Multiple sequence alignment - TraesCS3B01G575800

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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 TraesCS3B01G575800 chr3B 100.000 8976 0 0 1 8976 806004812 805995837 0.000000e+00 16576.0
1 TraesCS3B01G575800 chr3B 97.374 7008 135 12 1987 8976 681023332 681016356 0.000000e+00 11876.0
2 TraesCS3B01G575800 chr3B 94.129 528 31 0 1144 1671 805812101 805811574 0.000000e+00 804.0
3 TraesCS3B01G575800 chr3B 94.118 527 31 0 1145 1671 806058704 806058178 0.000000e+00 802.0
4 TraesCS3B01G575800 chr3B 88.832 591 40 6 2 580 2122684 2122108 0.000000e+00 702.0
5 TraesCS3B01G575800 chr3B 87.288 590 38 10 1 570 188234727 188235299 2.730000e-179 640.0
6 TraesCS3B01G575800 chr3B 88.596 456 28 5 1144 1596 805977588 805977154 4.770000e-147 532.0
7 TraesCS3B01G575800 chr3B 85.135 370 34 11 232 580 662459775 662460144 8.570000e-95 359.0
8 TraesCS3B01G575800 chr3B 87.676 284 27 7 1714 1994 805675754 805675476 3.130000e-84 324.0
9 TraesCS3B01G575800 chr3B 96.460 113 3 1 585 696 806058884 806058772 1.540000e-42 185.0
10 TraesCS3B01G575800 chr3B 94.737 38 1 1 660 696 806058734 806058697 3.500000e-04 58.4
11 TraesCS3B01G575800 chr6B 97.741 6995 132 14 1999 8976 669538567 669545552 0.000000e+00 12019.0
12 TraesCS3B01G575800 chr6B 88.557 603 45 10 1 580 127313509 127312908 0.000000e+00 710.0
13 TraesCS3B01G575800 chr6B 84.668 587 50 15 24 580 95441737 95441161 4.740000e-152 549.0
14 TraesCS3B01G575800 chr4A 97.571 7000 148 11 1993 8976 727888170 727881177 0.000000e+00 11965.0
15 TraesCS3B01G575800 chr5B 96.815 7002 192 21 1993 8976 516067818 516074806 0.000000e+00 11666.0
16 TraesCS3B01G575800 chr5B 97.733 3794 74 6 1991 5775 34749855 34753645 0.000000e+00 6519.0
17 TraesCS3B01G575800 chr5B 88.284 606 45 9 1 580 659735209 659735814 0.000000e+00 702.0
18 TraesCS3B01G575800 chr2B 96.534 7010 202 21 1993 8976 53201005 53207999 0.000000e+00 11561.0
19 TraesCS3B01G575800 chr2B 96.104 7007 230 21 1991 8976 656380850 656387834 0.000000e+00 11387.0
20 TraesCS3B01G575800 chr2B 96.574 4174 117 16 1993 6148 53222982 53227147 0.000000e+00 6892.0
21 TraesCS3B01G575800 chr2B 97.528 3802 81 5 1994 5786 96165802 96162005 0.000000e+00 6488.0
22 TraesCS3B01G575800 chr2B 97.253 3823 90 7 1980 5790 782557638 782561457 0.000000e+00 6464.0
23 TraesCS3B01G575800 chr2B 97.431 3114 70 6 5868 8976 782561648 782564756 0.000000e+00 5299.0
24 TraesCS3B01G575800 chr2B 96.871 3132 86 10 5853 8976 662366939 662363812 0.000000e+00 5230.0
25 TraesCS3B01G575800 chr2B 87.669 592 51 10 10 580 727543125 727542535 0.000000e+00 669.0
26 TraesCS3B01G575800 chr2B 86.623 613 48 19 1 580 25795198 25794587 0.000000e+00 647.0
27 TraesCS3B01G575800 chr1B 96.624 4650 137 13 2980 7621 416752221 416756858 0.000000e+00 7699.0
28 TraesCS3B01G575800 chr1B 88.275 597 53 7 1 580 677252862 677252266 0.000000e+00 699.0
29 TraesCS3B01G575800 chr1B 87.245 588 56 8 1 580 608992992 608993568 0.000000e+00 652.0
30 TraesCS3B01G575800 chr1B 91.777 377 28 3 7 383 513159366 513158993 1.030000e-143 521.0
31 TraesCS3B01G575800 chr3D 95.265 528 25 0 1144 1671 598726319 598725792 0.000000e+00 837.0
32 TraesCS3B01G575800 chr3D 95.238 105 4 1 593 696 598726415 598726311 2.000000e-36 165.0
33 TraesCS3B01G575800 chr3D 91.489 47 3 1 1148 1194 575774815 575774770 7.520000e-06 63.9
34 TraesCS3B01G575800 chr7B 89.298 598 43 8 1 580 664320847 664321441 0.000000e+00 730.0
35 TraesCS3B01G575800 chr7B 89.130 598 43 7 1 580 664349042 664349635 0.000000e+00 725.0
36 TraesCS3B01G575800 chr7B 94.235 451 19 4 694 1143 44604400 44604844 0.000000e+00 682.0
37 TraesCS3B01G575800 chr7B 87.565 579 58 8 7 580 726148951 726148382 0.000000e+00 658.0
38 TraesCS3B01G575800 chr7B 86.304 606 52 17 1 580 720486937 720487537 1.640000e-176 630.0
39 TraesCS3B01G575800 chr7B 83.520 625 57 24 1 580 600700537 600699914 7.930000e-150 542.0
40 TraesCS3B01G575800 chr7B 88.571 245 28 0 1427 1671 73176689 73176933 1.890000e-76 298.0
41 TraesCS3B01G575800 chr7B 83.871 186 21 5 1138 1314 664399076 664398891 1.550000e-37 169.0
42 TraesCS3B01G575800 chr7A 85.321 545 57 8 1144 1671 566989434 566989972 7.930000e-150 542.0
43 TraesCS3B01G575800 chr7A 91.346 104 7 2 595 696 566989339 566989442 3.380000e-29 141.0
44 TraesCS3B01G575800 chr7A 100.000 29 0 0 660 688 566910197 566910225 5.000000e-03 54.7
45 TraesCS3B01G575800 chr6D 87.611 452 35 14 697 1143 18304175 18304610 1.040000e-138 505.0
46 TraesCS3B01G575800 chr6D 89.922 387 24 10 761 1143 18302920 18303295 1.350000e-132 484.0
47 TraesCS3B01G575800 chr6D 87.215 438 35 14 697 1129 18305502 18305923 6.300000e-131 479.0
48 TraesCS3B01G575800 chr7D 87.935 431 33 10 718 1143 19106505 19106921 2.910000e-134 490.0
49 TraesCS3B01G575800 chr4D 89.572 374 28 7 774 1143 452396216 452396582 1.770000e-126 464.0
50 TraesCS3B01G575800 chr2D 85.872 453 43 12 697 1144 19381942 19382378 6.350000e-126 462.0
51 TraesCS3B01G575800 chr2D 85.714 455 46 11 697 1146 573454042 573453602 6.350000e-126 462.0
52 TraesCS3B01G575800 chr2D 88.679 371 29 8 778 1143 573455296 573454934 2.970000e-119 440.0
53 TraesCS3B01G575800 chr1D 84.835 455 35 18 696 1143 422884987 422885414 2.320000e-115 427.0
54 TraesCS3B01G575800 chr3A 89.213 343 29 1 1144 1486 728925280 728924946 1.080000e-113 422.0
55 TraesCS3B01G575800 chr3A 91.489 188 16 0 1484 1671 728915280 728915093 8.940000e-65 259.0
56 TraesCS3B01G575800 chr3A 95.146 103 4 1 595 696 728925374 728925272 2.590000e-35 161.0
57 TraesCS3B01G575800 chrUn 81.544 531 51 17 1169 1671 86611945 86612456 2.350000e-105 394.0
58 TraesCS3B01G575800 chr4B 88.462 52 6 0 1661 1712 300162269 300162320 7.520000e-06 63.9


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G575800 chr3B 805995837 806004812 8975 True 16576.000000 16576 100.000000 1 8976 1 chr3B.!!$R6 8975
1 TraesCS3B01G575800 chr3B 681016356 681023332 6976 True 11876.000000 11876 97.374000 1987 8976 1 chr3B.!!$R2 6989
2 TraesCS3B01G575800 chr3B 805811574 805812101 527 True 804.000000 804 94.129000 1144 1671 1 chr3B.!!$R4 527
3 TraesCS3B01G575800 chr3B 2122108 2122684 576 True 702.000000 702 88.832000 2 580 1 chr3B.!!$R1 578
4 TraesCS3B01G575800 chr3B 188234727 188235299 572 False 640.000000 640 87.288000 1 570 1 chr3B.!!$F1 569
5 TraesCS3B01G575800 chr3B 806058178 806058884 706 True 348.466667 802 95.105000 585 1671 3 chr3B.!!$R7 1086
6 TraesCS3B01G575800 chr6B 669538567 669545552 6985 False 12019.000000 12019 97.741000 1999 8976 1 chr6B.!!$F1 6977
7 TraesCS3B01G575800 chr6B 127312908 127313509 601 True 710.000000 710 88.557000 1 580 1 chr6B.!!$R2 579
8 TraesCS3B01G575800 chr6B 95441161 95441737 576 True 549.000000 549 84.668000 24 580 1 chr6B.!!$R1 556
9 TraesCS3B01G575800 chr4A 727881177 727888170 6993 True 11965.000000 11965 97.571000 1993 8976 1 chr4A.!!$R1 6983
10 TraesCS3B01G575800 chr5B 516067818 516074806 6988 False 11666.000000 11666 96.815000 1993 8976 1 chr5B.!!$F2 6983
11 TraesCS3B01G575800 chr5B 34749855 34753645 3790 False 6519.000000 6519 97.733000 1991 5775 1 chr5B.!!$F1 3784
12 TraesCS3B01G575800 chr5B 659735209 659735814 605 False 702.000000 702 88.284000 1 580 1 chr5B.!!$F3 579
13 TraesCS3B01G575800 chr2B 53201005 53207999 6994 False 11561.000000 11561 96.534000 1993 8976 1 chr2B.!!$F1 6983
14 TraesCS3B01G575800 chr2B 656380850 656387834 6984 False 11387.000000 11387 96.104000 1991 8976 1 chr2B.!!$F3 6985
15 TraesCS3B01G575800 chr2B 53222982 53227147 4165 False 6892.000000 6892 96.574000 1993 6148 1 chr2B.!!$F2 4155
16 TraesCS3B01G575800 chr2B 96162005 96165802 3797 True 6488.000000 6488 97.528000 1994 5786 1 chr2B.!!$R2 3792
17 TraesCS3B01G575800 chr2B 782557638 782564756 7118 False 5881.500000 6464 97.342000 1980 8976 2 chr2B.!!$F4 6996
18 TraesCS3B01G575800 chr2B 662363812 662366939 3127 True 5230.000000 5230 96.871000 5853 8976 1 chr2B.!!$R3 3123
19 TraesCS3B01G575800 chr2B 727542535 727543125 590 True 669.000000 669 87.669000 10 580 1 chr2B.!!$R4 570
20 TraesCS3B01G575800 chr2B 25794587 25795198 611 True 647.000000 647 86.623000 1 580 1 chr2B.!!$R1 579
21 TraesCS3B01G575800 chr1B 416752221 416756858 4637 False 7699.000000 7699 96.624000 2980 7621 1 chr1B.!!$F1 4641
22 TraesCS3B01G575800 chr1B 677252266 677252862 596 True 699.000000 699 88.275000 1 580 1 chr1B.!!$R2 579
23 TraesCS3B01G575800 chr1B 608992992 608993568 576 False 652.000000 652 87.245000 1 580 1 chr1B.!!$F2 579
24 TraesCS3B01G575800 chr3D 598725792 598726415 623 True 501.000000 837 95.251500 593 1671 2 chr3D.!!$R2 1078
25 TraesCS3B01G575800 chr7B 664320847 664321441 594 False 730.000000 730 89.298000 1 580 1 chr7B.!!$F3 579
26 TraesCS3B01G575800 chr7B 664349042 664349635 593 False 725.000000 725 89.130000 1 580 1 chr7B.!!$F4 579
27 TraesCS3B01G575800 chr7B 726148382 726148951 569 True 658.000000 658 87.565000 7 580 1 chr7B.!!$R3 573
28 TraesCS3B01G575800 chr7B 720486937 720487537 600 False 630.000000 630 86.304000 1 580 1 chr7B.!!$F5 579
29 TraesCS3B01G575800 chr7B 600699914 600700537 623 True 542.000000 542 83.520000 1 580 1 chr7B.!!$R1 579
30 TraesCS3B01G575800 chr7A 566989339 566989972 633 False 341.500000 542 88.333500 595 1671 2 chr7A.!!$F2 1076
31 TraesCS3B01G575800 chr6D 18302920 18305923 3003 False 489.333333 505 88.249333 697 1143 3 chr6D.!!$F1 446
32 TraesCS3B01G575800 chr2D 573453602 573455296 1694 True 451.000000 462 87.196500 697 1146 2 chr2D.!!$R1 449
33 TraesCS3B01G575800 chrUn 86611945 86612456 511 False 394.000000 394 81.544000 1169 1671 1 chrUn.!!$F1 502

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
796 1357 0.031043 CACACACACATGCACCAAGG 59.969 55.000 0.00 0.0 0.00 3.61 F
1180 1856 0.174389 CTGTGGATCCGACTCTGGTG 59.826 60.000 7.39 0.0 0.00 4.17 F
1715 2902 0.250858 TGCCAGCACATACACTGCTT 60.251 50.000 0.00 0.0 42.54 3.91 F
1716 2903 1.003003 TGCCAGCACATACACTGCTTA 59.997 47.619 0.00 0.0 42.54 3.09 F
2045 3232 1.134694 GCTTCAAATCCGCACGACC 59.865 57.895 0.00 0.0 0.00 4.79 F
2341 3535 1.471119 GACTGGTGGATACGGTGAGA 58.529 55.000 0.00 0.0 42.51 3.27 F
3768 4969 1.737838 CATCGTGTTATGGGTGTGCT 58.262 50.000 0.00 0.0 0.00 4.40 F
4197 5398 1.242076 GCTGATGAACTGCACAAGGT 58.758 50.000 0.00 0.0 41.89 3.50 F
5223 6436 2.014335 TTCACATGCATCTCGTCAGG 57.986 50.000 0.00 0.0 0.00 3.86 F
5680 6905 2.706339 CTTAGCCAGCAAGGTCTGAT 57.294 50.000 0.00 0.0 40.61 2.90 F
7198 8548 4.337145 TGTTGTCACAGGTTGGTAACTTT 58.663 39.130 0.00 0.0 37.61 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2057 3244 0.830648 GGTCCGTTGGATCTGGATCA 59.169 55.000 11.93 0.00 39.54 2.92 R
2445 3640 2.633481 AGCCGGCCTTAATCTAACCTAG 59.367 50.000 26.15 0.00 0.00 3.02 R
2748 3944 4.072131 ACATCCACAACAGTAACACCATC 58.928 43.478 0.00 0.00 0.00 3.51 R
3510 4711 4.388499 GCGGAGGAGGGCGTTTCA 62.388 66.667 0.00 0.00 0.00 2.69 R
3768 4969 0.107703 GACATCATTCCCTCCACGCA 60.108 55.000 0.00 0.00 0.00 5.24 R
4197 5398 1.065600 GGCTTGCGTTTCAACAGCA 59.934 52.632 5.48 5.48 36.93 4.41 R
5680 6905 1.079819 GCCTCAGCTTGCGTGTCTA 60.080 57.895 0.00 0.00 35.50 2.59 R
5706 6931 1.143305 CACCGCTTGACAGAAGAGTG 58.857 55.000 0.00 0.00 0.00 3.51 R
6380 7727 1.251251 CCCTTAGCAGCAGCAACTTT 58.749 50.000 3.17 0.00 45.49 2.66 R
7356 8707 0.539051 CCAGGGGTGCTCAACTCTAG 59.461 60.000 0.00 0.00 0.00 2.43 R
8759 10121 0.820871 GTGGTTTGTGCAAGGGTTGA 59.179 50.000 0.00 0.00 0.00 3.18 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
204 214 0.955428 ACTACGTCCGCGAACAGGTA 60.955 55.000 8.23 6.38 42.00 3.08
417 511 3.754965 ACAAGCTTCTTGGCATGTAGAA 58.245 40.909 10.54 5.69 41.37 2.10
557 679 1.766069 AATCGCCGAGTTTGCAAAAC 58.234 45.000 14.67 10.24 0.00 2.43
580 702 2.619147 TGAAACGAACTTCACCGAACA 58.381 42.857 0.00 0.00 30.31 3.18
581 703 2.349275 TGAAACGAACTTCACCGAACAC 59.651 45.455 0.00 0.00 30.31 3.32
583 705 2.012937 ACGAACTTCACCGAACACAA 57.987 45.000 0.00 0.00 0.00 3.33
613 736 2.003548 GGAGGGGAAGAGGGCATGT 61.004 63.158 0.00 0.00 0.00 3.21
688 811 0.179059 TCGACTTGCTTTGCTGGTCA 60.179 50.000 12.54 0.00 33.37 4.02
690 813 1.267806 CGACTTGCTTTGCTGGTCAAT 59.732 47.619 12.54 0.00 34.12 2.57
691 814 2.666619 CGACTTGCTTTGCTGGTCAATC 60.667 50.000 12.54 0.00 34.12 2.67
692 815 1.615392 ACTTGCTTTGCTGGTCAATCC 59.385 47.619 0.00 0.00 34.12 3.01
693 816 1.891150 CTTGCTTTGCTGGTCAATCCT 59.109 47.619 0.00 0.00 34.12 3.24
694 817 1.250328 TGCTTTGCTGGTCAATCCTG 58.750 50.000 0.00 0.00 38.06 3.86
695 818 1.251251 GCTTTGCTGGTCAATCCTGT 58.749 50.000 0.00 0.00 37.45 4.00
696 819 1.615392 GCTTTGCTGGTCAATCCTGTT 59.385 47.619 0.00 0.00 37.45 3.16
698 821 2.363306 TTGCTGGTCAATCCTGTTGT 57.637 45.000 0.00 0.00 37.45 3.32
702 825 1.270550 CTGGTCAATCCTGTTGTTGCC 59.729 52.381 0.00 0.00 37.07 4.52
703 826 0.240945 GGTCAATCCTGTTGTTGCCG 59.759 55.000 0.00 0.00 0.00 5.69
706 829 2.625823 AATCCTGTTGTTGCCGCCG 61.626 57.895 0.00 0.00 0.00 6.46
707 830 3.842925 ATCCTGTTGTTGCCGCCGT 62.843 57.895 0.00 0.00 0.00 5.68
709 832 2.411290 CTGTTGTTGCCGCCGTTT 59.589 55.556 0.00 0.00 0.00 3.60
733 1294 0.869454 CAGCGCCGCTCTTCTTCTAG 60.869 60.000 9.54 0.00 36.40 2.43
738 1299 1.269051 GCCGCTCTTCTTCTAGCTCTC 60.269 57.143 0.00 0.00 36.56 3.20
739 1300 2.020720 CCGCTCTTCTTCTAGCTCTCA 58.979 52.381 0.00 0.00 36.56 3.27
741 1302 2.421775 CGCTCTTCTTCTAGCTCTCACA 59.578 50.000 0.00 0.00 36.56 3.58
742 1303 3.119673 CGCTCTTCTTCTAGCTCTCACAA 60.120 47.826 0.00 0.00 36.56 3.33
743 1304 4.617067 CGCTCTTCTTCTAGCTCTCACAAA 60.617 45.833 0.00 0.00 36.56 2.83
744 1305 4.625311 GCTCTTCTTCTAGCTCTCACAAAC 59.375 45.833 0.00 0.00 35.80 2.93
745 1306 5.777802 CTCTTCTTCTAGCTCTCACAAACA 58.222 41.667 0.00 0.00 0.00 2.83
746 1307 5.533482 TCTTCTTCTAGCTCTCACAAACAC 58.467 41.667 0.00 0.00 0.00 3.32
747 1308 4.937201 TCTTCTAGCTCTCACAAACACA 57.063 40.909 0.00 0.00 0.00 3.72
748 1309 4.621991 TCTTCTAGCTCTCACAAACACAC 58.378 43.478 0.00 0.00 0.00 3.82
750 1311 3.717707 TCTAGCTCTCACAAACACACAC 58.282 45.455 0.00 0.00 0.00 3.82
751 1312 2.401583 AGCTCTCACAAACACACACA 57.598 45.000 0.00 0.00 0.00 3.72
752 1313 2.923121 AGCTCTCACAAACACACACAT 58.077 42.857 0.00 0.00 0.00 3.21
754 1315 2.287188 GCTCTCACAAACACACACATGG 60.287 50.000 0.00 0.00 0.00 3.66
755 1316 2.945008 CTCTCACAAACACACACATGGT 59.055 45.455 0.00 0.00 0.00 3.55
767 1328 3.299340 ACACATGGTGACGAACTCTAC 57.701 47.619 2.98 0.00 36.96 2.59
768 1329 2.626266 ACACATGGTGACGAACTCTACA 59.374 45.455 2.98 0.00 36.96 2.74
772 1333 1.002142 TGGTGACGAACTCTACACACG 60.002 52.381 0.00 0.00 35.33 4.49
774 1335 0.664224 TGACGAACTCTACACACGCA 59.336 50.000 0.00 0.00 0.00 5.24
776 1337 0.659417 ACGAACTCTACACACGCACG 60.659 55.000 0.00 0.00 0.00 5.34
780 1341 1.660264 CTCTACACACGCACGCACA 60.660 57.895 0.00 0.00 0.00 4.57
796 1357 0.031043 CACACACACATGCACCAAGG 59.969 55.000 0.00 0.00 0.00 3.61
801 1362 2.165167 CACACATGCACCAAGGAAGAT 58.835 47.619 0.00 0.00 0.00 2.40
802 1363 2.094906 CACACATGCACCAAGGAAGATG 60.095 50.000 0.00 0.00 0.00 2.90
805 1366 1.747355 CATGCACCAAGGAAGATGACC 59.253 52.381 0.00 0.00 0.00 4.02
806 1367 0.770499 TGCACCAAGGAAGATGACCA 59.230 50.000 0.00 0.00 0.00 4.02
808 1369 2.238521 GCACCAAGGAAGATGACCAAA 58.761 47.619 0.00 0.00 0.00 3.28
809 1370 2.627699 GCACCAAGGAAGATGACCAAAA 59.372 45.455 0.00 0.00 0.00 2.44
810 1371 3.259123 GCACCAAGGAAGATGACCAAAAT 59.741 43.478 0.00 0.00 0.00 1.82
811 1372 4.813027 CACCAAGGAAGATGACCAAAATG 58.187 43.478 0.00 0.00 0.00 2.32
832 1393 3.018598 GCTTTGCCAAGAGAAACTTCC 57.981 47.619 0.86 0.00 36.61 3.46
833 1394 2.625314 GCTTTGCCAAGAGAAACTTCCT 59.375 45.455 0.86 0.00 36.61 3.36
834 1395 3.068732 GCTTTGCCAAGAGAAACTTCCTT 59.931 43.478 0.86 0.00 36.61 3.36
835 1396 4.614946 CTTTGCCAAGAGAAACTTCCTTG 58.385 43.478 10.99 10.99 36.61 3.61
836 1397 3.576078 TGCCAAGAGAAACTTCCTTGA 57.424 42.857 16.09 2.45 37.51 3.02
837 1398 4.104383 TGCCAAGAGAAACTTCCTTGAT 57.896 40.909 16.09 0.00 37.51 2.57
838 1399 3.822735 TGCCAAGAGAAACTTCCTTGATG 59.177 43.478 16.09 7.08 37.51 3.07
840 1401 3.192212 CCAAGAGAAACTTCCTTGATGCC 59.808 47.826 16.09 0.00 37.51 4.40
844 1405 1.546029 GAAACTTCCTTGATGCCCACC 59.454 52.381 0.00 0.00 0.00 4.61
858 1419 1.305219 CCCACCGTGGCTACATTGTG 61.305 60.000 12.54 4.40 35.79 3.33
860 1421 1.338294 CCACCGTGGCTACATTGTGTA 60.338 52.381 4.16 0.00 32.37 2.90
861 1422 2.627945 CACCGTGGCTACATTGTGTAT 58.372 47.619 0.00 0.00 31.66 2.29
863 1424 2.500098 ACCGTGGCTACATTGTGTATCT 59.500 45.455 0.00 0.00 31.66 1.98
871 1432 4.039245 GCTACATTGTGTATCTAGCCCTCA 59.961 45.833 0.00 0.00 31.66 3.86
874 1435 2.139323 TGTGTATCTAGCCCTCACGT 57.861 50.000 0.00 0.00 32.55 4.49
878 1439 1.881324 GTATCTAGCCCTCACGTCCTC 59.119 57.143 0.00 0.00 0.00 3.71
888 1449 3.447586 CCCTCACGTCCTCTTTCTCATTA 59.552 47.826 0.00 0.00 0.00 1.90
926 1487 0.548926 TACAAGGGGATGGCCTCACA 60.549 55.000 3.32 0.00 36.99 3.58
1013 1575 2.175715 GGAATCCCTCCCAGCTAACAAT 59.824 50.000 0.00 0.00 38.44 2.71
1060 1622 0.804364 TGCATGCATTTGACTCGACC 59.196 50.000 18.46 0.00 0.00 4.79
1115 1677 1.678635 CACAACCCGGCCATCACAT 60.679 57.895 2.24 0.00 0.00 3.21
1180 1856 0.174389 CTGTGGATCCGACTCTGGTG 59.826 60.000 7.39 0.00 0.00 4.17
1192 1872 4.335647 CTGGTGGAGGCCGCAAGT 62.336 66.667 9.31 0.00 35.42 3.16
1270 1964 2.543641 CATGATGTACGAGCAGCTCAA 58.456 47.619 22.49 6.79 0.00 3.02
1472 2623 3.755628 GCCTGCGTCTACCGGTGA 61.756 66.667 19.93 10.15 36.94 4.02
1488 2639 2.419159 CGGTGATCATGAGAAGAAGCCA 60.419 50.000 0.00 0.00 0.00 4.75
1492 2643 2.609427 TCATGAGAAGAAGCCATCGG 57.391 50.000 0.00 0.00 0.00 4.18
1507 2658 1.906105 ATCGGGCGCCACCTTCTTTA 61.906 55.000 30.85 1.90 39.10 1.85
1534 2685 1.338200 GGGATGACTTCGCTGACAACT 60.338 52.381 0.00 0.00 34.56 3.16
1557 2708 2.360980 CTCCCTCTGACCGACCCT 59.639 66.667 0.00 0.00 0.00 4.34
1558 2709 1.613610 CTCCCTCTGACCGACCCTA 59.386 63.158 0.00 0.00 0.00 3.53
1614 2773 1.141881 CTCCAACTACGCCGATGCT 59.858 57.895 0.00 0.00 34.43 3.79
1659 2846 3.127533 CCCGGCCGCTTCTCAAAG 61.128 66.667 22.85 1.77 35.47 2.77
1671 2858 4.872691 CGCTTCTCAAAGTACAAGATCCAT 59.127 41.667 0.00 0.00 34.79 3.41
1672 2859 5.220548 CGCTTCTCAAAGTACAAGATCCATG 60.221 44.000 0.00 0.00 34.79 3.66
1674 2861 6.036953 GCTTCTCAAAGTACAAGATCCATGAG 59.963 42.308 0.00 0.00 34.79 2.90
1676 2863 7.244886 TCTCAAAGTACAAGATCCATGAGAA 57.755 36.000 0.00 0.00 39.11 2.87
1677 2864 7.679783 TCTCAAAGTACAAGATCCATGAGAAA 58.320 34.615 0.00 0.00 39.11 2.52
1679 2866 8.099364 TCAAAGTACAAGATCCATGAGAAAAC 57.901 34.615 0.00 0.00 0.00 2.43
1680 2867 6.727824 AAGTACAAGATCCATGAGAAAACG 57.272 37.500 0.00 0.00 0.00 3.60
1681 2868 5.178797 AGTACAAGATCCATGAGAAAACGG 58.821 41.667 0.00 0.00 0.00 4.44
1682 2869 2.749621 ACAAGATCCATGAGAAAACGGC 59.250 45.455 0.00 0.00 0.00 5.68
1686 2873 2.270352 TCCATGAGAAAACGGCTTGT 57.730 45.000 0.00 0.00 0.00 3.16
1688 2875 1.879380 CCATGAGAAAACGGCTTGTCA 59.121 47.619 0.00 1.88 33.59 3.58
1689 2876 2.293122 CCATGAGAAAACGGCTTGTCAA 59.707 45.455 0.00 0.00 32.89 3.18
1690 2877 3.057315 CCATGAGAAAACGGCTTGTCAAT 60.057 43.478 0.00 0.00 32.89 2.57
1692 2879 2.948979 TGAGAAAACGGCTTGTCAATGT 59.051 40.909 0.00 0.00 0.00 2.71
1693 2880 3.380004 TGAGAAAACGGCTTGTCAATGTT 59.620 39.130 0.00 0.00 0.00 2.71
1696 2883 4.097892 AGAAAACGGCTTGTCAATGTTTCT 59.902 37.500 9.71 7.01 32.02 2.52
1697 2884 3.354089 AACGGCTTGTCAATGTTTCTG 57.646 42.857 0.00 0.00 0.00 3.02
1699 2886 1.666888 CGGCTTGTCAATGTTTCTGCC 60.667 52.381 0.00 0.00 36.14 4.85
1700 2887 1.340889 GGCTTGTCAATGTTTCTGCCA 59.659 47.619 5.18 0.00 38.99 4.92
1701 2888 2.608752 GGCTTGTCAATGTTTCTGCCAG 60.609 50.000 5.18 0.00 38.99 4.85
1702 2889 2.669364 CTTGTCAATGTTTCTGCCAGC 58.331 47.619 0.00 0.00 0.00 4.85
1703 2890 1.689984 TGTCAATGTTTCTGCCAGCA 58.310 45.000 0.00 0.00 0.00 4.41
1704 2891 1.337703 TGTCAATGTTTCTGCCAGCAC 59.662 47.619 0.00 0.00 0.00 4.40
1706 2893 2.029649 GTCAATGTTTCTGCCAGCACAT 60.030 45.455 4.10 4.10 0.00 3.21
1707 2894 3.191162 GTCAATGTTTCTGCCAGCACATA 59.809 43.478 9.09 0.00 0.00 2.29
1709 2896 2.268762 TGTTTCTGCCAGCACATACA 57.731 45.000 0.00 0.00 0.00 2.29
1710 2897 1.879380 TGTTTCTGCCAGCACATACAC 59.121 47.619 0.00 0.00 0.00 2.90
1711 2898 2.154462 GTTTCTGCCAGCACATACACT 58.846 47.619 0.00 0.00 0.00 3.55
1712 2899 1.812235 TTCTGCCAGCACATACACTG 58.188 50.000 0.00 0.00 0.00 3.66
1713 2900 0.674581 TCTGCCAGCACATACACTGC 60.675 55.000 0.00 0.00 32.37 4.40
1714 2901 0.675837 CTGCCAGCACATACACTGCT 60.676 55.000 0.00 0.00 46.21 4.24
1715 2902 0.250858 TGCCAGCACATACACTGCTT 60.251 50.000 0.00 0.00 42.54 3.91
1716 2903 1.003003 TGCCAGCACATACACTGCTTA 59.997 47.619 0.00 0.00 42.54 3.09
1717 2904 1.667724 GCCAGCACATACACTGCTTAG 59.332 52.381 0.00 0.00 42.54 2.18
1718 2905 2.936993 GCCAGCACATACACTGCTTAGT 60.937 50.000 0.00 0.00 42.54 2.24
1719 2906 2.932614 CCAGCACATACACTGCTTAGTC 59.067 50.000 0.00 0.00 42.54 2.59
1720 2907 2.932614 CAGCACATACACTGCTTAGTCC 59.067 50.000 0.00 0.00 42.54 3.85
1721 2908 2.567169 AGCACATACACTGCTTAGTCCA 59.433 45.455 0.00 0.00 42.54 4.02
1722 2909 3.007940 AGCACATACACTGCTTAGTCCAA 59.992 43.478 0.00 0.00 42.54 3.53
1723 2910 3.751175 GCACATACACTGCTTAGTCCAAA 59.249 43.478 0.00 0.00 0.00 3.28
1724 2911 4.378459 GCACATACACTGCTTAGTCCAAAC 60.378 45.833 0.00 0.00 0.00 2.93
1725 2912 4.754618 CACATACACTGCTTAGTCCAAACA 59.245 41.667 0.00 0.00 0.00 2.83
1726 2913 5.412594 CACATACACTGCTTAGTCCAAACAT 59.587 40.000 0.00 0.00 0.00 2.71
1727 2914 6.003950 ACATACACTGCTTAGTCCAAACATT 58.996 36.000 0.00 0.00 0.00 2.71
1728 2915 6.490040 ACATACACTGCTTAGTCCAAACATTT 59.510 34.615 0.00 0.00 0.00 2.32
1729 2916 5.852282 ACACTGCTTAGTCCAAACATTTT 57.148 34.783 0.00 0.00 0.00 1.82
1730 2917 6.220726 ACACTGCTTAGTCCAAACATTTTT 57.779 33.333 0.00 0.00 0.00 1.94
1772 2959 8.094798 ACTTAAACTCAATTTATCAAGCGACA 57.905 30.769 0.00 0.00 32.71 4.35
1773 2960 8.564574 ACTTAAACTCAATTTATCAAGCGACAA 58.435 29.630 0.00 0.00 32.71 3.18
1774 2961 8.948853 TTAAACTCAATTTATCAAGCGACAAG 57.051 30.769 0.00 0.00 32.71 3.16
1775 2962 7.537306 TTAAACTCAATTTATCAAGCGACAAGC 59.463 33.333 0.00 0.00 38.16 4.01
1930 3117 9.696917 AAAGCTACTAAATTTTTGAGTCATTGG 57.303 29.630 0.00 0.00 0.00 3.16
1931 3118 7.315890 AGCTACTAAATTTTTGAGTCATTGGC 58.684 34.615 0.00 0.00 0.00 4.52
1932 3119 6.531594 GCTACTAAATTTTTGAGTCATTGGCC 59.468 38.462 0.00 0.00 0.00 5.36
1933 3120 5.793817 ACTAAATTTTTGAGTCATTGGCCC 58.206 37.500 0.00 0.00 0.00 5.80
1934 3121 4.980339 AAATTTTTGAGTCATTGGCCCT 57.020 36.364 0.00 0.00 0.00 5.19
1935 3122 4.980339 AATTTTTGAGTCATTGGCCCTT 57.020 36.364 0.00 0.00 0.00 3.95
1936 3123 6.432403 AAATTTTTGAGTCATTGGCCCTTA 57.568 33.333 0.00 0.00 0.00 2.69
1937 3124 6.432403 AATTTTTGAGTCATTGGCCCTTAA 57.568 33.333 0.00 0.00 0.00 1.85
1938 3125 5.878406 TTTTTGAGTCATTGGCCCTTAAA 57.122 34.783 0.00 0.00 0.00 1.52
1939 3126 5.878406 TTTTGAGTCATTGGCCCTTAAAA 57.122 34.783 0.00 2.33 0.00 1.52
1940 3127 4.864704 TTGAGTCATTGGCCCTTAAAAC 57.135 40.909 0.00 0.00 0.00 2.43
1941 3128 3.838565 TGAGTCATTGGCCCTTAAAACA 58.161 40.909 0.00 0.00 0.00 2.83
1942 3129 4.415596 TGAGTCATTGGCCCTTAAAACAT 58.584 39.130 0.00 0.00 0.00 2.71
1943 3130 4.462483 TGAGTCATTGGCCCTTAAAACATC 59.538 41.667 0.00 0.00 0.00 3.06
1944 3131 4.677182 AGTCATTGGCCCTTAAAACATCT 58.323 39.130 0.00 0.00 0.00 2.90
1945 3132 5.086621 AGTCATTGGCCCTTAAAACATCTT 58.913 37.500 0.00 0.00 0.00 2.40
1946 3133 6.252995 AGTCATTGGCCCTTAAAACATCTTA 58.747 36.000 0.00 0.00 0.00 2.10
1947 3134 6.723977 AGTCATTGGCCCTTAAAACATCTTAA 59.276 34.615 0.00 0.00 0.00 1.85
1948 3135 7.400052 AGTCATTGGCCCTTAAAACATCTTAAT 59.600 33.333 0.00 0.00 0.00 1.40
1949 3136 8.040727 GTCATTGGCCCTTAAAACATCTTAATT 58.959 33.333 0.00 0.00 0.00 1.40
1950 3137 9.261035 TCATTGGCCCTTAAAACATCTTAATTA 57.739 29.630 0.00 0.00 0.00 1.40
1951 3138 9.883142 CATTGGCCCTTAAAACATCTTAATTAA 57.117 29.630 0.00 0.00 0.00 1.40
2045 3232 1.134694 GCTTCAAATCCGCACGACC 59.865 57.895 0.00 0.00 0.00 4.79
2057 3244 2.597805 ACGACCCGACAGCTGTCT 60.598 61.111 36.78 23.34 42.66 3.41
2341 3535 1.471119 GACTGGTGGATACGGTGAGA 58.529 55.000 0.00 0.00 42.51 3.27
2445 3640 6.255887 CGAATCTGGTAGATTGTTGTTCCTAC 59.744 42.308 8.66 0.00 44.41 3.18
2748 3944 6.435904 TGGTTGGTTCTAATAGGGATTTTGTG 59.564 38.462 0.00 0.00 0.00 3.33
3113 4310 5.050126 TGGTGATGGTTTTACACTTACCA 57.950 39.130 0.00 0.00 45.32 3.25
3312 4509 9.764363 CAGTCTCACATGCTTTTTATATACCTA 57.236 33.333 0.00 0.00 0.00 3.08
3510 4711 3.570912 TGAGGTTCCTTCGAAAAAGGT 57.429 42.857 0.00 0.00 38.55 3.50
3628 4829 6.679327 ATGGATTTAACTAGCCTTCGAAAC 57.321 37.500 0.00 0.00 0.00 2.78
3640 4841 3.129287 GCCTTCGAAACATCCAATGTGAT 59.871 43.478 0.00 0.00 44.07 3.06
3768 4969 1.737838 CATCGTGTTATGGGTGTGCT 58.262 50.000 0.00 0.00 0.00 4.40
4197 5398 1.242076 GCTGATGAACTGCACAAGGT 58.758 50.000 0.00 0.00 41.89 3.50
4494 5695 5.047377 TGTTCAGGCTGACAAAGTTTCTTTT 60.047 36.000 18.55 0.00 0.00 2.27
5223 6436 2.014335 TTCACATGCATCTCGTCAGG 57.986 50.000 0.00 0.00 0.00 3.86
5263 6476 3.227276 CTCCTCTGCCGCCCGTAT 61.227 66.667 0.00 0.00 0.00 3.06
5571 6796 3.139397 ACCAAATGTTGAAGACACCCCTA 59.861 43.478 0.00 0.00 42.04 3.53
5680 6905 2.706339 CTTAGCCAGCAAGGTCTGAT 57.294 50.000 0.00 0.00 40.61 2.90
5706 6931 4.400961 AAGCTGAGGCGGCCACTC 62.401 66.667 23.09 15.68 44.37 3.51
5757 6982 7.047271 TGAGCTTTTGAAAAATTTGGCTTACT 58.953 30.769 3.40 0.00 29.39 2.24
6221 7564 7.813645 AGGTATTCAAATTGTTACTTCCGTTC 58.186 34.615 0.00 0.00 0.00 3.95
6251 7595 6.751425 TCAGCAGTTATTTTGTTCTTGTTGTG 59.249 34.615 0.00 0.00 0.00 3.33
6380 7727 6.647334 TTTCATTCAGTGCACCTATGAAAA 57.353 33.333 29.79 20.64 40.35 2.29
6563 7910 9.244292 CTGGATGCTACTTATACCTGAAGTATA 57.756 37.037 0.00 0.00 41.97 1.47
7142 8492 5.422331 ACAATATGCCTACTGATACGGCTAT 59.578 40.000 0.00 0.00 44.09 2.97
7198 8548 4.337145 TGTTGTCACAGGTTGGTAACTTT 58.663 39.130 0.00 0.00 37.61 2.66
7356 8707 2.093216 GCAGTAGCTGACCATGCAC 58.907 57.895 0.00 0.00 36.88 4.57
7358 8709 1.134699 GCAGTAGCTGACCATGCACTA 60.135 52.381 0.00 0.00 36.88 2.74
7422 8774 1.903877 GCCACCCAGCTGCTCTCTTA 61.904 60.000 8.66 0.00 0.00 2.10
7642 8994 2.283966 AGCTACTGGCCCTGACGT 60.284 61.111 0.00 0.00 43.05 4.34
7785 9137 1.730064 GTGTCTTCGCTTTTATGCCGA 59.270 47.619 0.00 0.00 0.00 5.54
7865 9217 7.655328 TGTGCTCTTTTTATTTATGTGTTTGGG 59.345 33.333 0.00 0.00 0.00 4.12
8118 9473 6.434340 TGATACGTACATCTCCTATCATTGCT 59.566 38.462 0.00 0.00 0.00 3.91
8273 9628 6.323203 ACTCAAATGTTCAAATCCTGTCAG 57.677 37.500 0.00 0.00 0.00 3.51
8444 9802 4.340617 TGTTCCTTAAAAGGCCCATACAG 58.659 43.478 0.00 0.00 46.06 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
306 335 1.070105 ACGTGGTTAGGCGCTTGAA 59.930 52.632 7.64 0.00 0.00 2.69
316 345 2.050168 GTCGCCGACACGTGGTTA 60.050 61.111 21.57 0.00 32.09 2.85
375 404 0.319297 GAAGCGGGTGTAGTTGTCGT 60.319 55.000 0.00 0.00 0.00 4.34
380 474 2.612221 GCTTGTAGAAGCGGGTGTAGTT 60.612 50.000 9.06 0.00 45.12 2.24
476 593 7.969314 ACAAAAACGTAAAAACATGCAAGAAT 58.031 26.923 0.00 0.00 0.00 2.40
557 679 3.936902 TCGGTGAAGTTCGTTTCAAAG 57.063 42.857 0.00 1.29 38.69 2.77
580 702 0.535102 CCTCCTCCACGCTGTTTTGT 60.535 55.000 0.00 0.00 0.00 2.83
581 703 1.237285 CCCTCCTCCACGCTGTTTTG 61.237 60.000 0.00 0.00 0.00 2.44
583 705 2.750350 CCCTCCTCCACGCTGTTT 59.250 61.111 0.00 0.00 0.00 2.83
613 736 0.688749 TGGCCAGCTGCTCATCTCTA 60.689 55.000 8.66 0.00 40.92 2.43
658 781 0.097150 GCAAGTCGAAATCGGGCTTC 59.903 55.000 2.63 0.85 40.29 3.86
688 811 2.625823 CGGCGGCAACAACAGGATT 61.626 57.895 10.53 0.00 0.00 3.01
690 813 4.555709 ACGGCGGCAACAACAGGA 62.556 61.111 13.24 0.00 0.00 3.86
691 814 2.999363 GAAACGGCGGCAACAACAGG 62.999 60.000 13.24 0.00 0.00 4.00
692 815 1.657181 GAAACGGCGGCAACAACAG 60.657 57.895 13.24 0.00 0.00 3.16
693 816 2.054140 GAGAAACGGCGGCAACAACA 62.054 55.000 13.24 0.00 0.00 3.33
694 817 1.370051 GAGAAACGGCGGCAACAAC 60.370 57.895 13.24 0.00 0.00 3.32
695 818 2.887889 CGAGAAACGGCGGCAACAA 61.888 57.895 13.24 0.00 38.46 2.83
696 819 3.342627 CGAGAAACGGCGGCAACA 61.343 61.111 13.24 0.00 38.46 3.33
715 1276 1.435515 CTAGAAGAAGAGCGGCGCT 59.564 57.895 37.11 37.11 43.88 5.92
718 1279 0.744281 AGAGCTAGAAGAAGAGCGGC 59.256 55.000 0.00 0.00 43.72 6.53
719 1280 2.020720 TGAGAGCTAGAAGAAGAGCGG 58.979 52.381 0.00 0.00 43.72 5.52
723 1284 5.069119 TGTGTTTGTGAGAGCTAGAAGAAGA 59.931 40.000 0.00 0.00 0.00 2.87
733 1294 2.287188 CCATGTGTGTGTTTGTGAGAGC 60.287 50.000 0.00 0.00 0.00 4.09
738 1299 2.790812 CGTCACCATGTGTGTGTTTGTG 60.791 50.000 12.26 1.47 45.61 3.33
739 1300 1.400142 CGTCACCATGTGTGTGTTTGT 59.600 47.619 12.26 0.00 45.61 2.83
741 1302 2.031258 TCGTCACCATGTGTGTGTTT 57.969 45.000 12.26 0.00 45.61 2.83
742 1303 1.668751 GTTCGTCACCATGTGTGTGTT 59.331 47.619 12.26 0.00 45.61 3.32
743 1304 1.134521 AGTTCGTCACCATGTGTGTGT 60.135 47.619 12.26 0.00 45.61 3.72
744 1305 1.526887 GAGTTCGTCACCATGTGTGTG 59.473 52.381 12.26 4.61 45.61 3.82
745 1306 1.412710 AGAGTTCGTCACCATGTGTGT 59.587 47.619 12.26 0.00 45.61 3.72
746 1307 2.154854 AGAGTTCGTCACCATGTGTG 57.845 50.000 7.72 7.72 46.88 3.82
747 1308 2.626266 TGTAGAGTTCGTCACCATGTGT 59.374 45.455 0.00 0.00 34.79 3.72
748 1309 2.987149 GTGTAGAGTTCGTCACCATGTG 59.013 50.000 0.00 0.00 34.45 3.21
750 1311 2.987149 GTGTGTAGAGTTCGTCACCATG 59.013 50.000 0.00 0.00 0.00 3.66
751 1312 2.351447 CGTGTGTAGAGTTCGTCACCAT 60.351 50.000 0.00 0.00 0.00 3.55
752 1313 1.002142 CGTGTGTAGAGTTCGTCACCA 60.002 52.381 0.00 0.00 0.00 4.17
754 1315 1.050767 GCGTGTGTAGAGTTCGTCAC 58.949 55.000 0.00 0.00 0.00 3.67
755 1316 0.664224 TGCGTGTGTAGAGTTCGTCA 59.336 50.000 0.00 0.00 0.00 4.35
756 1317 1.050767 GTGCGTGTGTAGAGTTCGTC 58.949 55.000 0.00 0.00 0.00 4.20
757 1318 0.659417 CGTGCGTGTGTAGAGTTCGT 60.659 55.000 0.00 0.00 0.00 3.85
758 1319 1.930816 GCGTGCGTGTGTAGAGTTCG 61.931 60.000 0.00 0.00 0.00 3.95
759 1320 0.937699 TGCGTGCGTGTGTAGAGTTC 60.938 55.000 0.00 0.00 0.00 3.01
760 1321 1.066752 TGCGTGCGTGTGTAGAGTT 59.933 52.632 0.00 0.00 0.00 3.01
761 1322 1.660575 GTGCGTGCGTGTGTAGAGT 60.661 57.895 0.00 0.00 0.00 3.24
762 1323 1.660264 TGTGCGTGCGTGTGTAGAG 60.660 57.895 0.00 0.00 0.00 2.43
763 1324 1.947146 GTGTGCGTGCGTGTGTAGA 60.947 57.895 0.00 0.00 0.00 2.59
764 1325 2.234335 TGTGTGCGTGCGTGTGTAG 61.234 57.895 0.00 0.00 0.00 2.74
765 1326 2.202756 TGTGTGCGTGCGTGTGTA 60.203 55.556 0.00 0.00 0.00 2.90
766 1327 3.860125 GTGTGTGCGTGCGTGTGT 61.860 61.111 0.00 0.00 0.00 3.72
767 1328 3.858989 TGTGTGTGCGTGCGTGTG 61.859 61.111 0.00 0.00 0.00 3.82
768 1329 3.860125 GTGTGTGTGCGTGCGTGT 61.860 61.111 0.00 0.00 0.00 4.49
772 1333 2.726912 GCATGTGTGTGTGCGTGC 60.727 61.111 0.00 0.00 39.89 5.34
774 1335 2.715005 GTGCATGTGTGTGTGCGT 59.285 55.556 0.00 0.00 44.11 5.24
776 1337 0.595567 CTTGGTGCATGTGTGTGTGC 60.596 55.000 0.00 0.00 41.61 4.57
780 1341 1.133823 TCTTCCTTGGTGCATGTGTGT 60.134 47.619 0.00 0.00 0.00 3.72
796 1357 3.681417 GCAAAGCCATTTTGGTCATCTTC 59.319 43.478 2.28 0.00 45.09 2.87
825 1386 1.632589 GGTGGGCATCAAGGAAGTTT 58.367 50.000 0.00 0.00 0.00 2.66
826 1387 0.609131 CGGTGGGCATCAAGGAAGTT 60.609 55.000 0.00 0.00 0.00 2.66
827 1388 1.002134 CGGTGGGCATCAAGGAAGT 60.002 57.895 0.00 0.00 0.00 3.01
829 1390 1.303236 CACGGTGGGCATCAAGGAA 60.303 57.895 0.00 0.00 0.00 3.36
830 1391 2.350895 CACGGTGGGCATCAAGGA 59.649 61.111 0.00 0.00 0.00 3.36
831 1392 2.751436 CCACGGTGGGCATCAAGG 60.751 66.667 19.63 0.00 32.67 3.61
840 1401 0.605319 ACACAATGTAGCCACGGTGG 60.605 55.000 22.87 22.87 41.55 4.61
844 1405 3.736252 GCTAGATACACAATGTAGCCACG 59.264 47.826 0.00 0.00 46.74 4.94
858 1419 1.881324 GAGGACGTGAGGGCTAGATAC 59.119 57.143 0.00 0.00 0.00 2.24
860 1421 0.553819 AGAGGACGTGAGGGCTAGAT 59.446 55.000 0.00 0.00 0.00 1.98
861 1422 0.331954 AAGAGGACGTGAGGGCTAGA 59.668 55.000 0.00 0.00 0.00 2.43
863 1424 1.183549 GAAAGAGGACGTGAGGGCTA 58.816 55.000 0.00 0.00 0.00 3.93
871 1432 5.723672 TCAAGTAATGAGAAAGAGGACGT 57.276 39.130 0.00 0.00 33.04 4.34
874 1435 7.795047 TGCATATCAAGTAATGAGAAAGAGGA 58.205 34.615 0.00 0.00 42.53 3.71
888 1449 9.453572 CCCTTGTATATATGTTGCATATCAAGT 57.546 33.333 17.77 5.61 34.91 3.16
944 1505 0.391263 GGAGTTAGTGGCCGAACCTG 60.391 60.000 10.48 0.00 40.22 4.00
945 1506 0.834687 TGGAGTTAGTGGCCGAACCT 60.835 55.000 10.48 1.06 40.22 3.50
946 1507 0.672711 GTGGAGTTAGTGGCCGAACC 60.673 60.000 10.48 2.53 39.84 3.62
1013 1575 4.235079 AGTTAGTGGCTGCATGGATAAA 57.765 40.909 0.50 0.00 0.00 1.40
1060 1622 6.749578 TGCAAACTACAACAGTATTGTGTTTG 59.250 34.615 23.39 23.39 43.73 2.93
1100 1662 2.044053 CCATGTGATGGCCGGGTT 60.044 61.111 2.18 0.00 44.70 4.11
1180 1856 3.682292 AATCGGACTTGCGGCCTCC 62.682 63.158 0.00 0.00 0.00 4.30
1192 1872 2.875933 AGCAAAACAAGTCGAAATCGGA 59.124 40.909 2.63 0.00 40.29 4.55
1414 2562 0.033991 CTCAGGACGAGGAGGAGGAA 60.034 60.000 0.00 0.00 38.18 3.36
1462 2613 3.898482 TCTTCTCATGATCACCGGTAGA 58.102 45.455 6.87 8.11 0.00 2.59
1472 2623 2.224475 CCCGATGGCTTCTTCTCATGAT 60.224 50.000 0.00 0.00 0.00 2.45
1488 2639 1.906105 TAAAGAAGGTGGCGCCCGAT 61.906 55.000 26.77 7.51 38.26 4.18
1492 2643 1.671328 GAAGATAAAGAAGGTGGCGCC 59.329 52.381 22.73 22.73 37.58 6.53
1507 2658 0.105039 GCGAAGTCATCCCCGAAGAT 59.895 55.000 0.00 0.00 0.00 2.40
1534 2685 1.609501 CGGTCAGAGGGAGGTTCCA 60.610 63.158 0.00 0.00 38.64 3.53
1557 2708 1.652563 CCGCGACATCTCGGTGATA 59.347 57.895 8.23 0.00 39.22 2.15
1558 2709 2.413351 CCGCGACATCTCGGTGAT 59.587 61.111 8.23 0.00 39.22 3.06
1614 2773 2.361104 GGCCGCAGAAACCCATCA 60.361 61.111 0.00 0.00 0.00 3.07
1642 2805 2.515996 TACTTTGAGAAGCGGCCGGG 62.516 60.000 29.38 0.00 36.29 5.73
1659 2846 4.201822 GCCGTTTTCTCATGGATCTTGTAC 60.202 45.833 0.00 0.00 0.00 2.90
1671 2858 2.948979 ACATTGACAAGCCGTTTTCTCA 59.051 40.909 0.00 0.00 0.00 3.27
1672 2859 3.626028 ACATTGACAAGCCGTTTTCTC 57.374 42.857 0.00 0.00 0.00 2.87
1674 2861 4.207019 CAGAAACATTGACAAGCCGTTTTC 59.793 41.667 12.01 7.62 30.32 2.29
1676 2863 3.705604 CAGAAACATTGACAAGCCGTTT 58.294 40.909 11.04 11.04 32.72 3.60
1677 2864 2.543653 GCAGAAACATTGACAAGCCGTT 60.544 45.455 0.00 0.00 0.00 4.44
1679 2866 1.666888 GGCAGAAACATTGACAAGCCG 60.667 52.381 0.00 0.00 0.00 5.52
1680 2867 1.340889 TGGCAGAAACATTGACAAGCC 59.659 47.619 5.62 5.62 41.15 4.35
1681 2868 2.669364 CTGGCAGAAACATTGACAAGC 58.331 47.619 9.42 0.00 32.10 4.01
1682 2869 2.034939 TGCTGGCAGAAACATTGACAAG 59.965 45.455 20.86 0.00 32.10 3.16
1686 2873 1.689984 TGTGCTGGCAGAAACATTGA 58.310 45.000 20.86 0.00 0.00 2.57
1688 2875 3.057315 GTGTATGTGCTGGCAGAAACATT 60.057 43.478 29.39 18.63 35.07 2.71
1689 2876 2.489329 GTGTATGTGCTGGCAGAAACAT 59.511 45.455 28.10 28.10 37.11 2.71
1690 2877 1.879380 GTGTATGTGCTGGCAGAAACA 59.121 47.619 20.86 20.96 0.00 2.83
1692 2879 2.153645 CAGTGTATGTGCTGGCAGAAA 58.846 47.619 20.86 1.81 0.00 2.52
1693 2880 1.812235 CAGTGTATGTGCTGGCAGAA 58.188 50.000 20.86 4.21 0.00 3.02
1696 2883 3.985877 GCAGTGTATGTGCTGGCA 58.014 55.556 0.00 0.00 37.96 4.92
1701 2888 2.972625 TGGACTAAGCAGTGTATGTGC 58.027 47.619 0.00 0.00 41.54 4.57
1702 2889 4.754618 TGTTTGGACTAAGCAGTGTATGTG 59.245 41.667 0.00 0.00 34.21 3.21
1703 2890 4.968259 TGTTTGGACTAAGCAGTGTATGT 58.032 39.130 0.00 0.00 34.21 2.29
1704 2891 6.500684 AATGTTTGGACTAAGCAGTGTATG 57.499 37.500 0.00 0.00 34.21 2.39
1706 2893 6.952773 AAAATGTTTGGACTAAGCAGTGTA 57.047 33.333 0.00 0.00 34.21 2.90
1707 2894 5.852282 AAAATGTTTGGACTAAGCAGTGT 57.148 34.783 0.00 0.00 34.21 3.55
1746 2933 9.210329 TGTCGCTTGATAAATTGAGTTTAAGTA 57.790 29.630 0.00 0.00 35.98 2.24
1747 2934 8.094798 TGTCGCTTGATAAATTGAGTTTAAGT 57.905 30.769 0.00 0.00 35.98 2.24
1748 2935 8.948853 TTGTCGCTTGATAAATTGAGTTTAAG 57.051 30.769 0.00 0.00 35.98 1.85
1749 2936 7.537306 GCTTGTCGCTTGATAAATTGAGTTTAA 59.463 33.333 0.00 0.00 34.27 1.52
1750 2937 7.021196 GCTTGTCGCTTGATAAATTGAGTTTA 58.979 34.615 0.00 0.00 34.71 2.01
1751 2938 5.858581 GCTTGTCGCTTGATAAATTGAGTTT 59.141 36.000 0.00 0.00 35.14 2.66
1752 2939 5.393962 GCTTGTCGCTTGATAAATTGAGTT 58.606 37.500 0.00 0.00 35.14 3.01
1753 2940 4.974591 GCTTGTCGCTTGATAAATTGAGT 58.025 39.130 0.00 0.00 35.14 3.41
1837 3024 9.868277 TTTCAATGAGTATTTTGTGAAAACACT 57.132 25.926 0.00 0.00 32.37 3.55
1904 3091 9.696917 CCAATGACTCAAAAATTTAGTAGCTTT 57.303 29.630 0.00 0.00 0.00 3.51
1905 3092 7.814587 GCCAATGACTCAAAAATTTAGTAGCTT 59.185 33.333 0.00 0.00 0.00 3.74
1906 3093 7.315890 GCCAATGACTCAAAAATTTAGTAGCT 58.684 34.615 0.00 0.00 0.00 3.32
1907 3094 6.531594 GGCCAATGACTCAAAAATTTAGTAGC 59.468 38.462 0.00 0.00 0.00 3.58
1908 3095 7.035612 GGGCCAATGACTCAAAAATTTAGTAG 58.964 38.462 4.39 0.00 0.00 2.57
1909 3096 6.723977 AGGGCCAATGACTCAAAAATTTAGTA 59.276 34.615 6.18 0.00 0.00 1.82
1910 3097 5.543790 AGGGCCAATGACTCAAAAATTTAGT 59.456 36.000 6.18 0.00 0.00 2.24
1911 3098 6.041423 AGGGCCAATGACTCAAAAATTTAG 57.959 37.500 6.18 0.00 0.00 1.85
1912 3099 6.432403 AAGGGCCAATGACTCAAAAATTTA 57.568 33.333 6.18 0.00 0.00 1.40
1913 3100 4.980339 AGGGCCAATGACTCAAAAATTT 57.020 36.364 6.18 0.00 0.00 1.82
1914 3101 4.980339 AAGGGCCAATGACTCAAAAATT 57.020 36.364 6.18 0.00 0.00 1.82
1915 3102 6.432403 TTTAAGGGCCAATGACTCAAAAAT 57.568 33.333 6.18 0.00 0.00 1.82
1916 3103 5.878406 TTTAAGGGCCAATGACTCAAAAA 57.122 34.783 6.18 0.00 0.00 1.94
1917 3104 5.129485 TGTTTTAAGGGCCAATGACTCAAAA 59.871 36.000 6.18 0.00 0.00 2.44
1918 3105 4.651503 TGTTTTAAGGGCCAATGACTCAAA 59.348 37.500 6.18 0.00 0.00 2.69
1919 3106 4.219115 TGTTTTAAGGGCCAATGACTCAA 58.781 39.130 6.18 0.00 0.00 3.02
1920 3107 3.838565 TGTTTTAAGGGCCAATGACTCA 58.161 40.909 6.18 0.00 0.00 3.41
1921 3108 4.706962 AGATGTTTTAAGGGCCAATGACTC 59.293 41.667 6.18 0.00 0.00 3.36
1922 3109 4.677182 AGATGTTTTAAGGGCCAATGACT 58.323 39.130 6.18 0.00 0.00 3.41
1923 3110 5.405935 AAGATGTTTTAAGGGCCAATGAC 57.594 39.130 6.18 0.00 0.00 3.06
1924 3111 7.732222 ATTAAGATGTTTTAAGGGCCAATGA 57.268 32.000 6.18 0.00 0.00 2.57
1925 3112 9.883142 TTAATTAAGATGTTTTAAGGGCCAATG 57.117 29.630 6.18 0.00 0.00 2.82
1986 3173 9.976511 CTGGTGGATAGATTAGTCGTTTATTTA 57.023 33.333 0.00 0.00 0.00 1.40
1987 3174 8.483758 ACTGGTGGATAGATTAGTCGTTTATTT 58.516 33.333 0.00 0.00 0.00 1.40
1988 3175 8.019656 ACTGGTGGATAGATTAGTCGTTTATT 57.980 34.615 0.00 0.00 0.00 1.40
1989 3176 7.598759 ACTGGTGGATAGATTAGTCGTTTAT 57.401 36.000 0.00 0.00 0.00 1.40
1990 3177 7.035840 GACTGGTGGATAGATTAGTCGTTTA 57.964 40.000 0.00 0.00 0.00 2.01
1991 3178 5.903810 GACTGGTGGATAGATTAGTCGTTT 58.096 41.667 0.00 0.00 0.00 3.60
2053 3240 1.482182 CCGTTGGATCTGGATCAGACA 59.518 52.381 11.93 0.00 43.63 3.41
2057 3244 0.830648 GGTCCGTTGGATCTGGATCA 59.169 55.000 11.93 0.00 39.54 2.92
2445 3640 2.633481 AGCCGGCCTTAATCTAACCTAG 59.367 50.000 26.15 0.00 0.00 3.02
2748 3944 4.072131 ACATCCACAACAGTAACACCATC 58.928 43.478 0.00 0.00 0.00 3.51
3068 4265 9.425248 ACCATGATAATTCAACCATAACAAGAT 57.575 29.630 0.00 0.00 34.96 2.40
3113 4310 5.012239 TGGTAACTACGGTAAGATGACAGT 58.988 41.667 0.00 0.00 37.61 3.55
3510 4711 4.388499 GCGGAGGAGGGCGTTTCA 62.388 66.667 0.00 0.00 0.00 2.69
3628 4829 8.161699 TGTTGAATAGATGATCACATTGGATG 57.838 34.615 0.00 0.00 36.82 3.51
3640 4841 7.332678 CACACACTGAGATTGTTGAATAGATGA 59.667 37.037 0.00 0.00 0.00 2.92
3768 4969 0.107703 GACATCATTCCCTCCACGCA 60.108 55.000 0.00 0.00 0.00 5.24
4197 5398 1.065600 GGCTTGCGTTTCAACAGCA 59.934 52.632 5.48 5.48 36.93 4.41
5131 6344 1.522806 GCCATGGCGGACGTGAATA 60.523 57.895 23.48 0.00 38.41 1.75
5223 6436 1.992170 ACGTTCAATCCAGCGTCTAC 58.008 50.000 0.00 0.00 31.54 2.59
5263 6476 1.208358 CGCGTAGTCCTTGACGTCA 59.792 57.895 15.76 15.76 41.13 4.35
5547 6772 2.955660 GGGTGTCTTCAACATTTGGTCA 59.044 45.455 0.00 0.00 40.80 4.02
5680 6905 1.079819 GCCTCAGCTTGCGTGTCTA 60.080 57.895 0.00 0.00 35.50 2.59
5706 6931 1.143305 CACCGCTTGACAGAAGAGTG 58.857 55.000 0.00 0.00 0.00 3.51
6216 7559 4.685169 AATAACTGCTGAACATGAACGG 57.315 40.909 0.00 0.00 0.00 4.44
6221 7564 7.436080 ACAAGAACAAAATAACTGCTGAACATG 59.564 33.333 0.00 0.00 0.00 3.21
6380 7727 1.251251 CCCTTAGCAGCAGCAACTTT 58.749 50.000 3.17 0.00 45.49 2.66
7058 8407 7.537306 CGGAAAAAGATTAAACACATCGTCAAT 59.463 33.333 0.00 0.00 0.00 2.57
7142 8492 4.908601 TCATTCTTTTCACCTCCAGCTA 57.091 40.909 0.00 0.00 0.00 3.32
7356 8707 0.539051 CCAGGGGTGCTCAACTCTAG 59.461 60.000 0.00 0.00 0.00 2.43
7358 8709 1.152030 TCCAGGGGTGCTCAACTCT 60.152 57.895 0.00 0.00 0.00 3.24
7380 8731 7.554835 TGGCATAAAATTACCATCGTAGTTTCT 59.445 33.333 0.00 0.00 34.37 2.52
7422 8774 1.637553 ACCAAAGATGTCATCCAGCCT 59.362 47.619 9.29 0.00 0.00 4.58
7642 8994 3.064987 GCTGCGAGCCCTAGAACGA 62.065 63.158 0.00 0.00 34.48 3.85
7785 9137 6.781507 TGACATATCTCAATCCATCACTCTCT 59.218 38.462 0.00 0.00 0.00 3.10
7865 9217 6.201044 CCATACACACGGAATGATAGAAAGTC 59.799 42.308 0.00 0.00 0.00 3.01
8273 9628 9.722056 GAGTTATTGTGTCAATGGATCATAAAC 57.278 33.333 5.40 0.59 0.00 2.01
8606 9967 2.432628 CGACCAGCTTCCGGTGTC 60.433 66.667 0.00 0.00 36.69 3.67
8759 10121 0.820871 GTGGTTTGTGCAAGGGTTGA 59.179 50.000 0.00 0.00 0.00 3.18
8906 10268 1.271762 GGGGGTTGTCTGGTAGAAACC 60.272 57.143 11.27 11.27 46.98 3.27


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

AutoCloner maintained by Alex Coulton.