Multiple sequence alignment - TraesCS5D01G498700

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 TraesCS5D01G498700 chr5D 100.000 3100 0 0 787 3886 528414954 528418053 0.000000e+00 5725.0
1 TraesCS5D01G498700 chr5D 94.569 2044 67 20 787 2821 528586940 528588948 0.000000e+00 3120.0
2 TraesCS5D01G498700 chr5D 89.657 1721 157 18 1070 2781 528296423 528294715 0.000000e+00 2172.0
3 TraesCS5D01G498700 chr5D 100.000 350 0 0 1 350 528414168 528414517 0.000000e+00 647.0
4 TraesCS5D01G498700 chr5D 84.236 203 13 4 2958 3144 528403469 528403668 3.080000e-41 180.0
5 TraesCS5D01G498700 chr5D 85.380 171 13 6 4 167 528586276 528586441 2.400000e-37 167.0
6 TraesCS5D01G498700 chr5D 86.667 105 11 3 3753 3857 398371362 398371463 3.170000e-21 113.0
7 TraesCS5D01G498700 chr5D 89.610 77 7 1 161 237 71884484 71884559 3.200000e-16 97.1
8 TraesCS5D01G498700 chr5D 94.340 53 3 0 166 218 565813368 565813420 8.950000e-12 82.4
9 TraesCS5D01G498700 chr5D 77.333 150 24 10 3737 3881 27805952 27805808 3.220000e-11 80.5
10 TraesCS5D01G498700 chr5D 97.059 34 1 0 3041 3074 528425219 528425252 1.510000e-04 58.4
11 TraesCS5D01G498700 chr5B 96.485 2020 60 6 802 2821 665539481 665541489 0.000000e+00 3326.0
12 TraesCS5D01G498700 chr5B 93.944 2163 90 18 805 2962 665173457 665171331 0.000000e+00 3230.0
13 TraesCS5D01G498700 chr5B 89.159 1725 161 18 1070 2781 665026437 665024726 0.000000e+00 2126.0
14 TraesCS5D01G498700 chr5B 95.189 291 13 1 2958 3247 665171302 665171012 3.540000e-125 459.0
15 TraesCS5D01G498700 chr5B 86.916 321 30 8 3570 3886 665170735 665170423 2.220000e-92 350.0
16 TraesCS5D01G498700 chr5B 94.152 171 10 0 3241 3411 93472268 93472098 1.070000e-65 261.0
17 TraesCS5D01G498700 chr5B 93.491 169 9 2 3407 3575 665171012 665170846 2.320000e-62 250.0
18 TraesCS5D01G498700 chr5B 84.236 203 13 4 2958 3144 665207314 665207115 3.080000e-41 180.0
19 TraesCS5D01G498700 chr5B 83.740 123 17 2 3760 3881 616730785 616730665 3.170000e-21 113.0
20 TraesCS5D01G498700 chr5A 93.822 2169 112 15 802 2962 656493954 656496108 0.000000e+00 3243.0
21 TraesCS5D01G498700 chr5A 94.874 2029 88 12 802 2821 656670815 656672836 0.000000e+00 3157.0
22 TraesCS5D01G498700 chr5A 90.082 1714 150 10 1070 2781 656222598 656220903 0.000000e+00 2206.0
23 TraesCS5D01G498700 chr5A 91.988 337 21 4 3407 3738 656530790 656531125 5.880000e-128 468.0
24 TraesCS5D01G498700 chr5A 84.236 203 13 4 2958 3144 656468453 656468652 3.080000e-41 180.0
25 TraesCS5D01G498700 chr5A 91.818 110 6 2 2982 3088 656530587 656530696 2.420000e-32 150.0
26 TraesCS5D01G498700 chr5A 94.667 75 3 1 3169 3242 656530714 656530788 8.820000e-22 115.0
27 TraesCS5D01G498700 chr7B 86.878 442 53 4 1637 2074 706991894 706991454 1.250000e-134 490.0
28 TraesCS5D01G498700 chr7B 84.466 103 13 3 160 260 743918491 743918592 8.890000e-17 99.0
29 TraesCS5D01G498700 chr7B 84.466 103 13 3 160 260 743963767 743963868 8.890000e-17 99.0
30 TraesCS5D01G498700 chr2D 81.015 611 50 20 1637 2235 645597822 645598378 3.590000e-115 425.0
31 TraesCS5D01G498700 chr6D 94.118 170 10 0 3242 3411 260024676 260024507 3.850000e-65 259.0
32 TraesCS5D01G498700 chr6A 94.118 170 10 0 3242 3411 370675438 370675607 3.850000e-65 259.0
33 TraesCS5D01G498700 chr6A 90.860 186 15 2 3244 3428 60016873 60016689 8.340000e-62 248.0
34 TraesCS5D01G498700 chr4B 94.048 168 10 0 3244 3411 575778321 575778154 4.980000e-64 255.0
35 TraesCS5D01G498700 chr4B 86.667 105 11 3 3753 3857 519408657 519408758 3.170000e-21 113.0
36 TraesCS5D01G498700 chr3B 93.567 171 11 0 3242 3412 778386309 778386479 4.980000e-64 255.0
37 TraesCS5D01G498700 chr3B 89.062 192 20 1 3220 3410 176100732 176100923 1.800000e-58 237.0
38 TraesCS5D01G498700 chr3B 89.831 59 6 0 2439 2497 537434386 537434328 4.160000e-10 76.8
39 TraesCS5D01G498700 chr4A 92.529 174 11 2 3239 3410 346686824 346686997 8.340000e-62 248.0
40 TraesCS5D01G498700 chr4D 91.160 181 14 2 3235 3415 75782045 75782223 1.080000e-60 244.0
41 TraesCS5D01G498700 chr3D 91.304 92 7 1 3416 3506 160622959 160622868 1.470000e-24 124.0
42 TraesCS5D01G498700 chr3D 85.714 105 14 1 3753 3857 495686649 495686546 4.100000e-20 110.0
43 TraesCS5D01G498700 chr1D 85.088 114 14 3 3753 3866 339297501 339297391 3.170000e-21 113.0
44 TraesCS5D01G498700 chr1D 88.298 94 9 2 3753 3845 211662041 211661949 1.140000e-20 111.0
45 TraesCS5D01G498700 chr6B 83.333 114 15 4 3763 3874 647174071 647174182 6.870000e-18 102.0
46 TraesCS5D01G498700 chr7D 82.301 113 16 4 3754 3866 115084321 115084213 1.150000e-15 95.3
47 TraesCS5D01G498700 chr7D 95.122 41 2 0 3409 3449 19770045 19770085 9.010000e-07 65.8
48 TraesCS5D01G498700 chr7D 95.122 41 2 0 3409 3449 19831507 19831547 9.010000e-07 65.8
49 TraesCS5D01G498700 chr7D 95.122 41 2 0 3409 3449 19903521 19903561 9.010000e-07 65.8
50 TraesCS5D01G498700 chr7D 95.122 41 2 0 3409 3449 19920723 19920763 9.010000e-07 65.8
51 TraesCS5D01G498700 chr7D 92.683 41 3 0 3409 3449 19848228 19848268 4.190000e-05 60.2
52 TraesCS5D01G498700 chr3A 82.524 103 14 4 1394 1494 32426561 32426661 1.920000e-13 87.9


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G498700 chr5D 528414168 528418053 3885 False 3186.000000 5725 100.000000 1 3886 2 chr5D.!!$F6 3885
1 TraesCS5D01G498700 chr5D 528294715 528296423 1708 True 2172.000000 2172 89.657000 1070 2781 1 chr5D.!!$R2 1711
2 TraesCS5D01G498700 chr5D 528586276 528588948 2672 False 1643.500000 3120 89.974500 4 2821 2 chr5D.!!$F7 2817
3 TraesCS5D01G498700 chr5B 665539481 665541489 2008 False 3326.000000 3326 96.485000 802 2821 1 chr5B.!!$F1 2019
4 TraesCS5D01G498700 chr5B 665024726 665026437 1711 True 2126.000000 2126 89.159000 1070 2781 1 chr5B.!!$R3 1711
5 TraesCS5D01G498700 chr5B 665170423 665173457 3034 True 1072.250000 3230 92.385000 805 3886 4 chr5B.!!$R5 3081
6 TraesCS5D01G498700 chr5A 656493954 656496108 2154 False 3243.000000 3243 93.822000 802 2962 1 chr5A.!!$F2 2160
7 TraesCS5D01G498700 chr5A 656670815 656672836 2021 False 3157.000000 3157 94.874000 802 2821 1 chr5A.!!$F3 2019
8 TraesCS5D01G498700 chr5A 656220903 656222598 1695 True 2206.000000 2206 90.082000 1070 2781 1 chr5A.!!$R1 1711
9 TraesCS5D01G498700 chr5A 656530587 656531125 538 False 244.333333 468 92.824333 2982 3738 3 chr5A.!!$F4 756
10 TraesCS5D01G498700 chr2D 645597822 645598378 556 False 425.000000 425 81.015000 1637 2235 1 chr2D.!!$F1 598

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
183 191 0.107508 TGGCAGAGCTATGTTGAGGC 60.108 55.000 10.55 0.0 0.0 4.70 F
185 193 0.107508 GCAGAGCTATGTTGAGGCCA 60.108 55.000 10.55 0.0 0.0 5.36 F
309 317 0.171231 GATTTGTCTTTCGCCCCAGC 59.829 55.000 0.00 0.0 0.0 4.85 F
916 1111 1.172812 GCCTCACACCAAGAACCACC 61.173 60.000 0.00 0.0 0.0 4.61 F
1469 1705 1.748122 GCTCCTCTCCACCGTCGTA 60.748 63.158 0.00 0.0 0.0 3.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1469 1705 1.528776 GACGAGGCCGAGGAGGTAT 60.529 63.158 0.00 0.00 43.70 2.73 R
1526 1762 4.314440 GGCACAGAGACACCGCCA 62.314 66.667 0.00 0.00 42.50 5.69 R
2258 2510 4.094646 ACGGTGGCGATCATGGCA 62.095 61.111 0.00 0.00 42.76 4.92 R
2821 3073 0.663568 CGGTCTATCGATGCCGGAAC 60.664 60.000 22.01 11.58 40.45 3.62 R
3395 3689 0.329596 ACCGTACTACTCCCTCCGTT 59.670 55.000 0.00 0.00 0.00 4.44 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
48 49 3.913089 TGCATATCATACTGCACGTAGG 58.087 45.455 0.00 0.00 43.11 3.18
49 50 2.668457 GCATATCATACTGCACGTAGGC 59.332 50.000 0.00 0.00 38.28 3.93
50 51 3.615110 GCATATCATACTGCACGTAGGCT 60.615 47.826 0.00 0.00 38.28 4.58
62 65 6.127535 ACTGCACGTAGGCTATTAAAGAAGTA 60.128 38.462 0.00 0.00 34.04 2.24
117 125 9.921637 AGATAGTACAAGCTATATCAAAGAAGC 57.078 33.333 0.00 0.00 32.32 3.86
144 152 9.243105 TGTATCTACACTAGATATGCTGCATTA 57.757 33.333 21.56 6.40 46.25 1.90
174 182 1.285078 TCTAGGTCAGTGGCAGAGCTA 59.715 52.381 13.08 13.08 43.07 3.32
175 183 2.091610 TCTAGGTCAGTGGCAGAGCTAT 60.092 50.000 13.84 0.00 42.95 2.97
178 186 1.065854 GGTCAGTGGCAGAGCTATGTT 60.066 52.381 10.55 0.00 0.00 2.71
179 187 2.005451 GTCAGTGGCAGAGCTATGTTG 58.995 52.381 10.55 4.35 0.00 3.33
181 189 2.093816 TCAGTGGCAGAGCTATGTTGAG 60.094 50.000 10.55 0.00 0.00 3.02
183 191 0.107508 TGGCAGAGCTATGTTGAGGC 60.108 55.000 10.55 0.00 0.00 4.70
185 193 0.107508 GCAGAGCTATGTTGAGGCCA 60.108 55.000 10.55 0.00 0.00 5.36
186 194 1.679944 GCAGAGCTATGTTGAGGCCAA 60.680 52.381 10.55 0.00 0.00 4.52
187 195 2.286872 CAGAGCTATGTTGAGGCCAAG 58.713 52.381 5.01 0.00 32.06 3.61
229 237 4.221482 GCCTTGGACCAATTTCTGAAGAAT 59.779 41.667 7.54 0.00 33.54 2.40
230 238 5.279657 GCCTTGGACCAATTTCTGAAGAATT 60.280 40.000 7.54 0.00 33.54 2.17
231 239 6.742363 GCCTTGGACCAATTTCTGAAGAATTT 60.742 38.462 7.54 0.00 33.54 1.82
279 287 2.849294 TTTTTACATTTGGCAGCCCC 57.151 45.000 9.64 0.00 0.00 5.80
280 288 1.722034 TTTTACATTTGGCAGCCCCA 58.278 45.000 9.64 0.00 43.51 4.96
288 296 2.203480 GGCAGCCCCAAACACTGA 60.203 61.111 0.00 0.00 33.10 3.41
290 298 1.588082 GCAGCCCCAAACACTGATG 59.412 57.895 0.00 0.00 33.10 3.07
293 301 2.173519 CAGCCCCAAACACTGATGATT 58.826 47.619 0.00 0.00 33.10 2.57
295 303 2.564062 AGCCCCAAACACTGATGATTTG 59.436 45.455 0.00 0.00 33.90 2.32
297 305 3.614870 GCCCCAAACACTGATGATTTGTC 60.615 47.826 0.00 0.00 32.53 3.18
298 306 3.828451 CCCCAAACACTGATGATTTGTCT 59.172 43.478 0.00 0.00 32.53 3.41
299 307 4.281688 CCCCAAACACTGATGATTTGTCTT 59.718 41.667 0.00 0.00 32.53 3.01
300 308 5.221501 CCCCAAACACTGATGATTTGTCTTT 60.222 40.000 0.00 0.00 32.53 2.52
301 309 5.922544 CCCAAACACTGATGATTTGTCTTTC 59.077 40.000 0.00 0.00 32.53 2.62
302 310 5.626543 CCAAACACTGATGATTTGTCTTTCG 59.373 40.000 0.00 0.00 32.53 3.46
304 312 3.189287 ACACTGATGATTTGTCTTTCGCC 59.811 43.478 0.00 0.00 0.00 5.54
305 313 2.749621 ACTGATGATTTGTCTTTCGCCC 59.250 45.455 0.00 0.00 0.00 6.13
306 314 2.091541 TGATGATTTGTCTTTCGCCCC 58.908 47.619 0.00 0.00 0.00 5.80
307 315 2.091541 GATGATTTGTCTTTCGCCCCA 58.908 47.619 0.00 0.00 0.00 4.96
308 316 1.533625 TGATTTGTCTTTCGCCCCAG 58.466 50.000 0.00 0.00 0.00 4.45
309 317 0.171231 GATTTGTCTTTCGCCCCAGC 59.829 55.000 0.00 0.00 0.00 4.85
312 320 2.436824 GTCTTTCGCCCCAGCTCC 60.437 66.667 0.00 0.00 36.60 4.70
313 321 3.717294 TCTTTCGCCCCAGCTCCC 61.717 66.667 0.00 0.00 36.60 4.30
314 322 4.803908 CTTTCGCCCCAGCTCCCC 62.804 72.222 0.00 0.00 36.60 4.81
337 526 3.761218 CACTCTCTAGGTGTGATGTGAGT 59.239 47.826 7.31 0.00 40.61 3.41
345 534 3.118261 AGGTGTGATGTGAGTGTGAGTTT 60.118 43.478 0.00 0.00 0.00 2.66
916 1111 1.172812 GCCTCACACCAAGAACCACC 61.173 60.000 0.00 0.00 0.00 4.61
989 1187 2.408565 TGGACTTTGGAGAGAGGTTGT 58.591 47.619 0.00 0.00 0.00 3.32
991 1189 3.142174 GGACTTTGGAGAGAGGTTGTTG 58.858 50.000 0.00 0.00 0.00 3.33
992 1190 3.181454 GGACTTTGGAGAGAGGTTGTTGA 60.181 47.826 0.00 0.00 0.00 3.18
993 1191 3.809905 ACTTTGGAGAGAGGTTGTTGAC 58.190 45.455 0.00 0.00 0.00 3.18
1204 1407 4.322650 GCCAGATCTCTCTGTCTTTGTCTT 60.323 45.833 0.00 0.00 46.33 3.01
1252 1488 3.500448 TGGCAGTTCTTGTTGTATGGA 57.500 42.857 0.00 0.00 0.00 3.41
1469 1705 1.748122 GCTCCTCTCCACCGTCGTA 60.748 63.158 0.00 0.00 0.00 3.43
2351 2603 2.121538 CGGGATCAGCGTCCTCAGA 61.122 63.158 0.00 0.00 38.38 3.27
2360 2612 3.197614 GTCCTCAGACGCATCGGA 58.802 61.111 0.00 0.00 32.18 4.55
2860 3112 2.984471 CGTACAATCACAAGTGCGTACT 59.016 45.455 0.00 0.00 38.69 2.73
2956 3213 0.817229 GGCCAGGCATTAGCAGAGAC 60.817 60.000 15.19 0.00 44.61 3.36
3089 3382 3.003394 TCAATGTTGCCGATTCATCCT 57.997 42.857 0.00 0.00 0.00 3.24
3130 3423 3.744530 GCTGTTCAACCTAGGTGTGAACT 60.745 47.826 36.78 18.33 39.44 3.01
3167 3460 2.971330 AGCATCTCTAACTCATCCCCTG 59.029 50.000 0.00 0.00 0.00 4.45
3172 3465 6.632672 GCATCTCTAACTCATCCCCTGTAAAA 60.633 42.308 0.00 0.00 0.00 1.52
3183 3476 4.637600 TCCCCTGTAAAATTAGAGCCCTA 58.362 43.478 0.00 0.00 0.00 3.53
3242 3536 7.721402 ACAGGAGTATATGTGCTCTTCTAAAG 58.279 38.462 7.45 0.00 37.27 1.85
3246 3540 8.852135 GGAGTATATGTGCTCTTCTAAAGTACT 58.148 37.037 7.45 0.00 37.27 2.73
3247 3541 9.887406 GAGTATATGTGCTCTTCTAAAGTACTC 57.113 37.037 0.00 0.00 34.62 2.59
3248 3542 8.852135 AGTATATGTGCTCTTCTAAAGTACTCC 58.148 37.037 0.00 0.00 31.49 3.85
3249 3543 4.803098 TGTGCTCTTCTAAAGTACTCCC 57.197 45.455 0.00 0.00 31.49 4.30
3250 3544 4.417437 TGTGCTCTTCTAAAGTACTCCCT 58.583 43.478 0.00 0.00 31.49 4.20
3251 3545 4.463186 TGTGCTCTTCTAAAGTACTCCCTC 59.537 45.833 0.00 0.00 31.49 4.30
3252 3546 4.024670 TGCTCTTCTAAAGTACTCCCTCC 58.975 47.826 0.00 0.00 0.00 4.30
3253 3547 3.067040 GCTCTTCTAAAGTACTCCCTCCG 59.933 52.174 0.00 0.00 0.00 4.63
3254 3548 4.271661 CTCTTCTAAAGTACTCCCTCCGT 58.728 47.826 0.00 0.00 0.00 4.69
3255 3549 4.670765 TCTTCTAAAGTACTCCCTCCGTT 58.329 43.478 0.00 0.00 0.00 4.44
3256 3550 4.704057 TCTTCTAAAGTACTCCCTCCGTTC 59.296 45.833 0.00 0.00 0.00 3.95
3257 3551 4.313020 TCTAAAGTACTCCCTCCGTTCT 57.687 45.455 0.00 0.00 0.00 3.01
3258 3552 4.268359 TCTAAAGTACTCCCTCCGTTCTC 58.732 47.826 0.00 0.00 0.00 2.87
3259 3553 2.599408 AAGTACTCCCTCCGTTCTCA 57.401 50.000 0.00 0.00 0.00 3.27
3260 3554 2.599408 AGTACTCCCTCCGTTCTCAA 57.401 50.000 0.00 0.00 0.00 3.02
3261 3555 2.885616 AGTACTCCCTCCGTTCTCAAA 58.114 47.619 0.00 0.00 0.00 2.69
3262 3556 3.442076 AGTACTCCCTCCGTTCTCAAAT 58.558 45.455 0.00 0.00 0.00 2.32
3263 3557 4.607239 AGTACTCCCTCCGTTCTCAAATA 58.393 43.478 0.00 0.00 0.00 1.40
3264 3558 5.209659 AGTACTCCCTCCGTTCTCAAATAT 58.790 41.667 0.00 0.00 0.00 1.28
3265 3559 5.661759 AGTACTCCCTCCGTTCTCAAATATT 59.338 40.000 0.00 0.00 0.00 1.28
3266 3560 5.437191 ACTCCCTCCGTTCTCAAATATTT 57.563 39.130 0.00 0.00 0.00 1.40
3267 3561 5.186198 ACTCCCTCCGTTCTCAAATATTTG 58.814 41.667 20.13 20.13 39.48 2.32
3268 3562 5.174037 TCCCTCCGTTCTCAAATATTTGT 57.826 39.130 23.95 0.00 39.18 2.83
3269 3563 5.183228 TCCCTCCGTTCTCAAATATTTGTC 58.817 41.667 23.95 13.65 39.18 3.18
3270 3564 5.045869 TCCCTCCGTTCTCAAATATTTGTCT 60.046 40.000 23.95 0.00 39.18 3.41
3271 3565 5.648092 CCCTCCGTTCTCAAATATTTGTCTT 59.352 40.000 23.95 0.00 39.18 3.01
3272 3566 6.151144 CCCTCCGTTCTCAAATATTTGTCTTT 59.849 38.462 23.95 0.00 39.18 2.52
3273 3567 7.244192 CCTCCGTTCTCAAATATTTGTCTTTC 58.756 38.462 23.95 12.84 39.18 2.62
3274 3568 7.119846 CCTCCGTTCTCAAATATTTGTCTTTCT 59.880 37.037 23.95 0.00 39.18 2.52
3275 3569 9.151471 CTCCGTTCTCAAATATTTGTCTTTCTA 57.849 33.333 23.95 5.84 39.18 2.10
3276 3570 9.151471 TCCGTTCTCAAATATTTGTCTTTCTAG 57.849 33.333 23.95 14.05 39.18 2.43
3277 3571 9.151471 CCGTTCTCAAATATTTGTCTTTCTAGA 57.849 33.333 23.95 15.80 39.18 2.43
3302 3596 9.485591 GACATTTTAAATGGACTACAACATACG 57.514 33.333 20.00 0.00 0.00 3.06
3303 3597 8.455682 ACATTTTAAATGGACTACAACATACGG 58.544 33.333 20.00 0.00 0.00 4.02
3304 3598 8.670135 CATTTTAAATGGACTACAACATACGGA 58.330 33.333 9.63 0.00 0.00 4.69
3305 3599 8.795842 TTTTAAATGGACTACAACATACGGAT 57.204 30.769 0.00 0.00 0.00 4.18
3306 3600 7.780008 TTAAATGGACTACAACATACGGATG 57.220 36.000 5.94 5.94 39.16 3.51
3308 3602 6.474140 AATGGACTACAACATACGGATGTA 57.526 37.500 15.10 0.00 45.93 2.29
3309 3603 6.665992 ATGGACTACAACATACGGATGTAT 57.334 37.500 15.10 8.21 45.93 2.29
3310 3604 7.770366 ATGGACTACAACATACGGATGTATA 57.230 36.000 15.10 8.98 45.93 1.47
3311 3605 7.770366 TGGACTACAACATACGGATGTATAT 57.230 36.000 15.10 5.13 45.93 0.86
3312 3606 7.599171 TGGACTACAACATACGGATGTATATG 58.401 38.462 15.10 11.56 45.93 1.78
3313 3607 7.033791 GGACTACAACATACGGATGTATATGG 58.966 42.308 15.10 7.14 45.93 2.74
3314 3608 7.094075 GGACTACAACATACGGATGTATATGGA 60.094 40.741 15.10 4.55 45.93 3.41
3315 3609 7.600065 ACTACAACATACGGATGTATATGGAC 58.400 38.462 15.10 0.00 45.93 4.02
3316 3610 6.413783 ACAACATACGGATGTATATGGACA 57.586 37.500 15.10 0.00 45.93 4.02
3317 3611 7.004555 ACAACATACGGATGTATATGGACAT 57.995 36.000 15.10 0.00 45.93 3.06
3318 3612 8.129496 ACAACATACGGATGTATATGGACATA 57.871 34.615 15.10 0.00 45.93 2.29
3319 3613 8.758829 ACAACATACGGATGTATATGGACATAT 58.241 33.333 15.10 9.53 45.93 1.78
3320 3614 9.599866 CAACATACGGATGTATATGGACATATT 57.400 33.333 15.10 0.00 45.93 1.28
3326 3620 9.219603 ACGGATGTATATGGACATATTTTCAAG 57.780 33.333 9.84 6.25 40.18 3.02
3327 3621 8.177663 CGGATGTATATGGACATATTTTCAAGC 58.822 37.037 9.84 5.45 40.18 4.01
3328 3622 8.177663 GGATGTATATGGACATATTTTCAAGCG 58.822 37.037 9.84 0.00 40.18 4.68
3329 3623 8.621532 ATGTATATGGACATATTTTCAAGCGT 57.378 30.769 9.84 0.00 38.29 5.07
3330 3624 9.719355 ATGTATATGGACATATTTTCAAGCGTA 57.281 29.630 9.84 0.00 38.29 4.42
3331 3625 9.203421 TGTATATGGACATATTTTCAAGCGTAG 57.797 33.333 9.84 0.00 35.71 3.51
3332 3626 9.419297 GTATATGGACATATTTTCAAGCGTAGA 57.581 33.333 9.84 0.00 35.71 2.59
3334 3628 7.807977 ATGGACATATTTTCAAGCGTAGATT 57.192 32.000 0.00 0.00 35.16 2.40
3335 3629 7.246674 TGGACATATTTTCAAGCGTAGATTC 57.753 36.000 0.00 0.00 27.80 2.52
3336 3630 6.821160 TGGACATATTTTCAAGCGTAGATTCA 59.179 34.615 0.00 0.00 27.80 2.57
3337 3631 7.126398 GGACATATTTTCAAGCGTAGATTCAC 58.874 38.462 0.00 0.00 27.80 3.18
3338 3632 7.011482 GGACATATTTTCAAGCGTAGATTCACT 59.989 37.037 0.00 0.00 27.80 3.41
3339 3633 7.910304 ACATATTTTCAAGCGTAGATTCACTC 58.090 34.615 0.00 0.00 27.80 3.51
3340 3634 7.549134 ACATATTTTCAAGCGTAGATTCACTCA 59.451 33.333 0.00 0.00 27.80 3.41
3341 3635 6.992063 ATTTTCAAGCGTAGATTCACTCAT 57.008 33.333 0.00 0.00 27.80 2.90
3342 3636 6.801539 TTTTCAAGCGTAGATTCACTCATT 57.198 33.333 0.00 0.00 27.80 2.57
3343 3637 6.801539 TTTCAAGCGTAGATTCACTCATTT 57.198 33.333 0.00 0.00 27.80 2.32
3344 3638 6.801539 TTCAAGCGTAGATTCACTCATTTT 57.198 33.333 0.00 0.00 27.80 1.82
3345 3639 6.169419 TCAAGCGTAGATTCACTCATTTTG 57.831 37.500 0.00 0.00 27.80 2.44
3346 3640 4.606457 AGCGTAGATTCACTCATTTTGC 57.394 40.909 0.00 0.00 0.00 3.68
3347 3641 4.256920 AGCGTAGATTCACTCATTTTGCT 58.743 39.130 0.00 0.00 0.00 3.91
3348 3642 4.697352 AGCGTAGATTCACTCATTTTGCTT 59.303 37.500 0.00 0.00 0.00 3.91
3349 3643 5.024555 GCGTAGATTCACTCATTTTGCTTC 58.975 41.667 0.00 0.00 0.00 3.86
3350 3644 5.251081 CGTAGATTCACTCATTTTGCTTCG 58.749 41.667 0.00 0.00 0.00 3.79
3351 3645 5.163953 CGTAGATTCACTCATTTTGCTTCGT 60.164 40.000 0.00 0.00 0.00 3.85
3352 3646 6.034577 CGTAGATTCACTCATTTTGCTTCGTA 59.965 38.462 0.00 0.00 0.00 3.43
3353 3647 6.992063 AGATTCACTCATTTTGCTTCGTAT 57.008 33.333 0.00 0.00 0.00 3.06
3354 3648 6.779117 AGATTCACTCATTTTGCTTCGTATG 58.221 36.000 0.00 0.00 0.00 2.39
3355 3649 5.940192 TTCACTCATTTTGCTTCGTATGT 57.060 34.783 0.00 0.00 0.00 2.29
3356 3650 7.549134 AGATTCACTCATTTTGCTTCGTATGTA 59.451 33.333 0.00 0.00 0.00 2.29
3357 3651 6.647212 TCACTCATTTTGCTTCGTATGTAG 57.353 37.500 0.00 0.00 0.00 2.74
3358 3652 6.163476 TCACTCATTTTGCTTCGTATGTAGT 58.837 36.000 0.00 0.00 0.00 2.73
3359 3653 6.310467 TCACTCATTTTGCTTCGTATGTAGTC 59.690 38.462 0.00 0.00 0.00 2.59
3360 3654 6.090763 CACTCATTTTGCTTCGTATGTAGTCA 59.909 38.462 0.00 0.00 0.00 3.41
3361 3655 6.090898 ACTCATTTTGCTTCGTATGTAGTCAC 59.909 38.462 0.00 0.00 0.00 3.67
3362 3656 6.163476 TCATTTTGCTTCGTATGTAGTCACT 58.837 36.000 0.00 0.00 0.00 3.41
3363 3657 6.649141 TCATTTTGCTTCGTATGTAGTCACTT 59.351 34.615 0.00 0.00 0.00 3.16
3364 3658 5.839262 TTTGCTTCGTATGTAGTCACTTG 57.161 39.130 0.00 0.00 0.00 3.16
3365 3659 4.514781 TGCTTCGTATGTAGTCACTTGT 57.485 40.909 0.00 0.00 0.00 3.16
3366 3660 4.878439 TGCTTCGTATGTAGTCACTTGTT 58.122 39.130 0.00 0.00 0.00 2.83
3367 3661 4.684242 TGCTTCGTATGTAGTCACTTGTTG 59.316 41.667 0.00 0.00 0.00 3.33
3368 3662 4.921515 GCTTCGTATGTAGTCACTTGTTGA 59.078 41.667 0.00 0.00 0.00 3.18
3369 3663 5.404366 GCTTCGTATGTAGTCACTTGTTGAA 59.596 40.000 0.00 0.00 35.39 2.69
3370 3664 6.073980 GCTTCGTATGTAGTCACTTGTTGAAA 60.074 38.462 0.00 0.00 35.39 2.69
3371 3665 7.360101 GCTTCGTATGTAGTCACTTGTTGAAAT 60.360 37.037 0.00 0.00 35.39 2.17
3372 3666 7.576750 TCGTATGTAGTCACTTGTTGAAATC 57.423 36.000 0.00 0.00 35.39 2.17
3373 3667 7.375834 TCGTATGTAGTCACTTGTTGAAATCT 58.624 34.615 0.00 0.00 35.39 2.40
3374 3668 7.541091 TCGTATGTAGTCACTTGTTGAAATCTC 59.459 37.037 0.00 0.00 35.39 2.75
3375 3669 7.542477 CGTATGTAGTCACTTGTTGAAATCTCT 59.458 37.037 0.00 0.00 35.39 3.10
3376 3670 9.856488 GTATGTAGTCACTTGTTGAAATCTCTA 57.144 33.333 0.00 0.00 35.39 2.43
3378 3672 9.778741 ATGTAGTCACTTGTTGAAATCTCTAAA 57.221 29.630 0.00 0.00 35.39 1.85
3379 3673 9.607988 TGTAGTCACTTGTTGAAATCTCTAAAA 57.392 29.630 0.00 0.00 35.39 1.52
3382 3676 9.396022 AGTCACTTGTTGAAATCTCTAAAAAGA 57.604 29.630 0.00 0.00 35.39 2.52
3383 3677 9.439537 GTCACTTGTTGAAATCTCTAAAAAGAC 57.560 33.333 0.00 0.00 35.39 3.01
3384 3678 9.173021 TCACTTGTTGAAATCTCTAAAAAGACA 57.827 29.630 0.00 0.00 0.00 3.41
3385 3679 9.787532 CACTTGTTGAAATCTCTAAAAAGACAA 57.212 29.630 0.00 0.00 0.00 3.18
3402 3696 7.625828 AAAGACAAATATTTAGGAACGGAGG 57.374 36.000 0.00 0.00 0.00 4.30
3403 3697 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
3404 3698 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
3405 3699 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
3419 3713 3.682718 CGGAGGGAGTAGTACGGTTTCTA 60.683 52.174 0.00 0.00 0.00 2.10
3445 3739 6.103057 ACCAAACCCCTAAACTTAACTCCTTA 59.897 38.462 0.00 0.00 0.00 2.69
3489 3783 7.022979 CGATGCAAATTTGATCAAACTAGTCA 58.977 34.615 22.71 16.07 32.51 3.41
3566 3975 9.658475 CATAAAAACGAAACAAACTACTCATCA 57.342 29.630 0.00 0.00 0.00 3.07
3575 3984 7.559590 AACAAACTACTCATCATTGCTATCC 57.440 36.000 0.00 0.00 0.00 2.59
3600 4009 1.688884 TCGGCCATCATCCTGTCCA 60.689 57.895 2.24 0.00 0.00 4.02
3673 4083 7.748513 ATGACCCTCATCTTCTTGAATTCAAGT 60.749 37.037 35.56 21.04 42.38 3.16
3683 4093 2.942804 TGAATTCAAGTGAAGGTGGCA 58.057 42.857 5.45 0.00 37.48 4.92
3685 4095 3.896888 TGAATTCAAGTGAAGGTGGCAAT 59.103 39.130 5.45 0.00 37.48 3.56
3693 4107 4.568956 AGTGAAGGTGGCAATTTTATTGC 58.431 39.130 14.36 14.36 44.22 3.56
3704 4118 6.694844 TGGCAATTTTATTGCATGTATACACG 59.305 34.615 21.72 0.00 46.58 4.49
3745 4159 4.827835 GCAATATTTAAGGAACTCCCCTCC 59.172 45.833 0.00 0.00 38.49 4.30
3746 4160 5.386060 CAATATTTAAGGAACTCCCCTCCC 58.614 45.833 0.00 0.00 38.49 4.30
3747 4161 1.677490 TTTAAGGAACTCCCCTCCCC 58.323 55.000 0.00 0.00 38.49 4.81
3748 4162 0.253488 TTAAGGAACTCCCCTCCCCC 60.253 60.000 0.00 0.00 38.49 5.40
3779 4193 2.795297 GCGTCGTCTCCTCTGAGG 59.205 66.667 17.84 17.84 39.23 3.86
3807 4221 4.126524 GGCAACCCTAGCATCGTC 57.873 61.111 0.00 0.00 0.00 4.20
3808 4222 1.883084 GGCAACCCTAGCATCGTCG 60.883 63.158 0.00 0.00 0.00 5.12
3809 4223 2.526120 GCAACCCTAGCATCGTCGC 61.526 63.158 0.00 0.00 0.00 5.19
3814 4228 2.727647 CTAGCATCGTCGCCTCGC 60.728 66.667 0.00 0.00 0.00 5.03
3820 4234 2.539338 ATCGTCGCCTCGCTCTCTC 61.539 63.158 0.00 0.00 0.00 3.20
3840 4254 2.443016 CCCTCTCACTCCCCTCCG 60.443 72.222 0.00 0.00 0.00 4.63
3850 4264 3.072468 CCCCTCCGTCGCTACCAA 61.072 66.667 0.00 0.00 0.00 3.67
3859 4273 2.124695 CGCTACCAAAGGGGCTCC 60.125 66.667 0.00 0.00 42.05 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 9.970395 CATTAAATATGCATCCACATACAACTT 57.030 29.630 0.19 0.00 35.42 2.66
39 40 5.080969 ACTTCTTTAATAGCCTACGTGCA 57.919 39.130 0.00 0.00 0.00 4.57
92 95 9.921637 AGCTTCTTTGATATAGCTTGTACTATC 57.078 33.333 0.00 0.00 40.91 2.08
160 168 1.901833 TCAACATAGCTCTGCCACTGA 59.098 47.619 0.00 0.00 0.00 3.41
161 169 2.277969 CTCAACATAGCTCTGCCACTG 58.722 52.381 0.00 0.00 0.00 3.66
162 170 1.209019 CCTCAACATAGCTCTGCCACT 59.791 52.381 0.00 0.00 0.00 4.00
163 171 1.661341 CCTCAACATAGCTCTGCCAC 58.339 55.000 0.00 0.00 0.00 5.01
164 172 0.107508 GCCTCAACATAGCTCTGCCA 60.108 55.000 0.00 0.00 0.00 4.92
166 174 0.107508 TGGCCTCAACATAGCTCTGC 60.108 55.000 3.32 0.00 0.00 4.26
167 175 2.286872 CTTGGCCTCAACATAGCTCTG 58.713 52.381 3.32 0.00 0.00 3.35
168 176 1.211457 CCTTGGCCTCAACATAGCTCT 59.789 52.381 3.32 0.00 0.00 4.09
169 177 1.673168 CCTTGGCCTCAACATAGCTC 58.327 55.000 3.32 0.00 0.00 4.09
174 182 2.772924 CCCCCTTGGCCTCAACAT 59.227 61.111 3.32 0.00 0.00 2.71
204 212 2.517959 TCAGAAATTGGTCCAAGGCTG 58.482 47.619 18.29 18.29 0.00 4.85
205 213 2.978156 TCAGAAATTGGTCCAAGGCT 57.022 45.000 10.72 4.31 0.00 4.58
206 214 3.157087 TCTTCAGAAATTGGTCCAAGGC 58.843 45.455 10.72 1.98 0.00 4.35
260 268 2.050144 TGGGGCTGCCAAATGTAAAAA 58.950 42.857 22.05 0.00 0.00 1.94
261 269 1.722034 TGGGGCTGCCAAATGTAAAA 58.278 45.000 22.05 0.00 0.00 1.52
262 270 1.722034 TTGGGGCTGCCAAATGTAAA 58.278 45.000 22.05 0.63 0.00 2.01
263 271 1.346068 GTTTGGGGCTGCCAAATGTAA 59.654 47.619 22.05 2.91 39.00 2.41
264 272 0.972883 GTTTGGGGCTGCCAAATGTA 59.027 50.000 22.05 0.00 39.00 2.29
265 273 1.053264 TGTTTGGGGCTGCCAAATGT 61.053 50.000 22.05 0.00 39.00 2.71
268 276 1.382420 AGTGTTTGGGGCTGCCAAA 60.382 52.632 22.05 10.57 35.21 3.28
272 280 0.895100 TCATCAGTGTTTGGGGCTGC 60.895 55.000 0.00 0.00 0.00 5.25
273 281 1.843368 ATCATCAGTGTTTGGGGCTG 58.157 50.000 0.00 0.00 0.00 4.85
274 282 2.564062 CAAATCATCAGTGTTTGGGGCT 59.436 45.455 0.00 0.00 31.08 5.19
279 287 5.116074 GCGAAAGACAAATCATCAGTGTTTG 59.884 40.000 3.16 3.16 38.46 2.93
280 288 5.215160 GCGAAAGACAAATCATCAGTGTTT 58.785 37.500 0.00 0.00 32.36 2.83
281 289 4.320494 GGCGAAAGACAAATCATCAGTGTT 60.320 41.667 0.00 0.00 40.66 3.32
282 290 3.189287 GGCGAAAGACAAATCATCAGTGT 59.811 43.478 0.00 0.00 40.66 3.55
283 291 3.426695 GGGCGAAAGACAAATCATCAGTG 60.427 47.826 0.00 0.00 45.40 3.66
284 292 2.749621 GGGCGAAAGACAAATCATCAGT 59.250 45.455 0.00 0.00 45.40 3.41
285 293 2.098117 GGGGCGAAAGACAAATCATCAG 59.902 50.000 0.00 0.00 45.40 2.90
288 296 2.094675 CTGGGGCGAAAGACAAATCAT 58.905 47.619 0.00 0.00 45.40 2.45
290 298 0.171231 GCTGGGGCGAAAGACAAATC 59.829 55.000 0.00 0.00 45.40 2.17
293 301 1.302511 GAGCTGGGGCGAAAGACAA 60.303 57.895 0.00 0.00 45.40 3.18
295 303 2.436824 GGAGCTGGGGCGAAAGAC 60.437 66.667 0.00 0.00 44.37 3.01
297 305 4.803908 GGGGAGCTGGGGCGAAAG 62.804 72.222 0.00 0.00 44.37 2.62
304 312 2.243774 TAGAGAGTGGGGGAGCTGGG 62.244 65.000 0.00 0.00 0.00 4.45
305 313 0.758685 CTAGAGAGTGGGGGAGCTGG 60.759 65.000 0.00 0.00 0.00 4.85
306 314 0.758685 CCTAGAGAGTGGGGGAGCTG 60.759 65.000 0.00 0.00 0.00 4.24
307 315 1.225403 ACCTAGAGAGTGGGGGAGCT 61.225 60.000 0.00 0.00 0.00 4.09
308 316 1.045911 CACCTAGAGAGTGGGGGAGC 61.046 65.000 0.00 0.00 28.94 4.70
309 317 0.336737 ACACCTAGAGAGTGGGGGAG 59.663 60.000 0.00 0.00 39.63 4.30
312 320 1.759445 CATCACACCTAGAGAGTGGGG 59.241 57.143 0.00 0.00 39.21 4.96
313 321 2.167281 CACATCACACCTAGAGAGTGGG 59.833 54.545 0.00 0.00 40.13 4.61
314 322 3.092301 TCACATCACACCTAGAGAGTGG 58.908 50.000 0.00 0.00 39.63 4.00
315 323 3.761218 ACTCACATCACACCTAGAGAGTG 59.239 47.826 0.00 0.00 41.15 3.51
316 324 3.761218 CACTCACATCACACCTAGAGAGT 59.239 47.826 0.00 0.00 35.66 3.24
318 326 3.507622 CACACTCACATCACACCTAGAGA 59.492 47.826 0.00 0.00 0.00 3.10
843 1033 2.291043 GGTGGGACATGGACGGAGT 61.291 63.158 0.00 0.00 45.62 3.85
916 1111 2.492019 TGGACGTAGCAGATTGATCG 57.508 50.000 0.00 0.00 0.00 3.69
989 1187 1.066858 GCTTCCTCATCACCGAGTCAA 60.067 52.381 0.00 0.00 0.00 3.18
991 1189 0.532573 TGCTTCCTCATCACCGAGTC 59.467 55.000 0.00 0.00 0.00 3.36
992 1190 0.534412 CTGCTTCCTCATCACCGAGT 59.466 55.000 0.00 0.00 0.00 4.18
993 1191 0.809241 GCTGCTTCCTCATCACCGAG 60.809 60.000 0.00 0.00 0.00 4.63
1046 1244 1.766059 TCCCACTCCCCATCATCGG 60.766 63.158 0.00 0.00 0.00 4.18
1204 1407 4.112634 CAAACGAACAGAGACAGAGACAA 58.887 43.478 0.00 0.00 0.00 3.18
1252 1488 3.005554 CTGAACTCGATCACTGCCAAAT 58.994 45.455 0.00 0.00 0.00 2.32
1469 1705 1.528776 GACGAGGCCGAGGAGGTAT 60.529 63.158 0.00 0.00 43.70 2.73
1526 1762 4.314440 GGCACAGAGACACCGCCA 62.314 66.667 0.00 0.00 42.50 5.69
1670 1906 5.047021 CCAGTTGAAGTAGGACATCTTCTGA 60.047 44.000 0.00 0.00 40.20 3.27
2258 2510 4.094646 ACGGTGGCGATCATGGCA 62.095 61.111 0.00 0.00 42.76 4.92
2351 2603 3.785859 ATGCCCACTCCGATGCGT 61.786 61.111 0.00 0.00 0.00 5.24
2821 3073 0.663568 CGGTCTATCGATGCCGGAAC 60.664 60.000 22.01 11.58 40.45 3.62
2823 3075 3.351450 CGGTCTATCGATGCCGGA 58.649 61.111 22.01 8.41 40.45 5.14
2832 3084 4.267928 GCACTTGTGATTGTACGGTCTATC 59.732 45.833 4.79 0.00 0.00 2.08
2837 3089 1.144969 CGCACTTGTGATTGTACGGT 58.855 50.000 4.79 0.00 0.00 4.83
2860 3112 1.002624 CCAAAAGCGCTCCCCTGTA 60.003 57.895 12.06 0.00 0.00 2.74
2956 3213 1.135972 CATCAACGTTCAAGGCTTCCG 60.136 52.381 0.00 2.69 0.00 4.30
3089 3382 1.110442 CACCCTTTCTTGGTGTTGCA 58.890 50.000 1.27 0.00 46.62 4.08
3121 3414 2.158957 TCACCACTTCTCAGTTCACACC 60.159 50.000 0.00 0.00 0.00 4.16
3130 3423 4.285020 AGATGCTCTATCACCACTTCTCA 58.715 43.478 0.00 0.00 38.31 3.27
3161 3454 3.470868 AGGGCTCTAATTTTACAGGGGA 58.529 45.455 0.00 0.00 0.00 4.81
3172 3465 8.338418 ACTCCTCTAAATTTTAGGGCTCTAAT 57.662 34.615 6.94 0.00 35.61 1.73
3183 3476 4.393990 CCGCCGTTTACTCCTCTAAATTTT 59.606 41.667 0.00 0.00 0.00 1.82
3242 3536 3.889520 ATTTGAGAACGGAGGGAGTAC 57.110 47.619 0.00 0.00 0.00 2.73
3246 3540 5.045869 AGACAAATATTTGAGAACGGAGGGA 60.046 40.000 30.18 0.00 40.55 4.20
3247 3541 5.186198 AGACAAATATTTGAGAACGGAGGG 58.814 41.667 30.18 4.03 40.55 4.30
3248 3542 6.743575 AAGACAAATATTTGAGAACGGAGG 57.256 37.500 30.18 4.51 40.55 4.30
3249 3543 8.034058 AGAAAGACAAATATTTGAGAACGGAG 57.966 34.615 30.18 5.19 40.55 4.63
3250 3544 7.979444 AGAAAGACAAATATTTGAGAACGGA 57.021 32.000 30.18 0.00 40.55 4.69
3251 3545 9.151471 TCTAGAAAGACAAATATTTGAGAACGG 57.849 33.333 30.18 14.46 40.55 4.44
3276 3570 9.485591 CGTATGTTGTAGTCCATTTAAAATGTC 57.514 33.333 0.00 0.00 0.00 3.06
3277 3571 8.455682 CCGTATGTTGTAGTCCATTTAAAATGT 58.544 33.333 0.00 0.00 0.00 2.71
3278 3572 8.670135 TCCGTATGTTGTAGTCCATTTAAAATG 58.330 33.333 0.00 0.00 0.00 2.32
3279 3573 8.795842 TCCGTATGTTGTAGTCCATTTAAAAT 57.204 30.769 0.00 0.00 0.00 1.82
3280 3574 8.670135 CATCCGTATGTTGTAGTCCATTTAAAA 58.330 33.333 0.00 0.00 0.00 1.52
3281 3575 7.825270 ACATCCGTATGTTGTAGTCCATTTAAA 59.175 33.333 0.00 0.00 44.07 1.52
3282 3576 7.332557 ACATCCGTATGTTGTAGTCCATTTAA 58.667 34.615 0.00 0.00 44.07 1.52
3283 3577 6.880484 ACATCCGTATGTTGTAGTCCATTTA 58.120 36.000 0.00 0.00 44.07 1.40
3284 3578 5.741011 ACATCCGTATGTTGTAGTCCATTT 58.259 37.500 0.00 0.00 44.07 2.32
3285 3579 5.353394 ACATCCGTATGTTGTAGTCCATT 57.647 39.130 0.00 0.00 44.07 3.16
3286 3580 6.665992 ATACATCCGTATGTTGTAGTCCAT 57.334 37.500 0.00 0.00 44.07 3.41
3287 3581 7.309560 CCATATACATCCGTATGTTGTAGTCCA 60.310 40.741 0.00 0.00 44.07 4.02
3288 3582 7.033791 CCATATACATCCGTATGTTGTAGTCC 58.966 42.308 0.00 0.00 44.07 3.85
3289 3583 7.754027 GTCCATATACATCCGTATGTTGTAGTC 59.246 40.741 0.00 0.00 44.07 2.59
3290 3584 7.231925 TGTCCATATACATCCGTATGTTGTAGT 59.768 37.037 0.00 0.00 44.07 2.73
3291 3585 7.599171 TGTCCATATACATCCGTATGTTGTAG 58.401 38.462 0.00 0.00 44.07 2.74
3292 3586 7.527568 TGTCCATATACATCCGTATGTTGTA 57.472 36.000 0.00 0.00 44.07 2.41
3293 3587 6.413783 TGTCCATATACATCCGTATGTTGT 57.586 37.500 0.00 0.00 44.07 3.32
3294 3588 9.599866 AATATGTCCATATACATCCGTATGTTG 57.400 33.333 0.00 0.00 45.66 3.33
3300 3594 9.219603 CTTGAAAATATGTCCATATACATCCGT 57.780 33.333 0.41 0.00 40.52 4.69
3301 3595 8.177663 GCTTGAAAATATGTCCATATACATCCG 58.822 37.037 0.41 0.00 40.52 4.18
3302 3596 8.177663 CGCTTGAAAATATGTCCATATACATCC 58.822 37.037 0.41 0.00 40.52 3.51
3303 3597 8.721478 ACGCTTGAAAATATGTCCATATACATC 58.279 33.333 0.41 1.63 40.52 3.06
3304 3598 8.621532 ACGCTTGAAAATATGTCCATATACAT 57.378 30.769 0.41 0.00 42.62 2.29
3305 3599 9.203421 CTACGCTTGAAAATATGTCCATATACA 57.797 33.333 0.41 0.64 33.86 2.29
3306 3600 9.419297 TCTACGCTTGAAAATATGTCCATATAC 57.581 33.333 0.41 0.00 33.86 1.47
3308 3602 9.507329 AATCTACGCTTGAAAATATGTCCATAT 57.493 29.630 0.00 0.00 35.63 1.78
3309 3603 8.902540 AATCTACGCTTGAAAATATGTCCATA 57.097 30.769 0.00 0.00 0.00 2.74
3310 3604 7.498900 TGAATCTACGCTTGAAAATATGTCCAT 59.501 33.333 0.00 0.00 0.00 3.41
3311 3605 6.821160 TGAATCTACGCTTGAAAATATGTCCA 59.179 34.615 0.00 0.00 0.00 4.02
3312 3606 7.011482 AGTGAATCTACGCTTGAAAATATGTCC 59.989 37.037 0.00 0.00 0.00 4.02
3313 3607 7.910304 AGTGAATCTACGCTTGAAAATATGTC 58.090 34.615 0.00 0.00 0.00 3.06
3314 3608 7.549134 TGAGTGAATCTACGCTTGAAAATATGT 59.451 33.333 0.00 0.00 0.00 2.29
3315 3609 7.909267 TGAGTGAATCTACGCTTGAAAATATG 58.091 34.615 0.00 0.00 0.00 1.78
3316 3610 8.668510 ATGAGTGAATCTACGCTTGAAAATAT 57.331 30.769 0.00 0.00 0.00 1.28
3317 3611 8.492673 AATGAGTGAATCTACGCTTGAAAATA 57.507 30.769 0.00 0.00 0.00 1.40
3318 3612 6.992063 ATGAGTGAATCTACGCTTGAAAAT 57.008 33.333 0.00 0.00 0.00 1.82
3319 3613 6.801539 AATGAGTGAATCTACGCTTGAAAA 57.198 33.333 0.00 0.00 0.00 2.29
3320 3614 6.801539 AAATGAGTGAATCTACGCTTGAAA 57.198 33.333 0.00 0.00 0.00 2.69
3321 3615 6.602179 CAAAATGAGTGAATCTACGCTTGAA 58.398 36.000 0.00 0.00 0.00 2.69
3322 3616 5.390885 GCAAAATGAGTGAATCTACGCTTGA 60.391 40.000 0.00 0.00 0.00 3.02
3323 3617 4.790140 GCAAAATGAGTGAATCTACGCTTG 59.210 41.667 0.00 0.00 0.00 4.01
3324 3618 4.697352 AGCAAAATGAGTGAATCTACGCTT 59.303 37.500 0.00 0.00 0.00 4.68
3325 3619 4.256920 AGCAAAATGAGTGAATCTACGCT 58.743 39.130 0.00 0.00 0.00 5.07
3326 3620 4.606457 AGCAAAATGAGTGAATCTACGC 57.394 40.909 0.00 0.00 0.00 4.42
3327 3621 5.163953 ACGAAGCAAAATGAGTGAATCTACG 60.164 40.000 0.00 0.00 0.00 3.51
3328 3622 6.170675 ACGAAGCAAAATGAGTGAATCTAC 57.829 37.500 0.00 0.00 0.00 2.59
3329 3623 7.549134 ACATACGAAGCAAAATGAGTGAATCTA 59.451 33.333 0.00 0.00 0.00 1.98
3330 3624 6.372659 ACATACGAAGCAAAATGAGTGAATCT 59.627 34.615 0.00 0.00 0.00 2.40
3331 3625 6.546395 ACATACGAAGCAAAATGAGTGAATC 58.454 36.000 0.00 0.00 0.00 2.52
3332 3626 6.500684 ACATACGAAGCAAAATGAGTGAAT 57.499 33.333 0.00 0.00 0.00 2.57
3333 3627 5.940192 ACATACGAAGCAAAATGAGTGAA 57.060 34.783 0.00 0.00 0.00 3.18
3334 3628 6.163476 ACTACATACGAAGCAAAATGAGTGA 58.837 36.000 0.00 0.00 0.00 3.41
3335 3629 6.090763 TGACTACATACGAAGCAAAATGAGTG 59.909 38.462 0.00 0.00 0.00 3.51
3336 3630 6.090898 GTGACTACATACGAAGCAAAATGAGT 59.909 38.462 0.00 0.00 0.00 3.41
3337 3631 6.311445 AGTGACTACATACGAAGCAAAATGAG 59.689 38.462 0.00 0.00 0.00 2.90
3338 3632 6.163476 AGTGACTACATACGAAGCAAAATGA 58.837 36.000 0.00 0.00 0.00 2.57
3339 3633 6.408858 AGTGACTACATACGAAGCAAAATG 57.591 37.500 0.00 0.00 0.00 2.32
3340 3634 6.426937 ACAAGTGACTACATACGAAGCAAAAT 59.573 34.615 0.00 0.00 0.00 1.82
3341 3635 5.756347 ACAAGTGACTACATACGAAGCAAAA 59.244 36.000 0.00 0.00 0.00 2.44
3342 3636 5.294356 ACAAGTGACTACATACGAAGCAAA 58.706 37.500 0.00 0.00 0.00 3.68
3343 3637 4.878439 ACAAGTGACTACATACGAAGCAA 58.122 39.130 0.00 0.00 0.00 3.91
3344 3638 4.514781 ACAAGTGACTACATACGAAGCA 57.485 40.909 0.00 0.00 0.00 3.91
3345 3639 4.921515 TCAACAAGTGACTACATACGAAGC 59.078 41.667 0.00 0.00 0.00 3.86
3346 3640 7.402811 TTTCAACAAGTGACTACATACGAAG 57.597 36.000 0.00 0.00 35.39 3.79
3347 3641 7.870954 AGATTTCAACAAGTGACTACATACGAA 59.129 33.333 0.00 0.00 35.39 3.85
3348 3642 7.375834 AGATTTCAACAAGTGACTACATACGA 58.624 34.615 0.00 0.00 35.39 3.43
3349 3643 7.542477 AGAGATTTCAACAAGTGACTACATACG 59.458 37.037 0.00 0.00 35.39 3.06
3350 3644 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
3352 3646 9.778741 TTTAGAGATTTCAACAAGTGACTACAT 57.221 29.630 0.00 0.00 35.39 2.29
3353 3647 9.607988 TTTTAGAGATTTCAACAAGTGACTACA 57.392 29.630 0.00 0.00 35.39 2.74
3356 3650 9.396022 TCTTTTTAGAGATTTCAACAAGTGACT 57.604 29.630 0.00 0.00 35.39 3.41
3357 3651 9.439537 GTCTTTTTAGAGATTTCAACAAGTGAC 57.560 33.333 0.00 0.00 35.39 3.67
3358 3652 9.173021 TGTCTTTTTAGAGATTTCAACAAGTGA 57.827 29.630 0.00 0.00 0.00 3.41
3359 3653 9.787532 TTGTCTTTTTAGAGATTTCAACAAGTG 57.212 29.630 0.00 0.00 0.00 3.16
3376 3670 8.520351 CCTCCGTTCCTAAATATTTGTCTTTTT 58.480 33.333 11.05 0.00 0.00 1.94
3377 3671 7.122204 CCCTCCGTTCCTAAATATTTGTCTTTT 59.878 37.037 11.05 0.00 0.00 2.27
3378 3672 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
3379 3673 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
3380 3674 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
3381 3675 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
3382 3676 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
3383 3677 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
3384 3678 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
3385 3679 6.141790 ACTACTCCCTCCGTTCCTAAATATT 58.858 40.000 0.00 0.00 0.00 1.28
3386 3680 5.713807 ACTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
3387 3681 5.134725 ACTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
3388 3682 3.991683 ACTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
3389 3683 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
3390 3684 3.682718 CGTACTACTCCCTCCGTTCCTAA 60.683 52.174 0.00 0.00 0.00 2.69
3391 3685 2.158900 CGTACTACTCCCTCCGTTCCTA 60.159 54.545 0.00 0.00 0.00 2.94
3392 3686 1.407989 CGTACTACTCCCTCCGTTCCT 60.408 57.143 0.00 0.00 0.00 3.36
3393 3687 1.020437 CGTACTACTCCCTCCGTTCC 58.980 60.000 0.00 0.00 0.00 3.62
3394 3688 1.020437 CCGTACTACTCCCTCCGTTC 58.980 60.000 0.00 0.00 0.00 3.95
3395 3689 0.329596 ACCGTACTACTCCCTCCGTT 59.670 55.000 0.00 0.00 0.00 4.44
3396 3690 0.329596 AACCGTACTACTCCCTCCGT 59.670 55.000 0.00 0.00 0.00 4.69
3397 3691 1.403323 GAAACCGTACTACTCCCTCCG 59.597 57.143 0.00 0.00 0.00 4.63
3398 3692 2.732763 AGAAACCGTACTACTCCCTCC 58.267 52.381 0.00 0.00 0.00 4.30
3399 3693 4.097135 GGTTAGAAACCGTACTACTCCCTC 59.903 50.000 0.00 0.00 42.62 4.30
3400 3694 4.019858 GGTTAGAAACCGTACTACTCCCT 58.980 47.826 0.00 0.00 42.62 4.20
3401 3695 4.377839 GGTTAGAAACCGTACTACTCCC 57.622 50.000 0.00 0.00 42.62 4.30
3419 3713 5.103387 AGGAGTTAAGTTTAGGGGTTTGGTT 60.103 40.000 0.00 0.00 0.00 3.67
3538 3832 8.829514 TGAGTAGTTTGTTTCGTTTTTATGTG 57.170 30.769 0.00 0.00 0.00 3.21
3575 3984 0.668706 GGATGATGGCCGAGATCACG 60.669 60.000 6.40 5.49 32.68 4.35
3600 4009 1.153168 CCATGCCCGACGAGGAATT 60.153 57.895 0.00 0.00 45.00 2.17
3634 4043 7.861629 AGATGAGGGTCATGTTTCTGTAATAA 58.138 34.615 0.00 0.00 37.20 1.40
3673 4083 4.613925 TGCAATAAAATTGCCACCTTCA 57.386 36.364 18.99 0.00 44.32 3.02
3761 4175 2.401592 CTCAGAGGAGACGACGCG 59.598 66.667 3.53 3.53 44.26 6.01
3791 4205 2.526120 GCGACGATGCTAGGGTTGC 61.526 63.158 0.00 0.00 34.26 4.17
3792 4206 1.883084 GGCGACGATGCTAGGGTTG 60.883 63.158 0.00 0.00 34.52 3.77
3794 4208 2.442272 AGGCGACGATGCTAGGGT 60.442 61.111 0.00 0.00 34.52 4.34
3797 4211 2.727647 GCGAGGCGACGATGCTAG 60.728 66.667 0.00 0.00 35.09 3.42
3798 4212 3.182472 GAGCGAGGCGACGATGCTA 62.182 63.158 4.90 0.00 37.13 3.49
3799 4213 4.560856 GAGCGAGGCGACGATGCT 62.561 66.667 4.57 4.57 39.14 3.79
3800 4214 4.560856 AGAGCGAGGCGACGATGC 62.561 66.667 0.00 0.00 35.09 3.91
3801 4215 2.352915 GAGAGCGAGGCGACGATG 60.353 66.667 0.00 0.00 35.09 3.84
3803 4217 3.196394 GAGAGAGCGAGGCGACGA 61.196 66.667 0.00 0.00 35.09 4.20
3804 4218 4.244802 GGAGAGAGCGAGGCGACG 62.245 72.222 0.00 0.00 0.00 5.12
3805 4219 3.894947 GGGAGAGAGCGAGGCGAC 61.895 72.222 0.00 0.00 0.00 5.19
3824 4238 1.755008 GACGGAGGGGAGTGAGAGG 60.755 68.421 0.00 0.00 0.00 3.69
3830 4244 2.439883 GTAGCGACGGAGGGGAGT 60.440 66.667 0.00 0.00 0.00 3.85
3840 4254 1.449778 GAGCCCCTTTGGTAGCGAC 60.450 63.158 0.00 0.00 36.04 5.19


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

AutoCloner maintained by Alex Coulton.