Multiple sequence alignment - TraesCS7D01G134000

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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 TraesCS7D01G134000 chr7D 100.000 3009 0 0 2964 5972 85204272 85207280 0.000000e+00 5557.0
1 TraesCS7D01G134000 chr7D 100.000 2631 0 0 1 2631 85201309 85203939 0.000000e+00 4859.0
2 TraesCS7D01G134000 chr7D 83.871 403 35 15 5359 5754 84803036 84803415 2.050000e-94 357.0
3 TraesCS7D01G134000 chr7B 90.545 2570 124 50 23 2536 34707707 34710213 0.000000e+00 3290.0
4 TraesCS7D01G134000 chr7B 93.025 1405 74 12 3580 4972 34710821 34712213 0.000000e+00 2030.0
5 TraesCS7D01G134000 chr7B 88.325 591 55 9 5384 5964 34821678 34822264 0.000000e+00 697.0
6 TraesCS7D01G134000 chr7B 86.835 395 27 11 5363 5754 34516441 34516813 9.260000e-113 418.0
7 TraesCS7D01G134000 chr7B 84.901 404 28 14 5359 5754 34497401 34497779 1.570000e-100 377.0
8 TraesCS7D01G134000 chr7B 86.243 189 14 7 5123 5301 34712292 34712478 1.700000e-45 195.0
9 TraesCS7D01G134000 chr7B 84.906 159 19 3 3085 3238 289354218 289354060 8.010000e-34 156.0
10 TraesCS7D01G134000 chr7B 86.777 121 15 1 5494 5613 34990499 34990619 3.750000e-27 134.0
11 TraesCS7D01G134000 chr7A 90.602 2160 99 47 2964 5101 86225321 86227398 0.000000e+00 2769.0
12 TraesCS7D01G134000 chr7A 87.540 1260 80 34 686 1923 86223144 86224348 0.000000e+00 1386.0
13 TraesCS7D01G134000 chr7A 92.244 722 46 10 5148 5861 86227393 86228112 0.000000e+00 1014.0
14 TraesCS7D01G134000 chr7A 88.822 501 32 9 123 604 86222618 86223113 1.430000e-165 593.0
15 TraesCS7D01G134000 chr7A 91.268 355 23 5 2090 2444 86224640 86224986 1.510000e-130 477.0
16 TraesCS7D01G134000 chr7A 92.105 266 18 1 5702 5964 86228001 86228266 7.310000e-99 372.0
17 TraesCS7D01G134000 chr7A 82.586 379 30 14 5377 5754 85964811 85965154 9.730000e-78 302.0
18 TraesCS7D01G134000 chr7A 90.647 139 6 4 1925 2062 86224510 86224642 1.710000e-40 178.0
19 TraesCS7D01G134000 chr7A 90.551 127 7 4 2446 2567 86225070 86225196 4.790000e-36 163.0
20 TraesCS7D01G134000 chr7A 82.635 167 26 3 5506 5670 86426086 86426251 1.730000e-30 145.0
21 TraesCS7D01G134000 chr2D 87.805 287 14 4 214 482 570257868 570257585 3.470000e-82 316.0
22 TraesCS7D01G134000 chr2D 89.542 153 9 3 33 184 570258009 570257863 2.840000e-43 187.0
23 TraesCS7D01G134000 chr2D 83.784 148 22 2 4292 4438 353160614 353160760 8.070000e-29 139.0
24 TraesCS7D01G134000 chr3B 77.449 439 62 23 3090 3517 6966477 6966889 1.670000e-55 228.0
25 TraesCS7D01G134000 chr3D 80.546 293 35 16 3089 3360 32288470 32288179 7.850000e-49 206.0
26 TraesCS7D01G134000 chr3D 93.233 133 6 2 350 482 73653051 73653180 6.110000e-45 193.0
27 TraesCS7D01G134000 chr6A 83.628 226 21 4 3089 3309 536430414 536430200 1.310000e-46 198.0
28 TraesCS7D01G134000 chr2B 76.952 269 44 13 4166 4419 419628029 419628294 2.900000e-28 137.0
29 TraesCS7D01G134000 chr4A 84.444 90 14 0 3439 3528 685828604 685828693 8.240000e-14 89.8


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 TraesCS7D01G134000 chr7D 85201309 85207280 5971 False 5208.000000 5557 100.000000 1 5972 2 chr7D.!!$F2 5971
1 TraesCS7D01G134000 chr7B 34707707 34712478 4771 False 1838.333333 3290 89.937667 23 5301 3 chr7B.!!$F5 5278
2 TraesCS7D01G134000 chr7B 34821678 34822264 586 False 697.000000 697 88.325000 5384 5964 1 chr7B.!!$F3 580
3 TraesCS7D01G134000 chr7A 86222618 86228266 5648 False 869.000000 2769 90.472375 123 5964 8 chr7A.!!$F3 5841

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
791 838 0.602562 CATCGATCTCCCTCTGCCTC 59.397 60.0 0.00 0.0 0.0 4.70 F
2088 2327 0.038526 CAGGTTCGGCGTCTACAGTT 60.039 55.0 6.85 0.0 0.0 3.16 F
3430 3815 0.032017 GCTGGGAGGAGGAGGTAGAA 60.032 60.0 0.00 0.0 0.0 2.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2589 2920 0.108138 GAGGACAATCGTGGGAGTGG 60.108 60.0 0.0 0.0 42.35 4.00 R
3514 3899 0.030369 GGCTATACGTCGGTCCACTG 59.970 60.0 0.0 0.0 0.00 3.66 R
5098 5790 0.178533 ACGGTCGTCCACCTTTCAAA 59.821 50.0 0.0 0.0 44.21 2.69 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
65 66 4.521130 TGAGTGGCTACAAACTGAGTAG 57.479 45.455 2.02 0.00 41.41 2.57
212 224 9.347240 CCTTACTTAAAGTGGATCATCATTCAT 57.653 33.333 0.00 0.00 32.89 2.57
286 298 2.496070 CACGTAATCAGACCTCTCCCAA 59.504 50.000 0.00 0.00 0.00 4.12
287 299 2.761208 ACGTAATCAGACCTCTCCCAAG 59.239 50.000 0.00 0.00 0.00 3.61
288 300 3.024547 CGTAATCAGACCTCTCCCAAGA 58.975 50.000 0.00 0.00 0.00 3.02
289 301 3.447586 CGTAATCAGACCTCTCCCAAGAA 59.552 47.826 0.00 0.00 0.00 2.52
302 328 6.550108 CCTCTCCCAAGAATCATTCATTCATT 59.450 38.462 0.00 0.00 43.27 2.57
393 419 2.960659 CTCGCGATCTGCTGCCAG 60.961 66.667 10.36 0.00 43.27 4.85
413 439 2.689771 ATCCCCCACACCCCGTAC 60.690 66.667 0.00 0.00 0.00 3.67
415 441 3.712907 CCCCCACACCCCGTACAG 61.713 72.222 0.00 0.00 0.00 2.74
516 545 1.342496 TCATCGTCTCATCATGGAGCC 59.658 52.381 0.00 0.00 34.84 4.70
604 635 2.529780 TTGATGGGTACGTTCGTGTT 57.470 45.000 8.14 0.00 0.00 3.32
605 636 3.657015 TTGATGGGTACGTTCGTGTTA 57.343 42.857 8.14 0.00 0.00 2.41
606 637 3.872511 TGATGGGTACGTTCGTGTTAT 57.127 42.857 8.14 0.00 0.00 1.89
607 638 3.772932 TGATGGGTACGTTCGTGTTATC 58.227 45.455 8.14 7.24 0.00 1.75
608 639 2.261037 TGGGTACGTTCGTGTTATCG 57.739 50.000 8.14 0.00 0.00 2.92
609 640 1.539388 TGGGTACGTTCGTGTTATCGT 59.461 47.619 8.14 0.00 39.74 3.73
610 641 1.913403 GGGTACGTTCGTGTTATCGTG 59.087 52.381 8.14 0.00 37.66 4.35
611 642 2.584791 GGTACGTTCGTGTTATCGTGT 58.415 47.619 8.14 0.00 37.66 4.49
673 708 5.834239 CATCCATGCTTTTCTTGTTGTTC 57.166 39.130 0.00 0.00 0.00 3.18
689 724 5.788450 TGTTGTTCTTGTCATGGTTTGTTT 58.212 33.333 0.00 0.00 0.00 2.83
722 758 8.589701 TTTTTCAAATAAGATTAGGAGGGACC 57.410 34.615 0.00 0.00 39.35 4.46
725 761 6.841601 TCAAATAAGATTAGGAGGGACCATG 58.158 40.000 0.00 0.00 42.04 3.66
734 770 3.254960 AGGAGGGACCATGGAATAGATG 58.745 50.000 21.47 0.00 42.04 2.90
756 792 6.985653 TGGTCTTTTTCCACCATTAAATGA 57.014 33.333 0.00 0.00 37.78 2.57
776 815 3.127376 TGATGTGAATGAAGGCAACATCG 59.873 43.478 8.95 0.00 37.01 3.84
777 816 2.777094 TGTGAATGAAGGCAACATCGA 58.223 42.857 0.00 0.00 37.01 3.59
778 817 3.346315 TGTGAATGAAGGCAACATCGAT 58.654 40.909 0.00 0.00 37.01 3.59
779 818 3.374988 TGTGAATGAAGGCAACATCGATC 59.625 43.478 0.00 0.00 37.01 3.69
791 838 0.602562 CATCGATCTCCCTCTGCCTC 59.397 60.000 0.00 0.00 0.00 4.70
874 921 4.683501 TTGATGTGACATTGTTCATCCG 57.316 40.909 21.70 0.00 36.75 4.18
1173 1220 2.444706 CGGAGGGGATCAGGCTCA 60.445 66.667 0.00 0.00 0.00 4.26
1296 1343 2.047844 GTCAGCGCTCTCTGGCAA 60.048 61.111 7.13 0.00 38.50 4.52
1414 1464 2.258591 CGTCCGTGGAGGTGAGTG 59.741 66.667 0.44 0.00 41.99 3.51
1415 1465 2.561956 CGTCCGTGGAGGTGAGTGT 61.562 63.158 0.44 0.00 41.99 3.55
1416 1466 1.746517 GTCCGTGGAGGTGAGTGTT 59.253 57.895 0.00 0.00 41.99 3.32
1417 1467 0.600255 GTCCGTGGAGGTGAGTGTTG 60.600 60.000 0.00 0.00 41.99 3.33
1418 1468 1.961277 CCGTGGAGGTGAGTGTTGC 60.961 63.158 0.00 0.00 34.51 4.17
1419 1469 1.961277 CGTGGAGGTGAGTGTTGCC 60.961 63.158 0.00 0.00 0.00 4.52
1420 1470 1.148273 GTGGAGGTGAGTGTTGCCA 59.852 57.895 0.00 0.00 0.00 4.92
1421 1471 1.148273 TGGAGGTGAGTGTTGCCAC 59.852 57.895 0.00 0.00 42.17 5.01
1424 1474 3.660111 GGTGAGTGTTGCCACCGC 61.660 66.667 0.00 0.00 42.73 5.68
1425 1475 3.660111 GTGAGTGTTGCCACCGCC 61.660 66.667 0.00 0.00 42.88 6.13
1445 1495 4.016706 CCGGTGGGTTCTTCCGCT 62.017 66.667 0.00 0.00 42.48 5.52
1448 1498 2.281484 GTGGGTTCTTCCGCTGCA 60.281 61.111 0.00 0.00 37.00 4.41
1449 1499 2.281484 TGGGTTCTTCCGCTGCAC 60.281 61.111 0.00 0.00 37.00 4.57
1457 1507 1.134818 TCTTCCGCTGCACGTATCATT 60.135 47.619 0.00 0.00 41.42 2.57
1468 1518 3.666001 CACGTATCATTAACCGTGTTGC 58.334 45.455 0.00 0.00 44.04 4.17
1470 1520 3.998341 ACGTATCATTAACCGTGTTGCTT 59.002 39.130 0.00 0.00 31.43 3.91
1471 1521 4.092383 ACGTATCATTAACCGTGTTGCTTC 59.908 41.667 0.00 0.00 31.43 3.86
1472 1522 3.740044 ATCATTAACCGTGTTGCTTCG 57.260 42.857 0.23 0.00 0.00 3.79
1552 1602 0.322546 GGAGCAAGGTGGTTTCGGAT 60.323 55.000 0.00 0.00 0.00 4.18
1605 1655 1.940883 CTGAGCAATGCCGGCACAAT 61.941 55.000 35.50 18.99 31.64 2.71
1651 1701 8.565896 TGATTTACTCATCTGCACAACTATTT 57.434 30.769 0.00 0.00 0.00 1.40
1670 1720 5.717078 ATTTGTGACATTGTTGATCTGCT 57.283 34.783 0.00 0.00 0.00 4.24
1698 1748 8.882415 TTTCGAAAGATAGGAAATAATACGCT 57.118 30.769 6.47 0.00 41.60 5.07
1716 1766 2.552315 CGCTTACATTTTCCACACCACT 59.448 45.455 0.00 0.00 0.00 4.00
1721 1771 6.622896 GCTTACATTTTCCACACCACTCATAC 60.623 42.308 0.00 0.00 0.00 2.39
1739 1789 5.504853 TCATACGGATCTGCTCATCTATCT 58.495 41.667 0.00 0.00 0.00 1.98
1740 1790 5.948758 TCATACGGATCTGCTCATCTATCTT 59.051 40.000 0.00 0.00 0.00 2.40
1741 1791 7.112779 TCATACGGATCTGCTCATCTATCTTA 58.887 38.462 0.00 0.00 0.00 2.10
1742 1792 7.611855 TCATACGGATCTGCTCATCTATCTTAA 59.388 37.037 0.00 0.00 0.00 1.85
1792 1846 8.302438 GGTACCTCACACATATAGTATTGTACC 58.698 40.741 4.06 0.00 0.00 3.34
1847 1910 2.665519 CGACACTAAACATGGCTTGCAC 60.666 50.000 0.00 0.00 0.00 4.57
2063 2302 6.018180 GCACCTCGTTAAAATTAGGAGTATGG 60.018 42.308 0.00 0.00 33.16 2.74
2084 2323 2.508663 GGCAGGTTCGGCGTCTAC 60.509 66.667 6.85 3.86 0.00 2.59
2086 2325 1.805945 GCAGGTTCGGCGTCTACAG 60.806 63.158 6.85 2.40 0.00 2.74
2088 2327 0.038526 CAGGTTCGGCGTCTACAGTT 60.039 55.000 6.85 0.00 0.00 3.16
2092 2331 2.601763 GGTTCGGCGTCTACAGTTTATG 59.398 50.000 6.85 0.00 0.00 1.90
2096 2335 3.043586 CGGCGTCTACAGTTTATGCTAG 58.956 50.000 0.00 0.00 0.00 3.42
2123 2362 2.417257 TATGCGGCGTCGGTAGGTT 61.417 57.895 13.05 0.00 36.79 3.50
2146 2385 1.493134 GGCGGCGTAAAGTAATCGGG 61.493 60.000 9.37 0.00 0.00 5.14
2202 2441 2.203070 ATGGCAGATTCGGCGGTC 60.203 61.111 7.21 6.04 0.00 4.79
2242 2481 3.883830 TGTGTTTTCAATTGGTGTGCT 57.116 38.095 5.42 0.00 0.00 4.40
2293 2532 1.914634 CCTCAGATACGACTGTGTGC 58.085 55.000 0.00 0.00 38.79 4.57
2401 2645 6.925165 CCTTAATTCAGTGAACTTGCATGTTT 59.075 34.615 17.99 1.26 0.00 2.83
2413 2657 0.373716 GCATGTTTGATCGGACGGAC 59.626 55.000 0.00 0.00 0.00 4.79
2459 2785 0.243636 GACTGCATTTTTGGGACCGG 59.756 55.000 0.00 0.00 0.00 5.28
2527 2858 4.363999 GTCTGTTAGATCTCCATCCAACG 58.636 47.826 0.00 0.00 34.37 4.10
2567 2898 1.697432 TGTTCATGTTCTTCCTCCCGT 59.303 47.619 0.00 0.00 0.00 5.28
2578 2909 4.020617 CTCCCGTGCTGCCCTTCA 62.021 66.667 0.00 0.00 0.00 3.02
2579 2910 3.965539 CTCCCGTGCTGCCCTTCAG 62.966 68.421 0.00 0.00 45.62 3.02
2586 2917 3.930504 CTGCCCTTCAGCCCATTC 58.069 61.111 0.00 0.00 35.78 2.67
2587 2918 2.045045 TGCCCTTCAGCCCATTCG 60.045 61.111 0.00 0.00 0.00 3.34
2991 3322 2.786495 CGCCTAGGACGCCACATCT 61.786 63.158 14.75 0.00 0.00 2.90
3002 3333 2.178273 CACATCTCGCGGACGACA 59.822 61.111 6.13 0.00 45.12 4.35
3006 3337 3.685214 ATCTCGCGGACGACACAGC 62.685 63.158 6.13 0.00 45.12 4.40
3011 3342 4.406173 CGGACGACACAGCGAGCT 62.406 66.667 0.00 0.00 34.83 4.09
3030 3361 1.079405 GCGTCGTCCCCATCTTCAA 60.079 57.895 0.00 0.00 0.00 2.69
3073 3453 2.853003 GGCTTCGTCTAAATCGACTGAC 59.147 50.000 0.00 0.00 37.05 3.51
3080 3460 4.106197 GTCTAAATCGACTGACGCTTGAT 58.894 43.478 0.00 0.00 42.26 2.57
3121 3506 8.988934 GCTATACATCAGTGAAAATCCGATTTA 58.011 33.333 6.79 0.00 0.00 1.40
3123 3508 6.683974 ACATCAGTGAAAATCCGATTTAGG 57.316 37.500 6.79 0.00 0.00 2.69
3131 3516 4.730949 AAATCCGATTTAGGTCAGTCGA 57.269 40.909 4.46 0.00 36.25 4.20
3141 3526 5.593679 TTAGGTCAGTCGATTTTCCCTAG 57.406 43.478 0.00 0.00 0.00 3.02
3142 3527 3.709587 AGGTCAGTCGATTTTCCCTAGA 58.290 45.455 0.00 0.00 0.00 2.43
3143 3528 4.094476 AGGTCAGTCGATTTTCCCTAGAA 58.906 43.478 0.00 0.00 0.00 2.10
3144 3529 4.160626 AGGTCAGTCGATTTTCCCTAGAAG 59.839 45.833 0.00 0.00 32.35 2.85
3145 3530 4.159879 GGTCAGTCGATTTTCCCTAGAAGA 59.840 45.833 0.00 0.00 32.35 2.87
3146 3531 5.337330 GGTCAGTCGATTTTCCCTAGAAGAA 60.337 44.000 0.00 0.00 32.35 2.52
3147 3532 6.164176 GTCAGTCGATTTTCCCTAGAAGAAA 58.836 40.000 0.00 0.00 32.35 2.52
3148 3533 6.311690 GTCAGTCGATTTTCCCTAGAAGAAAG 59.688 42.308 7.64 0.00 34.84 2.62
3149 3534 5.582665 CAGTCGATTTTCCCTAGAAGAAAGG 59.417 44.000 7.64 0.00 34.84 3.11
3150 3535 5.484290 AGTCGATTTTCCCTAGAAGAAAGGA 59.516 40.000 7.64 5.44 36.08 3.36
3151 3536 6.157123 AGTCGATTTTCCCTAGAAGAAAGGAT 59.843 38.462 7.64 1.87 36.08 3.24
3152 3537 6.258947 GTCGATTTTCCCTAGAAGAAAGGATG 59.741 42.308 7.64 2.43 36.08 3.51
3165 3550 2.272146 GGATGCGCCTGAGGGAAA 59.728 61.111 4.18 0.00 33.58 3.13
3172 3557 1.731720 CGCCTGAGGGAAAGAAGAAG 58.268 55.000 0.00 0.00 33.58 2.85
3177 3562 2.571202 CTGAGGGAAAGAAGAAGGAGCT 59.429 50.000 0.00 0.00 0.00 4.09
3183 3568 0.399454 AAGAAGAAGGAGCTGCAGCA 59.601 50.000 38.24 0.00 45.16 4.41
3228 3613 7.394816 ACCCCATTATCTATCTTATGGTTTCG 58.605 38.462 0.00 0.00 36.61 3.46
3231 3616 6.316390 CCATTATCTATCTTATGGTTTCGGGC 59.684 42.308 0.00 0.00 34.23 6.13
3233 3618 2.960384 TCTATCTTATGGTTTCGGGCGA 59.040 45.455 0.00 0.00 0.00 5.54
3261 3646 2.597510 GGGGTGGTGGTGCACTTC 60.598 66.667 17.98 9.86 34.40 3.01
3264 3649 2.591715 GTGGTGGTGCACTTCGCT 60.592 61.111 17.98 0.00 43.06 4.93
3426 3811 3.547787 AACGCTGGGAGGAGGAGGT 62.548 63.158 0.00 0.00 0.00 3.85
3428 3813 1.830408 CGCTGGGAGGAGGAGGTAG 60.830 68.421 0.00 0.00 0.00 3.18
3429 3814 1.621377 GCTGGGAGGAGGAGGTAGA 59.379 63.158 0.00 0.00 0.00 2.59
3430 3815 0.032017 GCTGGGAGGAGGAGGTAGAA 60.032 60.000 0.00 0.00 0.00 2.10
3431 3816 2.032151 GCTGGGAGGAGGAGGTAGAAG 61.032 61.905 0.00 0.00 0.00 2.85
3432 3817 1.571457 CTGGGAGGAGGAGGTAGAAGA 59.429 57.143 0.00 0.00 0.00 2.87
3433 3818 2.008400 TGGGAGGAGGAGGTAGAAGAA 58.992 52.381 0.00 0.00 0.00 2.52
3434 3819 2.592512 TGGGAGGAGGAGGTAGAAGAAT 59.407 50.000 0.00 0.00 0.00 2.40
3435 3820 3.014110 TGGGAGGAGGAGGTAGAAGAATT 59.986 47.826 0.00 0.00 0.00 2.17
3436 3821 3.389656 GGGAGGAGGAGGTAGAAGAATTG 59.610 52.174 0.00 0.00 0.00 2.32
3437 3822 3.181459 GGAGGAGGAGGTAGAAGAATTGC 60.181 52.174 0.00 0.00 0.00 3.56
3438 3823 3.452627 GAGGAGGAGGTAGAAGAATTGCA 59.547 47.826 0.00 0.00 0.00 4.08
3439 3824 3.454082 AGGAGGAGGTAGAAGAATTGCAG 59.546 47.826 0.00 0.00 0.00 4.41
3440 3825 3.432890 GGAGGAGGTAGAAGAATTGCAGG 60.433 52.174 0.00 0.00 0.00 4.85
3441 3826 3.452627 GAGGAGGTAGAAGAATTGCAGGA 59.547 47.826 0.00 0.00 0.00 3.86
3442 3827 3.454082 AGGAGGTAGAAGAATTGCAGGAG 59.546 47.826 0.00 0.00 0.00 3.69
3453 3838 1.734655 TTGCAGGAGGAAGAAGGACT 58.265 50.000 0.00 0.00 0.00 3.85
3455 3840 0.392327 GCAGGAGGAAGAAGGACTGC 60.392 60.000 0.00 0.00 43.50 4.40
3465 3850 3.310860 AAGGACTGCGGGCCGTTAG 62.311 63.158 28.82 26.05 0.00 2.34
3478 3863 1.336056 GCCGTTAGATCTCCATCCGAC 60.336 57.143 0.00 0.00 0.00 4.79
3486 3871 2.704464 TCTCCATCCGACGTCTAGAA 57.296 50.000 14.70 0.00 0.00 2.10
3514 3899 4.274950 TCGACTGACCCAATTTCAGAAAAC 59.725 41.667 11.68 1.72 42.81 2.43
3515 3900 4.036262 CGACTGACCCAATTTCAGAAAACA 59.964 41.667 11.68 0.00 42.81 2.83
3516 3901 5.520376 ACTGACCCAATTTCAGAAAACAG 57.480 39.130 11.68 6.02 42.81 3.16
3517 3902 4.956075 ACTGACCCAATTTCAGAAAACAGT 59.044 37.500 11.68 6.55 42.81 3.55
3518 3903 5.163519 ACTGACCCAATTTCAGAAAACAGTG 60.164 40.000 11.68 0.00 42.81 3.66
3519 3904 4.099266 TGACCCAATTTCAGAAAACAGTGG 59.901 41.667 0.00 5.65 0.00 4.00
3520 3905 4.285863 ACCCAATTTCAGAAAACAGTGGA 58.714 39.130 15.14 0.00 30.78 4.02
3521 3906 4.099419 ACCCAATTTCAGAAAACAGTGGAC 59.901 41.667 15.14 0.00 30.78 4.02
3522 3907 4.501400 CCCAATTTCAGAAAACAGTGGACC 60.501 45.833 15.14 0.00 30.78 4.46
3523 3908 4.290155 CAATTTCAGAAAACAGTGGACCG 58.710 43.478 0.00 0.00 0.00 4.79
3524 3909 2.992124 TTCAGAAAACAGTGGACCGA 57.008 45.000 0.00 0.00 0.00 4.69
3525 3910 2.234300 TCAGAAAACAGTGGACCGAC 57.766 50.000 0.00 0.00 0.00 4.79
3526 3911 0.859232 CAGAAAACAGTGGACCGACG 59.141 55.000 0.00 0.00 0.00 5.12
3527 3912 0.462789 AGAAAACAGTGGACCGACGT 59.537 50.000 0.00 0.00 0.00 4.34
3539 3924 1.949525 GACCGACGTATAGCCTAACCA 59.050 52.381 0.00 0.00 0.00 3.67
3617 4290 7.585286 TGATACGTCCACACTAAACAAATAC 57.415 36.000 0.00 0.00 0.00 1.89
3654 4329 1.447489 GAGCAGCATGAGCACGACT 60.447 57.895 12.28 0.00 45.49 4.18
3855 4531 0.965866 TCGTCAGAGTCCTCGGCAAT 60.966 55.000 0.00 0.00 34.09 3.56
4125 4801 3.213402 CGGAGGGCGGAGAGAGTC 61.213 72.222 0.00 0.00 0.00 3.36
4353 5029 0.747283 GGGTCCAGATGAAGCTGCTG 60.747 60.000 1.35 0.00 34.56 4.41
4447 5123 2.437359 CCAAGAAGCAGGGCCTCG 60.437 66.667 0.95 0.00 0.00 4.63
4452 5128 3.672295 GAAGCAGGGCCTCGTGGAG 62.672 68.421 0.95 0.00 34.57 3.86
4560 5242 1.359848 ATGGAATCGCTCGTGTTGAC 58.640 50.000 0.00 0.00 0.00 3.18
4575 5257 0.750249 TTGACGTCAGCAAGAGGACA 59.250 50.000 19.11 0.00 35.59 4.02
4580 5262 1.011451 GTCAGCAAGAGGACAGACGC 61.011 60.000 0.00 0.00 34.22 5.19
4584 5266 0.108424 GCAAGAGGACAGACGCAGAT 60.108 55.000 0.00 0.00 0.00 2.90
4691 5379 4.928398 CTGGAGCTACAGCACTGG 57.072 61.111 14.40 0.00 45.16 4.00
4717 5405 3.204526 GCTTCCAAGGAGATGATGACAG 58.795 50.000 0.00 0.00 0.00 3.51
4760 5448 3.319198 GGACAGCAGGGGAACGGA 61.319 66.667 0.00 0.00 0.00 4.69
4763 5451 1.229082 ACAGCAGGGGAACGGAGTA 60.229 57.895 0.00 0.00 45.00 2.59
4767 5455 3.446570 AGGGGAACGGAGTACGCG 61.447 66.667 3.53 3.53 45.00 6.01
4815 5503 0.042731 TGGAGGAATCGGAAGGAGGT 59.957 55.000 0.00 0.00 0.00 3.85
4817 5505 0.386113 GAGGAATCGGAAGGAGGTCG 59.614 60.000 0.00 0.00 0.00 4.79
4980 5668 2.295253 ATACGGCCTGAGAGAAAACG 57.705 50.000 0.00 0.00 0.00 3.60
5021 5709 0.598680 GGAGCGATGAGTTGGATCGG 60.599 60.000 0.00 0.00 42.42 4.18
5025 5713 1.290203 CGATGAGTTGGATCGGTTGG 58.710 55.000 0.00 0.00 39.23 3.77
5077 5769 1.897560 CTTGTGGGTTCAGTCTTCCC 58.102 55.000 0.00 0.00 41.41 3.97
5094 5786 1.084289 CCCGGACGACCATTCTTTTC 58.916 55.000 0.73 0.00 35.59 2.29
5095 5787 1.338769 CCCGGACGACCATTCTTTTCT 60.339 52.381 0.73 0.00 35.59 2.52
5096 5788 2.423577 CCGGACGACCATTCTTTTCTT 58.576 47.619 0.00 0.00 35.59 2.52
5097 5789 2.812011 CCGGACGACCATTCTTTTCTTT 59.188 45.455 0.00 0.00 35.59 2.52
5098 5790 3.252458 CCGGACGACCATTCTTTTCTTTT 59.748 43.478 0.00 0.00 35.59 2.27
5099 5791 4.261447 CCGGACGACCATTCTTTTCTTTTT 60.261 41.667 0.00 0.00 35.59 1.94
5122 5814 4.764896 GGTGGACGACCGTTCTTT 57.235 55.556 2.33 0.00 39.42 2.52
5123 5815 2.996444 GGTGGACGACCGTTCTTTT 58.004 52.632 2.33 0.00 39.42 2.27
5124 5816 0.863799 GGTGGACGACCGTTCTTTTC 59.136 55.000 2.33 0.00 39.42 2.29
5125 5817 1.539712 GGTGGACGACCGTTCTTTTCT 60.540 52.381 2.33 0.00 39.42 2.52
5126 5818 2.207590 GTGGACGACCGTTCTTTTCTT 58.792 47.619 2.33 0.00 39.42 2.52
5127 5819 2.610833 GTGGACGACCGTTCTTTTCTTT 59.389 45.455 2.33 0.00 39.42 2.52
5128 5820 3.064408 GTGGACGACCGTTCTTTTCTTTT 59.936 43.478 2.33 0.00 39.42 2.27
5129 5821 3.690628 TGGACGACCGTTCTTTTCTTTTT 59.309 39.130 2.33 0.00 39.42 1.94
5161 5853 4.571176 GGACGACCATTCTTTCATAGGAAC 59.429 45.833 0.00 0.00 35.97 3.62
5381 6083 3.469739 TGATCAGATGTGCGCAATATGT 58.530 40.909 14.00 5.59 0.00 2.29
5386 6088 3.747529 CAGATGTGCGCAATATGTCCATA 59.252 43.478 14.00 0.00 0.00 2.74
5423 6126 7.977490 ACTATAATATCACGAAGCATCATCG 57.023 36.000 0.00 0.00 45.47 3.84
5532 6236 3.277142 AGCGTTTGGAAATAGTAGGGG 57.723 47.619 0.00 0.00 0.00 4.79
5580 6284 5.573146 CGAAAAGCTAGGAATTTAAGCTGG 58.427 41.667 9.94 0.15 45.61 4.85
5588 6292 2.169144 GGAATTTAAGCTGGCTGGCATT 59.831 45.455 3.74 0.00 34.17 3.56
5617 6322 0.311790 AAGCTGGTGTTGAATGTGCG 59.688 50.000 0.00 0.00 0.00 5.34
5666 6371 4.164988 CCTGGACCACTAGAGGATTCATTT 59.835 45.833 13.71 0.00 0.00 2.32
5682 6387 0.674895 ATTTGGAGCAGCAGTCGGTC 60.675 55.000 0.00 0.00 0.00 4.79
5720 6425 0.883833 CACTGGCCACATCCTGTTTC 59.116 55.000 0.00 0.00 36.34 2.78
5729 6434 3.539604 CACATCCTGTTTCATCTCCTCC 58.460 50.000 0.00 0.00 0.00 4.30
5746 6451 2.163815 CCTCCTTTTCATCAGCTGCAAG 59.836 50.000 9.47 5.74 0.00 4.01
5802 6558 4.374399 CTTTTCATCAGCTGCAAACCTTT 58.626 39.130 9.47 0.00 0.00 3.11
5817 6573 1.308069 CCTTTCACTGGCCACATCCG 61.308 60.000 0.00 0.00 0.00 4.18
5839 6598 5.182001 CCGGTTTGATCTCTTTTTCATCAGT 59.818 40.000 0.00 0.00 0.00 3.41
5841 6600 7.094805 CCGGTTTGATCTCTTTTTCATCAGTTA 60.095 37.037 0.00 0.00 0.00 2.24
5842 6601 7.959651 CGGTTTGATCTCTTTTTCATCAGTTAG 59.040 37.037 0.00 0.00 0.00 2.34
5930 6693 4.937620 GGTTCTCACTTGCAATAGATGTGA 59.062 41.667 15.26 15.26 36.42 3.58
5964 6727 3.099141 CCATGCCATTTCCCTAACAAGT 58.901 45.455 0.00 0.00 0.00 3.16
5965 6728 4.264172 ACCATGCCATTTCCCTAACAAGTA 60.264 41.667 0.00 0.00 0.00 2.24
5966 6729 4.097892 CCATGCCATTTCCCTAACAAGTAC 59.902 45.833 0.00 0.00 0.00 2.73
5967 6730 4.374689 TGCCATTTCCCTAACAAGTACA 57.625 40.909 0.00 0.00 0.00 2.90
5968 6731 4.076394 TGCCATTTCCCTAACAAGTACAC 58.924 43.478 0.00 0.00 0.00 2.90
5969 6732 4.076394 GCCATTTCCCTAACAAGTACACA 58.924 43.478 0.00 0.00 0.00 3.72
5970 6733 4.705023 GCCATTTCCCTAACAAGTACACAT 59.295 41.667 0.00 0.00 0.00 3.21
5971 6734 5.883673 GCCATTTCCCTAACAAGTACACATA 59.116 40.000 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 9.899661 TGTAGCCACTCAAAAATATAATACAGT 57.100 29.630 0.00 0.00 0.00 3.55
44 45 4.521130 CTACTCAGTTTGTAGCCACTCA 57.479 45.455 0.00 0.00 32.29 3.41
71 72 9.382275 TGTTGCATGCATATATTGGTAGTATAG 57.618 33.333 23.37 0.00 0.00 1.31
74 75 8.349245 GTTTGTTGCATGCATATATTGGTAGTA 58.651 33.333 23.37 0.00 0.00 1.82
75 76 6.957920 TTGTTGCATGCATATATTGGTAGT 57.042 33.333 23.37 0.00 0.00 2.73
76 77 6.642131 GGTTTGTTGCATGCATATATTGGTAG 59.358 38.462 23.37 0.00 0.00 3.18
134 138 0.734889 GGCCAACGAATCTGGACATG 59.265 55.000 0.00 0.00 42.14 3.21
135 139 0.744414 CGGCCAACGAATCTGGACAT 60.744 55.000 2.24 0.00 42.78 3.06
212 224 0.036388 GATTGGTCAGCCGGAGAACA 60.036 55.000 5.05 8.60 37.67 3.18
286 298 8.799367 TGTGTTTCTGAATGAATGAATGATTCT 58.201 29.630 6.73 0.00 41.16 2.40
287 299 8.975410 TGTGTTTCTGAATGAATGAATGATTC 57.025 30.769 0.00 0.00 40.99 2.52
288 300 9.767228 TTTGTGTTTCTGAATGAATGAATGATT 57.233 25.926 0.00 0.00 34.24 2.57
289 301 9.938280 ATTTGTGTTTCTGAATGAATGAATGAT 57.062 25.926 0.00 0.00 34.24 2.45
302 328 5.361427 TGTCGGACTAATTTGTGTTTCTGA 58.639 37.500 9.88 0.00 0.00 3.27
379 405 3.472943 ATCCCTGGCAGCAGATCGC 62.473 63.158 9.56 1.92 42.91 4.58
410 436 0.753262 AGGATGATGGACGCCTGTAC 59.247 55.000 0.00 0.00 0.00 2.90
413 439 4.451241 CAGGATGATGGACGCCTG 57.549 61.111 0.00 0.00 39.69 4.85
415 441 0.249657 GAGACAGGATGATGGACGCC 60.250 60.000 0.00 0.00 39.69 5.68
516 545 1.585668 CTGCGCAGTCTTAACTCATCG 59.414 52.381 29.24 0.00 31.71 3.84
656 687 5.964758 TGACAAGAACAACAAGAAAAGCAT 58.035 33.333 0.00 0.00 0.00 3.79
657 688 5.384063 TGACAAGAACAACAAGAAAAGCA 57.616 34.783 0.00 0.00 0.00 3.91
658 689 5.232838 CCATGACAAGAACAACAAGAAAAGC 59.767 40.000 0.00 0.00 0.00 3.51
659 690 6.332630 ACCATGACAAGAACAACAAGAAAAG 58.667 36.000 0.00 0.00 0.00 2.27
660 691 6.279513 ACCATGACAAGAACAACAAGAAAA 57.720 33.333 0.00 0.00 0.00 2.29
667 702 6.720012 AAAACAAACCATGACAAGAACAAC 57.280 33.333 0.00 0.00 0.00 3.32
673 708 5.542616 TTGCAAAAACAAACCATGACAAG 57.457 34.783 0.00 0.00 0.00 3.16
722 758 6.183360 GGTGGAAAAAGACCATCTATTCCATG 60.183 42.308 20.35 0.00 45.79 3.66
725 761 5.261216 TGGTGGAAAAAGACCATCTATTCC 58.739 41.667 12.92 12.92 40.35 3.01
734 770 7.331687 CACATCATTTAATGGTGGAAAAAGACC 59.668 37.037 20.52 0.00 45.62 3.85
749 785 6.990798 TGTTGCCTTCATTCACATCATTTAA 58.009 32.000 0.00 0.00 0.00 1.52
751 787 5.471556 TGTTGCCTTCATTCACATCATTT 57.528 34.783 0.00 0.00 0.00 2.32
754 790 3.127376 CGATGTTGCCTTCATTCACATCA 59.873 43.478 10.36 0.00 34.04 3.07
756 792 3.346315 TCGATGTTGCCTTCATTCACAT 58.654 40.909 0.00 0.00 0.00 3.21
776 815 1.398958 AAGCGAGGCAGAGGGAGATC 61.399 60.000 0.00 0.00 0.00 2.75
777 816 1.382420 AAGCGAGGCAGAGGGAGAT 60.382 57.895 0.00 0.00 0.00 2.75
778 817 2.038007 AAGCGAGGCAGAGGGAGA 59.962 61.111 0.00 0.00 0.00 3.71
779 818 1.612395 AAGAAGCGAGGCAGAGGGAG 61.612 60.000 0.00 0.00 0.00 4.30
791 838 5.220681 GCTTTACTGGAAGGAATAAGAAGCG 60.221 44.000 0.00 0.00 36.06 4.68
874 921 4.393371 GGAATCAAGAAGCAGTACTTGGAC 59.607 45.833 0.00 0.00 42.27 4.02
924 971 4.870991 GGTGTTAGGCTATGTCAAGAAGTC 59.129 45.833 0.00 0.00 0.00 3.01
926 973 4.832248 TGGTGTTAGGCTATGTCAAGAAG 58.168 43.478 0.00 0.00 0.00 2.85
984 1031 1.678635 CATTGCCGCCTTCCCTTCA 60.679 57.895 0.00 0.00 0.00 3.02
988 1035 3.830192 CAGCATTGCCGCCTTCCC 61.830 66.667 4.70 0.00 0.00 3.97
989 1036 2.751436 TCAGCATTGCCGCCTTCC 60.751 61.111 4.70 0.00 0.00 3.46
990 1037 2.768492 CCTCAGCATTGCCGCCTTC 61.768 63.158 4.70 0.00 0.00 3.46
1143 1190 4.778415 CTCCGGTGGAGCGACACG 62.778 72.222 0.00 0.00 43.29 4.49
1296 1343 2.040544 CAAGCCGCCCTCGTTCATT 61.041 57.895 0.00 0.00 0.00 2.57
1428 1478 4.016706 AGCGGAAGAACCCACCGG 62.017 66.667 0.00 0.00 45.66 5.28
1430 1480 3.056328 GCAGCGGAAGAACCCACC 61.056 66.667 0.00 0.00 34.64 4.61
1431 1481 2.281484 TGCAGCGGAAGAACCCAC 60.281 61.111 0.00 0.00 34.64 4.61
1432 1482 2.281484 GTGCAGCGGAAGAACCCA 60.281 61.111 0.00 0.00 34.64 4.51
1433 1483 2.775032 TACGTGCAGCGGAAGAACCC 62.775 60.000 0.00 0.00 46.52 4.11
1434 1484 0.739813 ATACGTGCAGCGGAAGAACC 60.740 55.000 0.00 0.00 46.52 3.62
1437 1487 0.459899 ATGATACGTGCAGCGGAAGA 59.540 50.000 0.00 0.00 46.52 2.87
1440 1490 2.198406 GTTAATGATACGTGCAGCGGA 58.802 47.619 0.00 5.06 46.52 5.54
1448 1498 3.592059 AGCAACACGGTTAATGATACGT 58.408 40.909 0.00 0.00 40.60 3.57
1449 1499 4.574759 GAAGCAACACGGTTAATGATACG 58.425 43.478 0.00 0.00 34.82 3.06
1468 1518 3.376234 ACATCATCATCAAACTGCCGAAG 59.624 43.478 0.00 0.00 0.00 3.79
1470 1520 2.989909 ACATCATCATCAAACTGCCGA 58.010 42.857 0.00 0.00 0.00 5.54
1471 1521 3.119743 ACAACATCATCATCAAACTGCCG 60.120 43.478 0.00 0.00 0.00 5.69
1472 1522 4.445452 ACAACATCATCATCAAACTGCC 57.555 40.909 0.00 0.00 0.00 4.85
1483 1533 3.312421 CCACATACGGGAACAACATCATC 59.688 47.826 0.00 0.00 0.00 2.92
1552 1602 2.914756 AATGGCGCCCATGATCAGCA 62.915 55.000 26.77 0.00 44.40 4.41
1605 1655 6.302535 TCAAGAGTTGATTAATTACCCCGA 57.697 37.500 0.00 0.00 34.08 5.14
1651 1701 5.518848 AAAAGCAGATCAACAATGTCACA 57.481 34.783 0.00 0.00 0.00 3.58
1698 1748 5.410132 CGTATGAGTGGTGTGGAAAATGTAA 59.590 40.000 0.00 0.00 0.00 2.41
1716 1766 5.504853 AGATAGATGAGCAGATCCGTATGA 58.495 41.667 0.00 0.00 0.00 2.15
1721 1771 8.465999 ACTAATTAAGATAGATGAGCAGATCCG 58.534 37.037 5.37 0.00 0.00 4.18
1792 1846 7.877097 CCCTATACCACTAGTAGTAGTACTGTG 59.123 44.444 18.75 20.36 39.96 3.66
1897 1968 5.045797 AGTTGGTTAGAAAGCCTAGTTAGGG 60.046 44.000 7.29 0.00 43.82 3.53
2006 2245 2.223572 GGCCTCGCCTAATCAAACAATG 60.224 50.000 0.00 0.00 46.69 2.82
2084 2323 7.556433 GCATACGTCTAAACTAGCATAAACTG 58.444 38.462 0.00 0.00 0.00 3.16
2086 2325 6.345565 CCGCATACGTCTAAACTAGCATAAAC 60.346 42.308 0.00 0.00 37.70 2.01
2088 2327 5.217393 CCGCATACGTCTAAACTAGCATAA 58.783 41.667 0.00 0.00 37.70 1.90
2092 2331 1.785430 GCCGCATACGTCTAAACTAGC 59.215 52.381 0.00 0.00 37.70 3.42
2096 2335 2.657336 ACGCCGCATACGTCTAAAC 58.343 52.632 0.00 0.00 40.28 2.01
2123 2362 0.108709 ATTACTTTACGCCGCCGTCA 60.109 50.000 0.00 0.00 46.39 4.35
2146 2385 2.681344 ACGGTCAAGTTCCAACTGAAAC 59.319 45.455 0.00 0.00 39.66 2.78
2202 2441 2.701073 AGTGTCAACTAACTCGGACG 57.299 50.000 0.00 0.00 33.79 4.79
2255 2494 0.747283 GCTGTCATGGCCCTCTTGAG 60.747 60.000 0.00 0.00 31.35 3.02
2401 2645 2.546778 GCATTTTAGTCCGTCCGATCA 58.453 47.619 0.00 0.00 0.00 2.92
2434 2678 4.379652 GTCCCAAAAATGCAGTCATGTTT 58.620 39.130 0.00 0.00 39.97 2.83
2444 2770 1.111277 ATAGCCGGTCCCAAAAATGC 58.889 50.000 1.90 0.00 0.00 3.56
2459 2785 7.807977 TTTTTCCAGGTGATAGATGAATAGC 57.192 36.000 0.00 0.00 0.00 2.97
2489 2815 4.404507 ACAGACCAAAATTCGATTGACG 57.595 40.909 0.00 0.00 44.09 4.35
2490 2816 7.129109 TCTAACAGACCAAAATTCGATTGAC 57.871 36.000 0.00 0.00 0.00 3.18
2491 2817 7.824289 AGATCTAACAGACCAAAATTCGATTGA 59.176 33.333 0.00 0.00 0.00 2.57
2492 2818 7.978982 AGATCTAACAGACCAAAATTCGATTG 58.021 34.615 0.00 0.00 0.00 2.67
2493 2819 7.281100 GGAGATCTAACAGACCAAAATTCGATT 59.719 37.037 0.00 0.00 0.00 3.34
2497 2823 7.012799 GGATGGAGATCTAACAGACCAAAATTC 59.987 40.741 0.00 0.00 0.00 2.17
2499 2825 6.069440 TGGATGGAGATCTAACAGACCAAAAT 60.069 38.462 17.80 0.42 0.00 1.82
2580 2911 3.727258 TGGGAGTGGCCGAATGGG 61.727 66.667 0.00 0.00 37.63 4.00
2581 2912 2.438434 GTGGGAGTGGCCGAATGG 60.438 66.667 0.00 0.00 37.63 3.16
2582 2913 2.593468 ATCGTGGGAGTGGCCGAATG 62.593 60.000 0.00 0.00 37.63 2.67
2583 2914 1.910580 AATCGTGGGAGTGGCCGAAT 61.911 55.000 0.00 0.00 37.63 3.34
2584 2915 2.589157 AATCGTGGGAGTGGCCGAA 61.589 57.895 0.00 0.00 37.63 4.30
2585 2916 3.000819 AATCGTGGGAGTGGCCGA 61.001 61.111 0.00 0.00 37.63 5.54
2586 2917 2.819595 CAATCGTGGGAGTGGCCG 60.820 66.667 0.00 0.00 34.72 6.13
2587 2918 1.745489 GACAATCGTGGGAGTGGCC 60.745 63.158 0.00 0.00 40.38 5.36
2589 2920 0.108138 GAGGACAATCGTGGGAGTGG 60.108 60.000 0.00 0.00 42.35 4.00
2591 2922 1.605058 CGGAGGACAATCGTGGGAGT 61.605 60.000 0.00 0.00 0.00 3.85
2593 2924 3.014085 GCGGAGGACAATCGTGGGA 62.014 63.158 0.00 0.00 0.00 4.37
2594 2925 2.511600 GCGGAGGACAATCGTGGG 60.512 66.667 0.00 0.00 0.00 4.61
2969 3300 3.458163 TGGCGTCCTAGGCGAAGG 61.458 66.667 23.94 6.98 39.82 3.46
2975 3306 1.360551 CGAGATGTGGCGTCCTAGG 59.639 63.158 0.82 0.82 0.00 3.02
2978 3309 4.498520 CGCGAGATGTGGCGTCCT 62.499 66.667 11.15 0.00 45.01 3.85
3008 3339 4.148825 GATGGGGACGACGCAGCT 62.149 66.667 4.20 0.00 45.87 4.24
3010 3341 1.519455 GAAGATGGGGACGACGCAG 60.519 63.158 4.20 0.00 45.87 5.18
3011 3342 1.822114 TTGAAGATGGGGACGACGCA 61.822 55.000 4.20 4.33 46.77 5.24
3012 3343 1.079405 TTGAAGATGGGGACGACGC 60.079 57.895 0.00 0.00 0.00 5.19
3013 3344 1.076533 CGTTGAAGATGGGGACGACG 61.077 60.000 0.00 0.00 35.90 5.12
3061 3441 5.856126 AAAATCAAGCGTCAGTCGATTTA 57.144 34.783 0.00 0.00 46.04 1.40
3114 3499 4.270325 GGAAAATCGACTGACCTAAATCGG 59.730 45.833 0.00 0.00 35.31 4.18
3121 3506 3.709587 TCTAGGGAAAATCGACTGACCT 58.290 45.455 0.00 0.00 0.00 3.85
3123 3508 5.326200 TCTTCTAGGGAAAATCGACTGAC 57.674 43.478 0.00 0.00 0.00 3.51
3131 3516 4.884164 CGCATCCTTTCTTCTAGGGAAAAT 59.116 41.667 11.07 3.45 33.17 1.82
3141 3526 1.012841 CTCAGGCGCATCCTTTCTTC 58.987 55.000 10.83 0.00 44.75 2.87
3142 3527 0.393537 CCTCAGGCGCATCCTTTCTT 60.394 55.000 10.83 0.00 44.75 2.52
3143 3528 1.222936 CCTCAGGCGCATCCTTTCT 59.777 57.895 10.83 0.00 44.75 2.52
3144 3529 1.821332 CCCTCAGGCGCATCCTTTC 60.821 63.158 10.83 0.00 44.75 2.62
3145 3530 1.852157 TTCCCTCAGGCGCATCCTTT 61.852 55.000 10.83 0.00 44.75 3.11
3146 3531 1.852157 TTTCCCTCAGGCGCATCCTT 61.852 55.000 10.83 0.00 44.75 3.36
3148 3533 1.821332 CTTTCCCTCAGGCGCATCC 60.821 63.158 10.83 0.00 0.00 3.51
3149 3534 0.392998 TTCTTTCCCTCAGGCGCATC 60.393 55.000 10.83 0.00 0.00 3.91
3150 3535 0.393537 CTTCTTTCCCTCAGGCGCAT 60.394 55.000 10.83 0.00 0.00 4.73
3151 3536 1.003355 CTTCTTTCCCTCAGGCGCA 60.003 57.895 10.83 0.00 0.00 6.09
3152 3537 0.321653 TTCTTCTTTCCCTCAGGCGC 60.322 55.000 0.00 0.00 0.00 6.53
3157 3542 2.304180 CAGCTCCTTCTTCTTTCCCTCA 59.696 50.000 0.00 0.00 0.00 3.86
3165 3550 0.036199 CTGCTGCAGCTCCTTCTTCT 60.036 55.000 36.61 0.00 42.66 2.85
3203 3588 7.394816 CGAAACCATAAGATAGATAATGGGGT 58.605 38.462 5.29 0.00 42.66 4.95
3238 3623 2.754375 CACCACCACCCCACTACC 59.246 66.667 0.00 0.00 0.00 3.18
3239 3624 2.033602 GCACCACCACCCCACTAC 59.966 66.667 0.00 0.00 0.00 2.73
3240 3625 2.448736 TGCACCACCACCCCACTA 60.449 61.111 0.00 0.00 0.00 2.74
3241 3626 4.204028 GTGCACCACCACCCCACT 62.204 66.667 5.22 0.00 0.00 4.00
3242 3627 3.731766 AAGTGCACCACCACCCCAC 62.732 63.158 14.63 0.00 36.38 4.61
3243 3628 3.425014 AAGTGCACCACCACCCCA 61.425 61.111 14.63 0.00 36.38 4.96
3244 3629 2.597510 GAAGTGCACCACCACCCC 60.598 66.667 14.63 0.00 36.38 4.95
3245 3630 2.978010 CGAAGTGCACCACCACCC 60.978 66.667 14.63 0.00 36.38 4.61
3246 3631 3.660111 GCGAAGTGCACCACCACC 61.660 66.667 14.63 0.00 45.45 4.61
3261 3646 1.599419 CGTTTGGGTTTTTCTCCAGCG 60.599 52.381 0.00 0.00 34.17 5.18
3264 3649 0.382515 CGCGTTTGGGTTTTTCTCCA 59.617 50.000 0.00 0.00 0.00 3.86
3411 3796 0.032017 TTCTACCTCCTCCTCCCAGC 60.032 60.000 0.00 0.00 0.00 4.85
3414 3799 2.850695 TTCTTCTACCTCCTCCTCCC 57.149 55.000 0.00 0.00 0.00 4.30
3426 3811 5.338708 CCTTCTTCCTCCTGCAATTCTTCTA 60.339 44.000 0.00 0.00 0.00 2.10
3428 3813 3.693578 CCTTCTTCCTCCTGCAATTCTTC 59.306 47.826 0.00 0.00 0.00 2.87
3429 3814 3.331889 TCCTTCTTCCTCCTGCAATTCTT 59.668 43.478 0.00 0.00 0.00 2.52
3430 3815 2.915604 TCCTTCTTCCTCCTGCAATTCT 59.084 45.455 0.00 0.00 0.00 2.40
3431 3816 3.013219 GTCCTTCTTCCTCCTGCAATTC 58.987 50.000 0.00 0.00 0.00 2.17
3432 3817 2.646798 AGTCCTTCTTCCTCCTGCAATT 59.353 45.455 0.00 0.00 0.00 2.32
3433 3818 2.026449 CAGTCCTTCTTCCTCCTGCAAT 60.026 50.000 0.00 0.00 0.00 3.56
3434 3819 1.349026 CAGTCCTTCTTCCTCCTGCAA 59.651 52.381 0.00 0.00 0.00 4.08
3435 3820 0.979665 CAGTCCTTCTTCCTCCTGCA 59.020 55.000 0.00 0.00 0.00 4.41
3436 3821 0.392327 GCAGTCCTTCTTCCTCCTGC 60.392 60.000 0.00 0.00 38.58 4.85
3437 3822 0.108424 CGCAGTCCTTCTTCCTCCTG 60.108 60.000 0.00 0.00 0.00 3.86
3438 3823 1.261238 CCGCAGTCCTTCTTCCTCCT 61.261 60.000 0.00 0.00 0.00 3.69
3439 3824 1.219393 CCGCAGTCCTTCTTCCTCC 59.781 63.158 0.00 0.00 0.00 4.30
3440 3825 1.219393 CCCGCAGTCCTTCTTCCTC 59.781 63.158 0.00 0.00 0.00 3.71
3441 3826 2.960688 GCCCGCAGTCCTTCTTCCT 61.961 63.158 0.00 0.00 0.00 3.36
3442 3827 2.436824 GCCCGCAGTCCTTCTTCC 60.437 66.667 0.00 0.00 0.00 3.46
3453 3838 2.792947 GGAGATCTAACGGCCCGCA 61.793 63.158 1.23 0.00 0.00 5.69
3455 3840 0.038159 GATGGAGATCTAACGGCCCG 60.038 60.000 0.00 0.00 0.00 6.13
3465 3850 2.768698 TCTAGACGTCGGATGGAGATC 58.231 52.381 10.46 0.00 0.00 2.75
3478 3863 4.283678 GGTCAGTCGATTCATTCTAGACG 58.716 47.826 0.00 0.00 36.97 4.18
3486 3871 4.588899 TGAAATTGGGTCAGTCGATTCAT 58.411 39.130 0.00 0.00 0.00 2.57
3514 3899 0.030369 GGCTATACGTCGGTCCACTG 59.970 60.000 0.00 0.00 0.00 3.66
3515 3900 0.106819 AGGCTATACGTCGGTCCACT 60.107 55.000 0.00 0.00 0.00 4.00
3516 3901 1.597742 TAGGCTATACGTCGGTCCAC 58.402 55.000 0.00 0.00 0.00 4.02
3517 3902 1.949525 GTTAGGCTATACGTCGGTCCA 59.050 52.381 0.00 0.00 0.00 4.02
3518 3903 1.268079 GGTTAGGCTATACGTCGGTCC 59.732 57.143 0.00 0.00 0.00 4.46
3519 3904 1.949525 TGGTTAGGCTATACGTCGGTC 59.050 52.381 0.00 0.00 0.00 4.79
3520 3905 1.952296 CTGGTTAGGCTATACGTCGGT 59.048 52.381 0.00 0.00 0.00 4.69
3521 3906 2.224606 TCTGGTTAGGCTATACGTCGG 58.775 52.381 0.00 0.00 0.00 4.79
3522 3907 4.500603 AATCTGGTTAGGCTATACGTCG 57.499 45.455 0.00 0.00 0.00 5.12
3633 4306 0.808847 TCGTGCTCATGCTGCTCATC 60.809 55.000 0.00 0.00 40.48 2.92
3654 4329 8.458573 ACCTGTTTGTTCAATTAGTATTGTCA 57.541 30.769 0.00 0.00 41.54 3.58
3855 4531 3.444417 TCTCCCGGCCCCCAGATA 61.444 66.667 0.00 0.00 0.00 1.98
3976 4652 4.500116 GAGCTCCACCGTCTCGCC 62.500 72.222 0.87 0.00 0.00 5.54
4452 5128 3.512516 GCGGCAGGTGATTCCAGC 61.513 66.667 0.00 0.00 46.16 4.85
4482 5161 2.126071 TCGTGAGTAGCTTGGCGC 60.126 61.111 0.00 0.00 39.57 6.53
4560 5242 0.730834 CGTCTGTCCTCTTGCTGACG 60.731 60.000 8.91 8.91 45.27 4.35
4575 5257 1.983196 CTCCGTCGTCATCTGCGTCT 61.983 60.000 0.00 0.00 0.00 4.18
4580 5262 0.748367 TCCTCCTCCGTCGTCATCTG 60.748 60.000 0.00 0.00 0.00 2.90
4584 5266 1.453379 GGATCCTCCTCCGTCGTCA 60.453 63.158 3.84 0.00 32.53 4.35
4689 5377 3.551496 CTCCTTGGAAGCGGTGCCA 62.551 63.158 11.24 11.24 0.00 4.92
4690 5378 2.543067 ATCTCCTTGGAAGCGGTGCC 62.543 60.000 4.07 4.07 0.00 5.01
4691 5379 1.078143 ATCTCCTTGGAAGCGGTGC 60.078 57.895 0.00 0.00 0.00 5.01
4760 5448 3.524606 CCCACGGATCCGCGTACT 61.525 66.667 33.62 11.56 44.19 2.73
4980 5668 4.500887 CCATGCCAAACCAATCTCATCATC 60.501 45.833 0.00 0.00 0.00 2.92
5021 5709 1.448717 GGGAGAAGAGAGCGCCAAC 60.449 63.158 2.29 0.00 0.00 3.77
5025 5713 0.247736 TTCAAGGGAGAAGAGAGCGC 59.752 55.000 0.00 0.00 0.00 5.92
5077 5769 4.483476 AAAAGAAAAGAATGGTCGTCCG 57.517 40.909 0.00 0.00 36.30 4.79
5096 5788 1.671845 CGGTCGTCCACCTTTCAAAAA 59.328 47.619 0.00 0.00 44.21 1.94
5097 5789 1.301423 CGGTCGTCCACCTTTCAAAA 58.699 50.000 0.00 0.00 44.21 2.44
5098 5790 0.178533 ACGGTCGTCCACCTTTCAAA 59.821 50.000 0.00 0.00 44.21 2.69
5099 5791 0.178533 AACGGTCGTCCACCTTTCAA 59.821 50.000 0.00 0.00 44.21 2.69
5100 5792 1.824658 AACGGTCGTCCACCTTTCA 59.175 52.632 0.00 0.00 44.21 2.69
5101 5793 2.525422 GAACGGTCGTCCACCTTTC 58.475 57.895 0.00 0.00 44.01 2.62
5102 5794 0.466963 AAGAACGGTCGTCCACCTTT 59.533 50.000 0.00 0.00 44.21 3.11
5103 5795 0.466963 AAAGAACGGTCGTCCACCTT 59.533 50.000 0.00 0.00 44.21 3.50
5104 5796 0.466963 AAAAGAACGGTCGTCCACCT 59.533 50.000 0.00 0.00 44.21 4.00
5105 5797 0.863799 GAAAAGAACGGTCGTCCACC 59.136 55.000 0.00 0.00 42.69 4.61
5106 5798 1.861971 AGAAAAGAACGGTCGTCCAC 58.138 50.000 0.00 0.00 0.00 4.02
5107 5799 2.607631 AAGAAAAGAACGGTCGTCCA 57.392 45.000 0.00 0.00 0.00 4.02
5108 5800 3.957671 AAAAGAAAAGAACGGTCGTCC 57.042 42.857 0.00 0.00 0.00 4.79
5126 5818 2.724454 TGGTCGTCCACCTTTCAAAAA 58.276 42.857 0.00 0.00 46.98 1.94
5127 5819 2.421751 TGGTCGTCCACCTTTCAAAA 57.578 45.000 0.00 0.00 46.98 2.44
5161 5853 9.445786 AGTTTTATGTACAAAAACAGAATGACG 57.554 29.630 28.23 0.00 45.17 4.35
5195 5887 4.998671 TTGCAGGAACATCTTGTTTGAA 57.001 36.364 0.00 0.00 41.28 2.69
5423 6126 7.136772 GTGGTCAAGTTATGTTTTTGTACCTC 58.863 38.462 0.00 0.00 0.00 3.85
5532 6236 6.699575 TCCTAGCTCCAAATGCTTATTTTC 57.300 37.500 0.00 0.00 41.46 2.29
5580 6284 3.131755 AGCTTCCTATTTCAAATGCCAGC 59.868 43.478 0.00 0.00 0.00 4.85
5588 6292 4.724399 TCAACACCAGCTTCCTATTTCAA 58.276 39.130 0.00 0.00 0.00 2.69
5617 6322 1.929836 CATCAAACTAGAGTGCGGCTC 59.070 52.381 0.00 0.00 44.45 4.70
5623 6328 3.054802 AGGAAGCCCATCAAACTAGAGTG 60.055 47.826 0.00 0.00 33.88 3.51
5666 6371 3.695606 GGACCGACTGCTGCTCCA 61.696 66.667 0.00 0.00 0.00 3.86
5683 6388 2.417719 GTGAAACTCCAGGTGCTACTG 58.582 52.381 1.80 1.80 38.21 2.74
5720 6425 3.878103 CAGCTGATGAAAAGGAGGAGATG 59.122 47.826 8.42 0.00 0.00 2.90
5729 6434 1.544691 AGGCTTGCAGCTGATGAAAAG 59.455 47.619 20.43 12.68 41.99 2.27
5746 6451 0.464554 GGATGTGGCTAGTGGAAGGC 60.465 60.000 0.00 0.00 42.19 4.35
5802 6558 2.063015 AAACCGGATGTGGCCAGTGA 62.063 55.000 9.46 0.00 0.00 3.41
5817 6573 9.003658 TCTAACTGATGAAAAAGAGATCAAACC 57.996 33.333 0.00 0.00 0.00 3.27
5839 6598 5.534654 CAGGTGGTCATTGGAAGTTTTCTAA 59.465 40.000 0.00 0.00 34.56 2.10
5841 6600 3.891366 CAGGTGGTCATTGGAAGTTTTCT 59.109 43.478 0.00 0.00 0.00 2.52
5842 6601 3.552890 GCAGGTGGTCATTGGAAGTTTTC 60.553 47.826 0.00 0.00 0.00 2.29
5846 6605 0.606401 CGCAGGTGGTCATTGGAAGT 60.606 55.000 0.00 0.00 0.00 3.01
5854 6613 2.046988 CTGATGCGCAGGTGGTCA 60.047 61.111 18.32 13.52 41.07 4.02


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

AutoCloner maintained by Alex Coulton.