Multiple sequence alignment - TraesCS7D01G471300

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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 TraesCS7D01G471300 chr7D 100.000 5989 0 0 1 5989 584858482 584852494 0.000000e+00 11060.0
1 TraesCS7D01G471300 chr7D 90.000 1390 71 33 2589 3951 92810272 92808924 0.000000e+00 1735.0
2 TraesCS7D01G471300 chr7D 86.965 514 38 11 2172 2658 92810801 92810290 8.770000e-153 551.0
3 TraesCS7D01G471300 chr7D 87.500 352 17 12 1122 1468 92811399 92811070 1.220000e-101 381.0
4 TraesCS7D01G471300 chr7D 90.995 211 18 1 1463 1673 92810981 92810772 3.530000e-72 283.0
5 TraesCS7D01G471300 chr7D 83.607 183 12 15 544 721 92811664 92811495 8.040000e-34 156.0
6 TraesCS7D01G471300 chr7D 93.750 48 1 2 3974 4020 92808925 92808879 2.990000e-08 71.3
7 TraesCS7D01G471300 chr7D 100.000 38 0 0 1062 1099 92811432 92811395 2.990000e-08 71.3
8 TraesCS7D01G471300 chr7B 89.941 4066 227 81 1602 5576 653020747 653016773 0.000000e+00 5075.0
9 TraesCS7D01G471300 chr7B 82.787 1435 93 66 84 1454 653022261 653020917 0.000000e+00 1140.0
10 TraesCS7D01G471300 chr7B 89.800 902 65 15 3237 4129 660062062 660062945 0.000000e+00 1131.0
11 TraesCS7D01G471300 chr7B 91.558 308 18 5 5684 5984 653016756 653016450 9.280000e-113 418.0
12 TraesCS7D01G471300 chr7B 89.247 93 6 3 1483 1571 653020920 653020828 4.910000e-21 113.0
13 TraesCS7D01G471300 chr7A 90.964 2490 127 43 2580 5005 675229669 675232124 0.000000e+00 3262.0
14 TraesCS7D01G471300 chr7A 91.649 922 47 8 5078 5986 675232177 675233081 0.000000e+00 1249.0
15 TraesCS7D01G471300 chr7A 85.619 1196 115 22 1464 2642 675228496 675229651 0.000000e+00 1203.0
16 TraesCS7D01G471300 chr7A 90.939 905 56 13 3237 4132 630247595 630246708 0.000000e+00 1194.0
17 TraesCS7D01G471300 chr7A 89.183 906 70 15 3237 4132 305700484 305699597 0.000000e+00 1105.0
18 TraesCS7D01G471300 chr7A 88.985 463 30 11 1013 1468 675227966 675228414 2.440000e-153 553.0
19 TraesCS7D01G471300 chr7A 92.877 351 19 3 1 350 675223182 675223527 6.930000e-139 505.0
20 TraesCS7D01G471300 chr7A 83.929 392 30 18 365 739 675226996 675227371 1.600000e-90 344.0
21 TraesCS7D01G471300 chr6A 89.823 904 67 12 3237 4132 546621493 546620607 0.000000e+00 1136.0
22 TraesCS7D01G471300 chr6A 92.000 425 31 3 3278 3700 376681342 376680919 1.440000e-165 593.0
23 TraesCS7D01G471300 chr6A 84.436 514 50 12 2172 2658 376682075 376681565 4.200000e-131 479.0
24 TraesCS7D01G471300 chr6A 87.198 414 27 11 1066 1468 376682742 376682344 1.180000e-121 448.0
25 TraesCS7D01G471300 chr6A 89.573 211 21 1 1463 1673 376682255 376682046 3.560000e-67 267.0
26 TraesCS7D01G471300 chr2D 93.499 723 31 8 2983 3700 87982324 87981613 0.000000e+00 1061.0
27 TraesCS7D01G471300 chr2D 89.952 418 16 10 1062 1468 87983372 87982970 3.200000e-142 516.0
28 TraesCS7D01G471300 chr2D 80.652 491 79 12 2741 3223 536921734 536921252 3.410000e-97 366.0
29 TraesCS7D01G471300 chr2D 92.670 191 14 0 1463 1653 87982881 87982691 5.910000e-70 276.0
30 TraesCS7D01G471300 chr2D 81.948 349 33 12 2172 2494 87982701 87982357 9.890000e-68 268.0
31 TraesCS7D01G471300 chr6B 93.874 653 24 9 2906 3553 173904643 173905284 0.000000e+00 970.0
32 TraesCS7D01G471300 chr1B 86.523 512 41 12 2172 2658 621201285 621201793 6.830000e-149 538.0
33 TraesCS7D01G471300 chr1B 87.290 417 28 18 1062 1468 621200615 621201016 2.540000e-123 453.0
34 TraesCS7D01G471300 chr1B 90.047 211 20 1 1463 1673 621201105 621201314 7.650000e-69 272.0
35 TraesCS7D01G471300 chr2A 79.675 492 82 12 2741 3223 679512407 679511925 7.440000e-89 339.0
36 TraesCS7D01G471300 chr2A 89.024 82 3 4 551 629 97848607 97848529 4.940000e-16 97.1
37 TraesCS7D01G471300 chr2B 81.928 249 39 6 2972 3217 89555882 89556127 7.870000e-49 206.0


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 TraesCS7D01G471300 chr7D 584852494 584858482 5988 True 11060.000000 11060 100.000000 1 5989 1 chr7D.!!$R1 5988
1 TraesCS7D01G471300 chr7D 92808879 92811664 2785 True 464.085714 1735 90.402429 544 4020 7 chr7D.!!$R2 3476
2 TraesCS7D01G471300 chr7B 653016450 653022261 5811 True 1686.500000 5075 88.383250 84 5984 4 chr7B.!!$R1 5900
3 TraesCS7D01G471300 chr7B 660062062 660062945 883 False 1131.000000 1131 89.800000 3237 4129 1 chr7B.!!$F1 892
4 TraesCS7D01G471300 chr7A 630246708 630247595 887 True 1194.000000 1194 90.939000 3237 4132 1 chr7A.!!$R2 895
5 TraesCS7D01G471300 chr7A 675223182 675233081 9899 False 1186.000000 3262 89.003833 1 5986 6 chr7A.!!$F1 5985
6 TraesCS7D01G471300 chr7A 305699597 305700484 887 True 1105.000000 1105 89.183000 3237 4132 1 chr7A.!!$R1 895
7 TraesCS7D01G471300 chr6A 546620607 546621493 886 True 1136.000000 1136 89.823000 3237 4132 1 chr6A.!!$R1 895
8 TraesCS7D01G471300 chr6A 376680919 376682742 1823 True 446.750000 593 88.301750 1066 3700 4 chr6A.!!$R2 2634
9 TraesCS7D01G471300 chr2D 87981613 87983372 1759 True 530.250000 1061 89.517250 1062 3700 4 chr2D.!!$R2 2638
10 TraesCS7D01G471300 chr6B 173904643 173905284 641 False 970.000000 970 93.874000 2906 3553 1 chr6B.!!$F1 647
11 TraesCS7D01G471300 chr1B 621200615 621201793 1178 False 421.000000 538 87.953333 1062 2658 3 chr1B.!!$F1 1596

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
945 4469 0.106419 CCTAACCTCGCTCTCTCCCT 60.106 60.0 0.00 0.00 0.00 4.20 F
1394 5238 0.257039 ATTCATTCCTGGCTTCGGCT 59.743 50.0 0.00 0.00 41.44 5.52 F
2380 6404 0.307760 CCCTTTGTCTGCGTCAACAC 59.692 55.0 0.00 0.00 0.00 3.32 F
2423 6448 0.398318 AACTCTGAACCCAGACAGCC 59.602 55.0 0.00 0.00 44.01 4.85 F
2716 6950 1.214367 CTGTAAACTGACGGCGTGTT 58.786 50.0 21.19 14.23 0.00 3.32 F
3887 8170 2.169144 CCAAGGCCTTCATTTCCATTCC 59.831 50.0 17.29 0.00 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2732 6969 0.179111 CGCGAAATAGCACTCTGGGA 60.179 55.000 0.00 0.00 36.85 4.37 R
3075 7317 1.014564 CCCGGAAGCTCTTGACGAAC 61.015 60.000 0.73 0.00 0.00 3.95 R
3887 8170 0.249868 TCTTGTCTGACCGGCAGTTG 60.250 55.000 20.54 11.89 45.14 3.16 R
4165 8452 1.067295 AGGGGAGAAACATGAGCACA 58.933 50.000 0.00 0.00 0.00 4.57 R
4288 8589 1.418264 GAAGTATGGAAGGGAGGAGGC 59.582 57.143 0.00 0.00 0.00 4.70 R
5632 9991 0.036732 GGTGATGCTCCACTGTCCAA 59.963 55.000 8.51 0.00 37.24 3.53 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
72 73 3.807071 CACCAAACCAAATAGCCAAACAC 59.193 43.478 0.00 0.00 0.00 3.32
262 272 3.649986 GCGACTTTGCTGTGCCGT 61.650 61.111 0.00 0.00 0.00 5.68
341 352 4.208686 CGCGGCCTACTCCTGGAC 62.209 72.222 0.00 0.00 0.00 4.02
377 3842 4.314440 GGCTGTCACGAGCACCCA 62.314 66.667 0.00 0.00 41.08 4.51
418 3883 0.391597 TGGGTTCTCGAGACAACACC 59.608 55.000 21.07 21.07 0.00 4.16
449 3920 1.668101 ATCTCACGACTTCCGAGCCC 61.668 60.000 0.00 0.00 41.76 5.19
450 3921 2.599281 TCACGACTTCCGAGCCCA 60.599 61.111 0.00 0.00 41.76 5.36
451 3922 2.154798 CTCACGACTTCCGAGCCCAA 62.155 60.000 0.00 0.00 41.76 4.12
488 3959 0.944311 GTCGCGCTCTGTTTTCCTGA 60.944 55.000 5.56 0.00 0.00 3.86
505 3976 2.159226 CCTGACTCGGCTTAACTCGATT 60.159 50.000 0.00 0.00 34.77 3.34
506 3977 2.854777 CTGACTCGGCTTAACTCGATTG 59.145 50.000 0.00 0.00 34.77 2.67
507 3978 2.230508 TGACTCGGCTTAACTCGATTGT 59.769 45.455 0.00 0.00 34.77 2.71
508 3979 2.853003 GACTCGGCTTAACTCGATTGTC 59.147 50.000 0.00 0.00 34.77 3.18
509 3980 1.846782 CTCGGCTTAACTCGATTGTCG 59.153 52.381 0.00 0.00 42.10 4.35
525 3996 5.508573 CGATTGTCGATTCCGTCTCATATAC 59.491 44.000 0.00 0.00 43.74 1.47
531 4002 7.222031 TGTCGATTCCGTCTCATATACTTTTTG 59.778 37.037 0.00 0.00 37.05 2.44
539 4012 6.490534 GTCTCATATACTTTTTGCTTCCAGC 58.509 40.000 0.00 0.00 42.82 4.85
629 4117 3.044305 GCTCCCACGCACACTGAC 61.044 66.667 0.00 0.00 0.00 3.51
630 4118 2.734723 CTCCCACGCACACTGACG 60.735 66.667 0.00 0.00 0.00 4.35
631 4119 4.293648 TCCCACGCACACTGACGG 62.294 66.667 0.00 0.00 0.00 4.79
632 4120 4.293648 CCCACGCACACTGACGGA 62.294 66.667 0.00 0.00 0.00 4.69
633 4121 3.036084 CCACGCACACTGACGGAC 61.036 66.667 0.00 0.00 0.00 4.79
634 4122 3.394874 CACGCACACTGACGGACG 61.395 66.667 0.00 0.00 0.00 4.79
635 4123 4.640855 ACGCACACTGACGGACGG 62.641 66.667 0.00 0.00 0.00 4.79
650 4138 2.734723 CGGGCAGACAGACACACG 60.735 66.667 0.00 0.00 0.00 4.49
651 4139 2.734591 GGGCAGACAGACACACGA 59.265 61.111 0.00 0.00 0.00 4.35
652 4140 1.664965 GGGCAGACAGACACACGAC 60.665 63.158 0.00 0.00 0.00 4.34
662 4150 4.436998 CACACGACCCTCCTCCGC 62.437 72.222 0.00 0.00 0.00 5.54
680 4168 3.330720 CCCCCTGTCGCCTTCCTT 61.331 66.667 0.00 0.00 0.00 3.36
703 4205 1.222113 CCCGCCTCTCTTTCCCTTC 59.778 63.158 0.00 0.00 0.00 3.46
730 4239 2.032030 CACGTCACTTAACCCAAGCAAG 60.032 50.000 0.00 0.00 37.83 4.01
747 4256 2.595463 GCAGCCAGCTGACACCAA 60.595 61.111 23.40 0.00 46.30 3.67
748 4257 2.195567 GCAGCCAGCTGACACCAAA 61.196 57.895 23.40 0.00 46.30 3.28
749 4258 1.656441 CAGCCAGCTGACACCAAAC 59.344 57.895 17.39 0.00 46.30 2.93
750 4259 1.893808 AGCCAGCTGACACCAAACG 60.894 57.895 17.39 0.00 0.00 3.60
751 4260 2.639286 CCAGCTGACACCAAACGC 59.361 61.111 17.39 0.00 0.00 4.84
752 4261 2.639286 CAGCTGACACCAAACGCC 59.361 61.111 8.42 0.00 0.00 5.68
753 4262 2.594592 AGCTGACACCAAACGCCC 60.595 61.111 0.00 0.00 0.00 6.13
754 4263 4.025401 GCTGACACCAAACGCCCG 62.025 66.667 0.00 0.00 0.00 6.13
755 4264 4.025401 CTGACACCAAACGCCCGC 62.025 66.667 0.00 0.00 0.00 6.13
775 4284 3.842923 CGCGACCTCCATCAGCCT 61.843 66.667 0.00 0.00 0.00 4.58
776 4285 2.107953 GCGACCTCCATCAGCCTC 59.892 66.667 0.00 0.00 0.00 4.70
806 4330 0.512952 GCAGTACACTCCAAGCAACG 59.487 55.000 0.00 0.00 0.00 4.10
907 4431 2.296190 GGCAAGAACCGAACCATTTCTT 59.704 45.455 0.00 0.00 39.62 2.52
909 4433 4.368315 GCAAGAACCGAACCATTTCTTTT 58.632 39.130 0.00 0.00 37.46 2.27
914 4438 3.154710 ACCGAACCATTTCTTTTCTCCC 58.845 45.455 0.00 0.00 0.00 4.30
915 4439 2.492088 CCGAACCATTTCTTTTCTCCCC 59.508 50.000 0.00 0.00 0.00 4.81
941 4465 0.684805 CCCACCTAACCTCGCTCTCT 60.685 60.000 0.00 0.00 0.00 3.10
942 4466 0.741915 CCACCTAACCTCGCTCTCTC 59.258 60.000 0.00 0.00 0.00 3.20
943 4467 0.741915 CACCTAACCTCGCTCTCTCC 59.258 60.000 0.00 0.00 0.00 3.71
944 4468 0.396001 ACCTAACCTCGCTCTCTCCC 60.396 60.000 0.00 0.00 0.00 4.30
945 4469 0.106419 CCTAACCTCGCTCTCTCCCT 60.106 60.000 0.00 0.00 0.00 4.20
956 4480 1.221021 CTCTCCCTACCAAACGCCC 59.779 63.158 0.00 0.00 0.00 6.13
962 4486 3.675619 CTACCAAACGCCCCCTCGG 62.676 68.421 0.00 0.00 0.00 4.63
974 4499 3.738481 CCTCGGCCAATTCCCCCA 61.738 66.667 2.24 0.00 0.00 4.96
991 4516 3.805307 ACTCTCTCGACAGCCGCG 61.805 66.667 0.00 0.00 38.37 6.46
1041 4867 3.110178 CCGTTCTTGGCCGTCGTC 61.110 66.667 0.00 0.00 0.00 4.20
1042 4868 2.355363 CGTTCTTGGCCGTCGTCA 60.355 61.111 0.00 0.00 0.00 4.35
1220 5052 4.849329 CGTCGTGCTCTACCCGGC 62.849 72.222 0.00 0.00 0.00 6.13
1317 5149 2.803670 CGCGGAGGTACACACACG 60.804 66.667 0.00 0.00 0.00 4.49
1318 5150 3.110178 GCGGAGGTACACACACGC 61.110 66.667 0.00 0.00 36.92 5.34
1323 5155 1.219522 GAGGTACACACACGCCACAC 61.220 60.000 0.00 0.00 0.00 3.82
1365 5205 2.381911 AGCCATTAACCCTGCTGATTG 58.618 47.619 0.00 0.00 31.70 2.67
1366 5206 2.025037 AGCCATTAACCCTGCTGATTGA 60.025 45.455 0.00 0.00 31.70 2.57
1367 5207 2.961062 GCCATTAACCCTGCTGATTGAT 59.039 45.455 0.00 0.00 0.00 2.57
1394 5238 0.257039 ATTCATTCCTGGCTTCGGCT 59.743 50.000 0.00 0.00 41.44 5.52
1395 5239 0.908910 TTCATTCCTGGCTTCGGCTA 59.091 50.000 0.00 0.00 41.44 3.93
1414 5258 0.678048 AGCAATTCTCACGGGGAAGC 60.678 55.000 0.00 0.00 0.00 3.86
1415 5259 1.657751 GCAATTCTCACGGGGAAGCC 61.658 60.000 0.00 0.00 0.00 4.35
1416 5260 0.322456 CAATTCTCACGGGGAAGCCA 60.322 55.000 0.00 0.00 0.00 4.75
1417 5261 0.625849 AATTCTCACGGGGAAGCCAT 59.374 50.000 0.00 0.00 0.00 4.40
1418 5262 0.625849 ATTCTCACGGGGAAGCCATT 59.374 50.000 0.00 0.00 0.00 3.16
1419 5263 0.322456 TTCTCACGGGGAAGCCATTG 60.322 55.000 0.00 0.00 0.00 2.82
1451 5299 1.612469 CGTGACTGTGCGAGCTTGAG 61.612 60.000 4.70 0.00 0.00 3.02
1555 5501 7.205992 TCCAACTCAGATATGAGAGATTTTCG 58.794 38.462 23.69 0.59 39.14 3.46
1573 5521 4.434713 TTCGGAAGCTTTTTAATCTGCC 57.565 40.909 0.00 0.00 0.00 4.85
1574 5522 3.417101 TCGGAAGCTTTTTAATCTGCCA 58.583 40.909 0.00 0.00 0.00 4.92
1577 5561 4.142403 CGGAAGCTTTTTAATCTGCCATGA 60.142 41.667 0.00 0.00 0.00 3.07
1606 5606 7.086685 AGGGACTTTACAAGTGGAGATAAAA 57.913 36.000 0.00 0.00 43.03 1.52
1653 5653 9.931210 CAGTTGTTTTGTACTAAAAGGTAGAAG 57.069 33.333 4.01 0.00 0.00 2.85
1654 5654 9.895138 AGTTGTTTTGTACTAAAAGGTAGAAGA 57.105 29.630 4.01 0.00 0.00 2.87
1659 5659 8.767478 TTTGTACTAAAAGGTAGAAGAATCGG 57.233 34.615 0.00 0.00 0.00 4.18
1679 5681 3.653344 GGGACTTTTCTTGGTTGAATGC 58.347 45.455 0.00 0.00 0.00 3.56
1801 5803 7.076842 ACATACACACTTTTGATGATGCTAC 57.923 36.000 0.00 0.00 0.00 3.58
1805 5807 6.000219 ACACACTTTTGATGATGCTACTCTT 59.000 36.000 0.00 0.00 0.00 2.85
1807 5809 7.013655 ACACACTTTTGATGATGCTACTCTTTT 59.986 33.333 0.00 0.00 0.00 2.27
1834 5836 5.897050 TGCCTTATTATAAGCGGTTTTTGG 58.103 37.500 4.64 0.40 0.00 3.28
1835 5837 4.743151 GCCTTATTATAAGCGGTTTTTGGC 59.257 41.667 4.64 6.78 0.00 4.52
1836 5838 5.451381 GCCTTATTATAAGCGGTTTTTGGCT 60.451 40.000 4.64 0.00 42.33 4.75
1838 5840 7.682501 GCCTTATTATAAGCGGTTTTTGGCTAA 60.683 37.037 4.64 0.00 38.88 3.09
1893 5895 9.965824 ATGTCGAAATGAAATTACTCAAGTTTT 57.034 25.926 0.00 0.00 33.67 2.43
1901 5903 9.691362 ATGAAATTACTCAAGTTTTAATTGCGT 57.309 25.926 0.00 0.00 31.13 5.24
1902 5904 8.963130 TGAAATTACTCAAGTTTTAATTGCGTG 58.037 29.630 0.00 0.00 29.17 5.34
1903 5905 9.176181 GAAATTACTCAAGTTTTAATTGCGTGA 57.824 29.630 0.00 0.00 29.17 4.35
1904 5906 8.728088 AATTACTCAAGTTTTAATTGCGTGAG 57.272 30.769 12.25 12.25 41.88 3.51
1939 5942 4.657055 TGATTTATGGCGAATTTGTGTCG 58.343 39.130 0.00 0.00 41.46 4.35
1952 5955 7.337718 CGAATTTGTGTCGATATCTTGGTAAG 58.662 38.462 0.34 0.00 41.02 2.34
2015 6018 7.380602 GCTAATCTTAAATAGGCAAACATGCTG 59.619 37.037 0.00 0.00 34.73 4.41
2040 6043 4.698583 ACTTTAGTGCCACTAGTCGTAG 57.301 45.455 4.51 2.46 31.47 3.51
2081 6084 4.286297 TGTGGATTGGTCTCCAACTTAG 57.714 45.455 3.23 0.00 46.95 2.18
2082 6085 3.907474 TGTGGATTGGTCTCCAACTTAGA 59.093 43.478 3.23 0.00 46.95 2.10
2083 6086 4.536090 TGTGGATTGGTCTCCAACTTAGAT 59.464 41.667 3.23 0.00 46.95 1.98
2084 6087 5.724370 TGTGGATTGGTCTCCAACTTAGATA 59.276 40.000 3.23 0.00 46.95 1.98
2188 6192 6.830838 GGTCATTGAAAAGGTAGAATCAGGAT 59.169 38.462 0.00 0.00 0.00 3.24
2286 6292 8.505625 CAAAAATCAAATGTAAATCTTGTGGGG 58.494 33.333 0.00 0.00 0.00 4.96
2305 6311 1.668628 GGACGCGCCAAATTCAAATGT 60.669 47.619 5.73 0.00 36.34 2.71
2309 6316 3.857093 ACGCGCCAAATTCAAATGTAATC 59.143 39.130 5.73 0.00 0.00 1.75
2339 6363 7.027161 ACGCACCAAACTAATATTTTCATGAC 58.973 34.615 0.00 0.00 0.00 3.06
2363 6387 4.645136 GGATTATCTTCAGTTTGTTCCCCC 59.355 45.833 0.00 0.00 0.00 5.40
2380 6404 0.307760 CCCTTTGTCTGCGTCAACAC 59.692 55.000 0.00 0.00 0.00 3.32
2423 6448 0.398318 AACTCTGAACCCAGACAGCC 59.602 55.000 0.00 0.00 44.01 4.85
2463 6505 3.767902 TGCATGCAGTATACAGCCATA 57.232 42.857 18.46 0.00 0.00 2.74
2464 6506 4.290711 TGCATGCAGTATACAGCCATAT 57.709 40.909 18.46 2.22 0.00 1.78
2597 6640 2.989840 GACAGAATCAGACAGACCAACG 59.010 50.000 0.00 0.00 0.00 4.10
2626 6751 8.284945 TGTCTCATCCTTCCTTGATTAATTTG 57.715 34.615 0.00 0.00 0.00 2.32
2694 6923 9.436957 ACATAAAAGATGAACGAATTACTCTGT 57.563 29.630 0.00 0.00 0.00 3.41
2700 6929 5.386958 TGAACGAATTACTCTGTAGCTGT 57.613 39.130 0.00 0.00 0.00 4.40
2714 6948 1.491563 GCTGTAAACTGACGGCGTG 59.508 57.895 21.19 6.53 41.65 5.34
2716 6950 1.214367 CTGTAAACTGACGGCGTGTT 58.786 50.000 21.19 14.23 0.00 3.32
2719 6956 3.391965 TGTAAACTGACGGCGTGTTAAT 58.608 40.909 21.19 4.95 0.00 1.40
2732 6969 4.212636 GGCGTGTTAATGTTTGTACTGTCT 59.787 41.667 0.00 0.00 0.00 3.41
2745 6983 2.541233 ACTGTCTCCCAGAGTGCTAT 57.459 50.000 0.00 0.00 44.49 2.97
3887 8170 2.169144 CCAAGGCCTTCATTTCCATTCC 59.831 50.000 17.29 0.00 0.00 3.01
3941 8226 4.665142 CGATGAACTTCTGACGAGCTTTTG 60.665 45.833 0.00 0.00 0.00 2.44
4165 8452 2.223900 GCGCTAGGAAAATACTACCGGT 60.224 50.000 13.98 13.98 0.00 5.28
4299 8600 1.686110 CGGTACAGCCTCCTCCCTT 60.686 63.158 0.00 0.00 34.25 3.95
4302 8603 0.617820 GTACAGCCTCCTCCCTTCCA 60.618 60.000 0.00 0.00 0.00 3.53
4343 8651 6.937436 GTTTCACTTAGGAAACCTCTGAAA 57.063 37.500 12.24 0.00 46.88 2.69
4361 8673 3.376234 TGAAACTCATCGTCTACCTACCG 59.624 47.826 0.00 0.00 0.00 4.02
4407 8720 1.821061 CTCTGAACCAGGACACGGCT 61.821 60.000 0.00 0.00 31.51 5.52
4468 8781 1.539827 GCCACAAATGCGAAGGTAAGT 59.460 47.619 0.00 0.00 0.00 2.24
4469 8782 2.414161 GCCACAAATGCGAAGGTAAGTC 60.414 50.000 0.00 0.00 0.00 3.01
4502 8816 1.863662 TTCCTCGCCGAGACTGACAC 61.864 60.000 17.19 0.00 0.00 3.67
4654 8968 0.036765 GCAACCAGGTGTACATCCGA 60.037 55.000 1.47 0.00 0.00 4.55
4783 9097 2.501723 CAAGTACAGGCTCAGGGTATGT 59.498 50.000 0.00 0.00 0.00 2.29
4784 9098 3.682592 AGTACAGGCTCAGGGTATGTA 57.317 47.619 0.00 0.00 0.00 2.29
4785 9099 4.200447 AGTACAGGCTCAGGGTATGTAT 57.800 45.455 0.00 0.00 0.00 2.29
4786 9100 3.898123 AGTACAGGCTCAGGGTATGTATG 59.102 47.826 0.00 0.00 0.00 2.39
4862 9181 6.110033 TCTAGTGCAACAAAAACTGACTGTA 58.890 36.000 0.00 0.00 41.43 2.74
4863 9182 5.835113 AGTGCAACAAAAACTGACTGTAT 57.165 34.783 0.00 0.00 41.43 2.29
4864 9183 6.207691 AGTGCAACAAAAACTGACTGTATT 57.792 33.333 0.00 0.00 41.43 1.89
4886 9205 9.431887 GTATTGTGTTTCATTTCCTACTAGTCA 57.568 33.333 0.00 0.00 0.00 3.41
5026 9350 4.161565 CAGCCAAATGTGTCCTAGTAGGTA 59.838 45.833 16.02 4.11 36.53 3.08
5037 9361 5.116882 GTCCTAGTAGGTAACCAATGCAAG 58.883 45.833 16.02 0.00 36.53 4.01
5039 9363 5.128827 TCCTAGTAGGTAACCAATGCAAGAG 59.871 44.000 16.02 0.00 36.53 2.85
5041 9365 5.700402 AGTAGGTAACCAATGCAAGAGAT 57.300 39.130 0.00 0.00 37.17 2.75
5076 9400 1.476488 CTAAACCGCCCCTGAAAATGG 59.524 52.381 0.00 0.00 0.00 3.16
5100 9433 2.615912 GCATCTTATGAACAGGGAGCAC 59.384 50.000 0.00 0.00 0.00 4.40
5150 9502 2.237392 GCAGAGTCTTCAACCATACCCT 59.763 50.000 0.00 0.00 0.00 4.34
5249 9602 6.153680 ACAAGAGAACCATGGTTTGTACAAAA 59.846 34.615 30.33 8.83 38.60 2.44
5253 9606 4.320608 ACCATGGTTTGTACAAAAGCAG 57.679 40.909 22.14 12.53 40.38 4.24
5336 9689 4.002982 TGGATCACAACACATTAGACAGC 58.997 43.478 0.00 0.00 0.00 4.40
5387 9740 6.767423 TGTGATGTACAATGGATGATAACCAG 59.233 38.462 0.00 0.00 36.17 4.00
5511 9868 6.492007 AGTGCTACAGTTTCAGAATCAATG 57.508 37.500 0.00 0.00 0.00 2.82
5512 9869 5.413833 AGTGCTACAGTTTCAGAATCAATGG 59.586 40.000 0.00 0.00 0.00 3.16
5513 9870 5.182001 GTGCTACAGTTTCAGAATCAATGGT 59.818 40.000 0.00 0.00 0.00 3.55
5514 9871 6.371548 GTGCTACAGTTTCAGAATCAATGGTA 59.628 38.462 0.00 0.00 0.00 3.25
5515 9872 6.371548 TGCTACAGTTTCAGAATCAATGGTAC 59.628 38.462 0.00 0.00 0.00 3.34
5516 9873 6.595716 GCTACAGTTTCAGAATCAATGGTACT 59.404 38.462 0.00 0.00 0.00 2.73
5517 9874 7.764443 GCTACAGTTTCAGAATCAATGGTACTA 59.236 37.037 0.00 0.00 0.00 1.82
5518 9875 9.823647 CTACAGTTTCAGAATCAATGGTACTAT 57.176 33.333 0.00 0.00 0.00 2.12
5549 9908 6.316390 GCATACAGGTGATAACTTGCTACTTT 59.684 38.462 0.00 0.00 0.00 2.66
5550 9909 7.148239 GCATACAGGTGATAACTTGCTACTTTT 60.148 37.037 0.00 0.00 0.00 2.27
5591 9950 5.981915 GGTAACCCGACTTTATTAGTAGCTG 59.018 44.000 0.00 0.00 37.17 4.24
5592 9951 5.927281 AACCCGACTTTATTAGTAGCTGA 57.073 39.130 0.00 0.00 37.17 4.26
5593 9952 5.517322 ACCCGACTTTATTAGTAGCTGAG 57.483 43.478 0.00 0.00 37.17 3.35
5594 9953 4.202131 ACCCGACTTTATTAGTAGCTGAGC 60.202 45.833 0.00 0.00 37.17 4.26
5595 9954 4.038162 CCCGACTTTATTAGTAGCTGAGCT 59.962 45.833 13.25 13.25 43.41 4.09
5603 9962 1.214062 GTAGCTGAGCTGCGTGAGT 59.786 57.895 18.79 0.00 40.10 3.41
5614 9973 2.159181 GCGTGAGTTACCATGCGTT 58.841 52.632 0.00 0.00 39.00 4.84
5623 9982 2.665649 TACCATGCGTTGTCCTACAG 57.334 50.000 0.00 0.00 0.00 2.74
5632 9991 2.233922 CGTTGTCCTACAGTCCATTCCT 59.766 50.000 0.00 0.00 0.00 3.36
5678 10037 0.677288 AGGTTTGTCCACGTCGATCA 59.323 50.000 0.00 0.00 39.02 2.92
5826 10201 7.147655 CCATAATAGAAGAGGAAAGAGACCACA 60.148 40.741 0.00 0.00 0.00 4.17
5852 10227 7.891712 ACCATGATCATTCAAGCATCCATTATA 59.108 33.333 5.16 0.00 34.96 0.98
5867 10242 8.834465 GCATCCATTATATCATTAGTGCCTTAG 58.166 37.037 0.00 0.00 0.00 2.18
5894 10269 0.771755 AGGGAGTTTCAGGGTTGTCC 59.228 55.000 0.00 0.00 0.00 4.02
5918 10293 0.165944 CAAATGGCGACGACACTTCC 59.834 55.000 4.98 0.00 0.00 3.46
5986 10361 6.578944 ACTTTCCCAGTGTTTTTATTTGTCC 58.421 36.000 0.00 0.00 32.83 4.02
5987 10362 6.155393 ACTTTCCCAGTGTTTTTATTTGTCCA 59.845 34.615 0.00 0.00 32.83 4.02
5988 10363 6.546428 TTCCCAGTGTTTTTATTTGTCCAA 57.454 33.333 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 8.865420 TTCTAATATAGCTCCGACTCTACATT 57.135 34.615 0.00 0.00 0.00 2.71
13 14 9.750783 ACCTAGTATTTTCTAATATAGCTCCGA 57.249 33.333 0.00 0.00 0.00 4.55
72 73 1.682854 TGCCTTGCCTTCACTTTTCAG 59.317 47.619 0.00 0.00 0.00 3.02
114 115 4.884164 GGTGCTAAAGGAAAGTATGCATCT 59.116 41.667 0.19 0.00 0.00 2.90
236 246 1.957186 GCAAAGTCGCCACCGTGTA 60.957 57.895 0.00 0.00 35.54 2.90
262 272 6.310956 CGGTACATCATCCGTTTACTTTTACA 59.689 38.462 0.00 0.00 41.58 2.41
327 338 2.363925 ACGGTCCAGGAGTAGGCC 60.364 66.667 0.00 0.00 0.00 5.19
341 352 2.046892 CTTCTGGGCCTCACACGG 60.047 66.667 4.53 0.00 0.00 4.94
377 3842 0.319641 GTCGAGTCTTGTTTCGGCCT 60.320 55.000 0.00 0.00 35.53 5.19
418 3883 1.373602 CGTGAGATTCGCGTACGTAG 58.626 55.000 17.90 11.60 44.47 3.51
488 3959 2.731341 CGACAATCGAGTTAAGCCGAGT 60.731 50.000 0.00 0.53 43.74 4.18
505 3976 6.387041 AAAGTATATGAGACGGAATCGACA 57.613 37.500 0.00 0.00 40.11 4.35
506 3977 7.556433 CAAAAAGTATATGAGACGGAATCGAC 58.444 38.462 0.00 0.00 40.11 4.20
507 3978 6.200286 GCAAAAAGTATATGAGACGGAATCGA 59.800 38.462 0.00 0.00 40.11 3.59
508 3979 6.201044 AGCAAAAAGTATATGAGACGGAATCG 59.799 38.462 0.00 0.00 43.02 3.34
509 3980 7.484035 AGCAAAAAGTATATGAGACGGAATC 57.516 36.000 0.00 0.00 0.00 2.52
510 3981 7.012421 GGAAGCAAAAAGTATATGAGACGGAAT 59.988 37.037 0.00 0.00 0.00 3.01
511 3982 6.315393 GGAAGCAAAAAGTATATGAGACGGAA 59.685 38.462 0.00 0.00 0.00 4.30
580 4054 1.601759 GCTGGTGGCGGATGCATAT 60.602 57.895 0.00 0.00 45.35 1.78
626 4114 3.680786 CTGTCTGCCCGTCCGTCA 61.681 66.667 0.00 0.00 0.00 4.35
629 4117 3.680786 TGTCTGTCTGCCCGTCCG 61.681 66.667 0.00 0.00 0.00 4.79
630 4118 2.048127 GTGTCTGTCTGCCCGTCC 60.048 66.667 0.00 0.00 0.00 4.79
631 4119 1.664965 GTGTGTCTGTCTGCCCGTC 60.665 63.158 0.00 0.00 0.00 4.79
632 4120 2.421739 GTGTGTCTGTCTGCCCGT 59.578 61.111 0.00 0.00 0.00 5.28
633 4121 2.734723 CGTGTGTCTGTCTGCCCG 60.735 66.667 0.00 0.00 0.00 6.13
634 4122 1.664965 GTCGTGTGTCTGTCTGCCC 60.665 63.158 0.00 0.00 0.00 5.36
635 4123 1.664965 GGTCGTGTGTCTGTCTGCC 60.665 63.158 0.00 0.00 0.00 4.85
636 4124 1.664965 GGGTCGTGTGTCTGTCTGC 60.665 63.158 0.00 0.00 0.00 4.26
637 4125 0.039074 GAGGGTCGTGTGTCTGTCTG 60.039 60.000 0.00 0.00 0.00 3.51
665 4153 1.842381 AAGGAAGGAAGGCGACAGGG 61.842 60.000 0.00 0.00 0.00 4.45
668 4156 1.677552 GGAAGGAAGGAAGGCGACA 59.322 57.895 0.00 0.00 0.00 4.35
670 4158 2.656069 CGGGAAGGAAGGAAGGCGA 61.656 63.158 0.00 0.00 0.00 5.54
672 4160 2.438614 GCGGGAAGGAAGGAAGGC 60.439 66.667 0.00 0.00 0.00 4.35
673 4161 2.258748 GAGGCGGGAAGGAAGGAAGG 62.259 65.000 0.00 0.00 0.00 3.46
674 4162 1.222113 GAGGCGGGAAGGAAGGAAG 59.778 63.158 0.00 0.00 0.00 3.46
676 4164 1.686110 GAGAGGCGGGAAGGAAGGA 60.686 63.158 0.00 0.00 0.00 3.36
677 4165 1.268283 AAGAGAGGCGGGAAGGAAGG 61.268 60.000 0.00 0.00 0.00 3.46
678 4166 0.615850 AAAGAGAGGCGGGAAGGAAG 59.384 55.000 0.00 0.00 0.00 3.46
679 4167 0.613777 GAAAGAGAGGCGGGAAGGAA 59.386 55.000 0.00 0.00 0.00 3.36
680 4168 1.265454 GGAAAGAGAGGCGGGAAGGA 61.265 60.000 0.00 0.00 0.00 3.36
703 4205 0.872388 GGTTAAGTGACGTGCAAGGG 59.128 55.000 4.26 0.00 0.00 3.95
730 4239 2.195567 TTTGGTGTCAGCTGGCTGC 61.196 57.895 20.86 12.14 43.31 5.25
735 4244 2.639286 GGCGTTTGGTGTCAGCTG 59.361 61.111 7.63 7.63 0.00 4.24
736 4245 2.594592 GGGCGTTTGGTGTCAGCT 60.595 61.111 3.30 0.00 0.00 4.24
738 4247 4.025401 GCGGGCGTTTGGTGTCAG 62.025 66.667 0.00 0.00 0.00 3.51
758 4267 3.781770 GAGGCTGATGGAGGTCGCG 62.782 68.421 0.00 0.00 0.00 5.87
759 4268 2.107953 GAGGCTGATGGAGGTCGC 59.892 66.667 0.00 0.00 0.00 5.19
760 4269 1.743321 GAGGAGGCTGATGGAGGTCG 61.743 65.000 0.00 0.00 0.00 4.79
761 4270 1.406860 GGAGGAGGCTGATGGAGGTC 61.407 65.000 0.00 0.00 0.00 3.85
762 4271 1.383803 GGAGGAGGCTGATGGAGGT 60.384 63.158 0.00 0.00 0.00 3.85
763 4272 1.383664 TGGAGGAGGCTGATGGAGG 60.384 63.158 0.00 0.00 0.00 4.30
764 4273 1.828768 GTGGAGGAGGCTGATGGAG 59.171 63.158 0.00 0.00 0.00 3.86
765 4274 2.060383 CGTGGAGGAGGCTGATGGA 61.060 63.158 0.00 0.00 0.00 3.41
766 4275 2.503061 CGTGGAGGAGGCTGATGG 59.497 66.667 0.00 0.00 0.00 3.51
767 4276 2.503061 CCGTGGAGGAGGCTGATG 59.497 66.667 0.00 0.00 45.00 3.07
773 4282 4.463879 CTGCTGCCGTGGAGGAGG 62.464 72.222 0.00 0.00 45.00 4.30
774 4283 2.351244 TACTGCTGCCGTGGAGGAG 61.351 63.158 6.98 11.03 45.00 3.69
775 4284 2.283604 TACTGCTGCCGTGGAGGA 60.284 61.111 6.98 0.00 45.00 3.71
776 4285 2.125512 GTACTGCTGCCGTGGAGG 60.126 66.667 6.98 0.00 44.97 4.30
820 4344 3.537874 GATGACGACGGGAGGGGG 61.538 72.222 0.00 0.00 0.00 5.40
821 4345 2.088674 GATGATGACGACGGGAGGGG 62.089 65.000 0.00 0.00 0.00 4.79
866 4390 2.580867 GCTCCTACTGCTCGTGCG 60.581 66.667 4.84 2.63 43.34 5.34
867 4391 2.202810 GGCTCCTACTGCTCGTGC 60.203 66.667 1.71 1.71 40.20 5.34
907 4431 2.687566 GGGCTCGGAGGGGAGAAA 60.688 66.667 7.20 0.00 36.08 2.52
909 4433 4.779733 GTGGGCTCGGAGGGGAGA 62.780 72.222 7.20 0.00 36.08 3.71
914 4438 2.732619 GGTTAGGTGGGCTCGGAGG 61.733 68.421 7.20 0.00 0.00 4.30
915 4439 1.677637 GAGGTTAGGTGGGCTCGGAG 61.678 65.000 0.00 0.00 0.00 4.63
941 4465 3.332385 GGGGGCGTTTGGTAGGGA 61.332 66.667 0.00 0.00 0.00 4.20
942 4466 3.335729 AGGGGGCGTTTGGTAGGG 61.336 66.667 0.00 0.00 0.00 3.53
943 4467 2.271173 GAGGGGGCGTTTGGTAGG 59.729 66.667 0.00 0.00 0.00 3.18
944 4468 2.125269 CGAGGGGGCGTTTGGTAG 60.125 66.667 0.00 0.00 0.00 3.18
945 4469 3.708544 CCGAGGGGGCGTTTGGTA 61.709 66.667 0.00 0.00 0.00 3.25
956 4480 4.522975 GGGGGAATTGGCCGAGGG 62.523 72.222 0.00 0.00 0.00 4.30
962 4486 0.106967 GAGAGAGTGGGGGAATTGGC 60.107 60.000 0.00 0.00 0.00 4.52
970 4495 2.716017 GGCTGTCGAGAGAGTGGGG 61.716 68.421 14.74 0.00 43.49 4.96
974 4499 3.805307 CGCGGCTGTCGAGAGAGT 61.805 66.667 14.74 0.00 43.49 3.24
1025 4851 1.736645 ATGACGACGGCCAAGAACG 60.737 57.895 2.24 2.90 0.00 3.95
1200 5032 4.849329 GGGTAGAGCACGACGCCG 62.849 72.222 0.00 0.00 44.04 6.46
1220 5052 1.750399 CATCCGGTGGCCTTCTTGG 60.750 63.158 3.32 4.36 39.35 3.61
1251 5083 1.264288 GACTTGGACTTGAACTTGGCG 59.736 52.381 0.00 0.00 0.00 5.69
1342 5178 3.890527 AGCAGGGTTAATGGCTGAG 57.109 52.632 0.00 0.00 34.83 3.35
1365 5205 6.158023 AGCCAGGAATGAATCAATCAAATC 57.842 37.500 0.40 0.00 42.54 2.17
1366 5206 6.555463 AAGCCAGGAATGAATCAATCAAAT 57.445 33.333 0.40 0.00 42.54 2.32
1367 5207 5.393352 CGAAGCCAGGAATGAATCAATCAAA 60.393 40.000 0.40 0.00 42.54 2.69
1394 5238 1.406887 GCTTCCCCGTGAGAATTGCTA 60.407 52.381 0.00 0.00 0.00 3.49
1395 5239 0.678048 GCTTCCCCGTGAGAATTGCT 60.678 55.000 0.00 0.00 0.00 3.91
1396 5240 1.657751 GGCTTCCCCGTGAGAATTGC 61.658 60.000 0.00 0.00 0.00 3.56
1414 5258 1.133598 ACGCATCAGCAATGTCAATGG 59.866 47.619 1.66 0.00 42.27 3.16
1415 5259 2.159490 TCACGCATCAGCAATGTCAATG 60.159 45.455 1.66 0.00 42.27 2.82
1416 5260 2.086094 TCACGCATCAGCAATGTCAAT 58.914 42.857 1.66 0.00 42.27 2.57
1417 5261 1.197492 GTCACGCATCAGCAATGTCAA 59.803 47.619 1.66 0.00 42.27 3.18
1418 5262 0.798159 GTCACGCATCAGCAATGTCA 59.202 50.000 1.66 0.00 42.27 3.58
1419 5263 1.081892 AGTCACGCATCAGCAATGTC 58.918 50.000 1.66 0.00 42.27 3.06
1451 5299 2.850321 TGTACGTAATCGTCGGACAAC 58.150 47.619 9.10 0.00 46.84 3.32
1555 5501 5.329035 TCATGGCAGATTAAAAAGCTTCC 57.671 39.130 0.00 0.00 30.55 3.46
1573 5521 5.886960 CTTGTAAAGTCCCTTTCCTCATG 57.113 43.478 0.00 0.00 39.70 3.07
1653 5653 3.818773 TCAACCAAGAAAAGTCCCGATTC 59.181 43.478 0.00 0.00 0.00 2.52
1654 5654 3.827722 TCAACCAAGAAAAGTCCCGATT 58.172 40.909 0.00 0.00 0.00 3.34
1656 5656 3.284793 TTCAACCAAGAAAAGTCCCGA 57.715 42.857 0.00 0.00 0.00 5.14
1657 5657 3.857010 GCATTCAACCAAGAAAAGTCCCG 60.857 47.826 0.00 0.00 0.00 5.14
1658 5658 3.554960 GGCATTCAACCAAGAAAAGTCCC 60.555 47.826 0.00 0.00 0.00 4.46
1659 5659 3.069443 TGGCATTCAACCAAGAAAAGTCC 59.931 43.478 0.00 0.00 33.12 3.85
1679 5681 2.396590 ACTTTAGGCCACGTACATGG 57.603 50.000 5.01 2.89 43.26 3.66
1697 5699 9.888637 TTTTGTAAATTTCGTTTGAATTCGAAC 57.111 25.926 23.53 23.53 43.89 3.95
1728 5730 4.657436 TTGCGTTTGAATTTGGTACCTT 57.343 36.364 14.36 0.00 0.00 3.50
1729 5731 4.657436 TTTGCGTTTGAATTTGGTACCT 57.343 36.364 14.36 0.00 0.00 3.08
1801 5803 9.612620 CCGCTTATAATAAGGCAAATAAAAGAG 57.387 33.333 0.00 0.00 0.00 2.85
1807 5809 9.522804 CAAAAACCGCTTATAATAAGGCAAATA 57.477 29.630 0.00 0.00 0.00 1.40
1821 5823 4.328536 TGAGATTAGCCAAAAACCGCTTA 58.671 39.130 0.00 0.00 36.53 3.09
1822 5824 3.153919 TGAGATTAGCCAAAAACCGCTT 58.846 40.909 0.00 0.00 36.53 4.68
1823 5825 2.790433 TGAGATTAGCCAAAAACCGCT 58.210 42.857 0.00 0.00 39.17 5.52
1824 5826 3.128589 TCATGAGATTAGCCAAAAACCGC 59.871 43.478 0.00 0.00 0.00 5.68
1832 5834 5.131642 AGTTCATTCCTCATGAGATTAGCCA 59.868 40.000 24.62 0.00 43.15 4.75
1834 5836 6.054295 ACAGTTCATTCCTCATGAGATTAGC 58.946 40.000 24.62 4.53 43.15 3.09
1835 5837 7.767659 TCAACAGTTCATTCCTCATGAGATTAG 59.232 37.037 24.62 11.00 43.15 1.73
1836 5838 7.623630 TCAACAGTTCATTCCTCATGAGATTA 58.376 34.615 24.62 8.90 43.15 1.75
1838 5840 6.058553 TCAACAGTTCATTCCTCATGAGAT 57.941 37.500 24.62 7.71 43.15 2.75
1893 5895 1.327460 GCAATCGAGCTCACGCAATTA 59.673 47.619 15.40 0.00 39.10 1.40
1895 5897 1.709147 GGCAATCGAGCTCACGCAAT 61.709 55.000 15.40 0.00 39.10 3.56
1897 5899 2.815211 GGCAATCGAGCTCACGCA 60.815 61.111 15.40 0.00 39.10 5.24
1898 5900 3.918220 CGGCAATCGAGCTCACGC 61.918 66.667 15.40 9.65 42.43 5.34
1899 5901 2.202610 TCGGCAATCGAGCTCACG 60.203 61.111 15.40 7.92 43.74 4.35
1907 5909 2.725759 CGCCATAAATCATCGGCAATCG 60.726 50.000 0.00 0.00 45.14 3.34
1930 5933 5.234329 CGCTTACCAAGATATCGACACAAAT 59.766 40.000 0.00 0.00 0.00 2.32
1939 5942 3.984633 GCTCTGACGCTTACCAAGATATC 59.015 47.826 0.00 0.00 0.00 1.63
1952 5955 0.649475 CAACAGCATAGCTCTGACGC 59.351 55.000 7.84 0.00 36.40 5.19
1963 5966 4.032960 TGACTTAACCCATCAACAGCAT 57.967 40.909 0.00 0.00 0.00 3.79
1968 5971 4.218417 AGCACATTGACTTAACCCATCAAC 59.782 41.667 0.00 0.00 35.28 3.18
2015 6018 5.648572 ACGACTAGTGGCACTAAAGTAATC 58.351 41.667 26.12 15.43 29.00 1.75
2047 6050 6.721208 AGACCAATCCACATCATAAAACAAGT 59.279 34.615 0.00 0.00 0.00 3.16
2081 6084 9.929722 GATCACAATGTCTCTCGTATATCTATC 57.070 37.037 0.00 0.00 0.00 2.08
2082 6085 9.454859 TGATCACAATGTCTCTCGTATATCTAT 57.545 33.333 0.00 0.00 0.00 1.98
2083 6086 8.722394 GTGATCACAATGTCTCTCGTATATCTA 58.278 37.037 21.07 0.00 0.00 1.98
2084 6087 7.229506 TGTGATCACAATGTCTCTCGTATATCT 59.770 37.037 26.02 0.00 38.56 1.98
2261 6267 8.435982 TCCCCACAAGATTTACATTTGATTTTT 58.564 29.630 0.00 0.00 0.00 1.94
2265 6271 5.125417 CGTCCCCACAAGATTTACATTTGAT 59.875 40.000 0.00 0.00 0.00 2.57
2273 6279 1.022451 GCGCGTCCCCACAAGATTTA 61.022 55.000 8.43 0.00 0.00 1.40
2279 6285 4.877619 TTTGGCGCGTCCCCACAA 62.878 61.111 8.89 1.26 30.65 3.33
2286 6292 1.696988 ACATTTGAATTTGGCGCGTC 58.303 45.000 2.29 2.29 0.00 5.19
2335 6359 6.316390 GGAACAAACTGAAGATAATCCGTCAT 59.684 38.462 0.00 0.00 0.00 3.06
2339 6363 4.335594 GGGGAACAAACTGAAGATAATCCG 59.664 45.833 0.00 0.00 0.00 4.18
2363 6387 3.181511 TGAAAGTGTTGACGCAGACAAAG 60.182 43.478 0.00 0.00 44.34 2.77
2380 6404 3.559242 GCAGGCTAGCAGTTATCTGAAAG 59.441 47.826 18.24 2.45 43.76 2.62
2423 6448 5.658468 TGCATGTCTGAATCTACTCTTCTG 58.342 41.667 0.00 0.00 0.00 3.02
2597 6640 5.549742 ATCAAGGAAGGATGAGACAGATC 57.450 43.478 0.00 0.00 0.00 2.75
2626 6751 5.294060 TGGAATTGTTTCTTTCTTTGCTTGC 59.706 36.000 0.00 0.00 32.16 4.01
2643 6768 8.330302 GTTTCTTGAAATGAAAGTGTGGAATTG 58.670 33.333 0.00 0.00 40.13 2.32
2683 6912 7.008447 CGTCAGTTTACAGCTACAGAGTAATTC 59.992 40.741 0.00 0.00 0.00 2.17
2684 6913 6.807230 CGTCAGTTTACAGCTACAGAGTAATT 59.193 38.462 0.00 0.00 0.00 1.40
2686 6915 5.335426 CCGTCAGTTTACAGCTACAGAGTAA 60.335 44.000 0.00 0.00 0.00 2.24
2687 6916 4.155462 CCGTCAGTTTACAGCTACAGAGTA 59.845 45.833 0.00 0.00 0.00 2.59
2688 6917 3.057456 CCGTCAGTTTACAGCTACAGAGT 60.057 47.826 0.00 0.00 0.00 3.24
2689 6918 3.502920 CCGTCAGTTTACAGCTACAGAG 58.497 50.000 0.00 0.00 0.00 3.35
2690 6919 2.352421 GCCGTCAGTTTACAGCTACAGA 60.352 50.000 0.00 0.00 0.00 3.41
2691 6920 1.993370 GCCGTCAGTTTACAGCTACAG 59.007 52.381 0.00 0.00 0.00 2.74
2692 6921 1.667756 CGCCGTCAGTTTACAGCTACA 60.668 52.381 0.00 0.00 0.00 2.74
2693 6922 0.989890 CGCCGTCAGTTTACAGCTAC 59.010 55.000 0.00 0.00 0.00 3.58
2694 6923 0.599558 ACGCCGTCAGTTTACAGCTA 59.400 50.000 0.00 0.00 0.00 3.32
2695 6924 0.944311 CACGCCGTCAGTTTACAGCT 60.944 55.000 0.00 0.00 0.00 4.24
2696 6925 1.219522 ACACGCCGTCAGTTTACAGC 61.220 55.000 0.00 0.00 0.00 4.40
2700 6929 3.391965 ACATTAACACGCCGTCAGTTTA 58.608 40.909 0.00 0.00 0.00 2.01
2714 6948 6.481954 CTGGGAGACAGTACAAACATTAAC 57.518 41.667 0.00 0.00 42.42 2.01
2732 6969 0.179111 CGCGAAATAGCACTCTGGGA 60.179 55.000 0.00 0.00 36.85 4.37
2745 6983 2.307309 CCACGACTTGAGCGCGAAA 61.307 57.895 12.10 0.00 0.00 3.46
2853 7091 1.293963 TGTCGAGGTACCGAGTGTCG 61.294 60.000 12.90 12.90 39.43 4.35
3024 7266 1.227999 CGTCGTTGCTGTTGGTCCAT 61.228 55.000 0.00 0.00 0.00 3.41
3075 7317 1.014564 CCCGGAAGCTCTTGACGAAC 61.015 60.000 0.73 0.00 0.00 3.95
3290 7537 1.403249 GCACACCCAGCAACATCATTC 60.403 52.381 0.00 0.00 0.00 2.67
3646 7900 4.101448 AGCGTGGGCAGGATGGTC 62.101 66.667 0.00 0.00 43.41 4.02
3737 8012 3.817084 ACCACACAATCATGTCAGTTCTG 59.183 43.478 0.00 0.00 37.82 3.02
3827 8110 3.114616 CAGACTTGCGGCTCGGTG 61.115 66.667 0.00 0.00 0.00 4.94
3862 8145 1.632589 GAAATGAAGGCCTTGGTGGT 58.367 50.000 26.25 3.59 38.35 4.16
3887 8170 0.249868 TCTTGTCTGACCGGCAGTTG 60.250 55.000 20.54 11.89 45.14 3.16
3941 8226 1.517257 CGTCTCCATGTCTGCGGAC 60.517 63.158 19.20 19.20 42.42 4.79
4117 8404 4.319766 CGTGTGAATGAAGAGAAAAGTGGG 60.320 45.833 0.00 0.00 0.00 4.61
4118 8405 4.511454 TCGTGTGAATGAAGAGAAAAGTGG 59.489 41.667 0.00 0.00 0.00 4.00
4165 8452 1.067295 AGGGGAGAAACATGAGCACA 58.933 50.000 0.00 0.00 0.00 4.57
4288 8589 1.418264 GAAGTATGGAAGGGAGGAGGC 59.582 57.143 0.00 0.00 0.00 4.70
4299 8600 4.873010 ACTCTGAAGGCTAGAAGTATGGA 58.127 43.478 0.00 0.00 0.00 3.41
4302 8603 6.635755 GTGAAACTCTGAAGGCTAGAAGTAT 58.364 40.000 0.00 0.00 0.00 2.12
4343 8651 2.996249 TCGGTAGGTAGACGATGAGT 57.004 50.000 0.00 0.00 0.00 3.41
4361 8673 4.888326 AGGTTAGCAGAGATCATGGATC 57.112 45.455 0.00 0.00 39.17 3.36
4429 8742 3.435186 GTCGCCTTGGAAGCCTGC 61.435 66.667 0.00 0.00 0.00 4.85
4431 8744 4.394712 CCGTCGCCTTGGAAGCCT 62.395 66.667 0.00 0.00 0.00 4.58
4468 8781 2.423898 GGAATCGGTGGAGCGAGGA 61.424 63.158 7.07 0.00 0.00 3.71
4469 8782 2.107141 GGAATCGGTGGAGCGAGG 59.893 66.667 7.07 0.00 0.00 4.63
4502 8816 1.535028 CCCTCTCTCGATCATGTCTCG 59.465 57.143 12.28 12.28 37.47 4.04
4783 9097 2.764010 AGGACGGTGCTGAACATACATA 59.236 45.455 0.00 0.00 0.00 2.29
4784 9098 1.555075 AGGACGGTGCTGAACATACAT 59.445 47.619 0.00 0.00 0.00 2.29
4785 9099 0.973632 AGGACGGTGCTGAACATACA 59.026 50.000 0.00 0.00 0.00 2.29
4786 9100 2.000447 GAAGGACGGTGCTGAACATAC 59.000 52.381 1.94 0.00 0.00 2.39
4837 9151 5.590259 ACAGTCAGTTTTTGTTGCACTAGAT 59.410 36.000 0.00 0.00 0.00 1.98
4863 9182 9.431887 GTATGACTAGTAGGAAATGAAACACAA 57.568 33.333 0.00 0.00 0.00 3.33
4864 9183 8.590204 TGTATGACTAGTAGGAAATGAAACACA 58.410 33.333 0.00 0.00 0.00 3.72
4886 9205 3.513119 CCATGATCTCCGAGTCCATGTAT 59.487 47.826 20.64 0.00 34.43 2.29
5076 9400 2.877168 CTCCCTGTTCATAAGATGCAGC 59.123 50.000 0.00 0.00 0.00 5.25
5100 9433 3.225104 CATACCCAAACCCATCTCCATG 58.775 50.000 0.00 0.00 0.00 3.66
5150 9502 4.711399 AGCATCATAGCAAAGTATCTGCA 58.289 39.130 0.00 0.00 42.48 4.41
5511 9868 4.021368 CACCTGTATGCCTACCATAGTACC 60.021 50.000 0.00 0.00 37.10 3.34
5512 9869 4.831155 TCACCTGTATGCCTACCATAGTAC 59.169 45.833 0.00 0.00 37.10 2.73
5513 9870 5.069518 TCACCTGTATGCCTACCATAGTA 57.930 43.478 0.00 0.00 37.10 1.82
5514 9871 3.923648 TCACCTGTATGCCTACCATAGT 58.076 45.455 0.00 0.00 37.10 2.12
5515 9872 6.211584 AGTTATCACCTGTATGCCTACCATAG 59.788 42.308 0.00 0.00 37.10 2.23
5516 9873 6.082031 AGTTATCACCTGTATGCCTACCATA 58.918 40.000 0.00 0.00 35.34 2.74
5517 9874 4.907875 AGTTATCACCTGTATGCCTACCAT 59.092 41.667 0.00 0.00 37.97 3.55
5518 9875 4.295201 AGTTATCACCTGTATGCCTACCA 58.705 43.478 0.00 0.00 0.00 3.25
5549 9908 5.259632 GTTACCAGTGAGGACCTACTAGAA 58.740 45.833 0.00 0.00 41.22 2.10
5550 9909 4.324874 GGTTACCAGTGAGGACCTACTAGA 60.325 50.000 0.00 0.00 41.22 2.43
5591 9950 1.002366 CATGGTAACTCACGCAGCTC 58.998 55.000 0.00 0.00 37.61 4.09
5592 9951 1.021390 GCATGGTAACTCACGCAGCT 61.021 55.000 0.00 0.00 37.61 4.24
5593 9952 1.425428 GCATGGTAACTCACGCAGC 59.575 57.895 0.00 0.00 37.61 5.25
5594 9953 1.014044 ACGCATGGTAACTCACGCAG 61.014 55.000 0.00 0.00 37.61 5.18
5595 9954 0.601576 AACGCATGGTAACTCACGCA 60.602 50.000 0.00 0.00 37.61 5.24
5603 9962 2.300723 ACTGTAGGACAACGCATGGTAA 59.699 45.455 0.00 0.00 0.00 2.85
5614 9973 3.981071 CAAGGAATGGACTGTAGGACA 57.019 47.619 0.00 0.00 0.00 4.02
5632 9991 0.036732 GGTGATGCTCCACTGTCCAA 59.963 55.000 8.51 0.00 37.24 3.53
5678 10037 2.774234 AGGATCATCAGAATCACCCGTT 59.226 45.455 0.00 0.00 0.00 4.44
5692 10060 4.079558 AGTCTTGTGCCCAAATAGGATCAT 60.080 41.667 0.00 0.00 41.22 2.45
5805 10180 4.468153 GGTGTGGTCTCTTTCCTCTTCTAT 59.532 45.833 0.00 0.00 0.00 1.98
5808 10183 2.368875 TGGTGTGGTCTCTTTCCTCTTC 59.631 50.000 0.00 0.00 0.00 2.87
5826 10201 3.905968 TGGATGCTTGAATGATCATGGT 58.094 40.909 9.46 0.00 34.96 3.55
5867 10242 1.339535 CCTGAAACTCCCTTGCCTCTC 60.340 57.143 0.00 0.00 0.00 3.20
5873 10248 2.230660 GACAACCCTGAAACTCCCTTG 58.769 52.381 0.00 0.00 0.00 3.61
5894 10269 2.478894 AGTGTCGTCGCCATTTGTTTAG 59.521 45.455 0.00 0.00 0.00 1.85
5918 10293 9.443283 GATTTTCCTATCGTCATTTTGATTCTG 57.557 33.333 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.