Multiple sequence alignment - TraesCS1D01G138800

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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 TraesCS1D01G138800 chr1D 100.000 3134 0 0 1 3134 190480069 190483202 0.000000e+00 5788.0
1 TraesCS1D01G138800 chr1D 89.646 396 28 8 2748 3134 88241362 88240971 2.810000e-135 492.0
2 TraesCS1D01G138800 chr1D 86.967 422 19 17 2748 3134 84804068 84803648 2.870000e-120 442.0
3 TraesCS1D01G138800 chr1D 85.132 417 35 14 2742 3134 229605187 229604774 4.870000e-108 401.0
4 TraesCS1D01G138800 chr1D 85.124 121 15 3 2379 2496 22602214 22602094 1.530000e-23 121.0
5 TraesCS1D01G138800 chr1D 85.841 113 14 2 2385 2496 307448352 307448463 5.490000e-23 119.0
6 TraesCS1D01G138800 chr1D 84.746 118 16 1 2386 2501 401286463 401286346 1.970000e-22 117.0
7 TraesCS1D01G138800 chr1D 84.298 121 16 3 2379 2496 22620148 22620028 7.100000e-22 115.0
8 TraesCS1D01G138800 chr1A 90.944 2363 140 44 110 2415 212019051 212016706 0.000000e+00 3110.0
9 TraesCS1D01G138800 chr1A 90.234 256 16 5 2501 2748 212016570 212016316 3.010000e-85 326.0
10 TraesCS1D01G138800 chr1A 97.674 43 1 0 1 43 212019161 212019119 1.210000e-09 75.0
11 TraesCS1D01G138800 chr1B 93.260 994 38 10 1 970 263947830 263948818 0.000000e+00 1437.0
12 TraesCS1D01G138800 chr1B 96.380 663 20 3 1717 2376 263980688 263981349 0.000000e+00 1088.0
13 TraesCS1D01G138800 chr1B 90.711 689 53 6 958 1641 263979257 263979939 0.000000e+00 907.0
14 TraesCS1D01G138800 chr1B 90.725 593 27 13 1679 2265 263980091 263980661 0.000000e+00 765.0
15 TraesCS1D01G138800 chr1B 87.715 407 29 3 2748 3134 614712962 614712557 3.680000e-124 455.0
16 TraesCS1D01G138800 chr1B 92.218 257 11 5 2501 2748 263981440 263981696 3.840000e-94 355.0
17 TraesCS1D01G138800 chr2D 90.215 419 10 4 2746 3134 623460683 623460266 4.630000e-143 518.0
18 TraesCS1D01G138800 chr2D 86.998 423 24 6 2742 3134 333199924 333200345 6.170000e-122 448.0
19 TraesCS1D01G138800 chr5D 89.706 408 18 12 2748 3134 2802005 2801601 1.680000e-137 499.0
20 TraesCS1D01G138800 chr5D 89.270 233 16 4 2501 2725 232006495 232006264 1.840000e-72 283.0
21 TraesCS1D01G138800 chr5D 87.745 204 9 10 2555 2747 3592827 3592629 1.130000e-54 224.0
22 TraesCS1D01G138800 chr4D 89.435 407 22 3 2748 3134 336252348 336251943 7.810000e-136 494.0
23 TraesCS1D01G138800 chr4D 88.480 408 24 5 2748 3134 487201947 487201542 3.660000e-129 472.0
24 TraesCS1D01G138800 chr4D 90.873 252 20 3 2745 2996 243712259 243712011 5.010000e-88 335.0
25 TraesCS1D01G138800 chr7D 88.698 407 24 4 2746 3131 575584555 575584960 7.860000e-131 477.0
26 TraesCS1D01G138800 chr7D 82.908 392 51 15 2748 3134 154204643 154205023 3.870000e-89 339.0
27 TraesCS1D01G138800 chr7D 84.956 113 13 4 2388 2498 560589920 560589810 9.190000e-21 111.0
28 TraesCS1D01G138800 chr6D 87.923 414 22 7 2748 3134 462608426 462608838 2.200000e-126 462.0
29 TraesCS1D01G138800 chr6D 83.375 397 52 13 2748 3134 21358997 21359389 3.840000e-94 355.0
30 TraesCS1D01G138800 chr4A 87.186 398 39 9 2748 3134 468761663 468761267 2.870000e-120 442.0
31 TraesCS1D01G138800 chr7A 85.608 403 35 11 2742 3134 686198006 686198395 4.870000e-108 401.0
32 TraesCS1D01G138800 chr7A 89.157 332 20 7 2743 3058 92396452 92396783 1.750000e-107 399.0
33 TraesCS1D01G138800 chr7A 88.194 288 23 5 2742 3018 689909785 689909498 1.800000e-87 333.0
34 TraesCS1D01G138800 chr7A 86.364 110 12 3 2385 2491 538573560 538573451 1.970000e-22 117.0
35 TraesCS1D01G138800 chr2A 85.106 423 30 8 2742 3133 104268818 104268398 4.870000e-108 401.0
36 TraesCS1D01G138800 chr2A 84.248 419 33 12 2748 3134 489835154 489835571 8.200000e-101 377.0
37 TraesCS1D01G138800 chr2A 87.879 231 22 3 2499 2724 193729569 193729340 1.850000e-67 267.0
38 TraesCS1D01G138800 chr2A 86.134 238 18 9 2502 2728 16067671 16067438 3.120000e-60 243.0
39 TraesCS1D01G138800 chr5A 81.975 405 49 11 2750 3131 158186791 158186388 3.900000e-84 322.0
40 TraesCS1D01G138800 chr5A 90.385 52 5 0 329 380 135154603 135154552 5.610000e-08 69.4
41 TraesCS1D01G138800 chr2B 90.411 219 14 4 2513 2725 94204086 94203869 6.620000e-72 281.0
42 TraesCS1D01G138800 chr2B 89.130 230 17 4 2501 2725 525628551 525628777 2.380000e-71 279.0
43 TraesCS1D01G138800 chr3B 86.667 240 14 10 2501 2728 526735343 526735576 1.870000e-62 250.0
44 TraesCS1D01G138800 chr3A 85.656 244 19 11 2501 2730 408023468 408023227 3.120000e-60 243.0
45 TraesCS1D01G138800 chr3A 81.853 259 24 16 2510 2747 466113869 466114125 2.470000e-46 196.0
46 TraesCS1D01G138800 chr3D 86.179 123 13 2 2379 2497 318513641 318513763 2.540000e-26 130.0
47 TraesCS1D01G138800 chr7B 84.821 112 16 1 2386 2496 115373268 115373157 9.190000e-21 111.0
48 TraesCS1D01G138800 chr5B 82.927 123 17 4 2379 2498 564446373 564446494 1.190000e-19 108.0
49 TraesCS1D01G138800 chr5B 90.385 52 5 0 329 380 136018677 136018626 5.610000e-08 69.4


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 TraesCS1D01G138800 chr1D 190480069 190483202 3133 False 5788.000000 5788 100.000000 1 3134 1 chr1D.!!$F1 3133
1 TraesCS1D01G138800 chr1A 212016316 212019161 2845 True 1170.333333 3110 92.950667 1 2748 3 chr1A.!!$R1 2747
2 TraesCS1D01G138800 chr1B 263947830 263948818 988 False 1437.000000 1437 93.260000 1 970 1 chr1B.!!$F1 969
3 TraesCS1D01G138800 chr1B 263979257 263981696 2439 False 778.750000 1088 92.508500 958 2748 4 chr1B.!!$F2 1790

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
574 646 0.534877 TCAATGCCACGAGTGCTGTT 60.535 50.0 0.0 0.0 0.0 3.16 F
1023 1117 0.103937 CGCAGGTTGGGCTTTCAAAA 59.896 50.0 0.0 0.0 0.0 2.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1677 1908 0.689412 TGTGAGTCTGTCCCCACACA 60.689 55.0 0.0 0.0 34.96 3.72 R
2981 3856 0.039764 GGAGGGAAGTGGGGGAAAAG 59.960 60.0 0.0 0.0 0.00 2.27 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
80 112 8.884124 ATTTCATCTTGGAAGTGGAGATAAAA 57.116 30.769 0.00 0.00 0.00 1.52
574 646 0.534877 TCAATGCCACGAGTGCTGTT 60.535 50.000 0.00 0.00 0.00 3.16
654 726 2.821366 CATGCCTGCTCCGGTGTC 60.821 66.667 0.00 0.00 0.00 3.67
723 810 2.223595 TGTCCGATCGATGCTTCTCTTC 60.224 50.000 18.66 0.00 0.00 2.87
728 815 3.058293 CGATCGATGCTTCTCTTCTAGCT 60.058 47.826 10.26 0.00 38.22 3.32
752 843 6.168164 AGAGCGCGTAATAGTTATAGAGAC 57.832 41.667 8.43 0.00 0.00 3.36
806 897 3.131755 CCTCCCCATTTCTTGCAAGATTC 59.868 47.826 28.89 0.00 34.49 2.52
818 909 5.413833 TCTTGCAAGATTCAGACTCCAAATC 59.586 40.000 25.16 0.00 0.00 2.17
902 993 1.853319 GTGTGAGCGTTGTCTTCGG 59.147 57.895 0.00 0.00 0.00 4.30
941 1035 2.352715 GGAAGGGAAATTTTCGTGCCTG 60.353 50.000 8.75 0.00 0.00 4.85
982 1076 2.023404 TCTAGAGATGGGCTGGGTTGTA 60.023 50.000 0.00 0.00 0.00 2.41
983 1077 1.898863 AGAGATGGGCTGGGTTGTAT 58.101 50.000 0.00 0.00 0.00 2.29
984 1078 2.208872 AGAGATGGGCTGGGTTGTATT 58.791 47.619 0.00 0.00 0.00 1.89
985 1079 2.092212 AGAGATGGGCTGGGTTGTATTG 60.092 50.000 0.00 0.00 0.00 1.90
986 1080 1.640670 AGATGGGCTGGGTTGTATTGT 59.359 47.619 0.00 0.00 0.00 2.71
987 1081 1.750778 GATGGGCTGGGTTGTATTGTG 59.249 52.381 0.00 0.00 0.00 3.33
997 1091 2.747446 GGTTGTATTGTGTGAGCCGAAT 59.253 45.455 0.00 0.00 0.00 3.34
1003 1097 1.026182 TGTGTGAGCCGAATGGATGC 61.026 55.000 0.00 0.00 37.49 3.91
1004 1098 1.451927 TGTGAGCCGAATGGATGCC 60.452 57.895 0.00 0.00 37.49 4.40
1023 1117 0.103937 CGCAGGTTGGGCTTTCAAAA 59.896 50.000 0.00 0.00 0.00 2.44
1024 1118 1.472376 CGCAGGTTGGGCTTTCAAAAA 60.472 47.619 0.00 0.00 0.00 1.94
1025 1119 1.939934 GCAGGTTGGGCTTTCAAAAAC 59.060 47.619 0.00 0.00 0.00 2.43
1028 1122 4.260985 CAGGTTGGGCTTTCAAAAACTTT 58.739 39.130 0.00 0.00 0.00 2.66
1043 1137 1.222387 CTTTACCGGCCCGATCCAA 59.778 57.895 3.71 0.00 0.00 3.53
1046 1140 0.256464 TTACCGGCCCGATCCAAAAT 59.744 50.000 3.71 0.00 0.00 1.82
1047 1141 0.256464 TACCGGCCCGATCCAAAATT 59.744 50.000 3.71 0.00 0.00 1.82
1050 1144 1.102978 CGGCCCGATCCAAAATTCTT 58.897 50.000 0.00 0.00 0.00 2.52
1051 1145 1.202290 CGGCCCGATCCAAAATTCTTG 60.202 52.381 0.00 0.00 0.00 3.02
1052 1146 1.136891 GGCCCGATCCAAAATTCTTGG 59.863 52.381 11.15 11.15 40.87 3.61
1170 1264 0.252467 AGCCTCTCAGGTAGCCAAGT 60.252 55.000 0.00 0.00 37.80 3.16
1202 1296 1.205460 GGCCCCTCCTACTTCCACAA 61.205 60.000 0.00 0.00 0.00 3.33
1246 1342 2.068831 TTCCTTTCCCCACCAGGTAT 57.931 50.000 0.00 0.00 0.00 2.73
1423 1521 1.474077 CCTGTTTGCTGTATTGCCTCC 59.526 52.381 0.00 0.00 0.00 4.30
1438 1536 0.170339 CCTCCGCGAAAATGGAAACC 59.830 55.000 8.23 0.00 32.89 3.27
1452 1550 3.843422 TGGAAACCCATTCAACAGATGT 58.157 40.909 0.00 0.00 39.98 3.06
1481 1580 1.421480 AGGGGGCGATTTCCTAGTAC 58.579 55.000 0.00 0.00 0.00 2.73
1483 1582 1.421480 GGGGCGATTTCCTAGTACCT 58.579 55.000 0.00 0.00 0.00 3.08
1484 1583 1.767088 GGGGCGATTTCCTAGTACCTT 59.233 52.381 0.00 0.00 0.00 3.50
1487 1586 4.041321 GGGGCGATTTCCTAGTACCTTTAT 59.959 45.833 0.00 0.00 0.00 1.40
1488 1587 4.995487 GGGCGATTTCCTAGTACCTTTATG 59.005 45.833 0.00 0.00 0.00 1.90
1489 1588 4.451435 GGCGATTTCCTAGTACCTTTATGC 59.549 45.833 0.00 0.00 0.00 3.14
1494 1593 7.441157 CGATTTCCTAGTACCTTTATGCAATGA 59.559 37.037 0.00 0.00 0.00 2.57
1495 1594 9.120538 GATTTCCTAGTACCTTTATGCAATGAA 57.879 33.333 0.00 0.00 0.00 2.57
1497 1596 8.871629 TTCCTAGTACCTTTATGCAATGAAAA 57.128 30.769 0.00 0.00 0.00 2.29
1512 1611 5.163972 GCAATGAAAACATAAAATGCGCAGA 60.164 36.000 18.32 0.69 0.00 4.26
1537 1636 5.083533 AGACTCAATTCAGGAAGTAGCTG 57.916 43.478 0.00 0.00 0.00 4.24
1555 1654 5.590530 AGCTGGTGATAACTAGTCTTCAG 57.409 43.478 7.71 6.24 0.00 3.02
1586 1685 9.352784 CATCTCTCTATGGTTATCGAGAATTTC 57.647 37.037 0.00 0.00 35.47 2.17
1596 1697 7.095229 TGGTTATCGAGAATTTCACTGTTTGAG 60.095 37.037 0.00 0.00 34.94 3.02
1597 1698 7.117812 GGTTATCGAGAATTTCACTGTTTGAGA 59.882 37.037 0.00 0.00 34.94 3.27
1615 1716 8.352201 TGTTTGAGATGAAGTTTTAGAACATGG 58.648 33.333 0.00 0.00 38.26 3.66
1620 1721 7.637511 AGATGAAGTTTTAGAACATGGGAGAT 58.362 34.615 0.00 0.00 38.26 2.75
1622 1723 5.415701 TGAAGTTTTAGAACATGGGAGATGC 59.584 40.000 0.00 0.00 38.26 3.91
1625 1726 3.459232 TTAGAACATGGGAGATGCTCG 57.541 47.619 0.00 0.00 0.00 5.03
1627 1728 2.388735 AGAACATGGGAGATGCTCGTA 58.611 47.619 0.00 0.00 0.00 3.43
1632 1733 3.006967 ACATGGGAGATGCTCGTATTACC 59.993 47.826 0.00 0.00 0.00 2.85
1634 1735 3.035363 TGGGAGATGCTCGTATTACCAA 58.965 45.455 0.00 0.00 0.00 3.67
1636 1737 4.058817 GGGAGATGCTCGTATTACCAAAG 58.941 47.826 0.00 0.00 0.00 2.77
1662 1893 2.368439 GTGTTAGCATGCTGGGATCAA 58.632 47.619 30.42 12.40 0.00 2.57
1677 1908 3.572539 CAACGCGTGTGCAGTGGT 61.573 61.111 14.98 0.00 42.97 4.16
1682 1913 2.708865 CGTGTGCAGTGGTGTGTG 59.291 61.111 0.00 0.00 0.00 3.82
1697 1928 2.440946 TGTGGGGACAGACTCACAG 58.559 57.895 0.00 0.00 44.46 3.66
1707 2495 3.417101 ACAGACTCACAGACTAGAGTGG 58.583 50.000 12.91 8.43 44.61 4.00
1708 2496 3.181438 ACAGACTCACAGACTAGAGTGGT 60.181 47.826 12.91 8.91 44.61 4.16
1710 2498 4.393680 CAGACTCACAGACTAGAGTGGTAC 59.606 50.000 12.91 1.59 44.61 3.34
1775 2568 6.096705 ACCAACTGATTTGATGTTCTGAAACA 59.903 34.615 0.00 0.00 39.11 2.83
1899 2692 4.013267 GGCATCTCTGGCATACTTACAT 57.987 45.455 0.00 0.00 46.77 2.29
1900 2693 4.392940 GGCATCTCTGGCATACTTACATT 58.607 43.478 0.00 0.00 46.77 2.71
1905 2698 6.406692 TCTCTGGCATACTTACATTACTCC 57.593 41.667 0.00 0.00 0.00 3.85
1916 2709 6.827727 ACTTACATTACTCCTTGTGAACAGT 58.172 36.000 0.00 0.00 0.00 3.55
2036 2830 0.391597 AAGACGGGAAGTTGCTCGAA 59.608 50.000 11.09 0.00 0.00 3.71
2063 2857 2.104451 CCAGAGGGAATCAGGACATGAG 59.896 54.545 0.00 0.00 37.66 2.90
2114 2908 0.462403 ACGTTGTTGTACAAGCCGGT 60.462 50.000 8.98 2.60 39.00 5.28
2312 3106 3.492102 TTCTCTTTGCTGCTGTACCTT 57.508 42.857 0.00 0.00 0.00 3.50
2351 3145 3.022406 ACTACTCCCTCCGTCACATAAC 58.978 50.000 0.00 0.00 0.00 1.89
2357 3151 3.386726 TCCCTCCGTCACATAACATAAGG 59.613 47.826 0.00 0.00 0.00 2.69
2359 3153 3.131396 CTCCGTCACATAACATAAGGGC 58.869 50.000 0.00 0.00 0.00 5.19
2376 3170 1.265905 GGGCGTTTTTGACACTACAGG 59.734 52.381 0.00 0.00 0.00 4.00
2377 3171 1.265905 GGCGTTTTTGACACTACAGGG 59.734 52.381 0.00 0.00 0.00 4.45
2379 3173 2.841215 CGTTTTTGACACTACAGGGGA 58.159 47.619 0.00 0.00 0.00 4.81
2385 3192 2.667470 TGACACTACAGGGGAGATAGC 58.333 52.381 0.00 0.00 0.00 2.97
2415 3222 3.797353 GGCCTCCATGGAAGCCGA 61.797 66.667 33.49 3.38 41.23 5.54
2417 3224 1.152881 GCCTCCATGGAAGCCGATT 60.153 57.895 22.79 0.00 38.35 3.34
2419 3226 1.476833 GCCTCCATGGAAGCCGATTTA 60.477 52.381 22.79 0.00 38.35 1.40
2420 3227 2.930950 CCTCCATGGAAGCCGATTTAA 58.069 47.619 17.00 0.00 38.35 1.52
2421 3228 3.287222 CCTCCATGGAAGCCGATTTAAA 58.713 45.455 17.00 0.00 38.35 1.52
2422 3229 3.699038 CCTCCATGGAAGCCGATTTAAAA 59.301 43.478 17.00 0.00 38.35 1.52
2423 3230 4.159506 CCTCCATGGAAGCCGATTTAAAAA 59.840 41.667 17.00 0.00 38.35 1.94
2466 3273 8.661352 ATTTCGGTTTCAAAACAATCTGAAAT 57.339 26.923 7.82 10.26 42.01 2.17
2467 3274 8.485976 TTTCGGTTTCAAAACAATCTGAAATT 57.514 26.923 7.82 0.00 42.01 1.82
2468 3275 8.485976 TTCGGTTTCAAAACAATCTGAAATTT 57.514 26.923 7.82 0.00 42.01 1.82
2496 3303 5.048846 ACAAGTAAACAAGGATGTGAGGT 57.951 39.130 0.00 0.00 40.46 3.85
2498 3305 4.974645 AGTAAACAAGGATGTGAGGTGA 57.025 40.909 0.00 0.00 40.46 4.02
2507 3373 3.267812 AGGATGTGAGGTGAATCATGGTT 59.732 43.478 0.00 0.00 0.00 3.67
2523 3389 6.455360 TCATGGTTTTGAAGGATGAATAGC 57.545 37.500 0.00 0.00 0.00 2.97
2545 3411 4.623647 GCATCATGTGTTAAAAAGCCCCAT 60.624 41.667 0.00 0.00 0.00 4.00
2695 3570 5.565455 TGAATTTTGAATTTGGAGGCCTT 57.435 34.783 6.77 0.00 0.00 4.35
2725 3600 1.273327 CGGCCTCCAAAAGCAATTTCT 59.727 47.619 0.00 0.00 0.00 2.52
2729 3604 3.258123 GCCTCCAAAAGCAATTTCTGGTA 59.742 43.478 0.00 0.00 33.58 3.25
2783 3658 2.286121 CCCAACAGGCCCTCCCTA 60.286 66.667 0.00 0.00 44.09 3.53
2784 3659 2.378634 CCCAACAGGCCCTCCCTAG 61.379 68.421 0.00 0.00 44.09 3.02
2785 3660 2.378634 CCAACAGGCCCTCCCTAGG 61.379 68.421 0.06 0.06 44.09 3.02
2791 3666 2.675371 GCCCTCCCTAGGCGTTTT 59.325 61.111 2.05 0.00 42.14 2.43
2792 3667 1.001269 GCCCTCCCTAGGCGTTTTT 60.001 57.895 2.05 0.00 42.14 1.94
2793 3668 1.313091 GCCCTCCCTAGGCGTTTTTG 61.313 60.000 2.05 0.00 42.14 2.44
2794 3669 1.313091 CCCTCCCTAGGCGTTTTTGC 61.313 60.000 2.05 0.00 42.14 3.68
2816 3691 4.490575 CCGGCGCCCAAAAATCGG 62.491 66.667 23.46 12.32 0.00 4.18
2818 3693 4.812476 GGCGCCCAAAAATCGGCC 62.812 66.667 18.11 0.00 42.53 6.13
2819 3694 4.812476 GCGCCCAAAAATCGGCCC 62.812 66.667 0.00 0.00 42.53 5.80
2820 3695 3.377759 CGCCCAAAAATCGGCCCA 61.378 61.111 0.00 0.00 42.53 5.36
2821 3696 2.578664 GCCCAAAAATCGGCCCAG 59.421 61.111 0.00 0.00 39.39 4.45
2822 3697 2.282783 GCCCAAAAATCGGCCCAGT 61.283 57.895 0.00 0.00 39.39 4.00
2823 3698 1.890174 CCCAAAAATCGGCCCAGTC 59.110 57.895 0.00 0.00 0.00 3.51
2824 3699 1.506262 CCAAAAATCGGCCCAGTCG 59.494 57.895 0.00 0.00 0.00 4.18
2825 3700 1.154035 CAAAAATCGGCCCAGTCGC 60.154 57.895 0.00 0.00 0.00 5.19
2826 3701 2.686816 AAAAATCGGCCCAGTCGCG 61.687 57.895 0.00 0.00 0.00 5.87
2835 3710 3.449227 CCAGTCGCGCCTCCAGTA 61.449 66.667 0.00 0.00 0.00 2.74
2836 3711 2.103143 CAGTCGCGCCTCCAGTAG 59.897 66.667 0.00 0.00 0.00 2.57
2837 3712 3.827898 AGTCGCGCCTCCAGTAGC 61.828 66.667 0.00 0.00 0.00 3.58
2838 3713 4.874977 GTCGCGCCTCCAGTAGCC 62.875 72.222 0.00 0.00 0.00 3.93
2842 3717 3.771160 CGCCTCCAGTAGCCCGTT 61.771 66.667 0.00 0.00 0.00 4.44
2843 3718 2.669240 GCCTCCAGTAGCCCGTTT 59.331 61.111 0.00 0.00 0.00 3.60
2844 3719 1.002502 GCCTCCAGTAGCCCGTTTT 60.003 57.895 0.00 0.00 0.00 2.43
2845 3720 0.608308 GCCTCCAGTAGCCCGTTTTT 60.608 55.000 0.00 0.00 0.00 1.94
2846 3721 1.450025 CCTCCAGTAGCCCGTTTTTC 58.550 55.000 0.00 0.00 0.00 2.29
2847 3722 1.076332 CTCCAGTAGCCCGTTTTTCG 58.924 55.000 0.00 0.00 39.52 3.46
2848 3723 0.952010 TCCAGTAGCCCGTTTTTCGC 60.952 55.000 0.00 0.00 38.35 4.70
2849 3724 1.500396 CAGTAGCCCGTTTTTCGCC 59.500 57.895 0.00 0.00 38.35 5.54
2850 3725 2.030958 AGTAGCCCGTTTTTCGCCG 61.031 57.895 0.00 0.00 38.35 6.46
2851 3726 2.743149 TAGCCCGTTTTTCGCCGG 60.743 61.111 0.00 0.00 43.82 6.13
2854 3729 4.097863 CCCGTTTTTCGCCGGCTC 62.098 66.667 26.68 6.70 42.87 4.70
2855 3730 4.439472 CCGTTTTTCGCCGGCTCG 62.439 66.667 26.68 17.41 37.43 5.03
2868 3743 4.699522 GCTCGGGCCGAAACTGGT 62.700 66.667 30.59 0.00 34.74 4.00
2869 3744 2.742372 CTCGGGCCGAAACTGGTG 60.742 66.667 30.59 12.56 34.74 4.17
2924 3799 2.429069 GCCGGCACAAGCGAAAAG 60.429 61.111 24.80 0.00 43.41 2.27
2925 3800 2.255252 CCGGCACAAGCGAAAAGG 59.745 61.111 0.00 0.00 43.41 3.11
2926 3801 2.255252 CGGCACAAGCGAAAAGGG 59.745 61.111 0.00 0.00 43.41 3.95
2927 3802 2.650778 GGCACAAGCGAAAAGGGG 59.349 61.111 0.00 0.00 43.41 4.79
2928 3803 2.049156 GCACAAGCGAAAAGGGGC 60.049 61.111 0.00 0.00 0.00 5.80
2929 3804 2.255252 CACAAGCGAAAAGGGGCG 59.745 61.111 0.00 0.00 0.00 6.13
2930 3805 2.203294 ACAAGCGAAAAGGGGCGT 60.203 55.556 0.00 0.00 0.00 5.68
2931 3806 2.255252 CAAGCGAAAAGGGGCGTG 59.745 61.111 0.00 0.00 32.72 5.34
2932 3807 2.983592 AAGCGAAAAGGGGCGTGG 60.984 61.111 0.00 0.00 0.00 4.94
2950 3825 4.838486 GGCCGCTCTGTCGACGAG 62.838 72.222 23.94 23.94 0.00 4.18
2951 3826 4.104417 GCCGCTCTGTCGACGAGT 62.104 66.667 26.57 0.00 0.00 4.18
2952 3827 2.098680 CCGCTCTGTCGACGAGTC 59.901 66.667 26.57 20.41 0.00 3.36
2962 3837 4.211986 GACGAGTCGAGAGCCTCT 57.788 61.111 21.50 0.00 0.00 3.69
2963 3838 2.473457 GACGAGTCGAGAGCCTCTT 58.527 57.895 21.50 0.00 0.00 2.85
2964 3839 0.375803 GACGAGTCGAGAGCCTCTTC 59.624 60.000 21.50 0.00 0.00 2.87
2965 3840 1.027792 ACGAGTCGAGAGCCTCTTCC 61.028 60.000 21.50 0.00 0.00 3.46
2966 3841 1.720694 CGAGTCGAGAGCCTCTTCCC 61.721 65.000 6.73 0.00 0.00 3.97
2967 3842 1.720694 GAGTCGAGAGCCTCTTCCCG 61.721 65.000 0.00 0.00 0.00 5.14
2968 3843 3.141488 TCGAGAGCCTCTTCCCGC 61.141 66.667 0.00 0.00 0.00 6.13
2969 3844 4.214327 CGAGAGCCTCTTCCCGCC 62.214 72.222 0.00 0.00 0.00 6.13
2970 3845 4.214327 GAGAGCCTCTTCCCGCCG 62.214 72.222 0.00 0.00 0.00 6.46
2972 3847 4.083862 GAGCCTCTTCCCGCCGTT 62.084 66.667 0.00 0.00 0.00 4.44
2973 3848 3.607370 GAGCCTCTTCCCGCCGTTT 62.607 63.158 0.00 0.00 0.00 3.60
2974 3849 3.125573 GCCTCTTCCCGCCGTTTC 61.126 66.667 0.00 0.00 0.00 2.78
2975 3850 2.663196 CCTCTTCCCGCCGTTTCT 59.337 61.111 0.00 0.00 0.00 2.52
2976 3851 1.003718 CCTCTTCCCGCCGTTTCTT 60.004 57.895 0.00 0.00 0.00 2.52
2977 3852 1.019805 CCTCTTCCCGCCGTTTCTTC 61.020 60.000 0.00 0.00 0.00 2.87
2978 3853 1.004200 TCTTCCCGCCGTTTCTTCC 60.004 57.895 0.00 0.00 0.00 3.46
2979 3854 2.032987 TTCCCGCCGTTTCTTCCC 59.967 61.111 0.00 0.00 0.00 3.97
2980 3855 3.887335 TTCCCGCCGTTTCTTCCCG 62.887 63.158 0.00 0.00 0.00 5.14
2983 3858 3.047877 CGCCGTTTCTTCCCGCTT 61.048 61.111 0.00 0.00 0.00 4.68
2984 3859 2.613506 CGCCGTTTCTTCCCGCTTT 61.614 57.895 0.00 0.00 0.00 3.51
2985 3860 1.658114 GCCGTTTCTTCCCGCTTTT 59.342 52.632 0.00 0.00 0.00 2.27
2986 3861 0.386858 GCCGTTTCTTCCCGCTTTTC 60.387 55.000 0.00 0.00 0.00 2.29
2987 3862 0.240145 CCGTTTCTTCCCGCTTTTCC 59.760 55.000 0.00 0.00 0.00 3.13
2988 3863 0.240145 CGTTTCTTCCCGCTTTTCCC 59.760 55.000 0.00 0.00 0.00 3.97
2989 3864 0.601558 GTTTCTTCCCGCTTTTCCCC 59.398 55.000 0.00 0.00 0.00 4.81
2990 3865 0.541063 TTTCTTCCCGCTTTTCCCCC 60.541 55.000 0.00 0.00 0.00 5.40
2991 3866 1.721093 TTCTTCCCGCTTTTCCCCCA 61.721 55.000 0.00 0.00 0.00 4.96
2992 3867 1.977009 CTTCCCGCTTTTCCCCCAC 60.977 63.158 0.00 0.00 0.00 4.61
2993 3868 2.426305 CTTCCCGCTTTTCCCCCACT 62.426 60.000 0.00 0.00 0.00 4.00
2994 3869 2.014033 TTCCCGCTTTTCCCCCACTT 62.014 55.000 0.00 0.00 0.00 3.16
2995 3870 1.977009 CCCGCTTTTCCCCCACTTC 60.977 63.158 0.00 0.00 0.00 3.01
2996 3871 1.977009 CCGCTTTTCCCCCACTTCC 60.977 63.158 0.00 0.00 0.00 3.46
2997 3872 1.977009 CGCTTTTCCCCCACTTCCC 60.977 63.158 0.00 0.00 0.00 3.97
2998 3873 1.465172 GCTTTTCCCCCACTTCCCT 59.535 57.895 0.00 0.00 0.00 4.20
2999 3874 0.612174 GCTTTTCCCCCACTTCCCTC 60.612 60.000 0.00 0.00 0.00 4.30
3000 3875 0.039764 CTTTTCCCCCACTTCCCTCC 59.960 60.000 0.00 0.00 0.00 4.30
3001 3876 1.440362 TTTTCCCCCACTTCCCTCCC 61.440 60.000 0.00 0.00 0.00 4.30
3002 3877 2.662971 TTTCCCCCACTTCCCTCCCA 62.663 60.000 0.00 0.00 0.00 4.37
3003 3878 2.287194 CCCCCACTTCCCTCCCAT 60.287 66.667 0.00 0.00 0.00 4.00
3004 3879 1.935931 CCCCCACTTCCCTCCCATT 60.936 63.158 0.00 0.00 0.00 3.16
3005 3880 1.615262 CCCCACTTCCCTCCCATTC 59.385 63.158 0.00 0.00 0.00 2.67
3006 3881 0.921256 CCCCACTTCCCTCCCATTCT 60.921 60.000 0.00 0.00 0.00 2.40
3007 3882 0.548510 CCCACTTCCCTCCCATTCTC 59.451 60.000 0.00 0.00 0.00 2.87
3008 3883 1.589414 CCACTTCCCTCCCATTCTCT 58.411 55.000 0.00 0.00 0.00 3.10
3009 3884 1.488393 CCACTTCCCTCCCATTCTCTC 59.512 57.143 0.00 0.00 0.00 3.20
3010 3885 1.488393 CACTTCCCTCCCATTCTCTCC 59.512 57.143 0.00 0.00 0.00 3.71
3011 3886 1.135960 CTTCCCTCCCATTCTCTCCC 58.864 60.000 0.00 0.00 0.00 4.30
3012 3887 0.725133 TTCCCTCCCATTCTCTCCCT 59.275 55.000 0.00 0.00 0.00 4.20
3013 3888 0.266152 TCCCTCCCATTCTCTCCCTC 59.734 60.000 0.00 0.00 0.00 4.30
3014 3889 0.766288 CCCTCCCATTCTCTCCCTCC 60.766 65.000 0.00 0.00 0.00 4.30
3015 3890 0.766288 CCTCCCATTCTCTCCCTCCC 60.766 65.000 0.00 0.00 0.00 4.30
3016 3891 1.075226 TCCCATTCTCTCCCTCCCG 60.075 63.158 0.00 0.00 0.00 5.14
3017 3892 2.812619 CCCATTCTCTCCCTCCCGC 61.813 68.421 0.00 0.00 0.00 6.13
3018 3893 1.764054 CCATTCTCTCCCTCCCGCT 60.764 63.158 0.00 0.00 0.00 5.52
3019 3894 1.745264 CATTCTCTCCCTCCCGCTC 59.255 63.158 0.00 0.00 0.00 5.03
3020 3895 1.830408 ATTCTCTCCCTCCCGCTCG 60.830 63.158 0.00 0.00 0.00 5.03
3052 3927 3.880846 GCCATGCCGCCGAAGAAG 61.881 66.667 0.00 0.00 0.00 2.85
3053 3928 2.436646 CCATGCCGCCGAAGAAGT 60.437 61.111 0.00 0.00 0.00 3.01
3054 3929 1.153449 CCATGCCGCCGAAGAAGTA 60.153 57.895 0.00 0.00 0.00 2.24
3055 3930 1.429148 CCATGCCGCCGAAGAAGTAC 61.429 60.000 0.00 0.00 0.00 2.73
3056 3931 1.518572 ATGCCGCCGAAGAAGTACG 60.519 57.895 0.00 0.00 0.00 3.67
3057 3932 2.126189 GCCGCCGAAGAAGTACGT 60.126 61.111 0.00 0.00 0.00 3.57
3058 3933 2.442188 GCCGCCGAAGAAGTACGTG 61.442 63.158 0.00 0.00 0.00 4.49
3059 3934 1.210931 CCGCCGAAGAAGTACGTGA 59.789 57.895 0.00 0.00 0.00 4.35
3060 3935 0.179145 CCGCCGAAGAAGTACGTGAT 60.179 55.000 0.00 0.00 0.00 3.06
3061 3936 1.189403 CGCCGAAGAAGTACGTGATC 58.811 55.000 0.00 0.00 0.00 2.92
3062 3937 1.557651 GCCGAAGAAGTACGTGATCC 58.442 55.000 0.00 0.00 0.00 3.36
3063 3938 1.801765 GCCGAAGAAGTACGTGATCCC 60.802 57.143 0.00 0.00 0.00 3.85
3064 3939 1.202382 CCGAAGAAGTACGTGATCCCC 60.202 57.143 0.00 0.00 0.00 4.81
3065 3940 1.202382 CGAAGAAGTACGTGATCCCCC 60.202 57.143 0.00 0.00 0.00 5.40
3066 3941 0.822164 AAGAAGTACGTGATCCCCCG 59.178 55.000 0.00 0.00 0.00 5.73
3067 3942 1.227176 GAAGTACGTGATCCCCCGC 60.227 63.158 0.00 0.00 0.00 6.13
3068 3943 2.948840 GAAGTACGTGATCCCCCGCG 62.949 65.000 0.00 0.00 44.66 6.46
3113 3988 3.393970 CCCAGCCGAAGCAGAGGA 61.394 66.667 0.00 0.00 43.56 3.71
3114 3989 2.665000 CCAGCCGAAGCAGAGGAA 59.335 61.111 0.00 0.00 43.56 3.36
3115 3990 1.449246 CCAGCCGAAGCAGAGGAAG 60.449 63.158 0.00 0.00 43.56 3.46
3116 3991 2.105466 CAGCCGAAGCAGAGGAAGC 61.105 63.158 0.00 0.00 43.56 3.86
3117 3992 2.821810 GCCGAAGCAGAGGAAGCC 60.822 66.667 0.00 0.00 39.53 4.35
3118 3993 2.510238 CCGAAGCAGAGGAAGCCG 60.510 66.667 0.00 0.00 0.00 5.52
3119 3994 2.573869 CGAAGCAGAGGAAGCCGA 59.426 61.111 0.00 0.00 0.00 5.54
3120 3995 1.518133 CGAAGCAGAGGAAGCCGAG 60.518 63.158 0.00 0.00 0.00 4.63
3121 3996 1.153469 GAAGCAGAGGAAGCCGAGG 60.153 63.158 0.00 0.00 0.00 4.63
3122 3997 2.585791 GAAGCAGAGGAAGCCGAGGG 62.586 65.000 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 112 1.991230 CCCAGGGAAGGAACATCGT 59.009 57.895 0.00 0.00 0.00 3.73
107 139 1.583967 CGAGATCGTGGTGAGCGTC 60.584 63.158 0.00 0.00 38.28 5.19
108 140 2.485582 CGAGATCGTGGTGAGCGT 59.514 61.111 0.00 0.00 38.28 5.07
244 276 1.731700 CATTTGATCCTGCCAGCCG 59.268 57.895 0.00 0.00 0.00 5.52
574 646 1.337167 CGCCGCCTCATTCTCATCATA 60.337 52.381 0.00 0.00 0.00 2.15
723 810 4.407496 AACTATTACGCGCTCTAGCTAG 57.593 45.455 15.01 15.01 39.32 3.42
728 815 6.870439 TGTCTCTATAACTATTACGCGCTCTA 59.130 38.462 5.73 0.00 0.00 2.43
739 826 9.647918 TGAGATTGAAGGTGTCTCTATAACTAT 57.352 33.333 0.00 0.00 39.24 2.12
752 843 7.173907 ACACAAGTTAAGATGAGATTGAAGGTG 59.826 37.037 0.00 0.00 0.00 4.00
806 897 4.319766 CGAAACTTGTGGATTTGGAGTCTG 60.320 45.833 0.00 0.00 0.00 3.51
818 909 1.439679 GAGGTAGCCGAAACTTGTGG 58.560 55.000 0.00 0.00 0.00 4.17
924 1018 0.389817 GGCAGGCACGAAAATTTCCC 60.390 55.000 0.00 0.00 0.00 3.97
982 1076 2.019249 CATCCATTCGGCTCACACAAT 58.981 47.619 0.00 0.00 0.00 2.71
983 1077 1.452110 CATCCATTCGGCTCACACAA 58.548 50.000 0.00 0.00 0.00 3.33
984 1078 1.026182 GCATCCATTCGGCTCACACA 61.026 55.000 0.00 0.00 0.00 3.72
985 1079 1.718757 GGCATCCATTCGGCTCACAC 61.719 60.000 0.00 0.00 0.00 3.82
986 1080 1.451927 GGCATCCATTCGGCTCACA 60.452 57.895 0.00 0.00 0.00 3.58
987 1081 2.537560 CGGCATCCATTCGGCTCAC 61.538 63.158 0.00 0.00 0.00 3.51
997 1091 4.738998 CCCAACCTGCGGCATCCA 62.739 66.667 1.75 0.00 0.00 3.41
1003 1097 1.743321 TTTGAAAGCCCAACCTGCGG 61.743 55.000 0.00 0.00 0.00 5.69
1004 1098 0.103937 TTTTGAAAGCCCAACCTGCG 59.896 50.000 0.00 0.00 0.00 5.18
1023 1117 1.222661 GGATCGGGCCGGTAAAGTT 59.777 57.895 27.98 2.13 0.00 2.66
1024 1118 1.555477 TTGGATCGGGCCGGTAAAGT 61.555 55.000 27.98 5.32 0.00 2.66
1025 1119 0.393267 TTTGGATCGGGCCGGTAAAG 60.393 55.000 27.98 0.00 0.00 1.85
1028 1122 0.256464 AATTTTGGATCGGGCCGGTA 59.744 50.000 27.98 8.20 0.00 4.02
1043 1137 3.012518 CTCATCGTCCTGCCAAGAATTT 58.987 45.455 0.00 0.00 0.00 1.82
1046 1140 0.250234 CCTCATCGTCCTGCCAAGAA 59.750 55.000 0.00 0.00 0.00 2.52
1047 1141 1.900351 CCTCATCGTCCTGCCAAGA 59.100 57.895 0.00 0.00 0.00 3.02
1050 1144 4.147449 CGCCTCATCGTCCTGCCA 62.147 66.667 0.00 0.00 0.00 4.92
1051 1145 4.899239 CCGCCTCATCGTCCTGCC 62.899 72.222 0.00 0.00 0.00 4.85
1052 1146 3.838271 TCCGCCTCATCGTCCTGC 61.838 66.667 0.00 0.00 0.00 4.85
1202 1296 5.600484 AGAGACGAGATCAATCAAAGGGTAT 59.400 40.000 0.00 0.00 0.00 2.73
1438 1536 7.114811 CCTTTTCGTTTTACATCTGTTGAATGG 59.885 37.037 0.00 0.00 0.00 3.16
1445 1543 3.824443 CCCCCTTTTCGTTTTACATCTGT 59.176 43.478 0.00 0.00 0.00 3.41
1448 1546 2.414957 CGCCCCCTTTTCGTTTTACATC 60.415 50.000 0.00 0.00 0.00 3.06
1449 1547 1.542472 CGCCCCCTTTTCGTTTTACAT 59.458 47.619 0.00 0.00 0.00 2.29
1452 1550 2.203470 ATCGCCCCCTTTTCGTTTTA 57.797 45.000 0.00 0.00 0.00 1.52
1481 1580 9.493206 GCATTTTATGTTTTCATTGCATAAAGG 57.507 29.630 0.00 0.00 42.36 3.11
1483 1582 7.691463 GCGCATTTTATGTTTTCATTGCATAAA 59.309 29.630 0.30 0.00 39.11 1.40
1484 1583 7.148523 TGCGCATTTTATGTTTTCATTGCATAA 60.149 29.630 5.66 0.00 39.11 1.90
1487 1586 4.450080 TGCGCATTTTATGTTTTCATTGCA 59.550 33.333 5.66 0.00 39.11 4.08
1488 1587 4.955617 TGCGCATTTTATGTTTTCATTGC 58.044 34.783 5.66 0.00 41.25 3.56
1489 1588 6.392353 TCTGCGCATTTTATGTTTTCATTG 57.608 33.333 12.24 0.00 41.25 2.82
1494 1593 5.858581 GTCTCTTCTGCGCATTTTATGTTTT 59.141 36.000 12.24 0.00 0.00 2.43
1495 1594 5.182001 AGTCTCTTCTGCGCATTTTATGTTT 59.818 36.000 12.24 0.00 0.00 2.83
1497 1596 4.256920 AGTCTCTTCTGCGCATTTTATGT 58.743 39.130 12.24 0.00 0.00 2.29
1501 1600 2.771089 TGAGTCTCTTCTGCGCATTTT 58.229 42.857 12.24 0.00 0.00 1.82
1506 1605 2.341257 TGAATTGAGTCTCTTCTGCGC 58.659 47.619 0.00 0.00 0.00 6.09
1512 1611 5.483583 AGCTACTTCCTGAATTGAGTCTCTT 59.516 40.000 0.65 0.00 0.00 2.85
1537 1636 5.105716 TGCTGTCTGAAGACTAGTTATCACC 60.106 44.000 11.55 0.00 44.99 4.02
1555 1654 5.182190 TCGATAACCATAGAGAGATGCTGTC 59.818 44.000 0.00 0.00 0.00 3.51
1563 1662 8.356657 AGTGAAATTCTCGATAACCATAGAGAG 58.643 37.037 0.00 0.00 41.92 3.20
1567 1666 8.425577 AACAGTGAAATTCTCGATAACCATAG 57.574 34.615 0.00 0.00 0.00 2.23
1569 1668 7.390440 TCAAACAGTGAAATTCTCGATAACCAT 59.610 33.333 0.00 0.00 31.51 3.55
1586 1685 8.397906 TGTTCTAAAACTTCATCTCAAACAGTG 58.602 33.333 0.00 0.00 36.30 3.66
1596 1697 7.680588 GCATCTCCCATGTTCTAAAACTTCATC 60.681 40.741 0.00 0.00 36.30 2.92
1597 1698 6.096001 GCATCTCCCATGTTCTAAAACTTCAT 59.904 38.462 0.00 0.00 36.30 2.57
1615 1716 4.694339 ACTTTGGTAATACGAGCATCTCC 58.306 43.478 0.00 0.00 0.00 3.71
1620 1721 4.751060 CCAGTACTTTGGTAATACGAGCA 58.249 43.478 0.00 0.00 33.38 4.26
1632 1733 3.753272 AGCATGCTAACACCAGTACTTTG 59.247 43.478 21.21 0.00 0.00 2.77
1634 1735 3.338249 CAGCATGCTAACACCAGTACTT 58.662 45.455 22.19 0.00 0.00 2.24
1636 1737 2.009774 CCAGCATGCTAACACCAGTAC 58.990 52.381 22.19 0.00 31.97 2.73
1662 1893 4.830765 ACACCACTGCACACGCGT 62.831 61.111 5.58 5.58 42.97 6.01
1677 1908 0.689412 TGTGAGTCTGTCCCCACACA 60.689 55.000 0.00 0.00 34.96 3.72
1682 1913 2.096248 CTAGTCTGTGAGTCTGTCCCC 58.904 57.143 0.00 0.00 0.00 4.81
1697 1928 2.937799 CTCTCACCGTACCACTCTAGTC 59.062 54.545 0.00 0.00 0.00 2.59
1705 2493 4.819105 ATCATTTTCTCTCACCGTACCA 57.181 40.909 0.00 0.00 0.00 3.25
1707 2495 8.169268 CACTTTAATCATTTTCTCTCACCGTAC 58.831 37.037 0.00 0.00 0.00 3.67
1708 2496 7.148474 GCACTTTAATCATTTTCTCTCACCGTA 60.148 37.037 0.00 0.00 0.00 4.02
1710 2498 6.024049 GCACTTTAATCATTTTCTCTCACCG 58.976 40.000 0.00 0.00 0.00 4.94
1775 2568 9.533831 AGTTCAAAGTTGACATAAAATATCCCT 57.466 29.630 0.00 0.00 36.83 4.20
1899 2692 6.071334 CCAGAGATACTGTTCACAAGGAGTAA 60.071 42.308 0.00 0.00 44.40 2.24
1900 2693 5.419155 CCAGAGATACTGTTCACAAGGAGTA 59.581 44.000 0.00 0.00 44.40 2.59
1905 2698 3.930336 TGCCAGAGATACTGTTCACAAG 58.070 45.455 0.00 0.00 44.40 3.16
2024 2818 1.149148 GGTGGTCTTCGAGCAACTTC 58.851 55.000 4.02 0.00 43.41 3.01
2036 2830 1.577736 CTGATTCCCTCTGGTGGTCT 58.422 55.000 0.00 0.00 0.00 3.85
2063 2857 1.967779 GAGGAATCCCTAGAGCTGGTC 59.032 57.143 0.00 0.00 44.53 4.02
2143 2937 3.311871 GCACATACTCTTGCTTCCATCTG 59.688 47.826 0.00 0.00 35.74 2.90
2312 3106 6.183360 GGAGTAGTACGCAAGGTTCACTATAA 60.183 42.308 6.37 0.00 46.39 0.98
2351 3145 3.915437 AGTGTCAAAAACGCCCTTATG 57.085 42.857 0.00 0.00 39.30 1.90
2357 3151 1.265905 CCCTGTAGTGTCAAAAACGCC 59.734 52.381 0.00 0.00 39.30 5.68
2359 3153 2.806244 CTCCCCTGTAGTGTCAAAAACG 59.194 50.000 0.00 0.00 0.00 3.60
2376 3170 1.134371 AGAGCCAAAACGCTATCTCCC 60.134 52.381 0.00 0.00 39.87 4.30
2377 3171 2.205911 GAGAGCCAAAACGCTATCTCC 58.794 52.381 0.00 0.00 42.53 3.71
2379 3173 1.471676 CCGAGAGCCAAAACGCTATCT 60.472 52.381 3.99 0.00 43.42 1.98
2437 3244 8.940952 TCAGATTGTTTTGAAACCGAAATTTTT 58.059 25.926 4.32 0.00 38.11 1.94
2467 3274 8.740906 TCACATCCTTGTTTACTTGTACAAAAA 58.259 29.630 10.03 5.59 34.17 1.94
2468 3275 8.282455 TCACATCCTTGTTTACTTGTACAAAA 57.718 30.769 10.03 0.00 34.17 2.44
2496 3303 6.914654 TTCATCCTTCAAAACCATGATTCA 57.085 33.333 0.00 0.00 0.00 2.57
2498 3305 7.124599 TGCTATTCATCCTTCAAAACCATGATT 59.875 33.333 0.00 0.00 0.00 2.57
2523 3389 4.533919 TGGGGCTTTTTAACACATGATG 57.466 40.909 0.00 0.00 0.00 3.07
2670 3538 4.637091 GGCCTCCAAATTCAAAATTCATGG 59.363 41.667 0.00 0.00 0.00 3.66
2695 3570 3.157252 GGAGGCCGAGCTCCATGA 61.157 66.667 8.47 0.00 39.45 3.07
2765 3640 3.962530 TAGGGAGGGCCTGTTGGGG 62.963 68.421 12.95 0.00 35.12 4.96
2766 3641 2.286121 TAGGGAGGGCCTGTTGGG 60.286 66.667 12.95 0.00 38.36 4.12
2767 3642 2.378634 CCTAGGGAGGGCCTGTTGG 61.379 68.421 12.95 1.54 39.48 3.77
2768 3643 3.049080 GCCTAGGGAGGGCCTGTTG 62.049 68.421 12.95 0.00 43.97 3.33
2769 3644 2.692741 GCCTAGGGAGGGCCTGTT 60.693 66.667 12.95 0.00 43.97 3.16
2772 3647 3.945064 AAACGCCTAGGGAGGGCCT 62.945 63.158 5.25 5.25 46.24 5.19
2773 3648 2.494777 AAAAACGCCTAGGGAGGGCC 62.495 60.000 11.72 0.00 46.24 5.80
2774 3649 1.001269 AAAAACGCCTAGGGAGGGC 60.001 57.895 11.72 0.00 43.97 5.19
2775 3650 1.313091 GCAAAAACGCCTAGGGAGGG 61.313 60.000 11.72 0.00 43.97 4.30
2776 3651 2.180674 GCAAAAACGCCTAGGGAGG 58.819 57.895 11.72 0.00 46.93 4.30
2799 3674 4.490575 CCGATTTTTGGGCGCCGG 62.491 66.667 22.54 12.00 0.00 6.13
2805 3680 1.890174 GACTGGGCCGATTTTTGGG 59.110 57.895 0.00 0.00 0.00 4.12
2806 3681 1.506262 CGACTGGGCCGATTTTTGG 59.494 57.895 0.00 0.00 0.00 3.28
2807 3682 1.154035 GCGACTGGGCCGATTTTTG 60.154 57.895 0.00 0.00 0.00 2.44
2808 3683 2.686816 CGCGACTGGGCCGATTTTT 61.687 57.895 0.00 0.00 0.00 1.94
2809 3684 3.124921 CGCGACTGGGCCGATTTT 61.125 61.111 0.00 0.00 0.00 1.82
2818 3693 3.417275 CTACTGGAGGCGCGACTGG 62.417 68.421 25.24 12.47 0.00 4.00
2819 3694 2.103143 CTACTGGAGGCGCGACTG 59.897 66.667 25.24 8.05 0.00 3.51
2820 3695 3.827898 GCTACTGGAGGCGCGACT 61.828 66.667 18.34 18.34 0.00 4.18
2821 3696 4.874977 GGCTACTGGAGGCGCGAC 62.875 72.222 12.10 7.34 41.55 5.19
2827 3702 1.450025 GAAAAACGGGCTACTGGAGG 58.550 55.000 0.00 0.00 0.00 4.30
2828 3703 1.076332 CGAAAAACGGGCTACTGGAG 58.924 55.000 0.00 0.00 38.46 3.86
2829 3704 0.952010 GCGAAAAACGGGCTACTGGA 60.952 55.000 0.00 0.00 42.83 3.86
2830 3705 1.500396 GCGAAAAACGGGCTACTGG 59.500 57.895 0.00 0.00 42.83 4.00
2831 3706 1.500396 GGCGAAAAACGGGCTACTG 59.500 57.895 0.00 0.00 42.83 2.74
2832 3707 2.030958 CGGCGAAAAACGGGCTACT 61.031 57.895 0.00 0.00 42.83 2.57
2833 3708 2.477396 CGGCGAAAAACGGGCTAC 59.523 61.111 0.00 0.00 42.83 3.58
2834 3709 2.743149 CCGGCGAAAAACGGGCTA 60.743 61.111 9.30 0.00 46.08 3.93
2839 3714 4.439472 CCGAGCCGGCGAAAAACG 62.439 66.667 23.20 19.15 41.17 3.60
2840 3715 4.097863 CCCGAGCCGGCGAAAAAC 62.098 66.667 23.20 8.62 46.86 2.43
2851 3726 4.699522 ACCAGTTTCGGCCCGAGC 62.700 66.667 5.73 3.62 37.14 5.03
2852 3727 2.742372 CACCAGTTTCGGCCCGAG 60.742 66.667 5.73 0.00 37.14 4.63
2907 3782 2.429069 CTTTTCGCTTGTGCCGGC 60.429 61.111 22.73 22.73 35.36 6.13
2908 3783 2.255252 CCTTTTCGCTTGTGCCGG 59.745 61.111 0.00 0.00 35.36 6.13
2909 3784 2.255252 CCCTTTTCGCTTGTGCCG 59.745 61.111 0.00 0.00 35.36 5.69
2910 3785 2.650778 CCCCTTTTCGCTTGTGCC 59.349 61.111 0.00 0.00 35.36 5.01
2911 3786 2.049156 GCCCCTTTTCGCTTGTGC 60.049 61.111 0.00 0.00 0.00 4.57
2912 3787 2.255252 CGCCCCTTTTCGCTTGTG 59.745 61.111 0.00 0.00 0.00 3.33
2913 3788 2.203294 ACGCCCCTTTTCGCTTGT 60.203 55.556 0.00 0.00 0.00 3.16
2914 3789 2.255252 CACGCCCCTTTTCGCTTG 59.745 61.111 0.00 0.00 0.00 4.01
2915 3790 2.983592 CCACGCCCCTTTTCGCTT 60.984 61.111 0.00 0.00 0.00 4.68
2933 3808 4.838486 CTCGTCGACAGAGCGGCC 62.838 72.222 17.16 0.00 30.94 6.13
2934 3809 4.104417 ACTCGTCGACAGAGCGGC 62.104 66.667 26.39 0.00 39.23 6.53
2935 3810 2.098680 GACTCGTCGACAGAGCGG 59.901 66.667 26.39 12.60 39.23 5.52
2948 3823 1.720694 CGGGAAGAGGCTCTCGACTC 61.721 65.000 19.03 11.41 46.21 3.36
2949 3824 1.751162 CGGGAAGAGGCTCTCGACT 60.751 63.158 19.03 0.91 42.10 4.18
2950 3825 2.802106 CGGGAAGAGGCTCTCGAC 59.198 66.667 19.03 12.05 42.10 4.20
2951 3826 3.141488 GCGGGAAGAGGCTCTCGA 61.141 66.667 23.35 0.00 42.10 4.04
2952 3827 4.214327 GGCGGGAAGAGGCTCTCG 62.214 72.222 19.03 17.84 42.42 4.04
2953 3828 4.214327 CGGCGGGAAGAGGCTCTC 62.214 72.222 19.03 11.12 0.00 3.20
2955 3830 3.607370 AAACGGCGGGAAGAGGCTC 62.607 63.158 13.24 6.34 0.00 4.70
2956 3831 3.607370 GAAACGGCGGGAAGAGGCT 62.607 63.158 13.24 0.00 0.00 4.58
2957 3832 3.125573 GAAACGGCGGGAAGAGGC 61.126 66.667 13.24 0.00 0.00 4.70
2958 3833 1.003718 AAGAAACGGCGGGAAGAGG 60.004 57.895 13.24 0.00 0.00 3.69
2959 3834 1.019805 GGAAGAAACGGCGGGAAGAG 61.020 60.000 13.24 0.00 0.00 2.85
2960 3835 1.004200 GGAAGAAACGGCGGGAAGA 60.004 57.895 13.24 0.00 0.00 2.87
2961 3836 2.038837 GGGAAGAAACGGCGGGAAG 61.039 63.158 13.24 0.00 0.00 3.46
2962 3837 2.032987 GGGAAGAAACGGCGGGAA 59.967 61.111 13.24 0.00 0.00 3.97
2963 3838 4.382320 CGGGAAGAAACGGCGGGA 62.382 66.667 13.24 0.00 0.00 5.14
2966 3841 2.125202 AAAAGCGGGAAGAAACGGCG 62.125 55.000 4.80 4.80 38.93 6.46
2967 3842 0.386858 GAAAAGCGGGAAGAAACGGC 60.387 55.000 0.00 0.00 34.78 5.68
2968 3843 0.240145 GGAAAAGCGGGAAGAAACGG 59.760 55.000 0.00 0.00 0.00 4.44
2969 3844 0.240145 GGGAAAAGCGGGAAGAAACG 59.760 55.000 0.00 0.00 0.00 3.60
2970 3845 0.601558 GGGGAAAAGCGGGAAGAAAC 59.398 55.000 0.00 0.00 0.00 2.78
2971 3846 0.541063 GGGGGAAAAGCGGGAAGAAA 60.541 55.000 0.00 0.00 0.00 2.52
2972 3847 1.076014 GGGGGAAAAGCGGGAAGAA 59.924 57.895 0.00 0.00 0.00 2.52
2973 3848 2.157452 TGGGGGAAAAGCGGGAAGA 61.157 57.895 0.00 0.00 0.00 2.87
2974 3849 1.977009 GTGGGGGAAAAGCGGGAAG 60.977 63.158 0.00 0.00 0.00 3.46
2975 3850 2.014033 AAGTGGGGGAAAAGCGGGAA 62.014 55.000 0.00 0.00 0.00 3.97
2976 3851 2.420466 GAAGTGGGGGAAAAGCGGGA 62.420 60.000 0.00 0.00 0.00 5.14
2977 3852 1.977009 GAAGTGGGGGAAAAGCGGG 60.977 63.158 0.00 0.00 0.00 6.13
2978 3853 1.977009 GGAAGTGGGGGAAAAGCGG 60.977 63.158 0.00 0.00 0.00 5.52
2979 3854 1.977009 GGGAAGTGGGGGAAAAGCG 60.977 63.158 0.00 0.00 0.00 4.68
2980 3855 0.612174 GAGGGAAGTGGGGGAAAAGC 60.612 60.000 0.00 0.00 0.00 3.51
2981 3856 0.039764 GGAGGGAAGTGGGGGAAAAG 59.960 60.000 0.00 0.00 0.00 2.27
2982 3857 1.440362 GGGAGGGAAGTGGGGGAAAA 61.440 60.000 0.00 0.00 0.00 2.29
2983 3858 1.855451 GGGAGGGAAGTGGGGGAAA 60.855 63.158 0.00 0.00 0.00 3.13
2984 3859 2.204244 GGGAGGGAAGTGGGGGAA 60.204 66.667 0.00 0.00 0.00 3.97
2985 3860 2.446337 AATGGGAGGGAAGTGGGGGA 62.446 60.000 0.00 0.00 0.00 4.81
2986 3861 1.935931 AATGGGAGGGAAGTGGGGG 60.936 63.158 0.00 0.00 0.00 5.40
2987 3862 0.921256 AGAATGGGAGGGAAGTGGGG 60.921 60.000 0.00 0.00 0.00 4.96
2988 3863 0.548510 GAGAATGGGAGGGAAGTGGG 59.451 60.000 0.00 0.00 0.00 4.61
2989 3864 1.488393 GAGAGAATGGGAGGGAAGTGG 59.512 57.143 0.00 0.00 0.00 4.00
2990 3865 1.488393 GGAGAGAATGGGAGGGAAGTG 59.512 57.143 0.00 0.00 0.00 3.16
2991 3866 1.626631 GGGAGAGAATGGGAGGGAAGT 60.627 57.143 0.00 0.00 0.00 3.01
2992 3867 1.135960 GGGAGAGAATGGGAGGGAAG 58.864 60.000 0.00 0.00 0.00 3.46
2993 3868 0.725133 AGGGAGAGAATGGGAGGGAA 59.275 55.000 0.00 0.00 0.00 3.97
2994 3869 0.266152 GAGGGAGAGAATGGGAGGGA 59.734 60.000 0.00 0.00 0.00 4.20
2995 3870 0.766288 GGAGGGAGAGAATGGGAGGG 60.766 65.000 0.00 0.00 0.00 4.30
2996 3871 0.766288 GGGAGGGAGAGAATGGGAGG 60.766 65.000 0.00 0.00 0.00 4.30
2997 3872 1.118356 CGGGAGGGAGAGAATGGGAG 61.118 65.000 0.00 0.00 0.00 4.30
2998 3873 1.075226 CGGGAGGGAGAGAATGGGA 60.075 63.158 0.00 0.00 0.00 4.37
2999 3874 2.812619 GCGGGAGGGAGAGAATGGG 61.813 68.421 0.00 0.00 0.00 4.00
3000 3875 1.753368 GAGCGGGAGGGAGAGAATGG 61.753 65.000 0.00 0.00 0.00 3.16
3001 3876 1.745264 GAGCGGGAGGGAGAGAATG 59.255 63.158 0.00 0.00 0.00 2.67
3002 3877 1.830408 CGAGCGGGAGGGAGAGAAT 60.830 63.158 0.00 0.00 0.00 2.40
3003 3878 2.440430 CGAGCGGGAGGGAGAGAA 60.440 66.667 0.00 0.00 0.00 2.87
3035 3910 3.880846 CTTCTTCGGCGGCATGGC 61.881 66.667 9.69 9.69 40.44 4.40
3036 3911 1.153449 TACTTCTTCGGCGGCATGG 60.153 57.895 10.53 0.00 0.00 3.66
3037 3912 1.752501 CGTACTTCTTCGGCGGCATG 61.753 60.000 10.53 0.00 0.00 4.06
3038 3913 1.518572 CGTACTTCTTCGGCGGCAT 60.519 57.895 10.53 0.00 0.00 4.40
3039 3914 2.126228 CGTACTTCTTCGGCGGCA 60.126 61.111 10.53 0.00 0.00 5.69
3040 3915 2.126189 ACGTACTTCTTCGGCGGC 60.126 61.111 7.21 0.00 0.00 6.53
3041 3916 0.179145 ATCACGTACTTCTTCGGCGG 60.179 55.000 7.21 0.00 0.00 6.13
3042 3917 1.189403 GATCACGTACTTCTTCGGCG 58.811 55.000 0.00 0.00 0.00 6.46
3043 3918 1.557651 GGATCACGTACTTCTTCGGC 58.442 55.000 0.00 0.00 0.00 5.54
3044 3919 1.202382 GGGGATCACGTACTTCTTCGG 60.202 57.143 0.00 0.00 0.00 4.30
3045 3920 1.202382 GGGGGATCACGTACTTCTTCG 60.202 57.143 0.00 0.00 0.00 3.79
3046 3921 1.202382 CGGGGGATCACGTACTTCTTC 60.202 57.143 0.00 0.00 0.00 2.87
3047 3922 0.822164 CGGGGGATCACGTACTTCTT 59.178 55.000 0.00 0.00 0.00 2.52
3048 3923 1.673808 GCGGGGGATCACGTACTTCT 61.674 60.000 0.00 0.00 0.00 2.85
3049 3924 1.227176 GCGGGGGATCACGTACTTC 60.227 63.158 0.00 0.00 0.00 3.01
3050 3925 2.897972 GCGGGGGATCACGTACTT 59.102 61.111 0.00 0.00 0.00 2.24
3051 3926 3.524606 CGCGGGGGATCACGTACT 61.525 66.667 0.00 0.00 0.00 2.73
3096 3971 2.866085 CTTCCTCTGCTTCGGCTGGG 62.866 65.000 0.00 0.00 42.37 4.45
3097 3972 1.449246 CTTCCTCTGCTTCGGCTGG 60.449 63.158 0.00 0.00 42.37 4.85
3098 3973 2.105466 GCTTCCTCTGCTTCGGCTG 61.105 63.158 0.00 0.00 42.37 4.85
3099 3974 2.267324 GCTTCCTCTGCTTCGGCT 59.733 61.111 0.00 0.00 42.37 5.52
3100 3975 2.821810 GGCTTCCTCTGCTTCGGC 60.822 66.667 0.00 0.00 42.19 5.54
3101 3976 2.510238 CGGCTTCCTCTGCTTCGG 60.510 66.667 0.00 0.00 0.00 4.30
3102 3977 1.518133 CTCGGCTTCCTCTGCTTCG 60.518 63.158 0.00 0.00 0.00 3.79
3103 3978 1.153469 CCTCGGCTTCCTCTGCTTC 60.153 63.158 0.00 0.00 0.00 3.86
3104 3979 2.664081 CCCTCGGCTTCCTCTGCTT 61.664 63.158 0.00 0.00 0.00 3.91
3105 3980 3.080121 CCCTCGGCTTCCTCTGCT 61.080 66.667 0.00 0.00 0.00 4.24
3106 3981 4.847444 GCCCTCGGCTTCCTCTGC 62.847 72.222 0.00 0.00 46.69 4.26


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

AutoCloner maintained by Alex Coulton.