Multiple sequence alignment - TraesCS7A01G556800

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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 TraesCS7A01G556800 chr7A 100.000 4548 0 0 1 4548 727851735 727847188 0.000000e+00 8399
1 TraesCS7A01G556800 chr7A 97.205 644 18 0 1504 2147 727838868 727838225 0.000000e+00 1090
2 TraesCS7A01G556800 chr7D 96.248 3305 77 19 611 3892 638259535 638262815 0.000000e+00 5373
3 TraesCS7A01G556800 chr7D 95.425 459 9 6 1 454 638259087 638259538 0.000000e+00 721
4 TraesCS7A01G556800 chr7D 90.090 111 7 2 3942 4048 638262814 638262924 1.710000e-29 141
5 TraesCS7A01G556800 chr7B 95.236 2834 96 18 628 3454 734683686 734686487 0.000000e+00 4449
6 TraesCS7A01G556800 chr7B 90.964 332 19 7 3566 3892 734686503 734686828 1.940000e-118 436
7 TraesCS7A01G556800 chr7B 78.854 506 90 8 4041 4543 748663357 748663848 4.390000e-85 326
8 TraesCS7A01G556800 chr7B 81.882 287 47 5 4258 4543 734698683 734698965 2.110000e-58 237
9 TraesCS7A01G556800 chr7B 93.525 139 8 1 118 256 734683388 734683525 5.960000e-49 206
10 TraesCS7A01G556800 chr6B 79.121 728 142 10 1083 1805 717537685 717538407 1.140000e-135 494
11 TraesCS7A01G556800 chr6B 78.846 624 128 4 2813 3434 717539230 717539851 7.040000e-113 418
12 TraesCS7A01G556800 chr6B 77.228 505 94 10 4041 4543 630859348 630859833 4.480000e-70 276
13 TraesCS7A01G556800 chr6B 96.364 165 6 0 451 615 699977610 699977446 5.800000e-69 272
14 TraesCS7A01G556800 chr6B 93.889 180 8 2 442 621 139468721 139468545 7.500000e-68 268
15 TraesCS7A01G556800 chr6D 79.133 623 128 2 2813 3434 472526658 472527279 3.250000e-116 429
16 TraesCS7A01G556800 chr6D 96.933 163 5 0 451 613 15801110 15801272 1.610000e-69 274
17 TraesCS7A01G556800 chr6A 78.710 620 130 2 2816 3434 617182709 617182091 3.270000e-111 412
18 TraesCS7A01G556800 chr3A 81.065 507 81 10 4041 4543 655724558 655725053 1.530000e-104 390
19 TraesCS7A01G556800 chr5B 80.864 486 85 8 4041 4521 41908030 41908512 4.300000e-100 375
20 TraesCS7A01G556800 chr5B 79.098 488 81 13 4041 4521 53739859 53740332 2.640000e-82 316
21 TraesCS7A01G556800 chr5B 75.624 521 96 19 4041 4543 704987609 704987102 3.540000e-56 230
22 TraesCS7A01G556800 chr2D 79.568 509 96 7 4041 4546 608535752 608535249 1.560000e-94 357
23 TraesCS7A01G556800 chr3B 79.727 513 82 10 4041 4546 104804998 104804501 7.240000e-93 351
24 TraesCS7A01G556800 chr3B 95.882 170 6 1 444 612 19992006 19991837 1.610000e-69 274
25 TraesCS7A01G556800 chr4A 77.778 486 99 7 4043 4521 701101890 701102373 1.600000e-74 291
26 TraesCS7A01G556800 chr2B 95.376 173 8 0 449 621 237581573 237581401 4.480000e-70 276
27 TraesCS7A01G556800 chr4B 96.914 162 5 0 451 612 63754002 63753841 5.800000e-69 272
28 TraesCS7A01G556800 chr5D 96.341 164 6 0 450 613 537178187 537178350 2.090000e-68 270
29 TraesCS7A01G556800 chr4D 95.833 168 6 1 451 618 230542711 230542545 2.090000e-68 270
30 TraesCS7A01G556800 chr4D 80.556 324 56 5 4143 4462 471193436 471193116 4.550000e-60 243
31 TraesCS7A01G556800 chr1D 94.286 175 9 1 451 625 427826921 427827094 2.700000e-67 267
32 TraesCS7A01G556800 chr1B 75.962 520 93 19 4041 4543 14129238 14129742 5.880000e-59 239


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 TraesCS7A01G556800 chr7A 727847188 727851735 4547 True 8399.000000 8399 100.000000 1 4548 1 chr7A.!!$R2 4547
1 TraesCS7A01G556800 chr7A 727838225 727838868 643 True 1090.000000 1090 97.205000 1504 2147 1 chr7A.!!$R1 643
2 TraesCS7A01G556800 chr7D 638259087 638262924 3837 False 2078.333333 5373 93.921000 1 4048 3 chr7D.!!$F1 4047
3 TraesCS7A01G556800 chr7B 734683388 734686828 3440 False 1697.000000 4449 93.241667 118 3892 3 chr7B.!!$F3 3774
4 TraesCS7A01G556800 chr6B 717537685 717539851 2166 False 456.000000 494 78.983500 1083 3434 2 chr6B.!!$F2 2351
5 TraesCS7A01G556800 chr6D 472526658 472527279 621 False 429.000000 429 79.133000 2813 3434 1 chr6D.!!$F2 621
6 TraesCS7A01G556800 chr6A 617182091 617182709 618 True 412.000000 412 78.710000 2816 3434 1 chr6A.!!$R1 618
7 TraesCS7A01G556800 chr5B 704987102 704987609 507 True 230.000000 230 75.624000 4041 4543 1 chr5B.!!$R1 502
8 TraesCS7A01G556800 chr2D 608535249 608535752 503 True 357.000000 357 79.568000 4041 4546 1 chr2D.!!$R1 505
9 TraesCS7A01G556800 chr1B 14129238 14129742 504 False 239.000000 239 75.962000 4041 4543 1 chr1B.!!$F1 502

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
722 752 0.462047 GATAAGTGAGGCACGGTGGG 60.462 60.000 10.6 0.0 39.64 4.61 F
775 809 0.462581 CGGTGGGACTCCATGTGATG 60.463 60.000 0.0 0.0 46.09 3.07 F
1051 1096 1.064017 TCTCTTCTCCCTCCTCTGCTC 60.064 57.143 0.0 0.0 0.00 4.26 F
2758 2921 0.320683 TCATCACCTTGTGCCTGACG 60.321 55.000 0.0 0.0 32.98 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1819 1864 2.561956 CGTCACCGTGTCCCTCTGT 61.562 63.158 0.00 0.00 0.00 3.41 R
2740 2903 0.603707 ACGTCAGGCACAAGGTGATG 60.604 55.000 0.00 0.00 35.23 3.07 R
2801 2964 0.736325 GGAGAACTGCATGCGTACGT 60.736 55.000 17.90 4.56 0.00 3.57 R
4062 4244 0.033504 CACTAGTGTCCACGCCACTT 59.966 55.000 15.06 0.00 42.83 3.16 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
27 28 6.042777 GCATCTCCTTTAATAAAAGTTGGGC 58.957 40.000 0.00 0.00 40.51 5.36
272 273 9.289782 AGGCATATATTGGTCTAAAAACATCTC 57.710 33.333 0.00 0.00 0.00 2.75
369 370 5.688807 ACTGGGGACAATAAGATCTCAATG 58.311 41.667 0.00 0.00 42.06 2.82
371 372 3.823304 GGGGACAATAAGATCTCAATGCC 59.177 47.826 0.00 1.87 0.00 4.40
374 375 5.360714 GGGACAATAAGATCTCAATGCCAAA 59.639 40.000 0.00 0.00 0.00 3.28
375 376 6.460676 GGGACAATAAGATCTCAATGCCAAAG 60.461 42.308 0.00 0.00 0.00 2.77
455 463 9.601217 AAGAAAGATGTGTGTAATGTATACTCC 57.399 33.333 4.17 0.00 0.00 3.85
456 464 8.204836 AGAAAGATGTGTGTAATGTATACTCCC 58.795 37.037 4.17 0.00 0.00 4.30
457 465 7.676683 AAGATGTGTGTAATGTATACTCCCT 57.323 36.000 4.17 0.00 0.00 4.20
458 466 7.291411 AGATGTGTGTAATGTATACTCCCTC 57.709 40.000 4.17 0.00 0.00 4.30
459 467 5.864418 TGTGTGTAATGTATACTCCCTCC 57.136 43.478 4.17 0.00 0.00 4.30
460 468 4.340097 TGTGTGTAATGTATACTCCCTCCG 59.660 45.833 4.17 0.00 0.00 4.63
461 469 4.340381 GTGTGTAATGTATACTCCCTCCGT 59.660 45.833 4.17 0.00 0.00 4.69
462 470 4.957954 TGTGTAATGTATACTCCCTCCGTT 59.042 41.667 4.17 0.00 0.00 4.44
463 471 5.068198 TGTGTAATGTATACTCCCTCCGTTC 59.932 44.000 4.17 0.00 0.00 3.95
464 472 4.586001 TGTAATGTATACTCCCTCCGTTCC 59.414 45.833 4.17 0.00 0.00 3.62
465 473 3.614568 ATGTATACTCCCTCCGTTCCT 57.385 47.619 4.17 0.00 0.00 3.36
466 474 4.736611 ATGTATACTCCCTCCGTTCCTA 57.263 45.455 4.17 0.00 0.00 2.94
467 475 4.524802 TGTATACTCCCTCCGTTCCTAA 57.475 45.455 4.17 0.00 0.00 2.69
468 476 4.870636 TGTATACTCCCTCCGTTCCTAAA 58.129 43.478 4.17 0.00 0.00 1.85
469 477 5.461327 TGTATACTCCCTCCGTTCCTAAAT 58.539 41.667 4.17 0.00 0.00 1.40
470 478 6.613699 TGTATACTCCCTCCGTTCCTAAATA 58.386 40.000 4.17 0.00 0.00 1.40
471 479 7.243824 TGTATACTCCCTCCGTTCCTAAATAT 58.756 38.462 4.17 0.00 0.00 1.28
472 480 8.393259 TGTATACTCCCTCCGTTCCTAAATATA 58.607 37.037 4.17 0.00 0.00 0.86
473 481 9.247861 GTATACTCCCTCCGTTCCTAAATATAA 57.752 37.037 0.00 0.00 0.00 0.98
474 482 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
475 483 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
476 484 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
477 485 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
478 486 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
479 487 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
480 488 8.645110 CCCTCCGTTCCTAAATATAAGTCTTTA 58.355 37.037 0.00 0.00 0.00 1.85
508 516 8.353684 AGAGATTTCACTATGAACTACATACGG 58.646 37.037 0.00 0.00 35.89 4.02
509 517 8.234136 AGATTTCACTATGAACTACATACGGA 57.766 34.615 0.00 0.00 35.89 4.69
510 518 8.353684 AGATTTCACTATGAACTACATACGGAG 58.646 37.037 0.00 0.00 35.89 4.63
511 519 5.434352 TCACTATGAACTACATACGGAGC 57.566 43.478 0.00 0.00 40.07 4.70
512 520 4.885325 TCACTATGAACTACATACGGAGCA 59.115 41.667 0.00 0.00 40.07 4.26
513 521 5.358725 TCACTATGAACTACATACGGAGCAA 59.641 40.000 0.00 0.00 40.07 3.91
514 522 6.040247 CACTATGAACTACATACGGAGCAAA 58.960 40.000 0.00 0.00 40.07 3.68
515 523 6.533723 CACTATGAACTACATACGGAGCAAAA 59.466 38.462 0.00 0.00 40.07 2.44
516 524 7.224753 CACTATGAACTACATACGGAGCAAAAT 59.775 37.037 0.00 0.00 40.07 1.82
517 525 5.794687 TGAACTACATACGGAGCAAAATG 57.205 39.130 0.00 0.00 0.00 2.32
518 526 5.483811 TGAACTACATACGGAGCAAAATGA 58.516 37.500 0.00 0.00 0.00 2.57
519 527 5.580691 TGAACTACATACGGAGCAAAATGAG 59.419 40.000 0.00 0.00 0.00 2.90
520 528 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
521 529 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
522 530 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
523 531 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
524 532 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
525 533 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
526 534 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
527 535 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
528 536 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
529 537 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
530 538 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
543 551 8.430801 AGTGAATCTACACTCTAAAATGCATC 57.569 34.615 0.00 0.00 46.36 3.91
544 552 8.263640 AGTGAATCTACACTCTAAAATGCATCT 58.736 33.333 0.00 0.00 46.36 2.90
545 553 9.534565 GTGAATCTACACTCTAAAATGCATCTA 57.465 33.333 0.00 0.00 37.73 1.98
546 554 9.534565 TGAATCTACACTCTAAAATGCATCTAC 57.465 33.333 0.00 0.00 0.00 2.59
547 555 9.534565 GAATCTACACTCTAAAATGCATCTACA 57.465 33.333 0.00 0.00 0.00 2.74
550 558 9.967346 TCTACACTCTAAAATGCATCTACATAC 57.033 33.333 0.00 0.00 0.00 2.39
551 559 9.750125 CTACACTCTAAAATGCATCTACATACA 57.250 33.333 0.00 0.00 0.00 2.29
553 561 9.265901 ACACTCTAAAATGCATCTACATACATC 57.734 33.333 0.00 0.00 0.00 3.06
554 562 8.715998 CACTCTAAAATGCATCTACATACATCC 58.284 37.037 0.00 0.00 0.00 3.51
555 563 7.600375 ACTCTAAAATGCATCTACATACATCCG 59.400 37.037 0.00 0.00 0.00 4.18
556 564 7.441836 TCTAAAATGCATCTACATACATCCGT 58.558 34.615 0.00 0.00 0.00 4.69
557 565 8.581578 TCTAAAATGCATCTACATACATCCGTA 58.418 33.333 0.00 0.00 0.00 4.02
558 566 9.371136 CTAAAATGCATCTACATACATCCGTAT 57.629 33.333 0.00 0.00 38.96 3.06
569 577 6.951256 CATACATCCGTATGTGGTTCATAG 57.049 41.667 3.56 0.00 46.70 2.23
570 578 6.455647 CATACATCCGTATGTGGTTCATAGT 58.544 40.000 3.56 0.00 46.70 2.12
571 579 4.693283 ACATCCGTATGTGGTTCATAGTG 58.307 43.478 0.00 0.00 44.79 2.74
572 580 4.404394 ACATCCGTATGTGGTTCATAGTGA 59.596 41.667 0.00 0.00 44.79 3.41
573 581 5.105106 ACATCCGTATGTGGTTCATAGTGAA 60.105 40.000 0.00 0.00 44.79 3.18
574 582 5.408880 TCCGTATGTGGTTCATAGTGAAA 57.591 39.130 0.00 0.00 38.22 2.69
575 583 5.984725 TCCGTATGTGGTTCATAGTGAAAT 58.015 37.500 0.00 0.00 38.22 2.17
576 584 6.411376 TCCGTATGTGGTTCATAGTGAAATT 58.589 36.000 0.00 0.00 38.22 1.82
577 585 6.537301 TCCGTATGTGGTTCATAGTGAAATTC 59.463 38.462 0.00 0.00 38.22 2.17
578 586 6.238374 CCGTATGTGGTTCATAGTGAAATTCC 60.238 42.308 0.00 0.00 38.22 3.01
579 587 6.538742 CGTATGTGGTTCATAGTGAAATTCCT 59.461 38.462 0.00 0.00 38.22 3.36
580 588 7.254455 CGTATGTGGTTCATAGTGAAATTCCTC 60.254 40.741 0.00 0.00 38.22 3.71
581 589 5.253330 TGTGGTTCATAGTGAAATTCCTCC 58.747 41.667 0.00 0.00 38.22 4.30
582 590 5.222027 TGTGGTTCATAGTGAAATTCCTCCA 60.222 40.000 0.00 0.00 38.22 3.86
583 591 5.710099 GTGGTTCATAGTGAAATTCCTCCAA 59.290 40.000 0.00 0.00 38.22 3.53
584 592 6.208599 GTGGTTCATAGTGAAATTCCTCCAAA 59.791 38.462 0.00 0.00 38.22 3.28
585 593 6.434028 TGGTTCATAGTGAAATTCCTCCAAAG 59.566 38.462 0.00 0.00 38.22 2.77
586 594 6.659242 GGTTCATAGTGAAATTCCTCCAAAGA 59.341 38.462 0.00 0.00 38.22 2.52
587 595 7.362142 GGTTCATAGTGAAATTCCTCCAAAGAC 60.362 40.741 0.00 0.00 38.22 3.01
588 596 7.020827 TCATAGTGAAATTCCTCCAAAGACT 57.979 36.000 0.00 0.00 0.00 3.24
589 597 7.461749 TCATAGTGAAATTCCTCCAAAGACTT 58.538 34.615 0.00 0.00 0.00 3.01
590 598 8.602424 TCATAGTGAAATTCCTCCAAAGACTTA 58.398 33.333 0.00 0.00 0.00 2.24
591 599 9.401058 CATAGTGAAATTCCTCCAAAGACTTAT 57.599 33.333 0.00 0.00 0.00 1.73
594 602 9.981460 AGTGAAATTCCTCCAAAGACTTATATT 57.019 29.630 0.00 0.00 0.00 1.28
601 609 9.901172 TTCCTCCAAAGACTTATATTTAGGAAC 57.099 33.333 0.00 0.00 32.50 3.62
602 610 8.202137 TCCTCCAAAGACTTATATTTAGGAACG 58.798 37.037 0.00 0.00 26.20 3.95
603 611 7.441458 CCTCCAAAGACTTATATTTAGGAACGG 59.559 40.741 0.00 0.00 0.00 4.44
604 612 8.081517 TCCAAAGACTTATATTTAGGAACGGA 57.918 34.615 0.00 0.00 0.00 4.69
605 613 8.202137 TCCAAAGACTTATATTTAGGAACGGAG 58.798 37.037 0.00 0.00 0.00 4.63
606 614 7.441458 CCAAAGACTTATATTTAGGAACGGAGG 59.559 40.741 0.00 0.00 0.00 4.30
607 615 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
608 616 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
609 617 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
610 618 6.141790 ACTTATATTTAGGAACGGAGGGAGT 58.858 40.000 0.00 0.00 0.00 3.85
611 619 7.300658 ACTTATATTTAGGAACGGAGGGAGTA 58.699 38.462 0.00 0.00 0.00 2.59
612 620 7.232330 ACTTATATTTAGGAACGGAGGGAGTAC 59.768 40.741 0.00 0.00 0.00 2.73
613 621 3.463048 TTTAGGAACGGAGGGAGTACT 57.537 47.619 0.00 0.00 0.00 2.73
681 693 1.583404 CAAAACAGAGCAAACACACGC 59.417 47.619 0.00 0.00 0.00 5.34
722 752 0.462047 GATAAGTGAGGCACGGTGGG 60.462 60.000 10.60 0.00 39.64 4.61
725 755 3.626924 GTGAGGCACGGTGGGAGT 61.627 66.667 10.60 0.00 0.00 3.85
743 773 1.001974 AGTGCATGTGACCGTGTATGT 59.998 47.619 0.00 0.00 0.00 2.29
754 784 2.359354 TGTATGTGGCACGGTGGC 60.359 61.111 25.93 25.93 44.03 5.01
775 809 0.462581 CGGTGGGACTCCATGTGATG 60.463 60.000 0.00 0.00 46.09 3.07
822 856 3.432051 GACCGACCGAGGCTGGATG 62.432 68.421 9.53 2.41 33.69 3.51
891 929 3.178046 GAAGGAGGAGGAGGAAGACTTT 58.822 50.000 0.00 0.00 0.00 2.66
997 1036 6.295462 CCATATGATCCATTTTCCCATCCAAC 60.295 42.308 3.65 0.00 0.00 3.77
1051 1096 1.064017 TCTCTTCTCCCTCCTCTGCTC 60.064 57.143 0.00 0.00 0.00 4.26
1390 1435 4.148825 GTGCTCCTCATCGCCCGT 62.149 66.667 0.00 0.00 0.00 5.28
2464 2589 1.264749 ACCTGCACGAGGAAGGCATA 61.265 55.000 5.88 0.00 46.33 3.14
2587 2712 3.083997 ATCGGACAGAGCCCCACC 61.084 66.667 0.00 0.00 0.00 4.61
2740 2903 5.405571 CCAGCAGGTACGTGTTCAATATATC 59.594 44.000 16.36 0.00 0.00 1.63
2745 2908 7.359264 GCAGGTACGTGTTCAATATATCATCAC 60.359 40.741 16.36 0.00 0.00 3.06
2752 2915 7.134815 GTGTTCAATATATCATCACCTTGTGC 58.865 38.462 0.00 0.00 32.98 4.57
2758 2921 0.320683 TCATCACCTTGTGCCTGACG 60.321 55.000 0.00 0.00 32.98 4.35
2793 2956 2.182842 GCTGACATGGATCCCACGC 61.183 63.158 9.90 2.37 35.80 5.34
2801 2964 2.359850 GATCCCACGCTGCCAACA 60.360 61.111 0.00 0.00 0.00 3.33
2802 2965 2.672996 ATCCCACGCTGCCAACAC 60.673 61.111 0.00 0.00 0.00 3.32
2931 3094 0.678395 CCACCTCCATCCTCATCTCG 59.322 60.000 0.00 0.00 0.00 4.04
2994 3157 1.059098 TGTGGCTCATGGACTTGTCT 58.941 50.000 0.00 0.00 0.00 3.41
3153 3316 1.508088 CTTCGTCATGGGCTTTGGC 59.492 57.895 0.00 0.00 37.82 4.52
3351 3514 4.135493 GCGCTTGTCTTCGTCGCC 62.135 66.667 0.00 0.00 39.91 5.54
3451 3618 8.006564 TCCCAGAGCAGATGGATTAATTAATTT 58.993 33.333 11.92 1.28 40.51 1.82
3452 3619 9.300681 CCCAGAGCAGATGGATTAATTAATTTA 57.699 33.333 11.92 0.00 40.51 1.40
3494 3661 2.330440 TGGTCGATGATCCAACCATG 57.670 50.000 9.55 0.00 36.88 3.66
3508 3675 7.684186 TGATCCAACCATGAGGAGGTAATATAT 59.316 37.037 0.00 0.00 38.76 0.86
3509 3676 9.213777 GATCCAACCATGAGGAGGTAATATATA 57.786 37.037 0.00 0.00 38.76 0.86
3510 3677 8.609617 TCCAACCATGAGGAGGTAATATATAG 57.390 38.462 0.00 0.00 38.76 1.31
3584 3752 1.615384 GGGTCTCTTGCTCCATGCTTT 60.615 52.381 0.00 0.00 43.37 3.51
3599 3767 0.595825 GCTTTGCTATTCATGCGGCC 60.596 55.000 0.00 0.00 0.00 6.13
3612 3780 4.621068 CATGCGGCCATGTTATATTAGG 57.379 45.455 2.24 0.00 43.07 2.69
3613 3781 2.432444 TGCGGCCATGTTATATTAGGC 58.568 47.619 2.24 0.00 44.48 3.93
3614 3782 2.039746 TGCGGCCATGTTATATTAGGCT 59.960 45.455 2.24 0.00 44.60 4.58
3616 3784 4.258543 GCGGCCATGTTATATTAGGCTAA 58.741 43.478 9.79 9.79 44.60 3.09
3805 3978 9.962783 TTGAATTTTATTCCTTTTTGCCAATTG 57.037 25.926 0.00 0.00 0.00 2.32
3806 3979 9.347240 TGAATTTTATTCCTTTTTGCCAATTGA 57.653 25.926 7.12 0.00 0.00 2.57
3808 3981 8.922931 ATTTTATTCCTTTTTGCCAATTGAGT 57.077 26.923 7.12 0.00 0.00 3.41
3816 3989 7.338957 TCCTTTTTGCCAATTGAGTTGAATTTT 59.661 29.630 7.12 0.00 40.37 1.82
3862 4040 9.546909 GCATGCATGTATTAAGTGTTGTATATC 57.453 33.333 26.79 0.46 0.00 1.63
3875 4053 8.954950 AGTGTTGTATATCCTTTCATTCTGAG 57.045 34.615 0.00 0.00 0.00 3.35
3916 4094 4.320608 CCCCCGTTTATCCATTTTGATG 57.679 45.455 0.00 0.00 0.00 3.07
3917 4095 3.069443 CCCCCGTTTATCCATTTTGATGG 59.931 47.826 0.00 0.00 43.01 3.51
3918 4096 3.492482 CCCCGTTTATCCATTTTGATGGC 60.492 47.826 0.52 0.00 41.43 4.40
3919 4097 3.131933 CCCGTTTATCCATTTTGATGGCA 59.868 43.478 0.00 0.00 41.43 4.92
3920 4098 4.382470 CCCGTTTATCCATTTTGATGGCAA 60.382 41.667 0.00 0.00 41.43 4.52
3921 4099 5.358922 CCGTTTATCCATTTTGATGGCAAT 58.641 37.500 0.00 0.00 41.43 3.56
3922 4100 5.816777 CCGTTTATCCATTTTGATGGCAATT 59.183 36.000 0.00 0.00 41.43 2.32
3923 4101 6.983307 CCGTTTATCCATTTTGATGGCAATTA 59.017 34.615 0.00 0.00 41.43 1.40
3924 4102 7.656948 CCGTTTATCCATTTTGATGGCAATTAT 59.343 33.333 0.00 0.00 41.43 1.28
3925 4103 9.044150 CGTTTATCCATTTTGATGGCAATTATT 57.956 29.630 0.00 0.00 41.43 1.40
3930 4108 9.635404 ATCCATTTTGATGGCAATTATTTTCAT 57.365 25.926 0.00 0.00 41.43 2.57
3933 4111 9.852481 CATTTTGATGGCAATTATTTTCATACG 57.148 29.630 0.00 0.00 33.25 3.06
3934 4112 8.417780 TTTTGATGGCAATTATTTTCATACGG 57.582 30.769 0.00 0.00 33.25 4.02
3935 4113 6.951062 TGATGGCAATTATTTTCATACGGA 57.049 33.333 0.00 0.00 0.00 4.69
3936 4114 6.969366 TGATGGCAATTATTTTCATACGGAG 58.031 36.000 0.00 0.00 0.00 4.63
3937 4115 5.766150 TGGCAATTATTTTCATACGGAGG 57.234 39.130 0.00 0.00 0.00 4.30
3938 4116 4.582656 TGGCAATTATTTTCATACGGAGGG 59.417 41.667 0.00 0.00 0.00 4.30
3939 4117 4.825085 GGCAATTATTTTCATACGGAGGGA 59.175 41.667 0.00 0.00 0.00 4.20
3940 4118 5.048713 GGCAATTATTTTCATACGGAGGGAG 60.049 44.000 0.00 0.00 0.00 4.30
3966 4146 3.987220 TCACTCACATGTCACAACGTATG 59.013 43.478 0.00 0.00 0.00 2.39
3969 4149 2.478514 TCACATGTCACAACGTATGCAC 59.521 45.455 0.00 0.00 0.00 4.57
3973 4153 3.372660 TGTCACAACGTATGCACTACA 57.627 42.857 0.00 0.00 0.00 2.74
4075 4257 4.980805 GCGGAAGTGGCGTGGACA 62.981 66.667 0.00 0.00 0.00 4.02
4087 4269 0.589708 CGTGGACACTAGTGACGACA 59.410 55.000 28.85 19.22 34.84 4.35
4122 4304 1.621317 TGGAGTTGTTGCCGATGAGTA 59.379 47.619 0.00 0.00 0.00 2.59
4126 4308 4.491676 GAGTTGTTGCCGATGAGTAGTTA 58.508 43.478 0.00 0.00 0.00 2.24
4134 4316 4.577693 TGCCGATGAGTAGTTATAGACGTT 59.422 41.667 0.00 0.00 0.00 3.99
4139 4321 3.382546 TGAGTAGTTATAGACGTTGCCCC 59.617 47.826 0.00 0.00 0.00 5.80
4153 4335 1.324005 TGCCCCGTATGTCGATGTCA 61.324 55.000 0.00 0.00 42.86 3.58
4160 4342 3.314357 CCGTATGTCGATGTCAAGGTAGA 59.686 47.826 0.00 0.00 42.86 2.59
4191 4403 0.821517 TAGCCGTGGTCGATGATGTT 59.178 50.000 0.00 0.00 39.71 2.71
4198 4410 1.271102 TGGTCGATGATGTTGTCGTCA 59.729 47.619 0.00 0.00 42.00 4.35
4211 4423 5.487433 TGTTGTCGTCATGGATAATGAAGT 58.513 37.500 0.00 0.00 46.90 3.01
4212 4424 5.937540 TGTTGTCGTCATGGATAATGAAGTT 59.062 36.000 0.00 0.00 46.90 2.66
4225 4437 1.021202 TGAAGTTGCACAAAGTCGGG 58.979 50.000 0.00 0.00 0.00 5.14
4229 4441 3.723097 TTGCACAAAGTCGGGGGCA 62.723 57.895 0.00 0.00 0.00 5.36
4297 4510 3.101209 CACATTGCGGATGTCGGG 58.899 61.111 2.81 0.00 45.88 5.14
4321 4534 0.103208 GCCTTCGACGATGAGTCCAT 59.897 55.000 11.97 0.00 46.92 3.41
4336 4549 3.511477 AGTCCATCGGCTATGTAAGGAT 58.489 45.455 0.00 0.00 33.34 3.24
4337 4550 3.259374 AGTCCATCGGCTATGTAAGGATG 59.741 47.826 0.00 0.00 35.44 3.51
4382 4595 1.669440 GTCTTGCCAGGACCGTGTA 59.331 57.895 0.00 0.00 0.00 2.90
4383 4596 0.249398 GTCTTGCCAGGACCGTGTAT 59.751 55.000 0.00 0.00 0.00 2.29
4389 4602 1.317431 CCAGGACCGTGTATCCGTGA 61.317 60.000 0.00 0.00 41.52 4.35
4390 4603 0.528924 CAGGACCGTGTATCCGTGAA 59.471 55.000 0.00 0.00 41.52 3.18
4396 4609 1.087771 CGTGTATCCGTGAAAGGGGC 61.088 60.000 0.00 0.00 43.54 5.80
4405 4618 0.035739 GTGAAAGGGGCCGTCACTAA 59.964 55.000 20.33 0.00 38.87 2.24
4407 4620 1.353022 TGAAAGGGGCCGTCACTAAAT 59.647 47.619 0.00 0.00 0.00 1.40
4410 4623 0.034477 AGGGGCCGTCACTAAATTGG 60.034 55.000 0.00 0.00 0.00 3.16
4413 4626 1.303091 GGCCGTCACTAAATTGGCGT 61.303 55.000 0.00 0.00 46.66 5.68
4414 4627 0.519961 GCCGTCACTAAATTGGCGTT 59.480 50.000 0.00 0.00 43.18 4.84
4430 4644 1.414378 CGTTGTGTCATGCAGTCGTA 58.586 50.000 0.00 0.00 0.00 3.43
4438 4652 0.097499 CATGCAGTCGTACCGTCGTA 59.903 55.000 0.00 0.00 0.00 3.43
4442 4656 1.063174 GCAGTCGTACCGTCGTAGATT 59.937 52.381 0.00 0.00 40.67 2.40
4446 4660 4.025396 CAGTCGTACCGTCGTAGATTACAT 60.025 45.833 0.00 0.00 40.67 2.29
4451 4665 3.018856 ACCGTCGTAGATTACATGGTCA 58.981 45.455 0.00 0.00 40.67 4.02
4457 4671 4.126437 CGTAGATTACATGGTCAATGCCA 58.874 43.478 0.00 0.00 40.22 4.92
4462 4676 1.838112 ACATGGTCAATGCCATCGTT 58.162 45.000 6.29 0.00 45.47 3.85
4467 4681 1.745087 GGTCAATGCCATCGTTGTGAT 59.255 47.619 0.00 0.00 39.58 3.06
4478 4692 1.202639 TCGTTGTGATGCAGTCCTTGT 60.203 47.619 0.00 0.00 0.00 3.16
4479 4693 1.603802 CGTTGTGATGCAGTCCTTGTT 59.396 47.619 0.00 0.00 0.00 2.83
4486 4700 0.176910 TGCAGTCCTTGTTGTCGTCA 59.823 50.000 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
96 97 1.860950 CATGGATGTTTCGTAGGCTCG 59.139 52.381 0.00 0.00 0.00 5.03
102 103 5.556915 AGAGGTTTTCATGGATGTTTCGTA 58.443 37.500 0.00 0.00 0.00 3.43
354 355 8.991243 TTTTCTTTGGCATTGAGATCTTATTG 57.009 30.769 0.00 0.49 0.00 1.90
454 462 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
482 490 8.353684 CCGTATGTAGTTCATAGTGAAATCTCT 58.646 37.037 0.00 0.00 38.22 3.10
483 491 8.350722 TCCGTATGTAGTTCATAGTGAAATCTC 58.649 37.037 0.00 0.00 38.22 2.75
484 492 8.234136 TCCGTATGTAGTTCATAGTGAAATCT 57.766 34.615 0.00 0.00 38.22 2.40
485 493 7.115095 GCTCCGTATGTAGTTCATAGTGAAATC 59.885 40.741 0.00 0.00 38.22 2.17
486 494 6.924060 GCTCCGTATGTAGTTCATAGTGAAAT 59.076 38.462 0.00 0.00 38.22 2.17
487 495 6.127563 TGCTCCGTATGTAGTTCATAGTGAAA 60.128 38.462 0.00 0.00 38.22 2.69
488 496 5.358725 TGCTCCGTATGTAGTTCATAGTGAA 59.641 40.000 0.00 0.00 39.36 3.18
489 497 4.885325 TGCTCCGTATGTAGTTCATAGTGA 59.115 41.667 0.00 0.00 39.36 3.41
490 498 5.183014 TGCTCCGTATGTAGTTCATAGTG 57.817 43.478 0.00 0.00 39.36 2.74
491 499 5.847111 TTGCTCCGTATGTAGTTCATAGT 57.153 39.130 0.00 0.00 39.36 2.12
492 500 7.438160 TCATTTTGCTCCGTATGTAGTTCATAG 59.562 37.037 0.00 0.00 39.36 2.23
493 501 7.269316 TCATTTTGCTCCGTATGTAGTTCATA 58.731 34.615 0.00 0.00 37.91 2.15
494 502 6.112734 TCATTTTGCTCCGTATGTAGTTCAT 58.887 36.000 0.00 0.00 40.25 2.57
495 503 5.483811 TCATTTTGCTCCGTATGTAGTTCA 58.516 37.500 0.00 0.00 0.00 3.18
496 504 5.581085 ACTCATTTTGCTCCGTATGTAGTTC 59.419 40.000 0.00 0.00 0.00 3.01
497 505 5.351465 CACTCATTTTGCTCCGTATGTAGTT 59.649 40.000 0.00 0.00 0.00 2.24
498 506 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
499 507 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
500 508 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
501 509 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
502 510 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
503 511 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
504 512 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
505 513 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
506 514 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
507 515 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
508 516 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
519 527 8.430801 AGATGCATTTTAGAGTGTAGATTCAC 57.569 34.615 0.00 0.00 38.46 3.18
520 528 9.534565 GTAGATGCATTTTAGAGTGTAGATTCA 57.465 33.333 0.00 0.00 0.00 2.57
521 529 9.534565 TGTAGATGCATTTTAGAGTGTAGATTC 57.465 33.333 0.00 0.00 0.00 2.52
524 532 9.967346 GTATGTAGATGCATTTTAGAGTGTAGA 57.033 33.333 0.00 0.00 0.00 2.59
525 533 9.750125 TGTATGTAGATGCATTTTAGAGTGTAG 57.250 33.333 0.00 0.00 0.00 2.74
527 535 9.265901 GATGTATGTAGATGCATTTTAGAGTGT 57.734 33.333 0.00 0.00 35.26 3.55
528 536 8.715998 GGATGTATGTAGATGCATTTTAGAGTG 58.284 37.037 0.00 0.00 35.26 3.51
529 537 7.600375 CGGATGTATGTAGATGCATTTTAGAGT 59.400 37.037 0.00 0.00 35.26 3.24
530 538 7.600375 ACGGATGTATGTAGATGCATTTTAGAG 59.400 37.037 0.00 0.00 35.26 2.43
531 539 7.441836 ACGGATGTATGTAGATGCATTTTAGA 58.558 34.615 0.00 0.00 35.26 2.10
532 540 7.658179 ACGGATGTATGTAGATGCATTTTAG 57.342 36.000 0.00 1.10 35.26 1.85
547 555 6.266786 TCACTATGAACCACATACGGATGTAT 59.733 38.462 14.23 5.54 44.82 2.29
548 556 5.595133 TCACTATGAACCACATACGGATGTA 59.405 40.000 14.23 0.00 44.82 2.29
549 557 5.105106 TTCACTATGAACCACATACGGATGT 60.105 40.000 7.68 7.68 37.89 3.06
550 558 4.944048 TCACTATGAACCACATACGGATG 58.056 43.478 5.94 5.94 40.07 3.51
551 559 5.607939 TTCACTATGAACCACATACGGAT 57.392 39.130 0.00 0.00 40.07 4.18
552 560 5.408880 TTTCACTATGAACCACATACGGA 57.591 39.130 0.00 0.00 35.89 4.69
553 561 6.238374 GGAATTTCACTATGAACCACATACGG 60.238 42.308 0.00 0.00 35.89 4.02
554 562 6.538742 AGGAATTTCACTATGAACCACATACG 59.461 38.462 0.00 0.00 35.89 3.06
555 563 7.012421 GGAGGAATTTCACTATGAACCACATAC 59.988 40.741 0.00 0.00 35.89 2.39
556 564 7.054124 GGAGGAATTTCACTATGAACCACATA 58.946 38.462 0.00 0.00 35.89 2.29
557 565 5.888161 GGAGGAATTTCACTATGAACCACAT 59.112 40.000 0.00 0.00 35.89 3.21
558 566 5.222027 TGGAGGAATTTCACTATGAACCACA 60.222 40.000 0.00 0.00 35.89 4.17
559 567 5.253330 TGGAGGAATTTCACTATGAACCAC 58.747 41.667 0.00 0.00 35.89 4.16
560 568 5.512942 TGGAGGAATTTCACTATGAACCA 57.487 39.130 0.00 0.00 35.89 3.67
561 569 6.659242 TCTTTGGAGGAATTTCACTATGAACC 59.341 38.462 0.00 0.00 35.89 3.62
562 570 7.391833 AGTCTTTGGAGGAATTTCACTATGAAC 59.608 37.037 0.00 0.00 35.89 3.18
563 571 7.461749 AGTCTTTGGAGGAATTTCACTATGAA 58.538 34.615 0.00 0.00 34.03 2.57
564 572 7.020827 AGTCTTTGGAGGAATTTCACTATGA 57.979 36.000 0.00 0.00 0.00 2.15
565 573 7.693969 AAGTCTTTGGAGGAATTTCACTATG 57.306 36.000 0.00 0.00 0.00 2.23
568 576 9.981460 AATATAAGTCTTTGGAGGAATTTCACT 57.019 29.630 0.00 0.00 0.00 3.41
575 583 9.901172 GTTCCTAAATATAAGTCTTTGGAGGAA 57.099 33.333 0.00 0.00 37.10 3.36
576 584 8.202137 CGTTCCTAAATATAAGTCTTTGGAGGA 58.798 37.037 0.00 0.00 0.00 3.71
577 585 7.441458 CCGTTCCTAAATATAAGTCTTTGGAGG 59.559 40.741 0.00 0.00 0.00 4.30
578 586 8.202137 TCCGTTCCTAAATATAAGTCTTTGGAG 58.798 37.037 0.00 0.00 0.00 3.86
579 587 8.081517 TCCGTTCCTAAATATAAGTCTTTGGA 57.918 34.615 0.00 0.00 0.00 3.53
580 588 7.441458 CCTCCGTTCCTAAATATAAGTCTTTGG 59.559 40.741 0.00 0.00 0.00 3.28
581 589 7.441458 CCCTCCGTTCCTAAATATAAGTCTTTG 59.559 40.741 0.00 0.00 0.00 2.77
582 590 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
583 591 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
584 592 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
585 593 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
586 594 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
587 595 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
588 596 7.300658 AGTACTCCCTCCGTTCCTAAATATAA 58.699 38.462 0.00 0.00 0.00 0.98
589 597 6.856757 AGTACTCCCTCCGTTCCTAAATATA 58.143 40.000 0.00 0.00 0.00 0.86
590 598 5.713807 AGTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
591 599 5.134725 AGTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
592 600 3.991683 AGTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
593 601 3.463048 AGTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
594 602 4.467769 CATAGTACTCCCTCCGTTCCTAA 58.532 47.826 0.00 0.00 0.00 2.69
595 603 3.749954 GCATAGTACTCCCTCCGTTCCTA 60.750 52.174 0.00 0.00 0.00 2.94
596 604 2.946785 CATAGTACTCCCTCCGTTCCT 58.053 52.381 0.00 0.00 0.00 3.36
597 605 1.340568 GCATAGTACTCCCTCCGTTCC 59.659 57.143 0.00 0.00 0.00 3.62
598 606 2.029623 TGCATAGTACTCCCTCCGTTC 58.970 52.381 0.00 0.00 0.00 3.95
599 607 2.154567 TGCATAGTACTCCCTCCGTT 57.845 50.000 0.00 0.00 0.00 4.44
600 608 1.964223 CATGCATAGTACTCCCTCCGT 59.036 52.381 0.00 0.00 0.00 4.69
601 609 1.337260 GCATGCATAGTACTCCCTCCG 60.337 57.143 14.21 0.00 0.00 4.63
602 610 1.974236 AGCATGCATAGTACTCCCTCC 59.026 52.381 21.98 0.00 0.00 4.30
603 611 2.896685 AGAGCATGCATAGTACTCCCTC 59.103 50.000 21.98 3.65 0.00 4.30
604 612 2.896685 GAGAGCATGCATAGTACTCCCT 59.103 50.000 21.98 0.00 0.00 4.20
605 613 2.028567 GGAGAGCATGCATAGTACTCCC 60.029 54.545 21.98 14.52 37.17 4.30
606 614 2.896685 AGGAGAGCATGCATAGTACTCC 59.103 50.000 21.98 22.80 41.58 3.85
607 615 5.652014 AGATAGGAGAGCATGCATAGTACTC 59.348 44.000 21.98 16.09 0.00 2.59
608 616 5.579047 AGATAGGAGAGCATGCATAGTACT 58.421 41.667 21.98 12.08 0.00 2.73
609 617 5.913137 AGATAGGAGAGCATGCATAGTAC 57.087 43.478 21.98 4.74 0.00 2.73
610 618 8.601047 ATTTAGATAGGAGAGCATGCATAGTA 57.399 34.615 21.98 4.88 0.00 1.82
611 619 6.924913 TTTAGATAGGAGAGCATGCATAGT 57.075 37.500 21.98 0.00 0.00 2.12
612 620 9.478768 CATATTTAGATAGGAGAGCATGCATAG 57.521 37.037 21.98 0.00 0.00 2.23
613 621 8.985922 ACATATTTAGATAGGAGAGCATGCATA 58.014 33.333 21.98 4.25 0.00 3.14
681 693 3.120060 CCTCATCTCTTTTTCCGCAACTG 60.120 47.826 0.00 0.00 0.00 3.16
722 752 1.660607 CATACACGGTCACATGCACTC 59.339 52.381 0.00 0.00 0.00 3.51
725 755 1.437625 CACATACACGGTCACATGCA 58.562 50.000 0.00 0.00 0.00 3.96
754 784 4.082523 ACATGGAGTCCCACCGCG 62.083 66.667 6.74 0.00 46.98 6.46
755 785 2.257409 ATCACATGGAGTCCCACCGC 62.257 60.000 6.74 0.00 46.98 5.68
775 809 3.623510 GCCTCTTTTCTGCTACATACACC 59.376 47.826 0.00 0.00 0.00 4.16
822 856 2.725008 CGAGACCAGCGGAGATCC 59.275 66.667 1.50 0.00 0.00 3.36
891 929 2.295070 GAGCTAAACTTGGGCCGAAAAA 59.705 45.455 0.54 0.00 0.00 1.94
997 1036 3.787001 GAGGGCCTCTTCCGTGGG 61.787 72.222 26.44 0.00 0.00 4.61
1051 1096 2.845752 TAAAGGTGCGCACTAGCCGG 62.846 60.000 36.84 0.00 37.52 6.13
1067 1112 3.605634 CCCTCATTGATCACCACGTAAA 58.394 45.455 0.00 0.00 0.00 2.01
1705 1750 3.680196 ACGTCCTCCCTGCCCCTA 61.680 66.667 0.00 0.00 0.00 3.53
1819 1864 2.561956 CGTCACCGTGTCCCTCTGT 61.562 63.158 0.00 0.00 0.00 3.41
2499 2624 4.189188 CGTACTCGCCAGGTCCGG 62.189 72.222 0.00 0.00 0.00 5.14
2740 2903 0.603707 ACGTCAGGCACAAGGTGATG 60.604 55.000 0.00 0.00 35.23 3.07
2745 2908 1.961277 GTCCACGTCAGGCACAAGG 60.961 63.158 0.00 0.00 0.00 3.61
2793 2956 1.132436 CATGCGTACGTGTTGGCAG 59.868 57.895 17.90 0.00 39.00 4.85
2801 2964 0.736325 GGAGAACTGCATGCGTACGT 60.736 55.000 17.90 4.56 0.00 3.57
2802 2965 1.742900 CGGAGAACTGCATGCGTACG 61.743 60.000 14.09 11.84 0.00 3.67
2803 2966 1.421410 CCGGAGAACTGCATGCGTAC 61.421 60.000 14.09 4.59 0.00 3.67
2804 2967 1.153647 CCGGAGAACTGCATGCGTA 60.154 57.895 14.09 0.00 0.00 4.42
3153 3316 0.995675 AGAGGATGTTGGGGATGGGG 60.996 60.000 0.00 0.00 0.00 4.96
3509 3676 8.968969 ACGTTATTATCTTTCTTCTCACCTACT 58.031 33.333 0.00 0.00 0.00 2.57
3510 3677 9.583765 AACGTTATTATCTTTCTTCTCACCTAC 57.416 33.333 0.00 0.00 0.00 3.18
3520 3687 9.294030 CGTACTAACCAACGTTATTATCTTTCT 57.706 33.333 0.00 0.00 33.98 2.52
3584 3752 0.466007 ACATGGCCGCATGAATAGCA 60.466 50.000 9.94 0.00 36.48 3.49
3599 3767 7.936847 TGGTCTGGTTTAGCCTAATATAACATG 59.063 37.037 0.00 0.00 38.35 3.21
3606 3774 6.569127 TCATTGGTCTGGTTTAGCCTAATA 57.431 37.500 0.00 0.00 38.35 0.98
3607 3775 5.450818 TCATTGGTCTGGTTTAGCCTAAT 57.549 39.130 0.00 0.00 38.35 1.73
3608 3776 4.919774 TCATTGGTCTGGTTTAGCCTAA 57.080 40.909 0.00 0.00 38.35 2.69
3611 3779 2.689983 CCATCATTGGTCTGGTTTAGCC 59.310 50.000 0.00 0.00 38.30 3.93
3636 3805 9.485206 TGAAGGAAGTAAAACTGACATACTAAC 57.515 33.333 0.00 0.00 30.03 2.34
3775 3947 9.838339 TGGCAAAAAGGAATAAAATTCAACTAA 57.162 25.926 2.36 0.00 0.00 2.24
3783 3955 8.922931 ACTCAATTGGCAAAAAGGAATAAAAT 57.077 26.923 3.01 0.00 0.00 1.82
3816 3989 6.016360 GCATGCATCACTGGTATAATAAACCA 60.016 38.462 14.21 0.00 44.75 3.67
3825 3998 2.940158 ACATGCATGCATCACTGGTAT 58.060 42.857 30.07 4.31 33.90 2.73
3828 4001 5.009310 ACTTAATACATGCATGCATCACTGG 59.991 40.000 30.07 20.17 33.90 4.00
3829 4002 5.912955 CACTTAATACATGCATGCATCACTG 59.087 40.000 30.07 22.27 33.90 3.66
3862 4040 7.583898 AGAGTTCCTCGCTCAGAATGAAAGG 62.584 48.000 0.00 0.00 39.33 3.11
3867 4045 2.957491 AGAGTTCCTCGCTCAGAATG 57.043 50.000 0.00 0.00 35.36 2.67
3871 4049 5.353123 GGAGTATATAGAGTTCCTCGCTCAG 59.647 48.000 0.00 0.00 35.36 3.35
3875 4053 3.695556 GGGGAGTATATAGAGTTCCTCGC 59.304 52.174 0.00 0.00 35.36 5.03
3895 4073 4.320608 CATCAAAATGGATAAACGGGGG 57.679 45.455 0.00 0.00 0.00 5.40
3907 4085 9.852481 CGTATGAAAATAATTGCCATCAAAATG 57.148 29.630 0.00 0.00 35.56 2.32
3908 4086 9.044150 CCGTATGAAAATAATTGCCATCAAAAT 57.956 29.630 0.00 0.00 35.56 1.82
3909 4087 8.253810 TCCGTATGAAAATAATTGCCATCAAAA 58.746 29.630 0.00 0.00 35.56 2.44
3910 4088 7.776107 TCCGTATGAAAATAATTGCCATCAAA 58.224 30.769 0.00 0.00 35.56 2.69
3911 4089 7.340122 TCCGTATGAAAATAATTGCCATCAA 57.660 32.000 0.00 0.00 36.51 2.57
3912 4090 6.016360 CCTCCGTATGAAAATAATTGCCATCA 60.016 38.462 0.00 0.00 0.00 3.07
3913 4091 6.381801 CCTCCGTATGAAAATAATTGCCATC 58.618 40.000 0.00 0.00 0.00 3.51
3914 4092 5.243730 CCCTCCGTATGAAAATAATTGCCAT 59.756 40.000 0.00 0.00 0.00 4.40
3915 4093 4.582656 CCCTCCGTATGAAAATAATTGCCA 59.417 41.667 0.00 0.00 0.00 4.92
3916 4094 4.825085 TCCCTCCGTATGAAAATAATTGCC 59.175 41.667 0.00 0.00 0.00 4.52
3917 4095 5.531287 ACTCCCTCCGTATGAAAATAATTGC 59.469 40.000 0.00 0.00 0.00 3.56
3918 4096 8.848474 ATACTCCCTCCGTATGAAAATAATTG 57.152 34.615 0.00 0.00 0.00 2.32
3919 4097 9.503399 GAATACTCCCTCCGTATGAAAATAATT 57.497 33.333 0.00 0.00 0.00 1.40
3920 4098 8.656806 TGAATACTCCCTCCGTATGAAAATAAT 58.343 33.333 0.00 0.00 0.00 1.28
3921 4099 7.929785 GTGAATACTCCCTCCGTATGAAAATAA 59.070 37.037 0.00 0.00 0.00 1.40
3922 4100 7.289317 AGTGAATACTCCCTCCGTATGAAAATA 59.711 37.037 0.00 0.00 28.79 1.40
3923 4101 6.099845 AGTGAATACTCCCTCCGTATGAAAAT 59.900 38.462 0.00 0.00 28.79 1.82
3924 4102 5.424252 AGTGAATACTCCCTCCGTATGAAAA 59.576 40.000 0.00 0.00 28.79 2.29
3925 4103 4.960469 AGTGAATACTCCCTCCGTATGAAA 59.040 41.667 0.00 0.00 28.79 2.69
3926 4104 4.543689 AGTGAATACTCCCTCCGTATGAA 58.456 43.478 0.00 0.00 28.79 2.57
3927 4105 4.142790 GAGTGAATACTCCCTCCGTATGA 58.857 47.826 0.00 0.00 46.14 2.15
3928 4106 4.506886 GAGTGAATACTCCCTCCGTATG 57.493 50.000 0.00 0.00 46.14 2.39
3939 4117 4.686091 CGTTGTGACATGTGAGTGAATACT 59.314 41.667 1.15 0.00 40.66 2.12
3940 4118 4.447724 ACGTTGTGACATGTGAGTGAATAC 59.552 41.667 1.15 0.00 0.00 1.89
3953 4131 3.054166 GTGTAGTGCATACGTTGTGACA 58.946 45.455 0.00 0.00 37.17 3.58
3969 4149 5.856126 TTTTGACCGAAGCAATAGTGTAG 57.144 39.130 0.00 0.00 0.00 2.74
3973 4153 9.998106 ATACTATATTTTGACCGAAGCAATAGT 57.002 29.630 0.00 0.00 0.00 2.12
4022 4204 4.026052 GGGAACTGGTGATGATCCAATTT 58.974 43.478 0.00 0.00 34.35 1.82
4028 4210 1.141858 GGGAGGGAACTGGTGATGATC 59.858 57.143 0.00 0.00 44.43 2.92
4062 4244 0.033504 CACTAGTGTCCACGCCACTT 59.966 55.000 15.06 0.00 42.83 3.16
4075 4257 3.251729 ACAACGTATGTGTCGTCACTAGT 59.748 43.478 13.77 5.93 41.93 2.57
4089 4271 2.295349 ACAACTCCAGTCGACAACGTAT 59.705 45.455 19.50 0.00 40.69 3.06
4090 4272 1.677576 ACAACTCCAGTCGACAACGTA 59.322 47.619 19.50 0.00 40.69 3.57
4094 4276 1.295792 GCAACAACTCCAGTCGACAA 58.704 50.000 19.50 1.52 0.00 3.18
4098 4280 0.670546 ATCGGCAACAACTCCAGTCG 60.671 55.000 0.00 0.00 0.00 4.18
4122 4304 1.188863 ACGGGGCAACGTCTATAACT 58.811 50.000 0.44 0.00 45.08 2.24
4126 4308 1.068127 GACATACGGGGCAACGTCTAT 59.932 52.381 9.71 0.00 45.08 1.98
4134 4316 1.324005 TGACATCGACATACGGGGCA 61.324 55.000 0.00 0.00 42.82 5.36
4139 4321 4.280461 GTCTACCTTGACATCGACATACG 58.720 47.826 0.00 0.00 38.80 3.06
4153 4335 4.021894 GGCTACATCATGATCGTCTACCTT 60.022 45.833 4.86 0.00 0.00 3.50
4160 4342 1.269778 CCACGGCTACATCATGATCGT 60.270 52.381 4.86 9.34 0.00 3.73
4191 4403 4.332543 GCAACTTCATTATCCATGACGACA 59.667 41.667 0.00 0.00 41.98 4.35
4198 4410 6.594788 ACTTTGTGCAACTTCATTATCCAT 57.405 33.333 0.00 0.00 38.04 3.41
4211 4423 2.909965 GCCCCCGACTTTGTGCAA 60.910 61.111 0.00 0.00 0.00 4.08
4212 4424 4.196778 TGCCCCCGACTTTGTGCA 62.197 61.111 0.00 0.00 0.00 4.57
4241 4454 5.983720 GCAACTCCGTGATATACAACATAGT 59.016 40.000 0.00 0.00 0.00 2.12
4252 4465 0.885879 ACGACTGCAACTCCGTGATA 59.114 50.000 0.00 0.00 33.69 2.15
4255 4468 3.234390 CACGACTGCAACTCCGTG 58.766 61.111 12.90 12.90 44.66 4.94
4297 4510 2.511600 CATCGTCGAAGGCACCCC 60.512 66.667 0.00 0.00 0.00 4.95
4321 4534 2.248248 CTCCCATCCTTACATAGCCGA 58.752 52.381 0.00 0.00 0.00 5.54
4325 4538 3.008485 GGCTTCCTCCCATCCTTACATAG 59.992 52.174 0.00 0.00 0.00 2.23
4327 4540 1.777272 GGCTTCCTCCCATCCTTACAT 59.223 52.381 0.00 0.00 0.00 2.29
4330 4543 2.945718 GGGCTTCCTCCCATCCTTA 58.054 57.895 0.00 0.00 45.82 2.69
4331 4544 3.761182 GGGCTTCCTCCCATCCTT 58.239 61.111 0.00 0.00 45.82 3.36
4337 4550 2.825264 CTCGATGGGCTTCCTCCC 59.175 66.667 0.00 0.00 46.73 4.30
4366 4579 0.462047 GGATACACGGTCCTGGCAAG 60.462 60.000 0.00 0.00 32.85 4.01
4374 4587 1.636988 CCTTTCACGGATACACGGTC 58.363 55.000 0.00 0.00 38.39 4.79
4382 4595 3.325201 GACGGCCCCTTTCACGGAT 62.325 63.158 0.00 0.00 0.00 4.18
4383 4596 4.011517 GACGGCCCCTTTCACGGA 62.012 66.667 0.00 0.00 0.00 4.69
4389 4602 2.167662 CAATTTAGTGACGGCCCCTTT 58.832 47.619 0.00 0.00 0.00 3.11
4390 4603 1.615919 CCAATTTAGTGACGGCCCCTT 60.616 52.381 0.00 0.00 0.00 3.95
4396 4609 1.533731 ACAACGCCAATTTAGTGACGG 59.466 47.619 0.00 0.00 0.00 4.79
4405 4618 0.672889 TGCATGACACAACGCCAATT 59.327 45.000 0.00 0.00 0.00 2.32
4407 4620 1.100463 ACTGCATGACACAACGCCAA 61.100 50.000 0.00 0.00 0.00 4.52
4410 4623 1.154599 CGACTGCATGACACAACGC 60.155 57.895 0.00 0.00 0.00 4.84
4413 4626 1.790755 GGTACGACTGCATGACACAA 58.209 50.000 0.00 0.00 0.00 3.33
4414 4627 3.507597 GGTACGACTGCATGACACA 57.492 52.632 0.00 0.00 0.00 3.72
4430 4644 3.018856 TGACCATGTAATCTACGACGGT 58.981 45.455 0.00 0.00 32.08 4.83
4446 4660 0.880441 CACAACGATGGCATTGACCA 59.120 50.000 21.46 2.90 45.82 4.02
4457 4671 2.079158 CAAGGACTGCATCACAACGAT 58.921 47.619 0.00 0.00 33.27 3.73
4462 4676 2.221169 GACAACAAGGACTGCATCACA 58.779 47.619 0.00 0.00 0.00 3.58
4467 4681 0.176910 TGACGACAACAAGGACTGCA 59.823 50.000 0.00 0.00 0.00 4.41
4474 4688 2.418628 ACACAACCTTGACGACAACAAG 59.581 45.455 0.00 0.00 42.72 3.16
4478 4692 2.675844 CAAGACACAACCTTGACGACAA 59.324 45.455 0.00 0.00 42.57 3.18
4479 4693 2.276201 CAAGACACAACCTTGACGACA 58.724 47.619 0.00 0.00 42.57 4.35
4486 4700 5.470098 CAGTATAACTGCAAGACACAACCTT 59.530 40.000 0.00 0.00 39.62 3.50


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

AutoCloner maintained by Alex Coulton.