Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006719.1 Hibiscus syriacus cultivar Beakdansim tig00016801_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 65826
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Found at i:67 original size:19 final size:19
Alignment explanation
Indices: 27--69 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
17 ATCTCACATG
* *
27 AAATTTATAAATCTTCATA
1 AAATTTATAAATCTTAAAA
46 AAATTTAATAAATC-TAAAA
1 AAATTT-ATAAATCTTAAAA
65 AAATT
1 AAATT
70 ACTTGATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (19 bp):
AAATTTATAAATCTTAAAA
Found at i:3966 original size:26 final size:26
Alignment explanation
Indices: 3935--4083 Score: 93
Period size: 23 Copynumber: 6.0 Consensus size: 26
3925 TTTGTGGAAG
* * *
3935 AGAAGAAAGGAGTTTGTGGAAGAAAA
1 AGAAGAAACGAGTTTATGAAAGAAAA
3961 AGAAGAAACGAGTTTATGAAAG--AA
1 AGAAGAAACGAGTTTATGAAAGAAAA
* * *
3985 A-AATAAATGAGTTTATG---GAAGA
1 AGAAGAAACGAGTTTATGAAAGAAAA
*
4007 AGAAGAAAC-ATGTTTATGGAAGAACAAGA
1 AGAAGAAACGA-GTTTATGAAAG-A-AA-A
* *
4036 AGAAGAAATGAGTTTATG---GAAGA
1 AGAAGAAACGAGTTTATGAAAGAAAA
* *
4059 AGAAGAAATGGGTTTATGAAAGAAA
1 AGAAGAAACGAGTTTATGAAAGAAA
4084 GTAATGAGTT
Statistics
Matches: 96, Mismatches: 13, Indels: 28
0.70 0.09 0.20
Matches are distributed among these distances:
20 1 0.01
22 3 0.03
23 44 0.46
24 4 0.04
25 1 0.01
26 24 0.25
27 1 0.01
28 1 0.01
29 16 0.17
30 1 0.01
ACGTcount: A:0.51, C:0.02, G:0.28, T:0.19
Consensus pattern (26 bp):
AGAAGAAACGAGTTTATGAAAGAAAA
Found at i:4000 original size:23 final size:23
Alignment explanation
Indices: 3956--4110 Score: 138
Period size: 23 Copynumber: 6.6 Consensus size: 23
3946 GTTTGTGGAA
*
3956 GAAA-AAGAAGAAACGAGTTTAT
1 GAAAGAAGAAGAAATGAGTTTAT
* *
3978 GAAAGAAAAATAAATGAGTTTAT
1 GAAAGAAGAAGAAATGAGTTTAT
* *
4001 GGAAGAAGAAGAAA-CATGTTTAT
1 GAAAGAAGAAGAAATGA-GTTTAT
4024 GGAAGAACAAGAAGAAGAAATGAGTTTAT
1 ----G-A-AAGAAGAAGAAATGAGTTTAT
* *
4053 GGAAGAAGAAGAAATGGGTTTAT
1 GAAAGAAGAAGAAATGAGTTTAT
*
4076 GAAAG-A-AAGTAATGAGTTTAT
1 GAAAGAAGAAGAAATGAGTTTAT
*
4097 GGAAGAAGAAGAAA
1 GAAAGAAGAAGAAA
4111 ATGTTTATTG
Statistics
Matches: 106, Mismatches: 16, Indels: 21
0.74 0.11 0.15
Matches are distributed among these distances:
21 17 0.16
22 7 0.07
23 61 0.58
25 1 0.01
27 1 0.01
29 18 0.17
30 1 0.01
ACGTcount: A:0.52, C:0.02, G:0.26, T:0.20
Consensus pattern (23 bp):
GAAAGAAGAAGAAATGAGTTTAT
Found at i:4013 original size:29 final size:28
Alignment explanation
Indices: 3980--4066 Score: 94
Period size: 29 Copynumber: 3.2 Consensus size: 28
3970 GAGTTTATGA
3980 AAGAAAAATAAATGAGTTTATGGAAGAAG
1 AAGAAAAA-AAATGAGTTTATGGAAGAAG
* *
4009 AAG---AAACAT--GTTTATGGAAGAAC
1 AAGAAAAAAAATGAGTTTATGGAAGAAG
*
4032 AAGAAGAAGAAATGAGTTTATGGAAGAAG
1 AAGAA-AAAAAATGAGTTTATGGAAGAAG
4061 AAGAAA
1 AAGAAA
4067 TGGGTTTATG
Statistics
Matches: 47, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
23 16 0.34
25 3 0.06
26 2 0.04
27 4 0.09
28 1 0.02
29 21 0.45
ACGTcount: A:0.54, C:0.02, G:0.25, T:0.18
Consensus pattern (28 bp):
AAGAAAAAAAATGAGTTTATGGAAGAAG
Found at i:4045 original size:52 final size:48
Alignment explanation
Indices: 3979--4125 Score: 162
Period size: 52 Copynumber: 3.0 Consensus size: 48
3969 CGAGTTTATG
*
3979 AAAGAAAAATAAATGAGTTTATGGAAGAAGAAGAAACATGTTTATGGAAGA
1 AAAG-AAAAGAAATGAGTTTATGGAAGAAGAAGAAA-ATGTTTAT-GAAGA
4030 ACAAGAAGAAGAAATGAGTTTATGGAAGAAGAAG-AAATGGGTTTAT---G-
1 A-AAGAA-AAGAAATGAGTTTATGGAAGAAGAAGAAAAT--GTTTATGAAGA
*
4077 AAAG-AAAGTAATGAGTTTATGGAAGAAGAAGAAAATGTTTATTGAAGA
1 AAAGAAAAGAAATGAGTTTATGGAAGAAGAAGAAAATGTTTA-TGAAGA
4125 A
1 A
4126 GAATGGTTCA
Statistics
Matches: 84, Mismatches: 2, Indels: 23
0.77 0.02 0.21
Matches are distributed among these distances:
43 5 0.06
44 26 0.31
45 5 0.06
46 3 0.04
47 2 0.02
48 2 0.02
50 2 0.02
51 5 0.06
52 34 0.40
ACGTcount: A:0.50, C:0.01, G:0.26, T:0.22
Consensus pattern (48 bp):
AAAGAAAAGAAATGAGTTTATGGAAGAAGAAGAAAATGTTTATGAAGA
Found at i:4068 original size:75 final size:72
Alignment explanation
Indices: 3906--4109 Score: 206
Period size: 75 Copynumber: 2.8 Consensus size: 72
3896 TCTCAGACGA
* * *
3906 ATGGAAGAAGAAGAACA--AGTTTGTGGAAG-AGAAGAAAGGAGTTTGTGGAAGAAAAAGAAGAA
1 ATGGAAGAAGAAGAA-ATGAGTTTATGGAAGAAGAAGAAAGCAGTTTATGGAAGAAAAAGAAGAA
3968 ACGAGTTT
65 ACGAGTTT
* * *
3976 ATGAAAGAAAAATAAATGAGTTTATGGAAGAAGAAGAAA-CATGTTTATGGAAGAACAAGAAGAA
1 ATGGAAGAAGAAGAAATGAGTTTATGGAAGAAGAAGAAAGCA-GTTTATGGAAG-A-AA-AAGAA
*
4040 GAAATGAGTTT
62 GAAACGAGTTT
* * * *
4051 ATGGAAGAAGAAGAAATGGGTTTATGAAAG-A-AAGTAATG-AGTTTATGGAAGAAGAAGAA
1 ATGGAAGAAGAAGAAATGAGTTTATGGAAGAAGAAG-AAAGCAGTTTATGGAAGAAAAAGAA
4110 AATGTTTATT
Statistics
Matches: 111, Mismatches: 14, Indels: 18
0.78 0.10 0.13
Matches are distributed among these distances:
69 1 0.01
70 17 0.15
71 13 0.12
72 19 0.17
73 15 0.14
74 6 0.05
75 40 0.36
ACGTcount: A:0.50, C:0.02, G:0.29, T:0.20
Consensus pattern (72 bp):
ATGGAAGAAGAAGAAATGAGTTTATGGAAGAAGAAGAAAGCAGTTTATGGAAGAAAAAGAAGAAA
CGAGTTT
Found at i:4094 original size:21 final size:21
Alignment explanation
Indices: 4034--4103 Score: 88
Period size: 21 Copynumber: 3.3 Consensus size: 21
4024 GGAAGAACAA
4034 GAAG-AAGAAATGAGTTTATG
1 GAAGAAAGAAATGAGTTTATG
*
4054 GAAGAAGAAGAAATGGGTTTATG
1 GAAG-A-AAGAAATGAGTTTATG
* *
4077 AAAGAAAGTAATGAGTTTATG
1 GAAGAAAGAAATGAGTTTATG
4098 GAAGAA
1 GAAGAA
4104 GAAGAAAATG
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
20 4 0.10
21 19 0.45
22 1 0.02
23 18 0.43
ACGTcount: A:0.47, C:0.00, G:0.30, T:0.23
Consensus pattern (21 bp):
GAAGAAAGAAATGAGTTTATG
Found at i:7526 original size:13 final size:13
Alignment explanation
Indices: 7508--7532 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7498 ACCCGACCAA
7508 GGACTATCAGGAG
1 GGACTATCAGGAG
7521 GGACTATCAGGA
1 GGACTATCAGGA
7533 CCATCAACGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.36, T:0.16
Consensus pattern (13 bp):
GGACTATCAGGAG
Found at i:10835 original size:63 final size:61
Alignment explanation
Indices: 10767--10893 Score: 175
Period size: 63 Copynumber: 2.0 Consensus size: 61
10757 AATAACTAGA
* * *
10767 TTCTTCTATAGATAATTATGGACATAATATTAAATATTAAAATAT-CATCTAATAAATATTTTT
1 TTCTTCTATAGATAATTATAGACAT-ATATTAAATA-TAAAAAATCCACCTAA-AAATATTTTT
* *
10830 TTCTTCTATAGATAATTCTAGATATATATTAAATATAAAAAATCCACCTAAAAATATTTTT
1 TTCTTCTATAGATAATTATAGACATATATTAAATATAAAAAATCCACCTAAAAATATTTTT
10891 TTC
1 TTC
10894 AAAGTTTTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
61 20 0.34
62 16 0.28
63 22 0.38
ACGTcount: A:0.43, C:0.10, G:0.04, T:0.43
Consensus pattern (61 bp):
TTCTTCTATAGATAATTATAGACATATATTAAATATAAAAAATCCACCTAAAAATATTTTT
Found at i:13148 original size:21 final size:21
Alignment explanation
Indices: 13122--13174 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
13112 GTTTCCAGCT
13122 TCGCAACGCGAACATCAACTA
1 TCGCAACGCGAACATCAACTA
* *
13143 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACATCAACTA
*
13164 TCGCAATGCGA
1 TCGCAACGCGA
13175 TTTTCCAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.32, C:0.32, G:0.19, T:0.17
Consensus pattern (21 bp):
TCGCAACGCGAACATCAACTA
Found at i:13194 original size:19 final size:19
Alignment explanation
Indices: 13178--13473 Score: 160
Period size: 21 Copynumber: 14.3 Consensus size: 19
13168 AATGCGATTT
13178 TCCAAATTCGTTGCGATAG
1 TCCAAATTCGTTGCGATAG
* *
13197 TCCAAGTTCGCGTTGCGATTTAT
1 TCCAAATT--CGTTGCGA--TAG
13220 TCCAAATTCGTTGCGATAG
1 TCCAAATTCGTTGCGATAG
13239 TCCAAATTCGCGTTGCGATAG
1 TCCAAATT--CGTTGCGATAG
*
13260 TCCAAGTTCGTTGCGATAG
1 TCCAAATTCGTTGCGATAG
* *
13279 TCGAAGTTCGCGTTGCGATAG
1 TCCAAATT--CGTTGCGATAG
* * * *
13300 TCGAAGTTCACGTTGTGATTTAT
1 TCCAAATT--CGTTGCGA--TAG
* *
13323 TCCAAGTTCGTTACGATAG
1 TCCAAATTCGTTGCGATAG
* * *
13342 TCGAAGTTCGCGTTGCGATTTAT
1 TCCAAATT--CGTTGCGA--TAG
*
13365 TCCAAGTTCGTTGCGATAG
1 TCCAAATTCGTTGCGATAG
* * *
13384 TCGAAGTTCGCGTTGCGATTTAT
1 TCCAAATT--CGTTGCGA--TAG
*
13407 TCCAAGTTCGTTGCGATAG
1 TCCAAATTCGTTGCGATAG
* * * *
13426 TCGAAGTCCGCGTTGCGATTTAT
1 TCCAAAT--TCGTTGCGA--TAG
*
13449 TCCAAATTCATTGCGATAG
1 TCCAAATTCGTTGCGATAG
13468 TCCAAA
1 TCCAAA
13474 ATCGCAACGA
Statistics
Matches: 225, Mismatches: 30, Indels: 44
0.75 0.10 0.15
Matches are distributed among these distances:
19 69 0.31
21 113 0.50
23 43 0.19
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (19 bp):
TCCAAATTCGTTGCGATAG
Found at i:13212 original size:21 final size:21
Alignment explanation
Indices: 13186--13444 Score: 241
Period size: 21 Copynumber: 12.4 Consensus size: 21
13176 TTTCCAAATT
13186 CGTTGCGATAGTCCAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
* *
13207 CGTTGCGATTTATTCCAAATT--
1 CGTTGCGA--TAGTCCAAGTTCG
*
13228 CGTTGCGATAGTCCAAATTCG
1 CGTTGCGATAGTCCAAGTTCG
13249 CGTTGCGATAGTCCAAGTT--
1 CGTTGCGATAGTCCAAGTTCG
*
13268 CGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
* *
13289 CGTTGCGATAGTCGAAGTTCA
1 CGTTGCGATAGTCCAAGTTCG
* *
13310 CGTTGTGATTTATTCCAAGTT--
1 CGTTGCGA--TAGTCCAAGTTCG
* *
13331 CGTTACGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
*
13352 CGTTGCGATTTATTCCAAGTT--
1 CGTTGCGA--TAGTCCAAGTTCG
*
13373 CGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
*
13394 CGTTGCGATTTATTCCAAGTT--
1 CGTTGCGA--TAGTCCAAGTTCG
* *
13415 CGTTGCGATAGTCGAAGTCCG
1 CGTTGCGATAGTCCAAGTTCG
13436 CGTTGCGAT
1 CGTTGCGAT
13445 TTATTCCAAA
Statistics
Matches: 197, Mismatches: 23, Indels: 36
0.77 0.09 0.14
Matches are distributed among these distances:
19 54 0.27
21 107 0.54
23 36 0.18
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (21 bp):
CGTTGCGATAGTCCAAGTTCG
Found at i:13267 original size:63 final size:59
Alignment explanation
Indices: 13178--13472 Score: 229
Period size: 63 Copynumber: 4.7 Consensus size: 59
13168 AATGCGATTT
* * *
13178 TCCAAATT-CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT-CGTTGCGATAG
1 TCCAAGTTCCGTTGCGATAGTCCAAGTT--CGTTGCGA--TAGTCCAAGTTCCGTTGCGATAG
* *
13239 TCCAAATTCGCGTTGCGATAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATAG
1 TCCAAGTTC-CGTTGCGATAGTCCAAGTTCGTTGCGATAGTCCAAGTTC-CGTTGCGATAG
* * * * * *
13300 TCGAAGTTCACGTTGTGATTTATTCCAAGTTCGTTACGATAGTCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTC-CGTTGCGA--TAGTCCAAGTTCGTTGCGATAGTCCAAGTTC-CGTTGCGA--TAG
* *
13365 TCCAAGTT-CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTT-CGTTGCGATAG
1 TCCAAGTTCCGTTGCGATAGTCCAAGTT--CGTTGCGA--TAGTCCAAGTTCCGTTGCGATAG
* * * * *
13426 TCGAAGTCCGCGTTGCGATTTATTCCAAATTCATTGCGATAGTCCAA
1 TCCAAGTTC-CGTTGCGA--TAGTCCAAGTTCGTTGCGATAGTCCAA
13473 AATCGCAACG
Statistics
Matches: 193, Mismatches: 25, Indels: 32
0.77 0.10 0.13
Matches are distributed among these distances:
59 8 0.04
61 65 0.34
63 94 0.49
65 26 0.13
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (59 bp):
TCCAAGTTCCGTTGCGATAGTCCAAGTTCGTTGCGATAGTCCAAGTTCCGTTGCGATAG
Found at i:13341 original size:42 final size:42
Alignment explanation
Indices: 13249--13469 Score: 315
Period size: 42 Copynumber: 5.3 Consensus size: 42
13239 TCCAAATTCG
* * *
13249 CGTTGCGATAGTCCAAGTT--CGTTGCGA--TAGTCGAAGTT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTT
* *
13287 CGCGTTGCGATAGTCGAAGTTCACGTTGTGATTTATTCCAAGTT
1 --CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTT
*
13331 CGTTACGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTT
13373 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTT
* *
13415 CGTTGCGATAGTCGAAGTCCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTT
*
13457 CATTGCGATAGTC
1 CGTTGCGATAGTC
13470 CAAAATCGCA
Statistics
Matches: 166, Mismatches: 11, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
40 18 0.11
42 139 0.84
44 9 0.05
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.34
Consensus pattern (42 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTT
Found at i:14352 original size:21 final size:21
Alignment explanation
Indices: 14328--14437 Score: 93
Period size: 21 Copynumber: 5.2 Consensus size: 21
14318 TGAACTATCA
14328 CAACGAATTTGGAATAAATCG
1 CAACGAATTTGGAATAAATCG
* * *
14349 CAACGCGAACTTAGACT--ATCG
1 CAA--CGAATTTGGAATAAATCG
*
14370 CAACGAATTTGTAATAAATCG
1 CAACGAATTTGGAATAAATCG
* *
14391 CAACGCAAACTTGGACT--ATCG
1 CAACG--AATTTGGAATAAATCG
*
14412 CAACAAATTTGGAATAAATCG
1 CAACGAATTTGGAATAAATCG
14433 CAACG
1 CAACG
14438 CGATAGTCGA
Statistics
Matches: 67, Mismatches: 14, Indels: 16
0.69 0.14 0.16
Matches are distributed among these distances:
19 16 0.24
21 35 0.52
23 16 0.24
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.22
Consensus pattern (21 bp):
CAACGAATTTGGAATAAATCG
Found at i:14380 original size:42 final size:42
Alignment explanation
Indices: 14321--14440 Score: 195
Period size: 42 Copynumber: 2.9 Consensus size: 42
14311 GCGATTTTGA
*
14321 ACTATCACAACGAATTTGGAATAAATCGCAACGCGAACTTAG
1 ACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTAG
* * *
14363 ACTATCGCAACGAATTTGTAATAAATCGCAACGCAAACTTGG
1 ACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTAG
*
14405 ACTATCGCAACAAATTTGGAATAAATCGCAACGCGA
1 ACTATCGCAACGAATTTGGAATAAATCGCAACGCGA
14441 TAGTCGAAGT
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.22
Consensus pattern (42 bp):
ACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTAG
Found at i:18929 original size:22 final size:22
Alignment explanation
Indices: 18904--18989 Score: 76
Period size: 19 Copynumber: 4.2 Consensus size: 22
18894 AACATTCATA
18904 AAACCAATCACTTCATATAATT
1 AAACCAATCACTTCATATAATT
*
18926 AAA-C-A-CAGTTCATATAATT
1 AAACCAATCACTTCATATAATT
* * ** *
18945 --ATCATTCA-TTCAGCTAATA
1 AAACCAATCACTTCATATAATT
18964 AAACCAATCACTTCATATAATT
1 AAACCAATCACTTCATATAATT
18986 AAAC
1 AAAC
18990 ACAGTTTAGA
Statistics
Matches: 48, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
17 1 0.02
18 1 0.02
19 21 0.44
20 3 0.06
21 7 0.15
22 15 0.31
ACGTcount: A:0.45, C:0.21, G:0.02, T:0.31
Consensus pattern (22 bp):
AAACCAATCACTTCATATAATT
Found at i:26336 original size:30 final size:30
Alignment explanation
Indices: 26302--26367 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 30
26292 ATAATTATTT
*
26302 TAATCGGTAT-TTTTTTCAA-ATATTACAAAA
1 TAATCAGTATATTTTTT-AACAT-TTACAAAA
*
26332 TAATCATTATATTTTTTAAGCATTTACAAAA
1 TAATCAGTATATTTTTTAA-CATTTACAAAA
26363 TAATC
1 TAATC
26368 TTCATTCGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
30 10 0.32
31 19 0.61
32 2 0.06
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.44
Consensus pattern (30 bp):
TAATCAGTATATTTTTTAACATTTACAAAA
Found at i:29689 original size:23 final size:23
Alignment explanation
Indices: 29663--29710 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
29653 ATAAAGTACA
*
29663 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
29686 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
29709 AT
1 AT
29711 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:30492 original size:23 final size:23
Alignment explanation
Indices: 30466--30528 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
30456 ATATAATCAT
30466 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
30489 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
30512 TACCTATTACATCATAT
1 TACCTATTACATTATAT
30529 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:30931 original size:25 final size:25
Alignment explanation
Indices: 30874--30939 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
30864 CACTCAAAAG
*
30874 ATGTATATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
***
30899 ACAAACATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
*
30924 TTGTACATACCTAAAT
1 ATGTACATACCTAAAT
30940 TTAATGATAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (25 bp):
ATGTACATACCTAAATATGTAGTTA
Found at i:33882 original size:365 final size:366
Alignment explanation
Indices: 33397--34104 Score: 1310
Period size: 365 Copynumber: 1.9 Consensus size: 366
33387 TTAAAATTAC
* *
33397 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTGCCGACACAAT
1 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
* *
33462 ATTATAAAGTGTCGATATAGGTTGTAGACCTATTTGCGCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
33527 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGTCGACACTTTTTT
131 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGTCGACACTTTTTT
33592 AAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGT
196 AAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGT
33657 CGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTATATTACAAAAT
261 CGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTATATTACAAAAT
*
33722 TATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
326 TACCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
* *
33763 CGACACTTTTTTAAATTGTATCGACACA-TTTTCTTCCAATATGGACATAAAGTACCGGCACAAT
1 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
33827 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
33892 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGTCGACACTTTTTT
131 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGTCGACACTTTTTT
33957 AAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGT
196 AAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGT
* *
34022 CGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTATATTGCAAATT
261 CGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTATATTACAAAAT
**
34087 TACCTATTTTATTATAAT
326 TACCTATTACATTATAAT
34105 ATGTTGAAAG
Statistics
Matches: 331, Mismatches: 11, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
365 304 0.92
366 27 0.08
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.35
Consensus pattern (366 bp):
CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGTCGACACTTTTTT
AAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGT
CGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTATATTACAAAAT
TACCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
Found at i:33905 original size:182 final size:183
Alignment explanation
Indices: 33397--34104 Score: 1301
Period size: 183 Copynumber: 3.9 Consensus size: 183
33387 TTAAAATTAC
* * *
33397 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTGCCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
* *
33462 ATTATAAAGTGTCGATATAGGTTGTAGACCTATTTGCGCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
33527 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
33580 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
33645 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
33710 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
* *
33763 CGACACTTTTTTAAATTGTATCGACACA-TTTTCTTCCAATATGGACATAAAGTACCGGCACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
33827 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
33892 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
33945 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
34010 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
* * * **
34075 ATATTGCAAATTTACCTATTTTATTATAAT
131 ATATTACAAAATTATCTATTACATTATAAT
34105 ATGTTGAAAG
Statistics
Matches: 510, Mismatches: 14, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
182 180 0.35
183 330 0.65
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.35
Consensus pattern (183 bp):
CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
Found at i:35525 original size:3 final size:3
Alignment explanation
Indices: 35517--35597 Score: 72
Period size: 3 Copynumber: 27.0 Consensus size: 3
35507 ACTTGTTTGG
* * * **
35517 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * * * *
35565 AGC TTC ATC GTC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
35598 GTCAGCTTCA
Statistics
Matches: 59, Mismatches: 19, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.23, C:0.35, G:0.06, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:35534 original size:12 final size:12
Alignment explanation
Indices: 35521--35609 Score: 88
Period size: 12 Copynumber: 7.4 Consensus size: 12
35511 GTTTGGATCA
* *
35521 TCATCTTCATCA
1 TCATCGTCATCT
* *
35533 TCATCATCATCA
1 TCATCGTCATCT
* *
35545 TCGTCATCATCT
1 TCATCGTCATCT
* *
35557 TCATCGCCAGCT
1 TCATCGTCATCT
*
35569 TCATCGTCATCA
1 TCATCGTCATCT
35581 TCATCGTCATCT
1 TCATCGTCATCT
*
35593 TCATCGTCAGCT
1 TCATCGTCATCT
35605 TCATC
1 TCATC
35610 TTCTGCGACC
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 65 1.00
ACGTcount: A:0.21, C:0.35, G:0.08, T:0.36
Consensus pattern (12 bp):
TCATCGTCATCT
Found at i:35540 original size:18 final size:18
Alignment explanation
Indices: 35521--35612 Score: 76
Period size: 18 Copynumber: 5.1 Consensus size: 18
35511 GTTTGGATCA
* *
35521 TCATCTTCATCATCATCA
1 TCATCATCATCATCATCT
*
35539 TCATCATCGTCATCATCT
1 TCATCATCATCATCATCT
** * * *
35557 TCATCGCCAGCTTCATCG
1 TCATCATCATCATCATCT
*
35575 TCATCATCATCGTCATCT
1 TCATCATCATCATCATCT
* * *
35593 TCATCGTCAGCTTCATCT
1 TCATCATCATCATCATCT
35611 TC
1 TC
35613 TGCGACCGCT
Statistics
Matches: 57, Mismatches: 17, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 57 1.00
ACGTcount: A:0.21, C:0.35, G:0.08, T:0.37
Consensus pattern (18 bp):
TCATCATCATCATCATCT
Found at i:35573 original size:36 final size:36
Alignment explanation
Indices: 35533--35609 Score: 118
Period size: 36 Copynumber: 2.1 Consensus size: 36
35523 ATCTTCATCA
*
35533 TCATCATCATCATCGTCATCATCTTCATCGCCAGCT
1 TCATCATCATCATCATCATCATCTTCATCGCCAGCT
* * *
35569 TCATCGTCATCATCATCGTCATCTTCATCGTCAGCT
1 TCATCATCATCATCATCATCATCTTCATCGCCAGCT
35605 TCATC
1 TCATC
35610 TTCTGCGACC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.21, C:0.35, G:0.09, T:0.35
Consensus pattern (36 bp):
TCATCATCATCATCATCATCATCTTCATCGCCAGCT
Found at i:35612 original size:6 final size:6
Alignment explanation
Indices: 35521--35612 Score: 67
Period size: 6 Copynumber: 15.3 Consensus size: 6
35511 GTTTGGATCA
* * * * * * * *
35521 TCATCT TCATCA TCATCA TCATCA TCGTCA TCATCT TCATCG CCAGCT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
* * * * *
35569 TCATCG TCATCA TCATCG TCATCT TCATCG TCAGCT TCATCT TC
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TC
35613 TGCGACCGCT
Statistics
Matches: 68, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 68 1.00
ACGTcount: A:0.21, C:0.35, G:0.08, T:0.37
Consensus pattern (6 bp):
TCATCT
Found at i:37891 original size:197 final size:199
Alignment explanation
Indices: 37061--38422 Score: 2526
Period size: 198 Copynumber: 6.9 Consensus size: 199
37051 TTTAAATTAG
*
37061 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCAGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
37126 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
37191 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCATCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
37256 AAAA
196 AAAA
37260 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
37325 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
37390 CGACACTTTTTATATATGGATCGACACTTTAAGGGTGCACCCTGTTTTCCATTCATTCTGG-AAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
37454 AAAA
196 AAAA
* *
37458 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAAACCGGTAAA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
37523 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
37588 CGACACTTTTTATATATGGATCAACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
37652 AAAA
196 AAAA
37656 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
37721 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATAC-TTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
37785 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCA-TCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
37849 AAAA
196 AAAA
*
37853 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCAGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
37918 ATTGTACCGGTTAGATTGAAAAATTACATA-TACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
37982 CGACAC-TTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
38046 AAAA
196 AAAA
*
38050 TATCGACACAAACTATATTAGTGTTGACACATTATTTAGACATATTCTCTCATAAAACCGGTAT-
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
38114 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
38179 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
**
38244 AAGG
196 AAAA
*
38248 TATCGACACAAACTATATGAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
* *
38313 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATA-TTTTGGTTTTCGATGTTTTTGGGA
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGATTTTGGGA
*
38377 TTGACACTTTTT-TATATGGATCGACACTTTATGGGTGCACCCTGTT
130 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
38423 GGCCATATTG
Statistics
Matches: 1136, Mismatches: 20, Indels: 15
0.97 0.02 0.01
Matches are distributed among these distances:
196 93 0.08
197 322 0.28
198 467 0.41
199 254 0.22
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.36
Consensus pattern (199 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
AAAA
Found at i:37923 original size:395 final size:398
Alignment explanation
Indices: 37061--38422 Score: 2526
Period size: 395 Copynumber: 3.4 Consensus size: 398
37051 TTTAAATTAG
37061 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCAGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCAGTATA
37126 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
37191 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCATCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
37256 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGG
196 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGG
37321 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
261 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
*
37386 GGATCGACACTTTTTATATATGGATCGACACTTTAAGGGTGCACCCTGTTTTCCATTCATTCTGG
326 GGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG
37451 -AAAAAAA
391 AAAAAAAA
* * *
37458 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAAACCGGTAAA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCAGTATA
37523 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
37588 CGACACTTTTTATATATGGATCAACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
37652 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGG
196 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGG
37717 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATAC-TTTGGGTTCGATGATTTTG
261 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
37781 GGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCA-TCTGG
326 GGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG
37845 AAAAAAAA
391 AAAAAAAA
37853 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCAGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCAGTATA
37918 ATTGTACCGGTTAGATTGAAAAATTACATA-TACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
37982 CGACAC-TTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
*
38046 AAAATATCGACACAAACTATATTAGTGTTGACACATTATTTAGACATATTCTCTCATAAAACCGG
196 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGG
38111 TAT-ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
261 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
38175 GGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG
326 GGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG
**
38240 AAAAAAGG
391 AAAAAAAA
* *
38248 TATCGACACAAACTATATGAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCAGTATA
* *
38313 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATA-TTTTGGTTTTCGATGTTTTTGGGA
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGATTTTGGGA
*
38377 TTGACACTTTTT-TATATGGATCGACACTTTATGGGTGCACCCTGTT
130 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
38423 GGCCATATTG
Statistics
Matches: 940, Mismatches: 18, Indels: 15
0.97 0.02 0.02
Matches are distributed among these distances:
393 94 0.10
394 193 0.21
395 286 0.30
396 177 0.19
397 190 0.20
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.36
Consensus pattern (398 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCAGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGG
TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
GGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG
AAAAAAAA
Found at i:38564 original size:19 final size:18
Alignment explanation
Indices: 38540--38585 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
38530 TTATATTCAC
38540 ATACAAAAATATAAATCGT
1 ATACAAAAATAT-AATCGT
* *
38559 ATACAAAATTATAATCTT
1 ATACAAAAATATAATCGT
38577 ATA-AAAAAT
1 ATACAAAAAT
38586 TAACCCTACA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 5 0.21
18 8 0.33
19 11 0.46
ACGTcount: A:0.59, C:0.09, G:0.02, T:0.30
Consensus pattern (18 bp):
ATACAAAAATATAATCGT
Found at i:38566 original size:18 final size:18
Alignment explanation
Indices: 38540--38587 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
38530 TTATATTCAC
*
38540 ATACAAAAATATAAATCGT
1 ATACAAAATTAT-AATCGT
*
38559 ATACAAAATTATAATCTT
1 ATACAAAATTATAATCGT
*
38577 ATAAAAAATTA
1 ATACAAAATTA
38588 ACCCTACATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 15 0.58
19 11 0.42
ACGTcount: A:0.58, C:0.08, G:0.02, T:0.31
Consensus pattern (18 bp):
ATACAAAATTATAATCGT
Found at i:40404 original size:33 final size:33
Alignment explanation
Indices: 40367--40432 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
40357 TATCTTAATA
*
40367 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
40400 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
40433 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:40506 original size:21 final size:21
Alignment explanation
Indices: 40466--40530 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
40456 CCCCTTATGC
* *
40466 CTCTCGAGTGTATCTTCGACT
1 CTCTCGAGTTTCTCTTCGACT
*
40487 CTCTCGAGTTTCTCTACGACT
1 CTCTCGAGTTTCTCTTCGACT
* *
40508 -TGATCAAGTTTCTCTTCGACT
1 CT-CTCGAGTTTCTCTTCGACT
40529 CT
1 CT
40531 TGATTGTCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.15, C:0.29, G:0.15, T:0.40
Consensus pattern (21 bp):
CTCTCGAGTTTCTCTTCGACT
Found at i:43426 original size:224 final size:227
Alignment explanation
Indices: 43024--43455 Score: 721
Period size: 225 Copynumber: 1.9 Consensus size: 227
43014 CTTTTAAAGT
43024 TGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATATTTTCCACCTACAATATTAATTTAATA
1 TGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATATTTTCCACCTACAATATTAATTTAATA
* *
43089 ATTTAATTTACACAAAATTTTATTTGATTGTTTTGATATTTTATAAAATATTTTTAGAATTTAAA
66 ATTTAATTTACACAAAATATTATTTGATTATTTTGATATTTTATAAAATATTTTTAGAATTTAAA
* * *
43154 TTTAACAATATTAACCAATATAATAATAAATATGTTTTCAACAGTGAAATAAGTATGAACAC-TT
131 TTTAACAATATTAACAAAGATAATAATAAATATATTTTCAACAGTGAAATAAGTATGAACACTTT
*
43218 TATAAAAATGATATATACTTTTTTGAAAGTTA
196 TATAAAAAGGATATATACTTTTTTGAAAGTTA
*
43250 TGTAATTTATGTTTCAATTT-TTTAATAGTGTTTCATGTTTTCCACCTACAATATTAA-TTAATA
1 TGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATATTTTCCACCTACAATATTAATTTAATA
* *
43313 ATTTTATTTACACAAAA-ATTATTTGATTATTTTGATATTTTATAAAATATTATTTAGATTTTAA
66 ATTTAATTTACACAAAATATTATTTGATTATTTTGATATTTTATAAAATATT-TTTAGAATTTAA
*
43377 ATTTAACAATATTAACTAAAGATAATAATAAATATATTTTC-ACAGTGAAATAAGTATGGACACT
130 ATTTAACAATATTAAC-AAAGATAATAATAAATATATTTTCAACAGTGAAATAAGTATGAACACT
43441 TTTATAAAAAGGATA
194 TTTATAAAAAGGATA
43456 GATAATTTAC
Statistics
Matches: 193, Mismatches: 10, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
223 32 0.17
224 70 0.36
225 71 0.37
226 20 0.10
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.45
Consensus pattern (227 bp):
TGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATATTTTCCACCTACAATATTAATTTAATA
ATTTAATTTACACAAAATATTATTTGATTATTTTGATATTTTATAAAATATTTTTAGAATTTAAA
TTTAACAATATTAACAAAGATAATAATAAATATATTTTCAACAGTGAAATAAGTATGAACACTTT
TATAAAAAGGATATATACTTTTTTGAAAGTTA
Found at i:47490 original size:14 final size:14
Alignment explanation
Indices: 47471--47500 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
47461 ATGTTTTTAA
47471 GAGTGACCGAAACC
1 GAGTGACCGAAACC
47485 GAGTGACCGAAACC
1 GAGTGACCGAAACC
47499 GA
1 GA
47501 TTTGATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.27, G:0.30, T:0.07
Consensus pattern (14 bp):
GAGTGACCGAAACC
Found at i:59995 original size:30 final size:29
Alignment explanation
Indices: 59961--60053 Score: 80
Period size: 30 Copynumber: 3.0 Consensus size: 29
59951 GTGAGCCACC
59961 TTTCAAATGTTAGAAAATAATTATTGAACT
1 TTTCAAATGTTA-AAAATAATTATTGAACT
* * * *
59991 TTTCAAATGATTAAAAATAGTCACTGAAAT
1 TTTCAAATG-TTAAAAATAATTATTGAACT
*
60021 TTATTAAATAGTTATAAAATAATCT-TTGAACT
1 TT-TCAAAT-GTTA-AAAATAAT-TATTGAACT
60053 T
1 T
60054 ATTAAACTAT
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
30 24 0.49
31 11 0.22
32 14 0.29
ACGTcount: A:0.44, C:0.08, G:0.09, T:0.40
Consensus pattern (29 bp):
TTTCAAATGTTAAAAATAATTATTGAACT
Found at i:60565 original size:2 final size:2
Alignment explanation
Indices: 60560--60603 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
60550 CGTATCAAAT
60560 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
60601 TA T
1 TA T
60604 GAATTATCTG
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:61615 original size:15 final size:16
Alignment explanation
Indices: 61595--61627 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
61585 TATGTTCATA
61595 TAAAAT-AATATATTT
1 TAAAATCAATATATTT
61610 TAAAATCGAATATATTT
1 TAAAATC-AATATATTT
61627 T
1 T
61628 TGTATGATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
17 10 0.62
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (16 bp):
TAAAATCAATATATTT
Found at i:64221 original size:18 final size:17
Alignment explanation
Indices: 64188--64221 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
64178 GTAATCTGAG
*
64188 ATATAATTTAATTAAAT
1 ATATAATTTAAATAAAT
64205 ATATAATTTTAAATAAA
1 ATATAA-TTTAAATAAA
64222 AATAATAAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATATAATTTAAATAAAT
Done.