Multiple sequence alignment - TraesCS3D01G316400

Loading Multiple Alignment...

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 TraesCS3D01G316400 chr3D 100.000 5572 0 0 1 5572 429629325 429634896 0.000000e+00 10290
1 TraesCS3D01G316400 chr3B 92.133 2682 156 26 670 3306 561568406 561571077 0.000000e+00 3733
2 TraesCS3D01G316400 chr3B 93.480 1365 61 11 3307 4653 561590433 561591787 0.000000e+00 2002
3 TraesCS3D01G316400 chr3B 95.833 480 18 1 131 608 561567929 561568408 0.000000e+00 774
4 TraesCS3D01G316400 chr3B 83.077 390 37 13 4909 5294 615297989 615297625 1.500000e-85 327
5 TraesCS3D01G316400 chr3B 91.905 210 9 3 4461 4670 561695145 561695346 2.540000e-73 287
6 TraesCS3D01G316400 chr3B 94.792 96 1 2 1 92 561567845 561567940 4.500000e-31 147
7 TraesCS3D01G316400 chr3A 90.186 2629 174 36 757 3306 556360671 556358048 0.000000e+00 3349
8 TraesCS3D01G316400 chr3A 94.105 1374 55 11 3307 4666 556356322 556354961 0.000000e+00 2065
9 TraesCS3D01G316400 chr3A 88.660 582 53 11 4998 5572 24773989 24773414 0.000000e+00 697
10 TraesCS3D01G316400 chr3A 82.186 494 51 22 4666 5127 213778811 213779299 1.880000e-104 390
11 TraesCS3D01G316400 chr3A 84.848 231 30 5 2528 2756 144472417 144472644 1.560000e-55 228
12 TraesCS3D01G316400 chr7D 92.451 914 40 16 4666 5572 453106593 453105702 0.000000e+00 1279
13 TraesCS3D01G316400 chr6D 92.105 912 53 11 4666 5572 3594754 3593857 0.000000e+00 1267
14 TraesCS3D01G316400 chr6D 87.446 231 24 5 2528 2756 429164259 429164032 1.540000e-65 261
15 TraesCS3D01G316400 chr7B 88.553 926 87 13 4660 5572 745225351 745224432 0.000000e+00 1105
16 TraesCS3D01G316400 chr7B 83.406 229 27 6 2528 2754 709784617 709784398 9.470000e-48 202
17 TraesCS3D01G316400 chr2B 86.681 916 94 17 4666 5572 500186327 500185431 0.000000e+00 990
18 TraesCS3D01G316400 chr2A 90.191 734 55 10 4847 5572 718134536 718135260 0.000000e+00 941
19 TraesCS3D01G316400 chr2A 87.184 593 51 15 4666 5250 760309565 760310140 0.000000e+00 651
20 TraesCS3D01G316400 chr1D 87.338 616 64 11 4908 5514 415985613 415985003 0.000000e+00 693
21 TraesCS3D01G316400 chr1D 83.631 336 36 9 2528 2859 1851716 1852036 1.170000e-76 298
22 TraesCS3D01G316400 chr1B 87.197 578 54 10 4680 5250 4081525 4082089 1.690000e-179 640
23 TraesCS3D01G316400 chr1B 84.682 346 34 11 4797 5131 603277346 603277009 1.500000e-85 327
24 TraesCS3D01G316400 chr6A 85.854 410 48 9 2528 2934 37838387 37838789 1.430000e-115 427
25 TraesCS3D01G316400 chr5B 80.103 387 39 18 3685 4070 441129501 441129850 2.580000e-63 254
26 TraesCS3D01G316400 chr6B 81.879 298 50 4 4664 4958 77895203 77895499 1.200000e-61 248
27 TraesCS3D01G316400 chr6B 81.000 300 53 4 4662 4958 77996791 77997089 9.330000e-58 235


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 TraesCS3D01G316400 chr3D 429629325 429634896 5571 False 10290.000000 10290 100.000000 1 5572 1 chr3D.!!$F1 5571
1 TraesCS3D01G316400 chr3B 561590433 561591787 1354 False 2002.000000 2002 93.480000 3307 4653 1 chr3B.!!$F1 1346
2 TraesCS3D01G316400 chr3B 561567845 561571077 3232 False 1551.333333 3733 94.252667 1 3306 3 chr3B.!!$F3 3305
3 TraesCS3D01G316400 chr3A 556354961 556360671 5710 True 2707.000000 3349 92.145500 757 4666 2 chr3A.!!$R2 3909
4 TraesCS3D01G316400 chr3A 24773414 24773989 575 True 697.000000 697 88.660000 4998 5572 1 chr3A.!!$R1 574
5 TraesCS3D01G316400 chr7D 453105702 453106593 891 True 1279.000000 1279 92.451000 4666 5572 1 chr7D.!!$R1 906
6 TraesCS3D01G316400 chr6D 3593857 3594754 897 True 1267.000000 1267 92.105000 4666 5572 1 chr6D.!!$R1 906
7 TraesCS3D01G316400 chr7B 745224432 745225351 919 True 1105.000000 1105 88.553000 4660 5572 1 chr7B.!!$R2 912
8 TraesCS3D01G316400 chr2B 500185431 500186327 896 True 990.000000 990 86.681000 4666 5572 1 chr2B.!!$R1 906
9 TraesCS3D01G316400 chr2A 718134536 718135260 724 False 941.000000 941 90.191000 4847 5572 1 chr2A.!!$F1 725
10 TraesCS3D01G316400 chr2A 760309565 760310140 575 False 651.000000 651 87.184000 4666 5250 1 chr2A.!!$F2 584
11 TraesCS3D01G316400 chr1D 415985003 415985613 610 True 693.000000 693 87.338000 4908 5514 1 chr1D.!!$R1 606
12 TraesCS3D01G316400 chr1B 4081525 4082089 564 False 640.000000 640 87.197000 4680 5250 1 chr1B.!!$F1 570

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
220 221 0.178068 TTCCATAGCCCAACTCGAGC 59.822 55.000 13.61 0.0 0.0 5.03 F
548 551 0.608308 TGGACGAGAAAGGAGCGAGA 60.608 55.000 0.00 0.0 0.0 4.04 F
1575 1612 1.068741 CCAGTACAGGATAAGTCGGGC 59.931 57.143 0.00 0.0 0.0 6.13 F
1686 1729 0.464554 GGGAGGCTGCAATACTGGAC 60.465 60.000 8.68 0.0 0.0 4.02 F
2042 2088 0.472925 TACACTCCCAACCCTGCTGA 60.473 55.000 0.00 0.0 0.0 4.26 F
3403 5222 0.770499 TTGACACAATGCTCCAGGGA 59.230 50.000 0.00 0.0 0.0 4.20 F
3831 5652 0.613012 GGGACCTGAAGCCAAGCAAT 60.613 55.000 0.00 0.0 0.0 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1612 1649 0.319405 GAGCTGCCTGTGCCATTTTT 59.681 50.00 0.00 0.00 36.33 1.94 R
1649 1692 0.326048 CCTGTCCCTCACTCCCATCT 60.326 60.00 0.00 0.00 0.00 2.90 R
3268 3351 0.516877 TTTGCCGAACTGCTTGATCG 59.483 50.00 3.78 3.78 40.07 3.69 R
3384 5203 0.770499 TCCCTGGAGCATTGTGTCAA 59.230 50.00 0.00 0.00 0.00 3.18 R
3523 5342 1.055849 TGCAGCAACCTAAGAGTCCA 58.944 50.00 0.00 0.00 0.00 4.02 R
4464 6290 2.287393 ACGAAACCAGGTTGTTTTGC 57.713 45.00 5.30 0.00 41.39 3.68 R
5439 7287 3.794028 TGTTAGTGTTCAAAAATGCGTGC 59.206 39.13 0.00 0.00 0.00 5.34 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
47 48 3.074412 GACGTCATTTCCCAGTGAATGT 58.926 45.455 11.55 0.00 31.67 2.71
66 67 8.388103 GTGAATGTATGTACTTGTATGTTCACC 58.612 37.037 0.00 0.00 37.06 4.02
68 69 9.162764 GAATGTATGTACTTGTATGTTCACCTT 57.837 33.333 0.00 0.00 0.00 3.50
124 125 8.822805 AGTGTAATAGGGTTCTTTATTCAGTCA 58.177 33.333 0.00 0.00 0.00 3.41
125 126 9.444600 GTGTAATAGGGTTCTTTATTCAGTCAA 57.555 33.333 0.00 0.00 0.00 3.18
164 165 1.752501 CGAGCTGCGGTATTCGTTGG 61.753 60.000 0.00 0.00 41.72 3.77
195 196 2.076100 CTTCATACGAACCAGCTGCAA 58.924 47.619 8.66 0.00 0.00 4.08
201 202 0.877071 CGAACCAGCTGCAACAGAAT 59.123 50.000 8.66 0.00 32.44 2.40
220 221 0.178068 TTCCATAGCCCAACTCGAGC 59.822 55.000 13.61 0.00 0.00 5.03
227 228 2.269241 CCAACTCGAGCCCCTTCC 59.731 66.667 13.61 0.00 0.00 3.46
234 235 2.360585 GAGCCCCTTCCCCTTTGG 59.639 66.667 0.00 0.00 0.00 3.28
236 237 3.997952 GCCCCTTCCCCTTTGGCT 61.998 66.667 0.00 0.00 39.05 4.75
323 326 2.393768 CGATTTCCGCTGCACTGCT 61.394 57.895 1.98 0.00 0.00 4.24
384 387 2.672307 AACTCCGGAGCGTCGTCT 60.672 61.111 31.56 7.06 0.00 4.18
410 413 1.000955 CTACAGTTCGAACCTGGTGCT 59.999 52.381 24.22 9.37 0.00 4.40
462 465 9.547753 TGTTAGAGATTCTTGGCTTATTATGTC 57.452 33.333 0.00 0.00 0.00 3.06
466 469 6.904626 AGATTCTTGGCTTATTATGTCTGGT 58.095 36.000 0.00 0.00 0.00 4.00
489 492 7.065085 TGGTTTTCCATAATTTTGTGTGTTGTG 59.935 33.333 0.00 0.00 46.22 3.33
533 536 1.135112 GCAAAAATGGGGTCGATGGAC 60.135 52.381 0.00 0.00 42.66 4.02
548 551 0.608308 TGGACGAGAAAGGAGCGAGA 60.608 55.000 0.00 0.00 0.00 4.04
554 557 1.402259 GAGAAAGGAGCGAGATCACGA 59.598 52.381 17.02 0.00 35.09 4.35
565 568 2.687566 ATCACGACACCCCTCCCC 60.688 66.667 0.00 0.00 0.00 4.81
596 599 4.006319 CCAGTCCTCCACTCATTTTCTTC 58.994 47.826 0.00 0.00 30.26 2.87
608 611 4.464008 TCATTTTCTTCTGGAAGTGCTGT 58.536 39.130 9.73 0.00 39.38 4.40
609 612 4.889409 TCATTTTCTTCTGGAAGTGCTGTT 59.111 37.500 9.73 0.00 39.38 3.16
611 614 6.716628 TCATTTTCTTCTGGAAGTGCTGTTAT 59.283 34.615 9.73 0.00 39.38 1.89
614 617 5.489792 TCTTCTGGAAGTGCTGTTATTCT 57.510 39.130 9.73 0.00 39.38 2.40
616 619 5.934625 TCTTCTGGAAGTGCTGTTATTCTTC 59.065 40.000 9.73 0.00 39.38 2.87
617 620 5.489792 TCTGGAAGTGCTGTTATTCTTCT 57.510 39.130 0.00 0.00 37.18 2.85
618 621 5.240891 TCTGGAAGTGCTGTTATTCTTCTG 58.759 41.667 0.00 0.00 37.18 3.02
619 622 4.326826 TGGAAGTGCTGTTATTCTTCTGG 58.673 43.478 0.00 0.00 37.18 3.86
620 623 4.041567 TGGAAGTGCTGTTATTCTTCTGGA 59.958 41.667 0.00 0.00 37.18 3.86
621 624 4.633565 GGAAGTGCTGTTATTCTTCTGGAG 59.366 45.833 0.00 0.00 37.18 3.86
622 625 5.482908 GAAGTGCTGTTATTCTTCTGGAGA 58.517 41.667 0.00 0.00 35.06 3.71
624 627 5.869579 AGTGCTGTTATTCTTCTGGAGAAA 58.130 37.500 1.83 0.00 46.90 2.52
625 628 6.299141 AGTGCTGTTATTCTTCTGGAGAAAA 58.701 36.000 1.83 0.00 46.90 2.29
626 629 6.944862 AGTGCTGTTATTCTTCTGGAGAAAAT 59.055 34.615 1.83 0.00 46.90 1.82
627 630 8.103305 AGTGCTGTTATTCTTCTGGAGAAAATA 58.897 33.333 1.83 0.00 46.90 1.40
628 631 8.178313 GTGCTGTTATTCTTCTGGAGAAAATAC 58.822 37.037 1.83 2.47 46.90 1.89
629 632 8.103305 TGCTGTTATTCTTCTGGAGAAAATACT 58.897 33.333 1.83 0.00 46.90 2.12
630 633 8.394121 GCTGTTATTCTTCTGGAGAAAATACTG 58.606 37.037 1.83 6.61 46.90 2.74
631 634 9.442047 CTGTTATTCTTCTGGAGAAAATACTGT 57.558 33.333 1.83 0.00 46.90 3.55
632 635 9.793259 TGTTATTCTTCTGGAGAAAATACTGTT 57.207 29.630 1.83 0.00 46.90 3.16
654 657 3.823369 TTTTTGCGGGGTGGAGTAA 57.177 47.368 0.00 0.00 0.00 2.24
655 658 2.068834 TTTTTGCGGGGTGGAGTAAA 57.931 45.000 0.00 0.00 0.00 2.01
656 659 2.296073 TTTTGCGGGGTGGAGTAAAT 57.704 45.000 0.00 0.00 0.00 1.40
657 660 3.436577 TTTTGCGGGGTGGAGTAAATA 57.563 42.857 0.00 0.00 0.00 1.40
658 661 2.406596 TTGCGGGGTGGAGTAAATAC 57.593 50.000 0.00 0.00 0.00 1.89
659 662 1.575419 TGCGGGGTGGAGTAAATACT 58.425 50.000 0.00 0.00 39.71 2.12
660 663 1.208535 TGCGGGGTGGAGTAAATACTG 59.791 52.381 0.00 0.00 36.50 2.74
661 664 1.208776 GCGGGGTGGAGTAAATACTGT 59.791 52.381 0.00 0.00 36.50 3.55
662 665 2.355412 GCGGGGTGGAGTAAATACTGTT 60.355 50.000 0.00 0.00 36.50 3.16
663 666 3.118665 GCGGGGTGGAGTAAATACTGTTA 60.119 47.826 0.00 0.00 36.50 2.41
664 667 4.443881 GCGGGGTGGAGTAAATACTGTTAT 60.444 45.833 0.00 0.00 36.50 1.89
665 668 5.677567 CGGGGTGGAGTAAATACTGTTATT 58.322 41.667 0.00 0.00 36.50 1.40
666 669 5.756833 CGGGGTGGAGTAAATACTGTTATTC 59.243 44.000 0.00 0.00 36.50 1.75
667 670 6.407752 CGGGGTGGAGTAAATACTGTTATTCT 60.408 42.308 0.00 0.00 36.50 2.40
668 671 7.344134 GGGGTGGAGTAAATACTGTTATTCTT 58.656 38.462 0.00 0.00 36.50 2.52
669 672 7.498239 GGGGTGGAGTAAATACTGTTATTCTTC 59.502 40.741 0.00 0.00 36.50 2.87
670 673 8.265764 GGGTGGAGTAAATACTGTTATTCTTCT 58.734 37.037 0.00 0.00 36.50 2.85
671 674 9.099454 GGTGGAGTAAATACTGTTATTCTTCTG 57.901 37.037 0.00 0.00 36.50 3.02
672 675 9.099454 GTGGAGTAAATACTGTTATTCTTCTGG 57.901 37.037 0.00 0.00 36.50 3.86
673 676 9.042450 TGGAGTAAATACTGTTATTCTTCTGGA 57.958 33.333 0.00 0.00 36.50 3.86
674 677 9.886132 GGAGTAAATACTGTTATTCTTCTGGAA 57.114 33.333 0.00 0.00 36.50 3.53
678 681 7.617041 AATACTGTTATTCTTCTGGAAGTGC 57.383 36.000 9.73 0.00 39.38 4.40
679 682 5.234466 ACTGTTATTCTTCTGGAAGTGCT 57.766 39.130 9.73 0.55 39.38 4.40
680 683 4.999950 ACTGTTATTCTTCTGGAAGTGCTG 59.000 41.667 9.73 4.86 39.38 4.41
681 684 4.973168 TGTTATTCTTCTGGAAGTGCTGT 58.027 39.130 9.73 0.00 39.38 4.40
767 770 5.826601 TGCAGATTACAACAGTTTCACAA 57.173 34.783 0.00 0.00 0.00 3.33
1112 1140 5.783111 ACAAAAAGTTCATACCATCTTGCC 58.217 37.500 0.00 0.00 0.00 4.52
1130 1158 5.350365 TCTTGCCACGATTACAACAAGTATC 59.650 40.000 0.00 0.00 36.69 2.24
1183 1213 5.986501 ACTTCGAGAAACTCAGAGGTATT 57.013 39.130 1.53 0.00 28.59 1.89
1190 1220 7.331934 TCGAGAAACTCAGAGGTATTGAAATTG 59.668 37.037 1.53 0.00 0.00 2.32
1196 1226 7.637511 ACTCAGAGGTATTGAAATTGGAGATT 58.362 34.615 1.53 0.00 0.00 2.40
1213 1243 4.584325 GGAGATTTGCTTATGTTATGCCCA 59.416 41.667 0.00 0.00 0.00 5.36
1214 1244 5.244626 GGAGATTTGCTTATGTTATGCCCAT 59.755 40.000 0.00 0.00 0.00 4.00
1216 1246 4.935352 TTTGCTTATGTTATGCCCATCC 57.065 40.909 0.00 0.00 0.00 3.51
1223 1257 7.289782 TGCTTATGTTATGCCCATCCTTTTAAT 59.710 33.333 0.00 0.00 0.00 1.40
1251 1285 7.217906 TCTTTCTCTCCCTCTTTACTGTTTTC 58.782 38.462 0.00 0.00 0.00 2.29
1321 1355 5.786401 AATAAGCTACTTGAAGAAGTGCG 57.214 39.130 0.00 0.00 42.66 5.34
1368 1405 7.877612 TCTGTGTTAGCAATAAGATGTTTCTCA 59.122 33.333 0.00 0.00 0.00 3.27
1376 1413 6.238320 GCAATAAGATGTTTCTCAGCTACCAG 60.238 42.308 0.00 0.00 42.33 4.00
1434 1471 3.091545 TGATGGGCAGAATCTTGTTTCC 58.908 45.455 0.00 0.00 0.00 3.13
1438 1475 3.073798 TGGGCAGAATCTTGTTTCCAGTA 59.926 43.478 0.00 0.00 0.00 2.74
1470 1507 1.751351 GTGCTTGGATTCTTTAGCCCC 59.249 52.381 0.00 0.00 32.73 5.80
1520 1557 6.315393 GGTGTATGGTATAACAGTGTTCCAAG 59.685 42.308 12.82 0.00 0.00 3.61
1521 1558 7.101054 GTGTATGGTATAACAGTGTTCCAAGA 58.899 38.462 12.82 4.21 0.00 3.02
1537 1574 1.207089 CAAGAGGAACGGCTGTATGGA 59.793 52.381 0.00 0.00 0.00 3.41
1575 1612 1.068741 CCAGTACAGGATAAGTCGGGC 59.931 57.143 0.00 0.00 0.00 6.13
1593 1630 3.680937 CGGGCGTACTTAAGTTTGATGAA 59.319 43.478 14.49 0.00 0.00 2.57
1612 1649 6.546034 TGATGAAGTCGGTAATCTGATAGTCA 59.454 38.462 0.00 0.00 0.00 3.41
1634 1671 4.254709 TGGCACAGGCAGCTCGTT 62.255 61.111 0.00 0.00 43.71 3.85
1649 1692 4.864806 CAGCTCGTTTATAGTTGCTTCTGA 59.135 41.667 0.00 0.00 0.00 3.27
1651 1694 5.103000 GCTCGTTTATAGTTGCTTCTGAGA 58.897 41.667 0.00 0.00 0.00 3.27
1684 1727 0.465097 CAGGGAGGCTGCAATACTGG 60.465 60.000 8.68 0.00 0.00 4.00
1686 1729 0.464554 GGGAGGCTGCAATACTGGAC 60.465 60.000 8.68 0.00 0.00 4.02
1698 1741 3.508845 ATACTGGACACTGGCAACTTT 57.491 42.857 0.00 0.00 37.61 2.66
1711 1757 2.819608 GGCAACTTTGTGCTAAGGATGA 59.180 45.455 0.00 0.00 44.31 2.92
1714 1760 2.699954 ACTTTGTGCTAAGGATGACCG 58.300 47.619 0.00 0.00 41.83 4.79
1718 1764 0.527817 GTGCTAAGGATGACCGACCG 60.528 60.000 0.00 0.00 41.83 4.79
1725 1771 1.071071 AGGATGACCGACCGTTCAAAA 59.929 47.619 0.00 0.00 41.83 2.44
1737 1783 5.504010 CGACCGTTCAAAAATCATATGGGAG 60.504 44.000 2.13 0.00 0.00 4.30
1748 1794 2.105477 TCATATGGGAGAGCTTTGCCTC 59.895 50.000 16.00 3.99 0.00 4.70
1767 1813 3.900601 CCTCTCCTACTGATACATGGCTT 59.099 47.826 0.00 0.00 0.00 4.35
1770 1816 3.643320 CTCCTACTGATACATGGCTTCCA 59.357 47.826 0.00 0.00 38.19 3.53
1789 1835 7.420800 GCTTCCAGGAATGAATATTACACTTG 58.579 38.462 1.09 0.00 28.86 3.16
1868 1914 0.733150 GGTTTTGGACCGAGCATAGC 59.267 55.000 0.00 0.00 39.00 2.97
1873 1919 3.386768 TTGGACCGAGCATAGCTAATC 57.613 47.619 0.00 0.00 39.88 1.75
1875 1921 1.402984 GGACCGAGCATAGCTAATCCG 60.403 57.143 0.00 0.00 39.88 4.18
1898 1944 7.445096 TCCGTCAGCATCACAATTCATTATTAT 59.555 33.333 0.00 0.00 0.00 1.28
1899 1945 7.536281 CCGTCAGCATCACAATTCATTATTATG 59.464 37.037 0.00 0.00 0.00 1.90
1910 1956 9.300681 ACAATTCATTATTATGTGGAATCGGAT 57.699 29.630 0.00 0.00 33.34 4.18
1928 1974 4.824537 TCGGATTTCATTTTGGACAAGTGA 59.175 37.500 0.00 0.00 0.00 3.41
1964 2010 4.021104 TGACACGAATTCTCTCATTCCAGT 60.021 41.667 3.52 0.00 30.38 4.00
1978 2024 7.730084 TCTCATTCCAGTACTGAAATCTATGG 58.270 38.462 24.68 3.68 0.00 2.74
2042 2088 0.472925 TACACTCCCAACCCTGCTGA 60.473 55.000 0.00 0.00 0.00 4.26
2107 2153 6.241207 ACATAACACAGTTCAATTCGGAAG 57.759 37.500 0.00 0.00 0.00 3.46
2189 2235 4.699735 TGGAGTTAATGGTGTATGCAACAG 59.300 41.667 7.79 0.00 46.57 3.16
2194 2240 4.751539 GTGTATGCAACAGCAGCG 57.248 55.556 0.00 0.00 42.36 5.18
2196 2242 1.075542 GTGTATGCAACAGCAGCGTA 58.924 50.000 0.00 0.00 42.36 4.42
2206 2252 1.407618 ACAGCAGCGTATCCGTATCAA 59.592 47.619 0.00 0.00 36.15 2.57
2224 2270 7.226523 CCGTATCAACATCAGAATCCATTTGTA 59.773 37.037 0.00 0.00 0.00 2.41
2225 2271 8.611757 CGTATCAACATCAGAATCCATTTGTAA 58.388 33.333 0.00 0.00 0.00 2.41
2253 2299 3.318839 CAGAAGGATTTGCACCACAAGAA 59.681 43.478 0.00 0.00 40.06 2.52
2280 2326 0.779997 ATTCCAGGAAAGGGTGCACT 59.220 50.000 17.98 0.00 0.00 4.40
2284 2330 1.351017 CCAGGAAAGGGTGCACTAGAA 59.649 52.381 17.98 0.00 0.00 2.10
2313 2359 4.383010 CCACTGCAGTGTAATGGTGATAGA 60.383 45.833 37.55 0.00 44.21 1.98
2401 2447 5.104374 GTGAATGTGAATTTGCCTGTATGG 58.896 41.667 0.00 0.00 39.35 2.74
2405 2451 5.798125 TGTGAATTTGCCTGTATGGAAAA 57.202 34.783 0.00 0.00 46.81 2.29
2473 2519 4.794003 GCTTATGGCATGGCAATCTAACAC 60.794 45.833 27.04 9.29 41.35 3.32
2482 2528 2.813754 GGCAATCTAACACACTTGCAGA 59.186 45.455 8.21 0.00 44.41 4.26
2509 2555 5.914085 AGTTGAAACTCTTCATCTTCGTG 57.086 39.130 0.00 0.00 41.22 4.35
2525 2571 2.814269 TCGTGTAGCTGCATCAGAATC 58.186 47.619 8.05 0.00 32.44 2.52
2768 2815 6.782494 AGGTAACCATTCTGAGTTGGAAAAAT 59.218 34.615 13.68 0.96 36.79 1.82
2774 2821 9.492973 ACCATTCTGAGTTGGAAAAATAATTTG 57.507 29.630 13.68 0.00 36.79 2.32
2798 2846 7.592938 TGTAGTTAAAGAAATGACATGCCTTG 58.407 34.615 0.00 0.00 0.00 3.61
2807 2855 3.548745 TGACATGCCTTGGTCTGATAG 57.451 47.619 0.00 0.00 35.11 2.08
2816 2864 4.444022 GCCTTGGTCTGATAGACACATGAT 60.444 45.833 10.75 0.00 46.79 2.45
2843 2891 3.259123 CCCCTTTTGTGAATCAGGGAAAG 59.741 47.826 6.12 6.14 38.82 2.62
2853 2901 2.746279 TCAGGGAAAGGAAAACAGCA 57.254 45.000 0.00 0.00 0.00 4.41
2884 2932 2.101415 CCTCGTCATGGCTTCAGATGTA 59.899 50.000 0.00 0.00 0.00 2.29
2890 2938 5.065090 CGTCATGGCTTCAGATGTAATGAAA 59.935 40.000 0.00 0.00 36.30 2.69
2935 2983 4.880696 GGCTCTCACTTTATGATGCTTTCT 59.119 41.667 0.00 0.00 36.48 2.52
2975 3023 3.133901 TGCCACAGACAACTTCTCAACTA 59.866 43.478 0.00 0.00 28.96 2.24
2992 3040 6.601613 TCTCAACTAAAAACAAGCTTGGAGAA 59.398 34.615 29.18 10.42 0.00 2.87
3024 3072 4.043059 TGGCCCTGTGTACAAGGTTAATTA 59.957 41.667 17.46 0.00 30.14 1.40
3062 3134 9.907576 TTTGTTCGTTAAAATGTTTGCTAATTG 57.092 25.926 0.00 0.00 0.00 2.32
3064 3136 8.535592 TGTTCGTTAAAATGTTTGCTAATTGTG 58.464 29.630 0.00 0.00 0.00 3.33
3077 3149 8.788813 GTTTGCTAATTGTGATAATTTCGTCTG 58.211 33.333 0.00 0.00 0.00 3.51
3100 3172 6.218746 TGAAGCATGTAGTCAGCATGTATAG 58.781 40.000 7.06 0.00 43.93 1.31
3107 3179 6.042777 TGTAGTCAGCATGTATAGCTTTGTC 58.957 40.000 0.00 0.00 41.14 3.18
3109 3181 5.114780 AGTCAGCATGTATAGCTTTGTCTG 58.885 41.667 0.00 0.00 41.14 3.51
3131 3203 7.928706 GTCTGTAGCCAAGTAATGATAGTGAAT 59.071 37.037 0.00 0.00 0.00 2.57
3196 3279 4.142609 TGGAGCATATCTTTGTCCAGTC 57.857 45.455 0.00 0.00 32.21 3.51
3219 3302 7.338703 AGTCGTCCTGTAAGATGTTCATAGTTA 59.661 37.037 0.00 0.00 34.07 2.24
3222 3305 7.432545 CGTCCTGTAAGATGTTCATAGTTACAG 59.567 40.741 23.52 23.52 45.30 2.74
3230 3313 5.939764 TGTTCATAGTTACAGCATCCTCT 57.060 39.130 0.00 0.00 0.00 3.69
3256 3339 5.621197 TGTTAGTCATGTGTGGCAAATAC 57.379 39.130 0.00 0.00 30.45 1.89
3263 3346 2.017782 TGTGTGGCAAATACGTTGTGT 58.982 42.857 0.00 0.00 39.63 3.72
3268 3351 3.484285 GTGGCAAATACGTTGTGTTGTTC 59.516 43.478 0.00 0.00 39.63 3.18
3281 3364 3.002246 TGTGTTGTTCGATCAAGCAGTTC 59.998 43.478 9.14 0.00 0.00 3.01
3294 3377 2.950433 AGCAGTTCGGCAAATTCAATG 58.050 42.857 0.00 0.00 35.83 2.82
3300 3383 5.863397 CAGTTCGGCAAATTCAATGTACATT 59.137 36.000 15.47 15.47 0.00 2.71
3331 5139 6.772605 TCAACTCAATATCATGGATAGTGGG 58.227 40.000 10.93 10.93 43.84 4.61
3333 5141 6.617782 ACTCAATATCATGGATAGTGGGAG 57.382 41.667 17.46 9.58 41.74 4.30
3334 5142 5.046014 ACTCAATATCATGGATAGTGGGAGC 60.046 44.000 17.46 0.00 41.74 4.70
3337 5145 2.477104 TCATGGATAGTGGGAGCTGA 57.523 50.000 0.00 0.00 0.00 4.26
3338 5146 2.763039 TCATGGATAGTGGGAGCTGAA 58.237 47.619 0.00 0.00 0.00 3.02
3339 5147 3.321039 TCATGGATAGTGGGAGCTGAAT 58.679 45.455 0.00 0.00 0.00 2.57
3340 5148 3.326006 TCATGGATAGTGGGAGCTGAATC 59.674 47.826 0.00 0.00 0.00 2.52
3346 5165 6.101734 TGGATAGTGGGAGCTGAATCTATTTT 59.898 38.462 0.00 0.00 0.00 1.82
3348 5167 7.040823 GGATAGTGGGAGCTGAATCTATTTTTG 60.041 40.741 0.00 0.00 0.00 2.44
3350 5169 6.430007 AGTGGGAGCTGAATCTATTTTTGAT 58.570 36.000 0.00 0.00 0.00 2.57
3383 5202 9.781834 CTGTACTAATGTTTGACTGTTGAAAAA 57.218 29.630 0.00 0.00 0.00 1.94
3403 5222 0.770499 TTGACACAATGCTCCAGGGA 59.230 50.000 0.00 0.00 0.00 4.20
3523 5342 5.520376 AGCTTCAACACAGCAATTTAGTT 57.480 34.783 0.00 0.00 39.99 2.24
3530 5349 4.718961 ACACAGCAATTTAGTTGGACTCT 58.281 39.130 0.00 0.00 38.29 3.24
3621 5440 8.406297 GGATTTCTTCCTATTTGGTATGTTCAC 58.594 37.037 0.00 0.00 41.78 3.18
3625 5444 8.335532 TCTTCCTATTTGGTATGTTCACTTTG 57.664 34.615 0.00 0.00 37.07 2.77
3672 5493 5.537674 AGCTATATTTTCCTTCCATGCCTTG 59.462 40.000 0.00 0.00 0.00 3.61
3822 5643 5.749462 AGAATTATTCACAGGGACCTGAAG 58.251 41.667 24.31 15.46 46.30 3.02
3831 5652 0.613012 GGGACCTGAAGCCAAGCAAT 60.613 55.000 0.00 0.00 0.00 3.56
3867 5688 6.015856 ACACTGATATGAACCCTAAGATCTCG 60.016 42.308 0.00 0.00 0.00 4.04
3873 5694 3.700038 TGAACCCTAAGATCTCGGACTTC 59.300 47.826 11.55 11.21 0.00 3.01
3999 5820 6.240549 AGAACCACTATACTGAGAAATGGG 57.759 41.667 0.00 0.00 0.00 4.00
4139 5962 5.164620 TCATCAGTGGACTAAGAAATGCA 57.835 39.130 0.00 0.00 0.00 3.96
4157 5980 3.503363 GCAGCTCGTGGACATGGC 61.503 66.667 0.00 0.00 0.00 4.40
4430 6256 1.281867 TCCATGGCCGAAGTCATTTCT 59.718 47.619 6.96 0.00 33.44 2.52
4578 6404 4.447470 GCCTGGATGGTAGGTAGTACTACT 60.447 50.000 27.71 17.79 42.29 2.57
4579 6405 5.222007 GCCTGGATGGTAGGTAGTACTACTA 60.222 48.000 27.71 16.93 42.29 1.82
4580 6406 6.523844 GCCTGGATGGTAGGTAGTACTACTAT 60.524 46.154 27.71 20.05 44.58 2.12
4617 6443 7.426929 AGATAAAGAGTGTTACTGTTGCTTG 57.573 36.000 0.00 0.00 31.59 4.01
4654 6480 8.066612 TCAGACAACAGAGTATCATGTTATCA 57.933 34.615 0.00 0.00 34.42 2.15
4925 6754 5.472148 CCTCTTGCATGCATTGTAAAAGAA 58.528 37.500 23.37 0.63 28.96 2.52
5171 7011 5.387279 TCAAAGTTTGTGTCGTTTGACTTC 58.613 37.500 15.08 0.00 45.70 3.01
5174 7014 5.217895 AGTTTGTGTCGTTTGACTTCTTC 57.782 39.130 0.00 0.00 45.70 2.87
5379 7227 7.165154 GTCGACAAATTTTTGACATTTCTCGAA 59.835 33.333 11.55 0.00 40.44 3.71
5439 7287 6.000891 TGTTCCATCTCTCGTGAAAATTTG 57.999 37.500 0.00 0.00 0.00 2.32
5442 7290 4.083324 TCCATCTCTCGTGAAAATTTGCAC 60.083 41.667 18.08 18.08 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
98 99 8.822805 TGACTGAATAAAGAACCCTATTACACT 58.177 33.333 0.00 0.00 0.00 3.55
99 100 9.444600 TTGACTGAATAAAGAACCCTATTACAC 57.555 33.333 0.00 0.00 0.00 2.90
104 105 9.533831 ACATTTTGACTGAATAAAGAACCCTAT 57.466 29.630 0.00 0.00 0.00 2.57
105 106 8.934023 ACATTTTGACTGAATAAAGAACCCTA 57.066 30.769 0.00 0.00 0.00 3.53
106 107 7.039714 GGACATTTTGACTGAATAAAGAACCCT 60.040 37.037 0.00 0.00 0.00 4.34
107 108 7.090808 GGACATTTTGACTGAATAAAGAACCC 58.909 38.462 0.00 0.00 0.00 4.11
108 109 7.595130 GTGGACATTTTGACTGAATAAAGAACC 59.405 37.037 0.00 0.00 0.00 3.62
109 110 8.352942 AGTGGACATTTTGACTGAATAAAGAAC 58.647 33.333 0.00 0.00 0.00 3.01
110 111 8.463930 AGTGGACATTTTGACTGAATAAAGAA 57.536 30.769 0.00 0.00 0.00 2.52
111 112 8.352201 CAAGTGGACATTTTGACTGAATAAAGA 58.648 33.333 0.00 0.00 0.00 2.52
112 113 8.352201 TCAAGTGGACATTTTGACTGAATAAAG 58.648 33.333 0.00 0.00 0.00 1.85
113 114 8.231692 TCAAGTGGACATTTTGACTGAATAAA 57.768 30.769 0.00 0.00 0.00 1.40
114 115 7.502226 ACTCAAGTGGACATTTTGACTGAATAA 59.498 33.333 0.00 0.00 0.00 1.40
115 116 6.998074 ACTCAAGTGGACATTTTGACTGAATA 59.002 34.615 0.00 0.00 0.00 1.75
116 117 5.829924 ACTCAAGTGGACATTTTGACTGAAT 59.170 36.000 0.00 0.00 0.00 2.57
117 118 5.192927 ACTCAAGTGGACATTTTGACTGAA 58.807 37.500 0.00 0.00 0.00 3.02
118 119 4.780815 ACTCAAGTGGACATTTTGACTGA 58.219 39.130 0.00 0.00 0.00 3.41
119 120 5.505173 AACTCAAGTGGACATTTTGACTG 57.495 39.130 0.00 0.00 0.00 3.51
120 121 6.238759 GCTTAACTCAAGTGGACATTTTGACT 60.239 38.462 0.00 0.00 36.55 3.41
121 122 5.915196 GCTTAACTCAAGTGGACATTTTGAC 59.085 40.000 0.00 0.00 36.55 3.18
122 123 5.277779 CGCTTAACTCAAGTGGACATTTTGA 60.278 40.000 0.00 0.00 40.46 2.69
123 124 4.911610 CGCTTAACTCAAGTGGACATTTTG 59.088 41.667 0.00 0.00 40.46 2.44
124 125 4.819630 TCGCTTAACTCAAGTGGACATTTT 59.180 37.500 0.00 0.00 43.66 1.82
125 126 4.385825 TCGCTTAACTCAAGTGGACATTT 58.614 39.130 0.00 0.00 43.66 2.32
126 127 3.997021 CTCGCTTAACTCAAGTGGACATT 59.003 43.478 0.00 0.00 43.66 2.71
127 128 3.589988 CTCGCTTAACTCAAGTGGACAT 58.410 45.455 0.00 0.00 43.66 3.06
128 129 2.866460 GCTCGCTTAACTCAAGTGGACA 60.866 50.000 0.00 0.00 43.66 4.02
129 130 1.727335 GCTCGCTTAACTCAAGTGGAC 59.273 52.381 0.00 0.00 43.66 4.02
195 196 3.682718 CGAGTTGGGCTATGGAATTCTGT 60.683 47.826 5.23 0.00 0.00 3.41
201 202 0.178068 GCTCGAGTTGGGCTATGGAA 59.822 55.000 15.13 0.00 0.00 3.53
220 221 2.037847 CAGCCAAAGGGGAAGGGG 59.962 66.667 0.00 0.00 40.01 4.79
227 228 3.944250 ATCGGTGCCAGCCAAAGGG 62.944 63.158 0.00 0.00 37.18 3.95
323 326 7.870445 GTCCAGGTAAAATGACAGCAATAAAAA 59.130 33.333 0.00 0.00 0.00 1.94
384 387 3.493699 CCAGGTTCGAACTGTAGACCAAA 60.494 47.826 26.32 0.00 34.16 3.28
462 465 7.279758 ACAACACACAAAATTATGGAAAACCAG 59.720 33.333 0.00 0.00 0.00 4.00
466 469 7.604164 ACACACAACACACAAAATTATGGAAAA 59.396 29.630 0.00 0.00 0.00 2.29
472 475 5.971763 ACCACACACAACACACAAAATTAT 58.028 33.333 0.00 0.00 0.00 1.28
489 492 0.971386 TCCGTCTTTCCCTACCACAC 59.029 55.000 0.00 0.00 0.00 3.82
533 536 1.833860 GTGATCTCGCTCCTTTCTCG 58.166 55.000 0.00 0.00 0.00 4.04
548 551 2.687566 GGGGAGGGGTGTCGTGAT 60.688 66.667 0.00 0.00 0.00 3.06
596 599 4.394300 CCAGAAGAATAACAGCACTTCCAG 59.606 45.833 0.00 0.00 39.33 3.86
636 639 2.068834 TTTACTCCACCCCGCAAAAA 57.931 45.000 0.00 0.00 0.00 1.94
637 640 2.296073 ATTTACTCCACCCCGCAAAA 57.704 45.000 0.00 0.00 0.00 2.44
638 641 2.306512 AGTATTTACTCCACCCCGCAAA 59.693 45.455 0.00 0.00 0.00 3.68
639 642 1.910671 AGTATTTACTCCACCCCGCAA 59.089 47.619 0.00 0.00 0.00 4.85
640 643 1.208535 CAGTATTTACTCCACCCCGCA 59.791 52.381 0.00 0.00 33.46 5.69
641 644 1.208776 ACAGTATTTACTCCACCCCGC 59.791 52.381 0.00 0.00 33.46 6.13
642 645 3.622166 AACAGTATTTACTCCACCCCG 57.378 47.619 0.00 0.00 33.46 5.73
643 646 6.896883 AGAATAACAGTATTTACTCCACCCC 58.103 40.000 0.00 0.00 33.46 4.95
644 647 8.265764 AGAAGAATAACAGTATTTACTCCACCC 58.734 37.037 0.00 0.00 33.46 4.61
645 648 9.099454 CAGAAGAATAACAGTATTTACTCCACC 57.901 37.037 0.00 0.00 33.46 4.61
646 649 9.099454 CCAGAAGAATAACAGTATTTACTCCAC 57.901 37.037 0.00 0.00 33.46 4.02
647 650 9.042450 TCCAGAAGAATAACAGTATTTACTCCA 57.958 33.333 0.00 0.00 33.46 3.86
648 651 9.886132 TTCCAGAAGAATAACAGTATTTACTCC 57.114 33.333 0.00 0.00 33.46 3.85
652 655 9.162764 GCACTTCCAGAAGAATAACAGTATTTA 57.837 33.333 14.19 0.00 40.79 1.40
653 656 7.885399 AGCACTTCCAGAAGAATAACAGTATTT 59.115 33.333 14.19 0.00 40.79 1.40
654 657 7.335422 CAGCACTTCCAGAAGAATAACAGTATT 59.665 37.037 14.19 0.00 40.79 1.89
655 658 6.820656 CAGCACTTCCAGAAGAATAACAGTAT 59.179 38.462 14.19 0.00 40.79 2.12
656 659 6.166279 CAGCACTTCCAGAAGAATAACAGTA 58.834 40.000 14.19 0.00 40.79 2.74
657 660 4.999950 CAGCACTTCCAGAAGAATAACAGT 59.000 41.667 14.19 0.00 40.79 3.55
658 661 4.999950 ACAGCACTTCCAGAAGAATAACAG 59.000 41.667 14.19 0.78 40.79 3.16
659 662 4.973168 ACAGCACTTCCAGAAGAATAACA 58.027 39.130 14.19 0.00 40.79 2.41
660 663 5.948992 AACAGCACTTCCAGAAGAATAAC 57.051 39.130 14.19 0.00 40.79 1.89
661 664 6.874134 GTCTAACAGCACTTCCAGAAGAATAA 59.126 38.462 14.19 0.00 40.79 1.40
662 665 6.014584 TGTCTAACAGCACTTCCAGAAGAATA 60.015 38.462 14.19 0.00 40.79 1.75
663 666 5.221722 TGTCTAACAGCACTTCCAGAAGAAT 60.222 40.000 14.19 0.00 40.79 2.40
664 667 4.100963 TGTCTAACAGCACTTCCAGAAGAA 59.899 41.667 14.19 0.00 40.79 2.52
665 668 3.641436 TGTCTAACAGCACTTCCAGAAGA 59.359 43.478 14.19 0.00 40.79 2.87
666 669 3.743396 GTGTCTAACAGCACTTCCAGAAG 59.257 47.826 5.85 5.85 43.79 2.85
667 670 3.728845 GTGTCTAACAGCACTTCCAGAA 58.271 45.455 0.00 0.00 33.22 3.02
668 671 2.288213 CGTGTCTAACAGCACTTCCAGA 60.288 50.000 0.00 0.00 33.78 3.86
669 672 2.061773 CGTGTCTAACAGCACTTCCAG 58.938 52.381 0.00 0.00 33.78 3.86
670 673 1.872237 GCGTGTCTAACAGCACTTCCA 60.872 52.381 0.00 0.00 33.78 3.53
671 674 0.790814 GCGTGTCTAACAGCACTTCC 59.209 55.000 0.00 0.00 33.78 3.46
672 675 1.457303 CAGCGTGTCTAACAGCACTTC 59.543 52.381 0.00 0.00 33.78 3.01
673 676 1.202533 ACAGCGTGTCTAACAGCACTT 60.203 47.619 0.00 0.00 33.78 3.16
674 677 0.389391 ACAGCGTGTCTAACAGCACT 59.611 50.000 0.00 0.00 33.78 4.40
675 678 1.986378 CTACAGCGTGTCTAACAGCAC 59.014 52.381 0.00 0.00 32.81 4.40
676 679 1.883926 TCTACAGCGTGTCTAACAGCA 59.116 47.619 0.00 0.00 32.81 4.41
677 680 2.631418 TCTACAGCGTGTCTAACAGC 57.369 50.000 0.00 0.00 0.00 4.40
678 681 4.346970 CTGATCTACAGCGTGTCTAACAG 58.653 47.826 0.00 0.00 39.86 3.16
679 682 4.357018 CTGATCTACAGCGTGTCTAACA 57.643 45.455 0.00 0.00 39.86 2.41
701 704 7.254185 GCAATTACCATGCTCAAATATTGTGTG 60.254 37.037 0.00 0.00 40.64 3.82
729 732 2.268076 GCATCACAAGGGCGTGGTT 61.268 57.895 0.00 0.00 37.50 3.67
767 770 6.311935 CGCAATCTTCATTCATTTTCCACAAT 59.688 34.615 0.00 0.00 0.00 2.71
1130 1158 1.078143 GGTGAGCAGGGTAAGCAGG 60.078 63.158 0.00 0.00 0.00 4.85
1183 1213 9.806203 CATAACATAAGCAAATCTCCAATTTCA 57.194 29.630 0.00 0.00 0.00 2.69
1190 1220 4.584325 TGGGCATAACATAAGCAAATCTCC 59.416 41.667 0.00 0.00 0.00 3.71
1196 1226 4.183223 AGGATGGGCATAACATAAGCAA 57.817 40.909 0.00 0.00 0.00 3.91
1214 1244 9.285359 AGAGGGAGAGAAAGATAATTAAAAGGA 57.715 33.333 0.00 0.00 0.00 3.36
1223 1257 8.437274 AACAGTAAAGAGGGAGAGAAAGATAA 57.563 34.615 0.00 0.00 0.00 1.75
1225 1259 6.943899 AACAGTAAAGAGGGAGAGAAAGAT 57.056 37.500 0.00 0.00 0.00 2.40
1242 1276 5.520649 GGGAAAATTGCAAACGAAAACAGTA 59.479 36.000 1.71 0.00 0.00 2.74
1251 1285 5.614449 GCATAAACTGGGAAAATTGCAAACG 60.614 40.000 1.71 0.00 0.00 3.60
1368 1405 0.545309 TGTCTCTTGGCCTGGTAGCT 60.545 55.000 3.32 0.00 0.00 3.32
1376 1413 2.109126 GCGATGGTGTCTCTTGGCC 61.109 63.158 0.00 0.00 0.00 5.36
1434 1471 6.272318 TCCAAGCACAAATTTCTTGTTACTG 58.728 36.000 13.88 2.89 36.41 2.74
1438 1475 6.585416 AGAATCCAAGCACAAATTTCTTGTT 58.415 32.000 13.88 5.86 36.41 2.83
1470 1507 3.121030 CGGTGGCTTGAAGCTCCG 61.121 66.667 27.59 27.59 45.32 4.63
1498 1535 6.761714 CCTCTTGGAACACTGTTATACCATAC 59.238 42.308 0.00 0.00 39.29 2.39
1520 1557 2.213499 CAATCCATACAGCCGTTCCTC 58.787 52.381 0.00 0.00 0.00 3.71
1521 1558 1.747206 GCAATCCATACAGCCGTTCCT 60.747 52.381 0.00 0.00 0.00 3.36
1529 1566 6.057533 TCATTCCTGTTAGCAATCCATACAG 58.942 40.000 0.00 0.00 36.77 2.74
1563 1600 3.067320 ACTTAAGTACGCCCGACTTATCC 59.933 47.826 6.26 0.00 38.76 2.59
1572 1609 4.694037 ACTTCATCAAACTTAAGTACGCCC 59.306 41.667 8.92 0.00 30.62 6.13
1575 1612 5.632347 ACCGACTTCATCAAACTTAAGTACG 59.368 40.000 8.92 3.17 32.51 3.67
1593 1630 7.495934 CCATTTTTGACTATCAGATTACCGACT 59.504 37.037 0.00 0.00 0.00 4.18
1612 1649 0.319405 GAGCTGCCTGTGCCATTTTT 59.681 50.000 0.00 0.00 36.33 1.94
1634 1671 5.663106 ACTCCCATCTCAGAAGCAACTATAA 59.337 40.000 0.00 0.00 0.00 0.98
1649 1692 0.326048 CCTGTCCCTCACTCCCATCT 60.326 60.000 0.00 0.00 0.00 2.90
1651 1694 1.307343 CCCTGTCCCTCACTCCCAT 60.307 63.158 0.00 0.00 0.00 4.00
1684 1727 0.740737 AGCACAAAGTTGCCAGTGTC 59.259 50.000 0.00 0.00 44.14 3.67
1686 1729 2.287788 CCTTAGCACAAAGTTGCCAGTG 60.288 50.000 0.00 0.00 44.14 3.66
1698 1741 0.535335 GGTCGGTCATCCTTAGCACA 59.465 55.000 0.00 0.00 0.00 4.57
1711 1757 4.095782 CCATATGATTTTTGAACGGTCGGT 59.904 41.667 3.65 0.00 0.00 4.69
1714 1760 5.588648 TCTCCCATATGATTTTTGAACGGTC 59.411 40.000 3.65 0.00 0.00 4.79
1718 1764 6.705863 AGCTCTCCCATATGATTTTTGAAC 57.294 37.500 3.65 0.00 0.00 3.18
1725 1771 3.139770 AGGCAAAGCTCTCCCATATGATT 59.860 43.478 3.65 0.00 0.00 2.57
1737 1783 1.827969 TCAGTAGGAGAGGCAAAGCTC 59.172 52.381 0.00 0.00 0.00 4.09
1748 1794 3.643320 TGGAAGCCATGTATCAGTAGGAG 59.357 47.826 0.00 0.00 0.00 3.69
1767 1813 7.206789 TCCAAGTGTAATATTCATTCCTGGA 57.793 36.000 0.00 0.00 0.00 3.86
1789 1835 6.400568 TCTTCCATGATTTCAGCAAATTTCC 58.599 36.000 0.00 0.00 31.94 3.13
1824 1870 2.026822 AGTGTAATCTCCTGTTGCTGGG 60.027 50.000 0.00 0.00 0.00 4.45
1868 1914 4.571984 TGAATTGTGATGCTGACGGATTAG 59.428 41.667 0.00 0.00 0.00 1.73
1873 1919 3.770263 AATGAATTGTGATGCTGACGG 57.230 42.857 0.00 0.00 0.00 4.79
1875 1921 9.177304 CACATAATAATGAATTGTGATGCTGAC 57.823 33.333 2.10 0.00 38.58 3.51
1898 1944 4.769488 TCCAAAATGAAATCCGATTCCACA 59.231 37.500 0.00 0.00 0.00 4.17
1899 1945 5.102313 GTCCAAAATGAAATCCGATTCCAC 58.898 41.667 0.00 0.00 0.00 4.02
1910 1956 6.462768 CCAGGATTCACTTGTCCAAAATGAAA 60.463 38.462 9.26 0.00 36.96 2.69
1928 1974 1.628340 TCGTGTCACCATTCCAGGATT 59.372 47.619 0.00 0.00 0.00 3.01
1978 2024 5.888161 ACTGAAATGAAACAGGGATGATACC 59.112 40.000 0.00 0.00 38.30 2.73
2101 2147 1.243902 GTCCACAATTTGGCTTCCGA 58.756 50.000 0.78 0.00 46.47 4.55
2107 2153 4.630940 CCATAACAATGTCCACAATTTGGC 59.369 41.667 0.78 0.00 46.47 4.52
2194 2240 6.455647 TGGATTCTGATGTTGATACGGATAC 58.544 40.000 0.00 0.00 0.00 2.24
2196 2242 5.551305 TGGATTCTGATGTTGATACGGAT 57.449 39.130 0.00 0.00 0.00 4.18
2206 2252 6.375455 GGACACTTACAAATGGATTCTGATGT 59.625 38.462 0.00 0.00 0.00 3.06
2224 2270 2.887152 GTGCAAATCCTTCTGGACACTT 59.113 45.455 0.00 0.00 46.51 3.16
2225 2271 2.508526 GTGCAAATCCTTCTGGACACT 58.491 47.619 0.00 0.00 46.51 3.55
2245 2291 5.010922 TCCTGGAATTTGATTGTTCTTGTGG 59.989 40.000 0.00 0.00 0.00 4.17
2253 2299 4.284234 CACCCTTTCCTGGAATTTGATTGT 59.716 41.667 10.45 0.00 0.00 2.71
2280 2326 2.582052 CACTGCAGTGGGGTTTTTCTA 58.418 47.619 34.65 0.00 42.10 2.10
2338 2384 3.118261 AGCTTCTGTCTGTTGTCAGGAAA 60.118 43.478 0.00 0.00 41.59 3.13
2401 2447 3.552604 TGCCGTACAAGAGCAATTTTC 57.447 42.857 0.00 0.00 32.56 2.29
2405 2451 2.549754 GCATATGCCGTACAAGAGCAAT 59.450 45.455 17.26 0.00 40.46 3.56
2473 2519 4.037208 AGTTTCAACTCCATTCTGCAAGTG 59.963 41.667 0.00 0.00 32.86 3.16
2509 2555 3.250280 CCATGTGATTCTGATGCAGCTAC 59.750 47.826 2.53 0.00 0.00 3.58
2525 2571 3.270877 GGCACTAGTCCTTTACCATGTG 58.729 50.000 0.00 0.00 0.00 3.21
2640 2686 3.196463 CAAAGCATTTTGTGACCTGCAA 58.804 40.909 0.00 0.00 35.03 4.08
2641 2687 2.483363 CCAAAGCATTTTGTGACCTGCA 60.483 45.455 0.00 0.00 41.68 4.41
2732 2778 8.713708 TCAGAATGGTTACCTTTATTTTTCCA 57.286 30.769 2.07 0.00 36.16 3.53
2773 2820 7.309133 CCAAGGCATGTCATTTCTTTAACTACA 60.309 37.037 0.00 0.00 0.00 2.74
2774 2821 7.029563 CCAAGGCATGTCATTTCTTTAACTAC 58.970 38.462 0.00 0.00 0.00 2.73
2794 2842 4.743057 TCATGTGTCTATCAGACCAAGG 57.257 45.455 3.97 0.00 44.44 3.61
2798 2846 6.451393 GGACTTATCATGTGTCTATCAGACC 58.549 44.000 3.97 0.00 44.44 3.85
2843 2891 1.478105 GGGGTGATCATGCTGTTTTCC 59.522 52.381 0.00 0.00 0.00 3.13
2853 2901 0.761187 CATGACGAGGGGGTGATCAT 59.239 55.000 0.00 0.00 0.00 2.45
2884 2932 3.140325 TCGCTCTCCCAAAGTTTCATT 57.860 42.857 0.00 0.00 0.00 2.57
2890 2938 1.048601 TGTCTTCGCTCTCCCAAAGT 58.951 50.000 0.00 0.00 0.00 2.66
2935 2983 7.014134 TCTGTGGCATTTTCTATCTGTGAAAAA 59.986 33.333 5.87 0.00 43.62 1.94
2975 3023 3.638627 CCTCCTTCTCCAAGCTTGTTTTT 59.361 43.478 24.35 0.00 0.00 1.94
3048 3096 9.638239 ACGAAATTATCACAATTAGCAAACATT 57.362 25.926 0.00 0.00 0.00 2.71
3062 3134 6.111768 ACATGCTTCAGACGAAATTATCAC 57.888 37.500 0.00 0.00 0.00 3.06
3064 3136 7.222805 TGACTACATGCTTCAGACGAAATTATC 59.777 37.037 0.00 0.00 0.00 1.75
3072 3144 1.923204 GCTGACTACATGCTTCAGACG 59.077 52.381 18.40 0.00 39.36 4.18
3073 3145 2.964740 TGCTGACTACATGCTTCAGAC 58.035 47.619 18.40 11.85 39.36 3.51
3100 3172 4.695455 TCATTACTTGGCTACAGACAAAGC 59.305 41.667 0.00 0.00 43.43 3.51
3107 3179 7.712639 ACATTCACTATCATTACTTGGCTACAG 59.287 37.037 0.00 0.00 0.00 2.74
3109 3181 8.438676 AACATTCACTATCATTACTTGGCTAC 57.561 34.615 0.00 0.00 0.00 3.58
3155 3238 6.628175 GCTCCATTTTCCCCTTTCAATTAGTC 60.628 42.308 0.00 0.00 0.00 2.59
3196 3279 7.255569 TGTAACTATGAACATCTTACAGGACG 58.744 38.462 10.97 0.00 0.00 4.79
3219 3302 4.772624 TGACTAACAAGTAGAGGATGCTGT 59.227 41.667 0.00 0.00 33.61 4.40
3222 3305 5.521735 CACATGACTAACAAGTAGAGGATGC 59.478 44.000 0.00 0.00 33.61 3.91
3230 3313 4.344359 TGCCACACATGACTAACAAGTA 57.656 40.909 0.00 0.00 0.00 2.24
3256 3339 2.286125 TGCTTGATCGAACAACACAACG 60.286 45.455 3.72 0.00 0.00 4.10
3263 3346 1.798223 CCGAACTGCTTGATCGAACAA 59.202 47.619 7.93 7.93 42.45 2.83
3268 3351 0.516877 TTTGCCGAACTGCTTGATCG 59.483 50.000 3.78 3.78 40.07 3.69
3281 3364 6.587990 TGGTTTAATGTACATTGAATTTGCCG 59.412 34.615 27.62 0.00 30.66 5.69
3319 5127 3.327172 AGATTCAGCTCCCACTATCCATG 59.673 47.826 0.00 0.00 0.00 3.66
3357 5176 9.781834 TTTTTCAACAGTCAAACATTAGTACAG 57.218 29.630 0.00 0.00 0.00 2.74
3369 5188 7.412781 GCATTGTGTCAATTTTTCAACAGTCAA 60.413 33.333 0.00 0.00 0.00 3.18
3383 5202 1.355381 TCCCTGGAGCATTGTGTCAAT 59.645 47.619 0.00 0.00 0.00 2.57
3384 5203 0.770499 TCCCTGGAGCATTGTGTCAA 59.230 50.000 0.00 0.00 0.00 3.18
3403 5222 6.976934 ACATCTTGTCCATTTGGTAAGTTT 57.023 33.333 12.61 4.11 34.50 2.66
3490 5309 5.393461 GCTGTGTTGAAGCTTGGCTATTAAT 60.393 40.000 2.10 0.00 38.25 1.40
3523 5342 1.055849 TGCAGCAACCTAAGAGTCCA 58.944 50.000 0.00 0.00 0.00 4.02
3530 5349 1.164411 CCGTCAATGCAGCAACCTAA 58.836 50.000 0.00 0.00 0.00 2.69
3659 5480 1.273327 GGTTCAACAAGGCATGGAAGG 59.727 52.381 0.00 0.00 0.00 3.46
3672 5493 6.305638 GCAAAATAAGACTTGATCGGTTCAAC 59.694 38.462 0.00 0.00 39.44 3.18
3831 5652 6.283694 GTTCATATCAGTGTCCAGCAGAATA 58.716 40.000 0.00 0.00 0.00 1.75
3867 5688 1.821216 TTCTTGCCATTCCGAAGTCC 58.179 50.000 0.00 0.00 0.00 3.85
3873 5694 5.242393 AGGATCAAATATTCTTGCCATTCCG 59.758 40.000 0.00 0.00 0.00 4.30
4139 5962 2.267006 CCATGTCCACGAGCTGCT 59.733 61.111 0.00 0.00 0.00 4.24
4157 5980 3.073274 CCAAGGAGGTTTAGGGAGTTG 57.927 52.381 0.00 0.00 0.00 3.16
4330 6156 4.395625 CACCATATTCTCAGGACATGCAT 58.604 43.478 0.00 0.00 0.00 3.96
4430 6256 7.051623 AGGTGGCATTTTCGTTAGTAATCATA 58.948 34.615 0.00 0.00 0.00 2.15
4464 6290 2.287393 ACGAAACCAGGTTGTTTTGC 57.713 45.000 5.30 0.00 41.39 3.68
4579 6405 9.303116 ACACTCTTTATCTAATGGATACTCGAT 57.697 33.333 0.00 0.00 36.72 3.59
4580 6406 8.693120 ACACTCTTTATCTAATGGATACTCGA 57.307 34.615 0.00 0.00 36.72 4.04
4609 6435 7.390162 TGTCTGAACATATATTCACAAGCAACA 59.610 33.333 0.00 0.00 34.84 3.33
4617 6443 8.709386 ACTCTGTTGTCTGAACATATATTCAC 57.291 34.615 0.00 0.00 34.84 3.18
4654 6480 7.915923 CGTGTCACAGTCTAGTTAATATCATGT 59.084 37.037 3.42 0.00 0.00 3.21
4658 6484 5.395778 CGCGTGTCACAGTCTAGTTAATATC 59.604 44.000 0.00 0.00 0.00 1.63
5013 6849 8.437575 AGTTTTCTCTATAAACTGGGTCAAAGA 58.562 33.333 0.00 0.00 42.54 2.52
5398 7246 6.227522 TGGAACAATAGTCTTTCGTCAATGA 58.772 36.000 0.00 0.00 31.92 2.57
5439 7287 3.794028 TGTTAGTGTTCAAAAATGCGTGC 59.206 39.130 0.00 0.00 0.00 5.34
5442 7290 5.116983 GTCCATGTTAGTGTTCAAAAATGCG 59.883 40.000 0.00 0.00 0.00 4.73


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

AutoCloner maintained by Alex Coulton.