Multiple sequence alignment - TraesCS1D01G036200

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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 TraesCS1D01G036200 chr1D 100.000 2494 0 0 1 2494 16893670 16896163 0.000000e+00 4606.0
1 TraesCS1D01G036200 chr1D 87.370 1251 113 21 648 1885 16978666 16977448 0.000000e+00 1393.0
2 TraesCS1D01G036200 chr1D 81.944 1080 179 9 842 1909 17021594 17020519 0.000000e+00 900.0
3 TraesCS1D01G036200 chr1D 79.771 1137 176 24 789 1909 17052301 17051203 0.000000e+00 776.0
4 TraesCS1D01G036200 chr1D 84.010 763 113 6 1154 1909 17061841 17061081 0.000000e+00 725.0
5 TraesCS1D01G036200 chr1D 82.133 347 30 12 1868 2184 16977434 16977090 4.820000e-68 268.0
6 TraesCS1D01G036200 chr1D 100.000 71 0 0 2863 2933 16896532 16896602 6.600000e-27 132.0
7 TraesCS1D01G036200 chr1B 86.109 1483 140 36 763 2210 30844142 30845593 0.000000e+00 1537.0
8 TraesCS1D01G036200 chr1B 82.264 857 118 18 1067 1909 24793136 24792300 0.000000e+00 710.0
9 TraesCS1D01G036200 chr1B 91.011 89 8 0 2406 2494 30845592 30845680 1.430000e-23 121.0
10 TraesCS1D01G036200 chr1B 94.915 59 1 2 2877 2933 30846018 30846076 1.120000e-14 91.6
11 TraesCS1D01G036200 chr1B 100.000 42 0 0 570 611 626147098 626147139 8.710000e-11 78.7
12 TraesCS1D01G036200 chr1A 90.265 904 76 3 1307 2198 18082314 18083217 0.000000e+00 1171.0
13 TraesCS1D01G036200 chr1A 80.458 1136 184 20 806 1908 18321284 18320154 0.000000e+00 833.0
14 TraesCS1D01G036200 chr1A 89.180 573 48 7 1639 2198 18100092 18100663 0.000000e+00 702.0
15 TraesCS1D01G036200 chr1A 86.741 626 58 10 694 1311 18048961 18049569 0.000000e+00 673.0
16 TraesCS1D01G036200 chr1A 78.239 1011 170 27 788 1774 18298880 18299864 1.160000e-168 603.0
17 TraesCS1D01G036200 chr1A 88.783 419 43 4 16 432 18048338 18048754 7.250000e-141 510.0
18 TraesCS1D01G036200 chr7D 100.000 42 0 0 570 611 462673296 462673255 8.710000e-11 78.7
19 TraesCS1D01G036200 chr7B 100.000 42 0 0 570 611 485833155 485833114 8.710000e-11 78.7
20 TraesCS1D01G036200 chr7A 92.727 55 3 1 567 621 136127052 136126999 8.710000e-11 78.7
21 TraesCS1D01G036200 chr6D 95.833 48 2 0 568 615 10765737 10765784 8.710000e-11 78.7
22 TraesCS1D01G036200 chr6B 97.778 45 1 0 571 615 20360129 20360173 8.710000e-11 78.7
23 TraesCS1D01G036200 chr2D 95.745 47 2 0 570 616 534729917 534729963 3.130000e-10 76.8
24 TraesCS1D01G036200 chr6A 95.556 45 2 0 571 615 12326045 12326089 4.050000e-09 73.1
25 TraesCS1D01G036200 chr6A 95.556 45 2 0 571 615 12331100 12331144 4.050000e-09 73.1


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 TraesCS1D01G036200 chr1D 16893670 16896602 2932 False 2369.0 4606 100.000000 1 2933 2 chr1D.!!$F1 2932
1 TraesCS1D01G036200 chr1D 17020519 17021594 1075 True 900.0 900 81.944000 842 1909 1 chr1D.!!$R1 1067
2 TraesCS1D01G036200 chr1D 16977090 16978666 1576 True 830.5 1393 84.751500 648 2184 2 chr1D.!!$R4 1536
3 TraesCS1D01G036200 chr1D 17051203 17052301 1098 True 776.0 776 79.771000 789 1909 1 chr1D.!!$R2 1120
4 TraesCS1D01G036200 chr1D 17061081 17061841 760 True 725.0 725 84.010000 1154 1909 1 chr1D.!!$R3 755
5 TraesCS1D01G036200 chr1B 24792300 24793136 836 True 710.0 710 82.264000 1067 1909 1 chr1B.!!$R1 842
6 TraesCS1D01G036200 chr1B 30844142 30846076 1934 False 583.2 1537 90.678333 763 2933 3 chr1B.!!$F2 2170
7 TraesCS1D01G036200 chr1A 18082314 18083217 903 False 1171.0 1171 90.265000 1307 2198 1 chr1A.!!$F1 891
8 TraesCS1D01G036200 chr1A 18320154 18321284 1130 True 833.0 833 80.458000 806 1908 1 chr1A.!!$R1 1102
9 TraesCS1D01G036200 chr1A 18100092 18100663 571 False 702.0 702 89.180000 1639 2198 1 chr1A.!!$F2 559
10 TraesCS1D01G036200 chr1A 18298880 18299864 984 False 603.0 603 78.239000 788 1774 1 chr1A.!!$F3 986
11 TraesCS1D01G036200 chr1A 18048338 18049569 1231 False 591.5 673 87.762000 16 1311 2 chr1A.!!$F4 1295

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
36 37 0.034089 GCCTCCCACTAATGCCTGTT 60.034 55.0 0.0 0.00 0.0 3.16 F
382 383 0.107017 TTGGAGCTTAGGCATGGAGC 60.107 55.0 0.0 0.92 41.7 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1380 1492 0.461339 ATACGAACGTGATGTGCCCC 60.461 55.0 10.14 0.0 0.0 5.80 R
2380 2591 0.324275 GATAGCCCAACCTGCCCAAA 60.324 55.0 0.00 0.0 0.0 3.28 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
30 31 0.254178 AGCACTGCCTCCCACTAATG 59.746 55.000 0.00 0.00 0.00 1.90
32 33 0.749454 CACTGCCTCCCACTAATGCC 60.749 60.000 0.00 0.00 0.00 4.40
33 34 0.916358 ACTGCCTCCCACTAATGCCT 60.916 55.000 0.00 0.00 0.00 4.75
36 37 0.034089 GCCTCCCACTAATGCCTGTT 60.034 55.000 0.00 0.00 0.00 3.16
55 56 2.463589 TTTGGTCCGCCACTGCTAGG 62.464 60.000 0.00 0.00 46.01 3.02
88 89 0.179000 GTGCTTCATCCTCCCACGAT 59.821 55.000 0.00 0.00 0.00 3.73
97 98 3.622166 TCCTCCCACGATTAAGAAACC 57.378 47.619 0.00 0.00 0.00 3.27
100 101 3.371595 CCTCCCACGATTAAGAAACCCAT 60.372 47.826 0.00 0.00 0.00 4.00
106 107 6.092748 CCACGATTAAGAAACCCATTGAAAG 58.907 40.000 0.00 0.00 0.00 2.62
112 113 3.500343 AGAAACCCATTGAAAGTCCCTG 58.500 45.455 0.00 0.00 0.00 4.45
113 114 3.140144 AGAAACCCATTGAAAGTCCCTGA 59.860 43.478 0.00 0.00 0.00 3.86
115 116 3.091633 ACCCATTGAAAGTCCCTGATG 57.908 47.619 0.00 0.00 0.00 3.07
118 119 2.756760 CCATTGAAAGTCCCTGATGGTG 59.243 50.000 0.00 0.00 34.77 4.17
119 120 3.561960 CCATTGAAAGTCCCTGATGGTGA 60.562 47.826 0.00 0.00 34.77 4.02
140 141 4.024133 TGACAAGTGACACACATGTATTGC 60.024 41.667 8.59 2.51 44.47 3.56
145 146 0.521291 ACACACATGTATTGCGCCAC 59.479 50.000 4.18 0.12 37.26 5.01
161 162 1.067142 GCCACGTATCACCACAAGAGA 60.067 52.381 0.00 0.00 0.00 3.10
177 178 6.317391 CCACAAGAGAAGATTGAGAATAACCC 59.683 42.308 0.00 0.00 0.00 4.11
185 186 8.166726 AGAAGATTGAGAATAACCCTTTCAAGT 58.833 33.333 0.00 0.00 0.00 3.16
188 189 6.633500 TTGAGAATAACCCTTTCAAGTGTG 57.367 37.500 0.00 0.00 0.00 3.82
207 208 7.683437 AGTGTGCCCTTTAACTAGTAATTTC 57.317 36.000 0.00 0.00 0.00 2.17
219 220 6.786967 ACTAGTAATTTCGGTCACATAGGT 57.213 37.500 0.00 0.00 0.00 3.08
317 318 2.954868 GTCGTGAGCGTATGGGCG 60.955 66.667 0.00 0.00 39.49 6.13
331 332 2.270352 TGGGCGGGCTATAATTCTTG 57.730 50.000 0.26 0.00 0.00 3.02
332 333 0.881796 GGGCGGGCTATAATTCTTGC 59.118 55.000 0.26 0.00 0.00 4.01
334 335 1.266989 GGCGGGCTATAATTCTTGCAC 59.733 52.381 0.00 0.00 0.00 4.57
339 340 5.591099 CGGGCTATAATTCTTGCACAAAAT 58.409 37.500 0.97 0.00 0.00 1.82
356 357 2.930826 AATTATGGGCCGTCTGTAGG 57.069 50.000 0.00 0.00 0.00 3.18
382 383 0.107017 TTGGAGCTTAGGCATGGAGC 60.107 55.000 0.00 0.92 41.70 4.70
404 405 2.353109 GCATGGGCTTTTCCTCTTTGAC 60.353 50.000 0.00 0.00 36.96 3.18
409 410 3.497942 GGGCTTTTCCTCTTTGACACCTA 60.498 47.826 0.00 0.00 34.39 3.08
417 418 1.961394 TCTTTGACACCTACAGCGACT 59.039 47.619 0.00 0.00 0.00 4.18
425 426 3.498397 ACACCTACAGCGACTCAAAAATG 59.502 43.478 0.00 0.00 0.00 2.32
426 427 3.074412 ACCTACAGCGACTCAAAAATGG 58.926 45.455 0.00 0.00 0.00 3.16
427 428 2.420022 CCTACAGCGACTCAAAAATGGG 59.580 50.000 0.00 0.00 0.00 4.00
428 429 0.598065 ACAGCGACTCAAAAATGGGC 59.402 50.000 0.00 0.00 0.00 5.36
429 430 0.109132 CAGCGACTCAAAAATGGGCC 60.109 55.000 0.00 0.00 0.00 5.80
430 431 1.154035 GCGACTCAAAAATGGGCCG 60.154 57.895 0.00 0.00 0.00 6.13
431 432 1.506262 CGACTCAAAAATGGGCCGG 59.494 57.895 0.00 0.00 0.00 6.13
432 433 0.958382 CGACTCAAAAATGGGCCGGA 60.958 55.000 5.05 0.00 0.00 5.14
433 434 1.253100 GACTCAAAAATGGGCCGGAA 58.747 50.000 5.05 0.00 0.00 4.30
434 435 1.616374 GACTCAAAAATGGGCCGGAAA 59.384 47.619 5.05 0.00 0.00 3.13
435 436 2.036604 GACTCAAAAATGGGCCGGAAAA 59.963 45.455 5.05 0.00 0.00 2.29
436 437 2.436173 ACTCAAAAATGGGCCGGAAAAA 59.564 40.909 5.05 0.00 0.00 1.94
469 470 7.281991 CTAAAACTGGCATTAGCATTTTGTC 57.718 36.000 0.00 0.00 44.61 3.18
480 502 7.765819 GCATTAGCATTTTGTCTTTATTTCCCT 59.234 33.333 0.00 0.00 41.58 4.20
489 511 6.309389 TGTCTTTATTTCCCTTCCTCCTAC 57.691 41.667 0.00 0.00 0.00 3.18
490 512 5.105064 TGTCTTTATTTCCCTTCCTCCTACG 60.105 44.000 0.00 0.00 0.00 3.51
491 513 5.028131 TCTTTATTTCCCTTCCTCCTACGT 58.972 41.667 0.00 0.00 0.00 3.57
492 514 6.097412 GTCTTTATTTCCCTTCCTCCTACGTA 59.903 42.308 0.00 0.00 0.00 3.57
493 515 5.859205 TTATTTCCCTTCCTCCTACGTAC 57.141 43.478 0.00 0.00 0.00 3.67
494 516 2.905415 TTCCCTTCCTCCTACGTACA 57.095 50.000 0.00 0.00 0.00 2.90
495 517 3.393426 TTCCCTTCCTCCTACGTACAT 57.607 47.619 0.00 0.00 0.00 2.29
496 518 2.662866 TCCCTTCCTCCTACGTACATG 58.337 52.381 0.00 0.00 0.00 3.21
497 519 1.687123 CCCTTCCTCCTACGTACATGG 59.313 57.143 0.00 0.00 0.00 3.66
498 520 1.687123 CCTTCCTCCTACGTACATGGG 59.313 57.143 0.00 0.00 0.00 4.00
499 521 1.687123 CTTCCTCCTACGTACATGGGG 59.313 57.143 0.00 0.00 0.00 4.96
500 522 0.928505 TCCTCCTACGTACATGGGGA 59.071 55.000 0.84 0.67 0.00 4.81
501 523 1.038280 CCTCCTACGTACATGGGGAC 58.962 60.000 0.84 0.00 0.00 4.46
502 524 1.411216 CCTCCTACGTACATGGGGACT 60.411 57.143 0.84 0.00 0.00 3.85
503 525 2.385803 CTCCTACGTACATGGGGACTT 58.614 52.381 0.00 0.00 0.00 3.01
504 526 2.361438 CTCCTACGTACATGGGGACTTC 59.639 54.545 0.00 0.00 0.00 3.01
505 527 1.411612 CCTACGTACATGGGGACTTCC 59.588 57.143 0.00 0.00 0.00 3.46
506 528 2.385803 CTACGTACATGGGGACTTCCT 58.614 52.381 0.00 0.00 35.95 3.36
507 529 1.192428 ACGTACATGGGGACTTCCTC 58.808 55.000 0.00 0.00 36.90 3.71
573 595 4.088823 GGTAATCACCGTATAGCTACCG 57.911 50.000 0.00 1.14 34.36 4.02
574 596 2.719426 AATCACCGTATAGCTACCGC 57.281 50.000 0.00 0.00 0.00 5.68
575 597 1.612676 ATCACCGTATAGCTACCGCA 58.387 50.000 0.00 0.00 39.10 5.69
576 598 1.612676 TCACCGTATAGCTACCGCAT 58.387 50.000 0.00 0.00 39.10 4.73
577 599 1.268625 TCACCGTATAGCTACCGCATG 59.731 52.381 0.00 3.54 39.10 4.06
578 600 0.601558 ACCGTATAGCTACCGCATGG 59.398 55.000 0.00 0.00 42.84 3.66
579 601 0.108804 CCGTATAGCTACCGCATGGG 60.109 60.000 2.06 2.06 40.75 4.00
580 602 0.885879 CGTATAGCTACCGCATGGGA 59.114 55.000 12.02 0.00 40.75 4.37
581 603 1.402456 CGTATAGCTACCGCATGGGAC 60.402 57.143 12.02 0.00 40.75 4.46
595 617 2.666272 TGGGACATGTGGTTAGCAAA 57.334 45.000 1.15 0.00 0.00 3.68
596 618 2.950781 TGGGACATGTGGTTAGCAAAA 58.049 42.857 1.15 0.00 0.00 2.44
597 619 3.505386 TGGGACATGTGGTTAGCAAAAT 58.495 40.909 1.15 0.00 0.00 1.82
598 620 3.509575 TGGGACATGTGGTTAGCAAAATC 59.490 43.478 1.15 0.00 0.00 2.17
599 621 3.509575 GGGACATGTGGTTAGCAAAATCA 59.490 43.478 1.15 0.00 0.00 2.57
600 622 4.021544 GGGACATGTGGTTAGCAAAATCAA 60.022 41.667 1.15 0.00 0.00 2.57
601 623 5.510520 GGGACATGTGGTTAGCAAAATCAAA 60.511 40.000 1.15 0.00 0.00 2.69
602 624 5.988561 GGACATGTGGTTAGCAAAATCAAAA 59.011 36.000 1.15 0.00 0.00 2.44
603 625 6.650390 GGACATGTGGTTAGCAAAATCAAAAT 59.350 34.615 1.15 0.00 0.00 1.82
604 626 7.173047 GGACATGTGGTTAGCAAAATCAAAATT 59.827 33.333 1.15 0.00 0.00 1.82
605 627 8.086851 ACATGTGGTTAGCAAAATCAAAATTC 57.913 30.769 0.00 0.00 0.00 2.17
606 628 7.714377 ACATGTGGTTAGCAAAATCAAAATTCA 59.286 29.630 0.00 0.00 0.00 2.57
607 629 8.723311 CATGTGGTTAGCAAAATCAAAATTCAT 58.277 29.630 0.00 0.00 0.00 2.57
608 630 9.941325 ATGTGGTTAGCAAAATCAAAATTCATA 57.059 25.926 0.00 0.00 0.00 2.15
609 631 9.941325 TGTGGTTAGCAAAATCAAAATTCATAT 57.059 25.926 0.00 0.00 0.00 1.78
646 668 3.440872 CACCGTATAGCTATCAGGACTCC 59.559 52.174 25.48 0.00 0.00 3.85
676 719 2.038837 GCACGAAACCCTAGCCACC 61.039 63.158 0.00 0.00 0.00 4.61
677 720 1.740296 CACGAAACCCTAGCCACCG 60.740 63.158 0.00 0.00 0.00 4.94
678 721 1.909781 ACGAAACCCTAGCCACCGA 60.910 57.895 0.00 0.00 0.00 4.69
679 722 1.262640 ACGAAACCCTAGCCACCGAT 61.263 55.000 0.00 0.00 0.00 4.18
795 853 3.509659 GCCTTGTATGGCCGGAAC 58.490 61.111 5.05 0.00 46.82 3.62
811 875 2.680974 GAACAGCAGCCTCACCACCA 62.681 60.000 0.00 0.00 0.00 4.17
879 957 3.585862 TCTTTTGGATCGTCTAGTGTGC 58.414 45.455 0.00 0.00 0.00 4.57
900 978 6.760770 TGTGCAAAATTTCCTTTCGATCTTTT 59.239 30.769 0.00 0.00 0.00 2.27
905 994 8.650714 CAAAATTTCCTTTCGATCTTTTGGATC 58.349 33.333 0.00 0.00 45.37 3.36
951 1045 7.627585 TTTGATTGTACGTACAGTGAGTAAC 57.372 36.000 26.04 12.23 37.52 2.50
971 1065 1.148273 GAGGCACAACCACCACAGA 59.852 57.895 0.00 0.00 43.14 3.41
1017 1111 3.387962 TCCTATGGATTCTGCTGTCCTT 58.612 45.455 2.59 0.00 35.49 3.36
1027 1121 1.071385 CTGCTGTCCTTCAGTTCAGGT 59.929 52.381 0.00 0.00 45.23 4.00
1029 1123 1.876156 GCTGTCCTTCAGTTCAGGTTG 59.124 52.381 0.00 0.00 45.23 3.77
1042 1136 1.689813 TCAGGTTGGACTACGAGCAAA 59.310 47.619 0.00 0.00 33.25 3.68
1060 1154 2.472695 AATCAAGCACCTTAGCGTCA 57.527 45.000 0.00 0.00 40.15 4.35
1063 1157 0.517316 CAAGCACCTTAGCGTCAACC 59.483 55.000 0.00 0.00 40.15 3.77
1069 1163 0.320374 CCTTAGCGTCAACCAGGTCA 59.680 55.000 0.00 0.00 0.00 4.02
1102 1196 3.228017 TCTCCGTCGGCCAACACA 61.228 61.111 6.34 0.00 0.00 3.72
1141 1235 1.814169 CCGCGGGGACTAGAAAAGC 60.814 63.158 20.10 0.00 34.06 3.51
1182 1276 6.184789 TGGAAATTATGTTTCCCTGTACCTC 58.815 40.000 17.06 0.00 45.59 3.85
1231 1325 2.115291 GCCATCTTGGACGCCTTCC 61.115 63.158 0.00 0.00 46.13 3.46
1266 1360 1.750399 CAACCCATCAGAAGCCCGG 60.750 63.158 0.00 0.00 0.00 5.73
1352 1464 0.673644 AATCGGTTCGTGGCCAGAAG 60.674 55.000 5.11 0.00 0.00 2.85
1359 1471 2.895424 CGTGGCCAGAAGGGTCCTT 61.895 63.158 5.11 1.27 42.20 3.36
1380 1492 5.182001 CCTTGAGGAAAACTATGTTGTGGAG 59.818 44.000 0.00 0.00 37.39 3.86
1446 1564 4.980805 GTCACCGTGCCGCCTTCA 62.981 66.667 0.00 0.00 0.00 3.02
1605 1730 1.522569 GTCCATGGCCGAAGCTACT 59.477 57.895 6.96 0.00 39.73 2.57
1653 1778 2.132740 TGCCTTCAACATTCAAACGC 57.867 45.000 0.00 0.00 0.00 4.84
1836 1979 6.412943 CAGTTATTGATATTCAAGCTTGTGCG 59.587 38.462 25.19 0.29 40.05 5.34
1964 2153 3.554934 TCATGGATTATGGTTGGTGAGC 58.445 45.455 0.00 0.00 37.39 4.26
2000 2193 7.177568 AGAGTGCTCGAATATAATGTACTGGAT 59.822 37.037 0.00 0.00 34.09 3.41
2022 2219 8.629158 TGGATTATTTTTACACAGGTGCATATC 58.371 33.333 0.00 0.00 0.00 1.63
2026 2223 9.634021 TTATTTTTACACAGGTGCATATCCATA 57.366 29.630 0.00 0.00 0.00 2.74
2027 2224 7.946381 TTTTTACACAGGTGCATATCCATAA 57.054 32.000 0.00 0.00 0.00 1.90
2049 2246 8.636213 CATAAGGGATTCTATTTGTGCTTTGAT 58.364 33.333 0.00 0.00 0.00 2.57
2077 2280 9.112725 AGAATTACGGTTTGTTTAACAAGTACT 57.887 29.630 10.51 2.54 39.53 2.73
2210 2421 8.465971 AGGATTCCCTACTATCTAACCTATGTT 58.534 37.037 0.00 0.00 42.15 2.71
2211 2422 8.532819 GGATTCCCTACTATCTAACCTATGTTG 58.467 40.741 0.00 0.00 35.87 3.33
2212 2423 9.091220 GATTCCCTACTATCTAACCTATGTTGT 57.909 37.037 0.00 0.00 35.87 3.32
2215 2426 9.750783 TCCCTACTATCTAACCTATGTTGTATC 57.249 37.037 0.00 0.00 35.87 2.24
2216 2427 9.529823 CCCTACTATCTAACCTATGTTGTATCA 57.470 37.037 0.00 0.00 35.87 2.15
2222 2433 8.783660 ATCTAACCTATGTTGTATCAAGAGGA 57.216 34.615 10.16 0.00 35.87 3.71
2223 2434 8.783660 TCTAACCTATGTTGTATCAAGAGGAT 57.216 34.615 10.16 0.00 36.65 3.24
2224 2435 9.213777 TCTAACCTATGTTGTATCAAGAGGATT 57.786 33.333 10.16 5.71 35.33 3.01
2225 2436 9.838339 CTAACCTATGTTGTATCAAGAGGATTT 57.162 33.333 10.16 1.90 35.33 2.17
2226 2437 8.511604 AACCTATGTTGTATCAAGAGGATTTG 57.488 34.615 10.16 0.00 33.61 2.32
2227 2438 7.633789 ACCTATGTTGTATCAAGAGGATTTGT 58.366 34.615 10.16 0.00 37.44 2.83
2228 2439 7.554118 ACCTATGTTGTATCAAGAGGATTTGTG 59.446 37.037 10.16 0.00 37.44 3.33
2229 2440 7.770433 CCTATGTTGTATCAAGAGGATTTGTGA 59.230 37.037 0.00 0.00 37.44 3.58
2230 2441 9.166173 CTATGTTGTATCAAGAGGATTTGTGAA 57.834 33.333 0.00 0.00 37.44 3.18
2231 2442 7.439157 TGTTGTATCAAGAGGATTTGTGAAG 57.561 36.000 0.00 0.00 37.44 3.02
2232 2443 7.223584 TGTTGTATCAAGAGGATTTGTGAAGA 58.776 34.615 0.00 0.00 37.44 2.87
2233 2444 7.719193 TGTTGTATCAAGAGGATTTGTGAAGAA 59.281 33.333 0.00 0.00 37.44 2.52
2234 2445 8.567948 GTTGTATCAAGAGGATTTGTGAAGAAA 58.432 33.333 0.00 0.00 37.44 2.52
2235 2446 8.327941 TGTATCAAGAGGATTTGTGAAGAAAG 57.672 34.615 0.00 0.00 37.44 2.62
2236 2447 5.695851 TCAAGAGGATTTGTGAAGAAAGC 57.304 39.130 0.00 0.00 0.00 3.51
2237 2448 4.520492 TCAAGAGGATTTGTGAAGAAAGCC 59.480 41.667 0.00 0.00 40.97 4.35
2241 2452 4.853924 GGATTTGTGAAGAAAGCCTGAA 57.146 40.909 0.32 0.00 38.20 3.02
2242 2453 5.200368 GGATTTGTGAAGAAAGCCTGAAA 57.800 39.130 0.32 0.00 38.20 2.69
2243 2454 5.600696 GGATTTGTGAAGAAAGCCTGAAAA 58.399 37.500 0.32 0.00 38.20 2.29
2244 2455 5.693555 GGATTTGTGAAGAAAGCCTGAAAAG 59.306 40.000 0.32 0.00 38.20 2.27
2245 2456 5.659440 TTTGTGAAGAAAGCCTGAAAAGT 57.341 34.783 0.00 0.00 0.00 2.66
2246 2457 5.659440 TTGTGAAGAAAGCCTGAAAAGTT 57.341 34.783 0.00 0.00 0.00 2.66
2247 2458 5.659440 TGTGAAGAAAGCCTGAAAAGTTT 57.341 34.783 0.00 0.00 0.00 2.66
2248 2459 5.650543 TGTGAAGAAAGCCTGAAAAGTTTC 58.349 37.500 0.00 0.00 37.69 2.78
2249 2460 5.184864 TGTGAAGAAAGCCTGAAAAGTTTCA 59.815 36.000 6.33 6.33 44.31 2.69
2261 2472 6.975196 TGAAAAGTTTCAGAATCCAATGGA 57.025 33.333 3.67 3.67 41.88 3.41
2271 2482 6.748132 TCAGAATCCAATGGAAAACAAAGAC 58.252 36.000 5.89 0.00 34.34 3.01
2272 2483 6.550854 TCAGAATCCAATGGAAAACAAAGACT 59.449 34.615 5.89 0.00 34.34 3.24
2273 2484 7.723616 TCAGAATCCAATGGAAAACAAAGACTA 59.276 33.333 5.89 0.00 34.34 2.59
2274 2485 8.359642 CAGAATCCAATGGAAAACAAAGACTAA 58.640 33.333 5.89 0.00 34.34 2.24
2275 2486 9.093458 AGAATCCAATGGAAAACAAAGACTAAT 57.907 29.630 5.89 0.00 34.34 1.73
2278 2489 9.753674 ATCCAATGGAAAACAAAGACTAATAGA 57.246 29.630 5.89 0.00 34.34 1.98
2279 2490 9.010029 TCCAATGGAAAACAAAGACTAATAGAC 57.990 33.333 0.00 0.00 0.00 2.59
2280 2491 7.962918 CCAATGGAAAACAAAGACTAATAGACG 59.037 37.037 0.00 0.00 0.00 4.18
2281 2492 7.611213 ATGGAAAACAAAGACTAATAGACGG 57.389 36.000 0.00 0.00 0.00 4.79
2282 2493 6.761312 TGGAAAACAAAGACTAATAGACGGA 58.239 36.000 0.00 0.00 0.00 4.69
2283 2494 7.218614 TGGAAAACAAAGACTAATAGACGGAA 58.781 34.615 0.00 0.00 0.00 4.30
2284 2495 7.716123 TGGAAAACAAAGACTAATAGACGGAAA 59.284 33.333 0.00 0.00 0.00 3.13
2285 2496 8.562052 GGAAAACAAAGACTAATAGACGGAAAA 58.438 33.333 0.00 0.00 0.00 2.29
2286 2497 9.595357 GAAAACAAAGACTAATAGACGGAAAAG 57.405 33.333 0.00 0.00 0.00 2.27
2287 2498 8.672823 AAACAAAGACTAATAGACGGAAAAGT 57.327 30.769 0.00 0.00 0.00 2.66
2288 2499 9.768662 AAACAAAGACTAATAGACGGAAAAGTA 57.231 29.630 0.00 0.00 0.00 2.24
2289 2500 8.754230 ACAAAGACTAATAGACGGAAAAGTAC 57.246 34.615 0.00 0.00 0.00 2.73
2290 2501 8.362639 ACAAAGACTAATAGACGGAAAAGTACA 58.637 33.333 0.00 0.00 0.00 2.90
2291 2502 9.199982 CAAAGACTAATAGACGGAAAAGTACAA 57.800 33.333 0.00 0.00 0.00 2.41
2292 2503 9.768662 AAAGACTAATAGACGGAAAAGTACAAA 57.231 29.630 0.00 0.00 0.00 2.83
2293 2504 8.983307 AGACTAATAGACGGAAAAGTACAAAG 57.017 34.615 0.00 0.00 0.00 2.77
2294 2505 7.544915 AGACTAATAGACGGAAAAGTACAAAGC 59.455 37.037 0.00 0.00 0.00 3.51
2295 2506 7.384477 ACTAATAGACGGAAAAGTACAAAGCT 58.616 34.615 0.00 0.00 0.00 3.74
2296 2507 8.526147 ACTAATAGACGGAAAAGTACAAAGCTA 58.474 33.333 0.00 0.00 0.00 3.32
2297 2508 9.530633 CTAATAGACGGAAAAGTACAAAGCTAT 57.469 33.333 0.00 0.00 0.00 2.97
2302 2513 9.477484 AGACGGAAAAGTACAAAGCTATATATG 57.523 33.333 0.00 0.00 0.00 1.78
2303 2514 9.257651 GACGGAAAAGTACAAAGCTATATATGT 57.742 33.333 0.00 0.00 0.00 2.29
2350 2561 9.299963 TGTTTAGTTGATGACAAATTTGAGTTG 57.700 29.630 24.64 0.00 37.77 3.16
2351 2562 9.301153 GTTTAGTTGATGACAAATTTGAGTTGT 57.699 29.630 24.64 1.87 41.84 3.32
2354 2565 8.225603 AGTTGATGACAAATTTGAGTTGTAGT 57.774 30.769 24.64 0.00 39.29 2.73
2355 2566 9.337396 AGTTGATGACAAATTTGAGTTGTAGTA 57.663 29.630 24.64 0.00 39.29 1.82
2356 2567 9.382244 GTTGATGACAAATTTGAGTTGTAGTAC 57.618 33.333 24.64 7.49 39.29 2.73
2357 2568 8.094798 TGATGACAAATTTGAGTTGTAGTACC 57.905 34.615 24.64 2.24 39.29 3.34
2358 2569 7.717436 TGATGACAAATTTGAGTTGTAGTACCA 59.283 33.333 24.64 0.00 39.29 3.25
2359 2570 7.867305 TGACAAATTTGAGTTGTAGTACCAA 57.133 32.000 24.64 0.00 39.29 3.67
2360 2571 8.282455 TGACAAATTTGAGTTGTAGTACCAAA 57.718 30.769 24.64 1.73 39.29 3.28
2361 2572 8.740906 TGACAAATTTGAGTTGTAGTACCAAAA 58.259 29.630 24.64 0.00 39.29 2.44
2362 2573 9.575783 GACAAATTTGAGTTGTAGTACCAAAAA 57.424 29.630 24.64 0.00 39.29 1.94
2386 2597 6.866010 AAGATGAAAAATTTGACTTTGGGC 57.134 33.333 0.00 0.00 0.00 5.36
2387 2598 5.927819 AGATGAAAAATTTGACTTTGGGCA 58.072 33.333 0.00 0.00 0.00 5.36
2388 2599 5.993441 AGATGAAAAATTTGACTTTGGGCAG 59.007 36.000 0.00 0.00 0.00 4.85
2389 2600 4.450053 TGAAAAATTTGACTTTGGGCAGG 58.550 39.130 0.00 0.00 0.00 4.85
2390 2601 4.080638 TGAAAAATTTGACTTTGGGCAGGT 60.081 37.500 0.00 0.00 0.00 4.00
2391 2602 4.502105 AAAATTTGACTTTGGGCAGGTT 57.498 36.364 0.00 0.00 0.00 3.50
2392 2603 3.473923 AATTTGACTTTGGGCAGGTTG 57.526 42.857 0.00 0.00 0.00 3.77
2393 2604 1.118838 TTTGACTTTGGGCAGGTTGG 58.881 50.000 0.00 0.00 0.00 3.77
2394 2605 0.758685 TTGACTTTGGGCAGGTTGGG 60.759 55.000 0.00 0.00 0.00 4.12
2395 2606 2.524148 ACTTTGGGCAGGTTGGGC 60.524 61.111 0.00 0.00 0.00 5.36
2396 2607 2.203684 CTTTGGGCAGGTTGGGCT 60.204 61.111 0.00 0.00 0.00 5.19
2397 2608 1.076549 CTTTGGGCAGGTTGGGCTA 59.923 57.895 0.00 0.00 0.00 3.93
2398 2609 0.324645 CTTTGGGCAGGTTGGGCTAT 60.325 55.000 0.00 0.00 0.00 2.97
2399 2610 0.324275 TTTGGGCAGGTTGGGCTATC 60.324 55.000 0.00 0.00 0.00 2.08
2400 2611 1.214305 TTGGGCAGGTTGGGCTATCT 61.214 55.000 0.00 0.00 0.00 1.98
2401 2612 1.152881 GGGCAGGTTGGGCTATCTG 60.153 63.158 0.00 0.00 0.00 2.90
2402 2613 1.609783 GGCAGGTTGGGCTATCTGT 59.390 57.895 3.15 0.00 0.00 3.41
2403 2614 0.749454 GGCAGGTTGGGCTATCTGTG 60.749 60.000 3.15 0.00 0.00 3.66
2404 2615 1.379642 GCAGGTTGGGCTATCTGTGC 61.380 60.000 3.15 0.00 0.00 4.57
2405 2616 1.091771 CAGGTTGGGCTATCTGTGCG 61.092 60.000 0.00 0.00 0.00 5.34
2406 2617 1.078426 GGTTGGGCTATCTGTGCGT 60.078 57.895 0.00 0.00 0.00 5.24
2407 2618 0.676782 GGTTGGGCTATCTGTGCGTT 60.677 55.000 0.00 0.00 0.00 4.84
2447 2658 7.178274 ACAGATTAGTTGTTAATTTGCCCATCA 59.822 33.333 0.00 0.00 37.36 3.07
2452 2663 2.836372 TGTTAATTTGCCCATCATGCCA 59.164 40.909 0.00 0.00 0.00 4.92
2454 2665 2.922740 AATTTGCCCATCATGCCATC 57.077 45.000 0.00 0.00 0.00 3.51
2460 2671 2.309613 GCCCATCATGCCATCTAAACA 58.690 47.619 0.00 0.00 0.00 2.83
2468 2679 1.992557 TGCCATCTAAACAGAAGGGGT 59.007 47.619 0.00 0.00 0.00 4.95
2470 2681 3.785887 TGCCATCTAAACAGAAGGGGTAT 59.214 43.478 0.00 0.00 0.00 2.73
2485 2696 9.930693 CAGAAGGGGTATGTTTATTATCTCTAC 57.069 37.037 0.00 0.00 0.00 2.59
2904 3115 8.647143 AGAACATTTTGAACTACAACCAAATG 57.353 30.769 0.00 0.00 38.81 2.32
2930 3141 9.884465 GTATATGCTTTATGTTTTGCTAAGAGG 57.116 33.333 0.00 0.00 0.00 3.69
2931 3142 5.059404 TGCTTTATGTTTTGCTAAGAGGC 57.941 39.130 0.00 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.526917 GCAGTGCTGGGTCACTTGT 60.527 57.895 8.18 0.00 44.26 3.16
1 2 2.263741 GGCAGTGCTGGGTCACTTG 61.264 63.158 16.11 0.00 44.26 3.16
2 3 2.113986 GGCAGTGCTGGGTCACTT 59.886 61.111 16.11 0.00 44.26 3.16
4 5 2.359230 GAGGCAGTGCTGGGTCAC 60.359 66.667 16.11 0.00 37.24 3.67
5 6 3.640407 GGAGGCAGTGCTGGGTCA 61.640 66.667 16.11 0.00 0.00 4.02
6 7 4.416738 GGGAGGCAGTGCTGGGTC 62.417 72.222 16.11 6.90 0.00 4.46
8 9 4.729918 GTGGGAGGCAGTGCTGGG 62.730 72.222 16.11 0.00 0.00 4.45
9 10 1.841302 TTAGTGGGAGGCAGTGCTGG 61.841 60.000 16.11 0.00 0.00 4.85
10 11 0.254178 ATTAGTGGGAGGCAGTGCTG 59.746 55.000 16.11 0.00 0.00 4.41
11 12 0.254178 CATTAGTGGGAGGCAGTGCT 59.746 55.000 16.11 0.33 0.00 4.40
12 13 1.379642 GCATTAGTGGGAGGCAGTGC 61.380 60.000 6.55 6.55 0.00 4.40
13 14 0.749454 GGCATTAGTGGGAGGCAGTG 60.749 60.000 0.00 0.00 0.00 3.66
14 15 0.916358 AGGCATTAGTGGGAGGCAGT 60.916 55.000 0.00 0.00 0.00 4.40
30 31 2.909965 TGGCGGACCAAAACAGGC 60.910 61.111 0.00 0.00 45.37 4.85
61 62 0.322277 AGGATGAAGCACCACTGCAG 60.322 55.000 13.48 13.48 46.97 4.41
66 67 0.678048 GTGGGAGGATGAAGCACCAC 60.678 60.000 0.00 0.00 41.18 4.16
68 69 1.450312 CGTGGGAGGATGAAGCACC 60.450 63.158 0.00 0.00 0.00 5.01
79 80 3.343941 TGGGTTTCTTAATCGTGGGAG 57.656 47.619 0.00 0.00 0.00 4.30
81 82 4.013728 TCAATGGGTTTCTTAATCGTGGG 58.986 43.478 0.00 0.00 0.00 4.61
88 89 5.538433 CAGGGACTTTCAATGGGTTTCTTAA 59.462 40.000 0.00 0.00 34.60 1.85
97 98 2.756760 CACCATCAGGGACTTTCAATGG 59.243 50.000 0.00 0.00 41.15 3.16
100 101 2.441375 TGTCACCATCAGGGACTTTCAA 59.559 45.455 0.00 0.00 41.15 2.69
106 107 1.347707 TCACTTGTCACCATCAGGGAC 59.652 52.381 0.00 0.00 41.15 4.46
112 113 2.560504 TGTGTGTCACTTGTCACCATC 58.439 47.619 4.27 0.00 35.11 3.51
113 114 2.708216 TGTGTGTCACTTGTCACCAT 57.292 45.000 4.27 0.00 35.11 3.55
115 116 2.288666 ACATGTGTGTCACTTGTCACC 58.711 47.619 13.12 0.00 45.26 4.02
118 119 4.466828 GCAATACATGTGTGTCACTTGTC 58.533 43.478 19.32 6.97 45.26 3.18
140 141 0.389296 TCTTGTGGTGATACGTGGCG 60.389 55.000 0.00 0.00 0.00 5.69
145 146 5.410924 TCAATCTTCTCTTGTGGTGATACG 58.589 41.667 0.00 0.00 0.00 3.06
161 162 7.725844 ACACTTGAAAGGGTTATTCTCAATCTT 59.274 33.333 0.00 0.00 40.45 2.40
177 178 4.918810 AGTTAAAGGGCACACTTGAAAG 57.081 40.909 0.00 0.00 0.00 2.62
185 186 5.644636 CCGAAATTACTAGTTAAAGGGCACA 59.355 40.000 0.00 0.00 0.00 4.57
188 189 5.876460 TGACCGAAATTACTAGTTAAAGGGC 59.124 40.000 0.00 0.58 0.00 5.19
207 208 6.990349 AGAATTGGTAAATACCTATGTGACCG 59.010 38.462 10.77 0.00 46.58 4.79
317 318 8.981647 CATAATTTTGTGCAAGAATTATAGCCC 58.018 33.333 16.49 0.00 35.38 5.19
331 332 1.476488 AGACGGCCCATAATTTTGTGC 59.524 47.619 0.00 0.00 0.00 4.57
332 333 2.491693 ACAGACGGCCCATAATTTTGTG 59.508 45.455 0.00 0.00 0.00 3.33
334 335 3.315191 CCTACAGACGGCCCATAATTTTG 59.685 47.826 0.00 0.00 0.00 2.44
339 340 1.827394 GCCTACAGACGGCCCATAA 59.173 57.895 0.00 0.00 41.73 1.90
356 357 1.090728 GCCTAAGCTCCAACTGAAGC 58.909 55.000 0.00 0.00 35.50 3.86
361 362 1.211457 CTCCATGCCTAAGCTCCAACT 59.789 52.381 0.00 0.00 40.80 3.16
362 363 1.673168 CTCCATGCCTAAGCTCCAAC 58.327 55.000 0.00 0.00 40.80 3.77
382 383 0.890683 AAAGAGGAAAAGCCCATGCG 59.109 50.000 0.00 0.00 44.33 4.73
385 386 2.893489 GTGTCAAAGAGGAAAAGCCCAT 59.107 45.455 0.00 0.00 37.37 4.00
404 405 3.120199 CCATTTTTGAGTCGCTGTAGGTG 60.120 47.826 0.00 0.00 0.00 4.00
409 410 0.598065 GCCCATTTTTGAGTCGCTGT 59.402 50.000 0.00 0.00 0.00 4.40
433 434 1.343142 CAGTTTTAGCCGGCCCTTTTT 59.657 47.619 26.15 5.68 0.00 1.94
434 435 0.966179 CAGTTTTAGCCGGCCCTTTT 59.034 50.000 26.15 6.59 0.00 2.27
435 436 0.898326 CCAGTTTTAGCCGGCCCTTT 60.898 55.000 26.15 7.06 0.00 3.11
436 437 1.304134 CCAGTTTTAGCCGGCCCTT 60.304 57.895 26.15 7.52 0.00 3.95
437 438 2.355115 CCAGTTTTAGCCGGCCCT 59.645 61.111 26.15 8.44 0.00 5.19
441 442 1.065551 GCTAATGCCAGTTTTAGCCGG 59.934 52.381 0.00 0.00 42.80 6.13
451 452 8.483307 AAATAAAGACAAAATGCTAATGCCAG 57.517 30.769 0.00 0.00 38.71 4.85
466 467 5.105064 CGTAGGAGGAAGGGAAATAAAGACA 60.105 44.000 0.00 0.00 0.00 3.41
467 468 5.105023 ACGTAGGAGGAAGGGAAATAAAGAC 60.105 44.000 0.00 0.00 0.00 3.01
469 470 5.354842 ACGTAGGAGGAAGGGAAATAAAG 57.645 43.478 0.00 0.00 0.00 1.85
480 502 1.288633 TCCCCATGTACGTAGGAGGAA 59.711 52.381 0.50 0.00 0.00 3.36
489 511 1.191535 TGAGGAAGTCCCCATGTACG 58.808 55.000 0.00 0.00 36.42 3.67
490 512 3.713826 TTTGAGGAAGTCCCCATGTAC 57.286 47.619 0.00 0.00 36.42 2.90
491 513 4.733077 TTTTTGAGGAAGTCCCCATGTA 57.267 40.909 0.00 0.00 36.42 2.29
492 514 3.611025 TTTTTGAGGAAGTCCCCATGT 57.389 42.857 0.00 0.00 36.42 3.21
514 536 3.068448 GGTTTGTCCCCATGTACGTTTTT 59.932 43.478 0.00 0.00 0.00 1.94
515 537 2.624364 GGTTTGTCCCCATGTACGTTTT 59.376 45.455 0.00 0.00 0.00 2.43
516 538 2.232399 GGTTTGTCCCCATGTACGTTT 58.768 47.619 0.00 0.00 0.00 3.60
544 566 8.191534 AGCTATACGGTGATTACCTTTAAGAT 57.808 34.615 4.98 0.00 45.22 2.40
545 567 7.592885 AGCTATACGGTGATTACCTTTAAGA 57.407 36.000 4.98 0.00 45.22 2.10
546 568 7.811713 GGTAGCTATACGGTGATTACCTTTAAG 59.188 40.741 4.98 0.00 45.22 1.85
548 570 6.072508 CGGTAGCTATACGGTGATTACCTTTA 60.073 42.308 4.98 0.00 45.22 1.85
550 572 4.217118 CGGTAGCTATACGGTGATTACCTT 59.783 45.833 4.98 0.00 45.22 3.50
551 573 3.755378 CGGTAGCTATACGGTGATTACCT 59.245 47.826 4.98 0.00 45.22 3.08
552 574 3.671702 GCGGTAGCTATACGGTGATTACC 60.672 52.174 18.43 0.00 41.09 2.85
553 575 3.058016 TGCGGTAGCTATACGGTGATTAC 60.058 47.826 18.43 4.84 45.42 1.89
554 576 3.148412 TGCGGTAGCTATACGGTGATTA 58.852 45.455 18.43 0.00 45.42 1.75
555 577 1.958579 TGCGGTAGCTATACGGTGATT 59.041 47.619 18.43 0.00 45.42 2.57
556 578 1.612676 TGCGGTAGCTATACGGTGAT 58.387 50.000 18.43 0.00 45.42 3.06
557 579 1.268625 CATGCGGTAGCTATACGGTGA 59.731 52.381 18.43 0.00 45.42 4.02
558 580 1.668919 CCATGCGGTAGCTATACGGTG 60.669 57.143 18.43 7.04 45.42 4.94
559 581 0.601558 CCATGCGGTAGCTATACGGT 59.398 55.000 18.43 0.00 45.42 4.83
560 582 0.108804 CCCATGCGGTAGCTATACGG 60.109 60.000 18.43 6.42 45.42 4.02
561 583 0.885879 TCCCATGCGGTAGCTATACG 59.114 55.000 14.25 14.25 45.42 3.06
562 584 1.616865 TGTCCCATGCGGTAGCTATAC 59.383 52.381 0.00 0.00 45.42 1.47
563 585 2.003937 TGTCCCATGCGGTAGCTATA 57.996 50.000 0.00 0.00 45.42 1.31
564 586 1.002430 CATGTCCCATGCGGTAGCTAT 59.998 52.381 0.00 0.00 45.42 2.97
565 587 0.392706 CATGTCCCATGCGGTAGCTA 59.607 55.000 0.00 0.00 45.42 3.32
566 588 1.146930 CATGTCCCATGCGGTAGCT 59.853 57.895 0.00 0.00 45.42 3.32
567 589 1.153168 ACATGTCCCATGCGGTAGC 60.153 57.895 4.19 0.00 45.41 3.58
568 590 0.815213 CCACATGTCCCATGCGGTAG 60.815 60.000 0.00 0.00 0.00 3.18
569 591 1.223211 CCACATGTCCCATGCGGTA 59.777 57.895 0.00 0.00 0.00 4.02
570 592 2.045045 CCACATGTCCCATGCGGT 60.045 61.111 0.00 0.00 0.00 5.68
571 593 0.393673 TAACCACATGTCCCATGCGG 60.394 55.000 9.19 9.19 0.00 5.69
572 594 1.016627 CTAACCACATGTCCCATGCG 58.983 55.000 0.00 0.00 0.00 4.73
573 595 0.740737 GCTAACCACATGTCCCATGC 59.259 55.000 0.00 0.00 0.00 4.06
574 596 2.127271 TGCTAACCACATGTCCCATG 57.873 50.000 0.00 2.77 0.00 3.66
575 597 2.897271 TTGCTAACCACATGTCCCAT 57.103 45.000 0.00 0.00 0.00 4.00
576 598 2.666272 TTTGCTAACCACATGTCCCA 57.334 45.000 0.00 0.00 0.00 4.37
577 599 3.509575 TGATTTTGCTAACCACATGTCCC 59.490 43.478 0.00 0.00 0.00 4.46
578 600 4.782019 TGATTTTGCTAACCACATGTCC 57.218 40.909 0.00 0.00 0.00 4.02
579 601 7.656707 ATTTTGATTTTGCTAACCACATGTC 57.343 32.000 0.00 0.00 0.00 3.06
580 602 7.714377 TGAATTTTGATTTTGCTAACCACATGT 59.286 29.630 0.00 0.00 0.00 3.21
581 603 8.085720 TGAATTTTGATTTTGCTAACCACATG 57.914 30.769 0.00 0.00 0.00 3.21
582 604 8.851541 ATGAATTTTGATTTTGCTAACCACAT 57.148 26.923 0.00 0.00 0.00 3.21
583 605 9.941325 ATATGAATTTTGATTTTGCTAACCACA 57.059 25.926 0.00 0.00 0.00 4.17
614 636 9.639601 CTGATAGCTATACGGTGATTATTTTCA 57.360 33.333 6.13 0.00 0.00 2.69
615 637 9.088512 CCTGATAGCTATACGGTGATTATTTTC 57.911 37.037 6.13 0.00 0.00 2.29
616 638 8.812972 TCCTGATAGCTATACGGTGATTATTTT 58.187 33.333 6.13 0.00 0.00 1.82
617 639 8.251721 GTCCTGATAGCTATACGGTGATTATTT 58.748 37.037 6.13 0.00 0.00 1.40
618 640 7.616150 AGTCCTGATAGCTATACGGTGATTATT 59.384 37.037 6.13 0.00 0.00 1.40
627 649 2.678836 CCGGAGTCCTGATAGCTATACG 59.321 54.545 6.13 0.45 0.00 3.06
646 668 3.589654 TTCGTGCTCTTGGCCTCCG 62.590 63.158 3.32 0.00 40.92 4.63
652 695 1.726853 CTAGGGTTTCGTGCTCTTGG 58.273 55.000 0.00 0.00 0.00 3.61
795 853 1.303888 ATTGGTGGTGAGGCTGCTG 60.304 57.895 0.00 0.00 0.00 4.41
879 957 7.945033 TCCAAAAGATCGAAAGGAAATTTTG 57.055 32.000 0.00 0.00 40.38 2.44
900 978 4.219944 AGCAACAGTTAACTAGACGATCCA 59.780 41.667 8.04 0.00 0.00 3.41
905 994 6.467723 AATCAAGCAACAGTTAACTAGACG 57.532 37.500 8.04 0.00 0.00 4.18
1017 1111 2.557056 CTCGTAGTCCAACCTGAACTGA 59.443 50.000 0.00 0.00 0.00 3.41
1027 1121 2.742053 GCTTGATTTGCTCGTAGTCCAA 59.258 45.455 0.00 0.00 0.00 3.53
1029 1123 2.094417 GTGCTTGATTTGCTCGTAGTCC 59.906 50.000 0.00 0.00 0.00 3.85
1042 1136 2.076863 GTTGACGCTAAGGTGCTTGAT 58.923 47.619 0.00 0.00 0.00 2.57
1060 1154 2.183679 GTCAGAGGAGATGACCTGGTT 58.816 52.381 0.00 0.00 40.99 3.67
1063 1157 1.403679 GACGTCAGAGGAGATGACCTG 59.596 57.143 11.55 0.00 43.36 4.00
1069 1163 1.658994 GAGACGACGTCAGAGGAGAT 58.341 55.000 28.31 6.29 34.60 2.75
1102 1196 2.431057 GGTAACAGTCGATCCTCCACAT 59.569 50.000 0.00 0.00 0.00 3.21
1133 1227 2.631062 TCCTTGTCGGAGTGCTTTTCTA 59.369 45.455 0.00 0.00 36.69 2.10
1141 1235 1.001974 TCCATTGTCCTTGTCGGAGTG 59.998 52.381 0.00 0.00 44.20 3.51
1182 1276 2.436292 GAGCTGCTCAGGTGCCTG 60.436 66.667 24.02 11.82 44.86 4.85
1231 1325 5.439721 TGGGTTGTCATTTCTATCCATCAG 58.560 41.667 0.00 0.00 0.00 2.90
1266 1360 2.129823 TGTGAAGTTCCGTCGTCTTC 57.870 50.000 0.00 12.13 38.30 2.87
1314 1408 0.535780 TATATCCCCAGTCGTCGCGT 60.536 55.000 5.77 0.00 0.00 6.01
1352 1464 4.302559 ACATAGTTTTCCTCAAGGACCC 57.697 45.455 0.00 0.00 45.39 4.46
1359 1471 4.506625 CCCTCCACAACATAGTTTTCCTCA 60.507 45.833 0.00 0.00 0.00 3.86
1380 1492 0.461339 ATACGAACGTGATGTGCCCC 60.461 55.000 10.14 0.00 0.00 5.80
1446 1564 1.137086 CCGAGATGGTTTCCGATGTCT 59.863 52.381 0.00 0.00 0.00 3.41
1563 1687 2.498644 AAAGCTCTGCCCTAAAGACC 57.501 50.000 0.00 0.00 0.00 3.85
1569 1694 0.777446 ACCCAAAAAGCTCTGCCCTA 59.223 50.000 0.00 0.00 0.00 3.53
1605 1730 1.138661 TGCAGCGTGATGGATGACATA 59.861 47.619 0.00 0.00 40.72 2.29
1653 1778 3.184379 CCGTGTATATGAACCGAAGCATG 59.816 47.826 0.00 0.00 0.00 4.06
1836 1979 1.134220 TCGGGGCAATTGTACATCTCC 60.134 52.381 7.40 0.00 0.00 3.71
1964 2153 2.360844 TCGAGCACTCTCTAGTCCAAG 58.639 52.381 0.00 0.00 37.19 3.61
2000 2193 7.946381 TGGATATGCACCTGTGTAAAAATAA 57.054 32.000 0.00 0.00 0.00 1.40
2022 2219 6.966534 AAGCACAAATAGAATCCCTTATGG 57.033 37.500 0.00 0.00 0.00 2.74
2026 2223 8.593945 TTATCAAAGCACAAATAGAATCCCTT 57.406 30.769 0.00 0.00 0.00 3.95
2027 2224 8.055181 TCTTATCAAAGCACAAATAGAATCCCT 58.945 33.333 0.00 0.00 32.36 4.20
2058 2255 7.022384 TGTGAAAGTACTTGTTAAACAAACCG 58.978 34.615 9.34 0.00 37.69 4.44
2101 2304 6.315714 TCCCCATTGATACACCTTACAAAAA 58.684 36.000 0.00 0.00 0.00 1.94
2106 2309 7.228706 CAGTAAATCCCCATTGATACACCTTAC 59.771 40.741 0.00 0.00 0.00 2.34
2180 2391 7.935405 AGGTTAGATAGTAGGGAATCCTCTAG 58.065 42.308 0.00 0.00 43.66 2.43
2190 2401 9.529823 TGATACAACATAGGTTAGATAGTAGGG 57.470 37.037 0.00 0.00 34.87 3.53
2210 2421 7.094634 GCTTTCTTCACAAATCCTCTTGATACA 60.095 37.037 0.00 0.00 31.83 2.29
2211 2422 7.247019 GCTTTCTTCACAAATCCTCTTGATAC 58.753 38.462 0.00 0.00 31.83 2.24
2212 2423 6.375455 GGCTTTCTTCACAAATCCTCTTGATA 59.625 38.462 0.00 0.00 31.83 2.15
2213 2424 5.184671 GGCTTTCTTCACAAATCCTCTTGAT 59.815 40.000 0.00 0.00 34.22 2.57
2214 2425 4.520492 GGCTTTCTTCACAAATCCTCTTGA 59.480 41.667 0.00 0.00 0.00 3.02
2215 2426 4.522022 AGGCTTTCTTCACAAATCCTCTTG 59.478 41.667 0.00 0.00 27.52 3.02
2216 2427 4.522022 CAGGCTTTCTTCACAAATCCTCTT 59.478 41.667 0.00 0.00 30.86 2.85
2217 2428 4.077822 CAGGCTTTCTTCACAAATCCTCT 58.922 43.478 0.00 0.00 30.86 3.69
2218 2429 4.074970 TCAGGCTTTCTTCACAAATCCTC 58.925 43.478 0.00 0.00 30.86 3.71
2219 2430 4.104383 TCAGGCTTTCTTCACAAATCCT 57.896 40.909 0.00 0.00 33.04 3.24
2220 2431 4.853924 TTCAGGCTTTCTTCACAAATCC 57.146 40.909 0.00 0.00 0.00 3.01
2221 2432 6.276091 ACTTTTCAGGCTTTCTTCACAAATC 58.724 36.000 0.00 0.00 0.00 2.17
2222 2433 6.225981 ACTTTTCAGGCTTTCTTCACAAAT 57.774 33.333 0.00 0.00 0.00 2.32
2223 2434 5.659440 ACTTTTCAGGCTTTCTTCACAAA 57.341 34.783 0.00 0.00 0.00 2.83
2224 2435 5.659440 AACTTTTCAGGCTTTCTTCACAA 57.341 34.783 0.00 0.00 0.00 3.33
2225 2436 5.184864 TGAAACTTTTCAGGCTTTCTTCACA 59.815 36.000 0.07 0.00 41.88 3.58
2226 2437 5.650543 TGAAACTTTTCAGGCTTTCTTCAC 58.349 37.500 0.07 0.00 41.88 3.18
2227 2438 5.913137 TGAAACTTTTCAGGCTTTCTTCA 57.087 34.783 0.07 0.00 41.88 3.02
2238 2449 6.975196 TCCATTGGATTCTGAAACTTTTCA 57.025 33.333 0.00 4.39 44.31 2.69
2239 2450 8.551205 GTTTTCCATTGGATTCTGAAACTTTTC 58.449 33.333 17.14 0.00 37.69 2.29
2240 2451 8.046107 TGTTTTCCATTGGATTCTGAAACTTTT 58.954 29.630 21.75 0.00 32.11 2.27
2241 2452 7.563906 TGTTTTCCATTGGATTCTGAAACTTT 58.436 30.769 21.75 0.00 32.11 2.66
2242 2453 7.123355 TGTTTTCCATTGGATTCTGAAACTT 57.877 32.000 21.75 0.00 32.11 2.66
2243 2454 6.729690 TGTTTTCCATTGGATTCTGAAACT 57.270 33.333 21.75 0.00 32.11 2.66
2244 2455 7.710475 TCTTTGTTTTCCATTGGATTCTGAAAC 59.290 33.333 17.41 17.41 31.74 2.78
2245 2456 7.710475 GTCTTTGTTTTCCATTGGATTCTGAAA 59.290 33.333 6.15 0.75 0.00 2.69
2246 2457 7.069826 AGTCTTTGTTTTCCATTGGATTCTGAA 59.930 33.333 6.15 0.00 0.00 3.02
2247 2458 6.550854 AGTCTTTGTTTTCCATTGGATTCTGA 59.449 34.615 6.15 0.00 0.00 3.27
2248 2459 6.752168 AGTCTTTGTTTTCCATTGGATTCTG 58.248 36.000 6.15 0.00 0.00 3.02
2249 2460 6.983906 AGTCTTTGTTTTCCATTGGATTCT 57.016 33.333 6.15 0.00 0.00 2.40
2252 2463 9.753674 TCTATTAGTCTTTGTTTTCCATTGGAT 57.246 29.630 6.15 0.00 0.00 3.41
2253 2464 9.010029 GTCTATTAGTCTTTGTTTTCCATTGGA 57.990 33.333 0.00 0.00 0.00 3.53
2254 2465 7.962918 CGTCTATTAGTCTTTGTTTTCCATTGG 59.037 37.037 0.00 0.00 0.00 3.16
2255 2466 7.962918 CCGTCTATTAGTCTTTGTTTTCCATTG 59.037 37.037 0.00 0.00 0.00 2.82
2256 2467 7.881232 TCCGTCTATTAGTCTTTGTTTTCCATT 59.119 33.333 0.00 0.00 0.00 3.16
2257 2468 7.391620 TCCGTCTATTAGTCTTTGTTTTCCAT 58.608 34.615 0.00 0.00 0.00 3.41
2258 2469 6.761312 TCCGTCTATTAGTCTTTGTTTTCCA 58.239 36.000 0.00 0.00 0.00 3.53
2259 2470 7.662604 TTCCGTCTATTAGTCTTTGTTTTCC 57.337 36.000 0.00 0.00 0.00 3.13
2260 2471 9.595357 CTTTTCCGTCTATTAGTCTTTGTTTTC 57.405 33.333 0.00 0.00 0.00 2.29
2261 2472 9.117183 ACTTTTCCGTCTATTAGTCTTTGTTTT 57.883 29.630 0.00 0.00 0.00 2.43
2271 2482 7.829378 AGCTTTGTACTTTTCCGTCTATTAG 57.171 36.000 0.00 0.00 0.00 1.73
2276 2487 9.477484 CATATATAGCTTTGTACTTTTCCGTCT 57.523 33.333 0.00 0.00 0.00 4.18
2277 2488 9.257651 ACATATATAGCTTTGTACTTTTCCGTC 57.742 33.333 0.00 0.00 0.00 4.79
2324 2535 9.299963 CAACTCAAATTTGTCATCAACTAAACA 57.700 29.630 17.47 0.00 32.93 2.83
2325 2536 9.301153 ACAACTCAAATTTGTCATCAACTAAAC 57.699 29.630 17.47 0.00 31.30 2.01
2328 2539 9.337396 ACTACAACTCAAATTTGTCATCAACTA 57.663 29.630 17.47 0.00 38.21 2.24
2329 2540 8.225603 ACTACAACTCAAATTTGTCATCAACT 57.774 30.769 17.47 0.00 38.21 3.16
2330 2541 9.382244 GTACTACAACTCAAATTTGTCATCAAC 57.618 33.333 17.47 3.96 38.21 3.18
2331 2542 8.564574 GGTACTACAACTCAAATTTGTCATCAA 58.435 33.333 17.47 0.00 38.21 2.57
2332 2543 7.717436 TGGTACTACAACTCAAATTTGTCATCA 59.283 33.333 17.47 0.00 38.21 3.07
2333 2544 8.094798 TGGTACTACAACTCAAATTTGTCATC 57.905 34.615 17.47 0.42 38.21 2.92
2334 2545 8.458573 TTGGTACTACAACTCAAATTTGTCAT 57.541 30.769 17.47 2.32 38.21 3.06
2335 2546 7.867305 TTGGTACTACAACTCAAATTTGTCA 57.133 32.000 17.47 0.00 38.21 3.58
2336 2547 9.575783 TTTTTGGTACTACAACTCAAATTTGTC 57.424 29.630 17.47 0.00 38.21 3.18
2360 2571 8.190122 GCCCAAAGTCAAATTTTTCATCTTTTT 58.810 29.630 0.00 0.00 0.00 1.94
2361 2572 7.338957 TGCCCAAAGTCAAATTTTTCATCTTTT 59.661 29.630 0.00 0.00 0.00 2.27
2362 2573 6.827762 TGCCCAAAGTCAAATTTTTCATCTTT 59.172 30.769 0.00 0.00 0.00 2.52
2363 2574 6.355747 TGCCCAAAGTCAAATTTTTCATCTT 58.644 32.000 0.00 0.00 0.00 2.40
2364 2575 5.927819 TGCCCAAAGTCAAATTTTTCATCT 58.072 33.333 0.00 0.00 0.00 2.90
2365 2576 5.179929 CCTGCCCAAAGTCAAATTTTTCATC 59.820 40.000 0.00 0.00 0.00 2.92
2366 2577 5.065235 CCTGCCCAAAGTCAAATTTTTCAT 58.935 37.500 0.00 0.00 0.00 2.57
2367 2578 4.080638 ACCTGCCCAAAGTCAAATTTTTCA 60.081 37.500 0.00 0.00 0.00 2.69
2368 2579 4.450976 ACCTGCCCAAAGTCAAATTTTTC 58.549 39.130 0.00 0.00 0.00 2.29
2369 2580 4.502105 ACCTGCCCAAAGTCAAATTTTT 57.498 36.364 0.00 0.00 0.00 1.94
2370 2581 4.198530 CAACCTGCCCAAAGTCAAATTTT 58.801 39.130 0.00 0.00 0.00 1.82
2371 2582 3.433456 CCAACCTGCCCAAAGTCAAATTT 60.433 43.478 0.00 0.00 0.00 1.82
2372 2583 2.104622 CCAACCTGCCCAAAGTCAAATT 59.895 45.455 0.00 0.00 0.00 1.82
2373 2584 1.693606 CCAACCTGCCCAAAGTCAAAT 59.306 47.619 0.00 0.00 0.00 2.32
2374 2585 1.118838 CCAACCTGCCCAAAGTCAAA 58.881 50.000 0.00 0.00 0.00 2.69
2375 2586 0.758685 CCCAACCTGCCCAAAGTCAA 60.759 55.000 0.00 0.00 0.00 3.18
2376 2587 1.152567 CCCAACCTGCCCAAAGTCA 60.153 57.895 0.00 0.00 0.00 3.41
2377 2588 2.574018 GCCCAACCTGCCCAAAGTC 61.574 63.158 0.00 0.00 0.00 3.01
2378 2589 1.725169 TAGCCCAACCTGCCCAAAGT 61.725 55.000 0.00 0.00 0.00 2.66
2379 2590 0.324645 ATAGCCCAACCTGCCCAAAG 60.325 55.000 0.00 0.00 0.00 2.77
2380 2591 0.324275 GATAGCCCAACCTGCCCAAA 60.324 55.000 0.00 0.00 0.00 3.28
2381 2592 1.214305 AGATAGCCCAACCTGCCCAA 61.214 55.000 0.00 0.00 0.00 4.12
2382 2593 1.619363 AGATAGCCCAACCTGCCCA 60.619 57.895 0.00 0.00 0.00 5.36
2383 2594 1.152881 CAGATAGCCCAACCTGCCC 60.153 63.158 0.00 0.00 0.00 5.36
2384 2595 0.749454 CACAGATAGCCCAACCTGCC 60.749 60.000 0.00 0.00 0.00 4.85
2385 2596 1.379642 GCACAGATAGCCCAACCTGC 61.380 60.000 0.00 0.00 0.00 4.85
2386 2597 1.091771 CGCACAGATAGCCCAACCTG 61.092 60.000 0.00 0.00 0.00 4.00
2387 2598 1.221840 CGCACAGATAGCCCAACCT 59.778 57.895 0.00 0.00 0.00 3.50
2388 2599 0.676782 AACGCACAGATAGCCCAACC 60.677 55.000 0.00 0.00 0.00 3.77
2389 2600 0.727398 GAACGCACAGATAGCCCAAC 59.273 55.000 0.00 0.00 0.00 3.77
2390 2601 0.323302 TGAACGCACAGATAGCCCAA 59.677 50.000 0.00 0.00 0.00 4.12
2391 2602 0.541392 ATGAACGCACAGATAGCCCA 59.459 50.000 0.00 0.00 0.00 5.36
2392 2603 0.940126 CATGAACGCACAGATAGCCC 59.060 55.000 0.00 0.00 0.00 5.19
2393 2604 1.939974 TCATGAACGCACAGATAGCC 58.060 50.000 0.00 0.00 0.00 3.93
2394 2605 2.932614 AGTTCATGAACGCACAGATAGC 59.067 45.455 28.18 4.76 45.50 2.97
2395 2606 5.230936 CACTAGTTCATGAACGCACAGATAG 59.769 44.000 28.18 23.20 45.50 2.08
2396 2607 5.102313 CACTAGTTCATGAACGCACAGATA 58.898 41.667 28.18 14.84 45.50 1.98
2397 2608 3.928992 CACTAGTTCATGAACGCACAGAT 59.071 43.478 28.18 14.52 45.50 2.90
2398 2609 3.005367 TCACTAGTTCATGAACGCACAGA 59.995 43.478 28.18 20.82 45.50 3.41
2399 2610 3.317150 TCACTAGTTCATGAACGCACAG 58.683 45.455 28.18 24.00 45.50 3.66
2400 2611 3.378911 TCACTAGTTCATGAACGCACA 57.621 42.857 28.18 15.99 45.50 4.57
2401 2612 4.053903 GTTCACTAGTTCATGAACGCAC 57.946 45.455 28.18 16.99 43.72 5.34
2406 2617 9.208022 CAACTAATCTGTTCACTAGTTCATGAA 57.792 33.333 3.38 3.38 33.39 2.57
2407 2618 8.367911 ACAACTAATCTGTTCACTAGTTCATGA 58.632 33.333 0.00 0.00 33.39 3.07
2447 2658 2.582636 ACCCCTTCTGTTTAGATGGCAT 59.417 45.455 0.00 0.00 43.50 4.40
2460 2671 9.102453 GGTAGAGATAATAAACATACCCCTTCT 57.898 37.037 0.00 0.00 0.00 2.85
2862 3073 8.647143 AAATGTTCTAATTTCAACCAAGTGTG 57.353 30.769 0.00 0.00 0.00 3.82
2863 3074 9.097257 CAAAATGTTCTAATTTCAACCAAGTGT 57.903 29.630 0.00 0.00 0.00 3.55
2864 3075 9.311916 TCAAAATGTTCTAATTTCAACCAAGTG 57.688 29.630 0.00 0.00 0.00 3.16
2865 3076 9.883142 TTCAAAATGTTCTAATTTCAACCAAGT 57.117 25.926 0.00 0.00 0.00 3.16
2867 3078 9.883142 AGTTCAAAATGTTCTAATTTCAACCAA 57.117 25.926 0.00 0.00 30.03 3.67
2904 3115 9.884465 CCTCTTAGCAAAACATAAAGCATATAC 57.116 33.333 0.00 0.00 0.00 1.47


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

AutoCloner maintained by Alex Coulton.