Multiple sequence alignment - TraesCS3A01G052300

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3A01G052300 chr3A 100.000 3350 0 0 1 3350 28128107 28124758 0.000000e+00 6187.0
1 TraesCS3A01G052300 chr3A 80.690 927 156 18 233 1152 20491933 20492843 0.000000e+00 699.0
2 TraesCS3A01G052300 chr3A 90.769 65 2 2 3158 3222 27909274 27909214 2.140000e-12 84.2
3 TraesCS3A01G052300 chr3D 91.697 1626 87 23 1456 3071 20346745 20345158 0.000000e+00 2211.0
4 TraesCS3A01G052300 chr3D 94.654 1085 50 7 190 1271 20347819 20346740 0.000000e+00 1676.0
5 TraesCS3A01G052300 chr3D 88.824 170 10 2 3142 3303 20342938 20342770 2.040000e-47 200.0
6 TraesCS3A01G052300 chr3D 90.769 65 2 2 3158 3222 20232566 20232506 2.140000e-12 84.2
7 TraesCS3A01G052300 chr3B 92.653 1225 68 12 50 1271 32749578 32748373 0.000000e+00 1744.0
8 TraesCS3A01G052300 chr3B 92.685 1121 62 9 1453 2567 32748381 32747275 0.000000e+00 1598.0
9 TraesCS3A01G052300 chr3B 80.856 888 145 18 272 1152 23032898 23032029 0.000000e+00 675.0
10 TraesCS3A01G052300 chr3B 89.032 465 36 8 2575 3032 32747056 32746600 2.260000e-156 562.0
11 TraesCS3A01G052300 chr3B 88.073 109 7 4 1346 1451 27055056 27054951 1.260000e-24 124.0
12 TraesCS3A01G052300 chr3B 91.026 78 4 2 3148 3222 32801376 32801299 5.910000e-18 102.0
13 TraesCS3A01G052300 chr1D 89.451 929 95 3 226 1152 446647556 446646629 0.000000e+00 1170.0
14 TraesCS3A01G052300 chr1D 84.554 628 95 1 1716 2341 446644341 446643714 3.670000e-174 621.0
15 TraesCS3A01G052300 chr1D 87.850 107 11 1 1335 1439 247242552 247242658 1.260000e-24 124.0
16 TraesCS3A01G052300 chr1A 88.474 937 103 5 219 1152 542371365 542370431 0.000000e+00 1127.0
17 TraesCS3A01G052300 chr1A 89.744 117 11 1 1335 1451 492020138 492020023 7.490000e-32 148.0
18 TraesCS3A01G052300 chr1B 88.260 937 105 5 219 1152 611675883 611676817 0.000000e+00 1116.0
19 TraesCS3A01G052300 chr1B 84.665 626 96 0 1716 2341 611680706 611681331 2.840000e-175 625.0
20 TraesCS3A01G052300 chr1B 87.736 106 12 1 1346 1451 304186505 304186401 4.540000e-24 122.0
21 TraesCS3A01G052300 chr7A 81.405 925 157 10 228 1150 546060947 546060036 0.000000e+00 741.0
22 TraesCS3A01G052300 chr2D 77.467 750 152 12 343 1080 589318426 589317682 1.850000e-117 433.0
23 TraesCS3A01G052300 chr2D 89.381 113 11 1 1340 1451 435339109 435338997 1.250000e-29 141.0
24 TraesCS3A01G052300 chr5B 93.333 105 7 0 1346 1450 213632249 213632145 4.480000e-34 156.0
25 TraesCS3A01G052300 chr2A 91.509 106 9 0 1346 1451 751097544 751097439 2.690000e-31 147.0
26 TraesCS3A01G052300 chr2B 87.903 124 11 4 1340 1461 37108490 37108369 3.480000e-30 143.0
27 TraesCS3A01G052300 chr5A 88.889 108 11 1 1346 1453 564391650 564391756 7.540000e-27 132.0
28 TraesCS3A01G052300 chr7D 80.000 105 11 7 2407 2504 595937856 595937957 6.000000e-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 TraesCS3A01G052300 chr3A 28124758 28128107 3349 True 6187.000000 6187 100.000000 1 3350 1 chr3A.!!$R2 3349
1 TraesCS3A01G052300 chr3A 20491933 20492843 910 False 699.000000 699 80.690000 233 1152 1 chr3A.!!$F1 919
2 TraesCS3A01G052300 chr3D 20342770 20347819 5049 True 1362.333333 2211 91.725000 190 3303 3 chr3D.!!$R2 3113
3 TraesCS3A01G052300 chr3B 32746600 32749578 2978 True 1301.333333 1744 91.456667 50 3032 3 chr3B.!!$R4 2982
4 TraesCS3A01G052300 chr3B 23032029 23032898 869 True 675.000000 675 80.856000 272 1152 1 chr3B.!!$R1 880
5 TraesCS3A01G052300 chr1D 446643714 446647556 3842 True 895.500000 1170 87.002500 226 2341 2 chr1D.!!$R1 2115
6 TraesCS3A01G052300 chr1A 542370431 542371365 934 True 1127.000000 1127 88.474000 219 1152 1 chr1A.!!$R2 933
7 TraesCS3A01G052300 chr1B 611675883 611681331 5448 False 870.500000 1116 86.462500 219 2341 2 chr1B.!!$F1 2122
8 TraesCS3A01G052300 chr7A 546060036 546060947 911 True 741.000000 741 81.405000 228 1150 1 chr7A.!!$R1 922
9 TraesCS3A01G052300 chr2D 589317682 589318426 744 True 433.000000 433 77.467000 343 1080 1 chr2D.!!$R2 737

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
40 41 0.106918 AAAGGAACACTTCACCCGCA 60.107 50.0 0.0 0.0 38.85 5.69 F
41 42 0.106918 AAGGAACACTTCACCCGCAA 60.107 50.0 0.0 0.0 32.85 4.85 F
1385 4998 0.104356 TGTCCTCCCCTTACACCCAA 60.104 55.0 0.0 0.0 0.00 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1366 4979 0.104356 TTGGGTGTAAGGGGAGGACA 60.104 55.0 0.00 0.0 0.00 4.02 R
1960 6144 0.321298 ACGAAGTAGCCGCCAACAAT 60.321 50.0 0.00 0.0 41.94 2.71 R
3048 7459 0.247894 TTCACACTTGACGCGCAAAC 60.248 50.0 5.73 0.0 35.74 2.93 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
19 20 2.715737 GGCGTGCAAGTGGAATAAAA 57.284 45.000 0.59 0.00 0.00 1.52
20 21 2.324860 GGCGTGCAAGTGGAATAAAAC 58.675 47.619 0.59 0.00 0.00 2.43
21 22 2.287909 GGCGTGCAAGTGGAATAAAACA 60.288 45.455 0.59 0.00 0.00 2.83
22 23 3.376540 GCGTGCAAGTGGAATAAAACAA 58.623 40.909 0.59 0.00 0.00 2.83
23 24 3.799420 GCGTGCAAGTGGAATAAAACAAA 59.201 39.130 0.59 0.00 0.00 2.83
24 25 4.085107 GCGTGCAAGTGGAATAAAACAAAG 60.085 41.667 0.59 0.00 0.00 2.77
25 26 4.444056 CGTGCAAGTGGAATAAAACAAAGG 59.556 41.667 0.00 0.00 0.00 3.11
26 27 5.596845 GTGCAAGTGGAATAAAACAAAGGA 58.403 37.500 0.00 0.00 0.00 3.36
27 28 6.045955 GTGCAAGTGGAATAAAACAAAGGAA 58.954 36.000 0.00 0.00 0.00 3.36
28 29 6.019075 GTGCAAGTGGAATAAAACAAAGGAAC 60.019 38.462 0.00 0.00 0.00 3.62
29 30 6.045955 GCAAGTGGAATAAAACAAAGGAACA 58.954 36.000 0.00 0.00 0.00 3.18
30 31 6.019075 GCAAGTGGAATAAAACAAAGGAACAC 60.019 38.462 0.00 0.00 0.00 3.32
31 32 7.264947 CAAGTGGAATAAAACAAAGGAACACT 58.735 34.615 0.00 0.00 37.07 3.55
32 33 7.418337 AGTGGAATAAAACAAAGGAACACTT 57.582 32.000 0.00 0.00 42.52 3.16
33 34 7.489160 AGTGGAATAAAACAAAGGAACACTTC 58.511 34.615 0.00 0.00 38.85 3.01
34 35 7.123547 AGTGGAATAAAACAAAGGAACACTTCA 59.876 33.333 0.00 0.00 38.85 3.02
35 36 7.222031 GTGGAATAAAACAAAGGAACACTTCAC 59.778 37.037 0.00 0.00 38.85 3.18
36 37 6.700081 GGAATAAAACAAAGGAACACTTCACC 59.300 38.462 0.00 0.00 38.85 4.02
37 38 4.465632 AAAACAAAGGAACACTTCACCC 57.534 40.909 0.00 0.00 38.85 4.61
38 39 1.675552 ACAAAGGAACACTTCACCCG 58.324 50.000 0.00 0.00 38.85 5.28
39 40 0.310854 CAAAGGAACACTTCACCCGC 59.689 55.000 0.00 0.00 38.85 6.13
40 41 0.106918 AAAGGAACACTTCACCCGCA 60.107 50.000 0.00 0.00 38.85 5.69
41 42 0.106918 AAGGAACACTTCACCCGCAA 60.107 50.000 0.00 0.00 32.85 4.85
42 43 0.535102 AGGAACACTTCACCCGCAAG 60.535 55.000 0.00 0.00 0.00 4.01
43 44 0.534203 GGAACACTTCACCCGCAAGA 60.534 55.000 0.00 0.00 43.02 3.02
44 45 1.305201 GAACACTTCACCCGCAAGAA 58.695 50.000 0.00 0.00 43.02 2.52
45 46 1.264288 GAACACTTCACCCGCAAGAAG 59.736 52.381 0.00 0.00 45.14 2.85
46 47 0.468226 ACACTTCACCCGCAAGAAGA 59.532 50.000 13.54 0.00 42.95 2.87
47 48 1.134220 ACACTTCACCCGCAAGAAGAA 60.134 47.619 13.54 0.00 42.95 2.52
48 49 1.532868 CACTTCACCCGCAAGAAGAAG 59.467 52.381 13.54 0.00 42.95 2.85
104 105 1.368641 TTGCTATCATGCGGTGTGAC 58.631 50.000 0.00 0.00 35.36 3.67
105 106 0.805711 TGCTATCATGCGGTGTGACG 60.806 55.000 0.00 0.00 35.36 4.35
126 127 3.466836 GCGCTACTGTTTTTCAACTACG 58.533 45.455 0.00 0.00 33.58 3.51
131 132 5.693555 GCTACTGTTTTTCAACTACGGTAGT 59.306 40.000 14.89 14.89 46.31 2.73
134 135 6.809869 ACTGTTTTTCAACTACGGTAGTACT 58.190 36.000 20.34 0.00 38.26 2.73
135 136 6.920210 ACTGTTTTTCAACTACGGTAGTACTC 59.080 38.462 20.34 8.35 38.26 2.59
136 137 6.215845 TGTTTTTCAACTACGGTAGTACTCC 58.784 40.000 20.34 0.00 38.26 3.85
151 152 7.776969 CGGTAGTACTCCTATATATAAAGGCCA 59.223 40.741 5.01 0.00 32.55 5.36
163 164 1.597797 AAAGGCCACATGCATCCACG 61.598 55.000 5.01 0.00 43.89 4.94
164 165 4.197498 GGCCACATGCATCCACGC 62.197 66.667 0.00 0.00 43.89 5.34
205 206 4.551702 TGTTTGAAGCTAGGCAGTGATA 57.448 40.909 0.00 0.00 0.00 2.15
206 207 4.507710 TGTTTGAAGCTAGGCAGTGATAG 58.492 43.478 0.00 0.00 0.00 2.08
207 208 4.222810 TGTTTGAAGCTAGGCAGTGATAGA 59.777 41.667 0.00 0.00 0.00 1.98
208 209 5.104776 TGTTTGAAGCTAGGCAGTGATAGAT 60.105 40.000 0.00 0.00 0.00 1.98
364 373 3.186680 TTTCCTCCGGGCCCCAAA 61.187 61.111 18.66 4.78 0.00 3.28
873 898 1.813192 GGAGTTCTCGAGGCTCCTG 59.187 63.158 31.62 1.83 43.93 3.86
1065 1096 4.416738 GGCCTGCTCGCCTTCCTT 62.417 66.667 7.31 0.00 46.10 3.36
1193 3345 7.396339 ACTGGTATACTATCTCTGTTCACACAA 59.604 37.037 2.25 0.00 30.36 3.33
1208 3360 4.051237 TCACACAATCTCACGAACTTCAG 58.949 43.478 0.00 0.00 0.00 3.02
1282 4895 8.416485 ACGGAGTACTAATACAAAAATGCTAC 57.584 34.615 0.00 0.00 41.94 3.58
1284 4897 8.325997 CGGAGTACTAATACAAAAATGCTACAC 58.674 37.037 0.00 0.00 33.30 2.90
1287 4900 6.431198 ACTAATACAAAAATGCTACACGGG 57.569 37.500 0.00 0.00 0.00 5.28
1289 4902 4.957759 ATACAAAAATGCTACACGGGAC 57.042 40.909 0.00 0.00 0.00 4.46
1291 4904 3.219281 ACAAAAATGCTACACGGGACTT 58.781 40.909 0.00 0.00 0.00 3.01
1292 4905 3.634910 ACAAAAATGCTACACGGGACTTT 59.365 39.130 0.00 0.00 0.00 2.66
1293 4906 4.822896 ACAAAAATGCTACACGGGACTTTA 59.177 37.500 0.00 0.00 0.00 1.85
1294 4907 5.299782 ACAAAAATGCTACACGGGACTTTAA 59.700 36.000 0.00 0.00 0.00 1.52
1296 4909 5.622770 AAATGCTACACGGGACTTTAAAG 57.377 39.130 13.76 13.76 0.00 1.85
1298 4911 1.736126 GCTACACGGGACTTTAAAGGC 59.264 52.381 19.14 16.33 0.00 4.35
1299 4912 2.614734 GCTACACGGGACTTTAAAGGCT 60.615 50.000 20.36 3.05 33.40 4.58
1300 4913 1.892209 ACACGGGACTTTAAAGGCTG 58.108 50.000 20.36 15.14 33.40 4.85
1302 4915 2.227194 CACGGGACTTTAAAGGCTGTT 58.773 47.619 20.36 2.27 33.40 3.16
1303 4916 3.181452 ACACGGGACTTTAAAGGCTGTTA 60.181 43.478 20.36 0.00 33.40 2.41
1304 4917 3.187842 CACGGGACTTTAAAGGCTGTTAC 59.812 47.826 20.36 3.47 33.40 2.50
1305 4918 3.181452 ACGGGACTTTAAAGGCTGTTACA 60.181 43.478 20.36 0.00 33.40 2.41
1306 4919 3.435671 CGGGACTTTAAAGGCTGTTACAG 59.564 47.826 20.36 8.18 33.40 2.74
1307 4920 4.648651 GGGACTTTAAAGGCTGTTACAGA 58.351 43.478 20.36 0.00 33.40 3.41
1308 4921 4.454847 GGGACTTTAAAGGCTGTTACAGAC 59.545 45.833 20.36 14.23 40.37 3.51
1318 4931 3.933332 GGCTGTTACAGACTCATAACACC 59.067 47.826 17.40 0.00 36.41 4.16
1319 4932 3.933332 GCTGTTACAGACTCATAACACCC 59.067 47.826 17.40 0.00 36.59 4.61
1320 4933 4.504858 CTGTTACAGACTCATAACACCCC 58.495 47.826 6.50 0.00 36.59 4.95
1321 4934 3.262405 TGTTACAGACTCATAACACCCCC 59.738 47.826 5.18 0.00 36.59 5.40
1340 4953 2.518349 CCCCCACACACACACACC 60.518 66.667 0.00 0.00 0.00 4.16
1341 4954 2.518349 CCCCACACACACACACCC 60.518 66.667 0.00 0.00 0.00 4.61
1342 4955 2.595095 CCCACACACACACACCCT 59.405 61.111 0.00 0.00 0.00 4.34
1343 4956 1.525995 CCCACACACACACACCCTC 60.526 63.158 0.00 0.00 0.00 4.30
1344 4957 1.525995 CCACACACACACACCCTCC 60.526 63.158 0.00 0.00 0.00 4.30
1345 4958 1.223211 CACACACACACACCCTCCA 59.777 57.895 0.00 0.00 0.00 3.86
1346 4959 0.179020 CACACACACACACCCTCCAT 60.179 55.000 0.00 0.00 0.00 3.41
1347 4960 0.550914 ACACACACACACCCTCCATT 59.449 50.000 0.00 0.00 0.00 3.16
1348 4961 1.064017 ACACACACACACCCTCCATTT 60.064 47.619 0.00 0.00 0.00 2.32
1349 4962 2.031120 CACACACACACCCTCCATTTT 58.969 47.619 0.00 0.00 0.00 1.82
1350 4963 2.430332 CACACACACACCCTCCATTTTT 59.570 45.455 0.00 0.00 0.00 1.94
1351 4964 3.634448 CACACACACACCCTCCATTTTTA 59.366 43.478 0.00 0.00 0.00 1.52
1352 4965 4.280677 CACACACACACCCTCCATTTTTAT 59.719 41.667 0.00 0.00 0.00 1.40
1353 4966 4.280677 ACACACACACCCTCCATTTTTATG 59.719 41.667 0.00 0.00 0.00 1.90
1354 4967 3.831911 ACACACACCCTCCATTTTTATGG 59.168 43.478 0.00 0.00 43.01 2.74
1355 4968 3.195396 CACACACCCTCCATTTTTATGGG 59.805 47.826 4.46 0.00 41.95 4.00
1356 4969 2.765699 CACACCCTCCATTTTTATGGGG 59.234 50.000 4.46 0.77 41.90 4.96
1357 4970 2.657459 ACACCCTCCATTTTTATGGGGA 59.343 45.455 5.62 0.00 45.09 4.81
1358 4971 3.274690 ACACCCTCCATTTTTATGGGGAT 59.725 43.478 5.62 0.00 45.09 3.85
1359 4972 3.642848 CACCCTCCATTTTTATGGGGATG 59.357 47.826 5.62 0.00 45.09 3.51
1360 4973 3.242011 CCCTCCATTTTTATGGGGATGG 58.758 50.000 5.62 0.00 45.09 3.51
1361 4974 3.242011 CCTCCATTTTTATGGGGATGGG 58.758 50.000 5.62 0.00 45.09 4.00
1362 4975 2.634453 CTCCATTTTTATGGGGATGGGC 59.366 50.000 0.00 0.00 45.09 5.36
1363 4976 1.699083 CCATTTTTATGGGGATGGGCC 59.301 52.381 0.00 0.00 38.04 5.80
1372 4985 2.517919 GGATGGGCCCATGTCCTC 59.482 66.667 42.21 26.98 37.08 3.71
1373 4986 2.517919 GATGGGCCCATGTCCTCC 59.482 66.667 42.21 22.21 37.08 4.30
1374 4987 3.105928 ATGGGCCCATGTCCTCCC 61.106 66.667 37.06 0.00 37.08 4.30
1377 4990 3.023735 GGCCCATGTCCTCCCCTT 61.024 66.667 0.00 0.00 0.00 3.95
1378 4991 1.696314 GGCCCATGTCCTCCCCTTA 60.696 63.158 0.00 0.00 0.00 2.69
1379 4992 1.532238 GCCCATGTCCTCCCCTTAC 59.468 63.158 0.00 0.00 0.00 2.34
1380 4993 1.279025 GCCCATGTCCTCCCCTTACA 61.279 60.000 0.00 0.00 0.00 2.41
1381 4994 0.546598 CCCATGTCCTCCCCTTACAC 59.453 60.000 0.00 0.00 0.00 2.90
1382 4995 0.546598 CCATGTCCTCCCCTTACACC 59.453 60.000 0.00 0.00 0.00 4.16
1383 4996 0.546598 CATGTCCTCCCCTTACACCC 59.453 60.000 0.00 0.00 0.00 4.61
1384 4997 0.120377 ATGTCCTCCCCTTACACCCA 59.880 55.000 0.00 0.00 0.00 4.51
1385 4998 0.104356 TGTCCTCCCCTTACACCCAA 60.104 55.000 0.00 0.00 0.00 4.12
1386 4999 1.296002 GTCCTCCCCTTACACCCAAT 58.704 55.000 0.00 0.00 0.00 3.16
1387 5000 1.212195 GTCCTCCCCTTACACCCAATC 59.788 57.143 0.00 0.00 0.00 2.67
1388 5001 1.203505 TCCTCCCCTTACACCCAATCA 60.204 52.381 0.00 0.00 0.00 2.57
1389 5002 1.638589 CCTCCCCTTACACCCAATCAA 59.361 52.381 0.00 0.00 0.00 2.57
1390 5003 2.042433 CCTCCCCTTACACCCAATCAAA 59.958 50.000 0.00 0.00 0.00 2.69
1391 5004 3.501385 CCTCCCCTTACACCCAATCAAAA 60.501 47.826 0.00 0.00 0.00 2.44
1392 5005 4.156477 CTCCCCTTACACCCAATCAAAAA 58.844 43.478 0.00 0.00 0.00 1.94
1393 5006 3.898741 TCCCCTTACACCCAATCAAAAAC 59.101 43.478 0.00 0.00 0.00 2.43
1394 5007 3.901222 CCCCTTACACCCAATCAAAAACT 59.099 43.478 0.00 0.00 0.00 2.66
1395 5008 4.262420 CCCCTTACACCCAATCAAAAACTG 60.262 45.833 0.00 0.00 0.00 3.16
1396 5009 4.306600 CCTTACACCCAATCAAAAACTGC 58.693 43.478 0.00 0.00 0.00 4.40
1397 5010 2.908688 ACACCCAATCAAAAACTGCC 57.091 45.000 0.00 0.00 0.00 4.85
1398 5011 2.114616 ACACCCAATCAAAAACTGCCA 58.885 42.857 0.00 0.00 0.00 4.92
1399 5012 2.158971 ACACCCAATCAAAAACTGCCAC 60.159 45.455 0.00 0.00 0.00 5.01
1400 5013 2.114616 ACCCAATCAAAAACTGCCACA 58.885 42.857 0.00 0.00 0.00 4.17
1401 5014 2.705127 ACCCAATCAAAAACTGCCACAT 59.295 40.909 0.00 0.00 0.00 3.21
1402 5015 3.244181 ACCCAATCAAAAACTGCCACATC 60.244 43.478 0.00 0.00 0.00 3.06
1403 5016 3.244146 CCCAATCAAAAACTGCCACATCA 60.244 43.478 0.00 0.00 0.00 3.07
1404 5017 4.378774 CCAATCAAAAACTGCCACATCAA 58.621 39.130 0.00 0.00 0.00 2.57
1405 5018 4.815308 CCAATCAAAAACTGCCACATCAAA 59.185 37.500 0.00 0.00 0.00 2.69
1406 5019 5.470777 CCAATCAAAAACTGCCACATCAAAT 59.529 36.000 0.00 0.00 0.00 2.32
1407 5020 6.347888 CCAATCAAAAACTGCCACATCAAATC 60.348 38.462 0.00 0.00 0.00 2.17
1408 5021 5.273674 TCAAAAACTGCCACATCAAATCA 57.726 34.783 0.00 0.00 0.00 2.57
1409 5022 5.668471 TCAAAAACTGCCACATCAAATCAA 58.332 33.333 0.00 0.00 0.00 2.57
1410 5023 6.289834 TCAAAAACTGCCACATCAAATCAAT 58.710 32.000 0.00 0.00 0.00 2.57
1411 5024 6.424509 TCAAAAACTGCCACATCAAATCAATC 59.575 34.615 0.00 0.00 0.00 2.67
1412 5025 5.471556 AAACTGCCACATCAAATCAATCA 57.528 34.783 0.00 0.00 0.00 2.57
1413 5026 5.670792 AACTGCCACATCAAATCAATCAT 57.329 34.783 0.00 0.00 0.00 2.45
1414 5027 5.006153 ACTGCCACATCAAATCAATCATG 57.994 39.130 0.00 0.00 0.00 3.07
1415 5028 4.464951 ACTGCCACATCAAATCAATCATGT 59.535 37.500 0.00 0.00 0.00 3.21
1421 5034 7.221452 GCCACATCAAATCAATCATGTAAACTC 59.779 37.037 0.00 0.00 0.00 3.01
1424 5037 8.464404 ACATCAAATCAATCATGTAAACTCCTG 58.536 33.333 0.00 0.00 0.00 3.86
1431 5044 9.911788 ATCAATCATGTAAACTCCTGTAGAAAT 57.088 29.630 0.00 0.00 0.00 2.17
1444 5057 8.361139 ACTCCTGTAGAAATATGTATGTGTAGC 58.639 37.037 0.00 0.00 0.00 3.58
1445 5058 8.245195 TCCTGTAGAAATATGTATGTGTAGCA 57.755 34.615 0.00 0.00 0.00 3.49
1446 5059 8.870116 TCCTGTAGAAATATGTATGTGTAGCAT 58.130 33.333 0.00 0.00 41.42 3.79
1449 5062 8.773645 TGTAGAAATATGTATGTGTAGCATTGC 58.226 33.333 0.00 0.00 38.94 3.56
1450 5063 8.993121 GTAGAAATATGTATGTGTAGCATTGCT 58.007 33.333 16.63 16.63 43.41 3.91
1451 5064 8.092521 AGAAATATGTATGTGTAGCATTGCTC 57.907 34.615 15.81 7.72 40.44 4.26
1553 5667 7.545362 AGCGTCTATCCATAATATGAAATGC 57.455 36.000 1.10 0.36 0.00 3.56
1581 5695 5.022282 AGAATTTCCACACCCACAAAAAG 57.978 39.130 0.00 0.00 0.00 2.27
1584 5698 4.464069 TTTCCACACCCACAAAAAGAAG 57.536 40.909 0.00 0.00 0.00 2.85
1585 5699 3.374042 TCCACACCCACAAAAAGAAGA 57.626 42.857 0.00 0.00 0.00 2.87
1586 5700 3.702792 TCCACACCCACAAAAAGAAGAA 58.297 40.909 0.00 0.00 0.00 2.52
1599 5713 9.480053 CACAAAAAGAAGAAATTCCACACATAT 57.520 29.630 0.00 0.00 0.00 1.78
1624 5741 9.679661 ATTTAAAAAGAGTTCCATTTGTTTGGT 57.320 25.926 0.00 0.00 38.01 3.67
1634 5751 9.054922 AGTTCCATTTGTTTGGTTTTATCATTG 57.945 29.630 0.00 0.00 38.01 2.82
1654 5771 9.601810 ATCATTGTACTGGTATATGACTTCCTA 57.398 33.333 0.00 0.00 0.00 2.94
1723 5907 3.313012 TGTACGGCATATAGGACATGC 57.687 47.619 0.00 0.00 46.50 4.06
1821 6005 2.670934 CGGCTGCAGCAGGAACTT 60.671 61.111 37.63 0.00 44.36 2.66
1842 6026 2.911143 GATGTGGTGGGGCTCGAT 59.089 61.111 0.00 0.00 0.00 3.59
1886 6070 1.065854 CGACAAGCTCCCTTTCCTCAT 60.066 52.381 0.00 0.00 0.00 2.90
2010 6194 2.499520 CGCGTGTTGGTCAATGCG 60.500 61.111 0.00 11.29 43.08 4.73
2238 6422 0.040067 GTTTCAACTGGAAGCTGCCG 60.040 55.000 6.16 3.45 37.60 5.69
2239 6423 0.179032 TTTCAACTGGAAGCTGCCGA 60.179 50.000 6.16 0.00 37.60 5.54
2508 6700 0.167251 GTTTGGCCCGTTATCACGTG 59.833 55.000 9.94 9.94 45.62 4.49
2509 6701 0.250381 TTTGGCCCGTTATCACGTGT 60.250 50.000 16.51 5.66 45.62 4.49
2510 6702 0.250381 TTGGCCCGTTATCACGTGTT 60.250 50.000 16.51 10.15 45.62 3.32
2511 6703 0.250381 TGGCCCGTTATCACGTGTTT 60.250 50.000 16.51 7.21 45.62 2.83
2569 6761 3.270027 GTCATTGTGAACCATCATCGGA 58.730 45.455 0.00 0.00 38.01 4.55
2661 7067 7.334421 GGTCTTACAAATGCTGATCTTCTTGTA 59.666 37.037 0.00 0.00 0.00 2.41
2692 7099 9.804758 ATTTTGTAATGTTTGACTTCGGTAAAA 57.195 25.926 0.00 0.00 0.00 1.52
2782 7193 0.179189 GTAAGTGGCATCGCACAAGC 60.179 55.000 0.00 0.00 37.42 4.01
2800 7211 0.583917 GCATACGAGCTGGCTAAAGC 59.416 55.000 0.00 0.00 43.88 3.51
2816 7227 4.991687 GCTAAAGCTAGATGGGTATGTGAC 59.008 45.833 0.00 0.00 38.21 3.67
2817 7228 6.027098 GCTAAAGCTAGATGGGTATGTGACC 61.027 48.000 0.00 0.00 42.18 4.02
2858 7269 5.428184 ACCAGAACCTAAAATCTCCTCAG 57.572 43.478 0.00 0.00 0.00 3.35
2896 7307 7.269477 AGAAAAATCTTCTCCACAGACAAAG 57.731 36.000 0.00 0.00 0.00 2.77
2947 7358 5.367945 TGTTGTATTTACTCTGATCCCCC 57.632 43.478 0.00 0.00 0.00 5.40
2970 7381 3.316573 GACTTGGACTGGGGGAGCG 62.317 68.421 0.00 0.00 0.00 5.03
2990 7401 0.316772 CGACCGCGACTACCATACAG 60.317 60.000 8.23 0.00 40.82 2.74
3046 7457 1.617755 GCGTCGGAGATGTGTGTGTG 61.618 60.000 0.00 0.00 46.97 3.82
3047 7458 1.008875 CGTCGGAGATGTGTGTGTGG 61.009 60.000 0.00 0.00 40.67 4.17
3048 7459 0.670546 GTCGGAGATGTGTGTGTGGG 60.671 60.000 0.00 0.00 40.67 4.61
3049 7460 1.118965 TCGGAGATGTGTGTGTGGGT 61.119 55.000 0.00 0.00 0.00 4.51
3062 7473 2.515057 TGGGTTTGCGCGTCAAGT 60.515 55.556 8.43 0.00 35.84 3.16
3063 7474 2.051345 GGGTTTGCGCGTCAAGTG 60.051 61.111 8.43 0.00 35.84 3.16
3064 7475 2.713154 GGTTTGCGCGTCAAGTGT 59.287 55.556 8.43 0.00 35.84 3.55
3065 7476 1.654137 GGTTTGCGCGTCAAGTGTG 60.654 57.895 8.43 0.00 35.84 3.82
3067 7478 0.247894 GTTTGCGCGTCAAGTGTGAA 60.248 50.000 8.43 0.00 34.87 3.18
3076 9392 2.481276 CGTCAAGTGTGAACAGGAGTCA 60.481 50.000 0.00 0.00 34.87 3.41
3090 9406 0.031449 GAGTCACATCTCCTAGGCGC 59.969 60.000 2.96 0.00 0.00 6.53
3110 9426 2.259818 CACAGGAGCGAGCTCGTT 59.740 61.111 34.46 30.61 43.59 3.85
3111 9427 1.373497 CACAGGAGCGAGCTCGTTT 60.373 57.895 34.46 23.97 43.59 3.60
3112 9428 0.109272 CACAGGAGCGAGCTCGTTTA 60.109 55.000 34.46 0.00 43.59 2.01
3114 9430 0.526524 CAGGAGCGAGCTCGTTTAGG 60.527 60.000 34.46 18.64 43.59 2.69
3115 9431 0.966370 AGGAGCGAGCTCGTTTAGGT 60.966 55.000 34.46 13.77 43.59 3.08
3116 9432 0.737219 GGAGCGAGCTCGTTTAGGTA 59.263 55.000 34.46 0.00 43.59 3.08
3239 9800 4.216472 CAGGTAGTCAGATTAGCTATGCGA 59.784 45.833 4.47 0.00 0.00 5.10
3241 9802 4.216687 GGTAGTCAGATTAGCTATGCGACT 59.783 45.833 15.62 15.62 36.33 4.18
3244 9805 5.948588 AGTCAGATTAGCTATGCGACTATG 58.051 41.667 11.70 0.00 30.79 2.23
3287 9856 3.749954 GCTAGCATGGTTCATCAATCCCT 60.750 47.826 10.63 0.00 0.00 4.20
3296 9865 1.063183 CATCAATCCCTCCCTCTCCC 58.937 60.000 0.00 0.00 0.00 4.30
3303 9872 3.632420 TCCCTCCCTCTCCCTAAATAC 57.368 52.381 0.00 0.00 0.00 1.89
3304 9873 3.148331 TCCCTCCCTCTCCCTAAATACT 58.852 50.000 0.00 0.00 0.00 2.12
3305 9874 3.116707 TCCCTCCCTCTCCCTAAATACTG 60.117 52.174 0.00 0.00 0.00 2.74
3306 9875 2.635427 CCTCCCTCTCCCTAAATACTGC 59.365 54.545 0.00 0.00 0.00 4.40
3307 9876 3.309296 CTCCCTCTCCCTAAATACTGCA 58.691 50.000 0.00 0.00 0.00 4.41
3308 9877 3.906846 CTCCCTCTCCCTAAATACTGCAT 59.093 47.826 0.00 0.00 0.00 3.96
3309 9878 3.904339 TCCCTCTCCCTAAATACTGCATC 59.096 47.826 0.00 0.00 0.00 3.91
3310 9879 3.906846 CCCTCTCCCTAAATACTGCATCT 59.093 47.826 0.00 0.00 0.00 2.90
3311 9880 4.262808 CCCTCTCCCTAAATACTGCATCTG 60.263 50.000 0.00 0.00 0.00 2.90
3312 9881 4.314121 CTCTCCCTAAATACTGCATCTGC 58.686 47.826 0.00 0.00 42.50 4.26
3313 9882 3.969976 TCTCCCTAAATACTGCATCTGCT 59.030 43.478 3.53 0.00 42.66 4.24
3314 9883 4.410228 TCTCCCTAAATACTGCATCTGCTT 59.590 41.667 3.53 0.00 42.66 3.91
3315 9884 4.708177 TCCCTAAATACTGCATCTGCTTC 58.292 43.478 3.53 0.00 42.66 3.86
3316 9885 4.410228 TCCCTAAATACTGCATCTGCTTCT 59.590 41.667 3.53 0.00 42.66 2.85
3317 9886 4.514441 CCCTAAATACTGCATCTGCTTCTG 59.486 45.833 3.53 0.00 42.66 3.02
3318 9887 5.121811 CCTAAATACTGCATCTGCTTCTGT 58.878 41.667 3.53 0.87 42.66 3.41
3319 9888 5.587844 CCTAAATACTGCATCTGCTTCTGTT 59.412 40.000 3.53 0.00 42.66 3.16
3320 9889 5.557891 AAATACTGCATCTGCTTCTGTTC 57.442 39.130 3.53 0.00 42.66 3.18
3321 9890 2.855209 ACTGCATCTGCTTCTGTTCT 57.145 45.000 3.53 0.00 42.66 3.01
3322 9891 3.969287 ACTGCATCTGCTTCTGTTCTA 57.031 42.857 3.53 0.00 42.66 2.10
3323 9892 3.594134 ACTGCATCTGCTTCTGTTCTAC 58.406 45.455 3.53 0.00 42.66 2.59
3324 9893 2.935201 CTGCATCTGCTTCTGTTCTACC 59.065 50.000 3.53 0.00 42.66 3.18
3325 9894 2.284190 GCATCTGCTTCTGTTCTACCC 58.716 52.381 0.00 0.00 38.21 3.69
3326 9895 2.355108 GCATCTGCTTCTGTTCTACCCA 60.355 50.000 0.00 0.00 38.21 4.51
3327 9896 3.683847 GCATCTGCTTCTGTTCTACCCAT 60.684 47.826 0.00 0.00 38.21 4.00
3328 9897 4.443457 GCATCTGCTTCTGTTCTACCCATA 60.443 45.833 0.00 0.00 38.21 2.74
3329 9898 5.295950 CATCTGCTTCTGTTCTACCCATAG 58.704 45.833 0.00 0.00 0.00 2.23
3330 9899 3.133003 TCTGCTTCTGTTCTACCCATAGC 59.867 47.826 0.00 0.00 0.00 2.97
3331 9900 3.107601 TGCTTCTGTTCTACCCATAGCT 58.892 45.455 0.00 0.00 0.00 3.32
3332 9901 3.133003 TGCTTCTGTTCTACCCATAGCTC 59.867 47.826 0.00 0.00 0.00 4.09
3333 9902 3.386402 GCTTCTGTTCTACCCATAGCTCT 59.614 47.826 0.00 0.00 0.00 4.09
3334 9903 4.739137 GCTTCTGTTCTACCCATAGCTCTG 60.739 50.000 0.00 0.00 0.00 3.35
3335 9904 3.982516 TCTGTTCTACCCATAGCTCTGT 58.017 45.455 0.00 0.00 0.00 3.41
3336 9905 4.353777 TCTGTTCTACCCATAGCTCTGTT 58.646 43.478 0.00 0.00 0.00 3.16
3337 9906 4.777896 TCTGTTCTACCCATAGCTCTGTTT 59.222 41.667 0.00 0.00 0.00 2.83
3338 9907 5.248477 TCTGTTCTACCCATAGCTCTGTTTT 59.752 40.000 0.00 0.00 0.00 2.43
3339 9908 5.876357 TGTTCTACCCATAGCTCTGTTTTT 58.124 37.500 0.00 0.00 0.00 1.94
3340 9909 5.938125 TGTTCTACCCATAGCTCTGTTTTTC 59.062 40.000 0.00 0.00 0.00 2.29
3341 9910 6.174049 GTTCTACCCATAGCTCTGTTTTTCT 58.826 40.000 0.00 0.00 0.00 2.52
3342 9911 5.978814 TCTACCCATAGCTCTGTTTTTCTC 58.021 41.667 0.00 0.00 0.00 2.87
3343 9912 4.917906 ACCCATAGCTCTGTTTTTCTCT 57.082 40.909 0.00 0.00 0.00 3.10
3344 9913 4.837972 ACCCATAGCTCTGTTTTTCTCTC 58.162 43.478 0.00 0.00 0.00 3.20
3345 9914 4.195416 CCCATAGCTCTGTTTTTCTCTCC 58.805 47.826 0.00 0.00 0.00 3.71
3346 9915 4.080638 CCCATAGCTCTGTTTTTCTCTCCT 60.081 45.833 0.00 0.00 0.00 3.69
3347 9916 4.874966 CCATAGCTCTGTTTTTCTCTCCTG 59.125 45.833 0.00 0.00 0.00 3.86
3348 9917 5.486526 CATAGCTCTGTTTTTCTCTCCTGT 58.513 41.667 0.00 0.00 0.00 4.00
3349 9918 4.429854 AGCTCTGTTTTTCTCTCCTGTT 57.570 40.909 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.287909 TGTTTTATTCCACTTGCACGCC 60.288 45.455 0.00 0.00 0.00 5.68
1 2 3.006659 TGTTTTATTCCACTTGCACGC 57.993 42.857 0.00 0.00 0.00 5.34
2 3 4.444056 CCTTTGTTTTATTCCACTTGCACG 59.556 41.667 0.00 0.00 0.00 5.34
3 4 5.596845 TCCTTTGTTTTATTCCACTTGCAC 58.403 37.500 0.00 0.00 0.00 4.57
4 5 5.860941 TCCTTTGTTTTATTCCACTTGCA 57.139 34.783 0.00 0.00 0.00 4.08
5 6 6.019075 GTGTTCCTTTGTTTTATTCCACTTGC 60.019 38.462 0.00 0.00 0.00 4.01
6 7 7.264947 AGTGTTCCTTTGTTTTATTCCACTTG 58.735 34.615 0.00 0.00 0.00 3.16
7 8 7.418337 AGTGTTCCTTTGTTTTATTCCACTT 57.582 32.000 0.00 0.00 0.00 3.16
8 9 7.123547 TGAAGTGTTCCTTTGTTTTATTCCACT 59.876 33.333 0.00 0.00 32.03 4.00
9 10 7.222031 GTGAAGTGTTCCTTTGTTTTATTCCAC 59.778 37.037 0.00 0.00 32.03 4.02
10 11 7.262048 GTGAAGTGTTCCTTTGTTTTATTCCA 58.738 34.615 0.00 0.00 32.03 3.53
11 12 6.700081 GGTGAAGTGTTCCTTTGTTTTATTCC 59.300 38.462 0.00 0.00 32.03 3.01
12 13 6.700081 GGGTGAAGTGTTCCTTTGTTTTATTC 59.300 38.462 0.00 0.00 32.03 1.75
13 14 6.578944 GGGTGAAGTGTTCCTTTGTTTTATT 58.421 36.000 0.00 0.00 32.03 1.40
14 15 5.221165 CGGGTGAAGTGTTCCTTTGTTTTAT 60.221 40.000 0.00 0.00 32.03 1.40
15 16 4.096682 CGGGTGAAGTGTTCCTTTGTTTTA 59.903 41.667 0.00 0.00 32.03 1.52
16 17 3.119280 CGGGTGAAGTGTTCCTTTGTTTT 60.119 43.478 0.00 0.00 32.03 2.43
17 18 2.425668 CGGGTGAAGTGTTCCTTTGTTT 59.574 45.455 0.00 0.00 32.03 2.83
18 19 2.021457 CGGGTGAAGTGTTCCTTTGTT 58.979 47.619 0.00 0.00 32.03 2.83
19 20 1.675552 CGGGTGAAGTGTTCCTTTGT 58.324 50.000 0.00 0.00 32.03 2.83
20 21 0.310854 GCGGGTGAAGTGTTCCTTTG 59.689 55.000 0.00 0.00 32.03 2.77
21 22 0.106918 TGCGGGTGAAGTGTTCCTTT 60.107 50.000 0.00 0.00 32.03 3.11
22 23 0.106918 TTGCGGGTGAAGTGTTCCTT 60.107 50.000 0.00 0.00 35.59 3.36
23 24 0.535102 CTTGCGGGTGAAGTGTTCCT 60.535 55.000 0.00 0.00 0.00 3.36
24 25 0.534203 TCTTGCGGGTGAAGTGTTCC 60.534 55.000 0.00 0.00 0.00 3.62
25 26 1.264288 CTTCTTGCGGGTGAAGTGTTC 59.736 52.381 0.00 0.00 36.04 3.18
26 27 1.134220 TCTTCTTGCGGGTGAAGTGTT 60.134 47.619 0.00 0.00 40.20 3.32
27 28 0.468226 TCTTCTTGCGGGTGAAGTGT 59.532 50.000 0.00 0.00 40.20 3.55
28 29 1.532868 CTTCTTCTTGCGGGTGAAGTG 59.467 52.381 0.00 0.00 40.20 3.16
29 30 1.416401 TCTTCTTCTTGCGGGTGAAGT 59.584 47.619 0.00 0.00 40.20 3.01
30 31 2.169832 TCTTCTTCTTGCGGGTGAAG 57.830 50.000 0.00 0.00 40.53 3.02
31 32 2.631160 TTCTTCTTCTTGCGGGTGAA 57.369 45.000 0.00 0.00 0.00 3.18
32 33 2.631160 TTTCTTCTTCTTGCGGGTGA 57.369 45.000 0.00 0.00 0.00 4.02
33 34 3.708563 TTTTTCTTCTTCTTGCGGGTG 57.291 42.857 0.00 0.00 0.00 4.61
61 62 2.095415 GCAAACGAGGCCGACTATTTTT 60.095 45.455 0.00 0.00 39.50 1.94
62 63 1.467342 GCAAACGAGGCCGACTATTTT 59.533 47.619 0.00 0.00 39.50 1.82
79 80 1.750206 ACCGCATGATAGCAATTGCAA 59.250 42.857 30.89 14.41 45.16 4.08
104 105 2.663279 AGTTGAAAAACAGTAGCGCG 57.337 45.000 0.00 0.00 0.00 6.86
105 106 3.466836 CGTAGTTGAAAAACAGTAGCGC 58.533 45.455 0.00 0.00 0.00 5.92
126 127 8.911965 GTGGCCTTTATATATAGGAGTACTACC 58.088 40.741 20.01 11.35 33.70 3.18
131 132 7.401782 TGCATGTGGCCTTTATATATAGGAGTA 59.598 37.037 20.01 5.31 43.89 2.59
134 135 6.634889 TGCATGTGGCCTTTATATATAGGA 57.365 37.500 20.01 2.86 43.89 2.94
135 136 6.488006 GGATGCATGTGGCCTTTATATATAGG 59.512 42.308 2.46 13.37 43.89 2.57
136 137 7.012704 GTGGATGCATGTGGCCTTTATATATAG 59.987 40.741 2.46 0.00 43.89 1.31
163 164 0.651031 GAAACTCCGCTGTTATCCGC 59.349 55.000 0.00 0.00 0.00 5.54
164 165 2.295253 AGAAACTCCGCTGTTATCCG 57.705 50.000 0.00 0.00 0.00 4.18
169 170 3.013921 TCAAACAAGAAACTCCGCTGTT 58.986 40.909 0.00 0.00 0.00 3.16
223 224 3.350219 AAGGTCGCCATTGACAATACT 57.650 42.857 0.00 0.00 40.72 2.12
307 308 1.432270 GCCTCTGCATGGCTACGAAC 61.432 60.000 19.77 0.00 46.38 3.95
337 346 2.890371 GGAGGAAACGGCGCTCTA 59.110 61.111 6.90 0.00 0.00 2.43
376 385 3.204827 AGCGCCATGTTGCCGATC 61.205 61.111 2.29 0.00 0.00 3.69
990 1015 1.142748 CCTCCTCATGTGCTCGTCC 59.857 63.158 0.00 0.00 0.00 4.79
1065 1096 3.858868 GACTGGGTTCGCGTCAGCA 62.859 63.158 5.77 0.00 45.49 4.41
1193 3345 3.753294 ACCAACTGAAGTTCGTGAGAT 57.247 42.857 0.00 0.00 41.60 2.75
1262 4875 7.278424 TCCCGTGTAGCATTTTTGTATTAGTAC 59.722 37.037 0.00 0.00 0.00 2.73
1263 4876 7.278424 GTCCCGTGTAGCATTTTTGTATTAGTA 59.722 37.037 0.00 0.00 0.00 1.82
1264 4877 6.093082 GTCCCGTGTAGCATTTTTGTATTAGT 59.907 38.462 0.00 0.00 0.00 2.24
1265 4878 6.315393 AGTCCCGTGTAGCATTTTTGTATTAG 59.685 38.462 0.00 0.00 0.00 1.73
1267 4880 5.007682 AGTCCCGTGTAGCATTTTTGTATT 58.992 37.500 0.00 0.00 0.00 1.89
1268 4881 4.585879 AGTCCCGTGTAGCATTTTTGTAT 58.414 39.130 0.00 0.00 0.00 2.29
1269 4882 4.010667 AGTCCCGTGTAGCATTTTTGTA 57.989 40.909 0.00 0.00 0.00 2.41
1270 4883 2.858745 AGTCCCGTGTAGCATTTTTGT 58.141 42.857 0.00 0.00 0.00 2.83
1271 4884 3.915437 AAGTCCCGTGTAGCATTTTTG 57.085 42.857 0.00 0.00 0.00 2.44
1273 4886 5.048294 CCTTTAAAGTCCCGTGTAGCATTTT 60.048 40.000 14.03 0.00 0.00 1.82
1278 4891 1.736126 GCCTTTAAAGTCCCGTGTAGC 59.264 52.381 14.03 3.38 0.00 3.58
1279 4892 3.000727 CAGCCTTTAAAGTCCCGTGTAG 58.999 50.000 14.03 0.00 0.00 2.74
1280 4893 2.369532 ACAGCCTTTAAAGTCCCGTGTA 59.630 45.455 14.03 0.00 0.00 2.90
1281 4894 1.142262 ACAGCCTTTAAAGTCCCGTGT 59.858 47.619 14.03 6.84 0.00 4.49
1282 4895 1.892209 ACAGCCTTTAAAGTCCCGTG 58.108 50.000 14.03 6.29 0.00 4.94
1284 4897 3.404899 TGTAACAGCCTTTAAAGTCCCG 58.595 45.455 14.03 0.02 0.00 5.14
1287 4900 5.989777 TGAGTCTGTAACAGCCTTTAAAGTC 59.010 40.000 14.03 0.81 0.00 3.01
1289 4902 8.443937 GTTATGAGTCTGTAACAGCCTTTAAAG 58.556 37.037 8.32 8.32 32.45 1.85
1291 4904 7.386848 GTGTTATGAGTCTGTAACAGCCTTTAA 59.613 37.037 16.75 0.00 40.37 1.52
1292 4905 6.872020 GTGTTATGAGTCTGTAACAGCCTTTA 59.128 38.462 16.75 0.00 40.37 1.85
1293 4906 5.701290 GTGTTATGAGTCTGTAACAGCCTTT 59.299 40.000 16.75 0.00 40.37 3.11
1294 4907 5.238583 GTGTTATGAGTCTGTAACAGCCTT 58.761 41.667 16.75 0.00 40.37 4.35
1296 4909 3.933332 GGTGTTATGAGTCTGTAACAGCC 59.067 47.826 24.77 19.95 46.01 4.85
1298 4911 4.504858 GGGGTGTTATGAGTCTGTAACAG 58.495 47.826 16.75 0.00 40.37 3.16
1299 4912 3.262405 GGGGGTGTTATGAGTCTGTAACA 59.738 47.826 13.97 13.97 38.19 2.41
1300 4913 3.870274 GGGGGTGTTATGAGTCTGTAAC 58.130 50.000 10.31 10.31 0.00 2.50
1323 4936 2.518349 GGTGTGTGTGTGTGGGGG 60.518 66.667 0.00 0.00 0.00 5.40
1324 4937 2.518349 GGGTGTGTGTGTGTGGGG 60.518 66.667 0.00 0.00 0.00 4.96
1325 4938 1.525995 GAGGGTGTGTGTGTGTGGG 60.526 63.158 0.00 0.00 0.00 4.61
1326 4939 1.525995 GGAGGGTGTGTGTGTGTGG 60.526 63.158 0.00 0.00 0.00 4.17
1327 4940 0.179020 ATGGAGGGTGTGTGTGTGTG 60.179 55.000 0.00 0.00 0.00 3.82
1328 4941 0.550914 AATGGAGGGTGTGTGTGTGT 59.449 50.000 0.00 0.00 0.00 3.72
1329 4942 1.691196 AAATGGAGGGTGTGTGTGTG 58.309 50.000 0.00 0.00 0.00 3.82
1330 4943 2.452600 AAAATGGAGGGTGTGTGTGT 57.547 45.000 0.00 0.00 0.00 3.72
1331 4944 4.321899 CCATAAAAATGGAGGGTGTGTGTG 60.322 45.833 0.00 0.00 44.39 3.82
1332 4945 3.831911 CCATAAAAATGGAGGGTGTGTGT 59.168 43.478 0.00 0.00 44.39 3.72
1333 4946 3.195396 CCCATAAAAATGGAGGGTGTGTG 59.805 47.826 5.97 0.00 44.39 3.82
1334 4947 3.440127 CCCATAAAAATGGAGGGTGTGT 58.560 45.455 5.97 0.00 44.39 3.72
1335 4948 2.765699 CCCCATAAAAATGGAGGGTGTG 59.234 50.000 5.97 0.00 44.39 3.82
1336 4949 2.657459 TCCCCATAAAAATGGAGGGTGT 59.343 45.455 5.97 0.00 44.39 4.16
1337 4950 3.396685 TCCCCATAAAAATGGAGGGTG 57.603 47.619 5.97 0.00 44.39 4.61
1338 4951 3.375207 CCATCCCCATAAAAATGGAGGGT 60.375 47.826 5.97 0.00 42.46 4.34
1339 4952 3.242011 CCATCCCCATAAAAATGGAGGG 58.758 50.000 5.97 0.00 44.39 4.30
1340 4953 3.242011 CCCATCCCCATAAAAATGGAGG 58.758 50.000 5.97 5.92 44.39 4.30
1341 4954 2.634453 GCCCATCCCCATAAAAATGGAG 59.366 50.000 5.97 0.00 44.39 3.86
1342 4955 2.688477 GCCCATCCCCATAAAAATGGA 58.312 47.619 5.97 0.00 44.39 3.41
1343 4956 1.699083 GGCCCATCCCCATAAAAATGG 59.301 52.381 0.00 0.00 41.34 3.16
1355 4968 2.517919 GAGGACATGGGCCCATCC 59.482 66.667 35.42 32.56 33.90 3.51
1356 4969 2.517919 GGAGGACATGGGCCCATC 59.482 66.667 35.42 25.15 33.90 3.51
1357 4970 3.105928 GGGAGGACATGGGCCCAT 61.106 66.667 32.75 32.75 40.39 4.00
1360 4973 1.696314 TAAGGGGAGGACATGGGCC 60.696 63.158 0.00 0.00 0.00 5.80
1361 4974 1.279025 TGTAAGGGGAGGACATGGGC 61.279 60.000 0.00 0.00 0.00 5.36
1362 4975 0.546598 GTGTAAGGGGAGGACATGGG 59.453 60.000 0.00 0.00 0.00 4.00
1363 4976 0.546598 GGTGTAAGGGGAGGACATGG 59.453 60.000 0.00 0.00 0.00 3.66
1364 4977 0.546598 GGGTGTAAGGGGAGGACATG 59.453 60.000 0.00 0.00 0.00 3.21
1365 4978 0.120377 TGGGTGTAAGGGGAGGACAT 59.880 55.000 0.00 0.00 0.00 3.06
1366 4979 0.104356 TTGGGTGTAAGGGGAGGACA 60.104 55.000 0.00 0.00 0.00 4.02
1367 4980 1.212195 GATTGGGTGTAAGGGGAGGAC 59.788 57.143 0.00 0.00 0.00 3.85
1368 4981 1.203505 TGATTGGGTGTAAGGGGAGGA 60.204 52.381 0.00 0.00 0.00 3.71
1369 4982 1.295020 TGATTGGGTGTAAGGGGAGG 58.705 55.000 0.00 0.00 0.00 4.30
1370 4983 3.449746 TTTGATTGGGTGTAAGGGGAG 57.550 47.619 0.00 0.00 0.00 4.30
1371 4984 3.898741 GTTTTTGATTGGGTGTAAGGGGA 59.101 43.478 0.00 0.00 0.00 4.81
1372 4985 3.901222 AGTTTTTGATTGGGTGTAAGGGG 59.099 43.478 0.00 0.00 0.00 4.79
1373 4986 4.799255 GCAGTTTTTGATTGGGTGTAAGGG 60.799 45.833 0.00 0.00 0.00 3.95
1374 4987 4.306600 GCAGTTTTTGATTGGGTGTAAGG 58.693 43.478 0.00 0.00 0.00 2.69
1375 4988 4.202202 TGGCAGTTTTTGATTGGGTGTAAG 60.202 41.667 0.00 0.00 0.00 2.34
1376 4989 3.706594 TGGCAGTTTTTGATTGGGTGTAA 59.293 39.130 0.00 0.00 0.00 2.41
1377 4990 3.068873 GTGGCAGTTTTTGATTGGGTGTA 59.931 43.478 0.00 0.00 0.00 2.90
1378 4991 2.114616 TGGCAGTTTTTGATTGGGTGT 58.885 42.857 0.00 0.00 0.00 4.16
1379 4992 2.158986 TGTGGCAGTTTTTGATTGGGTG 60.159 45.455 0.00 0.00 0.00 4.61
1380 4993 2.114616 TGTGGCAGTTTTTGATTGGGT 58.885 42.857 0.00 0.00 0.00 4.51
1381 4994 2.906691 TGTGGCAGTTTTTGATTGGG 57.093 45.000 0.00 0.00 0.00 4.12
1382 4995 3.992643 TGATGTGGCAGTTTTTGATTGG 58.007 40.909 0.00 0.00 0.00 3.16
1383 4996 5.987777 TTTGATGTGGCAGTTTTTGATTG 57.012 34.783 0.00 0.00 0.00 2.67
1384 4997 6.289834 TGATTTGATGTGGCAGTTTTTGATT 58.710 32.000 0.00 0.00 0.00 2.57
1385 4998 5.856156 TGATTTGATGTGGCAGTTTTTGAT 58.144 33.333 0.00 0.00 0.00 2.57
1386 4999 5.273674 TGATTTGATGTGGCAGTTTTTGA 57.726 34.783 0.00 0.00 0.00 2.69
1387 5000 5.987777 TTGATTTGATGTGGCAGTTTTTG 57.012 34.783 0.00 0.00 0.00 2.44
1388 5001 6.289834 TGATTGATTTGATGTGGCAGTTTTT 58.710 32.000 0.00 0.00 0.00 1.94
1389 5002 5.856156 TGATTGATTTGATGTGGCAGTTTT 58.144 33.333 0.00 0.00 0.00 2.43
1390 5003 5.471556 TGATTGATTTGATGTGGCAGTTT 57.528 34.783 0.00 0.00 0.00 2.66
1391 5004 5.046878 ACATGATTGATTTGATGTGGCAGTT 60.047 36.000 0.00 0.00 0.00 3.16
1392 5005 4.464951 ACATGATTGATTTGATGTGGCAGT 59.535 37.500 0.00 0.00 0.00 4.40
1393 5006 5.006153 ACATGATTGATTTGATGTGGCAG 57.994 39.130 0.00 0.00 0.00 4.85
1394 5007 6.527057 TTACATGATTGATTTGATGTGGCA 57.473 33.333 0.00 0.00 31.56 4.92
1395 5008 7.037438 AGTTTACATGATTGATTTGATGTGGC 58.963 34.615 0.00 0.00 31.56 5.01
1396 5009 7.703621 GGAGTTTACATGATTGATTTGATGTGG 59.296 37.037 0.00 0.00 31.56 4.17
1397 5010 8.464404 AGGAGTTTACATGATTGATTTGATGTG 58.536 33.333 0.00 0.00 31.56 3.21
1398 5011 8.464404 CAGGAGTTTACATGATTGATTTGATGT 58.536 33.333 0.00 0.00 33.64 3.06
1399 5012 8.464404 ACAGGAGTTTACATGATTGATTTGATG 58.536 33.333 0.00 0.00 0.00 3.07
1400 5013 8.585471 ACAGGAGTTTACATGATTGATTTGAT 57.415 30.769 0.00 0.00 0.00 2.57
1401 5014 9.166173 CTACAGGAGTTTACATGATTGATTTGA 57.834 33.333 0.00 0.00 0.00 2.69
1402 5015 9.166173 TCTACAGGAGTTTACATGATTGATTTG 57.834 33.333 0.00 0.00 0.00 2.32
1403 5016 9.739276 TTCTACAGGAGTTTACATGATTGATTT 57.261 29.630 0.00 0.00 0.00 2.17
1404 5017 9.739276 TTTCTACAGGAGTTTACATGATTGATT 57.261 29.630 0.00 0.00 0.00 2.57
1405 5018 9.911788 ATTTCTACAGGAGTTTACATGATTGAT 57.088 29.630 0.00 0.00 0.00 2.57
1421 5034 9.494271 AATGCTACACATACATATTTCTACAGG 57.506 33.333 0.00 0.00 38.34 4.00
1424 5037 8.993121 AGCAATGCTACACATACATATTTCTAC 58.007 33.333 5.69 0.00 38.34 2.59
1431 5044 4.944048 ACGAGCAATGCTACACATACATA 58.056 39.130 8.12 0.00 39.88 2.29
1434 5047 4.360563 AGTACGAGCAATGCTACACATAC 58.639 43.478 8.12 6.72 39.88 2.39
1437 5050 4.443913 TTAGTACGAGCAATGCTACACA 57.556 40.909 8.12 0.00 39.88 3.72
1439 5052 8.573885 AGTATTATTAGTACGAGCAATGCTACA 58.426 33.333 8.12 0.00 39.88 2.74
1440 5053 8.967552 AGTATTATTAGTACGAGCAATGCTAC 57.032 34.615 8.12 2.64 39.88 3.58
1489 5600 2.640826 ACTCCCTCGGTTCCAAAATACA 59.359 45.455 0.00 0.00 0.00 2.29
1530 5644 7.545362 AGCATTTCATATTATGGATAGACGC 57.455 36.000 3.89 0.00 0.00 5.19
1553 5667 6.155475 TGTGGGTGTGGAAATTCTTTTTAG 57.845 37.500 0.00 0.00 0.00 1.85
1563 5677 4.090090 TCTTCTTTTTGTGGGTGTGGAAA 58.910 39.130 0.00 0.00 0.00 3.13
1599 5713 9.508642 AACCAAACAAATGGAACTCTTTTTAAA 57.491 25.926 0.00 0.00 43.54 1.52
1607 5724 8.831715 ATGATAAAACCAAACAAATGGAACTC 57.168 30.769 0.00 0.00 43.54 3.01
1682 5803 0.532573 AGATAGCCACGTCACCACAG 59.467 55.000 0.00 0.00 0.00 3.66
1723 5907 1.470979 CGTCTCCGGTCCACCAAATAG 60.471 57.143 0.00 0.00 35.14 1.73
1755 5939 4.778143 GCCATCGCCCACTCGGTT 62.778 66.667 0.00 0.00 0.00 4.44
1818 6002 2.034066 CCCACCACATCGGCAAGT 59.966 61.111 0.00 0.00 39.03 3.16
1842 6026 0.391130 CGGATTCTTCAACAGCCCGA 60.391 55.000 0.00 0.00 37.87 5.14
1886 6070 2.338620 CCTCCTTGACGACGCACA 59.661 61.111 0.00 0.00 0.00 4.57
1960 6144 0.321298 ACGAAGTAGCCGCCAACAAT 60.321 50.000 0.00 0.00 41.94 2.71
2048 6232 0.948623 TGCTGGTCGAAATGTGTCGG 60.949 55.000 0.00 0.00 41.43 4.79
2095 6279 1.686110 CCTTGAGGTCTAGCCCGGT 60.686 63.158 0.00 0.00 38.26 5.28
2213 6397 1.340889 GCTTCCAGTTGAAACCATGCA 59.659 47.619 0.00 0.00 31.06 3.96
2511 6703 6.920758 GTGTTATGCTTGTCACATACCAAAAA 59.079 34.615 0.00 0.00 29.89 1.94
2516 6708 5.220854 GGATGTGTTATGCTTGTCACATACC 60.221 44.000 17.50 16.13 46.77 2.73
2569 6761 3.776969 TCTCTCTCTCTCTCTCTCAAGCT 59.223 47.826 0.00 0.00 0.00 3.74
2665 7071 9.804758 TTTACCGAAGTCAAACATTACAAAATT 57.195 25.926 0.00 0.00 0.00 1.82
2705 7112 8.071368 TGAATGGTATTCTGTTTTGAAACGTAC 58.929 33.333 0.00 3.58 41.74 3.67
2810 7221 2.030027 TGAACTCCTCCAGGTCACAT 57.970 50.000 0.00 0.00 44.58 3.21
2816 7227 3.118592 GGTATGACTTGAACTCCTCCAGG 60.119 52.174 0.00 0.00 0.00 4.45
2817 7228 3.515502 TGGTATGACTTGAACTCCTCCAG 59.484 47.826 0.00 0.00 0.00 3.86
2896 7307 1.996292 TAGCTCGCTCACATGTCAAC 58.004 50.000 0.00 0.00 0.00 3.18
2947 7358 1.221840 CCCCAGTCCAAGTCATCGG 59.778 63.158 0.00 0.00 0.00 4.18
2970 7381 1.656569 GTATGGTAGTCGCGGTCGC 60.657 63.158 6.13 5.16 35.26 5.19
2981 7392 1.206132 CGTCTTGGGCACTGTATGGTA 59.794 52.381 0.00 0.00 0.00 3.25
2986 7397 1.414919 AGTTTCGTCTTGGGCACTGTA 59.585 47.619 0.00 0.00 0.00 2.74
2990 7401 1.464997 GATCAGTTTCGTCTTGGGCAC 59.535 52.381 0.00 0.00 0.00 5.01
3046 7457 2.051345 CACTTGACGCGCAAACCC 60.051 61.111 5.73 0.00 35.74 4.11
3047 7458 1.654137 CACACTTGACGCGCAAACC 60.654 57.895 5.73 0.00 35.74 3.27
3048 7459 0.247894 TTCACACTTGACGCGCAAAC 60.248 50.000 5.73 0.00 35.74 2.93
3049 7460 0.247894 GTTCACACTTGACGCGCAAA 60.248 50.000 5.73 0.00 35.74 3.68
3062 7473 3.667497 GAGATGTGACTCCTGTTCACA 57.333 47.619 7.58 7.58 46.47 3.58
3076 9392 3.917760 GGCGCGCCTAGGAGATGT 61.918 66.667 41.71 0.00 0.00 3.06
3096 9412 0.966370 ACCTAAACGAGCTCGCTCCT 60.966 55.000 34.83 18.81 44.43 3.69
3097 9413 0.737219 TACCTAAACGAGCTCGCTCC 59.263 55.000 34.83 0.00 44.43 4.70
3153 9714 2.050350 CATGGCAGCAGGTTCCTGG 61.050 63.158 18.81 5.97 34.85 4.45
3156 9717 0.685458 AATCCATGGCAGCAGGTTCC 60.685 55.000 6.96 0.00 0.00 3.62
3180 9741 2.359478 GTGGCGGTTGGGTAGTGG 60.359 66.667 0.00 0.00 0.00 4.00
3182 9743 2.850130 TGGTGGCGGTTGGGTAGT 60.850 61.111 0.00 0.00 0.00 2.73
3208 9769 2.060050 TCTGACTACCTGCCTAGAGC 57.940 55.000 0.00 0.00 44.14 4.09
3239 9800 2.497675 CCTACTGACAGTGGTGCATAGT 59.502 50.000 18.58 0.00 0.00 2.12
3241 9802 2.815158 TCCTACTGACAGTGGTGCATA 58.185 47.619 18.58 0.00 0.00 3.14
3244 9805 2.622436 GAATCCTACTGACAGTGGTGC 58.378 52.381 18.58 7.71 0.00 5.01
3287 9856 3.414759 TGCAGTATTTAGGGAGAGGGA 57.585 47.619 0.00 0.00 0.00 4.20
3296 9865 6.538021 AGAACAGAAGCAGATGCAGTATTTAG 59.462 38.462 7.68 0.00 45.16 1.85
3303 9872 2.935201 GGTAGAACAGAAGCAGATGCAG 59.065 50.000 7.68 0.00 45.16 4.41
3304 9873 2.355108 GGGTAGAACAGAAGCAGATGCA 60.355 50.000 7.68 0.00 45.16 3.96
3305 9874 2.284190 GGGTAGAACAGAAGCAGATGC 58.716 52.381 0.00 0.00 42.49 3.91
3306 9875 3.616956 TGGGTAGAACAGAAGCAGATG 57.383 47.619 0.00 0.00 0.00 2.90
3307 9876 4.202305 GCTATGGGTAGAACAGAAGCAGAT 60.202 45.833 0.00 0.00 33.45 2.90
3308 9877 3.133003 GCTATGGGTAGAACAGAAGCAGA 59.867 47.826 0.00 0.00 33.45 4.26
3309 9878 3.133721 AGCTATGGGTAGAACAGAAGCAG 59.866 47.826 0.00 0.00 34.83 4.24
3310 9879 3.107601 AGCTATGGGTAGAACAGAAGCA 58.892 45.455 0.00 0.00 34.83 3.91
3311 9880 3.386402 AGAGCTATGGGTAGAACAGAAGC 59.614 47.826 0.00 0.00 33.43 3.86
3312 9881 4.404073 ACAGAGCTATGGGTAGAACAGAAG 59.596 45.833 13.85 0.00 0.00 2.85
3313 9882 4.353777 ACAGAGCTATGGGTAGAACAGAA 58.646 43.478 13.85 0.00 0.00 3.02
3314 9883 3.982516 ACAGAGCTATGGGTAGAACAGA 58.017 45.455 13.85 0.00 0.00 3.41
3315 9884 4.744795 AACAGAGCTATGGGTAGAACAG 57.255 45.455 13.85 0.00 0.00 3.16
3316 9885 5.499004 AAAACAGAGCTATGGGTAGAACA 57.501 39.130 13.85 0.00 0.00 3.18
3317 9886 6.174049 AGAAAAACAGAGCTATGGGTAGAAC 58.826 40.000 13.85 0.00 0.00 3.01
3318 9887 6.213600 AGAGAAAAACAGAGCTATGGGTAGAA 59.786 38.462 13.85 0.00 0.00 2.10
3319 9888 5.721960 AGAGAAAAACAGAGCTATGGGTAGA 59.278 40.000 13.85 0.00 0.00 2.59
3320 9889 5.983540 AGAGAAAAACAGAGCTATGGGTAG 58.016 41.667 13.85 0.00 0.00 3.18
3321 9890 5.104900 GGAGAGAAAAACAGAGCTATGGGTA 60.105 44.000 13.85 0.00 0.00 3.69
3322 9891 4.323868 GGAGAGAAAAACAGAGCTATGGGT 60.324 45.833 13.85 0.00 0.00 4.51
3323 9892 4.080638 AGGAGAGAAAAACAGAGCTATGGG 60.081 45.833 13.85 0.00 0.00 4.00
3324 9893 4.874966 CAGGAGAGAAAAACAGAGCTATGG 59.125 45.833 13.85 0.00 0.00 2.74
3325 9894 5.486526 ACAGGAGAGAAAAACAGAGCTATG 58.513 41.667 6.84 6.84 0.00 2.23
3326 9895 5.753721 ACAGGAGAGAAAAACAGAGCTAT 57.246 39.130 0.00 0.00 0.00 2.97
3327 9896 5.552870 AACAGGAGAGAAAAACAGAGCTA 57.447 39.130 0.00 0.00 0.00 3.32
3328 9897 4.429854 AACAGGAGAGAAAAACAGAGCT 57.570 40.909 0.00 0.00 0.00 4.09


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

AutoCloner maintained by Alex Coulton.