Multiple sequence alignment - TraesCS6A01G124800

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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 TraesCS6A01G124800 chr6A 100.000 5159 0 0 1 5159 98310971 98305813 0.000000e+00 9527.0
1 TraesCS6A01G124800 chr6A 84.023 3361 493 34 967 4305 98315986 98312648 0.000000e+00 3192.0
2 TraesCS6A01G124800 chr6A 82.260 3371 545 37 967 4306 98888129 98884781 0.000000e+00 2863.0
3 TraesCS6A01G124800 chr6A 81.968 3344 541 47 974 4285 98813630 98810317 0.000000e+00 2778.0
4 TraesCS6A01G124800 chr6A 82.808 2536 411 21 1786 4305 98916425 98913899 0.000000e+00 2244.0
5 TraesCS6A01G124800 chr6A 83.622 751 114 4 977 1718 98917171 98916421 0.000000e+00 697.0
6 TraesCS6A01G124800 chr6A 96.581 117 4 0 4265 4381 98306669 98306553 1.470000e-45 195.0
7 TraesCS6A01G124800 chr6A 96.581 117 4 0 4303 4419 98306707 98306591 1.470000e-45 195.0
8 TraesCS6A01G124800 chr6A 94.937 79 4 0 4265 4343 98306631 98306553 1.950000e-24 124.0
9 TraesCS6A01G124800 chr6A 94.937 79 4 0 4341 4419 98306707 98306629 1.950000e-24 124.0
10 TraesCS6A01G124800 chr6A 86.667 60 6 1 860 917 98250330 98250271 1.200000e-06 65.8
11 TraesCS6A01G124800 chr6A 100.000 31 0 0 4606 4636 98913715 98913685 2.010000e-04 58.4
12 TraesCS6A01G124800 chr6D 93.662 3471 167 16 859 4305 81774002 81770561 0.000000e+00 5142.0
13 TraesCS6A01G124800 chr6D 83.549 3173 502 15 974 4133 81759726 81756561 0.000000e+00 2950.0
14 TraesCS6A01G124800 chr6D 82.719 3339 533 36 989 4305 81926176 81922860 0.000000e+00 2929.0
15 TraesCS6A01G124800 chr6D 82.930 3304 507 38 981 4256 82139151 82135877 0.000000e+00 2924.0
16 TraesCS6A01G124800 chr6D 82.662 3328 515 46 981 4272 81935399 81932098 0.000000e+00 2892.0
17 TraesCS6A01G124800 chr6D 82.365 3357 538 40 977 4306 82203996 82200667 0.000000e+00 2870.0
18 TraesCS6A01G124800 chr6D 90.034 883 53 13 1 858 81774942 81774070 0.000000e+00 1110.0
19 TraesCS6A01G124800 chr6D 83.995 756 107 10 975 1718 82209744 82208991 0.000000e+00 713.0
20 TraesCS6A01G124800 chr6D 95.489 133 6 0 5027 5159 81770017 81769885 4.050000e-51 213.0
21 TraesCS6A01G124800 chr6D 87.978 183 9 5 4533 4713 81770258 81770087 2.440000e-48 204.0
22 TraesCS6A01G124800 chr6B 92.709 3525 214 15 822 4305 156551140 156547618 0.000000e+00 5046.0
23 TraesCS6A01G124800 chr6B 82.977 3319 522 29 977 4272 156654846 156651548 0.000000e+00 2959.0
24 TraesCS6A01G124800 chr6B 82.844 3305 512 39 981 4256 157027423 157024145 0.000000e+00 2911.0
25 TraesCS6A01G124800 chr6B 82.089 3361 543 42 977 4306 157109400 157106068 0.000000e+00 2817.0
26 TraesCS6A01G124800 chr6B 89.264 652 43 9 227 858 156551802 156551158 0.000000e+00 791.0
27 TraesCS6A01G124800 chr6B 83.862 756 108 10 975 1718 157130859 157130106 0.000000e+00 708.0
28 TraesCS6A01G124800 chr6B 90.537 391 23 8 4779 5159 156547168 156546782 5.960000e-139 505.0
29 TraesCS6A01G124800 chr6B 93.249 237 15 1 4531 4767 156547452 156547217 1.060000e-91 348.0
30 TraesCS6A01G124800 chr6B 92.308 169 10 2 4379 4547 156547658 156547493 2.400000e-58 237.0
31 TraesCS6A01G124800 chr6B 100.000 31 0 0 4606 4636 157127401 157127371 2.010000e-04 58.4
32 TraesCS6A01G124800 chr5D 80.633 2055 372 15 975 3016 372064126 372062085 0.000000e+00 1567.0


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 TraesCS6A01G124800 chr6A 98305813 98310971 5158 True 9527.00 9527 100.00000 1 5159 1 chr6A.!!$R2 5158
1 TraesCS6A01G124800 chr6A 98312648 98315986 3338 True 3192.00 3192 84.02300 967 4305 1 chr6A.!!$R3 3338
2 TraesCS6A01G124800 chr6A 98884781 98888129 3348 True 2863.00 2863 82.26000 967 4306 1 chr6A.!!$R5 3339
3 TraesCS6A01G124800 chr6A 98810317 98813630 3313 True 2778.00 2778 81.96800 974 4285 1 chr6A.!!$R4 3311
4 TraesCS6A01G124800 chr6A 98913685 98917171 3486 True 999.80 2244 88.81000 977 4636 3 chr6A.!!$R7 3659
5 TraesCS6A01G124800 chr6D 81756561 81759726 3165 True 2950.00 2950 83.54900 974 4133 1 chr6D.!!$R1 3159
6 TraesCS6A01G124800 chr6D 81922860 81926176 3316 True 2929.00 2929 82.71900 989 4305 1 chr6D.!!$R2 3316
7 TraesCS6A01G124800 chr6D 82135877 82139151 3274 True 2924.00 2924 82.93000 981 4256 1 chr6D.!!$R4 3275
8 TraesCS6A01G124800 chr6D 81932098 81935399 3301 True 2892.00 2892 82.66200 981 4272 1 chr6D.!!$R3 3291
9 TraesCS6A01G124800 chr6D 82200667 82203996 3329 True 2870.00 2870 82.36500 977 4306 1 chr6D.!!$R5 3329
10 TraesCS6A01G124800 chr6D 81769885 81774942 5057 True 1667.25 5142 91.79075 1 5159 4 chr6D.!!$R7 5158
11 TraesCS6A01G124800 chr6D 82208991 82209744 753 True 713.00 713 83.99500 975 1718 1 chr6D.!!$R6 743
12 TraesCS6A01G124800 chr6B 156651548 156654846 3298 True 2959.00 2959 82.97700 977 4272 1 chr6B.!!$R1 3295
13 TraesCS6A01G124800 chr6B 157024145 157027423 3278 True 2911.00 2911 82.84400 981 4256 1 chr6B.!!$R2 3275
14 TraesCS6A01G124800 chr6B 157106068 157109400 3332 True 2817.00 2817 82.08900 977 4306 1 chr6B.!!$R3 3329
15 TraesCS6A01G124800 chr6B 156546782 156551802 5020 True 1385.40 5046 91.61340 227 5159 5 chr6B.!!$R4 4932
16 TraesCS6A01G124800 chr6B 157127371 157130859 3488 True 383.20 708 91.93100 975 4636 2 chr6B.!!$R5 3661
17 TraesCS6A01G124800 chr5D 372062085 372064126 2041 True 1567.00 1567 80.63300 975 3016 1 chr5D.!!$R1 2041

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
21 22 0.105039 ATTCGACGCCTCCTTCATCC 59.895 55.0 0.00 0.00 0.00 3.51 F
604 615 0.108804 TGGACGAGACCAAAGATCGC 60.109 55.0 0.00 0.00 40.02 4.58 F
1265 1387 0.178953 ACCCATGTCTTGCTGCCTTT 60.179 50.0 0.00 0.00 0.00 3.11 F
2094 2300 0.035152 TCAGCGGCACAATTCCAGAT 60.035 50.0 1.45 0.00 0.00 2.90 F
2382 2588 0.659957 GAGGATGCGAATTGTCTGGC 59.340 55.0 0.00 0.00 0.00 4.85 F
3379 3597 1.207791 ACTACCTGATGGCTCCAAGG 58.792 55.0 5.34 5.34 36.63 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1355 1477 0.523072 CACCAATTCCAACGGCAGAG 59.477 55.000 0.00 0.00 0.00 3.35 R
1517 1642 0.809385 GACCAGATTCTCCGTCGTGA 59.191 55.000 0.00 0.00 0.00 4.35 R
2895 3101 1.546029 GGCCCTTTGAGGTCATTGTTC 59.454 52.381 0.00 0.00 31.93 3.18 R
2974 3180 2.414824 CGAGTACAGAACCACAGAGCTC 60.415 54.545 5.27 5.27 0.00 4.09 R
4003 4224 2.787473 TCATTTCCTGTGCCTCGAAT 57.213 45.000 0.00 0.00 0.00 3.34 R
4936 5465 0.755686 GGACCAACCAAACATTGCCA 59.244 50.000 0.00 0.00 38.79 4.92 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
21 22 0.105039 ATTCGACGCCTCCTTCATCC 59.895 55.000 0.00 0.00 0.00 3.51
25 26 2.587194 CGCCTCCTTCATCCAGCG 60.587 66.667 0.00 0.00 37.39 5.18
90 92 2.378028 GCAGGTGAATGCTCGACTC 58.622 57.895 0.00 0.00 43.07 3.36
99 101 1.267574 ATGCTCGACTCCATGGTGGT 61.268 55.000 17.76 14.53 39.03 4.16
143 145 1.429148 AATCGCGGGAGAAATGTCGC 61.429 55.000 6.13 0.00 44.04 5.19
150 152 2.221169 GGGAGAAATGTCGCATATGCA 58.779 47.619 26.52 11.60 42.21 3.96
151 153 2.816087 GGGAGAAATGTCGCATATGCAT 59.184 45.455 26.52 10.62 42.21 3.96
152 154 3.365666 GGGAGAAATGTCGCATATGCATG 60.366 47.826 26.52 12.01 42.21 4.06
168 170 1.331756 GCATGCTACATCGTGGAAAGG 59.668 52.381 11.37 0.00 0.00 3.11
199 201 1.965754 CTGCTCCTGTCTACCCCAGC 61.966 65.000 0.00 0.00 0.00 4.85
207 209 0.471617 GTCTACCCCAGCATCTGCAT 59.528 55.000 4.79 0.00 45.16 3.96
225 227 6.572519 TCTGCATAATAAAACAATCCAAGCC 58.427 36.000 0.00 0.00 0.00 4.35
245 247 2.592308 GGCTTCTCCGCCTCCATT 59.408 61.111 0.00 0.00 46.63 3.16
405 414 2.677228 CATCGGAACCAAGGGCCT 59.323 61.111 0.00 0.00 0.00 5.19
443 452 2.938838 CCACCCCAGTTTACTGTCAAA 58.061 47.619 8.91 0.00 42.27 2.69
454 463 2.793278 ACTGTCAAATTTGAACGGCC 57.207 45.000 22.07 10.22 39.21 6.13
473 482 3.505293 GGCCTCAGAATTCAGATAATGGC 59.495 47.826 16.13 16.13 36.27 4.40
475 484 4.722220 CCTCAGAATTCAGATAATGGCCA 58.278 43.478 8.56 8.56 0.00 5.36
476 485 4.518211 CCTCAGAATTCAGATAATGGCCAC 59.482 45.833 8.16 0.00 0.00 5.01
477 486 5.114764 TCAGAATTCAGATAATGGCCACA 57.885 39.130 8.16 0.00 0.00 4.17
478 487 5.698104 TCAGAATTCAGATAATGGCCACAT 58.302 37.500 8.16 3.95 39.54 3.21
479 488 6.840527 TCAGAATTCAGATAATGGCCACATA 58.159 36.000 8.16 4.77 35.94 2.29
480 489 7.464273 TCAGAATTCAGATAATGGCCACATAT 58.536 34.615 8.16 10.47 35.94 1.78
521 531 2.244117 ATAGTGTGCCAGTGGAGCCG 62.244 60.000 15.20 0.00 0.00 5.52
572 583 1.066136 CAGACAGAGCACGTGTGATG 58.934 55.000 18.38 14.86 29.46 3.07
589 600 2.768527 TGATGAGGTCAAGAGGATGGAC 59.231 50.000 0.00 0.00 32.78 4.02
604 615 0.108804 TGGACGAGACCAAAGATCGC 60.109 55.000 0.00 0.00 40.02 4.58
605 616 0.806492 GGACGAGACCAAAGATCGCC 60.806 60.000 0.00 0.00 40.02 5.54
606 617 0.806492 GACGAGACCAAAGATCGCCC 60.806 60.000 0.00 0.00 40.02 6.13
607 618 1.878522 CGAGACCAAAGATCGCCCG 60.879 63.158 0.00 0.00 0.00 6.13
608 619 2.125106 AGACCAAAGATCGCCCGC 60.125 61.111 0.00 0.00 0.00 6.13
658 669 2.594321 GCAGATGATTCCTCTCGATCG 58.406 52.381 9.36 9.36 0.00 3.69
714 739 1.815003 CTCTGCAAATCTCCACCAACC 59.185 52.381 0.00 0.00 0.00 3.77
744 770 1.852067 GAATGCGTGGCGTTTCCTGT 61.852 55.000 0.00 0.00 37.94 4.00
760 786 1.202405 CCTGTTCACAAAAGGGTGCAC 60.202 52.381 8.80 8.80 38.66 4.57
775 802 2.550855 GGTGCACCAAGAAGTGATCAGA 60.551 50.000 31.23 0.00 40.34 3.27
780 807 4.083590 GCACCAAGAAGTGATCAGAGAAAC 60.084 45.833 0.00 0.00 40.34 2.78
782 809 5.049818 CACCAAGAAGTGATCAGAGAAACAC 60.050 44.000 0.00 0.00 40.34 3.32
783 810 5.163258 ACCAAGAAGTGATCAGAGAAACACT 60.163 40.000 0.00 0.00 43.92 3.55
809 838 5.303747 TGGCACGTGGTAAAAATTCTATG 57.696 39.130 18.88 0.00 0.00 2.23
849 878 4.698583 GTAGACGGCTACAAAAGAGAGA 57.301 45.455 23.78 0.00 45.10 3.10
894 990 2.577449 ACCGTTTTTCCTTTGTGCTG 57.423 45.000 0.00 0.00 0.00 4.41
957 1061 6.237781 CGTCAAGCTCTTCAATGATTAGACAG 60.238 42.308 0.00 0.00 0.00 3.51
1008 1115 1.069022 CACCAGAAAACCATGCAGACG 60.069 52.381 0.00 0.00 0.00 4.18
1080 1199 2.633509 CCTTGCCCTTGTGCTGCTC 61.634 63.158 0.00 0.00 0.00 4.26
1112 1231 1.218585 CTCTCACCAGCTCCTGCAG 59.781 63.158 6.78 6.78 42.74 4.41
1157 1276 4.083862 GTTCCTCGCCGGGCTCTT 62.084 66.667 18.34 0.00 0.00 2.85
1170 1289 1.301716 GCTCTTGCAAGACGGTGGA 60.302 57.895 25.16 3.53 39.41 4.02
1249 1371 0.179081 GCAAGATAGGACGGTCACCC 60.179 60.000 10.76 0.00 0.00 4.61
1265 1387 0.178953 ACCCATGTCTTGCTGCCTTT 60.179 50.000 0.00 0.00 0.00 3.11
1281 1403 0.909623 CTTTTAAGGGCCTCGAGGGA 59.090 55.000 32.06 0.00 37.23 4.20
1283 1405 1.591768 TTTAAGGGCCTCGAGGGAAT 58.408 50.000 32.06 0.00 37.23 3.01
1284 1406 1.591768 TTAAGGGCCTCGAGGGAATT 58.408 50.000 32.06 10.97 37.23 2.17
1309 1431 1.115930 ACGATCCCTTGGGATCCTCG 61.116 60.000 31.77 26.70 41.01 4.63
1310 1432 0.827925 CGATCCCTTGGGATCCTCGA 60.828 60.000 31.77 3.62 41.01 4.04
1355 1477 3.414700 CAACTCGCTGTCCGGTGC 61.415 66.667 0.00 3.93 37.59 5.01
1443 1568 2.031163 GCACTCCACGAGTTGCCT 59.969 61.111 0.00 0.00 41.37 4.75
1450 1575 1.291877 CCACGAGTTGCCTTCTTCGG 61.292 60.000 0.00 0.00 0.00 4.30
1521 1646 2.009774 GGACACTTTCCATCCATCACG 58.990 52.381 0.00 0.00 45.10 4.35
1522 1647 2.354704 GGACACTTTCCATCCATCACGA 60.355 50.000 0.00 0.00 45.10 4.35
1523 1648 2.673368 GACACTTTCCATCCATCACGAC 59.327 50.000 0.00 0.00 0.00 4.34
1738 1872 6.012508 TGGAGTAATCCCAAATGAACTCTTCT 60.013 38.462 6.78 0.00 34.99 2.85
1741 1875 7.918076 AGTAATCCCAAATGAACTCTTCTACA 58.082 34.615 0.00 0.00 0.00 2.74
1776 1910 5.642491 GGAGTACCTGTCATTTCCTAACAAC 59.358 44.000 0.00 0.00 0.00 3.32
2094 2300 0.035152 TCAGCGGCACAATTCCAGAT 60.035 50.000 1.45 0.00 0.00 2.90
2174 2380 2.159324 GGCAGCTTTCTCCACAAATAGC 60.159 50.000 0.00 0.00 0.00 2.97
2382 2588 0.659957 GAGGATGCGAATTGTCTGGC 59.340 55.000 0.00 0.00 0.00 4.85
2391 2597 2.752354 CGAATTGTCTGGCCAAATACCA 59.248 45.455 7.01 0.00 35.40 3.25
2895 3101 6.418819 ACTTTCTTTCAGCATTCAACATTTCG 59.581 34.615 0.00 0.00 0.00 3.46
3201 3419 4.095483 GGAGACGTTGATGCATCTTCATTT 59.905 41.667 26.32 9.26 0.00 2.32
3379 3597 1.207791 ACTACCTGATGGCTCCAAGG 58.792 55.000 5.34 5.34 36.63 3.61
3455 3673 1.277557 AGAGGTTGATGCACTCTCCAC 59.722 52.381 0.00 0.00 36.96 4.02
3861 4082 1.661112 GTTGCTACATTGAGAGGCGAC 59.339 52.381 0.00 0.00 0.00 5.19
4003 4224 0.178876 TGAGGTCCTGGATCCAACCA 60.179 55.000 29.39 13.20 38.33 3.67
4018 4239 0.400213 AACCATTCGAGGCACAGGAA 59.600 50.000 0.00 0.00 0.00 3.36
4134 4355 1.000827 CTGGCCAGTATAGACGCTGAG 60.001 57.143 25.53 0.00 34.87 3.35
4297 4552 6.436218 TCACTTTGTACAGAGCCTAACAGATA 59.564 38.462 13.09 0.00 0.00 1.98
4298 4553 6.754209 CACTTTGTACAGAGCCTAACAGATAG 59.246 42.308 13.09 0.00 0.00 2.08
4299 4554 4.920640 TGTACAGAGCCTAACAGATAGC 57.079 45.455 0.00 0.00 0.00 2.97
4300 4555 3.637229 TGTACAGAGCCTAACAGATAGCC 59.363 47.826 0.00 0.00 0.00 3.93
4301 4556 2.752030 ACAGAGCCTAACAGATAGCCA 58.248 47.619 0.00 0.00 0.00 4.75
4302 4557 3.312890 ACAGAGCCTAACAGATAGCCAT 58.687 45.455 0.00 0.00 0.00 4.40
4303 4558 3.713764 ACAGAGCCTAACAGATAGCCATT 59.286 43.478 0.00 0.00 0.00 3.16
4304 4559 4.164988 ACAGAGCCTAACAGATAGCCATTT 59.835 41.667 0.00 0.00 0.00 2.32
4305 4560 4.514441 CAGAGCCTAACAGATAGCCATTTG 59.486 45.833 0.00 0.00 0.00 2.32
4306 4561 4.164988 AGAGCCTAACAGATAGCCATTTGT 59.835 41.667 0.00 0.00 31.07 2.83
4307 4562 4.455606 AGCCTAACAGATAGCCATTTGTC 58.544 43.478 0.00 0.00 28.55 3.18
4308 4563 4.164988 AGCCTAACAGATAGCCATTTGTCT 59.835 41.667 0.00 0.00 28.55 3.41
4309 4564 4.884164 GCCTAACAGATAGCCATTTGTCTT 59.116 41.667 0.00 0.00 28.55 3.01
4310 4565 5.358160 GCCTAACAGATAGCCATTTGTCTTT 59.642 40.000 0.00 0.00 28.55 2.52
4311 4566 6.127619 GCCTAACAGATAGCCATTTGTCTTTT 60.128 38.462 0.00 0.00 28.55 2.27
4312 4567 7.067008 GCCTAACAGATAGCCATTTGTCTTTTA 59.933 37.037 0.00 0.00 28.55 1.52
4313 4568 8.398665 CCTAACAGATAGCCATTTGTCTTTTAC 58.601 37.037 0.00 0.00 28.55 2.01
4314 4569 9.167311 CTAACAGATAGCCATTTGTCTTTTACT 57.833 33.333 0.00 0.00 28.55 2.24
4315 4570 8.409358 AACAGATAGCCATTTGTCTTTTACTT 57.591 30.769 0.00 0.00 28.55 2.24
4316 4571 8.409358 ACAGATAGCCATTTGTCTTTTACTTT 57.591 30.769 0.00 0.00 0.00 2.66
4317 4572 8.299570 ACAGATAGCCATTTGTCTTTTACTTTG 58.700 33.333 0.00 0.00 0.00 2.77
4318 4573 8.299570 CAGATAGCCATTTGTCTTTTACTTTGT 58.700 33.333 0.00 0.00 0.00 2.83
4319 4574 9.515226 AGATAGCCATTTGTCTTTTACTTTGTA 57.485 29.630 0.00 0.00 0.00 2.41
4320 4575 9.556030 GATAGCCATTTGTCTTTTACTTTGTAC 57.444 33.333 0.00 0.00 0.00 2.90
4321 4576 7.341445 AGCCATTTGTCTTTTACTTTGTACA 57.659 32.000 0.00 0.00 0.00 2.90
4322 4577 7.425606 AGCCATTTGTCTTTTACTTTGTACAG 58.574 34.615 0.00 0.00 0.00 2.74
4323 4578 7.284489 AGCCATTTGTCTTTTACTTTGTACAGA 59.716 33.333 0.00 0.00 0.00 3.41
4324 4579 7.591426 GCCATTTGTCTTTTACTTTGTACAGAG 59.409 37.037 11.68 11.68 0.00 3.35
4325 4580 7.591426 CCATTTGTCTTTTACTTTGTACAGAGC 59.409 37.037 13.09 0.00 0.00 4.09
4326 4581 6.613755 TTGTCTTTTACTTTGTACAGAGCC 57.386 37.500 13.09 0.00 0.00 4.70
4327 4582 5.925509 TGTCTTTTACTTTGTACAGAGCCT 58.074 37.500 13.09 0.00 0.00 4.58
4328 4583 7.058023 TGTCTTTTACTTTGTACAGAGCCTA 57.942 36.000 13.09 0.00 0.00 3.93
4329 4584 7.502696 TGTCTTTTACTTTGTACAGAGCCTAA 58.497 34.615 13.09 3.30 0.00 2.69
4330 4585 7.440255 TGTCTTTTACTTTGTACAGAGCCTAAC 59.560 37.037 13.09 5.57 0.00 2.34
4331 4586 7.440255 GTCTTTTACTTTGTACAGAGCCTAACA 59.560 37.037 13.09 0.00 0.00 2.41
4332 4587 7.656137 TCTTTTACTTTGTACAGAGCCTAACAG 59.344 37.037 13.09 8.03 0.00 3.16
4333 4588 6.659745 TTACTTTGTACAGAGCCTAACAGA 57.340 37.500 13.09 0.00 0.00 3.41
4334 4589 5.746990 ACTTTGTACAGAGCCTAACAGAT 57.253 39.130 13.09 0.00 0.00 2.90
4335 4590 6.852420 ACTTTGTACAGAGCCTAACAGATA 57.148 37.500 13.09 0.00 0.00 1.98
4336 4591 6.868622 ACTTTGTACAGAGCCTAACAGATAG 58.131 40.000 13.09 0.00 0.00 2.08
4337 4592 4.920640 TGTACAGAGCCTAACAGATAGC 57.079 45.455 0.00 0.00 0.00 2.97
4338 4593 3.637229 TGTACAGAGCCTAACAGATAGCC 59.363 47.826 0.00 0.00 0.00 3.93
4339 4594 2.752030 ACAGAGCCTAACAGATAGCCA 58.248 47.619 0.00 0.00 0.00 4.75
4340 4595 3.312890 ACAGAGCCTAACAGATAGCCAT 58.687 45.455 0.00 0.00 0.00 4.40
4341 4596 3.713764 ACAGAGCCTAACAGATAGCCATT 59.286 43.478 0.00 0.00 0.00 3.16
4342 4597 4.164988 ACAGAGCCTAACAGATAGCCATTT 59.835 41.667 0.00 0.00 0.00 2.32
4343 4598 4.514441 CAGAGCCTAACAGATAGCCATTTG 59.486 45.833 0.00 0.00 0.00 2.32
4344 4599 4.164988 AGAGCCTAACAGATAGCCATTTGT 59.835 41.667 0.00 0.00 31.07 2.83
4345 4600 4.455606 AGCCTAACAGATAGCCATTTGTC 58.544 43.478 0.00 0.00 28.55 3.18
4346 4601 4.164988 AGCCTAACAGATAGCCATTTGTCT 59.835 41.667 0.00 0.00 28.55 3.41
4347 4602 4.884164 GCCTAACAGATAGCCATTTGTCTT 59.116 41.667 0.00 0.00 28.55 3.01
4348 4603 5.358160 GCCTAACAGATAGCCATTTGTCTTT 59.642 40.000 0.00 0.00 28.55 2.52
4349 4604 6.127619 GCCTAACAGATAGCCATTTGTCTTTT 60.128 38.462 0.00 0.00 28.55 2.27
4350 4605 7.067008 GCCTAACAGATAGCCATTTGTCTTTTA 59.933 37.037 0.00 0.00 28.55 1.52
4351 4606 8.398665 CCTAACAGATAGCCATTTGTCTTTTAC 58.601 37.037 0.00 0.00 28.55 2.01
4352 4607 9.167311 CTAACAGATAGCCATTTGTCTTTTACT 57.833 33.333 0.00 0.00 28.55 2.24
4353 4608 8.409358 AACAGATAGCCATTTGTCTTTTACTT 57.591 30.769 0.00 0.00 28.55 2.24
4354 4609 8.409358 ACAGATAGCCATTTGTCTTTTACTTT 57.591 30.769 0.00 0.00 0.00 2.66
4355 4610 8.299570 ACAGATAGCCATTTGTCTTTTACTTTG 58.700 33.333 0.00 0.00 0.00 2.77
4356 4611 8.299570 CAGATAGCCATTTGTCTTTTACTTTGT 58.700 33.333 0.00 0.00 0.00 2.83
4357 4612 9.515226 AGATAGCCATTTGTCTTTTACTTTGTA 57.485 29.630 0.00 0.00 0.00 2.41
4358 4613 9.556030 GATAGCCATTTGTCTTTTACTTTGTAC 57.444 33.333 0.00 0.00 0.00 2.90
4359 4614 7.341445 AGCCATTTGTCTTTTACTTTGTACA 57.659 32.000 0.00 0.00 0.00 2.90
4360 4615 7.425606 AGCCATTTGTCTTTTACTTTGTACAG 58.574 34.615 0.00 0.00 0.00 2.74
4361 4616 7.284489 AGCCATTTGTCTTTTACTTTGTACAGA 59.716 33.333 0.00 0.00 0.00 3.41
4362 4617 7.591426 GCCATTTGTCTTTTACTTTGTACAGAG 59.409 37.037 11.68 11.68 0.00 3.35
4363 4618 7.591426 CCATTTGTCTTTTACTTTGTACAGAGC 59.409 37.037 13.09 0.00 0.00 4.09
4364 4619 6.613755 TTGTCTTTTACTTTGTACAGAGCC 57.386 37.500 13.09 0.00 0.00 4.70
4365 4620 5.925509 TGTCTTTTACTTTGTACAGAGCCT 58.074 37.500 13.09 0.00 0.00 4.58
4366 4621 7.058023 TGTCTTTTACTTTGTACAGAGCCTA 57.942 36.000 13.09 0.00 0.00 3.93
4367 4622 7.502696 TGTCTTTTACTTTGTACAGAGCCTAA 58.497 34.615 13.09 3.30 0.00 2.69
4368 4623 7.440255 TGTCTTTTACTTTGTACAGAGCCTAAC 59.560 37.037 13.09 5.57 0.00 2.34
4369 4624 7.440255 GTCTTTTACTTTGTACAGAGCCTAACA 59.560 37.037 13.09 0.00 0.00 2.41
4370 4625 7.656137 TCTTTTACTTTGTACAGAGCCTAACAG 59.344 37.037 13.09 8.03 0.00 3.16
4371 4626 6.659745 TTACTTTGTACAGAGCCTAACAGA 57.340 37.500 13.09 0.00 0.00 3.41
4372 4627 5.746990 ACTTTGTACAGAGCCTAACAGAT 57.253 39.130 13.09 0.00 0.00 2.90
4373 4628 6.852420 ACTTTGTACAGAGCCTAACAGATA 57.148 37.500 13.09 0.00 0.00 1.98
4374 4629 6.868622 ACTTTGTACAGAGCCTAACAGATAG 58.131 40.000 13.09 0.00 0.00 2.08
4375 4630 4.920640 TGTACAGAGCCTAACAGATAGC 57.079 45.455 0.00 0.00 0.00 2.97
4376 4631 3.637229 TGTACAGAGCCTAACAGATAGCC 59.363 47.826 0.00 0.00 0.00 3.93
4377 4632 2.752030 ACAGAGCCTAACAGATAGCCA 58.248 47.619 0.00 0.00 0.00 4.75
4378 4633 3.312890 ACAGAGCCTAACAGATAGCCAT 58.687 45.455 0.00 0.00 0.00 4.40
4379 4634 3.713764 ACAGAGCCTAACAGATAGCCATT 59.286 43.478 0.00 0.00 0.00 3.16
4380 4635 4.164988 ACAGAGCCTAACAGATAGCCATTT 59.835 41.667 0.00 0.00 0.00 2.32
4381 4636 4.514441 CAGAGCCTAACAGATAGCCATTTG 59.486 45.833 0.00 0.00 0.00 2.32
4382 4637 4.164988 AGAGCCTAACAGATAGCCATTTGT 59.835 41.667 0.00 0.00 31.07 2.83
4383 4638 4.455606 AGCCTAACAGATAGCCATTTGTC 58.544 43.478 0.00 0.00 28.55 3.18
4384 4639 4.164988 AGCCTAACAGATAGCCATTTGTCT 59.835 41.667 0.00 0.00 28.55 3.41
4385 4640 4.884164 GCCTAACAGATAGCCATTTGTCTT 59.116 41.667 0.00 0.00 28.55 3.01
4386 4641 5.358160 GCCTAACAGATAGCCATTTGTCTTT 59.642 40.000 0.00 0.00 28.55 2.52
4387 4642 6.127619 GCCTAACAGATAGCCATTTGTCTTTT 60.128 38.462 0.00 0.00 28.55 2.27
4388 4643 7.067008 GCCTAACAGATAGCCATTTGTCTTTTA 59.933 37.037 0.00 0.00 28.55 1.52
4389 4644 8.398665 CCTAACAGATAGCCATTTGTCTTTTAC 58.601 37.037 0.00 0.00 28.55 2.01
4390 4645 9.167311 CTAACAGATAGCCATTTGTCTTTTACT 57.833 33.333 0.00 0.00 28.55 2.24
4391 4646 8.409358 AACAGATAGCCATTTGTCTTTTACTT 57.591 30.769 0.00 0.00 28.55 2.24
4392 4647 8.409358 ACAGATAGCCATTTGTCTTTTACTTT 57.591 30.769 0.00 0.00 0.00 2.66
4393 4648 8.299570 ACAGATAGCCATTTGTCTTTTACTTTG 58.700 33.333 0.00 0.00 0.00 2.77
4394 4649 8.299570 CAGATAGCCATTTGTCTTTTACTTTGT 58.700 33.333 0.00 0.00 0.00 2.83
4395 4650 9.515226 AGATAGCCATTTGTCTTTTACTTTGTA 57.485 29.630 0.00 0.00 0.00 2.41
4396 4651 9.556030 GATAGCCATTTGTCTTTTACTTTGTAC 57.444 33.333 0.00 0.00 0.00 2.90
4397 4652 7.341445 AGCCATTTGTCTTTTACTTTGTACA 57.659 32.000 0.00 0.00 0.00 2.90
4398 4653 7.425606 AGCCATTTGTCTTTTACTTTGTACAG 58.574 34.615 0.00 0.00 0.00 2.74
4399 4654 7.284489 AGCCATTTGTCTTTTACTTTGTACAGA 59.716 33.333 0.00 0.00 0.00 3.41
4400 4655 7.591426 GCCATTTGTCTTTTACTTTGTACAGAG 59.409 37.037 11.68 11.68 0.00 3.35
4401 4656 7.591426 CCATTTGTCTTTTACTTTGTACAGAGC 59.409 37.037 13.09 0.00 0.00 4.09
4402 4657 6.613755 TTGTCTTTTACTTTGTACAGAGCC 57.386 37.500 13.09 0.00 0.00 4.70
4403 4658 5.676552 TGTCTTTTACTTTGTACAGAGCCA 58.323 37.500 13.09 0.00 0.00 4.75
4404 4659 6.116806 TGTCTTTTACTTTGTACAGAGCCAA 58.883 36.000 13.09 5.31 0.00 4.52
4405 4660 6.600032 TGTCTTTTACTTTGTACAGAGCCAAA 59.400 34.615 13.09 10.57 0.00 3.28
4406 4661 6.910972 GTCTTTTACTTTGTACAGAGCCAAAC 59.089 38.462 13.09 1.85 0.00 2.93
4407 4662 6.600032 TCTTTTACTTTGTACAGAGCCAAACA 59.400 34.615 13.09 0.00 0.00 2.83
4408 4663 6.371809 TTTACTTTGTACAGAGCCAAACAG 57.628 37.500 13.09 0.00 0.00 3.16
4409 4664 4.150897 ACTTTGTACAGAGCCAAACAGA 57.849 40.909 13.09 0.00 0.00 3.41
4410 4665 4.718961 ACTTTGTACAGAGCCAAACAGAT 58.281 39.130 13.09 0.00 0.00 2.90
4516 4771 5.179368 TGCAAGAACCTTTAGATGTTTCTCG 59.821 40.000 0.00 0.00 33.17 4.04
4519 4774 7.291567 CAAGAACCTTTAGATGTTTCTCGAAC 58.708 38.462 0.00 0.00 38.78 3.95
4524 4779 9.503399 AACCTTTAGATGTTTCTCGAACTTATT 57.497 29.630 0.00 0.00 39.08 1.40
4581 5029 6.091577 GGACAACGTATACACATGTGAAATGA 59.908 38.462 31.94 11.52 0.00 2.57
4636 5126 3.248266 GTTTCCATTCAAGTGCAGATGC 58.752 45.455 0.00 0.00 42.50 3.91
4644 5136 2.749076 TCAAGTGCAGATGCCATGTAAC 59.251 45.455 1.72 0.00 41.18 2.50
4646 5138 0.248215 GTGCAGATGCCATGTAACGC 60.248 55.000 1.72 0.00 41.18 4.84
4749 5241 8.727910 GGAACCTTTAAATGTTTCTCGAAGTAT 58.272 33.333 9.78 0.00 0.00 2.12
4750 5242 9.756461 GAACCTTTAAATGTTTCTCGAAGTATC 57.244 33.333 9.78 0.00 0.00 2.24
4783 5312 8.307882 GCTTAAGTTTCACAAGCATGGATACAC 61.308 40.741 4.02 0.00 41.95 2.90
4802 5331 9.113838 GGATACACATGTGAAATGACTATCTTT 57.886 33.333 31.94 6.94 0.00 2.52
4831 5360 2.030274 CCGTGGAAGGTTGAAAATGGAC 60.030 50.000 0.00 0.00 0.00 4.02
4901 5430 5.449041 CGTATCAGCTGTTTTTACATGCCAT 60.449 40.000 14.67 0.00 0.00 4.40
4909 5438 6.403866 TGTTTTTACATGCCATCAGAGTTT 57.596 33.333 0.00 0.00 0.00 2.66
4910 5439 6.215121 TGTTTTTACATGCCATCAGAGTTTG 58.785 36.000 0.00 0.00 0.00 2.93
4937 5466 8.240883 GGTGAATTACCGAATTACTAGCTATG 57.759 38.462 0.00 0.00 40.26 2.23
4939 5468 6.872020 TGAATTACCGAATTACTAGCTATGGC 59.128 38.462 0.00 0.00 35.33 4.40
4942 5471 5.228945 ACCGAATTACTAGCTATGGCAAT 57.771 39.130 3.10 0.00 41.70 3.56
4943 5472 4.997395 ACCGAATTACTAGCTATGGCAATG 59.003 41.667 3.10 0.00 41.70 2.82
4945 5474 5.470098 CCGAATTACTAGCTATGGCAATGTT 59.530 40.000 3.10 0.00 41.70 2.71
4947 5476 6.852853 CGAATTACTAGCTATGGCAATGTTTG 59.147 38.462 3.10 0.00 41.70 2.93
4948 5477 6.639632 ATTACTAGCTATGGCAATGTTTGG 57.360 37.500 3.10 0.00 41.70 3.28
4949 5478 3.968265 ACTAGCTATGGCAATGTTTGGT 58.032 40.909 3.10 0.00 41.70 3.67
4950 5479 4.344104 ACTAGCTATGGCAATGTTTGGTT 58.656 39.130 3.10 0.00 41.70 3.67
4951 5480 3.598019 AGCTATGGCAATGTTTGGTTG 57.402 42.857 3.10 0.00 41.70 3.77
4952 5481 2.234414 AGCTATGGCAATGTTTGGTTGG 59.766 45.455 3.10 0.00 41.70 3.77
4953 5482 2.028203 GCTATGGCAATGTTTGGTTGGT 60.028 45.455 0.00 0.00 38.54 3.67
4995 5534 6.359804 TGACCAGGAAATTGAGGATCTAATG 58.640 40.000 0.00 0.00 34.92 1.90
4997 5536 5.135383 CCAGGAAATTGAGGATCTAATGCA 58.865 41.667 0.00 0.00 34.92 3.96
5006 5545 3.220110 AGGATCTAATGCAACTGCCATG 58.780 45.455 0.00 0.00 41.18 3.66
5007 5546 2.295349 GGATCTAATGCAACTGCCATGG 59.705 50.000 7.63 7.63 41.18 3.66
5008 5547 2.512692 TCTAATGCAACTGCCATGGT 57.487 45.000 14.67 0.00 41.18 3.55
5118 5666 2.066262 ACAAGCGGTATTTCGACACTG 58.934 47.619 0.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 1.135257 AGAATGAGTTCGTCCTCGCTG 60.135 52.381 0.91 0.00 39.38 5.18
25 26 1.656095 CGCAAGAATGAGTTCGTCCTC 59.344 52.381 0.00 0.00 39.38 3.71
62 64 0.106819 ATTCACCTGCTCATGCTCCC 60.107 55.000 0.00 0.00 40.48 4.30
65 67 2.490165 GCATTCACCTGCTCATGCT 58.510 52.632 0.00 0.00 39.20 3.79
99 101 2.668212 CGACGCCTTGCCTTGGAA 60.668 61.111 0.00 0.00 0.00 3.53
106 108 2.054140 TTGTTTGTCCGACGCCTTGC 62.054 55.000 0.00 0.00 0.00 4.01
143 145 3.328505 TCCACGATGTAGCATGCATATG 58.671 45.455 21.98 6.79 43.13 1.78
150 152 1.210478 AGCCTTTCCACGATGTAGCAT 59.790 47.619 0.00 0.00 0.00 3.79
151 153 0.613260 AGCCTTTCCACGATGTAGCA 59.387 50.000 0.00 0.00 0.00 3.49
152 154 2.596904 TAGCCTTTCCACGATGTAGC 57.403 50.000 0.00 0.00 0.00 3.58
153 155 5.360591 AGAAATAGCCTTTCCACGATGTAG 58.639 41.667 5.90 0.00 0.00 2.74
155 157 4.192317 GAGAAATAGCCTTTCCACGATGT 58.808 43.478 5.90 0.00 0.00 3.06
156 158 4.034510 GTGAGAAATAGCCTTTCCACGATG 59.965 45.833 5.90 0.00 0.00 3.84
157 159 4.192317 GTGAGAAATAGCCTTTCCACGAT 58.808 43.478 5.90 0.00 0.00 3.73
158 160 3.596214 GTGAGAAATAGCCTTTCCACGA 58.404 45.455 5.90 0.00 0.00 4.35
159 161 2.678336 GGTGAGAAATAGCCTTTCCACG 59.322 50.000 16.09 0.00 33.96 4.94
168 170 2.093235 ACAGGAGCAGGTGAGAAATAGC 60.093 50.000 0.00 0.00 0.00 2.97
199 201 7.170320 GGCTTGGATTGTTTTATTATGCAGATG 59.830 37.037 0.00 0.00 0.00 2.90
207 209 3.181495 CCGCGGCTTGGATTGTTTTATTA 60.181 43.478 14.67 0.00 0.00 0.98
233 235 1.227674 GCTACCAATGGAGGCGGAG 60.228 63.158 6.16 0.00 0.00 4.63
235 237 2.588877 CGCTACCAATGGAGGCGG 60.589 66.667 25.59 13.49 40.68 6.13
268 270 2.825836 CATTGCAGGGCGGTCTCC 60.826 66.667 0.00 0.00 0.00 3.71
392 401 2.583441 GCCAAAGGCCCTTGGTTCC 61.583 63.158 29.77 13.20 46.53 3.62
405 414 2.844451 GCGTGTGAGGCTTGCCAAA 61.844 57.895 14.54 0.00 0.00 3.28
409 418 4.030452 GTGGCGTGTGAGGCTTGC 62.030 66.667 0.00 0.00 37.59 4.01
443 452 3.420893 TGAATTCTGAGGCCGTTCAAAT 58.579 40.909 7.05 0.00 0.00 2.32
454 463 5.128205 TGTGGCCATTATCTGAATTCTGAG 58.872 41.667 9.72 4.07 0.00 3.35
473 482 2.959507 TGGACTGTGACGATATGTGG 57.040 50.000 0.00 0.00 0.00 4.17
475 484 2.766263 ACCATGGACTGTGACGATATGT 59.234 45.455 21.47 0.00 0.00 2.29
476 485 3.384668 GACCATGGACTGTGACGATATG 58.615 50.000 21.47 0.00 0.00 1.78
477 486 2.365617 GGACCATGGACTGTGACGATAT 59.634 50.000 21.47 0.00 0.00 1.63
478 487 1.754803 GGACCATGGACTGTGACGATA 59.245 52.381 21.47 0.00 0.00 2.92
479 488 0.537188 GGACCATGGACTGTGACGAT 59.463 55.000 21.47 0.00 0.00 3.73
480 489 0.830023 TGGACCATGGACTGTGACGA 60.830 55.000 21.47 0.00 0.00 4.20
521 531 1.235281 GCTTGTGTTTCCGTCCTCCC 61.235 60.000 0.00 0.00 0.00 4.30
559 570 0.038251 TGACCTCATCACACGTGCTC 60.038 55.000 17.22 0.00 29.99 4.26
572 583 1.407258 CTCGTCCATCCTCTTGACCTC 59.593 57.143 0.00 0.00 0.00 3.85
589 600 1.878522 CGGGCGATCTTTGGTCTCG 60.879 63.158 0.00 0.00 35.57 4.04
638 649 2.594321 CGATCGAGAGGAATCATCTGC 58.406 52.381 10.26 0.00 0.00 4.26
639 650 2.594321 GCGATCGAGAGGAATCATCTG 58.406 52.381 21.57 0.00 0.00 2.90
714 739 2.097444 GCCACGCATTCAAAAAGAAACG 60.097 45.455 0.00 0.00 42.30 3.60
744 770 1.480137 CTTGGTGCACCCTTTTGTGAA 59.520 47.619 32.62 16.26 38.55 3.18
760 786 5.303971 AGTGTTTCTCTGATCACTTCTTGG 58.696 41.667 0.00 0.00 37.81 3.61
775 802 2.552315 CCACGTGCCATAAAGTGTTTCT 59.448 45.455 10.91 0.00 33.14 2.52
780 807 4.491234 TTTTACCACGTGCCATAAAGTG 57.509 40.909 10.91 0.00 0.00 3.16
782 809 6.386654 AGAATTTTTACCACGTGCCATAAAG 58.613 36.000 10.91 0.00 0.00 1.85
783 810 6.334102 AGAATTTTTACCACGTGCCATAAA 57.666 33.333 10.91 11.34 0.00 1.40
809 838 5.688176 GTCTACTATTTCTGACTCAATCCGC 59.312 44.000 0.00 0.00 0.00 5.54
846 875 2.413453 GACTCTGACCGTGCAAAATCTC 59.587 50.000 0.00 0.00 0.00 2.75
849 878 2.146342 CAGACTCTGACCGTGCAAAAT 58.854 47.619 0.00 0.00 32.44 1.82
894 990 3.037485 GCTCCTTGCAGTCGTAGTC 57.963 57.895 0.00 0.00 42.31 2.59
919 1015 1.807142 GCTTGACGGGAAAGAAGAAGG 59.193 52.381 0.00 0.00 0.00 3.46
1008 1115 4.105486 GTGTCTTGTTTGAAAACTGGAGC 58.895 43.478 7.39 0.00 39.59 4.70
1080 1199 1.138661 GTGAGAGAGGCCAAGGAGATG 59.861 57.143 5.01 0.00 0.00 2.90
1157 1276 2.338620 CGAGTCCACCGTCTTGCA 59.661 61.111 0.00 0.00 0.00 4.08
1170 1289 2.348620 TGCCATGAAGCAGCGAGT 59.651 55.556 0.00 0.00 38.00 4.18
1249 1371 3.367703 CCCTTAAAAGGCAGCAAGACATG 60.368 47.826 3.03 0.00 45.10 3.21
1265 1387 1.591768 AATTCCCTCGAGGCCCTTAA 58.408 50.000 26.87 13.82 34.51 1.85
1309 1431 2.362120 AAGGTGCTGCAGCCCATC 60.362 61.111 33.78 21.18 41.18 3.51
1310 1432 2.509931 ATCAAGGTGCTGCAGCCCAT 62.510 55.000 33.78 25.43 41.18 4.00
1355 1477 0.523072 CACCAATTCCAACGGCAGAG 59.477 55.000 0.00 0.00 0.00 3.35
1517 1642 0.809385 GACCAGATTCTCCGTCGTGA 59.191 55.000 0.00 0.00 0.00 4.35
1521 1646 1.546476 AGTGTGACCAGATTCTCCGTC 59.454 52.381 4.22 4.22 0.00 4.79
1522 1647 1.546476 GAGTGTGACCAGATTCTCCGT 59.454 52.381 0.00 0.00 0.00 4.69
1523 1648 1.546029 TGAGTGTGACCAGATTCTCCG 59.454 52.381 0.00 0.00 0.00 4.63
1570 1704 6.919775 ACTACAGAGTTGAGTTGGTATCTT 57.080 37.500 0.00 0.00 28.61 2.40
1738 1872 5.012664 ACAGGTACTCCAATGATGTTGTGTA 59.987 40.000 0.00 0.00 34.60 2.90
1741 1875 4.041567 TGACAGGTACTCCAATGATGTTGT 59.958 41.667 0.00 0.00 34.60 3.32
1776 1910 4.564372 CCATCGATAGCTCCATGTAAATCG 59.436 45.833 0.00 5.15 38.00 3.34
1918 2124 2.154462 CTCCCCTGACATGTTGTTGTC 58.846 52.381 0.00 0.00 45.05 3.18
2028 2234 3.537337 TCTTAGATTGGGAAGGTGGGAA 58.463 45.455 0.00 0.00 0.00 3.97
2094 2300 5.930569 CAGATTGCTGCAAGAGTATATGCTA 59.069 40.000 20.72 0.00 42.97 3.49
2174 2380 4.020218 TGAAGGTGAGGTACTTCAGATTGG 60.020 45.833 8.10 0.00 45.76 3.16
2382 2588 6.460123 GCTTTGATATCCAGTGTGGTATTTGG 60.460 42.308 0.00 0.00 39.03 3.28
2391 2597 5.957771 TTCCTAGCTTTGATATCCAGTGT 57.042 39.130 0.00 0.00 0.00 3.55
2445 2651 1.678101 GCTGGTATTGACCCATTGAGC 59.322 52.381 0.00 0.00 46.32 4.26
2895 3101 1.546029 GGCCCTTTGAGGTCATTGTTC 59.454 52.381 0.00 0.00 31.93 3.18
2974 3180 2.414824 CGAGTACAGAACCACAGAGCTC 60.415 54.545 5.27 5.27 0.00 4.09
3201 3419 8.429641 ACTAATGTTTTCTCTGAACTGGAGTAA 58.570 33.333 0.00 0.00 33.06 2.24
3379 3597 4.819769 TCATGGAGCTTTTTAATTGCCAC 58.180 39.130 0.00 0.00 0.00 5.01
3455 3673 5.851177 GGTACAAGATTTTGATGTTGTGTCG 59.149 40.000 10.92 0.00 38.31 4.35
3861 4082 5.821516 AGACTACTCCGAAACTGTAGATG 57.178 43.478 0.00 0.00 37.62 2.90
4003 4224 2.787473 TCATTTCCTGTGCCTCGAAT 57.213 45.000 0.00 0.00 0.00 3.34
4134 4355 8.114927 ATCATGACTGATCTTTGCATCTGTGC 62.115 42.308 0.00 0.00 44.00 4.57
4273 4527 4.883083 TCTGTTAGGCTCTGTACAAAGTG 58.117 43.478 0.00 0.00 0.00 3.16
4297 4552 7.284489 TCTGTACAAAGTAAAAGACAAATGGCT 59.716 33.333 0.00 0.00 32.33 4.75
4298 4553 7.422399 TCTGTACAAAGTAAAAGACAAATGGC 58.578 34.615 0.00 0.00 0.00 4.40
4299 4554 7.591426 GCTCTGTACAAAGTAAAAGACAAATGG 59.409 37.037 0.00 0.00 0.00 3.16
4300 4555 7.591426 GGCTCTGTACAAAGTAAAAGACAAATG 59.409 37.037 0.00 0.00 0.00 2.32
4301 4556 7.502561 AGGCTCTGTACAAAGTAAAAGACAAAT 59.497 33.333 0.00 0.00 0.00 2.32
4302 4557 6.826741 AGGCTCTGTACAAAGTAAAAGACAAA 59.173 34.615 0.00 0.00 0.00 2.83
4303 4558 6.354130 AGGCTCTGTACAAAGTAAAAGACAA 58.646 36.000 0.00 0.00 0.00 3.18
4304 4559 5.925509 AGGCTCTGTACAAAGTAAAAGACA 58.074 37.500 0.00 0.00 0.00 3.41
4305 4560 7.440255 TGTTAGGCTCTGTACAAAGTAAAAGAC 59.560 37.037 0.00 0.00 0.00 3.01
4306 4561 7.502696 TGTTAGGCTCTGTACAAAGTAAAAGA 58.497 34.615 0.00 0.00 0.00 2.52
4307 4562 7.656137 TCTGTTAGGCTCTGTACAAAGTAAAAG 59.344 37.037 0.00 0.00 0.00 2.27
4308 4563 7.502696 TCTGTTAGGCTCTGTACAAAGTAAAA 58.497 34.615 0.00 0.00 0.00 1.52
4309 4564 7.058023 TCTGTTAGGCTCTGTACAAAGTAAA 57.942 36.000 0.00 0.00 0.00 2.01
4310 4565 6.659745 TCTGTTAGGCTCTGTACAAAGTAA 57.340 37.500 0.00 0.00 0.00 2.24
4311 4566 6.852420 ATCTGTTAGGCTCTGTACAAAGTA 57.148 37.500 0.00 0.00 0.00 2.24
4312 4567 5.746990 ATCTGTTAGGCTCTGTACAAAGT 57.253 39.130 0.00 0.00 0.00 2.66
4313 4568 5.751028 GCTATCTGTTAGGCTCTGTACAAAG 59.249 44.000 0.00 0.00 0.00 2.77
4314 4569 5.661458 GCTATCTGTTAGGCTCTGTACAAA 58.339 41.667 0.00 0.00 0.00 2.83
4315 4570 5.263968 GCTATCTGTTAGGCTCTGTACAA 57.736 43.478 0.00 0.00 0.00 2.41
4316 4571 4.920640 GCTATCTGTTAGGCTCTGTACA 57.079 45.455 0.00 0.00 0.00 2.90
4325 4580 7.396540 AAAAGACAAATGGCTATCTGTTAGG 57.603 36.000 0.00 0.00 29.55 2.69
4326 4581 9.167311 AGTAAAAGACAAATGGCTATCTGTTAG 57.833 33.333 0.00 0.00 29.55 2.34
4327 4582 9.515226 AAGTAAAAGACAAATGGCTATCTGTTA 57.485 29.630 0.00 0.00 29.55 2.41
4328 4583 8.409358 AAGTAAAAGACAAATGGCTATCTGTT 57.591 30.769 0.00 0.00 29.55 3.16
4329 4584 8.299570 CAAAGTAAAAGACAAATGGCTATCTGT 58.700 33.333 0.00 0.00 29.55 3.41
4330 4585 8.299570 ACAAAGTAAAAGACAAATGGCTATCTG 58.700 33.333 0.00 0.00 29.55 2.90
4331 4586 8.409358 ACAAAGTAAAAGACAAATGGCTATCT 57.591 30.769 0.00 0.00 29.55 1.98
4332 4587 9.556030 GTACAAAGTAAAAGACAAATGGCTATC 57.444 33.333 0.00 0.00 29.55 2.08
4333 4588 9.073475 TGTACAAAGTAAAAGACAAATGGCTAT 57.927 29.630 0.00 0.00 29.55 2.97
4334 4589 8.453238 TGTACAAAGTAAAAGACAAATGGCTA 57.547 30.769 0.00 0.00 29.55 3.93
4335 4590 7.284489 TCTGTACAAAGTAAAAGACAAATGGCT 59.716 33.333 0.00 0.00 32.33 4.75
4336 4591 7.422399 TCTGTACAAAGTAAAAGACAAATGGC 58.578 34.615 0.00 0.00 0.00 4.40
4337 4592 7.591426 GCTCTGTACAAAGTAAAAGACAAATGG 59.409 37.037 0.00 0.00 0.00 3.16
4338 4593 7.591426 GGCTCTGTACAAAGTAAAAGACAAATG 59.409 37.037 0.00 0.00 0.00 2.32
4339 4594 7.502561 AGGCTCTGTACAAAGTAAAAGACAAAT 59.497 33.333 0.00 0.00 0.00 2.32
4340 4595 6.826741 AGGCTCTGTACAAAGTAAAAGACAAA 59.173 34.615 0.00 0.00 0.00 2.83
4341 4596 6.354130 AGGCTCTGTACAAAGTAAAAGACAA 58.646 36.000 0.00 0.00 0.00 3.18
4342 4597 5.925509 AGGCTCTGTACAAAGTAAAAGACA 58.074 37.500 0.00 0.00 0.00 3.41
4343 4598 7.440255 TGTTAGGCTCTGTACAAAGTAAAAGAC 59.560 37.037 0.00 0.00 0.00 3.01
4344 4599 7.502696 TGTTAGGCTCTGTACAAAGTAAAAGA 58.497 34.615 0.00 0.00 0.00 2.52
4345 4600 7.656137 TCTGTTAGGCTCTGTACAAAGTAAAAG 59.344 37.037 0.00 0.00 0.00 2.27
4346 4601 7.502696 TCTGTTAGGCTCTGTACAAAGTAAAA 58.497 34.615 0.00 0.00 0.00 1.52
4347 4602 7.058023 TCTGTTAGGCTCTGTACAAAGTAAA 57.942 36.000 0.00 0.00 0.00 2.01
4348 4603 6.659745 TCTGTTAGGCTCTGTACAAAGTAA 57.340 37.500 0.00 0.00 0.00 2.24
4349 4604 6.852420 ATCTGTTAGGCTCTGTACAAAGTA 57.148 37.500 0.00 0.00 0.00 2.24
4350 4605 5.746990 ATCTGTTAGGCTCTGTACAAAGT 57.253 39.130 0.00 0.00 0.00 2.66
4351 4606 5.751028 GCTATCTGTTAGGCTCTGTACAAAG 59.249 44.000 0.00 0.00 0.00 2.77
4352 4607 5.661458 GCTATCTGTTAGGCTCTGTACAAA 58.339 41.667 0.00 0.00 0.00 2.83
4353 4608 5.263968 GCTATCTGTTAGGCTCTGTACAA 57.736 43.478 0.00 0.00 0.00 2.41
4354 4609 4.920640 GCTATCTGTTAGGCTCTGTACA 57.079 45.455 0.00 0.00 0.00 2.90
4363 4618 7.396540 AAAAGACAAATGGCTATCTGTTAGG 57.603 36.000 0.00 0.00 29.55 2.69
4364 4619 9.167311 AGTAAAAGACAAATGGCTATCTGTTAG 57.833 33.333 0.00 0.00 29.55 2.34
4365 4620 9.515226 AAGTAAAAGACAAATGGCTATCTGTTA 57.485 29.630 0.00 0.00 29.55 2.41
4366 4621 8.409358 AAGTAAAAGACAAATGGCTATCTGTT 57.591 30.769 0.00 0.00 29.55 3.16
4367 4622 8.299570 CAAAGTAAAAGACAAATGGCTATCTGT 58.700 33.333 0.00 0.00 29.55 3.41
4368 4623 8.299570 ACAAAGTAAAAGACAAATGGCTATCTG 58.700 33.333 0.00 0.00 29.55 2.90
4369 4624 8.409358 ACAAAGTAAAAGACAAATGGCTATCT 57.591 30.769 0.00 0.00 29.55 1.98
4370 4625 9.556030 GTACAAAGTAAAAGACAAATGGCTATC 57.444 33.333 0.00 0.00 29.55 2.08
4371 4626 9.073475 TGTACAAAGTAAAAGACAAATGGCTAT 57.927 29.630 0.00 0.00 29.55 2.97
4372 4627 8.453238 TGTACAAAGTAAAAGACAAATGGCTA 57.547 30.769 0.00 0.00 29.55 3.93
4373 4628 7.284489 TCTGTACAAAGTAAAAGACAAATGGCT 59.716 33.333 0.00 0.00 32.33 4.75
4374 4629 7.422399 TCTGTACAAAGTAAAAGACAAATGGC 58.578 34.615 0.00 0.00 0.00 4.40
4375 4630 7.591426 GCTCTGTACAAAGTAAAAGACAAATGG 59.409 37.037 0.00 0.00 0.00 3.16
4376 4631 7.591426 GGCTCTGTACAAAGTAAAAGACAAATG 59.409 37.037 0.00 0.00 0.00 2.32
4377 4632 7.284489 TGGCTCTGTACAAAGTAAAAGACAAAT 59.716 33.333 0.00 0.00 0.00 2.32
4378 4633 6.600032 TGGCTCTGTACAAAGTAAAAGACAAA 59.400 34.615 0.00 0.00 0.00 2.83
4379 4634 6.116806 TGGCTCTGTACAAAGTAAAAGACAA 58.883 36.000 0.00 0.00 0.00 3.18
4380 4635 5.676552 TGGCTCTGTACAAAGTAAAAGACA 58.323 37.500 0.00 0.00 0.00 3.41
4381 4636 6.613755 TTGGCTCTGTACAAAGTAAAAGAC 57.386 37.500 0.00 0.00 0.00 3.01
4382 4637 6.600032 TGTTTGGCTCTGTACAAAGTAAAAGA 59.400 34.615 0.00 0.00 37.27 2.52
4383 4638 6.791303 TGTTTGGCTCTGTACAAAGTAAAAG 58.209 36.000 0.00 0.00 37.27 2.27
4384 4639 6.600032 TCTGTTTGGCTCTGTACAAAGTAAAA 59.400 34.615 0.00 0.00 37.27 1.52
4385 4640 6.116806 TCTGTTTGGCTCTGTACAAAGTAAA 58.883 36.000 0.00 0.00 37.27 2.01
4386 4641 5.676552 TCTGTTTGGCTCTGTACAAAGTAA 58.323 37.500 0.00 0.00 37.27 2.24
4387 4642 5.284861 TCTGTTTGGCTCTGTACAAAGTA 57.715 39.130 0.00 0.00 37.27 2.24
4388 4643 4.150897 TCTGTTTGGCTCTGTACAAAGT 57.849 40.909 0.00 0.00 37.27 2.66
4389 4644 5.455392 CAATCTGTTTGGCTCTGTACAAAG 58.545 41.667 0.00 0.00 37.27 2.77
4390 4645 4.261572 GCAATCTGTTTGGCTCTGTACAAA 60.262 41.667 0.00 0.00 35.75 2.83
4391 4646 3.253188 GCAATCTGTTTGGCTCTGTACAA 59.747 43.478 0.00 0.00 35.75 2.41
4392 4647 2.813754 GCAATCTGTTTGGCTCTGTACA 59.186 45.455 0.00 0.00 35.75 2.90
4393 4648 3.477899 GCAATCTGTTTGGCTCTGTAC 57.522 47.619 1.08 0.00 35.75 2.90
4401 4656 3.434299 GCTCAAAATGGCAATCTGTTTGG 59.566 43.478 0.00 0.00 35.75 3.28
4402 4657 4.312443 AGCTCAAAATGGCAATCTGTTTG 58.688 39.130 0.00 0.00 38.43 2.93
4403 4658 4.612264 AGCTCAAAATGGCAATCTGTTT 57.388 36.364 0.00 0.00 0.00 2.83
4404 4659 5.927281 ATAGCTCAAAATGGCAATCTGTT 57.073 34.783 0.00 0.00 0.00 3.16
4405 4660 5.008019 CGTATAGCTCAAAATGGCAATCTGT 59.992 40.000 0.00 0.00 0.00 3.41
4406 4661 5.008019 ACGTATAGCTCAAAATGGCAATCTG 59.992 40.000 0.00 0.00 0.00 2.90
4407 4662 5.126067 ACGTATAGCTCAAAATGGCAATCT 58.874 37.500 0.00 0.00 0.00 2.40
4408 4663 5.424121 ACGTATAGCTCAAAATGGCAATC 57.576 39.130 0.00 0.00 0.00 2.67
4409 4664 6.055588 AGTACGTATAGCTCAAAATGGCAAT 58.944 36.000 0.00 0.00 0.00 3.56
4410 4665 5.424757 AGTACGTATAGCTCAAAATGGCAA 58.575 37.500 0.00 0.00 0.00 4.52
4581 5029 5.827797 TCTTTCACAGCTAAAACAAGATGGT 59.172 36.000 0.00 0.00 37.20 3.55
4636 5126 0.881118 AAACAGCTGGCGTTACATGG 59.119 50.000 19.93 0.00 0.00 3.66
4644 5136 2.486203 TGGTATGTAAAAACAGCTGGCG 59.514 45.455 19.93 0.00 0.00 5.69
4646 5138 3.119990 CGGTGGTATGTAAAAACAGCTGG 60.120 47.826 19.93 0.00 0.00 4.85
4715 5207 8.103935 AGAAACATTTAAAGGTTCCCACAAAAA 58.896 29.630 17.68 0.00 30.85 1.94
4758 5250 7.023575 GTGTATCCATGCTTGTGAAACTTAAG 58.976 38.462 0.00 0.00 38.04 1.85
4803 5332 6.466885 TTTTCAACCTTCCACGGATAAAAA 57.533 33.333 0.00 0.00 0.00 1.94
4811 5340 2.884639 AGTCCATTTTCAACCTTCCACG 59.115 45.455 0.00 0.00 0.00 4.94
4868 5397 3.045601 ACAGCTGATACGAAGCAAACT 57.954 42.857 23.35 0.00 43.37 2.66
4869 5398 3.813529 AACAGCTGATACGAAGCAAAC 57.186 42.857 23.35 0.00 43.37 2.93
4870 5399 4.829064 AAAACAGCTGATACGAAGCAAA 57.171 36.364 23.35 0.00 43.37 3.68
4901 5430 3.071479 GGTAATTCACCGCAAACTCTGA 58.929 45.455 0.00 0.00 37.63 3.27
4929 5458 4.440525 CCAACCAAACATTGCCATAGCTAG 60.441 45.833 0.00 0.00 40.80 3.42
4930 5459 3.446873 CCAACCAAACATTGCCATAGCTA 59.553 43.478 0.00 0.00 40.80 3.32
4931 5460 2.234414 CCAACCAAACATTGCCATAGCT 59.766 45.455 0.00 0.00 40.80 3.32
4932 5461 2.028203 ACCAACCAAACATTGCCATAGC 60.028 45.455 0.00 0.00 40.48 2.97
4933 5462 3.368323 GGACCAACCAAACATTGCCATAG 60.368 47.826 0.00 0.00 38.79 2.23
4934 5463 2.564947 GGACCAACCAAACATTGCCATA 59.435 45.455 0.00 0.00 38.79 2.74
4935 5464 1.347378 GGACCAACCAAACATTGCCAT 59.653 47.619 0.00 0.00 38.79 4.40
4936 5465 0.755686 GGACCAACCAAACATTGCCA 59.244 50.000 0.00 0.00 38.79 4.92
4937 5466 0.755686 TGGACCAACCAAACATTGCC 59.244 50.000 0.00 0.00 46.75 4.52
4945 5474 6.043012 ATTCATTTGAATCTTGGACCAACCAA 59.957 34.615 1.69 3.01 46.65 3.67
4947 5476 5.467035 TTCATTTGAATCTTGGACCAACC 57.533 39.130 1.69 0.00 39.54 3.77
4948 5477 7.116805 GTCAATTCATTTGAATCTTGGACCAAC 59.883 37.037 1.69 0.00 45.71 3.77
4949 5478 7.153985 GTCAATTCATTTGAATCTTGGACCAA 58.846 34.615 6.76 6.76 45.71 3.67
4950 5479 6.295236 GGTCAATTCATTTGAATCTTGGACCA 60.295 38.462 23.79 0.00 45.71 4.02
4951 5480 6.101997 GGTCAATTCATTTGAATCTTGGACC 58.898 40.000 19.31 19.31 45.71 4.46
4952 5481 6.690530 TGGTCAATTCATTTGAATCTTGGAC 58.309 36.000 6.27 10.75 45.71 4.02
4953 5482 6.071221 CCTGGTCAATTCATTTGAATCTTGGA 60.071 38.462 6.27 0.98 45.71 3.53
4959 5498 8.377034 TCAATTTCCTGGTCAATTCATTTGAAT 58.623 29.630 0.00 0.00 45.71 2.57
4977 5516 6.501781 CAGTTGCATTAGATCCTCAATTTCC 58.498 40.000 0.00 0.00 0.00 3.13
4995 5534 2.070783 CATTTTGACCATGGCAGTTGC 58.929 47.619 13.04 0.00 41.14 4.17
4997 5536 5.714333 TGTATACATTTTGACCATGGCAGTT 59.286 36.000 13.04 0.00 0.00 3.16
5006 5545 7.065324 TCCATTCGACTTGTATACATTTTGACC 59.935 37.037 6.36 0.00 0.00 4.02
5007 5546 7.970384 TCCATTCGACTTGTATACATTTTGAC 58.030 34.615 6.36 0.00 0.00 3.18
5008 5547 7.822334 ACTCCATTCGACTTGTATACATTTTGA 59.178 33.333 6.36 3.47 0.00 2.69
5065 5613 7.492669 TGAGTTATATGTGTTTCAGAAGCTAGC 59.507 37.037 6.62 6.62 0.00 3.42
5118 5666 1.363744 CATTCCTCTCGTGTTCTGCC 58.636 55.000 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.