Multiple sequence alignment - TraesCS7A01G442000

Loading Multiple Alignment...

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 TraesCS7A01G442000 chr7A 100.000 2342 0 0 1 2342 635950126 635947785 0.000000e+00 4325.0
1 TraesCS7A01G442000 chr7A 82.677 508 70 10 1 495 536258902 536259404 3.570000e-118 435.0
2 TraesCS7A01G442000 chr7A 81.100 418 59 7 1 401 506104323 506103909 1.350000e-82 316.0
3 TraesCS7A01G442000 chr7A 83.276 293 34 6 211 493 534490419 534490706 2.990000e-64 255.0
4 TraesCS7A01G442000 chr4D 92.374 577 34 3 1776 2342 429098021 429098597 0.000000e+00 813.0
5 TraesCS7A01G442000 chr3D 91.508 577 38 4 1776 2342 266839709 266840284 0.000000e+00 784.0
6 TraesCS7A01G442000 chr3D 81.858 452 67 7 1 440 432813651 432814099 1.320000e-97 366.0
7 TraesCS7A01G442000 chr3D 87.347 245 19 2 211 444 541486427 541486670 1.070000e-68 270.0
8 TraesCS7A01G442000 chr6B 87.544 570 61 2 1070 1630 223983982 223983414 0.000000e+00 651.0
9 TraesCS7A01G442000 chr6B 87.040 571 65 2 1070 1631 223860913 223860343 9.130000e-179 636.0
10 TraesCS7A01G442000 chr3B 90.909 451 30 2 1903 2342 117444603 117445053 1.550000e-166 595.0
11 TraesCS7A01G442000 chr3B 89.352 216 14 2 2136 2342 449942315 449942530 1.780000e-66 263.0
12 TraesCS7A01G442000 chr3B 97.826 46 1 0 1788 1833 449942270 449942315 1.930000e-11 80.5
13 TraesCS7A01G442000 chr5D 87.377 507 49 5 1 495 97896130 97896633 3.380000e-158 568.0
14 TraesCS7A01G442000 chr5D 87.179 78 8 2 1828 1904 282962994 282962918 1.150000e-13 87.9
15 TraesCS7A01G442000 chr1B 89.888 445 34 2 1909 2342 534828861 534828417 1.570000e-156 562.0
16 TraesCS7A01G442000 chr1B 79.963 539 91 15 538 1066 384567534 384567003 4.720000e-102 381.0
17 TraesCS7A01G442000 chr1B 82.968 411 59 5 1 402 497019402 497019810 6.150000e-96 361.0
18 TraesCS7A01G442000 chr6A 93.130 262 18 0 1 262 427502257 427501996 3.650000e-103 385.0
19 TraesCS7A01G442000 chr1D 81.858 452 67 7 1 440 215038541 215038989 1.320000e-97 366.0
20 TraesCS7A01G442000 chr1D 82.025 395 60 5 1 385 471204589 471204982 2.240000e-85 326.0
21 TraesCS7A01G442000 chr1A 83.333 396 53 4 1 385 355748041 355748434 1.030000e-93 353.0
22 TraesCS7A01G442000 chr2B 82.278 395 58 3 1 385 622284678 622285070 4.820000e-87 331.0
23 TraesCS7A01G442000 chr7D 82.071 396 60 4 1 385 267814484 267814089 6.240000e-86 327.0
24 TraesCS7A01G442000 chr7D 84.716 229 22 5 277 495 120005343 120005118 1.410000e-52 217.0
25 TraesCS7A01G442000 chr7D 83.158 190 27 4 1377 1561 450841043 450840854 4.000000e-38 169.0
26 TraesCS7A01G442000 chr4A 85.942 313 30 6 194 495 206126944 206127253 2.900000e-84 322.0
27 TraesCS7A01G442000 chr4A 80.147 136 25 2 1875 2009 413736641 413736775 1.480000e-17 100.0
28 TraesCS7A01G442000 chr2A 84.591 318 32 8 138 441 385782521 385782835 1.360000e-77 300.0
29 TraesCS7A01G442000 chr2A 85.765 281 30 3 2069 2340 131204197 131203918 2.940000e-74 289.0
30 TraesCS7A01G442000 chr2A 85.909 220 31 0 1788 2007 372107536 372107317 3.890000e-58 235.0
31 TraesCS7A01G442000 chr4B 88.843 242 15 4 211 441 12559086 12559326 1.060000e-73 287.0
32 TraesCS7A01G442000 chr7B 88.333 240 16 4 213 441 528347152 528347390 6.370000e-71 278.0


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 TraesCS7A01G442000 chr7A 635947785 635950126 2341 True 4325 4325 100.000 1 2342 1 chr7A.!!$R2 2341
1 TraesCS7A01G442000 chr7A 536258902 536259404 502 False 435 435 82.677 1 495 1 chr7A.!!$F2 494
2 TraesCS7A01G442000 chr4D 429098021 429098597 576 False 813 813 92.374 1776 2342 1 chr4D.!!$F1 566
3 TraesCS7A01G442000 chr3D 266839709 266840284 575 False 784 784 91.508 1776 2342 1 chr3D.!!$F1 566
4 TraesCS7A01G442000 chr6B 223983414 223983982 568 True 651 651 87.544 1070 1630 1 chr6B.!!$R2 560
5 TraesCS7A01G442000 chr6B 223860343 223860913 570 True 636 636 87.040 1070 1631 1 chr6B.!!$R1 561
6 TraesCS7A01G442000 chr5D 97896130 97896633 503 False 568 568 87.377 1 495 1 chr5D.!!$F1 494
7 TraesCS7A01G442000 chr1B 384567003 384567534 531 True 381 381 79.963 538 1066 1 chr1B.!!$R1 528

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
532 545 0.031716 TCATCTCCAGCAGCTACCCT 60.032 55.0 0.0 0.0 0.0 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1701 1732 0.108138 CCTCTTTCTACCACGGCCTG 60.108 60.0 0.0 0.0 0.0 4.85 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 6.575244 TGGATTTCACTGGATATGTTAGGT 57.425 37.500 0.00 0.00 0.00 3.08
95 96 2.910199 CGGAGTTGATGATCACCATGT 58.090 47.619 0.00 0.00 35.17 3.21
101 102 5.319453 AGTTGATGATCACCATGTTGAAGT 58.681 37.500 0.00 0.00 35.17 3.01
115 116 7.149973 CCATGTTGAAGTTGAAATCAATCACT 58.850 34.615 0.00 0.00 37.82 3.41
117 118 6.506147 TGTTGAAGTTGAAATCAATCACTGG 58.494 36.000 0.00 0.00 37.82 4.00
118 119 6.096705 TGTTGAAGTTGAAATCAATCACTGGT 59.903 34.615 0.00 0.00 37.82 4.00
128 129 1.480212 AATCACTGGTGAGTCGGCCA 61.480 55.000 2.24 6.16 43.61 5.36
129 130 1.267574 ATCACTGGTGAGTCGGCCAT 61.268 55.000 2.24 0.00 43.61 4.40
139 140 3.473647 TCGGCCATGGGAGCAGAG 61.474 66.667 15.13 0.00 30.73 3.35
151 152 1.381056 AGCAGAGAGATGAGCCGGT 60.381 57.895 1.90 0.00 0.00 5.28
172 173 2.667199 GGCGTTGTAAGCCGGTGT 60.667 61.111 1.90 0.00 45.58 4.16
178 179 1.746322 TTGTAAGCCGGTGTGGACGA 61.746 55.000 1.90 0.00 42.00 4.20
179 180 1.005867 GTAAGCCGGTGTGGACGAA 60.006 57.895 1.90 0.00 42.00 3.85
224 225 2.433491 CGTGGACGGGCGAATCAA 60.433 61.111 0.00 0.00 35.37 2.57
295 296 1.889105 CAGCACGGCACAGACAAGT 60.889 57.895 0.00 0.00 0.00 3.16
464 477 3.924114 TTGTGGGATGAACGTGGATAT 57.076 42.857 0.00 0.00 0.00 1.63
467 480 3.198853 TGTGGGATGAACGTGGATATTGA 59.801 43.478 0.00 0.00 0.00 2.57
475 488 7.012327 GGATGAACGTGGATATTGAGATCAAAA 59.988 37.037 0.00 0.00 39.55 2.44
495 508 8.394971 TCAAAACATATCAACTGTCTGATGTT 57.605 30.769 12.59 8.96 36.69 2.71
496 509 8.291740 TCAAAACATATCAACTGTCTGATGTTG 58.708 33.333 15.58 15.58 43.28 3.33
502 515 4.176271 TCAACTGTCTGATGTTGATAGCG 58.824 43.478 18.51 0.00 44.89 4.26
503 516 3.170791 ACTGTCTGATGTTGATAGCGG 57.829 47.619 0.00 0.00 0.00 5.52
504 517 1.863454 CTGTCTGATGTTGATAGCGGC 59.137 52.381 0.00 0.00 0.00 6.53
505 518 1.482182 TGTCTGATGTTGATAGCGGCT 59.518 47.619 7.98 7.98 0.00 5.52
506 519 2.131183 GTCTGATGTTGATAGCGGCTC 58.869 52.381 5.39 0.00 0.00 4.70
507 520 1.756538 TCTGATGTTGATAGCGGCTCA 59.243 47.619 5.39 0.00 0.00 4.26
508 521 2.366590 TCTGATGTTGATAGCGGCTCAT 59.633 45.455 5.39 2.86 0.00 2.90
509 522 2.735663 CTGATGTTGATAGCGGCTCATC 59.264 50.000 17.14 17.14 34.28 2.92
510 523 2.366590 TGATGTTGATAGCGGCTCATCT 59.633 45.455 21.74 2.94 34.63 2.90
511 524 2.229675 TGTTGATAGCGGCTCATCTG 57.770 50.000 5.39 0.00 0.00 2.90
512 525 1.756538 TGTTGATAGCGGCTCATCTGA 59.243 47.619 5.39 0.00 0.00 3.27
513 526 2.366590 TGTTGATAGCGGCTCATCTGAT 59.633 45.455 5.39 0.00 0.00 2.90
514 527 2.992543 GTTGATAGCGGCTCATCTGATC 59.007 50.000 5.39 3.28 0.00 2.92
515 528 2.242043 TGATAGCGGCTCATCTGATCA 58.758 47.619 5.39 6.25 0.00 2.92
516 529 2.830321 TGATAGCGGCTCATCTGATCAT 59.170 45.455 5.39 0.00 0.00 2.45
517 530 3.119209 TGATAGCGGCTCATCTGATCATC 60.119 47.826 5.39 0.89 0.00 2.92
518 531 1.340088 AGCGGCTCATCTGATCATCT 58.660 50.000 0.00 0.00 0.00 2.90
519 532 1.273048 AGCGGCTCATCTGATCATCTC 59.727 52.381 0.00 0.00 0.00 2.75
520 533 1.672441 GCGGCTCATCTGATCATCTCC 60.672 57.143 0.00 0.00 0.00 3.71
521 534 1.617357 CGGCTCATCTGATCATCTCCA 59.383 52.381 0.00 0.00 0.00 3.86
522 535 2.352912 CGGCTCATCTGATCATCTCCAG 60.353 54.545 0.00 0.00 0.00 3.86
523 536 2.613474 GGCTCATCTGATCATCTCCAGC 60.613 54.545 0.00 0.60 0.00 4.85
524 537 2.037381 GCTCATCTGATCATCTCCAGCA 59.963 50.000 0.00 0.00 0.00 4.41
525 538 3.863021 GCTCATCTGATCATCTCCAGCAG 60.863 52.174 0.00 0.00 0.00 4.24
526 539 2.037381 TCATCTGATCATCTCCAGCAGC 59.963 50.000 0.00 0.00 0.00 5.25
527 540 1.790818 TCTGATCATCTCCAGCAGCT 58.209 50.000 0.00 0.00 0.00 4.24
528 541 2.954792 TCTGATCATCTCCAGCAGCTA 58.045 47.619 0.00 0.00 0.00 3.32
529 542 2.627221 TCTGATCATCTCCAGCAGCTAC 59.373 50.000 0.00 0.00 0.00 3.58
530 543 1.690893 TGATCATCTCCAGCAGCTACC 59.309 52.381 0.00 0.00 0.00 3.18
531 544 1.001860 GATCATCTCCAGCAGCTACCC 59.998 57.143 0.00 0.00 0.00 3.69
532 545 0.031716 TCATCTCCAGCAGCTACCCT 60.032 55.000 0.00 0.00 0.00 4.34
533 546 0.835941 CATCTCCAGCAGCTACCCTT 59.164 55.000 0.00 0.00 0.00 3.95
534 547 1.211457 CATCTCCAGCAGCTACCCTTT 59.789 52.381 0.00 0.00 0.00 3.11
535 548 0.905357 TCTCCAGCAGCTACCCTTTC 59.095 55.000 0.00 0.00 0.00 2.62
536 549 0.107459 CTCCAGCAGCTACCCTTTCC 60.107 60.000 0.00 0.00 0.00 3.13
537 550 0.547712 TCCAGCAGCTACCCTTTCCT 60.548 55.000 0.00 0.00 0.00 3.36
538 551 0.329596 CCAGCAGCTACCCTTTCCTT 59.670 55.000 0.00 0.00 0.00 3.36
539 552 1.272147 CCAGCAGCTACCCTTTCCTTT 60.272 52.381 0.00 0.00 0.00 3.11
540 553 2.519013 CAGCAGCTACCCTTTCCTTTT 58.481 47.619 0.00 0.00 0.00 2.27
541 554 2.229784 CAGCAGCTACCCTTTCCTTTTG 59.770 50.000 0.00 0.00 0.00 2.44
542 555 2.108250 AGCAGCTACCCTTTCCTTTTGA 59.892 45.455 0.00 0.00 0.00 2.69
543 556 2.229062 GCAGCTACCCTTTCCTTTTGAC 59.771 50.000 0.00 0.00 0.00 3.18
544 557 3.756117 CAGCTACCCTTTCCTTTTGACT 58.244 45.455 0.00 0.00 0.00 3.41
545 558 4.145052 CAGCTACCCTTTCCTTTTGACTT 58.855 43.478 0.00 0.00 0.00 3.01
546 559 4.022849 CAGCTACCCTTTCCTTTTGACTTG 60.023 45.833 0.00 0.00 0.00 3.16
547 560 4.141251 AGCTACCCTTTCCTTTTGACTTGA 60.141 41.667 0.00 0.00 0.00 3.02
548 561 4.767409 GCTACCCTTTCCTTTTGACTTGAT 59.233 41.667 0.00 0.00 0.00 2.57
549 562 5.106118 GCTACCCTTTCCTTTTGACTTGATC 60.106 44.000 0.00 0.00 0.00 2.92
550 563 5.066913 ACCCTTTCCTTTTGACTTGATCT 57.933 39.130 0.00 0.00 0.00 2.75
551 564 4.829492 ACCCTTTCCTTTTGACTTGATCTG 59.171 41.667 0.00 0.00 0.00 2.90
552 565 4.829492 CCCTTTCCTTTTGACTTGATCTGT 59.171 41.667 0.00 0.00 0.00 3.41
553 566 5.048434 CCCTTTCCTTTTGACTTGATCTGTC 60.048 44.000 10.95 10.95 35.21 3.51
554 567 5.532406 CCTTTCCTTTTGACTTGATCTGTCA 59.468 40.000 14.90 14.90 41.94 3.58
555 568 6.208204 CCTTTCCTTTTGACTTGATCTGTCAT 59.792 38.462 18.03 0.00 42.95 3.06
556 569 7.391554 CCTTTCCTTTTGACTTGATCTGTCATA 59.608 37.037 18.03 12.85 42.95 2.15
566 579 9.538508 TGACTTGATCTGTCATATGAATACTTG 57.461 33.333 7.07 0.00 39.23 3.16
580 593 6.117911 TGAATACTTGATGTTGTATTGCCG 57.882 37.500 0.00 0.00 38.85 5.69
583 596 3.620488 ACTTGATGTTGTATTGCCGGAT 58.380 40.909 5.05 0.00 0.00 4.18
584 597 4.776349 ACTTGATGTTGTATTGCCGGATA 58.224 39.130 5.05 0.00 0.00 2.59
586 599 3.472652 TGATGTTGTATTGCCGGATACC 58.527 45.455 5.05 0.00 32.68 2.73
596 609 3.414759 TGCCGGATACCCCAGATATAT 57.585 47.619 5.05 0.00 34.14 0.86
599 612 2.035961 CCGGATACCCCAGATATATGCG 59.964 54.545 0.00 0.00 39.14 4.73
601 614 3.132289 CGGATACCCCAGATATATGCGTT 59.868 47.826 0.00 0.00 35.98 4.84
603 616 4.161565 GGATACCCCAGATATATGCGTTGA 59.838 45.833 0.00 0.00 34.14 3.18
604 617 5.163301 GGATACCCCAGATATATGCGTTGAT 60.163 44.000 0.00 0.00 34.14 2.57
612 625 7.298122 CCAGATATATGCGTTGATTTGGTTAC 58.702 38.462 0.00 0.00 0.00 2.50
618 631 2.230266 GCGTTGATTTGGTTACCCATGT 59.770 45.455 0.00 0.00 41.49 3.21
630 643 5.063880 GGTTACCCATGTATAAGCTTCAGG 58.936 45.833 0.00 0.00 0.00 3.86
634 647 4.413520 ACCCATGTATAAGCTTCAGGTCAT 59.586 41.667 0.00 0.00 0.00 3.06
639 652 5.614308 TGTATAAGCTTCAGGTCATCCATG 58.386 41.667 0.00 0.00 35.89 3.66
679 692 4.210120 CGACTTAGCAGATGCATAAACTCC 59.790 45.833 7.68 0.00 45.16 3.85
680 693 5.102953 ACTTAGCAGATGCATAAACTCCA 57.897 39.130 7.68 0.00 45.16 3.86
689 702 1.737838 CATAAACTCCAGCGGCTCAA 58.262 50.000 0.00 0.00 0.00 3.02
690 703 2.292267 CATAAACTCCAGCGGCTCAAT 58.708 47.619 0.00 0.00 0.00 2.57
717 731 7.025963 GCTCATATTCTCTTTCTGGTGTTTTG 58.974 38.462 0.00 0.00 0.00 2.44
756 776 6.071503 TCACTAAAAGCAGAACTAGTACTCCC 60.072 42.308 0.00 0.00 0.00 4.30
757 777 4.554960 AAAAGCAGAACTAGTACTCCCC 57.445 45.455 0.00 0.00 0.00 4.81
768 789 0.391793 GTACTCCCCTCAACAGCAGC 60.392 60.000 0.00 0.00 0.00 5.25
773 794 1.003839 CCCTCAACAGCAGCGGTAA 60.004 57.895 0.00 0.00 0.00 2.85
774 795 1.298859 CCCTCAACAGCAGCGGTAAC 61.299 60.000 0.00 0.00 0.00 2.50
775 796 0.320771 CCTCAACAGCAGCGGTAACT 60.321 55.000 0.00 0.00 0.00 2.24
778 799 3.064207 CTCAACAGCAGCGGTAACTTAA 58.936 45.455 0.00 0.00 0.00 1.85
787 808 4.392138 GCAGCGGTAACTTAACAGATCTTT 59.608 41.667 0.00 0.00 0.00 2.52
790 811 7.201617 GCAGCGGTAACTTAACAGATCTTTTAT 60.202 37.037 2.24 0.00 0.00 1.40
791 812 8.116753 CAGCGGTAACTTAACAGATCTTTTATG 58.883 37.037 11.17 11.17 0.00 1.90
792 813 8.038944 AGCGGTAACTTAACAGATCTTTTATGA 58.961 33.333 17.03 0.00 0.00 2.15
793 814 8.662141 GCGGTAACTTAACAGATCTTTTATGAA 58.338 33.333 17.03 6.12 0.00 2.57
799 820 8.718734 ACTTAACAGATCTTTTATGAAACCGTC 58.281 33.333 17.03 0.00 0.00 4.79
800 821 6.496338 AACAGATCTTTTATGAAACCGTCC 57.504 37.500 0.00 0.00 0.00 4.79
801 822 5.556915 ACAGATCTTTTATGAAACCGTCCA 58.443 37.500 0.00 0.00 0.00 4.02
802 823 5.643777 ACAGATCTTTTATGAAACCGTCCAG 59.356 40.000 0.00 0.00 0.00 3.86
804 825 4.627284 TCTTTTATGAAACCGTCCAGGA 57.373 40.909 0.00 0.00 45.00 3.86
805 826 4.320870 TCTTTTATGAAACCGTCCAGGAC 58.679 43.478 9.92 9.92 45.00 3.85
806 827 4.041198 TCTTTTATGAAACCGTCCAGGACT 59.959 41.667 17.95 0.00 45.00 3.85
810 831 3.842007 TGAAACCGTCCAGGACTTTTA 57.158 42.857 17.95 6.38 45.00 1.52
821 842 2.031157 CAGGACTTTTAACCCTTGCACG 60.031 50.000 0.00 0.00 0.00 5.34
826 847 1.504359 TTTAACCCTTGCACGACTCG 58.496 50.000 0.00 0.00 0.00 4.18
827 848 0.947180 TTAACCCTTGCACGACTCGC 60.947 55.000 0.00 0.00 0.00 5.03
846 867 2.433664 CGTGTTGGTACGGAGGCC 60.434 66.667 0.00 0.00 40.22 5.19
852 873 3.766691 GGTACGGAGGCCAGCGAA 61.767 66.667 5.01 0.00 0.00 4.70
864 885 4.443266 AGCGAAGGCGGCTCAGAC 62.443 66.667 13.70 2.22 46.35 3.51
887 908 1.304134 AGGGCGGTTTAGGCAAAGG 60.304 57.895 0.00 0.00 38.57 3.11
899 920 1.372997 GCAAAGGTGAGCGACGAGA 60.373 57.895 0.00 0.00 0.00 4.04
901 922 1.081376 AAAGGTGAGCGACGAGACG 60.081 57.895 0.00 0.00 0.00 4.18
910 931 2.202531 GACGAGACGGGCCGTAAC 60.203 66.667 34.29 25.78 41.37 2.50
913 934 2.968206 GAGACGGGCCGTAACAGT 59.032 61.111 34.29 14.34 41.37 3.55
952 973 4.519437 CAGCTCAGGCCATCGCGA 62.519 66.667 13.09 13.09 39.73 5.87
955 976 2.279120 CTCAGGCCATCGCGAGAC 60.279 66.667 16.66 3.46 46.97 3.36
956 977 3.068064 TCAGGCCATCGCGAGACA 61.068 61.111 16.66 0.00 46.97 3.41
966 987 2.881352 GCGAGACAGTGTAGGCGC 60.881 66.667 17.28 17.28 37.60 6.53
967 988 2.577112 CGAGACAGTGTAGGCGCG 60.577 66.667 0.00 0.00 0.00 6.86
974 995 4.729856 GTGTAGGCGCGGTCGGTT 62.730 66.667 8.83 0.00 35.95 4.44
990 1012 3.185797 GTCGGTTTACTGGTGTTAGCTTG 59.814 47.826 0.00 0.00 0.00 4.01
994 1016 5.516996 GGTTTACTGGTGTTAGCTTGAAAC 58.483 41.667 0.00 0.00 0.00 2.78
996 1018 3.188159 ACTGGTGTTAGCTTGAAACGA 57.812 42.857 0.00 0.00 0.00 3.85
1004 1026 1.153958 GCTTGAAACGAGCCATGGC 60.154 57.895 30.12 30.12 42.33 4.40
1010 1032 1.589716 AAACGAGCCATGGCAGAAGC 61.590 55.000 37.18 19.16 44.88 3.86
1012 1034 2.758089 CGAGCCATGGCAGAAGCAC 61.758 63.158 37.18 17.21 44.61 4.40
1014 1036 3.058160 GCCATGGCAGAAGCACGT 61.058 61.111 32.08 0.00 44.61 4.49
1018 1040 0.095245 CATGGCAGAAGCACGTAACG 59.905 55.000 0.00 0.00 44.61 3.18
1020 1042 2.474712 GCAGAAGCACGTAACGGC 59.525 61.111 0.00 0.00 41.58 5.68
1022 1044 3.110178 AGAAGCACGTAACGGCGC 61.110 61.111 6.90 0.00 34.88 6.53
1042 1064 0.319555 CGGCGACTCAGAAGTGGAAA 60.320 55.000 0.00 0.00 35.28 3.13
1044 1066 1.540363 GGCGACTCAGAAGTGGAAACA 60.540 52.381 0.00 0.00 35.28 2.83
1055 1077 2.115911 TGGAAACAAGCAACGGCGT 61.116 52.632 6.77 6.77 39.91 5.68
1066 1088 0.732880 CAACGGCGTAGGTGTCTCAG 60.733 60.000 15.20 0.00 0.00 3.35
1067 1089 0.892358 AACGGCGTAGGTGTCTCAGA 60.892 55.000 15.20 0.00 0.00 3.27
1068 1090 0.892358 ACGGCGTAGGTGTCTCAGAA 60.892 55.000 12.58 0.00 0.00 3.02
1091 1113 2.649034 GACTCAAGGCCACGACGA 59.351 61.111 5.01 0.00 0.00 4.20
1097 1119 3.575351 AAGGCCACGACGACAGCTC 62.575 63.158 5.01 0.00 0.00 4.09
1151 1173 4.699522 GAGGCGGCGGGTTGAAGT 62.700 66.667 9.78 0.00 0.00 3.01
1161 1183 0.393132 GGGTTGAAGTAGAGCCCAGC 60.393 60.000 0.00 0.00 39.13 4.85
1172 1194 2.034687 GCCCAGCTGTGGTGATGT 59.965 61.111 13.81 0.00 43.23 3.06
1176 1198 0.745845 CCAGCTGTGGTGATGTAGGC 60.746 60.000 13.81 0.00 39.30 3.93
1180 1202 0.246360 CTGTGGTGATGTAGGCGACA 59.754 55.000 2.11 2.11 43.97 4.35
1194 1216 2.883828 CGACAGGGTGGCTCAAGGT 61.884 63.158 0.00 0.00 0.00 3.50
1208 1230 3.850098 AAGGTGAGGCCAAGTGCGG 62.850 63.158 5.01 0.00 42.61 5.69
1290 1321 1.303074 CTGCTCAGAGGCAAAGGCA 60.303 57.895 0.00 0.00 43.71 4.75
1291 1322 0.892358 CTGCTCAGAGGCAAAGGCAA 60.892 55.000 0.00 0.00 43.71 4.52
1293 1324 1.174712 GCTCAGAGGCAAAGGCAACA 61.175 55.000 0.00 0.00 43.71 3.33
1331 1362 2.202987 GCCACATCGGAGGCTCAG 60.203 66.667 17.69 13.08 46.05 3.35
1365 1396 1.301009 GCGGCTATGAGTAGGTGCC 60.301 63.158 0.00 0.00 40.14 5.01
1373 1404 4.715130 AGTAGGTGCCGGCCCTCA 62.715 66.667 31.94 19.00 33.35 3.86
1375 1406 4.392166 TAGGTGCCGGCCCTCAGA 62.392 66.667 31.94 17.35 33.35 3.27
1406 1437 1.301716 GTCAAGGGCAGCACGAGAA 60.302 57.895 0.00 0.00 0.00 2.87
1408 1439 2.357517 AAGGGCAGCACGAGAACG 60.358 61.111 0.00 0.00 45.75 3.95
1444 1475 0.956633 CTGCAGCAGAAGAAAAGGCA 59.043 50.000 18.42 0.00 32.44 4.75
1461 1492 1.296392 CAGAGTCGAACCATGGCCA 59.704 57.895 13.04 8.56 0.00 5.36
1515 1546 2.733218 TTCGAGGCGAACACAGCG 60.733 61.111 0.00 0.00 41.05 5.18
1522 1553 3.470567 CGAACACAGCGACTCGGC 61.471 66.667 0.00 0.00 0.00 5.54
1531 1562 4.862092 CGACTCGGCGCAGATGCT 62.862 66.667 11.52 0.00 39.32 3.79
1539 1570 2.767445 GCGCAGATGCTCAATGGCA 61.767 57.895 0.30 0.00 46.63 4.92
1567 1598 3.319198 GGTGAGGCCGGTGAAGGA 61.319 66.667 1.90 0.00 0.00 3.36
1570 1601 1.918293 TGAGGCCGGTGAAGGATGT 60.918 57.895 1.90 0.00 0.00 3.06
1571 1602 1.450312 GAGGCCGGTGAAGGATGTG 60.450 63.158 1.90 0.00 0.00 3.21
1584 1615 0.461548 GGATGTGGCTCTCATCACGA 59.538 55.000 14.81 0.00 42.16 4.35
1590 1621 0.171455 GGCTCTCATCACGACGACTT 59.829 55.000 0.00 0.00 0.00 3.01
1595 1626 1.447838 CATCACGACGACTTGGGGG 60.448 63.158 0.00 0.00 0.00 5.40
1631 1662 1.228124 CGGGAAGGTCAAAGTGGCA 60.228 57.895 0.00 0.00 0.00 4.92
1632 1663 0.821711 CGGGAAGGTCAAAGTGGCAA 60.822 55.000 0.00 0.00 0.00 4.52
1633 1664 1.408969 GGGAAGGTCAAAGTGGCAAA 58.591 50.000 0.00 0.00 0.00 3.68
1634 1665 1.760029 GGGAAGGTCAAAGTGGCAAAA 59.240 47.619 0.00 0.00 0.00 2.44
1635 1666 2.224042 GGGAAGGTCAAAGTGGCAAAAG 60.224 50.000 0.00 0.00 0.00 2.27
1636 1667 2.430694 GGAAGGTCAAAGTGGCAAAAGT 59.569 45.455 0.00 0.00 0.00 2.66
1637 1668 3.118775 GGAAGGTCAAAGTGGCAAAAGTT 60.119 43.478 0.00 0.00 0.00 2.66
1638 1669 3.801114 AGGTCAAAGTGGCAAAAGTTC 57.199 42.857 0.00 0.00 0.00 3.01
1639 1670 2.430694 AGGTCAAAGTGGCAAAAGTTCC 59.569 45.455 0.00 0.00 0.00 3.62
1640 1671 2.430694 GGTCAAAGTGGCAAAAGTTCCT 59.569 45.455 0.00 0.00 0.00 3.36
1641 1672 3.490933 GGTCAAAGTGGCAAAAGTTCCTC 60.491 47.826 0.00 0.00 0.00 3.71
1642 1673 2.357637 TCAAAGTGGCAAAAGTTCCTCG 59.642 45.455 0.00 0.00 0.00 4.63
1643 1674 2.052782 AAGTGGCAAAAGTTCCTCGT 57.947 45.000 0.00 0.00 0.00 4.18
1644 1675 1.594331 AGTGGCAAAAGTTCCTCGTC 58.406 50.000 0.00 0.00 0.00 4.20
1645 1676 1.141053 AGTGGCAAAAGTTCCTCGTCT 59.859 47.619 0.00 0.00 0.00 4.18
1646 1677 1.531578 GTGGCAAAAGTTCCTCGTCTC 59.468 52.381 0.00 0.00 0.00 3.36
1647 1678 1.140052 TGGCAAAAGTTCCTCGTCTCA 59.860 47.619 0.00 0.00 0.00 3.27
1648 1679 1.801178 GGCAAAAGTTCCTCGTCTCAG 59.199 52.381 0.00 0.00 0.00 3.35
1649 1680 1.195674 GCAAAAGTTCCTCGTCTCAGC 59.804 52.381 0.00 0.00 0.00 4.26
1650 1681 1.801178 CAAAAGTTCCTCGTCTCAGCC 59.199 52.381 0.00 0.00 0.00 4.85
1651 1682 1.048601 AAAGTTCCTCGTCTCAGCCA 58.951 50.000 0.00 0.00 0.00 4.75
1652 1683 0.318762 AAGTTCCTCGTCTCAGCCAC 59.681 55.000 0.00 0.00 0.00 5.01
1653 1684 1.444553 GTTCCTCGTCTCAGCCACG 60.445 63.158 0.00 0.00 38.67 4.94
1654 1685 2.636412 TTCCTCGTCTCAGCCACGG 61.636 63.158 0.00 0.00 37.85 4.94
1655 1686 3.062466 CCTCGTCTCAGCCACGGA 61.062 66.667 0.00 0.00 37.85 4.69
1656 1687 2.487428 CTCGTCTCAGCCACGGAG 59.513 66.667 0.00 0.00 37.85 4.63
1657 1688 3.057547 CTCGTCTCAGCCACGGAGG 62.058 68.421 0.00 0.00 37.85 4.30
1666 1697 4.514577 CCACGGAGGCAGTAGGCG 62.515 72.222 0.00 0.00 46.16 5.52
1669 1700 4.148825 CGGAGGCAGTAGGCGCTT 62.149 66.667 7.64 0.52 46.16 4.68
1670 1701 2.512515 GGAGGCAGTAGGCGCTTG 60.513 66.667 7.64 2.20 46.16 4.01
1671 1702 2.579201 GAGGCAGTAGGCGCTTGA 59.421 61.111 7.64 0.00 46.16 3.02
1672 1703 1.079127 GAGGCAGTAGGCGCTTGAA 60.079 57.895 7.64 0.00 46.16 2.69
1673 1704 1.078848 AGGCAGTAGGCGCTTGAAG 60.079 57.895 7.64 0.00 46.16 3.02
1674 1705 2.754995 GGCAGTAGGCGCTTGAAGC 61.755 63.158 7.64 7.20 46.16 3.86
1675 1706 2.034879 GCAGTAGGCGCTTGAAGCA 61.035 57.895 18.22 0.00 42.58 3.91
1676 1707 1.577328 GCAGTAGGCGCTTGAAGCAA 61.577 55.000 18.22 0.00 42.58 3.91
1677 1708 0.445436 CAGTAGGCGCTTGAAGCAAG 59.555 55.000 18.22 2.70 42.58 4.01
1678 1709 0.674895 AGTAGGCGCTTGAAGCAAGG 60.675 55.000 18.22 1.92 42.58 3.61
1679 1710 2.040544 TAGGCGCTTGAAGCAAGGC 61.041 57.895 18.22 13.68 42.58 4.35
1680 1711 4.426112 GGCGCTTGAAGCAAGGCC 62.426 66.667 18.22 17.35 44.11 5.19
1681 1712 3.673484 GCGCTTGAAGCAAGGCCA 61.673 61.111 18.22 0.00 42.58 5.36
1682 1713 2.256461 CGCTTGAAGCAAGGCCAC 59.744 61.111 18.22 0.00 42.58 5.01
1683 1714 2.554636 CGCTTGAAGCAAGGCCACA 61.555 57.895 18.22 0.00 42.58 4.17
1684 1715 1.741525 GCTTGAAGCAAGGCCACAA 59.258 52.632 13.09 0.53 41.89 3.33
1685 1716 0.319297 GCTTGAAGCAAGGCCACAAG 60.319 55.000 13.09 11.31 41.89 3.16
1686 1717 0.316204 CTTGAAGCAAGGCCACAAGG 59.684 55.000 5.01 0.00 37.77 3.61
1687 1718 1.114722 TTGAAGCAAGGCCACAAGGG 61.115 55.000 5.01 0.00 40.85 3.95
1699 1730 4.697756 CAAGGGCGGCGAAGGTGA 62.698 66.667 12.98 0.00 0.00 4.02
1700 1731 4.394712 AAGGGCGGCGAAGGTGAG 62.395 66.667 12.98 0.00 0.00 3.51
1708 1739 4.379243 CGAAGGTGAGCAGGCCGT 62.379 66.667 0.00 0.00 0.00 5.68
1709 1740 2.743928 GAAGGTGAGCAGGCCGTG 60.744 66.667 0.00 0.00 0.00 4.94
1710 1741 4.335647 AAGGTGAGCAGGCCGTGG 62.336 66.667 0.00 0.00 0.00 4.94
1712 1743 3.702048 GGTGAGCAGGCCGTGGTA 61.702 66.667 0.00 0.00 36.87 3.25
1713 1744 2.125512 GTGAGCAGGCCGTGGTAG 60.126 66.667 0.00 0.00 36.87 3.18
1714 1745 2.283604 TGAGCAGGCCGTGGTAGA 60.284 61.111 0.00 0.00 36.87 2.59
1715 1746 1.911269 TGAGCAGGCCGTGGTAGAA 60.911 57.895 0.00 0.00 36.87 2.10
1716 1747 1.295423 GAGCAGGCCGTGGTAGAAA 59.705 57.895 0.00 0.00 36.87 2.52
1717 1748 0.741221 GAGCAGGCCGTGGTAGAAAG 60.741 60.000 0.00 0.00 36.87 2.62
1718 1749 1.192146 AGCAGGCCGTGGTAGAAAGA 61.192 55.000 0.00 0.00 34.15 2.52
1719 1750 0.741221 GCAGGCCGTGGTAGAAAGAG 60.741 60.000 0.00 0.00 0.00 2.85
1720 1751 0.108138 CAGGCCGTGGTAGAAAGAGG 60.108 60.000 0.00 0.00 0.00 3.69
1721 1752 1.449778 GGCCGTGGTAGAAAGAGGC 60.450 63.158 0.00 0.00 43.47 4.70
1722 1753 1.295423 GCCGTGGTAGAAAGAGGCA 59.705 57.895 0.00 0.00 43.65 4.75
1723 1754 0.741221 GCCGTGGTAGAAAGAGGCAG 60.741 60.000 0.00 0.00 43.65 4.85
1724 1755 0.741221 CCGTGGTAGAAAGAGGCAGC 60.741 60.000 0.00 0.00 0.00 5.25
1725 1756 1.078759 CGTGGTAGAAAGAGGCAGCG 61.079 60.000 0.00 0.00 0.00 5.18
1726 1757 1.079127 TGGTAGAAAGAGGCAGCGC 60.079 57.895 0.00 0.00 0.00 5.92
1757 1788 4.385405 GCAGCAGCGGTGAGGAGT 62.385 66.667 20.69 0.00 32.22 3.85
1758 1789 2.345244 CAGCAGCGGTGAGGAGTT 59.655 61.111 20.69 0.00 32.22 3.01
1759 1790 1.739562 CAGCAGCGGTGAGGAGTTC 60.740 63.158 20.69 0.00 32.22 3.01
1760 1791 2.811317 GCAGCGGTGAGGAGTTCG 60.811 66.667 20.69 0.00 0.00 3.95
1761 1792 2.125912 CAGCGGTGAGGAGTTCGG 60.126 66.667 9.50 0.00 0.00 4.30
1762 1793 2.282958 AGCGGTGAGGAGTTCGGA 60.283 61.111 0.00 0.00 0.00 4.55
1763 1794 2.182030 GCGGTGAGGAGTTCGGAG 59.818 66.667 0.00 0.00 0.00 4.63
1764 1795 2.182030 CGGTGAGGAGTTCGGAGC 59.818 66.667 0.00 0.00 0.00 4.70
1765 1796 2.579738 GGTGAGGAGTTCGGAGCC 59.420 66.667 0.00 0.00 0.00 4.70
1766 1797 2.579738 GTGAGGAGTTCGGAGCCC 59.420 66.667 0.00 0.00 0.00 5.19
1801 1832 2.997897 GTGACTGAGGCCGAGGGT 60.998 66.667 9.39 1.99 0.00 4.34
1873 1904 1.279840 GAACAGCAGTTGTGACCGC 59.720 57.895 0.00 0.00 40.74 5.68
1928 1959 1.981636 CAGAAGCCTGCTCAGAGGT 59.018 57.895 0.00 0.00 35.29 3.85
2000 2031 2.861935 TGTGTTTTCCTTCGAGTCGTTC 59.138 45.455 13.12 0.00 0.00 3.95
2065 2096 3.554692 CGGCTTGAAGCGCGGTAG 61.555 66.667 12.91 6.74 43.62 3.18
2120 2151 2.345244 CGCAGCTTGGACAGAGGT 59.655 61.111 0.00 0.00 0.00 3.85
2337 2377 4.588899 ACAACCAAAGTAGCATGCTGATA 58.411 39.130 30.42 7.62 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 4.139786 ACTCCGCGGTAGATAATTACTGA 58.860 43.478 27.15 0.00 32.72 3.41
70 71 1.107945 TGATCATCAACTCCGCGGTA 58.892 50.000 27.15 11.20 0.00 4.02
95 96 6.320926 TCACCAGTGATTGATTTCAACTTCAA 59.679 34.615 0.00 0.00 38.86 2.69
101 102 4.452114 CGACTCACCAGTGATTGATTTCAA 59.548 41.667 0.04 0.00 39.13 2.69
115 116 3.716195 CCCATGGCCGACTCACCA 61.716 66.667 6.09 0.00 41.06 4.17
117 118 2.187946 CTCCCATGGCCGACTCAC 59.812 66.667 6.09 0.00 0.00 3.51
118 119 3.785859 GCTCCCATGGCCGACTCA 61.786 66.667 6.09 0.00 0.00 3.41
128 129 1.050204 GCTCATCTCTCTGCTCCCAT 58.950 55.000 0.00 0.00 0.00 4.00
129 130 1.047596 GGCTCATCTCTCTGCTCCCA 61.048 60.000 0.00 0.00 0.00 4.37
172 173 3.394800 CGATTGACTCGTTCGTCCA 57.605 52.632 0.00 0.00 42.56 4.02
220 221 1.300311 TCAACACGACGCGGTTGAT 60.300 52.632 23.66 3.21 46.01 2.57
224 225 0.731514 CTACATCAACACGACGCGGT 60.732 55.000 12.47 0.00 0.00 5.68
427 440 8.748412 CATCCCACAAAAGAAAAATATCAGGTA 58.252 33.333 0.00 0.00 0.00 3.08
433 446 7.598493 CACGTTCATCCCACAAAAGAAAAATAT 59.402 33.333 0.00 0.00 0.00 1.28
441 454 2.226330 TCCACGTTCATCCCACAAAAG 58.774 47.619 0.00 0.00 0.00 2.27
448 461 4.336889 TCTCAATATCCACGTTCATCCC 57.663 45.455 0.00 0.00 0.00 3.85
464 477 8.724229 CAGACAGTTGATATGTTTTGATCTCAA 58.276 33.333 0.00 0.00 0.00 3.02
467 480 8.890718 CATCAGACAGTTGATATGTTTTGATCT 58.109 33.333 0.00 0.00 36.08 2.75
484 497 1.863454 GCCGCTATCAACATCAGACAG 59.137 52.381 0.00 0.00 0.00 3.51
495 508 2.242043 TGATCAGATGAGCCGCTATCA 58.758 47.619 0.00 0.00 0.00 2.15
496 509 3.130869 AGATGATCAGATGAGCCGCTATC 59.869 47.826 0.09 0.00 0.00 2.08
497 510 3.098377 AGATGATCAGATGAGCCGCTAT 58.902 45.455 0.09 0.00 0.00 2.97
498 511 2.491298 GAGATGATCAGATGAGCCGCTA 59.509 50.000 0.09 0.00 0.00 4.26
499 512 1.273048 GAGATGATCAGATGAGCCGCT 59.727 52.381 0.09 0.00 0.00 5.52
500 513 1.672441 GGAGATGATCAGATGAGCCGC 60.672 57.143 0.09 0.00 0.00 6.53
501 514 1.617357 TGGAGATGATCAGATGAGCCG 59.383 52.381 0.09 0.00 0.00 5.52
502 515 2.613474 GCTGGAGATGATCAGATGAGCC 60.613 54.545 0.09 0.00 33.11 4.70
503 516 2.037381 TGCTGGAGATGATCAGATGAGC 59.963 50.000 0.09 5.64 33.11 4.26
504 517 3.863021 GCTGCTGGAGATGATCAGATGAG 60.863 52.174 0.09 0.00 33.11 2.90
505 518 2.037381 GCTGCTGGAGATGATCAGATGA 59.963 50.000 0.09 0.00 33.11 2.92
506 519 2.037902 AGCTGCTGGAGATGATCAGATG 59.962 50.000 0.00 0.00 33.11 2.90
507 520 2.331166 AGCTGCTGGAGATGATCAGAT 58.669 47.619 0.00 0.00 33.11 2.90
508 521 1.790818 AGCTGCTGGAGATGATCAGA 58.209 50.000 0.00 0.00 33.11 3.27
509 522 2.288948 GGTAGCTGCTGGAGATGATCAG 60.289 54.545 13.43 0.00 0.00 2.90
510 523 1.690893 GGTAGCTGCTGGAGATGATCA 59.309 52.381 13.43 0.00 0.00 2.92
511 524 1.001860 GGGTAGCTGCTGGAGATGATC 59.998 57.143 13.43 0.00 0.00 2.92
512 525 1.055040 GGGTAGCTGCTGGAGATGAT 58.945 55.000 13.43 0.00 0.00 2.45
513 526 0.031716 AGGGTAGCTGCTGGAGATGA 60.032 55.000 13.43 0.00 0.00 2.92
514 527 0.835941 AAGGGTAGCTGCTGGAGATG 59.164 55.000 13.43 0.00 0.00 2.90
515 528 1.488393 GAAAGGGTAGCTGCTGGAGAT 59.512 52.381 13.43 0.00 0.00 2.75
516 529 0.905357 GAAAGGGTAGCTGCTGGAGA 59.095 55.000 13.43 0.00 0.00 3.71
517 530 0.107459 GGAAAGGGTAGCTGCTGGAG 60.107 60.000 13.43 0.00 0.00 3.86
518 531 0.547712 AGGAAAGGGTAGCTGCTGGA 60.548 55.000 13.43 0.00 0.00 3.86
519 532 0.329596 AAGGAAAGGGTAGCTGCTGG 59.670 55.000 13.43 0.00 0.00 4.85
520 533 2.206576 AAAGGAAAGGGTAGCTGCTG 57.793 50.000 13.43 0.00 0.00 4.41
521 534 2.108250 TCAAAAGGAAAGGGTAGCTGCT 59.892 45.455 7.57 7.57 0.00 4.24
522 535 2.229062 GTCAAAAGGAAAGGGTAGCTGC 59.771 50.000 0.00 0.00 0.00 5.25
523 536 3.756117 AGTCAAAAGGAAAGGGTAGCTG 58.244 45.455 0.00 0.00 0.00 4.24
524 537 4.141251 TCAAGTCAAAAGGAAAGGGTAGCT 60.141 41.667 0.00 0.00 0.00 3.32
525 538 4.142038 TCAAGTCAAAAGGAAAGGGTAGC 58.858 43.478 0.00 0.00 0.00 3.58
526 539 6.150140 CAGATCAAGTCAAAAGGAAAGGGTAG 59.850 42.308 0.00 0.00 0.00 3.18
527 540 6.003950 CAGATCAAGTCAAAAGGAAAGGGTA 58.996 40.000 0.00 0.00 0.00 3.69
528 541 4.829492 CAGATCAAGTCAAAAGGAAAGGGT 59.171 41.667 0.00 0.00 0.00 4.34
529 542 4.829492 ACAGATCAAGTCAAAAGGAAAGGG 59.171 41.667 0.00 0.00 0.00 3.95
530 543 5.532406 TGACAGATCAAGTCAAAAGGAAAGG 59.468 40.000 15.93 0.00 42.57 3.11
531 544 6.624352 TGACAGATCAAGTCAAAAGGAAAG 57.376 37.500 15.93 0.00 42.57 2.62
541 554 9.755804 TCAAGTATTCATATGACAGATCAAGTC 57.244 33.333 4.48 10.42 38.69 3.01
547 560 9.842775 ACAACATCAAGTATTCATATGACAGAT 57.157 29.630 4.48 0.00 0.00 2.90
553 566 9.616634 GGCAATACAACATCAAGTATTCATATG 57.383 33.333 0.00 0.00 38.50 1.78
554 567 8.506437 CGGCAATACAACATCAAGTATTCATAT 58.494 33.333 0.00 0.00 38.50 1.78
555 568 7.041440 CCGGCAATACAACATCAAGTATTCATA 60.041 37.037 0.00 0.00 38.50 2.15
556 569 6.238731 CCGGCAATACAACATCAAGTATTCAT 60.239 38.462 0.00 0.00 38.50 2.57
566 579 2.812011 GGGTATCCGGCAATACAACATC 59.188 50.000 13.61 0.00 34.42 3.06
570 583 1.142060 CTGGGGTATCCGGCAATACAA 59.858 52.381 13.61 0.87 38.76 2.41
571 584 0.762418 CTGGGGTATCCGGCAATACA 59.238 55.000 13.61 1.04 38.76 2.29
572 585 1.053424 TCTGGGGTATCCGGCAATAC 58.947 55.000 0.00 0.00 41.78 1.89
580 593 4.161565 TCAACGCATATATCTGGGGTATCC 59.838 45.833 9.51 0.00 33.66 2.59
583 596 5.755409 AATCAACGCATATATCTGGGGTA 57.245 39.130 9.51 0.00 33.66 3.69
584 597 4.640771 AATCAACGCATATATCTGGGGT 57.359 40.909 9.51 0.36 33.66 4.95
586 599 4.761739 ACCAAATCAACGCATATATCTGGG 59.238 41.667 3.92 3.92 35.37 4.45
612 625 4.422073 TGACCTGAAGCTTATACATGGG 57.578 45.455 0.00 0.00 0.00 4.00
618 631 4.042062 CCCATGGATGACCTGAAGCTTATA 59.958 45.833 15.22 0.00 37.04 0.98
630 643 0.034059 CGCTACTCCCCATGGATGAC 59.966 60.000 15.22 0.00 40.80 3.06
634 647 3.161450 GGCGCTACTCCCCATGGA 61.161 66.667 15.22 0.00 38.75 3.41
649 662 2.317149 ATCTGCTAAGTCGCCAGGGC 62.317 60.000 0.00 0.00 37.85 5.19
651 664 1.156645 GCATCTGCTAAGTCGCCAGG 61.157 60.000 0.00 0.00 38.21 4.45
655 668 3.557595 AGTTTATGCATCTGCTAAGTCGC 59.442 43.478 0.19 0.00 42.66 5.19
656 669 4.210120 GGAGTTTATGCATCTGCTAAGTCG 59.790 45.833 0.19 0.00 42.66 4.18
659 672 4.024218 GCTGGAGTTTATGCATCTGCTAAG 60.024 45.833 0.19 2.85 42.66 2.18
661 674 3.470709 GCTGGAGTTTATGCATCTGCTA 58.529 45.455 0.19 0.00 42.66 3.49
662 675 2.295885 GCTGGAGTTTATGCATCTGCT 58.704 47.619 0.19 0.00 42.66 4.24
689 702 7.372260 ACACCAGAAAGAGAATATGAGCTAT 57.628 36.000 0.00 0.00 0.00 2.97
690 703 6.798427 ACACCAGAAAGAGAATATGAGCTA 57.202 37.500 0.00 0.00 0.00 3.32
696 709 6.681777 GTGCAAAACACCAGAAAGAGAATAT 58.318 36.000 0.00 0.00 44.02 1.28
703 716 5.712302 GTGTTCGTGCAAAACACCAGAAAG 61.712 45.833 25.29 0.00 46.88 2.62
707 721 1.544686 GTGTTCGTGCAAAACACCAG 58.455 50.000 25.29 0.00 46.88 4.00
717 731 3.870723 TTAGTGAATGTGTGTTCGTGC 57.129 42.857 0.00 0.00 0.00 5.34
723 737 5.590259 AGTTCTGCTTTTAGTGAATGTGTGT 59.410 36.000 0.00 0.00 0.00 3.72
756 776 0.320771 AGTTACCGCTGCTGTTGAGG 60.321 55.000 1.15 0.00 0.00 3.86
757 777 1.512926 AAGTTACCGCTGCTGTTGAG 58.487 50.000 1.15 0.00 0.00 3.02
773 794 8.617290 ACGGTTTCATAAAAGATCTGTTAAGT 57.383 30.769 9.44 0.00 0.00 2.24
774 795 8.175716 GGACGGTTTCATAAAAGATCTGTTAAG 58.824 37.037 9.44 5.55 0.00 1.85
775 796 7.662258 TGGACGGTTTCATAAAAGATCTGTTAA 59.338 33.333 9.44 0.00 0.00 2.01
778 799 5.556915 TGGACGGTTTCATAAAAGATCTGT 58.443 37.500 0.00 0.00 0.00 3.41
787 808 4.360951 AAAGTCCTGGACGGTTTCATAA 57.639 40.909 20.49 0.00 37.67 1.90
790 811 2.721425 AAAAGTCCTGGACGGTTTCA 57.279 45.000 20.49 0.00 37.67 2.69
791 812 3.251729 GGTTAAAAGTCCTGGACGGTTTC 59.748 47.826 25.17 16.31 37.67 2.78
792 813 3.216800 GGTTAAAAGTCCTGGACGGTTT 58.783 45.455 24.94 24.94 37.67 3.27
793 814 2.487805 GGGTTAAAAGTCCTGGACGGTT 60.488 50.000 20.49 19.08 37.67 4.44
794 815 1.072806 GGGTTAAAAGTCCTGGACGGT 59.927 52.381 20.49 10.45 37.67 4.83
795 816 1.350019 AGGGTTAAAAGTCCTGGACGG 59.650 52.381 20.49 0.00 37.67 4.79
797 818 2.557056 GCAAGGGTTAAAAGTCCTGGAC 59.443 50.000 19.20 19.20 0.00 4.02
799 820 2.296190 GTGCAAGGGTTAAAAGTCCTGG 59.704 50.000 0.00 0.00 0.00 4.45
800 821 2.031157 CGTGCAAGGGTTAAAAGTCCTG 60.031 50.000 0.00 0.00 0.00 3.86
801 822 2.158726 TCGTGCAAGGGTTAAAAGTCCT 60.159 45.455 0.00 0.00 0.00 3.85
802 823 2.031420 GTCGTGCAAGGGTTAAAAGTCC 60.031 50.000 0.00 0.00 0.00 3.85
803 824 2.876550 AGTCGTGCAAGGGTTAAAAGTC 59.123 45.455 0.00 0.00 0.00 3.01
804 825 2.876550 GAGTCGTGCAAGGGTTAAAAGT 59.123 45.455 0.00 0.00 0.00 2.66
805 826 2.096417 CGAGTCGTGCAAGGGTTAAAAG 60.096 50.000 3.82 0.00 0.00 2.27
806 827 1.868498 CGAGTCGTGCAAGGGTTAAAA 59.132 47.619 3.82 0.00 0.00 1.52
810 831 2.665185 GCGAGTCGTGCAAGGGTT 60.665 61.111 15.08 0.00 0.00 4.11
821 842 2.429571 TACCAACACGCGCGAGTC 60.430 61.111 39.36 0.00 0.00 3.36
826 847 3.475774 CTCCGTACCAACACGCGC 61.476 66.667 5.73 0.00 40.59 6.86
827 848 2.807895 CCTCCGTACCAACACGCG 60.808 66.667 3.53 3.53 40.59 6.01
828 849 3.116531 GCCTCCGTACCAACACGC 61.117 66.667 0.00 0.00 40.59 5.34
836 857 2.202756 CTTCGCTGGCCTCCGTAC 60.203 66.667 3.32 0.00 0.00 3.67
837 858 3.458163 CCTTCGCTGGCCTCCGTA 61.458 66.667 3.32 0.00 0.00 4.02
846 867 4.441695 TCTGAGCCGCCTTCGCTG 62.442 66.667 0.00 0.00 0.00 5.18
868 889 1.595093 CCTTTGCCTAAACCGCCCTG 61.595 60.000 0.00 0.00 0.00 4.45
875 896 1.197036 GTCGCTCACCTTTGCCTAAAC 59.803 52.381 0.00 0.00 0.00 2.01
899 920 4.692475 GCCACTGTTACGGCCCGT 62.692 66.667 15.63 15.63 42.82 5.28
907 928 1.292223 GTGCCTCGAGCCACTGTTA 59.708 57.895 18.70 0.00 42.71 2.41
916 937 4.180946 CCTCGTCGGTGCCTCGAG 62.181 72.222 5.13 5.13 46.77 4.04
936 957 4.218578 CTCGCGATGGCCTGAGCT 62.219 66.667 10.36 0.00 39.73 4.09
949 970 2.881352 GCGCCTACACTGTCTCGC 60.881 66.667 0.00 6.80 35.82 5.03
952 973 2.989824 ACCGCGCCTACACTGTCT 60.990 61.111 0.00 0.00 0.00 3.41
966 987 2.331194 CTAACACCAGTAAACCGACCG 58.669 52.381 0.00 0.00 0.00 4.79
967 988 2.071540 GCTAACACCAGTAAACCGACC 58.928 52.381 0.00 0.00 0.00 4.79
974 995 4.695396 TCGTTTCAAGCTAACACCAGTAA 58.305 39.130 0.00 0.00 0.00 2.24
990 1012 0.449388 CTTCTGCCATGGCTCGTTTC 59.551 55.000 35.53 7.32 42.51 2.78
994 1016 2.437180 TGCTTCTGCCATGGCTCG 60.437 61.111 35.53 25.71 42.51 5.03
996 1018 2.184020 TACGTGCTTCTGCCATGGCT 62.184 55.000 35.53 15.88 42.51 4.75
1004 1026 2.769617 CGCCGTTACGTGCTTCTG 59.230 61.111 14.06 0.00 0.00 3.02
1020 1042 4.421479 ACTTCTGAGTCGCCGGCG 62.421 66.667 42.13 42.13 41.35 6.46
1022 1044 2.125912 CCACTTCTGAGTCGCCGG 60.126 66.667 0.00 0.00 32.54 6.13
1024 1046 1.149148 GTTTCCACTTCTGAGTCGCC 58.851 55.000 0.00 0.00 32.54 5.54
1025 1047 1.865865 TGTTTCCACTTCTGAGTCGC 58.134 50.000 0.00 0.00 32.54 5.19
1029 1051 3.546815 CGTTGCTTGTTTCCACTTCTGAG 60.547 47.826 0.00 0.00 0.00 3.35
1042 1064 1.959226 CACCTACGCCGTTGCTTGT 60.959 57.895 0.00 0.00 34.43 3.16
1044 1066 1.666872 GACACCTACGCCGTTGCTT 60.667 57.895 0.00 0.00 34.43 3.91
1055 1077 1.890894 GCCGCTTCTGAGACACCTA 59.109 57.895 0.00 0.00 0.00 3.08
1061 1083 1.524008 TTGAGTCGCCGCTTCTGAGA 61.524 55.000 0.00 0.00 0.00 3.27
1066 1088 3.491652 GCCTTGAGTCGCCGCTTC 61.492 66.667 0.00 0.00 0.00 3.86
1088 1110 4.104417 GACGCCTCGAGCTGTCGT 62.104 66.667 16.30 16.21 46.85 4.34
1091 1113 3.671411 AACGACGCCTCGAGCTGT 61.671 61.111 12.14 7.24 43.06 4.40
1142 1164 0.393132 GCTGGGCTCTACTTCAACCC 60.393 60.000 0.00 0.00 41.24 4.11
1151 1173 0.618680 ATCACCACAGCTGGGCTCTA 60.619 55.000 19.93 0.00 42.74 2.43
1161 1183 0.246360 TGTCGCCTACATCACCACAG 59.754 55.000 0.00 0.00 31.43 3.66
1172 1194 3.075005 GAGCCACCCTGTCGCCTA 61.075 66.667 0.00 0.00 0.00 3.93
1176 1198 2.046892 CCTTGAGCCACCCTGTCG 60.047 66.667 0.00 0.00 0.00 4.35
1180 1202 2.227036 CCTCACCTTGAGCCACCCT 61.227 63.158 0.00 0.00 42.98 4.34
1269 1300 2.034687 TTTGCCTCTGAGCAGCCC 59.965 61.111 0.00 0.00 45.13 5.19
1273 1304 1.151221 TTGCCTTTGCCTCTGAGCA 59.849 52.632 0.00 0.00 42.17 4.26
1279 1310 1.576421 CGAGTGTTGCCTTTGCCTC 59.424 57.895 0.00 0.00 36.33 4.70
1290 1321 3.883744 CTGGCCGCTTCCGAGTGTT 62.884 63.158 0.00 0.00 36.29 3.32
1291 1322 4.379243 CTGGCCGCTTCCGAGTGT 62.379 66.667 0.00 0.00 36.29 3.55
1353 1384 3.480133 GGGCCGGCACCTACTCAT 61.480 66.667 30.85 0.00 0.00 2.90
1436 1467 1.878953 TGGTTCGACTCTGCCTTTTC 58.121 50.000 0.00 0.00 0.00 2.29
1444 1475 1.296715 GTGGCCATGGTTCGACTCT 59.703 57.895 9.72 0.00 0.00 3.24
1522 1553 1.063649 GTGCCATTGAGCATCTGCG 59.936 57.895 3.64 0.00 46.24 5.18
1531 1562 3.834013 TTCACCGCCGTGCCATTGA 62.834 57.895 0.00 0.00 40.04 2.57
1539 1570 4.003788 CCTCACCTTCACCGCCGT 62.004 66.667 0.00 0.00 0.00 5.68
1567 1598 0.179127 CGTCGTGATGAGAGCCACAT 60.179 55.000 0.00 0.00 33.13 3.21
1570 1601 0.960861 AGTCGTCGTGATGAGAGCCA 60.961 55.000 0.00 0.00 0.00 4.75
1571 1602 0.171455 AAGTCGTCGTGATGAGAGCC 59.829 55.000 0.00 0.00 0.00 4.70
1613 1644 0.821711 TTGCCACTTTGACCTTCCCG 60.822 55.000 0.00 0.00 0.00 5.14
1617 1648 3.118775 GGAACTTTTGCCACTTTGACCTT 60.119 43.478 0.00 0.00 0.00 3.50
1631 1662 1.416401 TGGCTGAGACGAGGAACTTTT 59.584 47.619 0.00 0.00 41.55 2.27
1632 1663 1.048601 TGGCTGAGACGAGGAACTTT 58.951 50.000 0.00 0.00 41.55 2.66
1633 1664 0.318762 GTGGCTGAGACGAGGAACTT 59.681 55.000 0.00 0.00 41.55 2.66
1635 1666 1.444553 CGTGGCTGAGACGAGGAAC 60.445 63.158 0.00 0.00 39.21 3.62
1636 1667 2.636412 CCGTGGCTGAGACGAGGAA 61.636 63.158 0.00 0.00 39.21 3.36
1637 1668 3.062466 CCGTGGCTGAGACGAGGA 61.062 66.667 0.00 0.00 39.21 3.71
1638 1669 3.057547 CTCCGTGGCTGAGACGAGG 62.058 68.421 0.00 0.00 39.21 4.63
1639 1670 2.487428 CTCCGTGGCTGAGACGAG 59.513 66.667 0.00 0.00 39.21 4.18
1640 1671 3.062466 CCTCCGTGGCTGAGACGA 61.062 66.667 0.00 0.00 39.21 4.20
1649 1680 4.514577 CGCCTACTGCCTCCGTGG 62.515 72.222 0.00 0.00 36.24 4.94
1652 1683 4.148825 AAGCGCCTACTGCCTCCG 62.149 66.667 2.29 0.00 36.24 4.63
1653 1684 2.512515 CAAGCGCCTACTGCCTCC 60.513 66.667 2.29 0.00 36.24 4.30
1654 1685 1.079127 TTCAAGCGCCTACTGCCTC 60.079 57.895 2.29 0.00 36.24 4.70
1655 1686 1.078848 CTTCAAGCGCCTACTGCCT 60.079 57.895 2.29 0.00 36.24 4.75
1656 1687 2.754995 GCTTCAAGCGCCTACTGCC 61.755 63.158 2.29 0.00 36.24 4.85
1657 1688 1.577328 TTGCTTCAAGCGCCTACTGC 61.577 55.000 2.29 4.37 46.26 4.40
1658 1689 0.445436 CTTGCTTCAAGCGCCTACTG 59.555 55.000 2.29 0.00 46.26 2.74
1659 1690 0.674895 CCTTGCTTCAAGCGCCTACT 60.675 55.000 2.29 0.00 46.26 2.57
1660 1691 1.796796 CCTTGCTTCAAGCGCCTAC 59.203 57.895 2.29 0.00 46.26 3.18
1661 1692 2.040544 GCCTTGCTTCAAGCGCCTA 61.041 57.895 2.29 0.00 46.26 3.93
1662 1693 3.368571 GCCTTGCTTCAAGCGCCT 61.369 61.111 2.29 0.00 46.26 5.52
1663 1694 4.426112 GGCCTTGCTTCAAGCGCC 62.426 66.667 10.60 10.60 46.26 6.53
1664 1695 3.673484 TGGCCTTGCTTCAAGCGC 61.673 61.111 4.57 0.00 46.26 5.92
1665 1696 2.074230 TTGTGGCCTTGCTTCAAGCG 62.074 55.000 4.57 0.00 46.26 4.68
1666 1697 0.319297 CTTGTGGCCTTGCTTCAAGC 60.319 55.000 1.04 1.04 39.85 4.01
1667 1698 0.316204 CCTTGTGGCCTTGCTTCAAG 59.684 55.000 3.32 8.95 40.75 3.02
1668 1699 1.114722 CCCTTGTGGCCTTGCTTCAA 61.115 55.000 3.32 0.00 0.00 2.69
1669 1700 1.531365 CCCTTGTGGCCTTGCTTCA 60.531 57.895 3.32 0.00 0.00 3.02
1670 1701 3.369921 CCCTTGTGGCCTTGCTTC 58.630 61.111 3.32 0.00 0.00 3.86
1682 1713 4.697756 TCACCTTCGCCGCCCTTG 62.698 66.667 0.00 0.00 0.00 3.61
1683 1714 4.394712 CTCACCTTCGCCGCCCTT 62.395 66.667 0.00 0.00 0.00 3.95
1691 1722 4.379243 ACGGCCTGCTCACCTTCG 62.379 66.667 0.00 0.00 0.00 3.79
1692 1723 2.743928 CACGGCCTGCTCACCTTC 60.744 66.667 0.00 0.00 0.00 3.46
1693 1724 4.335647 CCACGGCCTGCTCACCTT 62.336 66.667 0.00 0.00 0.00 3.50
1695 1726 3.665675 CTACCACGGCCTGCTCACC 62.666 68.421 0.00 0.00 0.00 4.02
1696 1727 2.125512 CTACCACGGCCTGCTCAC 60.126 66.667 0.00 0.00 0.00 3.51
1697 1728 1.476845 TTTCTACCACGGCCTGCTCA 61.477 55.000 0.00 0.00 0.00 4.26
1698 1729 0.741221 CTTTCTACCACGGCCTGCTC 60.741 60.000 0.00 0.00 0.00 4.26
1699 1730 1.192146 TCTTTCTACCACGGCCTGCT 61.192 55.000 0.00 0.00 0.00 4.24
1700 1731 0.741221 CTCTTTCTACCACGGCCTGC 60.741 60.000 0.00 0.00 0.00 4.85
1701 1732 0.108138 CCTCTTTCTACCACGGCCTG 60.108 60.000 0.00 0.00 0.00 4.85
1702 1733 1.900545 GCCTCTTTCTACCACGGCCT 61.901 60.000 0.00 0.00 0.00 5.19
1703 1734 1.449778 GCCTCTTTCTACCACGGCC 60.450 63.158 0.00 0.00 0.00 6.13
1704 1735 0.741221 CTGCCTCTTTCTACCACGGC 60.741 60.000 0.00 0.00 38.01 5.68
1705 1736 0.741221 GCTGCCTCTTTCTACCACGG 60.741 60.000 0.00 0.00 0.00 4.94
1706 1737 1.078759 CGCTGCCTCTTTCTACCACG 61.079 60.000 0.00 0.00 0.00 4.94
1707 1738 1.362406 GCGCTGCCTCTTTCTACCAC 61.362 60.000 0.00 0.00 0.00 4.16
1708 1739 1.079127 GCGCTGCCTCTTTCTACCA 60.079 57.895 0.00 0.00 0.00 3.25
1709 1740 1.815840 GGCGCTGCCTCTTTCTACC 60.816 63.158 7.64 0.00 46.69 3.18
1710 1741 3.801129 GGCGCTGCCTCTTTCTAC 58.199 61.111 7.64 0.00 46.69 2.59
1740 1771 3.890936 AACTCCTCACCGCTGCTGC 62.891 63.158 5.34 5.34 0.00 5.25
1741 1772 1.739562 GAACTCCTCACCGCTGCTG 60.740 63.158 0.00 0.00 0.00 4.41
1742 1773 2.659610 GAACTCCTCACCGCTGCT 59.340 61.111 0.00 0.00 0.00 4.24
1743 1774 2.811317 CGAACTCCTCACCGCTGC 60.811 66.667 0.00 0.00 0.00 5.25
1744 1775 2.125912 CCGAACTCCTCACCGCTG 60.126 66.667 0.00 0.00 0.00 5.18
1745 1776 2.282958 TCCGAACTCCTCACCGCT 60.283 61.111 0.00 0.00 0.00 5.52
1746 1777 2.182030 CTCCGAACTCCTCACCGC 59.818 66.667 0.00 0.00 0.00 5.68
1747 1778 2.182030 GCTCCGAACTCCTCACCG 59.818 66.667 0.00 0.00 0.00 4.94
1748 1779 2.579738 GGCTCCGAACTCCTCACC 59.420 66.667 0.00 0.00 0.00 4.02
1749 1780 2.579738 GGGCTCCGAACTCCTCAC 59.420 66.667 0.00 0.00 0.00 3.51
1772 1803 3.699894 AGTCACCTGAGCCGCCAG 61.700 66.667 2.75 2.75 0.00 4.85
1773 1804 4.007644 CAGTCACCTGAGCCGCCA 62.008 66.667 0.00 0.00 41.50 5.69
1774 1805 3.695606 TCAGTCACCTGAGCCGCC 61.696 66.667 0.00 0.00 42.80 6.13
1780 1811 1.979155 CTCGGCCTCAGTCACCTGA 60.979 63.158 0.00 0.00 45.44 3.86
1781 1812 2.575993 CTCGGCCTCAGTCACCTG 59.424 66.667 0.00 0.00 40.25 4.00
1782 1813 2.681778 CCTCGGCCTCAGTCACCT 60.682 66.667 0.00 0.00 0.00 4.00
1783 1814 3.775654 CCCTCGGCCTCAGTCACC 61.776 72.222 0.00 0.00 0.00 4.02
1784 1815 2.997897 ACCCTCGGCCTCAGTCAC 60.998 66.667 0.00 0.00 0.00 3.67
1785 1816 2.997315 CACCCTCGGCCTCAGTCA 60.997 66.667 0.00 0.00 0.00 3.41
1786 1817 3.775654 CCACCCTCGGCCTCAGTC 61.776 72.222 0.00 0.00 0.00 3.51
1801 1832 3.371063 GTCACCTCCGACGAGCCA 61.371 66.667 0.00 0.00 34.49 4.75
1883 1914 1.085091 CTCTACTGCTACGTCGTGGT 58.915 55.000 8.47 4.46 0.00 4.16
1884 1915 0.377554 CCTCTACTGCTACGTCGTGG 59.622 60.000 8.47 6.20 0.00 4.94
1887 1918 0.938713 CCTCCTCTACTGCTACGTCG 59.061 60.000 0.00 0.00 0.00 5.12
1892 1923 0.255033 TGCGACCTCCTCTACTGCTA 59.745 55.000 0.00 0.00 0.00 3.49
1928 1959 2.244117 GACTTGGGCTGCGATCTCCA 62.244 60.000 0.00 0.00 0.00 3.86
1979 2010 2.589798 ACGACTCGAAGGAAAACACA 57.410 45.000 5.20 0.00 0.00 3.72
2000 2031 2.751436 CGGCCCACCATGGAAGTG 60.751 66.667 21.47 6.27 40.96 3.16
2109 2140 2.879233 GCCGGTCACCTCTGTCCAA 61.879 63.158 1.90 0.00 0.00 3.53
2191 2222 0.171455 ACACGACTCTTCATCCTCGC 59.829 55.000 0.00 0.00 0.00 5.03
2200 2231 1.267261 CAAGACGAGGACACGACTCTT 59.733 52.381 0.00 0.00 37.31 2.85
2252 2284 5.126384 AGGACAGATGAGCTACACTAGAAAC 59.874 44.000 0.00 0.00 0.00 2.78


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

AutoCloner maintained by Alex Coulton.