Multiple sequence alignment - TraesCS5D01G465400

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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 TraesCS5D01G465400 chr5D 100.000 5960 0 0 491 6450 508109824 508115783 0.000000e+00 11007.0
1 TraesCS5D01G465400 chr5D 100.000 186 0 0 1 186 508109334 508109519 1.720000e-90 344.0
2 TraesCS5D01G465400 chr5D 94.382 178 10 0 2614 2791 119768980 119768803 2.290000e-69 274.0
3 TraesCS5D01G465400 chr5D 92.982 57 4 0 1694 1750 380840908 380840964 4.140000e-12 84.2
4 TraesCS5D01G465400 chr5B 92.770 3693 137 53 1464 5085 638842123 638838490 0.000000e+00 5221.0
5 TraesCS5D01G465400 chr5B 91.768 413 15 7 1007 1415 638842514 638842117 2.030000e-154 556.0
6 TraesCS5D01G465400 chr5B 87.118 458 35 11 5246 5687 638838381 638837932 1.250000e-136 497.0
7 TraesCS5D01G465400 chr5B 91.549 213 9 7 773 977 638843006 638842795 1.060000e-72 285.0
8 TraesCS5D01G465400 chr5B 86.207 203 11 4 1 186 638843731 638843529 3.050000e-48 204.0
9 TraesCS5D01G465400 chr5B 78.333 300 35 16 6128 6404 638836797 638836505 4.000000e-37 167.0
10 TraesCS5D01G465400 chr5B 91.011 89 4 2 561 645 638843422 638843334 4.090000e-22 117.0
11 TraesCS5D01G465400 chr5B 97.959 49 1 0 642 690 638843098 638843050 1.150000e-12 86.1
12 TraesCS5D01G465400 chr5A 94.804 2887 78 19 2833 5682 635772809 635775660 0.000000e+00 4434.0
13 TraesCS5D01G465400 chr5A 89.035 1368 88 32 1091 2448 635771448 635772763 0.000000e+00 1639.0
14 TraesCS5D01G465400 chr5A 89.701 670 23 14 5772 6407 635775962 635776619 0.000000e+00 813.0
15 TraesCS5D01G465400 chr5A 88.636 528 14 13 491 1002 635770616 635771113 9.250000e-168 601.0
16 TraesCS5D01G465400 chr5A 92.697 178 13 0 2614 2791 130138587 130138410 2.310000e-64 257.0
17 TraesCS5D01G465400 chr5A 90.526 190 14 1 1 186 635770346 635770535 1.390000e-61 248.0
18 TraesCS5D01G465400 chr5A 88.525 122 13 1 1646 1766 489497653 489497532 5.210000e-31 147.0
19 TraesCS5D01G465400 chr5A 97.826 46 1 0 561 606 635770641 635770686 5.360000e-11 80.5
20 TraesCS5D01G465400 chr5A 100.000 32 0 0 2800 2831 635772758 635772789 6.980000e-05 60.2
21 TraesCS5D01G465400 chr2D 94.444 180 9 1 2614 2792 628591803 628591982 6.370000e-70 276.0
22 TraesCS5D01G465400 chr2D 90.323 186 13 1 2611 2791 634056165 634056350 8.360000e-59 239.0
23 TraesCS5D01G465400 chr4A 95.322 171 8 0 2621 2791 448515230 448515060 8.240000e-69 272.0
24 TraesCS5D01G465400 chr4A 90.164 122 11 1 1646 1766 245814923 245814802 2.410000e-34 158.0
25 TraesCS5D01G465400 chr4A 88.333 60 7 0 2546 2605 652856329 652856388 8.970000e-09 73.1
26 TraesCS5D01G465400 chr4D 94.220 173 8 1 2621 2791 122199877 122200049 4.960000e-66 263.0
27 TraesCS5D01G465400 chr7A 91.848 184 13 2 2618 2800 469986543 469986361 8.300000e-64 255.0
28 TraesCS5D01G465400 chr7A 87.838 74 8 1 2530 2603 83720189 83720261 1.150000e-12 86.1
29 TraesCS5D01G465400 chr7D 91.304 184 12 3 2618 2800 409459290 409459110 1.390000e-61 248.0
30 TraesCS5D01G465400 chr7D 100.000 28 0 0 2450 2477 81231771 81231798 1.200000e-02 52.8
31 TraesCS5D01G465400 chr7D 100.000 28 0 0 2450 2477 81647230 81647257 1.200000e-02 52.8
32 TraesCS5D01G465400 chr3D 91.620 179 15 0 2612 2790 463808653 463808831 1.390000e-61 248.0
33 TraesCS5D01G465400 chr7B 87.500 184 21 2 2614 2797 750591675 750591494 1.820000e-50 211.0
34 TraesCS5D01G465400 chr7B 88.462 78 7 2 2530 2606 28624876 28624952 6.890000e-15 93.5
35 TraesCS5D01G465400 chr7B 85.075 67 9 1 2546 2612 664034309 664034374 4.170000e-07 67.6
36 TraesCS5D01G465400 chr6B 90.164 122 11 1 1646 1766 699123992 699124113 2.410000e-34 158.0
37 TraesCS5D01G465400 chr6B 92.500 40 3 0 6409 6448 22236517 22236478 2.510000e-04 58.4
38 TraesCS5D01G465400 chr6A 86.713 143 15 2 1641 1782 198259 198120 8.660000e-34 156.0
39 TraesCS5D01G465400 chr1B 89.344 122 12 1 1646 1766 665781884 665781763 1.120000e-32 152.0
40 TraesCS5D01G465400 chr1B 89.831 59 4 2 2552 2608 412899130 412899188 2.490000e-09 75.0
41 TraesCS5D01G465400 chr1B 83.333 72 11 1 2546 2616 222296559 222296488 1.500000e-06 65.8
42 TraesCS5D01G465400 chr2A 87.402 127 15 1 1641 1766 40760659 40760785 1.870000e-30 145.0
43 TraesCS5D01G465400 chr2A 80.606 165 23 8 2450 2605 177668970 177669134 1.140000e-22 119.0
44 TraesCS5D01G465400 chr1A 88.333 120 14 0 2468 2587 201861431 201861312 1.870000e-30 145.0
45 TraesCS5D01G465400 chr1D 84.892 139 13 3 2468 2606 127221822 127221692 4.060000e-27 134.0
46 TraesCS5D01G465400 chr3A 86.364 110 13 1 2479 2588 9880784 9880677 1.140000e-22 119.0
47 TraesCS5D01G465400 chrUn 83.333 114 7 4 2475 2588 288188000 288187899 1.910000e-15 95.3
48 TraesCS5D01G465400 chr2B 91.935 62 5 0 2547 2608 743335057 743335118 3.200000e-13 87.9


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 TraesCS5D01G465400 chr5D 508109334 508115783 6449 False 5675.5000 11007 100.000000 1 6450 2 chr5D.!!$F2 6449
1 TraesCS5D01G465400 chr5B 638836505 638843731 7226 True 891.6375 5221 89.589375 1 6404 8 chr5B.!!$R1 6403
2 TraesCS5D01G465400 chr5A 635770346 635776619 6273 False 1125.1000 4434 92.932571 1 6407 7 chr5A.!!$F1 6406

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
707 1008 0.397816 CCAACCCCCAACCAAGACAA 60.398 55.000 0.00 0.00 0.00 3.18 F
1611 2189 0.313987 GTTTCCACCTTCCGCCAAAG 59.686 55.000 0.00 0.00 0.00 2.77 F
2585 3174 0.314302 CCCAGAACGACTTGTCGACT 59.686 55.000 26.65 20.55 36.85 4.18 F
2587 3176 1.001706 CCAGAACGACTTGTCGACTCA 60.002 52.381 26.65 2.31 36.85 3.41 F
3430 4084 0.756903 TAAGCTAGCCCCACGGAATC 59.243 55.000 12.13 0.00 0.00 2.52 F
4787 5456 1.404851 GCTAGAGCTCACCAGTTGGTC 60.405 57.143 17.77 0.00 41.77 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2348 2937 0.108585 GCAGTTTGAGGTCAGGGTCA 59.891 55.000 0.0 0.0 0.00 4.02 R
2683 3290 0.597637 AGTCGCAACTTCAGTGTCGG 60.598 55.000 0.0 0.0 28.74 4.79 R
3430 4084 2.153645 TGCATAGCACAAGTTCCACAG 58.846 47.619 0.0 0.0 31.71 3.66 R
4540 5208 2.362736 CACAGAAGATCACACATGGGG 58.637 52.381 0.0 0.0 0.00 4.96 R
5205 5909 1.559682 GCCAACAGGTCCTCCTATTCA 59.440 52.381 0.0 0.0 43.07 2.57 R
6249 7864 0.178068 ACGTATTGCAGAATCGGCCT 59.822 50.000 0.0 0.0 0.00 5.19 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
33 34 6.854091 ACCTACTAGCTGCCTATAATAACC 57.146 41.667 0.00 0.00 0.00 2.85
35 36 5.651139 CCTACTAGCTGCCTATAATAACCGA 59.349 44.000 0.00 0.00 0.00 4.69
150 168 1.808411 TGGAGCGAAAAGGATGACAC 58.192 50.000 0.00 0.00 0.00 3.67
155 173 2.301870 AGCGAAAAGGATGACACTACCA 59.698 45.455 0.00 0.00 0.00 3.25
530 548 8.520351 GCATAGTTCAAATGGTTAGGTTTAGTT 58.480 33.333 0.00 0.00 0.00 2.24
533 551 8.762481 AGTTCAAATGGTTAGGTTTAGTTTCT 57.238 30.769 0.00 0.00 0.00 2.52
534 552 9.856162 AGTTCAAATGGTTAGGTTTAGTTTCTA 57.144 29.630 0.00 0.00 0.00 2.10
537 555 9.238368 TCAAATGGTTAGGTTTAGTTTCTATGG 57.762 33.333 0.00 0.00 0.00 2.74
538 556 9.238368 CAAATGGTTAGGTTTAGTTTCTATGGA 57.762 33.333 0.00 0.00 0.00 3.41
539 557 9.990868 AAATGGTTAGGTTTAGTTTCTATGGAT 57.009 29.630 0.00 0.00 0.00 3.41
540 558 8.980481 ATGGTTAGGTTTAGTTTCTATGGATG 57.020 34.615 0.00 0.00 0.00 3.51
541 559 6.826741 TGGTTAGGTTTAGTTTCTATGGATGC 59.173 38.462 0.00 0.00 0.00 3.91
542 560 7.054751 GGTTAGGTTTAGTTTCTATGGATGCT 58.945 38.462 0.00 0.00 0.00 3.79
543 561 7.012421 GGTTAGGTTTAGTTTCTATGGATGCTG 59.988 40.741 0.00 0.00 0.00 4.41
544 562 5.440610 AGGTTTAGTTTCTATGGATGCTGG 58.559 41.667 0.00 0.00 0.00 4.85
545 563 5.191722 AGGTTTAGTTTCTATGGATGCTGGA 59.808 40.000 0.00 0.00 0.00 3.86
546 564 6.064717 GGTTTAGTTTCTATGGATGCTGGAT 58.935 40.000 0.00 0.00 0.00 3.41
547 565 6.547510 GGTTTAGTTTCTATGGATGCTGGATT 59.452 38.462 0.00 0.00 0.00 3.01
548 566 7.068716 GGTTTAGTTTCTATGGATGCTGGATTT 59.931 37.037 0.00 0.00 0.00 2.17
549 567 7.572523 TTAGTTTCTATGGATGCTGGATTTG 57.427 36.000 0.00 0.00 0.00 2.32
550 568 5.513233 AGTTTCTATGGATGCTGGATTTGT 58.487 37.500 0.00 0.00 0.00 2.83
551 569 5.954150 AGTTTCTATGGATGCTGGATTTGTT 59.046 36.000 0.00 0.00 0.00 2.83
552 570 7.118723 AGTTTCTATGGATGCTGGATTTGTTA 58.881 34.615 0.00 0.00 0.00 2.41
553 571 7.781693 AGTTTCTATGGATGCTGGATTTGTTAT 59.218 33.333 0.00 0.00 0.00 1.89
554 572 7.750229 TTCTATGGATGCTGGATTTGTTATC 57.250 36.000 0.00 0.00 0.00 1.75
555 573 6.840527 TCTATGGATGCTGGATTTGTTATCA 58.159 36.000 0.00 0.00 0.00 2.15
556 574 7.289310 TCTATGGATGCTGGATTTGTTATCAA 58.711 34.615 0.00 0.00 0.00 2.57
557 575 6.989155 ATGGATGCTGGATTTGTTATCAAT 57.011 33.333 0.00 0.00 33.32 2.57
558 576 6.795144 TGGATGCTGGATTTGTTATCAATT 57.205 33.333 0.00 0.00 33.32 2.32
559 577 7.185318 TGGATGCTGGATTTGTTATCAATTT 57.815 32.000 0.00 0.00 33.32 1.82
560 578 8.303780 TGGATGCTGGATTTGTTATCAATTTA 57.696 30.769 0.00 0.00 33.32 1.40
561 579 8.926374 TGGATGCTGGATTTGTTATCAATTTAT 58.074 29.630 0.00 0.00 33.32 1.40
562 580 9.199982 GGATGCTGGATTTGTTATCAATTTATG 57.800 33.333 0.00 0.00 33.32 1.90
563 581 9.199982 GATGCTGGATTTGTTATCAATTTATGG 57.800 33.333 0.00 0.00 33.32 2.74
564 582 8.076910 TGCTGGATTTGTTATCAATTTATGGT 57.923 30.769 0.00 0.00 33.32 3.55
565 583 8.538701 TGCTGGATTTGTTATCAATTTATGGTT 58.461 29.630 0.00 0.00 33.32 3.67
622 683 3.660970 TTTATTACCAGCCAGCCATCA 57.339 42.857 0.00 0.00 0.00 3.07
638 699 3.309954 GCCATCAAGATCTACCACGAAAC 59.690 47.826 0.00 0.00 0.00 2.78
640 701 4.806247 CCATCAAGATCTACCACGAAACTC 59.194 45.833 0.00 0.00 0.00 3.01
652 953 9.453572 TCTACCACGAAACTCTACTTTATTCTA 57.546 33.333 0.00 0.00 0.00 2.10
696 997 2.525629 CAACCCAACCCAACCCCC 60.526 66.667 0.00 0.00 0.00 5.40
700 1001 2.525629 CCAACCCAACCCCCAACC 60.526 66.667 0.00 0.00 0.00 3.77
701 1002 2.283809 CAACCCAACCCCCAACCA 59.716 61.111 0.00 0.00 0.00 3.67
702 1003 1.383248 CAACCCAACCCCCAACCAA 60.383 57.895 0.00 0.00 0.00 3.67
703 1004 1.074850 AACCCAACCCCCAACCAAG 60.075 57.895 0.00 0.00 0.00 3.61
704 1005 1.595058 AACCCAACCCCCAACCAAGA 61.595 55.000 0.00 0.00 0.00 3.02
705 1006 1.533033 CCCAACCCCCAACCAAGAC 60.533 63.158 0.00 0.00 0.00 3.01
706 1007 1.231641 CCAACCCCCAACCAAGACA 59.768 57.895 0.00 0.00 0.00 3.41
707 1008 0.397816 CCAACCCCCAACCAAGACAA 60.398 55.000 0.00 0.00 0.00 3.18
708 1009 1.039856 CAACCCCCAACCAAGACAAG 58.960 55.000 0.00 0.00 0.00 3.16
709 1010 0.930726 AACCCCCAACCAAGACAAGA 59.069 50.000 0.00 0.00 0.00 3.02
735 1036 1.219124 CACTCGTAGTGGGCAGCAT 59.781 57.895 0.00 0.00 42.35 3.79
758 1059 2.580867 CCTTCCTTCGCTCGCTCG 60.581 66.667 0.00 0.00 0.00 5.03
760 1061 3.691744 CTTCCTTCGCTCGCTCGCT 62.692 63.158 0.00 0.00 0.00 4.93
761 1062 3.685214 TTCCTTCGCTCGCTCGCTC 62.685 63.158 0.00 0.00 0.00 5.03
762 1063 4.186433 CCTTCGCTCGCTCGCTCT 62.186 66.667 0.00 0.00 0.00 4.09
763 1064 2.650602 CTTCGCTCGCTCGCTCTC 60.651 66.667 0.00 0.00 0.00 3.20
764 1065 4.180946 TTCGCTCGCTCGCTCTCC 62.181 66.667 0.00 0.00 0.00 3.71
767 1068 4.567385 GCTCGCTCGCTCTCCCTG 62.567 72.222 0.00 0.00 0.00 4.45
768 1069 3.898509 CTCGCTCGCTCTCCCTGG 61.899 72.222 0.00 0.00 0.00 4.45
769 1070 4.742649 TCGCTCGCTCTCCCTGGT 62.743 66.667 0.00 0.00 0.00 4.00
770 1071 3.764466 CGCTCGCTCTCCCTGGTT 61.764 66.667 0.00 0.00 0.00 3.67
771 1072 2.125350 GCTCGCTCTCCCTGGTTG 60.125 66.667 0.00 0.00 0.00 3.77
858 1160 3.801997 CAGCCGGGCTCCAATCCT 61.802 66.667 20.97 0.00 36.40 3.24
1126 1691 3.672295 CTCCCTCTCTTGCCGGTGC 62.672 68.421 1.90 0.00 38.26 5.01
1313 1878 0.874175 GTTTTTCGGTGGTTGCTGGC 60.874 55.000 0.00 0.00 0.00 4.85
1375 1940 2.470196 CAATTGATTGCTGCTCGAGG 57.530 50.000 15.58 0.00 0.00 4.63
1376 1941 1.065102 CAATTGATTGCTGCTCGAGGG 59.935 52.381 15.58 0.00 0.00 4.30
1412 1977 3.261580 CTCACGCAAGGTCACATTGATA 58.738 45.455 6.32 0.00 46.39 2.15
1413 1978 3.872696 TCACGCAAGGTCACATTGATAT 58.127 40.909 6.32 0.00 46.39 1.63
1414 1979 4.260985 TCACGCAAGGTCACATTGATATT 58.739 39.130 6.32 0.00 46.39 1.28
1415 1980 4.332543 TCACGCAAGGTCACATTGATATTC 59.667 41.667 6.32 0.00 46.39 1.75
1416 1981 3.627577 ACGCAAGGTCACATTGATATTCC 59.372 43.478 6.32 0.00 46.39 3.01
1417 1982 3.879295 CGCAAGGTCACATTGATATTCCT 59.121 43.478 6.32 0.00 0.00 3.36
1418 1983 4.260907 CGCAAGGTCACATTGATATTCCTG 60.261 45.833 6.32 0.00 0.00 3.86
1419 1984 4.498682 GCAAGGTCACATTGATATTCCTGC 60.499 45.833 6.32 0.00 0.00 4.85
1420 1985 4.508551 AGGTCACATTGATATTCCTGCA 57.491 40.909 0.00 0.00 0.00 4.41
1421 1986 5.057843 AGGTCACATTGATATTCCTGCAT 57.942 39.130 0.00 0.00 0.00 3.96
1422 1987 4.825634 AGGTCACATTGATATTCCTGCATG 59.174 41.667 0.00 0.00 0.00 4.06
1423 1988 4.823442 GGTCACATTGATATTCCTGCATGA 59.177 41.667 0.00 0.00 0.00 3.07
1424 1989 5.048921 GGTCACATTGATATTCCTGCATGAG 60.049 44.000 0.00 0.00 0.00 2.90
1425 1990 5.761726 GTCACATTGATATTCCTGCATGAGA 59.238 40.000 0.00 0.00 0.00 3.27
1426 1991 5.761726 TCACATTGATATTCCTGCATGAGAC 59.238 40.000 0.00 0.00 0.00 3.36
1427 1992 5.763698 CACATTGATATTCCTGCATGAGACT 59.236 40.000 0.00 0.00 0.00 3.24
1428 1993 5.996513 ACATTGATATTCCTGCATGAGACTC 59.003 40.000 0.00 0.00 0.00 3.36
1429 1994 5.619132 TTGATATTCCTGCATGAGACTCA 57.381 39.130 7.80 7.80 0.00 3.41
1430 1995 4.953667 TGATATTCCTGCATGAGACTCAC 58.046 43.478 7.47 0.00 0.00 3.51
1445 2010 0.867753 CTCACGCAGCGATGTAGTCC 60.868 60.000 24.65 0.00 0.00 3.85
1446 2011 1.139734 CACGCAGCGATGTAGTCCT 59.860 57.895 24.65 0.00 0.00 3.85
1456 2024 3.181503 GCGATGTAGTCCTGTTTCTACGA 60.182 47.826 0.00 0.00 39.25 3.43
1458 2026 5.396484 CGATGTAGTCCTGTTTCTACGAAA 58.604 41.667 0.00 0.00 39.25 3.46
1466 2034 3.060895 CCTGTTTCTACGAAATCGCTGAC 59.939 47.826 2.15 0.00 44.43 3.51
1483 2051 2.192608 GACTTTTGGCAGCTGCTCCG 62.193 60.000 35.82 21.65 41.70 4.63
1521 2095 1.999648 TTGGCAGCTGGTTGATCTTT 58.000 45.000 17.12 0.00 0.00 2.52
1523 2097 1.251251 GGCAGCTGGTTGATCTTTGT 58.749 50.000 17.12 0.00 0.00 2.83
1532 2109 3.139397 TGGTTGATCTTTGTTGGGGTAGT 59.861 43.478 0.00 0.00 0.00 2.73
1611 2189 0.313987 GTTTCCACCTTCCGCCAAAG 59.686 55.000 0.00 0.00 0.00 2.77
1612 2190 1.460273 TTTCCACCTTCCGCCAAAGC 61.460 55.000 0.00 0.00 0.00 3.51
1667 2248 6.438425 AGGTTACCATTGATTTTGCTCTGATT 59.562 34.615 3.51 0.00 0.00 2.57
1891 2475 5.335127 CATTTTGGTATTCAGAGAAAGCCG 58.665 41.667 0.00 0.00 0.00 5.52
2337 2926 8.947055 AAAACAATATGCTCCAATATTGAACC 57.053 30.769 17.23 4.87 46.60 3.62
2348 2937 1.961133 TATTGAACCGGGTCTCCCTT 58.039 50.000 22.56 3.31 42.67 3.95
2494 3083 2.263741 GCACTGCCAGGGTTGACTG 61.264 63.158 0.00 0.00 38.21 3.51
2506 3095 1.509703 GTTGACTGAAACCCCTCGAC 58.490 55.000 0.00 0.00 0.00 4.20
2528 3117 0.726256 GTCGAGACTAGTCGTGACCC 59.274 60.000 26.94 12.75 40.93 4.46
2575 3164 1.202964 TGAGTCACTACCCCAGAACGA 60.203 52.381 0.00 0.00 0.00 3.85
2578 3167 1.617357 GTCACTACCCCAGAACGACTT 59.383 52.381 0.00 0.00 0.00 3.01
2582 3171 0.599558 TACCCCAGAACGACTTGTCG 59.400 55.000 19.74 19.74 39.31 4.35
2583 3172 1.111116 ACCCCAGAACGACTTGTCGA 61.111 55.000 26.65 0.00 36.85 4.20
2584 3173 0.666577 CCCCAGAACGACTTGTCGAC 60.667 60.000 26.65 19.00 36.85 4.20
2585 3174 0.314302 CCCAGAACGACTTGTCGACT 59.686 55.000 26.65 20.55 36.85 4.18
2586 3175 1.666311 CCCAGAACGACTTGTCGACTC 60.666 57.143 26.65 20.60 36.85 3.36
2587 3176 1.001706 CCAGAACGACTTGTCGACTCA 60.002 52.381 26.65 2.31 36.85 3.41
2588 3177 2.351835 CCAGAACGACTTGTCGACTCAT 60.352 50.000 26.65 9.29 36.85 2.90
2589 3178 2.911723 CAGAACGACTTGTCGACTCATC 59.088 50.000 26.65 15.86 36.85 2.92
2630 3237 2.428888 ACCAAGGTTTACGAGTCGAC 57.571 50.000 21.50 7.70 0.00 4.20
2664 3271 5.504994 CGAGGTTGAGACTCATAGACTAAGC 60.505 48.000 5.87 0.00 34.66 3.09
2678 3285 7.713942 TCATAGACTAAGCGTGAGTAATCTACA 59.286 37.037 0.00 0.00 0.00 2.74
2679 3286 6.121613 AGACTAAGCGTGAGTAATCTACAC 57.878 41.667 0.00 0.00 0.00 2.90
2680 3287 5.881443 AGACTAAGCGTGAGTAATCTACACT 59.119 40.000 0.00 0.00 33.13 3.55
2681 3288 7.046652 AGACTAAGCGTGAGTAATCTACACTA 58.953 38.462 0.00 0.00 33.13 2.74
2682 3289 7.225145 AGACTAAGCGTGAGTAATCTACACTAG 59.775 40.741 0.00 0.00 33.13 2.57
2683 3290 4.555348 AGCGTGAGTAATCTACACTAGC 57.445 45.455 0.00 0.00 33.13 3.42
2684 3291 3.315749 AGCGTGAGTAATCTACACTAGCC 59.684 47.826 0.00 0.00 33.13 3.93
2685 3292 3.848917 GCGTGAGTAATCTACACTAGCCG 60.849 52.174 0.00 0.00 33.13 5.52
2686 3293 3.558829 CGTGAGTAATCTACACTAGCCGA 59.441 47.826 0.00 0.00 33.13 5.54
2687 3294 4.552378 CGTGAGTAATCTACACTAGCCGAC 60.552 50.000 0.00 0.00 33.13 4.79
2693 3300 2.786777 TCTACACTAGCCGACACTGAA 58.213 47.619 0.00 0.00 0.00 3.02
2726 3333 1.542030 AGACTAGTCGGCACTGAAGTG 59.458 52.381 17.07 6.08 40.74 3.16
2787 3407 5.598830 TGACTAGTCCTTGGACTCATAATCC 59.401 44.000 23.80 9.47 36.68 3.01
2831 3451 6.061022 TGGAAGATTGCTACTGGTATTTCA 57.939 37.500 0.00 0.00 0.00 2.69
3029 3676 2.071540 ACACTGCATGATGTCTGTTCG 58.928 47.619 0.00 0.00 0.00 3.95
3054 3701 3.672808 CTCCTGAAGTCTGTGCATTCTT 58.327 45.455 0.00 0.00 0.00 2.52
3113 3760 6.089249 ACATGCCTTCCAAAGAAAAACTAG 57.911 37.500 0.00 0.00 0.00 2.57
3138 3789 3.023119 TCCTGAACAACACAAGCAATGT 58.977 40.909 0.00 0.00 45.34 2.71
3217 3868 4.614555 TGAACTAATAAATGCAGCCACG 57.385 40.909 0.00 0.00 0.00 4.94
3319 3970 9.014297 GGTTTTGGATAGAATATACAAGATGGG 57.986 37.037 0.00 0.00 0.00 4.00
3430 4084 0.756903 TAAGCTAGCCCCACGGAATC 59.243 55.000 12.13 0.00 0.00 2.52
3474 4128 8.806146 GCAATGACCCCTTCATATAATTATGTT 58.194 33.333 8.28 0.00 44.86 2.71
3515 4169 4.038642 ACACGATTGGGTTATTGTTTTGCT 59.961 37.500 0.00 0.00 0.00 3.91
3527 4181 7.041440 GGTTATTGTTTTGCTGGCAGTTTTAAT 60.041 33.333 17.16 11.53 0.00 1.40
3674 4331 2.762887 TGTTCATGTTCCTTTGTGCCAA 59.237 40.909 0.00 0.00 0.00 4.52
3675 4332 3.181477 TGTTCATGTTCCTTTGTGCCAAG 60.181 43.478 0.00 0.00 0.00 3.61
3700 4357 8.465999 AGTTCTTGAGTCATCTATAGTGAAGTG 58.534 37.037 0.00 0.00 0.00 3.16
3701 4358 8.462811 GTTCTTGAGTCATCTATAGTGAAGTGA 58.537 37.037 0.00 0.00 0.00 3.41
3702 4359 7.990917 TCTTGAGTCATCTATAGTGAAGTGAC 58.009 38.462 0.00 7.89 36.98 3.67
3703 4360 7.831690 TCTTGAGTCATCTATAGTGAAGTGACT 59.168 37.037 18.18 18.18 46.26 3.41
3704 4361 7.326968 TGAGTCATCTATAGTGAAGTGACTG 57.673 40.000 20.76 3.05 44.35 3.51
3705 4362 7.112779 TGAGTCATCTATAGTGAAGTGACTGA 58.887 38.462 20.76 14.86 44.35 3.41
3706 4363 7.611855 TGAGTCATCTATAGTGAAGTGACTGAA 59.388 37.037 20.76 12.44 44.35 3.02
3707 4364 7.995289 AGTCATCTATAGTGAAGTGACTGAAG 58.005 38.462 17.79 0.00 43.15 3.02
3708 4365 7.613801 AGTCATCTATAGTGAAGTGACTGAAGT 59.386 37.037 17.79 0.00 43.15 3.01
3721 4378 5.304101 AGTGACTGAAGTCTGATCTTCACTT 59.696 40.000 11.55 0.00 45.62 3.16
3778 4435 7.067737 CCGGATACAAATTACTTGTTTATGGGT 59.932 37.037 0.00 0.00 46.49 4.51
3832 4489 5.108103 CGAAACTGTCACGGTAAGAGTTAAC 60.108 44.000 0.00 0.00 0.00 2.01
3844 4501 7.626144 GGTAAGAGTTAACGAGCAATATCTC 57.374 40.000 0.00 0.00 0.00 2.75
4007 4665 4.323553 AAGCCGACAGGTAGATTATCAC 57.676 45.455 0.00 0.00 40.50 3.06
4016 4674 6.432581 ACAGGTAGATTATCACACTCCTACA 58.567 40.000 0.00 0.00 0.00 2.74
4131 4795 7.782049 TCACTCAAGTTTATGGATTCTACGAT 58.218 34.615 0.00 0.00 0.00 3.73
4540 5208 2.751806 CCAAGAAGTTCCTCATGAAGGC 59.248 50.000 0.00 0.00 45.78 4.35
4663 5331 6.892310 ACAGAAAATTCTTGTTTGCTCAAC 57.108 33.333 0.00 0.00 34.74 3.18
4677 5345 5.574891 TTGCTCAACGTATTATGCCAATT 57.425 34.783 0.00 0.00 0.00 2.32
4787 5456 1.404851 GCTAGAGCTCACCAGTTGGTC 60.405 57.143 17.77 0.00 41.77 4.02
5050 5719 9.166173 TCTACATTTGTTCTGGTAGATTTGATG 57.834 33.333 0.00 0.00 37.80 3.07
5134 5838 2.289565 GTTAGGTGATGGGCAGTTAGC 58.710 52.381 0.00 0.00 44.65 3.09
5159 5863 5.868258 CACTGATACATGGATGAGTAGATGC 59.132 44.000 9.94 0.00 0.00 3.91
5162 5866 6.461640 TGATACATGGATGAGTAGATGCAAG 58.538 40.000 0.00 0.00 0.00 4.01
5163 5867 4.767578 ACATGGATGAGTAGATGCAAGT 57.232 40.909 0.00 0.00 0.00 3.16
5299 6003 6.391227 AGTCTAACCAAAATGTTTGACCAG 57.609 37.500 12.53 0.00 45.75 4.00
5313 6017 4.431416 TTGACCAGTGCTTTTCTCCTTA 57.569 40.909 0.00 0.00 0.00 2.69
5457 6170 3.470709 ACTATTTCCTGTGATGATGCGG 58.529 45.455 0.00 0.00 0.00 5.69
5507 6220 5.813157 GGTCTGATAACTAGCTGAAGTTTCC 59.187 44.000 7.18 1.60 40.20 3.13
5657 6383 1.123928 CCTACCTACAGCTGGAAGGG 58.876 60.000 30.20 19.34 34.52 3.95
5683 6409 5.869888 CCATTGTGTTACTCACCTCTCTAAC 59.130 44.000 0.00 0.00 45.61 2.34
5687 6413 5.473846 TGTGTTACTCACCTCTCTAACTGAG 59.526 44.000 0.00 0.00 45.61 3.35
5698 6463 3.114809 CTCTAACTGAGCTTGAGCATCG 58.885 50.000 5.70 0.00 45.16 3.84
5718 6483 2.094258 CGAGCAGCGTTTGTATTGTGAT 59.906 45.455 0.00 0.00 34.64 3.06
5719 6484 3.419915 GAGCAGCGTTTGTATTGTGATG 58.580 45.455 0.00 0.00 0.00 3.07
5720 6485 3.073678 AGCAGCGTTTGTATTGTGATGA 58.926 40.909 0.00 0.00 0.00 2.92
5721 6486 3.120199 AGCAGCGTTTGTATTGTGATGAC 60.120 43.478 0.00 0.00 0.00 3.06
5723 6488 4.397382 CAGCGTTTGTATTGTGATGACAG 58.603 43.478 0.00 0.00 32.26 3.51
5725 6490 3.435327 GCGTTTGTATTGTGATGACAGGA 59.565 43.478 0.00 0.00 32.26 3.86
5726 6491 4.083537 GCGTTTGTATTGTGATGACAGGAA 60.084 41.667 0.00 0.00 32.26 3.36
5727 6492 5.621422 CGTTTGTATTGTGATGACAGGAAG 58.379 41.667 0.00 0.00 32.26 3.46
5728 6493 5.393962 GTTTGTATTGTGATGACAGGAAGC 58.606 41.667 0.00 0.00 32.26 3.86
5729 6494 3.609853 TGTATTGTGATGACAGGAAGCC 58.390 45.455 0.00 0.00 32.26 4.35
5730 6495 2.885135 ATTGTGATGACAGGAAGCCA 57.115 45.000 0.00 0.00 32.26 4.75
5732 6497 2.885135 TGTGATGACAGGAAGCCATT 57.115 45.000 0.00 0.00 0.00 3.16
5733 6498 3.159213 TGTGATGACAGGAAGCCATTT 57.841 42.857 0.00 0.00 0.00 2.32
5734 6499 3.084039 TGTGATGACAGGAAGCCATTTC 58.916 45.455 0.00 0.00 34.93 2.17
5735 6500 3.084039 GTGATGACAGGAAGCCATTTCA 58.916 45.455 0.00 0.00 37.54 2.69
5737 6502 4.159135 GTGATGACAGGAAGCCATTTCATT 59.841 41.667 0.00 0.00 37.54 2.57
5738 6503 4.773674 TGATGACAGGAAGCCATTTCATTT 59.226 37.500 0.00 0.00 37.54 2.32
5743 6512 1.486310 GGAAGCCATTTCATTTCCCCC 59.514 52.381 0.00 0.00 37.54 5.40
5943 6920 4.657013 TGGCTGTGGTATGAATGTTTGTA 58.343 39.130 0.00 0.00 0.00 2.41
5989 6970 3.433343 TGAATGATGCAAAGATGTGGGT 58.567 40.909 0.00 0.00 0.00 4.51
5990 6971 3.193903 TGAATGATGCAAAGATGTGGGTG 59.806 43.478 0.00 0.00 0.00 4.61
5992 6973 2.596346 TGATGCAAAGATGTGGGTGTT 58.404 42.857 0.00 0.00 0.00 3.32
6007 6988 5.055265 TGGGTGTTATCCACAAAGAAGAA 57.945 39.130 0.00 0.00 46.44 2.52
6010 6991 5.048713 GGGTGTTATCCACAAAGAAGAACAG 60.049 44.000 0.00 0.00 46.44 3.16
6135 7743 7.706281 TTGTGTTTTAATCGCATGTGAATTT 57.294 28.000 13.91 6.70 0.00 1.82
6147 7755 8.627487 TCGCATGTGAATTTAAAAATACCATC 57.373 30.769 6.47 0.00 0.00 3.51
6148 7756 8.246871 TCGCATGTGAATTTAAAAATACCATCA 58.753 29.630 6.47 0.00 0.00 3.07
6161 7769 1.460504 ACCATCACTCTGCATGCTTG 58.539 50.000 20.33 11.88 0.00 4.01
6164 7772 2.688446 CCATCACTCTGCATGCTTGATT 59.312 45.455 20.33 8.60 0.00 2.57
6166 7774 4.023963 CCATCACTCTGCATGCTTGATTAG 60.024 45.833 20.33 6.69 0.00 1.73
6167 7775 3.538591 TCACTCTGCATGCTTGATTAGG 58.461 45.455 20.33 7.77 0.00 2.69
6168 7776 2.033049 CACTCTGCATGCTTGATTAGGC 59.967 50.000 20.33 0.00 0.00 3.93
6180 7795 3.671008 TGATTAGGCAACGTGTACTGT 57.329 42.857 0.00 0.00 46.39 3.55
6185 7800 2.914059 AGGCAACGTGTACTGTTTTCT 58.086 42.857 0.00 0.00 46.39 2.52
6245 7860 2.354510 GCAGCCACAAATCATAGCGTAA 59.645 45.455 0.00 0.00 0.00 3.18
6246 7861 3.788797 GCAGCCACAAATCATAGCGTAAC 60.789 47.826 0.00 0.00 0.00 2.50
6248 7863 3.623060 AGCCACAAATCATAGCGTAACAG 59.377 43.478 0.00 0.00 0.00 3.16
6249 7864 3.621268 GCCACAAATCATAGCGTAACAGA 59.379 43.478 0.00 0.00 0.00 3.41
6251 7866 4.271049 CCACAAATCATAGCGTAACAGAGG 59.729 45.833 0.00 0.00 0.00 3.69
6253 7868 2.821991 ATCATAGCGTAACAGAGGCC 57.178 50.000 0.00 0.00 39.91 5.19
6409 8038 3.410631 AACATCAATGGTGACGGTACA 57.589 42.857 0.00 0.00 36.31 2.90
6410 8039 3.627395 ACATCAATGGTGACGGTACAT 57.373 42.857 0.00 0.00 36.31 2.29
6411 8040 4.746535 ACATCAATGGTGACGGTACATA 57.253 40.909 0.00 0.00 36.31 2.29
6412 8041 5.290493 ACATCAATGGTGACGGTACATAT 57.710 39.130 0.00 0.00 36.31 1.78
6413 8042 5.056480 ACATCAATGGTGACGGTACATATG 58.944 41.667 0.00 0.00 36.31 1.78
6414 8043 4.746535 TCAATGGTGACGGTACATATGT 57.253 40.909 13.93 13.93 0.00 2.29
6415 8044 4.438148 TCAATGGTGACGGTACATATGTG 58.562 43.478 18.81 4.37 0.00 3.21
6416 8045 2.971660 TGGTGACGGTACATATGTGG 57.028 50.000 18.81 9.81 0.00 4.17
6417 8046 1.134640 TGGTGACGGTACATATGTGGC 60.135 52.381 18.81 10.66 0.00 5.01
6418 8047 1.205657 GTGACGGTACATATGTGGCG 58.794 55.000 18.81 9.61 0.00 5.69
6419 8048 0.818938 TGACGGTACATATGTGGCGT 59.181 50.000 18.81 12.21 0.00 5.68
6420 8049 2.022934 TGACGGTACATATGTGGCGTA 58.977 47.619 18.81 0.00 0.00 4.42
6421 8050 2.624364 TGACGGTACATATGTGGCGTAT 59.376 45.455 18.81 0.00 0.00 3.06
6422 8051 2.984471 GACGGTACATATGTGGCGTATG 59.016 50.000 18.81 6.77 38.76 2.39
6423 8052 2.624364 ACGGTACATATGTGGCGTATGA 59.376 45.455 18.81 0.00 36.96 2.15
6424 8053 3.257375 ACGGTACATATGTGGCGTATGAT 59.743 43.478 18.81 0.00 36.96 2.45
6425 8054 4.242475 CGGTACATATGTGGCGTATGATT 58.758 43.478 18.81 0.00 36.96 2.57
6426 8055 5.047872 ACGGTACATATGTGGCGTATGATTA 60.048 40.000 18.81 0.00 36.96 1.75
6427 8056 5.865013 CGGTACATATGTGGCGTATGATTAA 59.135 40.000 18.81 0.00 36.96 1.40
6428 8057 6.034577 CGGTACATATGTGGCGTATGATTAAG 59.965 42.308 18.81 0.82 36.96 1.85
6429 8058 7.094631 GGTACATATGTGGCGTATGATTAAGA 58.905 38.462 18.81 0.00 36.96 2.10
6430 8059 7.601130 GGTACATATGTGGCGTATGATTAAGAA 59.399 37.037 18.81 0.00 36.96 2.52
6431 8060 7.421530 ACATATGTGGCGTATGATTAAGAAC 57.578 36.000 7.78 0.00 36.96 3.01
6432 8061 6.145534 ACATATGTGGCGTATGATTAAGAACG 59.854 38.462 7.78 0.00 36.96 3.95
6433 8062 3.191669 TGTGGCGTATGATTAAGAACGG 58.808 45.455 0.00 0.00 35.93 4.44
6434 8063 3.119065 TGTGGCGTATGATTAAGAACGGA 60.119 43.478 0.00 0.00 35.93 4.69
6435 8064 3.244579 GTGGCGTATGATTAAGAACGGAC 59.755 47.826 0.00 0.00 35.93 4.79
6436 8065 3.131577 TGGCGTATGATTAAGAACGGACT 59.868 43.478 0.00 0.00 35.93 3.85
6437 8066 3.489785 GGCGTATGATTAAGAACGGACTG 59.510 47.826 0.00 0.00 35.93 3.51
6438 8067 3.489785 GCGTATGATTAAGAACGGACTGG 59.510 47.826 0.00 0.00 35.93 4.00
6439 8068 4.735578 GCGTATGATTAAGAACGGACTGGA 60.736 45.833 0.00 0.00 35.93 3.86
6440 8069 4.976731 CGTATGATTAAGAACGGACTGGAG 59.023 45.833 0.00 0.00 0.00 3.86
6441 8070 3.887621 TGATTAAGAACGGACTGGAGG 57.112 47.619 0.00 0.00 0.00 4.30
6442 8071 3.170717 TGATTAAGAACGGACTGGAGGT 58.829 45.455 0.00 0.00 0.00 3.85
6443 8072 3.581332 TGATTAAGAACGGACTGGAGGTT 59.419 43.478 0.00 0.00 0.00 3.50
6444 8073 4.773674 TGATTAAGAACGGACTGGAGGTTA 59.226 41.667 0.00 0.00 0.00 2.85
6445 8074 4.796038 TTAAGAACGGACTGGAGGTTAG 57.204 45.455 0.00 0.00 0.00 2.34
6446 8075 0.896226 AGAACGGACTGGAGGTTAGC 59.104 55.000 0.00 0.00 0.00 3.09
6447 8076 0.458025 GAACGGACTGGAGGTTAGCG 60.458 60.000 0.00 0.00 0.00 4.26
6448 8077 2.202756 CGGACTGGAGGTTAGCGC 60.203 66.667 0.00 0.00 0.00 5.92
6449 8078 2.187163 GGACTGGAGGTTAGCGCC 59.813 66.667 2.29 0.00 0.00 6.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 2.401766 GGAGCATGTTGGGCAGTCG 61.402 63.158 0.00 0.00 0.00 4.18
35 36 1.303888 CTGGAGCATGTTGGGCAGT 60.304 57.895 0.00 0.00 0.00 4.40
150 168 2.125673 CTCGCCCCGTGTTGGTAG 60.126 66.667 0.00 0.00 35.15 3.18
155 173 1.671054 CATGAACTCGCCCCGTGTT 60.671 57.895 4.97 4.97 44.23 3.32
530 548 7.289310 TGATAACAAATCCAGCATCCATAGAA 58.711 34.615 0.00 0.00 0.00 2.10
531 549 6.840527 TGATAACAAATCCAGCATCCATAGA 58.159 36.000 0.00 0.00 0.00 1.98
532 550 7.514784 TTGATAACAAATCCAGCATCCATAG 57.485 36.000 0.00 0.00 32.73 2.23
533 551 8.481492 AATTGATAACAAATCCAGCATCCATA 57.519 30.769 0.00 0.00 39.54 2.74
534 552 6.989155 ATTGATAACAAATCCAGCATCCAT 57.011 33.333 0.00 0.00 39.54 3.41
535 553 6.795144 AATTGATAACAAATCCAGCATCCA 57.205 33.333 0.00 0.00 39.54 3.41
536 554 9.199982 CATAAATTGATAACAAATCCAGCATCC 57.800 33.333 0.00 0.00 39.54 3.51
537 555 9.199982 CCATAAATTGATAACAAATCCAGCATC 57.800 33.333 0.00 0.00 39.54 3.91
538 556 8.707449 ACCATAAATTGATAACAAATCCAGCAT 58.293 29.630 0.00 0.00 39.54 3.79
539 557 8.076910 ACCATAAATTGATAACAAATCCAGCA 57.923 30.769 0.00 0.00 39.54 4.41
540 558 8.947055 AACCATAAATTGATAACAAATCCAGC 57.053 30.769 0.00 0.00 39.54 4.85
552 570 9.990868 AGGAACTAAACCTAACCATAAATTGAT 57.009 29.630 0.00 0.00 36.02 2.57
555 573 9.387257 CGTAGGAACTAAACCTAACCATAAATT 57.613 33.333 0.00 0.00 45.48 1.82
556 574 8.953368 CGTAGGAACTAAACCTAACCATAAAT 57.047 34.615 0.00 0.00 45.48 1.40
616 674 2.890808 TCGTGGTAGATCTTGATGGC 57.109 50.000 0.00 0.00 0.00 4.40
622 683 6.837471 AAGTAGAGTTTCGTGGTAGATCTT 57.163 37.500 0.00 0.00 0.00 2.40
638 699 9.053840 TGTATGTCGAGGTAGAATAAAGTAGAG 57.946 37.037 0.00 0.00 0.00 2.43
640 701 9.828852 GATGTATGTCGAGGTAGAATAAAGTAG 57.171 37.037 0.00 0.00 0.00 2.57
696 997 3.754850 TGATGATGCTCTTGTCTTGGTTG 59.245 43.478 0.00 0.00 0.00 3.77
700 1001 3.306434 CGAGTGATGATGCTCTTGTCTTG 59.694 47.826 0.00 0.00 0.00 3.02
701 1002 3.056250 ACGAGTGATGATGCTCTTGTCTT 60.056 43.478 0.00 0.00 0.00 3.01
702 1003 2.495270 ACGAGTGATGATGCTCTTGTCT 59.505 45.455 0.00 0.00 0.00 3.41
703 1004 2.886081 ACGAGTGATGATGCTCTTGTC 58.114 47.619 0.00 0.00 0.00 3.18
704 1005 3.445450 ACTACGAGTGATGATGCTCTTGT 59.555 43.478 0.00 0.00 32.46 3.16
705 1006 4.039151 ACTACGAGTGATGATGCTCTTG 57.961 45.455 0.00 0.00 0.00 3.02
735 1036 0.108804 CGAGCGAAGGAAGGTTGCTA 60.109 55.000 0.00 0.00 35.73 3.49
758 1059 0.890996 CAACCACAACCAGGGAGAGC 60.891 60.000 0.00 0.00 0.00 4.09
760 1061 0.472471 GACAACCACAACCAGGGAGA 59.528 55.000 0.00 0.00 0.00 3.71
761 1062 0.474184 AGACAACCACAACCAGGGAG 59.526 55.000 0.00 0.00 0.00 4.30
762 1063 0.472471 GAGACAACCACAACCAGGGA 59.528 55.000 0.00 0.00 0.00 4.20
763 1064 0.537371 GGAGACAACCACAACCAGGG 60.537 60.000 0.00 0.00 0.00 4.45
764 1065 0.884704 CGGAGACAACCACAACCAGG 60.885 60.000 0.00 0.00 0.00 4.45
765 1066 1.507141 GCGGAGACAACCACAACCAG 61.507 60.000 0.00 0.00 0.00 4.00
766 1067 1.525077 GCGGAGACAACCACAACCA 60.525 57.895 0.00 0.00 0.00 3.67
767 1068 2.604174 CGCGGAGACAACCACAACC 61.604 63.158 0.00 0.00 0.00 3.77
768 1069 2.935955 CGCGGAGACAACCACAAC 59.064 61.111 0.00 0.00 0.00 3.32
769 1070 2.970324 GCGCGGAGACAACCACAA 60.970 61.111 8.83 0.00 0.00 3.33
858 1160 0.400213 AATTGCGGTCTGGTCTGGAA 59.600 50.000 0.00 0.00 0.00 3.53
1126 1691 1.023513 CGGCAAGAGAGAAAGGCAGG 61.024 60.000 0.00 0.00 0.00 4.85
1251 1816 2.363683 GCCATTTCTGAGCAAGCTAGT 58.636 47.619 0.00 0.00 0.00 2.57
1412 1977 2.306341 CGTGAGTCTCATGCAGGAAT 57.694 50.000 9.12 0.00 0.00 3.01
1413 1978 3.820595 CGTGAGTCTCATGCAGGAA 57.179 52.632 9.12 0.00 0.00 3.36
1419 1984 0.527169 ATCGCTGCGTGAGTCTCATG 60.527 55.000 22.48 16.50 36.50 3.07
1420 1985 0.527169 CATCGCTGCGTGAGTCTCAT 60.527 55.000 22.48 2.14 0.00 2.90
1421 1986 1.153958 CATCGCTGCGTGAGTCTCA 60.154 57.895 22.48 0.00 0.00 3.27
1422 1987 0.098905 TACATCGCTGCGTGAGTCTC 59.901 55.000 22.48 0.00 0.00 3.36
1423 1988 0.099613 CTACATCGCTGCGTGAGTCT 59.900 55.000 22.48 6.36 0.00 3.24
1424 1989 0.179161 ACTACATCGCTGCGTGAGTC 60.179 55.000 22.48 0.00 0.00 3.36
1425 1990 0.179161 GACTACATCGCTGCGTGAGT 60.179 55.000 22.48 18.70 0.00 3.41
1426 1991 0.867753 GGACTACATCGCTGCGTGAG 60.868 60.000 22.48 15.88 0.00 3.51
1427 1992 1.138883 GGACTACATCGCTGCGTGA 59.861 57.895 22.48 3.55 0.00 4.35
1428 1993 1.139734 AGGACTACATCGCTGCGTG 59.860 57.895 22.48 19.99 0.00 5.34
1429 1994 1.139734 CAGGACTACATCGCTGCGT 59.860 57.895 22.48 5.32 0.00 5.24
1430 1995 0.458543 AACAGGACTACATCGCTGCG 60.459 55.000 17.25 17.25 31.99 5.18
1445 2010 3.921021 AGTCAGCGATTTCGTAGAAACAG 59.079 43.478 1.55 0.00 45.90 3.16
1446 2011 3.909430 AGTCAGCGATTTCGTAGAAACA 58.091 40.909 1.55 0.00 45.90 2.83
1456 2024 1.336240 GCTGCCAAAAGTCAGCGATTT 60.336 47.619 0.00 0.00 44.94 2.17
1458 2026 1.878775 GCTGCCAAAAGTCAGCGAT 59.121 52.632 0.00 0.00 44.94 4.58
1466 2034 2.564975 CGGAGCAGCTGCCAAAAG 59.435 61.111 34.39 17.66 43.38 2.27
1483 2051 5.197549 GCCAAAATTCGTTTCTTTTTCAGC 58.802 37.500 0.00 0.00 0.00 4.26
1521 2095 1.358152 CTCCTCCAACTACCCCAACA 58.642 55.000 0.00 0.00 0.00 3.33
1523 2097 1.132657 TGACTCCTCCAACTACCCCAA 60.133 52.381 0.00 0.00 0.00 4.12
1532 2109 2.583441 CCCTGCGTGACTCCTCCAA 61.583 63.158 0.00 0.00 0.00 3.53
1611 2189 1.227943 TATGGAAGGCAGGCATCGC 60.228 57.895 0.00 0.00 0.00 4.58
1612 2190 0.394192 TCTATGGAAGGCAGGCATCG 59.606 55.000 0.00 0.00 0.00 3.84
1667 2248 5.410355 ACCTGTACGGCAAGTATTAAAGA 57.590 39.130 0.00 0.00 37.69 2.52
1940 2528 8.789881 TTGTTCAATGTTCATAAAACCTTACG 57.210 30.769 7.34 0.00 0.00 3.18
2022 2611 3.601443 CAGAGTTCTGTTACCTCAGGG 57.399 52.381 0.00 0.00 39.09 4.45
2348 2937 0.108585 GCAGTTTGAGGTCAGGGTCA 59.891 55.000 0.00 0.00 0.00 4.02
2561 3150 1.617357 GACAAGTCGTTCTGGGGTAGT 59.383 52.381 0.00 0.00 0.00 2.73
2563 3152 0.599558 CGACAAGTCGTTCTGGGGTA 59.400 55.000 14.03 0.00 46.99 3.69
2582 3171 3.219052 AGGTTTTCGAGTCGATGAGTC 57.781 47.619 17.34 5.76 35.23 3.36
2583 3172 3.318017 CAAGGTTTTCGAGTCGATGAGT 58.682 45.455 17.34 0.00 35.23 3.41
2584 3173 2.668457 CCAAGGTTTTCGAGTCGATGAG 59.332 50.000 17.34 2.73 35.23 2.90
2585 3174 2.036733 ACCAAGGTTTTCGAGTCGATGA 59.963 45.455 17.34 5.52 35.23 2.92
2586 3175 2.157668 CACCAAGGTTTTCGAGTCGATG 59.842 50.000 17.34 10.23 35.23 3.84
2587 3176 2.036733 TCACCAAGGTTTTCGAGTCGAT 59.963 45.455 17.34 0.00 35.23 3.59
2588 3177 1.409790 TCACCAAGGTTTTCGAGTCGA 59.590 47.619 12.09 12.09 0.00 4.20
2589 3178 1.525619 GTCACCAAGGTTTTCGAGTCG 59.474 52.381 6.09 6.09 0.00 4.18
2630 3237 2.202492 CAACCTCGGAGCGACTCG 60.202 66.667 0.00 0.00 0.00 4.18
2636 3243 0.820871 ATGAGTCTCAACCTCGGAGC 59.179 55.000 6.64 0.00 32.38 4.70
2637 3244 3.314080 GTCTATGAGTCTCAACCTCGGAG 59.686 52.174 6.64 0.00 0.00 4.63
2664 3271 3.558829 TCGGCTAGTGTAGATTACTCACG 59.441 47.826 0.00 0.00 37.20 4.35
2678 3285 1.605712 GCAACTTCAGTGTCGGCTAGT 60.606 52.381 0.00 0.00 0.00 2.57
2679 3286 1.071605 GCAACTTCAGTGTCGGCTAG 58.928 55.000 0.00 0.00 0.00 3.42
2680 3287 0.666274 CGCAACTTCAGTGTCGGCTA 60.666 55.000 0.00 0.00 0.00 3.93
2681 3288 1.956170 CGCAACTTCAGTGTCGGCT 60.956 57.895 0.00 0.00 0.00 5.52
2682 3289 1.954146 TCGCAACTTCAGTGTCGGC 60.954 57.895 0.00 0.00 0.00 5.54
2683 3290 0.597637 AGTCGCAACTTCAGTGTCGG 60.598 55.000 0.00 0.00 28.74 4.79
2684 3291 0.778815 GAGTCGCAACTTCAGTGTCG 59.221 55.000 0.00 0.00 35.28 4.35
2685 3292 1.852942 TGAGTCGCAACTTCAGTGTC 58.147 50.000 0.00 0.00 35.28 3.67
2686 3293 2.533266 ATGAGTCGCAACTTCAGTGT 57.467 45.000 0.00 0.00 35.28 3.55
2687 3294 3.610242 GTCTATGAGTCGCAACTTCAGTG 59.390 47.826 0.00 0.00 35.28 3.66
2693 3300 4.886247 GACTAGTCTATGAGTCGCAACT 57.114 45.455 15.91 0.00 38.88 3.16
2726 3333 1.218316 CAACTCCAGGGCCGACTAC 59.782 63.158 0.00 0.00 0.00 2.73
2787 3407 4.154737 CCATACTTGTCAGTTGTCACCATG 59.845 45.833 0.00 0.00 34.06 3.66
2978 3617 1.942657 CCCACATATTCAGGAAGTGCG 59.057 52.381 0.00 0.00 0.00 5.34
3029 3676 0.871057 GCACAGACTTCAGGAGCAAC 59.129 55.000 0.00 0.00 0.00 4.17
3054 3701 4.202461 GGCTATATCCCATCACCTTTGTCA 60.202 45.833 0.00 0.00 0.00 3.58
3113 3760 1.604278 GCTTGTGTTGTTCAGGAGACC 59.396 52.381 0.00 0.00 0.00 3.85
3138 3789 2.027561 GGTACAGTCAACCAGTGCCATA 60.028 50.000 0.00 0.00 37.86 2.74
3217 3868 5.065218 CCAACTACCATTATCAGCAAGACAC 59.935 44.000 0.00 0.00 0.00 3.67
3319 3970 2.216898 GCATGAGTTCTGATAGTGGCC 58.783 52.381 0.00 0.00 0.00 5.36
3394 4048 2.749466 GCTTAAGTCTGCATGGCCCATA 60.749 50.000 0.00 0.00 0.00 2.74
3430 4084 2.153645 TGCATAGCACAAGTTCCACAG 58.846 47.619 0.00 0.00 31.71 3.66
3515 4169 7.454260 AAAAACACCAAAATTAAAACTGCCA 57.546 28.000 0.00 0.00 0.00 4.92
3674 4331 8.465999 CACTTCACTATAGATGACTCAAGAACT 58.534 37.037 6.78 0.00 0.00 3.01
3675 4332 8.462811 TCACTTCACTATAGATGACTCAAGAAC 58.537 37.037 6.78 0.00 0.00 3.01
3704 4361 6.306837 CGTCAGTAAAGTGAAGATCAGACTTC 59.693 42.308 0.00 0.00 44.31 3.01
3705 4362 6.153067 CGTCAGTAAAGTGAAGATCAGACTT 58.847 40.000 0.00 0.00 0.00 3.01
3706 4363 5.241949 ACGTCAGTAAAGTGAAGATCAGACT 59.758 40.000 7.59 0.00 31.19 3.24
3707 4364 5.462405 ACGTCAGTAAAGTGAAGATCAGAC 58.538 41.667 7.59 0.00 31.19 3.51
3708 4365 5.473846 AGACGTCAGTAAAGTGAAGATCAGA 59.526 40.000 19.50 0.00 31.19 3.27
3721 4378 8.139350 TGATAAAAACAGAGAAGACGTCAGTAA 58.861 33.333 19.50 0.00 0.00 2.24
3778 4435 7.939784 ATAGTAGCCACGATCTACATAATCA 57.060 36.000 12.99 0.00 39.00 2.57
3832 4489 4.250116 AGCTACAAGGAGATATTGCTCG 57.750 45.455 0.00 0.00 35.74 5.03
3844 4501 6.583806 CACAAATTTCTTGCTAAGCTACAAGG 59.416 38.462 18.64 8.35 42.82 3.61
3874 4531 9.804758 GTCACAAGAGCTACTATAGTAACAAAT 57.195 33.333 13.51 0.00 0.00 2.32
4007 4665 6.876257 AGAACATTAGAAGCTTTGTAGGAGTG 59.124 38.462 0.00 0.00 0.00 3.51
4131 4795 5.304614 AGACACTTACTTCCTTAAGCACTCA 59.695 40.000 0.00 0.00 36.05 3.41
4540 5208 2.362736 CACAGAAGATCACACATGGGG 58.637 52.381 0.00 0.00 0.00 4.96
4663 5331 7.703328 ACTGACCTAAAAATTGGCATAATACG 58.297 34.615 0.00 0.00 0.00 3.06
4787 5456 2.025863 GCCCAGTTGAATCCCTCCATG 61.026 57.143 0.00 0.00 0.00 3.66
5077 5747 8.774183 ACTTATGTCACTTGGGGTACATAATTA 58.226 33.333 7.09 0.00 41.47 1.40
5134 5838 6.396450 CATCTACTCATCCATGTATCAGTGG 58.604 44.000 0.00 0.00 36.82 4.00
5159 5863 7.490402 GGAAAATAATCTGCCAATCTCAACTTG 59.510 37.037 0.00 0.00 0.00 3.16
5162 5866 6.866480 TGGAAAATAATCTGCCAATCTCAAC 58.134 36.000 0.00 0.00 0.00 3.18
5163 5867 6.664816 ACTGGAAAATAATCTGCCAATCTCAA 59.335 34.615 0.00 0.00 0.00 3.02
5205 5909 1.559682 GCCAACAGGTCCTCCTATTCA 59.440 52.381 0.00 0.00 43.07 2.57
5299 6003 5.691754 CCAATTTGTGTAAGGAGAAAAGCAC 59.308 40.000 0.00 0.00 0.00 4.40
5313 6017 7.879160 AGATGTGCAAAAATATCCAATTTGTGT 59.121 29.630 0.00 0.00 36.63 3.72
5507 6220 4.565564 GCAAAAAGATTTATCTGCAGCCAG 59.434 41.667 9.47 0.00 37.19 4.85
5683 6409 0.459759 TGCTCGATGCTCAAGCTCAG 60.460 55.000 3.32 0.00 43.37 3.35
5687 6413 2.708255 GCTGCTCGATGCTCAAGC 59.292 61.111 8.07 0.00 43.37 4.01
5698 6463 3.125146 TCATCACAATACAAACGCTGCTC 59.875 43.478 0.00 0.00 0.00 4.26
5704 6469 5.605564 TTCCTGTCATCACAATACAAACG 57.394 39.130 0.00 0.00 29.82 3.60
5718 6483 3.511146 GGAAATGAAATGGCTTCCTGTCA 59.489 43.478 0.00 0.00 35.46 3.58
5719 6484 3.118992 GGGAAATGAAATGGCTTCCTGTC 60.119 47.826 0.00 0.00 37.94 3.51
5720 6485 2.833943 GGGAAATGAAATGGCTTCCTGT 59.166 45.455 0.00 0.00 37.94 4.00
5721 6486 2.169144 GGGGAAATGAAATGGCTTCCTG 59.831 50.000 0.00 0.00 37.94 3.86
5723 6488 1.486310 GGGGGAAATGAAATGGCTTCC 59.514 52.381 0.00 0.00 37.25 3.46
5760 6529 1.570347 CGAAATGTGCGAACGGGGAA 61.570 55.000 0.00 0.00 0.00 3.97
5761 6530 2.030401 CGAAATGTGCGAACGGGGA 61.030 57.895 0.00 0.00 0.00 4.81
5764 6533 1.355796 TAGGCGAAATGTGCGAACGG 61.356 55.000 0.00 0.00 0.00 4.44
5765 6534 0.440758 TTAGGCGAAATGTGCGAACG 59.559 50.000 0.00 0.00 0.00 3.95
5844 6786 1.422402 GGGTTCACAACACCTAAGGGA 59.578 52.381 0.00 0.00 34.36 4.20
5989 6970 6.353323 TGTCTGTTCTTCTTTGTGGATAACA 58.647 36.000 0.00 0.00 36.85 2.41
5990 6971 6.861065 TGTCTGTTCTTCTTTGTGGATAAC 57.139 37.500 0.00 0.00 0.00 1.89
5992 6973 9.739276 AATAATGTCTGTTCTTCTTTGTGGATA 57.261 29.630 0.00 0.00 0.00 2.59
6025 7018 3.506067 GGTCGGGAGTGAAAATCATTTGT 59.494 43.478 0.00 0.00 28.43 2.83
6041 7034 3.241067 TCGAAGAAAATACTGGTCGGG 57.759 47.619 0.00 0.00 0.00 5.14
6135 7743 5.887598 AGCATGCAGAGTGATGGTATTTTTA 59.112 36.000 21.98 0.00 0.00 1.52
6147 7755 2.033049 GCCTAATCAAGCATGCAGAGTG 59.967 50.000 21.98 12.04 0.00 3.51
6148 7756 2.295885 GCCTAATCAAGCATGCAGAGT 58.704 47.619 21.98 18.19 0.00 3.24
6161 7769 5.178809 AGAAAACAGTACACGTTGCCTAATC 59.821 40.000 0.00 0.00 0.00 1.75
6164 7772 3.805422 CAGAAAACAGTACACGTTGCCTA 59.195 43.478 0.00 0.00 0.00 3.93
6166 7774 2.610374 TCAGAAAACAGTACACGTTGCC 59.390 45.455 0.00 0.00 0.00 4.52
6167 7775 3.844943 GCTCAGAAAACAGTACACGTTGC 60.845 47.826 0.00 0.00 0.00 4.17
6168 7776 3.308595 TGCTCAGAAAACAGTACACGTTG 59.691 43.478 0.00 0.00 0.00 4.10
6180 7795 3.303990 GCTGACGAACATTGCTCAGAAAA 60.304 43.478 0.00 0.00 33.30 2.29
6185 7800 1.291184 CCGCTGACGAACATTGCTCA 61.291 55.000 0.00 0.00 43.93 4.26
6245 7860 0.254178 ATTGCAGAATCGGCCTCTGT 59.746 50.000 18.77 0.35 42.01 3.41
6246 7861 1.869767 GTATTGCAGAATCGGCCTCTG 59.130 52.381 14.65 14.65 42.73 3.35
6248 7863 0.861837 CGTATTGCAGAATCGGCCTC 59.138 55.000 0.00 0.00 0.00 4.70
6249 7864 0.178068 ACGTATTGCAGAATCGGCCT 59.822 50.000 0.00 0.00 0.00 5.19
6251 7866 1.268032 CCAACGTATTGCAGAATCGGC 60.268 52.381 0.00 0.00 34.17 5.54
6253 7868 2.276201 TCCCAACGTATTGCAGAATCG 58.724 47.619 0.00 0.00 34.17 3.34
6318 7943 3.991051 AGAGCACGTCACCACCCG 61.991 66.667 0.00 0.00 0.00 5.28
6319 7944 2.357517 CAGAGCACGTCACCACCC 60.358 66.667 0.00 0.00 0.00 4.61
6321 7946 1.227556 AACCAGAGCACGTCACCAC 60.228 57.895 0.00 0.00 0.00 4.16
6322 7947 1.227527 CAACCAGAGCACGTCACCA 60.228 57.895 0.00 0.00 0.00 4.17
6324 7949 1.934463 CACAACCAGAGCACGTCAC 59.066 57.895 0.00 0.00 0.00 3.67
6325 7950 1.887242 GCACAACCAGAGCACGTCA 60.887 57.895 0.00 0.00 33.66 4.35
6326 7951 1.835483 CTGCACAACCAGAGCACGTC 61.835 60.000 0.00 0.00 38.96 4.34
6327 7952 1.889105 CTGCACAACCAGAGCACGT 60.889 57.895 0.00 0.00 38.96 4.49
6329 7954 2.912624 GCCTGCACAACCAGAGCAC 61.913 63.158 0.00 0.00 38.96 4.40
6330 7955 2.595463 GCCTGCACAACCAGAGCA 60.595 61.111 0.00 0.00 41.66 4.26
6332 7957 0.892358 ACATGCCTGCACAACCAGAG 60.892 55.000 0.00 0.00 34.77 3.35
6333 7958 0.890542 GACATGCCTGCACAACCAGA 60.891 55.000 0.00 0.00 34.77 3.86
6334 7959 1.582968 GACATGCCTGCACAACCAG 59.417 57.895 0.00 0.00 0.00 4.00
6407 8036 6.145534 CGTTCTTAATCATACGCCACATATGT 59.854 38.462 1.41 1.41 32.75 2.29
6408 8037 6.401047 CCGTTCTTAATCATACGCCACATATG 60.401 42.308 0.00 0.00 32.97 1.78
6409 8038 5.637810 CCGTTCTTAATCATACGCCACATAT 59.362 40.000 0.00 0.00 32.97 1.78
6410 8039 4.986034 CCGTTCTTAATCATACGCCACATA 59.014 41.667 0.00 0.00 32.97 2.29
6411 8040 3.807622 CCGTTCTTAATCATACGCCACAT 59.192 43.478 0.00 0.00 32.97 3.21
6412 8041 3.119065 TCCGTTCTTAATCATACGCCACA 60.119 43.478 0.00 0.00 32.97 4.17
6413 8042 3.244579 GTCCGTTCTTAATCATACGCCAC 59.755 47.826 0.00 0.00 32.97 5.01
6414 8043 3.131577 AGTCCGTTCTTAATCATACGCCA 59.868 43.478 0.00 0.00 32.97 5.69
6415 8044 3.489785 CAGTCCGTTCTTAATCATACGCC 59.510 47.826 0.00 0.00 32.97 5.68
6416 8045 3.489785 CCAGTCCGTTCTTAATCATACGC 59.510 47.826 0.00 0.00 32.97 4.42
6417 8046 4.928601 TCCAGTCCGTTCTTAATCATACG 58.071 43.478 0.00 0.00 0.00 3.06
6418 8047 5.163437 ACCTCCAGTCCGTTCTTAATCATAC 60.163 44.000 0.00 0.00 0.00 2.39
6419 8048 4.960469 ACCTCCAGTCCGTTCTTAATCATA 59.040 41.667 0.00 0.00 0.00 2.15
6420 8049 3.775316 ACCTCCAGTCCGTTCTTAATCAT 59.225 43.478 0.00 0.00 0.00 2.45
6421 8050 3.170717 ACCTCCAGTCCGTTCTTAATCA 58.829 45.455 0.00 0.00 0.00 2.57
6422 8051 3.889520 ACCTCCAGTCCGTTCTTAATC 57.110 47.619 0.00 0.00 0.00 1.75
6423 8052 4.382793 GCTAACCTCCAGTCCGTTCTTAAT 60.383 45.833 0.00 0.00 0.00 1.40
6424 8053 3.056322 GCTAACCTCCAGTCCGTTCTTAA 60.056 47.826 0.00 0.00 0.00 1.85
6425 8054 2.494870 GCTAACCTCCAGTCCGTTCTTA 59.505 50.000 0.00 0.00 0.00 2.10
6426 8055 1.275573 GCTAACCTCCAGTCCGTTCTT 59.724 52.381 0.00 0.00 0.00 2.52
6427 8056 0.896226 GCTAACCTCCAGTCCGTTCT 59.104 55.000 0.00 0.00 0.00 3.01
6428 8057 0.458025 CGCTAACCTCCAGTCCGTTC 60.458 60.000 0.00 0.00 0.00 3.95
6429 8058 1.590147 CGCTAACCTCCAGTCCGTT 59.410 57.895 0.00 0.00 0.00 4.44
6430 8059 3.003113 GCGCTAACCTCCAGTCCGT 62.003 63.158 0.00 0.00 0.00 4.69
6431 8060 2.202756 GCGCTAACCTCCAGTCCG 60.203 66.667 0.00 0.00 0.00 4.79
6432 8061 2.187163 GGCGCTAACCTCCAGTCC 59.813 66.667 7.64 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.