Multiple sequence alignment - TraesCS5A01G000700

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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 TraesCS5A01G000700 chr5A 100.000 3041 0 0 1 3041 643931 646971 0.000000e+00 5616.0
1 TraesCS5A01G000700 chr5D 93.079 968 34 8 1145 2088 935266 934308 0.000000e+00 1386.0
2 TraesCS5A01G000700 chr5D 92.260 646 34 2 2369 2998 934060 933415 0.000000e+00 902.0
3 TraesCS5A01G000700 chr5D 82.128 470 24 26 1 430 936331 935882 6.240000e-92 348.0
4 TraesCS5A01G000700 chr5D 93.293 164 7 2 2206 2366 934269 934107 3.920000e-59 239.0
5 TraesCS5A01G000700 chr5D 100.000 46 0 0 475 520 935776 935731 5.400000e-13 86.1
6 TraesCS5A01G000700 chr5D 100.000 35 0 0 2999 3033 932509 932475 7.040000e-07 65.8
7 TraesCS5A01G000700 chr5B 87.388 1229 72 36 1182 2356 216516 217715 0.000000e+00 1334.0
8 TraesCS5A01G000700 chr5B 88.037 652 41 6 2369 2998 217793 218429 0.000000e+00 737.0
9 TraesCS5A01G000700 chr5B 96.373 193 2 3 1 192 215243 215431 2.280000e-81 313.0
10 TraesCS5A01G000700 chr5B 98.182 55 1 0 479 533 215748 215802 2.500000e-16 97.1
11 TraesCS5A01G000700 chr5B 92.063 63 5 0 632 694 215837 215899 4.180000e-14 89.8
12 TraesCS5A01G000700 chr5B 92.857 56 4 0 534 589 657192717 657192772 6.990000e-12 82.4
13 TraesCS5A01G000700 chr5B 91.379 58 1 1 534 591 493512499 493512446 3.250000e-10 76.8
14 TraesCS5A01G000700 chr5B 100.000 39 0 0 591 629 604023971 604024009 4.210000e-09 73.1
15 TraesCS5A01G000700 chr5B 89.655 58 2 1 534 591 114693816 114693763 1.510000e-08 71.3
16 TraesCS5A01G000700 chr5B 85.714 70 6 1 522 591 641227636 641227701 1.510000e-08 71.3
17 TraesCS5A01G000700 chr7A 90.909 550 39 8 1092 1634 728649966 728650511 0.000000e+00 728.0
18 TraesCS5A01G000700 chr7A 100.000 39 0 0 592 630 348209695 348209733 4.210000e-09 73.1
19 TraesCS5A01G000700 chr7A 89.655 58 2 1 534 591 506283078 506283025 1.510000e-08 71.3
20 TraesCS5A01G000700 chr2A 80.105 955 135 34 1086 1996 763450867 763449924 0.000000e+00 660.0
21 TraesCS5A01G000700 chr2D 84.530 362 55 1 1635 1996 638456341 638455981 1.040000e-94 357.0
22 TraesCS5A01G000700 chr2B 91.803 61 1 1 531 591 289890674 289890730 6.990000e-12 82.4
23 TraesCS5A01G000700 chr2B 85.714 77 6 2 534 610 525826160 525826089 3.250000e-10 76.8
24 TraesCS5A01G000700 chr7D 100.000 42 0 0 591 632 55835112 55835071 9.040000e-11 78.7
25 TraesCS5A01G000700 chr6B 91.379 58 1 1 534 591 460065852 460065799 3.250000e-10 76.8
26 TraesCS5A01G000700 chr3A 88.060 67 4 1 534 600 82876787 82876725 3.250000e-10 76.8
27 TraesCS5A01G000700 chr6D 100.000 40 0 0 592 631 420707787 420707826 1.170000e-09 75.0
28 TraesCS5A01G000700 chr4D 100.000 39 0 0 591 629 20579950 20579988 4.210000e-09 73.1
29 TraesCS5A01G000700 chr1B 100.000 39 0 0 591 629 564788674 564788712 4.210000e-09 73.1
30 TraesCS5A01G000700 chr1B 95.349 43 2 0 592 634 555633613 555633571 5.440000e-08 69.4
31 TraesCS5A01G000700 chr7B 95.455 44 2 0 592 635 450640577 450640620 1.510000e-08 71.3
32 TraesCS5A01G000700 chr6A 100.000 38 0 0 592 629 23628711 23628748 1.510000e-08 71.3


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 TraesCS5A01G000700 chr5A 643931 646971 3040 False 5616.000000 5616 100.0000 1 3041 1 chr5A.!!$F1 3040
1 TraesCS5A01G000700 chr5D 932475 936331 3856 True 504.483333 1386 93.4600 1 3033 6 chr5D.!!$R1 3032
2 TraesCS5A01G000700 chr5B 215243 218429 3186 False 514.180000 1334 92.4086 1 2998 5 chr5B.!!$F4 2997
3 TraesCS5A01G000700 chr7A 728649966 728650511 545 False 728.000000 728 90.9090 1092 1634 1 chr7A.!!$F2 542
4 TraesCS5A01G000700 chr2A 763449924 763450867 943 True 660.000000 660 80.1050 1086 1996 1 chr2A.!!$R1 910

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
967 1330 0.105964 GACCAAACCCAAACCCAAGC 59.894 55.0 0.0 0.0 0.0 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2771 3352 0.320374 AAGAATTGCCACCTCGTCGA 59.68 50.0 0.0 0.0 0.0 4.2 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
54 58 3.036959 TCCCTCCCTCCCTCCCTC 61.037 72.222 0.00 0.00 0.00 4.30
55 59 4.179599 CCCTCCCTCCCTCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
56 60 4.179599 CCTCCCTCCCTCCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
57 61 3.039526 CTCCCTCCCTCCCTCCCT 61.040 72.222 0.00 0.00 0.00 4.20
250 271 3.544684 TGCAATGCATCCTTGGTAGTAG 58.455 45.455 2.72 0.00 31.71 2.57
251 272 2.880890 GCAATGCATCCTTGGTAGTAGG 59.119 50.000 0.00 0.00 0.00 3.18
253 274 3.845781 ATGCATCCTTGGTAGTAGGTG 57.154 47.619 0.00 0.00 34.29 4.00
254 275 2.827755 TGCATCCTTGGTAGTAGGTGA 58.172 47.619 0.00 0.00 34.29 4.02
256 277 3.134623 TGCATCCTTGGTAGTAGGTGATG 59.865 47.826 0.00 0.00 34.29 3.07
258 279 2.116238 TCCTTGGTAGTAGGTGATGGC 58.884 52.381 0.00 0.00 34.29 4.40
259 280 2.119495 CCTTGGTAGTAGGTGATGGCT 58.881 52.381 0.00 0.00 0.00 4.75
260 281 2.103263 CCTTGGTAGTAGGTGATGGCTC 59.897 54.545 0.00 0.00 0.00 4.70
261 282 2.848678 TGGTAGTAGGTGATGGCTCT 57.151 50.000 0.00 0.00 0.00 4.09
262 283 3.116096 TGGTAGTAGGTGATGGCTCTT 57.884 47.619 0.00 0.00 0.00 2.85
263 284 3.450904 TGGTAGTAGGTGATGGCTCTTT 58.549 45.455 0.00 0.00 0.00 2.52
264 285 3.197766 TGGTAGTAGGTGATGGCTCTTTG 59.802 47.826 0.00 0.00 0.00 2.77
265 286 3.451178 GGTAGTAGGTGATGGCTCTTTGA 59.549 47.826 0.00 0.00 0.00 2.69
266 287 3.902881 AGTAGGTGATGGCTCTTTGAG 57.097 47.619 0.00 0.00 0.00 3.02
267 288 3.177228 AGTAGGTGATGGCTCTTTGAGT 58.823 45.455 0.00 0.00 31.39 3.41
268 289 2.486472 AGGTGATGGCTCTTTGAGTG 57.514 50.000 0.00 0.00 31.39 3.51
269 290 1.980765 AGGTGATGGCTCTTTGAGTGA 59.019 47.619 0.00 0.00 31.39 3.41
294 315 6.846505 AGTCCTATTTATCCAGACCTGATTCA 59.153 38.462 0.00 0.00 0.00 2.57
308 329 2.161855 TGATTCATGTTGCTGACACCC 58.838 47.619 0.00 0.00 42.04 4.61
309 330 2.161855 GATTCATGTTGCTGACACCCA 58.838 47.619 0.00 0.00 42.04 4.51
310 331 2.064434 TTCATGTTGCTGACACCCAA 57.936 45.000 0.00 0.00 42.04 4.12
311 332 1.317613 TCATGTTGCTGACACCCAAC 58.682 50.000 7.10 7.10 42.04 3.77
312 333 0.314935 CATGTTGCTGACACCCAACC 59.685 55.000 10.23 0.00 42.04 3.77
313 334 0.827507 ATGTTGCTGACACCCAACCC 60.828 55.000 10.23 0.00 42.04 4.11
314 335 1.454847 GTTGCTGACACCCAACCCA 60.455 57.895 3.82 0.00 36.27 4.51
315 336 1.040339 GTTGCTGACACCCAACCCAA 61.040 55.000 3.82 0.00 36.27 4.12
316 337 1.040339 TTGCTGACACCCAACCCAAC 61.040 55.000 0.00 0.00 0.00 3.77
317 338 2.200337 GCTGACACCCAACCCAACC 61.200 63.158 0.00 0.00 0.00 3.77
318 339 1.530655 CTGACACCCAACCCAACCC 60.531 63.158 0.00 0.00 0.00 4.11
319 340 2.203582 GACACCCAACCCAACCCC 60.204 66.667 0.00 0.00 0.00 4.95
325 346 2.525629 CAACCCAACCCCAACCCC 60.526 66.667 0.00 0.00 0.00 4.95
327 368 2.647949 AACCCAACCCCAACCCCAA 61.648 57.895 0.00 0.00 0.00 4.12
333 374 3.610479 CCCCAACCCCAACCCCAT 61.610 66.667 0.00 0.00 0.00 4.00
418 492 2.680312 ACTGCAGCATCGATTGTAGT 57.320 45.000 15.27 13.18 35.78 2.73
420 494 2.094026 ACTGCAGCATCGATTGTAGTGA 60.094 45.455 16.87 0.00 38.55 3.41
430 507 5.666969 TCGATTGTAGTGAGTTTGTTTGG 57.333 39.130 0.00 0.00 0.00 3.28
431 508 5.361427 TCGATTGTAGTGAGTTTGTTTGGA 58.639 37.500 0.00 0.00 0.00 3.53
435 512 5.042463 TGTAGTGAGTTTGTTTGGATGGA 57.958 39.130 0.00 0.00 0.00 3.41
438 515 5.458041 AGTGAGTTTGTTTGGATGGATTG 57.542 39.130 0.00 0.00 0.00 2.67
458 563 7.178805 TGGATTGTGAATGAATGAATTTCCTCA 59.821 33.333 0.00 0.00 33.04 3.86
460 565 9.245962 GATTGTGAATGAATGAATTTCCTCATC 57.754 33.333 10.06 6.43 34.90 2.92
462 567 8.301252 TGTGAATGAATGAATTTCCTCATCAT 57.699 30.769 10.06 5.16 34.90 2.45
463 568 8.194769 TGTGAATGAATGAATTTCCTCATCATG 58.805 33.333 10.06 0.00 34.90 3.07
473 611 7.930325 TGAATTTCCTCATCATGTATCTGACTC 59.070 37.037 0.00 0.00 0.00 3.36
533 672 5.981088 TGTACCATGCATGTTTTTCATCT 57.019 34.783 24.58 0.00 34.09 2.90
534 673 5.953183 TGTACCATGCATGTTTTTCATCTC 58.047 37.500 24.58 4.58 34.09 2.75
535 674 5.711506 TGTACCATGCATGTTTTTCATCTCT 59.288 36.000 24.58 0.00 34.09 3.10
537 676 6.446781 ACCATGCATGTTTTTCATCTCTAG 57.553 37.500 24.58 7.06 34.09 2.43
538 677 6.182627 ACCATGCATGTTTTTCATCTCTAGA 58.817 36.000 24.58 0.00 34.09 2.43
554 693 8.706492 CATCTCTAGATGCATCTCCTTTTATC 57.294 38.462 31.92 0.00 44.44 1.75
555 694 7.238486 TCTCTAGATGCATCTCCTTTTATCC 57.762 40.000 31.92 0.00 38.32 2.59
556 695 6.784473 TCTCTAGATGCATCTCCTTTTATCCA 59.216 38.462 31.92 10.19 38.32 3.41
558 697 7.982252 TCTAGATGCATCTCCTTTTATCCATT 58.018 34.615 31.92 6.52 38.32 3.16
559 698 8.443176 TCTAGATGCATCTCCTTTTATCCATTT 58.557 33.333 31.92 5.86 38.32 2.32
560 699 7.909485 AGATGCATCTCCTTTTATCCATTTT 57.091 32.000 23.75 0.00 29.30 1.82
561 700 7.723324 AGATGCATCTCCTTTTATCCATTTTG 58.277 34.615 23.75 0.00 29.30 2.44
563 702 7.664552 TGCATCTCCTTTTATCCATTTTGAT 57.335 32.000 0.00 0.00 0.00 2.57
564 703 7.494211 TGCATCTCCTTTTATCCATTTTGATG 58.506 34.615 0.00 0.00 0.00 3.07
566 705 7.650903 GCATCTCCTTTTATCCATTTTGATGAC 59.349 37.037 0.00 0.00 32.05 3.06
600 739 3.948735 GACGGAGGGTCCATTTTGA 57.051 52.632 0.00 0.00 39.90 2.69
601 740 2.420058 GACGGAGGGTCCATTTTGAT 57.580 50.000 0.00 0.00 39.90 2.57
602 741 2.017049 GACGGAGGGTCCATTTTGATG 58.983 52.381 0.00 0.00 39.90 3.07
603 742 1.633432 ACGGAGGGTCCATTTTGATGA 59.367 47.619 0.00 0.00 35.91 2.92
604 743 2.017049 CGGAGGGTCCATTTTGATGAC 58.983 52.381 0.00 0.00 35.91 3.06
605 744 2.617788 CGGAGGGTCCATTTTGATGACA 60.618 50.000 0.00 0.00 35.91 3.58
606 745 3.430453 GGAGGGTCCATTTTGATGACAA 58.570 45.455 0.00 0.00 36.28 3.18
607 746 3.445096 GGAGGGTCCATTTTGATGACAAG 59.555 47.826 0.00 0.00 36.28 3.16
608 747 4.082125 GAGGGTCCATTTTGATGACAAGT 58.918 43.478 0.00 0.00 37.32 3.16
609 748 5.253330 GAGGGTCCATTTTGATGACAAGTA 58.747 41.667 0.00 0.00 37.32 2.24
610 749 5.831103 AGGGTCCATTTTGATGACAAGTAT 58.169 37.500 0.00 0.00 37.32 2.12
611 750 6.256053 AGGGTCCATTTTGATGACAAGTATT 58.744 36.000 0.00 0.00 37.32 1.89
612 751 6.725834 AGGGTCCATTTTGATGACAAGTATTT 59.274 34.615 0.00 0.00 37.32 1.40
613 752 7.235399 AGGGTCCATTTTGATGACAAGTATTTT 59.765 33.333 0.00 0.00 37.32 1.82
614 753 7.331687 GGGTCCATTTTGATGACAAGTATTTTG 59.668 37.037 0.00 0.00 37.32 2.44
615 754 7.331687 GGTCCATTTTGATGACAAGTATTTTGG 59.668 37.037 0.00 0.00 37.32 3.28
616 755 7.331687 GTCCATTTTGATGACAAGTATTTTGGG 59.668 37.037 0.00 0.00 37.32 4.12
617 756 7.234371 TCCATTTTGATGACAAGTATTTTGGGA 59.766 33.333 0.00 0.00 37.32 4.37
618 757 7.331687 CCATTTTGATGACAAGTATTTTGGGAC 59.668 37.037 0.00 0.00 37.32 4.46
619 758 5.621197 TTGATGACAAGTATTTTGGGACG 57.379 39.130 0.00 0.00 0.00 4.79
620 759 4.006989 TGATGACAAGTATTTTGGGACGG 58.993 43.478 0.00 0.00 0.00 4.79
621 760 3.773418 TGACAAGTATTTTGGGACGGA 57.227 42.857 0.00 0.00 0.00 4.69
622 761 3.670625 TGACAAGTATTTTGGGACGGAG 58.329 45.455 0.00 0.00 0.00 4.63
623 762 3.007635 GACAAGTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
675 814 7.325660 ACATTCCTGCTAAAATACAGACATG 57.674 36.000 0.00 0.00 35.90 3.21
683 822 6.883756 TGCTAAAATACAGACATGTCCATGAA 59.116 34.615 22.21 4.46 41.20 2.57
694 833 5.121811 ACATGTCCATGAAAGCTAAGCTAG 58.878 41.667 13.93 0.00 38.38 3.42
695 834 4.024218 CATGTCCATGAAAGCTAAGCTAGC 60.024 45.833 6.62 6.62 45.38 3.42
698 837 9.228454 CATGTCCATGAAAGCTAAGCTAGCAAA 62.228 40.741 18.83 2.91 46.42 3.68
710 849 2.056094 CTAGCAAAGCAGTTTGGCAC 57.944 50.000 0.00 0.00 42.99 5.01
711 850 1.610522 CTAGCAAAGCAGTTTGGCACT 59.389 47.619 0.00 0.00 42.99 4.40
713 852 0.932399 GCAAAGCAGTTTGGCACTTG 59.068 50.000 0.00 0.00 42.99 3.16
714 853 1.740043 GCAAAGCAGTTTGGCACTTGT 60.740 47.619 0.00 0.00 42.99 3.16
715 854 2.481104 GCAAAGCAGTTTGGCACTTGTA 60.481 45.455 0.00 0.00 42.99 2.41
718 933 1.133792 AGCAGTTTGGCACTTGTACCT 60.134 47.619 0.00 0.00 30.92 3.08
720 935 2.882137 GCAGTTTGGCACTTGTACCTTA 59.118 45.455 0.00 0.00 30.92 2.69
724 939 5.473504 CAGTTTGGCACTTGTACCTTATCTT 59.526 40.000 0.00 0.00 30.92 2.40
726 941 6.549736 AGTTTGGCACTTGTACCTTATCTTTT 59.450 34.615 0.00 0.00 27.32 2.27
730 945 7.878036 TGGCACTTGTACCTTATCTTTTTAAC 58.122 34.615 0.00 0.00 0.00 2.01
737 952 9.752961 TTGTACCTTATCTTTTTAACTTTTGCC 57.247 29.630 0.00 0.00 0.00 4.52
740 955 8.657074 ACCTTATCTTTTTAACTTTTGCCAAC 57.343 30.769 0.00 0.00 0.00 3.77
741 956 8.261522 ACCTTATCTTTTTAACTTTTGCCAACA 58.738 29.630 0.00 0.00 0.00 3.33
743 958 9.914923 CTTATCTTTTTAACTTTTGCCAACAAC 57.085 29.630 0.00 0.00 34.87 3.32
746 961 8.696410 TCTTTTTAACTTTTGCCAACAACTAG 57.304 30.769 0.00 0.00 34.87 2.57
817 1032 9.458374 TGTACAATCAGTCAATACATATGTACG 57.542 33.333 17.69 11.94 32.72 3.67
818 1033 9.673454 GTACAATCAGTCAATACATATGTACGA 57.327 33.333 17.69 13.94 32.72 3.43
821 1036 9.893305 CAATCAGTCAATACATATGTACGAGTA 57.107 33.333 17.69 9.42 32.72 2.59
889 1252 0.520847 GAAAGCAGAGCAGTTGGAGC 59.479 55.000 0.00 0.00 0.00 4.70
911 1274 2.281208 GGCGTACAAGTGGCCACA 60.281 61.111 36.39 14.48 46.13 4.17
912 1275 2.613506 GGCGTACAAGTGGCCACAC 61.614 63.158 36.39 24.08 46.13 3.82
921 1284 3.884774 TGGCCACACCTCCACCAC 61.885 66.667 0.00 0.00 40.22 4.16
923 1286 3.884774 GCCACACCTCCACCACCA 61.885 66.667 0.00 0.00 0.00 4.17
924 1287 3.170362 CCACACCTCCACCACCAT 58.830 61.111 0.00 0.00 0.00 3.55
925 1288 1.460255 CCACACCTCCACCACCATT 59.540 57.895 0.00 0.00 0.00 3.16
926 1289 0.895100 CCACACCTCCACCACCATTG 60.895 60.000 0.00 0.00 0.00 2.82
928 1291 1.978617 CACCTCCACCACCATTGCC 60.979 63.158 0.00 0.00 0.00 4.52
931 1294 1.535204 CCTCCACCACCATTGCCAAC 61.535 60.000 0.00 0.00 0.00 3.77
932 1295 1.532794 TCCACCACCATTGCCAACC 60.533 57.895 0.00 0.00 0.00 3.77
933 1296 1.836158 CCACCACCATTGCCAACCA 60.836 57.895 0.00 0.00 0.00 3.67
935 1298 0.247185 CACCACCATTGCCAACCATC 59.753 55.000 0.00 0.00 0.00 3.51
936 1299 0.904394 ACCACCATTGCCAACCATCC 60.904 55.000 0.00 0.00 0.00 3.51
937 1300 0.903924 CCACCATTGCCAACCATCCA 60.904 55.000 0.00 0.00 0.00 3.41
939 1302 0.114954 ACCATTGCCAACCATCCACT 59.885 50.000 0.00 0.00 0.00 4.00
940 1303 1.269012 CCATTGCCAACCATCCACTT 58.731 50.000 0.00 0.00 0.00 3.16
942 1305 1.205417 CATTGCCAACCATCCACTTCC 59.795 52.381 0.00 0.00 0.00 3.46
944 1307 0.187117 TGCCAACCATCCACTTCCAA 59.813 50.000 0.00 0.00 0.00 3.53
946 1309 0.881118 CCAACCATCCACTTCCAACG 59.119 55.000 0.00 0.00 0.00 4.10
950 1313 1.002087 ACCATCCACTTCCAACGAGAC 59.998 52.381 0.00 0.00 0.00 3.36
951 1314 1.676014 CCATCCACTTCCAACGAGACC 60.676 57.143 0.00 0.00 0.00 3.85
952 1315 1.001974 CATCCACTTCCAACGAGACCA 59.998 52.381 0.00 0.00 0.00 4.02
953 1316 1.124780 TCCACTTCCAACGAGACCAA 58.875 50.000 0.00 0.00 0.00 3.67
955 1318 1.602377 CCACTTCCAACGAGACCAAAC 59.398 52.381 0.00 0.00 0.00 2.93
959 1322 0.547075 TCCAACGAGACCAAACCCAA 59.453 50.000 0.00 0.00 0.00 4.12
960 1323 1.064611 TCCAACGAGACCAAACCCAAA 60.065 47.619 0.00 0.00 0.00 3.28
961 1324 1.066454 CCAACGAGACCAAACCCAAAC 59.934 52.381 0.00 0.00 0.00 2.93
962 1325 1.066454 CAACGAGACCAAACCCAAACC 59.934 52.381 0.00 0.00 0.00 3.27
963 1326 0.466739 ACGAGACCAAACCCAAACCC 60.467 55.000 0.00 0.00 0.00 4.11
964 1327 0.466555 CGAGACCAAACCCAAACCCA 60.467 55.000 0.00 0.00 0.00 4.51
965 1328 1.783071 GAGACCAAACCCAAACCCAA 58.217 50.000 0.00 0.00 0.00 4.12
966 1329 1.686587 GAGACCAAACCCAAACCCAAG 59.313 52.381 0.00 0.00 0.00 3.61
967 1330 0.105964 GACCAAACCCAAACCCAAGC 59.894 55.000 0.00 0.00 0.00 4.01
968 1331 1.341913 ACCAAACCCAAACCCAAGCC 61.342 55.000 0.00 0.00 0.00 4.35
969 1332 1.068921 CAAACCCAAACCCAAGCCG 59.931 57.895 0.00 0.00 0.00 5.52
970 1333 2.137528 AAACCCAAACCCAAGCCGG 61.138 57.895 0.00 0.00 0.00 6.13
971 1334 2.591193 AAACCCAAACCCAAGCCGGA 62.591 55.000 5.05 0.00 36.56 5.14
972 1335 2.989253 CCCAAACCCAAGCCGGAC 60.989 66.667 5.05 0.00 36.56 4.79
973 1336 2.203422 CCAAACCCAAGCCGGACA 60.203 61.111 5.05 0.00 36.56 4.02
974 1337 2.268076 CCAAACCCAAGCCGGACAG 61.268 63.158 5.05 0.00 36.56 3.51
975 1338 1.228124 CAAACCCAAGCCGGACAGA 60.228 57.895 5.05 0.00 36.56 3.41
976 1339 0.609131 CAAACCCAAGCCGGACAGAT 60.609 55.000 5.05 0.00 36.56 2.90
977 1340 0.988832 AAACCCAAGCCGGACAGATA 59.011 50.000 5.05 0.00 36.56 1.98
978 1341 0.541863 AACCCAAGCCGGACAGATAG 59.458 55.000 5.05 0.00 36.56 2.08
979 1342 0.325296 ACCCAAGCCGGACAGATAGA 60.325 55.000 5.05 0.00 36.56 1.98
980 1343 1.051812 CCCAAGCCGGACAGATAGAT 58.948 55.000 5.05 0.00 36.56 1.98
981 1344 1.001406 CCCAAGCCGGACAGATAGATC 59.999 57.143 5.05 0.00 36.56 2.75
982 1345 1.001406 CCAAGCCGGACAGATAGATCC 59.999 57.143 5.05 0.00 36.56 3.36
983 1346 1.688735 CAAGCCGGACAGATAGATCCA 59.311 52.381 5.05 0.00 34.35 3.41
984 1347 2.088104 AGCCGGACAGATAGATCCAA 57.912 50.000 5.05 0.00 34.35 3.53
985 1348 1.689273 AGCCGGACAGATAGATCCAAC 59.311 52.381 5.05 0.00 34.35 3.77
986 1349 1.412710 GCCGGACAGATAGATCCAACA 59.587 52.381 5.05 0.00 34.35 3.33
987 1350 2.158957 GCCGGACAGATAGATCCAACAA 60.159 50.000 5.05 0.00 34.35 2.83
988 1351 3.722147 CCGGACAGATAGATCCAACAAG 58.278 50.000 0.00 0.00 34.35 3.16
989 1352 3.384789 CCGGACAGATAGATCCAACAAGA 59.615 47.826 0.00 0.00 34.35 3.02
990 1353 4.500545 CCGGACAGATAGATCCAACAAGAG 60.501 50.000 0.00 0.00 34.35 2.85
991 1354 4.376146 GGACAGATAGATCCAACAAGAGC 58.624 47.826 0.00 0.00 34.87 4.09
992 1355 4.376146 GACAGATAGATCCAACAAGAGCC 58.624 47.826 0.00 0.00 0.00 4.70
993 1356 3.776969 ACAGATAGATCCAACAAGAGCCA 59.223 43.478 0.00 0.00 0.00 4.75
994 1357 4.411540 ACAGATAGATCCAACAAGAGCCAT 59.588 41.667 0.00 0.00 0.00 4.40
995 1358 4.996122 CAGATAGATCCAACAAGAGCCATC 59.004 45.833 0.00 0.00 0.00 3.51
996 1359 4.657504 AGATAGATCCAACAAGAGCCATCA 59.342 41.667 0.00 0.00 0.00 3.07
1039 1408 1.152139 CTCCTCCCTCCCTCCATCC 60.152 68.421 0.00 0.00 0.00 3.51
1045 1414 1.532794 CCTCCCTCCATCCTCTCCG 60.533 68.421 0.00 0.00 0.00 4.63
1046 1415 1.532794 CTCCCTCCATCCTCTCCGG 60.533 68.421 0.00 0.00 0.00 5.14
1047 1416 3.237741 CCCTCCATCCTCTCCGGC 61.238 72.222 0.00 0.00 0.00 6.13
1048 1417 3.610669 CCTCCATCCTCTCCGGCG 61.611 72.222 0.00 0.00 0.00 6.46
1067 1436 4.394712 CGCCACCTCCACCTCCAC 62.395 72.222 0.00 0.00 0.00 4.02
1068 1437 3.249189 GCCACCTCCACCTCCACA 61.249 66.667 0.00 0.00 0.00 4.17
1069 1438 2.750350 CCACCTCCACCTCCACAC 59.250 66.667 0.00 0.00 0.00 3.82
1073 1442 2.650116 CCTCCACCTCCACACCTCG 61.650 68.421 0.00 0.00 0.00 4.63
1099 1468 2.347114 CAGCACCGATCCACCACA 59.653 61.111 0.00 0.00 0.00 4.17
1130 1502 1.541379 ATCACAAGCAGCAGCATCAA 58.459 45.000 3.17 0.00 45.49 2.57
1133 1505 1.800315 CAAGCAGCAGCATCAACGC 60.800 57.895 3.17 0.00 45.49 4.84
1134 1506 2.263021 AAGCAGCAGCATCAACGCA 61.263 52.632 3.17 0.00 45.49 5.24
1136 1508 2.084681 GCAGCAGCATCAACGCAAC 61.085 57.895 0.00 0.00 41.58 4.17
1137 1509 1.283487 CAGCAGCATCAACGCAACA 59.717 52.632 0.00 0.00 0.00 3.33
1138 1510 1.000233 CAGCAGCATCAACGCAACAC 61.000 55.000 0.00 0.00 0.00 3.32
1141 1513 0.308684 CAGCATCAACGCAACACAGT 59.691 50.000 0.00 0.00 0.00 3.55
1142 1514 0.588252 AGCATCAACGCAACACAGTC 59.412 50.000 0.00 0.00 0.00 3.51
1143 1515 0.588252 GCATCAACGCAACACAGTCT 59.412 50.000 0.00 0.00 0.00 3.24
1153 1525 1.974236 CAACACAGTCTTCCTCCTCCT 59.026 52.381 0.00 0.00 0.00 3.69
1174 1546 4.619227 CCACACCCGCGACAACCT 62.619 66.667 8.23 0.00 0.00 3.50
1344 1734 2.531942 ACCCTCCCCAACTCCCAC 60.532 66.667 0.00 0.00 0.00 4.61
1348 1738 2.856988 TCCCCAACTCCCACCCAC 60.857 66.667 0.00 0.00 0.00 4.61
1794 2250 3.138798 GAGGACGCCGTGGAGCTA 61.139 66.667 0.00 0.00 0.00 3.32
1857 2313 3.119096 GAGTTCGACGCCAAGGGC 61.119 66.667 0.00 0.00 46.75 5.19
2034 2535 8.870075 ATTCATCAACATCATCATCATCATCT 57.130 30.769 0.00 0.00 0.00 2.90
2046 2547 9.819267 TCATCATCATCATCTTCATAGATTAGC 57.181 33.333 0.00 0.00 39.11 3.09
2073 2574 6.477688 CCATTCTCCATTCATATTGCAACAAC 59.522 38.462 0.00 0.00 0.00 3.32
2075 2576 6.778834 TCTCCATTCATATTGCAACAACAT 57.221 33.333 0.00 0.00 0.00 2.71
2079 2580 8.291191 TCCATTCATATTGCAACAACATAAGA 57.709 30.769 0.00 0.00 0.00 2.10
2084 2585 7.751732 TCATATTGCAACAACATAAGACAGAC 58.248 34.615 0.00 0.00 0.00 3.51
2088 2589 4.511454 TGCAACAACATAAGACAGACAGAC 59.489 41.667 0.00 0.00 0.00 3.51
2090 2591 5.007626 GCAACAACATAAGACAGACAGACAA 59.992 40.000 0.00 0.00 0.00 3.18
2092 2593 6.604735 ACAACATAAGACAGACAGACAAAC 57.395 37.500 0.00 0.00 0.00 2.93
2093 2594 6.112734 ACAACATAAGACAGACAGACAAACA 58.887 36.000 0.00 0.00 0.00 2.83
2094 2595 6.258727 ACAACATAAGACAGACAGACAAACAG 59.741 38.462 0.00 0.00 0.00 3.16
2095 2596 6.161855 ACATAAGACAGACAGACAAACAGA 57.838 37.500 0.00 0.00 0.00 3.41
2096 2597 6.219473 ACATAAGACAGACAGACAAACAGAG 58.781 40.000 0.00 0.00 0.00 3.35
2097 2598 3.742433 AGACAGACAGACAAACAGAGG 57.258 47.619 0.00 0.00 0.00 3.69
2098 2599 2.366916 AGACAGACAGACAAACAGAGGG 59.633 50.000 0.00 0.00 0.00 4.30
2099 2600 2.365617 GACAGACAGACAAACAGAGGGA 59.634 50.000 0.00 0.00 0.00 4.20
2100 2601 2.366916 ACAGACAGACAAACAGAGGGAG 59.633 50.000 0.00 0.00 0.00 4.30
2101 2602 1.974236 AGACAGACAAACAGAGGGAGG 59.026 52.381 0.00 0.00 0.00 4.30
2102 2603 1.002544 GACAGACAAACAGAGGGAGGG 59.997 57.143 0.00 0.00 0.00 4.30
2103 2604 0.322008 CAGACAAACAGAGGGAGGGC 60.322 60.000 0.00 0.00 0.00 5.19
2104 2605 0.768221 AGACAAACAGAGGGAGGGCA 60.768 55.000 0.00 0.00 0.00 5.36
2149 2655 6.237901 ACTCCATCTAGACATGCTCTAGTAG 58.762 44.000 21.51 17.84 46.35 2.57
2150 2656 6.043822 ACTCCATCTAGACATGCTCTAGTAGA 59.956 42.308 21.51 17.18 46.35 2.59
2151 2657 6.842676 TCCATCTAGACATGCTCTAGTAGAA 58.157 40.000 21.51 10.55 46.35 2.10
2152 2658 7.465960 TCCATCTAGACATGCTCTAGTAGAAT 58.534 38.462 21.51 11.75 46.35 2.40
2153 2659 8.606830 TCCATCTAGACATGCTCTAGTAGAATA 58.393 37.037 21.51 9.84 46.35 1.75
2154 2660 9.407380 CCATCTAGACATGCTCTAGTAGAATAT 57.593 37.037 21.51 11.06 46.35 1.28
2353 2896 6.997239 ATAACCATTCCATCATCATCATCG 57.003 37.500 0.00 0.00 0.00 3.84
2429 3004 3.682292 GAATTGCCCGCCGGAGTCT 62.682 63.158 5.05 0.00 0.00 3.24
2495 3070 3.134127 GCCGTGACCAATCCCTGC 61.134 66.667 0.00 0.00 0.00 4.85
2502 3077 2.202236 GACCAATCCCTGCTGCTCCA 62.202 60.000 0.00 0.00 0.00 3.86
2531 3112 1.355066 CCTTGCCGACGAAGAAGAGC 61.355 60.000 0.00 0.00 0.00 4.09
2534 3115 2.875485 CCGACGAAGAAGAGCCGA 59.125 61.111 0.00 0.00 0.00 5.54
2615 3196 2.040544 CACCTTGTCGGCCATGGAC 61.041 63.158 18.40 13.35 40.10 4.02
2622 3203 4.873129 CGGCCATGGACTCGACGG 62.873 72.222 18.40 0.00 0.00 4.79
2741 3322 3.849951 AGCACGTAGATGGGCGGG 61.850 66.667 0.00 0.00 34.21 6.13
2747 3328 4.490606 TAGATGGGCGGGGCTCCA 62.491 66.667 1.96 0.00 34.50 3.86
2872 3469 1.202903 GGATCGTAGACCCCTAGAGCA 60.203 57.143 0.00 0.00 42.51 4.26
2919 3516 2.672651 CTTGTGCATCACCGGGCA 60.673 61.111 6.32 1.81 37.77 5.36
2942 3539 0.807496 GCAGCAGGACATTCTGAACC 59.193 55.000 0.00 0.00 36.93 3.62
2956 3553 3.708220 GAACCCGCTCTGCTCCTCG 62.708 68.421 0.00 0.00 0.00 4.63
3033 4535 1.142314 CTCCAGAGCAGAGCAGAGC 59.858 63.158 0.00 0.00 0.00 4.09
3034 4536 1.605971 CTCCAGAGCAGAGCAGAGCA 61.606 60.000 0.00 0.00 0.00 4.26
3035 4537 1.153529 CCAGAGCAGAGCAGAGCAG 60.154 63.158 0.00 0.00 0.00 4.24
3036 4538 1.605971 CCAGAGCAGAGCAGAGCAGA 61.606 60.000 0.00 0.00 0.00 4.26
3037 4539 0.179121 CAGAGCAGAGCAGAGCAGAG 60.179 60.000 0.00 0.00 0.00 3.35
3038 4540 0.323633 AGAGCAGAGCAGAGCAGAGA 60.324 55.000 0.00 0.00 0.00 3.10
3039 4541 0.179129 GAGCAGAGCAGAGCAGAGAC 60.179 60.000 0.00 0.00 0.00 3.36
3040 4542 1.516821 GCAGAGCAGAGCAGAGACG 60.517 63.158 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 58 3.412386 ACAACTTGCTGCTTTACTAGGG 58.588 45.455 0.00 0.00 0.00 3.53
55 59 6.403636 CCATAACAACTTGCTGCTTTACTAGG 60.404 42.308 0.00 0.00 0.00 3.02
56 60 6.371548 TCCATAACAACTTGCTGCTTTACTAG 59.628 38.462 0.00 0.00 0.00 2.57
57 61 6.234920 TCCATAACAACTTGCTGCTTTACTA 58.765 36.000 0.00 0.00 0.00 1.82
101 105 4.297510 TGCAACATTTTCATTCCAACTCG 58.702 39.130 0.00 0.00 0.00 4.18
244 265 4.160626 ACTCAAAGAGCCATCACCTACTAC 59.839 45.833 0.00 0.00 32.04 2.73
250 271 2.289945 ACTCACTCAAAGAGCCATCACC 60.290 50.000 0.00 0.00 36.58 4.02
251 272 2.999355 GACTCACTCAAAGAGCCATCAC 59.001 50.000 0.00 0.00 36.58 3.06
253 274 2.235898 AGGACTCACTCAAAGAGCCATC 59.764 50.000 0.00 0.00 36.58 3.51
254 275 2.264455 AGGACTCACTCAAAGAGCCAT 58.736 47.619 0.00 0.00 36.58 4.40
256 277 4.479786 AATAGGACTCACTCAAAGAGCC 57.520 45.455 0.00 0.00 36.58 4.70
258 279 7.786030 TGGATAAATAGGACTCACTCAAAGAG 58.214 38.462 0.00 0.00 39.04 2.85
259 280 7.619698 TCTGGATAAATAGGACTCACTCAAAGA 59.380 37.037 0.00 0.00 0.00 2.52
260 281 7.708752 GTCTGGATAAATAGGACTCACTCAAAG 59.291 40.741 0.00 0.00 0.00 2.77
261 282 7.364762 GGTCTGGATAAATAGGACTCACTCAAA 60.365 40.741 0.00 0.00 0.00 2.69
262 283 6.098409 GGTCTGGATAAATAGGACTCACTCAA 59.902 42.308 0.00 0.00 0.00 3.02
263 284 5.598830 GGTCTGGATAAATAGGACTCACTCA 59.401 44.000 0.00 0.00 0.00 3.41
264 285 5.836358 AGGTCTGGATAAATAGGACTCACTC 59.164 44.000 0.00 0.00 0.00 3.51
265 286 5.600484 CAGGTCTGGATAAATAGGACTCACT 59.400 44.000 0.00 0.00 0.00 3.41
266 287 5.598830 TCAGGTCTGGATAAATAGGACTCAC 59.401 44.000 0.00 0.00 0.00 3.51
267 288 5.777449 TCAGGTCTGGATAAATAGGACTCA 58.223 41.667 0.00 0.00 0.00 3.41
268 289 6.926630 ATCAGGTCTGGATAAATAGGACTC 57.073 41.667 0.00 0.00 0.00 3.36
269 290 6.846505 TGAATCAGGTCTGGATAAATAGGACT 59.153 38.462 0.00 0.00 0.00 3.85
294 315 0.827507 GGGTTGGGTGTCAGCAACAT 60.828 55.000 4.12 0.00 40.80 2.71
308 329 2.525629 GGGGTTGGGGTTGGGTTG 60.526 66.667 0.00 0.00 0.00 3.77
309 330 2.647949 TTGGGGTTGGGGTTGGGTT 61.648 57.895 0.00 0.00 0.00 4.11
310 331 3.036959 TTGGGGTTGGGGTTGGGT 61.037 61.111 0.00 0.00 0.00 4.51
311 332 2.525629 GTTGGGGTTGGGGTTGGG 60.526 66.667 0.00 0.00 0.00 4.12
312 333 2.525629 GGTTGGGGTTGGGGTTGG 60.526 66.667 0.00 0.00 0.00 3.77
313 334 2.525629 GGGTTGGGGTTGGGGTTG 60.526 66.667 0.00 0.00 0.00 3.77
314 335 3.852421 GGGGTTGGGGTTGGGGTT 61.852 66.667 0.00 0.00 0.00 4.11
316 337 3.610479 ATGGGGTTGGGGTTGGGG 61.610 66.667 0.00 0.00 0.00 4.96
317 338 2.038813 GATGGGGTTGGGGTTGGG 59.961 66.667 0.00 0.00 0.00 4.12
318 339 2.038813 GGATGGGGTTGGGGTTGG 59.961 66.667 0.00 0.00 0.00 3.77
319 340 2.038813 GGGATGGGGTTGGGGTTG 59.961 66.667 0.00 0.00 0.00 3.77
325 346 0.265553 AATGGGATGGGATGGGGTTG 59.734 55.000 0.00 0.00 0.00 3.77
327 368 0.630175 TGAATGGGATGGGATGGGGT 60.630 55.000 0.00 0.00 0.00 4.95
333 374 6.467490 AATATACACATGAATGGGATGGGA 57.533 37.500 0.00 0.00 34.60 4.37
390 464 7.483307 ACAATCGATGCTGCAGTAATTAAAAT 58.517 30.769 16.64 0.00 0.00 1.82
418 492 4.892345 TCACAATCCATCCAAACAAACTCA 59.108 37.500 0.00 0.00 0.00 3.41
420 494 5.867903 TTCACAATCCATCCAAACAAACT 57.132 34.783 0.00 0.00 0.00 2.66
430 507 8.202137 AGGAAATTCATTCATTCACAATCCATC 58.798 33.333 0.00 0.00 39.98 3.51
431 508 8.086143 AGGAAATTCATTCATTCACAATCCAT 57.914 30.769 0.00 0.00 39.98 3.41
435 512 8.755028 TGATGAGGAAATTCATTCATTCACAAT 58.245 29.630 11.64 0.00 39.98 2.71
438 515 8.195436 ACATGATGAGGAAATTCATTCATTCAC 58.805 33.333 0.00 3.34 39.98 3.18
458 563 5.832595 ACTAGCAGTGAGTCAGATACATGAT 59.167 40.000 0.00 0.00 0.00 2.45
460 565 5.067023 TGACTAGCAGTGAGTCAGATACATG 59.933 44.000 9.92 0.00 46.49 3.21
462 567 4.589908 TGACTAGCAGTGAGTCAGATACA 58.410 43.478 9.92 0.00 46.49 2.29
473 611 7.603024 ACATAATCATCATCATGACTAGCAGTG 59.397 37.037 0.00 0.00 42.05 3.66
533 672 7.565190 ATGGATAAAAGGAGATGCATCTAGA 57.435 36.000 28.78 10.98 37.25 2.43
534 673 8.632906 AAATGGATAAAAGGAGATGCATCTAG 57.367 34.615 28.78 0.00 37.25 2.43
535 674 8.853126 CAAAATGGATAAAAGGAGATGCATCTA 58.147 33.333 28.78 12.98 37.25 1.98
537 676 7.719483 TCAAAATGGATAAAAGGAGATGCATC 58.281 34.615 19.37 19.37 33.50 3.91
538 677 7.664552 TCAAAATGGATAAAAGGAGATGCAT 57.335 32.000 0.00 0.00 35.84 3.96
540 679 7.650903 GTCATCAAAATGGATAAAAGGAGATGC 59.349 37.037 0.00 0.00 33.42 3.91
542 681 8.827832 TGTCATCAAAATGGATAAAAGGAGAT 57.172 30.769 0.00 0.00 33.42 2.75
543 682 8.648698 TTGTCATCAAAATGGATAAAAGGAGA 57.351 30.769 0.00 0.00 33.42 3.71
582 721 2.017049 CATCAAAATGGACCCTCCGTC 58.983 52.381 0.00 0.00 40.17 4.79
584 723 2.017049 GTCATCAAAATGGACCCTCCG 58.983 52.381 0.00 0.00 40.17 4.63
585 724 3.085952 TGTCATCAAAATGGACCCTCC 57.914 47.619 0.00 0.00 36.96 4.30
586 725 4.082125 ACTTGTCATCAAAATGGACCCTC 58.918 43.478 0.00 0.00 33.42 4.30
587 726 4.118168 ACTTGTCATCAAAATGGACCCT 57.882 40.909 0.00 0.00 33.42 4.34
588 727 6.530019 AATACTTGTCATCAAAATGGACCC 57.470 37.500 0.00 0.00 33.42 4.46
589 728 7.331687 CCAAAATACTTGTCATCAAAATGGACC 59.668 37.037 0.00 0.00 33.42 4.46
590 729 7.331687 CCCAAAATACTTGTCATCAAAATGGAC 59.668 37.037 0.00 0.00 33.42 4.02
591 730 7.234371 TCCCAAAATACTTGTCATCAAAATGGA 59.766 33.333 0.00 0.00 33.42 3.41
592 731 7.331687 GTCCCAAAATACTTGTCATCAAAATGG 59.668 37.037 0.00 0.00 33.42 3.16
593 732 7.062138 CGTCCCAAAATACTTGTCATCAAAATG 59.938 37.037 0.00 0.00 32.87 2.32
594 733 7.090173 CGTCCCAAAATACTTGTCATCAAAAT 58.910 34.615 0.00 0.00 32.87 1.82
595 734 6.442952 CGTCCCAAAATACTTGTCATCAAAA 58.557 36.000 0.00 0.00 32.87 2.44
596 735 5.048364 CCGTCCCAAAATACTTGTCATCAAA 60.048 40.000 0.00 0.00 32.87 2.69
597 736 4.457603 CCGTCCCAAAATACTTGTCATCAA 59.542 41.667 0.00 0.00 0.00 2.57
598 737 4.006989 CCGTCCCAAAATACTTGTCATCA 58.993 43.478 0.00 0.00 0.00 3.07
599 738 4.258543 TCCGTCCCAAAATACTTGTCATC 58.741 43.478 0.00 0.00 0.00 2.92
600 739 4.261801 CTCCGTCCCAAAATACTTGTCAT 58.738 43.478 0.00 0.00 0.00 3.06
601 740 3.558321 CCTCCGTCCCAAAATACTTGTCA 60.558 47.826 0.00 0.00 0.00 3.58
602 741 3.007635 CCTCCGTCCCAAAATACTTGTC 58.992 50.000 0.00 0.00 0.00 3.18
603 742 2.290705 CCCTCCGTCCCAAAATACTTGT 60.291 50.000 0.00 0.00 0.00 3.16
604 743 2.026636 TCCCTCCGTCCCAAAATACTTG 60.027 50.000 0.00 0.00 0.00 3.16
605 744 2.238898 CTCCCTCCGTCCCAAAATACTT 59.761 50.000 0.00 0.00 0.00 2.24
606 745 1.838077 CTCCCTCCGTCCCAAAATACT 59.162 52.381 0.00 0.00 0.00 2.12
607 746 1.558294 ACTCCCTCCGTCCCAAAATAC 59.442 52.381 0.00 0.00 0.00 1.89
608 747 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
609 748 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
610 749 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
611 750 0.115745 AGTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
612 751 1.002069 TAGTACTCCCTCCGTCCCAA 58.998 55.000 0.00 0.00 0.00 4.12
613 752 1.002069 TTAGTACTCCCTCCGTCCCA 58.998 55.000 0.00 0.00 0.00 4.37
614 753 2.149973 TTTAGTACTCCCTCCGTCCC 57.850 55.000 0.00 0.00 0.00 4.46
615 754 2.292845 CGATTTAGTACTCCCTCCGTCC 59.707 54.545 0.00 0.00 0.00 4.79
616 755 2.287487 GCGATTTAGTACTCCCTCCGTC 60.287 54.545 0.00 0.00 0.00 4.79
617 756 1.680207 GCGATTTAGTACTCCCTCCGT 59.320 52.381 0.00 0.00 0.00 4.69
618 757 1.955080 AGCGATTTAGTACTCCCTCCG 59.045 52.381 0.00 0.00 0.00 4.63
619 758 3.637694 AGAAGCGATTTAGTACTCCCTCC 59.362 47.826 0.00 0.00 0.00 4.30
620 759 4.338682 TGAGAAGCGATTTAGTACTCCCTC 59.661 45.833 0.00 0.00 0.00 4.30
621 760 4.279145 TGAGAAGCGATTTAGTACTCCCT 58.721 43.478 0.00 0.00 0.00 4.20
622 761 4.650754 TGAGAAGCGATTTAGTACTCCC 57.349 45.455 0.00 0.00 0.00 4.30
623 762 9.562583 CTATAATGAGAAGCGATTTAGTACTCC 57.437 37.037 0.00 0.00 0.00 3.85
667 806 3.430042 AGCTTTCATGGACATGTCTGT 57.570 42.857 24.50 11.26 39.72 3.41
671 810 3.960571 AGCTTAGCTTTCATGGACATGT 58.039 40.909 0.00 0.00 33.89 3.21
694 833 0.932399 CAAGTGCCAAACTGCTTTGC 59.068 50.000 0.00 0.00 39.81 3.68
695 834 2.298411 ACAAGTGCCAAACTGCTTTG 57.702 45.000 0.00 0.00 39.81 2.77
698 837 1.133792 AGGTACAAGTGCCAAACTGCT 60.134 47.619 9.97 0.00 39.81 4.24
699 838 1.318576 AGGTACAAGTGCCAAACTGC 58.681 50.000 9.97 0.00 39.81 4.40
700 839 5.003804 AGATAAGGTACAAGTGCCAAACTG 58.996 41.667 9.97 0.00 39.81 3.16
703 842 6.969993 AAAAGATAAGGTACAAGTGCCAAA 57.030 33.333 9.97 0.00 37.85 3.28
704 843 6.969993 AAAAAGATAAGGTACAAGTGCCAA 57.030 33.333 9.97 0.00 37.85 4.52
705 844 7.722285 AGTTAAAAAGATAAGGTACAAGTGCCA 59.278 33.333 9.97 0.00 37.85 4.92
706 845 8.107399 AGTTAAAAAGATAAGGTACAAGTGCC 57.893 34.615 0.00 0.00 35.42 5.01
707 846 9.961265 AAAGTTAAAAAGATAAGGTACAAGTGC 57.039 29.630 0.00 0.00 0.00 4.40
711 850 9.752961 GGCAAAAGTTAAAAAGATAAGGTACAA 57.247 29.630 0.00 0.00 0.00 2.41
713 852 9.752961 TTGGCAAAAGTTAAAAAGATAAGGTAC 57.247 29.630 0.00 0.00 0.00 3.34
714 853 9.752961 GTTGGCAAAAGTTAAAAAGATAAGGTA 57.247 29.630 0.00 0.00 0.00 3.08
715 854 8.261522 TGTTGGCAAAAGTTAAAAAGATAAGGT 58.738 29.630 0.00 0.00 0.00 3.50
718 933 9.660180 AGTTGTTGGCAAAAGTTAAAAAGATAA 57.340 25.926 0.00 0.00 36.22 1.75
720 935 9.313118 CTAGTTGTTGGCAAAAGTTAAAAAGAT 57.687 29.630 0.00 0.00 36.22 2.40
724 939 6.311690 GCACTAGTTGTTGGCAAAAGTTAAAA 59.688 34.615 0.00 0.00 36.22 1.52
726 941 5.105716 TGCACTAGTTGTTGGCAAAAGTTAA 60.106 36.000 0.00 0.00 36.22 2.01
730 945 3.115554 GTGCACTAGTTGTTGGCAAAAG 58.884 45.455 10.32 0.00 36.22 2.27
734 949 1.979855 ATGTGCACTAGTTGTTGGCA 58.020 45.000 19.41 0.95 0.00 4.92
735 950 3.751175 TCTAATGTGCACTAGTTGTTGGC 59.249 43.478 19.41 0.00 0.00 4.52
736 951 5.940192 TTCTAATGTGCACTAGTTGTTGG 57.060 39.130 19.41 5.71 0.00 3.77
745 960 9.836864 TGACTGATAATAATTCTAATGTGCACT 57.163 29.630 19.41 0.28 0.00 4.40
863 1176 3.482156 ACTGCTCTGCTTTCTCTCAAA 57.518 42.857 0.00 0.00 0.00 2.69
868 1181 2.075338 CTCCAACTGCTCTGCTTTCTC 58.925 52.381 0.00 0.00 0.00 2.87
869 1182 1.881498 GCTCCAACTGCTCTGCTTTCT 60.881 52.381 0.00 0.00 0.00 2.52
870 1183 0.520847 GCTCCAACTGCTCTGCTTTC 59.479 55.000 0.00 0.00 0.00 2.62
872 1185 1.303155 GGCTCCAACTGCTCTGCTT 60.303 57.895 0.00 0.00 0.00 3.91
873 1186 2.350514 GGCTCCAACTGCTCTGCT 59.649 61.111 0.00 0.00 0.00 4.24
874 1187 3.123620 CGGCTCCAACTGCTCTGC 61.124 66.667 0.00 0.00 0.00 4.26
875 1188 2.435586 CCGGCTCCAACTGCTCTG 60.436 66.667 0.00 0.00 0.00 3.35
876 1189 2.604686 TCCGGCTCCAACTGCTCT 60.605 61.111 0.00 0.00 0.00 4.09
889 1252 2.125673 CCACTTGTACGCCTCCGG 60.126 66.667 0.00 0.00 39.22 5.14
909 1272 1.228552 GCAATGGTGGTGGAGGTGT 60.229 57.895 0.00 0.00 0.00 4.16
910 1273 1.978617 GGCAATGGTGGTGGAGGTG 60.979 63.158 0.00 0.00 0.00 4.00
911 1274 2.017668 TTGGCAATGGTGGTGGAGGT 62.018 55.000 0.00 0.00 0.00 3.85
912 1275 1.228831 TTGGCAATGGTGGTGGAGG 60.229 57.895 0.00 0.00 0.00 4.30
915 1278 1.193462 ATGGTTGGCAATGGTGGTGG 61.193 55.000 1.92 0.00 0.00 4.61
921 1284 1.205417 GAAGTGGATGGTTGGCAATGG 59.795 52.381 1.92 0.00 0.00 3.16
923 1286 1.203162 TGGAAGTGGATGGTTGGCAAT 60.203 47.619 1.92 0.00 0.00 3.56
924 1287 0.187117 TGGAAGTGGATGGTTGGCAA 59.813 50.000 0.00 0.00 0.00 4.52
925 1288 0.187117 TTGGAAGTGGATGGTTGGCA 59.813 50.000 0.00 0.00 0.00 4.92
926 1289 0.603065 GTTGGAAGTGGATGGTTGGC 59.397 55.000 0.00 0.00 0.00 4.52
928 1291 1.806542 CTCGTTGGAAGTGGATGGTTG 59.193 52.381 0.00 0.00 0.00 3.77
931 1294 1.676014 GGTCTCGTTGGAAGTGGATGG 60.676 57.143 0.00 0.00 0.00 3.51
932 1295 1.001974 TGGTCTCGTTGGAAGTGGATG 59.998 52.381 0.00 0.00 0.00 3.51
933 1296 1.348064 TGGTCTCGTTGGAAGTGGAT 58.652 50.000 0.00 0.00 0.00 3.41
935 1298 1.602377 GTTTGGTCTCGTTGGAAGTGG 59.398 52.381 0.00 0.00 0.00 4.00
936 1299 1.602377 GGTTTGGTCTCGTTGGAAGTG 59.398 52.381 0.00 0.00 0.00 3.16
937 1300 1.476291 GGGTTTGGTCTCGTTGGAAGT 60.476 52.381 0.00 0.00 0.00 3.01
939 1302 0.547075 TGGGTTTGGTCTCGTTGGAA 59.453 50.000 0.00 0.00 0.00 3.53
940 1303 0.547075 TTGGGTTTGGTCTCGTTGGA 59.453 50.000 0.00 0.00 0.00 3.53
942 1305 1.066454 GGTTTGGGTTTGGTCTCGTTG 59.934 52.381 0.00 0.00 0.00 4.10
944 1307 0.466739 GGGTTTGGGTTTGGTCTCGT 60.467 55.000 0.00 0.00 0.00 4.18
946 1309 1.686587 CTTGGGTTTGGGTTTGGTCTC 59.313 52.381 0.00 0.00 0.00 3.36
950 1313 1.449782 GGCTTGGGTTTGGGTTTGG 59.550 57.895 0.00 0.00 0.00 3.28
951 1314 1.068921 CGGCTTGGGTTTGGGTTTG 59.931 57.895 0.00 0.00 0.00 2.93
952 1315 2.137528 CCGGCTTGGGTTTGGGTTT 61.138 57.895 0.00 0.00 0.00 3.27
953 1316 2.523168 CCGGCTTGGGTTTGGGTT 60.523 61.111 0.00 0.00 0.00 4.11
955 1318 2.989253 GTCCGGCTTGGGTTTGGG 60.989 66.667 0.00 0.00 38.76 4.12
959 1322 0.541863 CTATCTGTCCGGCTTGGGTT 59.458 55.000 0.00 0.00 38.76 4.11
960 1323 0.325296 TCTATCTGTCCGGCTTGGGT 60.325 55.000 0.00 0.00 38.76 4.51
961 1324 1.001406 GATCTATCTGTCCGGCTTGGG 59.999 57.143 0.00 0.00 38.76 4.12
962 1325 1.001406 GGATCTATCTGTCCGGCTTGG 59.999 57.143 0.00 0.00 40.09 3.61
963 1326 1.688735 TGGATCTATCTGTCCGGCTTG 59.311 52.381 0.00 0.00 37.32 4.01
964 1327 2.088104 TGGATCTATCTGTCCGGCTT 57.912 50.000 0.00 0.00 37.32 4.35
965 1328 1.689273 GTTGGATCTATCTGTCCGGCT 59.311 52.381 0.00 0.00 37.32 5.52
966 1329 1.412710 TGTTGGATCTATCTGTCCGGC 59.587 52.381 0.00 0.00 37.32 6.13
967 1330 3.384789 TCTTGTTGGATCTATCTGTCCGG 59.615 47.826 0.00 0.00 37.32 5.14
968 1331 4.615949 CTCTTGTTGGATCTATCTGTCCG 58.384 47.826 0.00 0.00 37.32 4.79
969 1332 4.376146 GCTCTTGTTGGATCTATCTGTCC 58.624 47.826 0.00 0.00 35.02 4.02
970 1333 4.141846 TGGCTCTTGTTGGATCTATCTGTC 60.142 45.833 0.00 0.00 0.00 3.51
971 1334 3.776969 TGGCTCTTGTTGGATCTATCTGT 59.223 43.478 0.00 0.00 0.00 3.41
972 1335 4.412796 TGGCTCTTGTTGGATCTATCTG 57.587 45.455 0.00 0.00 0.00 2.90
973 1336 4.657504 TGATGGCTCTTGTTGGATCTATCT 59.342 41.667 0.00 0.00 0.00 1.98
974 1337 4.965814 TGATGGCTCTTGTTGGATCTATC 58.034 43.478 0.00 0.00 0.00 2.08
975 1338 4.746089 GCTGATGGCTCTTGTTGGATCTAT 60.746 45.833 0.00 0.00 38.06 1.98
976 1339 3.432749 GCTGATGGCTCTTGTTGGATCTA 60.433 47.826 0.00 0.00 38.06 1.98
977 1340 2.683152 GCTGATGGCTCTTGTTGGATCT 60.683 50.000 0.00 0.00 38.06 2.75
978 1341 1.674962 GCTGATGGCTCTTGTTGGATC 59.325 52.381 0.00 0.00 38.06 3.36
979 1342 1.684248 GGCTGATGGCTCTTGTTGGAT 60.684 52.381 0.00 0.00 41.46 3.41
980 1343 0.322816 GGCTGATGGCTCTTGTTGGA 60.323 55.000 0.00 0.00 41.46 3.53
981 1344 0.609957 TGGCTGATGGCTCTTGTTGG 60.610 55.000 0.00 0.00 41.46 3.77
982 1345 1.134367 CATGGCTGATGGCTCTTGTTG 59.866 52.381 0.00 0.00 41.46 3.33
983 1346 1.471119 CATGGCTGATGGCTCTTGTT 58.529 50.000 0.00 0.00 41.46 2.83
984 1347 0.395311 CCATGGCTGATGGCTCTTGT 60.395 55.000 0.00 0.00 45.58 3.16
985 1348 2.415825 CCATGGCTGATGGCTCTTG 58.584 57.895 0.00 0.00 45.58 3.02
1016 1385 2.955246 AGGGAGGGAGGAGCCTGA 60.955 66.667 0.00 0.00 36.66 3.86
1019 1388 3.418623 ATGGAGGGAGGGAGGAGCC 62.419 68.421 0.00 0.00 0.00 4.70
1050 1419 4.394712 GTGGAGGTGGAGGTGGCG 62.395 72.222 0.00 0.00 0.00 5.69
1051 1420 3.249189 TGTGGAGGTGGAGGTGGC 61.249 66.667 0.00 0.00 0.00 5.01
1052 1421 2.750350 GTGTGGAGGTGGAGGTGG 59.250 66.667 0.00 0.00 0.00 4.61
1053 1422 1.831652 GAGGTGTGGAGGTGGAGGTG 61.832 65.000 0.00 0.00 0.00 4.00
1054 1423 1.536662 GAGGTGTGGAGGTGGAGGT 60.537 63.158 0.00 0.00 0.00 3.85
1055 1424 2.650116 CGAGGTGTGGAGGTGGAGG 61.650 68.421 0.00 0.00 0.00 4.30
1056 1425 2.973899 CGAGGTGTGGAGGTGGAG 59.026 66.667 0.00 0.00 0.00 3.86
1058 1427 4.394712 GGCGAGGTGTGGAGGTGG 62.395 72.222 0.00 0.00 0.00 4.61
1059 1428 4.742201 CGGCGAGGTGTGGAGGTG 62.742 72.222 0.00 0.00 0.00 4.00
1061 1430 4.436998 GACGGCGAGGTGTGGAGG 62.437 72.222 16.62 0.00 0.00 4.30
1062 1431 4.778415 CGACGGCGAGGTGTGGAG 62.778 72.222 16.62 0.00 40.82 3.86
1084 1453 2.746277 GGTGTGGTGGATCGGTGC 60.746 66.667 0.00 0.00 0.00 5.01
1099 1468 1.819305 GCTTGTGATTCTGGTGGTGGT 60.819 52.381 0.00 0.00 0.00 4.16
1130 1502 0.249911 GGAGGAAGACTGTGTTGCGT 60.250 55.000 3.66 0.00 0.00 5.24
1133 1505 1.974236 AGGAGGAGGAAGACTGTGTTG 59.026 52.381 0.00 0.00 0.00 3.33
1134 1506 2.252714 GAGGAGGAGGAAGACTGTGTT 58.747 52.381 0.00 0.00 0.00 3.32
1136 1508 1.190643 GGAGGAGGAGGAAGACTGTG 58.809 60.000 0.00 0.00 0.00 3.66
1137 1509 0.787084 TGGAGGAGGAGGAAGACTGT 59.213 55.000 0.00 0.00 0.00 3.55
1138 1510 1.190643 GTGGAGGAGGAGGAAGACTG 58.809 60.000 0.00 0.00 0.00 3.51
1141 1513 0.252284 GTGGTGGAGGAGGAGGAAGA 60.252 60.000 0.00 0.00 0.00 2.87
1142 1514 0.545309 TGTGGTGGAGGAGGAGGAAG 60.545 60.000 0.00 0.00 0.00 3.46
1143 1515 0.836400 GTGTGGTGGAGGAGGAGGAA 60.836 60.000 0.00 0.00 0.00 3.36
1213 1594 1.893808 ACAGCCAGCCGTTGAACTG 60.894 57.895 0.00 4.44 37.04 3.16
1370 1784 1.812922 GTGATGAGCAGCAGGTCGG 60.813 63.158 3.76 0.00 45.10 4.79
1812 2268 1.447838 CATGGGCACGACGTAGCTT 60.448 57.895 17.60 5.37 0.00 3.74
2034 2535 7.565190 ATGGAGAATGGAGCTAATCTATGAA 57.435 36.000 0.00 0.00 0.00 2.57
2046 2547 6.040054 TGTTGCAATATGAATGGAGAATGGAG 59.960 38.462 0.59 0.00 0.00 3.86
2073 2574 5.636965 CCTCTGTTTGTCTGTCTGTCTTATG 59.363 44.000 0.00 0.00 0.00 1.90
2075 2576 4.039245 CCCTCTGTTTGTCTGTCTGTCTTA 59.961 45.833 0.00 0.00 0.00 2.10
2079 2580 2.366916 CTCCCTCTGTTTGTCTGTCTGT 59.633 50.000 0.00 0.00 0.00 3.41
2084 2585 0.322008 GCCCTCCCTCTGTTTGTCTG 60.322 60.000 0.00 0.00 0.00 3.51
2088 2589 1.615392 CTTTTGCCCTCCCTCTGTTTG 59.385 52.381 0.00 0.00 0.00 2.93
2090 2591 1.149101 TCTTTTGCCCTCCCTCTGTT 58.851 50.000 0.00 0.00 0.00 3.16
2092 2593 2.521547 AATCTTTTGCCCTCCCTCTG 57.478 50.000 0.00 0.00 0.00 3.35
2093 2594 3.193782 AGTAATCTTTTGCCCTCCCTCT 58.806 45.455 0.00 0.00 0.00 3.69
2094 2595 3.653835 AGTAATCTTTTGCCCTCCCTC 57.346 47.619 0.00 0.00 0.00 4.30
2095 2596 3.593780 AGAAGTAATCTTTTGCCCTCCCT 59.406 43.478 0.00 0.00 33.39 4.20
2096 2597 3.969553 AGAAGTAATCTTTTGCCCTCCC 58.030 45.455 0.00 0.00 33.39 4.30
2097 2598 6.415573 TCTAAGAAGTAATCTTTTGCCCTCC 58.584 40.000 0.00 0.00 46.39 4.30
2098 2599 7.824779 TCTTCTAAGAAGTAATCTTTTGCCCTC 59.175 37.037 0.00 0.00 46.39 4.30
2099 2600 7.690256 TCTTCTAAGAAGTAATCTTTTGCCCT 58.310 34.615 0.00 0.00 46.39 5.19
2100 2601 7.923414 TCTTCTAAGAAGTAATCTTTTGCCC 57.077 36.000 0.00 0.00 46.39 5.36
2101 2602 9.004717 AGTTCTTCTAAGAAGTAATCTTTTGCC 57.995 33.333 10.39 0.00 46.39 4.52
2353 2896 1.006805 CTCGCCGGATGAGGATGAC 60.007 63.158 5.05 0.00 0.00 3.06
2376 2951 2.151049 CTGCTGCAGTCCTTTTGGGC 62.151 60.000 21.21 0.00 46.74 5.36
2474 3049 2.818274 GGATTGGTCACGGCGTCC 60.818 66.667 10.85 10.68 0.00 4.79
2483 3058 1.452833 GGAGCAGCAGGGATTGGTC 60.453 63.158 0.00 0.00 40.21 4.02
2517 3092 1.514443 GTCGGCTCTTCTTCGTCGG 60.514 63.158 0.00 0.00 0.00 4.79
2553 3134 4.101448 GCAGGTGATCCAGGCGGT 62.101 66.667 0.00 0.00 35.89 5.68
2747 3328 2.045926 GTCCTGACGGGCAGCAAT 60.046 61.111 4.98 0.00 43.50 3.56
2771 3352 0.320374 AAGAATTGCCACCTCGTCGA 59.680 50.000 0.00 0.00 0.00 4.20
2919 3516 0.677098 CAGAATGTCCTGCTGCTGCT 60.677 55.000 17.00 0.00 40.48 4.24
2942 3539 4.544689 CGTCGAGGAGCAGAGCGG 62.545 72.222 0.00 0.00 0.00 5.52
2984 3581 1.663173 GGATAGTCGAGAGCTGGGC 59.337 63.158 0.00 0.00 0.00 5.36


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

AutoCloner maintained by Alex Coulton.