Multiple sequence alignment - TraesCS3A01G288000

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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 TraesCS3A01G288000 chr3A 100.000 3461 0 0 1 3461 516240627 516237167 0.000000e+00 6392.0
1 TraesCS3A01G288000 chr3A 97.944 535 11 0 1 535 24190686 24190152 0.000000e+00 928.0
2 TraesCS3A01G288000 chr3A 84.830 323 41 7 543 861 729670548 729670230 5.570000e-83 318.0
3 TraesCS3A01G288000 chr3A 97.959 49 1 0 879 927 516291172 516291124 6.150000e-13 86.1
4 TraesCS3A01G288000 chr3B 95.562 1645 63 7 863 2504 522031940 522030303 0.000000e+00 2625.0
5 TraesCS3A01G288000 chr3B 90.691 333 13 8 2561 2876 522030310 522029979 8.880000e-116 427.0
6 TraesCS3A01G288000 chr3D 94.891 1644 61 11 864 2504 396673700 396672077 0.000000e+00 2549.0
7 TraesCS3A01G288000 chr3D 92.308 325 15 6 2561 2876 396672084 396671761 1.460000e-123 453.0
8 TraesCS3A01G288000 chr3D 80.496 605 68 22 2883 3461 577485461 577484881 5.340000e-113 418.0
9 TraesCS3A01G288000 chr3D 80.402 597 68 23 2881 3451 275838624 275838051 3.220000e-110 409.0
10 TraesCS3A01G288000 chr3D 79.335 571 86 19 2884 3451 73449633 73450174 4.220000e-99 372.0
11 TraesCS3A01G288000 chr3D 87.227 321 28 12 543 861 466745767 466745458 1.530000e-93 353.0
12 TraesCS3A01G288000 chr3D 82.816 419 47 5 2883 3300 70683501 70683895 5.500000e-93 351.0
13 TraesCS3A01G288000 chr5D 83.658 1438 184 33 1042 2461 408852609 408854013 0.000000e+00 1306.0
14 TraesCS3A01G288000 chr5D 80.212 566 57 20 2913 3451 406324927 406325464 1.170000e-99 374.0
15 TraesCS3A01G288000 chr5D 79.236 602 66 26 2883 3461 127275942 127275377 7.060000e-97 364.0
16 TraesCS3A01G288000 chr5D 84.735 321 40 9 543 861 37640477 37640790 2.590000e-81 313.0
17 TraesCS3A01G288000 chr5B 83.460 1445 186 35 1042 2461 490769702 490771118 0.000000e+00 1295.0
18 TraesCS3A01G288000 chr5B 95.556 45 1 1 1 44 389988777 389988733 1.720000e-08 71.3
19 TraesCS3A01G288000 chr5A 83.391 1439 189 31 1042 2461 519904267 519905674 0.000000e+00 1288.0
20 TraesCS3A01G288000 chr5A 98.000 550 10 1 1 550 374081833 374082381 0.000000e+00 953.0
21 TraesCS3A01G288000 chr5A 98.343 543 9 0 1 543 519535659 519536201 0.000000e+00 953.0
22 TraesCS3A01G288000 chr5A 95.359 237 11 0 311 547 519530514 519530278 9.070000e-101 377.0
23 TraesCS3A01G288000 chr7A 96.577 555 16 3 1 555 732732289 732731738 0.000000e+00 917.0
24 TraesCS3A01G288000 chr7A 98.077 312 5 1 236 547 25053359 25053049 3.040000e-150 542.0
25 TraesCS3A01G288000 chr7A 81.250 592 73 15 2884 3461 620178685 620178118 8.810000e-121 444.0
26 TraesCS3A01G288000 chr7A 96.203 237 8 1 311 547 732735451 732735686 1.510000e-103 387.0
27 TraesCS3A01G288000 chr7A 79.466 599 66 29 2884 3451 700069294 700069866 4.220000e-99 372.0
28 TraesCS3A01G288000 chr7D 95.513 312 14 0 1 312 46783591 46783902 1.850000e-137 499.0
29 TraesCS3A01G288000 chr7D 96.170 235 7 1 311 543 46784752 46784986 1.950000e-102 383.0
30 TraesCS3A01G288000 chr7D 85.340 382 32 12 2923 3303 575191903 575191545 1.170000e-99 374.0
31 TraesCS3A01G288000 chr7D 78.511 591 66 25 2885 3451 80354656 80355209 7.160000e-87 331.0
32 TraesCS3A01G288000 chr2D 95.513 312 14 0 1 312 165487303 165486992 1.850000e-137 499.0
33 TraesCS3A01G288000 chr2D 81.958 521 46 16 2957 3451 470063661 470063163 6.960000e-107 398.0
34 TraesCS3A01G288000 chr2D 95.781 237 9 1 311 547 165491481 165491716 7.010000e-102 381.0
35 TraesCS3A01G288000 chr2D 78.297 599 70 28 2889 3457 196860884 196861452 7.160000e-87 331.0
36 TraesCS3A01G288000 chr2D 85.449 323 41 5 543 861 636211222 636210902 7.160000e-87 331.0
37 TraesCS3A01G288000 chr2D 85.139 323 41 7 543 861 119370106 119370425 1.200000e-84 324.0
38 TraesCS3A01G288000 chr2D 84.969 326 39 8 543 861 97278118 97277796 4.310000e-84 322.0
39 TraesCS3A01G288000 chr2D 84.663 326 37 9 542 861 556233431 556233749 2.590000e-81 313.0
40 TraesCS3A01G288000 chr2D 84.568 324 38 11 543 861 246550410 246550094 9.330000e-81 311.0
41 TraesCS3A01G288000 chr2D 87.008 254 32 1 2883 3136 644672715 644672967 5.650000e-73 285.0
42 TraesCS3A01G288000 chr2A 83.218 578 61 15 2884 3448 38150468 38151022 6.670000e-137 497.0
43 TraesCS3A01G288000 chr4D 81.176 595 60 13 2883 3451 77117057 77116489 6.860000e-117 431.0
44 TraesCS3A01G288000 chr4D 83.294 425 42 6 2880 3300 469505966 469506365 7.060000e-97 364.0
45 TraesCS3A01G288000 chr4D 92.500 160 12 0 3302 3461 304462150 304461991 2.690000e-56 230.0
46 TraesCS3A01G288000 chr1D 80.985 589 62 12 2889 3451 16338329 16337765 4.130000e-114 422.0
47 TraesCS3A01G288000 chr1D 80.541 591 68 18 2884 3451 338913174 338913740 8.940000e-111 411.0
48 TraesCS3A01G288000 chr1D 82.452 416 48 6 2889 3303 16348516 16348125 1.190000e-89 340.0
49 TraesCS3A01G288000 chr4A 81.113 593 50 22 2884 3461 585522107 585522652 5.340000e-113 418.0
50 TraesCS3A01G288000 chr6D 80.570 597 62 23 2883 3451 3826098 3825528 8.940000e-111 411.0
51 TraesCS3A01G288000 chr6D 84.663 326 37 10 543 861 154344495 154344176 2.590000e-81 313.0
52 TraesCS3A01G288000 chr6B 81.748 515 52 16 2957 3451 213319951 213319459 3.240000e-105 392.0
53 TraesCS3A01G288000 chrUn 82.452 416 48 6 2889 3303 305007883 305007492 1.190000e-89 340.0
54 TraesCS3A01G288000 chr2B 82.979 329 47 8 545 866 741256483 741256157 4.370000e-74 289.0
55 TraesCS3A01G288000 chr2B 97.590 83 2 0 70 152 276080626 276080544 3.600000e-30 143.0
56 TraesCS3A01G288000 chr2B 100.000 38 0 0 1 38 276082085 276082048 1.720000e-08 71.3
57 TraesCS3A01G288000 chr1B 96.032 126 2 3 29 152 430784881 430785005 5.860000e-48 202.0
58 TraesCS3A01G288000 chr1B 79.355 155 27 4 1188 1341 11182346 11182196 1.700000e-18 104.0
59 TraesCS3A01G288000 chr1B 100.000 38 0 0 1 38 12442311 12442348 1.720000e-08 71.3
60 TraesCS3A01G288000 chr7B 95.238 126 3 3 29 152 346880582 346880706 2.730000e-46 196.0


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 TraesCS3A01G288000 chr3A 516237167 516240627 3460 True 6392 6392 100.0000 1 3461 1 chr3A.!!$R2 3460
1 TraesCS3A01G288000 chr3A 24190152 24190686 534 True 928 928 97.9440 1 535 1 chr3A.!!$R1 534
2 TraesCS3A01G288000 chr3B 522029979 522031940 1961 True 1526 2625 93.1265 863 2876 2 chr3B.!!$R1 2013
3 TraesCS3A01G288000 chr3D 396671761 396673700 1939 True 1501 2549 93.5995 864 2876 2 chr3D.!!$R4 2012
4 TraesCS3A01G288000 chr3D 577484881 577485461 580 True 418 418 80.4960 2883 3461 1 chr3D.!!$R3 578
5 TraesCS3A01G288000 chr3D 275838051 275838624 573 True 409 409 80.4020 2881 3451 1 chr3D.!!$R1 570
6 TraesCS3A01G288000 chr3D 73449633 73450174 541 False 372 372 79.3350 2884 3451 1 chr3D.!!$F2 567
7 TraesCS3A01G288000 chr5D 408852609 408854013 1404 False 1306 1306 83.6580 1042 2461 1 chr5D.!!$F3 1419
8 TraesCS3A01G288000 chr5D 406324927 406325464 537 False 374 374 80.2120 2913 3451 1 chr5D.!!$F2 538
9 TraesCS3A01G288000 chr5D 127275377 127275942 565 True 364 364 79.2360 2883 3461 1 chr5D.!!$R1 578
10 TraesCS3A01G288000 chr5B 490769702 490771118 1416 False 1295 1295 83.4600 1042 2461 1 chr5B.!!$F1 1419
11 TraesCS3A01G288000 chr5A 519904267 519905674 1407 False 1288 1288 83.3910 1042 2461 1 chr5A.!!$F3 1419
12 TraesCS3A01G288000 chr5A 374081833 374082381 548 False 953 953 98.0000 1 550 1 chr5A.!!$F1 549
13 TraesCS3A01G288000 chr5A 519535659 519536201 542 False 953 953 98.3430 1 543 1 chr5A.!!$F2 542
14 TraesCS3A01G288000 chr7A 732731738 732732289 551 True 917 917 96.5770 1 555 1 chr7A.!!$R3 554
15 TraesCS3A01G288000 chr7A 620178118 620178685 567 True 444 444 81.2500 2884 3461 1 chr7A.!!$R2 577
16 TraesCS3A01G288000 chr7A 700069294 700069866 572 False 372 372 79.4660 2884 3451 1 chr7A.!!$F1 567
17 TraesCS3A01G288000 chr7D 46783591 46784986 1395 False 441 499 95.8415 1 543 2 chr7D.!!$F2 542
18 TraesCS3A01G288000 chr7D 80354656 80355209 553 False 331 331 78.5110 2885 3451 1 chr7D.!!$F1 566
19 TraesCS3A01G288000 chr2D 196860884 196861452 568 False 331 331 78.2970 2889 3457 1 chr2D.!!$F3 568
20 TraesCS3A01G288000 chr2A 38150468 38151022 554 False 497 497 83.2180 2884 3448 1 chr2A.!!$F1 564
21 TraesCS3A01G288000 chr4D 77116489 77117057 568 True 431 431 81.1760 2883 3451 1 chr4D.!!$R1 568
22 TraesCS3A01G288000 chr1D 16337765 16338329 564 True 422 422 80.9850 2889 3451 1 chr1D.!!$R1 562
23 TraesCS3A01G288000 chr1D 338913174 338913740 566 False 411 411 80.5410 2884 3451 1 chr1D.!!$F1 567
24 TraesCS3A01G288000 chr4A 585522107 585522652 545 False 418 418 81.1130 2884 3461 1 chr4A.!!$F1 577
25 TraesCS3A01G288000 chr6D 3825528 3826098 570 True 411 411 80.5700 2883 3451 1 chr6D.!!$R1 568

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
860 1714 0.039798 TTCGTTTCCGAGGAGTCACG 60.04 55.0 11.86 11.86 45.24 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2546 3422 0.234625 AAATAGCACACACACACGCG 59.765 50.0 3.53 3.53 0.0 6.01 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
183 184 1.334149 GGTCAAAAGAGTTGCTGCGAC 60.334 52.381 12.16 12.16 0.00 5.19
470 1324 1.265635 GCAAGTTATGCGACCACAACA 59.734 47.619 0.00 0.00 46.87 3.33
543 1397 5.008712 TGTGACTGCTAGTGATATTACCTCG 59.991 44.000 0.00 0.00 0.00 4.63
546 1400 6.096423 TGACTGCTAGTGATATTACCTCGTTT 59.904 38.462 0.00 0.00 0.00 3.60
547 1401 6.273825 ACTGCTAGTGATATTACCTCGTTTG 58.726 40.000 0.00 0.00 0.00 2.93
549 1403 6.636705 TGCTAGTGATATTACCTCGTTTGTT 58.363 36.000 0.00 0.00 0.00 2.83
550 1404 7.101054 TGCTAGTGATATTACCTCGTTTGTTT 58.899 34.615 0.00 0.00 0.00 2.83
551 1405 8.252417 TGCTAGTGATATTACCTCGTTTGTTTA 58.748 33.333 0.00 0.00 0.00 2.01
552 1406 9.090692 GCTAGTGATATTACCTCGTTTGTTTAA 57.909 33.333 0.00 0.00 0.00 1.52
568 1422 9.212687 CGTTTGTTTAAAACGTTTTATCTCTCA 57.787 29.630 28.69 20.04 45.45 3.27
572 1426 9.505995 TGTTTAAAACGTTTTATCTCTCAAACC 57.494 29.630 28.69 16.10 33.12 3.27
573 1427 8.675888 GTTTAAAACGTTTTATCTCTCAAACCG 58.324 33.333 28.69 0.00 33.12 4.44
574 1428 5.996669 AAACGTTTTATCTCTCAAACCGT 57.003 34.783 7.96 0.00 30.37 4.83
575 1429 5.996669 AACGTTTTATCTCTCAAACCGTT 57.003 34.783 0.00 0.00 31.19 4.44
576 1430 5.996669 ACGTTTTATCTCTCAAACCGTTT 57.003 34.783 0.00 0.00 30.37 3.60
577 1431 5.744490 ACGTTTTATCTCTCAAACCGTTTG 58.256 37.500 16.53 16.53 41.96 2.93
578 1432 5.295045 ACGTTTTATCTCTCAAACCGTTTGT 59.705 36.000 20.71 6.59 41.36 2.83
579 1433 5.844396 CGTTTTATCTCTCAAACCGTTTGTC 59.156 40.000 20.71 3.22 41.36 3.18
580 1434 5.934935 TTTATCTCTCAAACCGTTTGTCC 57.065 39.130 20.71 0.00 41.36 4.02
581 1435 2.992124 TCTCTCAAACCGTTTGTCCA 57.008 45.000 20.71 4.19 41.36 4.02
582 1436 3.269538 TCTCTCAAACCGTTTGTCCAA 57.730 42.857 20.71 3.87 41.36 3.53
583 1437 3.611970 TCTCTCAAACCGTTTGTCCAAA 58.388 40.909 20.71 3.54 41.36 3.28
584 1438 4.204012 TCTCTCAAACCGTTTGTCCAAAT 58.796 39.130 20.71 0.00 41.36 2.32
585 1439 4.274950 TCTCTCAAACCGTTTGTCCAAATC 59.725 41.667 20.71 0.00 41.36 2.17
586 1440 4.204012 TCTCAAACCGTTTGTCCAAATCT 58.796 39.130 20.71 0.00 41.36 2.40
587 1441 4.274950 TCTCAAACCGTTTGTCCAAATCTC 59.725 41.667 20.71 0.00 41.36 2.75
588 1442 3.948473 TCAAACCGTTTGTCCAAATCTCA 59.052 39.130 20.71 0.00 41.36 3.27
589 1443 4.399618 TCAAACCGTTTGTCCAAATCTCAA 59.600 37.500 20.71 0.00 41.36 3.02
590 1444 4.993029 AACCGTTTGTCCAAATCTCAAA 57.007 36.364 0.00 0.00 32.36 2.69
591 1445 5.529581 AACCGTTTGTCCAAATCTCAAAT 57.470 34.783 0.00 0.00 34.41 2.32
592 1446 5.121221 ACCGTTTGTCCAAATCTCAAATC 57.879 39.130 0.00 0.00 34.41 2.17
593 1447 4.158384 CCGTTTGTCCAAATCTCAAATCG 58.842 43.478 0.00 0.00 34.41 3.34
594 1448 3.603770 CGTTTGTCCAAATCTCAAATCGC 59.396 43.478 0.00 0.00 34.41 4.58
595 1449 4.613622 CGTTTGTCCAAATCTCAAATCGCT 60.614 41.667 0.00 0.00 34.41 4.93
596 1450 5.222631 GTTTGTCCAAATCTCAAATCGCTT 58.777 37.500 0.00 0.00 34.41 4.68
597 1451 4.685169 TGTCCAAATCTCAAATCGCTTC 57.315 40.909 0.00 0.00 0.00 3.86
598 1452 3.440173 TGTCCAAATCTCAAATCGCTTCC 59.560 43.478 0.00 0.00 0.00 3.46
599 1453 3.440173 GTCCAAATCTCAAATCGCTTCCA 59.560 43.478 0.00 0.00 0.00 3.53
600 1454 3.440173 TCCAAATCTCAAATCGCTTCCAC 59.560 43.478 0.00 0.00 0.00 4.02
601 1455 3.428045 CCAAATCTCAAATCGCTTCCACC 60.428 47.826 0.00 0.00 0.00 4.61
602 1456 1.656652 ATCTCAAATCGCTTCCACCG 58.343 50.000 0.00 0.00 0.00 4.94
603 1457 0.320374 TCTCAAATCGCTTCCACCGT 59.680 50.000 0.00 0.00 0.00 4.83
604 1458 1.156736 CTCAAATCGCTTCCACCGTT 58.843 50.000 0.00 0.00 0.00 4.44
605 1459 0.871722 TCAAATCGCTTCCACCGTTG 59.128 50.000 0.00 0.00 0.00 4.10
606 1460 0.109781 CAAATCGCTTCCACCGTTGG 60.110 55.000 0.00 0.00 45.56 3.77
618 1472 3.747099 CACCGTTGGATTTCTCACATC 57.253 47.619 0.00 0.00 0.00 3.06
619 1473 2.094258 CACCGTTGGATTTCTCACATCG 59.906 50.000 0.00 0.00 0.00 3.84
620 1474 2.028476 ACCGTTGGATTTCTCACATCGA 60.028 45.455 0.00 0.00 31.12 3.59
621 1475 2.604914 CCGTTGGATTTCTCACATCGAG 59.395 50.000 0.00 0.00 43.80 4.04
633 1487 5.171476 TCTCACATCGAGATCTTCAAAACC 58.829 41.667 0.00 0.00 46.18 3.27
634 1488 5.047021 TCTCACATCGAGATCTTCAAAACCT 60.047 40.000 0.00 0.00 46.18 3.50
635 1489 6.152831 TCTCACATCGAGATCTTCAAAACCTA 59.847 38.462 0.00 0.00 46.18 3.08
636 1490 6.333416 TCACATCGAGATCTTCAAAACCTAG 58.667 40.000 0.00 0.00 0.00 3.02
637 1491 6.152831 TCACATCGAGATCTTCAAAACCTAGA 59.847 38.462 0.00 0.00 0.00 2.43
638 1492 6.983307 CACATCGAGATCTTCAAAACCTAGAT 59.017 38.462 0.00 0.00 0.00 1.98
639 1493 7.168972 CACATCGAGATCTTCAAAACCTAGATC 59.831 40.741 0.00 0.00 42.86 2.75
640 1494 6.150396 TCGAGATCTTCAAAACCTAGATCC 57.850 41.667 0.00 0.00 43.32 3.36
641 1495 5.069251 TCGAGATCTTCAAAACCTAGATCCC 59.931 44.000 0.00 0.00 43.32 3.85
642 1496 5.163405 CGAGATCTTCAAAACCTAGATCCCA 60.163 44.000 0.00 0.00 43.32 4.37
643 1497 6.463614 CGAGATCTTCAAAACCTAGATCCCAT 60.464 42.308 0.00 0.00 43.32 4.00
644 1498 6.599445 AGATCTTCAAAACCTAGATCCCATG 58.401 40.000 0.00 0.00 43.32 3.66
645 1499 5.779241 TCTTCAAAACCTAGATCCCATGT 57.221 39.130 0.00 0.00 0.00 3.21
646 1500 6.139679 TCTTCAAAACCTAGATCCCATGTT 57.860 37.500 0.00 0.00 0.00 2.71
647 1501 5.945784 TCTTCAAAACCTAGATCCCATGTTG 59.054 40.000 0.00 0.00 0.00 3.33
648 1502 5.512942 TCAAAACCTAGATCCCATGTTGA 57.487 39.130 0.00 0.00 0.00 3.18
649 1503 6.078456 TCAAAACCTAGATCCCATGTTGAT 57.922 37.500 0.00 0.00 0.00 2.57
650 1504 7.206789 TCAAAACCTAGATCCCATGTTGATA 57.793 36.000 0.00 0.00 0.00 2.15
651 1505 7.282585 TCAAAACCTAGATCCCATGTTGATAG 58.717 38.462 0.00 0.00 0.00 2.08
652 1506 5.832539 AACCTAGATCCCATGTTGATAGG 57.167 43.478 8.64 8.64 0.00 2.57
653 1507 4.832492 ACCTAGATCCCATGTTGATAGGT 58.168 43.478 9.54 9.54 29.99 3.08
654 1508 5.227593 ACCTAGATCCCATGTTGATAGGTT 58.772 41.667 9.54 0.00 30.45 3.50
655 1509 5.672194 ACCTAGATCCCATGTTGATAGGTTT 59.328 40.000 9.54 0.00 30.45 3.27
656 1510 6.160459 ACCTAGATCCCATGTTGATAGGTTTT 59.840 38.462 9.54 0.00 30.45 2.43
657 1511 6.488006 CCTAGATCCCATGTTGATAGGTTTTG 59.512 42.308 0.00 0.00 0.00 2.44
658 1512 6.078456 AGATCCCATGTTGATAGGTTTTGA 57.922 37.500 0.00 0.00 0.00 2.69
659 1513 5.888161 AGATCCCATGTTGATAGGTTTTGAC 59.112 40.000 0.00 0.00 0.00 3.18
660 1514 4.006989 TCCCATGTTGATAGGTTTTGACG 58.993 43.478 0.00 0.00 0.00 4.35
661 1515 3.756434 CCCATGTTGATAGGTTTTGACGT 59.244 43.478 0.00 0.00 0.00 4.34
662 1516 4.379394 CCCATGTTGATAGGTTTTGACGTG 60.379 45.833 0.00 0.00 0.00 4.49
663 1517 4.215399 CCATGTTGATAGGTTTTGACGTGT 59.785 41.667 0.00 0.00 0.00 4.49
664 1518 5.278266 CCATGTTGATAGGTTTTGACGTGTT 60.278 40.000 0.00 0.00 0.00 3.32
665 1519 5.821516 TGTTGATAGGTTTTGACGTGTTT 57.178 34.783 0.00 0.00 0.00 2.83
666 1520 6.197364 TGTTGATAGGTTTTGACGTGTTTT 57.803 33.333 0.00 0.00 0.00 2.43
667 1521 6.622549 TGTTGATAGGTTTTGACGTGTTTTT 58.377 32.000 0.00 0.00 0.00 1.94
723 1577 4.856801 CCGAACCGGGAGCATGGG 62.857 72.222 6.32 0.00 44.15 4.00
724 1578 4.096003 CGAACCGGGAGCATGGGT 62.096 66.667 6.32 0.00 34.99 4.51
725 1579 2.355115 GAACCGGGAGCATGGGTT 59.645 61.111 6.32 3.29 46.26 4.11
726 1580 1.304134 GAACCGGGAGCATGGGTTT 60.304 57.895 6.32 0.00 43.76 3.27
727 1581 0.898326 GAACCGGGAGCATGGGTTTT 60.898 55.000 6.32 0.00 43.76 2.43
728 1582 1.184970 AACCGGGAGCATGGGTTTTG 61.185 55.000 6.32 0.00 41.07 2.44
729 1583 1.606313 CCGGGAGCATGGGTTTTGT 60.606 57.895 0.00 0.00 0.00 2.83
730 1584 1.595093 CCGGGAGCATGGGTTTTGTC 61.595 60.000 0.00 0.00 0.00 3.18
731 1585 1.595093 CGGGAGCATGGGTTTTGTCC 61.595 60.000 0.00 0.00 0.00 4.02
743 1597 5.196341 GGGTTTTGTCCCTTTTCTGTAAG 57.804 43.478 0.00 0.00 43.85 2.34
744 1598 4.891168 GGGTTTTGTCCCTTTTCTGTAAGA 59.109 41.667 0.00 0.00 42.52 2.10
745 1599 5.009710 GGGTTTTGTCCCTTTTCTGTAAGAG 59.990 44.000 0.00 0.00 43.94 2.85
746 1600 7.911921 GGGTTTTGTCCCTTTTCTGTAAGAGG 61.912 46.154 0.00 0.00 43.94 3.69
753 1607 2.978824 TCTGTAAGAGGCACGCCC 59.021 61.111 3.95 0.00 38.67 6.13
754 1608 2.509336 CTGTAAGAGGCACGCCCG 60.509 66.667 3.95 0.00 39.21 6.13
755 1609 3.296709 CTGTAAGAGGCACGCCCGT 62.297 63.158 3.95 0.00 39.21 5.28
757 1611 3.307906 TAAGAGGCACGCCCGTGT 61.308 61.111 20.25 3.34 46.90 4.49
763 1617 4.357947 GCACGCCCGTGTCTCTCA 62.358 66.667 20.25 0.00 46.90 3.27
764 1618 2.430921 CACGCCCGTGTCTCTCAC 60.431 66.667 12.31 0.00 40.91 3.51
777 1631 6.257169 GTGTCTCTCACGAAATTATAACCG 57.743 41.667 0.00 0.00 37.31 4.44
778 1632 5.803967 GTGTCTCTCACGAAATTATAACCGT 59.196 40.000 0.00 4.25 37.31 4.83
783 1637 3.935450 CACGAAATTATAACCGTGCCTG 58.065 45.455 17.82 2.66 44.24 4.85
784 1638 3.372822 CACGAAATTATAACCGTGCCTGT 59.627 43.478 17.82 0.00 44.24 4.00
785 1639 4.004982 ACGAAATTATAACCGTGCCTGTT 58.995 39.130 8.11 0.00 33.69 3.16
786 1640 4.142773 ACGAAATTATAACCGTGCCTGTTG 60.143 41.667 8.11 0.00 33.69 3.33
787 1641 3.775661 AATTATAACCGTGCCTGTTGC 57.224 42.857 0.00 0.00 41.77 4.17
788 1642 1.080298 TTATAACCGTGCCTGTTGCG 58.920 50.000 0.00 0.00 45.60 4.85
793 1647 2.051345 CGTGCCTGTTGCGGAAAC 60.051 61.111 0.00 0.00 45.60 2.78
794 1648 2.829206 CGTGCCTGTTGCGGAAACA 61.829 57.895 0.79 0.79 46.66 2.83
800 1654 3.330766 TGTTGCGGAAACAAAACCG 57.669 47.368 0.00 0.00 45.85 4.44
801 1655 0.526662 TGTTGCGGAAACAAAACCGT 59.473 45.000 0.00 0.00 45.85 4.83
802 1656 1.741706 TGTTGCGGAAACAAAACCGTA 59.258 42.857 0.00 0.00 45.85 4.02
803 1657 2.163010 TGTTGCGGAAACAAAACCGTAA 59.837 40.909 0.00 0.00 45.85 3.18
808 1662 4.541085 CGGAAACAAAACCGTAACTCTT 57.459 40.909 0.00 0.00 43.53 2.85
809 1663 5.655893 CGGAAACAAAACCGTAACTCTTA 57.344 39.130 0.00 0.00 43.53 2.10
810 1664 5.434706 CGGAAACAAAACCGTAACTCTTAC 58.565 41.667 0.00 0.00 43.53 2.34
858 1712 2.894763 TTTTCGTTTCCGAGGAGTCA 57.105 45.000 0.00 0.00 45.24 3.41
859 1713 2.144482 TTTCGTTTCCGAGGAGTCAC 57.856 50.000 0.00 0.00 45.24 3.67
860 1714 0.039798 TTCGTTTCCGAGGAGTCACG 60.040 55.000 11.86 11.86 45.24 4.35
861 1715 2.087009 CGTTTCCGAGGAGTCACGC 61.087 63.158 7.37 0.00 35.63 5.34
862 1716 1.289380 GTTTCCGAGGAGTCACGCT 59.711 57.895 0.00 0.00 0.00 5.07
866 1720 0.965866 TCCGAGGAGTCACGCTGATT 60.966 55.000 0.00 0.00 0.00 2.57
942 1796 2.687935 GCGATTTGGCTGGAGGATAAAA 59.312 45.455 0.00 0.00 0.00 1.52
953 1807 2.007608 GAGGATAAAACACCACGGAGC 58.992 52.381 0.00 0.00 0.00 4.70
974 1828 2.448582 TTCCCGGTTCAGTGGTGCT 61.449 57.895 0.00 0.00 0.00 4.40
983 1837 0.880278 TCAGTGGTGCTGCGAGAAAC 60.880 55.000 0.00 0.00 44.66 2.78
1425 2279 1.238439 CCAAGGTGAGCAACGTCATT 58.762 50.000 0.00 0.00 0.00 2.57
1865 2719 2.202610 CGCTCTCGACGCCATCAA 60.203 61.111 0.00 0.00 38.10 2.57
2179 3054 1.267806 CAGTACCGTACCACGTCAACT 59.732 52.381 5.02 0.00 40.58 3.16
2445 3320 1.191489 TTGACAGATGGACCTCGCCA 61.191 55.000 0.00 0.00 43.23 5.69
2467 3342 2.817396 GCAAGCTCTGACTCCGCC 60.817 66.667 0.00 0.00 0.00 6.13
2473 3348 1.153289 CTCTGACTCCGCCCCATTG 60.153 63.158 0.00 0.00 0.00 2.82
2503 3379 5.509771 CGCATTTCGTGGATGAATATTTCA 58.490 37.500 0.00 0.00 45.01 2.69
2532 3408 9.772973 TCACAAAACATCTTAGTACTAATGTGT 57.227 29.630 26.77 23.35 32.42 3.72
2544 3420 7.611213 AGTACTAATGTGTAAGTCAAATGGC 57.389 36.000 0.00 0.00 0.00 4.40
2545 3421 7.394816 AGTACTAATGTGTAAGTCAAATGGCT 58.605 34.615 0.00 0.00 0.00 4.75
2546 3422 6.743575 ACTAATGTGTAAGTCAAATGGCTC 57.256 37.500 0.00 0.00 0.00 4.70
2547 3423 4.685169 AATGTGTAAGTCAAATGGCTCG 57.315 40.909 0.00 0.00 0.00 5.03
2548 3424 1.804151 TGTGTAAGTCAAATGGCTCGC 59.196 47.619 0.00 0.00 0.00 5.03
2549 3425 1.075542 TGTAAGTCAAATGGCTCGCG 58.924 50.000 0.00 0.00 0.00 5.87
2550 3426 1.076332 GTAAGTCAAATGGCTCGCGT 58.924 50.000 5.77 0.00 0.00 6.01
2551 3427 1.075542 TAAGTCAAATGGCTCGCGTG 58.924 50.000 5.77 4.44 0.00 5.34
2552 3428 0.884704 AAGTCAAATGGCTCGCGTGT 60.885 50.000 5.77 0.00 0.00 4.49
2553 3429 1.154413 GTCAAATGGCTCGCGTGTG 60.154 57.895 5.77 0.00 0.00 3.82
2554 3430 1.596752 TCAAATGGCTCGCGTGTGT 60.597 52.632 5.77 0.00 0.00 3.72
2555 3431 1.440850 CAAATGGCTCGCGTGTGTG 60.441 57.895 5.77 0.00 0.00 3.82
2556 3432 1.891919 AAATGGCTCGCGTGTGTGT 60.892 52.632 5.77 0.00 0.00 3.72
2557 3433 2.116736 AAATGGCTCGCGTGTGTGTG 62.117 55.000 5.77 0.00 0.00 3.82
2558 3434 3.807631 ATGGCTCGCGTGTGTGTGT 62.808 57.895 5.77 0.00 0.00 3.72
2559 3435 4.000557 GGCTCGCGTGTGTGTGTG 62.001 66.667 5.77 0.00 0.00 3.82
2570 3446 4.346970 CGTGTGTGTGTGCTATTTCAAAA 58.653 39.130 0.00 0.00 0.00 2.44
2783 3676 7.189079 ACTTTGGAAAATAAAGTTGGACCAA 57.811 32.000 1.69 1.69 43.71 3.67
2789 3682 8.802267 TGGAAAATAAAGTTGGACCAATAGAAG 58.198 33.333 10.83 0.00 0.00 2.85
2791 3684 6.775594 AATAAAGTTGGACCAATAGAAGGC 57.224 37.500 10.83 0.00 0.00 4.35
2792 3685 3.806949 AAGTTGGACCAATAGAAGGCA 57.193 42.857 10.83 0.00 0.00 4.75
2793 3686 4.322057 AAGTTGGACCAATAGAAGGCAT 57.678 40.909 10.83 0.00 0.00 4.40
2795 3688 5.450818 AGTTGGACCAATAGAAGGCATTA 57.549 39.130 10.83 0.00 0.00 1.90
2796 3689 5.193679 AGTTGGACCAATAGAAGGCATTAC 58.806 41.667 10.83 0.00 0.00 1.89
2811 3706 1.397390 ATTACCGTAGCGACAGGGGG 61.397 60.000 11.19 0.93 0.00 5.40
2812 3707 2.786512 TTACCGTAGCGACAGGGGGT 62.787 60.000 11.19 6.24 0.00 4.95
2813 3708 1.920734 TACCGTAGCGACAGGGGGTA 61.921 60.000 11.19 5.40 0.00 3.69
2814 3709 2.487532 CCGTAGCGACAGGGGGTAG 61.488 68.421 0.00 0.00 0.00 3.18
2815 3710 1.452651 CGTAGCGACAGGGGGTAGA 60.453 63.158 0.00 0.00 0.00 2.59
2817 3712 1.108132 GTAGCGACAGGGGGTAGAGG 61.108 65.000 0.00 0.00 0.00 3.69
2876 3771 8.087982 TGATTTGATTTTACTGAGACTGTCAC 57.912 34.615 10.88 4.28 0.00 3.67
2877 3772 7.714813 TGATTTGATTTTACTGAGACTGTCACA 59.285 33.333 10.88 9.16 0.00 3.58
2878 3773 6.844696 TTGATTTTACTGAGACTGTCACAC 57.155 37.500 10.88 1.99 0.00 3.82
2879 3774 6.161855 TGATTTTACTGAGACTGTCACACT 57.838 37.500 10.88 1.93 0.00 3.55
2880 3775 6.216569 TGATTTTACTGAGACTGTCACACTC 58.783 40.000 10.88 0.00 0.00 3.51
2881 3776 4.585955 TTTACTGAGACTGTCACACTCC 57.414 45.455 10.88 0.00 0.00 3.85
2886 3781 4.075682 CTGAGACTGTCACACTCCTAGAA 58.924 47.826 10.88 0.00 0.00 2.10
2910 3805 3.434319 CAGCCGCGCCTTCAACAT 61.434 61.111 0.00 0.00 0.00 2.71
2964 3866 2.967740 AAAAACGTCTCAGTCGCGT 58.032 47.368 5.77 0.00 40.81 6.01
2967 3869 3.590443 AACGTCTCAGTCGCGTCCG 62.590 63.158 5.77 1.36 37.92 4.79
2992 3894 1.570347 CGCCGAAATTCACCGGTTCA 61.570 55.000 2.97 0.00 46.84 3.18
2995 3897 1.156736 CGAAATTCACCGGTTCAGCT 58.843 50.000 2.97 0.00 0.00 4.24
3006 3908 1.029681 GGTTCAGCTCGTTTTTGGGT 58.970 50.000 0.00 0.00 0.00 4.51
3014 3916 1.299544 CGTTTTTGGGTCCGGCAAC 60.300 57.895 0.00 0.00 0.00 4.17
3108 4013 2.798283 CCGTCAAGCGAAAAGTCAAGTA 59.202 45.455 0.00 0.00 44.77 2.24
3119 4026 5.390567 CGAAAAGTCAAGTATTTCTTCCCGG 60.391 44.000 0.00 0.00 33.63 5.73
3127 4034 2.198304 ATTTCTTCCCGGCTCGCCTT 62.198 55.000 6.35 0.00 0.00 4.35
3226 4136 0.466189 CACCGCCAGATAGCCCATTT 60.466 55.000 0.00 0.00 0.00 2.32
3256 4166 1.228657 AAGAACAGAGGTTTCGCCGC 61.229 55.000 0.00 0.00 43.70 6.53
3364 4301 0.390860 CCTAGGCAATGGACTCGGAG 59.609 60.000 2.83 2.83 37.15 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 6.262273 GGACAAATTGACCTTAAGTGAACAGA 59.738 38.462 7.22 0.00 0.00 3.41
222 223 6.875195 CAGCAACTATTTTGACCAAATTGGAT 59.125 34.615 20.25 3.66 40.96 3.41
546 1400 9.505995 GGTTTGAGAGATAAAACGTTTTAAACA 57.494 29.630 30.92 22.50 36.35 2.83
547 1401 8.675888 CGGTTTGAGAGATAAAACGTTTTAAAC 58.324 33.333 30.92 27.16 41.77 2.01
556 1410 6.140786 GGACAAACGGTTTGAGAGATAAAAC 58.859 40.000 33.41 13.81 43.26 2.43
557 1411 5.823570 TGGACAAACGGTTTGAGAGATAAAA 59.176 36.000 33.41 10.37 43.26 1.52
558 1412 5.369833 TGGACAAACGGTTTGAGAGATAAA 58.630 37.500 33.41 11.66 43.26 1.40
559 1413 4.963373 TGGACAAACGGTTTGAGAGATAA 58.037 39.130 33.41 12.94 43.26 1.75
560 1414 4.610605 TGGACAAACGGTTTGAGAGATA 57.389 40.909 33.41 14.28 43.26 1.98
561 1415 3.485463 TGGACAAACGGTTTGAGAGAT 57.515 42.857 33.41 15.44 43.26 2.75
562 1416 2.992124 TGGACAAACGGTTTGAGAGA 57.008 45.000 33.41 15.15 43.26 3.10
563 1417 4.275936 AGATTTGGACAAACGGTTTGAGAG 59.724 41.667 33.41 12.81 43.26 3.20
564 1418 4.204012 AGATTTGGACAAACGGTTTGAGA 58.796 39.130 33.41 16.95 43.26 3.27
565 1419 4.036262 TGAGATTTGGACAAACGGTTTGAG 59.964 41.667 33.41 13.81 43.26 3.02
566 1420 3.948473 TGAGATTTGGACAAACGGTTTGA 59.052 39.130 33.41 15.68 43.26 2.69
567 1421 4.300189 TGAGATTTGGACAAACGGTTTG 57.700 40.909 27.21 27.21 45.95 2.93
568 1422 4.993029 TTGAGATTTGGACAAACGGTTT 57.007 36.364 0.00 0.00 32.51 3.27
569 1423 4.993029 TTTGAGATTTGGACAAACGGTT 57.007 36.364 0.00 0.00 32.51 4.44
570 1424 4.320202 CGATTTGAGATTTGGACAAACGGT 60.320 41.667 0.00 0.00 36.57 4.83
571 1425 4.158384 CGATTTGAGATTTGGACAAACGG 58.842 43.478 0.00 0.00 36.57 4.44
572 1426 3.603770 GCGATTTGAGATTTGGACAAACG 59.396 43.478 0.00 0.00 36.57 3.60
573 1427 4.798574 AGCGATTTGAGATTTGGACAAAC 58.201 39.130 0.00 0.00 36.57 2.93
574 1428 5.452078 AAGCGATTTGAGATTTGGACAAA 57.548 34.783 0.00 0.00 37.79 2.83
575 1429 4.082787 GGAAGCGATTTGAGATTTGGACAA 60.083 41.667 0.00 0.00 0.00 3.18
576 1430 3.440173 GGAAGCGATTTGAGATTTGGACA 59.560 43.478 0.00 0.00 0.00 4.02
577 1431 3.440173 TGGAAGCGATTTGAGATTTGGAC 59.560 43.478 0.00 0.00 0.00 4.02
578 1432 3.440173 GTGGAAGCGATTTGAGATTTGGA 59.560 43.478 0.00 0.00 0.00 3.53
579 1433 3.428045 GGTGGAAGCGATTTGAGATTTGG 60.428 47.826 0.00 0.00 0.00 3.28
580 1434 3.762779 GGTGGAAGCGATTTGAGATTTG 58.237 45.455 0.00 0.00 0.00 2.32
598 1452 2.094258 CGATGTGAGAAATCCAACGGTG 59.906 50.000 0.00 0.00 0.00 4.94
599 1453 2.028476 TCGATGTGAGAAATCCAACGGT 60.028 45.455 0.00 0.00 0.00 4.83
600 1454 2.616960 TCGATGTGAGAAATCCAACGG 58.383 47.619 0.00 0.00 0.00 4.44
611 1465 5.174395 AGGTTTTGAAGATCTCGATGTGAG 58.826 41.667 0.00 0.00 46.72 3.51
612 1466 5.152623 AGGTTTTGAAGATCTCGATGTGA 57.847 39.130 0.00 0.00 0.00 3.58
613 1467 6.333416 TCTAGGTTTTGAAGATCTCGATGTG 58.667 40.000 0.00 0.00 0.00 3.21
614 1468 6.531503 TCTAGGTTTTGAAGATCTCGATGT 57.468 37.500 0.00 0.00 0.00 3.06
615 1469 6.644592 GGATCTAGGTTTTGAAGATCTCGATG 59.355 42.308 0.00 0.00 36.55 3.84
616 1470 6.239458 GGGATCTAGGTTTTGAAGATCTCGAT 60.239 42.308 0.00 0.00 36.55 3.59
617 1471 5.069251 GGGATCTAGGTTTTGAAGATCTCGA 59.931 44.000 0.00 0.00 36.55 4.04
618 1472 5.163405 TGGGATCTAGGTTTTGAAGATCTCG 60.163 44.000 0.00 0.00 38.84 4.04
619 1473 6.240549 TGGGATCTAGGTTTTGAAGATCTC 57.759 41.667 0.00 7.75 37.11 2.75
620 1474 6.159398 ACATGGGATCTAGGTTTTGAAGATCT 59.841 38.462 10.44 0.00 36.55 2.75
621 1475 6.360618 ACATGGGATCTAGGTTTTGAAGATC 58.639 40.000 0.00 3.49 35.83 2.75
622 1476 6.332976 ACATGGGATCTAGGTTTTGAAGAT 57.667 37.500 0.00 0.00 0.00 2.40
623 1477 5.779241 ACATGGGATCTAGGTTTTGAAGA 57.221 39.130 0.00 0.00 0.00 2.87
624 1478 5.945784 TCAACATGGGATCTAGGTTTTGAAG 59.054 40.000 0.00 0.00 0.00 3.02
625 1479 5.886609 TCAACATGGGATCTAGGTTTTGAA 58.113 37.500 0.00 0.00 0.00 2.69
626 1480 5.512942 TCAACATGGGATCTAGGTTTTGA 57.487 39.130 0.00 0.00 0.00 2.69
627 1481 6.488006 CCTATCAACATGGGATCTAGGTTTTG 59.512 42.308 5.52 0.00 32.06 2.44
628 1482 6.160459 ACCTATCAACATGGGATCTAGGTTTT 59.840 38.462 14.00 0.00 32.37 2.43
629 1483 5.672194 ACCTATCAACATGGGATCTAGGTTT 59.328 40.000 14.00 0.18 32.37 3.27
630 1484 5.227593 ACCTATCAACATGGGATCTAGGTT 58.772 41.667 14.00 0.00 32.37 3.50
631 1485 4.832492 ACCTATCAACATGGGATCTAGGT 58.168 43.478 14.00 14.00 34.16 3.08
632 1486 5.832539 AACCTATCAACATGGGATCTAGG 57.167 43.478 13.10 13.10 34.16 3.02
633 1487 7.227512 GTCAAAACCTATCAACATGGGATCTAG 59.772 40.741 5.52 0.40 34.16 2.43
634 1488 7.054124 GTCAAAACCTATCAACATGGGATCTA 58.946 38.462 5.52 0.00 34.16 1.98
635 1489 5.888161 GTCAAAACCTATCAACATGGGATCT 59.112 40.000 5.52 0.00 34.16 2.75
636 1490 5.220854 CGTCAAAACCTATCAACATGGGATC 60.221 44.000 5.52 0.00 34.16 3.36
637 1491 4.640201 CGTCAAAACCTATCAACATGGGAT 59.360 41.667 0.00 2.37 34.16 3.85
638 1492 4.006989 CGTCAAAACCTATCAACATGGGA 58.993 43.478 0.00 0.00 34.16 4.37
639 1493 3.756434 ACGTCAAAACCTATCAACATGGG 59.244 43.478 0.00 0.00 36.68 4.00
640 1494 4.215399 ACACGTCAAAACCTATCAACATGG 59.785 41.667 0.00 0.00 0.00 3.66
641 1495 5.356882 ACACGTCAAAACCTATCAACATG 57.643 39.130 0.00 0.00 0.00 3.21
642 1496 6.385649 AAACACGTCAAAACCTATCAACAT 57.614 33.333 0.00 0.00 0.00 2.71
643 1497 5.821516 AAACACGTCAAAACCTATCAACA 57.178 34.783 0.00 0.00 0.00 3.33
701 1555 0.538746 ATGCTCCCGGTTCGGTTTTT 60.539 50.000 0.00 0.00 46.80 1.94
702 1556 1.074248 ATGCTCCCGGTTCGGTTTT 59.926 52.632 0.00 0.00 46.80 2.43
703 1557 1.674322 CATGCTCCCGGTTCGGTTT 60.674 57.895 0.00 0.00 46.80 3.27
704 1558 2.046314 CATGCTCCCGGTTCGGTT 60.046 61.111 0.00 0.00 46.80 4.44
705 1559 4.096003 CCATGCTCCCGGTTCGGT 62.096 66.667 0.00 0.00 46.80 4.69
707 1561 3.622060 AACCCATGCTCCCGGTTCG 62.622 63.158 0.00 0.00 34.80 3.95
708 1562 0.898326 AAAACCCATGCTCCCGGTTC 60.898 55.000 0.00 0.00 38.96 3.62
709 1563 1.155155 AAAACCCATGCTCCCGGTT 59.845 52.632 0.00 0.00 41.68 4.44
710 1564 1.606313 CAAAACCCATGCTCCCGGT 60.606 57.895 0.00 0.00 0.00 5.28
711 1565 1.595093 GACAAAACCCATGCTCCCGG 61.595 60.000 0.00 0.00 0.00 5.73
712 1566 1.595093 GGACAAAACCCATGCTCCCG 61.595 60.000 0.00 0.00 0.00 5.14
713 1567 2.276869 GGACAAAACCCATGCTCCC 58.723 57.895 0.00 0.00 0.00 4.30
722 1576 5.009710 CCTCTTACAGAAAAGGGACAAAACC 59.990 44.000 0.00 0.00 0.00 3.27
723 1577 5.507482 GCCTCTTACAGAAAAGGGACAAAAC 60.507 44.000 0.00 0.00 0.00 2.43
724 1578 4.583073 GCCTCTTACAGAAAAGGGACAAAA 59.417 41.667 0.00 0.00 0.00 2.44
725 1579 4.142038 GCCTCTTACAGAAAAGGGACAAA 58.858 43.478 0.00 0.00 0.00 2.83
726 1580 3.137544 TGCCTCTTACAGAAAAGGGACAA 59.862 43.478 0.00 0.00 0.00 3.18
727 1581 2.708861 TGCCTCTTACAGAAAAGGGACA 59.291 45.455 0.00 0.00 0.00 4.02
728 1582 3.075148 GTGCCTCTTACAGAAAAGGGAC 58.925 50.000 0.00 0.00 41.97 4.46
729 1583 2.289444 CGTGCCTCTTACAGAAAAGGGA 60.289 50.000 0.00 0.00 0.00 4.20
730 1584 2.076863 CGTGCCTCTTACAGAAAAGGG 58.923 52.381 0.00 0.00 0.00 3.95
731 1585 1.464997 GCGTGCCTCTTACAGAAAAGG 59.535 52.381 0.00 0.00 0.00 3.11
732 1586 1.464997 GGCGTGCCTCTTACAGAAAAG 59.535 52.381 2.98 0.00 0.00 2.27
733 1587 1.519408 GGCGTGCCTCTTACAGAAAA 58.481 50.000 2.98 0.00 0.00 2.29
734 1588 0.321298 GGGCGTGCCTCTTACAGAAA 60.321 55.000 11.25 0.00 36.10 2.52
735 1589 1.295423 GGGCGTGCCTCTTACAGAA 59.705 57.895 11.25 0.00 36.10 3.02
736 1590 2.978824 GGGCGTGCCTCTTACAGA 59.021 61.111 11.25 0.00 36.10 3.41
737 1591 2.509336 CGGGCGTGCCTCTTACAG 60.509 66.667 11.25 0.00 36.10 2.74
738 1592 3.307906 ACGGGCGTGCCTCTTACA 61.308 61.111 11.25 0.00 36.10 2.41
739 1593 2.813908 CACGGGCGTGCCTCTTAC 60.814 66.667 11.25 0.00 39.39 2.34
754 1608 5.803967 ACGGTTATAATTTCGTGAGAGACAC 59.196 40.000 9.55 0.00 43.69 3.67
755 1609 5.957798 ACGGTTATAATTTCGTGAGAGACA 58.042 37.500 9.55 0.00 43.69 3.41
760 1614 9.914419 CAACAGGCACGGTTATAATTTCGTGAG 62.914 44.444 27.34 20.96 46.59 3.51
761 1615 8.258842 CAACAGGCACGGTTATAATTTCGTGA 62.259 42.308 27.34 0.00 46.59 4.35
762 1616 4.142773 AACAGGCACGGTTATAATTTCGTG 60.143 41.667 22.79 22.79 46.42 4.35
763 1617 3.602483 ACAGGCACGGTTATAATTTCGT 58.398 40.909 5.90 5.90 27.95 3.85
764 1618 4.339429 CAACAGGCACGGTTATAATTTCG 58.661 43.478 0.00 0.00 46.59 3.46
765 1619 4.102649 GCAACAGGCACGGTTATAATTTC 58.897 43.478 0.00 0.00 46.59 2.17
766 1620 3.426963 CGCAACAGGCACGGTTATAATTT 60.427 43.478 0.00 0.00 46.59 1.82
767 1621 2.096819 CGCAACAGGCACGGTTATAATT 59.903 45.455 0.00 0.00 46.59 1.40
768 1622 1.668751 CGCAACAGGCACGGTTATAAT 59.331 47.619 0.00 0.00 46.59 1.28
769 1623 1.080298 CGCAACAGGCACGGTTATAA 58.920 50.000 0.00 0.00 46.59 0.98
770 1624 0.741574 CCGCAACAGGCACGGTTATA 60.742 55.000 0.00 0.00 46.59 0.98
771 1625 2.038269 CCGCAACAGGCACGGTTAT 61.038 57.895 0.00 0.00 46.59 1.89
772 1626 2.661840 TTCCGCAACAGGCACGGTTA 62.662 55.000 0.00 0.00 46.59 2.85
774 1628 4.555709 TTCCGCAACAGGCACGGT 62.556 61.111 0.00 0.00 46.92 4.83
776 1630 2.051345 GTTTCCGCAACAGGCACG 60.051 61.111 0.00 0.00 45.17 5.34
777 1631 0.179124 TTTGTTTCCGCAACAGGCAC 60.179 50.000 0.00 0.00 46.37 5.01
778 1632 0.532573 TTTTGTTTCCGCAACAGGCA 59.467 45.000 0.00 0.00 46.37 4.75
779 1633 0.927537 GTTTTGTTTCCGCAACAGGC 59.072 50.000 0.00 0.00 46.37 4.85
780 1634 1.566404 GGTTTTGTTTCCGCAACAGG 58.434 50.000 0.00 0.00 46.37 4.00
781 1635 1.196200 CGGTTTTGTTTCCGCAACAG 58.804 50.000 0.00 0.00 46.37 3.16
782 1636 3.330766 CGGTTTTGTTTCCGCAACA 57.669 47.368 0.00 0.00 44.11 3.33
844 1698 1.009389 CAGCGTGACTCCTCGGAAAC 61.009 60.000 0.00 0.00 0.00 2.78
845 1699 1.176619 TCAGCGTGACTCCTCGGAAA 61.177 55.000 0.00 0.00 0.00 3.13
846 1700 0.965866 ATCAGCGTGACTCCTCGGAA 60.966 55.000 0.00 0.00 0.00 4.30
847 1701 0.965866 AATCAGCGTGACTCCTCGGA 60.966 55.000 0.00 0.00 0.00 4.55
848 1702 0.526524 GAATCAGCGTGACTCCTCGG 60.527 60.000 0.00 0.00 0.00 4.63
849 1703 0.526524 GGAATCAGCGTGACTCCTCG 60.527 60.000 7.84 0.00 39.53 4.63
850 1704 0.532573 TGGAATCAGCGTGACTCCTC 59.467 55.000 13.82 0.98 42.84 3.71
851 1705 1.198713 ATGGAATCAGCGTGACTCCT 58.801 50.000 13.82 1.57 42.84 3.69
852 1706 2.029838 AATGGAATCAGCGTGACTCC 57.970 50.000 8.07 8.07 42.73 3.85
853 1707 5.741388 ATAAAATGGAATCAGCGTGACTC 57.259 39.130 0.00 0.00 0.00 3.36
854 1708 5.415701 ACAATAAAATGGAATCAGCGTGACT 59.584 36.000 0.00 0.00 0.00 3.41
855 1709 5.512788 CACAATAAAATGGAATCAGCGTGAC 59.487 40.000 0.00 0.00 0.00 3.67
856 1710 5.639757 CACAATAAAATGGAATCAGCGTGA 58.360 37.500 0.00 0.00 0.00 4.35
857 1711 4.266029 GCACAATAAAATGGAATCAGCGTG 59.734 41.667 0.00 0.00 0.00 5.34
858 1712 4.158394 AGCACAATAAAATGGAATCAGCGT 59.842 37.500 0.00 0.00 0.00 5.07
859 1713 4.675510 AGCACAATAAAATGGAATCAGCG 58.324 39.130 0.00 0.00 0.00 5.18
860 1714 5.045872 GGAGCACAATAAAATGGAATCAGC 58.954 41.667 0.00 0.00 0.00 4.26
861 1715 6.461110 AGGAGCACAATAAAATGGAATCAG 57.539 37.500 0.00 0.00 0.00 2.90
862 1716 5.066375 CGAGGAGCACAATAAAATGGAATCA 59.934 40.000 0.00 0.00 0.00 2.57
866 1720 3.689161 CACGAGGAGCACAATAAAATGGA 59.311 43.478 0.00 0.00 0.00 3.41
914 1768 3.338250 AGCCAAATCGCCCCAGGA 61.338 61.111 0.00 0.00 0.00 3.86
942 1796 4.309950 GGAACCGCTCCGTGGTGT 62.310 66.667 0.00 0.00 46.56 4.16
956 1810 2.112297 GCACCACTGAACCGGGAA 59.888 61.111 6.32 0.00 0.00 3.97
983 1837 2.009042 GCATTCCAACAGGAGGACGAG 61.009 57.143 0.00 0.00 34.19 4.18
1227 2081 3.380637 GCTCCGACTGGATGAAGTAGTAA 59.619 47.826 0.00 0.00 45.33 2.24
1516 2370 2.108168 CCACTTCTCGAGGAATACCCA 58.892 52.381 13.56 0.00 37.41 4.51
1665 2519 1.228367 CTGCAGGTTCAGCTTGGGT 60.228 57.895 5.57 0.00 0.00 4.51
1865 2719 1.827399 GATGTCGGTGGTGACCAGGT 61.827 60.000 3.58 0.00 43.33 4.00
2131 3006 3.115892 GTCGTGCCGGAAATGCGA 61.116 61.111 5.05 0.00 0.00 5.10
2199 3074 2.357034 CCGTTGTACACCAGCGCT 60.357 61.111 2.64 2.64 45.25 5.92
2418 3293 2.616256 GGTCCATCTGTCAAGCATGTCA 60.616 50.000 0.00 0.00 0.00 3.58
2445 3320 3.308014 GAGTCAGAGCTTGCCGGCT 62.308 63.158 29.70 6.86 46.11 5.52
2506 3382 9.772973 ACACATTAGTACTAAGATGTTTTGTGA 57.227 29.630 31.03 7.22 33.66 3.58
2518 3394 9.158233 GCCATTTGACTTACACATTAGTACTAA 57.842 33.333 17.41 17.41 0.00 2.24
2519 3395 8.537016 AGCCATTTGACTTACACATTAGTACTA 58.463 33.333 0.00 0.00 0.00 1.82
2520 3396 7.394816 AGCCATTTGACTTACACATTAGTACT 58.605 34.615 0.00 0.00 0.00 2.73
2521 3397 7.464178 CGAGCCATTTGACTTACACATTAGTAC 60.464 40.741 0.00 0.00 0.00 2.73
2522 3398 6.533723 CGAGCCATTTGACTTACACATTAGTA 59.466 38.462 0.00 0.00 0.00 1.82
2523 3399 5.351465 CGAGCCATTTGACTTACACATTAGT 59.649 40.000 0.00 0.00 0.00 2.24
2524 3400 5.727791 GCGAGCCATTTGACTTACACATTAG 60.728 44.000 0.00 0.00 0.00 1.73
2525 3401 4.094294 GCGAGCCATTTGACTTACACATTA 59.906 41.667 0.00 0.00 0.00 1.90
2526 3402 3.119849 GCGAGCCATTTGACTTACACATT 60.120 43.478 0.00 0.00 0.00 2.71
2527 3403 2.420022 GCGAGCCATTTGACTTACACAT 59.580 45.455 0.00 0.00 0.00 3.21
2528 3404 1.804151 GCGAGCCATTTGACTTACACA 59.196 47.619 0.00 0.00 0.00 3.72
2529 3405 1.201921 CGCGAGCCATTTGACTTACAC 60.202 52.381 0.00 0.00 0.00 2.90
2530 3406 1.075542 CGCGAGCCATTTGACTTACA 58.924 50.000 0.00 0.00 0.00 2.41
2531 3407 1.076332 ACGCGAGCCATTTGACTTAC 58.924 50.000 15.93 0.00 0.00 2.34
2532 3408 1.075542 CACGCGAGCCATTTGACTTA 58.924 50.000 15.93 0.00 0.00 2.24
2533 3409 0.884704 ACACGCGAGCCATTTGACTT 60.885 50.000 15.93 0.00 0.00 3.01
2534 3410 1.301716 ACACGCGAGCCATTTGACT 60.302 52.632 15.93 0.00 0.00 3.41
2535 3411 1.154413 CACACGCGAGCCATTTGAC 60.154 57.895 15.93 0.00 0.00 3.18
2536 3412 1.596752 ACACACGCGAGCCATTTGA 60.597 52.632 15.93 0.00 0.00 2.69
2537 3413 1.440850 CACACACGCGAGCCATTTG 60.441 57.895 15.93 0.00 0.00 2.32
2538 3414 1.891919 ACACACACGCGAGCCATTT 60.892 52.632 15.93 0.00 0.00 2.32
2539 3415 2.280797 ACACACACGCGAGCCATT 60.281 55.556 15.93 0.00 0.00 3.16
2540 3416 3.043713 CACACACACGCGAGCCAT 61.044 61.111 15.93 0.00 0.00 4.40
2541 3417 4.522689 ACACACACACGCGAGCCA 62.523 61.111 15.93 0.00 0.00 4.75
2542 3418 4.000557 CACACACACACGCGAGCC 62.001 66.667 15.93 0.00 0.00 4.70
2543 3419 4.649954 GCACACACACACGCGAGC 62.650 66.667 15.93 0.00 0.00 5.03
2544 3420 1.008875 ATAGCACACACACACGCGAG 61.009 55.000 15.93 7.88 0.00 5.03
2545 3421 0.598942 AATAGCACACACACACGCGA 60.599 50.000 15.93 0.00 0.00 5.87
2546 3422 0.234625 AAATAGCACACACACACGCG 59.765 50.000 3.53 3.53 0.00 6.01
2547 3423 1.262950 TGAAATAGCACACACACACGC 59.737 47.619 0.00 0.00 0.00 5.34
2548 3424 3.600717 TTGAAATAGCACACACACACG 57.399 42.857 0.00 0.00 0.00 4.49
2570 3446 3.443976 GACACACGAGCCATTTTGTTTT 58.556 40.909 0.00 0.00 0.00 2.43
2588 3464 6.365247 GTGAAGCAACTATTTCTAAGTCGACA 59.635 38.462 19.50 0.00 0.00 4.35
2760 3653 9.423061 CTATTGGTCCAACTTTATTTTCCAAAG 57.577 33.333 6.41 0.00 37.28 2.77
2767 3660 6.723977 TGCCTTCTATTGGTCCAACTTTATTT 59.276 34.615 6.41 0.00 0.00 1.40
2770 3663 5.249780 TGCCTTCTATTGGTCCAACTTTA 57.750 39.130 6.41 0.00 0.00 1.85
2783 3676 2.889045 TCGCTACGGTAATGCCTTCTAT 59.111 45.455 0.00 0.00 34.25 1.98
2789 3682 0.874607 CCTGTCGCTACGGTAATGCC 60.875 60.000 0.00 0.00 0.00 4.40
2791 3684 0.249322 CCCCTGTCGCTACGGTAATG 60.249 60.000 0.00 0.00 0.00 1.90
2792 3685 1.397390 CCCCCTGTCGCTACGGTAAT 61.397 60.000 0.00 0.00 0.00 1.89
2793 3686 2.053865 CCCCCTGTCGCTACGGTAA 61.054 63.158 0.00 0.00 0.00 2.85
2795 3688 3.286694 TACCCCCTGTCGCTACGGT 62.287 63.158 0.00 0.00 0.00 4.83
2796 3689 2.440796 TACCCCCTGTCGCTACGG 60.441 66.667 0.00 0.00 0.00 4.02
2873 3768 4.019858 CTGGAGATGTTCTAGGAGTGTGA 58.980 47.826 0.00 0.00 31.17 3.58
2876 3771 2.102252 GGCTGGAGATGTTCTAGGAGTG 59.898 54.545 0.00 0.00 35.11 3.51
2877 3772 2.393646 GGCTGGAGATGTTCTAGGAGT 58.606 52.381 0.00 0.00 35.11 3.85
2878 3773 1.339610 CGGCTGGAGATGTTCTAGGAG 59.660 57.143 0.00 0.00 35.11 3.69
2879 3774 1.403814 CGGCTGGAGATGTTCTAGGA 58.596 55.000 0.00 0.00 35.11 2.94
2880 3775 0.249657 GCGGCTGGAGATGTTCTAGG 60.250 60.000 0.00 0.00 35.11 3.02
2881 3776 0.596083 CGCGGCTGGAGATGTTCTAG 60.596 60.000 0.00 0.00 37.45 2.43
2903 3798 1.338105 CGTCTGAGAGGGCATGTTGAA 60.338 52.381 0.00 0.00 0.00 2.69
2910 3805 1.048601 AAAAGTCGTCTGAGAGGGCA 58.951 50.000 9.56 0.00 0.00 5.36
2992 3894 1.599797 CCGGACCCAAAAACGAGCT 60.600 57.895 0.00 0.00 0.00 4.09
2995 3897 1.453379 TTGCCGGACCCAAAAACGA 60.453 52.632 5.05 0.00 0.00 3.85
3108 4013 2.124695 GGCGAGCCGGGAAGAAAT 60.125 61.111 2.18 0.00 0.00 2.17
3213 4122 1.230635 CGGCGGAAATGGGCTATCTG 61.231 60.000 0.00 0.00 0.00 2.90
3322 4259 2.156098 GGCAAATCACCGAACACCTTA 58.844 47.619 0.00 0.00 0.00 2.69
3395 4332 4.083862 GTCGGCCTCGGCTTCCTT 62.084 66.667 8.00 0.00 41.60 3.36


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

AutoCloner maintained by Alex Coulton.