Multiple sequence alignment - TraesCS2A01G173200

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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 TraesCS2A01G173200 chr2A 100.000 4394 0 0 1 4394 130722246 130726639 0.000000e+00 8115
1 TraesCS2A01G173200 chr2D 90.013 3024 122 67 565 3499 124808029 124810961 0.000000e+00 3746
2 TraesCS2A01G173200 chr2D 93.846 390 18 5 139 525 124807630 124808016 2.280000e-162 582
3 TraesCS2A01G173200 chr2B 87.185 1826 103 59 565 2347 177597251 177598988 0.000000e+00 1954
4 TraesCS2A01G173200 chr2B 89.885 1305 55 34 2388 3651 177598989 177600257 0.000000e+00 1607
5 TraesCS2A01G173200 chr2B 91.636 538 26 13 2 525 177596706 177597238 0.000000e+00 726
6 TraesCS2A01G173200 chr5A 88.999 709 55 3 3707 4394 671479054 671478348 0.000000e+00 856
7 TraesCS2A01G173200 chr6B 86.521 779 65 9 3652 4394 470913144 470912370 0.000000e+00 821
8 TraesCS2A01G173200 chr6D 87.840 699 51 7 3726 4394 356195567 356196261 0.000000e+00 789
9 TraesCS2A01G173200 chr4A 88.694 628 61 9 3650 4270 617724515 617725139 0.000000e+00 758
10 TraesCS2A01G173200 chr4A 84.821 784 69 16 3650 4394 617789995 617790767 0.000000e+00 743
11 TraesCS2A01G173200 chr4A 84.566 784 72 15 3650 4394 617757718 617758491 0.000000e+00 732
12 TraesCS2A01G173200 chr4A 85.455 110 10 3 4285 4394 617725186 617725289 4.650000e-20 110
13 TraesCS2A01G173200 chrUn 88.376 628 61 11 3650 4270 235771616 235772238 0.000000e+00 745
14 TraesCS2A01G173200 chrUn 83.598 378 22 14 4051 4394 325321294 325321665 7.090000e-83 318
15 TraesCS2A01G173200 chrUn 86.364 110 9 3 4285 4394 235772285 235772388 9.990000e-22 115
16 TraesCS2A01G173200 chr7D 84.217 792 66 16 3652 4393 560756397 560757179 0.000000e+00 715
17 TraesCS2A01G173200 chr3B 83.162 778 92 15 3650 4394 16324342 16323571 0.000000e+00 675
18 TraesCS2A01G173200 chr1B 82.592 764 101 24 3655 4394 476694716 476693961 0.000000e+00 645
19 TraesCS2A01G173200 chr4B 79.445 793 109 18 3652 4394 75637487 75638275 3.030000e-141 512
20 TraesCS2A01G173200 chr3D 82.857 350 26 18 4071 4394 305604869 305605210 2.590000e-72 283
21 TraesCS2A01G173200 chr7B 79.070 301 37 16 4112 4388 238369455 238369157 2.700000e-42 183


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 TraesCS2A01G173200 chr2A 130722246 130726639 4393 False 8115 8115 100.000000 1 4394 1 chr2A.!!$F1 4393
1 TraesCS2A01G173200 chr2D 124807630 124810961 3331 False 2164 3746 91.929500 139 3499 2 chr2D.!!$F1 3360
2 TraesCS2A01G173200 chr2B 177596706 177600257 3551 False 1429 1954 89.568667 2 3651 3 chr2B.!!$F1 3649
3 TraesCS2A01G173200 chr5A 671478348 671479054 706 True 856 856 88.999000 3707 4394 1 chr5A.!!$R1 687
4 TraesCS2A01G173200 chr6B 470912370 470913144 774 True 821 821 86.521000 3652 4394 1 chr6B.!!$R1 742
5 TraesCS2A01G173200 chr6D 356195567 356196261 694 False 789 789 87.840000 3726 4394 1 chr6D.!!$F1 668
6 TraesCS2A01G173200 chr4A 617789995 617790767 772 False 743 743 84.821000 3650 4394 1 chr4A.!!$F2 744
7 TraesCS2A01G173200 chr4A 617757718 617758491 773 False 732 732 84.566000 3650 4394 1 chr4A.!!$F1 744
8 TraesCS2A01G173200 chr4A 617724515 617725289 774 False 434 758 87.074500 3650 4394 2 chr4A.!!$F3 744
9 TraesCS2A01G173200 chrUn 235771616 235772388 772 False 430 745 87.370000 3650 4394 2 chrUn.!!$F2 744
10 TraesCS2A01G173200 chr7D 560756397 560757179 782 False 715 715 84.217000 3652 4393 1 chr7D.!!$F1 741
11 TraesCS2A01G173200 chr3B 16323571 16324342 771 True 675 675 83.162000 3650 4394 1 chr3B.!!$R1 744
12 TraesCS2A01G173200 chr1B 476693961 476694716 755 True 645 645 82.592000 3655 4394 1 chr1B.!!$R1 739
13 TraesCS2A01G173200 chr4B 75637487 75638275 788 False 512 512 79.445000 3652 4394 1 chr4B.!!$F1 742

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
724 756 0.243636 CTTGCATTCCGTTCCAACCC 59.756 55.0 0.00 0.0 0.0 4.11 F
1484 1559 0.103026 TAGAGCTGGCTATGTGTGCG 59.897 55.0 0.00 0.0 0.0 5.34 F
2770 2884 0.037882 ATGCACGACTGTCTCACTGG 60.038 55.0 6.21 0.0 0.0 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2678 2789 0.248289 AAGAGCATTGTGGGCATTGC 59.752 50.0 0.0 0.0 46.48 3.56 R
3149 3286 0.670854 GTTGAGGTCGAGGTTGAGGC 60.671 60.0 0.0 0.0 0.00 4.70 R
3670 3841 0.315886 TAAGACAAACGAGCCAGCGA 59.684 50.0 0.0 0.0 34.83 4.93 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
68 69 3.117360 ACCCCCATTCAGATTCATCCTTC 60.117 47.826 0.00 0.00 0.00 3.46
73 76 4.523173 CCATTCAGATTCATCCTTCCATGG 59.477 45.833 4.97 4.97 0.00 3.66
87 90 3.726557 TCCATGGCTGGGATCATAATC 57.273 47.619 6.96 0.00 43.34 1.75
105 108 6.325028 TCATAATCAAACACAAAAACTCCCCA 59.675 34.615 0.00 0.00 0.00 4.96
119 122 8.364142 CAAAAACTCCCCAAACAAATCTACATA 58.636 33.333 0.00 0.00 0.00 2.29
156 159 2.597455 CCATGACCAACCTTTCCAGTT 58.403 47.619 0.00 0.00 0.00 3.16
161 164 0.951558 CCAACCTTTCCAGTTCCACG 59.048 55.000 0.00 0.00 0.00 4.94
167 170 2.484770 CCTTTCCAGTTCCACGTCTTGA 60.485 50.000 0.00 0.00 0.00 3.02
218 221 2.618241 ACGGCATGCACTACCAATTATG 59.382 45.455 21.36 0.00 0.00 1.90
264 270 0.916809 ACCCTTACGAATTCCCTGGG 59.083 55.000 6.33 6.33 39.06 4.45
344 356 0.312416 CTAGCCTGCTAGCCAGTACG 59.688 60.000 13.29 0.00 39.42 3.67
345 357 0.395311 TAGCCTGCTAGCCAGTACGT 60.395 55.000 13.29 0.00 40.06 3.57
372 384 1.218875 TTTGTAGTGTGTGGCGCGAG 61.219 55.000 12.10 0.00 0.00 5.03
405 417 2.708497 TCGTGCGGTGTACGAAAACAC 61.708 52.381 7.64 10.56 46.19 3.32
498 515 1.436195 GAGAAACCAGCGTGCACACA 61.436 55.000 18.64 0.00 0.00 3.72
520 540 0.665670 CAGTGTCACGTCAGCTCCTG 60.666 60.000 0.00 0.00 0.00 3.86
523 543 0.464036 TGTCACGTCAGCTCCTGTTT 59.536 50.000 0.00 0.00 32.61 2.83
526 546 1.412710 TCACGTCAGCTCCTGTTTCTT 59.587 47.619 0.00 0.00 32.61 2.52
527 547 2.158957 TCACGTCAGCTCCTGTTTCTTT 60.159 45.455 0.00 0.00 32.61 2.52
528 548 2.614057 CACGTCAGCTCCTGTTTCTTTT 59.386 45.455 0.00 0.00 32.61 2.27
529 549 3.065371 CACGTCAGCTCCTGTTTCTTTTT 59.935 43.478 0.00 0.00 32.61 1.94
561 581 2.698168 GGGGGTAGCTCCTGTTTCT 58.302 57.895 2.72 0.00 36.25 2.52
562 582 0.992695 GGGGGTAGCTCCTGTTTCTT 59.007 55.000 2.72 0.00 36.25 2.52
563 583 1.065345 GGGGGTAGCTCCTGTTTCTTC 60.065 57.143 2.72 0.00 36.25 2.87
568 588 0.695347 AGCTCCTGTTTCTTCCCTGG 59.305 55.000 0.00 0.00 0.00 4.45
573 593 1.608283 CCTGTTTCTTCCCTGGTCGAC 60.608 57.143 7.13 7.13 0.00 4.20
689 721 2.432628 GGCGTCACCACTTCCTCG 60.433 66.667 0.00 0.00 38.86 4.63
715 747 1.135972 CCAACGTCTTCTTGCATTCCG 60.136 52.381 0.00 0.00 0.00 4.30
716 748 1.531149 CAACGTCTTCTTGCATTCCGT 59.469 47.619 0.00 0.00 0.00 4.69
717 749 1.878953 ACGTCTTCTTGCATTCCGTT 58.121 45.000 0.00 0.00 0.00 4.44
718 750 1.798813 ACGTCTTCTTGCATTCCGTTC 59.201 47.619 0.00 0.00 0.00 3.95
719 751 1.128692 CGTCTTCTTGCATTCCGTTCC 59.871 52.381 0.00 0.00 0.00 3.62
720 752 2.151202 GTCTTCTTGCATTCCGTTCCA 58.849 47.619 0.00 0.00 0.00 3.53
721 753 2.552315 GTCTTCTTGCATTCCGTTCCAA 59.448 45.455 0.00 0.00 0.00 3.53
722 754 2.552315 TCTTCTTGCATTCCGTTCCAAC 59.448 45.455 0.00 0.00 0.00 3.77
723 755 1.243902 TCTTGCATTCCGTTCCAACC 58.756 50.000 0.00 0.00 0.00 3.77
724 756 0.243636 CTTGCATTCCGTTCCAACCC 59.756 55.000 0.00 0.00 0.00 4.11
726 758 0.468214 TGCATTCCGTTCCAACCCAA 60.468 50.000 0.00 0.00 0.00 4.12
740 772 1.612146 CCCAACCCAACCCATTCCC 60.612 63.158 0.00 0.00 0.00 3.97
743 775 0.614697 CAACCCAACCCATTCCCTCC 60.615 60.000 0.00 0.00 0.00 4.30
745 781 1.214992 ACCCAACCCATTCCCTCCTC 61.215 60.000 0.00 0.00 0.00 3.71
748 784 0.548510 CAACCCATTCCCTCCTCCTC 59.451 60.000 0.00 0.00 0.00 3.71
761 797 3.384146 CCTCCTCCTCCATATCATCATCG 59.616 52.174 0.00 0.00 0.00 3.84
763 799 2.480932 CCTCCTCCATATCATCATCGCG 60.481 54.545 0.00 0.00 0.00 5.87
765 801 2.094545 TCCTCCATATCATCATCGCGTG 60.095 50.000 5.77 3.96 0.00 5.34
766 802 1.657594 CTCCATATCATCATCGCGTGC 59.342 52.381 5.77 0.00 0.00 5.34
809 845 0.901114 TGGTGCCAGTAACGCCTAGA 60.901 55.000 0.00 0.00 38.55 2.43
812 848 1.877165 GCCAGTAACGCCTAGACGC 60.877 63.158 0.00 0.00 36.19 5.19
982 1026 1.738350 CGATCTGACCTACACACTCGT 59.262 52.381 0.00 0.00 0.00 4.18
984 1028 3.502920 GATCTGACCTACACACTCGTTG 58.497 50.000 0.00 0.00 0.00 4.10
1054 1098 4.954970 CCGTGGTGCTGGGCTTGT 62.955 66.667 0.00 0.00 0.00 3.16
1326 1370 1.589196 GTACAGGTGAGGCGATCGC 60.589 63.158 31.52 31.52 41.06 4.58
1465 1540 5.188555 TCTCAACAGCCATTTCTAGTCATCT 59.811 40.000 0.00 0.00 0.00 2.90
1466 1541 6.381133 TCTCAACAGCCATTTCTAGTCATCTA 59.619 38.462 0.00 0.00 0.00 1.98
1467 1542 6.577103 TCAACAGCCATTTCTAGTCATCTAG 58.423 40.000 0.00 0.00 43.48 2.43
1475 1550 3.874383 TCTAGTCATCTAGAGCTGGCT 57.126 47.619 5.80 5.80 45.11 4.75
1476 1551 4.984146 TCTAGTCATCTAGAGCTGGCTA 57.016 45.455 7.32 7.32 45.11 3.93
1477 1552 5.512942 TCTAGTCATCTAGAGCTGGCTAT 57.487 43.478 7.88 0.00 45.11 2.97
1478 1553 5.252547 TCTAGTCATCTAGAGCTGGCTATG 58.747 45.833 7.88 4.10 45.11 2.23
1479 1554 3.843422 AGTCATCTAGAGCTGGCTATGT 58.157 45.455 0.00 0.00 0.00 2.29
1480 1555 3.573538 AGTCATCTAGAGCTGGCTATGTG 59.426 47.826 0.00 0.00 0.00 3.21
1481 1556 3.320541 GTCATCTAGAGCTGGCTATGTGT 59.679 47.826 0.00 0.00 0.00 3.72
1482 1557 3.320256 TCATCTAGAGCTGGCTATGTGTG 59.680 47.826 0.00 0.00 0.00 3.82
1483 1558 1.410517 TCTAGAGCTGGCTATGTGTGC 59.589 52.381 0.00 0.00 0.00 4.57
1484 1559 0.103026 TAGAGCTGGCTATGTGTGCG 59.897 55.000 0.00 0.00 0.00 5.34
1485 1560 1.448540 GAGCTGGCTATGTGTGCGT 60.449 57.895 0.00 0.00 0.00 5.24
1486 1561 1.003355 AGCTGGCTATGTGTGCGTT 60.003 52.632 0.00 0.00 0.00 4.84
1487 1562 1.135315 GCTGGCTATGTGTGCGTTG 59.865 57.895 0.00 0.00 0.00 4.10
1488 1563 1.135315 CTGGCTATGTGTGCGTTGC 59.865 57.895 0.00 0.00 0.00 4.17
1489 1564 2.485122 GGCTATGTGTGCGTTGCC 59.515 61.111 0.00 0.00 43.13 4.52
1490 1565 2.040544 GGCTATGTGTGCGTTGCCT 61.041 57.895 5.32 0.00 45.07 4.75
1491 1566 1.135315 GCTATGTGTGCGTTGCCTG 59.865 57.895 0.00 0.00 0.00 4.85
1492 1567 1.135315 CTATGTGTGCGTTGCCTGC 59.865 57.895 0.00 0.00 0.00 4.85
1546 1621 3.827008 TTCTATCTTAGTGCCTGCAGG 57.173 47.619 29.34 29.34 38.53 4.85
1572 1647 4.878397 ACACAATGCAGGCTCTACTAAATC 59.122 41.667 0.00 0.00 0.00 2.17
1602 1677 4.096984 GTGTGCTGCTTCTAATTAGGCAAT 59.903 41.667 12.54 0.00 34.21 3.56
1652 1727 3.809832 CACGGATGAATACAGAATGGGTC 59.190 47.826 0.00 0.00 43.62 4.46
1675 1750 7.962373 GGTCCTTTTTGTTGAACAATTCTTTTG 59.038 33.333 11.97 0.00 38.00 2.44
1721 1817 0.552363 CATGGGATGTGGTGGATGGA 59.448 55.000 0.00 0.00 0.00 3.41
1942 2038 3.597728 CCGGCTCTACCTCTCCGC 61.598 72.222 0.00 0.00 40.49 5.54
1989 2091 2.413371 GCCTCTTGCTTCGAAATGTGAC 60.413 50.000 0.00 0.00 36.87 3.67
2004 2106 5.657470 AATGTGACATGTGTATATGCGTC 57.343 39.130 1.15 0.00 0.00 5.19
2006 2108 3.113322 GTGACATGTGTATATGCGTCGT 58.887 45.455 1.15 0.00 0.00 4.34
2007 2109 4.201930 TGTGACATGTGTATATGCGTCGTA 60.202 41.667 1.15 0.00 0.00 3.43
2008 2110 4.145928 GTGACATGTGTATATGCGTCGTAC 59.854 45.833 1.15 0.00 0.00 3.67
2009 2111 3.294102 ACATGTGTATATGCGTCGTACG 58.706 45.455 9.53 9.53 45.88 3.67
2010 2112 3.242837 ACATGTGTATATGCGTCGTACGT 60.243 43.478 16.05 0.00 44.73 3.57
2011 2113 2.707392 TGTGTATATGCGTCGTACGTG 58.293 47.619 16.05 10.38 44.73 4.49
2012 2114 2.039085 GTGTATATGCGTCGTACGTGG 58.961 52.381 16.05 9.43 44.73 4.94
2254 2356 7.174946 GGTACTGAAAGATTGTCCAAGATTTGA 59.825 37.037 0.00 0.00 37.43 2.69
2261 2363 7.893124 AGATTGTCCAAGATTTGATATTGCT 57.107 32.000 0.00 0.00 30.44 3.91
2288 2390 6.876789 TCAATACGTTCTTGTGTATCAACCAT 59.123 34.615 0.00 0.00 31.15 3.55
2289 2391 6.662414 ATACGTTCTTGTGTATCAACCATG 57.338 37.500 0.00 0.00 32.18 3.66
2305 2407 3.937814 ACCATGCACATTTTCTCTACGA 58.062 40.909 0.00 0.00 0.00 3.43
2307 2409 5.670485 ACCATGCACATTTTCTCTACGATA 58.330 37.500 0.00 0.00 0.00 2.92
2343 2445 5.793457 GCTAGGTAAAAATTAGTTGTGCACG 59.207 40.000 13.13 0.00 0.00 5.34
2355 2457 3.252215 AGTTGTGCACGCTGCTTTTATAA 59.748 39.130 13.13 0.00 45.31 0.98
2356 2458 4.082787 AGTTGTGCACGCTGCTTTTATAAT 60.083 37.500 13.13 0.00 45.31 1.28
2357 2459 5.123186 AGTTGTGCACGCTGCTTTTATAATA 59.877 36.000 13.13 0.00 45.31 0.98
2358 2460 4.904116 TGTGCACGCTGCTTTTATAATAC 58.096 39.130 13.13 0.04 45.31 1.89
2359 2461 4.201871 TGTGCACGCTGCTTTTATAATACC 60.202 41.667 13.13 0.00 45.31 2.73
2360 2462 3.942115 TGCACGCTGCTTTTATAATACCA 59.058 39.130 10.54 0.00 45.31 3.25
2361 2463 4.201871 TGCACGCTGCTTTTATAATACCAC 60.202 41.667 10.54 0.00 45.31 4.16
2362 2464 4.035208 GCACGCTGCTTTTATAATACCACT 59.965 41.667 0.00 0.00 40.96 4.00
2363 2465 5.501715 CACGCTGCTTTTATAATACCACTG 58.498 41.667 0.00 0.00 0.00 3.66
2364 2466 5.064707 CACGCTGCTTTTATAATACCACTGT 59.935 40.000 0.00 0.00 0.00 3.55
2365 2467 6.256975 CACGCTGCTTTTATAATACCACTGTA 59.743 38.462 0.00 0.00 0.00 2.74
2366 2468 6.479001 ACGCTGCTTTTATAATACCACTGTAG 59.521 38.462 0.00 0.00 0.00 2.74
2367 2469 6.700081 CGCTGCTTTTATAATACCACTGTAGA 59.300 38.462 0.00 0.00 0.00 2.59
2368 2470 7.223971 CGCTGCTTTTATAATACCACTGTAGAA 59.776 37.037 0.00 0.00 0.00 2.10
2369 2471 9.057089 GCTGCTTTTATAATACCACTGTAGAAT 57.943 33.333 0.00 0.00 0.00 2.40
2404 2506 6.712095 CCATAGGCTACTATTTTGATGCTGAA 59.288 38.462 0.00 0.00 37.82 3.02
2552 2654 4.144297 TCCATTTCTTACAGCAAGCACTT 58.856 39.130 0.00 0.00 33.94 3.16
2554 2656 4.261741 CCATTTCTTACAGCAAGCACTTGT 60.262 41.667 11.77 0.00 42.31 3.16
2619 2727 3.055591 CTCTCTAGCATGTATTGTGGCG 58.944 50.000 0.00 0.00 0.00 5.69
2678 2789 0.753262 ATCCGGTAGCTAGGCACAAG 59.247 55.000 0.00 0.00 0.00 3.16
2679 2790 1.521681 CCGGTAGCTAGGCACAAGC 60.522 63.158 0.00 0.00 40.40 4.01
2680 2791 1.218047 CGGTAGCTAGGCACAAGCA 59.782 57.895 0.00 0.00 44.61 3.91
2681 2792 0.391130 CGGTAGCTAGGCACAAGCAA 60.391 55.000 0.00 0.00 44.61 3.91
2748 2862 4.436584 GGTCACATTCTCTTTGCAATCTCG 60.437 45.833 0.00 0.00 0.00 4.04
2764 2878 2.433145 CGGCATGCACGACTGTCT 60.433 61.111 21.36 0.00 0.00 3.41
2765 2879 2.447887 CGGCATGCACGACTGTCTC 61.448 63.158 21.36 0.00 0.00 3.36
2766 2880 1.374631 GGCATGCACGACTGTCTCA 60.375 57.895 21.36 1.87 0.00 3.27
2767 2881 1.630244 GGCATGCACGACTGTCTCAC 61.630 60.000 21.36 0.00 0.00 3.51
2768 2882 0.668706 GCATGCACGACTGTCTCACT 60.669 55.000 14.21 0.00 0.00 3.41
2769 2883 1.066136 CATGCACGACTGTCTCACTG 58.934 55.000 6.21 0.00 0.00 3.66
2770 2884 0.037882 ATGCACGACTGTCTCACTGG 60.038 55.000 6.21 0.00 0.00 4.00
2773 2887 2.262915 CGACTGTCTCACTGGCCC 59.737 66.667 0.00 0.00 0.00 5.80
2774 2888 2.262915 GACTGTCTCACTGGCCCG 59.737 66.667 0.00 0.00 0.00 6.13
2775 2889 2.203640 ACTGTCTCACTGGCCCGA 60.204 61.111 0.00 0.00 0.00 5.14
2776 2890 1.816863 GACTGTCTCACTGGCCCGAA 61.817 60.000 0.00 0.00 0.00 4.30
2780 2894 1.202879 TGTCTCACTGGCCCGAAAAAT 60.203 47.619 0.00 0.00 0.00 1.82
2786 2900 4.062293 TCACTGGCCCGAAAAATATATCG 58.938 43.478 0.00 0.00 38.74 2.92
2815 2933 2.287965 TGTCAACGAACGCGACGTC 61.288 57.895 27.49 18.93 43.16 4.34
2842 2960 1.259770 CATGCATGCTGCTACAGTACG 59.740 52.381 20.33 0.00 45.31 3.67
2843 2961 0.246360 TGCATGCTGCTACAGTACGT 59.754 50.000 20.33 0.00 45.31 3.57
2875 2997 2.359792 CGATGAACGGGAACTGACG 58.640 57.895 0.00 0.00 38.67 4.35
2883 3009 0.878523 CGGGAACTGACGACTTTGCA 60.879 55.000 0.00 0.00 36.31 4.08
2884 3010 1.523758 GGGAACTGACGACTTTGCAT 58.476 50.000 0.00 0.00 0.00 3.96
2885 3011 1.197721 GGGAACTGACGACTTTGCATG 59.802 52.381 0.00 0.00 0.00 4.06
2886 3012 2.143122 GGAACTGACGACTTTGCATGA 58.857 47.619 0.00 0.00 0.00 3.07
2887 3013 2.548057 GGAACTGACGACTTTGCATGAA 59.452 45.455 0.00 0.00 0.00 2.57
2888 3014 3.545633 GAACTGACGACTTTGCATGAAC 58.454 45.455 0.00 0.00 0.00 3.18
2889 3015 2.838736 ACTGACGACTTTGCATGAACT 58.161 42.857 0.00 0.00 0.00 3.01
2890 3016 2.802816 ACTGACGACTTTGCATGAACTC 59.197 45.455 0.00 0.00 0.00 3.01
3137 3263 1.736645 CGCCAGGACCAAGTACGTG 60.737 63.158 0.00 1.33 0.00 4.49
3140 3266 0.670546 CCAGGACCAAGTACGTGCTG 60.671 60.000 7.01 12.03 46.03 4.41
3149 3286 3.449227 TACGTGCTGCTCCCCTCG 61.449 66.667 0.00 0.00 0.00 4.63
3169 3312 0.037232 CCTCAACCTCGACCTCAACC 60.037 60.000 0.00 0.00 0.00 3.77
3232 3375 4.183865 GGCTGAGCTTTTTCTTGTTGTTT 58.816 39.130 3.72 0.00 0.00 2.83
3233 3376 4.268644 GGCTGAGCTTTTTCTTGTTGTTTC 59.731 41.667 3.72 0.00 0.00 2.78
3234 3377 4.864247 GCTGAGCTTTTTCTTGTTGTTTCA 59.136 37.500 0.00 0.00 0.00 2.69
3235 3378 5.521372 GCTGAGCTTTTTCTTGTTGTTTCAT 59.479 36.000 0.00 0.00 0.00 2.57
3236 3379 6.509039 GCTGAGCTTTTTCTTGTTGTTTCATG 60.509 38.462 0.00 0.00 0.00 3.07
3237 3380 5.811613 TGAGCTTTTTCTTGTTGTTTCATGG 59.188 36.000 0.00 0.00 0.00 3.66
3369 3534 1.046472 TCGGCCGGGACTACATCAAT 61.046 55.000 27.83 0.00 0.00 2.57
3395 3560 0.892755 CAGTGGCTCCGGTTGTAGTA 59.107 55.000 0.00 0.00 0.00 1.82
3499 3670 6.365520 TCTCTCCACTGCAGATAATGTACTA 58.634 40.000 23.35 0.00 0.00 1.82
3500 3671 6.263392 TCTCTCCACTGCAGATAATGTACTAC 59.737 42.308 23.35 0.00 0.00 2.73
3501 3672 6.129874 TCTCCACTGCAGATAATGTACTACT 58.870 40.000 23.35 0.00 0.00 2.57
3526 3697 0.175989 GTGGTGGTAGTAGCAGCTCC 59.824 60.000 26.54 14.72 43.70 4.70
3530 3701 1.338655 GTGGTAGTAGCAGCTCCTAGC 59.661 57.143 15.46 15.46 42.84 3.42
3532 3703 1.479757 GGTAGTAGCAGCTCCTAGCCT 60.480 57.143 12.13 0.00 43.77 4.58
3547 3718 0.541863 AGCCTACATGTGGTAGCACC 59.458 55.000 21.65 4.97 46.73 5.01
3611 3782 1.118838 TTGTTGGCCCTGTGAAAAGG 58.881 50.000 0.00 0.00 37.05 3.11
3620 3791 5.309282 TGGCCCTGTGAAAAGGAATTATTTT 59.691 36.000 0.00 1.52 40.02 1.82
3669 3840 8.357402 TCTTTGATCCTAAAACCTAAAAAGTGC 58.643 33.333 0.00 0.00 0.00 4.40
3670 3841 7.833285 TTGATCCTAAAACCTAAAAAGTGCT 57.167 32.000 0.00 0.00 0.00 4.40
3818 3995 2.029369 CGGTCGAAACCCGTTGGA 59.971 61.111 4.86 0.00 43.21 3.53
3853 4031 0.402121 GGGTCCCTGCAGTTCTTCTT 59.598 55.000 13.81 0.00 0.00 2.52
3866 4045 2.108425 GTTCTTCTTCCCTCCCCACTTT 59.892 50.000 0.00 0.00 0.00 2.66
3878 4066 0.608308 CCCACTTTCGTTTCCTCCCC 60.608 60.000 0.00 0.00 0.00 4.81
3924 4113 3.436728 GGCGCATCCCATTTCCTC 58.563 61.111 10.83 0.00 0.00 3.71
3937 4126 0.623723 TTTCCTCTTCCAATCCCCCG 59.376 55.000 0.00 0.00 0.00 5.73
3996 4185 3.760035 TCTTCCGCCGGAGTGAGC 61.760 66.667 5.05 0.00 31.21 4.26
4012 4201 0.108138 GAGCAAGGGATAGCGTGTGT 60.108 55.000 0.00 0.00 35.48 3.72
4149 4341 3.744719 CCGAGGAGGAACGACGCA 61.745 66.667 0.00 0.00 45.00 5.24
4190 4383 1.517257 CGCGAAGGAGCAGAATCGT 60.517 57.895 0.00 0.00 37.60 3.73
4296 4544 3.466836 TGCCCTTGTAAGAGATTATGCG 58.533 45.455 0.00 0.00 0.00 4.73
4316 4564 5.064558 TGCGTAGGTTAACTGATTTGGAAA 58.935 37.500 5.42 0.00 0.00 3.13
4331 4580 2.356135 TGGAAAGGATTAAGCACTCGC 58.644 47.619 0.00 0.00 38.99 5.03
4359 4619 2.714250 TGGTTTGGGTACTGGTGAGATT 59.286 45.455 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.971167 TTGGGTCCAAGCACGATGC 60.971 57.895 0.00 0.00 45.46 3.91
73 76 5.581126 TTGTGTTTGATTATGATCCCAGC 57.419 39.130 0.00 0.00 0.00 4.85
87 90 4.319177 TGTTTGGGGAGTTTTTGTGTTTG 58.681 39.130 0.00 0.00 0.00 2.93
105 108 5.116882 GCGAGGGAGTATGTAGATTTGTTT 58.883 41.667 0.00 0.00 0.00 2.83
240 246 4.566070 CCAGGGAATTCGTAAGGGTTACAA 60.566 45.833 0.00 0.00 35.89 2.41
343 355 4.089493 CCACACACTACAAAAGTCGATACG 59.911 45.833 0.00 0.00 35.76 3.06
344 356 4.143179 GCCACACACTACAAAAGTCGATAC 60.143 45.833 0.00 0.00 35.76 2.24
345 357 3.991773 GCCACACACTACAAAAGTCGATA 59.008 43.478 0.00 0.00 35.76 2.92
372 384 1.485032 CGCACGAATACCCCGTTAGC 61.485 60.000 0.00 0.00 38.29 3.09
410 424 3.071459 CTAAAGCGCGCGTGAGGTG 62.071 63.158 32.35 13.54 0.00 4.00
498 515 1.571919 GAGCTGACGTGACACTGTTT 58.428 50.000 3.68 0.00 0.00 2.83
543 563 0.992695 AAGAAACAGGAGCTACCCCC 59.007 55.000 0.00 0.00 40.05 5.40
544 564 1.065345 GGAAGAAACAGGAGCTACCCC 60.065 57.143 0.00 0.00 40.05 4.95
545 565 1.065345 GGGAAGAAACAGGAGCTACCC 60.065 57.143 0.00 0.00 40.05 3.69
546 566 1.909986 AGGGAAGAAACAGGAGCTACC 59.090 52.381 0.00 0.00 39.35 3.18
547 567 2.355209 CCAGGGAAGAAACAGGAGCTAC 60.355 54.545 0.00 0.00 0.00 3.58
548 568 1.909302 CCAGGGAAGAAACAGGAGCTA 59.091 52.381 0.00 0.00 0.00 3.32
549 569 0.695347 CCAGGGAAGAAACAGGAGCT 59.305 55.000 0.00 0.00 0.00 4.09
550 570 0.402121 ACCAGGGAAGAAACAGGAGC 59.598 55.000 0.00 0.00 0.00 4.70
551 571 1.338200 CGACCAGGGAAGAAACAGGAG 60.338 57.143 0.00 0.00 0.00 3.69
552 572 0.685097 CGACCAGGGAAGAAACAGGA 59.315 55.000 0.00 0.00 0.00 3.86
553 573 0.685097 TCGACCAGGGAAGAAACAGG 59.315 55.000 0.00 0.00 0.00 4.00
554 574 1.797025 GTCGACCAGGGAAGAAACAG 58.203 55.000 3.51 0.00 0.00 3.16
555 575 0.032952 CGTCGACCAGGGAAGAAACA 59.967 55.000 10.58 0.00 0.00 2.83
556 576 0.316204 TCGTCGACCAGGGAAGAAAC 59.684 55.000 10.58 0.00 0.00 2.78
557 577 1.203994 GATCGTCGACCAGGGAAGAAA 59.796 52.381 10.58 0.00 0.00 2.52
558 578 0.815734 GATCGTCGACCAGGGAAGAA 59.184 55.000 10.58 0.00 0.00 2.52
559 579 1.374343 CGATCGTCGACCAGGGAAGA 61.374 60.000 10.58 0.00 43.74 2.87
560 580 1.064296 CGATCGTCGACCAGGGAAG 59.936 63.158 10.58 0.00 43.74 3.46
561 581 1.377594 TCGATCGTCGACCAGGGAA 60.378 57.895 15.94 0.00 44.82 3.97
562 582 2.269883 TCGATCGTCGACCAGGGA 59.730 61.111 15.94 1.18 44.82 4.20
689 721 1.668151 AAGAAGACGTTGGAGGCGC 60.668 57.895 0.00 0.00 0.00 6.53
715 747 1.404479 GGGTTGGGTTGGGTTGGAAC 61.404 60.000 0.00 0.00 0.00 3.62
716 748 1.075151 GGGTTGGGTTGGGTTGGAA 60.075 57.895 0.00 0.00 0.00 3.53
717 749 1.669927 ATGGGTTGGGTTGGGTTGGA 61.670 55.000 0.00 0.00 0.00 3.53
718 750 0.766288 AATGGGTTGGGTTGGGTTGG 60.766 55.000 0.00 0.00 0.00 3.77
719 751 0.684535 GAATGGGTTGGGTTGGGTTG 59.315 55.000 0.00 0.00 0.00 3.77
720 752 0.472925 GGAATGGGTTGGGTTGGGTT 60.473 55.000 0.00 0.00 0.00 4.11
721 753 1.157513 GGAATGGGTTGGGTTGGGT 59.842 57.895 0.00 0.00 0.00 4.51
722 754 1.612146 GGGAATGGGTTGGGTTGGG 60.612 63.158 0.00 0.00 0.00 4.12
723 755 0.614697 GAGGGAATGGGTTGGGTTGG 60.615 60.000 0.00 0.00 0.00 3.77
724 756 0.614697 GGAGGGAATGGGTTGGGTTG 60.615 60.000 0.00 0.00 0.00 3.77
726 758 1.151361 AGGAGGGAATGGGTTGGGT 60.151 57.895 0.00 0.00 0.00 4.51
740 772 3.181477 GCGATGATGATATGGAGGAGGAG 60.181 52.174 0.00 0.00 0.00 3.69
743 775 2.165234 ACGCGATGATGATATGGAGGAG 59.835 50.000 15.93 0.00 0.00 3.69
745 781 2.265683 CACGCGATGATGATATGGAGG 58.734 52.381 15.93 0.00 0.00 4.30
748 784 1.127397 GTGCACGCGATGATGATATGG 59.873 52.381 15.93 0.00 0.00 2.74
761 797 3.490759 CGGAGTGATGGTGCACGC 61.491 66.667 11.45 4.50 43.42 5.34
763 799 0.108186 TGATCGGAGTGATGGTGCAC 60.108 55.000 8.80 8.80 37.47 4.57
765 801 1.224075 CATGATCGGAGTGATGGTGC 58.776 55.000 0.00 0.00 37.47 5.01
766 802 2.159057 TGACATGATCGGAGTGATGGTG 60.159 50.000 0.00 0.00 37.47 4.17
925 969 2.202919 CTGGATGGTGATCGCGCA 60.203 61.111 8.75 0.00 0.00 6.09
982 1026 3.300388 CCATGGACTCCTAGCTCTACAA 58.700 50.000 5.56 0.00 0.00 2.41
984 1028 1.616374 GCCATGGACTCCTAGCTCTAC 59.384 57.143 18.40 0.00 0.00 2.59
1326 1370 4.570663 GACTGGACGGGCGGATCG 62.571 72.222 0.00 0.00 0.00 3.69
1347 1391 2.825836 GATTGAGGGGCAGCGGTG 60.826 66.667 10.98 10.98 0.00 4.94
1465 1540 0.103026 CGCACACATAGCCAGCTCTA 59.897 55.000 0.00 0.00 0.00 2.43
1466 1541 1.153489 CGCACACATAGCCAGCTCT 60.153 57.895 0.00 0.00 0.00 4.09
1467 1542 1.021390 AACGCACACATAGCCAGCTC 61.021 55.000 0.00 0.00 0.00 4.09
1468 1543 1.003355 AACGCACACATAGCCAGCT 60.003 52.632 0.00 0.00 0.00 4.24
1469 1544 1.135315 CAACGCACACATAGCCAGC 59.865 57.895 0.00 0.00 0.00 4.85
1470 1545 1.135315 GCAACGCACACATAGCCAG 59.865 57.895 0.00 0.00 0.00 4.85
1471 1546 2.331893 GGCAACGCACACATAGCCA 61.332 57.895 0.00 0.00 41.63 4.75
1472 1547 2.040544 AGGCAACGCACACATAGCC 61.041 57.895 0.00 0.00 46.39 3.93
1473 1548 1.135315 CAGGCAACGCACACATAGC 59.865 57.895 0.00 0.00 46.39 2.97
1474 1549 1.135315 GCAGGCAACGCACACATAG 59.865 57.895 0.00 0.00 46.39 2.23
1475 1550 2.331893 GGCAGGCAACGCACACATA 61.332 57.895 0.00 0.00 46.39 2.29
1476 1551 3.673484 GGCAGGCAACGCACACAT 61.673 61.111 0.00 0.00 46.39 3.21
1521 1596 3.817647 GCAGGCACTAAGATAGAAATGGG 59.182 47.826 0.00 0.00 36.02 4.00
1546 1621 1.936547 GTAGAGCCTGCATTGTGTAGC 59.063 52.381 0.00 0.00 0.00 3.58
1572 1647 2.739885 AGAAGCAGCACACTCTACAG 57.260 50.000 0.00 0.00 0.00 2.74
1581 1656 4.907879 ATTGCCTAATTAGAAGCAGCAC 57.092 40.909 14.28 0.00 36.44 4.40
1618 1693 9.897744 CTGTATTCATCCGTGCATAATAAAAAT 57.102 29.630 0.00 0.00 0.00 1.82
1619 1694 9.114952 TCTGTATTCATCCGTGCATAATAAAAA 57.885 29.630 0.00 0.00 0.00 1.94
1620 1695 8.669946 TCTGTATTCATCCGTGCATAATAAAA 57.330 30.769 0.00 0.00 0.00 1.52
1624 1699 6.149973 CCATTCTGTATTCATCCGTGCATAAT 59.850 38.462 0.00 0.00 0.00 1.28
1634 1709 7.093771 ACAAAAAGGACCCATTCTGTATTCATC 60.094 37.037 0.00 0.00 0.00 2.92
1637 1712 6.590234 ACAAAAAGGACCCATTCTGTATTC 57.410 37.500 0.00 0.00 0.00 1.75
1638 1713 6.553100 TCAACAAAAAGGACCCATTCTGTATT 59.447 34.615 0.00 0.00 0.00 1.89
1652 1727 8.288913 ACACAAAAGAATTGTTCAACAAAAAGG 58.711 29.630 7.14 0.00 41.96 3.11
1675 1750 5.298347 AGCTTGTTAGTTCAGTCCTTACAC 58.702 41.667 0.00 0.00 0.00 2.90
1679 1754 4.563786 GCCTAGCTTGTTAGTTCAGTCCTT 60.564 45.833 0.00 0.00 0.00 3.36
1680 1755 3.055747 GCCTAGCTTGTTAGTTCAGTCCT 60.056 47.826 0.00 0.00 0.00 3.85
1721 1817 1.599047 CGTCACCTTCTCCCTGCAT 59.401 57.895 0.00 0.00 0.00 3.96
1919 2015 3.412879 GAGGTAGAGCCGGACGTGC 62.413 68.421 5.05 0.00 43.70 5.34
1921 2017 1.451747 GAGAGGTAGAGCCGGACGT 60.452 63.158 5.05 0.00 43.70 4.34
1922 2018 2.188161 GGAGAGGTAGAGCCGGACG 61.188 68.421 5.05 0.00 43.70 4.79
1923 2019 2.188161 CGGAGAGGTAGAGCCGGAC 61.188 68.421 5.05 0.00 43.70 4.79
1924 2020 2.192443 CGGAGAGGTAGAGCCGGA 59.808 66.667 5.05 0.00 43.70 5.14
1925 2021 3.597728 GCGGAGAGGTAGAGCCGG 61.598 72.222 0.00 0.00 43.73 6.13
1989 2091 3.928252 CGTACGACGCATATACACATG 57.072 47.619 10.44 0.00 33.65 3.21
2004 2106 2.736343 TTCTGCACCGACCACGTACG 62.736 60.000 15.01 15.01 37.88 3.67
2006 2108 1.007038 GTTCTGCACCGACCACGTA 60.007 57.895 0.00 0.00 37.88 3.57
2007 2109 2.279918 GTTCTGCACCGACCACGT 60.280 61.111 0.00 0.00 37.88 4.49
2008 2110 2.022129 GAGTTCTGCACCGACCACG 61.022 63.158 0.00 0.00 39.43 4.94
2009 2111 2.022129 CGAGTTCTGCACCGACCAC 61.022 63.158 0.00 0.00 0.00 4.16
2010 2112 2.338620 CGAGTTCTGCACCGACCA 59.661 61.111 0.00 0.00 0.00 4.02
2011 2113 2.432628 CCGAGTTCTGCACCGACC 60.433 66.667 0.00 0.00 0.00 4.79
2012 2114 3.112709 GCCGAGTTCTGCACCGAC 61.113 66.667 0.00 0.00 0.00 4.79
2254 2356 6.818644 ACACAAGAACGTATTGAGAGCAATAT 59.181 34.615 17.53 0.00 45.75 1.28
2261 2363 6.588756 GGTTGATACACAAGAACGTATTGAGA 59.411 38.462 17.53 5.26 39.30 3.27
2288 2390 6.458206 GGCAAATATCGTAGAGAAAATGTGCA 60.458 38.462 9.60 0.00 43.63 4.57
2289 2391 5.909610 GGCAAATATCGTAGAGAAAATGTGC 59.090 40.000 0.00 0.00 43.63 4.57
2305 2407 7.416964 TTTTACCTAGCAACATGGCAAATAT 57.583 32.000 0.00 0.00 35.83 1.28
2307 2409 5.736951 TTTTACCTAGCAACATGGCAAAT 57.263 34.783 0.00 0.00 35.83 2.32
2343 2445 8.433421 TTCTACAGTGGTATTATAAAAGCAGC 57.567 34.615 0.00 0.00 0.00 5.25
2355 2457 6.998673 GGGAGCAAAATATTCTACAGTGGTAT 59.001 38.462 0.00 0.00 0.00 2.73
2356 2458 6.069905 TGGGAGCAAAATATTCTACAGTGGTA 60.070 38.462 0.00 0.00 0.00 3.25
2357 2459 5.193679 GGGAGCAAAATATTCTACAGTGGT 58.806 41.667 0.00 0.00 0.00 4.16
2358 2460 5.192927 TGGGAGCAAAATATTCTACAGTGG 58.807 41.667 0.00 0.00 0.00 4.00
2359 2461 6.949352 ATGGGAGCAAAATATTCTACAGTG 57.051 37.500 0.00 0.00 0.00 3.66
2360 2462 7.227156 CCTATGGGAGCAAAATATTCTACAGT 58.773 38.462 0.00 0.00 33.58 3.55
2361 2463 6.150140 GCCTATGGGAGCAAAATATTCTACAG 59.850 42.308 0.00 0.00 33.58 2.74
2362 2464 6.003950 GCCTATGGGAGCAAAATATTCTACA 58.996 40.000 0.00 0.00 33.58 2.74
2363 2465 6.241645 AGCCTATGGGAGCAAAATATTCTAC 58.758 40.000 0.00 0.00 33.58 2.59
2364 2466 6.454223 AGCCTATGGGAGCAAAATATTCTA 57.546 37.500 0.00 0.00 33.58 2.10
2365 2467 5.330648 AGCCTATGGGAGCAAAATATTCT 57.669 39.130 0.00 0.00 33.58 2.40
2366 2468 6.241645 AGTAGCCTATGGGAGCAAAATATTC 58.758 40.000 0.00 0.00 33.58 1.75
2367 2469 6.206180 AGTAGCCTATGGGAGCAAAATATT 57.794 37.500 0.00 0.00 33.58 1.28
2368 2470 5.850046 AGTAGCCTATGGGAGCAAAATAT 57.150 39.130 0.00 0.00 33.58 1.28
2369 2471 6.952605 ATAGTAGCCTATGGGAGCAAAATA 57.047 37.500 0.00 0.00 32.53 1.40
2370 2472 5.850046 ATAGTAGCCTATGGGAGCAAAAT 57.150 39.130 0.00 0.00 32.53 1.82
2371 2473 5.646692 AATAGTAGCCTATGGGAGCAAAA 57.353 39.130 0.00 0.00 34.07 2.44
2372 2474 5.646692 AAATAGTAGCCTATGGGAGCAAA 57.353 39.130 0.00 0.00 34.07 3.68
2373 2475 5.131977 TCAAAATAGTAGCCTATGGGAGCAA 59.868 40.000 0.00 0.00 34.07 3.91
2374 2476 4.658435 TCAAAATAGTAGCCTATGGGAGCA 59.342 41.667 0.00 0.00 34.07 4.26
2375 2477 5.228945 TCAAAATAGTAGCCTATGGGAGC 57.771 43.478 0.00 0.00 34.07 4.70
2376 2478 5.645497 GCATCAAAATAGTAGCCTATGGGAG 59.355 44.000 0.00 0.00 34.07 4.30
2377 2479 5.310594 AGCATCAAAATAGTAGCCTATGGGA 59.689 40.000 0.00 0.00 34.07 4.37
2463 2565 2.721231 CAACCCACAGTGCAACGG 59.279 61.111 0.00 0.00 45.86 4.44
2552 2654 3.442273 GTGAGGAAACCAAGTGTCAAACA 59.558 43.478 0.00 0.00 0.00 2.83
2554 2656 3.963129 AGTGAGGAAACCAAGTGTCAAA 58.037 40.909 0.00 0.00 0.00 2.69
2606 2714 0.523968 GCTGTGCGCCACAATACATG 60.524 55.000 4.18 0.00 44.08 3.21
2612 2720 1.454572 AATCAAGCTGTGCGCCACAA 61.455 50.000 4.18 0.00 44.08 3.33
2643 2751 3.967987 ACCGGATTTCCACTAATCTAGCT 59.032 43.478 9.46 0.00 35.37 3.32
2678 2789 0.248289 AAGAGCATTGTGGGCATTGC 59.752 50.000 0.00 0.00 46.48 3.56
2679 2790 2.004583 CAAGAGCATTGTGGGCATTG 57.995 50.000 0.00 0.00 0.00 2.82
2680 2791 0.248289 GCAAGAGCATTGTGGGCATT 59.752 50.000 3.93 0.00 41.58 3.56
2681 2792 1.895238 GCAAGAGCATTGTGGGCAT 59.105 52.632 3.93 0.00 41.58 4.40
2748 2862 1.374631 TGAGACAGTCGTGCATGCC 60.375 57.895 16.68 5.63 0.00 4.40
2764 2878 4.062293 CGATATATTTTTCGGGCCAGTGA 58.938 43.478 4.39 0.00 0.00 3.41
2765 2879 4.404507 CGATATATTTTTCGGGCCAGTG 57.595 45.455 4.39 0.00 0.00 3.66
2773 2887 8.388103 ACACTTTGACTTCCGATATATTTTTCG 58.612 33.333 0.00 0.00 35.19 3.46
2774 2888 9.704098 GACACTTTGACTTCCGATATATTTTTC 57.296 33.333 0.00 0.00 0.00 2.29
2775 2889 9.226606 TGACACTTTGACTTCCGATATATTTTT 57.773 29.630 0.00 0.00 0.00 1.94
2776 2890 8.786826 TGACACTTTGACTTCCGATATATTTT 57.213 30.769 0.00 0.00 0.00 1.82
2780 2894 5.803461 CGTTGACACTTTGACTTCCGATATA 59.197 40.000 0.00 0.00 0.00 0.86
2786 2900 3.543460 CGTTCGTTGACACTTTGACTTCC 60.543 47.826 0.00 0.00 0.00 3.46
2787 2901 3.594312 CGTTCGTTGACACTTTGACTTC 58.406 45.455 0.00 0.00 0.00 3.01
2797 2911 2.278077 ACGTCGCGTTCGTTGACA 60.278 55.556 21.14 0.00 36.35 3.58
2875 2997 1.135859 CCTGCGAGTTCATGCAAAGTC 60.136 52.381 0.00 0.00 41.22 3.01
3140 3266 4.475135 GGTTGAGGCGAGGGGAGC 62.475 72.222 0.00 0.00 0.00 4.70
3149 3286 0.670854 GTTGAGGTCGAGGTTGAGGC 60.671 60.000 0.00 0.00 0.00 4.70
3169 3312 3.484407 GGATTTCCTCCATGATCAGGTG 58.516 50.000 6.62 6.48 44.26 4.00
3191 3334 2.430921 CACGCGTCACTCTCCCAC 60.431 66.667 9.86 0.00 0.00 4.61
3197 3340 3.406361 CAGCCACACGCGTCACTC 61.406 66.667 9.86 0.00 44.76 3.51
3232 3375 4.758251 CGTCCTGCACGCCCATGA 62.758 66.667 0.00 0.00 42.87 3.07
3395 3560 6.433404 TCTCTCTTTATTTACACCGTCTGTCT 59.567 38.462 0.00 0.00 33.91 3.41
3499 3670 4.927049 TGCTACTACCACCACTAGTAAGT 58.073 43.478 0.00 0.00 35.91 2.24
3500 3671 4.202030 GCTGCTACTACCACCACTAGTAAG 60.202 50.000 0.00 0.00 0.00 2.34
3501 3672 3.698040 GCTGCTACTACCACCACTAGTAA 59.302 47.826 0.00 0.00 0.00 2.24
3515 3686 1.215673 TGTAGGCTAGGAGCTGCTACT 59.784 52.381 19.93 19.93 41.99 2.57
3526 3697 2.224066 GGTGCTACCACATGTAGGCTAG 60.224 54.545 12.53 13.00 45.97 3.42
3530 3701 0.179084 CCGGTGCTACCACATGTAGG 60.179 60.000 0.00 5.37 45.97 3.18
3532 3703 1.219664 GCCGGTGCTACCACATGTA 59.780 57.895 1.90 0.00 43.88 2.29
3554 3725 2.652530 GACGTGTCAGGCCCGTTA 59.347 61.111 0.00 0.00 34.51 3.18
3625 3796 4.888038 AAGAAACCTTGGTACGACAAAC 57.112 40.909 0.00 0.00 0.00 2.93
3669 3840 0.946221 AAGACAAACGAGCCAGCGAG 60.946 55.000 0.00 0.00 34.83 5.03
3670 3841 0.315886 TAAGACAAACGAGCCAGCGA 59.684 50.000 0.00 0.00 34.83 4.93
3808 3985 0.679960 GCCTAAGCATCCAACGGGTT 60.680 55.000 0.00 0.00 39.53 4.11
3818 3995 2.186903 CCACGACCGCCTAAGCAT 59.813 61.111 0.00 0.00 39.83 3.79
3866 4045 2.961531 TTGAAATGGGGAGGAAACGA 57.038 45.000 0.00 0.00 0.00 3.85
3878 4066 0.878416 TCGGGAGCGGTTTTGAAATG 59.122 50.000 0.00 0.00 0.00 2.32
3924 4113 2.092429 TCTGAATTCGGGGGATTGGAAG 60.092 50.000 14.33 0.00 0.00 3.46
3937 4126 1.424493 CCGTCGGCTGCTCTGAATTC 61.424 60.000 0.00 0.00 0.00 2.17
3996 4185 1.369091 GCCACACACGCTATCCCTTG 61.369 60.000 0.00 0.00 0.00 3.61
4012 4201 4.974438 ACCCCTCCCTTCACGCCA 62.974 66.667 0.00 0.00 0.00 5.69
4190 4383 1.228124 CCTCCGCCCAACAACAAGA 60.228 57.895 0.00 0.00 0.00 3.02
4296 4544 7.939784 ATCCTTTCCAAATCAGTTAACCTAC 57.060 36.000 0.88 0.00 0.00 3.18
4331 4580 3.181437 ACCAGTACCCAAACCAAACCTAG 60.181 47.826 0.00 0.00 0.00 3.02
4335 4595 2.621526 CTCACCAGTACCCAAACCAAAC 59.378 50.000 0.00 0.00 0.00 2.93
4359 4619 0.623194 TTGAATGCCCCTCGAATCCA 59.377 50.000 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.