Multiple sequence alignment - TraesCS3A01G300000

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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 TraesCS3A01G300000 chr3A 100.000 2495 0 0 1 2495 534185039 534187533 0.000000e+00 4608.0
1 TraesCS3A01G300000 chr3A 84.768 1208 98 34 362 1501 534199648 534200837 0.000000e+00 1133.0
2 TraesCS3A01G300000 chr3A 91.279 172 14 1 2323 2494 20553255 20553085 1.490000e-57 233.0
3 TraesCS3A01G300000 chr3B 87.227 963 68 22 620 1530 542730623 542729664 0.000000e+00 1046.0
4 TraesCS3A01G300000 chr3B 91.077 594 29 19 1 588 542731533 542730958 0.000000e+00 782.0
5 TraesCS3A01G300000 chr3B 89.591 538 43 5 987 1511 542722590 542722053 0.000000e+00 671.0
6 TraesCS3A01G300000 chr3B 83.412 633 56 20 368 970 542723257 542722644 2.180000e-150 542.0
7 TraesCS3A01G300000 chr3B 88.800 250 23 3 1 246 542724689 542724441 4.030000e-78 302.0
8 TraesCS3A01G300000 chr3B 90.643 171 14 1 2324 2494 434734606 434734438 2.500000e-55 226.0
9 TraesCS3A01G300000 chr3B 79.861 144 26 3 2322 2465 747515841 747515981 4.390000e-18 102.0
10 TraesCS3A01G300000 chr7A 96.025 629 23 2 1695 2323 418607364 418606738 0.000000e+00 1022.0
11 TraesCS3A01G300000 chr7A 91.167 634 39 4 1690 2323 106955971 106956587 0.000000e+00 845.0
12 TraesCS3A01G300000 chr7A 92.568 148 10 1 2323 2470 364383991 364383845 6.990000e-51 211.0
13 TraesCS3A01G300000 chr7A 85.792 183 24 2 2313 2494 644484370 644484189 2.530000e-45 193.0
14 TraesCS3A01G300000 chr7A 90.000 60 5 1 2323 2381 89782371 89782430 2.660000e-10 76.8
15 TraesCS3A01G300000 chr1A 95.171 642 29 2 1682 2323 398111066 398111705 0.000000e+00 1013.0
16 TraesCS3A01G300000 chr7D 82.838 1043 62 39 1 968 6439270 6438270 0.000000e+00 826.0
17 TraesCS3A01G300000 chr7D 88.447 528 33 7 987 1504 6438212 6437703 1.640000e-171 612.0
18 TraesCS3A01G300000 chr3D 86.486 703 57 13 987 1655 416199131 416198433 0.000000e+00 737.0
19 TraesCS3A01G300000 chr3D 89.623 530 43 3 987 1504 416193256 416192727 0.000000e+00 664.0
20 TraesCS3A01G300000 chr3D 81.795 780 60 33 230 968 416194052 416193314 1.660000e-161 579.0
21 TraesCS3A01G300000 chr3D 93.069 404 15 5 1 401 416211082 416210689 1.660000e-161 579.0
22 TraesCS3A01G300000 chr3D 81.744 367 32 19 592 939 416199553 416199203 8.790000e-70 274.0
23 TraesCS3A01G300000 chr3D 84.677 248 33 3 1 243 416196048 416195801 2.480000e-60 243.0
24 TraesCS3A01G300000 chr3D 92.453 159 10 2 2316 2474 121383475 121383631 2.500000e-55 226.0
25 TraesCS3A01G300000 chr3D 83.333 198 16 12 387 581 416210626 416210443 1.530000e-37 167.0
26 TraesCS3A01G300000 chr3D 95.385 65 3 0 284 348 416195329 416195265 1.220000e-18 104.0
27 TraesCS3A01G300000 chr7B 86.104 403 39 10 1689 2085 138151043 138150652 3.840000e-113 418.0
28 TraesCS3A01G300000 chr7B 85.960 349 40 4 1737 2085 649348859 649348520 5.070000e-97 364.0
29 TraesCS3A01G300000 chr7B 92.000 250 17 2 2077 2323 138150628 138150379 5.110000e-92 348.0
30 TraesCS3A01G300000 chr7B 90.323 248 20 3 2077 2321 649348496 649348250 3.100000e-84 322.0
31 TraesCS3A01G300000 chr7B 90.141 142 13 1 1944 2085 649349102 649348962 1.520000e-42 183.0
32 TraesCS3A01G300000 chr7B 95.000 60 2 1 1694 1752 41065342 41065283 2.640000e-15 93.5
33 TraesCS3A01G300000 chr5A 92.829 251 14 3 2077 2323 372935063 372935313 6.560000e-96 361.0
34 TraesCS3A01G300000 chr2B 81.119 143 24 2 2323 2465 95793630 95793769 7.290000e-21 111.0
35 TraesCS3A01G300000 chr2B 88.732 71 4 3 1676 1746 755403740 755403674 1.590000e-12 84.2
36 TraesCS3A01G300000 chr2A 86.364 88 7 5 1693 1777 72510391 72510476 9.500000e-15 91.6
37 TraesCS3A01G300000 chrUn 88.732 71 4 3 1676 1746 271478693 271478627 1.590000e-12 84.2
38 TraesCS3A01G300000 chrUn 88.732 71 4 3 1676 1746 319547626 319547560 1.590000e-12 84.2
39 TraesCS3A01G300000 chrUn 88.732 71 4 3 1676 1746 319551028 319550962 1.590000e-12 84.2
40 TraesCS3A01G300000 chr5B 85.938 64 8 1 2319 2381 669560884 669560947 1.600000e-07 67.6


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 TraesCS3A01G300000 chr3A 534185039 534187533 2494 False 4608.000000 4608 100.000000 1 2495 1 chr3A.!!$F1 2494
1 TraesCS3A01G300000 chr3A 534199648 534200837 1189 False 1133.000000 1133 84.768000 362 1501 1 chr3A.!!$F2 1139
2 TraesCS3A01G300000 chr3B 542729664 542731533 1869 True 914.000000 1046 89.152000 1 1530 2 chr3B.!!$R3 1529
3 TraesCS3A01G300000 chr3B 542722053 542724689 2636 True 505.000000 671 87.267667 1 1511 3 chr3B.!!$R2 1510
4 TraesCS3A01G300000 chr7A 418606738 418607364 626 True 1022.000000 1022 96.025000 1695 2323 1 chr7A.!!$R2 628
5 TraesCS3A01G300000 chr7A 106955971 106956587 616 False 845.000000 845 91.167000 1690 2323 1 chr7A.!!$F2 633
6 TraesCS3A01G300000 chr1A 398111066 398111705 639 False 1013.000000 1013 95.171000 1682 2323 1 chr1A.!!$F1 641
7 TraesCS3A01G300000 chr7D 6437703 6439270 1567 True 719.000000 826 85.642500 1 1504 2 chr7D.!!$R1 1503
8 TraesCS3A01G300000 chr3D 416192727 416199553 6826 True 433.500000 737 86.618333 1 1655 6 chr3D.!!$R1 1654
9 TraesCS3A01G300000 chr3D 416210443 416211082 639 True 373.000000 579 88.201000 1 581 2 chr3D.!!$R2 580
10 TraesCS3A01G300000 chr7B 138150379 138151043 664 True 383.000000 418 89.052000 1689 2323 2 chr7B.!!$R2 634
11 TraesCS3A01G300000 chr7B 649348250 649349102 852 True 289.666667 364 88.808000 1737 2321 3 chr7B.!!$R3 584

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
825 7668 0.10412 CCACGGATATGAACGCCAGA 59.896 55.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2351 9324 0.036022 GCACTGTTCCTCTCTGCCTT 59.964 55.0 0.0 0.0 0.0 4.35 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
119 3638 1.482553 CGGTAGGGGATATGGACTGGT 60.483 57.143 0.00 0.00 0.00 4.00
197 3720 4.021719 TCCAGTAGAAGAAAAATCGACGGT 60.022 41.667 0.00 0.00 0.00 4.83
219 3742 4.857037 GTGGCGATCTGGTTAATTTTCAAC 59.143 41.667 0.00 0.00 0.00 3.18
276 5593 5.297776 CCCGAGAAACATGAATAATTGCTCT 59.702 40.000 0.00 0.00 0.00 4.09
315 5632 3.242944 CACATCTCCGTATGTTAACGCTG 59.757 47.826 0.26 0.00 41.51 5.18
401 6835 3.072944 CTGCTTTCTCTTTGGTCCTCTG 58.927 50.000 0.00 0.00 0.00 3.35
439 6883 2.407090 GCAAGTGGCCAATCAGAAAAC 58.593 47.619 7.24 0.00 36.11 2.43
443 6887 5.625197 GCAAGTGGCCAATCAGAAAACATAT 60.625 40.000 7.24 0.00 36.11 1.78
444 6888 6.405731 GCAAGTGGCCAATCAGAAAACATATA 60.406 38.462 7.24 0.00 36.11 0.86
445 6889 7.685155 GCAAGTGGCCAATCAGAAAACATATAT 60.685 37.037 7.24 0.00 36.11 0.86
446 6890 8.849168 CAAGTGGCCAATCAGAAAACATATATA 58.151 33.333 7.24 0.00 0.00 0.86
447 6891 8.995027 AGTGGCCAATCAGAAAACATATATAA 57.005 30.769 7.24 0.00 0.00 0.98
448 6892 9.420118 AGTGGCCAATCAGAAAACATATATAAA 57.580 29.630 7.24 0.00 0.00 1.40
499 6948 2.838202 TCCCTCAGGAGACATGGTTTAC 59.162 50.000 0.00 0.00 37.19 2.01
500 6949 2.092914 CCCTCAGGAGACATGGTTTACC 60.093 54.545 0.00 0.00 33.47 2.85
501 6950 4.648169 CCCTCAGGAGACATGGTTTACCA 61.648 52.174 3.71 3.71 43.31 3.25
502 6951 6.439562 CCCTCAGGAGACATGGTTTACCAG 62.440 54.167 7.77 2.85 42.67 4.00
521 6972 2.028130 AGGAGCTACCAGACAATCGAG 58.972 52.381 0.00 0.00 42.04 4.04
535 6986 3.193691 ACAATCGAGACAGTAGAGGTTGG 59.806 47.826 0.00 0.00 0.00 3.77
614 7398 0.523966 TTTACCGGCCGAATTGCAAG 59.476 50.000 30.73 9.82 0.00 4.01
627 7412 0.865218 TTGCAAGAACGCACGCAAAG 60.865 50.000 0.00 0.00 42.87 2.77
706 7524 2.499205 CGAGTTGGCCAGCCGATA 59.501 61.111 16.95 0.00 39.42 2.92
708 7526 0.946221 CGAGTTGGCCAGCCGATATC 60.946 60.000 16.95 5.84 39.42 1.63
709 7527 0.603975 GAGTTGGCCAGCCGATATCC 60.604 60.000 16.95 0.00 39.42 2.59
710 7528 1.056700 AGTTGGCCAGCCGATATCCT 61.057 55.000 16.95 0.00 39.42 3.24
751 7592 5.499139 TTCCTGCGAATCCATCAAAATAC 57.501 39.130 0.00 0.00 0.00 1.89
753 7594 4.816385 TCCTGCGAATCCATCAAAATACTC 59.184 41.667 0.00 0.00 0.00 2.59
762 7603 3.058914 CCATCAAAATACTCGCCGATTCC 60.059 47.826 0.00 0.00 0.00 3.01
767 7608 2.126417 ATACTCGCCGATTCCGACCG 62.126 60.000 0.00 0.00 38.22 4.79
783 7624 0.177373 ACCGTTTCCCTCTTATCCGC 59.823 55.000 0.00 0.00 0.00 5.54
798 7639 1.523032 CCGCCCGGTACAGAAATCC 60.523 63.158 0.00 0.00 0.00 3.01
824 7667 0.880278 CCCACGGATATGAACGCCAG 60.880 60.000 0.00 0.00 0.00 4.85
825 7668 0.104120 CCACGGATATGAACGCCAGA 59.896 55.000 0.00 0.00 0.00 3.86
903 7779 8.503486 CACGGAATGGAAGCGTATATATATAC 57.497 38.462 19.12 19.12 36.15 1.47
959 7835 3.200593 GCAGCCAGCCATCGAGTG 61.201 66.667 0.00 0.00 37.23 3.51
982 7876 4.737352 GCAAAGGCAAGATCTTGTGTTTCA 60.737 41.667 30.88 0.00 42.31 2.69
984 7878 2.549754 AGGCAAGATCTTGTGTTTCACG 59.450 45.455 30.88 8.09 42.31 4.35
985 7879 2.290641 GGCAAGATCTTGTGTTTCACGT 59.709 45.455 30.88 0.00 42.31 4.49
991 7908 2.475818 TCTTGTGTTTCACGTACGCAT 58.524 42.857 16.72 0.00 37.14 4.73
1091 8008 0.039798 GCGTGTGACCTCTACGTGAA 60.040 55.000 0.00 0.00 39.79 3.18
1198 8125 4.208686 GGGCGAGCTCGGATCGTT 62.209 66.667 35.10 0.00 42.13 3.85
1277 8204 0.460459 GTAGGGGCAGCGAAGAAGAC 60.460 60.000 0.00 0.00 0.00 3.01
1355 8288 2.278013 GACCATCGACGAGGACGC 60.278 66.667 11.71 0.00 43.96 5.19
1530 8463 3.778718 CACACGCGCATGATAAAACTTAC 59.221 43.478 11.87 0.00 0.00 2.34
1531 8464 3.433957 ACACGCGCATGATAAAACTTACA 59.566 39.130 11.87 0.00 0.00 2.41
1532 8465 4.094294 ACACGCGCATGATAAAACTTACAT 59.906 37.500 11.87 0.00 0.00 2.29
1533 8466 4.666176 CACGCGCATGATAAAACTTACATC 59.334 41.667 5.73 0.00 0.00 3.06
1534 8467 3.894288 CGCGCATGATAAAACTTACATCG 59.106 43.478 8.75 0.00 0.00 3.84
1535 8468 4.317769 CGCGCATGATAAAACTTACATCGA 60.318 41.667 8.75 0.00 0.00 3.59
1536 8469 5.498159 GCGCATGATAAAACTTACATCGAA 58.502 37.500 0.30 0.00 0.00 3.71
1537 8470 5.963004 GCGCATGATAAAACTTACATCGAAA 59.037 36.000 0.30 0.00 0.00 3.46
1538 8471 6.632834 GCGCATGATAAAACTTACATCGAAAT 59.367 34.615 0.30 0.00 0.00 2.17
1539 8472 7.165812 GCGCATGATAAAACTTACATCGAAATT 59.834 33.333 0.30 0.00 0.00 1.82
1540 8473 9.009327 CGCATGATAAAACTTACATCGAAATTT 57.991 29.630 0.00 0.00 0.00 1.82
1554 8487 3.993508 GAAATTTCGACCGGTTCTCTC 57.006 47.619 9.42 0.00 0.00 3.20
1555 8488 2.381725 AATTTCGACCGGTTCTCTCC 57.618 50.000 9.42 0.00 0.00 3.71
1556 8489 0.535797 ATTTCGACCGGTTCTCTCCC 59.464 55.000 9.42 0.00 0.00 4.30
1557 8490 1.538687 TTTCGACCGGTTCTCTCCCC 61.539 60.000 9.42 0.00 0.00 4.81
1558 8491 3.459063 CGACCGGTTCTCTCCCCC 61.459 72.222 9.42 0.00 0.00 5.40
1559 8492 2.039137 GACCGGTTCTCTCCCCCT 59.961 66.667 9.42 0.00 0.00 4.79
1560 8493 2.039137 ACCGGTTCTCTCCCCCTC 59.961 66.667 0.00 0.00 0.00 4.30
1561 8494 2.364961 CCGGTTCTCTCCCCCTCT 59.635 66.667 0.00 0.00 0.00 3.69
1562 8495 1.306226 CCGGTTCTCTCCCCCTCTT 60.306 63.158 0.00 0.00 0.00 2.85
1563 8496 1.617947 CCGGTTCTCTCCCCCTCTTG 61.618 65.000 0.00 0.00 0.00 3.02
1564 8497 0.614979 CGGTTCTCTCCCCCTCTTGA 60.615 60.000 0.00 0.00 0.00 3.02
1565 8498 1.886422 GGTTCTCTCCCCCTCTTGAT 58.114 55.000 0.00 0.00 0.00 2.57
1566 8499 2.200955 GGTTCTCTCCCCCTCTTGATT 58.799 52.381 0.00 0.00 0.00 2.57
1567 8500 3.385115 GGTTCTCTCCCCCTCTTGATTA 58.615 50.000 0.00 0.00 0.00 1.75
1568 8501 3.134985 GGTTCTCTCCCCCTCTTGATTAC 59.865 52.174 0.00 0.00 0.00 1.89
1569 8502 4.034410 GTTCTCTCCCCCTCTTGATTACT 58.966 47.826 0.00 0.00 0.00 2.24
1570 8503 4.354208 TCTCTCCCCCTCTTGATTACTT 57.646 45.455 0.00 0.00 0.00 2.24
1571 8504 4.290942 TCTCTCCCCCTCTTGATTACTTC 58.709 47.826 0.00 0.00 0.00 3.01
1572 8505 4.016105 TCTCTCCCCCTCTTGATTACTTCT 60.016 45.833 0.00 0.00 0.00 2.85
1573 8506 4.699994 TCTCCCCCTCTTGATTACTTCTT 58.300 43.478 0.00 0.00 0.00 2.52
1574 8507 4.471386 TCTCCCCCTCTTGATTACTTCTTG 59.529 45.833 0.00 0.00 0.00 3.02
1575 8508 4.175962 TCCCCCTCTTGATTACTTCTTGT 58.824 43.478 0.00 0.00 0.00 3.16
1576 8509 4.601857 TCCCCCTCTTGATTACTTCTTGTT 59.398 41.667 0.00 0.00 0.00 2.83
1577 8510 4.702131 CCCCCTCTTGATTACTTCTTGTTG 59.298 45.833 0.00 0.00 0.00 3.33
1578 8511 5.514834 CCCCCTCTTGATTACTTCTTGTTGA 60.515 44.000 0.00 0.00 0.00 3.18
1579 8512 5.412904 CCCCTCTTGATTACTTCTTGTTGAC 59.587 44.000 0.00 0.00 0.00 3.18
1580 8513 5.997746 CCCTCTTGATTACTTCTTGTTGACA 59.002 40.000 0.00 0.00 0.00 3.58
1581 8514 6.148480 CCCTCTTGATTACTTCTTGTTGACAG 59.852 42.308 0.00 0.00 0.00 3.51
1582 8515 6.931281 CCTCTTGATTACTTCTTGTTGACAGA 59.069 38.462 0.00 0.00 0.00 3.41
1583 8516 7.605691 CCTCTTGATTACTTCTTGTTGACAGAT 59.394 37.037 0.00 0.00 0.00 2.90
1584 8517 8.908786 TCTTGATTACTTCTTGTTGACAGATT 57.091 30.769 0.00 0.00 0.00 2.40
1585 8518 9.342308 TCTTGATTACTTCTTGTTGACAGATTT 57.658 29.630 0.00 0.00 0.00 2.17
1586 8519 9.604626 CTTGATTACTTCTTGTTGACAGATTTC 57.395 33.333 0.00 0.00 0.00 2.17
1587 8520 8.908786 TGATTACTTCTTGTTGACAGATTTCT 57.091 30.769 0.00 0.00 0.00 2.52
1588 8521 9.342308 TGATTACTTCTTGTTGACAGATTTCTT 57.658 29.630 0.00 0.00 0.00 2.52
1647 8580 4.685824 GAAATTTCGAAACCACCAAACG 57.314 40.909 13.81 0.00 0.00 3.60
1648 8581 4.352887 GAAATTTCGAAACCACCAAACGA 58.647 39.130 13.81 0.00 0.00 3.85
1649 8582 2.828874 TTTCGAAACCACCAAACGAC 57.171 45.000 6.47 0.00 32.89 4.34
1650 8583 1.015868 TTCGAAACCACCAAACGACC 58.984 50.000 0.00 0.00 32.89 4.79
1651 8584 0.107800 TCGAAACCACCAAACGACCA 60.108 50.000 0.00 0.00 0.00 4.02
1652 8585 0.948678 CGAAACCACCAAACGACCAT 59.051 50.000 0.00 0.00 0.00 3.55
1653 8586 1.335496 CGAAACCACCAAACGACCATT 59.665 47.619 0.00 0.00 0.00 3.16
1654 8587 2.223618 CGAAACCACCAAACGACCATTT 60.224 45.455 0.00 0.00 0.00 2.32
1655 8588 3.377439 GAAACCACCAAACGACCATTTC 58.623 45.455 0.00 0.00 0.00 2.17
1656 8589 2.358322 ACCACCAAACGACCATTTCT 57.642 45.000 0.00 0.00 0.00 2.52
1657 8590 2.227194 ACCACCAAACGACCATTTCTC 58.773 47.619 0.00 0.00 0.00 2.87
1658 8591 2.158667 ACCACCAAACGACCATTTCTCT 60.159 45.455 0.00 0.00 0.00 3.10
1659 8592 3.071892 ACCACCAAACGACCATTTCTCTA 59.928 43.478 0.00 0.00 0.00 2.43
1660 8593 4.261801 CCACCAAACGACCATTTCTCTAT 58.738 43.478 0.00 0.00 0.00 1.98
1661 8594 4.332819 CCACCAAACGACCATTTCTCTATC 59.667 45.833 0.00 0.00 0.00 2.08
1662 8595 5.178797 CACCAAACGACCATTTCTCTATCT 58.821 41.667 0.00 0.00 0.00 1.98
1663 8596 5.643777 CACCAAACGACCATTTCTCTATCTT 59.356 40.000 0.00 0.00 0.00 2.40
1664 8597 6.149474 CACCAAACGACCATTTCTCTATCTTT 59.851 38.462 0.00 0.00 0.00 2.52
1665 8598 6.371825 ACCAAACGACCATTTCTCTATCTTTC 59.628 38.462 0.00 0.00 0.00 2.62
1666 8599 6.183360 CCAAACGACCATTTCTCTATCTTTCC 60.183 42.308 0.00 0.00 0.00 3.13
1667 8600 5.941555 ACGACCATTTCTCTATCTTTCCT 57.058 39.130 0.00 0.00 0.00 3.36
1668 8601 5.908341 ACGACCATTTCTCTATCTTTCCTC 58.092 41.667 0.00 0.00 0.00 3.71
1669 8602 5.659079 ACGACCATTTCTCTATCTTTCCTCT 59.341 40.000 0.00 0.00 0.00 3.69
1670 8603 6.834451 ACGACCATTTCTCTATCTTTCCTCTA 59.166 38.462 0.00 0.00 0.00 2.43
1671 8604 7.507616 ACGACCATTTCTCTATCTTTCCTCTAT 59.492 37.037 0.00 0.00 0.00 1.98
1672 8605 8.026607 CGACCATTTCTCTATCTTTCCTCTATC 58.973 40.741 0.00 0.00 0.00 2.08
1673 8606 9.088987 GACCATTTCTCTATCTTTCCTCTATCT 57.911 37.037 0.00 0.00 0.00 1.98
1674 8607 9.088987 ACCATTTCTCTATCTTTCCTCTATCTC 57.911 37.037 0.00 0.00 0.00 2.75
1675 8608 9.312904 CCATTTCTCTATCTTTCCTCTATCTCT 57.687 37.037 0.00 0.00 0.00 3.10
1754 8687 3.125316 CCCTCTTACGTCGTTGTTTTCA 58.875 45.455 1.78 0.00 0.00 2.69
1829 8767 7.239763 TCGGCACCTAATAAATAGATCATGA 57.760 36.000 0.00 0.00 33.04 3.07
1853 8791 2.613691 CTGCCCTAATTTTTGCTGCAG 58.386 47.619 10.11 10.11 38.78 4.41
1979 8917 2.300152 TCCTCCCATGATCTCGCATTAC 59.700 50.000 0.00 0.00 0.00 1.89
2106 9075 2.182014 CATCAAACGCACGATCGAGTA 58.818 47.619 24.34 4.53 0.00 2.59
2327 9300 4.479993 GCATGGAGAGCGGGCTGT 62.480 66.667 0.00 0.00 0.00 4.40
2328 9301 2.513204 CATGGAGAGCGGGCTGTG 60.513 66.667 0.00 0.00 0.00 3.66
2329 9302 3.790437 ATGGAGAGCGGGCTGTGG 61.790 66.667 0.00 0.00 0.00 4.17
2331 9304 3.474570 GGAGAGCGGGCTGTGGAT 61.475 66.667 0.00 0.00 0.00 3.41
2332 9305 2.586792 GAGAGCGGGCTGTGGATT 59.413 61.111 0.00 0.00 0.00 3.01
2333 9306 1.522580 GAGAGCGGGCTGTGGATTC 60.523 63.158 0.00 0.00 0.00 2.52
2334 9307 1.965754 GAGAGCGGGCTGTGGATTCT 61.966 60.000 0.00 0.00 0.00 2.40
2335 9308 1.522580 GAGCGGGCTGTGGATTCTC 60.523 63.158 0.00 0.00 0.00 2.87
2336 9309 1.965754 GAGCGGGCTGTGGATTCTCT 61.966 60.000 0.00 0.00 0.00 3.10
2337 9310 1.817099 GCGGGCTGTGGATTCTCTG 60.817 63.158 0.00 0.00 0.00 3.35
2338 9311 1.817099 CGGGCTGTGGATTCTCTGC 60.817 63.158 0.00 0.00 0.00 4.26
2339 9312 1.452833 GGGCTGTGGATTCTCTGCC 60.453 63.158 14.00 14.00 45.02 4.85
2340 9313 1.606531 GGCTGTGGATTCTCTGCCT 59.393 57.895 14.85 0.00 43.53 4.75
2341 9314 0.034670 GGCTGTGGATTCTCTGCCTT 60.035 55.000 14.85 0.00 43.53 4.35
2342 9315 1.093159 GCTGTGGATTCTCTGCCTTG 58.907 55.000 0.00 0.00 0.00 3.61
2343 9316 1.093159 CTGTGGATTCTCTGCCTTGC 58.907 55.000 0.00 0.00 0.00 4.01
2344 9317 0.694771 TGTGGATTCTCTGCCTTGCT 59.305 50.000 0.00 0.00 0.00 3.91
2345 9318 1.093159 GTGGATTCTCTGCCTTGCTG 58.907 55.000 0.00 0.00 0.00 4.41
2346 9319 0.694771 TGGATTCTCTGCCTTGCTGT 59.305 50.000 0.00 0.00 0.00 4.40
2347 9320 1.093159 GGATTCTCTGCCTTGCTGTG 58.907 55.000 0.00 0.00 0.00 3.66
2348 9321 1.093159 GATTCTCTGCCTTGCTGTGG 58.907 55.000 0.00 0.00 0.00 4.17
2358 9331 2.195411 TGCTGTGGCAAAGGCAGA 59.805 55.556 6.84 0.00 46.36 4.26
2361 9334 4.806936 TGTGGCAAAGGCAGAGAG 57.193 55.556 0.00 0.00 43.71 3.20
2362 9335 1.073722 TGTGGCAAAGGCAGAGAGG 59.926 57.895 0.00 0.00 43.71 3.69
2363 9336 1.376466 GTGGCAAAGGCAGAGAGGA 59.624 57.895 0.00 0.00 43.71 3.71
2364 9337 0.250901 GTGGCAAAGGCAGAGAGGAA 60.251 55.000 0.00 0.00 43.71 3.36
2365 9338 0.250901 TGGCAAAGGCAGAGAGGAAC 60.251 55.000 0.00 0.00 43.71 3.62
2366 9339 0.250901 GGCAAAGGCAGAGAGGAACA 60.251 55.000 0.00 0.00 43.71 3.18
2367 9340 1.163554 GCAAAGGCAGAGAGGAACAG 58.836 55.000 0.00 0.00 40.72 3.16
2368 9341 1.544314 GCAAAGGCAGAGAGGAACAGT 60.544 52.381 0.00 0.00 40.72 3.55
2369 9342 2.149578 CAAAGGCAGAGAGGAACAGTG 58.850 52.381 0.00 0.00 0.00 3.66
2370 9343 0.036022 AAGGCAGAGAGGAACAGTGC 59.964 55.000 0.00 0.00 0.00 4.40
2371 9344 1.376553 GGCAGAGAGGAACAGTGCC 60.377 63.158 0.00 0.00 46.49 5.01
2372 9345 1.676384 GCAGAGAGGAACAGTGCCT 59.324 57.895 0.00 0.00 38.81 4.75
2378 9351 1.562783 GAGGAACAGTGCCTCTACCT 58.437 55.000 19.79 0.00 46.70 3.08
2379 9352 1.903183 GAGGAACAGTGCCTCTACCTT 59.097 52.381 19.79 0.00 46.70 3.50
2380 9353 2.303311 GAGGAACAGTGCCTCTACCTTT 59.697 50.000 19.79 0.00 46.70 3.11
2381 9354 2.303311 AGGAACAGTGCCTCTACCTTTC 59.697 50.000 0.00 0.00 0.00 2.62
2382 9355 2.615747 GGAACAGTGCCTCTACCTTTCC 60.616 54.545 0.00 0.00 0.00 3.13
2383 9356 2.031495 ACAGTGCCTCTACCTTTCCT 57.969 50.000 0.00 0.00 0.00 3.36
2384 9357 1.903183 ACAGTGCCTCTACCTTTCCTC 59.097 52.381 0.00 0.00 0.00 3.71
2385 9358 2.183679 CAGTGCCTCTACCTTTCCTCT 58.816 52.381 0.00 0.00 0.00 3.69
2386 9359 3.245658 ACAGTGCCTCTACCTTTCCTCTA 60.246 47.826 0.00 0.00 0.00 2.43
2387 9360 3.131400 CAGTGCCTCTACCTTTCCTCTAC 59.869 52.174 0.00 0.00 0.00 2.59
2388 9361 3.011934 AGTGCCTCTACCTTTCCTCTACT 59.988 47.826 0.00 0.00 0.00 2.57
2389 9362 3.770388 GTGCCTCTACCTTTCCTCTACTT 59.230 47.826 0.00 0.00 0.00 2.24
2390 9363 4.223255 GTGCCTCTACCTTTCCTCTACTTT 59.777 45.833 0.00 0.00 0.00 2.66
2391 9364 4.844655 TGCCTCTACCTTTCCTCTACTTTT 59.155 41.667 0.00 0.00 0.00 2.27
2392 9365 6.021030 TGCCTCTACCTTTCCTCTACTTTTA 58.979 40.000 0.00 0.00 0.00 1.52
2393 9366 6.154706 TGCCTCTACCTTTCCTCTACTTTTAG 59.845 42.308 0.00 0.00 0.00 1.85
2394 9367 6.154877 GCCTCTACCTTTCCTCTACTTTTAGT 59.845 42.308 0.00 0.00 0.00 2.24
2395 9368 7.631161 GCCTCTACCTTTCCTCTACTTTTAGTC 60.631 44.444 0.00 0.00 0.00 2.59
2396 9369 7.388460 TCTACCTTTCCTCTACTTTTAGTCG 57.612 40.000 0.00 0.00 0.00 4.18
2397 9370 6.944862 TCTACCTTTCCTCTACTTTTAGTCGT 59.055 38.462 0.00 0.00 0.00 4.34
2398 9371 6.416631 ACCTTTCCTCTACTTTTAGTCGTT 57.583 37.500 0.00 0.00 0.00 3.85
2399 9372 6.221659 ACCTTTCCTCTACTTTTAGTCGTTG 58.778 40.000 0.00 0.00 0.00 4.10
2400 9373 5.638234 CCTTTCCTCTACTTTTAGTCGTTGG 59.362 44.000 0.00 0.00 0.00 3.77
2401 9374 6.409524 TTTCCTCTACTTTTAGTCGTTGGA 57.590 37.500 0.00 0.00 0.00 3.53
2402 9375 6.600882 TTCCTCTACTTTTAGTCGTTGGAT 57.399 37.500 0.00 0.00 0.00 3.41
2403 9376 6.600882 TCCTCTACTTTTAGTCGTTGGATT 57.399 37.500 0.00 0.00 0.00 3.01
2404 9377 6.395629 TCCTCTACTTTTAGTCGTTGGATTG 58.604 40.000 0.00 0.00 0.00 2.67
2405 9378 6.209986 TCCTCTACTTTTAGTCGTTGGATTGA 59.790 38.462 0.00 0.00 0.00 2.57
2406 9379 6.531948 CCTCTACTTTTAGTCGTTGGATTGAG 59.468 42.308 0.00 0.00 0.00 3.02
2407 9380 7.223260 TCTACTTTTAGTCGTTGGATTGAGA 57.777 36.000 0.00 0.00 0.00 3.27
2408 9381 7.663827 TCTACTTTTAGTCGTTGGATTGAGAA 58.336 34.615 0.00 0.00 0.00 2.87
2409 9382 8.311836 TCTACTTTTAGTCGTTGGATTGAGAAT 58.688 33.333 0.00 0.00 0.00 2.40
2410 9383 7.133891 ACTTTTAGTCGTTGGATTGAGAATG 57.866 36.000 0.00 0.00 0.00 2.67
2411 9384 6.149474 ACTTTTAGTCGTTGGATTGAGAATGG 59.851 38.462 0.00 0.00 0.00 3.16
2412 9385 3.981071 AGTCGTTGGATTGAGAATGGA 57.019 42.857 0.00 0.00 0.00 3.41
2413 9386 3.600388 AGTCGTTGGATTGAGAATGGAC 58.400 45.455 0.00 0.00 0.00 4.02
2414 9387 2.678336 GTCGTTGGATTGAGAATGGACC 59.322 50.000 0.00 0.00 0.00 4.46
2415 9388 1.665679 CGTTGGATTGAGAATGGACCG 59.334 52.381 0.00 0.00 0.00 4.79
2416 9389 1.401905 GTTGGATTGAGAATGGACCGC 59.598 52.381 0.00 0.00 0.00 5.68
2417 9390 0.107214 TGGATTGAGAATGGACCGCC 60.107 55.000 0.00 0.00 0.00 6.13
2418 9391 0.819666 GGATTGAGAATGGACCGCCC 60.820 60.000 0.00 0.00 0.00 6.13
2426 9399 2.354729 TGGACCGCCCAGATTTGG 59.645 61.111 0.00 0.00 40.82 3.28
2427 9400 3.140814 GGACCGCCCAGATTTGGC 61.141 66.667 0.00 0.00 43.58 4.52
2432 9405 2.125952 GCCCAGATTTGGCGCAAC 60.126 61.111 10.83 0.00 43.58 4.17
2433 9406 2.929903 GCCCAGATTTGGCGCAACA 61.930 57.895 10.83 0.00 43.58 3.33
2434 9407 1.213537 CCCAGATTTGGCGCAACAG 59.786 57.895 10.83 0.00 43.58 3.16
2435 9408 1.213537 CCAGATTTGGCGCAACAGG 59.786 57.895 10.83 0.00 37.73 4.00
2436 9409 1.243342 CCAGATTTGGCGCAACAGGA 61.243 55.000 10.83 0.00 37.73 3.86
2437 9410 0.109597 CAGATTTGGCGCAACAGGAC 60.110 55.000 10.83 0.00 0.00 3.85
2438 9411 1.212751 GATTTGGCGCAACAGGACC 59.787 57.895 10.83 0.00 0.00 4.46
2439 9412 1.523154 GATTTGGCGCAACAGGACCA 61.523 55.000 10.83 0.00 0.00 4.02
2440 9413 1.805428 ATTTGGCGCAACAGGACCAC 61.805 55.000 10.83 0.00 0.00 4.16
2441 9414 2.902423 TTTGGCGCAACAGGACCACT 62.902 55.000 10.83 0.00 0.00 4.00
2464 9437 8.311650 ACTGAAAACAGTGATATGAACAGTAC 57.688 34.615 0.00 0.00 34.01 2.73
2465 9438 7.931407 ACTGAAAACAGTGATATGAACAGTACA 59.069 33.333 0.00 0.00 34.01 2.90
2466 9439 8.083462 TGAAAACAGTGATATGAACAGTACAC 57.917 34.615 0.00 0.00 0.00 2.90
2467 9440 6.706055 AAACAGTGATATGAACAGTACACG 57.294 37.500 0.00 0.00 34.16 4.49
2468 9441 5.638596 ACAGTGATATGAACAGTACACGA 57.361 39.130 0.00 0.00 34.16 4.35
2469 9442 5.641709 ACAGTGATATGAACAGTACACGAG 58.358 41.667 0.00 0.00 34.16 4.18
2470 9443 4.500837 CAGTGATATGAACAGTACACGAGC 59.499 45.833 0.00 0.00 34.16 5.03
2471 9444 4.399618 AGTGATATGAACAGTACACGAGCT 59.600 41.667 0.00 0.00 34.16 4.09
2472 9445 5.589050 AGTGATATGAACAGTACACGAGCTA 59.411 40.000 0.00 0.00 34.16 3.32
2473 9446 5.681982 GTGATATGAACAGTACACGAGCTAC 59.318 44.000 0.00 0.00 0.00 3.58
2474 9447 5.355910 TGATATGAACAGTACACGAGCTACA 59.644 40.000 0.00 0.00 0.00 2.74
2475 9448 3.994204 TGAACAGTACACGAGCTACAA 57.006 42.857 0.00 0.00 0.00 2.41
2476 9449 4.514781 TGAACAGTACACGAGCTACAAT 57.485 40.909 0.00 0.00 0.00 2.71
2477 9450 4.234574 TGAACAGTACACGAGCTACAATG 58.765 43.478 0.00 0.00 0.00 2.82
2478 9451 3.936372 ACAGTACACGAGCTACAATGT 57.064 42.857 0.00 0.00 0.00 2.71
2479 9452 4.252971 ACAGTACACGAGCTACAATGTT 57.747 40.909 0.00 0.00 0.00 2.71
2480 9453 3.987868 ACAGTACACGAGCTACAATGTTG 59.012 43.478 0.00 0.00 0.00 3.33
2481 9454 3.987868 CAGTACACGAGCTACAATGTTGT 59.012 43.478 3.64 3.64 44.86 3.32
2482 9455 5.158494 CAGTACACGAGCTACAATGTTGTA 58.842 41.667 5.57 5.57 42.35 2.41
2483 9456 5.805486 CAGTACACGAGCTACAATGTTGTAT 59.195 40.000 6.10 0.00 42.26 2.29
2484 9457 5.805486 AGTACACGAGCTACAATGTTGTATG 59.195 40.000 6.10 4.49 42.26 2.39
2485 9458 4.816392 ACACGAGCTACAATGTTGTATGA 58.184 39.130 6.10 0.00 42.26 2.15
2486 9459 5.234752 ACACGAGCTACAATGTTGTATGAA 58.765 37.500 6.10 0.00 42.26 2.57
2487 9460 5.120208 ACACGAGCTACAATGTTGTATGAAC 59.880 40.000 6.10 0.00 42.26 3.18
2488 9461 5.120053 CACGAGCTACAATGTTGTATGAACA 59.880 40.000 6.10 0.00 42.26 3.18
2489 9462 5.348724 ACGAGCTACAATGTTGTATGAACAG 59.651 40.000 6.10 0.00 42.26 3.16
2490 9463 5.348724 CGAGCTACAATGTTGTATGAACAGT 59.651 40.000 6.10 0.00 42.26 3.55
2492 9465 5.088739 GCTACAATGTTGTATGAACAGTGC 58.911 41.667 15.67 1.08 46.44 4.40
2493 9466 5.334802 GCTACAATGTTGTATGAACAGTGCA 60.335 40.000 15.67 6.32 46.44 4.57
2494 9467 5.710513 ACAATGTTGTATGAACAGTGCAT 57.289 34.783 15.67 0.00 46.44 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
107 3626 1.071471 CCGGCCACCAGTCCATATC 59.929 63.158 2.24 0.00 0.00 1.63
129 3649 1.079750 GAAGCACTGGTCCTCCGAC 60.080 63.158 0.00 0.00 38.38 4.79
197 3720 4.378978 CGTTGAAAATTAACCAGATCGCCA 60.379 41.667 0.00 0.00 0.00 5.69
276 5593 0.250467 GTGGACTTTGGAGCAGAGCA 60.250 55.000 0.00 0.00 0.00 4.26
315 5632 0.179137 GCAAAGCAATTAGGGACGGC 60.179 55.000 0.00 0.00 0.00 5.68
401 6835 2.602257 GCCCCTTGATTTTGGCATAC 57.398 50.000 0.00 0.00 43.46 2.39
446 6890 9.471084 CCGTCACTGTTCCTTTTATTTTATTTT 57.529 29.630 0.00 0.00 0.00 1.82
447 6891 8.635328 ACCGTCACTGTTCCTTTTATTTTATTT 58.365 29.630 0.00 0.00 0.00 1.40
448 6892 8.173542 ACCGTCACTGTTCCTTTTATTTTATT 57.826 30.769 0.00 0.00 0.00 1.40
449 6893 7.754851 ACCGTCACTGTTCCTTTTATTTTAT 57.245 32.000 0.00 0.00 0.00 1.40
450 6894 7.095102 GCTACCGTCACTGTTCCTTTTATTTTA 60.095 37.037 0.00 0.00 0.00 1.52
464 6908 0.173708 GAGGGAAGCTACCGTCACTG 59.826 60.000 0.00 0.00 42.28 3.66
470 6914 0.395862 TCTCCTGAGGGAAGCTACCG 60.396 60.000 0.00 0.00 41.69 4.02
499 6948 1.202463 CGATTGTCTGGTAGCTCCTGG 60.202 57.143 0.00 0.00 36.08 4.45
500 6949 1.751351 TCGATTGTCTGGTAGCTCCTG 59.249 52.381 0.00 0.00 37.07 3.86
501 6950 2.028130 CTCGATTGTCTGGTAGCTCCT 58.972 52.381 0.00 0.00 37.07 3.69
502 6951 2.025155 TCTCGATTGTCTGGTAGCTCC 58.975 52.381 0.00 0.00 0.00 4.70
503 6952 2.423892 TGTCTCGATTGTCTGGTAGCTC 59.576 50.000 0.00 0.00 0.00 4.09
504 6953 2.425312 CTGTCTCGATTGTCTGGTAGCT 59.575 50.000 0.00 0.00 0.00 3.32
505 6954 2.164624 ACTGTCTCGATTGTCTGGTAGC 59.835 50.000 0.00 0.00 0.00 3.58
509 6960 3.066064 CCTCTACTGTCTCGATTGTCTGG 59.934 52.174 0.00 0.00 0.00 3.86
521 6972 3.306156 GGAAGACACCAACCTCTACTGTC 60.306 52.174 0.00 0.00 32.92 3.51
535 6986 2.159627 CACGTAAGCCATTGGAAGACAC 59.840 50.000 6.95 0.00 45.62 3.67
598 7370 1.602323 TTCTTGCAATTCGGCCGGT 60.602 52.632 27.83 12.19 0.00 5.28
614 7398 1.721133 CCGTTCTTTGCGTGCGTTC 60.721 57.895 0.00 0.00 0.00 3.95
627 7412 2.921126 GCATATGCATGTTAGCCGTTC 58.079 47.619 22.84 0.00 41.59 3.95
706 7524 0.037734 GTCCACGGGTTTTGGAGGAT 59.962 55.000 0.00 0.00 44.06 3.24
708 7526 0.466555 TTGTCCACGGGTTTTGGAGG 60.467 55.000 0.00 0.00 44.06 4.30
709 7527 1.394618 TTTGTCCACGGGTTTTGGAG 58.605 50.000 0.00 0.00 44.06 3.86
710 7528 2.074729 ATTTGTCCACGGGTTTTGGA 57.925 45.000 0.00 0.00 41.06 3.53
751 7592 3.695022 AACGGTCGGAATCGGCGAG 62.695 63.158 17.22 0.87 42.74 5.03
753 7594 2.795389 GAAACGGTCGGAATCGGCG 61.795 63.158 0.00 0.00 42.74 6.46
762 7603 1.535437 CGGATAAGAGGGAAACGGTCG 60.535 57.143 0.00 0.00 0.00 4.79
767 7608 0.532196 CGGGCGGATAAGAGGGAAAC 60.532 60.000 0.00 0.00 0.00 2.78
783 7624 1.523032 GGCGGATTTCTGTACCGGG 60.523 63.158 6.32 0.00 45.66 5.73
824 7667 3.447742 CTTGGTGTTGACCTTTTTGCTC 58.552 45.455 0.00 0.00 43.58 4.26
825 7668 2.418609 GCTTGGTGTTGACCTTTTTGCT 60.419 45.455 0.00 0.00 43.58 3.91
878 7722 7.594015 GGTATATATATACGCTTCCATTCCGTG 59.406 40.741 21.29 0.00 39.48 4.94
882 7726 8.347771 TCGTGGTATATATATACGCTTCCATTC 58.652 37.037 21.29 8.97 39.48 2.67
903 7779 1.219124 CACCTCCATCACCTCGTGG 59.781 63.158 0.99 0.99 39.83 4.94
915 7791 1.279271 AGAGTGTACAATGGCACCTCC 59.721 52.381 0.00 0.00 36.35 4.30
959 7835 3.375782 AACACAAGATCTTGCCTTTGC 57.624 42.857 30.95 0.00 44.03 3.68
968 7844 2.729882 GCGTACGTGAAACACAAGATCT 59.270 45.455 17.90 0.00 35.74 2.75
982 7876 2.164827 TCATCCTTGTGTATGCGTACGT 59.835 45.455 17.90 0.00 33.36 3.57
984 7878 4.430007 TCTTCATCCTTGTGTATGCGTAC 58.570 43.478 9.25 9.25 0.00 3.67
985 7879 4.729227 TCTTCATCCTTGTGTATGCGTA 57.271 40.909 0.00 0.00 0.00 4.42
991 7908 3.009033 CCACCCTTCTTCATCCTTGTGTA 59.991 47.826 0.00 0.00 0.00 2.90
1077 7994 1.324383 TGCAGTTCACGTAGAGGTCA 58.676 50.000 0.00 0.00 0.00 4.02
1197 8124 4.367023 CGGACAAGGCCGTCGGAA 62.367 66.667 17.49 0.00 46.07 4.30
1257 8184 1.153349 CTTCTTCGCTGCCCCTACC 60.153 63.158 0.00 0.00 0.00 3.18
1260 8187 2.665603 GTCTTCTTCGCTGCCCCT 59.334 61.111 0.00 0.00 0.00 4.79
1277 8204 2.584608 CCTGGCTAAGGTGGACCG 59.415 66.667 0.00 0.00 41.74 4.79
1374 8307 2.746277 GGACGTTTCAGCGGGCAT 60.746 61.111 0.00 0.00 35.98 4.40
1508 8441 2.525750 AGTTTTATCATGCGCGTGTG 57.474 45.000 27.72 14.58 0.00 3.82
1534 8467 2.671888 GGAGAGAACCGGTCGAAATTTC 59.328 50.000 8.04 8.20 0.00 2.17
1535 8468 2.614734 GGGAGAGAACCGGTCGAAATTT 60.615 50.000 8.04 0.00 0.00 1.82
1536 8469 1.066358 GGGAGAGAACCGGTCGAAATT 60.066 52.381 8.04 0.00 0.00 1.82
1537 8470 0.535797 GGGAGAGAACCGGTCGAAAT 59.464 55.000 8.04 0.00 0.00 2.17
1538 8471 1.538687 GGGGAGAGAACCGGTCGAAA 61.539 60.000 8.04 0.00 0.00 3.46
1539 8472 1.980772 GGGGAGAGAACCGGTCGAA 60.981 63.158 8.04 0.00 0.00 3.71
1540 8473 2.362120 GGGGAGAGAACCGGTCGA 60.362 66.667 8.04 0.00 0.00 4.20
1541 8474 3.459063 GGGGGAGAGAACCGGTCG 61.459 72.222 8.04 0.00 0.00 4.79
1542 8475 2.039137 AGGGGGAGAGAACCGGTC 59.961 66.667 8.04 0.95 0.00 4.79
1543 8476 2.039137 GAGGGGGAGAGAACCGGT 59.961 66.667 0.00 0.00 0.00 5.28
1544 8477 1.306226 AAGAGGGGGAGAGAACCGG 60.306 63.158 0.00 0.00 0.00 5.28
1545 8478 0.614979 TCAAGAGGGGGAGAGAACCG 60.615 60.000 0.00 0.00 0.00 4.44
1546 8479 1.886422 ATCAAGAGGGGGAGAGAACC 58.114 55.000 0.00 0.00 0.00 3.62
1547 8480 4.034410 AGTAATCAAGAGGGGGAGAGAAC 58.966 47.826 0.00 0.00 0.00 3.01
1548 8481 4.354208 AGTAATCAAGAGGGGGAGAGAA 57.646 45.455 0.00 0.00 0.00 2.87
1549 8482 4.016105 AGAAGTAATCAAGAGGGGGAGAGA 60.016 45.833 0.00 0.00 0.00 3.10
1550 8483 4.294347 AGAAGTAATCAAGAGGGGGAGAG 58.706 47.826 0.00 0.00 0.00 3.20
1551 8484 4.354208 AGAAGTAATCAAGAGGGGGAGA 57.646 45.455 0.00 0.00 0.00 3.71
1552 8485 4.226168 ACAAGAAGTAATCAAGAGGGGGAG 59.774 45.833 0.00 0.00 0.00 4.30
1553 8486 4.175962 ACAAGAAGTAATCAAGAGGGGGA 58.824 43.478 0.00 0.00 0.00 4.81
1554 8487 4.576330 ACAAGAAGTAATCAAGAGGGGG 57.424 45.455 0.00 0.00 0.00 5.40
1555 8488 5.412904 GTCAACAAGAAGTAATCAAGAGGGG 59.587 44.000 0.00 0.00 0.00 4.79
1556 8489 5.997746 TGTCAACAAGAAGTAATCAAGAGGG 59.002 40.000 0.00 0.00 0.00 4.30
1557 8490 6.931281 TCTGTCAACAAGAAGTAATCAAGAGG 59.069 38.462 0.00 0.00 0.00 3.69
1558 8491 7.953158 TCTGTCAACAAGAAGTAATCAAGAG 57.047 36.000 0.00 0.00 0.00 2.85
1559 8492 8.908786 AATCTGTCAACAAGAAGTAATCAAGA 57.091 30.769 0.00 0.00 0.00 3.02
1560 8493 9.604626 GAAATCTGTCAACAAGAAGTAATCAAG 57.395 33.333 0.00 0.00 0.00 3.02
1561 8494 9.342308 AGAAATCTGTCAACAAGAAGTAATCAA 57.658 29.630 0.00 0.00 0.00 2.57
1562 8495 8.908786 AGAAATCTGTCAACAAGAAGTAATCA 57.091 30.769 0.00 0.00 0.00 2.57
1626 8559 4.205588 GTCGTTTGGTGGTTTCGAAATTTC 59.794 41.667 14.69 8.20 32.56 2.17
1627 8560 4.106909 GTCGTTTGGTGGTTTCGAAATTT 58.893 39.130 14.69 0.00 32.56 1.82
1628 8561 3.489568 GGTCGTTTGGTGGTTTCGAAATT 60.490 43.478 14.69 0.00 32.56 1.82
1629 8562 2.033675 GGTCGTTTGGTGGTTTCGAAAT 59.966 45.455 14.69 0.00 32.56 2.17
1630 8563 1.401199 GGTCGTTTGGTGGTTTCGAAA 59.599 47.619 6.47 6.47 32.56 3.46
1631 8564 1.015868 GGTCGTTTGGTGGTTTCGAA 58.984 50.000 0.00 0.00 32.56 3.71
1632 8565 0.107800 TGGTCGTTTGGTGGTTTCGA 60.108 50.000 0.00 0.00 0.00 3.71
1633 8566 0.948678 ATGGTCGTTTGGTGGTTTCG 59.051 50.000 0.00 0.00 0.00 3.46
1634 8567 3.067601 AGAAATGGTCGTTTGGTGGTTTC 59.932 43.478 0.00 0.00 0.00 2.78
1635 8568 3.028130 AGAAATGGTCGTTTGGTGGTTT 58.972 40.909 0.00 0.00 0.00 3.27
1636 8569 2.621526 GAGAAATGGTCGTTTGGTGGTT 59.378 45.455 0.00 0.00 0.00 3.67
1637 8570 2.158667 AGAGAAATGGTCGTTTGGTGGT 60.159 45.455 0.00 0.00 0.00 4.16
1638 8571 2.504367 AGAGAAATGGTCGTTTGGTGG 58.496 47.619 0.00 0.00 0.00 4.61
1639 8572 5.178797 AGATAGAGAAATGGTCGTTTGGTG 58.821 41.667 0.00 0.00 0.00 4.17
1640 8573 5.422214 AGATAGAGAAATGGTCGTTTGGT 57.578 39.130 0.00 0.00 0.00 3.67
1641 8574 6.183360 GGAAAGATAGAGAAATGGTCGTTTGG 60.183 42.308 0.00 0.00 0.00 3.28
1642 8575 6.595716 AGGAAAGATAGAGAAATGGTCGTTTG 59.404 38.462 0.00 0.00 0.00 2.93
1643 8576 6.712276 AGGAAAGATAGAGAAATGGTCGTTT 58.288 36.000 0.00 0.00 0.00 3.60
1644 8577 6.155393 AGAGGAAAGATAGAGAAATGGTCGTT 59.845 38.462 0.00 0.00 0.00 3.85
1645 8578 5.659079 AGAGGAAAGATAGAGAAATGGTCGT 59.341 40.000 0.00 0.00 0.00 4.34
1646 8579 6.155475 AGAGGAAAGATAGAGAAATGGTCG 57.845 41.667 0.00 0.00 0.00 4.79
1647 8580 9.088987 AGATAGAGGAAAGATAGAGAAATGGTC 57.911 37.037 0.00 0.00 0.00 4.02
1648 8581 9.088987 GAGATAGAGGAAAGATAGAGAAATGGT 57.911 37.037 0.00 0.00 0.00 3.55
1649 8582 9.312904 AGAGATAGAGGAAAGATAGAGAAATGG 57.687 37.037 0.00 0.00 0.00 3.16
1829 8767 3.814842 GCAGCAAAAATTAGGGCAGTTTT 59.185 39.130 0.00 0.00 0.00 2.43
1853 8791 5.291128 ACGGACGATTTTTACAGACATGATC 59.709 40.000 0.00 0.00 0.00 2.92
2042 8980 2.494073 TCACGTAGGTATGCACACATGA 59.506 45.455 0.00 0.00 37.04 3.07
2106 9075 2.025155 ACGATAGACACGAGCCAAGAT 58.975 47.619 0.00 0.00 41.38 2.40
2300 9273 0.807667 CTCTCCATGCGTACACTGCC 60.808 60.000 0.00 0.00 0.00 4.85
2323 9296 1.093159 CAAGGCAGAGAATCCACAGC 58.907 55.000 0.00 0.00 33.66 4.40
2324 9297 1.093159 GCAAGGCAGAGAATCCACAG 58.907 55.000 0.00 0.00 33.66 3.66
2325 9298 0.694771 AGCAAGGCAGAGAATCCACA 59.305 50.000 0.00 0.00 33.66 4.17
2326 9299 1.093159 CAGCAAGGCAGAGAATCCAC 58.907 55.000 0.00 0.00 33.66 4.02
2327 9300 0.694771 ACAGCAAGGCAGAGAATCCA 59.305 50.000 0.00 0.00 33.66 3.41
2328 9301 1.093159 CACAGCAAGGCAGAGAATCC 58.907 55.000 0.00 0.00 33.66 3.01
2329 9302 1.093159 CCACAGCAAGGCAGAGAATC 58.907 55.000 0.00 0.00 0.00 2.52
2330 9303 3.261250 CCACAGCAAGGCAGAGAAT 57.739 52.632 0.00 0.00 0.00 2.40
2331 9304 4.806936 CCACAGCAAGGCAGAGAA 57.193 55.556 0.00 0.00 0.00 2.87
2342 9315 1.584380 CTCTCTGCCTTTGCCACAGC 61.584 60.000 0.00 0.00 40.48 4.40
2343 9316 0.959372 CCTCTCTGCCTTTGCCACAG 60.959 60.000 0.00 0.00 36.33 3.66
2344 9317 1.073722 CCTCTCTGCCTTTGCCACA 59.926 57.895 0.00 0.00 36.33 4.17
2345 9318 0.250901 TTCCTCTCTGCCTTTGCCAC 60.251 55.000 0.00 0.00 36.33 5.01
2346 9319 0.250901 GTTCCTCTCTGCCTTTGCCA 60.251 55.000 0.00 0.00 36.33 4.92
2347 9320 0.250901 TGTTCCTCTCTGCCTTTGCC 60.251 55.000 0.00 0.00 36.33 4.52
2348 9321 1.163554 CTGTTCCTCTCTGCCTTTGC 58.836 55.000 0.00 0.00 38.26 3.68
2349 9322 2.149578 CACTGTTCCTCTCTGCCTTTG 58.850 52.381 0.00 0.00 0.00 2.77
2350 9323 1.544314 GCACTGTTCCTCTCTGCCTTT 60.544 52.381 0.00 0.00 0.00 3.11
2351 9324 0.036022 GCACTGTTCCTCTCTGCCTT 59.964 55.000 0.00 0.00 0.00 4.35
2352 9325 1.676384 GCACTGTTCCTCTCTGCCT 59.324 57.895 0.00 0.00 0.00 4.75
2353 9326 1.376553 GGCACTGTTCCTCTCTGCC 60.377 63.158 0.00 0.00 40.68 4.85
2354 9327 0.390998 GAGGCACTGTTCCTCTCTGC 60.391 60.000 17.67 0.00 45.13 4.26
2355 9328 3.830679 GAGGCACTGTTCCTCTCTG 57.169 57.895 17.67 0.00 45.13 3.35
2358 9331 1.077993 AGGTAGAGGCACTGTTCCTCT 59.922 52.381 27.71 27.71 45.96 3.69
2359 9332 1.562783 AGGTAGAGGCACTGTTCCTC 58.437 55.000 17.31 17.31 45.96 3.71
2360 9333 3.796866 AGGTAGAGGCACTGTTCCT 57.203 52.632 0.00 0.00 44.28 3.36
2361 9334 2.615747 GGAAAGGTAGAGGCACTGTTCC 60.616 54.545 0.00 0.00 41.55 3.62
2362 9335 2.303311 AGGAAAGGTAGAGGCACTGTTC 59.697 50.000 0.00 0.00 41.55 3.18
2363 9336 2.303311 GAGGAAAGGTAGAGGCACTGTT 59.697 50.000 0.00 0.00 41.55 3.16
2364 9337 1.903183 GAGGAAAGGTAGAGGCACTGT 59.097 52.381 0.00 0.00 41.55 3.55
2365 9338 2.183679 AGAGGAAAGGTAGAGGCACTG 58.816 52.381 0.00 0.00 41.55 3.66
2367 9340 3.367321 AGTAGAGGAAAGGTAGAGGCAC 58.633 50.000 0.00 0.00 0.00 5.01
2368 9341 3.759815 AGTAGAGGAAAGGTAGAGGCA 57.240 47.619 0.00 0.00 0.00 4.75
2369 9342 5.423704 AAAAGTAGAGGAAAGGTAGAGGC 57.576 43.478 0.00 0.00 0.00 4.70
2370 9343 7.415429 CGACTAAAAGTAGAGGAAAGGTAGAGG 60.415 44.444 0.00 0.00 0.00 3.69
2371 9344 7.121020 ACGACTAAAAGTAGAGGAAAGGTAGAG 59.879 40.741 0.00 0.00 0.00 2.43
2372 9345 6.944862 ACGACTAAAAGTAGAGGAAAGGTAGA 59.055 38.462 0.00 0.00 0.00 2.59
2373 9346 7.155655 ACGACTAAAAGTAGAGGAAAGGTAG 57.844 40.000 0.00 0.00 0.00 3.18
2374 9347 7.373493 CAACGACTAAAAGTAGAGGAAAGGTA 58.627 38.462 0.00 0.00 0.00 3.08
2375 9348 6.221659 CAACGACTAAAAGTAGAGGAAAGGT 58.778 40.000 0.00 0.00 0.00 3.50
2376 9349 5.638234 CCAACGACTAAAAGTAGAGGAAAGG 59.362 44.000 0.00 0.00 0.00 3.11
2377 9350 6.453092 TCCAACGACTAAAAGTAGAGGAAAG 58.547 40.000 0.00 0.00 30.88 2.62
2378 9351 6.409524 TCCAACGACTAAAAGTAGAGGAAA 57.590 37.500 0.00 0.00 30.88 3.13
2379 9352 6.600882 ATCCAACGACTAAAAGTAGAGGAA 57.399 37.500 0.00 0.00 34.59 3.36
2380 9353 6.209986 TCAATCCAACGACTAAAAGTAGAGGA 59.790 38.462 0.00 7.89 35.03 3.71
2381 9354 6.395629 TCAATCCAACGACTAAAAGTAGAGG 58.604 40.000 0.00 0.00 0.00 3.69
2382 9355 7.313646 TCTCAATCCAACGACTAAAAGTAGAG 58.686 38.462 0.00 0.00 0.00 2.43
2383 9356 7.223260 TCTCAATCCAACGACTAAAAGTAGA 57.777 36.000 0.00 0.00 0.00 2.59
2384 9357 7.884816 TTCTCAATCCAACGACTAAAAGTAG 57.115 36.000 0.00 0.00 0.00 2.57
2385 9358 7.333423 CCATTCTCAATCCAACGACTAAAAGTA 59.667 37.037 0.00 0.00 0.00 2.24
2386 9359 6.149474 CCATTCTCAATCCAACGACTAAAAGT 59.851 38.462 0.00 0.00 0.00 2.66
2387 9360 6.371548 TCCATTCTCAATCCAACGACTAAAAG 59.628 38.462 0.00 0.00 0.00 2.27
2388 9361 6.148811 GTCCATTCTCAATCCAACGACTAAAA 59.851 38.462 0.00 0.00 0.00 1.52
2389 9362 5.642063 GTCCATTCTCAATCCAACGACTAAA 59.358 40.000 0.00 0.00 0.00 1.85
2390 9363 5.175859 GTCCATTCTCAATCCAACGACTAA 58.824 41.667 0.00 0.00 0.00 2.24
2391 9364 4.382685 GGTCCATTCTCAATCCAACGACTA 60.383 45.833 0.00 0.00 0.00 2.59
2392 9365 3.600388 GTCCATTCTCAATCCAACGACT 58.400 45.455 0.00 0.00 0.00 4.18
2393 9366 2.678336 GGTCCATTCTCAATCCAACGAC 59.322 50.000 0.00 0.00 0.00 4.34
2394 9367 2.676750 CGGTCCATTCTCAATCCAACGA 60.677 50.000 0.00 0.00 0.00 3.85
2395 9368 1.665679 CGGTCCATTCTCAATCCAACG 59.334 52.381 0.00 0.00 0.00 4.10
2396 9369 1.401905 GCGGTCCATTCTCAATCCAAC 59.598 52.381 0.00 0.00 0.00 3.77
2397 9370 1.681780 GGCGGTCCATTCTCAATCCAA 60.682 52.381 0.00 0.00 0.00 3.53
2398 9371 0.107214 GGCGGTCCATTCTCAATCCA 60.107 55.000 0.00 0.00 0.00 3.41
2399 9372 0.819666 GGGCGGTCCATTCTCAATCC 60.820 60.000 0.00 0.00 35.00 3.01
2400 9373 0.107214 TGGGCGGTCCATTCTCAATC 60.107 55.000 0.00 0.00 41.46 2.67
2401 9374 0.107017 CTGGGCGGTCCATTCTCAAT 60.107 55.000 0.00 0.00 46.01 2.57
2402 9375 1.198094 TCTGGGCGGTCCATTCTCAA 61.198 55.000 0.00 0.00 46.01 3.02
2403 9376 0.982852 ATCTGGGCGGTCCATTCTCA 60.983 55.000 0.00 0.00 46.01 3.27
2404 9377 0.181350 AATCTGGGCGGTCCATTCTC 59.819 55.000 0.00 0.00 46.01 2.87
2405 9378 0.625849 AAATCTGGGCGGTCCATTCT 59.374 50.000 0.00 0.00 46.01 2.40
2406 9379 0.740737 CAAATCTGGGCGGTCCATTC 59.259 55.000 0.00 0.00 46.01 2.67
2407 9380 0.684153 CCAAATCTGGGCGGTCCATT 60.684 55.000 0.00 0.00 46.01 3.16
2408 9381 1.076777 CCAAATCTGGGCGGTCCAT 60.077 57.895 0.00 0.00 46.01 3.41
2409 9382 2.354729 CCAAATCTGGGCGGTCCA 59.645 61.111 0.00 0.00 44.79 4.02
2410 9383 3.140814 GCCAAATCTGGGCGGTCC 61.141 66.667 0.00 0.00 43.74 4.46
2416 9389 1.213537 CTGTTGCGCCAAATCTGGG 59.786 57.895 4.18 0.00 43.74 4.45
2417 9390 1.213537 CCTGTTGCGCCAAATCTGG 59.786 57.895 4.18 0.57 46.65 3.86
2418 9391 0.109597 GTCCTGTTGCGCCAAATCTG 60.110 55.000 4.18 0.00 0.00 2.90
2419 9392 1.244019 GGTCCTGTTGCGCCAAATCT 61.244 55.000 4.18 0.00 0.00 2.40
2420 9393 1.212751 GGTCCTGTTGCGCCAAATC 59.787 57.895 4.18 0.00 0.00 2.17
2421 9394 1.530419 TGGTCCTGTTGCGCCAAAT 60.530 52.632 4.18 0.00 0.00 2.32
2422 9395 2.124109 TGGTCCTGTTGCGCCAAA 60.124 55.556 4.18 0.00 0.00 3.28
2423 9396 2.904866 GTGGTCCTGTTGCGCCAA 60.905 61.111 4.18 0.00 32.26 4.52
2424 9397 3.872603 AGTGGTCCTGTTGCGCCA 61.873 61.111 4.18 0.00 0.00 5.69
2425 9398 3.357079 CAGTGGTCCTGTTGCGCC 61.357 66.667 4.18 0.00 36.37 6.53
2426 9399 1.444119 TTTCAGTGGTCCTGTTGCGC 61.444 55.000 0.00 0.00 42.19 6.09
2427 9400 1.021202 TTTTCAGTGGTCCTGTTGCG 58.979 50.000 0.00 0.00 42.19 4.85
2428 9401 1.748493 TGTTTTCAGTGGTCCTGTTGC 59.252 47.619 0.00 0.00 42.19 4.17
2429 9402 3.698029 CTGTTTTCAGTGGTCCTGTTG 57.302 47.619 0.00 0.00 42.19 3.33
2441 9414 7.095816 CGTGTACTGTTCATATCACTGTTTTCA 60.096 37.037 0.00 0.00 0.00 2.69
2442 9415 7.115805 TCGTGTACTGTTCATATCACTGTTTTC 59.884 37.037 0.00 0.00 0.00 2.29
2443 9416 6.926826 TCGTGTACTGTTCATATCACTGTTTT 59.073 34.615 0.00 0.00 0.00 2.43
2444 9417 6.452242 TCGTGTACTGTTCATATCACTGTTT 58.548 36.000 0.00 0.00 0.00 2.83
2445 9418 6.020971 TCGTGTACTGTTCATATCACTGTT 57.979 37.500 0.00 0.00 0.00 3.16
2446 9419 5.638596 TCGTGTACTGTTCATATCACTGT 57.361 39.130 0.00 1.20 0.00 3.55
2447 9420 4.500837 GCTCGTGTACTGTTCATATCACTG 59.499 45.833 0.00 0.00 0.00 3.66
2448 9421 4.399618 AGCTCGTGTACTGTTCATATCACT 59.600 41.667 0.00 0.00 0.00 3.41
2449 9422 4.673441 AGCTCGTGTACTGTTCATATCAC 58.327 43.478 0.00 0.00 0.00 3.06
2450 9423 4.983671 AGCTCGTGTACTGTTCATATCA 57.016 40.909 0.00 0.00 0.00 2.15
2451 9424 5.817988 TGTAGCTCGTGTACTGTTCATATC 58.182 41.667 0.00 0.00 0.00 1.63
2452 9425 5.830000 TGTAGCTCGTGTACTGTTCATAT 57.170 39.130 0.00 0.00 0.00 1.78
2453 9426 5.632244 TTGTAGCTCGTGTACTGTTCATA 57.368 39.130 0.00 0.00 0.00 2.15
2454 9427 4.514781 TTGTAGCTCGTGTACTGTTCAT 57.485 40.909 0.00 0.00 0.00 2.57
2455 9428 3.994204 TTGTAGCTCGTGTACTGTTCA 57.006 42.857 0.00 0.00 0.00 3.18
2456 9429 4.235360 ACATTGTAGCTCGTGTACTGTTC 58.765 43.478 0.00 0.00 0.00 3.18
2457 9430 4.252971 ACATTGTAGCTCGTGTACTGTT 57.747 40.909 0.00 0.00 0.00 3.16
2458 9431 3.936372 ACATTGTAGCTCGTGTACTGT 57.064 42.857 0.00 0.00 0.00 3.55
2459 9432 3.987868 ACAACATTGTAGCTCGTGTACTG 59.012 43.478 0.00 0.00 40.16 2.74
2460 9433 4.252971 ACAACATTGTAGCTCGTGTACT 57.747 40.909 0.00 0.00 40.16 2.73
2461 9434 5.803461 TCATACAACATTGTAGCTCGTGTAC 59.197 40.000 10.09 0.00 45.80 2.90
2462 9435 5.956642 TCATACAACATTGTAGCTCGTGTA 58.043 37.500 10.09 0.00 45.80 2.90
2463 9436 4.816392 TCATACAACATTGTAGCTCGTGT 58.184 39.130 10.09 0.00 45.80 4.49
2464 9437 5.120053 TGTTCATACAACATTGTAGCTCGTG 59.880 40.000 10.09 3.91 45.80 4.35
2465 9438 5.234752 TGTTCATACAACATTGTAGCTCGT 58.765 37.500 10.09 0.00 45.80 4.18
2466 9439 5.348724 ACTGTTCATACAACATTGTAGCTCG 59.651 40.000 10.09 0.39 45.80 5.03
2467 9440 6.537566 CACTGTTCATACAACATTGTAGCTC 58.462 40.000 10.09 2.68 45.80 4.09
2468 9441 5.106555 GCACTGTTCATACAACATTGTAGCT 60.107 40.000 10.09 0.00 45.80 3.32
2469 9442 5.088739 GCACTGTTCATACAACATTGTAGC 58.911 41.667 10.09 2.54 45.80 3.58
2470 9443 6.239908 TGCACTGTTCATACAACATTGTAG 57.760 37.500 10.09 0.48 45.80 2.74
2471 9444 6.816134 ATGCACTGTTCATACAACATTGTA 57.184 33.333 6.92 6.92 46.55 2.41
2472 9445 5.710513 ATGCACTGTTCATACAACATTGT 57.289 34.783 2.32 2.32 44.86 2.71


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

AutoCloner maintained by Alex Coulton.