGACGAAGCAAAGGTATTCT 59.000 47.619 0.00 0.00 37.05 2.40
249 255 2.860735 CGAAGCAAAGGTATTCTCTCGG 59.139 50.000 0.00 0.00 0.00 4.63
250 256 2.990066 AGCAAAGGTATTCTCTCGGG 57.010 50.000 0.00 0.00 0.00 5.14
257 263 3.983821 AGGTATTCTCTCGGGTTCTTCT 58.016 45.455 0.00 0.00 0.00 2.85
258 264 3.955551 AGGTATTCTCTCGGGTTCTTCTC 59.044 47.826 0.00 0.00 0.00 2.87
259 265 3.068448 GGTATTCTCTCGGGTTCTTCTCC 59.932 52.174 0.00 0.00 0.00 3.71
260 266 2.606751 TTCTCTCGGGTTCTTCTCCT 57.393 50.000 0.00 0.00 0.00 3.69
264 275 1.893801 TCTCGGGTTCTTCTCCTGTTC 59.106 52.381 0.00 0.00 33.44 3.18
269 280 1.669211 GGTTCTTCTCCTGTTCCGTCG 60.669 57.143 0.00 0.00 0.00 5.12
282 293 1.682740 TCCGTCGGTAGCATGATACA 58.317 50.000 21.76 0.13 0.00 2.29
283 294 1.607148 TCCGTCGGTAGCATGATACAG 59.393 52.381 21.76 17.94 0.00 2.74
285 296 2.551032 CCGTCGGTAGCATGATACAGTA 59.449 50.000 21.76 6.42 0.00 2.74
286 297 3.552541 CGTCGGTAGCATGATACAGTAC 58.447 50.000 21.76 15.41 0.00 2.73
288 299 4.450080 CGTCGGTAGCATGATACAGTACTA 59.550 45.833 21.76 0.21 0.00 1.82
290 301 6.312180 CGTCGGTAGCATGATACAGTACTATA 59.688 42.308 21.76 0.00 0.00 1.31
291 302 7.462731 GTCGGTAGCATGATACAGTACTATAC 58.537 42.308 21.76 7.88 0.00 1.47
292 303 7.333921 GTCGGTAGCATGATACAGTACTATACT 59.666 40.741 21.76 0.00 40.28 2.12
293 304 7.881751 TCGGTAGCATGATACAGTACTATACTT 59.118 37.037 21.76 0.00 36.76 2.24
294 305 8.176365 CGGTAGCATGATACAGTACTATACTTC 58.824 40.741 21.76 0.01 36.76 3.01
296 307 7.147143 AGCATGATACAGTACTATACTTCGG 57.853 40.000 0.00 0.00 36.76 4.30
297 308 6.940867 AGCATGATACAGTACTATACTTCGGA 59.059 38.462 0.00 0.00 36.76 4.55
298 309 7.612244 AGCATGATACAGTACTATACTTCGGAT 59.388 37.037 0.00 0.00 36.76 4.18
299 310 7.698550 GCATGATACAGTACTATACTTCGGATG 59.301 40.741 0.00 0.00 36.76 3.51
300 311 8.731605 CATGATACAGTACTATACTTCGGATGT 58.268 37.037 0.00 1.96 36.76 3.06
301 312 8.095937 TGATACAGTACTATACTTCGGATGTG 57.904 38.462 6.78 0.00 36.76 3.21
302 313 7.935210 TGATACAGTACTATACTTCGGATGTGA 59.065 37.037 6.78 0.00 36.76 3.58
305 316 7.833786 ACAGTACTATACTTCGGATGTGAAAA 58.166 34.615 6.78 0.00 36.76 2.29
306 317 8.475639 ACAGTACTATACTTCGGATGTGAAAAT 58.524 33.333 6.78 0.00 36.76 1.82
307 318 8.755941 CAGTACTATACTTCGGATGTGAAAATG 58.244 37.037 6.78 0.00 36.76 2.32
308 319 7.926555 AGTACTATACTTCGGATGTGAAAATGG 59.073 37.037 6.78 0.00 34.86 3.16
309 320 4.900635 ATACTTCGGATGTGAAAATGGC 57.099 40.909 6.78 0.00 0.00 4.40
310 321 1.468520 ACTTCGGATGTGAAAATGGCG 59.531 47.619 0.00 0.00 0.00 5.69
311 322 0.170116 TTCGGATGTGAAAATGGCGC 59.830 50.000 0.00 0.00 0.00 6.53
312 323 0.676466 TCGGATGTGAAAATGGCGCT 60.676 50.000 7.64 0.00 0.00 5.92
313 324 0.523968 CGGATGTGAAAATGGCGCTG 60.524 55.000 7.64 0.00 0.00 5.18
314 325 0.803380 GGATGTGAAAATGGCGCTGC 60.803 55.000 7.64 0.00 0.00 5.25
315 326 1.135699 GATGTGAAAATGGCGCTGCG 61.136 55.000 19.17 19.17 0.00 5.18
316 327 2.504681 GTGAAAATGGCGCTGCGG 60.505 61.111 24.61 5.63 0.00 5.69
317 328 2.671276 TGAAAATGGCGCTGCGGA 60.671 55.556 24.61 0.00 0.00 5.54
329 340 1.895707 CTGCGGATTCATCCTGCCC 60.896 63.158 15.53 0.00 44.93 5.36
334 345 0.536915 GGATTCATCCTGCCCTCTGC 60.537 60.000 0.00 0.00 43.73 4.26
346 359 1.742268 GCCCTCTGCTCTGTTTGATTC 59.258 52.381 0.00 0.00 36.87 2.52
349 362 2.613977 CCTCTGCTCTGTTTGATTCGGT 60.614 50.000 0.00 0.00 0.00 4.69
373 412 7.222999 GGTGATAGTTTTGCACATAGTAGAGAC 59.777 40.741 0.00 0.00 34.33 3.36
407 446 3.064820 ACACTTGCCAGTAGAAAAACGTG 59.935 43.478 0.00 0.00 0.00 4.49
408 447 2.032924 ACTTGCCAGTAGAAAAACGTGC 59.967 45.455 0.00 0.00 0.00 5.34
411 450 1.398071 GCCAGTAGAAAAACGTGCGTC 60.398 52.381 0.00 0.00 0.00 5.19
412 451 1.862201 CCAGTAGAAAAACGTGCGTCA 59.138 47.619 0.00 0.00 0.00 4.35
439 478 1.685148 GGGGCTGATTGATCCTCAAC 58.315 55.000 0.00 0.00 39.45 3.18
444 504 3.118482 GGCTGATTGATCCTCAACTCTGA 60.118 47.826 0.00 0.00 39.45 3.27
453 513 3.067106 TCCTCAACTCTGATTCGCAAAC 58.933 45.455 0.00 0.00 0.00 2.93
477 537 6.030228 CGCGCTAGATCTATATGACATGAAA 58.970 40.000 5.56 0.00 0.00 2.69
512 573 3.132467 AGAATTCCTAGGTTGTAGCGGTC 59.868 47.826 9.08 0.00 0.00 4.79
561 622 0.798776 GTGGTTTCATCTGGACTGCG 59.201 55.000 0.00 0.00 0.00 5.18
562 623 0.684535 TGGTTTCATCTGGACTGCGA 59.315 50.000 0.00 0.00 0.00 5.10
570 631 3.638627 TCATCTGGACTGCGAGATTGTAT 59.361 43.478 0.00 0.00 37.47 2.29
598 659 3.886123 CGATGGGGGAAACAGATTTACT 58.114 45.455 0.00 0.00 0.00 2.24
619 682 1.353609 AACCCGCGTAACGTGTATGC 61.354 55.000 4.92 10.20 41.42 3.14
673 736 3.612004 CGGGAACAGACAGTCTCTAACAC 60.612 52.174 0.00 0.00 0.00 3.32
674 737 3.574826 GGGAACAGACAGTCTCTAACACT 59.425 47.826 0.00 0.00 0.00 3.55
675 738 4.551388 GGAACAGACAGTCTCTAACACTG 58.449 47.826 0.00 0.00 45.86 3.66
676 739 4.278669 GGAACAGACAGTCTCTAACACTGA 59.721 45.833 0.00 0.00 43.54 3.41
677 740 5.221263 GGAACAGACAGTCTCTAACACTGAA 60.221 44.000 0.00 0.00 43.54 3.02
678 741 5.189659 ACAGACAGTCTCTAACACTGAAC 57.810 43.478 0.00 1.38 43.54 3.18
679 742 4.890581 ACAGACAGTCTCTAACACTGAACT 59.109 41.667 0.00 3.41 43.54 3.01
680 743 5.218885 CAGACAGTCTCTAACACTGAACTG 58.781 45.833 0.00 10.65 43.54 3.16
681 744 4.279671 AGACAGTCTCTAACACTGAACTGG 59.720 45.833 6.83 0.00 43.54 4.00
709 780 4.331717 ACTGAACACGAAACAAGGTTGTAG 59.668 41.667 0.00 0.00 41.31 2.74
710 781 3.064271 TGAACACGAAACAAGGTTGTAGC 59.936 43.478 0.00 0.00 41.31 3.58
711 782 2.914059 ACACGAAACAAGGTTGTAGCT 58.086 42.857 0.00 0.00 41.31 3.32
712 783 4.062677 ACACGAAACAAGGTTGTAGCTA 57.937 40.909 0.00 0.00 41.31 3.32
713 784 4.638304 ACACGAAACAAGGTTGTAGCTAT 58.362 39.130 0.00 0.00 41.31 2.97
714 785 4.451096 ACACGAAACAAGGTTGTAGCTATG 59.549 41.667 0.00 0.00 41.31 2.23
715 786 4.451096 CACGAAACAAGGTTGTAGCTATGT 59.549 41.667 0.00 0.00 41.31 2.29
716 787 5.636121 CACGAAACAAGGTTGTAGCTATGTA 59.364 40.000 0.00 0.00 41.31 2.29
717 788 6.146510 CACGAAACAAGGTTGTAGCTATGTAA 59.853 38.462 0.00 0.00 41.31 2.41
725 796 7.063934 AGGTTGTAGCTATGTAATTAGGTCC 57.936 40.000 0.00 0.00 32.47 4.46
762 874 4.324135 CACGCAACAATTTATGACCACATG 59.676 41.667 0.00 0.00 37.87 3.21
791 903 5.591643 ACGCTGTAAAGTGTAAACTGATG 57.408 39.130 0.00 0.00 0.00 3.07
816 928 4.247258 GGATTGTTGCATGCTTGAAATCA 58.753 39.130 20.33 0.26 0.00 2.57
943 1055 6.820152 TGTAGTTACGTGCTACTTATCTGAGA 59.180 38.462 23.25 0.00 39.47 3.27
979 1091 2.434336 TCCTCTGGTGGGTATTGATTCG 59.566 50.000 0.00 0.00 0.00 3.34
993 1105 2.571212 TGATTCGTTTGCCTGTCTGTT 58.429 42.857 0.00 0.00 0.00 3.16
1037 1149 4.618920 ACAGGAGTCGTTCAAGGTAAAT 57.381 40.909 0.00 0.00 0.00 1.40
1039 1151 6.105397 ACAGGAGTCGTTCAAGGTAAATAA 57.895 37.500 0.00 0.00 0.00 1.40
1041 1153 5.929992 CAGGAGTCGTTCAAGGTAAATAACA 59.070 40.000 0.00 0.00 0.00 2.41
1048 1160 9.417284 GTCGTTCAAGGTAAATAACATTTATCG 57.583 33.333 0.00 0.00 27.18 2.92
1131 1245 8.102484 TCTGGCTCTAATTTTAGGGAGTAATT 57.898 34.615 1.31 0.00 32.90 1.40
1132 1246 7.993183 TCTGGCTCTAATTTTAGGGAGTAATTG 59.007 37.037 1.31 0.00 32.90 2.32
1133 1247 7.867921 TGGCTCTAATTTTAGGGAGTAATTGA 58.132 34.615 1.31 0.00 32.90 2.57
1134 1248 8.502738 TGGCTCTAATTTTAGGGAGTAATTGAT 58.497 33.333 1.31 0.00 32.90 2.57
1236 1350 7.068226 TGGTTTATCATCTCGTCTAACTGATCA 59.932 37.037 0.00 0.00 0.00 2.92
1277 1391 4.979039 TCTCTACAGAGGGAGAGGTAATCT 59.021 45.833 6.41 0.00 42.30 2.40
1414 1529 1.340017 CCATGGACAAGGGAATCACGT 60.340 52.381 5.56 0.00 0.00 4.49
1429 1544 1.950909 TCACGTGGATTTGGGTTTGTC 59.049 47.619 17.00 0.00 0.00 3.18
1531 1646 5.596361 TGTTGAGAAGGTATTGCCAAAAGAA 59.404 36.000 0.00 0.00 40.61 2.52
1940 2061 3.029320 TCGCGTGGTAAGTTATTGTGT 57.971 42.857 5.77 0.00 0.00 3.72
1976 2097 8.141909 TCTTCGATACCTTAGTACCATGAATTG 58.858 37.037 0.00 0.00 0.00 2.32
1983 2104 5.163723 CCTTAGTACCATGAATTGTGTGCTG 60.164 44.000 0.00 0.00 0.00 4.41
1991 2112 3.023119 TGAATTGTGTGCTGGAAAGTGT 58.977 40.909 0.00 0.00 0.00 3.55
2005 2126 3.649986 GTGTGCACCGCTGACACC 61.650 66.667 15.69 0.00 35.04 4.16
2012 2133 1.068588 GCACCGCTGACACCTCATATA 59.931 52.381 0.00 0.00 0.00 0.86
2260 2417 1.139095 GCGAAGGTCCTACTCACCG 59.861 63.158 0.00 0.00 39.13 4.94
2275 2432 2.409055 ACCGTACGACAGGCGCATA 61.409 57.895 18.76 0.00 46.04 3.14
2289 2446 1.070134 GCGCATATCTTACTCACCCCA 59.930 52.381 0.30 0.00 0.00 4.96
2299 2456 1.002134 CTCACCCCACCATGGTCAC 60.002 63.158 16.53 0.00 35.17 3.67
2332 2489 4.954202 TCAAGATCTCCATACCGTTACAGT 59.046 41.667 0.00 0.00 0.00 3.55
2670 2827 0.167251 GCCACCGTATTTCCGTTGTG 59.833 55.000 0.00 0.00 0.00 3.33
2687 2844 6.039941 TCCGTTGTGATGTTGGAATTTTAGTT 59.960 34.615 0.00 0.00 0.00 2.24
2691 2848 9.744468 GTTGTGATGTTGGAATTTTAGTTACTT 57.256 29.630 0.00 0.00 0.00 2.24
2694 2851 8.699749 GTGATGTTGGAATTTTAGTTACTTTGC 58.300 33.333 0.00 0.00 0.00 3.68
2707 2864 5.985781 AGTTACTTTGCATGTTTGTAGACG 58.014 37.500 0.00 0.00 0.00 4.18
2781 5724 2.092267 TCTGGACTTGCATGCCATATGT 60.092 45.455 16.68 4.95 0.00 2.29
2799 5742 7.170489 GCCATATGTATGCTATATGCTGTACTG 59.830 40.741 1.24 0.00 43.37 2.74
2810 5753 6.985653 ATATGCTGTACTGGATACTTCTGT 57.014 37.500 14.62 0.00 34.56 3.41
2811 5754 4.456280 TGCTGTACTGGATACTTCTGTG 57.544 45.455 1.65 0.00 34.56 3.66
2812 5755 3.832490 TGCTGTACTGGATACTTCTGTGT 59.168 43.478 1.65 0.00 34.56 3.72
2813 5756 4.082190 TGCTGTACTGGATACTTCTGTGTC 60.082 45.833 1.65 0.00 34.56 3.67
2871 5814 6.484818 TTTGGCTAACGGATAGTTTTGTAC 57.515 37.500 0.00 0.00 43.86 2.90
2872 5815 5.410355 TGGCTAACGGATAGTTTTGTACT 57.590 39.130 0.00 0.00 43.86 2.73
2873 5816 5.413499 TGGCTAACGGATAGTTTTGTACTC 58.587 41.667 0.00 0.00 43.86 2.59
2874 5817 4.807834 GGCTAACGGATAGTTTTGTACTCC 59.192 45.833 0.00 0.00 43.86 3.85
2875 5818 4.807834 GCTAACGGATAGTTTTGTACTCCC 59.192 45.833 0.00 0.00 43.86 4.30
2876 5819 5.394993 GCTAACGGATAGTTTTGTACTCCCT 60.395 44.000 0.00 0.00 43.86 4.20
2877 5820 4.732672 ACGGATAGTTTTGTACTCCCTC 57.267 45.455 0.00 0.00 38.33 4.30
2878 5821 4.351127 ACGGATAGTTTTGTACTCCCTCT 58.649 43.478 0.00 0.00 38.33 3.69
2879 5822 4.159879 ACGGATAGTTTTGTACTCCCTCTG 59.840 45.833 0.00 0.00 38.33 3.35
2880 5823 4.159879 CGGATAGTTTTGTACTCCCTCTGT 59.840 45.833 0.00 0.00 38.33 3.41
2881 5824 5.662456 GGATAGTTTTGTACTCCCTCTGTC 58.338 45.833 0.00 0.00 38.33 3.51
2882 5825 5.395435 GGATAGTTTTGTACTCCCTCTGTCC 60.395 48.000 0.00 0.88 38.33 4.02
2883 5826 2.638363 AGTTTTGTACTCCCTCTGTCCC 59.362 50.000 0.00 0.00 28.23 4.46
2884 5827 2.370849 GTTTTGTACTCCCTCTGTCCCA 59.629 50.000 0.00 0.00 0.00 4.37
2885 5828 2.642171 TTGTACTCCCTCTGTCCCAT 57.358 50.000 0.00 0.00 0.00 4.00
2886 5829 1.866015 TGTACTCCCTCTGTCCCATG 58.134 55.000 0.00 0.00 0.00 3.66
2887 5830 0.466124 GTACTCCCTCTGTCCCATGC 59.534 60.000 0.00 0.00 0.00 4.06
2888 5831 0.339859 TACTCCCTCTGTCCCATGCT 59.660 55.000 0.00 0.00 0.00 3.79
2889 5832 0.339859 ACTCCCTCTGTCCCATGCTA 59.660 55.000 0.00 0.00 0.00 3.49
2890 5833 1.061812 ACTCCCTCTGTCCCATGCTAT 60.062 52.381 0.00 0.00 0.00 2.97
2891 5834 2.180086 ACTCCCTCTGTCCCATGCTATA 59.820 50.000 0.00 0.00 0.00 1.31
2892 5835 3.181402 ACTCCCTCTGTCCCATGCTATAT 60.181 47.826 0.00 0.00 0.00 0.86
2893 5836 3.176411 TCCCTCTGTCCCATGCTATATG 58.824 50.000 0.00 0.00 0.00 1.78
2894 5837 3.176411 CCCTCTGTCCCATGCTATATGA 58.824 50.000 0.00 0.00 0.00 2.15
2895 5838 3.779183 CCCTCTGTCCCATGCTATATGAT 59.221 47.826 0.00 0.00 0.00 2.45
2896 5839 4.383880 CCCTCTGTCCCATGCTATATGATG 60.384 50.000 0.00 0.00 0.00 3.07
2897 5840 4.224594 CCTCTGTCCCATGCTATATGATGT 59.775 45.833 0.00 0.00 0.00 3.06
2898 5841 5.280368 CCTCTGTCCCATGCTATATGATGTT 60.280 44.000 0.00 0.00 0.00 2.71
2899 5842 6.070596 CCTCTGTCCCATGCTATATGATGTTA 60.071 42.308 0.00 0.00 0.00 2.41
2900 5843 7.365384 CCTCTGTCCCATGCTATATGATGTTAT 60.365 40.741 0.00 0.00 0.00 1.89
2901 5844 8.608185 TCTGTCCCATGCTATATGATGTTATA 57.392 34.615 0.00 0.00 0.00 0.98
2902 5845 9.217336 TCTGTCCCATGCTATATGATGTTATAT 57.783 33.333 0.00 0.00 0.00 0.86
2903 5846 9.842775 CTGTCCCATGCTATATGATGTTATATT 57.157 33.333 0.00 0.00 0.00 1.28
2917 5860 8.491045 TGATGTTATATTATGTGACAGAGGGA 57.509 34.615 0.00 0.00 0.00 4.20
2918 5861 8.588472 TGATGTTATATTATGTGACAGAGGGAG 58.412 37.037 0.00 0.00 0.00 4.30
2919 5862 7.914427 TGTTATATTATGTGACAGAGGGAGT 57.086 36.000 0.00 0.00 0.00 3.85
2920 5863 9.601810 ATGTTATATTATGTGACAGAGGGAGTA 57.398 33.333 0.00 0.00 0.00 2.59
2921 5864 8.857098 TGTTATATTATGTGACAGAGGGAGTAC 58.143 37.037 0.00 0.00 0.00 2.73
2922 5865 6.919775 ATATTATGTGACAGAGGGAGTACC 57.080 41.667 0.00 0.00 40.67 3.34
2936 5879 4.130286 GGAGTACCCATGCTATATGCTC 57.870 50.000 0.00 0.00 37.46 4.26
2937 5880 3.772025 GGAGTACCCATGCTATATGCTCT 59.228 47.826 0.00 0.00 37.46 4.09
2938 5881 4.223923 GGAGTACCCATGCTATATGCTCTT 59.776 45.833 0.00 0.00 37.46 2.85
2939 5882 5.157940 AGTACCCATGCTATATGCTCTTG 57.842 43.478 0.00 0.00 43.37 3.02
2940 5883 4.594920 AGTACCCATGCTATATGCTCTTGT 59.405 41.667 0.00 0.00 43.37 3.16
2941 5884 5.780282 AGTACCCATGCTATATGCTCTTGTA 59.220 40.000 0.00 0.00 43.37 2.41
2942 5885 5.768980 ACCCATGCTATATGCTCTTGTAT 57.231 39.130 0.00 0.00 43.37 2.29
2943 5886 6.131972 ACCCATGCTATATGCTCTTGTATT 57.868 37.500 0.00 0.00 43.37 1.89
2944 5887 7.257790 ACCCATGCTATATGCTCTTGTATTA 57.742 36.000 0.00 0.00 43.37 0.98
2945 5888 7.106239 ACCCATGCTATATGCTCTTGTATTAC 58.894 38.462 0.00 0.00 43.37 1.89
2946 5889 6.256539 CCCATGCTATATGCTCTTGTATTACG 59.743 42.308 0.00 0.00 43.37 3.18
2947 5890 6.813649 CCATGCTATATGCTCTTGTATTACGT 59.186 38.462 0.00 0.00 43.37 3.57
2948 5891 7.201470 CCATGCTATATGCTCTTGTATTACGTG 60.201 40.741 0.00 0.00 43.37 4.49
2949 5892 6.977213 TGCTATATGCTCTTGTATTACGTGA 58.023 36.000 0.00 0.00 43.37 4.35
2950 5893 6.861572 TGCTATATGCTCTTGTATTACGTGAC 59.138 38.462 0.00 0.00 43.37 3.67
2951 5894 6.032565 GCTATATGCTCTTGTATTACGTGACG 59.967 42.308 2.24 2.24 38.95 4.35
2952 5895 2.871133 TGCTCTTGTATTACGTGACGG 58.129 47.619 10.66 0.00 0.00 4.79
2953 5896 2.488937 TGCTCTTGTATTACGTGACGGA 59.511 45.455 10.66 0.00 0.00 4.69
2954 5897 3.106672 GCTCTTGTATTACGTGACGGAG 58.893 50.000 10.66 4.61 0.00 4.63
2958 5901 2.019249 TGTATTACGTGACGGAGGGAG 58.981 52.381 10.66 0.00 0.00 4.30
2978 5921 4.050553 GAGTATGTTCTGCTGATCTGCTC 58.949 47.826 23.02 12.36 0.00 4.26
2981 5924 1.066358 TGTTCTGCTGATCTGCTCTGG 60.066 52.381 23.02 11.86 0.00 3.86
2985 5928 0.689055 TGCTGATCTGCTCTGGTGTT 59.311 50.000 23.02 0.00 0.00 3.32
2986 5929 1.338484 TGCTGATCTGCTCTGGTGTTC 60.338 52.381 23.02 0.00 0.00 3.18
2988 5931 2.619147 CTGATCTGCTCTGGTGTTCTG 58.381 52.381 0.00 0.00 0.00 3.02
2989 5932 1.277273 TGATCTGCTCTGGTGTTCTGG 59.723 52.381 0.00 0.00 0.00 3.86
2990 5933 1.277557 GATCTGCTCTGGTGTTCTGGT 59.722 52.381 0.00 0.00 0.00 4.00
2992 5935 2.325484 TCTGCTCTGGTGTTCTGGTTA 58.675 47.619 0.00 0.00 0.00 2.85
2994 5937 3.055819 TCTGCTCTGGTGTTCTGGTTATC 60.056 47.826 0.00 0.00 0.00 1.75
2997 5940 3.686726 GCTCTGGTGTTCTGGTTATCTTG 59.313 47.826 0.00 0.00 0.00 3.02
2998 5941 3.674997 TCTGGTGTTCTGGTTATCTTGC 58.325 45.455 0.00 0.00 0.00 4.01
3000 5943 3.411446 TGGTGTTCTGGTTATCTTGCAG 58.589 45.455 0.00 0.00 0.00 4.41
3001 5944 2.162408 GGTGTTCTGGTTATCTTGCAGC 59.838 50.000 0.00 0.00 0.00 5.25
3002 5945 2.162408 GTGTTCTGGTTATCTTGCAGCC 59.838 50.000 0.00 0.00 0.00 4.85
3003 5946 1.398390 GTTCTGGTTATCTTGCAGCCG 59.602 52.381 0.00 0.00 0.00 5.52
3004 5947 0.744414 TCTGGTTATCTTGCAGCCGC 60.744 55.000 0.00 0.00 39.24 6.53
3017 5960 0.381801 CAGCCGCACTGTGTTTTCTT 59.618 50.000 9.86 0.00 41.86 2.52
3020 5963 1.597937 GCCGCACTGTGTTTTCTTCAG 60.598 52.381 9.86 0.00 35.60 3.02
3021 5964 1.597937 CCGCACTGTGTTTTCTTCAGC 60.598 52.381 9.86 0.00 33.12 4.26
3023 5966 1.064060 GCACTGTGTTTTCTTCAGCGT 59.936 47.619 9.86 0.00 33.12 5.07
3025 5968 3.100817 CACTGTGTTTTCTTCAGCGTTG 58.899 45.455 0.00 0.00 33.12 4.10
3027 5970 1.403679 TGTGTTTTCTTCAGCGTTGGG 59.596 47.619 0.00 0.00 0.00 4.12
3029 5972 2.614983 GTGTTTTCTTCAGCGTTGGGTA 59.385 45.455 0.00 0.00 0.00 3.69
3030 5973 3.065648 GTGTTTTCTTCAGCGTTGGGTAA 59.934 43.478 0.00 0.00 0.00 2.85
3031 5974 3.065648 TGTTTTCTTCAGCGTTGGGTAAC 59.934 43.478 0.00 4.01 0.00 2.50
3033 5976 2.922740 TCTTCAGCGTTGGGTAACTT 57.077 45.000 0.00 0.00 34.60 2.66
3034 5977 4.339872 TTCTTCAGCGTTGGGTAACTTA 57.660 40.909 0.00 0.00 34.60 2.24
3035 5978 3.921677 TCTTCAGCGTTGGGTAACTTAG 58.078 45.455 0.00 0.00 34.60 2.18
3036 5979 2.088950 TCAGCGTTGGGTAACTTAGC 57.911 50.000 0.00 0.00 34.60 3.09
3037 5980 1.345089 TCAGCGTTGGGTAACTTAGCA 59.655 47.619 0.00 0.00 34.60 3.49
3038 5981 1.463444 CAGCGTTGGGTAACTTAGCAC 59.537 52.381 0.00 0.00 34.60 4.40
3040 5983 1.730612 GCGTTGGGTAACTTAGCACTC 59.269 52.381 0.62 0.00 34.60 3.51
3041 5984 1.990563 CGTTGGGTAACTTAGCACTCG 59.009 52.381 0.62 0.00 34.60 4.18
3043 5986 3.366273 CGTTGGGTAACTTAGCACTCGTA 60.366 47.826 0.62 0.00 34.60 3.43
3044 5987 4.171754 GTTGGGTAACTTAGCACTCGTAG 58.828 47.826 0.62 0.00 33.94 3.51
3046 6212 3.019564 GGGTAACTTAGCACTCGTAGGA 58.980 50.000 0.62 0.00 0.00 2.94
3049 6215 4.157472 GGTAACTTAGCACTCGTAGGAACT 59.843 45.833 0.00 0.00 46.37 3.01
3054 6220 6.752168 ACTTAGCACTCGTAGGAACTAAAAA 58.248 36.000 0.00 0.00 45.48 1.94
3107 6273 9.712305 ATGAGATATTTAACCTGAATTCCTACG 57.288 33.333 2.27 0.00 0.00 3.51
3109 6275 7.450903 AGATATTTAACCTGAATTCCTACGGG 58.549 38.462 2.27 0.00 38.40 5.28
3110 6276 5.703730 ATTTAACCTGAATTCCTACGGGA 57.296 39.130 2.27 0.00 40.36 5.14
3111 6277 5.703730 TTTAACCTGAATTCCTACGGGAT 57.296 39.130 2.27 0.00 41.87 3.85
3112 6278 3.840124 AACCTGAATTCCTACGGGATC 57.160 47.619 2.27 0.00 41.87 3.36
3117 6283 5.163332 ACCTGAATTCCTACGGGATCTAAAC 60.163 44.000 2.27 0.00 41.87 2.01
3118 6284 5.163343 CCTGAATTCCTACGGGATCTAAACA 60.163 44.000 2.27 0.00 41.87 2.83
3119 6285 5.667466 TGAATTCCTACGGGATCTAAACAC 58.333 41.667 2.27 0.00 41.87 3.32
3120 6286 5.188163 TGAATTCCTACGGGATCTAAACACA 59.812 40.000 2.27 0.00 41.87 3.72
3122 6288 4.730949 TCCTACGGGATCTAAACACAAG 57.269 45.455 0.00 0.00 36.57 3.16
3123 6289 4.346730 TCCTACGGGATCTAAACACAAGA 58.653 43.478 0.00 0.00 36.57 3.02
3124 6290 4.159135 TCCTACGGGATCTAAACACAAGAC 59.841 45.833 0.00 0.00 36.57 3.01
3134 6312 7.280876 GGATCTAAACACAAGACTTATGATGCA 59.719 37.037 0.00 0.00 0.00 3.96
3246 6431 7.201582 GCAGAAATTTTCCTATGGATTGCTTTG 60.202 37.037 5.52 0.00 0.00 2.77
3281 6466 7.969536 ATTTCATAGGAATATTGGTGAGTCG 57.030 36.000 0.00 0.00 31.93 4.18
3307 6513 3.855255 TTGTTTCAGATGACCCAGTCA 57.145 42.857 0.00 0.00 46.90 3.41
3324 6530 6.447084 ACCCAGTCAGGATTTTTCTATAGGAA 59.553 38.462 0.00 0.00 41.22 3.36
3325 6531 7.129504 ACCCAGTCAGGATTTTTCTATAGGAAT 59.870 37.037 0.00 0.00 41.22 3.01
3326 6532 8.001292 CCCAGTCAGGATTTTTCTATAGGAATT 58.999 37.037 0.00 0.00 41.22 2.17
3327 6533 9.061435 CCAGTCAGGATTTTTCTATAGGAATTC 57.939 37.037 0.00 0.00 41.22 2.17
3328 6534 8.768955 CAGTCAGGATTTTTCTATAGGAATTCG 58.231 37.037 0.00 0.00 33.53 3.34
3571 6995 2.170187 CCACCCTCTCAATCCTCTGAAG 59.830 54.545 0.00 0.00 0.00 3.02
3572 6996 1.836802 ACCCTCTCAATCCTCTGAAGC 59.163 52.381 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 2.091541 TCAAATCCGGTTGAATCAGCC 58.908 47.619 6.02 6.02 34.59 4.85
20 21 5.070001 ACTTTCTCAAATCCGGTTGAATCA 58.930 37.500 8.66 0.00 37.08 2.57
21 22 5.412904 AGACTTTCTCAAATCCGGTTGAATC 59.587 40.000 8.66 3.05 37.08 2.52
54 55 1.604915 GGAAGGTTCTGGAGGGAGC 59.395 63.158 0.00 0.00 0.00 4.70
56 57 1.612442 CGGGAAGGTTCTGGAGGGA 60.612 63.158 0.00 0.00 0.00 4.20
79 80 4.921515 GCGCGTGTGAATAAATAGATAGGA 59.078 41.667 8.43 0.00 0.00 2.94
83 84 3.060540 CACGCGCGTGTGAATAAATAGAT 60.061 43.478 45.19 13.64 42.55 1.98
115 120 2.897350 CCGCCTCTGATTTCCCGC 60.897 66.667 0.00 0.00 0.00 6.13
143 148 0.917259 GCGTCTGTCTATCAGTTGCG 59.083 55.000 0.00 0.00 43.97 4.85
145 150 3.433709 CTCTGCGTCTGTCTATCAGTTG 58.566 50.000 0.00 0.00 43.97 3.16
150 155 3.560826 GCCTCTGCGTCTGTCTATC 57.439 57.895 0.00 0.00 0.00 2.08
174 179 1.466697 CCTCTCGAGTCGCTGTCTTTC 60.467 57.143 13.13 0.00 0.00 2.62
175 180 0.523966 CCTCTCGAGTCGCTGTCTTT 59.476 55.000 13.13 0.00 0.00 2.52
183 188 2.042520 CTCCGAAGCCTCTCGAGTCG 62.043 65.000 13.13 13.45 41.44 4.18
243 249 1.551452 ACAGGAGAAGAACCCGAGAG 58.449 55.000 0.00 0.00 0.00 3.20
244 250 1.893801 GAACAGGAGAAGAACCCGAGA 59.106 52.381 0.00 0.00 0.00 4.04
249 255 1.669211 CGACGGAACAGGAGAAGAACC 60.669 57.143 0.00 0.00 0.00 3.62
250 256 1.669211 CCGACGGAACAGGAGAAGAAC 60.669 57.143 8.64 0.00 0.00 3.01
257 263 0.968901 ATGCTACCGACGGAACAGGA 60.969 55.000 23.38 15.42 0.00 3.86
258 264 0.806102 CATGCTACCGACGGAACAGG 60.806 60.000 23.38 12.91 0.00 4.00
259 265 0.172578 TCATGCTACCGACGGAACAG 59.827 55.000 23.38 14.94 0.00 3.16
260 266 0.821517 ATCATGCTACCGACGGAACA 59.178 50.000 23.38 15.35 0.00 3.18
264 275 1.337071 ACTGTATCATGCTACCGACGG 59.663 52.381 13.61 13.61 0.00 4.79
269 280 8.176365 CGAAGTATAGTACTGTATCATGCTACC 58.824 40.741 5.39 0.00 39.39 3.18
282 293 7.926555 CCATTTTCACATCCGAAGTATAGTACT 59.073 37.037 0.00 0.00 41.73 2.73
283 294 7.307219 GCCATTTTCACATCCGAAGTATAGTAC 60.307 40.741 0.00 0.00 0.00 2.73
285 296 5.527582 GCCATTTTCACATCCGAAGTATAGT 59.472 40.000 0.00 0.00 0.00 2.12
286 297 5.333339 CGCCATTTTCACATCCGAAGTATAG 60.333 44.000 0.00 0.00 0.00 1.31
288 299 3.312421 CGCCATTTTCACATCCGAAGTAT 59.688 43.478 0.00 0.00 0.00 2.12
290 301 1.468520 CGCCATTTTCACATCCGAAGT 59.531 47.619 0.00 0.00 0.00 3.01
291 302 1.795162 GCGCCATTTTCACATCCGAAG 60.795 52.381 0.00 0.00 0.00 3.79
292 303 0.170116 GCGCCATTTTCACATCCGAA 59.830 50.000 0.00 0.00 0.00 4.30
293 304 0.676466 AGCGCCATTTTCACATCCGA 60.676 50.000 2.29 0.00 0.00 4.55
294 305 0.523968 CAGCGCCATTTTCACATCCG 60.524 55.000 2.29 0.00 0.00 4.18
296 307 1.135699 CGCAGCGCCATTTTCACATC 61.136 55.000 2.29 0.00 0.00 3.06
297 308 1.153978 CGCAGCGCCATTTTCACAT 60.154 52.632 2.29 0.00 0.00 3.21
298 309 2.254951 CGCAGCGCCATTTTCACA 59.745 55.556 2.29 0.00 0.00 3.58
299 310 2.270297 ATCCGCAGCGCCATTTTCAC 62.270 55.000 10.07 0.00 0.00 3.18
300 311 1.594194 AATCCGCAGCGCCATTTTCA 61.594 50.000 10.07 0.00 0.00 2.69
301 312 0.867329 GAATCCGCAGCGCCATTTTC 60.867 55.000 10.07 3.65 0.00 2.29
302 313 1.139520 GAATCCGCAGCGCCATTTT 59.860 52.632 10.07 0.00 0.00 1.82
305 316 2.203252 ATGAATCCGCAGCGCCAT 60.203 55.556 10.07 6.83 0.00 4.40
306 317 2.896854 GATGAATCCGCAGCGCCA 60.897 61.111 10.07 4.56 0.00 5.69
307 318 3.654020 GGATGAATCCGCAGCGCC 61.654 66.667 10.07 0.00 37.19 6.53
316 327 3.018479 GCAGAGGGCAGGATGAATC 57.982 57.895 0.00 0.00 43.97 2.52
329 340 2.414481 CACCGAATCAAACAGAGCAGAG 59.586 50.000 0.00 0.00 0.00 3.35
334 345 6.727824 AAACTATCACCGAATCAAACAGAG 57.272 37.500 0.00 0.00 0.00 3.35
346 359 6.040247 TCTACTATGTGCAAAACTATCACCG 58.960 40.000 0.00 0.00 0.00 4.94
349 362 7.265673 GGTCTCTACTATGTGCAAAACTATCA 58.734 38.462 0.00 0.00 0.00 2.15
373 412 0.962356 GCAAGTGTGGGTCTCATGGG 60.962 60.000 0.00 0.00 0.00 4.00
411 450 2.983879 AATCAGCCCCCGAACCCTG 61.984 63.158 0.00 0.00 0.00 4.45
412 451 2.614013 AATCAGCCCCCGAACCCT 60.614 61.111 0.00 0.00 0.00 4.34
453 513 5.162000 TCATGTCATATAGATCTAGCGCG 57.838 43.478 8.70 0.00 0.00 6.86
477 537 7.173032 ACCTAGGAATTCTCGGTTTAATTTGT 58.827 34.615 17.98 0.00 38.25 2.83
512 573 3.255642 AGAACACGAATTGGGGAAACATG 59.744 43.478 0.00 0.00 0.00 3.21
561 622 3.921021 CCCATCGCGTTAGATACAATCTC 59.079 47.826 5.77 0.00 40.76 2.75
562 623 3.306088 CCCCATCGCGTTAGATACAATCT 60.306 47.826 5.77 0.00 43.33 2.40
570 631 0.108041 GTTTCCCCCATCGCGTTAGA 60.108 55.000 5.77 0.00 0.00 2.10
619 682 0.871722 TCCCAGCAATTCAACGTTCG 59.128 50.000 0.00 0.00 0.00 3.95
673 736 2.289002 GTGTTCAGTTCAGCCAGTTCAG 59.711 50.000 0.00 0.00 0.00 3.02
674 737 2.288666 GTGTTCAGTTCAGCCAGTTCA 58.711 47.619 0.00 0.00 0.00 3.18
675 738 1.261619 CGTGTTCAGTTCAGCCAGTTC 59.738 52.381 0.00 0.00 0.00 3.01
676 739 1.134521 TCGTGTTCAGTTCAGCCAGTT 60.135 47.619 0.00 0.00 0.00 3.16
677 740 0.464036 TCGTGTTCAGTTCAGCCAGT 59.536 50.000 0.00 0.00 0.00 4.00
678 741 1.581934 TTCGTGTTCAGTTCAGCCAG 58.418 50.000 0.00 0.00 0.00 4.85
679 742 1.668751 GTTTCGTGTTCAGTTCAGCCA 59.331 47.619 0.00 0.00 0.00 4.75
680 743 1.668751 TGTTTCGTGTTCAGTTCAGCC 59.331 47.619 0.00 0.00 0.00 4.85
681 744 3.354397 CTTGTTTCGTGTTCAGTTCAGC 58.646 45.455 0.00 0.00 0.00 4.26
725 796 1.950630 GCGTGTGCAAAAGCTTGGG 60.951 57.895 7.63 0.00 42.15 4.12
791 903 1.273048 TCAAGCATGCAACAATCCACC 59.727 47.619 21.98 0.00 0.00 4.61
816 928 1.446792 CCGATCACTGCGACAGCTT 60.447 57.895 6.74 0.00 45.42 3.74
943 1055 5.125739 CACCAGAGGACTCGTATAGAAAACT 59.874 44.000 0.00 0.00 34.09 2.66
979 1091 2.292103 TGCAAAACAGACAGGCAAAC 57.708 45.000 0.00 0.00 0.00 2.93
993 1105 3.186909 CCTCGAATACGACATCTGCAAA 58.813 45.455 0.00 0.00 43.81 3.68
1047 1159 9.935682 ACAAACATAATATTAGCATTTCTGACG 57.064 29.630 1.02 0.00 0.00 4.35
1134 1248 9.374711 TCCTAACACATTACATGGATATCACTA 57.625 33.333 4.83 0.00 33.60 2.74
1135 1249 8.262601 TCCTAACACATTACATGGATATCACT 57.737 34.615 4.83 0.00 33.60 3.41
1136 1250 8.150945 ACTCCTAACACATTACATGGATATCAC 58.849 37.037 4.83 0.00 33.60 3.06
1277 1391 6.662865 TTCCTCAGCAAACATTTCCATAAA 57.337 33.333 0.00 0.00 0.00 1.40
1429 1544 3.181461 CCTCCTTAAGAGTAGCCATGGTG 60.181 52.174 14.67 0.00 41.47 4.17
1531 1646 9.911788 AATGGACAAATATCAGAGAGTTAACAT 57.088 29.630 8.61 0.00 0.00 2.71
1672 1788 2.629137 TGAATTGATGCCAAACAGCTGT 59.371 40.909 15.25 15.25 35.06 4.40
1777 1897 9.887862 ATAAATTATTGGGGATCTGAAGAACAT 57.112 29.630 0.00 0.00 0.00 2.71
1957 2078 5.878116 GCACACAATTCATGGTACTAAGGTA 59.122 40.000 0.00 0.00 0.00 3.08
1976 2097 2.105984 TGCACACTTTCCAGCACAC 58.894 52.632 0.00 0.00 31.05 3.82
1983 2104 1.891919 TCAGCGGTGCACACTTTCC 60.892 57.895 20.43 0.00 0.00 3.13
1991 2112 1.540435 TATGAGGTGTCAGCGGTGCA 61.540 55.000 10.38 8.68 35.66 4.57
2260 2417 2.135664 AAGATATGCGCCTGTCGTAC 57.864 50.000 4.18 0.00 41.07 3.67
2275 2432 1.846439 CCATGGTGGGGTGAGTAAGAT 59.154 52.381 2.57 0.00 32.67 2.40
2289 2446 4.344865 GGTGGCGGTGACCATGGT 62.345 66.667 19.89 19.89 43.01 3.55
2299 2456 1.079127 AGATCTTGAACGGTGGCGG 60.079 57.895 0.00 0.00 0.00 6.13
2670 2827 8.810652 TGCAAAGTAACTAAAATTCCAACATC 57.189 30.769 0.00 0.00 0.00 3.06
2687 2844 4.212425 CACCGTCTACAAACATGCAAAGTA 59.788 41.667 0.00 0.00 0.00 2.24
2691 2848 2.289274 CACACCGTCTACAAACATGCAA 59.711 45.455 0.00 0.00 0.00 4.08
2694 2851 2.761559 TCCACACCGTCTACAAACATG 58.238 47.619 0.00 0.00 0.00 3.21
2704 2861 2.755650 GATCATACCATCCACACCGTC 58.244 52.381 0.00 0.00 0.00 4.79
2707 2864 2.483876 CACGATCATACCATCCACACC 58.516 52.381 0.00 0.00 0.00 4.16
2799 5742 5.992217 ACTGAAAACAGACACAGAAGTATCC 59.008 40.000 0.00 0.00 34.88 2.59
2810 5753 3.278574 CCAACCAGACTGAAAACAGACA 58.721 45.455 3.32 0.00 0.00 3.41
2811 5754 2.033424 GCCAACCAGACTGAAAACAGAC 59.967 50.000 3.32 0.00 0.00 3.51
2812 5755 2.297701 GCCAACCAGACTGAAAACAGA 58.702 47.619 3.32 0.00 0.00 3.41
2813 5756 2.023673 TGCCAACCAGACTGAAAACAG 58.976 47.619 3.32 0.00 0.00 3.16
2891 5834 9.104713 TCCCTCTGTCACATAATATAACATCAT 57.895 33.333 0.00 0.00 0.00 2.45
2892 5835 8.491045 TCCCTCTGTCACATAATATAACATCA 57.509 34.615 0.00 0.00 0.00 3.07
2893 5836 8.589338 ACTCCCTCTGTCACATAATATAACATC 58.411 37.037 0.00 0.00 0.00 3.06
2894 5837 8.497910 ACTCCCTCTGTCACATAATATAACAT 57.502 34.615 0.00 0.00 0.00 2.71
2895 5838 7.914427 ACTCCCTCTGTCACATAATATAACA 57.086 36.000 0.00 0.00 0.00 2.41
2896 5839 8.305317 GGTACTCCCTCTGTCACATAATATAAC 58.695 40.741 0.00 0.00 0.00 1.89
2897 5840 8.418597 GGTACTCCCTCTGTCACATAATATAA 57.581 38.462 0.00 0.00 0.00 0.98
2899 5842 6.919775 GGTACTCCCTCTGTCACATAATAT 57.080 41.667 0.00 0.00 0.00 1.28
2926 5869 6.032565 CGTCACGTAATACAAGAGCATATAGC 59.967 42.308 0.00 0.00 46.19 2.97
2927 5870 6.523546 CCGTCACGTAATACAAGAGCATATAG 59.476 42.308 0.00 0.00 0.00 1.31
2928 5871 6.205270 TCCGTCACGTAATACAAGAGCATATA 59.795 38.462 0.00 0.00 0.00 0.86
2929 5872 5.009310 TCCGTCACGTAATACAAGAGCATAT 59.991 40.000 0.00 0.00 0.00 1.78
2930 5873 4.336153 TCCGTCACGTAATACAAGAGCATA 59.664 41.667 0.00 0.00 0.00 3.14
2931 5874 3.129813 TCCGTCACGTAATACAAGAGCAT 59.870 43.478 0.00 0.00 0.00 3.79
2932 5875 2.488937 TCCGTCACGTAATACAAGAGCA 59.511 45.455 0.00 0.00 0.00 4.26
2933 5876 3.106672 CTCCGTCACGTAATACAAGAGC 58.893 50.000 0.00 0.00 0.00 4.09
2934 5877 3.488721 CCCTCCGTCACGTAATACAAGAG 60.489 52.174 0.00 0.00 0.00 2.85
2935 5878 2.424601 CCCTCCGTCACGTAATACAAGA 59.575 50.000 0.00 0.00 0.00 3.02
2936 5879 2.424601 TCCCTCCGTCACGTAATACAAG 59.575 50.000 0.00 0.00 0.00 3.16
2937 5880 2.424601 CTCCCTCCGTCACGTAATACAA 59.575 50.000 0.00 0.00 0.00 2.41
2938 5881 2.019249 CTCCCTCCGTCACGTAATACA 58.981 52.381 0.00 0.00 0.00 2.29
2939 5882 2.019984 ACTCCCTCCGTCACGTAATAC 58.980 52.381 0.00 0.00 0.00 1.89
2940 5883 2.425143 ACTCCCTCCGTCACGTAATA 57.575 50.000 0.00 0.00 0.00 0.98
2941 5884 2.425143 TACTCCCTCCGTCACGTAAT 57.575 50.000 0.00 0.00 0.00 1.89
2942 5885 2.019249 CATACTCCCTCCGTCACGTAA 58.981 52.381 0.00 0.00 0.00 3.18
2943 5886 1.065199 ACATACTCCCTCCGTCACGTA 60.065 52.381 0.00 0.00 0.00 3.57
2944 5887 0.323178 ACATACTCCCTCCGTCACGT 60.323 55.000 0.00 0.00 0.00 4.49
2945 5888 0.815734 AACATACTCCCTCCGTCACG 59.184 55.000 0.00 0.00 0.00 4.35
2946 5889 2.100989 AGAACATACTCCCTCCGTCAC 58.899 52.381 0.00 0.00 0.00 3.67
2947 5890 2.100197 CAGAACATACTCCCTCCGTCA 58.900 52.381 0.00 0.00 0.00 4.35
2948 5891 1.202428 GCAGAACATACTCCCTCCGTC 60.202 57.143 0.00 0.00 0.00 4.79
2949 5892 0.824759 GCAGAACATACTCCCTCCGT 59.175 55.000 0.00 0.00 0.00 4.69
2950 5893 1.115467 AGCAGAACATACTCCCTCCG 58.885 55.000 0.00 0.00 0.00 4.63
2951 5894 2.111384 TCAGCAGAACATACTCCCTCC 58.889 52.381 0.00 0.00 0.00 4.30
2952 5895 3.640967 AGATCAGCAGAACATACTCCCTC 59.359 47.826 0.00 0.00 0.00 4.30
2953 5896 3.387374 CAGATCAGCAGAACATACTCCCT 59.613 47.826 0.00 0.00 0.00 4.20
2954 5897 3.726607 CAGATCAGCAGAACATACTCCC 58.273 50.000 0.00 0.00 0.00 4.30
2958 5901 3.803231 CAGAGCAGATCAGCAGAACATAC 59.197 47.826 13.03 0.00 36.85 2.39
2978 5921 3.411446 TGCAAGATAACCAGAACACCAG 58.589 45.455 0.00 0.00 0.00 4.00
2981 5924 2.162408 GGCTGCAAGATAACCAGAACAC 59.838 50.000 0.50 0.00 34.07 3.32
2985 5928 0.744414 GCGGCTGCAAGATAACCAGA 60.744 55.000 14.08 0.00 42.15 3.86
2986 5929 1.723870 GCGGCTGCAAGATAACCAG 59.276 57.895 14.08 0.00 42.15 4.00
3000 5943 0.380378 TGAAGAAAACACAGTGCGGC 59.620 50.000 0.00 0.00 0.00 6.53
3001 5944 1.597937 GCTGAAGAAAACACAGTGCGG 60.598 52.381 0.00 0.00 34.60 5.69
3002 5945 1.746760 GCTGAAGAAAACACAGTGCG 58.253 50.000 0.00 0.00 34.60 5.34
3003 5946 1.064060 ACGCTGAAGAAAACACAGTGC 59.936 47.619 0.00 0.00 43.20 4.40
3004 5947 3.100817 CAACGCTGAAGAAAACACAGTG 58.899 45.455 0.00 0.00 44.40 3.66
3005 5948 2.097466 CCAACGCTGAAGAAAACACAGT 59.903 45.455 0.00 0.00 34.60 3.55
3009 5952 1.757682 ACCCAACGCTGAAGAAAACA 58.242 45.000 0.00 0.00 0.00 2.83
3010 5953 3.314357 AGTTACCCAACGCTGAAGAAAAC 59.686 43.478 0.00 0.00 39.78 2.43
3011 5954 3.547746 AGTTACCCAACGCTGAAGAAAA 58.452 40.909 0.00 0.00 39.78 2.29
3012 5955 3.202829 AGTTACCCAACGCTGAAGAAA 57.797 42.857 0.00 0.00 39.78 2.52
3017 5960 1.345089 TGCTAAGTTACCCAACGCTGA 59.655 47.619 0.00 0.00 39.78 4.26
3020 5963 1.730612 GAGTGCTAAGTTACCCAACGC 59.269 52.381 0.00 0.00 39.78 4.84
3021 5964 1.990563 CGAGTGCTAAGTTACCCAACG 59.009 52.381 0.00 0.00 39.78 4.10
3023 5966 3.194116 CCTACGAGTGCTAAGTTACCCAA 59.806 47.826 0.00 0.00 0.00 4.12
3025 5968 3.019564 TCCTACGAGTGCTAAGTTACCC 58.980 50.000 0.00 0.00 0.00 3.69
3027 5970 5.307926 AGTTCCTACGAGTGCTAAGTTAC 57.692 43.478 0.00 0.00 0.00 2.50
3029 5972 5.972107 TTAGTTCCTACGAGTGCTAAGTT 57.028 39.130 0.00 0.00 0.00 2.66
3030 5973 5.972107 TTTAGTTCCTACGAGTGCTAAGT 57.028 39.130 0.00 0.00 0.00 2.24
3081 6247 9.712305 CGTAGGAATTCAGGTTAAATATCTCAT 57.288 33.333 7.93 0.00 0.00 2.90
3103 6269 5.326200 AGTCTTGTGTTTAGATCCCGTAG 57.674 43.478 0.00 0.00 0.00 3.51
3104 6270 5.733620 AAGTCTTGTGTTTAGATCCCGTA 57.266 39.130 0.00 0.00 0.00 4.02
3105 6271 4.618920 AAGTCTTGTGTTTAGATCCCGT 57.381 40.909 0.00 0.00 0.00 5.28
3106 6272 6.338146 TCATAAGTCTTGTGTTTAGATCCCG 58.662 40.000 8.94 0.00 0.00 5.14
3107 6273 7.254932 GCATCATAAGTCTTGTGTTTAGATCCC 60.255 40.741 8.94 0.00 0.00 3.85
3109 6275 8.201554 TGCATCATAAGTCTTGTGTTTAGATC 57.798 34.615 8.94 0.00 0.00 2.75
3110 6276 7.201679 GCTGCATCATAAGTCTTGTGTTTAGAT 60.202 37.037 8.94 0.00 0.00 1.98
3111 6277 6.092670 GCTGCATCATAAGTCTTGTGTTTAGA 59.907 38.462 8.94 0.00 0.00 2.10
3112 6278 6.128200 TGCTGCATCATAAGTCTTGTGTTTAG 60.128 38.462 8.94 5.62 0.00 1.85
3117 6283 4.895224 ATGCTGCATCATAAGTCTTGTG 57.105 40.909 9.81 3.03 0.00 3.33
3118 6284 5.678583 ACTATGCTGCATCATAAGTCTTGT 58.321 37.500 19.90 2.59 0.00 3.16
3119 6285 6.427974 CAACTATGCTGCATCATAAGTCTTG 58.572 40.000 19.90 9.10 0.00 3.02
3120 6286 6.615264 CAACTATGCTGCATCATAAGTCTT 57.385 37.500 19.90 0.20 0.00 3.01
3153 6331 5.652452 AGATGCAACCCACTACCTATTTTTC 59.348 40.000 0.00 0.00 0.00 2.29
3197 6377 6.019762 GCGTTTTTCCTTTGTAGTATGCTAC 58.980 40.000 13.52 13.52 45.85 3.58
3213 6397 6.866248 TCCATAGGAAAATTTCTGCGTTTTTC 59.134 34.615 5.65 0.00 38.19 2.29
3281 6466 5.067805 ACTGGGTCATCTGAAACAAAGAAAC 59.932 40.000 0.00 0.00 0.00 2.78
3325 6531 9.567848 GAAATAAAGGAAAATTGCAGTATCGAA 57.432 29.630 0.00 0.00 0.00 3.71
3326 6532 8.735315 TGAAATAAAGGAAAATTGCAGTATCGA 58.265 29.630 0.00 0.00 0.00 3.59
3327 6533 8.909708 TGAAATAAAGGAAAATTGCAGTATCG 57.090 30.769 0.00 0.00 0.00 2.92
3507 6912 3.722555 TTCGACAAATGATGTTCGAGC 57.277 42.857 0.00 0.00 44.12 5.03
3571 6995 0.942884 GCTTTTGCACAGGAAGCAGC 60.943 55.000 14.76 0.00 43.89 5.25
3572 6996 3.190337 GCTTTTGCACAGGAAGCAG 57.810 52.632 14.76 0.00 43.89 4.24


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

AutoCloner maintained by Alex Coulton.